title: input  DNA

city: Research Triangle Park

first: Sylvia

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

data_processing:
Each raw dataset was filtered to remove any reads with average base quality score <20 after trimming all reads to 36mers.
Filtered reads were mapped against the mm10 reference genome via Bowtie v0.12.8 with default parameters and '-m 1' option.
Duplicate mapped reads were removed with Picard tools v1.110 MarkDuplicates.jar.
Uniquely-mapped non-duplicate reads were extended to the estimated average fragment length (150nt) then converted to bedGraph format for visualization of coverage.
Genome_build: mm10
Supplementary_files_format_and_content: Mapped read depth in bedGraph format.

source_name: uterus

extract_protocol:
Uteri were submersed in PBS + 1% formaldehyde, cut into small (~1 mm3) pieces with a razor blade and incubed at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated from the sample by adding 5-10 ml lysis buffer containing PIPES, Igepal, PMSF and Protease Inhibitor Cocktail, followed by disruption with a Dounce homogenizer. Samples were pelleted by centrifugation and resuspended in buffer containing Na deoxycholate, SDS, and Triton X-100. Lysates were sonicated using a Misonix Sonicator 3000 equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and the chromatin suspensions were transferred to new tubes and stored at -80 C. Prior to use in ChIP, protein A agarose beads (Invitrogen) were preblocked using blocking proteins and nucleic acids for 3 hr. For each ChIP reaction, an aliquot of chromatin (20-30 ug) was precleared with 30 ul preblocked protein A agarose beads for 1-2 hr. ChIP reactions were set up using precleared chromatin and antibody Eralpha (sc-542, Lot# D1310) in a buffer containing Na deoxycholate and incubated overnight at 4 C. Preblocked protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Agarose beads containing the immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. An SDS-containing buffer was added to elute the immune complexes from the beads, and the eluates were subjected to RNase treatment at 37 C for 20 min and proteinase K treatment at 37 C for 3 hr. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNAs were purified by phenolchloroform extraction and ethanol precipitation. Quality of ChIP enrichment was assayed by qPCR using primers against candidate EREs in the Igf1 and Stat5a promoters. Input DNA was queried at the same sites in parallel
ChIP DNA was amplified by following the Illumina ChIP-Seq DNA Sample Prep Kit protocol. In brief, DNA ends were polished and 5’-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. After addition of 3’-A to the ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was sizefractionated (200-250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles,Phusion polymerase), the resulting DNA libraries were quantified and tested by QPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions. DNA libraries were sequenced on a Genome Analyzer II.

treatment_protocol: Mice were ovariectomized, rested for 10-14 days to clear endogenouse ovarian hormones and then injected with 100 ul of saline (Vehicle, V) or 100 ul of saline containing 250 ng of estradiol (E2). Uterine tissue was collected 1 hour later and snap frozen. ERa ChIP-seq was done at Active Motif using antibody sc-542 (Santa Cruz Biotech)

value: uterus

tag: chip antibody


title: Sample_402_Brd2_rep2

status: Public on Apr 01 2017

type: SRA

city: New York

first: Rajal

last: Sharma

state: NY

address: 1425 Madison Ave., Room 16-52

country: USA

institute: ISMMS

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Read sequences were filtered by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
Peaks were called using MACS with Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
For RNA-Seq: Tophat (v2.1.0) alignment was performed using the mm9 reference genome. HT-seq was used to find read counts across genes. DESeq2 was used to find differentially expressed genes with FDR < 0.1 and Fold-change > 1.5.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files generated by computing feature density over a 5 bp window across the genome. http://genome.ucsc.edu/goldenPath/help/wiggle.html For RNA-Seq: Tab-delimited text file of normalized counts for all samples.

molecule: genomic DNA

organism: Mus musculus

source_name: primary T cells

growth_protocol: CD4+ T cells were purified from spleen. Naïve T cells were activated with plate bound anti-CD3 and anti-CD28 plus IL6(20ng/mL), TGFb(2.5ng/mL) . The cells were cultured for 48-72h and treated with JQ1 and MS402 for 2 hours before harvesting for further analysis.

extract_protocol:
For ChIP-Seq: Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies. For RNA-Seq: Compound treated cells were collected and RNA was extracted using a Nucleospin RNA kit (Clontech).
ChIP-Seq: ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size. RNA-Seq: Extracted RNA was subjected to polyA selection and standard Illumina RNA-seq library prep procedures.

tag: strain

tag: cell type

value: primary T cells

tag: chip-antibody

value: Brd2 (Bethyl; IHC-00612)


title: IRJ2-T47D_Y537S_FM_RNAseq

city: New York City

first: MacIntosh

middle: Grant

last: Cornwell

department: School of Medicine

institute: New York University

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to hg19 genome using STAR v2.5.1, and a raw count file was generated using STAR output
Transcipt Assembly and FPKM values were determined using cufflinks v2.2.1 and a normzlized RPKM matrix was generated using the cufflinks output
Quality Control steps tp ensure read quality were performed using rRNA STAR v2.5.1 and RseQC v2.6.2
Further differential expressions analysis was done using DEseq2 v1.1, gage v2.21, clusterprofiler 2.4.3, gostats v2.36; heatmaps were generated using complexheatmap v1.6
All analysis was performed by inputting fastq files into VIPER: https://bitbucket.org/cfce/viper/overview
Association of ChIP-seq data with RNAseq data was done using BETA v1.0.7
Genome_build: hg19
Supplementary_files_format_and_content: bed files for ER ChIP
Supplementary_files_format_and_content: Count Matrix Files for two separate experiments, one for MCF7 Parental and Tamoxifen Resistant lines, and anotherr for RUNX2 with and without DOX

molecule: total RNA

organism: Homo sapiens

growth_protocol: MCF7 cells were grown in DMEM supplemented with Penstrep and L-glutamine and 10% FBS.

extract_protocol: Cell lines were extracted using the Rneasy (Qiagen # 74104) kit with the substitution of Trizol instead of Buffer RLT. Preparation for sequaencing is done using the Illumina Truseq RNAseq v2 kit (15025063)

tag: cell subtype - mutation

tag: condition

value: Full Medium

tag: treatment


title: IRJ1-T47D_Y537S_FM_RNAseq


title: EAAE V

middle: C

tag: genotype/variation

value: DBD-mutant ERa (EAAE)

tag: treated with

value: saline (Vehicle, V)

tag: tissue

value: Eralpha, Santa Cruz sc-542


title: IRJ13-T47D_Y537S_WM_E2_RNAseq

value: White Medium


title: EAAE 1h E2

value: 250 ng of estradiol (E2)


title: IN528_culture_pol2

city: Cleveland

first: Tyler

middle: E

last: Miller

state: Ohio

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Sequencing of H3K27ac and JMJD6 ChIP and an unenriched chromatin control library (input) was performed on a NextSeq, with read lengths of 50bp
Reads were aligned to hg19 using BWA (Li, et. al., 2009)
Identical ChIP-seq sequence reads were collapsed to a single read to avoid PCR duplicates.
Peaks were called using HOMER v4.6 (Heinz, et. al., 2010) using matched inputs with the following parameters : H3K27ac, –histone –tagThreshold 50; JMJD6, –factor .
Genome_build: Hg19
Supplementary_files_format_and_content: Peak file (bed file) and bigwig file was generated for each sample by HOMER v4.6.

source_name: Primary Patient Derived Tumor Model

growth_protocol: IN528 cells from a primary patient derived GBM tumor model were grown in serum free cell culture conditions

extract_protocol:
For histone modification and transcription factor ChIP-Seq, 2 million cells (H3K27Ac), 15-20 million cells (JMJD6), or 5 million cells (Pol2) were crosslinked in PBS + 1% fresh formaldehyde for 10 minutes at 37 C, quenched for 5 minutes with 125 mM glycine, washed twice in cold PBS with protease inhibitors (complete PI, Roche), and stored at -80 C. Pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g , resuspended in cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes, sonicated to an average fragment size of 200-400 bp on a Branson sonifier, and cleared of debris by centrifugation. Samples were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 0.25% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4 C overnight with 2-5 ug of antibody towards: H3K27ac (Active Motif, 39133), JMJD6 (Abcam, ab64575, lot GR54735-1), and total Pol II (Santa Cruz, sc-899-X, lot H0510). Antigen-antibody complexes were collected with protein G Dynabeads (Life technologies) for 4 hours at 4 C, and sequentially washed with RIPA buffer (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 140 Mm NaCl), RIPA/High salt (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 360 mM NaCl), LiCl Wash Buffer (250mM LiCl, 0.5% NP40, 0.5% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.0), and TE Buffer (10mM Tris-HCl pH 8.0, 1mM EDTA). Beads were resuspended in Low SDS ChIP elution buffer (10mM Tris-HCl pH 8.0, 0.5M EDTA, 300mM NaCl, 0.1% SDS, 5mM DTT) and incubated for 6 hours at 65 C to elute DNA and reverse crosslinking. Samples were treated with RNAase for 30 minutes and proteinase K for 2 hours at 37 C. ChIP DNA was then purified from supernatants with AMPure beads (Beckman-Coulter). Input DNA was prepared in parallel by adding unenriched, diluted chromatin directly into the elution / reverse crosslinking step.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated to barcoded illumina adaptors (Quick T4 DNA ligase, NEB). Each reaction was followed by clean-up with AMPure beads (Beckman-Coulter). Ligation products were amplified by PCR for 14-18 cycles with illumina primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection or gel purification (E-Gel SizeSelect 2%, Life technologies).

treatment_protocol: cell isolation: Cells were collected

value: IN528 cells

tag: antibody


title: IN528_IC_pol2

treatment_protocol: cell isolation: Cells were dissociated from the tumor, depleted of mouse cells twice by Miltenyi mouse depletion kit and MACS magnetic sorting


title: IN528_IC_pol2 input


title: 3565_culture_pol2

growth_protocol: 3565 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

value: 3565 cells


title: 3565culture_JMJD6


title: 3565culture_H3K27Ac


title: 3565culture_H3K27Ac input


title: 3565_IC_JMJD6


title: siNC_RNA-seq_replicate1

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

data_processing:
Basecalls performed using Illumina software
Reads were aligned using TopHat v2.0.9 in Galaxy, using default parameters and hg19 as the reference genome.
Raw counts per exon (mapped to hg19_genes_2012-03-09.gtf) were estimated using htseq-count.
Subsequently, DESeq2 (implemented in Bioconductor v2.12, R v3.0.1) was used to identify differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Text file containing normalized read counts. Read counts were normalized using the DESeq2 rlog transformation algorithm

source_name: LNCaP

growth_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).

extract_protocol:
Total RNA was extracted using Trizol, according to the manufacturer's instructions.
Libraries were generated using 10 ng of RNA and NEXTflex Rapid Illumina Directional RNA-Seq Library Prep Kits

value: LNCaP

tag: transfection

value: siNC


title: 3565_IC_pol2


title: siGRHL2_RNA-seq_replicate3

treatment_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).


title: siGRHL2_RNA-seq_replicate2


title: 3565_IC_H3K27Ac input


title: siNC_RNA-seq_replicate2


title: GRHL2_ChIP-seq_replicate2

data_processing:
Basecalls performed in BaseSpace
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2, with default parameters.
Reads were filtered using minimum MAPQ quality score of 15.
Peaks were called using MACS with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated in Galaxy

extract_protocol:
LNCaP cells were seeded at 3x10^6 cells/plate in 15cm plates in RMPI 1640 + 10% FBS and allowed to grow for 3 days prior to fixation with formaldehyde. Nuclear pellets were sonicated on ice for 10 cycles (30 sec on, 30 sec off) using a Diagenode Bioruptor. Lysates were immunoprecipitated with 4 ug GRHL2 antibody (Sigma HPA004820) or 5 ug AR antibody (Santa Cruz sc-816 X), which had been pre-coupled to Protein G Dynabeads (Life Technologies, 10004D). DNA was purified using a PCR purification kit (Qiagen) and eluted in 100 µl.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Prep Kit

tag: cell line

value: Sigma HPA004820


title: GRHL2_ChIP-seq_replicate1


title: AR_ChIP-seq_replicate1

value: Santa Cruz sc-816 X


title: IN528ic input

growth_protocol: IN528 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

extract_protocol:
For histone modification and transcription factor ChIP-Seq, 2 million cells (H3K27Ac) or 20 million cells (JMJD6) were crosslinked in PBS + 1% fresh formaldehyde for 10 minutes at 37 C, quenched for 5 minutes with 125 mM glycine, washed twice in cold PBS with protease inhibitors (complete PI, Roche), and stored at -80 C. Pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g , resuspended in cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes, sonicated to an average fragment size of 200-400 bp on a Branson sonifier, and cleared of debris by centrifugation. Samples were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 0.25% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4 C overnight with 2-5 ug of antibody towards H3K27ac (Active Motif, 39133) or JMJD6 (Abcam, ab64575). Antigen-antibody complexes were collected with protein G Dynabeads (Life technologies) for 4 hours at 4 C, and sequentially washed with RIPA buffer (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 140 Mm NaCl), RIPA/High salt (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 360 mM NaCl), LiCl Wash Buffer (250mM LiCl, 0.5% NP40, 0.5% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.0), and TE Buffer (10mM Tris-HCl pH 8.0, 1mM EDTA). Beads were resuspended in Low SDS ChIP elution buffer (10mM Tris-HCl pH 8.0, 0.5M EDTA, 300mM NaCl, 0.1% SDS, 5mM DTT) and incubated for 6 hours at 65 C to elute DNA and reverse crosslinking. Samples were treated with RNAase for 30 minutes and proteinase K for 2 hours at 37 C. ChIP DNA was then purified from supernatants with AMPure beads (Beckman-Coulter). Input DNA was prepared in parallel by adding unenriched, diluted chromatin directly into the elution / reverse crosslinking step.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated to barcoded illumina adaptors (Quick T4 DNA ligase, NEB). Each reaction was followed by clean-up with AMPure beads (Beckman-Coulter). Ligation products were amplified by PCR for 14-18 cycles with illumina primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection or gel purification (E-Gel SizeSelect 2%, Life technologies).

tag: microenvironment

value: in vivo intrancranial tumor


title: 3565_IC_H3K27Ac


title: Clone_3_RNA_rep2

city: Jerusalem

first: Yehudit

last: Bergman

address: Hebrew University Medical School, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
ATAC-seq: Basecalls were derived from the standard illumina Nextseq 500 software. Adapter sequences and low quality bases were removed from reads using trim_galore. Processed reads were mapped using bowtie2 to the mm10 mouse genome, where nucleotides located on SNPs from the castaneous genome were masked (Sanger mouse genome project - release 1505). Reads falling on SNPs were then sorted to genome of origin using SNPsplit (Babraham institute) and PCR-duplicate reads were removed with Picard. Peaks of open chromatin were called from all of the mapped reads using Homer software43. Allelic reads within peaks were counted using HTseq-count.
Nuclear RNA-seq - Basecalls were derived from the standard Illumina Nextseq 500 software or HiSeq1000 RTA software. Adapter sequences and low quality bases were removed from reads using trim_galore. Reads were mapped to the mm10 mouse genome using bowtie2, after masking nucleotides located on SNPs from the cast genome (Sanger mouse genome project - release 1505). Reads falling on SNPs were then sorted to genome of origin using SNPsplit (Babraham institute) and PCR duplicates removed using Picard (Broad institute). Read coverage tracks were made using bedtools. Reads over ENSEMBL genes were counted with HTseq-count.
Kappa-VJ-seq - Basecalls were derived from the standard illumina Miseq software. sequences were quality trimmed (trim_galore) and aligned to a hybrid B6/Cast genome assembly using bowtie2, with Cast polymorphic sites substituted based on the Sanger Mouse Genome Project database (release 1505). Reads over each Vκ segment were counted (HTseq-count) and normalized to the total mapped rearranged fragment number to allow comparison of the Vκ repertoire contribution between different libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Total and allelically sorted alignments from ATAC-seq and RNA-seq - bedgraph format. Mapped allelic Vkappa rearrangement read counts from Igk-VJ-seq - txt format

source_name: Bone marrow derived pre-B cell

growth_protocol: Cells isolated from the bone marrow of B6/Cast mice were grown in RPMI 1640 + 10% FBS, penicillin-streptomycin (Gibco), L-glutamine (Gibco) and 50 μM of β-Mercaptoethanol (Gibco) on irradiated ST2 feeder cells. IL-7 was added to conditioned medium collected from J558L-IL7 secreting cells (as provided by A. Rolink) in order to select for pre-B cell populations.

extract_protocol: ATAC-seq - Nuclei from ~50,000 cells were isolated using NP-40-containing buffer. Extracted nuclei were treated with transposed with Nextera (illumina) Tn5 transposase for 30 minutes. Following clean-up transposed fragments were directly amplified and barcoded using Nextera indexes. Libraries were then sequenced using Illumina NextSeq 500 with 2x75 bp or 2x35 reads. Nuclear RNA-seq - Nuclei were obtained from 16 million cells per sample by incubation in 4 ml 50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% NP40, 5 min on ice, followed by a wash with the same solution without NP40. RNA was isolated with RNeasy mini kit (Qiagen) and treated with Turbo DNAse (Ambion). RNA was depleted of Ribosomal RNA with RiboZero-gold (Illumina). Stranded RNA-seq libraries were prepared following standard second-strand dU incorperating protocols (Parkhomchuk et al., 2009). Kappa-VJ-seq - RNA was extracted from cells with Highpure RNA isolation kit (Roche). RNA was poly-A enriched using poly-dT beads (Life technologies) in two selection cycles and RT then performed using AffinityScript QPCR cDNA Synthesis Kit (Agilent) with an RT primer specific for the Cκ region 5’-ATGCTGTAGGTGCTGTCTTT-3’. The residual RNA was degraded with 0.1N NaOH, neutralized with 0.1M acetic acid and the single strand cDNA then purified using Silane beads (Life technologies). A 3TR3 adapter ('5-/Phos/ AGATCGGAAGAGCACACGTCTG/3SpC3/-3') was ligated to the 3’ end by overnight incubation with T4 RNA ligase (NEB) at 22°C, and the cDNA then purified from excess adapter with Silane beads and PCR amplified for 12 cycles using the reverse complement of the 3RT3 adapter as the forward primer and the upstream Cκ region as the reverse primer with the partial Truseq illumina adapter added to the beginning (5’-TACACGACGCTCTTCCGATCT-ACTGGATGGTGGGAAGATGGAT-3’). The PCR product was cleaned with 0.7x ampure XT beads, amplified with indexed universal Illumina adapter primers for an additional 7 cycles to obtain ~550 bp libraries.

tag: ex-vivo vs cell culture

value: Cell Culture


title: IN528culture JMJD6

value: serum free cell culture


title: Clone_3_RNA_rep1


title: BM_FrD_ATAC_rep2

value: Ex-vivo sorted B220+IgM-CD43-CD25+ cells

value: C57BL6/Castaneous backcrossed (note - only small sections of genome are castaneous, including IgK locus on chr6, which was used for analysis)


title: IN528culture input


title: Clone_B52_ATAC_rep2


title: Clone_3_ATAC_rep2


title: AR_ChIP-seq_replicate2


title: siNC_RNA-seq_replicate3


title: siGRHL2_RNA-seq_replicate1


title: Clone_B52_ATAC_rep1


title: pool_ATAC_rep2


title: BM_FrD_RNA_rep1


title: Clone_8_ATAC_rep1


title: Clone_3_ATAC_rep1


title: IN528ic JMJD6


title: pool_ATAC_rep1


title: IN528culture H3K27Ac


title: Clone_4_ATAC_rep2


title: Clone_4_ATAC_rep1


title: Cyanidioschyzon merolae strain 10D H3_2

city: Berlin

first: Pawel

last: Mikulski

address: Koenigin-Luise-Str. 12-16

department: Biology

country: Germany

institute: Free University Berlin

description: biological replicate 2

data_processing:
Quality of paired-end raw reads was assessed using FastQC v0.11.4. The reads were trimmed according to the quality and mapped to the reference in Bowtie v2.2.6, with standard options.
Peaks were called using MACS v2.1 with exclusion of clonal reads.
Identified H3K27me3 peaks were annotated by intersection with the reference using Bedtools v2.17
Genome_build: Cyanidioschyzon merolae Genome Project v3 (http://merolae.biol.s.u-tokyo.ac.jp/)
Supplementary_files_format_and_content: Files are an output of MACS2 peak calling and are in the broadpeak format. The columns of the tables are as in MACS2 manual. Each biological replicate for H3K27me3 IP is represented by two files - one for peak calling with the input sample used for normalization, the other one with the H3 sample used for normalization.

organism: Cyanidioschyzon merolae strain 10D

source_name: Liquid cell culture

growth_protocol: Cyanidioschyzon merolae cells were grown at 42°C with shaking at 150 rpm. The cultures were kept under continuous light, with light intensity of 70 µmol.

extract_protocol:
The samples were fixed (Formaldehyde, 1% (v/v)) for 10 min, until addition of glycine (to final concentration of 125 mM, 5 min incubation). Superfluous formaldehyde was removed by three washes with ice cold PBS buffer and the remaining cell pellet was resuspended in 4 ml of Extraction Buffer (50 mm Tris-HCl pH 8, 10 mm EDTA, 1% SDS) with Protease Inhibitor Cocktail (Roche). The samples were sonicated for 5 min with 30 sec ON/ 30 sec OFF cycle using Bioruptor Plus device (Diagenode) and cleared by two rounds of centrifugation (13000 rpm, 4°C, 10 min). Subsequent steps were performed as in the Plant ChIP-seq kit protocol (Diagenode) with higher volume of sample taken aside as an input (1:5 of chromatin for IP).
According to the MicroPlex Library preparation kit v1 (Diagenode)


title: BM_FrD_RNA_rep2


title: Cyanidioschyzon merolae strain 10D H3_3

description: biological replicate 3


title: IN528ic H3K27Ac


title: Cyanidioschyzon merolae strain 10D input

description: input from IP of biological replicate 1


title: Clone_8_ATAC_rep2


title: Cyanidioschyzon merolae strain 10D H3_1

description: biological replicate 1


title: BM_FrD_ATAC_rep1


title: Cyanidioschyzon merolae strain 10D H3K27me3_3

description: biological replicate 3


title: Cyanidioschyzon merolae strain 10D H3K27me3_2

description: biological replicate 2


title: Cyanidioschyzon merolae strain 10D H3K27me3_1

description: biological replicate 1


title: Cyanidioschyzon merolae strain 10D RNAseq_3

description: biological replicate 3

data_processing:
A quality of paired-end raw sequencing reads were analyzed using Galaxy implementation (usegalaxy.org) of FastQC programme.
Reads' mapping and FPKM calculation was performed using Galaxy implementations of Tuxedo protocol.
Genome_build: Cyanidioschyzon merolae Genome Project v3 (http://merolae.biol.s.u-tokyo.ac.jp/)
Supplementary_files_format_and_content: Cufflinks output file. Tab-delimited tile containing FPKM values of the genomic loci. Each replicate is represented by separate file.

molecule: polyA RNA

extract_protocol:
According to RNeasy Plant Mini kit (Qiagen)
According to the TruSeq RNA Library Prep kit (Illumina)


title: Cyanidioschyzon merolae strain 10D RNAseq_1

description: biological replicate 1


title: P. stewartii, Plate 1

city: Blacksburg

first: Holly

last: Packard

state: VA

address: 926 West Campus Drive

department: Biological Sciences

institute: Virginia Tech

data_processing:
data received, downloaded, and unzipped into the program Geneious v. 9.1
fastq files aligned to the annotated coding sequences of P. stewartii DC283 reference sequence NZ_AHIE00000000.1
aligned sequences uploaded into Microsoft Excel
Genome_build: reference sequence NZ_AHIE00000000.1 from NCBI
Supplementary_files_format_and_content: .xlsx file containing sequence counts, gene names, and identifiers

organism: Pantoea stewartii subsp. stewartii DC283

source_name: in vitro RM agar plate

extract_protocol:
Pellets were resuspended in TE buffer with lysozyme and proteinase K, then a Qiagen miRNeasy kit used for total RNA extraction.  RNA integrity was measured by the Agilant Bioanalyzer 2100.
The stranded RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit' by University of Illinois

treatment_protocol: All samples stored pelleted at -20°C after washing in RNA-Protect Bacterial Reagent

tag: growth substrate

value: in vitro RM agar plate

tag: culture time

value: 18 hours


title: P. stewartii, Liquid 2

source_name: in vitro LB broth

value: in vitro LB broth


title: P. stewartii, Planta 1

source_name: Zea mays xylem

value: Zea mays xylem

value: 10 days in planta


title: P. stewartii, Liquid 1


title: WT cerebellum 3

status: Public on Mar 31 2017

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: Wildtype cerebellum

data_processing:
Reads were aligned using the TopHat2 application in BaseSpace (Illumina). This procedure involved first filtering out mitochondrial and ribosomal sequences, followed by trimming of 2 bases from the 5’ end of each read, and alignment to the mm10 build of the mouse genome using the Bowtie 1 aligner.
After alignment, quantification of transcript abundance was performed using Cufflinks for all annotated reference genes and transcripts that were detected in the samples, with data reported as Reads Per Kilobase of exon per Million reads (FPKM) values. Differential expression was then performed with Cuffdiff 2.1.1, with results reported as log2 (Heterozygous/Wildtype), and p values adjusted using the FDR.
Genome_build: mm10
Supplementary_files_format_and_content: .BAM files were generated for each sample
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: cerebellum

extract_protocol:
Total RNA was obtained from the mouse cerebellum samples using the RNeasy Mini Kit (Qiagen). Samples were given a number and all processing was done in a double-blinded fashion. Reads were aligned using the TopHat2 application in BaseSpace (Illumina). This procedure involved first filtering out mitochondrial and ribosomal sequences, followed by trimming of 2 bases from the 5’ end of each read, and alignment to the Mm10 build of the mouse genome using the Bowtie 1 aligner. After alignment, quantification of transcript abundance was performed using Cufflinks for all annotated reference genes and transcripts that were detected in the samples, with data reported as Fragments Per Kilobase of exon per Million fragments (FPKM) values. Differential expression was then performed with Cuffdiff 2.1.1, with results reported as log2 (Heterozygous/Wildtype), and p values adjusted using the FDR..
Libraries were prepared using the Stranded Total RNA kit (Illumina) and validated on the 2100 Bioanalyzer (Agilent). The libraries were run on the Illumina NextSeq 500 instrument using the NextSeq 75 cycle High Output Reagent kit. Seventy-five base pair single end reads were performed with libraries loaded at 1.9pM with 1% Phi X control, according to standard Illumina protocol.
Stranded RNA-seq

tag: Sex

value: male

tag: age

value: 6 weeks postnatal


title: HET cerebellum 2

description: Reln HET cerebellum

tag: strain

value: Orl/BalbC


title: WT cerebellum 1

description: Wildtype cerebellum


title: WT cerebellum 2

description: Wildtype cerebellum


title: HET cerebellum 1

description: Reln HET cerebellum


title: HET cerebellum 3

description: Reln HET cerebellum


title: C8_BRD2KO G1E-ER4 uninduced replicate 2 HiC

city: Philadelphia

first: Gerd

last: Blobel

state: PA

address: 3615 Civic Center Blvd, ARC 315

department: Pediatrics/Hematology

institute: University of Pennsylvania	Children's Hospital of Philadelphia

description:
HiC
10kb_C8_BRD2KO_G1E-ER4_uninduced_raw_interchromosomal_contact_matrices.tar.gz
10kb_C8_BRD2KO_G1E-ER4_uninduced_iced_interchromosomal_contact_matrices.tar.gz
10kb_C8_BRD2KO_G1E-ER4_uninduced_qnormed_interchromosomal_contact_matrices.tar.gz
40kb_C8_BRD2KO_G1E-ER4_uninduced_raw_interchromosomal_contact_matrices.tar.gz
40kb_C8_BRD2KO_G1E-ER4_uninduced_iced_interchromosomal_contact_matrices.tar.gz
40kb_C8_BRD2KO_G1E-ER4_uninduced_qnormed_interchromosomal_contact_matrices.tar.gz

data_processing:
Paired-end reads were aligned independently to mm9 mouse genome using bowtie2 (global parameters: --very-sensitive –L 30 –score-min L,-0.6,-0.2 –end-to-end --reorder;  local parameters:  --very-sensitive –L 20 –score-min L,-0.6,-0.2 –end-to-end --reorder) through the HiC-Pro software (Servant et al., 2015). Unmapped reads, non-uniquely mapped reads, and PCR duplicates were filtered, and uniquely aligned reads were paired. Reads from the five sequencing runs (SR1-SR5) and two replicates (Rep1, Rep2) were pooled, then used to construct contact matrices at 10kb and 40kb resolution. Contact matrices were balanced using the iterative correction and eigenvector decomposition (ICED) technique (Imakaev et al., 2012). The lowest-interacting 10% of bins were removed prior to balancing to facilitate convergence. Interchromosomal contact matrices were quantile normalized, with any bin-bin pairs with ICED values lower than 0.01 being excluded from the quantile normalization and downstream analysis.
Genome_build: mm9
The processed data files (<resolution>_<condition>_<stage>_interchromosomal_contact_matrices.tar.gz) are gzipped tarballs containing the contact matrices at <resolution> (either 10kb or 40kb) for the pooled HiC libraries of <condition> (G1E-ER4_uninduced, C8_BRD2KO_G1E-ER4_uninduced, or D_BRD2KO_G1E-ER4_uninduced) at the <stage> (raw, iced, or qnormed) step of the data processing. The tarballs contain files <resolution>_<condition>_<stage>_<chromosome>.matrix, which contain the interchromosomal contact matrix for each chromosome. Each line of a .matrix file represents an interaction between two bins on that chromosome. The .matrix files are formatted as tab delimited files with three columns, which represent the start coordinate of the upstream bin, the start coordinate of the downstream bin, and the value of the interaction, respectively. The end coordinates of the bins can be determined by adding the matrix resolution (10000 or 40000) to the start coordinate. For example, the line "10000<tab>40000<tab>10" in a 10kb resolution matrix file for chr1 should be interpreted to mean that the bin chr1:10000-20000 interacts with the bin chr1:40000-50000 with quantitative value 10. Bin-bin pairs with zero reads, or values that have been filtered out during processing are not listed in the matrix files. Therefore not every possible bin-bin pair has a corresponding line in the matrix file. Such bin-bin pairs can be assumed to have zero reads (raw stage matrices) or to have been excluded by filtering during processing (iced and qnormed stage matrices).

source_name: G1E-ER4 cells

growth_protocol:
G1E-ER4 cells are a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al., 1997) in which GATA1-ER is stably expressed. G1E-ER4 cells can be induced to differentiate through the addition of estradiol to the culture medium. Here we refer to the undifferentiated (i.e. -GATA1) state as "uninduced." G1E-ER4 cells were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997). To generate BRD2 KO cells, we transfected G1E-ER4 cells with guide RNA and Cas9 constructs, and isolated single cell clones with undetectable BRD2 expression by Western blot
G1E-ER4 cells are a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al., 1997) in which GATA1-ER is stably expressed. G1E-ER4 cells can be induced to differentiate through the addition of estradiol to the culture medium. Here we refer to the undifferentiated (i.e. -GATA1) state as "uninduced." G1E-ER4 cells were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
10 million uninduced G1E-ER4 cells (-GATA1), either unedited control cells or BRD2 KO clonal sublines, were fixed in 2% formaldehyde at room temperature for 10 minutes then quenched with 0.25M glycine for 5 minutes. Cells were washed with PBS, pelleted, resuspended in 1mL cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) and incubated on ice for 10 minutes. Nuclei were pelleted and washed once with 800ul of cold 1.2X NEB Buffer DpnII, pelleted and resuspended in 500ul 1.2X NEB Buffer DpnII. SDS was added to a final concentration of 0.3% and samples were incubated with shaking at 950rpm at 37C. 40ul of water was added to each sample, followed by 300U of DpnII (NEB R0543M), and samples were incubated overnight at 37C with shaking. An additional 300U of DpnII was added, and samples were incubated for 2 more hours at 37C, followed by incubation at 65C for 20 minutes. Nuclei were cooled on ice, pelleted and resuspended in 1X NEB Buffer2 with biotin-14-dATP, dCTP, dGTP, dTTP and DNA Polymerase I, Large (Klenow) Fragment (NEB M0210), and incubated at 37C with shaking for 1.5 hours. Fragments were ligated in a total volume of 1.2mL with T4 DNA Ligase (NEB) for 4 hours at 16C, then at room temperature for 30 minutes. Proteinase K (20ul of 20mg/mL) and SDS (120ul of 10% SDS) were added and crosslinks were reversed overnight at 65C. An additional 10ul of proteinase K was added and samples were incubated at 55C for 2hrs. DNase-free RNaseA was added and samples were incubated at 37C for 30 minutes. DNA was purified by phenol chloroform extraction. To prepare the sequencing library, DNA was sonicated to 200-300bp fragments and purified using Ampure XP beads (Beckman Coulter). Ligation junctions were pulled down using streptavidin beads (50ul of Dynabeads MyOne Streptavidine C1 beads/10 million cells).
Libraries were prepared using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB E6040) as per manufacturer’s instructions. Briefly, fragmented DNA was subjected to blunt end repair and dA tailing, followed by adaptor ligation. Following ligation, DNA was purified using AMPure XP beads (Beckman Coulter) and eluted in 15ul of water. Libraries were amplified for 6 cycles and PCR products were purified using AMPure XP beads (Beckman Coulter).

treatment_protocol:
none (uninduced)
none (uninduced)

tag: cell type

value: erythroid


title: G1E-ER4 uninduced replicate 1 HiC

description:
HiC
10kb_G1E-ER4_uninduced_raw_interchromosomal_contact_matrices.tar.gz
10kb_G1E-ER4_uninduced_iced_interchromosomal_contact_matrices.tar.gz
10kb_G1E-ER4_uninduced_qnormed_interchromosomal_contact_matrices.tar.gz
40kb_G1E-ER4_uninduced_raw_interchromosomal_contact_matrices.tar.gz
40kb_G1E-ER4_uninduced_iced_interchromosomal_contact_matrices.tar.gz
40kb_G1E-ER4_uninduced_qnormed_interchromosomal_contact_matrices.tar.gz

growth_protocol:
G1E-ER4 cells are a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al., 1997) in which GATA1-ER is stably expressed. G1E-ER4 cells can be induced to differentiate through the addition of estradiol to the culture medium. Here we refer to the undifferentiated (i.e. -GATA1) state as "uninduced." G1E-ER4 cells were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).
G1E-ER4 cells are a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al., 1997) in which GATA1-ER is stably expressed. G1E-ER4 cells can be induced to differentiate through the addition of estradiol to the culture medium. Here we refer to the undifferentiated (i.e. -GATA1) state as "uninduced." G1E-ER4 cells were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).


title: D_BRD2KO G1E-ER4 uninduced replicate 1 HiC

description:
HiC
10kb_D_BRD2KO_G1E-ER4_uninduced_raw_interchromosomal_contact_matrices.tar.gz
10kb_D_BRD2KO_G1E-ER4_uninduced_iced_interchromosomal_contact_matrices.tar.gz
10kb_D_BRD2KO_G1E-ER4_uninduced_qnormed_interchromosomal_contact_matrices.tar.gz
40kb_D_BRD2KO_G1E-ER4_uninduced_raw_interchromosomal_contact_matrices.tar.gz
40kb_D_BRD2KO_G1E-ER4_uninduced_iced_interchromosomal_contact_matrices.tar.gz
40kb_D_BRD2KO_G1E-ER4_uninduced_qnormed_interchromosomal_contact_matrices.tar.gz


title: G1E-ER4+E2 24 hr input

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2  --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file with read coverage, peaks in broadpeak format

growth_protocol: G1E-ER4 cells were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degreses with 5% CO2 (as described in Weiss et al., 1997)

extract_protocol:
G1E-ER4 cells were crosslinked with 1% formaldehyde in PBS with gentle agitation for 10 minutes at room temperature and then quenched with glycine. Fixed cells were resuspended in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal) prepared fresh with protease inhibitors (Sigma P8340) and 1mM phenylmethylsulfonyl fluoride (PMSF) and incubated on ice for 10 minutes. Nuclei were pelleted and resuspended in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS, prepared fresh with protease inhibitors and PMSF), and incubated on ice for 20 minutes. Samples were then diluted with 0.6mL IP Dilution Buffer (20mM Tris-HCl pH 8, 2mM EDTA pH 8, 150mM NaCl, 1% Triton X-100, 0.01% SDS, prepared fresh with protease inhibitors and PMSF), and sonicated at 4 degrees C (Epishear, Active Motif). After sonication, samples were spun at 4 degrees C to remove debris and added to preclearing reactions containing 3.4mL IP Dilution Buffer, protein A/G agarose beads, and isotope-matched IgG. Samples were precleared for ?2 hours.
Antibody (anti-CTCF, Millipore (07-729, lot 2517762) was prebound to protein A/G agarose beads. Precleared chromatin was added to beads and IPs were performed overnight at 4 degrees C with rotation. Beads were washed once with IP Wash 1 (20mM Tris-HCl pH 8, 2mM EDTA pH 8, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20 mM Tris-HCl pH 8, 2mM EDTA pH 8, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP Wash Buffer 2 (10 mM Tris-HCl pH 8, 1mM EDTA pH 8, 0.25 M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate), and twice with TE (10mM Tris-HCl pH 8, 1mM EDTA pH 8). All washes were performed on ice. Following the final wash, beads were moved to room temperature and eluted twice with 100ul of Elution Buffer (100mM NaHCO3, 1%SDS, prepared fresh) for a final eluate volume of 200ul. The following were added to each sample: 12ul of 5M NaCl, 2ul RNaseA (10mg/ml) and samples were incubated at 65C for ?1 hour. 3ul of Proteinase K (20mg/ml) was added and samples were incubated at 65C overnight.
Following overnight incubation, 10ul of 3M sodium acetate pH 5 was added to each sample and DNA was purified using the QIAquick PCR Purification kit per the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions accompanying TruSeq ChIP-seq Sample Preparation Kit. (Part#  IP-202-1012). In brief, ChIP-enriched, fragmented DNA was subjected to end repair to generate blunt-end double stranded DNA, adenylation of 3’ ends, and adaptor ligation. Following ligation, SPRIselect (Beckman Coulter) beads were used at 0.9X and 0.6X for left and right side selection, respectively, to obtain an average library target size of ~300 bp. After size selection, fragments were amplified for 16 cycles, and PCR products were purified using Agencourt AMPureXP beads (Beckman Coulter).

treatment_protocol: Cells were induced to differentiate (activate GATA1) by the addition of 100nM estradiol for 24 hours

tag: chip ab

value: wild type G1E-ER4 cells


title: CTCF C8_Brd2KO G1E-ER4+E2 24 hr

source_name: C8_Brd2KO G1E-ER4 cells

value: C8_Brd2KO G1E-ER4


title: CTCF G1E-ER4+E2 24 hr


title: CTCF D_Brd2KO G1E-ER4+E2 24 hr

source_name: D_Brd2KO G1E-ER4 cells

value: D_Brd2KO G1E-ER4


title: C8_Brd2KO G1E-ER4+E2 24 hr input


title: Cyanidioschyzon merolae strain 10D RNAseq_2

description: biological replicate 2


title: G1E-ER4 uninduced replicate 2 HiC


title: NBM cells IL3 rep 1

city: Lund

first: Pablo

last: Peña-Martínez

address: Klinikgatan 28

department: Clinical Genetics

country: Sweden

institute: Lund University

description: processed data file: NBM_IL4_TMM.txt

data_processing:
Bcl2FastQ software was used for basecalling.
Sequenced reads were mapped to the mm10 referece genome using Tophat 2.0.13 with parameters -p 2 --keep-fasta-order --bowtie1 --no-coverage-search
BAM files were imported to  the Qlucore Omics Explorer 3.0 software and normalized using the TMM (Trimmed Mean of M-values) method.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt file of TMM values for all samples

source_name: NBM cells IL3

extract_protocol:
Bone marrow of leukemic or healthy mice were crushed followed by CD117 selection (Miltenyi Biotec, Bergisch Gladbach, Germany). RNA was extracted using the QIAshredder and RNeasy Microkit (QIAgen, Hilden, Germany). Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

value: Mouse normal bone marrow

value: c-Kit enriched normal bone marrow

tag: grown in

value: 20 ng/mL IL3 for 18hrs


title: Leukemia cells IL4 rep4

description: processed data file: MLL_IL4_TMM.txt

source_name: Leukemia cells IL4

tag: variation

value: Actin-dsRed

value: Mouse leukemic bone marrow

value: c-Kit enriched MLL-AF9 leukemia cells

value: 20 ng/mL  IL3 and IL4 for 18hrs


title: NBM cells IL3 rep 2

description: processed data file: NBM_IL4_TMM.txt


title: NBM cells IL4 rep 4

description: processed data file: NBM_IL4_TMM.txt

source_name: NBM cells IL4


title: NBM cells IL4 rep 1

description: processed data file: NBM_IL4_TMM.txt


title: NBM cells IL4 rep 3

description: processed data file: NBM_IL4_TMM.txt


title: NBM cells IL3 rep 3

description: processed data file: NBM_IL4_TMM.txt


title: NBM cells IL4 rep 2

description: processed data file: NBM_IL4_TMM.txt


title: Leukemia cells IL4 rep3

description: processed data file: MLL_IL4_TMM.txt


title: P. stewartii, Plate 2

value: in vitro RM agar plate

value: 18 hours


title: Leukemia cells IL3 rep3

description: processed data file: MLL_IL4_TMM.txt

source_name: Leukemia cells IL3


title: P. stewartii, Planta 2

value: Zea mays xylem

value: 10 days in planta


title: Leukemia cells IL4 rep2

description: processed data file: MLL_IL4_TMM.txt


title: Leukemia cells IL3 rep1

description: processed data file: MLL_IL4_TMM.txt


title: C8_BRD2KO G1E-ER4 uninduced replicate 1 HiC


title: D_BRD2KO G1E-ER4 uninduced replicate 2 HiC


title: WTSORTD8RNA1_rep1

city: Göttingen

first: Ashish

last: Rajput

state: Niedersachsen

address: Von-Siebold-Straße 3A

department: Research Group for Computational Systems Biology

institute: German Center for Neurodegenerative Diseases (DZNE)

description: WT aSyn-IRES-GFP (Set:E)

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the hg19 genome assembly using STAR aligner version 2.3.0e_r291 with default options
Genome_build: hg19
Supplementary_files_format_and_content: Read counts for all genes and all exons (Ensembl annotation v72) were obtained using FeaturesCount. DEGs were calculated using DESEQ2

source_name: LUHMES cells

growth_protocol: differentiation day 8

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) or NucleoSpin RNA (Macherey-Nagel) according to manufacturer instructions
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: proliferating LUHMES cells were infected with equimolar amounts of lentiviral particles encoding for: IRES-GFP (samples set C); full-length human wild-type (WT) aSyn (SNCA, NM_000345), WT aSyn-IRES-GFP (samples set E) or familial mutant A30P aSyn, A30P aSyn-IRES-GFP (samples set A)

tag: condition

value: WT aSyn-IRES-GFP (Set:E)

value: Lund Human Mesencephalic (LUHMES) cells


title: WTSORTD8RNA3_rep3

description: WT aSyn-IRES-GFP (Set:E)


title: WTSORTD8RNA2_rep2

description: WT aSyn-IRES-GFP (Set:E)


title: GFPSORTD8RNA3_rep3

description: IRES-GFP (Set:C)

value: IRES-GFP (Set:C)


title: D_Brd2KO G1E-ER4+E2 24 hr input

value: erythroid

tag: genotype/variation


title: Leukemia cells IL4 rep1

description: processed data file: MLL_IL4_TMM.txt

tag: tissue


title: A30PSORTD8RNA1_rep1

description: A30P aSyn-IRES-GFP (Set:A)

value: A30P aSyn-IRES-GFP (Set:A)


title: GFPSORTD8RNA2_rep2

description: IRES-GFP (Set:C)


title: A30PSORTD8RNA2_rep2

description: A30P aSyn-IRES-GFP (Set:A)


title: A30PSORTD8RNA3_rep3

description: A30P aSyn-IRES-GFP (Set:A)


title: GFPSORTD8RNA1_rep1

description: IRES-GFP (Set:C)


title: Leukemia cells IL3 rep2

description: processed data file: MLL_IL4_TMM.txt


title: SCC_t0_n2_m3

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

data_processing:
Illumina sequencing reads were trimmed to the 18nt barcode sequence using the galaxy genome browser (https://usegalaxy.org/) and shRNAs were matched to their 18nt barcode using the Barcode Deconvolution Software (Cellecta), with a maximum barcode mismatch of 1bp.
Differential representation of each shRNA in the three modules was determined using DESeq2
The DESeq2 data from each shRNA module was merged into an output file containing for each shRNA the gene annotation, the Illumina sequencing reads from each individual experiment at t=0 and t=14, the Benjamini-Hochberg multiple test corrected p value, and the mean fold change in abundance when comparing t=14 vs t=0
Supplementary_files_format_and_content: csv file includes Illumina sequencing reads from each individual experiment at t=0 and t=14, the Benjamini-Hochberg multiple test corrected p value, and the mean fold change in abundance when comparing t=14 vs t=0. The reads report the abundance of a given shRNA integrated in the genome.

source_name: Skin primary cells

growth_protocol: NHKs and SCC13 cells were cultured in complete FAD medium on a feeder layer of 3T3-J2 fibroblasts, pre-treated with 4 µg ml−1 mitomycin-C (Sigma-Aldrich). 1.2 x 10^8 NHKs or SCC13 cells were infected at a MOI of 0.5 (so that 50% of cells carried a single shRNA construct) for each shRNA module (1, 2 and 3). Therefore, each individual shRNA was represented by ~2,000 cells. 24h after infection, half of the infected cell population (60,000,000 cells per module) was collected for genomic DNA purification (t=0). The other half was seeded at clonal density (600,000 cells per 175 cm2 feeder layer) into 10 layer 175cm2 Corning® HYPERflasks® (Sigma-Aldrich) and cells were cultured for two weeks (t=14).

extract_protocol:
Genomic DNA (gDNA) was isolated from NHK and SCC13 cells by phenol/chloroform purification
400 µg of gDNA per replicate was used as template in a pre-amplification PCR reaction with Phusion® High Fidelity Polymerase (NEB) to amplify an 180bp amplicon containing the 18nt barcode sequence, which is unique to each shRNA construct. The 180bp PCR products containing Illumina sequencing adapters were run on a 2% (w/v) agarose gel, and a clean band was excised and purified using QIAquick Gel Extraction kit as recommended by the manufacturer (Qiagen).

value: cutaneous SCC facial epidermis

tag: passages

tag: decipher module

value: module 3

tag: time

value: 0 days


title: SCC_t0_n2_m2

tag: cell line

value: module 2


title: SCC_t14_n2_m3

value: 14 days


title: SCC_t0_n2_m1

value: module 1


title: SCC_t14_n1_m2


title: SCC_t14_n1_m3


title: SCC_t14_n2_m2


title: NHK_t14_n2_m2

value: Primary normal human keratinocytes

value: Km


title: NHK_t14_n2_m1


title: SCC_t0_n1_m1


title: NHK_t0_n2_m3


title: SCC_t0_n1_m2


title: SCC_t14_n2_m1


title: NHK_t0_n2_m1


title: SCC_t14_n1_m1


title: NHK_t14_n1_m3


title: NHK_t0_n2_m2


title: NHK_t14_n2_m3


title: NHK_t0_n1_m2


title: NHK_t0_n1_m3


title: NHK_t14_n1_m1


title: NHK_t0_n1_m1


title: NHK_t14_n1_m2


title: ICM_1

city: Salt Lake City

first: Peter

middle: G

last: Hendrickson

state: UT

address: 2000 Circle of Hope Dr.

department: HHMI/Oncological Sciences

institute: University of Utah

description:
Cavitated embryo
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X4_130419_700179R_0412_AD1YHYACXX_4_1.txt.gz
9741X4_130419_700179R_0412_AD1YHYACXX_4_2.txt.gz
9741X19_130419_700179R_0412_AD1YHYACXX_8_1.txt.gz
9741X19_130419_700179R_0412_AD1YHYACXX_8_2.txt.gz

data_processing:
Raw sequencing reads were aligned to the human genome hg19 using Novoalign (v2.8, Novocraft) with the follow parameters; [-k –H –r All 50 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG]. The index also included all known splice junctions as generated with the MakeTranscriptome application (USeq package, v8.8.8) based on Ensembl gene annotation.
Alignments from the 12 and 14 cycle libraries from the same sample were merged. Splice junction alignments were converted to genomic coordinates and low quality and non-unique reads were removed using the SamTranscriptomeParser application (USeq package, v8.8.8) with the parameters [-a 240 –b –r –p –n 1].
Stranded differential expression analysis on merged sample replicates was calculated with the DefinedRegionDifferentialSeq application (Useq package, v8.8.8), which uses the DESeq2 R package for variance normalization and differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data is an excel spreadsheet containing a list of all expressed genes with expression data for sample replicates (raw count, normalize raw count, and FPKM). This file also contains the differential expression statistics for all expressed genes in all paired comparisons calculated by DESeq2.

source_name: Embryo

extract_protocol:
RNA extraction from pooled oocytes and embryos was preformed using the Qiagen AllPrep kit according to manufacturers instructions.
Two stranded libraries were prepared for each stage using the TotalScript RNA-Seq kit (Epicentre, Cat. num. TSRNA1296). This approach enabled low inputs (5ng of total RNA/reaction), and random hexamer priming facilitated transcript coverage balance. Each cDNA library was then split and amplified for 12 or 14 PCR cycles, resulting in four technical replicates per developmental stage.

treatment_protocol: Within 3 hours of collection, GV, MI, and MII oocytes were completely denuded of their cumulous cells. Denuded oocytes were then stored in 10 uL of protein free media in slow freeze 250 uL straws and kept at -80C until RNA preparation. Likewise, preimplantation embryos used for this study were cryopreserved according to standard IVF protocols. Prior to RNA preparation, the embryos were thawed and pooled according to developmental stage. Embryos that failed to survive thawing were discarded. Blastocyst stage embryos were hatched and, using laser microdissection, were manually separated into Inner Cell mass (ICM) and mural trophectoderm.

tag: developmental stage

value: Blastocyst; ICM and polar trophectoderm

tag: combined analysis name


title: Trophectoderm_2

description:
Cavitated embryo
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X10_130419_700179R_0412_AD1YHYACXX_6_1.txt.gz
9741X10_130419_700179R_0412_AD1YHYACXX_6_2.txt.gz
9741X15_130419_700179R_0412_AD1YHYACXX_7_1.txt.gz
9741X15_130419_700179R_0412_AD1YHYACXX_7_2.txt.gz

value: Blastocyst; mural trophectoderm


title: ICM_2

description:
Cavitated embryo
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X9_130419_700179R_0412_AD1YHYACXX_6_1.txt.gz
9741X9_130419_700179R_0412_AD1YHYACXX_6_2.txt.gz
9741X14_130419_700179R_0412_AD1YHYACXX_7_1.txt.gz
9741X14_130419_700179R_0412_AD1YHYACXX_7_2.txt.gz


title: SCC_t0_n1_m3


title: Morula_2

description:
Compacted, uncavitated embryo
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X8_130419_700179R_0412_AD1YHYACXX_5_1.txt.gz
9741X8_130419_700179R_0412_AD1YHYACXX_5_2.txt.gz
9741X13_130419_700179R_0412_AD1YHYACXX_7_1.txt.gz
9741X13_130419_700179R_0412_AD1YHYACXX_7_2.txt.gz

value: Morula


title: Trophectoderm_1

description:
Cavitated embryo
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X5_130419_700179R_0412_AD1YHYACXX_5_1.txt.gz
9741X5_130419_700179R_0412_AD1YHYACXX_5_2.txt.gz
9741X20_130419_700179R_0412_AD1YHYACXX_8_1.txt.gz
9741X20_130419_700179R_0412_AD1YHYACXX_8_2.txt.gz


title: MII oocyte_2

description:
Presence of a polar body
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9740X6_130419_700179R_0412_AD1YHYACXX_2_1.txt.gz
9740X6_130419_700179R_0412_AD1YHYACXX_2_2.txt.gz
9740X12_130419_700179R_0412_AD1YHYACXX_3_1.txt.gz
9740X12_130419_700179R_0412_AD1YHYACXX_3_2.txt.gz

source_name: Oocyte

value: Mature oocyte


title: Morula_1

description:
Compacted, uncavitated embryo
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X3_130419_700179R_0412_AD1YHYACXX_4_1.txt.gz
9741X3_130419_700179R_0412_AD1YHYACXX_4_2.txt.gz
9741X18_130419_700179R_0412_AD1YHYACXX_8_1.txt.gz
9741X18_130419_700179R_0412_AD1YHYACXX_8_2.txt.gz


title: Cleavage_2

description:
2-,4-,8-cell embryo
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X7_130419_700179R_0412_AD1YHYACXX_5_1.txt.gz
9741X7_130419_700179R_0412_AD1YHYACXX_5_2.txt.gz
9741X12_130419_700179R_0412_AD1YHYACXX_6_1.txt.gz
9741X12_130419_700179R_0412_AD1YHYACXX_6_2.txt.gz

value: 2-,4-,and 8-cell embryo


title: Pronuclear_1

description:
Presence of two visible pronuclei
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X1_130419_700179R_0412_AD1YHYACXX_4_1.txt.gz
9741X1_130419_700179R_0412_AD1YHYACXX_4_2.txt.gz
9741X17_130419_700179R_0412_AD1YHYACXX_8_1.txt.gz
9741X17_130419_700179R_0412_AD1YHYACXX_8_2.txt.gz

value: 1-cell embryo


title: Cleavage_1

description:
2-,4-,8-cell embryo
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X2_130419_700179R_0412_AD1YHYACXX_4_1.txt.gz
9741X2_130419_700179R_0412_AD1YHYACXX_4_2.txt.gz
9741X16_130419_700179R_0412_AD1YHYACXX_7_1.txt.gz
9741X16_130419_700179R_0412_AD1YHYACXX_7_2.txt.gz


title: MI oocyte_2

description:
Absence of a germinal vesicle and polar body
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9740X5_130419_700179R_0412_AD1YHYACXX_2_1.txt.gz
9740X5_130419_700179R_0412_AD1YHYACXX_2_2.txt.gz
9740X11_130419_700179R_0412_AD1YHYACXX_3_1.txt.gz
9740X11_130419_700179R_0412_AD1YHYACXX_3_2.txt.gz

value: Immature oocyte


title: MI oocyte_1

description:
Absence of a germinal vesicle and polar body
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9740X2_130419_700179R_0412_AD1YHYACXX_1_1.txt.gz
9740X2_130419_700179R_0412_AD1YHYACXX_1_2.txt.gz
9740X8_130419_700179R_0412_AD1YHYACXX_2_1.txt.gz
9740X8_130419_700179R_0412_AD1YHYACXX_2_2.txt.gz


title: Pronuclear_2

description:
Presence of two visible pronuclei
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9741X6_130419_700179R_0412_AD1YHYACXX_5_1.txt.gz
9741X6_130419_700179R_0412_AD1YHYACXX_5_2.txt.gz
9741X11_130419_700179R_0412_AD1YHYACXX_6_1.txt.gz
9741X11_130419_700179R_0412_AD1YHYACXX_6_2.txt.gz


title: Germinal Vesicle_1

description:
Presence of a germinal vesicle
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9740X1_130419_700179R_0412_AD1YHYACXX_1_1.txt.gz
9740X1_130419_700179R_0412_AD1YHYACXX_1_2.txt.gz
9740X7_130419_700179R_0412_AD1YHYACXX_2_1.txt.gz
9740X7_130419_700179R_0412_AD1YHYACXX_2_2.txt.gz


title: MII oocyte_1

description:
Presence of a polar body
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9740X3_130419_700179R_0412_AD1YHYACXX_1_1.txt.gz
9740X3_130419_700179R_0412_AD1YHYACXX_1_2.txt.gz
9740X9_130419_700179R_0412_AD1YHYACXX_3_1.txt.gz
9740X9_130419_700179R_0412_AD1YHYACXX_3_2.txt.gz


title: Chaf1a_si308-rep2

data_processing:
Raw RNA sequencing reads were aligned to a custom genome index using Novoalign (v2.8, Novocraft).
Splice junction alignments were converted to genomic coordinates and low quality and non-unique reads were removed using the SamTranscriptomeParser application (USeq package, v8.8.8).
Raw reads were counted across all individual exons and repeat elements and subsequently merged by corresponsing ensembl gene or repeat masker subfamily annotation. Differential gene and subfamily expression was called using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file contains read coverage and DESeq2 differential expression statistics for all Ensemble genes (mm10) and repetitive elements (by subfamily annotation). Each siRNA treatment condition (siChaf1a, siChaf1a +si308, siChaf1a +si309) was compared in a pairwise manner to mESCs treated only with negative control siRNA (NC).

source_name: mouse embryonic stem cells

growth_protocol: mESCs containing a MERVL::EGFP reporter were cultured on gelatin in ES-DMEM supplemented with serum, leukemia Inhibitory Factor, and 2i (CHIR99021, PD0325901).

extract_protocol:
RNA was extracted using TRIzol and purified using the Direct-zol RNA MiniPrep Kit by Zymo Research
Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis. Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4paired-end flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001).  Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61),  a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003).

treatment_protocol: Cells were transfected with 20pmol of total siRNA (10pmol of each) using RNAiMax (Life Technologies). Transfections were performed twice on consecutive days to ensure efficient knockdown.

value: mouse embryonic stem cells (in 2i media)

tag: transgene

value: siChaf1a (10pmol) +si308 (10pmol)


title: Chaf1a_si308-rep1


title: NC_Chaf1a-rep2

value: Negative Control siRNA (10pmol) + siChaf1a (10pmol)


title: Chaf1a_si309-rep2


title: NC-rep2

value: Negative Control siRNA (20pmol)


title: NC_Chaf1a-rep1


title: NC-rep1


title: Unsorted-plusDox-HAChIP-18hr-rep2

description:
Antibody: abcam9110
mDUX-HA-rep2.bw

data_processing:
Raw read squences were trimmed to remove low quality bases and adapter sequences (Trim Galore!) before aligning to mm10 using Bowtie2 (v2.2.6) with the following parameters: (-t –q –N1 –L 25 –X 2000 –no-mixed –no-discordant) (*non-unique reads assigned to 1 location).
A read-normalized bedgraph file for the ChIPs and input control were generated with MACS2 callpeak (-B -SPMR). Replicates from the 12hr dox-induction and 18hr dox-induction were merged.
Genome_build: mm10
Supplementary_files_format_and_content: The read normalized bedGraph files were  converted into bigwig format for genome browser visulization.

growth_protocol: mESCs containing two stably integrated transgenes (TRE::3xHA-mDux; MERVL::EGFP) were cultured on gelatin in ES-DMEM supplemented with serum, leukemia Inhibitory Factor, and 2i (CHIR99021, PD0325901).

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10 minutes. Cells were then washed in PBS (x2) and resuspended in lysis buffer (10mM Tris,100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) to extract chromatin. Lysates were then sonicated using a BioRuptor, centrifuged to pellet cellular debris, and immunoprecipitated.
After reversing crosslinks, libraries were prepped using the NEBnext DNA Library Prep Kit (NEB, E7370L). Adapter ligated DNA was size selected and purified using AMPure XP beads (Beckman Coulter, A63881) before sequencing.

treatment_protocol: Cells were kept under constant drug selection (Puromycin, G418) and induced with doxycycline for 12 or 18hrs prior to crosslinking.

value: mDuxCA

tag: tag

value: 18hr dox-induction


title: Unsorted-plusDox-HAChIP-18hr-rep1

description:
Antibody: abcam9110
mDUX-HA-rep2.bw


title: Unsorted-plusDox-Input

description:
Input
mDux-HA-Input.bw


title: Unsorted-plusDox-HAChIP-12hr-rep2

description:
Antibody: abcam9110
mDUX-HA-rep1.bw

value: 12hr dox-induction


title: Unsorted-plusDox-HAChIP-12hr-rep1

description:
Antibody: abcam9110
mDUX-HA-rep1.bw


title: SRC-2 KO-4

city: Dallas

first: Shruthy

last: Suresh

state: Texas

address: 6000 Harry Hines Blvd NA6.300

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Illumina Hiseq 2500 used for basecalling
Reads were trimmed to remove low-quality regions in the ends
Trimmed reads were mapped to the mouse genome (mm10) using TopHat v2.0.1227 guided by iGenomes GTF file. Alignments with mapping quality less than 10 were discarded.
Expression abundance estimation and differential expression analysis were carried out using Cufflinks/Cuffdiff (v2.1.1) software
Genome_build: mm10
Supplementary_files_format_and_content: fold changes in expression and statistics results of Group A (WT) vs Group B (SRC-2 KO) generated with cuttdiff

source_name: SRC-2 KO_liver tumor

growth_protocol: Src-2+/-; LAPtTA females were bred with Src-2+/-; tet-o-MYC males to obtain tet-o-MYC; LAPtTA mice with SRC-2 WT or homozygous null alleles.

extract_protocol:
Total RNA was isolated from liver tumors using Trizol (Invitrogen) followed by additional cleanup and DNase digestion using the RNeasy Mini Kit (Qiagen).
Four micrograms of total DNAse treated RNA were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis.  cDNA were A-tailed and indexed adapters were ligated. Samples were PCR amplified and purified with AmpureXP beads and validated on the Agilent 2100 Bioanalyzer. Before being normalized and pooled, samples were quantified by Qubit (Invitrogen). Sequencing was performed on a Illumina Hiseq 2500 to generate 51-bp single-end reads. Four g of total DNAse treated RNA was prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina.   Poly-A RNA was purified and fragmented before strand specific cDNA synthesis.  cDNA was A-tailed and indexed adapters were ligated.  Samples were PCR amplified and purified with AmpureXP beads and validated on the Agilent 2100 Bioanalyzer.  Samples were quantified by Qubit (Invitrogen) prior to normalization and pooling.  Sequencing was performed on an Illumina Hiseq 2500 to generate 51-bp single-end reads.  Reads were trimmed to remove low-quality regions in the ends.  Trimmed reads were mapped to the mouse genome (mm10) using TopHat v2.0.1227 guided by iGenomes GTF file (https://ccb.jhu.edu/software/tophat/igenomes.shtml).  Alignments with mapping quality less than 10 were discarded.  Expression abundance estimation and differential expression analysis were carried out using Cufflinks/Cuffdiff (v2.1.1) software.

treatment_protocol: Doxycycline was withdrawn at 6 weeks of age, mice were monitored for 9 weeks of MYC induction. Mice were euthanized and dissected at 15 weeks of age.

value: Src-2+/-; LAPtTA female bred with Src-2+/-; tet-o-MYC male

value: tet-o-MYC; LAPtTA; Src-2-/-; homozygous null alleles

tag: age

value: 15 weeks

value: liver tumor


title: SRC-2 KO-1


title: SRC-2 KO-2


title: SRC-2 KO-3


title: SRC-2 KO-5


title: WT-5

source_name: WT_liver tumor

value: tet-o-MYC; LAPtTA; Src-2+/+; SRC-2 WT


title: Germinal Vesicle_2

description:
Presence of a germinal vesicle
Original raw file names (see readme_fastq_sequence_library.txt which is linked as a supplementary file on the Series record):
9740X4_130419_700179R_0412_AD1YHYACXX_1_1.txt.gz
9740X4_130419_700179R_0412_AD1YHYACXX_1_2.txt.gz
9740X10_130419_700179R_0412_AD1YHYACXX_3_1.txt.gz
9740X10_130419_700179R_0412_AD1YHYACXX_3_2.txt.gz


title: Chaf1a_si309-rep1

tag: cell type

value: siChaf1a (10pmol) +si309 (10pmol)


title: WT-4


title: WT-3


title: WT-2


title: ATACseq_E10.5-Mx-Ezh2cKO_1

city: Basel

first: Filippo

middle: M.

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Library strategy: ATAC-Seq
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Read pairs were aligned to the GRCm38/mm10 reference genome using the QuasR Bioconductor package (PMID: 25417205, version 1.12.0) by the qAlign function with parameters maxHits=10 (allowing up to 10 hits per read, reporting one randomly), which internally uses bowtie (version 1.1.1, PMID: 19261174).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and binsize=100. The scores in the wig file therefore represent the number of alignment pairs per 100bp window and per million reads in the library.

source_name: Cranial neural crest cells

extract_protocol:
To profile for open chromatin, we used the Assay for Transposase Accessible Chromatin (ATACseq) protocol, performed according to Buenrostro et al., 2015 with minor modifications.  The dissected samples were incubated in trypsin 0.5%/EDTA 1X at 37 °C for 10 minutes and rinsed in DMEM 1X/ FBS 10%. Cranial neural crest cells (CNCCs) were then dissociated with a pipette, filtered and collected by FACS. 50.000 CNCCs were used per transposition reaction. After sorting, CNCCs were pelleted by centrifugation (500 g for 5 minutes at 4°C), washed with cold 1X PBS buffer and pelleted again by centrifugation (500 g for 5 minutes at 4°C). They were then re-suspended in cold lysis buffer (10mM Tris-HCl pH 8.0; 10mM NaCl; 3mM MgCl2; 0.5% NP40) and pelleted by centrifugation (5 minutes, 500 g at 4°C). The supernatant was discarded.
The transposition reaction was performed as reported in Buenrostro et al., 2015, steps 6 – 12, using the Nextera Sample preparation kit from Illumina. PCR Amplification was done according to Buenrostro et al., 2015, steps 13 – 18. The indexing PCR primers mentioned in the supplemental material from Buenrostro et al., 2013 were used. Amplified libraries were cleaned up using AMPure XP beads in a DNA / beads ratio of 1 / 1.8. The Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, paired-end) according to Illumina standards.

value: Mx

tag: genotype


title: ATACseq_E10.5-Mx_1

value: WT


title: 5FU_Day8_Rep2_92

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts (.txt)

source_name: Bone Marrow

extract_protocol:
Six- to 12-weeks-old C57Bl/6 wilt type mice were treated with a single dose of 150 mg/kg 5-FU (Sigma-Aldrich) or with PBS control and were analyzed at different time points (0, 8, 10, 12 and 14 days) post-treatment. Bone marrow (BM) cells were obtained by either crushing leg, arm and pelvic bones or just flushing leg bones in Hanks’ Buffered Saline Solution (HBSS) containing 2% heat-inactivated FBS (Sigma-Aldrich). HBSS/2% FBS was used for all incubation and wash steps. Erythrocytes and contaminating bone material were removed by ACK lysis followed by centrifugation on a Ficoll gradient (Histopaque 1119, Sigma-Aldrich) for crushed bones. BM cells were first pre-enriched for c-Kit+ cells using c-Kit microbeads (Miltenyi Biotec, 130-091-224) and MACS Separation LS Columns (Miltenyi Biotec, 130-042-401), and incubated with purified, unconjugated-lineage antibodies (CD3 from Biolegend, and CD4, CD5, CD8, B220, Ter119, Mac-1 and Gr-1 from eBioscience) followed by goat anti-rat-PE-Cy5 (Invitrogen, A10691) and subsequently blocked with purified rat IgG (Sigma-Aldrich). Cells were then stained with c-Kit-APC-eFluor780 (eBioscience, 47-1171-82), Sca-1-PB (BioLegend, 108120), CD48-A647 (BioLegend, 103416), CD150-PE (BioLegend, 115904), CD34-FITC (eBioscience, 11-0341-85) and FcγR-PerCP-eFluor710 (eBioscience, 46-0161-82) after 5-FU treatment. Single GMPs (lin-/c-kit+/sca-1-/cd34+/fcgr+) were directly sorted into individual wells of a 96-well PCR plate containing 2.3 µl of 0.2% Triton-X100 (Sigma-Aldrich, Cat. no. 93443) and 2.3 U of SUPERase-In RNase Inhibitor (Ambion, Cat no. AM2694). cDNA was obtained and amplified following the described SMARTSEQ2 protocol (Picelli et al., 2014). Libraries were prepared for sequencing from 125 ng of cDNA using the Illumina Nextera XT DNA preparation kit. Pooled libraries were run on the Illumina Hi-Seq 2500.
Libraries were prepared for sequencing from 125 ng of cDNA using the Illumina Nextera XT DNA preparation kit.

tag: strain

value: GMP

tag: treatment


title: 5FU_Day8_Rep2_87


title: 5FU_Day8_Rep2_89


title: WT-1

tag: strain background


title: 5FU_Day8_Rep2_91


title: ATACseq_E10.5-Mx_2


title: 5FU_Day8_Rep2_93


title: 5FU_Day8_Rep2_9


title: 5FU_Day8_Rep2_85


title: 5FU_Day8_Rep2_82


title: 5FU_Day8_Rep2_88


title: 5FU_Day8_Rep2_94


title: 5FU_Day8_Rep2_84


title: 5FU_Day8_Rep2_90


title: 5FU_Day8_Rep2_83


title: 5FU_Day8_Rep2_7


title: 5FU_Day8_Rep2_80


title: 5FU_Day8_Rep2_81


title: 5FU_Day8_Rep2_86


title: 5FU_Day8_Rep2_78


title: 5FU_Day8_Rep2_79


title: 5FU_Day8_Rep2_76


title: 5FU_Day8_Rep2_75


title: 5FU_Day8_Rep2_74


title: 5FU_Day8_Rep2_73


title: 5FU_Day8_Rep2_72


title: 5FU_Day8_Rep2_8


title: 5FU_Day8_Rep2_70


title: 5FU_Day8_Rep2_68


title: 5FU_Day8_Rep2_69


title: 5FU_Day8_Rep2_67


title: 5FU_Day8_Rep2_63


title: 5FU_Day8_Rep2_58


title: 5FU_Day8_Rep2_60


title: 5FU_Day8_Rep2_5


title: 5FU_Day8_Rep2_59


title: 5FU_Day8_Rep2_61


title: 5FU_Day8_Rep2_64


title: 5FU_Day8_Rep2_66


title: 5FU_Day8_Rep2_57


title: 5FU_Day8_Rep2_65


title: 5FU_Day8_Rep2_62


title: 5FU_Day8_Rep2_77


title: 5FU_Day8_Rep2_52


title: 5FU_Day8_Rep2_55


title: 5FU_Day8_Rep2_53


title: 5FU_Day8_Rep2_56


title: 5FU_Day8_Rep2_54


title: 5FU_Day8_Rep2_50


title: 5FU_Day8_Rep2_51


title: 5FU_Day8_Rep2_71


title: 5FU_Day8_Rep2_48


title: 5FU_Day8_Rep2_4


title: 5FU_Day8_Rep2_47


title: 5FU_Day8_Rep2_6


title: 5FU_Day8_Rep2_46


title: 5FU_Day8_Rep2_45


title: 5FU_Day8_Rep2_44


title: 5FU_Day8_Rep2_43


title: 5FU_Day8_Rep2_39


title: 5FU_Day8_Rep2_42


title: 5FU_Day8_Rep2_38


title: 5FU_Day8_Rep2_3


title: 5FU_Day8_Rep2_37


title: 5FU_Day8_Rep2_33


title: 5FU_Day8_Rep2_28


title: 5FU_Day8_Rep2_41


title: 5FU_Day8_Rep2_29


title: 5FU_Day8_Rep2_40


title: 5FU_Day8_Rep2_32


title: 5FU_Day8_Rep2_31


title: 5FU_Day8_Rep2_35


title: 5FU_Day8_Rep2_49


title: 5FU_Day8_Rep2_27


title: 5FU_Day8_Rep2_24


title: 5FU_Day8_Rep2_26


title: 5FU_Day8_Rep2_22


title: 5FU_Day8_Rep2_20


title: 5FU_Day8_Rep2_23


title: 5FU_Day8_Rep2_21


title: 5FU_Day8_Rep2_1


title: 5FU_Day8_Rep2_19


title: 5FU_Day8_Rep2_18


title: 5FU_Day8_Rep2_34


title: 5FU_Day8_Rep2_36


title: 5FU_Day8_Rep2_17


title: 5FU_Day8_Rep2_2


title: 5FU_Day8_Rep2_30


title: 5FU_Day8_Rep2_25


title: Tcell input

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

description: murine Tcell input DNA, genomic

data_processing:
Reads were aligned to the mouse mm10 reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 1.119.
Peaks were called for total RNA-Pol2 samples using MACS2 version  2.1.0 with a FDR threshold of 0.05.
Annotation of called peaks with ChIPpeakAnno package (Version 3.8.9) in R.
Genome_build: mm10
Supplementary_files_format_and_content: 1. Bed files contain the peak positional information derived from MACS2. Its a 5-coulmn bed format containing chr, peak start, peak end, peak name, FE.
Supplementary_files_format_and_content: 2. CSV files contain the annotated peaks from MACS2. Peaks were annotated to the closest gene using ChIPpeakAnno package in R.

source_name: primary T-cells

growth_protocol: Peripheral CD4+ T cells were isolated with CD4 Dynabeads (Invitrogen) and kept in RPMI medium (supplemented with 10% (vol/vol), FCS, β-mercaptoethanol (0.05 mM, Gibco), penicillin-streptomycin (100 U/ml, Gibco), Sodium Pyruvate (1 mM, Lonza), Non-Essential Amino Acids (1x, Gibco), MEM Vitamin Solution (1x, Gibco), Glutamax (1x, Gibco) and HEPES pH 7.2 (10 mM, Gibco)). Naïve CD4+ T cells were stimulated for 36–48h under Th1 conditions (on surfaces coated with goat anti–hamster immunoglobulin G (55397, MP Biomedicals)) with soluble anti-CD3 (0.1 μg/ml; 145-2C11) and anti CD28 (1 μg/ml; 37N), interleukin 4 (anti-IL-4, 10 μg/ml; IIB11), all produced and purified in-house (Kremmer, E.) and recombinant IL-12 (10 ng/ml, R&D Systems). Stimulation of naïve CD4+ T cells under Th0 conditions was done with soluble anti-CD3 (0.1 μg/ml) and anti CD28 (1 μg/ml) on surfaces coated with goat anti-hamster.

extract_protocol:
30x106 T cells were crosslinked with 1% Formaldehyde (10min, RT) and crosslinking reaction was stopped by the addition of glycine to a final concentration of 0.125 M. Chromatin immunoprecipitation assays were performed as described (DeKoter RP et al., 2002) with minor changes. After sonification for 25 Cycles (Bioruptor; 30s on, 30s off at high) chromatin was diluted to 1ml total volume in nuclei-lysis buffer with protease inhibitors and added to 3ml Chip IP buffer (0.01%SDS; 1.1% Triton X-100;1.2mM EDTA; 16.7mM Tris-HCl,pH8.1; 16.7mM NaCl) with protease inhibitors. 10μg antibody were coupled to 80μl Dynabeads Protein G (10004D) for at least 1h at RT and further blocked with sonicated salmon sperm DNA for 30min before washing. Beads and diluted Chromatin were incubated at 4°C over night and washed with 1ml of the following buffers each at RT for 5min with rotation: Buffer I (0.1% SDS; 1% Triton X-100; 2mM EDTA; 20mM Tris-HCL pH8.1; 150mM NaCl), Buffer II (0.1% SDS; 1% Triton X-100; 2mM EDTA; 20mM Tris-HCL pH8.1; 500mM NaCl), Buffer III (0.25M LiCl; 1% NP-40; 1mM EDTA; 10mM Tris-HCl, pH8.1), 2x TE ph 8.0. DNA purification was done according to Ronnie Blecher-Gonen et al., 2013.
Library preperation was performed from 2 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

treatment_protocol: After being stimulated for at least 36h cell populations were expanded in RPMI medium (as described above) supplemented with Proleukin S (200 IE/ml, IL2-analog, Novartis) for additional 2 or 3 days. One day before activation, cells were cultured in RPMI medium (as described above), but without Proleukin S. Th1 cells were activated with plate-bound CD3 (5 μg/ml) and suluble anti-CD28 (2.5 μg/ml).

value: Balb/c DO11.10

tag: chip antibody

value: input

tag: fixation

value: 10min 1% Formaldehyde

value: primary Th1 cells


title: 5FU_Day8_Rep2_16


title: H3K36me3 2h_1

description: ChIP-Seq against H3K36me3 in treated murine Tcells after 2h, replicate 1

value: anti-Histone H3 K36me3 ab9050


title: 5FU_Day8_Rep2_11


title: 5FU_Day8_Rep2_13


title: totPol2 2h_2

description: ChIP-Seq against RNA-Pol2 in treated murine Tcells after 2h, replicate 2

value: anti-RNA Pol II(8WG16) ab817


title: 5FU_Day8_Rep2_15


title: H3K36me3 NR_1

description: ChIP-Seq against H3K36me3 in non-restimulated murine Tcells, replicate 1


title: 5FU_Day8_Rep2_12


title: H3K36me3 30min_1

description: ChIP-Seq against H3K36me3 in treated murine Tcells after 30min, replicate 1


title: totPol2 2h_1

description: ChIP-Seq against RNA-Pol2 in treated murine Tcells after 2h, replicate 1


title: 5FU_Day8_Rep2_10


title: totPol2 30min_1

description: ChIP-Seq against RNA-Pol2 in treated murine Tcells after 30min, replicate 1


title: totPol2 NR_2

description: ChIP-Seq against RNA-Pol2 in non-restimulated murine Tcells, replicate 2


title: 5FU_Day8_Rep1_9


title: totPol2 30min_2

description: ChIP-Seq against RNA-Pol2 in treated murine Tcells after 30min, replicate 2


title: 5FU_Day8_Rep1_96


title: 5FU_Day8_Rep1_95


title: totPol2 NR_1

description: ChIP-Seq against RNA-Pol2 in non-restimulated murine Tcells, replicate 1


title: 5FU_Day8_Rep1_93


title: 5FU_Day8_Rep1_92


title: Control_9

extract_protocol:
C57Bl/6 Scl-tTA::TRE-BCR/ABL (BA)  mice as previously described (Reynaud, D et al., Cancer Cell, 2011), were bred in the presence of 20mg/L doxycycline in their drinking water, and induced for CML-like MPN development at 5 weeks of age by doxycycline withdrawal. BA and control mice were analyzed 5-6 weeks after BCR/ABL induction. Bone marrow (BM) cells were obtained by either crushing leg, arm and pelvic bones or just flushing leg bones in Hanks’ Buffered Saline Solution (HBSS) containing 2% heat-inactivated FBS (Sigma-Aldrich). HBSS/2% FBS was used for all incubation and wash steps. Erythrocytes and contaminating bone material were removed by ACK lysis followed by centrifugation on a Ficoll gradient (Histopaque 1119, Sigma-Aldrich) for crushed bones. BM cells were first pre-enriched for c-Kit+ cells using c-Kit microbeads (Miltenyi Biotec, 130-091-224) and MACS Separation LS Columns (Miltenyi Biotec, 130-042-401), and incubated with purified, unconjugated-lineage antibodies (CD3 from Biolegend, and CD4, CD5, CD8, B220, Ter119, Mac-1 and Gr-1 from eBioscience) followed by goat anti-rat-PE-Cy5 (Invitrogen, A10691) and subsequently blocked with purified rat IgG (Sigma-Aldrich). Cells were then stained with c-Kit-APC-eFluor780 (eBioscience, 47-1171-82), Sca-1-PB (BioLegend, 108120), CD48-A647 (BioLegend, 103416), CD150-PE (BioLegend, 115904), CD34-FITC (eBioscience, 11-0341-85) and FcγR-PerCP-eFluor710 (eBioscience, 46-0161-82). Single GMPs (lin-/c-kit+/sca-1-/cd34+/fcgr+) were directly sorted into individual wells of a 96-well PCR plate containing 2.3 µl of 0.2% Triton-X100 (Sigma-Aldrich, Cat. no. 93443) and 2.3 U of SUPERase-In RNase Inhibitor (Ambion, Cat no. AM2694). cDNA was obtained and amplified following the described SMARTSEQ2 protocol (Picelli et al., 2014). Libraries were prepared for sequencing from 125 ng of cDNA using the Illumina Nextera XT DNA preparation kit. Pooled libraries were run on the Illumina Hi-Seq 4000.
Libraries were prepared for sequencing from 125 ng of cDNA using the Illumina Nextera XT DNA preparation kit.

value: control


title: 5FU_Day8_Rep1_91


title: 5FU_Day8_Rep2_14


title: Control_96


title: 5FU_Day8_Rep1_8


title: 5FU_Day8_Rep1_94


title: Control_95


title: Control_94


title: 5FU_Day8_Rep1_89


title: 5FU_Day8_Rep1_88


title: Control_90


title: Control_91


title: 5FU_Day8_Rep1_86


title: 5FU_Day8_Rep1_85


title: Control_8


title: 5FU_Day8_Rep1_87


title: Control_88


title: Control_89


title: 5FU_Day8_Rep1_84


title: 5FU_Day8_Rep1_82


title: Control_87


title: 5FU_Day8_Rep1_90


title: 5FU_Day8_Rep1_83


title: 5FU_Day8_Rep1_81


title: 5178-4DPI

city: Davis

first: Payam

last: Vahmani

state: California

address: One Shields Avenue

department: Department of Animal Science

institute: University of California Davis

data_processing:
Sequence reads with base quality scores were produced by the Illumina sequencer. RNA-Seq reads flagged as low quality by the chastity filter in CASAVA 1.8 were removed. In addition, we removed reads with an average read quality score below 15 and reads in which over 5 of the last 10 bases had a PHRED quality score below 2.
Sequence reads were aligned to pig reference genome sequence assembly (Sscrofa10.2) using Tophat 2.0.12 with default parameters which included: enable use of GTF file, set minimum anchor length of 8, accept zero mismatches in the anchor region, allow intron length between 50 and 500,000, and allow up to 20 alignments to the reference for a given read. For annotation of genes, we used the GTF file for Sscrofa10.2 from Ensembl version 71.
The number of reads uniquely mapped to each gene was determined using Htseq-count (v0.5.3.p3). Reads that were assigned to more than one gene were not counted by Htseq-count.
The read counts per gene were normalised to counts per million (CPM). Genes expressed at very low levels were removed by keeping only those genes that achieve CPM above four in at least half the samples. Trimmed mean of M-values (TMM) normalisation was applied to this dataset to account for compositional differences between the libraries. Genes that respond to PRRSV infection at any of the day after infection compared to the day 0 baseline were determined in edgeR using a generalized linear model that takes into account the following: dpi, gender, batch (separate experiment on PHGC3 and PHGC5 animals), post globin depletion RIN score, population structure (three PCAs based on genotype of 44 animals).
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample.

organism: Sus scrofa

source_name: 4 DPI_whole blood

extract_protocol:
Three mL of whole blood were collected into the Tempus Blood RNA tubes (Life Technologies, Carlsbad, CA, USA). Total RNA of trial 3 and 5 was isolated using the Tempus Spin RNA isolation Kit (Life Technologies, Carlsbad, CA, USA) and MagMax for Stabilized Blood Tubes RNA Isolation Kit for Tempus tubes (Life Technologies), respectively, according to the respective manufacturer's instructions. RNA concentration was quantified using a ND-1000 spectrophotometer (Nano-Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed using either Agilent 2100 Bioanalyzer or 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA, USA). The globin transcripts (HBA and HBB) were reduced using an RNase H based globin reduction method 24 and RNA quality was assessed again.
Poly (A)+ fractions from the globin depleted RNA samples (1.0 µg RNA each) were purified by oligo-dT purification beads (Illumina, Inc., San Diego, USA) and then used to construct cDNA libraries following the TruSeq RNA Sample Preparation Guide (Illumina, Inc., San Diego, USA). Sequencing was performed on HiSeq 2000 System (Illumina, Inc.) using the TruSeqTM Pair End (PE) 100bp Kit (Illumina, Inc.).

tag: animal id

tag: gender

value: F

tag: days post infection

value: 4 DPI

tag: wur marker type

value: AA

tag: viremia level

tag: body weight (kg)

tag: tissue

value: peripheral blood


title: 5178-28DPI

source_name: 28 DPI_whole blood

value: 28 DPI


title: 5178-7DPI

source_name: 7 DPI_whole blood

value: 7 DPI


title: Control_86


title: 5186-7DPI

value: AG


title: 5186-10DPI

source_name: 10 DPI_whole blood

value: 10 DPI


title: 5FU_Day8_Rep1_80

tag: time


title: Control_92


title: Control_85


title: 5FU_Day8_Rep1_7


title: Control_93


title: 5178-10DPI


title: 5178-14DPI

source_name: 14 DPI_whole blood

value: 14 DPI


title: 5178-0DPI

source_name: 0 DPI_whole blood

value: 0 DPI


title: 5170-7DPI

value: M


title: 5178-21DPI

source_name: 21 DPI_whole blood

value: 21 DPI


title: Control_84

value: GMP


title: 5170-21DPI


title: 5170-4DPI


title: Control_82


title: 5186-4DPI


title: 5170-0DPI


title: 5170-10DPI


title: 5170-14DPI


title: 5159-7DPI


title: 5159-4DPI


title: 5159-28DPI


title: 5159-21DPI


title: 5FU_Day8_Rep1_74


title: 5170-28DPI


title: Control_83


title: 5159-10DPI


title: 5FU_Day8_Rep1_73


title: 5FU_Day8_Rep1_76


title: 5FU_Day8_Rep1_75


title: Control_81


title: 5159-0DPI


title: 5FU_Day8_Rep1_79


title: 5FU_Day8_Rep1_78


title: 5155-7DPI


title: 5FU_Day8_Rep1_77


title: 5155-21DPI


title: 5FU_Day8_Rep1_71


title: 5155-14DPI


title: Control_80


title: Control_79


title: Control_77


title: Control_7


title: Control_78


title: 5155-11DPI

source_name: 11 DPI_whole blood

value: 11 DPI


title: Control_76


title: 5155-0DPI


title: 5FU_Day8_Rep1_70


title: 5159-14DPI


title: 5145-7DPI


title: 5FU_Day8_Rep1_6


title: Control_74


title: 5145-28DPI


title: 5FU_Day8_Rep1_69


title: 5155-4DPI


title: 5FU_Day8_Rep1_72


title: Control_73


title: 5145-10DPI


title: Control_72


title: 5145-21DPI


title: 5FU_Day8_Rep1_68


title: 5142-4DPI


title: 5145-0DPI


title: 5142-7DPI


title: 5FU_Day8_Rep1_67


title: 5FU_Day8_Rep1_66


title: Control_71


title: Control_70


title: Control_75


title: Control_6


title: 5142-10DPI


title: 5142-0DPI


title: 5142-14DPI


title: Control_69


title: 5119-4DPI


title: 5FU_Day8_Rep1_64


title: 5119-7DPI


title: 5119-28DPI


title: 5145-14DPI


title: 5119-14DPI


title: 5119-21DPI


title: 5FU_Day8_Rep1_62


title: 5FU_Day8_Rep1_63


title: 5FU_Day8_Rep1_61


title: 5119-0DPI


title: 5142-21DPI


title: 5090-4DPI


title: 5FU_Day8_Rep1_65


title: 5090-28DPI


title: 5FU_Day8_Rep1_60


title: 5090-21DPI


title: Control_65


title: 5119-10DPI


title: Control_67


title: 5FU_Day8_Rep1_5


title: 5090-10DPI


title: 5090-0DPI


title: Control_64


title: 5089-7DPI


title: 5FU_Day8_Rep1_59


title: Control_63


title: 5089-4DPI


title: 5FU_Day8_Rep1_58


title: Control_62


title: 5FU_Day8_Rep1_57


title: Control_61


title: 5089-14DPI


title: 5089-21DPI


title: Control_68


title: 5FU_Day8_Rep1_56


title: 5090-7DPI


title: 5FU_Day8_Rep1_54


title: 5082-10DPI


title: 5089-10DPI


title: 5082-7DPI


title: 5082-4DPI


title: 5089-0DPI


title: 5FU_Day8_Rep1_53


title: 5FU_Day8_Rep1_52


title: Control_60


title: Control_58


title: 5081-7DPI


title: 5082-28DPI


title: Control_5


title: Control_57


title: 5082-0DPI


title: Control_66


title: 5090-14DPI


title: 5FU_Day8_Rep1_51


title: 5FU_Day8_Rep1_50


title: Control_56


title: 5081-28DPI


title: Control_55


title: 5081-14DPI


title: 5081-21DPI


title: 5FU_Day8_Rep1_55


title: 5082-21DPI


title: 5081-10DPI


title: 5FU_Day8_Rep1_4


title: 5FU_Day8_Rep1_49


title: Control_54


title: 5FU_Day8_Rep1_47


title: 5072-7DPI


title: 5072-10DPI


title: 5072-21DPI


title: 5072-14DPI


title: 5072-0DPI


title: 5072-4DPI


title: Control_51


title: Control_53


title: 5FU_Day8_Rep1_46


title: Control_52


title: Control_50


title: 5059-4DPI


title: 5081-4DPI


title: 5059-7DPI


title: 5FU_Day8_Rep1_45


title: 5059-21DPI


title: 5059-28DPI


title: Control_59


title: 5FU_Day8_Rep1_44


title: Control_49


title: 5FU_Day8_Rep1_48


title: 5FU_Day8_Rep1_43


title: 5072-28DPI


title: 5041-7DPI


title: 5059-10DPI


title: 5082-14DPI


title: 5041-4DPI


title: 5FU_Day8_Rep1_41


title: 5041-14DPI


title: Control_48


title: 5FU_Day8_Rep1_42


title: Control_46


title: Control_4


title: 5059-14DPI


title: Control_45


title: 5089-28DPI


title: 5041-0DPI


title: 5059-0DPI


title: 5FU_Day8_Rep1_3


title: 5041-28DPI


title: 5037-7DPI


title: Control_44


title: 5FU_Day8_Rep1_40


title: 5037-4DPI


title: 5041-21DPI


title: 5041-10DPI


title: 5FU_Day8_Rep1_39


title: Control_43


title: 5037-28DPI


title: 5037-21DPI


title: 5FU_Day8_Rep1_38


title: Control_47


title: 5FU_Day8_Rep1_37


title: 5037-14DPI


title: Control_42


title: 5FU_Day8_Rep1_36


title: Control_41


title: 5036-28DPI

value: GG


title: Control_40


title: 5036-4DPI


title: 5037-0DPI


title: 5036-7DPI


title: 5036-21DPI


title: 5FU_Day8_Rep1_35


title: 5036-14DPI


title: Control_3


title: Control_39


title: 5036-0DPI


title: Control_38


title: 5036-10DPI


title: 5035-7DPI


title: 5035-4DPI


title: 5FU_Day8_Rep1_33


title: 5FU_Day8_Rep1_34


title: 5035-28DPI


title: 5FU_Day8_Rep1_32


title: Control_37


title: 5037-10DPI


title: 5035-14DPI


title: 5035-21DPI


title: 5FU_Day8_Rep1_30


title: 5FU_Day8_Rep1_31


title: 5035-10DPI


title: 5035-0DPI


title: 5FU_Day8_Rep1_2


title: 5FU_Day8_Rep1_29


title: 5033-10DPI


title: 5033-7DPI


title: 5033-4DPI


title: 5033-14DPI


title: 5FU_Day8_Rep1_28


title: Control_34


title: Control_32


title: 5033-0DPI


title: Control_35


title: Control_33


title: 5FU_Day8_Rep1_26


title: Control_31


title: Control_36


title: 5028-7DPI


title: Control_30


title: 5028-10DPI


title: 5FU_Day8_Rep1_25


title: 5027-7DPI


title: 5027-4DPI


title: 5027-28DPI


title: Control_2


title: 5FU_Day8_Rep1_24


title: Control_29


title: 5027-21DPI


title: 5027-14DPI


title: 5FU_Day8_Rep1_23


title: 5FU_Day8_Rep1_27


title: Control_28


title: 5028-14DPI


title: 5028-4DPI


title: 5027-10DPI


title: 5028-28DPI


title: 5FU_Day8_Rep1_22


title: 5026-4DPI


title: Control_26


title: 5FU_Day8_Rep1_21


title: 5026-7DPI


title: 5FU_Day8_Rep1_20


title: 5026-10DPI


title: 5026-14DPI


title: 5026-0DPI


title: 5FU_Day8_Rep1_1


title: 5019-7DPI


title: Control_24


title: 5FU_Day8_Rep1_19


title: 5019-28DPI


title: 5019-4DPI


title: Control_23


title: 5019-21DPI


title: 5019-10DPI


title: 5FU_Day8_Rep1_18


title: Control_22


title: 5027-0DPI


title: Control_27


title: 5009-7DPI


title: Control_21


title: Control_20


title: 5FU_Day8_Rep1_17


title: 5FU_Day8_Rep1_15


title: 5009-4DPI


title: 5026-28DPI


title: 5009-14DPI


title: 5FU_Day8_Rep1_16


title: 5019-0DPI


title: 5FU_Day8_Rep1_14


title: Control_25


title: 5009-0DPI


title: Control_19


title: 5FU_Day8_Rep1_13


title: 5005-7DPI


title: Control_18


title: 5005-4DPI


title: 5009-21DPI


title: 5009-10DPI


title: 5FU_Day8_Rep1_12


title: 5005-21DPI


title: Control_17


title: 5005-14DPI


title: 5FU_Day8_Rep1_11


title: 5005-10DPI


title: 5009-28DPI


title: Control_1


title: 5FU_Day8_Rep1_10


title: 5005-0DPI


title: Control_15


title: Control_16


title: 5004-4DPI


title: 5FU_Day14_9


title: 5004-21DPI


title: 5004-28DPI


title: 5FU_Day14_96


title: Control_14


title: 5004-14DPI


title: 5005-28DPI


title: 5FU_Day14_95


title: 5FU_Day14_94


title: Control_11


title: Control_12


title: 5002-4DPI


title: 5002-7DPI


title: Control_13


title: 5002-28DPI


title: Control_10


title: 5002-14DPI


title: 5FU_Day14_92


title: 5002-21DPI


title: 5004-7DPI


title: 5002-10DPI


title: BA-4_9

value: BCR/ABL induction


title: 5002-0DPI


title: 5FU_Day14_91


title: 5001-21DPI


title: BA-4_96


title: 5FU_Day14_8


title: 5004-0DPI


title: BA-4_95


title: 5004-10DPI


title: 5001-14DPI


title: 5001-0DPI


title: 5FU_Day14_93


title: BA-4_93


title: 5FU_Day14_89


title: 5FU_Day14_86


title: 5FU_Day14_88


title: BA-4_90


title: 5FU_Day14_87


title: BA-4_91


title: BA-4_92


title: 5FU_Day14_85


title: 5FU_Day14_84


title: BA-4_89


title: BA-4_88


title: 5FU_Day14_83


title: 5001-28DPI


title: BA-4_87


title: 5FU_Day14_82


title: 5FU_Day14_90


title: 5FU_Day14_81


title: BA-4_94


title: BA-4_86


title: 5FU_Day14_7


title: BA-4_84


title: BA-4_83


title: BA-4_85


title: 5FU_Day14_79


title: 5FU_Day14_77


title: 5FU_Day14_78


title: BA-4_81


title: BA-4_80


title: BA-4_82


title: BA-4_8


title: BA-4_79


title: BA-4_7


title: BA-4_78


title: 5FU_Day14_74


title: 5FU_Day14_76


title: 5FU_Day14_75


title: 5FU_Day14_73


title: 5FU_Day14_71


title: BA-4_75


title: 5FU_Day14_80


title: BA-4_76


title: 5FU_Day14_6


title: 5FU_Day14_70


title: BA-4_74


title: BA-4_77


title: 5FU_Day14_69


title: BA-4_73


title: BA-4_71


title: 5FU_Day14_66


title: 5FU_Day14_68


title: BA-4_70


title: 5FU_Day14_67


title: 5FU_Day14_65


title: BA-4_6


title: BA-4_72


title: BA-4_67


title: 5FU_Day14_63


title: BA-4_68


title: 5FU_Day14_72


title: BA-4_66


title: 5FU_Day14_60


title: 5FU_Day14_62


title: 5FU_Day14_64


title: BA-4_65


title: 5FU_Day14_59


title: BA-4_63


title: 5FU_Day14_5


title: 5FU_Day14_58


title: 5FU_Day14_57


title: BA-4_62


title: 5FU_Day14_56


title: BA-4_61


title: BA-4_69