title: OPC_rep2

data_processing:
Illumina Casava software used for basecalling.
We sequenced primary mouse OPCs and OLs induced to differentiate for 1 day (referred as iOL) and 3 days (referred as mOL) in duplicates (60–80 million mate pairs each) to be used for ab initio transcirptome assembly with Cufflinks v2.2.1. In Brief, Cufflinks were run with the following options: -u, -N, -g (mm10 GTF file provided as guide), and -M (rRNA and 7SK RNA mask file provided). We generated transcriptome assemblies for each sample separately and then utilized Cuffmerge to combine all annotations. Any transcripts that overlapped and transcribed in the same orientation as a known coding region (RefSeq NM entries) were removed and then merged the annotations using Cuffmerge. We removed any single-exonic transcripts to reduce transcriptional noise. Any transcripts with a length < 200 nt including miRNA and snRNA host genes were removed. Next, we used the CPAT algorithm (Wang et al., 2013) to predict protein-coding potential of the remaining transcripts. Any transcript with a CPAT scores greater than 0.44 was removed. The resulting OL-expressing lncRNA annotation was then compared to the RefSeq or lncRNA annotation in order to determine the number of novel genes discovered here. Transcripts were considered divergent if their TSS was less than 2.5 kb from a RefSeq_NM TSS on the opposite strand. All other lncRNAs were considered to be intergenic. This T-ALL lncRNA annotation was merged with the RefSeqNM annotation using Cuffmerge and used for all subsequent RNA-Seq expression analyses. For a copy of this annotation in GTF format, see supplemental information.
Genome_build: mm10
Supplementary_files_format_and_content: [.fpkm_tracking] tab-delimited text files include lncRNA FPKM values for each Sample

source_name: OPC

growth_protocol: primary mouse oligodendrocyte precursor cells are cultured with the presence of PDGFAA, or differentiated for one day or three days with T3

extract_protocol:
total RNA was harvested using Trizol reagent
Strand-specific RNA libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded Total RNA Library Prep Kit (Cat# RS-122-2201)

value: Oligodendrocyte Precursor Cell


title: lncOL1KO_rep1

status: Public on Dec 28 2016

type: SRA

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: [.txt] tab-delimited text files include FPKM values of all UCSC_mm10 annotated genes and differential gene expression analysis

molecule: total RNA

organism: Mus musculus

source_name: mouse primary oligodendrocyte

growth_protocol: primary mouse oligodendrocyte precursor cells are  differentiated for one day with T3

extract_protocol:
total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

tag: cell type

value: Primary oligodendrocyte

tag: genotype

tag: strain

value: mixed background


title: iOL_rep2

source_name: iOL

value: Immature oligodendrocyte


title: Ctrl_rep2

value: lncOL1+/+, lncOL1+/-


title: mOL_rep1

source_name: mOL

value: Mature oligodendrocyte


title: mOL_rep2


title: OPC_rep1


title: iOL_rep1


title: p6_CD74_H3K4Me2

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description: processed data file: p6_CD74_activation_H3K4Me2_versus_input.bed

library_source: genomic

data_processing:
Reads were demultiplexed
Adapters were trimmed using the cutadapt tool
The reads were aligned uniquely to the human genome (hg19)
Bound regions were detected using MACS2 (version 2.0.10.20131216)
Genome_build: hg19
Supplementary_files_format_and_content: bed files of MACS2 peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: Cll cells

growth_protocol: B cells were obtained from CLL patients using a RosettSep antibody mixture.

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
In-house ChIP-Seq protocol, Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of y samples on one lane.

treatment_protocol: Cells were activated with either CD74 Ab or IgG control Ab

tag: diagnosis

value: CLL

tag: patient number

tag: patient age

tag: patient sex

value: Male

tag: disease level

value: Binet B

tag: chip ab

value: H3K4Me2 (abcam ab32356)

tag: activation

value: B cells


title: L-Input-1

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

description: Total RNA rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
The RIP-seq reads were aligned against the hg19 human reference genome with the UCSC known gene transcript annotation using TopHat v2.0.9. The RIP-seq peaks were identified for + and – strand separately using macs2 v2.0.10 (Zhang et al., 2008), with a scanning window size of 100 bps, but without shifting the reads (peak length≥150, FDR≤0.01 and fold change≥4 and RIP read count ≥50)
Genome_build: hg19

source_name: Prostate cancer cell line

growth_protocol: LNCaP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Cells were crosslinked with 0.3% formaldehyde for 10 min at room temperature and lysed with RIPA lysis buffer for 10 min on ice before sonication. The supernatant was collected and incubated with RIP antibodies for 4 to 6 hours. After washing with RIPA buffer, RNA was eluted from the beads with 100 µl NaHCO3 and 1% SDS in the presence of proteinase K and RNase inhibitor at room temperature for 10 min with occasional vortex. The eluted material was de-crosslinked at 65°C for 45 – 60 min before purification of RNA using Trizol LS reagent (Life Technology). DNase I treatment was performed to remove any residual DNA.
RNA-seq libraries were constructed with TruSeq Stranded mRNA Library Prep Kit from Illumina according to the manufacturer’s manual.

tag: cell line

value: LNCaP


title: L-Input-2

description: Total RNA rep2


title: HNRNPL RIP rep1

description: HNRNPL RIP rep1


title: HNRNPL RIP rep2

description: HNRNPL RIP rep2


title: Cripto KO F/A

status: Public on Dec 27 2016

city: Naples

first: ALESSANDRO

last: FIORENZANO

state: Naples

address: Castellino 111

department: IGB institute CNR

country: Italy

institute: I.G.B. Institute, CNR

data_processing:
Illumina casava base calling
BAM format was used for the read alignments. Sequenced reads were mapped to mm9 whole genome using TopHat v 2.0.13 using the annotation file (Mus musculus NCBIM37 release 67) as guide (parameter -G). All the other parameters are set as default.
raw counts have been obtained using HTSeq  (version 0.6.1p1) on intersection-nonempty mode
individual raw count were comnined in a single table of counts and underwent to ful quantile normalization and proportional test filtering
normalization of combined raw counts, filtering and the analysis of differentially expressed genes was performad using RNAseqGUI (ver 0.99.3)
Genome_build: mm9
Supplementary_files_format_and_content: [T_counts.txt] Table of combined raw counts; [Proportion_T_counts_FQUA.txt] Table of normalized and filtered counts

source_name: Cripto KO F/A

growth_protocol: Wild-Type (WT) and Cripto KO R1 mESCs were cultured in serum/LIF. EpiSCs were generated from ESCs, seeded at low density in N2B27 supplemented with Activin A (20 ng/ml, Invitrogen) and bFGF and cultured for 6 days.

extract_protocol:
Total RNAs were isolated using RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Cripto KO

tag: culture protocol

value: F/A (bFGF and Activin)

value: EpiSC


title: WT F/A

source_name: WT F/A

value: WT


title: VCaP Input DNA

city: Boston

first: Fen

last: Ma

state: MA

address: 3 Blackfan Circle

department: Hem/Onc

institute: BIDMC

data_processing:
Basecalls performed using RTA 1.13.48.0 as primary analysis and CASAVA version 1.8.2 as secondary analysis.
ChIP-seq reads were aligned to the hg18 genome assembly with illumina's ELAND aligner.
NonPF reads were filtered.
Peaks were called using MACs version 2.0.10.20120703 with the default setting, detailed as: effective genome size=2.70e+09, band width=300, model fold=[5,50], qvalue cutoff=5.00e-02, larger dataset will be scaled towards smaller dataset, range for calculating regional lambda is:1000 bps and 10000 bps, broad region calling is off.
Genome_build: hg18
Supplementary_files_format_and_content: BED files were generate

source_name: VCaP Prostate Cancer Cell line

growth_protocol: VCaP cells were cultured in DMEM medium with 10% FBS

extract_protocol:
Cell was fixed by 1% formaldehyde for 10min and then lysed. Lysates were sonicated and Input DNA were set aside. Lysates were then clarified from sonicated nuclei and SOX9-DNA complexes were isolated with SOX9 antibody. Cross-linking of the DNA were reversed by heating for both Input and immunoprecipitated DNA. All DNA were purified by Qiagen PCR purification kit before library construction.
Libraries were prepared according to Illumina's instructions accompanying the ChIP Sample Prep Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: VCaP

tag: chip antibody

value: none (input)


title: ASH1 Rep2

city: Chiyodaku

first: Yujiro

last: Tanaka

state: Tokyo

address: 2-3-10 Kandasurugadai

department: School of Biomedical Science

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Alignment to hg19 by BWA.
MACS14 peak detection software with p-value 1x10^-7.
Statistical analysis by Genomatix suite, CLC Main Workbench, Galaxy portal, and ngs.plot.
Gene ontology analysis by DAVID server.
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: WIG, BED (peak calls)

growth_protocol: K562 cells were cultured in DMEM with 10% fetal calf serum.

extract_protocol:
Approximately 1x108 K562 cells were fixed by 10% formaldehyde in 50 mM Hepes-KOH, pH7.5, 100 mM NaCl, 1 mM EDTA, ph8.0, 0.5 mM EGTA, pH8.0 for 10 min at room temperature, quenched by one tenth volume of 2.5 M Glycine, rinsed sequentially with LB1 (50 mM Hepes-KOH, pH7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), LB2 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, pH8.0), and resuspended in LB3 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA, pH8.0 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) containing Protease Inhibotor Cocktail (Roche). Cell suspension was then sonciated by Covaris S2 Acoustic Solbilyzer with Duty Cycle 20%, Intensity 5, Cycles per Burst 200, and 20-30 cycles. Lysates were cleared by centrifugation, and immunoprecipitated with anti-ASH1 antibodies fixed on Dynabeads M-280 sheep anti-rabbit/mouse IgG (Invitrogen), washed with LiCl buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40, 1% Na-Deoxycholate) and then with TE, and eluted in 1% SDS, 0.1 M NaHCO3. After overnight de-crosslinking, DNA was purified with PCR Cleanup column (QIAGEN). Fragment sizes were checked by 2100 BioAnalyzer (Agilent).
Sequencing libraries were constructed using ChIP-Seq Sample Prep Kit (Illumina) according to the manufacture's protocol.

value: leukemia cell line K562

value: anti-ASH1 (made in-house)

tag: chip antibody batch


title: Cripto KO Serum/LIF

source_name: Cripto KO Serum/LIF

value: Serum/LIF

value: ESC


title: VCaP SOX9 ChIP-seq

value: SOX9:Millipore AB5535


title: WT Serum/LIF

source_name: WT Serum/LIF


title: C93; single cell

city: Philadelphia

first: Diana

middle: Elena

last: Stanescu

state: PA

address: 3400 Civic Center Blvd

department: IDOM

institute: University of Pennsylvania

description:
FGC0930_s_1_TCCTGAGCCTAAGCCT.fastq
FGC0930_s_2_TCCTGAGCCTAAGCCT.fastq

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome to obtain transcript quantitation.
Genome_build: mm9
Supplementary_files_format_and_content: File with FPKM values

source_name: pancreas

extract_protocol:
Embryos at e13.5 were dissected in cold PBS, the pancreas was isolated and then disociated into single cells using trypsin. Single cells suspension at a concentration of 200cell/ul was loaded on a microfluidic device. cDNA was prepared from each cell using the SMARTer Kit (Takara-Clontech, CA)
Single cell RNA libraries were prepared for sequencing using the low throughput Nextera XT SNA library prep kit (Illumina, CA), according to the manufacturers protocol

tag: tissue

value: pancreata

tag: age

value: embryonic day e13.5


title: C95; single cell

description:
FGC0930_s_1_AAGAGGCACTAAGCCT.fastq
FGC0930_s_2_AAGAGGCACTAAGCCT.fastq


title: C92; single cell

description:
FGC0930_s_1_GGACTCCTCTAAGCCT.fastq
FGC0930_s_2_GGACTCCTCTAAGCCT.fastq


title: C96; single cell

description:
FGC0930_s_1_CGAGGCTGCTAAGCCT.fastq
FGC0930_s_2_CGAGGCTGCTAAGCCT.fastq


title: p6_IgG_H3K4Me2

description: processed data file: p6_IgG_activation_H3K4Me2_versus_input.bed

value: CLL

value: Male

value: Binet B

value: IgG

tag: cell type


title: C91; single cell

description:
FGC0930_s_1_TAGGCATGCTAAGCCT.fastq
FGC0930_s_2_TAGGCATGCTAAGCCT.fastq


title: C86; single cell

description:
FGC0930_s_1_GGACTCCTAAGGAGTA.fastq
FGC0930_s_2_GGACTCCTAAGGAGTA.fastq


title: C84; single cell

description:
FGC0930_s_1_CGAGGCTGACTGCATA.fastq
FGC0930_s_2_CGAGGCTGACTGCATA.fastq


title: C82; single cell

description:
FGC0930_s_1_GTAGAGGAACTGCATA.fastq
FGC0930_s_2_GTAGAGGAACTGCATA.fastq


title: C83; single cell

description:
FGC0930_s_1_AAGAGGCAACTGCATA.fastq
FGC0930_s_2_AAGAGGCAACTGCATA.fastq


title: C88; single cell

description:
FGC0930_s_1_GTAGAGGAAAGGAGTA.fastq
FGC0930_s_2_GTAGAGGAAAGGAGTA.fastq


title: C90; single cell

description:
FGC0930_s_1_CGAGGCTGAAGGAGTA.fastq
FGC0930_s_2_CGAGGCTGAAGGAGTA.fastq


title: Suz12_OPC

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the rn5 genome assembly using Bowtie2 with the default configuration
Peak calling was performed using MACS (Model-based Analysis of ChIP-Seq) (http://liulab.dfci.harvard.edu/MACS) with a p value cut off of 1x e9.
Genome_build: rn5
Supplementary_files_format_and_content: [.bed] peaks file generated using Macs14

organism: Rattus norvegicus

growth_protocol: primary rat oligodendrocyte progenitors were cultured with the presence of PDGFAA and FGF

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
OLs (~20 million cells) were cross-linked in 1% formaldehyde at room temperature for 10 min and then quenched with 125 mM glycine for 5 min. Cells were rinsed, resuspended in lysis buffer (50 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.25% Triton X-100 and 0.5% NP-40 and protease inhibitor cocktail) and incubated on ice for 10 min. Lysates were centrifuged and pellets were resuspended in nuclei washing buffer  (200 mM NaCl, 1 mM EDTA, 1 mM EGTA, 10 mM Tris pH 8.0, and protease inhibitor cocktail) with gentle rocking at 4°C. Nuclei were pelleted and resuspended in 1 ml of sonication buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA and protease inhibitor cocktail). Nuclear suspensions were sonicated with a Covaris S220 sonicator (total time 8 min). Antibody (chromatin: antibody = 4:1) was added to chromatin and incubated at 4°C overnight. Chromatin-protein complex was immunoprecipitated with protein A/G plus agarose beads and washed sequentially, twice with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 150 mM NaCl), twice with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 500 mM NaCl) and twice with LiCl buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris [pH 8.0]) and once with 1xTE buffer. Immunoprecipitates were then eluted in elution buffer at 65°C for 1 h. Eluted chromatin was subjected to reverse-crosslink and chromatin fragment purification with QIAGEN PCR purification columns. ChIP-Seq libraries were prepared using NEBNext ChIP-Seq Library Prep Kit according to manufacturer’s instructions.

value: anti-SUZ12 (D39F6) XP Rabbit mAb (CST, catalog# 3737, lot# 3)

value: Oligodendrocyte Precursor Cell

value: Brown Norway Rat


title: C89; single cell

description:
FGC0930_s_1_AAGAGGCAAAGGAGTA.fastq
FGC0930_s_2_AAGAGGCAAAGGAGTA.fastq


title: C81; single cell

description:
FGC0930_s_1_TCCTGAGCACTGCATA.fastq
FGC0930_s_2_TCCTGAGCACTGCATA.fastq


title: C8; single cell

description:
FGC0930_s_1_CGTACTAGCTCTCTAT.fastq
FGC0930_s_2_CGTACTAGCTCTCTAT.fastq


title: C76; single cell

description:
FGC0930_s_1_GTAGAGGAGTAAGGAG.fastq
FGC0930_s_2_GTAGAGGAGTAAGGAG.fastq


title: C77; single cell

description:
FGC0930_s_1_AAGAGGCAGTAAGGAG.fastq
FGC0930_s_2_AAGAGGCAGTAAGGAG.fastq


title: C74; single cell

description:
FGC0930_s_1_GGACTCCTGTAAGGAG.fastq
FGC0930_s_2_GGACTCCTGTAAGGAG.fastq


title: C75; single cell

description:
FGC0930_s_1_TCCTGAGCGTAAGGAG.fastq
FGC0930_s_2_TCCTGAGCGTAAGGAG.fastq


title: C79; single cell

description:
FGC0930_s_1_TAGGCATGACTGCATA.fastq
FGC0930_s_2_TAGGCATGACTGCATA.fastq


title: C71; single cell

description:
FGC0930_s_1_AAGAGGCAAGAGTAGA.fastq
FGC0930_s_2_AAGAGGCAAGAGTAGA.fastq


title: C70; single cell

description:
FGC0930_s_1_CGAGGCTGAGAGTAGA.fastq
FGC0930_s_2_CGAGGCTGAGAGTAGA.fastq


title: C7; single cell

description:
FGC0930_s_1_AGGCAGAACTCTCTAT.fastq
FGC0930_s_2_AGGCAGAACTCTCTAT.fastq


title: C65; single cell

description:
FGC0930_s_1_AAGAGGCATATCCTCT.fastq
FGC0930_s_2_AAGAGGCATATCCTCT.fastq


title: C67; single cell

description:
FGC0930_s_1_TCCTGAGCAGAGTAGA.fastq
FGC0930_s_2_TCCTGAGCAGAGTAGA.fastq


title: C63; single cell

description:
FGC0930_s_1_TAGGCATGTATCCTCT.fastq
FGC0930_s_2_TAGGCATGTATCCTCT.fastq


title: C66; single cell

description:
FGC0930_s_1_GTAGAGGATATCCTCT.fastq
FGC0930_s_2_GTAGAGGATATCCTCT.fastq


title: C87; single cell

description:
FGC0930_s_1_TCCTGAGCAAGGAGTA.fastq
FGC0930_s_2_TCCTGAGCAAGGAGTA.fastq


title: C61; single cell

description:
FGC0930_s_1_TCCTGAGCTATCCTCT.fastq
FGC0930_s_2_TCCTGAGCTATCCTCT.fastq


title: C62; single cell

description:
FGC0930_s_1_GGACTCCTTATCCTCT.fastq
FGC0930_s_2_GGACTCCTTATCCTCT.fastq


title: C80; single cell

description:
FGC0930_s_1_GGACTCCTACTGCATA.fastq
FGC0930_s_2_GGACTCCTACTGCATA.fastq


title: C59; single cell

description:
FGC0930_s_1_AAGAGGCACTCTCTAT.fastq
FGC0930_s_2_AAGAGGCACTCTCTAT.fastq


title: C56; single cell

description:
FGC0930_s_1_GGACTCCTCTCTCTAT.fastq
FGC0930_s_2_GGACTCCTCTCTCTAT.fastq


title: C94; single cell

description:
FGC0930_s_1_GTAGAGGACTAAGCCT.fastq
FGC0930_s_2_GTAGAGGACTAAGCCT.fastq


title: C6; single cell

description:
FGC0930_s_1_CTCTCTACTAGATCGC.fastq
FGC0930_s_2_CTCTCTACTAGATCGC.fastq


title: C54; single cell

description:
FGC0930_s_1_GTAGAGGATAGATCGC.fastq
FGC0930_s_2_GTAGAGGATAGATCGC.fastq


title: C50; single cell

description:
FGC0930_s_1_GGACTCCTTAGATCGC.fastq
FGC0930_s_2_GGACTCCTTAGATCGC.fastq


title: C52; single cell

description:
FGC0930_s_1_CGAGGCTGTAGATCGC.fastq
FGC0930_s_2_CGAGGCTGTAGATCGC.fastq


title: sek-1(km4) DR (replicate 3)

city: Shanghai

first: Ziyun

last: Wu

state: Shanghai

address: 800 Dongchuan RD

department: Food Science and Engineering

country: China

institute: Shanghai Jiao Tong University

description: matrixWZY.csv

data_processing:
Align reads to C. elegans genome with SMALT (Wellcome Trust Sanger Institute) aligner
Import raw data into RStudio/Bioconductor
Quantification of mapped reads with featureCounts (Subread)
Genome_build: WBcel246 (Dec 2014)
Supplementary_files_format_and_content: comma separated values (raw counts of sequencing reads)

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized populations of L1 animals were obtained by hypochlorite treatment, then allowed to develop at 20°C on standard NGM plates seeded with OP50

extract_protocol:
Day 6 adult were snap frozen in liquid nitrogen. Total RNA was extracted using TRIzol (Sigma-Aldrich, St. Louis, MO), and purified with Direct-zol™ RNA Kits (Zymo Research, Irvine, CA). Purified RNA samples were DNase treated before sending for sequencing.
RNA libraries were prepared with poly(A) enrichment and sequencing using standard Illumina protocols (50 bp single end).

treatment_protocol: L4/young adult animals were transferred to NGM agar plates containing 5 mg/L cholesterol, 50 mg/L ampicillin, 10 mg/L kanamycin, 1 mg/L tetracycline, 50mg/L nystatin, and 100 mg/L FUdR, and seeded with the cold- and antibiotic- treated OP50.  Day 3 adult animals were washed twice in S basal, and transferred to a 24 well plate containing 1 ml cold- and antibiotic- arrested OP50 at different concentrations (AL OD = 3; DR OD = 0.1). 10–20 worms were placed in each well.

tag: treatment

value: DR

tag: biological replicate

value: day 6 adult


title: C51; single cell

description:
FGC0930_s_1_TAGGCATGTAGATCGC.fastq
FGC0930_s_2_TAGGCATGTAGATCGC.fastq

tag: strain


title: C60; single cell

description:
FGC0930_s_1_GTAGAGGACTCTCTAT.fastq
FGC0930_s_2_GTAGAGGACTCTCTAT.fastq


title: C49; single cell

description:
FGC0930_s_1_TCCTGAGCTAGATCGC.fastq
FGC0930_s_2_TCCTGAGCTAGATCGC.fastq


title: C47; single cell

description:
FGC0930_s_1_CAGAGAGGCTAAGCCT.fastq
FGC0930_s_2_CAGAGAGGCTAAGCCT.fastq


title: C45; single cell

description:
FGC0930_s_1_AGGCAGAACTAAGCCT.fastq
FGC0930_s_2_AGGCAGAACTAAGCCT.fastq


title: C73; single cell

description:
FGC0930_s_1_TAGGCATGGTAAGGAG.fastq
FGC0930_s_2_TAGGCATGGTAAGGAG.fastq


title: sek-1(km4) DR (replicate 2)

description: matrixWZY.csv


title: C43; single cell

description:
FGC0930_s_1_TAAGGCGACTAAGCCT.fastq
FGC0930_s_2_TAAGGCGACTAAGCCT.fastq


title: sek-1(km4) DR (replicate 1)

description: matrixWZY.csv


title: C72; single cell

description:
FGC0930_s_1_GTAGAGGAAGAGTAGA.fastq
FGC0930_s_2_GTAGAGGAAGAGTAGA.fastq


title: C46; single cell

description:
FGC0930_s_1_CTCTCTACCTAAGCCT.fastq
FGC0930_s_2_CTCTCTACCTAAGCCT.fastq


title: sek-1(km4) AL (replicate 3)

description: matrixWZY.csv

value: AL


title: sek-1(km4) AL (replicate 2)

description: matrixWZY.csv


title: C41; single cell

description:
FGC0930_s_1_CAGAGAGGAAGGAGTA.fastq
FGC0930_s_2_CAGAGAGGAAGGAGTA.fastq


title: C40; single cell

description:
FGC0930_s_1_CTCTCTACAAGGAGTA.fastq
FGC0930_s_2_CTCTCTACAAGGAGTA.fastq


title: C55; single cell

description:
FGC0930_s_1_TCCTGAGCCTCTCTAT.fastq
FGC0930_s_2_TCCTGAGCCTCTCTAT.fastq


title: C39; single cell

description:
FGC0930_s_1_AGGCAGAAAAGGAGTA.fastq
FGC0930_s_2_AGGCAGAAAAGGAGTA.fastq


title: C4; single cell

description:
FGC0930_s_1_GCTACGCTTAGATCGC.fastq
FGC0930_s_2_GCTACGCTTAGATCGC.fastq


title: C69; single cell

description:
FGC0930_s_1_TAGGCATGAGAGTAGA.fastq
FGC0930_s_2_TAGGCATGAGAGTAGA.fastq


title: C38; single cell

description:
FGC0930_s_1_CGTACTAGAAGGAGTA.fastq
FGC0930_s_2_CGTACTAGAAGGAGTA.fastq


title: C36; single cell

description:
FGC0930_s_1_GCTACGCTACTGCATA.fastq
FGC0930_s_2_GCTACGCTACTGCATA.fastq


title: N2 DR (replicate 2)

description: matrixWZY.csv


title: N2 DR (replicate 3)

description: matrixWZY.csv


title: C34; single cell

description:
FGC0930_s_1_CTCTCTACACTGCATA.fastq
FGC0930_s_2_CTCTCTACACTGCATA.fastq


title: C35; single cell

description:
FGC0930_s_1_CAGAGAGGACTGCATA.fastq
FGC0930_s_2_CAGAGAGGACTGCATA.fastq


title: C37; single cell

description:
FGC0930_s_1_TAAGGCGAAAGGAGTA.fastq
FGC0930_s_2_TAAGGCGAAAGGAGTA.fastq


title: N2 DR (replicate 1)

description: matrixWZY.csv


title: C3; single cell

description:
FGC0930_s_1_TAAGGCGATAGATCGC.fastq
FGC0930_s_2_TAAGGCGATAGATCGC.fastq


title: N2 AL (replicate 3)

description: matrixWZY.csv


title: C31; single cell

description:
FGC0930_s_1_TAAGGCGAACTGCATA.fastq
FGC0930_s_2_TAAGGCGAACTGCATA.fastq


title: N2 AL (replicate 1)

description: matrixWZY.csv


title: C30; single cell

description:
FGC0930_s_1_GCTACGCTGTAAGGAG.fastq
FGC0930_s_2_GCTACGCTGTAAGGAG.fastq


title: C28; single cell

description:
FGC0930_s_1_CTCTCTACGTAAGGAG.fastq
FGC0930_s_2_CTCTCTACGTAAGGAG.fastq


title: C25; single cell

description:
FGC0930_s_1_TAAGGCGAGTAAGGAG.fastq
FGC0930_s_2_TAAGGCGAGTAAGGAG.fastq


title: N2 AL (replicate 2)

description: matrixWZY.csv


title: C29; single cell

description:
FGC0930_s_1_CAGAGAGGGTAAGGAG.fastq
FGC0930_s_2_CAGAGAGGGTAAGGAG.fastq


title: C24; single cell

description:
FGC0930_s_1_CTCTCTACAGAGTAGA.fastq
FGC0930_s_2_CTCTCTACAGAGTAGA.fastq


title: C42; single cell

description:
FGC0930_s_1_GCTACGCTAAGGAGTA.fastq
FGC0930_s_2_GCTACGCTAAGGAGTA.fastq


title: sek-1(km4) AL (replicate 1)

description: matrixWZY.csv


title: C21; single cell

description:
FGC0930_s_1_TAAGGCGAAGAGTAGA.fastq
FGC0930_s_2_TAAGGCGAAGAGTAGA.fastq


title: C22; single cell

description:
FGC0930_s_1_GCTACGCTAGAGTAGA.fastq
FGC0930_s_2_GCTACGCTAGAGTAGA.fastq


title: iDeptor

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

institute: Italian National Cancer Institute "Regina Elena"

data_processing:
Base-calling and quality-control was performed using the Illumina BCL2FASTQ software.
RNA-seq was analyzed via the web pipeline RAP, which employs the Tuxedo suite for mapping (Tophat) and transcripts reconstruction (Cufflinks, Cuffdiff)
genome build: hg19
processed data files format and content: FPKM

extract_protocol:
total RNA was extracted from KMS27 cells using Qiazol (Invitrogen), purified from genomic DNA contamination through a DNase I (Qiagen) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and by Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.
RNA libraries for sequencing were generated in triplicate according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, Inc., San Diego, CA, US). Starting material was 500ng of total RNA.

value: Multiple Myeloma cells

tag: sirna

value: siDEPTOR


title: CN

value: siRNA control


title: C20; single cell

description:
FGC0930_s_1_CGTACTAGAGAGTAGA.fastq
FGC0930_s_2_CGTACTAGAGAGTAGA.fastq


title: C2; single cell

description:
FGC0930_s_1_CGTACTAGTAGATCGC.fastq
FGC0930_s_2_CGTACTAGTAGATCGC.fastq


title: C19; single cell

description:
FGC0930_s_1_AGGCAGAAAGAGTAGA.fastq
FGC0930_s_2_AGGCAGAAAGAGTAGA.fastq


title: C18; single cell

description:
FGC0930_s_1_CTCTCTACTATCCTCT.fastq
FGC0930_s_2_CTCTCTACTATCCTCT.fastq


title: C33; single cell

description:
FGC0930_s_1_AGGCAGAAACTGCATA.fastq
FGC0930_s_2_AGGCAGAAACTGCATA.fastq


title: C17; single cell

description:
FGC0930_s_1_CAGAGAGGTATCCTCT.fastq
FGC0930_s_2_CAGAGAGGTATCCTCT.fastq


title: C16; single cell

description:
FGC0930_s_1_GCTACGCTTATCCTCT.fastq
FGC0930_s_2_GCTACGCTTATCCTCT.fastq


title: C32; single cell

description:
FGC0930_s_1_CGTACTAGACTGCATA.fastq
FGC0930_s_2_CGTACTAGACTGCATA.fastq


title: sample 1 of 6-week age Cherry Valley Pekin duck

city: Beijing

first: Liyuan

last: Wang

state: China

address: No.2 of Yuanmingyuan West Road, Haidian District

department: Animal Sciencie and Technology

institute: China Agricultura University

data_processing:
Quality control through Phred score, GC content, and filtering of raw data
Reads mapping to the reference genome using TopHat2
Quantification of gene expression level was evaluated by RPKM in Htseq
Differential expression analysis using DEseq2
GO and KEGG enrichment analysis of differentially expressed genes using GOseq and KOBAS (2.0)
Genome_build: BGI_duck_1.0
Supplementary_files_format_and_content: Distribution of FPKM in BD3, BD6, CD3, and CD6

organism: Anas platyrhynchos

source_name: 6-week age Cherry Valley Pekin duck

growth_protocol: Grow healthy before slaughter

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Cherry Valley Pekin

value: breast muscle

value: 6-weeks old


title: sample 2 of 6-week age Cherry Valley Pekin duck


title: C14; single cell

description:
FGC0930_s_1_CGTACTAGTATCCTCT.fastq
FGC0930_s_2_CGTACTAGTATCCTCT.fastq

value: pancreata

value: embryonic day e13.5


title: C15; single cell

description:
FGC0930_s_1_TAAGGCGATATCCTCT.fastq
FGC0930_s_2_TAAGGCGATATCCTCT.fastq


title: sample 2 of 6-week age native Pekin duck

source_name: 6-week age native Pekin duck

value: native Pekin


title: C13; single cell

description:
FGC0930_s_1_AGGCAGAATATCCTCT.fastq
FGC0930_s_2_AGGCAGAATATCCTCT.fastq


title: C12; single cell

description:
FGC0930_s_1_CTCTCTACCTCTCTAT.fastq
FGC0930_s_2_CTCTCTACCTCTCTAT.fastq


title: sample 1 of 3-week age Cherry Valley Pekin duck

source_name: 3-week age Cherry Valley Pekin duck

value: 3-weeks old


title: sample 1 of 6-week age native Pekin duck


title: sample 2 of 3-week age native Pekin duck

source_name: 3-week age native Pekin duck


title: C1; single cell

description:
FGC0930_s_1_AGGCAGAATAGATCGC.fastq
FGC0930_s_2_AGGCAGAATAGATCGC.fastq


title: RICCexpt3-0gy-lib3

status: Public on Dec 26 2016

city: Stanford

first: William

middle: J

last: Greenleaf

state: CA

address: 279 Campus Drive, Beckman Center B257

department: Genetics

institute: Stanford University

description:
No-irradiation cell control
ctcfbjocc_expt3_0gy_vplot.dat
ctcfbjunocc_expt3_0gy_vplot.dat
tsspluscage_expt3_0gy_vplot.dat
tssnoatac_expt3_0gy_vplot.dat

data_processing:
Adapter sequences were trimmed using a custom Python script that aligns Read 1 and Read 2 to each other.
Paired-end alignment was performed on hg19 using bowtie2 with parameters "-X 2000 -p18".
Reads were filtered for all scaffolds except chromosomes 1-22 and X.
Reads were filtered for mapping quality with a threshold of 30 using samtools 0.1.19 and for reads falling within ENCODE DAC and Duke blacklists using bedtools 2.20.1.
Duplicates were removed with Picard tools (version 1.117) MarkDuplicates.
Simple histograms were generated with Picard Tools Collect Insert Size Metrics (version 1.117).
Technical replicates were pooled (for most downstream analysis) as BAM files using samtools 0.1.19.
V-plots were generated using custom python code using PySam version 0.8.3.
Fragment length histograms were calculated within windows tiling the genome in using custom Python code using PySam version 0.8.3.
Histograms were background-subtracted (with background quantified in 0 Gy samples) and normalized against GC-content matched regions using custom MATLAB code (version 2013a). A further normalization was done by dividing each enrichment trace from the 300 gy sample by its corresponding enrichment trace from the same window in the 300 gy lysed dechromatinized DNA sample.  These dechromatinized DNA traces were smoothed with a 30 bp sliding window to compensate for lower sequencing coverage.
Biological histogram data was merged from the first two (higher quality) biological replicates to boost sequencing coverage per window.
Window histograms were clustered using k-means and then PCA was run on cluster averages using MATLAB (version 2013a).
The first principal component of variation was compared with the fragment length fold enrichment (normalized histogram ratio) in sliding windows across the genome to create a track of PC1 similarity score (using custom code in MATLAB version 2013a and the same custom python code to analyze window histograms).
genome build: hg19
processed data files format and content: Processed data file (1) (*.pc1dotproduct.*) is a hg19 genome track of principal component 1 similarity score calculated in 0.3 Mb windows sliding by 60kb.  This signal represents the compaction level of chromatin in tri-nucleosome units (arising from stacking of alternating nucleosomes). It is positive in open chromatin and negative in compacted chromatin  File format for both is bigwig.
processed data files format and content: Processed data file (2) (*.numfrags.*) is a track of RICC-seq filtered fragment counts within 0.3 Mb windows sliding by 60kb.  File format is bigwig.
processed data files format and content: Processed data files *.log are insert size histograms generated by PicardTools from BAM files. Format is tab delimited text with headers with two columns: insert size and counts. The log files contain insert size histograms from shallowly sequenced data sets which were used as a control in the case of Samples 24/25 and as an exploratory experiment to test whether the method can capture longer fragments with size selection (Samples 26-29).  The figures in the paper just show the insert size histograms (24/25), or the histograms with a fitted and then subtracted baseline (26-29). There wasn't any further processing for those libraries because they weren't deep enough to support the other analyses in the pipeline. The histogram captures the information we needed from those experiments.
processed data files format and content: Processed data files ctcf*vplot.dat are tab-delimited text files containing a matrix with 1000 rows and 2000 columns representing a V-plot around occupied or unoccupied (based on ENCODE CTCF ChIP) CTCF motifs. Matrix rows represent fragment lengths (length = zero-based row index) and matrix columns represent relative base pair positions around the CTCF motif, which is at the center column of each matrix.
processed data files format and content: Processed data files tssf*vplot.dat are tab-delimited text files containing a matrix with 1000 rows and 2000 columns representing a V-plot around active transcription start sites determined using RefGene and  ENCODE RNA-CAGE data or around inactive transcription start sites determined via a lack of an ATAC-seq peak (from ATAC-seq peaks called in pooled BJ ATAC data, file BJatac2pooled.peaks.bed) at the TSS. Matrix rows  (length = zero-based row index) represent fragment lengths and matrix columns represent relative base pair positions around the RefGene TSS which is at the center column of each matrix.

source_name: Neonatal foreskin

growth_protocol: Cells were grown in EMEM media (ATCC) supplemented with 10% Heat-inactivated Fetal Bovine Serum and 100 U/mL penicillin-streptomycin in T175 flasks. They were harvested at 80% confluence by incubation with Accutase and washed in cold PBS, with centrifugation for 5 min at 500 x g to collect cells prior to lysis.

extract_protocol:
Cells were lysed in agarose plugs by incubating with 0.4M EDTA pH 8.0, 2% (w/v) Sarkosyl, 0.5 mg/mL Proteinase K at 50˚C for 24-48 hours, then washed 3x with TE(10 mM Tris, 1 mM EDTA, pH 8), for 1 hour each wash at room temperature), 2x with TE containing 0.1 mg/mL RNase A at 37˚C, and 2x with TE at room temperature.
Agarose-embedded genomic DNA was treated with shrimp alkaline phosphatase, then the enzyme was inactivated with lysis buffer (0.4M EDTA pH 8, 2% (w/v) Sarkosyl, 0.5 mg/mL Proteinase K) at 50˚C for 18 hours. Samples were washed 5x with TE at room temperature, then treated with ~0.4 U/µL T4 polynucleotide kinase in 70 mM Tris, 10 mM MgCl2, 5 mM DTT, 1 mM spermidine and 5 µM ATP for 30 min at 37˚C, and washed 4x with TE.  ssDNA fragments were eluted from agarose plugs by passive diffusion into TE following thermal denaturation at 95˚C and an ice quench. A truncated version of Illumina TruSeq adapters with random hexamer overhangs were ligated to concentrated ssDNA fragments using T4 DNA ligase (50 pmol each adapter per ssDNA from 1.5 million cells). After removing excess adapters, the resulting library was made double stranded using Taq-B polymerase (Enzymatics), size selected on an agarose gel, amplified and barcoded via PCR, and size selected again on an agarose gel.

treatment_protocol: Cells were embedded in agarose and gamma-irradiated in cold PBS. Control samples were lysed and washed (see extract protocol) prior to irradiation.

value: human foreskin fibroblast

value: BJ

tag: passages

tag: pre-processing

value: Embedded in agarose

tag: radiation dose

value: 0 Gy


title: sample 1 of 3-week age native Pekin duck


title: RICCexpt3-0gy-lib1


title: RICCexpt3-300lys-lib2

description:
Dechromatinized DNA (lysed cell) control
ctcfbjocc_expt3_300lys_vplot.dat
ctcfbjunocc_expt3_300lys_vplot.dat
tsspluscage_expt3_300lys_vplot.dat
tssnoatac_expt3_300lys_vplot.dat

value: Embedded in agarose, lysed and digested protein & RNA, washed.


title: RICCexpt3-0gy-lib2


title: WT-MBP-mRNA-Seq

first: Chenjiang

last: You

address: 2005 Songhu Rd

institute: Fudan University

description:
Exon.RPM.txt.gz
5UTR.RPM.txt.gz
3UTR.RPM.txt.gz

data_processing:
Raw reads were processed by first trimming polyA tails (≥9 nt)  using custom Perl script. Reads without polyA tails (Ribo-Seq) or less than 18 nucleotides after trimming were discarded from further analysis.
Trimmed reads were collapsed into unique reads prior to genome alignment using Tophat 2.0 with default parameters (Trapnell et al., 2012)
Files containing genomic coordinates (e.g., 5’ UTR, exon, intron) were obtained from the TAIR website (www.arabidopsis.org). Reads were associated with a genomic feature using bedtools v2.23.0 (Quinlan and Hall, 2010) with overlap ≥ 80%.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Files containing RPM values of each gene feature and the associated library

organism: Arabidopsis thaliana

source_name: 13-day old seedlings

growth_protocol: 13-day-old seedlings grown on ½ Murashige and Skoog (MS) plates under 16h light/8h dark cycle

extract_protocol:
RNA was extracted with TRI Reagent (MRC)
Membrane bound polysomes (MBP) were isolated as described (Li et al. 2013). MBP was digested with RNase I (Ambion) and the digestion product was centrifuged in a 15-50% sucrose density gradient. A gradient fractionation system (ISCO) was used to collect the monosome fraction. Monosomal RNA was extracted and resolved on 15% Urea-PAGE. 23-35 nt RNAs were recovered from the gel and phosphorylated by T4 polynucleotide kinase (NEB) and polyadenylated with polyA polymerase (NEB) and reverse transcribed with oligodT linkerM followed by cDNA circularization with CircLigase (Epicenter). rRNAs were removed by hybridization with biotin-conjugated DNA probes followed by capture with Dynabead M-280 Stretavidin (Invitrogen). The remaining cDNA were subjected to library construction following the NEBNext Library Prep kit (NEB).

tag: cell fraction

value: Membrane bound polysome (MBP)

tag: genotype

value: WT


title: WT-MBP-Ribo-Seq

data_processing:
Library strategy: Ribo-seq
Raw reads were processed by first trimming polyA tails (≥9 nt)  using custom Perl script. Reads without polyA tails (Ribo-Seq) or less than 18 nucleotides after trimming were discarded from further analysis.
Trimmed reads were collapsed into unique reads prior to genome alignment using Tophat 2.0 with default parameters (Trapnell et al., 2012)
Files containing genomic coordinates (e.g., 5’ UTR, exon, intron) were obtained from the TAIR website (www.arabidopsis.org). Reads were associated with a genomic feature using bedtools v2.23.0 (Quinlan and Hall, 2010) with overlap ≥ 80%.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Files containing RPM values of each gene feature and the associated library


title: RICCexpt3-300lys-lib1

tag: cell line


title: RICCexpt3-300gy-lib7

description:
Main RICC-seq sample
ctcfbjocc_expt3_300gy_vplot.dat
ctcfbjunocc_expt3_300gy_vplot.dat
tsspluscage_expt3_300gy_vplot.dat
tssnoatac_expt3_300gy_vplot.dat


title: RICCexpt3-300gy-lib6


title: RICCexpt3-300gy-lib5


title: RICCexpt3-300gy-lib4


title: RICCexpt3-300gy-lib3


title: RICCexpt3-300gy-lib1


title: RICCexpt3-300gy-lib2


title: RICCexpt2-0gy-lib1

description:
No-irradiation cell control
ctcfbjocc_expt2_0gy_vplot.dat
ctcfbjunocc_expt2_0gy_vplot.dat
tsspluscage_expt2_0gy_vplot.dat
tssnoatac_expt2_0gy_vplot.dat
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw

value: human foreskin fibroblast (hTERT immortalized)


title: sample 2 of 3-week age Cherry Valley Pekin duck


title: RICCexpt2-0gy-lib2


title: C11; single cell

description:
FGC0930_s_1_CAGAGAGGCTCTCTAT.fastq
FGC0930_s_2_CAGAGAGGCTCTCTAT.fastq


title: RICCexpt1-0gy-lib2

description:
No-irradiation cell control
ctcfbjocc_expt1_0gy_vplot.dat
ctcfbjunocc_expt1_0gy_vplot.dat
tsspluscage_expt1_0gy_vplot.dat
tssnoatac_expt1_0gy_vplot.dat
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw


title: RICCexpt2-300lys-lib1

description:
Dechromatinized DNA (lysed cell) control
ctcfbjocc_expt2_300lys_vplot.dat
ctcfbjunocc_expt2_300lys_vplot.dat
tsspluscage_expt2_300lys_vplot.dat
tssnoatac_expt2_300lys_vplot.dat
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw


title: RICCexpt2-300gy-lib2

description:
Main RICC-seq sample
ctcfbjocc_expt2_300gy_vplot.dat
ctcfbjunocc_expt2_300gy_vplot.dat
tsspluscage_expt2_300gy_vplot.dat
tssnoatac_expt2_300gy_vplot.dat
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw


title: RICCexpt1-0gy-lib1


title: RICCexpt1-300lys-lib1

description:
Dechromatinized DNA (lysed cell) control
ctcfbjocc_expt1_300lys_vplot.dat
ctcfbjunocc_expt1_300lys_vplot.dat
tsspluscage_expt1_300lys_vplot.dat
tssnoatac_expt1_300lys_vplot.dat
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw


title: RICCexpt1-300lys-lib2


title: RICCSizeSel-300lys

description: Dechromatinized DNA (lysed cell) control


title: RICCSizeSel-300gy-lib2

description: Main RICC-seq sample


title: RICCexpt1-300gy-lib2

description:
Main RICC-seq sample
ctcfbjocc_expt1_300gy_vplot.dat
ctcfbjunocc_expt1_300gy_vplot.dat
tsspluscage_expt1_300gy_vplot.dat
tssnoatac_expt1_300gy_vplot.dat
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw
PCScore_win300kbsliding60kb_Smooth30Range50to500_combined.pc1dotproduct.st.fix.bw


title: RICCexpt1-300gy-lib1


title: RICCSizeSel-300gy-lib1

description: Main RICC-seq sample


title: RICCXlink-300gy

description: Main RICC-seq sample

value: Crosslinked with EGS, then 1% formaldehyde, then embedded in agarose.


title: BJATAClib7

description: cultured cells used to prepare ATAC-seq library for nucleosome calling and open chromatin mapping

data_processing:
Library strategy: ATAC-seq
Adapter sequences were trimmed using a custom Python script that aligns Read 1 and Read 2 to each other.
Paired-end alignment was performed on hg19 using bowtie2 with parameters "-X 2000 -p18".
Reads were filtered for all scaffolds except chromosomes 1-22 and X.
Reads were filtered for mapping quality with a threshold of 30 using samtools 0.1.19 and for reads falling within ENCODE DAC and Duke blacklists using bedtools 2.20.1.
Duplicates were removed with Picard tools (version 1.117) MarkDuplicates.
Technical replicates were pooled as BAM files using samtools 0.1.19.
Broad peaks were called using MACS2 (version 2.1.0.20140616) using parameters "--nomodel --nolambda --keep-dup all --broad --call-summits -slocal 10000"
Peaks were extended by 120 bp on both sides, filtered to remove peaks of less than 500 bp, then merged peaks within 120 bp using bedtools (version 2.20.1).
Nucleosomes were then called within these peaks using NucleoATAC using default parameters (Schep et al., Genome Research 2015).
ATAC-seq insertions were calculated over the genome and converted to a bigwig file using UCSC tool bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: .bw file is a bigwig file containing ATAC-seq insertion density.
Supplementary_files_format_and_content: BJatac2pooled.peaks.bed file is a BED file containing MACS2 called broad peaks after extension, filtering and merging.
Supplementary_files_format_and_content: BJatacNucCalls_DefaultParams.nucpos.occscore.bed file is a BED file of nucleosome calls with the occupancy score in column 5

extract_protocol:
Simultaneously lysed and transposed with 0.01% w/v digitonin in ATAC-seq transposition reaction.
Libraries were constructed by transposition of permeabilized cells with Illumina Nextera Tn5 transposase that inserts short sequencing adapters.  The transposed DNA was purified using a Qiagen MinElute PCR cleanup kit and overhangs were extended by 5 minute incubation at 72˚C, followed by PCR with barcoding primers to introduce the remaining adapter sequence. i7 barcodes were used for multiplexing (TAAGGCGA, CGTACTAG, AGGCAGAA, TCCTGAGC, GGACTCCT, TAGGCATG, CGAGGCTG, AAGAGGCA).


title: BJATAClib6


title: BJATAClib4


title: BJATAClib3


title: BJATAClib2


title: BJATAClib1


title: tj_BAC_OSC_rep2

city: Vienna

first: Alexander

last: Stark

address: Dr Bohr-Gasse 7

country: Austria

institute: Research Institute for Molecular Pathology (IMP), Vienna Biocenter VBC

description: PCR amplified cDNA (STAP-seq transcript)

data_processing:
library strategy: STAP-Seq
Basecall where performed using Real-Time Analysis (RTA) version 1.12.4.2 or CASAVA 1.9.1
Paired-end STAP-seq reads were trimmed to 44bp, with the first 8bp as the unique molecular barcode identifier. The reads were mapped using the remaining 36bp to dm3 and dp3 (for spike-in controls) genome assemblies using Bowtie 0.12.9 (bowtie -p 4 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa). For paired-end reads that are mapped to the same positions, we collapsed those that have the exact barcodes as well as those with 1bp mismatch, and removed all mapped reads containing N’s in their barcodes. For comparison of focused (BAC) STAP-seq screens in S2 cells, we subsampled all reads at 700,000 reads before mapping and removed fragments outside of the focused regions from analysis. For comparison of BAC STAP-seq screens across cell lines, we subsampled at 300,000 mapped reads.
Genome_build: dm3
Supplementary_files_format_and_content: Processed data file is in plain text. We report for each experimentally-determined TSS the chromosome, the +1 position, the ranking and strand

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells

extract_protocol: Genomic DNA (source: embryos of the sequenced strain: y; cn bw sp) or BAC DNA was isolated, sheared and size selected (~100-250bp). Following the instructions of NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB; cat. no. E7645L) ,Illumina NEBnext Multiplexing Adaptors (NEB; cat. no. E7335 or E7500) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STAP-seq vectors. To construct the STAP-seq vector, the sequence between BglII and FseI from the pGL3-Promoter backbone (Promega; cat. no. E1751) was replaceda ccdB suicide gene flanked by homology arms (used for cloning the promoter candidates during library generation), an intron (mhc16), an ORF (truncated sgGFP, Qbiogene, Inc), followed by the pGL3’s SV40 late polyA-signal. The enhancers were cloned between the KpnI and BglII sites. The control screens were performed with a vector not harboring an enhancer. The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.

value: Ovarian Somatic Cells

tag: experimental procedure

value: STAP-Seq


title: RICCexpt2-300gy-lib1


title: ham_BAC_S2_rep2

source_name: S2 cells

value: S2 cells


title: tj_BAC_OSC_rep1


title: ssp3_BAC_S2_rep2


title: ncm_BAC_S2_rep2


title: sgl_BAC_S2_rep2


title: zfh1_BAC_S2_rep3

description:
PCR amplified cDNA (STAP-seq transcript)
processed data file: zfh1_BAC_eTSS.txt


title: RICCSizeSel-0gy

description: No-irradiation cell control


title: zfh1_BAC_S2_rep2


title: ncm_BAC_S2_rep1

description:
PCR amplified cDNA (STAP-seq transcript)
polyA+ RNA

data_processing:
Library strategy: STAP-seq
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STAP-Seq
Paired-end STAP-seq reads were trimmed to 44bp, with the first 8bp as the unique molecular barcode identifier. The reads were mapped using the remaining 36bp to dm3 and dp3 (for spike-in controls) genome assemblies using Bowtie 0.12.9 (bowtie -p 4 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa). For paired-end reads that are mapped to the same positions, we collapsed those that have the exact barcodes as well as those with 1bp mismatch, and removed all mapped reads containing N’s in their barcodes. For focused STAP-seq screens, we subsampled all reads at 700,000 reads before mapping and removed fragments outside of the focused regions from analysis.
Genome_build: dm3
Supplementary_files_format_and_content: Processed data file is in plain text. We report for each eTSS the chromosome, the +1 position, the core promoter strength, and p-value.
Analyses on Samples sgl, ham, ncm and ssp3_BAC were based on zfh1_BAC_eTSS.txt in the manuscript, and hence no corresponding files are generated.

source_name: STAP-seq screen using ncm enhancer, with library derived from BAC fragments


title: ctrl_BAC_S2_rep1

description:
PCR amplified cDNA (STAP-seq transcript)
polyA+ RNA
zfh1_BAC_eTSS.txt

source_name: STAP-seq screen using no enhancer, with library derived from BAC fragments


title: sgl_BAC_S2_rep1

source_name: STAP-seq screen using sgl enhancer, with library derived from BAC fragments


title: RICCLive-300gy

description: Main RICC-seq sample


title: ctrl_genome-wide_rep1

description:
PCR amplified cDNA (STAP-seq transcript)
polyA+ RNA
zfh1_genome-wide_eTSS.txt

source_name: STAP-seq screen using no enhancer, with library derived from genome-wide Drosophila melanogaster fragments


title: zfh1_BAC_S2_rep1

source_name: STAP-seq screen using zfh1 enhancer, with library derived from BAC fragments


title: ctrl_genome-wide_rep2


title: ham_BAC_S2_rep1

source_name: STAP-seq screen using ham enhancer, with library derived from BAC fragments


title: zfh1_genome-wide_rep1

source_name: STAP-seq screen using zfh1 enhancer, with library derived from genome-wide Drosophila melanogaster fragments


title: zfh1_genome-wide_rep2


title: BJATAClib8


title: BJATAClib5


title: MIX_31_JLW8_BR2

city: Seattle

first: Sascha

last: Krause

state: Washington

address: 616 NE Northlake Place

department: Microbiology

institute: University of Washington

data_processing:
raw reads were aligned to the combined isolate genomes, as appropriate for each sample, using BWA version 0.7.12-r1044 with default parameters
The alignments were post-processed into sorted BAM files with SAMTools version 1.2-232-g87cdc4a
Reads were attributed to open reading frames (ORFs) using the htseq-count tool from the ‘HTSeq’ framework version 0.5.4p5 in the ‘intersection-nonempty’ mode
Differential abundance analysis was performed with DESeq2 1.2.10 using R 3.2.4
Genome_build: Genebank: JQMG00000000, JUHH01000001, JPOH00000000
Supplementary_files_format_and_content: tab-delimited text files include DESeq raw counts for differernt organisms in pure and mixed culture
Supplementary_files_format_and_content: 001_methanotroph_count: MB_31_BR1, First biological replicate of Methylobacter 31/32 pure culture; MB_31_BR2, Second biological replicate of Methylobacter 31/32 pure culture; MIX_31_13_BR1, First biological replicate of Methylobacter 31/32 and Methylotenera #13 co-culture; MIX_31_13_BR2, Second biological replicate of Methylobacter 31/32 and Methylotenera #13 co-culture; MIX_31_JLW8_BR1, First biological replicate of Methylobacter 31/32 and Methylotenera JLW8 co-culture; MIX_31_JLW8_BR2, Second biological replicate of Methylobacter 31/32 and Methylotenera JLW8 co-culture.
Supplementary_files_format_and_content: 001_nonmethanotroph_MT13: MIX_31_JLW8_BR1, First biological replicate of Methylotenera #13 pure culture; MIX_31_JLW8_BR2, Second biological replicate of Methylotenera #13 pure culture; MT_JLW8_BR1, First biological replicate of Methylobacter 31/32 and Methylotenera #13 co-culture; MT_JLW8_BR2, Second biological replicate of Methylobacter 31/32 and Methylotenera #13 co-culture
Supplementary_files_format_and_content: 001_nonmethanotroph_MTJLW8: MIX_31_JLW8_BR1, First biological replicate of Methylotenera JLW8 pure culture; MIX_31_JLW8_BR2, Second biological replicate of Methylotenera JLW8 pure culture; MT_JLW8_BR1, First biological replicate of Methylobacter 31/32 and Methylotenera JLW8 co-culture; MT_JLW8_BR2, Second biological replicate of Methylobacter 31/32 and Methylotenera JLW8 co-culture

organism:
Methylobacter tundripaludum
Methylotenera mobilis

source_name: bacterial meta-transcriptome

growth_protocol: M. tundripaludum 31/32 was pre-grown in nitrate mineral salt (NMS) medium, 30 µM lanthanum chloride and 25 % methane, 5 % air and 70 % nitrogen in the headspace. Methylotenera strains were pre-grown in the same way but with 0.1% methanol instead. We established co-cultures and controls in duplicates or triplicates in autoclaved vials in NMS medium. Different strains were  mixed together in equal starting densities (107 cells per ml). All vials were sealed with rubber stoppers and capped with crimp seals. The headspace was exchanged daily according to the following scheme: (1) Flushing with N2 gas for 30 sec (flow rate > 1.28 L/min), (2) Equalizing pressure, by removing the excess volume of N2 gas with a syringe, (3) Removing 60 ml of headspace and adding back 50 ml of methane and 10 ml of air, corresponding to an initial dissolved O2 concentration of approximately 15 µM. All vials were incubated in a shaker (200 RPM) at 18 °C.

extract_protocol:
RNA was extracted from co-cultures and pure cultures grown with and without lanthanum. Cells were grown to an optical density 600 of approximately 0.5 for extracting RNA. We followed the procedure described earlier Chu et al 2016 Journal of Bacteriology with the following exception: we used the MPBio FastPrep® Lysing E matrix tubes. The purified RNA was tested for DNA contamination using 16S PCR. Afterwards, samples were stored at -80°C for subsequent analyses.
RNA was submitted for transcriptomics analysis to GENEWIZ (Seattle, USA). 1 x 50 bp were sequenced in single-read configuration in Rapid Run mode on a HiSeq 2500 System.

tag: culture

value: M. tundripaludum + M. mobilis JLW8

tag: agent

value: 25% (v/v) methane added


title: MIX_31_13_BR2

value: M. tundripaludum + M. mobilis #13


title: MIX_31_JLW8_BR1


title: MT_JLW8_BR1

organism: Methylotenera mobilis

source_name: bacterial transcriptome

value: Methylotenera mobilis JLW8

value: 0.1% (v/v) methanol added


title: MT_JLW8_BR2


title: MT_13_BR2

value: Methylotenera mobilis #13


title: MIX_31_13_BR1


title: MB_31_BR2

organism: Methylobacter tundripaludum

value: Methylobacter trundripaludum 31/32


title: MT_13_BR1


title: ssp3_BAC_S2_rep1

source_name: STAP-seq screen using ssp3 enhancer, with library derived from BAC fragments


title: MB_31_BR1


title: rough microsome fraction

status: Public on Dec 25 2016

city: Kyoto city

first: Takanari

last: Umegawachi

state: Kyoto

address: Sakyo-ku

institute: Kyoto Institute of Technology

data_processing:
The deep sequencing data were mapped to the reference D. melanogaster genome sequence (UCSC version dm3) by the TopHat (Kim D et al., 2013) program version 1.3.2 with default parameters.
The Cufflinks (Trapnell C et al., 2013) program version 2.0.0 was then used to assemble transcripts and to calculate fragments per kilobase of transcript per million mapped fragments (FPKM) with option ‘-library-type fr-secondstrand’.
Genome_build: UCSC dm3

source_name: macrophage-like cells

growth_protocol: S2-DRSC cells were maintained at 25˚C in Schneider's Drosophila medium supplemented with 10% fetal bovine serum.

extract_protocol:
After fractionation, total RNAs were isolated using Trizol reagent.
Isolated RNAs were used for library construction with TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: After homogenization of S2-DRSC cell, cell extracts were subject to the sedimental centrifugation and sucrose density gradient centrifugation to fractionate rough microsome (RM) and cytoplasm (C) fractions. The RM fraction was separated into naked microsome (NM) and stripped ribosome (SR) fractions by centrifugation following treatment with EDTA and puromycin in high-salt buffer.

value: S2-DRSC cells


title: naked microsome fraction


title: cytoplasm fraction


title: stripped ribosome fraction


title: C2C12_overexpressed

first: Tingting

last: Li

address: 38 Xueyuan Rd

department: Medical informatics

institute: Peking University

data_processing:
TopHat v1.4.1 default
rpkm values were got by  DEGseq
Genome_build: mm9

source_name: differentiating C2C12 myoblasts - Linc-RAM overexpressed

growth_protocol: C2C12 were cultured in DMEM medium containing 10% FBS, changed for differentiation medium containing 2% HS when the confluence up to 80-85%.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C2C12 cells were infected with lentivirus containing Linc-RAM, sh-Linc-RAM or empty vector, respectively, and selected by blasticidin. The stable cells were cultured in DMEM medium containing 10% FBS, changed for differentiation medium containing 2% HS when the confluence up to 80-85%. RNA were isolated from the differentiating cells (DM12h).


title: C2C12_knocked-down

source_name: differentiating C2C12 myoblasts - Linc-RAM knockdown


title: K562 WT CTCF ChIP

status: Public on Dec 24 2016

city: Cambridge

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Leukemia

growth_protocol: Cells were maintained in 10% FCS RPMI with P/S

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
sonication

value: Leukemia

tag: chip antibody

value: CTCF

tag: antibody manufacturer

value: Millipore

tag: antibody catalog number

tag: system

value: Bone


title: HEK293_H3K27Ac

source_name: Embryonic Kidney (HEK)

growth_protocol: H293T cells were cultured in DMEM + serum at 37°C / 5% CO2

treatment_protocol: normal HEK293T cells

tag: cell type

value: Embryonic Kidney (HEK)

value: Abcam

value: Kidney


title: K562-Input

growth_protocol: Cells were cultured in 10% FCS RPMI with P/S


title: K562 210-delta CTCF ChIP

treatment_protocol: +DOX for 3 days

tag: treatment

value: +DOX 3 days


title: WT1plusKTS cells replicate 1 input

city: Lund

first: Linnea

last: Järvstråt

state: Scania

address: Klinikgatan 26

department: Department of Hematology and Transfusion Medicine

country: Sweden

institute: Lund University

data_processing:
Illumina RTA 1.17.21.3 was used for base-calling
ChIP-seq reads were aligned to hg19 using Bowtie2-2.2.7 with parameters –local –no-unal
Peaks where called using MACS2-2.1.1.20160226 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: BED files with the found peaks

source_name: K562 cell line

growth_protocol: Cultured in RPMI 1640 medium w 10% FBS w 1 mg/ml G418

extract_protocol:
After crosslinking with 1% formaldehyde for 10 minutes, chromatin shearing was done by sonication in a Bioruptor UCD-200 (Diagenode, Liège, Belgium). The resulting lysate was divided into one aliquot for streptavidin capture (the equivalent of 9-10 million cells), another for Histone 3 K4 tri-methylation (H3K4me3; ab 8580, Abcam, Cambridge, UK) immunoprecipitation (the equivalent of 1-2 million cells) and a third aliquot for non-immunoprecipitated lysate to use as input control. The H3K4me3 immunoprecipitation and the input control preparation were done using the MagnaChip kit, according to the manufacturer’s instructions, increasing the reaction volumes to accommodate the input cell number. For the streptavidin capture, Dynabeads M-280 Streptavidin (Invitrogen) were used, according to the manufacturer’s recommendations with minor modifications. Briefly, beads were washed with PBS three times prior to use, 3 mg of beads were used for each sample, incubation was done at room temperature, and washing after incubation was done five times with PBS with 0.1% BSA. After washing, the streptavidin beads were resuspended in Chip Elution Buffer from the MagnaChip kit and all samples proceeded to Proteinase K treatment and DNA purification according to the MagnaChip protocol.
ThruPlex DNA-seq kit (Rubicon Genomics, Ann Arbor, Michigan, USA) according to manufacturer’s recommendations.

treatment_protocol: Stable transfectants w pEF1aBirAv5-neo plasmid

tag: transfections apart from pef1abirav5-neo


title: FB_RNA

city: chengdu

first: li

last: li

state: sichuan

address: wai nan guo xue xiang #37

department: dermatology

institute: west china hospital

data_processing:
The library products were used for sequencing using IlluminaHiSeqTM 2000. By base calling, the original image data produced by the sequencer was transferred into sequences, which were defined as “raw reads”.
Prior to mapping these reads to the reference database, we filtered all sequences to remove adaptor sequences, N sequences (in which the percentage of unknown bases (N) was greater than 10%) and low-quality sequences (the percentages of low quality bases with a quality value ≤ 5 was greater than 50% in a read). The remaining reads were mapped to the mice genome using SOAPaligner/SOAP2
The gene expression level was calculated by using RPKM (Reads Per Kb per Million reads) method.
Software for functional annotation was BLAST(2.2.23) and Blast2GO(2.2.5).
Software for expression pattern analysis was Cluster (3.0) and Java Tree View (1.1.6r2).
Genome_build: mm9
Supplementary_files_format_and_content: files contain statistics of mapped reads, RPKM values for 2 samples, all genes with different expression and list of genes with different expression between 2 samples. SVG files show distribution of reads on reference genes, sequencing saturation analysis results and distribution of reads sequencing quality.

source_name: fibroblasts

growth_protocol: SKPs were cultured in proliferation medium (DMEM/F12 (3:1) containing 0.1% penicillin/streptomycin, 40 ng/ml FGF2 (Collaborative, USA), 20 ng/ml EGF (Collaborative, USA) and 2% B27 supplement (Invitrogen, USA)) at a 37°C incubator.Fibroblasts were cultured in DMEM containing 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent.The total RNA was firstly treated with DNase I to degrade DNA contamination. Then the mRNA was enriched by using oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: BALB/c

tag: tissue

value: dermis

tag: age

value: post natal day 3

value: fibroblast


title: SKP_RNA

source_name: skin derived precursors

value: post natal day 4

value: skin-derived precursor


title: NoTagged replicate 2 input


title: WT1plusKTS cells replicate 3 input


title: NoTagged replicate 3 input


title: NoTagged replicate 1 input


title: WT1plusKTS cells replicate 2 input


title: WT1plusKTS cells replicate 2 H3K4me3 IP

description: antibody: H3K4me3; ab 8580, Abcam, Cambridge, UK) i


title: WT1plusKTS cells replicate 1 H3K4me3 IP


title: NoTagged replicate 3 Streptavidin


title: C2C12_control

source_name: differentiating C2C12 myoblasts - control


title: NoTagged replicate 2 Streptavidin


title: NoTagged replicate 1 Streptavidin


title: WT1plusKTS cells replicate 3 Streptavidin


title: WT1plusKTS cells replicate 2 Streptavidin


title: WT1plusKTS cells replicate 1 Streptavidin


title: WT1minusKTS cells replicate 3 input


title: HCT116-WT-CTCF

first: Richard

source_name: Colon Carcinoma

growth_protocol: Cells were maintained in 10% FCS DMEM with P/S

value: Colon Carcinoma

value: Colon


title: WT1minusKTS cells replicate 1 H3K4me3 IP


title: WT1minusKTS cells replicate 3 H3K4me3 IP


title: WT1minusKTS cells replicate 1 input


title: WT1minusKTS cells replicate 2 input


title: WT1minusKTS cells replicate 2 H3K4me3 IP


title: WT1minusKTS cells replicate 1 Streptavidin


title: WT1minusKTS cells replicate 2 Streptavidin


title: GFP_H3K4me3_B

city: Davis

first: Gina

middle: Marie

last: Turco

address: University of California, Davis

institute: UC Davis

description: input sample: GFP_INPUT_B

data_processing:
low quality reads were filtered
WGA adaptors were trimmed from biorep A&B before mappings
Bowtie software was used for the mapping to the Arabidopsis TAIR10 reference genome
SICER.SH ran at "redundancy threshold" (1), "window size" (200), "fragment size" (300), "effective genome fraction" (0.85), "gap size" (200), "FDR" (0.01)
Windowbed was used for the identification of the genes affected by the histone modification
Genome_build: Tair 10
Supplementary_files_format_and_content: wig

source_name: GFP positive protoplast (pWOL:GFP marker line)

growth_protocol: Plants were grown under standard conditions at 24ºC in a 16-h light 8-h dark cycle.

extract_protocol:
Root protoplast were prepared as described in (Brady et al., 2007). The MoFlo cell sorter’s electronic configuration was modified to identify intact protoplasts above electronic and sample buffer “noise” levels by choosing a side scatter electronic threshold and by applying logarithmic scaling to the forward angle and side angle 488nm laser light scatter signals.  To collect the GFP positive protoplasts, the green fluorescence of the GFP (530/50 detection filter) was separated from the red fluorescence (emission 670/30) of chlorophyl. Protoplast chromatin was crosslinked with 0.1% formaldehyde for 5 min and the reaction was stopped by adding glycine (0.125M final concentration). The chromatin immunoprecipitation assay performed in this study is a modification of the protocol described in (Bouyer et al., 2011). We used four independent biological replicates (100,000 GFP positive protoplast each) and two antibodies: H3K27me3 (Millipore 07-449) and H3K4me3 (Millipore 07-473).
DNA recovered after ChIP and the input chromatin were both amplified using SeqPlex Enhanced DNA amplification kit (SEQXE – Sigma) for the bioreps 1&2 and GenomePlex Complete (WGA-Sigma) for the bioreps A&B, following the manufacturer’s instructions. Amplified DNA was used to synthesize a barcoded Illumina-compatible library (Kumar et al., 2012). Libraries were pooled and sequenced on the HiSeq2500 50SR. WGA adaptors from bioreps A&B were trimmed before mapping to the refference genome.

value: root

value: FACS treated GFP positive root protoplasts

tag: genetic background/cultivar

value: ColO

value: H3K4me3 (Millipore 07-473)


title: GFP_H3K27me3_B

description: input sample: GFP_INPUT_B

value: H3K27me3 (Millipore 07-449)


title: GFP_INPUT_A


title: GFP_INPUT_B


title: GFP_H3K4me3_A

description: input sample: GFP_INPUT_A


title: HET.18_3

city: Wilrijk (Antwerp)

first: Peter Paul

last: De Deyn

state: Antwerpen

address: universiteitsplein 1

country: Belgium

institute: University of Antwerp

data_processing:
The data was inspected with FASTQC (v0.10.1) and trimmed when necessary with FASTX trimmer
Alignment was performed with STAR (2.3.1l) (Dobin et al., 2013) with 2 mismatches allowed to the ensemble reference genome version 37 of the 1000Genome project.
Data was quantified with HT-Seq count (0.5.4) (Anders et al., 2015)
Genome_build: ensemble reference genome version 37 of the 1000Genome project
Supplementary_files_format_and_content: txt-file containing the HT-Seq count for the individual samples; raw counts of sequencing reads

extract_protocol:
The brain was harvested and dissected on ice into three parts: 2 hemi-forebrains and the cerebellum (olfactory bulbs were discarded). The frozen hemi-forebrains were lysed in QIAzol (Qiagen), followed by total RNA isolation using the RNeasy Lipid Tissue Mini Kit (Qiagen, 74804).
Sequence libraries were generated with the TruSeq RNA sample prep kit V2 (Illumina) using the Sciclone NGS liquid handler (Perkin Elmer).

tag: strain background

tag: genotype/variation

value: heterozygous APP23 (+/-)

value: 18 months

value: brain; Hemi-forebrain


title: WT.24_2

value: Wild type

value: 24 months


title: HET.24_2


title: GFP_H3K27me3_A

description: input sample: GFP_INPUT_A

tag: genotype


title: HET.24_3


title: WT.24_1


title: WT.24_3


title: HET.18_2


title: HET.24_1


title: HET.18_1


title: HET.06_1

value: 6 months


title: WT.18_1


title: HET.06_2


title: WT.18_3


title: WT.18_2


title: HET.06_3


title: HET.02_3

value: 1.5 months


title: WT.06_1


title: WT.06_2


title: HET.02_1


title: WT.06_3


title: HET.02_2


title: WT.02_3


title: WT.02_2


title: WT.02_1


title: HSC 95 rep3 w/ spike

city: New Haven

first: Sherman

last: Weissman

state: CT

address: 1 Gilbert street

institute: Yale University

description:
single-cell RNA-seq in HSC biorep3 w/ RNA spike-in
FPKM_table_single-cell_RNA-seq_HSCspike.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were mapped to the mouse genome (mm9 from UCSC database) by Tophat (v1.3.3) with “–r 100” option
Gene expression values were then calculated by Cufflinks (v1.2.1), using RefSeq genes as reference annotation with “-G” option
RNA-seq reads were also mapped to ArrayControl RNA spikes by bowtie2 (2.2.1) with “--local -D 15 -R 3 -N 1 -L 20 -i S,1,0.50 -k 1" option
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RefSeq gene id, gene symbol, chromosome and FPKM value for each sample

source_name: Hematopoietic stem cells

growth_protocol: Bone Marrow cells from both normal mice and bled mice were isolated from 6-8 weeks C57BL6 mice.

extract_protocol:
Total RNA was isolated by RNeasy mini kit (Qiagen) and Pan et al. 2013 protocol for bulk RNA-seq ;  C1 Fluidigm for mRNA seq protocol for single-cell RNA-seq. For single cell RNA-seq, we also used ArrayControl RNA spikes (Thermo Fisher Cat# AM1780) and prepared RNA spike mixture  following the instruction.
Bulk RNA-seq library preparation was conducted using standard Tru-Seq Illumina kits. Single cell RNA-seq library is constructed by using Nextera XT DNA Library Preparation Kit (96 samples).

treatment_protocol: 18 different populations and HSC and MPP1 populations (both normal and bled mice) for single cell experiment from mouse BM cells were sorted by FACS AriaII (BD Biosciences) from the Yale cell sorter Core Facility.

tag: marker

tag: barcodes

value: TCCTGAGC-TAGATCGC

tag: cell count

tag: well id


title: HSC 96 rep3 w/ spike

value: TCCTGAGC-TATCCTCT


title: HSC 92 rep3 w/ spike

value: TCCTGAGC-CTAAGCCT


title: HSC 94 rep3 w/ spike

value: TCCTGAGC-GTAAGGAG


title: HSC 88 rep3 w/ spike

value: TAGGCATG-TATCCTCT


title: HSC 89 rep3 w/ spike

value: TCCTGAGC-AAGGAGTA


title: HSC 90 rep3 w/ spike

value: TCCTGAGC-ACTGCATA


title: HSC 91 rep3 w/ spike

value: TCCTGAGC-AGAGTAGA


title: HSC 87 rep3 w/ spike

value: TAGGCATG-TAGATCGC


title: HSC 86 rep3 w/ spike

value: TAGGCATG-GTAAGGAG


title: HSC 83 rep3 w/ spike

value: TAGGCATG-AGAGTAGA


title: HSC 78 rep3 w/ spike

value: TAAGGCGA-GTAAGGAG


title: HSC 81 rep3 w/ spike

value: TAGGCATG-AAGGAGTA


title: HSC 79 rep3 w/ spike

value: TAAGGCGA-TAGATCGC


title: HSC 77 rep3 w/ spike

value: TAAGGCGA-CTCTCTAT


title: HSC 80 rep3 w/ spike

value: TAAGGCGA-TATCCTCT


title: HSC 73 rep3 w/ spike

value: TAAGGCGA-AAGGAGTA


title: HSC 75 rep3 w/ spike

value: TAAGGCGA-AGAGTAGA


title: HSC 72 rep3 w/ spike

value: GTAGAGGA-TATCCTCT


title: HSC 69 rep3 w/ spike

value: GTAGAGGA-CTCTCTAT


title: HSC 93 rep3 w/ spike

value: TCCTGAGC-CTCTCTAT


title: HSC 68 rep3 w/ spike

value: GTAGAGGA-CTAAGCCT


title: HSC 71 rep3 w/ spike

value: GTAGAGGA-TAGATCGC


title: HSC 66 rep3 w/ spike

value: GTAGAGGA-ACTGCATA


title: HSC 64 rep3 w/ spike

value: GGACTCCT-TATCCTCT


title: HSC 67 rep3 w/ spike

value: GTAGAGGA-AGAGTAGA


title: HSC 63 rep3 w/ spike

value: GGACTCCT-TAGATCGC


title: HSC 74 rep3 w/ spike

value: TAAGGCGA-ACTGCATA


title: HSC 85 rep3 w/ spike

value: TAGGCATG-CTCTCTAT


title: HSC 62 rep3 w/ spike

value: GGACTCCT-GTAAGGAG


title: HSC 84 rep3 w/ spike

value: TAGGCATG-CTAAGCCT


title: HSC 60 rep3 w/ spike

value: GGACTCCT-CTAAGCCT


title: HSC 58 rep3 w/ spike

value: GGACTCCT-ACTGCATA


title: HSC 59 rep3 w/ spike

value: GGACTCCT-AGAGTAGA


title: HSC 82 rep3 w/ spike

value: TAGGCATG-ACTGCATA


title: HSC 65 rep3 w/ spike

value: GTAGAGGA-AAGGAGTA


title: HSC 56 rep3 w/ spike

value: GCTACGCT-TATCCTCT


title: HSC 57 rep3 w/ spike

value: GGACTCCT-AAGGAGTA


title: HSC 52 rep3 w/ spike

value: GCTACGCT-CTAAGCCT


title: HSC 54 rep3 w/ spike

value: GCTACGCT-GTAAGGAG


title: HSC 55 rep3 w/ spike

value: GCTACGCT-TAGATCGC


title: HSC 53 rep3 w/ spike

value: GCTACGCT-CTCTCTAT


title: HSC 70 rep3 w/ spike

value: GTAGAGGA-GTAAGGAG


title: HSC 76 rep3 w/ spike

value: TAAGGCGA-CTAAGCCT


title: HSC 51 rep3 w/ spike

value: GCTACGCT-AGAGTAGA


title: HSC 48 rep3 w/ spike

value: CTCTCTAC-TATCCTCT


title: HSC 50 rep3 w/ spike

value: GCTACGCT-ACTGCATA


title: HSC 49 rep3 w/ spike

value: GCTACGCT-AAGGAGTA


title: HSC 45 rep3 w/ spike

value: CTCTCTAC-CTCTCTAT


title: HSC 46 rep3 w/ spike

value: CTCTCTAC-GTAAGGAG


title: HSC 47 rep3 w/ spike

value: CTCTCTAC-TAGATCGC


title: HSC 44 rep3 w/ spike

value: CTCTCTAC-CTAAGCCT


title: HSC 40 rep3 w/ spike

value: CGTACTAG-TATCCTCT


title: HSC 39 rep3 w/ spike

value: CGTACTAG-TAGATCGC


title: HSC 61 rep3 w/ spike

value: GGACTCCT-CTCTCTAT


title: HSC 41 rep3 w/ spike

value: CTCTCTAC-AAGGAGTA


title: HSC 38 rep3 w/ spike

value: CGTACTAG-GTAAGGAG


title: HSC 37 rep3 w/ spike

value: CGTACTAG-CTCTCTAT


title: HSC 32 rep3 w/ spike

value: CGAGGCTG-TATCCTCT


title: HSC 42 rep3 w/ spike

value: CTCTCTAC-ACTGCATA


title: HSC 30 rep3 w/ spike

value: CGAGGCTG-GTAAGGAG


title: HSC 36 rep3 w/ spike

value: CGTACTAG-CTAAGCCT


title: HSC 34 rep3 w/ spike

value: CGTACTAG-ACTGCATA


title: HSC 29 rep3 w/ spike

value: CGAGGCTG-CTCTCTAT


title: HSC 31 rep3 w/ spike

value: CGAGGCTG-TAGATCGC


title: HSC 35 rep3 w/ spike

value: CGTACTAG-AGAGTAGA


title: HSC 33 rep3 w/ spike

value: CGTACTAG-AAGGAGTA


title: HSC 28 rep3 w/ spike

value: CGAGGCTG-CTAAGCCT


title: HSC 26 rep3 w/ spike

value: CGAGGCTG-ACTGCATA


title: HSC 27 rep3 w/ spike

value: CGAGGCTG-AGAGTAGA


title: HSC 25 rep3 w/ spike

value: CGAGGCTG-AAGGAGTA


title: HSC 23 rep3 w/ spike

value: CAGAGAGG-TAGATCGC


title: HSC 21 rep3 w/ spike

value: CAGAGAGG-CTCTCTAT


title: HSC 20 rep3 w/ spike

value: CAGAGAGG-CTAAGCCT


title: HSC 24 rep3 w/ spike

value: CAGAGAGG-TATCCTCT


title: HSC 17 rep3 w/ spike

value: CAGAGAGG-AAGGAGTA


title: HSC 16 rep3 w/ spike

value: AGGCAGAA-TATCCTCT


title: HSC 19 rep3 w/ spike

value: CAGAGAGG-AGAGTAGA


title: HSC 18 rep3 w/ spike

value: CAGAGAGG-ACTGCATA


title: HSC 15 rep3 w/ spike

value: AGGCAGAA-TAGATCGC


title: HSC 43 rep3 w/ spike

value: CTCTCTAC-AGAGTAGA


title: HSC 13 rep3 w/ spike

value: AGGCAGAA-CTCTCTAT


title: HSC 14 rep3 w/ spike

value: AGGCAGAA-GTAAGGAG


title: HSC 12 rep3 w/ spike

value: AGGCAGAA-CTAAGCCT


title: HSC 9 rep3 w/ spike

value: AGGCAGAA-AAGGAGTA


title: HSC 10 rep3 w/ spike

value: AGGCAGAA-ACTGCATA


title: HSC 7 rep3 w/ spike

value: AAGAGGCA-TAGATCGC


title: HSC 11 rep3 w/ spike

value: AGGCAGAA-AGAGTAGA


title: HSC 8 rep3 w/ spike

value: AAGAGGCA-TATCCTCT


title: HSC 6 rep3 w/ spike

value: AAGAGGCA-GTAAGGAG


title: HSC 5 rep3 w/ spike

value: AAGAGGCA-CTCTCTAT


title: HSC 1 rep3 w/ spike

value: AAGAGGCA-AAGGAGTA


title: HSC 3 rep3 w/ spike

value: AAGAGGCA-AGAGTAGA


title: HSC 22 rep3 w/ spike

value: CAGAGAGG-GTAAGGAG


title: bled MPP1 95

description: single-cell RNA-seq in bled  MPP1

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were mapped to the mouse genome (mm9 from UCSC database) by Tophat (v1.3.3) with “–r 100” option
Gene expression values were then calculated by Cufflinks (v1.2.1), using RefSeq genes as reference annotation with “-G” option
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RefSeq gene id, gene symbol, chromosome and FPKM value for each sample

source_name: Multipotent precursors 1

extract_protocol:
Total RNA was isolated with Smart-seq protocol for single-cell RNA-seq and Pan et al. 2013 protocol for bulk RNA-seq
library preparation was conducted using standard Tru-Seq Illumina kits.

treatment_protocol: 18 different populations of mouse BM cells were sorted by FACS AriaII (BD Biosciences) from the Yale cell sorter Core Facility.

value: TCCTGAGC-GTAAGGAG


title: bled MPP1 96

description: single-cell RNA-seq in bled  MPP1

value: TCCTGAGC-TATCCTCT


title: bled MPP1 94

description: single-cell RNA-seq in bled  MPP1

value: TCCTGAGC-GCGTAAGA


title: bled MPP1 93

description: single-cell RNA-seq in bled  MPP1

value: TCCTGAGC-CTCTCTAT


title: bled MPP1 91

description: single-cell RNA-seq in bled  MPP1

value: TCCTGAGC-AGAGTAGA


title: bled MPP1 90

description: single-cell RNA-seq in bled  MPP1

value: TCCTGAGC-ACTGCATA


title: bled MPP1 88

description: single-cell RNA-seq in bled  MPP1

value: TAGGCATG-TATCCTCT


title: bled MPP1 84

description: single-cell RNA-seq in bled  MPP1

value: TAGGCATG-CTAAGCCT


title: bled MPP1 85

description: single-cell RNA-seq in bled  MPP1

value: TAGGCATG-CTCTCTAT


title: bled MPP1 87

description: single-cell RNA-seq in bled  MPP1

value: TAGGCATG-GTAAGGAG


title: bled MPP1 86

description: single-cell RNA-seq in bled  MPP1

value: TAGGCATG-GCGTAAGA


title: bled MPP1 83

description: single-cell RNA-seq in bled  MPP1

value: TAGGCATG-AGAGTAGA


title: bled MPP1 82

description: single-cell RNA-seq in bled  MPP1

value: TAGGCATG-ACTGCATA


title: HSC 4 rep3 w/ spike

value: AAGAGGCA-CTAAGCCT


title: bled MPP1 78

description: single-cell RNA-seq in bled  MPP1

value: TAAGGCGA-GCGTAAGA


title: HSC 2 rep3 w/ spike

value: AAGAGGCA-ACTGCATA


title: bled MPP1 77

description: single-cell RNA-seq in bled  MPP1

value: TAAGGCGA-CTCTCTAT


title: bled MPP1 73

description: single-cell RNA-seq in bled  MPP1

value: TAAGGCGA-AAGGAGTA


title: bled MPP1 76

description: single-cell RNA-seq in bled  MPP1

value: TAAGGCGA-CTAAGCCT


title: bled MPP1 75

description: single-cell RNA-seq in bled  MPP1

value: TAAGGCGA-AGAGTAGA


title: bled MPP1 72

description: single-cell RNA-seq in bled  MPP1

value: GTAGAGGA-TATCCTCT


title: bled MPP1 74

description: single-cell RNA-seq in bled  MPP1

value: TAAGGCGA-ACTGCATA


title: bled MPP1 70

description: single-cell RNA-seq in bled  MPP1

value: GTAGAGGA-GCGTAAGA


title: bled MPP1 71

description: single-cell RNA-seq in bled  MPP1

value: GTAGAGGA-GTAAGGAG


title: bled MPP1 92

description: single-cell RNA-seq in bled  MPP1

value: TCCTGAGC-CTAAGCCT


title: bled MPP1 69

description: single-cell RNA-seq in bled  MPP1

value: GTAGAGGA-CTCTCTAT


title: bled MPP1 66

description: single-cell RNA-seq in bled  MPP1

value: GTAGAGGA-ACTGCATA


title: bled MPP1 62

description: single-cell RNA-seq in bled  MPP1

value: GGACTCCT-GCGTAAGA


title: bled MPP1 64

description: single-cell RNA-seq in bled  MPP1

value: GGACTCCT-TATCCTCT


title: bled MPP1 65

description: single-cell RNA-seq in bled  MPP1

value: GTAGAGGA-AAGGAGTA


title: bled MPP1 63

description: single-cell RNA-seq in bled  MPP1

value: GGACTCCT-GTAAGGAG


title: bled MPP1 61

description: single-cell RNA-seq in bled  MPP1

value: GGACTCCT-CTCTCTAT


title: bled MPP1 81

description: single-cell RNA-seq in bled  MPP1

value: TAGGCATG-AAGGAGTA


title: bled MPP1 80

description: single-cell RNA-seq in bled  MPP1

value: TAAGGCGA-TATCCTCT


title: bled MPP1 57

description: single-cell RNA-seq in bled  MPP1

value: GGACTCCT-AAGGAGTA


title: bled MPP1 60

description: single-cell RNA-seq in bled  MPP1

value: GGACTCCT-CTAAGCCT


title: bled MPP1 56

description: single-cell RNA-seq in bled  MPP1

value: GCTACGCT-TATCCTCT


title: bled MPP1 58

description: single-cell RNA-seq in bled  MPP1

value: GGACTCCT-ACTGCATA


title: bled MPP1 59

description: single-cell RNA-seq in bled  MPP1

value: GGACTCCT-AGAGTAGA


title: bled MPP1 79

description: single-cell RNA-seq in bled  MPP1

value: TAAGGCGA-GTAAGGAG


title: bled MPP1 55

description: single-cell RNA-seq in bled  MPP1

value: GCTACGCT-GTAAGGAG


title: bled MPP1 53

description: single-cell RNA-seq in bled  MPP1

value: GCTACGCT-CTCTCTAT


title: bled MPP1 49

description: single-cell RNA-seq in bled  MPP1

value: GCTACGCT-AAGGAGTA


title: bled MPP1 50

description: single-cell RNA-seq in bled  MPP1

value: GCTACGCT-ACTGCATA


title: bled MPP1 48

description: single-cell RNA-seq in bled  MPP1

value: CTCTCTAC-TATCCTCT


title: bled MPP1 47

description: single-cell RNA-seq in bled  MPP1

value: CTCTCTAC-GTAAGGAG


title: bled MPP1 51

description: single-cell RNA-seq in bled  MPP1

value: GCTACGCT-AGAGTAGA


title: bled MPP1 68

description: single-cell RNA-seq in bled  MPP1

value: GTAGAGGA-CTAAGCCT


title: bled MPP1 52

description: single-cell RNA-seq in bled  MPP1

value: GCTACGCT-CTAAGCCT


title: bled MPP1 67

description: single-cell RNA-seq in bled  MPP1

value: GTAGAGGA-AGAGTAGA


title: bled MPP1 46

description: single-cell RNA-seq in bled  MPP1

value: CTCTCTAC-GCGTAAGA


title: bled MPP1 44

description: single-cell RNA-seq in bled  MPP1

value: CTCTCTAC-CTAAGCCT


title: bled MPP1 43

description: single-cell RNA-seq in bled  MPP1

value: CTCTCTAC-AGAGTAGA


title: bled MPP1 42

description: single-cell RNA-seq in bled  MPP1

value: CTCTCTAC-ACTGCATA


title: bled MPP1 41

description: single-cell RNA-seq in bled  MPP1

value: CTCTCTAC-AAGGAGTA


title: bled MPP1 40

description: single-cell RNA-seq in bled  MPP1

value: CGTACTAG-TATCCTCT


title: bled MPP1 39

description: single-cell RNA-seq in bled  MPP1

value: CGTACTAG-GTAAGGAG


title: bled MPP1 38

description: single-cell RNA-seq in bled  MPP1

value: CGTACTAG-GCGTAAGA


title: bled MPP1 37

description: single-cell RNA-seq in bled  MPP1

value: CGTACTAG-CTCTCTAT


title: bled MPP1 34

description: single-cell RNA-seq in bled  MPP1

value: CGTACTAG-ACTGCATA


title: bled MPP1 32

description: single-cell RNA-seq in bled  MPP1

value: CGAGGCTG-TATCCTCT


title: bled MPP1 36

description: single-cell RNA-seq in bled  MPP1

value: CGTACTAG-CTAAGCCT


title: bled MPP1 35

description: single-cell RNA-seq in bled  MPP1

value: CGTACTAG-AGAGTAGA


title: bled MPP1 54

description: single-cell RNA-seq in bled  MPP1

value: GCTACGCT-GCGTAAGA


title: bled MPP1 89

description: single-cell RNA-seq in bled  MPP1

value: TCCTGAGC-AAGGAGTA


title: bled MPP1 30

description: single-cell RNA-seq in bled  MPP1

value: CGAGGCTG-GCGTAAGA


title: bled MPP1 29

description: single-cell RNA-seq in bled  MPP1

value: CGAGGCTG-CTCTCTAT


title: bled MPP1 28

description: single-cell RNA-seq in bled  MPP1

value: CGAGGCTG-CTAAGCCT


title: bled MPP1 45

description: single-cell RNA-seq in bled  MPP1

value: CTCTCTAC-CTCTCTAT


title: bled MPP1 27

description: single-cell RNA-seq in bled  MPP1

value: CGAGGCTG-AGAGTAGA


title: bled MPP1 26

description: single-cell RNA-seq in bled  MPP1

value: CGAGGCTG-ACTGCATA


title: bled MPP1 25

description: single-cell RNA-seq in bled  MPP1

value: CGAGGCTG-AAGGAGTA


title: bled MPP1 23

description: single-cell RNA-seq in bled  MPP1

value: CAGAGAGG-GTAAGGAG


title: bled MPP1 22

description: single-cell RNA-seq in bled  MPP1

value: CAGAGAGG-GCGTAAGA


title: bled MPP1 21

description: single-cell RNA-seq in bled  MPP1

value: CAGAGAGG-CTCTCTAT


title: bled MPP1 20

description: single-cell RNA-seq in bled  MPP1

value: CAGAGAGG-CTAAGCCT


title: bled MPP1 24

description: single-cell RNA-seq in bled  MPP1

value: CAGAGAGG-TATCCTCT


title: bled MPP1 19

description: single-cell RNA-seq in bled  MPP1

value: CAGAGAGG-AGAGTAGA


title: bled MPP1 18

description: single-cell RNA-seq in bled  MPP1

value: CAGAGAGG-ACTGCATA


title: bled MPP1 15

description: single-cell RNA-seq in bled  MPP1

value: AGGCAGAA-GTAAGGAG


title: bled MPP1 17

description: single-cell RNA-seq in bled  MPP1

value: CAGAGAGG-AAGGAGTA


title: bled MPP1 31

description: single-cell RNA-seq in bled  MPP1

value: CGAGGCTG-GTAAGGAG


title: bled MPP1 33

description: single-cell RNA-seq in bled  MPP1

value: CGTACTAG-AAGGAGTA


title: bled MPP1 14

description: single-cell RNA-seq in bled  MPP1

value: AGGCAGAA-GCGTAAGA


title: bled MPP1 9

description: single-cell RNA-seq in bled  MPP1

value: AGGCAGAA-AAGGAGTA


title: bled MPP1 13

description: single-cell RNA-seq in bled  MPP1

value: AGGCAGAA-CTCTCTAT


title: bled MPP1 16

description: single-cell RNA-seq in bled  MPP1

value: AGGCAGAA-TATCCTCT


title: bled MPP1 11

description: single-cell RNA-seq in bled  MPP1

value: AGGCAGAA-AGAGTAGA


title: bled MPP1 6

description: single-cell RNA-seq in bled  MPP1

value: AAGAGGCA-GCGTAAGA


title: bled MPP1 4

description: single-cell RNA-seq in bled  MPP1

value: AAGAGGCA-CTAAGCCT


title: bled MPP1 7

description: single-cell RNA-seq in bled  MPP1

value: AAGAGGCA-GTAAGGAG


title: bled MPP1 3

description: single-cell RNA-seq in bled  MPP1

value: AAGAGGCA-AGAGTAGA


title: bled MPP1 8

description: single-cell RNA-seq in bled  MPP1

value: AAGAGGCA-TATCCTCT


title: bled MPP1 2

description: single-cell RNA-seq in bled  MPP1

value: AAGAGGCA-ACTGCATA


title: bled MPP1 1

description: single-cell RNA-seq in bled  MPP1

value: AAGAGGCA-AAGGAGTA


title: bled HSC 96

description: single-cell RNA-seq in bled  HSC

value: TCCTGAGC-TATCCTCT


title: bled HSC 91

description: single-cell RNA-seq in bled  HSC

value: TCCTGAGC-AGAGTAGA


title: bled HSC 93

description: single-cell RNA-seq in bled  HSC

value: TCCTGAGC-CTCTCTAT


title: bled HSC 92

description: single-cell RNA-seq in bled  HSC

value: TCCTGAGC-CTAAGCCT


title: bled HSC 90

description: single-cell RNA-seq in bled  HSC

value: TCCTGAGC-ACTGCATA


title: bled HSC 95

description: single-cell RNA-seq in bled  HSC

value: TCCTGAGC-GTAAGGAG


title: bled HSC 89

description: single-cell RNA-seq in bled  HSC

value: TCCTGAGC-AAGGAGTA


title: bled HSC 88

description: single-cell RNA-seq in bled  HSC

value: TAGGCATG-TATCCTCT


title: bled HSC 87

description: single-cell RNA-seq in bled  HSC

value: TAGGCATG-GTAAGGAG


title: bled MPP1 12

description: single-cell RNA-seq in bled  MPP1

value: AGGCAGAA-CTAAGCCT


title: bled MPP1 10

description: single-cell RNA-seq in bled  MPP1

value: AGGCAGAA-ACTGCATA


title: bled HSC 85

description: single-cell RNA-seq in bled  HSC

value: TAGGCATG-CTCTCTAT


title: bled HSC 86

description: single-cell RNA-seq in bled  HSC

value: TAGGCATG-GCGTAAGA


title: bled HSC 84

description: single-cell RNA-seq in bled  HSC

value: TAGGCATG-CTAAGCCT


title: bled HSC 83

description: single-cell RNA-seq in bled  HSC

value: TAGGCATG-AGAGTAGA


title: bled HSC 82

description: single-cell RNA-seq in bled  HSC

value: TAGGCATG-ACTGCATA


title: bled HSC 81

description: single-cell RNA-seq in bled  HSC

value: TAGGCATG-AAGGAGTA


title: bled HSC 78

description: single-cell RNA-seq in bled  HSC

value: TAAGGCGA-GCGTAAGA


title: bled HSC 79

description: single-cell RNA-seq in bled  HSC

value: TAAGGCGA-GTAAGGAG


title: bled HSC 80

description: single-cell RNA-seq in bled  HSC

value: TAAGGCGA-TATCCTCT


title: bled HSC 76

description: single-cell RNA-seq in bled  HSC

value: TAAGGCGA-CTAAGCCT


title: bled HSC 74

description: single-cell RNA-seq in bled  HSC

value: TAAGGCGA-ACTGCATA


title: bled HSC 73

description: single-cell RNA-seq in bled  HSC

value: TAAGGCGA-AAGGAGTA


title: bled HSC 75

description: single-cell RNA-seq in bled  HSC

value: TAAGGCGA-AGAGTAGA


title: bled MPP1 5

description: single-cell RNA-seq in bled  MPP1

value: AAGAGGCA-CTCTCTAT


title: bled HSC 72

description: single-cell RNA-seq in bled  HSC

value: GTAGAGGA-TATCCTCT


title: bled HSC 71

description: single-cell RNA-seq in bled  HSC

value: GTAGAGGA-GTAAGGAG


title: bled HSC 69

description: single-cell RNA-seq in bled  HSC

value: GTAGAGGA-CTCTCTAT


title: bled HSC 70

description: single-cell RNA-seq in bled  HSC

value: GTAGAGGA-GCGTAAGA


title: bled HSC 66

description: single-cell RNA-seq in bled  HSC

value: GTAGAGGA-ACTGCATA


title: bled HSC 62

description: single-cell RNA-seq in bled  HSC

value: GGACTCCT-GCGTAAGA


title: bled HSC 64

description: single-cell RNA-seq in bled  HSC

value: GGACTCCT-TATCCTCT


title: bled HSC 63

description: single-cell RNA-seq in bled  HSC

value: GGACTCCT-GTAAGGAG


title: bled HSC 61

description: single-cell RNA-seq in bled  HSC

value: GGACTCCT-CTCTCTAT


title: bled HSC 65

description: single-cell RNA-seq in bled  HSC

value: GTAGAGGA-AAGGAGTA


title: bled HSC 60

description: single-cell RNA-seq in bled  HSC

value: GGACTCCT-CTAAGCCT


title: bled HSC 59

description: single-cell RNA-seq in bled  HSC

value: GGACTCCT-AGAGTAGA


title: bled HSC 58

description: single-cell RNA-seq in bled  HSC

value: GGACTCCT-ACTGCATA


title: bled HSC 56

description: single-cell RNA-seq in bled  HSC

value: GCTACGCT-TATCCTCT


title: bled HSC 55

description: single-cell RNA-seq in bled  HSC

value: GCTACGCT-GTAAGGAG


title: bled HSC 54

description: single-cell RNA-seq in bled  HSC

value: GCTACGCT-GCGTAAGA


title: bled HSC 77

description: single-cell RNA-seq in bled  HSC

value: TAAGGCGA-CTCTCTAT


title: bled HSC 51

description: single-cell RNA-seq in bled  HSC

value: GCTACGCT-AGAGTAGA


title: bled HSC 53

description: single-cell RNA-seq in bled  HSC

value: GCTACGCT-CTCTCTAT


title: bled HSC 52

description: single-cell RNA-seq in bled  HSC

value: GCTACGCT-CTAAGCCT


title: bled HSC 49

description: single-cell RNA-seq in bled  HSC

value: GCTACGCT-AAGGAGTA


title: bled HSC 94

description: single-cell RNA-seq in bled  HSC

value: TCCTGAGC-GCGTAAGA


title: bled HSC 47

description: single-cell RNA-seq in bled  HSC

value: CTCTCTAC-GTAAGGAG


title: bled HSC 48

description: single-cell RNA-seq in bled  HSC

value: CTCTCTAC-TATCCTCT


title: bled HSC 46

description: single-cell RNA-seq in bled  HSC

value: CTCTCTAC-GCGTAAGA


title: bled HSC 44

description: single-cell RNA-seq in bled  HSC

value: CTCTCTAC-CTAAGCCT


title: bled HSC 45

description: single-cell RNA-seq in bled  HSC

value: CTCTCTAC-CTCTCTAT


title: bled HSC 43

description: single-cell RNA-seq in bled  HSC

value: CTCTCTAC-AGAGTAGA


title: bled HSC 68

description: single-cell RNA-seq in bled  HSC

value: GTAGAGGA-CTAAGCCT


title: bled HSC 42

description: single-cell RNA-seq in bled  HSC

value: CTCTCTAC-ACTGCATA


title: bled HSC 67

description: single-cell RNA-seq in bled  HSC

value: GTAGAGGA-AGAGTAGA


title: bled HSC 41

description: single-cell RNA-seq in bled  HSC

value: CTCTCTAC-AAGGAGTA


title: bled HSC 40

description: single-cell RNA-seq in bled  HSC

value: CGTACTAG-TATCCTCT


title: bled HSC 37

description: single-cell RNA-seq in bled  HSC

value: CGTACTAG-CTCTCTAT


title: bled HSC 57

description: single-cell RNA-seq in bled  HSC

value: GGACTCCT-AAGGAGTA


title: bled HSC 36

description: single-cell RNA-seq in bled  HSC

value: CGTACTAG-CTAAGCCT


title: bled HSC 34

description: single-cell RNA-seq in bled  HSC

value: CGTACTAG-ACTGCATA


title: bled HSC 38

description: single-cell RNA-seq in bled  HSC

value: CGTACTAG-GCGTAAGA


title: bled HSC 39

description: single-cell RNA-seq in bled  HSC

value: CGTACTAG-GTAAGGAG


title: bled HSC 35

description: single-cell RNA-seq in bled  HSC

value: CGTACTAG-AGAGTAGA


title: bled HSC 33

description: single-cell RNA-seq in bled  HSC

value: CGTACTAG-AAGGAGTA


title: bled HSC 50

description: single-cell RNA-seq in bled  HSC

value: GCTACGCT-ACTGCATA


title: bled HSC 30

description: single-cell RNA-seq in bled  HSC

value: CGAGGCTG-GCGTAAGA


title: bled HSC 29

description: single-cell RNA-seq in bled  HSC

value: CGAGGCTG-CTCTCTAT


title: bled HSC 31

description: single-cell RNA-seq in bled  HSC

value: CGAGGCTG-GTAAGGAG


title: bled HSC 28

description: single-cell RNA-seq in bled  HSC

value: CGAGGCTG-CTAAGCCT


title: bled HSC 27

description: single-cell RNA-seq in bled  HSC

value: CGAGGCTG-AGAGTAGA


title: bled HSC 26

description: single-cell RNA-seq in bled  HSC

value: CGAGGCTG-ACTGCATA


title: bled HSC 25

description: single-cell RNA-seq in bled  HSC

value: CGAGGCTG-AAGGAGTA


title: bled HSC 22

description: single-cell RNA-seq in bled  HSC

value: CAGAGAGG-GCGTAAGA


title: bled HSC 20

description: single-cell RNA-seq in bled  HSC

value: CAGAGAGG-CTAAGCCT


title: bled HSC 21

description: single-cell RNA-seq in bled  HSC

value: CAGAGAGG-CTCTCTAT


title: bled HSC 24

description: single-cell RNA-seq in bled  HSC

value: CAGAGAGG-TATCCTCT


title: bled HSC 17

description: single-cell RNA-seq in bled  HSC

value: CAGAGAGG-AAGGAGTA


title: bled HSC 18

description: single-cell RNA-seq in bled  HSC

value: CAGAGAGG-ACTGCATA


title: bled HSC 15

description: single-cell RNA-seq in bled  HSC

value: AGGCAGAA-GTAAGGAG


title: bled HSC 19

description: single-cell RNA-seq in bled  HSC

value: CAGAGAGG-AGAGTAGA


title: bled HSC 14

description: single-cell RNA-seq in bled  HSC

value: AGGCAGAA-GCGTAAGA


title: bled HSC 16

description: single-cell RNA-seq in bled  HSC

value: AGGCAGAA-TATCCTCT


title: bled HSC 13

description: single-cell RNA-seq in bled  HSC

value: AGGCAGAA-CTCTCTAT


title: bled HSC 32

description: single-cell RNA-seq in bled  HSC

value: CGAGGCTG-TATCCTCT


title: bled HSC 9

description: single-cell RNA-seq in bled  HSC

value: AGGCAGAA-AAGGAGTA


title: bled HSC 7

description: single-cell RNA-seq in bled  HSC

value: AAGAGGCA-GTAAGGAG


title: bled HSC 12

description: single-cell RNA-seq in bled  HSC

value: AGGCAGAA-CTAAGCCT


title: bled HSC 11

description: single-cell RNA-seq in bled  HSC

value: AGGCAGAA-AGAGTAGA


title: bled HSC 6

description: single-cell RNA-seq in bled  HSC

value: AAGAGGCA-GCGTAAGA


title: bled HSC 10

description: single-cell RNA-seq in bled  HSC

value: AGGCAGAA-ACTGCATA


title: bled HSC 8

description: single-cell RNA-seq in bled  HSC

value: AAGAGGCA-TATCCTCT


title: bled HSC 5

description: single-cell RNA-seq in bled  HSC

value: AAGAGGCA-CTCTCTAT


title: bled HSC 4

description: single-cell RNA-seq in bled  HSC

value: AAGAGGCA-CTAAGCCT


title: bled HSC 3

description: single-cell RNA-seq in bled  HSC

value: AAGAGGCA-AGAGTAGA


title: bled HSC 23

description: single-cell RNA-seq in bled  HSC

value: CAGAGAGG-GTAAGGAG


title: bled HSC 1

description: single-cell RNA-seq in bled  HSC

value: AAGAGGCA-AAGGAGTA


title: bled HSC 2

description: single-cell RNA-seq in bled  HSC

value: AAGAGGCA-ACTGCATA


title: CFU-E population

description: PMA-RNA-seq in CFU-E

source_name: erythoid colony forming unit

growth_protocol: Bone Marrow cells were isolated from 6-8 weeks C57BL6 mice


title: GMP-11 population

description: PMA-RNA-seq in GMP-11

source_name: granulocyte-macrophage progenitor


title: ProEry population

description: PMA-RNA-seq in ProEry

source_name: Pro-erythrocyte


title: Mature Meg population

description: PMA-RNA-seq in Mature Meg

source_name: Mature megakaryocyte


title: GMP-7 population

description: PMA-RNA-seq in GMP-7

source_name: granuloctye-macrophage progenitor


title: PreCFU-E population

description: PMA-RNA-seq in PreCFU-E

source_name: pre-erythoid colony forming unit


title: preMegE population

description: PMA-RNA-seq in preMegE

source_name: pre-megakaryocyte-erythrocyte


title: MPP4 population

description: PMA-RNA-seq in MPP4

source_name: Multipotent precursors 4


title: CLP Sca1 high population

description: PMA-RNA-seq in CLP Sca1 high

source_name: common lymphoid progenitor (sorted sca-1 hi )


title: CMP population

description: PMA-RNA-seq in CMP

source_name: common myeloid progenitor


title: CLP population

description: PMA-RNA-seq in CLP

source_name: common lymphoid progenitor


title: MKP population

description: PMA-RNA-seq in MKP

source_name: megakarycyte-committed progenitor


title: MEP population

description: PMA-RNA-seq in MEP

source_name: megakaryocyte-erythroid progenitor


title: MPP2 population

description: PMA-RNA-seq in MPP2

source_name: Multipotent precursors 2


title: MPP1 population

description: PMA-RNA-seq in MPP1