title: Fibroblasts_TNF+ACP_24 hours [TNF.PRP_rep4]

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description:
Sample_OOO_OOO_Fb_4_TNF.PRP
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

data_processing:
1. RNASeq: Quality of all RNA and library preparations were evaluated with BioAnalyzer 2100 (Agilent). Sequencing libraries were sequenced by the Genomics Core Facility at Weill Cornell Medicine using a Illumina Hiseq 4000
2. RNASeq: 50-bp single-end reads at a depth of ~ 22-30 million reads per sample. Read quality was assessed and adapters were trimmed using FASTP. Reads were then mapped to the mouse genome (mm10) and reads in exons were counted against Gencode v27 with STAR2.7
3. RNAseq: Differential gene expression analysis was performed in R using edgeR3.24.3. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. Replica-associated batch correction was performed by directly incorporating a batch-specific term into a linear model. Differential expression was estimated using quasi-likelihood framework. Benhamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with an unadjusted p-value less than 0.01 were considered differentially expressed
Genome_build: hg38
Supplementary_files_format_and_content: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx : unfiltered count matrix, filtered  count matrix, log-transformed normalized matrix, differential expression statistics for fibroblast exposed to PRP, TNF or combination thereof
Supplementary_files_format_and_content: edgeR_DEGs_xmf_batch_2019-06-04.xlsx  : unfiltered count matrix, filtered  count matrix, log-transformed normalized matrix, differential expression statistics for macrophages exposed to PRP, TNF or combination thereof

source_name: Fibroblasts_TNF+ACP_24 hours

growth_protocol: Human primary fibroblasts were isolated from synovial tissues retrieved at the time of total knee replacement surgery, under IRB approval and patient consent. Cells were grown in MEM Alpha (1X, # 12561-056 with L-Glut), with 10% FBS and 1% Pen/Strep. Fibroblasts between passages 4 and 7 were used for experimental purposes. Human CD14+ monocytes were isolated from whole blood samples and cultured in RPMI (1X, # 11875119 with L-Glut) with 10% defined serum and 1% Pen/Strep and 10 ng/ml of monocyte colony stimulating factor (M-CSF) for 24 hours to promote a pro-macrophage lineage. At 24 h after M-CSF treatment, macrophages and fibroblasts were co-cultured in a 0.4 mm polyester trans-well system, in serum-defined RPMI with 1% L-Glut and 1% Pen/Strep. The co-cultured cells were left untreated (control, medium) or incubated with 10% v:v of activated ACP, 20ng/ml of recombinant human TNF, or ACP+TNF for an additional 24 hours.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) from co-cultures of macrophages and fibroblasts (control, ACP, TNF, or ACP+TNF for 24h; n=4/ea). A total of 100 ng of high-quality RNA (RIN>8 and A260/280>1.8) were used to construct libraries.
RNA-Seq library preparations were done using established Illumina methods for mRNA-Seq (Part #RS-122-2001). Briefly, poly A+ RNA was purified from 100 ng of total RNA with oligo-dT beads and fragmented with divalent cations at elevated temperature. First strand cDNA synthesis was performed with random hexamer priming and SuperScript II Reverse transcriptase (Invitrogen, part # 18064-014). Second strand cDNA synthesis was performed using RNAseH and DNA PolI. Following dscDNA synthesis, the double stranded products are end repaired, followed by addition of a single ‘A’ base and then ligation of the Illumina TruSeq adaptors. The resulting product was amplified with 15 cycles of PCR. Each library was made with a unique Index sequence and libraries are pooled for sequencing.

treatment_protocol: Macrophages and fibroblasts (n=4/ea) were (1) left untreated (control, medium), (2) incubated with 10% v:v of activated ACP, (3) incubated with 20ng/ml of recombinant human TNF, or (4) incubated with 10% v:v of activated ACP and 20ng/ml of TNF for 24 hours.

tag: donor age

value: adult

tag: tissue

value: synovial tissue

value: Primary fibroblast-like synoviocytes (fibroblasts)

value: TNF+ACP_24 hours


title: Hep3B_sh1_3

status: Public on Sep 02 2021

type: SRA

city: Nanjing

first: Anliang

last: Xia

address: 321 Zhongshan Road

country: China

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

library_source: transcriptomic

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Hep3B cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Hep3B cells

tag: cell type

value: HCC-derived cells

tag: treatment

value: treated with shlnc-CTHCC lentivirus for 72 hours


title: Fibroblasts_ACP_24 hours [PRP_rep4]

country: USA

description:
Sample_OOO_OOO_Fb_4_PRP
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

molecule: polyA RNA

source_name: Fibroblasts_ACP_24 hours

value: ACP_24 hours


title: Fibroblasts_untreated [FBS_rep4]

description:
Sample_OOO_OOO_Fb_4_FBS
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: untreated


title: PHH-ETV-7d-3

city: SHANGHAI

first: Wenjing

last: Zai

address: Dongan Road

institute: Fudan University

data_processing:
The sequencing reads from all RNA-seq experiments were trimmed by Cutadapt v3.1 (https://cutadapt.readthedocs.io/en/stable/), then aligned to the human (hg19) reference genome by Hisat2 (https://daehwankimlab.github.io/hisat2/)
The resulting files were sorted by SAMtools (http://samtools.sourceforge.net/) and analyzed for expression using FeatureCounts (http://subread.sourceforge.net/).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Primary human hepatocytes

growth_protocol: 5C-PHH were cultured as described in Xiang C, et al., Science 2019. In brief, Cell were  cultured with 5C medium (Null medium (Williams’ medium E containing B27, Glutamax, and Pen Strep) supplemented with Forskolin (20 μM), SB431542 (10 μM), IWP2 (0.5 μM), DAPT (5 μM), and LDN193189 (0.1 μM))

extract_protocol: RNA libraries were prepared for sequencing using the Illumina mRNA-Seq Prep Kit (Illumina)

treatment_protocol: The day after plating, 5C-PHH were infected with concentrated HBV particles (ayw) collected from HepAD38 supernatant at a multiplicity of infection (MOI) 200, in Null medium containing 4 % PEG8000. For mock- infection groups, cells were treated with Null medium containing 4 % PEG8000. 20 h later, the medium was removed, and cells were rinsed with PBS for three times. Cell were then cultured with 5C medium for indicated time before harvesting and testing.

value: Primary human hepatocytes

tag: culture

value: Five chemicals-cultured PHH (5C-PHH)

value: HBV-infected (ayw, MOI 200), ETV (100 nM)-treated

tag: time

value: 7 days post infection


title: PHH-Mock-28d-2

value: Mock-infected

value: 28 days post infection


title: PHH-ETV-28d-3


title: PHH-HBV-28d-2

value: HBV-infected (ayw, MOI 200)


title: PHH-HBV-28d-3


title: PHH-Mock-28d-3


title: Fibroblasts_TNF+ACP_24 hours [TNF.PRP_rep3]

description:
Sample_OOO_OOO_Fb_3_TNF.PRP
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx


title: Fibroblasts_TNF_24 hours [TNF_rep4]

description:
Sample_OOO_OOO_Fb_4_TNF
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

source_name: Fibroblasts_TNF_24 hours

value: TNF_24 hours


title: PHH-ETV-28d-1


title: PHH-Mock-28d-1


title: PHH-ETV-28d-2


title: PHH-ETV-7d-2


title: PHH-HBV-28d-1


title: Fibroblasts_TNF+ACP_24 hours [TNF.PRP_rep2]

description:
Sample_OOO_OOO_Fb_2_TNF.PRP
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: adult


title: PHH-HBV-7d-3


title: PHH-HBV-7d-2


title: Fibroblasts_ACP_24 hours [PRP_rep3]

description:
Sample_OOO_OOO_Fb_3_PRP
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: synovial tissue


title: Fibroblasts_TNF_24 hours [TNF_rep3]

description:
Sample_OOO_OOO_Fb_3_TNF
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: Primary fibroblast-like synoviocytes (fibroblasts)


title: PHH-ETV-7d-1


title: Hep3B_shNC2

value: treated with shNC lentivirus for 72 hours


title: Fibroblasts_ACP_24 hours [PRP_rep2]

description:
Sample_OOO_OOO_Fb_2_PRP
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx


title: Fibroblasts_TNF_24 hours [TNF_rep2]

description:
Sample_OOO_OOO_Fb_2_TNF
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx


title: PHH-HBV-2d-2

value: 2 days post infection


title: PHH-HBV-7d-1


title: CLL618_mRNA

type: RNA

city: Memphis

first: Jared

last: Andrews

state: Tennessee

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

hyb_protocol: Products were hybridized to Affymetrix Human Gene 2.0 ST arrays according to the manufacturer's protocol

data_processing:
Gene expression levels were determined using the Applied Biosystems Transcriptome Analysis Console (v4.0.2.15) using rma normalization, HuGene2.0.na36 annotations, and default settings.
probe group file: HuGene-2_0-st.pgf
meta-probeset file: HuGene-2_0-st-v1.na36.transcript.csv

label: biotin

source_name: CD19+ B cells

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

extract_protocol: RNA was purified using Qiagen RNAeasy Kits according to the manufacturer's protocol

value: Peripheral blood

tag: disease state

value: chronic lymphocytic leukemia


title: PHH-Mock-7d-3


title: Macrophages_TNF_24 hours [TNF_rep4]

description:
Macrophage_4_TNFa_S30_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx

source_name: Macrophages_TNF_24 hours

value: blood

value: Primary macrophages differentiated from cd14+ monocytes


title: PHH-Mock-2d-3

value: Primary human hepatocytes


title: Fibroblasts_ACP_24 hours [PRP_rep1]

description:
Sample_OOO_OOO_Fb_1_PRP
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: ACP_24 hours


title: Macrophages_ACP+TNF_24 hours [TNF.PRP_rep4]

description:
Macrophage_4_TNFa_plus_PRP_S31_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx

source_name: Macrophages_ACP+TNF_24 hours

value: ACP+TNF_24 hours


title: Fibroblasts_untreated [FBS_rep2]

description:
Sample_OOO_OOO_Fb_2_FBS
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: untreated


title: PHH-Mock-7d-1

value: Five chemicals-cultured PHH (5C-PHH)

value: Mock-infected

value: 7 days post infection


title: PHH-Mock-7d-2


title: Mp-uMT_5

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description:
rep1-6: independent library preparations;
Tumor_CD11b+F4/80high

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assembly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of clusters for each gene was counted, which provides the number of molecules detected for each gene
The number of RNA molecules for each gene and index was listed
Genome_build: mm10
Supplementary_files_format_and_content: The copy number of detected RNA molecules for genes and indexes (tubes) are summarized

organism: Mus musculus

source_name: Tumor macrophages in muMt-/- mice

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction
Libraries were prepared by using molecular barcoding technique. First, for normalization, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: One hundred of CD45+CD11b+F4/80high or CD45+TCRbeta+CD8+ cells were isolated from tumor using FACS cell sorter

tag: cell markers

value: Tumor macrophages

tag: genotype

value: muMt-/-


title: PHH-Mock-2d-2


title: Fibroblasts_untreated [FBS_rep3]

description:
Sample_OOO_OOO_Fb_3_FBS
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: adult

value: synovial tissue


title: Fibroblasts_untreated [FBS_rep1]

description:
Sample_OOO_OOO_Fb_1_FBS
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: Primary fibroblast-like synoviocytes (fibroblasts)


title: Fibroblasts_TNF_24 hours [TNF_rep1]

description:
Sample_OOO_OOO_Fb_1_TNF
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: TNF_24 hours


title: Fibroblasts_TNF+ACP_24 hours [TNF.PRP_rep1]

description:
Sample_OOO_OOO_Fb_1_TNF.PRP
processed data file: edgeR_DEGs_xFibroblasts_batch_2019-06-04.xlsx

value: TNF+ACP_24 hours


title: PHH-HBV-2d-3

value: HBV-infected (ayw, MOI 200)

value: 2 days post infection


title: PHH-HBV-2d-1


title: 4hr Vehicle H3K4me3

city: Ann Arbor

first: Sunil

last: Tomar

address: 109 Zina Pitcher Place

institute: University of Michigan

data_processing:
We used BioWardrobe for the analysis (MACS pipeline)
Genome_build: GRCh37
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: peaks
Supplementary_files_format_and_content: narrowPeak
Supplementary_files_format_and_content: bed

source_name: EPC2 Cells

growth_protocol: After 5 days of ALI culture, EPC2 cells were treated with IL-13 (100 ng/mL) for 30 minutes for STAT6 ChIP. Cells were collected and then lysed and sonicated for 10 minutes (peak power, 175 W; duty factor, 10%; cycles/burst, 200 count) at 1.5°C with a Covaris S series Sonicator (Covaris, Woburn, Mass), yielding chromatin fragments of 200 to 300 bp in size. Each chromatin sample was precleared with 10 μL of Dynabeads Protein G magnetic beads (Life Technologies, Carlsbad, Calif) for 45 minutes at 4°C on a rotating wheel to remove nonspecific binding. Anti-H3K4me3 (1 μL; ChIPAb+ Trimethyl-Histone H3 [Lys4]; Millipore, Temecula, Calif) or anti-STAT6 (2.5 μg; sc-621; Santa Cruz Biotechnology, Santa Cruz, Calif) were bound to 20 μL of Dynabeads Protein G magnetic beads (Life Technologies) for 1 hour at RT on a rotating wheel. Chromatin complexes (5 μg for histone mark or 25 μg for STAT6 ChIP) were then added to the antibody-coated beads and immunoprecipitated for 14 to 16 hours at 4°C on a rotating wheel. Precipitates were washed with 500 μL of each of the following buffers in succession: low-salt wash buffer (10 mmol/L Tris-HCl [pH 7.6], 1 mmol/L EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and 150 mmol/L NaCl), high-salt wash buffer (10 mmol/L Tris-HCl [pH 7.6], 1 mmol/L EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, and 400 mmol/L NaCl), LiCl wash buffer (10 mmol/L Tris-HCl [pH 7.6], 1 mmol/L EDTA, 250 mmol/L LiCl, 0.5% sodium deoxycholate, and 0.5% Nonidet P-40), and Triton X-100 buffer (10 mmol/L Tris-HCl [pH 7.6], 1 mmol/L EDTA, and 0.2% Triton X-100)

extract_protocol:
Chromatin complexes were eluted in 100 μL of elution buffer (10 mmol/L Tris-HCl [pH 7.6], 1 mmol/L EDTA, 250 mmol/L NaCl, and 0.3% SDS) and incubated at 37°C for 1 hour with shaking. For protein degradation and reverse cross-linking, 5 μL of Proteinase K solution (Life Technologies) was added to the eluates and incubated at 37°C for 1 hour, followed by incubation at 65°C for 6 hours. DNA was purified with the QIAquick PCR Purification Kit (Qiagen, Valencia, Calif), eluted in 30 μL of molecular biology grade water (Sigma, St Louis, Mo), and processed for qPCR before sequencing.
Libraries were created, as described previously,38 and sequenced by the CCHMC Gene Discovery and Genetic Variation Core.

treatment_protocol: 30 min with IL13 and  Vehicle

tag: antibody

tag: agent

value: Vehicle

tag: time point


title: 30min IL13 treatment STAT6chipseq


title: 4hr IL13 H3K4me3


title: PHH-Mock-2d-1

value: Primary human hepatocytes


title: Macrophages_untreated [FBS_rep4]

description:
Macrophage_4_FBS_S29_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx

value: blood

value: Primary macrophages differentiated from cd14+ monocytes


title: Macrophages_TNF_24 hours [TNF_rep3]

description:
Macrophage_3_TNFa_S26_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: Macrophages_ACP_24 hours [PRP_rep4]

description:
Macrophage_4_PRP_S32_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx

source_name: Macrophages_ACP_24 hours

value: ACP_24 hours


title: Macrophages_untreated [FBS_rep3]

description:
Macrophage_3_FBS_S25_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx

value: untreated


title: Macrophages_TNF_24 hours [TNF_rep2]

description:
Macrophage_2_TNFa_S22_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: FL313_rnaseq

data_processing:
bcl2fastq (v1.8.4) was used to demultiplex and convert base call files into FASTQ files.
Read quantification was performed by salmon (v0.14.1) to gencode.v31lift37 annotations with the -validateMappings and -seqBias parameters.
Differential gene expression analyses and normalized gene-level counts were generated with DESeq2 (v1.26.0).
Genome_build: hg19
Supplementary_files_format_and_content: Raw transcript counts as quantified by salmon (v0.14.1) using gencode.v31lift37 annotations. Contains transcriptID, Length, effectiveLength, TPM, and NumReads columns.

extract_protocol:
RNA was extracted with a Qiagen RNeasy kit.
rRNA-depleted (Ribo-Zero) libraries were prepared using TruSeq RNA Sample kits with indexed adaptors.

value: lymph node

value: follicular lymphoma


title: TS121511B_rnaseq

value: tonsil

value: healthy


title: TS072611B_rnaseq


title: TS081111A_rnaseq


title: Macrophages_ACP+TNF_24 hours [TNF.PRP_rep2]

description:
Macrophage_2_TNFa_plus_PRP_S23_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx

value: adult

value: ACP+TNF_24 hours


title: Macrophages_ACP_24 hours [PRP_rep2]

description:
Macrophage_2_PRP_S24_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: Macrophages_ACP+TNF_24 hours [TNF.PRP_rep1]

description:
Macrophage_1_TNFa_plus_PRP_S19_L001
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: TS121511A_rnaseq


title: 30min Vehicle treatment STAT6chipseq


title: Macrophages_untreated [FBS_rep2]

description:
Macrophage_2_FBS_S21_L001
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: TS072111A_rnaseq


title: Macrophages_ACP_24 hours [PRP_rep1]

description:
Macrophage_1_PRP_S20_L001
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: Macrophages_untreated [FBS_rep1]

description:
Macrophage_1_FBS_S17_L001
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: TS060911A_rnaseq


title: Macrophages_ACP+TNF_24 hours [TNF.PRP_rep3]

description:
Macrophage_3_TNFa_plus_PRP_S27_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: FL301_rnaseq


title: Macrophages_TNF_24 hours [TNF_rep1]

description:
Macrophage_1_TNFa_S18_L001
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: CD8T-WT_1

description:
rep1-6: independent library preparations;
Tumor_CD8+

source_name: Tumor CD8+ T cells in WT mice

value: Tumor CD8+ T cells

value: WT


title: FL255_rnaseq


title: FL303_rnaseq


title: Macrophages_ACP_24 hours [PRP_rep3]

description:
Macrophage_3_PRP_S28_L003
processed data file: edgeR_DEGs_xmf_batch_2019-06-04.xlsx


title: FL202_rnaseq


title: FL238_rnaseq


title: FL120_rnaseq


title: FL174_rnaseq


title: ChIPseq_E9_5_HeadSATB2_BR1

city: Pune

first: Sanjeev

last: Galande

state: Maharashtra

address: Dr. Homi bhabha road, Pashan

department: Biology

country: India

institute: IISER Pune

description:
processed data file:
E9_5_Head_SATB2_merged_subtract.bw

library_source: genomic

data_processing:
Sequencing reads were trimmed using TrimmomaticPE for Truseq2:PE adapters and reads with quality greater than phred 33 were retained. Quality of sequencing reads were determined using fastQC91. High quality sequencing reads were aligned to the zebrafish danRer10 genome version using default parameters of BWA. Aligned reads were subsampled to 40 million reads in each sample using BBMap. RPKM normalized Input signal subtracted BigWig tracks for visualization were generated using the bamCompare tool from deepTools 3.3.2.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

molecule: genomic DNA

source_name: Head tissue

extract_protocol:
To obtain genome wide binding sites for SATB2 during early neurogenesis, SWR/J mice were incrossed and embryos were isolated at desired stage of development. For experiments with E9.5 head tissue and trunk (visceral organs were discarded) were dissected under stereo microscopes with fine forceps and collected in ice chilled 1x PBS containing 0.5% glucose. Tissues from 10-12 embryos were pooled together for each replicate and crosslinked using 1% methanol free formaldehyde for 8 minutes followed by quenching with 125 mM glycine for an additional 5 minutes at RT. For experiments at E13.5, dorsal telencephalon was isolated and processed as described above. Chromatin isolation and ChIP experiment was performed as described in experiments for zebrafish Satb2 with modifications as follows. 100 µg of precleared chromatin was used for each IP reaction and 10 µg of anti-Human SATB2 antibody was used for pulldown. Equal amount of anti-Rabbit IgG (Invitrogen) was used as a control for each ChIP experiment. Antibody-protein complex was captured using 100 µl of pre-blocked Dynabeads protein A:G mixture for 4 hours at 4oC. Samples were processed further as described in the earlier section.
Equal amount of DNA (~5 ng) was used as an input for library preparation and libraries were prepared using NEB ultra II DNA library prep kit (NEB, USA). Sequencing reads (76 bp PE) were obtained on the Nextseq 550 platform at IISER, Pune.  Sequencing reads were trimmed using TrimmomaticPE for Truseq2:PE adapters and were aligned to mouse mm10 genome using default parameters of BWA. Aligned reads were subsampled to 25 million reads for each sample using BBMap. QC, peak calling and BigWig generation was performed as described in the above sections.  Equal amount of DNA (~5 ng) was used as an input for library preparation and libraries were prepared using NEB ultra II DNA library prep kit (NEB, USA). Sequencing reads (76 bp PE) were obtained on the Nextseq 550 platform at IISER, Pune.  Sequencing reads were trimmed using TrimmomaticPE for Truseq2:PE adapters and were aligned to mouse mm10 genome using default parameters of BWA. Aligned reads were subsampled to 25 million reads for each sample using BBMap. QC, peak calling and BigWig generation was performed as described in the above sections.

tag: genotype/varaition

value: Wild-Type

tag: strain

value: SWR/J

value: anti-Human Satb2(generated in this study)

tag: Stage


title: DL551_rnaseq

value: diffuse large B cell lymphoma


city: Paris

first: Aurélien

last: Sutra del Galy

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSEhigh
Antigen_experienced_CFSEhighcohort1_Rep3

hyb_protocol: Labelled DNA was hybrized on the Affymetrix Mouse Gene 2.1 ST processed on an Affymetrix GeneTitan device.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Microarray data were carried out with R (version 3.1.0) using packages from the Bioconductor. Raw data CEL files were used and the quality control analysis was performed using ArrayQualityMetrics package. The raw data were preprocessed using the RMA (Robust Multi-array Average) method available in oligo package. Gene expression levels were analyzed on a base-2 logarithmic scale.

label: Biotin

source_name: dividing or not antigen experienced Marilyn CD4 T cells from lymph node

label_protocol: For each condition, RNA was employed to synthetize cDNA according to the standard Affymetrix protocol.Affymetrix GeneTitan device.

growth_protocol: Naïve or antigen experienced Marilyn CD4 T cells were intravenously injected into C57BL6 mice vaccinated and cells were sorted by flow cytometry from draining lymph nodes on the basis of their CFSE profiles.

extract_protocol: RNA was extracted using Single Cell RNA Purification Kit (Cat. 51800) Norgen Biotek according to the manufacturer protocol. A column DNAse treatment was included (QIAGEN).

treatment_protocol: Marilyn cells expansion in vivo was studied in the absence or presence of a first cohort

tag: gender

value: female


title: FL153_rnaseq


title: DL237_rnaseq


title: DL273_rnaseq


title: FL3A145_rnaseq


title: DL191_rnaseq


title: DL252_rnaseq


title: DL3A193_rnaseq


title: DL135_rnaseq


title: Yellow-white_WingDisc_MS_Replicate1

city: Nashville

last: Nordman

state: TN

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

data_processing:
Bam files were aligned to dm6 (Dos Santos et al., 2015) by BWA mem (v0.7.17) (Li, 2013) and duplicate reads are marked with Picard Tools command ‘MarkDuplicates’.
Coordinates of uniquely-mapping, non-duplicate, reads with a MAPQ >10 were extracted with samtools (Li et al., 2009) view (v1.11) (-F 1024 -F 256 -F 128 -q 10).
RT was generated from a modified version of TIGER (Koren et al., 2021). Alignability filtering was performed against dm6 using a read length of 100bp. The uniquely aligning sample reads were then partitioned into windows of 1000 uniquely alignable base pairs. GC correction was performed with standard segmentation (TIGER command ‘TIGER_segment_filt’, using the MATLAB function ‘segment’) parameters which temporarily removed eUR and PH regions for determining GC content bias. GC correction was then applied to all data (PH and eUR included). From the GC-corrected data in 1kbp windows, eUR regions were defined in WT fat body and salivary gland samples as regions of continuous low DNA copy number. In this, the raw DNA copy number data in 1kb windows were segmented (TIGER command ‘TIGER_segment_filt’, R2 = 0.04, standard deviation threshold = 1) to identify regions of at least one standard deviation below the mean.  From these regions, only those ≥ 50 kbp in length without gaps ≥10 kbp (≥10 continuous 1kbp windows above the segmentation standard deviation cutoff) were called as eUR regions. This method provided the most accurate prediction of eUR regions by visual inspection. These predicted eUR regions overlapped with the smaller panel of previously published UR regions (J. Nordman et al., 2011) in fat body and salivary glands. The predicted and previously published eUR regions were merged with bedtools (Quinlan & Hall, 2010) merge (v2.29.2) to finalize eUR zones in fat body and salivary gland. Standard TIGER data filtering removes outlier windows attributed to noise or copy number variations. To still filter outliers, eUR and PH regions must be removed and filtered separately from the rest of the chromosome (arm regions). The eUR (as defined in the previous paragraph) and PH regions were removed from the GC-corrected data. In the arm-only regions, outliers were removed with segmentation (standard deviation threshold = 2, R2 = 0.06). eUR regions then separately filtered for outliers in a similar manner (standard deviation threshold = 3, R2 = 0.06). All segmentation parameters were chosen to optimize outlier removal via visual interpretation. The segmentation filtered arm, PH, and eUR regions were merged to form the final rawRT data. This data was used for all the statistical analysis including variant calling between salivary gland and fat body samples. RT values were generated by smoothing the filtered data with a cubic smoothing spline (MatLab command ‘csaps’, smoothing parameter = 1x10-15). Only zones of >20 continuous 1kbp windows were included and smoothing was not performed over gaps of >5kpb. The smoothed profiles were then normalized to an individual chromosomal mean of zero and a standard deviation of one. In comparing TIGER profiles of salivary glands and fat body to G1/S profiles of wind disc and follicle cells, the variable copy number of eUR and PH regions distorts normalization. Therefore, a second normalization was performed based only on the arm regions of chromosomes. The arm regions were first normalized to a mean of zero and a standard deviation of one. The mean shift and standard deviation values based on the arm regions were then applied to the eUR and PH regions. All regions were then merged and smoothed for visualization using identical parameters.
Quantile normalization was performed for comparisons between TIGER and non-TIGER samples through the preprocess Core R package to equalize the dynamic range of RT values (Bolstad 2016).
The stats (v3.6.2) statistical package was used to identify 50-kb windows with significantly altered RT values, by one-way ANOVA test [aov, P value adjusted for multiple testing with BH post-HOC correction {P < (0.01/2400)}]. Adjacent windows were merged and >200kb regions were called as variant.
BEDTools intersect (v2.26.0) was used to determine overlap of windows with -f 0.5 parameters (Quinlan and Hall 2010).
Merging of adjacent RT windows was done by BEDTools merge (v2.27.1) with -d 11 parameters.
Genome_build: dm6
Supplementary_files_format_and_content: text

organism: Drosophila melanogaster

source_name: female 3rd instar larval wing disc

extract_protocol:
Tissue was disrupted by douncing and filtered over a 30 mM filter to collect follicle cell nuclei. DAPI-stained nuclei were sorted by 5-Laser FACS Aria III and G1 and S-phase populations were collected. Genomic DNA was fragmented by sonication and extracted by using a standard Phenol-Chloroform extraction protocol and precipitated with sodium acetate, glycogen, and isopropanol.
Libraries were prepared according to the protocol accompanying Rubicon Thruplex DNA-seq kit (R400427).

value: Wing disc

value: Yellow-white

tag: Sex

value: Female

tag: developmental stage

value: 3rd instar larvae

tag: phase

value: S phase


description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSEhigh
Antigen_experienced_CFSEhighcohort1_Rep2


title: ago2_35S-EVD

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: contains Amplicons: At2G20610, 35S-EVD_EVD-gag

data_processing:
Library strategy: BSA-seq [Bisulfite converted PCR-amplified Amplicon Sequencing]
Raw reads were trimmed for adapters and mapped using methylpy to all the amplicons pooled together for sequencing.
The allC file generated by methylpy was used to calculate methylation percentage for a locus.
Supplementary_files_format_and_content: tab delimited allC file showing total number of reads (total) and reads reporting methylation (mc_count) for each cytosine in the amplicon pool.

organism: Arabidopsis thaliana

growth_protocol: Plants were grown under 16-hour day conditions at 22°C in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds unless otherwise noted.

extract_protocol:
Genomic DNA was treated with RNAse A, recovered with phenol chloroform isolation and then treated with sodium bisulfite using the EZ DNA methylation kit (Zymo Research).
PCR-amplified amplicons were gel-purified and pooled in equimolar ratios. The Illumina Nextera DNA Flex kit (https://doi.org/10.1101/779215) was used to prepare the library.
Single-end Illumina sequencing of 300 bp with an Illumina MiSeq.

tag: ecotype

value: Columbia

tag: tissue

tag: molecule subtype

value: PCR amplified DNA


title: ago6_35S-EVD

source_name: inflorescence (stage 1-12) immature flower buds


title: Antigen_experienced_CFSEhigh_Rep1

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSEhigh
Antigen_experienced_CFSEhigh_Rep1


title: CLL412B_rnaseq

value: peripheral blood

value: chronic lymphocytic leukemia


title: CLL347B_rnaseq


title: Col_EVD-only_BR4

description: contains Amplicons: At2G20610, EVD-only

value: inflorescence (stage 1-12) immature flower buds


title: Col_EVD-only_BR5

description: contains Amplicons: At2G20610, EVD-only


title: Antigen_experienced_CFSEhigh_Rep3

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSEhigh
Antigen_experienced_CFSEhigh_Rep3


title: Naive_CFSElow_Rep1

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSElow
Naive_CFSElow_Rep1


description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSEhigh
Antigen_experienced_CFSEhighcohort1_Rep1


title: Antigen_experienced_CFSElow_Rep3

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSElow
Antigen_experienced_CFSElow_Rep3


title: CLL144_rnaseq


title: Naive_CFSElow_Rep3

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSElow
Naive_CFSElow_Rep3


title: Naive_CFSElow_Rep2

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSElow
Naive_CFSElow_Rep2


title: Antigen_experienced_CFSEhigh_Rep2

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSEhigh
Antigen_experienced_CFSEhigh_Rep2


title: Antigen_experienced_CFSElow_Rep2

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSElow
Antigen_experienced_CFSElow_Rep2


title: Antigen_experienced_CFSElow_Rep1

description:
female,C57BL/6,Lymph node, Marilyn CD4 T cells, CFSElow
Antigen_experienced_CFSElow_Rep1


title: Col_EVD-only_BR3

description: contains Amplicons: At2G20610, EVD-only


title: CLL158_rnaseq


title: Col_EVD-only_BR2

description: contains Amplicons: At2G20610, EVD-only


title: Yellow-white_WingDisc_MS_Replicate2


title: Col_35S-EVD_EVD-only_BR4

description: contains Amplicons: At2G20610, 35S-EVD_EVD-gag, EVD-only


title: DL166_rnaseq

value: lymph node


title: TS121511B_X_FAIRE-seq

data_processing:
Reads were aligned to hg19 with bowtie2 (v2.2.5) using default settings.
Reads in ENCODE blacklisted regions were removed with samtools (v1.9).
Peaks were called with MACS2 (v2.1.0.20150420) with the parameters --nomodel --shiftsize=150 (ChIP) or --nomodel --shiftsize=50 (FAIRE) and input controls.
DiffBind (v2.14.0) was used to derive consensus peak sets for each histone mark and accessible chromatin, requiring peaks to overlap in at least three samples for each ChIP-seq or FAIRE-seq assay in order to be merged and retained. The consensus peaksets for each assay were then concatenated and merged to derive a list of putative regulatory elements with bedtools2 (v2.29.2).
DiffBind was then used to determine differentially bound/accessible regions between sample groups for each assay. ChIPseeker (v1.22.0) was used to annotate peaks with hg19 UCSC knownGene annotations.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak format files containing peaks for each sample as called by MACS2.

extract_protocol:
Cells were formaldehyde cross-linked (1% final concentration) for 10 minutes in RPMI with 10% FBS. Quenching was performed by addition of 1M glycine (125 mM final concentration) with gentle mixing for 10 minutes at room temperature. Chromatin was lysed for 10 minutes sequentially in L1 buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 5% NP40 and 0.25% Triton X-100) followed by L2 buffer (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 1M and Tris pH 8.0). The pellets were resuspended in 300 ul of buffer L3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 1M Tris pH 8.0, 100mM NaCl, 0.1% Na-deoxycholate and 5mg/ml N-lauroyl sarcosine) and sonicated to an average size of 500bp using a Diagenode Bioruptor. The soluble DNA fraction was isolated by performing two consecutive phenol:chloroform:isoamylalcohol (25:24:1, pH 8) extractions followed by a chloroform-isoamyl alcohol (24:1) extraction. Precipitated DNA was resuspended in 10mM Tris-HCl (pH 7.4) and incubated with 10 µg of RNase A for 1hr. DNA was purified with QIAquick PCR purification columns.
Cells were formaldehyde cross-linked (1% final concentration) for 10 minutes in RPMI with 10% FBS. Quenching was performed by addition of 1M glycine (125 mM final concentration) with gentle mixing for 10 minutes at room temperature. Cells were washed with cold PBS and lysed in an SDS buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0) with protease inhibitors before chromatin was fragmented using a Diagenode Bioruptor to an average size of less than 300 bp as determined using an Agilent Bioanalyzer 2100. Lysates were immunoprecipitated with the listed antibodies conjugated to Protein-A Dynabeads (5 ug antibody incubated with beads for 2-4 hours at 4°C) overnight at 4°C. The beads were then washed with the following buffers each for 3 minutes at 4°C - low salt buffer (150 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), high salt buffer (500 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), LiCl buffer (250 mM LiCl, 50 mM Tris pH 8.0, 0.5% Na deoxycholate, 1% NP40), and TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). After washing, crosslinks were reversed overnight at 65°C in 250 uL elution buffer (1% SDS, 100 mM NaHCO3) followed by addition of proteinaseK and incubation at 56°C for 1 hour.  DNA was purified with QIAquick PCR purification columns.
At least 3 ng of DNA was used to for indexed library preparation using Illumina TruSeq adapters and standard Illumina protocols. Fragments were size selected (average fragment-size: 200-400 bp for ChIP; 50-200 for FAIRE) using Agencourt AMPure XP beads prior to amplification. Samples were pooled (6-10 per lane) and sequenced.

value: tonsil

value: healthy


title: TS121511A_X_FAIRE-seq


title: sqk1-1_SQK1-IR_dCas9

description:
PCR amplified DNA
contains Amplicons: At2G20610, sqk1-1-amplicon-1

data_processing:
Raw reads were trimmed for adapters and mapped using methylpy to all the amplicons pooled together for sequencing.
The allC file generated by methylpy was used to calculate methylation percentage for a locus.
Supplementary_files_format_and_content: tab delimited allC file showing total number of reads (total) and reads reporting methylation (mc_count) for each cytosine in the amplicon pool.


title: CLL140_rnaseq


title: TS081111A_X_FAIRE-seq


title: sqk1-1_SQK1-IR


title: TS111711_X_FAIRE-seq


title: Col_35S-EVD_EVD-only_BR3


title: TS102711A_X_FAIRE-seq


title: sqk1-1


title: TS020212A_X_FAIRE-seq


title: TS061611B_X_FAIRE-seq


title: sqk1-1_dCas9


title: TS072611B_X_FAIRE-seq


title: suvh2-suvh9_35S-EVD_BR1_BSA-seq


title: Col_35S-EVD_EVD-only_BR2


title: suvh2-suvh9_35S-EVD_BR3_BSA-seq


title: ago469_SQK1-IR

description:
PCR amplified DNA
contains Amplicons: At2G20610, SQK1-amplicon-1


title: suvh2-suvh9_35S-EVD_BR2_BSA-seq


title: TS060911A_X_FAIRE-seq


title: drm1-drm2_35S-EVD_BR2

description:
PCR amplified DNA
contains Amplicons: At2G20610, 35S-EVD_EVD-gag


title: TS020212B_X_FAIRE-seq


title: Col_T3_35S-EVD_BSA-seq


title: TS072111A_X_FAIRE-seq


title: pol5_SQK1-IR_BR1_BSA-seq

description: contains Amplicons: At2G20610, SQK-amplicon-1


title: pol5_RHD6-IR_BSA-seq

description: contains Amplicons: At2G20610, RHD6-amplicon-1


title: FL433_X_FAIRE-seq

value: follicular lymphoma


title: TS042811A_X_FAIRE-seq


title: TS012612B_X_FAIRE-seq


title: pol5_Fig5_BSA-seq


title: pol5_35S-EVD_BR3_BSA-seq

description: contains Amplicons: At2G20610, 35S-EVD_EVD-gag


title: FL404_X_FAIRE-seq


title: pol5_SQK1-IR_BR2_BSA-seq


title: TS072611A_X_FAIRE-seq


title: FL395_X_FAIRE-seq


title: TS012612A_X_FAIRE-seq


title: FL420_X_FAIRE-seq


title: TS050411_X_FAIRE-seq


title: pol5_35S-EVD_BR2_BSA-seq


title: FL255_X_FAIRE-seq


title: pol4_35S-EVD_BSA-seq


title: pol4_Supplemental_BSA-seq

description: contains Amplicons: At2G20610, EVD5


title: FL238_X_FAIRE-seq


title: FL174_X_FAIRE-seq


title: FL372_X_FAIRE-seq


title: pol5_35S-EVD_BR1_BSA-seq


title: pol5_Fig6_BSA-seq


title: FL202_X_FAIRE-seq


title: DL487_X_FAIRE-seq


title: met1_35S-EVD_BSA-seq


title: FL301_X_FAIRE-seq


title: pol5_Supplemental_BSA-seq

description: contains Amplicons: At2G20610, SimpleHat2, Tas3a, EVD5, At1G56090, At5G52070


title: dcl2-dcl4_35S-EVD_BSA-seq


title: drm2_35S-EVD_BSA-seq


title: dcl3_35S-EVD_BSA-seq


title: DL551_X_FAIRE-seq


title: drm1-drm2_35S-EVD_BSA-seq


title: dcl2-dcl3-dcl4_35S-EVD_BSA-seq


title: drm1-drm2_Supplemental_BSA-seq

description: contains Amplicons: At2G20610, SimpleHat2, Tas3a, EVD5


title: DL3A538_X_FAIRE-seq


title: dcl1_35S-EVD_BSA-seq


title: DL252_X_FAIRE-seq


title: FL313_X_FAIRE-seq


title: DL237_X_FAIRE-seq


title: dcl1-het-dcl2-dcl3-dcl4_35S-EVD_BSA-seq


title: dcl1-dcl2-dcl3-dcl4_35S-EVD_BSA-seq


title: CLL396_X_FAIRE-seq


title: CLL378_X_FAIRE-seq


title: ago4-ago6_35S-EVD_BSA-seq


title: cmt2_35S-EVD_BSA-seq


title: cmt2-cmt3_35S-EVD_BSA-seq


title: CLL347_X_FAIRE-seq


title: DL273_X_FAIRE-seq


title: ago4-6_35S-EVD_BSA-seq


title: ago4-ago6-ago9_35S-EVD_BSA-seq


title: CLL144_X_FAIRE-seq


title: Col_Supplemental_BSA-seq


title: Col_T3A-EVD_BSA-seq

description: contains Amplicons: At2G20610, T3A-EVD


title: Col_root_BSA-seq

source_name: roots

value: roots


title: TS081414_NAIVE_K27AC_ChIP

source_name: CD19+CD27-CD5- B cells

extract_protocol:
Cells were formaldehyde cross-linked (1% final concentration) for 10 minutes in RPMI with 10% FBS. Quenching was performed by addition of 1M glycine (125 mM final concentration) with gentle mixing for 10 minutes at room temperature. Cells were washed with cold PBS and lysed in an SDS buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0) with protease inhibitors before chromatin was fragmented using a Diagenode Bioruptor to an average size of less than 300 bp as determined using an Agilent Bioanalyzer 2100. Lysates were immunoprecipitated with the listed antibodies conjugated to Protein-A Dynabeads (5 ug antibody incubated with beads for 2-4 hours at 4°C) overnight at 4°C. The beads were then washed with the following buffers each for 3 minutes at 4°C - low salt buffer (150 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), high salt buffer (500 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), LiCl buffer (250 mM LiCl, 50 mM Tris pH 8.0, 0.5% Na deoxycholate, 1% NP40), and TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). After washing, crosslinks were reversed overnight at 65°C in 250 uL elution buffer (1% SDS, 100 mM NaHCO3) followed by addition of proteinaseK and incubation at 56°C for 1 hour.  DNA was purified with QIAquick PCR purification columns.
At least 3 ng of DNA was used to for indexed library preparation using Illumina TruSeq adapters and standard Illumina protocols. Fragments were size selected (average fragment-size: 200-400 bp for ChIP; 50-200 for FAIRE) using Agencourt AMPure XP beads prior to amplification. Samples were pooled (6-10 per lane) and sequenced.

value: H3K27ac (Abcam ab4729)


title: TS102214_MEMORY_K27AC_ChIP

source_name: CD19+CD27+CD5- B cells


title: TS121511A_K27AC_ChIP


title: Col_RHD6-IR_BR2_BSA-seq


title: Col_RHD6-IR_root_BSA-seq


title: Col_SQK1-IR_Fig6_BSA-seq

description: contains Amplicons: At2G20610, SQK-amplicon-1, SQK-amplicon-2


title: ago4-4_35S-EVD_BSA-seq


title: TS102214_NAIVE_K27AC_ChIP


title: CLL140_X_FAIRE-seq


title: Col_SQK1-IR_BR2_BSA-seq


title: Col_SQK1-IR_BR1_BSA-seq


title: TS072611A_K27AC_ChIP


title: TS072111A_K27AC_ChIP


title: Col_RHD6-IR_BR1_BSA-seq


title: TS121511B_K27AC_ChIP


title: TS060911A_K27AC_ChIP


title: Col_BR2_Fig5_BSA-seq


title: TS050411_K27AC_ChIP


title: TS081111A_K27AC_ChIP


title: TS040611B_K27AC_ChIP


title: Col_BR1_Fig5_BSA-seq


title: TS012612B_K27AC_ChIP


title: TS012612A_K27AC_ChIP


title: FL301_K27AC_ChIP


title: FL174_K27AC_ChIP


title: TS072611B_K27AC_ChIP


title: Col_35S-EVD_BR3_BSA-seq


title: Col_BR2_Fig6_BSA-seq


title: FL238_K27AC_ChIP


title: CLL412_X_FAIRE-seq


title: Col_35S-EVD_T3A-EVD_BSA-seq

description: contains Amplicons: At2G20610, 35S-EVD_EVD-gag, T3A-EVD


title: Col_BR1_Fig6_BSA-seq


title: Col_EVD-only_BSA-seq

description: contains Amplicons: At2G20610, EVD-only


title: DL551_K27AC_ChIP

value: diffuse large B cell lymphoma


title: MPP4-1013/1013 1 [SHMN43]

city: Toronto

first: Vincent

last: Rondeau

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

data_processing:
Sequencing reads (50 bp) were generated on the GenomEast platform (Illumina). RNAseq libraries have been sequenced in Paired-End mode.
Briefly, reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) and reads shorter than 40 bases were discarded for further analysis. Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR.
Gene expression quantiﬁcation was performed from uniquely aligned reads using htseq-count with annotations from Ensembl and “union” mode. Only non-ambiguously assigned reads have been retained for further analyses.
Read counts have been normalized across samples with the median-of-ratios method proposed by Anders and Huber, to make these counts comparable between samples.
RNA-seq analyses yielded robust and reproducible data for all samples with more than 8 x 107 reads per sample.
Genome_build: mm10
Supplementary_files_format_and_content: Excel tables with raw and normalized gene counts for every gene and every sample

source_name: RNA has been prepared from sorted MPP subpopulations (MPP1, MPP2, MPP3, MPP4)

extract_protocol:
Pools of 3 x 103 MPP1-4 were sorted directly into RLT buffer (Qiagen) enriched with 1% of β-mercaptoethanol. Total RNA isolation and DNAse treatment were performed using RNeasy Micro Kit (Qiagen). Full length cDNAs were generated from 350 to 1,000 pg of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain-en-Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase.
Six hundred pg of pre-amplified cDNAs were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP and SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoresis.

tag: cell type

value: Bone marrow


title: TS061611B_K27AC_ChIP

tag: disease state


title: DL3A538_K27AC_ChIP


title: MPP4-+/1013 2 [SHMN41]


title: DL252_K27AC_ChIP


title: MPP4-+/1013 3 [SHMN42]


title: Col_35S-EVD_EVD-only_BSA-seq


title: MPP4-+/1013 1 [SHMN40]


title: TS020212B_K27AC_ChIP


title: MPP4-1013/1013 2 [SHMN48]


title: DL237_K27AC_ChIP


title: Col_35S-EVD_BR1_BSA-seq


title: MPP4-WT 3 [SHMN39]

value: wild type


title: CLL674_K27AC_ChIP


title: MPP4-WT 1 [SHMN37]


title: MPP3-1013/1013 2 [SHMN52]


title: DL135_K27AC_ChIP


title: CLL679_K27AC_ChIP


title: CLL668_K27AC_ChIP


title: CLL618_K27AC_ChIP


title: MPP3-1013/1013 1 [SHMN35]


title: CLL633_K27AC_ChIP


title: CLL612_K27AC_ChIP


title: MPP3-WT 3 [SHMN30]


title: CLL589_K27AC_ChIP


title: MPP4-WT 2 [SHMN38]


title: MPP3-+/1013 1 [SHMN31]


title: Col_35S-EVD_BR4_BSA-seq


title: MPP3-+/1013 3 [SHMN33]


title: CLL583_K27AC_ChIP


title: MPP3-+/1013 2 [SHMN32]


title: MPP3-WT 1 [SHMN28]


title: MPP3-WT 2 [SHMN29]


title: DL273_K27AC_ChIP


title: CLL378_K27AC_ChIP


title: Col_35S-EVD_BR2_BSA-seq


title: CLL144_K27AC_ChIP


title: CLL396_K27AC_ChIP


title: CLL347_K27AC_ChIP


title: MPP2-1013/1013 2 [SHMN27]


title: MPP2-1013/1013 1 [SHMN25]


title: MPP2-+/1013 3 [SHMN24]


title: CLL634_K27AC_ChIP


title: MPP2-WT 3 [SHMN21]


title: MPP2-+/1013 1 [SHMN22]


title: CLL412_K27AC_ChIP


title: MPP1-1013/1013 2 [SHMN49]


title: CC021314_K27AC_ChIP

source_name: CD19+CD10+CD44lowCXCR4- B cells


title: CB021314_K27AC_ChIP

source_name: CD19+CD10+CD44lowCXCR4+ B cells


title: TS111711_K4ME1_ChIP

source_name: CD19+ B cells

value: H3K4me1 (Abcam ab8895)


title: TS121511A_K4ME1_ChIP


title: MPP2-WT 1 [SHMN19]


title: MPP2-+/1013 2 [SHMN23]


title: TS121511B_K4ME1_ChIP


title: MPP2-WT 2 [SHMN20]


title: CLL140_K27AC_ChIP


title: MPP1-+/1013 1 [SHMN13]


title: TS081111A_K4ME1_ChIP


title: MPP1-WT 3 [SHMN46]


title: TS102711A_K4ME1_ChIP


title: MPP1-1013/1013 1 [SHMN17]


title: TS072111A_K4ME1_ChIP


title: TS061611A_K4ME1_ChIP


title: TS072611B_K4ME1_ChIP


title: MPP1-WT 2 [SHMN11]


title: TS060911A_K4ME1_ChIP


title: MPP1-+/1013 2 [SHMN14]


title: MPP1-+/1013 3 [SHMN47]


title: TS050411_K4ME1_ChIP


title: TS061611B_K4ME1_ChIP


title: TS040611B_K4ME1_ChIP


title: TS020212B_K4ME1_ChIP


title: TS020212A_K4ME1_ChIP


title: MPP1-WT 1 [SHMN10]


title: caki cl2a_(Clariom_D_Human)

city: Donsotia-San Sebastian

first: charles

last: lawrie

address: Paseo Mikeletegi, 83- planta 3

department: Oncology

country: Spain

institute: Biodonostia Research Institute

description: Gene expression data from  clone 2 of Caki sunitinib resistant ccRCC cell line

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA processed in affymetrix TAC (v.4.0.2)

source_name: ccRCC Caki sunitinib resistant cell line

label_protocol: standard Affymetrix protocol

growth_protocol: cells were grown over several months either with sunitinib (two clones per cell line) or without (parental cell lines).

extract_protocol: RNA was extracted for cells with Trizol using standard protocols

treatment_protocol: Sunitinib concentrations were increased incrementally by 0.5uM steps until the IC50 values reached >10uM

tag: cell line

value: clear cell renal cell carcinoma (ccRCC)

tag: drug resistance

value: sunitinib resistant


title: W1_S57

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

description: Wild type bone marrow tissue

data_processing:
Data is mapping to genome UCSC mm10 using STAR software
counts data are extract using featureCounts
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Gene counts and log cpm for each sample in spreadsheet

source_name: whole bone marrow mononuclear cells

growth_protocol: Not applicate

extract_protocol:
RNA was extracted from Bone Marrow Cells harvested from bones of respective genotyped mice, and washed twice with PBS. RNA was collected using Trizol reagent (Catlog#15596026, Ambion), then treated with DNAse using DNAse supplied in TURBO DNA-free™ Kit (Catlog#AM1907, Ambion).The obtained RNA was re-purified using RNeasy kit (Catalog# 74106, Qiagen).
RNA was first treated with GlobinClear (Mouse/Rat) to remove any possible globin mRNA, then Illumina TruSeq Stranded TotalRNA Lib Prep Kit. SingleIndex.

treatment_protocol: Not applicate

tag: genetic condition

value: Wild type


title: caki cl2b_(Clariom_D_Human)


title: TS012612A_K4ME1_ChIP

tag: antibody


title: W2_S58

description: Wild type bone marrow tissue


title: TFD3_S68

description: Tet2/Flt3/Dnmt3a knockdown leukemia bone marrow tissue

value: Tet2+/-/Flt3ITD/+ Dnmt3aFlox/+; MxCre


title: TFD1_S66


title: caki cl1b_(Clariom_D_Human)

description: Gene expression data from  clone 1 of Caki sunitinib resistant ccRCC cell line


title: caki cl2c_(Clariom_D_Human)


title: 786c2a_(Clariom_D_Human)

description: Gene expression data from  clone 2 of 786-O sunitinib resistant ccRCC cell line

source_name: ccRCC 786 sunitinib resistant cell line


title: Caki Parental 3_(Clariom_D_Human)

description: Gene expression data from Caki-1 ccRCC cell line

source_name: ccRCC Caki cell line

value: sunitinib sensitive


title: 786c2c_(Clariom_D_Human)


title: 786c1b_(Clariom_D_Human)

description: Gene expression data from  clone 1 of 786-O sunitinib resistant ccRCC cell line


title: W3_S59

description: Wild type bone marrow tissue


title: caki cl1c_(Clariom_D_Human)


title: 786c2b_(Clariom_D_Human)


title: FL255_K4ME1_ChIP


title: FL313_K4ME1_ChIP


title: TF2_S64

description: Tet2/Flt3 knockdown leukemia bone marrow tissue


title: Caki Parental 1_(Clariom_D_Human)


title: 786c1a_(Clariom_D_Human)


title: Post injury with FAK inhibitor day 14 3

city: Mobile

first: Steve

last: Lim

state: AL

address: 5851 USA Drive North MSB 2320

department: Biochemistry and molecular biology

institute: University of South Alabama

data_processing:
HiSeq 2x150 PE HO HiSeq 2x150bp
Sample sequencing statistics
Overall sequencing statistics
Mapping sequence reads to the reference genome
Extracting gene hit counts
Genome_build: mm10, GRCm38

source_name: Media of femoral artery

extract_protocol:
Mice were treated with or without FAK-I for 2 weeks after wire injury. Femoral arteries were isolated, and the fat and adventitia layers were carefully removed under surgical microscope. To remove endothelial and immune cells, the artery lumen was quickly flushed with 150 µl TRIzol lysis reagent (Invitrogen) using a 29-gauge insulin syringe. Media were frozen in liquid nitrogen and lysed in 500 µl TRIzol  per artery, and total RNA was isolated using the RNeasy column.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated twice daily with vehicle (10 mM citrate, pH 6.0) or FAK inhibitor VS-4718 (50 mg/kg) by oral gavage.

value: Media of femoral artery

tag: treatment

value: Post injury with FAK inhibitor day 14


title: TFD2_S67


title: DF3_S62

description: Dnmt3a/Flt3 knockdown leukemia bone marrow tissue

value: Dnmt3aFlox/+:MxCre /Flt3 ITD/+


title: Caki Parental 2_(Clariom_D_Human)


title: TS012612B_K4ME1_ChIP

value: tonsil


title: FL301_K4ME1_ChIP

value: lymph node


title: caki cl1a_(Clariom_D_Human)


title: DF2_S61


title: 786Pa_(Clariom_D_Human)

description: Gene expression data from 786-O ccRCC cell line

source_name: ccRCC 786 cell line


title: TF3_S65


title: TF1_S63


title: FL238_K4ME1_ChIP

value: follicular lymphoma


title: 786Pc_(Clariom_D_Human)


title: FL174_K4ME1_ChIP


title: Post injury with FAK inhibitor day 14 2


title: Post injury with FAK inhibitor day 14 1


title: Mouse pancreatic islet cells from Ngn3-CreERT lineage traced mice

city: London

first: Rocio

last: Sancho

address: Floor 28 Guy's Hospital

department: Centre for Stem Cells and Regenerative Medicine

country: United Kingdom

institute: King's College London

data_processing:
Alignment and Quantification: Cell Ranger 3.2.0
Read quality control: FastQC 0.11.8
Read Trimming: Cutadapt 2.5
Cell Quality Control: Scater 3.9
Dimensionality Reduction & Analysis: Seurat  3
Genome_build: mm10: TdTomato Sequence
Supplementary_files_format_and_content: Raw Count Matrix

source_name: Ngn3-expressing cells in the adult mouse pancreas

growth_protocol: Islets were isolated directly from mice

extract_protocol:
Approximately 10,000 cells were loaded into a channel of the 10x Chromium Chip B - according to the 10x Genomics Single Cell 3’ Reagent Kit v3 GEM protocol
RNA was reverse transcribed via 11 PCR cycles, followed by a further 12 PCR cycles for cDNA amplification
10X 3' end scRNA-Seq

treatment_protocol: Islets cells were isolated by performing collagenase digestion, histopaque gradient and dissociated to single cells using TypLE Express

tag: genotype/variation

value: pancreatic islet cells

tag: time point

value: 10 days post-tamoxifen


title: DL3A538_K4ME1_ChIP

value: diffuse large B cell lymphoma


title: Mouse pancreatic islet cells from Ngn3-CreERT lineage traced mice (2 mice pooled)_1

description:
GRI264A4 & GRI264A5
Processed data file: counts.csv includes data for both GSMnnn…..

data_processing:
Alignment and Quantification: Cell Ranger 5.0.0
Read quality control: FastQC 0.11.8
Read Trimming: Cutadapt 2.5
Cell Quality Control: Scater 3.9
Dimensionality Reduction & Analysis: Seurat 4.0.0
Genome_build: mm10: TdTomato Sequence
Supplementary_files_format_and_content: Raw Count Matrix

extract_protocol:
Approximately 10,000 cells were loaded into a channel of the 10x Chromium Chip B - according to the 10x Genomics Single Cell 3’ Reagent Kit v3 GEM protocol
RNA was reverse transcribed via 11 PCR cycles, followed by a further 12 PCR cycles for cDNA amplification


title: FL153_K4ME1_ChIP


title: 786c1c_(Clariom_D_Human)


title: Post injury day 14 2

tag: strain

value: Post injury day 14


title: DF1_S60


title: Post injury day 14 3


title: A498 cl1c_(Clariom_D_Human)

description: Gene expression data from  clone 1 of  498 sunitinib resistant ccRCC cell line

source_name: ccRCC A498 sunitinib resistantcell line


title: Sham control 2

value: Sham control


title: A498 cl2c_(Clariom_D_Human)

description: Gene expression data from  clone 2  of  498 sunitinib resistant ccRCC cell line


title: DL551_K4ME1_ChIP

value: H3K4me1 (Abcam ab8895)


title: Post injury day 14 1


title: 786Pb_(Clariom_D_Human)

value: clear cell renal cell carcinoma (ccRCC)


title: DL273_K4ME1_ChIP


title: A498 cl2a_(Clariom_D_Human)

value: sunitinib resistant


title: Sham control 3


title: A498 cl2b_(Clariom_D_Human)


title: DL252_K4ME1_ChIP


title: DL237_K4ME1_ChIP


title: Sham control 1


title: DMI_MET3

city: Nanjing，Zhenjiang

first: Zhicong

last: Zhao

state: Jiangsu province

address: 163 Xianlin Avenue，438 Jiefang Road

institute: School of life sciences, Nanjing university, Affiliated Hospital of Jiangsu University

description: 3T3-L1 adipocyte D6 metformin re3

data_processing:
Illumina pipeline CASAVA v1.8.2 used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster  Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to  the manufacturer’s instructions. After cluster generation, the library preparations were  sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were  generated
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and iscurrently the most commonly used method for estimating gene expression levels
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: 3T3-L1 cells

growth_protocol: Mouse embryonic fibroblast 3T3-L1 cells were obtained from the American Type Culture Collection (Manassas, VA) and cultivated in DMEM (Gibco, Gaithersburg, MD, USA) containing 10% FBS and 1% penicillin/streptomycin (Life Technologies, Grand Island, NY, USA). 3T3-L1 preadipocytes were seeded into 6 well plates when contact inhibition occurred. Then cells were induced by 1-methyl-3-isobutyl xanthine, dexamethasone and insulin according to Anil Kumar's method

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Invitrogen, Carlsbad, CA).Total RNA was extracted from cells using Trizol reagent (Invitrogen, Carlsbad, CA) Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: metformin (dissolved in phosphate-buffered saline, PBS) at 5 mM was added to the medium for every 2 days with Dexamethasone/3-isobutyl-1-methylxanthine/Insulin

value: murine preadipocyte cells


title: A498 cl1b_(Clariom_D_Human)


title: DL188_K4ME1_ChIP


title: 217 DC

city: Ridgefield

first: Li

last: Li

state: Connecticut

address: PO Box 368

institute: Boehringer Ingelheim Pharmaceuticals, Inc.

data_processing: All samples were normalized to the same concentration and a total of 100 ng of RNA per sample were used for hybridization and run on the XT_PGX_MmV2_Inflammation_CSO 248 gene panel (NanoString Item No. 115000082)

source_name: TRUC mouse

extract_protocol: distal colons were preserved snap frozen in RNAlater, homogenized in 1 mL of Trizol Reagent (Invitrogen cat. #15596-026) with a 5 mm stainless steel bead (Qiagen cat. #69989) in RNase-free tubes (Ambion) on a tissue homogenizer (Tissue Lyser II) for 3 runs X 2 minutes at frequency 25.0 for 5 minutes at room temperature to permit complete dissociation. 200 μL of chloroform (EM Science cat. # CX1055-6) per mL of Trizol Reagent was added, capped securely and shaken vigorously by hand for 15 seconds. Tubes were incubated at room temperature for 15 minutes and then centrifuged at 10,000 x g for 10 min. at 4 degrees C. The top aqueous phase was harvested after centrifugation and transferred to 96 well deep well plates and stored at -80 degrees C until RNA isolation. RNA was isolated with automation on the Biomek using Agencourt RNAdvance Tissue Kit (Beckman Coulter #14073200). Yield and quality of RNA were determined using Nanodrop and RNA Integrity Number (RIN) values were determined using Tapestation (Agilent)

value: Mouse distal colons

tag: treatment group

value: oral vehicle


title: DL135_K4ME1_ChIP


title: 220 DC


title: A498 Pc_(Clariom_D_Human)

description: Gene expression data from  498 ccRCC cell line

source_name: ccRCC A498 cell line

value: sunitinib sensitive


title: CLL412_K4ME1_ChIP

value: peripheral blood

value: chronic lymphocytic leukemia


title: A498 cl1a_(Clariom_D_Human)

source_name: ccRCC A498 sunitinib resistant cell line


title: 219 DC


title: Mouse pancreatic islet cells from Ngn3-CreERT lineage traced mice (2 mice pooled)_2

description:
GRI264A6 & GRI264A7
Processed data file: counts.csv includes data for both GSMnnn…..


title: CLL396_K4ME1_ChIP


title: A498 Pb_(Clariom_D_Human)


title: DMI3

description: 3T3-L1 adipocyte D6 control re3


title: DMI_MET1

description: 3T3-L1 adipocyte D6 metformin re1


title: CLL347_K4ME1_ChIP


title: DMI2

description: 3T3-L1 adipocyte D6 control re2


title: A498 Pa_(Clariom_D_Human)


title: DMI1

description: 3T3-L1 adipocyte D6 control re1


title: 214 DC


title: 213 DC


title: 193 DC


title: 173 DC


title: DMI_MET2

description: 3T3-L1 adipocyte D6 metformin re2


title: CLL144_K4ME1_ChIP


title: CLL140_K4ME1_ChIP


title: CLL378_K4ME1_ChIP


title: NC2

description: 3T3-L1 preadipocyte D6 re2

value: untreated


title: 172 DC

value: isotype control


title: 169 DC


title: TS121511A_H3AC_ChIP

value: tonsil

value: healthy

value: H3K9/K14ac (EMD-Millipore 06-599)


title: NC1

description: 3T3-L1 preadipocyte D6 re1


title: 216 DC


title: Testis from WT mouse_rep2

city: Shanghai

first: Wenfeng

last: Xiong

state: Shanghai

address: Ruijin er road

department: Research Center for Experimental Medicine

institute: Ruijin hospital

description: Gene expression in testis from 6-8 weeks old WT mouse

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: Testis, WT mouse

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: Testis

tag: gender

value: Male

tag: age

value: 6-8 weeks

tag: strain background


title: 168 DC


title: TS111711_H3AC_ChIP


title: NC3

description: 3T3-L1 preadipocyte D6 re3


title: Testis from WT mouse_rep1


title: B15_L3_132132

city: Nanning

first: Rilan

last: Chen

address: Department of Acupuncture, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine Guangxi Zhuang Autonomous Region, China

department: Department of Acupuncture

description: Differential expression of osteoarthritis-related genes (Osteoarthritis)

data_processing:
Basecalls performed using Illumina HiSeq2500
Through fastp software to obtain a clean read
Align the fastq files against the library’s sgRNAs sequences list using TopHat
The DEGSeq R package (1.20.0) was used to perform differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Rattus norvegicus

source_name: Rat

extract_protocol:
Total RNA was isolated from cartilage tissue using TRIzol (Invitrogen, Carlsbad, CA, USA), and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the instructions provided by the manufacturer.
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Xiaogu San (XGS) was obtained from Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine (Nanning, Guangxi Zhuang Autonomous Region, China). Male Sprague Dawley (SD) rats were purchased from the Experimental Animal Center, Sun yat-sen University (Guangzhou, China). Rats (weight 140-230 g, age 8-12 weeks) were placed in an air-conditioned room at 22 ± 2 ℃ with a humidity of 50±10%, a 12 h light-/dark cycle and free access to sterile water and food. All animal procedures were certified by the Guangzhou Forevergen Medical Experimental Animal Center Animal Ethics Committee (Approval No. GFAC-AEWC-119) and animals were treated in accordance with Guide for the Care and Use of Laboratory Animals (8th edition, National Academies Press).

value: Sprague Dawley

tag: Sex

value: male

tag: weight

value: 8-12 weeks

value: Cartilage

value: osteoarthritis

value: XGS


title: B11_L3_131131

institute: Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine

growth_protocol: Rats (weight 140-230 g, age 8-12 weeks) were placed in an air-conditioned room at 22 ± 2 ℃ with a humidity of 50±10%, a 12 h light-/dark cycle and free access to sterile water and food.

tag: tissue


title: 166 DC

value: Mouse distal colons


title: TS121511A_snp

type: genomic

hyb_protocol: 0.5 ug of DNA was hybridized according to manufacturer's instructions.

data_processing: Genotypes were called from CEL files using the Affymetrix Genotyping Console (v4.2.0.26) with the BIRDSEED v2 algorithm with default settings. Copy number analysis was performed with the Affymetrix Genotyping Console using regional GC correction and default settings. The DNAcopy R package was used for circular binary segmentation on raw data. cnvkit and the copynumber R package were used for CNV thresholding using log2 ratio values of -0.2 and 0.2.

label_protocol: Per manufacturer's instructions

extract_protocol: Genomic DNA was extracted from sorted B CD19+ B cells using a Qiagen Dneasy Blood and Tissue kit.


title: B3_L3_130130

description: Differential expression of osteoarthritis-related genes (control)

value: control


title: TS120310_snp


title: B2_L3_129129


title: TS102711A_H3AC_ChIP


title: TS072611B_H3AC_ChIP


title: 153 DC


title: Testis from Prss37KO mouse_rep1

description: Gene expression in testis from 6-8 weeks old Prss55KO mouse

source_name: Testis, Prss37KO mouse


title: TS111711_snp


title: Testis from WT mouse_rep3


title: Testis from Prss37KO mouse_rep3


title: TS061611B_H3AC_ChIP


title: TS081111A_H3AC_ChIP


title: TS072111A_H3AC_ChIP


title: TS081111A_snp


title: Testis from Prss37KO mouse_rep2


title: TS050411_H3AC_ChIP


title: MCL004: genomic DNA from MCL (FFPE)

first: Daniel

last: Xia

address: 200 Elizabeth Street

description: MCL

hyb_protocol: Labeled DNA was incubated at 48°C for 16–24 hours

scan_protocol: Arrays were imaged using an Illumina iScan instrument

data_processing:
Methylation data were extracted and normalized using the Bioconductor package minfi v1.30
Average Beta or normalized (Illumina method) Average Beta (beta_TGL51_illumina_annot_geo.csv)

label: Cy3 and Cy5

source_name: mantle cell lymphoma (MCL)

label_protocol: 250ng of DNA were subjected to bisulphite conversion using the Zymo EZ DNA Methylation kit, followed by amplification, fragmentation and fluorophore-labeled

extract_protocol: Genomic DNA was extracted and purified from FFPE samples using Qiagen QIAamp DNA FFPE Tissue Kit and processed with the FFPE DNA Restoration Kit (Illumina)

value: Lymphoma

tag: disease subtype

value: MCL


title: TS121511B_snp

last: Andrews

address: 262 Danny Thomas Pl

source_name: CD19+ B cells

tag: disease state


title: SLL005: genomic DNA from CLL/SLL (FFPE)

description: CLL/SLL

source_name: chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL)

value: CLL/SLL


title: TS072611A_snp

value: tonsil


title: 146 DC


title: TS072111A_snp

value: healthy


title: TS072611A_H3AC_ChIP

value: H3K9/K14ac (EMD-Millipore 06-599)


title: TS040611B_H3AC_ChIP


title: 135 DC

value: isotype control


title: 162 DC


title: TS102711_snp


title: 163 DC


title: 143 DC


title: 150 DC


title: FL005: genomic DNA from FL (FFPE)

description: FL

source_name: follicular lymphoma (FL)

value: FL


title: TS072611B_snp


title: MCL003: genomic DNA from MCL (FFPE)

description: MCL


title: TS060911B_snp


title: TS061611A_snp


title: SLL001: genomic DNA from CLL/SLL (FFPE)

description: CLL/SLL


title: TS061611A_H3AC_ChIP


title: WT-3

city: Houston

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

description: rRNA depleted (mRNA-seq)

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic version 0.17 for mRNA-seq or Cutadapt for sRNA-seq
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2 version 2.0.0-beta7
Read counting was performed with HTSeq
Differential Gene expression analysis performed with DESeq2
Genome_build: Streptococcus pneumoniae D39 (RefSeq NC_008533) genome and D39 plasmid pDP1 sequence (RefSeq NC_005022)

organism: Streptococcus pneumoniae D39

growth_protocol: Strains were grown in Difco Brain Heart Infusion Broth at 37oC in atmosphere of 5% CO2 to an OD620 of 0.1 - 0.15

extract_protocol:
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
For samples 1-6, the library was generated by first removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria. Samples were then subjected to RNA fragmentation using the Ambion RNA fragmentation kit (AM8740). Fragmented RNA was subjected to RNA 5' polyphosphatase (Epicenter) treatment, which was performed to facilitate the 5' adapter ligation step. Small RNA libraries were generated by Macrogen using TruSeq® small RNA library kit (Illumina).  For samples 7-14, rRNA-depleted samples were directly used for mRNA-seq library preparation using ScriptSeqTM v2 RNA-seq Library preparation kit (Epicenter).

tag: genotype

value: Wildtype parent


title: 138 DC


title: TS061611B_snp

city: Memphis

first: Jared

institute: St. Jude Children's Research Hospital


title: FL002: genomic DNA from FL (FFPE)

description: FL


title: TS012612A_H3AC_ChIP


title: WT-2

description: rRNA depleted (mRNA-seq)


title: MCL002: genomic DNA from MCL (FFPE)

description: MCL


title: 127 DC


title: MZL045: genomic DNA from small B-cell lymphoma, favor CLL/SLL (FFPE)

description: SBCL, favor CLL/SLL

source_name: small B-cell lymphoma, favor chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL)

value: SBCL, favor CLL/SLL


title: 139 DC


title: FL006: genomic DNA from FL (FFPE)

description: FL


title: FL004: genomic DNA from FL (FFPE)

description: FL


title: TS042811A_H3AC_ChIP


title: TS040611B_snp


title: TS012612B_H3AC_ChIP


title: 126 DC


title: TS020212A_H3AC_ChIP


title: FL313_H3AC_ChIP

value: lymph node

value: follicular lymphoma


title: TS060911A_snp


title: TS050411_snp


title: TS020212B_H3AC_ChIP


title: FL301_H3AC_ChIP


title: FL3A145_H3AC_ChIP


title: TS042811A_snp


title: 118 DC


title: TS012612B_snp


title: UNK005: genomic DNA from B-cell lymphoma, favor MZL (FFPE)

description: BCL, favor MZL

source_name: B-cell lymphoma, favor marginal zone lymphoma (MZL)

value: BCL, favor MZL


title: FL255_H3AC_ChIP


title: FL003: genomic DNA from FL (FFPE)

description: FL


title: MZL034: genomic DNA from nodal MZL (FFPE)

description: NMZL

source_name: nodal marginal zone lymphoma (MZL)

value: NMZL


title: FL238_H3AC_ChIP


title: pnp-3 mRNA

description: rRNA depleted (mRNA-seq)

value: pnp deletion mutant


title: WT-1

description: rRNA depleted (mRNA-seq)


title: TS020212B_snp


title: FL202_H3AC_ChIP


title: TS020212A_snp


title: rny-2 mRNA

description: rRNA depleted (mRNA-seq)

value: rny deletion mutant


title: MZL029: genomic DNA from MZL (FFPE)

description: MZL

source_name: marginal zone lymphoma (MZL)

value: MZL


title: MZL033: genomic DNA from MZL (FFPE)

description: MZL

value: Lymphoma


title: rny-3 mRNA

description: rRNA depleted (mRNA-seq)


title: MZL028: genomic DNA from MZL (FFPE)

description: MZL


title: pnp-1 mRNA

description: rRNA depleted (mRNA-seq)


title: FL301_2_snp


title: MZL030: genomic DNA from extranodal MZL (FFPE)

description: EMZL

source_name: extranodal marginal zone lymphoma (MZL)

value: EMZL


title: pnp-2 mRNA

description: rRNA depleted (mRNA-seq)


title: MZL027: genomic DNA from nodal MZL (FFPE)

description: NMZL


title: FL153_H3AC_ChIP


title: MZL032: genomic DNA from MZL (FFPE)

description: MZL


title: TS012612A_snp


title: FL3A119_H3AC_ChIP


title: FL139_H3AC_ChIP


title: FL174_H3AC_ChIP


title: UNK002: genomic DNA from extranodal MZL (FFPE)

description: EMZL


title: Satb2_ChIPseq_Sox10_pos_Rep2

description:
processed data file:
Sox10_Positive_Satb2_Rep1_10M_subtract_Over_Neg.bw
Sox10_Positive_Satb2_Rep2_10M_subtract_Over_Neg.bw

data_processing:
Sequencing reads were trimmed using TrimmomaticPE for Truseq2:PE adapters and reads with quality greater than phred 33 were retained. Quality of sequencing reads were determined using fastQC. High quality sequencing reads were aligned to the zebrafish danRer10 genome version using default parameters of BWA88. Aligned reads were subsampled to keep equal number of  reads in each sample using BBMap. RPKM normalized Input signal subtracted BigWig tracks for visualization were generated using the bamCompare tool from deepTools 3.3.2.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

organism: Danio rerio

source_name: FACS sorted cell population

extract_protocol:
To perform neural crest specific ChIP-seq for Satb2, Sox10pos and Sox10neg cells were isolated from Tg: sox10:GFP transgenic fish using high speed flow cytometry sorting (FACS ARIA III, Becton Dickinson). Cells were directly lysed in the lysis buffer to isolate chromatin by sonication. ChIP experiment was performed as described in the above section.
1.5 pM of the denatured libraries was used as an input to obtain sequencing reads using 28 cycles for read1, 8 cycles for indexes and 101 cycles for read2 on NextSeq 550 at IISER Pune.

tag: genotype/varaition

value: TU

value: anti-zebrafish Satb2(generated in this study)

tag: Stage

value: 14 somite (16hpf)


title: WT_sibs_14ss_scRNAseq

description: processed data file:

data_processing:
Sequencing data was further processed with default parameters using cell Ranger 6.0 (10X Genomics). Sequencing reads were aligned to the danRer10 genome using STAR aligner. Feature matrices generated using cell Ranger were utilized for further integrated analysis using Seurat 4.0.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

source_name: Whole embryo

extract_protocol:
embryos from the cross of satb2+/- fish were raised to 14 ss at 28.5oC, hand dechorinated and dissociated further in 1x DMEM-F12 (Sigma Aldrich) + 125 mM EGTA by hand tapping. Cells were collected by centrifugation at 300 xg for 2 minutes and resuspended in 1X DPBS (Gibco) + 0.1% BSA (Himedia). Genotype of each embryo was assessed by genomic PCR as described above. Cell suspension was passed through 70-μm Flowmi cell strainers (Sigma). Cell viability was estimated using CountessII automated cell counter and  samples with more than 95% viability were processed further with 10X Genomics Chromium.
Approximately 8000 cells were captured in GEMs. scRNA-seq libraries were prepared as described in 10X Genomics manuals (Single Cell 3′ Reagent Kits V3.2). Immediately following GEM generation, reverse transcription reaction was carried out using eppendorf mastercycler pro by incubating at 53oC for 45 minutes followed by denaturation at 85oC for 5 min. Single-stranded cDNA was purified using DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, USA). cDNA amplification was performed for 11 cycles with initial denaturation at 98oC 3 minutes followed by repeated cycles of 98oC for 15 seconds, 63oC for 20 seconds and 72oC for 1 minute. Final extension was performed at 72oC for 1 minute. cDNA quality was determined using Bioanalyzer 2100 dsDNA high sensitivity assay kit (Agilent). cDNA was further fragmented, end repaired and A-tailed according to the manufacturer's instructions. Before proceeding for adapter ligation, samples were purified using double-side clean up protocol with SPRI beads (Beckman Coulter). Adapter ligated sample was subjected to amplification for 11 cycles using indexing primer from Chromium i7 Multiplex Kit (PN-120262). Amplified libraries were again subjected to double-side purification using SPRI and quantified using Qubit fluorometer (Thermo Fisher Scientific, USA) and the library size was estimated using Bioanalyzer 2100.

value: Wild-Type


title: FL120_H3AC_ChIP

data_processing:
Reads were aligned to hg19 with bowtie2 (v2.2.5) using default settings.
Reads in ENCODE blacklisted regions were removed with samtools (v1.9).
Peaks were called with MACS2 (v2.1.0.20150420) with the parameters --nomodel --shiftsize=150 (ChIP) or --nomodel --shiftsize=50 (FAIRE) and input controls.
DiffBind (v2.14.0) was used to derive consensus peak sets for each histone mark and accessible chromatin, requiring peaks to overlap in at least three samples for each ChIP-seq or FAIRE-seq assay in order to be merged and retained. The consensus peaksets for each assay were then concatenated and merged to derive a list of putative regulatory elements with bedtools2 (v2.29.2).
DiffBind was then used to determine differentially bound/accessible regions between sample groups for each assay. ChIPseeker (v1.22.0) was used to annotate peaks with hg19 UCSC knownGene annotations.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak format files containing peaks for each sample as called by MACS2.

tag: antibody

value: H3K9/K14ac (EMD-Millipore 06-599)


title: FL301_snp


title: Satb2_MUT_14ss_scRNAseq

description: processed data file:

extract_protocol:
embryos from the cross of satb2+/- fish were raised to 14 ss at 28.5oC, hand dechorinated and dissociated further in 1x DMEM-F12 (Sigma Aldrich) + 125 mM EGTA by hand tapping. Cells were collected by centrifugation at 300 xg for 2 minutes and resuspended in 1X DPBS (Gibco) + 0.1% BSA (Himedia). Genotype of each embryo was assessed by genomic PCR as described above. Cell suspension was passed through 70-μm Flowmi cell strainers (Sigma). Cell viability was estimated using CountessII automated cell counter and  samples with more than 95% viability were processed further with 10X Genomics Chromium.
1.5 pM of the denatured libraries was used as an input to obtain sequencing reads using 28 cycles for read1, 8 cycles for indexes and 101 cycles for read2 on Nextseq 550 (Illumina) at IISER Pune.


title: FL255_snp


title: MZL026: genomic DNA from nodal MZL (FFPE)

description: NMZL


title: MZL025: genomic DNA from splenic MZL (FFPE)

description: SMZL

source_name: splenic marginal zone lymphoma (MZL)

value: SMZL


title: FL313_snp


title: Satb2_ChIPseq_Sox10_pos_Rep3


title: FL202_snp


title: Sox10_Positive_input


title: DL3A538_H3AC_ChIP

extract_protocol:
Cells were formaldehyde cross-linked (1% final concentration) for 10 minutes in RPMI with 10% FBS. Quenching was performed by addition of 1M glycine (125 mM final concentration) with gentle mixing for 10 minutes at room temperature. Cells were washed with cold PBS and lysed in an SDS buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0) with protease inhibitors before chromatin was fragmented using a Diagenode Bioruptor to an average size of less than 300 bp as determined using an Agilent Bioanalyzer 2100. Lysates were immunoprecipitated with the listed antibodies conjugated to Protein-A Dynabeads (5 ug antibody incubated with beads for 2-4 hours at 4°C) overnight at 4°C. The beads were then washed with the following buffers each for 3 minutes at 4°C - low salt buffer (150 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), high salt buffer (500 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), LiCl buffer (250 mM LiCl, 50 mM Tris pH 8.0, 0.5% Na deoxycholate, 1% NP40), and TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). After washing, crosslinks were reversed overnight at 65°C in 250 uL elution buffer (1% SDS, 100 mM NaHCO3) followed by addition of proteinaseK and incubation at 56°C for 1 hour.  DNA was purified with QIAquick PCR purification columns.
At least 3 ng of DNA was used to for indexed library preparation using Illumina TruSeq adapters and standard Illumina protocols. Fragments were size selected (average fragment-size: 200-400 bp for ChIP; 50-200 for FAIRE) using Agencourt AMPure XP beads prior to amplification. Samples were pooled (6-10 per lane) and sequenced.

value: diffuse large B cell lymphoma


title: MZL024: genomic DNA from splenic MZL (FFPE)

description: SMZL


title: Satb2_ChIPseq_Sox10_pos_Rep1


title: MZL022: genomic DNA from splenic MZL (FFPE)

description: SMZL


title: FL238_snp


title: Satb2_ChIPseq_Sox10_neg_Rep2


title: DL3A193_H3AC_ChIP


title: DL273_H3AC_ChIP


title: DL252_H3AC_ChIP


title: UNK001: genomic DNA from small B-cell lymphoma, favor SLL (FFPE)

description: SBCL, favor SLL

source_name: small B-cell lymphoma, favor small lymphocytic lymphoma (SLL)

value: SBCL, favor SLL


title: FL125_snp

value: lymph node


title: DL237_H3AC_ChIP


title: MZL016: genomic DNA from extranodal MZL (FFPE)

description: EMZL


title: Satb2_ChIPseq_Sox10_neg_Rep3


title: FL120_snp

value: follicular lymphoma


title: DL551_H3AC_ChIP


title: scRNAseq_FLAG_SATB2

description: processed data file:

data_processing:
Sequencing data was further processed with default parameters using cell Ranger 3.0.2 (10X Genomics). Sequencing reads were aligned to the danRer10 genome using STAR aligner. Feature matrices generated using cell Ranger were utilized for further analysis using Seurat 3.0.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

extract_protocol:
a mosaic over expression system was generated by injecting one cell of 16 cell stage embryos with 200 pg of 3xFLAG-Satb2. Only one cell per embryo was injected randomly irrespective of its spatial arrangement. Embryos were raised at 28.5oC, hand dechorinated and dissociated further in 1x DMEM-F12 (Sigma Aldrich, USA) + 125 mM EGTA by hand tapping. Cells were collected by centrifugation at 300 xg for 2 minutes and resuspended in 1X DPBS (Gibco) + 0.1% BSA. Cell suspension was passed through 70 μm Flowmi cell strainers (Sigma). Cell viability was estimated using CountessII automated cell counters and samples with more than 95% viability were processed further with 10X Genomics Chromium.
Approximately 8000 cells were captured in GEMs. scRNA-seq libraries were prepared as described in the 10X Genomics manual (Single Cell 3′ Reagent Kits V3, User Guide PN-1000092). Immediately following GEM generation, reverse transcription reaction was carried out using thermal cycler (Eppendorf Mastercycler pro) by incubating at 53oC for 45 minutes followed by denaturation at 85oC for 5 minutes. Single-stranded cDNA was purified using DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, USA). cDNA amplification was performed for 11 cycles with initial denaturation at 98oC for 3 minutes followed by repeated cycles of 98oC for 15 seconds, 63oC for 20 seconds and 72oC for 1 minute. Final extension was performed at 72oC for 1 minute. cDNA quality was determined on a Bioanalyzer 2100 high sensitivity assay. cDNA was further fragmented, end repaired and A-tailed according to manufacturer's instructions. Before proceeding for adapter ligation, samples were purified using double-side clean up protocol with SPRI bead (Beckman Coulter). Adapter ligated sample was subjected to amplification for 11 cycles using indexing primer from Chromium i7 Multiplex Kit (PN-120262). Amplified libraries were again subjected to double-side purification using SPRI and quantified using Qubit fluorometer and library size was estimated using Bioanalyzer 2100.

treatment_protocol: overexpression of 3XFLAG-SATB2 from 16 cell stage

value: AB/TU

value: Dome (4.5 hpf)


title: MZL021: genomic DNA from splenic MZL (FFPE)

description: SMZL


title: FL3A145_snp


title: MZL014: genomic DNA from extranodal MZL (FFPE)

description: EMZL


title: ATACseq_SATB2mut_Som_14_BR1

description:
processed data file:
SATB2mut_Som_14_merged_ATAC.bw
SATB2mut_som14_filtered_consensus.bed

data_processing:
Sequencing reads (41 bp PE) were obtained on NextSeq-550 at IISER Pune and trimmed for Nextera adapters using default parameters of Trimmomatic PE. Trimmed reads were aligned to danRer10 using default parameters of Bowtie2. Briefly, BAM files were subsampled to 55 million reads in each sample using BBMap and sorted by name. Paired end bed files were obtained using the bamtobed function of bedtools. Reads were displaced by +4 bp and -5 bp. Peak calling was performed using MACS2 callpeak -f BEDPE -q 0.05 --nomodel --extsize 200 --gsize 1.3e9 --keep-dup 2 parameters. Consensus peaks were obtained using a custom R script used for ChIPseq analysis. BigWig files were generated using bamCoverage (deepTools). Peaks were annotated to the nearest gene using Homer and classified into promoter (+/- 2 Kb) and non-promoter regions. K-means clustering was performed around +/- 2 Kb of Satb2 peak center using deepTools. Clusters were annotated using Homer and gene ontology analysis was performed using webGestalt. Motif analysis was performed using findMotifsGenome.pl from Homer.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

extract_protocol:
cells were washed with 1x DPBS and resuspended in cell lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM KCl, 0.1 % NP-40, 0.1% Tween20 and 0.01% Digitonin) and incubated on ice for 3 minutes. Further, cells were washed with a wash buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM KCl and 0.1% Tween20) by centrifugation at 500 xg for 10 minutes at 4oC. Supernatant was discarded and pellet was resuspended in 25 µl 2x Tagmentation buffer (Illumina, catalog #15027866), 16.5 µl DPBS, 0.5 µl 10% Tween 20, 0.5 µl 1% Digitonin, 5 µl nuclease and 2.5 µl Tn5 transposase enzyme (TDE1, Illumina, catalog # 15027865) and incubated for 28 minutes at 37oC. After the tagmentation reaction, DNA was isolated using the Zymo DNA clean and concentrator kit (Zymo).
Purified DNA was used as an input to generate a library by amplifying with 2x Q5 DNA polymerase mix (NEB) and indexing primers. Optimal cycles were determined using qPCR analysis. Amplified libraries were purified using Agencourt ampure XP beads to remove adapters and larger fragments.


title: FL174_snp


title: FL139_snp


title: Sox10_Negative_input


title: MZL006: genomic DNA from extranodal MZL (FFPE)

description: EMZL


title: CLL378_H3AC_ChIP

value: peripheral blood

value: chronic lymphocytic leukemia


title: CLL347_H3AC_ChIP


title: MZL008: genomic DNA from splenic MZL (FFPE)

description: SMZL


title: DL135_H3AC_ChIP


title: DL273_snp

value: diffuse large b cell lymphoma


title: ATACseq_WT_Som_14_BR2

description:
processed data file:
WT_Som_14_merged_ATAC.bw
WT_som14_filtered_consensus.bed


title: DL191_H3AC_ChIP


title: ATACseq_SATB2OE_Dome_BR2

description:
processed data file:
SATB2OE_Dome_merged_ATAC.bw
SATB2OE_Dome_filtered_consensus.bed

treatment_protocol: overexpression of 3XFLAG-SATB2 from 1 cell stage


title: DL237_snp


title: DL252_snp


title: CLL396_H3AC_ChIP


title: DL166_snp


title: Satb2_ChIPseq_Sox10_neg_Rep1


title: ATACseq_SATB2mut_Som_14_BR2


title: MZL001: genomic DNA from splenic MZL (FFPE)

description: SMZL

value: Lymphoma


title: MCL001: genomic DNA from MCL (FFPE)

description: MCL

value: MCL


title: ATACseq_SATB2OE_Dome_BR1


title: CLL158_H3AC_ChIP


title: MZL002: genomic DNA from splenic MZL (FFPE)

description: SMZL


title: DL191_snp


title: CLL144_snp


title: TS111711_INPUT

value: tonsil

value: healthy

value: input


title: CLL144_H3AC_ChIP


title: donor3_cytokinetriplet

city: Boulder

first: Thomas

last: LaRocca

state: CO

address: 1725 Pleasant St

institute: University of Colorado Boulder

data_processing:
QC and adapters trimmed using fastp.
Reads aligned and counted using STAR.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene counts for each sample.

source_name: Primary human astrocytes

growth_protocol: Primary astrocytes were grown in astrocyte-specific growth medium (from corresponding suppliers) and sub-cultured when semi-confluent.

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns.
PolyA libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit.

treatment_protocol: Passage 2-3 cells were treated when semi-confluent for 24 h with combinations of Aβ, C1q, TNF-α and IL-1α pre-diluted in fresh media.

tag: treatment

value: 10 nm C1q TNF-α IL-1α

tag: donor age

value: fetal

tag: supplier/gender

value: Sciencell/male


title: RNAseq_Dome_Satb2_Momix_BR3

last: Galande

address: Dr. Homi bhabha road, Pashan

description:
processed data file:
Dome_Satb2OE_normCPM_SATB2OE.txt
Dome_Satb2MO_normCPM.txt

data_processing:
Sequencing reads were trimmed for quality using Trimmomatic and aligned to daRer10 genome assembly using HISAT2 aligner. Counts for each gene feature was estimated using the FeatureCounts package from Rsubread. Differential expression analysis was performed for replicates using EdgeR. A volcano plot for significantly differentially expressed genes was generated using the PlotVolcano tool from the Galaxy server. Gene ontology analysis for upregulated and downregulated genes were performed using a web-based tool, gProfiler.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

extract_protocol:
For Satb2 overexpression studies, 3x-Flag-Satb2 mRNA was injected at 1 cell stage and embryos were harvested at 4.5 hpf and were lysed in RNA iso plus (DSS-Takara, India) to extract total RNA. Each sample consisted of at least 10 embryos per experiment. For Satb2 knock-down studies, 4 ng morpholino mix was injected at 1 cell stage and embryos were harvested at 4.5 hpf.
Approximately 500 ng of Total RNA with RIN > 9 was used as a starting material to prepare mRNA sequencing libraries using the SENSE mRNA seq kit (Lexogen GMBH, Austria). All cDNA samples were amplified for 10-15 cycles depending on cycle number estimation by qPCR using the PCR add-on kit (Lexogen GMBH, Austria). Amplified libraries were purified using two rounds of 0.8x volume of Hi-prep PCR purification kit. The concentration of libraries was estimated using the Qubit 4 DNA HS system (Thermo Scientific). Finally, all the libraries were pooled and subjected to high throughput sequencing using 100 bp PE chemistry on Hiseq 2500 (Macrogen, Korea).

treatment_protocol: Knockdown using  SATB2 morpholinos from 1 cell stage

value: Wild-Type

tag: strain


title: TS102711A_INPUT


title: ATACseq_WT_Som_14_BR1

value: TU

value: 14 somite (16hpf)


title: RNAseq_Dome_Satb2_Momix_BR2


title: MZL010: genomic DNA from extranodal MZL (FFPE)

description: EMZL

value: EMZL


title: TS081111A_INPUT


title: CLL140_H3AC_ChIP

value: H3K9/K14ac (EMD-Millipore 06-599)


title: DL135_snp

value: lymph node


title: Quantseq_14som_WT_BR2

description:
3' mRNA quantseq Lexogen
processed data file:
14_somite_quantseq_normCPM.txt

data_processing:
Sequencing reads were trimmed for quality using Trimmomatic and aligned to the daRer10 genome assembly using STAR aligner. Counts for each gene feature was estimated using the FeatureCounts package from Rsubread. Differential expression analysis was performed for replicates using EdgeR.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

growth_protocol: embryos were grown at 28.5 degrees till the desired stage is reached. Stages were determined visually

extract_protocol:
Single embryos were harvested in 100 μl RNA iso-plus total RNA extraction reagent (DSS Takara, India) at 80% epiboly, 6 ss and 14 ss stages of zebrafish embryonic development. Samples were homogenized by vigorous vortexing to assure complete lysis followed by addition of 15 ul of CHCl3. Aqueous layer was separated by centrifugation at 12000 xg for 15 minutes at 4oC. The aqueous layer was collected in a separate tube and an equal volume of isopropanol containing GlycoBlue coprecipitant (Invitrogen, USA) was added. The aqueous fraction was stored at -20oC until further processing. Meanwhile, the organic fraction was processed for DNA extraction by precipitating with 150 μl of 100% ethanol and incubated for 10 minutes at RT. Samples were centrifuged for 10 minutes at high speed and the pellet was washed with 70% ethanol (twice). After drying, DNA pellets were resuspended in low TE and used for genotyping as described before. Once the genotype for each embryo was confirmed, the corresponding RNA fractions were processed further. RNA from 2-3 samples were pooled to get sufficient amounts to prepare libraries.
Extracted RNA samples were quantified using Nanodrop 2000 and RNA integrity was determined using Agilent bioanalyzer 2100. Samples with RNA integrity number (RIN) > 8 were used to prepare sequencing libraries using Quantseq 3’ mRNA seq library kit (Lexogen GMBH, Austria) as per the instructions from the manufacturer. Briefly, 300 ng of RNA was used for poly-A capturing and subjected to first and second-strand synthesis. All cDNA samples were amplified for 10-15 cycles depending on cycle number estimation by qPCR (PCR add-on kit, Lexogen GMBH, Austria). Amplified libraries were purified using two rounds of 0.8x volume of Hi-prep PCR purification kit (MagBio Genomics, USA). The concentration of libraries was estimated using the Qubit dsDNA HS system (Thermo Fisher Scientific). Finally, all the libraries were pooled and subjected to high throughput sequencing using 76 bp SE chemistry on Nextseq 550.


title: CLL158_snp

value: peripheral blood


title: SLL007: genomic DNA from CLL/SLL (FFPE)

description: CLL/SLL

value: CLL/SLL


title: Quantseq_14som_WT_BR1


title: ATACseq_WT_Dome_BR1

description:
processed data file:
WT_Dome_merged_ATAC.bw
WT_Dome_filtered_consensus.bed

value: AB/TU

value: Dome (4.5 hpf)


title: Quantseq_14som_SATB2_MUT_BR2


title: TS121511B_INPUT