title: Healthy 2

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

description:
single cell
liver19

data_processing:
Raw sequences were demultiplexed, aligned, filtered, barcode counting, unique molecular identifier (UMI) counting with Cell Ranger software v3.1 (10XGenomics) to digitalize the expression of each gene for each cell.
The outlier cells with very low number of gene features (<500), or high number of gene features as doublets (>5000),  or low total UMI (<1000) and high mitochondrial ratio (>10%) from each data set were removed.
Samples were combined based on the  identified anchors for the following integrated analysis.
Genome_build: hg19
Supplementary_files_format_and_content: CSV files include mRNA molecule count values and single cell barcodes for each Sample

source_name: liver immune cells

extract_protocol:
Single-cell suspensions of FACS-sorted CD45+ liver cells were resuspended and washed in 0.05% RNase-free BSA in PBS for single-cell library preparation.
10x Chromium Next GEM Single Cell 3' Kit.

tag: diagnosis

value: healthy

tag: tissue

value: liver

value: immune


title: 2_SPF_24_V_S28 [PBMC vaccine transcriptome]

status: Public on Oct 23 2021

type: SRA

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

country: USA

institute: University of Minnesota

library_source: transcriptomic

data_processing:
SAMPLE 1 AND 2: Sequencing reads were mapped to the mouse genome (GRCm38) using Bowtie aligner (bowtie2 version 2.3.4.1) with local mode, -L 22 and -N 1 parameters (Langmead and Salzberg, 2012). Reads were assigned to Ensembl gene models (Mus_musculus.GRCm38.87.gtf) with featureCounts of the Subread software package (version 1.5.1) (Liao et al., 2014). The reads count matrices were organized corresponding to experimental design and used for subsequent statistical analysis using the bioconductor package edgeR (version 3.24.3) (McCarthy et al., 2012; Robinson et al., 2010). The raw reads count table were normalized by using default method in the package prior to generating statistics. Multidimensional scaling was performed with edgeR using the top 500 differentially expressed genes across samples. The regression model in the edgeR package with block design and interaction model was used for statistical analysis to select the corresponding significant genes.
SAMPLE 1 ONLY: The normalized reads table of mouse blood samples were reformatted to meet the requirements for the subsequent GSEA analysis (Mootha et al., 2003; Subramanian et al., 2005). The gene lists were prepared from human vaccination data and merged into an immune geneset (c7.immune.datasets.gmt) to generate a customized geneset (c7.custom.immune.datasets.gmt) (Mootha et al., 2003; Subramanian et al., 2005). The mouse datasets originated from either SPF or dirty mouse models were computed against the customized geneset by using desktop GSEA analysis engine with default parameters except the enrichment plot generation.
Bowtie 2 mapping
FeatureCounts for reads assignment
edgeR for statistical analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: rawcounts matrix

molecule: total RNA

organism: Mus musculus

source_name: PBMC

extract_protocol:
SAMPLE GROUP 1: Mouse PBMCs were isolated using FicolÒ-Paque PREMIUM (Millipore Sigma) and RNA was extracted using RNeasy Micro Plus Kit (Qiagen).
SAMPLE GROUP 1: The cDNA library was prepared using strand-specific RNA-sequencing protocols.
SAMPLE GROUP 1: Samples were run on an Illumina NovaSeq (150 bp paired-end). We obtained an average of 35 million read pairs per sample.
SAMPLE GROUP 2: Whole lungs were harvested and RNA was extracted using AllPrep DNA/RNA kit (Qiagen).
SAMPLE GROUP 2: The cDNA library was prepared using strand-specific RNA-sequencing protocols.
SAMPLE GROUP 2: Samples were run on an Illumina NovaSeq (50 bp paired-end). We obtained an average of 27 million read pairs per sample.

treatment_protocol:
SAMPLE GROUP 1: Mice were vaccinated intramuscularly (i.m.) with 180 ug of 2019-2020 seasonal quadrivalent influenza vaccine (Sanofi Pasteur) with or without 25 uL AddaVax (InvivoGen).
SAMPLE GROUP 2: For IAV infections, mice were anesthetized using a weight-based dose of ketamine/xylazine delivered intraperitoneally (i.p.). Mice were vaccinated intranasally (i.n.) with 1000 PFU of X31. For challenge, mice were infected i.n. with 1000 PFU of PR8.

tag: tissue/cell type

value: PBMC

tag: strain

tag: treatment (spf or dirty)

value: SPF

tag: treatment vaccination/infection

tag: treatment time point

value: 24 hours post vaccination


title: 2_SPF_0_Naive_S2 [PBMC vaccine transcriptome]

value: Naïve


title: 3_SPF_0_Naive_S3 [PBMC vaccine transcriptome]


title: Cohort1_005E_7_cTfhTET

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
Cohort1_005E_7_cTfhTET
Cohort1.vsn.normalised.csv

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform, with 6 samples pooled per lane.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the human GRCh38 genome assembly including ERCC spike-ins using HISAT2 2.1.0 (no soft clipping). BAM files were imported to Seqmonk v1.45.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count quantitation file was generated by counting reads using Rsubread, normalisation with RUVseq package (k = 3, with model.matrix ~d$sex +d$group) followed by vsd normalisation using ‘varianceStabilzingTransformation’ within DESeq2 package. Row names are Ensembl_IDs, with each sample included as columns.

organism: Homo sapiens

source_name: cTfhTET

extract_protocol:
PBMCs were isolated at the Babraham Institute by density gradient centrifugation and cryopreserved in liquid nitrogen. Before sorting, ~10-30 million PBMC cells were thawed in culture media and rested for 2 hours at 37 degrees C, after which influenza HLADR tetramers (TET)added along with a panel of cell surface antibodies. Live CD3+ CD4+ CD45RA- TET+ cells were sorted on a BD Aria Fusion sorter directly into 1x lysis buffer as per the SmartseqV4 Ultra low input RNA kit for sequencing from Takara Clontech. Cells from day 7 after vaccination (cTfhTet) were also sorted on the basis of expressing PD1 and CXCR5 markers.
cDNA was prepared directly from cells (40-1000 max) lysed in 1x lysis buffer, and amplified acccording to the protocol for the SmartseqV4 Ultra low input RNA kit for sequencing from Takara Clontech. Between 16 and 18 PCR cycles were used for each sample, depending on cell input. Quality of cDNA was confirmed using an Agilent Bioanalyser.
Libraries were generated from amplified cDNA using the NexteraXTDNA library preparation kit from Illumina, with nexteraXT indexes. Library quantitatation was performed using Agilent Bioanalyser, KAPA qPCR and Qubit High-sensitivity kits.

tag: cell type

value: cTfhTET

tag: group

tag: cohort

tag: pid

tag: day

value: YOUNG

tag: Sex

value: F

tag: lane

tag: cells

tag: bleed

tag: genotype


title: 3_SPF_24_V_S29 [PBMC vaccine transcriptome]

value: 2019-2020 seasonal quadrivalent influenza vaccine


title: THP-1 MTB 6h ctrl whole

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

country: China

institute: ablife

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 and bowtie2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue < =0.01
Genome_build: GRCh38, BCG NC_012207.1,MTB NZ_CP013475.1

source_name: THP-1, uninfected Control

extract_protocol:
For pathogens and the second biological replicates of THP-1, 1.5μg of total RNA was used for RNA-seq library preparation. rRNA was removed from total RNA using Ribo-Zero rRNA Removal Kit. Ribo-Zero RNAs were iron fragmented at 85℃. First-strand cDNA was synthesized with random primers harboring adaptor sequence, the randomized hexamer and Terminal-Tagging oligo cDNA using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (epicentre). The cDNAs were then purified and amplified. PCR products corresponding to 150-350 bps were purified by 12% PAGE gel, quantified and stored at -80℃ until used for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and BCG were first sequenced with illumina GAIIx system for 33 nt single-end sequencing by ABlife. Inc (Wuhan, China). MTB were applied to Hiseq 2000 system for 101 nt pair-end sequencing by Majorbio. Inc (Shanghai, China). The second biological replicates of THP-1 were applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China).For the first biological replicates of THP-1, total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis. For each sample, 5μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80℃ until used for sequencing. For high-throughput sequencing, the first biological replicates of THP-1 were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: uninfected Control

tag: time

tag: library type

value: Ribo-Zero


title: Fig_1d_PRNP_subs_opti_PE3_rep1

city: Beijing

first: Hao

last: Wu

address: HaiDian, Beijing

department: Peking University

institute: Peking University

description: Amplified from the human PRNP locus

library_source: genomic

data_processing:
Removed-adapter reads were aligned to corresponding amplicon reference with BWA MEM algorithm (v0.7.17-r1188).
After alignment, mapped reads were sorted by positions and converted into mpileup format with samtools (v1.10).
Targeted amplicon sequencing data was analyzed using the published toolkit CRlSPResso2 (v2.0.45).
Graphpad prism 9 was used to analyze the data.
Sanger sequencing data was analyzed using the Snapgene.
The.mpileup files were converted into.bmat files by Python scripts of "Detect-Seq" pipeline (http://detect-seq.com/).
Potential off-target sites were predicted using Cas-OFFinder (V2.4).
Genome_build: WT amplicon sequences were used as WT amplicon genome references, HDR amplicon sequences were used as HDR (insertion and deletion) amplicon references.
Supplementary_files_format_and_content: MPILEUP format: mutation information.

molecule: genomic DNA

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured and maintained at 37 °C in DMEM medium plus additional 10% FBS. For HCT116 cells, they were maintained in RPMI medium supplementing with 10% FBS.

extract_protocol:
Genomic DNA was extracted with CWBIO universal genomic DNA kit (CWbiotech, CW2298M) following the manufacturer’s protocol.
Genomic sites to be identified were amplified from genomic DNA samples and sequenced on the Illumina NovaSeq platform.
Targeted amplicon based high throughput sequencing

treatment_protocol: Plasmid transfections into HEK293T or HCT116 cells were conducted with lipofectamine 2000 as the manufacturer’s instructions.

value: human embryonic kidney 293 cells

tag: treatment

value: transfected with PE3 vectors for 72 h

tag: cell line

value: HEK293T cells


title: 1_SPF_72_V_S53 [PBMC vaccine transcriptome]

tag: tissue/cell type

tag: strain

tag: treatment (spf or dirty)

tag: treatment vaccination/infection

value: 72 hours post vaccination


title: Healthy 1

description:
single cell
liver15

tag: diagnosis

value: healthy

tag: tissue

tag: cell type


title: THP-1 BCG 24h polyA

source_name: THP-1, infected

value: Mycobacterium bovis BCG str. Tokyo 172

value: polyA-capture


title: Fig_1d_PRNP_subs_AS_PE2_rep1

description: Amplified from the human PRNP locus

value: transfected with PE2 vectors for 72 h


title: 4_SPF_24_V_S30 [PBMC vaccine transcriptome]

value: PBMC

value: SPF

tag: treatment time point


title: Cohort1_328F_7_cTfhTET

description:
Cohort1_328F_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: group

tag: cohort

tag: pid

tag: day

tag: Sex

tag: lane


title: Fig_1d_PRNP_subs_S_PE2_rep1

description: Amplified from the human PRNP locus


title: THP-1 MTB 6h whole

tag: agent

value: Mycobacterium tuberculosis M1458

tag: time

tag: library type


title: Cohort1_484A_7_cTfhTET

description:
Cohort1_484A_7_cTfhTET
Cohort1.vsn.normalised.csv

value: cTfhTET

tag: cells

tag: bleed

tag: genotype


title: Cohort1_389X_7_cTfhTET

description:
Cohort1_389X_7_cTfhTET
Cohort1.vsn.normalised.csv

value: YOUNG


title: Cohort1_329G_7_cTfhTET

description:
Cohort1_329G_7_cTfhTET
Cohort1.vsn.normalised.csv

value: OLD

value: M


title: Fig_1d_PRNP_subs_cor_PE3_rep1

description: Amplified from the human PRNP locus

tag: treatment

tag: cell line


title: THP-1 MTB 24h whole

tag: tissue


title: NAFLD 1

description:
single cell
liver9

tag: diagnosis

value: NAFLD

value: liver

tag: cell type

value: immune


title: THP-1 MTB 24h ctrl whole

value: uninfected Control

value: Ribo-Zero


title: hematopoietic stem cells from G0 mice treated with a control oligonucleotide

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced using a NovaSeq6000 SP 100-cycle flow cell (Illumina).
Fastq files were generated using Cellranger mkfastq (version 3.0.2). The raw reads were mapped to the mouse (mm10) or human (hg38) genomes using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: csv file with raw gene counts for every gene and every cell

molecule: polyA RNA

extract_protocol:
BM samples were first processed and enriched as described above, and cells were sorted by FACS. Sample preparation and sequencing were performed at MD Anderson’s Advanced Technology Genomics Core. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific).
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics), in which single cells were lysed and barcoded for reverse-transcription. Equal amounts of each uniquely indexed sample library were pooled together.
scRNA-seq

value: hematopoietic stem cells

value: Tert ER/+ or Tert+/+

tag: age

value: 2 month-old

value: control

tag: generation


title: NAFLD 3

description:
single cell
liver13


title: hematopoietic stem cells from G5/G6 mice treated with the oligonucleotide A151

value: Tert ER/ER

value: oligonucleotide A151


title: Donor 2 DMSO

data_processing:
Illumina software used for basecalling.
Sequences were aligned to the human genome using Tophat2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: hg19
Supplementary_files_format_and_content: CSV files include mRNA molecule count values and single cell barcodes for each Sample

source_name: sorted kupffer cells

extract_protocol:
Qiagen Rneasy micro kit
KAPA mRNA HyperPrep Kit

treatment_protocol: Purified kupffer cells were treated wth DMSO or DPI (500nM) for 24hrs

value: kupffer

value: DMSO

tag: donor


title: NAFLD 2

description:
single cell
liver12


title: hematopoietic stem cells from G0 mice treated with the oligonucleotide A151


title: Donor 1 DPI

value: DPI


title: Cohort1_061Q_7_cTfhTET

description:
Cohort1_061Q_7_cTfhTET
Cohort1.vsn.normalised.csv

value: cTfhTET

tag: group

tag: cohort

tag: pid

tag: day

value: F


title: 1_SPF_0_Naive_S1 [PBMC vaccine transcriptome]

tag: tissue/cell type

value: PBMC

tag: strain

tag: treatment (spf or dirty)

value: SPF

tag: treatment vaccination/infection

value: Naïve

tag: treatment time point


title: 1_SPF_24_V_S27 [PBMC vaccine transcriptome]

value: 2019-2020 seasonal quadrivalent influenza vaccine

value: 24 hours post vaccination


title: Cohort1_406Q_7_cTfhTET

description:
Cohort1_406Q_7_cTfhTET
Cohort1.vsn.normalised.csv

value: YOUNG

tag: Sex

value: M

tag: lane

tag: cells

tag: bleed

tag: genotype


title: G5/G6 R26-LSL HSCs plus vehicle (Exp2)

source_name: Hematopoietic Stem cells from G5/G6 mice 3 months after vehicle treatment

extract_protocol:
BM samples were first processed and enriched as described above, and cells were sorted by FACS. Sample preparation and sequencing were performed at MD Anderson’s Advanced Technology Genomics Core. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific).
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics), in which single cells were lysed and barcoded for reverse-transcription. Equal amounts of each uniquely indexed sample library were pooled together.

tag: cell type

value: bone marrow hematopoietic cells

value: G5/G6 R26CreER/CreER/TERT-LSL/LSL

tag: age

value: five months at the endpoint


title: hematopoietic stem cells from G5/G6 mice treated with a control  oligonucleotide

value: hematopoietic stem cells

value: Tert ER/ER

value: 2 month-old

tag: treatment

value: control

tag: generation


title: THP-1 BCG 6h ctrl whole

tag: tissue

tag: agent

value: uninfected Control

tag: time

tag: library type

value: Ribo-Zero


title: G5/G6 R26-LSL HSCs plus vehicle (Exp1)


title: Cohort1_357M_7_cTfhTET

description:
Cohort1_357M_7_cTfhTET
Cohort1.vsn.normalised.csv

value: cTfhTET

tag: group

tag: cohort

tag: pid

tag: day

value: OLD


title: Donor 2 DPI

value: liver

value: kupffer

value: DPI

tag: donor


title: Healthy 3

description:
single cell
liver2

tag: diagnosis

value: healthy

value: immune


title: Kera_L.v_6

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

description: RNA-seq

data_processing:
Reads were quality checked with FastQC (Babraham Institute), aligned with STAR (Dobin et al. 2013) against the hg19 human genome build and GENCODE19 transcriptome.
Uniquely mapping reads were summarised into counts against the GENCODE19 gene reference using featureCounts from subread (Liao, Smyth and Shi 2013).
Raw counts were summed across resequenced samples and used for differential expression analysis using edgeR (Robinson, McCarthy and Smyth 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Keratinocyte

growth_protocol: Human diploid fibroblasts (HDFs) (IMR90, WI38 and BJ) were cultured in phenol-red-free DMEM with 10% FBS under physiological 5% O2. Primary normal human keratinocytes were isolated from normal human skin. All procedures involving human subjects were approved by the ethics committee of the Ehime University Graduate School of Medicine, Toon, Ehime, Japan, and all subjects provided written informed consent. The keratinocytes were cultured in Epilife medium (Gibco) supplemented with human keratinocyte growth supplement (HKGS, Gibco) under 21% atmospheric O2.

extract_protocol:
Qiagen RNeasy plus kit according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: p16-induced Senescence was induced in IMR90 cells by overexpression of p16 via retroviral infection. RIS was induced by lentivirus-mediated expression of HRASG12V in human keratinocytes.

tag: passage

tag: vector

value: pLenti vector


title: THP-1 BCG 6h whole

value: Mycobacterium bovis BCG str. Tokyo 172


title: Cohort1_364V_7_cTfhTET

description:
Cohort1_364V_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: Sex

value: M

tag: lane

tag: cells

tag: bleed

tag: genotype


title: THP-1 BCG 24h ctrl whole

tag: tissue


title: Cohort1_393B_7_cTfhTET

description:
Cohort1_393B_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: cell type

value: YOUNG

value: F


title: G5/G6 R26-LSL HSCs plus OHT (Exp2)

source_name: Hematopoietic Stem cells from G5/G6 mice 3 months after 4-OHT treatment

value: bone marrow hematopoietic cells

value: G5/G6 R26CreER/CreER/TERT-LSL/LSL

tag: age

value: five months at the endpoint


title: Kera_L.v_5

description: RNA-seq


title: Cohort1_425L_7_cTfhTET

description:
Cohort1_425L_7_cTfhTET
Cohort1.vsn.normalised.csv


title: THP-1 BCG 24h whole

tag: agent

tag: time

tag: library type


title: Cohort1_368Z_7_cTfhTET

description:
Cohort1_368Z_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: group

tag: cohort

tag: pid


title: Cohort1_069Z_7_cTfhTET

description:
Cohort1_069Z_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: day


title: G5/G6 R26-LSL HSCs plus OHT (Exp1)


title: Cohort1_402L_7_cTfhTET

description:
Cohort1_402L_7_cTfhTET
Cohort1.vsn.normalised.csv


title: rep1_AI_K27_input

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using bowtie2 -N 1. Uniq mapped reads were remained.
macs14 was used to peakcalling with  default parameters
Genome_build: GRCh38

growth_protocol: Androgen-dependent prostate cancer cells LNCaP (AD) were cultured in RPMI1640 medium, while androgen-independent prostate cancer cells LNCaP (AI) were maintained in RPMI1640 medium with charcoal stripped serum.

extract_protocol:
Androgen-dependent prostate cancer and its androgen-independent derivative cell lines was used to do the ChIP-Seq library construction. Approximately 1 × 107 cells were fixed with 1% formaldehyd, and were resuspended in 1 mL SDS Lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1). DNA was sonicated to 200 – 500 b. After centrifugation, we took 60ul supernatant and diluted tenfold with ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl). The lysate was then incubated with anti-EZH2 antibody(source: Millipore, cat# 17-662, lot# 2366583) or anti-H3K27me3 antibody(source: Millipore,cat#07-449,lot# 2382150) at 4 ◦ C overnight. The immunuprecipitates were further incubated with Pierce™ Protein A/G Magnetic Beads (Thermo, 88803) for 2 hours at 4 oC. After applying to magnet and removing the supernatants, we washed beads once with Low Salt Immune Complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl) and added 1 ml of buffer to each tube, rotated at 4 ℃ for 5 min; we then placed the tube on the DynaMag-2 magnet for 30 s, then discarded supernatant. We repeated washing first with High Salt Immune Complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl) and LiCl Immune Complex wash buffer(0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 10 mM Tris, pH 8.1) and second with TE Buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) for a total of 5 washes. The immunoprecipitates were eluted from the beads with elution buffer (50 nM Tris 8.0, 10 mM EDTA and 1% SDS) and incubated at 65 oC overnight. After sequential RNase A and proteinase K treatment, DNA fragments were purified by phenol extraction and ethanol precipitation.
ChIP-Seq was performed by using ThruPLEX® DNA-seq kit (R400427; Rubicon Genomics) according to manufacturer’s instructions. The PCR products corresponding to 300-500 bps were gel purified, quantified and stored at -80 oC until used for sequencing. ChIP-Seq sequencing was performed on NextSeq500 platform with 151 bp paired-end sequencing.

tag: cell line

value: LNCaP

value: prostate cancer cells

tag: growth type

value: androgen-independent growth


title: Donor 1 DMSO

tag: treatment

value: DMSO

tag: donor


title: rep2_AI_K27_input


title: rep2_AD_K27_input

value: androgen-dependent growth


title: rep2_AI_K27_ChIP


title: Cohort1_366X_7_cTfhTET

description:
Cohort1_366X_7_cTfhTET
Cohort1.vsn.normalised.csv

value: cTfhTET

value: OLD

tag: Sex

tag: lane

tag: cells


title: G0 R26-LSL HSCs plus vehicle (Exp2)

source_name: Hematopoietic Stem cells from G0 mice 3 months after vehicle treatment

tag: genotype

value: G0 R26CreER/CreER/TERT-LSL/+ or R26CreER/CreER/TERT-LSL+/+


title: rep1_AI_K27_ChIP

tag: cell type


title: Cohort1_333L_7_cTfhTET

description:
Cohort1_333L_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: bleed


title: Kera_L.v_1

description: RNA-seq

tag: passage

tag: vector


title: Kera_L.v_4

description: RNA-seq


title: rep1_AD_K27_input


title: Kera_L.Ras_6

description: RNA-seq

value: pLenti HRASG12V


title: G5/G6 R26-LSL HSCs

tag: age

value: two months


title: Kera_L.Ras_5

description: RNA-seq


title: Cohort1_408S_7_cTfhTET

description:
Cohort1_408S_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: group


title: Kera_L.v_3

description: RNA-seq

value: pLenti vector


title: Kera_L.v_2

description: RNA-seq


title: G0 R26-LSL HSCs plus vehicle (Exp1)

source_name: Hematopoietic Stem cells from G0 mice 3 months after 4-OHT treatment


title: G0 R26-LSL HSCs plus OHT (Exp2)


title: Kera_L.Ras_3

description: RNA-seq


title: Cohort1_326D_7_cTfhTET

description:
Cohort1_326D_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: cohort

value: M


title: rep2_AD_K27_ChIP


title: G5/G6 HSCs after vehicle treatment

source_name: Hematopoietic Stem cells from G5/G6 mice isolated 1 week after vehicle treatment

value: TERT-ER/ER


title: G5/G6 HSCs 8 hr after pI:pC treatment

source_name: Hematopoietic Stem cells from G5/G6 mice isolated 8 hours after pI:pC treatment


title: Cohort1_044X_7_cTfhTET

description:
Cohort1_044X_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: pid

value: F


title: Cohort1_362S_7_cTfhTET

description:
Cohort1_362S_7_cTfhTET
Cohort1.vsn.normalised.csv

tag: day


title: AI_EZH2_ChIP

tag: cell line


title: Cohort1_456V_7_cTfhTET

description:
Cohort1_456V_7_cTfhTET
Cohort1.vsn.normalised.csv

value: YOUNG


title: G0 R26-LSL HSCs plus OHT (Exp1)

source_name: Hematopoietic Stem cells from G0 mice

value: bone marrow hematopoietic cells


title: G0 R26-LSL HSCs


title: AI_EZH2_input

tag: growth type


title: G5/G6 HSCs 24 hr after pI:pC treatment

source_name: Hematopoietic Stem cells from G5/G6 mice isolated 24 hours after pI:pC treatment


title: Kera_L.Ras_4

description: RNA-seq


title: IM_v_3

description: RNA-seq

value: pWZL vector


title: rep2_AD_EZH2_input

value: LNCaP


title: Cohort1_326D_0_TET

description:
Cohort1_326D_0_TET
Cohort1.vsn.normalised.csv

source_name: TET

value: TET


title: rep1_AD_EZH2_input

value: prostate cancer cells


title: rep1_AD_EZH2_ChIP


title: rep1_AD_K27_ChIP


title: G5/G6 HSCs 48 hr after pI:pC treatment

source_name: Hematopoietic Stem cells from G5/G6 mice isolated 48 hours after pI:pC treatment


title: Kera_L.Ras_2

description: RNA-seq


title: Kera_L.Ras_1

description: RNA-seq


title: Cohort1_065V_7_cTfhTET

description:
Cohort1_065V_7_cTfhTET
Cohort1.vsn.normalised.csv


title: Cohort1_074E_7_cTfhTET

description:
Cohort1_074E_7_cTfhTET
Cohort1.vsn.normalised.csv


title: Cohort1_393B_0_TET

description:
Cohort1_393B_0_TET
Cohort1.vsn.normalised.csv


title: IM_v_2

description: RNA-seq


title: rep2_AD_EZH2_ChIP


title: G5/G6 HSCs 1 week after pI:pC treatment

source_name: Hematopoietic Stem cells from G5/G6 mice isolated 1 week after pI:pC treatment


title: Cohort1_456V_0_TET

description:
Cohort1_456V_0_TET
Cohort1.vsn.normalised.csv


title: G0 HSCs 8 hr after pI:pC treatment

source_name: Hematopoietic Stem cells from G0 mice isolated 8 hours after pI:pC treatment

value: TERT-ER/+ or TERT+/+


title: rep2_AD_NC_RNAseq

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue < =0.01
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample

extract_protocol:
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For RNA-seq, total RNA was extracted from each embryo, 10 mg of total RNA was used for RNA sequencing (RNA-seq) library preparation. Polyadenylated mRNAs were purified and concentrated with Magnetic Beads Oligo (dT) (Invitrogen, Carlsbad, CA, USA) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and applied to Illumine NextSeq 500 system 151 nt pair-end sequencing by ABlife, Inc. (Wuhan, China).

treatment_protocol: siRNAmock (NC) or siRNAEZH2 (siEZH2) were transfected into LNCaP/abl by Lipofectamine 2000 (Invitrogen). After 24 hours, cells were collected and qRT-PCR was performed to confirm RNA knockdown.

value: androgen-dependent growth


title: rep1_AI_NC_RNAseq

value: androgen-independent growth


title: G0 HSCs after vehicle treatment

source_name: Hematopoietic Stem cells from G0 mice isolated 1 week after vehicle treatment


title: Cohort1_005E_0_TET

description:
Cohort1_005E_0_TET
Cohort1.vsn.normalised.csv


title: IM_v_1

description: RNA-seq


title: rep1_AD_NC_RNAseq


title: rep2_AI_NC_RNAseq


title: Cohort1_072C_0_TET

description:
Cohort1_072C_0_TET
Cohort1.vsn.normalised.csv

value: OLD


title: G0 HSCs 48 hr after pI:pC treatment

source_name: Hematopoietic Stem cells from G0 mice isolated 48 hours after pI:pC treatment


title: rep2_AI_siEZH2_RNAseq


title: IM_p16_2

description: RNA-seq

value: pWZL p16


title: Cohort1_061Q_0_TET

description:
Cohort1_061Q_0_TET
Cohort1.vsn.normalised.csv


title: IM_p16_3

description: RNA-seq


title: G0 HSCs 1 week after pI:pC treatment

source_name: Hematopoietic Stem cells from G0 mice isolated 1 week after pI:pC treatment


title: IM_p16_1

description: RNA-seq


title: G0 HSCs 24 hr after pI:pC treatment

source_name: Hematopoietic Stem cells from G0 mice isolated 24 hours after pI:pC treatment


title: rep1_AI_siEZH2_RNAseq


title: UPN16 Lin-CD34+ cells

source_name: Stem and Progenitor cells from a patients with a pathogenic mutation in TERT

value: TERT c.2110C>T

value: 49 years old


title: G5/G6 HSCs after transplantation

source_name: Hematopoietic Stem cells from G5/G6 mice after transpantation in wild type recipients

value: two months


title: Cohort1_074E_0_TET

description:
Cohort1_074E_0_TET
Cohort1.vsn.normalised.csv


title: rep2_AD_siEZH2_RNAseq


title: Cohort1_377J_0_TET

description:
Cohort1_377J_0_TET
Cohort1.vsn.normalised.csv

value: M


title: NIH6 Lin-CD34+ cells

source_name: Stem and Progenitor cells from a patients with a pathogenic mutation in TERC

value: TERC minus 58 C>G

value: 42 years old


title: G5/G6 HSCs

source_name: Hematopoietic Stem cells from G5/G6 mice

value: TERT-ER/ER


title: Cohort1_065V_0_TET

description:
Cohort1_065V_0_TET
Cohort1.vsn.normalised.csv

value: F


title: rep1_AD_siEZH2_RNAseq


title: G0 HSCs after transplantation

source_name: Hematopoietic Stem cells from G0 mice after transpantation in wild type recipients

value: bone marrow hematopoietic cells


title: NIH1 Lin-CD34+ cells

value: TERT c.570-586dup

value: 58 years old


title: rep2_AI_RNAseq

value: LNCaP

value: prostate cancer cells


title: Cohort1_349D_0_TET

description:
Cohort1_349D_0_TET
Cohort1.vsn.normalised.csv

value: TET


title: rep1_AI_RNAseq

value: androgen-independent growth


title: HD4 (937) Lin-CD34+ cells

source_name: Stem and Progenitor cells from a healthy donor

value: 25 years old


title: Cohort1_406Q_0_TET

description:
Cohort1_406Q_0_TET
Cohort1.vsn.normalised.csv

value: YOUNG


title: Cohort1_328F_0_TET

description:
Cohort1_328F_0_TET
Cohort1.vsn.normalised.csv


title: HD3 (177) Lin-CD34+ cells

value: 20 years old


title: rep2_AD_RNAseq

value: androgen-dependent growth


title: G5/G6 MPP4 cells

source_name: Multipotent Progenitor Cells Type 4 from G5/G6 mice

value: two months


title: rep1_AD_RNAseq


title: NIH5 Lin-CD34+ cells

value: TERT c.1892G>A


title: G5/G6 LK cells

source_name: Lineage-cKit+ cells from G5/G6 mice


title: Cohort1_044X_0_TET

description:
Cohort1_044X_0_TET
Cohort1.vsn.normalised.csv

value: OLD

value: M


title: HD2 (58) Lin-CD34+ cells

value: 51 years old


title: G5/G6 LSK cells

source_name: Lineage-cKit+Sca1+ cells from G5/G6 mice

value: TERT-ER/ER


title: Cohort1_332K_0_TET

description:
Cohort1_332K_0_TET
Cohort1.vsn.normalised.csv

source_name: TET


title: HD1 (600) Lin-CD34+ cells

value: bone marrow hematopoietic cells

value: 54 years old


title: BCG 6h ex

organism: Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172

source_name: BCG, extracellular

tag: tissue

value: BCG, extracellular

tag: agent

value: Mycobacterium bovis BCG str. Tokyo 172

tag: time

tag: library type

value: Ribo-Zero


title: G0 MPP4 cells

source_name: Multipotent Progenitor Cells Type 4 from G0 mice

value: TERT-ER/+ or TERT+/+


title: Cohort1_402L_0_TET

description:
Cohort1_402L_0_TET
Cohort1.vsn.normalised.csv

value: TET

tag: Sex

value: F

tag: lane

tag: cells


title: rep2_AI_IgG

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with fastx_clipper
Reads were mapped using tophat2 -N 2. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
detecting different expression gene using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes gene RPKM values for each sample

growth_protocol: Androgen-dependent prostate cancer cells LNCaP (AD) were cultured in RPMI1640 medium, while androgen-independent prostate cancer cells LNCaP (AI) were maintained in RPMI1640 medium with charcoal stripped   serum.

extract_protocol:
Cells were irradiated once for 400 mJ/cm2. Take up crosslinked cells in ice-cold lysis buffer, then add RQ I DNaseat incubated at 37 °C for 3 min at 1,000g. The mixture was then centrifuged at 10,000 x g at 4 °C for 10 min to remove cell debris. The supernatant was incubated with DynaBeads protein G conjugated with anti-EZH2 antibody (source: Millipore, cat# 17-662, lot# 2366583) or IgG (source: Millipore, cat# 17-662, lot# 2366583) at 4 °C for 2 hours. The beads were washed with Wash buffer, High-salt Wash buffer and 1X PNK Buffer, respectively. Resuspend the beads in dephosphorylation mix and wash the beads 3 times with 1X PNK Buffer. Then resuspend the beads in phosphorylation mix and wash the beads 2 times with 1X PNK Buffer. Resuspend the beads in Elution Buffer. The supernatant was used to run gels. A region 30 kDa above the protein size is excised. Add PK buffer (900 µl) and 10mg/ML proteinase K (100 µl) to the membrane pieces, the isolated RNA was used for prepare sequencing library.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing and Illumina Genome Analyzer Iix for single-end sequencing by ABlife. Inc (Wuhan, China).

value: prostate cancer cell line LNCaP (AI)

tag: growth protocol

value: androgen-independent growth

tag: rip antibody

value: anti-IgG (Millipore, cat# 17-662, lot# 2366583)


title: BCG 6h in

source_name: BCG, intracellular

value: BCG, intracellular


title: Cohort1_357M_0_TET

description:
Cohort1_357M_0_TET
Cohort1.vsn.normalised.csv

tag: cell type

tag: bleed

tag: genotype


title: rep2_AD_IgG

value: prostate cancer cell line LNCaP (AD)

value: androgen-dependent growth


title: G0 HSCs

source_name: Hematopoietic Stem cells from G0 mice

tag: age

value: two months


title: G0 LK cells

source_name: Lineage-cKit+ cells from G0 mice


title: Cohort1_449M_0_TET

description:
Cohort1_449M_0_TET
Cohort1.vsn.normalised.csv

tag: group

tag: cohort

tag: pid

value: YOUNG

value: M


title: rep1_AI_IgG

tag: cell line


title: BCG 24h ex

tag: tissue


title: rep1_AD_IgG


title: 10X-Zheng-CDC42-Rescue

city: Cincinnati

first: Zheng

last: Zhang

state: OH

address: 8760 Sturbridge Dr

department: Division of Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: Single cell RNAseq

data_processing:
Sample demultiplexing, barcode processing, and UMI counting were performed using Cell Ranger 1.3.0 (10x Genomics).
Using default setting by Cell ranger

source_name: Small intestinal crypts

extract_protocol:
4000-5000 cells from each sample were harvested for library construction
single cell RNA-seq libraries were prepared using 10x Genomics Chromium Single Cell 3ʹReagent Kits v3

treatment_protocol: Small intestinal crypts were harvested from 2-3 months old adult mice, and then treated with 3x TripLE for 1 hour to get single cell suspension

tag: strain

tag: short name

value: Rescue

value: Adult

value: Olfm4-IRES-eGFPCreERT2; CDC42flox/flox; Yapflox/flox; Tazflox/+


title: Cohort1_364V_0_TET

description:
Cohort1_364V_0_TET
Cohort1.vsn.normalised.csv

tag: day

value: OLD


title: 10X-Zheng-CDC42-KO

description: Single cell RNAseq

value: KO

value: Olfm4-IRES-eGFPCreERT2; CDC42flox/flox


title: Stress -27

city: Jakarta Timur

first: Ardha

last: Apriyanto

state: DKI Jakarta

address: Puloayang Raya Blok OR I

country: Indonesia

institute: Astra Agro Lestari

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequences were not trimming due to high quality reads.
The software HISAT2 (v2.1.0) was used to align sequencing reads to the reference genome of oil palm (GCF_000442705.1).
The estimated read counts and calculated Fragments Per Kilobase Million (FPKM) were quantified using StringTie (v1.3.4)
Statistical analysis of differential gene expression was conducted with DESeq2 (v1.18.1)
Genome_build: GCF_000442705.1
Supplementary_files_format_and_content: Normalized counts FPKM

organism: Elaeis guineensis

source_name: Inflorescense at leaf axil -27

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen). About 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Defoliation stress treatment was conducted as described by Durand-Gasselin et al. [1999]. In general, all of the leaves were cut down. The trees were later felled 45 days after complete defoliation, and the inflorescence samples were collected for transcriptomic analysis.

value: Primordial Inflorescense

tag: leaf axil position

tag: treatment

value: stress

value: Indonesia:Kalimantan Tengah


title: G0 LSK cells

source_name: Lineage-cKit+Sca1+ cells from G0 mice

value: bone marrow hematopoietic cells

value: TERT-ER/+ or TERT+/+


title: 10X-Zheng-CDC42-HET

description: Single cell RNAseq

value: Het

value: Olfm4-IRES-eGFPCreERT2; CDC42+/flox


title: BCG 24h in

value: BCG, intracellular

tag: agent

value: Mycobacterium bovis BCG str. Tokyo 172

tag: time

tag: library type

value: Ribo-Zero


title: rep1_AI_EZH2

value: prostate cancer cell line LNCaP (AI)

tag: growth protocol

value: androgen-independent growth

tag: rip antibody

value: anti-EZH2 (Millipore, cat# 17-662, lot# 2366583)


title: Cohort1_066W_0_TET

description:
Cohort1_066W_0_TET
Cohort1.vsn.normalised.csv

tag: cell type

value: TET

tag: Sex

value: M

tag: lane

tag: cells

tag: bleed

tag: genotype


title: Stress -20

source_name: Inflorescense at leaf axil -20

tag: tissue


title: Cohort1_329G_0_TET

description:
Cohort1_329G_0_TET
Cohort1.vsn.normalised.csv

tag: group

tag: cohort

tag: pid

value: OLD


title: HB15

data_processing:
Illumina Casava1.5 software used for basecalling.
3' adapter(TTAGATCAG) trimmed with cutadapt -e 0.12 -O 6 --trimmed-only -m 15 -M 25
mapped using bowtie2 -t -N 1 -p 24
detecting different expression gene using edgeR
Genome_build: Gossypium_hirsutum_v1.1
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample

organism: Gossypium barbadense

source_name: Gossypium barbadense 15 DPA

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at A260/A280 and A260/A230 using smartspec plus (BioRad)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 15 DPA

value: fiber


title: rep2_AD_EZH2

tag: cell line

value: prostate cancer cell line LNCaP (AD)

value: androgen-dependent growth


title: HB25

source_name: Gossypium barbadense 20 DPA

value: 20 DPA


title: Stress +5

source_name: Inflorescense at leaf axil +5

value: Primordial Inflorescense

tag: leaf axil position

tag: treatment

value: stress

value: Indonesia:Kalimantan Tengah


title: Control -27

value: control


title: Cohort1_425L_0_TET

description:
Cohort1_425L_0_TET
Cohort1.vsn.normalised.csv

tag: day

value: YOUNG

value: F


title: rep1_AD_EZH2

tag: growth protocol


title: Cohort1_333L_0_TET

description:
Cohort1_333L_0_TET
Cohort1.vsn.normalised.csv


title: ATAC-seq_G5 HSCs

data_processing:
Equal molar concentrations of uniquely indexed samples were pooled together. Pooled libraries were sequenced using a NextSeq500 150-cycle flow cell (Illumina).
Reads were aligned to the mouse (mm10) or human (hg38) genomes, and peaks were called using the cellranger-atac count pipeline.
Individual samples were merged using the cellranger-atac pipeline to generate the peak-barcode matrix and TF-barcode matrix.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: A sparse matrix with the number of reads in each peak for each cell, a sparse matrix with the transcription factor (TF) activity for each cell, and a fragment file with the number of reads in each peaks for each cell

source_name: Stem cells from G5/G6 mice

extract_protocol:
The scATAC Low Cell Input Nuclei Isolation protocol (10X Genomics) was used to isolate nuclei from FACS-purified cells. The trypan blue exclusion assay was performed to check for intact nuclei.
The remaining extracted nuclei were used for the consecutive steps of the scATAC-seq library preparation protocol following 10X Genomics guidelines.

value: bone marrow hematopoietic cells

value: TERT-ER/ER


title: Cohort1_389X_0_TET

description:
Cohort1_389X_0_TET
Cohort1.vsn.normalised.csv


title: HB10

source_name: Gossypium barbadense 10 DPA

value: 10 DPA


title: Cohort1_408S_0_TET

description:
Cohort1_408S_0_TET
Cohort1.vsn.normalised.csv

value: TET


title: Control -20


title: ATAC-seq_G0 HSCs

source_name: Stem cells from G0 mice

value: TERT-ER/+ or TERT+/+


title: rep2_AI_EZH2

value: prostate cancer cell line LNCaP (AI)

value: androgen-independent growth

tag: rip antibody

value: anti-EZH2 (Millipore, cat# 17-662, lot# 2366583)


title: Control +5


title: HB5

source_name: Gossypium barbadense 5 DPA

value: 5 DPA

value: fiber


title: Type-2 diabetic adipocyte Exosomes (T2D) 1

status: Public on Oct 22 2021

type: RNA

city: Boston

first: Naser

last: Jafari

address: 72 East Concord

department: Hem Onc

institute: Boston University

description: Test

data_processing: Ct values were generated by ABI 7500 Fast System Software

label: SYBR Green

source_name: MCF7 cells

growth_protocol: MCF7 cells were cultured in DMEM including 10% FBS and 1% antibiotics for an over night

extract_protocol: RNA isolated using Qiagen RNA purification protocol and reagents

treatment_protocol: MCF7 Cancer cells were treated with ND or T2D adipocytes exosomes for 5 days

tag: cell type

value: breast cancer


title: Type-2 diabetic adipocyte Exosomes (T2D) 2

description: Test


title: Type-2 diabetic adipocyte Exosomes (T2D) 3

description: Test


title: Control replicate 3

description: Control

value: Control


title: Non diabetic adipocyte Exosomes (ND) 1

description: Test

value: Non diabetic adipocyte Exosomes (ND) 1


title: Control replicate 2

description: Control


title: Control replicate 1

description: Control


title: Non diabetic adipocyte Exosomes (ND) 3

description: Test

value: Non diabetic adipocyte Exosomes (ND) 3


title: JK-XC-4-2

city: Chicago

first: Xiufen

last: Chen

state: IL

address: 900 E 57th Street KCBD 6230A

institute: The University of Chicago

data_processing:
Illumina sequencing was converted to fastq using bcl2fastq
Estimated counts and TPM values generated using kallisto with mm10/GRCm38.97 using sequence bias correction (--bias flag), 100 bootstrap samples (-b 100), seed of 10 (--seed=10), and estimated fragment length of 50 (-l 50).
Genome_build: mm10/GRCm38.97
Supplementary_files_format_and_content: tab-delimited text files include estimated counts and TPM values for each sample

source_name: spleen

extract_protocol:
TCRTg101 in livers and spleens of leukemia-bearing mice were isolated at various time points following adoptive transfer (day 0, day 6-7, day 13-14, day 16-18) by FACS and were re-suspended in Trizol (Life Technologies). TCRTg101 RNA was isolated via chloroform extraction. Low input RNA sequencing was performed in the University of Chicago Genomic. Genes with fewer than 10 reads in at least 6 samples were filtered out, resulting in a dataset of 11,164 genes. Differential gene expression analysis was performed on raw aligned read counts using DESeq2 (Love et al., 2014), with batch effects accounted for in the design formula. Genes were considered to be differentially expressed if they had an adjusted p-value < 0.05 using a Benjamini-Hochberg test (FDR). Counts per gene were regular log (rlog)-transformed, and batch effects were removed using the removeBatchEffect function from limma (Ritchie et al., 2015) for principal component analysis (PCA), sample clustering based on Euclidean distance, and heatmaps depicting z-scores of gene expression. rlog-transformed, batch-corrected counts were also used for weighted gene correlation network analysis (WGCNA) (Langfelder and Horvath, 2008) while additionally filtering out the 50% of genes with the lowest variance to reduce noise, resulting in a set of 5,582 genes. Adjacency was determined using a signed analysis and a soft thresholding power of 14, which was determined by scale-free fit index (Zhang and Horvath, 2005). 12 clusters of genes were initially identified, 2 of which contained a combined 4,269 genes (76.5% of the dataset), and roughly corresponded to genes whose expression increased or decreased over the experimental time course. Of the other 10 clusters, 2 were identified as containing genes which were transiently upregulated or downregulated. These two clusters contained 448 genes, combined. The remaining 865 genes were assigned to eight different clusters, which appeared to be the result of high variance within sample groups, either due to low overall gene expression or low outlier values. No conclusions were drawn regarding these clusters due to uncertainty in the data. Core Facility on the Illumina HiSeq 2500 platform in two batches. Reads were mapped onto the University of California Santa Cruz mouse genome using kallisto (Bray et al., 2016)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: spleen

tag: age

value: 6 week old

value: wild type

value: Tg101 from leukemia bearing mice at d7


title: JK-XC-8

source_name: liver

value: liver

value: Tg101 from leukemia bearing mice at d14


title: JK-XC-7

value: Tg101 from leukemia bearing mice at d13


title: JK-XC-9-2

value: Tg101 from leukemia bearing mice at d16


title: JK-XC-11

value: Tg101 from untreated mice at d18


title: JK-XC-13


title: JK-XC-12-2

value: undivied Tg101 (CTVhi) from leukemia bearing mice at 18


title: JK-XC-9


title: JK-XC-13-2


title: JK-XC-3-2


title: JK-XC-4


title: JK-XC-6


title: Non diabetic adipocyte Exosomes (ND) 2

description: Test

value: Non diabetic adipocyte Exosomes (ND) 2


title: JK-XC-3


title: JK-XC-1-2

value: naive Tg101 (d0)


title: JK-TG-13-2

value: Tg101 from leukemia bearing mice at d18


title: JK-TG-12-2


title: JK-XC-5-2


title: JK-XC-5


title: JK-XC-12


title: JK-XC-1


title: JK-XC-11-2


title: EDL_Input_rep1

city: Oslo

first: Mads

last: Bengtsen

address: Blindernveien 31

country: Norway

institute: University of Oslo

data_processing:
Reads were trimmed and adaptors removed with Trim Galore and mapped to the mouse genome (mm9) with BWA MEM (v0.7.13) using default parameters. Duplicated and low-quality reads (-q >10) were removed using Samtools (v0.1.19) in addition mitochondrial reads were also removed. Peak calling was conducted with PePr (v.1.18) for each histone modification over the respective input sample using the following parameters --sharp and a p-value threshold of 0.05.  Differently enriched regions were identified with PePr --diff with the histone modification of interest over the respective input for each sample, using a threshold on 1.5 or above and a FDR-value on < 1x10-5 for H3K4me3 and  < 1x10-7 for H3K27ac in addition to intersect with peaks identified in their respective sample. BedGraph files were generated with Deeptools (v.3.3.1).
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraphs of histone enrichment, peaks files, differentially enriched regions files

source_name: EDL

extract_protocol:
Animals were sedated with 2 % isoflurane. Following deep anaesthesia, soleus and EDL were surgically removed, frozen in liquid nitrogen and stored at -80 °C. Muscles were equilibrated to -20 °C and lysed using gentleMACS M-tubes (Miltenyi Biotec). The myonuclei were isolated with PCM1 (HPA023370, Sigma Aldrich) from the whole muscle lysate, cross-linked and sonicated using a Bioruptor pico (Diagenode). The Histone/DNA complexes were isolated using antibodies against H3K4me3 (C15410003, Diagenode) or H3K27ac (C15410196, Diagenode) , respectively. DNA was decrosslinked and purified with Zymo ChIP DNA Clean & Concentrator kit (Zymogen).
Libraries were generated with Swift Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) following the recommendations from the manufacturer with the exception that the ratio of beads and PEG was 1.5 and 1.3 in step Repair step I and II, respectively, and amplified with 12 PCR cycles. Libraries were sequenced on Illumina HiSeq 2500 40 bp paired-end at the Oslo University Hospital Genomics Core Facility (oslo.genomics.no).

value: EDL

value: NMRI

tag: population

value: Myonuclei

tag: chip antibody

value: none (input)


title: SOL_H3K27ac_rep3

description:
SOL_1_H3K27ac.bedgraph
SOL_Myonuclei_H3K27ac_peaks.txt

source_name: Soleus

value: Soleus

value: H3K27ac (C15410196, Diagenode)


title: EDL_H3K27ac_rep2

description:
EDL_1_H3K27ac.bedgraph
EDL_Myonuclei_H3K27ac_peaks.txt


title: JK-TG-12

value: 6 week old

tag: genotype

value: wild type


title: SOL_H3K4me3_rep1

description:
SOL_1_H3K4me3.bedgraph
SOL_Myonuclei_H3K4me3_peaks.txt

tag: tissue

value: H3K4me3 (C15410003, Diagenode)


title: EDL_H3K27ac_rep3


title: JK-TG-10

value: spleen


title: JK-TG-13

value: liver


title: EDL_Input_rep3


title: EDL_Input_rep2


title: JK-Tg-10-DT

value: naive Tg101 Oligo-dT regular sequencing


title: EDL_H3K27ac_rep1


title: EDL_H3K4me3_rep3

description:
EDL_1_H3K4me3.bedgraph
EDL_Myonuclei_H3K4me3_peaks.txt


title: SOL_Input_rep2


title: EDL_H3K4me3_rep2


title: Whole postnatal pancreas from 1 day old mouse donor 30

city: Edmonton

first: Patrick

middle: E

last: MacDonald

state: AB

address: 6-040 Li Ka Shing Centre

country: Canada

institute: University of Alberta

data_processing:
RTA 2.4.11 used for basecalling
Sequencing was performed on the Illumina NextSeq 500 with Paired End 42bp × 42bp reads.
Sequencing data was demultiplexed using Illumina's bcl2fastq2.
De-multiplexed read sequences were then aligned to the reference sequence using salmon aligner v 0.13.1 using the gcBias, validateMappings, and rangeFactorizationBins (with 4 as the binning parameter) options
Analysis of differentially expressed genes was performed using the DESeq2 package (version 1.24.0) in R
Genome_build: mm10 release 96
Supplementary_files_format_and_content: Supplementary files contain salmon output files, which have been renamed for clarity. These files may be loaded into R using the tximport package. Counts.csv is a matrix table with normalized gene counts for filtered genes and every sample

source_name: pancreas

growth_protocol: Mice were bred and raised to 1 day postnatal using standard approved animal care committee methodology.

extract_protocol:
RNA from the pancreata of 1-day old mice was isolated using a 526 protocol specific for pancreatic RNA isolations. Sample quality control was performed using the Agilent 2100 Bioanalyzer.
Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs).

value: pancreas

value: WT


title: Whole postnatal pancreas from 1 day old mouse donor 29


title: Whole postnatal pancreas from 1 day old mouse donor 20

value: KO


title: Single cell RNA-seq mouse islets mouse # 621670

data_processing:
Library strategy: scRNA-seq
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger v3.1.0 mkfastq command with bclfastq2.
Samples were trimmed using cutadapt version 2.10 with default options except for a maximum error rate of 0.1
Subsequent UMI and cell barcode de-convolution along with mapping to the genome was performed using 10X Genomics’ cellranger v4.0.0 software package count command to generate the final digital gene expression matrices
The Seurat SCTransform pipeline was used for aggregation and subsequent processing.
Integrated data was used for principal component analysis and UMAP analysis
The barcode/UMI information is captured in R1, while transcript/biological info is captured in R2; UMI: 10bp + Barcode:16bp
Genome_build: mm10 (GRCm38 release 101)
Supplementary_files_format_and_content: Supplementary files contain Cellranger output files, which have been renamed to ensure clarity. Change file names to 'matrix.mtx.gz', 'barcodes.tsv.gz' and 'features.tsv.gz' after separating files into donor specific folders. This is necessary to allow Seurat to read these files. Seurat cannot read files named in their current form. scaled_gene_expression_matrix.csv is a VST normalized gene expression count matrix of all the samples compiled into one file after quality control.

source_name: Islets

growth_protocol: Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology, then transferred to 60% kcal/fat high fat diet for 9 weeks.

extract_protocol:
Cells were counted and inspected using a NucleoCounter-200 before input to the 10X Chromium library preparation pipeline and subsequent NGS.
Single Cell Suspension was loaded on the 10x genomics single cell controller for capture in droplet emulsion. Libraries were prepped using the Chromium Single Cell 3’ Reagent v3.1 Chemistry kit and the standard protocol was followed for all steps.

treatment_protocol: Adult animals 8 weeks of age were exposed to 60% high fat diet for 9 weeks before islets were isolated.

value: Islets


title: Whole postnatal pancreas from 1 day old mouse donor 19


title: EDL_H3K4me3_rep1


title: SOL_Input_rep1


title: SOL_H3K27ac_rep2


title: SOL_H3K4me3_rep3


title: Single cell RNA-seq mouse islets mouse # 621669


title: SOL_H3K27ac_rep1


title: Aorta of ApoE KO mice2, Gpnmb vaccine

city: Niigata

first: Masayoshi

last: Suda

address: 1-757 Asahimachi-dori, Chuo-ku

department: Department of Cardiovascular Biology and Medicine

country: Japan

institute: Niigata University

data_processing:
these libraries were analyzed on a NextSeq500 with a NextSeq 500/550 High Output Kit v2 (Illumina).
TopHat 2 (version 2.0.13) was used for mapping reads to the reference genome (Ensembl GRCm38/mm10) with annotation data downloaded from the Ensembl Asia website (URL https://asia.ensembl.org/).
Expression of each transcript was quantified as the number of fragments per kilobase of transcript per million fragments mapped (FPKM), and expression was compared among 3 groups by Cuffdiff (included in Cufflinks version 2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Aorta

extract_protocol:
Total RNA was isolated from tissue samples with an RNeasy Mini Kit (Qiagen, 74104) and its quality was assessed by using the Agilent 2100 Bioanalyzer with the Agilent RNA6000 pico Kit (Agilent Technologies).
The TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) was employed to construct four libraries according to the specifications of the manufacturer.

treatment_protocol: We fed the HFD to ApoE KO mice from 4 weeks of age, administered Gpnmb vaccine or control vaccine at 8 weeks of age, and analyzed these mice at 16 weeks.

value: Aorta

value: ApoE -/-

value: Gpnmb vaccine


title: SOL_H3K4me3_rep2

value: NMRI

value: Myonuclei


title: Aorta of ApoE KO mice3, control vaccine

value: control vaccine


title: WCE control in v6.5 mouse ESCs

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina bcl2fastq version 2.17.1.14 software to generate fastq files.
reads were aligned to mouse mm10 reference genome using bowtie2 software, with default parameters.
for transcription factors, peaks were identified with MACS version 1.4.2-157.  Whole-cell extract was used as control to define a background model. Duplicate reads aligned to the exact same location are excluded by MACS default configuration.
Genome_build: mm10
Supplementary_files_format_and_content: bed file, contains the peaks detected by MACS software

source_name: WCE control in v6.5 mouse ESCs

growth_protocol: cells were grown in 2i/LIF for 4 passages

extract_protocol:
ChIP-seq was done based on how it was described earlier in PMID: 24048479. After harvesting, washing and centrifugate, the cell pellets were crosslinked in 1% formaldehyde for 10 minutes at room temperature, and then quenched with 2.5 M Glycine for 5 minutes at room temperature. Fixated cells were then lysed in a Lysis buffer (140 mM NaCl, 50 mM HEPES KOH pH 7.5, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton X-100, 1 mM EDTA, supplemented with a complete protease inhibitor cocktail tablet (Roche) and 20 mM NEM) at 4°C. The lysates were then centrifuged at 1000g for 10 minutes at 4°C, and the pellet was resuspended in a Sonication Solution (140 mM NaCl, 10 mM Tris HCl, 0.1% DOC, 0.2% SDS and complete protease inhibitor cocktail and 20 mM NEM) and were sonicated with Sonifier (model S-450D) at 4°C  to achieve size ranges between 200 and 800 bp and then precipitated at full speed for 10 minutes by a cooled centrifuge. Supernatant lysates were extracted and diluted. Small amount of lysate was saved for whole cell extract (input) at this point. Antibodies were pre-bound by incubating with Protein-G Dynabeads (Invitrogen) in blocking buffer (0.5% Tween and 0.5% BSA in PBS) for 1 hour at room temperature. Washed beads were added to the lysates for incubation, as detailed below per antibody. Following incubations, the samples were washed five times with the Lysis buffer, twice with modified Lysis buffer (500 mM NaCl, 50 mM HEPES KOH pH 7.5, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton X-100, 1 mM EDTA, supplemented with a complete protease inhibitor cocktail tablet (Roche), twice with LiCl buffer (0.5% NP-40, , 250 mM LiCl, 10 mM TE, 0.5% DOC), once with TE (10 mM Tris-HCl pH 8.0, 1mM EDTA), and then eluted in Elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0). Eluate were treated sequentially with RNaseA (Roche,) for 30 minutes in 37 °C and Proteinase K (NEB) for 2 hours at 37°C and were then de-crosslinked at 65 °C for 8 hours. DNA was purified with Agencourt AMPure XP system (Beckman Coulter Genomics).
Libraries were then prepared according to a modified version of the Illumina Genomic DNA protocol, as detailed previously in PMID: 24048479. H3K27ac: 5 million cells, 5ug ab4729 (Abcam), incubation 6 hours incubation time at 4°C. SUMO1: 5 million cells, 5ug 4930 (Cell Signaling Technologies), incubation 12 hours incubation time at 4°C.

treatment_protocol: For Ubc9 depletion DOX was added for 72 hours

value: mouse embryonics stem cells

tag: antibody


title: SOL_Input_rep3

value: Soleus

value: none (input)


title: Whole postnatal pancreas from 1 day old mouse donor 16


title: Single cell RNA-seq mouse islets mouse # 621666


title: JK-TG-10-2

value: 6 week old

value: wild type

value: naive Tg101 (d0)


title: Aorta of ApoE KO mice3, Gpnmbl vaccine


title: WCE control in Ubc9-control mouse ESCs, replicate 1

source_name: WCE control in Ubc9-control mouse ESCs1


title: H3K27ac chip-seq in Ubc9-depleted mouse ESCs, replicate 1

source_name: H3K27ac chip-seq in Ubc9-depleted mouse ESCs1

value: DOX inuced Ubc9 depletion(TET-OFF)

tag: matched control file


title: WCE control in Ubc9-control mouse ESCs, replicate 2

source_name: WCE control in Ubc9-control mouse ESCs2


title: H3K27ac chip-seq in Ubc9-depleted mouse ESCs, replicate 2

source_name: H3K27ac chip-seq in Ubc9-depleted mouse ESCs2


title: Sumo1 chip-seq in v6.5 mouse ESCs

source_name: Sumo1 chip-seq in v6.5 mouse ESCs


title: Whole postnatal pancreas from 1 day old mouse donor 25

value: pancreas


title: Aorta of ApoE KO mice1, control vaccine


title: ATAC_Ubc9-control mESCs, replicate 2

description:
wo-2_S7
ATAC_Ubc9-control_REP2

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were trimmed with Trim using python script (https://github.com/TheJacksonLaboratory/ATAC-seq/blob/master/auyar/pyadapter_trim.py)
Reads were aligned to mm10 mouse genome using Bowtie2 with the parameter -X2000 (allowing fragments up to 2 kb to align).
Duplicated aligned reads were removed using Picard MarkDuplicates tool with the command REMOVE_DUPLICATES=true.
To identify chromatin accessibility signal we considered only short reads (≤ 120bp) that correspond to nucleosome free region. To detect and separate accessible loci in each sample, we used MACS version 1.4.2-1 with --call-subpeaks flag (PeakSplitter version 1.0).
peaks that appear in both replicates are kept for further processing
Genome_build: mm10
Supplementary_files_format_and_content: bed files containing peaks that appear in both replicates in each condition

source_name: Ubc9-control mESCs

extract_protocol:
Cells were harvested using trypsin and counted. 50000 cells were centrifuged at 300g for 5 minutes, followed by a wash in PBS, and were centrifuged again at 300g for 5 minutes.
Cells then were lysed in 50 μl of lysis buffer (10mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA) while being centrifuged at 250g for 10 minutes in 4 °C. The pellet was resuspended in a 50 μl of transposition reaction (25 μl of X2 TD Buffer (Illumina), 2.5 μl transposase and 22.5 μl of nuclease-free water). The reaction was performed at 37 °C for 30 minutes. Immediately after, the DNA products were purified using a MiniElute kit (Qiagen). Purified transposed DNA was amplified and barcoded using custom Nextera PCR primers 1 and 2, in a 12 cycle PCR reaction in KAPA HiFi HotStart (Roche). The libraries were purified using a MiniElute kit (Qiagen) and sequenced using Illumina NGS.

value: mouse Embryonic Stem Cells


title: H3K27ac chip-seq in Ubc9-control mouse ESCs, replicate 1

source_name: H3K27ac chip-seq in Ubc9-control mouse ESCs1


title: ATAC_H1 WT mESCs, replicate 1

description:
ATAC_H1_WT_REP1_S1
ATAC_H1-WT_REP1

source_name: H1 WT mESCs

value: taken from PMID 16377562


title: ATAC_H1 WT mESCs, replicate 2

description:
ATAC_H1_WT_REP2_S2
ATAC_H1-WT_REP2


title: H3K27ac chip-seq in Ubc9-control mouse ESCs, replicate 2

source_name: H3K27ac chip-seq in Ubc9-control mouse ESCs2


title: ATAC_Ubc9-depleted mESCs, replicate 2

description:
dox-2_S9
ATAC_Ubc9-depleted_REP2

source_name: Ubc9-depleted mESCs


title: WCE control in Ubc9-depleted mouse ESCs, replicate 2

source_name: WCE control in Ubc9-depleted mouse ESCs2


title: Aorta of ApoE KO mice2, control vaccine


title: ATAC_Ubc9-depleted mESCs, replicate 1

description:
dox-1_S8
ATAC_Ubc9-depleted_REP1


title: Y812 T6-2

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

data_processing:
Trimmed reads with Trimmomatic 0.3
Reading mapping to S288C pan genome with Bowtie 2 version 2.2.2
Read counts calculated with HTSeq 0.60
Genome_build: S288C pan genome
Supplementary_files_format_and_content: text file; raw HTSeq counts

organism: Saccharomyces cerevisiae

source_name: frozen stock

growth_protocol: Grown in anaerobic MMAS media with 10% glucose. Samples collected at 4, 10, 26 hours (T3, T6, T14) of growth.

extract_protocol:
Hot acid-phenol RNA exraction
Illumina TruSeq Stranded mRNA HT kit

tag: time point

value: T6 - hour 10

tag: replicate


title: Y799 T6-3


title: ATAC_H1 triple-KO mESCs, replicate 2

description:
ATAC_H1_TKO_REP2_S4
ATAC_H1-TKO_REP2

source_name: H1 triple-KO mESCs

tag: cell line


title: Y812 T6-1


title: WCE control in Ubc9-depleted mouse ESCs, replicate 1

source_name: WCE control in Ubc9-depleted mouse ESCs1


title: Y797 T6-2


title: Single cell RNA-seq mouse islets mouse # 621665

source_name: Islets

value: Islets


title: Y797 T6-1


title: ATAC_Ubc9-control mESCs, replicate 1

description:
wo-1_S6
ATAC_Ubc9-control_REP1


title: ChIP-SPT5-RAMOS-noDIVAC

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

institute: Bar-Ilan University

description: input used:ChIP-INPUT-RAMOS-noDIVAC

data_processing:
For DT40 data, ChIP-seq reads were aligned to Gallus_gallus-4.0 genome with the region spanning pseudoV and IgL locus (chr15:7,921,694–7,955,323) replaced with respective reporter construct sequence; for Ramos data ChIP-seq reads were aligned to the human GRCh38 genome with the lentivirus reporter appended as an extra chromosome.
Alignment done using Bowtie (version 1.1.2) with seed length 50 and 2, 3, and 3 mismatches allowed, respectively
Peaks were called using MACS 1.4.3 (Zhang et al., 2008). Default parameters were used (p value cutoff for peak detection = 1x10e-5;–keep-dup = auto), with corresponding DNA input as a control.
Genome_build: human GRCh37/hg19;GalGal4
Supplementary_files_format_and_content: Aligned-reads bed files were first converted to bedgraph files using bedtools genomecov (Quinlan and Hall, 2010) following by bedGraphToBigWig to make a bigwig file (Kent et al., 2010).

source_name: Ramos cell line

growth_protocol: Ramos cells were propagated in RPMI 1640 medium (Sigma), supplemented with 10 % fetal bovine serum (Gibco), 1X GlutaMAX (Gibco) and 1 % antibiotic mixture (Sigma) in a 5 % CO2 atmosphere at 37 °C.  DT40 cells were propagated in RPMI 1640 medium (Sigma), supplemented with 10 % fetal bovine serum (Hyclone), 1 % chicken serum (Biowest), 1X GlutaMAX (Gibco), 50 µM β-mercaptoethanol (Gibco) and 1 % antibiotic mixture (Sigma) in a 5 % CO2 atmosphere at 41 °C.

extract_protocol:
Chromatin Immunoprecipitation was performed using the following protocol. 4 x 107 formaldehyde-fixed cells were lysed in SDS lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, supplemented with Complete, EDTA free protease inhibitor cocktail (Roche)) and diluted 4-fold with dilution buffer (16.4 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, supplemented with inhibitors). The lysate was sonicated in aliquots using a water bath sonicator (Diagenode Bioruptor Pico) for 11 cycles (30s on/30s off) and cleared by centrifugation. The combined sonicated material was further diluted 1.5-fold in dilution buffer and 1.7 x 107 cell equivalents were subjected to immunoprecipitation with 5 μg (α-H3K27Ac, α-H3.3, α-RPB1, α-S5P CTD and α-S2P CTD), 7 μg (α-Spt5) or 1:50 dilution (α-H3K36me3) of antibodies at 4°C overnight. The next day, immune complexes were incubated with 30 µl magnetic beads (Protein G Dynabeads, Thermo Fisher Scientific) or (Protein A/G magnetic beads, Pierce). The magnetic beads were washed twice with low salt wash buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with ChIP wash buffer (50 mM HEPS, pH 7.6, 500 mM LiCl, 1 mM EDTA, 0.7% sodium deoxycholate and 1 % Igepal CA-630) and twice with TE buffer with 50 mM NaCl.     Chromatin Immunoprecipitation was performed with the SimpleChIP Enzymatic Chromatin IP Kit (#9003) according to the manufacturer’s protocol with minor modifications. In brief, 40 x 10e6 Ramos cells were spun down at 90xg for 10 min before the pellet was reconstituted in 9 ml of RPMI with 2% FBS in a 15 ml conical tube. Then, 0.6 ml of 16% Formaldehyde (Pierce/ThermoFisher #28906) was added and the cells were placed on a rocker for 10 min at RT. One ml of 10x glycine solution was added to quench the reaction, and the cells were then returned to the rocker for 5 min at RT before being spun down at 300xg and washed 2x with PBS. All following steps were performed on ice or at 4°C unless otherwise noted. Cells were reconstituted in 10 ml of Buffer A with protease inhibitors and allowed to rest for 10 minutes and the lysed cells were spun down at 2000xg for 5 min to pellet nuclei. Pelleted nuclei were washed with 10 ml of Buffer B, pelleted at 2000xg for 5 min, and then resuspended in 1 ml of Buffer B. 1.7 µl of micrococcal nuclease (CST #10011) was added to the nuclei and the tube incubated in a 37°C water bath for 20 min. The reaction was stopped with 100 µl of 0.5 ml of EDTA, and the nuclei pelleted at 16,000xg for 1 min. The pellet was then resuspended in 1 ml of 1x ChIP Buffer with protease inhibitors and sonicated in 200 µl aliquots in a Qsonica sonicator for 2 cycles of 15 s on, 45 s off at 20% power. The lysate was then clarified at 10,000xg for 10 min before the supernatant was removed and diluted five-fold in 1x ChIP Buffer with protease inhibitors. For each ChIP, 500 µl of chromatin was incubated with 1-2 µg of antibody in a 1.5 ml Eppendorf tube at 4°C overnight on a rotator. The next day, 30 µl of Protein G Magnetic beads (CST #70024) was added to each tube and the mixture incubated at 4°C for 2 hours on a rotator. The beads were pelleted using a magnetic separation rack and the supernatant discarded.  The beads were then washed 3x with a low-salt wash and 1x with a high-salt wash using 5 min incubations on a rotator. Chromatin was eluted from beads with the addition of 150 µl of 1x Elution Buffer and incubation at 1200 rpm on a thermal mixer for 2 hours at 65°C. The beads were pelleted and the supernatant was moved to a new 1.5 ml Eppendorf tube and 2 µl of Proteinase K (CST #10012) added. The mixture was incubated for 2 hr at 65°C and then DNA was purified using SimpleChIP DNA Purification Buffers and Columns (CST #14209) and eluted in a volume of 50 µl.
ChIP-seq libraries were prepared for each ChIP from three independent ChIP experiments using TruSeq ChIP Sample Preparation kit (Illumina) or NEBNext Ultra II DNA Library Prep kit (New England Biolabs) according to manufacturer’s instructions.

value: B lymphocyte

value: WT

value: Burkitt's lymphoma-derived cell line, EBV-negative

value: Unknown

tag: Sex

value: male

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: ChIP-INPUT-RAMOS-DIVAC

value: INPUT


title: Y795 T6-3

value: CEN.PK113-5D URA3+


title: Y799 T6-2


title: ChIP-INPUT-RAMOS-noDIVAC


title: Y812 T3-2

value: T3 - hour 4


title: Y812 T3-1


title: Y812 T3-3


title: ATAC_H1 triple-KO mESCs, replicate 1

description:
ATAC_H1_TKO_REP1_S3
ATAC_H1-TKO_REP1


title: Y797 T6-3


title: Y799 T3-1


title: ChIP-S5P-RAMOS-noDIVAC

description: input used:ChIP-INPUT-RAMOS-noDIVAC

value: Abcam


title: Y799 T3-3


title: ChIP-S5P-RAMOS-DIVAC

description: input used:ChIP-INPUT-RAMOS-DIVAC


title: Y799 T6-1


title: ChIP-SPT5-RAMOS-DIVAC

description: input used:ChIP-INPUT-RAMOS-DIVAC


title: Y795 T6-1


title: ChIP-H3K27ac-RAMOS-noDIVAC

description: input used:ChIP-INPUT-RAMOS-noDIVAC


title: ChIP-H3K27ac-RAMOS-DIVAC

description: input used:ChIP-INPUT-RAMOS-DIVAC


title: Y797 T3-3


title: ChIP-POL2-RAMOS-DIVAC

description: input used:ChIP-INPUT-RAMOS-DIVAC


title: Y797 T3-2


title: ChIP-POL2-RAMOS-noDIVAC

description: input used:ChIP-INPUT-RAMOS-noDIVAC


title: TAF7_RIP_1

city: Bethesda

first: Dinah

middle: S.

last: Singer

state: MD

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

data_processing:
RIP-seq reads were aligned to human reference genome (hg19) with STAR aligner. Raw read counts were obtained using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of sequencing reads for each sample

source_name: HeLa TAF7 (WT) cells

growth_protocol: HeLa TAF7 (WT) cells were cultured in F12K medium supplemented with 10% fetal bovine serum.

extract_protocol:
TAF7-RNA complexes in HeLa TAF7 (WT) cytoplasmic extracts were immunoprecipitated using Protein A-Sepharose (MilliporeSigma, P3391) that coated with an anti-TAF7 antibody (generated in our lab). RNA was released from the TAF7-RNA complexes by proteinase K treatment followed by an acid phenol: chloroform (pH 4.5) extraction.
Libraries were prepared using the SMARTer Ultra Low RNA Kit for Illumina Sequencing and Illumina® Nextera XT DNA Library Preparation Kit according to manufacturers' instructions.

value: HeLa

tag: expressing

tag: rna population

value: Cytoplasmic RNA


title: TAF7_RIP_2

tag: rip antibody


title: Y795 T3-3


title: Y797 T3-1


title: Y795 T6-2


title: Synechocystis_PCC6803_2h_mock_control_1

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: mock 2h 1

label_protocol: The DNAse treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Synechocystis sp. PCC 6803 PCC-M strain (Trautmann, 2012) was grown photoautotrophically (40 µmol photons·m-2·s-1) at 30°C in BG-11 medium (Rippka, 1979) supplemented with 20 mM HEPES-NaOH (pH 7.5).

extract_protocol: Synechocystis 6803 cells were harvested by rapid filtration on hydrophilic polyethersulfone filters (Supor 800 Filter, 0.8 μm, Pall, New York, NY, USA). The filter covered with cells was immediately immersed in 1 ml of PGTX solution (Pinto, 2009)and frozen in liquid nitrogen. Total RNA was extracted as described previously (Hein, 2013).

treatment_protocol: Exponentially growing cells (density of 2 x 107 cells ml-1) were transferred to a plastic dish and irradiated with UV-C (254 nm) using UV lamps (UVP Inc., Upland, CA, USA) at a dose rate of 400 J/m2

tag: treatment

value: mock 2h


title: Synechocystis_PCC6803_2h_UV_stress_1

source_name: UV 2h 1

value: UV 2h


title: Y795 T3-2


title: Synechocystis_PCC6803_2h_UV_stress_2

source_name: UV 2h 2


title: Synechocystis_PCC6803_2h_mock_control_2

source_name: mock 2h 2


title: Aorta of ApoE KO mice1, Gpnmb vaccine

source_name: Aorta

tag: strain

value: Aorta

tag: age

value: ApoE -/-

value: Gpnmb vaccine


title: Y812 T14-2

value: T14 - hour 26


title: Y795 T3-1


title: Y799 T14-3


title: Synechocystis_PCC6803_1h_UV_stress_2

source_name: UV 1h 2

value: UV 1h


title: KATO/DDP_rep2

city: Chiangmai

first: Supachai

last: Yodkeeree

state: Chiangmai

address: 110 Intrawarorote

department: Biochemistry

country: Thailand

institute: Chiangmai University

description: Gastric cancer

data_processing:
Data generated from Illumina HiSeq TM were transformed into sequence reads by base calling using HWI-ST1276
Sequences were analyzed by using CLC genomic workbench version 10.0 which include quality control, trimming of adaptor and mapping to reference genome.
GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz was used as a reference genome.
Genome_build: Hg38
Supplementary_files_format_and_content: text file including TPM for every gene and every sample

source_name: Stomach

growth_protocol: KATOIII and KATO/DDP cell lines were grown in complete DMEM. KATO/DDP cells were grown were maintaine in low dose cisplatin and cultured in drug free madia for at least two passages before each experiment.

extract_protocol:
Total RNA was extracted by Nucleozol Ref 740404.200 and the quality of total RNA was checkedd by nanodrop and agarose gel electrophoresis.
Total RNA extracted was checked for quality and then mRNA was enriched from total RNA by using oilgodT beads. Then, mRNA was fragmented and cDNA was synthesized. After first strand synthesis, custom second strand synthesis buffer (illumina) was used to generate the second strand by nick translation. After that it undergoes purification, adapters ligation and PCR enrichment.

tag: histological type

value: Signet ring cell

tag: phenotype

value: Cisplatin resistance


title: KATO/DDP_rep3

description: Gastric cancer


title: Y799 T14-2

tag: genotype


title: Synechocystis_PCC6803_1h_mock_control_2

source_name: mock 1h 2

value: mock 1h


title: Synechocystis_PCC6803_1h_UV_stress_1

source_name: UV 1h 1


title: Y799 T14-1


title: KATO/DDP_rep1

description: Gastric cancer


title: A_6 [20207_S30]

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12
then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab)
Remaining reads were aligned to the Mesocricetus auratus genome assembly version 1.0 using Hisat2 (Kim et al., 2015)
Reads mapping to genes were counted using htseq-count (Anders et al., 2015)
Differential expression analysis was performed using the Bioconductor package DESeq2  (Love et al., 2014)
Genome_build: NC_041754.1 Macaca mulatta :  JF416958.1 Kyasanur forest disease virus strain P9605 :  JF416954.1 Alkhumra hemorrhagic fever virus strain 200300001
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample and matrix table with normalized gene counts.

organism: Macaca nemestrina

source_name: Macaca nemestrina infected with Alkhumra hemorrhagic fever virus at day 6

growth_protocol: Twelve female PTMs aged 10 to 16 years of age were housed in a humidity, temperature, and light controlled facility in adjacent cages for social interaction. Virus seed stocks were propagated once on Vero cells, and virus working stocks were aliquoted and frozen in liquid nitrogen tanks.

extract_protocol:
RNA was extracted from 140 ml plasma using the QIAamp Viral RNA Mini Kit (Qiagen). RNA was irradiated (10 megarad) for removal from the BSL4 according to established sample removal protocols (54). Following removal, cDNA was generated using SuperScript VILO cDNA Synthesis Kit (ThermoFisher).
100 ng of RNA was used for initial treatment with the Qiagen FastSelect -H/M/R and -Globin kit to inhibit cDNA synthesis of rRNA and globin transcripts.  The two viral stocks were not rRNA/Globin treated.  The only modification was to reduce the initial fragmentation step to 2 minutes to account for the degradation of the RNA.  After incubation with the probes from the FastSelect kit, the samples proceeded with cDNA synthesis and library preparation following the Illumina Stranded RNA Prep, Ligation kit.

treatment_protocol: Virus inoculations were performed with the indicated virus diluted in sterile PBS. For subcutaneous (sc) infections, 1x105 pfu was delivered in a single injection between the shoulder blades (1 ml volume)

tag: agent

value: Alkhumra hemorrhagic fever virus

value: day 6


title: A_0 [20205_S28]

source_name: Macaca nemestrina infected with Alkhumra hemorrhagic fever virus at day 0

value: day 0


title: A_6 [20204_S27]


title: A_2 [20206_S29]

source_name: Macaca nemestrina infected with Alkhumra hemorrhagic fever virus at day 2

value: day 2


title: A_2 [20203_S26]


title: A_0 [20202_S25]


title: KATOIII_rep2

description: Gastric cancer

value: Cisplatin sensitive


title: Y797 T14-3

source_name: frozen stock


title: A_6 [20201_S24]


title: Y797 T14-1


title: KATOIII_rep3

description: Gastric cancer


title: Y797 T14-2


title: KATOIII_rep1

description: Gastric cancer


title: Y795 T14-3

value: CEN.PK113-5D URA3+


title: A_2 [20200_S23]


title: A_6 [20198_S21]


title: Synechocystis_PCC6803_1h_mock_control_1

source_name: mock 1h 1


title: Yeast extract - peptone (YP)_9d_rep2

first: Evan

last: Shepherdson

state: Ontario

address: 1280 Main St W

institute: McMaster University

data_processing:
RNA-seq reads were aligned to the Streptomyces venezuelae genome GCA_001886595.1 using Bowtie2
Aligned reads were sorted using Samtools sort and a counts file was generated using HTseq-count
Counts files were processed using DESeq2 to generate a table of normalized transcript abundance measurements and to analyze statistical changes in expression between sample conditions
Genome_build: GCA_001886595.1
Supplementary_files_format_and_content: Matrix table with normalized transcript abundance for every gene and every sample in .csv file format

organism: Streptomyces venezuelae

source_name: Bacterial cells

growth_protocol: 10 uL of a Streptomyces venezuelae overnight culture were spotted to solid growth medium and incubated at 30 degrees Celsius. After specified incubation times, total RNA was extracted from cell lysates.

extract_protocol:
Lysates were generated by vortexing bacterial cells with glass beads in a guanidinium thiocyanate saturated lysis buffer. Total RNA was extracted with acidified phenol:chloroform
rRNA was depleted from total RNA samples using a Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. Libraries were constructed using an NEBNext Ultra II Direcitonal RNA Library Prep Kit for Illumina.

tag: growth medium

value: Yeast extract - peptone (YP)

tag: incubation time

value: 9 days


title: A_0 [20196_S19]

tag: time point


title: H1299 siRNA

city: Albuquerque

first: Steven

middle: A

last: Belinsky

state: NM

address: 2425 Ridgecrest Dr SE

department: Lung Cancer Program

institute: Lovelace Respiratory Research Institute

description:
H1299 TET1 KD
9992580024_K

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were transformed using variance stablizing transformation (VST), normalized using robust spline normalization (RSN) and converted to log2 using the lumi package in R

label: biotin

source_name: lung bronchial epithelium

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: genomic DNA was treated with proteinase K, digested with Rnase and phenol chloroform extracted

tag: sirna

value: siRNA TET1 knockdown

tag: cell line


title: A_0 [20199_S22]


title: Y795 T14-1

tag: replicate


title: Y795 T14-2


title: H1299 cells

description:
H1299 parent cell line
9992580024_J

value: vehicle


title: Y812 T14-1


title: Yeast extract - peptone (YP)_5d_rep2

value: 5 days


title: A_2 [20197_S20]


title: Yeast extract - peptone (YP)_5d_rep1


title: K_6 [20195_S18]

source_name: Macaca nemestrina infected with Kyasanur forest disease virus at day 6

value: Kyasanur forest disease virus


title: Yeast extract - peptone (YP)_2d_rep2

value: 2 days


title: Yeast extract - peptone (YP)_9d_rep1


title: K_2 [20194_S17]

source_name: Macaca nemestrina infected with Kyasanur forest disease virus at day 2


title: K_6 [20192_S15]


title: K_0 [20193_S16]

source_name: Macaca nemestrina infected with Kyasanur forest disease virus at day 0


title: Halofuginone, sample 4

city: New York

first: Jonathan

middle: W.

last: Snow

state: New York

address: 3009 Broadway

department: Biology

institute: Barnard College

description:
H4
PolyA enriched
C3vH4.csv

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The reads were then mapped to the A. mellifera reference genome available on NCBI using the STAR aligner.
The RNA-seq aligner is executed using a splice aligner, which detects splice junctions and incorporating them to help align the entire read sequences. BAM files were generated as a result of this step.
Gene hit counts were calculated using Feature counts from the Subread package.
After mapping and total gene hit counts calculation, the total gene hit counts table was used for downstream differential expression analysis using DESeq2 and groups were compared.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: *.csv: Comma-separated values, normalized read counts for paired samples.

organism: Apis mellifera

source_name: honey bee midgut

extract_protocol:
Midguts were removed, stored in RNAlater, and RNA was harvested using Trizol reagent. RNA was submitted to additional quality control analysis before mRNA was enriched by polyA selection.
Library preparation was performed using a NEBNext Ultra RNA library preparation kit. Sequencing was then performed using Illumina HiSeq platform.

treatment_protocol: Honey bees were fed sucrose solution containing 200 uM Halofuginone (0.5% DMSO) or 0.5% DMSO alone for 24 hours.

tag: tissue

value: midgut

value: 200 uM Halofuginone (0.5% DMSO) for 24 hours


title: Hei193 Nf18001 1uM 2days

city: BUSAN

first: Bum-Joon

last: Park

address: Busandaehak-ro 63

department: Molecular Biology

country: South Korea

institute: Pusan National University

description: Gene expression data from Nf18001 treated Hei193 cells. (1uM, 2day)

hyb_protocol: Following fragmentation, 50-500 ng of cRNA were hybridized on AffymetrixGeneChip® Human Gene 2.0 ST Array X 6. GeneChips were washed and stained in the Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix GeneChip® Command Console® Software (AGCC).

source_name: Hei193 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HEI-193 cells were cultured in liquid DEME medium containing 10% FBS and 1% antibiotics.

extract_protocol: Total cellular RNA was extracted using the Qiagen (Hilden, Germany) RNA extraction kit.

treatment_protocol: For Chemical treatment, Nf18001 (1, 2μΜ) or TEW7197(10 μΜ) was treated for 2 or 4 or 6 day in SF condition.

tag: cell

value: human vestibular schwannoma cells

value: 1 uM Nf18001 for 2 days


title: Hei193 TEW7197 10uM 6days

description: Gene expression data from TEW7197 treated Hei193 cells. (10uM, 6day)

value: 10uM TEW7197 for 6 days


title: Hei193 Nf18001 1uM 6days

description: Gene expression data from Nf18001 treated Hei193 cells. (1uM, 6day)

value: 1 uM Nf18001 for 6 days


title: Hei193 Nf18001 1uM 4days

description: Gene expression data from Nf18001 treated Hei193 cells. (1uM, 4day)

value: 1 uM Nf18001 for 4 days


title: Hei193 Control

description: Gene expression data from control Hei193 cells.

value: control


title: A549 siRNA

description:
A549 TET1 KD
9992580024_I


title: Hei193 Nf18001 2uM 6days

description: Gene expression data from Nf18001 treated Hei193 cells. (2uM, 6day)

value: 2 uM Nf18001 for 6 days


title: Halofuginone, sample 3

description:
H3
PolyA enriched
C2vH3.csv


title: A549 cells

description:
A549 parent cell line
9992580024_H


title: Yeast extract - peptone (YP)_2d_rep1


title: K_2 [20191_S14]

value: day 2


title: K_0 [20190_S13]

value: day 0


title: Halofuginone, sample 2

description:
H2
PolyA enriched
C1vH2.csv


title: Control (dmso), sample 3

description:
C3
PolyA enriched
C3vH4.csv

value: 0.5% DMSO alone for 24 hours


title: Control (dmso), sample 2

description:
C2
PolyA enriched
C2vH3.csv


title: Preteated PBD150 inhibitor before the addition LPS (4μg/ml) treatment biol rep 3 tech rep 1

city: Taipei

first: Chen

middle: Yi

last: Ling

address: 128 Academia Road, Section 2

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1104 control probes, spotted onto glass slides using a proprietary non-contact printing method.

hyb_protocol: HOA v4.3 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 600~630 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: The raw data were adjust by Rosetta Resolver® error model calculation. The statistic values were calculated after the replicated probes queezing and median scaling normalization.

source_name: U937 cell line (human histiocytic lymphoma cell)

label_protocol: 2.5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: The U937 cells were maintained at 2-3 × 106 cells/ml in a RPMI 1640 medium  supplemented with 10% FBS, the incubation time of the culture was 48 hours.

extract_protocol: RNA extraction by column based extraction kit (RiboPure-Blood, Ambion). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN>8).

treatment_protocol: Human macrophage cells were untreatment, LPS (4μg/ml) only, preteated PBD150 inhibitor (10μM) for 2 hrs before the addition LPS (4μg/ml) treatment, the incubation time of the culture was 48 hours.


title: K_0 [20187_S10]


title: Preteated PBD150 inhibitor before the addition LPS (4μg/ml) treatment biol rep 3 tech rep 3

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1106 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: K_6 [20189_S12]

value: day 6


title: Preteated PBD150 inhibitor before the addition LPS (4μg/ml) treatment biol rep 3 tech rep 2

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1105 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: K_2 [20188_S11]


title: Control (dmso), sample 1

description:
C1
PolyA enriched
C1vH2.csv


title: DKO+NAC mice lung sample T453.3

city: Salamanca

first: Eugenio

last: Santos

address: Campus Miguel de Unamuno

department: Instituto de Biología Celular y Molecular del Cáncer

country: Spain

institute: Universidad de Salamanca y CBERONC

description: Gene expression data from whole HRAS and NRAS-deficient lung extracts treated antenatally with N-acetyl cysteine.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data.

source_name: DKO Lung + NAC 4

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Animals were housed in type IIL individually ventilated cages, in a temperature- and humidity-controlled room with a 12h light/dark cycle, with food (Teklad 2014, Harlan Laboratories) and water available ad libitum.  All the lung samples were collected from postnatal day 0 mice.

extract_protocol: Manually selected lungs of Control, HRas-KO, NRas-KO and DKO from postnatal day 0 were used for RNA extraction using the TRIZOL protocol. RNA was further purified using Qiagen Rneasy mini kit. Each RNA sample for each microarray was obtained from one individual animal.

treatment_protocol: Pregnant females were treated throughout the pregnancy with 0.5% N-acetyl cysteine (NAC) pH 7.4 (Only in SAMPLES 15, 16 and 17)

tag: genotype/variation

value: DKO

value: Lung tissue obtained from postnatal day 0 mice

value: N-acetyl cysteine (NAC)


title: Preteated PBD150 inhibitor before the addition LPS (4μg/ml) treatment biol rep 2 tech rep 3

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1103 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: S72 [P15763_138]

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

data_processing:
NOT PROVIDED; REQUESTED
Genome_build: MesAur1.0.101
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mesocricetus auratus

source_name: Liver_HFD + MI_D2

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: 22 weeks

value: HFD + MI_D2


title: Preteated PBD150 inhibitor before the addition LPS (4μg/ml) treatment biol rep 1 tech rep 3

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1100 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: DKO+NAC mice lung sample T317.3

source_name: DKO Lung + NAC 2


title: Preteated PBD150 inhibitor before the addition LPS (4μg/ml) treatment biol rep 2 tech rep 1

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1101 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: DKO+NAC mice lung sample T195.2

source_name: DKO Lung + NAC 1


title: Preteated PBD150 inhibitor before the addition LPS (4μg/ml) treatment biol rep 2 tech rep 2

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1102 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: DKO+NAC mice lung sample T445.4

source_name: DKO Lung + NAC 3


title: DKO mice Lung sample  H797.2A

description: Gene expression data from whole HRAS and NRAS-deficient lung extracts.

source_name: DKO Lung 5


title: Preteated PBD150 inhibitor before the addition LPS (4μg/ml) treatment biol rep 1 tech rep 2

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1099 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: K_6 [20186_S9]

value: Kyasanur forest disease virus


title: S71 [P15763_137]


title: S70 [P15763_136]


title: only LPS (4μg/ml) treatment biol rep 3 tech rep 3

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1097 control probes, spotted onto glass slides using a proprietary non-contact printing method.

value: only LPS (4μg/ml)


title: DKO mice Lung sample  G186.1A

source_name: DKO Lung 4


title: only LPS (4μg/ml) treatment biol rep 3 tech rep 2

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1096 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: Preteated PBD150 inhibitor before the addition LPS (4μg/ml) treatment biol rep 1 tech rep 1

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1098 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: DKO mice Lung sample  G185.7A

source_name: DKO Lung 2