title: JB1 WT NPCs Rep2

city: Naples

first: Ankit

last: Verma

state: Naples

address: Via Pietro Castellino, 111

country: Italy

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

description: JB1_WT NPCs

data_processing:
Basecalls to fastq generation was performed by Blc2fastq v2.0.2 software (Illumina). The raw sequencing reads were checked for read quality using FastQC tool and trimmed for adapter sequences using Trimmomatic v.0.36 and only the good quality reads were aligned to mm10 version of mouse reference genome (GRCm38) using STAR-2.5.4a (--outFilterMultimapNmax 1). Reads were assigned to features using featurecounts from Subread package v.1.6.0. Differential expression was performed using DESeq2 v.1.24.0. The functional enrichment analysis of deregulated genes was performed using gprofiler2 R package. The allele-specific RNA-Seq analysis was performed by utilizing the SNPs present between B6 and JF1 genome. SNPs were derived from Takada et al. (Takada et al., 2013) and converted to mm10 using CrossMap v-0.2.5 (Zhao et al., 2013). To strengthen, the conversion possibilities, these SNPs were overlapped with JF1 SNPs downloaded from the Sanger Institute website (ftp://ftp-mouse.sanger.ac.uk/REL-1807-SNPs_Indels/mgp.v6.merged.norm.snp.indels.sfiltered.vcf.gz) which revealed ~11 millions SNP positions. These SNPs were used for creating N-masked genomes using custom Python script by incorporating ‘Ns’ at the SNP positions. The alignment was performed using STAR with specific parameters (--alignEndsTypeEndToEnd, --outSAMattributes All, --outFilterMultimapNmax 1 --outFilterMismatchNmax 3). The aligned reads were assigned to maternal (JF1) or paternal (B6) allele using SNPSplit v0.3.2 (Krueger & Andrews, 2016), along with a file containing SNPs. For visualization purposes, bigwig files were generated and uploaded to UCSC genome browser (mouse genome version GRCm38/mm10). The reads were assigned to the features using featurecounts (Liao et al. 2013) and imported to DESeq2 for further normalization. The factor for normalization was calculated from bulk RNA-Seq and used for both B6 and JF1 counts normalization
Genome_build: mm10
Supplementary_files_format_and_content: contains 1) unnormalized read count matrix for Bulk and Allele Specific data, The matrix has gene Ensembl ID and counts for each sample,   2). Bigwig files: “Bulk” denotes Total RNA-Seq while “B6” and “JF1” prefix shows allele specific bigwig files. 1 and 2 shows replicates. R and F represents reverse and forward strands respectively.

source_name: Neural precursor cells

growth_protocol: Wildtype hybrid JB1 (♀JF1 × ♂ C57BL/6) F1 ESCs and Zfp57-knock-out hybrid were cultured under standard-free conditions on gelatinized tissue culture dishes and  maintained in ESGRO Complete Plus Serum-free Clonal Grade 1i Medium (MerckMillipore) with the addition of Gsk3 inhibitor CHIR99021 (3μm). The cells were cultured at 37°C under an atmosphere of 5% CO2.

extract_protocol:
RNA was extracted from cultured NPCs by lysing the cells with the addition of the TRI reagent (Sigma-Aldrich)  and following the manufacturer’s instructions
~1μg of high quality RNA (260/280 > 1.80) samples in biological duplicates were subjected to library preparation using TruSeq Stranded Total RNA Ribo-Zero Gold Kit (Illumina Inc. USA) and sequencing with 2x125bp paired end (PE) mode on Illumina HiSeq2500 platform (IGA Technology Services, Italy).

treatment_protocol: JB1 WT and Zfp57-/- mESCs were plated onto gelatin-coated dishes at the optimal density of 7.500 ES cells/cm2. Next day, ESC media was changed for DDM as described (Gaspard et al.,Nat Protocol 2009). DDM was supplemented with cyclopamine (1 μm) from days 2 to 10 to enhance dorsalization of telencephalic progenitors . At day 12 of culture, corticogenesis was stopped.

value: ES-derived neural progenitor cells

value: Wildtype


title: JB1 ZFP57KO NPCs Rep2

status: Public on Jul 06 2021

type: SRA

description: JB1 Zfp57-/- NPCs

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: strain

tag: genotype


title: RB203 (SNP_370K)

type: genomic

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 21

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
The B allele frequency  and log-ratio signals were smoothes and analyzed using the Geneome Alteration Print (GAP) algorithm (Popova et al., 2009).
1.Raw data file :
X raw and Y raw : raw coordinates ; X and Y: normalized coordinates
1.Processed  data file :
score: GenomeStudio score; Theta: GenomeStudio genotype metric; R: GenomeStudio intensity metric; B allele frequency: GenomeStudio B allele frequency estimate; Log R ratio: GenomeStudio signal intensity estimate

molecule: genomic DNA

organism: Homo sapiens

source_name: retinblastoma sample RB203

label_protocol: Standard Illumina Protocol

extract_protocol: For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A.  DNA was then extracted using a standard phenol-chloroform protocol

tag: geo dataset

value: SAMPLE 60

tag: batch name

tag: tissue

value: retinoblastoma


title: IgAN_01_077

city: Beijing

first: Ping

last: Lu

address: 5 Yiheyuan Road

country: China

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
scRNA-Seq：Sequencing read pairs were split into single-cell RNA-seq read pairs according to the 8bp barcode of read2, followed by corresponding extraction of read1. Unique Molecular Identifiers (UMIs) were added to sequence identifier of read1 in order to correctly identify PCR duplicates later. We subsequently trimmed template switch oligo (TSO) sequence and ployA tail sequence in read1. After removing adapter contaminants and low-quality bases (N > 10%), we aligned clean reads to hg19 human reference genome from UCSC using TopHat (version 2.0.12). Then, the htseq-count script developed with HTSeq (version 0.6.0) was used to count uniquely aligned reads with genes. Transcripts of the same gene with identical UMIs were regarded as PCR duplicates and removed in this process.
Genome_build: hg19
Supplementary_files_format_and_content: A  comma-separated values (csv) file include UMI counts for each single cell RNA samples

molecule: polyA RNA

source_name: IgAN patients’ renal biopsies

growth_protocol: Paracancerous tissues from renal carcinoma were diced and incubated with 0.5mg/ml type II (SIGMA, C6885) and 0.5mg/ml type IV (SIGMA, C5138) collagenase at 37℃ for 15 min. The glomeruli were transferred by pipetting to RPMI 1640 with 25 mM HEPES (Gibco, 22400-089) supplemented with 100 U/mL penicillin, 100 ug/mL streptomycin, 2 mM L-glutamine and 10% fetal bovine serum. After 7-10 days’ incubation, mesangial cells were seen at the edges of glomeruli that attached to the plate and passaged when confluent using 0.05% trypsin. Mesangial cells after 4~5 weeks of subculture still remains homogenous, the morphologically was characterized by phase contrast microscopy. Immunofluorescence staining of Desmin (Abcam, ab32362, 1:100) and Vimentin (Abcam, ab8978, 1:100) were used to identify mesangium. All experiments were performed using confluent mesangial cells from the 2nd to 4th passage. In an attempt to mimic the microenvironment around mesangial cells in vivo, mesangial cells were cultured with serum collected from normal volunteers or IgAN patients. In order to avoid influence of complement, all human serums were heat-inactivated by 56℃ water bath for 30 min before using.

extract_protocol:
Single-cell RNA sequencing was conducted using a modified high throughput STRT method. Single cell was transferred to lysis buffer containing a 25-bp RT primer that consists of poly T and a fragment of cell barcode and unique molecular identifier (UMI). The reverse transcription was then initiated by SSII, the synthesized cDNA was further amplified by 19 cycles of PCR to generate double-strand DNA. Then, the purified DNA was further amplified by another four cycles of PCR using a biotinylationed primer to add biotin modification to the 3’ terminal of the synthesized DNA. Subsequently, the modified double-strand DNA were fragmented to 300 bp by super sonication, the 3’ terminal fragments were then coupled to streptavidin C1 beads with one hour’s incubation. After washing by 2X B&W buffer, 3’ terminal of reverse transcribed DNA on C1 beads were used for library construction.
Preparation of library was based on the instruction of Kapa Hyper Prep Kit.
All sequencing data were generated by 150-bp pair-end sequencing through an Illumina Hiseq-4000 platform.

treatment_protocol: Sample collection procedure was approved by the Medicine Ethics Committee of the Chinese People’s Liberation Army General Hospital (S2017-102-01). 13 IgAN patients’ renal biopsies and 6 renal paracancerous tissue were collected. To capture cells inside glomerulus, renal biopsies were first cut into millimeter-sized pieces, the treated tissues were then transferred to 1ml 0.5mg/ml collagenase II and collagenase IV mixtures and digested for 5 min at 37°C with slight shaking. Digested tissues were then transferred to a 2 cm dish and diluted by 1 ml DMEM cell culture medium. Glomerulus were quickly picked using 100 µm inner-diameter mouth pipette and transferred to a 20 µl DPBS dro in 2 cm dish, after slightly treating with needle, the glomerulus were transferred to 200 µl mixtures containing 0.5mg/ml collagenase II, 0.5 mg/ml collagenase IV and 0.0125% tyrisin for 15 minutes’ digestion at 37°C with 900 rpm shaking. Meanwhile, the rest tissues were collected and centrifuged at 500g for 3min, after removing supernatant, tissues were resuspeded by 500 µl 0.5mg/ml collagenase II and collagenase IV mixtures and digested at 37°C with 900 rpm shaking for 10 min. After digestion, cells were centrifuged at 800g for 5min. For glomerulus cells, about 80~90 µl supernatant was discarded and resuspended by 200 µl DMEM culture medium. For the rest renal cells, all supernatant was removed and the pellets were then resuspended by 100 µl DMEM. To capture the major cell types, the non-glomerulus renal cells were first incubated with 100 µl buffer containing 10 µl CD14+ MicroBeads (Miltenyi, 130-050-021) for 15 min at 4°C. Cells were then washed by 1X DPBS and macrophages were isolated on magnetic rack using MS column, 300 µl DMEM was added to the column to flush out macrophages. The negative selected cells were then resuspended by 100 µl DMEM, after 15 min’s incubation with 100 µl buffer that contains 10 µl CD326 (EPCAM) beads at 4°C, epithelium were isolated using MS column on magnetic rack. To cover all the cell types, the last negative selected cells were also collected. All collected cells were diluted to 300 µl using DMEM. For monocytes collection, we took 5 ml peripheral blood from each of the 5 normal people and 5 of the 13 IgAN patients. Peripheral blood samples were collected into EDTA vacutainers. Peripheral blood monocytes were first isolated by Ficoll-Paque (Solarbio, P8680). The PBMC cell layer was collected and washed three times with PBS. After centrifugation with 800g for 5 min, cell pellets were resuspended in 300 µL buffer which contains 30 µl CD14+ beads and incubated for 15 min at 4℃. Cells were washed by PBS and monocytes were isolated using LS Column on MACS Separator (Miltenyi, 130-042-302). 5 mL of DMEM were added to the column to flush out positive cells using the plunger supplied with the column. Cell suspension was centrifuged and resuspended to 500 µl.

tag: patients

tag: disease state

value: IgAN

value: renal biopsies


title: IgAN_01_079


title: JB1 ZFP57KO NPCs Rep1

description: JB1 Zfp57-/- NPCs


title: IgAN_01_076


title: RB214 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 29

source_name: retinblastoma sample RB214

value: SAMPLE 71


title: RB202 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 20

source_name: retinblastoma sample RB202

value: SAMPLE 59


title: JB1 WT NPCs Rep1

description: JB1_WT NPCs


title: RB218 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 31

source_name: retinblastoma sample RB218

value: SAMPLE 75


title: PEER cell line - H3K27ac - CRISPR-Cas9 editing

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

description: CRISPR-Cas9 TAL1 upstream 12bp insertion

library_source: genomic

data_processing:
FASTQ files were processed by pipeline available at BLUEPRINT Data Coordination Center Portal (http://dcc.blueprint-epigenome.eu/).
Raw read counts were collected using Genomic Analysis Toolkit v4.2 in 200bp bins and normalized by average number of reads per a bin.
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig with normalized read count

source_name: Cell line

extract_protocol:
10^7 cells  were incubated with 1% formaldehyde in RPMI medium for 10 minutes at room temperature, followed by addition of glycine to a final concentration of 0.125M. Cells were washed three times with cold PBS-BSA 0.5% before being pelleted and frozen at -80 ºC.
ChIP-seq for the histone marks H3K4me3 and H3K27Ac (Diagenode) were included in this study.

value: T-cells

tag: antibody, verndor, catalog number

value: H3K27ac Antibody, Diagenode, C15410196


title: PEER cell line - H3K4me3 - CRISPR-Cas9 editing

value: H3K4me3 Antibody, Diagenode, C15410003


title: RB208 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 25

source_name: retinblastoma sample RB208

value: SAMPLE 65


title: ATAC-seq mouse CD8+ T EV rep2

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: NIH

description: ATAC-seq mouse CD8+ T EV rep2

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.1.1
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. MACS v1.4.2 is used to call peaks using the BED files. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes or differential ATAC-Seq peaks among different conditions.
Genome_build: mm10 and hg19

source_name: spleen

growth_protocol: CD8+ T lymphocytes or draining lymph nodes were isolated using the EasySep Mouse CD8+ T cell isolation kit (STEMCELL #19853) and cultured in RPMI-1640 medium (ATCC) supplemented with 10% FBS and 50 mM b-mercaptoethanol. For RNA-seq using cells isolated from lymph nodes, CD90.1+ CD8 + cells were sorted and cell libraries were prepared with SMART-Seq Ultra low Input RNA kit (Takara, #634889). For human CD8+ T cells related assays, naïve CD8+ T cells were isolated with EasySep™ Human Naïve CD8+ T Cell Isolation Kit II (STEMCELL, #17968), and activated with Dynabeads Human T-Activator CD3/CD28 (Thermo Fisher Scientific, #111.31D) for two days, and cells were isolated by a magnet per the manufacturer’s protocol.

extract_protocol:
For ChIP-seq, DNA libraries were prepared with the KAPA LTP Library Preparation Kit and barcoded with NEXTflex DNA barcodes. For ATAC-seq, Nuclei were then used for the transposition reaction with the Nextera DNA Library Preparation kit at 37C for 30 min. DNA was purified with the Zymo DNA recovery kit. For RNA-seq, RNA was extracted using the Zymo RNA miniprep kit (Zymo Research), and 500 ng RNA was used for library preparation with the Kapa mRNA HyperPrep Kit (KK8580, Kapa Biosystems) and indexed with NEXTflex DNA Barcodes-24. After the final amplification, samples were loaded onto 2% E-Gel pre-cast gels (ThermoFisher), and 250 to 400 bp DNA fragments were recovered and purified with Zymoclean Gel DNA Recovery Kit (Zymo Research).
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina HiSeq3000 system.

treatment_protocol: Purified cells were activated using plate-bound anti-CD3 (2 mg/ml) plus soluble anti-CD28 (1 mg/ml) monoclonal antibodies for two days. After resting overnight in the absence of cytokine, cells were washed and cultured with 1 mg/ml MSA conjugated IL-2, H9 or H9T (unless otherwise specified).

tag: antibody

value: CD8+ T cells


title: IgAN_01_075


title: RB200 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 19

source_name: retinblastoma sample RB200

value: SAMPLE 57


title: RB205 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 23

source_name: retinblastoma sample RB205

value: SAMPLE 62


title: PEER cell line - H3K27ac

description: wild type


title: ATAC-seq mouse CD8+ T STAT5CA rep2

description: ATAC-seq mouse CD8+ T STAT5CA rep2


title: RB206 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 24

source_name: retinblastoma sample RB206

value: SAMPLE 63


title: RB210 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 27

source_name: retinblastoma sample RB210

value: SAMPLE 67


title: IgAN_01_074


title: RB204 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 22

source_name: retinblastoma sample RB204

value: SAMPLE 61


title: ATAC-seq mouse CD8+ T EV rep1

description: ATAC-seq mouse CD8+ T EV rep1


title: 74-Post-xRT

city: Charlestown

first: David

middle: T

last: Ting

state: MA

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw and normalized read counts in Text format

source_name: metastatic tumor

growth_protocol: biopsies were taken from out of field metastatic tumor sites

extract_protocol:
RNA extraction from fresh frozen samples was done using the  AllPrep DNA/RNA kit fron Qiagen
The Smarter Stranded Total RNA-Seq kit v2 (634413, Illumina) was used with 10 ng RNA input, according to the manufacturer instructions to generate libraries.
Dual-indexed pooled libraries were sequenced on the Illumina NextSeq 500 platform using a 150 cycles kit with paired end read mode.

treatment_protocol: samples were snap frozen in liquid nitrogen

value: metastatic tumor

tag: cancer type

value: MSS CRC

tag: time point

value: Post-xRT

tag: sequencning run


title: IgAN_01_073

value: IgAN

value: renal biopsies


title: RB56 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 17

source_name: retinblastoma sample RB56

value: SAMPLE 46

value: retinoblastoma


title: ATAC-seq mouse CD8+ T STAT5CA rep1

description: ATAC-seq mouse CD8+ T STAT5CA rep1


title: RB52 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 16

source_name: retinblastoma sample RB52

value: SAMPLE 43


title: 73-Pre-xRT

value: Pre-xRT


title: RB57 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 18

source_name: retinblastoma sample RB57

value: SAMPLE 47


title: 74-Pre-Tx

value: Pre-Tx


title: RNA-seq mouse CD8+ T H9T 24h rep2

description: RNA-seq mouse CD8+ T H9T 24h rep2

value: CD8+ T cells


title: RNA-seq mouse CD8+ T IL7+IL15 24h rep2

description: RNA-seq mouse CD8+ T IL7+IL15 24h rep2


title: 74-Pre-xRT


title: RB40 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 15

source_name: retinblastoma sample RB40

value: SAMPLE 31


title: IgAN_01_069

source_name: IgAN patients’ renal biopsies


title: RB38 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 14

source_name: retinblastoma sample RB38

value: SAMPLE 29


title: RNA-seq mouse CD8+ T IL15 24h rep2

description: RNA-seq mouse CD8+ T IL15 24h rep2


title: 71-Pre-xRT


title: IgAN_01_070


title: RNA-seq mouse CD8+ T IL2 24h rep2

description: RNA-seq mouse CD8+ T IL2 24h rep2


title: PEER cell line - H3K4me3

description: wild type

value: T-cells

value: H3K4me3 Antibody, Diagenode, C15410003


title: IgAN_01_071


title: RB34 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 12

source_name: retinblastoma sample RB34

value: SAMPLE 26


title: 73-Pre-Tx

value: metastatic tumor


title: 71-Pre-Tx

value: MSS CRC


title: RNA-seq mouse CD8+ T IL7+IL15 24h rep1

description: RNA-seq mouse CD8+ T IL7+IL15 24h rep1


title: IgAN_01_068


title: RB30 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 11

source_name: retinblastoma sample RB30

value: SAMPLE 22


title: RB24 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 9

source_name: retinblastoma sample RB24

value: SAMPLE 17


title: IgAN_01_072

value: IgAN

value: renal biopsies


title: IgAN_01_067


title: RNA-seq mouse CD8+ T IL15 24h rep1

description: RNA-seq mouse CD8+ T IL15 24h rep1


title: RB28 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 10

source_name: retinblastoma sample RB28

value: SAMPLE 20

value: retinoblastoma


title: IgAN_01_066


title: RNA-seq mouse CD8+ T H9T 24h rep1

description: RNA-seq mouse CD8+ T H9T 24h rep1

source_name: spleen


title: RNA-seq mouse CD8+ T IL2 24h rep1

description: RNA-seq mouse CD8+ T IL2 24h rep1


title: RB23 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 8

source_name: retinblastoma sample RB23

value: SAMPLE 16


title: IgAN_01_065


title: 68-Pre-xRT

value: Pre-xRT


title: IgAN_01_064


title: RNA-seq mouse CD8+ T 2-DG rep3

description: RNA-seq mouse CD8+ T 2-DG rep3


title: 68-Pre-Tx

value: Pre-Tx


title: RB12 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 6

source_name: retinblastoma sample RB12

value: SAMPLE 10


title: IgAN_01_063


title: 63-Pre-xRT

value: PDAC


title: RNA-seq mouse CD8+ T 2-DG rep2

description: RNA-seq mouse CD8+ T 2-DG rep2

value: CD8+ T cells


title: IgAN_01_062


title: RB14 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 7

source_name: retinblastoma sample RB14

value: SAMPLE 12


title: RNA-seq mouse CD8+ T Cont rep3

description: RNA-seq mouse CD8+ T Cont rep3


title: RNA-seq mouse CD8+ T Cont rep2

description: RNA-seq mouse CD8+ T Cont rep2


title: 36-Pre-Tx


title: RB6 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 4

source_name: retinblastoma sample RB6

value: SAMPLE 5


title: 52-Post-xRT

value: Post-xRT


title: 68-Post-xRT

value: metastatic tumor


title: RB10 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 5

source_name: retinblastoma sample RB10

value: SAMPLE 8


title: IgAN_01_061


title: IgAN_01_060


title: RNA-seq mouse CD8+ T 2-DG rep1

description: RNA-seq mouse CD8+ T 2-DG rep1


title: RB4 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 3

source_name: retinblastoma sample RB4

value: SAMPLE 4


title: 56-Pre-xRT

source_name: metastatic tumor


title: RB3 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 2

source_name: retinblastoma sample RB3

value: SAMPLE 3


title: 63-Pre-Tx


title: IgAN_01_059

value: IgAN


title: RNA-seq mouse EV rep2

description: RNA-seq mouse EV rep2


title: 50-Post-xRT


title: RB109 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 22

source_name: retinblastoma sample RB109

value: SAMPLE 55


title: IgAN_01_058

value: renal biopsies


title: RNA-seq mouse STAT5CA rep2

description: RNA-seq mouse STAT5CA rep2


title: IgAN_01_057


title: RB2 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 1

source_name: retinblastoma sample RB2

value: SAMPLE 2

value: retinoblastoma


title: 56-Pre-Tx


title: RB63 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 21

source_name: retinblastoma sample RB63

value: SAMPLE 53


title: IgAN_01_056

source_name: IgAN patients’ renal biopsies


title: 52-Pre-xRT

value: Pre-xRT


title: RNA-seq mouse STAT5CA rep1

description: RNA-seq mouse STAT5CA rep1


title: IgAN_01_055


title: RB62 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 20

source_name: retinblastoma sample RB62

value: SAMPLE 52


title: RNA-seq mouse EV rep1

description: RNA-seq mouse EV rep1


title: RNA-seq mouse CD8+ T Cont rep1

description: RNA-seq mouse CD8+ T Cont rep1


title: RB60 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 19

source_name: retinblastoma sample RB60

value: SAMPLE 50


title: RNA-seq mouse CD90.1+ H9T rep3

description: RNA-seq mouse CD90.1+ H9T rep3

source_name: draining lymph nodes

value: CD8+ T cells


title: 54-Pre-Tx

value: PDAC

value: Pre-Tx


title: 52-Pre-Tx

value: MSS CRC


title: RNA-seq mouse CD90.1+ H9 rep3

description: RNA-seq mouse CD90.1+ H9 rep3


title: IgAN_01_053


title: IgAN_01_052


title: RB59 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 18

source_name: retinblastoma sample RB59

value: SAMPLE 49


title: RNA-seq mouseCD90.1+ IL2 rep3

description: RNA-seq mouseCD90.1+ IL2 rep3


title: 51-Pre-xRT

value: metastatic tumor


title: RB51 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 17

source_name: retinblastoma sample RB51

value: SAMPLE 42


title: IgAN_01_050


title: RB50 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 16

source_name: retinblastoma sample RB50

value: SAMPLE 41


title: IgAN_01_051

value: IgAN


title: 50-Pre-Tx


title: RNA-seq mouse CD90.1+ IL2 rep2

description: RNA-seq mouse CD90.1+ IL2 rep2


title: RB46 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 14

source_name: retinblastoma sample RB46

value: SAMPLE 37


title: RNA-seq mouse CD90.1+ H9 rep2

description: RNA-seq mouse CD90.1+ H9 rep2


title: IgAN_01_054

value: renal biopsies


title: 44-Pre-Tx


title: 41-Post-xRT

value: Post-xRT


title: 44-Pre-xRT


title: IgAN_01_049


title: IgAN_01_048


title: 41-Pre-Tx


title: RNA-seq mouse CD90.1+ H9T rep1

description: RNA-seq mouse CD90.1+ H9T rep1


title: RB45 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 13

source_name: retinblastoma sample RB45

value: SAMPLE 36

value: retinoblastoma


title: IgAN_01_047


title: 36-Pre-xRT

value: Pre-xRT


title: RNA-seq mouse CD90.1+ H9 rep1

description: RNA-seq mouse CD90.1+ H9 rep1


title: RB43 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 12

source_name: retinblastoma sample RB43

value: SAMPLE 34


title: IgAN_01_046


title: RNA-seq mouse CD90.1+ IL2 rep1

description: RNA-seq mouse CD90.1+ IL2 rep1


title: RB42 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 11

source_name: retinblastoma sample RB42

value: SAMPLE 33


title: RNA-seq mouse CD90.1+ H9T rep2

description: RNA-seq mouse CD90.1+ H9T rep2

value: CD8+ T cells


title: 33-Post-xRT

value: PDAC


title: RB49 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 15

source_name: retinblastoma sample RB49

value: SAMPLE 40


title: IgAN_01_045


title: RB41 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 10

source_name: retinblastoma sample RB41

value: SAMPLE 32


title: 30-Post-xRT

source_name: metastatic tumor

value: MSS CRC


title: IgAN_01_044


title: 33-Pre-xRT

value: metastatic tumor


title: RB39 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 9

source_name: retinblastoma sample RB39

value: SAMPLE 30


title: ATAC-Seq H9 d6

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.2.1
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. MACS v1.4.2 is used to call peaks using the BED files. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes or differential ATAC-Seq peaks among different conditions.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements, bed

source_name: spleen

growth_protocol: CD8+ T lymphocytes were isolated using the EasySep Mouse CD8+ T cell isolation kit (STEMCELL #19853) and cultured in RPMI-1640 medium (ATCC) supplemented with 10% FBS and 50 mM b-mercaptoethanol

extract_protocol:
For ChIP-seq, DNA libraries were prepared with the KAPA LTP Library Preparation Kit and barcoded with NEXTflex DNA barcodes. For ATAC-seq, Nuclei were then used for the transposition reaction with the Nextera DNA Library Preparation kit at 37C for 30 min. DNA was purified with the Zymo DNA recovery kit. For RNA-seq, RNA was extracted using the Zymo RNA miniprep kit (Zymo Research), and 500 ng RNA was used for library preparation with the Kapa mRNA HyperPrep Kit (KK8580, Kapa Biosystems) and indexed with NEXTflex DNA Barcodes-24. After the final amplification, samples were loaded onto 2% E-Gel pre-cast gels (ThermoFisher), and 250 to 400 bp DNA fragments were recovered and purified with Zymoclean Gel DNA Recovery Kit (Zymo Research).
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina Hi Seq3000 system.

tag: treatment

value: pre-activated, H9 d6


title: ATAC-Seq H9T d6

value: pre-activated, H9T d6


title: 34-Pre-Tx

value: Pre-Tx


title: RB32 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 8

source_name: retinblastoma sample RB32

value: SAMPLE 24


title: ATAC-Seq IL2 d6

value: pre-activated, IL-2 d6


title: 30-Pre-xRT


title: RB31 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 7

source_name: retinblastoma sample RB31

value: SAMPLE 23


title: IgAN_01_043

source_name: IgAN patients’ renal biopsies

value: IgAN

value: renal biopsies


title: 4-Post-xRT

value: Post-xRT


title: ATAC-Seq d0

value: pre-activated, no cytokine, d0


title: ChIP-Seq H3K27ac H9 d6

value: CD8+ T cells

tag: chip antibody

value: anti-H3K27ac (diagenode, pAb-196-050)


title: ChIP-Seq H3K27ac H9T d6


title: IgAN_01_042


title: RB25 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 5

source_name: retinblastoma sample RB25

value: SAMPLE 18

value: retinoblastoma


title: RB27 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 6

source_name: retinblastoma sample RB27

value: SAMPLE 19


title: IgAN_01_040


title: IgAN_01_041


title: 33-Pre-Tx

value: metastatic tumor

value: PDAC


title: ChIP-Seq H3K27ac IL2 d6


title: IgAN_01_039


title: RB21 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 4

source_name: retinblastoma sample RB21

value: SAMPLE 14


title: 27-Pre-xRT

value: MSS CRC

value: Pre-xRT


title: IgAN_01_038


title: ChIP-Seq H3K27ac d0


title: RB11 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 3

source_name: retinblastoma sample RB11

value: SAMPLE 9


title: IgAN_01_037


title: RNA-Seq preA H9T d6 rep2

value: pre-activated, H9T d6


title: RB7 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 2

source_name: retinblastoma sample RB7

value: SAMPLE 6


title: IgAN_01_036

value: IgAN


title: RB1 (SNP_610K)

description:
SNP array data from retinoblastoma samples
data_proc_610k.RData
data_raw_610k.RData
processed_data_i_GPL8887_retino_all_samples.csv
raw_data_i_GPL8887_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 1

source_name: retinblastoma sample RB1

value: SAMPLE 1


title: RNA-Seq preA H9 d6 rep2

value: pre-activated, H9 d6


title: 25-Pre-xRT


title: IgAN_01_034

value: renal biopsies


title: RNA-Seq preA IL-2 d6 rep2

value: CD8+ T cells

value: pre-activated, IL-2 d6


title: IgAN_01_032


title: IgAN_01_033


title: RET215 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 74

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

data_processing:
R Software, MinFi R package
Average Beta

label: Cy5 and Cy3

source_name: foetal retina samples RET215

extract_protocol: For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A. DNA was then extracted using a standard phenol-chloroform protocol.

tag: batch

tag: geo dataset serie sample id

value: SAMPLE 118


title: RET2 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 73

source_name: foetal retina samples RET2

value: SAMPLE 117

value: retinoblastoma


title: RET1 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 72

source_name: foetal retina samples RET1

value: SAMPLE 116


title: 27-Pre-Tx

value: metastatic tumor

value: Pre-Tx


title: RNA-Seq preA IL-2 d4 rep2

tag: cell type

value: pre-activated, IL-2 d4


title: 12-Post-xRT

value: MSS CRC

value: Post-xRT


title: RNA-Seq preA H9 d4 rep2

tag: strain

value: pre-activated, H9 d4


title: IgAN_01_031


title: 18-Post-xRT


title: RB304 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 70

source_name: retinoblastoma sample RB304

value: SAMPLE 87


title: RBsjd7 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 71

source_name: retinoblastoma sample RBsjd7

value: SAMPLE 113


title: IgAN_01_030

value: IgAN


title: RNA-Seq preA H9T d2 rep2

value: pre-activated, H9T d2


title: 30-Pre-Tx

source_name: metastatic tumor


title: RB35 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 13

source_name: retinblastoma sample RB35

value: SAMPLE 27


title: RB225 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 68

source_name: retinoblastoma sample RB225

value: SAMPLE 82


title: 18-Pre-xRT

value: Pre-xRT


title: 3-Post-xRT

value: PDAC


title: IgAN_01_035

value: renal biopsies


title: RNA-Seq preA H9 d2 rep2

source_name: spleen

value: CD8+ T cells

value: pre-activated, H9 d2


title: RB300 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 69

source_name: retinoblastoma sample RB300

value: SAMPLE 83

value: retinoblastoma


title: RNA-Seq preA IL-2 d2 rep2

value: pre-activated, IL-2 d2


title: IgAN_01_029

source_name: IgAN patients’ renal biopsies


title: RNA-Seq preA H9T d4 rep2

value: pre-activated, H9T d4


title: RB223 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 66

source_name: retinoblastoma sample RB223

value: SAMPLE 80


title: RB224 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 67

source_name: retinoblastoma sample RB224

value: SAMPLE 81


title: 12-Pre-xRT

value: metastatic tumor

value: MSS CRC


title: IgAN_01_028

value: IgAN


title: IgAN_01_027


title: RNA-Seq preA H9T d6 rep1

value: pre-activated, H9T d6


title: IgAN_01_026


title: RNA-Seq preA d0 rep2

value: pre-activated, no cytokine, d0


title: RB222 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 65

source_name: retinoblastoma sample RB222

value: SAMPLE 79


title: IgAN_01_025


title: RB221 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 64

source_name: retinoblastoma sample RB221

value: SAMPLE 78


title: RNA-Seq preA H9 d6 rep1

value: pre-activated, H9 d6


title: 3-Pre-xRT

value: PDAC

value: Pre-xRT


title: 17-Pre-Tx

value: Pre-Tx


title: RNA-Seq preA H9T d4 rep1

value: CD8+ T cells


title: RNA-Seq preA IL-2 d6 rep1

value: pre-activated, IL-2 d6


title: RB220 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 63

source_name: retinoblastoma sample RB220

value: SAMPLE 77

value: retinoblastoma


title: IgAN_01_023

value: renal biopsies


title: RNA-Seq preA H9 d4 rep1

value: pre-activated, H9 d4


title: 18-Pre-Tx

value: metastatic tumor


title: 12-Pre-Tx

value: MSS CRC


title: 4-Pre-xRT


title: RB219 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 62

source_name: retinoblastoma sample RB219

value: SAMPLE 76


title: RNA-Seq preA IL-2 d4 rep1

value: pre-activated, IL-2 d4


title: IgAN_01_022

value: IgAN


title: 11-Pre-Tx


title: RB218 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 61

source_name: retinoblastoma sample RB218

value: SAMPLE 75


title: RB217 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 60

source_name: retinoblastoma sample RB217

value: SAMPLE 74


title: IgAN_01_021


title: RB216 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 59

source_name: retinoblastoma sample RB216

value: SAMPLE 73


title: RNA-Seq preA H9T d2 rep1

value: pre-activated, H9T d2


title: IgAN_01_020


title: RNA-Seq preA H9 d2 rep1

value: pre-activated, H9 d2


title: 4-Pre-Tx

value: Pre-Tx


title: IgAN_01_024


title: IgAN_01_019


title: RNA-Seq preA IL-2 d2 rep1

value: CD8+ T cells

value: pre-activated, IL-2 d2


title: Reticular Dysgenesis patient 2 bone marrow

city: Stanford

first: Wenqing

last: Wang

state: CA

address: 2500 BMI, 1291 Welch Rd

department: Department of Pediatrics

institute: Stanford University School of Medicine

data_processing:
Reads alignment, cell barcode calling and UMI count were performed using cellranger 3.0.0
Genome_build: hg19
Supplementary_files_format_and_content: Barcode-UMI count matrix for each sample in csv

source_name: Whole bone marrow

extract_protocol: Single cell RNA-seq libraries were prepared using 10X Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.

treatment_protocol: Cryopreserved bone marrow samples from 2 RD patients and 1 healthy donor were thawed in RPMI with 10% FBS, and red blood cell lysis was performed using amonium chloride solution. CD45+ cells were FACS sorted into PBS for 10X single cells RNA-seq library preparation.

value: bone marrow

value: Reticular Dysgenesis

tag: Sex

value: M

tag: age

value: 6 months


title: IgAN_01_017

value: renal biopsies


title: RB212 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 57

source_name: retinoblastoma sample RB212

value: SAMPLE 69

value: retinoblastoma


title: Reticular Dysgenesis patient 1 bone marrow


title: IgAN_01_018


title: RNA-Seq preA d0 rep1

value: pre-activated, no cytokine, d0


title: RB211 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 56

source_name: retinoblastoma sample RB211

value: SAMPLE 68


title: Healthy donor bone marrow

value: healthy

value: F

value: 15 years


title: RB209 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 55

source_name: retinoblastoma sample RB209

value: SAMPLE 66


title: IgAN_01_016

value: IgAN


title: IgAN_01_015


title: processes_ptx_rep2

city: Zurich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: HEST

country: Switzerland

institute: ETH Zürich

description: ribosomal depletion

data_processing:
Mapping was performed with STAR
featureCounts was used for reads counting
DEA analysis was conducted in R with edgeR
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: counts of each sample and DEA analysis (edgeR output), .csv files

organism: Rattus norvegicus

growth_protocol: Rat hippocampal neurons, cultured on cell culture inserts

extract_protocol:
RNA was extracted from HC using peqGOLD Isolation Systems TriFast™ (Peqlab) following the manufacturer’s protocol.
NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina

treatment_protocol: In the treatment conditions, cell media was supplemented with the GabaA-receptor antagonist Picrotoxin (PTX) for 48h from DIV18-20.

value: Sprague-Dawley

tag: compartment

value: Processes

value: Primary Hippocampal Neurons


title: Resistant STAT3 inh rep2

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

description:
Bulk RNA-seq on viable drug resistant K562 using Nextera library prep
K562_LLL12_Rx_Bulk_Gene_counts

data_processing:
Basecalls performed using Partek Flow software, version 8.0
For Bulk RNA-seq: double-ended sequencing reads were aligned to human (hg38) using Spliced Transcripts Alignment to a Reference (STAR 2.6.1d). Aligned reads were then quantified to the transcriptome (ensembl release99) and normalized
Genome_build: hg38
Supplementary_files_format_and_content: text counts table, coverage bigwig files

growth_protocol: K562 lines were obtained from ATCC (CCL-243). The parental cells were made resistant to and maintained at 1µM imatinib (IM) as previously described (Eiring et al., 2015)

extract_protocol:
RNA was isolated using the RNeasy Plus mini kit (Qiagen) for bulk RNA-seq
Libraries were prepared according to Illumina's Nextera XT instructions

treatment_protocol: Cells are left untreated OR treated with 1uM imatinib/1uM LL12

value: Cell line

tag: organ

value: Bone marrow

tag: treatement

value: 1uM LLL12


title: Resistant STAT3 inh rep3


title: processes_ptx_rep1

description: ribosomal depletion

value: GabaA-receptor antagonist Picrotoxin (PTX) for 48h


title: 3-Pre-Tx

source_name: metastatic tumor

tag: tissue

value: metastatic tumor

value: PDAC

value: Pre-Tx


title: processes_ctrl_rep2

description: ribosomal depletion

value: control


title: RB213 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 58

source_name: retinoblastoma sample RB213

value: SAMPLE 70

value: retinoblastoma


title: processes_ctrl_rep1

description: ribosomal depletion


title: somata_ptx_rep2

description: ribosomal depletion

value: Somata


title: RB206 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 53

source_name: retinoblastoma sample RB206

value: SAMPLE 63


title: RB203 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 52

source_name: retinoblastoma sample RB203

value: SAMPLE 60


title: Sensitive STAT3 inh rep2

description:
Bulk RNA-seq on viable drug sensitive K562 using Nextera library prep
K562_LLL12_Rx_Bulk_Gene_counts


title: Resistant STAT3 inh rep1


title: somata_ptx_rep1

description: ribosomal depletion


title: RB200 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 51

source_name: retinoblastoma sample RB200

value: SAMPLE 57


title: IgAN_01_011

source_name: IgAN patients’ renal biopsies

tag: patients

tag: disease state

value: IgAN

value: renal biopsies


title: Sensitive STAT3 inh rep1


title: IgAN_01_012


title: RB111 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 50

source_name: retinoblastoma sample RB111

value: SAMPLE 56


title: somata_ctrl_rep2

description: ribosomal depletion

value: Sprague-Dawley

value: Primary Hippocampal Neurons


title: IgAN_01_010


title: RB208 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 54

source_name: retinoblastoma sample RB208

value: SAMPLE 65


title: somata_ctrl_rep1

description: ribosomal depletion


title: Resistant rep2

value: Cell line

value: Bone marrow

value: 1uM imatinib


title: RB109 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 49

source_name: retinoblastoma sample RB109

value: SAMPLE 55


title: IgAN_01_014


title: IgAN_01_013


title: RB64 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 48

source_name: retinoblastoma sample RB64

value: SAMPLE 54


title: Resistant rep1


title: IgAN_01_009


title: IgAN_01_008


title: Sensitive rep3

value: Untreated


title: IgAN_01_007


title: RB62 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 46

source_name: retinoblastoma sample RB62

value: SAMPLE 52

value: retinoblastoma


title: RB63 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 47

source_name: retinoblastoma sample RB63

value: SAMPLE 53


title: Sensitive rep2


title: IgAN_01_006


title: RB61 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 45

source_name: retinoblastoma sample RB61

value: SAMPLE 51


title: IgAN_01_005


title: Sensitive rep1


title: asthenozoospermia patients

city: Hangzhou

first: yanqian

last: wu

address: 8 Yikang Road, Lin’an District, Hangzhou, Zhejiang, P.R.China

institute: hangzhou medical college

data_processing:
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers.
The libraries were denatured and diluted to a loading volume of 1.3ml and loading concentration of 1.8pM
Diluted libraries were loaded onto reagent cartridge and forwarded to sequencing run  on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (#FC-404-2005, Illumina), according to the manufacturer’s instructions
Data Collection and Analysis

source_name: sperm-asthenozoospermia patients

extract_protocol:
total RNA was extracted from pooled sperm samples of fertile controls and asthenozoospermia patients (each pooled from 10 individuals) using TRIzol Reagent (Takara, Dalian, China)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: sperm

value: sperm-asthenozoospermia patients


title: Resistant rep3


title: RB60 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 44

source_name: retinoblastoma sample RB60

value: SAMPLE 50


title: fertile controls

source_name: sperm-fertile controls

value: sperm-fertile controls


title: RB59 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 43

source_name: retinoblastoma sample RB59

value: SAMPLE 49


title: Rat_HDLI_Test9

type: RNA

city: Seoul

first: Soo-Jong

last: Hong

state: Seoul

address: Department of Medicine, 88, OLYMPIC-RO 43-GIL, SONGPA-GU

country: South Korea

institute: University of Ulsan Collage of Medicine

description: Gene expression data from frozen lung

hyb_protocol: 5.5 μg of labeled DNA target was hybridized to the GeneChip® Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) at 45°C for 16hour for human samples, and hybridized to the GeneChip® Rat Gene 2.0 ST Array (Affymetrix) at 45°C for 16hour for rat samples.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: Lung of rat exposed to humidifier disinfectant

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: For rat experimenmt, twelve-week-old nulliparous female and male Sprague-Dawley rats were purchased from Orient Bio (Seoul, Korea).

extract_protocol: mRNAs were extracted from FFPE of human lung tissues and frozen rat lung tissues with a miRNeasy FFPE kit (Qiagen, Hilden, Germany) and TRIzol reagent (Invitrogen, Carlsbad, CA, USA), respectively, according to the manufacturer’s protocol.

treatment_protocol: All patients were confirmed to have HDLI based on both pathological and radiological findings. In the case of rat experiment, PHMG phosphate was exposed to whole-body target PHMG phosphate concentrations of 0 (Control) or 3.20 mg/m3 for 6 hours per day, 7 days per week, from day 6 to day 20.

value: Lung

value: 11 weeks


title: IgAN_01_003

value: IgAN

value: renal biopsies


title: D6stMED: moDC unstimulated control

city: Bilthoven

first: Alberto

last: Miranda-Bedate

state: Utrecht

address: Antonie van Leeuwenhoeklaan 9

department: Department of Immune Mechanisms (IMM)

country: Netherlands

institute: RIVM

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq2 Conversion Software v2.20
RNAseq reads were aligned to the Homo sapiens reference genome (GRCh38) and most recent transcript annotations using STAR (2.6.1a)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_counts_moDC_all_samples.txt: Tab-delimited text file includes raw gene counts of all moDC samples

source_name: peripheral blood mononuclear cells

growth_protocol: CD14 positive monocytes were isolated from  peripherial blood of healthy humans and cultured for 6d with 500U/ml GM-CSF and 800U/ml IL-4 to generate monocyte-derived dendritic cells

extract_protocol:
The column-based miRNeasy RNA isolation kit (Qiagen) was used. RNA was isolated according to the manufacturer’s instructions with minor modifications (extra column-washing step with 80% ethanol before extracting the RNA with RNase-free water)
To determine RNA quality and integrity we used Lab-on-Chip analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with an RNA integrity number above 8 were used.
The TruSeq Stranded mRNA Library Prep Kit from Illumina was used to construct libraries

treatment_protocol: human monocyte-derived dendritic cells were stimulated with live B. pertussis at MOI 10 for 3 hours

value: moDC

tag: donor

tag: stimulated with b . pertussis

value: No

tag: b. pertussis strain

tag: b. pertussis year of isolation

tag: pertactin genotype

tag: batch of sequencing

tag: sample name in supplementary file


title: IgAN_01_002


title: Rat_HDLI_Test8

description: Gene expression data from frozen lung


title: Rat_HDLI_Test10

description: Gene expression data from frozen lung


title: Rat_HDLI_Test7

description: Gene expression data from frozen lung


title: D3stMED: moDC unstimulated control

tag: cell type


title: RB57 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 41

source_name: retinoblastoma sample RB57

tag: batch

tag: geo dataset serie sample id

value: SAMPLE 47


title: RB56 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 40

source_name: retinoblastoma sample RB56

value: SAMPLE 46


title: RB58 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 42

source_name: retinoblastoma sample RB58

value: SAMPLE 48


title: IgAN_01_001

source_name: IgAN patients’ renal biopsies


title: IgAN_01_004


title: Rat_HDLI_Test6

description: Gene expression data from frozen lung

tag: age


title: D2: moDC unstimulated control


title: D1stMED: moDC unstimulated control


title: Rat_HDLI_Test5

description: Gene expression data from frozen lung


title: Control mice Replicate 4

city: guangzhou

first: canming

last: li

state: guangdong

address: NO 600, Tianhe ave.

institute: The Third Affiliated Hospital of Sun Yat-sen University

description: Biological replicate 4 of 4. Control mice, untreated, harvested 3 days after administration of saline.

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar  Mouse mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Data was extracted using Agilent Feature Extraction software. The probe signals passing "P" or "M" QC flags in at least 4 samples were retained for further analysis.
IP (Cy5-labelled) intensities were normalized as relative intensities by the RNA spike-in calibration controls.  Differentially m6A-methylated mRNAs, lncRNAs and other ncRNAs passing fold change and statistical significance cutoffs were identified and compiled.

source_name: RNAs that binded to the magnetic beads with anti-N6-methyadenosine (m6A) antibody

label_protocol: Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated "IP" fraction contained enriched m6A methylated RNAs, and the supernatant " Sup" fraction contained unmodified RNAs."IP" and "Sup" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: All mice were maintained in a temperature-controlled room under a 12 h light dark schedule and received food and water ad libitum.

extract_protocol: Total RNA was extracted from the kidney specimens using TRIzol reagent (Invitrogen, USA) in accordance with the manufacturer’s instructions.

treatment_protocol: The mice in Cis-AKI group were injected intraperitoneal with a single dose of cisplatin (20 mg/kg body weight;) as described previously. Control mice received saline only.

tag: treatment

value: control

value: about 10 weeks

value: kidney

tag: strain

tag: molecule

value: m6a modified RNAs

source_name: RNAs that without binding to the magnetic beads with anti-N6-methyadenosine (m6A) antibody

value: unmodified RNAs


title: Rat_HDLI_Test4

description: Gene expression data from frozen lung

tag: tissue


title: RB52 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 38

source_name: retinoblastoma sample RB52

value: SAMPLE 43

value: retinoblastoma


title: Rat_HDLI_Test2

description: Gene expression data from frozen lung


title: RB54 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 39

source_name: retinoblastoma sample RB54

value: SAMPLE 44


title: Control mice Replicate 2

description: Biological replicate 2 of 4. Control mice, untreated, harvested 3 days after administration of saline.


title: A1: moDC unstimulated control


title: RB51 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 37

source_name: retinoblastoma sample RB51

value: SAMPLE 42


title: Control mice Replicate 1

description: Biological replicate 1 of 4. Control mice, untreated, harvested 3 days after administration of saline.


title: RB49 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 35

source_name: retinoblastoma sample RB49

value: SAMPLE 40


title: RB50 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 36

source_name: retinoblastoma sample RB50

value: SAMPLE 41


title: Rat_HDLI_Test3

description: Gene expression data from frozen lung

value: Lung

value: 11 weeks


title: Mice treated with cisplatin Replicate 3

description: Biological replicate 3 of 4. Mice with kidney injury, treated with cisplatin, harvested 3 days after administration of cisplatin.

value: cisplatin


title: Control mice Replicate 3

description: Biological replicate 3 of 4. Control mice, untreated, harvested 3 days after administration of saline.


title: 25-Pre-Tx

source_name: metastatic tumor

value: metastatic tumor

tag: cancer type

value: MSS CRC

tag: time point

value: Pre-Tx

tag: sequencning run


title: D3stL: moDC stimulated with B. pertussis strain L

value: moDC

tag: donor

tag: stimulated with b . pertussis

value: Yes

value: L

value: Positive


title: Rat_Lung_Control10

description: Gene expression data from frozen lung

source_name: Lung of rat


title: Mice treated with cisplatin Replicate 2

description: Biological replicate 2 of 4. Mice with kidney injury, treated with cisplatin, harvested 3 days after administration of cisplatin.

value: about 10 weeks

value: kidney

value: m6a modified RNAs

value: unmodified RNAs


title: Rat_Lung_Control9

description: Gene expression data from frozen lung


title: Rat_Lung_Control8

description: Gene expression data from frozen lung


title: Rat_HDLI_Test1

description: Gene expression data from frozen lung


title: RB46 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 33

source_name: retinoblastoma sample RB46

value: SAMPLE 37

value: retinoblastoma


title: Rat_Lung_Control7

description: Gene expression data from frozen lung


title: D2stMED: moDC unstimulated control

value: No

tag: b. pertussis strain

tag: b. pertussis year of isolation


title: D6stL: moDC stimulated with B. pertussis strain L

tag: pertactin genotype

tag: batch of sequencing


title: Mice treated with cisplatin Replicate 1

description: Biological replicate 1 of 4. Mice with kidney injury, treated with cisplatin, harvested 3 days after administration of cisplatin.


title: Rat_Lung_Control5

description: Gene expression data from frozen lung

value: Lung


title: B2: moDC stimulated with B. pertussis strain L

tag: cell type

tag: sample name in supplementary file


title: Mice treated with cisplatin Replicate 4

description: Biological replicate 4 of 4. Mice with kidney injury, treated with cisplatin, harvested 3 days after administration of cisplatin.


title: D4stL: moDC stimulated with B. pertussis strain L


title: RB43 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 31

source_name: retinoblastoma sample RB43

tag: batch

tag: geo dataset serie sample id

value: SAMPLE 34


title: RB42 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 30

source_name: retinoblastoma sample RB42

value: SAMPLE 33


title: RB41 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 29

source_name: retinoblastoma sample RB41

value: SAMPLE 32


title: Rat_Lung_Control4

description: Gene expression data from frozen lung

tag: age

value: 11 weeks


title: Rat_Lung_Control3

description: Gene expression data from frozen lung


title: D6stK: moDC stimulated with B. pertussis strain K

source_name: peripheral blood mononuclear cells

value: K


title: D3stK: moDC stimulated with B. pertussis strain K

value: moDC


title: RB48 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 34

source_name: retinoblastoma sample RB48

value: SAMPLE 39


title: D1stK: moDC stimulated with B. pertussis strain K

value: Yes


title: D2stL: moDC stimulated with B. pertussis strain L

value: L

value: Positive


title: HA.Pex_RNASeq, biological rep2

city: Gothenburg

first: Yanyan

address: Chalmersplatsen 4

country: Sweden

institute: Chalmers University of Technology

description:
Yeast strain HA.Pex was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
BP2_S11_L001_R1_001

data_processing:
The raw reads from each sample were mapped to the CEN.PK 113-7D reference genome (http://cenpk.tudelft.nl) using TopHat (v 2.0.12), with 80.2—90.8% of the reads successfully mapped.
Cufflinks version 2.2.166 was used to calculate FPKM values, and the feature Counts module of the Subread package (v 1.4.6) was used to determine raw read counts.
Genome_build: CEN.PK 113-7D

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Shake flask 30 ˚C, 200rpm

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit with a FastPrep homogenizer to disrupt cells.
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 2500 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 24.7-29.8 million.

treatment_protocol: Samples of cells were frozen rapidly in liquid nitrogen to prevent mRNA turnover.

tag: strain

tag: genotype

value: Evolved strain derived from LA by UV mutagenesis with plasmid pCP-Pex

tag: protein tag


title: HA.Pex_RNASeq, biological rep3

description:
Yeast strain HA.Pex was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
BP3_S12_L001_R1_001


title: RB39 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 27

source_name: retinoblastoma sample RB39

value: SAMPLE 30

tag: tissue


title: Rat_Lung_Control6

description: Gene expression data from frozen lung


title: RB45 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 32

source_name: retinoblastoma sample RB45

value: SAMPLE 36


title: RB38 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 26

source_name: retinoblastoma sample RB38

value: SAMPLE 29


title: RB40 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 28

source_name: retinoblastoma sample RB40

value: SAMPLE 31

value: retinoblastoma


title: D2stK: moDC stimulated with B. pertussis strain K


title: Rat_Lung_Control1

description: Gene expression data from frozen lung

value: Lung


title: Rat_Lung_Control2

description: Gene expression data from frozen lung


title: HA.Nan_RNASeq, biological rep3

description:
Yeast strain HA.Nan was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
BV3_S9_L001_R1_001

value: Evolved strain derived from LA by UV mutagenesis with plasmid pCP-Nan


title: A2: moDC stimulated with B. pertussis strain K


title: HA.Pex_RNASeq, biological rep1

description:
Yeast strain HA.Pex was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
BP1_S10_L001_R1_001


title: H1: moDC stimulated with B. pertussis strain J

value: J


title: RB34 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 24

source_name: retinoblastoma sample RB34

value: SAMPLE 26


title: D1stL: moDC stimulated with B. pertussis strain L


title: HA.Nan_RNASeq, biological rep2

description:
Yeast strain HA.Nan was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
BV2_S8_L001_R1_001


title: HA.Nan_RNASeq, biological rep1

description:
Yeast strain HA.Nan was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
BV1_S7_L001_R1_001


title: RB37 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 25

source_name: retinoblastoma sample RB37

value: SAMPLE 28


title: RB31 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 23

source_name: retinoblastoma sample RB31

value: SAMPLE 23


title: LA.Pex_RNASeq, biological rep3

description:
Yeast strain LA.Pex was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
CP3_S6_L001_R1_001

value: MATa URA3 HIS3 LEU2 TRP1 SUC2 MAL2-8c tpi1(41-707)::loxP-KanMX4-loxP with plasmid pCP-Pex


title: RB30 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 22

source_name: retinoblastoma sample RB30

value: SAMPLE 22


title: D3stJ: moDC stimulated with B. pertussis strain J

value: moDC

value: Yes


title: LA.Pex_RNASeq, biological rep2

description:
Yeast strain LA.Pex was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
CP2_S5_L001_R1_001


title: A3: moDC stimulated with B. pertussis strain K

value: K

value: Positive


title: D3: moDC stimulated with B. pertussis strain J


title: RB28 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 21

source_name: retinoblastoma sample RB28

value: SAMPLE 20


title: D2stJ: moDC stimulated with B. pertussis strain J


title: RB27_REP2 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 20

source_name: retinoblastoma sample RB27 replicat 2

value: SAMPLE 19


title: LA.Pex_RNASeq, biological rep1

description:
Yeast strain LA.Pex was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
CP1_S4_L001_R1_001


title: infected A549 cells rep3 (miRNA)

city: Harbin

first: Zhiyuan

last: Qu

address: Haping road 678

department: State Key Laboratory of Veterinary Biotechnology

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.Bowtie2(2.2.8) was used for mapping reads to ribosome RNA database.The remaining reads were further used in assembly and analysis of mRNAs and circRNAs.
The rRNA removed reads of each sample were then mapped to reference genome by Tophat2(2.1.1). The alignment parameters were as follows: 1) maximum read mismatch is 2. 2) Diables the coverage based search for junctions. 3) The distance between mate-pair reads is 50 bp. 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80 bp. The mapped reads were used for mRNA analysis and the unmapped reads were used for circRNA analysis
The reconstruction of mRNA was carried out with software Cufflinks(2.2.1), and then we used Cuffmerge to merge mRNA from different replicas of a group into comprehensive set of mRNA, and then merge the mRNA for further downstream differential expression analysis
20mers from both ends of the unmapped reads that aligned to GRCh38.p12 in the reversed orientation (head-to-tail) were extracted and then were subjected to find_circ to identify circRNAs
All of the clean tags of miRNA were then searched against miRBase database (release 21) to identify known miRNAs.
The mRNA expression level was normalized by using FPKM (Fragments per kilobase of transcript per million mapped reads) and the circRNAs expression level was normalized by RPM (Reads per million mapped reads). The miRNA expression level was calculated and normalized to TPM (transcripts per million).
The edge R package was used for differentially expression of mRNAs and circRNAs and miRNAs.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each mRNA Sample.
tab-delimited text files include RPM values for each circRNA Sample.
tab-delimited text files include TPM values for each miRNA Sample.

source_name: A549 cells

growth_protocol: A549 cells were grown in nutrient mixture F-12 Ham Kaighn’s modified medium or Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum  at 37℃ in a humidified 5% CO2 atmosphere.

extract_protocol:
RNA was harvested using Trizol reagent.
After removing the rRNAs, half of the total enriched RNA was used for circRNA and mRNA library construction, and the other half was size-selected by polyacrylamide gel electrophoresis to enrich for 18–30 nt RNAs for small RNA library construction. To construct circRNA and mRNA libraries, fragmented RNAs were reverse-transcribed into cDNA by using random primers, and the cDNA fragments were purified with a QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to illumina sequencing adapters. Then, Uracil-N-Glycosylase was used to digest the second-strand cDNA. The digested products were amplified by PCR.To construct the small RNA library, the 3’ and 5’ illumina sequencing adaptors were ligated to the RNAs, and the ligation products were reverse-transcribed, amplified.

treatment_protocol: A549 cells were mock-infected or infected with H9N2 virus for 12 h

tag: cell line

tag: infection

value: H9N2 virus infected for 12 h


title: D1stJ: moDC stimulated with B. pertussis strain J

tag: donor


title: LA.Nan_RNASeq, biological rep3

description:
Yeast strain LA.Nan was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
CV3_S3_L001_R1_001

value: MATa URA3 HIS3 LEU2 TRP1 SUC2 MAL2-8c tpi1(41-707)::loxP-KanMX4-loxP with plasmid pCP-Nan


title: infected A549 cells rep2 (miRNA)


title: RB25 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 18

source_name: retinoblastoma sample RB25

value: SAMPLE 18

value: retinoblastoma


title: RB27_REP1 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 19

source_name: retinoblastoma sample RB27 replicat 1


title: LA.Nan_RNASeq, biological rep2

description:
Yeast strain LA.Nan was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
CV2_S2_L001_R1_001


title: G1: moDC stimulated with B. pertussis strain H

tag: stimulated with b . pertussis

value: H


title: infected A549 cells rep1 (miRNA)


title: LA.Nan_RNASeq, biological rep1

description:
Yeast strain LA.Nan was cultured in SD-2xSCAA medium, cells were collected at OD600 1.0
CV1_S1_L001_R1_001


title: RB24 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 17

source_name: retinoblastoma sample RB24

value: SAMPLE 17


title: Hela WT, biological replicate 3 reanalysis

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description: Gene expression data from hela WT cells

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on Affymetrix Human Genome U133 Plus 2.0 Array

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 .

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: hela WT cells

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: The hela stable clones overexpressing TFEB-3xFLAG and hela WT were grown in standard conditions.

extract_protocol: Total RNAs from either WT and TFEB-3xFLAG hela cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

value: HeLa


title: D6stH: moDC stimulated with B. pertussis strain H

source_name: peripheral blood mononuclear cells

tag: b. pertussis strain


title: TFEB-3xFLAG, biological replicate2

description: Gene expression data from hela stable clone overexpressing TFEB-3xFLAG

treatment_protocol: The hela stable clones overexpressing TFEB-3xFLAG and hela WT were grown in standard conditions.


title: uninfected A549 cells rep3 (miRNA)

value: untreated


title: RBsjd9 (SNP_CytoScan)

description: SNP array data from retinoblastoma samples

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
SNP arrays were analyzed using the Genome Alteration Print method71 (Popova et al., 2009), which takes into account both the log ratio and B allele frequency signals to determine normal cell contamination, tumor ploidy and the absolute copy-number of each segment.
CN : Copy Number, BA : B allete Frequency

source_name: retinoblastoma sample RBsjd9

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Immediately following enucleation, a needle was inserted through the anterior chamber of the eye to extract a tumor sample by aspiration. The tumor specimen was placed in RPMI medium on ice, cells were re-suspended, counted and separated into two tubes (for DNA and RNA preparation). The tubes were then centrifuged to remove all media and snap frozen for later extraction.

extract_protocol: For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A.  DNA was then extracted using a standard phenol-chloroform protocol

tag: geo dataset serie

value: SAMPLE 115


title: TFEB-3xFLAG, biological replicate3

source_name: hela stable clone overexpressing TFEB-3xFLAG


title: Hela WT, biological replicate 2 reanalysis

description: Gene expression data from hela WT cells


title: RB23 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 16

source_name: retinoblastoma sample RB23

value: SAMPLE 16


title: uninfected A549 cells rep2 (miRNA)


title: RB21_REP2 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 15

source_name: retinoblastoma sample RB21 replicat 2

value: SAMPLE 14


title: RB21_REP1 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 14

source_name: retinoblastoma sample RB21 replicat 1


title: D1stH: moDC stimulated with B. pertussis strain H

value: moDC

tag: b. pertussis year of isolation

tag: pertactin genotype


title: RBsjd8 (SNP_CytoScan)

source_name: retinoblastoma sample RBsjd8

value: SAMPLE 114


title: D2stH: moDC stimulated with B. pertussis strain H

tag: cell type

value: Yes

tag: batch of sequencing


title: RBsjd3 (SNP_CytoScan)

source_name: retinoblastoma sample RBsjd3

value: SAMPLE 112


title: D6stJ: moDC stimulated with B. pertussis strain J

value: J

value: Positive

tag: sample name in supplementary file


title: Monocytes primed with heat-killed L. plantarum HK3_6d

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description:
Monocytes primed with heat-killed L. plantarum
Group_3

data_processing:
FASTQ files were aligned to Genome data base using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/],and read counts obtained for each gene
Differential Expression was estimated using DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281] and edgeR [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/]
Genome_build: human (hg38)
Supplementary_files_format_and_content: A plain text file (*.tsv) was generated for the whole project, consisting in a matrix with two sort of columns: 1st column contains gene IDs (ENTREZ_GENE_ID), and then, from the 2nd to the 10th columns, the numbers of raw counts obtained by STAR per gene and per sample are depicted

source_name: Monocytes

growth_protocol: Monocytes were obtained from buffy coats from healthy human donors

extract_protocol:
RNA was extracted using NucleoSpin RNA extraction kit from Macherey-Nagel
Sequencing libraries were prepared following the protocol NuGEN Universal Plus mRNA-Seq kit (PART NO. 0508, 9133, 9134) (Tecan Genomics, Inc.; NuGEN) following the manufacturer’s instructions.
mRNA stranded library sequencing

treatment_protocol: Monocytes were stimulated with culture medium alone or in the presence of either live or heat-killed L. plantarum for 24 h. Stimuli were washed away and cells were rested for 6 days. After that, all monocytes were re-stimulated with live L. plantarum for 24 h.

value: Monocytes

tag: treatment

value: Heat-killed L. plantarum-Live L. plantarum


title: RBsjd2 (SNP_CytoScan)

source_name: retinoblastoma sample RBsjd2

value: SAMPLE 111


title: RB14_REP2 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 12

source_name: retinoblastoma sample RB14 replicat 2

tag: batch

tag: geo dataset serie sample id

value: SAMPLE 12

value: retinoblastoma


title: RB15 (methylation)

description:
Genome methylation data from retinoblastoma samples
Methylation_processed_data.RData
Methylation_raw_data.RData
format_data_for_GEO_submission_methylation_data_retino.R
Raw_data_i_methylation_retino_all_samples.csv
processed_data_i_methylation_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 13

source_name: retinoblastoma sample RB15

value: SAMPLE 13


title: F1: moDC stimulated with B. pertussis strain G

value: G


title: TFEB-3xFLAG, biological replicate1

value: HeLa


title: Monocytes primed with heat-killed L. plantarum HK2_6d


title: Hela WT, biological replicate 1 reanalysis

description: Gene expression data from hela WT cells