title: w1118_fatBody_T=ZT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB3_Oct_2

data_processing:
Multiple fastq files for each library were merged by samtools v1.3,
after which they were subjected to demultiplexing using BRB-seq tools v1.1.
Then samples were mapped to the reference genome using STAR v.2.5.0b in the alignReads mode with the following parameters: --outFilterScoreMinOverLread 0.20, --outFilterMatchNminOverLread 0.20, --outFilterMultimapNmax 1.
RefSeq Genes annotation track (UCSC, annotation database for dm3) was used to index the reference genome.
Samtools was used to remove reads with an insert size > 1kb.
Number of reads falling into each of the 16,995 genes was counted using the Python package HTSeq v0.6.1
Samples with < 300,000 reads assigned to the genes (no feature, ambiguous, low quality, not aligned or mapped to the multiple locations reads were not considered) were excluded from the analysis
Genes, expressed in less than 80% of the samples were removed from the analysis.
The count table was quantile normalized with the voom function from the limma v3.32.5 package.
Batch effects from different libraries were removed with ComBat from SVA v3.24.4 package.
Genome_build: dm3, UCSC, BDGP Release 5, Apr 2006
Supplementary_files_format_and_content: *.csv.gz with raw (integer) count values for each sample as well as quantile-normalized and batch corrected counts:
raw_counts_all_samples: raw (integer) counts for all samples
w1118_time_series_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the reference w1118 time series
w1118_time_series_fatbody_norm: normalized by voom and batch corrected by Combat counts for fat body samples of the reference w1118 time series
w1118_time_series_gut_norm: normalized by voom and batch corrected by Combat counts for gut samples of the reference w1118 time series
w1118_time_series_malpighiantubules_norm: normalized by voom and batch corrected by Combat counts for malpighiantubules samples of the reference w1118 time series
w1118_time_series_all_DGRPs_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the reference w1118 time series and all DGRP samples
w1118_time_series_all_DGRPs_fatbody_norm: normalized by voom and batch corrected by Combat counts for fat body samples of the reference w1118 time series and all DGRP samples
w1118_time_series_all_DGRPs_gut_norm: normalized by voom and batch corrected by Combat counts for gut samples of the reference w1118 time series and all DGRP samples
DGRP-796_time_series_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the DGRP-796 time series
DGRP-796_time_series_gut_norm: normalized by voom and batch corrected by Combat counts for fat body samples of theDGRP-796 time series
w1118_and_DGRP-796_time_series_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the reference w1118 time series and DGRP-796 time series
w1118_and_DGRP-796_time_series_gut_norm: normalized by voom and batch corrected by Combat counts for gut samples of the reference w1118 time series and DGRP-796 time series

tag: time series type


title: LPS 30 minutes 1

status: Public on Dec 10 2020

type: SRA

city: Charlestown

first: Mahesh Chandra

last: Kodali

state: MA

department: Neurology

country: USA

institute: Massachusetts General Hospital / Harvard Medical School

description:
one male and one female pooled together
DESeq2_normalized_counts.txt

library_source: transcriptomic

data_processing:
Transcript abundance from RNA-seq reads was quantified using Salmon, and gene-level counts were obtained using tximport, against the C57BL/6J mouse genome annotation Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6), obtained from the National Center for Biotechnology Information. Subsequently, raw counts were processed with DESeq2 to determine differentially expressed genes.
salmon version 1.2.1
Genome_build: Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: DESeq2 normalized count matrix

molecule: total RNA

organism: Mus musculus

source_name: Cerebral Vessels

extract_protocol:
RNA was extracted from mouse cerebral vessels after trizol homogenization, and then using QIAGEN miRNeasy micro Kit. Samples were later DNAse treated and cleaned up using RNEasy minelute clean up kit, finally eluted in RNAse free water from Qiagen.
Isolated RNA sample quality was determined using High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and concentration was measured using Qubit 2.0 RNA High Sensitivity assay (ThermoFisher, Massachusetts, USA). Libraries were then constructed following manufacturer’s instructions for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio USA Inc., California, USA) followed by Nextera® XT DNA Library Prep Kit (Illumina, California, USA). Final library quantities were measured by KAPA SYBR® FAST qPCR and quality was assessed using TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). Resulting final library size was about 430bp with an insert size of about 200bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed basing on QC values and sequencing was performed on an Illumina® NovaSeq 6000 (Illumina, California, USA). The read length configuration was 150 PE for 20M PE reads per sample (10M in each direction).

tag: genotype

value: wild type

tag: strain

tag: treatment

value: 10mg/kg LPS for 30 min

tag: Sex

value: pooled male and female


title: RNA-seq_Case6_A

city: Chongqing

first: Guanghui

last: Li

state: Chongqing

address: Xinqiao Street No. 2r

department: Xinqiao Hospital

country: China

institute: Army Medical University

data_processing:
RNA-seq were performed in the Illumina Novaseq System. All libraries were sequenced on the Novaseq using 2×150 bp paired-end sequencing.
Adaptor sequences were trimmed, and reads were processed into clean reads. Each RNA-seq data required approxiimately 10 G.
A novel network flow algorithm used in StringTie (version 2.2.1)  was applied to perform transcript assembly and quantify gene expression in fragments per kilobase of transcript per million fragment mapped units for RNA-seq.
DESeq (version 1.24.0)  was used to identify differentially expressed genes (DEGs)
Genome_build: genome GRCh37.75
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from tumor tissues using TRIzol™ Reagent (Life Technologies) for transcriptome analyses. RNA integrity, purity, and concentration were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). Nanodrop and Qubit 3.0. RNA-seq libraries were constructed using KAPA mRNA HyperPrep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Computed tomography-guided puncture biopsy of the lung deposit was performed a week before SBRT, and were then placed in the refrigerator (-80°C) to preserve sample integrity.

tag: tissue

value: colorectal cancer

tag: diagnosis

tag: histology

value: Adenocarcinoma

value: Fraction of radiotherapy:60Gy/14F


title: H3K115Q - rep2

city: San Francisco

first: Hannes

last: Braberg

state: CA

institute: UCSF

description: RNA-Seq.xlsx

data_processing:
RNA-Seq: Reads were filtered for quality and aligned to the yeast genome using tophat.
RNA-Seq: Non-unique reads and reads mapping to ribosomal RNA were removed prior to analysis.
RNA-Seq: Transcript counts were extracted using htseq-count
RNA-Seq: Differential expression was measured using the Dseq2 package in R
ATAC-Seq: Sequence reads were trimmed and aligned to the genome of S.cerevisiae
ATAC-Seq: Reads with a length <100bp were removed
ATAC-Seq: Replicates belonging to an allele (wt, H3K36A, H3K122A, set2∆) were merged and normalized to the smallest read number.
ATAC-Seq: Count files were generated with “featureCounts v1.5.3”
Genome_build: SacCer3 from http://hgdownload.cse.ucsc.edu/downloads.html
Supplementary_files_format_and_content: RNA-seq: Gene-Expression-Data.xlsx contains two tabs in matrix format: 1) Raw counts separately for each mutant and replicate. 2) log2 fold-change over wt for each histone mutant, with replicates averaged.
Supplementary_files_format_and_content: ATAC-seq: One BedGraph (.bdg, http://genome.ucsc.edu/goldenPath/help/bedgraph.html) file for each mutant and wt. The chromosomes are labeled by their NCBI accession numbers, and the last ("dataValue") column contains the read counts.

organism: Saccharomyces cerevisiae

source_name: Budding yeast cells

extract_protocol:
RNA-Seq: RNA was extracted with hot acidic phenol  as described in "M. A. Collart, S. Oliviero, Preparation of yeast RNA. Curr Protoc Mol Biol Chapter 13, Unit13 12 (2001)". ATAC-Seq: DNA was purified (Qiagen MinElute DNA Purification Kit), amplified and barcoded by PCR.
RNA-Seq: RNA-seq libraries were generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). ATAC-Seq: See treatment and extract protocols. Purified PCR-products were then sequenced.

treatment_protocol: ATAC-Seq:  Yeast cells (2.5x106) were grown to mid-log phase, pelleted, washed with SB-buffer (1.4 M Sorbitol, 40 mM HEPES-KOH pH 7.5, 0.5 mM MgCl2), resuspended in 200 μl SB buffer + 10 mM DTT with 10 μl of 10 mg/ml 100T zymolyase (MP Biomedicals) solution and incubated for 5min at 30 °C. Spheroblasted cells were washed with SB-buffer and incubated for 15 min at 37 °C in 25 μl transposase solution (12.5 μl 2x TD buffer, 1.25 μl Nextera enzyme, 11.25 μl water).

tag: strain background

value: MSY196 (based on S288C)

tag: replicate


title: RNA-seq_Case5_B

source_name: Computed tomography-guided puncture biopsy of the lung deposit

value: non-small-cell lung cancer

value: NO


title: LPS 30 minutes 3


title: w1118_fatBody_T=ZT5_Rep1

city: Lausanne

first: Bart

last: Deplancke

state: Vaud

address: EPFL-SV-IBI-UPDEPLA, Station 19

department: Biology

country: Switzerland

institute: École polytechnique fédérale de Lausanne (EPFL)

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB15_Oct_2

organism: Drosophila melanogaster

growth_protocol: Flies were raised on standard food at 25 °C and under 12 hours light: 12 hours dark (LD) cycles.

extract_protocol:
Standart Trizol extraction was performed, followed by Direct-zol™-96 RNA Purification (Zymo Resaearch) RNA purification
BRB-seq libraries were prepared according to Alpern et al 2019

value: whole fat body

tag: time of harvesting

tag: library

tag: bloomington

value: Time-series for w1118


title: RNA-seq_Case5_A

value: Fraction of radiotherapy:60Gy/13F


title: RNA-seq_Case4_B

value: Metastasis


title: LPS 15 minutes 2

value: 10mg/kg LPS for 15 min


title: PBS Control 2

value: PBS


title: PBS Control 3


title: LPS 15 minutes 3


title: PBS Control 1


title: LPS 15 minutes 1


title: RNA-seq_Case4_A

value: Fraction of radiotherapy:60Gy/12F


title: w1118_fatBody_T=ZT3_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB2_Oct_2


title: w1118_fatBody_T=ZT1_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB1_Oct_2


title: w1118_fatBody_T=ZT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB2_Jan_2


title: MEF low As treated H3K27ac ChIP-seq

city: Boston

first: Yanqiang

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

library_source: genomic

data_processing:
High-throughput sequencing generated sequences for each  sample and the raw reads passed quality filtering (Q > 17 and length >= 25 bp). Raw reads were first subject to 3’ adapter removal. Clean reads of fastq file were transferred into fasta file.
RNA-seq reads were mapped to the to the mouse genome build mm10 using topHat(Trapnell et al., 2009). Read counts of annotated genes were obtained by the Python software HTSeq-count(Anders et al., 2015).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
ChIP reads were mapped to the mm10 genome using Bowtie aligner allowing up to two mismatches(Langmead, 2010). Only the uniquely mapping reads were used for further analysis. The function bamCoverage of deepTools(Ramírez et al., 2014) was used to convert the bam file to normalized bigwig file to shown on genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include RPKM(Reads Per Kilobase Million) values for 4 Samples .The bigwig(.bw) files were generated by the bamCoverage, the score represents reads per genomic content (1x normalization).

molecule: genomic DNA

source_name: low dose sodium arsenite (As) treated WT MEF

growth_protocol: MEF and Dot1L− /− cells are diploid and nontumorigenic. Both cells were cultured in high glucose Dulbecco's Modified Eagle Medium (DMEM) with 10% (v/v) fetal bovine serum (FBS) in an incubator at 37 °C with 5% CO2.

extract_protocol:
Total RNAs from exposed and control groups of two cell lines were isolated and quality controlled with protocols from Illumina. A total amount of 2μg RNA per sample was used as input material for library construction.Chromatin immunoprecipitation (ChIP) was performed as described previously (Wang et al., 2 009b; Wang et al., 2 008). In brief, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with 125 mM glycine. After chromatin fragmented to 200 to 500bp by sonication, chromatin templates from 20 million cells were used for ChIP experiment. Samples were immunoprecipitated with 2- 4μg of H3K27ac antibody overnight at 4 °C followed by washing steps.
Ribosomal RNA (rRNA) was removed through Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA) according to the manu- facturer's instructions. Strand-specific sequencing libraries were gener- ated through the dUTP method by using the resulting RNA from NEB- Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer' s recommendations. RNA-seq was performed on an Illumina Hiseq 2000 platform and 100 bp paired-end reads were gen- erated according to Illumina' s protocol.  After reverse crosslinking, the ChIP DNA fragments were purified and repaired using End-ItTM DNA End-Repair Kit (Epicentre) followed by treatment with Taq polymerase to generate single-base 3′ overhangs used for adaptor ligation. Follow- ing ligation of a pair of Illumina adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers. Amplified DNA fragments around 300bp were isolated from agarose gel prior to sequencing.

treatment_protocol: At approximately 80% confluent, cells were treated with fresh medium containing 0 or 5, 10 μM As for 24 h. After exposure, cells were collected for following experiments.

tag: cell type

value: primary mouse embryonic fibroblasts (MEF)

tag: genotype/variation

tag: chip antibody


title: MEF Control H3K27ac ChIP-seq

source_name: untreated control WT MEF

value: wild type


title: Dot1L low As treated RNA-seq

description:
Dot1L_As
processed data file: MEF_Dot1L_As_treated.RNAseq.rpkm.txt

molecule: polyA RNA

source_name: low dose sodium arsenite (As) treated Dot1L mutant MEF


title: RNA-seq_Case3_B


title: LPS 30 minutes 2

value: 10mg/kg LPS for 30 min


title: w1118_fatBody_T=ZT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB1_Jan_2


title: Dot1L Control RNA-seq

description:
Dot1L_CK
processed data file: MEF_Dot1L_As_treated.RNAseq.rpkm.txt

source_name: untreated control Dot1L mutant MEF


title: RNA-seq_Case3_A

value: Fraction of radiotherapy:60Gy/11F


title: w1118_fatBody_T=ZT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB13_Oct_2


title: MEF low As treated RNA-seq

description:
MEF_As
processed data file: MEF_Dot1L_As_treated.RNAseq.rpkm.txt


title: MEF Control RNA-seq

description:
MEF_CK
processed data file: MEF_Dot1L_As_treated.RNAseq.rpkm.txt


title: RNA-seq_Case2_A

value: Cervical cancer

value: Squamous cell carcinoma

value: Fraction of radiotherapy:60Gy/10F


title: w1118_brain_T=CT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN48_Oct_1

value: whole brain


title: w1118_fatBody_T=ZT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_fatbody_norm.csv.gz
w1118_time_series_all_DGRPs_fatbody_norm.csv.gz
FB14_Oct_2


title: Primary human NK cells from a 24 yo M donor

city: Athens

first: Adam

middle: W.

last: Barb

state: GA

address: 180 E. Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

data_processing:
Read mapping to human ribosomal RNA reference: rRNA sequence filtering against human NCBI rRNA accessions, Bowtie2 ver. 2.3.4.1
Read mapping to hg38: Reads not mapped to rRNA were aligned to human genome using STAR ver. 2.7.1a
Raw count extraction: Raw counts extracted from STAR alignment BAM files using HTSEQ v0.9.1
Manual matrix count filtering: Summation of row counts in raw matrix ≥ 50 counts
Count matrix normalization, DESeq2
Genome_build: UCSC (Dec. 2013 GRCh/38hg38)
Supplementary_files_format_and_content: Tab-delimited txt file, raw count matrix
Supplementary_files_format_and_content: Tab-delimited txt file, manually filtered count matrix.  Input count matrix for RNA-Seq

source_name: total RNA

growth_protocol: NK cells were isolated by negative selection using the RosetteSep Enrichment Mixture following the recommended protocol (Stem Cell Tech) with the following minor changes: LRS filters were drained into a sterile 50-ml tube, and the contents were diluted to 30 ml using PBS with 2% IgG-depleted FBS. The cell suspension was then split into 2 × 15-ml aliquots, and each was mixed with 750 μl of the negative selection mixture. After a 20-min incubation, the steps mentioned in the protocol were followed. Contaminating erythrocytes were then removed by incubating the cells with erythrocyte lysis buffer (155 mM ammonium chloride, 12 mM sodium bicarbonate, and 0.1 mM EDTA, pH 7.4) for 10 min at room temperature. HEK293F, NK92 and YTS cells were grown in a pure culture and separated from the culture medium prior to RNA isolation.

extract_protocol: QuantSeq 3’ mRNA-Seq library kit (Lexogen, Vienna, Austria)

value: Primary human NK cell


title: Primary human NK cells from a 35 yo M donor


title: Primary human NK cells from a 40 yo M donor


title: Case11_A

data_processing:
Library strategy: exome-seq
The paired-end reads were mapped to the human reference genome GRCh37.75 using BWA (version 0.7.15-r1140) with default parameters.
Variant calling was executed with GATK mutect2(v3.7-0-gcfedb67),vardict(v1.4.8-0),varscan(v2.4.2)and low-quality variants.Variants were annotated with ANNOVAR (2016-02-01), according to the genomic coordinates GRCh37.75 and complex variants were  further annotated with SnpEff (v4.3). Then we evaluated if the variants were present in the dbSNP (v147) common database. Variants not found in the dbSNP database were further filtered with the ClinVar (20181028)
database,Cosmic(70),1000g_EAS,ExAC_ALL,ExAC_EAS. Pathogenic variants were annotated as “likely-pathogenic” “pathogenic”or“drug response” by the ClinVar database.Raw exome sequencing data were also used to analysis copy number variations (CNV), which was performed by using mainly the software CNVkit.
TMB(Tumor Mutational Burden) was defined as the number of somatic mutations. The TMB value was obtained according to the TMB algorithm from FMI①. The FMI test method (FoundationOneCDxTM) was approved by the FDA in 2017 for clinical drug selection decision making. It is defined as TMB-high when the tissue sample TMB is >10. Finally, we get a result table for each sample.
Genome_build: genome GRCh37.75
Supplementary_files_format_and_content: Matrix table with CNV  for every sample
Supplementary_files_format_and_content: Matrix table with SNV  for every sample
Supplementary_files_format_and_content: Matrix table with TMB  for every sample

extract_protocol:
Purity of the extracted DNA was assessed by electrophoresis of the DNA through a 1% agarose gel, and DNA concentration was quantified with a Qubit Fluorometer using the QubitTM dsDNA HS Assay Kit(Themo Fisher Scientific)Kit.
Ten paired DNA libraries were constructed using Agilent 60M sample preparation kit following the manufacturer’s instructions and separately sequenced on Illumina NextSeq500 with 2x150 bp. Adaptor sequences were trimmed and reads were processed.

value: non-small-cell lung cancer

tag: patient diagnosis

value: non-small cell lung cancer (NSCLC)

tag: tissue disease state

value: Adenocarcinoma

value: Fraction of radiotherapy:60Gy/21F


title: YTS cell replicate 7

value: YTS


title: NK92 cell replicate 7


title: w1118_brain_T=CT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN36_Oct_1

tag: time series type

value: Time-series for w1118


title: Case10_A

value: colorectal cancer

value: Metastasis

value: Fraction of radiotherapy:60Gy/20F


title: HEK293F replicate 1

tag: strain


title: Case9_A

tag: treatment

value: Fraction of radiotherapy:60Gy/19F


title: w1118_brain_T=CT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN35_Oct_1


title: w1118_brain_T=CT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN47_Oct_1


title: Case8_A

value: Fraction of radiotherapy:60Gy/18F


title: w1118_brain_T=CT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN46_Oct_1


title: RNA-seq_Case2_B

value: NO


title: w1118_brain_T=CT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN34_Oct_1


title: Case7_A

value: Fraction of radiotherapy:60Gy/17F


title: w1118_brain_T=CT17_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN33_Jan_7


title: w1118_brain_T=CT21_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN35_Jan_8


title: Case5_A

value: Fraction of radiotherapy:60Gy/15F


title: Case4_A

value: Fraction of radiotherapy:60Gy/14F


title: w1118_brain_T=CT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN33_Oct_1

value: whole brain


title: w1118_brain_T=CT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN45_Oct_1


title: Case3_A

value: Fraction of radiotherapy:60Gy/13F


title: Case2_A

value: Cervical cancer

value: Squamous cell carcinoma

value: Fraction of radiotherapy:60Gy/12F


title: Case6_A

value: non-small cell lung cancer (NSCLC)

value: Adenocarcinoma

value: Fraction of radiotherapy:60Gy/16F


title: Case1_A

value: Esophageal cancer

value: Adenosquamous cancer.

value: Fraction of radiotherapy:60Gy/11F


title: Spleen_12_NAIVE_44

type: RNA

city: Cambridge

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

hyb_protocol: The Mouse 430_2 GeneChip probe arrays were pre-hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol. 15 ug of labeled cRNA was fragmented in 30 uL 1X fragmentation buffer 100 mM KOAc, 30 mM MgOAc at 95°C for 35 minutes. The fragmented labeled cRNA was resuspended in 300 uL 1X hybridization buffer containing 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20, 0.5 mg/mL Aceylated BSA, 0.1 mg/mL herring sperm DNA, control oligo B2, and control transcripts bioB 1.5 pM, bioC 5 pM, bioD 25 pM, and cre 100 pM, and hybridized to Genechip probe arrays according to manufacturer’s protocol (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip probe arrays were scanned using GeneArray Scanner (Hewlett Packard, Corvallis, OR).

data_processing: CEL files were subjected to GC-content-based Robust Multi-array Average (GCRMA) normalization (version 2.20.0).  Expression levels were log (base 2) transformed.  All calculations and analyses were carried out using R (version 2.11.1) and Bioconductor computational tools.  Analyses were applied to discover genes that were differentially expressed between specific sets of tissue.  First, to identify differentially expressed genes between groups of samples, we applied the linear modeling approach (limma) to fit gene expression levels (log2 transformed) according to the defined groups of samples and Bayesian posterior error analysis (limma version 3.4.5).  Genes that exhibited a log-odds score greater than zero and fold change greater then 1.5 were considered significantly different.

label: Biotin

label_protocol: Five ug of purified total RNA was used in a 20 uL first strand reaction with 200U SuperScript II (Invitrogen, Carlsbad,CA) and 0.5ug (dT) T7primer[5’GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(T)24] in 1X first strand buffer (Invitrogen Life Technologies, Carlsbad, CA) with a 42°C incubation for 1 hour. Second strand synthesis was carried out by the addition of 40 U E. coli DNA Polymerase, 2 U E. coli RNase H, 10 U E. coli DNA Ligase in 1X second strand buffer (Invitrogen Life Technologies, Carlsbad, CA) followed by incubation at 16°C for 2 hrs.  The second strand synthesis reaction was purified using the Genechip Sample Cleanup Module according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA). The purified cDNA was amplified using BioArray high yield RNA transcription labeling kit (Enzo Life Sciences, Inc., Parmingdale, NY) according to manufacturer’s protocol to produce 70-120 ?g of biotin labeled cRNA (compliment RNA).

extract_protocol: Mice were sacrificed after specified time points and indicated organs were harvested for total RNA.

value: Spleen


title: w1118_brain_T=CT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN44_Oct_1

value: Time-series for w1118


title: Spleen_12_VEH_7


title: w1118_brain_T=CT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN32_Oct_1


title: Spleen_12_VEH_5


title: Spleen_12_MEF79_2_31


title: Spleen_12_VEH_2


title: Case11_B

value: non-small-cell lung cancer

value: NO


title: w1118_brain_T=CT13_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN31_Jan_9


title: Spleen_12_VEH_1


title: Spleen_12_MEF79_2_27


title: Spleen_12_NAIVE_41


title: Spleen_12_MEF79_2_26


title: Spleen_12_NAIVE_47


title: Spleen_12_MEF79_2_32


title: Spleen_12_VEH_4


title: Case10_B

value: colorectal cancer

value: Metastasis


title: Spleen_12_VEH_6


title: Spleen_12_VEH_3


title: w1118_brain_T=CT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN31_Oct_1

value: whole brain


title: Spleen_12_MEF79_2_28


title: w1118_brain_T=CT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN43_Oct_1


title: Spleen_12_MEF79_2_25


title: Spleen_12_DMF179_2_21


title: Spleen_12_DMF179_2_23


title: w1118_brain_T=CT11_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN42_Oct_1


title: Spleen_12_MEF79_2_29


title: Spleen_12_MEF79_2_30


title: Spleen_12_DMF179_2_22


title: Spleen_12_DMF179_2_20


title: Spleen_12_DMF179_2_24


title: Case8_B


title: Case7_B


title: w1118_brain_T=CT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN30_Oct_1


title: Case6_B


title: Case5_B


title: Case9_B


title: w1118_brain_T=CT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN29_Oct_1


title: Case4_B


title: w1118_brain_T=CT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN41_Oct_1


title: w1118_brain_T=CT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN40_Oct_1


title: w1118_brain_T=CT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN28_Oct_1


title: Case3_B


title: Spleen_12_DMF179_2_19


title: Spleen_12_DMF179_2_18


title: w1118_brain_T=CT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN39_Oct_1


title: Spleen_12_DMF100_9


title: Case2_B


title: Case1_B


title: Spleen_12_DMF100_11


title: Spleen_12_DMF100_13


title: Spleen_12_DMF100_MEF79_2_36


title: Spleen_12_DMF100_MEF79_2_33


title: Spleen_12_DMF100_12


title: Spleen_12_DMF100_MEF79_2_34


title: Spleen_12_DMF100_14


title: w1118_brain_T=CT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN27_Oct_1


title: Spleen_12_DMF179_2_17


title: Spleen_6_VEH_57


title: Spleen_12_DMF100_MEF79_2_35


title: Spleen_12_DMF100_15


title: Spleen_12_DMF100_10


title: Case11_T

source_name: Peripheral blood samples

value: Peripheral blood

value: normal


title: w1118_brain_T=CT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN38_Oct_1


title: Spleen_6_VEH_58


title: Spleen_12_DMF100_16


title: Case10_T


title: Spleen_6_VEH_56


title: Case9_T


title: Spleen_6_VEH_55


title: Case8_T


title: w1118_brain_T=CT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN25_Oct_1


title: w1118_brain_T=CT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN37_Oct_3


title: w1118_brain_T=CT1_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN25_Jan_7


title: w1118_brain_T=ZT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN24_Oct_1


title: Spleen_6_VEH_52


title: Case6_T


title: Case7_T


title: Case5_T


title: Case4_T


title: Spleen_6_VEH_54


title: Spleen_6_VEH_51


title: w1118_brain_T=ZT21_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN11_Jan_7


title: w1118_brain_T=ZT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN12_Oct_1


title: Case3_T


title: Spleen_6_VEH_53


title: Spleen_6_MEF79_2_79


title: Spleen_6_MEF79_2_81


title: w1118_brain_T=ZT23_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN12_Jan_7


title: Spleen_6_MEF79_2_80


title: Spleen_6_MEF79_2_78


title: Spleen_6_MEF79_2_76


title: Spleen_6_MEF79_2_82


title: w1118_brain_T=ZT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN23_Oct_1


title: Case2_T


title: Spleen_6_MEF79_2_77


title: Case1_T


title: w1118_brain_T=ZT19_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN10_Jan_7


title: Spleen_6_DMF179_2_74


title: w1118_brain_T=ZT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN11_Oct_1


title: w1118_brain_T=ZT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN22_Oct_1


title: 20uM BAM15 5

city: Baton Rouge

first: John

middle: P

last: Kirwan

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

description: Sample 19

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.3.1056 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: human
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

source_name: Epithelial adenocarcinoma of the breast

growth_protocol: MDA-MB-231 cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (100 U/mL), and 0.2% amphotericin B. Cells (0.3x106) were seeded into 6-well plates, grown to 80% confluence.

extract_protocol:
RNA was harvested using the TRIzol Reagent, isopropanol precipitation, 3 washes with 75% ethanol, and solubulized in RNase-free water.
Lexogen Quant-Seq
indexed and pooled samples, 50bp forward read

treatment_protocol: Cells at 80% confluence were treated with 0.1% DMSO Vehicle, 1uM BAM15 (in 0.1% DMSO), 10uM BAM15 (in 0.1% DMSO), 20uM BAM15 (in 0.1% DMSO) or 20uM DNP (in 0.1% DMSO) for 16 hours.

tag: passages


title: 20uM BAM15 4

description: Sample 18


title: w1118_brain_T=CT9_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN29_Jan_7

tag: tissue


title: Spleen_6_DMF179_2_72


title: Spleen_6_DMF179_2_70


title: w1118_brain_T=ZT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN10_Oct_1


title: 20uM BAM15 2

description: Sample 16


title: 20uM BAM15 3

description: Sample 17


title: w1118_brain_T=ZT17_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN9_Jan_7


title: Spleen_6_DMF179_2_69


title: Spleen_6_DMF179_2_71


title: w1118_brain_T=ZT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN9_Oct_1


title: Spleen_6_DMF179_2_67


title: 20uM BAM15 1

description: Sample 15


title: Spleen_6_MEF79_2_75


title: w1118_brain_T=ZT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN21_Oct_1


title: Spleen_6_DMF179_2_68


title: Vehicle 6

description: Sample 4


title: Spleen_6_DMF100_66


title: Spleen_6_DMF100_MEF79_2_83


title: w1118_brain_T=ZT15_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN8_Jan_8


title: Spleen_6_DMF100_61


title: Spleen_6_DMF100_62


title: Spleen_6_DMF100_64


title: Spleen_6_DMF100_60


title: w1118_brain_T=ZT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN8_Oct_1


title: MLN_12_VEH_5

value: Mesenteric Lymph Node (MLN)


title: Vehicle 2

description: Sample 2


title: MLN_12_VEH_7


title: Vehicle 1

description: Sample 1


title: Spleen_6_DMF100_59


title: w1118_brain_T=ZT13_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN7_Jan_7


title: w1118_brain_T=ZT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN20_Oct_1


title: Spleen_6_DMF100_65


title: MLN_12_VEH_4


title: MLN_12_VEH_8


title: senescent, METTL3 knockout, mutant METTL3 knock-in, replicate 2 [rna.M3]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against hg19 version of the human genome and RSEM v1.2.12 software was used to estimate raw read counts and RPKM values using Ensemble transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contain raw counts for each gene

source_name: IMR90 cell lines

extract_protocol:
Cells were harvested 48 hours later and RNA was extracted using RNeasy mini Kit (Qiagen, 74106) and digested with DNase I (Qiagen, 79254)
Libraries were generated using KAPA RNA HyperPrep library preparation kit

treatment_protocol: At day 4 post vector control or RAS expressing retrovirus infection, IMR90 cells were seeded and transfected with non-targeted siControl or siMETTL14 using Lipofectamine™ RNAiMAX. Cells were transfected with siRNA again and infected with lentivirus encoding wildtype or a R298P mutant METTL14 on the next day

tag: experiment

value: RNA-seq

tag: sirna


title: Spleen_6_DMF100_MEF79_2_84


title: Spleen_6_DMF100_MEF79_2_86


title: Spleen_6_DMF100_MEF79_2_85


title: w1118_brain_T=ZT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN7_Oct_1


title: senescent, METTL3 knockout, mutant METTL3 knock-in, replicate 1 [rna.M3]


title: w1118_brain_T=ZT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN19_Oct_1


title: senescent, METTL3 knockout, wild type METTL3 knock-in, replicate 2 [rna.M3]


title: w1118_brain_T=ZT11_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN6_Jan_7


title: MLN_12_NAIVE_47


title: senescent, METTL3 knockout, wild type METTL3 knock-in, replicate 1 [rna.M3]


title: senescent, METTL3 knockout, replicate 2 [rna.M3]

value: senescent, METTL3 knockout


title: MLN_12_VEH_6


title: MLN_12_VEH_1


title: MLN_12_VEH_3


title: senescent, METTL3 knockout, replicate 1 [rna.M3]


title: MLN_12_NAIVE_44


title: MLN_12_NAIVE_43


title: w1118_brain_T=ZT11_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN6_Oct_1


title: MLN_12_NAIVE_41


title: senescent, control knockout, replicate 2 [rna.M3]

value: senescent, control knockout


title: w1118_brain_T=ZT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN18_Oct_1


title: MLN_12_NAIVE_46


title: w1118_brain_T=ZT9_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN5_Jan_8


title: senescent, control knockout, replicate 1 [rna.M3]


title: w1118_brain_T=ZT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN17_Oct_1


title: w1118_brain_T=ZT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN5_Oct_1


title: MLN_12_MEF79_2_32


title: MLN_12_NAIVE_48


title: MLN_12_MEF79_2_28


title: MLN_12_MEF79_2_27


title: MLN_12_MEF79_2_30


title: MLN_12_NAIVE_42


title: MLN_12_DMF179_2_24


title: MLN_12_MEF79_2_25


title: MLN_12_MEF79_2_29


title: MLN_12_MEF79_2_31


title: MLN_12_NAIVE_45


title: MLN_12_MEF79_2_26


title: control, replicate 2 [rna.M3]

value: control


title: w1118_brain_T=ZT7_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN4_Jan_8


title: carm6A.shM3.m6A

data_processing:
Library strategy: MeRIP-seq
Raw sequencing data was aligned using bowtie2 against hg19 version of the human genome. HOMER was used to generate bigwig files and call m6A peaks (FDR<5%, at least 4 fold) in in control and senescent cells with vector, METTL3 and METTL14 knockdown versus corresponding total RNA input
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contain alignment tracks in bigwig format

source_name: m6a pulldown, senesent cells, METTL3 knockout

extract_protocol:
Total RNA was isolated from control or oncogenic RAS-induced senescent IMR90 cells 9 days post infection (three independent batches of cells were collected) using the RNeasy maxi kit (Qiagen, 75162) and digested with DNase I (Qiagen, 79254). polyA+ RNA was purified using the GenElute mRNA Miniprep kit (Sigma).
rRNA-depleted caRNA (QIAseq FastSelect kit) was used for library preparation

tag: group

value: senescent

tag: condition

tag: cell line


title: MLN_12_DMF179_2_23


title: w1118_brain_T=ZT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN16_Oct_1

tag: time of harvesting

tag: replicate

tag: library


title: control, replicate 1 [rna.M3]


title: carm6A.shM14.m6A

source_name: m6a pulldown, senesent cells, METTL14 knockout


title: carm6A.RAS.m6A

source_name: m6a pulldown, senesent cells, WT

value: WT


title: w1118_brain_T=ZT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN3_Oct_1

tag: bloomington


title: w1118_brain_T=ZT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN4_Oct_1


title: MLN_12_DMF179_2_20


title: w1118_brain_T=ZT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN15_Oct_1


title: MLN_12_DMF179_2_22


title: carm6A.ctr.m6A

source_name: m6a pulldown, control cells, WT


title: w1118_brain_T=ZT3_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN2_Jan_8


title: carm6A.shM3.input

source_name: input RNA, senesent cells, METTL3 knockout

value: input


title: w1118_brain_T=ZT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN2_Oct_1


title: carm6A.shM14.input

source_name: input RNA, senesent cells, METTL14 knockout


title: MLN_12_DMF179_2_21


title: carm6A.RAS.input

source_name: input RNA, senesent cells, WT


title: w1118_brain_T=ZT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN14_Oct_1


title: MLN_12_DMF179_2_19


title: w1118_brain_T=ZT1_Rep3

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN1_Jan_7


title: MLN_12_DMF100_MEF79_2_38


title: carm6A.ctr.input

source_name: input RNA, control cells, WT


title: w1118_brain_T=ZT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN1_Oct_3


title: MLN_12_DMF100_MEF79_2_33


title: MLN_12_DMF100_9


title: MLN_12_DMF100_16


title: MLN_12_DMF100_MEF79_2_35


title: MLN_12_DMF100_MEF79_2_39


title: MLN_12_DMF179_2_18


title: YTS cell replicate 6

value: YTS


title: w1118_brain_T=ZT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_brain_norm.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN13_Oct_3

value: Time-series for w1118


title: YTS cell replicate 5


title: MLN_12_DMF100_15


title: MLN_12_DMF100_13


title: MLN_12_DMF100_14


title: RAL-796_gut_T=CT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT48_Jan18_2_28233

value: whole gut

value: Time-series for RAL-796


title: MLN_12_DMF179_2_17


title: MLN_12_DMF100_MEF79_2_40


title: MLN_12_DMF100_MEF79_2_37


title: MLN_12_DMF100_MEF79_2_36


title: MLN_12_DMF100_MEF79_2_34


title: MLN_12_DMF100_12


title: MLN_12_DMF100_11


title: MLN_6_VEH_58


title: MLN_12_VEH_2


title: RAL-796_gut_T=CT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT47_Jan18_2_28233


title: YTS cell replicate 3


title: YTS cell replicate 4


title: YTS cell replicate 1


title: RAL-796_gut_T=CT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT36_Jan18_2_28233


title: NK92 cell replicate 5


title: NK92 cell replicate 4


title: Vehicle 4

description: Sample 3

tag: cell type


title: RAL-796_gut_T=CT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT45_Jan18_2_28233


title: RAL-796_gut_T=CT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT34_Jan18_2_28233


title: RAL-796_gut_T=CT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT33_Jan18_2_28233


title: MLN_6_VEH_57


title: MLN_6_VEH_53


title: MLN_12_DMF100_10


title: MLN_6_VEH_56


title: MLN_6_VEH_52


title: MLN_6_VEH_54


title: MLN_6_VEH_51


title: NK92 cell replicate 6


title: MLN_6_MEF79_2_78


title: MLN_6_VEH_55


title: RAL-796_gut_T=CT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT46_Jan18_2_28233


title: NK92 cell replicate 3


title: MLN_6_MEF79_2_82


title: RAL-796_gut_T=CT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT44_Jan18_2_28233


title: MLN_6_MEF79_2_81


title: MLN_6_MEF79_2_80


title: RAL-796_gut_T=CT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT32_Jan18_2_28233


title: NK92 cell replicate 2


title: MLN_6_MEF79_2_77


title: RAL-796_gut_T=CT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT43_Jan18_2_28233


title: MLN_6_MEF79_2_76


title: RAL-796_gut_T=CT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT31_Jan18_2_28233


title: HEK293F replicate 6


title: HEK293F replicate 5


title: MLN_6_MEF79_2_79


title: MLN_6_DMF179_2_74


title: MLN_6_DMF179_2_71


title: MLN_6_DMF179_2_72


title: MLN_6_DMF179_2_70


title: MLN_6_DMF179_2_73


title: MLN_6_DMF179_2_68


title: HEK293F replicate 4


title: HEK293F replicate 7


title: RAL-796_gut_T=CT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT41_Jan18_2_28233


title: RAL-796_gut_T=CT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT30_Jan18_2_28233


title: NK92 cell replicate 1


title: MLN_6_MEF79_2_75


title: RAL-796_gut_T=CT11_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT42_Jan18_2_28233


title: HEK293F replicate 2


title: RAL-796_gut_T=CT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT29_Jan18_2_28233


title: RAL-796_gut_T=CT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT40_Jan18_2_28233


title: input RNA, senescent cells

data_processing:
Library strategy: MeRIP-seq
Raw sequencing data was aligned using bowtie2 against hg19 version of the human genome. HOMER was used to generate bigwig files and call m6A peaks (FDR<5%, at least 4 fold) in control and senescent cell lines versus corresponding total RNA input.
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contain alignment tracks in bigwig format

extract_protocol:
Total RNA was isolated from control or oncogenic RAS-induced senescent IMR90 cells 9 days post infection (three independent batches of cells were collected) using the RNeasy maxi kit (Qiagen, 75162) and digested with DNase I (Qiagen, 79254). polyA+ RNA was purified using the GenElute mRNA Miniprep kit (Sigma).
Purified mRNA was fragmented using ZnCl2 buffer into ~100 nt and subjected to immunoprecipitation with an anti-m6A antibody (Synaptic Systems, Cat. No: 202 111). m6A-containing mRNAs eluted by free m6A and input fragments from control and senescent cells were used for library preparation

tag: sample type

tag: cell phenotype


title: input RNA, control cells


title: RAL-796_gut_T=CT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT28_Jan18_2_28233

tag: time series type


title: HEK293F replicate 3

tag: strain


title: MLN_6_DMF100_MEF79_2_90


title: m6A pulldown, senescent cells

value: m6A MeRIP


title: MLN_6_DMF100_MEF79_2_89


title: MLN_6_DMF179_2_67


title: MLN_6_DMF100_MEF79_2_87


title: RAL-796_gut_T=CT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT39_Jan18_2_28233


title: MLN_6_DMF179_2_69


title: RAL-796_gut_T=CT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT27_Jan18_2_28233


title: MLN_6_DMF100_MEF79_2_85


title: MLN_6_DMF100_MEF79_2_88


title: MLN_6_DMF100_MEF79_2_84


title: MLN_6_DMF100_MEF79_2_86


title: m6A pulldown, control cells


title: MLN_6_DMF100_65


title: MLN_6_DMF100_63


title: MLN_6_DMF100_66


title: MLN_6_DMF100_64


title: MLN_6_DMF100_60


title: MLN_6_DMF100_61


title: RAL-796_gut_T=CT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT38_Jan18_2_28233


title: MLN_6_DMF100_MEF79_2_83


title: MLN_6_DMF100_59


title: p65 binding in senescent cells

data_processing:
Library strategy: cut-and-run
Cut-and-run and CHIP-seq data was aligned using bowtie against hg19 version of the human genome and HOMER was used to generate bigwig files with default normalization parameters and call significant peaks vs IgG control using options “-style histone” for  factors METLL3, METTL14, p65
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contain alignment tracks in bigwig format

extract_protocol:
For cut-and-run cells were harvested, and gently washed twice using wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and EDTA-free Protease Inhibitor Cocktail). Cells were then incubated with the antibody overnight in the buffer (Wash buffer supplemented with 0.05% digitonin and 2 mM EDTA) at 4°C. The next day, supernatant was removed by centrifuge and cell pellets were washed once with Dig-wash buffer (Wash buffer containing 0.05% digitonin). Cell pellets were then incubated with Protein A-MNase (700 ng/ml in Dig-wash buffer) for 1 hour by rotation at 4°C. After three times of wash, cell pellets were resuspended in 100 l Dig-wash buffer with 2 l 100 mM CaCl2, incubated at 0°C for 30 mins, and then reactions were stopped by addition of 100 l 2 x STOP buffer (340 mM NaCl, 20 mM EDTA pH 8.0, 4 mM EGTA, 0.05% digitonin, 50 g/ml RNase A, 50 g/ml glycogen and 2 pg/ml heterologous spike-in yeast DNA). For CHIP-seq, DNA was eluted by incubation of the beads with TE buffer plus 1% SDS for 15 mins at 65 °C. The samples were then incubated overnight at 65 °C to reverse crosslinking. The next day, the samples were digested with proteinase K and the DNA was purified using a Wizard SV Gel and PCR Clean Up kit (Promega)
10 ng of ChIP DNA was used for ChIP-seq library construction using NEBNext Ultra DNA Library Prep Kit (NEB, E7645)

tag: chip antibody

tag: knockdown

value: no


title: RAL-796_gut_T=CT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT37_Jan18_2_28233

tag: tissue


title: RAL-796_gut_T=CT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT26_Jan18_2_28233


title: METTL14 binding in senescent cells


title: MLN_6_DMF100_62


title: METTL3 binding in senescent cells


title: IgG binding in senescent cells

value: IgG


title: Kidney_12_VEH_7

value: Kidney


title: p65 binding in control cells


title: RAL-796_gut_T=ZT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT12_Jan18_2_28233


title: Kidney_12_VEH_5


title: Kidney_12_VEH_8


title: Kidney_12_VEH_6


title: METTL14 binding in control cells


title: Kidney_12_VEH_2


title: Kidney_12_VEH_3


title: RAL-796_gut_T=ZT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT23_Jan18_2_28233


title: METTL3 binding in control cells


title: RAL-796_gut_T=CT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT25_Jan18_2_28233


title: Kidney_12_NAIVE_47


title: Kidney_12_VEH_4


title: RAL-796_gut_T=ZT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT11_Jan18_2_28233


title: Kidney_12_NAIVE_46


title: IgG binding in control cells


title: Kidney_12_NAIVE_42


title: Kidney_12_NAIVE_45


title: Kidney_12_NAIVE_43


title: RAL-796_gut_T=CT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT35_Jan18_2_28233


title: YTS cell replicate 2


title: Kidney_12_MEF79_2_32


title: Pol2 binding in senescent cells, shMETTL3 knockdown

data_processing:
Cut-and-run and CHIP-seq data was aligned using bowtie against hg19 version of the human genome and HOMER was used to generate bigwig files with default normalization parameters and call significant peaks vs IgG control using options “-style histone” for  factors METLL3, METTL14, p65
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contain alignment tracks in bigwig format


title: Kidney_12_VEH_1


title: Kidney_12_MEF79_2_31


title: Kidney_12_MEF79_2_30


title: RAL-796_gut_T=ZT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT9_Jan18_2_28233


title: Pol2 binding in senescent cells, vector knockdown

value: vector


title: Pol2 binding in senescent cells, shMETTL14 knockdown


title: RAL-796_gut_T=ZT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT10_Jan18_2_28233


title: RAL-796_gut_T=ZT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT21_Jan18_2_28233


title: RAL-796_gut_T=ZT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT22_Jan18_2_28233


title: RAL-796_gut_T=ZT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT8_Jan18_2_28233


title: Pol2 binding in control cells, vector knockdown


title: input DNA of senescent cells, vector knockdown


title: Kidney_12_MEF79_2_29


title: Kidney_12_NAIVE_41


title: input DNA of control cells, vector knockdown


title: RAL-796_gut_T=ZT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT20_Jan18_2_28233


title: Kidney_12_MEF79_2_28


title: RAL-796_gut_T=ZT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT7_Jan18_2_28233


title: Kidney_12_MEF79_2_25


title: RAL-796_gut_T=ZT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT19_Jan18_2_28233


title: Kidney_12_MEF79_2_27


title: senescent, METTL14 knockout, mutant METTL14 knock-in, replicate 3

extract_protocol:
Cells were harvested 48 hours later and RNA was extracted using RNeasy mini Kit (Qiagen, 74106) and digested with DNase I (Qiagen, 79254)
Libraries were generated using Lexogen Quantseq library preparation kit

tag: genotype/variation


title: senescent, METTL14 knockout, mutant METTL14 knock-in, replicate 2


title: RAL-796_gut_T=ZT11_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT6_Jan18_2_28233


title: RAL-796_gut_T=ZT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT18_Jan18_2_28233


title: Kidney_12_DMF179_2_20


title: senescent, METTL14 knockout, mutant METTL14 knock-in, replicate 1


title: Kidney_12_DMF179_2_24


title: Kidney_12_DMF179_2_21


title: senescent, METTL14 knockout, wild type METTL14 knock-in, replicate 3


title: Kidney_12_DMF179_2_23


title: Kidney_12_DMF179_2_22


title: Kidney_12_DMF179_2_19


title: Kidney_12_DMF100_MEF79_2_36


title: Kidney_12_DMF100_MEF79_2_34


title: Kidney_12_DMF179_2_17


title: Kidney_12_DMF100_MEF79_2_35


title: senescent, METTL14 knockout, wild type METTL14 knock-in, replicate 2


title: Kidney_12_DMF179_2_18


title: Kidney_12_DMF100_MEF79_2_33


title: Kidney_12_DMF100_15


title: RAL-796_gut_T=ZT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT5_Jan18_2_28233


title: Kidney_12_DMF100_9


title: RAL-796_gut_T=ZT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT17_Jan18_2_28233


title: senescent, METTL14 knockout, wild type METTL14 knock-in, replicate 1


title: Kidney_12_DMF100_13


title: Kidney_12_DMF100_12


title: senescent, METTL14 knockout, replicate 2

source_name: senescent, METTL14 knockout

value: senescent, METTL14 knockout


title: Kidney_12_DMF100_10


title: RAL-796_gut_T=ZT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT16_Jan18_2_28233


title: RAL-796_gut_T=ZT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT3_Jan18_2_28233


title: senescent, METTL14 knockout, replicate 1


title: RAL-796_gut_T=ZT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT4_Jan18_2_28233


title: senescent, control knockout, replicate 3

source_name: senescent, control knockout


title: RAL-796_gut_T=ZT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT2_Jan18_2_28233


title: RAL-796_gut_T=ZT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT14_Jan18_2_28233


title: senescent, METTL14 knockout, replicate 3


title: Kidney_6_VEH_55


title: Kidney_6_VEH_56


title: RAL-796_gut_T=ZT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT1_Jan18_2_28233


title: senescent, control knockout, replicate 1


title: Kidney_6_VEH_53


title: control, replicate 3

source_name: control


title: Kidney_12_DMF100_11


title: RAL-796_gut_T=ZT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT15_Jan18_2_28233


title: Kidney_6_VEH_57


title: Kidney_6_VEH_54


title: Kidney_6_MEF79_2_81


title: RAL-796_gut_T=ZT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT13_Jan18_2_28233


title: Kidney_6_VEH_51


title: Kidney_6_VEH_52


title: senescent, control knockout, replicate 2


title: control, replicate 2


title: Kidney_6_MEF79_2_82


title: Kidney_6_MEF79_2_80


title: RAL-796_brain_T=CT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN48_Jan18_1_28233

value: whole brain


title: Kidney_6_MEF79_2_79


title: control, replicate 1


title: Kidney_6_MEF79_2_78


title: Kidney_6_DMF179_2_74


title: Kidney_6_MEF79_2_75


title: Kidney_6_MEF79_2_77


title: RAL-796_brain_T=CT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN36_Jan18_1_28233


title: Gastric cancer cell line SNU1750 (Short-read RNA-seq)

city: Singapore

first: Kie Kyon

last: Huang

state: Select State/Province

address: 8 College Road

country: Singapore

institute: Duke-NUS Graduate Medical School

description: Short-read RNA-seq

data_processing:
We used CCS module of IsoSeq3 program (https://github.com/PacificBiosciences/IsoSeq3) to generate circular consensus sequence (CCS) reads from the sub-reads generated from the sequencing run.
Reads that were identified as full length were considered for de-novo clustering of reads using cluster module of IsoSeq3 to identify unique isoforms.
Isoforms were mapped to human genome (version hg38) using GMAP and only high-quality isoforms (supported by at least two FLNC reads) were considered for further analysis.
Isoforms identified across all cell lines were merged into a single non-redundant transcriptome using gffcompare (https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) and annotated using SQANTI2.
Transcript-level expression in the unit of transcript per million (tpm) were estimated for each identified isoform using Kallisto applied on short-read sequencing data and reference transcriptome defined using Iso-seq.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gtf file containing the merged, non-redundant gastric cancer transcriptome.
Supplementary_files_format_and_content: Matrix table with tpm value for every isoform and every sample.

source_name: Gastric cancer cell line

extract_protocol:
Total RNA was extracted from 10 gastric cell-lines using RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.
For long-read Iso-seq, amplified cDNA products were made into SMRTbell template libraries according to the Iso-Seq protocol by Pacific Biosciences.
For short-read RNA-seq, two micrograms of total RNA was used to create libraries with Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, California, USA) according to manufacturer’s instructions.

value: Gastric cancer cell line


title: RAL-796_gut_T=ZT23_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_gut_norm.csv.gz
w1118_and_DGRP-796_time_series_gut_norm.csv.gz
GUT24_Jan18_2_28233


title: RAL-796_brain_T=CT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN47_Jan18_1_28233


title: RAL-796_brain_T=CT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN46_Jan18_1_28233


title: RAL-796_brain_T=CT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN45_Jan18_1_28233


title: RAL-796_brain_T=CT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN34_Jan18_1_28233


title: Kidney_6_DMF179_2_73


title: RAL-796_brain_T=CT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN33_Jan18_1_28233


title: RAL-796_brain_T=CT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN44_Jan18_1_28233


title: Kidney_6_DMF179_2_70


title: Kidney_6_DMF179_2_72


title: Kidney_6_DMF179_2_71


title: Kidney_6_MEF79_2_76


title: Kidney_6_DMF179_2_69


title: RAL-796_brain_T=CT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN35_Jan18_1_28233


title: RAL-796_brain_T=CT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN32_Jan18_1_28233


title: Kidney_6_DMF100_MEF79_2_86


title: Kidney_6_DMF179_2_67


title: Kidney_6_DMF100_66


title: Kidney_6_DMF100_MEF79_2_90


title: Kidney_6_DMF100_65


title: Kidney_6_DMF100_61


title: Kidney_6_DMF100_MEF79_2_89


title: Kidney_6_DMF100_MEF79_2_83


title: Kidney_6_DMF179_2_68


title: Kidney_6_DMF100_63


title: Kidney_6_DMF100_62


title: Kidney_6_DMF100_64


title: Kidney_6_DMF100_MEF79_2_84


title: Kidney_6_DMF100_59


title: Kidney_6_DMF100_60


title: GC4_PB_H11.DecP.30_H.DZ

city: New York

first: Gabriel

last: Victora

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_H11

data_processing:
Raw fastq sequence files generated from Smartseq2 libraries were aligned to mouse genome (v. mm10) with the annotated transcriptome (v. gencode M22) using STAR (v. 2.6)(Dobin et al., 2013). Subsequently, genome-mapped BAM files were processed through RSEM (v. 1.3.1)(Li and Dewey, 2011) for gene quantification. The matrix of gene counts was then, used as input for analysis by the R package Seurat (v. 3.1.4.)(Stuart et al., 2019). Next, the dataset was corrected by using the regularized negative binomial regression (SCTransform) implemented by Seurat (Hafemeister and Satija, 2019). To control the dataset for unwanted sources of experimental variation, we fed the mitochondrial gene abundance and the experimental batches information into SCTransform. Additionally, cells containing more than 20% of sequence reads aligned to mitochondrial genes were excluded prior to normalization. Next, single cells were clustered and gene expression were evaluated with the Seurat workflow. Gene signature scoring was performed by using Seurat’s AddModuleScore function (See Supplemental Spreadsheet 1 for the complete list).
Genome_build: mm10
Supplementary_files_format_and_content: txt files contain raw, individual quantification matrices per experiment
Supplementary_files_format_and_content: tsv files contain metadata tables, umap/pca embeddings, and quality filtered raw and normalized quantification

source_name: Germinal Centers

extract_protocol:
Cell suspensions were resuspended in PBE and incubated on ice for 30 min with fluorescently-labeled antibodies (Table S2) along with 1 mg/mL of anti-CD16/32 (24G2, eBioscience). For detection of cells in early S of the cell cycle, we performed dual nucleotide pulse and staining as previously described (Gitlin et al., 2014). Briefly, mice were injected i.v. with 1 mg of EdU (A10044, Thermo Fisher Scientific) and one hour later with 2 mg of BrdU (B5002, Sigma). 30 min after the second injection, lymph nodes were harvested, and single cell suspensions were prepared. After cell surface receptor staining as described above, cells were fixed and permeabilized using BD Cytofix/Cytoperm™ fixation and permeabilization solution and BD Cytoperm Permeabilization Buffer PLUS, respectively. EdU and BrdU incorporation into DNA was assayed using the Click-iT Plus EdU Alexa Fluor 647 Flow Cytometry Assay Kit (Invitrogen) and FITC BrdU Flow Kit (BD), respectively. For single cell sorting, cells were stained as above and index-sorted directly into 96 well plates containing Buffer TCL (Qiagen) supplemented with 1% -mercaptoethanol using a BD FACS Aria II. Each plate contained all conditions assayed in each replicate. Cells were washed, filtered, and resuspended in PBE prior to analysis or sorting on BD FACS LSR II, FACS Symphony or FACS ARIA II cytometers. All data were analyzed using Flowjo software v.10.
Libraries were prepared as previously described (Trombetta et al., 2014). Briefly, nucleic acids were extracted from sorted single cell using RNAClean XP SPRI beads (Beckman Coulter), and RNA was hybridized first using RT primer (/5BiosG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) then reverse-transcribed into cDNA using TSO primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG) and RT maxima reverse transcriptase (Thermo Fisher Scientific). cDNA was amplified using ISPCR primer (AAGCAGTGGTATCAACGCAGAGT) and KAPA HiFi HotStart ReadyMix (Fisher Scientific), cleaned up using RNAClean XP SPRI beads three times, and tagmented using Nextera XT DNA Library Preparation Kit (Illumina). For each sequencing batch, up to four plates were barcoded at a time with Nextera XT Index Kit v2 Sets A-D (Illumina). Finally, dual-barcoded libraries were pooled and sequenced using Illumina Hiseq2500 (experiment 1)/Nextseq 550 (experiments 2-4) platform.
Smartseq2

tag: dec

tag: timepoint

tag: zone

tag: sequencing

tag: genotype


title: RAL-796_brain_T=CT11_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN42_Jan18_1_28233

tag: time of harvesting

tag: replicate


title: RAL-796_brain_T=CT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN31_Jan18_1_28233

tag: library

tag: bloomington


title: RAL-796_brain_T=CT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN43_Jan18_1_28233


title: GC4_PB_H10.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_H10


title: GC4_PB_H09.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_H09


title: RAL-796_brain_T=CT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN30_Jan18_1_28233


title: RAL-796_brain_T=CT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN41_Jan18_1_28233


title: GC4_PB_H08.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_H08


title: GC4_PB_H07.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_H07


title: RAL-796_brain_T=CT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN40_Jan18_1_28233


title: GC4_PB_G11.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_G11


title: Kidney_6_DMF100_MEF79_2_85


title: Jejunum_12_VEH_7

value: Jejunum


title: Jejunum_12_VEH_4


title: RAL-796_brain_T=CT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN28_Jan18_1_28233


title: Jejunum_12_VEH_6


title: Jejunum_12_VEH_8


title: Jejunum_12_NAIVE_48


title: Jejunum_12_VEH_1


title: Jejunum_12_VEH_2


title: Jejunum_12_VEH_5


title: GC4_PB_G09.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_G09


title: Jejunum_12_VEH_3


title: RAL-796_brain_T=CT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN39_Jan18_1_28233


title: Jejunum_12_NAIVE_47


title: Jejunum_12_NAIVE_43


title: Jejunum_12_NAIVE_45


title: Jejunum_12_NAIVE_46


title: Jejunum_12_NAIVE_42


title: RAL-796_brain_T=CT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN27_Jan18_1_28233


title: GC4_PB_G10.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_G10


title: Jejunum_12_MEF79_2_32


title: RAL-796_brain_T=CT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN29_Jan18_1_28233


title: Jejunum_12_NAIVE_41


title: RAL-796_brain_T=CT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN38_Jan18_1_28233


title: GC4_PB_F11.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_F11


title: GC4_PB_G08.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_G08


title: RAL-796_brain_T=CT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN37_Jan18_1_28233


title: GC4_PB_G07.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_G07


title: Jejunum_12_MEF79_2_31


title: Jejunum_12_MEF79_2_28


title: Jejunum_12_MEF79_2_30


title: Jejunum_12_MEF79_2_26


title: Jejunum_12_MEF79_2_27


title: Jejunum_12_MEF79_2_29


title: GC4_PB_F10.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_F10


title: RAL-796_brain_T=ZT21_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN23_Jan18_1_28233


title: Jejunum_12_DMF179_2_24


title: GC4_PB_F07.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_F07


title: Jejunum_12_DMF179_2_23


title: Jejunum_12_DMF179_2_22


title: RAL-796_brain_T=CT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN25_Jan18_1_28233


title: Jejunum_12_DMF179_2_17


title: RAL-796_brain_T=ZT19_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN22_Jan18_1_28233


title: GC4_PB_F09.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_F09


title: RAL-796_brain_T=ZT23_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN24_Jan18_1_28233


title: RAL-796_brain_T=CT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN26_Jan18_1_28233


title: Jejunum_12_DMF179_2_20


title: Jejunum_12_DMF179_2_21


title: Jejunum_12_DMF179_2_19


title: RAL-796_brain_T=ZT21_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN11_Jan18_1_28233


title: RAL-796_brain_T=ZT17_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN21_Jan18_1_28233


title: Jejunum_12_DMF179_2_18


title: GC4_PB_E11.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_E11


title: Jejunum_12_DMF100_MEF79_2_40


title: Jejunum_12_DMF100_MEF79_2_36


title: Jejunum_12_DMF100_MEF79_2_37


title: GC4_PB_F08.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_F08


title: GC4_PB_D11.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_D11


title: Jejunum_12_DMF100_MEF79_2_34


title: Jejunum_12_DMF100_16


title: GC4_PB_E10.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_E10


title: Kidney_6_DMF100_MEF79_2_87


title: RAL-796_brain_T=ZT15_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN20_Jan18_1_28233


title: Jejunum_12_DMF100_9


title: Jejunum_12_DMF100_MEF79_2_38


title: RAL-796_brain_T=ZT19_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN10_Jan18_1_28233


title: GC4_PB_E09.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_E09


title: Jejunum_12_DMF100_14


title: Jejunum_12_DMF100_MEF79_2_35


title: Jejunum_12_DMF100_MEF79_2_39


title: GC4_PB_E08.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_E08


title: RAL-796_brain_T=ZT17_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN9_Jan18_1_28233


title: Jejunum_12_DMF100_10


title: Jejunum_12_DMF100_11


title: Jejunum_12_DMF100_MEF79_2_33


title: RAL-796_brain_T=ZT11_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN18_Jan18_1_28233


title: GC4_PB_E07.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_E07


title: Jejunum_6_VEH_58


title: RAL-796_brain_T=ZT15_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN8_Jan18_1_28233


title: GC4_PB_D09.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_D09


title: GC4_PB_D10.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_D10


title: Jejunum_12_DMF100_15


title: GC4_PB_C10.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_C10


title: Jejunum_12_DMF100_13


title: Jejunum_6_VEH_55


title: GC4_PB_C09.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_C09


title: Jejunum_6_VEH_51


title: RAL-796_brain_T=ZT13_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN7_Jan18_1_28233


title: RAL-796_brain_T=ZT13_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN19_Jan18_1_28233


title: Jejunum_6_MEF79_2_81


title: RAL-796_brain_T=ZT5_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN3_Jan18_1_28233


title: GC4_PB_C07.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_C07


title: Jejunum_6_MEF79_2_80


title: Jejunum_6_VEH_57


title: Jejunum_12_DMF100_12


title: Jejunum_6_MEF79_2_78


title: Jejunum_6_DMF179_2_74


title: GC4_PB_D08.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_D08


title: Jejunum_6_VEH_56


title: GC4_PB_D07.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_D07


title: GC4_PB_B11.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_B11


title: Jejunum_6_VEH_54


title: RAL-796_brain_T=ZT9_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN5_Jan18_1_28233


title: Jejunum_6_VEH_53


title: GC4_PB_C11.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_C11


title: Jejunum_6_MEF79_2_79


title: RAL-796_brain_T=ZT9_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN17_Jan18_1_28233


title: Jejunum_6_MEF79_2_82


title: RAL-796_brain_T=ZT7_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN16_Jan18_1_28233


title: RAL-796_brain_T=ZT7_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN4_Jan18_1_28233


title: Jejunum_6_DMF179_2_68


title: RAL-796_brain_T=ZT5_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN15_Jan18_1_28233


title: GC4_PB_A11.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_A11


title: GC4_PB_B07.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_B07


title: Jejunum_6_DMF179_2_73


title: GC4_PB_C08.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_C08


title: Jejunum_6_DMF179_2_72


title: Jejunum_6_VEH_52


title: RAL-796_brain_T=ZT3_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN2_Jan18_1_28233


title: GC4_PB_B10.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_B10


title: RAL-320_gut_T=23h21m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_29654

value: Single observation


title: Jejunum_6_DMF179_2_71


title: RAL-796_brain_T=ZT3_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN14_Jan18_1_28233


title: Jejunum_6_DMF179_2_70


title: GC4_PB_B09.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_B09


title: RAL-409_gut_T=22h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28278


title: RAL-796_brain_T=ZT1_Rep2

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN1_Jan18_1_28233


title: GC4_PB_B08.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_B08


title: Jejunum_6_DMF179_2_69


title: RAL-796_brain_T=ZT1_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
DGRP-796_time_series_brain_norm.csv.gz
w1118_and_DGRP-796_time_series_brain_norm.csv.gz
BRAIN13_Jan18_1_28233


title: Jejunum_6_DMF100_60


title: Jejunum_6_DMF179_2_67


title: Jejunum_6_DMF100_59


title: RAL-235_gut_T=22h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28275


title: Jejunum_6_DMF100_MEF79_2_89


title: Jejunum_6_DMF100_MEF79_2_85


title: Jejunum_6_DMF100_MEF79_2_86


title: RAL-913_gut_T=22h14m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28265


title: RAL-057_gut_T=23h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_29652


title: GC4_DZ_H06.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_H06


title: GC4_DZ_H05.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_H05


title: GC4_PB_A09.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_A09


title: RAL-040_gut_T=22h52m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_29651


title: Jejunum_6_DMF100_MEF79_2_83


title: ILN_12_VEH_1

value: Inguinal Lymph Node (ILN)


title: Jejunum_6_DMF100_MEF79_2_84


title: Jejunum_6_DMF100_61


title: RAL-908_gut_T=21h55m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28263


title: RAL-907_gut_T=21h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28262


title: GC4_PB_A08.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_A08


title: Jejunum_6_DMF100_64


title: GC4_PB_A10.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_A10


title: ILN_12_VEH_8


title: ILN_12_VEH_7


title: ILN_12_NAIVE_45


title: ILN_12_NAIVE_43


title: ILN_12_NAIVE_41


title: GC4_DZ_H02.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_H02


title: ILN_12_VEH_6


title: GC4_DZ_H01.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_H01


title: RAL-897_gut_T=21h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28260


title: ILN_12_MEF79_2_32


title: ILN_12_MEF79_2_31


title: GC4_DZ_H03.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_H03


title: GC4_PB_A07.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_PB_A07


title: ILN_12_NAIVE_48


title: RAL-911_gut_T=22h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28264


title: ILN_12_MEF79_2_30


title: ILN_12_MEF79_2_29


title: ILN_12_NAIVE_46


title: ILN_12_NAIVE_44


title: ILN_12_NAIVE_47


title: RAL-900_gut_T=21h36m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28261


title: RAL-855_gut_T=20h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28251


title: RAL-892_gut_T=21h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28258


title: ILN_12_MEF79_2_25


title: ILN_12_NAIVE_42


title: RAL-890_gut_T=21h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28257


title: ILN_12_DMF179_2_23


title: ILN_12_DMF179_2_22


title: GC4_DZ_G06.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_G06


title: GC4_DZ_H04.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_H04


title: RAL-857_gut_T=20h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28252


title: GC4_DZ_G05.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_G05


title: ILN_12_DMF179_2_24


title: GC4_DZ_G04.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_G04


title: GC4_DZ_G01.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_G01


title: RAL-853_gut_T=20h0m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28250


title: RAL-832_gut_T=19h31m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28245


title: ILN_12_DMF100_MEF79_2_40


title: ILN_12_DMF179_2_21


title: ILN_12_DMF179_2_19


title: ILN_12_DMF100_MEF79_2_38


title: ILN_12_DMF100_MEF79_2_36


title: GC4_DZ_G03.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_G03


title: ILN_12_DMF100_MEF79_2_37


title: GC4_DZ_F06.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_F06


title: GC4_DZ_G02.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_G02


title: RAL-821_gut_T=19h12m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28243


title: RAL-819_gut_T=19h2m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28242


title: RAL-849_gut_T=19h50m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28248


title: ILN_12_DMF179_2_20


title: RAL-810_gut_T=18h43m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28239


title: GC4_DZ_F05.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_F05


title: RAL-808_gut_T=18h33m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28238


title: ILN_12_DMF100_MEF79_2_33


title: GC4_DZ_F04.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_F04


title: ILN_12_DMF100_9


title: ILN_12_DMF100_13


title: GC4_DZ_F03.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_F03


title: ILN_12_DMF100_12


title: ILN_12_DMF100_11


title: ILN_12_DMF100_10


title: ILN_12_DMF100_MEF79_2_34


title: RAL-805_gut_T=18h24m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28237


title: RAL-802_gut_T=18h4m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28235


title: ILN_12_DMF100_MEF79_2_35


title: GC4_DZ_E06.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_E06


title: GC4_DZ_F01.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_F01


title: RAL-790_gut_T=17h45m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28232


title: ILN_12_DMF100_16


title: GC4_DZ_E04.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_E04


title: ILN_6_VEH_57


title: ILN_6_VEH_53


title: ILN_6_VEH_55


title: ILN_6_VEH_54


title: ILN_6_VEH_52


title: ILN_6_MEF79_2_82


title: RAL-776_gut_T=17h16m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB4_Gut_n_28229


title: GC4_DZ_E05.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_E05


title: RAL-783_gut_T=17h26m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28230


title: ILN_6_MEF79_2_79


title: ILN_6_MEF79_2_81


title: GC4_DZ_E02.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_E02


title: ILN_6_VEH_56


title: RAL-748_gut_T=17h7m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28224


title: GC4_DZ_E01.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_E01


title: ILN_6_MEF79_2_78


title: RAL-738_gut_T=16h57m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28223


title: ILN_6_MEF79_2_77


title: GC4_DZ_E03.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_E03


title: ILN_6_DMF179_2_73


title: ILN_6_MEF79_2_80


title: GC4_DZ_D06.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_D06


title: RAL-703_gut_T=16h19m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28218


title: ILN_6_MEF79_2_76


title: RAL-716_gut_T=16h28m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB6_Gut_n_28219


title: ILN_6_MEF79_2_75


title: ILN_6_DMF179_2_72


title: RAL-646_gut_T=16h9m_Rep1

description:
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_gut_norm.csv.gz
BRB5_Gut_n_28217


title: GC4_DZ_D03.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_D03


title: ILN_6_DMF179_2_71


title: GC4_DZ_D04.DecP.30_H.DZ

description:
1dec_07082018-scRNAseq.txt.gz
GC4_DZ_D04