title: CF 7D post-MI, biological rep3

city: Cincinnati

first: Vikram

last: Prasad

state: OH

address: 240, Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
CF_7D MI-3
Gene expression data from cardiac fibroblasts isolated from infarct area 7 days post-MI.

hyb_protocol: 3.0 ug of fragmented cDNA were hybridized to Clariom S Arrays, Mouse (Applied Biosystems). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0007. The Stain and Antibody solutions are produced by Applied Biosystems and contained in the Genechip Hybridization Wash and Stain Kit.

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

data_processing: The .cel were created by Command Console (Affymetrix). The .cel files were analyzed by Expression Console (Affymetrix) to create .sst-rma-gene-full.chp files.

label_protocol: The GeneChip 3’ IVT Pico Reagent Kit is used to create biotin – labeled double -strand cDNA targets for hybridization to the Clariom S Arrays, Mouse.

growth_protocol: cell isolation protocol: Heart tissue from tamoxifen-treated TCF21-MerCreMer;R26GFP mice were digested by collagenase D and Dispase II. GFP positive TCF21 cardiac fibroblasts were sorted out by FACS.

extract_protocol: Trizol-based extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain background

tag: genotype/variation

value: sorted TCF21 lineage-traced cardiac fibroblasts


title: CF 4W post-MI, biological rep3

status: Public on Feb 24 2018

type: RNA

country: USA

description:
CF_4W MI-3
Gene expression data from cardiac fibroblasts isolated from infarct area 4 weeks post-MI.

label: biotin

molecule: total RNA

organism: Mus musculus

tag: cell type


title: CF 3D post-MI, biological rep3

description:
CF_3D MI-3
Gene expression data from cardiac fibroblasts isolated from infarct area 3 days post-MI.


title: Mouse lung_homogenates_rep1

city: Hamamatsu

first: Yasunori

last: Enomoto

state: Shizuoka

address: 1-20-1 Handayama

department: Department of Regenerative and Infectious Pathology

country: Japan

institute: Hamamatsu University School of Medicine

description:
Lung homogenates-1
Gene expression of lung homogenates in untreated lung

hyb_protocol: 2.0ug of Cy3-labelled cRNA was fragmented at 60 degrees for 30 min in a reaction volume of 25ul containing 1x Agilent fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SuperPrint G3 Human GE 8x60K Microarray ver2.0 (Agilent) for 17 h at 65 degrees in a rotating Agilent hybridization oven. After hybridization, microaarays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37 degrees GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Mouse lung_homogenates_replicate1

label_protocol: Cy3 labeled cRNA was prepared from 5.8ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacture's protocol, followed by Rneasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA extraction protocol not provided.

tag: tissue

value: Lung

value: lung homogenate

tag: treatment

value: untreated

tag: gender

value: Male


title: CF 4W post-MI, biological rep2

description:
CF_4W MI-2
Gene expression data from cardiac fibroblasts isolated from infarct area 4 weeks post-MI.


title: Mouse lung_homogenates_rep2

description:
Lung homogenates-2
Gene expression of lung homogenates in untreated lung

source_name: Mouse lung_homogenates_replicate2


title: CD_4

type: SRA

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

country: China

institute: Fudan University

library_source: transcriptomic

data_processing:
Quality control: 1) remove reads with adaptors; 2)remove reads in which unkown bases are more than 10%; 3)remove low qulity reads(the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5)
Hisat2 was used to align clean reads to the mouse genome
Htseq was used to estimate raw counts for each gene
FPKM was calculated using Stringtie
Edgr was use to detect differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: HT-seq counts and FPKM are provided in Excel files. Column headers are found in the 'description' field.

source_name: brain

extract_protocol:
Total RNA was extracted from brain homogenate using the TriPure Isolation Reagent (Roche) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.  We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: Mice were treated by either PLX5622, control diet (CD), PLX5622 + CD (RP = PLX5622 treated for 14 days, followed by CD (control diet) treatment for several days), LPS or vehicle

tag: strain

value: brain

tag: age

value: adult

value: CD

tag: time


title: Mouse lung_CD140a+Lin-cells_rep2

description:
Steady-state fibroblasts-2
Gene expression of steady-state fibroblasts in untreated lung

source_name: Mouse lung_CD140a+Lin-cells_replicate2

value: steady-state fibroblasts


title: CF 7D post-MI, biological rep2

description:
CF_7D MI-2
Gene expression data from cardiac fibroblasts isolated from infarct area 7 days post-MI.


title: CF 4W post-MI, biological rep1

description:
CF_4W MI-1
Gene expression data from cardiac fibroblasts isolated from infarct area 4 weeks post-MI.


title: Nrd1-AA BrdU-seq -Rap rep1

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

library_source: genomic

data_processing:
Library strategy: BrdU-Seq
fastq files were processed through the mapping function of HTS EPFL station.PCR duplicates were discarded from the analysis.
bigwig were generated using HTS EPFL station. Strands were merged by 125bp for BrdU-seq.
Genome_build: saccer3
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Nrd1-AA BrdU-seq -Rap

growth_protocol: Cells grown at 30°C to an OD600= 0.4 were synchronized in G1-phase with α-factor (20 ng/ml, Sigma) for 3h in total. After two washes with distilled water, cells were released into S-phase at 18°C. Depending on the experiment, cells were released or not in YEPD medium containing BrdU (100 μg/ml, Sigma) and treated or not with rapamycin. Cells were then collected at t=70min 18°C after G1-release and treated with 0.1% Sodium Azide (Sigma).

extract_protocol:
BrdU immunoprecipitation was mainly performed as described in (Soudet et al., 2014) with the following modifications. Genomic DNA was sonicated into 300-400 bp fragments and denatured. 5 μg  BrdU antibody (BD PharMingen, 555627) coupled to 75μl of Dynabeads Protein G (Invitrogen) were added to 5μg of denatured BrdU-containing genomic DNA in BrdU IP buffer (PBS + 0.0625% Triton X-100). After 1 hour incubation at room temperature on a wheel, beads were washed twice with BrdU IP buffer and eluted in Tris-HCl 10mM (pH 8.0), EDTA 1mM, 1% SDS. Eluates were cleared of SDS using the NucleoSpin Gel and PCR Clean-up (Macherey-Nagel).
iDeal library preparation kit was used for library construction.

value: -Rap

tag: chip antibody

value: BrdU antibody (BD PharMingen, 555627)


title: CF 2W post-MI, biological rep1

description:
CF_2W MI-1
Gene expression data from cardiac fibroblasts isolated from infarct area 2 weeks post-MI.


title: CD

description: SRA accessions include 3 reads per sample: barcode, Forward and Reverse.

data_processing:
Fastq files were generated using CellRanger v2.1.0 using the Illumina BCL files as input
Read alignment and count summarization were performed using CellRanger v2.1.0  CellRanger count
Counts from different samples were aggregated using CellRanger aggr in CellRanger software
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells. Aggregated processed data files are available on the series record.

source_name: brain microglia

extract_protocol: C57BL/6J mouse was perfused by 20 mL L15 culture medium. Brain was quickly minced on ice. Then the tissue was dissociated with papain (Sigma) for 20 min at 37℃, followed by the termination of ovomucoid containing L15 culture medium (2 mg/mL). Next, myelin was removed from the single cell suspension by Percoll density gradient centrifugation (25% v/v, SolarBio). Then the cells were reacted with 1:250 PE rat anti-mouse CD11b (BD Pharmingen, 553311) and 1:250 APC anti-mouse CD45 (BD Pharmingen, 561018) on ice for 1 h. After FACS buffer rinse for 3 times, the cells were reacted with 7-AAD (1:80, BD Pharmingen, 559925) on ice for 10 min to exclude the dead cells. Microglia were sorted as CD11b+/CD45+ cells30 by BD FACS Aria III (BD Biosciences). Then the harvested cells were sent to prepare library through 10X genomics, followed by the pair-end 100 sequencing via Illumina HiSeq 4000. 609 cells from 4 CD-treated mice were sequenced at 0.544 M mean reads of sequencing depth per cell, while 585 cells from 6 mice of repopulation day 5 were sequenced at 0.564 M raw reads of sequencing depth per cell.

treatment_protocol: CD mice were treated by control diet (CD) for 19 days. Repopulation mice were treated with PLX5622 for 14 days, followed by CD treated for 5 days

value: CD11b+/CD45+ microglia

value: CD treated for 19 days


title: CF 2W post-MI, biological rep2

description:
CF_2W MI-2
Gene expression data from cardiac fibroblasts isolated from infarct area 2 weeks post-MI.


title: Mouse lung_CD140a+Lin-cells_rep1

description:
Steady-state fibroblasts-1
Gene expression of steady-state fibroblasts in untreated lung

source_name: Mouse lung_CD140a+Lin-cells_replicate1


title: Nrd1-AA dSet2 BrdU-seq +Rap rep1

description: BrdUseq_Nrd1dSet2_PlusRap_merged_final.bigWig

source_name: Nrd1-AA dSet2 BrdU-seq +Rap

value: Nrd1-AA dSet2

value: +Rap


title: CF uninjured, biological rep1

description:
CF_uninjured-1
Gene expression data from quiescent cardiac fibroblasts isolated from uninjured heart.

source_name: cardiac fibroblasts isolated from left ventricle of uninjured heart


title: Nrd1-AA BrdU-seq +Rap rep2

source_name: Nrd1-AA BrdU-seq +Rap


title: CF 7D post-MI, biological rep1

description:
CF_7D MI-1
Gene expression data from cardiac fibroblasts isolated from infarct area 7 days post-MI.


title: CF 3D post-MI, biological rep2

description:
CF_3D MI-2
Gene expression data from cardiac fibroblasts isolated from infarct area 3 days post-MI.


title: Nrd1-AA BrdU-seq -Rap rep2


title: Mouse lung_CD49e+Sca1-Lin-cells_rep1

description:
Myofibroblasts-1
Gene expression of myofibroblasts in bleomycin-treated lung

value: myofibroblasts

value: bleomycin


title: Mouse lung_CD49e+Sca1-Lin-cells_rep2

description:
Myofibroblasts-2
Gene expression of myofibroblasts in bleomycin-treated lung


title: CF uninjured, biological rep3

description:
CF_uninjured-3
Gene expression data from quiescent cardiac fibroblasts isolated from uninjured heart.

value: sorted TCF21 lineage-traced cardiac fibroblasts


title: CF 3D post-MI, biological rep1

description:
CF_3D MI-1
Gene expression data from cardiac fibroblasts isolated from infarct area 3 days post-MI.


title: DFosB A

status: Public on Feb 23 2018

city: Boston

first: Anna

last: Idelevich

address: 188 Longwood

institute: HSDM

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were maintained at Harvard animal facilities in compliance with theStudies were approved by Institutional the Harvard University Institutional Animal Care and Use Committee (IACUC)

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

treatment_protocol: No treatment


title: Control B

source_name: wild-type

value: wild-type


title: CF uninjured, biological rep2

description:
CF_uninjured-2
Gene expression data from quiescent cardiac fibroblasts isolated from uninjured heart.


title: CaM1_3: Tumor tissue vs adjacent tissue from obese women

city: Mexico City

first: Esau

middle: Floriano

last: Sanchez

address: Cerrada de Palomas SN

department: Military School of Graduate of Health

country: Mexico

institute: SEDENA

description: Pool 2 of 2.

hyb_protocol: A hybridization mixture is prepared with each aliquot of marked cRNA, for each of the 8 microarray micromatrixes of the micro-arrangement.The protocol for gene expression analysis used is based on two-color microarray (Low Input Quick Amp Labeling, Agilent Technologies) for RNA preparation and hybridization. Agilent SurePrint G3 Human GE v2 8x60K microarrays were used with model ID 039494 and probe version 039381, synthesized with on-site oligonucleotide technology, Homo sapiens organism, manufacturer Agilent Technologies, construction format 8 x 60 K, IS-62976-8-V2_60kby8_GX_E control grid: hg19: GRCh37: Feb2009.

scan_protocol: Microarray scanning was performed with the Roche Nimblescan MS200 high-resolution scanner, using feature extraction software to analyze the image by identifying probes and analyzing fluorescence to define and measure gene expression characteristics afterwards.

data_processing: Genespring GX 14.8 (Agilent Technologies) software was used to identify the common expression profile of invasive breast carcinoma of Mexican women with excess fatty tissue  and identify signaling pathways related to adipokines. The Ontological Analysis was performed using the National Institute of Allergy and Infectious Diseases (NIAID) database DAVID v6.8, NIH.

organism: Homo sapiens

source_name: A pool of 2 samples from obese patients

label_protocol: Non-tumour tissue cRNA (peripheral) was marked with cyanine 3 and tumoral tissue cRNA (CaM) was marked with cyanine 5 according to the protocol.

extract_protocol: Secondary to each patient's surgical procedure, 3 cubic millimeters of tumor tissue (CaM) and 3 cubic millimeters of non-tumor (peripheral) tissue were collected. In total, 36 samples of breast glandular tissue were collected, of which 18 were from tumour tissue (CaM) and the other 18 were from non-tumour (peripheral) tissue.  Biological samples were collected within the first 45 minutes after the surgical procedure, placed in sterile cryotubes with RNA latter and immediately frozen at -70 °C until use. RNA extraction of 100 mg of tissue was performed from the biological samples collected with the TRIzol reagent (Invitrogen ®). TissueRuptor® was used to disrupt tissue. According to the protocol of the supplier quality and integrity of RNA was quantified and determined. The RNA concentration and 260/280 ratio was determined by triplicate in high-speed UV/VIS microfluidic spectrophotometry with QIAxpert® (QIAGEN) using 1 μL for each measurement. Verification of the integrity of total RNA was performed by capillary electrophoresis using QIAxcel® equipment (QIAGEN). The aliquots of total RNA of tumor and non-tumor tissue were paired and organized into 8 groups in order to make the comparison between tissues from the same patient during the hybridization process. 5 μL of an RNA aliquot at a 70 ng/μL concentration were taken to make the total RNA pool for each group. The RNA needed for amplification and marking was taken from each pool.

value: breast glandular tissue:tumor

tag: phenotype

value: obese

value: female

source_name: A pool of 2 samples from obese  patients

value: breast glandular tissue:non-tumor (peripheral)


title: CaM2_1: Tumor tissue vs adjacent tissue from overweight women

description: Pool 4 of 4.

source_name: A pool of 2 samples from overweight  patients

value: overweight


title: Model group 3

city: Tianjin

first: Weiying

last: Liu

address: Qi-Xiang-Tai Road 42

institute: Tianjin Medical University

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mice Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene Chip 2 Scanner 300 7G.

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: APP/PS1 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: The mice were euthanized and their brains were taken out rapidly on the ice table and stored in -80℃.

treatment_protocol: For RNA isolation, all the brain tissues were placed on ice in the Trizol solution (Sigma).

value: APP/PS1 transgenic

value: brain


title: CaM2_3: Tumor tissue vs adjacent tissue from obese women

description: Pool 1 of 2.

source_name: A pool of 3 samples from obese  patients

source_name: A pool of 3 samples from obese patients


title: CaM1_2: Tumor tissue vs adjacent tissue from overweight women

description: Pool 2 of 4.


title: Control A


title: CaM1_1: Tumor tissue vs adjacent tissue from overweight women

description: Pool 3 of 4.

source_name: A pool of 3 samples from overweight  patients


title: CaM2_2: Tumor tissue vs adjacent tissue from overweight women

description: Pool 1 of 4.


title: DFosB B


title: Model group 1


title: Control group 3

source_name: C57/6J mice

value: control; wild type


title: HPYD group 3

source_name: APP/PS1 mice treatment with HPYD

tag: treated with

value: polypeptides HPYD


title: Control group 2


title: Control group 1


title: HPYD group 1


title: Model group 2


title: HPYD group 2


title: Stable_5016_v4_Muco

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

description:
STA-1year
US82400123_252800420130_S01_GE2_107_Sep09_2_2

hyb_protocol: cRNA samples were hybridized to a Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarrays according manufacturer’s instructions.

scan_protocol: Scanned with an Agilent Technologies Microarray Scanner using default parameters. Each sample represents one channel of a dual-channel array.

data_processing: Data extraction of median feature intensity was performed with Feature Extraction software v10.7 (Agilent Technologies). In order to remove signal intensity bias between each array, median feature intensities were normalized with the lowess (locally weighted scatterplot smoothing) method, then spots for which half of the samples exhibited a signal less than the mean of all median signals were removed. Correction between 2 microarray hybridization batches was performed on the 28,867 remaining spots with Combat algorithm available through the R package sva.

source_name: whole blood

label_protocol: The cRNA labeling and hybridizations were performed according to Protocol from Agilent Technologies Inc (Agilent Technologies Inc, Palo Alto, CA, USA), using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the two-colour manufacturer’s protocol. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the PAXgene blood RNA system kit with an on-column DNase digestion protocol according to the manufacturer’s instructions. Quantity and quality of total RNA were determined using a 2100 Bioanalyzer (Agilent Technologies Incorporation). Microarrays were performed on RNA with a RNA integrity number (RIN) above 6.5.

treatment_protocol: Peripheral blood samples were collected in PAXgene tubes (PreAnalytix, Qiagen), and stored at −80°C. No infection or acute rejection were reported within one month before or after blood collection.

tag: clinical group

value: STA

tag: hybridization batch number


title: Stable_4011_v4_BPCO

description:
STA-1year
US82400123_252800421617_S01_GE2_107_Sep09_2_3


title: Stable_MISA6031_v4_Muco

description:
STA-1year
US82400123_252800421001_S01_GE2_107_Sep09_2_4


title: Stable_7018_v4_BPCO

description:
STA-1year
US82400123_252800421585_S01_GE2_107_Sep09_2_1


title: Stable_6003_v4_Muco

description:
STA-1year
US82400123_252800421617_S01_GE2_107_Sep09_1_2


title: Stable_7024_v4_Bronch

description:
STA-1year
US82400123_252800421618_S01_GE2_107_Sep09_2_3


title: Stable_1038_v4_Muco

description:
STA-1year
US82400123_252800421595_S01_GE2_107_Sep09_1_2


title: Stable_7011_v4_Muco

description:
STA-1year
US82400123_252800421618_S01_GE2_107_Sep09_1_3


title: Stable_3047_v4_BPCO

description:
STA-1year
US82400123_252800421001_S01_GE2_107_Sep09_1_2


title: Stable_3055_v4_Muco


title: Stable_9

description:
STA-1year
US82400123_252800418519_S01_GE2_107_Sep09_1_3


title: Stable_2012_v4_BPCO

description:
STA-1year
US82400123_252800421596_S01_GE2_107_Sep09_1_4


title: Stable_2008_v4_Muco

description:
STA-1year
US82400123_252800421618_S01_GE2_107_Sep09_2_2


title: Stable_86

description:
STA-1year
US82400123_252800421003_S01_GE2_107_Sep09_1_4


title: Stable_2003_v4_Muco

description:
STA-1year
US82400123_252800421001_S01_GE2_107_Sep09_2_3


title: 850K_GBM64

type: genomic

first: Dan

last: Zhou

address: 131 Dong 'an Road, Xuhui District

description:
genomic DNA from PDX tumor
tumor tissue from Patient Derived Xenograph

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Tumor tissue from Patient-Derived Xenograft (PDX) were mechanically dissociated and selected in stem cell culture medium (ThermoFisher, StemPro NSC SFM A1050901) containing L-glutamin and Penicillin-Streptomycin in laminin (#L2020) -coated flasks to reduce culture condition-introduced heterogeneity. Neural stem cells were expanded on Matrigel (CORNING 356230) or fibronectin-coated 6-well plate in stem cell growth medium (GM) containing DEME/F12 plus Glutamax (Life Technologies 10565-018), BIT9500 Serum Substitute (1x, Stem Cell Technologies 09500), Heparin (20ug/mL Sigma H3149), Primocin (1x, InvivoGen ant-pm-1), human bFGF (20ng/Ml, Stemgent 03-0002), human EGF (20ng/mL, R&D Biosystems 236-EG).

extract_protocol: Genomic DNA was isolated and purified from homogenized liver tissue using a serial phenol: chloroform extraction. Trizol reagent was used for extracting total RNA following the manufacturer’s protocol.

value: genomic DNA


title: Stable_69

description:
STA-1year
US82400123_252800420238_S01_GE2_107_Sep09_2_2


title: Stable_92_h2

description:
STA-1year
US82400123_252800421002_S01_GE2_107_Sep09_2_3


title: 850K_GBM184

source_name: tumor tissue from Patient Derived Xenograph


title: Stable_90

description:
STA-1year
US82400123_252800418519_S01_GE2_107_Sep09_2_2


title: Stable_51

description:
STA-1year
US82400123_252800420240_S01_GE2_107_Sep09_2_1


title: Stable_75

description:
STA-1year
US82400123_252800418519_S01_GE2_107_Sep09_2_3


title: Stable_82

description:
STA-1year
US82400123_252800420239_S01_GE2_107_Sep09_1_3


title: Stable_49

description:
STA-1year
US82400123_252800418518_S01_GE2_107_Sep09_2_1


title: 850K_GBM102

value: tumor tissue from Patient Derived Xenograph


title: Stable_78

description:
STA-1year
US82400123_252800418519_S01_GE2_107_Sep09_1_2


title: Stable_67

description:
STA-1year
US82400123_252800418519_S01_GE2_107_Sep09_2_1


title: Stable_88

description:
STA-1year
US82400123_252800418518_S01_GE2_107_Sep09_2_3


title: Stable_65mean

description:
STA-1year
US82400123_252800420238_S01_GE2_107_Sep09_2_4


title: 850K_GBM6


title: Stable_80

description:
STA-1year
US82400123_252800420238_S01_GE2_107_Sep09_1_1


title: Stable_31

description:
STA-1year
US82400123_252800418518_S01_GE2_107_Sep09_1_1


title: 850K_GBM10


title: 850K_GBM187


title: Stable_29

description:
STA-1year
US82400123_252800421003_S01_GE2_107_Sep09_1_2


title: Stable_4

description:
STA-1year
US82400123_252800420240_S01_GE2_107_Sep09_2_2


title: Stable_44

description:
STA-1year
US82400123_252800418519_S01_GE2_107_Sep09_1_4


title: Stable_27

description:
STA-1year
US82400123_252800412630_S01_GE2_107_Sep09_1_3


title: Stable_39

description:
STA-1year
US82400123_252800418518_S01_GE2_107_Sep09_2_2


title: Stable_20

description:
STA-1year
US82400123_252800420238_S01_GE2_107_Sep09_1_2


title: Stable_128

description:
STA-1year
US82400123_252800420240_S01_GE2_107_Sep09_2_3


title: Stable_109

description:
STA-1year
US82400123_252800420238_S01_GE2_107_Sep09_1_4


title: 850K_GBM143

description:
genomic DNA from PDX tumor
tumor tissue from Patient Derived Xenograph


title: Stable_2

description:
STA-1year
US82400123_252800420238_S01_GE2_107_Sep09_2_1


title: Stable_16

description:
STA-1year
US82400123_252800418518_S01_GE2_107_Sep09_2_4


title: Stable_11

description:
STA-1year
US82400123_252800420239_S01_GE2_107_Sep09_2_2


title: Stable_18

description:
STA-1year
US82400123_252800420239_S01_GE2_107_Sep09_2_3


title: BOS_71

description:
BOS-timeReplicate
US82400123_252800420239_S01_GE2_107_Sep09_2_1

value: BOS


title: BOS_103

description:
BOS-timeReplicate
US82400123_252800418517_S01_GE2_107_Sep09_1_2


title: Stable_42

description:
STA-1year
US82400123_252800412630_S01_GE2_107_Sep09_2_4


title: BOS_9022_v4_FI

description:
BOS-PRED
US82400123_252800421617_S01_GE2_107_Sep09_1_4


title: 850K_GBM80


title: 850K_GBM14


title: BOS_55

description:
BOS-timeReplicate
US82400123_252800418518_S01_GE2_107_Sep09_1_4


title: 850K_GBM84


title: BOS_4017_v3_Muco

description:
BOS-PRED
US82400123_252800421618_S01_GE2_107_Sep09_1_4


title: 850K_GBM12


title: BOS_7035_v3_BPCO

description:
BOS-PRED
US82400123_252800421616_S01_GE2_107_Sep09_2_3


title: BOS_3060_v3_Bronch

description:
BOS-PRED
US82400123_252800421596_S01_GE2_107_Sep09_2_3


title: Stable_100

description:
STA-1year
US82400123_252800412630_S01_GE2_107_Sep09_1_2


title: Stable_111

description:
STA-1year
US82400123_252800420240_S01_GE2_107_Sep09_1_3


title: 850K_GBM39


title: Stable_116

description:
STA-1year
US82400123_252800418519_S01_GE2_107_Sep09_2_4


title: Stable_107

description:
STA-1year
US82400123_252800420240_S01_GE2_107_Sep09_1_4


title: BOS_9022_v3_FI

description:
BOS-timeReplicate
US82400123_252800421595_S01_GE2_107_Sep09_2_1


title: BOS_58

description:
BOS-PRED
US82400123_252800420240_S01_GE2_107_Sep09_2_3


title: BOS_113

description:
BOS-timeReplicate
US82400123_252800418517_S01_GE2_107_Sep09_1_1


title: BOS_12

description:
BOS-PRED
US82400123_252800418519_S01_GE2_107_Sep09_2_4


title: BOS_8043_v3_SIP


title: BOS_37

description:
BOS-timeReplicate
US82400123_252800421003_S01_GE2_107_Sep09_1_4


title: BOS_118

description:
BOS-timeReplicate
US82400123_252800418517_S01_GE2_107_Sep09_2_4


title: BOS_7028_v3_Other

description:
BOS-timeReplicate
US82400123_252800421001_S01_GE2_107_Sep09_1_3


title: BOS_4017_v4_Muco

description:
BOS-timeReplicate
US82400123_252800421618_S01_GE2_107_Sep09_2_3


title: BOS_102

description:
BOS-PRED
US82400123_252800418519_S01_GE2_107_Sep09_2_3


title: Stable_126

description:
STA-1year
US82400123_252800420239_S01_GE2_107_Sep09_1_1


title: BOS_24

description:
BOS-PRED
US82400123_252800418519_S01_GE2_107_Sep09_1_1


title: BOS_PEFR5008_v3_BPCO

description:
BOS-PRED
US82400123_252800421596_S01_GE2_107_Sep09_1_2


title: BOS_36

description:
BOS-PRED
US82400123_252800412630_S01_GE2_107_Sep09_1_3


title: BOS_MEST5011_v4_Muco

description:
BOS-PRED
US82400123_252800420130_S01_GE2_107_Sep09_2_3


title: BOS_97

description:
BOS-PRED
US82400123_252800420238_S01_GE2_107_Sep09_1_4


title: BOS_117

description:
BOS-PRED
US82400123_252800412630_S01_GE2_107_Sep09_1_2


title: BOS_70

description:
BOS-PRED
US82400123_252800420240_S01_GE2_107_Sep09_1_2


title: BOS_8043_v4_SIP

description:
BOS-timeReplicate
US82400123_252800421595_S01_GE2_107_Sep09_1_4


title: BOS_3080_v3_BPCO

description:
BOS-PRED
US82400123_252800421617_S01_GE2_107_Sep09_2_1


title: BOS_83

description:
BOS-PRED
US82400123_252800418517_S01_GE2_107_Sep09_2_4


title: BOS_73

description:
BOS-PRED
US82400123_252800418518_S01_GE2_107_Sep09_2_3


title: BOS_54

description:
BOS-PRED
US82400123_252800412630_S01_GE2_107_Sep09_2_3


title: BOS_8043_v7_SIP

description:
BOS-PRED
US82400123_252800421617_S01_GE2_107_Sep09_1_3


title: BOS_DUMI8016_v4_BPCO

description:
BOS-PRED
US82400123_252800421619_S01_GE2_107_Sep09_1_2


title: BOS_5017_v3_Sarco

description:
BOS-PRED
US82400123_252800421595_S01_GE2_107_Sep09_2_4


title: BOS_108

description:
BOS-PRED
US82400123_252800418519_S01_GE2_107_Sep09_1_3


title: BOS_7035_v4_BPCO

description:
BOS-PRED
US82400123_252800421619_S01_GE2_107_Sep09_2_3


title: BOS_7028_v4_Other

description:
BOS-PRED
US82400123_252800421617_S01_GE2_107_Sep09_1_1


title: BOS_112mean

description:
BOS-PRED
US82400123_252800418518_S01_GE2_107_Sep09_2_2


title: BOS_52

description:
BOS-PRED
US82400123_252800418517_S01_GE2_107_Sep09_2_1


title: BOS_59

description:
BOS-PRED
US82400123_252800421003_S01_GE2_107_Sep09_2_1


title: BOS_40

description:
BOS-PRED
US82400123_252800418518_S01_GE2_107_Sep09_2_4


title: BOS_1004_v3_Muco

description:
BOS-PRED
US82400123_252800421618_S01_GE2_107_Sep09_1_2


title: BOS_3080_v4_BPCO


title: BOS_84

description:
BOS-PRED
US82400123_252800418517_S01_GE2_107_Sep09_2_2


title: BOS_9022_v7_FI

description:
BOS-DIAG
US82400123_252800421620_S01_GE2_107_Sep09_1_1


title: BOS_9040_v7_BPCO

description:
BOS-DIAG
US82400123_252800421585_S01_GE2_107_Sep09_1_4


title: BOS_25


title: BOS_32

description:
BOS-PRED
US82400123_252800418519_S01_GE2_107_Sep09_1_2


title: BOS_PEFR5008_v4_BPCO

description:
BOS-DIAG
US82400123_252800421618_S01_GE2_107_Sep09_2_1


title: BOS_93

description:
BOS-PRED
US82400123_252800420239_S01_GE2_107_Sep09_2_3


title: BOS_60

description:
BOS-PRED
US82400123_252800412630_S01_GE2_107_Sep09_2_2


title: Stable_122

description:
STA-1year
US82400123_252800412630_S01_GE2_107_Sep09_2_2


title: BOS_14

description:
BOS-PRED
US82400123_252800412630_S01_GE2_107_Sep09_1_4


title: BOS_98mean

description:
BOS-PRED
US82400123_252800421003_S01_GE2_107_Sep09_2_2


title: BOS_1057_v4_BPCO

description:
BOS-PRED
US82400123_252800421001_S01_GE2_107_Sep09_2_4


title: BOS_8029_v5_Muco

description:
BOS-DIAG
US82400123_252800421619_S01_GE2_107_Sep09_1_1


title: BOS_8016_v6_BPCO

description:
BOS-DIAG
US82400123_252800421619_S01_GE2_107_Sep09_2_3


title: BOS_8001_v7_BPCO

description:
BOS-DIAG
US82400123_252800421620_S01_GE2_107_Sep09_1_2


title: BOS_7052_v6_FI

description:
BOS-DIAG
US82400123_252800421596_S01_GE2_107_Sep09_2_2


title: BOS_7035_v6_BPCO

description:
BOS-DIAG
US82400123_252800421596_S01_GE2_107_Sep09_2_1


title: BOS_4020_v7_Muco

description:
BOS-DIAG
US82400123_252800421620_S01_GE2_107_Sep09_1_4


title: BOS_5011_v6_Muco

description:
BOS-DIAG
US82400123_252800421585_S01_GE2_107_Sep09_1_1


title: BOS_5017_v5_Sarco

description:
BOS-DIAG
US82400123_252800421619_S01_GE2_107_Sep09_1_4


title: BOS_1006_v6_Muco

description:
BOS-DIAG
US82400123_252800421617_S01_GE2_107_Sep09_2_4


title: BOS_3124_v6_Sclero

description:
BOS-DIAG
US82400123_252800421616_S01_GE2_107_Sep09_2_3


title: BOS_61

description:
BOS-DIAG
US82400123_252800421003_S01_GE2_107_Sep09_2_4


title: BOS_4017_v8_Muco

description:
BOS-DIAG
US82400123_252800421596_S01_GE2_107_Sep09_1_2


title: BOS_1004_v5_Muco

description:
BOS-DIAG
US82400123_252800421596_S01_GE2_107_Sep09_1_4


title: Stable_7018_v3_BPCO

description:
STA-6months
US82400123_252800421595_S01_GE2_107_Sep09_1_2


title: BOS_53

description:
BOS-DIAG
US82400123_252800420239_S01_GE2_107_Sep09_1_2


title: BOS_3060_v8_Bronch

description:
BOS-DIAG
US82400123_252800421616_S01_GE2_107_Sep09_2_4


title: BOS_5mean

description:
BOS-DIAG
US82400123_252800420240_S01_GE2_107_Sep09_1_1


title: Stable_5016_v3_Muco

description:
STA-6months
US82400123_252800421585_S01_GE2_107_Sep09_2_1


title: BOS_21

description:
BOS-DIAG
US82400123_252800420238_S01_GE2_107_Sep09_1_3


title: BOS_57mean

description:
BOS-DIAG
US82400123_252800418518_S01_GE2_107_Sep09_1_2


title: Stable_4011_v3_BPCO

description:
STA-6months
US82400123_252800420130_S01_GE2_107_Sep09_1_4


title: Stable_3047_v3_BPCO

description:
STA-6months
US82400123_252800421619_S01_GE2_107_Sep09_1_2


title: BOS_114

description:
BOS-DIAG
US82400123_252800420240_S01_GE2_107_Sep09_2_1


title: Stable_7024_v3_Bronch

description:
STA-6months
US82400123_252800420130_S01_GE2_107_Sep09_1_2


title: Stable_6003_v3_Muco

description:
STA-6months
US82400123_252800421617_S01_GE2_107_Sep09_1_1


title: Stable_3063_v3_Muco

description:
STA-6months
US82400123_252800421001_S01_GE2_107_Sep09_1_4


title: BOS_1028_v7_Muco

description:
BOS-DIAG
US82400123_252800421001_S01_GE2_107_Sep09_1_4


title: Stable_2012_v3_BPCO

description:
STA-6months
US82400123_252800421585_S01_GE2_107_Sep09_2_3


title: BOS_33

description:
BOS-DIAG
US82400123_252800421003_S01_GE2_107_Sep09_1_3


title: Stable_89

description:
STA-6months
US82400123_252800418517_S01_GE2_107_Sep09_2_2


title: BOS_23

description:
BOS-DIAG
US82400123_252800420238_S01_GE2_107_Sep09_2_2


title: Stable_2008_v3_Muco

description:
STA-6months
US82400123_252800421001_S01_GE2_107_Sep09_2_2


title: Stable_99

description:
STA-6months
US82400123_252800421003_S01_GE2_107_Sep09_1_1


title: Stable_87_h2

description:
STA-6months
US82400123_252800421002_S01_GE2_107_Sep09_2_4


title: BOS_10007_v5_HTAP

description:
BOS-DIAG
US82400123_252800421596_S01_GE2_107_Sep09_2_1


title: Stable_7011_v3_Muco

description:
STA-6months
US82400123_252800421619_S01_GE2_107_Sep09_2_1


title: P7731_C

city: Herston

first: Fares

last: Al-Ejeh

state: QLD

address: 300 Herston Road

department: Cancer

country: Australia

institute: QIMR Berghofer

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were quantile normalised to the baseline of the mean of all samples and then filtered using an Illumina detection score of ≥ 0.95 (p-value ≤ 0.05) and an average raw signal of ≥ 150 using GeneSpring v11.5.1 (Agilent Technologies).

source_name: P7731 cell line

label_protocol: Biotinylated RNA was generated using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to manufacturer's instructions.

growth_protocol: P7731 cells were maintained in RPMI1640 + 10% FBS.

extract_protocol: RNA from P7731 cells was extracted using the RNeasy “animal cells spin” protocol (Qiagen) according to manufacturer’s instructions. Primary tumour RNA was extracted with TriReagent (SIGMA) and isopropanal precipitated.

tag: cell line

value: breast cancer bone metastasis

tag: disease state

value: carcinoma


title: Stable_77

description:
STA-6months
US82400123_252800418517_S01_GE2_107_Sep09_2_3


title: Stable_79mean

description:
STA-6months
US82400123_252800418518_S01_GE2_107_Sep09_1_2


title: Primary_Tumour_B

description: Replicate 2

source_name: Right breast primary tumor

value: primary breast tumor

value: invasive ductal carcinoma


title: P7731_A

description: Replicate 1


title: Stable_91

description:
STA-6months
US82400123_252800412630_S01_GE2_107_Sep09_1_4


title: Stable_8

description:
STA-6months
US82400123_252800418518_S01_GE2_107_Sep09_1_1


title: Stable_66

description:
STA-6months
US82400123_252800418517_S01_GE2_107_Sep09_1_1


title: Stable_43mean

description:
STA-6months
US82400123_252800420238_S01_GE2_107_Sep09_2_4


title: Stable_76

description:
STA-6months
US82400123_252800420239_S01_GE2_107_Sep09_1_3


title: Stable_30

description:
STA-6months
US82400123_252800418517_S01_GE2_107_Sep09_1_2


title: Stable_50

description:
STA-6months
US82400123_252800420239_S01_GE2_107_Sep09_1_4


title: Stable_81

description:
STA-6months
US82400123_252800420238_S01_GE2_107_Sep09_1_3


title: prostate_cancer_sample_32

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

country: Canada

institute: GenomeDx

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathological re-review by an expert genitourinary pathologist, tumor was macrodissected from surrounding stroma from 3–4 10 µm tissue sections from a region with maximum tumor content for total RNA extraction.

tag: annotation

value: Adenocarcinoma

tag: patient id


title: prostate_cancer_sample_31


title: P7731_B

description: Replicate 2


title: prostate_cancer_sample_26


title: Stable_68

description:
STA-6months
US82400123_252800420239_S01_GE2_107_Sep09_1_2


title: prostate_cancer_sample_30


title: prostate_cancer_sample_29


title: Stable_48

description:
STA-6months
US82400123_252800421003_S01_GE2_107_Sep09_2_3


title: prostate_cancer_sample_27


title: prostate_cancer_sample_33

value: Adenocarcinoma with Neuroendocrine Differentiation


title: Stable_74

description:
STA-6months
US82400123_252800418519_S01_GE2_107_Sep09_1_4


title: prostate_cancer_sample_28


title: Stable_3


title: Stable_41mean

description:
STA-6months
US82400123_252800421003_S01_GE2_107_Sep09_2_2


title: Stable_28

description:
STA-6months
US82400123_252800420240_S01_GE2_107_Sep09_1_4


title: Stable_19

description:
STA-6months
US82400123_252800420238_S01_GE2_107_Sep09_1_1


title: prostate_cancer_sample_24


title: Primary_Tumour_A

description: Replicate 1

value: female


title: prostate_cancer_sample_23


title: prostate_cancer_sample_25


title: Stable_26

description:
STA-6months
US82400123_252800420239_S01_GE2_107_Sep09_2_1


title: Stable_17

description:
STA-6months
US82400123_252800420239_S01_GE2_107_Sep09_1_1


title: Stable_115

description:
STA-6months
US82400123_252800420240_S01_GE2_107_Sep09_2_2


title: prostate_cancer_sample_22


title: Stable_10

description:
STA-6months
US82400123_252800421003_S01_GE2_107_Sep09_2_4


title: Stable_106

description:
STA-6months
US82400123_252800418518_S01_GE2_107_Sep09_1_3


title: Stable_1


title: prostate_cancer_sample_9

value: Small cell carcinoma sample from patient with mixed histology


title: Stable_125

description:
STA-6months
US82400123_252800418519_S01_GE2_107_Sep09_2_2


title: prostate_cancer_sample_13

value: Adenocarcinoma sample from patient with mixed histology


title: prostate_cancer_sample_20

value: Small cell carcinoma


title: Stable_127_h2

description:
STA-6months
US82400123_252800421002_S01_GE2_107_Sep09_2_3


title: prostate_cancer_sample_21


title: prostate_cancer_sample_19


title: Stable_110mean

description:
STA-6months
US82400123_252800420240_S01_GE2_107_Sep09_1_1


title: prostate_cancer_sample_10


title: prostate_cancer_sample_6


title: prostate_cancer_sample_12


title: prostate_cancer_sample_17


title: prostate_cancer_sample_14


title: prostate_cancer_sample_3


title: Blood Neu ZT13 Replicate 3

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description: mRNA seq

data_processing:
RNA-Seq data in the form of FASTQ files were subsequently mapped to the mouse genome build mm10 using the STAR alignment software. The mapped reads were then counted using featureCounts (part of Subread package) based on the GENCODE M7 annotations
The raw counts were then used for a differential gene expression analysis (DEG) using edgeR (R version 3.1.2) with FDR<0.05 and log2FC>2 to identify genes differentially regulated in neutrophil subsets to generate volcano plots.
Count per million reads (CPM) values were calculated from raw counts using edgeR (R version 3.1.2). The CPM values were then log2-transformed in R (x -> log2(1+x)).
For PCA, hierarchical clustering and correlation matrices, the gene expression matrix was first subsetted using the top 20% variable genes (as measured by standard deviation across samples) and then those that were significantly associated with a cell population (FDR-corrected ANOVA, q-value <0.05) resulting in 4820 DEGs
Genome_build: GRCm38

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using the Arctus Picopure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer's protocol.
cDNA libraries were prepared using 2ng of total RNA and 1µL of a 1:50000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol (Picelli et al., 2014), except for the following modifications: (1) use of 20μM TSO; and (2) use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent kit on the Perkin Elmer Labchip

tag: developmental stage

value: Adult (7 weeks)

tag: microbiota status

value: Specfic-pathogen-free (SPF)

value: Blood Neutrophil ZT13


title: Blood Neu ZT13 Replicate 1

description: mRNA seq

tag: cell type


title: Stable_15

description:
STA-6months
US82400123_252800420240_S01_GE2_107_Sep09_1_2

value: STA


title: prostate_cancer_sample_15


title: prostate_cancer_sample_7


title: Blood Neu ZT13 Replicate 2

description: mRNA seq


title: prostate_cancer_sample_4


title: prostate_cancer_sample_5


title: prostate_cancer_sample_11


title: Mature Neu Replicate 3

description: mRNA seq

value: Mature Neutrophil


title: Blood Neu ZT5 Replicate 1

description: mRNA seq

value: Blood Neutrophil ZT5


title: Mature Neu Replicate 2

description: mRNA seq


title: Mature Neu Replicate 1

description: mRNA seq


title: Immature Neu Replicate 3

description: mRNA seq

value: Immature Neutrophil


title: prostate_cancer_sample_16


title: Immature Neu Replicate 2

description: mRNA seq


title: preNeu Replicate 2

description: mRNA seq

value: preNeutrophil


title: GMP Replicate 3

description: mRNA seq

value: GMP


title: Immature Neu Replicate 1

description: mRNA seq


title: prostate_cancer_sample_18


title: prostate_cancer_sample_8


title: preNeu Replicate 1

description: mRNA seq


title: Blood Neu ZT5 Replicate 2

description: mRNA seq


title: preNeu Replicate 3

description: mRNA seq


title: prostate_cancer_sample_1


title: GMP Replicate 2

description: mRNA seq


title: Blood Neu ZT5 Replicate 3

description: mRNA seq


title: GMP Replicate 1

description: mRNA seq


title: V43DNA_R409_24hours_post1stALVAC

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

description: transcriptional profilling of blood taken 24 hours after the 1st ALVAC boost  (week 12)

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using Genome Studio software (Illumina).

data_processing: Raw probe intensities were preprocessed using the R (version 3.4.3) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.50.1). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.32.10).

organism: Macaca mulatta

source_name: blood sample from donor R409 taken 24 hours after the 1st ALVAC boost

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: Total RNA was extracted using Agencourt RNAdvance Blood Kit. The isolated total RNA was checked for quantity and quality using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System. Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification. Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.

tag: donor

tag: immunization

tag: time after immunization

value: 24 hours

tag: prime

tag: number of siv challenge to infection

tag: tissue

value: blood


title: V43DNA_R409_2weeks_post1stALVAC

description: transcriptional profilling of blood taken 2 weeks after the 1st ALVAC boost  (week 14)

source_name: blood sample from donor R409 taken 2 weeks after the 1st ALVAC boost

value: 2 weeks


title: V43DNA_R278_24hours_post1stALVAC

source_name: blood sample from donor R278 taken 24 hours after the 1st ALVAC boost

value: DNA


title: prostate_cancer_sample_2


title: V43DNA_R278_prevax

description: transcriptional profilling of blood taken pre-vaccination (week -1)

source_name: blood sample from donor R278 taken pre-vaccination

value: prevax


title: V43DNA_R278_1week_post2ndALVAC

description: transcriptional profilling of blood taken 1 week after the 2nd ALVAC boost  (week 25)

source_name: blood sample from donor R278 taken 1 week after the 2nd ALVAC boost

value: 1 week


title: V43DNA_R409_24hours_post2ndALVAC

description: transcriptional profilling of blood taken 24 hours after the 2nd ALVAC boost  (week 24)

source_name: blood sample from donor R409 taken 24 hours after the 2nd ALVAC boost


title: V43DNA_R409_prevax

source_name: blood sample from donor R409 taken pre-vaccination


title: V43DNA_R278_2weeks_post1stALVAC

source_name: blood sample from donor R278 taken 2 weeks after the 1st ALVAC boost


title: V43DNA_R278_24hours_post2ndALVAC

source_name: blood sample from donor R278 taken 24 hours after the 2nd ALVAC boost


title: V43DNA_R275_2weeks_post1stALVAC

source_name: blood sample from donor R275 taken 2 weeks after the 1st ALVAC boost


title: V43DNA_R275_prevax

source_name: blood sample from donor R275 taken pre-vaccination


title: V43DNA_R275_1week_post2ndALVAC

source_name: blood sample from donor R275 taken 1 week after the 2nd ALVAC boost


title: V43DNA_R409_1week_post2ndALVAC

source_name: blood sample from donor R409 taken 1 week after the 2nd ALVAC boost


title: V43DNA_R275_24hours_post1stALVAC

source_name: blood sample from donor R275 taken 24 hours after the 1st ALVAC boost


title: V43DNA_R273_1week_post2ndALVAC

source_name: blood sample from donor R273 taken 1 week after the 2nd ALVAC boost

value: neg


title: V43DNA_R275_24hours_post2ndALVAC

source_name: blood sample from donor R275 taken 24 hours after the 2nd ALVAC boost


title: V43DNA_R273_24hours_post2ndALVAC

source_name: blood sample from donor R273 taken 24 hours after the 2nd ALVAC boost


title: WH028_Control

first: Michael

middle: S.

last: Kobor

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

extract_protocol: Genomic DNA was isolated using the Isohelix DNA isolation kit and bisulfite converted with the Zymo EZ DNA Methylation Kit, as per manufacturer’s instructions.

tag: individual

value: Buccal epithelial cells

tag: Sex

value: F

tag: disease status

value: Control

tag: disease subgroup

tag: age

tag: self-reported ethnicity

value: Caucasian

tag: sentrix id

tag: sentrix position


title: WH024B_Control

value: Canadian


title: WH017_Control


title: WH018_Control

value: M

value: Irish/English/German/Ukrainian


title: WH027_Control


title: WH021_Control

value: British/Chinese


title: V43DNA_R273_2weeks_post1stALVAC

source_name: blood sample from donor R273 taken 2 weeks after the 1st ALVAC boost


title: V43DNA_R273_prevax

source_name: blood sample from donor R273 taken pre-vaccination


title: V43DNA_R268_1week_post2ndALVAC

source_name: blood sample from donor R268 taken 1 week after the 2nd ALVAC boost


title: WH023_Control

value: Dutch


title: WH015B_Control


title: WH026_Control

value: English/Irish/Scottish


title: V43DNA_R268_2weeks_post1stALVAC

source_name: blood sample from donor R268 taken 2 weeks after the 1st ALVAC boost


title: WH014_Control


title: V43DNA_R268_24hours_post1stALVAC

source_name: blood sample from donor R268 taken 24 hours after the 1st ALVAC boost

value: 24 hours


title: WH024A_Control


title: WH015A_Control


title: V43DNA_R268_24hours_post2ndALVAC

source_name: blood sample from donor R268 taken 24 hours after the 2nd ALVAC boost

value: blood


title: WH019_Control


title: V43DNA_R268_prevax

source_name: blood sample from donor R268 taken pre-vaccination


title: WH008A_Control

value: Canadian/Italian/Swedish


title: V43DNA_R265_1week_post2ndALVAC

source_name: blood sample from donor R265 taken 1 week after the 2nd ALVAC boost


title: V43DNA_R265_24hours_post1stALVAC

source_name: blood sample from donor R265 taken 24 hours after the 1st ALVAC boost


title: V43DNA_R265_prevax

source_name: blood sample from donor R265 taken pre-vaccination


title: V43DNA_R265_2weeks_post1stALVAC

source_name: blood sample from donor R265 taken 2 weeks after the 1st ALVAC boost

value: 2 weeks


title: WH022_Control


title: WH004_rep1_Control

value: Canada/USA/German


title: WH009_Control

value: First Nations


title: WH006A_Control

value: German/Mennonite/English


title: WH007_Control

value: Buccal epithelial cells


title: WH006B_Control


title: V43DNA_R273_24hours_post1stALVAC

source_name: blood sample from donor R273 taken 24 hours after the 1st ALVAC boost

value: DNA

value: neg


title: V43DNA_R265_24hours_post2ndALVAC

source_name: blood sample from donor R265 taken 24 hours after the 2nd ALVAC boost


title: WH008B_Control

value: F

value: Control


title: V43DNA_R261_24hours_post1stALVAC

source_name: blood sample from donor R261 taken 24 hours after the 1st ALVAC boost


title: Spleen CD4+ T cells_single_cells_10X

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
CellRanger 2.0
cellranger count --id=spleens --fastqs directory_to_fastq_chunks --transcriptome refdata-cellranger-mm10-1.2.0 --mempercore=8 --nosecondary
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts. The key to the cell barcode can be found in the file "10XGenomics_MouseSpleenCD4_metadata.txt" on the series record.

source_name: spleen

growth_protocol: Live cells were sorted by flow cytometry from the spleen of a mouse.

extract_protocol:
Spleen were mechanically dissociated to single cell suspensions. CD4+ T cells were sorted by flow cytometry as DAPI- CD45+ TCRb+ CD4+ cells. Single cells were then encapsulated in nanodroplets according to the 10x Genomics protocol.
RNA libraries were prepared for sequencing using standard 10X Genomics Chromium prep

tag: strain

value: spleen

value: CD4+ T cells

value: Male

value: 9 weeks


title: WH005A_Control

value: M

value: Caucasian


title: V43DNA_R261_2weeks_post1stALVAC

source_name: blood sample from donor R261 taken 2 weeks after the 1st ALVAC boost

value: blood


title: WH003C_Control

value: German/Ukrainian


title: WD366_FASD

value: FASD

value: pFAS


title: V43DNA_R261_24hours_post2ndALVAC

source_name: blood sample from donor R261 taken 24 hours after the 2nd ALVAC boost

value: 24 hours


title: WH005B_Control


title: V43DNA_R261_prevax

source_name: blood sample from donor R261 taken pre-vaccination

value: prevax


title: WH004_rep2_Control

value: Buccal epithelial cells

value: Canada/USA/German


title: WD363_FASD

value: ARND

value: Russian/Caucasian


title: WH003A_Control

value: F

value: Control


title: V43DNA_R259_1week_post2ndALVAC

source_name: blood sample from donor R259 taken 1 week after the 2nd ALVAC boost

value: 1 week


title: WH003B_Control


title: Phf8 Knockout-3

first: Xuemei

last: Chen

address: 320 Yueyang Road

department: State Key Laboratory of Molecular Biology

institute: Chinese Academy of Sciences

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 645 and Fluidics Station 450 followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 4.0 with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.

source_name: phf8 KO_10 wk-old_hippocampus

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: hippocampus from Phf8 knock out and wild type mice

extract_protocol: Total RNA was extracted using Takara RNAiso Plus Kit following the manufacturer’s instructions， and Qualified total RNA was further purified by NucleoSpin RNA Clean-up XS kit and RNase-Free DNase Set.

tag: strain background

tag: genotype/variation

value: Phf8 knockout

value: 10 weeks

value: hippocampus


title: V43DNA_R259_24hours_post2ndALVAC

source_name: blood sample from donor R259 taken 24 hours after the 2nd ALVAC boost

tag: donor


title: WD360_FASD

tag: cell type

value: First Nations


title: V43DNA_R259_24hours_post1stALVAC

source_name: blood sample from donor R259 taken 24 hours after the 1st ALVAC boost

tag: immunization

tag: time after immunization

value: blood


title: Phf8 Knockout-1


title: WD310D_FASD

value: M

value: Native/French/Thai


title: V43DNA_R259_prevax

source_name: blood sample from donor R259 taken pre-vaccination

tag: prime

tag: number of siv challenge to infection


title: Wild Type-3

source_name: WT_10 wk-old_hippocampus

value: wild type

tag: tissue


title: WD357_FASD

tag: individual

tag: Sex

value: FASD


title: V43DNA_R257_1week_post2ndALVAC

source_name: blood sample from donor R257 taken 1 week after the 2nd ALVAC boost

value: DNA

value: neg


title: V43DNA_R259_2weeks_post1stALVAC

source_name: blood sample from donor R259 taken 2 weeks after the 1st ALVAC boost

value: 2 weeks


title: WD313_FASD

value: Buccal epithelial cells

tag: disease status

tag: disease subgroup

value: ARND


title: Targeted ShapeMaP R749H pol II nascent RNA untreated control for DMS treated samples

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

description:
nascent nuclear RNA
Anti-pol II nascent RNA treated with 1M7 and PCR enriched for RD histone transcripts and 18s rRNA

data_processing:
Single-end 50 base reads (after removing barcodes) or 125 base reads (after removing barcodes and trimming adaptor sequences) were uniquely mapped to the hg19 UCSC human genome or a custom rRNA genome with Bowtie2 version 2.1.0
Genome_build: GRCh37/hg19 assembly or custom 18s rRNA genome
Supplementary_files_format_and_content: ChIPseq data sets were processed into BigWig files.  Targeted shape map data was processed into a text files using pysamstats to create text files containing coverage and mutations (insertions, deletions and mismatches)counts  across all positions.  1M7 and DMS replicates were combined to create tables.

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H

growth_protocol: Rpb1 WT and mutant cells were grown in DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin, and pen/strep

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
targeted ShapeMap on nascent RNA: IP's were prepared from DNAseI solublilized nuclear extracts (~1.5X 10E7 cells). Precipitated RNA was treated with 1M7 or DMS. RNA was purified by Trizol extraction. Prufied RNA was random primed and cDNA was PCR enriched for the 3' region of RD hisone transcripts and the 5' region of 18S rRNA. PCR fragments were converted to sequencing libraries using ChIP-seq library construction protocol.
ChIP-seq: 1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: Amr Rpb1 was induced with doxycycline (2.0 mg/ml)  for 12-16 hr then treated with a-amanitin (2.5 mg/ml) for a further 42 hr before cross-linking and harvesting for ChIP-seq.

tag: growth conditions

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: Targeted ShapeMaP R749H pol II nascent RNA untreated control for 1M7 treated samples

description:
nascent nuclear RNA
Anti-pol II nascent RNA untreated control PCR enriched for RD histone transcripts and 18s rRNA


title: Wild Type-2

tag: age


title: WD319_FASD

value: F

tag: self-reported ethnicity

tag: sentrix id

tag: sentrix position


title: WD294_FASD


title: V43DNA_R261_1week_post2ndALVAC

source_name: blood sample from donor R261 taken 1 week after the 2nd ALVAC boost

tag: donor

value: 1 week


title: V43DNA_R257_24hours_post2ndALVAC

source_name: blood sample from donor R257 taken 24 hours after the 2nd ALVAC boost

value: 24 hours


title: Targeted ShapeMaP R749H pol II nascent RNA 1M7 treated


title: Wild Type-1

tag: strain background

tag: genotype/variation

value: 10 weeks


title: WD310B_FASD

tag: cell type


title: V43DNA_R257_prevax

source_name: blood sample from donor R257 taken pre-vaccination

tag: immunization

value: prevax

tag: time after immunization

tag: prime


title: V43DNA_R255_1week_post2ndALVAC

source_name: blood sample from donor R255 taken 1 week after the 2nd ALVAC boost

tag: number of siv challenge to infection

tag: tissue


title: WD247_FASD

tag: individual

tag: Sex

tag: disease status

value: FAS

value: First nations


title: V43DNA_R257_24hours_post1stALVAC

source_name: blood sample from donor R257 taken 24 hours after the 1st ALVAC boost

value: blood


title: Targeted ShapeMaP WT pol II nascent RNA untreated control for DMS treated samples

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

tag: growth conditions

tag: antibody


title: Targeted ShapeMaP WT pol II nascent RNA untreated control for 1M7 treated samples

description:
nascent nuclear RNA
Anti-pol II nascent RNA treated with DMS and PCR enriched for RD histone transcripts and 18s rRNA


title: WD284_FASD

tag: disease subgroup

value: pFAS

tag: age


title: V43DNA_R257_2weeks_post1stALVAC

source_name: blood sample from donor R257 taken 2 weeks after the 1st ALVAC boost


title: Targeted ShapeMaP WT pol II nascent RNA 1M7 treated


title: WD263_FASD

tag: self-reported ethnicity

value: Cree

tag: sentrix id

tag: sentrix position


title: Targeted ShapeMaP WT pol II nascent RNA DMS treated


title: Targeted ShapeMaP R749H pol II nascent RNA DMS treated


title: V43DNA_R255_24hours_post2ndALVAC

source_name: blood sample from donor R255 taken 24 hours after the 2nd ALVAC boost

tag: donor


title: WD216_FASD

tag: cell type

value: FASD

value: First Nations


title: Phf8 Knockout-2

tag: strain background

tag: genotype/variation

value: Phf8 knockout

value: hippocampus


title: V43DNA_R255_24hours_post1stALVAC

source_name: blood sample from donor R255 taken 24 hours after the 1st ALVAC boost

tag: immunization

tag: time after immunization

tag: prime

value: DNA


title: NELF-A ChIP-seq WT pol II

description: Chromatin IP against NELF-A

value: rabbit anti NELF-A (this study)


title: V43DNA_R255_2weeks_post1stALVAC

source_name: blood sample from donor R255 taken 2 weeks after the 1st ALVAC boost

value: 2 weeks

tag: number of siv challenge to infection

tag: tissue


title: V43DNA_R255_prevax

source_name: blood sample from donor R255 taken pre-vaccination


title: V43DNA_R254_1week_post2ndALVAC

source_name: blood sample from donor R254 taken 1 week after the 2nd ALVAC boost


title: CSst77 ChIP-seq WT pol II

description: Chromatin IP against CstF77

value: rabbit anti CstF77 (Glover-Cutter et al. 2008)


title: WD192_FASD

tag: individual

value: Buccal epithelial cells

tag: Sex

value: M

tag: disease status

value: ARND

value: Metis


title: CstF77 ChIP-seq R749H slow pol II

description: Chromatin IP against CstF77

tag: growth conditions

tag: antibody


title: WD210_FASD

tag: disease subgroup

tag: age

tag: self-reported ethnicity


title: SLBP ChIP-seq R749H slow pol II Rep2

description: Chromatin IP against SLBP

value: rabbit anti SLBP (gift of Z. Dominski)


title: SLBP ChIP-seq R749H slow pol II Rep1

description: Chromatin IP against SLBP


title: V43DNA_R254_2weeks_post1stALVAC

source_name: blood sample from donor R254 taken 2 weeks after the 1st ALVAC boost

tag: donor


title: WD182_FASD

tag: cell type

value: F

value: French/White

tag: sentrix id

tag: sentrix position


title: V43DNA_R254_24hours_post2ndALVAC

source_name: blood sample from donor R254 taken 24 hours after the 2nd ALVAC boost

tag: immunization

value: 24 hours

value: blood


title: SLBP ChIP-seq WT pol II Rep1

description: Chromatin IP against SLBP


title: WD121_FASD

value: FASD


title: V43DNA_R254_24hours_post1stALVAC

source_name: blood sample from donor R254 taken 24 hours after the 1st ALVAC boost

tag: time after immunization


title: WD110_FASD

value: First Nations


title: V43DNA_R254_prevax

source_name: blood sample from donor R254 taken pre-vaccination

value: prevax

tag: prime


title: SLBP ChIP-seq WT pol II Rep2

description: Chromatin IP against SLBP


title: V43DNA_R239_24hours_post2ndALVAC

source_name: blood sample from donor R239 taken 24 hours after the 2nd ALVAC boost

tag: number of siv challenge to infection


title: V43DNA_R239_1week_post2ndALVAC

source_name: blood sample from donor R239 taken 1 week after the 2nd ALVAC boost

value: 1 week

tag: tissue


title: R32_L4.N708

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq33
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11c- IgD+ CD38int Naive B cells

growth_protocol: Peripheral blood B cells from SLE patients, healthy subjects or RA patients were isolated using human B cell enrichment kit (StemCell Technologies) and stained for indicated markers. The purity of the sorted populations was routinely >90%.

extract_protocol:
RNA was isolated using PicoPure RNA isolation kit (Thermo Fisher Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diagnosis

value: Healthy subject

tag: collection

tag: cell surface marker

value: CD19+ CD11c- IgD+ CD27-CD38int

value: CD19+ CD11c- IgD+ CD38int Naive B cells


title: WD084_FASD

tag: individual

tag: Sex

tag: disease status


title: V43DNA_R239_2weeks_post1stALVAC

source_name: blood sample from donor R239 taken 2 weeks after the 1st ALVAC boost

value: 2 weeks

value: DNA


title: V43DNA_R239_24hours_post1stALVAC

source_name: blood sample from donor R239 taken 24 hours after the 1st ALVAC boost


title: R31_L4.N707

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq32
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11c- IgD- CD38int Memory B cells

value: CD19+ CD11c- IgD- CD27+CD38int


title: R30_L4.N706

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq31
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11c- IgD- CD38- Memory B cells

value: CD19+ CD11c- IgD- CD38- Memory B cells


title: 450K_H1228

description:
genomic DNA from H1228 glioma stem cells
glioma stem cells from primary tumor

source_name: glioma stem cells from primary tumor

tag: age

value: glioma stem cells from primary tumor

tag: gender

value: genomic DNA


title: R29_L4.N705

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq30
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11chi IgD- CD38- B cells

value: CD19+ CD11chi IgD- CD27-CD38-

value: CD19+ CD11chi IgD- CD38- B cells


title: WD135_FASD

value: Buccal epithelial cells

value: M

tag: disease subgroup

value: ARND

tag: self-reported ethnicity

value: Caucasian/First Nations


title: WD107_rep2_FASD

tag: cell type

value: FASD

value: First Nations

tag: sentrix id


title: WD107_rep1_FASD

tag: sentrix position


title: WD015_FASD

value: pFAS


title: V43DNA_R239_prevax

source_name: blood sample from donor R239 taken pre-vaccination

tag: donor

tag: immunization

value: prevax

tag: time after immunization

value: blood


title: V43DNA_R237_24hours_post2ndALVAC

source_name: blood sample from donor R237 taken 24 hours after the 2nd ALVAC boost

value: 24 hours

tag: prime

tag: number of siv challenge to infection

tag: tissue


title: WD033_FASD


title: WD007_FASD

value: F

value: Scottish/Irish/German/First Nations


title: R28_L4.N704

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq29
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

tag: diagnosis

value: Healthy subject

tag: collection

tag: cell surface marker

value: CD19+ CD11c- IgD+ CD27-CD38int

value: CD19+ CD11c- IgD+ CD38int Naive B cells


title: 450K_043white

description:
genomic DNA from white matter
human tissue

source_name: human tissue

value: human tissue

value: genomic DNA


title: V43DNA_R237_1week_post2ndALVAC

source_name: blood sample from donor R237 taken 1 week after the 2nd ALVAC boost

value: 1 week


title: WD031_FASD

tag: individual

value: Buccal epithelial cells

tag: Sex

tag: disease status


title: V43DNA_R237_2weeks_post1stALVAC

source_name: blood sample from donor R237 taken 2 weeks after the 1st ALVAC boost

value: 2 weeks


title: R27_L4.N703

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq28
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

value: CD19+ CD11c- IgD- CD27+CD38int

value: CD19+ CD11c- IgD- CD38int Memory B cells


title: 450K_022C+W

description:
genomic DNA from mixed cortex and white matter
human tissue

tag: age

tag: gender


title: V43DNA_R237_24hours_post1stALVAC

source_name: blood sample from donor R237 taken 24 hours after the 1st ALVAC boost


title: R26_L3.N702

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq27
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

tag: cell type

value: CD19+ CD11c- IgD- CD38- Memory B cells


title: NELF-A ChIP-seq R749H slow pol II

description: Chromatin IP against NELF-A

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H

tag: growth conditions

tag: antibody

value: rabbit anti NELF-A (this study)


title: R25_L4.N701

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq26
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

value: CD19+ CD11chi IgD- CD27-CD38-

value: CD19+ CD11chi IgD- CD38- B cells


title: R22_L3.N710

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq23
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: 450K_043gray

description:
genomic DNA from gray matter
human tissue

data_processing: Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi


title: R24_L4.N712

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq25
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: 450K_052cort

description:
genomic DNA from cortex
human tissue


title: R23_L3.N711

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq24
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: 450K_Normalhumanastrocyte

description:
genomic DNA from Normalhumanastrocyte
normal human astrocyte cell line

source_name: normal human astrocyte cell line

value: normal human astrocyte cell line


title: 450K_HOPC

description:
genomic DNA from human oligodedrocye precursor cells
human oligodendrocyte precursor cells

source_name: human oligodendrocyte precursor cells

value: human oligodendrocyte precursor cells


title: V43DNA_R237_prevax

data_processing: Raw probe intensities were preprocessed using the R (version 3.4.3) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.50.1). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.32.10).

source_name: blood sample from donor R237 taken pre-vaccination

tag: donor

value: prevax

value: blood


title: R20_L3.N708

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq21
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11c- IgD+ CD38int Naive B cells

value: Subject with Rheumatoid arthritis (RA)

value: CD19+ CD11c- IgD+ CD27-CD38int


title: R21_L3.N709

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq22
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

value: Healthy subject


title: R19_L3.N707

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq20
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: 450K_052white

value: human tissue

value: genomic DNA


title: V43DNA_R235_1week_post2ndALVAC

source_name: blood sample from donor R235 taken 1 week after the 2nd ALVAC boost

tag: immunization

value: 1 week

value: DNA


title: V43DNA_R235_24hours_post1stALVAC

source_name: blood sample from donor R235 taken 24 hours after the 1st ALVAC boost

tag: time after immunization

value: 24 hours


title: 450K_HumanFetalBrain

description:
genomic DNA from human feta brain
human tissue


title: V43DNA_R235_24hours_post2ndALVAC

source_name: blood sample from donor R235 taken 24 hours after the 2nd ALVAC boost

tag: prime


title: V43DNA_R235_2weeks_post1stALVAC

source_name: blood sample from donor R235 taken 2 weeks after the 1st ALVAC boost

value: 2 weeks

tag: number of siv challenge to infection


title: 450K_H9ES

description:
genomic DNA from H9ES
human H9 embryonic cells

source_name: human H9 embryonic cells

value: human H9 embryonic cells


title: V43DNA_R233_2weeks_post1stALVAC

source_name: blood sample from donor R233 taken 2 weeks after the 1st ALVAC boost

tag: tissue


title: R18_L3.N706

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq19
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11c- IgD- CD38- Memory B cells

tag: diagnosis

value: CD19+ CD11c- IgD- CD38- Memory B cells


title: V43DNA_R235_prevax

source_name: blood sample from donor R235 taken pre-vaccination


title: R16_L2.N704

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq17
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

tag: collection

value: CD19+ CD11c- IgD+ CD38int Naive B cells


title: V43DNA_R233_1week_post2ndALVAC

source_name: blood sample from donor R233 taken 1 week after the 2nd ALVAC boost


title: R15_L2.N703

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq16
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11c- IgD- CD38int Memory B cells

tag: cell surface marker

value: CD19+ CD11c- IgD- CD27+CD38int


title: 450K_NSC27

description:
genomic DNA from primary neural stem cells
fetal brain-derived neural stem/progenitor cells


title: 450K_H1ES

description:
genomic DNA from H1ES
human H1 embryonic cells

source_name: human H1 embryonic cells

value: human H1 embryonic cells


title: V43DNA_R233_24hours_post2ndALVAC

source_name: blood sample from donor R233 taken 24 hours after the 2nd ALVAC boost


title: 450K_NSC30

source_name: fetal brain-derived neural stem/progenitor cells


title: R17_L3.N705

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq18
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11chi IgD- CD38- B cells

value: CD19+ CD11chi IgD- CD27-CD38-

value: CD19+ CD11chi IgD- CD38- B cells


title: V43DNA_R233_24hours_post1stALVAC

description: transcriptional profilling of blood taken 24 hours after the 1st ALVAC boost  (week 12)

source_name: blood sample from donor R233 taken 24 hours after the 1st ALVAC boost

value: blood


title: R12_L2.N712

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq13
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

value: Subject with Rheumatoid arthritis (RA)


title: V43DNA_R231_1week_post2ndALVAC

source_name: blood sample from donor R231 taken 1 week after the 2nd ALVAC boost


title: 450K_GSC195

description:
genomic DNA from PDX-derived glioma stem cells
patient-derived Xenograph glioma stem cells


title: R14_L2.N702

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq15
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: V43DNA_R233_prevax

description: transcriptional profilling of blood taken pre-vaccination (week -1)

source_name: blood sample from donor R233 taken pre-vaccination

value: prevax


title: R13_L2.N701

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq14
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: V43DNA_R231_24hours_post2ndALVAC

description: transcriptional profilling of blood taken 24 hours after the 2nd ALVAC boost  (week 24)

source_name: blood sample from donor R231 taken 24 hours after the 2nd ALVAC boost


title: 450K_NSC23

value: fetal brain-derived neural stem/progenitor cells


title: R10_L2.N710

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq11
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: 450K_GSC143

source_name: patient-derived Xenograph glioma stem cells


title: R11_L2.N711

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq12
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

value: CD19+ CD11c- IgD- CD38int Memory B cells


title: R9_L2.N709

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq10
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: 450K_GSC182

data_processing: Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi

value: patient-derived Xenograph glioma stem cells

value: genomic DNA


title: 450K_GSC154


title: V43DNA_R231_2weeks_post1stALVAC

description: transcriptional profilling of blood taken 2 weeks after the 1st ALVAC boost  (week 14)

source_name: blood sample from donor R231 taken 2 weeks after the 1st ALVAC boost

value: DNA


title: R8_L1.N708

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq9
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11c- IgD+ CD38int Naive B cells

value: CD19+ CD11c- IgD+ CD27-CD38int


title: 450K_GSC187


title: 450K_GSC184


title: R7_L1.N707

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq8
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: 450K_GSC22


title: V43DNA_R231_24hours_post1stALVAC

data_processing: Raw probe intensities were preprocessed using the R (version 3.4.3) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.50.1). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.32.10).

source_name: blood sample from donor R231 taken 24 hours after the 1st ALVAC boost

value: 24 hours


title: V43DNA_R230_24hours_post2ndALVAC

source_name: blood sample from donor R230 taken 24 hours after the 2nd ALVAC boost


title: V43DNA_R231_prevax

source_name: blood sample from donor R231 taken pre-vaccination


title: V43DNA_R230_1week_post2ndALVAC

description: transcriptional profilling of blood taken 1 week after the 2nd ALVAC boost  (week 25)

source_name: blood sample from donor R230 taken 1 week after the 2nd ALVAC boost

value: 1 week


title: R5_L1.N705

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq6
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: R6_L1.N706

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq7
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11c- IgD- CD38- Memory B cells

value: CD19+ CD11c- IgD- CD38- Memory B cells


title: V43DNA_R230_2weeks_post1stALVAC

source_name: blood sample from donor R230 taken 2 weeks after the 1st ALVAC boost

value: 2 weeks


title: R4_L1.N704

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq5
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

value: Healthy subject

value: CD19+ CD11c- IgD+ CD38int Naive B cells


title: V43DNA_R230_24hours_post1stALVAC

source_name: blood sample from donor R230 taken 24 hours after the 1st ALVAC boost


title: 450K_GSC59


title: V43DNA_R227_1week_post2ndALVAC

source_name: blood sample from donor R227 taken 1 week after the 2nd ALVAC boost


title: R3_L1.N703

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq4
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11c- IgD- CD38int Memory B cells

value: CD19+ CD11c- IgD- CD27+CD38int


title: V43DNA_R227_2weeks_post1stALVAC

source_name: blood sample from donor R227 taken 2 weeks after the 1st ALVAC boost


title: 450K_GSC61


title: 450K_GSC108


title: R1_L1.N701

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq2
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19

source_name: CD19+ CD11chi IgD- CD38- B cells

value: CD19+ CD11chi IgD- CD27-CD38-

value: CD19+ CD11chi IgD- CD38- B cells


title: R2_L1.N702

data_processing:
Fastq files were generated using bcl2fastq
For sorted healthy subject or RA B cell subsets, STAR 2.5.2a was used to map reads to human genome (HG19)
For sorted healthy subject or RA B cell subsets,  rlog transformed and normalized values were generated using DEseq3
processed data files format and content: rlog.deseq2.txt
Genome_build: hg19


title: 450K_GSC84


title: V43DNA_R230_prevax

source_name: blood sample from donor R230 taken pre-vaccination

value: blood


title: RMS28901-16

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-16.sort.readcount.txt
Genome_build: hg19

source_name: CD19+ CD11c- CD27- IgD+ Naïve B cells

value: Subject with Systemic lupus erythematosus (SLE)

value: CD19+ CD11c- CD27- IgD+

value: CD19+ CD11c- CD27- IgD+ naive B cells


title: 450K_GSC12

value: patient-derived Xenograph glioma stem cells


title: 450K_GSC43

value: genomic DNA


title: RMS28901-15

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-15.sort.readcount.txt
Genome_build: hg19

source_name: CD19+ CD11c- CD27+ IgD- Memory B cells

value: CD19+ CD11c- CD27+ IgD-

value: CD19+ CD11c- CD27+ IgD-  Memory B cells


title: V43DNA_R227_prevax

source_name: blood sample from donor R227 taken pre-vaccination

value: prevax


title: 450K_GSC39

source_name: patient-derived Xenograph glioma stem cells


title: V43DNA_R227_24hours_post1stALVAC

source_name: blood sample from donor R227 taken 24 hours after the 1st ALVAC boost

value: 24 hours


title: RMS28901-13

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-13.sort.readcount.txt
Genome_build: hg19

source_name: CD19+CD11chi IgD+ B cells

value: CD19+ CD11chi CD27- IgD+

value: CD19+ CD11chi CD27- IgD+ B cells


title: RMS28901-12

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-12.sort.readcount.txt
Genome_build: hg19


title: RMS28901-11

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-11.sort.readcount.txt
Genome_build: hg19


title: RMS28901-10

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-10.sort.readcount.txt
Genome_build: hg19

source_name: CD19+CD11chi IgD- B cells

value: CD19+ CD11chi CD27- IgD-

value: CD19+ CD11chi CD27- IgD-  B cells


title: RMS28901-9

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-9.sort.readcount.txt
Genome_build: hg19


title: 450K_GSC102

data_processing: Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi


title: RMS28901-14

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-14.sort.readcount.txt
Genome_build: hg19


title: V43DNA_R226_1week_post2ndALVAC

source_name: blood sample from donor R226 taken 1 week after the 2nd ALVAC boost

value: 1 week

value: DNA


title: 450K_GSC14


title: V43DNA_R226_2weeks_post1stALVAC

source_name: blood sample from donor R226 taken 2 weeks after the 1st ALVAC boost

value: 2 weeks


title: V43DNA_R226_24hours_post2ndALVAC

source_name: blood sample from donor R226 taken 24 hours after the 2nd ALVAC boost

value: blood


title: V43DNA_R226_24hours_post1stALVAC

source_name: blood sample from donor R226 taken 24 hours after the 1st ALVAC boost


title: V43DNA_R227_24hours_post2ndALVAC

source_name: blood sample from donor R227 taken 24 hours after the 2nd ALVAC boost


title: RMS28901-8

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-8.sort.readcount.txt
Genome_build: hg19

value: Subject with Systemic lupus erythematosus (SLE)


title: RMS28901-7

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-7.sort.readcount.txt
Genome_build: hg19


title: V43DNA_R224_1week_post2ndALVAC

data_processing: Raw probe intensities were preprocessed using the R (version 3.4.3) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.50.1). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.32.10).

source_name: blood sample from donor R224 taken 1 week after the 2nd ALVAC boost


title: RMS28901-6

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-6.sort.readcount.txt
Genome_build: hg19


title: V43DNA_R226_prevax

source_name: blood sample from donor R226 taken pre-vaccination


title: RMS28901-4

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-4.sort.readcount.txt
Genome_build: hg19

value: CD19+ CD11c- CD27- IgD+


title: V43DNA_R224_24hours_post2ndALVAC

source_name: blood sample from donor R224 taken 24 hours after the 2nd ALVAC boost


title: V43DNA_R224_2weeks_post1stALVAC

source_name: blood sample from donor R224 taken 2 weeks after the 1st ALVAC boost


title: 450K_GSC80


title: 450K_GSC64


title: RMS28901-1

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-1.sort.readcount.txt
Genome_build: hg19


title: V43DNA_R224_prevax

source_name: blood sample from donor R224 taken pre-vaccination


title: 450K_GSC6


title: V43DNA_R222_1week_post2ndALVAC

source_name: blood sample from donor R222 taken 1 week after the 2nd ALVAC boost


title: V43DNA_R222_24hours_post2ndALVAC

source_name: blood sample from donor R222 taken 24 hours after the 2nd ALVAC boost


title: RMS28901-3

data_processing:
Fastq files were generated using bcl2fastq
For sorted SLE B cell subsets, sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
For sorted SLE B cell subsets, count tables were generated using HTseq.
processed data files format and content: RMS28901-3.sort.readcount.txt
Genome_build: hg19

source_name: CD19+ CD11c- CD27+ IgD- Memory B cells


title: 450K_GSC76

source_name: patient-derived Xenograph glioma stem cells


title: V43DNA_R222_2weeks_post1stALVAC

source_name: blood sample from donor R222 taken 2 weeks after the 1st ALVAC boost


title: V43DNA_R220_24hours_post1stALVAC

source_name: blood sample from donor R220 taken 24 hours after the 1st ALVAC boost


title: V43DNA_R220_2weeks_post1stALVAC

source_name: blood sample from donor R220 taken 2 weeks after the 1st ALVAC boost


title: 450K_GSC164


title: V43DNA_R220_1week_post2ndALVAC

source_name: blood sample from donor R220 taken 1 week after the 2nd ALVAC boost


title: V43DNA_R220_24hours_post2ndALVAC

source_name: blood sample from donor R220 taken 24 hours after the 2nd ALVAC boost


title: V43DNA_R222_prevax

source_name: blood sample from donor R222 taken pre-vaccination


title: V43DNA_R218_24hours_post1stALVAC

source_name: blood sample from donor R218 taken 24 hours after the 1st ALVAC boost


title: V43DNA_R218_1week_post2ndALVAC

source_name: blood sample from donor R218 taken 1 week after the 2nd ALVAC boost


title: V43DNA_R220_prevax

source_name: blood sample from donor R220 taken pre-vaccination


title: 450K_GSC10