title: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 1

description: Rab11a DN replicate 1


title: G68D18A

status: Public on Feb 22 2021

type: SRA

city: Cincinnati

first: Biplab

last: Dasgupta

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: run1768_lane2_indexD705-D506=G68D18A-human_align

library_source: transcriptomic

data_processing:
Post Binary Alignment/Map (BAM) aligned files of RNASeq data were analyzed using Avadis® NGS software, Version 1.3.0. Reads were filtered to remove 1) duplicate reads, 2) non-primary-matched reads and 3) reads with alignment scores <95. Quantification was performed on the filtered reads against the RefSeq annotation.
Data normalization was performed with DESeq. The sequencing depth is estimated by the read count of the gene with the median read count ratio across all genes. The method is based on the negative binomial distribution, which allows for less restrictive variance parameter assumptions than does the Poisson distribution. The false discovery rate (FDR) was calculated according to the Benjamini and Hochberg algorithm.  1.5 FC with an FDR of 0.05 was used as selection criteria
Supplementary_files_format_and_content: Tab-delimited text files include DESeq normalized values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Brain Tumor

extract_protocol:
Rneasy Mini Kit from Qiagen
RNA-Seq as per Illumina protocol

tag: tissue

value: Brain Tumor

tag: cell type

value: acquired resistant cells

tag: time point

value: day 18


title: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description: Rab11a DN Control replicate 3

data_processing:
Raw fastq files were aligned to Ensembl reference zv11 using STAR
Aligned reads were cleaned using samtools
Normalized read counts were obtained using HTSeq and edgeR
Genome_build: Danio Rerio Ensembl zv11
Supplementary_files_format_and_content: Counts per million normalized reads are available as a tab-delimited file (Normalized_expression.txt), and include YapS87A and WT samples from GSE71681

molecule: polyA RNA

organism: Danio rerio

source_name: 36hpf zebrafish eyes

extract_protocol:
Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol.
polyA RNA; RNA libraries were prepared using standard Illumina protocols.
Illumina HiSeq 2000; 50bp Single-end reads

tag: genotype

value: Rab11aDN Control

tag: age

value: eyes


title: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3

description: NICD replicate 3

value: NICD overexpression


title: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2

description: Rab11a DN Control replicate 2


title: OIR_retina_P30_3

city: Montreal

first: Mike

last: Sapieha

state: Quebec

address: 5415 Boul. L'Assomption

country: Canada

institute: Hôpital Maisonneuve-Rosemont

data_processing:
Analysis was performed using the Torrent Suite software v5.4 (Thermo Fisher) and the RNASeqAnalysis plugins (Thermo Fisher)
The RNASeqAnalysis plugins aligns reads on mouse reference genome (mm10) using STAR, and then unmapped reads are aligned using Bowtie2 and merged together.
Gene level expression is calculated using HTSeq and Picard to report raw read counts and FPKM (fragment per kilobase of transcript per million).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw read counts for each Sample

organism: Mus musculus

source_name: OIR P30 retina lysate

extract_protocol:
Total RNA was isolated from freshly dissected retina lysates using the RNeasy Mini Kit (QIAGEN). The mRNA was then purified from 1μg of total RNA using the Dynabeads® mRNA DIRECT™ Micro Kit (Thermo Fisher). Whole transcriptome libraries were prepared using the Ion Total RNA-seq Kit v2. The yield and size distribution of the amplified libraries were assessed with an Agilent Bioanalyzer using a DNA 1000 Kit. Sequencing was performed on an Ion Proton Instrument (Ion Torrent™, Thermo Fisher).
Analysis was performed using the Torrent Suite software v5.4.0 (Thermo Fisher Scientific) and the RNASeqAnalysis plugins (Thermo Fisher Scientific). The RNASeqAnalysis plugins aligns reads on mouse reference genome (mm10) using STAR, and then unmapped reads are aligned using Bowtie2 and merged together. Gene level expression is calculated using HTSeq and Picard to report raw read counts and FPKM (fragment per kilobase of transcript per million).

treatment_protocol: Mice undergoing OIR (oxygen-induced retinophaty) were subjected to 75% oxygen from postnatal 7 to postnatal 12 and then brought up to air room condition (21% oxygen). Control animals were kept all the time at air room (21% oxygen).

tag: strain

value: Wildtype

value: Retina

tag: disease state

value: OIR


title: G82D1B

description: run1768_lane2_indexD708-D503=G82D1B-human_align

value: parental

value: day 1


title: G82R (AqR)

library_source: genomic

data_processing:
QC perfomed using FastQC(v0.11.2)
Adapter sequence (if present) removed using TrimGalore (v0.4.2) and cutadapt(v1.8.1)
Quality controlled reads aligned to hg19 genome using bowtie2(v2.3.4.1)
Aligned reads sorted using samttols (v1.8.0) and duplicate reads removed using picard(v1.89)
Peaks were called using MACS2(v2.1.0)
Genome_build: hg19

molecule: genomic DNA

extract_protocol:
Cells were prepared previous to the transposition reaction and purification (Qiagen MinElute PCR Purification Kit). Samples were PCR amplified and purified using the same kit as before.
as per Illumina protocol


title: Pan3.W.N15.0hr.pos

city: Utrecht

first: Joep

last: de Ligt

address: Universiteitsweg 100

department: Genetics

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Illumina software used for basecalling.
Sequenced reads mappend and analysed as specified here;https://github.com/UMCUGenetics/RNASeq/releases/tag/2.1.0
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file with metadata
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreas

growth_protocol: Organoids from human the small intestine, colon, liver ducts, pancreas and stomach were grown is expansion medium as described in earlier publications (23, 48–50). Small intestine, colon, liver and pancreas organoids were grown in Matrigel (BD

extract_protocol:
Total RNA was extracted using the RNAeasy mini kit (Qiagen) according to manufecter's protocol including DNAse treatment.
Library preparation was started with 500ng of Total RNA using the Truseq Stranded Total RNA kit with Ribo-Zero Human/Mouse/Rat set A and B by Illumina (Cat. RS-122-2201 and RS-122-2202
Libraries were equimolar pooled to 2 nM. And sequenced on the Illumina Nextseq, 1x75bp high output, and 1.0-1.4 pM of library pools was loaded.

treatment_protocol: On day 3 post splitting xpansion medium was replaced by Wnt inhibitory medium, lacking Wnt and/or R-spondin (see Table 7) and addition of DKK1 (200 ng/μl - Peprotech) and IWP2 (3 μM - Tocris).

tag: line

value: Pancreas

tag: timepoint (hr)

tag: wnt yes or no

value: yes


title: Li3.W.6hr.neg

source_name: Liver

value: Liver

value: no


title: Li3.W.24hr.neg


title: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 2

description: Rab11a DN replicate 2

value: Rab11aDN overexpression


title: G82 (parental)


title: Col3.W.P26N.6hr.neg

source_name: Colon

value: Colon


title: Control_retina_P30_3

source_name: Normoxia P30 retina lysate

value: Control


title: Control_retina_P30_1


title: OIR_retina_P17_3

source_name: OIR P17 retina lysate


title: OIR_retina_P30_2


title: OIR_retina_P17_2


title: G68D1B

description: run1773_lane92_indexD709-D501=G68D1B-human_align

value: Brain Tumor


title: Col3.W.P26N.24hr.neg


title: OIR_retina_P17_1


title: G68D1A

description: run1768_lane2_indexD708-D502=G68D1A-human_align


title: Control_retina_P17_3

source_name: Normoxia P17 retina lysate


title: Col3.W.P26N.0hr.pos


title: Li3.W.0hr.pos


title: D39 Δtcs09 mutant strain_replicate 3 [4164]

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
Sequencing on NovaSeq 6000 (Illumina) followed in paired-end mode with 50 cycles. Fastq files were assessed for sequence quality using FastQC (version 0.11.5) and an index from the genome from the file NC_008533 (D39) was created with bowtie2 (version 2.3.4.3). The mapping of the reads to the index was performed also with bowtie2. Reads were counted and assigned to the corresponding genome using function featureCounts of R package Rsubread (version 2.2.2). Contrasts were calculated using R package DESeq2 (version 1.28.1). R version 3.4.4 was used.
Genome_build: NC_008533
Supplementary_files_format_and_content: Raw.Counts.csv, Comma seperated text file containing counts of all samples

organism: Streptococcus pneumoniae D39

source_name: Δtcs09 mutant grown in CDM mid-log phase (OD 0.6)

growth_protocol: Each bacterial strain was cultured in a blood agar plate for 10 hours at 37ºC and 5% CO2. The bacteria were then inoculated into liquid CDM at a starting OD600nm of 0.1 and grown in a water bath at 37ºC until a final OD600nm of 0,6.

extract_protocol:
The pellets were processed for total RNA extraction using acid phenol-chloroform and DNase treatment to remove genomic DNA. The products were purified using the RNA Clean-Up and Concentration kit (NORGEN BIOTEK CORP), the quality of the RNA was determined by agarose gel electrophoresis and the amount was quantified using a Nanodrop ND-1000 (PeqLab)
RNA samples were fragmented, depleted of genomic DNA and dephosphorylated prior to their ligation to 5' phosphorylated barcoded adapters, Barcodes RNAs were pooled, depleted of rRNA using RiboZero and converted to Illumina cDNA libraries in 2 steps. First, the RNA was reverse transcribed using a primer targeting the ligated adapter. During cDNA synthesis, a second adapter was added to the 3' end of cDNAs through template switching. Second, cDNAs were PCR amplified with primers targeting the ligated adapters and carrying the full sequence of the Illumina sequencing adapters.

treatment_protocol: 30 ml of the bacterial culture was added into a vial containing ice cold killing buffer. Tubes were immediately centrifuged for 10 min at 3200g and 4ºC, the supernatant was removed and the vials with the pellet were flash frozen in liquid nitrogen and stored at -80ºC

tag: genotype/variation

value: {delta}tcs09 mutant

tag: growth phase

value: CDM mid-log phase (OD 0.6)


title: OIR_retina_P30_1


title: Control_retina_P17_2


title: Control_retina_P17_1


title: OIR_retina_P14_2

source_name: OIR P14 retina lysate


title: Control_retina_P30_2


title: SI2.W.74.6hr.neg

source_name: Intestine

value: Intestine


title: SI2.W.74.24hr.neg


title: Control_retina_P14_1

source_name: Normoxia P14 retina lysate


title: D39 Δhk09 mutant strain_replicate 4 [5221]

source_name: Δhk09 mutant grown in CDM mid-log phase (OD 0.6)

value: {delta}hk09 mutant


title: D39 Δtcs09 mutant strain_replicate 2 [2366]


title: Control_retina_P14_2

value: Wildtype


title: OIR_retina_P14_1

value: Retina


title: SI2.W.74.0hr.pos


title: D39 Δhk09 mutant strain_replicate 3 [3565]


title: Pan2.W.N8.6hr.neg


title: Severe mutant null #5

city: Solna

first: Florian

middle: Andreas

last: Schober

address: Solnavägen 9

department: Department of Medical Biochemistry and Biophysics (MBB)

country: Sweden

institute: Karolinska Institutet

description:
DESeq2_NullvsCtrl.txt
Null.5

data_processing:
Paired-end RNA sequencing reads were quasi-mapped against a cDNA library of BDGP6 (release 94) with salmon v0.11.3 and a --gcbias flag (Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Meth. 2017;14: 417–419. doi:10.1038/nmeth.4197).
Differential gene expression analysis was performed with DESeq2 version 1.26.0 (Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and  dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550) and Independent Hypothesis Weighing version 1.14.1 (Ignatiadis, N., Klaus, B., Zaugg, J.B., and Huber, W. (2016). Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nat Meth 13, 577–580).
Genome_build: BDGP6 (release 94)
Supplementary_files_format_and_content: DESeq2_I172GvsCtrl.txt
DESeq2_P223LvsCtrl.txt
DESeq2_NullvsCtrl.txt
SAMC_counts.Rdata (R file for txi import)

organism: Drosophila melanogaster

source_name: total larvae

growth_protocol: All genomically engineered fly lines were maintained and experiments performed at 25°C and 60% humidity on a 12h:12h light:dark cycle and fed on a standard yeast–sugar–agar (10-5-1) medium.

extract_protocol:
Total RNA wasDrosophila RNA was extracted, and on-column DNase digested with the miRNeasy Mini kit (QIAGEN/Germany). RNA integrity was certified on a Bioanalyzer (Agilent Technologies/US).
2 µg RNA were subjected to 2x75bp ribo-zero RNAseq at a depth of 3M reads per sample on a HiSeq4000.

value: 4 day-old at 25°C

tag: genetic background

value: wDah


title: Severe mutant null #4

description:
DESeq2_NullvsCtrl.txt
Null.4


title: GFP +2b + WUS (1)

city: Hefei

first: Zhong

last: Zhao

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

description:
small RNA
library strategy: siRNA-Seq

data_processing:
Basecalls performed using CASAVA version 1.4
3' and 5' adaptor were removed by home perl scripts
uniq reads number were count
reads great than 18 nt were kept for small RNA analysis
Supplementary_files_format_and_content: tab-delimited text files include read number for each Sample

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: Seeds pretreated for 2 days at 4°C were grown in soil in the greenhouse for another 4-weeks  (22°C, 16 h light /8 h dark photoperiod).

extract_protocol:
Total RNA were extracted from the leaves using the mirVana™ miRNA Isolation Kit (lif tetechnology) with two biological replicates. Total RNA was fractionated by electrophoresis. RNA from 10 to 30 nt was sliced and recovered.
The 18-30 nt small RNA were selected for library building.The purified small RNA was subjected to adapter ligation, reverse transcription, PCR amplification with NEXTflex Small RNA Sequencing Kit (Bioo Scientific), and the resulting libraries sent for deep sequencing by Illumina HiSeq2000.

treatment_protocol: 3-week-old N. benthamiana were infiltrated with the mixture of Agrobacterium tumefaciens harbored different constructs, including 35S::GFP + 35S::GUS, 35S::GFP + 35S::2b + 35S::GUS, 35S::GFP + 35S::2b + 35S::WUS.The leaves from plants were harvested six days after infiltration.

tag: group

value: leaves


title: D39 Δhk09 mutant strain_replicate 2 [8067]


title: Pan2.W.N8.24hr.neg

value: Pancreas


title: Severe mutant null #3

description:
DESeq2_NullvsCtrl.txt
Null.3


title: D39 Δhk09 mutant strain_replicate 1 [7793]


title: Pan2.W.N8.0hr.pos

value: yes


title: GFP +2b +GUS (2)

description:
small RNA
library strategy: siRNA-Seq


title: Severe mutant null #2

description:
DESeq2_NullvsCtrl.txt
Null.2


title: D39 Δrr09 mutant strain_replicate 4 [2106]

source_name: Δrr09 mutant grown in CDM mid-log phase (OD 0.6)

value: {delta}rr09 mutant


title: GFP +2b +GUS (1)

description:
small RNA
library strategy: siRNA-Seq


title: D39 Δtcs09 mutant strain_replicate 1 [5088]


title: Li2.W.6hr.neg

value: Liver

value: no


title: D39 Δrr09 mutant strain_replicate 3 [6764]


title: Severe mutant p223l #5

description:
DESeq2_P223LvsCtrl.txt
P223L.5


title: GFP + GUS (2)

description:
small RNA
library strategy: siRNA-Seq


title: D39 Δrr09 mutant strain_replicate 2 [4795]


title: Li2.W.0hr.pos


title: GFP + GUS (1)

description:
small RNA
library strategy: siRNA-Seq


title: Severe mutant p223l #4

description:
DESeq2_P223LvsCtrl.txt
P223L.4


title: D39 Δrr09 mutant strain_replicate 1 [6924]


title: EGFP-Positive_3

city: Ota-ku

first: Takashi

last: Nishina

state: Tokyo

address: 5-21-16 Omori-nishi

department: Biochemistry

country: Japan

institute: Toho University

data_processing:
Adapter trimming and quality filtering of resulting fastq files were performed by using Cutadapt-v1.18
Trimmed reads were mapped to the Refseq mm10 RNA by using Bowtie2-2.2.5 with the following parameters: t -p 16 –N 1 -D 200 –R 20 -L 20 -i S,1,0.50 --nofw. Tag numbers of each gene represented the expression level of each gene and were used as count data.
Genes with tag number ≥10 were deemed low expressed and were excluded from analysis. The sample to sample normalization was performed with R (version 3.5.1) and TCC package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw tag-count values for each sample

source_name: Stromal cells

extract_protocol:
To isolate IL-11+ EGFP+ cells or IL-11- EGFP- cells, the colon was removed from DSS-treated Il11-Egfp reporter mice on Day 7. Then, the colon was minced with scissors and digested in RPMI 1640 containing 100 U/mL Penicillin and 0.1 mg/mL Streptomycin, 0.25 mg/mL Liberase (Merck), 0.05 mg/mL DNase (Roche), and 2% (v/v) fetal bovine serum (FBS, Gibco) for 60 min. EGFP+ and EGFP- cells among Ter119- CD45- CD31- EpCAM- cell populations were enriched using MojoSort Mouse anti-APC Nanobeads (BioLegend) and MojoSort Magnet (BioLegend), and sorted by BD FACSAriaTM III Cell Sorter (BD Biosciences).
RNA-seq analysis were performed using the 5’Tag-seq method as described previously (Shichino etal., JCI Insight, 2019). Briefly, polyA RNA were trapped by oligo-dT-immobilized magnetic beads and reverse-transcribed by using Superscript IV (Thermo Fisher Scientific). Then, polyC tailing and 2nd strand synthesis were performed, and cDNA was amplified by PCR. Resulted cDNA products were converted to Ion Torrent sequencing libraries by using NEBNext UltraII FS library prep kit (New England Biolabs). RNA sequencing was performed with Ion 540 Kit-Chef, Ion 540 Chip Kit and Ion Genestudio S5 Sequencer (Thermo Fisher Scientific) according to the manufacturer's instructions.

treatment_protocol: Nine- to fifteen-week-old wild-type or Il11-Egfp reporter mice received 1.5 % DSS (MW: 36,000-50,000 D; MP Biomedicals) ad libitum in drinking water for 5 days, which then was changed to regular water.

value: Colon

value: Lineage (CD45, CD31, EpCAM, Ter119) negative, DAPI-negative

tag: expression

value: EGFP-Positive


title: GFP +2b + WUS (2)

description:
small RNA
library strategy: siRNA-Seq


title: Severe mutant p223l #3

description:
DESeq2_P223LvsCtrl.txt
P223L.3


title: Col2.W.P11N.6hr.neg


title: D39 wild-type strain_replicate 4 [9287]

source_name: wild-type grown in CDM mid-log phase (OD 0.6)

value: wild-type


title: EGFP-Positive_2


title: Severe mutant p223l #2

description:
DESeq2_P223LvsCtrl.txt
P223L.2


title: EGFP-Positive_1


title: Col2.W.P11N.0hr.pos


title: Severe mutant p223l #1

description:
DESeq2_P223LvsCtrl.txt
P223L.1


title: EGFP-Negative_3

value: EGFP-Negative


title: Severe mutant null #1

description:
DESeq2_NullvsCtrl.txt
Null.1


title: SI1.W.72.6hr.neg

value: Intestine


title: Mild mutant i172g #5

description:
DESeq2_I172GvsCtrl.txt
I172G.5


title: D39 wild-type strain_replicate 1 [9375]

value: CDM mid-log phase (OD 0.6)


title: EGFP-Negative_2


title: SI1.W.72.24hr.neg


title: Li2.W.24hr.neg


title: Mild mutant i172g #4

description:
DESeq2_I172GvsCtrl.txt
I172G.4


title: SI1.W.72.0hr.pos


title: Mild mutant i172g #3

description:
DESeq2_I172GvsCtrl.txt
I172G.3


title: Col2.W.P11N.24hr.neg


title: Mild mutant i172g #2

description:
DESeq2_I172GvsCtrl.txt
I172G.2


title: D39 wild-type strain_replicate 3 [1545]


title: T3 sample 2 snRNA-seq

city: Tromsø

first: Alexander

middle: Christopher

last: West

state: Troms

address: Framstredet 39, Tromsø

department: Arctic Chronobiology and Physiology

country: Norway

institute: Universitetet i Tromsø

data_processing:
Gene-cell matrices were generated by mapping sequence reads to ICSASG_v2 with Cell Ranger 3.0.1
Genome_build: ICSASG_v2
Supplementary_files_format_and_content: Processed data files are simple gene-cell matrices (genes as rows, cell indexes as columns).

organism: Salmo salar

source_name: Atlantic salmon Gill

extract_protocol:
Nuclei were released by detergent mechanical lysis, then samples were homogenized (30s) and nuclei isolated by sucrose gradient as Matson et al (2018)
Libraries were created using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (10x technologies) by University of Manchester genomic technology core facility (UK). Raw data was converted to counts per cell using Cell Ranger (10x Technologies, ver. 3.1.0) and processed using NCBI annotations. The R package Seurat (ver. 3.1.5) was used to perform an integrated analysis using all snRNAseq data

value: Gill

tag: treatment

value: Parr constant light -> 8 week short photoperiod -> 8 week constant light


title: Mild mutant i172g #1

description:
DESeq2_I172GvsCtrl.txt
I172G.1

value: 4 day-old at 25°C


title: Pan1.W.RP325.24hr.neg

source_name: Pancreas


title: T4 sample 1 snRNA-seq

value: Parr constant light -> 8 week short photoperiod -> 8 week constant light -> 24h seawater


title: T4 sample 2 snRNA-seq


title: T3 sample 1 snRNA-seq


title: D39 wild-type strain_replicate 2 [2988]


title: T2 sample 2 snRNA-seq

value: Parr constant light -> 8 week short photoperiod


title: Pan1.W.RP325.0hr.neg

value: Pancreas


title: Li1.W.6hr.neg

source_name: Liver


title: Control #5

description:
DESeq2_I172GvsCtrl.txt, DESeq2_P223LvsCtrl.txt, DESeq2_NullvsCtrl.txt
wDah.5

value: wDah

value: control


title: Control #4

description:
DESeq2_I172GvsCtrl.txt, DESeq2_P223LvsCtrl.txt, DESeq2_NullvsCtrl.txt
wDah.4


title: Li1.W.24hr.neg

value: Liver


title: Control #3

description:
DESeq2_I172GvsCtrl.txt, DESeq2_P223LvsCtrl.txt, DESeq2_NullvsCtrl.txt
wDah.3


title: T1 sample 2 snRNA-seq

value: Parr constant light


title: T2 sample 1 snRNA-seq


title: EGFP-Negative_1

value: Colon


title: Pan1.W.RP325.6hr.neg

value: no


title: dSTINGknock-24h_starved-rep3

type: RNA

city: Birmingham

first: Katarina

last: Akhmetova

state: AL

address: 720 20th St S, Kaul 548

institute: University of Alabama at Birmingham

description:
mut-ST-3
Gene expression data for dSTING knockout 24 hour starved male flies.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Drosophila Gene 1.0 ST array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.48.0), using R version 3.2.0 and the Brainarray drogene10stdmentrezgcdf R package (version 20.0.0).

label: biotin

source_name: males, whole body, 5-days old, 24 h starved

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Flies were grown at standard conditions.

extract_protocol: Whole bodies of ten males were used to extract total RNA. RNA was extracted using ZR Tissue and Insect RNA MicroPrep™ (Zymo Research, #R2030) according to the manufacturer's instructions.

treatment_protocol: Flies were grown for 4 days on regular food. Then, flies were either left on regular food, or placed into empty vials with moist whatman paper for 24 hours.

value: whole body

value: dSTINGknock

tag: Sex

value: male

value: 5 days after eclosion

value: Starved 24h


title: Li1.W.0hr.pos

tag: tissue

value: yes


title: Control #2

description:
DESeq2_I172GvsCtrl.txt, DESeq2_P223LvsCtrl.txt, DESeq2_NullvsCtrl.txt
wDah.2


title: dSTINGknock-24h_starved-rep1

description:
mut-ST-1
Gene expression data for dSTING knockout 24 hour starved male flies.


title: dSTINGknock-24h_starved-rep2

description:
mut-ST-2
Gene expression data for dSTING knockout 24 hour starved male flies.


title: w1118-24h_starved-rep3

description:
wt-ST-3
Gene expression data for w1118 24 hour starved male flies.


title: Col1.W.P7N.6hr.neg

source_name: Colon


title: w1118-24h_starved-rep2

description:
wt-ST-2
Gene expression data for w1118 24 hour starved male flies.


title: T1 sample 1 snRNA-seq

value: Gill


title: Control #1

description:
DESeq2_I172GvsCtrl.txt, DESeq2_P223LvsCtrl.txt, DESeq2_NullvsCtrl.txt
wDah.1

value: 4 day-old at 25°C


title: WTT3

city: Wuhan

first: Fanfan

last: Zeng

state: Hubei

address: No.13, Hangkong Road

department: Department of Immunology

institute: Tongji Medical College, Huazhong University of Science and Technology

description:
gene_all_counts.txt
gene_all_fpkm.txt
transcript_all_counts.txt
transcript_all_fpkm.txt

data_processing:
The software installed on the Illumina HiSeq X10 System used for basecalling.
FastQC v0.11.7 was used to perform quality control checks on raw sequence data.
The raw reads were aligned to the mm10 reference genome by using HISAT2 software (version 2.1.0). The mapping rate was more than 90% overall across all the samples.
StringTie v1.3.4d was used to quantify the gene expression counts.
Differential expression analysis was performed on the count data using R package DESeq2 1.18.1. Benjamini-Hochberg step-up method to control false discovery rate. Significant genes are defined by a Benjamini and Hochberg corrected P value of cut-off of 0.05 and fold-change of at least 1.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts and FPKM values for each sample

source_name: Mouse primary keratinocytes, treated with recombinant IL-33

growth_protocol: Primary keratinocytes were isolated from newborn mice by incubating in 154CF medium (GIBCO, # M-154CF-500) containing 2 mg / mL Dispase II at 4 ° C for 10 hours. The epidermis was gently peeled and the cells were washed with cold HBSS (GIBCO, # 14175-095). Primary keratinocytes were then isolated by digestion with 0.05% trypsin for 10 minutes and seeded in 48-well plates and cultured in a 5% CO2 incubator for recombinant IL-33 treatment.

extract_protocol:
Total RNA from primary keratinocytes was extracted using TRIzol (Invitrogen, USA), VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, China) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary keratinocytes were treated with or without recombinant IL-33 for 12 h.

value: skin epidermis

value: post natal 0-2 days

value: wild type


title: w1118-24h_starved-rep1

description:
wt-ST-1
Gene expression data for w1118 24 hour starved male flies.


title: Pst-mm3

city: Durham

first: Joshua

middle: Aaron

last: Granek

state: NC

address: Box 3568, 213 Research Drive

department: Department of Biostatistics and Bioinformatics

institute: Duke University School of Medicine

data_processing:
General read quality was evaluated using FastQC v0.11.2
Genome and GTF files were downloaded from NCBI and indexed using bowtie2-build (Bowtie2 v2.3.1).
FASTQs were filtered and trimmed using fastq-mcf (ea-utils v1.1.2) using paramteres "-q 20 -x 0.5" and adapter sequences from the NEBNext manual.
Filtered and trimmed reads were mapped using tophat2 (v2.1.1) using parameters "--library-type fr-firststrand --max-intron-length 5 --min-intron-length 4 --transcriptome-max-hits 1 --max-multihits 1 --no-coverage-search --no-novel-juncs --no-sort-bam
samtools v0.1.19 was used to merge and sort the accepted_hits.bam and unmapped.bam files output by tophat using commands "samtools merge -n" and "samtools sort -n"
htseq-count (htseq v0.6.1) was used to count reads per gene with the parameters "--order=name --format=bam --stranded=reverse --type=gene --idattr=locus_tag" $TH_DIR/${SAMPLE}/merged.name.bam
A Jupyter notebook containing the analysis pipeline is available at <https://gitlab.oit.duke.edu/Biostatistics_and_Bioinformatics/HTS_SummerCourse_2017/-/blob/master/Materials/Computation/Wk4_Day4_AM/analysis_nb/2017_generate_pilot_counts.ipynb>
Genome_build: GCF_000007805.1_ASM780v1
Supplementary_files_format_and_content: tab-delimited text files containing raw read counts per gene

organism: Pseudomonas syringae

source_name: bacterial culture

extract_protocol: rRNA was depleted from purified total RNA using the Ribo-Zero Gram-Negative Bacteria kit (Illumina). rRNA-depleted samples were then cleaned up with the RNA Clean & Concentrator-5 (Zymo Research) and eluted in 15ul.    library strategy RNA-Seq.  RNA-Seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420; New England BioLabs).

value: pv. tomato DC3000

tag: media


title: Pst-mm4


title: Col1.W.P7N.0hr.pos


title: dSTINGknock-fed-rep3

description:
mut-F-3
Gene expression data for dSTING knockout fed male flies.

source_name: males, whole body, 5-days old, fed

value: Fed


title: WTT1


title: Pst-mm1


title: WTT2


title: Pst-kb3


title: WTC3

source_name: Mouse primary keratinocytes, untreated


title: D39 Δtcs09 mutant strain_replicate 4 [6128]

source_name: Δtcs09 mutant grown in CDM mid-log phase (OD 0.6)

value: {delta}tcs09 mutant

value: CDM mid-log phase (OD 0.6)


title: dSTINGknock-fed-rep2

description:
mut-F-2
Gene expression data for dSTING knockout fed male flies.


title: w1118-fed-rep3

description:
wt-F-3
Gene expression data for w1118 fed male flies.


title: Pst-kb1


title: dSTINGknock-fed-rep1

description:
mut-F-1
Gene expression data for dSTING knockout fed male flies.


title: WTC1


title: WTC2


title: w1118-fed-rep2

description:
wt-F-2
Gene expression data for w1118 fed male flies.


title: Basenji_blood_WGBS

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

data_processing:
Adaptor sequences and low quality bases were removed using trimmomatic tool (Bolger et al, 2014)
Sequencing reads were aligned to in-silico bisulphite-converted reference genome Canis lupus basenji using WALT mapping tool (Chen et al, 2016)
DNA methylation calling was performed using MethylDackel (https://github.com/dpryan79/MethylDackel)
Genome_build: Canis lupus basenji: GCA_013276365.1_UNSW_CanFamBas_1.0_genomic.fa
Supplementary_files_format_and_content: bedGraph / The file contains 1. Chromosome / Scaffold; 2. CpG start coordinate; 3. CpG end coordinate; 4. The methylation percentage rounded to an integer; 5. The number of alignments/pairs reporting methylated bases; 6. The number of alignments/pairs reporting unmethylated bases
Supplementary_files_format_and_content: bigtable.tsv / For bigtable.tsv" processed data files the column headers are as follows: column 1 - assembly (chromosome). column 2 - position: coordinate for the cytosine position on the chromosome. column 3 (.C) - number of reads depicting a methylated cytosine. column 4 (.cov) - total number of reads at that position.

organism: Canis lupus

source_name: Blood-derived DNA subject to WGBS

growth_protocol: Basenji's whole blood

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue kit (Qiagen, USA).
MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 300 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA).

treatment_protocol: no treatment

tag: tissue type

value: blood


title: Human_skin_fib_rep1

city: Singapore

first: Eleonora

last: Adami

address: 8 College Road

department: CVMD

country: Singapore

institute: Duke-NUS Medical School

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to human genome hg38 using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -p -R -G
Genome_build: Homo sapiens hg38 Ensembl release 92
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: human dermal fibroblasts from a healthy donor

extract_protocol:
The total RNA of primary human dermal fibroblasts, extracted using the RNeasy mini kit (Qiagen), was quantified using Qubit RNA high sensitivity assay kit (Thermo Fisher Scientific) and RNA integrity number (RIN) was assessed using the LabChip GX RNA Assay Reagent Kit (Perkin Elmer).
Libraries prepared using the TruSeq Stranded mRNA Kit (Illumina) were pooled and sequenced on a NextSeq 500 sequencer (Illumina) using NextSeq 500 High Output v2 kit and paired-end 75–base pair sequencing chemistry.

tag: subject status

value: healthy donor

tag: cell type

value: dermal fibroblasts

tag: rin


title: COX4I1 knockdown rep4 [3D]

status: Public on Feb 21 2021

city: Jerusalem

first: Ann

last: Saada (Reisch)

department: Department of Genetics

country: Israel

institute: Hadassah Medical Center

data_processing:
Demultiplexing was done by the Technion Genome Center, resulting in fastq files of 50 bp reads.
Using Cutadapt (v1.18) quality trimming was done at the 3’ end with a cutoff of 10, and adapter & poly-A sequences were removed. The error rate was set to zero. Reads that became shorter than 28 nt were filtered out. Command : cutadapt -e 0 -q 10 -a "A{100}" -a "A{15}N{100}" -a GATCGTCGGACT -n 3 -m 28
The processed files were aligned to the Homo Sapiens transcriptome and genome using TopHat  (v2.1.1). The genome version was GRCh38 with annotations from Ensembl release 95. Strand information was taken into consideration. Alignment allowed up to 2 mismatches per read, and a total edit distance of 5. Command : tophat --library-type fr-secondstrand -N 2 --read-edit-dist 5
Quantification was done using htseq-count (v0.6.1p1). Reads that aligned with a quality lower than 10 were skipped. Strand information was taken into consideration. An annotation file that lacked information for genes of type IG, TR, Artifact, miRNA, Mt_rRNA, Mt_tRNA, ncRNA, piRNA, pre_miRNA, rRNA, ribozyme, sRNA, scRNA, scaRNA, siRNA, snRNA, snoRNA, tRNA and vaultRNA was used. Command : htseq-count --type=exon  --idattr=gene_id  -a 10  --mode=union  --stranded=yes
Genes with a sum of counts less than 10 over all samples were filtered out. Differential expression analysis was done with the DESeq2 package (v1.22.1). Differential expression was calculated with default parameters except not using the independentFiltering algorithm.
Genome_build: GRCh38
Supplementary_files_format_and_content: An Excel file. 'rawc.' columns are raw counts,  'normc.'  columns are the values after DESeq2 normalization.  'baseMean, Log2FoldChange, lfcSE, stat, pvalue, padj' are corresponding result of DESeq2 analysis. 'sig' indicates significance according to our threshold (padj<0.1).

source_name: HFF_COX4I1 knockdown

growth_protocol: 10,000 cells per well were seeded on 6-well plate in high-glucose media and incubated in 37°C, 5% CO2. Following 72 hours, total RNA was isolated from both knockdown and control.

extract_protocol:
RNA was harvested using Tri-reagent (Sigma-Aldrich), according to manufacturer's instructions. RNA concentration and qualification were determined using Tapestation (The minimal RNA concentration that was suitable for HiSeq analysis was higher than at least 2.5ng/μl, for each plicate).
Libraries were prepared using the CEL-Seq2 protocol, and sequenced on Illumina HiSeq 2500.

treatment_protocol: No treatment

tag: cell line/type

value: human foreskin fibroblasts (HFF)

tag: tissue source

value: Skin; foreskin

value: COX4I1 knockdown


title: COX4I1 knockdown rep5 [3E]


title: COX4I1 knockdown rep3 [3C]


title: COX4I1 knockdown rep2 [3B]


title: Control rep4 [1D]

value: Control


title: Control rep5 [1E]


title: COX4I1 knockdown rep1 [3A]


title: Control rep3 [1C]


title: Control rep2 [1B]


title: Control rep1 [1A]


title: w1118-fed-rep1

description:
wt-F-1
Gene expression data for w1118 fed male flies.

value: whole body

tag: genotype

value: male

tag: age

value: 5 days after eclosion


title: Pst-kb2

tag: strain

tag: genotype/variation


title: P6I3

city: Strasbourg

first: Helene

last: Burckel

address: 3 rue de la porte de l'hopital

country: France

institute: ICANS

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto a chimeric genome composed of hg38 assembly of human genome and mm10 assembly of mouse genome using STAR 2.5.3a.
Quantification : Gene expression was quantified using HTSeq v0.6.1p1 (union mode) and Ensembl release 93 annotations.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values file containing raw read counts in each sample.

source_name: Subcutaneous human pancreatic tumour resected from mice flank

extract_protocol:
Animals were euthanized 24 hours after irradiation by either proton or photon beams. Tumor was then harvested, flash frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted using RNeasy Plus Universal Tissue Mini kit (Qiagen, Hilden, Germany) as per manufacturer’s instructions. RNA integrity was performed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA). RNA quantification and quality (ratio of OD260/230 and OD260/280) were assessed using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, USA).
RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Gemcitabine (40 mg/kg) and olaparib (50 mg/kg) were administered via intra-peritoneal injections 24 hours and 1 hour before irradiation, respectively (Figure 1). Gemcitabine (Selleck Chemicals LLC, Houston, USA) was dissolved in dimethyl sulfoxide (DMSO) and diluted in PBS at 40 mg/ml. Olaparib (Selleck Chemicals LLC) was dissolved in DMSO at a concentration of 50 mg/ml then diluted in PBS and 10% 2-hydroxypropyl--cyclodextrin (Sigma) at 4 mg/ml.   Mice were irradiated with either clinical photon beams or clinical proton beams under anaesthesia (ketamine 100 mg/kg and xylazine 10 mg/kg). Tumors were irradiated with a single fraction of 10 Gy of physical dose and a dose rate of 8 Gy/min.   Photon irradiation were carried out using a Novalis Tx (Varian Medical Systems, Palo Alto, CA, U.S.A), with 6 MV energy photon in Paul Strauss Comprehensive Cancer Center (ICANS, Strasbourg, France). Animals presented a tumor toward the irradiation beam. The whole body of the mouse, apart from the tumor, was protected with lied shield (XRaystore, La Garde, France) to avoid radiation toxicity.   The proton beams irradiation were extracted from CYRCé (CYclotron pour la ReCherche et l’Enseignement) in Institut Pluridisciplinaire Hubert Curien (Strasbourg, France) with an averaged energy beam of 25 MeV. Using an in-house immobilization bed, tumor was irradiated directly in contact with the collimator. Dosimetry and characterization of the beam have recently been published.

tag: cell line

value: PTOG :proton therapy + olaparib + gemcitabine


title: P3E4

value: Subcutaneous human pancreatic tumour resected from mice flank

value: RTOG :radiotherapy + olaparib + gemcitabine


title: P3C5

value: RTG :radiotherapy + gemcitabine


title: P10I7


title: P10I8


title: P6H6

value: PTO :proton therapy + olaparib


title: P6H3


title: P6H4


title: P6H2


title: P10G10

value: PTG :proton therapy + gemcitabine


title: P10G11


title: P6H1


title: P10G9


title: P10G7


title: P3D2

value: RTO :radiotherapy + olaparib


title: P6I1


title: P6G3


title: P10F7

value: PT :proton therapy


title: P6F2


title: P6F6


title: P11E8


title: P11D9


title: P11E7


title: P11D7


title: P11E9


title: P11D8


title: P3D8


title: P6F5


title: P3C3


title: P3C4


title: P3C6


title: P11B8

value: RT :radiotherapy


title: P3C2


title: P6F1


title: P11B7


title: P3B6


title: P3B3


title: P3B2


title: P11D10


title: P3E6B


title: P11A7

value: CTL :control - no irradiation - no treatment


title: P3A4


title: P11A8


title: P3A5


title: P3A3


title: 72h_no_RAD

city: Belfast

first: Francesca

last: Amoroso

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

data_processing:
Sequencing was performed on Illumina Next Seq 500 (High out output (150)) at 75 P.E at 25M reads/ sample.
Fastq files were generated using bcl2fastq version 2.19 using the default thresholds.
Reads were aligned to version GRCh37/hg19 of the human reference genome using STAR (version 2.4.2a).
Raw counts of reads mapped to genes were calculated using HT‐Seq (http://www‐huber.embl.de/users/anders/HTSeq/doc/overview.html)
Raw counts were used as input for differential expression analysis using DESeq2.
Read counts per genes files were generate and principal component analysis (PCA) (RStudio, Boston, USA) performed.
Genome_build: mm8
Supplementary_files_format_and_content: Gene sets were filtered to contain genes upregulated with radiation (ratio >1.5) and downregulated with ONC201 (ratio <0.5).

source_name: Prostate Cancer cells

growth_protocol: Cells were seaded as standard protocol, treated as described above and harvasted at different time points.

extract_protocol:
The RNA was extracted from the cells and collected utilizing the column-based method through the RNeasy MinElute Clean-up Kit (QIAGEN, Hilden, Germany).
The RNA library preparations were performed with the KAPA RNA HyperPrep Kit (KAPA Biosystems, Roche Holding AG) according to the manufacturer’s instructions.

tag: treatments

value: untreated cells, harvested at 72h

tag: experiment

value: in vitro


title: 72h_8Gy

value: cells irradiated with 4Gy and harvested at 72h


title: 72h_V

value: cells treated with DMSO 0.1% for 72h


title: 72h_8Gy_15uM

value: cells irradiated with 8Gy and ONC201 15uM, harvested at 72h


title: 72h_8Gy_5uM

value: cells irradiated with 8Gy and ONC201 5uM, harvested at 72h


title: 72h_5uM

value: cells treated with ONC201 5uM for 72h


title: 72h_8Gy_10uM

value: cells irradiated with 8Gy and ONC201 10uM, harvested at 72h


title: ZX18

city: Bandar Baru Bangi

first: Siew-Eng

last: Ooi

state: Selangor

address: 6 Persiaran Institusi

department: Advanced Biotechnology and Breeding Centre

country: Malaysia

institute: Malaysian Palm Oil Board

data_processing:
Basecalls performed using RTA (Real Time Analysis); Basecalls binary is converted to FASTQ using bcl2fastq.
Quality trimming was done with flexbar with options: --qtrim-post-removal –aa TruSeq –x 12 –hr A –hi 5 –qt 20
Processed reads were mapped to Pisifera P5 reference genome with STAR 2.7.2b, with options –outFilterMultimapNmax 20  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverReadLmax 0.05 –alignIntronMin 20 –alignIntronMax 30000.
Read counts tabulated with HTSeq-Count ver. 0.11.2  to the gene feature of gff file NCBI Elaeis guineensis Annotation Release 101 with options -t gene -m intersection-nonempty.
Genome_build: E. guineensis P5-build of an AVROS pisifera palm (Singh et al., 2015) (BioProject PRJNA192219).
Supplementary_files_format_and_content: text files of read counts for gene feature in NCBI Elaeis guineensis Annotation Release 101.

organism: Elaeis guineensis

source_name: spear leaf (frond F0)

extract_protocol:
Total RNA was extracted from leaf tissues using InnuPREP Plant RNA kit (Analytik Jena AG) or a CTAB-extraction method (Liao et al 2004, Prep Biochem Biotechnol 34:209–214). DNAse1 treatment was  carried out using an on column digestion method with RNeasy Mini kit (Qiagen) to remove genomic DNA carryover.
Total RNA (500 ng) was used to generate RNA sequencing libraries using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). Adapter sequences are Illumina compatible.
RNA-Seq on Illumina platform to generate 7 million – 10 million SE50 (Agency L2 samples) or SE100 (L1 samples) reads.

value: spear leaf (frond F0)

tag: embryogenesis group

value: low

tag: number of embryoid lines

tag: palm tree id

tag: agency

tag: rna isolation method

value: InnuPREP Plant RNA kit


title: ZX12

tag: tissue


title: 72h_4Gy


title: W13_ctab

value: zero

value: CTAB-extraction method


title: ZX9


title: ZX18_ctab


title: U62_ctab

value: high

value: Jen Avros


title: Y46

value: Jen Avros Yangambi


title: W57_ctab


title: ZX9_ctab


title: Y46_ctab


title: Y25


title: 72h_4Gy_5uM

value: cells irradiated with 4Gy and ONC201 5uM, harvested at 72h


title: 72h_4Gy_15uM

value: cells irradiated with 4Gy and ONC201 15uM, harvested at 72h


title: X36


title: X17


title: 72h_4Gy_10uM

value: cells irradiated with 4Gy and ONC201 10uM, harvested at 72h

value: in vitro


title: 72h_2Gy

value: cells irradiated with 2Gy and harvested at 72h


title: W57


title: 72h_2Gy_5uM

value: cells irradiated with 2Gy and ONC201 5uM, harvested at 72h


title: W34


title: W32


title: 72h_2Gy_15uM

value: cells irradiated with 2Gy and ONC201 15uM, harvested at 72h


title: W54


title: 72h_15uM

value: cells treated with ONC201 15uM for 72h


title: W13


title: 72h_10uM

value: cells treated with ONC201 10uM for 72h


title: W11

value: spear leaf (frond F0)


title: 24h_no_RAD

value: untreated cells, harvested at 24h


title: 24h_8Gy_5uM

value: cells irradiated with 8Gy and ONC201 5uM, harvested at 24h


title: 24h_V

value: cells treated with DMSO 0.1% for 24h


title: U73

value: InnuPREP Plant RNA kit


title: U90

value: high


title: 24h_5uM

value: cells treated with ONC201 5uM for 24h


title: 24h_8Gy

value: cells irradiated with 8Gy and harvested at 24h


title: U68

value: Jen Avros


title: 24h_8Gy_15uM

value: cells irradiated with 8Gy and ONC201 15uM, harvested at 24h


title: 24h_4Gy

value: cells irradiated with 4Gy and harvested at 24h


title: U64


title: AM95

value: zero

value: Dumpy Yangambi Avros

value: CTAB-extraction method


title: U53


title: 24h_4Gy_5uM

value: cells irradiated with 4Gy and ONC201 5uM, harvested at 24h

value: in vitro


title: 24h_8Gy_10uM

value: cells irradiated with 8Gy and ONC201 10uM, harvested at 24h


title: AM94

value: spear leaf (frond F0)


title: 24h_4Gy_15uM

value: cells irradiated with 4Gy and ONC201 15uM, harvested at 24h


title: 72h_2Gy_10uM

value: cells irradiated with 2Gy and ONC201 10uM, harvested at 72h


title: AM93

value: low


title: 24h_4Gy_10uM

value: cells irradiated with 4Gy and ONC201 10uM, harvested at 24h


title: AM92


title: 24h_2Gy

value: cells irradiated with 2Gy and harvested at 24h


title: AM91

value: Dumpy Avros


title: AM90


title: 24h_2Gy_5uM

value: cells irradiated with 2Gy and ONC201 5uM, harvested at 24h


title: U59

value: high

value: Jen Avros

value: InnuPREP Plant RNA kit


title: U62


title: 24h_2Gy_15uM

value: cells irradiated with 2Gy and ONC201 15uM, harvested at 24h


title: 24h_2Gy_10uM

value: cells irradiated with 2Gy and ONC201 10uM, harvested at 24h


title: AM89

value: CTAB-extraction method


title: AM81


title: AM82

value: Dumpy Yangambi Avros


title: 24h_10uM

value: cells treated with ONC201 10uM for 24h

value: in vitro


title: 24h_15uM

value: cells treated with ONC201 15uM for 24h


title: KO_72hrstim_rep3

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Adapters were trimmed from the 3' end of reads using cutadapt
Transcript abundances were calculated using salmon against mm10
Gene abundances were calculated from transcript abundances using tximport
Reads were mapped to mouse genome (mm10 or hg38) using STAR
Genome_build: mm10
Supplementary_files_format_and_content: transcript abundances in txt format

source_name: Marginal zone B cells

extract_protocol:
RNA extracted using Rneasy Micro Kit (Qiagen)
Clontech SMART-Seq v4 Ultra Low Input

value: Marginal zone B cells

tag: stimulation

value: 72 hr stimulation

value: Srpk3 conditional knockout


title: AM73

value: spear leaf (frond F0)

value: low


title: KO_72hrstim_rep1


title: KO_8hrstim_rep3

value: 8 hr stimulation


title: KO_72hrstim_rep2


title: AM70

value: Dumpy Avros


title: control-knockdown NSFs

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the naked mole rat reference genome sequences (HetGla_female_1.0) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: GCA_000247695.1
Supplementary_files_format_and_content: FPKM

organism: Heterocephalus glaber

source_name: control-knockdown NSFs

extract_protocol:
Total RNA was extracted using Sepasol-G (Nacalai) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

tag: cell type

value: Naked mole rats skin fibroblasts (NSF)

value: control-knockdown


title: AM68


title: β-catenin-knockdown NSFs

source_name: β-catenin-knockdown NSFs

value: beta-catenin-knockdown


title: AM66

value: zero


title: AM59


title: KO_8hrstim_rep1


title: KO_8hrstim_rep2


title: AM56


title: AM58


title: KO_unstim_rep6

value: unstimulated


title: AM54

value: CTAB-extraction method


title: KO_unstim_rep5


title: HDMSCs_NC_rep3

city: Shenzhen

first: Wenhui

last: Yu

state: Guangdong

address: 3025# Shen Nan Road

department: Department of Orthopedics

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

data_processing:
The sequencing data were filtered with SOAPnuke (v1.5.2)11 by (1) removing reads containing sequencing adaptors; (2) removing reads whose low-quality base ratio (base quality less than or equal to 5) was more than 20%; and (3) removing reads whose unknown base ('N' base) ratio was more than 5%
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5)13 was used to align the clean reads to the reference coding gene set, and then the expression level of the gene was calculated by RSEM (v1.2.12)
Differential expression analysis was performed using DESeq2 (v1.4.5)15 with a Q value ≤ 0.05
Genome_build: Grch38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: MSCs were seeded in 12-well plates at a density of 5×104/well and cultured with DMEM (1000 mg/L glucose) with 10% FBS

extract_protocol:
Total RNA was extracted from MSCs using TRIzol (Invitrogen), and 1 μg of isolated RNA was the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was  generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on  the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the  final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300  copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Culture medium was changed to osteogenic medium (OM) to induce osteogenic differentiation, consisting of DMEM (glucose 1000 mg/L) with 10% FBS, 100 IU/mL penicillin, 100 IU/mL streptomycin, 0.1 μM dexamethasone, 10 mM β-glycerol phosphate, and 50 μM ascorbic acid (Sigma-Aldrich). The OM was changed every 3 days thereafter for 7 days

tag: disease state

value: Healthy

value: Bone marrow

value: Mesenchymal stem cells


title: HDMSCs_NC_rep2


title: AM46

value: Dumpy Yangambi Avros


title: KO_unstim_rep4

value: Marginal zone B cells


title: AM45


title: High fat diet-fed Ldlr–/– mice #2

city: Tokyo

first: Takuro

last: Miyazaki

address: 1-5-8 Hatanodai, Shinagawa-ku

institute: Showa University School of Medicine

hyb_protocol: Standard hybridization protocol onto Mouse Oligo chip 24k (TORAY Industries Inc.) and

scan_protocol: Standard scanning protocol using a 3D-Gene® Scanner (TORAY Industries Inc.)

data_processing: Fluorescent intensity exceeding 2SD are subtracted with the averaged background, and normalized to achieve median 25.

source_name: Lymph node

label_protocol: Standard labeling protocol

extract_protocol: Total RNA in cocultured Tregs were isolated using an RNeasy mini kit (Qiagen) with on-column DNaseI digestion.

treatment_protocol: Mice were subjected to chow or high fat diet for 12 weeks

value: Mesenteric lymph node

value: Ldlr -/-

tag: diet

value: high fat diet


title: High fat diet-fed Ldlr–/– mice #3

tag: genotype


title: KO_unstim_rep3

value: Srpk3 conditional knockout


title: AM41

value: spear leaf (frond F0)


title: ASMSCs_NC_rep3

value: Ankylosing spondylitis


title: KO_unstim_rep2


title: HDMSCs_H3K27ac

data_processing:
Raw reads were filtered and trimmed to remove sequencing adaptors and low-quality reads
Clean reads were mapped to the human genome version hg38 using Bowtie2 (v2.5.1)
Peaks were called using MACS2 (v.2.1.1) and normalization (reads per kilobase per million or RPKM) of the ChIP-seq data and heatmap plotting were performed using deepTools (v2.3.6.0)
The normalized ChIP-seq data were visualized on Integrative Genomics Viewer (IGV)
Genome_build: Grch38
Supplementary_files_format_and_content: peaks txt files
Supplementary_files_format_and_content: bw files were generated by deepTools (v2.3.6.0)

source_name: Bone marrow

extract_protocol:
Cells were harvested and cross-linked with 1% formaldehyde for 10 min and quenched with 0.125 M glycine for 5 min. Cells were lysed in 1 mL lysis buffer and rotated for 30 min at 4°C. Cell lysates were centrifuged at 2,400 g for 10 min at 4°C to isolate the nuclei. Nuclei were resuspended in digestion buffer and subjected to enzymatic digestion to shear chromatin fragments to an average size between 200 bp and 500 bp by incubating the tube at 37°C for 10-15 min. The shearing reaction was stopped, and the fragmented chromatin was centrifuged at 18000 g for 10 min at 4°C. The supernatant was transferred to a new Eppendorf tube, and the ChIP reaction mix containing protein A/G magnetic beads, ChIP IP buffer, antibody, and protease inhibitor cocktail was added and rotated at 4°C overnight. After overnight incubation, protein A/G magnetic beads were washed. The chromatin was eluted in reverse cross-linking buffer followed by incubation of the tube at 65°C for 3 h. Then, the ChIP DNA was treated with RNase A and protease K at 37°C for 30 min and purified using phenol chloroform.
ChIP DNA was processed for library generation using the QIAseq Ultralow Input Library Kit (QIAGEN) following the manufacturer’s instructions.

tag: chip antibody


title: ASMSCs_NC_rep2


title: KO_unstim_rep1


title: ASMSCs_NC_rep1


title: ASMSCs_H3K27ac


title: WT_72hrstim_rep3

value: 72 hr stimulation

value: wildtype


title: Chow-fed Ldlr–/– mice #1

tag: strain

value: chow


title: HDMSCs_input


title: Chow-fed Ldlr–/– mice #3


title: Chow-fed Ldlr–/– mice #2


title: KO_matureB_rep3

source_name: Mature B cells

extract_protocol:
RNA extracted using Rneasy Micro Kit (Qiagen)
Nugen Universal Plus mRNA

value: Mature B cells


title: AM31

value: zero

value: Dumpy Avros


title: KO_matureB_rep2

value: unstimulated


title: ASMSCs_input

value: Bone marrow


title: High fat diet-fed Ldlr–/– mice #1


title: HDMSCs_NC_rep1

value: Healthy

value: Mesenchymal stem cells


title: AM134

value: low

value: CTAB-extraction method


title: WT_72hrstim_rep1

value: Marginal zone B cells


title: KO_matureB_rep1


title: AM39

value: Dumpy Yangambi Avros


title: WT_8hrstim_rep3

value: 8 hr stimulation


title: AM126

value: spear leaf (frond F0)


title: KO_immatureB_rep3

source_name: Immature B cells

value: Immature B cells

value: Srpk3 conditional knockout


title: WT_8hrstim_rep1

value: wildtype


title: AM122


title: WT_8hrstim_rep2


title: AM36


title: WT_unstim_rep6


title: WT_unstim_rep5


title: WT_matureB_rep2


title: AM111


title: WT_matureB_rep3


title: AM109


title: WT_72hrstim_rep2

value: 72 hr stimulation


title: AM105


title: WT_unstim_rep3


title: WT_immatureB_rep3


title: AM103


title: WT_unstim_rep2


title: AM123


title: KO_immatureB_rep2


title: WT_unstim_rep1


title: KO_immatureB_rep1


title: WT_immatureB_rep1


title: WT_unstim_rep4


title: Aged

city: Obu

first: Yosuke

last: Shikama

state: Aichi

address: 7-430 Morioka-cho

institute: National Center for Geriatrics and Gerontology

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Ver.2.0 Microarray (Agilent, G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 074809_D_F_20171030) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX 14.9.

source_name: aged epithelial cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the RNeasy mini kit according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Submandibular gland

tag: gender

value: Female

tag: age

value: 24 months


title: HEK 293T mock transduced 2h rep1

status: Public on Feb 20 2021

city: Nyíregyháza

first: Judit

last: Dobránszki

state: Szabolcs-Szatmár-Bereg

address: Westsik Vilmos út 4-6.

department: Centre for Agricultural Genomics and Biotechnology

country: Hungary

institute: University of Debrecen

data_processing:
DNBSEQ G400 sequencer built-in software was used for basecalling
Sequenced reads were trimmed for adaptor sequences, and filtered for low-complexity or low-quality sequence using Trimmomatic v0.36.
Trimmed eads were mapped to Ensembl GRCh38 whole genome using HISAT2 v.2.1.0 with default parameters.
Raw read counts were generated with featureCounts v1.6.2 with default settings using the Ensembl Build GRCh38.101 annotation gtf file. Read counts were normalized using the median-of-ratios method introduced with the DESeq2 v4.0.3 R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table including normalized gene counts for every sample and every gene, generated using the median-of-ratios method

source_name: Embrionic Kidney  - HEK 293T

growth_protocol: HEK293T cells (Invitrogen, CA, USA) were maintained in DMEM media supplemented with 10%FBS, 1% L-Glutamine and 1% penicilin/streptomicin. Day before transduction, cells were plated into 6-well plate with 5*10^5 cell/ well in 1500 µl of DMEM.

extract_protocol:
Cells were collected at 0-2 hours after transduction, media was discarded and cells were washed with 500 µl PBS, and then suspended into 500 µl TRIzol Reagent (Thermo Fisher Scientific, MA, USA). RNA isolation was carried out according to the manufacturer's instructions.
RNA quality was determined by Agilent RNA 6000 Nano kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). Thereafter,  sequencing was performed on the DNBSEQ G400 sequencer using MGIEasy RNA Library Prep Set.

treatment_protocol: Medium was discarded and the cells were transduced with 5 ng RT-equivalent of HIV-1 / HIV-2, or mock pseudovirions in 1500 µl serum- and antibiotic-free media, complemented with 8 µg/ml polybrene.

value: epithelial cells

tag: treatment

value: treated with VSV.G-MOCK for 2 hours


title: HEK 293T HIV-2 transduced 0h rep1

value: treated with HIV-2 for 0 hours


title: HEK 293T HIV-1 transduced 0h rep1

value: treated with HIV-1 for 0 hours


title: HEK 293T HIV-1 transduced 0h rep2


title: HEK 293T HIV-2 transduced 0h rep2


title: HEK 293T mock transduced 2h rep2


title: HEK 293T mock transduced 0h rep2

value: treated with VSV.G-MOCK for 0 hours


title: HEK 293T mock transduced 0h rep1


title: HEK 293T HIV-1 transduced 2h rep2

value: treated with HIV-1 for 2 hours


title: AM116

value: zero

value: CTAB-extraction method


title: WT_immatureB_rep2

value: unstimulated


title: Thyroid-wt43

city: Los Angeles

first: Kailtyn

middle: Yan-Yun

last: Liu

state: CA

address: 10833 Le Conte Ave

department: Medicine

institute: UCLA/VA

data_processing:
TMM (trimmed mean of M-values) was used to normalize the gene expression.
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
the gene expression level was estimated using RSEM v1.2.15.
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Wt

extract_protocol:
Tissues were desected and snap frozen in liquid N2. Total RNA was isolated using Qiagen RNAase kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Thyroid

value: 3 months


title: Thyroid-wt1


title: Thyroid-Hb83

source_name: TRbK146Q mutant


title: Thyroid-wt2


title: HEK 293T HIV-2 transduced 2h rep1

value: treated with HIV-2 for 2 hours


title: Pituitary-Hb83

value: Pituitary


title: Pituitary-Hb60


title: HEK 293T HIV-1 transduced 2h rep1


title: HEK 293T HIV-2 transduced 2h rep2


title: Pituitary-Hb62


title: Pituitary-Wt2


title: Pituitary-Wt43


title: Pituitary-Wt1


title: Thyroid-Hb62


title: Thyroid-Hb60


title: Hypothalamus-Hb60

value: Hypothalamus


title: Young

source_name: young epithelial cell

value: Submandibular gland

value: 9 weeks


title: Hypothalamus-Wt2


title: Hypothalamus-Hb62


title: Hypothalamus-Wt1


title: Hypothalamus-Wt43


title: patient 599, RCC tumor tissue

city: Lyon

first: Jean-Noel

last: Hubert

address: 150 cours Albert Thomas

institute: International Agency For Research on Cancer

description:
sample_id: 2020_599TU
non-normalized data in non_norm_matrix13.txt.gz

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was processed using vst transformation and quantile normalisation with the lumi package in R (Bioconductor).

source_name: kidney

label_protocol: Biotin labeled single-stranded cRNAs (Illumina TotalPrep RNA Amplification Kit from Ambion®).

extract_protocol: RNA was extracted withTotal RNA Isolation NucleoSpin® RNA II kit (Macherey Nagel) in accordance with the prescribed protocol provided with the kit. Quality control was performed withAgilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).

value: kidney

tag: type

value: tumor

tag: Sex

value: female

tag: histo

value: conventional RCC

tag: Stage

tag: grade


title: patient 604, RCC tumor tissue

description:
sample_id: 2020_604TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 598, RCC tumor tissue

description:
sample_id: 2020_598TU
non-normalized data in non_norm_matrix13.txt.gz

value: male


title: patient 600, RCC tumor tissue

description:
sample_id: 2020_600TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 601, RCC tumor tissue

description:
sample_id: 2020_601TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 595, RCC tumor tissue

description:
sample_id: 2020_595TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 594, RCC tumor tissue

description:
sample_id: 2020_594TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 602, RCC tumor tissue

description:
sample_id: 2020_602TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 603, RCC tumor tissue

description:
sample_id: 2020_603TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 596, RCC tumor tissue

description:
sample_id: 2020_596TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 597, RCC tumor tissue

description:
sample_id: 2020_597TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 591, RCC tumor tissue

description:
sample_id: 2020_591TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 590, RCC tumor tissue

description:
sample_id: 2020_590TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 592, RCC tumor tissue

description:
sample_id: 2020_592TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 593, RCC tumor tissue

description:
sample_id: 2020_593TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 589, RCC tumor tissue

description:
sample_id: 2020_589TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 588, RCC tumor tissue

description:
sample_id: 2020_588TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 586, RCC tumor tissue

description:
sample_id: 2020_586TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 587, RCC tumor tissue

description:
sample_id: 2020_587TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 584, RCC tumor tissue

description:
sample_id: 2020_584TU
non-normalized data in non_norm_matrix13.txt.gz


title: WT_matureB_rep1

value: Mature B cells

value: wildtype


title: Hypothalamus-Hb83


title: patient 585, RCC tumor tissue

description:
sample_id: 2020_585TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 578, RCC tumor tissue

description:
sample_id: 2020_578TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 580, RCC tumor tissue

description:
sample_id: 2020_580TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 581, RCC tumor tissue

description:
sample_id: 2020_581TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 579, RCC tumor tissue

description:
sample_id: 2020_579TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 577, RCC tumor tissue

description:
sample_id: 2020_577TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 582, RCC tumor tissue

description:
sample_id: 2020_582TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 572, RCC tumor tissue

description:
sample_id: 2020_572TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 575, RCC tumor tissue

description:
sample_id: 2020_575TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 574, RCC tumor tissue

description:
sample_id: 2020_574TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 573, RCC tumor tissue

description:
sample_id: 2020_573TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 571, RCC tumor tissue

description:
sample_id: 2020_571TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 566, RCC tumor tissue

description:
sample_id: 2020_566TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 570, RCC tumor tissue

description:
sample_id: 2020_570TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 564, RCC tumor tissue

description:
sample_id: 2020_564TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 563, RCC tumor tissue

description:
sample_id: 2020_563TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 562, RCC tumor tissue

description:
sample_id: 2020_562TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 565, RCC tumor tissue

description:
sample_id: 2020_565TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 567, RCC tumor tissue

description:
sample_id: 2020_567TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 568, RCC tumor tissue

description:
sample_id: 2020_568TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 556, RCC tumor tissue

description:
sample_id: 2020_556TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 560, RCC tumor tissue

description:
sample_id: 2020_560TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 557, RCC tumor tissue

description:
sample_id: 2020_557TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 576, RCC tumor tissue

description:
sample_id: 2020_576TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 551, RCC tumor tissue

description:
sample_id: 2020_551TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 558, RCC tumor tissue

description:
sample_id: 2020_558TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 559, RCC tumor tissue

description:
sample_id: 2020_559TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 550, RCC tumor tissue

description:
sample_id: 2020_550TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 561, RCC tumor tissue

description:
sample_id: 2020_561TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 583, RCC tumor tissue

description:
sample_id: 2020_583TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 548, RCC tumor tissue

description:
sample_id: 2020_548TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 555, RCC tumor tissue

description:
sample_id: 2020_555TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 554, RCC tumor tissue

description:
sample_id: 2020_554TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 547, RCC tumor tissue

description:
sample_id: 2020_547TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 569, RCC tumor tissue

description:
sample_id: 2020_569TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 552, RCC tumor tissue

description:
sample_id: 2020_552TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 546, RCC tumor tissue

description:
sample_id: 2020_546TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 553, RCC tumor tissue

description:
sample_id: 2020_553TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 544, RCC tumor tissue

description:
sample_id: 2020_544TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 538, RCC tumor tissue

description:
sample_id: 2020_538TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 543, RCC tumor tissue

description:
sample_id: 2020_543TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 534, RCC tumor tissue

description:
sample_id: 2020_534TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 537, RCC tumor tissue

description:
sample_id: 2020_537TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 540, RCC tumor tissue

description:
sample_id: 2020_540TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 539, RCC tumor tissue

description:
sample_id: 2020_539TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 542, RCC tumor tissue

description:
sample_id: 2020_542TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 536, RCC tumor tissue

description:
sample_id: 2020_536TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 535, RCC tumor tissue

description:
sample_id: 2020_535TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 531, RCC tumor tissue

description:
sample_id: 2020_531TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 545, RCC tumor tissue

description:
sample_id: 2020_545TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 549, RCC tumor tissue

description:
sample_id: 2020_549TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 533, RCC tumor tissue

description:
sample_id: 2020_533TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 532, RCC tumor tissue

description:
sample_id: 2020_532TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 529, RCC tumor tissue

description:
sample_id: 2020_529TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 525, RCC tumor tissue

description:
sample_id: 2020_525TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 522, RCC tumor tissue

description:
sample_id: 2020_522TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 521, RCC tumor tissue

description:
sample_id: 2020_521TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 530, RCC tumor tissue

description:
sample_id: 2020_530TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 541, RCC tumor tissue

description:
sample_id: 2020_541TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 519, RCC tumor tissue

description:
sample_id: 2020_519TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 518, RCC tumor tissue

description:
sample_id: 2020_518TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 517, RCC tumor tissue

description:
sample_id: 2020_517TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 516, RCC tumor tissue

description:
sample_id: 2020_516TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 528, RCC tumor tissue

description:
sample_id: 2020_528TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 527, RCC tumor tissue

description:
sample_id: 2020_527TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 515, RCC tumor tissue

description:
sample_id: 2020_515TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 509, RCC tumor tissue

description:
sample_id: 2020_509TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 512, RCC tumor tissue

description:
sample_id: 2020_512TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 514, RCC tumor tissue

description:
sample_id: 2020_514TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 526, RCC tumor tissue

description:
sample_id: 2020_526TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 524, RCC tumor tissue

description:
sample_id: 2020_524TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 506, RCC tumor tissue

description:
sample_id: 2020_506TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 504, RCC tumor tissue

description:
sample_id: 2020_504TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 503, RCC tumor tissue

description:
sample_id: 2020_503TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 502, RCC tumor tissue

description:
sample_id: 2020_502TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 513, RCC tumor tissue

description:
sample_id: 2020_513TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 500, RCC tumor tissue

description:
sample_id: 2020_500TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 511, RCC tumor tissue

description:
sample_id: 2020_511TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 499, RCC tumor tissue

description:
sample_id: 2020_499TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 498, RCC tumor tissue

description:
sample_id: 2020_498TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 510, RCC tumor tissue

description:
sample_id: 2020_510TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 508, RCC tumor tissue

description:
sample_id: 2020_508TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 505, RCC tumor tissue

description:
sample_id: 2020_505TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 491, RCC tumor tissue

description:
sample_id: 2020_491TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 501, RCC tumor tissue

description:
sample_id: 2020_501TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 520, RCC tumor tissue

description:
sample_id: 2020_520TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 487, RCC tumor tissue

description:
sample_id: 2020_487TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 507, RCC tumor tissue

description:
sample_id: 2020_507TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 496, RCC tumor tissue

description:
sample_id: 2020_496TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 523, RCC tumor tissue

description:
sample_id: 2020_523TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 497, RCC tumor tissue

description:
sample_id: 2020_497TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 495, RCC tumor tissue

description:
sample_id: 2020_495TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 493, RCC tumor tissue

description:
sample_id: 2020_493TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 483, RCC tumor tissue

description:
sample_id: 2020_483TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 494, RCC tumor tissue

description:
sample_id: 2020_494TU
non-normalized data in non_norm_matrix10.txt.gz


title: patient 482, RCC tumor tissue

description:
sample_id: 2020_482TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 480, RCC tumor tissue

description:
sample_id: 2020_480TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 477, RCC tumor tissue

description:
sample_id: 2020_477TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 479, RCC tumor tissue

description:
sample_id: 2020_479TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 476, RCC tumor tissue

description:
sample_id: 2020_476TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 473, RCC tumor tissue

description:
sample_id: 2020_473TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 492, RCC tumor tissue

description:
sample_id: 2020_492TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 472, RCC tumor tissue

description:
sample_id: 2020_472TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 470, RCC tumor tissue

description:
sample_id: 2020_470TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 466, RCC tumor tissue

description:
sample_id: 2020_466TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 489, RCC tumor tissue

description:
sample_id: 2020_489TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 490, RCC tumor tissue

description:
sample_id: 2020_490TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 488, RCC tumor tissue

description:
sample_id: 2020_488TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 486, RCC tumor tissue

description:
sample_id: 2020_486TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 458, RCC tumor tissue

description:
sample_id: 2020_458TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 485, RCC tumor tissue

description:
sample_id: 2020_485TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 478, RCC tumor tissue

description:
sample_id: 2020_478TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 484, RCC tumor tissue

description:
sample_id: 2020_484TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 481, RCC tumor tissue

description:
sample_id: 2020_481TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 456, RCC tumor tissue

description:
sample_id: 2020_456TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 475, RCC tumor tissue

description:
sample_id: 2020_475TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 455, RCC tumor tissue

description:
sample_id: 2020_455TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 474, RCC tumor tissue

description:
sample_id: 2020_474TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 454, RCC tumor tissue

description:
sample_id: 2020_454TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 471, RCC tumor tissue

description:
sample_id: 2020_471TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 469, RCC tumor tissue

description:
sample_id: 2020_469TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 451, RCC tumor tissue

description:
sample_id: 2020_451TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 468, RCC tumor tissue

description:
sample_id: 2020_468TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 457, RCC tumor tissue

description:
sample_id: 2020_457TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 450, RCC tumor tissue

description:
sample_id: 2020_450TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 465, RCC tumor tissue

description:
sample_id: 2020_465TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 464, RCC tumor tissue

description:
sample_id: 2020_464TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 448, RCC tumor tissue

description:
sample_id: 2020_448TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 462, RCC tumor tissue

description:
sample_id: 2020_462TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 463, RCC tumor tissue

description:
sample_id: 2020_463TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 461, RCC tumor tissue

description:
sample_id: 2020_461TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 445, RCC tumor tissue

description:
sample_id: 2020_445TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 446, RCC tumor tissue

description:
sample_id: 2020_446TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 443, RCC tumor tissue

description:
sample_id: 2020_443TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 441, RCC tumor tissue

description:
sample_id: 2020_441TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 440, RCC tumor tissue

description:
sample_id: 2020_440TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 439, RCC tumor tissue

description:
sample_id: 2020_439TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 460, RCC tumor tissue

description:
sample_id: 2020_460TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 459, RCC tumor tissue

description:
sample_id: 2020_459TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 438, RCC tumor tissue

description:
sample_id: 2020_438TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 437, RCC tumor tissue

description:
sample_id: 2020_437TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 467, RCC tumor tissue

description:
sample_id: 2020_467TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 453, RCC tumor tissue

description:
sample_id: 2020_453TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 435, RCC tumor tissue

description:
sample_id: 2020_435TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 432, RCC tumor tissue

description:
sample_id: 2020_432TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 434, RCC tumor tissue

description:
sample_id: 2020_434TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 429, RCC tumor tissue

description:
sample_id: 2020_429TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 426, RCC tumor tissue

description:
sample_id: 2020_426TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 420, RCC tumor tissue

description:
sample_id: 2020_420TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 417, RCC tumor tissue

description:
sample_id: 2020_417TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 418, RCC tumor tissue

description:
sample_id: 2020_418TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 452, RCC tumor tissue

description:
sample_id: 2020_452TU
non-normalized data in non_norm_matrix8.txt.gz


title: patient 416, RCC tumor tissue

description:
sample_id: 2020_416TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 413, RCC tumor tissue

description:
sample_id: 2020_413TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 414, RCC tumor tissue

description:
sample_id: 2020_414TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 449, RCC tumor tissue

description:
sample_id: 2020_449TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 412, RCC tumor tissue

description:
sample_id: 2020_412TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 410, RCC tumor tissue

description:
sample_id: 2020_410TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 447, RCC tumor tissue

description:
sample_id: 2020_447TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 433, RCC tumor tissue

description:
sample_id: 2020_433TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 444, RCC tumor tissue

description:
sample_id: 2020_444TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 442, RCC tumor tissue

description:
sample_id: 2020_442TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 436, RCC tumor tissue

description:
sample_id: 2020_436TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 431, RCC tumor tissue

description:
sample_id: 2020_431TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 430, RCC tumor tissue

description:
sample_id: 2020_430TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 403, RCC tumor tissue

description:
sample_id: 2020_403TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 404, RCC tumor tissue

description:
sample_id: 2020_404TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 401, RCC tumor tissue

description:
sample_id: 2020_401TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 428, RCC tumor tissue

description:
sample_id: 2020_428TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 407, RCC tumor tissue

description:
sample_id: 2020_407TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 397, RCC tumor tissue

description:
sample_id: 2020_397TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 427, RCC tumor tissue

description:
sample_id: 2020_427TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 396, RCC tumor tissue

description:
sample_id: 2020_396TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 393, RCC tumor tissue

description:
sample_id: 2020_393TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 425, RCC tumor tissue

description:
sample_id: 2020_425TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 424, RCC tumor tissue

description:
sample_id: 2020_424TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 423, RCC tumor tissue

description:
sample_id: 2020_423TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 422, RCC tumor tissue

description:
sample_id: 2020_422TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 421, RCC tumor tissue

description:
sample_id: 2020_421TU
non-normalized data in non_norm_matrix6.txt.gz


title: patient 390, RCC tumor tissue

description:
sample_id: 2020_390TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 387, RCC tumor tissue

description:
sample_id: 2020_387TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 419, RCC tumor tissue

description:
sample_id: 2020_419TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 415, RCC tumor tissue

description:
sample_id: 2020_415TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 409, RCC tumor tissue

description:
sample_id: 2020_409TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 411, RCC tumor tissue

description:
sample_id: 2020_411TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 408, RCC tumor tissue

description:
sample_id: 2020_408TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 385, RCC tumor tissue

description:
sample_id: 2020_385TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 406, RCC tumor tissue

description:
sample_id: 2020_406TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 405, RCC tumor tissue

description:
sample_id: 2020_405TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 402, RCC tumor tissue

description:
sample_id: 2020_402TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 400, RCC tumor tissue

description:
sample_id: 2020_400TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 378, RCC tumor tissue

description:
sample_id: 2020_378TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 377, RCC tumor tissue

description:
sample_id: 2020_377TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 376, RCC tumor tissue

description:
sample_id: 2020_376TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 375, RCC tumor tissue

description:
sample_id: 2020_375TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 374, RCC tumor tissue

description:
sample_id: 2020_374TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 399, RCC tumor tissue

description:
sample_id: 2020_399TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 373, RCC tumor tissue

description:
sample_id: 2020_373TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 371, RCC tumor tissue

description:
sample_id: 2020_371TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 398, RCC tumor tissue

description:
sample_id: 2020_398TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 395, RCC tumor tissue

description:
sample_id: 2020_395TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 367, RCC tumor tissue

description:
sample_id: 2020_367TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 394, RCC tumor tissue

description:
sample_id: 2020_394TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 365, RCC tumor tissue

description:
sample_id: 2020_365TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 392, RCC tumor tissue

description:
sample_id: 2020_392TU
non-normalized data in non_norm_matrix4.txt.gz


title: Col1.W.P7N.24hr.neg

city: Utrecht

first: Joep

last: de Ligt

address: Universiteitsweg 100

institute: University Medical Center Utrecht

data_processing:
Illumina software used for basecalling.
Sequenced reads mappend and analysed as specified here;https://github.com/UMCUGenetics/RNASeq/releases/tag/2.1.0
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file with metadata
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Colon

extract_protocol:
Total RNA was extracted using the RNAeasy mini kit (Qiagen) according to manufecter's protocol including DNAse treatment.
Library preparation was started with 500ng of Total RNA using the Truseq Stranded Total RNA kit with Ribo-Zero Human/Mouse/Rat set A and B by Illumina (Cat. RS-122-2201 and RS-122-2202
Libraries were equimolar pooled to 2 nM. And sequenced on the Illumina Nextseq, 1x75bp high output, and 1.0-1.4 pM of library pools was loaded.

tag: line

value: Colon

tag: timepoint (hr)

tag: wnt yes or no

value: no


title: patient 358, RCC tumor tissue

description:
sample_id: 2020_358TU
non-normalized data in non_norm_matrix3.txt.gz

tag: tissue


title: patient 363, RCC tumor tissue

description:
sample_id: 2020_363TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 362, RCC tumor tissue

description:
sample_id: 2020_362TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 391, RCC tumor tissue

description:
sample_id: 2020_391TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 357, RCC tumor tissue

description:
sample_id: 2020_357TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 366, RCC tumor tissue

description:
sample_id: 2020_366TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 354, RCC tumor tissue

description:
sample_id: 2020_354TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 361, RCC tumor tissue

description:
sample_id: 2020_361TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 359, RCC tumor tissue

description:
sample_id: 2020_359TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 389, RCC tumor tissue

description:
sample_id: 2020_389TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 386, RCC tumor tissue

description:
sample_id: 2020_386TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 388, RCC tumor tissue

description:
sample_id: 2020_388TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 384, RCC tumor tissue

description:
sample_id: 2020_384TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 383, RCC tumor tissue

description:
sample_id: 2020_383TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 381, RCC tumor tissue

description:
sample_id: 2020_381TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 345, RCC tumor tissue

description:
sample_id: 2020_345TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 380, RCC tumor tissue

description:
sample_id: 2020_380TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 379, RCC tumor tissue

description:
sample_id: 2020_379TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 372, RCC tumor tissue

description:
sample_id: 2020_372TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 344, RCC tumor tissue

description:
sample_id: 2020_344TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 370, RCC tumor tissue

description:
sample_id: 2020_370TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 343, RCC tumor tissue

description:
sample_id: 2020_343TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 382, RCC tumor tissue

description:
sample_id: 2020_382TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 369, RCC tumor tissue

description:
sample_id: 2020_369TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 339, RCC tumor tissue

description:
sample_id: 2020_339TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 340, RCC tumor tissue

description:
sample_id: 2020_340TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 364, RCC tumor tissue

description:
sample_id: 2020_364TU
non-normalized data in non_norm_matrix3.txt.gz