title: Human pleural mesothelioma cell line Meso163 CNV

city: Nantes

first: Jean-Francois

last: Fonteneau

address: 8 quai Moncousu BP70721

country: France

institute: INSERM

description: Hybridized to CytoscanHD

hyb_protocol: DNA (500 ng) was processed and hybridized to Affymetrix CytoScanHD Array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneChip Scanner 3000 7G

data_processing:
The detection, determination and visualization of gains, losses were performed using Affymetrix Chromosome Analysis Suite software (ChAS v3.1.1.27).
primary data description: Copy number variant using CN and SNP probe

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Human pleural mesothelioma were established from pleural effusions cells cultured in RPMI containing 10% heat-inactivated fetal calf serum, 100U/mL penicillin, 100μg/mL streptomycin and 2mM L-glutamine (all reagents from Gibco-Invitrogen) and cultured at 37°C in a 5% CO2 atmosphere.

extract_protocol: Genomic DNA was extracted with Nucleospin® Blood kit (Macherey-Nagel) according to the manufacturer's instructions.

value: pleural mesothelioma cell line


title: Ptpn2-2 sgRNA Sample 1 Rep 3 [T20DP_r3_C12]

status: Public on Jul 17 2019

type: SRA

city: Boston

first: Brian

middle: Christopher

last: Miller

state: MA

address: 77 Avenue Louis Pasteur

department: Immunology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Basecalls performed using Illumina NextSeq500 and converted to fastq files using Bcl2fastq
Fastq files trimmed for poor quality reads using Trimmomatic with the parameters LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:16
Trimmed Fastq files were aligned to the mouse genome mm10 using Bowtie2
Aligned reads aggregated to a gene count matrix using HTSeq
Count normalization and differential expression analysis performed using DESeq2 (quality filter: gene expression threshold of 100,000)
Genome_build: mm10
Supplementary_files_format_and_content: normalized count matrix, tab-delimited text

molecule: total RNA

organism: Mus musculus

source_name: Ptpn2-2 sgRNA Sample 1

growth_protocol: Antigen specific T cells (OT-1 specific for SIINFEKL peptide within OVA) were transferred to MC38-OVA tumors and allowed to respond and proliferate in response to the tumor for 7 days

extract_protocol:
Cells were sorted in pools of 500 cells into 25uL Qiagen RLT + 1%beta-mercaptoethanol (v/v) and frozen at -80C
Lysates were converted to cDNA following capture with Agencourt RNA Clean beads using the SmartSeq2 protocol as previously described (Trombetta et al, Curr Protoc Mol Biol, 2014)

tag: strain

tag: cell type

value: CD8+ T cells; tumor infiltrating T cells

tag: timepoint

value: Day 7


title: 677_N

type: RNA

city: London

first: Long

last: Hoang

address: Dovehouse Street

department: Genomic Medicine

country: United Kingdom

institute: Imperial College London

description: Global gene expression data for each extracted RNA sample was generated using Affymetrix Human Gene 1.1ST arrays and the GeneTitan system following Affymetrix protocols (Affymetrix, California, USA). Briefly taking 200ng of RNA amplified sense-strand complementary DNA (cDNA) was generated using the Ambion® WT Expression Kit (Life Technologies, California, USA).  This was then fragmented and labelled using the Affymetrix GeneChip® WT Terminal Labeling Kit (Affymetrix, California, USA) before hybridization onto the arrays and subsequent scanning on the GeneTitan system.  Poly-A RNA controls were included as per Affymetrix’s recommendations.

scan_protocol: GeneTitan system

data_processing: Quality of the expression data generated was assessed through arrayQualityMetrics (3.30.0) and the RLE (Relative Log Expression) and NUSE (Normalised Unscaled Standard Errors) metrics calculated within the Bioconductor package Oligo (1.38.0)

label: Biotin

organism: Homo sapiens

source_name: Normal Tissue

extract_protocol: Total RNA was extracted from tissues (stored in RNAlater) using the Qiagen RNeasy fibrous midi kit including the recommended homogenisation step with the Qiagen TissueRuptor® and disposable probes (Qiagen, Crawley, UK)

treatment_protocol: stored at -80°C

tag: age

tag: gender

tag: group

value: LUSC


title: 1008_N

hyb_protocol: hybridization onto the arrays and subsequent scanning on the GeneTitan system

label_protocol: 200ng of RNA amplified sense-strand complementary DNA (cDNA) was generated using the Ambion® WT Expression Kit (Life Technologies, California, USA).  This was then fragmented and labelled using the Affymetrix GeneChip® WT Terminal Labeling Kit (Affymetrix, California, USA)


title: 64_N


title: 965_T

source_name: Tumour

value: LUAD


title: Control-1 sgRNA Sample 1 Rep 1 [T19a8SP_r1_F11]

source_name: Control-1 sgRNA Sample 1


title: wt2_HA-TFIIS

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

library_source: genomic

data_processing:
Read file QC: Total reads were analysed with FastQC and visually inspected to make sure each sequenced sample met the adequate quality standards.
Adapter clipping, quality trimming and filtering: Fastx clipper and Fastx collapser were used to remove Illumina adapters, filter reads shorter than 20 bases, and discard the ones with more than 30 Ns.
Genome alignment: Filtered reads were mapped to the yeast genome with Bowtie2 (ChIP-seq) using the yeast R64 (sacCer3) genome as reference
Genome_build: R64 (sacCer3)
Supplementary_files_format_and_content: RPKM-normalised coverage bigWig tracks for the individual ChIP-seq datasets generated with the suite of Python tools deepTools.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Strains were grown at 30°C, with liquid cultures growing in an orbital shaking incubator at 180 rpm in YPD medium

extract_protocol:
The ChIP experiments were performed as previously described (Rodríguez-Gil et al., 2010), except that anti-Rpb3 (ab81859; Abcam) or anti-HA (3F10 Roche) antibodies and Sheep anti-Mouse or anti-Rat IgG Dynabeads (Invitrogen) were used.
Samples were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina, following the manufacturer's instructions.

tag: genotype/variation

value: WT

tag: chip antibody

value: anti-HA (3F10 Roche)

tag: molecule subtype

value: IP DNA


title: 983_T


title: 476_N


title: CD40L Treated 18h Rep.3

first: Benjamin

last: Gewurz

state: Massachusetts

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCh37.83
Supplementary_files_format_and_content: tab-delimited text files include Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj). Separate tab-delimited text files are also provided for raw counts and normalized counts of genes, respectively

molecule: polyA RNA

source_name: Blood

growth_protocol: Freshly isolated primary human B cells were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% fetal calf serum (FCS) and 10 mM HEPES in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
Total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: Primary B cells were treated either untreated or treated with CD40L at xxx ng/ml. At 1h and 18h, cells were collected and subject to total RNA extraction

value: Primary B cells

tag: treatment

value: CD40L Treated 18h


title: Human pleural mesothelioma cell line Meso225 CNV

type: genomic

description: Hybridized to CytoscanHD


title: 851_T


title: 954_N


title: Human pleural mesothelioma cell line Meso76 CNV

description: Hybridized to CytoscanHD


title: Human pleural mesothelioma cell line Meso96 CNV

description: Hybridized to CytoscanHD


title: 835_T


title: CD40L Treated 18h Rep.2


title: wt1_Rpb3

value: anti-Rpb3 (ab81859; Abcam)


title: Human pleural mesothelioma cell line Meso173 CNV

description: Hybridized to CytoscanHD


title: wt2_Rpb3


title: Human pleural mesothelioma cell line Meso61 CNV

description: Hybridized to CytoscanHD


title: CD40L Treated 18h Rep.1


title: Human pleural mesothelioma cell line Meso47 CNV

description: Hybridized to CytoscanHD


title: Untreated Rep.3

value: untreated


title: CD40L Treated 1h Rep.2

value: CD40L Treated 1h


title: CD40L Treated 1h Rep.1


title: Ptpn2-2 sgRNA Sample 1 Rep 2 [T20DP_r2_D11]


title: Human pleural mesothelioma cell line Meso45 CNV

description: Hybridized to CytoscanHD


title: Untreated Rep.2


title: Human pleural mesothelioma cell line Meso31 CNV

description: Hybridized to CytoscanHD


title: 677_T


title: rst1-3_rep1

city: Strasbourg

first: Heike

last: Lange

address: 12 Rue de général Zimmer

department: IBMP

institute: CNRS

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence with cutadapt v1.18, then mapped to TAIR10 reference genome using ShortStack v3.8.5 with parameters --mismatches 0 --mmap u --pad 75 --mincov 5 --dicermin 18 --dicermax 26
Reads of 21nt and 22nt falling in mRNA annotations were extracted for differential expression analysis (DEseq2)
Genome_build: TAIR10
Supplementary_files_format_and_content: table of raw counts of 21 and 22 siRNA

organism: Arabidopsis thaliana

source_name: small RNA libraries prepared from wildtype + six mutants, three biological replicates each

growth_protocol: all plants were grown on soil, 20°C, 3 weeks with 12h/12h  and 3 weeks with 16h/8h light/darkness.  For each genotype, three biological replicates were grown at different dates in different growth chambers. Closed flower buds from 4 plants/replicate were pooled and stored at -80°C

extract_protocol:
RNA was extracted with TRI-reagent (MRC) following the manufacturers instructions. After precipitation with 0.8 Vol isopropanol for 1-3 h at -80 °C, RNAs were collected by centrifugation (30 min 16000 x g, 4 °C), washed twice with 70% EtOH, resupended in water and further purified by adding 1 Vol of Phenol:Chloroform:Isoaylalkohol (25:24:1). The aqueaous phase was transferred in a fresh tube, RNAs were precipitated over night with 2.5 Vol of EtOH at -80 °C, collected by centrifugation, washed twice with 70 % EtOH and resupended in water to approx. 2,5 µg/µl.
Libraries were prepared from 1 µg of total RNA using the NEB Next Multiplex Small RNA Library Prep Set for Illumina (NEB #E7300S and #E7580S) following the manufacturer’s instructions. After ligation of primers, cDNA synthesis and PCR amplification, pooled libraries were loaded on a NOVEX 6% polyacrylamide gel with 100 mM Tris, 100 mM Borate, 2 mM EDTA. Five fractions corresponding to 130-180 nt products were excised and eluted over night in water. After EtOH precipitation, size and concentration of the fractions were checked with an Agilent 2100 Bioanalyzer (Agilent Technologies). The fraction of 140-150 nt containing the 21-22 nt small RNAs of interest was sequenced on a HiSeq 4000 sequencer (single-end mode 1x50bp).

tag: tissue

value: flower buds

tag: genotype


title: 954_T


title: rst1-2_rep3


title: rst1-3_rep2


title: Human pleural mesothelioma cell line Meso11 CNV

description: Hybridized to CytoscanHD


title: rst1-3_rep3


title: Human pleural mesothelioma cell line Meso13 CNV

description: Hybridized to CytoscanHD


title: 64_T


title: Porcine ovarian granulosa cells at 144h of culture 1

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

description: Gene expression data from porcine ovarian granulosa cells at 144h of culture

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to the Affymetrix® Porcine Gene 1.1 ST Array Strip (48°C/20 h). Microarrays were then washed and stained according to the technical protocol using the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: The array strips were scanned employing Imaging Station of the GeneAtlas System.

data_processing: Obtained cell files were submied to bioconductor and R programing lenguage. Each CEL file was merged with a description file.  In order to correct background, normalize, and summarize results, we used the Robust Multiarray Averaging (RMA) algorithm.

label: biotin

organism: Sus scrofa domesticus

source_name: Crossbred Landrace gilts with a median age of 170 days and weight of 98 kg

label_protocol: Biotin labeling and fragmentation were performed by Affymetrix GeneChip® WT Terminal Labeling and Hybridization (Affymetrix).

growth_protocol: A total of 43 crossbred Landrace gilts with a median age of 170 days and weight of 98 kg were used in this study. All animals were housed under identical conditions.

extract_protocol: For reverse transcription, 1 µg of each RNA sample was used. Reverse transcription was based on the protocols and reagents of SABiosciences (RT2 First Stand Kit - 330401), using a Veritimer 96 well Thermal Cycler. Real-time PCR was performed using the Light Cycler® 96 (Roche Diagnostic GmbH, Germany), RT2 SYBR® Green ROXTM qPCR Master Mix (Qiagen Sciences, Maryland, USA)

treatment_protocol: GCs was washed twice using Dulbecco’s Phosphate Buffered Saline  (DPBS, Sigma-Aldrich, USA), and centrifugation at 200 x g for 10 min at RT. The culture medium consisted of Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma-Aldrich, USA), 2% fetal bovine serum FBS (FBS; Sigma-Aldrich Co., St. Louis, MO, USA), 4 mM L-glutamine (stock 200 mM, Invitrogen, USA), 10 mg/mL gentamicin (Invitrogen, USA), 10,000 units/mL penicillin, and 10,000 μg/mL streptomycin (Invitrogen, USA). GCs were cultivated at 37° C under aerobic conditions (5% CO2). GCs were cultivated for 30 days; total RNA was isolated after 0h, 48h, 96h and 144h of culture.

value: Porcine ovarian granulosa

tag: breed

value: Landrace gilts

tag: time point


title: CD40L Treated 1h Rep.3


title: Porcine ovarian granulosa cells at 144h of culture 2


title: Human pleural mesothelioma cell line Meso4 CNV

description: Hybridized to CytoscanHD


title: 1008_T


title: 476_T


title: cyto_24h_1

city: Kuopio

first: Mikko

middle: P

last: Turunen

address: Yliopistonranta 1 E

department: A. I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalling and demultiplexing were performed using the bcl2fastq Conversion Software from Illumina (service from Exiqon A/S, Vedbaek, Denmark).
Trim FastQ files using Trimmomatic (service from Exiqon A/S, Vedbaek, Denmark)
Align to reference genome Bowtie2 version 2.1.0, parameters  min_length 15, max_length 51, n_ceil “L,0,0.15”, iterations @adapter.length+1, seed mismatch 1 (service from Exiqon A/S, Vedbaek, Denmark)
Differential expression and data normalization was performed using DESeq2
Genome_build: miRBase v20 (GRCm38/mm10)
Supplementary_files_format_and_content: bam files were generated by Exiqon A/S, Vedbaek, Denmark and further processed to xlsx file by authors

source_name: Endothelial cell line

growth_protocol: C166 cells were grown on 150 mm cell culture dish in DMEM containing 10 % FBS and 1 % penicillin-streptomycin. Cells were split for experiments two days prior treatment so that they reach 80% confluency at the time of treatment.

extract_protocol:
Cells were fractionated into nuclear and cytoplasmic fractions and RNA isolated according to a protocol by Gagnon et al. (Gagnon K, Li L, Janowski BA, Corey DR. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nature Protocols 2014, vol. 9, no. 9, p.2045-60).
Library was prepared using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit (service from Exiqon A/S, Vedbaek, Denmark).

treatment_protocol: Cells were treated with hypoxia (2h or 24h) or normoxia (control). Hypoxia treatment was done using 1 % oxygen (InvivO2 Baker Ruskinn hypoxia chamber). Normoxia (control) cells were grown in normal humidified incubator (atmospheric oxygen levels, +37 °C, 5 % CO2).

value: Yolk sac -derived endothelial cell line

tag: cell line

value: Cytoplasmic RNA


title: skin_CL21

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

description:
Amorim_GEO_raw.txt
Amorim_GEO_normalized.txt
studydesign.csv

data_processing:
Raw reads from fastq files were mapped to the human reference transcriptome (Ensembl; Homo sapiens version 86) using Kallisto, version 0.44.0
All subsequent analyses were carried out using the statistical computing environment, R version 3.5.1 in RStudio version 1.1.456 and Bioconductor, version 3.8
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package
Differentially expressed genes (³2-fold and £1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Data was normalized using the TMM method in EdgeR
Normalized data was variance stabilized using the VOOM function in limma
Genome_build: Ensembl; Homo sapiens version 86
Supplementary_files_format_and_content:  [Amorim_GEO_raw.txt]  Tab-delimited text raw data includes raw gene counts summarized by tximport package
Supplementary_files_format_and_content:  [Amorim_GEO_normalized.txt]  Tab-delimited text normalized data includes gene expression for each sample after normalization with EdgeR package (TMM method)
Supplementary_files_format_and_content:  [studydesign.csv]  Comma-separated values file with study design including healthy subjects and cutaneous leishmaniasis patients clinical metadata

source_name: cutaneous leishmaniasis lesion

growth_protocol: 4mm biopsies were stored in RNAlater in -80 until sample processing

extract_protocol:
RNA was extracted from 20-30 mg of skin lesion using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer instructions.
RNA was used to prepare sequence-ready libraries using the Illumina TruSeq Total Transcriptome kit with RiboZero Gold rRNA depletion (Illumina)
[sample quality control]  Quality assessment and quantification of RNA preparations and libraries was carried out using an Agilent Tapestation 4200 and Qubit 3, respectively

tag: subject

value: cutaneous leishmaniasis patient

tag: infection

value: Leishmania braziliensis

value: cure

tag: Sex

value: M

tag: lesion size (mm^3)

tag: dth (mm^3)

tag: number of parasite transcripts (rna-seq)

tag: number of parasites (qpcr)

tag: time to cure (days)

value: skin lesion


title: Porcine ovarian granulosa cells at 96h of culture 2

description: Gene expression data from porcine ovarian granulosa cells at 96h of culture


title: rst1-2_rep2


title: Porcine ovarian granulosa cells at 48h of culture 1

description: Gene expression data from porcine ovarian granulosa cells at 48h of culture


title: Porcine ovarian granulosa cells at 48h of culture 2


title: Porcine ovarian granulosa cells at 0h of culture 1

description: Gene expression data from porcine ovarian granulosa cells at 0h of culture


title: rst1-2_rep1


title: Porcine ovarian granulosa cells at 96h of culture 1


title: 6bKO ATAC-seq 3

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

institute: Washington University School of Medicine

data_processing:
For ATAC-seq, reads were processed with an in-house pipeline for QC.  Cutadapt version 1.16 was used to trim reads
For ATAC-seq, reads were aliegned to mm10 with bwa version 0.7.16a
For ATAC-seq, quantification was performed with methylQA v 0.2.1 with paramaters methylQA atac
For ATAC-seq, peaks were called using macs2 with paramaters callpeak, q=0.01, --keep-dup 1000 --nomodel --shift 0 --extsize 150
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for ATA0seq 6bKO

source_name: Hematopoietic Stem Cell

extract_protocol:
1.0x104 HSCs were sorted into PBS+10% FBS, lyzed in ATAC-RSB buffer for 3-minutes, and then tagmented for 30-minutes at 37°C using the Nextera TD/Transposase
NebNext with custom primers was used for library amplification of the ATAC DNA (12-14 cycles of PCR as determined by qPCR).  Libraries were again purified with Ampure XP beads and run on an Illumina Hiseq 3000 (PE2X150).

tag: strain

value: Wild-type

tag: age

tag: cre-driver

value: Vav

tag: cell type

value: Hematopoietic stem cell


title: skin_CL19

tag: tissue


title: 6bKO ATAC-seq 1

tag: genotype


title: riprT_rep2

value: riprT


title: Control ATAC-seq 3


title: skin_CL18

value: failure


title: 6bKO ATAC-seq 2


title: Untreated Rep.1

value: Primary B cells

tag: treatment

value: untreated


title: AP2-G SCC gametocytes input, rep 1

city: University Park

first: Manuel

last: Llinas

address: Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Read were trimmed using Trimmomatic 0.32.3.
Reads were mapped to the P. falciparum 3D7 genome (Pf 3D7 v28, obtained from PlasmoDB) using BWA-MEM 0.4.1.
Duplicate reads were removed using samtools 1.1.2.
MACS2 (version 2.1.1.20160309) was used to call peaks with a q value cutoff of 0.01.
Genome_build: Pf 3D7 v28
Supplementary_files_format_and_content: Bam files were converted to bigwig files using bamCoverage from the deeptools suite  3.1.2.0.0.

organism: Plasmodium falciparum

source_name: AP2-G SCC gametocytes input

growth_protocol: Parasites were cultured at 37°C in the presence of 5% oxygen and 7% carbon dioxide, in RPMI 1640 media supplemented with hypoxanthine, 0.5% Albumax II (Invitrogen), and 2.5 nM WR99210

extract_protocol:
ChIP was performed as previously described (PMID:28618269) with minor modifications. Shld1 was added to AP2-G-DD cultures at 24 hpi or 6 hpi to stabilize AP2-G and nuclei were harvested 60 (stage I gametocytes) hours later following sorbitol treatment to remove trophozoites and schizonts.  Crosslinked nuclei were then resuspended in Covaris shearing buffer (0.1% SDS, 10 mM Tris pH 8.1, 1 mM EDTA) and sonicated using an M220 ultrasonicator (Covaris) and the following conditions: 5% duty cycle, 75 W peak incident power, 200 cycles per burst, treatment time 300 seconds.  The sonicated chromatin was diluted ten-fold with dilution buffer and precleared with Protein A/G magnetic beads (Pierce) for two hours. The pre-cleared material was then incubated with antibody and magnetic beads overnight, with a small volume of non-immunoprecipitated input material kept separately. For immunoprecipitations with AP2-G-DD, rat α HA (Roche 3F10) was used. The next day, beads were washed and the bound DNA eluted in elution buffer. Crosslinking was reversed by incubating overnight at 45°C and DNA was subsequently treated with RNase A at 37° for 30 minutes and Proteinase K at 45° for two hours. DNA was purified the Qiagen MinElute kit and quantified using the Qubit HS DNA assay.
Barcoded libraries for Illumina TruSeq single-end sequencing were constructed using NEBNext DNA library Prep reagents (New England Biolabs) by following the standard Illumina library preparation protocol. The DNA was first end-repaired for 30 min at 20°C, purified using Agencourt AMPure XP beads (Beckman Coulter) and then dA-tailed for 30 min at 37°C, and purified using Ampure XP beads. NEXTflex Illumina DNA barcodes (diluted 1/10) were then ligated to the DNA fragments using T4 DNA ligase at 20°C for 15 min. The resulting DNA was then size selected for 250 bp inserts using Ampure XP beads PCR-amplified (12 cycles) using Kapa HiFi (Kapa biosystems) and purified using AMPure XP beads.

treatment_protocol: 0.5 μM Shld1 was added at 24 hpi (trophozoites) or 6 hpi (early rings) the following cycle to stabilise the AP2-G-DD protein for NCC and SCC, respectively.

tag: Stage

value: Stage I gametocytes (SCC)

tag: chip antibody


title: AP2-G SCC gametocytes anti HA, rep 2

source_name: AP2-G SCC gametocytes anti HA

value: HA (Roche 3F10)


title: AP2-G SCC gametocytes input, rep 2


title: AP2-G NCC gametocytes input, rep 2

source_name: AP2-G NCC gametocytes input

value: Stage I gametocytes (NCC)


title: riprT_rep3

value: flower buds


title: skin_CL17

tag: subject


title: riprC_rep3

value: riprC


title: riprT_rep1


title: skin_CL16

value: cutaneous leishmaniasis patient

tag: infection


title: skin_CL20

value: Leishmania braziliensis

tag: Sex

value: F


title: riprC_rep2


title: Porcine ovarian granulosa cells at 0h of culture 2

value: Porcine ovarian granulosa

tag: breed

value: Landrace gilts

tag: time point


title: skin_CL15

value: M

tag: lesion size (mm^3)

tag: dth (mm^3)

tag: number of parasite transcripts (rna-seq)

value: skin lesion


title: Input

data_processing:
For ChIP-seq reads were aligned to the mm10 using Bowtie2 v1.2.1.1
For ChIP-seq peak calling was performed with hiddenDomains v3.0
ChIPQC v3.6 was used for QC
supplementary_files_format_and_content: bigWig files for H3K27me3 and H3K4me3
Genome_build: mm10

extract_protocol:
1.0x104 HSCs were sorted into PBS+10% FBS, and then crosslinked at room temperature for 8 minutes using 1% paraformaldehyde (VWR #J531).  Chromatin was sheared using a Covaris E220 Focused-ultrasonicator until the DNA fragments were between 200 – 700 base pairs.  Chromatin samples were incubated overnight at 4°C with either the H3K27me3 antibody (Diagenode # pAb-195-050) or the H3K4me3 antibody (Diagenode #pAb-003-050).  Following overnight incubation, protein G dynabeads (Life Technologies #130-099-508) were added for 2-hours at 4°C.  The beads were washed, and tagmented for 10-minutes at 37°C using the Nextera DNA Library Preperation Kit (Illumina #FC-121-1030).  After additional washes, an overnight decrosslinking was performed immunoprecipiated DNA was isolated using Ampure XP beads
2xKapa HiFi HotStart Ready Mix (Kapa #KB KK2601), along with Nextera custom primers, was used for library amplification of the ChIP DNA(12 cycles of PCR as determined by qPCR).  Libraries were again purified with Ampure XP beads and run on an Illumina Hiseq 3000 (PE2X150).

tag: strain

value: Wild-type

value: Vav

value: Hematopoietic stem cell


title: riprC_rep1


title: AP2-G NCC gametocytes anti HA, rep 1

source_name: AP2-G NCC gametocytes anti HA


title: 6bKO H3K4me3-ChIP 1

tag: age

value: H3K4me3 (Diagenode #pAb-003-050)


title: skin_CL14

value: cure

tag: number of parasites (qpcr)

tag: time to cure (days)


title: col0_rep2

tag: tissue


title: skin_CL13


title: col0_rep3

tag: genotype


title: skin_CL12


title: Control ATAC-seq 2

tag: cre-driver

tag: cell type


title: Control H3K4me3-ChIP 1

tag: chip antibody


title: Control H3K4me3-ChIP 2


title: skin_CL11

tag: subject

value: failure


title: 6bKO H3K27me3-ChIP 2

value: H3K27me3 (Diagenode #pAb-069-050)


title: cer7-sail_rep3


title: col0_rep1


title: AP2-G NCC gametocytes anti HA, rep 2

tag: Stage

value: Stage I gametocytes (NCC)

value: HA (Roche 3F10)


title: skin_CL10

tag: infection

tag: Sex


title: 6bKO H3K27me3-ChIP 1


title: AP2-G NCC gametocytes input, rep 1


title: cer7-sail_rep1

value: flower buds


title: skin_CL9

value: cutaneous leishmaniasis patient


title: Control H3K27me3-ChIP 2


title: cer7-gabi_rep3


title: cer7-gabi_rep2


title: skin_CL8

value: Leishmania braziliensis


title: skin_CL7

value: F


title: cer7-gabi_rep1


title: skin_CL6


title: 6bKO RNA-seq 2

data_processing:
For RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4
For RNA-seq gene counts were derived with Subread:featureCount v1.4.5 as well as htseq-count v0.8.0
For RNA-seq QC was performed with RSeQC v2.3
For RNA-seq quantification and normalization of gene RPKM was performed using Partek Genomics Suite Software version 6.6
supplementary_files_format_and_content: tab-delimited file with raw gene counts
Genome_build: mm10

extract_protocol:
For RNA-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-) were sorted from a pooled sample of 3 male and 3 female 8-week old miceHSCs were purified from three biological replicates (composed of pooled WBM from three male and three female mice) of either Vav-CRE:Kdm6b+/+ or Vav-CRE:Kdm6bfl/fl mice.  Total RNA was isolated from the samples using the NucleoSpin RNA XS kit
The SMARTer Ultra Low RNA kit (Clontech) was used to prepare the libraries from 3-5ng of total RNA.


title: 6bKO RNA-seq 3


title: skin_CL5


title: MM progressed from paired sample 6

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: active MM

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

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

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure.  The custom CDF GENECODEG version 22 was used from BrainArray.

source_name: Highly purified PCs from MM patient

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100 nanograms of total RNA, according to the Affymetrix WT Plus Expression Protocol.

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

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

value: Bone marrow

value: plasma cells

tag: patient diagnosis

value: active MM


title: 6bKO RNA-seq 1


title: SMM at diagnosis, sample 7

description: progressed SMM

value: progressed SMM


title: SMM at diagnosis, non-progressed sample 12

description: non-progressed SMM

value: non-progressed SMM


title: skin_CL4

value: M

tag: lesion size (mm^3)

value: skin lesion


title: Control RNA-seq 3

value: Wild-type

value: Vav

value: Hematopoietic stem cell


title: Comb_NA-07-Zefi8-BloodR-SAL-3_S7

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
Raw sequences were mapped to the Taeniopygia guttata genome assembly (Tg.fa) using tophat2 v2.0.13 generating alignments in bam format, using an Ensembl gene and transcript gtf as a guide.
Mapped reads were assembled according to the Ensembl taeGut3.2.4.84.gtf file using cufflinks v2.2.1.
The resulting mapped files from cufflinks were normalized and concatenated into a single tab-delimited gene matrix file using cuffnorm.
Differentially expressed genes were identified using cuffdiff v2.2.1.
Genome_build: taeGut3
Supplementary_files_format_and_content: FPKM

organism: Taeniopygia guttata

source_name: RBC/Saline

extract_protocol:
Birds were euthanized at 2 h post-injection and tissue samples collected. Red blood cells were extracted from the trunk.The density gradient media Polymorphprep (Axis-Shield) was used to separate whole blood into the components of plasma, mononuclear white blood cells, polymorphonuclear white blood cells, and red blood cells. This media allowed the removal of polymorphonuclear white blood cells that would remain within the red blood cell layer by other separation methods. Total RNA was isolated using an RNeasy Kit (Qiagen) with a modified protocol involving Trizol (Life Technologies).
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit; Clonetech Catalog# 634889 and Nextera XT DNA; Illumina Catalog# FC-131-1024

treatment_protocol: For hypothalamus and spleen samples, four birds from the from the captive colony at Western Kentucky University were injected i.p. with bacterial lipopolysaccharide (Escherichia coli) at a dose of 2 mg/kg BW. An additional four birds served as controls, and were injected with vehicle (0.9% saline). For red blood cell samples, six male zebra finch from the captive colony were injected i.p. with bacterial lipopolysaccharide (Escherichia coli) at a dose of 2mg/kg BW (dissolved in 0.9% saline). An additional six males served as controls injected with vehicle (0.9% saline).

tag: agent

value: 0.9 percent saline

tag: time point

value: 2 hours post-injection

value: red blood cells (trunk)


title: Comb_NA-06-Zefi4-BloodR-SAL-2_S6


title: Comb_NA-08-Zefi14-BloodR-SAL-4_S8


title: Control H3K27me3-ChIP 1

tag: strain

value: H3K27me3 (Diagenode #pAb-069-050)


title: Control RNA-seq 2

tag: age


title: Comb_NA-05-Zefi2-BloodR-SAL-1_S5


title: MM progressed from paired sample 8

description: active MM


title: skin_CL3

value: cutaneous leishmaniasis patient

value: failure

tag: dth (mm^3)

tag: number of parasite transcripts (rna-seq)

tag: number of parasites (qpcr)


title: SMM at diagnosis, non-progressed sample 11

description: non-progressed SMM

tag: tissue


title: SMM at diagnosis, non-progressed sample 10

description: non-progressed SMM


title: MM progressed from paired sample 4

description: active MM


title: Control ATAC-seq 1

tag: genotype

tag: cre-driver


title: skin_CL2

value: Leishmania braziliensis

tag: time to cure (days)


title: SMM at diagnosis, non-progressed sample 8

description: non-progressed SMM

value: Bone marrow

tag: cell type


title: Control RNA-seq 1


title: SMM at diagnosis, non-progressed sample 9

description: non-progressed SMM

value: plasma cells


title: SMM at diagnosis, non-progressed sample 6

description: non-progressed SMM


title: SMM at diagnosis, non-progressed sample 7

description: non-progressed SMM


title: Comb_NA-03-Zefi7-BloodR-LPS-3_S3

source_name: RBC/LPS

value: bacterial LPS (E. coli) at a dose of 2 mg/kg BW


title: skin_HS7

source_name: healthy skin

tag: subject

value: not-infected subject

value: not-infected

value: skin


title: MM progressed from paired sample 3

description: active MM

value: active MM


title: skin_CL1

tag: infection

value: F

value: skin lesion


title: SMM at diagnosis, sample 6

description: progressed SMM

value: progressed SMM


title: KO6

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

description: RNA was purified using Rneasy Fibrous Tissue Kit

hyb_protocol: The reaction mixes were loaded onto the Nanostring nCounter Prep Station for binding and wahing.

scan_protocol: The resulting cartridge was transferred to the Nanostring nCounter digital analyzer for scanning

data_processing: The data collection was done by Nanostring nCounter digital analyzer. Quantified expression data were analyzed using Nanostring nSolver Analysis software v2.0. Data were normalized by scaling with the geometric mean of built-in control gene probes for each sample.

source_name: Pan-cancer immune profiling in Siah2 KO6

label_protocol: For each Nanostring assay, an aliquot of 100ng RNA was mixed with a Nanostring code set mix and incubated at 65 C for overnight (16hr).

growth_protocol: YUMMER 1.7 cells wer cultured in DMEM media supplemented with 10% FBS and Amp/Pen.

extract_protocol: RNA from tumors was purified using Rneasy Fibrous Tissue Kit.Purity and concentration of extracted RNA were checked and quantified by reading at 260 and 280 nm in a NanoDrop spectrophotometer (Thermo Fisher)

treatment_protocol: YUMMER1.7 tumor cells were injected into WT or Siah2-/- mice.The tumor were collected at day 11 after injection.

tag: genotype/variation

value: Siah2 KO

value: melanoma


title: Comb_NA-01-Zefi1-BloodR-LPS-1_S1

value: 2 hours post-injection

value: red blood cells (trunk)


title: Comb_NA-02-Zefi3-BloodR-LPS-2_S2


title: KO5

source_name: Pan-cancer immune profiling in Siah2 KO5


title: skin_HS5

tag: Sex


title: skin_HS4

tag: lesion size (mm^3)


title: Comb_NA-04-Zefi13-BloodR-LPS-4_S4

tag: agent


title: KO3

source_name: Pan-cancer immune profiling in Siah2 KO3


title: skin_HS6


title: NA-15-7-LPS-SPL_S15

source_name: Spleen/LPS

tag: time point

value: spleen


title: skin_HS3


title: NA-16-8-LPS-SPL_S16


title: AP2-G SCC gametocytes anti HA, rep 1

tag: strain

tag: Stage

value: Stage I gametocytes (SCC)

tag: chip antibody

value: HA (Roche 3F10)


title: KO2

source_name: Pan-cancer immune profiling in Siah2 KO2


title: NA-14-6-LPS-SPL_S14


title: skin_HS2

tag: age

tag: dth (mm^3)

tag: number of parasite transcripts (rna-seq)


title: KO1

source_name: Pan-cancer immune profiling in Siah2 KO1

tag: tissue


title: WT6

source_name: Pan-cancer immune profiling in Siah2 WT6

value: Siah2 WT


title: skin_HS1

tag: number of parasites (qpcr)


title: WT5

source_name: Pan-cancer immune profiling in Siah2 WT5


title: NA-12-4-SAL-SPL_S12

source_name: Spleen/Saline

value: 0.9 percent saline


title: WT4

source_name: Pan-cancer immune profiling in Siah2 WT4


title: SMM at diagnosis, non-progressed sample 5

description: non-progressed SMM

value: Bone marrow

value: plasma cells

tag: patient diagnosis

value: non-progressed SMM


title: SMM at diagnosis, sample 3

description: progressed SMM

tag: cell type


title: WT3

source_name: Pan-cancer immune profiling in Siah2 WT3


title: NA-11-3-SAL-SPL_S11


title: MM progressed from paired sample 1

description: active MM


title: MM progressed from paired sample 2

description: active MM


title: SMM at diagnosis, sample 1

description: progressed SMM


title: DAPT1

city: Providence

first: Gary

last: Wessel

state: RI

address: 185 Meeting St

department: Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

description: Single-cell mRNA

data_processing:
The Cell Ranger Single Cell Software Suite 2.1.0 was used to perform single cells demultiplexing and UMI counting.The custom transcriptome reference was generated from assembly Spur_4.2 using CellRanger. Cells that have at least 400 or at most 2,500 genes detected were included in the downstream analysis using Seurat 2.3.0. The union of the top 1,000 highest dispersion genes from the compared datasets were selected for the alignment. T‐SNE projection and clustering analysis (dims = 1:20 and resolution = 0.5) were performed using Seurat. Markers were found using FindConservedMarkers and FindMarkers functions.
Genome_build: Spur_4.2
Supplementary_files_format_and_content: tab-delimited text files include matrices that contain UMI-corrected counts for each cell

organism: Strongylocentrotus purpuratus

extract_protocol: The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v2 chemistry and cells were loaded on a GemCode Single Cell Instrument (10× Genomics, Pleasanton, CA). Approximately 5,000 single cells were targeted from each sample. Libraries were sequenced on Illumina HiSeq 2,500 with the custom configuration of read 1 (26 bp) and read 2 (98 bp), i7 index (8 bp) and i5 index (0 bp)

treatment_protocol: Adult S. purpuratus were obtained from South Coast Bio‐Marine info@scbiomarine.com and were spawned using 0.5 M KCl injections intracoelomically. DAPT (Tocris) was added at fertilization to 8 μM, a concentration previously determined to effectively perturb Delta/Notch signaling without affecting overall development (Materna & Davidson, 2012). C59 (Cellagen) was added at 0.5 μM at fertilization as previously described (Cui et al., 2014). Embryos were cultured and, at appropriate developmental stages, were dissociated into single cells as described (McClay, 2004). We started with 50 ml cultures containing 0.25% of embryos (125 ul of embryos in 50 ml). The full volume was dissociated into single cells. We obtained 12 million single cells from which 5,000 were used for the DropSeq. Briefly, embryos were washed 2× in calcium‐free seawater (CaFSW; 4°C) by gentle centrifugation (500g), and then resuspended in hyaline extraction media (HEM; 4°C) containing 1 mM EGTA. Note: do not use EDTA since some of the early steps in the 10× protocol use enzymes that rely on magnesium for function. The embryos in HEM were inverted every few minutes while remaining at 4°C and monitored for an indication of loss of adhesion (the cells transition from a cuboidal or squamous epithelium to a rounded morphology). At that point, the embryos are washed 1× with CaFSW (4°C) and replaced with 0.5 M NaCl and dissociated by several passes through a loose fitting Dounce homogenizer. Gentle shear force is sufficient to achieve near complete dissociation with no detectable lysis. The cell suspension is then passed through a 40 uM Nitex filter to remove undissociated embryos, counted on a haemocytometer (see Figure S5), and then diluted into an appropriate concentration of 0.5 M NaCl (4°C) for the 10× protocol.

tag: developmental stage

value: adult

tag: treatment

value: DAPT


title: MM progressed from paired sample 5

description: active MM

value: active MM


title: MM progressed from paired sample 9

description: active MM


title: W1

description: Single-cell mRNA


title: NA-10-2-SAL-SPL_S10


title: WT2

source_name: Pan-cancer immune profiling in Siah2 WT2

tag: genotype/variation


title: SMM at diagnosis, sample 8

description: progressed SMM


title: NA-13-5-LPS-SPL_S13

value: bacterial LPS (E. coli) at a dose of 2 mg/kg BW


title: NA-08-8-LPS-HYP_S8

source_name: Hypothalamus/LPS

value: hypothalamus


title: NA-09-1-SAL-SPL_S9


title: DMSO1

description: Single-cell mRNA

value: DMSO


title: NA-07-7-LPS-HYP_S7


title: SMM at diagnosis, non-progressed sample 4

description: non-progressed SMM

source_name: Highly purified PCs from MM patient


title: MM progressed from paired sample 7

description: active MM


title: FC-2

city: Milwaukee

first: Sarah

last: Logan

state: Wisconsin

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: Gene expression throughout differentiation process

hyb_protocol: labeled cRNAs were hybridized onto the human LncRNA Array v3.0 (8 x 60K, Arraystar)

scan_protocol: arrays were scanned by the Agilent Scanner G2505C.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, mRNAs that at least 2 out of 8 samples have flags in Present or Marginal (“All Targets Value - mRNAs”) were chosen for differentially expressed mRNAs screening

source_name: brain

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar

growth_protocol: iPSCs were differentiated into cerebral organoids following the Lancaster (2013) protocol

extract_protocol: After cerebral organoids were lysed in the QIAzol lysis reagent (Qiagen Inc., Valencia, CA), chloroform was thoroughly mixed with the samples, set for 5 minutes before centrifuged.  Supernatants were transferred into a new tube and mixed with isopropanol and centrifuged again for pellets. After washed with 75% ethanol for one time, the pellets were dried and dissolved in RNase free water. The quantity and purity of RNA were validated using a Nanodrop spectrophotometer (Thermo scientific).

treatment_protocol: iPSCs, 1 month, and 2 month cerebral organoids were lysed at the respective time points without treatment besides the normal diferentiation protocol

value: fetal brain tissue


title: NA-06-6-LPS-HYP_S6

value: 2 hours post-injection


title: NA-05-LPS-HYP_S5


title: SMM at diagnosis, sample 4

description: progressed SMM

value: progressed SMM


title: FT-2-2


title: old/high-fat diet Ad-MSCs-1

city: Kyoto

first: Taichiro

last: Nishikawa

address: 465 Kajii-cho, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

description: Gene expression in Ad-MSCs

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60˚C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarry 8x60K Ver. 2.0 (G4858A #74809, Agilent Technologies) for 17 hours at 65˚C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37˚C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: adipose tissue derived mesenchymal stem cells, 24w, high-fat diet, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Abdominal subcutaneous adipose tissue was obtained from each mice. Minced tissues were digested in Hanks’ balanced salt solution containing 0.2 % collagenase D (Roche Diagnostics K.K., Tokyo, Japan) at 37°C for 1 h in a shaking incubator. The solution then was separated into two phases by centrifugation at 400xg. Erythrocytes were eliminated by suspending the pellet in erythrocyte lysis solution (0.16 M NH4Cl). After passing through a 40 µm mesh filter into a new tube, the cells were suspended in a Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum, seeded on uncoated culture plates at 10^6 cells/25 cm2, and maintained at 37 degree in 5% CO2. The adherent cells were cultured and harvested at 70–80 % confluence. Two or three passages were conducted to achieve a morphologically homogenous cell population, then the cells were used as adipose tissue derived mesenchymal stem cells.

treatment_protocol: Six-week-old male C57BL/6 mice were fed control chow (C) or high-fat diet (60% fat; HF) for 12 or 24 weeks.

value: Six-week-old

tag: Sex

value: male

value: subcutaneous fat tissue

tag: cell

value: mesenchymal stem cells

tag: gender

tag: diet

value: high-fat diet

tag: period


title: FT-1-1


title: NA-04-4-SAL-HYP_S4

source_name: Hypothalamus/Saline

tag: agent

value: 0.9 percent saline

tag: time point


title: SMM at diagnosis, non-progressed sample 3

description: non-progressed SMM

value: Bone marrow

value: plasma cells


title: old/high-fat diet Ad-MSCs-2

description: Gene expression in Ad-MSCs

source_name: adipose tissue derived mesenchymal stem cells, 24w, high-fat diet, replicate 2

tag: age

tag: strain


title: NA-02-2-SAL-HYP_S2


title: old/control Ad-MSCs-2

description: Gene expression in Ad-MSCs

source_name: adipose tissue derived mesenchymal stem cells, 24w, control diet, replicate 2

value: control chow


title: AB-1

value: adult brain tissue


title: AT-3


title: CO2-3

source_name: iPSC-derived cerebral organoid

value: cerebral organoid


title: young/high-fat diet Ad-MSCs-2

description: Gene expression in Ad-MSCs

source_name: adipose tissue derived mesenchymal stem cells, 12w, high-fat diet, replicate 2


title: NA-03-3-SAL-HYP_S3


title: SMM at diagnosis, sample 5

description: progressed SMM


title: SMM at diagnosis, sample 9

description: progressed SMM


title: young/control Ad-MSCs-2

description: Gene expression in Ad-MSCs

source_name: adipose tissue derived mesenchymal stem cells, 12w, control diet, replicate 2


title: NA-01-1-SAL-HYP_S1


title: MM progressed from paired sample 10

description: active MM

value: active MM


title: SMM at diagnosis, sample 2

description: progressed SMM


title: young/high-fat diet Ad-MSCs-1

description: Gene expression in Ad-MSCs

source_name: adipose tissue derived mesenchymal stem cells, 12w, high-fat diet, replicate 1


title: old/control Ad-MSCs-1

description: Gene expression in Ad-MSCs

source_name: adipose tissue derived mesenchymal stem cells, 24w, control diet, replicate 1


title: CO2-2


title: SMM at diagnosis, non-progressed sample 2

description: non-progressed SMM

value: non-progressed SMM


title: AT-2


title: SMM at diagnosis, sample 10

description: progressed SMM


title: CO2-1


title: SMM at diagnosis, non-progressed sample 1

description: non-progressed SMM


title: neuron_with PGC-1α_rep 2

status: Public on Jul 16 2019

city: Tianjin

first: Bin

last: Han

address: 154 Anshan Road, Heping District

country: China

institute: Tianjin Medical University General Hospital

description: Gene expression in hippocampus with neuronal PGC-1α overexpression

hyb_protocol: Labeled controls and test samples labeled with Cy3-dCTP were dissolved in 80 μL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: After washing, slides were scanned immediately using G2565CA (Agilent Technologies).

data_processing: The array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13 (Agilent). To select the differentially expressed genes, we used thresholdvalues of ≥2 and ≤−2-fold change and Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage. Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

source_name: Hippocampus

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. The procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

extract_protocol: Total RNA was extracted from hippocampus by using  the Trizol reagent (Invitrogen) and purified with a NucleoSpin® RNA clean-up kit (MACHEREY- NAGEL, Germany) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Only RNA extracts with RNA integrity number values >6 underwent in further analysis.

value: Hippocampus

value: neuron

value: with neuronal PGC-1α overexpression


title: neuron_with PGC-1α_rep 3


title: young/control Ad-MSCs-1

description: Gene expression in Ad-MSCs

source_name: adipose tissue derived mesenchymal stem cells, 12w, control diet, replicate 1


title: neuron_with PGC-1α_rep 5


title: neuron_without PGC-1α_rep 1

description: Gene expression in hippocampus without neuronal PGC-1α overexpression

value: without neuronal PGC-1α overexpression


title: neuron_without PGC-1α_rep 4


title: neuron_with PGC-1α_rep 4


title: S4058WT

city: beijing

first: yongli

last: song

state: china

address: west road2,yuanmingyuan

department: college of life science

institute: china agricultural university

description: Gene expression

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Normal colon

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: genotype

value: wildtype

value: colonic epithelium


title: neuron_without PGC-1α_rep 5

tag: tissue

value: male


title: S405131KO

description: Gene expression

source_name: knockout colon

value: miR-31 knockout


title: MDS patient#296

city: Taipei City

first: Huai-Hsuan

last: Huang

state: Taiwan

address: No.7, Chong-Shan South Road, Zhongzheng Dist.

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: According to the protocols of Affymetrix Gene Expression Service Lab, Academia Sinica, Taiwan

data_processing:
Data were processed using Expression Console software with RMA normalization.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

source_name: MDS patient

growth_protocol: Mononucleated cells from the bone marrow samples of the MDS patients and the healthy controls

extract_protocol: TRIzol

treatment_protocol: not applicable

tag: subject status

value: MDS patient#296

tag: subject id

value: Myelodysplastic syndromes (MDS)

value: bone marrow

value: mononucleated cells


title: MDS patient#300

scan_protocol: According to the protocols of Affymetrix Gene Expression Service Lab, Academia Sinica, Taiwan

value: MDS patient#300

tag: cell type


title: neuron_without PGC-1α_rep 3


title: S450831KO

description: Gene expression


title: S4056WT

description: Gene expression


title: MDS patient#292

label_protocol: According to the protocols of Affymetrix Gene Expression Service Lab, Academia Sinica, Taiwan

value: MDS patient#292


title: MDS patient#295

value: MDS patient#295


title: MDS patient#299

value: MDS patient#299


title: neuron_with PGC-1α_rep 1


title: MDS patient#297

value: MDS patient#297


title: MDS patient#294

value: MDS patient#294


title: MDS patient#293

value: MDS patient#293


title: neuron_without PGC-1α_rep 2

value: Hippocampus

value: neuron


title: MDS patient#291

value: MDS patient#291


title: MDS patient#298

value: MDS patient#298


title: MDS patient#289

value: MDS patient#289


title: S4838WT

description: Gene expression

value: wildtype

value: colonic epithelium

value: male


title: MDS patient#288

value: MDS patient#288

value: Myelodysplastic syndromes (MDS)

value: bone marrow


title: MDS patient#285

value: MDS patient#285

value: mononucleated cells


title: MDS patient#287

value: MDS patient#287


title: MDS patient#286

value: MDS patient#286


title: MDS patient#281

value: MDS patient#281


title: MDS patient#282

value: MDS patient#282


title: MDS patient#284

value: MDS patient#284


title: MDS patient#279

value: MDS patient#279


title: MDS patient#290

value: MDS patient#290


title: MDS patient#275

value: MDS patient#275


title: MDS patient#272

value: MDS patient#272


title: MDS patient#278

value: MDS patient#278


title: MDS patient#274

value: MDS patient#274


title: MDS patient#273

value: MDS patient#273


title: MDS patient#277

value: MDS patient#277


title: MDS patient#280

value: MDS patient#280

value: Myelodysplastic syndromes (MDS)


title: MDS patient#270

value: MDS patient#270

value: bone marrow


title: MDS patient#269

value: MDS patient#269

value: mononucleated cells


title: MDS patient#271

value: MDS patient#271


title: MDS patient#267

value: MDS patient#267


title: MDS patient#266

value: MDS patient#266


title: MDS patient#276

value: MDS patient#276


title: MDS patient#262

value: MDS patient#262


title: MDS patient#268

value: MDS patient#268


title: MDS patient#263

value: MDS patient#263


title: MDS patient#264

value: MDS patient#264


title: MDS patient#261

value: MDS patient#261


title: MDS patient#259

value: MDS patient#259


title: MDS patient#258

value: MDS patient#258


title: MDS patient#260

value: MDS patient#260


title: MDS patient#257

value: MDS patient#257

value: Myelodysplastic syndromes (MDS)


title: MDS patient#256

value: MDS patient#256

value: bone marrow


title: MDS patient#251

value: MDS patient#251

value: mononucleated cells


title: MDS patient#254

value: MDS patient#254


title: S405731KO

description: Gene expression

value: miR-31 knockout

value: colonic epithelium

value: male


title: MDS patient#248

value: MDS patient#248


title: MDS patient#265

value: MDS patient#265


title: MDS patient#252

value: MDS patient#252


title: MDS patient#247

value: MDS patient#247


title: MDS patient#249

value: MDS patient#249


title: MDS patient#255

value: MDS patient#255


title: MDS patient#250

value: MDS patient#250


title: MDS patient#245

value: MDS patient#245


title: MDS patient#239

value: MDS patient#239

value: Myelodysplastic syndromes (MDS)


title: MDS patient#253

value: MDS patient#253

value: bone marrow


title: MDS patient#246

value: MDS patient#246

value: mononucleated cells


title: MDS patient#283

value: MDS patient#283


title: MDS patient#243

value: MDS patient#243


title: MDS patient#235

value: MDS patient#235


title: MDS patient#232

value: MDS patient#232


title: MDS patient#226

value: MDS patient#226


title: MDS patient#236

value: MDS patient#236


title: MDS patient#230

value: MDS patient#230


title: MDS patient#240

value: MDS patient#240


title: MDS patient#233

value: MDS patient#233


title: MDS patient#231

value: MDS patient#231


title: MDS patient#237

value: MDS patient#237


title: MDS patient#224

value: MDS patient#224


title: MDS patient#222

value: MDS patient#222

value: Myelodysplastic syndromes (MDS)


title: MDS patient#241

value: MDS patient#241

value: bone marrow


title: MDS patient#225

value: MDS patient#225

value: mononucleated cells


title: MDS patient#234

value: MDS patient#234


title: MDS patient#219

value: MDS patient#219


title: MDS patient#244

value: MDS patient#244


title: MDS patient#223

value: MDS patient#223


title: MDS patient#228

value: MDS patient#228


title: MDS patient#242

value: MDS patient#242


title: MDS patient#227

value: MDS patient#227


title: MDS patient#217

value: MDS patient#217


title: MDS patient#220

value: MDS patient#220


title: MDS patient#215

value: MDS patient#215


title: MDS patient#221

value: MDS patient#221


title: MDS patient#229

value: MDS patient#229


title: MDS patient#216

value: MDS patient#216

value: Myelodysplastic syndromes (MDS)


title: MDS patient#214

value: MDS patient#214

value: bone marrow


title: MDS patient#209

value: MDS patient#209

value: mononucleated cells


title: MDS patient#208

value: MDS patient#208


title: MDS patient#204

value: MDS patient#204


title: MDS patient#207

value: MDS patient#207


title: MDS patient#201

value: MDS patient#201


title: MDS patient#199

value: MDS patient#199


title: MDS patient#202

value: MDS patient#202


title: MDS patient#200

value: MDS patient#200


title: MDS patient#212

value: MDS patient#212


title: MDS patient#210

value: MDS patient#210


title: MDS patient#205

value: MDS patient#205


title: MDS patient#218

value: MDS patient#218


title: MDS patient#197

value: MDS patient#197


title: MDS patient#195

value: MDS patient#195

value: Myelodysplastic syndromes (MDS)


title: MDS patient#211

value: MDS patient#211

value: bone marrow


title: MDS patient#206

value: MDS patient#206

value: mononucleated cells


title: MDS patient#191

value: MDS patient#191


title: MDS patient#189

value: MDS patient#189


title: MDS patient#194

value: MDS patient#194


title: MDS patient#196

value: MDS patient#196


title: MDS patient#198

value: MDS patient#198


title: MDS patient#213

value: MDS patient#213


title: MDS patient#203

value: MDS patient#203


title: MDS patient#192

value: MDS patient#192


title: MDS patient#190

value: MDS patient#190


title: MDS patient#238

value: MDS patient#238


title: MDS patient#177

value: MDS patient#177


title: MDS patient#185

value: MDS patient#185


title: MDS patient#187

value: MDS patient#187

value: Myelodysplastic syndromes (MDS)


title: MDS patient#172

value: MDS patient#172

value: bone marrow


title: MDS patient#186

value: MDS patient#186

value: mononucleated cells


title: MDS patient#171

value: MDS patient#171


title: MDS patient#175

value: MDS patient#175


title: MDS patient#181

value: MDS patient#181


title: MDS patient#173

value: MDS patient#173


title: MDS patient#183

value: MDS patient#183


title: MDS patient#174

value: MDS patient#174


title: MDS patient#188

value: MDS patient#188


title: MDS patient#193

value: MDS patient#193


title: MDS patient#179

value: MDS patient#179


title: MDS patient#184

value: MDS patient#184


title: MDS patient#178

value: MDS patient#178


title: MDS patient#176

value: MDS patient#176


title: MDS patient#170

value: MDS patient#170

value: Myelodysplastic syndromes (MDS)


title: MDS patient#162

value: MDS patient#162

value: bone marrow


title: MDS patient#180

value: MDS patient#180

value: mononucleated cells


title: MDS patient#168

value: MDS patient#168


title: MDS patient#164

value: MDS patient#164


title: MDS patient#159

value: MDS patient#159


title: MDS patient#161

value: MDS patient#161


title: MDS patient#169

value: MDS patient#169


title: MDS patient#163

value: MDS patient#163


title: MDS patient#167

value: MDS patient#167


title: MDS patient#166

value: MDS patient#166


title: MDS patient#165

value: MDS patient#165


title: MDS patient#158

value: MDS patient#158


title: MDS patient#153

value: MDS patient#153


title: MDS patient#152

value: MDS patient#152


title: MDS patient#151

value: MDS patient#151

value: Myelodysplastic syndromes (MDS)


title: MDS patient#182

value: MDS patient#182

value: bone marrow


title: MDS patient#148

value: MDS patient#148

value: mononucleated cells


title: MDS patient#154

value: MDS patient#154


title: MDS patient#155

value: MDS patient#155


title: MDS patient#149

value: MDS patient#149


title: MDS patient#145

value: MDS patient#145


title: MDS patient#146

value: MDS patient#146


title: MDS patient#144

value: MDS patient#144


title: MDS patient#147

value: MDS patient#147


title: MDS patient#157

value: MDS patient#157


title: MDS patient#156

value: MDS patient#156


title: MDS patient#150

value: MDS patient#150


title: MDS patient#139

value: MDS patient#139


title: MDS patient#143

value: MDS patient#143


title: MDS patient#160

value: MDS patient#160

value: Myelodysplastic syndromes (MDS)


title: MDS patient#141

value: MDS patient#141

value: bone marrow


title: MDS patient#135

value: MDS patient#135

value: mononucleated cells


title: MDS patient#132

value: MDS patient#132


title: MDS patient#136

value: MDS patient#136


title: MDS patient#140

value: MDS patient#140


title: MDS patient#142

value: MDS patient#142


title: MDS patient#126

value: MDS patient#126


title: MDS patient#127

value: MDS patient#127


title: MDS patient#133

value: MDS patient#133


title: MDS patient#137

value: MDS patient#137


title: MDS patient#123

value: MDS patient#123


title: MDS patient#134

value: MDS patient#134


title: MDS patient#138

value: MDS patient#138


title: MDS patient#129

value: MDS patient#129


title: MDS patient#128

value: MDS patient#128

value: Myelodysplastic syndromes (MDS)


title: MDS patient#124

value: MDS patient#124

value: bone marrow


title: MDS patient#122

value: MDS patient#122

value: mononucleated cells


title: MDS patient#115

value: MDS patient#115


title: MDS patient#117

value: MDS patient#117


title: MDS patient#131

value: MDS patient#131


title: MDS patient#118

value: MDS patient#118


title: MDS patient#116

value: MDS patient#116


title: MDS patient#121

value: MDS patient#121


title: MDS patient#120

value: MDS patient#120


title: MDS patient#130

value: MDS patient#130


title: MDS patient#119

value: MDS patient#119


title: MDS patient#125

value: MDS patient#125


title: MDS patient#112

value: MDS patient#112


title: MDS patient#110

value: MDS patient#110


title: MDS patient#113

value: MDS patient#113

value: Myelodysplastic syndromes (MDS)


title: MDS patient#105

value: MDS patient#105

value: bone marrow


title: MDS patient#095

value: MDS patient#095

value: mononucleated cells


title: MDS patient#097

value: MDS patient#097


title: MDS patient#106

value: MDS patient#106


title: MDS patient#107

value: MDS patient#107


title: MDS patient#094

value: MDS patient#094


title: MDS patient#098

value: MDS patient#098


title: MDS patient#108

value: MDS patient#108


title: MDS patient#096

value: MDS patient#096


title: MDS patient#093

value: MDS patient#093


title: MDS patient#102

value: MDS patient#102


title: MDS patient#100

value: MDS patient#100


title: MDS patient#092

value: MDS patient#092


title: MDS patient#091

value: MDS patient#091


title: MDS patient#099

value: MDS patient#099

value: Myelodysplastic syndromes (MDS)


title: MDS patient#086

value: MDS patient#086

value: bone marrow


title: MDS patient#101

value: MDS patient#101

value: mononucleated cells


title: MDS patient#088

value: MDS patient#088


title: MDS patient#090

value: MDS patient#090


title: MDS patient#104

value: MDS patient#104


title: MDS patient#103

value: MDS patient#103


title: MDS patient#089

value: MDS patient#089


title: MDS patient#111

value: MDS patient#111


title: MDS patient#087

value: MDS patient#087


title: MDS patient#082

value: MDS patient#082


title: MDS patient#085

value: MDS patient#085


title: MDS patient#080

value: MDS patient#080


title: MDS patient#083

value: MDS patient#083


title: MDS patient#079

value: MDS patient#079


title: MDS patient#081

value: MDS patient#081

value: Myelodysplastic syndromes (MDS)


title: MDS patient#060

value: MDS patient#060

value: bone marrow


title: MDS patient#078

value: MDS patient#078

value: mononucleated cells


title: MDS patient#069

value: MDS patient#069


title: MDS patient#077

value: MDS patient#077


title: MDS patient#068

value: MDS patient#068


title: MDS patient#067

value: MDS patient#067


title: MDS patient#076

value: MDS patient#076


title: MDS patient#071

value: MDS patient#071


title: MDS patient#070

value: MDS patient#070


title: MDS patient#065

value: MDS patient#065


title: MDS patient#114

value: MDS patient#114


title: MDS patient#064

value: MDS patient#064


title: MDS patient#084

value: MDS patient#084


title: MDS patient#061

value: MDS patient#061


title: MDS patient#062

value: MDS patient#062

value: Myelodysplastic syndromes (MDS)


title: MDS patient#074

value: MDS patient#074

value: bone marrow


title: MDS patient#075

value: MDS patient#075

value: mononucleated cells


title: MDS patient#073

value: MDS patient#073


title: MDS patient#054

value: MDS patient#054


title: MDS patient#055

value: MDS patient#055


title: MDS patient#057

value: MDS patient#057


title: MDS patient#058

value: MDS patient#058


title: MDS patient#056

value: MDS patient#056


title: MDS patient#066

value: MDS patient#066


title: MDS patient#072

value: MDS patient#072


title: MDS patient#052

value: MDS patient#052


title: MDS patient#048

value: MDS patient#048


title: MDS patient#051

value: MDS patient#051


title: MDS patient#047

value: MDS patient#047


title: MDS patient#050

value: MDS patient#050

value: Myelodysplastic syndromes (MDS)


title: MDS patient#109

value: MDS patient#109

value: bone marrow


title: MDS patient#053

value: MDS patient#053

value: mononucleated cells


title: MDS patient#044

value: MDS patient#044


title: MDS patient#063

value: MDS patient#063


title: MDS patient#046

value: MDS patient#046


title: MDS patient#049

value: MDS patient#049


title: MDS patient#040

value: MDS patient#040


title: MDS patient#042

value: MDS patient#042


title: MDS patient#059

value: MDS patient#059


title: MDS patient#036

value: MDS patient#036


title: MDS patient#045

value: MDS patient#045


title: MDS patient#043

value: MDS patient#043


title: MDS patient#038

value: MDS patient#038


title: MDS patient#041

value: MDS patient#041


title: MDS patient#035

value: MDS patient#035

value: Myelodysplastic syndromes (MDS)


title: MDS patient#033

value: MDS patient#033

value: bone marrow


title: MDS patient#037

value: MDS patient#037

value: mononucleated cells


title: MDS patient#026

value: MDS patient#026


title: MDS patient#034

value: MDS patient#034


title: MDS patient#022

value: MDS patient#022


title: MDS patient#032

value: MDS patient#032


title: MDS patient#024

value: MDS patient#024


title: MDS patient#027

value: MDS patient#027


title: MDS patient#021

value: MDS patient#021


title: MDS patient#025

value: MDS patient#025


title: MDS patient#018

value: MDS patient#018


title: MDS patient#016

value: MDS patient#016


title: MDS patient#019

value: MDS patient#019


title: MDS patient#030

value: MDS patient#030


title: MDS patient#020

value: MDS patient#020

value: Myelodysplastic syndromes (MDS)


title: MDS patient#029

value: MDS patient#029

value: bone marrow


title: MDS patient#039

value: MDS patient#039

value: mononucleated cells


title: MDS patient#031

value: MDS patient#031


title: MDS patient#017

value: MDS patient#017


title: MDS patient#028

value: MDS patient#028


title: MDS patient#015

value: MDS patient#015


title: MDS patient#023

value: MDS patient#023


title: MDS patient#012

value: MDS patient#012


title: MDS patient#011

value: MDS patient#011


title: MDS patient#014

value: MDS patient#014


title: MDS patient#009

value: MDS patient#009


title: MDS patient#013

value: MDS patient#013


title: N16 [re-analyzed]

source_name: healthy donor

value: healthy donor#16

value: healthy donor


title: MDS patient#004

value: MDS patient#004

value: Myelodysplastic syndromes (MDS)


title: MDS patient#008

value: MDS patient#008

value: bone marrow


title: N20 [re-analyzed]

value: healthy donor#20

value: mononucleated cells


title: MDS patient#007

value: MDS patient#007


title: MDS patient#001

value: MDS patient#001


title: MDS patient#010

value: MDS patient#010


title: N12 [re-analyzed]

value: healthy donor#12


title: MDS patient#003

value: MDS patient#003


title: MDS patient#002

value: MDS patient#002


title: N13 [re-analyzed]

value: healthy donor#13


title: N14 [re-analyzed]

value: healthy donor#14


title: N10 [re-analyzed]

value: healthy donor#10


title: N08 [re-analyzed]

value: healthy donor#08


title: N19 [re-analyzed]

value: healthy donor#19

value: healthy donor


title: MDS patient#006

value: MDS patient#006

value: Myelodysplastic syndromes (MDS)


title: N18 [re-analyzed]

value: healthy donor#18

value: bone marrow


title: N15 [re-analyzed]

value: healthy donor#15

value: mononucleated cells


title: N17 [re-analyzed]

value: healthy donor#17


title: N09 [re-analyzed]

value: healthy donor#09


title: N11 [re-analyzed]

value: healthy donor#11


title: N07 [re-analyzed]

value: healthy donor#07


title: N06 [re-analyzed]

value: healthy donor#06


title: Healthy donor#20

growth_protocol: Mononucleated cells from the bone marrow samples of the AML patients and the healthy controls

value: Healthy donor#20


title: Healthy donor#17

value: Healthy donor#17


title: N01 [re-analyzed]

value: healthy donor#01


title: Healthy donor#18

value: Healthy donor#18


title: Healthy donor#12

value: Healthy donor#12


title: Healthy donor#06

value: healthy donor

value: Healthy donor#06


title: N05 [re-analyzed]

value: healthy donor#05


title: N03 [re-analyzed]

value: healthy donor#03


title: Healthy donor#15

value: Healthy donor#15

value: bone marrow


title: AML patient#194

source_name: AML patient

value: acute myeloid leukemia (AML)

value: AML patient#194

value: mononucleated cells


title: Healthy donor#14

value: Healthy donor#14


title: Healthy donor#08

value: Healthy donor#08


title: Healthy donor#04

value: Healthy donor#04


title: AML patient#193

value: AML patient#193


title: Healthy donor#02

value: Healthy donor#02


title: Healthy donor#11

value: Healthy donor#11


title: Healthy donor#05

value: Healthy donor#05


title: Healthy donor#07

value: Healthy donor#07


title: Healthy donor#13

value: healthy donor

value: Healthy donor#13


title: Healthy donor#03

value: Healthy donor#03


title: Healthy donor#01

value: Healthy donor#01


title: AML patient#192

value: AML patient#192


title: N04 [re-analyzed]

value: healthy donor#04

value: bone marrow


title: Healthy donor#09

value: Healthy donor#09


title: Healthy donor#19

value: Healthy donor#19

value: mononucleated cells


title: AML patient#191

value: acute myeloid leukemia (AML)

value: AML patient#191


title: Healthy donor#10

value: Healthy donor#10


title: MDS patient#005

value: MDS patient#005

value: Myelodysplastic syndromes (MDS)


title: AML patient#189

value: AML patient#189


title: AML patient#180

value: AML patient#180


title: AML patient#190

value: AML patient#190


title: N02 [re-analyzed]

value: healthy donor#02

value: healthy donor


title: Healthy donor#16

value: Healthy donor#16


title: AML patient#179

value: AML patient#179


title: AML patient#188

value: AML patient#188


title: AML patient#175

value: AML patient#175

value: bone marrow


title: AML patient#185

value: AML patient#185


title: AML patient#187

value: AML patient#187

value: mononucleated cells


title: AML patient#172

value: acute myeloid leukemia (AML)

value: AML patient#172


title: AML patient#181

value: AML patient#181


title: AML patient#182

value: AML patient#182


title: AML patient#183

value: AML patient#183


title: AML patient#167

value: AML patient#167


title: AML patient#184

value: AML patient#184


title: AML patient#173

value: AML patient#173


title: AML patient#168

value: AML patient#168


title: AML patient#174

value: AML patient#174


title: AML patient#169

value: AML patient#169


title: AML patient#176

value: AML patient#176


title: AML patient#171

value: AML patient#171


title: AML patient#170

value: AML patient#170

value: bone marrow


title: AML patient#166

value: AML patient#166


title: AML patient#186

value: AML patient#186

value: mononucleated cells


title: AML patient#164

value: acute myeloid leukemia (AML)

value: AML patient#164


title: AML patient#165

value: AML patient#165


title: AML patient#178

value: AML patient#178


title: AML patient#177

value: AML patient#177


title: AML patient#163

value: AML patient#163


title: AML patient#162

value: AML patient#162


title: AML patient#161

value: AML patient#161


title: AML patient#158

value: AML patient#158


title: AML patient#160

value: AML patient#160


title: AML patient#159

value: AML patient#159


title: AML patient#155

value: AML patient#155


title: AML patient#145

value: AML patient#145


title: AML patient#147

value: AML patient#147

value: bone marrow


title: AML patient#152

value: AML patient#152


title: AML patient#157

value: AML patient#157

value: mononucleated cells


title: AML patient#156

value: acute myeloid leukemia (AML)

value: AML patient#156


title: AML patient#151

value: AML patient#151


title: AML patient#153

value: AML patient#153


title: AML patient#146

value: AML patient#146


title: AML patient#142

value: AML patient#142


title: AML patient#144

value: AML patient#144


title: AML patient#143

value: AML patient#143


title: AML patient#135

value: AML patient#135


title: AML patient#154

value: AML patient#154


title: AML patient#134

value: AML patient#134


title: AML patient#137

value: AML patient#137


title: AML patient#139

value: AML patient#139


title: AML patient#133

value: AML patient#133

value: bone marrow


title: AML patient#141

value: AML patient#141


title: AML patient#149

value: AML patient#149

value: mononucleated cells


title: AML patient#136

value: acute myeloid leukemia (AML)

value: AML patient#136


title: AML patient#150

value: AML patient#150


title: AML patient#132

value: AML patient#132


title: AML patient#138

value: AML patient#138


title: AML patient#148

value: AML patient#148


title: AML patient#129

value: AML patient#129


title: AML patient#130

value: AML patient#130


title: AML patient#131

value: AML patient#131


title: AML patient#128

value: AML patient#128


title: AML patient#126

value: AML patient#126


title: AML patient#140

value: AML patient#140


title: AML patient#125

value: AML patient#125


title: AML patient#124

value: AML patient#124

value: bone marrow


title: AML patient#122

value: AML patient#122


title: AML patient#127

value: AML patient#127

value: mononucleated cells


title: AML patient#123

value: acute myeloid leukemia (AML)

value: AML patient#123


title: AML patient#118

value: AML patient#118


title: AML patient#121

value: AML patient#121


title: AML patient#119

value: AML patient#119


title: AML patient#117

value: AML patient#117


title: AML patient#114

value: AML patient#114


title: AML patient#105

value: AML patient#105


title: AML patient#116

value: AML patient#116


title: AML patient#112

value: AML patient#112


title: AML patient#120

value: AML patient#120


title: AML patient#115

value: AML patient#115


title: AML patient#113

value: AML patient#113


title: AML patient#106

value: AML patient#106

value: bone marrow


title: AML patient#102

value: AML patient#102


title: AML patient#109

value: AML patient#109

value: mononucleated cells


title: AML patient#104

value: acute myeloid leukemia (AML)

value: AML patient#104


title: AML patient#107

value: AML patient#107


title: AML patient#097

value: AML patient#097


title: AML patient#098

value: AML patient#098


title: AML patient#101

value: AML patient#101


title: AML patient#103

value: AML patient#103


title: AML patient#099

value: AML patient#099


title: AML patient#110

value: AML patient#110


title: AML patient#100

value: AML patient#100


title: AML patient#111

value: AML patient#111


title: AML patient#092

value: AML patient#092


title: AML patient#091

value: AML patient#091


title: AML patient#093

value: AML patient#093

value: bone marrow


title: AML patient#090

value: AML patient#090


title: AML patient#088

value: AML patient#088

value: mononucleated cells


title: AML patient#094

value: acute myeloid leukemia (AML)

value: AML patient#094


title: AML patient#096

value: AML patient#096


title: AML patient#095

value: AML patient#095


title: AML patient#086

value: AML patient#086


title: AML patient#081

value: AML patient#081


title: AML patient#078

value: AML patient#078


title: AML patient#070

value: AML patient#070


title: AML patient#079

value: AML patient#079


title: AML patient#082

value: AML patient#082


title: AML patient#069

value: AML patient#069


title: AML patient#080

value: AML patient#080


title: AML patient#077

value: AML patient#077


title: AML patient#074

value: AML patient#074

value: bone marrow


title: AML patient#084

value: AML patient#084


title: AML patient#108

value: AML patient#108

value: mononucleated cells


title: AML patient#064

value: acute myeloid leukemia (AML)

value: AML patient#064


title: AML patient#075

value: AML patient#075


title: AML patient#063

value: AML patient#063


title: AML patient#073

value: AML patient#073


title: AML patient#061

value: AML patient#061


title: AML patient#065

value: AML patient#065


title: AML patient#083

value: AML patient#083


title: AML patient#068

value: AML patient#068


title: AML patient#062

value: AML patient#062


title: AML patient#076

value: AML patient#076


title: AML patient#089

value: AML patient#089


title: AML patient#067

value: AML patient#067


title: AML patient#072

value: AML patient#072

value: bone marrow


title: AML patient#071

value: AML patient#071


title: AML patient#066

value: AML patient#066

value: mononucleated cells


title: AML patient#085

value: acute myeloid leukemia (AML)

value: AML patient#085


title: AML patient#060

value: AML patient#060


title: AML patient#059

value: AML patient#059


title: AML patient#058

value: AML patient#058


title: AML patient#057

value: AML patient#057


title: AML patient#052

value: AML patient#052


title: AML patient#046

value: AML patient#046


title: AML patient#050

value: AML patient#050


title: AML patient#049

value: AML patient#049


title: AML patient#056

value: AML patient#056


title: AML patient#045

value: AML patient#045


title: AML patient#047

value: AML patient#047


title: AML patient#044

value: AML patient#044

value: bone marrow


title: AML patient#051

value: AML patient#051


title: AML patient#054

value: AML patient#054

value: mononucleated cells


title: AML patient#038

value: acute myeloid leukemia (AML)

value: AML patient#038


title: AML patient#055

value: AML patient#055


title: AML patient#037

value: AML patient#037


title: AML patient#053

value: AML patient#053


title: AML patient#040

value: AML patient#040


title: AML patient#041

value: AML patient#041


title: AML patient#033

value: AML patient#033


title: AML patient#048

value: AML patient#048


title: AML patient#043

value: AML patient#043


title: AML patient#042

value: AML patient#042


title: AML patient#039

value: AML patient#039


title: AML patient#036

value: AML patient#036


title: AML patient#030

value: AML patient#030

value: bone marrow


title: AML patient#031

value: AML patient#031


title: AML patient#034

value: AML patient#034

value: mononucleated cells


title: AML patient#035

value: acute myeloid leukemia (AML)

value: AML patient#035


title: AML patient#032

value: AML patient#032


title: AML patient#028

value: AML patient#028


title: AML patient#087

value: AML patient#087


title: AML patient#022

value: AML patient#022


title: AML patient#020

value: AML patient#020


title: AML patient#025

value: AML patient#025


title: AML patient#024

value: AML patient#024


title: AML patient#027

value: AML patient#027


title: AML patient#023

value: AML patient#023


title: AML patient#021

value: AML patient#021


title: AML patient#004

value: AML patient#004


title: AML patient#009

value: AML patient#009

value: bone marrow


title: AML patient#012

value: AML patient#012


title: AML patient#029

value: AML patient#029

value: mononucleated cells


title: AML patient#026

value: acute myeloid leukemia (AML)

value: AML patient#026


title: AML patient#005

value: AML patient#005


title: AML patient#007

value: AML patient#007


title: AML patient#013

value: AML patient#013


title: AML patient#011

value: AML patient#011


title: AML patient#003

value: AML patient#003


title: AML patient#008

value: AML patient#008


title: AML patient#006

value: AML patient#006


title: AML patient#010

value: AML patient#010


title: AML patient#015

value: AML patient#015


title: AML patient#018

value: AML patient#018


title: AML patient#017

value: AML patient#017


title: shHOXB-AS3#2

data_processing:
Data were processed using Expression Console software with RMA normalization.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

growth_protocol: OCI/AML3 cell lines infected by the lentivirus with shRNA, and underwent drug selection

extract_protocol: Total RNA was extracted with kit, Neucleospin RNA.

tag: cell line

tag: shRNA


title: AML patient#002

value: AML patient#002

value: bone marrow


title: AML patient#019

value: AML patient#019


title: AML patient#016

value: AML patient#016

value: mononucleated cells


title: RH4 Ent6 H2BK5ac

city: Bethesda

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq peaks were called by MACS2 version 2.1.0.
Spike in normalization was done by dividing the number of human reads in each bin according to million mapped dm3 reads.
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Genome_build: hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: Cells were grown to 80% confluence, treated with either DMSO (0.05% by volume) or HDAC inhibitor Entinostat (final concentration 1 uM) for 1 or 6 hours. Samples were then harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen). Spike in of drosophila chromatin was performed using the Active Motif components (cat # 61686, cat # 53083).

tag: antibody

value: anti-H2BK5ac (Active Motif, Cat# 39123)

tag: enrichment target

tag: target function

value: Histone modification

tag: treatment

value: Entinostat 1 ╡M


title: RH4 D6 H2BK5ac

value: DMSO


title: RH4 Merck60 H3K27ac

value: H3K27ac (39133, Active Motif)

value: Active enhancers

value: HDAC3 inhibitor Merck60 1 ╡M


title: RH4 Ent6 MYOG

value: Thermo (cat # MA1-41042)

value: MYOG

value: Transcription Factor

value: Entinostat


title: RH4 D6 H4K16ac

value: anti-H4K16ac (Millipore, Cat# 07-327)


title: RH4 Ent6 SOX8

value: SOX8 (Abcam, ab104245)


title: RH4 D6 MYOG


title: RH4 D6 r2 H3K27ac


title: RH4 Ent6 MYOD

value: MYOD SantaCruz (M-318) sc-760

value: MYOD

value: Myogenic Transcription Factor


title: RH4 Ent6 H4K16ac


title: AML patient#014

value: acute myeloid leukemia (AML)

value: AML patient#014

value: bone marrow

value: mononucleated cells


title: RH4 D6 MYOD

value: DMSO


title: AML patient#001

value: AML patient#001


title: RH4 D6 PAX3FOXO1

value: antiP3F (in house)

value: Fusion Transcription Factor


title: RH4 D6 HDAC3

value: HDAC3 (Abcam, ab7030)

value: Epigenetic Enzyme


title: RH4 LW3 H3K27ac

value: H3K27ac (39133, Active Motif)

value: Active enhancers

value: HDAC3 inhibitor LW3 1 ╡M


title: shHOXB-AS3#1


title: RH4 Ent6 YY1

description: DNA (ChIP-enriched)

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0.  DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.  ATAC-seq DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: Cells were grown to 80% confluence, treated with either DMSO (0.05% by volume) or HDAC inhibitor Entinostat (final concentration 1 uM) for 1 or 6 hours. Samples were then harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).

value: YY-1 antibody (ab109237)

value: Acetylated Lysine Reader, Active Enhancers

value: Entinostat, 1 µM, 6 hours


title: control#1


title: RH4 Ent 6hr ATAC

description: DNA (ATAC-enriched)

value: ATAC

value: Open Chromatin


title: control#2


title: RH4 DMSO 6hr ATAC

description: DNA (ATAC-enriched)

value: DMSO, 6 hours


title: RH4 Ent 1hr ATAC

description: DNA (ATAC-enriched)

value: Entinostat, 1 µM, 1 hour


title: RH4 D6 RAD21 Rep2

description: DNA (ChIP-enriched)

value: Rad21 (Santa Cruz, ChIP Grade ab992)

value: Cohesin Complex


title: RH4 D6 HDAC1

description: DNA (ChIP-enriched)

value: Anti-HDAC1, Abcam (ab7028)

value: NuRD Complex


title: RH4 Ent6 RAD21 Rep2

description: DNA (ChIP-enriched)


title: RH4 D6 YY1

description: DNA (ChIP-enriched)


title: RH4 D6 SOX8

value: SOX8 (Abcam, ab104245)

value: Transcription Factor

value: DMSO


title: RH4 Ent6 PAX3FOXO1

value: antiP3F (in house)

value: Fusion Transcription Factor

value: Entinostat


title: RH4 D6 bioMerck

description: DNA (ChIP-enriched)

value: Biotinylated HDAC inhibitor Merck60, Bradner lab

value: HDAC Chemseq (bioMerck)


title: RH30 input

description: DNA (input control)

value: input

value: control

value: untreated


title: RH4 Ent6 H3K36ac

description: DNA (ChIP-enriched)

value: H3K36ac (Active Motif, 39379)

value: Active promoters

value: Entinostat, 1 µM, 6 hours


title: RH4 Ent6 Pol2

description: DNA (ChIP-enriched)

value: Transcription


title: RH4 Ent1 Pol2

description: DNA (ChIP-enriched)

value: Entinostat, 1 µM, 1 hour


title: RH30 H3K27ac

description: DNA (ChIP-enriched)

value: H3K27ac (Active Motif, 39133)

value: Active enhancers


title: RH4 D6 HDAC2

description: DNA (ChIP-enriched)

value: HDAC2, Abcam (cat7029 lotGR88809-14 pAb)

value: NuRD Complex

value: DMSO, 6 hours


title: RH4 D6 H3K36ac

description: DNA (ChIP-enriched)


title: RH4 D6 RAD21 Rep1

description: DNA (ChIP-enriched)

value: Rad21 (Santa Cruz, ChIP Grade ab992)

value: Cohesin Complex


title: RH4 Ent6 RAD21 Rep1

description: DNA (ChIP-enriched)


title: RH4 D6 Pol2

description: DNA (ChIP-enriched)


title: RH4 Ent6 H3K27ac

description: DNA (ChIP-enriched)


title: RH4 Ent1 H3K27ac

description: DNA (ChIP-enriched)


title: RH4 D6 H3K27ac

description: DNA (ChIP-enriched)


title: RH4 bioJQ1

description: DNA (ChIP-enriched)

value: Biotinylated JQ1, Bradner lab

value: BET Bromodomain Binder Chemseq


title: RH3 input

description: DNA (input control)

value: input


title: RH4 SOX8

description: DNA (ChIP-enriched)

value: Abcam (ab104245, rabbit pAb)

value: Transcription Factor


title: RH4 HDAC2

description: DNA (ChIP-enriched)

value: untreated


title: ATAC-MW-0041: Donor_10_stim_veh_d7

city: Seattle

first: Timothy

middle: George

last: Johnstone

state: WA

address: 400 Dexter Ave N #605

department: Computational Genomics & Data Science

institute: Juno Therapeutics

description: tagmented DNA

data_processing:
Trimming was performed with Trimmomatic 0.36 using paired-end mode with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10
Reads were mapped using bowtie2 2.3.4 using parameters --very-sensitive -X 1500 in reference mode
Duplicates were removed usiing PicardTools MarkDuplicates 2.17.6. mtDNA reads were filtered and reads were shifted to account for transposase shift. Sub-nucleosomal fragments (<100nt) were length-selected
Peaks were called with MACS2 2.1.1.20160309 with parameters --nomodel -shift 100 --extsize 200 -q 0.01
Raw counts were FrIP-normalized with DESeq2 1.18.1
Consensus peaks and counts in peaks were collated with DiffBind 2.6.6
Genome_build: hg38
Supplementary_files_format_and_content: matrix of normalized accessibility counts with narrowPeak name as bed coordinates

source_name: Mixed CD4 and CD8 CAR-T cells

extract_protocol: Libraries were generated with an Illumina Nextera DNA Preparation kit according to Buenrostro et al. 2015.

value: Mixed CD4 and CD8 CAR-T cells

tag: donor

tag: stimulation

value: stim

value: veh

tag: time-point


title: ATAC-MW-0039: Donor_6_stim_veh_d7

description: tagmented DNA


title: RH3 H3K27ac

description: DNA (ChIP-enriched)

value: H3K27ac, Active Motif (39133, pAb)


title: ATAC-MW-0037: Donor_3_stim_veh_d7

description: tagmented DNA


title: ATAC-MW-0038: Donor_3_stim_len_d7

description: tagmented DNA

value: len


title: ATAC-MW-0042: Donor_10_stim_len_d7

description: tagmented DNA


title: RH4 Ent6 bioMerck

description: DNA (ChIP-enriched)

value: Biotinylated HDAC inhibitor Merck60, Bradner lab

value: HDAC Chemseq (bioMerck)

value: Entinostat, 1 µM, 6 hours


title: ATAC-MW-0040: Donor_6_stim_len_d7

description: tagmented DNA


title: RH4 Ent6 HDAC2

description: DNA (ChIP-enriched)

value: HDAC2, Abcam (cat7029 lotGR88809-14 pAb)

value: NuRD Complex


title: ATAC-MW-0033: Donor_10_stim_veh_24hr

description: tagmented DNA


title: ATAC-MW-0034: Donor_10_stim_len_24hr

description: tagmented DNA


title: ATAC-MW-0035: Donor_1_stim_veh_d7

description: tagmented DNA


title: ATAC-MW-0027: Donor_6_nostim_veh_24hr

description: tagmented DNA

value: nostim


title: ATAC-MW-0026: Donor_3_stim_len_24hr

description: tagmented DNA


title: ATAC-MW-0028: Donor_6_nostim_len_24hr

description: tagmented DNA


title: ATAC-MW-0025: Donor_3_stim_veh_24hr

description: tagmented DNA


title: ATAC-MW-0036: Donor_1_stim_len_d7

description: tagmented DNA


title: ATAC-MW-0024: Donor_3_nostim_len_24hr

description: tagmented DNA


title: RH4 Ent6 HDAC3

value: HDAC3 (Abcam, ab7030)

value: Epigenetic Enzyme

value: Entinostat


title: ATAC-MW-0023: Donor_3_nostim_veh_24hr

description: tagmented DNA


title: ATAC-MW-0022: Donor_1_stim_len_24hr

description: tagmented DNA


title: ATAC-MW-0019: Donor_1_nostim_veh_24hr

description: tagmented DNA


title: 309_14.6_stim_len_d7

data_processing:
Strand-specific, poly-A-selected RNA-seq reads were trimmed (minimum quality 2), mapped to hg38 (OmicSoft OSA4 default parameters using OmicSoft GenCodeV24 transcript models as reference), and quantified using ArrayStudio (OmicSoft)
Reads per gene were quantified in a strand-specific manner using ArrayStudio (OmicSoft) to output expression values in the form of TPM-scaled FPKM
Genome_build: hg38
Supplementary_files_format_and_content: tab separated table of TPM-normalized expression values per-gene

source_name: Cultured T cell

growth_protocol: Anti-BCMA CAR T cells were cultured in the presence or absence of BCMA beads for either 24 hours or 7 days with or without 1 µM lenalidomide.

extract_protocol:
RNA was extracted using Promega Maxwell HT simplyRNA custom kit
Libraries were prepared with NEB UltraII directional kit using the polyA enrichment module

value: T-cell

tag: stim-status

tag: sample-donor

tag: timepoint


title: ATAC-MW-0021: Donor_1_stim_veh_24hr

description: tagmented DNA


title: ATAC-MW-0020: Donor_1_nostim_len_24hr

description: tagmented DNA


title: 310_14.1_stim_len_d7


title: 304_14.3_stim_veh_d7


title: 305_14.6_stim_veh_d7


title: 307_14.1_stim_len_d7


title: 283_14.6_no_stim_len_24hr


title: 284_14.6_stim_len_24hr


title: ATAC-MW-0029: Donor_6_stim_veh_24hr

description: tagmented DNA


title: ATAC-MW-0030: Donor_6_stim_len_24hr

description: tagmented DNA


title: ATAC-MW-0031: Donor_10_nostim_veh_24hr

description: tagmented DNA


title: 303_14.1_stim_veh_d7


title: ATAC-MW-0032: Donor_10_nostim_len_24hr

description: tagmented DNA


title: 285_14.1_no_stim_len_24hr


title: 280_14.1_stim_len_24hr


title: 279_14.1_no_stim_len_24hr


title: 278_14.1_stim_veh_24hr


title: 281_14.3_no_stim_len_24hr


title: 275_14.6_no_stim_veh_24hr


title: 277_4.1_no_stim_veh_24hr


title: 274_14.3_stim_veh_24hr


title: 272_14.1_stim_veh_24hr


title: 271_14.1_no_stim_veh_24hr


title: 308_14.3_stim_len_d7