title: S1-3

description:
hypoblast
bulk_Readcount_matix.txt


title: wt_24_1_4

status: Public on May 06 2020

type: SRA

city: Adelaide

first: Nhi

last: Hin

address: North Terrace

country: Australia

institute: University of Adelaide

description: Wild type 24-month-old zebrafish brain under hypoxia 4

library_source: transcriptomic

data_processing:
Trimming done using default parameters on AdapterRemoval 2.2.1
Pseudoalignment to zebrafish GRCz11 reference assembly transcriptome using kallisto version 0.45.0 with default parameters in single-end rf-stranded mode
Transcript estimated counts for each library were summarised into a count matrix using catchKallisto function from the edgeR package
Transcript estimated counts were summarised to gene-level estimated counts by summing transcript-level counts of transcripts associated with the same gene
Genome_build: GRCz11
Supplementary_files_format_and_content: Estimated raw counts provided in tab delimited file format:
counts_t.txt: estimated transcript count
counts_g.txt: estimated gene count

molecule: polyA RNA

organism: Danio rerio

source_name: Whole-brain

growth_protocol: Tübingen strain zebrafish were maintained in a recirculated water system. To generate a family of heterozygous Q96K97del allele (i.e. Q96K97del/+ at psen1) and wild type (+/+) sibling fish, we mated a psen1Q96K97del/+ individual with a +/+ individual and raised the progeny from a single spawning event together in one tank.

extract_protocol:
Adult fish were euthanized by sudden immersion in an ice water slurry for at least ~30 seconds before decapitation and removal of the entire brain for immediate RNA or protein extraction. Each zebrafish brain has a mass of approximately 7mg. All fish brains were removed during late morning/noon to minimise any influence of circadian rhythms.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: brain

tag: background strain

value: Tubingen

tag: age (months)

tag: psen1 genotype

tag: oxygen condition

value: hypoxia


title: q96_24_1_1

description: Heterozygous mutant 24-month-old zebrafish brain under hypoxia 1


title: Hippocampus memory impaired. Biological replicate 1

status: Public on May 07 2020

type: RNA

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

country: Spain

institute: Cima

description: B6.Cg-Tg(APPswe)E1-2Dbo/J  mice 18-20 mont-old

hyb_protocol: Labeled sense cDNA was hybridized to the GeneChip® Mouse Clariom S Arrays, washed and stained on a GeneChip® Fluidics 450 workstation (Affymetrix) according to the manufacturer protocols.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000 7G

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse hippocampi after morris water maze

label_protocol: The sense cDNA was prepared from 1 ng of total RNA using the Affymetrix GeneChip® WT Pico Kit (PN902623). The sense strand cDNA was then fragmented and biotinylated according to the manufacturer's instructions.

growth_protocol: Hippocampus of mouse  that underwent  Morris water maze test before sacrificed.

extract_protocol: The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Mice were sacrificed by cervical dislocation, brain was extracted and the hippocampus was dissected and kept in dry ice immediately. Tissue was stored at -80 C until RNA extraction.

value: hippocampus

tag: memory status

value: impaired

tag: genotype

tag: age

value: 18-20 months


title: Hippocampus memory impaired. Biological replicate 4


title: q96_24_1_4

description: Heterozygous mutant 24-month-old zebrafish brain under hypoxia 4


title: wt_24_1_2

description: Wild type 24-month-old zebrafish brain under hypoxia 2


title: wt_24_1_3

description: Wild type 24-month-old zebrafish brain under hypoxia 3


title: q96_24_1_2

description: Heterozygous mutant 24-month-old zebrafish brain under hypoxia 2


title: q96_24_1_3

description: Heterozygous mutant 24-month-old zebrafish brain under hypoxia 3


title: q96_24_0_2

description: Heterozygous mutant 24-month-old zebrafish brain under normoxia 2

value: normoxia


title: q96_24_0_4

description: Heterozygous mutant 24-month-old zebrafish brain under normoxia 4


title: q96_24_0_3

description: Heterozygous mutant 24-month-old zebrafish brain under normoxia 3


title: wt_24_0_3

description: Wild type 24-month-old zebrafish brain under normoxia 3


title: wt_24_1_1

description: Wild type 24-month-old zebrafish brain under hypoxia 1


title: S1-1

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

description:
hypoblast
bulk_Readcount_matix.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_fascicularis_5.0.91 whole genome using STAR v2.3.4 with default parameters
Reads of exon  were calculated using RSEM
Genome_build: Macaca_fascicularis_5.0.91
Supplementary_files_format_and_content: tab-delimited text files include mapped reads values for each Sample

organism: Macaca fascicularis

source_name: embryo

extract_protocol:
Monkey embryos with decidua were collected and embedded in optimal cutting temperature compound (OCT; 4583, Tissue-Tek OCT, skura). Embryos were cryo-sectioned along the anterior-posterior axis. Populations of approximately 20 cells from putative EPI, TE, EXMC or VE/YE were collected by laser microdissection and processed for low-input RNA sequencing based on Smart-seq2 method.
RNA libraries were prepared for sequencing using standard SMART-seq2 protocols for ILLUMINA

value: embryo

value: Day 18


title: wt_24_0_1

description: Wild type 24-month-old zebrafish brain under normoxia 1


title: wt_24_0_4

description: Wild type 24-month-old zebrafish brain under normoxia 4


title: q96_6_1_1

description: Heterozygous mutant 6-month-old zebrafish brain under hypoxia 1


title: wt_6_1_4

description: Wild type 6-month-old zebrafish brain under hypoxia 4


title: wt_6_1_3

description: Wild type 6-month-old zebrafish brain under hypoxia 3


title: wt_6_1_2

description: Wild type 6-month-old zebrafish brain under hypoxia 2


title: wt_6_1_1

description: Wild type 6-month-old zebrafish brain under hypoxia 1


title: q96_6_1_3

description: Heterozygous mutant 6-month-old zebrafish brain under hypoxia 3


title: q96_6_0_4_reanalyzed

description:
Heterozygous mutant 6-month-old zebrafish brain under normoxia 4
GSM3591573


title: wt_24_0_2

description: Wild type 24-month-old zebrafish brain under normoxia 2


title: q96_6_0_1_reanalyzed

description:
Heterozygous mutant 6-month-old zebrafish brain under normoxia 1
GSM3591570


title: q96_6_0_2_reanalyzed

description:
Heterozygous mutant 6-month-old zebrafish brain under normoxia 2
GSM3591571


title: q96_6_1_2

description: Heterozygous mutant 6-month-old zebrafish brain under hypoxia 2


title: wt_6_0_1_reanalyzed

description:
Wild type 6-month-old zebrafish brain under normoxia 1
GSM3591566


title: HT3

city: El Paso

first: Anita

middle: Maria

last: Quintana

state: Texas

address: 500 West University Avenue

department: Biological Sciences

country: USA

institute: University of Texas at El Paso

data_processing:
Sequences were trimmed with Trimmomatic
Alignment was performed using Tophat2
Cufflinks was used to determine differential gene expression patterns
Genome_build: GRCz11
Supplementary_files_format_and_content: excel

source_name: Brain Homogenate

extract_protocol:
Trizol
TruSeq

tag: days post fertilization

tag: strain

value: hcfc1a mutant


title: q96_6_0_3_reanalyzed

description:
Heterozygous mutant 6-month-old zebrafish brain under normoxia 3
GSM3591572


title: q96_24_0_1

description: Heterozygous mutant 24-month-old zebrafish brain under normoxia 1


title: HT2


title: forearm_hgps_patient7

type: genomic

city: Heidelberg

first: Julian

last: Gutekunst

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center

description:
HGADFN122
200784530084_R06C01

hyb_protocol: Bisulphite treated DNA was amplified, fragmented and hybridised onto Illumina Infinium Human MethylationEPIC Beadchips following the standard Illumina protocol

scan_protocol: Using Illumina iScan scanning systems with recommended settings

data_processing: Raw idat files were processed using the minfi pipeline and filtered for sex chromosomes, self-hybridizing probes, SNP containing probes and low detection p-values

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: disease state

value: Hutchinson-Gilford Progeria Syndrome (HGPS)

tag: gender

value: female

value: skin

tag: cell type

value: skin fibroblast


title: wt_6_0_3_reanalyzed

description:
Wild type 6-month-old zebrafish brain under normoxia 3
GSM3591568


title: WT4

value: wild type


title: HT4


title: wt_6_0_2_reanalyzed

description:
Wild type 6-month-old zebrafish brain under normoxia 2
GSM3591567


title: q96_6_1_4

description: Heterozygous mutant 6-month-old zebrafish brain under hypoxia 4


title: HT1


title: forearm_hgps_patient9

description:
HGADFN169
200784530084_R08C01

value: male


title: WT1


title: WT2


title: forearm_hgps_patient4

description:
HGADFN167
200392810037_R04C01


title: forearm_hgps_patient8

description:
HGADFN178
200784530084_R07C01


title: forearm_control_patient3

description:
GM05659
200784530084_R01C01

value: normal


title: forearm_control_patient4

description:
GM00969
200784530084_R02C01


title: forearm_control_patient6

description:
GM02036
200784530084_R04C01


title: forearm_control_patient5

description:
GM01864
200784530084_R03C01


title: forearm_hgps_patient2

description:
HGADFN271
200392810037_R02C01


title: RORgt KO Th17, biological rep3

city: Seoul

first: Sungkyu

last: Lee

address: Gwanak-gu, Gwanak-ro 1

country: South Korea

institute: Seoul National University

description: Gene expression data from Th17 cells

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: Th17 cells

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Naïve CD4+ T cells were purified from spleen by using Sony cell sorter SH800. In short, red blood cells were removed with ACK lysis buffer and B cells were depleted of single-cell suspensions using anti-biotin magnetic beads (Miltenyi biotech). Thereafter, cells were stained with antibodies against CD4, CD25, CD44 and CD62L, and FACS-sorted to isolate CD4+CD25-CD44lowCD62Lhigh naïve T cells. Cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco) supplemented with 10% heat-inactivated FBS (Gibco), 50U penicillin-streptomycin and 50μM β-mercaptoethanol. For Th17(β) cell polarization, naïve CD4+ T cells were cultured for 60 h in 96-well flat-bottom plates pre-coated with anti-CD3 (145-2C11;10μg/ml) and anti-CD28 (37.51;10μg/ml) antibody under TH17(β) conditions (TGF-β1(1ng/ml), IL-6(30μg/ml), anti-IL-4(11B11;2μg/ml),anti-IFN-γ(XMG1.2;2μg/ml))

value: Th17 cells

value: RORgt-deficient


title: SRG3 cKO Th17, biological rep1

description: Gene expression data from Th17 cells


title: RORgt KO Th17, biological rep1

description: Gene expression data from Th17 cells


title: WT Th17, biological rep1

description: Gene expression data from Th17 cells

value: WT


title: SRG3 cKO Th17, biological rep3

description: Gene expression data from Th17 cells


title: RORgt KO Th17, biological rep2

description: Gene expression data from Th17 cells


title: SRG3 cKO Th17, biological rep2

description: Gene expression data from Th17 cells


title: forearm_hgps_patient6

description:
HGADFN164
200784530084_R05C01


title: WT Th17, biological rep3

description: Gene expression data from Th17 cells


title: WT Th17, biological rep2

description: Gene expression data from Th17 cells


title: forearm_control_patient1

description:
HGMDFN090
200392810037_R07C01


title: wt_6_0_4_reanalyzed

description:
Wild type 6-month-old zebrafish brain under normoxia 4
GSM3591569

value: brain

value: Tubingen


title: forearm_hgps_patient1

description:
HGADFN155
200392810037_R01C01


title: forearm_hgps_patient5

description:
HGADFN143
200392810037_R05C01


title: KO set 2  UUO [3899]

city: Oslo

first: Guttorm

last: Haraldsen

address: Sognsvannsveien 20

department: Pathology

country: Norway

institute: Oslo University Hospital

hyb_protocol: 750 ng of biotin-labeled cRNA was hybridized to the Illumina MouseRef-8 v2 Expression BeadChip

scan_protocol: Standard Illumina scanning protocol

data_processing:
The raw data was pre-processed by Illumina´s BeadStudio software V2
Data were normalized by Quantile Normalization of micrarraoy data, please refer to below paper (https://academic.oup.com/bioinformatics/article/19/2/185/372664)

source_name: kidney

label_protocol: Illumina Total Prep 96 RNA Amp Kit

extract_protocol: RNA from tissue homogenates was isolated with the RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen). RNA purification was performed using an RNase-Free DNAse Set (Qiagen¨)

treatment_protocol: Unilateral ureteral obstruction in IL-33-deficient and wild type C57/BL6 mice, tissue harvest 24h after ligation.

value: kidney

value: IL-33 KO

tag: treatment

value: UUO


title: WT set 2  UUO [3892]


title: forearm_control_patient2

description:
HGFDFN168
200392810037_R08C01


title: WT set 2  UUO [3895]


title: WT set 2  UUO [3893]


title: forearm_hgps_patient3

description:
HGADFN188
200392810037_R03C01


title: WT set 1  UUO [3820]


title: WT3


title: KO set 2  UUO [3897]


title: WT set 2  UUO [3894]


title: KO control  [3813]

value: control


title: WT control  [3811]


title: KO set 2  UUO [3898]


title: WT set 1  UUO [3819]


title: KO set 1  UUO [3821]


title: Wild Type C57BL6 T-cells, Naïve, Biological Replicate 3

city: Tampa

first: Matthew

middle: S

last: Beatty

state: FL

address: 12902 USF Magnolia Drive

department: Immunology

institute: Moffitt Cancer Center & Research Institute

description: Gene expression data from naïve murine T-cells

hyb_protocol: Hybridization with the biotin-labeled RNA and staining  of Affymetrix GeneChip Mouse Genome 430 2.0 Array followed the prescribed procedure outlined in the Affymetrix technical manual and has been previously described Warrington JA, Nair A, Mahadevappa M, Tsyganskaya M. (2000) Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genomics 2(3):143-7.

scan_protocol: Scanning of the chips utilizing GeneChip Scanner 3000 (Affymetrix) followed the prescribed procedure outlined in the Affymetrix technical manual and has been previously described Warrington JA, Nair A, Mahadevappa M, Tsyganskaya M. (2000) Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genomics 2(3):143-7.

data_processing: Scanned image data was visually inspected for hybridization artifacts and processed using Affymetrix GCOS software to generate Cel file data. CEL data was then processed using the RMA algorithm implemented by Partek Genomics Suite (St. Louis, MO). Using Partek, differential gene expression of normalized data was determined by two-way ANOVA and contrasts between geneotype and treatment conditions were applied to calculate fold-change values along with the statistical p-value and false descovery rate (FDR) values. Lists of significantly changed transcripts (2-fold change and FDR < 0.5) were uploaded to MetaCore (GeneGo), for gene ontology analysis and network mapping.

source_name: Purified splenic T-cells

label_protocol: One hundred nanograms of total RNA served as the mRNA source for microarray analysis.  The poly(A) RNA was specifically converted to cDNA and then amplified and labeled with biotin using the Ambion Message Amp Premier RNA Amplification Kit (Life Technologies, Grand Island, NY) following the manufacturer’s protocol initially described by Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH. Amplified RNA synthesized from limited quantities of heterogeneous cDNA.  Proc Natl Acad Sci U S A. 1990 Mar;87(5):1663-7

growth_protocol: Splenic T-cells were isolated from C57BL6 wild type or cereblon knock out mice using negative magnetic bead selection (Pan T cell Kit II, Miltenyi) and grown in complete RPMI-10 media.

extract_protocol: T-cells were collected and lysed in TRIzol (Invitrogen) to extract total RNA according to manufactures protocol.

treatment_protocol: Purified T-cells were then collected in their naïve, unactivated state or treated with anti-CD3 (5µg/ml plate bound) and anti-CD28 (1µg/ml soluble) for 12 hours.

value: Splenic T-cells

value: 3-4 months of age

tag: Sex

value: Female


title: Wild Type C57BL6 T-cells, Naïve, Biological Replicate 1


title: SiRNA IFNγ TGFβ_rep3

hyb_protocol: 750 ng of biotin-labeled cRNA was hybridized to the Illumina HumanHT-12 v4 Expression BeadChip

data_processing:
The raw data was pre-processed by Illumina‚s BeadStudio software V2
Data were normalized by Quantile Normalization of micrarray data, please refer to below paper (https://academic.oup.com/bioinformatics/article/19/2/185/372664)

source_name: Fibroblast

growth_protocol: Primary normal human dermal fibroblasts (NHDF) were purchased from PromoCell (Heidelberg, Germany) and cultured in Fibroblast Growth Medium supplemented with one vial of SupplementMix (PromoCell), 5 % FCS, 100 μg/ml amphotericin B and 100 μg/ml gentamicin (Thermo Fisher Scientific).

extract_protocol: RNA from  cell cultures was isolated with the RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen). RNA purification was performed using an RNase-Free DNAse Set (Qiagen¨)

treatment_protocol: Human IL-33 (#4392422) and Silencer Select Negative Control No. 2 siRNA (#4390846) were purchased from Thermo Fisher Scientific. Fibroblasts were transfected with 30 nM siRNA using Lipofectamine RNAimax (Invitrogen) in Opti-MEM for 12 hours followed by a change to serum free fibroblast growth medium, containing cytokines for another 12 hours before harvest and RNA extraction.

value: Fibroblast

tag: knockdown

value: si IFNgamma, TGF Beta


title: WT set1 UUO [3818]


title: CRBN KO T-cells, Naïve, Biological Replicate 3

value: C57BL6 crbn-/-


title: CRBN KO T-cells, Activated AntiCD3/CD28, 12 hours, Biological Replicate 3

description: Gene expression data from activated murine T-cells


title: WT control  [3812]


title: Wild Type C57BL6 T-cells, Activated AntiCD3/CD28, 12 hours, Biological Replicate 1


title: CRBN KO T-cells, Naïve, Biological Replicate 1


title: Scr IFNγ_rep3

value: Scrambled IFNgamma


title: CRBN KO T-cells, Activated AntiCD3/CD28, 12 hours, Biological Replicate 1


title: Wild Type C57BL6 T-cells, Activated AntiCD3/CD28, 12 hours, Biological Replicate 2


title: CRBN KO T-cells, Activated AntiCD3/CD28, 12 hours, Biological Replicate 2


title: KO control  [3814]


title: Chronic lymphocytic leukemia 9; from the CLL11 trial [11_CLL009up]

city: London

first: Jennifer

last: Edelmann

address: Charterhouse Square

department: Centre for Haemato-/Oncology

country: United Kingdom

institute: Barts Cancer Institute

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix® fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL-files and chp-files (generated by Affymetrix GTYPE using the DM algorithm and by the birdseed algorithm in Affymetrix Genotyping Console version 4.0, respectively) were processed by dChip and model-based expression performed using the PM/MM model.
affymetrix-algorithm-name = birdseed-v2
affymetrix-algorithm-version = 2.4
affymetrix-array-type = GenomeWideSNP_6
program-name = Genotyping Console
program-version = 3.0.3190.24001
Signal' = Summarized signal; Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

label: Biotin

source_name: peripherel blood

label_protocol: As per manufacturer (Affymetrix®)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations from peripheral blood using the Qiagen® DNA Blood Mini Kit (Hilden, Germany). Immunomagnetic tumor cell enrichment was performed for all samples (Midi MACS, Miltenyi Biotec®; Bergisch Gladbach, Germany) so that 146 CD19-positive fractions, and 91 CD19-negative fractions were used. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: mononuclear cells CD19+

tag: cohort

value: treatment-naïve

tag: tp53 status

value: TP53 aberration

tag: atm status

value: no ATM deletion


title: CRBN KO T-cells, Naïve, Biological Replicate 2

tag: tissue


title: SiRNA IFNγ TGFβ_rep2


title: Chronic lymphocytic leukemia 8; from the CLL11 trial [11_CLL008up]


title: Chronic lymphocytic leukemia 4; from the CLL11 trial [11_CLL004]


title: Scr IFNγ TGFβ_rep2

value: Scrambled IFNgamma, TGF Beta


title: Scr IFNγ TGFβ_rep3


title: Chronic lymphocytic leukemia 6; from the CLL11 trial [11_CLL006up]


title: SiRNA IFNγ_rep3

value: si IFNgamma


title: Chronic lymphocytic leukemia 5; from the CLL11 trial [11_CLL005up]


title: Chronic lymphocytic leukemia 3 paired normal; from the CLL11 trial [11_CLL003pn]

value: mononuclear cells CD19-

value: not annotated


title: C/EBPa_168h_rep2_ChIPSeq

city: Göttingen

first: Jinmi

last: Choi

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

description: Chromatin sonication for 16 min with Covaris S220 Ultrasonicator

library_source: genomic

data_processing:
Sequencing data preprocessing. Paired-end reads with additional 6 base reads of barcodes were obtained for each of the samples. Reads from TT-seq/RNA-seq or ChIP-seq/ATAC-seq were demultiplexed, trimmed using Cutadapt 1.9.1 (Martin, 2012) and trim_galore_v0.4.1, and mapped with STAR 2.3.0 (Dobin et al., 2013) or Bowtie2.2.5/Bowtie1.0.0 (Langmead and Salzberg, 2012), respectively, to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). For ATAC-seq, chromosome M was removed. Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
For ChIP-seq , we used the 'callpeak' function of MACS2.1.1 (Zhang et al., 2008) with ‘--BAMPE’ options. To catalogue all the C/EBPα, BRD4 or H3K4me1 binding sites over all the time points, we merged and reduced all peaks from all the time points. Duplicates were removed. To obtain the enriched signal (count matrix), read count within the merged peaks were normalized by library size followed by a normalization with counts in corresponding input.
For ATAC-seq, TT-seq and Total RNA-seq, bigwig files were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X options and/or --filterRNAstrand options.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: BRD4allPeaks_reduced.txt:Merged BRD4 peaks from all the time points.; BRD4mat.txt: BRD4 count table normalized with size factors and input on the genomic coordinates in BRD4allPeaks_reduced.txt.
Supplementary_files_format_and_content: CEBPallPeaks_reduced.txt:Merged CEBPa peaks from all the time points; CEBPmat.txt: CEBP coverage normalized to size factors and input on the genomic coordinates in CEBPallPeaks_reduced.txt
Supplementary_files_format_and_content: H3K4me1allpeaks_reduced.txt:Merged H3K4me1 peaks from all the time points; H3K4me1mat.txt: H3K4me1 coverage normalized to size factors and input on the genomic coordinates in H3K4me1allPeaks_reduced.txt
Supplementary_files_format_and_content: Bigwig files of ATAC-seq normalized by sizefactor.
Supplementary_files_format_and_content: Strand specific bigwig files of TT-seq and RNA-seq normalized by size factors.

source_name: BLaER

extract_protocol:
ChIP-seq: At each time point, 3x10^7 cells were harvested and fixed with 1% of formaldehyde for 8 minutes (Thermo Scientific, 28908). Formaldehyde was quenched with 0.2M glycine for 5 min. Chromatin was sheared to 200-500 bp in size using the Covaris S220 ultrasonicator (16min for C/EBPα and BRD4, 18min for H3K4me1). A fraction of the resulting chromatin was used as input control. Sheared chromatin (50ug for C/EBPα and BRD4, 30ul for H3K4me1) was incubated with 5 ug of antibodies - anti-C/EBPα (Santa Cruz, sc-61), anti-H3K4me1 (abcam, ab8895), anti-BRD4 (Bethyl Laboratories, A301–985A100)- bound to protein-A beads (Life Technologies, 9999-01). Samples were incubated at 65ºC overnight to reverse the crosslinks, followed by RNase and proteinase K treatments.
ATAC-seq: ATAC-seq was performed as described (Buenrostro et al., 2013). Briefly, 5 x 10^4 cells were harvested and treated with Nextera Tn5 Transposase (Illumina, FC-121-1030) for 45 min at 37°C.
Total RNA-seq: Total RNA was extracted from the cells labelled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min. RNA prepared using QIAzol according to the manufacturer’s instructions was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator before the library preparation.
At each time point, 1-2.2 x 10^8 cells were labeled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min and harvested by centrifuging at 500g for 2 min. Harvested pellets were lysed with QIAzol (Qiagen, 79306). Following addition of 5ng of spike-in mix per 1 x 10^8 cells, total RNA was purified using QIAzol (Qiagen, 79306) according to the manufacturer’s instructions. Total RNA (300ug) was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator. Newly synthesized RNAs were purified as described (Schwalb et al., 2016) with the following modifications. After streptavidin pull down, the resulting RNA was purified with RNeasy Micro Kit (Qiagen, 74004), together with DNase treatment (Qiagen, 79254).
ChIP-seq: NEB Ultra DNA Library kit (NEB, E7370S) ; ATAC-seq:Nextera Tn5 Transposase ((Illumina, FC-121-1030)) NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S) ; Total RNA-seq and TT-seq Ovation Universal RNA-seq System (Nugen, 0343)

value: RCH-ACV stably expressing estrogen inducible C/EBPa

tag: extract protocol

value: NEB Ultra DNA Library kit (NEB, E7370S)

value: Beta-estradiol (100nM) treatment 0h

tag: chip antibody

value: anti-C/EBPa (Santa Cruz, sc-61)


title: Chronic lymphocytic leukemia 2 paired normal; from the CLL11 trial [11_CLL002pn]


title: Chronic lymphocytic leukemia 4 paired normal; from the CLL11 trial [11_CLL004pn]


title: Input_16min_168h_rep2_ChIPSeq

value: Beta-estradiol (100nM) treatment 96h

value: none (input)


title: Input_16min_168h_rep1_ChIPSeq


title: C/EBPa_168h_rep1_ChIPSeq


title: Chronic lymphocytic leukemia 2; from the CLL11 trial [11_CLL002]


title: SiRNA IFNγ_rep2

value: Fibroblast


title: Wild Type C57BL6 T-cells, Naïve, Biological Replicate 2

value: Splenic T-cells

value: 3-4 months of age

value: Female


title: Scr IFNγ_rep2

value: Scrambled IFNgamma


title: 168h_ATAC_rep2

city: Barcelona

first: Maria

last: Vila-Casadesús

state: Barcelona

address: Carrer del Dr. Aiguader, 88

institute: CRG

data_processing:
Reads were mapped to the UCSC human genome build (hg38) using Bowtie2 46 with standard settings.
Reads mapping to multiple locations in the genome were removed using SAMtools.
PCR duplicates were filtered using Picard.
Bam files were parsed to deepTools for downstream analyses and browser visualization.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files used for browser exploration data

source_name: Leukaemia cell line

growth_protocol: B and CEBPA induced cells were grown in RPMI medium

extract_protocol:
Cells were collected by centrifugation.
Briefly, 5 million cells were harvested and treated with Nextera Tn5 Transposase (Illumina, FC-121-1030) for 45 min at 37°C. Library fragments were amplified using 1x NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S) and 1.25uM of custom Nextera PCR primers 1 and 2. PCR amplification was done with 11 cycles, determined by KAPA Real-Time Library Amplication Kit (Peqlab, KK2701) to stop prior to saturation. Then, the samples were purified using Qiagen MinElute PCR Purification Kit (Qiagen, 28004) and with Agencourt AMPure XP beads (Beckman Coulter, A63881) in 3:1 ratio.
The libraries were sequenced paired-end (50bp) on a HiSeq2000 instrument

treatment_protocol: C/EBPa was induced with beta-estradiol;

tag: cell line

value: BLaER

value: CEBPA

tag: time


title: 168h_ATAC_rep1


title: Scr IFNγ_rep1


title: SiRNA IFNγ TGFβ_rep1

value: si IFNgamma, TGF Beta


title: Scr IFNγ TGFβ_rep1

value: Scrambled IFNgamma, TGF Beta


title: SiRNA IFNγ_rep1

value: si IFNgamma


title: Chronic lymphocytic leukemia 7; from the CLL11 trial [11_CLL007up]

value: mononuclear cells CD19+

value: treatment-naïve

value: TP53 aberration

value: no ATM deletion


title: BLaER cell line, 168h_CTCF_ChIPseq_rep2

data_processing:
Reads were aligned using STAR (outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.06 -sjdbOverhang 100 –outFilterType BySJout -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000)
Gene expression was quantified using STAR (--quantMode GeneCounts)
Sample scaling and statistical analysis were performed using the R package DESeq2 (1.6.3) (R 3.1.0 and bioconductor 3.0)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files used for browser exploration data; narrowPeak

source_name: Leukemia cell line

extract_protocol:
Cells were cross-linked for 10 min using 1% formaldehyde and quenched using a final concentration of 0.125M glycin. Cell pellets were lysed by incubating 10 min on ice with 5mM Pipes pH 8, 85 mM KCL, 0.5 % IGEPAL, 1X protease inhibitor (Roche®). After centrifugation, pellets were incubated in 1% SDS, 10 mM EDTA pH 8, 50 mM Tris-HCL pH 8.1 and 1X PIC for 10 min on ice. Chromatin was sheared on a Bioruptor360 pico sonicator (Diagenode) at 4oC for 14 cycles of 30 sec ON and 30 sec OFF. After sonication, the solution was left on ice for 1h to allow SDS precipitation and clarified by centrifugation at 16,000g at for 10 min at 4oC. Supernatant was transferred in a new tube, 10 % was saved as input and the rest was diluted to 1.2 mL with 1X cold IP buffer (Diagenode). 10μg of anti-CTCF (Milipore, 07-729) was added followed by overnight incubation at 4oC on a rotator. 42 μL of beads (Unblocked Protein A beads, kch-503-008, Diagenode) were used per IP after blocking them using 1% bovine serum albumin cold IP buffer for 15 min at 4oC under rotation. Blocked beads were added to the chromatin solution and incubated 3h at 4oC with rotation. Beads were then collected by centrifugation for 2 min at 3000 rpm at 4oC and washed 3 times with cold IP buffer and 2 times with cold TE buffer (10mM Tris pH 8, 1mM EDTA). Beads were then eluted with freshly prepared elution buffer (1% SDS, 0.1M NaHCO 3 ) and incubated 25 min at RT. The supernatant was transferred into a new tube and cross-linking was reversed by adding NaCl (final concentration 200mM) and incubating overnight at 65oC. Protein digestion was achieved by adding Tris pH 6.5 (40mM), EDTA pH 8 (10mM) and proteinase K (4μg/μL) and incubating 1h at 45oC. DNA was then purified by phenol chloroform isoamyl (25:24:1) extraction. The entire DNA sample was used to construct Illumina sequencing libraries.
Library preparation was performed using the NEBNext DNA Library Prep Kit (New England BioLabs) with 2 μL NEBNext adaptor in the ligation step. Libraries were amplified for 14 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (> 200 bp).

treatment_protocol: C/EBPa was induced with beta-estradiol; CTCF depletion was induced with auxin


title: BLaER cell line, 168h_CTCF_ChIPseq_rep1


title: Chronic lymphocytic leukemia 1; from the CLL11 trial [11_CLL001]

value: ATM deletion


title: Chronic lymphocytic leukemia 3; from the CLL11 trial [11_CLL003]


title: BLaER cell line, 96h_CTCF_ChIPseq_rep1


title: BLaER cell line, 96h_CTCF_ChIPseq_rep2


title: BLaER cell line, 24h_CTCF_ChIPseq_rep2


title: Chronic lymphocytic leukemia 342; from the CLL8 trial [8_CLL342up]


title: Chronic lymphocytic leukemia 314; from the CLL8 trial [8_CLL314up]


title: Chronic lymphocytic leukemia 300; from the CLL8 trial [8_CLL300up]


title: Chronic lymphocytic leukemia 287; from the CLL8 trial [8_CLL287up]


title: Chronic lymphocytic leukemia 324; from the CLL8 trial [8_CLL324up]


title: BLaER cell line, 24h_CTCF_ChIPseq_rep1


title: BLaER cell line, B_CTCF_ChIPseq_rep1

value: Non-treated


title: BLaER cell line, B_CTCF_ChIPseq_rep2


title: Chronic lymphocytic leukemia 277; from the CLL8 trial [8_CLL277up]


title: Chronic lymphocytic leukemia 268; from the CLL8 trial [8_CLL268up]


title: Chronic lymphocytic leukemia 263; from the CLL8 trial [8_CLL263up]


title: BLaER subclone, 24h_CTCF_AID_AUX_HiC_rep2

description: in-situ Hi-C

data_processing:
50kb contact matrices with raw contacts
Genome_build: hg38
Supplementary_files_format_and_content: 50kb contact matrices with raw contacts

extract_protocol:
Cells were collected by centrifugation. Crosslinked nuclei were digested with MboI followed by fill-in with bio-dATP, in-situ ligation and DNA extraction.
DNA was sonicated and libraries were constructed using the the NEBNext DNA Library Prep Kit (New England Biolabs).

tag: subclone

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

value: CEBPA+DMSO


title: Chronic lymphocytic leukemia 260; from the CLL8 trial [8_CLL260up]


title: BLaER subclone, 168h_CTCF_AID_DMSO_HiC_rep2

description: in-situ Hi-C

value: CEBPA+auxin


title: BLaER subclone, 168h_CTCF_AID_AUX_HiC_rep2

description: in-situ Hi-C


title: BLaER subclone, 168h_CTCF_AID_AUX_HiC_rep1

description: in-situ Hi-C


title: BLaER subclone, 168h_CTCF_AID_DMSO_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 254; from the CLL8 trial [2_CLL254up]


title: BLaER subclone, 24h_CTCF_AID_DMSO_HiC_rep2

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 343; from the CLL8 trial [8_CLL343up]


title: KO set 1  UUO [3822]

value: kidney

tag: genotype

value: IL-33 KO

value: UUO


title: BLaER subclone, 24h_CTCF_AID_AUX_HiC_rep1

description: in-situ Hi-C


title: BLaER subclone, 24h_CTCF_AID_DMSO_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 253; from the CLL8 trial [8_CLL253up]


title: Chronic lymphocytic leukemia 250; from the CLL8 trial [8_CLL250up]


title: BLaER subclone, B_CTCF_AID_HiC

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 224; from the CLL8 trial [8_CLL224up]


title: Chronic lymphocytic leukemia 241; from the CLL8 trial [8_CLL241up]


title: BLaER cell line, 144h_HiC_rep2

description: in-situ Hi-C

value: BLaER


title: Chronic lymphocytic leukemia 207; from the CLL8 trial [8_CLL207up]


title: BLaER cell line, 168h_HiC_rep2

description: in-situ Hi-C

value: CEBPA


title: BLaER cell line, 120h_HiC_rep2

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 170; from the CLL8 trial [8_CLL170up]


title: Chronic lymphocytic leukemia 147; from the CLL8 trial [8_CLL147up]


title: BLaER cell line, 72h_HiC_rep2

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 259; from the CLL8 trial [8_CLL259up]


title: Chronic lymphocytic leukemia 87 paired normal; from the CLL8 trial [8_CLL087pn]

value: mononuclear cells CD19-

value: not annotated


title: Chronic lymphocytic leukemia 80 paired normal; from the CLL8 trial [8_CLL080pn]


title: BLaER cell line, 18h_HiC_rep2

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 87; from the CLL8 trial [8_CLL087]


title: BLaER cell line, B_HiC_rep2

description: in-situ Hi-C


title: BLaER cell line, 168h_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 80; from the CLL8 trial [8_CLL080]


title: BLaER cell line, 96h_HiC_rep2

description: in-situ Hi-C


title: BLaER cell line, 144h_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 77 paired normal; from the CLL8 trial [8_CLL077pn]


title: Chronic lymphocytic leukemia 77; from the CLL8 trial [8_CLL077]


title: BLaER cell line, 120h_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 88 paired normal; from the CLL8 trial [8_CLL088pn]


title: Chronic lymphocytic leukemia 73 paired normal; from the CLL8 trial [8_CLL073pn]


title: BLaER cell line, 96h_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 64 paired normal; from the CLL8 trial [8_CLL064pn]


title: BLaER cell line, 24h_HiC_rep1

description: in-situ Hi-C


title: BLaER cell line, 72h_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 73; from the CLL8 trial [8_CLL073]


title: Chronic lymphocytic leukemia 64; from the CLL8 trial [8_CLL064]


title: Chronic lymphocytic leukemia 88; from the CLL8 trial [8_CLL088]


title: Chronic lymphocytic leukemia 36 paired normal; from the CLL8 trial [8_CLL036pn]


title: BLaER cell line, 24h_HiC_rep2

description: in-situ Hi-C


title: BLaER cell line, 9h_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 29 paired normal; from the CLL8 trial [8_CLL029pn]


title: BLaER cell line, B_HiC_rep1

description: in-situ Hi-C


title: BLaER cell line, 18h_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 110; from the CLL2O trial [2O_CLL110up]

value: refractory


title: Chronic lymphocytic leukemia 29; from the CLL8 trial [8_CLL029]

value: mononuclear cells CD19+


title: Chronic lymphocytic leukemia 109; from the CLL2O trial [2O_CLL109up]

value: treatment-naïve


title: BLaER cell line, 48h_HiC_rep1

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 107; from the CLL2O trial [2O_CLL107up]

value: relapsed

value: TP53 aberration


title: Chronic lymphocytic leukemia 108; from the CLL2O trial [2O_CLL108up]

value: no ATM deletion


title: BLaER cell line, 9h_HiC_rep2

description: in-situ Hi-C


title: Chronic lymphocytic leukemia 104; from the CLL2O trial [2O_CLL104up]


title: Chronic lymphocytic leukemia 105; from the CLL2O trial [2O_CLL105up]


title: ATAC_24h_rep2

data_processing:
Sequencing data preprocessing. Paired-end reads with additional 6 base reads of barcodes were obtained for each of the samples. Reads from TT-seq/RNA-seq or ChIP-seq/ATAC-seq were demultiplexed and mapped with STAR 2.3.0 (Dobin et al., 2013) or Bowtie2.2.5/Bowtie1.0.0 (Langmead and Salzberg, 2012), respectively, to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). For ATAC-seq, chromosome M was removed. Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
For ChIP-seq , we used the 'callpeak' function of MACS2.1.1 (Zhang et al., 2008) with ‘--BAMPE’ options. To catalogue all the C/EBPα, BRD4 or H3K4me1 binding sites over all the time points, we merged and reduced all peaks, and removed those falling +/- 4Mb of centromeric heterochromatin regions. Duplicates were removed. To obtain the enriched signal (count matrix), read count within the merged peaks were normalized by library size followed by a normalization with counts in corresponding input.
For ATAC-seq, reads were aligned to GRCh38 genome assembly without mitochondrial chromosome (ChrM) using Bowtie1.0.0 (Langmead et al., 2009). Bigwig files were generated by Deeptools 2.3.4 .
For TT-seq, we used a spike-in (RNAs) as described in (Schwalb et al., 2016) to allow antisense bias determination (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) in TT-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015).
For Total RNA-seq, reads were aligned to GRCh38 genome assembly with STAR2.4.2 ((Dobin et al., 2013).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: BRD4allPeaks_reduced.txt:Merged BRD4 peaks from all the time points.; BRD4mat.txt: BRD4 count table for genomic coordinates in BRD4allPeaks_reduced.txt, normalized with size factors and input
Supplementary_files_format_and_content: CEBPallPeaks_reduced.txt:Merged CEBPa peaks from all the time points; CEBPmat.txt: CEBP coverage normalized to size factors and input on the genomic coordinates in CEBPallPeaks_reduced.txt
Supplementary_files_format_and_content: H3K4me1allpeaks_reduced.txt:Merged H3K4me1 peaks from all the time points; H3K4me1mat.txt: H3K4me1 coverage normalized to size factors and input on the genomic coordinates in H3K4me1allPeaks_reduced.txt
Supplementary_files_format_and_content: The bigwig files of ATAC-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X options.
Supplementary_files_format_and_content: Strand specific bigwig files of TT-seq and RNA-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X --filterRNAstrand options.

extract_protocol:
ChIP-seq: At each time point, 3x10^7 cells were harvested and fixed with 1% of formaldehyde for 8 minutes (Thermo Scientific, 28908). Formaldehyde was quenched with 0.2M glycine for 5 min. Chromatin was sheared to 200-500 bp in size using the Covaris S220 ultrasonicator (16min for C/EBPα and BRD4, 18min for H3K4me1). A fraction of the resulting chromatin was used as input control. Sheared chromatin (50ug for C/EBPα and BRD4, 30ul for H3K4me1) was incubated with 5 ug of antibodies - anti-C/EBPα (Santa Cruz, sc-61), anti-H3K4me1 (abcam, ab8895), anti-BRD4 (Bethyl Laboratories, A301–985A100)- bound to protein-A beads (Life Technologies, 9999-01). Samples were incubated at 65ºC overnight to reverse the crosslinks, followed by RNase and proteinase K treatments.
ATAC-seq: ATAC-seq was performed as described (Buenrostro et al., 2013). Briefly, 5 x 10^4 cells were harvested and treated with Nextera Tn5 Transposase (Illumina, FC-121-1030) for 45 min at 37°C.
Total RNA-seq: Total RNA was extracted from the cells labelled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min. RNA prepared using QIAzol according to the manufacturer’s instructions was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator before the library preparation.
At each time point, 1-2.2 x 10^8 cells were labeled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min and harvested by centrifuging at 500g for 2 min. Harvested pellets were lysed with QIAzol (Qiagen, 79306). Following addition of 5ng of spike-in mix per 1 x 10^8 cells, total RNA was purified using QIAzol (Qiagen, 79306) according to the manufacturer’s instructions. Total RNA (300ug) was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator. Newly synthesized RNAs were purified as described (Schwalb et al., 2016) with the following modifications. After streptavidin pull down, the resulting RNA was purified with RNeasy Micro Kit (Qiagen, 74004), together with DNase treatment (Qiagen, 79254).
ChIP-seq: NEB Ultra DNA Library kit (NEB, E7370S) ; ATAC-seq:Nextera Tn5 Transposase ((Illumina, FC-121-1030)) 1x NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S) ; Total RNA-seq and TT-seq Ovation Universal RNA-seq System (Nugen, 0343)

value: RCH-ACV stably expressing estrogen inducible C/EBPa

value: Nextera Tn5 Transposase-1x NEBNext High-Fidelity 2x PCR Master Mix

value: Beta-estradiol (100nM) treatment 24h


title: ATAC_12h_rep2

value: Beta-estradiol (100nM) treatment 12h


title: Chronic lymphocytic leukemia 36; from the CLL8 trial [8_CLL036]


title: ATAC_96h_rep1

value: Beta-estradiol (100nM) treatment 96h


title: ATAC_12h_rep1


title: Chronic lymphocytic leukemia 102; from the CLL2O trial [2O_CLL102up]


title: ATAC_0h_rep2

value: Beta-estradiol (100nM) treatment 0h


title: ATAC_24h_rep1


title: ATAC_96h_rep2


title: Chronic lymphocytic leukemia 100; from the CLL2O trial [2O_CLL100up]


title: Input_16min_96h_rep1_ChIPSeq

description: Chromatin sonication for 16 min with Covaris

value: NEB Ultra DNA Library kit


title: Input_16min_96h_rep2_ChIPSeq


title: Chronic lymphocytic leukemia 99; from the CLL2O trial [2O_CLL099up]


title: Chronic lymphocytic leukemia 101; from the CLL2O trial [2O_CLL101up]


title: Chronic lymphocytic leukemia 98; from the CLL2O trial [2O_CLL098up]


title: Input_16min_12h_rep2_ChIPSeq


title: Input_16min_24h_rep1_ChIPSeq


title: Chronic lymphocytic leukemia 106; from the CLL2O trial [2O_CLL106up]


title: Input_16min_24h_rep2_ChIPSeq


title: ATAC_0h_rep1


title: Chronic lymphocytic leukemia 97; from the CLL2O trial [2O_CLL097up]

value: no TP53 aberration


title: Chronic lymphocytic leukemia 103; from the CLL2O trial [2O_CLL103up]


title: Input_16min_0h_rep1_ChIPSeq


title: BLaER cell line, 48h_HiC_rep2

description: in-situ Hi-C

value: BLaER

value: CEBPA


title: Input_16min_0h_rep2_ChIPSeq


title: Chronic lymphocytic leukemia 96; from the CLL2O trial [2O_CLL096up]

value: ATM deletion


title: Chronic lymphocytic leukemia 95; from the CLL2O trial [2O_CLL095up]

value: refractory


title: Chronic lymphocytic leukemia 93; from the CLL2O trial [2O_CLL093up]

value: mononuclear cells CD19+


title: Chronic lymphocytic leukemia 94; from the CLL2O trial [2O_CLL094up]


title: Chronic lymphocytic leukemia 91; from the CLL2O trial [2O_CLL091up]


title: C/EBPa_96h_rep2_ChIPSeq

value: anti-C/EBPalpha (Santa Cruz, sc-61)


title: C/EBPa_96h_rep1_ChIPSeq


title: Chronic lymphocytic leukemia 90; from the CLL2O trial [2O_CLL090up]


title: C/EBPa_24h_rep1_ChIPSeq


title: C/EBPa_24h_rep2_ChIPSeq


title: Input_16min_12h_rep1_ChIPSeq


title: C/EBPa_12h_rep2_ChIPSeq


title: C/EBPa_0h_rep1_ChIPSeq


title: Chronic lymphocytic leukemia 88; from the CLL2O trial [2O_CLL088up]

value: relapsed


title: Chronic lymphocytic leukemia 85 paired normal; from the CLL2O trial [2O_CLL085pn]

value: mononuclear cells CD19-

value: not annotated


title: C/EBPa_12h_rep1_ChIPSeq

value: RCH-ACV stably expressing estrogen inducible C/EBPa


title: Chronic lymphocytic leukemia 86; from the CLL2O trial [2O_CLL086up]

value: TP53 aberration


title: MDA231_MMS_Srfnb_8h

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: MDA213 breast cancer cell-line

growth_protocol: MDA-MB231 breast cancer cells lines were obtained from ATCC and grown in DMEM supplemented with 10% inactivated FBS plus antibiotics in a 37°C humidified incubator at 5% O2 and 95% CO2 atmosphere. Cells were kept and treated in the exponential phase of growing (60-70% confluence).

extract_protocol:
RNA was harvested using the RNeasy protocol (Qiagen) and the purity of prepared RNA was determined using Agilent 2100 BioAnalyzer.
Total RNA samples about 1-2 ug were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 100bp single-end (SE) sequencing protocol.

treatment_protocol: Sorafenib (1µM) was used as a pretreatment 24 hours prior to MMS exposure, MMS exposure was 40 µg/mL final concentration in fresh medium with or without sorafenib as appropriate.

value: Sorafenib and MMS


title: MDA231_MMS_Srfnb_24h


title: C/EBPa_0h_rep2_ChIPSeq


title: MDA231_Srfnb_8h

value: Sorafenib


title: Chronic lymphocytic leukemia 83 paired normal; from the CLL2O trial [2O_CLL083pn]


title: Chronic lymphocytic leukemia 84; from the CLL2O trial [2O_CLL084]

value: treatment-naïve


title: Chronic lymphocytic leukemia 84 paired normal; from the CLL2O trial [2O_CLL084pn]


title: MDA231_MMS_24h

value: MMS


title: MDA231_MMS_8h


title: Chronic lymphocytic leukemia 92; from the CLL2O trial [2O_CLL092up]

value: no ATM deletion


title: Chronic lymphocytic leukemia 85; from the CLL2O trial [2O_CLL085]

value: no TP53 aberration


title: MDA231_Ctrl_24h

value: Control


title: Chronic lymphocytic leukemia 83; from the CLL2O trial [2O_CLL083]


title: MDA231_Ctrl_8h


title: Chronic lymphocytic leukemia 82 paired normal; from the CLL2O trial [2O_CLL082pn]


title: Chronic lymphocytic leukemia 89; from the CLL2O trial [2O_CLL089up]


title: Chronic lymphocytic leukemia 87; from the CLL2O trial [2O_CLL-087up]


title: Chronic lymphocytic leukemia 81 paired normal; from the CLL2O trial [2O_CLL081pn]


title: MDA213_2_Srfnb_24h


title: Chronic lymphocytic leukemia 81; from the CLL2O trial [2O_CLL081]


title: MDA213_2_MMS_Srfnb_8h


title: MDA213_2_MMS_Srfnb_24h


title: Chronic lymphocytic leukemia 80 paired normal; from the CLL2O trial [2O_CLL080pn]


title: MDA213_2_Srfnb_8h


title: MDA213_2_MMS_24h


title: Chronic lymphocytic leukemia 80; from the CLL2O trial [2O_CLL080]


title: MDA213_2_Ctrl_24h


title: Chronic lymphocytic leukemia 79 paired normal; from the CLL2O trial [2O_CLL079pn]


title: MDA213_2_MMS_8h


title: MDA231_Srfnb_24h


title: MDA213_2_Ctrl_8h


title: Chronic lymphocytic leukemia 79; from the CLL2O trial [2O_CLL079]


title: Chronic lymphocytic leukemia 77 paired normal; from the CLL2O trial [2O_CLL077pn]


title: Chronic lymphocytic leukemia 82; from the CLL2O trial [2O_CLL082]


title: Chronic lymphocytic leukemia 76; from the CLL2O trial [2O_CLL076]


title: FECD-NR_3

city: Dallas

first: Venkateswara

last: Mootha

address: 5323 Harry Hines

department: Ophthalmology

institute: UT Southwestern

description: FECD_NR: advanced FECD without the expanded repeat

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, sequenced reads were mapped to hg38 whole genome using STAR-2.5.3a. Transcriptome reconstruction and differential analysis were carried with Cufflinks-2.2.1.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Cornea

extract_protocol:
Corneal endothelium layer was removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina Whole Transcriptome RNA Sample Prep Kit (strand specific) was used with 50 ng-1 ug of total RNA for the construction of library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Corneal endothelium cells

value: F


title: FECD-NR_2


title: FECD-NR_0


title: Chronic lymphocytic leukemia 77; from the CLL2O trial [2O_CLL077]


title: FECD-NR_1


title: RNA-seq ctrl replicate 1

first: Björn

last: Schwalb

address: Fassberg 11

institute: MPI

description: RNA

data_processing:
Direct RNA nanopore sequencing data preprocessing of synthetic RNAs. Direct RNA nanopore sequencing reads were obtained for each of the samples (Supplementary Table 1).  FAST5 files were base-called using Guppy 3.1.5 (Oxford Nanopore Technologies) with the following parameters: guppy_basecaller -c rna_r9.4.1_70bps_hac.cfg. Direct RNA nanopore sequencing reads were mapped with GraphMap 0.5.2 46 to the synthetic RNA reference sequence with the following parameters: graphmap align --evalue 1e-10. Further data processing was carried out using the R/Bioconductor environment.
Direct RNA nanopore sequencing data preprocessing of human K562 cells. Direct RNA nanopore sequencing reads were obtained for each of the samples (Supplementary Table 1).  FAST5 files were base-called using Guppy 3.1.5 (Oxford Nanopore Technologies) with the following parameters: guppy_basecaller -c rna_r9.4.1_70bps_hac.cfg. Direct RNA nanopore sequencing reads were mapped with Minimap2 2.10 47 to the GRCh38/hg38 genome assembly (Human Genome Reference Consortium) with the following parameters: minimap2 -ax splice -k14 --secondary=no. Samtools 1.3.1 48 was used to quality filter SAM files, whereby alignments with MAPQ smaller than 20 (-q 20) were skipped. Further data processing was carried out using the R/Bioconductor environment and custom python scripts.
RNA-seq data preprocessing and antisense bias correction. Paired-end 75 base reads with additional 6 base reads of barcodes were obtained for each of the samples (Supplementary Table 1).  Reads were demultiplexed and mapped with STAR 2.3.0 (Dobin and Gingeras 2015) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li, Handsaker et al. 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. We used a spike-in (RNAs) normalization strategy essentially as described (Schwalb, Michel et al. 2016) to allow observation of antisense bias ratio  (ratio of spurious reads originating from the opposite strand introduced by the reverse transcription reaction). Read counts (kij) for spike-ins were calculated using HTSeq (Anders, Pyl et al. 2015). The number of transcribed bases (tbj) for all samples was calculated as the sum of the coverage of evident (sequenced) fragment parts (read pairs only) for all fragments with an inner mate interval not entirely overlapping a Refseq annotated intron (UCSC RefSeq GRCh38) in addition to the sum of the coverage of non-evident fragment parts (entire fragment). The number of transcribed bases (tbj) or read counts (kj) for all features (RefSeq-TUs) were corrected for antisense bias cj as follows using the parameter calculated as described above. RPKs were calculated upon antisense bias corrected read counts (kj) falling into the region of a RefSeq-TU divided by its length in kilobases. Coverages were calculated upon antisense bias corrected number of transcribed bases (tbj) falling into the region of a RefSeq-TU divided by its length in bases.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig files containing the coverage

source_name: K562 erythroleukemia cells

growth_protocol: Human K562 erythroleukemia cells were obtained from DSMZ (Cat. # ACC-10). K562 cells were cultured antibiotic-free in accordance with the DSMZ Cell Culture standards in RPMI 1640 medium (Thermo Fisher Scientific) containing 10 % heat inactivated fetal bovine serum (FBS) (Thermo Fisher Scientific), and 1x GlutaMAX supplement (Thermo Fisher Scientific) at 37 °C in a humidified 5 % CO2 incubator. Cells used in this study display the phenotypic properties, including morphology and proliferation rate, that have been described in literature. Cells were verified to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen). Biological replicates were cultured independently.

extract_protocol:
Ovation Universal RNA-Seq System (NuGEN)
Nanopore: Total RNA was extracted from K562 cells using QIAzol (Quiagen) according to manufacturer’s instructions. Poly(A) RNA was purified from 1 mg of total RNA using the µMACS mRNA Isolation Kit (Milteny Biotec) following the manufacturer’s protocol. The quality of poly(A) RNA selection was assessed using the TapeStation System (Agilent). Poly(A) selected RNAs were subsequently subjected to direct RNA nanopore sequencing library preparation (SQK-RNA001, SQK-RNA002, Oxford Nanopore Technologies) following manufacturer’s protocol with 1000 ng input. All libraries were sequenced on a MinION Mk1B (MIN-101B) for 48 h, unless reads sequenced per second stagnated dramatically.
RNA-seq: Total RNA was extracted from K562 cells using QIAzol according to manufacturer’s instructions except for the addition of 150 ng RNA spike-in mix 25 together with QIAzol. To isolate polyA RNA from 75 µg of total RNA, two subsequent rounds of purification by Dynabeads Oligo (dT)25 (invitrogen) were performed. Purification based on manufacturer’s instructions was performed twice, using 1 mg of Dynabeads Oligo (dT)25 beads for the first round and 0.5 mg for the second round of purification. The quality of polyadenylated RNA selection was assessed using RNA ScreenTape on a TapeStation (Agilent). Sequencing libraries were prepared using the NuGEN Ovation Universal RNA-seq kit according to manufacturer’s instructions. Fragments were amplified by 10 cycles of PCR, and sequenced on an Illumina NextSeq 550 in paired-end mode with 75 bp read length.

treatment_protocol:
Nanopore: K562 cells were kept at low passage numbers (<6) and at optimal densities (3x10^5 - 8x10^5) during all experimental setups. Per biological replicate, K562 cells were diluted 24 h before the experiment was performed (Supplementary Table 1). Per 5EU 60 min sample (6 replicates), cells were incubated at 37 °C, 5 % CO2 for 1 h after a final concentration of 500 µM 5-Ethynyluridine (5EU, Jena Bioscience) was added. Per 5EU 24 h sample (3 replicates), cells were incubated at 37 °C, 5% CO2 for 24 h. 5EU was added 3 times during the 24h incubation, i.e. every 8 hours (0h, 8h, 16h) at a final concentration of 500 µM. Control samples were not labeled (3 replicates). Per 5EU 60 min HS (heat shock) sample (5 replicates), cells were incubated at 42 °C for 5 min (until cell suspension reached 42 °C), and then 5EU was added at a final concentration of 500 µM. Further, heat shock treatments were performed in a water bath (LAUDA, Aqualine AL12) at 42 °C. for 1 h. Temperature was monitored by thermometer. To avoid transcriptional changes by freshly added growth medium, fresh growth medium was added 24 h prior to heat shock treatments 45. Exactly after the labeling duration, cells were centrifuged at 37 °C and 1,500 x g for 2 min.
RNA-seq: Two biological replicates of K562 cells were diluted 24 h before the experiment was performed. Per replicate, 3.6 x 107 cells in growth medium were labeled at a final concentration of 500 µM 4-thio-uracil (4sU, Sigma-Aldrich), and incubated at 37 °C, 5 % CO2 for 5 min. Exactly after 5 min of labeling, cells were harvested at 37 °C and 1,500 x g for 2 min.

tag: method protocol

value: RNA-seq

value: K562 erythroleukemia cells

tag: treatment condition


title: RNA-seq ctrl replicate 2

description: RNA


title: FECD_REP_5

tag: gender


title: FECD_REP_4

tag: cell type


title: Chronic lymphocytic leukemia 75 paired normal; from the CLL2O trial [2O_CLL075pn]


title: Chronic lymphocytic leukemia 74; from the CLL2O trial [2O_CLL074up]

value: mononuclear cells CD19+

value: refractory

value: ATM deletion


title: FECD_REP_3


title: Chronic lymphocytic leukemia 73; from the CLL2O trial [2O_CLL073up]


title: FECD_REP_2


title: Chronic lymphocytic leukemia 1 paired normal; from the CLL11 trial [11_CLL001pn]

value: mononuclear cells CD19-

value: not annotated


title: Chronic lymphocytic leukemia 72 paired normal; from the CLL2O trial [2O_CLL072pn]


title: Chronic lymphocytic leukemia 78; from the CLL2O trial [2O_CLL078]

value: relapsed

value: TP53 aberration


title: FECD_REP_0


title: Pre_S_5


title: Chronic lymphocytic leukemia 78 paired normal; from the CLL2O trial [2O_CLL078pn]


title: Pre_S_4


title: Chronic lymphocytic leukemia 76 paired normal; from the CLL2O trial [2O_CLL076pn]


title: Chronic lymphocytic leukemia 71; from the CLL2O trial [2O_CLL071]


title: Chronic lymphocytic leukemia 72; from the CLL2O trial [2O_CLL072]


title: Chronic lymphocytic leukemia 71 paired normal; from the CLL2O trial [2O_CLL071pn]


title: Chronic lymphocytic leukemia 69 paired normal; from the CLL2O trial [2O_CLL069pn]


title: Pre_S_3

value: M


title: Pre_S_1


title: Pre_S_2


title: Pre_S_0


title: Chronic lymphocytic leukemia 69; from the CLL2O trial [2O_CLL069]


title: Chronic lymphocytic leukemia 68 paired normal; from the CLL2O trial [2O_CLL068pn]


title: Chronic lymphocytic leukemia 67 paired normal; from the CLL2O trial [2O_CLL067pn]


title: Control_7


title: Chronic lymphocytic leukemia 67; from the CLL2O trial [2O_CLL067]


title: Control_5


title: Control_6


title: Chronic lymphocytic leukemia 66 paired normal; from the CLL2O trial [2O_CLL066pn]


title: FECD_REP_1


title: Control_4


title: Chronic lymphocytic leukemia 68; from the CLL2O trial [2O_CLL068]

value: treatment-naïve


title: Control_3


title: Control_2


title: Chronic lymphocytic leukemia 70; from the CLL2O trial [2O_CLL070]


title: Chronic lymphocytic leukemia 70 paired normal; from the CLL2O trial [2O_CLL070pn]


title: Control_1


title: Chronic lymphocytic leukemia 66; from the CLL2O trial [2O_CLL066]


title: Chronic lymphocytic leukemia 65 paired normal; from the CLL2O trial [2O_CLL065pn]


title: Chronic lymphocytic leukemia 64 paired normal; from the CLL2O trial [2O_CLL064pn]


title: Chronic lymphocytic leukemia 65; from the CLL2O trial [2O_CLL065]


title: Chronic lymphocytic leukemia 64; from the CLL2O trial [2O_CLL064]


title: Control_0


title: BLaER subclone, Bcell_CTCF-AID_AUX_24h_ChIPseq

value: BLaER subclone CTCF-AID (Auxin Inducible Degron)

tag: treatment

value: CEBPA+auxin


title: Chronic lymphocytic leukemia 63; from the CLL2O trial [2O_CLL063]

value: no ATM deletion


title: Chronic lymphocytic leukemia 63 paired normal; from the CLL2O trial [2O_CLL063pn]


title: BLaER subclone, Bcell_CTCF-AID_DMSO_24h_ChIPseq

value: CEBPA+DMSO


title: Chronic lymphocytic leukemia 62 paired normal; from the CLL2O trial [2O_CLL062pn]


title: 000008512269_F12

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

data_processing:
Data was separated by barcode and aligned using Tophat version 2.0.10 (Kim et al. 2013) with default settings.
Transcripts were quantified by the Broad Technology Labs computational pipeline using Cuffquant version 2.2.1 (Trapnell et al. 2012).
Data were processed through CuffNorm if 50% of the reads aligned and if at least 100,000 pairs were aligned per sample. Normalization used the default settings, including “geometric” normalization, and expression level information as FPKM (Fragments per kilobase of transcript per million mapped fragments) are provided.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including FPKM for each sample

source_name: TEM

extract_protocol:
Naïve (CD45RA+CD28+), EM (CD45RA-CD28-) and TEMRA (CD45RA+CD28-) CD3+CD8+ were FACS-sorted (FACSAria, BD Biosciences; purity greater than 95%) from freshly isolated human PBMCs obtained from 8 healthy donors (obtained by the Establissement Français du Sang). After sorting, total RNA was extracted using the RecoverAll Total Nucleic Acid Isolation Kit (Ambion). RNA quantity was measured with a Nanodrop ND1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was assessed using an Agilent 2100 Bioanalyser.
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform according to the SmartSeq2 protocol (Picelli et al, 2013, 2014) with some modifications (Trombetta et al, 2014). Briefly, total RNA was purified using RNA-SPRI beads, polyA mRNA was converted to cDNA and amplified cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Sequencing was carried out as paired-end 2x25bp with an additional 8 cycles for each index.

value: CD8+ T cells

tag: cell subtype

value: TEM

tag: cell markers

tag: volunteer

tag: rin


title: Control_8

value: Corneal endothelium cells

value: F


title: Chronic lymphocytic leukemia 62; from the CLL2O trial [2O_CLL062]

value: mononuclear cells CD19+

tag: cohort

tag: tp53 status

tag: atm status


title: 000008512269_F11


title: Chronic lymphocytic leukemia 61 paired normal; from the CLL2O trial [2O_CLL061pn]


title: 000008512269_E11


title: 000008512269_D11


title: Chronic lymphocytic leukemia 60 paired normal; from the CLL2O trial [2O_CLL060pn]


title: 000008512269_C11


title: 000008512269_C12


title: 000008512269_B11


title: Chronic lymphocytic leukemia 60; from the CLL2O trial [2O_CLL060]


title: Chronic lymphocytic leukemia 59 paired normal; from the CLL2O trial [2O_CLL059pn]


title: Chronic lymphocytic leukemia 59; from the CLL2O trial [2O_CLL059]

value: refractory


title: 000008512269_F09

source_name: Naive

value: Naive


title: Chronic lymphocytic leukemia 58 paired normal; from the CLL2O trial [2O_CLL058pn]

value: mononuclear cells CD19-


title: 000008512269_E09


title: 000008512269_A11


title: 000008512269_D12


title: Chronic lymphocytic leukemia 57; from the CLL2O trial [2O_CLL057]


title: Chronic lymphocytic leukemia 58; from the CLL2O trial [2O_CLL058]


title: 000008512269_D09


title: 000008512269_B09


title: Chronic lymphocytic leukemia 56; from the CLL2O trial [2O_CLL056]


title: Chronic lymphocytic leukemia 56 paired normal; from the CLL2O trial [2O_CLL056pn]

value: not annotated


title: Chronic lymphocytic leukemia 54; from the CLL2O trial [2O_CLL054up]


title: Chronic lymphocytic leukemia 57 paired normal; from the CLL2O trial [2O_CLL057pn]


title: 000008512269_A09


title: Chronic lymphocytic leukemia 53 paired normal; from the CLL2O trial [2O_CLL053pn]


title: Chronic lymphocytic leukemia 55; from the CLL2O trial [2O_CLL055up]


title: 000008512269_E12

source_name: EM

value: EM


title: 000008512269_F10


title: 000008512269_E10


title: Chronic lymphocytic leukemia 52 paired normal; from the CLL2O trial [2O_CLL052pn]


title: 000008512269_D10


title: Chronic lymphocytic leukemia 52; from the CLL2O trial [2O_CLL052]

value: no TP53 aberration


title: Chronic lymphocytic leukemia 51 paired normal; from the CLL2O trial [2O_CLL051pn]


title: 000008512269_C09


title: 000008512269_C10


title: Chronic lymphocytic leukemia 50 paired normal; from the CLL2O trial [2O_CLL050pn]


title: Chronic lymphocytic leukemia 51; from the CLL2O trial [2O_CLL051]

value: TP53 aberration


title: Chronic lymphocytic leukemia 49 paired normal; from the CLL2O trial [2O_CLL049pn]


title: CML-BC15

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with fastx_clipper
mapped to hg19 whole genome using tophat2 with parameters
Reads per kilobase of exon model per million mapped reads (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
detecting different expression gene using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: text file with RPKM abundance measurements

source_name: Peripheral blood mononuclear cells

extract_protocol:
Peripheral blood  mononuclear cells were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA-Seq Library Preparation Kit forWhole Transcriptome Discovery–Illumina Compatible (K02421) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Blast crisis of chronic myeloid leukemia

tag: tissue

value: Peripheral blood

value: mononuclear

tag: bcr/abl fusion gene

value: Positive


title: Chronic lymphocytic leukemia 50; from the CLL2O trial [2O_CLL050]

value: ATM deletion


title: 000008512269_B12

value: CD8+ T cells


title: Chronic lymphocytic leukemia 49; from the CLL2O trial [2O_CLL049]


title: 000008512269_A10


title: 000008512269_A12


title: Chronic lymphocytic leukemia 48 paired normal; from the CLL2O trial [2O_CLL048pn]


title: Chronic lymphocytic leukemia 53; from the CLL2O trial [2O_CLL053]


title: Chronic lymphocytic leukemia 48; from the CLL2O trial [2O_CLL048]

value: treatment-naïve

value: no ATM deletion


title: CML-BC11


title: Chronic lymphocytic leukemia 47; from the CLL2O trial [2O_CLL047]


title: CML-CP10

value: Chronic phase of chronic myeloid leukemia


title: CML-BC13


title: CML-CP9


title: Chronic lymphocytic leukemia 61; from the CLL2O trial [2O_CLL061]

value: mononuclear cells CD19+


title: Chronic lymphocytic leukemia 46 paired normal; from the CLL2O trial [2O_CLL046pn]


title: CML-CP8


title: Chronic lymphocytic leukemia 46; from the CLL2O trial [2O_CLL046]


title: 000008512269_B10


title: Chronic lymphocytic leukemia 45 paired normal; from the CLL2O trial [2O_CLL045pn]


title: CML-CP7


title: CML-CP6


title: Chronic lymphocytic leukemia 45; from the CLL2O trial [2O_CLL045]


title: Chronic lymphocytic leukemia 44 paired normal; from the CLL2O trial [2O_CLL044pn]


title: Ctrl4

value: Healthy

value: Negative


title: Chronic lymphocytic leukemia 44; from the CLL2O trial [2O_CLL044]


title: CML-BC14


title: Chronic lymphocytic leukemia 43 paired normal; from the CLL2O trial [2O_CLL043pn]

value: mononuclear cells CD19-


title: CML-BC12


title: Chronic lymphocytic leukemia 43; from the CLL2O trial [2O_CLL043]

value: refractory


title: Ctrl5


title: Ctrl2


title: Ctrl3


title: Ctrl1


title: Chronic lymphocytic leukemia 42 paired normal; from the CLL2O trial [2O_CLL042pn]

value: not annotated


title: Chronic lymphocytic leukemia 42; from the CLL2O trial [2O_CLL042]


title: Chronic lymphocytic leukemia 41 paired normal; from the CLL2O trial [2O_CLL041pn]


title: Chronic lymphocytic leukemia 47 paired normal; from the CLL2O trial [2O_CLL047pn]


title: Chronic lymphocytic leukemia 41; from the CLL2O trial [2O_CLL041]


title: Chronic lymphocytic leukemia 40 paired normal; from the CLL2O trial [2O_CLL040pn]


title: Chronic lymphocytic leukemia 40; from the CLL2O trial [2O_CLL040]

value: relapsed


title: Sample6: PFN1_KO.2

city: Gainesvile

first: Kristen

last: Skruber

state: Florida

address: 1333 Center Drive

institute: university of florida

description: RNA-seq of Control vs PFN1 Knock-Out Cells

data_processing:
Illumina Casava software was used for base calling.
For RNA-seq, reads were aligned to the human transcriptome using RSEM followed by mapping to the human genome (hg19) using Bowtie and TopHat.
Uniquely mapped reads were counted using Quantas.
Identification of differentially expressed genes was computed using EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: The final processed data is found in the file "CAD-PFN1KO.xlsx"

source_name: Cath.a differentiated cell line

growth_protocol: Undifferentiated CAD cells cultured in 8% FBS.

extract_protocol:
Total RNA was extracted from Wild-type or PFN1 KO Cath.a differentiated cells (four biological replicates/condition). RNA was isolated using Direct-Zol RNA miniprep kit.
Libraries were generated using KAPA stranded RNA-Seq kit with RiboErase HMR.

treatment_protocol: Crispr-Cas9 mediated PFN1 deletion.

value: Cath.a differentiated cell line

tag: genotype/variation

value: PFN1 KO


title: Sample8: PFN1_KO.4


title: Sample5: PFN1_KO.1


title: Sample3: WT-Control.3

value: Control KO


title: Chronic lymphocytic leukemia 39 paired normal; from the CLL2O trial [2O_CLL039pn]


title: Sample7: PFN1_KO.3


title: Sample4: WT-Control.4


title: Sample2: WT-Control.2


title: Chronic lymphocytic leukemia 39; from the CLL2O trial [2O_CLL039]

value: TP53 aberration


title: Sample1: WT-Control.1


title: Chronic lymphocytic leukemia 38; from the CLL2O trial [2O_CLL038up]


title: Chronic lymphocytic leukemia 37; from the CLL2O trial [2O_CLL037]


title: Chronic lymphocytic leukemia 37 paired normal; from the CLL2O trial [2O_CLL037pn]


title: Chronic lymphocytic leukemia 36 paired normal; from the CLL2O trial [2O_CLL036pn]


title: Chronic lymphocytic leukemia 36; from the CLL2O trial [2O_CLL036]


title: KO Ebf3 1

city: Kyoto city

first: Mao

last: Kuriki

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Regenerative immunity

country: Japan

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

description: Group2- KYT_010_04

data_processing:
Illumina NextSeq500 software used for basecalling.
Sequencing (Long-read: High/Mid-output kit v2, 2x76, 2x151 or 1x160)  was performed with the Illumina NextSeq-500 platform (San Diego, CA, USA), which generated raw sequencing reads.
8 gz-compressed FASTQ files per sample (4 imaging sections x Read 1+2)
8 FASTQ files are concatenated by cat command in Linux into 2 files (Read 1 and Read 2) ,Imported to CLC GW as paired-end reads,
Reads were mapped to the reference genome and transcript annotation was performed (Mouse, mm 10,49,585 genes, 103,982 transcripts) (ENSEMBLE, provided by CLC). PCA plot and box plot of total count (N>1 experiment) or RPKM (N=1 experiment),For drawing graph and plot, normalization is performed by quantile method for total count or RPKM
Genome_build: UCSC MM9
Supplementary_files_format_and_content: After statistical analysis (explained in next page), CLC files are exported in Excel format.

source_name: Thoracic LPM

extract_protocol:
LPMs were isolated from Prx1-Cre Ebf3-KO mice with those from Prx1-Cre Ebf3 heterozygous mice. Trunks without limb buds, heart and other organs in thoracic /abdominal cavity were isolated, and then thoracic wall tissues were excised. Prx1-Cre R26RTdtomato-activated LPMs were isolated from these thoracic wall tissues by fluorescence-activated cell sorting (FACS). Total RNA was extracted from the cells isolated by FACS in cell lysis buffer (TRIzol LS Reagent, Life Technologies, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

tag: genotype

value: Prx1-Cre Ebf3 flox/flox


title: Herero Ebf3 3

description: Group1- KYT_010_03

value: Prx1-Cre Ebf3 flox/+


title: KO Ebf3 3

description: Group2- KYT_010_06


title: Chronic lymphocytic leukemia 35; from the CLL2O trial [2O_CLL035]

value: no TP53 aberration


title: Herero Ebf3 1

description: Group1- KYT_010_01


title: KO Ebf3 2

description: Group2- KYT_010_05


title: Chronic lymphocytic leukemia 34 paired normal; from the CLL2O trial [2O_CLL034pn]


title: Herero Ebf3 2

description: Group1- KYT_010_02


title: Chronic lymphocytic leukemia 34; from the CLL2O trial [2O_CLL034]


title: Chronic lymphocytic leukemia 35 paired normal; from the CLL2O trial [2O_CLL035pn]


title: Neonatal sciatic nerve, (myelin removal beads)

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

country: Canada

institute: Hospital for Sick Children

data_processing:
FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/) with settings as described in the Drop-seq Alignment Cookbook (version 1.2 Jan2016, http://mccarrolllab.com/dropseq/).
The number of cell barcodes per sample was identified by calculating the cumulative fraction of reads attributable to each individual cell barcode and arranging these in decreasing order.
A total of 2500 barcodes were selected for the 3d injured nerve dataset, 2500 barcodes for the neonatal FACS dataset, 6200 barcodes for the neonatal myelin removal beads dataset, and 2000 barcodes for the uninjured nerve dataset.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are tab-delimited text files containing raw digital gene expression for each sample. Processed data files for the 3 d injured sciatic nerve, FACS sorted neonatal sciatic nerve,  myelin removal bead treated neonatal sciatic nerve, and uninjured sciatic nerve are included. The processed data file for the uninjured sciatic nerve includes mesenchymal cell data previously published in Carr et al., 2019, Cell Stem Cell.

source_name: Sciatic nerve

extract_protocol:
Cells were extracted from the sciatic nerves of adult and neonatal CD1 mice. Nerves were dissociated with collagenase and trypsin and cells were either FACS sorted or processed through myelin removal beads prior to collection of single-cell transcriptomes as described by Macosko et al., 2015, Cell. Injured sciatic nerve samples were isolated from the distal segment 3 days following nerve resection.
Standard Illumina libraries were generated as described by Macosko et al., 2015, Cell.

value: sciatic nerve

value: neonatal (P2-P3)

value: Wildtype CD1


title: Uninjured sciatic nerve, (myelin removal beads)

value: adult


title: Chronic lymphocytic leukemia 33 paired normal; from the CLL2O trial [2O_CLL033pn]


title: Neonatal sciatic nerve, (FACS sorted)

value: neonatal (P3-P4)


title: Chronic lymphocytic leukemia 32 paired normal; from the CLL2O trial [2O_CLL032pn]


title: Sciatic nerve, 3 days post injury, (myelin removal beads)

value: distal sciatic nerve


title: Chronic lymphocytic leukemia 33; from the CLL2O trial [2O_CLL033]

value: mononuclear cells CD19+

value: ATM deletion


title: KO10

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

data_processing:
Basecalls performed using CASAVA version 1.8
For RNA-seq reads were mapped on mm9 using TOPHAT v2.0.6 with the following parameters :--min-anchor=5 --min-isoform-fraction=0.01 --max-multihits=10 --bowtie1. The number of reads covered by each gene is calculated by HTSeq-Count with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Htseq-count text file

source_name: cortical primordia (E15.5)

extract_protocol:
Mouse cortical primordia were collected and dissected on ice, then flash-frozen in liquid nitrogen and stored at -80°C.
PolyA+ RNA-seq were performed by using the TruSeq RNA Sample Prep kit, following manufacturer instructions.

value: cortical primordia (E15.5)

value: Nr2f1 Knock Out


title: KO5


title: Chronic lymphocytic leukemia 31 paired normal; from the CLL2O trial [2O_CLL031pn]

value: mononuclear cells CD19-

value: not annotated


title: Chronic lymphocytic leukemia 32; from the CLL2O trial [2O_CLL032]

value: relapsed

value: no ATM deletion


title: KO4


title: Chronic lymphocytic leukemia 31; from the CLL2O trial [2O_CLL031]

value: refractory


title: WT3

value: WT


title: Chronic lymphocytic leukemia 30 paired normal; from the CLL2O trial [2O_CLL030pn]


title: WT2


title: Chronic lymphocytic leukemia 29 paired normal; from the CLL2O trial [2O_CLL029pn]


title: Chronic lymphocytic leukemia 30; from the CLL2O trial [2O_CLL030]

value: treatment-naïve

value: TP53 aberration


title: Chronic lymphocytic leukemia 29; from the CLL2O trial [2O_CLL029]


title: Uninjured Control

city: Durham

first: James

last: White

state: NC

address: 300 N. Duke St.

institute: Duke University

data_processing:
Basecalling and fastq files generated using 10X Cellranger v2.1.1 with default parameters
Alignment, counting, filtering, of single cell RNA-Seq of samples:- Uninjured Control & Injured(1d) , using 10X Cellranger v2.1.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for Mus musculus Uninjured Control & Injured(1d)  tibialis anterior muscle cells. Columns correspond to individual cells(barcodes), while rows correspond to genes.
genes.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.

source_name: Tibialis Anterior muscle

growth_protocol: Mice fed on standard chow

extract_protocol:
Muscle protease digestion
10X Single Cell 3' v2

treatment_protocol: IM injection of 1.2% BaCl

value: young (12 weeks)

value: Tibialis Anterior muscle


title: embryo (8-cell stage), MUT.RME814.P200

city: Singapore

first: Brenda

middle: Yuyuan

last: Han

address: 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology, A*STAR

data_processing:
RNA-seq data was processed using the ENCODE STAR-RSEM pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/ STAR_RSEM.sh).
Sequence reads were mapped to the mouse genome build GRCm38.p6 using STAR (v2.6.0c)
Gene-level transcript abundances were quantified by RSEM8 (v1.3.1) against the GENCODE mouse vM18 annotation set
DESeq2 (v1.22.2) was used for differential expression analysis. Multi-factor analysis was used to account for batch effects (P200 samples vs P226 samples).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: [Quant.genes.results]  Gene-level expression estimates (generated by RSEM)
[MUT.vs.CTL_MF.DE.txt]  differential expression (DESeq2)

source_name: mouse embryo (8-cell stage)

growth_protocol: Naturally mated timed pregnant females from Prdm10Δ/+ intercrosses were sacrificed at E2.5, and 8-cell stage embryos were collected from the oviduct.

extract_protocol:
Embryos were individually snap frozen in 4 ul lysis buffer containing dNTP mix, oligo-dT primer and SUPERase-In RNase inhibitor (Invitrogen).
RNA-seq library preparation was performed according to the Smart-seq2 protocol with slight modifications. Embryos were isolated and processed in two separate batches. To pre-screen cDNA samples for downstream library preparation, mutant (Prdm10Δ/Δ) and control (Prdm10+/+, Prdm10Δ/+) embryos were identified by qRT-PCR detection of Prdm10 exon 5. 16 cycles of PCR pre-amplification were carried out for batch 1 (P200) and 13 cycles for batch 2 (P226). 1 ng of cDNA was used for tagmentation with the Nextera XT DNA Library Prep Kit (Illumina). Final libraries were amplified and pooled for single-end Illumina sequencing.

value: Prdm10 KO

tag: age (embryonic day)

value: embryo (8-cell stage)


title: WT9

tag: cell type


title: embryo (8-cell stage), CTL.RME806.P226

value: Prdm10 WT/HET


title: Injured (1d)


title: WT #3.4

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Gene ontology process enrichment analysis (Huang et al., 2009) was performed to assess differential expression of genes between contrasts.
Genome_build: mm10
Supplementary_files_format_and_content: library-size normalized counts per sample

source_name: cauda epididymidis

extract_protocol:
Tissues were removed, snap frozen in liquid nitrogen and lysed using metal beads, Trizol reagent and chloroform. Subsequently, RNA-phase was prepared using RNeasy Mini kit including on-column DNase digestion.
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech) following standard instructions.

value: 10-12 weeks

value: wildtype


title: WT #2.4


title: embryo (8-cell stage), MUT.RME804.P226


title: WT #1.4


title: embryo (8-cell stage), CTL.RME811.P200


title: embryo (8-cell stage), CTL_RME813.P200


title: embryo (8-cell stage), MUT.RME810.P226


title: embryo (8-cell stage), CTL.RME809.P226


title: embryo (8-cell stage), CTL_RME815.P200


title: embryo (8-cell stage), MUT.RME805.P226


title: embryo (8-cell stage), MUT.RME812.P200


title: WT #3.3

source_name: corpus epididymidis


title: WT #2.3


title: Chronic lymphocytic leukemia 22; from the CLL2O trial [2O_CLL022]

data_processing:
CEL-files and chp-files (generated by Affymetrix GTYPE using the DM algorithm and by the birdseed algorithm in Affymetrix Genotyping Console version 4.0, respectively) were processed by dChip and model-based expression performed using the PM/MM model.
affymetrix-algorithm-name = birdseed-v2
affymetrix-algorithm-version = 2.4
affymetrix-array-type = GenomeWideSNP_6
program-name = Genotyping Console
program-version = 3.0.3190.24001
Signal' = Summarized signal; Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

source_name: peripherel blood

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations from peripheral blood using the Qiagen® DNA Blood Mini Kit (Hilden, Germany). Immunomagnetic tumor cell enrichment was performed for all samples (Midi MACS, Miltenyi Biotec®; Bergisch Gladbach, Germany) so that 146 CD19-positive fractions, and 91 CD19-negative fractions were used. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: mononuclear cells CD19+


title: Chronic lymphocytic leukemia 21 paired normal; from the CLL2O trial [2O_CLL021pn]


title: Chronic lymphocytic leukemia 24; from the CLL2O trial [2O_CLL024]

value: no TP53 aberration


title: Chronic lymphocytic leukemia 24 paired normal; from the CLL2O trial [2O_CLL024pn]

value: mononuclear cells CD19-


title: Chronic lymphocytic leukemia 28; from the CLL2O trial [2O_CLL028]


title: Chronic lymphocytic leukemia 28 paired normal; from the CLL2O trial [2O_CLL028pn]

value: not annotated


title: Chronic lymphocytic leukemia 25; from the CLL2O trial [2O_CLL025]

value: relapsed

value: ATM deletion


title: Chronic lymphocytic leukemia 25 paired normal; from the CLL2O trial [2O_CLL025pn]


title: Chronic lymphocytic leukemia 26 paired normal; from the CLL2O trial [2O_CLL026pn]


title: WT #1.3


title: Chronic lymphocytic leukemia 27; from the CLL2O trial [2O_CLL027]

value: refractory

value: no ATM deletion


title: Chronic lymphocytic leukemia 27 paired normal; from the CLL2O trial [2O_CLL027pn]


title: Chronic lymphocytic leukemia 26; from the CLL2O trial [2O_CLL026]


title: Chronic lymphocytic leukemia 22 paired normal; from the CLL2O trial [2O_CLL022pn]


title: Chronic lymphocytic leukemia 23 paired normal; from the CLL2O trial [2O_CLL023pn]


title: Chronic lymphocytic leukemia 23; from the CLL2O trial [2O_CLL023]


title: Chronic lymphocytic leukemia 20; from the CLL2O trial [2O_CLL020]


title: embryo (8-cell stage), CTL.RME808.P226


title: Chronic lymphocytic leukemia 19 paired normal; from the CLL2O trial [2O_CLL019pn]


title: WT #3.2

source_name: caput epididymidis


title: WT #1.2


title: WT #2.2


title: WT #3.1

source_name: whole testis


title: Chronic lymphocytic leukemia 18 paired normal; from the CLL2O trial [2O_CLL018pn]


title: WT #2.1


title: Chronic lymphocytic leukemia 75; from the CLL2O trial [2O_CLL075]

value: treatment-naïve


title: Chronic lymphocytic leukemia 21; from the CLL2O trial [2O_CLL021]

value: TP53 aberration


title: Chronic lymphocytic leukemia 18; from the CLL2O trial [2O_CLL018]


title: Chronic lymphocytic leukemia 20 paired normal; from the CLL2O trial [2O_CLL020pn]


title: Day4_OHT.1

description:
Prdm10 KO mESCs, Day 4
d4_KO.vs.WT_DE_pval.txt

data_processing:
RNA-seq data was processed using the ENCODE STAR-RSEM pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/ STAR_RSEM.sh).
Sequence reads were mapped to the mouse genome build GRCm38.p6 using STAR (v2.6.0c)
Gene-level transcript abundances were quantified by RSEM8 (v1.3.1) against the GENCODE mouse vM18 annotation set
DESeq2 (v1.22.2) was used for differential expression analysis
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Gene-level expression estimates (generated by RSEM)

source_name: mouse embryonic stem cells

growth_protocol: Prdm10F/F; Rosa26-CreERT2 mESCs were cultured on 0.1% gelatin-coated plates in Dulbecco’s Modified Eagle’s Medium supplemented with 15% fetal bovine serum, GlutaMAX, non-essential amino acids, 1 mM sodium pyruvate, 100 U/ml penicillin/ streptomycin, 5.5 μM 2-mercaptoethanol and 1000 U/ml LIF.

extract_protocol:
At Day 2 and Day 4 post-induction, mESCs were harvested in TRIzol and total RNA purified using the PureLink RNA Mini Kit (Life Technologies) with on-column DNase treatment.
Total RNA was quantified on a Nanodrop and RNA quality was assessed on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies). Libraries were constructed from 1 mg total RNA using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina). The resulting libraries were assessed by High Sensitivity DNA Assay on a Bioanalyzer and quantitative real-time PCR using the KAPA Library Quantification Kit (Roche).

treatment_protocol: Cells were treated for 24 h with 50 nM 4-OHT to induce Prdm10 deletion, or an equal volume of ethanol as vehicle control

value: mouse embryonic stem cells

value: Prdm10del/del; Rosa26-CreERT2

tag: treatment

tag: timepoint

value: Day 4


title: Day4_OHT.2


title: Chronic lymphocytic leukemia 15 paired normal; from the CLL2O trial [2O_CLL015pn]


title: Day4_EtOH.2

description:
Prdm10 WT mESCs, Day 4
d4_KO.vs.WT_DE_pval.txt

value: Prdm10F/F; Rosa26-CreERT2

value: ethanol


title: Chronic lymphocytic leukemia 14; from the CLL2O trial [2O_CLL014]


title: Chronic lymphocytic leukemia 17; from the CLL2O trial [2O_CLL017]


title: Day4_EtOH.1


title: Chronic lymphocytic leukemia 12 paired normal; from the CLL2O trial [2O_CLL012pn]


title: Chronic lymphocytic leukemia 13; from the CLL2O trial [2O_CLL013]


title: Chronic lymphocytic leukemia 15; from the CLL2O trial [2O_CLL015]


title: Day2_OHT.2

description:
Prdm10 KO mESCs, Day 2
d2_KO.vs.WT_DE_pval.txt

value: Day 2


title: Day4_EtOH.3


title: Chronic lymphocytic leukemia 14 paired normal; from the CLL2O trial [2O_CLL014pn]


title: Day2_OHT.1


title: Chronic lymphocytic leukemia 16 paired normal; from the CLL2O trial [2O_CLL016pn]


title: Chronic lymphocytic leukemia 19; from the CLL2O trial [2O_CLL019]


title: Day4_OHT.3


title: Day2_EtOH.2

description:
Prdm10 WT mESCs, Day 2
d2_KO.vs.WT_DE_pval.txt


title: Chronic lymphocytic leukemia 13 paired normal; from the CLL2O trial [2O_CLL013pn]


title: Day2_OHT.3


title: WT #1.1

value: 10-12 weeks

value: wildtype


title: Chronic lymphocytic leukemia 16; from the CLL2O trial [2O_CLL016]

value: mononuclear cells CD19+


title: Day2_EtOH.3


title: Chronic lymphocytic leukemia 11 paired normal; from the CLL2O trial [2O_CLL011pn]

value: mononuclear cells CD19-


title: Day2_EtOH.1


title: KO_input

description: input DNA from KO mESCs

data_processing:
ChIP-seq data were processed using the ENCODE Transcription Factor and Histone ChIP-Seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2; v1.1.7, commit 2f567e6e).
Fastq files were aligned with bwa (0.7.13), then filtered to remove duplicates (with Picard 2.10.6), multi-mapping reads and low-quality alignments (with samtools 1.2)
SPP (1.13) was used to call peaks from the filtered alignments; in addition to calling peaks on each individual sample, peaks were called on the pooled set of alignments across all samples, as well as two pseudo-replicates obtained from the pooled set by splitting alignments into two equal sets.
Peaks in the ENCODE mm10 blacklist were filtered out, and filtered peak sets were assessed for reproducibility using IDR (2.0.4.2).
Final peak set used was the ‘optimal’ peak set from the pipeline, which was obtained from the pooled pseudo-replicates with IDR cut-off of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig (signal tracks, fold-change over input); regionPeak (peak files generated by SPP/IDR)

extract_protocol:
Chromatin extracts were obtained by successive rounds of lysis in LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Nonidet-P40, 0.25% Triton X-100), LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine). Chromatin DNA was sheared to a size range of 100-500 bp by sonication. Chromatin immunoprecipitation was performed by incubating sonicated chromatin with anti-PRDM10 antibody at 4°C overnight, followed by incubation with Protein A Dynabeads. Beads were washed in low salt buffer, high salt buffer, LiCl buffer and TE buffer. Protein/DNA complexes were eluted, reverse-crosslinked overnight at 65°C and treated with RNase A and proteinase K. ChIP DNA was purified using Qiaquick PCR Purification kit (Qiagen).
Libraries were prepared from 4 ng of ChIP DNA using the NEBNext Ultra II DNA Library Preparation Kit for Illumina (NEB). All libraries were amplified for 9 PCR cycles and final elution volumes were reduced. Libraries were quantified by High Sensitivity DNA Assay on a Bioanalyzer and quantitative real-time PCR (KAPA Library Quantification Kit for Illumina, Roche).

treatment_protocol: Cells were treated for 24 h with 50 nM 4-OHT to induce Prdm10 deletion, or ethanol as vehicle control.

tag: chip antibody

value: 4-hydroxytamoxifen (4-OHT)


title: Chronic lymphocytic leukemia 17 paired normal; from the CLL2O trial [2O_CLL017pn]

value: not annotated


title: Chronic lymphocytic leukemia 11; from the CLL2O trial [2O_CLL011]


title: Chronic lymphocytic leukemia 12; from the CLL2O trial [2O_CLL012]


title: KO_ChIP.3

description:
Prdm10 ChIP rep 3 with KO mESCs
peaks.KO_IDR.optimal.regionPeak

value: anti-PRDM10 (Bethyl Laboratories, A303-204A)


title: Chronic lymphocytic leukemia 10; from the CLL2O trial [2O_CLL010]


title: WT_input

description: input DNA from WT mESCs


title: KO_ChIP.1

description:
Prdm10 ChIP rep 1 with KO mESCs
peaks.KO_IDR.optimal.regionPeak

value: anti-PRDM10 rabbit polyclonal 1 (generated in-house)


title: WT_ChIP.2

description:
Prdm10 ChIP rep 2 with WT mESCs
peaks.WT_IDR.optimal.regionPeak

value: anti-PRDM10 rabbit polyclonal 2 (generated in-house)


title: Chronic lymphocytic leukemia 7 paired normal; from the CLL2O trial [2O_CLL007pn]


title: KO_ChIP.2

description:
Prdm10 ChIP rep 2 with KO mESCs
peaks.KO_IDR.optimal.regionPeak


title: Chronic lymphocytic leukemia 9 paired normal; from the CLL2O trial [2O_CLL009pn]


title: WT_ChIP.1

description:
Prdm10 ChIP rep 1 with WT mESCs
peaks.WT_IDR.optimal.regionPeak


title: Chronic lymphocytic leukemia 8; from the CLL2O trial [2O_CLL008]

value: relapsed

value: no ATM deletion


title: Chronic lymphocytic leukemia 9; from the CLL2O trial [2O_CLL009]

value: TP53 aberration


title: Chronic lymphocytic leukemia 10 paired normal; from the CLL2O trial [2O_CLL010pn]


title: WT_ChIP.3

description:
Prdm10 ChIP rep 3 with WT mESCs
peaks.WT_IDR.optimal.regionPeak

value: mouse embryonic stem cells


title: Chronic lymphocytic leukemia 5 paired normal; from the CLL2O trial [2O_CLL005pn]


title: Chronic lymphocytic leukemia 4 paired normal; from the CLL2O trial [2O_CLL004pn]


title: Chronic lymphocytic leukemia 7; from the CLL2O trial [2O_CLL007]

value: refractory