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Protocol	Library Type	Single/Paired End	QC score	NRO score	Read Depth Post-Trimming

Control? (Relative to Dataset)	Condition Type	Treatment	Spike-in	Publication Year

Organism	Sample Type	Tissue	Cell Origin	Strain

Cell Type	Genotype	Construct

General Info
Is published
Disease cell type/tissue
Part of a timecourse
Is not an outlier
Is not unusable

Related Datasets
Any other short read data
ATAC-seq
RNA-seq
ChIP-seq
3D sequencing

Data Available
Was included in Tfit master file
Was included in dREG master file

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All
Bru-seq
ChRO-seq
ChRO-seq variant
EU-seq
GRO-cap
GRO-seq
GRO-seq variant
NET-seq
PRO-cap
PRO-cap variant
PRO-seq
PRO-seq variant
RNA-seq variant
TT-seq
other

All
circularization
ligation
not noted in GEO or publication
random primed

All
paired
single

All
1
2
3
4
5

All
1
2
3
4
5

All
> 10M
> 20M
> 30M
> 40M
> 50M
> 60M
> 70M
> 80M
> 90M
> 100M

All
control
experimental

All
no treatment
treatment
vehicle

All
1,6-hexanediol
1-NM-PP1
17-beta-estradiol
17-beta-estradiol withdrawal
2,5-hexanediol
3MB-PP1
4-thiouridine
5-aza-2'-deoxycytidine
7SK antisense oligonucleotide
A23187
A771726
AKTi-1/2
AZ'5576
Atxn10 exonic antisense oligonucleotide 1
Atxn10 intronic antisense oligonucleotide 1
BRM014
C3
C37 control drug
C646 CBP inhibitor
CH99021
CHIR99021
DMSO
DMSO
DMSO/ethanol
DRB
EGF
FCCP
G-CSF
GC-1
GDNF
GSK2879552
HCMV strain TB40/E
HCMV strain TB40/E IE2
HCMV strain TB40/E IE2F
HCMV strain Towne BAC
HCMV strain Towne IE2 BAC
HCMV strain Towne IE2F BAC
HCMV strain Towne varS
HSV-1
IBET151
ICI 182,780
IFN-gamma
INCB059872
JQ1
KCl
KL-1
KL-2
KM05283
Kdo2-Lipid A
LBH589
LG100268
LIF
MS417
Mock infection
NVP2
Nedd4 exonic antisense oligonucleotide 2
Nedd4 exonic antisense oligonucleotide 3
Nedd4 intronic antisense oligonucleotide 2
PBS
PD0325901
PJ34
R1881
RGFP966
RPMI/B27
SD70
STI-571
Spt5-Pol II small-molecule inhibitor 21
TGF-beta
THZ531
TNF-alpha
VEGF-A
VEGF-A165
Wnt3a
actinomycin D
activin
activin A
acyclovir
adeno-Cre virus
adipocyte differentiation protocol
alpha-amanitin
anti-CD180
anti-CD40
anti-IgD-dextran
anti-TAF1 C413 antibody
auxin
bromouridine
camptothecin
celastrol
cell sorting CD19+
cell sorting CD23+
cell sorting EGFP+
cell sorting EGFP-
cell sorting HV+
cell sorting HV-
charcoal-stripped FBS
cisplatin
cold stress
control antisense oligonucleotide
copper sulfate
cortistatin A
cycloheximide
dTAG47
dTAG7
dTAGV-1
dTag7
dexamethasone
differentiated
dihydrotestosterone
dimethyloxalylglycine
doxycycline
doxycycline withdrawal
dsRNA Bap170
dsRNA EGFP
dsRNA Fcp1
dsRNA Gaf
dsRNA Hsf
dsRNA IntS8
dsRNA IntS9
dsRNA LacI
dsRNA LacZ
dsRNA M1bp
dsRNA Msl2
dsRNA Nipped-B
dsRNA Nurf301
dsRNA Rad21
dsRNA Taf1
dsRNA beta-galactosidase
dsRNA control
duvelisib
embryoid body differentiation protocol
enterocyte differentiation protocol
estradiol
ethanol
ethynyl uridine
flavopiridol
gamma-secretase inhibitor
gestation
glucose-free media
growth media
heat pretreatment
heat shock
hepatocyte differentiation protocol 1
hepatocyte differentiation protocol 2
high fat diet
hydroxytamoxifen
hypoxia
idelalisib
indoleacetic acid
influenza A virus Flag-NS1
influenza A virus Flag-deltaPAF
influenza virus strain PR8-delta-NS1
interleukin-1b
interleukin-4
ionomycin
leflunomide
light cycle
lipopolysaccharide
low fat diet
mating
methanol
mock infection medium
mock treatment
myotube differentiation protocol
neutrophil differentiation protocol
nitro-octadec-9-enoic acid
nocodazole
non-permissive temperature
nucleotides
nutlin-3
oxPAPC
pancreatic differentiation protocol
permissive temperature
phenylephrine
phorbol 12-myristate 13-acetate
phorbol myristate acetate
phosphonoacetic acid
phosphonoformic acid
pinometostat
pladienolides B
reelin
replicatively passaging until senescent
retinoic acid
romidepsin
rosiglitazone
serum starvation
serum-free media
starvation
stromal cell co-culture
tetrodotoxin
thapsigargin
thermoneutrality
thymidine
treadmill exercise
trichostatin A
triptolide
ultraviolet C
various
vehicle
water

All
A. thaliana
D. melanogaster
G. gallus
H. sapiens
Luciferase/GFP/NeoR
Luciferase/Gal4/NeoR/GFP
M. musculus
S. cerevisiae
S. frugiperda
S. pombe
SIRV Set 3
other

All
2008
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2023

All
A. thaliana
C. elegans
C. griseus
C. lupus familiaris
D. melanogaster
E. caballus
E. coli
H. sapiens
M. esculenta
M. mulatta
M. musculus
M. velifer
P. falciparum
P. troglodytes
R. norvegicus
S. cerevisiae
S. pombe
S. scrofa
T. thermophila
Z. mays

All
cell line
organism
primary cell
tissue

All
adipose
blood
bone
brain
breast
embryo
eye
gonad
heart
inflorescence and meristem
intestine
kidney
leaf
liver
lung
micronucleus
multiple
muscle
nervous
ovary
pituitary
prostate
seed
seedling
shoot
skin
spleen
testis
umbilical cord
uterus
yolk sac

All
cardiomyoblast
embryonic stem cell
endothelial
epithelial
erythroblast
hematopoietic progenitor
lymphoblast
mesenchymal progenitor
myeloblast
myeloid progenitor
myoblast
neural progenitor
unknown

All
1.9wR x wK
129/SV-Jae x castaneus
129/Sv
129/Sve
129P2/OlaHsd
129S1/SvImJ x 129X1/SvJ
129S1/SvImJ x C57BL/6J
3D7
972 h-
B2086 x CU428
B73
BALB/cJ
BALBc/J
BY4733
BY4742
Black Swiss
C57BL/6
C57BL/6 x 129/Sv
C57BL/6 x CAST/EiJ
C57BL/6(f) x (C57BL/6 x CAST/EiJ)(m)
C57BL/6(f) x 129/Sv(m)
C57BL/6J
C57BL/6J mice(f) x PWK/PhJ(m)
C57BL/6J mice(f) x SPRET/EiJ(m)
C57BL/6J x CAST/EiJ
C57Bl/6EiJ
CS118 (Isk1as)
Chesapeake Bay retriever
Col 0
Col 0 x Wassilewskija
Col-0
FY10092 (dis2-11)
German shepherd
JS78
K-12
LV7 (cdk9as)
MS340 (mcs6as5)
N2
NF54
NOD/ShiLtJ
Nase 3
PP185 (cdk9as dis2-11)
PP20 (cdk9as lsk1as)
PP23 (cdk9as mcs6as5)
PWK/PhJ
Rhodesian ridgeback
SPRET/EiJ
W303-1-alpha
W303-1a
Wassilewskija
bloodhound
boxer
clp1-769-5
flat-coated retriever
golden retriever
lab cross
labrador retriever
mixed breed
ne4253
ok554
pit bull
sdc-2 (y93)
standard poodle
tm892
transgenic strain 1.9
transgenic strain 3.6
w1118
yellow-white
yw

All
3T3-L1
76NF2V
A2780
A375
A549
AC16
ARPE-19
AU565
AtT20
B cell
BEAS-2B
BJ
BJ5ta
C2C12
CD14+ macrophage
CD34+ erythroblast
CD4+ T cell
CH12F3
CHO-K1
CUTLL1
DL1
DLD1 Flp-In
Daudi
ECOMG
ESC
G401
GC pituitary cell
GM12878
HAEC
HAP1
HASM
HCC1806
HCC1937
HCC1954
HCEC
HCT116
HEK293
HEK293 Flp-In
HEK293T
HEK293T Flp-In
HEp2
HF1
HUVEC
HeLa
HeLa S3
HepG2
IMR90
Jurkat T cell
K562
KBM7
Kasumi-1
LC-2/ad
LNCaP
MCF10A
MCF7
MDA-MB-231
MDA-MB-361
MDA-MB-436
MDA-MB-468
MEF
MEL624
MHT
ML-DmBG3-c2
MRC5
MRC5VA
MV4-11
N2a
NHA
NSPC
NTera2/D1
NUDUL1
Nalm6
OCI-LY1
OCILY1
PCT 7134
RAW264.7
REH
RMG1
Ramos
S2
S2VP10
SEM
SHEP
SJSA
SKBR3
SKOV3
SUDHL4
SW480
T47D
T98G
THP1
TIG-3
TRExBCBL1
U2OS
U87
U936
UACC812
VCaP
ZR751
acute myeloid leukemia cell
bone marrow derived macrophage
brain
brown adipose tissue
cardiomyocyte
cortex
cortical neuron
early ring parasite
early schizont parasite
early trophozoite parasite
embryo
embryonic fibroblast
embryonic gonad
epididymal white adipose tissue
forebrain
foreskin fibroblast
gametoyte stage III parasite
head
hematopoietic progenitor cell
hepatocyte
iPSC
inflorescence and meristem
inguinal white adipose tissue
intestinal organoid
kidney
late ring parasite
late schizont parasite
late trophozoite parasite
leaf
liver
lung
lymphoblast
micronucleus
myoblast
myocardium (borderline ischemic)
myocardium (healthy)
myocardium (ischemic)
ovarian somatic cell
ovary
peritoneal macrophage
pre pro B cell
pro B cell
quadriceps muscle
seed
seedling
shoot
skin fibroblast
spleen
spleen hemangiosarcoma
splenic B cell
splenic germinal center B cell
v-Abl pro B cell
whole bacteria
whole fly
whole worm
whole yeast
yolk sac

All
Ago1 mut
Ago4 mut
Ago4 mut; Ago4 D762A exogenous (stable)
Ago4 mut; Ago4 exogenous (stable)
Ago4 mut; Ago6 mut; Ago9 mut
Ago4 mut; Ago6 mut; Ago9 mut; Ago4 D762A exogenous (stable)
Ago4 mut; Ago6 mut; Ago9 mut; Ago4 exogenous (stable)
Aid -/-
Aid -/-; 3' IgH CBE -/-
Aml1-ETO dTAG-inducible degron
Atm -/-
Bcl11a -/-
BirA (stable); Rev-erb-alpha BLRP (stable)
BirA knock-in
CH +/-; Aid -/-
CH +/-; Aid -/-; I-alpha -/-
CH +/-; Aid -/-; I-alpha -/-; 3xCTCF-binding element knock-in
CTCF binding site -/-
Cdk12 F813G/-
Cdk12 F813G/-; Cdk13 F791G/-
Cdk12 F813G/-; Cdk13 F791G/F791G
Cdk13 F791G/F791G
Cdk8 F97G
Csb CS1AN mut
Ctcf fl/fl; WapI fl/fl
Dcp1a -/-
Dmnt3a fl/fl
Dmnt3a fl/fl; Nestin-Cre
Drm3 mut
ER-alpha enhancer -/-
ER-beta flag (stable)
Ebf1 fl/+; Cd23-Cre
Ebf1 fl/-; Cd23-Cre
Esr1 (stable)
Esr1 L540Q (stable)
Frg1 mut; Frg2 mut
Fucci-EGFP+ (stable)
Gsk3 -/-
H2B G53D
HDAC3 +/+; Alb-Cre
HDAC3 fl/-; Alb-Cre
Hdac3 fl/fl
Hdac3 fl/fl; Myl1-Cre
Hdac3 fl/fl; adiponectin-Cre
Hdgf -/-
Hdgf -/-; Hdgf exogenous (stable)
Hsf1 -/-
Hsf1 -/-; Hsf2 -/-
Hsp70 promoter 10bp insert
Hsp70 promoter 5bp insert
I-TG transgene knock-in +/-
I-element fragment knock-in
Idn2 mut
Idn2 mut; Idnl1 mut; Idnl2 mut
Kdm1a +/gene trap
Kdm2a H212A HA-tag (stable)
Kdm2a HA-tag (stable)
Krabiner endogenous -/-
Krabiner endogenous -/-; dox-inducible Krabiner DBD mut exogenous (stable)
Krabiner endogenous -/-; dox-inducible Krabiner KRAB mut exogenous (stable)
Krabiner endogenous -/-; dox-inducible Krabiner exogenous (stable)
Lsd1 exon 8a fl/fl
Lsd1 exon 8a fl/fl; Nestin-Cre
Mecp2 -/Y
Mecp2 R106W Tavi-tag
Mecp2 R306C/Y
Mecp2 Tavi-tag
Med14 dTAG-inducible degron
Med26 mut
Mhd3 -/-
Mll2 -/-; shRNA Cxxc1 (stable)
Mll2 -/-; shRNA control (stable)
Mll2 fl/fl; tamoxifen-inducible Cre
Myc Wdr5-interaction-defective fl/fl; tamoxifen-inducible Cre
Myc fl/fl
Myc fl/fl; tamoxifen-inducible Cre/+
Myc truncation fl/fl; tamoxifen-inducible Cre
Myc-HA fl/fl; tamoxifen-inducible Cre
MyoD -/-
NCoR fl/fl
NCoR fl/fl; LysM-Cre +/-
NelfB -/-
Nrpd1 mut
Nrpd1 mut; Nrpe1 mut
Nrpe1 mut
PU.1 -/-
PU.1 -/-; tamoxifen-inducible PU.1 exogenous (stable)
Paf1 -/-; dox-inducible Paf1 exogenous (stable)
Pcif1 -/-
P{GAL4::VP16-nos.UTR}CG6325MVD1/P{y[+t7.7] v[+t1.8]=TRiP.GL00054}attP2
Rad21 +/+; tamoxifen-inducible Cre/+
Rad21 auxin-inducible degron
Rad21 fl/fl; tamoxifen-inducible Cre/+
Rag1 -/-
Rag1 -/-; Emu-Bcl2 +
Rag1 -/-; Emu-Bcl2 +; CTCF auxin-inducible degron
Rag1 -/-; Emu-Bcl2 +; Rad21 auxin-inducible degron
Rag1 -/-; Emu-Bcl2 +; dox-inducible Wapl auxin-inducible degron
Rag1 -/-; Igh VH inversion
Rag2 -/-
Rbfox2 -/-
Rev-erb-alpha -/-
Rev-erb-alpha fl/fl; Rev-erb-beta fl/fl
Rev-erb-alpha fl/fl; Rev-erb-beta fl/fl; Tie2-Cre
Rora fl/fl; Rorc fl/fl; AAV-TBG-Cre
RpII215 G3973A
Rpd1 -/-
SA -/-
Sirt6 -/-
Smarca4 -/-; Smarca2 dTAG-inducible degron
Smarca4 dTAG-inducible degron
Smcx -/-
Spt5 V1008D
Spt5l mut
Srf (stable)
Srf S103A (stable)
Srf S103D (stable)
Srsf1 -/-; dox-repressible Srsf1 exogenous (stable)
Suvr2 mut
Tcf3 -/-
Tdg -/-
Tdg fl/fl
Tff1 promoter -/-
Tir1 (Flp knock-in)
Tir1 (Flp knock-in); Nelf-C auxin-inducible degron
Tir1 (Flp knock-in); Nelf-E auxin-inducible degron
Tsix +/-
Vhb18 heavy chain knock-in
XX
XX; XX DSD insertion +/+
XX; XX DSD insertion +/-
XY; XX DSD insertion +/+
XY; XX DSD insertion +/-
Xpc XP67TMA mut
Xrcc4 -/-; p53 -/-
Xrcc4 -/-; p53 -/-; recurrent genomic break clusters
Zmynd8 fl/fl
Zmynd8 fl/fl; Cd19-Cre
Znf143 auxin-inducible degron; Tir1 knock-in
Znf143 auxin-inducible degron; Tir1 knock-in; Arf16-PB1 knock-in
alpha-amanitin resistant, dox-inducible Rpb1 N792D (Flp knock-in)
alpha-amanitin resistant, dox-inducible Rpb1 N792D/E1126G (Flp knock-in)
alpha-amanitin resistant, dox-inducible Rpb1 N792D/H1108Y (Flp knock-in)
alpha-amanitin resistant, dox-inducible Rpb1 N792D/R749H (Flp knock-in)
cdk9T120G::hphMX6 lsk1F353G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+
cdk9T120G::hphMX6 mcs6N84T-L87G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h-
cdk9T120G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+
cdk9T120G::natMx dis2-11 ura4-D18 leu1-32
copper-inducible FLAG-IntS8 (stable)
copper-inducible FLAG-IntS8-WFEF/A mut (stable)
csr-1 -/-
dis2-11 leu1-32 ura4-D18 h+
dox-inducible EGFP (stable)
dox-inducible Etv6-Runx1 fusion (stable)
dox-inducible Etv6-Runx1 fusion R518Q (stable)
dox-inducible Jun (stable); shRNA Gata3 (stable)
dox-inducible Jun (stable); shRNA control (stable)
dox-inducible Myc (stable)
dox-inducible OMO-MYC (stable)
dox-inducible Pax2 (stable)
dox-inducible RTA (stable)
dox-inducible Snf5 (stable)
dox-inducible TFIIS D282A, E283A (Flp knock-in)
dox-inducible Xist endogenous allele
dox-inducible luciferase (stable)
dox-inducible shRNA Ints11 endogenous (stable)
dox-inducible shRNA Paf1 (stable)
dox-inducible shRNA Phf5a (stable)
dox-inducible shRNA Srsf2 endogenous (stable); dox-inducible Srsf2 P95H exogenous (stable)
dox-inducible shRNA Srsf2 endogenous (stable); dox-inducible Srsf2 exogenous (stable)
dox-inducible shRNA U2af35 endogenous (stable); dox-inducible U2af35 Q157P exogenous (stable)
dox-inducible shRNA U2af35 endogenous (stable); dox-inducible U2af35 S34F exogenous (stable)
dox-inducible shRNA control (stable)
drh-3 -/-
elba1 mut
elba2 mut
elba3 mut
hNDF -/-
insv mut
lambda-N-CG9754 luciferase knock-in
linc1319 +15kb intronic pAS insertion (+/-)
linc1319 +2kb instronic pAS insertion (+/-)
linc1319 TSS +/-
linc1319 promoter +/-
linc1536 intronic pAS insertion (+/-)
linc1536 promoter +/-
lsk1F353G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M216 h-
luciferase knock-in
mcs6N84T-L87G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+
miR-1 (stable)
miR-122 (stable)
miR-133a (stable)
miR-155 (stable)
miR-302a (stable)
miR-372 (stable)
miR-373 (stable)
nanos promoter Gal4-responsive dsRNA CG9754 knock-in
nanos promoter Gal4-responsive dsRNA piwi knock-in
nanos promoter Gal4-responsive dsRNA piwi; Dcr2 constitutive knock-in
nanos promoter Gal4-responsive dsRNA white knock-in
nanos promoter Gal4-responsive dsRNA white; Dcr2 constitutive knock-in
p53 -/-
prg-1 -/-
sdc-2 mut
shRNA Brca1 (stable)
shRNA GFP
shRNA Gata3 (stable)
shRNA Jun (stable)
shRNA Lsd1 A (stable)
shRNA Lsd1 B (stable)
shRNA Parp1 (stable)
shRNA Recql5 endogenous (stable); dox-inducible Recql5 exogenous (stable)
shRNA Rhi
shRNA Rrp40 (stable)
shRNA Tead4 (stable)
shRNA Yap1 (stable)
shRNA control (stable)
shRNA luciferase (stable)
spt4 -/-
tamoxifen-inducible Cre/+
tamoxifen-inducible oncogenic H-RasV12
temperature-dependent Clp1 mut
traffic jam promoter Gal4-responsive dsRNA piwi
traffic jam promoter Gal4-responsive dsRNA white
w[1118]; P{w[+mC]=GAL4::VP16-nos.UTR}CG6325[MVD1]
zfp1 -/-

All
BirA; Rev-erb-alpha
Hdac3 -/-
Hhex-Venus reporter
Hif1-alpha
Hif2-alpha
Ints11 E203Q exogenous
Ints11 exogenous
RNAi L4440 control
RNAi Nelf
RNAi control
RNAi sdc-2
Rpb1 H1108Y
Rpb1 R749H
dox-inducible Tet-CD-GFP
dox-inducible shRNA Arid1A
dox-inducible shRNA Ints11
empty control
shRNA AP2-gamma
shRNA Hsf1
shRNA Nup358
shRNA Paf1
shRNA RAR-alpha/RAR-gamma
shRNA Rbm7
shRNA Rod1
shRNA control
shRNA luciferase
siRNA Ago1
siRNA Ago2
siRNA Brd4
siRNA Cpsf73
siRNA Cstf64
siRNA Cstf64; siRNA Cstf64tau
siRNA Cstf64tau
siRNA Foxa1
siRNA GFP
siRNA Gata3
siRNA Gps2
siRNA Hnrnph1
siRNA Hnrnpk
siRNA Hnrnpl
siRNA Hnrnpll
siRNA JMJD6
siRNA Jmjd6
siRNA Kdm2a
siRNA Kdm2a 5'UTR
siRNA Kdm5c
siRNA Ldb1
siRNA Mash1
siRNA Mll-Af4
siRNA Mre11
siRNA Ncapd3
siRNA Ncapg
siRNA NelfB
siRNA NelfE
siRNA Nkx3-1
siRNA Pcbp2
siRNA Pcgem1
siRNA Prncr1
siRNA Ptbp1
siRNA Pygo2
siRNA Rad21
siRNA Rbfox2
siRNA Rbm22
siRNA Rbm25
siRNA Setx
siRNA Smc3
siRNA Srsf4
siRNA Ssu72
siRNA Suz12
siRNA Tbx19
siRNA Top1
siRNA U2af1
siRNA U2af2
siRNA Xrcc5
siRNA Xrn2
siRNA Yap1
siRNA Yy1
siRNA beta-catenin; siRNA Satb1
siRNA control
siRNA luciferase
siRNA piwi