title: mESC6_H3K4me3_R1

city: La Jolla

first: Daria

last: Merkurjev

address: 9500 Gilman Drive, Mail Code 0648

institute: UCSD

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18 and mm9
Supplementary_files_format_and_content: bedGraph

source_name: single-cell 46C derived mESC#6 subline

growth_protocol: CVB and CVI lines and sublines as well as HUES9 hESC line and sublines were cultured on a feeder layer of gamma-irradiated mouse embryonic fibroblasts (MEFs), and maintained in hESC media made with knockout (KO) Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% Plasmanate from Talecris Biotherapeutics; 10% Knockout serum replacement (KOSR) from Gibco; 20 mM GlutaMax, 20 mM nonessential amino acids (NEAA) and 20 mM Pen/Strep from Invitrogen; and, 20 ng/µL FGF from Millipore. Mouse ESCs were prepared in feeder free condition with DMEM-KO supplemented with 15% ESC qualified-fetal bovine serum, 2 mM nonessential amino acids, glutamx, penicillin/streptomycin, 2-mercaptoethanol and 1000u/ml LIF.

extract_protocol:
Cells were fixed with 2mM disuccinimidyl glutarate (DSG) for 45 mins and 1% formaldehyde for 10mins, and followed by glycine for 5 mins. Chromatin DNA was sheared to 200–500 bp average in size by sonication and chromatin was immunoprecipitated with antibodies. Protein A/G beads Sigma were added and incubated overnight at 4°C. After washing and elution, the protein–DNA complex was reverse-crosslinked by heating at 65°C, and immunoprecipitated DNA was purified by using QIAquick Spin column.
ChIP-seq libraries were prepared using the KAPA Library Preparation Kit (KK8201)

treatment_protocol: No particular treatments were applied.

tag: cell line

value: 46C mESC subline

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: H3K4me3 (Millipore, 07-473)


title: mESC1_H3K4me3_R2

status: Public on Jul 29 2019

type: SRA

state: CA

department: Medicine

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: single-cell 46C derived mESC#1 subline


title: mESC2_H3K4me3_R2

source_name: single-cell 46C derived mESC#2 subline


title: mESC3_H3K4me3_R2

source_name: single-cell 46C derived mESC#3 subline


title: mESC5_H3K4me3_R2

source_name: single-cell 46C derived mESC#5 subline


title: wt_SMC_baseline_031617

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

library_source: transcriptomic

data_processing:
FASTQ files were generated by demultiplexing the Illumina sequencer's base call files (BCLs) using 10X CellRanger 'mkfastq' command.
For cell-gene matrix files, individual matrices were first generated using 10X Cell Ranger 'count' command. Individual matrices were then aggregated using the 10X Cell Ranger 'aggr' command. Sparse matrix was read into Seurat and a dense matrix was exported.
Genome_build: mm10
Supplementary_files_format_and_content: cell-gene readcount matrix; sample identity, corresponding to the 'sample number in processed data' numbers, is appended to each cell barcode column name

molecule: total RNA

extract_protocol:
Cells were enzymatically dissociated from the aortic root and ascending aorta (to the level of the brachiocephalic artery) of experimental mice
Cells were captured on a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using either the V2 or V3 chemistry for 3' whole transcriptome analysis. Manufacturer's instructions for GEM (Gelbead EMulsion) generation, downstream reverse transcription, cDNA isolation, PCR amplification and library preparation were followed without any significant alterations

tag: genotype/variation

value: Myh11(cre), ROSA(tdT), ApoE(-/-)

tag: treatment/timepoint

value: baseline

tag: number of animals included in sample

tag: tissue

value: aortic root and ascending aorta

tag: smc lineage status

value: SMC lineage

tag: sample number in processed data


title: mESC5_H3K4me3_R1


title: wt_nonSMC_baseline_031617

value: non-SMC


title: mESC3_H3K4me3_R1


title: wt_nonSMC_16wk_citeseq_antibody

data_processing:
FASTQ files were generated by demultiplexing the Illumina sequencer's base call files (BCLs) using 10X CellRanger 'mkfastq' command.
For cell-gene matrix files, individual matrices were first generated using 10X Cell Ranger 'count' command -antibody barcode-derived reads were read from the 'undetermined' FASTQ files. Individual matrices were then aggregated using the 10X Cell Ranger 'aggr' command. Sparse matrix was read into Seurat and a dense matrix was exported.
Genome_build: mm10
Supplementary_files_format_and_content: *RNA_wirka_et_al_GEO.txt: mRNA gene-cell matrix. Sample identity, corresponding to the 'sample number in processed data' numbers, is appended to each cell barcode column name
Supplementary_files_format_and_content: *ADT_wirka_et_al_GEO.txt: Antibody-derived tag(ADT)-cell matrix. Sample identity, corresponding to the 'sample number in processed data' numbers, is appended to each cell barcode column name

extract_protocol:
Cells were enzymatically dissociated from the aortic root and ascending aorta (to the level of the brachiocephalic artery) of experimental mice
Cells were captured on a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using either the V2 or V3 chemistry for 3' whole transcriptome analysis.  Manufacturer's instructions for GEM (Gelbead EMulsion) generation, downstream reverse transcription, cDNA isolation were followed. Prior to library construction, cDNA was separated using size selection into mRNA and antibody barcode fractions and PCR amplification and library preparation were conducted separately. For the mRNA fraction, PCR amplification and library preparation were performed following the manufacturer's instructions. For the antibody barcode fraction, PCR and library construction was performed according to the standard CITE-seq protocol (https://cite-seq.com/protocol/). Both library fractions were pooled together prior to sequencing.

tag: timepoint

value: 16 weeks high-fat diet


title: wt_SMC_16wk_citeseq_antibody

value: SMC-lineage


title: mESC6_H3K4me3_R2


title: mESC2_H3K4me3_R1


title: Acute_4_serum

city: Lexington

first: Shavahn

middle: C

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

data_processing:
The sequencing results were analyzed using an in-house small RNA analysis program - sRNAanalyzer (http://srnanalyzer.systemsbiology.net).  The adaptor sequences were trimmed and low-quality sequences such as low nucleotide complexity reads, homopolymer sequences or di-, tri-nucleotide repeat sequences were removed before the reads were mapped against various databases.
The processed reads were then sequentially mapped against databases including Equus caballus miRNA (mirBase; 74), novel Equus caballus miRNA not yet incorporated in mirBase (horse_novel, 75), transcripts, virus, plant and all miRNA (mirBase), coding transcripts (RefSeq), ribosomal and transfer RNA, equine non-coding RNA, equine coding transcripts (CDS) and equine genomic sequence (DNA)
Genome_build: EquCab 2.0
Supplementary_files_format_and_content: .xls - raw read counts

organism: Equus caballus

source_name: serum

extract_protocol:
Isolation of RNA from tissue was performed using RNeasy Mini Kit (Qiagen, Gaithersburg, MD, USA), per manufacturer’s instructions.  After extraction, RNA was analyzed by NanoDrop® (Thermo Fisher Scientific) and Bioanalyzer® (Agilent, Santa Clara, CA, USA) to evaluate concentration, purity and integrity.  All samples had a 230/260 ratio > 1.8, a 260/280 ratio > 2.0 and an RNA integrity number > 8.0.  Serum RNA was isolated using miRNeasy Micro Kit (Qiagen) per the manufacturer’s instructions for cell culture, with chloroform increased to 300 mL and the optional RWT wash included.  Bioanalyzer® analysis was performed to ensure there was no cellular RNA contamination.
Library preparation was performed using a modified small RNA sequencing library construction protocol 72. In brief, the in-house protocol used adapters with four degenerate bases at each ligation site.  Modified adapter sequences are based on Illumina adapter sequences and are listed in Supplementary Table 6.  The adapters were purchased from Integrated DNA Technologies (Coralville, IA, USA).  The 3’ adapter ligation reaction includes 5 ml of RNA, 1 ml of 3’ adapter at 10 nM, 1 ml of RNase inhibitor (Thermo Fisher Scientific), 1 ml of modified T4 RNA Ligase 2 (NEB, Ipswich, MA, USA) and 1 ml of 10 X ligase buffer.  The ligation was performed for 1 hour at 25oC, and was facilitated by the addition of 15% PEG 8000.  Before adding the 5’ adapter, 1 µL of single-strand binding protein (1µg/µl) (Promega, Madison, WI, USA), 1 uL of 5’-deadenylase (NEB) and 1uL of RecJ (NEB) were added, mixed and incubated at 37oC for 1 hour to remove adapter dimers.  For 5’ adapter ligation, 1 µl of 5’ adapter at 25 µM, 1 µL of T4 RNA Ligase (NEB, Ipswich MA), and 1 µL of 10 mM ATP were added then incubated for 1 hour at 25 oC. Complementary DNA (cDNA) was generated from ligated product with SuperScript III reverse transcriptase (Thermo Fisher Scientific) using primer complimentary to the 3’ adapter sequence.  The resulting cDNA was amplified with Illumina universal primer and indexed-primer.  Library size-selection was performed using a PippinHT instrument (Sage Science, Boston, MA, USA) with either a 3% agarose cassette or with 6% polyacrylamide gel. The library with proper insert size was sequenced with the NextSeq 500 (Illumina, San Diego, CA).

value: serum

tag: disease

value: acute placentitis

tag: region


title: ATAC-seq_E16.5_Hnf4_DKO_rep1

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
FastQC (version 0.11.3) was used to check the quality of raw sequencing reads (fastq)
Alignment: Bowtie2, version 2.2.6
Deeptools bamCoverage (v2.4.2, duplicate reads ignored, RPKM normalized and extended reads) was used to generate bigwig files from bam files.
Model-based Analysis of ChIP-Seq (MACS 1.4.1) was used for peak calling and to generate bed files from aligned reads.
Genome_build: mm9

source_name: Mouse midgut epithelial cells

extract_protocol:
Embryos were collected at E16.5, and the freshly harvested embryonic small intestine (caudal stomach to rostral caecum) was opened longitudinally with forceps, and cut into 1 cm pieces. Intestinal tissues were treated with pre-warmed 0.25% Trypsin for 8 min at 37°C on a vortex station (speed set between 6-7), neutralized with 10% FBS, and passed through a 70-μm cell strainer. Cells were stained with the anti-CD326 (EpCAM) magnetic microbeads antibody (Miltenyi Biotec, 130-105-958) for 40 min on ice. To obtain single magnetic antibody conjugated EpCAM positive epithelial cells, stained cells were passed through a 40-μm cell strainer and then collected over a MS column (Miltenyi Biotec, 130-042-201) in a magnetic field. 20,000 cells were used for ATAC-seq as described previously with slight modifications. Briefly, cells were resuspended in ice-cold lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40), and then centrifuged at 500 g for 10 min at 4°C. The isolated nuclei were incubated with Nextera Tn5 Transposase (Illumina FC-121-1030) at 37°C for 30 min. The transposed chromatin was purified with QIAquick PCR Purification Kit (QIAGEN).
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: E16.5 embryonic epithelial cells from the midgut

tag: genotype

value: Shh-Cre; Hnf4af/f; Hnf4gCrispr/Crispr


title: ATAC-seq_E16.5_Hnf4_ghet_Control


title: Acute_1_serum


title: Acute_5_serum


title: Acute_3_serum


title: Control_2_serum

value: control


title: Control_1_serum


title: SubAcute_4_serum

value: subacute placentitis


title: SubAcute_5_serum


title: SubAcute_3_serum


title: SubAcute_2_serum


title: Control_3_EN2

source_name: endometrium

value: endometrium

value: region 2 - gross inflammation without placental separation


title: Control_3_EN1

value: region 1 - main lesion by cervical star with placental separation


title: ATAC-seq_E16.5_Hnf4_DKO_rep2


title: wt_nonSMC_16wk_citeseq_RNA


title: Control_3_CA2

source_name: chorioallantois

value: chorioallantois


title: Control_3_CA1


title: wt_SMC_16wk_citeseq_RNA

value: Myh11(cre), ROSA(tdT), ApoE(-/-)


title: Control_3_serum


title: Control_2_EN2


title: SubAcute_1_serum


title: Control_2_EN1


title: Control_2_CA2


title: Control_2_CA1


title: Acute_2_serum


title: Control_1_EN2


title: SubAcute_5_CA2


title: SubAcute_5_EN1


title: SubAcute_5_EN2


title: Control_1_CA1


title: SubAcute_4_EN2


title: SubAcute_5_CA1


title: Control_1_EN1


title: SubAcute_4_EN1


title: SubAcute_4_CA2


title: SubAcute_3_EN2


title: SubAcute_4_CA1


title: SubAcute_3_EN1


title: SubAcute_3_CA1


title: SubAcute_2_EN1


title: SubAcute_3_CA2


title: SubAcute_2_EN2


title: SubAcute_1_EN2


title: SubAcute_1_EN1


title: SubAcute_2_CA1


title: SubAcute_2_CA2


title: SubAcute_1_CA1


title: mESC4_H3K4me3

source_name: single-cell 46C derived mESC#4 subline

value: 46C mESC subline

value: H3K4me3 (Millipore, 07-473)


title: mESC1_H3K4me3_R1


title: SubAcute_1_CA2


title: Control_1_CA2


title: WT_DOX_50_1

city: San Francisco

first: Ruilin

last: Tian

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California, San Francisco

description:
Quant-seq
XG_normalized_counts2.csv

data_processing:
Salmon v0.14.1 was used to obtain transcript abundance counts
Gene-level count estimates were obtained using tximport v1.8.0
Differential gene expression analysis using DESeq2 v1.20.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files are in "CSV(Comma-separated values)" format. Each row is a gene and each column is a sample. Values are normalzied counts

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted from cells using the Quick-RNA Miniprep Kit (Zymo; Cat. No. R1054)
Libraries were prepared by UC Davis Genome Center according to the 3'-Tag RNA seq protocol

tag: gene knockdown

tag: drug treatment

value: Doxycycline


title: OMA1_KD_oligomycin_2

description:
Quant-seq
XG_normalized_counts1.csv

value: oligomycin


title: WT_DOX_50_2

description:
Quant-seq
XG_normalized_counts2.csv


title: WT_DOX_0_2

description:
Quant-seq
XG_normalized_counts2.csv

value: untreated


title: OMA1_KD_oligomycin_3

description:
Quant-seq
XG_normalized_counts1.csv


title: OMA1_KD_untreated_2

description:
Quant-seq
XG_normalized_counts1.csv


title: wt_nonSMC_8wk_051717

value: 8wk high-fat diet

value: aortic root and ascending aorta

value: non-SMC


title: OMA1_KD_oligomycin_1

description:
Quant-seq
XG_normalized_counts1.csv


title: HRI_KD_oligomycin_2

description:
Quant-seq
XG_normalized_counts1.csv

value: HRI (sgRNA_i1)


title: OMA1_KD_untreated_1

description:
Quant-seq
XG_normalized_counts1.csv


title: HRI_KD_oligomycin_3

description:
Quant-seq
XG_normalized_counts1.csv


title: WT_DOX_0_1

description:
Quant-seq
XG_normalized_counts2.csv


title: OMA1_KD_untreated_3

description:
Quant-seq
XG_normalized_counts1.csv


title: HRI_KD_untreated_3

description:
Quant-seq
XG_normalized_counts1.csv


title: HRI_KD_oligomycin_1

description:
Quant-seq
XG_normalized_counts1.csv


title: HRI_KD_untreated_2

description:
Quant-seq
XG_normalized_counts1.csv


title: DELE1_KD_oligomycin_1

description:
Quant-seq
XG_normalized_counts1.csv

value: DELE1 (sgRNA_i1)


title: DELE1_KD_oligomycin_2

description:
Quant-seq
XG_normalized_counts1.csv


title: DELE1_KD_untreated_1

description:
Quant-seq
XG_normalized_counts1.csv


title: WT_oligomycin_3

description:
Quant-seq
XG_normalized_counts1.csv

value: Non targeting control(1872)


title: HRI_KD_untreated_1

description:
Quant-seq
XG_normalized_counts1.csv


title: WT_oligomycin_2

description:
Quant-seq
XG_normalized_counts1.csv


title: WT_oligomycin_1

description:
Quant-seq
XG_normalized_counts1.csv


title: WT_untreated_3

description:
Quant-seq
XG_normalized_counts1.csv


title: WT_untreated_1

description:
Quant-seq
XG_normalized_counts1.csv


title: WT_untreated_2

description:
Quant-seq
XG_normalized_counts1.csv


title: rca3-2

description: processed data file number = 6

data_processing:
FASTQ files were generated by demultiplexing the Illumina sequencer's base call files (BCLs) using 10X CellRanger 'mkfastq' command.
For cell-gene matrix files, individual matrices were first generated using 10X Cell Ranger 'count' command. Individual matrices were then aggregated using the 10X Cell Ranger 'aggr' command. Sparse matrix was read into Seurat and a dense matrix was exported.
Genome_build: GRCh38
Supplementary_files_format_and_content: cell-gene readcount matrix; sample identity, corresponding to the 'processed data file' numbers (indicated in the sample description field), is appended to each cell barcode column name

source_name: coronary artery from explanted heart

extract_protocol:
Cells were enzymatically dissociated from freshly-obtained human right coronary artery samples
Cells were captured on a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using either the V2 or V3 chemistry for 3' whole transcriptome analysis. Manufacturer's instructions for GEM (Gelbead EMulsion) generation, downstream reverse transcription, cDNA isolation, PCR amplification and library preparation were followed without any significant alterations

tag: subject status

value: patients undergoing heart transplantation

value: explanted hearts

value: proximal to mid right coronary artery (RCA)

tag: cell type

value: all cell types present in freshly dissociated artery

tag: sample preparation

value: enzymatic digestion, FACS


title: rca4-1

description: processed data file number = 8


title: rca1-2

description: processed data file number = 2


title: rca2-2

description: processed data file number = 4


title: DELE1_KD_oligomycin_3

description:
Quant-seq
XG_normalized_counts1.csv


title: rca1-1

description: processed data file number = 1


title: rca2-1

description: processed data file number = 3


title: MDA-MB-231 Engulfing4

city: Ann Arbor

first: Yu-Chih

last: Chen

state: MI

address: 1301 Beal Ave.

institute: University of Michigan

data_processing:
Bowtie and Tophat read aligner
Cufflink
Cuffdiff
Genome_build: hg19 genome
Supplementary_files_format_and_content: Cuffdiff output to compare the gene expression between wild-type and engulfing MDA-MB-231 cells

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231 cells were cultured in DMEM (Gibco 11965) with 10% FBS (Gibco 10082) and 1% penicillin/streptomycin (Gibco 15070).

extract_protocol:
Total RNA was extracted using the RNeasy kit from QIAGEN following the manufacturers protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Engulfing MDA-MB-231 cells were retrieved from microfluidic chip and expand the number of sequencing

tag: cell line

value: Breast cancer cell line

tag: phenotype

value: Engulfing


title: MDA-MB-231 Engulfing1


title: MDA-MB-231 Engulfing2


title: MDA-MB-231 Engulfing3


title: MDA-MB-231 WT2

value: wildtype


title: MDA-MB-231 Engulfing6


title: MDA-MB-231 Engulfing5


title: MDA-MB-231 WT1


title: DELE1_KD_untreated_2

description:
Quant-seq
XG_normalized_counts1.csv


title: DELE1_KD_untreated_3

description:
Quant-seq
XG_normalized_counts1.csv


title: MDA-MB-231 WT3


title: hESC_1_8_H3K4me3_R2

source_name: single-cell HUES9 derived hESC 1.8 subline

value: HUES9 hiPSC subline

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: H3K4me3 (Millipore, 07-473)


title: hESC_1_8_H3K4me3_R1


title: HUES9_hESC_Rad21

source_name: HUES9 hiPSC parental line

value: HUES9 hiPSC line

value: Rad21 (Abcam, ab992)


title: rca3-3

description: processed data file number = 7


title: HUES9_hESC_CTCF

value: CTCF (Millipore, 07-729)


title: rca3-1

description: processed data file number = 5


title: hiPSC_1_15_H3K4me3_R2

source_name: single-cell CVI derived hiPSC 1.15 subline

value: Craig Venter-I (CVI) hiPSC subline


title: hiPSC_1_7_H3K4me3_R2

source_name: single-cell CVB derived hiPSC 1.7 subline

value: Craig Venter-B (CVB) hiPSC subline


title: hiPSC_1_8_H3K4me3_R2

source_name: single-cell CVB derived hiPSC 1.8 subline


title: hiPSC_1_14_H3K4me3_R2

source_name: single-cell CVI derived hiPSC 1.14 subline


title: hiPSC4_JMJD2A

source_name: single-cell CVB derived hiPSC#4 subline (genome editing: PSEN1 deltaE9 -/-, IB12)

value: JMJD2A (Bethyl, A300-861A)


title: hiPSC3_JMJD2A

source_name: single-cell CVB derived hiPSC#3 subline (genome editing: PSEN1 deltaE9 +/-, IID12)


title: hESC_1_7_H3K4me3_R2

source_name: single-cell HUES9 derived hESC 1.7 subline


title: hiPSC_1_13_H3K4me3_R2

source_name: single-cell CVI derived hiPSC 1.13 subline


title: hiPSC5_JMJD2A

source_name: single-cell CVB derived hiPSC#5 subline (genome editing: PSEN1 deltaE9 -/-, IIA12)


title: hiPSC4_SMCDH1

value: SMCDH1 (Abcam, ab31865)


title: hiPSC3_SIN3A

value: SIN3A (Novus NB600-1263)


title: hiPSC2_SMCDH1

source_name: single-cell CVB derived hiPSC#2 subline (genome editing: PSEN1 deltaE9 +/-, IIA11)


title: hiPSC3_SMCDH1


title: hiPSC5_SIN3A


title: hiPSC4_REST

value: REST/NRSF (Millipore, CS200555)


title: HUES9_hESC_H3K4me3_R2


title: hiPSC5_REST


title: hiPSC2_SIN3A


title: hiPSC2_REST


title: hiPSC5_H2A_Z

value: H2A.Z (Millipore, 07-594)


title: hiPSC_1_9_H3K4me3_R2

source_name: single-cell CVB derived hiPSC 1.9 subline


title: hiPSC4_H2A_Z


title: hiPSC3_H2A_Z


title: hiPSC2_H2A_Z


title: hiPSC5_H3K9me3

value: H3K9me3 (Abcam, ab8898)


title: hiPSC3_H3K9me3


title: hiPSC5_H3K9ac

value: H3K9ac (Millipore 07-352 and Abcam, ab4441)


title: hiPSC2_JMJD2A


title: hiPSC2_H3K9me3


title: hiPSC4_H3K9ac


title: hiPSC4_SIN3A


title: hiPSC3_H3K9ac


title: hiPSC2_H3K9ac


title: hiPSC4_H3K4me2

value: H3K4me2 (Active Motif, 39141)


title: Spheroid_Rep3

city: St Louis

first: Lisa

middle: Jean

last: Funkhouser-Jones

state: MO

address: 660 S. Euclid Avenue

department: Molecular Microbiology

institute: Washington University School of Medicine

data_processing:
Base-calling was performed with RTA version 2.7.7
Five bases were trimmed from the 5' end of all reads. Trimmed reads were mapped to the mm10 genome build using the STAR aligner in Partek Flow with default parameters.
Counts per million (CPM) values were determined by dividing the number of reads per gene by the total number of reads in the sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include CPM values for each sample

source_name: ileal stem cell-derived spheroids

extract_protocol:
Cells were homogenized using a QiaShredder column (QIAGEN) and total RNA was purified using an RNeasy Mini kit (QIAGEN) followed by treatment with a DNase DNeasy kit (Thermo Fisher Scientific).
Ribosomal RNA was removed from 1 ug total RNA using a Ribo-ZERO kit (Illumina-EpiCentre) then RNA libraries were prepared using standard Illumina techniques

tag: strain

tag: growth protocol

value: Grown as spheroids in L-WRN media for 3 days


title: hiPSC5_H3K4me2


title: Spheroid_Rep2


title: hiPSC3_H3K4me2


title: ALI_Day3_Rep2

source_name: ileal stem cell-derived epithelium

value: Plated on transwells, submerged in L-WRN media for 7 days, ALI for 3 days


title: ALI_Day3_Rep3


title: ALI_Day3_Rep4


title: hiPSC7_Rad21_R2

source_name: single-cell CVB derived hiPSC#7 subline (genome editing: APP V717 -/-, IIIB12)


title: hiPSC8_Rad21_R2

source_name: single-cell CVB derived hiPSC#8 subline (failed genome editing, IB7)


title: hiPSC2_H3K4me2


title: Spheroid_Rep1


title: ALI_Day3_Rep1


title: hiPSC6_Rad21_R2

source_name: single-cell CVB derived hiPSC#6 subline (genome editing: APP V717 +/-, IV8)


title: hiPSC5_Rad21_R2


title: Non-ALI_Day3_Rep4

value: Plated on transwells and submerged in L-WRN media for 10 days


title: hiPSC5_SMCDH1


title: Non-ALI_Day3_Rep3


title: hiPSC4_Rad21_R2


title: hiPSC2_Rad21_R2


title: Non-ALI_Day0_Rep4

value: Plated on transwells and submerged in L-WRN media for 7 days


title: Non-ALI_Day3_Rep1


title: hiPSC1_Rad21_R2

source_name: single-cell CVB derived hiPSC#1 subline (failed genome editing, IID4)


title: hiPSC3_REST


title: Non-ALI_Day0_Rep3


title: CVB_hiPSC_Rad21_R2

source_name: CVB hiPSC parental line

value: Craig Venter-B (CVB) hiPSC line


title: Non-ALI_Day0_Rep2


title: hiPSC8_CTCF_R2


title: hiPSC4_H3K9me3


title: hiPSC4_CTCF_R2


title: hiPSC2_CTCF_R2


title: hiPSC1_CTCF_R2


title: hiPSC3_CTCF_R2


title: hiPSC5_CTCF_R2


title: hiPSC3_Rad21_R2

value: Rad21 (Abcam, ab992)


title: hiPSC6_H3K4me3

value: H3K4me3 (Millipore, 07-473)


title: hiPSC8_H3K4me3


title: CVB_hiPSC_CTCF_R2

value: CTCF (Millipore, 07-729)


title: ko_SMC_16wk_070617

tag: genotype/variation

value: Myh11(cre), Tcf21(flx/flx), ROSA(tdT), ApoE(-/-)

tag: treatment/timepoint

value: 16wk high-fat diet

tag: number of animals included in sample

tag: tissue

value: aortic root and ascending aorta

value: SMC lineage


title: hiPSC6_CTCF_R2

value: Craig Venter-B (CVB) hiPSC subline


title: Non-ALI_Day0_Rep1


title: Non-ALI_Day3_Rep2


title: 599K598 vs Vector BR1B

type: RNA

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

description: total RNA was directly labeled with the Micromax ASAP labeling kit, using 10 ug total RNA for each sample.

hyb_protocol: Combimatrix 100 ul volume cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner

data_processing: The raw total intensities were treated as follows to generate the M Log2 ratios for this work.  Background signal was calculated from a set of negative control spots incorporated into the array.  As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest.  To avoid this issue the negative control spots were ranked according to their total intensity.  The average of the lowest 30% was calculated.  Background signal was calculated as this mean + 2 standard deviations.  The background signal was then subtracted from the total intensity for each spot.  Probes whose signal was not greater than zero after background subtraction were omitted from further analysis.  For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3)  LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes.  Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001.  Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.

organism: Geobacter sulfurreducens

source_name: overexpression of GsuTCS1

label_protocol: Micromax ASAP direct RNA labeling protocol

extract_protocol: hot phenol method

tag: sample type

value: overexpression of GsuTCS1

tag: growth condition

value: Geobacter sulfurreducens was grown anaerobically to mid-log in batch NBAF media with kanamycin and IPTG

source_name: control with vector

value: control with vector


title: 599K598 vs Vector BR2B


title: 599K598 vs Vector BR3B


title: Right ventricle, MCT+NI, mouse 617

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).

label: biotin

source_name: right ventricle, MCT injection, nutritional intervention

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Female C57BL/6 mice (aged 8 weeks) were obtained from Janvier-Labs (Saint-Berthevin Cedex, France) and housed at identical conditions under a 12:12 h light/dark cycle with food and water provided ad libitum. After arrival mice were randomly allocated to one of the 3 experimental groups, and immedialtely fed the experimental diets for 2 wks until start of the injections.

extract_protocol: RNA from right ventricle was isolated (RNeasy Micro kit, Qiagen, Venlo, the Netherlands). Subsequently, RNA was quantified (Nanodrop ND1000, Nanodrop technologies Wilmington, DE, USA) and integrity was checked by an Agilent 2100 Bioanalyser with RNA 6000 microchips (Agilent Technologies, South Queensferry, UK).

treatment_protocol: From 10 weeks of age, monocrotaline (MCT, 600 mg/kg dissolved in saline) was given weekly by subcutaneous injection during 8 weeks. As control served sham-treated mice that received a matched volume of saline during 8 weeks and were fed the standard semi-synthetic control diet (AIN-93M) [reference group]. Mice in the MCT group were fed either the standard semi-synthetic control diet (AIN-93M) [MCT group], or an isocaloric semi-synthetic diet high in protein, leucine, oligosaccharides and fish oil [MCT+NI group].

tag: Sex

value: female

tag: mouseid

tag: muscle

value: right ventricle

tag: combined treatment group

value: monocrotaline (MCT), nutritional intervention

tag: monocrotaline (mct) (yes/no)

value: yes

tag: nutritional intervention (yes/no)

tag: group description

value: MCT+NI


title: 599K598 vs Vector BR1A


title: 599K598 vs Vector BR3A


title: dag W (weaning) 28groep 5 big 40

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

institute: Wageningen UR

hyb_protocol: The hybridization temperature is 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays are washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: The arrays where scanned using the DNA microarray scanner with SureScan High-Resolution Technology from Agilent Technologies. Agilent Scan Control with resolution of 5 µm, 16 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 colour gene expression.

data_processing: The data were analysed by using R (v3.0.2) by executing different packages, including LIMMA (Gentleman et al., 2005) and arrayQualityMetrics (Kauffmann et al., 2009). The data were read in and background corrected (method=normexp and offset=1) with functions from the R package LIMMA (Gentleman et al., 2005) from Bioconductor (Gentleman et al., 2004). Quantile normalisation of the data was done between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes were removed in a three-step procedure, 1) get the highest of the dark spots to get a base value, 2) multiply by 1.1, and 3) the gene/probe must be expressed in each of the samples in the experimental condition.

organism: Sus scrofa

source_name: jejunum, antibiotic, day W28

label_protocol: Labelling of RNA was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling. The input was 10 ng of total RNA and 600 ng of labelled cRNA is used on the eight pack array. Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies).

growth_protocol: Thirty-one Hypor gilts and sows divided over three different batches were allotted to one of two treatments based on body weight, backfat thickness and parity 4 weeks before farrowing (day 87 of gestation). From farrowing till weaning they were fed the standard lactation diet. Sows were housed at Trouw Nutrition Swine Research Centre in gestation group housing and lactation departments. During lactation sows were housed individually. Sows had free access to water and were fed according to a standard feeding scheme.

extract_protocol: Total RNA was extracted from 50 to 100 mg jejunum or colon tissue. All samples were homogenised using the TisuPrep Homogenizer Omni TP TH220P) in TRizol reagent (Life Technologies) as recommended by the manufacturer with minor modifications. The homogenised tissue samples were dissolved in 5 ml of TRizol reagent. After centrifugation the supernatant was transferred to a fresh tube. Subsequently, Direct-zol™ RNA MiniPrep Kit by Zymo Research was used as described by the manufacturer. The RNA was quantified by absorbance measurements at 260 nm. Quality Control was performed by Agilent Bioanalyser.

treatment_protocol: One treatment group (Control - C) received standard gestation feed and standard lactation feed within lactation (one week before expected day of farrowing until weaning). The second treatment group (antibiotic treatment – AB) received daily an oral antibiotic treatment with 15 mg / kg body weight of Paracillin® SP (amoxicillin) (MSD Animal Health, Boxmeer, The Netherlands) from one week before expected day of farrowing until farrowing as a topdressing to the standard lactation feed.

value: jejunum

tag: age (days)

tag: treatment

value: antibiotic


title: Right ventricle, MCT, mouse 644

source_name: right ventricle, MCT injection, standard diet

tag: strain

value: monocrotaline (MCT), standard diet

value: no

value: MCT


title: RNAseq in AtT-20 expressing active Creb3l2 and XBP1 replicate 3

city: Montreal

first: Amandine

last: Bemmo

state: QC

address: 110 Avenue des Pins

country: Canada

institute: IRCM

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 50bp reads were trimmed with trimmomatic v0.22 to obtain high quality reads and then mapped to the GRCm38 mouse genome build using TopHat v2.0.8
Gene expression raw count were calculated with HTSeq-count from HTSeq v0.5.4
Differential gene expression analysis was performed with the R package DeSeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene expression raw counts, fold changes (Log2), P-values and adjusted P-values (q-values)

source_name: AtT-20 cells expressing 3x flag-Creb3l2 and XBP1s

growth_protocol: AtT-20 cells were plated on adherent culture dishes to obtain about 70% confluence after 3 days. They are cultured in DMEM + 10% FBS.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
mRNA library preparation was done at the IRCM Molecular Biology facility following the TruSeq Stranded mRNA sample preparation guide (Illumina). Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 36bp paired end reads.

tag: cell type

value: pituitary corticotroph cell

tag: passages

tag: cell line

tag: mrna enrichment protocol

value: polyA


title: RNAseq in AtT-20 expressing active (ie spliced) XBP1 (XBP1s) replicate 3

source_name: AtT-20 cells expressing XBP1s


title: RNAseq in AtT-20 expressing active (ie spliced) XBP1 (XBP1s) replicate 1


title: Right ventricle, MCT+NI, mouse 615


title: Right ventricle, MCT, mouse 640


title: Right ventricle, MCT+NI, mouse 619


title: RNAseq in AtT-20 expressing active Creb3l2 and XBP1 replicate 1


title: Right ventricle, MCT, mouse 641


title: Right ventricle, sham, mouse 620

source_name: right ventricle, sham injection, standard diet

value: sham, standard diet

value: reference


title: 599K598 vs Vector BR2A

value: overexpression of GsuTCS1


title: RNAseq in AtT-20 expressing active (ie spliced) XBP1 (XBP1s) replicate 2


title: RNAseq in AtT-20 expressing active Creb3l2 and XBP1 replicate 2


title: dag W (weaning) 28 groep 5 big 39

tag: tissue


title: Right ventricle, sham, mouse 624


title: dag W (weaning) 28 groep 5 big 37


title: dag W (weaning) 4 groep 5 big 34

source_name: jejunum, antibiotic, day W4


title: RNAseq in AtT-20 expressing active (ie cleaved) Creb3l2 replicate 1

source_name: AtT-20 cells expressing 3x flag-Creb3l2


title: RNAseq in AtT-20 expressing Neo (control) replicate 3

source_name: AtT-20 cells expressing 3x flag-Neo


title: RNAseq in AtT-20 expressing Neo (control) replicate 2


title: dag W (weaning) 4 groep 5 big 33


title: RNAseq in AtT-20 expressing Neo (control) replicate 1


title: RNAseq in AtT-20 expressing active (ie cleaved) Creb3l2 replicate 3


title: dag W (weaning) 4 groep 5 big 32


title: FLAG ChIPseq in AtT-20 cells expressing 3x flag-Creb3l2 (cleaved form)

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 36bp (XBP1) or 50bp (flag-Creb3l2) reads were trimmed to obtain high quality reads and then mapped to the mm9 mouse genome build using Bowtie with the following parameter: -t -p 4 --trim5 1 --best mm9 –S
Peaks were identified by comparing Creb3I2 to flag ( GSM2324113) and XBP1 to IgG (GSM2324114) using MACS callpeak function with the parameters: --bw 250 -g mm --mfold 7,20 -p 1e-5 ; the parameter -f BAMPE was added for Creb3I2
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using HOMER
Supplementary_files_format_and_content: Text files were generated with MACS peak caller

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-400bp were kept for library preparation
The libraries and flowcells were prepared at the IRCM Molecular Biology Core facility following Illumina recommendations (Illumina, San Diego, CA) and then sequenced on Hiseq 2000 at the Génome Québec Innovation Centre.

tag: chip antibody

value: FLAG M2 SIGMA (F3165)


title: dag W (weaning) 4 groep 5 big 10


title: dag W (weaning) 28 groep 5 big 38


title: HS Rep 2 miRNA-seq

city: San Deigo

first: Amy

last: Pasquinelli

address: 9500 Gilman Drive

department: Biological Sciences

data_processing:
For piRNA analysis:   reads were trimmed for quality and length between (16-30nts) aligned to piRNAs (obtained from version WS235 of C. elegans genome from   worm base). Primary alignments were obtained with sam tools differential expression was determined by DESeq2
For miRNA analysis:
reads were trimmed
reads were aligned to C. elegans miRNAs obtained from Mirbase
Counts were generated with custom perl scripts
Genome_build: differential expression was determined with DESeq2
Supplementary_files_format_and_content: CSV; Contains DESeq2 output

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: WT Caenorhabditis elegans (N2 Bristol) animals were cultured on OP50 bacteria at 20°C, and collected at the last larval. Standard worm synchronization methods were used.

extract_protocol: RNA was extracted with Trizol and DNAse treated.

treatment_protocol: The experimental Group was treated with a 6hr HS of a Tempearture of 35ºC

tag: Stage

tag: genotype/variation

value: wildtype N2

value: 4 hr of 35C


title: XBP1 ChIPseq in AtT-20 cells

description: normal (non Tg) AtT-20 cells

source_name: AtT-20 cells

value: XBP1 M-186 Santa Cruz (Sc-7160)


title: HS Rep 1 miRNA-seq


title: CTRL Rep 2 miRNA-seq

description: control; 20ºC


title: CTRL Rep 1 miRNA-seq

description: control; 20ºC


title: dag W (weaning)  groep 5 big 8

source_name: jejunum, antibiotic, day W

value: W


title: dag 7 groep 5 big 21

source_name: jejunum, antibiotic, day 7


title: dag W (weaning)  groep 5 big 29


title: dag 7 groep 5 big 20


title: dag 7 groep 5 big 4


title: dag 1 groep 5 big 18

source_name: jejunum, antibiotic, day 1


title: dag W (weaning)  groep 5 big 25


title: dag W (weaning)  groep 5 big 7


title: dag 1 groep 5 big 17


title: Right ventricle, sham, mouse 625

tag: Sex

value: female

tag: mouseid

value: right ventricle


title: dag W (weaning) 28 groep 1 big 34

source_name: jejunum, control, day W28

value: jejunum

value: control


title: dag W (weaning) 4 groep 1 big 10

source_name: jejunum, control, day W4


title: dag W (weaning) 4 groep 1 big 31


title: dag W (weaning)  groep 1 big 24

source_name: jejunum, control, day W


title: dag W (weaning) 4 groep 1 big 29


title: dag 1 groep 5 big 21

value: antibiotic


title: dag 7 groep 1 big 23

source_name: jejunum, control, day 7


title: dag W (weaning) 4 groep 1 big 32


title: wild-type Ey+ INPs - replicate 3

city: Vienna

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
Bascalling performed using RTA 1.18.64.0
The unstranded reads were screened for ribosomal RNA by aligning with BWA (v0.7.12) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v2.1.1) against the Drosophila melanogaster genome (FlyBase r6.12). Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r6.12).
Reads arising from duplication events are marked as such in the alignment (SAM/BAM files) as follows. The different tags are counted at each genomic position. Thereafter, the diversity of tags at each position is examined. First, tags are sorted descending by their count. If several tags have the same occurrence, they are further sorted alphanumerically. Reads sharing the same tag, are sorted by the average PHRED quality. Again if several reads have the same quality, they are further sorted alphanumerically. Now the tags are cycled through by their counts. Within one tag, the read with the highest average PHRED quality is the unique correct read and all subsequent reads with the same tag are marked as duplicates. Furthermore, all reads which have tags with one mismatch difference compared the pool of valid read tags are also marked as duplicates.
snRNA, rRNA, tRNA, snoRNA and pseudogenes are masked from the GTF (FlyBase r6.12) with subtractBed from bedtools (v2.26.0).
The aligned reads were counted with HTSeq (v0.6.1; intersection-nonempty).
The genes were subjected to differential expression analysis with DESeq2 (v1.12.4).
Genome_build: FlyBase r6.12
Supplementary_files_format_and_content: Excel files (xlsx) containing the differential expression analysis (DESeq2 output); Htseq count files (txt)

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: Flies expressing UAS-cd8::tdTomato; erm-GAL4 were crossed with D-, Grh- or Ey-GFP flies. The crosses were at 25C for two night for egg-laying. Then, the egss were transferred to 29C for five days. Wandering L3 larval brains were collected and prepared for FACS-sorting.

extract_protocol:
For each samples, 6000-7000 INPs of different temporal stages were FACS sorted and total RNA was isolated using TRIzol LS reagent. Total RNA was converted to first strand (using oligo-(dT)20 primers) and second strand cDNA.
Library preparation was done using Illumina's protocol with Nextera DNA Library Preparation Kit using a modified Index primer 1 (i7), which included random octamere sequences for molecular barcoding.

value: brain

value: Ey+ INP

value: third instar larva

tag: marker

value: cells express membrane bound tdTomato and Eyeless protein tagged with GFP (UAS-cd8::tdTomato and Ey::GFP)


title: wild-type Ey+ INPs - replicate 2


title: dag W (weaning) 28 groep 1 big 13


title: dag W (weaning)  groep 1 big 25


title: dag W (weaning) 4 groep 1 big 30


title: dag W (weaning) 28 groep 1 big 37


title: dag 7 groep 1 big 22


title: dag 7 groep 1 big 20


title: dag 7 groep 1 big 4


title: dag 7 groep 1 big 21


title: dag 7 groep 5 big 24


title: dag 1 groep 5 big 2


title: wild-type Ey+ INPs - replicate 1


title: dag 7 groep 1 big 19


title: wild-type Grh+ INPs - replicate 3

value: Grh+ INP

value: cells express membrane bound tdTomato and Grainyhead protein tagged with GFP (UAS-cd8::tdTomato and Grh::GFP)


title: wild-type D+ INPs - replicate 3

value: D+ INP

value: cells express membrane bound tdTomato and Dichaete protein tagged with GFP (UAS-cd8::tdTomato and D::GFP)


title: wild-type Grh+ INPs - replicate 2


title: wild-type D+ INPs - replicate 1


title: wild-type D+ INPs - replicate 2


title: wild-type Grh+ INPs - replicate 1


title: dag W (weaning)  groep 1 big 7


title: dag 1 groep 1 big 19

source_name: jejunum, control, day 1


title: dag 1 groep 1 big 18


title: dag 1 groep 1 big 19B


title: dag 1 groep 1 big 17


title: dag 1 groep 1 big 20


title: dag 1 groep 1 big 16


title: CD8_47_Sepsis

city: Collegeville

first: James

middle: Raymond

last: Brown

state: PA

address: 1250 S. Collegeville Road

institute: GlaxoSmithKline

description: 47.024.Blood.CD8.8.17.2016.Sepsis.Late.AR027_ATTCCT_L001_001

data_processing:
An initial quality check of raw FASTQ data was performed using FastQC.
Reads that were either less than 25bp, or had a maximum quality score below Q15, or average quality score below Q10 were discarded. The quality filtered reads were mapped to the human reference genome GRCh38/hg38 (Dec 2013) using STAR.
The read counts were called using Subread.
Differential gene expression analysis was performed for CD4+, CD8+ and CD14+ samples using DESeq2 in R Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample

extract_protocol:
RNA was extracted and purified using Qiagen’s RNeasy Mini Kit on the QIAcube.
Starting with 350 nanograms of total RNA, barcoded libraries were prepared using Illumina’s TruSeq RNA Library Prep totalRNA kit. The quality of the libraries was confirmed using the Agilent Bioanalyzer DNA1000 Assay. The libraries were quantified and normalized by qPCR using KAPA Library Quantification Kit.

tag: patient group

value: Sepsis

tag: subjectid

tag: sepsis stage

value: Late

tag: sampleID


title: CD4_51_Crit-Ill

description: 51.029.Blood.CD4.9.7.2016.Crit-Ill.NA.AR002_CGATGT_L007_001

value: Crit-Ill


title: CD8_48_Sepsis

description: 48.025.Blood.CD8.8.24.2016.Sepsis.Late.AR004_TGACCA_L004_001


title: CD4_4_Sepsis

description: 4.026.Blood.CD4.8.24.2016.Sepsis.Late.AR027_ATTCCT_L001_001


title: CD8_6_Sepsis

description: 6.010B.Blood.CD8.7.12.2016.Sepsis.Late.AR023_GAGTGG_L006_001


title: CD8_44_Healthy

description: 44.020.Blood.CD8.8.12.2016.Healthy.NA.A018_GTCCGC_L008_001

value: Healthy


title: CD4_7_Cancer

description: 7.745.PBMC.CD4.9.13.2016.NA.NA.AR013_AGTCAA_L006_001

value: Cancer


title: CD8_46_Sepsis

description: 46.022.Blood.CD8.8.16.2016.Sepsis.Late.AR022_CGTACG_L004_001


title: CD4_40_Healthy

description: 40.018.Blood.CD4.8.2.2016.Healthy.NA.AR019_GTGAAA_L007_001


title: CD8_43_Sepsis

description: 43.019.Blood.CD8.8.3.2016.Sepsis.Early.AR011_GGCTAC_L007_001

value: Early


title: CD8_5_Sepsis

description: 5.010A.Blood.CD8.7.6.2016.Sepsis.Early.AR006_GCCAAT_L007_001


title: CD8_41_Healthy

description: 41.018.Blood.CD8.8.2.2016.Healthy.NA.AR025_ACTGAT_L001_001


title: CD4_49_Sepsis

description: 49.027.Blood.CD4.9.1.2016.Sepsis.Late.AR005_ACAGTG_L003_001


title: CD4_9_Cancer

description: 9.745.Tumor.CD4.9.13.2016.unknown.NA.AR006_GCCAAT_L003_001


title: CD8_39_Healthy

description: 39.017.Blood.CD8.8.2.2016.Healthy.NA.AR006_GCCAAT_L003_001


title: CD4_38_Healthy

description: 38.017.Blood.CD4.8.2.2016.Healthy.NA.AR008_ACTTGA_L007_001


title: CD8_8_Cancer

description: 8.745.PBMC.CD8.9.13.2016.NA.NA.A027_ATTCCT_L008_001


title: CD8_35_Crit-Ill

description: 35.015.Blood.CD8.NA.Crit-Ill.NA.AR008_ACTTGA_L004_001


title: CD8_52_Crit-Ill

description: 52.029.Blood.CD8.9.7.2016.Crit-Ill.NA.AR014_AGTTCC_L002_001


title: CD4_36_Crit-Ill

description: 36.016.Blood.CD4.NoDoD.Crit-Ill.NA.AR004_TGACCA_L007_001


title: CD4_34_Crit-Ill

description: 34.015.Blood.CD4.NoDoD.Crit-Ill.NA.AR013_AGTCAA_L006_001


title: CD8_33_Crit-Ill

description: 33.014.Blood.CD8.7.20.2016.Crit-Ill.NA.AR002_CGATGT_L006_001


title: CD8_50_Sepsis

description: 50.027.Blood.CD8.9.1.2016.Sepsis.Late.AR025_ACTGAT_L001_001


title: CD8_45_Healthy

description: 45.021.Blood.CD8.8.12.2016.Healthy.NA.AR003_TTAGGC_L002_001


title: CD8_31_Crit-Ill

description: 31.013.Blood.CD8.7.13.2016.Crit-Ill.NA.AR011_GGCTAC_L005_001


title: CD8_30_Crit-Ill

description: 30.011.Blood.CD8.7.12.2016.Crit-Ill.NA.AR003_TTAGGC_L002_001


title: CD4_3_Healthy

description: 3.023.Blood.CD4.8.16.2016.Healthy.NA.AR010_TAGCTT_L007_001


title: CD4_32_Crit-Ill

description: 32.014.Blood.CD4.7.20.2016.Crit-Ill.NA.A016_CCGTCC_L008_001


title: CD8_29_Sepsis

description: 29.009.Blood.CD8.6.29.2016.Sepsis.Early.AD013_AGTCAA_L008_001


title: CD8_28_Sepsis

description: 28.008.Blood.CD8.6.8.2016.Sepsis.Early.AR010_TAGCTT_L005_001


title: CD4_25_Sepsis

description: 25.007.Blood.CD4.6.1.2016.Sepsis.Early.AR005_ACAGTG_L003_001


title: CD8_26_Sepsis

description: 26.007.Blood.CD8.6.1.2016.Sepsis.Early.AR015_ATGTCA_L003_001


title: CD8_24_Sepsis

description: 24.026.Blood.CD8.8.24.2016.Sepsis.Late.AR001_ATCACG_L005_001


title: CD4_16_Sepsis

description: 16.010.Blood.CD4.7.12.2016.Sepsis.Late.AR011_GGCTAC_L005_001


title: CD4_17_Crit-Ill

description: 17.011.Blood.CD4.7.12.2016.Crit-Ill.NA.AR002_CGATGT_L006_001


title: CD4_2_Healthy

description: 2.021.HC.Blood.CD4.8.12.2016.Healthy.NA.AR023_GAGTGG_L006_001


title: CD8_98_Sepsis

description: 98_035_9_29_2016_Sepsis_CD8_Blood_Early_AR009_S27_L007_001


title: CD4_23_Sepsis

description: 23.025.Blood.CD4.8.24.2016.Sepsis.Late.AR018_GTCCGC_L001_001


title: CD4_18_Crit-Ill

description: 18.013.Blood.CD4.7.13.2016.Crit-Ill.NA.AD005_ACAGTG_L008_001


title: CD4_20_Sepsis

description: 20.022.Blood.CD4.8.16.2016.Sepsis.Late.AD012_CTTGTA_L008_001


title: CD4_15_Sepsis

description: 15.010.Blood.CD4.7.6.2016.Sepsis.Early.AR009_GATCAG_L002_001


title: CD8_99_Sepsis

description: 99_036_9_29_2016_Sepsis_Blood_Late_AR027_S29_L006_001


title: CD8_96_Sepsis

description: 96_032_9_21_2016_Sepsis_Blood_Late_AR005_S27_L006_001


title: CD8_10_Cancer

description: 10.745.Tumor.CD8.9.13.2016.unknown.NA.AR014_AGTTCC_L002_001


title: CD4_1_Sepsis

description: 1.009B.Blood.CD4.7.5.2016.Sepsis.Late.AR018_GTCCGC_L001_001


title: CD4_22_Sepsis

description: 22.024.Blood.CD4.8.17.2016.Sepsis.Late.AR010_TAGCTT_L005_001


title: CD8_11_Cancer

description: 11.655.Tumor.CD8.9.13.2016.NA.NA.A025_ACTGAT_L008_001


title: CD4_93_Crit-Ill

description: 93_76_Blood_CD4_20170511_CriticallyIll_Early_AR019_S33_L007_001


title: CD4_94_Sepsis

description: 94_77_Blood_CD4_20170511_Sepsis_Early_AR005_S28_L006_001


title: CD4_95_Sepsis

description: 95_78_Blood_CD4_20170511_Sepsis_Early_AR008_S6_L002_001


title: CD4_92_Sepsis

description: 92_75_Blood_CD4_20170511_Sepsis_Early_AR010_S23_L005_001


title: CD4_91_Crit-Ill

description: 91_74_Blood_CD4_20170511_CriticallyIll_Early_AR005_S3_L001_001


title: CD8_12_Cancer

description: 12.655.PBMC.CD8.9.13.2016.NA.NA.AD023_GAGTGG_L008_001


title: CD4_13_Sepsis

description: 13.009.Blood.CD4.6.29.2016.Sepsis.Early.AR001_ATCACG_L005_001


title: CD8_14_Sepsis

description: 14.009.Blood.CD8.7.5.2016.Sepsis.Late.AR015_ATGTCA_L003_001


title: CD4_88_Healthy

description: 88_68_Blood_CD4_3_29_2017_Hlthy_Early_AR008_S8_L006_001


title: CD4_90_Crit-Ill

description: 90_73_Blood_CD4_20170511_CriticallyIll_Early_AR003_S37_L008_001


title: CD4_86_Healthy

description: 86_66_Blood_CD4_3-16-2017_Hlthy_Early_AR013_S20_L008_001


title: CD4_85_Healthy

description: 85_65_Blood_CD4_3-16-2017_Healthy_Early_AR027_S29_L006_001


title: CD8_97_Sepsis

description: 97_033_9_26_2016_Sepsis_Blood_Late_AR014_S22_L005_001


title: CD4_82_Crit-Ill

description: 82_62_Blood_CD4_3_9_2017_CritIll_Early_AR027_S7_L005_001


title: CD4_84_Healthy

description: 84_64_Blood_CD4_3-15-2017_Healthy_Early_AR014_S24_L005_001


title: CD4_81_Sepsis

description: 81_61_Blood_CD4_3_6_2017_Sep_Late_AR002_S3_L005_001


title: CD4_77_Healthy

description: 77_58_Blood_CD4_3_3_2017_Hlthy_Early_AR015_S16_L007_001


title: CD4_79_Sepsis

description: 79_060A_Blood_CD4_3_6_2017_Sep_Early_AR014_S11_L006_001


title: CD4_75_Crit-Ill

description: 75_55_Blood_CD4_2_8_2017_CritIll_Early_AR013_S15_L007_001


title: CD4_71_Crit-Ill

description: 71_52_Blood_CD4_1_18_2017_CritIll_Early_AR015_S21_L008_001


title: CD4_78_Healthy

description: 78_59_Blood_CD4_3-3-2017_Healthy_Early_AR009_S22_L005_001


title: Pooled HCASMC_TCF21 ChIPseq

data_processing:
Fastq files were mapped to the Hg19 genome with the BWA-MEM aligner v.0.7.12
ChIPseq peaks were called with MACSv2 using default parameters
“Robust” peaks were selected by specifying a minimum fold-enrichment of 10 and a minimum log10 q-value of 60.
Genome_build: hg19
Supplementary_files_format_and_content: BED file. 1st: chromosome, 2nd: start position of peak, 3rd: end position of peak, 4th: peak name, 5th: peak height

source_name: human coronary artery

growth_protocol: A total of 65 primary human coronary artery smooth muscle cell (HCASMC) lines were purchased from PromoCell, Cell Applications, Lonza, Lifeline Cell Technology and ATCC. Cells were cultured in smooth muscle growth medium (Lonza catalog #CC-3182) supplemented with hEGF, insulin, hFGF-b, and 5% FBS, according to the manufacturer’s instructions. All HCASMC lines were used at passages 4-8.

extract_protocol:
Cells were cross linked in 1% formaldehyde for 10 min and then washed with PBS. Cell pellets were frozen at -80C. All cell pellets were thawed on ice, combined for a total of 19.5 million cross linked cells and resuspended in cold PBS. PBS was removed and replaced with hypotonic buffer (20mM Hepes pH 7.9, 10mM KCl, 1mM EDTA, pH 8, 10% glycerol) and cells incubated on ice for 6 min. Cells were dounce homogenized with 20 strokes on ice using a 7ml glass homogenizer. Nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 4, constant duty for 12 rounds of 20 second pulses), resulting in chromatin fragments of 250-400 bp. Lysate was treated overnight at 4C with 5ug of anti-Tcf21 antibody (Sigma #HPA013189). Protein-DNA complexes were captured on Protein G agarose beads (Millipore Sigma #16-266) and eluted in 1% SDS TE buffer at 65C. After reverse cross linking, RNase A and proteinase K digestion, chromatin was purified using Qiagen PCR purification kit (Catalog #28106)
sequencing libraries were generated according to Illumina DNA Sample Kit Instructions (Illumina Part # 0801– 0303, San Diego, CA)

tag: passage

value: passages 4-8

value: anti-Tcf21 antibody (Sigma #HPA013189)


title: CD4_80_Sepsis

description: 80_060B_Blood_CD4_3_13_2017_Sep_Late_AR010_S10_L006_001


title: CD4_74_Crit-Ill

description: 74_54_Blood_CD4_2-2-2017_Crit-Ill_Early_AR002_S25_L006_001


title: CD4_69_Crit-Ill

description: 69_50_Blood_CD4_1_11_2017_CritIll_Early_AR009_S9_L006_001


title: CD4_76_Crit-Ill

description: 76_56_Blood_CD4_2-23-2017_CritIll_Early_AR001_S15_L003_001


title: CD4_68_Sepsis

description: 68_49_Blood_CD4_1_11_2017_Sep_Early_AR004_S4_L005_001


title: CD4_89_Healthy

description: 89_69_Blood_CD4_3_30_2017_Hlthy_Early_AR013_S20_L008_001


title: CD4_66_Sepsis

description: 66_47_Blood_CD4_1_9_2017_Sep_Late_AR016_S17_L007_001


title: CD4_63_Crit-Ill

description: 63_43_Blood_CD4_11_11_2016_CritIll_Early_AR005_S5_L005_001


title: CD4_83_Healthy

description: 83_63_Blood_CD4_3-15-2017_Healthy_Early_AR006_S4_L001_001


title: CD4_65_Sepsis

description: 65_46_Blood_CD4_1_6_2017_Sep_Early_AR001_S13_L007_001


title: CD4_64_Sepsis

description: 64_45_Blood_CD4_12-14-2016_Sepsis_Late_AR012_S31_L007_001


title: CD4_70_Crit-Ill

description: 70_51_Blood_CD4_1-12-2017_Crit-Ill_Early_AR008_S21_L005_001


title: CD4_72_Sepsis

description: 72_053A_Blood_CD4_2-1-2017_Sepsis_Early_AR006_S28_L006_001


title: CD4_62_Crit-Ill

description: 62_42_Blood_CD4_11-11-2016_Crit-Ill_Early_AR025_S34_L007_001


title: CD4_58_Sepsis

description: 58_37-2_Blood_CD4_10-14-2016_Sepsis_Late_AR010_S23_L005_001


title: CD4_61_Crit-Ill

description: 61_41_Blood_CD4_11-3-2016_Crit-Ill_Early_AR022_S33_L007_001


title: CD4_60_Healthy

description: 60_39_Blood_CD4_10-25-2016_Healthy_Early_AR003_S36_L008_001


title: CD4_55_Sepsis

description: 55_35_Blood_CD4_9-29-2016_Sepsis_Early_AR004_S26_L006_001


title: CD4_56_Sepsis

description: 56_36_Blood_CD4_9_29_2016_Sep_Late_AR001_S18_L008_001


title: CD4_59_Healthy

description: 59_38_Blood_CD4_10_12_2016_Hlthy_Early_AR016_S22_L008_001


title: CD14_274_Sepsis

description: 274_094_Blood_CD14_6_27_2017_Sepsis_Early_AR010_S23_L005_001


title: CD14_271_Healthy

description: 271_091_Blood_CD14_6_23_2017_Healthy_Unkwn_AR023_S25_L005_001


title: CD4_54_Sepsis

description: 54_33_Blood_CD4_9-26-2016_Sepsis_Late_AR019_S32_L007_001


title: CD14_270_Healthy

description: 270_090_Blood_CD14_6_23_2017_Healthy_Unkwn_AR001_S16_L004_001


title: CD14_277_Sepsis

description: 277_097_Blood_CD14_6_30_2017_Sepsis_Early_AR002_S26_L006_001


title: CD14_266_Sepsis

description: 266_085_Blood_CD14_6_14_2017_Sepsis_Unkwn_AR019_S13_L003_001


title: CD4_57_Sepsis

description: 57_037A_Blood_CD4_10-7-2016_Sepsis_Early_AR018_S10_L005_001


title: CD14_264_Crit-Ill

description: 264_082_Blood_CD14_6_7_2017_Crit-Ill_Unkwn_AR012_S12_L003_001


title: CD4_67_Crit-Ill

description: 67_48_Blood_CD4_1_10_2017_CritIll_Early_AR003_S14_L007_001


title: CD14_261_Sepsis

description: 261_079_Blood_CD14_6_6_2017_Sepsis_Late_AR014_S22_L005_001


title: CD14_267_Healthy

description: 267_087_Blood_CD14_6_16_2017_Healthy_Unkwn_AR004_S2_L006_001


title: CD8_258_Sepsis

description: 258_097_Blood_CD8_6_30_2017_Sepsis_Early_AR003_S35_L008_001


title: CD14_262_Crit-Ill

description: 262_080_Blood_CD14_6_6_2017_Crit-Ill_Unkwn_AR006_S28_L006_001


title: CD8_255_Sepsis

description: 255_094_Blood_CD8_6_27_2017_Sepsis_Early_AR015_S19_L004_001


title: CD8_252_Healthy

description: 252_091_Blood_CD8_6_23_2017_Healthy_Unkwn_AR013_S36_L008_001


title: CD8_251_Healthy

description: 251_090_Blood_CD8_6_23_2017_Healthy_Unkwn_AR003_S17_L004_001


title: CD8_248_Healthy

description: 248_087_Blood_CD8_6_16_2017_Healthy_Unkwn_AR011_S11_L003_001


title: CD8_247_Sepsis

description: 247_085_Blood_CD8_6_14_2017_Sepsis_Unkwn_AR001_S34_L008_001


title: CD8_246_Healthy

description: 246_084_Blood_CD8_6_9_2007_Healthy_Unkwn_AR018_S10_L002_001


title: CD14_265_Healthy

description: 265_084_Blood_CD14_6_9_2007_Healthy_Unkwn_AR027_S29_L006_001


title: CD4_233_Healthy

description: 233_091_Blood_CD4_6_23_2017_Healthy_Unkwn_AR016_S20_L004_001


title: CD4_232_Healthy

description: 232_090_Blood_CD4_6_23_2017_Healthy_Unkwn_AR015_S37_L008_001


title: CD4_229_Healthy

description: 229_087_Blood_CD4_6_16_2017_Healthy_Unkwn_AR014_S9_L002_001


title: CD4_228_Sepsis

description: 228_085_Blood_CD4_6_14_2017_Sepsis_Unkwn_AR007_S21_L005_001


title: 24M_N16

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
Laser captured nvu from normal murine cortex
10 um cervical spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
From each individual 1000 motor neurons (MN) were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)

hyb_protocol: 12.5µg of cRNA molecules were heat fragmented and applied to the Mouse 430 2.0 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols

data_processing: Data were normalised using the RMA package in Expression console

source_name: Laser captured neurovvascular unit

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol: PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

tag: age group

value: 24 months

tag: gender

value: M


title: CD4_224_Crit-Ill

description: 224_080_Blood_CD4_6_6_2017_Crit-Ill_Unkwn_AR022_S14_L003_001

tag: cell type


title: CD4_227_Healthy

description: 227_084_Blood_CD4_6_9_2007_Healthy_Unkwn_AR025_S15_L003_001


title: CD4_223_Sepsis

description: 223_079_Blood_CD4_6_6_2017_Sepsis_Late_AR010_S8_L002_001


title: CD8_243_Crit-Ill

description: 243_080_Blood_CD8_6_6_2017_Crit-Ill_Unkwn_AR018_S24_L005_001


title: 12M_N14

value: 12 months


title: CD8_242_Sepsis

description: 242_079_Blood_CD8_6_6_2017_Sepsis_Late_AR005_S27_L006_001


title: CD14_222_Crit-Ill

description: 222_29_Blood_CD14_20160907_CriticallyIll_na_AR003_S17_L004_001


title: 24M_N23


title: 24M_N20


title: CD14_221_Sepsis

description: 221_27_Blood_CD14_20160901_Sepsis_Late_AR019_S13_L003_001


title: 12M_N17


title: 3M_N17

value: 3 months


title: CD14_220_Sepsis

description: 220_26_Blood_CD14_20160824_Sepsis_Late_AR012_S12_L003_001


title: 12M_N16


title: MDA-MB-231 tumorigenic cells treated with 2 Gy of proton dose - replicate5

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

description:
Biological replicate 5 of 6
MDA-MB-231_2Gy_proton_rep5

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Respective untreated cell lines, were used as a control. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from untreated cells was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: Non tumorigenic (MCF10A) and tumorigenic breast (MCF7 and MDA-MB-231) immortalized cell lines were collected after 24 hours post treatments.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: cell line

value: Human non-tumorigenic breast epithelial cell line

tag: harvest time post treatment

value: 24 hours

tag: original tissue

value: breast

source_name: MDA-MB-231 breast cancer cell line non exposed to proton tratments

tag: sample type

value: no treatment control


title: 3M_N15


title: MDA-MB-231 tumorigenic cells treated with 2 Gy of proton dose - replicate6

description:
Biological replicate 6 of 6
MDA-MB-231_2Gy_proton_rep6


title: MDA-MB-231 tumorigenic cells treated with 2 Gy of proton dose - replicate4

description:
Biological replicate 4 of 6
MDA-MB-231_2Gy_proton_rep4


title: CD14_219_Sepsis

description: 219_25_Blood_CD14_20160824_Sepsis_Late_AR015_S19_L004_001


title: 3M_N13


title: 3M_N14


title: CD14_218_Sepsis

description: 218_24_Blood_CD14_20160817_Sepsis_Late_AR002_S1_L001_001


title: MDA-MB-231 tumorigenic cells treated with 2 Gy of proton dose - replicate2

description:
Biological replicate 2 of 6
MDA-MB-231_2Gy_proton_rep2


title: CD14_217_Healthy

description: 217_23_Blood_CD14_20160816_Healthy_na_AR007_S21_L005_001


title: MDA-MB-231 tumorigenic cells treated with 2 Gy of proton dose - replicate3

description:
Biological replicate 3 of 6
MDA-MB-231_2Gy_proton_rep3


title: CD14_215_Healthy

description: 215_21_Blood_CD14_20160812_Healthy_na_AR004_S27_L006_001


title: MDA-MB-231 tumorigenic cells treated with 2 Gy of proton dose - replicate1

description:
Biological replicate 1 of 6
MDA-MB-231_2Gy_proton_rep1


title: CD14_214_Healthy

description: 214_20_Blood_CD14_20160812_Healthy_na_AR025_S35_L007_001


title: CD8_245_Crit-Ill

description: 245_082_Blood_CD8_6_7_2017_Crit-Ill_Unkwn_AR009_S7_L002_001


title: MDA-MB-231 tumorigenic cells treated with 0.5 Gy of proton dose - replicate6

description:
Biological replicate 6 of 6
MDA-MB-231_0,5Gy_proton_rep6


title: MDA-MB-231 tumorigenic cells treated with 0.5 Gy of proton dose - replicate5

description:
Biological replicate 5 of 6
MDA-MB-231_0,5Gy_proton_rep5


title: MDA-MB-231 tumorigenic cells treated with 0.5 Gy of proton dose - replicate4

description:
Biological replicate 4 of 6
MDA-MB-231_0,5Gy_proton_rep4


title: MDA-MB-231 tumorigenic cells treated with 0.5 Gy of proton dose - replicate2

description:
Biological replicate 2 of 6
MDA-MB-231_0,5Gy_proton_rep2


title: MDA-MB-231 tumorigenic cells treated with 0.5 Gy of proton dose - replicate1

description:
Biological replicate 1 of 6
MDA-MB-231_0,5Gy_proton_rep1


title: CD14_212_Healthy

description: 212_18_Blood_CD14_20160802_Healthy_na_AR016_S20_L004_001


title: CD14_211_Healthy

description: 211_17_Blood_CD14_20160802_Healthy_na_AR022_S14_L003_001


title: CD14_210_Crit-Ill

description: 210_16_Blood_CD14_na_CriticallyIll_na_AR009_S7_L002_001


title: CD4_73_Sepsis

description: 73_053B_Blood_CD4_2-8-2017_Sepsis_Late_AR005_S27_L006_001


title: MCF7 tumorigenic cells treated with 2 Gy of proton dose - replicate6

description:
Biological replicate 6 of 6
MCF7_2Gy_proton_rep6

value: Human tumorigenic breast cancer cell line

source_name: MCF7 breast cancer cell line non exposed to proton tratments


title: CD14_209_Crit-Ill

description: 209_15_Blood_CD14_na_CriticallyIll_na_AR004_S2_L001_001


title: CD14_216_Sepsis

description: 216_22_Blood_CD14_20160816_Sepsis_Late_AR013_S38_L008_001

value: Sepsis


title: CD14_208_Crit-Ill

description: 208_14_Blood_CD14_20160720_CriticallyIll_na_AR027_S30_L006_001


title: CD14_205_Sepsis

description: 205_010B_Blood_CD14_20160712_Sepsis_Late_AR011_S31_L007_001

value: Late


title: CD14_213_Sepsis

description: 213_019A_Blood_CD14_20160803_Sepsis_Early_AR010_S8_L002_001


title: MDA-MB-231 tumorigenic cells treated with 0.5 Gy of proton dose - replicate3

description:
Biological replicate 3 of 6
MDA-MB-231_0,5Gy_proton_rep3


title: MCF7 tumorigenic cells treated with 2 Gy of proton dose - replicate5

description:
Biological replicate 5 of 6
MCF7_2Gy_proton_rep5


title: MCF7 tumorigenic cells treated with 2 Gy of proton dose - replicate2

description:
Biological replicate 2 of 6
MCF7_2Gy_proton_rep2


title: MCF7 tumorigenic cells treated with 2 Gy of proton dose - replicate3

description:
Biological replicate 3 of 6
MCF7_2Gy_proton_rep3


title: CD14_201_Sepsis

description: 201_008A_Blood_CD14_20160608_Sepsis_Early_AR014_S9_L002_001


title: CD14_207_Crit-Ill

description: 207_13_Blood_CD14_20160713_CriticallyIll_na_AR025_S15_L003_001

value: Crit-Ill


title: MCF7 tumorigenic cells treated with 0.5 Gy of proton dose - replicate4

description:
Biological replicate 4 of 6
MCF7_0,5Gy_proton_rep4


title: MCF7 tumorigenic cells treated with 0.5 Gy of proton dose - replicate6

description:
Biological replicate 6 of 6
MCF7_0,5Gy_proton_rep6


title: CD14_200_Sepsis

description: 200_007A_Blood_CD14_20160601_Sepsis_Early_AR016_S40_L008_001


title: MCF7 tumorigenic cells treated with 0.5 Gy of proton dose - replicate5

description:
Biological replicate 5 of 6
MCF7_0,5Gy_proton_rep5


title: CD14_198_Sepsis

description: 198_77_Blood_CD14_20170511_Sepsis_Early_AR001_S16_L004_001


title: CD14_204_Sepsis

description: 204_010A_Blood_CD14_20160706_Sepsis_Early_AR022_S34_L007_001


title: CD14_197_Crit-Ill

description: 197_76_Blood_CD14_20170511_CriticallyIll_Early_AR001_S36_L008_001


title: MCF7 tumorigenic cells treated with 2 Gy of proton dose - replicate4

description:
Biological replicate 4 of 6
MCF7_2Gy_proton_rep4


title: CD14_203_Sepsis

description: 203_009B_Blood_CD14_20160705_Sepsis_Late_AR018_S24_L005_001


title: MCF7 tumorigenic cells treated with 2 Gy of proton dose - replicate1

description:
Biological replicate 1 of 6
MCF7_2Gy_proton_rep1


title: MCF7 tumorigenic cells treated with 0.5 Gy of proton dose - replicate3

description:
Biological replicate 3 of 6
MCF7_0,5Gy_proton_rep3


title: CD14_196_Sepsis

description: 196_75_Blood_CD14_20170511_Sepsis_Early_AR006_S29_L006_001


title: CD14_199_Sepsis

description: 199_78_Blood_CD14_20170511_Sepsis_na_AR006_S4_L001_001


title: CD14_195_Crit-Ill

description: 195_74_Blood_CD14_20170511_CriticallyIll_na_AR012_S32_L007_001


title: MCF7 tumorigenic cells treated with 0.5 Gy of proton dose - replicate2

description:
Biological replicate 2 of 6
MCF7_0,5Gy_proton_rep2


title: MCF7 tumorigenic cells treated with 0.5 Gy of proton dose - replicate1

description:
Biological replicate 1 of 6
MCF7_0,5Gy_proton_rep1


title: CD14_194_Crit-Ill

description: 194_73_Blood_CD14_20170511_CriticallyIll_na_AR023_S25_L005_001


title: MCF10A non tumorigenic cells treated with 2 Gy of proton dose - replicate5

description:
Biological replicate 5 of 6
MCF10A_2Gy_proton_rep5

source_name: MCF10A breast epithelial cell line no exposed to proton tratments


title: MCF10A non tumorigenic cells treated with 2 Gy of proton dose - replicate4

description:
Biological replicate 4 of 6
MCF10A_2Gy_proton_rep4


title: MCF10A non tumorigenic cells treated with 2 Gy of proton dose - replicate3

description:
Biological replicate 3 of 6
MCF10A_2Gy_proton_rep3


title: MCF10A non tumorigenic cells treated with 2 Gy of proton dose - replicate6

description:
Biological replicate 6 of 6
MCF10A_2Gy_proton_rep6


title: MCF10A non tumorigenic cells treated with 2 Gy of proton dose - replicate2

description:
Biological replicate 2 of 6
MCF10A_2Gy_proton_rep2


title: MCF10A non tumorigenic cells treated with 2 Gy of proton dose - replicate1

description:
Biological replicate 1 of 6
MCF10A_2Gy_proton_rep1


title: CD14_192_Cancer

description: 192_853_Blood_CD14_Unkwn_Cancer_Unkwn_AR022_S33_L007_001


title: MCF10A non tumorigenic cells treated with 0.5 Gy of proton dose - replicate6

description:
Biological replicate 6 of 6
MCF10A_0,5Gy_proton_rep6


title: CD14_190_Cancer

description: 190_822_Blood_CD14_Unkwn_Cancer_Unkwn_AR006_S4_L001_001


title: CD8_186_Cancer

description: 186_853_Blood_CD8_Unkwn_Cancer_Unkwn_AR027_S5_L001_001


title: MCF10A non tumorigenic cells treated with 0.5 Gy of proton dose - replicate5

description:
Biological replicate 5 of 6
MCF10A_0,5Gy_proton_rep5


title: CD8_184_Cancer

description: 184_822_Blood_CD8_Unkwn_Cancer_Unkwn_AR019_S32_L007_001


title: CD4_178_Cancer

description: 178_822_Blood_CD4_Unkwn_Cancer_Unkwn_AR002_S1_L001_001


title: Sample12_siHMGA1_T72H_rep3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

description:
MDA-MB-231 cells were tranfected with siHMGA1 siRNA reagent. After 72 Hours, RNA molecules were collected and processed.
processed data: countmatrix.txt

data_processing:
Basecalls performed using CASAVA (Illumina Inc.).
The reads were mapped to the reference genome (UCSC-hg19) using STAR (Dobin et al., 2013), version 2.0.1.
HTSeq-count (version 0.6.1) was used to generate gene counts.
Differential gene expression analysis was performed using EdgeR (version 1.10.1) comparing the different time points using a quantile-adjusted conditional maximum likelihood (qCML) method.
Genome_build: hg19 (GRCh37); homo_sapiens.release-75 from ENSEMBL database.
Supplementary_files_format_and_content: countmatrix.txt: Tab-delimited text file includes COUNTS values for each Sample.

growth_protocol: MDA-MB-231 cell lines were routinely grown in high glucose DMEM, with 10% tetracycline-free FBS, 2mM L-Glutamine, 100 U/ml Penicillin and 100 µg/ml Streptomycin (Euroclone).

extract_protocol:
RNA extracts were collected at 24 and 72 hours after the silencing. Total RNA was isolated following the manufacturer’s instructions of the TRIzol reagent (Thermo Fisher Scientific), subjected to DNase-I (Thermo Fisher Scientific) treatment and subsequently purified using phenol-chloroform.
Libraries were constructed with the Illumina TruSeq RNA kits pair reads.

treatment_protocol: LipofectamineTM RNAiMAX reagent (Thermo Fisher Scientific) was used for transfection of 30 pmol of siRNA/35-mm dish, following the manufacturer instructions.

tag: treatment

tag: time

value: 72 Hours


title: Sample13_siCTRL_T72H_rep1

description:
MDA-MB-231 cells were tranfected with siCTRL siRNA reagent. After 72 Hours, RNA molecules were collected and processed.
processed data: countmatrix.txt

value: siCTRL


title: Sample14_siCTRL_T72H_rep2


title: CD4_180_Cancer

description: 180_853_Blood_CD4_Unkwn_Cancer_Unkwn_AR012_S31_L007_001

value: Cancer


title: CD4_176_Cancer

description: 176_796_Blood_CD4_Unkwn_Cancer_Unkwn_AR011_S30_L007_001


title: CD14_175_Healthy

description: 175_069_Blood_CD14_3_30_2017_Healthy_AR018_S20_L004_001

value: Healthy


title: Sample11_siHMGA1_T72H_rep2


title: CD14_174_Healthy

description: 174_68_Blood_CD14_3-29-2017_Healthy_AR022_S9_L002_001


title: Sample10_siHMGA1_T72H_rep1


title: CD14_172_Healthy

description: 172_66_Blood_CD14_3-16-2017_Healthy_AR002_S1_L005_001


title: Sample9_siCTRL_T24H_rep3

description:
MDA-MB-231 cells were tranfected with siCTRL siRNA reagent. After 24 Hours, RNA molecules were collected and processed.
processed data: countmatrix.txt

value: 24 Hours


title: CD4_87_Healthy

description: 87_67_Blood_CD4_3_29_2017_Hlthy_Early_AR011_S10_L002_001


title: CD14_173_Healthy

description: 173_67_Blood_CD14_3-29-2017_Healthy_AR012_S7_L002_001


title: Sample8_siCTRL_T24H_rep2


title: CD14_171_Healthy

description: 171_65_Blood_CD14_3-16-2017_Healthy_AR016_S14_L003_001


title: CD14_188_Cancer

description: 188_796_Blood_CD14_Unkwn_Cancer_Unkwn_AR005_S3_L001_001


title: MCF10A non tumorigenic cells treated with 0.5 Gy of proton dose - replicate3

description:
Biological replicate 3 of 6
MCF10A_0,5Gy_proton_rep3


title: MCF10A non tumorigenic cells treated with 0.5 Gy of proton dose - replicate1

description:
Biological replicate 1 of 6
MCF10A_0,5Gy_proton_rep1


title: Sample7_siCTRL_T24H_rep1


title: MCF10A non tumorigenic cells treated with 0.5 Gy of proton dose - replicate4

description:
Biological replicate 4 of 6
MCF10A_0,5Gy_proton_rep4


title: CD14_170_Healthy

description: 170_064_Blood_CD14_3_15_2017_Healthy_AR009_S12_L003_001


title: Sample15_siCTRL_T72H_rep3


title: Sample6_siHMGA1_T24H_rep3

description:
MDA-MB-231 cells were tranfected with siHMGA1 siRNA reagent. After 24 Hours, RNA molecules were collected and processed.
processed data: countmatrix.txt


title: MCF10A non tumorigenic cells treated with 0.5 Gy of proton dose - replicate2

description:
Biological replicate 2 of 6
MCF10A_0,5Gy_proton_rep2


title: Sample5_siHMGA1_T24H_rep2


title: CD14_169_Healthy

description: 169_063_Blood_CD14_3_15_2017_Healthy_AR012_S6_L002_001


title: Sample4_siHMGA1_T24H_rep1


title: CD14_168_Crit-Ill

description: 168_062_Blood_CD14_3_9_2017_CriticallyIll_AR002_S1_L001_001


title: CD14_167_Sepsis

description: 167_61_Blood_CD14_3-6-2017_Sepsis_Late_AR003_S17_L008_001


title: Sample3_NotTreated_T00H_rep3

description:
RNA molecules from MDA-MB-231 were collected and processed at time zero in respect to all the other experiments.
processed data: countmatrix.txt

value: No treatment

value: 0 Hours


title: Sample2_NotTreated_T00H_rep2


title: CD14_165_Sepsis

description: 165_60_Blood_CD14_3-6-2017_Sepsis_Early_AR016_S19_L008_001

value: Early


title: CD14_164_Healthy

description: 164_059_Blood_CD14_3_3_2017_Healthy_AR027_S5_L001_001


title: MEC1 2B17 rep2

city: Québec

first: Chantal

last: Guillemette

state: Québec

address: 2705 blvd Laurier

department: Faculty of Pharmacy

institute: Laval University

data_processing:
Quality trimming with trimmomatic min quality = 30; min length = 32
Alignment with TopHat v2.0.14 to the hg38 human genome
Generation of count matrices with HTSeq
Normalization and differential expression analysis with DESeq2 and edgeR
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression analysis results for both DESeq2 and edgeR with raw and  normalized read counts for all samples for a given cell line. One tab-seperated file per cell line.

source_name: Leukemia

extract_protocol:
RNA was extracted from 5 million cells from each sample using QIAGEN RNeasy Mini Kit with DNAse I. 1 ug total RNA from each sample was used to prepare sequencing librairies with Illumina HiSeq RNA Sample Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: transfected with an expression vector containing the coding sequence of human UGT2B17


title: MEC1 2B17 rep3


title: CD14_166_Sepsis

description: 166_60_Blood_CD14_3-13-2017_Sepsis_Late_AR001_S16_L008_001


title: CD14_162_Crit-Ill

description: 162_056_Blood_CD14_2_23_2017_CriticallyIll_AR004_S2_L001_001


title: CD14_161_Crit-Ill

description: 161_055_Blood_CD14_2_8_2017_CriticallyIll_AR022_S8_L002_001


title: CD14_163_Healthy

description: 163_058_Blood_CD14_3_3_2017_Healthy_AR014_S19_L004_001


title: MEC1 CTRL rep1

value: stable repression of UGT2B17 by shRNA knock-down


title: MEC1 CTRL rep2


title: MEC1 CTRL rep3


title: CD14_158_Sepsis

description: 158_053_Blood_CD14_2_1_2017_Sepsis_Early_AR009_S17_L004_001


title: CD14_160_Crit-Ill

description: 160_054_Blood_CD14_2_2_2017_CriticallyIll_AR025_S9_L002_001


title: HCV patient 1 - HPC -repeat

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

data_processing:
Base calling accuracy was measured by the Phred quality score (Q score).
Distributions of the average read quality was calculated b ythe ShortRead 1.20.0 package from Bioconductor.
Quality trimming: We trim low quality ends (< Q20) with FastX 0.0.13. Adapter trimming: The adapters are trimmed only at the end (at least 10bp overlap and 90% match) with cutadapt 1.2.1 . Reads that are shorter than 15bp after adapter trimming are removed. Removal of contaminants: Using bowtie 2.1.0.
Read alignment: Tophat v2.0.8b
Quality filtering, sorting and indexing: samtools 0.1.19-44428cd
Genome_build: GRCh37
Supplementary_files_format_and_content: One tab-delimited text file with raw read counts per gene and per sample. Gene IDs are Ensembl IDs.

source_name: Hepatic progenitor cells

growth_protocol: Snap frozen tissue

extract_protocol:
Laser microdissection + Qiagen kit
NEBNext Ultra Kit

treatment_protocol: Aceton fixation/cresyl violet staining

tag: disease state

value: hepatitis C


title: CD14_157_Crit-Ill

description: 157_52_Blood_CD14_1-18-2017_CriticallyIll_AR025_S10_L002_001


title: PSC patient 5 - HPC

value: primary sclerosing cholangitis


title: PSC patient 6 - HPC


title: HCV patient 5 -HPC


title: CD14_156_Crit-Ill

description: 156_051_Blood_CD14_1_12_2017_CriticallyIll_AR010_S18_L004_001


title: MEC1 2B17 rep1


title: CD14_153_Crit-Ill

description: 153_048_Blood_CD14_1_10_2017_CriticallyIll_AR008_S11_L003_001


title: PSC patient 4 - HPC


title: CD14_154_Sepsis

description: 154_49_Blood_CD14_1-11-2017_Sepsis_AR015_S13_L003_001


title: CD14_152_Sepsis

description: 152_47_Blood_CD14_1-9-2017_Sepsis_Late_AR004_S2_L005_001


title: HCV patient 4 - HPC


title: CD14_159_Sepsis

description: 159_053_Blood_CD14_2_8_2017_Sepsis_Late_AR008_S16_L004_001


title: Sample1_NotTreated_T00H_rep1


title: HCV patient 3 - HEP

source_name: Hepatocytes


title: CD14_151_Sepsis

description: 151_46_Blood_CD14_1-6-2017_Sepsis_Early_AR005_S3_L005_001


title: HCV patient 2 - HEP


title: HCV patient 3 -HPC


title: CD14_149_Crit-Ill

description: 149_43_Blood_CD14_11-11-2016_CriticallyIll_AR011_S6_L002_001


title: HCV patient 2 -HPC


title: CD14_148_Crit-Ill

description: 148_42_Blood_CD14_11-11-2016_CriticallyIll_AR003_S11_L003_001


title: PSC patient 3 - HEP


title: CD14_147_Crit-Ill

description: 147_41_Blood_CD14_11-3-2016_CriticallyIll_AR027_S5_L005_001


title: CD14_146_Healthy

description: 146_039_Blood_CD14_10_25_2016_Healthy_AR018_S15_L003_001


title: PSC patient 2 - HEP


title: CD14_145_Healthy

description: 145_38_Blood_CD14_10-12-2016_Healthy_AR006_S4_L005_001


title: PSC patient 2- HPC


title: PSC patient 3 - HPC


title: CD14_144_Sepsis

description: 144_037_Blood_CD14_10_14_2016_Sepsis_Late_AR005_S3_L001_001


title: CD14_155_Crit-Ill

description: 155_050_Blood_CD14_1_11_2017_CriticallyIll_AR014_S14_L003_001


title: HCV patient 1 - HEP


title: HCV patient 1 -HPC


title: CD14_143_Sepsis

description: 143_037_Blood_CD14_10_7_2016_Sepsis_Early_AR006_S4_L001_001


title: CD14_141_Sepsis

description: 141_35_Blood_CD14_9-29-2016_Sepsis_Early_AR015_S18_L008_001


title: CD14_142_Sepsis

description: 142_036_Blood_CD14_9_29_2016_Sepsis_Late_AR010_S13_L003_001


title: PSC patient 1 - HPC


title: CD14_140_Sepsis

description: 140_33_Blood_CD14_9-26-2016_Sepsis_Late_AR019_S8_L002_001


title: CD8_137_Sepsis

description: 137_77_Blood_CD8_20170511_Sepsis_Early_AR027_S5_L001_001


title: PSC patient 1 - HEP


title: CD4_236_Sepsis

description: 236_094_Blood_CD4_6_27_2017_Sepsis_Early_AR016_S38_L008_001


title: CD8_135_Sepsis

description: 135_75_Blood_CD8_20170511_Sepsis_Early_AR015_S39_L008_001


title: hESC_1_7_H3K4me3_R1

city: La Jolla

first: Daria

last: Merkurjev

address: 9500 Gilman Drive, Mail Code 0648

institute: UCSD

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18 and mm9
Supplementary_files_format_and_content: bedGraph

source_name: single-cell HUES9 derived hESC 1.7 subline

extract_protocol:
Cells were fixed with 2mM disuccinimidyl glutarate (DSG) for 45 mins and 1% formaldehyde for 10mins, and followed by glycine for 5 mins. Chromatin DNA was sheared to 200–500 bp average in size by sonication and chromatin was immunoprecipitated with antibodies. Protein A/G beads Sigma were added and incubated overnight at 4°C. After washing and elution, the protein–DNA complex was reverse-crosslinked by heating at 65°C, and immunoprecipitated DNA was purified by using QIAquick Spin column.
ChIP-seq libraries were prepared using the KAPA Library Preparation Kit (KK8201)

value: HUES9 hiPSC subline

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: H3K4me3 (Millipore, 07-473)


title: CD14_150_Sepsis

description: 150_45_Blood_CD14_12-14-2016_Sepsis_Late_AR013_S12_L003_001

tag: patient group

value: Sepsis


title: hiPSC_1_15_H3K4me3_R1

source_name: single-cell CVI derived hiPSC 1.15 subline

value: Craig Venter-I (CVI) hiPSC subline


title: CD8_136_Crit-Ill

description: 136_76_Blood_CD8_20170511_CriticallyIll_Early_AR018_S10_L002_001

value: Crit-Ill

tag: subjectid


title: hESC_1_9_H3K4me3_R1

source_name: single-cell HUES9 derived hESC 1.9 subline


title: CD8_134_Crit-Ill

description: 134_74_Blood_CD8_20170511_CriticallyIll_Early_AR013_S18_L004_001

tag: sepsis stage


title: hiPSC_1_14_H3K4me3_R1

source_name: single-cell CVI derived hiPSC 1.14 subline


title: CD8_133_Crit-Ill

description: 133_73_Blood_CD8_20170511_CriticallyIll_Early_AR011_S11_L003_001

tag: sampleID


title: HUES9_hESC_H3K4me3_R1

source_name: HUES9 hiPSC parental line

value: HUES9 hiPSC line


title: CD8_130_Healthy

description: 130_067_3_29_2017_Healthy_Blood_AR007_S21_L005_001


title: CD8_129_Healthy

description: 129_066_3_16_2017_Healthy_CD8_Blood_AR008_S26_L007_001


title: CD8_132_Healthy

description: 132_069_3_30_2017_Healthy_CD8_Blood_AR005_S23_L006_001


title: CVI_hiPSC_CTCF

source_name: CVI hiPSC parental line

value: Craig Venter-I (CVI) hiPSC line

value: CTCF (Millipore, 07-729)


title: CVI_hiPSC_H3K4me3_R2


title: CD8_128_Healthy

description: 128_065_3_16_2017_Healthy_Blood_AR004_S26_L006_001

value: Healthy


title: hiPSC_1_13_H3K4me3_R1

source_name: single-cell CVI derived hiPSC 1.13 subline


title: CVI_hiPSC_H3K4me3_R1


title: hESC_1_9_H3K4me3_R2


title: CD8_127_Healthy

description: 127_064_3_15_2017_Healthy_CD8_Blood_AR013_S33_L008_001


title: hiPSC_1_8_H3K4me3_R1

source_name: single-cell CVB derived hiPSC 1.8 subline

value: Craig Venter-B (CVB) hiPSC subline


title: CD8_126_Healthy

description: 126_063_3_15_2017_Healthy_Blood_AR025_S15_L003_001


title: CD8_125_Crit-Ill

description: 125_062_3_9_2017_CriticallyIll_CD8_Blood_AR002_S21_L006_001


title: hiPSC_1_7_H3K4me3_R1

source_name: single-cell CVB derived hiPSC 1.7 subline


title: hiPSC_1_9_H3K4me3_R1

source_name: single-cell CVB derived hiPSC 1.9 subline


title: hiPSC8_Rad21_R1

source_name: single-cell CVB derived hiPSC#8 subline (failed genome editing, IB7)

value: Rad21 (Abcam, ab992)


title: CD8_124_Sepsis

description: 124_061_3_6_2017_Sepsis_CD8_Blood_Late_AR014_S29_L007_001

value: Late


title: CD8_123_Sepsis

description: 123_060B_3_13_2017_Sepsis_CD8_Blood_Late_AR004_S22_L006_001


title: hiPSC7_Rad21_R1

source_name: single-cell CVB derived hiPSC#7 subline (genome editing: APP V717 -/-, IIIB12)


title: CD8_122_Sepsis

description: 122_060A_3_6_2017_Sepsis_CD8_Blood_Early_AR006_S24_L006_001

value: Early


title: hiPSC6_Rad21_R1

source_name: single-cell CVB derived hiPSC#6 subline (genome editing: APP V717 +/-, IV8)


title: CD8_131_Healthy

description: 131_068_3_29_2017_Healthy_CD8_Blood_AR027_S25_L006_001


title: hiPSC5_Rad21_R1

source_name: single-cell CVB derived hiPSC#5 subline (genome editing: PSEN1 deltaE9 -/-, IIA12)


title: CD8_121_Healthy

description: 121_059_3_3_2017_Healthy_CD8_Blood_AR010_S28_L007_001


title: CD8_120_Healthy

description: 120_058_3_3_2017_Healthy_Blood_AR013_S37_L008_001


title: hiPSC4_Rad21_R1

source_name: single-cell CVB derived hiPSC#4 subline (genome editing: PSEN1 deltaE9 -/-, IB12)


title: CVI_hiPSC_Rad21


title: CD8_119_Crit-Ill

description: 119_056_2_23_2017_CriticallyIll_Blood_AR012_S31_L007_001


title: hiPSC2_Rad21_R1

source_name: single-cell CVB derived hiPSC#2 subline (genome editing: PSEN1 deltaE9 +/-, IIA11)


title: CD8_117_Crit-Ill

description: 117_054_2_2_2017_CriticallyIll_CD8_Blood_AR018_S30_L007_001


title: hiPSC3_Rad21_R1

source_name: single-cell CVB derived hiPSC#3 subline (genome editing: PSEN1 deltaE9 +/-, IID12)


title: hiPSC1_Rad21_R1

source_name: single-cell CVB derived hiPSC#1 subline (failed genome editing, IID4)


title: CD8_116_Sepsis

description: 116_053B_2_8_2017_Sepsis_Blood_Late_AR016_S39_L008_001


title: CVB_hiPSC_Rad21_R1

source_name: CVB hiPSC parental line

value: Craig Venter-B (CVB) hiPSC line


title: CD8_115_Sepsis

description: 115_053A_2_1_2017_Sepsis_Blood_Early_AR015_S38_L008_001


title: CD8_113_Crit-Ill

description: 113_051_1_12_2017_CriticallyIll_Blood_AR001_S35_L008_001


title: hiPSC6_CTCF_R1


title: CD8_112_Crit-Ill

description: 112_050_1_11_2017_CriticallyIll_Blood_AR003_S36_L008_001


title: CD8_114_Crit-Ill

description: 114_052_1_18_2017_CriticallyIll_CD8_Blood_AR003_S32_L008_001


title: hiPSC4_CTCF_R1


title: hiPSC2_CTCF_R1


title: hiPSC5_CTCF_R1


title: CD8_111_Sepsis

description: 111_049_1_11_2017_Sepsis_CD8_Blood_AR015_S34_L008_001


title: hiPSC7_CTCF


title: hiPSC1_CTCF_R1


title: CVB_hiPSC_CTCF_R1


title: CD8_107_Sepsis

description: 107_045_12_14_2016_Sepsis_Blood_Late_AR006_S28_L006_001


title: CD8_118_Crit-Ill

description: 118_055_2_8_2017_CriticallyIll_Blood_AR023_S24_L005_001


title: CD8_106_Crit-Ill

description: 106_043_11_11_2016_CriticallyIll_Blood_AR011_S11_L003_001


title: hiPSC5_H3K4me3


title: hiPSC7_H3K4me3


title: CD8_105_Crit-Ill

description: 105_042_11_11_2016_CriticallyIll_Blood_AR022_S33_L007_001


title: CD8_104_Crit-Ill

description: 104_041_11_3_2016_CriticallyIll_Blood_AR012_S12_L003_001


title: hiPSC4_H3K4me3


title: hiPSC8_CTCF_R1


title: CD8_103_Healthy

description: 103_039_10_25_2016_Healthy_Blood_AR025_S34_L007_001


title: hiPSC3_H3K4me3


title: hiPSC1_H3K4me3


title: hiPSC2_H3K4me3


title: CD8_101_Sepsis

description: 101_037_2_10_14_2016_Sepsis_Blood_Late_AR011_S30_L007_001


title: CD8_102_Healthy

description: 102_038_10_12_2016_Healthy_CD8_Blood_AR001_S31_L008_001


title: CD8_110_Crit-Ill

description: 110_048_1_10_2017_CriticallyIll_Blood_AR002_S25_L006_001


title: CVB_hiPSC_H3K4me3


title: CD8_109_Sepsis

description: 109_047_1_9_2017_Sepsis_CD8_Blood_Late_AR016_S35_L008_001


title: hiPSC3_CTCF_R1


title: RNAseq in POMC_ACreb3l2/AXBP1 double Tg IL replicate 2

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 50bp reads were trimmed to obtain high quality reads and then mapped to the GRCm38 mouse genome build using Star
Gene expression FPKM was determined using Cufflink
Gene expression raw count was performed with HTSeq-count
Differential gene expression analysis was performed with DeSeq
Genome_build: mm10
Supplementary_files_format_and_content: Fpkm.txt: tab-delimited text file containing the matrix table of FPKM values
Supplementary_files_format_and_content: gene.raw.count.txt: tab-delimited text files containing the matrix table of raw fragment counts

source_name: pool of 5 pituitary neuro-intermediate lobes (NIL)

extract_protocol:
NIL from WT or Tg mice were dissected and snapfreezed up to RNA extraction. Total RNA from pools of 5 NILs was extracted using the Qiagen RNeasy+ miniprep kit (including a genomic DNA removal step). Ribosomal depletion was performed on the extracted RNA.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2500 following the manufacturer's protocols to obtain 50bp paired end reads.

value: Melanotropes

tag: genotype

value: POMC_ACreb3l2/AXBP1 double Tg

tag: strain

tag: mrna enrichment protocol

value: Ribosomal depletion


title: CD8_108_Sepsis

description: 108_046_1_6_2017_Sepsis_Blood_Early_AR018_S23_L005_001

tag: cell type


title: RNAseq in POMC_ACreb3l2/AXBP1 double Tg IL replicate 1


title: JVM2 2B17 rep1

source_name: Leukemia

tag: cell line

value: transfected with an expression vector containing the coding sequence of human UGT2B17


title: Sample4_450K_rep2

type: genomic

city: Singapore

first: LI

last: ZHOU

address: 11 Mandalay Road

country: Singapore

institute: Lee Kong Chian School of Medicine, Nanyang Technological University

description: sample4 replicate 2

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip v1.2 and Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol.

scan_protocol: Illumina HiScan for Illumina HumanMethylation450 BeadChip and iScan for Illumina Infinium HumanMethylation850 BeadChip using standard recommended Illumina scanner setting.

data_processing:
Custom R scripts.
Raw data provided as Unmethylated and methylated signal intensities as well as in IDAT files.
Procesesd data files include raw BETA values.

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol.

extract_protocol: Bisulfite conversion of genomic DNA from peripheral blood was performed using the EZ DNA methylation kit according to manufacturer's instructions (Zymo Research).

tag: tissue

value: whole blood


title: RNAseq in POMC_AXBP1 Tg IL replicate 2

value: POMC_AXBP1 Tg


title: JVM2 CTRL rep3

value: transfected with an empty pcDNA6 vector


title: JVM2 CTRL rep2


title: RNAseq in POMC_ACreb3l2 Tg IL replicate 2

value: POMC_ACreb3l2 Tg


title: JVM2 CTRL rep1


title: RNAseq in POMC_AXBP1 Tg IL replicate 1


title: RNAseq in POMC_ACreb3l2 Tg IL replicate 1


title: Sample3_450K_rep1

description: sample3 replicate 1


title: Sample4_450K_rep1

description: sample4 replicate 1


title: RNAseq in WT IL replicate 2

value: WT


title: Sample2_450K_rep2

description: sample2 replicate 2


title: CD8_100_Sepsis

description: 100_037A_10_7_2016_Sepsis_Blood_Early_AR019_S32_L007_001

value: Sepsis


title: Neurons8_Prep2

description: Induced neuronal differentiation from hiPSCs

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph

growth_protocol: hiPSCs were seeded onto PA6 cells in PA differentiation medium for 12 days. Between days 12-14, when rosettes were visible, after dissociation, were  FACS-sorted based on the  CD184+/CD271-/CD44-/CD24+ cell-surface signature. Sorted NPCs were cultured on 20µg/mL poly-L-ornithine and 5µg/mL laminin coated plates in NPC medium until confluency was reached. To generate neurons, NPCs grown in 10 cm-plates at confluency were switched to NPC medium without FGF (day 1), and cultured afterwards for 3 weeks. Around day 21, neurons were sorted based on the CD184-/CD44-/CD24+ signature. For RNAseq experiments 1x106 CD24+ sorted neurons were plated on 20µg/mL poly-L-ornithine and 5µg/mL laminin coated 24-well plates in NPC media supplemented with 0.5mM dbcAMP from Sigma, and 20ng/µL BDNF and 20 ng/µL GDNF.

extract_protocol:
Total RNA was extracted using RNeasy Assay (Qiagen) and converted into cDNA using SuperScript First-Strand Synthesis System (Invitrogen) following manufacture’s protocols.
RNA quality was calculated on TapeStation (Agilent Technologies). Most of samples showed a RIN >7.0 and 7 out of 24 had an RIN between 6 and 7. PolyA+ RNA-seq libraries were generated using the Illumina TruSeq Stranded RNA LT kit and following manufacturer’s detailed instructions.

treatment_protocol: No particular treatment was applied after differentiation.

value: single-cell derived from CVB line prior to neuronal differentiation, preparation 2


title: Sample2_450K_rep1

description: sample2 replicate 1


title: RNAseq in WT IL replicate 1


title: Neurons8_Prep3

value: single-cell derived from CVB line prior to neuronal differentiation, preparation 3


title: JVM2 2B17 rep3


title: Sox2 ChIPseq in AtT-20 cells expressing Sox2

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads

growth_protocol: AtT-20 cells and αT3 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and antibiotics (penicillin/streptomycin)

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-400bp were kept for library preparation
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2500 following the manufacturer's protocols to obtain 50bp paired end reads.

value: expressing Sox2

tag: chip antibody

value: Sox2; Abcam (Ab59776)


title: JVM2 2B17 rep2


title: Neurons7_Prep3

value: Craig Venter-B (CVB) hiPSC subline


title: Neurod1 ChIPseq in AtT-20 cells

value: Neurod1; Poulin et al. Mol. Cell. Biol 20, 4826-4837 (2000)


title: Neurons7_Prep2


title: Input DNA in αT3 cells expressing Neo

value: expressing Neo


title: Sample3_450K_rep2

description: sample3 replicate 2


title: Sample1_450K_rep1

description: sample1 replicate 1


title: Neurons6_Prep3