title: Tumor, patient 3

city: Shenyang

first: Yunhong

last: Zhan

address: No. 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

description:
Test
long non-coding RNAs
Qiagen Custom RT²  lncRNA qPCR Assay

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/cn/analyze/
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (tumor/adjacent) ratios.

label: SYBR Green

source_name: bladder cancer

label_protocol: RT2 lncRNA qPCR Assay were performed using the Custom RT2 PCR Arrays (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. 1 mg RNA was reverse transcribed to cDNA in 20μl system by First Strand cDNA Synthesis Kit for RT-PCR (Merck & Co., Inc., Kenilworth, NJ, USA). Real-time PCR was performed using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR was carried out as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s and 72 °C for 20s.

growth_protocol: Tumor tissues and the corresponding adjacent tissues were collected simultaneously. All the resected samples were placed immediately into liquid nitrogen and stored at - 80°C.

extract_protocol: Total RNA was extracted by 1 mL TRIzol (Merck & Co., Inc., Kenilworth, NJ, USA)according to the manufacturer’s protocol.

value: bladder

value: bladder cancer patient

tag: gender

value: male


title: MCF-7, biological rep1 [circRNA]

status: Public on Nov 18 2020

type: RNA

city: Suzhou

first: Min

last: Jiang

state: Jiangsu

address: No. 188, Shi Zi Road

country: China

institute: The First Affiliated Hospital of Soochow University

description:
S-1
circRNA expression data from MCF-7 cells.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by quantile normalization.

molecule: total RNA

organism: Homo sapiens

source_name: MCF-7 cell

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: MCF-7, LCC2 and LCC9 cells were grown in phenol red free IMEM supplemented with 5% charcoal-stripped FBS and 1% penicillin/streptomycin in a cell culture incubator at 37 ℃ and 5% CO2.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: MCF-7, LCC2 or LCC9 cells were resuspended with phenol red free IMEM supplemented with 5% charcoal-stripped FBS and 1% penicillin/streptomycin and seeded in T75 flasks. Culture medium was changed once on day 2. Cells were washed with normal saline twice and harvested on day 4.

tag: cell line

tag: tamoxifen resistance

value: No

tag: fulvestrant resistance


title: Genomic DNA from blood 56

type: genomic

city: Exeter

first: Katie

last: Lunnon

state: Devon

address: RILD South, Barrack Road

country: United Kingdom

institute: University of Exeter

description: control sample

hyb_protocol: DNA was sodium-bisulfite treated using a Zymo EZ-96 DNA methylation kit, and was subsequently amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings

molecule: genomic DNA

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from whole blood samples using Qiagen DNeasy Kit according to standard instructions

tag: tissue

value: whole blood

tag: Sex

value: Male

tag: age

tag: disease state

value: control

tag: disease state2

value: Included


title: Genomic DNA from blood 53

description: control sample

value: Female


title: Tumor, patient 2


title: PCA.261: prostate_cancer_primary_261

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St, Suite 430

country: Canada

institute: Decipher Biosciences, Inc.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by 2 expert genitourinary pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

tag: psa

tag: grade group

tag: race

value: Black

tag: non-organ confined

tag: palsma cell content

tag: inflammation signature

tag: ifng signature

tag: igg production

tag: nk activity


title: PCA.260: prostate_cancer_primary_260

value: White

value: Yes


title: Genomic DNA from blood 49

description: control sample


title: Genomic DNA from blood 47

description: mild cognitive impairment sample

value: mild cognitive impairment

value: mild cognitive impairment stable


title: Adjacent, patient 3

description:
Control
long non-coding RNAs
Qiagen Custom RT²  lncRNA qPCR Assay

source_name: Adjacent tissue

tag: gender


title: Genomic DNA from blood 48

description: mild cognitive impairment sample


title: PCA.258: prostate_cancer_primary_258


title: Adjacent, patient 2


title: PCA.259: prostate_cancer_primary_259


title: PCA.257: prostate_cancer_primary_257


title: Genomic DNA from blood 50

description: control sample

value: Excluded


title: Genomic DNA from blood 46

description: control sample


title: Genomic DNA from blood 45

description: mild cognitive impairment sample

value: mild cognitive impairment to alzheimer's disease converter


title: Tumor, patient 1


title: LCC9, biological rep2 [circRNA]

description:
FUL-4
circRNA expression data from LCC9 cells.

source_name: LCC9 cell

tag: cell line

tag: tamoxifen resistance

value: tamoxifen-resistant

value: fulvestrant-resistant


title: Tumor, patient 3

description:
Test
miRNAs
Qiagen Custom miScript miRNA PCR Arrays

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/cn/analyze/
For the normalization it uses the average of five housekeeping genes: SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A, RNU6-2.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (tumor/adjacent) ratios.

label_protocol: Custom miScript miRNA PCR Arrays were performed using the Custom RT2 PCR Arrays (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. 1 mg RNA was reverse transcribed to cDNA in 20μl system by First Strand cDNA Synthesis Kit for RT-PCR (Merck & Co., Inc., Kenilworth, NJ, USA). Real-time PCR was performed using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR was carried out as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s and 72 °C for 20s.

tag: tissue

value: bladder

value: bladder cancer patient


title: LCC9, biological rep1 [circRNA]

description:
FUL-3
circRNA expression data from LCC9 cells.

tag: fulvestrant resistance


title: Adjacent, patient 1

value: male


title: PCA.255: prostate_cancer_primary_255

tag: age

value: No


title: PCA.256: prostate_cancer_primary_256


title: Tumor, patient 1

tag: disease state


title: Genomic DNA from blood 41

description: control sample

value: whole blood

tag: Sex

value: Male

tag: disease state2


title: Genomic DNA from blood 42

description: Alzheimer's disease sample

value: Alzheimer's disease

value: Included


title: Tumor, patient 2


title: PCA.252: prostate_cancer_primary_252

tag: psa

tag: grade group


title: PCA.253: prostate_cancer_primary_253

tag: race

tag: non-organ confined


title: Genomic DNA from blood 40

description: control sample

value: control


title: PCA.254: prostate_cancer_primary_254

value: White

tag: palsma cell content

tag: inflammation signature


title: Adjacent, patient 3

description:
Control
miRNAs
Qiagen Custom miScript miRNA PCR Arrays


title: Genomic DNA from blood 43

description: control sample

value: Female


title: Genomic DNA from blood 34

description: Alzheimer's disease sample


title: Genomic DNA from blood 36

description: control sample


title: Genomic DNA from blood 38

description: Alzheimer's disease sample


title: Genomic DNA from blood 39

description: mild cognitive impairment sample

value: mild cognitive impairment


title: Adjacent, patient 2


title: PCA.251: prostate_cancer_primary_251

tag: ifng signature

tag: igg production


title: Genomic DNA from blood 44

description: control sample


title: Genomic DNA from blood 35

description: control sample


title: Genomic DNA from blood 30

description: control sample


title: Genomic DNA from blood 31

description: mild cognitive impairment sample

value: mild cognitive impairment stable


title: Pooled MAN1A2 RNA-seq

type: SRA

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Drive

department: Bioengineering

country: USA

institute: UCSD

library_source: transcriptomic

data_processing:
The quality of the sequencing reads was verified using FastQC. Omicsoft Sequence Aligner 2 was used to align the sequencing reads to Zebrafish genome.
DEseq2, R package for RNAseq data, was used for differential analysis.
Genome_build: GRCz10
Supplementary_files_format_and_content: For each processed data file, there are 2 columns: the first column being Ensembl gene ID, and the second column being raw read counts.

organism: Danio rerio

source_name: liver tissue

growth_protocol: Embryos and adult fish were raised and maintained under standard laboratory conditions. We used the following transgenic lines: Tg(dusp6:d2EGFP)pt6,10 Tg(krt18:EGFP)p314,11 Tg(EPV.Tp1-Mmu.Hbb:EGFP)um14,12 Tg(EPV.Tp1-Mmu.Hbb:hist2h2l-mCherry)s939,13 and Tg(fabp10a:DsRed,ela3l:EGFP)gz15,14 [the last three referred to here as Tg(Tp1:GFP), Tg(Tp1:H2B-mCherry), and Tg(fabp10a:DsRed), respectively].

extract_protocol:
Total RNA was extracted from three different batches of 100 livers of uninjected control and man1a2 MO-injected larvae at 5 days post fertilization by using RNeasy Mini Kit.
The pooled RNA was used to generate mRNA sequencing libraries using Illumina TruSeq Stranded mRNA sample preparation kit. Poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads, mRNA fragmented into small pieces using divalent cations, and copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by using dUTP in the Second Strand Marking Mix, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments were ligated to single 'A' base and adapter, then purified and enriched with PCR to create the final cDNA libraries.

treatment_protocol: arf6-ATG MO (5’-GATCTTGGAAAGCATCTTCCCCATG-3’), man1a2-ATG MO (5’-CCGGCGTGGTCATATTTTGATGATC-3’), and man1a2-splicing MO (5’-AAGAATGTAAACTCACCTCTCTGAT-3’) were purchased from Gene Tools, LLC. Embryos were injected at the one-cell stage with man1a2-ATG MO (1.5 or 4.5 ng), man1a2-splicing MO (5 or 7.5 ng), or arf6-ATG MO (0.5 ng).

value: liver

tag: condition

value: MAN1A2 knockdown

tag: developmental stage

value: Larvae at 5 days post fertilization


title: Adjacent, patient 1

tag: gender


title: Pooled control RNA-seq

tag: tissue

value: Normal


title: PCA.249: prostate_cancer_primary_249

value: Yes

tag: nk activity


title: Genomic DNA from blood 25

description: mild cognitive impairment sample

tag: age


title: PCA.250: prostate_cancer_primary_250

value: Black


title: Genomic DNA from blood 33

description: Alzheimer's disease sample

tag: disease state


title: Genomic DNA from blood 32

description: mild cognitive impairment sample

tag: Sex


title: PCA.246: prostate_cancer_primary_246


title: Genomic DNA from blood 29

description: Alzheimer's disease sample

tag: disease state2


title: PCA.248: prostate_cancer_primary_248

tag: psa


title: Genomic DNA from blood 37

description: control sample


title: Genomic DNA from blood 24

description: Alzheimer's disease sample


title: Genomic DNA from blood 28

description: mild cognitive impairment sample


title: PCA.247: prostate_cancer_primary_247

tag: grade group


title: Genomic DNA from blood 26

description: Alzheimer's disease sample


title: Genomic DNA from blood 21

description: Alzheimer's disease sample


title: PCA.245: prostate_cancer_primary_245

tag: race


title: PCA.244: prostate_cancer_primary_244

tag: non-organ confined


title: Genomic DNA from blood 23

description: control sample


title: Genomic DNA from blood 27

description: Alzheimer's disease sample

value: Excluded


title: Genomic DNA from blood 22

description: Alzheimer's disease sample


title: Genomic DNA from blood 20

description: Alzheimer's disease sample


title: PCA.241: prostate_cancer_primary_241

value: No

tag: palsma cell content


title: PCA.242: prostate_cancer_primary_242

tag: inflammation signature


title: Genomic DNA from blood 12

description: control sample

value: whole blood


title: PCA.240: prostate_cancer_primary_240

tag: ifng signature


title: Genomic DNA from blood 11

description: Alzheimer's disease sample


title: Genomic DNA from blood 14

description: control sample

value: Male


title: Genomic DNA from blood 19

description: Alzheimer's disease sample

value: Alzheimer's disease


title: Genomic DNA from blood 16

description: mild cognitive impairment sample

value: Included


title: PCA.243: prostate_cancer_primary_243

tag: igg production


title: Genomic DNA from blood 13

description: mild cognitive impairment sample


title: PCA.239: prostate_cancer_primary_239


title: Genomic DNA from blood 17

description: mild cognitive impairment sample

value: mild cognitive impairment to alzheimer's disease converter


title: Genomic DNA from blood 8

description: control sample

value: control


title: Genomic DNA from blood 7

description: Alzheimer's disease sample

value: Female


title: Genomic DNA from blood 15

description: mild cognitive impairment sample

value: mild cognitive impairment


title: PCA.237: prostate_cancer_primary_237


title: Transgenic FUS(1-359) + DF402 treatment rep 4

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

data_processing:
Read quality trimming (with Phred score > 20 at least in 80% in read) with Trimmomatic v 0.32
Aligning reads with STAR (2.5.2) at reference genome GRCm38(mm10)
Read counting using featureCounts
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Processed files are standard output of HTSeq-count read counting (text format, tab-delimeted). Gene name is provided as RefSeq ID. Also, some supplemental information in the end of file included

molecule: polyA RNA

organism: Mus musculus

source_name: thoracic and lumbar spinal cord

extract_protocol:
For RNAseq analysis total RNA was extracted from the thoracic and lumbar spinal cords of experimental and control pre-symptomatic mice (70-day old, 4 animals per group) using Qiagen RNeasy Plus mini kit
cDNA libraries for the dual indexed single-end sequence analysis were prepared from equal amounts (270 ng) of each total RNA sample using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit

treatment_protocol: Animals received DF402 in the drinking water (70 µg/ml) from the age of 6 weeks

tag: genotype

value: FUS(1-359) transgenic

value: 70 day

tag: treatment

value: 70 ug/ml


title: PCA.234: prostate_cancer_primary_234


title: PCA.236: prostate_cancer_primary_236

value: White


title: PCA.235: prostate_cancer_primary_235


title: diffuse glioma_HD_part2_014

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: bisulphite conerted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k or EPIC Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

source_name: diffuse glioma IDH wt

extract_protocol: Genomic DNA was extracted and pruified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

tag: subject status

value: patient with glioblastoma

tag: gender

value: female

tag: tissue/sample type


title: Transgenic FUS(1-359) + DF402 treatment rep 3

tag: age


title: Genomic DNA from blood 2

description: Alzheimer's disease sample

tag: tissue

tag: disease state


title: Genomic DNA from blood 1

description: mild cognitive impairment sample

tag: Sex

tag: disease state2

value: mild cognitive impairment stable


title: Genomic DNA from blood 5

description: mild cognitive impairment sample


title: diffuse glioma_HD_part2_013

value: male


title: Genomic DNA from blood 9

description: control sample


title: Genomic DNA from blood 6

description: mild cognitive impairment sample


title: diffuse glioma_HD_part2_011


title: Transgenic FUS(1-359) + DF402 treatment rep 2


title: PCA.233: prostate_cancer_primary_233

tag: psa

tag: grade group

value: Yes

tag: nk activity


title: Genomic DNA from blood 3

description: Alzheimer's disease sample

value: whole blood


title: diffuse glioma_HD_part2_010


title: Transgenic FUS(1-359) + DF402 treatment rep 1


title: Genomic DNA from blood 4

description: control sample

value: Male


title: Transgenic FUS(1-359) rep 4

value: Untreated


title: diffuse glioma_HD_part2_006


title: diffuse glioma_HD_part2_008


title: diffuse glioma_HD_part2_005


title: Genomic DNA from blood 18

description: control sample

value: Included


title: PCA.232: prostate_cancer_primary_232

tag: race

tag: non-organ confined

value: No

tag: palsma cell content


title: PCA.231: prostate_cancer_primary_231

tag: inflammation signature

tag: ifng signature

tag: igg production


title: Transgenic FUS(1-359) rep 3

tag: genotype

tag: treatment


title: diffuse glioma_HD_part2_012

tag: subject status

tag: gender

tag: tissue/sample type


title: Transgenic FUS(1-359) rep 2

tag: age


title: Genomic DNA from blood 10

description: Alzheimer's disease sample

tag: tissue

tag: Sex

tag: disease state

value: Alzheimer's disease


title: diffuse glioma_HD_part2_002


title: PCA.230: prostate_cancer_primary_230

tag: psa

tag: grade group


title: diffuse glioma_HD_part2_003


title: Transgenic FUS(1-359) rep 1


title: Wild-type rep 4

value: Wild type


title: PCA.238: prostate_cancer_primary_238

tag: race

tag: nk activity


title: PCA.229: prostate_cancer_primary_229

tag: non-organ confined

tag: palsma cell content


title: diffuse glioma_HD_part2_004


title: PCA.228: prostate_cancer_primary_228

tag: inflammation signature

tag: ifng signature


title: Wild-type rep 3

tag: genotype


title: diffuse glioma_EORTC 26101_297

description:
tumor_DNA_FFPE
EORTC 26101_297

hyb_protocol: bisulphite conerted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol


title: Wild-type rep 2

tag: treatment


title: diffuse glioma_HD_part2_001

tag: subject status


title: diffuse glioma_HD_part2_007

tag: gender


title: diffuse glioma_EORTC 26101_295

description:
tumor_DNA_FFPE
EORTC 26101_295


title: Wild-type rep 1


title: PCA.226: prostate_cancer_primary_226

tag: igg production


title: PCA.227: prostate_cancer_primary_227

tag: age


title: PCA.225: prostate_cancer_primary_225


title: PCA.224: prostate_cancer_primary_224

value: Black


title: diffuse glioma_HD_part2_009

tag: tissue/sample type


title: PCA.223: prostate_cancer_primary_223


title: bulk RNA-seq_Map3k2-/- DSS_D1 replicate 3

city: Shanghai

first: Hongxiang

last: Sun

address: 280 South Chongqing Rd.

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University

description: MEKK2 KO RNASeq.xlsx

data_processing:
Illumina Bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
HTSeq-count was used to enumerate transcripts associated with each gene
Genome_build: mm10
Supplementary_files_format_and_content:tab-delimited text files include CPM values for each Sample

source_name: Colon

extract_protocol:
The frozen tissues were disaggregated using a motorized homogenizer followed by RNA extraction using the RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep Kit (Illumina)

tag: strain

tag: tissue

value: Colon

value: 16 Week

value: DSS

tag: Sex


title: diffuse glioma_EORTC 26101_296

description:
tumor_DNA_FFPE
EORTC 26101_296


title: single-cell RNA-seq_WT DSS_D3 10x

description: gp38+CD90+ total iMSC

data_processing:
Illumina Bcl2fastq software used for basecalling.
CellRanger was used to analyze the original single cell RNA sequencing results.Seurat was used to perform dimension reduction and pySCENIC was used to calculate TF activity score.
Genome_build: mm10
Supplementary_files_format_and_content:MTX,TSV,RDS

extract_protocol:
The single cell suspension of fresh colon lamina propria were processed by 10x Genomics 3'RNASeq V2
10x Genomics single cell RNA-Seq

value: 12 Week

value: wild type


title: bulk RNA-seq_Map3k2-/- DSS_D1 replicate 2

description: MEKK2 KO RNASeq.xlsx

value: female


title: diffuse glioma_EORTC 26101_291

description:
tumor_DNA_FFPE
EORTC 26101_291


title: diffuse glioma_EORTC 26101_292

description:
tumor_DNA_FFPE
EORTC 26101_292


title: PCA.221: prostate_cancer_primary_221

tag: psa

tag: grade group

value: White


title: PCA.222: prostate_cancer_primary_222

tag: race

tag: nk activity


title: diffuse glioma_EORTC 26101_287

description:
tumor_DNA_FFPE
EORTC 26101_287


title: diffuse glioma_EORTC 26101_294

description:
tumor_DNA_FFPE
EORTC 26101_294


title: diffuse glioma_EORTC 26101_290

description:
tumor_DNA_FFPE
EORTC 26101_290

value: male


title: bulk RNA-seq_Map3k2-/- DSS_D1 replicate 1

description: MEKK2 KO RNASeq.xlsx


title: diffuse glioma_EORTC 26101_285

description:
tumor_DNA_FFPE
EORTC 26101_285


title: diffuse glioma_EORTC 26101_286

description:
tumor_DNA_FFPE
EORTC 26101_286


title: diffuse glioma_EORTC 26101_288

description:
tumor_DNA_FFPE
EORTC 26101_288


title: diffuse glioma_EORTC 26101_279

description:
tumor_DNA_FFPE
EORTC 26101_279


title: diffuse glioma_EORTC 26101_284

description:
tumor_DNA_FFPE
EORTC 26101_284


title: diffuse glioma_EORTC 26101_289

description:
tumor_DNA_FFPE
EORTC 26101_289


title: PCA.220: prostate_cancer_primary_220

tag: non-organ confined

value: Yes

tag: palsma cell content


title: bulk RNA-seq_WT DSS_D1 replicate 3

description: MEKK2 KO RNASeq.xlsx


title: bulk RNA-seq_WT DSS_D1 replicate 2

description: MEKK2 KO RNASeq.xlsx


title: PCA.219: prostate_cancer_primary_219

tag: inflammation signature

tag: ifng signature


title: diffuse glioma_EORTC 26101_283

description:
tumor_DNA_FFPE
EORTC 26101_283


title: bulk RNA-seq_WT DSS_D1 rep1icate 1

description: MEKK2 KO RNASeq.xlsx

tag: genotype

tag: treatment


title: diffuse glioma_EORTC 26101_282

description:
tumor_DNA_FFPE
EORTC 26101_282

tag: gender


title: diffuse glioma_EORTC 26101_280

description:
tumor_DNA_FFPE
EORTC 26101_280


title: PCA.216: prostate_cancer_primary_216

tag: igg production


title: PCA.218: prostate_cancer_primary_218

tag: age


title: diffuse glioma_EORTC 26101_281

description:
tumor_DNA_FFPE
EORTC 26101_281


title: diffuse glioma_EORTC 26101_277

description:
tumor_DNA_FFPE
EORTC 26101_277


title: bulk RNA-seq_Map3k2-/- H2O replicate 2

description: MEKK2 KO RNASeq.xlsx


title: diffuse glioma_EORTC 26101_278

description:
tumor_DNA_FFPE
EORTC 26101_278


title: bulk RNA-seq_Map3k2-/- H2O replicate 3

description: MEKK2 KO RNASeq.xlsx


title: diffuse glioma_EORTC 26101_272

description:
tumor_DNA_FFPE
EORTC 26101_272


title: PCA.215: prostate_cancer_primary_215


title: diffuse glioma_EORTC 26101_274

description:
tumor_DNA_FFPE
EORTC 26101_274


title: diffuse glioma_EORTC 26101_276

description:
tumor_DNA_FFPE
EORTC 26101_276


title: diffuse glioma_EORTC 26101_273

description:
tumor_DNA_FFPE
EORTC 26101_273


title: diffuse glioma_EORTC 26101_275

description:
tumor_DNA_FFPE
EORTC 26101_275


title: PCA.214: prostate_cancer_primary_214


title: bulk RNA-seq_Map3k2-/- H2O replicate 1

description: MEKK2 KO RNASeq.xlsx


title: bulk RNA-seq_WT H2O replicate 3

description: MEKK2 KO RNASeq.xlsx


title: PCA.217: prostate_cancer_primary_217


title: PCA.213: prostate_cancer_primary_213


title: PCA.212: prostate_cancer_primary_212


title: genomic DNA from brain 96

city: Erlangen

first: Katja

last: Kobow

state: Deutschland

address: Schwabachanlage 6

department: Neuropathology

institute: Universitätsklinikum Erlangen

description:
structural brain lesion and epilepsy
Sample96

hyb_protocol: Arrays were imaged using iscan Reader using standard recommended Illumina scanner setting

scan_protocol: Differential DNA methylation analysis was performed with a self-customized Python wrapped cross R package pipeline, utilizing 'Champ,' 'watermelon,' 'DNAMarray,' and 'minfi' as R packages. 'MethQC' and 'Pymethylarray' were used as Python-based array analysis packages. Additional own implementations of lacking functionality were used where needed. All these packages were wrapped by using 'rpy2', an interface to R running embedded in a Python process.

data_processing: Data was stratified quantile normalized using the ‘minfi‘ ‘preprocessQuantile‘ function

label: Cy5 and Cy3

source_name: Cortex

label_protocol: Following FFPE restoration bisulphite converted DNA was hybridised to Illumina Infinium Human Methylation 850K Beadchip using standard Illumina protocol

extract_protocol: genomic DNA was extracted and purified from FFPE tissue punches using Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

value: Cortex

tag: diagnosis

value: TLE


title: bulk RNA-seq_WT H2O replicate 2

description: MEKK2 KO RNASeq.xlsx

tag: strain


title: genomic DNA from brain 95

description:
structural brain lesion and epilepsy
Sample95

tag: tissue


title: PCA.211: prostate_cancer_primary_211


title: diffuse glioma_EORTC 26101_264

description:
tumor_DNA_FFPE
EORTC 26101_264


title: diffuse glioma_EORTC 26101_271

description:
tumor_DNA_FFPE
EORTC 26101_271


title: diffuse glioma_EORTC 26101_293

description:
tumor_DNA_FFPE
EORTC 26101_293


title: genomic DNA from brain 94

description:
structural brain lesion and epilepsy
Sample94


title: Mirc11-/- hematopoietic myeloid progenitors_4

city: South Bend

first: Richard

last: Dahl

state: IN

address: Harper Hall 227, 1234 Notre Dame Ave.

department: Microbiology and Immunology

institute: Indiana University School of Medicine, South Bend

data_processing:
Raw sequences were trimmed of adapters with Trimmomatic (Bolger et al., 2014) and assessed for quality with FastQC (Andrews, 2014).  Trimmed sequences were aligned to the Mus_musculus.GRCm38.dna.primary_assembly Ensembl version of the mouse genome, using Mus_musculus.GRCm38.92, (Zerbino et al., 2018) with TopHat2 (Trapnell et al., 2009) using Bowtie 2 (Langmead et al., 2012).  Corresponding alignments were sorted with SAMtools (Li et al., 2009).  Read counts were generated with HTSeq-count (Ander et al., 2014) and were merged with a python script (Wheeler, 2013).  Subsequent statistics were completed in R (R Core Team, 2014) implementing the EdgeR library (McCarthy et al., 2012; Robinson et al., 2007; Robinson et al., 2008; Robinson et al., 2010).  Gene names and GO terms were identified using the Ensemble version of BioMart (Kinsella et al., 2011).
References:
Anders, S., Pyl, T. P., Huber, W.  HTSeq — A Python framework to work with high-throughput sequencing data. Bioinformatics, 2014, in print; online at doi:10.1093/bioinformatics/btu638
Andrews, S., Babraham bioinformatics.  Babraham institute.  http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Retrieved September 3, 2014.
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P. Ensembl BioMarts: a hub for data retrieval across taxonomic space.  Database (Oxford). Vol. 2011 Published online Jul 23, 2011
Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40, 4288-4297
R Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.  URL http://www.R-project.org/.
Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23, 2881-2887
Robinson MD and Smyth GK (2008). Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics, 9, 321-332
Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140
Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: Discovering splice junctions with RNA-seq. Bioinformatics (Oxford, England), 25(9), 1105-1111.
Wheeler, D.  (2013).  How to use DESeq to analyse RNAseq data.  David Wheeler lab page.  http://dwheelerau.com/2013/04/15/how-to-use-deseq-to-analyse-rnaseq-data/.  Retrieved October 3, 2014.
Genome_build: MM10
Supplementary_files_format_and_content: spread sheet and DE genes

source_name: Bone Marrow

growth_protocol: Bone marrow isolated from 6-8 week old mice

extract_protocol:
Total RNA prepared using Qiagen MirEasy Kit
cDNA libraries were generated using NEBNext Ultra II RNA Library Prep.

treatment_protocol: Isolated the Lin-Sca1-ckit+ population with celll sorting on FACSAria III

tag: cell type

value: Lin-Sca1-cKit+ myeloid progenitors


title: diffuse glioma_EORTC 26101_270

description:
tumor_DNA_FFPE
EORTC 26101_270


title: PCA.210: prostate_cancer_primary_210

tag: psa


title: Mirc11-/- hematopoietic myeloid progenitors_3


title: PCA.209: prostate_cancer_primary_209

tag: grade group


title: Mirc11-/- hematopoietic myeloid progenitors_2


title: genomic DNA from brain 93

description:
structural brain lesion and epilepsy
Sample93


title: genomic DNA from brain 92

description:
structural brain lesion and epilepsy
Sample92


title: PCA.208: prostate_cancer_primary_208

tag: race


title: Mirc11-/- hematopoietic myeloid progenitors_1


title: diffuse glioma_EORTC 26101_268

description:
tumor_DNA_FFPE
EORTC 26101_268


title: diffuse glioma_EORTC 26101_265

description:
tumor_DNA_FFPE
EORTC 26101_265


title: diffuse glioma_EORTC 26101_259

description:
tumor_DNA_FFPE
EORTC 26101_259


title: diffuse glioma_EORTC 26101_267

description:
tumor_DNA_FFPE
EORTC 26101_267


title: diffuse glioma_EORTC 26101_263

description:
tumor_DNA_FFPE
EORTC 26101_263


title: diffuse glioma_EORTC 26101_262

description:
tumor_DNA_FFPE
EORTC 26101_262


title: diffuse glioma_EORTC 26101_261

description:
tumor_DNA_FFPE
EORTC 26101_261


title: diffuse glioma_EORTC 26101_266

description:
tumor_DNA_FFPE
EORTC 26101_266


title: diffuse glioma_EORTC 26101_258

description:
tumor_DNA_FFPE
EORTC 26101_258


title: genomic DNA from brain 91

description:
structural brain lesion and epilepsy
Sample91


title: diffuse glioma_EORTC 26101_269

description:
tumor_DNA_FFPE
EORTC 26101_269


title: diffuse glioma_EORTC 26101_260

description:
tumor_DNA_FFPE
EORTC 26101_260


title: genomic DNA from brain 90

description:
structural brain lesion and epilepsy
Sample90


title: diffuse glioma_EORTC 26101_257

description:
tumor_DNA_FFPE
EORTC 26101_257


title: diffuse glioma_EORTC 26101_256

description:
tumor_DNA_FFPE
EORTC 26101_256


title: WT hematopoietic myeloid progenitors_3

value: WT


title: PCA.206: prostate_cancer_primary_206

value: No

tag: nk activity


title: PCA.207: prostate_cancer_primary_207

tag: non-organ confined


title: WT hematopoietic myeloid progenitors_2


title: PCA.205: prostate_cancer_primary_205

tag: palsma cell content


title: genomic DNA from brain 89

description:
structural brain lesion and epilepsy
Sample89


title: WT hematopoietic myeloid progenitors_1


title: diffuse glioma_EORTC 26101_255

description:
tumor_DNA_FFPE
EORTC 26101_255


title: genomic DNA from brain 88

description:
structural brain lesion and epilepsy
Sample88


title: diffuse glioma_EORTC 26101_254

description:
tumor_DNA_FFPE
EORTC 26101_254


title: genomic DNA from brain 86

description:
structural brain lesion and epilepsy
Sample86


title: Wt2262M2

data_processing:
The raw reads were mapped to mm9 genome using STAR-2.5.1 at default parameters
The Cufflinks program was used to evaluate the Expression values (FPKM) Fragment per kilo base per million mapped reads.
Differential Expression Analysis was done  for AkoM1 versus WtM1 and AkoM2 versus WtM2 using DESEQ.
Genome_build: MM9
Supplementary_files_format_and_content: spread sheet for DE genes and FPKM values

growth_protocol: Bone marrow derived macrophages (BMDM) were generated from bone marrow isolated (BM) from 6-8 week old wildtype and mirn23a-/- (Mirc11-/-) C57BL/6 mice. BM grown in DMEM, 10%FBS, 15% L929 conditioned media (M-CSF source), 10mM HEPES buffer, and 50 U/ml penicillin, and 50 ug/ml streptomycin for 7d.

extract_protocol:
RNA was isolated using Qiagen miRNeasy kit (Qiagen, Valencia, CA).
cDNA libraries were generated using NEBNext Ultra II RNA Library Prep.

treatment_protocol: After 7d, cells removed by TrypLE and replated at 1x106 cells/ml overnight. BMDMs were polarized for 24h under M1 (100 ng/ml LPS + 50 ng/ml mIFNγ)  or M2 (20ng/ml IL-4 + 20ng/ml IL-13) conditions for 24h.

tag: mouse strain

value: Macrophage (cultured)

value: 24h 100ng/ml LPS + 10ng/ml IFNg


title: WT hematopoietic myeloid progenitors_4


title: Wt2261M2


title: PCA.204: prostate_cancer_primary_204

tag: inflammation signature

tag: ifng signature


title: Wt2260M2

tag: treatment


title: bulk RNA-seq_WT H2O replicate 1

description: MEKK2 KO RNASeq.xlsx

tag: genotype

tag: Sex


title: diffuse glioma_EORTC 26101_252

description:
tumor_DNA_FFPE
EORTC 26101_252

tag: gender


title: PCA.200: prostate_cancer_primary_200

tag: age

tag: igg production


title: genomic DNA from brain 87

description:
structural brain lesion and epilepsy
Sample87

tag: tissue

tag: diagnosis


title: PCA.199: prostate_cancer_primary_199

tag: psa


title: PCA.202: prostate_cancer_primary_202

tag: grade group


title: genomic DNA from brain 85

description:
structural brain lesion and epilepsy
Sample85


title: genomic DNA from brain 83

description:
structural brain lesion and epilepsy
Sample83


title: diffuse glioma_EORTC 26101_251

description:
tumor_DNA_FFPE
EORTC 26101_251


title: diffuse glioma_EORTC 26101_250

description:
tumor_DNA_FFPE
EORTC 26101_250


title: diffuse glioma_EORTC 26101_253

description:
tumor_DNA_FFPE
EORTC 26101_253


title: PCA.203: prostate_cancer_primary_203

tag: race


title: genomic DNA from brain 82

description:
structural brain lesion and epilepsy
Sample82


title: genomic DNA from brain 84

description:
structural brain lesion and epilepsy
Sample84


title: Wt2260M1

tag: cell type


title: diffuse glioma_EORTC 26101_249

description:
tumor_DNA_FFPE
EORTC 26101_249


title: genomic DNA from brain 81

description:
structural brain lesion and epilepsy
Sample81

value: HME


title: Wt2262M1


title: Ako2273M2


title: Wt2261M1


title: PCA.197: prostate_cancer_primary_197

tag: non-organ confined

tag: nk activity


title: genomic DNA from brain 80

description:
structural brain lesion and epilepsy
Sample80


title: PCA.198: prostate_cancer_primary_198

tag: palsma cell content


title: diffuse glioma_EORTC 26101_248

description:
tumor_DNA_FFPE
EORTC 26101_248


title: PCA.201: prostate_cancer_primary_201

tag: inflammation signature


title: PCA.196: prostate_cancer_primary_196

tag: ifng signature


title: diffuse glioma_EORTC 26101_245

description:
tumor_DNA_FFPE
EORTC 26101_245


title: genomic DNA from brain 79

description:
structural brain lesion and epilepsy
Sample79


title: Ako2271M2

tag: mouse strain

tag: treatment


title: PCA.195: prostate_cancer_primary_195


title: Ako2272M2


title: diffuse glioma_EORTC 26101_247

description:
tumor_DNA_FFPE
EORTC 26101_247


title: genomic DNA from brain 78

description:
structural brain lesion and epilepsy
Sample78


title: PCA.194: prostate_cancer_primary_194


title: diffuse glioma_EORTC 26101_243

description:
tumor_DNA_FFPE
EORTC 26101_243


title: genomic DNA from brain 77

description:
structural brain lesion and epilepsy
Sample77


title: diffuse glioma_EORTC 26101_246

description:
tumor_DNA_FFPE
EORTC 26101_246


title: Ako2272M1


title: genomic DNA from brain 76

description:
structural brain lesion and epilepsy
Sample76


title: Ako2273M1


title: Ako2271M1


title: diffuse glioma_EORTC 26101_244

description:
tumor_DNA_FFPE
EORTC 26101_244


title: genomic DNA from brain 75

description:
structural brain lesion and epilepsy
Sample75

value: FCD 2B


title: diffuse glioma_EORTC 26101_242

description:
tumor_DNA_FFPE
EORTC 26101_242


title: PCA.193: prostate_cancer_primary_193


title: PCA.192: prostate_cancer_primary_192


title: genomic DNA from brain 74

description:
structural brain lesion and epilepsy
Sample74


title: CTCF CFUE

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

library_source: genomic

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2  --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
S3norm version 1(https://github.com/guanjue/S3norm) and default parameters except -r max1
CLIMB 0.1.0 with dependent Julia package cgibbs.jl version 0.1.0. CLIMB  was run at the default settings in all analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs, normalized read counts
Supplementary_files_format_and_content: bed, CLIMB classes

source_name: CFUE cells

extract_protocol:
Lysates were prepared from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s ChIP-seq Sample Preparation Kit.

value: bone marrow derived progenitor cells

tag: facs cell isolation sort markers

value: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119+, CD44+, FSCHigh

tag: strain

tag: chip antibody

value: Millipore 07-729


title: PCA.191: prostate_cancer_primary_191

tag: age

tag: igg production


title: genomic DNA from brain 73

description:
structural brain lesion and epilepsy
Sample73

tag: tissue

tag: diagnosis


title: PCA.190: prostate_cancer_primary_190

tag: psa

tag: grade group


title: diffuse glioma_EORTC 26101_241

description:
tumor_DNA_FFPE
EORTC 26101_241

tag: gender


title: genomic DNA from brain 72

description:
structural brain lesion and epilepsy
Sample72


title: PCA.189: prostate_cancer_primary_189

tag: race

tag: non-organ confined


title: CTCF GMP

source_name: GMP cells

tag: cell type


title: CTCF CMP

source_name: CMP cells


title: PCA.187: prostate_cancer_primary_187

tag: palsma cell content

tag: inflammation signature

tag: nk activity


title: CTCF MEP

source_name: MEP cells


title: CTCF iMk

source_name: iMk cells


title: diffuse glioma_EORTC 26101_239

description:
tumor_DNA_FFPE
EORTC 26101_239


title: genomic DNA from brain 69

description:
structural brain lesion and epilepsy
Sample69


title: PCA.185: prostate_cancer_primary_185

tag: ifng signature


title: CTCF LSK

source_name: LSK cells

tag: facs cell isolation sort markers


title: genomic DNA from brain 70

description:
structural brain lesion and epilepsy
Sample70


title: diffuse glioma_EORTC 26101_236

description:
tumor_DNA_FFPE
EORTC 26101_236


title: diffuse glioma_EORTC 26101_240

description:
tumor_DNA_FFPE
EORTC 26101_240


title: PCA.184: prostate_cancer_primary_184


title: diffuse glioma_EORTC 26101_238

description:
tumor_DNA_FFPE
EORTC 26101_238


title: CTCF CFUMk

source_name: CFUMk cells

tag: strain


title: PCA.188: prostate_cancer_primary_188


title: PCA.186: prostate_cancer_primary_186


title: diffuse glioma_EORTC 26101_235

description:
tumor_DNA_FFPE
EORTC 26101_235


title: genomic DNA from brain 67

description:
structural brain lesion and epilepsy
Sample67


title: KO_lung_3

data_processing:
Read quality was checked using Fastqc.
Alignment software used was STAR v.2.5.2a
DEseq2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: For each processed file, there are 2 columns: the first column being Ensembl gene ID, and the second column being raw read counts

source_name: lung tissue

growth_protocol: Man1a2 +/- mice (Man1a2tm1.1Ahe, #007672., Jackson Labs, Bar harbor, Maine, US) were bred to evaluate whether newborn Man1A2 -/- null mice demonstrated abnormal liver architecture in addition to the known lethal changes in the lung, compared with wild type

extract_protocol:
Total RNA was extracted from livers of mouse pups at first day of life using RNeasy Mini Kit (Qiagen, Valencia, CA) and reverse-transcribed to cDNA using High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific, Waltham, MA)
mRNA sequencing libraries using Illumina TruSeq Stranded mRNA sample preparation kit. Poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads, mRNA fragmented into small pieces using divalent cations, and copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by using dUTP in the Second Strand Marking Mix, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments were ligated to single 'A' base and adapter, then purified and enriched with PCR to create the final cDNA libraries which were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorometer. Quality was examined using Agilent Tapestation 2200.The cDNA libraries were pooled at a final concentration 1.8pM

treatment_protocol: Within 30-60 minutes of birth, newborn mice were decapitated, dissected through a midline incision extending from the pubic symphysis cranially into the thoracic cavity, and lung and liver tissue harvested for histological examination and RNA extraction

value: lung

tag: genotype

value: MAN1A2 knockout

value: newborn


title: diffuse glioma_EORTC 26101_233

description:
tumor_DNA_FFPE
EORTC 26101_233

value: male


title: genomic DNA from brain 66

description:
structural brain lesion and epilepsy
Sample66


title: diffuse glioma_EORTC 26101_234

description:
tumor_DNA_FFPE
EORTC 26101_234

value: female


title: diffuse glioma_EORTC 26101_237

description:
tumor_DNA_FFPE
EORTC 26101_237


title: PCA.183: prostate_cancer_primary_183

source_name: FFPE prostate cancer

tag: age

value: White


title: WT_lung_3

value: wildtype


title: diffuse glioma_EORTC 26101_231

description:
tumor_DNA_FFPE
EORTC 26101_231


title: CTCF G1E

description: Marit Vermunt and Gerd Blobel generated and shared the G1E CTCF ChIP-seq data for this work.

source_name: G1E cells

value: ES-derived erythroid progenitor cells

tag: chip antibody

tag: growth protocol

value: GATA1-null proerythroblast cell line G1E (Weiss et al., 1997). G1E cells were grown in IMDM+15% FBS, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37C degrees with 5% CO2 (as described in Weiss et al., 1997).


title: PCA.182: prostate_cancer_primary_182

value: No

tag: igg production


title: genomic DNA from brain 65

description:
structural brain lesion and epilepsy
Sample65

tag: tissue

value: Cortex

tag: diagnosis


title: genomic DNA from brain 64

description:
structural brain lesion and epilepsy
Sample64


title: genomic DNA from brain 63

description:
structural brain lesion and epilepsy
Sample63


title: WT_lung_2


title: diffuse glioma_EORTC 26101_232

description:
tumor_DNA_FFPE
EORTC 26101_232

tag: gender


title: PCA.180: prostate_cancer_primary_180

tag: psa

tag: grade group

tag: race

value: Black

value: Yes


title: diffuse glioma_EORTC 26101_229

description:
tumor_DNA_FFPE
EORTC 26101_229


title: KO_lung_2


title: PCA.179: prostate_cancer_primary_179

tag: non-organ confined

tag: palsma cell content


title: genomic DNA from brain 71

description:
structural brain lesion and epilepsy
Sample71

value: FCD 2B


title: KO_lung_1


title: PCA.178: prostate_cancer_primary_178

tag: inflammation signature

tag: nk activity


title: WT_lung_1


title: genomic DNA from brain 61

description:
structural brain lesion and epilepsy
Sample61


title: PCA.177: prostate_cancer_primary_177

tag: ifng signature


title: KO_liver_3

value: liver


title: genomic DNA from brain 60

description:
structural brain lesion and epilepsy
Sample60


title: genomic DNA from brain 62

description:
structural brain lesion and epilepsy
Sample62


title: WT_liver_3


title: KO_liver_2


title: diffuse glioma_EORTC 26101_230

description:
tumor_DNA_FFPE
EORTC 26101_230


title: diffuse glioma_EORTC 26101_226

description:
tumor_DNA_FFPE
EORTC 26101_226


title: genomic DNA from brain 58

description:
structural brain lesion and epilepsy
Sample58


title: PCA.176: prostate_cancer_primary_176


title: PCA.175: prostate_cancer_primary_175


title: diffuse glioma_EORTC 26101_227

description:
tumor_DNA_FFPE
EORTC 26101_227


title: genomic DNA from brain 59

description:
structural brain lesion and epilepsy
Sample59


title: WT_liver_2


title: genomic DNA from brain 57

description:
structural brain lesion and epilepsy
Sample57


title: PCA.173: prostate_cancer_primary_173


title: diffuse glioma_EORTC 26101_225

description:
tumor_DNA_FFPE
EORTC 26101_225


title: diffuse glioma_EORTC 26101_224

description:
tumor_DNA_FFPE
EORTC 26101_224


title: PCA.174: prostate_cancer_primary_174


title: diffuse glioma_EORTC 26101_228

description:
tumor_DNA_FFPE
EORTC 26101_228


title: diffuse glioma_EORTC 26101_223

description:
tumor_DNA_FFPE
EORTC 26101_223


title: PCA.172: prostate_cancer_primary_172


title: KO_liver_1


title: WT_liver_1


title: genomic DNA from brain 68

description:
structural brain lesion and epilepsy
Sample68


title: genomic DNA from brain 55

description:
structural brain lesion and epilepsy
Sample55

value: FCD 2A


title: genomic DNA from brain 56

description:
structural brain lesion and epilepsy
Sample56


title: diffuse glioma_EORTC 26101_222

description:
tumor_DNA_FFPE
EORTC 26101_222


title: genomic DNA from brain 53

description:
structural brain lesion and epilepsy
Sample53


title: genomic DNA from brain 54

description:
structural brain lesion and epilepsy
Sample54


title: genomic DNA from brain 51

description:
structural brain lesion and epilepsy
Sample51


title: genomic DNA from brain 52

description:
structural brain lesion and epilepsy
Sample52


title: diffuse glioma_EORTC 26101_221

description:
tumor_DNA_FFPE
EORTC 26101_221


title: PCA.167: prostate_cancer_primary_167


title: PCA.170: prostate_cancer_primary_170


title: PCA.168: prostate_cancer_primary_168


title: PCA.171: prostate_cancer_primary_171


title: diffuse glioma_EORTC 26101_219

description:
tumor_DNA_FFPE
EORTC 26101_219


title: PCA.169: prostate_cancer_primary_169


title: genomic DNA from brain 50

description:
structural brain lesion and epilepsy
Sample50


title: genomic DNA from brain 48

description:
structural brain lesion and epilepsy
Sample48


title: diffuse glioma_EORTC 26101_218

description:
tumor_DNA_FFPE
EORTC 26101_218


title: diffuse glioma_EORTC 26101_217

description:
tumor_DNA_FFPE
EORTC 26101_217


title: genomic DNA from brain 47

description:
structural brain lesion and epilepsy
Sample47


title: PCA.164: prostate_cancer_primary_164


title: PCA.166: prostate_cancer_primary_166


title: PCA.165: prostate_cancer_primary_165


title: PCA.181: prostate_cancer_primary_181


title: diffuse glioma_EORTC 26101_220

description:
tumor_DNA_FFPE
EORTC 26101_220


title: genomic DNA from brain 46

description:
structural brain lesion and epilepsy
Sample46


title: PCA.162: prostate_cancer_primary_162


title: genomic DNA from brain 45

description:
structural brain lesion and epilepsy
Sample45


title: diffuse glioma_EORTC 26101_215

description:
tumor_DNA_FFPE
EORTC 26101_215


title: genomic DNA from brain 44

description:
structural brain lesion and epilepsy
Sample44


title: diffuse glioma_EORTC 26101_216

description:
tumor_DNA_FFPE
EORTC 26101_216


title: PCA.163: prostate_cancer_primary_163


title: diffuse glioma_EORTC 26101_211

description:
tumor_DNA_FFPE
EORTC 26101_211


title: PBMC patient 8 high viremia

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
samples.txt
patients.txt

data_processing:
The MARS-seq pipeline scripts with a genome of hg19 + TB40/E were used.
In read1, the first 5 positions are ignored, the next 4 positions (6-9) are the batch barcode, and the next 37 positions (10-46) are the insert that was used for the alignment.
In read2, the first 7 positions (1-7) are the sample barcode, and the next 8 positions (8-15) are the UMI (unique molecular identifier).
Genome_build: hg19 + TB40/E (NCBI accession EF999921.1)
Supplementary_files_format_and_content: tab-delimited text files. Include number of umis for all genes, per sample.

source_name: PBMC from HSCT patient

growth_protocol: Primary human foreskin fibroblasts (HFF) (ATCC CRL-1634) were maintained in DMEM with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 100 units/ml penicillin and streptomycin (Beit-Haemek, Israel).

extract_protocol:
PBMC were isolated from fresh venous blood, obtained from HSCT patients, using Lymphoprep (Stemcell Technologies) density gradient
RNA libraries were generated from samples of ~10,000 cells according to the MARS-seq protocol (Jaitin et al., 2014; Keren-Shaul et al., 2019).
The library is 3' RNA-seq

treatment_protocol: Fibroblasts were infected with HCMV strain TB40/E

tag: cell type

value: PBMC


title: PCA.160: prostate_cancer_primary_160


title: PCA.159: prostate_cancer_primary_159


title: genomic DNA from brain 43

description:
structural brain lesion and epilepsy
Sample43


title: genomic DNA from brain 42

description:
structural brain lesion and epilepsy
Sample42


title: PCA.161: prostate_cancer_primary_161


title: diffuse glioma_EORTC 26101_209

description:
tumor_DNA_FFPE
EORTC 26101_209


title: diffuse glioma_EORTC 26101_214

description:
tumor_DNA_FFPE
EORTC 26101_214


title: diffuse glioma_EORTC 26101_213

description:
tumor_DNA_FFPE
EORTC 26101_213


title: genomic DNA from brain 40

description:
autoptic normal brain and no epilepsy
Sample40

source_name: White Matter

value: White Matter


title: genomic DNA from brain 41

description:
structural brain lesion and epilepsy
Sample41


title: PBMC patient 8 low viremia

description:
samples.txt
patients.txt


title: PCA.157: prostate_cancer_primary_157


title: PCA.158: prostate_cancer_primary_158


title: PCA.156: prostate_cancer_primary_156


title: diffuse glioma_EORTC 26101_208

description:
tumor_DNA_FFPE
EORTC 26101_208


title: diffuse glioma_EORTC 26101_210

description:
tumor_DNA_FFPE
EORTC 26101_210


title: genomic DNA from brain 39

description:
autoptic normal brain and no epilepsy
Sample39

value: CTRL - WM


title: PBMC patient 7 low viremia

description:
samples.txt
patients.txt


title: PCA.155: prostate_cancer_primary_155


title: PBMC patient 6 high viremia

description:
samples.txt
patients.txt


title: genomic DNA from brain 38

description:
autoptic normal brain and no epilepsy
Sample38


title: genomic DNA from brain 37

description:
autoptic normal brain and no epilepsy
Sample37


title: diffuse glioma_EORTC 26101_207

description:
tumor_DNA_FFPE
EORTC 26101_207


title: diffuse glioma_EORTC 26101_212

description:
tumor_DNA_FFPE
EORTC 26101_212


title: PBMC patient 7 high viremia

description:
samples.txt
patients.txt


title: PBMC patient 6 low viremia

description:
samples.txt
patients.txt


title: diffuse glioma_EORTC 26101_204

description:
tumor_DNA_FFPE
EORTC 26101_204


title: PCA.154: prostate_cancer_primary_154


title: diffuse glioma_EORTC 26101_206

description:
tumor_DNA_FFPE
EORTC 26101_206


title: PCA.153: prostate_cancer_primary_153


title: genomic DNA from brain 36

description:
autoptic normal brain and no epilepsy
Sample36


title: 131-O

city: Indianapolis

first: Steven

middle: P

last: Angus

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
Reads were aligned to the human reference genome (hg38) using STAR 2.4.2a
reads were translated to transcriptome coordinates using Salmon 0.60
Isoform data were collated to single gene IDs using the R package biomaRt, and abundance estimates were upper quartile normalized using R
Genome_build: hg38
Supplementary_files_format_and_content: Processed files (.xlsx) contain transcript abundance estimates, organized by official gene symbol--both pre-normalization (...genes.xlsx) and post upper quartile normalization (...genes.norm.xlsx)

source_name: Patient 131

extract_protocol:
Qiagen RNeasy Plus Mini with DNase treatment
KAPA Stranded mRNAseq Kit, 1 ug total RNA input, 10 cycles PCR amplification

value: breast tumor specimen

tag: disease state

tag: time point

value: post-treatment

tag: treatment

value: trastuzumab + lapatinib


title: 133-R

source_name: Patient 133

value: pre-treatment


title: genomic DNA from brain 34

description:
autoptic normal brain and no epilepsy
Sample34


title: diffuse glioma_EORTC 26101_202

description:
tumor_DNA_FFPE
EORTC 26101_202

source_name: diffuse glioma IDH wt

value: female


title: PCA.151: prostate_cancer_primary_151

tag: age


title: diffuse glioma_EORTC 26101_203

description:
tumor_DNA_FFPE
EORTC 26101_203

value: male


title: 124-O

source_name: Patient 124


title: PCA.152: prostate_cancer_primary_152

value: White

tag: igg production


title: PCA.150: prostate_cancer_primary_150

value: No


title: genomic DNA from brain 49

description:
structural brain lesion and epilepsy
Sample49

source_name: Cortex

tag: tissue

value: Cortex


title: diffuse glioma_EORTC 26101_201

description:
tumor_DNA_FFPE
EORTC 26101_201


title: 128-R

source_name: Patient 128


title: 128-O

value: pertuzumab


title: genomic DNA from brain 33

description:
autoptic normal brain and no epilepsy
Sample33

tag: diagnosis


title: diffuse glioma_EORTC 26101_199

description:
tumor_DNA_FFPE
EORTC 26101_199

tag: gender


title: genomic DNA from brain 35

description:
autoptic normal brain and no epilepsy
Sample35


title: 125-R

source_name: Patient 125


title: genomic DNA from brain 32

description:
autoptic normal brain and no epilepsy
Sample32

value: CTRL - NCx


title: diffuse glioma_EORTC 26101_200

description:
tumor_DNA_FFPE
EORTC 26101_200


title: genomic DNA from brain 31

description:
autoptic normal brain and no epilepsy
Sample31


title: 125-O


title: 123-R

source_name: Patient 123


title: genomic DNA from brain 29

description:
autoptic normal brain and no epilepsy
Sample29


title: 123-O

value: trastuzumab


title: diffuse glioma_EORTC 26101_198

description:
tumor_DNA_FFPE
EORTC 26101_198


title: 121-O

source_name: Patient 121


title: PCA.148: prostate_cancer_primary_148

tag: psa


title: genomic DNA from brain 28

description:
autoptic normal brain and no epilepsy
Sample28


title: diffuse glioma_EORTC 26101_194

description:
tumor_DNA_FFPE
EORTC 26101_194


title: diffuse glioma_EORTC 26101_205

description:
tumor_DNA_FFPE
EORTC 26101_205


title: PCA.146: prostate_cancer_primary_146

tag: grade group


title: PCA.147: prostate_cancer_primary_147

tag: race


title: PCA.144: prostate_cancer_primary_144

value: Black

tag: non-organ confined

value: Yes


title: genomic DNA from brain 27

description:
autoptic normal brain and no epilepsy
Sample27


title: diffuse glioma_EORTC 26101_197

description:
tumor_DNA_FFPE
EORTC 26101_197


title: genomic DNA from brain 26

description:
structural brain lesion and epilepsy
Sample26

value: PMG


title: PCA.145: prostate_cancer_primary_145

tag: palsma cell content


title: PCA.143: prostate_cancer_primary_143

tag: inflammation signature


title: diffuse glioma_EORTC 26101_195

description:
tumor_DNA_FFPE
EORTC 26101_195


title: diffuse glioma_EORTC 26101_196

description:
tumor_DNA_FFPE
EORTC 26101_196


title: 120-R

source_name: Patient 120


title: 120-O

value: trastuzumab + pertuzumab


title: 119-R

source_name: Patient 119


title: genomic DNA from brain 24

description:
structural brain lesion and epilepsy
Sample24


title: 119-O


title: genomic DNA from brain 25

description:
structural brain lesion and epilepsy
Sample25


title: genomic DNA from brain 23

description:
structural brain lesion and epilepsy
Sample23


title: PCA.139: prostate_cancer_primary_139

tag: nk activity


title: genomic DNA from brain 22

description:
structural brain lesion and epilepsy
Sample22


title: 118-O

source_name: Patient 118


title: genomic DNA from brain 21

description:
structural brain lesion and epilepsy
Sample21


title: PCA.149: prostate_cancer_primary_149

tag: ifng signature


title: PCA.137: prostate_cancer_primary_137


title: 117-R

source_name: Patient 117


title: PCA.138: prostate_cancer_primary_138

source_name: FFPE prostate cancer


title: PCA.140: prostate_cancer_primary_140


title: diffuse glioma_EORTC 26101_189

description:
tumor_DNA_FFPE
EORTC 26101_189


title: diffuse glioma_EORTC 26101_193

description:
tumor_DNA_FFPE
EORTC 26101_193


title: diffuse glioma_EORTC 26101_191

description:
tumor_DNA_FFPE
EORTC 26101_191


title: diffuse glioma_EORTC 26101_186

description:
tumor_DNA_FFPE
EORTC 26101_186


title: genomic DNA from brain 20

description:
structural brain lesion and epilepsy
Sample20


title: 116-R

source_name: Patient 116


title: diffuse glioma_EORTC 26101_190

description:
tumor_DNA_FFPE
EORTC 26101_190


title: diffuse glioma_EORTC 26101_187

description:
tumor_DNA_FFPE
EORTC 26101_187


title: diffuse glioma_EORTC 26101_192

description:
tumor_DNA_FFPE
EORTC 26101_192


title: diffuse glioma_EORTC 26101_188

description:
tumor_DNA_FFPE
EORTC 26101_188


title: PCA.136: prostate_cancer_primary_136


title: genomic DNA from brain 19

description:
structural brain lesion and epilepsy
Sample19


title: PCA.135: prostate_cancer_primary_135


title: 116-O


title: genomic DNA from brain 18

description:
structural brain lesion and epilepsy
Sample18


title: 115-O

source_name: Patient 115


title: diffuse glioma_EORTC 26101_183

description:
tumor_DNA_FFPE
EORTC 26101_183


title: genomic DNA from brain 17

description:
structural brain lesion and epilepsy
Sample17


title: PCA.133: prostate_cancer_primary_133


title: genomic DNA from brain 30

description:
autoptic normal brain and no epilepsy
Sample30


title: diffuse glioma_EORTC 26101_185

description:
tumor_DNA_FFPE
EORTC 26101_185


title: diffuse glioma_EORTC 26101_184

description:
tumor_DNA_FFPE
EORTC 26101_184


title: 113-R

source_name: Patient 113


title: PCA.134: prostate_cancer_primary_134


title: genomic DNA from brain 16

description:
structural brain lesion and epilepsy
Sample16


title: PCA.132: prostate_cancer_primary_132


title: diffuse glioma_EORTC 26101_181

description:
tumor_DNA_FFPE
EORTC 26101_181


title: diffuse glioma_EORTC 26101_182

description:
tumor_DNA_FFPE
EORTC 26101_182


title: 113-O


title: genomic DNA from brain 15

description:
structural brain lesion and epilepsy
Sample15


title: 112-O

source_name: Patient 112


title: genomic DNA from brain 14

description:
structural brain lesion and epilepsy
Sample14


title: PCA.142: prostate_cancer_primary_142


title: 117-O


title: PCA.130: prostate_cancer_primary_130


title: 111-R

source_name: Patient 111


title: genomic DNA from brain 13

description:
structural brain lesion and epilepsy
Sample13


title: PCA.131: prostate_cancer_primary_131


title: 111-O


title: genomic DNA from brain 12

description:
structural brain lesion and epilepsy
Sample12


title: diffuse glioma_EORTC 26101_179

description:
tumor_DNA_FFPE
EORTC 26101_179

source_name: diffuse glioma IDH wt


title: genomic DNA from brain 11

description:
structural brain lesion and epilepsy
Sample11


title: 109-O

source_name: Patient 109


title: PCA.129: prostate_cancer_primary_129


title: 108-R

source_name: Patient 108


title: genomic DNA from brain 10

description:
structural brain lesion and epilepsy
Sample10

source_name: Cortex


title: diffuse glioma_EORTC 26101_178

description:
tumor_DNA_FFPE
EORTC 26101_178


title: 108-O


title: genomic DNA from brain 9

description:
structural brain lesion and epilepsy
Sample9


title: 107-R

source_name: Patient 107


title: PCA.127: prostate_cancer_primary_127


title: PCA.126: prostate_cancer_primary_126


title: PCA.128: prostate_cancer_primary_128


title: PCA.125: prostate_cancer_primary_125


title: genomic DNA from brain 8

description:
structural brain lesion and epilepsy
Sample8


title: PCA.124: prostate_cancer_primary_124


title: diffuse glioma_EORTC 26101_177

description:
tumor_DNA_FFPE
EORTC 26101_177


title: PCA.141: prostate_cancer_primary_141


title: diffuse glioma_EORTC 26101_176

description:
tumor_DNA_FFPE
EORTC 26101_176


title: diffuse glioma_EORTC 26101_175

description:
tumor_DNA_FFPE
EORTC 26101_175


title: 107-O


title: genomic DNA from brain 7

description:
structural brain lesion and epilepsy
Sample7


title: 103-R

source_name: Patient 103


title: 103-O


title: diffuse glioma_EORTC 26101_174

description:
tumor_DNA_FFPE
EORTC 26101_174


title: 101-R

source_name: Patient 101


title: genomic DNA from brain 6

description:
structural brain lesion and epilepsy
Sample6


title: genomic DNA from brain 5

description:
structural brain lesion and epilepsy
Sample5


title: PCA.123: prostate_cancer_primary_123


title: 101-O


title: PCA.122: prostate_cancer_primary_122


title: diffuse glioma_EORTC 26101_173

description:
tumor_DNA_FFPE
EORTC 26101_173


title: genomic DNA from brain 3

description:
structural brain lesion and epilepsy
Sample3


title: genomic DNA from brain 4

description:
structural brain lesion and epilepsy
Sample4


title: diffuse glioma_EORTC 26101_169

description:
tumor_DNA_FFPE
EORTC 26101_169


title: human Periosteum-Derived Progenitor Cells group3

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

country: Italy

institute: University of Verona

description:
hPMSCs_3
35±2

data_processing:
Base-calling performed using bcl2fastq2.
Starting from raw FASTQ files, quality of reads obtained from each sample was assessed using FastQC software. Adapters were trimmed and reads with length <18bp or >27bp were filtered out with cutadapt (1.16).
Filtered reads were aligned to the miRBase 21 using SHRiMP2 (2.2.3) with the “mirna” option activated. Mature miRNAs were assigned to the fragments based on the mapping position on the hairpin miRNAs.
The number of unique-UMI mapped reads were counted for each mature miRNA.
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts values for every microRNAs and every sample.

source_name: Periosteum

growth_protocol: Cells were plated in T25 flasks and cultured in a complete culture medium DMEM/F-12  with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (100 U/ml) at 37°C and 5% CO2.

extract_protocol:
Stromal cells were harvested from healthy tissues and characterized according to the minimal criteria established by the International Society for Cellular Therapy (ISCT) for the identification of human mesenchymal stem cells. Total RNA was harvested using Total RNA Purification Kit (Norgen).
350ng RNA for each sample were processed in triplicate with the QiAseq miRNA kit (QIAGEN) according to manufacturer’s instruction for the generation of miRNA-seq libraries. miRNA-seq libraries were assessed by capillary electrophoretic analysis with the Agilent 4200 Tape station  and sequenced with  1X75bp-reads  on an Illumina NextSeq 500 platform.

tag: culture passage

value: Periosteum

tag: primary cell type

value: Mesenchymal stromal stem cells


title: diffuse glioma_EORTC 26101_170

description:
tumor_DNA_FFPE
EORTC 26101_170


title: diffuse glioma_EORTC 26101_171

description:
tumor_DNA_FFPE
EORTC 26101_171


title: diffuse glioma_EORTC 26101_172

description:
tumor_DNA_FFPE
EORTC 26101_172


title: human Periosteum-Derived Progenitor Cells group2

description:
hPMSCs_2
32±2


title: PCA.120: prostate_cancer_primary_120


title: PCA.119: prostate_cancer_primary_119


title: PCA.121: prostate_cancer_primary_121


title: human Periosteum-Derived Progenitor Cells group1

description:
hPMSCs_1
30±3


title: genomic DNA from brain 2

description:
structural brain lesion and epilepsy
Sample2


title: PCA.118: prostate_cancer_primary_118


title: PCA.116: prostate_cancer_primary_116


title: PCA.117: prostate_cancer_primary_117


title: diffuse glioma_EORTC 26101_168

description:
tumor_DNA_FFPE
EORTC 26101_168


title: diffuse glioma_EORTC 26101_167

description:
tumor_DNA_FFPE
EORTC 26101_167


title: PCA.115: prostate_cancer_primary_115


title: genomic DNA from brain 1

description:
structural brain lesion and epilepsy
Sample1


title: human Dental Pulp Stem Cells  group3

description:
hDPCs_3
36±2

source_name: Dental Pulp

value: Dental Pulp


title: human Dental Pulp Stem Cells  group2

description:
hDPCs_2
35±3


title: human Dental Pulp Stem Cells  group1

description:
hDPCs_1
34±2


title: diffuse glioma_EORTC 26101_166

description:
tumor_DNA_FFPE
EORTC 26101_166


title: OCI-Ly10_CU-O75_IC20_12h

city: New York

first: Matko

last: Kalac

state: New York

address: 1 Gustave L Levy Place

department: Tisch Cancer Institute

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Alignment with STARv2.5.3
Gene-level raw counts summarization with STARTv2.5.3 quant-mode
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature generation with limma (R bioconductor package)
Genome_build: GRCh38.v89
Supplementary_files_format_and_content: Tab delimited text output of raw counts from STAR alignment and gene count quantification

source_name: OCI-Ly10 Diffuse Large B Cell Lymphoma

growth_protocol: The cells were grown in logarithmic phase untill treatment

extract_protocol:
RNAs were extracted with using Qiagen Rneasy mini kit
Strand specific sequencing libraries were generated from rRNA depleted total RNAs using the NEBNext® Ultra Directional RNA Library Prep Kit for Illumina

treatment_protocol: All the samples were treated with indicated concentration of drugs for 0, 12 and 24 hours.

tag: cell line

tag: dose

tag: duration


title: OCI-Ly10_CU-O75_IC20_24h

tag: treatment


title: OCI-Ly10_CU-O75_IC20/10_24h


title: PCA.114: prostate_cancer_primary_114

tag: age

tag: igg production


title: PCA.112: prostate_cancer_primary_112


title: OCI-Ly10_CU-O75_IC20/10_12h


title: PCA.113: prostate_cancer_primary_113


title: diffuse glioma_EORTC 26101_164

description:
tumor_DNA_FFPE
EORTC 26101_164

tag: gender


title: diffuse glioma_EORTC 26101_162

description:
tumor_DNA_FFPE
EORTC 26101_162


title: PCA.111: prostate_cancer_primary_111

tag: psa


title: PCA.109: prostate_cancer_primary_109

tag: grade group


title: diffuse glioma_EORTC 26101_163

description:
tumor_DNA_FFPE
EORTC 26101_163


title: PCA.110: prostate_cancer_primary_110

tag: race


title: OCI-Ly10_DMSO_12h

value: DMSO


title: diffuse glioma_EORTC 26101_161

description:
tumor_DNA_FFPE
EORTC 26101_161


title: diffuse glioma_EORTC 26101_160

description:
tumor_DNA_FFPE
EORTC 26101_160


title: diffuse glioma_EORTC 26101_165

description:
tumor_DNA_FFPE
EORTC 26101_165


title: diffuse glioma_EORTC 26101_159

description:
tumor_DNA_FFPE
EORTC 26101_159


title: PCA.107: prostate_cancer_primary_107

tag: non-organ confined


title: 791_NC

data_processing:
Read quality was checked using Fastqc.
Alignment software used was STAR aligner
DEseq2 was used for differential expression analysis
Genome_build: hg19

source_name: liver tissue

extract_protocol:
Total RNA was extracted from four human BA recipient liver and three normal liver allografts using RNeasy Mini Kit (Qiagen, Valencia, CA)
Total RNA libraries were generated using Illumina TruSeq Stranded Total RNA Kit (Illumina, San Diego, CA)

tag: tissue

value: liver

tag: condition

value: Normal


title: 785_NC


title: PCA.108: prostate_cancer_primary_108

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

source_name: FFPE prostate cancer

tag: palsma cell content

tag: inflammation signature

tag: nk activity


title: diffuse glioma_HD_part2_016

tag: subject status

value: patient with glioblastoma

value: male

tag: tissue/sample type


title: 769_NC


title: diffuse glioma_HD_part2_017


title: 789_BA

value: Biliary atresia


title: OCI-Ly10_DMSO_24h

tag: cell line

tag: dose


title: 690_BA


title: diffuse glioma_EORTC 26101_157

description:
tumor_DNA_FFPE
EORTC 26101_157


title: diffuse glioma_EORTC 26101_155

description:
tumor_DNA_FFPE
EORTC 26101_155

value: female


title: PCA.105: prostate_cancer_primary_105

tag: ifng signature


title: 62_BA


title: diffuse glioma_HD_part2_018


title: diffuse glioma_EORTC 26101_156

description:
tumor_DNA_FFPE
EORTC 26101_156


title: diffuse glioma_EORTC 26101_153

description:
tumor_DNA_FFPE
EORTC 26101_153


title: diffuse glioma_EORTC 26101_158

description:
tumor_DNA_FFPE
EORTC 26101_158


title: diffuse glioma_HD_part2_015


title: U2OS cells_untreated_rep4 [WT-4.0]

city: Utrecht

first: Sanne

last: Boersma

state: (None)

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht institute

data_processing:
CEL-seq2 protocol (Hashimshony et al., 2016; Muraro et al., 2016)
Supplementary_files_format_and_content: excell sheet with nr of reads per gene

source_name: U2OS cells_untreated

growth_protocol: Human U2OS were grown in DMEM (4.5 g/L glucose, Gibco) supplemented with 5% fetal bovine serum (Sigma-Aldrich) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Cells were harvested and RNA was isolated using TRISure (Bioline), according to manufacturer’s guidelines.
CEL-seq2 protocol (Hashimshony et al., 2016; Muraro et al., 2016)

treatment_protocol: U2OS cells were seeded at 20% confluency in a 12-wells plate. One day after seeding, cells were incubated with 1000 U/ml IFN for 24h. As control, cells without IFN treatment were processed in parallel.

tag: cell type

tag: treatment

value: untreated


title: U2OS cells_IFNtreated_rep4 [IFN-4.0]

source_name: U2OS cells_IFNtreated

value: 24h 1000 U/ml IFNα2


title: diffuse glioma_EORTC 26101_154

description:
tumor_DNA_FFPE
EORTC 26101_154

tag: gender


title: PCA.101: prostate_cancer_primary_101

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by 2 expert genitourinary pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

tag: age

tag: psa

value: No

tag: igg production


title: PCA.103: prostate_cancer_primary_103

tag: grade group

tag: race

value: Black

tag: non-organ confined


title: HSCs collected from primary recipient [M283]

city: los angeles

first: Du

state: ca

address: 1425 san pablo st bcc 305

department: stem cell

institute: university of southern california

data_processing:
raw fastq files were generated by Illumina bcl2fastq software with default parameters
fastq files of each sample were processed separately using cellranger software (v2.1.0) "cellranger count" with default settings
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 file containing UMI matrix of each gene in each cell

source_name: HSCs collected from primary recipient

extract_protocol: Chromium Single Cell 3’ Library (10X Genomics V2)

tag: strain background

value: adult

tag: tissue

value: bone marrow

value: hematopoietic stem cells


title: HSCs collected from primary recipient [M285]


title: HSCs collected from primary recipient [M284]


title: HSCs collected from primary recipient [M282]


title: diffuse glioma_EORTC 26101_180

description:
tumor_DNA_FFPE
EORTC 26101_180


title: PCA.102: prostate_cancer_primary_102

tag: palsma cell content

tag: inflammation signature

tag: nk activity


title: PCA.104: prostate_cancer_primary_104

value: Yes


title: U2OS cells_untreated_rep1 [WT-3.0]


title: U2OS cells_IFNtreated_rep1 [IFN-3.0]


title: KLF3-OE-72h_rep2

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.6.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each sample

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs were cultured on 0.1% gelatin-coated plates in serum medium and leukemia inhibitory factor (1,000 unit /ml).

extract_protocol:
For RNA-seq,cells were treated with TRIzol and followed with phase seperation, RNA precipitation and RNA wash. Finally, RNA were dissolved in DEPC water.
For RNA-seq, total RNA was subjected to two rounds of purification using poly-T oligo-attached magnetic beads before the synthesis of double-stranded (ds) cDNA. The ds-cDNA was ligated to adaptors and sequenced with illumina Hiseq platform. For low-input KLF3-GFP positive and negative cells, Samrt-seq2 protocol was applied to construct RNA libraries.
RNA-seq and Smart-seq2

treatment_protocol: For KLF3-GFP positive and negative cells, 500 cells was sorted by flow cytometry into mild hypotonic lysis buffer.

tag: genotype

value: Mouse embryonic stem cell

tag: strain

tag: developmental

value: 3.5 days


title: PCA.96: prostate_cancer_primary_96

tag: ifng signature


title: PCA.97: prostate_cancer_primary_97


title: diffuse glioma_EORTC 26101_149

description:
tumor_DNA_FFPE
EORTC 26101_149

data_processing: BeadStudio software v3.2

extract_protocol: Genomic DNA was extracted and pruified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions


title: GFP-OE-72h_rep2

tag: cell type


title: PCA.100: prostate_cancer_primary_100


title: diffuse glioma_EORTC 26101_148

description:
tumor_DNA_FFPE
EORTC 26101_148

tag: gender


title: PCA.99: prostate_cancer_primary_99

tag: age


title: KLF3-OE-72h_rep1


title: PCA.98: prostate_cancer_primary_98

tag: psa


title: diffuse glioma_EORTC 26101_151

description:
tumor_DNA_FFPE
EORTC 26101_151


title: 421_BA

tag: condition


title: diffuse glioma_EORTC 26101_152

description:
tumor_DNA_FFPE
EORTC 26101_152


title: PCA.95: prostate_cancer_primary_95

tag: grade group

tag: igg production


title: GFP-positive_rep1

value: KLF3-GFP positive


title: PCA.106: prostate_cancer_primary_106

tag: race

tag: non-organ confined


title: GFP-OE-72h_rep1


title: GFP-negative_rep2

value: KLF3-GFP negative


title: wildtype [S7]

first: Paul

last: Schimmel

state: California

address: 10550 North Torrey Pines Road, BCC379

department: Molecular Medicine

institute: The Scripps Research Institute

description:
S7
Ribosome footprints
200911_SupplementaryTable4-6.xlsx

data_processing:
Library strategy: Ribo-Seq
Reads were processed as described in Ingolia et al. In brief, adapter sequences were trimmed using Trimgalore and one base on the 5’end was clipped off at the same time (Adapter sequence: CTGTAGGCACCATCAAT).
rRNA reads were mapped out using bowtie and remaining reads were aligned against the human transcriptome (v19 release, Genecode) for pausing analysis or against the hg19 human genome (index downloaded from Hisat2) for differential translation analysis, both with Hisat268.
Codon usage in the A-site of paused ribosomes were identified as described by Ishimura et al. with the following changes: First, bam files were merged and offsets were calculated with functions derived from riboWaltz69. P-sites were mapped for all reads belonging to transcripts with an average of 0.5 reads/codon, again with functionalities derived from riboWaltz. Finally, pause strength P was calculated as a z-score model assuming a poisson distribution of reads, where Z = (read density at codon I – max(background)/(max(background)**0.5) with a custom python script (Scott Adamson, Jeffrey Chuang, UConn, 50). All codons with P≥10 were taken into account. Codons were ranked by how often pausing was observed. For observed/expected, all transcripts with reads were used without minimal criteria for coverage. E, P, and A-sites were mapped, again with functionalities derived from riboWaltz. The frequency of codons in the A-site was compared to the hypothetical frequency of these codons according to their occurrence in the transcriptome (observed/expected) with a custom python script (Scott Adamson, Jeffrey Chuang, The Jackson Laboratory, 50).
Differential ribosomal occupancy was calculated using DESeq2. GO analysis was performed using Panther GO with all genes found in ribosome footprints as background.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: 200911_SupplementaryTable4-6.xlsx

growth_protocol: Ribosome footprinting was performed as described by Ingolia et al. In short, 5 x 10e6 cells seeded 18 hours prior were harvested.

extract_protocol:
RNaseI treated, and polysomes were isolated by ultracentrifugation through a 1 M sucrose gradient at 207,00 x g in a SW55 Ti rotor for 4 hours.
Fragments between 26 and 34 nt were isolated, dephosphorylated, and linkers were added. The isolated RNA was then reverse transcribed, circularized, and sequences derived from ribosomal RNAs depleted. Finally, fragments were amplified, and barcoding sequences were added.

treatment_protocol: gRNA targeted against exon 2 of ArgRS was designed following rules described by Ran et al. pSpCas9(BB)-2A-GFP (PX458) was a gift from Feng Zhang (Addgene plasmid # 48138; http://n2t.net/addgene:48138 ; RRID:Addgene_48138)63. Oligos were ordered from Eton Bioscience and inserted into pSpCas9(BB)-2A-GFP to obtain pSpCas9_gRNA_ex2. The plasmid was transfected into HEK 293T cells using Lipofectamine 2000 and immortalized murine embryonic fibroblasts were transfected with a murine version of the gRNA (pSpCas9_gRNA_mex2) using Calfectin. Positive cells were selected by GFP-expression with the help of the Scripps Research Institute Flow cytometry core facility on a MoFlo Astrios EQ jet-in-air sorting flow cytometer (BD Bioscience). Cells were sorted as single cells into a 96 well plate and expanded. The fastest growing 12 clones (HEK 293T) were picked and ArgRS expression was assessed using Western blot. 4/12 clones were found with truncated ArgRS corresponding to the expected size, one clone was further found with shorter than full-length ArgRS but not corresponding to the expected molecular weight of ΔLZ-ArgRS in HEK 293T cells. 2/17 clones with truncated ArgRS could be isolated from transfected MEF cells. DNA was isolated from clones with the desired ArgRS variant, the sequence flanking the gRNA-induced cutting site was amplified and sequenced using Sanger sequencing (Eton Bioscience). HEK 293T clone #4 was chosen for its defined frameshift inducing mutation while the exact nature of disruption could not be unambiguously assigned for the other clones. The PCR amplified genetic region flanking the gRNA target site was further subcloned into pET_28b for cleaner sequencing results.  gRNA against human RARS1 exon 2: attgaccggttgaaaaactg

tag: cell line

tag: genotype/variation

value: wildtype


title: delta LZ [S8]

description:
S8
Ribosome footprints
200911_SupplementaryTable4-6.xlsx

value: delta LZ


title: delta LZ + LZ_mCerulean [S9]

description:
S9
Ribosome footprints
200911_SupplementaryTable4-6.xlsx

value: delta LZ + LZ_mCerulean


title: delta LZ + LZ_mCerulean [S6]

description:
S6
Ribosome footprints
200911_SupplementaryTable4-6.xlsx


title: GFP-positive_rep2


title: PCA.94: prostate_cancer_primary_94

tag: palsma cell content

tag: inflammation signature


title: PCA.92: prostate_cancer_primary_92

tag: nk activity


title: PCA.93: prostate_cancer_primary_93


title: diffuse glioma_EORTC 26101_150

description:
tumor_DNA_FFPE
EORTC 26101_150

value: male


title: PCA.91: prostate_cancer_primary_91


title: diffuse glioma_EORTC 26101_140

description:
tumor_DNA_FFPE
EORTC 26101_140


title: diffuse glioma_EORTC 26101_146

description:
tumor_DNA_FFPE
EORTC 26101_146

value: female


title: delta LZ [S5]

description:
S5
Ribosome footprints
200911_SupplementaryTable4-6.xlsx


title: wildtype [S4]

description:
S4
Ribosome footprints
200911_SupplementaryTable4-6.xlsx


title: diffuse glioma_EORTC 26101_145

description:
tumor_DNA_FFPE
EORTC 26101_145


title: P7_Input_ChIP

city: Adelaide

first: Dale

last: McAninch

state: SA

address: North Terrace

country: Australia

institute: The University of Adelaide

data_processing:
Reads were aligned by Bowtie (V2.0.0), with options -n 2 -m 1, against mouse genome build mm9
Peaks were called for each biological replicate using MACS (V1.4.2), bandwidth of 300, a model fold of 10–30, using input sample as background control, and a p-value threshold of 1e-5.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP peak files in BED file format, with mm9 genomic coordinates of each peak

source_name: testis

extract_protocol:
Mixed background (129 sv/eV, MF1, CBA and C57Bl/6) Sox3 null mice were crossed onto the 129/SvJ genetic background and mice from the F6 generation were used. P7 testes were discected and mechanically dissociated into small fragments before fixation in 1% formaldehyde for 8 minutes at room temperature. Fixed tissue was lysed and sonicated (Bioruptor, Diagenode) for 15 minutes in 1-minute pulses on ice. SOX3 bound chromatin was immunoprecipitated by a goat polyclonal antibody raised against human SOX3 (R&D systems, AF2569). DNA was recovered by reversing crosslinks, and purified by PCR clean-up kit (QIAGEN). Three independent DNA libraries were produced with the KAPA HTP/LTP Library Preparation Kit as per manufacturer's instructions, and libraries were sequenced on the Illumina HiSeq producing 50 bp single end reads.
Libraries were prepared according to KAPA HTP/LTP Library Preparation Kits instruction manual (KK8230)

tag: strain

tag: tissue

value: testis

tag: chip antibody

value: none (input)


title: diffuse glioma_EORTC 26101_147

description:
tumor_DNA_FFPE
EORTC 26101_147

source_name: diffuse glioma IDH wt


title: GFP-negative_rep1

tag: genotype

tag: cell type

tag: developmental


title: P7_Testes_ChIP_Biol_3

tag: age

value: R&D hSOX3 (AF2569)


title: P7_Testes_ChIP_Biol_2


title: delta LZ [S2]

description:
S2
Ribosome footprints
200911_SupplementaryTable4-6.xlsx


title: PCA.89: prostate_cancer_primary_89

first: Elai

address: 1152 Mainland St, Suite 430

institute: Decipher Biosciences, Inc.

tag: psa

value: Black

tag: ifng signature


title: PCA.88: prostate_cancer_primary_88

tag: grade group

value: No

tag: igg production


title: diffuse glioma_EORTC 26101_142

description:
tumor_DNA_FFPE
EORTC 26101_142

tag: gender


title: PCA.90: prostate_cancer_primary_90

tag: race

tag: non-organ confined


title: wildtype [S1]

description:
S1
Ribosome footprints
200911_SupplementaryTable4-6.xlsx

tag: cell line

tag: genotype/variation


title: diffuse glioma_EORTC 26101_144

description:
tumor_DNA_FFPE
EORTC 26101_144


title: P7_Testes_ChIP_Biol_1


title: Cohort2_B_Patient19

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

data_processing:
Reads were mapped to the GRCh38.p10 Ensembl human genome using STAR v.2.5.2a with default parameters.
Cohort 1 and 2 were analyzed indenpendetly of one another. Genes with less than 10 raw counts in all conditions were excluded from the analysis to sort out lowly expressed genes.
Reads per kilobase million (RPKM) values were calculated and can be found in the processed data files.
Genome_build: GRCh38
Supplementary_files_format_and_content: Table with gene expression levels in excel format

source_name: Gut

extract_protocol:
Laser capture microdissection - please refer to paper for further details.
Illumina TruSeq Stranded mRNA Library Prep kit (#20020594, Illumina, San Diego, CA, USA)

tag: gut segment type

value: Biliopancreatic limb

tag: patient


title: diffuse glioma_EORTC 26101_143

description:
tumor_DNA_FFPE
EORTC 26101_143


title: diffuse glioma_EORTC 26101_141

description:
tumor_DNA_FFPE
EORTC 26101_141


title: PCA.87: prostate_cancer_primary_87

city: Vancouver

last: Davicioni

tag: palsma cell content

tag: inflammation signature

tag: nk activity


title: diffuse glioma_EORTC 26101_137

description:
tumor_DNA_FFPE
EORTC 26101_137


title: Cohort2_A_Patient17

value: Alimentary limb


title: PCA.85: prostate_cancer_primary_85

value: Yes


title: diffuse glioma_EORTC 26101_138

description:
tumor_DNA_FFPE
EORTC 26101_138


title: diffuse glioma_EORTC 26101_136

description:
tumor_DNA_FFPE
EORTC 26101_136


title: Cohort2_P_Patient26

value: Perioperative


title: Cohort2_C_Patient22

value: Common channel


title: diffuse glioma_EORTC 26101_139

description:
tumor_DNA_FFPE
EORTC 26101_139


title: PCA.84: prostate_cancer_primary_84


title: diffuse glioma_EORTC 26101_135

description:
tumor_DNA_FFPE
EORTC 26101_135


title: PCA.86: prostate_cancer_primary_86


title: Cohort2_C_Patient3


title: PCA.82: prostate_cancer_primary_82


title: PCA.83: prostate_cancer_primary_83


title: Positive DIF rep3

city: yokohama

first: Kinuka

last: Ohtaka

address: 1-7-22, suehiro-cho

country: Japan

institute: RIKEN

description: Gene expression without negative DIF 7 days

hyb_protocol: Hybridization was performed according to the manual of the Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

scan_protocol: We scanned tomato custom-designed microarray images with Agilent DNA Microarray Scanner G2565CA (Agilent Technologies).

data_processing: Scanned microarray images were converted to signal data with Feature Extraction software (Agilent Technologies).

organism: Solanum lycopersicum

source_name: Control high temperature

label_protocol: Target labeling was performed according to the manual of the Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

growth_protocol: Germination of Tomato (Solanum lycopersicum) seeds begun with absorption of water in dish at 28 ˚C under dark for 2 days. After imbibition, germinated seeds were picked up and were transferred to rock wool, which were cultivated in distilled water at 23°C/23°C (day temperature/night temperature, 16 h photoperiod) under 130 to 140 µmol photons m-2 s-1 of light for 5 days.

extract_protocol: Total RNA samples were prepared using Rneasy Plant Mini Kit (QIAGEN) following the manufacture's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Young sprouts of S. lycopersicum (fully opened cotyledon) were cultivated for 7 d in 30°C/25°C (+DIF) versus 25°C/30°C (-DIF) (DT/NT, 16 h photoperiod) under 300 µmol photons m-2 s-1.

tag: tissue

value: Epicotyl


title: Cohort2_A_Patient2


title: diffuse glioma_EORTC 26101_132

first: Tobias

address: Im Neuenheimer Feld 280

institute: DKFZ

description:
tumor_DNA_FFPE
EORTC 26101_132


title: diffuse glioma_EORTC 26101_133

description:
tumor_DNA_FFPE
EORTC 26101_133


title: Positive DIF rep1


title: Cohort2_P_Patient27


title: PCA.81: prostate_cancer_primary_81


title: diffuse glioma_EORTC 26101_134

description:
tumor_DNA_FFPE
EORTC 26101_134


title: diffuse glioma_EORTC 26101_131

description:
tumor_DNA_FFPE
EORTC 26101_131


title: Cohort2_C_Patient23


title: Negative DIF rep2

description: Gene expression after negative DIF 7 days

source_name: High temperature at night


title: diffuse glioma_EORTC 26101_129

description:
tumor_DNA_FFPE
EORTC 26101_129


title: diffuse glioma_EORTC 26101_130

description:
tumor_DNA_FFPE
EORTC 26101_130


title: m3_CTAL_a

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
For renal tubule RNA-seq, the sequencing reads were mapped to Ensembl Release 94 genome using STAR-2.5.4a.  For single-cell RNA-seq, the raw sequencing reads were mapped to Ensembl Release 96 using cellranger 3.0.2.
Transcript abundances in TPM were calculated by rsem 1.3.0. Single-cell RNA-seq data was processed by cellranger followed by SoupX and Seurat

source_name: CTAL

growth_protocol: Pathogen-free male C57BL/6 had free access to ad libitum drinking water and normal rodent chow before experiment.

extract_protocol: Total RNA was extracted using the Direct-zol(tm) RNA Kits (Zymo Research) and cDNA was synthesized by SMARTer V4 Ultra Low RNA kit (Clontech). The cDNA was then purified by AmPure XP magnetic beads (Beckman Coulter Genomics). The Nextera XT DNA Library Preparation Kits (Illumina) was used to generate the libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Kidney

tag: tissue preparation

value: Microdissected renal tubule

tag: Sex

value: 6-8 weeks


title: Negative DIF rep3

tag: age


title: m2_CTAL_a


title: Cohort2_B_Patient21


title: m3_CTAL_b


title: delta LZ + LZ_mCerulean [S3]

city: La Jolla

description:
S3
Ribosome footprints
200911_SupplementaryTable4-6.xlsx

value: delta LZ + LZ_mCerulean


title: PCA.80: prostate_cancer_primary_80

tag: psa

tag: grade group

tag: ifng signature


title: Negative DIF rep1


title: Cohort2_A_Patient21


title: PCA.79: prostate_cancer_primary_79

tag: race

tag: igg production


title: m4_CTAL_a

value: male


title: Positive DIF rep2


title: PCA.77: prostate_cancer_primary_77

tag: non-organ confined


title: PCA.78: prostate_cancer_primary_78


title: m4_CTAL_b


title: diffuse glioma_EORTC 26101_127

city: Heidelberg

last: Kessler

description:
tumor_DNA_FFPE
EORTC 26101_127

tag: gender


title: PCA.76: prostate_cancer_primary_76


title: Cohort2_B_Patient15

tag: gut segment type


title: Cohort2_C_Patient27

tag: patient


title: diffuse glioma_EORTC 26101_126

description:
tumor_DNA_FFPE
EORTC 26101_126


title: m5_CTAL_b


title: diffuse glioma_EORTC 26101_128

description:
tumor_DNA_FFPE
EORTC 26101_128


title: PCA.75: prostate_cancer_primary_75

tag: palsma cell content


title: Cohort2_B_Patient26


title: Cohort2_P_Patient19


title: Cohort2_A_Patient23_2


title: Cohort2_P_Patient21


title: PCA.74: prostate_cancer_primary_74

tag: inflammation signature


title: m2_PTS2_a


title: PCA.73: prostate_cancer_primary_73

tag: nk activity


title: m1_PTS2_a

tag: tissue


title: diffuse glioma_EORTC 26101_124

description:
tumor_DNA_FFPE
EORTC 26101_124

value: female


title: diffuse glioma_EORTC 26101_125

description:
tumor_DNA_FFPE
EORTC 26101_125


title: m3_PTS2_a

tag: strain


title: m1_CCD_a

source_name: CCD

tag: tissue preparation


title: Cohort2_C_Patient19


title: Cohort2_A_Patient20


title: diffuse glioma_EORTC 26101_123

description:
tumor_DNA_FFPE
EORTC 26101_123


title: PCA.71: prostate_cancer_primary_71


title: m5_CTAL_a

tag: Sex


title: PCA.72: prostate_cancer_primary_72

tag: age


title: PCA.70: prostate_cancer_primary_70

tag: psa


title: PCA.69: prostate_cancer_primary_69

tag: grade group


title: diffuse glioma_EORTC 26101_119

description:
tumor_DNA_FFPE
EORTC 26101_119


title: m3_PTS2_b


title: PCA.68: prostate_cancer_primary_68

tag: ifng signature


title: diffuse glioma_EORTC 26101_122

description:
tumor_DNA_FFPE
EORTC 26101_122


title: Cohort2_B_Patient17


title: m4_PTS2_b


title: Cohort2_P_Patient23


title: diffuse glioma_EORTC 26101_121

description:
tumor_DNA_FFPE
EORTC 26101_121


title: m5_PTS2_a


title: m4_PTS2_a


title: Cohort2_A_Patient27


title: m5_PTS2_b


title: PCA.66: prostate_cancer_primary_66

tag: race


title: Cohort2_C_Patient21


title: Cohort2_B_Patient20


title: PCA.67: prostate_cancer_primary_67

tag: igg production


title: PCA.64: prostate_cancer_primary_64

tag: non-organ confined


title: PCA.65: prostate_cancer_primary_65


title: m2_CCD_a


title: Cohort2_A_Patient19


title: diffuse glioma_EORTC 26101_116

description:
tumor_DNA_FFPE
EORTC 26101_116

tag: gender


title: m3_CCD_a


title: Cohort2_P_Patient4

tag: gut segment type


title: diffuse glioma_EORTC 26101_117

description:
tumor_DNA_FFPE
EORTC 26101_117


title: diffuse glioma_EORTC 26101_120

description:
tumor_DNA_FFPE
EORTC 26101_120


title: diffuse glioma_EORTC 26101_114

description:
tumor_DNA_FFPE
EORTC 26101_114


title: diffuse glioma_EORTC 26101_118

description:
tumor_DNA_FFPE
EORTC 26101_118


title: Cohort2_C_Patient26

tag: patient


title: diffuse glioma_EORTC 26101_115

description:
tumor_DNA_FFPE
EORTC 26101_115


title: m3_CCD_b


title: m4_CCD_b


title: Cohort2_B_Patient23


title: m5_CCD_a


title: diffuse glioma_EORTC 26101_111

description:
tumor_DNA_FFPE
EORTC 26101_111


title: Cohort2_A_Patient22


title: PCA.63: prostate_cancer_primary_63

tag: palsma cell content


title: m5_CCD_b


title: diffuse glioma_EORTC 26101_113

description:
tumor_DNA_FFPE
EORTC 26101_113


title: PCA.61: prostate_cancer_primary_61

tag: inflammation signature


title: PCA.60: prostate_cancer_primary_60

tag: nk activity


title: Cohort2_C_Patient17


title: PCA.59: prostate_cancer_primary_59


title: diffuse glioma_EORTC 26101_110

description:
tumor_DNA_FFPE
EORTC 26101_110


title: m1_PTS1_a

tag: tissue


title: PCA.56: prostate_cancer_primary_56


title: diffuse glioma_EORTC 26101_112

description:
tumor_DNA_FFPE
EORTC 26101_112


title: Cohort2_A_Patient23


title: PCA.58: prostate_cancer_primary_58


title: m1_CTAL_a

tag: strain


title: Cohort2_B_Patient27


title: m1_PTS1_b

tag: tissue preparation


title: m2_PTS1_a

tag: Sex


title: diffuse glioma_EORTC 26101_106

description:
tumor_DNA_FFPE
EORTC 26101_106


title: Cohort2_C_Patient20


title: diffuse glioma_EORTC 26101_108

description:
tumor_DNA_FFPE
EORTC 26101_108


title: Cohort2_P_Patient22


title: PCA.55: prostate_cancer_primary_55

tag: age


title: m2_PTS1_b


title: Cohort2_P_Patient17


title: m1_GL_a

source_name: Glomerulus


title: diffuse glioma_EORTC 26101_104

description:
tumor_DNA_FFPE
EORTC 26101_104


title: diffuse glioma_EORTC 26101_103

description:
tumor_DNA_FFPE
EORTC 26101_103


title: PCA.54: prostate_cancer_primary_54

tag: psa


title: PCA.53: prostate_cancer_primary_53

tag: grade group


title: Cohort2_C_Patient10


title: Cohort2_B_Patient9


title: diffuse glioma_EORTC 26101_105

description:
tumor_DNA_FFPE
EORTC 26101_105


title: m2_GL_a


title: diffuse glioma_EORTC 26101_102

description:
tumor_DNA_FFPE
EORTC 26101_102


title: diffuse glioma_EORTC 26101_101

description:
tumor_DNA_FFPE
EORTC 26101_101


title: PCA.52: prostate_cancer_primary_52

tag: ifng signature


title: Cohort2_A_Patient8


title: PCA.51: prostate_cancer_primary_51

tag: race


title: m2_GL_b


title: m1_GL_b