title: S1 PEO1 2

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: PEO1 cell line with SNAI1 over-expression, replicate 2

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: Data were normalized by Robust Multichip Average (RMA) using Affymetrix Powertools using default parameters

label: Biotin

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA

growth_protocol: All cell lines were cultured in DMEM supplemented with 10% FBS and 4-6µg/ml puromycin.

extract_protocol: Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

treatment_protocol: Lentiviral plasmids encoding full length wide type SNAI1 (#LVP314779), TWIST1 (#LV349265), ZEB1 (#LV362464), and ZEB2 (#LV362542) with pLenti-GIII-CMV-GFP-2A-Puro backbone (#LV590, all from ABM) were used for lentivirus production. Empty vector with no inserts was used as negative control. 24 hours after infection, cells were selected with puromycin.

tag: cell line

value: Ovarian cancer cell line

value: epithelial


title: EV PEO1 2

status: Public on May 25 2022

type: RNA

description: PEO1 cell line treated with empty vector, replicate 2

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: phenotype

tag: treatment

value: Empty vector


title: Th17_24h_LNA2_replicate3_LANE3

type: SRA

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6A

department: Turku Bioscience

country: Finland

institute: University of Turku

library_source: transcriptomic

data_processing:
FastQC was used to check the quality of the raw sequencing reads (Andrews, 2010), and Trimmomatic (Bolger et al., 2014) was used to trim the adapters and low-quality bases. Tophat2 (Kim et al., 2013) was used to align the trimmed reads to the human reference genome GRCh37.75 (Ensembl release 75). HTseq-count (Anders et al., 2015) was used to calculate the summarized read counts for each gene.
Genome_build: hg19
Supplementary_files_format_and_content: csv

source_name: cord blood

growth_protocol: Ficoll (GE Healthcare, cat# 17-1440-03) was used to isolate PBMCs from human umbilical cord blood samples from Turku University Central Hospital, which was followed by CD4+ T cells were isolation (Invitrogen (cat# 11331D).  CD4+ T cells were activated using a plate coated anti-CD3 antibody (Beckman Coulter, cat# IM-1304) (3750 ng/well in a six-well culture plate), and anti-CD28 antibody (Beckman Coulter, cat# IM1376) was added in the medium in a concentration of 1 μg/mL. X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) containing 0.5 million cells/mL complemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich) was used for the cultures. Cells were plated at a density of 2 million cells per well and cultured at 37° C in 5% CO2. For Th17 polarization of CD4+ cells, IL-6 (20 ng/mL; Roche, cat# 11138600 001), IL-1β (10 ng/mL, R&D Systems, cat# 201 LB) and TGFβ (10 ng/mL, R&D Systems, cat# 240) were used as the cytokine cocktail along with neutralizing antibodies against IFNγ (1 μg/mL, R&D Systems, cat# MAB-285) and IL4 (1 μg/mL, R&D Systems, cat# MAB204). Nonpolarizing control (Th0) cells were activated with anti-CD3 and anti-CD28 antibodies in the presence of the neutralizing antibodies without differentiating cytokines.

extract_protocol:
RNA was isolated (RNeasy Mini Kit, cat# 74106, QIAGEN) and treated in-column with DNase (RNase-Free DNase Set; QIAGEN) for 15 min. The removal of genomic DNA was ensured by an additional treatment of the samples with DNase I (Invitrogen). RNA quantification was performed using Nanodrop 2000 and quality control was performed using BioRad Experion or Agilent Bioanalyzer.
libraries for RNA-Seq were prepared using Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part #15031047). The quality of the libraries was confirmed with Advanced Analytical Fragment Analyzer, and the concentrations of the libraries were quantified with Qubit® Fluorometric Quantitation (Life Technologies).
24 samples pooled on one lane and sequence 3 lanes with 2x100bp read length (about 37 x _x000B_10^6 reads per sample). Sequencing was performed at the Finnish Functional Genomics Centre using the HiSeq2500 Next-Generation Sequencing platform.

treatment_protocol: For LNA transfections, 4 million cells mixed with 150 pmols of LNA, prepared in 100 μL volume of OptiMEM (Gibco by Life Technologies, cat # 31985-047), were used to transfect the cells using the Amaxa Nucleofector II system (Lonza). After transfection, cells were first rested at 37° C for 48 h in RPMI 1640 (Sigma-Aldrich) medium supplemented with 10% FCS, 50 U/mL penicillin, 50 μg/mL streptomycin, and 2 mM L-glutamine and then activated and cultured as described above. The following LNAs (provided by QIAGEN) were used:  LNA-NC (non-targeting control): 5´-AACACGTCTATACGC -3´;  LNA-1: 5'-ACTTTGGCATTCTAGG-3´;  LNA-4: 5'-AGGCTGGTAGGCTATG-3´.

value: In vitro differentiated Th17 cells

value: Nucleofected cells differentiated for 24 hour in Th17 media


title: Z2 429 2

description: OVCA429 cell line with ZEB2 over-expression, replicate 2

value: intermediate epithelial


title: Z1 429 1

description: OVCA429 cell line with ZEB1 over-expression, replicate 1


title: Z1 429 2

description: OVCA429 cell line with ZEB1 over-expression, replicate 2


title: Z2 PEO1 1

description: PEO1 cell line with ZEB2 over-expression, replicate 1


title: T1 PEO1 1

description: PEO1 cell line with TWIST1 over-expression, replicate 1


title: Z2 429 1

description: OVCA429 cell line with ZEB2 over-expression, replicate 1


title: T1 429 2

description: OVCA429 cell line with TWIST1 over-expression, replicate 2


title: Th17_24h_LNANT_replicate3_LANE1


title: EV PEO1 1

description: PEO1 cell line treated with empty vector, replicate 1


title: S1 PEO1 1

description: PEO1 cell line with SNAI1 over-expression, replicate 1


title: Th17_24h_LNA1_replicate3_LANE1


title: Th17_72h_LNA4_replicate2_LANE1

value: Nucleofected cells differentiated for 72 hour in Th17 media


title: T1 PEO1 2

description: PEO1 cell line with TWIST1 over-expression, replicate 2


title: Th17_24h_LNANT_replicate3_LANE2


title: Th17_72h_LNA4_replicate2_LANE3


title: EV 429 1

description: OVCA429 cell line treated with empty vector, replicate 1


title: Z2 410 1

description: OVCA420 cell line with ZEB2 over-expression, replicate 1


title: P209_NPPP_W3_LS [sam1116222]

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

country: USA

institute: The Rockefeller University

data_processing:
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Assembly: GRCh37
Supplementary files format and content: Tab delimited gene expression data of each sample

source_name: Skin

extract_protocol:
Qiagen miRNeasy micro kit (not performed by Regeneron)
KAPA Stranded mRNA-Seq Kit for Illumina® Platforms with 100ng input and 12 PCR cycles.

tag: subjectid

tag: condition

value: NPPP

tag: timepoint

tag: tissue

value: LS


title: Th17_72h_LNA2_replicate2_LANE1


title: S1 429 1

description: OVCA429 cell line with SNAI1 over-expression, replicate 1


title: EV 429 2

description: OVCA429 cell line treated with empty vector, replicate 2


title: Z2 420 2

description: OVCA420 cell line with ZEB2 over-expression, replicate 2


title: Th17_72h_LNA4_replicate2_LANE2


title: T1 429 1

description: OVCA429 cell line with TWIST1 over-expression, replicate 1


title: Th17_72h_LNA2_replicate2_LANE3


title: S1 429 2

description: OVCA429 cell line with SNAI1 over-expression, replicate 2


title: Z2 PEO1 2

description: PEO1 cell line with ZEB2 over-expression, replicate 2


title: Th17_72h_LNA2_replicate2_LANE2


title: Th17_72h_LNA1_replicate2_LANE3


title: Th17_72h_LNANT_replicate2_LANE1


title: Th17_72h_LNANT_replicate2_LANE3


title: Th17_72h_LNA1_replicate2_LANE1


title: 15 month old TMEM184B mutant hippocampus sample 1

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

department: Neuroscience

institute: University of Arizona

data_processing:
Alignment to mouse genome using Salmon (salmon-0.11.1-linux_x86_64)
Trim first column of Salmon output data to contain ENSMUST transcript identifiers. This was done using the Galaxy platform.
Created a file to convert ENSMUST identifiers to GeneID using Galaxy
Normalize count values and idnetify differentially expressed genes using DeSeq2. This was done using the Galaxy Platform.
Export data, and remove ribosomal RNA sequences.as necessary (rpl, rps).
Assembly: mm10
Supplementary files format and content: tabular text files containing normalized counts

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Mouse hippocampi were dissected, immediately homogenized in Trizol, and frozen. Total RNA was extracted using the manufacturer's protocol.
Illumina Platform PE150 library; 250-300bp insert cDNA library

value: hippocampus

tag: genotype

value: TMEM184B mutant (GT/GT)

tag: age

value: 15 months


title: 15 month old TMEM184B mutant hippocampus sample 3


title: Z1 420 2

description: OVCA420 cell line with ZEB1 over-expression, replicate 2


title: S1 420 2

description: OVCA420 cell line with SNAI1 over-expression, replicate 2


title: EV 420 2

description: OVCA420 cell line treated with empty vector, replicate 2


title: Th17_24h_LNA4_replicate2_LANE3


title: Th17_72h_LNA1_replicate2_LANE2


title: 15 month old TMEM184B mutant hippocampus sample 2


title: T1 420 2

description: OVCA420 cell line with TWIST1 over-expression, replicate 2


title: T1 420 1

description: OVCA420 cell line with TWIST1 over-expression, replicate 1


title: Th17_24h_LNA4_replicate2_LANE2


title: Th17_72h_LNANT_replicate2_LANE2


title: EV 420 1

description: OVCA420 cell line treated with empty vector, replicate 1


title: S1 420 1

description: OVCA420 cell line with SNAI1 over-expression, replicate 1


title: 5 month old TMEM184B mutant hippocampus sample 3

value: 5 months


title: Th17_24h_LNA4_replicate2_LANE1


title: 5 month old TMEM184B mutant hippocampus sample 1


title: 5 month old TMEM184B mutant hippocampus sample 2


title: 15 month old wild type hippocampus sample 2

value: Wild Type (C57BL/6)


title: Th17_24h_LNA2_replicate2_LANE2


title: 15 month old wild type hippocampus sample 1


title: 15 month old wild type hippocampus sample 3


title: Th17_24h_LNA1_replicate2_LANE1


title: Th17_24h_LNA1_replicate2_LANE2


title: Th17_24h_LNA1_replicate2_LANE3


title: 5 month old wild type hippocampus sample 3


title: Th17_24h_LNA2_replicate2_LANE3


title: Th17_24h_LNANT_replicate2_LANE2


title: Th17_24h_LNA2_replicate2_LANE1


title: 5 month old wild type hippocampus sample 1


title: Th17_24h_LNANT_replicate2_LANE3


title: Th17_24h_LNANT_replicate2_LANE1


title: 5 month old wild type hippocampus sample 4


title: 5 month old wild type hippocampus sample 2


title: Th17_72h_LNA4_replicate1_LANE3


title: APP/PS1 hippocampal dentate gyrus presented with both BCI-838 and physical exercise for a month, 4

first: Benjamin

middle: S

last: Glicksberg

address: 1 Gustave Levy Place

department: Genetics and Genomics

institute: Icahn School of Medicine at Mt Sinai

description:
borchelt.final
normalized.borchelt.final
APPPI321

data_processing:
Quality control of raw samples in .fastq format
Alignment of paired-end reads to mouse reference genome using STAR
Conversion of aligned reads to readcounts using htseq-count
Variation partitioning analysis using variationPartition package in R
Surrogate variable analysis using sva packagein R
DEG analysis of SVA-adjusted readcounts using DeSeq package in R
Assembly: Mus musculus mm10
Supplementary files format and content: Raw readcounts provided in matrix format as text file
Supplementary files format and content: Normalized readcounts via DeSeq package provided in matrix format as text file

source_name: Hippocampal dentate gyrus

extract_protocol: RNA isolation:   Snap frozen samples from the DG of 5 mice of each group were homogenized in QIAzol Lysis Reagent (Qiagen).  Total RNA purification was performed with the miRNeasy Mini kit (Qiagen). RNA quantification and quality were  evaluated by Agilent BioAnalyzer. RNA integrity was checked using the RNA 6000 Nano assay (Agilent, CA,  USA). All processed RNA samples had RQN/RIN value of 8.4 or greater and sent to NOVOGENE to be sequenced.

treatment_protocol: Administration of BCI-838 5 mg/kg daily per one month p.o.. Physical Activity via running wheels ad libitum per one month.

value: Hippocampal dentate gyrus

value: Presented with both BCI-838 and physcial exercise


title: APP/PS1 hippocampal dentate gyrus presented with both BCI-838 and physical exercise for a month, 5

description:
borchelt.final
normalized.borchelt.final
APPPI376


title: Th17_72h_LNA4_replicate1_LANE1


title: Th17_72h_LNA2_replicate1_LANE3


title: APP/PS1 hippocampal dentate gyrus presented with both BCI-838 and physical exercise for a month, 3

description:
borchelt.final
normalized.borchelt.final
APPPI320


title: Th17_72h_LNA4_replicate1_LANE2


title: APP/PS1 hippocampal dentate gyrus presented with both BCI-838 and physical exercise for a month, 2

description:
borchelt.final
normalized.borchelt.final
APPPI286


title: APP/PS1 hippocampal dentate gyrus presented with both BCI-838 and physical exercise for a month, 1

description:
borchelt.final
normalized.borchelt.final
APPPI182


title: Th17_72h_LNA2_replicate1_LANE2


title: Z1 420 1

description: OVCA420 cell line with ZEB1 over-expression, replicate 1


title: Th17_72h_LNA2_replicate1_LANE1


title: APP/PS1 hippocampal dentate gyrus exposed to physical exercise for a month, 5

description:
borchelt.final
normalized.borchelt.final
APPPI313

value: Exposed to physical exercise


title: Th17_72h_LNA1_replicate1_LANE3


title: APP/PS1 hippocampal dentate gyrus exposed to physical exercise for a month, 3

description:
borchelt.final
normalized.borchelt.final
APPPI264


title: Th17_72h_LNA1_replicate1_LANE2


title: APP/PS1 hippocampal dentate gyrus exposed to physical exercise for a month, 2

description:
borchelt.final
normalized.borchelt.final
APPPI236


title: Th17_72h_LNANT_replicate1_LANE3


title: APP/PS1 hippocampal dentate gyrus exposed to physical exercise for a month, 1

description:
borchelt.final
normalized.borchelt.final
APPPI224


title: APP/PS1 hippocampal dentate gyrus administered with BCI-838 for a month, 4

description:
borchelt.final
normalized.borchelt.final
APPPI322

value: Administered with BCI-838


title: Th17_72h_LNANT_replicate1_LANE2


title: APP/PS1 hippocampal dentate gyrus administered with BCI-838 for a month, 3

description:
borchelt.final
normalized.borchelt.final
APPPI288


title: Th17_72h_LNANT_replicate1_LANE1


title: Th17_24h_LNA4_replicate1_LANE2


title: APP/PS1 hippocampal dentate gyrus exposed to physical exercise for a month, 4

description:
borchelt.final
normalized.borchelt.final
APPPI275


title: Th17_24h_LNA2_replicate1_LANE3


title: APP/PS1 hippocampal dentate gyrus control, 3

description:
borchelt.final
normalized.borchelt.final
APPPI262

value: Control


title: Th17_24h_LNA4_replicate1_LANE3


title: APP/PS1 hippocampal dentate gyrus administered with BCI-838 for a month, 1

description:
borchelt.final
normalized.borchelt.final
APPPI198


title: Th17_24h_LNA4_replicate1_LANE1


title: Th17_24h_LNA2_replicate1_LANE1


title: APP/PS1 hippocampal dentate gyrus control, 2

description:
borchelt.final
normalized.borchelt.final
APPPI255


title: Th17_24h_LNA2_replicate1_LANE2


title: APP/PS1 hippocampal dentate gyrus control, 5

description:
borchelt.final
normalized.borchelt.final
APPPI318


title: APP/PS1 hippocampal dentate gyrus control, 1

description:
borchelt.final
normalized.borchelt.final
APPPI184


title: Th17_24h_LNA1_replicate1_LANE2


title: Th17_24h_LNA1_replicate1_LANE3


title: WT hippocampal dentate gyrus control, 4

description:
borchelt.final
normalized.borchelt.final
WT_218

value: WT


title: Th17_24h_LNA1_replicate1_LANE1

value: In vitro differentiated Th17 cells


title: Th17_24h_LNANT_replicate1_LANE3

value: Nucleofected cells differentiated for 24 hour in Th17 media


title: Th17_24h_LNANT_replicate1_LANE2


title: WT hippocampal dentate gyrus control, 3

description:
borchelt.final
normalized.borchelt.final
WT_214


title: WT hippocampal dentate gyrus control, 1

description:
borchelt.final
normalized.borchelt.final
WT_191


title: Stella-KO_HI-C

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
For Hi-C pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16). Then HiCPro (version 2.7) (Servant et al., 2015) was used to map, process and iteratively corrected normalization. Briefly, reads were independently aligned to the mouse reference genome (mm9) with the bowtie2 algorithm (Langmead and Salzberg, 2012). We discarded the uncut DNA reads, re-ligation reads, continuous reads and PCR artifacts. Unique mapped reads (MAPQ>10) were used to build the contact matrix.
Compartment analysis are used R package (HiTC) (Servant et al., 2012) pca.hic function to generate the PC1 eigenvectors using 400kb normalized matrices with following options: (normPerExpected=TRUE, npc=1)
TAD calling is done using Direction Index  method as previously described (Dixon et al., 2012)
Assembly: mm9
Supplementary files format and content: Tab-delimited text files

molecule: genomic DNA

source_name: Female germline stem cells (FGSCs)

growth_protocol: FGSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Life Technologies), 2 mM L-glutamine (Sigma), 30 mg/mL pyruvate (Amresco) and 50 mM -mercaptoethanol (Biotech)

extract_protocol:
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014)
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Female germline stem cells (FGSCs)

tag: passages

tag: strain

value: Stella-KO

tag: restriction enzyme

value: Dpn II


title: WT hippocampal dentate gyrus control, 5

description:
borchelt.final
normalized.borchelt.final
WT_225


title: Th17_24h_LNANT_replicate1_LANE1


title: APP/PS1 hippocampal dentate gyrus administered with BCI-838 for a month, 2

description:
borchelt.final
normalized.borchelt.final
APPPI245


title: Th17_72h_LNA1_replicate1_LANE1

value: Nucleofected cells differentiated for 72 hour in Th17 media


title: WT hippocampal dentate gyrus control, 2

description:
borchelt.final
normalized.borchelt.final
WT_207


title: ChIPseq-Ezh2-D6-Input

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

description: Calibrated ChIP-seq

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Cutadapt 1.9.1 with parameters -q 20 -m 20 used for quality-trimming RNA-Seq sequences. m 30 used for ChIP-Seq instead.
STAR_2.5.2b used for aligning RNA-Seq sequences to hg19 reference genome. Bowtie2 used for aligning ChIP-Seq sequences to hg19+mm9 reference genomes
Picard markduplicates used to mark RNA-Seq duplicates. Sambamba used to mark ChIP-Seq duplicates.
BamCompare 3.1.3 used to normalize with BPM method (only RNA-Seq) and to apply a smoothing of 10 bp. For ChIP-Seq samples, signal from input samples was sustracted to the samples signal. For RNA-Seq samples, signal from the reverse strand was sustracted to the signal in the forward strand.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-Seq, bigwig files containing Reads per Million (RPM) with a 10 bp smoothing. For ChIP-Seq, bigwig files containing calibrated reads with a 10 bp smoothing.ChIP-Seq signal was normalized against input signal. For RNA-Seq, signal in forward strand has positive values, while signal in reverse strand has negative values.

source_name: Human lung carcinoma A549 cell line

growth_protocol:
A549 cells were cultured in 5% CO2 at 37 ºC  in DMEM High glucose media supplemented with 10% FBS heat inactivated, penicillin/streptomycin (Gibco), L-glutamine (Gibco) and 2-mercaptoethanol (Gibco).
EMT-MET protocol: Cells treated during 6 days with TGF-B (10 ng/mL), EGF (50 ng/mL ) followed by additional 6 days upon removal of the cytokines from the media. Cells were mantained in the presence of 5uM GSK126 during the course of the experiment.  Cells were diluted 1:4 every 48h and GSK126 was refreshed every two days when the cells were diluted.

extract_protocol:
A549 cells were mixed with 1.4x10^5 mouse JM8 embryonic stem cells as spike-in control as described in Fursova et al 2019. ChIP assay were mainly performed as described previously (Brookes et al, 2012) with minor modifications described in Asenjo et al 2020.
cChIP-seq libraries were generated from 3 ng of immunoprecipitated DNA with the NEBNext Ultra DNA Library Prep kit for Illumina (#7370) according to manufacturer’s instructions.

treatment_protocol: Cells treated with TGF-B (10 ng/mL) and EGF (50 ng/mL) for 6 days

value: Lung carcinoma cell line

tag: chip anitbody

value: Ezh2 (Diagenode, C15410039, lot 003)


title: ChIPseq-Ezh2-D0-Input

description: Calibrated ChIP-seq


title: 24h_KO_Ipsil

city: Ulju-gun

first: Wonhyo

last: Lee

state: Ulsan

address: Unist-gil 50

department: Biological Sciences

country: South Korea

institute: UNIST

description: Prdx1 -/- tMCAO 24h ipsillateral hemisphere

data_processing:
The single cell RNA libraries constructed by 10x Single Cell chip A kit are sequenced by llumina HiSeq2500 Instrument
Illumina fastq files are aligned on mm10 reference genome by Cell ranger
barcode, feature, and matrix file which are output file of Cell ranger are imported to R with Read10x function of Seurat  package
10x data are converted to seurat object CreateSeuratObject function of seurat package
Multiplet data are eliminated by doubletFinder package
Genome_build: mm10
Supplementary_files_format_and_content: Matrix file of barcodes and genes which shows gene expression of each single cells.

source_name: brain hemisphere

extract_protocol:
The brain hemisphere was removed after cold PBS transcardial perfusion, and tissues were cut into pieces and transferred to the gentleMACSTM C tubes (Miltenyi Biotec) containing the Adult Brain Dissociation kit mouse and rat (Miltenyi Biotec, 130-107-677) enzyme mixture. The brain tissue dissociated with gentleMACSTM program 37°C _ABDK_1 with run 30 min incubations on the MACSmix tube rotator. The supernatant was aspirated, the pellet was resuspended in 8ml of 40% Percoll (GE Healthcare) and overlaid on the top of 4ml of 80% Percoll. The myelin debris was removed using Percoll separation. The gradient is centrifuged at 2200rpm for 20 min without brake at 22°C. Cells were collected 40% to 80% interface and washed with PBS and stained with Zombie NIRTM Fixable viability kit (Biolegend, 423106). The cells were washed by PBS for two times.
BD FACS Aria III (BD Biosciences) was used for sorting brain single live cells. Each cell suspension was subjected to 3′ single-cell RNA sequencing using Single Cell A Chip Kit, Single Cell 3′ Library and Gel Bead Kit V2, and i7 Multiplex Kit (10x Genomics) with a cell recovery target of 9000, following the manufacturer’s instructions

treatment_protocol: C57B6L/J male mice, aged 8-9 weeks Prdx1+/+, Prdx1-/- mice36, and weighing 20−24g, were used for focal brain ischemia experiments. There was no significant difference in weight and age between Prdx1+/+ mice and any Prdx1-/- mice groups. We used a transient (60 min) middle cerebral artery occlusion (tMCAO) model induced through an intraluminal suture (Doccol, 701956PK5Re) under anesthesia with 1.5% isoflurane (SomnosuiteR, Kent Scientific). The method of inducing this tMCAO model 10-20% reduction in cerebral blood flow was confirmed by Laser Doppler Flowmetry (LDF, Primed 3000 system). The rectal temperature was maintained at 37±0.5°C during surgery using a heating pad system. 60 min after MCAO, the brain blood flow was reperfused by the withdrawal of the intraluminal suture.

value: ipsillateral hemisphere

value: Prdx1 -/-


title: 48h_KO_Cont

description: Prdx1 -/- tMCAO 48h contralateral hemisphere

value: contralateral hemisphere


title: 48h_KO_Ipsil

description: Prdx1 -/- tMCAO 48h ipsillateral hemisphere


title: 24h_KO_Cont

description: Prdx1 -/- tMCAO 24h contralateral hemisphere


title: Rep2_Sample_R21055376-Over-Input-Over-Input

description: Over-Input

data_processing:
For MeDIP pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters.
PCR duplicates were removed using Samtools (version 2.0.1) (Li et al., 2009) and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file

source_name: female germline stem cells

growth_protocol: FGSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Life Technologies), 2 mM L-glutamine (Sigma), 30 mg/mL pyruvate (Amresco) and 50 mM -mercaptoethanol (Biotech).

extract_protocol:
MeDIP experiments were performed using a MagMEDIP kit (Diagenode, Seraing, Belgium). Briefly, genomic DNA (gDNA) was extracted from FGSCs and sonicated to shear chromatin. Fifty nanograms of fragmented genomic DNA was used for the library construction and purified. Methylated DNA was immunoprecipitated with anti-5-methylcytosine antibody overnight at 4℃. After washing and elution, immunoprecipitated DNA was amplified and subjected to Illumina sequencing.
Library was prepared with NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.

tag: genotype/variation

value: Stella-overexpression

tag: fraction

value: input


title: Rep2_Sample_R21055375-Over-con-Input-Over-con-Input

description: Over-con-Input


title: Rep2_Sample_R21055374-KO-2-Input-KO-2-Input

value: Stella-knockout


title: APP/PS1 hippocampal dentate gyrus control, 4

description:
borchelt.final
normalized.borchelt.final
APPPI307

value: Hippocampal dentate gyrus


title: Rep2_Sample_R21055370-KO-2-IP-KO-2-IP

value: IP


title: Rep2_Sample_R21055373-SgNC-Input-SgNC-Input

description: SgNC-Input

value: SgNC


title: Rep2_Sample_R21055372-Over-IP-Over-IP

description: Over-IP


title: Rep2_Sample_R21055369-sgNC-IP-sgNC-IP

description: sgNC-IP

value: sgNC


title: Rep2_Sample_R21055371-Over-con-IP-Over-con-IP

description: Over-con-IP


title: 157560571_2_H6_GTAGAGGA-GTAAGGAG_L008

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
Fastq files were processed with Kallisto v0.45.0 (9), and gene-level counts were generated from abundances scaled using the average transcript length, averaged over samples and to library size (lengthScaledTPM), using the tximport package v1.16.1 (10). Subsequent analysis was performed using a typical Bioconductor workflow (11). Briefly, the count matrix was imported of into R to create a SingleCellExperiment object. Cells with a library size of < 30,000 reads were removed from the analysis. After QC metric filtering, a total of 689 cells were kept for downstream analysis. The logNormCounts() function from the scater  package v1.16.2 (12) was used to generate log-transformed normalized expression values. PCA was performed using the top 4000 highly variable genes, and tSNE (13) and UMAP (14) was subsequently performed using the top 30 principal components for data visualization. The top 30 principal components were also used to build a shared nearest-neighbour (SNN) graph, and cell clusters were identified using the walktrap algorithm from the igraph package v1.2.5 (15). Differentially expressed genes between groups were identified using MAST v1.14.0 (16). Genes with a false discovery rate (FDR) of < 0.05 and a fold change of > 1.25 or < −1.25 were considered significantly differentially expressed between groups.
Supplementary_files_format_and_content: CSV and raw counts

source_name: PBMC

extract_protocol:
Samples were single-cell sorted into 96-well PCR plates containing 5 µL of DNA Suspension Buffer (Teknova) with 1% BSA (Sigma-Aldrich) per well. Plates were sealed and briefly vortexed before being spun at 800 × g for 1 minute and immediately transferred to dry ice. Plates were stored at -80°C for at least overnight before proceeding. Once ready to proceed, the plates were thawed on ice and spun at 800 × g for 1 minute to collect all liquid. We used a modified version of a previously published method to amplify the whole transcriptome (8). In brief, the reverse transcriptase that is used to make cDNA has a terminal transferase activity. Then, a “template‐switch” primer incorporates a second universal priming sequence yielding cDNA with two universal priming sequences.  Custom primers were synthesized by IDT using sequences published by Trombetta, et al. (8). In brief, reverse transcription occurred in two steps.  The initial step was conducted in 5 µL of the lysed cell, 2.4 µM 3’ SMART CDS Primer II A (IDT), 2.4 mM each dNTP mix (GeneAmp) and 6.32 U RNaseOUT (Invitrogen).  The samples were incubated at room temperature for 1 minute, 72°C for 3 minutes and held on ice before beginning the second step.  The next step was conducted with SuperScript II Reverse Transcriptase Kit (Invitrogen), using 7 µL of the step 1 product, 1× First Strand Buffer, 2.5 mM DTT, 110 U SuperScript II and an additional 11 U RNaseOUT, as well as 1 µM SMARTer II Oligonucleotide (IDT) and molecular-grade water to 11 µL. The samples were incubated at 42°C for 90 min, followed by a limited cycle amplification of 10 cycles at 50°C for 2 min and 42°C for 2 min, concluding with a final extension at 72°C for 15 minutes.
Whole transcriptome amplification (WTA) immediately proceeded with the 11 µL of the reverse transcription product, using 1× KAPA HiFi HotStart Ready Mix (Roche) and 0.5 µM IS PCR Primer (IDT).  Amplification parameters were 98°C for 3 min and 22 cycles of 98°C for 15 sec, 67°C for 20 sec and 72°C for 6 min, followed by a final extension of 72°C for 5 min.  The WTA product was cleaned using AMPure XP beads (Beckman Coulter).  The PCR product was incubated at room temperature for 5 min with 0.8 volumes of XP beads before being placed on a magnet.  The beads were washed three times with 100 µL of 80% ethanol.  After briefly drying, the beads were resuspended in 20 µL of 1× TE Buffer (Sigma Aldrich) and 18 µL of supernatant were was transferred to a new 96-well PCR plate. Quality and quantitation were measured by TapeStation using a High Sensitivity D5000 ScreenTape (Agilent).  Samples with a concentration ≥200 pg/µL were carried forward for sequencing according to the Nextera XT DNA Library Preparation Kit (Illumina) protocol.  Samples were dual-indexed using the Nextera Index XT Kit (Illumina) and a scheme that would allow for eight pools without overlapping indices. After pooling, the concentration of each pool was measured by Qubit dsDNA HS Assay Kit (Invitrogen) and sizing was determined by Fragment Analyzer HS Small Fragment Kit (Agilent).  A smear analysis was conducted in the range of 150 to 1000 bp, and the average peak size along with the Qubit results were used to determine the molarity.  Each pool was then diluted to a concentration of 2 nM.  The samples were sequenced on the Illumina HiSeq 2500 using PE50 on a high-output 8-lane flow cell with one pool per lane.

treatment_protocol: PBMCs were thawed RPMI media containing 10% FBS, L-Glut, Pen-Strep and rested overnight (16-18 hours). The cells were incubated with purified anti-CD40 monoclonal antibody (Miltenyi Biotec) for 10 minutes before being stimulated (Frentsch, M. et al Nat Med 2005).  The CD40L-PE-Cy7 antibody was added along with 1 μg/mL anti-human CD28/CD49d co-stimulatory antibody and either 2 g/mL vaccine-matched 92TH023-Env peptide pool or with peptide diluent (DMSO) only for 5 hours at 37C 5% CO2. PBMCs were then incubated with a mix of equal parts IFN- Catch Reagent (Miltenyi Biotec), IL-2 Catch Reagent (Miltenyi Biotec), IL-4 Catch Reagent (Miltenyi Biotec) on ice for 15 mins. R10 was added and PBMCs were incubated rotating at 37C 5% CO2 for 1 hour. Samples were washed with buffer (1x PBS, 2 mM EDTA, 0.5% BSA) and stained on ice with aqua viability dye followed by an antibody cocktail containing phenotyping markers as well as cytokine detection antibodies (Table 1). Live CD14- CD19- CD56- CD8- single cytokine+ CD154+, IFN-+, IL-2+ or CD154+IL2+ CD4+ T lymphocytes were single-cell sorted  with a FACSAria II cell sorter. PolyfunctionalityFull functional profiles wasere determined post-sorting using analysis usingof the individual cell level flow cytometry data (acquired by indexing).

value: PBMC

value: CD4 T cells

tag: vaccination

value: RV144 vaccine regimen


title: Rep1_Sample_R21055376-Over-Input-Over-Input

description: Over-Input


title: Rep1_Sample_R21055375-Over-con-Input-Over-con-Input

description: Over-con-Input


title: Rep1_Sample_R21055374-KO-2-Input-KO-2-Input


title: ChIPseq-Ezh2-D6

description: Calibrated ChIP-seq

tag: cell line


title: RNA-D0-R1

description: mRNA-seq

molecule: polyA RNA

extract_protocol:
Trizol extraction
Libraries were generated from 500 ng of  RNA using the TruSeq stranded mRNA Library Prep kit (#20020595) according to manufacturer’s instructions.


title: 157560571_2_H9_AGGCAGAA-ACTGCATA_L008

tag: cell type


title: 157560571_2_H8_CGTACTAG-ACTGCATA_L008


title: 157560571_2_H7_TAAGGCGA-ACTGCATA_L008


title: RNA-D6-R1

description: mRNA-seq


title: RNA-D12-R2

description: mRNA-seq

treatment_protocol: Cells treated during 6 days with TGF-B (10 ng/mL), EGF (50 ng/mL ) followed by additional 6 days upon removal of the cytokines from the media


title: RNA-D6_w_GSK126-R1

description: mRNA-seq

treatment_protocol: Cells treated with TGF-B (10 ng/mL), EGF (50 ng/mL)and GSK126 (5uM) for 6 days.


title: ChIPseq-Ezh2-D0

description: Calibrated ChIP-seq


title: RNA-D12_w_GSK126-R2

description: mRNA-seq

treatment_protocol: Cells treated during 6 days with TGF-B (10 ng/mL), EGF (50 ng/mL ) followed by additional 6 days upon removal of the cytokines from the media. Cells were mantained in the presence of 5uM GSK126 during the course of the experiment.


title: RNA-D12_w_GSK126-R1

description: mRNA-seq


title: RNA-D6_w_GSK126-R2

description: mRNA-seq


title: RNA-D6-R2

description: mRNA-seq


title: Rep1_Sample_R21055373-SgNC-Input-SgNC-Input

description: SgNC-Input-


title: Rep1_Sample_R21055372-Over-IP-Over-IP

description: Over-IP


title: RNA-D12-R1

description: mRNA-seq


title: RNA-D0-R2

description: mRNA-seq


title: Rep1_Sample_R21055369-sgNC-IP-sgNC-IP

description: sgNC-IP


title: 157560571_2_H2_CAGAGAGG-GTAAGGAG_L008


title: 157560571_2_H4_CGAGGCTG-GTAAGGAG_L008


title: 157560571_2_H10_TCCTGAGC-ACTGCATA_L008


title: 157560571_2_G8_GGACTCCT-GTAAGGAG_L008


title: dppa3-over-control2

data_processing:
RNA-seq data were trimmed and aligned to mouse genome (mm9), then Hisat2 was used to mapping the reads with default parameters.
DEseq2 was used to calculate the significant different genes under the parameters: adjust of p value < 0.05 and log2 fold change > 1.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent (Invitrogen, Carlsbard, CA, USA). RNA quantity and quality were determined with 2100 Bioanalyzer (Agilent Technologies).
RNA-Seq libraries was prepared using the KAPA Stranded mRNA-Seq kit (KAPA Biosystems, Wilmington, MA, USA), following the manufacturer's protocol

tag: genoype/variation


title: dppa3-over-control3


title: Rep1_Sample_R21055371-Over-con-IP-Over-con-IP

description: Over-con-IP


title: 157560571_2_G6_AGGCAGAA-GTAAGGAG_L008


title: DPAA3-over2


title: 157560571_2_G7_TCCTGAGC-GTAAGGAG_L008


title: dppa3-over-control1


title: DPAA3-over1


title: 157560571_2_H12_TAGGCATG-ACTGCATA_L008


title: 157560571_2_H11_GGACTCCT-ACTGCATA_L008


title: 157560571_2_H3_GCTACGCT-GTAAGGAG_L008


title: 157560571_2_H5_AAGAGGCA-GTAAGGAG_L008


title: 157560571_2_F9_TAGGCATG-AGAGTAGA_L008


title: 157560571_2_F8_GGACTCCT-AGAGTAGA_L008


title: DPPA3-ko-control1


title: Rep1_Sample_R21055370-KO-2-IP-KO-2-IP


title: dppa3-over-control Rep1

data_processing:
For Hi-C pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16). Then HiCPro (version 2.7) (Servant et al., 2015) was used to map, process and iteratively corrected normalization. Briefly, reads were independently aligned to the mouse reference genome (mm9) with the bowtie2 algorithm (Langmead and Salzberg, 2012). We discarded the uncut DNA reads, re-ligation reads, continuous reads and PCR artifacts. Unique mapped reads (MAPQ>10) were used to build the contact matrix.
Compartment analysis are used R package (HiTC) (Servant et al., 2012) pca.hic function to generate the PC1 eigenvectors using 400kb normalized matrices with following options: (normPerExpected=TRUE, npc=1)
TAD calling is done using Direction Index  method as previously described (Dixon et al., 2012)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files

source_name: Female germline stem cell

value: Dpn II


title: dppa3-ko2


title: dppa3-over-control Rep2


title: dppa3-ko3


title: DPPA3-ko-control2


title: DPPA3-ko-control3


title: DPAA3-over3


title: 157560571_2_G12_TAGGCATG-GTAAGGAG_L008


title: 157560571_2_G2_AAGAGGCA-AGAGTAGA_L008


title: 157560571_2_F3_GTAGAGGA-TATCCTCT_L008


title: input_rep2

data_processing:
For ChIP pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters.
PCR duplicates were removed using Samtools (version 2.0.1) (Li et al., 2009) and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 min at room temperature and quenched with 125mM glycine. Cells were then put on ice, resuspended in cold cell lysis buffer (140mM NaCl, 1mM EDTA pH 8.0, 1% TritonX-100 and 0.1% SDS and Protease Inhibitors (Roche)). Nuclei were sonicated into 200-1000 bp. The chromatin fragments were pre-cleared and then immunoprecipitated with Protein A+G Magnetic beads coupled with anti-STELLA (ab19878, Abcam).After reverse crosslinking, immunoprecipitated DNAs and input DNAs were end-repaired and ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.
Library was prepared with NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.

tag: antibody


title: 157560571_2_G3_GTAGAGGA-AGAGTAGA_L008


title: dppa3-over Rep2


title: 157560571_2_G1_CGAGGCTG-AGAGTAGA_L008


title: dppa3-over Rep1


title: 157560571_2_F1_CGAGGCTG-TATCCTCT_L008


title: 157560571_2_F12_GCTACGCT-AGAGTAGA_L008


title: stella_rep2

value: anti-STELLA (ab19878, Abcam)


title: 157560571_2_F7_TCCTGAGC-AGAGTAGA_L008


title: dppa3-ko1


title: 157560571_2_G5_CGTACTAG-GTAAGGAG_L008


title: 157560571_2_G4_TAAGGCGA-GTAAGGAG_L008


title: input_rep1


title: 157560571_2_F6_AGGCAGAA-AGAGTAGA_L008


title: 157560571_2_F2_AAGAGGCA-TATCCTCT_L008


title: stella_rep1


title: 157560571_2_F4_TAAGGCGA-AGAGTAGA_L008


title: ChIP-Seq - treated - neural progenitor cells - rep3

city: Pittsburgh

first: Donald

middle: B.

last: DeFranco

state: PA

address: 7041 Biomedical Sciences Tower 3

department: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
ATACseq reads were trimmed to remove the adapter using trim_galore. Short reads were aligned to the mouse reference genome (mm10) using bwa mem aligner version 0.7.17. Reads mapping to mitochondrial DNA were removed before analysis. PCR duplicates are removed with picard (v2.18.12). To identify peaks from ATAC-seq reads, we used the macs2 package (v2.1.1.20160309) with ‘-f BEDPE’ parameter.  To visualize individual ATAC-seq data on Integrative Genomics Viewer (IGV), we converted bam output files into normalized bigwig format using the bamCoverage function in deepTools (v3.3.0) with options “--binSize 10 --normalizeUsing RPKM -p=2”
Chipseq reads were trimmed to remove the adapter using trim_galore. Short reads were aligned to the mouse reference genome (mm10) using bowtie2 aligner version 2.4.1. To identify peaks from Chipseq reads, we used the macs2 package (v2.1.1.20160309) with ‘-B --SPMR --qvalue .05 --gsize mm --nomodel --extsize 200’ parameter.  To visualize individual chipseq data on Integrative Genomics Viewer (IGV), we converted bam output files into normalized bigwig format using the bamCoverage function in deepTools (v3.3.0) with options “--binSize 10 --normalizeUsing RPKM -p=2”
Genome_build: mm10
Supplementary_files_format_and_content: peak files, bigwig

source_name: neural progenitor cells

growth_protocol: NSPCs derived from the telencephalon were generated from individual C57Bl/6 female mouse embryos on   embryonic day 14.5 (E14.5), dissociated into single cells, and grown as three-dimensional neurosphere   cultures. Neurospheres were passaged every 3-4 days, and all experimental treatments were given at the end of the third passage.

extract_protocol:
(1) For ATAC-seq, a detailed protocol is described by Corces et al., 2017. In brief, nuclei were resuspended in transposase reaction mix containing 1:20 dilution of Transposase (Illumina) in 1X TD buffer (Illumina) and incubated at 37oC for 30 minutes with mixing.  Fragmented product was purified using a Zymo DNA Clean and Concentrator-5 kit prior to PCR amplification, adapter sequence incorporation, and library preparation. (2) For ChIP-seq, a detailed protocol is described by Rollins and Rogatsky et al., 2019. In brief, lysates were clarified from sonicated nuclei and GR-DNA complexes were isolated with antibody. Purified DNA was eluted using the QIAquick PCR Purification Kit according to manufacturer’s directions. DNA was stored at -20 oC until next generation sequencing using an Illumina HiSeq 2500 system.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with an ethanol vehicle or dexamethasone (10-7M) for a total of 4 hours.

value: ES-derived neural progenitor cells

value: cerebral cortex

value: embryonic day 14.5

tag: treatment

value: dexamethasone (10-7M)

tag: chip antibody

value: GR (ThermoFisher Cat.No. PA1-511A


title: ChIP-Seq - input - neural progenitor cells

value: ethanol vehicle


title: 157560571_2_F10_CTCTCTAC-AGAGTAGA_L008


title: 157560571_2_F11_CAGAGAGG-AGAGTAGA_L008


title: 157560571_2_E8_GCTACGCT-TATCCTCT_L008


title: 157560571_2_E6_CTCTCTAC-TATCCTCT_L008


title: ChIP-Seq - treated - neural progenitor cells - rep2


title: ChIP-Seq - treated - neural progenitor cells - rep1


title: ChIP-Seq - untreated - neural progenitor cells - rep3


title: 157560571_2_E5_TAGGCATG-TATCCTCT_L008


title: ChIP-Seq - untreated - neural progenitor cells - rep2


title: ChIP-Seq - untreated - neural progenitor cells - rep1


title: 157560571_2_E4_GGACTCCT-TATCCTCT_L008


title: 157560571_2_E3_TCCTGAGC-TATCCTCT_L008


title: 157560571_2_E2_AGGCAGAA-TATCCTCT_L008


title: 157560571_2_E1_CGTACTAG-TATCCTCT_L008


title: 157560571_2_D9_CGAGGCTG-CTCTCTAT_L008


title: NM_TE.3

city: shanghai

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 genome_tran using hisat2 (version 2.1.0) with default parameters. Only Reads with high quality (MAPQ>=60) were retained for futher analysis.
The reads count for every gene was counted by featureCounts (Version 1.6.1), and the normalized abundance was calculated as log2(reads per million +1 ) using R edgeR package.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with normalized abundance for every gene and every sample.
Supplementary_files_format_and_content: tab-delimited text files with raw counts for every gene and every sample

source_name: TE

growth_protocol: The BDF1 (C57BL/6N female × DBA2 male) mice were used to obtain embryos (the in vitro fertilization and in vitro culture embryos were defined as IVF embryos, the natural mating and in vivo development embryos were defined as NM embryos.

extract_protocol:
The prepared cells were transferred to lysis buffer by a mouth pipette. Reverse transcription was performed directly using Oligo (dT) primer in the lysate containg completely cytoplasm. The second-strand cDNAs were synthesised depending on the poly(A) tail attached to the 3′ end of the first-strand cDNAs.
Fragment cDNA was prepared using Covaris sonicator (Covaris S220, Woburn, MA, USA) for sequence library construction. Kapa Hyper Prep Kit（KAPA , KK8504, Switzerland）was used to complete the sequence libraries.

treatment_protocol: Single cell of pre-implatation embryos was collected without polar body by removing zone pellucida with 20mg/ml PE (Pronase E, Sigma), incubating in CZB without Ca2+ and gently pipetting with a firepolished glass tube. Single cell of E7.5 embryos (EXE, Epi) was collected by separating from decidua and digestng with 0.05% TE (Trypsin-EDTA, Gibco, 25300062). All the cells were washed at least three times with 0.5% BSA-PBS (MP Biomedicals ,USA) solution before used.

tag: developmental stage

value: embryonic day 3.5 (E3.5)

tag: fertilization

value: NM


title: NM_TE.2


title: NM_TE.1


title: NM_morula.3

source_name: morula

value: embryonic day 2.5 (E2.5)


title: NM_morula.2


title: NM_ICM.3

source_name: ICM


title: NM_morula.1


title: 157560571_2_E7_CAGAGAGG-TATCCTCT_L008

tag: tissue


title: 157560571_2_D3_TCCTGAGC-CTCTCTAT_L008


title: 157560571_2_D4_GGACTCCT-CTCTCTAT_L008


title: NM_ICM.2


title: NM_ICM.1


title: 157560571_2_D1_CGTACTAG-CTCTCTAT_L008


title: 157560571_2_D12_TAAGGCGA-TATCCTCT_L008


title: NM_ExE.3

source_name: ExE

value: embryonic day 7.5 (E7.5)


title: NM_ExE.2


title: 157560571_2_D5_TAGGCATG-CTCTCTAT_L008


title: 157560571_2_C7_CAGAGAGG-GCGTAAGA_L008


title: 157560571_2_D11_GTAGAGGA-CTCTCTAT_L008


title: 157560571_2_C6_CTCTCTAC-GCGTAAGA_L008


title: 157560571_2_C9_CGAGGCTG-GCGTAAGA_L008


title: NM_Epi.1

source_name: Epi


title: NM_2cell.3

value: embryonic day 1.5 (E1.5)


title: 157560571_2_D6_CTCTCTAC-CTCTCTAT_L008


title: NM_Epi.3


title: 157560571_2_C8_GCTACGCT-GCGTAAGA_L008


title: NM_2cell.2


title: NM_2cell.1


title: 157560571_2_C4_GGACTCCT-GCGTAAGA_L008


title: 157560571_2_C5_TAGGCATG-GCGTAAGA_L008


title: 157560571_2_C3_TCCTGAGC-GCGTAAGA_L008


title: 157560571_2_C1_CGTACTAG-GCGTAAGA_L008


title: 157560571_2_C2_AGGCAGAA-GCGTAAGA_L008


title: 157560571_2_C12_TAAGGCGA-CTCTCTAT_L008


title: IVF_ExE.2

value: IVF


title: IVF_ExE.3


title: NM_ExE.1


title: NM_Epi.2


title: IVF_Epi.3


title: 157560571_2_C11_GTAGAGGA-GCGTAAGA_L008

value: PBMC


title: 157560571_2_C10_AAGAGGCA-GCGTAAGA_L008

value: CD4 T cells


title: IVF_Epi.2


title: 157560571_2_B8_GCTACGCT-CTAAGCCT_L007

value: RV144 vaccine regimen


title: 157560571_2_B7_CAGAGAGG-CTAAGCCT_L007


title: IVF_TE.3


title: IVF_ExE.1


title: 157560571_2_B6_CTCTCTAC-CTAAGCCT_L007


title: IVF_TE.2


title: 157560571_2_B5_TAGGCATG-CTAAGCCT_L007


title: 157560571_2_B4_GGACTCCT-CTAAGCCT_L007


title: IVF_morula.3


title: IVF_ICM.3


title: IVF_morula.2


title: 157560571_2_B3_TCCTGAGC-CTAAGCCT_L007


title: 157560571_2_B2_AGGCAGAA-CTAAGCCT_L007


title: IVF_TE.1


title: 157560571_2_B12_TAAGGCGA-GCGTAAGA_L008


title: IVF_morula.1


title: 157560571_2_B1_CGTACTAG-CTAAGCCT_L007


title: IVF_Epi.1


title: IVF_2cell.3


title: IVF_ICM.1


title: 157560571_2_B9_CGAGGCTG-CTAAGCCT_L007


title: IVF_2cell.1


title: IVF_2cell.2


title: 157560571_2_B11_GTAGAGGA-CTAAGCCT_L007


title: 157560571_2_B10_AAGAGGCA-CTAAGCCT_L007


title: 157560571_2_A9_GTAGAGGA-AAGGAGTA_L007


title: IVF_ICM.2


title: NM_ExE_K27.3

description:
NM_IF_EXE_segments.bed
NM_IF_EXE_K27.logFE.bw

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome using bwa mem (0.7.12-r1039) with default paraments.
PCR duplicates were removed and only the reads with high quality (MAPQ>20) were retained for futher analysis.
Chromatin states were defined using ChromHMM (Version 1.15)  with paraments -b 500 -center.
The signal trackings were normalized by input values using macs2 (2.1.2) bdgcmp with paraments -m logFE -p 1
Genome_build: mm10
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: bigwig

extract_protocol:
About 500-1000 cells were used per library and about 1µg histone H3K4me3 antibody (Cell signaling Technology, 9727S, USA) or histone H3K27me3 antibody (Diagnode, C15410195, Belgium) were used for immunoprecipitation reaction.
The sequence libraries were generated by Kapa Hyper Prep Kit (KAPA, KK8504, Switzerland).


title: NM_ExE_K4.3

description:
NM_IF_EXE_segments.bed
NM_IF_EXE_K4.logFE.bw

value: H3K4me3 antibody (Cell signaling Technology, 9727S, USA)


title: 157560571_2_A5_CAGAGAGG-AAGGAGTA_L007


title: 157560571_2_A4_CTCTCTAC-AAGGAGTA_L007


title: 157560571_2_A3_TAGGCATG-AAGGAGTA_L007


title: 157560571_2_A6_GCTACGCT-AAGGAGTA_L007


title: 157560571_2_A8_AAGAGGCA-AAGGAGTA_L007


title: 157560571_2_A7_CGAGGCTG-AAGGAGTA_L007


title: 157560571_2_A2_GGACTCCT-AAGGAGTA_L007


title: NM_ExE_K4.2


title: NM_Epi_K4.4

description:
NM_IF_EPI_segments.bed
NM_IF_EPI_K4.logFE.bw


title: NM_ExE_K4.1


title: NM_ExE_K27.2

value: H3K27me3 antibody (Diagnode, C15410195, Belgium)


title: 157560571_1_H9_TAAGGCGA-AAGGAGTA_L007


title: NM_ExE_K27.1


title: NM_Epi_K4.3


title: NM_ExE_input


title: NM_Epi_K27.3

description:
NM_IF_EPI_segments.bed
NM_IF_EPI_K27.logFE.bw


title: 157560571_2_A10_TAAGGCGA-CTAAGCCT_L007


title: NM_Epi_K27.4


title: 157560571_2_F5_CGTACTAG-AGAGTAGA_L008


title: NM_Epi_K4.2


title: 157560571_1_H4_CGAGGCTG-ACTGCATA_L007


title: NM_Epi_K27.1


title: 157560571_1_H5_AAGAGGCA-ACTGCATA_L007


title: 157560571_1_H3_GCTACGCT-ACTGCATA_L007


title: NM_Epi_K4.1


title: 157560571_1_H2_CAGAGAGG-ACTGCATA_L007


title: 157560571_2_A1_TCCTGAGC-AAGGAGTA_L007


title: NM_Epi_K27.2


title: NM_ICM_K27.7

description:
NM_IF_ICM_segments.bed
NM_IF_ICM_K27.logFE.bw


title: 157560571_1_H10_CGTACTAG-AAGGAGTA_L007


title: 157560571_1_G8_CGTACTAG-ACTGCATA_L007


title: IVF_TE_K27_input.7


title: IVF_ICM_K27_input.6


title: 157560571_1_H1_CTCTCTAC-ACTGCATA_L007


title: 157560571_1_G6_TAAGGCGA-ACTGCATA_L007


title: 157560571_1_H8_GTAGAGGA-ACTGCATA_L007


title: NM_Epi_input


title: 157560571_1_H11_AGGCAGAA-AAGGAGTA_L007


title: 157560571_1_G12_TAGGCATG-ACTGCATA_L007


title: NM_ICM_K27.8


title: 157560571_1_G3_CGAGGCTG-GTAAGGAG_L007


title: NM_ICM_input.6


title: NM_TE_K4.4

description:
NM_IF_TE_segments.bed
NM_IF_TE_K4.logFE.bw


title: NM_TE_K27.7

description:
NM_IF_TE_segments.bed
NM_IF_TE_K27.logFE.bw


title: 157560571_1_G11_GGACTCCT-ACTGCATA_L007


title: NM_TE_K27_input.7


title: 157560571_1_G9_AGGCAGAA-ACTGCATA_L007


title: 157560571_1_G4_AAGAGGCA-GTAAGGAG_L007


title: IVF_TE_K27.8

description:
IVF_vit_TE_segments.bed
IVF_vit_TE_K27.logFE.bw


title: 157560571_1_F9_TCCTGAGC-GTAAGGAG_L007


title: NM_TE_K27.8


title: IVF_ICM_K27.7

description:
IVF_vit_ICM_segments.bed
IVF_vit_ICM_K27.logFE.bw


title: IVF_ICM_K27.8


title: 157560571_1_G10_TCCTGAGC-ACTGCATA_L007


title: 157560571_1_G5_GTAGAGGA-GTAAGGAG_L007


title: NM_TE_K4.2


title: 157560571_1_G2_GCTACGCT-GTAAGGAG_L007


title: NM_TE_K4.1


title: 157560571_1_F7_CGTACTAG-GTAAGGAG_L007


title: IVF_TE_K27.7


title: 157560571_1_F4_AAGAGGCA-AGAGTAGA_L007


title: 157560571_1_F5_GTAGAGGA-AGAGTAGA_L007


title: NM_morula_K4.4

description:
NM_IF_morula_segments.bed
NM_IF_morula_K4.logFE.bw


title: 157560571_1_F3_CGAGGCTG-AGAGTAGA_L007


title: 157560571_1_F8_AGGCAGAA-GTAAGGAG_L007


title: 157560571_1_F2_GCTACGCT-AGAGTAGA_L007


title: 157560571_1_F1_CAGAGAGG-AGAGTAGA_L007


title: 157560571_1_F12_CTCTCTAC-GTAAGGAG_L007


title: NM_morula_K4.1


title: 157560571_1_F11_TAGGCATG-GTAAGGAG_L007


title: 157560571_1_E9_TCCTGAGC-AGAGTAGA_L007


title: 157560571_1_F6_TAAGGCGA-GTAAGGAG_L007


title: NM_ICM_K4.3

description:
NM_IF_ICM_segments.bed
NM_IF_ICM_K4.logFE.bw


title: NM_ICM_K4.2


title: NM_morula_K4.2


title: NM_morula_K27.3

description:
NM_IF_morula_segments.bed
NM_IF_morula_K27.logFE.bw


title: NM_ICM_K4.1


title: NM_morula_K4.3


title: NM_TE_K4.3


title: 157560571_1_E1_CGAGGCTG-TATCCTCT_L007


title: NM_morula_K27.1


title: NM_TE_input.2


title: 157560571_1_E12_CTCTCTAC-AGAGTAGA_L007


title: 157560571_1_F10_GGACTCCT-GTAAGGAG_L007


title: 157560571_1_E8_AGGCAGAA-AGAGTAGA_L007


title: NM_morula_K27.2


title: 157560571_1_E10_GGACTCCT-AGAGTAGA_L007


title: 157560571_1_D3_GCTACGCT-TATCCTCT_L007


title: 157560571_1_E7_CGTACTAG-AGAGTAGA_L007


title: 157560571_1_D2_CAGAGAGG-TATCCTCT_L007


title: NM_TE_input.1


title: 157560571_1_D1_CTCTCTAC-TATCCTCT_L007


title: 157560571_1_E6_TAAGGCGA-AGAGTAGA_L007


title: IVF_morula_K4.2

description:
IVF_vit_morula_segments.bed
IVF_vit_morula_K4.logFE.bw


title: NM_ICM_input.1


title: 157560571_1_E11_TAGGCATG-AGAGTAGA_L007


title: IVF_morula_K4.1


title: NM_morula_input.1


title: NM_ICM_input.2


title: 157560571_1_E3_AAGAGGCA-TATCCTCT_L007


title: IVF_TE_K4.3

description:
IVF_vit_TE_segments.bed
IVF_vit_TE_K4.logFE.bw


title: NM_ICM_input


title: IVF_morula_K27.2

description:
IVF_vit_morula_segments.bed
IVF_vit_morula_K27.logFE.bw


title: IVF_TE_K4.2


title: IVF_TE_K4.1


title: 157560571_1_B1_CGTACTAG-TATCCTCT_L007


title: 157560362_2_H7_AAGAGGCA-ACTGCATA_L008


title: 157560571_1_C2_TAGGCATG-TATCCTCT_L007


title: IVF_TE_input


title: IVF_morula_input.1


title: IVF_ICM_K4.2

description:
IVF_vit_ICM_segments.bed
IVF_vit_ICM_K4.logFE.bw


title: 157560571_1_E4_GTAGAGGA-TATCCTCT_L007


title: 157560362_2_G5_CTCTCTAC-ACTGCATA_L008


title: IVF_morula_K27.1


title: IVF_ICM_K4.1


title: 157560571_1_B2_AGGCAGAA-TATCCTCT_L007


title: 157560571_1_C1_GGACTCCT-TATCCTCT_L007


title: 157560571_1_B3_TCCTGAGC-TATCCTCT_L007


title: 157560362_2_G10_GCTACGCT-ACTGCATA_L008


title: IVF_TE_input.2


title: IVF_morula_K27.3


title: IVF_ICM_K4.3


title: 157560362_2_E1_CAGAGAGG-ACTGCATA_L008


title: 157560571_1_A12_TAAGGCGA-TATCCTCT_L007


title: 157560362_2_D9_GCTACGCT-GCGTAAGA_L001


title: IVF_ExE_K4.3

description:
IVF_vitBT_EXE_segments.bed
IVF_vitBT_EXE_K4.logFE.bw


title: IVF_ICM_input


title: IVF_ICM_input.3


title: IVF_ExE_K4.2


title: IVF_ExE_K4.1


title: 157560362_2_D8_GCTACGCT-AAGGAGTA_L001


title: 157560362_2_D7_CAGAGAGG-TATCCTCT_L002


title: IVF_ExE_K27.3

description:
IVF_vitBT_EXE_segments.bed
IVF_vitBT_EXE_K27.logFE.bw


title: IVF_ExE_K27.2


title: 157560362_2_D12_GCTACGCT-ACTGCATA_L001


title: 157560362_2_C7_TAGGCATG-CTAAGCCT_L001


title: 157560362_2_H1_CGAGGCTG-ACTGCATA_L008


title: IVF_Epi_K4.1

description:
IVF_vitBT_EPI_segments.bed
IVF_vitBT_EPI_K4.logFE.bw


title: 157560362_2_B7_CAGAGAGG-GCGTAAGA_L002


title: IVF_ExE_K27.1


title: 157560362_1_H9_TAGGCATG-CTCTCTAT_L001


title: IVF_Epi_K4.3


title: IVF_ExE_input.1


title: 157560362_2_C5_TAGGCATG-GTAAGGAG_L001


title: 157560362_1_H9_CGAGGCTG-CTCTCTAT_L007


title: 157560362_2_D6_CAGAGAGG-CTCTCTAT_L002


title: IVF_Epi_K27.1

description:
IVF_vitBT_EPI_segments.bed
IVF_vitBT_EPI_K27.logFE.bw


title: 157560362_1_H5_TAGGCATG-CTCTCTAT_L007


title: IVF_Epi_K27.3


title: 157560362_1_H4_GGACTCCT-CTCTCTAT_L007


title: 157560362_1_H6_CTCTCTAC-CTCTCTAT_L007


title: 157560362_1_H7_CAGAGAGG-CTCTCTAT_L007


title: 157560362_1_H3_TCCTGAGC-CTCTCTAT_L007


title: 157560362_1_H8_GCTACGCT-CTCTCTAT_L007


title: IVF_Epi_input


title: IVF_Epi_K27.2


title: 157560362_1_H2_AGGCAGAA-CTCTCTAT_L007


title: IVF_Epi_K4.2


title: 157560362_1_H1_CGTACTAG-CTCTCTAT_L007


title: IVF_Epi_K27.4


title: 157560362_1_H12_TAGGCATG-TATCCTCT_L001


title: K27me3-H

city: Daegu

first: Sehyun

last: Chae

address: 61, Cheomdan-ro

department: Neurovascular Unit Research Group

institute: Korea Brain Research Institute

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences (TruSeq universal and indexed adapters) were removed using the cutadapt software (version 2.7), and the remaining reads were aligned to the human genome (GRCh38) using BOWTIE2 software (version 2.2.6) with the default parameters.
After the alignment, duplicated reads were marked with Picard v1.76
Enriched peak regions were determined using MACS2 algorithm with the following parameters: -f BAMPE -g hs -p 1e-3 --keep-dup=1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited bed files contain the genomic coordinates and read coount of each peak.

source_name: adipocyte-derived stem cells (hADSCs)

extract_protocol:
The cells were lysed by radioimmunoprecipitation assay (RIPA) buffer and the cell lysates were collected by centrifugation. Immunoprecipitated DNA was isolated with selected antibodies.  Libraries were prepared according to Illumina's instructions. Briefly, 10 ng of DNA was end-repaired using a combination of Klenow polymerase and T4 polynucleotide kinase to yield a protruding 3-d'A' overhang. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 100~500 bp were band isolated from an agarose gel. The purified DNA was captured on agilent bioanalyzer. Libraries were sequencedHiSeq 2000 platform following the manufacturer's protocols.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: hADSCs


title: IVF_Epi_input.1


title: K27me3-C

value: Clioquinol (50 μM, 48 h)


title: K9me3-C


title: K27me3-N


title: 157560362_1_H11_GTAGAGGA-CTCTCTAT_L007


title: K9me3-N


title: K9me3-H


title: 157560362_1_G9_CGAGGCTG-GCGTAAGA_L007


title: 157560362_1_G8_TAGGCATG-AGAGTAGA_L001


title: K4me3-N


title: 157560362_1_G8_GCTACGCT-GCGTAAGA_L007


title: K4me3-H


title: K4me3-C


title: 157560362_1_G7_CAGAGAGG-GCGTAAGA_L007


title: 157560362_1_G6_CTCTCTAC-GCGTAAGA_L007


title: 157560362_1_G7_TAGGCATG-GCGTAAGA_L001


title: 157560362_1_H10_AAGAGGCA-CTCTCTAT_L007


title: 157560362_1_G4_GGACTCCT-GCGTAAGA_L007


title: 157560362_1_G5_TAGGCATG-GCGTAAGA_L007


title: 157560362_1_G3_TCCTGAGC-GCGTAAGA_L007


title: ILM_S6_FC1

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (Gencode, release 35, hg38, all) with RNA STAR Galaxy Version 2.7.5b with default parameters using the Gencode main annotation file (Gencode, release 38, https://www.gencodegenes.org/human/releases.html).
Three BAM files for each sample (one for each lane) were combined in one BAM file per sample using Merge BAM files (Galaxy Version 1.2.0).
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 with default parameters using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.4.1103, R Version 4.0.3).
Gene symbols and gene types were determined based on ENSEMBL release 101 (Human genes, download on 10/28/2020). Genes with zero reads in all samples were removed from analysis. Principal component analysis (PCA) was applied to check for potential batch effects. Differential gene expression was analyzed using the R package DESeq2 Version 1.30.1 with default parameters (Benjamini-Hochberg adjusted p-values, lfcShrink: type = “normal”).
Genome_build: hg38
Supplementary_files_format_and_content: normalized reads

source_name: Macular hole

extract_protocol: RNA extraction, library preparation and RNA sequencing were performed of 28 samples in total at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de). In short, membranes for RNA extraction were directly transferred into 50 µl RNAlaterTM (ThermoFisher). After the shipping, RNAlaterTM was replaced by RLT Plus buffer and the obtained tissue homogenized by vortexing for 30 seconds. Using gDNA Eliminator spin columns eliminated Genomic DNA contamination. After adding ethanol the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Lastly, total RNA was eluted in 12 μl of nuclease-free water. 750 pg total RNA was converted to first-stranded cDNA using the SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc.) 12 cycles of LD PCR were performed to amplify double-stranded cDNA followed by purification via magnetic bead clean-up. The Library was prepared according to Illumina Nextera XT Sample Preparation Guide (Illumina, Inc.). 150 pg of cDNA were tagged and fragmented via Nextera XT transposome. After adding partial adapters a limited-cycle PCR program was used to amplification resulting in multiplexed sequencing libraries. The libraries were quantified with the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc.). The Illumina TruSe SR Cluster Kit v3 was used for cluster generation on the cBot with pooled equimolar amounts of each library. The products were sequenced on a HiSeq1000 instrument with TruSeq SBS Kit v3 according to the Illumina HiSeq 1000 System User Guide. Illumina image analysis and base calling were recorded and converted to Fastq files via the CASAVA1.8.2/ bcl2fastq v2.18 software.

value: Macular hole


title: ILM_S5_FC1


title: 157560362_1_G2_AGGCAGAA-GCGTAAGA_L007


title: 157560362_1_G1_CGTACTAG-GCGTAAGA_L007


title: ILM_S4_FC1


title: ILM_S3_FC1


title: ILM_S2_FC1


title: 157560362_1_G11_GTAGAGGA-GCGTAAGA_L007


title: 157560362_1_G12_TAAGGCGA-CTCTCTAT_L007


title: ILM_S1_FC1


title: 157560362_1_G10_AAGAGGCA-GCGTAAGA_L007


title: 157560362_1_F9_TAGGCATG-AAGGAGTA_L001


title: MEFs, RelB.KO_01

city: Delhi

first: Soumen

last: Basak

state: Delhi

address: Aruna Asaf Ali Road

department: Immunology

country: India

institute: National Institute of Immunology

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: By using illumina Bead Array Reader version 3.7.9.27572

data_processing: The raw data was extracted from illumina's Genome studio software and the same used to check the quality of data. The data were normalized using quantile normalization method.

label: Standard Illumina protocol using Cy3.

source_name: Mouse Embyonic fibroblast

label_protocol: Biotinylated cRNA were prepared with TargetAmpTM- Nano labelling Kit for illumina Expression Beadchip

extract_protocol: Total RNA was isolated using  RNeasy Kit (QIAGEN) and on column DNase digestion was performed according to manufacturer protocol. Quality control was performed using Agilent Bioanalyzer.

tag: genotype

value: RelB KO

value: MEFs


title: Gliosis_S10_FC1

source_name: Macular pucker

value: Macular pucker


title: Gliosis_S8_FC1


title: 157560362_1_F9_CGAGGCTG-CTAAGCCT_L006


title: MEFs, WT_02

description: replicate 2

value: WT


title: 157560362_1_F8_GCTACGCT-CTAAGCCT_L006


title: MEFs, WT_01

description: replicate 1


title: MEFs, RelB.KO_02

description: replicate 2


title: ILM_S7_FC1


title: 157560362_1_F6_CTCTCTAC-CTAAGCCT_L006


title: Gliosis_S6_FC1


title: 157560362_1_F5_TAGGCATG-CTAAGCCT_L006


title: Gliosis_S7_FC1


title: 157560362_1_F7_CAGAGAGG-CTAAGCCT_L006


title: Gliosis_S5_FC1


title: 157560362_1_F3_GGACTCCT-CTAAGCCT_L006


title: Gliosis_S4_FC1


title: Gliosis_S3_FC1


title: 157560362_1_F2_TCCTGAGC-CTAAGCCT_L006


title: 157560362_1_F12_TAAGGCGA-GCGTAAGA_L007


title: 157560362_1_F1_AGGCAGAA-CTAAGCCT_L006


title: Gliosis_S9_FC1


title: Gliosis_S1_FC1


title: 157560362_1_F10_AAGAGGCA-CTAAGCCT_L006


title: PVR S9

source_name: PVR

value: PVR


title: 157560362_1_E9_AAGAGGCA-AAGGAGTA_L006


title: 157560362_1_E8_CGAGGCTG-AAGGAGTA_L006


title: 157560362_1_F11_TAGGCATG-ACTGCATA_L001


title: PVR S7


title: PVR S8


title: PVR S5


title: PVR S3


title: 157560362_1_E6_CAGAGAGG-AAGGAGTA_L006


title: Gliosis_S2_FC1


title: S7WT_p6cell

city: Stockholm

first: Menghan

last: Wang

state: please select...

address: Karolinska Vägen 6

country: Sweden

institute: Karolinska Institute

data_processing:
used drop-seq pipeline to do the alignment, put barcode and UMI information into tag, trimmed adapter, 5’ primer and 3’ polyA from reads.
trimmed reads aligned to human genome with transcriptome annotation (GRCh38, ensemble 93) using STAR (version 2.6.0a).
merged tags with aligned SAM file. Repaired substitution and indel errors of barcodes.
got digital gene expression matrix from barcode-UMI-gene triplets.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each sample

source_name: S7WT_pancreatic beta cell

growth_protocol: ES cell–derived pancreatic β cells were routinely generated by  d 12 adherent differentiation cultures on Matrigel coated plastic 6-Well plate in RPMI1640 and DMEM medium  supplemented with 10ng/ml  ActivinA and NOGGIN.Then,the cells were  generated by  d 20 suspension culture on the low-attachment plate.

extract_protocol:
We performed single cell RNA-seq in  WT and KO β cells at both S6 (immature) and S7 (mature) stages sorted by fluorescence-activated cell sorter (FACS) as double-positive for both INS(GFP) and NKX6.1(mCherry)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hESC-derived pancreatic beta cell

value: wild type

tag: cell stage

value: S7 (mature)


title: 157560362_1_E12_CGTACTAG-CTAAGCCT_L006


title: PVR S6


title: 157560362_1_E2_TCCTGAGC-AAGGAGTA_L006


title: 157560362_1_E12_CTCTCTAC-CTAAGCCT_L002


title: 157560362_1_E4_TAGGCATG-AAGGAGTA_L006


title: 157560362_1_E1_AGGCAGAA-AAGGAGTA_L006


title: PVR S2


title: PVR S4


title: 157560362_1_E3_GGACTCCT-AAGGAGTA_L006


title: PVR S1


title: 157560362_1_F11_GTAGAGGA-CTAAGCCT_L006


title: 157560362_1_E10_GTAGAGGA-AAGGAGTA_L006


title: PVR S10


title: 157560362_1_E7_GCTACGCT-AAGGAGTA_L006


title: 157560362_1_E11_TAAGGCGA-CTAAGCCT_L006


title: 157560362_1_E5_CTCTCTAC-AAGGAGTA_L006


title: S7KO_p5cell

source_name: S7KO_pancreatic beta cell

value: ZnT8 KO


title: S7WT_p2cell


title: S7KO_p4cell


title: 157560362_1_D4_CAGAGAGG-GTAAGGAG_L001

value: PBMC


title: 157560362_1_E10_CAGAGAGG-CTAAGCCT_L001

value: CD4 T cells


title: S7WT_p1cell


title: S7WT_p3cell


title: 157560362_1_D2_AAGAGGCA-ACTGCATA_L006

value: RV144 vaccine regimen


title: S6WT_p2cell

source_name: S6WT_pancreatic beta cell

value: S6 (immature)


title: S7WT_p4cell


title: S6WT_p1cell


title: 157560362_1_D5_CGTACTAG-AAGGAGTA_L006


title: S7KO_p3cell


title: S6WT_p3cell


title: 157560362_1_D3_GTAGAGGA-ACTGCATA_L006


title: 157560362_1_D6_CTCTCTAC-AAGGAGTA_L002


title: S6K0_p2cell

source_name: S6K0_pancreatic beta cell


title: S7KO_p6cell


title: S7KO_p1cell


title: 157560362_1_D3_CAGAGAGG-CTCTCTAT_L001

source_name: PBMC


title: 157560362_1_D1_CGAGGCTG-ACTGCATA_L006


title: 157560362_1_C9_TAGGCATG-ACTGCATA_L006


title: 157560362_1_C4_TAAGGCGA-ACTGCATA_L006


title: 157560362_1_C5_CGTACTAG-ACTGCATA_L006


title: 157560362_1_C7_TCCTGAGC-ACTGCATA_L006


title: S6K0_p3cell


title: S6K0_p1cell


title: Prdm16-overexpressing Neural Stem Cells

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Reads were QC filtered and aligned with Bowtie version 2011-03-15
Peak-calling was performed with MACS v1.4 version 2013-02-19
Quantitate Coverage in Regions was performed with GeneProf version 2.151202
Gene calling was performed with GeneProf version 2.151202
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: E14.5 Forebrain

extract_protocol: Genomic DNA was isolated with QIAamp DNA Mini Kit (QIAGEN). DNA sequencing libraries were prepared using the TruSeq DNA LT Sample Prep Kit

value: neural stem cell

value: Prdm16 overexpressing


title: 157560362_1_C12_GCTACGCT-ACTGCATA_L006


title: Wild Type Neural Stem Cells


title: 157560362_1_C8_GGACTCCT-ACTGCATA_L006


title: 157560362_1_C11_CAGAGAGG-ACTGCATA_L006


title: S7KO_p2cell


title: 157560362_1_C10_CTCTCTAC-ACTGCATA_L006


title: 157560362_1_C6_AGGCAGAA-ACTGCATA_L006


title: 157560362_1_B8_CAGAGAGG-TATCCTCT_L001


title: 157560362_1_D4_TAAGGCGA-AAGGAGTA_L006


title: 157560362_1_A9_CAGAGAGG-GTAAGGAG_L006


title: RMS3-#2

city: Tsu

first: Noboru

last: Suzuki

state: Mie

address: 2-174 Edobashi

department: Department of Animal Functional Genomics of Advanced Science Research Promotion Center

country: Japan

institute: Organization for Research Initiative and Promotion at Mie University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentationand 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole mouse Genome Oligo Microarrays (4x44K)  17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software ver 8 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Tumors by subcutaneous injection of the PRMS cell line, RMS3, 2w after injection, Sample 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the Quick amp Labeling  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: 1 × 10^6 RMS3 cells were suspended 200µl PBS and injected in subcutaneous of a C57BL/6J mouse. At two weeks after injection, metastatic tumors were harvested.

value: tumor

tag: host strain

tag: Sex

value: male

tag: cell line source

value: PRMS cell line

tag: time point

value: At two weeks after injection


title: ISPY2_988665

city: San Francisco

first: Denise

middle: M

last: Wolf

state: CA

address: 2340 Sutter st

institute: University of California, San Francisco

hyb_protocol: Hybridization was performed by Agendia Inc (Irvine, CA). This company is referenced by the platforms used: GPL20078 and GPL30494 (updated version of GPL16233).

scan_protocol: Scanning was performed by Agendia Inc (Irvine, CA).

data_processing:
For each array, gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to its 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out; and a fixed value of 9.5 was added to avoid negative values. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified. Expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct raw files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding a normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes. The linear adjustment factors and updated probe annotation files per platform are provided, as is the ComBat-normalized data we used in our analysis (supplemental file "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt").
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt: Normalized, gene-level, batch-/platform- adjusted pre-treatment Agilent 44K expression data for patients from 10 arms of the neoadjuvant I-SPY 2 platform trial for early stage, aggressive breast cancer (n=988 samples for 987 patients). This is the dataset we used in our pan-arm analysis, and constitutes part of the I-SPY2-990 mRNA/RPPA Data Resource. To derive this matrix, probeset level expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were mean-collapsed by gene and combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct new files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding the resulting normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2_LinearFit_forCombiningExp_20078.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agendia32627_DPv1.14_SCFGplus [gene-collapsed using annotation GPL20078] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt, the normalized expression matrix in the I-SPY2-990 data resource.
ISPY2_LinearFit_forCombiningExp_GPL30493_wasGPL16233.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233)] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt.
ProbeAnnotation_ISPY2Edit_GPL30493_wasGPL16233.txt: This is the probeset annotation file for GPL30493, a minor update of GPL16233. For each probeset ID (row), the associated gene name, systematic name and DNA sequence is described (columns).

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: Labeling was performed by Agendia Inc (Irvine, CA).

extract_protocol: Extraction was performed by Agendia Inc (Irvine, CA).

tag: patient id

value: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

tag: pcr

tag: arm

value: Paclitaxel + Ganetespib

tag: adjustment method

value: ComBat Adjust


title: ISPY2_987995

value: Paclitaxel + AMG 386


title: ISPY2_995480

value: Paclitaxel + Pertuzumab + Trastuzumab


title: ISPY2_999264


title: 157560362_1_B11_CAGAGAGG-GCGTAAGA_L001

tag: cell type

tag: vaccination


title: 157560362_1_B6_CAGAGAGG-AGAGTAGA_L001


title: ISPY2_983841


title: 157560362_1_A6_GGACTCCT-GTAAGGAG_L006


title: 157560362_1_A12_AAGAGGCA-GTAAGGAG_L006


title: 157560362_1_A11_CGAGGCTG-GTAAGGAG_L006


title: ISPY2_987728

value: Paclitaxel + Ganitumab


title: ISPY2_987914

value: Paclitaxel


title: 157560362_1_A6_CAGAGAGG-AAGGAGTA_L001

value: PBMC


title: ISPY2_992609


title: 157560362_1_C3_GTAGAGGA-GTAAGGAG_L006

value: CD4 T cells


title: ISPY2_990443

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: 157560362_1_A8_CTCTCTAC-GTAAGGAG_L006

value: RV144 vaccine regimen


title: ISPY2_986734


title: ISPY2_991818


title: ISPY2_999733

value: Paclitaxel + MK-2206


title: 157560292_2_H8_AAGAGGCA-AGAGTAGA_L006


title: Prdm16-null Neural Stem Cells

value: neural stem cell

value: Prdm16 null


title: ISPY2_981461

value: T-DM1 + Pertuzumab


title: RMS3-#1

source_name: Tumors by subcutaneous injection of the PRMS cell line, RMS3, 2w after injection, Sample 1

value: tumor

value: male

value: PRMS cell line

value: At two weeks after injection


title: ISPY2_974181

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + AMG 386

value: ComBat Adjust


title: ISPY2_982505

value: Paclitaxel + Pertuzumab + Trastuzumab


title: 157560292_2_H3_TAGGCATG-AGAGTAGA_L006

value: PBMC


title: ISPY2_963604


title: 157560292_2_H5_CAGAGAGG-AGAGTAGA_L006

value: CD4 T cells


title: ISPY2_962664

value: Paclitaxel


title: 157560362_1_A10_GCTACGCT-GTAAGGAG_L006


title: 157560362_1_A5_TCCTGAGC-GTAAGGAG_L006


title: 157560292_2_H9_GTAGAGGA-AGAGTAGA_L006


title: ISPY2_981664


title: ISPY2_971492


title: 157560362_1_A7_TAGGCATG-GTAAGGAG_L006


title: ISPY2_960490

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: ISPY2_982086


title: 157560292_2_H7_CGAGGCTG-AGAGTAGA_L006

value: RV144 vaccine regimen


title: ISPY2_960029


title: ISPY2_966016

value: Paclitaxel + Ganitumab


title: ISPY2_965265


title: 157560292_2_G4_AAGAGGCA-TATCCTCT_L006


title: 157560292_2_G9_GTAGAGGA-TATCCTCT_L006


title: ISPY2_962153

value: Paclitaxel + AMG 386 + Trastuzumab


title: 157560292_2_H10_TAAGGCGA-GTAAGGAG_L006


title: ISPY2_963303


title: 157560292_2_H6_GCTACGCT-AGAGTAGA_L006


title: 157560292_2_H1_TCCTGAGC-AGAGTAGA_L006


title: ISPY2_970839


title: ISPY2_950742


title: ISPY2_955035


title: 157560292_2_H12_AGGCAGAA-GTAAGGAG_L006


title: 157560292_2_G1_GCTACGCT-TATCCTCT_L006


title: 157560292_2_H4_CTCTCTAC-AGAGTAGA_L006


title: 157560292_2_G2_CGAGGCTG-TATCCTCT_L006


title: ISPY2_949444


title: ISPY2_950131


title: 157560292_2_G11_CGTACTAG-AGAGTAGA_L006


title: 157560292_2_G12_AGGCAGAA-AGAGTAGA_L006


title: 157560292_2_F9_GGACTCCT-TATCCTCT_L006


title: ISPY2_947398

value: T-DM1 + Pertuzumab


title: 157560292_2_G10_TAAGGCGA-AGAGTAGA_L006


title: ISPY2_943633


title: ISPY2_941926


title: 157560292_2_F6_AGGCAGAA-TATCCTCT_L006


title: 157560292_2_F7_TCCTGAGC-TATCCTCT_L006


title: 157560292_2_F4_CGTACTAG-TATCCTCT_L006


title: 157560292_2_H11_CGTACTAG-GTAAGGAG_L006


title: 157560292_2_F3_TAAGGCGA-TATCCTCT_L006


title: ISPY2_934906


title: ISPY2_935460


title: 157560292_2_F2_GTAGAGGA-CTCTCTAT_L006


title: ISPY2_953885


title: ISPY2_940186

value: Paclitaxel + Ganetespib


title: 157560292_2_F1_AAGAGGCA-CTCTCTAT_L006


title: 157560292_2_F12_CAGAGAGG-TATCCTCT_L006


title: ISPY2_929391


title: ISPY2_930903


title: 157560292_2_H2_GGACTCCT-AGAGTAGA_L006


title: ISPY2_929980

value: Paclitaxel + MK-2206 + Trastuzumab


title: 157560292_2_E9_CTCTCTAC-CTCTCTAT_L006


title: ISPY2_928815


title: 157560292_2_F11_CTCTCTAC-TATCCTCT_L006


title: 157560292_2_E4_TAGGCATG-CTCTCTAT_L006


title: 157560292_2_E3_GGACTCCT-CTCTCTAT_L006


title: ISPY2_928446


title: ISPY2_943879


title: ISPY2_924895


title: ISPY2_924868


title: ISPY2_928170


title: 157560292_2_E2_TCCTGAGC-CTCTCTAT_L006


title: ISPY2_938719


title: 157560292_2_E12_CGAGGCTG-CTCTCTAT_L006


title: ISPY2_924071


title: 157560292_2_E11_GCTACGCT-CTCTCTAT_L006


title: ISPY2_922872


title: 157560292_2_F10_TAGGCATG-TATCCTCT_L006


title: ISPY2_918979


title: 157560292_2_E10_CAGAGAGG-CTCTCTAT_L006


title: 157560292_2_D9_AAGAGGCA-GCGTAAGA_L006


title: 157560292_2_D8_CGAGGCTG-GCGTAAGA_L006


title: ISPY2_917762


title: 157560292_2_D3_GCTACGCT-GCGTAAGA_L006


title: ISPY2_916586


title: ISPY2_914968


title: 157560292_2_D2_CAGAGAGG-GCGTAAGA_L006


title: ISPY2_912836


title: ISPY2_913527


title: 157560292_2_E1_AGGCAGAA-CTCTCTAT_L006


title: ISPY2_906795

value: Paclitaxel + Trastuzumab


title: ISPY2_910188


title: 157560292_2_D12_CGTACTAG-CTCTCTAT_L006


title: 157560292_2_D11_TAAGGCGA-CTCTCTAT_L006


title: 157560292_2_D10_GTAGAGGA-GCGTAAGA_L006


title: 157560292_2_D1_CTCTCTAC-GCGTAAGA_L006


title: 157560292_2_C1_AGGCAGAA-GCGTAAGA_L006


title: 157560292_2_C2_TCCTGAGC-GCGTAAGA_L006


title: ISPY2_923968


title: 157560292_2_C11_GGACTCCT-GCGTAAGA_L006


title: 157560292_2_B9_TAAGGCGA-GCGTAAGA_L006


title: ISPY2_901705


title: ISPY2_899692


title: ISPY2_899381


title: 157560292_2_B2_GTAGAGGA-CTAAGCCT_L005


title: ISPY2_896852


title: ISPY2_896939


title: 157560292_2_A9_CGAGGCTG-CTAAGCCT_L005


title: ISPY2_898618


title: 157560292_2_B12_CGTACTAG-GCGTAAGA_L006


title: 157560292_2_A5_GCTACGCT-CTAAGCCT_L005


title: ISPY2_905264


title: ISPY2_896621


title: ISPY2_892390


title: ISPY2_901807


title: 156560566_3_H6_CAGAGAGG-CTAAGCCT_L005


title: ISPY2_893874


title: 157560292_2_C12_TAGGCATG-GCGTAAGA_L006


title: 156560566_3_H1_GGACTCCT-CTAAGCCT_L005


title: 156560566_3_H5_CTCTCTAC-CTAAGCCT_L005


title: ISPY2_894673


title: 156560566_3_H3_TAGGCATG-CTAAGCCT_L005


title: ISPY2_895653


title: 156560566_2_H9_TAAGGCGA-CTAAGCCT_L005


title: ISPY2_890372


title: ISPY2_900959


title: 157560292_2_B1_AAGAGGCA-CTAAGCCT_L005


title: 156560566_2_H8_GTAGAGGA-AAGGAGTA_L005


title: ISPY2_887594

value: Paclitaxel + MK-2206


title: ISPY2_889721

value: Breast cancer biopsy (pre-treatment)


title: 156560566_2_H6_CGAGGCTG-AAGGAGTA_L005


title: ISPY2_885871


title: ISPY2_884266


title: 156560566_2_H4_CAGAGAGG-AAGGAGTA_L005


title: 156560566_2_H3_CTCTCTAC-AAGGAGTA_L005


title: ISPY2_882553

value: Paclitaxel + AMG 386


title: ISPY2_884011

value: ComBat Adjust


title: 156560566_2_H5_GCTACGCT-AAGGAGTA_L005


title: 156560566_2_H7_AAGAGGCA-AAGGAGTA_L005


title: ISPY2_879224


title: 156560566_2_H12_TCCTGAGC-CTAAGCCT_L005


title: ISPY2_877463


title: 156560566_2_H11_AGGCAGAA-CTAAGCCT_L005


title: 156560566_2_H2_TAGGCATG-AAGGAGTA_L005


title: ISPY2_875089


title: ISPY2_866660


title: 156560566_2_G8_TAAGGCGA-AAGGAGTA_L005


title: 156560566_2_H10_CGTACTAG-CTAAGCCT_L005


title: 156560566_2_G9_CGTACTAG-AAGGAGTA_L005


title: ISPY2_865416


title: ISPY2_870077


title: 156560566_2_G5_CGAGGCTG-ACTGCATA_L005


title: 156560566_2_G6_AAGAGGCA-ACTGCATA_L005


title: 156560566_2_G7_GTAGAGGA-ACTGCATA_L005


title: ISPY2_863161


title: 156560566_2_G4_GCTACGCT-ACTGCATA_L005


title: 156560566_2_G3_CAGAGAGG-ACTGCATA_L005


title: ISPY2_861745


title: 156560566_2_G1_TAGGCATG-ACTGCATA_L005


title: ISPY2_882538


title: 156560566_2_G2_CTCTCTAC-ACTGCATA_L005


title: ISPY2_860243


title: ISPY2_873686


title: ISPY2_862244

value: Paclitaxel + Pertuzumab + Trastuzumab


title: ISPY2_857165


title: 156560566_2_G11_TCCTGAGC-AAGGAGTA_L005

value: PBMC


title: ISPY2_847272


title: ISPY2_848003


title: ISPY2_847753


title: ISPY2_856159


title: 156560566_2_F9_CGTACTAG-ACTGCATA_L005

value: CD4 T cells


title: ISPY2_860901


title: ISPY2_851488


title: 156560566_2_F5_CGAGGCTG-GTAAGGAG_L005


title: 156560566_2_G10_AGGCAGAA-AAGGAGTA_L005


title: ISPY2_851223


title: 156560566_2_F6_AAGAGGCA-GTAAGGAG_L005


title: ISPY2_848371


title: 156560566_2_F3_CAGAGAGG-GTAAGGAG_L005


title: 156560566_2_F7_GTAGAGGA-GTAAGGAG_L005


title: ISPY2_845147


title: 156560566_2_F2_CTCTCTAC-GTAAGGAG_L005


title: 156560566_2_F8_TAAGGCGA-ACTGCATA_L005


title: ISPY2_845783


title: 156560566_2_F4_GCTACGCT-GTAAGGAG_L005


title: ISPY2_843554

value: Paclitaxel


title: 156560566_2_F1_TAGGCATG-GTAAGGAG_L005


title: 156560566_2_F11_TCCTGAGC-ACTGCATA_L005


title: ISPY2_845079


title: 156560566_2_G12_GGACTCCT-AAGGAGTA_L005


title: ISPY2_846156


title: ISPY2_841336


title: ISPY2_839274


title: 156560566_2_F12_GGACTCCT-ACTGCATA_L005


title: ISPY2_834418


title: 156560566_2_E9_CGTACTAG-GTAAGGAG_L005


title: 156560566_2_F10_AGGCAGAA-ACTGCATA_L005


title: 156560566_2_E8_TAAGGCGA-GTAAGGAG_L005


title: ISPY2_831702


title: ISPY2_825363


title: ISPY2_824512


title: ISPY2_829491


title: 156560566_2_E3_CAGAGAGG-AGAGTAGA_L005


title: 156560566_2_E5_CGAGGCTG-AGAGTAGA_L005


title: 156560566_2_E5_CTCTCTAC-ACTGCATA_L002


title: ISPY2_831848


title: 156560566_2_E2_CTCTCTAC-AGAGTAGA_L005


title: ISPY2_830486


title: ISPY2_832056

value: Paclitaxel + Pembrolizumab


title: 156560566_2_E12_GGACTCCT-GTAAGGAG_L005


title: 156560566_2_E11_TCCTGAGC-GTAAGGAG_L005


title: 156560566_2_E7_GTAGAGGA-AGAGTAGA_L005


title: 156560566_2_E4_CAGAGAGG-ACTGCATA_L001


title: 156560566_2_E6_AAGAGGCA-AGAGTAGA_L005


title: ISPY2_830958

value: Linear Adjustment Factor


title: ISPY2_824350


title: ISPY2_823618


title: ISPY2_820807


title: 156560566_2_E1_TAGGCATG-AGAGTAGA_L005

value: RV144 vaccine regimen


title: ISPY2_824234


title: ISPY2_820348


title: 156560566_2_D8_TAAGGCGA-AGAGTAGA_L005


title: 156560566_2_E10_AGGCAGAA-GTAAGGAG_L005


title: 156560566_2_D7_GTAGAGGA-TATCCTCT_L005


title: 156560566_2_D9_CGTACTAG-AGAGTAGA_L005


title: ISPY2_815493


title: 156560566_2_E4_GCTACGCT-AGAGTAGA_L005


title: 156560566_2_D6_AAGAGGCA-TATCCTCT_L005


title: ISPY2_805136


title: ISPY2_808714


title: ISPY2_804979

value: Paclitaxel + Ganitumab


title: 156560566_2_D3_CAGAGAGG-TATCCTCT_L005


title: ISPY2_810965


title: ISPY2_802105


title: 156560566_2_D4_GCTACGCT-TATCCTCT_L005


title: ISPY2_802308


title: ISPY2_801641


title: ISPY2_800447


title: 156560566_2_D10_AGGCAGAA-AGAGTAGA_L005


title: 156560566_2_D11_TCCTGAGC-AGAGTAGA_L005


title: 156560566_2_D2_CTCTCTAC-TATCCTCT_L005


title: ISPY2_803677


title: ISPY2_798604


title: ISPY2_797639


title: ISPY2_797499


title: 156560566_2_D12_GGACTCCT-AGAGTAGA_L005


title: 156560566_2_D1_TAGGCATG-TATCCTCT_L005


title: ISPY2_799149


title: ISPY2_796558


title: 156560566_2_C9_CGTACTAG-TATCCTCT_L005


title: 156560566_2_C7_GTAGAGGA-CTCTCTAT_L005


title: 156560566_2_C8_TAAGGCGA-TATCCTCT_L005


title: 156560566_2_C5_AAGAGGCA-CTCTCTAT_L005


title: ISPY2_795996


title: 156560566_2_D5_CGAGGCTG-TATCCTCT_L005


title: ISPY2_804233


title: ISPY2_794128


title: ISPY2_793684


title: 156560566_2_C3_GCTACGCT-CTCTCTAT_L005


title: 156560566_2_C2_CAGAGAGG-CTCTCTAT_L005


title: ISPY2_792181


title: 156560566_2_C1_CTCTCTAC-CTCTCTAT_L005


title: ISPY2_793155


title: ISPY2_792412


title: 156560566_2_B8_AGGCAGAA-CTCTCTAT_L005


title: 156560566_2_B5_GTAGAGGA-GCGTAAGA_L005


title: ISPY2_791321


title: 156560566_2_C12_GGACTCCT-TATCCTCT_L005


title: ISPY2_787415


title: 156560566_2_B9_TCCTGAGC-CTCTCTAT_L005


title: ISPY2_786753


title: ISPY2_788149

value: Paclitaxel + AMG 386 + Trastuzumab


title: 156560566_2_C11_TCCTGAGC-TATCCTCT_L005


title: ISPY2_790397

value: T-DM1 + Pertuzumab


title: ISPY2_786480

value: Paclitaxel + Ganetespib


title: 156560566_2_C4_CGAGGCTG-CTCTCTAT_L005


title: 156560566_2_B6_TAAGGCGA-CTCTCTAT_L005


title: 156560566_2_B7_CGTACTAG-CTCTCTAT_L005


title: ISPY2_783764


title: 156560566_2_B3_CGAGGCTG-GCGTAAGA_L005


title: ISPY2_783771


title: 156560566_2_B4_AAGAGGCA-GCGTAAGA_L005


title: 156560566_2_B2_GCTACGCT-GCGTAAGA_L005


title: ISPY2_783427


title: ISPY2_786003


title: 156560566_2_C10_AGGCAGAA-TATCCTCT_L005


title: 156560566_2_B1_CAGAGAGG-GCGTAAGA_L005


title: ISPY2_781642


title: 156560566_2_B12_TAGGCATG-CTCTCTAT_L005


title: 156560566_2_B10_GGACTCCT-CTCTCTAT_L005


title: ISPY2_780272


title: 156560566_2_A9_TCCTGAGC-GCGTAAGA_L005


title: ISPY2_779739

value: Paclitaxel + MK-2206 + Trastuzumab


title: ISPY2_778527


title: ISPY2_774840


title: 156560566_2_A2_GCTACGCT-CTAAGCCT_L004


title: ISPY2_771151


title: ISPY2_767934


title: 156560566_2_A7_CGTACTAG-GCGTAAGA_L005


title: ISPY2_768214


title: 156560566_2_A6_TAAGGCGA-GCGTAAGA_L005


title: 156560566_2_A5_GTAGAGGA-CTAAGCCT_L004


title: ISPY2_767081


title: ISPY2_769972


title: 156560566_2_A4_AAGAGGCA-CTAAGCCT_L004


title: ISPY2_760901


title: ISPY2_765773


title: 156560566_2_A12_CTCTCTAC-GCGTAAGA_L005


title: 156560566_2_A10_GGACTCCT-GCGTAAGA_L005


title: 156560566_2_A11_TAGGCATG-GCGTAAGA_L005


title: 156560566_2_A8_AGGCAGAA-GCGTAAGA_L005


title: 156560566_1_H9_TCCTGAGC-CTAAGCCT_L004


title: ISPY2_760011


title: ISPY2_753109


title: 156560566_1_H8_AGGCAGAA-CTAAGCCT_L004


title: 156560566_2_A1_CAGAGAGG-CTAAGCCT_L004


title: 156560566_1_H7_CGTACTAG-CTAAGCCT_L004


title: 156560566_1_H6_TAAGGCGA-CTAAGCCT_L004


title: ISPY2_759418


title: ISPY2_752469


title: 156560566_2_A3_CGAGGCTG-CTAAGCCT_L004


title: ISPY2_748583


title: 156560566_1_H5_GTAGAGGA-AAGGAGTA_L004


title: 156560566_1_H3_CGAGGCTG-AAGGAGTA_L004


title: ISPY2_755914


title: 156560566_1_H4_AAGAGGCA-AAGGAGTA_L004


title: 156560566_1_H2_GCTACGCT-AAGGAGTA_L004


title: 156560566_1_H1_CAGAGAGG-AAGGAGTA_L004


title: ISPY2_748611


title: ISPY2_752372


title: ISPY2_735673


title: ISPY2_738041


title: 156560566_1_H12_CTCTCTAC-CTAAGCCT_L001


title: ISPY2_741535


title: ISPY2_734997


title: 156560566_1_H11_TAGGCATG-CTAAGCCT_L004


title: ISPY2_733276


title: 156560566_1_H10_GGACTCCT-CTAAGCCT_L004


title: 156560566_1_G9_TCCTGAGC-AAGGAGTA_L004


title: ISPY2_745633


title: ISPY2_729732


title: 156560566_1_G8_AGGCAGAA-AAGGAGTA_L004


title: ISPY2_732137


title: ISPY2_728287


title: ISPY2_736721


title: 156560566_1_H12_CTCTCTAC-CTAAGCCT_L004


title: 156560566_1_G7_CGTACTAG-AAGGAGTA_L004


title: ISPY2_728149


title: 156560566_1_G4_AAGAGGCA-ACTGCATA_L004


title: ISPY2_726940


title: 156560566_1_G6_TAAGGCGA-AAGGAGTA_L004


title: ISPY2_727255


title: ISPY2_719713


title: 156560566_1_G1_CAGAGAGG-ACTGCATA_L004


title: ISPY2_727804


title: 156560566_1_G10_GGACTCCT-AAGGAGTA_L004


title: 156560566_1_F9_TCCTGAGC-ACTGCATA_L004


title: 156560566_1_G11_TAGGCATG-AAGGAGTA_L004


title: ISPY2_712785


title: 156560566_1_G3_CGAGGCTG-ACTGCATA_L004


title: 156560566_1_G2_GCTACGCT-ACTGCATA_L004


title: 156560566_1_G5_GTAGAGGA-ACTGCATA_L004


title: ISPY2_724384


title: 156560566_1_G12_CTCTCTAC-AAGGAGTA_L004


title: 156560566_1_F5_GTAGAGGA-GTAAGGAG_L004


title: ISPY2_724293


title: 156560566_1_F5_CTCTCTAC-GTAAGGAG_L001


title: ISPY2_712276


title: ISPY2_706169


title: 156560566_1_F4_CTCTCTAC-CTCTCTAT_L001


title: ISPY2_711476


title: 156560566_1_F7_CGTACTAG-ACTGCATA_L004


title: 156560566_1_F8_AGGCAGAA-ACTGCATA_L004


title: ISPY2_706639


title: ISPY2_706418


title: ISPY2_712917


title: 156560566_1_F4_AAGAGGCA-GTAAGGAG_L004


title: 156560566_1_F6_TAAGGCGA-ACTGCATA_L004


title: ISPY2_703401


title: ISPY2_705381


title: 156560566_1_F2_GCTACGCT-GTAAGGAG_L004


title: ISPY2_703455


title: 156560566_1_F3_CGAGGCTG-GTAAGGAG_L004


title: ISPY2_695521


title: ISPY2_701790


title: 156560566_1_F1_CAGAGAGG-GTAAGGAG_L004


title: ISPY2_721099


title: 156560566_1_F12_CTCTCTAC-ACTGCATA_L004


title: ISPY2_692885


title: ISPY2_691753


title: 156560566_1_F11_TAGGCATG-ACTGCATA_L004


title: 156560566_1_F10_GGACTCCT-ACTGCATA_L004


title: ISPY2_700549


title: 156560566_1_E9_TCCTGAGC-GTAAGGAG_L004


title: ISPY2_690410


title: 156560566_1_E8_AGGCAGAA-GTAAGGAG_L004


title: ISPY2_690089


title: ISPY2_689480


title: 156560566_1_E6_TAAGGCGA-GTAAGGAG_L004


title: 156560566_1_E7_CGTACTAG-GTAAGGAG_L004


title: ISPY2_689452


title: 156560566_1_E5_GTAGAGGA-AGAGTAGA_L004


title: ISPY2_689188


title: 156560566_1_E4_AAGAGGCA-AGAGTAGA_L004


title: Healthy donor, HD19

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchips using standard Illumina protocol.

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

data_processing:
Data was processed with the minfi package in R
Normalization was performed with the Noob method, followed by the Quantile method (minfi)

label: Cy3, Cy5

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from monocytes using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions

tag: donor

tag: age

value: F

tag: diagnosis baseline

value: HD

tag: prognosis

value: Peripheral blood

value: monocytes


title: Healthy donor, VAS83

value: M

tag: tissue


title: ISPY2_689076

value: Breast cancer biopsy (pre-treatment)

value: ComBat Adjust


title: Healthy donor, M5


title: 156560566_1_E3_CGAGGCTG-AGAGTAGA_L004

value: PBMC

value: CD4 T cells


title: UA17-S-01

source_name: synovial fluid

value: UA

value: Good

value: Synovial fluid


title: Healthy donor, M3


title: Healthy donor, CL06


title: UA19-S-01

value: Poor


title: Healthy donor, CL03


title: UA15-S-01


title: Healthy donor, M1


title: ISPY2_688955

value: Paclitaxel


title: UA10-S-01


title: Healthy donor, M2


title: 156560566_1_E1_CAGAGAGG-AGAGTAGA_L004

value: RV144 vaccine regimen


title: UA13-S-01


title: Healthy donor, CL07


title: 156560566_1_E2_GCTACGCT-AGAGTAGA_L004


title: Healthy donor, CL02


title: UA20-S-01


title: ISPY2_688291

value: Paclitaxel + AMG 386


title: UA11-S-01


title: ISPY2_687733

value: Paclitaxel + Ganetespib


title: 156560566_1_E12_CTCTCTAC-GTAAGGAG_L004


title: ISPY2_687288

value: T-DM1 + Pertuzumab


title: UA12-S-01


title: 156560566_1_E11_TAGGCATG-GTAAGGAG_L004


title: ISPY2_685795

value: Paclitaxel + AMG 386 + Trastuzumab


title: UA14-S-01


title: UA06-S-01


title: Healthy donor, CL05

value: F

value: HD

value: Peripheral blood


title: 156560566_1_E10_GGACTCCT-GTAAGGAG_L004


title: ISPY2_685182

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Pertuzumab + Trastuzumab


title: Healthy donor, CL08

value: monocytes


title: UA07-S-01


title: 156560566_1_D9_TCCTGAGC-AGAGTAGA_L004

value: PBMC

value: CD4 T cells


title: UA08-S-01

value: M

value: UA

value: Good


title: Healthy donor, M4


title: 156560566_1_D8_AGGCAGAA-AGAGTAGA_L004


title: ISPY2_683457

value: Paclitaxel + Ganitumab

value: ComBat Adjust


title: 156560566_1_D7_CGTACTAG-AGAGTAGA_L004

value: RV144 vaccine regimen


title: UA09-S-01

value: Poor

value: Synovial fluid


title: ISPY2_683173

value: Paclitaxel + Pembrolizumab

value: Linear Adjustment Factor


title: 156560566_1_D6_TAAGGCGA-AGAGTAGA_L004


title: ISPY2_679787

value: Paclitaxel