title: DLC16011232508 (re-analyzed)

description:
Complete data.txt.gz
Sample 151


title: DLC16011232503

status: Public on Jun 24 2019

type: SRA

city: Wuhan

first: xuewen

last: xu

state: Hubei

address: Shizishan street, No.1

country: China

institute: Huazhong Agricultural University

description:
Complete data.txt.gz
Sample 150

library_source: transcriptomic

data_processing:
Clean reads were obtained from the released raw reads through the following quality control steps: 1) remove reads containing adaptor; 2) remove reads containing more than 5% N; 3) remove low-quality reads
Alignment of RNA-seq data was conducted using Hisat2 V2.0.5 with the genome assembly Sscrofa11.1 (GCA_000003025) as the reference.
The aligned reads for each sample were then assembled into transcripts with StringTie v1.3.3 .
The generated transcripts from different samples were merged using the “merge” function of StringTie and yielded the final annotation file (the merged.gtf file)
The differential expression analysis was conducted with Ballgown.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample

molecule: polyA RNA

organism: Sus scrofa

source_name: longissimus dorsi muscle

growth_protocol: The experimental population was composed of 265 F1 animals from the crossing of 8 Duroc boars and 112 Luchuan sows, which were fed with the same diets at the same farm. All animals were slaughtered by a standardized procedure at the age of 210 days ± 6 days at the same abattoir.

extract_protocol:
Total RNA was extracted from longissimus dorsi muscle samples with Trizol reagent according to the product instructions. RNA samples were quantified using NanoDrop-2000 spectrophotometers (Thermo Scientific) and checked for purity and integrity using Agilent 2100 bioanalyzer.
The 150-bp paired-end RNA sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep kit for Illumina® (NEB, USA) according to the manufacturer’s protocols and sequenced on the Illumina Hiseq 4000 platform.

treatment_protocol: Twenty-five minutes postmortem, samples of the longissimus dorsi muscle at the thoracolumbar junction were taken for meat quality trait measurements and RNA extraction.

tag: breed

value: Duroc x Luchuan crossed pigs

tag: tissue

value: longissimus dorsi muscle

tag: imf content


title: DLC16011132702

description:
Complete data.txt.gz
Sample 149


title: DLC16011528906

description:
Complete data.txt.gz
Sample 164


title: R2G_16_rep2

first: Jun

last: You

address: Xudong 2nd Road

institute: Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences

description: Waterlogging tolerant genotype, waterlogging stress for 16 hours, replicate 2

data_processing:
Illumina Casava1.7 software used for basecalling.
The program FastQC was employed to determine the base quality of the raw reads (in FASTQ format) and we removed the paired-end reads containing more than 5% ambiguous residues (Ns) and those containing >10% bases with a Phred quality score of 10. Then, the raw reads were trimmed using Trimmomatic, version 0.32
The high-quality reads were mapped to the sesame (Sesamum indicum L.) reference genome v1.0 using the STAR software
Genome_build: GCF_000512975.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Sesamum indicum

source_name: root

extract_protocol:
Total RNA was extracted from 126 root samples using the TRIzol reagent (Invitrogen), and treated with DNase I and Oligo (dT) to isolate mRNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

tag: developmental stage

value: flowering stage

tag: genotype

tag: condition

value: waterlogging stress for 16 hours


title: EOL1.OTX015.8h_Rep3

city: Berlin

first: Bernard

last: Haendler

address: Muellerstr. 178

country: Germany

institute: Bayer AG

data_processing:
Illumina bcl2fastq v2.17 was used to convert bcl to fastqs.
RNA-seq reads were aligned to GRCh38 using STAR aligner.
RSEM was used to quantify reads in genes.
Expected counts were further analyzed in R, DESeq2 was used for differential gene expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes expected counts (obtained with RSEM) for all samples

organism: Homo sapiens

source_name: EOL-1 (AML)

growth_protocol: HL-60, Jurkat, MOLM-13, MOLM14, NOMO-1, KOPN-8, EOL-1 and OCI-AML3 were cultured in RPMI 1640 (FG1215). OCI-AML2, OCI-AML5 and RS4-11 were cultured in Alpha-Medium (F0915). MV4-11 and SEM were cultured in IMDM (21980-032). All above listed media were supplemented with 10% fetal bovine serum. Cell lines were cultured at 37C in 5% CO2.

extract_protocol:
RNA was extracted using using RNeasy-Plus Mini kit (Qiagen #74134).
Libraries were prepared using Illumina TruSeq Stranded mRNA Kit and sequenced on Illumina HiSeq2500 HTv4 (single-end, dual-indexing, 50 Cycles).

treatment_protocol: Cells were treated for 8h (P-TEFb - 0.05 µM, OTX015 - 1 µM), 24h (BAY-155 - 2 µM, Brequinar - 2 µM, DMSO – 0.1%) and 96h (EPZ-5676 - 3 µM, DMSO – 0.1%) prior to RNA extraction.

tag: cell line

tag: agent

tag: concentration

tag: time point (hours)

tag: mll fusion type

value: MLL-TD


title: R2G_16_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 16 hours, replicate 1


title: DLC16011129805 (re-analyzed)

description:
Complete data.txt.gz
Sample 148


title: EOL1.OTX015.8h_Rep2


title: DLC16011128512

description:
Complete data.txt.gz
Sample 145


title: DLC16011129801

description:
Complete data.txt.gz
Sample 146


title: DLC16011128506

description:
Complete data.txt.gz
Sample 144


title: R2G_14_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 14 hours, replicate 2

value: waterlogging stress for 14 hours


title: DLC16011128504

description:
Complete data.txt.gz
Sample 143


title: EOL1.OTX015.8h_Rep1


title: R2G_18_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 18 hours, replicate 1

value: waterlogging stress for 18 hours


title: R2G_14_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 14 hours, replicate 1


title: DLC16011128503

description:
Complete data.txt.gz
Sample 142


title: EOL1.BAY1251152.8h_Rep2


title: DLC16011128502 (re-analyzed)

description:
Complete data.txt.gz
Sample 141


title: DLC16011128501

description:
Complete data.txt.gz
Sample 140


title: EOL1.BAY1251152.8h_Rep1


title: DLC16011128402 (re-analyzed)

description:
Complete data.txt.gz
Sample 136


title: DLC16011128404

description:
Complete data.txt.gz
Sample 137


title: OCIAML3.OTX015.8h_Rep2

source_name: OCI-AML3 (AML)

value: NMP mut


title: DLC16011129804

description:
Complete data.txt.gz
Sample 147


title: DLC16011032109

description:
Complete data.txt.gz
Sample 134


title: OCIAML3.OTX015.8h_Rep1


title: DLC16011028005

description:
Complete data.txt.gz
Sample 132


title: DLC16011028201

description:
Complete data.txt.gz
Sample 133


title: R2G_10_rep3

description: Waterlogging tolerant  genotype, waterlogging stress for 10 hours, replicate 3

value: waterlogging stress for 10 hours


title: R2G_14_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 14 hours, replicate 3


title: EOL1.BAY1251152.8h_Rep3


title: OCIAML3.BAY1251152.8h_Rep3


title: DLC16011027407

description:
Complete data.txt.gz
Sample 129


title: R2G_10_rep2

description: Waterlogging tolerant  genotype, waterlogging stress for 10 hours, replicate 2


title: DLC16011027401 (re-analyzed)

description:
Complete data.txt.gz
Sample 128


title: DLC16011028004

description:
Complete data.txt.gz
Sample 131


title: OCIAML3.BAY1251152.8h_Rep2


title: R2G_10_rep1

description: Waterlogging tolerant  genotype, waterlogging stress for 10 hours, replicate 1


title: R2G_12_rep2

description: Waterlogging tolerant genotype, waterlogging stress for 12 hours, replicate 2

value: waterlogging stress for 12 hours


title: DLC16010930011

description:
Complete data.txt.gz
Sample 127


title: OCIAML3.BAY1251152.8h_Rep1


title: R2G_0_rep3

description: Waterlogging tolerant genotype, control condition for 0 hours, replicate 3

value: control condition for 0 hours


title: OCIAML3.OTX015.8h_Rep3


title: R2G_12_rep1

description: Waterlogging tolerant genotype, waterlogging stress for 12 hours, replicate 1


title: DLC16011033313

description:
Complete data.txt.gz
Sample 135


title: R2G_0_rep2

description: Waterlogging tolerant genotype, control condition for 0 hours, replicate 2


title: DLC16010930007

description:
Complete data.txt.gz
Sample 126


title: DLC16010930005

description:
Complete data.txt.gz
Sample 125


title: DLC16010930003

description:
Complete data.txt.gz
Sample 124


title: ML2.OTX015.8h_Rep3

source_name: ML2 (AML)

value: MLL-AF


title: R2G_0_rep1

description: Waterlogging tolerant genotype, control condition for 0 hours, replicate 1


title: ML2.OTX015.8h_Rep2


title: DLC16010929603

description:
Complete data.txt.gz
Sample 121


title: DLC16010929610

description:
Complete data.txt.gz
Sample 123


title: EG_8_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 8 hours, replicate 3

value: Ezhi No.2 (EG)

value: waterlogging stress for 8 hours


title: ML2.OTX015.8h_Rep1


title: DLC16011027409

description:
Complete data.txt.gz
Sample 130


title: DLC16011128411

description:
Complete data.txt.gz
Sample 139


title: R2G_12_rep3

description: Waterlogging tolerant genotype, waterlogging stress for 12 hours, replicate 3


title: DLC16010929605

description:
Complete data.txt.gz
Sample 122


title: DLC16010928108

description:
Complete data.txt.gz
Sample 120


title: EG_8_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 8 hours, replicate 2


title: ML2.BAY1251152.8h_Rep3


title: DLC16010928103

description:
Complete data.txt.gz
Sample 119


title: DLC16010928102 (re-analyzed)

description:
Complete data.txt.gz
Sample 118


title: EG_8_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 8 hours, replicate 1


title: DLC16010927912

description:
Complete data.txt.gz
Sample 117


title: ML2.BAY1251152.8h_Rep2


title: EG_6_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 6 hours, replicate 3

value: waterlogging stress for 6 hours


title: DLC16010927904

description:
Complete data.txt.gz
Sample 114


title: ML2.BAY1251152.8h_Rep1


title: DLC16010927906

description:
Complete data.txt.gz
Sample 116


title: DLC16010927901

description:
Complete data.txt.gz
Sample 113


title: EG_6_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 6 hours, replicate 2


title: Jurkat.DMSO.96h_Rep2

source_name: Jurkat (ALL)

value: Jurkat

value: DMSO

value: 0.10 percent

value: MLL-WT


title: DLC16010927308

description:
Complete data.txt.gz
Sample 111

value: Duroc x Luchuan crossed pigs

value: longissimus dorsi muscle


title: EG_6_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 6 hours, replicate 1

value: root

value: flowering stage


title: DLC16010927307

description:
Complete data.txt.gz
Sample 110


title: DLC16010927306

description:
Complete data.txt.gz
Sample 109


title: EG_48W_rep3

description: Waterlogging sensitive genotype, recovery for 12 hours, 48 hours after stress treatment, wilting, replicate 3


title: DLC16010927305

description:
Complete data.txt.gz
Sample 108


title: DLC16010927302

description:
Complete data.txt.gz
Sample 107


title: NOMO1.DMSO.96h_Rep3

source_name: NOMO-1 (AML)


title: EG_48W_rep2

description: Waterlogging sensitive genotype, recovery for 12 hours, 48 hours after stress treatment, wilting, replicate 2


title: DLC16010927301

description:
Complete data.txt.gz
Sample 106


title: NOMO1.DMSO.96h_Rep2


title: DLC16010837812

description:
Complete data.txt.gz
Sample 105


title: EG_48W_rep1

description: Waterlogging sensitive genotype, recovery for 12 hours, 48 hours after stress treatment, wilting, replicate 1


title: NOMO1.DMSO.96h_Rep1


title: DLC16010837810 (re-analyzed)

description:
Complete data.txt.gz
Sample 104


title: DLC16010837808

description:
Complete data.txt.gz
Sample 103


title: MOLM13.DMSO.96h_Rep3

source_name: MOLM-13 (AML)


title: DLC16010837803

description:
Complete data.txt.gz
Sample 102


title: EG_48_rep2

description: Waterlogging sensitive genotype, recovery for 12 hours, 48 hours after stress treatment, replicate 2


title: MOLM13.DMSO.96h_Rep2


title: DLC16010834002

description:
Complete data.txt.gz
Sample 101


title: EG_48_rep1

description: Waterlogging sensitive genotype, recovery for 12 hours, 48 hours after stress treatment, replicate 1


title: DLC16010737910

description:
Complete data.txt.gz
Sample 100


title: MOLM13.DMSO.96h_Rep1


title: DLC16010737907

description:
Complete data.txt.gz
Sample 98


title: DLC16010927309

description:
Complete data.txt.gz
Sample 112


title: DLC16010737906

description:
Complete data.txt.gz
Sample 97


title: DLC16010729908

description:
Complete data.txt.gz
Sample 92


title: EG_46_rep3

description: Waterlogging sensitive genotype, recovery for 10 hours, 46 hours after stress treatment, replicate 3


title: EG_48_rep3

description: Waterlogging sensitive genotype, recovery for 12 hours, 48 hours after stress treatment, replicate 3


title: MV411.DMSO.96h_Rep3


title: EG_46_rep1

description: Waterlogging sensitive genotype, recovery for 10 hours, 46 hours after stress treatment, replicate 1


title: DLC16010737903

description:
Complete data.txt.gz
Sample 94


title: EG_44_rep3

description: Waterlogging sensitive genotype, recovery for 8 hours, 44 hours after stress treatment, replicate 3


title: DLC16010927905

description:
Complete data.txt.gz
Sample 115


title: Jurkat.EPZ5676.96h_Rep3


title: DLC16010729912

description:
Complete data.txt.gz
Sample 93


title: MV411.DMSO.96h_Rep2


title: MV411.DMSO.96h_Rep1


title: DLC16010729904

description:
Complete data.txt.gz
Sample 90


title: EG_46_rep2

description: Waterlogging sensitive genotype, recovery for 10 hours, 46 hours after stress treatment, replicate 2


title: DLC16010629703

description:
Complete data.txt.gz
Sample 89


title: EG_44_rep1

description: Waterlogging sensitive genotype, recovery for 8 hours, 44 hours after stress treatment, replicate 1


title: DLC16010737904

description:
Complete data.txt.gz
Sample 95


title: EG_42_rep3

description: Waterlogging sensitive genotype, recovery for 6 hours, 42 hours after stress treatment, replicate 3


title: DLC16010737905

description:
Complete data.txt.gz
Sample 96


title: DLC16010729906

description:
Complete data.txt.gz
Sample 91


title: DLC16010629702

description:
Complete data.txt.gz
Sample 88


title: DLC16010533009

description:
Complete data.txt.gz
Sample 87


title: DLC16010430101

description:
Complete data.txt.gz
Sample 85


title: Jurkat.EPZ5676.96h_Rep1


title: DLC16010430102

description:
Complete data.txt.gz
Sample 86


title: DLC16010429107

description:
Complete data.txt.gz
Sample 82


title: DLC16010429106

description:
Complete data.txt.gz
Sample 81


title: DLC16010429104

description:
Complete data.txt.gz
Sample 80


title: EG_42_rep2

description: Waterlogging sensitive genotype, recovery for 6 hours, 42 hours after stress treatment, replicate 2


title: NOMO1.EPZ5676.96h_Rep1


title: NOMO1.EPZ5676.96h_Rep2


title: EG_44_rep2

description: Waterlogging sensitive genotype, recovery for 8 hours, 44 hours after stress treatment, replicate 2


title: MOLM13.EPZ5676.96h_Rep3


title: DLC16010329006

description:
Complete data.txt.gz
Sample 75


title: DLC16010329012

description:
Complete data.txt.gz
Sample 76


title: EG_40_rep2

description: Waterlogging sensitive genotype, recovery for 4 hours, 40 hours after stress treatment, replicate 2


title: MOLM13.EPZ5676.96h_Rep2


title: EG_40_rep3

description: Waterlogging sensitive genotype, recovery for 4 hours, 40 hours after stress treatment, replicate 3


title: EG_40_rep1

description: Waterlogging sensitive genotype, recovery for 4 hours, 40 hours after stress treatment, replicate 1


title: DLC16010130912

description:
Complete data.txt.gz
Sample 74


title: NOMO1.EPZ5676.96h_Rep3


title: EG_4_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 4 hours, replicate 3

value: waterlogging stress for 4 hours


title: DLC15123130310

description:
Complete data.txt.gz
Sample 71


title: DLC15123130412

description:
Complete data.txt.gz
Sample 72


title: MV411.EPZ5676.96h_Rep3


title: Jurkat.DMSO.96h_Rep1


title: DLC16010429103

description:
Complete data.txt.gz
Sample 79


title: MOLM13.EPZ5676.96h_Rep1


title: EG_42_rep1

description: Waterlogging sensitive genotype, recovery for 6 hours, 42 hours after stress treatment, replicate 1


title: EG_4_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 4 hours, replicate 2


title: DLC16010331007

description:
Complete data.txt.gz
Sample 78


title: MV411.EPZ5676.96h_Rep2


title: DLC15122931301

description:
Complete data.txt.gz
Sample 67


title: EG_4_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 4 hours, replicate 1


title: DLC15123130303

description:
Complete data.txt.gz
Sample 68


title: DLC15122921503

description:
Complete data.txt.gz
Sample 64


title: DLC15122921505

description:
Complete data.txt.gz
Sample 65


title: DLC15123130308

description:
Complete data.txt.gz
Sample 70


title: DLC15123130306 (re-analyzed)

description:
Complete data.txt.gz
Sample 69


title: MV411.EPZ5676.96h_Rep1


title: EG_38_rep3

description: Waterlogging sensitive genotype, recovery for 2 hours, 38 hours after stress treatment, replicate 3


title: Jurkat.DMSO.24h_Rep3


title: DLC15122732003

description:
Complete data.txt.gz
Sample 61


title: DLC15122831901 (re-analyzed)

description:
Complete data.txt.gz
Sample 63


title: Jurkat.DMSO.24h_Rep2


title: DLC15122731808 (re-analyzed)

description:
Complete data.txt.gz
Sample 59


title: Jurkat.DMSO.24h_Rep1


title: DLC15122831409

description:
Complete data.txt.gz
Sample 62


title: EG_38_rep2

description: Waterlogging sensitive genotype, recovery for 2 hours, 38 hours after stress treatment, replicate 2


title: EG_38_rep1

description: Waterlogging sensitive genotype, recovery for 2 hours, 38 hours after stress treatment, replicate 1


title: EG_36_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 36 hours, replicate 3

value: waterlogging stress for 36 hours


title: DLC15122632303

description:
Complete data.txt.gz
Sample 56


title: DLC15122731804

description:
Complete data.txt.gz
Sample 57


title: DLC15122731805

description:
Complete data.txt.gz
Sample 58


title: Jurkat.Brequinar.24h_Rep1

value: Brequinar


title: EG_36_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 36 hours, replicate 2


title: DLC15122436910

description:
Complete data.txt.gz
Sample 55


title: DLC15122436904

description:
Complete data.txt.gz
Sample 54


title: EG_36_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 36 hours, replicate 1


title: Jurkat.EPZ5676.96h_Rep2


title: Jurkat.BAY155.24h_Rep3


title: DLC15122432609

description:
Complete data.txt.gz
Sample 52


title: DLC15122436903

description:
Complete data.txt.gz
Sample 53


title: DLC15122432607

description:
Complete data.txt.gz
Sample 51


title: EG_32_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 32 hours, replicate 3

value: waterlogging stress for 32 hours


title: DLC15122432601

description:
Complete data.txt.gz
Sample 50


title: EG_32_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 32 hours, replicate 2


title: Jurkat.BAY155.24h_Rep2


title: Jurkat.BAY155.24h_Rep1


title: DLC15122432211

description:
Complete data.txt.gz
Sample 49


title: DLC15122423109

description:
Complete data.txt.gz
Sample 48


title: Jurkat.Brequinar.24h_Rep2


title: NOMO1.DMSO.24h_Rep3


title: DLC15122334305

description:
Complete data.txt.gz
Sample 45


title: EG_28_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 28 hours, replicate 3

value: waterlogging stress for 28 hours


title: DLC15122423103

description:
Complete data.txt.gz
Sample 46


title: EG_32_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 32 hours, replicate 1


title: NOMO1.DMSO.24h_Rep2

value: MLL-AF


title: EG_28_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 28 hours, replicate 2

value: Ezhi No.2 (EG)


title: DLC15122236604

description:
Complete data.txt.gz
Sample 43


title: NOMO1.DMSO.24h_Rep1


title: DLC15122236605

description:
Complete data.txt.gz
Sample 44


title: DLC15122236602

description:
Complete data.txt.gz
Sample 42


title: EG_28_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 28 hours, replicate 1


title: DLC15122123209

description:
Complete data.txt.gz
Sample 39


title: NOMO1.Brequinar.24h_Rep3


title: DLC15122236601

description:
Complete data.txt.gz
Sample 41


title: DLC15122123203

description:
Complete data.txt.gz
Sample 38


title: NOMO1.Brequinar.24h_Rep2


title: DLC15122732001

description:
Complete data.txt.gz
Sample 60


title: EG_24_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 24 hours, replicate 3

value: waterlogging stress for 24 hours


title: DLC15122423106

description:
Complete data.txt.gz
Sample 47


title: DLC15121923306

description:
Complete data.txt.gz
Sample 37


title: EG_24_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 24 hours, replicate 2


title: DLC15121923305

description:
Complete data.txt.gz
Sample 36


title: NOMO1.Brequinar.24h_Rep1


title: NOMO1.BAY155.24h_Rep3


title: DLC15121837310 (re-analyzed)

description:
Complete data.txt.gz
Sample 35


title: DLC15121638107 (re-analyzed)

description:
Complete data.txt.gz
Sample 33


title: EG_22_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 22 hours, replicate 3

value: waterlogging stress for 22 hours


title: NOMO1.BAY155.24h_Rep2


title: EG_22_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 22 hours, replicate 2


title: MOLM13.DMSO.24h_Rep3


title: EG_22_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 22 hours, replicate 1


title: EG_20_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 20 hours, replicate 3

value: waterlogging stress for 20 hours


title: MOLM13.DMSO.24h_Rep2

value: DMSO


title: NOMO1.BAY155.24h_Rep1


title: DLC15121537504

description:
Complete data.txt.gz
Sample 29


title: DLC15121526307

description:
Complete data.txt.gz
Sample 28


title: DLC15121537506

description:
Complete data.txt.gz
Sample 30


title: DLC15121526305

description:
Complete data.txt.gz
Sample 27


title: DLC15120937103

description:
Complete data.txt.gz
Sample 23


title: DLC15121137604

description:
Complete data.txt.gz
Sample 25


title: DLC15121124807

description:
Complete data.txt.gz
Sample 24


title: DLC15121638110 (re-analyzed)

description:
Complete data.txt.gz
Sample 34


title: DLC16010737909

description:
Complete data.txt.gz
Sample 99


title: DLC15121622707 (re-analyzed)

description:
Complete data.txt.gz
Sample 31


title: MOLM13.DMSO.24h_Rep1

value: 0.10 percent


title: EG_20_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 20 hours, replicate 2


title: EG_24_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 24 hours, replicate 1


title: EG_20_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 20 hours, replicate 1


title: DLC15120925503

description:
Complete data.txt.gz
Sample 18


title: MOLM13.Brequinar.24h_Rep3


title: DLC15120925901 (re-analyzed)

description:
Complete data.txt.gz
Sample 20


title: DLC15120925907

description:
Complete data.txt.gz
Sample 22


title: EG_2_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 2 hours, replicate 2

value: waterlogging stress for 2 hours


title: MOLM13.Brequinar.24h_Rep2


title: DLC15121525707

description:
Complete data.txt.gz
Sample 26

value: Duroc x Luchuan crossed pigs


title: CM_x_72h_rep2

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

country: USA

institute: Stanford University School of Medicine

data_processing:
Library strategy: Ampli-seq
Ampli-seq pipeline of Ion Torrent Server
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: iPSC

growth_protocol: induced pluripotent stem cells (iPSC)  derived cardiomyocytes were routinely cultured on Matrigel (BD bioscience, NJ, USA), coated plastic in RPMI 1640 (Gibco, NY, USA) supplemented with B27 (Gibco)

extract_protocol:
Qiazol
Libraries prepared from 10ng RNA.
Depth of reads about 30 million/sample.

treatment_protocol: Cells were incubated with Trypanosoma cruzi Y strain culture in RPMI 1640 (Gibco, NY, USA)

tag: disease state

value: Control

tag: time

tag: cell type

value: iPSC-derived cardiomyocytes


title: CM_x_72h_rep1


title: DLC15120625105 (re-analyzed)

description:
Complete data.txt.gz
Sample 17

value: longissimus dorsi muscle


title: MOLM13.Brequinar.24h_Rep1


title: EG_2_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 2 hours, replicate 1

value: root

value: flowering stage


title: MV411.DMSO.24h_Rep3


title: MV411.DMSO.24h_Rep2


title: EG_18_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 18 hours, replicate 2

value: waterlogging stress for 18 hours


title: DLC15120925905 (re-analyzed)

description:
Complete data.txt.gz
Sample 21


title: DLC15120624301

description:
Complete data.txt.gz
Sample 16


title: DLC15120624109

description:
Complete data.txt.gz
Sample 15


title: EG_2_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 2 hours, replicate 3


title: CM_x_48h_rep2


title: EG_18_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 18 hours, replicate 3


title: CM_x_48h_rep1


title: MV411.DMSO.24h_Rep1


title: EG_18_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 18 hours, replicate 1


title: CM_x_24h_rep2


title: DLC15120925505

description:
Complete data.txt.gz
Sample 19


title: MV411.Brequinar.24h_Rep3

value: Brequinar


title: DLC15120426404

description:
Complete data.txt.gz
Sample 13


title: DLC15120526205 (re-analyzed)

description:
Complete data.txt.gz
Sample 14


title: EG_16_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 16 hours, replicate 3

value: waterlogging stress for 16 hours


title: CM_x_24h_rep1


title: CM_x_0h_rep2


title: DLC15120423705

description:
Complete data.txt.gz
Sample 12


title: EG_16_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 16 hours, replicate 2


title: MV411.Brequinar.24h_Rep1

value: MLL-AF


title: MV411.Brequinar.24h_Rep2


title: EG_16_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 16 hours, replicate 1

value: Ezhi No.2 (EG)


title: MOLM13.BAY155.24h_Rep3


title: CM_x_0h_rep1


title: DLC15113025007

description:
Complete data.txt.gz
Sample 10


title: DLC16010331003

description:
Complete data.txt.gz
Sample 77


title: EG_14_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 14 hours, replicate 2

value: waterlogging stress for 14 hours


title: MOLM13.BAY155.24h_Rep2


title: DLC15113024701

description:
Complete data.txt.gz
Sample 9


title: EG_14_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 14 hours, replicate 1


title: DLC15112637008

description:
Complete data.txt.gz
Sample 8


title: CM_Try_48h_rep2

value: Chagas disease


title: MOLM13.BAY155.24h_Rep1


title: CM_Try_72h_rep2


title: CM_Try_48h_rep1


title: MV411.BAY155.24h_Rep3


title: EG_12_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 12 hours, replicate 3

value: waterlogging stress for 12 hours


title: DLC15112526003

description:
Complete data.txt.gz
Sample 7


title: EG_12_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 12 hours, replicate 2


title: MV411.BAY155.24h_Rep1


title: CM_Try_24h_rep2


title: DLC15120123008

description:
Complete data.txt.gz
Sample 11


title: DLC15111318902

description:
Complete data.txt.gz
Sample 5


title: EG_12_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 12 hours, replicate 1


title: MV411.BAY155.24h_Rep2


title: CM_Try_24h_rep1


title: Jurkat.OTX015.8h_Rep3

value: Jurkat

value: MLL-WT


title: DLC15111221605

description:
Complete data.txt.gz
Sample 4


title: Jurkat.OTX015.8h_Rep2


title: CM_Try_0h_rep2


title: EG_14_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 14 hours, replicate 3


title: DLC15111020504

description:
Complete data.txt.gz
Sample 3


title: EG_10_rep2

description: Waterlogging sensitive genotype, waterlogging stress for 10 hours, replicate 2

value: waterlogging stress for 10 hours


title: CM_Try_72h_rep1


title: Jurkat.OTX015.8h_Rep1


title: DLC15110318504

description:
Complete data.txt.gz
Sample 2

value: Duroc x Luchuan crossed pigs


title: EG_10_rep1

description: Waterlogging sensitive genotype, waterlogging stress for 10 hours, replicate 1


title: DLC15112524411

description:
Complete data.txt.gz
Sample 6


title: DLC15103121701

description:
Complete data.txt.gz
Sample 1


title: EG_0_rep2

description: Waterlogging sensitive genotype, control condition for 0 hours, replicate 2

value: control condition for 0 hours


title: Jurkat.BAY1251152.8h_Rep2


title: Jurkat.BAY1251152.8h_Rep1


title: Top12_veh_24min

city: GENEVA

first: Benjamin

last: Albert

address: 30, quai Ernest-Ansermet

department: Bimol

country: Switzerland

institute: University of Genevea

library_source: genomic

data_processing:
For ChIP-Seq raw reads were aligned to the sacCer3
For ChIP-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For ChIP-Seq, reads that mapped to both sacCer3
For ChIP-Seq, the reads were shifted by 100 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: wig and bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

molecule: genomic DNA

organism: Saccharomyces cerevisiae W303

source_name: whole organism

growth_protocol: cells were grown at 30 degrees in YPAD to mid-log phase before heat shock

extract_protocol:
TruSeq ChIP library preparation kit (Illumina)
ChIP-seq was performed as described previously (Ribaud et al., 2012) (PMID: 21952045).

tag: strain

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

tag: treatment

value: Vehicle

tag: antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

value: 24 minutes after treatment


title: NOMO1.OTX015.8h_Rep2


title: Top12_veh_12min

value: 12 minutes after treatment


title: EG_10_rep3

description: Waterlogging sensitive genotype, waterlogging stress for 10 hours, replicate 3

value: root

value: flowering stage


title: NOMO1.OTX015.8h_Rep3

value: MLL-AF


title: EG_0_rep1

description: Waterlogging sensitive genotype, control condition for 0 hours, replicate 1

value: Ezhi No.2 (EG)


title: Top12_veh_18min

value: 18 minutes after treatment


title: CK_R2G_8_rep2

description: Waterlogging tolerant genotype, control condition for 8 hours, replicate 2

value: control condition for 8 hours


title: Chicken 19, jejunum

type: RNA

city: bologna

first: PAOLO

middle: o

last: BOSI

state: BOLOGNA

address: Viale Fanin, 46

department: DISTAL

country: Italy

institute: UNIVERSITY OF BOLOGNA

description: Gene expression data from oxyntic mucosa

hyb_protocol: Total mRNA was hybridized on  Affymetrix© GeneChip Chicken 1.0 ST Array.  Affymetrix hybridization, wash, and stain Kit for WT GenerChip Array were used.

scan_protocol: Quantification of transcript expression on a GeneAtlas imaging station (Affymetrix).

data_processing: Performance quality tests of the arrays including the labelling, hybridization, scanning and background signals by a Robust Multichip Analysis were performed on the CEL files using Transcriptomic Analysis Console (TAC) Affymetrix© software (4.0.1.36) .

label: biotin

organism: Gallus gallus

source_name: Chicken 19, jejunum mucosa

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol

growth_protocol: Ross 308 male  chicks were reared at the experimental facility of the University of Bologna within an environmental controlled poultry house and randomly allotted in 6 pens of 6 m2 each (25 birds/pen, 11 birds/m2). All the chicks were vaccinated against coccidiosis, infectious bronchitis virus, Marek’s disease virus, Newcastle and Gumboro disease. Stocking density was defined according to the European legislation in force (European Commission, 2007) to simulate the environmental conditions usually adopted in the intensive production system. Each pen was equipped with 2 circular pan feeders able to guarantee at least 2 cm of front space/bird and 10 nipples, while the floor was covered with chopped straw (2 kg/m2). Birds received 23L:1D of artificial light from 0 to 7 d and in the last 3 days before slaughter, whereas a photoperiod of 18L:6D was adopted in the remaining days. All the birds received the same standard commercial diet composed by three feeding phases: Starter (0-10d), Grower (11-25d) and Finisher (26-42d)

extract_protocol: Total RNA was extracted using GeneJET RNA Purification Kit (Thermo Scientific) according to manufacturer’s instructions and RNA quantity and quality were evaluated using Nanodrop ND 1000 spectrophotometer (Nanodrop Technologies Inc., Wilmington, DE, USA) and agarose gel electrophoresis, respectively. After, RNA integrity was evaluated through Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, California, USA).

treatment_protocol: At slaughter age (day 42), on 38 birds, selected with a homogeneous body weight, jejunum and cecum mucosae were collected by gently scraping after tissues rinsing in PSB to remove residues of digesta, and immediately frozen in liquid nitrogen and then stored at -80°C.

value: Jejunum mucosa

tag: breed

value: Ross 308

tag: diet

value: standard 3-phase diets

tag: age

value: 6 weeks

tag: gender

value: male


title: Chicken 18, jejunum

source_name: Chicken 18, jejunum mucosa

tag: tissue


title: CK_R2G_8_rep3

description: Waterlogging tolerant genotype, control condition for 8 hours, replicate 3

tag: developmental stage

tag: genotype

tag: condition


title: NOMO1.OTX015.8h_Rep1

tag: cell line

tag: agent

tag: concentration


title: Top12_veh_6min

value: 6 minutes after treatment


title: NOMO1.BAY1251152.8h_Rep2

tag: time point (hours)

tag: mll fusion type


title: Chicken 16, jejunum

source_name: Chicken 16, jejunum mucosa


title: Chicken 17, jejunum

source_name: Chicken 17, jejunum mucosa


title: NOMO1.BAY1251152.8h_Rep3


title: CM_Try_0h_rep1

tag: disease state

value: Chagas disease

tag: time

tag: cell type

value: iPSC-derived cardiomyocytes


title: Veh_24_top1

tag: strain

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP1-AID-KanMX6 MAT[alpha]

tag: treatment

value: Vehicle

tag: antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)


title: Chicken 15, jejunum

source_name: Chicken 15, jejunum mucosa

tag: breed

tag: diet

tag: age


title: EG_0_rep3

description: Waterlogging sensitive genotype, control condition for 0 hours, replicate 3

tag: tissue

value: root

tag: developmental stage

value: control condition for 0 hours


title: Chicken 14, jejunum

source_name: Chicken 14, jejunum mucosa

tag: gender


title: CK_R2G_8_rep1

description: Waterlogging tolerant genotype, control condition for 8 hours, replicate 1

value: flowering stage

tag: genotype

tag: condition


title: CK_R2G_48_rep2

description: Waterlogging tolerant genotype, control condition for 48 hours, replicate 2

value: control condition for 48 hours


title: Veh_6_top1


title: CK_R2G_48_rep3

description: Waterlogging tolerant genotype, control condition for 48 hours, replicate 3


title: CK_R2G_48_rep1

description: Waterlogging tolerant genotype, control condition for 48 hours, replicate 1


title: CK_R2G_44_rep3

description: Waterlogging tolerant genotype, control condition for 44 hours, replicate 3

value: control condition for 44 hours


title: CK_R2G_44_rep2

description: Waterlogging tolerant genotype, control condition for 44 hours, replicate 2


title: Top12_aux_18min

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

value: Auxin

value: 18 minutes after treatment


title: Veh_18_top1


title: NOMO1.BAY1251152.8h_Rep1

tag: cell line

tag: agent

tag: concentration

value: MLL-AF


title: Veh_12_top1

value: 12 minutes after treatment


title: MOLM13.OTX015.8h_Rep3

tag: time point (hours)

tag: mll fusion type


title: MOLM13.OTX015.8h_Rep2


title: MOLM13.BAY1251152.8h_Rep3


title: MOLM13.OTX015.8h_Rep1


title: MOLM13.BAY1251152.8h_Rep2


title: Top12_aux_24min

tag: time

value: 24 minutes after treatment


title: Top12_aux_6min

tag: strain

value: 6 minutes after treatment


title: CK_R2G_40_rep3

description: Waterlogging tolerant genotype, control condition for 40 hours, replicate 3

value: control condition for 40 hours


title: MOLM13.BAY1251152.8h_Rep1


title: CK_R2G_40_rep1

description: Waterlogging tolerant genotype, control condition for 40 hours, replicate 1


title: Chicken 12, jejunum

source_name: Chicken 12, jejunum mucosa

value: Jejunum mucosa

value: Ross 308

value: standard 3-phase diets

value: 6 weeks

value: male


title: Aux_24_top1

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP1-AID-KanMX6 MAT[alpha]

tag: treatment

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)


title: Chicken 13, jejunum

source_name: Chicken 13, jejunum mucosa


title: Chicken 11, jejunum

source_name: Chicken 11, jejunum mucosa


title: MV411.OTX015.8h_Rep2


title: Chicken 8, jejunum

source_name: Chicken 8, jejunum mucosa


title: Chicken 7, jejunum

source_name: Chicken 7, jejunum mucosa


title: CK_R2G_40_rep2

description: Waterlogging tolerant genotype, control condition for 40 hours, replicate 2

source_name: root

value: root

value: flowering stage


title: Chicken 9, jejunum

source_name: Chicken 9, jejunum mucosa


title: MV411.OTX015.8h_Rep3


title: Top12_aux_12min

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

tag: antibody


title: Aux_18_top1

value: Auxin


title: CK_R2G_44_rep1

description: Waterlogging tolerant genotype, control condition for 44 hours, replicate 1

value: control condition for 44 hours


title: Aux_12_top1


title: MV411.OTX015.8h_Rep1

value: MLL-AF


title: Chicken 5, jejunum

source_name: Chicken 5, jejunum mucosa

tag: breed


title: Chicken 6, jejunum

source_name: Chicken 6, jejunum mucosa

tag: diet


title: Aux_6_top1


title: Chicken 4, jejunum

source_name: Chicken 4, jejunum mucosa

tag: age


title: CK_R2G_4_rep3

description: Waterlogging tolerant genotype, control condition for 4 hours, replicate 3

tag: tissue

value: control condition for 4 hours


title: CK_R2G_4_rep2

description: Waterlogging tolerant genotype, control condition for 4 hours, replicate 2

tag: developmental stage


title: Chicken 3, jejunum

source_name: Chicken 3, jejunum mucosa

tag: gender


title: CK_R2G_4_rep1

description: Waterlogging tolerant genotype, control condition for 4 hours, replicate 1

tag: genotype


title: MV411.BAY1251152.8h_Rep2


title: Top1_Aux_CHX

source_name: whole organism

value: Auxin and Cycloheximide  at the same time

value: 20 minutes after treatment


title: Chicken 10, jejunum

source_name: Chicken 10, jejunum mucosa


title: Top1_Aux


title: veh_20min

value: W303 background;leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100 MATa

value: Vehicle


title: Chicken 2, jejunum

source_name: Chicken 2, jejunum mucosa

value: Jejunum mucosa

value: Ross 308


title: CK_R2G_32_rep2

description: Waterlogging tolerant genotype, control condition for 32 hours, replicate 2

tag: condition

value: control condition for 32 hours


title: MV411.BAY1251152.8h_Rep1

tag: cell line


title: CK_R2G_32_rep3

description: Waterlogging tolerant genotype, control condition for 32 hours, replicate 3


title: CK_R2G_32_rep1

description: Waterlogging tolerant genotype, control condition for 32 hours, replicate 1


title: 3D_t20 rep3

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

data_processing:
Sequencer Software HiSeq Control Software 2.2.58 was used for base calling of samples processed on Illumina HiSeq 2000. Base calling of samples processed in NextSeq Sequencer was performed with the Real-Time Analysis (RTA) v2.
Sequence reads were trimmed for adapter sequence, and  masked for low-complexityy or low-quality sequence (bbduk v35.92). Read quality was checked for each sample using FastqC v0.11.5. High-quality reads were mapped to CRCh38 whole genome using STAR v2.5.2a aligner.
Counting reads mapped to each gene was performed with HTSeq-count v0.6.0 software. RseqC v2.6.4 was used to distribute reads mapping to annotated genes (CDS_Exons, 5'UTR_Exons, 3'UTR_Exons, Introns)
Genome_build: Human (GRCh38) Lexogen QuantSeq 2.2.3 FWD (genome version GRCh38.77)
Supplementary_files_format_and_content: Non-normalized read counts (tab-delimited text files including features (genes) and the number of reads mapped to each of them)

growth_protocol: 2D culture condition - Cells were seeded onto Matrigel coated 12-well tissue culture plates at a cell density of 4x10^5 cells/well in mTeSR1. Culture medium was changed daily until a confluence of around 90-95%. 3D culture condition- For 3D aggregates formation, cell were incubated with Accutase at 37ºC for 7 min. Cells were then resuspended in mTeSR1 supplemented with ROCKi followed by seeding onto AggrewellTM 800 plate with a cell density of 1.5x10^6 cells/well for a final volume of 1.5 mL/well. After the first 24h of culture medium was changed without ROCKi. Aggregates were maintained in the microwell plate until day 7 of differentiation, when they were transferred to a 6 Well Ultra-Low Attachment Multiple Well plate.

extract_protocol:
Samples from 2D monolayer and 3D aggregates at different stages of cardiac differentiation were singularized with 0.25% trypsin-EDTA at 37ºC for (7-15) min. For enzymatic digestion neutralization, RPMI+10% FBS was added. After centrifugation and washing the cells one time with PBS, the cell pellet was frozen at -80ºC. Total RNA from the samples was extracted using High Pure RNA Isolation Kit (Roche, Cat. 11828665001), according to manufacturer´s instructions. Lexogen QuantSeq 3'mRNA-Seq Library Prep Kit FWD for Illumina (Cat. No. 015.96) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Lexogen and Illumina standard protocols. Briefly, 500 ng of total RNA were primed with the oligo dT primer containing Illumina-compatible linker sequences. After first strand synthesis, the RNA is removed and second strand is synthesized with Illumina-compatible random primers. After magnetic bead-based purification the libraries were PCR amplified introducing the sequences required for cluster generation. Sequencing was performed using HiSeq (50 cycles protocol) or NextSeq (75 cycles protocol) platforms.

treatment_protocol: In both culture conditions, a temporal modulation of WNT signalling protocol was used. From day 0 to day 6, cells were cultured in RPMI 1640 medium supplemented with B27 minus insulin. At day 0 cells were supplemented with GSK3 inhibitor CHIR at a final concentration of 5 µM in 2D and 11 µM in 3D culture condition. After 24 hours, medium was changed to remove CHIR. At day 3, cells were supplemented with Wnt inhibitor IWP-4 at a final concentration of 5 µM. At day 5, medium was changed. From day 7 until the end of differentiation, cells were cultured in RPMI 1640 supplemented with B27, with medium changed every 3 days until cell harvest.

tag: cell type

value: induced pluripotent stem cells

tag: source

value: foreskin fibroblasts

tag: mode of growth

value: 3D aggregates

value: 20 days


title: Cyclo_20min

value: Cycloheximide

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)


title: Chicken 1, jejunum

description: Gene expression data from oxyntic mucosa

source_name: Chicken 1, jejunum mucosa

value: standard 3-phase diets

value: 6 weeks

value: male


title: Chicken 19, cecum

source_name: Chicken 19, cecum mucosa

value: cecum mucosa


title: 3D_t15 rep3

value: 15 days


title: CK_R2G_24_rep1

description: Waterlogging tolerant genotype, control condition for 24 hours, replicate 1

value: root

value: flowering stage

value: control condition for 24 hours


title: CK_R2G_24_rep3

description: Waterlogging tolerant genotype, control condition for 24 hours, replicate 3


title: Diaz_20min

value: W303 background;leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100 MATa

value: Diazaborine

value: 20 minutes after treatment


title: V_top12

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

value: Vehicle

value: 20 minutes after vehicle treatment


title: Chicken 18, cecum

source_name: Chicken 18, cecum mucosa

value: Ross 308


title: CK_R2G_24_rep2

description: Waterlogging tolerant genotype, control condition for 24 hours, replicate 2


title: Chicken 16, cecum

source_name: Chicken 16, cecum mucosa


title: Chicken 17, cecum

source_name: Chicken 17, cecum mucosa


title: 3D_t18 rep3

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 3D aggregates

value: 18 days


title: Chicken 15, cecum

source_name: Chicken 15, cecum mucosa

value: standard 3-phase diets

value: 6 weeks

value: male


title: 3D_t9 rep3

value: 9 days


title: CycAux_top12

value: auxin and cycloheximide at the same time

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

value: 20 minutes after auxin and cycloheximide treatment


title: 3D_t12 rep3

value: 12 days


title: CK_R2G_20_rep2

description: Waterlogging tolerant genotype, control condition for 20 hours, replicate 2

value: root

value: flowering stage

value: control condition for 20 hours


title: CK_R2G_20_rep1

description: Waterlogging tolerant genotype, control condition for 20 hours, replicate 1


title: 3D_t7 rep3

value: 7 days


title: Cyc_top12

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

value: cycloheximide

value: 20 minutes after cycloheximide treatment


title: 3D_t1 rep3

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 3D aggregates

value: 1 day


title: CK_R2G_20_rep3

description: Waterlogging tolerant genotype, control condition for 20 hours, replicate 3


title: Aux_top12

value: W303 background; leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

value: auxin

value: 20 minutes after auxin treatment


title: 3D_t3 rep3

value: 3 days


title: utp13_A

value: W303 background; leu2-3,112 his3-11,15 ura3-1::pADH1-OsTIR1-URA3 ade2-1 trp1-1 can1-100 UTP13-AID*-Myc-HPH MAT[alpha]

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

value: 20 minutes after treatment


title: utp13_v

value: vehicle


title: CK_R2G_16_rep3

description: Waterlogging tolerant genotype, control condition for 16 hours, replicate 3

value: root

value: flowering stage

value: control condition for 16 hours


title: 3D_t5 rep3

value: 5 days


title: Chicken 13, cecum

source_name: Chicken 13, cecum mucosa

value: cecum mucosa

value: Ross 308

value: standard 3-phase diets

value: 6 weeks

value: male


title: Chicken 14, cecum

source_name: Chicken 14, cecum mucosa


title: CK_R2G_16_rep2

description: Waterlogging tolerant genotype, control condition for 16 hours, replicate 2

source_name: root


title: Utp8_A

value: W303 background; leu2-3,112 his3-11,15 ura3-1::pADH1-OsTIR1-URA3 ade2-1 trp1-1 can1-100 UTP8-AID*-Myc-HPH MATa


title: CK_R2G_16_rep1

description: Waterlogging tolerant genotype, control condition for 16 hours, replicate 1


title: 3D_t20 rep2

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 3D aggregates

value: 20 days


title: 3D_t0 rep3

value: 0 days


title: CK_R2G_12_rep3

description: Waterlogging tolerant genotype, control condition for 12 hours, replicate 3

value: control condition for 12 hours


title: 3D_t18 rep2

value: 18 days


title: CK_R2G_12_rep2

description: Waterlogging tolerant genotype, control condition for 12 hours, replicate 2

value: root


title: ifh1AA_60_veh

value: W303 background;tor1-1 fpr1<delta>::Nat RPL13A-2xFKBP12-TRP1;leu2-3,112 his3-11,15 ura3-1::pADH1-OsTIR1-URA3 ade2-1 trp1-1 can1-100 IFH1-FRB-KanMX6 MAT[alpha]

value: Vehicle

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

value: 60min after Vehicle treatment


title: utp8_V

value: vehicle

value: 20 minutes after treatment


title: 3D_t15 rep2

value: 15 days


title: ifh1AA_60_rap

value: W303 background;tor1-1 fpr1<delta>::Nat RPL13A-2xFKBP12-TRP1; leu2-3,112 his3-11,15 ura3-1::pADH1-OsTIR1-URA3 ade2-1 trp1-1 can1-100 IFH1-FRB-KanMX6 MAT[alpha]

value: Rapamycin

value: 60min after Rapamycin treatment


title: ifh1_FRB_Top1_veh

value: W303 background;tor1-1 fpr1<delta>::Nat RPL13A-2xFKBP12-TRP1; leu2-3,112 his3-11,15 ura3-1::pADH1-OsTIR1-URA3 ade2-1 trp1-1 can1-100 IFH1-FRB-KanMX6 TOP1-AID-KanMX6 MAT[alpha]

value: 60 min Vehicle treatment


title: CK_R2G_12_rep1

description: Waterlogging tolerant genotype, control condition for 12 hours, replicate 1

value: flowering stage


title: CK_EG_8_rep3

description: Waterlogging sensitive genotype, control condition for 8 hours, replicate 3

value: Ezhi No.2 (EG)

value: control condition for 8 hours


title: ifh1_FRB_Top1_auxrap

growth_protocol: cells were grown at 30 degrees in YPAD to mid-log phase and pretreated with rapamycin 40 minutes before treatment.

value: rapamycin pretreatment 40min  followed by auxin treatment

value: (pretreatment_rapamycin 40min) 20min after auxin treatment


title: Chicken 10, cecum

source_name: Chicken 10, cecum mucosa

value: cecum mucosa

value: Ross 308

value: standard 3-phase diets

value: 6 weeks

value: male


title: 3D_t12 rep2

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 3D aggregates

value: 12 days


title: 3D_t9 rep2

value: 9 days


title: CK_EG_8_rep1

description: Waterlogging sensitive genotype, control condition for 8 hours, replicate 1

value: root


title: ifh1_FRB_Top1-2_veh

value: W303 background;tor1-1 fpr1<delta>::Nat RPL13A-2xFKBP12-TRP1; leu2-3,112 his3-11,15 ura3-1::pADH1-OsTIR1-URA3 ade2-1 trp1-1 can1-100 IFH1-FRB-KanMX6 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

value: Vehicle

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

value: 60 min Vehicle treatment


title: CK_EG_8_rep2

description: Waterlogging sensitive genotype, control condition for 8 hours, replicate 2

value: flowering stage

value: Ezhi No.2 (EG)

value: control condition for 8 hours


title: ifh1_FRB_Top1_aux

value: W303 background;tor1-1 fpr1<delta>::Nat RPL13A-2xFKBP12-TRP1; leu2-3,112 his3-11,15 ura3-1::pADH1-OsTIR1-URA3 ade2-1 trp1-1 can1-100 IFH1-FRB-KanMX6 TOP1-AID-KanMX6 MAT[alpha]

value: Auxin

value: 20 minutes after auxin treatment


title: Chicken 12, cecum

source_name: Chicken 12, cecum mucosa

value: cecum mucosa

value: Ross 308

value: standard 3-phase diets

value: 6 weeks

value: male


title: 3D_t7 rep2

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 3D aggregates

value: 7 days


title: 3D_t5 rep2

value: 5 days


title: 3D_t3 rep2

value: 3 days


title: 3D_t1 rep2

value: 1 day


title: ifh1_FRB_Top1-2_auxrap

value: W303 background;tor1-1 fpr1<delta>::Nat RPL13A-2xFKBP12-TRP1; leu2-3,112 his3-11,15 ura3-1::pADH1-OsTIR1-URA3 ade2-1 trp1-1 can1-100 IFH1-FRB-KanMX6 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

value: rapamycin pretreatment 40min  followed by auxin treatment

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

value: (pretreatment_rapamycin 40min) 20min after auxin treatment


title: veh20_merged

value: W303 background;leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100 MATa

value: Vehicle

value: 20min after Vehicle treatment


title: CK_EG_48_rep2

description: Waterlogging sensitive genotype, control condition for 48 hours, replicate 2

value: root

value: flowering stage

value: Ezhi No.2 (EG)

value: control condition for 48 hours


title: CK_EG_48_rep1

description: Waterlogging sensitive genotype, control condition for 48 hours, replicate 1


title: 3D_t0 rep2

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 0 days


title: 3D_t20 rep1

value: 3D aggregates

value: 20 days


title: Day 4 rep 1 (PAT-seq)

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

country: Australia

institute: Monash University

description:
Sample 7
barcode: bcB_009-3bcPCR CTGCCCCGGGTTCCTCATTCTCTAGGTTGCGACCTGCTGTACGGCCAAGGCG

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) and adaptor sequence (allowing for up to 1 in 5 sequencing errors).
Reads are aligned using SHRiMP (v2.2.3, http://compbio.cs.toronto.edu/shrimp/). Multi-mapping reads are assigned a location at random from the best alignments.
Alignments are extended where the stripped poly(A) sequence matches the reference genome. The remaining, untemplated, poly(A) length is taken as the poly(A) tail length for that read. A read is called as having a poly(A) tail if this length is at least 4 As.
Reads aligning to genes are counted. Transcript locations were downloaded from the ENSEMBL version 82 (Saccharomyces cerevisiae). Overlapping transcripts (mostly isoforms) were merged. As 3'UTR annotations are not always accurate, reads up to 400 bases down-strand of a gene are counted towards that gene. Where a read might be assigned to multiple genes, it is assigned to the gene with annotated 3' end nearest to the alignment's 3' end. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample.
Supplementary_files_format_and_content: tail_count.csv contains counts of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv.
Supplementary_files_format_and_content: tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample.
Supplementary_files_format_and_content: These files are sufficient for differential expression and differential tail length analysis with the statistics package ""Fitnoise"".
Supplementary_files_format_and_content: gene.csv lists the genomic locations of the genes that were used. Locations are 1-based.

organism: Saccharomyces cerevisiae

source_name: Yeast cells grown on solid media

growth_protocol: Wild-type yeast cells were grown in liquid media to mid log phase. These were then harvested (samples 1 & 2) or diluted and plated onto solid media for further growth and harvest after 2, 3  or 4 days of growth  as previously described (Traven, A., et al. Transcriptional profiling of a yeast colony provides new insight into the heterogeneity of multicellular fungal communities. PloS one 2012;7(9):e46243.)

extract_protocol:
Total RNA was extracted from snap frozen cell pellets and hot phenol extraction. 1 microgram of this was input into the library preperation.
Library construction was by the PAT-seq approach (Harrison, P.F., et al. PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA 2015;21(8):1502-1510.)
Bead preparation and 75-base SOLiD sequencing chemistry (SOLiD EZ bead System)
[Cluster Generation]  80ul of 500pM library pool was used for emulsion PCR.
[Sequencing chemistry]  5500 Series Genetic Analyzer protocol 4456991 Rev. H, May 2012

tag: strain backround

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

tag: growth phase

value: Day 4


title: Chicken 9, cecum

description: Gene expression data from oxyntic mucosa

source_name: Chicken 9, cecum mucosa

value: cecum mucosa

value: Ross 308

value: standard 3-phase diets

value: 6 weeks

value: male


title: Chicken 11, cecum

source_name: Chicken 11, cecum mucosa


title: Chicken 8, cecum

source_name: Chicken 8, cecum mucosa


title: Day 3 rep 1 (PAT-seq)

description:
Sample 5
barcode: bcB_007-3bcPCR CTGCCCCGGGTTCCTCATTCTCTGGGTTATGCCCTGCTGTACGGCCAAGGCG

value: Day 3


title: CK_EG_48_rep3

description: Waterlogging sensitive genotype, control condition for 48 hours, replicate 3

value: root


title: Chicken 5, cecum

source_name: Chicken 5, cecum mucosa


title: Chicken 2, cecum

source_name: Chicken 2, cecum mucosa


title: Chicken 3, cecum

source_name: Chicken 3, cecum mucosa


title: Chicken 7, cecum

source_name: Chicken 7, cecum mucosa


title: Chicken 6, cecum

source_name: Chicken 6, cecum mucosa


title: Chicken 4, cecum

source_name: Chicken 4, cecum mucosa


title: Day 3 rep 2 (PAT-seq)

description:
Sample 6
barcode: bcB_008-3bcPCR CTGCCCCGGGTTCCTCATTCTCTGAGCGAGGATCTGCTGTACGGCCAAGGCG


title: Chicken 1, cecum

source_name: Chicken 1, cecum mucosa


title: ifh1_FRB_Top1-2_aux

source_name: whole organism

tag: strain

value: W303 background;tor1-1 fpr1<delta>::Nat RPL13A-2xFKBP12-TRP1; leu2-3,112 his3-11,15 ura3-1::pADH1-OsTIR1-URA3 ade2-1 trp1-1 can1-100 IFH1-FRB-KanMX6 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

value: Auxin

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

tag: time

value: 20 minutes after auxin treatment


title: 3D_t15 rep1

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 15 days


title: veh5_merged

value: W303 background;leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100 MATa

tag: treatment

value: Vehicle

tag: antibody

value: 5min after Vehicle treatment


title: CK_EG_44_rep3

description: Waterlogging sensitive genotype, control condition for 44 hours, replicate 3

value: flowering stage

value: Ezhi No.2 (EG)

value: control condition for 44 hours


title: Day 2 rep 1 (PAT-seq)

description:
Sample 3
barcode: bcB_005-3bcPCR CTGCCCCGGGTTCCTCATTCTCTGTGGTGTAAGCTGCTGTACGGCCAAGGCG

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: Day 2


title: CK_EG_44_rep2

description: Waterlogging sensitive genotype, control condition for 44 hours, replicate 2


title: 3D_t18 rep1

value: 3D aggregates

value: 18 days


title: Day 4 rep 2 (PAT-seq)

description:
Sample 8
barcode: bcB_010-3bcPCR CTGCCCCGGGTTCCTCATTCTCTGCGGTAAGCTCTGCTGTACGGCCAAGGCG

value: Day 4


title: Day 2 rep 2 (PAT-seq)

description:
Sample 4
barcode: bcB_006-3bcPCR CTGCCCCGGGTTCCTCATTCTCTGCGAGGGACACTGCTGTACGGCCAAGGCG


title: CK_EG_44_rep1

description: Waterlogging sensitive genotype, control condition for 44 hours, replicate 1

value: root


title: CK_EG_40_rep2

description: Waterlogging sensitive genotype, control condition for 40 hours, replicate 2

value: control condition for 40 hours


title: rapa_20_cyclo

growth_protocol: cells were grown at 30 degrees in YPAD to mid-log phase and pretreated with cycloheximide 5minutes before treatment

value: Cycloheximide pre-treatment 5min  followed by Rapamycin treatment

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

value: (pretreatment_cycloheximide 5min)  20min after rapamycin treatment


title: 3D_t9 rep1

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 9 days


title: 3D_t12 rep1

value: 12 days


title: rapa_5_cyclo

value: W303 background;leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100 MATa

value: Cycloheximide pre-treatment 5min   followed by Rapamycin treatment

value: (pretreatment_cycloheximide 5min)  5 min after rapamycin treatment


title: CK_EG_40_rep3

description: Waterlogging sensitive genotype, control condition for 40 hours, replicate 3

value: flowering stage

value: Ezhi No.2 (EG)


title: rapa_5

value: rapamycin

value: 5 min after rapamycin treatment


title: 3D_t7 rep1

value: 3D aggregates

value: 7 days


title: no_Heatshock_cyclo

value: Cycloheximide pre-treatment 5min  followed by no heat shock

value: (pretreatment_cycloheximide 5min)  5 min after no heatshock (30C)


title: Log phase rep 2 (PAT-seq)

description:
Sample 2
barcode: bcB_004-3bcPCR CTGCCCCGGGTTCCTCATTCTCTGGATGCGGTCCTGCTGTACGGCCAAGGCG

source_name: Yeast cells grown in liquid culture

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: Log phase


title: rapa_20

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

value: 20min after rapamycin treatment


title: 3D_t5 rep1

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 5 days


title: CK_EG_40_rep1

description: Waterlogging sensitive genotype, control condition for 40 hours, replicate 1

value: root

value: control condition for 40 hours


title: CK_EG_4_rep3

description: Waterlogging sensitive genotype, control condition for 4 hours, replicate 3

value: flowering stage

value: control condition for 4 hours


title: no_Heatshock

value: W303 background;leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100 MATa

value: no heat shock (30C)

value: 5 min after no heatshock (30C)


title: Heatshock_cyclo

value: Cycloheximide pre-treatment 5min followed by heat shock

value: (pretreatment_cycloheximide 5min) 5 min after heatshock (40C)


title: 3D_t3 rep1

value: 3D aggregates

value: 3 days


title: CK_EG_4_rep2

description: Waterlogging sensitive genotype, control condition for 4 hours, replicate 2

value: Ezhi No.2 (EG)


title: Heatshock

value: heat shock (40C)

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

value: 5 min after heatshock (40C)


title: Log phase rep 1 (PAT-seq)

description:
Sample 1
barcode: bcB_003-3bcPCR CTGCCCCGGGTTCCTCATTCTCTATAGGTTATACTGCTGTACGGCCAAGGCG

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: Log phase


title: Kidney collecting duct cells, Sham rep3

city: Seattle

first: Neal

middle: A

last: Paragas

state: WA

address: 850 Republican St

institute: University of Washington

data_processing:
Illumina’s RTA (v1.18) software used for basecalling.
Demultiplexing and FASTQ format file generation and alignment was performed using HiSeq analysis software (TopHat v2.1.1 with UCSC mouse genome build mm10. Quality control was then performed with RNA-SeQC v1.1.8 and counts generated using HTSeq-counts v0.7.2.
Differential gene expression between IRI and sham conditions was determined using DESeq2 package in R environment
Genome_build: mm10
Supplementary_files_format_and_content: Excel file reports htseq abundance counts

organism: Mus musculus

source_name: Kidney collecting duct cells

extract_protocol:
Total RNA was eluted and purified using RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. RNA integrity number (RIN) was measured using the Agilent 2200 TapeStation (Agilent Technologies, TX) and only samples with a RIN than or equal to 6.8 was used. Approximately 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Kidney Ischemia-Reperfusion Injury (IRI) Model: The renal artery was clamped using vascular clamps for a period of 30 min according to an established model of warm IRI to induce ischemic acute renal failure. To determine gene expression in collecting duct cells during IRI we bred Gt(ROSA)26Sor-mCherry-Rpl10a (mCherryTRAP) mouse that labels ribosomes for immunoprecipitation isolation of RNA with a tissue specific Cre-recombinase mouse57. HoxB7-Cre (HoxB7TRAP/+) was used to label ribosomes in the collecting duct. Kidneys from RiboTRAP mice were harvested, flash frozen until homogenization. Frozen kidneys were homogenized and the lysate was added to Anti-RFP magnetic beads (MBL International, WA) and mCherry/TRAP bound beads were separated from the supernatant with a magnet.

value: Sham

value: Kidney

value: Kidney collecting duct cells


title: Kidney collecting duct cells, Sham rep2


title: 3D_t0 rep1

value: induced pluripotent stem cells

value: foreskin fibroblasts

value: 0 days


title: Kidney collecting duct cells, Sham rep4


title: CK_EG_4_rep1

description: Waterlogging sensitive genotype, control condition for 4 hours, replicate 1

source_name: root

value: root

value: flowering stage

value: control condition for 4 hours


title: CK_EG_32_rep3

description: Waterlogging sensitive genotype, control condition for 32 hours, replicate 3

value: control condition for 32 hours


title: Top1-AID HSF1-FRB _AuxRap

growth_protocol: cells were grown at 30 degrees in YPAD to mid-log phase before treatment

value: W303 background;tor1-1 fpr1<delta>::Nat RPL13A-2xFKBP12-TRP1 HSF1-FRB-KanMX6  TOP1-AID-KanMX6 MAT[alpha]

value: Auxin+rapamycin

value: 50min after treatment


title: Kidney collecting duct cells, Sham rep1


title: Top1-AID HSF1-FRB _Aux

value: Auxin

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)


title: CK_EG_32_rep2

description: Waterlogging sensitive genotype, control condition for 32 hours, replicate 2

value: Ezhi No.2 (EG)


title: Top1-AID HSF1-FRB _Veh

value: Vehicle


title: CK_EG_32_rep1

description: Waterlogging sensitive genotype, control condition for 32 hours, replicate 1


title: Kidney collecting duct cells, IRI rep4

value: IRI


title: 3D_t1 rep1

value: 3D aggregates

value: 1 day


title: Top1-AID HSF1-FRB _Rap

value: rapamycin


title: Kidney collecting duct cells, IRI rep1

value: Kidney

value: Kidney collecting duct cells


title: Kidney collecting duct cells, IRI rep3


title: CK_EG_24_rep1

description: Waterlogging sensitive genotype, control condition for 24 hours, replicate 1

value: root

value: control condition for 24 hours


title: Top2-AID 20min_Veh

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH  MAT[alpha]

value: 20min after treatment


title: BCL6 KO rep 2

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (mm10) using Tophat (v2.0.6) with default parameters
Raw count and RPKM were calcualted using RSeQC (v2.3.6)
Genome_build: mm10
Supplementary_files_format_and_content: text file

source_name: Neutrophils

extract_protocol:
Neutrophils were sorted from total lung cells of influenza-infected mice at day 6 post. Two pools per genotype were used for RNA-seq. RNA from the sorted neutrophils was extracted using RNeasy Plus Mini Kit (Qiagen) following the manufacture’s recommendation.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

value: lung

value: Neutrophils

tag: genotype/variation

value: BCL6 KO

tag: passages


title: CK_EG_24_rep3

description: Waterlogging sensitive genotype, control condition for 24 hours, replicate 3

tag: tissue

value: flowering stage


title: Top1-2-AID 60min_Veh

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)


title: Kidney collecting duct cells, IRI rep2


title: CK_EG_24_rep2

description: Waterlogging sensitive genotype, control condition for 24 hours, replicate 2

tag: developmental stage

value: Ezhi No.2 (EG)


title: Top2-AID 60min_Veh

value: Vehicle


title: BCL6 KO rep 1


title: CK_EG_20_rep3

description: Waterlogging sensitive genotype, control condition for 20 hours, replicate 3

value: control condition for 20 hours


title: Sample B3: HpH-Root-YC03-3-rep3

city: 广州

first: Chen

middle: Qian

last: Qian

state: 广东省

address: 天河区五山街道

institute: 华南农业大学

data_processing:
Oligo (dT) magnetic beads are used to select mRNA with polyA tail.
Remove reads with adaptors;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% inaread,we define the low quality base to be the base whose sequencing quality is no more than 5).
We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.
RSEM is a quantification tool and FPKM methodis usedincalculatedexpressionlevel.
Screening DEGs using NOISeq.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

organism: Glycine max

source_name: soybean root

extract_protocol:
Ethanol precipitation protocol and CTAB-PBIOZOL reagent for the purification of total RNA from the plant tissue
BGI RNA-Seq kit


title: Top2-AID 60min_Aux

value: auxin


title: Top1-2-AID 20min_Veh


title: DOM21A

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

description:
small RNA (15-50 nt)
Sample 21A.D

data_processing:
Single end sequencing reads were cleaned with quality filter, adapter cutter, and length filter, using ACGT101_miR_v4.2g from LC Sciences.
The cleaned reads were mapped to miRBase (miRBase v21) using Bowtie v1.1.1.
The un-mapped reads were mapped to multiple databases including mRNA (http://www.genoscope.cns.fr/trout-ggb/data/Oncorhynchus mykiss mrna.fa.gz build 05/19/2014), Rfam11, and genomic DNA (http://www.genoscope.cns.fr/trout-ggb/data/Oncorhynchus mykiss chr.fa.gz build 04/28/2014), using Bowtie v1.1.1.
Novel miRNA candidates were identified from genome mapped reads based on the propensity of hairpin formation in corresponding genome positions, using ACGT101_miR_v4.2g from LC Sciences.
Data were normalized by dividing sequence counts of individual samples by corresponding normalization factors which are the median values of the ratios between specific sample counts and geometric mean counts of all samples.
Genome_build: http://www.genoscope.cns.fr/trout-ggb/data/Oncorhynchus mykiss chr.fa.gz build 04/28/2014

organism: Oncorhynchus mykiss

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Walbaum

value: Liver

tag: age

value: Juvenille

value: wild type


title: BCL6 WT rep 1

value: BCL6 WT


title: CK_EG_20_rep1

description: Waterlogging sensitive genotype, control condition for 20 hours, replicate 1

value: root

tag: genotype


title: Sample B2: HpH-Root-YC03-3-rep2


title: DOM6B

description:
small RNA (15-50 nt)
Sample 6B.D


title: CK_EG_20_rep2

description: Waterlogging sensitive genotype, control condition for 20 hours, replicate 2

tag: condition


title: Top1-AID 60min_Veh

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP1-AID-KanMX6 MAT[alpha]

value: 20min after treatment


title: Sample B1: HpH-Root-YC03-3-rep1


title: Top1-2-AID 60min_Aux


title: Sample A3: LpH-Root-YC03-3-rep3


title: CK_EG_16_rep3

description: Waterlogging sensitive genotype, control condition for 16 hours, replicate 3

value: control condition for 16 hours


title: CK_EG_16_rep2

description: Waterlogging sensitive genotype, control condition for 16 hours, replicate 2


title: CK_EG_16_rep1

description: Waterlogging sensitive genotype, control condition for 16 hours, replicate 1


title: DOM4B

description:
small RNA (15-50 nt)
Sample 4B.D


title: CK_EG_12_rep3

description: Waterlogging sensitive genotype, control condition for 12 hours, replicate 3

value: control condition for 12 hours


title: CK_EG_12_rep2

description: Waterlogging sensitive genotype, control condition for 12 hours, replicate 2

value: flowering stage


title: Sample A2: LpH-Root-YC03-3-rep2


title: Top1-AID 60min_Aux


title: SUB6A

description:
small RNA (15-50 nt)
Sample 6A.S


title: BCL6 WT rep 2

value: lung

value: Neutrophils


title: Top1-AID 20min_Veh

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)


title: SUB4A

description:
small RNA (15-50 nt)
Sample 4A.S


title: CK_EG_12_rep1

description: Waterlogging sensitive genotype, control condition for 12 hours, replicate 1

value: Ezhi No.2 (EG)


title: Sample A1: LpH-Root-YC03-3-rep1


title: Top2-AID 20min_Aux

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH  MAT[alpha]


title: SUB1B

description:
small RNA (15-50 nt)
Sample 1B.S


title: Top1-2-AID 20min_Aux

value: W303 background;leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MAT[alpha]

value: auxin


title: 1mA miCLIP mouse brain AlkB replicate 2

status: Public on Jun 23 2019

city: New York

first: Anya

last: Grozhik

state: New York

address: 1300 York Ave, Room LC-523

institute: Weill Cornell Medicine

description:
mouse.brain.1mA.miCLIP.AlkB.clusters.bed
mouse.brain.1mA.miCLIP.AlkB.bedgraph
mouse.brain.1mA.miCLIP.AlkB.terminations.bedgraph

data_processing:
Reads resulting from 1mA miCLIP or RNA-Seq library sequencing were trimmed of the 3’ linker sequence (5’ AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGAC 3’) and barcoded reverse transcription primer sequences (5’ NNXXXXNNNAGATCGGAAGAGCGTCGTGT 3’, where N = random nucleotide, and XXXX = fixed barcode sequence; barcode sequences correspond to iCLIP barcodes in Konig et al., Nature Structural and Molecular Biology, 2010) using Flexbar (version 2.5). To demultiplex reads belonging to individual biological replicates, the pyBarcodeFilter.py script of the pyCRAC suite (version 1.2.2) was used to demultiplex the samples based on the fixed portion of the reverse transcription barcode. The random portion of the reverse transcription barcode was then moved into the sequence header using a custom awk script. PCR duplicates were collapsed using pyFastqDuplicateRemover.py of the pyCRAC suite. Finally, reads were aligned to hg19 for HEK 293T cells or mm10 for mouse brain using Bowtie (version 1.1.2; command: bowtie -f -s 0 -v 2 -m 10 --best --maxbts 800 --strata -S /genomeindex input.fasta output.sam). To view aligned reads in a genome browser, .sam files produced by Bowtie were converted to .bedgraph files of reads and 5’ ends of reads (“terminations”) using bedtools (version 2.25.0). 1mA miCLIP clusters of unique reads were generated using the CIMS software package for analysis of HITS-CLIP data (Moore, Zhang, et al., Nature Protocols, 2014); HEK 293T clusters have a minimum score of 20, and mouse brain clusters have a minimum score of 5.
Genome_build: Human: hg19; Mouse: mm10.
Supplementary_files_format_and_content: HEK293T.1mA.miCLIP.clusters.rep1.bed : Genomic coordinates of HEK 293T cell 1mA miCLIP clusters with score >/= 20, replicate 1  HEK293T.1mA.miCLIP.clusters.rep2.bed : Genomic coordinates of HEK 293T cell 1mA miCLIP clusters with score >/= 20, replicate 2  HEK293T.RNA_Seq.unique.reads.bed : Genomic coordinates of HEK 293T cell RNA-Seq unique reads  mouse.brain.1mA.miCLIP.CTL.clusters.bed : Genomic coordinates of mouse brain 1mA miCLIP clusters with score >/= 5, control  mouse.brain.1mA.miCLIP.AlkB.clusters.bed : Genomic coordinates of mouse brain 1mA miCLIP clusters with score >/= 5, AlkB-treated  HEK293T.1mA.miCLIP.rep1.bedgraph : Coverage file of HEK 293T cell 1mA miCLIP unique reads, replicate 1  HEK293T.1mA.miCLIP.rep2.bedgraph : Coverage file of HEK 293T cell 1mA miCLIP unique reads, replicate 2  HEK293T.RNA_Seq.bedgraph : Coverage file of HEK 293T cell RNA-Seq unique reads  mouse.brain.1mA.miCLIP.CTL.bedgraph : Coverage file of mouse brain 1mA miCLIP unique reads, control  mouse.brain.1mA.miCLIP.AlkB.bedgraph : Coverage file of mouse brain 1mA miCLIP unique reads, AlkB-treated  HEK293T.1mA.miCLIP.rep1.terminations.bedgraph : Coverage file of HEK 293T cell 1mA miCLIP terminations, replicate 1  HEK293T.1mA.miCLIP.rep2.terminations.bedgraph : Coverage file of HEK 293T cell 1mA miCLIP terminations, replicate 2  mouse.brain.1mA.miCLIP.CTL.terminations.bedgraph : Coverage file of mouse brain 1mA miCLIP terminations, control  mouse.brain.1mA.miCLIP.AlkB.terminations.bedgraph : Coverage file of mouse brain 1mA miCLIP terminations, AlkB-treated

source_name: Mouse brain poly(A) RNA

growth_protocol: HEK 293T cells were grown at 37°C in DMEM media that was supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA from HEK 293T cells (N = 2 biological replicates) or whole mouse brain (N = 3 biological replicates per experimental group) was extracted using TRIzol (ThermoFisher) and treated with RQ1 RNase-free DNase I (Promega) according to the manufacturers’ instructions. Poly(A) RNA was then isolated using one round of selection with oligo(dT) magnetic beads (New England Biolabs). This resulted in approximately 10 μg of poly(A) RNA for each replicate used in this study.
1mA miCLIP was performed exactly as previously described(Linder et al., Nature Methods, 2015), with the following modifications: mRNA was subjected to fragmentation using RNA Fragmentation Reagents (ThermoFisher). Fragmentation was allowed to proceed for exactly 12 minutes at 75°C. Fragmented RNA was then incubated with anti-1mA antibody and the antibody-RNA complexes were processed for crosslinking, immunoprecipitation, RNA linker ligation, purification, and reverse transcription exactly as previously described(Linder et al., Nature Methods, 2015). For mouse brain samples, immunoprecipitated antibody-RNA complexes were mock-treated or treated with AlkB prior to RNA linker ligation. Reverse transcription incorporated use of barcoded primers to allow downstream pooling of libraries. Following reverse transcription of RNA-peptide complexes, first-strand cDNA was circularized using CircLigase II ssDNA Ligase (EpiBio) to preserve the 3’ end of the cDNA, and thus, sites of 1mA-induced terminations of reverse transcription. To generate priming sites for library amplification, the cDNA was cut in the middle of its priming sequence (green bar in Fig. 2a) using a small single-stranded oligo complementary to the priming sequence and FastDigest BamHI restriction digest (ThermoFisher), as previously described(Linder et al., Nature Methods, 2015). This generated priming sites for the Illumina P5 and P3 primers on either side of the cDNA. For library amplification, Accuprime Supermix I (ThermoFisher) and Illumina P5 and P3 primers were used. PCR amplification cycle number was selected as previously described(Grozhik et al., Methods in Molecular Biology, 2017). Amplified libraries were then pooled and cleaned up using a 1.8X ratio of AMPure XP magnetic beads (Beckman Coulter). Libraries were subjected to next-generation sequencing at the Epigenomics Core of Weill Cornell Medicine. Libraries were sequenced on an Illumina HiSeq 2500 instrument in single-end mode to generate 50-base reads.

treatment_protocol: No treatments applied prior to RNA extraction.

tag: passage

value: Anti-1mA MBL D345-3

value: AlkB


title: 1mA miCLIP mouse brain CTL replicate 1

description:
mouse.brain.1mA.miCLIP.CTL.clusters.bed
mouse.brain.1mA.miCLIP.CTL.bedgraph
mouse.brain.1mA.miCLIP.CTL.terminations.bedgraph

value: control


title: 1mA miCLIP mouse brain CTL replicate 2


title: 1mA miCLIP mouse brain CTL replicate 3


title: pre-cDC1 H3K27Ac

city: Saint Louis

first: Vivek

last: Durai

state: MO

address: 4940 Parkview Place, Dock at CSRB, Murphy Lab 7766

department: Pathology and Immunology

institute: Washington University in St. Louis School of Medicine

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm10 genome assembly using  Bowtie 1.1.1.
Tag directories were made using makeTagDirectory program of the Homer Software package.
BEDGRAPH were made using makeUCSCfile program of the Homer Software package.
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH

source_name: Bone marrow

growth_protocol: Femurs and hips were isolated from wildtype mice and bone marrow cells were harvested with mortar and pestle. After lysing red blood cells using ACK Lysis buffer, whole bone marrow was stained with fluorescent antibodies to identify DC progenitors and then sort purified to >95% purity using a FACS AriaFusion. MDPs: Lin–CD117hiCD135+CD115+CD11c–MHCII–. CDPs: Lin–CD117intCD135+CD115+CD11c–MHCII–. pre-cDC1s: Lin–CD117intCD135+CD226+.

extract_protocol:
Sorted cells were cross-linked by incubating for 8 min at room temperature with 1% formaldehyde. Reactions were then quenched with 1.25 M glycine, cells were washed twice with PBS, and pellets were “flash frozen” for storage at -80°C. Chromatin was sonicated at 4°C in sonication buffer (10 mM Tris-HCl, pH 8.0; 100 nM NaCl; 1 mM EDTA, 0.5 mM EGTA; 0.1% sodium deoxycholate; and 0.5% N-lauroylsarcosine) for 24 cycles of 20 s on and 50 s off per cycle with a Vivra-Cell VCX130PB and CV188 (Sonics & Material) to obtain DNA fragments from 140 bp to 500 bp. Chromatin was then immunoprecipitated overnight at 4°C with Dynabeads Protein A that had been pre-incubated with 2.5 µg of the appropriate antibody: anti-H3K27ac (Ab 4729; Abcam) or H3K4me1 (Ab 8895; Abcam). Beads containing protein-DNA complexes were washed seven times with RIPA buffer (50 mM HEPES, pH 7.5; 500 mM LiCl; 1 mM EDTA; 1% NP-40; and 0.7% sodium deoxycholage). DNA fragments were eluted, and crosslinking was reversed by incubation in a solution containing 50 mM Tris-HCl, pH 8.0; 10 mM EDTA; 1% SDS; and 1 mg/mL of proteinase K (New England Biolabs) for 5 hours at 65°C. DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
Libraries for ChIP-Seq were prepared with a ThruPLEX-FD kit (Rubicon Genomics)

tag: cell type

tag: strain/genotype

value: C57BL/6 WT

tag: chip antibody

value: H3K27ac (Ab 4729; Abcam)


title: CDP H3K4me1

value: Common dendritic cell progenitor

value: H3K4me1 (Ab 8895; Abcam)


title: PTDSR-2

city: Sydney

first: matthew

middle: kwok kei

last: wong

state: New South Wales

address: Lowy cancer centre, University of New South Wales

department: histone modification group

institute: Children's Cancer Institute

description:
JMJD6_NT_common_peaks
NMYC_JMJD6_NT_common_peaks
enhancers_JMJD6-NT_merged
promoters_1kb_JMJD6-NT_merged
superenhancers_JMJD6-NT_merged
enhancers_BOTH-NT_merged
promoters_1kb_BOTH-NT_merged
superenhancers_BOTH-NT_merged

data_processing:
ChIP-Seq raw reads were aligned using the Burrows Wheeler Aligner (BWA) with default parameters. Files were further processed using SAMtools, BEDtools  and bedGraphToBigWig. Peaks were called with MACS2 ‘callpeak’ (version macs2 2.1.1.20160309) against input controls, with default parameters.  Common peaks of NMYC or JMJD6 were selected if a ChIP-seq peak was identified in all three replicates of either NMYC or JMJD6.
To find NMYC and JMJD6 genomic binding locations, gene promoters were selected as ± 1 kilobase from the transcription start site of genes from the RefSeq (refFlat) database, downloaded from the University of California Santa Cruz (UCSC) Table Browser.  Enhancer and superenhancer regions were identified using H3K27ac data (Series GSE113139) . Enhancer- and superenhancer-associated genes are the two nearest genes within 1000 kb, identified using the Genomic Regions Enrichment of Annotations Tool (GREAT). Promoters, enhancers and superenhancers bound by NMYC or JMJD6 were selected if they overlapped with a ChIP-seq peak identified from all three replicates of either NMYC or JMJD6.
The .bed files do not have a quantitative component as common peaks were only called if they were present in all three replicates.
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: CHP-134 neuroblastoma cells

growth_protocol: CHP-134 neuroblastoma cells were cultured in RPMI medium supplemented with 10% fetal bovine serum and l-glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA immunoprecipitated by the antibodies were purified and subjected to sequencing with Illumina HiSeq 2000 at Ramaciotti Centre for Genomics, University of New South Wales, Australia

treatment_protocol: Cells were treated with formaldehyde alone for DNA cross-linking for the NMYC antibody pulldown. For the JMJD6 antibody pulldown, cells were double cross-linked with DSG, followed by formaldehyde for chromatin immunoprecipitation. The chromatin immunoprecipitation experiements were done in triplicate.

tag: cell line

value: CHP-134 neuroblastoma cells

value: peripheral nervous system tumor cell

value: JMJD6 antibody (ab64575)


title: PTDSR-3


title: PTDSR-1


title: CDP H3K27Ac


title: 1mA miCLIP mouse brain AlkB replicate 1


title: pre-cDC1 H3K4me1


title: NMYC-1

description:
NMYC_NT_common_peaks
NMYC_JMJD6_NT_common_peaks
enhancers_NMYC-NT_merged
promoters_1kb_NMYC-NT_merged
superenhancers_NMYC-NT_merged
enhancers_BOTH-NT_merged
promoters_1kb_BOTH-NT_merged
superenhancers_BOTH-NT_merged

value: NMYC antibody (sc-53993)


title: NMYC-3


title: Sample_Input_NT

data_processing:
ChIP-Seq raw reads were aligned using the Burrows Wheeler Aligner (BWA) with default parameters. Files were further processed using SAMtools, BEDtools  and bedGraphToBigWig. Peaks were called with MACS2 ‘callpeak’ (version macs2 2.1.1.20160309) against input controls, with default parameters.  For analyzing the effect of JMJD6 on RNA polymerase 2 binding, all canonical transcription start sites (TSS) were obtained, and read counts were generated in 50bp windows leading into and out of the TSS (at x=0), spanning +/- 1000bp of the TSS.
Genome_build: hg19
Supplementary_files_format_and_content: To select genes with reduced RNA Pol II binding after DOX treatment, gene promoters ± 1 kilobase (kb) from the transcription start site of genes from the RefSeq (refFlat) database were downloaded from the University of California Santa Cruz Table Browser. RNA Pol II ChIP-seq experiments were performed in duplicate, and genes were designated as harbouring a RNA Pol II peak if they had a promoter which harboured a Pol2 peak in both NT samples and neither DOX sample. The resulting gene list was used as input for the Gene Set Enrichment Analysis (GSEA), performed with the ‘Investigate Gene Sets’ tool available via the Broad Institute (http://software.broadinstitute.org/gsea/) and the Molecular Signature Database (MSigDB).

source_name: doxycycline inducible JMJD6 shRNA CHP-134 neuroblastoma cells

growth_protocol: Doxycycline inducible JMJD6 shRNA CHP-134 neuroblastoma cells were cultured in RPMI medium supplemented with 10% fetal bovine serum and l-glutamine.

treatment_protocol: Doxycycline inducible JMJD6 shRNA CHP-134 neuroblastoma cells were treated with vehicle control or 2ug/ul doxycycline for 30 hours

value: vehicle control

value: peripheral nervous system tumour cell


title: Sample_pol2_NT

value: Go-ChIP-Grade Purified anti-RNA Polymerase II RPB1 Antibody (Biolegend, 664912)


title: Sample_pol2_NT_WON5767


title: Sample_pol2_DOX_WON5767

value: doxycycline


title: MDP H3K27Ac

value: Monocyte/dendric cell progenitor


title: MDP H3K4me1


title: Sample_pol2_DOX


title: rb IgG_WON3029

data_processing:
ChIP-Seq raw reads were aligned using the Burrows Wheeler Aligner (BWA) with default parameters. Files were further processed using SAMtools, BEDtools and bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: To view H3K27ac, H3K4me and H3K4me3 binding, BigWig files were normalized against the number of reads in each sample and also the size of the mappable genome.

treatment_protocol: No treatment

value: control rabbit IgG (sc-2027, Santa Cruz Biotech)


title: Sample_Input_DOX


title: Sample_Input_NT_WON5767


title: Sample_Input_DOX_WON5767


title: h3k4me3_WON3029

value: rabbit anti-H3K4me3 antibody (ab213224, Abcam)


title: P62 shBmi1&CHD7-2

city: Toronto

first: Michael

middle: D

last: Taylor

state: Ontario

address: 686 Bay St

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

data_processing:
Illumina's BaseSpace was used to perform TopHat alignment of all reads, and to run CuffLinks for gene expression estimation followed by differential expression analysis
Tophat (version 2.0.7) alignment of all reads was done with hg19 as the reference genome, and conducted with parameters:  --read-realign-edit-dist 1 --segment-length 24 -p 7 --rg-id 0 --rg-sample XZ-3 --library-type fr-firststrand --no-coverage-search --keep-fasta-order --fusion-search --fusion-min-dist 100000 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM,M
genome build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene id, locus, sample type being compared, expression of gene in each sample type, log2 fold change, and statistical information such as test statictic, p-value and q-value

scramble_vs_shBMI.gene_exp.diff: Differential Expression between scramble and BMI1 knockdown
scramble_vs_shBMIshCHD7.gene_exp.diff: Differential Expression between scramble and BMI1 and CHD7 knockdown
scramble_vs_shCHD7.gene_exp.diff: Differential Expression between scramble and CHD7 knockdown
shBMI_vs_shBMIshCHD7.gene_exp.diff: Differential Expression between BMI1 knockdown BMI1;CHD7 knockdown
shBMI_vs_shCHD7.gene_exp.diff: Differential Expression BMI1 knockdown and CHD7 knockdown
shCHD7_vs_shBMIshCHD7.gene_exp.diff: Differential Expression between CHD7 knockdown and BMI1;CHD7 knockdown

source_name: Group4 medulloblastoma cell line

growth_protocol: Cells were cultured in DMEM (high glucose, GlutaMAX™ Supplement, ThermoFisher) including 10% of fetal bovine serum and 1% of Penicillin-Streptomycin at 37ºC. Cells were subcultured every 3-4 days once they reached confluent.

extract_protocol:
Cell pellets were lysed in RLT buffer from the RNeasy Micro purification kit (Qiagen). Total RNA was isolated using the same kit and the extra On-column DNase.
Library construction protocol not provided.

treatment_protocol: A GIPZ-lentiviral shRNAmir vector containing a hairpin sequence targeting BMI1, CHD7 and MATH1 were purchased from Dharmacon, UK. Packaging, virus production and determination of titre were carried out as previously reported (Merve et al., 2014). Icb1299 cells were infected after mechanical dissociation at a multiplicity of infection (MOI) of 12. After 96h of incubation, puromycin selection at a concentration of 2.5µg/ml was applied to enrich for the trasduced population. The efficacy of gene silencing was assessed by qRT-PCR analysis at multiple time points after passaging, at specific timepoints protein analysis was also carried out either by immunocytochemistry or western blotting. All experiments were conducted at least in triplicates.

value: Group4 medulloblastoma

tag: knockdown

value: BMI1 and CHD7


title: P62 shBmi1&CHD7-1


title: h3k4me_WON3029

value: rabbit anti-H3K4me antibody (ab106165, Abcam)


title: 1mA miCLIP mouse brain AlkB replicate 3

tag: strain

value: Anti-1mA MBL D345-3

value: AlkB


title: input_WON3029


title: P62 shBmi1-1


title: P62 Scramble-1

value: scramble


title: P62 shBmi1-2


title: h3k27ac_WON3029

value: CHP-134 neuroblastoma cells

value: rabbit anti-H3K27ac antibody (ab4726, Abcam)


title: NMYC-2

value: peripheral nervous system tumor cell


title: MDP ATAC-seq biological replicate 3

description: Open chromatin

data_processing:
Illumina bcl2fastq version 2.18 was used for basecalling.
Paired-end reads were then trimmed with Seqpurge.
Paired-end reads were aligned to mm10 genome with bowtie2.
Aligned reads were filtered for mitochondrial, low-quality and duplicates with Picard tools.
Peak calls were performed on individual samples and merged to create a union peak set.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

extract_protocol:
MDPs, CDPs, and pre-cDC1s were sorted from bone marrow and lysed in ice-cold ATAC-RSB buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. Cells were incubated at 4° C for 3 min, then washed with ATAC-RSB buffer containing only 0.1% Tween-20. Nuclei were spun down by centrifugation and then incubated in 50 µL of transposition buffer (25 µL 2X TD buffer, 22.5 µL dH2O, 2.5 µL Tn5 transposase (Nextera DNA Library Prep Kit, Illumina)) and incubated at 37° C for 30 min. If 10,000 cells could not be obtained for a certain population then the quantity of Tn5 transposase was titrated down proportionately to the number of cells obtained but cells were still incubated in 50 µL total. Transposed DNA was purified with a DNA Clean & Concentrator kit (Zymo Research), eluted in 21 µL of elution buffer, and stored at -20° C until amplification.
Nextera DNA Library Prep Kit

value: C57BL/6 WT


title: CDP ATAC-seq biological replicate 2

description: Open chromatin

value: Common dendritic cell progenitor


title: pre-cDC1 ATAC-seq biological replicate 1

description: Open chromatin


title: CDP ATAC-seq biological replicate 1

description: Open chromatin


title: pre-cDC1 ATAC-seq biological replicate 3

description: Open chromatin


title: eV30

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

institute: University of Zurich

description:
ENS_counts.tsv
gene_counts.tsv
normalized_gene_counts.tsv

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file (ENS_counts.tsv) using custom Python code
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file (gene_counts.tsv)
Reads were normalized using scran, and normalized values are stored in normalized_gene_counts.tsv
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text files. ENS_counts.tsv contains raw counts, with genes labeled by their Ensembl ENS numbers. gene_counts.tsv contains raw counts, with genes labeled by their gene names. normalized_gene_counts.tsv contains normalized (scran) counts of cells that passed quality control

source_name: Neural embryonic cell

extract_protocol:
cytosol aspiration via patch-clamp pipettes
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neural embryonic cell

tag: driver line

value: Nex Cre line

value: Glutamatergic 1

tag: quality control

value: Passed


title: P62 shCHD7-2


title: MDP ATAC-seq biological replicate 2

description: Open chromatin

value: Monocyte/dendric cell progenitor


title: MDP ATAC-seq biological replicate 1

description: Open chromatin


title: eV27

value: Glutamatergic 2


title: P62 shCHD7-1

value: Group4 medulloblastoma


title: CDP ATAC-seq biological replicate 3

description: Open chromatin


title: P62 Scramble-2


title: pre-cDC1 ATAC-seq biological replicate 2

description: Open chromatin


title: eV29

value: Undefined


title: eV25


title: eV18


title: eV24


title: eV11


title: eV17


title: eV16

value: VZ-derived


title: eV26


title: eV14

description:
ENS_counts.tsv
gene_counts.tsv

value: Failed


title: eV10


title: eV13


title: eH144

value: Htr3a Cre line


title: eH142


title: eV5


title: eH140


title: eH145


title: eV1


title: eH141

description:
ENS_counts.tsv
gene_counts.tsv


title: eV9


title: eV3


title: eH138


title: eH137

value: CGE-derived


title: eV23


title: eH133

value: MGE-derived 1


title: eH132


title: eH131


title: eH130


title: eH129

value: MGE-derived 2


title: eH124

description:
ENS_counts.tsv
gene_counts.tsv

value: GABAergic


title: eH127

description:
ENS_counts.tsv
gene_counts.tsv


title: eH125


title: eH139


title: eH123


title: eH134


title: eH136


title: eH143


title: eH110


title: eH113

value: Cajal Retzius


title: eH116


title: eH111


title: eH114


title: eH105


title: eH108


title: eH107


title: eH120


title: eH104


title: eH103


title: eH101


title: eH100


title: eH99


title: eH128


title: eH102


title: eH96


title: eH97


title: eH91


title: eH94


title: eH89


title: eH119


title: eH109


title: eH106


title: eH87

description:
ENS_counts.tsv
gene_counts.tsv


title: eH85


title: eH75


title: eH73


title: eH78


title: eH80


title: eH82


title: eH79


title: eH77


title: eH84


title: eH69


title: eH72


title: eH66


title: eH71


title: eH65


title: eH61


title: eH62


title: eH63


title: eH59


title: eH64

description:
ENS_counts.tsv
gene_counts.tsv


title: eH57


title: eH90


title: eH56


title: eH55


title: eH54


title: eH53


title: eH52


title: eH51


title: eH76


title: eH49


title: eH50


title: eH47

description:
ENS_counts.tsv
gene_counts.tsv


title: eH46


title: 1mA miCLIP HEK 293T replicate 2

source_name: HEK 293T cell poly(A) RNA

value: HEK 293T

tag: antibody

value: Anti-1mA MBL D345-3


title: RNA-Seq HEK 293T


title: eH45

value: Neural embryonic cell


title: Top1-AID 20min_Aux

value: W303 background; leu2-3,112 HIS3,15 ura3-1::pADH1-OsTIR1-URA3 ADE2 trp1-1 can1-100 TOP1-AID-KanMX6 MAT[alpha]

tag: treatment

value: auxin

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

tag: time

value: 20min after treatment


title: eH44

value: Passed


title: eH43

value: Undefined


title: eH48


title: eH42

description:
ENS_counts.tsv
gene_counts.tsv


title: 1mA miCLIP HEK 293T replicate 1