title: Control participant 151

description:
MethylationEPIC (850 k)
X204088030086_R08C01

tag: age (days)

tag: bmi

tag: ch


title: Control participant 125

status: Public on Apr 28 2025

type: genomic

city: Budapest

first: Zsolt

last: Radák

address: Alkotás Street 44, building L3

country: Hungary

institute: Research Center for Molecular Exercise Science, Hungarian University of Sports Science

description:
MethylationEPIC (850 k)
X204086170062_R07C01

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
The raw methylation signal intensities were retrieved using the function read.metharray.exp of the minfi v1.40.0 R package, followed by linear dye bias correction and noob background correction to account for technical variation in background fluorescence signal. Specifically, the value was calculated from the intensity of the methylated and unmethylated sites, as the ratio of fluorescent signals.
*processed value definition: Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: standard protocol

extract_protocol: standard protocol

tag: tissue

value: Blood

tag: project batch

tag: gender

value: female

tag: olympic champion

value: no

tag: sport

value: controll

tag: date of sampling

tag: vo2 max est.

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: jumpmax[cm]

tag: jumpmax[cm/bh]

tag: cognition

tag: irisin

tag: ldl

tag: hdl

tag: tg


title: Control participant 120

description:
MethylationEPIC (850 k)
X204088020016_R02C01

value: male

tag: age (days)

tag: bmi

tag: ch


title: Control participant 122

description:
MethylationEPIC (850 k)
X204088030094_R07C01

tag: tissue

tag: project batch

tag: gender


title: Control participant 146

description:
MethylationEPIC (850 k)
X204086170062_R03C01

tag: olympic champion

tag: sport

tag: date of sampling


title: Control participant 121

description:
MethylationEPIC (850 k)
X204088030022_R08C01

tag: vo2 max est.

tag: gripmax[kg]

tag: gripmax[kg/bm]


title: Control participant 119

description:
MethylationEPIC (850 k)
X204073580111_R04C01

tag: jumpmax[cm]

tag: jumpmax[cm/bh]

tag: cognition


title: Control participant 118

description:
MethylationEPIC (850 k)
X204088030009_R03C01

tag: ldl

tag: hdl


title: Control participant 117

description:
MethylationEPIC (850 k)
X204088030152_R01C01

tag: age (days)

tag: tg


title: Control participant 116

description:
MethylationEPIC (850 k)
X204073580111_R01C01

tag: bmi

tag: irisin

tag: ch


title: Control participant 113

description:
MethylationEPIC (850 k)
X204088030153_R07C01

tag: tissue

tag: project batch

tag: gender


title: Control participant 114

description:
MethylationEPIC (850 k)
X204088030020_R07C01

tag: olympic champion

tag: sport

tag: date of sampling


title: Control participant 115

description:
MethylationEPIC (850 k)
X204086170008_R04C01

tag: vo2 max est.

tag: gripmax[kg]

tag: gripmax[kg/bm]


title: Control participant 112

description:
MethylationEPIC (850 k)
X204088030100_R03C01

tag: jumpmax[cm]

tag: jumpmax[cm/bh]

tag: cognition


title: Control participant 111

description:
MethylationEPIC (850 k)
X204088030009_R08C01

tag: age (days)

tag: ldl

tag: hdl


title: Control participant 131

description:
MethylationEPIC (850 k)
X204086170032_R01C01

tag: bmi

tag: tg


title: Control participant 110

description:
MethylationEPIC (850 k)
X204088020016_R07C01

tag: tissue

tag: irisin

tag: ch


title: Control participant 109

description:
MethylationEPIC (850 k)
X204088030124_R06C01

tag: project batch

tag: gender

tag: olympic champion


title: Control participant 108

description:
MethylationEPIC (850 k)
X204088020033_R03C01

tag: sport

tag: date of sampling

tag: vo2 max est.


title: Control participant 105

description:
MethylationEPIC (850 k)
X204086170008_R07C01

value: Low

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: jumpmax[cm]


title: Control participant 106

description:
MethylationEPIC (850 k)
X204074220153_R06C01

tag: age (days)

tag: jumpmax[cm/bh]

tag: cognition


title: Control participant 104

description:
MethylationEPIC (850 k)
X204088030086_R04C01

tag: bmi

tag: ldl

tag: hdl


title: Control participant 102

description:
MethylationEPIC (850 k)
X204088030065_R06C01

tag: tissue

tag: irisin

tag: tg


title: Control participant 101

description:
MethylationEPIC (850 k)
X204088030065_R03C01

tag: project batch

tag: gender

tag: ch


title: Control participant 99

description:
MethylationEPIC (850 k)
X204088010150_R04C01

tag: olympic champion

tag: sport

tag: date of sampling


title: Control participant 100

description:
MethylationEPIC (850 k)
X204088020033_R04C01

tag: vo2 max est.

tag: gripmax[kg]

tag: gripmax[kg/bm]


title: Control participant 97

description:
MethylationEPIC (850 k)
X204088030124_R03C01

tag: age (days)

tag: jumpmax[cm]

tag: jumpmax[cm/bh]


title: Control participant 96

description:
MethylationEPIC (850 k)
X204088030152_R06C01

tag: bmi

tag: cognition

tag: ldl


title: Control participant 98

description:
MethylationEPIC (850 k)
X204088010124_R04C01

tag: tissue

tag: irisin

tag: hdl


title: Control participant 95

description:
MethylationEPIC (850 k)
X204086170062_R02C01

tag: project batch

tag: gender

tag: tg


title: Control participant 94

description:
MethylationEPIC (850 k)
X204088020033_R06C01

tag: olympic champion

tag: sport

tag: ch


title: Control participant 91

description:
MethylationEPIC (850 k)
X204088030065_R04C01

tag: date of sampling

tag: vo2 max est.

tag: gripmax[kg]


title: Control participant 92

description:
MethylationEPIC (850 k)
X204088030100_R01C01

tag: age (days)

tag: gripmax[kg/bm]

tag: jumpmax[cm]


title: Control participant 90

description:
MethylationEPIC (850 k)
X204071680141_R06C01

tag: jumpmax[cm/bh]

tag: bmi

tag: cognition


title: Control participant 89

description:
MethylationEPIC (850 k)
X204073570112_R01C01

tag: tissue

tag: ldl


title: Control participant 87

description:
MethylationEPIC (850 k)
X204086170032_R02C01

tag: project batch

tag: irisin

tag: hdl


title: Control participant 86

description:
MethylationEPIC (850 k)
X204088030094_R05C01

tag: gender

tag: olympic champion

tag: tg


title: Control participant 85

description:
MethylationEPIC (850 k)
X204088030138_R02C01

tag: sport

tag: date of sampling

tag: ch


title: Control participant 93

description:
MethylationEPIC (850 k)
X204088030022_R03C01

tag: age (days)

tag: vo2 max est.

tag: gripmax[kg]


title: Control participant 83

description:
MethylationEPIC (850 k)
X204088030086_R06C01

tag: gripmax[kg/bm]

tag: jumpmax[cm]

tag: jumpmax[cm/bh]


title: Control participant 81

description:
MethylationEPIC (850 k)
X204088030124_R04C01

tag: tissue

tag: bmi

tag: cognition


title: Control participant 107

description:
MethylationEPIC (850 k)
X204088030086_R01C01

tag: project batch

tag: irisin

tag: ldl


title: Control participant 88

description:
MethylationEPIC (850 k)
X204086170032_R08C01

tag: gender

tag: olympic champion

tag: hdl


title: Control participant 84

description:
MethylationEPIC (850 k)
X204088030009_R06C01

tag: sport

tag: date of sampling

tag: tg


title: Control participant 80

description:
MethylationEPIC (850 k)
X204088010153_R01C01

tag: age (days)

tag: vo2 max est.

tag: ch


title: Control participant 78

description:
MethylationEPIC (850 k)
X204071680079_R01C01

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: jumpmax[cm]


title: Control participant 77

description:
MethylationEPIC (850 k)
X204071680091_R08C01

tag: tissue

tag: jumpmax[cm/bh]

tag: bmi


title: Control participant 103

description:
MethylationEPIC (850 k)
X204088030100_R07C01

tag: project batch

tag: cognition


title: Control participant 76

description:
MethylationEPIC (850 k)
X204071680091_R04C01

tag: gender

tag: ldl


title: Control participant 69

description:
MethylationEPIC (850 k)
X204088010124_R03C01

tag: olympic champion

tag: irisin

tag: hdl


title: Control participant 64

description:
MethylationEPIC (850 k)
X204088030022_R04C01

tag: sport

tag: date of sampling

tag: tg


title: Control participant 72

description:
MethylationEPIC (850 k)
X204086170032_R04C01

tag: age (days)

tag: vo2 max est.

tag: ch


title: Control participant 66

description:
MethylationEPIC (850 k)
X204073570112_R02C01

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: jumpmax[cm]


title: Control participant 73

description:
MethylationEPIC (850 k)
X204088020033_R02C01

tag: tissue

tag: jumpmax[cm/bh]

tag: bmi


title: Control participant 68

description:
MethylationEPIC (850 k)
X204088010124_R07C01

tag: project batch

tag: gender

tag: cognition


title: Control participant 75

description:
MethylationEPIC (850 k)
X204088030148_R03C01

tag: olympic champion

tag: irisin

tag: ldl


title: Control participant 74

description:
MethylationEPIC (850 k)
X204073580111_R08C01

tag: sport

tag: date of sampling

tag: hdl


title: Control participant 67

description:
MethylationEPIC (850 k)
X204073570112_R07C01

tag: age (days)

tag: vo2 max est.

tag: tg


title: Control participant 71

description:
MethylationEPIC (850 k)
X204088030148_R01C01

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: ch


title: Control participant 70

description:
MethylationEPIC (850 k)
X204088030020_R03C01

tag: tissue

tag: jumpmax[cm]

tag: jumpmax[cm/bh]


title: Control participant 65

description:
MethylationEPIC (850 k)
X204088020020_R07C01

tag: project batch

tag: gender

tag: bmi


title: Control participant 61

description:
MethylationEPIC (850 k)
X204088030086_R07C01

tag: olympic champion

tag: cognition


title: Control participant 59

description:
MethylationEPIC (850 k)
X204088030094_R03C01

tag: sport

tag: irisin

tag: ldl


title: Control participant 63

description:
MethylationEPIC (850 k)
X204088030143_R08C01

tag: date of sampling

tag: age (days)

tag: hdl


title: Control participant 60

description:
MethylationEPIC (850 k)
X204088010124_R02C01

tag: vo2 max est.

tag: gripmax[kg]

tag: tg


title: Control participant 54

description:
MethylationEPIC (850 k)
X204088030086_R03C01

tag: tissue

tag: gripmax[kg/bm]

tag: ch


title: Control participant 55

description:
MethylationEPIC (850 k)
X204088030094_R06C01

tag: project batch

tag: jumpmax[cm]

tag: jumpmax[cm/bh]


title: Control participant 56

description:
MethylationEPIC (850 k)
X204071680079_R08C01

tag: gender

tag: olympic champion

tag: bmi


title: Control participant 82

description:
MethylationEPIC (850 k)
X204088030100_R05C01

tag: sport

tag: cognition


title: Control participant 79

description:
MethylationEPIC (850 k)
X204088030153_R04C01

tag: date of sampling

tag: irisin

tag: ldl


title: Control participant 58

description:
MethylationEPIC (850 k)
X204088020020_R08C01

tag: age (days)

tag: vo2 max est.

tag: hdl


title: Control participant 52

description:
MethylationEPIC (850 k)
X204088020033_R05C01

tag: tissue

tag: gripmax[kg]

tag: tg


title: Control participant 57

description:
MethylationEPIC (850 k)
X204088020033_R08C01

tag: project batch

tag: gripmax[kg/bm]

tag: ch


title: Control participant 51

description:
MethylationEPIC (850 k)
X204074220153_R03C01

tag: gender

tag: jumpmax[cm]

tag: jumpmax[cm/bh]


title: Control participant 49

description:
MethylationEPIC (850 k)
X204086170062_R05C01

tag: olympic champion

tag: sport

tag: bmi


title: Control participant 50

description:
MethylationEPIC (850 k)
X204086170046_R05C01

tag: date of sampling

tag: cognition

tag: irisin


title: Control participant 48

description:
MethylationEPIC (850 k)
X204088020033_R01C01

tag: age (days)

tag: vo2 max est.

tag: ldl


title: Control participant 62

description:
MethylationEPIC (850 k)
X204088010150_R05C01

tag: tissue

tag: gripmax[kg]

tag: hdl


title: Control participant 46

description:
MethylationEPIC (850 k)
X204088030095_R01C01

tag: project batch

tag: gripmax[kg/bm]

tag: tg


title: Control participant 47

description:
MethylationEPIC (850 k)
X204088030095_R06C01

tag: gender

tag: jumpmax[cm]

tag: ch


title: Control participant 45

description:
MethylationEPIC (850 k)
X204088030080_R03C01

tag: olympic champion

tag: sport

tag: jumpmax[cm/bh]


title: Control participant 43

description:
MethylationEPIC (850 k)
X204071680091_R02C01

tag: date of sampling

tag: bmi

tag: cognition


title: Control participant 44

description:
MethylationEPIC (850 k)
X204073570112_R04C01

tag: age (days)

tag: vo2 max est.


title: Control participant 38

description:
MethylationEPIC (850 k)
X204088010050_R06C01

tag: tissue

tag: ldl


title: Control participant 40

description:
MethylationEPIC (850 k)
X204071680141_R04C01

tag: gripmax[kg]

tag: hdl


title: Control participant 39

description:
MethylationEPIC (850 k)
X204088030020_R02C01

tag: project batch

tag: gripmax[kg/bm]

tag: irisin


title: Control participant 34

description:
MethylationEPIC (850 k)
X204088020057_R03C01

tag: gender

tag: jumpmax[cm]

tag: tg


title: Control participant 37

description:
MethylationEPIC (850 k)
X204086170032_R03C01

tag: olympic champion

tag: sport

tag: ch


title: Control participant 33

description:
MethylationEPIC (850 k)
X204088010150_R06C01

tag: date of sampling

tag: jumpmax[cm/bh]

tag: bmi


title: Control participant 31

description:
MethylationEPIC (850 k)
X204088030148_R07C01

tag: age (days)

tag: vo2 max est.

tag: cognition


title: Control participant 30

description:
MethylationEPIC (850 k)
X204073580111_R02C01

tag: tissue

tag: gripmax[kg]

tag: ldl


title: Control participant 53

description:
MethylationEPIC (850 k)
X204088030080_R08C01

tag: project batch

tag: gripmax[kg/bm]

tag: hdl


title: Control participant 42

description:
MethylationEPIC (850 k)
X204086170062_R01C01

tag: gender

tag: jumpmax[cm]


title: Control participant 41

description:
MethylationEPIC (850 k)
X204071680079_R03C01

tag: olympic champion

tag: tg


title: Control participant 32

description:
MethylationEPIC (850 k)
X204071680091_R07C01

tag: sport

tag: ch


title: Control participant 36

description:
MethylationEPIC (850 k)
X204088030153_R05C01

tag: date of sampling

tag: jumpmax[cm/bh]

tag: irisin


title: Control participant 35

description:
MethylationEPIC (850 k)
X204088030124_R05C01

tag: age (days)

tag: vo2 max est.

tag: bmi


title: Control participant 29

description:
MethylationEPIC (850 k)
X204088030052_R07C01

tag: tissue

tag: gripmax[kg]

tag: cognition


title: Control participant 25

description:
MethylationEPIC (850 k)
X204071680091_R01C01

tag: project batch

tag: gripmax[kg/bm]

tag: ldl


title: Control participant 23

description:
MethylationEPIC (850 k)
X204088030009_R04C01

tag: gender

tag: jumpmax[cm]

tag: hdl


title: Control participant 24

description:
MethylationEPIC (850 k)
X204088030022_R06C01

tag: olympic champion

tag: sport

tag: tg


title: Control participant 27

description:
MethylationEPIC (850 k)
X204088030138_R01C01

tag: date of sampling

tag: jumpmax[cm/bh]

tag: ch


title: Control participant 28

description:
MethylationEPIC (850 k)
X204088010050_R03C01

tag: age (days)

tag: vo2 max est.

tag: irisin


title: Control participant 26

description:
MethylationEPIC (850 k)
X204086170032_R07C01

tag: tissue

tag: gripmax[kg]

tag: bmi


title: Control participant 22

description:
MethylationEPIC (850 k)
X204088030138_R06C01

tag: project batch

tag: gripmax[kg/bm]

tag: cognition


title: Control participant 21

description:
MethylationEPIC (850 k)
X204088030143_R07C01

tag: gender

tag: jumpmax[cm]

tag: ldl


title: Control participant 19

description:
MethylationEPIC (850 k)
X204088010124_R05C01

tag: olympic champion

tag: sport

tag: hdl


title: Control participant 20

description:
MethylationEPIC (850 k)
X204088030152_R08C01

tag: date of sampling

tag: jumpmax[cm/bh]

tag: tg


title: Control participant 18

description:
MethylationEPIC (850 k)
X204088030124_R07C01

tag: age (days)

tag: vo2 max est.

tag: ch


title: Control participant 17

description:
MethylationEPIC (850 k)
X204088020020_R04C01

tag: tissue

tag: gripmax[kg]

tag: irisin


title: Control participant 14

description:
MethylationEPIC (850 k)
X204086170062_R06C01

tag: project batch

tag: gripmax[kg/bm]

tag: bmi


title: Control participant 15

description:
MethylationEPIC (850 k)
X204088030138_R05C01

tag: gender

tag: jumpmax[cm]

tag: cognition


title: Control participant 16

description:
MethylationEPIC (850 k)
X204088030020_R08C01

tag: olympic champion

tag: sport

tag: ldl


title: Control participant 13

description:
MethylationEPIC (850 k)
X204073580111_R07C01

tag: date of sampling

tag: jumpmax[cm/bh]

tag: hdl


title: Control participant 11

description:
MethylationEPIC (850 k)
X204088030152_R02C01

tag: age (days)

tag: vo2 max est.

tag: tg


title: Control participant 12

description:
MethylationEPIC (850 k)
X204088030052_R05C01

tag: tissue

tag: gripmax[kg]

tag: ch


title: Control participant 10

description:
MethylationEPIC (850 k)
X204086170032_R06C01

tag: project batch

tag: gripmax[kg/bm]

tag: irisin


title: Control participant 9

description:
MethylationEPIC (850 k)
X204088030080_R01C01

tag: gender

tag: jumpmax[cm]

tag: bmi


title: Control participant 7

description:
MethylationEPIC (850 k)
X204086170046_R01C01

tag: olympic champion

tag: sport

tag: cognition


title: Control participant 4

description:
MethylationEPIC (850 k)
X204088030138_R08C01

tag: date of sampling

tag: jumpmax[cm/bh]

tag: ldl


title: Control participant 6

description:
MethylationEPIC (850 k)
X204088030065_R07C01

tag: age (days)

tag: vo2 max est.

tag: hdl


title: Control participant 3

description:
MethylationEPIC (850 k)
X204088030095_R05C01

tag: tissue

tag: gripmax[kg]

tag: tg


title: atg5_WSM_rep2

type: SRA

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the GCF_000001735.4/TAIR10.1 genome assembly using bowtie2
The number of reads falling in the genes  were counted using coveragebed software and normalized with DESeq2 software
Assembly: GCF_000001735.4
Supplementary files format and content: tab-delimited text file include the differential expression results of DESeq2 and raw and normalized counts  for each sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: A. thaliana thaliana (L.) Heynh Columbia-0 (Col-0) seeds and atg5 (SALK_020601C) mutant were germinated in 50 ml of Control medium or waterstress medium in 125 ml flasks at 21 °C, 16/8 h light/dark cycle, light intensity of 105 μmol photons m−2 s−1 an

extract_protocol: TruSeq Stranded mRNA Library Prep from Illumina  using 1 mg of total RNA for each sample. The libraries were analyzed by capillary electrophoresis using a Bioanalyzer 2100.Sequences were performed on an Illumina NextSeq 500 using a NextSeq 500/550 High Output Kit v2.5 (150 Cycles) in a 2X75 cycles configuration at the UUSMD (UNAM, Mexico)

treatment_protocol:
0.5X Murashige, 0,5% Sucrose for control medium. Water stress medium was complemented with glycerol 2.5% and Alginic acid 0.5%
mRNA was isolated using TRIzol

tag: strain

value: A. thaliana. Heynh Columbia-0

value: seedling


title: atg5_NM_rep1


title: atg5_WSM_rep3


title: Control participant 5

description:
MethylationEPIC (850 k)
X204088030020_R04C01

tag: project batch

tag: gripmax[kg/bm]

tag: irisin

tag: ch


title: Control participant 2

description:
MethylationEPIC (850 k)
X204088030094_R02C01

tag: gender

tag: olympic champion

tag: jumpmax[cm]

tag: bmi


title: atg5_NM_rep3


title: Control participant 1

description:
MethylationEPIC (850 k)
X204088030100_R02C01

tag: sport

tag: date of sampling

tag: jumpmax[cm/bh]

tag: cognition


title: atg5_NM_rep2


title: WT_WSM_rep3


title: WT_WSM_rep1


title: WT_WSM_rep2


title: WT_NM_rep1


title: WT_NM_rep2


title: neuron_NMDA_rep2

city: St Louis

first: Marianne

middle: Catherine

last: Kramer

state: MO

address: 975 N Warson Rd

country: USA

institute: Danforth Plant Science Center

data_processing:
3' adapter sequences were trimmed using cutadapt (version 1.2.1 with parameters -e 0.06 -O 6 -m 14)
Reads from all samples were aligned to the rn6 reference genome/annotation file  using STAR (v2.4.0) using default parameters.
Read counts in mapped bam files were assessed using HTSeq with parameters --format=bam --stranded=reverse --mode=intersection-strict.
DESeq2 was run on HTSeq count files using default parameters and a cutoff of  FDR < 0.05 for assigning significantly differentially abundant transcripts.
Assembly: rn6
Supplementary files format and content: bam files, htseq files, deseq files

molecule: polyA RNA

organism: Rattus norvegicus

source_name: cortical rat neurons

growth_protocol: Primary rat neuronal cultures were prepared from embryonic day 18 Sprague–Dawley CD rat embryos. Brains were isolated, cortices dissected and incubated for 25 min in HBSS containing 2.5% Trypsin. Cortices were then rinsed twice with HBSS, mechanically disaggregated in DMEM + 10% FBS, passed through a 70 μm strainer and resuspended in neurobasal medium supplemented with B27 and GlutaMAX

extract_protocol:
Control- and NMDA-treated cells collected and resuspended in QIAzol
Strand specific libraries were constructed as previously described (Silverman, et al, 2014)

treatment_protocol: On DIV7 and DIV15 (for DIV21 cultures), 40% of media was removed and replaced with fresh media. At DIV15 or DIV21 neurons were treated with 10 µM NMDA for 4 or 24 hours as stated.

tag: cell type

value: cortical rat neurons

tag: treatment

value: NMDA


title: neuron_NMDA_rep1


title: neuron_NMDA_rep3_ssRNase_protein

description:
neuron_NMDA_rep3_merged_merged.CSAR_PPS_FDR05.bed.gz
neuron_NMDA_rep3_noprotein_NR_structure_unspliced_std.bed12.gz

data_processing:
3' adapter sequences were trimmed using cutadapt (version 1.2.1 with parameters -e 0.06 -O 6 -m 14)
Redundant reads were compressed using an in-house perl (version 5.8.8) script
Trimmed and untrimmed reads were aligned to the Rattus norvegicus genome (rn6) using Tophat (version 2.0.10 with parameters --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --transcriptome-max-hits 10 --no-coverage-search –no-novel-juncs)
PPS files - PPSs were identified using a modified version of the CSAR software package, as previously described (Silverman et al., 2014; Gosai et al., 2015; Foley et al., 2017a; Shan et al., 2019). Briefly, read coverage is calculated at each nucleotide in the genome and a Poisson test was used to determine an enrichment score for footprint compared to structure-only samples. PPSs were then called with a false discovery rate of 5% as previously described (Silverman et al., 2014; Gosai et al., 2015; Foley et al., 2017a; Shan et al., 2019).
mRNA structure scores - The structure score for every nucleotide of detected mRNAs was calculated using all mapped and spliced reads. We only considered mRNAs with a ≥ 37 nt 5’ UTRs, ≥ 175 nt 3’ UTRs and a minimum coverage of 25 reads across the entire transcript in both conditions.
Assembly: rn6
Supplementary files format and content: BED format of protein protected sites (PPSs), bw for structure scores.
Library strategy: PIP-seq

extract_protocol:
Control- and NMDA-treated cells collected and resuspended in Lysis buffer
PIP-seq libraries were constructed as previously described (Kramer and Gregory, 2019). To summarize, INTACT purified nuclei from 3 grams of tissue per replicate were lysed and separated into footprinting and structure-only samples. The footprinting samples were then treated with either dsRNase (ds-P) or ssRNase (ss-P) before protein digestion by proteinase K and reversal of crosslinks. In the structure-only samples, proteins were first digested with proteinase K before treatment with either dsRNase (P-ds) or ssRNase (P-ss). Each sample resulted in 4 libraries: 2 footprinting libraries (ss-P, ds-P) and 2 structure-only libraries (P-ss, P-ds). All libraries were sequenced on an Illumina HiSeq2000 using the standard protocol for 50 base pair single read sequencing.

tag: rnase

value: ssRNase (Rnase ONE)

tag: protein-bound

value: yes


title: neuron_ctrl_rep2

value: control


title: Control participant 8

description:
MethylationEPIC (850 k)
X204088020016_R04C01

tag: tissue

tag: age (days)

tag: vo2 max est.

tag: gripmax[kg]

tag: ldl

tag: hdl

tag: tg


title: neuron_NMDA_rep3_ssRNase_noprotein


title: neuron_NMDA_rep3_dsRNase_protein

value: dsRNase (Rnase V1)


title: neuron_NMDA_rep3_dsRNase_noprotein


title: atg5_WSM_rep1

tag: strain


title: neuron_NMDA_rep2_ssRNase_protein

description:
neuron_NMDA_rep2_merged_merged.CSAR_PPS_FDR05.bed.gz
neuron_NMDA_rep2_noprotein_NR_structure_unspliced_std.bed12.gz


title: neuron_NMDA_rep2_dsRNase_noprotein


title: neuron_ctrl_rep3_ssRNase_protein

description:
neuron_ctrl_rep3_merged_merged.CSAR_PPS_FDR05.bed.gz
neuron_ctrl_rep3_noprotein_NR_structure_unspliced_std.bed12.gz


title: neuron_NMDA_rep2_dsRNase_protein


title: neuron_ctrl_rep3_dsRNase_protein


title: WT_NM_rep3


title: neuron_ctrl_rep3_dsRNase_noprotein


title: neuron_ctrl_rep2_ssRNase_noprotein

description:
neuron_ctrl_rep2_merged_merged.CSAR_PPS_FDR05.bed.gz
neuron_ctrl_rep2_noprotein_NR_structure_unspliced_std.bed12.gz


title: neuron_ctrl_rep2_dsRNase_protein


title: neuron_ctrl_rep2_ssRNase_protein


title: scRNAseq_Donor4_Replicate1_CMP

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Rd

department: Meinig School of Biomedical Engineering

institute: Cornell University

description:
Library name: scRNAseq_Donor4_Replicate1_CMP
CMP S7

library_source: other

data_processing:
Bulk RNA-seq reads were aligned to the human genome (GRCh38) using STAR, and gene expression counts were processed with DESeq2 for normalization and differential expression analysis. For single cell RNAseq, raw base call files were demultiplexed and converted to FASTQ files using Cell Ranger mkfastq. Reads were aligned to the GRCh38 reference genome using Cell Ranger multi (10X Genomics, v6.1.2), and UMI-based gene-barcode matrices were generated. Downstream processing, including quality control, normalization, clustering, and differential gene expression analysis, was performed using Scanpy (v1.10.1). Cells with fewer than 500 detected genes, fewer than 1,000 UMI counts, or >20% mitochondrial content were filtered out. Doublets were removed using Scrublet (v0.2.3), and data were normalized to 10,000 counts per cell and log-transformed for analysis.
Assembly: GRCh38 (GENCODE v38)
Supplementary files format and content: bulkRNA-seq: CSV files containing gene expression counts and sample meta data.
Supplementary files format and content: scRNA-seq: H5AD files containing raw gene expression profiles from cellranger as well as CSV file containing CellRanger multi config information for CellPlex experiments.

molecule: other

growth_protocol: Peripheral blood was collected from healthy adult volunteers under IRB-approved protocols. No in vitro expansion or culture of cells was performed. Peripheral blood mononuclear cells (PBMCs) were isolated directly from whole blood using Ficoll-Paque™ density gradient centrifugation.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. Cells were first lysed in RNAlater and RLT buffer containing β-mercaptoethanol, followed by RNA purification, DNase treatment, and elution. RNA integrity and concentration were assessed using a NanoDrop spectrophotometer. For single cell RNA-seq, live PBMCs were labeled using the 10X Genomics 3' CellPlex Kit Set A.
For bulk RNA sequencing, RNA samples were treated with DNase before library preparation using the TruSeq RNA Library Prep Kit (Illumina) and sequenced on a NovaSeq 6000 system. Single-cell RNA sequencing (scRNA-seq) was performed using the 10X Genomics 3’ Gene Expression platform and single-cell libraries were generated using the Chromium Single Cell 3’ v3.1 Reagent Kit with Feature Barcoding technology. All libraries were sequenced on an Illumina NovaSeq 6000 system.

treatment_protocol: PBMCs were incubated at 1×10⁶ cells/mL in RPMI-1640 medium under the following conditions for 16 hours: control (DMSO vehicle), 1000 nM BTP2, 2 µg/mL PHA, 2 µg/mL PHA + 1000 nM BTP2, or 2 µg/mL PHA + 1000 nM CM4620. Cells were incubated at 37°C with 5% CO₂.

value: PBMCs

value: Multiplexed and pooled


title: scRNAseq_Donor4_Replicate2_CMP

description:
Library name: scRNAseq_Donor4_Replicate2_CMP
CMP S8


title: scRNAseq_Donor3_Replicate1_CMP

description:
Library name: scRNAseq_Donor3_Replicate1_CMP
CMP S5


title: scRNAseq_Donor3_Replicate2_CMP

description:
Library name: scRNAseq_Donor3_Replicate2_CMP
CMP S6


title: scRNAseq_Donor2_Replicate2_CMP

description:
Library name: scRNAseq_Donor2_Replicate2_CMP
CMP S4


title: scRNAseq_Donor1_Replicate2_CMP

description:
Library name: scRNAseq_Donor1_Replicate2_CMP
CMP S2


title: scRNAseq_Donor2_Replicate1_CMP

description:
Library name: scRNAseq_Donor2_Replicate1_CMP
CMP S3


title: neuron_ctrl_rep1


title: scRNAseq_Donor1_Replicate1_CMP

description:
Library name: scRNAseq_Donor1_Replicate1_CMP
CMP S1


title: scRNAseq_Donor3_Replicate2_GEX

description:
Library name: scRNAseq_Donor3_Replicate2_GEX
S6

library_source: transcriptomic single cell


title: scRNAseq_Donor1_Replicate2_GEX

description:
Library name: scRNAseq_Donor1_Replicate2_GEX
S2


title: scRNAseq_Donor2_Replicate1_GEX

description:
Library name: scRNAseq_Donor2_Replicate1_GEX
S3


title: bulkRNAseq_Donor4_PBMC+PHA+CM4620

description:
Library name: bulkRNAseq_Donor4_Condition6
S45


title: scRNAseq_Donor2_Replicate2_GEX

description:
Library name: scRNAseq_Donor2_Replicate2_GEX
S4


title: bulkRNAseq_Donor4_PBMC+CM4620

description:
Library name: bulkRNAseq_Donor4_Condition5
S44


title: neuron_ctrl_rep2_dsRNase_noprotein


title: neuron_NMDA_rep2_ssRNase_noprotein

description:
neuron_NMDA_rep2_merged_merged.CSAR_PPS_FDR05.bed.gz
neuron_NMDA_rep2_noprotein_NR_structure_unspliced_std.bed12.gz


title: scRNAseq_Donor1_Replicate1_GEX

description:
Library name: scRNAseq_Donor1_Replicate1_GEX
S1


title: bulkRNAseq_Donor4_PBMC(Control)

description:
Library name: bulkRNAseq_Donor4_Condition1
S40

value: DMSO


title: bulkRNAseq_Donor4_PBMC+PHA

description:
Library name: bulkRNAseq_Donor4_Condition2
S41

value: Blood

value: PHA


title: bulkRNAseq_Donor3_PBMC+PHA+CM4620

description:
Library name: bulkRNAseq_Donor3_Condition6
S39


title: bulkRNAseq_Donor3_PBMC+CM4620

description:
Library name: bulkRNAseq_Donor3_Condition5
S38


title: bulkRNAseq_Donor4_PBMC+BTP2

description:
Library name: bulkRNAseq_Donor4_Condition3
S42


title: scRNAseq_Donor4_Replicate2_GEX

description:
Library name: scRNAseq_Donor4_Replicate2_GEX
S8


title: neuron_ctrl_rep3_ssRNase_noprotein

description:
neuron_ctrl_rep3_merged_merged.CSAR_PPS_FDR05.bed.gz
neuron_ctrl_rep3_noprotein_NR_structure_unspliced_std.bed12.gz

value: no


title: bulkRNAseq_Donor3_PBMC+PHA+BTP2

description:
Library name: bulkRNAseq_Donor3_Condition4
S37


title: scRNAseq_Donor3_Replicate1_GEX

description:
Library name: scRNAseq_Donor3_Replicate1_GEX
S5


title: bulkRNAseq_Donor4_PBMC+PHA+BTP2

description:
Library name: bulkRNAseq_Donor4_Condition4
S43


title: scRNAseq_Donor4_Replicate1_GEX

description:
Library name: scRNAseq_Donor4_Replicate1_GEX
S7


title: bulkRNAseq_Donor3_PBMC(Control)

description:
Library name: bulkRNAseq_Donor3_Condition1
S34


title: bulkRNAseq_Donor2_PBMC+CM4620

description:
Library name: bulkRNAseq_Donor2_Condition5
S32


title: bulkRNAseq_Donor2_PBMC+PHA+CM4620

description:
Library name: bulkRNAseq_Donor2_Condition6
S33


title: bulkRNAseq_Donor2_PBMC+PHA+BTP2

description:
Library name: bulkRNAseq_Donor2_Condition4
S31


title: bulkRNAseq_Donor2_PBMC+BTP2

description:
Library name: bulkRNAseq_Donor2_Condition3
S30


title: bulkRNAseq_Donor2_PBMC(Control)

description:
Library name: bulkRNAseq_Donor2_Condition1
S28


title: bulkRNAseq_Donor1_PBMC+PHA+CM4620

description:
Library name: bulkRNAseq_Donor1_Condition6
S27


title: bulkRNAseq_Donor1_PBMC+PHA+BTP2

description:
Library name: bulkRNAseq_Donor1_Condition4
S25


title: bulkRNAseq_Donor1_PBMC+PHA

description:
Library name: bulkRNAseq_Donor1_Condition2
S23


title: bulkRNAseq_Donor3_PBMC+BTP2

description:
Library name: bulkRNAseq_Donor3_Condition3
S36


title: 119ub1-OLD_Rep2

city: Tianjin

first: Liangyu

last: Xing

address: 22nd Qixiangtai Road

country: China

institute: Tianjin Medical University

description: Library name: Sample 4

library_source: genomic

data_processing:
Sequencing quality was checked by fastqc.
Use trim-galore to filter the adapters.
Clean reads were aligned to UCSC mm39 reference genome and λDNA (TD904, Vazyme Biotech Co.,Ltd), using bowtie2 with the following parameters: --phred33 --end-to-end --very-sensitive --no-mixed --no-discordant --no-unal -I 10 -X 700
Dupulicates were removed by sambamba.
Bam files were sorted and bulit index by samtools
Used deeptools to generate bigwig files, according to scale-factor to normalize.
Peak was calling by macs2, and annotated by ChIPseeker.
Assembly: mm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

organism: Mus musculus

source_name: femur

growth_protocol: Osteoblasts were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
The CUT&Tag assay of osteoblasts were performed using Hyperactive Universal CUT & Tag Assay Kit (TD904, Vazyme Biotech Co.,Ltd), the chromatin was incubated with H2AK119ub1 antibody.
The DNA Library of CUT&TAG were prepared according to the manufacturer's instructions (TD904, Vazyme).

treatment_protocol: In Aging CUT&Tag，osteoblats isolated from femur of 3-month and 18-month mice(C57BL/6J). In CKO CUT&Tag,Kdm2b-CxxC domain conditional knockout osteoblats isolated and screening from femur of Kdm2bfl/fl Ocncre Ai14 (C57BL/6J), osteoblats isolated from Ocncre Ai14 mice as control.

value: femur

tag: cell line

value: Osteoblast

value: mice femoral osteoblast


title: Fes_PBS_Biol_2

city: Kingston

first: Peter

middle: A

last: Greer

state: ON

address: 18 Stuart St.

department: Sinclair Cancer Research Institute

country: Canada

institute: Queen's University

description: Library name: Fes + PBS 2

data_processing:
STAR v2.7.8a, PICARD v2.9.0, RNASeQC v1.1.8, R v4.1.12, DESeq2 v1.34.0, pheatmap v1.0.12
The raw FASTQ reads were aligned to the GRCm38 genome with STAR (-- runMode alignReads --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate) with the --quantMode GeneCounts option to generate gene counts based on the Ensembl 102 Mouse exonic annotation. A raw count table was created using each samples stranded counts from the 2nd read strand.
Metrics and QCs were performed on the alignments with PICARD and RNASeQC.
QCs were performed on the raw counts in R using DESeq2 and pheatmap
TPM normalization was carried out in R.
Assembly: GRCm38 (Ensembl 102), mm9
Supplementary files format and content: Csv file containing raw gene counts for each sample
Supplementary files format and content: Csv file containing Transcripts per million for each sample

source_name: bone marrow

growth_protocol: BMDMs from fesFes+/+ and fesFes-/- mice were plated in 6-well flat bottom TC-treated plates (Corning, USA) at 2,500,000 cells per well in 2mL of complete macrophage media (RPMI 1640 supplemented with 15% FBS, 1% A/A, 50µM α-monothioglycerate, and 20ng/mL macrophage colony-stimulating factor) and kept in a humidified incubator at 5% CO2 and 37C.

extract_protocol:
RNA purification was performed according to Invitrogen’s TrizolTM Regent protocol. Purified RNA sample concentrations were determined with a NanoDrop ND-1000 spectrophotometer for downstream cDNA synthesis.
cDNA synthesis was carried out using the Maxima First Strand cDNA synthesis kit (Thermo Fisher Scientific, USA) according to manufacturer’s instructions, with 372ng of RNA as the starting template. RNA quality and quantity were confirmed via NanoDrop measurement. All samples possessed an A260/280 purity ratio >1.7 and were sent to Genome Quebec (Montreal, Canada; RRID:SCR_017703) for poly-A enriched RNA-sequencing.

treatment_protocol: The BMDMs were either left untreated, or they were stimulated with 1μg/mL LPS for 4 hours.

value: bone marrow

value: primary cells

value: macrophages

tag: genotype

value: Fes-/-

value: PBS

tag: time

value: 4 hours

tag: batch


title: Fes_LPS_Biol_3

description: Library name: Fes + LPS 3

value: LPS


title: Fes_PBS_Biol_3

description: Library name: Fes + PBS 3


title: Fes_LPS_Biol_2

description: Library name: Fes + LPS 2


title: 119ub1-YOUNG_Rep2

description: Library name: Sample 2


title: Fes_PBS_Biol_1

description: Library name: Fes + PBS 1


title: WT_LPS_Biol_2

description: Library name: WT + LPS 2

value: Fes+/+


title: WT_LPS_Biol_3

description: Library name: WT + LPS 3


title: Fes_LPS_Biol_1

description: Library name: Fes + LPS 1


title: bulkRNAseq_Donor2_PBMC+PHA

description:
Library name: bulkRNAseq_Donor2_Condition2
S29

value: PBMCs


title: WT_LPS_Biol_1

description: Library name: WT + LPS 1


title: CRISPR library from Cal27 derived tumor 1 from mouse replicate 3

city: Stanford

first: Luca

last: Ducoli

state: CA

address: 269 Campus Drive CCSR 2150

institute: Stanford University

description: Library name: LD_Cal27_T_3_1

data_processing:
In each screen, UMI was compressed using umi_tools extract, and adaptor sequences were removed using cutadapt. Subsequently, the remaining reads were aligned on the guide sequences using bowtie (maximum error: 1, minimum length: 16). The count for each guide was collected using umi_tools count, then transformed into scc format. For in vitro screen analysis, MaGeCK MLE was performed based on the guide counts with the design matrix of comparing the timepoint of the initial collection and the post-screen collection as described in (W. Li et al. 2015). In vivo and in vitro CRISPR screens were integrated by first determining the ß scores of each sample against plasmid DNA determined by miSeq (Illumina) using the MaGeCK MLE algorithm (W. Li et al. 2015). ß scores were normalized and visualized using the MaGeCKFlute R package (B. Wang et al. 2019) following the authors’ guidelines.
Assembly: hg38
Supplementary files format and content: tab separated txt file containing unnormalized feature (guide) counts
Library strategy: CRISPR Screen

growth_protocol: The human A431 and Cal27 cell lines were cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C

extract_protocol:
Three mice (a total of six tumors) were performed on each cell line. Based on the visual observation of subcutaneous tumor growths, the mice injected with the same cell lines were sacrificed on the same days after 3-4 weeks. (A431: 3.5 weeks, Cal27: 4.5 weeks) The tumors were surgically harvested, minced, and homogenized in an MP Biomedical lysing matrix A tube. Genomic DNA was isolated using QIAGEN DNeasy Blood and Tissue Kit
Sequencing library was made as described in (Mathiowetz et al. 2023, PMID: 37000620) with an adjustment of using <10g of gDNA in PCR1 reaction and a pair of primers matching with our sequences and manually determining PCR2 cycles based on a trial run to prevent overamplification.

treatment_protocol: The pooled oligo Lenti virus was made and transfected on dCas9-KRAB expressing A431 and Cal27 with MOI of 0.3.. After the 3 days of selection in puromycin, the transfection rates were chekced with Cell Titer Blue. Four million cells in 100ul were gently mixed with 50ul Matrigel (Corning) until it turned into a homogenous mixture and injected with 28G insulin syringe into both sides of rear flanks of SCID Hairless Outbred (SHO®) mice (Charles River). Triplicate of cells (with +1000x coverage) were collected, flash frozen, and stored at -80C for each replicate as the initial screen time point.

value: Lentivirus-mediated CRISPR library infection and a tumor grown in mouse


title: CRISPR library from Cal27 cells, week 0, replicate 3

description: Library name: LD_Cal27_W0_3

value: Lentivirus-mediated CRISPR library infection


title: CRISPR library from Cal27 cells, week 0, replicate 2

description: Library name: LD_Cal27_W0_2


title: CRISPR library from Cal27 cells, week 0, replicate 1

description: Library name: LD_Cal27_W0_1


title: bulkRNAseq_Donor1_PBMC(Control)

description:
Library name: bulkRNAseq_Donor1_Condition1
S22

value: Blood

value: DMSO


title: WT_PBS_Biol_2

description: Library name: WT + PBS 2


title: WT_PBS_Biol_3

description: Library name: WT + PBS 3


title: Single cell sequencing of transformed human KC with CDK4(R24C)-Ras(G12V)

description: Library name: scSeq_transformed_KC

data_processing:
Single-cell RNA-seq data from Cal27 xenograft (Ji et al. 2020) and CDK4(R24C)-Ras(G12V) transformed spheroids were mapped as described above. Seurat objects were generated, and expression values were normalized using the SCTransform() function from the Seurat R package (Satija et al. 2015).
Assembly: hg38
Supplementary files format and content: cellranger outputs including barcode, feature, matrix, and h5 files

source_name: Human Kertatinocyte

growth_protocol: The cultures were incubated at 37°C in a 5% CO2 incubator for a week.

extract_protocol:
Spheroids were then collected in a 15mL falcon tube and reduced to single-cell suspension using 0.25% trypsin with DNase I (0.2 mg/mL, Worthington) and Collagenase I (5 mg/mL, Gibco) for 30 minutes at 37°C. Cells were washed 3 times in DMEM containing 10% FBS. Cells were collected by centrifugation at 450g for 5min and finally resuspended in PBS (Gibco) containing 0.04% BSA. Cell count was determined using a Countess machine (Thermo Fisher). After passing through a cell strainer (Corning), 25’000 cells were loaded into a 10x Chromium machine (10x genomics).
Library preparation was performed using the Chromium GEM-X Single Cell 3’ Kit (10x Genomics), followed by sequencing at Novogene.

treatment_protocol: A 10mg/mL solution of Poly(2-hydroxyethyl methacrylate) (pHEMA, sigma) was prepared in 95% ethanol and warmed at 37°C until fully dissolved. Two layers of PHEMA were applied to 10cm dishes by spreading 5mL of the solution and allowing it to dry under a tissue culture hood for 24 hours per layer. The coated dishes were sterilized under UV light for at least 15 minutes prior to use. For spheroid formation, CDK4(R24C)-Ras(G12V) cells were seeded into pHEMA-coated 10cm dishes at a final concentration of 2.5x105 cells/mL in KGM medium for spheroid formation.

value: Human Kertatinocyte

value: Lentiviral transfection of CDK4(R24C)-Ras(G12V)


title: CRISPR library from Cal27 derived tumor 1 from mouse replicate 2

description: Library name: LD_Cal27_T_2_1


title: WT_PBS_Biol_1

description: Library name: WT + PBS 1


title: bulkRNAseq_Donor1_PBMC+CM4620

description:
Library name: bulkRNAseq_Donor1_Condition5
S26


title: bulkRNAseq_Donor1_PBMC+BTP2

description:
Library name: bulkRNAseq_Donor1_Condition3
S24


title: CRISPR library from Cal27 derived tumor 1 from mouse replicate 1

description: Library name: LD_Cal27_T_1_1


title: CRISPR library from Cal27 derived tumor 2 from mouse replicate 3

description: Library name: LD_Cal27_T_3_2


title: Lung, TTI-101, 2

city: Houston

first: Michael

middle: Joseph

last: Clowers

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Ancerson Cancer Center

description: Library name: C2

data_processing:
Sequence reads were analyzed with the STAR alignment–DESeq2 software pipeline
Assembly: mm10
Supplementary files format and content: gene counts

source_name: Lung

extract_protocol:
Mouse lung RNA was extracted by placing cryopreserved lung tissue into tubes containing chrome plated steel beads and QIAzol (Qiagen). Tubes were then shaken on a Mini-BeadBeater 16 (BioSpec) for 10-20 seconds twice, incubating samples on ice between each round. Homogenates were then passed through a QIAshredder (Qiagen) for further cellular lysis. RNA extraction was then performed using the RNeasy Mini kit (Qiagen) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594)

value: Lung

value: CC-LR


title: CRISPR library from A431 cells, week 0, replicate 3

description: Library name: LD_A431_W0_3


title: Lung, TTI-101, 4

description: Library name: D2


title: Lung, TTI-101, 1

description: Library name: C1


title: CRISPR library from A431 cells, week 0, replicate 2

description: Library name: LD_A431_W0_2


title: CRISPR library from A431 derived tumor 2 from mouse replicate 3

description: Library name: LD_A431_T_3_2


title: Lung, Control, 4

description: Library name: B2

value: Control


title: CRISPR library from Cal27 derived tumor 2 from mouse replicate 2

description: Library name: LD_Cal27_T_2_2


title: Lung, Control, 2

description: Library name: A2


title: CRISPR library from A431 derived tumor 2 from mouse replicate 1

description: Library name: LD_A431_T_1_2


title: CRISPR library from A431 derived tumor 1 from mouse replicate 3

description: Library name: LD_A431_T_3_1


title: Lung, Control, 1

description: Library name: A1


title: CRISPR library from A431 derived tumor 1 from mouse replicate 2

description: Library name: LD_A431_T_2_1


title: CRISPR library from A431 derived tumor 2 from mouse replicate 2

description: Library name: LD_A431_T_2_2


title: CRISPR library from A431 derived tumor 1 from mouse replicate 1

description: Library name: LD_A431_T_1_1


title: MA9_FLT3ITD_Setd1b_dSET_NC_H3K4me3

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description: Library name: sample15

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.1.0.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-1.56.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: mouse MLL-AF9 leukemia cells were grown in RPMI media supplemented with 10% FBS, penicillin/streptomycin, and 10 ng/ml rmIL-3.

extract_protocol:
Cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated. For histone modifications, DSG treatment was skipped.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: leukemia

value: Setd1b SET knockout

value: After wash with PBS, the cells were incubated without cytokines for 24 hr.

tag: chip antibody

value: H3K36me3 (abcam Cat#ab9050)


title: H3K4me3-CUTRUN_DMSO_MLF2-dTAG

city: Geneva

first: Simon

last: Braun

address: rue Michel Servet 1

country: Switzerland

institute: University of Geneva

description:
Library name: H3K4me3-CUTRUN_DMSO_MLF2-dTAG
CUT&RUN

data_processing:
Sequencing reads were trimmed using cutadapt 3.5 (adapters -m 20 -O 5 -p). Reads were aligned to the mouse mm10 and E. coli K12 MG1655 genomes using bowtie2 v2.4.4 (-p 8 --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000). Alignments were filtered using samtools v1.12 (view -h -F 1796 -q 20). Cut&Run peaks in mm10 were called using MACS2 v2.7.1 (callpeak --format BAMPE --nomodel --call-summits --shift -100 --extsize 200 --keep-dup all -B -g mm). Peaks from all replicates within 1 kb were merged using bedtools v2.30. Normalization scaling factors were calculated based on the spiked-in E. coli reads obtained from each replicate. Genome coverage files (bigwig) were generated with deepTools v3.5.2 (bamCoverage --binSize 10 --scaleFactor --normalizeUsing RPKM --ignoreForNormalization chrM ChrUn ChrRandom -p max). For IGV genome browser snapshots, average of replicates genome coverage files (bigwig) was generated with deepTools v3.5.2 (bigwigAverage for merging replicates). deepTools v3.5.2 was used to produce heat maps of SMARCA4 Cut&Run mean read density across Cut&Run and ATAC-seq peaks.
Assembly: mm10
Supplementary files format and content: bigwig file normalized to spike-in scale factor
Library strategy: Cut & Run

source_name: mESC

growth_protocol: mESCs were cultured in media containing DMEM media, supplemented with LIF, 15% FBS, 0.1 mM β-Mercapthoethanol, 1x non-essential amino acids, 100 mM Hepes buffer, 100 U/ml Penicillin-Streptomycin at 37°C and 5% CO2 on plates coated with 0.2% gelatin solution

extract_protocol:
For CUT&RUN analysis 500.00 cells were collected and directly processed. The experiment was conducted with the CUTANA ChIC/CUT&RUN Kit (Epicypher, 14-1048), according to the manufacturers instructions.
Sequencing libraries were prepared from 2ng uL of Cut&Run-enriched DNA using the Illumina TruSeq ChIP Library Preparation Kit and the IDT TruSeq RNA UD Indexes v2. No size selection was performed. Library molarity and quality were assessed by Qubit and Tapestation (DNA High sensitivity chip).
. Libraries were sequenced on a NovaSeq 6000 Illumina sequencer with paired-end 50 settings.

tag: cell type

value: mESC


title: IgG-CUTRUN_DMSO_MLF2-dTAG

description:
Library name: IgG-CUTRUN_DMSO_MLF2-dTAG
CUT&RUN

tag: treatment


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 1.5, replicate 3

description: Library name: LD_Kerat_W1_TSK3

source_name: Human Keratinocyte

growth_protocol: The human A431 and Cal27 cell line was cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C. Primary human keratinocytes were obtained from fresh, surgically discarded neonatal foreskin, cultured in Keratinocyte-SFM and Medium 154 with Keratinocyte supplement, and subcultured regularly before reaching high confluency for a few cycles.

extract_protocol:
DNA was isolated from the cell pellet using QIAGEN DNeasy Blood and Tissue Kit
The sequencing library was made as described in (Ji et al. 2020) [PMID: 32579974]

treatment_protocol: Lentivirus has been produced in Lenti-X cells seeded higher than 70% in 10cm (or 15cm) dish. Cells in each 10cm dish were transfected with 7.5ug CMV, 3.5ug MDG, 7.5ug Plasmid in 625ul OptiMEM mixed with another tube containing 25ul Lipofectamine in 625ul OptiMEM. (The volume or amount were doubled for cells in 15cm dish). The media was replaced after the overnight incubation, collected after every 24h with media replacement for two times, filtered through a 0.45um PES membrane, and concentrated with Lenti-X concentrator (Takara). Cas9 transfection was performed on A431, Cal27, and Primary Keratinocytes and selected with blasticidin. Pooled guide lentivirus was titrated in each of dCas9-KRAB expressing cell lines to achieve an MOI of 0.3. Following selection with puromycin for two to three days, the transfection rates were checked with Cell Titer Blue, and triplicate of cells (with +1000x coverage) were collected, flash frozen, and stored at -80°C for each replicate as the initial screen time point. Cells were cultured by maintaining at least 1000x coverage with regular basis of subculturing for three weeks (Primary Keratinocyte for 1.5 week due to inherently limited proliferation capacity).

value: Human Keratinocyte


title: MA9_FLT3ITD_Setd1b_WT_NC_H3K4me3

description: Library name: sample14

value: Setd1b SET wildtype


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 1.5, replicate 2

description: Library name: LD_Kerat_W1_TSK2


title: SMARCA4-CUTRUN_dTAG13_MLF2-dTAG_Rep3

description:
Library name: SMARCA4-CUTRUN_dTAG13_MLF2-dTAG_Rep3
CUT&RUN


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 1.5, replicate 1

description: Library name: LD_Kerat_W1_TSK1


title: CRISPR library from Cal27 derived tumor 2 from mouse replicate 1

description: Library name: LD_Cal27_T_1_2


title: Lung, TTI-101, 3

description: Library name: D1


title: SMARCA4-CUTRUN_dTAG13_MLF2-dTAG_Rep2

description:
Library name: SMARCA4-CUTRUN_dTAG13_MLF2-dTAG_Rep2
CUT&RUN


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 0, replicate 3

description: Library name: LD_Kerat_W0_TSK3


title: Lung, Control, 3

description: Library name: B1


title: SMARCA4-CUTRUN_dTAG13_MLF2-dTAG_Rep1

description:
Library name: SMARCA4-CUTRUN_dTAG13_MLF2-dTAG_Rep1
CUT&RUN


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 0, replicate 2

description: Library name: LD_Kerat_W0_TSK2


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 0, replicate 1

description: Library name: LD_Kerat_W0_TSK1


title: SMARCA4-CUTRUN_DMSO_MLF2-dTAG_Rep2

description:
Library name: SMARCA4-CUTRUN_DMSO_MLF2-dTAG_Rep2
CUT&RUN


title: SMARCA4-CUTRUN_DMSO_MLF2-dTAG_Rep3

description:
Library name: SMARCA4-CUTRUN_DMSO_MLF2-dTAG_Rep3
CUT&RUN


title: CRISPR library from A431 cells, week 0, replicate 1

description: Library name: LD_A431_W0_1


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 1.5, replicate 3

description: Library name: LD_Kerat_W1_KC3


title: SMARCA4-CUTRUN_DMSO_MLF2-dTAG_Rep1

description:
Library name: SMARCA4-CUTRUN_DMSO_MLF2-dTAG_Rep1
CUT&RUN


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 0, replicate 3

description: Library name: LD_Kerat_W0_KC3


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 1.5, replicate 1

description: Library name: LD_Kerat_W1_KC1


title: Top1-cKO_T-cells_Rep3

city: Bangalore

first: Kushagra

last: Bansal

state: Karnataka

address: Jakkur

department: MBGU

country: India

institute: JNCASR

description: RNA-seq

data_processing:
The fastq files were trimmed to 50bp and low-quality reads were removed using fastx (v0.0.13) and sickle (v1.33.0) respectively. These 50bp reads were aligned to mouse genome (mm10) using hisat2 (v2.2.1).
The read counts for each gene were generated using htseq (v0.12.4). Differential gene expression analysis was performed using the DESeq2 R package.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: CD4+ T cells

extract_protocol:
EpCAM+CD45-MHCIIhiLy51hi cTEChi and EpCAM+CD45-MHCIIhiLy51lo mTEChi cells were sorted from 2-weeks-old mice and TCRb+CD4+ T cells were sorted from spleen of 7-weeks-old mice. Total RNA was isolated using TRI reagent. RNA concentration and integrity was assessed using Tapestation.
~2ng of RNA was used to prepare RNA-seq library using Takara SMARTer® Stranded Total RNA-Seq Kit v2 according to manufacturer’s instructions.

value: CD4+ T cells


title: Top1-WT_T-cells_Rep3

description: RNA-seq


title: Top1-cKO_T-cells_Rep2

description: RNA-seq


title: CRISPR library from_Cal27 cells, TSK library, Week 3, replicate 3

description: Library name: LD_Cal27_W3_TSK3


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 1.5, replicate 2

description: Library name: LD_Kerat_W1_KC2


title: Top1-WT_T-cells_Rep2

description: RNA-seq


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 0, replicate 1

description: Library name: LD_Kerat_W0_KC1


title: CRISPR library from_Cal27 cells, TSK library, Week 3, replicate 2

description: Library name: LD_Cal27_W3_TSK2


title: Top1-WT_T-cells_Rep1

description: RNA-seq


title: Top1-cHet_mTECs_Rep2

description: RNA-seq

source_name: mTEChi

value: mTEChi


title: CRISPR library from_Cal27 cells, TSK library, Week 3, replicate 1

description: Library name: LD_Cal27_W3_TSK1

value: Lentivirus-mediated CRISPR library infection


title: CRISPR library from_Cal27 cells, TSK library, Week 0, replicate 3

description: Library name: LD_Cal27_W0_TSK3


title: Top1-cHet_mTECs_Rep1

description: RNA-seq


title: Top1-cHet_cTECs_Rep2

description: RNA-seq

source_name: cTEChi

value: cTEChi


title: CRISPR library from_Cal27 cells, TSK library, Week 0, replicate 2

description: Library name: LD_Cal27_W0_TSK2


title: CRISPR library from_Cal27 cells, TSK library, Week 0, replicate 1

description: Library name: LD_Cal27_W0_TSK1


title: Top1-cHet_cTECs_Rep1

description: RNA-seq


title: CRISPR library from_Cal27 cells, KC library, Week 3, replicate 3

description: Library name: LD_Cal27_W3_KC3


title: Top1-WT_mTECs_Rep1

description: RNA-seq


title: CRISPR library from_Cal27 cells, KC library, Week 3, replicate 2

description: Library name: LD_Cal27_W3_KC2


title: Top1-cKO_T-cells_Rep1

description: RNA-seq


title: Top1-WT_cTECs_Rep1

description: RNA-seq


title: Top1-WT_cTECs_Rep2

description: RNA-seq


title: CRISPR library from_Cal27 cells, KC library, Week 0, replicate 3

description: Library name: LD_Cal27_W0_KC3


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 0, replicate 2

description: Library name: LD_Kerat_W0_KC2


title: 24hdTAG13_SMARCA4-dTAG_RNA_Rep3

description:
3' mRNA seq
Brg1_12
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed

data_processing:
Sequencing reads were trimmed using cutadapt68 v3.5 (removal of truseq adapter sequences, polyA sequences, and low quality reads). Trimmed reads were aligned to the mouse genome (mm10) using STAR69 v2.7.5 (STARoptions, --readFilesCommand zcat --runThreadN 8 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000). Gene count matrices were obtained from the aligned reads using featureCounts70 v2.0.3 (-t exon -g gene_id -O -T 4 -s 1 -a GRCm38.102).
Differential gene expression analysis between conditions was determined using the R package DESeq271 after pre-filtering genes with low counts (rowSums > 10), with significance cut-offs set at FDR < 0.05 and fold change > 1.5 in either direction.
Assembly: mm10
Supplementary files format and content: bed file gene counts for all conditions

source_name: Embryonic stem cells (mESC)

extract_protocol:
For RNA-seq analysis cell pellets were collected and stored at -80°C. RNA was then isolated using the RNAeasy kit (Qiagen, 74106).
Sequencing libraries were generated using the Collibri 3’ mRNA Library Prep Kit for Illumina (Invitrogen, A38110024), according to the manufacturer’s instructions.
Libraries were sequenced on an NovaSeq 6000 Illumina sequencerwith single-end 100 settings.

value: Embryonic stem cells (mESC)


title: 24hdTAG13_SMARCA4-dTAG_RNA_Rep2

description:
3' mRNA seq
Brg1_11
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: CRISPR library from_A431 cells, TSK library, Week 3, replicate 3

description: Library name: LD_A431_W3_TSK3


title: CRISPR library from_Cal27 cells, KC library, Week 0, replicate 1

description: Library name: LD_Cal27_W0_KC1


title: CRISPR library from_A431 cells, TSK library, Week 3, replicate 2

description: Library name: LD_A431_W3_TSK2


title: CRISPR library from_Cal27 cells, KC library, Week 0, replicate 2

description: Library name: LD_Cal27_W0_KC2


title: 8hdTAG13_SMARCA4-dTAG_RNA_Rep3

description:
3' mRNA seq
Brg1_9
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: 8hdTAG13_SMARCA4-dTAG_RNA_Rep2

description:
3' mRNA seq
Brg1_8
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: 24hdTAG13_SMARCA4-dTAG_RNA_Rep1

description:
3' mRNA seq
Brg1_10
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: CRISPR library from_A431 cells, TSK library, Week 3, replicate 1

description: Library name: LD_A431_W3_TSK1


title: 8hdTAG13_SMARCA4-dTAG_RNA_Rep1

description:
3' mRNA seq
Brg1_7
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: CRISPR library from_A431 cells, TSK library, Week 0, replicate 3

description: Library name: LD_A431_W0_TSK3


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #2). Replicate 1

description: Library name: S16_1116_2_1

data_processing:
For analyzing differentially expressed genes compared to the control, raw reads were first quantified with Salmon (ver. 0.12.0) (Patro et al. 2017) using the gencode release v39 basic annotation with the following settings: -l A -p 8 --gcBias --numGibbsSamples 20 --validateMappings.
Assembly: hg38
Supplementary files format and content: Salmon count output files

growth_protocol: The human A431 cell line was cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C

extract_protocol:
After 48h of ASO transfection, cells were lysed in LRT plus lysis buffer (Qiagen), and RNA isolation was performed using an RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
From each sample, 500ng of RNA was used for the library preparation using the kit (QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI, Lexogen), pooled together with an equal concentration, and then sequenced on a NovaSeq X+, paired-end, 150 bp length, with ~30 M reads for each sample.

treatment_protocol: For each ASO, we performed a reverse transfection using Lipofectamine RNAiMAX (Thermo Fisher Scientific). In 10cm dishes, 2mL Opti-MEM, 20nM of scrambled control ASO or two ASOs targeting LINC00704 and LINC01116, and 25µL Lipofectamine RNAiMAX (Thermo) were mixed and incubated for 20min. Then, 1x106 A431 cells per dish were seeded into each 10cm dish and cultured for 48h in a 5% CO2 incubator.

value: LINC01116-ASO transfection with Lipofectamine reagents


title: Top1-WT_mTECs_Rep2

description: RNA-seq


title: 3hdTAG13_SMARCA4-dTAG_RNA_Rep3

description:
3' mRNA seq
Brg1_6
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #2). Replicate 2

description: Library name: S17_1116_2_2


title: CRISPR library from_A431 cells, TSK library, Week 0, replicate 2

description: Library name: LD_A431_W0_TSK2


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #1). Replicate 3

description: Library name: S15_1116_1_3


title: 3hdTAG13_SMARCA4-dTAG_RNA_Rep2

description:
3' mRNA seq
Brg1_5
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: CRISPR library from_Cal27 cells, KC library, Week 3, replicate 1

description: Library name: LD_Cal27_W3_KC1


title: CRISPR library from_A431 cells, TSK library, Week 0, replicate 1

description: Library name: LD_A431_W0_TSK1


title: 3hdTAG13_SMARCA4-dTAG_RNA_Rep1

description:
3' mRNA seq
Brg1_4
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #1). Replicate 2

description: Library name: S14_1116_1_2


title: CRISPR library from_A431 cells, KC library, Week 3, replicate 3

description: Library name: LD_A431_W3_KC1


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #2). Replicate 3

description: Library name: S12_704_2_3

value: LINC00704-ASO transfection with Lipofectamine reagents


title: DMSO_SMARCA4-dTAG_RNA_Rep3

description:
3' mRNA seq
Brg1_3
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed

value: DMSO


title: CRISPR library from_A431 cells, KC library, Week 3, replicate 2

description: Library name: LD_A431_W3_KC3


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #2). Replicate 1

description: Library name: S10_704_2_1


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #1). Replicate 2

description: Library name: S08_704_1_2


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #1). Replicate 3

description: Library name: S09_704_1_3


title: CRISPR library from_A431 cells, KC library, Week 3, replicate 1

description: Library name: LD_A431_W3_KC2


title: DMSO_SMARCA4-dTAG_RNA_Rep1

description:
3' mRNA seq
Brg1_1
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: Bulk RNA-seq in A431 control condition (Non-targeting ASO). Replicate 3

description: Library name: S03_Ctrl_3

value: Non-targeting ASO transfection with Lipofectamine reagents


title: CRISPR library from_A431 cells, KC library, Week 0, replicate 3

description: Library name: LD_A431_W0_KC3


title: DMSO_SMARCA4-dTAG_RNA_Rep2

description:
3' mRNA seq
Brg1_2
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: 24hdTAG13_MLF2-dTAG_RNA_Rep3

description:
3' mRNA seq
Mlf2_12
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #1). Replicate 1

description: Library name: S07_704_1_1


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #2). Replicate 3

description: Library name: S18_1116_2_3


title: CRISPR library from_A431 cells, KC library, Week 0, replicate 2

description: Library name: LD_A431_W0_KC2


title: CD69_TFP_cDNA

city: San Francisco

first: Arja

last: Ray

state: California

address: 513 Parnassus Avenue

department: Pathology

institute: UCSF

description: Library name: Sample 1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: .H5 Matrices

source_name: Primary tumor

extract_protocol:
Pooled 8:2 CD45+:CD45- cells were resuspended in Cell Staining Buffer (BioLegend) and stained with a pool of 137 TotalSeq-C antibodies (Table) according to the manufacturer’s protocol before loading onto the Chromium Controller (10X Genomics) for GEM generation.
The cDNA libraries were generated using all or a subset of Chromium Next GEM Single Cell 5′ Library Kit for gene expression (GEX), Chromium Single Cell V(D)J Enrichment kit (10X Genomics) for T cell receptor (TCR), and Chromium Single Cell 5′ Feature Barcode Library kit for antibody derived tag (ADT) according to the manufacturer’s instructions

value: Primary tumor

value: total RNA


title: CD69_TFP_ADT

description: Library name: Sample 2


title: Bulk RNA-seq in A431 control condition (Non-targeting ASO). Replicate 2

description: Library name: S02_Ctrl_2


title: 24hdTAG13_MLF2-dTAG_RNA_Rep2

description:
3' mRNA seq
Mlf2_11
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: Bulk RNA-seq in A431 control condition (Non-targeting ASO). Replicate 1

description: Library name: S01_Ctrl_1


title: CRISPR library from_A431 cells, KC library, Week 0, replicate 1

description: Library name: LD_A431_W0_KC1


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #1). Replicate 1

description: Library name: S13_1116_1_1


title: 24hdTAG13_MLF2-dTAG_RNA_Rep1

description:
3' mRNA seq
Mlf2_10
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: 8hdTAG13_MLF2-dTAG_RNA_Rep3

description:
3' mRNA seq
Mlf2_9
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: Mouse_Otx2_Atlas_Biological_Rep2_technical_Rep1

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

description:
Library name: Mouse_Otx2_Atlas_B2_T1
Mouse_Otx2_peaks.narrowPeak

data_processing:
Sequence reads were trimmed of low quality bases and adapters using cutadapt v3.5 76and Trim Galore v0.6.4_dev 77, using arguments ---paired --length 20 -e 0.1 --illumina -q 20 --stringency 3. Trimmed reads were aligned to mouse genome GRCm38 and 13LGS genome Itri_07Aug2017 using Bowtie2 78 with arguments -X 1000 --very-sensitive-local --no-mixed --no-discordant --no-dovetail. Unmapped reads with a MAPQ score of 30 or below were filtered from the analysis with SAMtools v1.12 79. Aligned reads were deduplicated using UMI-tools 80 dedup with parameters -chimeric-pairs="discard" --unpaired-reads="discard" --paired --ignore-umi. Technical replicates were collapsed into single biological replicates using samtools merge. For visualization, normalization was applied using deepTools bamCoverage v3.5.1 81 using arguments --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2311060300 (13LGS) or --effectiveGenomeSize 2651675564 (mouse). For each protein target, peaks were called jointly across replicates against IgG control using macs2 82 using arguments -f BAMPE --keep-dup all -q 0.05 -g 2311060300 (13LGS) or -g 2651675564 (mouse). For mouse samples, peaks on mitochondrial reads and blacklisted ENCODE regions 83 were filtered from analysis.
Assembly: GRCm38
Supplementary files format and content: txt for called peaks
Library strategy: CUT&Run

source_name: P2 retina

extract_protocol:
Nuclei were isolated according to the described protocol 75, using a lysis buffer modified to contain 0.01% Tween-20 and 0.01% Nonidet P40, as well as 1X protease inhibitor cocktail (Roche, 11873580001) in all solutions. Samples were lysed for 5 minutes in the lysis buffer with gentle trituration throughout, as described. CUT&RUN was performed using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher, 14-1048). For each reaction, either 500,000 13LGS nuclei or 385,000 mouse nuclei were used. The CUTANA protocol v4.0 protocol was followed with minor modifications. In brief, isolated nuclei were resuspended in CUT&RUN wash buffer and added directly to Concanavalin A beads. Then 0.5 µg of the following antibodies were added to each respective reaction: IgG control (EpiCypher, 13-0042), H3K4me1 (EpiCypher, 13-0057), H3K4me3 (EpiCypher, 13-0041), H3K27ac (EpiCypher, 13-0059), H3K27me3 (EpiCypher, 13-0055), NeuroD1 (Cell Signaling, 62953), Otx2 (R&D Systems, BAF1979), or Otx2 (Atlas Antibodies, HPA000633).  H3K9me3 (Abcam, ab8898) was used at 0.41 µg of antibody per reaction.
The total CUT&RUN DNA yield, up to 5 ng of total purified DNA, was used for library preparation, using reagents from CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001) or NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S). The EpiCypher CUTANA Library Prep Kit User Manual v1.3 was followed and indexing performed using NEBNext® Multiplex Oligos for Illumina® (NEB, E7395S) or Dual Index Kit TT Set A (10X Genomics, PN-1000215). Final libraries were sequenced at the Novogene sequencing core (Sacramento, CA, USA) on the NovaSeq X Plus (Illumina) to generate paired-end 150 base pair reads.

value: P2 retina


title: Mouse_Otx2_Atlas_Biological_Rep2_technical_Rep2

description:
Library name: Mouse_Otx2_Atlas_B2_T2
Mouse_Otx2_peaks.narrowPeak


title: Mouse_Otx2_RD_Biological_Rep2_technical_Rep2

description:
Library name: Mouse_Otx2_RD_B2_T2
Mouse_Otx2_peaks.narrowPeak


title: iNs and iMGLs cultured with CLU KO iAs

city: Boston

first: Courtney

last: Benoit

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description:
Library name: AL118
10X Genomics

data_processing:
Fastq files were mapped using the 10xGenomics Cellanger (v7.0.0) pipeline and a GRCh38 index and resulted in an average of >4K mapped and filtered reads per cell. Mappings and counts were analyzed using the Seurat package (v5.0.3) in R (v4.4.1) using RStudio (v1.4.1103). Briefly, imported Cellranger data were filtered to remove cells with <3000 or > 10000 mapped genes and with > 20% mapping to mitochondrial genes, and to remove suspected doublets. The remaining dataset has 52,078 cells (17,479 iMGs, 33,837 iNs, and 762 iAs) with an average number of mapped genes detected per cell of 1,924 for iMGs, 2,309 for iNs, and 2,684 for iAs, and average total unique molecular identifiers (UMIs) per cell of 3,644 iMGs, 4,199 iNs, and 5,477 iAs. After filtering, normalized and scaled data were clustered using the 3000 most highly variable features. Uniform Manifold Approximation and Projection (UMAP) was run on the first 20 principal components.
Assembly: Human hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iNs, iAs, iMGLs

extract_protocol:
Cells were dissociated with a 1:1 mixture of warm trypsin-EDTA:cold StemPro Accutase Cell Dissociation Reagent for 10min at 37°C. Trypsin was quenched with Trypsin Neutralization Solution (ScienCell, 0113-2) prior to collection of cell suspension. Four independent culture wells were combined for each culture condition. Cell suspensions were centrifuged for 5 min at 300 x g and resuspended in 1 mL of BrainPhys media. The cell pellet was triturated gently with a p1000 tip and passed through a 40µM Flowmi Cell Strainer (Millipore, BAH136800040-50) to remove debris. Cell suspensions were centrifuged at 200 rcf for 5min and resuspended in 0.04% BSA in PBS. Washes were repeated two more times. At the end of the final wash, cell suspension was passed through another 40µM Flowmi Cell Strainer.
Each triple-culture was loaded onto an individual 10X Chromium Chip well (60,000 cells per well) and resulting emulsions were used to generate scRNAseq libraries using the Chromium Next GEM Single Cell 3’ v3.1 chemistry. Libraries were multiplexed and sequenced on a NovaSeq to an average depth of >20K reads per filtered barcode before filtering.

value: iNs, iAs, iMGLs

value: CLU KO iAs


title: 8hdTAG13_MLF2-dTAG_RNA_Rep2

description:
3' mRNA seq
Mlf2_8
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: Mouse_Otx2_RD_Biological_Rep2_technical_Rep1

description:
Library name: Mouse_Otx2_RD_B2_T1
Mouse_Otx2_peaks.narrowPeak


title: 8hdTAG13_MLF2-dTAG_RNA_Rep1

description:
3' mRNA seq
Mlf2_7
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: HEK293T_SNAR_3

city: Urbana

first: Sihang

last: Zhou

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois Urbana-Champaign

description: Library name: sample24

data_processing:
poly(A)+ RNA reads were first trimmed using TrimGalore and then mapped to the transcriptome using quasi-mapper Salmon to generate read counts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Kidney

growth_protocol: HEK293T cells were maintained in DMEM supplied with 10% fetal bovine serum (FBS) and 1% Pen-Strep in the cell incubator with 5% CO₂ at 37°C. A549 cells were maintained in F-12K supplied with 10% fetal bovine serum (FBS) and 1% Pen-Strep in the cell incubator with 5% CO₂ at 37°C.

extract_protocol:
Total RNA extraction was performed using E.Z.N.A.® Total RNA Kit I (Omega Bio-tek) according to the manufacturer’s instructions
Total RNA was rRNA depleted and poly(A)+ RNA enriched. The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) according to the instructions.

treatment_protocol: HEK293T and A549 cells were transfected with U6-snaR, U6-scramble, GFP or SF3B2 plasmid using Lipofectamine 3000 for 48 hours at 37 °C with 5% CO2 before collection

value: Kidney

value: epithelial


title: HEK293T_SNAR_2

description: Library name: sample23


title: 3hdTAG13_MLF2-dTAG_RNA_Rep3

description:
3' mRNA seq
Mlf2_6
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: 3hdTAG13_MLF2-dTAG_RNA_Rep2

description:
3' mRNA seq
Mlf2_5
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: Mouse_H3K27ac_Biological_Rep2

description:
Library name: Mouse_H3K27ac_B2
Mouse_H3K27ac_peaks.narrowPeak


title: HEK293T_SNAR_1

description: Library name: sample22


title: Mouse_NeuroD1_Biological_Rep2_technical_Rep1

description:
Library name: Mouse_NeuroD1_B2_T1
Mouse_Neurod1_peaks.narrowPeak


title: HEK293T_SF3B2_3

description: Library name: sample21


title: bulkRNAseq_Donor3_PBMC+PHA

description:
Library name: bulkRNAseq_Donor3_Condition2
S35

source_name: Blood

value: Blood

value: PBMCs

value: PHA


title: 3hdTAG13_MLF2-dTAG_RNA_Rep1

description:
3' mRNA seq
Mlf2_4
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: DMSO_MLF2-dTAG_RNA_Rep3

description:
3' mRNA seq
Mlf2_3
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: HEK293T_SF3B2_1

description: Library name: sample19


title: Mouse_H3K4me1_Biological_Rep2

description:
Library name: Mouse_H3K4me1_B2
Mouse_H3K4me1_peaks.narrowPeak


title: Mouse_H3K4me3_Biological_Rep2

description:
Library name: Mouse_H3K4me3_B2
Mouse_H3K4me3_peaks.narrowPeak


title: DMSO_MLF2-dTAG_RNA_Rep2

description:
3' mRNA seq
Mlf2_2
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: HEK293T_SF3B2_2

description: Library name: sample20


title: HEK293T_SCR_3

description: Library name: sample18


title: Mouse_lgG_Biological_Rep2

description: Library name: Mouse_lgG_B2


title: DMSO_MLF2-dTAG_RNA_Rep1

description:
3' mRNA seq
Mlf2_1
Allsamples.SMARCA4.MLF2.dTAG.RNA.ESCs.raw.gene.count.bed


title: iNs and iMGLs cultured with CLU WT iAs

description:
Library name: AL117
10X Genomics

value: CLU WT iAs


title: Mouse_Otx2_Atlas_Biological_Rep1_technical_Rep1

description:
Library name: Mouse_Otx2_Atlas_B1_T1
Mouse_Otx2_peaks.narrowPeak


title: Mouse_Otx2_Atlas_Biological_Rep1_technical_Rep2

description:
Library name: Mouse_Otx2_Atlas_B1_T2
Mouse_Otx2_peaks.narrowPeak


title: 8hdTAG13_SMARCA4-dTAG_Rep3

description:
ATAC-seq
AllSamples.SMARCA4.MLF2.dTAG.ATAC.ESCs.chrALL.bed

data_processing:
Sequencing reads were trimmed using cutadapt 3.5 (adapters -m 20 -O 5 -p). Reads were aligned to the mm10 genome using bowtie2 v2.4.4 (--maxins 2000 -p 8 -N 1). Alignments were filtered using samtools v1.12 (view -h -F 1796 -q 20). ATAC peaks were called using MACS2 v2.7.1 (callpeak --format BAMPE --call-summits --shift -75 --extsize 150 --keep-dup all -B --SPMR -g mm -t ATAC.bam). Peaks from all replicates within 1 kb were merged using bedtools v2.30, filtered against the mouse blacklist, and the numbers of reads from each replicate overlapping with the peak set was counted using featureCounts v2.0.3 (-T 4 -O -p -a -t exon -g gene_id).
Differential ATAC peak calls were determined using the R software DESeq2 after pre-filtering peaks with low counts (rowSums > 100), with significance cut-offs set at FDR < 0.05 and fold change > 1.5 in either direction
Assembly: mm10
Supplementary files format and content: bed file with rawATAC peak counts for all conditions

extract_protocol:
For ATAC-seq 60.000 cells were collected and resuspended in 500 µl RSB buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2). Cells were pelleted at 500 rcf, at 4°C for 5 min. Supernatant was removed, cells were resuspended in 50 µl RSB buffer containing 0.1% Tween-20 and 0.1% NP40 and incubated on ice for 3 min. Lysis was washed out with 500 µl RSB buffer containing 0.1% Tween-20. Samples were centrifuged for 10 min at 4°C and 500 rcf. Supernatant was removed and pellets resuspended in 50 µl transposition mix (25 µl TD buffer (Diagenode, C01019043-1000), 2.5 µl Tagmentase (Diagenode, C01070012-200), 22.5 µl H2O). Samples were incubated for 30 min at 37°C at 1000 rpm. DNA was cleaned up using the MinElute kit (Qiagen, 28004).
Eluted DNA was amplified for 10 cycles, adding Nextera Ad PCR primers. DNA was cleaned up using the MinElute kit (Qiagen, 28004). Library molarity and quality were assessed by Qubit and Tapestation (DNA High sensitivity chip).
Libraries were sequenced on a NovaSeq 6000 Illumina sequencerwith paired-end 50 settings.


title: Mouse_NeuroD1_Biological_Rep2_technical_Rep2

description:
Library name: Mouse_NeuroD1_B2_T2
Mouse_Neurod1_peaks.narrowPeak


title: 8hdTAG13_SMARCA4-dTAG_Rep2


title: HEK293T_SCR_2

description: Library name: sample17


title: HEK293T_SCR_1

description: Library name: sample16


title: HEK293T_GFP_3

description: Library name: sample15


title: Mouse_Otx2_RD_Biological_Rep1_technical_Rep2

description:
Library name: Mouse_Otx2_RD_B1_T2
Mouse_Otx2_peaks.narrowPeak


title: Mouse_Otx2_RD_Biological_Rep1_technical_Rep1

description:
Library name: Mouse_Otx2_RD_B1_T1
Mouse_Otx2_peaks.narrowPeak


title: HEK293T_GFP_1

description: Library name: sample13


title: HEK293T_GFP_2

description: Library name: sample14


title: Mouse_NeuroD1_Biological_Rep1_technical_Rep2

description:
Library name: Mouse_NeuroD1_B1_T2
Mouse_Neurod1_peaks.narrowPeak


title: Mouse_NeuroD1_Biological_Rep1_technical_Rep1

description:
Library name: Mouse_NeuroD1_B1_T1
Mouse_Neurod1_peaks.narrowPeak


title: A549_SNAR_3

description: Library name: sample12


title: DMSO_SMARCA4-dTAG_Rep1


title: A549_SNAR_2

description: Library name: sample11

value: Lung


title: 8hdTAG13_MLF2-dTAG_Rep3

value: Embryonic stem cells (mESC)


title: Mouse_H3K4me3_Biological_Rep1

description:
Library name: Mouse_H3K4me3_B1
Mouse_H3K4me3_peaks.narrowPeak


title: A549_SF3B2_3

description: Library name: sample9


title: A549_SNAR_1

description: Library name: sample10


title: Mouse_H3K4me1_Biological_Rep1

description:
Library name: Mouse_H3K4me1_B1
Mouse_H3K4me1_peaks.narrowPeak


title: Mouse_lgG_Biological_Rep1

description: Library name: Mouse_lgG_B1


title: Mouse_H3K27ac_Biological_Rep1

description:
Library name: Mouse_H3K27ac_B1
Mouse_H3K27ac_peaks.narrowPeak


title: 8hdTAG13_MLF2-dTAG_Rep2


title: 8hdTAG13_MLF2-dTAG_Rep1


title: MOLM13_sgSETD1B_2_4d_SETD2

description: Library name: Sample17

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.2
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: leukemia

value: Setd1b SET knockout

value: SETD2 (Cell Signaling #80290)


title: DMSO_MLF2-dTAG_Rep3

value: DMSO


title: Astro_AAVsgAnxa1_4

first: Zhaorong

last: Li

institute: Dana Farber Cancer Institute

data_processing:
The raw sequences from all the samples were aligned to the GRCm38 transcriptome and quantified using kallisto.
Assembly: GRCm38
Supplementary files format and content: TAR gzipped folders of kallisto output

source_name: CNS

growth_protocol: Inbred C57BL/6J mice (The Jackson Laboratory, 000664) were used as a genetic background for all in vivo experiments. Mice were housed under standard conditions in a pathogen-free facility at the Hale Building for Transformative Medicine at 20–23°C and 50% humidity with access to water and food ad libitum and under a 12h light/dark cycle, in accordance with guidelines for care and experimentation defined by the Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Cell suspensions were stained extracellularly as described above with Live/dead stain  and Fc block, and finally with a mix of antibodies in FACS buffer for 30 min at 4°C. All antibodies were diluted 1:100 in FACS buffer. Prior to sorting, cell suspensions were filtered through tubes with 35µm cell strainer caps (Falcon, 352235). For RNA-seq analyses, cells were sorted directly into 100µL Picopure™ Extraction Buffer (Thermo Scientific, KIT0204), incubated 30 min at 42°C and then stored at -80°C until RNA isolation and sequencing was performed.
Library was constructed using  Smart-Seq 2 protocols

value: CNS

value: Astro


title: MOLM13_sgSETD1B_1_4d_SETD2

description: Library name: Sample16


title: A549_SF3B2_1

description: Library name: sample7


title: 8hdTAG13_SMARCA4-dTAG_Rep1


title: DMSO_MLF2-dTAG_Rep2


title: Astro_AAVsgAnxa1_3


title: MOLM13_sgAAVS_4d_SETD2

description: Library name: Sample15

value: Setd1b SET wildtype


title: A549_SCR_3

description: Library name: sample6


title: DMSO_SMARCA4-dTAG_Rep3


title: DMSO_SMARCA4-dTAG_Rep2


title: DMSO_MLF2-dTAG_Rep1


title: Astro_AAVsgAnxa1_2


title: A549_SCR_2

description: Library name: sample5


title: BM_FLT3ITD_2_H3K36me3

description: Library name: Sample14

source_name: Bone marrow

value: Bone marrow

value: H3K36me3 (abcam Cat#ab9050)


title: Astro_AAVsgAnxa1_1


title: A549_SCR_1

description: Library name: sample4


title: BM_FLT3ITD_1_H3K36me3

description: Library name: Sample13


title: Astro_AAVsgRosa_3


title: A549_SF3B2_2

description: Library name: sample8


title: GRIS-BD_Experiment_4-WTA

city: Xinxiang

first: Tianhan

state: Henan

address: No.601, Hualan Road

institute: Xinxiang Medical University

description:
BD Rhapsody
Subcutaneous injectionTyr knockout or Oca2 knockout or WT B16F10 cells.

data_processing:
Set up BD rhapsody local pepline on linux operating system according to the manufacter's instruction, then load with WTA and TAG raw data and run, finally analysis the processed data (“_RSEC_MolsPerCell.csv” and “_Sample_Tag_Calls.csv”) using Segeq software.
Assembly: GRCm39
Supplementary files format and content: tab-separated values file and matrix files

source_name: tumor

extract_protocol:
sort CD45+ cells from single cell suspension of tumor
each group was labelled with sample tag, then built the whole transcriptome analysis (WTA) and sample tag library (TAG) according to the manufacter's instructions (BD Rhapsody™ Single-Cell Analysis System Instrument User Guide (Doc ID 214062))

treatment_protocol: C57BL/6 female mice were divided into three groups of three mice each subcutaneous injected Tyr knockout or Oca2 knockout or WT B16F10 cells..  Cell samples from tumors were stained with antibody mixture and CD45+ cells were sorted for single cell sequencing.

value: tumor

value: CD45+ cell from tumor

value: tumor-infiltrating immune cells


title: A549_GFP_3

description: Library name: sample3

value: epithelial


title: BM_monosomy7_H3K36me3

description: Library name: Sample12


title: m6A-RIP-seq analysis of RBM15 deltaRRM1  mESCs replicate 2

data_processing:
Sequencing reads were trimmed using cutadapt 3.5 (adapters -m 20 -O 4 -e 0.2 -p). Reads were aligned to the mm10 genome wiusing STAR v2.7.5 (--readFilesCommand zcat --runThreadN 6 --genomeDir GRCm38.102 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard). m6A peaks enriched relative to input mRNA were called using MACS272 v2.7.1 (callpeak --nomodel --keep-dup all -B -q 0.05 --extsize 100 --shift -50 -g mm -t m6A.bam -c input.bam, filtered for score > 200). Peaks from NT, KO and ΔRRM1 datasets within 100 bp were merged using bedtools v2.30 and the numbers of reads from each replicate overlapping with the peak set was counted using featureCounts v2.0.3 (-T 4 -O -p -a -t exon -g gene_id).
Differential m6A peak calls were determined using the R software DESeq2 after pre-filtering peaks with low counts (rowSums > 50), with significance cut-offs set at FDR < 0.05 and fold change > 1.5 in either direction.
Assembly: mm10
Supplementary files format and content: bed files with raw m6A peak counts and gene counts for all conditions

extract_protocol:
RNA was isolated using the RNAeasy kit (Qiagen, 74106). Next, mRNA was isolated using the mRNA Isolation kit (NEB, S1550S). mRNA was fragmented using the NEBNext Magnesium RNA fragmentation module (NEB, E6150S) and purified using Monarch RNA Cleanup Kit (NEB, T2030S). 100 ng mRNA was aliquoted and stored as input at -80°C. For m6A-RIP, 50 µl of Dynabeads protein G (Invitrogen, 10004D) were aliquoted and placed on a magnet. Supernatant was removed and beads were washed in 500 µl of m6A-IP buffer (10 mM TrisHCl pH7.4, 150 mM NaCl, 0.1% NP-40). After the initial washing, beads were resuspended in 500 µl m6A-IP buffer and incubated for 45 min at RT on a rotating wheel. Next, supernatant was removed and beads were resuspended in 400 µl m6A-IP buffer. Samples were placed on ice and 5 µg of m6A-antibody (Supplementary table 6), 5 µl RiboLock RNase Inhibitor (Thermo Fisher Scientific, E00381), 20 µl fragmented mRNA, 100 µl 5X m6A-IP buffer (50 mM Tris-HCl pH7.4, 750 mM NaCl, 0.5% NP-40) and 370 µl H2O were added. Samples were incubated for 2 h, at 4°C on a rotating wheel. Next, samples were placed on a magnet and supernatant was removed. Samples were washed twice in 500 µl ice cold m6A-IP buffer for 30 sec. After washing samples were resuspended in 150 µl RNA cleanup binding buffer of the Monarch RNA Cleanup Kit (NEB, T2030S). Samples were incubated for 5 min at RT on a rotating wheel. The eluate was transferred to a new tube. m6A-RIP mRNA was purified using the Monarch RNA Cleanup Kit (NEB, T2030S). Samples were eluted in 8 µl elution buffer.
The sequencing libraries were made using the Illumina Stranded mRNA Prep Ligation kit and protocol starting from 100 ng of input mRNA and m6A-RIP mRNA. To start, 8.5 ul of RNA, 8.5 ulof Fragmentation master mix and 8 ul of First Strand Synthesis master mix were mixed for direct First strand cDNA synthesis. Then protocol instructions were followed as described.
Library molarity and quality were assessed by Qubit and Tapestation (DNA High sensitivity chip). Libraries were sequenced on a NovaSeq 6000 Illumina sequencerwith paired-end 50 settings.

value: RBM15 deltaRRM1

value: m6A antibody


title: Astro_AAVsgRosa_1


title: A549_GFP_2

description: Library name: sample2

value: Lung


title: BM_FLT3ITD_1_H3K4me3

description: Library name: Sample10

value: H3K4me3 (abcam Cat#ab8580)


title: Astro_AAVsgRosa_2


title: A549_GFP_1

description: Library name: sample1


title: m6A-RIP-seq analysis of RBM15 deltaRRM1  mESCs replicate 1

value: Embryonic stem cells (mESC)


title: m6A-RIP-seq analysis of RBM15 KO mESCs replicate 2

value: RBM15 KO


title: BM_FLT3ITD_2_H3K4me3

description: Library name: Sample11

value: leukemia


title: BM_monosomy7_H3K4me3

description: Library name: Sample9


title: m6A-RIP-seq analysis of RBM15 KO mESCs replicate 1


title: CD4_AAVsgAnxa1_4


title: CD4_AAVsgAnxa1_3


title: mouse2_unselected.CS

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_mouse2_unselected_filtered_feature_bc_matrix.h5
mouse_featurereference.csv

data_processing:
CellRanger was used to align reads to the Mus musculus reference (GENCODE vM23/Ensembl 98) and the Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85) from Ensembl70. Gene counts were analyzed with Seurat v471 for clustering, integration and differential gene expression and Monocle version 372 for clustering and pseudotime. Filtering cutoffs were set as follows: minimum genes per cell = 500, maximum genes = 5000, minimum UMIs per cell was set on a per-sample basis after inspecting a rank plot of UMI/cell. Cells with over 20% mitochondrial reads were also excluded. Differentially-expressed genes were identified via Seurat’s FindMarker function with default parameters. Samples were integrated using Seurat’s integration anchors and the first 30 principle components were used for integration and UMAP creation. Clusters were found using monocle (cluster_cells, resolution = 5 10-5, k = 8, partition_qval = 0.05). Psudotime was generated using Monocle’s learn_graph (default parameters). For ATAC analysis, peaks were called using Signac with MACS2, and gene activity scores were calculated with Signac.
Assembly: Mus musculus reference (GENCODE vM23/Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files
Supplementary files format and content: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: featurereference.csv
Assembly: Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85)
Supplementary files format and content: Contain mRNA+ADT or mRNA + ATAC counts as appropriate
Supplementary files format and content: ATAC fragment files
Supplementary files format and content: Contain ADT antibodies used & barcode sequences
Library strategy: CITE-Seq

source_name: testis

extract_protocol:
Rat cells were isolated from the testes of 3- to 4-month-old Sprague Dawley rats transgenic for the LacZ gene under the metallothionine promoter67. Mouse cells were isolated from C57BL/6 inbred mice also 3-4 months old. Tissue was chopped into fine pieces and incubated in collagenase (Sigma) at a concentration of 1mg/ml in HBSS (Gibco) for 15 minutes at 37C. Cells were spun down for 1 minute at 600 rcf, then resuspended in warm Trypsin (Gibco, 0.25%) with 20% DNase solution (Sigma, 7mg/ml dissolved in HBSS). Tissue was pipetted for 2 minutes with a 10 ml pipette and incubated at 37C for 5 minutes. Then tissue was pipetted for another 2 minutes and incubated at 37C for 3 minutes. FBS (Sigma F2442) was added to stop the digestion. Additional DNase was added until no turbidity was visible. Cells were washed in PBS-S twice (PBS [Gibco] with 1% FBS, 10 mM HEPES [Sigma Aldrich], 1 mg/ml glucose [Sigma Aldrich], 1 mM pyruvate [Gibco], 50 units/ml penicillin [Gibco], 50 ug/ml streptomycin [Gibco] prepared as described in 68). All centrifugation steps were 5 minutes at 600 rcf.   Cells were processed both as unselected samples and enriched for EPCAM as described below. Each biological replicate was then used for either encapsulation of cells with antibody treatment or further processed as nuclei for GEX+ATAC assay.
Cells were encapsulated and libraries generated for GEX+CITE using a Chromium Next GEM Single Cells 3’ Kit v3.1 with Feature Barcoding (10X Genomics) per manufacturer’s protocol. Prepared nuclei were encapsulated with the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit following manufacturer’s instructions. Each biological replicate was encapsulated individually. Libraries were sequenced on a NextSeq2000 sequencer (Illumina) using a 100-cycle sequencing kits to a minimum depth of 30k reads per cell.

value: testis

tag: Stage

value: Adult

tag: selection

value: unselected

tag: library type

value: ADT


title: MOLM13_KDM5C

description: Library name: Sample8

value: Setd1b SET wildtype

value: KDM5C (abcam Cat#ab190180)


title: mouse2_unselected

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_mouse2_unselected_filtered_feature_bc_matrix.h5

tag: tissue

value: mRNA


title: CD4_AAVsgAnxa1_2

value: CNS


title: GRIS-BD_Experiment_4-TAG

value: tumor

value: CD45+ cell from tumor

value: tumor-infiltrating immune cells


title: m6A-RIP-seq analysis of NT control mESCs replicate 2

value: WT

value: m6A antibody


title: MOLM13_sgSETD1B_2_4d_H3K36me3

description: Library name: Sample7

value: Setd1b SET knockout

value: H3K36me3 (abcam Cat#ab9050)


title: mouse1_unselected.CS

description:
h5 file contains both modalities, CITE antibodies used in featurereference.csv file
Count_output_mouse1_unselected_filtered_feature_bc_matrix.h5
mouse_featurereference.csv


title: m6A-RIP-seq analysis of NT control mESCs replicate 1

value: Embryonic stem cells (mESC)


title: CD4_AAVsgAnxa1_1


title: mRNA-seq analysis of RBM15 deltaRRM1  mESCs replicate 2

description: Input mRNA-seq

value: RBM15 deltaRRM1

value: none (input)


title: MOLM13_sgAAVS_4d_H3K36me3

description: Library name: Sample5

value: leukemia


title: MOLM13_sgSETD1B_1_4d_H3K36me3

description: Library name: Sample6


title: mouse1_unselected

description:
3' single-cell RNAseq with CITE. h5 file contains both modalities
Count_output_mouse1_unselected_filtered_feature_bc_matrix.h5

value: testis

value: Adult

value: unselected


title: CD4_AAVsgRosa_5


title: mRNA-seq analysis of RBM15 deltaRRM1  mESCs replicate 1

description: Input mRNA-seq


title: multiome6epcam_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
multiomeC57Eunselected_atac_fragments.tsv.gz
multiomeC57Eunselected_atac_fragments.tsv.gz.tbi

data_processing:
CellRanger was used to align reads to the Mus musculus reference (GENCODE vM23/Ensembl 98) and the Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85) from Ensembl70. Gene counts were analyzed with Seurat v471 for clustering, integration and differential gene expression and Monocle version 372 for clustering and pseudotime. Filtering cutoffs were set as follows: minimum genes per cell = 500, maximum genes = 5000, minimum UMIs per cell was set on a per-sample basis after inspecting a rank plot of UMI/cell. Cells with over 20% mitochondrial reads were also excluded. Differentially-expressed genes were identified via Seurat’s FindMarker function with default parameters. Samples were integrated using Seurat’s integration anchors and the first 30 principle components were used for integration and UMAP creation. Clusters were found using monocle (cluster_cells, resolution = 5 10-5, k = 8, partition_qval = 0.05). Psudotime was generated using Monocle’s learn_graph (default parameters). For ATAC analysis, peaks were called using Signac with MACS2, and gene activity scores were calculated with Signac.
Assembly: Mus musculus reference (GENCODE vM23/Ensembl 98)
Supplementary files format and content: filtered_feature_bc_matrix.h5 files
Supplementary files format and content: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi
Supplementary files format and content: featurereference.csv
Assembly: Rattus norvegicus 6.0 DNA primary assembly along with the corresponding GTF file (v6.0.85)
Supplementary files format and content: Contain mRNA+ADT or mRNA + ATAC counts as appropriate
Supplementary files format and content: ATAC fragment files
Supplementary files format and content: Contain ADT antibodies used & barcode sequences
Library strategy: single-cell multiome RNA + ATAC

value: EpCAM+

value: ATAC DNA


title: CD4_AAVsgRosa_4

value: CNS


title: MOLM13_sgSETD1B_1_4d_H3K4me3

description: Library name: Sample3

value: H3K4me3 (abcam Cat#ab8580)


title: mRNA-seq analysis of RBM15 KO mESCs replicate 1

description: Input mRNA-seq

value: RBM15 KO


title: MOLM13_sgSETD1B_2_4d_H3K4me3

description: Library name: Sample4


title: CD4_AAVsgRosa_3


title: CD4_AAVsgRosa_2


title: mRNA-seq analysis of RBM15 KO mESCs replicate 2

description: Input mRNA-seq


title: multiome6epcam_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
multiomeC57Eunselected_filtered_feature_bc_matrix.h5

value: mRNA


title: multiome5unselected_ATAC

description:
3' single-cell multiome ATAC. h5 file contains both modalities
multiomeC57Eepcam_atac_fragments.tsv.gz
multiomeC57Eepcam_atac_fragments.tsv.gz.tbi


title: multiome5unselected_RNA

description:
3' single-cell multiome RNA. h5 file contains both modalities
multiomeC57Eepcam_filtered_feature_bc_matrix.h5