title: 7A_L3 H358 lung cells

source_name: 7A_L3 H358 lung cells


title: UM1_ChIP_seq_Ab2

status: Public on Jan 23 2019

type: SRA

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description: UnMutCLL-H3K4me1_peaks.broadPeak.sorted.bam.bedgraph.gz

library_source: genomic

data_processing:
For ChIP seq, Raw reads containing adapter sequences, were removed using CutAdapt v2.2.1.
Cleaned reads were than aligned to GRCh38 reference genome, using Bowtie v1.0.0 --best -n 2 -k 1 -m 1 -t.
Aligned reads were used to call peaks with MACS v2.1.0 -f BAM --broad --broad-cutoff 0.05 -B -g hs, over corresponding inputs.
After peak calling for each sample, UCSC’s tool WigCorrelation was used on BED files, to estimate the correlation between samples.
For RNA seq, Raw reads containing adapter sequences, were removed, using CutAdapt v2.2.1. Cleaned reads were aligned using STAR v2.5.2b. Aligned reads were used for quantification, using SubRead v1.5.2 FeatureCount with Gencode v24 annotation. Normalization of read counts was performed with RPKM normalization, using an in-house script.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts, RPKM values

molecule: genomic DNA

organism: Homo sapiens

source_name: Human Peripheral Blood

extract_protocol:
For hMeDIP and MeDIP seq, genomic DNA was extracted using  DNA extraction kit, Total RNA for RNA seq was extracted using RNA extraction kit and then quality was asses using Bioanalyser. For ChIP seq chromatin was extracted, sponicated and specific antibody was used to pulldown the ChIP DNA.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: tissue

value: Human Peripheral Blood

tag: tumor type

value: Chronic lymphocytic leukemia

tag: tumor classification

value: IGHV unmutated CLL


title: M6_ChIP_seq_Ab2

description: MutCLL-H3K4me1_peaks.broadPeak.sorted.bam.bedgraph.gz

value: IGHV Mutated CLL


title: UM1_ChIP_seq_Ab1

description: UM-CLL-H3K27ac_peaks.broadPeak.sorted.bam.bedgraph.gz


title: M3_ChIP_seq_Ab1

description: M-CLL-H3K27ac_peaks.broadPeak.sorted.bam.bedgraph.gz


title: M4_ChIP_seq_Ab2


title: M2_ChIP_seq_Ab1


title: M6_ChIP_seq_Ab1


title: M4_ChIP_seq_Ab1


title: M1_ChIP_seq_Ab2


title: Bcell-N3-RNAseq

library_source: transcriptomic

molecule: total RNA

value: Normal healthy control

value: Normal B cell


title: Bcell-N2-RNAseq


title: Bcell-N5-RNAseq


title: M1_ChIP_seq_Ab1


title: Bcell-N4-RNAseq


title: B-cell-RNAseq


title: Bcell-N1-RNAseq


title: Mem-B-cell-RNAseq

value: Class switched memory B cell


title: Mar-B-cell-RNAseq

value: Non class switched memory B cell


title: M10-RNAseq


title: UM7_RNAseq


title: M8-RNAseq


title: UM1_RNAseq


title: UM2_RNAseq


title: M7_RNAseq


title: M6_RNAseq


title: M9-RNAseq


title: M4_RNAseq


title: M3_ChIP_seq_Ab2


title: Naive-B-cell-RNAseq

value: Naive B cell


title: M1_RNAseq


title: M2_RNAseq


title: UM-INPUT-MeDIP

description:
MeDIP seq
UM-new-MeDIP_peaks.broadPeak.sorted.bam.bedgraph.gz


title: UM3_RNAseq


title: Mem-B-INPUT-MeDIP

description:
MeDIP seq
Mem-Bcell-MeDIP-peaks_peaks.broadPeak.sorted.bam.bedgraph.gz


title: B-cell-INPUT-MeDIP

description:
MeDIP seq
Bcell-MeDIP-repeats_peaks.broadPeak.sorted.bam.bedgraph.gz


title: M3_RNAseq


title: Naive-B-INPUT-MeDIP

description:
MeDIP seq
Naive-Bcell-MeDIP-peaks_peaks.broadPeak.sorted.bam.bedgraph.gz


title: Naive-B-cell-MeDIP


title: UM7-MeDIP


title: Mar-B-cell-MeDIP

description:
MeDIP seq
Mar-Bcell-MeDIP-peaks_peaks.broadPeak.sorted.bam.bedgraph.gz


title: UM2_MeDIPSET2


title: UC-MSC6

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: primary cells were passaged to 5th generation before RNA extract

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence to get the clean reads
Then the clean reads were mapped to hg38 whole genome using HISAT2
FPKM and Count values were calculated using StringTie and Ballgown
Genome_build: hg38
Supplementary_files_format_and_content: xls file includes RPKM values and count values for each Sample …

source_name: umbilical cord mesenchymal stem cells

growth_protocol: Primary MSCs were isolated and the routinely cultured and spilt until passage 5.

extract_protocol:
Medium was removed, cells were washed with PBS, and RNA was harvested using Trizol reagent.
The sequencing library for Illumina HiSeq 4000 sequencer was constructed with 0.2 μg of total RNA of each sample by PE150 strategy.

treatment_protocol: No treatment

value: umbilical cord

tag: cell type

value: primary mesenchymal stem cells

tag: passage


title: P-MSC6

source_name: chorionic plate mesenchymal stem cells

value: chorionic plate


title: UC-MSC4


title: UC-MSC5


title: UM3_MeDIPSET2


title: UM5_MeDIPSET2


title: P-MSC5


title: P-MSC4


title: UC-MSC3


title: M9-MeDIP

description:
MeDIP seq
M-new-MeDIP_peaks.broadPeak.sorted.bam.bedgraph.gz


title: P-MSC3


title: Mar-B-INPUT-MeDIP


title: M8-MeDIP


title: B-cell-MeDIP


title: Mem-B-cell-MeDIP


title: M-INPUT-MeDIP


title: AM-MSC6

source_name: amnionic membrane mesenchymal stem cells

value: amnionic membrane


title: M6_MeDIPSET2


title: M5_MeDIPSET2


title: AM-MSC3


title: UM1_MeDIPSET2


title: M2_MeDIPSET2


title: AM-MSC4


title: M3_MeDIPSET2


title: Naive-B-cell-hMeDIP

description:
hMeDIP seq
Naive-Bcell-hMeDIP-peaks_peaks.broadPeak.sorted.bam.bedgraph.gz


title: UM7-hMeDIP

description:
hMeDIP seq
UnMutated-hMeDIP-peaks_peaks.broadPeak.sorted.bam.bedgraph.gz


title: AM-MSC5


title: M4_MeDIPSET2


title: Mem-B-cell-hMeDIP

description:
hMeDIP seq
Mem-Bcell-hMeDIP-peaks_peaks.broadPeak.sorted.bam.bedgraph.gz


title: M1_MeDIPSET2


title: UM2_hMeDIP


title: UM1_hMeDIP


title: M10-hMeDIP

description:
hMeDIP seq
Mutated-hMeDIP-peaks_peaks.broadPeak.sorted.bam.bedgraph.gz


title: M9-hMeDIP


title: UM5_hMeDIP


title: UM3_hMeDIP


title: M10-MeDIP


title: Mar-B-cell-hMeDIP

description:
hMeDIP seq
Mar-Bcell-hMeDIP-peaks_peaks.broadPeak.sorted.bam.bedgraph.gz


title: B-cell-hMeDIP

description:
hMeDIP seq
Bcell-MeDIP-peaks_peaks.broadPeak.sorted.bam.bedgraph.gz


title: M7-MeDIP


title: M6_hMeDIP


title: M4_hMeDIP


title: M5_hMeDIP


title: M7-hMeDIP


title: M8-hMeDIP


title: M3_hMeDIP


title: 28-T26-TTR-CII

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

data_processing:
Quality filtering was performed using cutadapt v. 1.7.1.
Reads were mapped against the human reference genome using the STAR aligner v.2.5.2a.
Read counts per gene were obtained using RSEM program v.1.2.31 and the Ensembl gtf annotation file.
Following analyses were performed using R. Differential expression analysis was performed with the limma v.3.34.5 and edger v.3.20.6 packages.
Genome_build: Ensembl gtf annotation file (release GRCh38.10)
Supplementary_files_format_and_content: *.genes.results: Tab-delimited text files include TPM and FPKM values for each Sample.

source_name: Colon biopsies

extract_protocol:
Tissue RNA was isolated by RNeasy Kit (Qiagen, Spain) according to the manufacturer's instructions. RNA were quantified by NanoDrop spectrophotometer (NanoDrop Technologies, USA). The purity and integrity of the total RNA were assessed via 2100 Bioanalyzer (Agilent, Germany). All RNA samples analyzed had a RNA Integrity Number ≥ 7.
Barcoded RNA sequencing libraries were prepared from 100 ng total RNA using Illumina’s TruSeq stranded mRNA kit according to the manufacturer’s instructions.
Libraries were subjected to paired-end sequencing (101 bp) on a HiSeq-4000 platform (Illumina, San Diego, CA).

tag: disease

value: Crohn's disease (CD)

value: Colon biopsy

tag: week of hsct treatment

tag: hsct responder

value: YES

tag: sescd global

tag: cdai

tag: Sex

value: female

tag: individual id


title: 28-T106-TTR-CII


title: 28-T52-TTR-CII


title: 31-T26-TTR-CIA

value: NO


title: 31-T52-TTR-CIA


title: osk_d8_c96

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts and transcripts per million(TPM) were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).

organism: Mus musculus

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: Mouse ESCs (mESCs) and iPS cell lines were cultured on feeder layers with mESC medium (high glucose DMEM, 15%FBS, NEAA, GlutaMAX, LIF) plus 2i (1 m PD0325901, 3 m CHIR99021). MEF cells were maintained in 10% FBS medium (high glucose DMEM supplemented with 10% FBS, GlutaMAX and NEAA). The reprogramming cells at different days were cultured in iCD1 medium.

extract_protocol:
For bulk cells, total RNAs were extracted by chloroform-isopropanol method; for single cell, following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).
Single cell libraries were constructed following the protocol of Using the C1 Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing (Fluidigm, PN 100-5950 B1).

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)

tag: strain background


title: osk_d8_c95


title: osk_d8_c85


title: osk_d8_c9


title: osk_d8_c88


title: osk_d8_c90


title: 26-T26-TTR-CII


title: 26-T52-TTR-CII


title: 27-S0-TTR-CII


title: 26-T106-TTR-CIA


title: 27-T26-TTR-CII


title: 27-T52-TTR-CIA


title: M2_hMeDIP

value: Human Peripheral Blood

value: Chronic lymphocytic leukemia


title: osk_d8_c83


title: osk_d8_c81


title: osk_d8_c79


title: 26-S0-TTR-CIA


title: osk_d8_c76


title: osk_d8_c75


title: osk_d8_c93


title: 28-S0-TTR-CIA


title: 31-S0-TTR-CIA


title: 22-T52-TTR-CII


title: osk_d8_c92


title: osk_d8_c91


title: 22-T26-TTR-CII


title: osk_d8_c73


title: osk_d8_c71


title: 22-T106-TTR-CII


title: osk_d8_c72


title: 22-S0-TTR-CIA


title: 21-S0-TTR-CI

value: male


title: osk_d8_c67


title: osk_d8_c68


title: 19-S0-TTR-CI


title: 18-T52-TTR-CII


title: 19-T26-TTR-CII


title: osk_d8_c61


title: osk_d8_c62


title: osk_d8_c63


title: osk_d8_c60


title: 18-T26-TTR-CIA


title: 18-S0-TTR-CI


title: osk_d8_c58


title: 16-T52-TTR-CII


title: osk_d8_c56


title: 16-T26-TTR-CII


title: osk_d8_c53


title: 16-T106-TTR-CII


title: osk_d8_c51


title: 16-S0-TTR-CI


title: 19-T52-TTR-CIA


title: osk_d8_c7


title: osk_d8_c5


title: osk_d8_c47


title: 14-T106-TTR-CII


title: 14-T26-TTR-CI


title: 13-T52-TTR-CI


title: osk_d8_c43


title: 13-T106-TTR-Cii


title: osk_d8_c52


title: osk_d8_c44


title: osk_d8_c42


title: PfsmallRNA

first: Zhensheng

last: Wang

address: Dongdan santiao

department: Microbiology and Parasitology

institute: Peking Union Medical College

data_processing:
Illumina Casava1.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, discard the 5’ adaptor contaminations, sequences containing the polyA tail as well as those smaller than 18 nt or bigger than 30 nt, then collapsed to remove the redundant reads to produce unique clean reads.
The clean reads were mapped to the plasmodium falciparum nuclear transfer RNA coding genes to produce transfer RNA derived fragments (tRFs) data by bowtie2 (v2.1.0.0) with the parameters -f -D 15 -R 2 -N 1 -L 10 -i S,1,1.75.
Genome_build: plasmodium falciparum strain 3D7 v28

organism: Plasmodium falciparum 3D7

source_name: Red blood cells infected with plasmodium falciparum parasite

growth_protocol: The standard Plasmodium falciparum strain 3D7 (Pf3D7) was maintained within fresh human red blood cells  at 5% hematocrit in RPMI-1640 medium supplemented with 0.5% (w/v) albumax II (Invitrogen, CA, USA),  Parasitemia was monitored by Giemsa staining of blood smears.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: developmental stage

value: mixed with ring, trophozoite, schizont stages


title: osk_d8_c40


title: 14-T52-TTR-CII


title: cerebral malaria F U133B array

type: RNA

city: Tübingen

first: Angelica

last: Boldt

address: Wilhelmnstr 27

country: Germany

institute: Institute for Tropical Medicine

description: Gene expression data from pooled RNA of whole blood from 4 children with cerebral malaria

hyb_protocol: After purification and precipitation at -20°C, we fragmented 20 µg of this cRNA by heat and ion-mediated hydrolysis at 94°C [200 mM Tris-acetate (pH 8.1), 500 mM KOAc, 150 mM MgOAc] and hybridized it to the microarray. We also added increasing concentrations of spiked controls expected to hybridize to the 5’ and 3’ transcript regions of the Escherichia coli genes bioB, bioC and bioD and of the cre gene of the P1 bacteriophage. We hybridized the arrays with the targets at 45°C for 16 h and then washed them at 25°C with 6 x saline sodium phosphate-EDTA (0.9 M NaCl, 60 mMNaH2PO4, 6 mM EDTA+0.01% Tween 20) for 10 min, followed by a stringent wash at 50°C with 100 mM MES, 0.1 M [Na+], 0.01% Tween 20 for 12 min. We then stained the arrays with 10 μg/ml phycoerythrin-conjugated streptavidin (Molecular Probes Europe BV, Leiden, Netherlands) during 10 min. We did the hybridization, washing and staining procedures using the GeneChip® Fluidics Station 400 (Affymetrix, Santa Clara, CA).

scan_protocol: We determined the fluorescence intensities using a laser confocal scanner (Agilent GeneArray ® Scanner), with excitation 488 nm, spot size 4 µm and pixel space 3µm and analyzed the scanned images using Affymetrix® Microarray Suite version 5.0 (Affymetrix, Santa Clara, CA).

data_processing: We standardized for sample loading and variations in staining by scaling the signals on all arrays to constant target intensity (TGT 150).All microarray results were homogeneous with respect to average background, noise (Raw Q) and percent of genes called present, had spiked control signals within the expected range and adequate 3’/5’ ratio values (under 3) of the signals of the housekeeping gene transcripts (GAPDH, 18SrRNA). The scaling factors of all arrays compared to each other did also not differ by a factor higher than 3.3. These facts allowed us to compare the signals between the microarrays of two groups, totalizing 25 AxCo, 25 UxA, 25 UxCo, 25 SxCo, 25 SxA, 25 SxU, 26 CexCo, 25 CexA, 25 CexU, and 25 SxU comparisons for U133A and U133B (but two U133B microarrays of asymptomatic infection and one of cerebral malaria could not be used due to low hybridization quality, in this case totalizing 15 AxCo and 20 CexCo, CexA, CexU and CexS U133B comparisons). We calculated the signals on the arrays, the signal ratios between them and the corresponding measure of likelihood of change and direction (called “change p-value”) with aid of the Affymetrix® Microarray Suite version 5.0 (Affymetrix, Santa Clara, CA). We excluded probe sets whose signal intensities reached values under 50 in all the investigated groups and considered the expression of a certain gene as increased or decreased if it varied positively by a factor ≥ 1.9 or negatively by a factor ≤ -1.9 and the corresponding change p-value resulted in decreases to lower than 0.15 or in increases to higher than 0.85, respectively, in at least 15 comparisons. We used the one class analysis of the Significance Analysis of Microarrays (SAM) program for the signal ratios (logged on base 2) to identify those genes having significant changes at a false discovery rate of 0.004%.

label: biotin

source_name: pooled whole blood RNA of 4 African children with cerebral malaria

label_protocol: We prepared cRNA and labeled it with biotinylated UTP and CTP by in vitro transcription using a T7 promoter-coupled double-stranded cDNA as template and the T7 RNA Transcript Labeling Kit (ENZO Diagnostics Inc., Farmingdale, NY).

extract_protocol: We extracted whole blood RNA using the PAXgene Blood RNA System (Qiagen, Hilden), pooled it in equal amounts to a total of 5 µg from four individuals and synthesized the first- and second-strand cDNA by using the SuperScript Double-Stranded cDNA Synthesis Kit (Life Technologies Inc., Rockville, MD) and an oligo-dT24-T7 primer.

value: pooled whole blood RNA of 4 samples

value: children

tag: diesease status

value: with cerebral malaria


title: severe malaria E U133B array

description: Gene expression data from pooled RNA of whole blood from 4 children with severe malaria

source_name: pooled whole blood RNA of 4 severely anemic African children with malaria

value: with malaria associated with severe anemia


title: cerebral malaria E U133B array


title: severe malaria D U133B array


title: osk_d8_c4


title: cerebral malaria C U133B array


title: cerebral malaria G U133B array


title: uncomplicated malaria H U133B array

source_name: pooled whole blood RNA of 4 African children with uncomplicated malaria

value: with uncomplicated malaria


title: osk_d8_c46


title: uncomplicated malaria G U133B array

description: Gene expression data from pooled RNA of whole blood from 4 children with uncomplicated malaria


title: severe malaria A U133B array


title: severe malaria C U133B array


title: severe malaria B U133B array


title: osk_d8_c31


title: uncomplicated malaria D U133B array


title: uncomplicated malaria F U133B array


title: osk_d8_c3


title: ILC2_CBFβ KO_rep3

city: ALBANY

first: Xiaofei

last: Shen

state: New York

address: 47 NEW SCOTLAND AVENUE

department: Immunology & Microbial Diseases

country: USA

institute: Albany Medical College

description: Gene expression data fromCBFβ CRISPR ILC2 line at 6 days post-transduction

hyb_protocol: Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA

data_processing: CDF: mogene20st_Mm_ENTREZG_17.1.0. Mouse Gene 2.0 ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affymetrix package (version 1.36.1). Differential expression was assessed using the moderated (empirical Bayesian) t test implemented in the limma package (version 3.14.4).

source_name: ILC2, CBFβ CRISPR, 6 days post-transduction

growth_protocol: C57BL/6J mice ILC2 lines were cultured with 10ng/ml of IL-2 and IL-33

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

treatment_protocol: gRNAs targeting CBFβ or Non-target control were inserted into LentiV2CRISPRGFP constructs to generate CRISPR knockout constructs. Lentivirus were prepared and transduced into ILC2 line cells.  GFP+ cells were sorted at 6 days post-transduction

tag: cell line

tag: growth for cell line

tag: background strain

tag: genotype

value: CBFBeta knock out


title: osk_d8_c29

tag: cell type


title: osk_d8_c27


title: uncomplicated malaria E U133B array

tag: tissue


title: osk_d8_c22


title: osk_d8_c23


title: osk_d8_c21


title: Female_CCI_rep2

city: Baltimore

first: Sean

last: Taverna

state: MD

address: 855 N Wolfe St

department: Pharmacology & Molecular Sciences

institute: Johns Hopkins University

data_processing:
Casava v1.8.2 used for base calling
Reads trimmed for adapter sequence
Reads mapped to rn6 genome using HISAT2
Genome_build: rn6
Supplementary_files_format_and_content: Count table contains raw transcript counts for each annotated genes generated uisng the summarizedOverlaps function of the Genomic Alignments package in R

organism: Rattus norvegicus

extract_protocol:
ipsilateral L4-L6 DRGs removed and flash frozen on dry ice, RNA extracted using Qiagen miniRNAeasy kit
RNA libraries constructed using NEBNext Ultra directional RNA library prep kit after poly(A)-RNA selection

treatment_protocol: CCI to sciatic nerve

value: Female

tag: group

value: CCI

value: Sprague-Dawley

value: DRG


title: ILC2_CBFβ KO_rep1

description: Gene expression data fromCBFβ CRISPR in ILC2 line at 6 days post-transduction

scan_protocol: Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA

value: ILC2 lines were cultured with 10ng/ml of IL-2 and IL-33


title: Col2CE_P0-2

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

description: FACS-sorted at P2

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and t-SNE), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10_trans_nono, available on the series record.
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz with UMI counts

source_name: Growth plate (femurs)

extract_protocol:
Femur growth plates were dissected, growth plate chondrocytes were enzymatically dissociated and tdTomato+ cells were FACS-isolated. ~18,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v3
10X Genomic Chromium Single Cell 3' v3 Libraries

value: Col2a1-creER; R26R(tdTomato/+)

value: Col2a1+ growth plate chondrocytes (tdTomato+)


title: osk_d8_c2

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)


title: Female_CCI_rep1


title: Asymptomatic G U133B array

source_name: pooled whole blood RNA of 4 African children with asymptomatic infection

value: with asymptomatic Plasmodium falciparum infection


title: ILC2_CBFβ KO_rep2

description: Gene expression data from CBFβ CRISPR ILC2 line at 6 days post-transduction

label_protocol: Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA


title: ILC2_control_rep2

description: Gene expression data from non-target control (NTC) CRISPR ILC2 line at 6 days post-transduction

source_name: ILC2, NTC CRISPR, 6 days post-transduction

treatment_protocol: gRNAs targeting CBFβ or Non-target control were inserted into LentiV2CRISPRGFP constructs to generate CRISPR knockout constructs. Lentivirus were prepared and transduced into ILC2 line cells.  GFP+ cells were sorted at 6 days post-transduction.

value: ILC2 cell lines were cultured with 10ng/ml of IL-2 and IL-33

value: Non-target Control


title: Asymptomatic C U133B array

description: Gene expression data from pooled RNA of whole blood from 4 children with asymptomatic infection

value: pooled whole blood RNA of 4 samples


title: Female_Naive_rep2

value: naive


title: Asymptomatic F U133B array

value: children


title: osk_d8_c19


title: ILC2_control_rep1


title: osk_d8_c24


title: ILC2_control_rep3


title: controls E U133B array

description: Gene expression data from pooled RNA of whole blood from 4 healthy children

source_name: pooled whole blood RNA of 4 healthy African children

value: healthy


title: osk_d8_c18


title: Female_Naive_rep1


title: controls C U133B array


title: osk_d8_c16


title: Male_CCI_rep2

value: Male


title: controls NA01 U133B array


title: EM23

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalized using quantile normalization with BeadStudio software v3.8

source_name: Formalin-fixed, paraffin-embedded (FFPE) tumor specimen

label_protocol: Illumina WG-DASL protocol

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: pfs_time (days)

tag: performance status

tag: Stage

value: IVA

tag: primary vs recurrent/metastatic tumor

value: R/M


title: osk_d8_c15


title: EM11

value: IV

value: primary


title: osk_d8_c12


title: Male_Naive_rep2

tag: Sex

value: Sprague-Dawley

value: DRG


title: EM21

value: III


title: FA35


title: Male_Naive_rep1


title: Male_CCI_rep1

value: CCI


title: osk_d8_c11

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)


title: osk_d8_c10


title: controls NA06 U133B array


title: osk_d8_c1


title: osk_d7_c24


title: EM14

value: II


title: EM15


title: osk_d5-c_c47


title: controls B U133B array


title: FA34


title: FA38


title: EM24


title: FA37


title: osk_d5-c_c46


title: EM25


title: EM13


title: FA39


title: osk_d5-c_c45


title: EM17


title: genomic DNA from tumor, ccRCC sample Pat6_2

type: genomic

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

institute: Umeå University

description: ccRCC Tumor Tissue Sample

hyb_protocol: bisulphite converted DNA (EZ DNA methylation gold) was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol.

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

data_processing: Fluorescence intensities were extracted using the Methylation module (1.9.0) in the Genome Studio software (V2011.1). CpG-sites at chromosome X and Y, detection p-value>0.05, nbeads <=3 or located within 3 bp from known SNP in any the samples 1-127 were filtered (set to NA) in samples 1-127. CpG-sites meeting the criteria in any of Pat1-Pat6 and Tumor free samples (116-127) were filtered in samples Pat1-Pat6. Bead types were normalized using the BMIQ method.

label: Cy5 and Cy3

source_name: ccRCC

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted accordint to standard protocols and DNA purity and concentration determined by spechtrophotometry.

treatment_protocol: Tumor samples were snap-frozen after extirpation and stored at -80 degrees celcius.

tag: age

tag: gender

tag: tnm stage

value: TNM II

tag: progress status (m0-pf

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):N/A


title: Lung Cancer 2424

city: Heidelberg

first: Sven

last: Diederichs

address: Im Neuenheimer Feld 280

department: RNA Biology & Cancer

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Agilent gene expression hybridization kit

scan_protocol: Agilent scanner

data_processing: Agilent Feature Extraction Software (FE) 10.7.3.1.

source_name: Lung Cancer

label_protocol: Invitrogen SuperScript Indirect cDNA labeling system

extract_protocol: Qiagen RNeasy Mini Kit from fresh frozen tissue samples cut into cryosections

value: Lung Adenocarcinoma


title: Lung Cancer 2041


title: genomic DNA from tumor, ccRCC sample Pat6_1

description: ccRCC Tumor Tissue Sample


title: Lung Cancer 2578


title: Lung Cancer 2299


title: Lung Cancer 2076


title: osk_d5-c_c44

tag: strain background


title: osk_d3-c_c53


title: Lung Cancer 2022


title: EM20

value: IVB


title: EM16


title: genomic DNA from tumor, ccRCC sample Pat4_1

description: ccRCC Tumor Tissue Sample

value: TNM I


title: EM30


title: Lung Cancer 0972


title: osk_d3-c_c48


title: osk_d3-c_c22


title: genomic DNA from tumor, ccRCC sample Pat5_2

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample Pat4_2

description: ccRCC Tumor Tissue Sample


title: osk_d3-b_c28


title: genomic DNA from tumor, ccRCC sample Pat4_3

description: ccRCC Tumor Tissue Sample


title: EM19


title: Lung Cancer 0817


title: genomic DNA from tumor, ccRCC sample Pat3_3

description: ccRCC Tumor Tissue Sample


title: osk_d3-b_c19


title: genomic DNA from tumor, ccRCC sample Pat5_3

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample Pat5_1

description: ccRCC Tumor Tissue Sample


title: osk_d3_c40


title: Lung Cancer 0603


title: Lung Cancer 0591


title: EM28


title: osk_d2-b_c48


title: FA36


title: genomic DNA from tumor, ccRCC sample Pat3_1

description: ccRCC Tumor Tissue Sample


title: EM12


title: osk_d2_c35


title: genomic DNA from tumor, ccRCC sample Pat2_3

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample Pat2_2

description: ccRCC Tumor Tissue Sample


title: EM22


title: genomic DNA from tumor, ccRCC sample Pat3_2

description: ccRCC Tumor Tissue Sample


title: EM27


title: Lung Cancer 0536


title: Lung Cancer 0535


title: osk_d1-b_c05


title: Lung Cancer 0666


title: genomic DNA from tumor, ccRCC sample Pat1_3

description: ccRCC Tumor Tissue Sample


title: EM10


title: genomic DNA from tumor, ccRCC sample Pat2_1

description: ccRCC Tumor Tissue Sample


title: Lung Cancer 0490


title: mef-b_c20


title: EM09


title: Lung Cancer 0489


title: mef-b_c19


title: EH36

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software v3.8

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

tag: suject status

value: squamous cell carcinoma of the head and neck (HNSCC) patient

tag: FDG/pet response

tag: array id


title: ER78


title: genomic DNA from tumor, ccRCC sample Pat1_2

description: ccRCC Tumor Tissue Sample


title: esc-b_c79

value: OG2 transgenic mouse embryonic stem cells (OG2-mESCs)


title: genomic DNA from tumor, ccRCC sample 127

description: Tumor Free Tissue

value: TumorFree


title: genomic DNA from tumor, ccRCC sample Pat1_1

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 126

description: Tumor Free Tissue


title: Lung Cancer 0378


title: mef-b_c07


title: esc-b_c55


title: Lung Cancer 0365


title: genomic DNA from tumor, ccRCC sample 125

description: Tumor Free Tissue


title: Lung Cancer 0397


title: Lung Cancer 0284


title: EH58


title: shRPRD1B-NIH3T3-Rep3

city: San Francisco

first: Melanie

last: Ott

state: CA

address: 1650 Owens Street, 5th Floor

department: Virology and Immunology

institute: Gladstone Institutes

description:
Replicate 3
Scr-vs-RPRD1B-2.xlsx

data_processing:
Differential expression was determined using the RNA Express v 1.1.0 package designed by Illumina.
Genome_build: mm10
Supplementary_files_format_and_content: Differential expression  and counts files were generated for each pair of biological replicates that were conducted in parallel.

growth_protocol: NIH3T3 cells were grown in 10% Bovine Calf Serum supplemented with L-Glutamine and Pen/Strep at 1x concentration. Cells were treated with scrambled shRNAs or RPRD1B shRNAs (indicated in sample section), and selected appropriately with puromycin for at 1 week.

extract_protocol:
RNA was purified from 1x10^6 NIH3T3 cells using Qiagen RNeasy Plus Kit (pn: 74106; lot:157057561). cDNA was synthesized with random hexamer primers.
Libraries were prepared with the Ovation Ultralow System V2 kit pn:7102-32/0344-32 and libraries were deep sequenced on the NextSeq 500 using paired-end 75pb sequencing

treatment_protocol: RPRD1B or Scrambled shRNA selected NIH3T3 cells were selected for at least 1 week with puromycin and validated by Western blot for knockdown prior to sequencing.

tag: cell line

value: Embryonic Fibroblasts

tag: treatment

value: RPRD1B shRNA

tag: genotype

value: RPRD1B knockdown


title: Lung Cancer 0571

tag: tissue


title: ER76


title: Lung Cancer 0276


title: shRPRD1B-NIH3T3-Rep4

description:
Replicate 4
Scr-vs-RPRD1B-2.xlsx

tag: cell type


title: genomic DNA from tumor, ccRCC sample 124

description: Tumor Free Tissue


title: shRPRD1B-NIH3T3-Rep2

description:
Replicate 2
Scr-vs-RPRD1B-1.xlsx


title: Lung Cancer 0271


title: genomic DNA from tumor, ccRCC sample 123

description: Tumor Free Tissue


title: EH53


title: EH44


title: EH60


title: Lung Cancer 0210


title: shScrambled-NIH3T3-Rep4

description:
Replicate 4
Scr-vs-RPRD1B-2.xlsx

value: Scrambled shRNA

value: control


title: shScrambled-NIH3T3-Rep3

description:
Replicate 3
Scr-vs-RPRD1B-2.xlsx


title: EH52


title: shScrambled-NIH3T3-Rep2

description:
Replicate 2
Scr-vs-RPRD1B-1.xlsx


title: Lung Cancer 0030


title: Lung Cancer 0074


title: genomic DNA from tumor, ccRCC sample 120

description: Tumor Free Tissue


title: genomic DNA from tumor, ccRCC sample 121

description: Tumor Free Tissue


title: genomic DNA from tumor, ccRCC sample 122

description: Tumor Free Tissue


title: EH42


title: Lung Cancer 0161


title: EH45


title: EH56


title: shScrambled-NIH3T3-Rep1

description:
Replicate 1
Scr-vs-RPRD1B-1.xlsx


title: genomic DNA from tumor, ccRCC sample 119

description: Tumor Free Tissue


title: genomic DNA from tumor, ccRCC sample 116

description: Tumor Free Tissue


title: Normal Lung 2578

source_name: Normal Lung

value: Normal


title: genomic DNA from tumor, ccRCC sample 118

description: Tumor Free Tissue


title: EI06


title: genomic DNA from tumor, ccRCC sample 117

description: Tumor Free Tissue


title: Lung Cancer 0016


title: Normal Lung 2424


title: EH51


title: ER80


title: EH37


title: genomic DNA from tumor, ccRCC sample 114

description: ccRCC Tumor Tissue Sample

value: Male

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: Normal Lung 2299


title: genomic DNA from tumor, ccRCC sample 112

description: ccRCC Tumor Tissue Sample

value: Female


title: genomic DNA from tumor, ccRCC sample 115

description: ccRCC Tumor Tissue Sample


title: Normal Lung 0972


title: Normal Lung 2076


title: EI08


title: shRPRD1B-NIH3T3-Rep1

description:
Replicate 1
Scr-vs-RPRD1B-1.xlsx


title: Wt_5K_H3K4Me3_R1

city: Mainz

first: Junaid

last: Akhtar

state: Rheinland-Pflaz

address: Johannes-Joachim-Becherweg, 32

department: Institute of Neurobiology and Developmental Biology

institute: University of Mainz

description: 5000 wild type NSCs H3K4Me3 Profile Replicate1

data_processing:
Library strategy: TAF-ChIP
De-multiplexing and fastq file conversion was performed using blc2fastq (v.1.8.4)
Mapping was performed using bowtie2 (v. 2.3.3) against ensembl release 84 of BDGP6 for Drosophila sample and K562 samples against hg38 (ensemble release 84).
The mapped bam files were normalized to RPKM using deepTools, and bigwig coverage file was generated
Genome_build: dm6 (Drosophila melanogaster), hg38 (K562 Cells)
Supplementary_files_format_and_content: UCSC compatible library size normalised bigwig tracks

organism: Drosophila melanogaster

source_name: Neural Stem Cells

extract_protocol:
Conventional libraries: After precipitating and pelleting, DNA was dissolved in 30 μl of TE buffer pH 8.0. The recovered DNA was converted into libraries using NebNext Ultra II DNA library preparation kit, following manufacturer’s protocol.
TAF-ChIP: Fixed cells were directly sorted in 240 μl of 140mM RIPA (10mM Tris-Cl pH 8.0, 140mM NaCl, 0.1mM EDTA pH8.0, 1% Triton X-100, and 0.1% SDS), and sonicated with 3 cycles at low power settings for breaking the nuclei. 15 μl of Protein A and G Dynabeads were coupled to 1 μg of specific antibody in the blocking buffer (RIPA 140mM supplemented with 0.2 mg/ml BSA, 0.05 mg/ml of glycogen and 0.2 mg/ml of yeast t-RNA) for 3 hrs at 4°C. The unfragmented chromatin were centrifuged at 14000 rpm for 10 minutes at 4°C, and the supernatant was transferred to the tube with blocked and antibody coupled beads. The samples were incubated at 4°C overnight with head over tail rotations. The samples were then washed twice briefly with 300 μl of home made tagmentation buffer (20 mM Tris(hydroxymethyl)aminomethane pH 7.6; 10 mM MgCl2; 20% (vol/vol) dimethylformamide) using magnetic rack for beads separation. The washed beads were resupended in 20 μl of 1X tagmentation DNA buffer (Nextera XT Kit) containing 1 μl of Nextera DNA tagmentation enzyme and incubated at 37 °C for 40 minutes with constant shaking in a thermoblock at 500 rpm. Following the tagmentation, the beads were washed as following; once with 140mM RIPA (10mM Tris-Cl pH 8.0, 140mM NaCl, 0.1mM EDTA pH8.0, 1% Triton X-100, and 0.1% SDS), four times with 250mM RIPA (10mM Tris-Cl pH 8.0, 250mM NaCl, 0.1mM EDTA pH8.0, 1% Triton X-100, and 0.1% SDS) and twice with TE buffer pH8.0 (10mM Tris-Cl pH 8.0 and 0.1mM EDTA pH8.0). The samples after proteinase K treatment for reverse-crosslinking were subjected to phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 μl of TE buffer pH 8.0. The DNA was amplified in a 100 μl reaction with 1X NEBNext High-Fidelity PCR Mix with primers containing molecular indices (listed in Table 1) with following program; 72 °C for 3min, {98 °C for 10 seconds, 63 °C for 30 seconds, 72 °C for 30 seconds} for 12 cycles, 72 °C for 5 minutes, and hold at 4 °C. The PCR reaction was purified with beads based size selection to remove any fragment that might be of larger than 1000 bp size. Ampure Xp beads were added to the PCR reaction in a ratio of 0.2X ratio to bind larger fragments. The magnetic beads were separated with the help of magnetic rack and supernatant was transferred to a fresh tube. Ampure Xp beads were added to the PCR reaction in a ration of 0.8X to bind the target library. After PCR purification, libraries were analyzed on Agilent Bioanalyzer for size distribution and the concentration was measured using Qubit fluorometer. The finished libraries were pooled in equimolar amounts and sequenced on illumina NextSeq 500.

value: Neural Stem Cells

tag: tissue type

value: Larval brain

tag: ip target

tag: chip antibody

value: ab8580 (Abcam)


title: genomic DNA from tumor, ccRCC sample 113

description: ccRCC Tumor Tissue Sample


title: EH75


title: EH57


title: Normal Lung 0817


title: Normal Lung 0666


title: genomic DNA from tumor, ccRCC sample 111

description: ccRCC Tumor Tissue Sample


title: Wt_1K_H3K4Me3_R2

description: 1000 wild type NSCs H3K4Me3 Profile Replicate2


title: Hif-1a KO + chemotherapy treatment

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

data_processing:
Fastq files were created using Cellranger 1.3
Reads were mapped and UMIs counted using CellRanger 1.3
Genome_build: mm10
Supplementary_files_format_and_content: A raw count matrix was generated using Seurat v2.3.4. Genes in the rows, and cells across the columns. -1 in the cellID denotes Kochemo, -2 WTchemo, -3 KOPBS. -4 WTPBS

source_name: MLL-AF9-induced leukemic cells

growth_protocol: c-Kit+ bone marrow cells (isolated with magnetic beads) from Hif-1alphaLox/Lox; CreERT2 mice were transduced with MLL-AF9-retrovirus and transplanted into wild type mice to generate primary leukemic cells.

extract_protocol:
3 days after end of treatment, bones (crista, femur, tibia) were collected from mice and bone marrow extracted by crushing bones in mortar. GFP+ cells (MLL-AF9-transduced) were sorted by flow cytometry on a BDFacsAriaII using 70 micron nozzle.
Libraries were constructed according to 10x genomics Chromium Single Cell 3' Reagents Kit V2 Protocol

treatment_protocol: Mice were transplanted with primary leukemias. Ten days later mice were treated intraperitoneal (ip) with 1mg tamoxifen or vehicle for 5 days. Afterwards, mice were treated ip with 100 mg/Kg cytarabine for 5 days and 3mg/kg doxorubicin for 3 days or PBS as control.

value: Bone Marrow

tag: strain

value: 11 weeks

tag: genotype/variation

value: Hif-1a KO

tag: agent

value: chemotherapy


title: Hif-1a wt + chemotherapy treatment

tag: age

value: Hif-1a wt


title: Normal Lung 2041


title: Hif-1a KO + PBS treatment

value: PBS


title: Hif-1a wt + PBS treatment


title: Normal Lung 0591


title: Normal Lung 0603


title: Wt_1K_H3K4Me3_R1

description: 1000 wild type NSCs H3K4Me3 Profile Replicate1


title: genomic DNA from tumor, ccRCC sample 109

description: ccRCC Tumor Tissue Sample

tag: gender

tag: tnm stage

value: TNM IV

tag: progress status (m0-pf

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: Normal Lung 0536


title: DMEM_Input

city: Salt Lake City

first: Donald

last: Ayer

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
ChIP-seq reads were aligned to human genome (hg19) using NovoAlign 3.08.02 with the following arguments: --NonC -r Random -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
Peaks were called using macs2 2.1.1.20160309 with the following arguments: macs2 callpeaks -g 3.1e9 -B --qvalue cutoff = 1.00e-02 --mfold=5 50
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files; pileup values for reads
Supplementary_files_format_and_content: Txt files; chromosome, start, stop, length, summits, p-value, fold enrichment, q-value, name value of peaks called by macs

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM (ThermoFisher Scientific, 11995-065) with 10% Fetal Bovine Serum (Gibco, A3160502) and 1X Penicillin-Streptomycin (Invitrogen, 15140122).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then were treated with 0.125M glycine for 5 min to stop cross-linking reaction. Cross-linked cells were washed with 1X cold PBS and scraped for harvest. MondoA-DNA complexes were isolated using MondoA antibody (Proteintech).
ChIP library was generated as described in Reddy et al. 2009.

treatment_protocol: HeLa cells were treated with either DMEM normal pH (3.7 g/L sodium bicarbonate) or acidic DMEM (0.37 g/L sodium bicarbonate) for 4 hours.

value: Cells were treated with DMEM with normal pH (~pH 7.2; 3.7 g/L sodium bicarbonate)

value: HeLa


title: Acidic DMEM_Input

value: Cells were treated with DMEM with low pH (~pH 6.7; 0.37 g/L sodium bicarbonate).


title: genomic DNA from tumor, ccRCC sample 103

description: ccRCC Tumor Tissue Sample

value: TNM II


title: genomic DNA from tumor, ccRCC sample 110

description: ccRCC Tumor Tissue Sample

value: Male

value: TNM III

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-P


title: Acidic DMEM_MondoA_ChIPseq

value: MLXIP Rabbit Polyclonal Antibody (Proteintech; 13614-1-AP)


title: genomic DNA from tumor, ccRCC sample 105

description: ccRCC Tumor Tissue Sample

value: Female


title: Colonic crypts rep3

city: Chapel Hill

first: Nancy

last: Allbritton

state: NC

address: Room 012, Chapman Hall

department: Kenan Professor and Chair of the UNC/NC State Joint Department of Biomedical Engineering and Kenan Professor of Chemistry at UNC

institute: UNC

data_processing:
Initial processing and basecalling was done using Casava v1.9
FASTQ files were trimmed with the TruSeq adapter and an additional 3bp on each end.
Alignment to the mm9 genome was performed using Tophat2
Reads were counted at mm10 genes using HTseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file contains read counts per gene for each replicate

source_name: WT mouse colon

growth_protocol: Crypts were isolated from a WT mouse (age 6-10 weeks). First, crypts were cultured on collagen as monolayers. Then to generate contiguous monolayers, colonic cells from monolayer cultures on collagen were plated on gradient cross-linked scaffolds. Contiguous monolayers were obtained by 3-5 days. To prepare samples for RNA sequencing whole monolayer was isolated using a lysis solution. Crypts were used for comparison.

extract_protocol: RNAaqueous Micro Kit Ambion

value: Colonic crypts


title: Colonic crypts rep2


title: DMEM_MondoA_ChIPSeq


title: Normal Lung 0490

value: Normal


title: genomic DNA from tumor, ccRCC sample 107

description: ccRCC Tumor Tissue Sample

value: TNM I

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: Normal Lung 2022


title: genomic DNA from tumor, ccRCC sample 108

description: ccRCC Tumor Tissue Sample


title: Normal Lung 0489


title: genomic DNA from tumor, ccRCC sample 104

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 102

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 106

description: ccRCC Tumor Tissue Sample


title: EH39

tag: suject status

value: squamous cell carcinoma of the head and neck (HNSCC) patient

tag: FDG/pet response


title: MS121_Chronic_Active

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

institute: Karolinska Institutet

description:
unbiased total nuclei isolation
10X_17_071_grch38

data_processing:
All individual samples were process with cellranger-2.1.1 with transcriptome reference refdata-cellranger-GRCh38-1.2.0
Each of the output filtered UMI count matrixes was used as input for Velocyto with the parameters, velocyto run10x -m repeatMasker_filtered_UMI_count_matrixes GRCh38-1.2.0_genes.gtf. For each of the samples, we combined the spliced and unspliced count matrices to get the final matrix.
genome build: GRCh38
processed data files format and content: Aligned output bam files and their correspondent index .bai files from CellRanger count output. Processed data includes raw UMI counts matrix with the assigned celltype clusters, where rows are geneIDs and columns cellIDs. Corresponding annotation text files, where rows are CellIDs and columns different annotation ( sample name, control/MS condition and Celltype)

source_name: MS patient_chronic active lesions

extract_protocol:
Nuclei were extracted with a Nuclei Isolation Buffer and the suspension was cleaned through density gradient centrifugation.
cDNA libraries have been constructed with the kit from 10x Genomics Single Cell 3' v2 and were compatible with standard Illumina sequencing

tag: health condition

value: MS patient

value: White Matter brain tissue

tag: tissue subtype

value: chronic active lesions

tag: molecule subtype

value: nuclear RNA


title: Colonic crypts rep1

tag: tissue


title: MS121_Active1

description:
unbiased total nuclei isolation
10X_17_070_grch38

source_name: MS patient_active

value: active


title: Colonic confluent monolayers at day 5 (407±53 Ω cm2) rep3

value: Colonic confluent monolayers at day 5


title: Colonic confluent monolayers at day 5 (407±53 Ω cm2) rep2


title: MS121_Active2

description:
unbiased total nuclei isolation
10X_17_069_grch38


title: Normal Lung 0535


title: genomic DNA from tumor, ccRCC sample 101

description: ccRCC Tumor Tissue Sample


title: Colonic confluent monolayers at day 5 (407±53 Ω cm2) rep1


title: MS121_NAWM

description:
unbiased total nuclei isolation
10X_17_068_grch38

source_name: MS patient_normal appearing white matter

value: normal appearing white matter


title: MS122_Active

description:
unbiased total nuclei isolation
10X_17_067_grch38


title: MS122_Chronic_Inactive

description:
unbiased total nuclei isolation
10X_17_066_grch38

source_name: MS patient_chronic inactive lesions

value: chronic inactive lesions


title: Colonic confluent monolayers at day 4 (623±15 Ω cm2) rep1

value: Colonic confluent monolayers at day 4


title: MS122_NAWM

description:
unbiased total nuclei isolation
10X_17_065_grch38


title: Normal Lung 0397


title: genomic DNA from tumor, ccRCC sample 97

description: ccRCC Tumor Tissue Sample

value: TNM IV

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: Normal Lung 0284


title: genomic DNA from tumor, ccRCC sample 98

description: ccRCC Tumor Tissue Sample

value: Female


title: Normal Lung 0271


title: Colonic confluent monolayers at day 3 (526±56 Ω cm2) rep3

value: Colonic confluent monolayers at day 3


title: Colonic confluent monolayers at day 4 (623±15 Ω cm2) rep3


title: Colonic confluent monolayers at day 4 (623±15 Ω cm2) rep2


title: Normal Lung 0272

value: Normal


title: genomic DNA from tumor, ccRCC sample 95

description: ccRCC Tumor Tissue Sample

value: Male

value: TNM I


title: SD48/16

description:
unbiased total nuclei isolation
10X_17_064_grch38

source_name: non-neurological control sample

value: non-neurological control sample


title: Normal Lung 0276


title: genomic DNA from tumor, ccRCC sample 100

description: ccRCC Tumor Tissue Sample

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: genomic DNA from tumor, ccRCC sample 96

description: ccRCC Tumor Tissue Sample

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-P


title: MS242 Remyelinating

description:
unbiased total nuclei isolation
10X_17_063_grch38

source_name: MS patient_remyelinating lesions

value: MS patient

value: White Matter brain tissue

value: remyelinating lesions


title: Normal Lung 0210


title: Normal Lung 0365


title: Colonic confluent monolayers at day 3 (526±56 Ω cm2) rep1


title: Wt_5K_H3K4Me3_R2

description: 5000 wild type NSCs H3K4Me3 Profile Replicate2

value: Neural Stem Cells

value: Larval brain

value: ab8580 (Abcam)


title: MS242_Chronic_Active1

description:
unbiased total nuclei isolation
10X_17_062_grch38

value: chronic active lesions

value: nuclear RNA


title: genomic DNA from tumor, ccRCC sample 94

description: ccRCC Tumor Tissue Sample

value: TNM III


title: genomic DNA from tumor, ccRCC sample 93

description: ccRCC Tumor Tissue Sample


title: MS242 Chronic_Inactive

description:
unbiased total nuclei isolation
10X_17_061_grch38

value: chronic inactive lesions


title: Normal Lung 0161


title: genomic DNA from tumor, ccRCC sample 92

description: ccRCC Tumor Tissue Sample

value: Female

value: TNM II


title: Normal Lung 0074

value: Normal


title: MS242_Chronic_Active2

description:
unbiased total nuclei isolation
10X_17_060_grch38


title: CO14

description:
unbiased total nuclei isolation
10X_17_059_grch38


title: msm_S3

city: Shenyang

first: Shengnan

last: Huang

address: 120 Dongling Road Shenhe District Shenyang P.R. China

institute: Shenyang Agricultural University

description: Chinese cabbage

data_processing:
Illumina HiSeq™ 2000 used for base calling
All raw reads were filtered by removing reads with adaptors and low-quality reads. Clean reads were mapped to the reference database for the B. rapa genome (Version 1.5, http://brassicadb.org/brad/) using SOAPaligner/SOAP2 (Li et al., 2009)
Gene expression levels were calculated using the RPKM (Reads Per kb per Million reads) method (Mortazavi et al., 2008) in six libraries
The DESeq software was applied to analyze DEGs based on the RPKM-derived baseMean for each gene between samples (Anders and Huber, 2010). To identify DEGs, the False Discovery Rate (FDR ≤ 0.001) method was used to determine the threshold of P-value in multiple tests (Benjamini and Hochberg, 1995)
Genome_build: Version 1.5, http://brassicadb.org/brad/
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values,length,coverage... for each gene

organism: Brassica rapa subsp. pekinensis

source_name: the developing flower buds

extract_protocol:
The developing flower buds of Chinese cabbage were sampled, total RNA was extracted using Trizol reagent
cDNA libraries were prepared for sequencing using standard Illumina protocols

value: the developing flower buds

tag: developmental stage

value: at the full-bloom stage

tag: genotype

value: mutant msm


title: msm_S2

description: Chinese cabbage


title: msm_S1

description: Chinese cabbage


title: genomic DNA from tumor, ccRCC sample 91

description: ccRCC Tumor Tissue Sample

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: wildtype_F4

description: Chinese cabbage

value: wild type 'FT'


title: Normal Lung 0016


title: wildtype_F2

description: Chinese cabbage


title: CO39

description:
unbiased total nuclei isolation
10X_17_058_grch38

value: non-neurological control sample

value: White Matter brain tissue


title: MS176_Chronic_Active

description:
unbiased total nuclei isolation
10X_17_057_grch38

value: MS patient


title: Normal Lung 0378


title: Normal Lung 0030


title: genomic DNA from tumor, ccRCC sample 88

description: ccRCC Tumor Tissue Sample

value: Male

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-P


title: MS176_Chronic_Inactive

description:
unbiased total nuclei isolation
10X_17_056_grch38


title: genomic DNA from tumor, ccRCC sample 90

description: ccRCC Tumor Tissue Sample

value: TNM I


title: Liver_Creb3l3_Ppara_DKO_fasted_replicate4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

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

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

source_name: Liver of a Creb3l3-Ppara double knockout mouse, fasted for 16hrs

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

growth_protocol: CREB3L3-/- mice were backcrossed onto a C57BL/6 background at least 10 times. PPARα-/- mice that had been backcrossed on a pure C57Bl/6J background for more than 10 generations were acquired from Jackson Laboratories (no. 008154, B6;129S4-Pparatm1Gonz/J). The two lines were interbred to generate combined PPARα/CREB3L3-/- mice. Mice were housed in a specific pathogen free facility at the Weill Cornell Medical College on a 12h light/dark cycles and fed ad libitum standard chow diet (PicoLab Rodent diet 20, #5058, Lab diet).

extract_protocol: Total RNA was extracted from cells using TRIzol reagent (Life Technologies, Bleiswijk, The Netherlands) and subsequently purified using the RNeasy Micro kit (Qiagen, Venlo, The Netherlands). RNA integrity was verified with RNA 6000 Nano chips on an Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: The four different mouse lines (wildtype, PPARα-/-, CREB3L3-/-, and PPARα/CREB3L3-/-) were either fasted for 16 hours or fed a ketogenic diet for 4 days (# F3666, Bio-Serv). The mice used for experiments were all male and approximately 8 weeks old. The euthanasia was carried out at around 10 a.m., with the ketogenic diet group being non-fasted (ad libitum fed). Livers were snap-frozen in liquid nitrogen.

tag: Sex

value: male

tag: treatment

value: fasting, 16hrs


title: Liver_Creb3l3_Ppara_DKO_fasted_replicate3


title: 100_K562_H3_R1

description:
TAF ChIP from 100 K562 cells for H3 Replicate 1
Used as control while processing

source_name: K562 Cell line

value: K562 Cell line

tag: tissue type

value: Cell Culture

tag: ip target

tag: chip antibody


title: 100_K562_H3_R2

description:
TAF ChIP from 100 K562 cells for H3 Replicate 2
Used as control while processing


title: Colonic confluent monolayers at day 3 (526±56 Ω cm2) rep2

value: Colonic confluent monolayers at day 3


title: wildtype_F1

description: Chinese cabbage


title: genomic DNA from tumor, ccRCC sample 85

description: ccRCC Tumor Tissue Sample

tag: age

value: Female

value: TNM II


title: MS176_NAWM

description:
unbiased total nuclei isolation
10X_17_054_grch38

value: normal appearing white matter

value: nuclear RNA


title: MS176_Remyelinating

description:
unbiased total nuclei isolation
10X_17_055_grch38

value: remyelinating lesions


title: Liver_Creb3l3_Ppara_DKO_fasted_replicate2


title: genomic DNA from tumor, ccRCC sample 89

description: ccRCC Tumor Tissue Sample

tag: gender

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: 100_K562_H3K27Me3_R1

description: TAF ChIP from 100 K562 cells for H3K27Me3 Replicate 1


title: genomic DNA from tumor, ccRCC sample 87

description: ccRCC Tumor Tissue Sample

tag: tnm stage


title: CO25

description:
unbiased total nuclei isolation
10X_17_053_grch38

value: non-neurological control sample


title: CO28

description:
unbiased total nuclei isolation
10X_17_052_grch38

value: White Matter brain tissue


title: Liver_PparaKO_fasted_replicate2

source_name: Liver of a Ppara knockout mouse, fasted for 16hrs

value: PPARalpha-/-


title: Liver_Creb3l3_Ppara_DKO_fasted_replicate1


title: genomic DNA from tumor, ccRCC sample 86

description: ccRCC Tumor Tissue Sample

source_name: ccRCC

tag: progress status (m0-pf


title: HeLa:MondoA-KO_DMEMAcidic rep2

middle: E

state: UT

department: Department of Oncological Sciences

data_processing:
STAR 2.6 was used to align the reads to GRCh38/hg38
featureCounts was used to obtain read counts for each gene
FastQC and MultiQC were used to assess sequencing and alignment quality
Genome_build: hg38
Supplementary_files_format_and_content: counts

growth_protocol: Cells were grown in standard 6-well dishes in DMEM with 10% FBS and 10% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted from cells using a Zymo Research Quick-RNA MiniPrep kit (cat #11-330T) according to the manufacturer's guidelines.
1 µg total RNA was used to generate libraries using a Kapa Stranded mRNA-Seq kit with mRNA capture beads (cat # KK8421) according to the manufacturer's guidelines.

treatment_protocol: Cells were treated with DMEM or DMEMAcidic for four hours prior to harvesting.

tag: cell line

value: HeLa

value: MondoA-KO

value: DMEMAcidic


title: HeLa:MondoA-KO_DMEMAcidic rep1


title: Liver_PparaKO_fasted_replicate1

value: male


title: genomic DNA from tumor, ccRCC sample 82

description: ccRCC Tumor Tissue Sample

value: Male

value: TNM I


title: genomic DNA from tumor, ccRCC sample 84

description: ccRCC Tumor Tissue Sample

value: TNM IV

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: 100_K562_H3K27Me3_R2

description: TAF ChIP from 100 K562 cells for H3K27Me3 Replicate 2

value: K562 Cell line

value: Cell Culture


title: genomic DNA from tumor, ccRCC sample 81

description: ccRCC Tumor Tissue Sample

value: TNM III

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-P


title: 100_K562_H3K9Me3_R2

description: TAF ChIP from 100 K562 cells for H3K9Me3 Replicate 2

value: Active Motif (Cat No- 39161)


title: genomic DNA from tumor, ccRCC sample 83

description: ccRCC Tumor Tissue Sample

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: Liver_PparaKO_fasted_replicate3

value: fasting, 16hrs


title: 100_K562_H3K9Me3_R1

description: TAF ChIP from 100 K562 cells for H3K9Me3 Replicate 1


title: Liver_Creb3l3KO_ketogenic_diet_replicate4

source_name: Liver of a Creb3l3 knockout mouse, fed a ketogenic diet for 4 days

value: ketogenic diet, 4 days


title: Liver_Creb3l3_Ppara_DKO_ketogenic_diet_replicate4

source_name: Liver of a Creb3l3-Ppara double knockout mouse, fed a ketogenic diet for 4 days


title: ABH inoculated cells Rep1

city: Chicago

first: Karla

middle: Jean Fullner

last: Satchell

state: IL

address: 303 East Chicago Ave

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC. Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered. The cleaned reads were aligned to the human reference genome using STAR. Read counts for each gene were calculated using htseq-count. Normalization and differential expression were determined using DESeq2. The cutoff for determining significantly differentially expressed genes was an FDR-adjusted p-value less than 0.05. A pathway analysis was performed on both gene lists using GeneCoDis to identify pathways that are enriched with genes that are upregulated and downregulated.
Genome_build: hg19
Supplementary_files_format_and_content: Each processed file is in .xlsx file type and contain offical gene symbol and description for each gene, read counts for each replicate, fold changes compared to PBS treated controls, and p-values indicating statistically significant or non-significant changes in gene expression compared to PBS treated controls.

source_name: ABH inoculated cells

growth_protocol: T84 cells were cultured in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM F12) with GlutaMAX supplement (ThermoFisher Gibco, #10565018) with 10% (w/v) fetal bovine serum (FBS, Gemini Bio-products, #900-108) and 0.1% penicillin/streptomycin (ThermoFisher Gibco). Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol:
Following bacterial challenge, T84 cells were washed once with cold 1x PBS and mRNA was extracted using the Qiagen RNeasy Kit (Qiagen, #74014) following manufacturers instructions.
The Illumina TruSeq Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 750 ng of high-quality RNA samples (RIN=10). The Kit procedure was performed without modifications. This procedure includes mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation. lllumina NextSeq 500 Sequencer was used to sequence the libraries with the production of single-end, 75 bp reads.

treatment_protocol: V. cholerae strains were grown at 30°C in LB medium supplemented with 100 mg mL-1 streptomycin. Overnight cultures were diluted 1:100 and grown at 30°C with shaking until exponential phase (OD600»0.40-0.60). Bacteria from 1 mL were pelleted by centrifugation and resuspended in phosphate buffered saline (PBS) to a final concentration of 5 x 108 bacterial cells mL-1. T84 cells (seeded the day before into cell culture-treated plates) were twice washed with PBS and then media changed to antibiotic- and FBS-free DMEM/F12. Resuspended V. cholerae was added to media over cells (multiplicity of infection = 5). Inoculations were synchronized by centrifugation at 500 xg for 3 min. T84 cells were subsequently incubated for 2 hours at 37°C in the presence of 5% CO2.

tag: cell type

value: colorectal carcinoma cells

tag: atcc catalog #

value: ATCC CCL-248

value: N16961 V. cholerae ΔhlyAΔhapA ABH only

tag: passage


title: RID inoculated cells Rep2

source_name: RID inoculated cells

value: N16961 V. cholerae ΔhlyAΔhapA RID only


title: HeLa:MondoA-KO_DMEM rep1

value: HeLa

value: MondoA-KO

value: DMEM


title: HeLa:MondoA-KO_DMEM rep2


title: ABH inoculated cells Rep2


title: Liver_Creb3l3KO_fasted_replicate4

source_name: Liver of a Creb3l3 knockout mouse, fasted for 16hrs

value: male


title: Liver_Creb3l3KO_fasted_replicate3


title: HeLa_DMEMAcidic rep2

source_name: HeLa

value: WT

value: DMEMAcidic


title: genomic DNA from tumor, ccRCC sample 80

description: ccRCC Tumor Tissue Sample

value: Male

value: TNM I


title: RID inoculated cells Rep1


title: ACD inoculated cells Rep2

source_name: ACD inoculated cells

value: N16961 V. cholerae ΔhlyAΔhapA ACD only


title: HeLa_DMEMAcidic rep1


title: genomic DNA from tumor, ccRCC sample 78

description: ccRCC Tumor Tissue Sample


title: Liver_Creb3l3KO_ketogenic_diet_replicate3


title: HeLa_DMEM rep2


title: HeLa_DMEM rep1


title: Liver_Creb3l3KO_fasted_replicate2


title: genomic DNA from tumor, ccRCC sample 77

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 76

description: ccRCC Tumor Tissue Sample


title: Liver_Creb3l3_Ppara_DKO_ketogenic_diet_replicate3


title: Liver_Creb3l3_Ppara_DKO_ketogenic_diet_replicate2


title: genomic DNA from tumor, ccRCC sample 75

description: ccRCC Tumor Tissue Sample

value: Female

value: TNM III

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-P


title: ACD inoculated cells Rep1


title: PGP1_RNASeq_Replicate3

city: Farmington

first: Travis

last: Hinson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
QC was run using fastqc and reads trimmed using Trimmomatic-0.32
Sequencing reads aligned to the human hg38 genome using STAR 2.5.1b
Raw counts were calculated using htseq-count
Differential expression using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Counts files generated with htseq-count

source_name: Human iPS Cardiomyocytes

extract_protocol:
RNA was isolated from fully differentiated iPS cardiomyocytes
Libraries were prepared according to the TruSeq Stranded mRNA LT Sample Prep Kit instructions.

value: Human iPS-derived Cardiomyocytes

tag: disease state


title: genomic DNA from tumor, ccRCC sample 79

description: ccRCC Tumor Tissue Sample

value: TNM II

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: genomic DNA from tumor, ccRCC sample 99

description: ccRCC Tumor Tissue Sample


title: DRTXA inoculated cells Rep1

source_name: DRTXA inoculated cells

value: colorectal carcinoma cells

value: ATCC CCL-248

value: N16961 V. cholerae ΔhlyAΔhapA rtxA deletion


title: PGP1_RNASeq_Replicate2


title: Liver_Creb3l3KO_ketogenic_diet_replicate2

value: ketogenic diet, 4 days


title: Liver_Creb3l3_Ppara_DKO_ketogenic_diet_replicate1


title: genomic DNA from tumor, ccRCC sample 73

description: ccRCC Tumor Tissue Sample

value: TNM IV

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: PGP1_RNASeq_Replicate1

value: WT


title: WT inoculated cells Rep2

source_name: WT inoculated cells

value: N16961 V. cholerae ΔhlyAΔhapA WT MARTX


title: Liver_Creb3l3KO_fasted_replicate1

value: male

value: fasting, 16hrs


title: 502G3_RNASeq_Replicate3

value: HCM


title: 502G3_RNASeq_Replicate2


title: PBS treated cells Rep1

source_name: PBS treated cells

value: PBS


title: Liver_wildtype_fasted_diet_replicate4

source_name: Liver of a wildtype mouse, fasted for 16hrs

value: wildtype (C57BL/6 )


title: WT inoculated cells Rep1


title: genomic DNA from tumor, ccRCC sample 69

description: ccRCC Tumor Tissue Sample

value: Male


title: Liver_PparaKO_ketogenic_diet_replicate3

source_name: Liver of a Ppara knockout mouse, fed a ketogenic diet for 4 days

value: PPARalpha-/-


title: genomic DNA from tumor, ccRCC sample 71

description: ccRCC Tumor Tissue Sample

value: TNM III


title: E2403A10_RNASeq_Replicate3

value: Human iPS-derived Cardiomyocytes


title: PBS treated cells Rep2

value: colorectal carcinoma cells


title: genomic DNA from tumor, ccRCC sample 72

description: ccRCC Tumor Tissue Sample

value: Female

value: TNM I

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: Bio21_2D_171566

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description:
sample_counts.txt
sample name in processed data file:
BIO21-2D.171566.bam

data_processing:
Reads were aligned to the hg38 genome using STAR v2.5.2b
Aligned data were read into R and summarized as counts per gene using the Bioconductor TxDb.Hsapiens.UCSC.hg38.knownGene package in concert with the GenomicAlignments package
Data were converted to counts/million counts, along with observation-level weights using the Bioconductor limma function voomWithQualityWeights
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a tab-delimited matrix of gene counts, with Entrez Gene IDs in the first column, and the BAM file names in the header

source_name: Kidney cells

growth_protocol: In brief, tissue was finely minced under sterile conditions, subjected to collagenase digestion with shaking at 37°C for 30 minutes, mixed 1:1 with horse serum, vortexed, and allowed to briefly settle, and supernatant was harvested. The cell suspension was centrifuged, washed, and plated in T25 flasks containing DMEM/F12 media supplemented with insulin, transferrin, selenium, and hydrocortisone. The Nortis devices were constructed with an extracellular matrix of type I collagen, and the cell chamber was coated with type IV collagen to facilitate cell adhesion. Cultures of primary renal epithelial cells, upon reaching greater than 80% confluency, were subjected to trypsin digestion and manual cell scraping to obtain single-cell suspensions. The cells were counted, washed, and resuspended at a concentration of 20 × 106 cells/ml, and 1–2 μl were injected into the Nortis device. Cells were incubated to allow matrix adhering for 12 hours before initiating flow at a rate of 0.5 μl/min. The integrity of the tubule cell structure was assessed grossly by light microscopy weekly.

extract_protocol:
Cells cultured within the kidney MPS were isolated after 48 hours of treatment, and total RNA was isolated using the Quagen RNeasy Micro Kit
The RNA library was prepared using a SMARTer Stranded Total RNA Sample Prep Kit - Low Input Mammalian (Takara 634861)

treatment_protocol: Kidney MPS were exposed to 50 μM of PMB, or 50 μM of NAB739, or 50μM of NAB741, or 10uM PMO, or 10uM PSO,or control for 48 hours

value: primary renal epithelial cells

tag: growth protocol

tag: donor


title: 502G3_RNASeq_Replicate1


title: Liver_Creb3l3KO_ketogenic_diet_replicate1

tag: genotype

value: ketogenic diet, 4 days


title: genomic DNA from tumor, ccRCC sample 68

description: ccRCC Tumor Tissue Sample


title: Liver_wildtype_fasted_diet_replicate3

tag: Sex


title: DRTXA inoculated cells Rep2

value: ATCC CCL-248

tag: treatment

value: N16961 V. cholerae ΔhlyAΔhapA rtxA deletion


title: genomic DNA from tumor, ccRCC sample 67

description: ccRCC Tumor Tissue Sample


title: Bio11_2D_171565

description:
sample_counts.txt
sample name in processed data file:
BIO11-2D.171565.bam


title: genomic DNA from tumor, ccRCC sample 70

description: ccRCC Tumor Tissue Sample


title: E2403A10_RNASeq_Replicate2


title: E2403A10_RNASeq_Replicate1


title: Liver_wildtype_ketogenic_diet_replicate4

source_name: Liver of a wildtype mouse, fed a ketogenic diet for 4 days

value: male


title: Liver_PparaKO_ketogenic_diet_replicate2


title: Bio26_Control_171559

description:
sample_counts.txt
sample name in processed data file:
9-0PMB.171559.bam

value: Control


title: IC10_RNASeq_Replicate3

value: HCM


title: Liver_wildtype_fasted_diet_replicate2

value: fasting, 16hrs


title: Bio26_Control_171558

description:
sample_counts.txt
sample name in processed data file:
2-0PMB.171558.bam


title: Bio26_Control_171557

description:
sample_counts.txt
sample name in processed data file:
6-0PMB.171557.bam


title: genomic DNA from tumor, ccRCC sample 74

description: ccRCC Tumor Tissue Sample


title: Bio26_Control_171556

description:
sample_counts.txt
sample name in processed data file:
3-0PMB.171556.bam


title: IC10_RNASeq_Replicate1


title: genomic DNA from tumor, ccRCC sample 65

description: ccRCC Tumor Tissue Sample

value: TNM IV

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: genomic DNA from tumor, ccRCC sample 66

description: ccRCC Tumor Tissue Sample

value: Male


title: Liver_wildtype_ketogenic_diet_replicate2

value: wildtype (C57BL/6 )


title: Bio26_Control_171555

description:
sample_counts.txt
sample name in processed data file:
8-0PMB.171555.bam


title: Bio26_50uM_PMB_171564

description:
sample_counts.txt
sample name in processed data file:
13-50PMB.171564.bam

value: 50 uM PMB


title: genomic DNA from tumor, ccRCC sample 63

description: ccRCC Tumor Tissue Sample

value: TNM II


title: Bio26_2D_171568

description:
sample_counts.txt
sample name in processed data file:
BIO26-2D.171568.bam


title: Liver_PparaKO_ketogenic_diet_replicate1

value: PPARalpha-/-


title: Liver_wildtype_fasted_diet_replicate1


title: genomic DNA from tumor, ccRCC sample 64

description: ccRCC Tumor Tissue Sample

value: TNM I


title: Liver_wildtype_ketogenic_diet_replicate3


title: Liver_wildtype_ketogenic_diet_replicate1


title: genomic DNA from tumor, ccRCC sample 62

description: ccRCC Tumor Tissue Sample

value: Female

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: Bio26_50uM_PMB_171563

description:
sample_counts.txt
sample name in processed data file:
10-50PMB.171563.bam

value: primary renal epithelial cells


title: RWPE-1 MIR205HG knockdown_rep3

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

institute: Fondazione IRCCS Istituto Nazionale Tumori

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v4. Raw expression data were log2-transformed and normalized using the robust spline normalization method. Datasets were filtered removing probes having detection p-value < 0.01 in less than one sample or not associated to official gene symbols; probes annotated with the same gene symbol were collapsed into the highest variance one. A robust spline normalization (rsn) of the expression levels was computed.

label: Biotin

source_name: RWPE-1 cells

label_protocol: Biotinylated cRNA were prepared with Illumina RNA TotalPrep amplification kit (Ambion)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: transfection

value: antisense gapmer directed against an exon-exon junction of MIR205HG transcript


title: Bio26_50uM_PMB_171562

description:
sample_counts.txt
sample name in processed data file:
1-50PMB.171562.bam


title: genomic DNA from tumor, ccRCC sample 60

description: ccRCC Tumor Tissue Sample

source_name: ccRCC


title: genomic DNA from tumor, ccRCC sample 61

description: ccRCC Tumor Tissue Sample


title: RWPE-1 control_rep3

value: scrambled oligomer


title: RWPE-1 MIR205HG knockdown_rep1


title: RWPE-1 MIR205HG knockdown_rep2


title: Bio21_Control_171551

description:
sample_counts.txt
sample name in processed data file:
14-0PMB.171551.bam


title: Bio26_50uM_PMB_171561

description:
sample_counts.txt
sample name in processed data file:
5-50PMB.171561.bam


title: Bio26_50uM_PMB_171560

description:
sample_counts.txt
sample name in processed data file:
4-50PMBBIO26.171560.bam


title: Bio21_Control_171550

description:
sample_counts.txt
sample name in processed data file:
4-0PMB.171550.bam


title: Bio21_Control_171549

description:
sample_counts.txt
sample name in processed data file:
7-0PMB.171549.bam


title: DU145 Alu-deleted MIR205HG transcript_rep3

source_name: DU145 cells

value: vector containing MIR205HG RefSeq sequence deleted for a portion of the Alu element


title: genomic DNA from tumor, ccRCC sample 58

description: ccRCC Tumor Tissue Sample


title: RWPE-1 control_rep1


title: Bio21_50uM_PMB_171554

description:
sample_counts.txt
sample name in processed data file:
27-0PMB.171554.bam


title: DU145 empty vector_rep3

value: empty vector


title: genomic DNA from tumor, ccRCC sample 55

description: ccRCC Tumor Tissue Sample


title: Bio21_50uM_PMB_171553

description:
sample_counts.txt
sample name in processed data file:
16-0PMB.171553.bam


title: DU145 Alu-deleted MIR205HG transcript_rep2


title: genomic DNA from tumor, ccRCC sample 54

description: ccRCC Tumor Tissue Sample

value: TNM III


title: Bio11_Control_171543

description:
sample_counts.txt
sample name in processed data file:
28-0PMB.171543.bam

value: Control


title: genomic DNA from tumor, ccRCC sample 52

description: ccRCC Tumor Tissue Sample

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-P


title: DU145 empty vector_rep2


title: genomic DNA from tumor, ccRCC sample 53

description: ccRCC Tumor Tissue Sample

value: TNM IV

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: Bio21_50uM_PMB_171552

description:
sample_counts.txt
sample name in processed data file:
13-0PMB.171552.bam


title: Bio11_Control_171541

description:
sample_counts.txt
sample name in processed data file:
27-0PMB.171541.bam


title: genomic DNA from tumor, ccRCC sample 57

description: ccRCC Tumor Tissue Sample


title: DU145 empty vector_rep1


title: genomic DNA from tumor, ccRCC sample 56

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 59

description: ccRCC Tumor Tissue Sample

value: Male


title: RWPE-1 control_rep2


title: Bio11_Control_171540

description:
sample_counts.txt
sample name in processed data file:
12-0PMB.171540.bam


title: DU145 Alu-deleted MIR205HG transcript_rep1


title: DU145 MIR205HG full length_rep4

value: MIR205HG full length sequence


title: Bio11_Control_171539

description:
sample_counts.txt
sample name in processed data file:
11-0PMB.171539.bam


title: DU145 MIR205HG RefSeq_rep4

value: MIR205HG RefSeq sequence


title: Bio11_Control_171538

description:
sample_counts.txt
sample name in processed data file:
10-0PMB.171538.bam


title: Bio11_50uM_PMB_171537

description:
sample_counts.txt
sample name in processed data file:
18-50PMB.171537.bam

value: 50 uM PMB


title: DU145 Empty vector_rep4


title: genomic DNA from tumor, ccRCC sample 46

description: ccRCC Tumor Tissue Sample

value: TNM I


title: genomic DNA from tumor, ccRCC sample 47

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 51

description: ccRCC Tumor Tissue Sample

value: Female


title: genomic DNA from tumor, ccRCC sample 48

description: ccRCC Tumor Tissue Sample

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: IC10_RNASeq_Replicate2

value: Human iPS-derived Cardiomyocytes

value: HCM


title: Bio11_50uM_PMB_171542

description:
sample_counts.txt
sample name in processed data file:
4-50PMB.171542.bam

value: primary renal epithelial cells


title: Bio11_50uM_PMB_171536

description:
sample_counts.txt
sample name in processed data file:
16-50PMB.171536.bam


title: DU145 MIR205HG RefSeq_rep3


title: DU145 Empty vector_rep3


title: Bio11_50uM_PMB_171535

description:
sample_counts.txt
sample name in processed data file:
15-50PMB.171535.bam


title: Bio11_50uM_PMB_171534

description:
sample_counts.txt
sample name in processed data file:
3-50PMB.171534.bam


title: DU145 MIR205HG RefSeq_rep2


title: Bio33_50uM_NAB741_187960

description:
sample_counts.txt
sample name in processed data file:
20-E_741.187960.bam

value: 50 uM NAB741


title: DU145 MIR205HG full length_rep3


title: genomic DNA from tumor, ccRCC sample 45

description: ccRCC Tumor Tissue Sample


title: Bio33_50uM_NAB741_187959

description:
sample_counts.txt
sample name in processed data file:
16-E_741.187959.bam


title: genomic DNA from tumor, ccRCC sample 44

description: ccRCC Tumor Tissue Sample

value: TNM II


title: genomic DNA from tumor, ccRCC sample 41

description: ccRCC Tumor Tissue Sample


title: DU145 MIR205HG full length_rep1


title: DU145 MIR205HG full length_rep2


title: Bio33_50uM_NAB741_187957

description:
sample_counts.txt
sample name in processed data file:
8-E_741.187957.bam


title: DU145 Empty vector_rep2

value: empty vector


title: Bio33_50uM_NAB741_187958

description:
sample_counts.txt
sample name in processed data file:
13-E_741.187958.bam


title: genomic DNA from tumor, ccRCC sample 43

description: ccRCC Tumor Tissue Sample

value: TNM III


title: DU145 MIR205HG RefSeq_rep1


title: DU145 Empty vector_rep1


title: Bio33_50uM_NAB741_187956

description:
sample_counts.txt
sample name in processed data file:
5-E_741.187956.bam


title: genomic DNA from tumor, ccRCC sample 49

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 40

description: ccRCC Tumor Tissue Sample


title: RWPE-1 control gapmer_rep3

value: control gapmer


title: Bio33_Control_187954

description:
sample_counts.txt
sample name in processed data file:
18-E_0PMB.187954.bam

value: Control


title: RWPE-1 MIR205HG intronic gapmer_rep3

value: gapmer directed against MIR205HG intron


title: Bio33_Control_187953

description:
sample_counts.txt
sample name in processed data file:
15-E_0PMB.187953.bam


title: genomic DNA from tumor, ccRCC sample 39

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 34

description: ccRCC Tumor Tissue Sample

value: Male


title: Bio33_50uM_NAB741_187955

description:
sample_counts.txt
sample name in processed data file:
2-E_741.187955.bam


title: genomic DNA from tumor, ccRCC sample 42

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 35

description: ccRCC Tumor Tissue Sample

value: TNM IV

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: RWPE-1 control gapmer_rep2


title: RWPE-1 MIR205HG intronic gapmer_rep1


title: RWPE-1 MIR205HG intronic gapmer_rep2


title: Bio33_Control_187952

description:
sample_counts.txt
sample name in processed data file:
9-E_0PMB.187952.bam


title: genomic DNA from tumor, ccRCC sample 36

description: ccRCC Tumor Tissue Sample


title: Bio33_Control_187951

description:
sample_counts.txt
sample name in processed data file:
6-E_0PMB.187951.bam


title: Bio33_Control_187950

description:
sample_counts.txt
sample name in processed data file:
3-E_0PMB.187950.bam


title: Bio33_50uM_PMB_187949

description:
sample_counts.txt
sample name in processed data file:
17-E_50PMB.187949.bam

value: 50 uM PMB


title: genomic DNA from tumor, ccRCC sample 29

description: ccRCC Tumor Tissue Sample

value: TNM I

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-P


title: genomic DNA from tumor, ccRCC sample 33

description: ccRCC Tumor Tissue Sample

value: Female


title: genomic DNA from tumor, ccRCC sample 37

description: ccRCC Tumor Tissue Sample


title: RWPE-1 control gapmer_rep1


title: Bio33_50uM_PMB_187948

description:
sample_counts.txt
sample name in processed data file:
12-E_50PMB.187948.bam


title: Bio33_50uM_PMB_187947

description:
sample_counts.txt
sample name in processed data file:
11-E_50PMB.187947.bam


title: RWPE-1 MIR205HG siRNA_rep3

value: MIR205HG siRNA


title: genomic DNA from tumor, ccRCC sample 31

description: ccRCC Tumor Tissue Sample

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: genomic DNA from tumor, ccRCC sample 38

description: ccRCC Tumor Tissue Sample


title: RWPE-1 control siRNA_rep3

value: control siRNA


title: RWPE-1 MIR205HG siRNA_rep2


title: Bio33_50uM_PMB_187946

description:
sample_counts.txt
sample name in processed data file:
7-E_50PMB.187946.bam

value: primary renal epithelial cells


title: RWPE-1 MIR205HG siRNA_rep1


title: genomic DNA from tumor, ccRCC sample 32

description: ccRCC Tumor Tissue Sample


title: Bio33_50uM_PMB_187945

description:
sample_counts.txt
sample name in processed data file:
4-E_50PMB.187945.bam


title: RWPE-1 control siRNA_rep2


title: genomic DNA from tumor, ccRCC sample 28

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 30

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 27

description: ccRCC Tumor Tissue Sample


title: RWPE-1 control siRNA_rep1


title: Bio49_50uM_NAB741_187943

description:
sample_counts.txt
sample name in processed data file:
20-E_NAB741.187943.bam


title: Bio33_50uM_PMB_187944

description:
sample_counts.txt
sample name in processed data file:
1-E_50PMB.187944.bam


title: Bio49_50uM_NAB741_187942

description:
sample_counts.txt
sample name in processed data file:
19-E_NAB741.187942.bam

value: 50 uM NAB741


title: genomic DNA from tumor, ccRCC sample 24

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 25

description: ccRCC Tumor Tissue Sample


title: Bio49_50uM_NAB741_187941

description:
sample_counts.txt
sample name in processed data file:
18-E_NAB741.187941.bam


title: Bio49_50uM_NAB741_187940

description:
sample_counts.txt
sample name in processed data file:
17-E_NAB741.187940.bam


title: F23 normal human diploid fibroblasts UVA-irradiated

city: Quebec city

first: Patrick

middle: J

last: Rochette

state: Quebec

address: 1050 chemin Ste-Foy - H2-10

department: Axe Médecine Régénératrice

country: Canada

institute: CHU de Québec – Université Laval

description: gene expression of chronically UVA-irradiated cells

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The file log2_and_linear_values.txt includes the log2 and linear values used to create heat maps. Linear values were used to calculate the fold change between control and UVA-irradiated samples.

source_name: chronically UVA-irradiated cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: All four fibroblasts cell strains were grown in the same culture medium : Dulbecco Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% antibiotics.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

treatment_protocol: Cells were chronically irradiated or not with 20 kJ/m^2 UVA, 2 times a day, 4 days a week for 5 weeks

tag: tissue

value: skin

value: Normal human diploid fibroblasts

value: female


title: F38 normal human diploid fibroblasts non-irradiated

description: gene expression of non-irradiated cells

source_name: non-irradiated cells


title: Bio49_50uM_NAB739_187937

description:
sample_counts.txt
sample name in processed data file:
14-E_NAB739.187937.bam

value: 50 uM NAB739


title: F21 normal human diploid fibroblasts non-irradiated

description: gene expression of non-irradiated cells


title: F23 normal human diploid fibroblasts non-irradiated

description: gene expression of non-irradiated cells


title: genomic DNA from tumor, ccRCC sample 20

description: ccRCC Tumor Tissue Sample

data_processing: Fluorescence intensities were extracted using the Methylation module (1.9.0) in the Genome Studio software (V2011.1). CpG-sites at chromosome X and Y, detection p-value>0.05, nbeads <=3 or located within 3 bp from known SNP in any the samples 1-127 were filtered (set to NA) in samples 1-127. CpG-sites meeting the criteria in any of Pat1-Pat6 and Tumor free samples (116-127) were filtered in samples Pat1-Pat6. Bead types were normalized using the BMIQ method.


title: F21 normal human diploid fibroblasts UVA-irradiated


title: genomic DNA from tumor, ccRCC sample 23

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 26

description: ccRCC Tumor Tissue Sample

value: TNM III


title: genomic DNA from tumor, ccRCC sample 22

description: ccRCC Tumor Tissue Sample

value: Male


title: genomic DNA from tumor, ccRCC sample 18

description: ccRCC Tumor Tissue Sample

value: TNM IV


title: genomic DNA from tumor, ccRCC sample 19

description: ccRCC Tumor Tissue Sample


title: IP_Trim71_rep1

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

description:
replicate1
Trim71_RIP.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using STAR v2.5.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.2.1
For RIP-seq,reads aligned to non-polyA transcripts were excluded. To calculate fold enrichment for RIP, we normalized the FPKM value of every transcript to the average of all transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample in txt file

source_name: embryonic stem cells

growth_protocol: Mouse ESCs were cultured on 0.1% gelatin-coated plates in 2i+LIF medium which is consist of N2B27 supplemented with MEK inhibitor PD0325901 (1.0 μM), GSK3 inhibitor CHIR99021 (3.0 μM) and leukemia inhibitory factor (1,000 unit /ml).

extract_protocol:
For RNA-seq,cells were treated with TRIzol and followed with phase seperation,  RNA precipitation and RNA wash. Finally, RNA were dissolved in DEPC water.For RIP-seq,The RNA in input lysis and  precipitated beads were extracted by TRIzol.
For RNA-seq,total RNA was subjected to two rounds of purification using poly-T oligo-attached magnetic beads before the synthesis of double-stranded (ds) cDNA. The ds cDNA was ligated to adaptors and sequenced with illumina Hiseq2000 platform.For RIP-seq,Input RNA were treated as the total RNA in RNA-seq,the IP RNA RNA from RIP experiment was directly used for the synthesis of ds-cDNA.

treatment_protocol: For PD+LIF experiments, ESCs were first plated in 2i+LIF for 24 hr, then washed once with 1xPBS and changed to N2B27 supplemented with PD+LIF, cultured for another 4 days before analysis with medium changed every other day.For RIP-seq, 3XFLag-Trim71 overexpressing and empty ESCs cultured in 2i+LIF medium were UV-crosslinked and lysed in lysis buffer. 1/40 lysis was taken as input. The remaining lysis was subjected to immunoprecipitation using FLAG antibody.

tag: strain

tag: developmental stage

value: 3.5 days

value: embryonic stem cells

tag: genotype/variation

value: Trim71 overexpression

tag: antibody

value: FLAG


title: IP_Trim71_rep2

description:
replicate2
Trim71_RIP.txt


title: genomic DNA from tumor, ccRCC sample 21

description: ccRCC Tumor Tissue Sample

extract_protocol: Genomic DNA was extracted accordint to standard protocols and DNA purity and concentration determined by spechtrophotometry.

tag: age

tag: gender

value: Female

tag: tnm stage

tag: progress status (m0-pf

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):TNM IV


title: Bio49_50uM_NAB739_187935

description:
sample_counts.txt
sample name in processed data file:
12-E_NAB739.187935.bam

tag: cell type


title: genomic DNA from tumor, ccRCC sample 17

description: ccRCC Tumor Tissue Sample

value: TNM II

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-PF


title: IP_empty_rep2

description:
replicate2
Trim71_RIP.txt

value: empty


title: Bio49_50uM_NAB739_187936

description:
sample_counts.txt
sample name in processed data file:
13-E_NAB739.187936.bam

value: primary renal epithelial cells


title: genomic DNA from tumor, ccRCC sample 14

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 50

description: ccRCC Tumor Tissue Sample


title: F38 normal human diploid fibroblasts UVA-irradiated

value: skin


title: Bio49_50uM_NAB739_187934

description:
sample_counts.txt
sample name in processed data file:
11-E_NAB739.187934.bam


title: Bio49_50uM_NAB739_187938

description:
sample_counts.txt
sample name in processed data file:
6-E_NAB739.187938.bam

value: 50 uM NAB741


title: Bio49_Control_187933

description:
sample_counts.txt
sample name in processed data file:
10-E_Ctrl.187933.bam

value: Control


title: Input_rep2

description:
replicate2
Trim71_RIP.txt


title: genomic DNA from tumor, ccRCC sample 16

description: ccRCC Tumor Tissue Sample


title: Input_rep1

description:
replicate1
Trim71_RIP.txt


title: Bio49_Control_187931

description:
sample_counts.txt
sample name in processed data file:
8-E_Ctrl.187931.bam


title: Trincr1-ko_PDL_rep2

description:
replicate2
WT_Trincr1-ko_2iL_PDL_FPKM.txt

tag: media

value: PDL


title: Trincr1-ko_PDL_rep1

description:
replicate1
WT_Trincr1-ko_2iL_PDL_FPKM.txt


title: Bio49_50uM_NAB741_187939

description:
sample_counts.txt
sample name in processed data file:
16-E_NAB741.187939.bam

tag: growth protocol


title: genomic DNA from tumor, ccRCC sample 11

description: ccRCC Tumor Tissue Sample


title: genomic DNA from tumor, ccRCC sample 13

description: ccRCC Tumor Tissue Sample

value: TNM III

value: non metastatic ccRCC at diagnosis and progress-free at follow up, M0-P:non metastatic ccRCC at diagnosis that later progress, M1:metastatic ccRCC at diagnosis):M0-P