title: ChIPseq_MCF10A_B-MYB_plusDOX

value: B-MYB (Santa Cruz sc-724)


title: 20_Day28eGFP_pos_1

status: Public on Jun 19 2019

type: SRA

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

country: USA

institute: University of Southern California

description:
processed data file:
D28MAFBeGFP+_vs_D28MAFBeGFP-.txt

library_source: transcriptomic

data_processing:
Fastq files were aligned to hg38 with TopHat2
Gene-level quantification was performed with Partek E/M through Partek Genomic Suite
Gene-level read couns was normalized to TPM through Partek Genomic Suite
Genome_build: hg38
Supplementary_files_format_and_content: TPM

molecule: total RNA

organism: Homo sapiens

source_name: FACS-sorted eGFP+ cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 1

growth_protocol: Kidney differentiation followed protocol described in Morizane et al., 2016

extract_protocol:
Ambion Recoverall Total Nucleic Acid Isolation Kit and QIAGEN Rneasy Micro Kit; Qiagen Rneasy micro kit
Kapa stranded mRNA-Seq library (#KK8420)

tag: cell line source

tag: source cell type

value: human embryonic stem cells

tag: differentiation day

value: Day 28

tag: cell line of origin

value: H9 human embryonic stem cell

tag: genotype/variation


title: ChIPseq_MCF10A_YAP_plusDOX

status: Public on Jun 18 2019

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

country: Germany

institute: University of Wuerzburg

library_source: genomic

data_processing:
For ChIP-seq analysis, reads were aligned to the human (hg19) or murine (mm10) genome with BOWTIE v1.1.2 (Langmead, 2010) using default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Genome-wide read density files ("bedgraph") were generated with the genomeCoverageBed function from the bedtools suite v2.26.0 (Quinlan et al., 2010).
For RNA-seq analysis, reads were aligned to the murine genome (mm10) with TopHat v2.1.0 (Kim et al., 2013) using BOWTIE2 (Langmead, 2010) and default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Reads per gene (Ensembl database GRCm38.p6) were counted with the "summarizeOverlaps" function in the R package {GenomicFeatures}.
Non- or weakly expressed genes were removed (threshold: mean read count per gene over all samples >1).
Differential gene expression was called using EdgeR and adjusting the calculated p-value with the Benjamini-Höchberg procedure.
Genome_build: mm10 (GRCm38) or hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-seq: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
Supplementary_files_format_and_content: RNA-seq: RNAseq_KPL_countmatrix.txt containing raw read counts for all samples and all genes.
Supplementary_files_format_and_content: RNA-seq: RNAseq_KPL_plusOHT_vs_minusOHT.txt containing gene names, gene description, log2FC, log2CPM, p-value, Benjamini-Höchberg-adjusted p-value (FDR).

molecule: genomic DNA

growth_protocol: KPL cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/ streptomycin. MCF10A-YAP5SA cells were cultured in DMEM/F-12 supplemented with 5% horse serum, 1% penicillin/ streptomycin, 10 µg/ml insulin, 500 ng/ml hydrocortisone, 20 ng/ml EGF and 100 ng/ml cholera toxin.

extract_protocol: For ChIP-Seq, chromatin from 2 x 10e7 KPL cells or 3.5 x 10e7 MCF10A-YAP5SA was isolated and immunoprecipitated as described above. Libraries for ChIP-Seq were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB) according to the manufacturer’s instructions. Size-selection was performed using Agencourt AMPure XP beads (Beckman Coulter) (150 bp). DNA fragments were amplified by 10-15 cycles of PCR and library quality was analyzed with the Biorad Experion system and the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using pico green.

treatment_protocol: To delete Lin9, KPL cells were treated with 10 nm 4-OHT (Sigma) for 72 hours. The expression of YAP5SA was induced in MCF10A-YAP5SA cells by the addition of 0.5 µg/ml doxycycline for 12 hours.

tag: cell line

tag: treatment

value: doxycycline

tag: chip antibody


title: ChIPseq_MCF10A_H3K4me1_minusDOX

value: ctrl

value: H3K4me1 (Abcam ab8895)


title: ChIPseq_MCF10A_B-MYB_minusDOX


title: Paraiba rep2 (miRNA-Seq)

city: La Jolla

first: Tariq

last: Rana

state: CA

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

description:
miRNA_DEGs.xlsx
PA-2

data_processing:
bowtie2 alignment to UCSC hg38 reference genome
Random 100 unmapped reads were generated and compared using BLAST
Partek was used to generate read counts, RPKM and mapping summary
Differential gene expression was calculated usig DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

source_name: iPSC derived neural stem cell

growth_protocol: hNSCs were purchased from ThermoFisher A15654 and cultured using StemPro NSC SFM media following manufacturer's instructions.

extract_protocol:
Total RNAs were collected using Qiagen RNeasy MiniKit following manufacturer's instructions
small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Neural stem cells were infected with Zika virus MR766 or Paraiba at MOI 1 for 3 days. Media was changed 4 hours post-infection.

tag: cell type

value: hNSC

tag: infection

value: Zika virus strain Paraiba


title: ChIPseq_MCF10A_input_plusDOX


title: ChIPseq_MCF10A_LIN9_minusDOX

value: LIN9 (Bethyl A300-BL3981)


title: ChIPseq_MCF10A_LIN9_plusDOX


title: ChIPseq_MCF10A_input_minusDOX


title: Paraiba rep1 (miRNA-Seq)

description:
miRNA_DEGs.xlsx
PA-1


title: NT rep1 (miRNA-Seq)

description:
miRNA_DEGs.xlsx
C1

value: mock


title: Paraiba rep3 (iCLIP-seq)

description:
Sample 6
ZIKV-AGO-iCLIP_mir_target_interaction.xlsx

data_processing:
Adapters trimmed with flexbar and demultiplexed with pyCRAC
PCR duplicates were collapsed with pyCRAC and concatenated reads aligned to hg38 using bowtie2
Reads from control (1-3) and Paraiba infected (4-6) samples were pooled separately and equal number of reads were subsampled to normalize CITS/CIMS calling between Control and Infected samples
CITS and CIMS algorithms were used to call truncation/mutation sites from pooled control and infected datasets
Differential gene expression was calculated usig DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Excel file includes baseMean values pooled control and infected samples

extract_protocol:
AGO-iCLIP-seq libraries were prepared following previously established iCLIP protocols (Konig, 2011). Briefly, hNSCs were UV crosslinked with 150mJ/cm2 254nm and cell pellets were lysed. RNAs were fragmented with RNaseI. Partially digested RNAs were incubated with AGO (Millipore MABE56) antibody overnight and immunoprecipitated the following day.
Preadenylated L3 linkers were ligated to 3' ends of RNAs and 5' ends were radiolabeled. RNA were resolved using SDS-PAGE and protein-RNA complexes were transfered to nitrocellulose membranes. RNAs were eluted and reverse transcribed using Superscript III reverse transcriptase. cDNAs were gel purified, circularized, linearized and amplified with P5/P3 Solexa primers for sequencing.

treatment_protocol: Neural stem cells were infected with Zika virus Paraiba at MOI 1 for 4 days. Media was changed 4 hours post-infection.

value: Zika virus stain Paraiba

tag: rip antibody

value: AGO (Millipore MABE56) antibody


title: MR766 rep1 (miRNA-Seq)

description:
miRNA_DEGs.xlsx
MR-1

value: Zika virus strain MR766


title: ChIPseq_MCF10A_YAP_minusDOX


title: Paraiba rep2 (iCLIP-seq)

description:
Sample 5
ZIKV-AGO-iCLIP_mir_target_interaction.xlsx


title: Paraiba rep1 (iCLIP-seq)

description:
Sample 4
ZIKV-AGO-iCLIP_mir_target_interaction.xlsx


title: NT rep3 (iCLIP-seq)

description:
Sample 3
ZIKV-AGO-iCLIP_mir_target_interaction.xlsx


title: Paraiba rep2 (RNA-Seq)

description:
Control.Vs.PA.DESeq_Analysis_summary.xlsx
PA-2

data_processing:
TopHat v1.4.1 alignment to UCSC hg19 reference genome
DUST scores calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads were filtered out
Alignment results were parsed using SAMtools and read counts were obtained using htseq-count program
Differential gene expression was calculated usig DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

extract_protocol:
Total RNAs were collected using Qiagen RNeasy MiniKit following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols


title: NT rep1 (iCLIP-seq)

description:
Sample 1
ZIKV-AGO-iCLIP_mir_target_interaction.xlsx


title: NT rep2 (iCLIP-seq)

description:
Sample 2
ZIKV-AGO-iCLIP_mir_target_interaction.xlsx


title: Paraiba rep1 (RNA-Seq)

description:
Control.Vs.PA.DESeq_Analysis_summary.xlsx
PA-1


title: MR766 rep1 (RNA-Seq)

description:
Control.Vs.PA.DESeq_Analysis_summary.xlsx
MR-1


title: NT rep1 (RNA-Seq)

description:
Control.Vs.PA.DESeq_Analysis_summary.xlsx
C1


title: NT rep2 (RNA-Seq)

description:
Control.Vs.PA.DESeq_Analysis_summary.xlsx
C2


title: LZ DEC-/- DEC-OVA/DEC-CS 1:3 [SF_9_S9]

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description:
L_OVA_CS_3_SF_9_S9
processed data file: pairwise_differential_expression.xlsx

data_processing:
For RNA-Seq data analysis, reads were pseudo-aligned to an index created from the Ensembl mouse GRCm38.p5 assembly and custom annotations of Igh locus features. Transcript-level abundances were quantified using kallisto v0.43.0 and subsequently summarized to the gene-level using the R package tximport. Differential gene expression analysis was performed using DESeq2.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: pairwise_differential_expression.xlsx: Excel file containing transcript abundances in TPM and pairwise differential expression.

organism: Mus musculus

source_name: Lymph node Germinal Center

extract_protocol:
Sorted cells were processed by extracting RNA using PicoPure RNA Isolation Kit (Thermo Fisher) according to manufacturer’s recommendations.
1 ng of total RNA was used to generate full length cDNA using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). 1 ng of cDNA was then used to prepare libraries using Nextera XT DNA sample preparation kit (Illumina).

tag: strain/background

value: B18hi DEC-/-

value: Germinal Center B cell


title: LZ DEC-/- DEC-OVA/DEC-CS 1:12 [SF_8_S8]

description:
L_OVA_CS_12_SF_8_S8
processed data file: pairwise_differential_expression.xlsx


title: LZ DEC-/- DEC-OVA/DEC-CS 1:40 [SF_7_S7]

description:
L_OVA_CS_40_SF_7_S7
processed data file: pairwise_differential_expression.xlsx


title: NT rep2 (miRNA-Seq)

description:
miRNA_DEGs.xlsx
C2


title: MR766 rep2 (miRNA-Seq)

description:
miRNA_DEGs.xlsx
MR-2


title: LZ Fucci- DEC-OVA [SF_30_S11]

description:
L_OVA_2_SF_30_S11
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-OVA/DEC-CS 1:12 [SF_3_S3]

description:
L_F_OVA_CS_12_SF_3_S3
processed data file: pairwise_differential_expression.xlsx

value: B18hi FUCCI+


title: LZ Fucci- DEC-OVA/DEC-CS 1:12 [SF_28_S9]

description:
L_OVA_CS_12_2_SF_28_S9
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci- DEC-CS [SF_26_S7]

description:
L_CS_2_SF_26_S7
processed data file: pairwise_differential_expression.xlsx


title: LZ DEC-/- DEC-OVA/DEC-CS 1:40 [SF_27_S8]

description:
L_OVA_CS_40_2_SF_27_S8
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-OVA [SF_5_S5]

description:
L_F_OVA_SF_5_S5
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci- DEC-OVA/DEC-CS 1:3 [SF_29_S10]

description:
L_OVA_CS_3_2_SF_29_S10
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-OVA/DEC-CS 1:12 [SF_23_S4]

description:
L_F_OVA_CS_12_SF_23_S4
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-OVA/DEC-CS 1:3 [SF_24_S5]

description:
L_F_OVA_CS_3_SF_24_S5
processed data file: pairwise_differential_expression.xlsx


title: MR766 rep2 (RNA-Seq)

description:
Control.Vs.PA.DESeq_Analysis_summary.xlsx
MR-2


title: LZ DEC-/- DEC-CS [SF_16_S15]

description:
L_CS_SF_16_S15
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-OVA/DEC-CS 1:3 [SF_14_S1]

description:
L_F_OVA_CS_3_SF_14_S1
processed data file: pairwise_differential_expression.xlsx


title: LZ DEC-/- DEC-OVA/DEC-CS 1:40 [SF_17_S16]

description:
L_OVA_CS_40_SF_17_S16
processed data file: pairwise_differential_expression.xlsx


title: LZ DEC-/- DEC-OVA [SF_20_S19]

description:
L_OVA_SF_20_S19
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-OVA/DEC-CS 1:12 [SF_13_S13]

description:
L_F_OVA_CS_12_SF_13_S13
processed data file: pairwise_differential_expression.xlsx


title: LZ DEC-/- DEC-OVA/DEC-CS 1:3 [SF_19_S18]

description:
L_OVA_CS_3_SF_19_S18
processed data file: pairwise_differential_expression.xlsx


title: LZ DEC-/- DEC-OVA/DEC-CS 1:12 [SF_18_S17]

description:
L_OVA_CS_12_SF_18_S17
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-CS [SF_11_S11]

description:
L_F_CS_SF_11_S11
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-OVA/DEC-CS 1:40 [SF_12_S12]

description:
L_F_OVA_CS_40_SF_12_S12
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-OVA [SF_15_S14]

description:
L_F_OVA_SF_15_S14
processed data file: pairwise_differential_expression.xlsx


title: LZ DEC-/- DEC-OVA [SF_10_S10]

description:
L_OVA_SF_10_S10
processed data file: pairwise_differential_expression.xlsx


title: LZ DEC-/- DEC-CS [SF_6_S6]

description:
L_CS_SF_6_S6
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-OVA/DEC-CS 1:3 [SF_4_S4]

description:
L_F_OVA_CS_3_SF_4_S4
processed data file: pairwise_differential_expression.xlsx


title: LZ Fucci+ DEC-CS [SF_1_S1]

description:
L_F_CS_SF_1_S1
processed data file: pairwise_differential_expression.xlsx


title: RNA GFP_d0

city: Guangzhou

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: reprogramming cells

growth_protocol: Mouse ESCs an iPSCs were cultured feeders-free with N2B27-2i medium (50% (v/v) DMEM (Hyclone), 50% (v/v) knock out DMEM (Gibco), N2 (Gibco), B27 (Gibco), 1mM sodium pyruvate (Gibco), 1mM non-essential amino acids (Gibco), 1 × GlutaMAX (Gibco), 0.1 mM 2 mercaptoethanol (Gibco), 1000 U/ml leukemia inhibitory factor (LIF) (Millipore), and the 2i inhibitors, 3 μM CHIR99021 (Sigma), and 1 μM PD0325901 (Sigma).  MEFs infected with 7 factors or single factor dropout retrovirus for 48 hours and then change the medium to iCD1 plus Rock inhibitor and induction for 7 days

extract_protocol:
Total RNAs were prepared with TRIzol. VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme) was used for library constructions and sequencing done with NextSeq500 Mid output 150 cycles (FC-404-2001, Illumina) for RNA-seq.
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.

value: reprogramming cells

tag: day of reprogramming


title: LZ Fucci+ DEC-OVA [SF_25_S6]

description:
L_F_OVA_SF_25_S6
processed data file: pairwise_differential_expression.xlsx


title: RNA MEF-Y'F-iPSC-6

source_name: iPSC cells

value: iPSC cells


title: RNA TTF-Y'F-iPSC-1


title: RNA MEF-rep2

source_name: Mouse Embyronic Fibroblast

value: Mouse Embyronic Fibroblast


title: LZ Fucci+ DEC-OVA/DEC-CS 1:40 [SF_2_S2]

description:
L_F_OVA_CS_40_SF_2_S2
processed data file: pairwise_differential_expression.xlsx


title: RNA MEF-rep1


title: RNA MEF-Y'F-iPSC-5


title: RNA MEF-Y'F-iPSC-4


title: RNA MEF-Y'F-iPSC-3


title: RNA MEF-7F-iPSC-5


title: RNA MEF-Y'F-iPSC-1


title: RNA MEF-Y'F-iPSC-2


title: RNA MEF-1


title: RNA MEF-7F-iPSC-3


title: RNA MEF-2


title: RNA MEF-7F-iPSC-2


title: RNA MEF-7F-iPSC-1


title: RNA MEF-3


title: RNA GFP-control-D7


title: RNA GFP-control-D1


title: RNA 7F-none-D7-rep2


title: RNA GFP-control-D3


title: RNA TTF-Y'F-iPSC-2


title: RNA 7F-none-D7-rep1


title: RNA 7F-none-D5-rep2


title: RNA 7F-none-D3-rep1


title: RNA 7F-none-D3-rep2


title: RNA 7F-none-D5-rep1


title: RNA MEF-7F-iPSC-4


title: RNA GFP-control-D5


title: RNA 7F-none-D1-rep2


title: RNA 7F-none-D0-rep1


title: RNA 7F-Sall4-D5


title: RNA 7F-none-D0-rep2


title: RNA 7F-Sall4-D0


title: RNA 7F-Sall4-D3


title: RNA 7F-Sall4-D7


title: RNA 7F-Sall4-D1


title: RNA 7F-Nanog-D7


title: RNA 7F-Nanog-D0


title: RNA 7F-Mkk6-D7


title: RNA 7F-Mkk6-D5


title: RNA 7F-Nanog-D1


title: RNA 7F-Mkk6-D3


title: RNA 7F-Mkk6-D1


title: RNA 7F-Kdm2b-D7


title: RNA 7F-none-D1-rep1


title: RNA 7F-Kdm2b-D5


title: RNA 7F-Nanog-D3


title: RNA 7F-Nanog-D5


title: SE-AX cell line

type: RNA

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

institute: Leibniz Institute DSMZ

hyb_protocol: Samples were prepared for and measured on Affymetrix HG-U133-plus2 Chip (Santa Clara/CA).

scan_protocol: GeneChips were scanned using the scanner GCS3000 and GCOS1.2 Software Suite (Affymetrix).

data_processing: After RMA-background correction with 9 further published samples (IMC-1 and KHYG1 from GEO:GSE19067; NK-92 from GEO:GSE53478; SNK6 from GEO:GSE19067 and 5 T-ALL cell lines i.e. ALL-SIL, CCRF-CEM, PEER, JURKAT, LOUCY from GSE87334), quantile normalisation of spot intensities, data were logarithmically transformed. Data processing was done via R/Bioconductor using limma and affy packages.

label: biotin

source_name: lymphoma cell line

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from total RNA.

extract_protocol: Total RNA was extracted using Trizol reagent.

value: SE-AX

tag: disease state

value: Cutaneous T-cell lymphoma


title: MAC-2B cell line


title: MAC-2A cell line


title: L-82 cell line

value: T-cell anaplastic large cell lymphoma


title: RNA 7F-Kdm2b-D3


title: MY-LA cell line

value: MY-LA


title: HH cell line

value: HH


title: MAC-1 cell line


title: FE-PD cell line

value: FE-PD


title: LOUCY cell line

value: LOUCY

value: T-cell acute lymphoblastic leukemia


title: RNA 7F-Kdm2b-D1


title: RNA 7F-Jdp2-D7


title: RNA 7F-Kdm2b-D0


title: RNA 7F-Jdp2-D5


title: RNA 7F-Jdp2-D1


title: RNA 7F-Jdp2-D3


title: RNA 7F-Glis1-D7


title: RNA 7F-Glis1-D5


title: RNA 7F-Glis1-D1


title: RNA 7F-Glis1-D0


title: RNA 7F-Glis1-D3


title: RNA 7F-Esrrb-D7


title: JURKAT cell line

value: JURKAT


title: DERL-7 cell line

value: Hodgkin lymphoma


title: RNA 7F-Jdp2-D0


title: RNA 7F-Mkk6-D0


title: ALL-SILL cell line

value: ALL-SILL


title: DERL-2 cell line


title: PEER cell line

value: PEER


title: RNA 7F-Esrrb-D5


title: RNA 7F-Esrrb-D3


title: ATAC 7F-Sall4-D5

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using run_dfilter15 with options -non-zero -bs=100 -ks=20 -lpval=3 -refine -std=5
Genome_build: mm10
Supplementary_files_format_and_content: bed file were generated with genomeCoverageBed and bedGraphToBigbed. Scores represent the number of fragments overlapping each genomic position.

extract_protocol:
For ATAC-seq, a total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers instructions.


title: CCRF-CEM cell line

value: CCRF-CEM


title: ATAC 7F-Sall4-D7


title: ATAC 7F-Mkk6-D7


title: ATAC 7F-Nanog-D0


title: ATAC 7F-Nanog-D7


title: ATAC 7F-Sall4-D3


title: ATAC 7F-Nanog-D5


title: ATAC 7F-Kdm2b-D5


title: ATAC 7F-Kdm2b-D7


title: ATAC 7F-Map2k6-D3


title: ATAC 7F-Map2k6-D0


title: RNA 7F-Esrrb-D1


title: ATAC 7F-Kdm2b-D0


title: ATAC 7F-Kdm2b-D3


title: ATAC 7F-Jdp2-D7


title: ATAC 7F-Jdp2-D3


title: ATAC 7F-Glis1-D7


title: ATAC 7F-Sall4-D0


title: ATAC 7F-Glis1-D3


title: RNA 7F-Esrrb-D0


title: EPCAM_7

city: Freiburg

first: Nadim

last: Aizarani

address: Stübeweg 51

department: Independent group leaders

institute: MPI-IE

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
Supplementary_files_format_and_content: Normalhumanliverdata.RData: A count table or expression matrix for all the normal human liver cells. Use readRDS function to load data in R.

source_name: Liver tissue

growth_protocol: Cells were isolated from human liver specimens obtained from surgical resections

extract_protocol:
Liver specimens were perfused and treated with collagenase followed by Percoll purifcation/clean up steps
The amplified RNA (aRNA) was reversely transcribed in order to generate libraries for sequencing. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.
CEL-Seq2 (Hasimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)

treatment_protocol: no treatment

tag: tissue

value: Normal liver resection specimen

tag: cause of resections

value: Colorectal cancer metastasis


title: EPCAM_8


title: ATAC 7F-Mkk6-D5

value: reprogramming cells


title: ATAC 7F-Glis1-D0


title: EPCAM_6


title: ATAC 7F-Nanog-D3


title: ATAC 7F-Jdp2-D5


title: EPCAM_5


title: ATAC 7F-Esrrb-D7


title: EPCAM_4


title: ATAC 7F-Esrrb-D3


title: ATAC 7F-Esrrb-D0


title: EPCAM_2


title: ATAC 7F-Esrrb-D5


title: EPCAM_3


title: ATAC 7F-D7-rep2


title: ATAC 7F-D5-rep1


title: ATAC 7F-Jdp2-D0


title: ORG_14

description: early stage organoid cells

source_name: Human liver organoid cells

value: Human liver organoid cells grown from EPCAM+ cells


title: ATAC 7F-Glis1-D5


title: ATAC 7F-D3-rep1


title: ORG_12

description: early stage organoid cells


title: ATAC 7F-D7-rep1


title: ORG_9

description: early stage organoid cells


title: ORG_11

description: early stage organoid cells


title: ORG_8

description: early stage organoid cells


title: ATAC 7F-D0-rep1


title: ORG_10

description: early stage organoid cells


title: ChIP_Ring1b_siSA1_10-human

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

description: genomic DNA

data_processing:
ChIP-Seq processing. Alignment of sequences to the reference mouse genome (mm9, February 2009) was performed using ‘Bowtie2’ under default settings (Langmead and Salzberg, 2012) . Duplicates were removed using Picardtools (version 2.13.2) and peak calling was carried out using MACS2 (version 2.1.1.20160309) after setting the qvalue (FDR) to 0.05 and using the ‘--extsize’ argument with the values obtained in the ‘macs2 predictd’ step (Zhang et al., 2008).
RNA-Seq processing. Fastq files with 51-nt single-end sequenced reads were quality-checked with FastQC (S. Andrews, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the mouse genome (mm9) with Nextpresso (Graña et al., 2018) executing TopHat-2.0.0 using Bowtie 0.12.7 and Samtools 0.1.16 allowing two mismatches and five multi-hits. Transcript assembly, estimation of their abundances and differential expression were calculated with Cufflinks 1.3.0 using the mouse genome annotation dataset NCBIM37/mm9 from Ensembl. To account for multiple-hypothesis testing, the estimated significance level (P value) was adjusted using Benjamini–Hochberg FDR correction. We consider significant those changes with FDR < 0.05.
HiC processing. HiC was performed as described (Rao et al., 2014) using MboI enzyme. Libraries from two different experiments were generated and sequenced per condition. (>200 million reads each). Data were processed using TADbit (Serra et al., 2017) for read quality control, read mapping, interaction detection, interaction filtering, and matrix normalization. After a FastQC protocol to discard artifacts, the remaining reads were mapped to the reference mouse genome (mm10) using a fragment-based strategy in TADbit, after discarding non- informative contacts -including self-circles, dangling-ends, errors, random breaks or duplicates
Genome_build: mm9 for ChIP-seq/RNA-seq; mm10 for HiC
Supplementary_files_format_and_content: bigwig files were generated using the tool bamCoverage of deeptools

source_name: mES cells SA1 depleted

growth_protocol: mESCs were grown in DMEM containing 10% fetal calf serum in the presence of LIF (serum-grown condition). MEK inhibitor PD0325901 (1μM) and GSK3 inhibitor CHIR99021 (3μM) were added (2i-grown). In both cases plates were coated with 0.1% gelatin and no feeder cells were present.

extract_protocol:
For ChIP-seq experiments, lysates were clarified from sonicated nuclei and cohesin-DNA complexes were isolated with antibody. HiC was performed as described (Rao et al., 2014) using MboI enzyme. For RNA-Seq,  RNA was extracted using the RNeasy Mini Kit and treated with DNaseI.
ChIP-Seq liibraries were prepared as follows: From 5 to 15 ng of immunoprecipitated chromatin (as quantitated by fluorometry) were electrophoresed on an agarose gel and independent sample-specific fractions of 100–200 bp were taken. Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers.  Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. HiC libraries were performed as described (Rao et al., 2014) using MboI enzyme. For RNA-seq libraries, RNA was extracted as described and treated with DNaseI (Ambion). polyA+RNA was purified with the Dynabeads mRNA purification kit (Invitrogen), randomly fragmented and converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation Guide" (Part # 15008136 Rev. A). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: ES cells with 20% of human chromatin

tag: passages

tag: strain

value: Ring1B (gift from L. Di Croce)


title: ORG_7

description: early stage organoid cells


title: ChIP_Ring1b_siSA2_5-human

description: genomic DNA

source_name: mES cells SA2 depleted

value: ES cells with 5% of human chromatin


title: ORG_6

description: late stage organoid cells


title: ChIP_Ring1b_Control_10-human

description: genomic DNA

source_name: mES cells


title: EPCAM_1


title: ORG_5

description: late stage organoid cells


title: ChIP_Ring1b_siSA2_10-human

description: genomic DNA


title: ORG_4

description: late stage organoid cells


title: ORG_13

description: early stage organoid cells


title: ChIP_Ring1b_siSA1_5-human

description: genomic DNA


title: ChIP_2i_SA2_rep3

description: genomic DNA

source_name: mES cells + 2i

value: ES cells with 2i

value: custom made antibody for SA2 (STAG2)


title: ORG_3

description: late stage organoid cells


title: ORG_2

description: late stage organoid cells


title: ChIP_2i_SA2_rep2

description: genomic DNA


title: ChIP_2i_SA1_rep3

description: genomic DNA

value: custom made antibody for SA1 (STAG1)


title: ATAC 7F-D1-rep1


title: Hmouse_18

source_name: Human cells from humanised mouse liver

value: Normal human liver cells from humanised mouse liver

value: Human liver cells from normal liver resection specimens transplanted and engrafted into mouse liver


title: ORG_1

description: late stage organoid cells


title: ChIP_2i_SA2_rep1

description: genomic DNA


title: ChIP_2i_SA1_rep1

description: genomic DNA


title: Hmouse_16


title: ChIP_2i_SA1_rep2

description: genomic DNA


title: Hmouse_17


title: RNAseq_KPL_plusOHT_rep3

description:
OHT_rep3
PolyA RNA
processed data file: RNAseq_KPL_countmatrix.txt
processed data file: RNAseq_KPL_plusOHT_vs_minusOHT.txt

source_name: KPL cells

extract_protocol:
For global gene expression analysis, total RNA was isolated from cells using the RNeasy Mini Kit with on-column DNase I digestion (Qiagen).
Libraries were generated with 1 µg RNA with the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions. Library quality was analyzed with the Biorad Experion system.

value: KPL


title: Hmouse_15


title: RNAseq_KPL_plusOHT_rep2

description:
OHT_rep2
PolyA RNA
processed data file: RNAseq_KPL_countmatrix.txt
processed data file: RNAseq_KPL_plusOHT_vs_minusOHT.txt


title: Hmouse_13


title: Hmouse_14


title: Hmouse_12


title: RNAseq_KPL_minusOHT_rep3

description:
EtOH_rep3
PolyA RNA
processed data file: RNAseq_KPL_countmatrix.txt
processed data file: RNAseq_KPL_plusOHT_vs_minusOHT.txt

value: ctrl


title: RNAseq_KPL_plusOHT_rep1

description:
OHT_rep1
PolyA RNA
processed data file: RNAseq_KPL_countmatrix.txt
processed data file: RNAseq_KPL_plusOHT_vs_minusOHT.txt


title: RNAseq_KPL_minusOHT_rep2

description:
EtOH_rep2
PolyA RNA
processed data file: RNAseq_KPL_countmatrix.txt
processed data file: RNAseq_KPL_plusOHT_vs_minusOHT.txt


title: Hmouse_8


title: Hmouse_9


title: Hmouse_7


title: ChIPseq_KPL_H3K4me3_plusOHT

value: H3K4me3 (Abcam ab8580)


title: ChIPseq_KPL_H3K27ac_plusOHT


title: Hmouse_11


title: ChIPseq_KPL_H3K27ac_minusOHT


title: ChIPseq_KPL_H3K4me3_minusOHT


title: Hmouse_5


title: ChIPseq_KPL_H3K4me1_plusOHT

value: H3K4me1 (Abcam ab8895)


title: Hmouse_6


title: ChIP_2i_Input

description: genomic DNA


title: Hmouse_2


title: ChIPseq_KPL_H3K4me1_minusOHT


title: Hmouse_3


title: ChIPseq_KPL_inputHistones


title: Hmouse_4


title: Hmouse_1


title: HCCP3_4

source_name: Liver cancer

value: HCC specimen

value: HCC


title: ChIPseq_KPL_Lin9_plusOHT

value: LIN9 (Bethyl A300-BL3981)


title: HCCP3_3


title: ChIPseq_KPL_Lin9_minusOHT


title: ChIPseq_KPL_input_plusOHT


title: HCCP3_1


title: ChIPseq_KPL_input_minusOHT


title: ChIPseq_KPL_Yap_minusOHT


title: HCCP2_5


title: Msi Positive – H3K27ac Peak

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

description: ChIP-seq of H3K27ac (Stem)

data_processing:
Sequences quality controlled and trimmed using FASTQC and trim-galore respectively.
ChIP sequencing data was aligned to the UCSC mm10 mouse genome using the 3 Bowtie2 aligner (version 2.1.0 49 ), removing reads with quality scores of <15. Non-unique and duplicate reads were removed using samtools (version 0.1.16) and Picard tools (version 1.98), respectively.
Absolute H3K27ac occupancy in stem 6 cells and non-stem cells was determined using the SICER-df algorithm without an input control (version 7 1.1; 50 ), using a redundancy threshold of 1, a window size of 200bp, a fragment size of 150, an effective 8 genome fraction of 0.75, a gap size of 200bp and an E-value of 1000.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base.  bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.  peak files were generated with SICER-df algorithm without an input control (version 7 1.1; 50 ), using a redundancy threshold of 1, a window size of 200bp, a fragment size of 150, an effective 8 genome fraction of 0.75, a gap size of 200bp and an E-value of 1000.

source_name: ChIP-seq of H3K27ac (Stem)

growth_protocol: 70,000 REM2+/EpCAM+ (stem) and REM2-/EpCAM+ (non-stem) cells were freshly isolated as described above. ChIP was performed as described previously - Fox, R. G. et al. "Image-based detection and targeting of therapy resistance in pancreatic adenocarcinoma." Nature 534, 407-411, doi:10.1038/nature17988 (2016)

extract_protocol:
Library preparation of eluted chromatin immunoprecipitated DNA fragments was performed using the NEBNext Ultra II DNA library prep kit (E7645S and E7600S- NEB) for Illumina as per the manufacturer’s protocol.
Library prepped DNA was subjected to single-end, 75-nucleotide reads sequencing on the Illumina NexSeq500 sequencer at a sequencing depth of 20 million reads per sample.

treatment_protocol: Cells were pelleted by centrifugation and crosslinked with 1% formalin in culture medium using the protocol described previously 48 . Fixed cells were then lysed in SDS buffer and sonicated on a Covaris S2 ultrasonicator. The following settings were used: Duty factor: 20%, Intensity: 4 and 200 Cycles/burst, Duration: 60 seconds for a total of 10 cycles to shear chromatin with an average fragment size of 200-400 bp. ChIP for H3K27Acetyl was performed using the antibody ab4729 (Abcam, Cambridge, UK) specific to the H3K27Ac modification.

value: REM2+/EpCAM+ (stem)

value: H3K27ac antibody ab4729 (Abcam, Cambridge, UK)


title: Msi Negative – H3K27ac Peak

description: ChIP-seq of H3K27ac (Non-stem)

source_name: ChIP-seq of H3K27ac (Non-stem)

value: REM2-/EpCAM+ (non-stem)


title: RNAseq_KPL_minusOHT_rep1

description:
EtOH_rep1
PolyA RNA
processed data file: RNAseq_KPL_countmatrix.txt
processed data file: RNAseq_KPL_plusOHT_vs_minusOHT.txt


title: Hmouse_10


title: HCCP2_4


title: ChIPseq_KPL_Yap_plusOHT


title: HCCP2_3


title: HCCP2_1


title: HCCP1_11


title: HCCP2_2


title: GBM CAF 1

city: San Francisco

first: Jordan

middle: Matthew

last: Spatz

address: 1450 3rd Street

department: Department of Neurosurgery

institute: UCSF

data_processing: GBM CAF RNASeq datasets were aligned (BowTie2) and gene exons counted (FeatureCounts) with standard inputs using the Galaxy public server

molecule: polyA RNA

source_name: Brain

extract_protocol:
Qiagen Total RNA
Illumina Poly-A Enrichment

value: Cancer Associated Fibroblast

tag: age

value: 62 years old

tag: Sex

value: female


title: HCCP1_10


title: HCCP1_9


title: HCCP1_8


title: HCCP1_7


title: HCCP1_6


title: PBS_d21_Veh_R6_skin

city: Pennington

first: Ron

last: Ammar

state: New Jersey

address: 311 Pennington Rocky Hill Road

institute: Bristol-Myers Squibb

data_processing:
Reads were aligned to the Mus musculus GRCm38 reference genome (NCBI assembly accession GCF_000001635.20) with the Omicsoft Sequence Aligner.
Gene and transcript abundance was determined with Ensembl R86 mouse gene models using RSEM.
All RNA-Seq data were processed in R with Bioconductor packages.
RNA-Seq samples were TMM normalized with the edgeR package.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files of counts and log2CPM

extract_protocol:
Total RNA was prepared using the RNeasy 96 kit (Qiagen, Germany) according to the manufacturer's instructions. cDNA synthesis was performed with high capacity RNA to cDNA kit (Life Technologies, Carlsbad, CA). Sequencing libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina, San Diego, CA) following manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: ~12 weeks old

value: PBS

tag: time point

value: skin

tag: tissue source

value: punch biopsy


title: BLM_d21_Veh_R5_skin

tag: treatment

value: BLM


title: PBS_d21_Veh_R8_skin


title: BLM_d28_SB525334_R7_skin


title: PBS_d14_R8_skin


title: BLM_d14_R1_skin


title: BLM_d28_SB525334_R3_skin


title: BLM_d7_R4_skin


title: HCCP3_2


title: GBM CAF 2

value: Cancer Assoicated Fibroblast

value: 67 years old


title: BLM_d21_SB525334_R9_skin


title: HCCP1_5


title: HCCP1_4


title: BLM_d7_R2_skin


title: HCCP1_1


title: PBS_d14_R7_skin


title: HCCP1_12


title: BLM_d28_SB525334_R2_skin


title: BP_4

value: normal liver resection specimen

value: Colorectal cancer metastasis


title: HCCP1_2

value: HCC specimen

value: HCC


title: PBS_d28_Veh_R6_skin


title: PBS_d7_R7_skin


title: BP_2


title: BP_3


title: PBS_d42_Veh_R7_skin


title: PBS_d28_Veh_R7_skin


title: P325_61


title: BLM_d14_R6_skin


title: BLM_d21_Veh_R6_skin


title: BLM_d7_R3_skin


title: PBS_d28_Veh_R4_skin


title: BLM_d21_SB525334_R7_skin


title: P325_59


title: BLM_d28_Veh_R3_skin


title: P325_58


title: BLM_d14_R7_skin


title: P325_55


title: P325_56


title: P325_57


title: BLM_d21_Veh_R4_skin


title: P325_53


title: P325_54


title: P325_52


title: PBS_d14_R6_skin


title: BLM_d21_Veh_R1_skin


title: P325_51


title: PBS_d21_Veh_R5_skin


title: P325_50


title: PBS_d7_R2_skin


title: BLM_d21_SB525334_R4_skin


title: BLM_d42_Veh_R5_skin


title: P325_49


title: BLM_d21_SB525334_R6_skin


title: BLM_d42_Veh_R1_skin


title: P325_47


title: P325_46


title: PBS_d7_R1_skin


title: P325_48


title: BLM_d28_Veh_R7_skin


title: P325_44


title: P325_45


title: BLM_d21_SB525334_R5_skin


title: P325_43


title: BLM_d14_R2_skin


title: P325_42


title: PBS_d14_R2_skin


title: PBS_d14_R3_skin


title: P325_41


title: P325_37


title: P325_38


title: PBS_d7_R4_skin


title: BLM_d42_Veh_R7_skin


title: BLM_d42_Veh_R6_skin


title: P325_35


title: BLM_d28_SB525334_R6_skin


title: P325_34


title: BLM_d28_Veh_R5_skin


title: P325_36


title: P325_32


title: PBS_d7_R3_skin


title: BLM_d14_R5_skin


title: PBS_d7_R6_skin


title: PBS_d28_Veh_R3_skin


title: P325_28


title: P325_30


title: P325_29


title: P325_33


title: PBS_d14_R4_skin


title: P325_31


title: BLM_d7_R7_skin


title: P325_26


title: BLM_d42_Veh_R8_skin


title: BLM_d28_SB525334_R4_skin


title: BLM_d7_R6_skin


title: P325_23


title: P325_22


title: BLM_d28_Veh_R1_skin


title: BLM_d42_Veh_R3_skin


title: BLM_d21_SB525334_R1_skin


title: BLM_d21_Veh_R3_skin


title: BLM_d28_SB525334_R5_skin


title: P325_20


title: P325_19


title: PBS_d42_Veh_R3_skin


title: BLM_d42_Veh_R2_skin


title: P325_25


title: P325_24


title: BLM_d14_R3_skin


title: PBS_d21_Veh_R1_skin


title: BLM_d28_Veh_R4_skin


title: P325_21


title: PBS_d14_R1_skin


title: BLM_d28_SB525334_R8_skin


title: PBS_d21_Veh_R7_skin


title: PBS_d42_Veh_R4_skin


title: PBS_d42_Veh_R5_skin


title: P325_13


title: BLM_d21_Veh_R7_skin


title: PBS_d21_Veh_R4_skin


title: P325_18


title: P325_16


title: P325_17


title: BLM_d42_Veh_R4_skin


title: PBS_d42_Veh_R6_skin


title: BLM_d21_SB525334_R8_skin


title: P325_6


title: P325_8


title: P325_11


title: P325_7


title: P325_12


title: PBS_d42_Veh_R8_skin


title: P325_4


title: P325_15


title: BLM_d14_R4_skin


title: P325_14


title: P325_5


title: PBS_d42_Veh_R2_skin


title: P325_3


title: BLM_d7_R5_skin


title: P325_10


title: P325_2


title: P325_1


title: PBS_d28_Veh_R2_skin


title: P325_9


title: BLM_d7_R1_skin


title: PBS_d28_Veh_R1_skin


title: P315_32


title: BLM_d28_Veh_R2_skin


title: BLM_d28_SB525334_R1_skin


title: PBS_d7_R8_skin


title: HCCP1_3


title: P315_30


title: P315_31


title: P315_28


title: PBS_d28_Veh_R5_skin


title: BLM_d21_SB525334_R3_skin


title: P315_26


title: P315_24


title: P325_60


title: P315_21


title: P315_23


title: P315_20


title: P315_19


title: BLM_d28_Veh_R6_skin


title: P315_17


title: P315_22


title: PBS_d21_Veh_R3_skin


title: P315_18


title: P315_27


title: P315_29


title: PBS_d7_R5_skin


title: BLM_d14_R8_skin


title: PBS_d14_R5_skin


title: P315_25


title: BP_1


title: P315_16


title: PBS_d21_Veh_R2_skin


title: BLM_d28_Veh_R5_lung

value: lung

value: superior lobe


title: BLM_d28_Veh_R1_lung


title: P315_14


title: P315_15


title: BLM_d21_Veh_R2_skin


title: P315_13


title: BLM_d28_SB525334_R3_lung


title: P315_12


title: BLM_d42_Veh_R7_lung


title: P315_11


title: PBS_d42_Veh_R1_skin


title: BLM_d28_SB525334_R1_lung


title: PBS_d28_Veh_R2_lung


title: PBS_d7_R1_lung


title: BLM_d42_Veh_R5_lung


title: BLM_d14_R6_lung


title: BLM_d42_Veh_R6_lung


title: PBS_d7_R8_lung


title: P315_7


title: P315_6


title: BLM_d28_SB525334_R5_lung


title: PBS_d28_Veh_R1_lung


title: P315_10


title: P311_23


title: P315_9


title: P315_8


title: P315_5


title: P315_3


title: P315_2


title: BLM_d21_Veh_R2_lung


title: BLM_d21_SB525334_R7_lung


title: P315_4


title: PBS_d14_R3_lung


title: P311_22


title: P315_1


title: BLM_d28_SB525334_R8_lung


title: P311_20


title: P311_21


title: P311_19


title: PBS_d21_Veh_R8_lung


title: BLM_d21_SB525334_R6_lung


title: P311_18


title: BLM_d28_SB525334_R6_lung


title: P311_17


title: PBS_d42_Veh_R4_lung


title: P311_16


title: PBS_d28_Veh_R6_lung


title: BLM_d28_Veh_R3_lung


title: BLM_d28_Veh_R6_lung


title: BLM_d14_R7_lung


title: PBS_d42_Veh_R6_lung


title: P311_12


title: BLM_d14_R1_lung


title: P311_13


title: PBS_d42_Veh_R8_lung


title: BLM_d7_R1_lung


title: P311_11


title: BLM_d28_Veh_R2_lung


title: P311_9


title: P311_10


title: P311_8


title: P311_7


title: PBS_d21_Veh_R5_lung


title: PBS_d14_R8_lung


title: PBS_d42_Veh_R3_lung


title: PBS_d21_Veh_R1_lung


title: P311_4


title: P311_6


title: P311_5


title: P311_2


title: P311_14


title: P311_3


title: BLM_d28_SB525334_R2_lung


title: BLM_d14_R2_lung


title: P310_28


title: PBS_d14_R7_lung


title: P310_27


title: P325_27


title: P310_26


title: BLM_d42_Veh_R8_lung


title: P310_25


title: PBS_d28_Veh_R3_lung


title: BLM_d21_Veh_R6_lung


title: BLM_d21_Veh_R1_lung


title: P310_22


title: P311_1


title: P310_23


title: P310_24


title: PBS_d28_Veh_R7_lung


title: P310_19


title: P310_21


title: BLM_d21_SB525334_R9_lung


title: BLM_d28_Veh_R7_lung


title: BLM_d14_R3_lung


title: BLM_d28_SB525334_R7_lung


title: PBS_d42_Veh_R1_lung


title: P310_20


title: P310_17


title: P310_18


title: BLM_d21_Veh_R3_lung


title: BLM_d42_Veh_R3_lung


title: PBS_d7_R3_lung


title: PBS_d28_Veh_R4_lung


title: P310_14


title: P310_16


title: P310_15


title: PBS_d7_R5_lung


title: PBS_d21_Veh_R3_lung


title: P310_13


title: P310_12


title: BLM_d14_R4_lung


title: BLM_d21_Veh_R7_lung


title: P310_10


title: P310_11


title: PBS_d21_Veh_R6_lung


title: P310_9


title: BLM_d28_Veh_R4_lung


title: BLM_d21_SB525334_R1_lung


title: PBS_d7_R7_lung


title: P310_7


title: BLM_d21_SB525334_R4_lung


title: P310_8


title: P310_4


title: BLM_d21_SB525334_R2_lung


title: P310_5


title: PBS_d14_R5_lung


title: P310_3


title: PBS_d7_R2_lung


title: BLM_d7_R6_lung


title: BLM_d21_SB525334_R8_lung


title: P310_1

value: Cholangiocarcinoma


title: P309_18


title: BLM_d14_R8_lung


title: BLM_d21_Veh_R5_lung


title: P309_16


title: PBS_d42_Veh_R7_lung


title: P310_6


title: P310_2


title: PBS_d14_R6_lung


title: PBS_d21_Veh_R2_lung


title: P309_14


title: PBS_d28_Veh_R5_lung


title: P309_13


title: Laser_Time60_rep2

city: Knoxville

first: Melinda

last: Hauser

address: 1311 Cumberland Ave

department: Microbiology

institute: The University of Tennessee

data_processing:
LaserGene SeqMan Ngen version# 14.1.0(115) DNASTAR, Inc. Madison WI
Assembly Workflow = Transcriptome.RNASeq
Assembly Type = Reference based assembly
Genome_build: S. cerevisiae S288C (NCBI Bioproject:PRJNA43747)
Supplementary_files_format_and_content: Excel file includes RPKM, p-values and fold change for each Sample .

organism: Saccharomyces cerevisiae

source_name: Cell pellet

growth_protocol: Yeast were grown in YEPD, harvested and suspended in PBS prior to irradiation

extract_protocol:
RNA extracted from frozen cell pellets by bead-beating in hot acid-phenol/chloroform
Tru-Seq Stranded mRNA kit (Illumina)

treatment_protocol: Yeast cells were irradiated with UV laser for 30s then transferred into fresh YEPD.  Cultures were incubated at 30C, aliquots were removed at 0, 15, 30 and 60 minutes and stored as frozen pellets.

tag: sample collection time (minutes post-transfer to yepd)

value: Laser Irradiated


title: PBS_d7_R4_lung


title: P309_12


title: P309_17


title: Laser_Time60_rep3


title: BLM_d7_R3_lung


title: Laser_Time30_rep3


title: Laser_Time60_rep1


title: P309_11


title: Laser_Time30_rep1


title: P309_10


title: Laser_Time30_rep2


title: BLM_d21_SB525334_R5_lung


title: P309_9


title: Laser_Time15_rep1


title: P309_15


title: Laser_Time15_rep2


title: P309_8


title: BLM_d21_SB525334_R2_skin


title: Laser_Time15_rep3


title: BLM_d14_R5_lung


title: BLM_d21_Veh_R4_lung


title: BLM_d28_SB525334_R4_lung


title: Laser_Time0_rep1


title: P309_7


title: Laser_Time0_rep3


title: Laser_Time0_rep2


title: BLM_d42_Veh_R2_lung


title: Control_Time60_rep3

value: Control


title: BLM_d42_Veh_R1_lung

value: female


title: Control_Time30_rep3


title: Control_Time60_rep2


title: PBS_d14_R4_lung

value: ~12 weeks old


title: Control_Time60_rep1


title: P309_5


title: Control_Time30_rep2


title: PBS_d14_R1_lung

value: PBS


title: Control_Time15_rep3


title: P309_6


title: Control_Time30_rep1


title: P309_3


title: P309_4


title: Control_Time15_rep1


title: PBS_d42_Veh_R2_lung


title: Control_Time15_rep2


title: P309_2


title: Control_Time0_rep3


title: PBS_d21_Veh_R7_lung


title: P309_1


title: BLM_d21_SB525334_R3_lung


title: Control_Time0_rep1


title: Control_Time0_rep2


title: P308_38


title: YRSK_d5_rep1ATAC

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
fastqc
Read were aligned to mouse genome assembly (mm10) using bowtie2 (--very-sensitive --end-to-end --no-unal --no-mixed -X 2000).
Low quality mapped reads were removed using samtools (view –q 30).
PCR duplicates were removed using samtools (rmdup) to keep uniquely mapped reads.
The BAM files of time point replicates of each sample were merged with samtools (merge) prior to peak calling with MACS2 (-g mm -f BAMPE).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file were generated with genomeCoverageBed followed by bedGraphToBigWig.

growth_protocol: OG2-MEF cells were transduced twice by pMX-Sox2, Klf4 along with Oct4 or Oc6 or engineered Oct4 (YR or Oct4defSox2) retroviruses produced using PlatE cells in DMEM + 10% FBS media supplemented with 1x NEAA and Glutamax. After second viral transduction, the medium was switched to highly efficient chemically defined (iCD1) reprogramming medium. The iCD media switch day was defined as day 0 and cells were further cultured with daily media change.

extract_protocol:
A total of 50,000 cells (reprogrammed with O4SK, O6SK and O4defS2SK retroviruses) were collected at days 1 and 5 of reprogramming in replicates. Cells were washed once with 50 μL of cold PBS; centrifuged at 500 x g for 5 min at 4°C and cell pellets were resuspended in 50 μL cold ATAC lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) by slowly pipetting up and down and immediately spun down at 500 x g for 10 min at 4°C to collect nuclei.  Nuclei were washed in 1x PBS and subsequently re-suspended in 50 μL transposition reaction mix (25 μL 2 x TD reaction buffer, 22.5 μL nuclease-free water, 2.5 μL Tn5 transposase) of Nextera DNA library preparation kit (FC-121-1030, Illumina). Samples were incubated at 37°C for 30 min and DNA was isolated using minElute Kit (Qiagen). The transposed DNA was then amplified with custom primers as described for 1 cycle of 72°C for 5 min, 98°C for 30 sec followed by 5 cycles of 98°C for 10 sec, 63°C for 30sec, 72°C for 1 min. To determine the suitable number of cycles required for next round of PCR the library was assessed by quantitative PCR. Libraries qualities were assessed using Bioanalyzer high sensivity DNA analysis kit (Agilent) followed by paired-end sequencing with the length of 150 nucleotides using Hiseq X10 (illumina) at Annoroad Gene Technology (http://en.annoroad.com/).
The libraries were generated using the Nextera DNA Library Prep kit (Illumina)

tag: cell type

value: reprogramming cells


title: YRSK_d5_rep2ATAC


title: YRSK_d1_rep2ATAC


title: PBS_d21_Veh_R4_lung


title: BLM_d7_R7_lung


title: YRSK_d1_rep1ATAC


title: PBS_d42_Veh_R5_lung


title: O6SK_d5_rep2ATAC


title: P308_35


title: O4SK_d5_rep2ATAC


title: O6SK_d1_rep2ATAC


title: O6SK_d1_rep1ATAC


title: O6SK_d5_rep1ATAC


title: BLM_d42_Veh_R4_lung


title: P308_36


title: O4SK_d5_rep1ATAC


title: O4SK_d1_rep2ATAC


title: O4SK_d1_rep1ATAC


title: BLM_d7_R5_lung


title: P308_33


title: PBS_d7_R6_lung


title: P308_37


title: P308_31


title: P308_30


title: P308_34


title: BLM_d7_R2_lung


title: P308_29


title: PBS_d14_R2_lung


title: P308_32


title: Test-null-Index29-OtA9458

city: Lubbock

first: Beverly

middle: S

last: Chilton

state: TX

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

description:
Index29_OtA9458
index29_CAACTA_L001-L002

data_processing:
Paired-end 106 nucleotide reads were mapped against the reference genome mm10 with star2.4.0j
Comparison of expression level (fpkm_tracking) and differential expression analysis was conducted with cufflinks.cuffdiff (2.2.1).
Exon quantification was performed to show the relative expression of all known Hltf exons in control tumors
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of RPKM values for each gene; RPKM values for alternative splicing of each gene

source_name: Hltf-deleted (-/-)_colorectal tumors

extract_protocol:
Individual samples [all tumors from an individual mouse/sample x 3 biological replicates for test and control male mice = 6 total samples] were flash frozen and sent to Otogenetics Corp.
Random-primed cDNA (rRNA depleted) using standard Ilumina Protocols

treatment_protocol: To recreate the aberrant crypt foci – adenoma – carcinoma sequence in human CRC, randomly selected six- to eight-week old Hltf-deleted and control male mice were given a single intraperitoneal (IP) injection of 10 mg/kg AOM, a potent carcinogen used to induce colon cancer in rodents. All experimental protocols began at 8 AM in the LARC housing facility. After 3-days of recovery, mice were given the first of four cycles of 3% DSS ad libitum. Each cycle lasted five days followed by a 16-day recovery period except for the last cycle in which mice were sacrificed 26-days after the last DSS treatment.  Mice were weighed every seven days throughout the treatment protocol.

tag: genotype/variation

value: Hltf-deleted (-/-) mice

value: colorectal tumors


title: Test-null-index34-OtA9895

description:
Index34_OtA9895
index34_CATGGC_L001-L002


title: P308_26


title: P308_27


title: Control Index 33-OtA9894

description:
Index33_OtA9894
index33_CAGGCG_L001-L002

source_name: control Hltf+/+_colorectal tumors

value: control Hltf+/+ mice


title: PCL.035: PCL at diagnosis, sample 14

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 2.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 21 for Human GeneChip Gene 2.0 ST transcript annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/ genecodet.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur. Only genes identified by probesets with 4 or more specifc probes within were retained.  The gained CDF results a umich GENCODEG-like annotation that retains only unambiguous signals for lncRNA and coding genes that partially overlap in thier genomic position.

source_name: Highly purified PCs from PCL patient

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100-250 nanograms of total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

value: Bone marrow plasma cells

tag: diagnosis

value: Plasma cell leukemia (PCL)


title: PCL.031: PCL at diagnosis, sample 11

value: MAF translocation


title: PCL.032: PCL at diagnosis, sample 12


title: PCL.033: PCL at diagnosis, sample 13

value: non-hyperdiploid karyotype, no major IgH (14q32) chromosomal translocations


title: PCL.028: PCL at diagnosis, sample 9


title: PCL.049: PCL at diagnosis, sample 15


title: PCL.020: PCL at diagnosis, sample 6


title: P308_25

value: normal liver resection specimen

value: Colorectal cancer metastasis


title: BLM_d7_R4_lung

value: BLM

value: lung

value: superior lobe


title: PCL.016: PCL at diagnosis, sample 4


title: P308_28


title: PCL.030: PCL at diagnosis, sample 10


title: Control Index 32-OtA9463

description:
Index32_OtA9463
index32_CACTCA_L001-L002


title: Test-null-Index30-OtA9459

description:
Index30_OtA9459
index30_CACCGG_L001-L002


title: PCL.018: PCL at diagnosis, sample 5


title: PCL.026: PCL at diagnosis, sample 8


title: PCL.011: PCL at diagnosis, sample 2


title: Control Index 31-OtA9461

description:
Index31_OtA9461
index31_CACGAT_L001-L002


title: P308_24


title: PCL.006: PCL at diagnosis, sample 1


title: P308_23


title: PCL.021: PCL at diagnosis, sample 7


title: MM.464: MM at diagnosis, sample 50

source_name: Highly purified PCs from MM patient

value: Multiple myeloma (MM)


title: MM.431: MM at diagnosis, sample 49


title: P308_22

source_name: Liver tissue


title: P308_21


title: P308_20


title: 9_NA_N4_1000

city: MINNEAPOLIS

first: Ryan

last: Langlois

state: MN

institute: University of Minnesota

description: 1,000 OT-I transferred into in B6 mice and infected with IAV-N4, control for clonal burst size. TRM sorted 35 days post infection

data_processing:
Sequencing reads were mapped to the mouse (mm10) genome using Bowtie aligner (bowtie2 version 2.2.4) with local mode, -L 22 and -N 1 parameters.
Reads were sorted and filtered by removing the PCR duplicates with Samtools (version 1.16) and assigned to Ensembl gene models (Mus_musculus.GRCm38.87.gtf) with featureCounts of the Subread software package (version 1.5)
Differentially expressed genes were compared between IAV_N4 and IAV_T4 samples. Statistical analysis was performed using the edgeR bioconductor package.
Genome_build: mm10

source_name: FACS-sorted TRM cells from lung

growth_protocol: OT-I CD8+ T cells were transferred into mice and animals were challenged with 40 PFU of IAV_N4 or IAV_T4. After 34 days, lungs were harvested after CD8-alpha iv staining, and single cell suspensions were sorted for live CD4-B220-F4/80-CD8+iv-CD45.1+CD45.2-Valpha2+CD44hi cells. Cells were FACS sorted directly into cell cysis buffer for RNA extraction.

extract_protocol:
OT-I cells from IAV_N4 and IAV_T4 infected mice were sorted and RNA was extracted using RNeasy Micro Plus kit (Qiagen).
The cDNA library was prepared using a strand-specific RNA-seq protocol.

treatment_protocol: Mice were infected with 40 PFU of IAV_N4 or IAV_T4

value: CD8+i.v.- OT-I TRM

tag: iav subtype

value: IAV-N4 (high affinity)

tag: # ot-i t cells injected into mice

tag: mouse age

value: 8-12 weeks

value: female

tag: body site


title: 8_NA_T4_50000

description: 50,000 OT-I transferred into in B6 mice and infected with IAV-T4. TRM sorted 35 days post infection

value: IAV-T4 (low affinity)


title: MM.402: MM at diagnosis, sample 46

tag: tissue


title: P308_19

tag: cause of resections


title: 7_NA_T4_50000

tag: strain


title: 6_NA_T4_50000


title: P308_18


title: P308_17


title: 10_NA_N4_1000


title: 11_NA_N4_1000


title: 4_NA_N4_50000

description: 50,000 OT-I transferred into in B6 mice and infected with IAV-N4. TRM sorted 35 days post infection


title: MM.313: MM at diagnosis, sample 38


title: MM.314: MM at diagnosis, sample 39


title: MM.302: MM at diagnosis, sample 36

value: hyperdiploid karyotype


title: MM.310: MM at diagnosis, sample 37


title: MM.413: MM at diagnosis, sample 48


title: MM.392: MM at diagnosis, sample 44


title: MM.375: MM at diagnosis, sample 43


title: MM.335: MM at diagnosis, sample 42


title: MM.398: MM at diagnosis, sample 45


title: 3_NA_N4_50000


title: MM.321: MM at diagnosis, sample 40


title: MM.295: MM at diagnosis, sample 34

value: no information about hyperdiploid status, no major IgH (14q32) chromosomal translocations


title: MM.330: MM at diagnosis, sample 41

value: Bone marrow plasma cells


title: MM.278: MM at diagnosis, sample 33


title: P308_16


title: P308_15


title: 2_NA_N4_50000


title: MM.301: MM at diagnosis, sample 35


title: P308_14


title: MM.274: MM at diagnosis, sample 32


title: P308_13


title: P308_11


title: P308_12


title: P308_10


title: MM.269: MM at diagnosis, sample 31


title: mm_rna_preb_il7minus-cxcl12plus-ERKinhibitorIIplus.2

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
genome alignment (RNA-seq): Raw reads were aligned to the reference genome using STAR
genome alignment (ATAC-seq): Raw reads were aligned to the reference genome using BWA MEM. Apparent PCR duplicates were removed using Picard MarkDuplicates.
gene expression quantification (RNA-seq): Counts per gene were generated using featureCounts.
peak calling (ATAC-seq): Read alignments were first adjusted to account for TAC transposon binding: +4bp for + strand alignments, -5bp for - strand alignments. The open chromatin enrichment track was generated by first creating a bedGraph from the raw reads using bedtools genomcov v2.18.2, then coverted to bigWig using UCSC tool bedGraphToBigWig; tracks were normalized by the sum of alignment lengths over 1 billion. The start position track was generated by taking just the first base of the alignment for + strand alignments or the last base of the alignment for - strand alignments, then creating bedGraph and bigWig tracks as for the open chromatin; tracks were normalized to counts per billion bases in the library. Open chromatin peaks were called using Macs2 with --nomodel set and no background provided; peaks with a score >5 were retained.
Genome_build: mouse: mm9
Supplementary_files_format_and_content: RNA-Seq: Read counts per gene: tab-delimited text table
Supplementary_files_format_and_content: ATAC Peak calls from Macs2: bed format
Supplementary_files_format_and_content: ATAC-seq open chromatin enrichment, normalized to counts per billion bases: bigWig format

source_name: IL- CXCL12+ ERK inhibitorII+ pre-B

extract_protocol: RNA was isolated from flow sorted B cell populations with the Qiagen RNeasy kit (Qiagen). Concentration and purity was analyzed on a Nanodrop 1000 Spectrophotometer. mRNA was isolated by oligo-dT beads and library was prepared using standard Illumina library protocol (Kit: RS-122-2101 TruSeq® Stranded mRNA LT-SetA). Libraries were sequenced on the Illumina Hiseq2500.

value: IL- CXCL12+ ERK inhibitorII+ pre-B


title: Fcmr+/+

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

country: Canada

institute: Princess Margaret Cancer Centre, University Health Network

data_processing:
The raw sequencing reads were processed for quality control, mapping (to mouse genome build GRCm38), and UMI (unique molecular identifier) count matrix assembly using the CellRanger bioinformatics pipeline v2.0.1 provided by 10xGenomics.
Normalization, clustering, and gene expression analysis were carried out using the Seurat R Package v2.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: Barcode, gene, and expression matrix

source_name: B16 melanoma tumor

extract_protocol:
B16 melanoma tumor-bearing mice were euthanized in accordance with animal use protocol guidelines. Tumors ranging in size from 500–1000 mm^3 were resected and weighed to the nearest 0.001g, diced into 1-2 mm3 pieces, and subjected to enzymatic digestion with a Tumor Dissociation Kit (Miltenyi Biotec) following the manufacturer’s protocol. Dissociation was performed in C-tubes (Miltenyi Biotec) at 37C on a GentleMACS Octo-MACS Dissociator with Heaters (Miltenyi, Biotec) prior to immune cell isolation via fluorescence-activated cell sorting (FACS). Tumor mononuclear phagocytes (TMPs) isolated via FACS, were washed, assessed for viability and morphology, and loaded onto a 10X Chromium instrument (10X Genomics) according to the manufacturer’s instructions.
Libraries were prepared using the 10X Genomics Chromium Single Cell 3’ v4 Chemistry Reagent Kit, as per the parameters recommended by 10X Genomics.

value: Fcmr+/+


title: S12_Filamentous_1

first: Yun

last: Fang

state: Guangzhou

address: 100 Central Xianlie Road

institute: Guangdong Institute of Microbiology

description: exposed to azo dye for 8h

data_processing:
After sequencing, four steps were taken to get a clean reads dataset with high quality. (1) Remove the reads with excess of "N"; (2) eliminate the reads caused by adapter contamination; (3) get rid of the reads that have more than 36 bases with low quality (quality score < 20); (4) Wipe away the duplicated reads generated by PCR amplification.
The clean data were mapped on the annotated genomic objects identified in the genome of S. decolorationis S12 using Tophat 2.0.11 and samtools 0.1.18.0, yielding BAM files (Trapnell et al., 2012; Li et al., 2009).
Sorted and indexed BAM files were analyzed by Cufflinks 2.0.0 (Trapnell et al., 2010) to calculate the number of fragments per kilobase of transcript permillion mapped reads (FPKM) for all genes and thereby detect differentially expressed genes.
Based on the calculations made by Cuffdiff, genes with |log2 fold changes (filamentous verse normal cell)| > 1 and FDR-p value < 0.05 were marked as significant.
Genome_build: AXZL01000000 (Shewanella decolorationis S12)
Supplementary_files_format_and_content: tab-delimited text files include FPKM value and Log2 (fold change)

organism: Shewanella decolorationis S12

growth_protocol: Shewanella decolorationis S12  was grown to a defined medium (pH 7.0) containing 7.64 g/L Na2HPO4, 3.00 g/L KH2PO4, 0.50 g/L NH4Cl, 1.00 g/L NaCl, 5.00 mmol/L sodium lactate, 0.5 g/L yeast extract, 0.50 mmol/L amaranth and statically cultivated at 30°C in anaerobic workstation (BugBox, Ruskinn Technologies).

extract_protocol:
Total RNA from the cell pellet was isolated using a TRIzol Reagent kit (Invitrogen, Carlsbad, USA) following the manufacturer’s instructions. RNA samples were treated with RNase-free DNaseI (QIAGEN, Carlsbad, USA) to digest residual genomic DNA and then purified by an RNeasy kit (Qiagen, Valencia, USA). Ribosomal RNA was removed by a RiboZero™ rRNA Removal kit (Epicenter, Madison, USA) following the manufacturer’s protocols (Bhagwat et al., 2014).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: taxonomy

value: Gammaproteobacteria

tag: cultivation

value: 8 h


title: S12_Filamentous_3

description: exposed to azo dye for 8h


title: mm_rna_preb_il7plus-cxcl12plus.2

source_name: IL+ CXCL12+ pre-B

value: IL+ CXCL12+ pre-B


title: 1_NA_N4_50000

tag: Sex


title: S12_Normal_3

description: exposed to azo dye for 0.5h


title: MM.268: MM at diagnosis, sample 30

value: non-hyperdiploid karyotype, no major IgH (14q32) chromosomal translocations


title: Fcmr-/-

value: Fcmr-/-


title: S12_Filamentous_2

description: exposed to azo dye for 8h


title: MM.263: MM at diagnosis, sample 29


title: IL23+IL15+IL1b_1

city: St. Louis

first: Marco

last: Colonna

address: 425 Euclide Ave

department: Pathology and Immunology

institute: Washington University in St.Louis

hyb_protocol: Products were hybridized to Affymetrix Human Gene 1.0 ST arrays according to the manufacturer’s protocol

data_processing: Data were analyzed with GenePattern software (Broad Institute). Raw data were normalized using standard RMA workflow.

source_name: tonsil ILC3 expanded in vitro stimulated ovenight with IL-23,IL-15 and IL-1b

label_protocol: Purified RNA was amplified using Nugen Ovation Pico SL or Ovation Pico kits and labeled using Nugen Encore Biotin kit.

growth_protocol: Cells were grown in IL-7 (10ng/ml)+SCF(10ng/ml) for 15-20 days. They were left unstimulated or stimulated with IL-23, IL-15 and IL-1b (all 50ng/ml)

extract_protocol: RNA was prepared with Micro RNAeasy kit following manufacturer instructions

value: tonsil

tag: markers


title: IL-7+SCF_2

source_name: tonsil ILC3 expanded in vitro


title: P308_8

value: normal liver resection specimen

value: Colorectal cancer metastasis


title: MM.243: MM at diagnosis, sample 28

value: Multiple myeloma (MM)


title: MM.239: MM at diagnosis, sample 27


title: MM.213: MM at diagnosis, sample 26


title: MM.212: MM at diagnosis, sample 25


title: IL23+IL15+IL1b_2

source_name: tonsil ILC3 expanded in vitro stimulated ovenight with IL-23, IL-15 and IL-1b


title: mm_rna_preb_il7plus-cxcl12plus.1


title: S12_Normal_2

description: exposed to azo dye for 0.5h


title: P308_7


title: P308_9


title: S12_Normal_1

description: exposed to azo dye for 0.5h


title: MM.206: MM at diagnosis, sample 24


title: IL7+SCF_1


title: mm_rna_spreb_cxcr4ko_il7minus.cxcl12plus.2

source_name: IL- CXCR4-/- CXCL12+ small pre-B

value: IL- CXCR4-/- CXCL12+ small pre-B


title: mm_rna_spreb_cxcr4ko_il7minus.cxcl12plus.1


title: mm_rna_spreb_cxcr4ko_il7minus.2

source_name: IL- CXCR4-/- small pre-B

value: IL- CXCR4-/- small pre-B


title: P308_5


title: P308_6


title: CTCF_ChIP-seq_Asynchronous

city: Tsukuba

first: Takeshi

last: SEKIYA

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: ChIP antibody: CTCF (Sci. Rep. 3, 2187)

data_processing:
Basecalls performed using Lifescope Genomemic Analysis Software 2.5.1
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope Genomemic Analysis Software 2.5.1
Peaks were called by MACS
BAM to BED conversion by bedtools
BED to BedGraph conversion by bedtools
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited BedGraph files format, containing column 1 to 4 defined in UCSC web site(https://genome.ucsc.edu/FAQ/FAQformat.html)

source_name: Mammary gland, epithelial

growth_protocol: MCF-7 cells were maintained at 37°C in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum

extract_protocol:
Cells were washed with cold PBS(-), and kept on ice for 5 min in a cold CSK buffer (10 mM PIPES-NaOH, pH 6.8, 100 mM NaCl, 3 mM MgCl2, 1 mM EGTA, 300 mM sucrose, 0.1% Triton X-100, 1 mM Na3VO4, 1 mM NaF, 5 mM beta-D-glycerophosphate).  After centrifugation at 2,300 ×g for 5 min, pellet fractions were incubated at 25°C for 10 min in CSK buffer containing 0.5% formaldehyde, and then incubated with 25°C for 5 min in 0.125 M glycine/PBS.  Immunoprecipitation assays were carried out according to the manufacture’s protocol (Chromatin Immunoprecipitation Assay Kit; Millipore).
Libraries were prepared according to Thermo fiser's instructions accompanying the 5500 SOLiD Fragment Library Core Kit (#4464412).

treatment_protocol: For mitotic cell preparation, MCF-7 cells were treated with 2.5 mM thymidine (Sigma) in the culture medium for 16 h.  After the excess thymidine block, cells were released into a fresh culture medium and incubated for 7 h, so that cells stayed in late S and G2 phases.  Then, cells were treated with nocodazole (Sigma) at a final concentration of 165 nM and further incubated for 6 h.  Mitotic cells were collected by gentle shaking of cell culture dishes.

tag: cell line

value: Breast cancer cells

tag: cell cycle stage

value: asynchronous


title: CTCF_ChIP-seq_Mitosis

description: ChIP antibody: CTCF (Sci. Rep. 3, 2187)

value: mitosis


title: P308_4


title: mm_rna_preb_il7minus-cxcl12plus.1

source_name: IL7- CXCL12+ pre-B

value: IL7- CXCL12+ pre-B


title: mm_rna_spreb_cxcr4ko_il7minus.1


title: P308_3


title: Input DNA

description: ChIP antibody: none


title: MM.179: MM at diagnosis, sample 23

value: Bone marrow plasma cells


title: P308_2


title: GS706 THP1 PB KDM6A+doxy H3K27ac ChIPseq

city: Planegg

first: Helena

last: Domínguez Moreno

state: Bavaria

address: Großhaderner Str. 9

department: Molecular Biology

institute: Biomedical Center of LMU

description: treated with doxocycline during 72; doxocycline was added freshly into the culture media every 24 hours

data_processing:
ChIP-seq reads were aligned to the human genome (hg38) using bowtie (Langmead et al., 2009) with options “-q -n 2 --best --chunkmbs 2000 -p 32 -m1”
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from homer tag directories using makeBigWig.pl

source_name: AML cell line THP-1

growth_protocol: cells were cultured following the recommendations of the dsmz; medium composition: for both, 90% RPMI 1640 + 10% h.i. FBS

extract_protocol:
formaldehyde-fixed cells (1% formaldehyde, 10min RT) were lysed in Buffer B (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0,3%SDS, 1x protease inhibitors -Roche) and sonicated in a microTUBE on a Covaris S220 until most of the DNA fragments were 200-500 base pairs long (settings: duty cycle 2%, peak incident power 105 Watts, cycles per burst 200, 25 min). After shearing lysates were centrifuged (10min 4°C 12000g) and supernatant diluted with 1 volume of Dilution Buffer (1mM EGTA 300 mM NaCl, 2% Triton x-100, 0.2% DOC, 1x protease inhibitors-Roche). In parallel, Dynabeads (Protein A) were conjugated to the antibody (2ul, H3K27ac, diagenode, cat no: C15410174, lot no: A.7071-001P; 1.5ul, H3K27me3, Active Motif, cat no: 39161, lot no: 21518003) in PCR tubes by rotating 1.5 hour at 4°C (30rpm). Antibody-conjugated magnetic beads were added to the tube containing the chromatin and incubated 3h at 4°C (30rpm). Beads were washed (20rpm; 10min) four times with 500 ul Buffer A (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1x protease inhibitors) and once with 500 ul Buffer C (10 mM Tris-HCl, pH 8.0, 10 mM EDTA). Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2μl of RNase (10mg/ml) for 30 min at 37°C, 900 rpm, then 1h with 2 μl of Proteinase K (20mg/ml) at 55°C, 900 rpm, and finally overnitht at 65°C to revert formaldehyde crosslinking; beads were magnetized and supernatant was transferred to a new tube. Another 30 μl of elution buffer + 1μl of proteinase K were added to the beads and the tubes were incubated 1h with the same conditions than before; the eluates were combined. Finally DNA was purified with AMPure XP beads.
Ultra II DNA Library prep kit for Illumina (NEB E7645S) was used for library preparation

treatment_protocol: THP-1 (WT and PiggyBac - PB - KDM6A) and K562 (WT, KDM6A KO PB DKM6A) were cultured for 72 h with or without doxycycline (0.5 ug/ml) Every 24 h cells were counted and 0.2 Mio cells/ml were cultured in fresh medium +/- doxycycline (0.5 ul/ml)

value: Acute myeloid leukemia (AML)

tag: chip antibody

tag: description

value: THP-1 KDM6A KO with KDM6A PB treated for 72h with doxycycline


title: mm_rna_preb_il7minus-cxcl12plus-ERKinhibitorIIplus.1

tag: cell type

value: IL- CXCL12+ ERK inhibitorII+ pre-B


title: P308_1

extract_protocol:
Liver specimens were perfused and treated with collagenase followed by Percoll purifcation/clean up steps
The amplified RNA (aRNA) was reversely transcribed in order to generate libraries for sequencing. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.
CEL-Seq2 (Hasimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)


title: GS704 K562 KDM6A KO PB KDM6A+doxy H3K27ac ChIPseq

source_name: AML cell line K562

value: K562 KDM6A KO with KDM6A PB treated for 72h with doxycycline


title: MM.154: MM at diagnosis, sample 22

tag: diagnosis

tag: genotype/variation

value: MAF translocation


title: GS705 THP1 PB KDM6A H3K27ac ChIPseq

value: THP-1 KDM6A KO with a doxocycline inducible PiggyBac (PB) KDM6A expression system


title: P304_26


title: GS703 K562 KDM6A KO PB KDM6A H3K27ac ChIPseq

value: K562 KDM6A KO with a doxocycline inducible PiggyBac (PB) KDM6A expression system


title: mm_rna_preb_il7minus.1

source_name: IL7- pre-B

value: IL7- pre-B


title: mm_rna_preb_il7minus.cxcl12plus.2


title: mm_rna_preb_il7plus.2

source_name: IL7+ pre-B

value: IL7+ pre-B


title: MM.078: MM at diagnosis, sample 18

source_name: Highly purified PCs from MM patient

value: Multiple myeloma (MM)

value: hyperdiploid karyotype


title: MM.115: MM at diagnosis, sample 20


title: MM.123: MM at diagnosis, sample 21


title: P304_25

source_name: Liver tissue

value: normal liver resection specimen

value: Colorectal cancer metastasis


title: MM.104: MM at diagnosis, sample 19


title: MM.074: MM at diagnosis, sample 17


title: P304_24


title: mm_rna_preb_il7plus.1


title: GS702 K562 WT H3K27ac ChIPseq

value: K562 WT


title: mm_rna_spreb_cxcr4ko.2

source_name: CXCR4-/- small pre-B

value: CXCR4-/- small pre-B


title: P304_23


title: P304_21


title: mm_rna_spreb_il7minus.2


title: mm_rna_spreb_cxcr4ko.1


title: MM.069: MM at diagnosis, sample 16


title: P304_22


title: GS216 MM6 H3K27me3 ChIPseq rep1

source_name: AML cell line MM6

growth_protocol: cells were cultured following the recommendations of the dsmz; medium composition: 90% RPMI 1640 + 10% h.i. FBS + 2 mM L-glutamine + 1x non-essential amino acids + 1 mM sodium pyruvate for MM1 and 90% RPMI 1640 + 10% h.i. FBS + 2 mM L-glutamine + non-essential amino acids + 1 mM sodium pyruvate + 10 µg/ml human insulin for MM6


title: GS700 MM1 H3K27me3 ChIPseq rep2

source_name: AML cell line MM1


title: MM.066: MM at diagnosis, sample 15


title: MM.056: MM at diagnosis, sample 14

value: no information about hyperdiploid status, no major IgH (14q32) chromosomal translocations


title: MM.052: MM at diagnosis, sample 12

value: Bone marrow plasma cells


title: GS701 MM6 H3K27me3 ChIPseq rep2

value: Acute myeloid leukemia (AML)


title: GS215 MM1 H3K27me3 ChIPseq rep1


title: P304_18


title: GS210 MM6 H3K27ac ChIPseq rep1


title: GS656 MM6 H3K27ac ChIPseq rep2


title: mm_rna_spreb_wt.1

source_name: small pre-B

value: small pre-B


title: GS654 MM1 H3K27ac ChIPseq rep2


title: MM.055: MM at diagnosis, sample 13


title: P304_20


title: MM.406: MM at diagnosis, sample 47


title: P304_17


title: MM.050: MM at diagnosis, sample 11


title: mm_atac_preb_il7minus-cxcl12plus.1

extract_protocol: To prepare Nuclei, respective flow sorted mouse primarey B cell progenitors or cultured pre-B cell were centrifuged at 500g for 5 min, which was followed by a wash with ice-cold PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min at 40C and supernatant removed. The nuclei pellet was resuspended in the transposase reaction mix (25 μL 2X Tagment buffer, 2.5 μL Tagment DNA enzyme (Illumina, FC-121-1030) and 22.5 μL nuclease-free water). The transposition reaction was carried out at 37 °C for 30 min. Directly following transposition the sample was purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10-12 cycles. The libraries were then purified using a Qiagen PCR cleanup kit. The amplified, adapter ligated libraries were size selected using Life Technologies' E-Gel® SizeSelect™ gel system in the 150-650bp range. The size-selected libraries were quantified using the Agilent Bioanalyzer and via q-PCR in triplicate using the KAPA Library Quantification Kit on the Life Technologies Step One System. Libraries were sequenced on the Illumina Hiseq2500 system.

value: IL7- CXCL12+ pre-B


title: GS187 MM1 H3K27ac ChIPseq rep1


title: mm_atac_preb_il7minus.2


title: PCL.013: PCL at diagnosis, sample 3

source_name: Highly purified PCs from PCL patient

value: Plasma cell leukemia (PCL)


title: MM.043: MM at diagnosis, sample 9

value: non-hyperdiploid karyotype, no major IgH (14q32) chromosomal translocations


title: mm_atac_preb_il7minus-cxcl12plus.2


title: mm_rna_spreb_wt.2


title: P304_15


title: P304_19


title: P304_14


title: mm_atac_preb_il7plus.2


title: Donor HU1016 HBV mono-infected for 28 days

city: Princeton

first: Alexander

last: Ploss

state: NJ

address: Washington Road

institute: Princeton University

data_processing:
The samples were run on two HiSeq 2500 Rapid Run mode flowcells. Basecalling was performed by Illumina RTA version 1.18.64.0. BCL files were then converted to fastq format using Illumina’s bcl2fastq version 1.8.4. Reads that aligned to phiX using Bowtie 1.1.1 (Langmead et al., 2009) were removed as well as reads that failed Illumina’s default chastity filter. The fastq files from each lane were then combined before splitting the reads from each sample using the barcode sequences allowing 1 mismatch, using the barcode_splitter program, version 0.18.2 (Leach and Parsons, 2017).
A reference genome was created using the NCBI GRCh38 human reference (iGenomes), the NCBI GRCm38 mouse reference (iGenomes), the NCBI U95551.1 Hepatitis B virus subtype ayw, complete genome, and the NCBI M21012.1 Hepatitis delta virus RNA, complete genome. The reference sequences (fasta) and gene annotations (gtf) were combined to form a single unified reference. The read alignment, quantification, and differential expression analysis was done using a locally installed instance of the Galaxy workflow platform (Afgan et al., 2016). The reads for each sample were then aligned to the combined reference using STAR (Galaxy Version 2.5.2b-1) with default parameters (Dobin et al., 2013). Quantification for each gene was then done using featurecounts (Galaxy Version 1.6.0.1) with default settings (Liao et al., 2014).
Genome_build: A reference genome was created using the NCBI GRCh38 human reference (iGenomes), the NCBI GRCm38 mouse reference (iGenomes), the NCBI U95551.1 Hepatitis B virus subtype ayw, complete genome, and the NCBI M21012.1 Hepatitis delta virus RNA, complete genome.
Supplementary_files_format_and_content: Tabular files of ENSEMBL gene ID and counts

organism:
Homo sapiens
Mus musculus

source_name: SACC-PHHs

growth_protocol: All SACC-PHHs were grown in Hurel Maintenance media containing 5% fetal bovine serum (FBS) and 1% v/v penicillin/streptomycin.

extract_protocol:
Total RNA extracted using Qiagen Rneasy Mini Kit per manufacturer's directions.
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Nano chip (Agilent Technologies, CA); only samples with RNA Integrity Number (RIN) greater than 9.0 were used for RNA-seq.  The poly-A containing RNA transcripts were enriched from 1μg of total RNA for each sample using oligo-dT bead, and further converted to cDNA then Illumina sequencing library using PrepX RNA-seq library kit on the automated Apollo 324TM NGS Library Prep System (Wafergen Biosystems, CA) according to the manufacturer's protocol.  Different DNA barcodes were added to each RNA-seq library.  The libraries were examined on Agilent Bioanalyzer DNA High Sensitivity chips for size distribution, and quantified by Qubit fluorometer (Invitrogen, CA).  The RNA-seq libraries were pooled at equal molar amount and sequenced on Illumina HiSeq 2500 Rapid flowcells as single-end 75 nucleotide reads following the standard protocol.  Raw sequencing reads were filtered by Illumina HiSeq Control Software, and only the Pass-Filter (PF) reads were used for further analysis.

treatment_protocol: PHHs (188,000 cells/well) were seeded along with 3T3 J mouse (30,000 cells/well) in a 24 well format.  Seven to ten days after seeding, SACC-PHHs were challenged with respective viruses.

value: Primary human hepatocytes co-cultured with mouse 3T3J non-parenchymal cells

tag: treatment

value: Mono-infected with HBV (MOI = 4,000)


title: Donor HU1016 HBV/HDV co-infected for 28 days

value: Co-infected with HBV (MOI = 4,000) and HDV (MOI = 1,000)


title: Donor HU1016 HBV/HDV co-infected for 8 days


title: MM.039: MM at diagnosis, sample 6


title: MM.040: MM at diagnosis, sample 7


title: P304_12

first: Nadim

last: Aizarani

institute: MPI-IE

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
Supplementary_files_format_and_content: Normalhumanliverdata.RData: A count table or expression matrix for all the normal human liver cells. Use readRDS function to load data in R.


title: mm_atac_spreb_cxcr4ko.2


title: mm_atac_preb_il7plus.1

value: IL7+ pre-B


title: mm_atac_spreb_cxcr4ko.1


title: Donor HU1016 HBV mono-infected for 8 days


title: MM.049: MM at diagnosis, sample 10

value: Multiple myeloma (MM)


title: MM.030: MM at diagnosis, sample 4

value: hyperdiploid karyotype


title: MM.035: MM at diagnosis, sample 5


title: MM.025: MM at diagnosis, sample 3

value: MAF translocation


title: Donor HU1020 (AKA BD405A) HBV/HDV co-infected, 28 days


title: P304_11

value: normal liver resection specimen

value: Colorectal cancer metastasis


title: Donor HU1020 (AKA BD405A) uninfected, 28 days

value: Uninfected


title: P304_9


title: Oct4SM_SMSK_d1

data_processing:
fastqc
Read were aligned to mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive –end-to-end.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read was retained.
Samtools was used to discard reads with mapping quality < 10
Peaks were called using MACS2 with options --call-summits --to-large -p 0.0001 –bdg options.
For each binding location, the read coverage for all libraries was calculated using the bedtools multicov function.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file were generated with genomeCoverageBed followed by bedGraphToBigWig.

growth_protocol: OG2-MEF cells were transduced twice by pMX-Sox2, Klf4 along with Oct4 or Oc6 or engineered Oct4 (YR or Oct4defSox2) retroviruses produced using PlatE cells in DMEM + 10% FBS media supplemented with 1x NEAA and Glutamax. After second viral transduction, the medium was switched to highly efficient chemically defined (iCD1) reprogramming medium. The iCD media switch day was defined as day 0 and cells were cultured for next 7 days with daily media change.

extract_protocol:
Reprogramming cells (7.5-10 x 10e6 cells per sample were collected by trypsinization at day 1, 5 and 7 days post transduction and washed twice with PBS (Gibco). Cells were resuspended in PBS at a density of 5 x 105/mL and then chemically crosslinked by the addition of 1% formaldehyde for 10 min at room temperature with gentle rotation. Crosslinking was stopped by the addition of glycine to a final concentration of 125 mM for 5 min at room temperature. Cells were washed twice with 10 mL cold PBS and lysed in 10 mL Lysis Buffer 1 (150 mM NaCl, 0.5% NP40; 1 mM EDTA, 10% glycerol, 0.25% triton-X100, freshly added complete proteinase inhibitor cocktail in 15 mL tubes at 4°C for 10 min with gentle rocking. The lysate was centrifuged for 10 min at 1350 x g at 4°C. The supernatant was discarded and the pellet was resuspended in 10 mL lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, protease inhibitor) incubated at 4°C for 10 min. The procedure was repeated using 10 mL lysis buffer 3 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, protease inhibitor) and 10 min rocking at RT. Nuclei were collected by centrifugation and washed twice with sonication buffer (10 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, protease inhibitor) and finally suspended in sonication buffer. Samples were sonicated using a Covaris S220 machine with settings to obtain DNA fragments with a length from 150 to 500 bp using microTUBEs (130 μL) for 5 cycles of 30 sec ON and 60 sec OFF using default settings recommended for microTUBEs. 10% Triton-X100 was added and the lysate was centrifuged at high speed (20000 x g for 10 min at 4°C). 1/10 of the supernatant was stored as input control. ChIP was performed in an automated fashion using the IP-Star compacted automated system (Diagenode) using 6 g ChIP-grade antibodies (Oct4 or Oct6) and 50 l protein G Dynabeads (Invitrogen). The coupling time for beads and antibody was 5 hours followed by incubation with lysate for 15 hours at 4°C. Automated wash steps of 10 minutes at 4°C were performed in the following order: low salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS 1% TritonX-100, 2 mM EDTA, 150 mM NaCl) , high salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS 1% TritonX-100, 2 mM EDTA, 500 mM NaCl), LiCl buffer (500 mM LiCl, 50 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% NP-40, 0.5% Na-deoxycholate), TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA) with final elution in 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS buffer. The eluted chromatin and input samples were reverse‐crosslinked by overnight incubation at 65°C. Samples were treated with RNaseA (0.2 mg/ml final concentration) at 37°C for 2h followed by proteinase K (0.2 g/ml final conc.) at 55°C for 3 hours. DNA was extracted by phenol:chloroform:isoamyl alcohol (25:24:1) and phase separated using heavy phase-lock tubes (TianGen) by centrifugation at 10000 rpm for 10 min at RT and precipitated with 100% ethanol with 20 μg/μl glycogen as co-precipitant. The precipitate was washed with 80% ethanol and finally eluted in 20ul water. DNA concentration was determined using Qubit dsDNA HS assay kit.
The libraries were generated using the Trueseq Nano DNA kit (Illumina)

value: reprogramming cells

tag: day of reprogramming

value: Oct4 Antibody

tag: antibody vendor, cat#, lot#

value: Santa Cruz biotech; sc-8628 X; 12415


title: mm_atac_preb_il7minus.1

value: IL7- pre-B


title: Oct6MS_MSSK_d1

value: Oct6 Antibody

value: Santa Cruz biotech;sc-11661 X; G0606


title: MM.004: MM at diagnosis, sample 1

tag: tissue

value: Bone marrow plasma cells


title: P304_13

tag: cause of resections


title: P304_10


title: Donor HU1020 (AKA BD405A) HBV/HDV co-infected, 8 days

value: Primary human hepatocytes co-cultured with mouse 3T3J non-parenchymal cells


title: Donor HU1020 (AKA BD405A) HBV mono-infected, 28 days

value: Mono-infected with HBV (MOI = 4,000)