title: CA3V_hippocampus_P120_Control_6


title: Pat56 Whole Blood

status: Public on Dec 20 2017

type: RNA

city: Paris

first: Hakim

last: hocini

address: 101 Rue de Tolbiac

country: France

institute: INSERM

description: SAMPLE 56

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: iScan Illumina scanning protocol using iScan control software

data_processing: neqc of limma package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Pat56 Whole Blood

label_protocol: In vitro transcription was generated from 150 ng of RNA using Ambion Illumina TotalPrep RNA Amplification Kits (Applied Biosystems/Ambion).

extract_protocol: RNA were purified using RNeasy Plus Micro Kit (Qiagen, France) and quantified using a ND-8000 spectrophotometer (NanoDrop Technologies) before being checked for integrity on the 2100 BioAnalyzer (Agilent Technologies).

tag: patient name

tag: groups

value: chronically HIV-1 infected individuals with controlled virus replication under combined antiretroviral therapy

tag: tissue

value: Whole Blood


title: Pat64 Whole Blood

description: SAMPLE 64

source_name: Pat64 Whole Blood


title: Pat57 Whole Blood

description: SAMPLE 57

source_name: Pat57 Whole Blood


title: Pat60 Whole Blood

description: SAMPLE 60

source_name: Pat60 Whole Blood


title: Pat54 Whole Blood

description: SAMPLE 54

source_name: Pat54 Whole Blood


title: CA3V_hippocampus_P120_Control_5

city: São Paulo

first: Hatylas

last: Azevedo

state: Sao Paulo

address: Doutor Arnaldo Avenue, 455

department: Pediatrics

country: Brazil

institute: University of São Paulo

description: Gene expression profiling of CA3 ventral hippocampus at P120

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028282_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: CA3 ventral hippocampus, P120, Normothermic Controls

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Microarray-Based Gene Expression Analysis - Low Input RNA (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol:
[experimental protocol] Brain tissue samples were collected from the ventral CA3 hippocampus at 1 (P12), 19 (P30), 49 (P60) and 109 (P120) days after hyperthermic-induced seizures. Brain microdissection was performed as described in (Gorter et al., 2006). Briefly, after decapitation, the temporal lobe and hippocampus were removed by incision at the ventrocaudal part underneath the rhinal fissure, until 5 mm posterior to bregma. Then, the hippocampus was cut into smaller pieces (200-300 uM) and the CA3 region was selected and removed in phosphate buffered saline (PBS) at 4°C under a dissecting microscope. The material obtained from the ventral CA3 region was placed in Eppendorf tubes containing RNA later (Qiagen) for subsequent extraction of total RNA
Total RNA was isolated from CA3 ventral hippocampus samples using Trizol reagent (Life Technologies) and purified using RNeasy Spin Columns (Qiagen, USA). RNA quantity was determined using a Nanovue spectrophotometer (GE Healthcare, USA). The RNA quality was performed using a 2100 Bioanalyzer with an RNA 6000 Nano kit and Ladder (Agilent Technologies, USA), according to the manufacturer’s instructions.

value: CA3 ventral hippocampus

tag: time period

tag: group

value: Normothermic Controls


title: Pat52 Whole Blood

description: SAMPLE 52

source_name: Pat52 Whole Blood

value: HIV Controllers

tag: sub group controller

value: Strong responders HIC


title: Pat53 Whole Blood

description: SAMPLE 53

source_name: Pat53 Whole Blood


title: Pat51 Whole Blood

description: SAMPLE 51

source_name: Pat51 Whole Blood

value: Weak responders HIC


title: Pat62 Whole Blood

description: SAMPLE 62

source_name: Pat62 Whole Blood


title: CA3V_hippocampus_P120_Control_3


title: Pat50 Whole Blood

description: SAMPLE 50

source_name: Pat50 Whole Blood


title: CA3V_hippocampus_P120_Control_4


title: Pat49 Whole Blood

description: SAMPLE 49

source_name: Pat49 Whole Blood


title: Pat55 Whole Blood

description: SAMPLE 55

source_name: Pat55 Whole Blood


title: Pat47 Whole Blood

description: SAMPLE 47

source_name: Pat47 Whole Blood


title: Pat48 Whole Blood

description: SAMPLE 48

source_name: Pat48 Whole Blood


title: CA3V_hippocampus_P120_Control_2


title: Pat45 Whole Blood

description: SAMPLE 45

source_name: Pat45 Whole Blood


title: CA3V_hippocampus_P120_Control_1


title: Pat44 Whole Blood

description: SAMPLE 44

source_name: Pat44 Whole Blood


title: Pat46 Whole Blood

description: SAMPLE 46

source_name: Pat46 Whole Blood


title: Pat37 Whole Blood

description: SAMPLE 37

source_name: Pat37 Whole Blood


title: Pat35 Whole Blood

description: SAMPLE 35

source_name: Pat35 Whole Blood


title: Pat39 Whole Blood

description: SAMPLE 39

source_name: Pat39 Whole Blood


title: Pat36 Whole Blood

description: SAMPLE 36

source_name: Pat36 Whole Blood


title: Pat38 Whole Blood

description: SAMPLE 38

source_name: Pat38 Whole Blood


title: Pat43 Whole Blood

description: SAMPLE 43

source_name: Pat43 Whole Blood


title: Pat40 Whole Blood

description: SAMPLE 40

source_name: Pat40 Whole Blood


title: Pat42 Whole Blood

description: SAMPLE 42

source_name: Pat42 Whole Blood


title: Pat31 Whole Blood

description: SAMPLE 31

source_name: Pat31 Whole Blood


title: Pat30 Whole Blood

description: SAMPLE 30

source_name: Pat30 Whole Blood


title: Pat26 Whole Blood

description: SAMPLE 26

source_name: Pat26 Whole Blood


title: Pat34 Whole Blood

description: SAMPLE 34

source_name: Pat34 Whole Blood


title: Pat27 Whole Blood

description: SAMPLE 27

source_name: Pat27 Whole Blood


title: Pat28 Whole Blood

description: SAMPLE 28

source_name: Pat28 Whole Blood


title: Pat32 Whole Blood

description: SAMPLE 32

source_name: Pat32 Whole Blood


title: Pat24 Whole Blood

description: SAMPLE 24

source_name: Pat24 Whole Blood


title: Pat29 Whole Blood

description: SAMPLE 29

source_name: Pat29 Whole Blood


title: Pat41 Whole Blood

description: SAMPLE 41

source_name: Pat41 Whole Blood


title: Pat25 Whole Blood

description: SAMPLE 25

source_name: Pat25 Whole Blood


title: Pat23 Whole Blood

description: SAMPLE 23

source_name: Pat23 Whole Blood


title: Pat33 Whole Blood

description: SAMPLE 33

source_name: Pat33 Whole Blood


title: Pat22 Whole Blood

description: SAMPLE 22

source_name: Pat22 Whole Blood


title: Pat21 Whole Blood

description: SAMPLE 21

source_name: Pat21 Whole Blood


title: Pat17 Whole Blood

description: SAMPLE 17

source_name: Pat17 Whole Blood


title: Pat19 Whole Blood

description: SAMPLE 19

source_name: Pat19 Whole Blood


title: CD8_d0_1

type: SRA

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

country: USA

institute: Cornell University

description: MCMV_RNA_NKCD8m45_rawCounts_knownGene.txt

library_source: transcriptomic

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.16-2.19)
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Genome_build: mm10
Supplementary_files_format_and_content: Text files are raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)

organism: Mus musculus

source_name: splenic CD8T cells

extract_protocol:
Cells were sorted directly into Trizol and total RNA underwent amplification using SMART-seq V4 (Clontech) Ultra Low Input RNA kit.
Subsequently, 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 47 million paired reads were generated per sample and the percent of mRNA bases was over to 72% on average.

tag: genotype

value: WT

tag: replicate

tag: condition

tag: cell type

value: splenic CD8T cells


title: CD8_d0_2


title: CD8m45_d7_1


title: CD8m45_d35_1


title: CD8m45_d35_2


title: CD8m45_d7_2


title: Pat18 Whole Blood

description: SAMPLE 18

source_name: Pat18 Whole Blood


title: CD8_d0_3


title: Pat12 Whole Blood

description: SAMPLE 12

source_name: Pat12 Whole Blood


title: Pat16 Whole Blood

description: SAMPLE 16

source_name: Pat16 Whole Blood


title: Pat14 Whole Blood

description: SAMPLE 14

source_name: Pat14 Whole Blood


title: Pat20 Whole Blood

description: SAMPLE 20

source_name: Pat20 Whole Blood


title: Pat13 Whole Blood

description: SAMPLE 13

source_name: Pat13 Whole Blood


title: NK_d35_2

source_name: splenic NK cells

value: HPOS

value: splenic NK cells


title: Pat15 Whole Blood

description: SAMPLE 15

source_name: Pat15 Whole Blood


title: NK_d35_1


title: Pat11 Whole Blood

description: SAMPLE 11

source_name: Pat11 Whole Blood


title: NK_d14_1


title: Pat8 Whole Blood

description: SAMPLE 8

source_name: Pat8 Whole Blood


title: Pat9 Whole Blood

description: SAMPLE 9

source_name: Pat9 Whole Blood


title: Pat5 Whole Blood

description: SAMPLE 5

source_name: Pat5 Whole Blood


title: Pat4 Whole Blood

description: SAMPLE 4

source_name: Pat4 Whole Blood


title: Pat7 Whole Blood

description: SAMPLE 7

source_name: Pat7 Whole Blood


title: Pat6 Whole Blood

description: SAMPLE 6

source_name: Pat6 Whole Blood


title: Pat3 Whole Blood

description: SAMPLE 3

source_name: Pat3 Whole Blood


title: STAT1KO_HPOS_D2_002

description: STAT1KOChimera_MCMV_Stat1Hpos_rawCounts_knownGene.txt


title: NK_d4_1


title: NK_d7_1


title: NK_d4_2


title: NK_d7_2


title: NK_d14_2


title: STAT1KO_HPOS_D2_001


title: STAT1KO_HPOS_D0_001


title: STAT1KO_HPOS_D0_002


title: Pat2 Whole Blood

description: SAMPLE 2

source_name: Pat2 Whole Blood


title: Pat10 Whole Blood

description: SAMPLE 10

source_name: Pat10 Whole Blood


title: Pat64 PBMC/36 pep stimulation/24H

description: SAMPLE 197

source_name: Pat64 PBMC

value: PBMC

tag: agent

value: HIV peptide pool of 36 peptides (15-mers overlapping by 11 amino acids peptides) covering 5 regions of HIV Gag, Pol and Nef {Richert, 2013}

tag: time point


title: Pat79 PBMC/36 pep stimulation/24H

description: SAMPLE 191

source_name: Pat79 PBMC


title: Pat67 PBMC/36 pep stimulation/24H

description: SAMPLE 198

source_name: Pat67 PBMC


title: Pat70 PBMC/36 pep stimulation/24H

description: SAMPLE 189

source_name: Pat70 PBMC


title: Pat54 PBMC/36 pep stimulation/24H

description: SAMPLE 193

source_name: Pat54 PBMC


title: Pat68 PBMC/36 pep stimulation/24H

description: SAMPLE 188

source_name: Pat68 PBMC


title: T3961 differ

city: Philadelphia

first: Yi

last: Fan

state: Pennsylvania

address: 3400 Civic Center Blvd, Smilow Center for Translational Research, Rm 8-132

department: Department of Radiation Oncology

institute: University of Pennsylvania

data_processing: Data analysis was performed in the core facility at University of Pennsylvania, and gene expression expressed as FPKM values. About 200 genes encoding all known human proteins associated with DNA damage and repair were classified (http://sciencepark.mdanderson.org/labs/wood/dna_repair_genes.html) and matched with the FPKM expression profile.

source_name: Matched non-stem cancer cells

growth_protocol: GSCs were cultured in serum-free Neurobasal-A medium (Gibco), supplemented with B-27 Supplement Minus Vitamin A (Gibco), GlutaMax (Gibco), sodium pyruvate (Gibco), fibroblastic growth factor (FGF, 5 ng/ml, R&D Systems), and epidermal growth factor (EGF, 20 ng/ml, R&D Systems).

extract_protocol:
Approximately 2 x 106 cells were lysed in 1 ml TRIzol (Thermo Fisher), followed by RNA extraction according to the manufacturer’s instructions. The isolated RNA was purified by using an RNeasy Plus Mini Kit (Qiagen).
Library was constructed by using a RiboZero protocol with TapeStation (Agilent), and subjected to deep sequencing (125 PE, about 40 megabyte reads for each sample, Illumina sequencer 2500) in the Next-Generation Sequencing Core at the University of Pennsylvania.

treatment_protocol: GSCs were cultured in stem cell medium. The matched non-GSCs were generated by brief treatment with serum (10% FBS)-containing medium for 24 h, and cultured back in stem cell medium.

value: Matched non-stem cancer cells


title: STAT1WT_HPOS_D2_002

source_name: splenic NK cells


title: Pat59 PBMC/36 pep stimulation/24H

description: SAMPLE 196

source_name: Pat59 PBMC


title: Pat1 Whole Blood

description: SAMPLE 1

source_name: Pat1 Whole Blood


title: Pat74 PBMC/36 pep stimulation/24H

description: SAMPLE 190

source_name: Pat74 PBMC


title: Pat66 PBMC/36 pep stimulation/24H

description: SAMPLE 187

source_name: Pat66 PBMC


title: Pat56 PBMC/36 pep stimulation/24H

description: SAMPLE 194

source_name: Pat56 PBMC


title: Pat58 PBMC/36 pep stimulation/24H

description: SAMPLE 195

source_name: Pat58 PBMC


title: STAT1WT_HPOS_D2_001


title: Pat80 PBMC/36 pep stimulation/24H

description: SAMPLE 192

source_name: Pat80 PBMC


title: T3961

source_name: Human patient-derived glioma stem cells

value: Human patient-derived glioma stem cells


title: Pat60 PBMC/36 pep stimulation/24H

description: SAMPLE 185

source_name: Pat60 PBMC


title: Pat95 PBMC/36 pep stimulation/24H

description: SAMPLE 182

source_name: Pat95 PBMC


title: T4121 differ


title: STAT1WT_HPOS_D0_001


title: T4121


title: Pat96 PBMC/36 pep stimulation/24H

description: SAMPLE 183

source_name: Pat96 PBMC


title: Pat65 PBMC/36 pep stimulation/24H

description: SAMPLE 186

source_name: Pat65 PBMC


title: Pat3 PBMC/36 pep stimulation/24H

description: SAMPLE 184

source_name: Pat3 PBMC


title: STAT1WT_HPOS_D0_002


title: Pat94 PBMC/36 pep stimulation/24H

description: SAMPLE 180

source_name: Pat94 PBMC


title: Pat104 PBMC/36 pep stimulation/24H

description: SAMPLE 181

source_name: Pat104 PBMC


title: IN528 differ

source_name: Matched non-stem cancer cells


title: IN528


title: Pat103 PBMC/36 pep stimulation/24H, 2

description: SAMPLE 179

source_name: Pat103 PBMC


title: Pat92 PBMC/36 pep stimulation/24H

description: SAMPLE 176

source_name: Pat92 PBMC


title: Pat38 PBMC/36 pep stimulation/24H

description: SAMPLE 175

source_name: Pat38 PBMC


title: Pat48 PBMC/36 pep stimulation/24H

description: SAMPLE 178

source_name: Pat48 PBMC


title: Pat103 PBMC/36 pep stimulation/24H

description: SAMPLE 177


title: Pat91 PBMC/36 pep stimulation/24H

description: SAMPLE 174

source_name: Pat91 PBMC


title: aSTAT1_STAT1WT_STIM_1_INPUT

library_source: genomic

data_processing:
BCL files were converted to fastq using bcl2fastq (v1.8.3 and v1.8.4)
ChIP-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to size-normalized BEDGRAPH files using bedtools (v2.26.0) and converted to bigWig using UCSC's bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files normalized by size factors calculated by DESeq2 among all ChIP (non-input) samples in peak regions or flank regions (see manuscript)

molecule: genomic DNA

source_name: splenic NK cells

extract_protocol:
Protein was cross-linked to DNA with 0.75% formaldehyde. Clarified supernatant from sonicated nuclei were applied to antibody-bound beads. After de-crosslinking and elution, DNA was isolated using Qiagen Gel Extraction Kit. Input samples were clarified supernatant that were not applied to antibody-bound beads.
Immunoprecipitated DNA was quantified by Picogreen and size was evaluated on a HighSense BioAnalyzer chip. When possible, fragments between 100 and 600 bp were size selected and Illumina Hiseq libraries were prepared using the Kapa DNA library preparation chemistry (Kapa Biosystems) using 12-15 cycles of PCR. Adaptors were diluted 1/10 or  1/50 depending on the starting amount of material available. Barcoded libraries were run on Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 57 million paired reads were generated per sample.

tag: chip antibody

value: IFNa


title: aSTAT1_STAT1WT_STIM_2_INPUT


title: Pat88 PBMC/36 pep stimulation/24H

description: SAMPLE 171

source_name: Pat88 PBMC


title: Pat101 PBMC/36 pep stimulation/24H

description: SAMPLE 165

source_name: Pat101 PBMC


title: Pat90 PBMC/36 pep stimulation/24H

description: SAMPLE 173

source_name: Pat90 PBMC


title: Pat85 PBMC/36 pep stimulation/24H

description: SAMPLE 166

source_name: Pat85 PBMC


title: Pat86 PBMC/36 pep stimulation/24H

description: SAMPLE 168

source_name: Pat86 PBMC


title: Pat89 PBMC/36 pep stimulation/24H

description: SAMPLE 172

source_name: Pat89 PBMC


title: Pat19 PBMC/36 pep stimulation/24H

description: SAMPLE 167

source_name: Pat19 PBMC


title: Pat102 PBMC/36 pep stimulation/24H

description: SAMPLE 169

source_name: Pat102 PBMC


title: Pat98 PBMC/36 pep stimulation/24H

description: SAMPLE 163

source_name: Pat98 PBMC


title: Pat56 PBMC/36 pep stimulation/6H

description: SAMPLE 154

source_name: Pat56 PBMC


title: Pat67 PBMC/36 pep stimulation/6H

description: SAMPLE 158

source_name: Pat67 PBMC


title: Pat87 PBMC/36 pep stimulation/24H

description: SAMPLE 170

source_name: Pat87 PBMC


title: Pat84 PBMC/36 pep stimulation/24H

description: SAMPLE 164

source_name: Pat84 PBMC


title: Pat83 PBMC/36 pep stimulation/24H

description: SAMPLE 161

source_name: Pat83 PBMC


title: Pat59 PBMC/36 pep stimulation/6H

description: SAMPLE 156

source_name: Pat59 PBMC


title: Pat58 PBMC/36 pep stimulation/6H

description: SAMPLE 155

source_name: Pat58 PBMC


title: Pat82 PBMC/36 pep stimulation/24H

description: SAMPLE 160

source_name: Pat82 PBMC


title: Pat74 PBMC/36 pep stimulation/6H

description: SAMPLE 150

source_name: Pat74 PBMC


title: Pat65 PBMC/36 pep stimulation/6H

description: SAMPLE 146

source_name: Pat65 PBMC


title: Pat68 PBMC/36 pep stimulation/6H

description: SAMPLE 148

source_name: Pat68 PBMC


title: Pat97 PBMC/36 pep stimulation/24H

description: SAMPLE 159

source_name: Pat97 PBMC


title: Pat99 PBMC/36 pep stimulation/24H

description: SAMPLE 162

source_name: Pat99 PBMC


title: Pat3 PBMC/36 pep stimulation/6H

description: SAMPLE 144

source_name: Pat3 PBMC


title: Pat54 PBMC/36 pep stimulation/6H

description: SAMPLE 153

source_name: Pat54 PBMC


title: Pat64 PBMC/36 pep stimulation/6H

description: SAMPLE 157

source_name: Pat64 PBMC


title: Pat70 PBMC/36 pep stimulation/6H

description: SAMPLE 149

source_name: Pat70 PBMC


title: Pat96 PBMC/36 pep stimulation/6H

description: SAMPLE 143

source_name: Pat96 PBMC


title: Pat95 PBMC/36 pep stimulation/6H

description: SAMPLE 142

source_name: Pat95 PBMC


title: Pat80 PBMC/36 pep stimulation/6H

description: SAMPLE 152

source_name: Pat80 PBMC


title: Pat60 PBMC/36 pep stimulation/6H

description: SAMPLE 145

source_name: Pat60 PBMC


title: Pat94 PBMC/36 pep stimulation/6H

description: SAMPLE 140

source_name: Pat94 PBMC


title: Pat92 PBMC/36 pep stimulation/6H

description: SAMPLE 136

source_name: Pat92 PBMC


title: Pat79 PBMC/36 pep stimulation/6H

description: SAMPLE 151

source_name: Pat79 PBMC


title: Pat91 PBMC/36 pep stimulation/6H

description: SAMPLE 134

source_name: Pat91 PBMC


title: Pat103 PBMC/36 pep stimulation/6H

description: SAMPLE 137

source_name: Pat103 PBMC


title: Pat104 PBMC/36 pep stimulation/6H

description: SAMPLE 141

source_name: Pat104 PBMC


title: Pat87 PBMC/36 pep stimulation/6H

description: SAMPLE 130

source_name: Pat87 PBMC


title: Pat48 PBMC/36 pep stimulation/6H

description: SAMPLE 138

source_name: Pat48 PBMC


title: Pat86 PBMC/36 pep stimulation/6H

description: SAMPLE 128

source_name: Pat86 PBMC


title: Pat89 PBMC/36 pep stimulation/6H

description: SAMPLE 132

source_name: Pat89 PBMC


title: Pat90 PBMC/36 pep stimulation/6H

description: SAMPLE 133

source_name: Pat90 PBMC


title: Pat84 PBMC/36 pep stimulation/6H

description: SAMPLE 124

source_name: Pat84 PBMC


title: Pat83 PBMC/36 pep stimulation/6H

description: SAMPLE 120

source_name: Pat83 PBMC


title: Pat98 PBMC/36 pep stimulation/6H

description: SAMPLE 123

source_name: Pat98 PBMC


title: Pat88 PBMC/36 pep stimulation/6H

description: SAMPLE 131

source_name: Pat88 PBMC


title: Pat82 PBMC/36 pep stimulation/6H

description: SAMPLE 119

source_name: Pat82 PBMC


title: Pat100 PBMC/36 pep stimulation/6H

description: SAMPLE 122

source_name: Pat100 PBMC


title: Pat102 PBMC/36 pep stimulation/6H

description: SAMPLE 129

source_name: Pat102 PBMC


title: Pat85 PBMC/36 pep stimulation/6H

description: SAMPLE 126

source_name: Pat85 PBMC


title: Pat19 PBMC/36 pep stimulation/6H

description: SAMPLE 127

source_name: Pat19 PBMC


title: Pat97 PBMC/36 pep stimulation/6H

description: SAMPLE 118

source_name: Pat97 PBMC


title: Pat99 PBMC/36 pep stimulation/6H

description: SAMPLE 121

source_name: Pat99 PBMC


title: Pat66 PBMC/36 pep stimulation/6H

description: SAMPLE 147

source_name: Pat66 PBMC


title: Pat38 PBMC/36 pep stimulation/6H

description: SAMPLE 135

source_name: Pat38 PBMC


title: Pat96 CD4

description: SAMPLE 116

source_name: Pat96 CD4


title: Pat98 CD4

description: SAMPLE 117

source_name: Pat98 CD4


title: Pat101 PBMC/36 pep stimulation/6H

description: SAMPLE 125

source_name: Pat101 PBMC


title: Magarach(GA)

city: Moscow

first: Sergei

last: Funikov

state: Moscow

address: Vavilov str. 32

country: Russia

institute: Engelhardt Insitute of Molecular Biology

description: small RNAs (21-29 nts)

data_processing:
As a result of deep-sequencing we obtained 5-14 million reads of small RNAs for each library. Pre-processing procedure included: 3’-adapter cropping, filtration of reads by length filtration (>18 nt) and quality (80% of nt have ≥ 20 Phred quality). Pre-processed reads were further subjected to subtraction of reads matching to all rRNA, tRNA, snRNA and miRNA sequences. The selected reads were mapped to the latest release of D. virilis genome by Bowtie (Langmead et al., 2009) with requiring of perfect match. In order to identify siRNAs and piRNAs, the sequenced reads were mapped to the canonical sequences of TEs obtained from combined libraries of annotated and computationally predicted D. virilis transposons and repeats sequences (Erwin et al., 2015). Length distribution and counting of siRNAs and piRNAs reads, nucleotide biases, ping-pong signatures, coverage of transposon sequence by piRNAs were analyzed with accordance to the well-described technique (Brennecke et al., 2007; Song et al., 2014) using custom scripts written in Python.
genome build: droVir2 (Aug, 2005)
Supplementary_files_format_and_content: Excel file with CPM

organism: Drosophila virilis

source_name: Magarach (N-strain)

extract_protocol:
Total RNA was extracted from ovaries of 7-10 days old females using Extract RNA reagent (Evrogen, Russia). To prepare small RNA fraction for cloning, total RNA from ovaries (~ 25 µg) was separated, using 15% polyacrylamide gel electrophoresis containing 8 M Urea. After incubation in an ethidium bromide solution (0.5 µg/ml) gel fragments corresponding to the small RNA fraction were excised, using chemically synthesized RNA corresponding to 21 and 29 nts as size markers.
Cloning of small RNA libraries was performed by Illumina TruSeq Small RNA prep kit (Illumina, USA) according to the manufacturer’s protocol.

value: Ovaries

tag: strain

value: Magarach (N-strain)

tag: rna fraction

value: Gel extraction of small RNAs (21-29 nts)


title: Pat94 CD4

description: SAMPLE 114

source_name: Pat94 CD4


title: Pat93 CD4

description: SAMPLE 113

source_name: Pat93 CD4


title: Pat91 CD4

description: SAMPLE 110

source_name: Pat91 CD4


title: Pat88 CD4

description: SAMPLE 107

source_name: Pat88 CD4


title: Pat48 CD4

description: SAMPLE 112

source_name: Pat48 CD4


title: Pat90 CD4

description: SAMPLE 109

source_name: Pat90 CD4


title: Pat92 CD4

description: SAMPLE 111

source_name: Pat92 CD4


title: Pat89 CD4

description: SAMPLE 108

source_name: Pat89 CD4


title: Pat83 CD4

description: SAMPLE 103

source_name: Pat83 CD4


title: Pat84 CD4

description: SAMPLE 104

source_name: Pat84 CD4


title: Pat97 CD8

description: SAMPLE 99

source_name: Pat97 CD8


title: Pat82 CD4

description: SAMPLE 102

source_name: Pat82 CD4


title: Pat81 CD4

description: SAMPLE 101

source_name: Pat81 CD4


title: Pat91 CD8

description: SAMPLE 92

source_name: Pat91 CD8


title: Pat86 CD4

description: SAMPLE 106

source_name: Pat86 CD4


title: Pat96 CD8

description: SAMPLE 98

source_name: Pat96 CD8


title: Pat89 CD8

description: SAMPLE 90

source_name: Pat89 CD8


title: Pat94 CD8

description: SAMPLE 96

source_name: Pat94 CD8


title: Pat48 CD8

description: SAMPLE 94

source_name: Pat48 CD8


title: Pat19 CD4

description: SAMPLE 105

source_name: Pat19 CD4


title: Pat92 CD8

description: SAMPLE 93

source_name: Pat92 CD8


title: Pat98 CD8

description: SAMPLE 100

source_name: Pat98 CD8


title: Pat95 CD8

description: SAMPLE 97

source_name: Pat95 CD8


title: Pat90 CD8

description: SAMPLE 91

source_name: Pat90 CD8


title: Pat93 CD8

description: SAMPLE 95

source_name: Pat93 CD8


title: Pat86 CD8

description: SAMPLE 87

source_name: Pat86 CD8


title: Pat88 CD8

description: SAMPLE 89

source_name: Pat88 CD8


title: Pat95 CD4

description: SAMPLE 115

source_name: Pat95 CD4


title: Pat87 CD8

description: SAMPLE 88

source_name: Pat87 CD8


title: Pat19 CD8

description: SAMPLE 86

source_name: Pat19 CD8


title: Pat85 CD8

description: SAMPLE 85

source_name: Pat85 CD8


title: Pat82 CD8

description: SAMPLE 82

source_name: Pat82 CD8


title: Pat83 CD8

description: SAMPLE 83

source_name: Pat83 CD8


title: Pat84 CD8

description: SAMPLE 84

source_name: Pat84 CD8


title: Pat81 CD8

description: SAMPLE 81

source_name: Pat81 CD8


title: MCF7 24h Hypoxia DMSO, Replicate 4

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description:
Sample name: 24 Hypoxia DMSO 4
Replicate 4

hyb_protocol: 750ng of cRNA from each sample was hybridized to Human HT-12 V4.0 BeadChip microarrays (Illumina) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina) at scan factor 2.

data_processing:
Probe intensities were background subtracted using BeadStudio Data Analysis Software v3.1.3.0 (Illumina) and normalized using the cross-correlation method (Chua et al., 2006) with MATLAB scripts. Gene probe sets with minimum 1.5- fold change (on a Log2 scale) over the average of the normoxia controls for each condition were identified.
Reference: Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

source_name: MCF7 Human Breast Cancer Cells, 24h Chronic Hypoxia, 0.1% DMSO

label_protocol: 500ng of high purity and integrity total RNA samples with 260/280 and 260/230 absorbance ratios >1.8 and RNA integrity numbers (RIN) >8.0 were reverse transcribed into cDNA and in vitro transcribed into biotin-labelled complementary RNA (cRNA) using the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: Cells were maintained in DMEM (Nacalai Tesque) containing 10% FBS (Sigma-Aldrich), 100 μg/ml penicillin, 100 μg/ml streptomycin, 2 mM GlutaMAX and 100 μM non-essential amino acids (Invitrogen).

extract_protocol: Total RNA was extracted from all cells using the RNeasy Mini kit (Qiagen) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >8).

treatment_protocol: Cells were plated at 2-2.5 x 10^4 cells/cm2. For acute hypoxia treatment, cells were cultured for 20 hours in normoxia (21% O2 and 5% CO2 at 37°C) followed by 4 hours of hypoxia in 1% O2 (Wang et al., 1995) and 5% CO2 at 37°C in an Invivo2 Hypoxia Workstation 400 (Ruskinn Technology). Chronic hypoxia treatments consist of continuous culture for 24 hours in hypoxia (Holmquist-Mengelbier et al., 2006) while the normoxia controls were carried out for 24 hours in 21% O2 and 5% CO2 at 37°C. For studies on the pharmacological inhibition of G9A using small molecules, cells were treated with media containing 6 μM BIX-01294 (Stemgent) in 0.1% dimethyl sulfoxide (DMSO, Sigma-Aldrich) for 24 hours with carrier controls consisting of only 0.1% DMSO in media or combined with concurrent acute/chronic hypoxia treatments as above.

tag: cell line

value: Breast cancer cell line

tag: hypoxia/normoxia

value: 24h Hypoxia

tag: drug treatment

value: 0.1% DMSO


title: Pat103 PBMC/36 pep stimulation/6H, 2

description: SAMPLE 139

source_name: Pat103 PBMC

tag: patient name

tag: groups

value: HIV Controllers


title: MCF7 4h Hypoxia BIX, Replicate 1

description:
Sample name: 4h Hypoxia BIX 1
Replicate 1

source_name: MCF7 Human Breast Cancer Cells, 4h Acute Hypoxia, 6 μM BIX-01294 in 0.1% DMSO

value: 20h Normoxia, 4h Hypoxia

value: 6 uM BIX-01294 in 0.1% DMSO


title: MCF7 24h Hypoxia No Treatment, Replicate 2

description:
Sample name: 24h Hypoxia NT 2
Replicate 2

source_name: MCF7 Human Breast Cancer Cells, 24h Chronic Hypoxia, No Treatment

value: No Treatment


title: MCF7 24h Hypoxia No Treatment, Replicate 1

description:
Sample name: 24h Hypoxia NT 1
Replicate 1


title: MCF7 24h Hypoxia BIX, Replicate 2

description:
Sample name: 24 Hypoxia BIX 2
Replicate 2

source_name: MCF7 Human Breast Cancer Cells, 24h Chronic Hypoxia, 6 μM BIX-01294 in 0.1% DMSO


title: MCF7 4h Hypoxia No Treatment, Replicate 4

description:
Sample name: 4h Hypoxia NT 4
Replicate 4

source_name: MCF7 Human Breast Cancer Cells, 4h Acute Hypoxia, No Treatment


title: MCF7 24h Hypoxia BIX, Replicate 4

description:
Sample name: 24 Hypoxia BIX 4
Replicate 4


title: MCF7 4h Hypoxia DMSO, Replicate 3

description:
Sample name: 4h Hypoxia DMSO 3
Replicate 3

source_name: MCF7 Human Breast Cancer Cells, 4h Acute Hypoxia, 0.1% DMSO


title: MCF7 4h Hypoxia DMSO, Replicate 1

description:
Sample name: 4h Hypoxia DMSO 1
Replicate 1


title: MCF7 4h Hypoxia No Treatment, Replicate 2

description:
Sample name: 4h Hypoxia NT 2
Replicate 2


title: MCF7 24h Hypoxia DMSO, Replicate 2

description:
Sample name: 24 Hypoxia DMSO 2
Replicate 2


title: MCF7 4h Hypoxia BIX, Replicate 2

description:
Sample name: 4h Hypoxia BIX 2
Replicate 2


title: MCF7 4h Hypoxia DMSO, Replicate 4

description:
Sample name: 4h Hypoxia DMSO 4
Replicate 4


title: MCF7 4h Hypoxia BIX, Replicate 3

description:
Sample name: 4h Hypoxia BIX 3
Replicate 3


title: MCF7 24h Hypoxia DMSO, Replicate 1

description:
Sample name: 24 Hypoxia DMSO 1
Replicate 1


title: MCF7 4h Hypoxia No Treatment, Replicate 3

description:
Sample name: 4h Hypoxia NT 3
Replicate 3


title: MCF7 Normoxia BIX, Replicate 4

description:
Sample name: Normoxia BIX 4
Replicate 4

source_name: MCF7 Human Breast Cancer Cells, 24h Normoxia, 6 μM BIX-01294 in 0.1% DMSO

value: 24h Normoxia


title: MCF7 Normoxia BIX, Replicate 1

description:
Sample name: Normoxia BIX 1
Replicate 1


title: MCF7 Normoxia BIX, Replicate 2

description:
Sample name: Normoxia BIX 2
Replicate 2


title: avelumab_200ug_NHS-muIL12_10ug_rep4

city: Billerica

first: Chunxiao

last: Xu

state: MA

address: 45A Middlesex Tpke

institute: EMD Serono Research and Development Institute

hyb_protocol: standard nanostring protocol

scan_protocol: standard nanostring protocol

data_processing: Per-sample background levels were calculated and subtracted from the samples. Samples were then normalized against the positive control probes such that geometric mean of the positive control probes was aligned across samples.  Samples were then normalized using the housekeeping gene probes such that the geometric mean of the housekeeping probes was aligned across samples.  Two samples (G3-4 and G4-1) were identified as outliers based on the counts distribution, PCA, and other analysis; these two samples were excluded from further analysis.

label: nanostring oligonucleotide probe

source_name: EMT-6 tumor

label_protocol: standard nanostring protocol

growth_protocol: BALB/c mice were injected with 0.5×10^6 EMT-6 tumor cells orthotopically in the mammary fat pad. Tumors were measured twice per week with digital calipers and tumor volumes were estimated using the spherical formula: volume = 0.5236 (length × width × height). Mice were randomized into treatment groups when tumor volume reached desired size of roughly 100mm^3 (day 0).

extract_protocol: total RNA extraction

treatment_protocol: NHS-muIL12 was given subcutaneously on day 0 (0ug groups 1 and 4.  2ug groups 2 and 5.  10ug groups 3 and 6).  Avelumab was given intravenously on days 0, 3, and 6 (0 ug groups 1, 2, 3.  200 ug groups 4, 5, 6)

value: NHS-muIL12, avelumab

tag: nhs-muil12 dose

tag: avelumab dose

value: BALB/c


title: MCF7 Normoxia DMSO, Replicate 3

description:
Sample name: Normoxia DMSO 3
Replicate 3

source_name: MCF7 Human Breast Cancer Cells, 24h Normoxia, 0.1% DMSO


title: avelumab_200ug_NHS-muIL12_10ug_rep3


title: MCF7 Normoxia DMSO, Replicate 4

description:
Sample name: Normoxia DMSO 4
Replicate 4


title: MCF7 Normoxia DMSO, Replicate 1

description:
Sample name: Normoxia DMSO 1
Replicate 1


title: MCF7 Normoxia No Treatment, Replicate 4

description:
Sample name: Normoxia NT 4
Replicate 4

source_name: MCF7 Human Breast Cancer Cells, 24h Normoxia, No Treatment


title: MCF7 Normoxia No Treatment, Replicate 1

description:
Sample name: Normoxia NT 1
Replicate 1


title: MCF7 24h Hypoxia BIX, Replicate 1

description:
Sample name: 24 Hypoxia BIX 1
Replicate 1


title: MCF7 Normoxia No Treatment, Replicate 2

description:
Sample name: Normoxia NT 2
Replicate 2


title: avelumab_200ug_NHS-muIL12_2ug_rep3


title: avelumab_200ug_NHS-muIL12_2ug_rep4


title: avelumab_200ug_NHS-muIL12_2ug_rep2


title: avelumab_200ug_NHS-muIL12_10ug_rep1


title: avelumab_200ug_NHS-muIL12_10ug_rep2


title: avelumab_200ug_NHS-muIL12_2ug_rep1


title: NHS-muIL12_2ug_rep3


title: NHS-muIL12_2ug_rep4


title: avelumab_200ug_rep4

value: avelumab


title: NHS-muIL12_10ug_rep1


title: NHS-muIL12_10ug_rep2


title: NHS-muIL12_10ug_rep3


title: avelumab_200ug_rep2


title: avelumab_200ug_rep3


title: NHS-muIL12_2ug_rep2


title: NT_culture_90

status: Public on Dec 19 2017

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description:
single cells isolated by FACS
rpkms_sc.txt

data_processing:
Fastq files were generated with bcl2fastq2 (2.18.0.12).
Reads were aligned to the chicken genome galGal4 from UCSC using Tophat 2.0.13 with -x 1 -g 1. Annotations were from Ensembl 80. Counts of reads on genes were calculated using bedtools intersect on unioned exons.
Data was read into R and differentially expressed genes were found using edgeR with TMM normalization.
Genome_build: galGal4
Supplementary_files_format_and_content: tab delimited text of TMM normalized, edgeR generated rpkms.

molecule: polyA RNA

organism: Gallus gallus

source_name: Cranial Neural Crest Cells

growth_protocol: Fertilized, white leghorn chicken eggs were incubated in a humidified chamber at 38C to the developmental desired stage. For additional information, please see methods in PMID: 29199959 DOI: 10.7554/eLife.28415

extract_protocol:
For scRNA-seq, the NC r4 stream was isolated by manual dissection at HHSt11, 13 and 15. HHSt11 r4 streams containing few migrating NC were pooled. For HHSt13 and 15 embryos, the r4 NC stream was further subdivided by manual dissection into three spatially distinct, non-overlapping portions: the most invasive front (5% of the stream, termed ‘Front’), the leading portion of the stream (25% of stream proximal of the most invasive front, termed ‘Lead’) and the proximal-most trailing portion of the stream (70% of the stream, termed ‘Trail’). Developmental stage- and stream position-matched tissues were pooled and dissociated before cytometric isolation. Cells were isolated by FACS, which included forward scatter, side scatter, pulse width, live/dead stain and YFP gates. Cells were sorted directly into 6 ul of Clontech lysis solution containing 0.05% RNAse inhibitor. Following lysis for 5 min at room temperature, lysates were immediately frozen on dry ice and stored at −80C.
Single-cell lysates were thawed on ice. cDNA synthesis and library preparation were performed with SMART-seq v4 Ultra Low Input RNA-seq (634892, Takara, Kusatsu, Shiga, Japan) and Nextera XT DNA dual indexing library preparation kits as recommended by the manufacturer (FC-131–1096, Illumina). Despite more cost-effective scRNAseq strategies, SMARTseq v4 was employed in order to detect the greatest number of genes per single cell, which is critical for distinguishing highly similar cell subpopulations (Ziegenhain et al., 2017; Dueck et al., 2016).

treatment_protocol: For NC cell isolations, pre-migratory NC were labeled by electroporation of a Gap43-YFP plasmid DNA into the dorsal neural tube of HHSt9 embryos as previously described (McLennan and Kulesa, 2007) and re-incubated (8, 16 and 24 hr for HHSt11, 13 and 15, respectively). After re-incubation, embryos were harvested into chilled 0.1% DEPC PBS and screened for health and transfection efficiency before tissue isolations were performed.

tag: location

value: In Vitro

tag: development stage

tag: type


title: NHS-muIL12_2ug_rep1


title: isotype_control_rep4


title: isotype_control_rep3


title: NT_culture_95


title: NT_culture_92


title: isotype_control_rep1


title: NT_culture_87


title: NT_culture_88


title: NT_culture_93


title: NT_culture_94


title: NT_culture_85


title: NT_culture_96


title: NT_culture_91


title: NT_culture_89


title: MCF7 24h Hypoxia No Treatment, Replicate 4

description:
Sample name: 24h Hypoxia NT 4
Replicate 4


title: NT_culture_81


title: NT_culture_84


title: isotype_control_rep2


title: NT_culture_83


title: NT_culture_76


title: NT_culture_86


title: NT_culture_79


title: NT_culture_82


title: NT_culture_75


title: NT_culture_78


title: NT_culture_77


title: NT_culture_74


title: NT_culture_73


title: NT_culture_71


title: NT_culture_64


title: NT_culture_65


title: NT_culture_72


title: NT_culture_66


title: NT_culture_63


title: NT_culture_61


title: NT_culture_67


title: NT_culture_70


title: NT_culture_60


title: NT_culture_68


title: NT_culture_59


title: NT_culture_62


title: NT_culture_80


title: NT_culture_56


title: NT_culture_57


title: NT_culture_58


title: NT_culture_53


title: NT_culture_54


title: NT_culture_52


title: NT_culture_69


title: NT_culture_49


title: NT_culture_47


title: NT_culture_51


title: NT_culture_46


title: NT_culture_45


title: NT_culture_50


title: NT_culture_44


title: NT_culture_43


title: NT_culture_41


title: NT_culture_39


title: NT_culture_42


title: NT_culture_38


title: NT_culture_40


title: NT_culture_37


title: NT_culture_55


title: NT_culture_30


title: NT_culture_28


title: NT_culture_29


title: NT_culture_32


title: NT_culture_31


title: NT_culture_34


title: NT_culture_33


title: NT_culture_48


title: NT_culture_27


title: NT_culture_25


title: NT_culture_26


title: NT_culture_24


title: NT_culture_20


title: NT_culture_18


title: NT_culture_22


title: NT_culture_17


title: NT_culture_36


title: NT_culture_16


title: NT_culture_19


title: NT_culture_14


title: NT_culture_13


title: NT_culture_15


title: NT_culture_23


title: NT_culture_35


title: NT_culture_11


title: NT_culture_10


title: NT_culture_12


title: NT_culture_3


title: NT_culture_9


title: NT_culture_8


title: NT_culture_6


title: NT_culture_2


title: NT_culture_4


title: NT_culture_7


title: NT_culture_5


title: HH15_Trailer_46

value: Trailer

value: Hamburger & Hamilton (HH) Stage 15

value: In Vivo


title: HH15_Trailer_47


title: NT_culture_1


title: HH15_Trailer_48


title: HH15_Trailer_49


title: NT_culture_21


title: HH15_Trailer_50


title: HH15_Trailer_45


title: HH15_Trailer_44


title: HH15_Trailer_40


title: HH15_Trailer_35


title: HH15_Trailer_41


title: HH15_Trailer_37


title: HH15_Trailer_38


title: HH15_Trailer_33


title: HH15_Trailer_34


title: HH15_Trailer_36


title: HH15_Trailer_31


title: HH15_Trailer_30


title: HH15_Trailer_28


title: HH15_Trailer_29


title: HH15_Trailer_26


title: HH15_Trailer_27


title: HH15_Trailer_25


title: HH15_Trailer_23


title: HH15_Trailer_24


title: HH15_Trailer_21


title: HH15_Trailer_17


title: HH15_Trailer_19


title: HH15_Trailer_22


title: HH15_Trailer_18


title: HH15_Trailer_43


title: HH15_Trailer_16


title: HH15_Trailer_42


title: HH15_Trailer_39


title: HH15_Trailer_20


title: HH15_Trailer_15


title: HH15_Trailer_14


title: HH15_Trailer_13


title: HH15_Trailer_32


title: HH15_Trailer_6


title: HH15_Trailer_7


title: HH15_Trailer_11


title: HH15_Trailer_10


title: HH15_Trailer_12


title: HH15_Trailer_5


title: HH15_Trailer_8


title: HH15_Trailer_4


title: HH15_Trailer_2


title: HH15_Trailer_3


title: HH15_Leader_50

value: Leader


title: HH15_Leader_49


title: HH15_Leader_48


title: HH15_Leader_45


title: HH15_Leader_46


title: HH15_Trailer_9


title: HH15_Leader_44


title: YC601-10d-litter7-HET

city: New York

first: Cem

last: Meydan

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

description:
YC651.8d.litter3.WT
YC601-10d-litter7-HET_IGO_08024_15_S26

data_processing:
RNAseq fastq files were aligned using STAR version 2.5.3a to the mouse genome (GRCm38/mm10) using Gencode M11 transcriptome assembly for junction points.
RNAseq counts were annotated by using subread version 1.4.5-p1 featureCounts. Counts were normalized to TPM (Transcripts Per Kilobase Million) for plotting. Differentially expressed genes were calculated using DESeq2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: gene counts; gene transcripts per million; exon counts

source_name: 10 dpp_Ythdc2+/em1 _whole testis

extract_protocol:
Total RNA from a single testis per animal, after removing the tunica albuginea, was extracted using the RNeasy Plus Mini Kit containing a genomic DNA eliminator column (Qiagen), according to manufacturers’ instructions.
Sequencing was performed at the Integrated Genomics Operation of MSKCC. 500 μg of total RNA underwent polyA capture and library preparation using the Truseq Stranded Total RNA library preparation chemistry (Illumina). Sequencing was performed using the Illumina HiSeq platform (2×50-bp paired-end reads) to generate on average, 44 million paired reads per sample.

tag: strain background

value: mixed; crossed to C57BL/6J five to six times

tag: mouse id

value: mouse a′

tag: genotype/variation

tag: age

value: 10 dpp

tag: littermate

value: litter 7

tag: tissue

value: whole testis


title: YC599-10d-litter7-MUT

description:
YC604.10d.litter7.MUT
YC599-10d-litter7-MUT_IGO_08024_14_S25

source_name: 10 dpp_Ythdc2em1/em1 _whole testis

value: mouse b


title: YC603-9d-litter6-MUT

description:
YC602.9d.litter6.WT
YC603-9d-litter6-MUT_IGO_08024_12_S23

source_name: 9 dpp_Ythdc2em1/em1 _whole testis

value: mouse a

value: 9 dpp

value: litter 6


title: YC604-10d-litter7-MUT

description:
YC654.8d.litter3.MUT
YC604-10d-litter7-MUT_IGO_08024_16_S27


title: YC598-10d-litter7-HET

description:
YC603.9d.litter6.MUT
YC598-10d-litter7-HET_IGO_08024_13_S24

value: mouse b′


title: HH15_Leader_43


title: YC602-9d-litter6-WT

description:
YC601.10d.litter7.HET
YC602-9d-litter6-WT_IGO_08024_11_S22

source_name: 9 dpp_Ythdc2+/+ _whole testis


title: HH15_Leader_37


title: HH15_Leader_39


title: YC577-9d-litter4-MUT

description:
YC594.9d.litter5.MUT
YC577-9d-litter4-MUT_IGO_08024_8_S37

value: mouse c

value: litter 4


title: HH15_Leader_40


title: YC592-9d-litter5-HET

description:
YC598.10d.litter7.HET
YC592-9d-litter5-HET_IGO_08024_9_S38

source_name: 9 dpp_Ythdc2+/em1 _whole testis

value: litter 5


title: HH15_Leader_38


title: HH15_Leader_36


title: YC578-9d-litter4-WT

description:
YC593.8d.litter2.WT
YC578-9d-litter4-WT_IGO_08024_7_S36

value: mouse c′


title: HH15_Leader_34

value: Hamburger & Hamilton (HH) Stage 15


title: HH15_Trailer_1

value: Trailer

value: In Vivo


title: HH15_Leader_47

value: Leader


title: YC654-8d-litter3-MUT

description:
YC592.9d.litter5.HET
YC654-8d-litter3-MUT_IGO_08024_6_S35

source_name: 8 dpp_Ythdc2em1/em1 _whole testis

value: mixed; crossed to C57BL/6J five to six times

value: 8 dpp

value: litter 3


title: HH15_Leader_35


title: HH15_Leader_33


title: YC594-9d-litter5-MUT

description:
YC599.10d.litter7.MUT
YC594-9d-litter5-MUT_IGO_08024_10_S21

value: whole testis


title: HH15_Leader_31


title: YC651-8d-litter3-WT

description:
YC591.8d.litter2.MUT
YC651-8d-litter3-WT_IGO_08024_5_S34

source_name: 8 dpp_Ythdc2+/+ _whole testis

value: mouse a′


title: YC591-8d-litter2-MUT

description:
YC578.9d.litter4.WT
YC591-8d-litter2-MUT_IGO_08024_4_S33

value: mouse b

value: litter 2


title: HH15_Leader_27


title: HH15_Leader_42


title: YC593-8d-litter2-WT

description:
YC577.9d.litter4.MUT
YC593-8d-litter2-WT_IGO_08024_3_S32


title: HH15_Leader_41


title: HH15_Leader_28


title: HH15_Leader_24


title: HH15_Leader_29


title: HH15_Leader_26


title: YC548-8d-litter1-MUT

description:
YC548.8d.litter1.MUT
YC548-8d-litter1-MUT_IGO_08024_2_S31

value: litter 1


title: HH15_Leader_25

description:
single cells isolated by FACS
rpkms_sc.txt


title: HH15_Leader_23


title: HH15_Leader_21


title: HH15_Leader_19


title: YC546-8d-litter1-WT

description:
YC546.8d.litter1.WT
YC546-8d-litter1-WT_IGO_08024_1_S30


title: HH15_Leader_20


title: HH15_Leader_18


title: HH15_Leader_32


title: HH15_Leader_30


title: HH15_Leader_12


title: HH15_Leader_13


title: HH15_Leader_15


title: HH15_Leader_14


title: HH15_Leader_17


title: HH15_Leader_16


title: HH15_Leader_9


title: HH15_Leader_8


title: HH15_Leader_7


title: HH15_Leader_22


title: HH15_Leader_10


title: HH15_Leader_4


title: HH15_Leader_6


title: HH15_Leader_3


title: HH15_Leader_5


title: HH15_Trailblazer_50

value: Invasive Front


title: HH15_Leader_2


title: HH15_Trailblazer_49


title: HH15_Leader_1


title: HH15_Trailblazer_48


title: HH15_Trailblazer_46


title: HH15_Trailblazer_42


title: HH15_Trailblazer_44


title: HH15_Trailblazer_47


title: HH15_Trailblazer_40


title: HH15_Trailblazer_43


title: HH15_Leader_11


title: HH15_Trailblazer_45


title: HH15_Trailblazer_35


title: HH15_Trailblazer_36


title: HH15_Trailblazer_39


title: HH15_Trailblazer_41


title: HH15_Trailblazer_31


title: HH15_Trailblazer_29


title: HH15_Trailblazer_32


title: HH15_Trailblazer_28


title: HH15_Trailblazer_24


title: HH15_Trailblazer_30


title: HH15_Trailblazer_20


title: HH15_Trailblazer_18


title: HH15_Trailblazer_19


title: HH15_Trailblazer_37


title: HH15_Trailblazer_38


title: HH15_Trailblazer_27


title: HH15_Trailblazer_26


title: HH15_Trailblazer_22


title: HH15_Trailblazer_25


title: HH15_Trailblazer_17


title: HH15_Trailblazer_21


title: HH15_Trailblazer_23


title: HH15_Trailblazer_11


title: HH15_Trailblazer_14


title: HH15_Trailblazer_16


title: HH15_Trailblazer_8


title: HH15_Trailblazer_34


title: HH15_Trailblazer_10


title: HH15_Trailblazer_12


title: HH15_Trailblazer_13


title: HH15_Trailblazer_9


title: HH15_Trailblazer_7


title: HH15_Trailblazer_5


title: HH15_Trailblazer_6


title: HH15_Trailblazer_1


title: HH15_Trailblazer_2


title: HH13_Trailer_60

value: Hamburger & Hamilton (HH) Stage 13


title: HH13_Trailer_58


title: HH13_Trailer_50


title: HH13_Trailer_59


title: HH15_Trailblazer_4


title: HH13_Trailer_54


title: HH15_Trailblazer_15


title: HH13_Trailer_48


title: HH13_Trailer_47


title: HH13_Trailer_53


title: HH13_Trailer_56


title: HH13_Trailer_43


title: HH13_Trailer_52


title: HH13_Trailer_55


title: HH13_Trailer_41


title: HH13_Trailer_44


title: HH13_Trailer_57


title: HH13_Trailer_45


title: HH15_Trailblazer_33


title: HH15_Trailblazer_3


title: HH13_Trailer_42


title: HH13_Trailer_46


title: HH13_Trailer_38


title: HH13_Trailer_37


title: HH13_Trailer_40


title: HH13_Trailer_51


title: HH13_Trailer_49


title: HH13_Trailer_35


title: HH13_Trailer_31


title: HH13_Trailer_34


title: HH13_Trailer_26


title: HH13_Trailer_36


title: HH13_Trailer_33


title: HH13_Trailer_22


title: HH13_Trailer_16


title: HH13_Trailer_18


title: HH13_Trailer_11


title: HH13_Trailer_29


title: HH13_Trailer_15


title: HH13_Trailer_10


title: HH13_Trailer_25


title: HH13_Trailer_20


title: HH13_Trailer_32


title: HH13_Trailer_27


title: HH13_Trailer_19


title: HH13_Trailer_30


title: HH13_Trailer_39


title: HH13_Trailer_28


title: HH13_Trailer_14


title: HH13_Trailer_13


title: HH13_Trailer_23


title: HH13_Trailer_21


title: HH13_Trailer_24


title: HH13_Trailer_17


title: HH13_Trailer_5


title: HH13_Trailer_6


title: HH13_Trailer_3


title: HH13_Trailer_4


title: HH13_Trailer_7


title: HH13_Trailer_9


title: HH13_Trailer_12


title: HH13_Leader_42


title: HH13_Leader_41


title: HH13_Trailer_1


title: HH13_Leader_45


title: HH13_Leader_49


title: HH13_Leader_48


title: HH13_Leader_46


title: HH13_Leader_31


title: HH13_Leader_36


title: HH13_Leader_50


title: HH13_Leader_32


title: HH13_Leader_37


title: HH13_Leader_35


title: HH13_Leader_29


title: HH13_Leader_38


title: HH13_Leader_34


title: HH13_Leader_39


title: HH13_Leader_28


title: HH13_Trailer_2


title: HH13_Leader_47


title: HH13_Leader_30


title: HH13_Leader_33


title: HH13_Leader_43


title: HH13_Leader_40


title: HH13_Leader_44


title: HH13_Leader_27


title: HH13_Leader_26


title: HH13_Leader_24


title: HH13_Leader_25


title: HH13_Leader_23


title: HH13_Leader_22


title: HH13_Trailer_8


title: HH13_Leader_20


title: HH13_Leader_15


title: HH13_Leader_19


title: HH13_Leader_11


title: HH13_Leader_12


title: HH13_Trailblazer_50


title: HH13_Leader_17


title: HH13_Leader_13


title: HH13_Leader_18


title: HH13_Leader_21


title: HH13_Leader_8


title: HH13_Trailblazer_49


title: HH13_Leader_16


title: HH13_Leader_5


title: HH13_Leader_14


title: HH13_Leader_6


title: HH13_Leader_3


title: HH13_Leader_7


title: HH13_Leader_4


title: HH13_Leader_9


title: HH13_Trailblazer_47


title: HH13_Trailblazer_46


title: HH13_Trailblazer_45


title: HH13_Trailblazer_48


title: HH13_Trailblazer_43


title: HH13_Trailblazer_42


title: HH13_Leader_10


title: HH13_Leader_2


title: HH13_Leader_1


title: HH13_Trailblazer_35


title: HH13_Trailblazer_40


title: HH13_Trailblazer_41


title: HH13_Trailblazer_37


title: HH13_Trailblazer_39


title: HH13_Trailblazer_32


title: HH13_Trailblazer_29


title: HH13_Trailblazer_36


title: HH13_Trailblazer_34


title: HH13_Trailblazer_44


title: HH13_Trailblazer_27


title: HH13_Trailblazer_22


title: HH13_Trailblazer_21


title: HH13_Trailblazer_28


title: HH13_Trailblazer_26


title: HH13_Trailblazer_25


title: HH13_Trailblazer_23


title: HH13_Trailblazer_19


title: HH13_Trailblazer_18


title: HH13_Trailblazer_20


title: HH13_Trailblazer_31


title: HH13_Trailblazer_30


title: HH13_Trailblazer_17


title: HH13_Trailblazer_16


title: HH13_Trailblazer_15


title: HH13_Trailblazer_38


title: HH13_Trailblazer_14


title: HH13_Trailblazer_24


title: HH13_Trailblazer_13


title: HH13_Trailblazer_33


title: HH13_Trailblazer_10


title: HH13_Trailblazer_12


title: HH13_Trailblazer_7


title: HH13_Trailblazer_8


title: HH13_Trailblazer_2


title: HH13_Trailblazer_6


title: HH13_Trailblazer_4


title: HH11_Trailblazer_94

value: Hamburger & Hamilton (HH) Stage 11


title: HH11_Trailblazer_90


title: HH13_Trailblazer_5


title: HH11_Trailblazer_92


title: HH13_Trailblazer_9


title: HH11_Trailblazer_95


title: HH13_Trailblazer_3


title: HH11_Trailblazer_96


title: HH13_Trailblazer_11


title: HH11_Trailblazer_89


title: HH13_Trailblazer_1


title: HH11_Trailblazer_88


title: HH11_Trailblazer_91


title: HH11_Trailblazer_86


title: HH11_Trailblazer_83


title: HH11_Trailblazer_93


title: HH11_Trailblazer_82


title: HH11_Trailblazer_87


title: HH11_Trailblazer_81


title: HH11_Trailblazer_79


title: HH11_Trailblazer_77


title: HH11_Trailblazer_84


title: HH11_Trailblazer_75


title: HH11_Trailblazer_85


title: HH11_Trailblazer_76


title: HH11_Trailblazer_80


title: HH11_Trailblazer_74


title: HH11_Trailblazer_73


title: HH11_Trailblazer_70


title: HH11_Trailblazer_69


title: HH11_Trailblazer_67


title: HH11_Trailblazer_71


title: HH11_Trailblazer_72


title: HH11_Trailblazer_78


title: control_dorsal_skin_7

city: Berlin

first: Ozlem

last: Akilli Ozturk

address: Robert Roesslestr. 10

department: Signal Transduction

country: Germany

institute: Max Delbruck Center

description:
replicate 14
9298740072_e

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio

source_name: Mouse dorsal skin_control

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplif Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: genotype

value: control

tag: strain

value: C57/BL6;129Ola mixed

value: 15 days

value: dorsal skin


title: HH11_Trailblazer_66

value: In Vivo


title: HH11_Trailblazer_65


title: control_dorsal_skin_5

description:
replicate 12
9298740072_a


title: control_dorsal_skin_9

description:
replicate 16
9298740072_g


title: control_dorsal_skin_2

description:
replicate 9
9298740070_d


title: Gab1_dorsal_skin_6

description:
replicate 6
9298740072_d

source_name: Mouse dorsal skin_Gab1_mutant

value: K14-cre; Gab1fl


title: HH11_Trailblazer_64


title: control_dorsal_skin_3

description:
replicate 10
9298740070_e


title: control_dorsal_skin_1

description:
replicate 8
9298740070_c


title: control_dorsal_skin_8

description:
replicate 15
9298740072_f


title: control_dorsal_skin_4

description:
replicate 11
9298740070_h


title: Gab1_dorsal_skin_4

description:
replicate 4
9298740070_g


title: control_dorsal_skin_6

description:
replicate 13
9298740072_b


title: Gab1_dorsal_skin_7

description:
replicate 7
9298740072_h


title: Gab1_dorsal_skin_5

description:
replicate 5
9298740072_c


title: Gab1_dorsal_skin_3

description:
replicate 3
9298740070_f


title: Gab1_dorsal_skin_2

description:
replicate 2
9298740070_b


title: HH11_Trailblazer_63


title: HH11_Trailblazer_68


title: HH11_Trailblazer_62


title: HH11_Trailblazer_60


title: HH11_Trailblazer_58


title: HH11_Trailblazer_59


title: HH11_Trailblazer_57


title: HH11_Trailblazer_55


title: HH11_Trailblazer_56


title: HH11_Trailblazer_61


title: HH11_Trailblazer_51


title: HH11_Trailblazer_52


title: HH11_Trailblazer_53


title: HH11_Trailblazer_54


title: HH11_Trailblazer_50


title: HH11_Trailblazer_49


title: HH11_Trailblazer_48


title: HH11_Trailblazer_46


title: HH11_Trailblazer_45


title: HH11_Trailblazer_47


title: Gab1_dorsal_skin_1

description:
replicate 1
9298740070_a


title: HH11_Trailblazer_44


title: HH11_Trailblazer_43


title: HH11_Trailblazer_42


title: HH11_Trailblazer_41


title: HH11_Trailblazer_40


title: genomic DNA from breast tissue 85

type: genomic

city: Research Triangle Park

first: Zongli

address: 111 tw alexander Dr.

institute: NIH/NIEHS

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: ENmix R package

label: Cy5 and Cy3

source_name: fresh frozen, histologically normal-appearing breast tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using DNeasy (Qiagen, Valencia, CA), according to the manufacturer’s instructions

value: never

tag: bmi

value: Benign

tag: race

value: White

value: normal breast


title: genomic DNA from breast tissue 79

value: former

value: Invasive

value: Black


title: genomic DNA from breast tissue 82

value: current

value: In Situ


title: genomic DNA from breast tissue 70


title: genomic DNA from breast tissue 83


title: genomic DNA from breast tissue 77


title: genomic DNA from breast tissue 81


city: Córdoba

first: Nathalie

last: Marquez

state: Córdoba

address: Camino 60 cuadras Km 5,5

country: Argentina

institute: INTA

description:
3 biological replicates. No technical replicates.
+AMF+Mp

hyb_protocol: Labelled cDNA targets were then hybridized (competitive hybridization) to the oligonucleotide arrays at 65 °C for 17 hours.

scan_protocol: Slides were scanned using the scanner Agilent G2505B at high resolution of 5 μm at 532 (Cy3) and 633 nm (Cy5) wavelengths (Agilent Technologies, Santa Clara, USA).

data_processing:
Data pre-processing was performed using the limma library (Smyth, 2005) from the R-package (R Core Team, 2012). Background correction was performed using background Correct function, using the “rma” algorithm. Between arrays normalization was performed using normalize Between Array function using “quantile” method. Finally, gene expressions were transformed to log2 scale and summarization of technical replicates was done calculating the median.
Estimated contrasts were expressed in log2 fold change scale. To express the contrasts differences as “fold change”, the following transformation was applied: FC= 2^contrast when the contrast was ≥ 0 and − 2^ –contrast when the contrast was < 0. This way, fold-changes have positive as well as negative value. A fold-change of 4 means a 4 times increase of gene expression, meanwhile a value of -4 means a 4 times decrease.

organism: Glycine max

source_name: Pre-mycorrhized soybean roots inoculated with M. phaseolina.

label_protocol: Synthesis of cDNA and labelling was performed with Quick Amp Labeling Kit as described in the protocol (Agilent Technologies Inc., USA). A two-colour microarray-based gene expression analysis protocol was used. Labelled cDNA targets (Cy3- and Cy5) were fragmented at 60 °C for 30 minutes.

growth_protocol: Soybean plantlets were cultivated in vitro conditions in a growth chamber set at 20/18°C (day/night), 70 % relative humidity, with a photoperiod of 16 h d-1 and a photosynthetic photon flux (PPF) of 225 µmol m−2 s−1.

extract_protocol: Total RNA extracted RNeasy plant mini kit (Qiagen, Valencia, USA) according to the manufacturer’s instructions.

tag: inoculation status

value: inoculated with M. phaseolina

value: whole root

source_name: pooled whole control soybean roots

value: not inoculated


title: genomic DNA from breast tissue 80


title: genomic DNA from breast tissue 71


title: HH11_Trailblazer_38

value: Invasive Front

value: Hamburger & Hamilton (HH) Stage 11


title: HH11_Trailblazer_37


title: genomic DNA from breast tissue 78

value: Other


title: genomic DNA from breast tissue 63


title: HH11_Trailblazer_36

value: In Vivo


title: genomic DNA from breast tissue 75


title: genomic DNA from breast tissue 69


title: genomic DNA from breast tissue 65


title: Pre-mycorrhized soybean roots

description:
3 biological replicates. Replicate 3 includes two technical replicates.
+AMF-Mp

source_name: Pre-mycorrhized soybean roots.


title: genomic DNA from breast tissue 64


title: genomic DNA from breast tissue 73


title: genomic DNA from breast tissue 74


title: genomic DNA from breast tissue 68


title: HH11_Trailblazer_39


title: HH11_Trailblazer_35


title: genomic DNA from breast tissue 61

value: Prophylactic


title: genomic DNA from breast tissue 62


title: genomic DNA from breast tissue 60

value: never


description:
3 biological replicates. No technical replicates.
-AMF+Mp

source_name: Soybean roots inoculated with M. phaseolina.


title: genomic DNA from breast tissue 59

value: Benign


title: genomic DNA from breast tissue 76

value: White


title: HH11_Trailblazer_34


title: genomic DNA from breast tissue 67

value: normal breast


title: HH11_Trailblazer_33


title: HH11_Trailblazer_31


title: HH11_Trailblazer_29


title: HH11_Trailblazer_30


title: genomic DNA from breast tissue 72

value: former


title: genomic DNA from breast tissue 58


title: genomic DNA from breast tissue 66


title: HH11_Trailblazer_26


title: HH11_Trailblazer_28


title: HH11_Trailblazer_27


title: HH11_Trailblazer_25


title: HH11_Trailblazer_24


title: HH11_Trailblazer_23


title: HH11_Trailblazer_20


title: HH11_Trailblazer_22


title: HH11_Trailblazer_21


title: HH11_Trailblazer_17


title: HH11_Trailblazer_18


title: genomic DNA from breast tissue 56

value: Invasive


title: HH11_Trailblazer_16


title: genomic DNA from breast tissue 55


title: Control soybean roots

description:
3 biological replicates. Replicate 3 includes two technical replicates.
-AMF-Mp

source_name: Control soybean roots.


title: HH11_Trailblazer_14


title: HH11_Trailblazer_15


title: genomic DNA from breast tissue 84


title: HH11_Trailblazer_19


title: HH11_Trailblazer_12


title: genomic DNA from breast tissue 57


title: HH11_Trailblazer_13


title: HH11_Trailblazer_10


title: genomic DNA from breast tissue 54


title: HH11_Trailblazer_9


title: HH11_Trailblazer_8


title: genomic DNA from breast tissue 49


title: HH11_Trailblazer_11


title: HH11_Trailblazer_7


title: genomic DNA from breast tissue 47


title: genomic DNA from breast tissue 46


title: genomic DNA from breast tissue 50


title: genomic DNA from breast tissue 48


title: genomic DNA from breast tissue 51


title: genomic DNA from breast tissue 41


title: HH11_Trailblazer_5


title: genomic DNA from breast tissue 39


title: genomic DNA from breast tissue 42


title: HH11_Trailblazer_4


title: genomic DNA from breast tissue 43


title: genomic DNA from breast tissue 52


title: genomic DNA from breast tissue 35


title: genomic DNA from breast tissue 40


title: genomic DNA from breast tissue 44

value: Black


title: genomic DNA from breast tissue 37

value: Reduction


title: HH11_Trailblazer_1


title: HH11_Trailblazer_2


title: genomic DNA from breast tissue 45

value: current


title: genomic DNA from breast tissue 38

value: In Situ


title: Stream_15_2

data_processing:
Fastq files were generated with bcl2fastq2 (2.18.0.12).
Reads were aligned to the chicken genome galGal4 from UCSC using Tophat 2.0.10 with -x 1 -g 1. Annotations were from Ensembl 84. Counts of reads on genes were calculated using bedtools intersect on unioned exons.
Data was read into R and differentially expressed genes were found using edgeR with TMM normalization.
Genome_build: galGal4
Supplementary_files_format_and_content: tab delimited text of TMM normalized, edgeR generated rpkms.

extract_protocol:
All manual dissections of Gap43-YFP transfected neural crest cells were performed using a fluorescent dissecting microscopy. For bulk RNA-seq samples, the neural crest streams adjacent to rhombomere 4 were isolated by manual dissection from Hamburger Hamilton Stage 13 and 15 embryos and divided into three biological replicates. The streams were subsequently cut into two spatially distinct, non-overlapping portions: the most invasive front (5% of the stream, termed ‘Front’) and the remaining proximal-most trailing portion of the stream (95% of the stream, termed ‘Stream’). Developmental stage- and stream position-matched pools of tissue were dissociated as previously described (Morrison et al., 2015).
Bulk RNA-seq lysates were thawed on ice. cDNA synthesis and library preparation were performed with SMART-seq v4 Ultra Low Input RNA-seq (634892, Takara, Kusatsu, Shiga, Japan) and Nextera XT DNA dual indexing library preparation kits as recommended by the manufacturer (FC-131–1096, Illumina, San Diego, CA). All 12 libraries were pooled and run across 2 lanes of an Illumina HiSeq 2500 generating 51 base single reads.

value: Remaining Stream

tag: developmental stage

value: Hamburger & Hamilton (HH) Stage 15


title: Stream_15_3


title: Stream_15_1


title: genomic DNA from breast tissue 34


title: genomic DNA from breast tissue 32


title: genomic DNA from breast tissue 53


title: HH11_Trailblazer_3

value: Invasive Front


title: Trailblazer_15_3


title: Trailblazer_15_2


title: genomic DNA from breast tissue 33


title: genomic DNA from breast tissue 36


title: Trailblazer_15_1


title: Stream_13_4

value: Hamburger & Hamilton (HH) Stage 13


title: genomic DNA from breast tissue 31


title: Stream_13_3


title: Stream_13_2


title: Trailblazer_13_4


title: genomic DNA from breast tissue 30


title: genomic DNA from breast tissue 28


title: Trailblazer_13_2


title: genomic DNA from breast tissue 26

value: Other


title: genomic DNA from breast tissue 27


title: HH11_Trailblazer_6

value: Hamburger & Hamilton (HH) Stage 11

value: In Vivo


title: genomic DNA from breast tissue 29


title: genomic DNA from breast tissue 24


title: iTreg_WT_1

first: Dan

middle: R

last: Littman

address: 430 East 29th Street, Alexandria West 4th Floor

department: Pathology

institute: New York University School of Medicine

data_processing:
RNA-seq reads were mapped to the Mus musculus genome Ensembl annotation release 87 with STAR (v2.5.2b).
Uniquely mapped reads were counted using featureCounts41 with parameters: -p -Q 20.
DESeq242 was used to identify differentially expressed genes across conditions with experimental design: ~Condition + Gender.
Read counts were normalized and transformed by functions varianceStabilizingTransformation and rlog in DESeq2 with the following parameter: blind=FALSE.
Gender differences were considered as batch effect, and were corrected by ComBat.
Genome_build: Ensembl annotation release 87
Supplementary_files_format_and_content: .txt files contain tab delimited matrix for all samples with either Raw counts or Read counts normalized and transformed by function varianceStabilizingTransformation; iTreg samples also contain DESeq2 comparison btween

source_name: LILP-derived CD3+CD4+Foxp3-YFP+ iTreg cells from Foxp3-Cre male donor mouse

extract_protocol:
A T cell reconstitution system was designed to purify c-Maf-sufficient or -deficient iTreg cells from compatible microenvironments. Briefly, Tnaive cells were isolated from the spleen of CD45.2 Foxp3creYFP or Maf∆Treg mice as CD4+CD3+CD44loCD62LhiFoxp3-YFP- and Treg cells were isolated from the spleens of CD45.1 WT B6 mice as CD4+CD3+CD25+ by FACS. Tnaive cells (2 ×105) and Treg cells (8 ×105) were simultaneously administered by retro-orbital injection into H. hepaticus-colonized Rag1_/_ mice. Two weeks after transfer, c-Maf-sufficient or -deficient iTreg cells were purified from the LI of reconstituted mice as CD4+CD3+CD45.1-CD45.2+Foxp3-YFP+ by FACS and collected into FBS. 20% of the sorted cells were stained for RORgt and Foxp3 and the remaining cells were saved in TRIzol (Invitrogen) for RNA extraction. To isolate H. hepaticus-specific colitogenic T effector (TEff) cells, HH7-2tg;Maf ∆Treg and HH7-2tg;Foxp3cre mice were colonized with H. hepaticus. HH7-2tg;Foxp3cre mice were further I.P. injected with 1mg anti-IL10RA antibody (clone 1B1.3A, Bioxcell) weekly from the day of colonization. HH7-2 TEff cells (CD3+CD4+TCRVβ6+Foxp3-YFP-) were sorted from the LILP two weeks after colonization. Homeostatic IL-23R-GFP+ T cells (CD3+CD4+IL-23R-GFP+) were sorted from both SILP and LILP of Il23rgfp/+ mice stably colonized with SFB.
Total RNA was extracted using TRIzol (Invitrogen) followed by DNase I treatment and cleanup with RNeasy MinElute kit (Qiagen). Treg RNA-seq libraries were prepared with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech cat # 634899 and 634888). TH17 RNA libraries were prepared using the Nugen Ovation Ultralow Library Systems V2 (cat # 7102 and 0344). All sequencing was performed using the Illumina NextSeq. RNAseq libraries were prepared and sequenced by the Genome Technology Core at New York University School of Medicine.

value: 2 months

tag: Sex

value: Male

value: Adult

tag: cell type

value: T cell

tag: cell subtype

value: CD3+CD4+Foxp3-YFP+ iTreg

value: Large intestine lamina propria


title: DP088

city: Atlanta

first: Elizabeth

middle: M

last: Kennedy

state: GA

address: 615 Michael Street, Suite 301

department: Human Genetics

institute: Emory University

data_processing: BeadStudio software v3.2

label: Cy3, Cy5

source_name: normal human bronchial epithelial cells

extract_protocol: Genomic DNA was isolated from cell pellets, previously held at -80°C, using the All Prep DNA/RNA kit (Qiagen #80204) according to the manufacturer’s instructions.

value: normal human bronchial epithelial cells

tag: radiation type

value: Si

tag: dose (gy)

tag: time (days)

tag: chip id

tag: row/col on chip


title: genomic DNA from breast tissue 23

value: former

value: Prophylactic

value: White

value: normal breast


title: iTreg_MafKO_1

source_name: LILP-derived CD3+CD4+Foxp3-YFP+ iTreg cells from Maf fl/fl Foxp3-Cre male donor mouse

tag: age

value: Maf fl/fl; Foxp3-Cre


title: genomic DNA from breast tissue 22

value: never

value: Invasive


title: genomic DNA from breast tissue 18

value: current

value: In Situ


title: genomic DNA from breast tissue 25


title: iTreg_WT_2

value: 2 months


title: DP043


title: IL23RGFP+_SI_2

source_name: SILP-derived CD3+CD4+IL23R-GFP+ T effector cells from  WT male mouse

value: Male

value: CD3+CD4+IL23R-GFP+ T effector cell

value: Small intestine lamina propria


title: genomic DNA from breast tissue 20

value: Benign


title: DP067


title: IL23RGFP+_SI_1

source_name: SILP-derived CD3+CD4+IL23R-GFP+ T effector cells from WT female mouse

value: Female

value: Adult

value: T cell


title: genomic DNA from breast tissue 14


title: Trailblazer_13_3

source_name: Cranial Neural Crest Cells

tag: location

value: Invasive Front

value: Hamburger & Hamilton (HH) Stage 13


title: genomic DNA from breast tissue 11

value: White

tag: tissue


title: genomic DNA from breast tissue 16

value: Black

value: normal breast


title: genomic DNA from breast tissue 13

value: former


title: iTreg_MafKO_2

value: CD3+CD4+Foxp3-YFP+ iTreg

tag: genotype

value: Maf fl/fl; Foxp3-Cre

value: Large intestine lamina propria


title: genomic DNA from breast tissue 12

value: never

value: Invasive


title: genomic DNA from breast tissue 9

value: current

value: In Situ


title: IL23RGFP+_LI_2

source_name: LILP-derived CD3+CD4+IL23R-GFP+ T effector cells from WT male mouse

tag: strain

value: 2 months

value: Male

value: CD3+CD4+IL23R-GFP+ T effector cell


title: DP066

value: normal human bronchial epithelial cells

value: Si


title: genomic DNA from breast tissue 15

tag: bmi


title: genomic DNA from breast tissue 19

tag: race


title: DP042


title: IL23RGFP+_LI_1

source_name: LILP-derived CD3+CD4+IL23R-GFP+ T effector cells from WT female mouse

value: Female

value: Adult

value: T cell


title: HH7-2_Teff_cMafKO_2

source_name: LILP-derived CD3+CD4+Vb6+Foxp3- T effector cells from HH7-2tg Maf fl/fl Foxp3-Cre male mouse

value: CD3+CD4+Vb6+Foxp3- T effector cell

value: HH7-2tg; Maf fl/fl; Foxp3-Cre


title: HH7-2_Teff_cMafKO_1

source_name: LILP-derived CD3+CD4+Vb6+Foxp3- T effector cells from HH7-2tg Maf fl/fl Foxp3-Cre female mouse


title: DP086


title: DP041


title: genomic DNA from breast tissue 17

value: White

value: normal breast


title: genomic DNA from breast tissue 6


title: HH7-2_Teff_WT_antiIL10_2

source_name: LILP-derived CD3+CD4+Vb6+Foxp3- T effector cells from HH7-2tg male mouse LILP treated with anti-IL10RA antibody

value: Large intestine lamina propria


title: DP082


title: genomic DNA from breast tissue 8

source_name: fresh frozen, histologically normal-appearing breast tissue

value: former


title: DP037


title: DP061


title: DP065


title: DP083


title: DP081


title: DP036


title: DP060


title: DP059


title: genomic DNA from breast tissue 5

value: never

value: Invasive


title: HH7-2_Teff_WT_antiIL10_1

source_name: LILP-derived CD3+CD4+Vb6+Foxp3- T effector cells from HH7-2tg female mouse treated with anti-IL10RA antibody


title: genomic DNA from breast tissue 10

value: current


title: DP055


title: DP078


title: genomic DNA from breast tissue 4

value: Prophylactic


title: DP054


title: DP031


title: DP077


title: genomic DNA from breast tissue 1

value: Benign


title: DP076


title: genomic DNA from breast tissue 3


title: DP053


title: DP030


title: DP035


title: DP029


title: genomic DNA from breast tissue 2

value: Black


title: DP073

value: normal human bronchial epithelial cells


title: DP087

value: Si


title: DP049


title: DP047


title: DP072


title: DP071


title: DP025


title: DP048


title: DP023


title: genomic DNA from breast tissue 7


title: DP171

value: xray


title: DP170


title: DP123


title: DP024


title: DP147


title: DP146


title: DP165


title: DP122


title: genomic DNA from breast tissue 21


title: DP141


title: DP117


title: DP140


title: DP164


title: DP159


title: DP135


title: DP158


title: DP111


title: DP105


title: DP129


title: DP153


title: DP104


title: DP128


title: DP152


title: DP169

value: Fe


title: DP134


title: DP121


title: DP145


title: Activin/FGF Hi 3

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description: Mouse embryonic stem cells cultured in Activin/FGF/N2B27, sorted for high Sox2 expression using FACS

data_processing: Quantile-normalization and low-quality probe filtering performed using the beadarray package in R, batch correction with ComBat

source_name: Activin/FGF Hi

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit for Illumina arrays

growth_protocol: ESCs were cultured in LIF/FCS/GMEM and adapted to other conditions for 4 passages (LIF/2i/N2B27, LIF/BMP/N2B27) or 9 passages (Activin/FGF/N2B27) before used for analysis.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's recommended protocol.

value: mouse embryonic stem cells

tag: condition

value: AFN

tag: sox2 expression in facs sorting

value: Hi

tag: array


title: Activin/FGF All 1

description: Mouse embryonic stem cells cultured in Activin/FGF/N2B27

source_name: Activin/FGF All

tag: cell type

value: All


title: LIF/BMP Hi 3

description: Mouse embryonic stem cells cultured in LIF/BMP/N2B27, sorted for high Sox2 expression using FACS

source_name: LIF/BMP Hi

value: LBN


title: Activin/FGF Lo 2

description: Mouse embryonic stem cells cultured in Activin/FGF/N2B27, sorted for low Sox2 expression using FACS

source_name: Activin/FGF Lo

value: Lo


title: DP168


title: LIF/FCS Hi 3

description: Mouse embryonic stem cells cultured in LIF/FCS/GMEM, sorted for high Sox2 expression using FACS

source_name: LIF/FCS Hi

value: LIF/FCS/GMEM

value: FCSL


title: DP144

source_name: normal human bronchial epithelial cells


title: Activin/FGF Lo 3


title: LIF/BMP Lo 3

description: Mouse embryonic stem cells cultured in LIF/BMP/N2B27, sorted for low Sox2 expression using FACS

source_name: LIF/BMP Lo


title: LIF/2i 3

description: Mouse embryonic stem cells cultured in LIF/2i/N2B27

value: PCLN


title: LIF/FCS Hi 2


title: LIF/FCS Hi 1


title: LIF/BMP Lo 1


title: Activin/FGF Hi 2


title: LIF/FCS Lo 3

description: Mouse embryonic stem cells cultured in LIF/FCS/GMEM, sorted for low Sox2 expression using FACS

source_name: LIF/FCS Lo


title: LIF/BMP Lo 2


title: LIF/2i 2


title: Activin/FGF All 2


title: LIF/2i 1


title: LIF/BMP Hi 2


title: LIF/FCS Lo 2


title: DP143


title: LIF/BMP Hi 1


title: LIF/FCS Lo 1


title: DP120


title: Activin/FGF Lo 1


title: DP142


title: Activin/FGF All 3


title: DP119


title: DP118


title: DP139


title: Activin/FGF Hi 1


title: DP163


title: DP162


title: DP115


title: DP161


title: DP138


title: DP114


title: DP160


title: DP112


title: DP113


title: LGSOC Patient3 metastasis tumor cells

city: Wuhan

first: Zongyuan

last: Yang

state: Hubei

address: Jiefang avenue 1095, Hankou,

department: Gyneconogical cancer

country: China

institute: cancer biology center

description: Gene expression data from metastatic tumor cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: PICR scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: LGSOC patient metastasis

label_protocol: Label protocol was carried out according to the Eukaryotic Target Preparation protocol in the Affymetrix technical manual (701021 Rev. 5) for Genechip Expression analysis (Affymetrix).

extract_protocol: Isolation of RNA was performed using the Trizol method (Invitrogen) and was purified using RNeasy spin columns (Qiagen) according to the manufacturers' protocols.

tag: tumor type

value: metastatic


title: DP136

tag: radiation type


title: LGSOC Patient3 primary tumor cells

description: Gene expression data from primary tumor cells.

source_name: LGSOC patient primary tumor

value: primary


title: LGSOC Patient3 ascites tumor cells

description: Gene expression data from ascitic tumor cells.

source_name: LGSOC patient ascites

value: ascitic


title: LGSOC Patient2 primary tumor cells


title: LGSOC Patient2 metastasis tumor cells


title: DP157

tag: dose (gy)


title: DP133

tag: time (days)


title: LGSOC Patient1 metastasis tumor cells


title: DP137

tag: chip id


title: DP156

tag: row/col on chip


title: LGSOC Patient1 primary tumor cells


title: LGSOC Patient1 ascites tumor cells


title: HGSOC Patient5 metastasis tumor cells

source_name: HGSOC patient metastasis


title: DP108


title: LGSOC Patient2 ascites tumor cells


title: DP132


title: DP155


title: HGSOC Patient3 metastasis tumor cells


title: HGSOC Patient5 primary tumor cells

source_name: HGSOC patient primary tumor


title: HGSOC Patient4 metastasis tumor cells


title: HGSOC Patient4 primary tumor cells


title: HGSOC Patient5 ascites tumor cells

source_name: HGSOC patient ascites


title: HGSOC Patient3 ascites tumor cells


title: DP131


title: DP107


title: DP109


title: HGSOC Patient2 metastasis tumor cells


title: HGSOC Patient4 ascites tumor cells


title: HGSOC Patient2 ascites tumor cells


title: DP154


title: DP106


title: DP151


title: DP103


title: HGSOC Patient1 metastasis tumor cells


title: DP150


title: HGSOC Patient2 primary tumor cells


title: CD14pos_monocyte_rep5 (r1)

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
SAMPLE 10
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep5

hyb_protocol: cRNA were hybridized to Human HT-12v3 or Human HT-12v4 BeadChip arrays (Illumina) using the standard Illumina hybridization protocol

scan_protocol: Imaging was performed on an Illumina iScan systemt using the standard Illumina scanning protocol

data_processing: Raw intensity values of datasets r1, r2 and r3 were pre-processed independently by the Gene Expression tool v1.9.0 in GenomeStudio V2011.1 (Illumina). Values for missing bead types were imputed, revealing 47,323 probesets for r1 and 48,803 probesets for r2 and r3. Datasets were exported by the Partek Report Plugin 2.16 (Partek) and imported into Partek® Genomics Suite® software, version 6.6 Copyright©; 2017 (PGS). From the publicly available dataset GSE35457, the raw intensity values of the specified samples of CD14+ and CD14+ CD16+ monocytes, as well as of CD1c+ and CD141+ DCs were used. The raw expression values for the CD14+ and CD14+ CD16+ monocyte samples were averaged always for the same donor, finally labeled as “CD14mix_Mono”. The resulting raw expression text file was also imported into PGS. Based on the Illumina Probe ID, 39,423 common probesets were identified on both HT12-V3 and HT12-V4 arrays. All datasets were filtered down to those probes to enable dataset assembly and comparability. Based on those probes, two different datasets were generated and normalized. Dataset n1 contains all samples from r1, r2 and the mentioned samples from GSE35457. Dataset n2 contains all samples from r3. The expression values of both datasets were independently quantile normalized and log2-transformed. In n1, the batch effect introduced by the combination of the three different datasets was removed using the CD14+ blood monocytes as bridging samples. Both datasets were finally filtered down to those probes being expressed across the samples of the corresponding dataset.  Probes with a maximum expression lower than 7 and 6.75 (all on log2 scale) were excluded as not expressed from datasets n1 and n2,  resulting in 21,250 and 18,857 present probes, respectively.

label_protocol: TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre) was utilized to generate biotin labeled anti-sense RNA (cRNA) according to the manufacturer’s protocol

growth_protocol: CD14+ monocytes were cultured in RPMI1640 medium supplemented with 10% FCS, 1% Penicillin-Streptomycin, 1% Sodiumpyruvate and 1% Glutamax (all from Gibco) for three days.

extract_protocol: Cells were harvested and lysed in TRIzol (Invitrogen) and RNA was isolated and concentration and purity was assessed using a NanoDrop 1000 UV-Vis Spectrophotometer (Thermo Scientific)

treatment_protocol: CD14+ monocytes were differentiated into Mo-MCSF or Mo-GMCSF in presence of 100 IU/ml rhMCSF or 800 IU/ml rhGMCSF respectively. Mo-MCSF[IL4] were generated by further culturing Mo-MCSF for 3d with 500 IU/ml rhGMCSF and 1000 IU/ml rhIL4. Mo-GMCSFIL4 were generated by the addition of 800 IU/ml rhGM-CSFGMCSF and 500 IU/ml rhIL4 and incubated for up to 6 days

value: CD14+ monocyte

tag: duration of total activation

value: 0 hours

tag: duration of activation with gmcsf + il4

value: blood


title: HGSOC Patient1 primary tumor cells


title: DP126

tag: tissue

value: normal human bronchial epithelial cells


title: CD14pos_monocyte_rep7 (r1)

description:
SAMPLE 12
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep7


title: DP130

value: Fe


title: DP149


title: HGSOC Patient1 ascites tumor cells


title: CD14pos_monocyte_rep6 (r1)

description:
SAMPLE 11
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep6


title: Mo_GMCSF_IL4_0to72h_rep3 (r3)

description:
SAMPLE 24
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 72 hours rep3

value: Mo-GMCSF[IL4 (0-72h)] cell

value: 72 hours

value: 0-72 hours


title: DP101


title: Mo_GMCSF_IL4_72to144h_rep1 (r3)

description:
SAMPLE 37
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro first with GM-CSF for 72 hours and then with the comibation of GM-CSF and IL-4 for further 72 hours rep1

value: Mo-GMCSF[IL4 (72-144h)] cell

value: 144 hours


title: Mo_GMCSF_IL4_72to144h_rep2 (r3)

description:
SAMPLE 38
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro first with GM-CSF for 72 hours and then with the comibation of GM-CSF and IL-4 for further 72 hours rep2


title: Mo_GMCSF_IL4_0to72h_rep2 (r3)

description:
SAMPLE 23
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 72 hours rep2


title: Mo_GMCSF_IL4_72to144h_rep3 (r3)

description:
SAMPLE 39
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro first with GM-CSF for 72 hours and then with the comibation of GM-CSF and IL-4 for further 72 hours rep3


title: Mo_GMCSF_IL4_0to72h_rep1 (r3)

description:
SAMPLE 22
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 72 hours rep1


title: Mo_GMCSF_IL4_0to144h_rep3 (r3)

description:
SAMPLE 21
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 144 hours rep3

value: Mo-GMCSF[IL4 (0-144h)] cell

value: 0-144 hours


title: CD14pos_monocyte_rep4 (r1)

description:
SAMPLE 9
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep4


title: CD14pos_monocyte_rep1 (r1)

description:
SAMPLE 6
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep1


title: CD45pos_lin_neg_HLADRhigh_cell_rep5 (r1)

description:
SAMPLE 5
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD45+ lin- HLA-DR[high] cell rep5

value: CD45+ lin- HLA-DR[high] cell

value: lung


title: Mo_GMCSF_IL4_0to144h_rep2 (r3)

description:
SAMPLE 20
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 144 hours rep2


title: CD14pos_monocyte_rep3 (r1)

description:
SAMPLE 8
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep3


title: DP100


title: Mo_GMCSF_rep3 (r3)

description:
SAMPLE 18
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF for 72 hours rep3

value: Mo-GMCSF


title: DP124


title: CD45pos_lin_neg_HLADRhigh_cell_rep4 (r1)

description:
SAMPLE 4
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD45+ lin- HLA-DR[high] cell rep4


title: CD14pos_monocyte_rep2 (r1)

description:
SAMPLE 7
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep2


title: DP148


title: CD45pos_lin_neg_HLADRhigh_cell_rep2 (r1)

description:
SAMPLE 2
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD45+ lin- HLA-DR[high] cell rep2


title: CD45pos_lin_neg_HLADRhigh_cell_rep1 (r1)

description:
SAMPLE 1
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD45+ lin- HLA-DR[high] cell rep1


title: CD45pos_lin_neg_HLADRhigh_cell_rep3 (r1)

description:
SAMPLE 3
non-normalized_dataset_r1.txt
normalized dataset n1
ex vivo FACS sorted CD45+ lin- HLA-DR[high] cell rep3


title: Mo_GMCSF_IL4_0to144h_rep1 (r3)

description:
SAMPLE 19
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 144 hours rep1


title: CD14pos_monocyte_rep10 (r3)

description:
SAMPLE 15
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte rep10


title: Mo_GMCSF_rep1 (r3)

description:
SAMPLE 16
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF for 72 hours rep1


title: CD14pos_monocyte_rep9 (r3)

description:
SAMPLE 14
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte rep9


title: Mo_GMCSF_rep2 (r3)

description:
SAMPLE 17
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF for 72 hours rep2


title: CD14pos_monocyte_rep8 (r3)

description:
SAMPLE 13
non-normalized_dataset_r3.txt
normalized dataset n2
ex vivo FACS sorted CD14+ monocyte rep8


title: 20_Ctrl_P10

first: Céline

last: Méhats

address: 24 rue du Faubourg St jacques

institute: Inserm

hyb_protocol: Following fragmentation, mirRNA targets were hybridized for 20 hr at 48C on mirRNA-40 Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were preprocessed and analyzing using Partek Genomic Suite.

source_name: whole lung

label_protocol: After validation of the RNA quality with Bioanalyzer 2100, 1 µg of total RNA was biotin labelled following the FlashTag Biotin HSR RNA labelling kit (Affymetrix).

extract_protocol: Total RNA was extracted using the Rneasy Qiagen kit (Qiagen, Courtaboeuf, France), according to the manufacturer's instructions.

tag: age

value: P10 of life

tag: sample origin

value: Ctrl diet during gestation


title: 19_Ctrl_P10


title: 18_Ctrl_J10


title: T_cell_rep3 (r2)

description:
SAMPLE 33
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted T cell rep3

value: T cell


title: Mo_MCSF_rep3 (r2)

description:
SAMPLE 36
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with M-CSF for 72 hours rep3

value: Mo-MCSF

value: 0 hours


title: Mo_MCSF_rep2 (r2)

description:
SAMPLE 35
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with M-CSF for 72 hours rep2

value: blood


title: T_cell_rep1 (r2)

description:
SAMPLE 31
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted T cell rep1


title: NK_cell_rep3 (r2)

description:
SAMPLE 30
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted NK cell rep3

value: NK cell


title: T_cell_rep2 (r2)

description:
SAMPLE 32
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted T cell rep2


title: 14_LPD_P10

value: Low protein diet during gestation


title: 13_LPD_P10


title: DP166

value: normal human bronchial epithelial cells

value: Fe


title: B_cell_rep3 (r2)

description:
SAMPLE 27
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted B cell rep3

value: B cell


title: 16_Ctrl_P10


title: 15_LPD_P10


title: 12_LPD_P10


title: 17_Ctrl_P10


title: 11_LPD_P10


title: 10_Ctrl_P21

value: P21 of life


title: Mo_MCSF_rep1 (r2)

description:
SAMPLE 34
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with M-CSF for 72 hours rep1

value: 72 hours


title: B_cell_rep2 (r2)

description:
SAMPLE 26
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted B cell rep2


title: B_cell_rep1 (r2)

description:
SAMPLE 25
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted B cell rep1


title: 8_Ctrl_P21


title: NK_cell_rep2 (r2)

description:
SAMPLE 29
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted NK cell rep2


title: 9_Ctrl_J21


title: Mo_GMCSF_IL4_0to72h_rep3 (r2)

description:
SAMPLE 24
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 72 hours rep3

value: Mo-GMCSF[IL4 (0-72h)] cell

value: 0-72 hours


title: NK_cell_rep1 (r2)

description:
SAMPLE 28
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted NK cell rep1


title: 6_Ctrl_P21


title: 5_LPD_P21


title: Mo_GMCSF_IL4_0to72h_rep2 (r2)

description:
SAMPLE 23
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 72 hours rep2


title: 7_Ctrl_P21


title: Mo_GMCSF_IL4_0to144h_rep3 (r2)

description:
SAMPLE 21
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 144 hours rep3

value: Mo-GMCSF[IL4 (0-144h)] cell

value: 144 hours

value: 0-144 hours


title: 4_LPD_P21


title: 3_LPD_P21


title: Mo_GMCSF_IL4_0to144h_rep2 (r2)

description:
SAMPLE 20
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 144 hours rep2


title: Mo_GMCSF_IL4_0to72h_rep1 (r2)

description:
SAMPLE 22
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 72 hours rep1


title: 1_LPD_P21


title: Mo_GMCSF_IL4_0to144h_rep1 (r2)

description:
SAMPLE 19
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF and IL-4 for 144 hours rep1


title: 2_LPD_P21


title: Mo_GMCSF_rep2 (r2)

description:
SAMPLE 17
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF for 72 hours rep2

value: Mo-GMCSF


title: Mo_GMCSF_rep3 (r2)

description:
SAMPLE 18
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF for 72 hours rep3


title: Mo_GMCSF_rep1 (r2)

description:
SAMPLE 16
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte, activated in vitro with GM-CSF for 72 hours rep1


title: CD14pos_monocyte_rep8 (r2)

description:
SAMPLE 13
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep8

value: CD14+ monocyte


title: CD14pos_monocyte_rep10 (r2)

description:
SAMPLE 15
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep10


title: CD14pos_monocyte_rep9 (r2)

description:
SAMPLE 14
non-normalized_dataset_r2.txt
normalized dataset n1
ex vivo FACS sorted CD14+ monocyte rep9


title: PBMC_NonResponder_Patient3_-3d

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description: Gene expression data from PBMCs of a non-responder patient three days before Sorafenib treatment.

hyb_protocol: Total RNA was hybridized to Affymetrix Clariom S arrays as described by the manufacturers (Affymetrix/Thermo Fisher Scientific, 168 Third Avenue, Waltham, MA USA 02451.)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor

label: Biotin

source_name: peripheral blood

label_protocol: RNA integrity was analyzed by capillary electrophoresis using a Fragment Analyser (Advanced Analytical Technologies, Inc. Ames, IA) and were further processed with the Affymetrix GeneChip Pico kit

extract_protocol: 2ug of total RNA from about 10^7 cells  per sample were incubated with DNaseI according the Qiagen manufacture and cleaned up with RNeasy Micro Kit (Qiagen, Hilden, Germany).

treatment_protocol: RNA from peripheral blood mononuclear cell of 8 patients at 2 different time points (3 days before and 6 days after Sorafenib treatment) were extractied from 8 ml of blood.

value: peripheral blood mononuclear cell

tag: treatment response

value: non-responder

tag: timepoint

value: -3 days

tag: treatment


title: PBMC_NonResponder_Patient4_-3d


title: PBMC_Responder_Patient3_6d

description: Gene expression data from PBMCs of a responder patient six days after Sorafenib treatment.

value: responder

value: 6 days

value: Sorafenib


title: PBMC_NonResponder_Patient2_-3d


title: PBMC_Responder_Patient4_-3d

description: Gene expression data from PBMCs of a responder patient three days before Sorafenib treatment.


title: PBMC_Responder_Patient3_-3d


title: PBMC_NonResponder_Patient4_6d

description: Gene expression data from PBMCs of a non-responder patient six days after Sorafenib treatment.


title: PBMC_NonResponder_Patient2_6d


title: PBMC_NonResponder_Patient1_-3d


title: PBMC_NonResponder_Patient3_6d


title: PBMC_Responder_Patient2_6d


title: PBMC_Responder_Patient1_-3d