title: 52_35d RNA-Seq

data_processing:
mRNA and miRNA: Basecalls and sample de-multiplexing performed by CASAVA with default parameters
mRNA: Sequenced reads were quality check with fastqc default parameters
mRNA: Sequenced reads were mapped with GSNAP using default algorithm parameters against hg19 genome
mRNA: The resulting SAM/BAM files were processed with SAMtools to yield count data for RefSeq transcript annotations
mRNA: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, the number of reads mapping to transcripts were counted and normalized by the size of the longest transcript of a gene and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and read count values for each mRNA sample, and RPM for each miRNA sample.

extract_protocol:
RNA-Seq: For mRNA sequencing, 100 ng input total RNA per sample were converted into cDNA libraries following the Illumina TruSeq® stranded total RNA sample preparation protocol with Ribo Zero Gold (cat RS-122-2301). The total RNA, once depleted from cytoplasmic and mitochondrial ribosomal RNA, was fragmented and converted into double-stranded cDNA. Single-stranded adaptors that include unique barcode sequences for sample identification were attached via ligation. The resulting molecules were amplified via polymerase chain reaction (PCR). The fragment size distribution of each library was quality-controlled using the Agilent Tapestation® 2200, and libraries were quantified using the Kapa® library quantification kit (Kapa Biosystems®, cat KK4835). The 20 libraries were normalized to 2 nM and pooled in 4 sets as per the randomization plan for each flow cell lane (4 lanes containing each 6 libraries). The pooled libraries were spiked in with 10% PhiX library and were bound to the surface of flow cells at equimolar concentrations of 13 picoM. Each template molecule was clonally amplified up to 1000-fold using a Cbot2® system (Illumina). Sequencing by synthesis was performed on the Illumina HiSeq2500®, using a strategy of 2x50bp paired-end sequencing with a minimal total read depth of 30 millions reads paired-end per sample after subtracting off-target sequences (residual ribosomal RNA, phiX, homopolymer repeats).
After cell lysis and total RNA extraction in phenol/chloroform, the aqueous phase was processeded using the RNeasy® Mini Kit (QIAGEN) with DNAse digestion as per the manufacturer’s instructions


title: 51_35d RNA-Seq

status: Public on Jun 20 2018

type: SRA

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Retinal epithelial cells

growth_protocol: Human primary Retinal Pigmented Epithelium (hpRPE) cells were purchased from Sciencell (6540). Cells were seeded in transwells (Costar, 3450 and 3460) previously coated with Laminin 521 (BioLamina, LN521-03). During the first week EpiCM 2% FBS (Sciencell, 0010F) media was employed to allow for attachment and proliferation (Sciencell, 4101). Four days after cell seeding, samples were decreased in FBS to a concentration of 1%. At day 7, cells were transferred to a media stimulating the differentiation of the cells that was a modification of the formulation previously reported to be effective for the culture of or primary RPE cells (Maminishkis et al., 2006; Sonoda et al., 2009). This medium is made with MEM Alpha media (Sigma, M-4526) supplemented with N1 supplement at 1% concentration (Sigma, N-6530), Glutamine-Penicillin-Streptomycin 1X (Sigma, G-1146), Non-essential Amino Acid (NEAA, M-7145), Taurine 0.25 mg/mL (Sigma, T-0625), Hydrocortisone 20 µg/L (Sigma, H-03966) and Triiodo-thyronin 13 ng/L (Sigma, T-5516). To enhance the differentiation of the RPE cells we cultured the apical side of the transwells with the supplemented media and added Bovine Serum Albumin (BSA) to a concentration of 0.1% (Sigma, A-9647). The basloateral side was cultured with the supplemented media with 1% FBS instead of BSA. Cells were cultured in a humidified incubator at 37°C with 5% CO2 atmosphere.

tag: tissue

value: Retinal epithelial cells

tag: age

value: differentiation day 35


title: 50_35d RNA-Seq


title: 40_28d RNA-Seq

value: differentiation day 28


title: 1_7d miRNA-Seq

data_processing:
mRNA and miRNA: Basecalls and sample de-multiplexing performed by CASAVA with default parameters
miRNA: Adapter trimming was performed by sRNABench.
miRNA: Trimmed sequence reads were mapped with sRNABench by "genome mode" using Bowtie onto hg19 including known micro RNAs from miRBase
miRNA: Read counts and normalized reads counts (RPM) were generated by sRNABench
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and read count values for each mRNA sample, and RPM for each miRNA sample.

extract_protocol:
miRNA-Seq: 1 microgram total RNA of every sample was processed following the Illumina TruSeq small RNAseq library prep protocol (cat. RS-200- 0012 – 0024). A single stranded 3’-RNA adapter and a single stranded 5’-RNA adapter were ligated to the total RNA of all samples. After reverse transcription, PCR-amplification of the resulting cDNA was performed using a unique primer pair for each sample. Each library was quantified before gel-purification based on Kapa® quantification (Kapa Biosystems®, cat KK4835) using 3 independent 10 -6 dilutions. The concentrations ranged 1.3-2.9 microgram cDNA with an average of 2.1 microgram. The fragment size distribution of each library was quality-controlled using the Agilent Tapestation® 2200. The 20 libraries were pooled and electrophoresed on a 10% acrylamide gel for purification of fragments spanning 140-160 base pairs. This fragment size covers the adaptor-ligated mature miRNAs, where the adaptors account for 120 bp. The content of this extract was quality-controlled using the Agilent Tapestation® 2200. The average library size was 150 bp. The concentration was determined with the Kapa® library quantification kit (Kapa Biosystems®, cat KK4835) using 3 independent 10 -6 dilutions of the gel-purified library pool. The concentration was normalized to 2nM, spiked in with 10% PhiX library and loaded onto two flow cell lanes of a rapid HiSeq2500 run at a concentration of 13 pM. Each template molecule was clonally amplified using a Cbot2® system (Illumina). Sequencing by synthesis was performed on the Illumina HiSeq2500®, using a strategy of 50bp single-end. The total read depth ranged 4.5-13.3 million reads per sample, with an average of 8.4 million reads after subtracting off-target sequences.
After cell lysis and total RNA extraction in phenol/chloroform, the aqueous phase was processeded using the RNeasy® Mini Kit (QIAGEN) with DNAse digestion as per the manufacturer’s instructions

value: differentiation day 7


title: 3_7d miRNA-Seq


title: 49_35d RNA-Seq


title: 2_7d miRNA-Seq


title: 39_28d RNA-Seq


title: 26_21d miRNA-Seq

value: differentiation day 21


title: 38_28d RNA-Seq


title: 37_28d RNA-Seq


title: 18_14d RNA-Seq

value: differentiation day 14


title: 25_21d RNA-Seq


title: 27_21d RNA-Seq


title: 14_14d RNA-Seq


title: 17_14d RNA-Seq


title: 4_7d RNA-Seq


title: 1_7d RNA-Seq


title: 3_7d RNA-Seq


title: 13_14d RNA-Seq


title: WP-NC

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

country: USA

institute: Saint John's Cancer Institute

data_processing:
Base calling and demultiplexing were processed using CASAVA v1.8 (Illumina).
Alignment to GRCh37/hg19 was performed using TopHat 2.0.10.
Expression values were generated using Cufflinks. Data represent RPKM for each cell line condition

source_name: WP-0614_over-expressing negative control hsa-miR_72 hrs

growth_protocol: Melanoma cell lines were cultured in RPMI-1640 supplemented with 10mM HEPES, 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
RNA extraction was performed with TRI-Reagent. The quality of RNA samples was estimated by RNA integrity number (RIN).
High quality RNA (RIN ≥ 8.0) was used to create mRNA libraries using the Illumina TruSeq RNA Sample Preparation Kit v2.

treatment_protocol: Melanoma cell lines (BD-0548, DP-0574, and WP-0614) were transfected with either 10nM of hsa-miR-200a or negative control hsa-miR precursors. Transfection were performed with Jet-PRIME transfection reagent according to the manufacturer’s instruction. After 72 hrs post-transfection, melanoma cells were washed twice with PBS and RNA extraction was performed.

tag: cell line

tag: cell type

value: metastatic melanoma cell line

tag: tissue source

value: cutaneous melanoma

tag: transfected with

value: hsa-miR negative control

tag: time point

value: 72 hrs post-transfection


title: WP-miR-200a

value: hsa-miR-200a-3p precursors


title: DP-NC

source_name: DP-0574_over-expressing negative control hsa-miR_72 hrs


title: BD-NC

source_name: BD-0548_over-expressing negative control hsa-miR_72 hrs


title: BD-miR-200a


title: 28_21d RNA-Seq


title: 26_21d RNA-Seq


title: RNA_trisomy4_147

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: processed data file: rpkm_table_ercc.xlsx, DEGs_020416.xlsx

data_processing:
RNA-seq alignment using Tophat 2.0.4, TAIR10 as library junction
Abundance counting using cuffdiff
Normalize count value using ERCC abundance
Calculate RPKM by dividing by union length of exons in kilbases and number of reads mapped in millions, as reported by cuffdiff
Calculate p-values with edgeR
genome build: TAIR10
processed data files format and content: Processed data (rpkm_table_ercc.xlsx) is in excel format include RPKM values for each samples; Processed data (DEGs_020416.xlsx) contains DEGs related to diploid samples.

organism: Arabidopsis thaliana

source_name: #147 trisomy4

extract_protocol:
Total RNA was isolated from rosette leaves using a Plant total RNA Purification kit Cat#TR02 (Gene Mark, Taiwan). The procedure involves cell lysis and protein precipitation followed by centrifugation. RNA in the supernatant is then bound on a filter column, where it is digested with DNaseI, followed by washing, and eluting with nuclease-free waster.
RNA was quantified with the Qubit RNA BR Assay and 0.4 μg of purified RNA with ERCC-ExFold mix(diploid with mix1 and others with mix2) spiked-in control was utilized as starting material for library construction, which was carried out with the Illumina TruSeq RNA Sample Preparation kit following the manufacturer's instructions. Libraries were sequenced using 100-bp reads on the HiSeq 2000 System (Illumina).

value: leaves

tag: ploidy


title: RNA_triploid_165

source_name: #165 triploid

value: triploid


title: RNA_trisomy5_118

source_name: #118 trisomy5


title: RNA_trisomy4_160

source_name: #160 trisomy4


title: RNA_triploid_164

source_name: #164 triploid


title: RNA_tetraploid_2

source_name: #2 tetraploid

value: tetraploid


title: RNA_trisomy2_7

source_name: #7 trisomy2


title: RNA_tetraploid_129

source_name: #129 tetraploid


title: RNA_tetraploid_143

source_name: #143 tetraploid


title: RNA_trisomy1_714

source_name: #714 trisomy1


title: RNA_trisomy1_640

source_name: #640 trisomy1


title: RNA_trisomy3_77

source_name: #77 trisomy3


title: RNA_diploid_134

source_name: #134 diploid

value: diploid


title: RNA_trisomy3_73

source_name: #73 trisomy3


title: RNA_diploid_131

source_name: #131 diploid


title: DP-miR-200a


title: RNA_diploid_87

source_name: #87 diploid


title: 2_7d RNA-Seq

source_name: Retinal epithelial cells


title: RNA_triploid_164a

description: processed data file: rpkm_table.txt, gene_exp.diff

data_processing:
RNA-seq alignment using Tophat 2.0.4, TAIR10 as library junction
Abundance counting using cuffdiff
Normalize count value using ERCC abundance
Calculate RPKM by dividing by union length of exons in kilbases and number of reads mapped in millions, as reported by cuffdiff
Calculate p-values with edgeR
genome build: TAIR10
processed data files format and content: Processed data (rpkm_table.txt) is in text format include RPKM values for each samples; Processed data (gene_exp.diff) contains DEGs related to diploid samples in cuffdiff format.

extract_protocol:
Total RNA was isolated from rosette leaves using a Plant total RNA Purification kit Cat#TR02 (Gene Mark, Taiwan). The procedure involves cell lysis and protein precipitation followed by centrifugation. RNA in the supernatant is then bound on a filter column, where it is digested with DNaseI, followed by washing, and eluting with nuclease-free waster.
RNA was quantified with the Qubit RNA BR Assay and 10 μg of purified RNA was utilized as starting material for library construction, which was carried out with the Dynabeads for polyA RNA enrichment, Superscript III cDNA synthesis, and barcoded with illumina index.  Libraries were sequenced using 100-bp reads on the HiSeq 2000 System (Illumina).


title: RNA_diploid_131a


title: WGBS_17chr_108a

library_source: genomic

data_processing:
BS-seq reads were aligned to the TAIR10 genome using BS Seeker2
If multiple alignments mapped to the same location only one is kept.
genome build: TAIR10
processed data files format and content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

molecule: genomic DNA

extract_protocol:
Genomic DNA was isolated from rosette leaves using a Wizard Genomic DNA Purification kit A1120 (Promega, USA). The procedure involves lysis of isolated nuclei, RNase digestion, protein precipitation, centrifugation, precipitation of DNA from the supernatant using isopropanol, followed by a wash step with 70% ethanol. After pelleting the precipitated DNA by centrifugation, it was dried under a vacuum and rehydrated in sterile nuclease free water.
genomic DNA was sheared by sonication to generate DNA fragments in the 100-300 bp size range. Bisulfite treatment and library preparation were carried out as described (Feng et al. 2011), except that the invitrogen methylcode bisulfite conversion kit was utilized for bisulfite treatment. The resulting libraries were sequenced with  Illumina sequencing technology (Illumna Hiseq 2000 sequencer).


title: WGBS_14chr_66a


title: RNA_triploid_141a

source_name: #141 triploid


title: WGBS_13chr_136a


title: RNA_trisomy5_195

source_name: #195 trisomy5


title: WGBS_16chr_121a


title: WGBS_tetraploid_143a


title: WGBS_tetraploid_129a


title: WGBS_triploid_165a

source_name: #165 triploid


title: RNA_trisomy2_3

source_name: #3 trisomy2


title: WGBS_trisomy4_144a

source_name: #144 trisomy4


title: WGBS_triploid_141a


title: WGBS_trisomy4_160a

source_name: #160 trisomy4


title: WGBS_diploid_134a


title: WGBS_trisomy4_147a

source_name: #147 trisomy4


title: d6_blue_post_3

city: WEST LAFAYETTE

first: Vikki

last: Weake

state: INDIANA

address: 175 S. University St.

department: Biochemisty

institute: Purdue University

data_processing:
Sanger / Illumina 1.9 used for basecalling.
Single-end sequenced reads were trimmed using Trimmomatic: trimmomatic SE LEADING:21 TRAILING:20 MINLEN:30 ILLUMINACLIP::2:40:10
Alignment to Ensemble Drosophila genome release 89 using Tophat with commands  --library-type fr-secondstrand
Sorting by read name using samtools sort with command -n
Read counting using HTSeq: htseq-count with options -s yes
Differential expression analysis and rpkm calculations using edgeR
Genome_build: BDGP6
Supplementary_files_format_and_content: Comma separated value (CSV) file of  normalized filtered counts (rpkm) for each sample.

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Retina

growth_protocol: Flies (genotype: w;cn bw;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion, flies were collected from 0 - 8h and then aged 12h (day 1) or 6 days. Flies were transferred to new food each 3 days if necessary. Mated male flies were used for all experiments.

extract_protocol:
Male flies were harvested and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. RNA was extracted from isolated GFP-tagged photoreceptor nuclei using previously described method by Ma J. and Weake V.M., J Vis Exp 2014 with minor modifications: nuclei were washed with PBS+300 mM NaCl following affinity purification. Control head homogenate (pre) samples were analyzed for day 1 dark samples.
Libraries were prepared using NuGen Ovation Drosophila RNA seq system. rRNA was depleted using InDA-C technology.

treatment_protocol: Male flies were exposed to 3h blue light (465nm; 8000 lux; 2mW/cm2) or dark control. A custom optical stimulator with temperature control (22 - 25C) was used for all experiments.

value: photoreceptor neurons

value: adult retina

value: 6 day old post eclosion

tag: Sex

value: male

tag: treatment

value: blue light

tag: genotype


title: d6_blue_post_2

value: w;cn bw;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]


title: d6_dark_post_3

value: dark (control)


title: d1_dark_post_3

value: 1 day old post eclosion


title: d1_dark_post_2


title: WGBS_diploid_87a


title: d6_dark_post_1


title: d6_blue_post_1


title: d1_blue_post_1


title: d1_dark_post_1


title: WGBS_diploid_131a


title: WT day 40 dissected eye rep3

data_processing:
Sanger / Illumina 1.9 used for basecalling.
Paired-end sequenced reads were trimmed using Trimmomatic with settings PE LEADING:20 TRAILING:20 MINLEN:30 ILLUMINACLIP:our_vector_file:2:40:10
Alignment to Ensemble Drosophila genome release 86 using Tophat with commands- -library-type fr-secondstrand --max-intron-length 141628 --mate-inner-dist 100
Exon and junction counts obtained using QoRTs QC with options --stranded_fr_secondstrand --minMAPQ 50 --maxReadLength 101
Novel splice sites identified using QoRTs mergeNovelSplices with options --minCount 6 --stranded_fr_secondstrand
Differential splicing  analysis using JunctionSeq: runJunctionSeqAnalyses with option analysis.type = "junctionsAndExons"
Genome_build: BDGP6
Supplementary_files_format_and_content: Comma separated value (CSV) file of all splicing event counts (junctions and exons) between day 10 and 40; text files for individual samples containing QoRTs splice junction and exon counts including novel splice junctions.

source_name: Dissected Eye

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 10 and 40 days with transfer to new food each 2-3 days.

extract_protocol:
Male flies were collected at indicated time point, anesthetized, and eyes were dissected and immediately stored in Trizol. RNA was extracted using Trizol according to the manufacturers' instructions.
Libraries were prepared using NuGen Ovation Drosophila RNA seq system. rRNA was depleted using InDA-C technology.
RNA sequencing by Illumina HiSeq2500 next generation sequencer

value: eye

value: 40 day old post eclosion


title: d6_dark_post_2


title: d1_blue_post_3


title: d1_dark_pre_3

source_name: Head

value: mixed cell types from whole head

value: Head


title: WT day 40 dissected eye rep2


title: d1_dark_pre_1


title: d1_blue_post_2


title: WT day 10 dissected eye rep3

value: 10 day old post eclosion


title: WT day 40 dissected eye rep1


title: d1_dark_pre_2


title: WGBS_triploid_164a

source_name: #164 triploid

value: leaves


title: WT day 10 dissected eye rep1


title: WT day 10 dissected eye rep2


title: MCF_plus_Decitabine_p53chip

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

description:
chipseq p53, Decitabine treated, 2hrs after IR
processed data file:
GEO2A.bed

data_processing:
ChIP-Seq: Alignment done with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6, reads were quantified within peaks and normalized across samples
RNA-Seq: reads were mapped and analyzed by TopHat/Cufflinks RNA-seq analysis pipeline38 using Tophat version 2.1.0 and cufflinks version 2.1.1. Alignment was done against hg19 genome and hg19 RefSeq.gtf transcript annotations were used.
Transposase/ATAC-Seq: fastq files were trimmed with CutAdapt ('TTCGTGCGTCAGTTCA' adapter), Alignment applied to trimmed files with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6
InVitro-Seq: fastq files were trimmed with CutAdapt ('TTCGTGCGTCAGTTCA' adapter), Alignment applied to trimmed files with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6.
Genome_build: hg19
Supplementary_files_format_and_content: TSV files, BED files

growth_protocol: Cells were passaged as at least twice post-thaw and used at a passage number of 6-14. ~70% confluent plates were treated and harvested

extract_protocol:
ChIPseq lysates were clarified from sonicated nuclei and IPed with DO-1 anti-p53 antibody. RNA samples were extracted with Trizol, purified on Zymo columns, and 500ng polyA selected.
DNA and mRNA libraries were prepared with standard illumina compatible protocols (NEBnext Kit), ATACseq and in vitro chip Lib was prepared by PCR of MuA tagmented DNA (Thermo).

treatment_protocol: Cell were Irradiated with a RS-2000 source (RadSource), 160KeV

value: Decitabine

tag: chip antibody

value: anti-p53 antibody (DO-1, Santa Cruz Biotechnology, SC-126X, Lot:G0115)


title: invitro_p53IP

description:
InVitro-Seq p53IP
processed data file:
GEO2B.bed

source_name: MCF7 Transposase Fragment Genomic DNA


title: MCF_Decitabine_ATACseq

description:
processed data file:
GEO2A.bed


title: MCF_minus_Decitabine_p53chip

description:
chipseq p53, no Decitabine, 2hrs after IR
processed data file:
GEO2A.bed


title: invitro_background

description:
InVitro-Seq background
processed data file:
GEO2B.bed


title: A549_mRNA, 3hrs 4Gy

description:
A549_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv

data_processing:
ChIP-Seq: Alignment done with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6, reads were quantified within peaks and normalized across samples
RNA-Seq: reads were mapped and analyzed by TopHat/Cufflinks RNA-seq analysis pipeline38 using Tophat version 2.1.0 and cufflinks version 2.1.1. Alignment was done against hg19 genome and hg19 RefSeq.gtf transcript annotations were used.
Transposase/ATAC-Seq: fastq files were trimmed with CutAdapt ('TTCGTGCGTCAGTTCA' adapter), Alignment applied to trimmed files with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6
Genome_build: hg19
Supplementary_files_format_and_content: TSV files

molecule: polyA RNA

extract_protocol:
ChIPseq lysates were clarified from sonicated nuclei and IPed with DO-1 anti-p53 antibody. RNA samples were extracted with Trizol, purified on Zymo columns, and 500ng polyA selected.
DNA and mRNA libraries were prepared with standard illumina compatible protocols (NEBnext Kit), ATACseq Lib was prepared by PCR of MuA tagmented DNA.

tag: treated with

value: 4Gy for 3hrs


title: SKMEL5_mRNA, 3hrs 4Gy

description:
SKMEL5_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: UACC62_mRNA, 3hrs 4Gy

description:
UACC62_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: HCT116_mRNA, 3hrs 4Gy

description:
HCT116_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: Rat-Control3-WTTS

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

data_processing:
WTTS reads were trimmed for adaptor sequence, and masked for low-quality sequence using FASTX-Toolkit.
WTTS reads were mapped to rat genome using the aligner Bowtie2 version 2.2.3 with setting"bowtie2 -L 25 -N 0 -i S,1,1.15 --no-unal".
The ends of mapped reads within 24bp of each other on the same strand were clustered to detect poly(A) sites .
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: mapped reads

organism: Rattus norvegicus

source_name: Hypothalamus

extract_protocol:
Total RNA was harvested using using Qiagen RNeasy Micro Purification Kit
WTTS libraries were constructed based on our previous protocols. The WTTS method includes several major steps: fragmentation, poly(A)+ RNA enrichment, 1st strand cDNA synthesis, Size selection and PCR amplication.

tag: strain

value: Long-Evans

value: Hypothalamus

tag: developmental stage

value: Adult

tag: disease state

value: control


title: H460_mRNA, 3hrs 4Gy

description:
H460_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: UACC257_mRNA, 3hrs 4Gy

description:
UACC257_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: Rat-Control4-WTTS


title: Rat-Control1-WTTS


title: MALME3_mRNA, 3hrs 4Gy

description:
MALME3_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: U2OS_mRNA, 3hrs 4Gy

description:
U2OS_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: Rat-OB3-WTTS

value: diet-induced obesity


title: MCF7_mRNA, 3hrs 4Gy

description:
MCF7_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: Rat-OB2-WTTS


title: Rat-OB1-WTTS


title: UACC257_RNA_NT

description:
UACC257_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv

value: none (untreated)


title: LOXIMVI_mRNA, 3hrs 4Gy

description:
LOXIMVI_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv

source_name: LOXIMVI

value: LOXIMVI


title: A549_RNA_NT

description:
A549_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: HCT116_RNA_NT

description:
HCT116_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: MALME3_RNA_NT

description:
MALME3_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: H460_RNA_NT

description:
H460_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: A498_mRNA, 3hrs 4Gy

description:
A498_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: U2OS_RNA_NT

description:
U2OS_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: UO31_mRNA, 3hrs 4Gy

description:
UO31_RNA_3h
mRNAseq_4gy_3hrs
processed data file:
mRNAseq.tsv


title: UACC62_RNA_NT

description:
UACC62_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: UO31_RNA_NT

description:
UO31_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: Rat-Control2-WTTS


title: LOXIMVI_RNA_NT

description:
LOXIMVI_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: RPE_p53ChIPseq_2h_4GY

description:
RPE_p53ChIPseq_2h_4GY
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv

source_name: RPE

value: RPE

value: 4GY for 2hrs

value: anti-p53  antibody (DO-1, Santa Cruz Biotechnology, SC-126X, Lot:G0115)


title: UACC257 p53 ChIPseq, 2hrs 4GY

description:
UACC257_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: UACC62 p53 ChIPseq, 2hrs 4GY

description:
UACC62_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: MCF7_p53ChIPseq_nutlin_2hr

description:
MCF7_p53ChIPseq_nutlin
chipseq p53, 2hrs after Nutlin
processed data file:
chipseq.tsv

value: nutlin for 2hrs


title: MCF7_RNA_NT

description:
MCF7_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: UACC257_p53ChIPseq_nutlin_2hr

description:
UACC257_p53ChIPseq_nutlin
chipseq p53, 2hrs after Nutlin
processed data file:
chipseq.tsv


title: Rat-OB4-WTTS


title: MALME3 p53 ChIPseq, 2hrs 4GY

description:
MALME3_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: U2OS p53 ChIPseq, 2hrs 4GY

description:
U2OS_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: A549 p53 ChIPseq, 2hrs 4GY

description:
A549_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: A498 p53 ChIPseq, 2hrs 4GY

description:
A498_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: WGBS_trisomy4_144_147

extract_protocol:
Genomic DNA was isolated from rosette leaves using a Wizard Genomic DNA Purification kit A1120 (Promega, USA). The procedure involves lysis of isolated nuclei, RNase digestion, protein precipitation, centrifugation, precipitation of DNA from the supernatant using isopropanol, followed by a wash step with 70% ethanol. After pelleting the precipitated DNA by centrifugation, it was dried under a vacuum and rehydrated in sterile nuclease free water.
genomic DNA was sheared by sonication to generate DNA fragments in the 100-300 bp size range. Bisulfite treatment and library preparation were carried out as described (Feng et al. 2011), except that the EpiTect Fast kit (QIAGEN) was utilized for bisulfite treatment. The resulting libraries were sequenced with  Illumina sequencing technology (Illumna NextSeq500 sequencer).


title: H460 p53 ChIPseq, 2hrs 4GY

description:
H460_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: LOXIMVI p53 ChIPseq, 2hrs 4GY

description:
LOXIMVI_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: MCF7 p53 ChIPseq, 2hrs 4GY

description:
MCF7_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: WGBS_trisomy4_128

source_name: #128 trisomy4


title: UO31 p53 ChIPseq, 2hrs 4GY

description:
UO31_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: SKMEL5_RNA_NT

description:
SKMEL5_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: A498_RNA_NT

description:
A498_RNA_NT
mRNAseq NT
processed data file:
mRNAseq.tsv


title: WGBS_tetraploid_2

source_name: #2 tetraploid

value: tetraploid


title: MCF7_Input

description:
MCF7_Input
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: WGBS_tetraploid_143

source_name: #143 tetraploid


title: HCT116 p53 ChIPseq, 2hrs 4GY

description:
HCT116_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: WGBS_triploid_164

value: triploid


title: LOXIMVI ATACseq

description:
LOXas
ATACseq
processed data file:
chipseq.tsv


title: WGBS_trisomy5_195

source_name: #195 trisomy5

value: leaves


title: LOXIMVI Transposase Fragment Genomic DNA

description:
LOXg
genomic DNA transposed
processed data file:
chipseq.tsv

data_processing:
library strategy: Transposase-seq
ChIP-Seq: Alignment done with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6, reads were quantified within peaks and normalized across samples
RNA-Seq: reads were mapped and analyzed by TopHat/Cufflinks RNA-seq analysis pipeline38 using Tophat version 2.1.0 and cufflinks version 2.1.1. Alignment was done against hg19 genome and hg19 RefSeq.gtf transcript annotations were used.
Transposase/ATAC-Seq: fastq files were trimmed with CutAdapt ('TTCGTGCGTCAGTTCA' adapter), Alignment applied to trimmed files with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6
Genome_build: hg19
Supplementary_files_format_and_content: TSV files


title: WGBS_triploid_165

source_name: #165 triploid


title: WGBS_trisomy3_73

source_name: #73 trisomy3


title: SKMEL5 p53 ChIPseq, 2hrs 4GY

description:
SKMEL5_p53cs
chipseq p53, 2hrs after IR
processed data file:
chipseq.tsv


title: WGBS_trisomy4_160


title: WGBS_trisomy5_118

source_name: #118 trisomy5


title: WGBS_trisomy2_3

source_name: #3 trisomy2


title: WGBS_trisomy1_640

source_name: #640 trisomy1


title: WGBS_diploid_134

source_name: #134 diploid

value: diploid


title: WGBS_diploid_87

source_name: #87 diploid


title: MCF7 ATACseq

description:
MCFas
ATACseq
processed data file:
chipseq.tsv


title: mcPC_DN2

city: paris

first: bruno

last: saubamea

address: 4 avenue de l'observatoire

department: Faculté de Pharmacie de Paris

country: France

institute: Université Paris Descartes

data_processing:
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded.
Transcript abundances (in Transcripts Per Million, TPM) and counts (in number of reads) were estimated using Salmon 0.8.0 (Patro R et al. Nat. Methods. 2017;14:417–419. )
Reads were aligned against the rat transcriptome using Rattus_norvegicus.Rnor_6.0.cdna.all.fa.gz Ensembl annotation file (ftp://ftp.ensembl.org/pub/release-87/fasta/rattus_norvegicus/cdna/).
Transcript-level estimates were summed within genes to obtain TPM and counts estimates at the gene level using the Tximport package (Soneson C et al. F1000Res. 2015;4:1521.).
The whole dataset contains  14607 genes with at least one read in each sample (after summation over technical replicates)
Differential gene expression was estimated using DESeq2 and was expressed as Log2FC, defined as the Log2 of the Fold Change between mean normalized counts in PC vs VSMC
Genome_build: Rnor_6.0 (Ensembl release 87)
Supplementary_files_format_and_content: File including Ensembl_Gene_ID, Entrez_Gene_ID, Gene_Symbol, Gene_Description, MeanTPM_VSMC, MeanTPM_mcPC, MeanCounts_VSMC, MeanCounts_mcPC, MeanLength_VSMC, MeanLength_mcPC, MeanCountsNorm_VSMC, MeanCountsNorm_mcPC, baseMean, log2FoldChange, lfcSE, lfc pvalue, lfc padj

source_name: Brain cortex

extract_protocol:
Total RNA was extracted using the RNeasy® Micro Kit (Qiagen). Messenger (polyA+) RNAs were purified from 100 ng of total RNA using oligo(dT). All samples had RNA integrity numbers ranging from 6.40 to 8.50 as assessed by Agilent Bioanalyzer.
Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina)

value: Sprague-Dawley

value: 4-5 weeks

tag: gender

value: male

value: Brain

value: PC


title: VSMC_DK4

tag: tissue

value: VSMC


title: mcPC_DL2


title: VSMC_DL4


title: VSMC_DN4


title: WGBS_trisomy3_77

source_name: #77 trisomy3


title: WGBS_trisomy1_714

source_name: #714 trisomy1


title: D10TDKO-1

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

description: All the neonates used were littermates by interbreeding heterozygous mice resulting from crosses of C57BL/6J (B6) and C57BL/6J.129P2-Tcrdtm1Mom/J (TCRδ-/-). Mice were infected intranasally with A/HKx31 (H3N2) in 10 µl (0.6 x 10e2 EID50 / g body weight for neonates) at age 7 days. Lungs were extracted at age 15 days.

data_processing:
Basecalls made using standard Illumina software.
Reads were mapped to the mm10 genome using STAR version 2.5.2b with default parameters.
Gene counts were obtained with HTSeq version 0.6.1p1 using Gencode comprehensive chromosomal annotations vM13.
Average insert sizes estimated using Picard 2.0.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_Aligned_GeneCounts.out.tab: Tab-delimited text files containing raw gene counts.

organism: Mus musculus

source_name: Lung, TCRδ-/-

extract_protocol:
TissueLyser homogenization of flash-frozen whole lung; Qiagen RNeasy Mini kit.
Illumina TruSeq Stranded Total RNA kit.

treatment_protocol: Infected with influenza at age 7 days; lungs extracted at age 15 days.

tag: strain/background

tag: genotype/variation

value: TCR<delta>-/-

value: lung

tag: age

value: postnatal day 15

tag: infection

value: influenza


title: D10TDKO-2


title: D10TDWT-3

source_name: Lung, WT

value: wild type


title: D10TDWT-2


title: MCF7 Transposase Fragment Genomic DNA

description:
MCFg
genomic DNA transposed
processed data file:
chipseq.tsv

tag: cell line


title: D10TDKO-3


title: D10TDWT-1


title: WGBS_trisomy2_7

source_name: #7 trisomy2


title: B188_iDC_1h_H3K4me3

status: Public on Jun 19 2018

city: Nijmegen

first: Simon

last: van Heeringen

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

description: ChIP-seq of H3K4me3 in monocyte-derived dendritic cells stimulated with R848 for 1 hour

data_processing:
Base-calling was performed by the Illumina CASAVA software.
Reads were aligned to the human genome (hg19) using bwa 0.6.1-r104 with default settings. Duplicate reads were marked using bamUtil 1.0.2.
Peaks were called using MACS2 version 2.0.10.20120913 with default settings.
Peaks common to all replicates were determined using BEDTools version 2.20.1.
Coverage files in bigWig format were created using bam2bw (https://bitbucket.org/simonvh/bam2bw/) with the -e auto and -c parameters
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 peak files in text format and BED format; Coverage files in bigWig format

source_name: monocyte-derived dendritic cells

growth_protocol: Human monocyte-derived dendritic cells were generated from buffy coats by Ficoll separation of PBMCs, followed by culturing of plastic-adherent cells for 6 days in RPMI 1640 supplemented with 10% FBS, ultra-glutamine, antibiotic-antimicotic, 300 U/mL IL-4, and 450 U/mL GM-CSF. Medium was refreshed on day 3.

extract_protocol:
Five million human moDCs were stimulated with R848, followed by cross-linking with 1% formaldehyde for 15 min at room temperature. The reaction was quenched with 0.125M glycine and washed at 4˚C with three buffers: 1) PBS; 2) buffer consisting of 0.2% Triton X-100, 0.2% NP-40, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris-HCl pH 7.5, 10 mM NaCl; and 3) buffer consisting of 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES pH 7.6. Cells were then resuspended in a ChIP-incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES, 1X protease inhibitor mixture [Roche], 0.1% BSA) and sheared using a Bioruptor Next Generation sonicator (Diagenode). Sonicated chromatin was centrifuged for 5 min at 4˚C and supernatant was snap-frozen and kept until ChIP. 10 ng of input or ChIP-enriched DNA were end-paired using T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase, New England Biolabs), and T4 polynucleotide kinase (New England Biolabs), followed by purification using the QIAquick PCR purification kit (Qiagen). Subsequently, DNA was dA-tailed using the Klenow fragment (3’ to 5’ exo minus, New England Biolabs), followed by purification using the MinElute Reaction Cleanup kit (Qiagen)
DNA was ligated to multiplex NEXTflex adapters (Bioo Scientific). IP and input DNA were purified by the MinElute reaction Cleanup kit, and amplified by PCR using the KAPA HiFi HotStart ReadyMix PCR kit (KAPA Biosystems) with the following program: 45 sec at 98°C for initial denaturation, 15 sec at 98C, 30 sec at 65C, 30 sec at 72°C for 4 cycles, followed by 1 minute at 72°C for final extension. Removal of excess adaptors and selection of 300bp bands was done using 2% E-Gel SizeSelect Agarose Gels (Invitrogen). Adapter-modified DNA fragments were enriched by PCR using the KAPA HiFi HotStart ReadyMix PCR kit for 8-10 cycles with the aforementioned program. To get rid of the 120bp adapterdimer, the PCR product was purified using Ampure beads (Beckman Coulter)

treatment_protocol:
Immature monocyte-derived DCs were stimulated with 4 µg/ml R848 (Axxora) for 1 hour.
Immature monocyte-derived DCs were stimulated with TLR-ligand R848 for 0h, 1h, or 24h

tag: cell type

value: monocyte-derived dendritic cells

tag: treatment time


title: B188_iDC_H3K4me3

description: ChIP-seq of H3K4me3 in immature monocyte-derived dendritic cells

treatment_protocol:
n/a
Immature monocyte-derived DCs were stimulated with TLR-ligand R848 for 0h, 1h, or 24h


title: B188_iDC_24h_H3K4me3

description: ChIP-seq of H3K4me3 in monocyte-derived dendritic cells stimulated with R848 for 24 hours

treatment_protocol:
Immature monocyte-derived Dcs were stimulated with 4 µg/ml R848 (Axxora) for 24 hours.
Immature monocyte-derived DCs were stimulated with TLR-ligand R848 for 0h, 1h, or 24h


title: B188_iDC_Input

description: ChIP-seq Input in immature monocyte-derived dendritic cells


title: B188_iDC_24h_H3K27ac

description: ChIP-seq of H3K27ac in monocyte-derived dendritic cells stimulated with R848 for 24 hours


title: B188_iDC_1h_H3K27ac

description: ChIP-seq of H3K27ac in monocyte-derived dendritic cells stimulated with R848 for 1 hour

treatment_protocol:
Immature monocyte-derived  Dcs were stimulated with 4 µg/ml R848 (Axxora) for 1 hour.
Immature monocyte-derived DCs were stimulated with TLR-ligand R848 for 0h, 1h, or 24h


title: mcPC_DK2


title: B198_iDC_24h_script

description: ChIP-seq of DC-SCRIPT in monocyte-derived dendritic cells stimulated with R848 for 24 hours

value: DC-SCRIPT/ZNF366 (cat# AF4707, lot# CALX011009A, R&D Systems)


title: B188_iDC_H3K27ac

description: ChIP-seq of H3K27ac in immature monocyte-derived dendritic cells


title: B198_iDC_1h_script

description: ChIP-seq of DC-SCRIPT in monocyte-derived dendritic cells stimulated with R848 for 1 hour


title: B198_iDC_script

description: ChIP-seq of DC-SCRIPT in immature monocyte-derived dendritic cells


title: B190_iDC_24h_script


title: B190_iDC_1h_script


title: B188_iDC_24h_script


title: B188_iDC_1h_script


title: B188_iDC_script


title: B188_iDC_1h_Input

description: ChIP-seq Input in monocyte-derived dendritic cells stimulated with R848 for 1 hour


title: HAEC_control_siRNA_3

city: New York

first: Jun

last: Zhu

address: 1 Gustave L. Levy Pl

department: Genetics and genomic sciences

institute: Icahn school of medicine at mount sinai

data_processing:
Sequencing reads were aligned to the human reference genome hg19 using TopHat
The mapped sequences was aligned with htseq-count to quantify the read count for each gene
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include number of counts for each sample

source_name: Human Aortic Endothelial Cells

growth_protocol: HAEC passage 5 were grown in endothelial growth medium (PeloBiotech, Cat# PB-C-MH-100-2199) containing 8% FCS on gelatine coated dishes

extract_protocol:
RNA from HAEC was extracted using RNA Mini Kit (Bio&Sell, Cat# BS67.311) and on column DNAse digestion (Qiagen, Cat# 79254)
Library construction (LncRNA library, Ribo-Zero), quality assessment and sequencing (HiSeqSE50) were performed by Novogene

treatment_protocol: HAEC were transfected with Lipofectamine RNAiMAX transfection reagent (Thermo Fisher, Cat# 13778150) for siRNA (50 nM) treatment. The following siRNAs were used (Stealth RNAi, Invitrogen, Cat#1299001): MTHFD2#1 (HSS116659), MTHFD2#2 (HSS116661), MTHFD2#3 (HSS173888), Ct#1 (Cat# 12935300), Ct#2 (Cat# 12935112), Ct#3 (Cat# 12935113). HAEC were cultured in endothelial growth medium (8 %FCS) until RNA isolation 72 h after transfection.

value: control


title: HAEC_MTHFD2_siRNA_2

value: MTHFD2 siRNA


title: HAEC_MTHFD2_siRNA_3


title: HAEC_control_siRNA_1


title: HAEC_MTHFD2_siRNA_1


title: IgG ChIP vehicle treated

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Alignment (BWA) Tool with the default configurations
Uniquely mapped reads with mis-match <= 2 were used for peak detection
Peaks were called usingMACS2 using the default setting.
Peaks with "pileup" >=6 and "fold_enrichment" >=5 were kept for further analysis
Genome_build: hg19
Supplementary_files_format_and_content: The peak files were generated using MACS2.

growth_protocol: human BEAS-2Bs were grown as recommended by Coriell

extract_protocol: Lysates were clarified from sonicated nuclei and NRF2-DNA complexes were isolated with antibody (Epitomics, Clone ID EP1808Y).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: human BEAS-2Bs were treated at a density of 900,000 cells/ml with 10 μM D,L-sulforaphane (Calbiochem) or 0.1% (v/v) DMSO as a vehicle control for 5 hours

value: vehicle

value: rabbit IgG antibody (Invitrogen)


title: NRF2 ChIP SFN treated rep1

value: SFN

value: rabbit monoclonal anti-NRF2 (Epitomics, Clone ID EP1808Y)


title: NRF2 ChIP SFN treated rep2


title: NRF2 ChIP vehicle treated rep1


title: NRF2 ChIP vehicle treated rep2


title: B188_iDC_24h_Input

description: ChIP-seq Input in monocyte-derived dendritic cells stimulated with R848 for 24 hours


title: HAEC_control_siRNA_2


title: BPA-replicate 4 [BRSEQ11]

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Sample 8 (BRSEQ11)

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Leading and trailing low quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15.
Reads with at least 30 bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000bp apart and keeping only unique, concordantly aligned read pairs for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.

growth_protocol: C57BL6/J offspring were exposed to control feed (low phytoestrogen diet) or BPA feed (low phytoestrogen + 50mg BPA/kg diet) throughout gestation and lactation. At weaning (postnatal day 21), all mice were placed on the control diet for the remainder of the experiment.

extract_protocol:
Total RNA was isolated from hippocampal tissue using RNeasy mini kit (Qiagen)
Following polyA selection using Dynabeads mRNA DIRECT protocol (Ambion), RNA was fragmented and tagged at both ends for stranded library preparation, using the Scriptseq v2 (Illumina) library preparation protocol.

treatment_protocol: Hippocampal tissues were rapidly dissected, flash frozen, and stored at -80˚C until further analysis.

tag: strain background

value: Wild-type

value: 20 weeks

value: male

value: 50 mg BPA/kg diet during gestation and lactation

value: brain; hippocampus


title: Lung_RNA polymerase II (Pol II)_ChIP-seq

city: Seattle

first: Karol

last: Bomsztyk

address: 850 Republican Street

department: Medicine

institute: University of Washington

data_processing:
Short reads were aligned to Mus musculus assembly mm10 using bowtie2 v2.2.8
). Peak calling, genome browser track generation, and data quality control were
performed using HOMER v4.8
Heart, kidney, liver and lung were done in duplicates and the two replicates for each organ were combined for peak calling
Genome_build: mm10
Supplementary_files_format_and_content: peak files

source_name: Lung

extract_protocol:
Hearts, kidneys, livers and lungs were recovered, flash frozen and stored at -80oC. Tissues were crosslinked and sheared.  Fragmented chromtin was used in ChIP with Pol II antibody.
Indexed libraries were constructed using Tn5 transposase tagmentations, as per Nextera protocol (Illumina)

value: Lung

value: Pol II CTD (4H8) Sc-47701 SantaCruz


title: Liver_RNA polymerase II (Pol II)_ChIP-seq

source_name: Liver

value: Liver


title: B190_iDC_script

tag: treatment


title: Heart_RNA polymerase II (Pol II)_ChIP-seq

source_name: Heart

value: Heart


title: Kidney_RNA polymerase II (Pol II)_ChIP-seq

source_name: Kidney

value: Kidney


title: Control-replicate 2 [BRSEQ03]

description: Sample 2 (BRSEQ03)

value: 0 mg BPA/kg diet during gestation and lactation


title: BPA-replicate 1 [BRSEQ04]

description: Sample 5 (BRSEQ04)


title: Control-replicate 4 [BRSEQ05]

description: Sample 4 (BRSEQ05)


title: Control-replicate 1 [BRSEQ08]

description: Sample 1 (BRSEQ08)


title: BPA-replicate 2 [BRSEQ09]

description: Sample 6 (BRSEQ09)


title: immature liver3

status: Public on Jun 18 2018

city: Yangling

first: Shengru

last: Wu

address: 22 St.XiNong

department: College of Animal Science and Technology

country: China

institute: Northwest A&F University

data_processing:
Reads mapping and transcriptome assembling:The 125 bp paired-end raw reads were firstly processed through FastQC to obtain the clean data, by removing the reads that contain sequencing adapter contaminations or poly-N and the low quality reads whose Q value were less than 20. At the same time, Q20, Q30 and GC content of the clean data were calculated. Index of the reference genome was built using Bowtie v2.0.6 and the clean reads from six cDNA libraries were merged and mapped to the Gallus gallus 4 (Ensembl 85; http://www.ensembl.org/Gallus_gallus/Info/Index) using TopHat. The mapped reads were assembled into transcripts using Cufflinks [29]. Briefly, ribosomal RNA in sequencing data was removed. We aligned all reads to ribosomal RNA of chicken download from ensemble by bowtie2. Then those aligned reads were removed from fastq files.
Coding potential and identification of lncRNAs:By using the Cuffcompare program, the assembled transcripts were annotated . The known protein-coding transcripts and the transcripts whose length were smaller than 200 bp were firstly removed, and the remaining unknown transcripts were used to screen for putative lncRNAs. Then, the coding potential for the remaining transcripts was calculated by CNCI  and CPC. A transcript was deemed to be lncRNA if the coding potentials were scored to be less than −1 by CPC software and the coding potentials were scored to be less than 0 by CNCI software, which suggest that this transcript has no capacity of coding for proteins. Briefly, those candidate transcripts whose length were longer than 200nt and the intersection between both coding prediction tools CPC and CNCI were deemed to be lncRNA.
Analysis of differential expression patterns:Expression levels of all transcripts, including putative lncRNAs and mRNAs, were quantified as FPKM using the Cuffdiff program from the Cufflinks package. Differential gene expression was determined using DESeq with a P value < 0.05 and log2foldchange >1 or < -1.
Genome_build: Gallus gallus 4

organism: Gallus gallus

source_name: liver sample from 1-day-old chicks

growth_protocol: Five adult healthy Arbor Acres breeder roosters (40 week of age) and Twenty one-day-old healthy Arbor Acres breeder roosters were collected from Experimental Teaching Center of Animal Science of the Northwest A&F University (Yangling, Shaanxi, China).

extract_protocol:
Total RNA from 3 adult roosters’ and 12 one-day-old rooster’ livers for RNA sequencing were extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s procedure. Specifically, the DNaseI was used during the RNA isolation process to avoid contamination with genomic DNA. The quantity and purity of total RNA were analyzed by a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific, MA, USA), and integrity of RNA was accessed with Bioanalyzer 2100 and RNA Nano6000 LabChip Kit (Agilent, CA, USA). Only samples that had the OD260/280 > 1.8, OD260/230 > 2.0, and the RNA Integrity Number (RIN) > 7.0 were used for further sequencing. Four RNA samples of one-day-old chicks’ liver were mixed equally together as a pooled RNA sample according to the purity of total RNA, and the RNA samples of adult chickens’ livers were directly used for library construction. In total, we gathered three RNA samples from three adult roosters and three pooled RNA samples from 12 one-day-old roosters for further library construction.
Approximately 3 μg of total RNA was used to prepare an LncRNA library. According to protocol of Epicentre Ribo-zero™ Gold Kit (Illumine, San Diego, USA), ribosomal RNA was removed and the rRNA-depleted RNA (Poly A+ and Poly A－ RNA) were collected [24, 25, 43]. Subsequently, high strand-specificity libraries were generated using the rRNA-depleted RNA and a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) following the manufacturer’s recommendations. Briefly, the rRNA-depleted RNA was fragmented using divalent cations under elevated temperature in NEBNext. First-strand cDNA was synthesized using random hexamer primers and M-MuLV reverse transcriptase (RNase H−). Subsequently, second-strand cDNA synthesis was performed using second-strand synthesis reaction buffer, DNA polymerase I, and RNase H. Remaining overhangs were converted into blunt ends by exonuclease/polymerase activity. After adenylation of the 3’ ends of the DNA fragments, NEBNext adaptors with hairpin loop structures were ligated to the fragments to prepare them for hybridization. To select cDNA fragments that are 150–200 bp in length, the fragments in each of the library were purified with an AMPure XP system (Beckman Coulter, Brea, CA, USA). Then 3 μl USER Enzyme (NEB, Ipswich, MA, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. The qPCRs were performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. The PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. After cluster generation, the paired-end sequencing (2*125bp) were performed on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China).

treatment_protocol: These randomly selected roosters were fed deprived for 12 hours, then killed and immediately dissected. The whole left side livers were collected into Eppendorf tubes, and frozen immediately in liquid nitrogen. For each liver sample we gathered, the liver was grinded and homogenized using liquid nitrogen, and then all the homogenized liver samples were stored at -80℃ until be analyzed. The livers of three adult roosters and twelve one-day-old roosters were selected randomly for RNA isolation and next generation sequencing analyses;

value: liver


title: mature liver1

source_name: liver sample from 40-week-old breeder cocks


title: mature liver3


title: mature liver2


title: immature liver2


title: immature liver1


title: non-targeting_293HEK_B

status: Public on Jun 17 2018

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description:
Flp-In T-REx-293 cells transfected with control, non-targeting siRNA (Invitrogen, Neg High GC Stealth)
processed data file: LstrandContribution.csv
NegH_B_ACAGTG_L007

data_processing:
Sequences of all RNA-seq reads were striped of adapters and trimmed from poor quality bases using cutadapt (version 1.9.2.dev0). Standard libraries were mapped using the GSNAP short read aligner (version 2016-05-01) allowing for spliced read alignment and settings. The assemblies were prepared genome reference human genome (GRCh38) facilitating the alignment of known splice junctions of the basic GENECODE v26 annotation and treating the mitochondrial genome as a circular DNA molecule to allow for mapping of all reads reads in the D-loop region.
Reads from short RNA-seq libraries were additionally merged and only ones which overlapped by at least 5 bases were further aligned to the genome using GSNAP short read aligner.
The quality control, read processing and filtering, visualization of the results and counting of reads for the annotation was performed using custom scripts incorporating elements of the RSeQC (version 2.6.1), BEDtools (version 2.23.0) and SAMtools packages
Reads mapping to were used to prepare pileups of with the expression corrected to the total number of reads mapping to both strands of the mitochondrial genome. The coverage over the non coding bases of the mitochondrial genome, additionally excluding regions antisense to rRNA and tRNA to avoid bleed-trough from the other strand, was summarized separately for the L-strand and H-strand utilizing custom scripts incorporating elements of the RSeQC and bwtool (version 1.0)  pakages.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files and csv containing cumulative expression

source_name: Flp-In T-REx-293_non-targeting

extract_protocol:
Total RNA was isolated with the TRI Reagent (T9424, Sigma) according to the manufacturer’s instructions. RNA was subjected to TURBO DNase (AM2238, Ambion) treatment. RNA dedicated for analysis of longer transcripts was subjected to rRNA depletion. Prior to rRNA depletion, to provide an internal performance control for further steps, 1 µg of RNA was mixed with 4 µl of 1:99 diluted ERCC RNA Spike-In Control Mix 1 (4456740, Ambion).
Libraries of long RNAs were constructed as previously described in Sultan et al., 2012 (PMID: 2609201) with minor modifications. Fragmentation and first strand cDNA synthesis were performed as in TruSeq RNA Library Prep kit v2 protocol (Illumina, RS-122-2001, instruction number 15026495 Rev. D), using SuperScript III reverse transcriptase (18080-085, Thermo Fisher Scientific). Ligation-based libraries for analysis of small RNAs were prepared as described by Labno et al (PMID: 27431325) with one modification – total RNA, which was not subjected to rRNA depletion, was used for library preparation. Enriched library quality was verified using 2100 Bioanalyzer and High Sensitivity DNA kit (5067-4626, Agilent). The libraries’ concentration was estimated by qPCR means with KAPA Universal Library Quantification Kit (KK4824, Kapa Biosystems), according to the supplied protocol. Sequencing was carried out on an Illumina sequencing platform, and standard libraries denaturation and pair-end sequencing procedures of 2x75 cycles.

tag: parental cells

value: 293 - ATCC  number CRL-1573

value: embrionic kidney (PubMed ID:886304)

value: Flp-In T-REx-293 (Invitrogen)

tag: experimental set

tag: sequenced rna species

value: long (> ~100 nucleotides); rRNA-depleted

tag: sample type

value: control


title: non-targeting_293HEK_C

description:
Flp-In T-REx-293 cells transfected with control, non-targeting siRNA (Invitrogen, Neg High GC Stealth)
processed data file: LstrandContribution.csv
NegH_C_GCCAAT_L007


title: GRSF1_silenced_C

description:
Flp-In T-REx-293 cells transfected with siRNA specific for GRSF1
processed data file: LstrandContribution.csv
GRSF1_C_GATCAG_L007

source_name: Flp-In T-REx-293_GRSF1_silenced


title: GRSF1_silenced_A

description:
Flp-In T-REx-293 cells transfected with siRNA specific for GRSF1
processed data file: LstrandContribution.csv
GRSF1_A_CAGATC_L007


title: non-targeting_293HEK_A

description:
Flp-In T-REx-293 cells transfected with control, non-targeting siRNA (Invitrogen, Neg High GC Stealth)
processed data file: LstrandContribution.csv
NegH_A_TGACCA_L007


title: untreated_293HEK_B

description:
untreated Flp-In T-REx-293 cells
processed data file: LstrandContribution.csv
293NGEM_B_CGATGT_L007

source_name: Flp-In T-REx-293_untreated


title: GRSF1_silenced_B

description:
Flp-In T-REx-293 cells transfected with siRNA specific for GRSF1
processed data file: LstrandContribution.csv
GRSF1_B_ACTTGA_L007


title: G207V_A

description:
transgenic 293 cells (293-G207V) which express catalytically inactive form of hSuv3 in the tetracycline-inducible manner (PMID: 19864255); treated with tetracycline in order to induce expression of hSuv3-G207V
processed data file: LstrandContribution.csv
G207V_A_TGACCA_L001

source_name: transgenic Flp-In T-REx-293_G207V

value: transgenic Flp-In T-REx-293

value: degradosome (hSuv3, PNPase)


title: Control-replicate 3 [BRSEQ10]

description: Sample 3 (BRSEQ10)

value: Wild-type

value: 20 weeks

value: male

tag: treated with


title: G207V_B

description:
transgenic 293 cells (293-G207V) which express catalytically inactive form of hSuv3 in the tetracycline-inducible manner (PMID: 19864255); treated with tetracycline in order to induce expression of hSuv3-G207V
processed data file: LstrandContribution.csv
G207V_B_ACAGTG_L001


title: BPA-replicate 3 [BRSEQ12]

description: Sample 7 (BRSEQ12)

value: 50 mg BPA/kg diet during gestation and lactation

value: brain; hippocampus


title: untreated_293HEK_C

description:
untreated Flp-In T-REx-293 cells
processed data file: LstrandContribution.csv
293NGEM_C_TTAGGC_L007


title: G207V_C

description:
transgenic 293 cells (293-G207V) which express catalytically inactive form of hSuv3 in the tetracycline-inducible manner (PMID: 19864255); treated with tetracycline in order to induce expression of hSuv3-G207V
processed data file: LstrandContribution.csv
G207V_C_GCCAAT_L003


title: PNPase_rescued_B

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase and concomitantly express siRNA-insensitive form of PNPase; treated with tetracycline in order to induce expression of exogenous form of PNPase
processed data file: LstrandContribution.csv
448siPN1tet_B_AGTTCC_L001


title: PNPase_silenced_C

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase (also known as PNPT1); untretaed with tetracycline
processed data file: LstrandContribution.csv
448siPN1_C_CTTGTA_L004


title: PNPase_rescued_A

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase and concomitantly express siRNA-insensitive form of PNPase; treated with tetracycline in order to induce expression of exogenous form of PNPase
processed data file: LstrandContribution.csv
448siPN1tet_A_AGTCAA_L004


title: untreated_293PN1res_C

description:
transgenic 293 cells (293PN1res) which express in the tet-inducible manner siRNA-insensitive form of PNPase-FLAG (PMID: 23221631); untreated cells
processed data file: LstrandContribution.csv
448_C_GATCAG_L002

source_name: transgenic Flp-In T-REx-293_untreated


title: untreated_293PN1res_B

description:
transgenic 293 cells (293PN1res) which express in the tet-inducible manner siRNA-insensitive form of PNPase-FLAG (PMID: 23221631); untreated cells
processed data file: LstrandContribution.csv
448_B_ACTTGA_L002


title: PNPase_silenced_A

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase (also known as PNPT1); untretaed with tetracycline
processed data file: LstrandContribution.csv
448siPN1_A_TAGCTT_L001


title: PNPase_silenced_B

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase (also known as PNPT1); untretaed with tetracycline
processed data file: LstrandContribution.csv
448siPN1_B_GGCTAC_L004


title: G207V_small_B

description:
transgenic 293 cells (293-G207V) which express catalytically inactive form of hSuv3 in the tetracycline-inducible manner (PMID: 19864255); treated with tetracycline in order to induce expression of hSuv3-G207V
G207V_B_small_CGTACG_L003

source_name: transgenic Flp-In T-REx-293_G207V_small

value: small (from ~20 to ~200 nucleotides)


title: PNPase_rescued_C

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase and concomitantly express siRNA-insensitive form of PNPase; treated with tetracycline in order to induce expression of exogenous form of PNPase
processed data file: LstrandContribution.csv
448siPN1tet_C_ATGTCA_L004


title: G207V_small_C

description:
transgenic 293 cells (293-G207V) which express catalytically inactive form of hSuv3 in the tetracycline-inducible manner (PMID: 19864255); treated with tetracycline in order to induce expression of hSuv3-G207V
G207V_C_small_GAGTGG_L004


title: G207V_small_A

description:
transgenic 293 cells (293-G207V) which express catalytically inactive form of hSuv3 in the tetracycline-inducible manner (PMID: 19864255); treated with tetracycline in order to induce expression of hSuv3-G207V
G207V_A_small_GTTTCG_L001


title: PNPase_rescued_small_A

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase and concomitantly express siRNA-insensitive form of PNPase; treated with tetracycline in order to induce expression of exogenous form of PNPase
448siPN1tet_A_small_TAGCTT_L002


title: PNPase_rescued_small_B

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase and concomitantly express siRNA-insensitive form of PNPase; treated with tetracycline in order to induce expression of exogenous form of PNPase
448siPN1tet_B_small_CCGTCC_L003


title: untreated_293HEK_A

description:
untreated Flp-In T-REx-293 cells
processed data file: LstrandContribution.csv
293NGEM_A_ATCACG_L007


title: PNPase_silenced_small_C

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase (also known as PNPT1); untretaed with tetracycline
448siPN1_C_small_GATCAG_L001


title: PNPase_silenced_small_B

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase (also known as PNPT1); untretaed with tetracycline
448siPN1_B_small_ACTTGA_L001


title: 8TR5

city: San Michele all'Adige

first: Carmen

last: Leida

address: E. Mach, 1

country: Italy

institute: Fondazione E. Mach

description: in field treated cluster

data_processing:
Sequenced reads were trimmed for adaptor sequence, and they showed high coverage and quality.
The resulting pre-processed reads were aligned to the reference transcriptome of Vitis vinifera (V2 grapevine annotation - http://genomes.cribi.unipd.it/grape/) using the bowtie2 aligner v2.2.3
Genome_build: Vitis vinifera (V2 grapevine annotation - http://genomes.cribi.unipd.it/grape/)
Supplementary_files_format_and_content: tab-delimited text files include summarized read counts values for each Sample. isoforms_attr_table.txt contains tcons corresponding to gene_id and gene_name

organism: Vitis vinifera

source_name: fruit cells_8_treated

growth_protocol: 8y plant of 'Pinot Noir' were grown in Pressano (TN) following standard agricoltural procedure. 1-MCP was applied on the 6th,7th,8th WAA at 5ppm injected in a wrapped bag for 24h and mock was used as reference. Clusters were sampled after 24h.

extract_protocol:
RNA was extracted usign Reith et al., 2014 method for Next Generation RNA sequencing from grapevine berry tissues.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fruit

tag: cultivar

value: Pinot Noir

tag: weeks after anthesis (waa)

value: 8 years


title: 7TR4

description: in field treated cluster

source_name: fruit cells_7_treated

tag: tissue


title: 7TR12

description: in field treated cluster


title: untreated_293PN1res_small_B

description:
transgenic 293 cells (293PN1res) which express in the tet-inducible manner siRNA-insensitive form of PNPase-FLAG (PMID: 23221631); untreated cells
448_B_small_ACAGTG_L004


title: untreated_293PN1res_small_A

description:
transgenic 293 cells (293PN1res) which express in the tet-inducible manner siRNA-insensitive form of PNPase-FLAG (PMID: 23221631); untreated cells
448_A_small_GGTAGC_L003


title: 8TR4

description: in field treated cluster


title: untreated_293PN1res_small_C

description:
transgenic 293 cells (293PN1res) which express in the tet-inducible manner siRNA-insensitive form of PNPase-FLAG (PMID: 23221631); untreated cells
448_C_small_GCCAAT_L004


title: 7TR3

description: in field treated cluster


title: 8TR3

description: in field treated cluster


title: 8TR1

description: in field treated cluster


title: 7TR1

description: in field treated cluster


title: 8TR2

description: in field treated cluster


title: 7TR2

description: in field treated cluster


title: 6TR3

description: in field treated cluster

source_name: fruit cells_6_treated


title: 8CR5

description: in field treated cluster

source_name: fruit cells_8_control


title: 8CR2

description: in field treated cluster


title: 6TR2

description: in field treated cluster


title: 8CR4

description: in field treated cluster


title: PNPase_rescued_small_C

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase and concomitantly express siRNA-insensitive form of PNPase; treated with tetracycline in order to induce expression of exogenous form of PNPase
448siPN1tet_C_small_GAGTGG_L002


title: 6TR1

description: in field treated cluster


title: 8CR1

description: in field treated cluster


title: 8CR3

description: in field treated cluster


title: 7CR12

description: in field treated cluster

source_name: fruit cells_7_control


title: 7CR4

description: in field treated cluster


title: 7CR3

description: in field treated cluster


title: PNPase_silenced_small_A

description:
transgenic 293 cells (293PN1res) which were transfected with siRNA specific for PNPase (also known as PNPT1); untretaed with tetracycline
448siPN1_A_small_CAGATC_L004


title: CL3_L1

city: Bristol

first: Lulu

state: State...

address: Academic Renal Unit,Dorothy Hodgkin Building,Whitson Street

department: School of Clinical Sciences

country: United Kingdom

institute: University of Bristol

description: The same library was run on 4 different lanes generating 4 pairs of fastq files per sample (paired-end sequencing)

data_processing:
The raw data was processed using Illumina software, RTA 1.17.21.3 with default filter and quality settings.
The reads were demultiplexed with CASAVA 1.8.2.
Read alignment is performed using Tophat. We use HTSeq to generate read counts, using the ENSEMBL GRCh37  annotations for reference.
Genome_build: GRCh37
Supplementary_files_format_and_content: csv file with abundance measurements. There are four counts per gene in each file because the same library was run on four different flowcell lanes.

source_name: Podocytes derived from human kidneys_1μM levamisole

growth_protocol: Conditionally immortalized human podocytes were established from three healthy kidney transplant donors. Cells were grown to 70%-80% confluence at 33 Celsius degree in 5% CO2 before thermo-switching to 37 Celsius degree in 5% CO2 and allowed to differentiate for 10 days.

extract_protocol:
Total RNA was extracted from levamisole-treated podocytes using the TRIzol method. RNA samples were then subjected to DNase treatment (Ambion TURBO DNase, Life Technologies) and purification (RNeasy Mini Kit, QIAGEN) according to the manufacturer’s instructions.
The cDNA library preparation and the sequencing were performed following manufacturer’s instructions at the Bristol Genomics Facility, University of Bristol. Briefly, approximately 1μg of purified total RNA was prepared for sequencing using the Illumina TruSeq mRNA Seq v2 kit.  Sequencing of 100bp paired-end reads was performed with the Illumina HiSeq 2500 instrument.

treatment_protocol: Differentiated cells were then treated with 1μM or 10μM levamisole (Sigma–Aldrich) for 24 hours, then subsequently used for RNA extraction and sequencing.

value: Podocytes

value: kidney


title: CL2_L1


title: CL2_L10

source_name: Podocytes derived from human kidneys_10μM levamisole


title: CL1_L1


title: CL1_L10


title: GRSF1_silenced_small_B

description:
Flp-In T-REx-293 cells transfected with siRNA specific for GRSF1
GRSF1small_B_L001

source_name: Flp-In T-REx-293_GRSF1_silenced_small

value: 293 - ATCC  number CRL-1573

value: embrionic kidney (PubMed ID:886304)


title: GRSF1_silenced_small_C

description:
Flp-In T-REx-293 cells transfected with siRNA specific for GRSF1
GRSF1small_C_L001

value: Flp-In T-REx-293 (Invitrogen)


title: 6CR2

description: in field treated cluster

source_name: fruit cells_6_control


title: 7CR1

description: in field treated cluster


title: 6CR3

description: in field treated cluster


title: GRSF1_silenced_small_A

description:
Flp-In T-REx-293 cells transfected with siRNA specific for GRSF1
GRSF1small_A_L001


title: non-targeting_293HEK_small_C

description:
Flp-In T-REx-293 cells transfected with control, non-targeting siRNA (Invitrogen, Neg High GC Stealth)
NegHsmall_C_L001

source_name: Flp-In T-REx-293_non-targeting_small

value: control


title: 6CR1

description: in field treated cluster


title: p53, Smarca4L/+ [LU8370]

city: Houston

first: Jennifer

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
Sequenced reads were mapped to mm10 genome using the Spliced Transcripts Alignment to a Reference (STAR) software tool
The HTSeq software tool was used to calculte the read count for each transcript
The Limma R package was used for assessment of transcript abundance measurements and doing differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: excel file includes transcript abundance measurements (read count) for each sample

source_name: GEMM tumor from PS cohort

extract_protocol:
RNA was extracted with Trizol reagent
RNA libraries were prepared for sequencing using the standard Illumina protocols

value: p53, Smarca4L/+


title: non-targeting_293HEK_small_B

description:
Flp-In T-REx-293 cells transfected with control, non-targeting siRNA (Invitrogen, Neg High GC Stealth)
NegHsmall_B_L001


title: Kras, p53 [LU8322]

source_name: GEMM tumor from KP cohort

value: Kras, p53


title: Kras, p53 [LU8315]


title: Kras, p53, Smarca4L/L [LU8314]

source_name: GEMM tumor from KPS cohort

value: Kras, p53, Smarca4L/L


title: Kras [LU8260]

value: Kras


title: Kras, p53, Smarca4L/L [LU8316]


title: untreated_293HEK_small_C

description:
untreated Flp-In T-REx-293 cells
293NGEMsmall_C_L001

source_name: Flp-In T-REx-293_untreated_small


title: Kras, p53, Smarca4L/+ [LU8252-2]

value: Kras, p53, Smarca4L/+


title: Kras, Smarca4L/+ [LU8165-2]

source_name: GEMM tumor from KS cohort

value: Kras, Smarca4L/+


title: Kras, Smarca4L/+ [LU8107]


title: non-targeting_293HEK_small_A

description:
Flp-In T-REx-293 cells transfected with control, non-targeting siRNA (Invitrogen, Neg High GC Stealth)
NegHsmall_A_L001


title: Kras, p53 [LU8185]


title: untreated_293HEK_small_A

description:
untreated Flp-In T-REx-293 cells
293NGEMsmall_A_L001


title: untreated_293HEK_small_B

description:
untreated Flp-In T-REx-293 cells
293NGEMsmall_B_L001


title: Kras, Smarca4L/L [LU8105-a]

value: Kras, Smarca4L/L


title: 7CR2

description: in field treated cluster


title: GDPOL1ctf4KO-5-rep2

status: Public on Jun 16 2018

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

description:
Okazaki Fragments
GAL1-DHFR-POL1-13xmyc, ctf4Δ

data_processing:
Bowtie2 (version 2.2.3) was used to align paired-end fastq files to the S. cerevisiae reference genome.
Sam files were converted to bam files using samtools, then reads were sorted.
Bam files were converted to bed files using bedtools paired end function and PCR duplicates were removed.
Printed columns for the chromosome, position of the start and stop of the read, and the strand information into output bed files.
Genome_build: Yeast S288C, build R64-1-1
Supplementary_files_format_and_content: bed files: chromosome, start and end positions of mapped reads, strand information.
Supplementary_files_format_and_content: OEM_position_timing.xls: Origin location (chromosome and base pair), origin efficiency metric for all replicates and conditions: calculated using methodology from (McGuffee et al. (2013) Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. Mol Cell 50, 123-135), and timing of origin firing during S phase (early or late).

organism: Saccharomyces cerevisiae

growth_protocol: 30°C, grow overnight in YEP + 3% raffinose + 0.5% galactose until log phase then switched into various galactose concentrations + 3% raffinose for four hours.

extract_protocol:
Okazaki fragments were enriched and purified as described previously (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).
Libraries were generated as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).

treatment_protocol: Add rapamycin for one hour.

tag: strain/background

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB

value: GAL1-DHFR-POL1-13xmyc, ctf4<delta>


title: GDPOL1ctf4KO-14-rep2

tag: genotype/variation


title: GDPOL1ctf4KO-5-rep1


title: GDPOL1ctf4KO-23-rep1


title: GDPOL1ctf4KO-23-rep2


title: Kras, Smarca4L/L [LU8245]


title: GDPOL1ctf4KO-41-rep1


title: GDPOL1ctf4KO-41-rep2


title: GDPOL1ctf4KO-500-rep2


title: GDPOL1ctf4KO-50-rep1


title: GDPOL1ctf4KO-50-rep2


title: GDPOL1-23-rep2

description: Okazaki Fragments


title: GDPOL1-500-rep2

description: Okazaki Fragments


title: GDPOL1ctf4KO-500-rep1


title: GDPOL1-32-rep1

description: Okazaki Fragments


title: Saureus_RsaE_HybridTrapSeq

city: Jouy-en-Josas

first: Tatiana

last: Rochat

address: Domaine de Vilvert

institute: INRA

description: RNA enriched in Hybrid-Trap-seq data with RsaE sRNA as bait.

data_processing:
FastQC (v0.10.1) quality control.
Mapping performed on Refseq CP000253.1 by Bowtie software with parameters -p 12 -S -m 1 -q .
The number of reads mapping to each predicted CDS retrieved from Genbank file CP000253.1 and 44 bona fide sRNAs (from Liu F. et al 2018, doi: 10.3389/fmicb.2018.00228) was calculated by HTSeq-count (Anders, Pyl et al. 2015).
Differential expression analysis (normalisation and fold change calculation) was performed with DESeq software. Fold changes were computed from normalized read number of condition A (defined by the three control sRNAs datasets) to normalized read number of condition B (defined by the RsaE dataset). Genes were considered as putative RsaE targets if with a fold change >= 10.
Genome_build: CP000253.1
Supplementary_files_format_and_content: The processed data file (putative_RsaE-targets_revised_20180425.csv) compiles read counts for the 4 RNA-seq samples and DEseq output for RsaE sample versus control samples.

organism: Staphylococcus aureus

extract_protocol:
Hybrid-trap-seq experiments were run in parallel with 4 sRNAs used as bait (RsaE compared to three control sRNAs ie RNAIII, RsaA and RsaH). The background noise due to nonspecific RNA binding was filtered out from RsaE dataset by a differential analysis using the three other sRNA datasets as control. Synthetic RNAs were generated with the T7 MEGAshortscript kit (Ambion) according to manufacturer’s instructions and using as DNA matrix sRNA gene PCR-amplified. Synthetic RNAs were 3’-end biotinylated as previously described (Jestin et al., 1997, DOI:10.1093/emboj/16.10.2945) using biotinamidocaproyl hydrazide (Sigma-Aldrich, B3770). After the biotinylation reaction, full length RNAs were purified on 5 % urea PAGE. Running Hybrid-trap-seq requires a pool of total RNA extracts to be used as prey. Total RNA samples were extracted in 16 different biological conditions (previously described in GEO and corresponding to submission GSE104971). Twenty µg of each of the 16 total RNA extracts were pooled to obtain the combined RNA extracts sample used during the procedure. For each Hybrid-trap-seq experiment, MasterBeads pre-coated with streptavidin (Ademtech, Pessac-France) were equilibrated in binding buffer (20 mM Tris-HCl, 0.5 M NaCl pH 8) and incubated 10 min at 20°C with 100 pmoles of biotinylated sRNA. Unbound sRNAs were removed by magnetic separation, and then sRNA-bound streptavidin beads were washed twice with binding buffer. 50 µg of pooled total RNA sample were mixed with the sRNA-bound beads. After 15 min at 45°C, followed by 15 min at room temperature, the unbound RNAs were removed by magnetic separation. The RNA-bound beads were washed twice with wash buffer (7 mM Tris-HCl pH 8, NaCl 0.17 M) before elution in RNase-free water.
Strand-specific RNA-seq libraries were generated with the TruSeq RNA-Seq Library Preparation Kit (Illumina), according to the manufacturer's instructions.

tag: strain


title: Saureus_RsaA_HybridTrapSeq

description: RNA enriched in Hybrid-Trap-seq data with RsaA sRNA as bait.


title: Saureus_RsaH_HybridTrapSeq

description: RNA enriched in Hybrid-Trap-seq data with RsaH sRNA as bait.


title: dRT5_2

description:
processed data file: Supplemental_table_2.txt
test condition replicat 2 (transcriptome comparison: HG003 ΔrsaE pRMC2RsaE induced relative to not-induced)

data_processing:
FastQC (v0.10.1) quality control.
Mapping performed on Refseq CP000253.1 with bowtie2 (v2.1.0) using default values.
The raw counts of the number of uniquely mapped reads to each CDS described in Refseq CP000253.1 were done with featureCounts (1.5.0-p1, with the options of both paired-end reads and stranded library) [Liao, 2014].
Differential expression analyzes (normalisation and statistical tests) were performed using the SARTools with DESeq2 software (Varet, Brillet-Gueguen et al. 2016) using two conditions (wild-type relative to rsaE mutant, and 5 min induced relative to non-induced RsaE expression). Genes with a BH-adjusted p-value < 0.05 and a fold change > 1.33 were considered as differentially expressed.
Genome_build: CP000253.1
Supplementary_files_format_and_content: Supplemental_table_1: Full results of the DEseq2 analysis "Wild-type relative to rsaE mutant" for all CDS. Column legends : Id=Accession number retrieved from Refseq CP000253.1 ; StrainReplicat= raw counts for 'StrainReplicat' sample ('strain' and 'replicat' take the possible values 'WT' for wild-type, 'dR' for rsaE mutant, '1' and '3' resp.); norm.StrainReplicat = Rounded normalized counts for 'StrainReplicat' sample; baseMean=Base mean over all samples ; FoldChange=Fold change of expression, calculated as 2log2(FC) ; log2FoldChange=Log2(FC) as estimated by the GLM model. pvalue=Raw p-value from the statistical test ; dispGeneEst=dispersion parameter estimated from feature counts ; dispFit=dispersion parameter estimated from the model ; dispMAP=dispersion parameter estimated from the Maximum A Posteriori model ; dispersion=final dispersion parameter used to perform the test ; betaConv=convergence of the coefficients of the model (TRUE or FALSE) ; maxCooks=maximum Cook's distance of the feature.
Supplementary_files_format_and_content: Supplemental_table_2: Full results of the DEseq2 analysis "Induced relative to non-induced RsaE expression" for all CDS. Column legends : Id=Accession number retrieved from Refseq CP000253.1 ; InductionReplicat= raw counts for 'InductionReplicat' sample ('Induction' and 'Replicat' take the possible values 'dRT0' for non-induced, 'dRT5' for induced, and '1', '2' and '3' are for triplicates, resp.); norm.InductionReplicat = Rounded normalized counts for 'InductionReplicat' sample; baseMean=Base mean over all samples ; FoldChange=Fold change of expression, calculated as 2log2(FC) ; log2FoldChange=Log2(FC) as estimated by the GLM model. pvalue=Raw p-value from the statistical test ; dispGeneEst=dispersion parameter estimated from feature counts ; dispFit=dispersion parameter estimated from the model ; dispMAP=dispersion parameter estimated from the Maximum A Posteriori model ; dispersion=final dispersion parameter used to perform the test ; betaConv=convergence of the coefficients of the model (TRUE or FALSE) ; maxCooks=maximum Cook's distance of the feature.

source_name: Staphylococcus aureus HG003

growth_protocol: Overnight cultures were diluted 1000 times and incubated in BHI at 37°C. For HG003 and HG003 ΔrsaE, strains were harvested at OD600 6. For HG003 ΔrsaE pRMC2RsaE, at OD600 0.5, the culture was split in two halves and anhydrotetracycline (aTc, 1 mM) was added to one of them. Induced and non-induced cultures were harvested 5 min after aTc addition.

extract_protocol:
Total RNAs were extracted as described (Bohn, C., Rigoulay, C. and Bouloc, P. 2007. BMC Microbiol, 7, 10). Samples were treated with TURBO DNase (Ambion) according to manufacturer’s instructions. Ten µg of RNA were depleted for ribosomal RNA with MICROBExpress (Ambion).
Strand-specific RNA-seq libraries were generated with the TruSeq SBS Kit v3 (Illumina), according to the manufacturer's instructions.

value: {delta}rsaE pRMC2-rsaE

tag: induction

value: induced 5 min


title: dRT5_1

description:
processed data file: Supplemental_table_2.txt
test condition replicat 1 (transcriptome comparison: HG003 ΔrsaE pRMC2RsaE induced relative to not-induced)


title: WT-5-rep1

description: Okazaki Fragments

value: WT


title: WT-5-rep2

description: Okazaki Fragments


title: dRT5_3

description:
processed data file: Supplemental_table_2.txt
test condition replicat 3 (transcriptome comparison: HG003 ΔrsaE pRMC2RsaE induced relative to not-induced)


title: dRT0_2

description:
processed data file: Supplemental_table_2.txt
reference condition replicat 2 (transcriptome comparison: HG003 ΔrsaE pRMC2RsaE induced relative to not-induced)

value: not-induced


title: GDPOL1ctf4KO-32-rep1


title: WT-50-rep2

description: Okazaki Fragments


title: Saureus_RNA3_HybridTrapSeq

description: RNA enriched in Hybrid-Trap-seq data with RNAIII sRNA as bait.


title: dRT0_1

description:
processed data file: Supplemental_table_2.txt
reference condition replicat 1 (transcriptome comparison: HG003 ΔrsaE pRMC2RsaE induced relative to not-induced)


title: dR1

description:
processed data file: Supplemental_table_1.txt
test condition replicat 1 (transcriptome comparison: ΔrsaE relative to wild-type)

data_processing:
FastQC (v0.10.1) quality control.
Mapping performed on Refseq CP000253.1 with bowtie2 (v2.1.0) using default values.
The raw counts of the number of uniquely mapped reads to each CDS described in Refseq CP000253.1 were done with featureCounts (1.5.0-p1, with the options of both paired-end reads and stranded library) [Liao, 2014].
Differential expression analyzes (normalisation and statistical tests) were performed using the SARTools with DESeq2 software (Varet, Brillet-Gueguen et al. 2016) using two conditions (rsaE mutant relative to wild-type, and 5 min induced relative to non-induced RsaE expression). Genes with a BH-adjusted p-value < 0.05 and a fold change > 1.33 were considered as differentially expressed.
Genome_build: CP000253.1
Supplementary_files_format_and_content: Supplemental_table_1: Full results of the DEseq2 analysis "rsaE mutant relative to wild-type" for all CDS. Column legends : Id=Accession number retrieved from Refseq CP000253.1 ; StrainReplicat= raw counts for 'StrainReplicat' sample ('strain' and 'replicat' take the possible values 'WT' for wild-type, 'dR' for rsaE mutant, '1' and '3' resp.); norm.StrainReplicat = Rounded normalized counts for 'StrainReplicat' sample; baseMean=Base mean over all samples ; FoldChange=Fold change of expression, calculated as 2log2(FC) ; log2FoldChange=Log2(FC) as estimated by the GLM model. pvalue=Raw p-value from the statistical test ; dispGeneEst=dispersion parameter estimated from feature counts ; dispFit=dispersion parameter estimated from the model ; dispMAP=dispersion parameter estimated from the Maximum A Posteriori model ; dispersion=final dispersion parameter used to perform the test ; betaConv=convergence of the coefficients of the model (TRUE or FALSE) ; maxCooks=maximum Cook's distance of the feature.
Supplementary_files_format_and_content: Supplemental_table_2: Full results of the DEseq2 analysis "Induced relative to non-induced RsaE expression" for all CDS. Column legends : Id=Accession number retrieved from Refseq CP000253.1 ; InductionReplicat= raw counts for 'InductionReplicat' sample ('Induction' and 'Replicat' take the possible values 'dRT0' for non-induced, 'dRT5' for induced, and '1', '2' and '3' are for triplicates, resp.); norm.InductionReplicat = Rounded normalized counts for 'InductionReplicat' sample; baseMean=Base mean over all samples ; FoldChange=Fold change of expression, calculated as 2log2(FC) ; log2FoldChange=Log2(FC) as estimated by the GLM model. pvalue=Raw p-value from the statistical test ; dispGeneEst=dispersion parameter estimated from feature counts ; dispFit=dispersion parameter estimated from the model ; dispMAP=dispersion parameter estimated from the Maximum A Posteriori model ; dispersion=final dispersion parameter used to perform the test ; betaConv=convergence of the coefficients of the model (TRUE or FALSE) ; maxCooks=maximum Cook's distance of the feature.

value: {delta}rsaE


title: GDPOL1-500-rep1

description: Okazaki Fragments


title: WT-500-rep2

description: Okazaki Fragments


title: WT1

description:
processed data file: Supplemental_table_1.txt
reference condition replicat 1 (transcriptome comparison: ΔrsaE relative to wild-type)

value: wild-type


title: dR3

description:
processed data file: Supplemental_table_1.txt
test condition replicat 3 (transcriptome comparison: ΔrsaE relative to wild-type)


title: WT-ypd-rep2

description: Okazaki Fragments

source_name: WT-ypd


title: WT-500-rep1

description: Okazaki Fragments


title: WT-50-rep1

description: Okazaki Fragments


title: dRT0_3

description:
processed data file: Supplemental_table_2.txt
reference condition replicat 3 (transcriptome comparison: HG003 ΔrsaE pRMC2RsaE induced relative to not-induced)


title: RgsD rep-2

city: Daejeon

first: Kwang-Soo

last: Shin

department: Life Science

country: South Korea

institute: Daejeon University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
genome build: Ensemble Aspergillus fumigatus CADRE
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Aspergillus fumigatus

source_name: asexual stage

growth_protocol: Incubate for 1 day in solid medium

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: genotype

value: rgsD deletion mutant

tag: sample

value: mycelium & conidia


title: RgsD rep-1


title: WT-ypd-rep1

description: Okazaki Fragments


title: WT3

description:
processed data file: Supplemental_table_1.txt
reference condition replicat 3 (transcriptome comparison: ΔrsaE relative to wild-type)


title: HT female hippocampus 2

status: Public on Jun 15 2018

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

data_processing:
Pre-processing of raw reads was carried out using Trimmomatic (version 0.35, options: LEADING:3 TRAILING:3 MAXINFO:80:0.4 MINLEN:36)
The trimmed reads were mapped to the Mus musculus genome (GRCm38) using TopHat2 (version 2.1.0, default options).
The gene-level read counts were created from the aligned reads by HTSeq then normalized on library size factors by using DEseq2 package.
Differential gene expression analysis was carried out using DEseq2 and the P-values were adjusted for multiple testing with the Benjamini–Hochberg correction.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using HTSeq and DESeq2.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CHD8 Asn2373LysfsX2 heterozygote mutant

tag: age

value: brain; hippocampus


title: HT female hippocampus 1

tag: strain background


title: HT male hippocampus 3


title: WT rep-2

value: Wild type


title: WT rep-1


title: HT male hippocampus 2


title: Rax1 rep-2

value: rax1 deletion mutant


title: WT female hippocampus 3

source_name: wild type_female_brain

value: wild type


title: WT female hippocampus 1


title: WT female hippocampus 2


title: HT male hippocampus 1


title: WT male hippocampus 3

source_name: wild type_male_brain


title: WT male hippocampus 2


title: TGFb 48h c

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

data_processing:
Raw sequence reads were pseudo aligned to the Homo sapiens transcriptome GRCh38 (Ensembl Build 79) using Kallisto (Version 0.43.0, Bray et al. Nat. Biotechnology 2016) running 100 bootstrap rounds.
Transcript expression were summarized to Ensembl gene expression using the R/Bioconductor tximport library.
Genome_build: Homo_sapiens.GRCh38.rel79
Supplementary_files_format_and_content: *_abundance.tsv: Tab-delimited text files per sample include effective read counts and transcript per million (TPM) values for each transcript.

source_name: SK-MES-1 cell line, TGF-beta, 48h

extract_protocol:
Total RNA was isolated from cultured cells using an RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The quantity of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, MA, USA). The quality of total RNA was assessed with an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, Boeblingen, Germany). Total RNA was considered to be sufficient for further analyses if it had an RNA integrity number (RIN) of at least 8.0.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Low-passage freshly thawed SK-MES-1 cells were kept in culture for two weeks and then seeded on 6-cm dishes (TPP, #93060) at a density of 1,000,000 cells/dish. Two days later, cells were serum-starved for 3 hours and stimulated with 2 ng/ml TGFβ1 (R&D Systems, #240-B-010) or left untreated. Total RNA was extracted at the indicated time points and sequenced using HiSeq 4000 (Illumina).

tag: cell line

tag: cell type

value: Squamous cell lung carcinoma cell line

tag: treatment

value: TGF-beta

tag: time

tag: replicate


title: WT male hippocampus 1


title: TGFb 48h b


title: TGFb 48h a


title: TGFb 24h c

source_name: SK-MES-1 cell line, TGF-beta, 24h


title: TGFb 24h b


title: Rax1 rep-1


title: TGFb 8h a

source_name: SK-MES-1 cell line, TGF-beta, 8h


title: HT female hippocampus 3


title: TGFb 24h a


title: TGFb 0h c

source_name: SK-MES-1 cell line, TGF-beta, 0h


title: TGFb 0h b


title: TGFb 0h a


title: TGFb 8h c


title: Control 48h a

source_name: SK-MES-1 cell line, control, 48h

value: control


title: Control 48h c


title: Control 48h b


title: Control 24h a

source_name: SK-MES-1 cell line, control, 24h


title: Control 24h b


title: Control 8h b

source_name: SK-MES-1 cell line, control, 8h


title: Control 0h b

source_name: SK-MES-1 cell line, control, 0h


title: Control 0h c


title: Control 0h a


title: Control 8h a


title: Control 8h c