title: Hepatocellular Carcinoma HC0264

description:
Hepatocellular Carcinoma
SH5X511_Cell1


title: Hepatocellular Carcinoma HC0277

status: Public on Oct 23 2018

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

description:
Hepatocellular Carcinoma
SH5X514_Cell2

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: tumor stage (figo)

tag: age

value: uncertain


title: Hepatocellular Carcinoma HC0234

description:
Hepatocellular Carcinoma
SH5X155_Cell3


title: Hepatocellular Carcinoma HC0212

description:
Hepatocellular Carcinoma
SH5X148_Cell1


title: Hepatocellular Carcinoma HC0221

description:
Hepatocellular Carcinoma
SH5X152_Cell2


title: Hepatocellular Carcinoma HC0206

description:
Hepatocellular Carcinoma
SH5X145_Cell2


title: Hepatocellular Carcinoma HC0219

description:
Hepatocellular Carcinoma
SH5YL19_Cell3


title: Hepatocellular Carcinoma HC0201

description:
Hepatocellular Carcinoma
SH55T64_Cell1


title: Hepatocellular Carcinoma HC0199

description:
Hepatocellular Carcinoma
SH55T63_Cell3


title: Hepatocellular Carcinoma HC0220

description:
Hepatocellular Carcinoma
SH5X152_Cell1


title: Hepatocellular Carcinoma HC0218

description:
Hepatocellular Carcinoma
SH5X151_Cell3


title: Hepatocellular Carcinoma HC0190

description:
Hepatocellular Carcinoma
SH55T58_Cell2


title: Hepatocellular Carcinoma HC0184

description:
Hepatocellular Carcinoma
SH55T55_Cell4


title: Hepatocellular Carcinoma HC0197

description:
Hepatocellular Carcinoma
SH55T63_Cell1


title: Hepatocellular Carcinoma HC0295

description:
Hepatocellular Carcinoma
SH5X519_Cell4


title: Hepatocellular Carcinoma HC0166

description:
Hepatocellular Carcinoma
SH56965_Cell1


title: Hepatocellular Carcinoma HC0167

description:
Hepatocellular Carcinoma
SH56965_Cell2


title: Hepatocellular Carcinoma HC0270

description:
Hepatocellular Carcinoma
SH5X512_Cell3


title: Hepatocellular Carcinoma HC0165

description:
Hepatocellular Carcinoma
SH56964_Cell4


title: Hepatocellular Carcinoma HC0254

description:
Hepatocellular Carcinoma
SH5X507_Cell3


title: Hepatocellular Carcinoma HC0173

description:
Hepatocellular Carcinoma
SH56966_Cell2


title: Hepatocellular Carcinoma HC0161

description:
Hepatocellular Carcinoma
SH56964_Cell3


title: Hepatocellular Carcinoma HC0163

description:
Hepatocellular Carcinoma
SH55T43_Cell3


title: Hepatocellular Carcinoma HC0162

description:
Hepatocellular Carcinoma
SH55T43_Cell2


title: Hepatocellular Carcinoma HC0158

description:
Hepatocellular Carcinoma
SH55T41_Cell2


title: Hepatocellular Carcinoma HC0153

description:
Hepatocellular Carcinoma
SH56963_Cell2


title: Hepatocellular Carcinoma HC0157

description:
Hepatocellular Carcinoma
SH55T41_Cell1


title: Hepatocellular Carcinoma HC0129

description:
Hepatocellular Carcinoma
SH55T31_Cell1


title: Hepatocellular Carcinoma HC0127

description:
Hepatocellular Carcinoma
SH55T28_Cell3


title: Hepatocellular Carcinoma HC0139

description:
Hepatocellular Carcinoma
SH55T35_Cell3


title: Hepatocellular Carcinoma HC0145

description:
Hepatocellular Carcinoma
SH55T37_Cell1


title: Hepatocellular Carcinoma HC0111

description:
Hepatocellular Carcinoma
SH55T24_Cell3


title: Hepatocellular Carcinoma HC0070

description:
Hepatocellular Carcinoma
SH54N45_Cell2


title: Hepatocellular Carcinoma HC0100

description:
Hepatocellular Carcinoma
SH54N58_Cell4


title: Hepatocellular Carcinoma HC0105

description:
Hepatocellular Carcinoma
SH55T23_Cell1


title: Hepatocellular Carcinoma HC0144

description:
Hepatocellular Carcinoma
SH55T36_Cell4


title: Hepatocellular Carcinoma HC0096

description:
Hepatocellular Carcinoma
SH54N57_Cell4


title: Hepatocellular Carcinoma HC0083

description:
Hepatocellular Carcinoma
SH54N54_Cell3


title: Hepatocellular Carcinoma HC0091

description:
Hepatocellular Carcinoma
SH54N56_Cell3


title: Hepatocellular Carcinoma HC0077

description:
Hepatocellular Carcinoma
SH54N53_Cell1


title: Hepatocellular Carcinoma HC0067

description:
Hepatocellular Carcinoma
SH54N44_Cell3


title: Hepatocellular Carcinoma HC0066

description:
Hepatocellular Carcinoma
SH54N44_Cell2


title: Hepatocellular Carcinoma HC0062

description:
Hepatocellular Carcinoma
SH54N43_Cell2


title: Hepatocellular Carcinoma HC0092

description:
Hepatocellular Carcinoma
SH54N56_Cell4


title: Hepatocellular Carcinoma HC0057

description:
Hepatocellular Carcinoma
SH54N41_Cell1


title: Hepatocellular Carcinoma HC0060

description:
Hepatocellular Carcinoma
SH54N41_Cell4


title: Hepatocellular Carcinoma HC0056

description:
Hepatocellular Carcinoma
SH54N40_Cell4


title: Hepatocellular Carcinoma HC0160

description:
Hepatocellular Carcinoma
SH56964_Cell2


title: Hepatocellular Carcinoma HC0053

description:
Hepatocellular Carcinoma
SH54N40_Cell1


title: Hepatocellular Carcinoma HC0048

description:
Hepatocellular Carcinoma
SH54N37_Cell4


title: Hepatocellular Carcinoma HC0041

description:
Hepatocellular Carcinoma
SH54N36_Cell1


title: Hepatocellular Carcinoma HC0040

description:
Hepatocellular Carcinoma
SH54N35_Cell4


title: Hepatocellular Carcinoma HC0038

description:
Hepatocellular Carcinoma
SH54N35_Cell2


title: Hepatocellular Carcinoma HC0037

description:
Hepatocellular Carcinoma
SH54N35_Cell1


title: Hepatocellular Carcinoma HC0035

description:
Hepatocellular Carcinoma
SH54N34_Cell3


title: Hepatocellular Carcinoma HC0029

description:
Hepatocellular Carcinoma
SH54N33_Cell1


title: Hepatocellular Carcinoma HC0025

description:
Hepatocellular Carcinoma
SH54N32_Cell1


title: Hepatocellular Carcinoma HC0023

description:
Hepatocellular Carcinoma
SH54N30_Cell3


title: Hepatocellular Carcinoma HC0024

description:
Hepatocellular Carcinoma
SH54N30_Cell4


title: Hepatocellular Carcinoma HC0007

description:
Hepatocellular Carcinoma
SH54N26_Cell3


title: Gastric Cancer GC1471

description:
Gastric Cancer
SH63Q18_Cell1


title: Hepatocellular Carcinoma HC0018

description:
Hepatocellular Carcinoma
SH54N29_Cell2


title: Hepatocellular Carcinoma HC0017

description:
Hepatocellular Carcinoma
SH54N29_Cell1


title: Gastric Cancer GC1444

description:
Gastric Cancer
SH63Q09_Cell2


title: Gastric Cancer GC1460

description:
Gastric Cancer
SH63Q15_Cell2


title: Gastric Cancer GC1469

description:
Gastric Cancer
SH63Q17_Cell3


title: Gastric Cancer GC1465

description:
Gastric Cancer
SH63Q16_Cell3


title: Gastric Cancer GC1453

description:
Gastric Cancer
SH63Q12_Cell3


title: Gastric Cancer GC1451

description:
Gastric Cancer
SH63Q12_Cell1


title: Hepatocellular Carcinoma HC0031

description:
Hepatocellular Carcinoma
SH54N33_Cell3


title: Gastric Cancer GC1443

description:
Gastric Cancer
SH63Q09_Cell1


title: Gastric Cancer GC1430

description:
Gastric Cancer
SH63Q04_Cell4


title: Hepatocellular Carcinoma HC0005

description:
Hepatocellular Carcinoma
SH54N26_Cell1


title: Gastric Cancer GC1435

description:
Gastric Cancer
SH63Q06_Cell1


title: Gastric Cancer GC1446

description:
Gastric Cancer
SH63Q09_Cell4


title: Gastric Cancer GC1439

description:
Gastric Cancer
SH63Q08_Cell1


title: Gastric Cancer GC1436

description:
Gastric Cancer
SH63Q06_Cell2


title: Gastric Cancer GC1414

description:
Gastric Cancer
SH63P63_Cell4


title: Gastric Cancer GC1422

description:
Gastric Cancer
SH63Q02_Cell4


title: Gastric Cancer GC1408

description:
Gastric Cancer
SH63P62_Cell2


title: Gastric Cancer GC1420

description:
Gastric Cancer
SH63Q02_Cell2


title: Hepatocellular Carcinoma HC0008

description:
Hepatocellular Carcinoma
SH54N26_Cell4


title: Hepatocellular Carcinoma HC0019

description:
Hepatocellular Carcinoma
SH54N29_Cell3


title: Gastric Cancer GC1405

description:
Gastric Cancer
SH63P61_Cell3


title: Gastric Cancer GC1402

description:
Gastric Cancer
SH63W52_Cell2


title: Gastric Cancer GC1432

description:
Gastric Cancer
SH63Q05_Cell2


title: Gastric Cancer GC1397

description:
Gastric Cancer
SH63P58_Cell3


title: Gastric Cancer GC1388

description:
Gastric Cancer
SH63P54_Cell2


title: Gastric Cancer GC1387

description:
Gastric Cancer
SH63P54_Cell1


title: Gastric Cancer GC1391

description:
Gastric Cancer
SH63P55_Cell1


title: Gastric Cancer GC1378

description:
Gastric Cancer
SH63P51_Cell4


title: Gastric Cancer GC1385

description:
Gastric Cancer
SH63P53_Cell3


title: Gastric Cancer GC1380

description:
Gastric Cancer
SH63P52_Cell2


title: Gastric Cancer GC1368

description:
Gastric Cancer
SH63P49_Cell2


title: Gastric Cancer GC1369

description:
Gastric Cancer
SH63P49_Cell3


title: Gastric Cancer GC1410

description:
Gastric Cancer
SH63P62_Cell4


title: Gastric Cancer GC1373

description:
Gastric Cancer
SH63P50_Cell3


title: Gastric Cancer GC1356

description:
Gastric Cancer
SH63P34_Cell1


title: Gastric Cancer GC1352

description:
Gastric Cancer
SH63P33_Cell1


title: Gastric Cancer GC1374

description:
Gastric Cancer
SH63P50_Cell4


title: Gastric Cancer GC1401

description:
Gastric Cancer
SH63P60_Cell3


title: Gastric Cancer GC1371

description:
Gastric Cancer
SH63P50_Cell1


title: Gastric Cancer GC1359

description:
Gastric Cancer
SH63P34_Cell4


title: Gastric Cancer GC1367

description:
Gastric Cancer
SH63P49_Cell1


title: Gastric Cancer GC1351

description:
Gastric Cancer
SH63P29_Cell4


title: Gastric Cancer GC1349

description:
Gastric Cancer
SH63P29_Cell2


title: Glu3

type: SRA

city: Kgs. Lyngby

first: Isotta

last: D'Arrigo

address: Kemitorvet

country: Denmark

institute: Technical University of Denmark

library_source: transcriptomic

data_processing:
Sequenced reads received from Beckman were already cut out from adapters.
The sequencing reads were checked for quality by evaluation of the average quality per reads Phred score.
For each sample the reads deriving from the two sequencing runs were merged. Then reads were mapped onto the P. putida KT2440 genome (RefSeq Accession No. NC_002947.3) with Bowtie2 by Rockhopper 2.0.3 software.
RPKM gene counts from Rockhopper analysis were used for differential expression analysis with the T-REx pipeline.
Genes were considered differentially expressed when they exhibited a P-value ≤ 0.05 and fold change greater than or equal to 2.
Genome_build: Pseudomonas putida KT2440 (RefSeq Accession No. NC_002947.3).
Supplementary_files_format_and_content: txt files including total gene reads, RPKM values etc. for each sample.

organism: Pseudomonas putida KT2440

source_name: Pseudomonas putida

growth_protocol: Pseudomonas putida strain KT2440 was cultivated in M9 minimal medium (10X solution: Na2HPO4·12H2O, 70 g/L; KH2PO4, 30 g/L; NH4Cl, 10 g/L; NaCl, 5 g/L) supplemented with ammonium iron citrate, magnesium sulfate, and trace metals (per liter: H3BO3, 300 mg; ZnCl2, 50 mg; MnCl2·4H2O, 30 mg; CoCl2, 200 mg; CuCl2·2H2O, 10 mg; NiCl2·6H2O, 20 mg; and NaMoO4·2H2O, 30 mg). Bacteria were grown in one of the chosen carbon sources: glucose (0.5% (w/v)), sodium citrate (10 mM), ferulic acid (10 mM), or serine (10 mM). Single colonies isolated from LB agar plates containing 25 µg/mL chloramphenicol and grown overnight at 30°C, were inoculated in 5 mL M9 medium. The overnight cultures were diluted to a starting OD600 of 0.01 (for ferulic acid and serine) and 0.1 (for glucose and sodium citrate) in 100 mL M9 medium in 250 mL Erlenmeyer flasks. All liquid cultures were grown at 30°C with vigorous shaking at 250 rpm.

extract_protocol:
Total RNA extraction and DNase I treatment for DNA removal were performed as described elsewhere (ref. 26 of the text). The integrity of total RNA, and DNA contamination were assessed with a RNA 6000 Nano chip on the Agilent 2100 Bioanalyzer (Agilent Technologies). Total RNA was extracted from three biological replicate cultures for each condition.
Sequencing libraries were constructed using the Illumina® TruSeq® Stranded mRNA Sample Preparation kit. The libraries were sequenced twice on the Illumina HiSeq2000 platform (Beckman Coulter Genomics), 100 bp, single-end.

treatment_protocol: P. putida KT2440 cells were harvested in mid-exponential phase, corresponding to OD600 ~ 0.6 for glucose, OD600 ~ 0.4 for citrate, OD600 ~ 0.3-0.4 for ferulic acid, and OD600 ~ 0.15-0.2 for serine. Cell harvest was performed by transferring 20 mL of each culture into 50-mL Falcon tubes containing 4 mL of stop solution (5% phenol in 95% ethanol, 4°C), vortexing for 15 sec and incubation on ice for 5 min. After centrifugation (3500 g, 10 min, 4°C) in a Multifuge X3 Fr centrifuge (Thermo Scientific), the supernatant was removed and the pellet was frozen in liquid nitrogen and stored at -80°C.

tag: strain

tag: carbon source

value: Growth in glucose

tag: growth phase

value: Mid-exponential phase


title: Ser1

value: Growth in serine


title: Glu2


title: Gastric Cancer GC1348

description:
Gastric Cancer
SH63P29_Cell1


title: Gastric Cancer GC1377

description:
Gastric Cancer
SH63P51_Cell3


title: Gastric Cancer GC1347

description:
Gastric Cancer
SH63P27_Cell4


title: Gastric Cancer GC1383

description:
Gastric Cancer
SH63P53_Cell1


title: Fer3

value: Growth in ferulic acid


title: Glu1


title: Fer2


title: Gastric Cancer GC1344

description:
Gastric Cancer
SH63P27_Cell1


title: Ser3


title: Gastric Cancer GC1337

description:
Gastric Cancer
SH63P24_Cell2


title: Gastric Cancer GC1342

description:
Gastric Cancer
SH63P26_Cell3


title: Cit1

value: Growth in citrate


title: Gastric Cancer GC1338

description:
Gastric Cancer
SH63P24_Cell3


title: Gastric Cancer GC1339

description:
Gastric Cancer
SH63W51_Cell4


title: Ser2


title: Cit3


title: Fer1


title: Gastric Cancer GC1336

description:
Gastric Cancer
SH63P24_Cell1


title: Gastric Cancer GC1340

description:
Gastric Cancer
SH63P26_Cell1


title: Snu114-8h-rep3

city: Manchester

first: Huw

middle: Batten

last: Thomas

state: Greater Manchester

address: Dover Street

department: Biological Sciences

country: United Kingdom

institute: University of Manchester

description:
Snu1_14-8h-12-14-16_S6
Mat α; his3△1; leu2△0; met15△0; lys2△0; ura3△0; PGAL1- YKL173w

data_processing:
Files were quality controlled using FastQ Screen
3' end trimming performed by Trimmomatic
Rerads mapped to S.cerevisiae using STAR aligner, mapping reads in pairs and using only uniqely mapped reads.
Mapped read counts produced using htseq-count against saccharomyces_cerevisiae.gff counting against gene regions and also intron regions
Differential expression carried out by DESeq2
Genome_build: sacCer3 (April 2011)
Supplementary_files_format_and_content: Tab de-limited excel spreadsheet for intron and exon expression values and treatments across all genes in yeast transcriptome

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD or YPGal for up to 8h

extract_protocol:
Total RNA was extracted using RiboPure Yeast RNA extraction kit (Ambion), and purified using Rneasy column purification kit (Qiagen), including a Dnase digestion step.
Quality and integrity of the RNA samples were assessed using a 2200 TapeStation (Agilent Technologies) and then libraries generated using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (0.1-4ug) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. The mRNA was then fragmented using divalent cations under elevated temperature and then reverse transcribed into first strand cDNA using random primers. Second strand cDNA was then synthesised using DNA Polymerase I and RNase H. Following a single 'A' base addition, adapters were ligated to the cDNA fragments, and the products then purified and enriched by PCR to create the final cDNA library. Adapter indices were used to multiplex libraries, which were pooled prior to paired-end sequencing (151:151 plus indices) on an Illumina NextSeq500 platform using a NextSeq 500/550 High Output Kit. Finally, the output data was demultiplexed (allowing one mismatch) and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.17.1.14

tag: strain background

tag: genotype/variation

value: Mat alpha; his3{delta}1; leu2{delta}0; met15{delta}0; lys2{delta}0; ura3{delta}0; PGAL1- YKL173w

tag: culture condition

value: Cultured in YPD for 8h


title: Gastric Cancer GC1330

description:
Gastric Cancer
SH63P22_Cell3


title: Snu114-8h-rep2

description:
S8-13B_S18
Mat α; his3△1; leu2△0; met15△0; lys2△0; ura3△0; PGAL1- YKL173w


title: Snu114-8h-rep1

description:
S8-13A_S12
Mat α; his3△1; leu2△0; met15△0; lys2△0; ura3△0; PGAL1- YKL173w


title: Gastric Cancer GC1324

description:
Gastric Cancer
SH63W51_Cell2


title: Gastric Cancer GC1323

description:
Gastric Cancer
SH63W51_Cell1


title: Gastric Cancer GC1333

description:
Gastric Cancer
SH63P23_Cell2


title: Snu114-6h-rep2

description:
S6-13B_S17
Mat α; his3△1; leu2△0; met15△0; lys2△0; ura3△0; PGAL1- YKL173w

value: Cultured in YPGal for 6h


title: Gastric Cancer GC1329

description:
Gastric Cancer
SH63P22_Cell2


title: Snu114-6h-rep3

description:
Snu1_14-6h-12-4-16_S5
Mat α; his3△1; leu2△0; met15△0; lys2△0; ura3△0; PGAL1- YKL173w


title: Snu114-6h-rep1

description:
S6-13A_S11
Mat α; his3△1; leu2△0; met15△0; lys2△0; ura3△0; PGAL1- YKL173w


title: Snu114-4h-rep3

description:
Snu1_14-4h-12-4-16_S4
Mat α; his3△1; leu2△0; met15△0; lys2△0; ura3△0; PGAL1- YKL173w

value: Cultured in YPD for 4h


title: Gastric Cancer GC1321

description:
Gastric Cancer
SH63P20_Cell2


title: Gastric Cancer GC1317

description:
Gastric Cancer
SH63P19_Cell2


title: Cit2


title: Gastric Cancer GC1315

description:
Gastric Cancer
SH63P18_Cell4


title: Gastric Cancer GC1314

description:
Gastric Cancer
SH63P18_Cell3


title: Snu114-4h-rep2

description:
S4-13B_S16
Mat α; his3△1; leu2△0; met15△0; lys2△0; ura3△0; PGAL1- YKL173w


title: Snu114-4h-rep1

description:
S4-13A_S10
Mat α; his3△1; leu2△0; met15△0; lys2△0; ura3△0; PGAL1- YKL173w


title: Gastric Cancer GC1313

description:
Gastric Cancer
SH63P18_Cell2


title: Dib1-6h-rep3

description:
Dib1-6h-12-4-16_S2
Mat α; his3△1; leu2△0; met15△0; LYS2; ura3△0; PGAL1- YPR082C

value: Mat alpha; his3{delta}1; leu2{delta}0; met15{delta}0; LYS2; ura3{delta}0; PGAL1- YPR082C


title: Gastric Cancer GC1309

description:
Gastric Cancer
SH63P17_Cell2


title: Dib1-8h-rep2

description:
D8-13B_S15
Mat α; his3△1; leu2△0; met15△0; LYS2; ura3△0; PGAL1- YPR082C


title: Dib1-8h-rep3

description:
Dib1-8h-12-4-16_S3
Mat α; his3△1; leu2△0; met15△0; LYS2; ura3△0; PGAL1- YPR082C


title: Dib1-8h-rep1

description:
D8-13A_S9
Mat α; his3△1; leu2△0; met15△0; LYS2; ura3△0; PGAL1- YPR082C


title: Gastric Cancer GC1307

description:
Gastric Cancer
SH63P16_Cell4


title: Dib1-6h-rep2

description:
D6-13B_S14
Mat α; his3△1; leu2△0; met15△0; LYS2; ura3△0; PGAL1- YPR082C


title: Gastric Cancer GC1305

description:
Gastric Cancer
SH63P16_Cell2


title: Dib1-4h-rep1

description:
D4-13A_S7
Mat α; his3△1; leu2△0; met15△0; LYS2; ura3△0; PGAL1- YPR082C


title: Gastric Cancer GC1290

description:
Gastric Cancer
SH63P12_Cell3


title: Gastric Cancer GC1296

description:
Gastric Cancer
SH63P14_Cell1


title: Gastric Cancer GC1293

description:
Gastric Cancer
SH63P13_Cell2


title: Dib1-4h-rep2

description:
D4-13B_S13
Mat α; his3△1; leu2△0; met15△0; LYS2; ura3△0; PGAL1- YPR082C


title: Gastric Cancer GC1316

description:
Gastric Cancer
SH63P19_Cell1


title: Dib1-4h-rep3

description:
Dib1-4h-12-14-16_S1
Mat α; his3△1; leu2△0; met15△0; LYS2; ura3△0; PGAL1- YPR082C


title: Gastric Cancer GC1269

description:
Gastric Cancer
SH63P07_Cell2


title: MRSA treated [12]

city: St. Lucia

first: Lisa

last: Bohlmann

address: University of Queensland

country: Australia

institute: University of Queensland

data_processing:
An average of 45 million reads per sample were generated and mapped to the reference genome using the 2-passmethod of the STAR aligner with default parameters.
Duplicate reads were denoted with the MarkDuplicates tool of Picard (http://broadinstitute.github.io/picard)
Differential gene expression was analysed using Degust (http://victorian-bioinformatics-438 consortium.github.io/degust/)
genome build: Streptococcus pyogenes: NZ_AFRY01000001.1, Staphylococcus aureus: NC_007793.1, Enterococcus faecium: Bioproject PRJNA497960
Supplementary_files_format_and_content: xlsx files for each bacterial strain, CPM

organism: Staphylococcus aureus

source_name: Bacteria

growth_protocol: Bacteria were grown in cation-adjusted Mueller-Hinton broth

extract_protocol:
RNA was isolated using the FastRNA® Pro Blue Kit (MP Biomedicals) and the SV Total RNA Isolation System (Promega)
RNASeq analysis was performed at the Australian Genome Research Facility. The library was prepared using a Ribo-zero stranded protocol. Libraries were sequenced with a HiSeq 2500 ultra-high-throughput sequencing system (Illumina) to produce 100-base-paired end reads.

treatment_protocol: Bacteria were grown in the presence or absense of PBT2 and zinc

tag: agent

value: PBT2 and zinc


title: MRSA treated [11]


title: MRSA treated [10]


title: Gastric Cancer GC1268

description:
Gastric Cancer
SH63P07_Cell1


title: Gastric Cancer GC1270

description:
Gastric Cancer
SH63P07_Cell3


title: MRSA untreated  [9]


title: Dib1-6h-rep1

description:
D6-13A_S8
Mat α; his3△1; leu2△0; met15△0; LYS2; ura3△0; PGAL1- YPR082C


title: MRSA untreated  [8]


title: MRSA untreated  [7]


title: Gastric Cancer GC1264

description:
Gastric Cancer
SH63W50_Cell3


title: Gastric Cancer GC1266

description:
Gastric Cancer
SH63P06_Cell3


title: Gastric Cancer GC1257

description:
Gastric Cancer
SH63P04_Cell2


title: Gastric Cancer GC1254

description:
Gastric Cancer
SH63P02_Cell3


title: SLX-11261.N712_S502.HGFMYBBXX.s_4.r_1

city: Cambridge

first: Thomas

middle: Pierre

last: Moreau

address: Long Road

department: Haematology

institute: Univeristy of Cambridge

description:
QC failed
Processed data file:
#NA
Single cell RNA sequencing

data_processing:
Raw sequencing reads (fastq files) were aligned with GSNAP30 to the human Ensembl reference genome GrCh38.81 to which was added entries for the 92 ERCC spike-in genes and the three fluorescent reporters eGFP, lssmOrange and dTomato expressed exogenously in FoP-MKs.
Read counts for each gene were then determined with HTSEQ-Count31 from the mapping files.
Quality check consisted in discarding all cells with less than 500 000 read counts and outlier cells showing high proportion of mitochondrial RNA reads or spike-in reads.
All non-captured genes (read count equal to zero for all cells) were removed from further analyses.
Read counts were then normalised to counts per million (CPM).
Genome_build: human Ensembl reference genome GrCh38.81
Supplementary_files_format_and_content: Single comma-delimited text file including CPM gene expression values for all QC-passed cells (n=111)

molecule: polyA RNA

source_name: Forward programmed megakaryocytes

growth_protocol: The hiPSC line A1ATD1c was forward programmed towards the megakaryocyte lineage using method describes in Moreau et al. 2016 (PMID: 27052461) and cell material collected after 40 days of standard culture. Rainbow vectors allowing fluorescence reporting of transcription factor expression (as described in Dalby et al. 2018) have been used to programme the cells.

extract_protocol:
The single cells were sorted in 96-well plates containing cell lysis buffer (2.3mL of 0.2% Triton X-100 with RNase inhibitor) and frozen to -80°C before library preparation.
The method for single cell cDNA library making has been adapted from Smartseq2 for full-length RNAseq from single cells and Fluidigm (PMID: 24385147). Briefly, the reverse transcription was initiated with oligo-dT primers using SuperScript-II reverse transcriptase (Thermo Scientific) and supplemented with ERCC RNA Spike-In. The cDNA was then PCR amplified for 21 cycles using the KAPA HiFi Hotstart ReadyMix and IS primers (Kappa biosystems). After purification of the amplified cDNA, the indexed library was made using the Illumina Nextera XT DNA kit, 96 cells eventually pooled and library quality checked on an Agilent high sensitivity DNA chip before sequencing on one lane of an HiSeq-4000 (Illumina).

treatment_protocol: The megakaryocytes have been sorted by FACS at day40 and 24 single cells of each rainbow transgene pattern (GFT, GF, GT, FT, G, F, T, Neg; G:GATA1, F:FLI1, T:TAL1) directly lysed in 0.2% Triton-X before NGS library preparation (see detailed methods in Dalby et al. 2018)

tag: hipsc line

tag: cell type

value: Forward programmed megakaryocytes

tag: differentiation day

value: Day 40

tag: transgene pattern

value: FT


title: Gastric Cancer GC1252

description:
Gastric Cancer
SH63P02_Cell1


title: SLX-11261.N711_S517.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1253

description:
Gastric Cancer
SH63P02_Cell2


title: SLX-11261.N711_S508.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1272

description:
Gastric Cancer
SH63P08_Cell1


title: SLX-11261.N711_S504.HGFMYBBXX.s_4.r_1


title: SLX-11261.N710_S517.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1245

description:
Gastric Cancer
SH63H63_Cell2


title: SLX-11261.N710_S507.HGFMYBBXX.s_4.r_1


title: SLX-11261.N709_S508.HGFMYBBXX.s_4.r_1

value: T


title: Gastric Cancer GC1241

description:
Gastric Cancer
SH63H62_Cell2


title: Gastric Cancer GC1244

description:
Gastric Cancer
SH63H63_Cell1


title: SLX-11261.N712_S503.HGFMYBBXX.s_4.r_1


title: SLX-11261.N709_S504.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1237

description:
Gastric Cancer
SH63H61_Cell2


title: SLX-11261.N709_S503.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1236

description:
Gastric Cancer
SH63H61_Cell1


title: Gastric Cancer GC1233

description:
Gastric Cancer
SH63H60_Cell2


title: SLX-11261.N709_S502.HGFMYBBXX.s_4.r_1


title: SLX-11261.N708_S517.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1232

description:
Gastric Cancer
SH63H60_Cell1


title: Gastric Cancer GC1231

description:
Gastric Cancer
SH63H59_Cell4


title: Gastric Cancer GC1248

description:
Gastric Cancer
SH63P01_Cell1


title: Gastric Cancer GC1230

description:
Gastric Cancer
SH63H59_Cell3


title: SLX-11261.N708_S504.HGFMYBBXX.s_4.r_1


title: SLX-11261.N708_S503.HGFMYBBXX.s_4.r_1


title: SLX-11261.N708_S505.HGFMYBBXX.s_4.r_1


title: SLX-11261.N711_S505.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1229

description:
Gastric Cancer
SH63H59_Cell2


title: Gastric Cancer GC1225

description:
Gastric Cancer
SH63H58_Cell2


title: Gastric Cancer GC1224

description:
Gastric Cancer
SH63H58_Cell1


title: Gastric Cancer GC1240

description:
Gastric Cancer
SH63H62_Cell1


title: SLX-11261.N709_S517.HGFMYBBXX.s_4.r_1


title: SLX-11261.N707_S517.HGFMYBBXX.s_4.r_1


title: SLX-11261.N708_S502.HGFMYBBXX.s_4.r_1


title: SLX-11261.N707_S507.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1234

description:
Gastric Cancer
SH63H60_Cell3


title: Gastric Cancer GC1223

description:
Gastric Cancer
SH63H57_Cell4


title: SLX-11261.N707_S505.HGFMYBBXX.s_4.r_1


title: SLX-11261.N707_S503.HGFMYBBXX.s_4.r_1


title: SLX-11261.N707_S504.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1218

description:
Gastric Cancer
SH63H56_Cell3


title: Gastric Cancer GC1214

description:
Gastric Cancer
SH63H55_Cell3


title: SLX-11261.N706_S517.HGFMYBBXX.s_4.r_1

value: F


title: Gastric Cancer GC1211

description:
Gastric Cancer
SH63H54_Cell4

value: uncertain


title: Gastric Cancer GC1210

description:
Gastric Cancer
SH63H54_Cell3


title: SLX-11261.N705_S517.HGFMYBBXX.s_4.r_1


title: SLX-11261.N705_S504.HGFMYBBXX.s_4.r_1


title: SLX-11261.N705_S507.HGFMYBBXX.s_4.r_1


title: SLX-11261.N705_S503.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1209

description:
Gastric Cancer
SH63H54_Cell2


title: Gastric Cancer GC1195

description:
Gastric Cancer
SH63H48_Cell4


title: SLX-11261.N705_S502.HGFMYBBXX.s_4.r_1


title: SLX-11261.N704_S508.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1205

description:
Gastric Cancer
SH63H52_Cell2


title: SLX-11261.N704_S504.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1189

description:
Gastric Cancer
SH63H46_Cell2


title: Gastric Cancer GC1188

description:
Gastric Cancer
SH63H46_Cell1


title: Gastric Cancer GC1222

description:
Gastric Cancer
SH63H57_Cell3


title: Gastric Cancer GC1203

description:
Gastric Cancer
SH63H51_Cell4


title: SLX-11261.N704_S503.HGFMYBBXX.s_4.r_1


title: SLX-11261.N703_S517.HGFMYBBXX.s_4.r_1

value: neg


title: Gastric Cancer GC1174

description:
Gastric Cancer
SH63P46_Cell1


title: SLX-11261.N704_S502.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1173

description:
Gastric Cancer
SH63P45_Cell4


title: Gastric Cancer GC1166

description:
Gastric Cancer
SH62G13_Cell3


title: Gastric Cancer GC1426

description:
Gastric Cancer
SH63Q03_Cell4


title: SLX-11261.N703_S508.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1208

description:
Gastric Cancer
SH63H54_Cell1


title: SLX-11261.N703_S507.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1149

description:
Gastric Cancer
SH62G05_Cell2


title: SLX-11261.N703_S505.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1154

description:
Gastric Cancer
SH62G06_Cell3


title: SLX-11261.N703_S503.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1156

description:
Gastric Cancer
SH62G07_Cell1


title: SLX-11261.N703_S504.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1151

description:
Gastric Cancer
SH63P44_Cell1


title: Esophageal Cancer EC0620

description:
Esophageal Cancer
SH57X17_Cell3


title: SLX-11261.N703_S502.HGFMYBBXX.s_4.r_1


title: SLX-11261.N702_S507.HGFMYBBXX.s_4.r_1


title: SLX-11261.N701_S517.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0589

description:
Esophageal Cancer
SH57X09_Cell1


title: Esophageal Cancer EC0574

description:
Esophageal Cancer
SH57X05_Cell2


title: Esophageal Cancer EC0599

description:
Esophageal Cancer
SH57X11_Cell3


title: SLX-11261.N701_S506.HGFMYBBXX.s_4.r_1


title: SLX-11261.N702_S504.HGFMYBBXX.s_4.r_1


title: SLX-11261.N702_S503.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0579

description:
Esophageal Cancer
SH57X06_Cell3


title: SLX-11261.N701_S508.HGFMYBBXX.s_4.r_1


title: Gastric Cancer GC1164

description:
Gastric Cancer
SH62G13_Cell1


title: Esophageal Cancer EC0559

description:
Esophageal Cancer
SH57T32_Cell3


title: Esophageal Cancer EC0555

description:
Esophageal Cancer
SH57T31_Cell3


title: Esophageal Cancer EC0535

description:
Esophageal Cancer
SH57T26_Cell3


title: SLX-11261.N702_S517.HGFMYBBXX.s_4.r_1


title: SLX-11261.N701_S503.HGFMYBBXX.s_4.r_1


title: SLX-11261.N701_S502.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0531

description:
Esophageal Cancer
SH57T25_Cell3


title: Esophageal Cancer EC0550

description:
Esophageal Cancer
SH57T30_Cell2


title: SLX-11261.N701_S505.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0528

description:
Esophageal Cancer
SH57T24_Cell4


title: Esophageal Cancer EC0547

description:
Esophageal Cancer
SH57T29_Cell3


title: Esophageal Cancer EC0542

description:
Esophageal Cancer
SH57T28_Cell2


title: SLX-11260.N712_S504.HGFMYBBXX.s_3.r_1

value: GFT


title: SLX-11260.N710_S505.HGFMYBBXX.s_3.r_1


title: SLX-11260.N710_S504.HGFMYBBXX.s_3.r_1


title: SLX-11260.N710_S503.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0513

description:
Esophageal Cancer
SH57T21_Cell1


title: Esophageal Cancer EC0493

description:
Esophageal Cancer
SH57T15_Cell1


title: Esophageal Cancer EC0503

description:
Esophageal Cancer
SH57T17_Cell3


title: SLX-11260.N712_S502.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0461

description:
Esophageal Cancer
SH57T02_Cell1


title: SLX-11261.N701_S504.HGFMYBBXX.s_4.r_1


title: SLX-11260.N710_S508.HGFMYBBXX.s_3.r_1


title: SLX-11260.N709_S508.HGFMYBBXX.s_3.r_1

value: GT


title: Esophageal Cancer EC0487

description:
Esophageal Cancer
SH57T12_Cell3


title: Esophageal Cancer EC0455

description:
Esophageal Cancer
SH57P67_Cell3


title: Esophageal Cancer EC0472

description:
Esophageal Cancer
SH57T05_Cell4


title: Esophageal Cancer EC0445

description:
Esophageal Cancer
SH57P65_Cell1


title: SLX-11260.N709_S505.HGFMYBBXX.s_3.r_1


title: SLX-11260.N709_S504.HGFMYBBXX.s_3.r_1


title: SLX-11260.N712_S508.HGFMYBBXX.s_3.r_1


title: SLX-11260.N708_S504.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0443

description:
Esophageal Cancer
SH57P63_Cell3


title: Esophageal Cancer EC0428

description:
Esophageal Cancer
SH57P59_Cell4


title: Esophageal Cancer EC0456

description:
Esophageal Cancer
SH57P67_Cell4


title: Esophageal Cancer EC0427

description:
Esophageal Cancer
SH57P59_Cell3


title: SLX-11260.N709_S503.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0421

description:
Esophageal Cancer
SH57P58_Cell1


title: SLX-11260.N708_S503.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0517

description:
Esophageal Cancer
SH57T22_Cell1


title: SLX-11260.N708_S508.HGFMYBBXX.s_3.r_1


title: SLX-11260.N708_S505.HGFMYBBXX.s_3.r_1


title: SLX-11260.N705_S504.HGFMYBBXX.s_3.r_1

value: GF


title: Esophageal Cancer EC0418

description:
Esophageal Cancer
SH57P57_Cell2


title: Esophageal Cancer EC0416

description:
Esophageal Cancer
SH57P56_Cell4


title: SLX-11260.N706_S517.HGFMYBBXX.s_3.r_1


title: SLX-11260.N704_S505.HGFMYBBXX.s_3.r_1


title: SLX-11260.N704_S503.HGFMYBBXX.s_3.r_1


title: SLX-11260.N704_S508.HGFMYBBXX.s_3.r_1


title: SLX-11260.N706_S508.HGFMYBBXX.s_3.r_1


title: SLX-11260.N702_S517.HGFMYBBXX.s_3.r_1

value: G


title: Esophageal Cancer EC0412

description:
Esophageal Cancer
SH57P55_Cell4


title: Esophageal Cancer EC0402

description:
Esophageal Cancer
SH57P53_Cell2


title: SLX-11260.N704_S504.HGFMYBBXX.s_3.r_1


title: SLX-11260.N702_S507.HGFMYBBXX.s_3.r_1


title: SLX-11260.N702_S505.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0387

description:
Esophageal Cancer
SH57P49_Cell3


title: SLX-11260.N702_S503.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0404

description:
Esophageal Cancer
SH57P53_Cell4


title: Esophageal Cancer EC0398

description:
Esophageal Cancer
SH57P52_Cell2


title: SLX-11260.N701_S517.HGFMYBBXX.s_3.r_1


title: SLX-11260.N701_S503.HGFMYBBXX.s_3.r_1


title: SLX-11260.N702_S508.HGFMYBBXX.s_3.r_1


title: SLX-11261.N712_S508.HGFMYBBXX.s_4.r_1

description:
QC passed
Processed data file:
ALD40_countqc.csv
Single cell RNA sequencing


title: SLX-11260.N702_S504.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0384

description:
Esophageal Cancer
SH57P48_Cell4


title: Esophageal Cancer EC0375

description:
Esophageal Cancer
SH57P46_Cell3


title: Esophageal Cancer EC0361

description:
Esophageal Cancer
SH57P43_Cell1


title: Esophageal Cancer EC0396

description:
Esophageal Cancer
SH57P51_Cell4


title: Esophageal Cancer EC0340

description:
Esophageal Cancer
SH57P32_Cell4


title: SLX-11261.N711_S507.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0410

description:
Esophageal Cancer
SH57P55_Cell2


title: Esophageal Cancer EC0338

description:
Esophageal Cancer
SH57P32_Cell2


title: SLX-11261.N712_S517.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0326

description:
Esophageal Cancer
SH57P29_Cell2


title: Esophageal Cancer EC0350

description:
Esophageal Cancer
SH57P38_Cell2


title: Esophageal Cancer EC0325

description:
Esophageal Cancer
SH57P29_Cell1


title: Esophageal Cancer EC0364

description:
Esophageal Cancer
SH57P43_Cell4


title: Esophageal Cancer EC0324

description:
Esophageal Cancer
SH57P27_Cell4


title: SLX-11261.N712_S507.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0403

description:
Esophageal Cancer
SH57P53_Cell3


title: Esophageal Cancer EC0347

description:
Esophageal Cancer
SH57P35_Cell3


title: Esophageal Cancer EC0346

description:
Esophageal Cancer
SH57P35_Cell2


title: Esophageal Cancer EC0341

description:
Esophageal Cancer
SH57P33_Cell1


title: SLX-11261.N712_S506.HGFMYBBXX.s_4.r_1


title: SLX-11261.N712_S505.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0313

description:
Esophageal Cancer
SH57P24_Cell1


title: Esophageal Cancer EC0314

description:
Esophageal Cancer
SH57P24_Cell2


title: SLX-11261.N712_S504.HGFMYBBXX.s_4.r_1


title: SLX-11261.N710_S504.HGFMYBBXX.s_4.r_1


title: SLX-11261.N710_S503.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0358

description:
Esophageal Cancer
SH57P41_Cell2


title: SLX-11261.N711_S502.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0323

description:
Esophageal Cancer
SH57P27_Cell3


title: SLX-11261.N710_S508.HGFMYBBXX.s_4.r_1


title: SLX-11261.N711_S503.HGFMYBBXX.s_4.r_1


title: SLX-11261.N710_S505.HGFMYBBXX.s_4.r_1


title: SLX-11261.N710_S506.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0280

description:
Esophageal Cancer
SH57P15_Cell4


title: Esophageal Cancer EC0315

description:
Esophageal Cancer
SH57P24_Cell3


title: Esophageal Cancer EC0290

description:
Esophageal Cancer
SH57P18_Cell2


title: Esophageal Cancer EC0318

description:
Esophageal Cancer
SH57P25_Cell2


title: Esophageal Cancer EC0274

description:
Esophageal Cancer
SH57N32_Cell3


title: Esophageal Cancer EC0272

description:
Esophageal Cancer
SH57N32_Cell1


title: Esophageal Cancer EC0265

description:
Esophageal Cancer
SH57N29_Cell2


title: SLX-11261.N711_S506.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0312

description:
Esophageal Cancer
SH57P23_Cell4


title: Esophageal Cancer EC0253

description:
Esophageal Cancer
SH57N24_Cell2


title: SLX-11261.N710_S502.HGFMYBBXX.s_4.r_1


title: SLX-11261.N709_S507.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0310

description:
Esophageal Cancer
SH57P23_Cell2


title: SLX-11261.N709_S506.HGFMYBBXX.s_4.r_1


title: SLX-11261.N707_S508.HGFMYBBXX.s_4.r_1


title: SLX-11261.N709_S505.HGFMYBBXX.s_4.r_1


title: SLX-11261.N707_S502.HGFMYBBXX.s_4.r_1


title: SLX-11261.N708_S507.HGFMYBBXX.s_4.r_1


title: SLX-11261.N708_S506.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0237

description:
Esophageal Cancer
SH57N20_Cell2


title: SLX-11261.N707_S506.HGFMYBBXX.s_4.r_1


title: SLX-11261.N706_S507.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0245

description:
Esophageal Cancer
SH57N22_Cell2


title: SLX-11261.N708_S508.HGFMYBBXX.s_4.r_1


title: SLX-11261.N706_S505.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0240

description:
Esophageal Cancer
SH57N21_Cell1


title: Esophageal Cancer EC0201

description:
Esophageal Cancer
SH57N05_Cell2


title: SLX-11261.N706_S508.HGFMYBBXX.s_4.r_1


title: SLX-11261.N706_S503.HGFMYBBXX.s_4.r_1


title: SLX-11261.N706_S502.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0225

description:
Esophageal Cancer
SH57N13_Cell2


title: SLX-11261.N705_S508.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0179

description:
Esophageal Cancer
SH57M66_Cell4


title: Esophageal Cancer EC0190

description:
Esophageal Cancer
SH57N02_Cell3


title: Esophageal Cancer EC0171

description:
Esophageal Cancer
SH57M64_Cell4


title: Esophageal Cancer EC0182

description:
Esophageal Cancer
SH57M67_Cell3


title: SLX-11261.N705_S505.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0152

description:
Esophageal Cancer
SH57Y01_Cell3


title: SLX-11261.N704_S517.HGFMYBBXX.s_4.r_1


title: SLX-11261.N704_S507.HGFMYBBXX.s_4.r_1


title: SLX-11261.N706_S506.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0149

description:
Esophageal Cancer
SH57M59_Cell2


title: Esophageal Cancer EC0140

description:
Esophageal Cancer
SH57M56_Cell1


title: Esophageal Cancer EC0196

description:
Esophageal Cancer
SH57N04_Cell1


title: SLX-11261.N704_S506.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0134

description:
Esophageal Cancer
SH57M54_Cell3


title: SLX-11261.N706_S504.HGFMYBBXX.s_4.r_1


title: SLX-11261.N703_S506.HGFMYBBXX.s_4.r_1


title: SLX-11261.N702_S506.HGFMYBBXX.s_4.r_1


title: SLX-11261.N702_S508.HGFMYBBXX.s_4.r_1


title: SLX-11261.N702_S505.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0123

description:
Esophageal Cancer
SH57M46_Cell4


title: Esophageal Cancer EC0167

description:
Esophageal Cancer
SH57M63_Cell4


title: SLX-11261.N705_S506.HGFMYBBXX.s_4.r_1


title: SLX-11261.N702_S502.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0121

description:
Esophageal Cancer
SH57M46_Cell2


title: Esophageal Cancer EC0112

description:
Esophageal Cancer
SH56F21_Cell1


title: Esophageal Cancer EC0102

description:
Esophageal Cancer
SH56F18_Cell3


title: Esophageal Cancer EC0099

description:
Esophageal Cancer
SH56F17_Cell4


title: SLX-11261.N701_S507.HGFMYBBXX.s_4.r_1


title: SLX-11260.N712_S517.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0100

description:
Esophageal Cancer
SH56H52_Cell3


title: Esophageal Cancer EC0088

description:
Esophageal Cancer
SH56F15_Cell1


title: SLX-11261.N704_S505.HGFMYBBXX.s_4.r_1


title: Esophageal Cancer EC0127

description:
Esophageal Cancer
SH57M51_Cell4


title: SLX-11260.N712_S506.HGFMYBBXX.s_3.r_1


title: Esophageal Cancer EC0084

description:
Esophageal Cancer
SH56F14_Cell1


title: Colorectal Cancer CC1606

description:
Colorectal Cancer
SH5YS07_Cell1


title: Colorectal Cancer CC1602

description:
Colorectal Cancer
SH5YS06_Cell1


title: SLX-11260.N712_S503.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1600

description:
Colorectal Cancer
SH5YY52_Cell3


title: SLX-11260.N711_S517.HGFMYBBXX.s_3.r_1


title: SLX-11260.N711_S508.HGFMYBBXX.s_3.r_1


title: SLX-11260.N711_S507.HGFMYBBXX.s_3.r_1


title: SLX-11260.N711_S506.HGFMYBBXX.s_3.r_1


title: SLX-11260.N711_S505.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1599

description:
Colorectal Cancer
SH5YS05_Cell2


title: Colorectal Cancer CC1586

description:
Colorectal Cancer
SH5YS01_Cell1


title: SLX-11260.N711_S504.HGFMYBBXX.s_3.r_1


title: SLX-11260.N710_S502.HGFMYBBXX.s_3.r_1


title: SLX-11260.N710_S507.HGFMYBBXX.s_3.r_1


title: SLX-11260.N711_S503.HGFMYBBXX.s_3.r_1


title: SLX-11260.N712_S507.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1583

description:
Colorectal Cancer
SH5YY52_Cell1


title: Colorectal Cancer CC1591

description:
Colorectal Cancer
SH5YS02_Cell2


title: Colorectal Cancer CC1584

description:
Colorectal Cancer
SH5YY52_Cell2


title: SLX-11260.N711_S502.HGFMYBBXX.s_3.r_1


title: SLX-11260.N710_S517.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1593

description:
Colorectal Cancer
SH5YS02_Cell4


title: Colorectal Cancer CC1595

description:
Colorectal Cancer
SH5YS03_Cell2


title: Colorectal Cancer CC1598

description:
Colorectal Cancer
SH5YS05_Cell1


title: Colorectal Cancer CC1575

description:
Colorectal Cancer
SH5YY51_Cell3


title: Colorectal Cancer CC1577

description:
Colorectal Cancer
SH5YY51_Cell4


title: SLX-11260.N712_S505.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1568

description:
Colorectal Cancer
SH5YY50_Cell4


title: Colorectal Cancer CC1558

description:
Colorectal Cancer
SH5YR45_Cell3


title: Colorectal Cancer CC1556

description:
Colorectal Cancer
SH5YR45_Cell1


title: Colorectal Cancer CC1554

description:
Colorectal Cancer
SH5YR44_Cell3


title: Colorectal Cancer CC1567

description:
Colorectal Cancer
SH5YY50_Cell3


title: SLX-11260.N708_S517.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1547

description:
Colorectal Cancer
SH5YR42_Cell4


title: SLX-11260.N710_S506.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1543

description:
Colorectal Cancer
SH5YR40_Cell4


title: SLX-11260.N709_S517.HGFMYBBXX.s_3.r_1


title: SLX-11260.N709_S507.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1562

description:
Colorectal Cancer
SH5YR46_Cell3


title: SLX-11260.N709_S506.HGFMYBBXX.s_3.r_1


title: SLX-11260.N709_S502.HGFMYBBXX.s_3.r_1


title: SLX-11260.N708_S506.HGFMYBBXX.s_3.r_1


title: SLX-11260.N708_S507.HGFMYBBXX.s_3.r_1


title: SLX-11260.N708_S502.HGFMYBBXX.s_3.r_1


title: SLX-11260.N707_S517.HGFMYBBXX.s_3.r_1


title: SLX-11260.N707_S505.HGFMYBBXX.s_3.r_1


title: SLX-11260.N707_S507.HGFMYBBXX.s_3.r_1


title: SLX-11260.N707_S508.HGFMYBBXX.s_3.r_1


title: SLX-11260.N707_S503.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1537

description:
Colorectal Cancer
SH5YR39_Cell2


title: Colorectal Cancer CC1541

description:
Colorectal Cancer
SH5YR40_Cell2


title: Colorectal Cancer CC1531

description:
Colorectal Cancer
SH5YR22_Cell4


title: Colorectal Cancer CC1536

description:
Colorectal Cancer
SH5YR39_Cell1


title: Colorectal Cancer CC1546

description:
Colorectal Cancer
SH5YR42_Cell3


title: SLX-11260.N706_S507.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1535

description:
Colorectal Cancer
SH5YR24_Cell4


title: Colorectal Cancer CC1527

description:
Colorectal Cancer
SH5YR20_Cell4


title: Colorectal Cancer CC1532

description:
Colorectal Cancer
SH5YR24_Cell1


title: Colorectal Cancer CC1516

description:
Colorectal Cancer
SH5YR18_Cell1


title: SLX-11260.N707_S504.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1515

description:
Colorectal Cancer
SH5YR16_Cell4


title: Colorectal Cancer CC1511

description:
Colorectal Cancer
SH5YR15_Cell4


title: SLX-11260.N706_S504.HGFMYBBXX.s_3.r_1


title: SLX-11260.N706_S503.HGFMYBBXX.s_3.r_1


title: SLX-11260.N707_S506.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1524

description:
Colorectal Cancer
SH5YR20_Cell1


title: SLX-11260.N707_S502.HGFMYBBXX.s_3.r_1


title: SLX-11260.N706_S506.HGFMYBBXX.s_3.r_1


title: SLX-11260.N706_S505.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1517

description:
Colorectal Cancer
SH5YR18_Cell2


title: Colorectal Cancer CC1503

description:
Colorectal Cancer
SH5YR13_Cell4


title: SLX-11260.N705_S508.HGFMYBBXX.s_3.r_1


title: SLX-11260.N705_S507.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1510

description:
Colorectal Cancer
SH5YR15_Cell3


title: Colorectal Cancer CC1491

description:
Colorectal Cancer
SH5YR08_Cell3


title: SLX-11260.N705_S503.HGFMYBBXX.s_3.r_1


title: SLX-11260.N705_S505.HGFMYBBXX.s_3.r_1


title: SLX-11260.N705_S517.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1475

description:
Colorectal Cancer
SH5YQ63_Cell4


title: Colorectal Cancer CC1474

description:
Colorectal Cancer
SH5YQ63_Cell3


title: Colorectal Cancer CC1473

description:
Colorectal Cancer
SH5YQ63_Cell2


title: SLX-11260.N706_S502.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1499

description:
Colorectal Cancer
SH5YR10_Cell4


title: Colorectal Cancer CC1525

description:
Colorectal Cancer
SH5YR20_Cell2


title: SLX-11260.N705_S506.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1487

description:
Colorectal Cancer
SH5YR07_Cell4


title: SLX-11260.N704_S506.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1467

description:
Colorectal Cancer
SH5YQ61_Cell4


title: Colorectal Cancer CC1476

description:
Colorectal Cancer
SH5YR01_Cell1


title: SLX-11260.N704_S517.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1470

description:
Colorectal Cancer
SH5YQ62_Cell3


title: Colorectal Cancer CC1505

description:
Colorectal Cancer
SH5YR14_Cell2


title: SLX-11260.N704_S502.HGFMYBBXX.s_3.r_1


title: SLX-11260.N703_S507.HGFMYBBXX.s_3.r_1


title: SLX-11260.N703_S506.HGFMYBBXX.s_3.r_1


title: SLX-11260.N704_S507.HGFMYBBXX.s_3.r_1


title: SLX-11260.N703_S504.HGFMYBBXX.s_3.r_1


title: SLX-11260.N703_S517.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1466

description:
Colorectal Cancer
SH5YQ61_Cell3


title: SLX-11260.N703_S503.HGFMYBBXX.s_3.r_1


title: SLX-11260.N702_S506.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1450

description:
Colorectal Cancer
SH5YQ57_Cell3


title: Colorectal Cancer CC1457

description:
Colorectal Cancer
SH5YQ59_Cell2


title: Colorectal Cancer CC1461

description:
Colorectal Cancer
SH5YQ60_Cell2


title: Colorectal Cancer CC1448

description:
Colorectal Cancer
SH5YQ57_Cell1


title: SLX-11260.N703_S508.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1441

description:
Colorectal Cancer
SH5YQ55_Cell2


title: SLX-11260.N705_S502.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1456

description:
Colorectal Cancer
SH5YQ59_Cell1


title: SLX-11260.N703_S505.HGFMYBBXX.s_3.r_1


title: SLX-11260.N701_S508.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1454

description:
Colorectal Cancer
SH5YQ58_Cell3


title: Colorectal Cancer CC1437

description:
Colorectal Cancer
SH5YQ54_Cell2


title: SLX-11260.N703_S502.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1453

description:
Colorectal Cancer
SH5YQ58_Cell2


title: SLX-11260.N701_S506.HGFMYBBXX.s_3.r_1


title: SLX-11260.N702_S502.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1438

description:
Colorectal Cancer
SH5YQ54_Cell3


title: Colorectal Cancer CC1435

description:
Colorectal Cancer
SH5YQ53_Cell4


title: Colorectal Cancer CC1440

description:
Colorectal Cancer
SH5YQ55_Cell1


title: SLX-11260.N701_S504.HGFMYBBXX.s_3.r_1


title: SLX-11260.N701_S505.HGFMYBBXX.s_3.r_1


title: Colorectal Cancer CC1436

description:
Colorectal Cancer
SH5YQ54_Cell1


title: SLX-11260.N701_S502.HGFMYBBXX.s_3.r_1


title: Patient1

city: La Jolla

first: Neil

last: Chi

state: CA

address: 9500 Gilman Drive

department: Medicine

country: USA

institute: University of California, San Diego

data_processing:
llumina Real Time Analysis (RTA) Version 1.13
Quality control was performed with FastQC version 0.11.2 and the dupRadar R package.
Reads were aligned to Gencode version 25 transcripts and quantitated with Kallisto version 0.43.0 with parameters -b 100 --single -l 300 -s 20.  Estimated counts and TPM values were output by Kallisto to abundance.tsv files.
Gene level counts were generated from the transcript counts using tximport R package.
[index file]  A Kallisto index file, gencode.v25.transcripts.idx,  was generated from Human Gencode version 25 transcript fasta file.  Transcripts on chromosome Y were removed.  Also only transcripts with the following biotypes were kept:  protein_coding, lincRNA, antisense, retained_intron, sense_intronic, and sense_overlapping.
Supplementary_files_format_and_content: Tab-delimited files for each sample from Kallisto with the following fields for each transcript:  target_id, length, effective length, estimated counts and tpm.
Supplementary_files_format_and_content: CSV file with read counts for each gene generated by tximport R package.

source_name: Patient, iPSC-derived cardiomyocytes

growth_protocol: Cell culture growth protocols as described in manuscript, previously reported in PMID 23257984 and PMID 23168164

extract_protocol:
RNA was extracted using TRIzol reagent and manufacturer's instructions for total RNA extraction
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA Library Prep Kit with Poly-A selection of cDNA

tag: disease state

value: cardiomyopathy

value: induced pluripotent stem cell-derived cardiomyocytes


title: WT3

source_name: WT, iPSC-derived cardiomyocytes

value: familial control


title: Colorectal Cancer CC1451

description:
Colorectal Cancer
SH5YQ57_Cell4


title: Colorectal Cancer CC1433

description:
Colorectal Cancer
SH5YQ53_Cell2


title: Colorectal Cancer CC1432

description:
Colorectal Cancer
SH5YQ53_Cell1


title: Colorectal Cancer CC1430

description:
Colorectal Cancer
SH5YQ52_Cell3


title: Colorectal Cancer CC1431

description:
Colorectal Cancer
SH5YY47_Cell4


title: WT1


title: Patient2


title: Colorectal Cancer CC1424

description:
Colorectal Cancer
SH5YQ51_Cell1


title: Colorectal Cancer CC1429

description:
Colorectal Cancer
SH5YQ52_Cell2


title: Patient3


title: Colorectal Cancer CC1428

description:
Colorectal Cancer
SH5YQ52_Cell1


title: Colorectal Cancer CC1413

description:
Colorectal Cancer
SH5YQ48_Cell2


title: WT2


title: PD0325901_6h_GnRH_8

city: Ste Anne de Beelvue

first: Yasmin

last: Schuermann

state: Quebec

address: 21 111 lakeshore Road

department: Animal Science

country: Canada

institute: McGill University

data_processing:
Sequencing was performed with Illumina HiSeq 2500 PE 125 with 250ng of RNA as input material per sample. All sampels had a RIN above 8.5.
FASTQC v0.11.5 was used to visualize quality of the seqeunce reads. The reads were cleaned using Trimmomatic v0.36, where illumina dapters and reads with average scores below 20 and lengths below 63 base pairs were removed. The index of the B.tau4.6.1  was built using Bowtie v.2.2.1.0 and aligned t othe genome using TopHat v2.0.11.
The following modifications were made to the default settings for alignment: removed reads having more than 3 mismatches, 100bp as the expecred inner distance between mate pairs, 50bp as the std deviation for the distribution on inner distances between mate paris, 5 as an anchor length, 1 as the max number of mismatches in the anchor, 50 as the minimum intron length, 2 as the number of threads to align reads, 3 as the segment alignment mismatches, 20 as a minimum intron length found during split-segment search.
The reads were counted using HTSeq v0.6.1
Genome_build: btau4.6.1
Supplementary_files_format_and_content: counts in a text file. Each gene is asscoaited with a number of counts

organism: Bos taurus

source_name: granulosa cells

extract_protocol:
granulosa cells were removed from the dominant follicle, flash frozen in liquid nitrogen, and RNA was harvested using NucleoSpin RNA Plus kit (Machery-Nagel, D-Mark BioSciences, ON, Canada). Illumina TruSeq RNA was used to construct the sequencing libraries using 250ng of RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The dominant follicle from cattle was treated either with a Vehicle Control (phosphate-buffered saline with DMSO) or the PD0325901 ERK1/2 signaling inhibitor at a concetration of 50µM in the absence or presence of GnRH. The volume of Vehicle or PD0325901 injected into the dominant follicle by ultrasound-guided intrafollicular  injection was determined by the following equation: V=-685.1 + 120.7D, where V corresponds to the estimated follicualr volume and D to the diameter of the follicle to be injected.

value: granulosa cells

tag: treatment

tag: time

value: 6h GnRH


title: PD0325901_6h_GnRH_6


title: PD0325901_6h_GnRH_7


title: Colorectal Cancer CC1427

description:
Colorectal Cancer
SH5YQ51_Cell4


title: Vehicle_6h_GnRH_5

value: Vehicle


title: SLX-11260.N701_S507.HGFMYBBXX.s_3.r_1

value: Forward programmed megakaryocytes


title: Colorectal Cancer CC1406

description:
Colorectal Cancer
SH5YQ45_Cell3


title: Colorectal Cancer CC1416

description:
Colorectal Cancer
SH5YQ49_Cell1


title: Colorectal Cancer CC1415

description:
Colorectal Cancer
SH5YQ48_Cell4


title: Colorectal Cancer CC1403

description:
Colorectal Cancer
SH5YQ44_Cell4


title: Vehicle_6h_GnRH_4


title: Colorectal Cancer CC1409

description:
Colorectal Cancer
SH5YQ46_Cell2


title: Colorectal Cancer CC1408

description:
Colorectal Cancer
SH5YQ46_Cell1


title: Colorectal Cancer CC1396

description:
Colorectal Cancer
SH5YQ42_Cell1


title: Vehicle_0h_GnRH_1

value: 0h GnRH


title: Colorectal Cancer CC1388

description:
Colorectal Cancer
SH5YQ40_Cell1


title: Colorectal Cancer CC1393

description:
Colorectal Cancer
SH5YQ41_Cell2


title: Colorectal Cancer CC1387

description:
Colorectal Cancer
SH5YQ39_Cell4


title: Colorectal Cancer CC1389

description:
Colorectal Cancer
SH5YQ40_Cell2


title: Colorectal Cancer CC1386

description:
Colorectal Cancer
SH5YQ39_Cell3


title: Vehicle_6h_GnRH_3


title: Colorectal Cancer CC1385

description:
Colorectal Cancer
SH5YQ39_Cell2


title: Colorectal Cancer CC1382

description:
Colorectal Cancer
SH5YQ37_Cell3


title: Vehicle_0h_GnRH_2


title: Colorectal Cancer CC1383

description:
Colorectal Cancer
SH5YQ37_Cell4


title: Colorectal Cancer CC1402

description:
Colorectal Cancer
SH5YQ44_Cell3


title: Colorectal Cancer CC1380

description:
Colorectal Cancer
SH5YQ37_Cell1


title: Colorectal Cancer CC1376

description:
Colorectal Cancer
SH5YQ36_Cell1


title: Colorectal Cancer CC1377

description:
Colorectal Cancer
SH5YQ36_Cell2


title: Colorectal Cancer CC1374

description:
Colorectal Cancer
SH5YQ35_Cell3


title: Colorectal Cancer CC1366

description:
Colorectal Cancer
SH5YQ33_Cell3


title: Colorectal Cancer CC1364

description:
Colorectal Cancer
SH5YQ33_Cell1


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H2A2)

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

description: Adult flies from 2nd hyperoxia-selected population

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Drosophila melanogaster

source_name: Adult flies from hyperoxia-selected population

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Invitrogen) according to the manufacturer's instructions.

tag: Strain

value: Drosophila melanogaster

tag: Developmental Stage

value: adult flies (25 male + 25 female)

tag: Tissue

value: Whole Organism


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H3A1)

description: Adult flies from 3rd hyperoxia-selected population


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H2A1)


title: Colorectal Cancer CC1358

description:
Colorectal Cancer
SH5YQ31_Cell3

tag: tumor stage (figo)

tag: age

value: uncertain


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C3A2)

description: Adult flies from 3rd control population

source_name: Adult flies from control population


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H3A2)


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C3A1)

description: Adult flies from 3rd control population


title: Colorectal Cancer CC1353

description:
Colorectal Cancer
SH5YQ30_Cell2


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H1A2)

description: Adult flies from 1st hyperoxia-selected population


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C2A2)

description: Adult flies from 2nd control population


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C2A1)

description: Adult flies from 2nd control population


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C1A2)

description: Adult flies from 1st control population


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H1A1)


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H3L2)

description: 3rd instar larvae from 3rd hyperoxia-selected population

source_name: 3rd instar larvae from hyperoxia-selected population

value: 3rd instar larvae


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H3L1)


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C1A1)

description: Adult flies from 1st control population


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H2L2)

description: 3rd instar larvae from 2nd hyperoxia-selected population


title: Colorectal Cancer CC1352

description:
Colorectal Cancer
SH5YQ30_Cell1


title: Colorectal Cancer CC1312

description:
Colorectal Cancer
SH5YQ15_Cell2


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H1L2)

description: 3rd instar larvae from 1st hyperoxia-selected population


title: Colorectal Cancer CC1359

description:
Colorectal Cancer
SH5YQ31_Cell4


title: Colorectal Cancer CC1310

description:
Colorectal Cancer
SH5YQ14_Cell4


title: Colorectal Cancer CC1307

description:
Colorectal Cancer
SH5YQ14_Cell1


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H2L1)


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C3L2)

description: 3rd instar larvae from 3rd control population

source_name: 3rd instar larvae from control population


title: AK250_RydC_rep3_10min

city: Urbana

first: Alisa

middle: Margaret

last: King

state: IL

address: 601 S Goodwin Ave Room C211

department: Microbiology

institute: University of Illinois at Urbana-Champaign

data_processing:
Libraries were quantitated by qPCR, pooled in equimolar concentration, and each pool sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq2000
TruSeq SBS sequencing kit version 3 was used
Fastq files were generated with Casava 1.8.2
Supplementary_files_format_and_content: files were analyzed using Rockhopper, where outputs include tab-delimited files with differentially expressed genes, non-codiing RNAs, and operons.
NC_000913_transcripts.txt: function of gene, start/stop for transcripts, expression levels, and q-value measuring differential expression between two experimental conditions
NC_000913_operons.txt: multi-gene operons
summary.txt: % of successfully aligned reads

organism: Escherichia coli str. K-12 substr. MG1655

source_name: overexpression of small RNA RydC

growth_protocol: Cells were grown in LB broth at 37 degrees Celsius for 1 hour 30 min and then RNA extracted after 10 min of RydC induction

extract_protocol:
RNA was extracted using the hot phenol method and ribosomal RNA removed using the Ribozero Bacteria kit (Illumina, CA)
Strand-specific librares were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'; DNA libraries for RNA-Seq were prepared with the Library Construction kit from Kapa Biosystems

tag: strain

value: K-12 substr. MG1655

tag: genotype

value: rydC +/+


title: Colorectal Cancer CC1277

description:
Colorectal Cancer
SH5YQ04_Cell3


title: AK250_vec_rep2_10min

source_name: no expression of small RNA RydC

value: rydC -/-


title: AK250_RydC_rep2_10min


title: Colorectal Cancer CC1250

description:
Colorectal Cancer
SH5YL33_Cell4


title: Colorectal Cancer CC1230

description:
Colorectal Cancer
SH5YL27_Cell4


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (H1L1)


title: Colorectal Cancer CC1251

description:
Colorectal Cancer
SH5YL36_Cell1


title: AK250_vec_rep1_10min


title: Colorectal Cancer CC1246

description:
Colorectal Cancer
SH5YL32_Cell4


title: Colorectal Cancer CC1278

description:
Colorectal Cancer
SH5YQ04_Cell4


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C3L1)


title: Colorectal Cancer CC1284

description:
Colorectal Cancer
SH5YQ07_Cell2


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C2L2)

description: 3rd instar larvae from 2nd control population


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C1L2)

description: 3rd instar larvae from control population


title: Expression profiling of Hyperoxia-Tolerant Drosophila melanogaster (C2L1)


title: AK250_RydC_rep1_10min


title: Expression profiling of hyperoxia-tolerant Drosophila melanogaster (C1L1)


title: AK250_vec_rep3_10min


title: Colorectal Cancer CC1306

description:
Colorectal Cancer
SH5YQ13_Cell4


title: Colorectal Cancer CC1241

description:
Colorectal Cancer
SH5YL31_Cell3


title: Colorectal Cancer CC1221

description:
Colorectal Cancer
SH5YL25_Cell3


title: Colorectal Cancer CC1196

description:
Colorectal Cancer
SH5X560_Cell4


title: Colorectal Cancer CC1266

description:
Colorectal Cancer
SH5YQ01_Cell4


title: P15-hyp-C9

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

library_source: genomic

data_processing:
alignment: Fastq files were aligned to the most current rat genome (Rn6, July 2014) using the Burrows-Wheeler Transform (BWA) tool to obtain .bam files (Li and Durbin, 2009).
filtering: Bam files were filtered using samtools to remove duplicate reads, unpaired reads, and reads with a minimum quality score below 10.
merging bam files: Following alignment and filtering, each the two runs for each sample were merged using samtools to obtain a single .bam file for each sample (Li et al., 2009).
peak calling: Model-based analysis of ChIP-seq (MACS2; version 2.1.0.20140616) was used to identify enriched regions of DNA methylation across the genome (Zhang et al., 2008). The peak calling to identify peak regions (DNA methylation windows) was performed using the ‘callpeaks’ function on paired end bam files with no control input and the following options: –f BAMPE –m 5 50 –bw 300 –g 2.9e9 –q 0.05. Each sample was modeled individually, generating 60 total peaksets. These were imported into R using the DiffBind package (Stark and Brown, 2011). As all samples had slightly different predicted peaks, peaksets were combined into common regions using the dba.count function in DiffBind, which removed peaks found in less than 3 samples across the entire dataset and provided the total number of reads within each peak/sample. This created a final dataset of 469,162 peaks and 48 samples from the developmental profile of the hypothalamus, and a final dataset of 350,960 peaks and 24 samples in the P22 hypothalamus and WBC (tissue-concordant) peakset.
Genome_build: rn6
Supplementary_files_format_and_content: peaks from MACS2, one/animal/age/tissue

molecule: genomic DNA

organism: Rattus norvegicus

extract_protocol:
Total RNA and DNA were simultaneously extracted from the hypothalamus and white blood cells (n=4/group/age/tissue; Qiagen AllPrep DNA/RNA Mini kit, Hilden, Germany). Frozen tissue was thawed on ice, quickly weighed and placed in lysis buffer for 5 minutes. Homogenization was performed by 5 strokes of an 18G needle, 10 strokes of a 20G needle, and 10 strokes of a 23G needle. The resulting homogenate was centrifuged at 21,000g for 3 minutes and the supernatant was collected for DNA and RNA extraction. White blood cells were thawed on ice and then centrifuged at 10,000g for 10 minutes. RNAlater was carefully removed without disturbing the cell pellet and cells were resuspended in lysis buffer. The cells were then frozen at -80˚C to disrupt cell membranes and then thawed on ice. The resulting homogenate was then used for DNA and RNA extraction. DNA concentration was assessed using Qubit Fluorometric Quantitation (Life Technologies, Carlsbad, USA). Full developmental data on the animals can be found in Supplementary Table 3.
For each sample, 500 ng of DNA were diluted in a total volume of 60µL of EB buffer (Qiagen, Hilden, Germany). DNA was then transferred to a 96-well plate and sheared for 1 hour using the Covaris Focused-ultrasonicator. DNA was purified using Ampure XP in 20% polyethylene glycol (PEG) beads to obtain fragments sized from 200-500 basepairs (Beckman-Coulter, Brea, USA). Library preparation was performed on the Bravo Automated Liquid Handling Platform (Agilent, Santa Clara, USA) using the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina, San Diego, USA). Following end-repair and A-tailing, adapters were ligated overnight at room temperature. PCR-free library preparation allowed for the conservation of methylated cytosines for subsequent methylated DNA immunoprecipitation. Finally, DNA was resuspended in 35µL of EB buffer (Qiagen, Hilden, Germany). DNA was quality controlled using Qubit Fluorometric Quantitation and the DNA 1000 Bioanalyzer 2100 kit (Agilent, Santa Clara, USA) to verify concentration and fragment size (250-550bp).
methylated DNA immunoprecipitation (meDIP): For each sample, 400ng of the sequencing library were diluted in a total volume of 50µL of IP Buffer (10mM sodium phosphate buffer, pH7.0, 140mM NaCl, 0.05% triton). DNA was denatured by incubation at 95˚C for 10 minutes, followed by the addition of 48µL ice-cold IP buffer and incubation on ice for 10 minutes. 2µL of anti-5-methylcytosine antibody (Eurogenetec, Liège, Belgium), diluted to 1/50 in IP buffer (1µL of antibody per 1µg of DNA ratio), was added to each sample. Immunoprecipitation reactions were incubated for 16 hours at 4˚C with overhead rotation. Following two 5 minute washes with 150uL of 0.1% BSA/PBS, 50µL of Dynabeads Protein G were incubated with 5µL of secondary antibody (rabbit anti-mouse IgG; Jackson Immunoresearch, West Grove, USA) in 45uL ice-cold IP buffer for 15 minutes at room temperature with overhead rotation. Beads were washed twice with IP buffer to remove unbound secondary antibody and resuspended in 50µL IP buffer. The antibody-bound beads were added to the immunoprecipitation reactions and incubated for 2 hours at 4˚C with overhead rotation. Beads were then washed 6 times with 150µL of ice-cold IP buffer and resuspended in 98.97µL of Proteinase K digestion buffer (TE with 0.5% SDS). Following the addition of 1.25µL Proteinase K (20mg/mL; Qiagen, Hilden, Germany), samples were incubated in a thermomixer for 2 hours at 55˚C with a rotation speed of 1250rpm. The reaction was then allowed to cool at room temperature for 15 minutes. Supernatant was collected and bead cleanup was performed using equal volume SeraMag beads with 30% PEG. DNA was resuspended in 35µL of EB buffer (Qiagen, Hilden, Germany). Two parallel rounds of the following PCR amplification cycle conditions were performed on each sample in order to reduce PCR amplification bias. The reaction mixes were as follows: 15µL DNA, 27µL H2O, 12µL 5X HF buffer, 1.5µL DMSO, 1.0µL paired-end primer (Illumina), 0.5µL Phusion High-Fidelity DNA polymerase (New England Biolabs), 2µL indexing primer (Illumina – specific to each sample). The amplification cycle was as follows: 98˚C for 1 minute, 12X (98˚C for 15 seconds, 65˚C for 30 seconds, 72˚C for 30 seconds), 72˚C for 5 minutes. Reactions from the same sample were pooled and bead cleanup was performed using SeraMag beads in 20% PEG (102µL of beads per 120µL of reaction). DNA was resuspended in a final volume of 35µL of EB buffer.
methylated DNA immunoprecipitation (meDIP): Indexed meDIP libraries were combined in 3 pools of 20 samples each, distributing samples evenly by tissue, age, and prenatal treatment across all three sets. Next-generation sequencing was performed on the pools by the Genome Sciences Centre in Vancouver, BC, Canada. Each sample pool was run on two HiSeq lanes, which produced approximately 600,000,000 paired-end reads of 125 bases per lane.

treatment_protocol: Prenatal treatment protocol: Details of the procedures for breeding and handling have been published previously (Bodnar et al., 2016). Briefly, outbred male and female Sprague-Dawley rats were obtained Charles River Laboratories (St. Constant, Quebec, Canada). Following a one-week habituation period, nulliparous females (n=39) were pair-housed with a male and vaginal lavage samples were collected daily for estrous cycle staging and to check for the presence of sperm, indicating gestation day (GD) 1. Pregnant dams were singly housed and assigned to one of three prenatal treatment groups: Prenatal alcohol exposure (PAE) - ad libitum access to liquid ethanol diet, 36% ethanol-derived calories, 6.37% v/v, n =13; Pair-fed (PF) - liquid-control diet, maltose-dextrin isocalorically substituted for ethanol, in the amount consumed by an PAE partner, g/kg body weight/GD, n =14; or Control (C) - pelleted version of the liquid control diet, ad libitum, n =12. All animals had ad libitum access to water. Experimental diets (Weinberg/Keiver Liquid Ethanol Diet #710324, Weinberg/Keiver Liquid Control Diet #710109, and Pelleted Control Diet #102698, Dyets Inc., Bethlehem, PA) were fed from gestation days 1-21, and then replaced with laboratory chow. Litters were weighed and culled at birth to 6 males and 6 females, when possible.   We focused our investigation of PAE-induced epigenetic alterations on female animals, as they show unique phenotypes in response to PAE and are generally underrepresented in molecular and genome-wide studies of FASD. On P1, 8, 15, and 22, female offspring (max 1/litter) were decapitated, trunk blood collected (at P22 only), and brains removed and weighed; the hypothalamus was then quickly dissected and frozen on dry ice in RNAlater (n=7-11/age/group; Qiagen, Hilden, Germany). WBCs were isolated using Ficoll-Paque (GE Healthcare, Uppsala, Sweden), which isolates peripheral blood mononuclear cells (PBMCs). All tissue collected was left at 4˚C for 24 hours to allow for complete permeation by RNAlater and then frozen at -80˚C until DNA extraction, as per manufacturer instructions. WBCs were stored in RNAlater at -80˚C until DNA extraction (Qiagen, Hilden, Germany). Due to the large number of animals associated with the experimental design of this study, animals were collected across four different cohorts (experimental breedings), spanning January 2012 – December 2013.

value: Sprague-Dawley

tag: animal id number

value: Control

tag: age (days)

tag: breeding

tag: tissue/cell type

value: hypothalamus

value: ttaggc


title: Colorectal Cancer CC1190

description:
Colorectal Cancer
SH5X559_Cell2


title: Colorectal Cancer CC1217

description:
Colorectal Cancer
SH5YL24_Cell3


title: P22-wbc-PF15

value: Pair-fed

value: White blood cells

value: ttcgaa


title: P22-hyp-PF15

value: tggcgc


title: P15-hyp-PF11

value: tgctgg


title: P22-hyp-C13

value: tgacca


title: P8-hyp-PF7

value: tgccat


title: Breast Cancer BC1596

description:
Breast Cancer
SH4YL63_Cell4


title: P0-hyp-PF3

value: NYB

value: tgaatg


title: Colorectal Cancer CC1170

description:
Colorectal Cancer
SH5X553_Cell2

value: uncertain


title: Breast Cancer BC1585

description:
Breast Cancer
SH4YM53_Cell2


title: Breast Cancer BC1584

description:
Breast Cancer
SH4YM53_Cell1


title: P15-hyp-PF10

value: tataat


title: P22-wbc-PF14

value: tcccga


title: P22-hyp-PF14

value: tcattc


title: Breast Cancer BC1583

description:
Breast Cancer
SH4YM50_Cell4


title: P8-hyp-C6

value: Sprague-Dawley

value: tagctt


title: Breast Cancer BC1581

description:
Breast Cancer
SH4YL63_Cell3


title: P8-hyp-PF6

value: hypothalamus

value: tacagc


title: P0-hyp-PF2

value: Pair-fed

value: taatcg


title: Breast Cancer BC1580

description:
Breast Cancer
SH4YM50_Cell2


title: P22-wbc-PF16

value: White blood cells

value: gtccgc


title: Breast Cancer BC1579

description:
Breast Cancer
SH4YM50_Cell1


title: P22-hyp-PF16

value: gtagag


title: P22-wbc-PF13

value: gcctta


title: P15-hyp-C10

value: Control

value: ggctac


title: Breast Cancer BC1577

description:
Breast Cancer
SH4YM49_Cell3


title: P22-hyp-PF13

value: gccgcg


title: Breast Cancer BC1575

description:
Breast Cancer
SH4YM49_Cell1

value: uncertain


title: Breast Cancer BC1572

description:
Breast Cancer
SH4YM48_Cell2


title: P15-hyp-PF9

value: gcactt


title: Breast Cancer BC1573

description:
Breast Cancer
SH4YM48_Cell3


title: Breast Cancer BC1582

description:
Breast Cancer
SH4YM50_Cell3


title: P0-hyp-PF1

value: gatgct


title: Breast Cancer BC1569

description:
Breast Cancer
SH4YM47_Cell3


title: Breast Cancer BC1568

description:
Breast Cancer
SH4YM47_Cell2


title: P8-hyp-PF5

value: gcaagg


title: P0-hyp-C2

value: Sprague-Dawley

value: gatcag


title: Breast Cancer BC1566

description:
Breast Cancer
SH4YM46_Cell4


title: Breast Cancer BC1567

description:
Breast Cancer
SH4YM47_Cell1


title: Breast Cancer BC1562

description:
Breast Cancer
SH4YM45_Cell4


title: Breast Cancer BC1565

description:
Breast Cancer
SH4YM46_Cell3


title: P22-hyp-E15

source_name: P22_hyp_prenatal alcohol exposed

value: Prenatal alcohol exposed

value: hypothalamus

value: gagtgg


title: P22-wbc-E16

source_name: P22_wbc_prenatal alcohol exposed

value: gaaacc


title: P22-hyp-E16

value: ctgctg


title: Breast Cancer BC1578

description:
Breast Cancer
SH4YM49_Cell4


title: P22-hyp-C14

value: cttgta


title: Breast Cancer BC1560

description:
Breast Cancer
SH4YM45_Cell2


title: Breast Cancer BC1559

description:
Breast Cancer
SH4YM45_Cell1


title: Breast Cancer BC1556

description:
Breast Cancer
SH4YM43_Cell4


title: Breast Cancer BC1555

description:
Breast Cancer
SH4YM43_Cell3


title: P0-hyp-E4

source_name: P0_hyp_prenatal alcohol exposed

value: NYB

value: ctagct


title: P8-hyp-C5

value: Control

value: cgatgt


title: P15-hyp-PF12

value: Pair-fed

value: ccgtcc


title: P22-wbc-E15

value: White blood cells

value: ccgcaa


title: P8-hyp-E7

source_name: P8_hyp_prenatal alcohol exposed

value: ccacgc


title: P15-hyp-E11

source_name: P15_hyp_prenatal alcohol exposed

value: Sprague-Dawley

value: cccatg


title: Breast Cancer BC1552

description:
Breast Cancer
SH4YM42_Cell4

source_name: Serum

value: uncertain


title: Breast Cancer BC1554

description:
Breast Cancer
SH4YM43_Cell2


title: P22-wbc-E14

value: Prenatal alcohol exposed

value: cactca


title: Breast Cancer BC1549

description:
Breast Cancer
SH4YM42_Cell1


title: P15-hyp-E12

value: hypothalamus

value: ctcaga


title: Breast Cancer BC1553

description:
Breast Cancer
SH4YM43_Cell1


title: Breast Cancer BC1548

description:
Breast Cancer
SH4YM41_Cell4


title: Breast Cancer BC1547

description:
Breast Cancer
SH4YM41_Cell3


title: Breast Cancer BC1550

description:
Breast Cancer
SH4YM42_Cell2


title: Breast Cancer BC1545

description:
Breast Cancer
SH4YM41_Cell1


title: Breast Cancer BC1543

description:
Breast Cancer
SH4YM40_Cell3


title: Breast Cancer BC1542

description:
Breast Cancer
SH4YM40_Cell2


title: P8-hyp-E6

value: caacta


title: P8-hyp-E8

value: ctatac


title: P8-hyp-PF8

value: atgtca


title: Breast Cancer BC1541

description:
Breast Cancer
SH4YM40_Cell1


title: P15-hyp-E10

value: caccgg


title: Breast Cancer BC1538

description:
Breast Cancer
SH4YM39_Cell2


title: P22-wbc-E13

value: atccta


title: P0-hyp-E3

value: NYB

value: ccaaca


title: P0-hyp-C1

value: Control

value: atcacg


title: Breast Cancer BC1537

description:
Breast Cancer
SH4YM39_Cell1


title: P22-hyp-E14

value: cacgat


title: P15-hyp-E9

value: Sprague-Dawley

value: ataatt


title: P22-hyp-E13

value: atacgg


title: Breast Cancer BC1536

description:
Breast Cancer
SH4YM37_Cell4

value: uncertain


title: Breast Cancer BC1544

description:
Breast Cancer
SH4YM40_Cell4


title: Breast Cancer BC1535

description:
Breast Cancer
SH4YM37_Cell3


title: P8-hyp-E5

value: Prenatal alcohol exposed

value: aggccg


title: Breast Cancer BC1534

description:
Breast Cancer
SH4YM37_Cell2


title: P0-hyp-E2

value: hypothalamus

value: caaaag


title: P22-wbc-C16

value: White blood cells

value: actgat


title: P0-hyp-E1

value: agcgct


title: Breast Cancer BC1540

description:
Breast Cancer
SH4YM39_Cell4


title: Breast Cancer BC1531

description:
Breast Cancer
SH4YM36_Cell3


title: Breast Cancer BC1533

description:
Breast Cancer
SH4YM37_Cell1


title: P22-hyp-C16

value: actctc


title: Breast Cancer BC1530

description:
Breast Cancer
SH4YM36_Cell2


title: Breast Cancer BC1532

description:
Breast Cancer
SH4YM36_Cell4


title: Breast Cancer BC1526

description:
Breast Cancer
SH4YM35_Cell2


title: P15-hyp-C12

value: acgata


title: Breast Cancer BC1522

description:
Breast Cancer
SH4YM34_Cell3


title: P8-hyp-C8

value: accggc


title: P0-hyp-C4

value: Control

value: NYB

value: acccag


title: P22-wbc-C13

value: Sprague-Dawley

value: acagtg


title: Breast Cancer BC1521

description:
Breast Cancer
SH4YM34_Cell2


title: Breast Cancer BC1520

description:
Breast Cancer
SH4YM34_Cell1


title: P22-wbc-C15

value: aaggac


title: P0-hyp-PF4

value: Pair-fed

value: agttcc


title: P22-hyp-C15

value: aagcga


title: Breast Cancer BC1519

description:
Breast Cancer
SH4YM31_Cell4

value: uncertain


title: P15-hyp-C11

value: hypothalamus

value: aagact


title: Breast Cancer BC1518

description:
Breast Cancer
SH4YM31_Cell3


title: P8-hyp-C7

value: aacttg


title: Breast Cancer BC1517

description:
Breast Cancer
SH4YL63_Cell1


title: Breast Cancer BC1516

description:
Breast Cancer
SH4YM31_Cell2


title: P22-wbc-C14

value: White blood cells

value: aaacat


title: Breast Cancer BC1515

description:
Breast Cancer
SH4YM31_Cell1


title: Breast Cancer BC1508

description:
Breast Cancer
SH4YM27_Cell3


title: Breast Cancer BC1505

description:
Breast Cancer
SH4YM26_Cell4


title: Breast Cancer BC1506

description:
Breast Cancer
SH4YM27_Cell1


title: Breast Cancer BC1495

description:
Breast Cancer
SH4YM23_Cell2


title: Breast Cancer BC1497

description:
Breast Cancer
SH4YM23_Cell4


title: Breast Cancer BC1511

description:
Breast Cancer
SH4YM29_Cell1


title: sister_S1

city: Caserta

first: Andrea

last: Riccio

address: Via Vivaldi

country: Italy

institute: Università degli Studi della Campania

data_processing:
RNA-seq reads were aligned to the human genome (hg19) by TopHat2 version.2.0.14,  using the annotation as guide. The RNA-seq quantification pipeline was used with default parameters and setting max. 1 mismatch for the alignment. Only uniquely mapped reads were considered for further analyses. The annotation, Homo_sapiens.GRCh37.75.gtf (www.ensembl.org)
Gene expression levels were quantified for each sample by FeatureCounts (Rsubread package version 1.24.2) and the annotation as guide, considering overall genes as associated features
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads on genes for each Sample

source_name: peripheral blood lymphocytes

extract_protocol:
Genomic DNA was isolated from peripheral blood lymphocytes either by using the salting-out procedure or by the AutopureLS system (Qiagen). Total RNA was extracted from peripheral blood collected in PAXgene Blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland), by using the RNA purification kit and following the instructions of the manufacturer. Nucleic acid concentration was determined by using the NanoDrop spectrophotometer (Termo Fisher Scientific, Italy)
RNA libraries were prepared for sequencing using kit TruSeq Stranded Total RNA Illumina protocols

value: control

tag: cell type

value: peripheral blood lymphocytes


title: Breast Cancer BC1493

description:
Breast Cancer
SH4YM22_Cell4


title: 1_S1

value: Long QT syndrome and Beckwith-Wiedemann syndrome


title: Breast Cancer BC1485

description:
Breast Cancer
SH4YM20_Cell4


title: Breast Cancer BC1489

description:
Breast Cancer
SH4YM21_Cell4


title: Breast Cancer BC1492

description:
Breast Cancer
SH4YM22_Cell3


title: Breast Cancer BC1483

description:
Breast Cancer
SH4YM20_Cell2


title: Testis_3w_BS

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: mRNA m5C profiles in 3-week-old mouse testis

data_processing:
Raw Reads were stripped of adaptor sequences and low quality bases were removed using Trimmomatic. Filtered paired-end RNA-BisSeq reads were mapped against mouse (mm10) reference genome by Bismark (version 0.13.0). The m5C sites calling was performed using Bismark (version 0.13.0).
Genome_build: mm10
Supplementary_files_format_and_content: txt format. Information of m5C positions and modified gene types (mm10).

organism: Mus musculus

source_name: 3-week-old Mouse testis

extract_protocol:
mRNAs of 3-week-old mouse testis were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.

tag: gender

value: male

tag: transfection

value: 3 weeks

tag: tissue

value: testis


title: P0-hyp-C3

value: Sprague-Dawley

value: Control

value: NYB

value: aacccc


title: T84 trametinib + JQ1 Rep1

city: Sutton

first: Steven

last: Whittaker

address: 15 Cotswold Road

institute: The Institute of Cancer Research

description:
Project_E04_All_Expressed_Genes.xlsx
T84_Combo_1_Normalised
T84_Combo_1_Raw

data_processing:
Bcl2fastq software (v1.8.4, Illumina) was used for converting the raw basecalls to fastqs and to further demultiplex the sequencing data.
Tophat2 spliced alignment software was used to align reads to the reference genome (GRCH37) in combination with Bowtie2.
Once the reads were aligned, HTSeq-count was used to count the number of reads mapping unambiguously to genomic feature in each sample.
Differential expression analysis of the count data was done in R using DESeq2 bioconductor package.
Genome_build: GRCH37
Supplementary_files_format_and_content: Raw count data was normalized to correct for library size and RNA composition bias. Reads per genomic feature are presented per sample.

source_name: T84 trametinib + JQ1, colorectal cancer cell line

growth_protocol: Cells were cultured in DMEM + 10% FBS

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen, Manchester, UK). NEB (Hitchin, UK) polyA kit was used to select the mRNA.
Strand specific libraries were generated from the mRNA using the NEB ultra directional kit. Illumina paired-end libraries were sequenced on a HiSeq2500 (Illumina, Little Chesterford, UK) using v4 chemistry acquiring 2 x 100 bp reads.

treatment_protocol: T84 cells were treated with DMSO, trametinib, JQ1 or the combination of trametinib and JQ1 for 24h.

tag: cell line

value: T84 colon carcinoma cell line

tag: treatment

value: Trametinib + JQ1

tag: time of treatment


title: T84 trametinib + JQ1 Rep3

description:
Project_E04_All_Expressed_Genes.xlsx
T84_Combo_3_Normalised
T84_Combo_3_Raw


title: T84 JQ1 Rep3

description:
Project_E04_All_Expressed_Genes.xlsx
T84_BRD4i_3_Normalised
T84_BRD4i_3_Raw

source_name: T84 JQ1, colorectal cancer cell line

value: JQ1 1µM


title: T84 trametinib + JQ1 Rep2

description:
Project_E04_All_Expressed_Genes.xlsx
T84_Combo_2_Normalised
T84_Combo_2_Raw


title: Breast Cancer BC1507

description:
Breast Cancer
SH4YM27_Cell2

value: uncertain


title: T84 JQ1 Rep2

description:
Project_E04_All_Expressed_Genes.xlsx
T84_BRD4i_2_Normalised
T84_BRD4i_2_Raw


title: Breast Cancer BC1502

description:
Breast Cancer
SH4YM26_Cell1


title: Breast Cancer BC1478

description:
Breast Cancer
SH4YM19_Cell1


title: T84 JQ1 Rep1

description:
Project_E04_All_Expressed_Genes.xlsx
T84_BRD4i_1_Normalised
T84_BRD4i_1_Raw


title: Breast Cancer BC1481

description:
Breast Cancer
SH4YM19_Cell4


title: T84 trametinib Rep3

description:
Project_E04_All_Expressed_Genes.xlsx
T84_MEKi_3_Normalised
T84_MEKi_3_Raw

source_name: T84 trametinib, colorectal cancer cell line

value: Trametinib 30nM


title: Breast Cancer BC1477

description:
Breast Cancer
SH4YM17_Cell4


title: Breast Cancer BC1475

description:
Breast Cancer
SH4YM17_Cell2


title: Breast Cancer BC1491

description:
Breast Cancer
SH4YM22_Cell2


title: Breast Cancer BC1480

description:
Breast Cancer
SH4YM19_Cell3


title: T84 trametinib Rep2

description:
Project_E04_All_Expressed_Genes.xlsx
T84_MEKi_2_Normalised
T84_MEKi_2_Raw


title: mRNA_PAPA_Skin_2

city: Bethesda

first: Hong-wei

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
Raw sequencing data were processed with bcl2fastq 1.8.4 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1
Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek6.6
Genome_build: hg19
Supplementary_files_format_and_content: excel for a RPKM file

source_name: Human skin

extract_protocol:
Normal density neutrophils were isolated by dextran sedimentation from control and PAPA patients. LDGs were isolated by negative selection from the PBMC fraction. Cells were resuspended in TriPure and RNA was isolated using the Zymo RNA Miniprep Kit.
cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina)
RNA seq data were generated on Illumina HiSeq 3000 instrument according to the manufacturer's instructions

value: skin

tag: healthy control or papa

value: PAPA

tag: sample id


title: Breast Cancer BC1490

description:
Breast Cancer
SH4YM22_Cell1

tag: tumor stage (figo)


title: T84 DMSO Rep3

description:
Project_E04_All_Expressed_Genes.xlsx
T84_DMSO_3_Normalised
T84_DMSO_3_Raw

source_name: T84 DMSO, colorectal cancer cell line

value: DMSO


title: Breast Cancer BC1473

description:
Breast Cancer
SH4YM15_Cell4

tag: age


title: mRNA_PAPA_LDG_1

source_name: Human LDGs

value: LDGs


title: Breast Cancer BC1472

description:
Breast Cancer
SH4YM15_Cell3


title: Breast Cancer BC1471

description:
Breast Cancer
SH4YM15_Cell2


title: T84 trametinib Rep1

description:
Project_E04_All_Expressed_Genes.xlsx
T84_MEKi_1_Normalised
T84_MEKi_1_Raw


title: T84 DMSO Rep2

description:
Project_E04_All_Expressed_Genes.xlsx
T84_DMSO_2_Normalised
T84_DMSO_2_Raw


title: mRNA_HC_Skin_2


title: Breast Cancer BC1467

description:
Breast Cancer
SH4YM14_Cell2


title: T84 DMSO Rep1

description:
Project_E04_All_Expressed_Genes.xlsx
T84_DMSO_1_Normalised
T84_DMSO_1_Raw


title: mRNA_HC_NDN_1

source_name: Human neutrophils

value: neutrophils


title: Breast Cancer BC1465

description:
Breast Cancer
SH4YM10_Cell4


title: Breast Cancer BC1459

description:
Breast Cancer
SH4YM09_Cell2


title: Breast Cancer BC1463

description:
Breast Cancer
SH4YM10_Cell2


title: GAS treated [33]

organism: Streptococcus pyogenes

source_name: Bacteria

tag: strain

tag: agent

value: PBT2 and zinc


title: HCT116_R4 Rep3

data_processing:
Bcl2fastq software (v1.8.4, Illumina) was used for converting the raw basecalls to fastqs and to further demultiplex the sequencing data.
Tophat2 spliced alignment software was used to align reads to the reference genome (GRCH37) in combination with Bowtie2.
Once the reads were aligned, HTSeq-count was used to count the number of reads mapping unambiguously to genomic feature in each sample.
Differential expression analysis of the count data was done in R using DESeq2 bioconductor package.
Genome_build: GRCH37
Supplementary_files_format_and_content: Raw count data was normalised to correct for library size and RNA composition bias. Reads per genomic feature are presented per sample.

source_name: Colorectal cancer cell line

treatment_protocol: Cells were treated with or without increasing concentrations of trametinib for upto 2 months and resistant clones isolated.


title: HCT116_R4 Rep2


title: GAS treated [31]


title: Breast Cancer BC1457

description:
Breast Cancer
SH4YM07_Cell4


title: Breast Cancer BC1454

description:
Breast Cancer
SH4YM07_Cell1


title: Breast Cancer BC1468

description:
Breast Cancer
SH4YM14_Cell3


title: GAS treated [32]


title: Breast Cancer BC1450

description:
Breast Cancer
SH4YM06_Cell1


title: Breast Cancer BC1452

description:
Breast Cancer
SH4YM06_Cell3


title: mRNA_PAPA_NDN_1


title: HCT116 Parental Rep2


title: HCT116 Parental Rep3


title: GAS untreated [29]


title: HCT116 Parental Rep1


title: HCT116_R4 Rep1


title: Ant_differentiated_donor_3

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

data_processing:
To process sequences, Illumina RTA-generated BCL files were converted to FASTQ files and sequence read and base quality were checked using the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sequences were aligned to hg19 using Tophat (26). Lane level bam data files were merged using the Picard MergeSamFiles tool and suspected PCR duplicates were marked, not removed, in the alignment files using the Picard MarkDuplicates tool (http://broadinstitute.github.io/picard/). Local realignment was performed around indels, and base quality score recalibration was run using GATK tools. Fragment counts were generated using the featureCounts function in the Bioconductor Rsubread package.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data consist of tab-delimited counts per gene for each sample. The first column contains the NCBI Gene ID, and the remaining columns are counts for each gene per sample.

source_name: differentiated anterior endothelial cells

growth_protocol: For cultured endothelial cells, the cell suspension was plated on gelatin coated T-75 flasks in EBM-2 medium supplemented with antibiotic/antimycotic (Invitrogen), 10% FBS (Invitrogen), 100 μg/ml ECGS (Millipore), 50 μg/ml Heparin (Invitrogen), and 40 ng/ml VEGF (R&D Systems). For kidney and lung samples, epithelial cells were removed from the cell suspension before plating using EpCAM microbeads (Miltenyi Biotec) to prevent epithelial cell overgrowth. Cells were cultured at 5% O2 until confluent and then endothelial cells as the CD144 positive and CD45 negative population were sorted on BD FACSAria II at the UW SLU Flow Cytometry Facility. After sorting, organ specific endothelial cells were cultured in EBM-2 supplemented with antibiotic/antimycotic, 10% FBS, 100 μg/ml ECGS, 50 μg/ml Heparin, and 20 ng/mL VEGF, on gelatin-coated plates and used for further experiments between passages 1-3.

extract_protocol:
Total RNA from cultured and freshly isolated organ specific endothelial cells was purified using the RNAeasy Mini Kit (Qiagen) and residual DNA was removed by on-column DNase digestion. RNA quality was assessed with the Agilent RNA 6000 Nano Kit using the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with RNA integrity number higher than 8 were kept for further analysis. RNA sequencing was performed on poly-A-enriched samples using Illumina TruSeq.
Each library was barcoded using the Illumina adapters, and amplified with 13 cycles of PCR. Library concentrations were quantified using the Quant-it dsDNA Assay (Life Technologies, Carlsbad, CA). Libraries were normalized and pooled based on Agilent 2100 Bioanalyzer results (Agilent Technologies, Santa Clara, CA), and the pools were sequenced on an Illumina HiSeq 2500.

treatment_protocol: Normal human fetal organs were obtained upon informed consent from abortion material (age 16-20 weeks) and the same donor tissues (kidney, lung, liver, and heart) were used to isolate organ specific endothelial cells. Tissues were minced finely in serum-free EBM-2 endothelial growth medium (Lonza) supplemented with 0.2 mg/ml Liberase and 100 U/ml DNase (Roche) and incubated for 30 min at 37 0C in a water bath with shaking. The resulting tissue homogenate was filtered twice through a 40 μm cell strainer to remove tissue debris and large vessels. For the isolation of fresh endothelial cells, EpCAM-positive cells were depleted first from the cell suspension using EpCAM microbeads (Miltenyi Biotec), followed by the depletion of CD45-positive cells using CD45 MicroBeads (Miltenyi Biotec). Then the CD144 positive cells were magnetically separated using CD144 MicroBeads (Miltenyi Biotec) on 2 different columns.

value: Anterior

value: Differentiated


title: Breast Cancer BC1449

description:
Breast Cancer
SH4YM05_Cell4


title: Breast Cancer BC1447

description:
Breast Cancer
SH4YM05_Cell2


title: Breast Cancer BC1444

description:
Breast Cancer
SH4YM03_Cell3


title: Ant_differentiated_donor_2


title: Ant_differentiated_donor_1


title: Breast Cancer BC1442

description:
Breast Cancer
SH4YM03_Cell1


title: U6_2

city: Hangzhou

first: Weiqiang

last: Lin

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Basecalls performed by BGISEQ-500 basecalling Software
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence to generate clean data using SOAPnuke V1.5.2 with parameters -l 15 -q 0.5 -n 0.1.
Clean data were mapped to the human genome (hg38) using the Bowtie2 tool
Expression levels of genes were measured by Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) using RSEM V1.2.12
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CRC cell line SW480

growth_protocol: SW480 CRC cell line (from the American Type Culture Collection, ATCC) was cultured in RPMI-1640 medium which was supplemented with 10% fetal bovine serum (GIBCO, Cat No. 10099), and 1% penicillin/streptomycin (GIBCO, Cat No. 15140). Cells were maintained in a 37 °C incubator with 5% CO2.

extract_protocol:
The cells were extracted with Trizol reageant (Invitrogen)
RNA libraries were prepared according the standard BGISEQ-500 library construction protocols

treatment_protocol: SW480 cells were infected with the recombinant lenti-viruses from control shRNA and CABLES2 shRNA vevtors  respectivly

value: colorectal cancer cell

tag: shRNA

value: control vehicle cells


title: U6_1


title: CAB_2

value: CABLES2 shRNA-1 cells


title: Post_differentiated_donor_3

source_name: differentiated posterior endothelial cells

value: Posterior


title: Breast Cancer BC1441

description:
Breast Cancer
SH4YM01_Cell4

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.


title: Post_differentiated_donor_2


title: CAB_1


title: GAS untreated [30]


title: GAS untreated [28]


title: Breast Cancer BC1439

description:
Breast Cancer
SH4YM01_Cell2


title: Breast Cancer BC1440

description:
Breast Cancer
SH4YM01_Cell3


title: Breast Cancer BC1438

description:
Breast Cancer
SH4YM01_Cell1


title: Post_differentiated_donor_1


title: Liver_fresh_tissue_donor_85

source_name: fresh liver tissue endothelial cells donor 85 (M, 122 d)

value: Liver

value: Fresh


title: Heart_fresh_tissue_donor_85

source_name: fresh heart tissue endothelial cells donor 85 (M, 122 d)

value: Heart