title: 2872 WT

status: Public on Mar 21 2019

data_processing:
RNA-Seq was performed using Illumina 4000 High-seq platform
Base-calling software: Illumina Casava 1.8 software
Alignment was conducted using TopHat (version 2.0.13) and Bowtie (version 2.2.1), with default parameter settings, with exception of: "---b2-very-sensitive" for additional search of valid alignments
Expression quantitation was performed with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: htseq raw counts

source_name: Layer6 of cortex

growth_protocol: Single housed

extract_protocol:
Qiagen RNeasy Plus Mini Kit
stranded TruSeq mRNA (poly A selection).

treatment_protocol: No treatment

tag: genotype

value: WT

value: Layer6 of cortex


title: 2772 WT

type: SRA

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue


title: 2333 WT


title: 2338 KO

value: Scn1b KO


title: 2771 WT


title: 2324 KO


title: 2337 KO


title: 2336 KO


title: HT1080_FUS-DDIT3-EGFP_p4

status: Public on Mar 12 2019

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

data_processing:
Alignment was performed using STAR version 2.6 using the ENSEMBL GRCh38 assembly reference genome
Gene expression was quantified using HTseq python framework version 0.9.1
Genome_build: ENSEMBL GRCh38
Supplementary_files_format_and_content: Tab-delimited file containing matrix of unnormalized reads mapped to each transcript as a result from HTseq analysis

organism: Homo sapiens

source_name: Fibrosarcoma cell line

growth_protocol: Culture media was supplemented with 5% or 10% fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin. Stable expression of EGFP constructs were maintained by addition of 500 µg/ml Geneticin.

extract_protocol:
RNA was extracted using Qiagen RNeasy micro kit, including DNase treatment
The library was generated using the Smart-seq2 protocol (Picelli, Faridani et al. 2014) with some modifications.

tag: cell line

tag: transfected gene


title: HT1080_FUS-DDIT3-EGFP_p1


title: HT1080_WT_p3


title: HT1080_WT_p2


title: HT1080_WT_p1


title: HT1080_WT_p4


title: Vehicle-Treated Lineage Depleted Bone Marrow, Replicate 2

status: Public on Feb 22 2019

first: Christopher

middle: Tai-Yi

last: Lee

address: 2406 Stone Road

department: Biostatistics

data_processing:
Illumina RTA2 for basecalling
TrimGalore low-quality bases and adapters
STAR to align reads to the mouse reference genome
Htseq to assemble aligned reads
edgeR to call differentially expressed genes (fold change > 1.5 and false-discovery rate < 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited txt for aligned counts for all samples and genes
Supplementary_files_format_and_content: RDS file for edgeR analysis results on all genes

source_name: DEK-KO Mouse Lineage Depleted Bone Marrow

extract_protocol:
Mouse BM was isolated from the femur of the indicated mouse strain immediately prior to use by flushing either in PBS (for transplantation studies; Lonza; Walkersville, MD, USA) or in Iscove’s Modified Dulbecco’s Medium (IMDM; Lonza) with hepes, L-Glutamine, and 10% fetal bovine serum (FBS; Fisher Scientific; Waltham, MA, USA) for all culture experiments. Lineage depletion of mouse BM was performed using a mouse lineage cell depletion kit following the manufacturer’s protocol (Miltenyi Biotec; Aurburn, CA, USA) using two sequential columns. The All Prep DNA/RNA Mini Kit (Qiagen) was utilized to isolate RNA from cell lysates. RNase-Free DNase (Qiagen) was used to eliminate contaminating genomic DNA.
Strand-specific libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Lineage depleted BM were treated with either exogenous DEK prior to RNA isolation.

tag: strain

value: Dek -/-

value: Bone marrow


title: Vehicle-Treated Lineage Depleted Bone Marrow, Replicate 1


title: NASH-diet-fed mouse (OA-NO2 minipump, Eartag#773)

status: Public on Feb 08 2019

data_processing:
We downloaded the reads files from the Indiana University Sequencing Core’s storage, and concatenated those into a single .fastq.gz file.
Adaptors and low-quality reads were trimmed by Trimmomatic v0.35
The trimmed high-quality reads were mapped to the mouse genome NCBI GRCm38 using HISAT2 v2.1.0
The resulting SAM files were sorted, indexed, and converted to BAM files using Samtools v1.2
The total number of reads that were mapped to gene were quantified using HTSeq-counts v0.6.0 under the union model with NCBI GRCm38 genome annotations.
Genome_build: NCBI GRCm38
Supplementary_files_format_and_content: raw mapped read counts

source_name: Liver

extract_protocol:
Total RNA of 12 liver samples were extracted with Trizol reagent and cleaned up with Qiagen clean-up kit (Cat# 74204).
Libraries were prepared with Roche KAPA mRNA HyperPrep Kit (KK8581) following the manufacturer’s protocol and being paired-end sequenced (2 x 76bp) on Illumina HiSeq 4000 platform. Quality control for the raw sequence reads were analyzed with FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adaptors and low-quality reads were trimmed by Trimmomatic v0.35.

treatment_protocol: C57BL/6J mice were fed standard chow diet (CD) or NASH-diet rich in saturated fat, trans-fat, fructose and cholesterol (40% of calories from fat, Research Diets D17010103) for 24 weeks. All mice were maintained on a 12-hour light/dark cycle and had ad libitum access to food and water. Mice were subjected to subcutaneous implantation of osmotic minipumps for delivery of polyethylenglycol (PEG), PEG-solvated oleic acid (OA),  or PEG-solvated OA-NO2 at an infusion rate of 5 mg/kg/day.

value: Liver

tag: protocol


title: Vehicle-Treated Lineage Depleted Bone Marrow, Replicate 3


title: DEK-Treated Lineage Depleted Bone Marrow, Replicate 1


title: NASH-diet-fed mouse (OA minipump, Eartag#761)


title: NASH-diet-fed mouse (OA minipump, Eartag#754)


title: NASH-diet-fed mouse (OA-NO2 minipump, Eartag#771)


title: NASH-diet-fed mouse (OA-NO2 minipump, Eartag#763)


title: male lung ILC2s_effector_rep2

status: Public on Mar 13 2019

type: RNA

city: Vancouver

first: Laura

last: Mathae

state: British Columbia

address: 675 W.10th Ave

country: Canada

institute: British Columbia Cancer Research Centre

hyb_protocol: cDNA was prepared from total RNA using GeneChip WT pico kit according to the manufacturer's protocol. Fragmented cDNA was labeled and hybridized to Affymetrix GeneChip Mouse Gene 2.0ST Array. Washing and staining were performed by Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were analyzed by Expression Console software by Affymetrix. Normalization was performed using RMA algorithm (by FlexArray 1.6.3).

label: biotin

source_name: Mus musculus male lung ILC2s one day after three consecutive days of intranasal IL-33 treatment

label_protocol: Labeling was performed using GeneChip WT pico kit according to the manufacturer's instructions.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: lung

tag: cell type

value: innate lymphoid cells (ILC2s)

tag: Sex

value: male

tag: treatment


title: male lung ILC2s_effector_rep1


title: male lung ILC2s_naïve_rep2

source_name: Mus musculus naïve male lung ILC2s

value: naïve


title: female lung ILC2s_effector_rep1

source_name: Mus musculus female lung ILC2s one day after three consecutive days of intranasal IL-33 treatment

value: female


title: female lung ILC2s_effector_rep3


title: female lung ILC2s_naïve_rep3

source_name: Mus musculus naïve female lung ILC2s


title: HT1080_FUS-DDIT3-EGFP_p3


title: female lung ILC2s_naïve_rep2


title: male lung ILC2s_naïve_rep3


title: female lung ILC2s_effector_rep2


title: male lung ILC2s_effector_rep3


title: NASH-diet-fed mouse (OA minipump, Eartag#751)


title: female lung ILC2s_naïve_rep1


title: male lung ILC2s_naïve_rep1


title: NASH-diet-fed mouse (PEG minipump, Eartag#750)


title: DEK-Treated Lineage Depleted Bone Marrow, Replicate 3


title: Chow diet-fed mouse (Eartag#735)

value: Chow diet-fed mouse (Eartag#735)


title: NASH-diet-fed mouse (PEG minipump, Eartag#741)


title: Chow diet-fed mouse (Eartag#732)

value: Chow diet-fed mouse (Eartag#732)


title: Chow diet-fed mouse (Eartag#729)

value: Chow diet-fed mouse (Eartag#729)


title: q96_6_0_4: Heterozygous mutant 6-month-old zebrafish brain 4

status: Public on Feb 06 2019

city: Adelaide

first: Nhi

last: Hin

address: North Terrace

country: Australia

institute: University of Adelaide

data_processing:
Trimming done using default parameters on AdapterRemoval 2.2.1
Pseudoalignment to zebrafish reference assembly transcriptome using kallisto version 0.44.0 with default parameters in single-end rf-stranded mode
Transcripts summarised to estimated counts using sleuth R package version 0.29.0 and the sleuth_to_matrix function
Genome_build: GRCz11
Supplementary_files_format_and_content: Estimated counts provided in comma delimited file format

molecule: polyA RNA

organism: Danio rerio

source_name: Whole brain

growth_protocol: Tübingen strain zebrafish were maintained in a recirculated water system. To generate a family of heterozygous Q96K97del allele (i.e. Q96K97del/+ at psen1) and wild type (+/+) sibling fish, we mated a psen1Q96K97del/+ individual with a +/+ individual and raised the progeny from a single spawning event together in one tank.

extract_protocol:
Adult fish were euthanized by sudden immersion in an ice water slurry for at least ~30 seconds before decapitation and removal of the entire brain for immediate RNA or protein extraction. Each zebrafish brain has a mass of approximately 7mg. All fish brains were removed during late morning/noon to minimise any influence of circadian rhythms.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole brain

tag: age

value: 6 months

value: psen1 heterozygous mutant (Q96K97/+)

tag: oxygen condition

value: normoxia


title: q96_6_0_3: Heterozygous mutant 6-month-old zebrafish brain 3


title: q96_6_0_2: Heterozygous mutant 6-month-old zebrafish brain 2


title: q96_6_0_1: Heterozygous mutant 6-month-old zebrafish brain 1


title: wt_6_0_2: Wild type 6-month-old zebrafish brain 2

value: psen1 wild type (+/+)


title: wt_6_0_3: Wild type 6-month-old zebrafish brain 3


title: wt_6_0_1: Wild type 6-month-old zebrafish brain 1


title: NASH-diet-fed mouse (PEG minipump, Eartag#748)


title: Preovulatory_follicle_G6.1M.G

status: Public on Nov 20 2018

city: Beijing

first: Zhiqiang

last: Yan

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

data_processing:
Illumina bcl2fastq version 2.19 were used to the basecalling.
Sequenced reads with 10% low quality bases, adapters and artificial sequences (including UP1, UP2, polyA sequences) introduced during the experimental processes were trimmed by in house scripts.
The trimmed clean reads were aligned to the UCSC human hg19 reference using Tophat2 (v2.1.0) with default settings (Trapnell et al., 2009).
Cufflinks (v2.2.1) with defualt settings was used to quantify transcription levels of annotated genes (Trapnell et al., 2010), and FPKM were calculated
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs

source_name: Granulosa cells from Preovulatory follicle

extract_protocol:
Each oocyte and 10 randomly selected granulosa cells were transferred into lysis buffer using a mouth pipette. The reverse transcription reaction was performed on the whole-cell lysate and terminal deoxynucleotidyl transferase was used to add a poly A tail to the 3′ end of the first-strand cDNAs, and then 20 cycles of PCR were performed to amplify the single-cell cDNA
RNA libraries were prepared according to instructions of Kappa Hyper Prep Kit (Kappa Biosystems).

value: Ovary

tag: developmental stage

value: Preovulatory


title: Preovulatory_follicle_G5.3M.G


title: Preovulatory_follicle_G4.2M.G


title: Preovulatory_follicle_G4.3M.G


title: Preovulatory_follicle_G3.2M.G


title: Preovulatory_follicle_G6.3M.G


title: Preovulatory_follicle_G3.3M.G


title: Preovulatory_follicle_G5.1M.G


title: Preovulatory_follicle_G6.2M.G


title: Preovulatory_follicle_G2.2M.G


title: Preovulatory_follicle_G5.2M.G


title: Preovulatory_follicle_G1.3M.G


title: Preovulatory_follicle_G1.2M.G


title: Preovulatory_follicle_G2.3M.G


title: Preovulatory_follicle_G3.1M.G


title: Preovulatory_follicle_G4.1M.G


title: Antral_follicle_S29G

source_name: Granulosa cells from antral follicle

value: Antral


title: Preovulatory_follicle_G1.1M.G


title: Antral_follicle_S25G


title: wt_6_0_4: Wild type 6-month-old zebrafish brain 4


title: Antral_follicle_C8C2G


title: Antral_follicle_C8G


title: Antral_follicle_S12G


title: Antral_follicle_C6C1G


title: Antral_follicle_C6C2G


title: Preovulatory_follicle_G2.1M.G


title: Antral_follicle_C8G2G


title: Antral_follicle_C4M1G


title: Antral_follicle_C1M1G


title: Antral_follicle_C2CG2G


title: Antral_follicle_C4GC2G


title: Antral_follicle_X21G


title: Antral_follicle_X9G


title: Antral_follicle_C4M2G


title: Antral_follicle_C2CG1G


title: Secondary_follicle_G8G

source_name: Granulosa cells from secondary follicle

value: Secondary


title: Antral_follicle_C1G2G


title: Antral_follicle_X4G


title: Antral_follicle_X4.2G


title: Antral_follicle_C1G1G


title: Secondary_follicle_E1G


title: Antral_follicle_X28G


title: Secondary_follicle_B33G


title: Antral_follicle_X10G


title: Primary_follicle_B7G

source_name: Granulosa cells from primary follicle

value: Primary


title: Antral_follicle_X20G


title: Secondary_follicle_G4G


title: Primary_follicle_B3G


title: Primary_follicle_B27G


title: Primary_follicle_B24G


title: Primary_follicle_B25G


title: Primary_follicle_b23G


title: Primary_follicle_B1G


title: Secondary_follicle_C3G


title: Secondary_follicle_G9G


title: Antral_follicle_X26G


title: Primary_follicle_B11G


title: Primary_follicle_A7G


title: Primary_follicle_X30G


title: Primordial_follicle_B35G

source_name: Granulosa cells from primordial follicle

value: Primordial


title: Primary_follicle_X17G


title: Primary_follicle_A14G


title: Primary_follicle_A11G


title: Primordial_follicle_A9G


title: Primary_follicle_A5G


title: Primordial_follicle_B2G


title: Primordial_follicle_A18G


title: Primordial_follicle_B26G


title: Primordial_follicle_A8G


title: Antral_follicle_S26O

source_name: Oocyte from antral follicle


title: Primordial_follicle_A3G


title: Antral_follicle_S12O


title: Antral_follicle_S25O


title: Antral_follicle_E4O


title: Antral_follicle_C8O


title: Antral_follicle_E1O


title: Antral_follicle_C5O


title: Primary_follicle_B13G


title: Antral_follicle_G3O


title: DEK-Treated Lineage Depleted Bone Marrow, Replicate 2

value: Dek -/-

value: Bone marrow


title: Antral_follicle_C4O


title: Antral_follicle_C1O


title: Antral_follicle_X29O


title: Antral_follicle_X30O


title: Antral_follicle_X27O


title: Primordial_follicle_B32G


title: Antral_follicle_X23O


title: Antral_follicle_X21O


title: Antral_follicle_X22O


title: Antral_follicle_X19O


title: Antral_follicle_X10O


title: Antral_follicle_X18O


title: Antral_follicle_E9O


title: Antral_follicle_E5O


title: Secondary_follicle_G9.2O

source_name: Oocyte from secondary follicle


title: Secondary_follicle_G6O


title: Secondary_follicle_G4O


title: Secondary_follicle_G5O


title: Secondary_follicle_G4.2O


title: Secondary_follicle_G3.1O


title: Secondary_follicle_G2O


title: Secondary_follicle_G2.2O


title: Secondary_follicle_G1O


title: Secondary_follicle_F26O


title: Primary_follicle_S8O

source_name: Oocyte from primary follicle


title: Primary_follicle_B7O


title: Primary_follicle_B6O


title: Primary_follicle_B3O


title: Primary_follicle_B35O


title: Primary_follicle_B2O


title: Antral_follicle_X17O


title: Primary_follicle_B28O


title: Primary_follicle_B33O


title: Primary_follicle_B1O


title: Primary_follicle_B20O


title: Primary_follicle_B16ORO


title: Antral_follicle_X16O


title: Secondary_follicle_G8O


title: Primary_follicle_B18O


title: Secondary_follicle_G6.2O


title: Primary_follicle_B11O


title: Primary_follicle_B10O


title: Primary_follicle_A5O


title: Primary_follicle_B13O


title: Primary_follicle_A18O


title: Primary_follicle_A3O


title: Primary_follicle_A20O


title: Primary_follicle_A2O


title: Primary_follicle_A19O


title: Primary_follicle_A11O


title: Primordial_follicle_F39O

source_name: Oocyte from primordial follicle


title: Primordial_follicle_F38O


title: Primordial_follicle_B5O


title: Primary_follicle_B25O


title: Primordial_follicle_B8O


title: Primordial_follicle_B33ORO


title: Primordial_follicle_B5ORO


title: Primordial_follicle_B32O


title: Primary_follicle_B27O


title: Primordial_follicle_B30O


title: Primordial_follicle_A8O


title: Primordial_follicle_B16O


title: Primordial_follicle_B26O


title: Primordial_follicle_B10ORO


title: Primordial_follicle_B14O


title: Primordial_follicle_A10O


title: C4.12ERaERE_E2.3

status: Public on Aug 30 2018

city: Duarte

first: Karineh

last: Petrossian

state: CA

address: 1500 E. Duarte Road

department: Cancer Biology

institute: Beckman Research Institute at City of Hope

description:
C4.12ERaERE_E2.3
RNA-Seq data, E2 treatment in C4-12 cells, replicate 3

data_processing:
Illumina RTA (1.18.64) was used to create .bcl files, and bcl2fastq v2.18 was used to generate FASTQ files.
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016), with strand was set to "reverse" for table of C4-12 samples and "no" for combined table with MCF7 / C4-12 samples
Genome_build: hg19
Supplementary_files_format_and_content: FPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count).  Log2(FPKM+0.1) values are anti-logged to provide linear values (with low FPKM values appearing as 0)
combined_unstranded_FPKM.txt (Table of Stranded FPKM Normalized Expression Values (both runs))
combined_unstranded_read_counts.txt (Table of Stranded HTSeq Read Counts (both runs))
stranded_FPKM.txt (Table of Stranded FPKM Normalized Expression Values (only C4-12 samples))
stranded_read_counts.txt (Table of Stranded HTSeq Read Counts (only C4-12 samples))

source_name: E2 treatment in C4-12 cells

growth_protocol: MCF7aro was cultured in phenol red MEM1x/10% FBS and C4-12ERaERE in phenol red-free high glucose DMEM/10% charcoal/dextran treated FBS. Both cell lines were supplemented with 1mM sodium pyruvate and 100 U/mL penicillin-streptomycin. C4-12ERaERE also received 1ul/mL of Hygromycin B, and MCF7aro received 50mg/mL G418.

extract_protocol:
RNA was extracted using RNeasy Extraction Kit
C4-12: Kapa stranded mRNA kit  MCF7: Illumina TruSeq unstranded V2 polyA kit
C4-12: stranded mRNA RNA-Seq  MCF7: unstranded RNA-Seq

treatment_protocol: Cells were treated 48h with DMSO or 1nM estrogen before RNA was extracted.

tag: library

value: Stranded polyA library


title: C4.12ERaERE_E2.1

description:
C4.12ERaERE_E2.1
RNA-Seq data, E2 treatment in C4-12 cells, replicate 1


title: Primordial_follicle_A6O


title: Primordial_follicle_A9O


title: Primary_follicle_A17O


title: C4.12ERaERE_control.3

description:
C4.12ERaERE_control.3
RNA-Seq data, Control treatment in C4-12 cells, replicate 3

source_name: DMSO treatment in C4-12 cells

value: DMSO


title: C4.12ERaERE_control.2

description:
C4.12ERaERE_control.2
RNA-Seq data, Control treatment in C4-12 cells, replicate 2


title: C4.12ERaERE_control.1

description:
C4.12ERaERE_control.1
RNA-Seq data, Control treatment in C4-12 cells, replicate 1


title: C4.12ERaERE_E2.2

description:
C4.12ERaERE_E2.2
RNA-Seq data, E2 treatment in C4-12 cells, replicate 2


title: E2Paro_3

description:
E2.plus.Paro.12
RNA-Seq data, E2+Paroxetine treatment in MCF7 cells, replicate 3

data_processing:
We believe Real Time Analysis (RTA) was used for base calling and bcl2fastq v1 was used to generate FASTQ files.
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Hsapiens.UCSC.hg19.knownGene (Bioconductor annotations, downloaded 6/8/2016), with strand was set to "reverse" for table of C4-12 samples and "no" for combined table with MCF7 / C4-12 samples
Genome_build: hg19
Supplementary_files_format_and_content: FPKM normalized expression (using quantified reads and TxDb annotations in R) and read counts (calculated using htseq-count).  Log2(FPKM+0.1) values are anti-logged to provide linear values (with low FPKM values appearing as 0)
combined_unstranded_FPKM.txt (Table of Stranded FPKM Normalized Expression Values (both runs))
combined_unstranded_read_counts.txt (Table of Stranded HTSeq Read Counts (both runs))
stranded_FPKM.txt (Table of Stranded FPKM Normalized Expression Values (only C4-12 samples))
stranded_read_counts.txt (Table of Stranded HTSeq Read Counts (only C4-12 samples))

source_name: E2+Paroxetine treatment in MCF7 cells

value: Unstranded polyA library


title: E2Paro_2

description:
E2.plus.Paro.11
RNA-Seq data, E2+Paroxetine treatment in MCF7 cells, replicate 2


title: Hsf1_ChIP_NHS

status: Public on Jul 26 2018

city: Chicago

first: David

last: Pincus

state: IL

institute: University of Chicago

library_source: genomic

data_processing:
bases called by Illumina software
aligned to sacCer3 by bowtie
processed data files format and content: bigwig files
Genome_build: saccer3

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol: Illumina tru-seq

tag: genotype/variation

value: WT

tag: perturbation

value: control 30C


title: E2Paro_1

description:
E2.plus.Paro.10
RNA-Seq data, E2+Paroxetine treatment in MCF7 cells, replicate 1


title: DMSO_3

description:
DMSO.3
RNA-Seq data, DMSO treatment in MCF7 cells, replicate 3

source_name: DMSO treatment in MCF7 cells


title: E2_2

description:
E2.8
RNA-Seq data, E2 treatment in MCF7 cells, replicate 2

source_name: E2 treatment in MCF7 cells


title: DMSO_2

description:
DMSO.2
RNA-Seq data, DMSO treatment in MCF7 cells, replicate 2


title: E2_1

description:
E2.7
RNA-Seq data, E2 treatment in MCF7 cells, replicate 1


title: E2_3

description:
E2.9
RNA-Seq data, E2 treatment in MCF7 cells, replicate 3


title: Primordial_follicle_A16O


title: Hsf1_ChIP_120min_HS

value: 120 min HS 39C


title: Patient_3_120minutes

status: Public on Jul 19 2018

city: Bethesda

first: Luis

middle: M

last: Franco

state: MD

address: 9000 Rockville Pike

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

data_processing:
bcl conversion was performed with bcl2fastq v. 2.17
Starting with the untrimmed FASTQ files (provided as raw files with this GEO entry), adapter-sequence trimming was performed with Cutadapt v. 1.10 on Python v. 2.7.9. Cutadapt parameters and adapter sequences: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 20
Alignment of the adapter-trimmed reads was performed with Bowtie2 v. 2.2.5 and TopHat v. 2.0.14. TopHat parameters: --no-mixed --mate-inner-dist 0 --mate-std-dev 50 -p 8 --library-type fr-firststrand. The reference genome file we used is a subset of the GRCh38 reference assembly, which excludes haplotype sequences (because Bowtie2 is not haplotype-aware). The transcriptome annotation file we used is a subset of the GENCODE23 annotation file, which excludes haplotype sequences (because Bowtie2 is not haplotype-aware).
Generation of a matrix of aligned-read counts was performed with featureCounts, which is part of the Subread package v. 1.5.1. featureCounts parameters: -p -B -s 2 -T 8 -O -t exon -g gene_name. The transcriptome annotation file we used is a subset of the GENCODE23 annotation file, which excludes haplotype sequences
Generation of abundance measurements normalized by library size was performed with the R package DESeq2 v. 1.16.1, in R v. 3.4.0. Platform: x86_64-pc-linux-gnu (64-bit)
Genome_build: GRCh38
Supplementary_files_format_and_content: RawReadCounts.txt: The values are raw read counts.
Supplementary_files_format_and_content: francohalpert_13MAR2018_NormalizedReadCounts.txt: The values correspond to read counts normalized by library size. The file contains a table with 58,765 rows and 13 columns. The first row is a header row and it is followed by 58,764 rows, each corresponding to one transcript. The first column has the transcript identifiers and it is followed by 12 columns, one for each sample.

source_name: Peripheral blood eosinophils

extract_protocol:
Total RNA was isolated from purified eosinophils by extraction with TRIzol Reagent (Thermo Fisher Scientific, Cat. No. 15596018) followed by column-based purification with the RNA Clean & Concentrator-5 kit (Zymo Research; Cat. No. R1016).
RNA libraries were prepared with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Preparation Kit (Illumina, Cat. No. RS-122-2303).

tag: individual

value: Patient 3

tag: disease state

value: hypereosinophilia of unknown significance

value: Peripheral blood eosinophils

value: single dose of oral prednisone, 1 mg/kg

tag: time

value: 120 minutes


title: Patient_3_60minutes

description: francohalpert_13MAR2018_NormalizedReadCounts.txt

value: 60 minutes


title: Patient_2_120minutes

value: Patient 2


title: Patient_3_30minutes

value: 30 minutes


title: Patient_3_Baseline

value: control

value: Baseline


title: Hsf1_ChIP_5min_HS

value: 5 min HS 39ºC


title: Paroxetine_3

description:
Paroxetine.6
RNA-Seq data, Paroxetine treatment in MCF7 cells, replicate 3

source_name: Paroxetine treatment in MCF7 cells

value: Paroxetine


title: Patient_2_60minutes


title: Paroxetine_1

description:
Paroxetine.4
RNA-Seq data, Paroxetine treatment in MCF7 cells, replicate 1


title: Paroxetine_2

description:
Paroxetine.5
RNA-Seq data, Paroxetine treatment in MCF7 cells, replicate 2


title: Patient_1_30minutes

value: Patient 1


title: Patient_1_60minutes


title: Patient_1_120minutes


title: Patient_2_30minutes


title: Patient_2_Baseline


title: R03_circRNA

status: Public on Jun 07 2018

first: Xiao

last: Chen

state: Beijing

address: Haidian Xiangshan Beigou No.1

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

data_processing:
For circRNA identification, unmapped reads were kept and 20-mers from 5’ and 3’ end of these reads were extracted and aligned independently to reference sequences by Bowtie. Anchor sequences were extended by find_circ such that the complete read aligned and the breakpoints were flanked by GU/AG splice sites. Then the back-spliced reads with at least two supporting reads were annotated as circRNAs.
Genome_build: Amel_4.5
Supplementary_files_format_and_content:Readcount_TPM_circRNA.txt

organism: Apis mellifera

source_name: ovaries

extract_protocol:
Trizol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA, according to the manufacturer’s instructions. CircRNA sequencing libraries were generated using the rRNA-depleted and RNase R digested RNAs by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols
For circRNA library preparation, a total amount of 5 μg RNA per sample was used as input material for RNA sample preparation. Firstly, ribosomal RNAs were depleted by using Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA) to get rRNA-depleted RNAs. rRNA-depleted RNAs were further treated with RNase R (Epicentre, USA) and then were subjected to Trizol extraction. Subsequently, sequencing libraries were generated using the rRNA-depleted and RNase R digested RNAs by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The library preparations were sequenced on an Illumina Hiseq 4000 platform and 150bp paired-end reads were generated. A total of twelve small libraries were constructed using ovaries of virgin queens, normal queens, caged queens and released queens. Reference genome was Amel_4.5.

tag: tissue

value: ovaries

value: egg-laying recovered queen

value: the queen was released after caged for seven days. And on the eighth day, the queen recovered to normal condition and laid eggs. Then, samples were collected.


title: R01_circRNA


title: R02_circRNA


title: DMSO_1

description:
DMSO.1
RNA-Seq data, DMSO treatment in MCF7 cells, replicate 1

tag: cell line

value: DMSO

value: Unstranded polyA library


title: C03_circRNA

value: egg-laying inhibited queen

value: Caged for 7 days


title: C02_circRNA


title: C01_circRNA


title: Q03_circRNA

value: normal egg-laying queen


title: Q02_circRNA


title: Q01_circRNA


title: V03_circRNA

value: virgin queen


title: V02_circRNA


title: V01_circRNA


title: JG_48

status: Public on Jan 24 2018

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description: Chi Sta - RPKM Rep3

data_processing:
The raw sequence data generated was converted into FASTQ files using Illumina CASSAVA 182, which were then imported into CLC Genomics Workbench 751 Low quality base pairs were trimmed from the ends and the sequence reads were mapped to the C japonicus reference genome with RPKM values calculated for genes Log2 transformation and quantile normalization was performed for the RPKM values and a Student’s T-test conducted to compare gene expression between various groups of samples Additional analysis and visualization of the data was performed using ArrayStar
Genome_build: GCA_0000192251
Supplementary_files_format_and_content: Tab-delimited text files includes comparative analysis for glucose vs xylan (exponential) samples, RPKM replicates, and RPKM means

organism: Cellvibrio japonicus

growth_protocol: MOPS defined medium

extract_protocol:
Standard extraction protocols
Sstandard Illumina protocols

treatment_protocol: 95%EtOH:5%Phenol to stop cellular metabolism

value: WT

tag: carbon source

value: chitin

tag: growth phase

value: stationary


title: JG_47

description: Chi Sta - RPKM Rep2


title: JG_43

description: Chi Exp - RPKM Rep1

value: exponential


title: Patient_1_Baseline

value: hypereosinophilia of unknown significance

value: Peripheral blood eosinophils

value: control

value: Baseline


title: JG_45

description: Chi Exp - RPKM Rep3


title: JG_46

description: Chi Sta - RPKM Rep1


title: JG_44

description: Chi Exp - RPKM Rep2


title: ES_Prdm15 Overexpression 3 serum/lif

status: Public on Jul 24 2017

city: Singapore

first: Jingxian

last: Zhang

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore

description: ES_Prdm15 Overexpression 3 serum/lif

data_processing:
The sequenced reads were mapped tomm9 build of the human genome using TopHat version 1.1.4 with the aligner Bowtie 0.12.7 with their default parameters except –m 1 and –segment-mismatches 2.
The mapped reads were further manipulated by removing the reads that mapped to multiple locations (-q 0) using SAMtools
FPKMs were calculated by Cufflink (2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: mESCs cultured in SL

growth_protocol: Serum+Lif

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PRDM15 overexpression

tag: strain

value: mESCs

tag: genotype

value: PRDM15 OE


title: ES_Prdm15 Overexpression 2 serum/lif

description: ES_Prdm15 Overexpression 2 serum/lif


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=96hr_rep1

status: Public on Jan 02 2018

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

description: SAMPLE 25

hyb_protocol: The labeled ss-cDNA samples were hybridized to Arabidopsis Gene 1.1 ST arrays (Affymetrix). The GeneTitan Hybridization Wash, and Stain for Wt Arrays (Affymetrix) was used for the hybridizations according to the protocol of the manufacturer.

scan_protocol: The Arabidopsis Gene 1.1 ST arrays were scanned using the Affymetrix GeneTitan scanner.

data_processing: The data were analyzed with the R statistical programming language (http://cran.r-project.org/) and the bioconductor oligo package. The raw data were normalized using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003; Biostatistics 4: 249-264).

organism: Arabidopsis thaliana

label_protocol: 100 ng total RNA was amplified using the GeneChip WT PLUS Reagent Kit (Affymetrix) generating biotinylated sense-strand DNA targets.

growth_protocol: Plants were grown for 2 weeks at 22C in short day conditions (11 hrs light, 13 hrs dark) on soil-perculite mixture.

extract_protocol: RNA was extracted from ground leaf material using Trizol Reagent (Sigma), which was followed by the RNAeasy mini kit (Qiagen).

treatment_protocol: Plants were shifted to the ambient temperature 28C and RNA was extracted at noon, (t=0), 24 hrs post the shift and 96 hrs post the shift.

value: pad4-1 sumo1-1 amiR-SUM2

value: SUMO mutant

tag: time point

value: t=96 hrs

value: leaf


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=24hr_rep3

description: SAMPLE 24

value: t=24 hrs


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=96hr_rep2

description: SAMPLE 26


title: leaf_pad4-1_siz1-2_t=96hr_rep3

description: SAMPLE 18

value: pad4-1 siz1-2


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=0hr_rep1

description: SAMPLE 19


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=24hr_rep2

description: SAMPLE 23


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=0hr_rep2

description: SAMPLE 20


title: leaf_pad4-1_siz1-2_t=24hr_rep2

description: SAMPLE 14


title: ES_Prdm15 Overexpression 1 serum/lif

description: ES_Prdm15 Overexpression 1 serum/lif


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=24hr_rep1

description: SAMPLE 22


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=96hr_rep3

description: SAMPLE 27


title: leaf_pad4-1_siz1-2_t=96hr_rep2

description: SAMPLE 17


title: leaf_pad4-1_t=96hr_rep2

description: SAMPLE 8


title: leaf_pad4-1_t=24hr_rep3

description: SAMPLE 6


title: leaf_pad4-1_siz1-2_t=0hr_rep1

description: SAMPLE 10


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=0hr_rep3

description: SAMPLE 21


title: leaf_pad4-1_t=0hr_rep2

description: SAMPLE 2


title: leaf_pad4-1_t=24hr_rep1

description: SAMPLE 4


title: leaf_pad4-1_t=0hr_rep3

description: SAMPLE 3


title: leaf_pad4-1_t=24hr_rep2

description: SAMPLE 5


title: leaf_pad4-1_t=96hr_rep1

description: SAMPLE 7


title: ES-Empty vector_serum/Lif 2

description: ES_ETOH 2 serum/lif 2

treatment_protocol: Empty Vector


title: ES-Empty vector_serum/Lif 3

description: ES_ETOH 3 serum/lif 3


title: leaf_pad4-1_siz1-2_t=0hr_rep3

description: SAMPLE 12


title: leaf_pad4-1_t=0hr_rep1

description: SAMPLE 1


title: leaf_pad4-1_siz1-2_t=96hr_rep1

description: SAMPLE 16


title: leaf_pad4-1_siz1-2_t=24hr_rep3

description: SAMPLE 15


title: leaf_pad4-1_siz1-2_t=0hr_rep2

description: SAMPLE 11


title: leaf_pad4-1_t=96hr_rep3

description: SAMPLE 9


title: leaf_pad4-1_siz1-2_t=24hr_rep1

description: SAMPLE 13


title: ES_OHT PRDM15KO 2 2i

data_processing:
The sequenced reads were mapped to mm9 build of the mouse genome using TopHat version 1.1.4 with the aligner Bowtie 0.12.7 with their default parameters except –m 1 and –segment-mismatches 2.
The mapped reads were further manipulated by removing the reads that mapped to multiple locations (-q 0) using SAMtools
FPKMs were calculated by Cufflink (2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: mESCs cultured in 2i+LIF

treatment_protocol: OHT (50nM)

tag: cell type

tag: passages


title: ChIP-Seq Input of PRDM15KO in Serum+lif  mES cells

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet –solexa1.3-quals
Peak calling was done by MACS 2.0.10 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated from the BAM alignment files, narrowpeak files were generated by MACS 2.0.10

extract_protocol:
Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody.
Single read - Illumina

treatment_protocol: OHT (50nM) 4 days before fixing the cell

value: ESCs

tag: chip antibody


title: ES_ETOH 3  2i

treatment_protocol: EtOH


title: ChIP-Seq analysis of PRDM15 in 2i Prdm15KO mES cells replicate 1

value: PRDM15 antibody (in house)


title: ES_OHT PRDM15KO 1 2i


title: ES-Empty vector_serum/Lif 1

description: ES_ETOH 1 serum/lif 1

tag: age


title: ChIP-Seq analysis of PRDM15 in 2i mES cells replicate 1


title: ChIP-Seq Input of PRDM15 in 2i mES cells


title: ChIP-Seq Input of PRDM15KO in 2i mES cells


title: ES_OHT PRDM15KO 3 2i


title: ChIP-Seq analysis of PRDM15 in serum+lif Prdm15KO mES cells replicate 1


title: ES_OHT PRDM15KO 1 Serum/Lif


title: ChIP-Seq analysis of PRDM15 in WT Serum+lif mES cells

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
Single read - Illumina


title: ChIP-Seq Input of PRDM15 in WT Serum+lif mES cells


title: ChIP-Seq analysis of PRDM15 in 2i Prdm15KO mES cells replicate 2


title: Husk rep 3 MPI

status: Public on Jul 03 2017

first: Maike

last: Stam

department: Swammerdam Institute for Life Sciences

description: (rRNA depleted)

data_processing:
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering of RNA-seq reads were done using Trimmomatic (Q20).
RNA-seq reads were aligned to the AGPv4 genome assembly using Tophat.
RNA-seq reads were assembled using Cufflink.
Gene expression level calculation and differential expression analysis was done using Cuffdiff.
Note: The strand polarity of the raw data at SRA is reversed.
Genome_build: AGPv4.32
Supplementary_files_format_and_content: Tab-delimited file containing gene expression level (FPKM) and differential expression data from Cuffdiff.

organism: Zea mays

source_name: Husk

growth_protocol: B73 maize plants were grown till stage V2 (Abendroth et al 2011) or till flowering (ears with emerging silks, before pollination) in greenhouse (16h of light per day, temperature above 22°C)

extract_protocol:
Plant tissues were ground in liquid Nitrogen and total RNA were extracted using TRIzol in combination with Quiagen RNeasy Plant kit.
A total of 500 ng of total RNA was treated with the Ribo-Zero rRNA Removal Kit, Plant Leaf (Epicentre) to specifically remove ribosomal RNAs. RNA-seq libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocol. Quality and quantity was assessed at all steps by capillary electrophoresis (Agilent Bioanalyser and Agilent TapeStation). Illumina Sequencing-by-synthesis libraries were quantified by fluorometry, immobilized and processed onto a flow cell with a cBot (Illumina) followed by sequencing-by-synthesis with TruSeq v3 chemistry on a HiSeq2500

treatment_protocol: V2 Seedlings were dissected to extract the inner stem tissue: the outer leaves, including sheath, and also exposed leaf blades were removed. Soft husk leaves were obtained after longitudinal section of the husk including ear, removal of the ear tissue as well as the lignified most external husk leaves layers.

value: inner layer husk, stage silk emerging 2-5 cm

tag: line


title: Husk rep 2 UvA

description: (rRNA depleted)


title: Husk rep 3 UvA

description: (rRNA depleted)


title: ChIP-Seq analysis of PRDM15 in 2i mES cells replicate 2


title: Husk rep 2 MPI

description: (rRNA depleted)


title: ES_ETOH 1  2i


title: ES_OHT PRDM15KO 2 Serum/Lif


title: ChIP-Seq analysis of PRDM15 in serum+lif Prdm15KO mES cells replicate 2


title: Husk rep 1 UvA

description: (rRNA depleted)


title: ES_ETOH 1 Serum/Lif


title: ES_ETOH 2  2i


title: ES_OHT PRDM15KO 3 Serum/Lif


title: ES_ETOH 2 Serum/Lif


title: ES_ETOH 3 Serum/Lif


title: IST rep 3 UvA

description: (rRNA depleted)

source_name: Seedling

value: inner stem tissue V2 seedling


title: Husk rep 1 MPI

description: (rRNA depleted)


title: IST rep 1 UvA

description: (rRNA depleted)


title: Dnmt3A ChIP-seq KO DMBA Back skin treated

status: Public on Jun 13 2017

city: Barcelona

first: Lorenzo

last: Rinaldi

state: Spain

address: Carrer Reixac Baldiri 10

department: Oncology

country: Spain

institute: IRB

description: Entire Epidermis isolated.

data_processing:
ChIP-seq datasets were aligned to the mouse genome build mm10 using BowTie (version 1.0.1) (Langmead et al. 2009); the parameters used were –k 1, –m 1, and –n 2. UCSC browser tracks (Kent et al. 2002) were created from the mapped bam file after converting it to bedGraph (normalized to 10 million reads) and subsequently bigWig format. Peak calling of Dnmt3A to determine regions of ChIP-seq enrichment over the background was done with the MACS version 1.4.1. For histone marks, MACS version 2 was used with parameters –broad, -q 0.01, and –g mm. ChIP-seq peaks were annotated using the annotatePeaks.pl script of the HOMER suite (version 4.6).
Peaks of Dnmt3A were called using MACS 1.4.1 using the parameters -p 1e-5, -w, -S and -g hs.
For H3k27ac, MACS2 was used with parameters -broad, -q 0.01 -g hs.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: The BED files were obtained from the output of MACS/MACS2.

source_name: Back skin, Dnmt3a KO, DMBA/TPA, Dnmt3A ChIP

extract_protocol:
To isolate pre-cancerous epidermal cells following short DMBA/TPA treatment, back skins were dissected and processed to singlecell suspensions as previously described (Jensen et al. 2010). For ChIP-seq, single-cell suspensions were cross-linked for 10 min at room temperature with 1% formaldehyde (methanol-free; Thermofisher, 28906) and quenched for 5 min to a final concentration of 0.125M glycine. Cells were washed 2x with cold PBS and frozen at -80°C.
Libraries for sequencing were prepared using NEBNext Ultra DNA Library Prep Kit from Illumina (E7370L) following the manufacturer's instructions.

treatment_protocol: The back skin of 8-week-old mice -- at which time hair follicles are in their resting phase (telogen) -- was shaved and treated with the mutagen 7,12-dimethylbenz[a]anthracene (DMBA; 200 µl of 0.25 mg/ml solution in acetone) and the pro-inflammatory and pro-proliferation agent 12-O-tetradecanoyl phorbol-13-acetate (TPA; 200 µl of 0.02 mg/ml solution in acetone) once weekly for 6 weeks. Specifically, DMBA was given on Monday and TPA always on the Friday of the same week. For short DMBA experiments, animals were sacrificed and back skins were processed three days after the sixth TPA application.

tag: genetic background

value: CU Black Six

tag: genotype/variation

value: Dnmt3a knockout

value: 14 weeks

tag: gender

value: Female

value: Back skin

tag: treatment

value: DMBA and TPA

value: Dnmt3a (Santa Cruz H-295)


title: IST rep 2 UvA

description: (rRNA depleted)


title: IST rep 3 MPI

description: (rRNA depleted)


title: IST rep 2 MPI

description: (rRNA depleted)


title: IST rep 1 MPI

description: (rRNA depleted)


title: H3K27ac ChIP-seq WT Belly skin untreated

description: Entire Epidermis isolated.

source_name: Belly skin, WT, untreated, H3K27ac ChIP

value: Wild-Type

value: Belly skin

value: H3K27ac (Merck Millipore. Cat 07-360)


title: Dnmt3A ChIP-seq WT DMBA Back skin treated

description: Entire Epidermis isolated.

source_name: Back skin, WT, DMBA/TPA, Dnmt3A ChIP


title: H3K27ac ChIP-seq WT DMBA Back skin treated

description: Entire Epidermis isolated.

source_name: Back skin, WT, DMBA/TPA, H3K27ac ChIP


title: RNA pol II tNET-seq Rpb1  R749H Rep3

status: Public on May 24 2017

city: Aurora

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

description:
nascent nuclear RNA
Anti-pol II tNET-seq
processed data file: R749H_tNetSeq_merge_negative_bedgraph.tdf, R749H_tNetSeq_merge_positive_bedgraph.tdf

data_processing:
Library strategy: tNET-Seq
Single-end 50 base reads (after removing barcodes) or 125 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome  or sacCer3 yeast genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for t-NET-seq
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: bigwig or TDF format

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H

growth_protocol: Rpb1 WT and mutant cells were grown in DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin, and pen/strep

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
IP's were prepared from DNAseI solublilized nuclear extracts (~1.5X 10E7 cells). RNA was purified by Trizol extraction and processed  using the KAPA RNA-seq kit (#07962169001) to create stand-specific random-primed libraries

treatment_protocol: Amr Rpb1 was induced with doxycycline (2.0 mg/ml)  for 12-16 hr then treated with a-amanitin (2.5 mg/ml) for a further 42 hr before cross-linking and harvesting for ChIP-seq.

tag: growth conditions

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: RNA pol II tNET-seq Rpb1  R749H Rep1

tag: cell line


title: RNA pol II tNET-seq Rpb1  R749H Rep2


title: RNA pol II tNET-seq Rpb1  WT Rep1

description:
nascent nuclear RNA
Anti-pol II tNET-seq
processed data file: WT_tNetSeq_merge_negative.bedgraph.tdf, WT_tNetSeq_merge_positive.bedgraph.tdf

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT


title: RNA pol II tNET-seq Rpb1  WT Rep2


title: RNA pol II tNET-seq Rpb1  WT Rep3


title: 19-9-11 Epi

status: Public on Dec 05 2016

city: West Lafayette

first: Xiaoping

last: Bao

state: Indiana

address: 480 Stadium Mall Drive

department: Chemical Engineering

institute: Purdue University

data_processing:
Casava1.8 software used for basecalling
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2
the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: hPSC-derived Epicardial cells

growth_protocol: hPSC-derived epicardial cells were generated from day 6 cardiac progenitors by treatment of CHIR99021 from day 7-9, and routinely passaged onto gelatin-coated plates with TGFβ inhibitor A83-01 or SB431542 after day 12.

extract_protocol:
RNA of hPSC-derived and primary epicardial cells was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Heart

tag: developmental stage

value: day 48 from hPSC


title: Donor9634

source_name: Primary Epicardial Cells

value: Adult


title: Donor9635


title: H9 Epi


title: Donor9605


title: Donor9633


title: 19-9-7 Epi

value: day 12 from hPSC


title: ES03 Epi


title: oex6977_A

status: Public on Jun 01 2015

city: Pasadena

first: Dianne

last: Newman

address: 1200 E California Blvd, MC 147-75

institute: Caltech

description:
SutA (PA14_69770) overexpression, replicate 1
Strain DKN1626 carrying the SutA (PA14_69770) gene under control of the arabinose-inducible promoter inserted into the att:Tn7 site on the chromosome

data_processing:
Image analysis, base calling, de-multiplexing, and conversion of sequencing to fastq format were carried out by HiSeq Control Software (HCS) version 2.0.12 and Real Time Analysis (RTA) version 1.17.21.3 on the Illumina HiSeq 2500 machine.
Reads were trimmed and filtered based on their quality scores using the Trimmomatic package v 0.30 (Bolger et al, Bioinformatics published online April1 2014). Leading and trailing quality cutoffs were set to 27, and a cutoff of 20 was set for a sliding window of 4 bases. Reads shorter than 35 bp after trimming were discarded.
Mapping trimmed reads to the Pseudomonas aeruginosa genome was carried out using Bowtie version 1.0.0 (Langmead et al., Genome biology 10, R25), with the following arguments: -n 2 --best -S. The .sam files generated by bowtie were converted to .bam files, sorted, and indexed using samtools version 0.1.19 (Li et al., Bioinformatics 25, 2078-2079).
Reads per feature were calculated using the easyRNASeq package version 1.4.2, part of the Bioconductor project for R (Delhomme et al., Bioinformatics 28, 2532-2533). Three different feature sets were used: genes, 100bp regions, and transcription units. See supplementary files for summaries
RPKM for genes, 100 bp regions, and transcription units were calculated by normalizing to reads mapped from each sample and size of each feature. Aggregated ratios and FDR values were calculated using the Degust web interface for the edgeR package (Robinson et al., Bioinformatics 26, 139-140).
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: Raw counts per gene are supplied as individual tab-delimited text files, one per sample. Genomic loci for each feature, aggregated ratios for replicates of each sample type, differential expression significance values, and rpkm values for each sample are supplied as tab-delimited supplementary files.

organism: Pseudomonas aeruginosa

source_name: planktonic cells

growth_protocol: Starter cultures of each of the three strains were grown for 8 hours in LB medium, then diluted 1:1000 into 5 ml minimal medium (14.15 mM KH2PO4, 35.85 mM K2HPO4, 42.8 mM NaCl, 9.3 mM NH4Cl, 1 mM MgSO4, 7.2 μM FeCl2 and trace elements (Glasser et al., 2014)) plus 40 mM sodium pyruvate and 25 mM arabinose. Cultures were grown at 37 degrees C with shaking for 21 hours, reaching an OD of approximately 1.

extract_protocol:
Total RNA was extracted using the RNEasy kit (Qiagen) according to the manufacturer's instructions with minor modifications. Briefly, frozen pellets were resuspeded in 215 ul TE buffer containing 15 mg/ml lysozyme (Sigma) and 1.4 mg/ml proteinase K (Qiagen). Samples were incubated with shaking for 8 minutes at 37 degrees C to disrupt the cell walls.  700 ul buffer RLT and 500 ul 100% ethanol were added and the mixture was applied to the Qiagen column. On-column DNA digestion, washing, and elution were carried out according to instructions. 10 ug total RNA was then further treated with the Turbo DNAse free kit (Ambion) according to instructions. 3.8 ug total RNA was subjected to ribosomal RNA depletion using the Ribo-Zero Magnetic Kit for gram negative bacteria (Epicentre).
Libraries for RNA Seq were constructed from the rRNA-depleted samples using the NEBNext mRNA Library Prep Master Mix Set for Illumina, according to the manufacturer's instructions.

treatment_protocol: 1 ml of culture was pelleted by centrifugation for 2.5 min. at 14000 rpm in a microfuge, the pellets were flash frozen in liquid nitrogen, and stored at -80 degrees C until RNA extraction.

tag: strain

tag: growth phase

value: late stationary

tag: medium

value: minimal medium plus 40mM sodium pyruvate and 25 mM arabinose


title: oex6977_C

description:
SutA (PA14_69770) overexpression, replicate 3
Strain DKN1626 carrying the SutA (PA14_69770) gene under control of the arabinose-inducible promoter inserted into the att:Tn7 site on the chromosome

tag: genotype


title: BJ-2

status: Public on Mar 01 2016

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8.4
Calculating insert size and standard deviation performed using Picard v.1.126
Reads were mapped to hg19 using TopHat v2.0.13 guided by GTF version GRCh37.70 with default parameters and calculated insert size and SD
read counting performed using HT-seq v0.6.0 (--mode=union --stranded=no --minaqual=30 --idattr=gene_name –type=exon)
Normalization and Deferential expression analysis performed using DEseq v3.0
BAM to bedgraph performed using bedtools v2.17.0
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.1.1
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (coverage for mapped reads), count tables (read counts for genomic features) and normalized count tables

source_name: Human forskin fibroblast, BJ (ATCC, CRL-2522)

extract_protocol:
Cells were harvested with Trizol reagent and stored at -80 °C until use. Total RNA was extracted using the Direct-zolTM Miniprep kit (R2052).
The standard Agilent SureSelect Strand-Specific RNA sequencing protocol was followed. Briefly, the polyA fraction was purified using two rounds of oligo dT-magnetic bead purification. The resulting polyA fraction was fragmented and first strand cDNA was done with random primers in the presence of Actinomycin D using standard techniques. The resulting first stand cDNA was purified using AMPure Beads and second strand cDNA and end repair was done using standard techniques.  The blunt ended double stranded cDNA was incubated with exo- E.coli DNA polymerase to add an adenosine to the ends for T/A cloning of the adaptors. PCR amplification was done in the presence of uracil DNA glycosylase to generate strand specificity.  A second round of PCR amplification was done to add unique 6-bp barcodes to each sample and add sequences necessary for flow cell attachment.  The resulting mRNA libraries were quantitated using qPCR following the manufacturer's instructions (Kapa Biosystems, Woburn MA).

treatment_protocol: Seed BJ cells into 6-well plate at 100,000 cells/well. Twenty-four hours post plating, add OSK (OCT4, 10 MOI; SOX2, 5 MOI and KLF4, 5 MOI) viruses with or without GFP or BRD3R viruses into respective wells. Incubate  overnight. Next morning, remove viruses by replacing virus-containing media with fresh fibroblast media. Seventy-two hour post transduction, harvest RNA.

value: BJ

tag: lentiviral transgenes

value: no

tag: passage number

value: passage 5

tag: cell type

value: fibroblasts

tag: harvest time

value: 48 hours post seeding


title: BJ-1

value: passage 8

tag: culture protocols

value: Human Fibroblast cells were cultured in fibroblast medium:DMEM, 10% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin, 0.1 mM MEM NEAA and 4 ng/ml human bFGF.


title: BJ-3

value: 72 hours post seeding


title: H1

source_name: human embryonic stem cells, WiCell

value: passage 40

value: embronic stem cells

value: Human ESCs (H1 and H9, WiCell, Wisconsin) and iPSCs were maintained in E8 medium [27] on MatrigelÂcoated tissue culture plates. E8 medium contained DMEM/F12, 64 mg/L LÂascorbic acid 2Âphosphate sesquimagnesium, 13.6 Âµg /L sodium selenium, 1.7 g/L NaHCO3, 1 g/L sodium chloride, 10 ng/ml FGF2, 20 Âµg/ml insulin, 10 Âµg/ml transferrin and 2 Âµg/L TGFÎ²1

value: 80% confluence


title: wild type - restricted - animal 421

status: Public on Sep 09 2016

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Hybridization to Affymetrix HT MG-430 PM Array Plates was performed at the Microarray Department of the University of Amsterdam, the Netherlands according to Affymetrix protocols.

scan_protocol: According to Affymetrix protocols.

data_processing: Raw data (CEL files) were normalized by robust multichip average (RMA) in the oligo BioConductor package, using a .CDF annotation file provided by Affymetrix using the R open statistical package (http://www.r-project.org/).

source_name: wild type, restricted

label_protocol: Labeling was performed at the Microarray Department of the University of Amsterdam, the Netherlands according to Affymetrix protocols.

growth_protocol: Ercc1Δ/- mice were obtained by crossing Ercc1Δ/+ (in a pure C57BL6J or FVB background) with Ercc1+/- mice (in a pure FVB or C57BL6J background respectively) to yield Ercc1Δ/- with an F1 C57BL6J/FVB hybrid background. Wild-type F1 littermates were used as controls.All animals used in the studies described in this paper were of the same F1 C57BL6J/FVB hybrid background. Typical unfavorable characteristics, like blindness in an FVB background or deafness in a C57BL6J background, do not occur in this hybrid background. Mice were weighed, visually inspected weekly, and scored for gross morphological and motor abnormalities. Experiments were performed in accordance with the Principles of Laboratory Animal Care and with the guidelines approved by the Dutch Ethical Committee in full accordance with European legislation.

extract_protocol: Total RNA was extracted from liver of 11 week old wild type and Ercc1Δ/- mice on AL and DR feeding regimen (n=5). Total RNA was extracted using QIAzol lysis Reagent and miRNAeasy Mini Kits (QIAGEN, Hilden, Germany), following Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNeasy program and stored at -80°C. The concentration of RNA was measured by Nanodrop (Thermo Fisher Scientific) and quality assessment of the RNA using the 2100 Bio-Analyzer (Agilent Technologies, Amstelveen, the Netherlands) following manufacturer’s instructions.

treatment_protocol: All animals were bred and maintained on AIN93G synthetic pellets (Research Diet Services B.V., Wijk bij Duurstede, The Netherlands). The amount of DR was determined in a prior pilot study but as control food intake of the AL-fed mice was continuously monitored. DR was initiated at 7 weeks of age with 10% (2.1 g/day), when animals almost reached the maximum bodyweight preventing disruption of development of young mice. DR was gradually increased weekly with 10%, until 30% DR (1.6 g/day) was reached at 9 weeks of age. Wild type mice ate on average 3.0 g food per day, resulting in 2.1 g/day for 30% DR. Food was given to the animals just before the start of the dark (active) period to avoid alterations in the biological clock.

value: F1 C57BL6J/FVB

tag: genotype/variation

value: wild type

tag: protocol

value: dietary restriction

value: liver


title: wild type - control - animal 403

source_name: wild type, control

value: control diet


title: wild type - restricted - animal 425


title: progeroid - restricted - animal 362

source_name: progeroid, restricted


title: wild type - control - animal 401


title: progeroid - control - animal 321

source_name: progeroid, control


title: wild type - restricted - animal 423


title: progeroid - control - animal 327


title: progeroid - restricted - animal 365


title: wild type - restricted - animal 424


title: wild type - restricted - animal 422


title: wild type - control - animal 405


title: progeroid - restricted - animal 366


title: wild type - control - animal 404


title: progeroid - restricted - animal 368


title: progeroid - control - animal 325


title: progeroid - control - animal 323


title: wild type - control - animal 402


title: oex6977_B

description:
SutA (PA14_69770) overexpression, replicate 2
Strain DKN1626 carrying the SutA (PA14_69770) gene under control of the arabinose-inducible promoter inserted into the att:Tn7 site on the chromosome

value: late stationary

value: minimal medium plus 40mM sodium pyruvate and 25 mM arabinose


title: H9

value: no

value: passage 43


title: d6977_C

description:
SutA (PA14_69770) delete, replicate 3
Strain DKN1625 carrying clean, unmarked deletion of SutA (PA14_69770)

value: delta-sutA


title: WT_C

description:
wild type, replicate 3
Wild type PA14, strain DKN263

value: WT


title: rpoA_empty1

description: rpoA ChIP in ∆sutA strain, replicate 1

data_processing:
Image analysis, base calling, de-multiplexing, and conversion of sequencing to fastq format were carried out by HiSeq Control Software (HCS) versions 2.0.12 and 2.2.38 and Real Time Analysis (RTA) versions 1.17.21.3 and 1.18.61 on the Illumina HiSeq 2500 machine.
Reads were trimmed and filtered based on their quality scores using the Trimmomatic package v 0.30 (Bolger et al, Bioinformatics published online April1 2014). Leading and trailing quality cutoffs were set to 27, and a cutoff of 20 was set for a sliding window of 4 bases. Reads shorter than 35 bp after trimming were discarded.
Mapping trimmed reads to the Pseudomonas aeruginosa genome was carried out using Bowtie version 1.0.0 (Langmead et al., Genome biology 10, R25), with the following arguments: -n 2 --best -S. The .sam files generated by bowtie were converted to .bam files, sorted, and indexed using samtools version 0.1.19 (Li et al., Bioinformatics 25, 2078-2079).
Reads per feature were calculated using the easyRNASeq package version 1.4.2, part of the Bioconductor project for R (Delhomme et al., Bioinformatics 28, 2532-2533). Three different feature sets were used: genes, 100bp regions, and transcription units. See supplementary files for summaries
RPKM for genes, 100 bp regions, and transcription units were calculated by normalizing to reads mapped from each sample and size of each feature. Aggregated ratios and FDR values were calculated using the Degust web interface for the edgeR package (Robinson et al., Bioinformatics 26, 139-140).
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: For each sample, a processed data file containing the counts per 100 bp in .wig format is provided. Additionally, supplementary files are provided that give the genomic loci, aggregated ratios of HASutA vs empty vector control ChIP signal, and rpkm values for each sample, for each gene in the PA14 genome; the aggregated ratios and rpkm values for each sample, for each 100 bp region; and the genomic loci and rpkm values for each transcriptional unit.

growth_protocol: Starter cultures of each of the three strains were grown overnight in LB medium, then diluted 1:1000 into 50 ml minimal medium (14.15 mM KH2PO4, 35.85 mM K2HPO4, 42.8 mM NaCl, 9.3 mM NH4Cl, 1 mM MgSO4, 7.2 μM FeCl2 and trace elements (Widdel et al., 1983)) plus 40 mM sodium pyruvate, 20 mM arabinose, and 100 µg/ml gentamicin. Cultures were grown at 37 degrees C with shaking for 24 hours, reaching an OD of approximately 1.

extract_protocol:
Pellets were lysed by treatment with 1 mg/ml lysozyme and sonicated with a microtip sonicator for 4 minutes, alternating 30 seconds on and 30 seconds off to shear DNA. Immunoprecipitation with an anti-HA antibody pre-conjugated to agarose beads or with an anti-RpoA antibody followed by protein A/G-conjugated agarose beads was carried out as descibed by Gilbert et al (Molecular microbiology 73, 1072-1085). Extracted, RNAse-treated DNA was purified using QIAquick columns and used for library construction.
Libraries for ChIP Seq were constructed from the fragmented genomic DNA samples using the NEBNext ChIP Library Prep Master Mix Set for Illumina, according to the manufacturer's instructions.

treatment_protocol: Cultures were fixed by incubation with 1% formaldehyde for 15 min, then quenched with 125 mM glycine for 10 min, pelleted, and frozen at -80⁰C.

value: delta-sutA carrying pMQ72

value: minimal medium plus 40mM sodium pyruvate, 20mM arabinose and 100 µg/ml gentamicin


title: rpoA_empty2

description: rpoA ChIP in ∆sutA strain, replicate 2


title: WT_B

description:
wild type, replicate 2
Wild type PA14, strain DKN263


title: d6977_B

description:
SutA (PA14_69770) delete, replicate 2
Strain DKN1625 carrying clean, unmarked deletion of SutA (PA14_69770)


title: d6977_A

description:
SutA (PA14_69770) delete, replicate 1
Strain DKN1625 carrying clean, unmarked deletion of SutA (PA14_69770)


title: HA69770_empty3

description: HA ChIP in ∆sutA strain, replicate 3


title: HA69770_empty2

description: HA ChIP in ∆sutA strain, replicate 2


title: HA69770_HA3

description: HA ChIP in HA-SutA expressing strain, replicate 3

value: delta-sutA carrying pMQ72_HASutA


title: rpoA_HA1

description: rpoA ChIP in HA-SutA expressing strain, replicate 1


title: HA69770_empty1

description: HA ChIP in ∆sutA strain, replicate 1


title: 5.0mm Anther, rep3

status: Public on Feb 11 2015

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
All reads from small RNA, PARE or RNA-seq libraries were trimmed to remove adapter sequences using a Perl script. After trimming off adapters, small RNA reads with the length between 18 and 34 were kept; PARE reads that are longer than 21-nt are discarded, and 21-nt PARE reads are chopped to 20-nt by removing the last nucleotide. Small RNA and PARE reads were mapped to the reference genome using bowtie, and RNA-seq reads were mapped using Tophat. We developed three websites and databases (for sRNA, PARE and RNA-seq, respectively) using the Maize AGPv2 genome, to store and analyze all libraries; we used these visualization tools extensively for this analysis. These Web sites are available at http://mpss.udel.edu/maize_sRNA2/ , http://mpss.udel.edu/maize_RNAseq2/ and http://mpss.udel.edu/maize_pare/ .  Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA). Small RNA and RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). PARE libraries were constructed as previously described (Zhai et al., Methods, 2013). All libraries were sequenced on an Illumina Hi-Seq 2000 instrument at the Delaware Biotechnology Institute, Newark, DE.
Genome_build: MAIZE_AGPv2_genome

organism: Zea mays subsp. mays

source_name: anther

growth_protocol: Fertile anthers of the W23 inbred line, mac1-Y211 and msca1 introgressed five times into W23, and ocl4 in the A188 inbred were grown in Stanford, CA under greenhouse conditions.

extract_protocol:
Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA).
Small RNA and RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). PARE libraries were constructed as previously described. All libraries were sequenced on an Illumina Hi-Seq 2000 instrument at the Delaware Biotechnology Institute, Newark, DE.

treatment_protocol: no treatment

value: Wildtype (W23)


title: 4.0mm Anther, rep3


title: Mature Pollen, rep2


title: 5.0mm Anther, rep2


title: 2.0mm Anther, rep3


title: HA69770_HA2

description: HA ChIP in HA-SutA expressing strain, replicate 2


title: rpoA_HA2

description: rpoA ChIP in HA-SutA expressing strain, replicate 2


title: Mature Pollen, rep3


title: progeroid - restricted - animal 369


title: progeroid - control - animal 326


title: 3.0mm Anther, rep2


title: rpoA_empty3

description: rpoA ChIP in ∆sutA strain, replicate 3


title: 3.0mm Anther, rep3


title: WT_A

description:
wild type, replicate 1
Wild type PA14, strain DKN263


title: 1.0mm Anther, rep2


title: 2.5mm Anther, rep3


title: rpoA_HA3

description: rpoA ChIP in HA-SutA expressing strain, replicate 3


title: 4.0mm Anther, rep2


title: 0.2mm Anther, rep2


title: 3.0mm Anther, rep1


title: Mature Pollen, rep1


title: 2.5mm Anther, rep2


title: 0.7mm Anther, rep2


title: 0.7mm Anther, rep1


title: 1.5mm Anther, rep2


title: 2.5mm Anther, rep1


title: 2.0mm Anther, rep2


title: 0.4mm Anther, rep1


title: Unrelated individual Ts5

status: Public on Apr 08 2014

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

description: processed data file: final_unr_QN_file.txt

data_processing:
Basecalling performed with CASAVA version 1.8
Mapping using GEM, default parameters
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: final_mouse_QN_file.txt: text file, chromosome, start, end, gene symbol, rpkm values, rpkm values after quantile normalization, log2 fold change (TsT1/TsN1)
Supplementary_files_format_and_content: final_QN_4rep_file.sorted.txt: text file, chromosome, start, end, gene type, gene symbol, rpkm values, rpkm values after quantile normalization, log2 fold change
Supplementary_files_format_and_content: final_unr_QN_file.txt: text file, chromosome, start, end, ensembl gene ID, gene symbol, rpkm values, rpkm values after quantile normalization, log2 fold change
Supplementary_files_format_and_content: Expression_iPS_cells.txt: text file, chromosome, start, end, strand, ensembl gene ID, gene symbol, rpkm values

extract_protocol:
Illumina mRNA-Seq Sample Preparation kit
Total RNA was collected using the TRIzol® reagent (Life Technologies) following the manufacturer’s instructions.

tag: disease/status

value: Trisomy 21 (T21)

value: Primary fibroblasts


title: Unrelated individual Ts7


title: 0.2mm Anther, rep1


title: 5.0mm Anther, rep1


title: 4.0mm Anther, rep1


title: 0.4mm Anther, rep2


title: Unrelated individual Ts2


title: 2.0mm Anther, rep1


title: Unrelated individual Ts4


title: Unrelated individual N8

value: Euploid


title: 1.5mm Anther, rep1


title: Unrelated individual Ts1


title: Unrelated individual Ts8


title: Unrelated individual Ts6


title: Unrelated individual Ts3


title: Unrelated individual N6


title: Unrelated individual N5


title: Unrelated individual N2


title: Unrelated individual N4


title: Unrelated individual N3


title: Unrelated individual N1


title: T1DS Rep3

description: processed data file: final_QN_4rep_file.sorted.txt

source_name: twin 1_T21_fetal primary fibroblasts

extract_protocol:
Illumina TruSeq RNA Sample Preparation Kit v2
Total RNA was collected using the TRIzol® reagent (Life Technologies) following the manufacturer’s instructions.

value: Trisomy 21

value: Fetal primary fibroblasts


title: 1.0mm Anther, rep1


title: T2N Rep1

source_name: twin 2_euploid_fetal primary fibroblasts


title: T1DS Rep1


title: T2N Rep3


title: T2N Rep2


title: RNASeq_polyA_DauerExit_N2_22hr

status: Public on Mar 01 2014

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute

data_processing:
The RNA-seq data (50bp read length) were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="opposite",selectReadPosition="end"). The library preparation protocol for polyA selected RNAs creates reads that correspond to the reverse complement of the original RNA and therefore we had to count the reads on the opposite strand of the actual gene. To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of reads and multiplied by the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts.
Genome_build: ce6
Supplementary_files_format_and_content: ce_geneExpression_polyA_rawCounts.txt: raw counts and ce_geneExpression_polyA_normalized.txt which contains normalized and log2 transformed values

organism: Caenorhabditis elegans

source_name: Whole-worm

growth_protocol: Continuous: Egg-prepped C. elegans eggs were allowed to hatch overnight, hatched L1s were plated on 2% NGM plates with OP50 for the desired period of time before harvesting ; Dauer-exit: Dauer larvae were grown as described in Hendriks & Gaidatzis et.al, introduction of food to the larvae, by plating them on 2% NGM plates with OP50, corresponds to the 0-hour timepoint.

extract_protocol:
total RNA isolation was performed using Tri-reagent (MRC)
Library preparation was performed using the Truseq stranded mRNA sample preparation kit (Illumina) according to the manufacturer's protocol

treatment_protocol: Worms were washed of the plates and subsequently washed three additional times with M9 before extraction of RNA

tag: time in development

value: 22 hours post-dauer

tag: growth protocol

value: Dauer-exit


title: T2N Rep0


title: RNASeq_polyA_DauerExit_N2_16hr

value: 16 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_21hr

value: 21 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_19hr

value: 19 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_15hr

value: 15 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_17hr

value: 17 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_20hr

value: 20 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_18hr

value: 18 hours post-dauer


title: Unrelated individual N7


title: RNASeq_polyA_DauerExit_N2_14hr

value: 14 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_11hr

value: 11 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_13hr

value: 13 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_9hr

value: 9 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_10hr

value: 10 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_8hr

value: 8 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_7hr

value: 7 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_3hr

value: 3 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_1hr

value: 1 hour post-dauer


title: RNASeq_polyA_DauerExit_N2_2hr

value: 2 hours post-dauer

value: Dauer-exit


title: T1DS Rep2

value: Trisomy 21

value: Fetal primary fibroblasts


title: RNASeq_polyA_DauerExit_N2_4hr

value: 4 hours post-dauer


title: RNASeq_polyA_DauerExit_N2_6hr

value: 6 hours post-dauer


title: T1DS Rep0


title: E16.5 WT BioRep1 Lane007

status: Public on Mar 29 2013

city: OMAHA

first: You

last: Li

state: NE

address: Emile St

department: Department of Genetics, Cell Biology and Anatomy

institute: University of Nebraska Medical Center

description: T3 G3

data_processing:
fastq quality control:fastQC v0.10.1
alignment: TopHat v1.4.1
transcriptome assembly, transcripts quantification and tests for differentially expression: Cufflinks v1.3.0
visualizing the output from Cufflinks: CummeRbund v1.2.0
Genome_build: mm9, NCBI build 37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Palate

extract_protocol:
Palates were removed from fetuses as duplicates at E14.5, E15.5, and E16,5 and stored in RNALater until extraction; and RNA was harvested from tissues using RNeasy Kit (Qiagen, CA) and evaluated the RNA for purity and concentration by NanoDrop (Wilmington, DE). RNA integrity numbers (RIN) were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Libraries were prepared using the Illumina mRNA-Seq Sample Preparation Kit (San Diego, CA) according to the manufacturer’s instructions. Briefly, poly(A) + RNA was recovered from 1 µg of total RNA using two rounds of isolation with oligo-dT-coated Sera-Mag magnetic beads. The recovered poly (A) + RNA was then chemically fragmented. RNA fragments were converted to cDNA using SuperScript II and random primers. The second strands were synthesized using RNaseH and DNA Pol I. The ends of the cDNA were repaired using T4 DNA polymerase, T4 polynucleotide kinase, and Klenow DNA polymerase. A single adenosine was added to the 3’ end using Klenow fragment (3’ to 5’ exo minus). Adaptors were attached to both ends of the cDNA using T4 DNA ligase. RNA fragments were extracted from a 2% low range ultra agarose sizing gel. The fragments were amplified by 15 cycles of PCR using Phusion DNA polymerase. Libraries were validated with Agilent Bioanalyzer (Palo Alto, CA).

value: Palatal shelves

tag: age

value: Embryonic day 16.5

value: TGF-beta3 +/+


title: E16.5 WT BioRep2 Lane007

description: T3 G3

tag: tissue


title: E16.5 WT BioRep2 Lane006

description: T3 G3


title: E16.5 TGFβ3-HT BioRep2 Lane007

description: T3 G2

value: TGF-beta3 +/-


title: RNASeq_polyA_DauerExit_N2_12hr

value: 12 hours post-dauer


title: E16.5 TGFβ3-HT BioRep1 Lane006

description: T3 G2


title: E16.5 TGFβ3-HT BioRep2 Lane006

description: T3 G2


title: E16.5 WT BioRep1 Lane006

description: T3 G3


title: E16.5 TGFβ3-KO BioRep2 Lane006

description: T3 G1

value: TGF-beta3 -/-


title: E16.5 TGFβ3-KO BioRep2 Lane007

description: T3 G1


title: E16.5 TGFβ3-HT BioRep1 Lane007

description: T3 G2


title: polyA RNA sequencing of STL011 Liver Cells; polyA-RNA-seq_STL011LI_r1a

status: Public on Jul 15 2013

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL011 Liver Cells
Library name: polyA-RNA-seq_STL011LI_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15285
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14778
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1067795_UCSD.Adult_Liver.mRNA-Seq.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL011LI_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Liver mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Adult Liver, Donor STL011 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16752
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 179,311,742
PERCENT_READS_MAPPING_TO_UCSC_GENES: 76.73
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.58

**********************************************************************

ANALYSIS FILE NAME: GSM1067795_UCSD.Adult_Liver.mRNA-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL011LI_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Adult Liver, Donor STL011 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16787
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: AL mRNA 01
BROWSER_TRACK_DESCRIPTION: UCSD Adult Liver mRNA-Seq Donor STL011 Library polyA-RNA-seq_STL011LI_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 179,311,742
PERCENT_READS_MAPPING_TO_UCSC_GENES: 76.73
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.58

**********************************************************************

extract_protocol: Library construction protocol: Four µg of total RNA was extracted from frozen cell pellets using the RNeasy Mini Kit (Qiagen, Valencia, CA). PolyA RNA was isolated from total RNA using Dynabeads oligo(dt)25 (Invitrogen). PolyA selected RNA was eluted in 2x Superscript III buffer supplemented with 10mM DTT and was fragmented by incubation at 94°C for 4 minutes. First-strand cDNA was synthesized with the following reaction composition: 0.5 µL random hexamer, 0.5 µL RNase Out, 1 µL DTT (100 mM), 0.5 µL dNTP (25 mM), 0.5 µL SuperScript III (20 µL final). The reaction was incubated at 25°C for 10 min then 50°C for 50 min.  Single-stranded cDNA was isolated by purification with RNAClean XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing second-strand was synthesized with the following reaction: 1.5 µL NEBuffer 2 (NEB), 1 µL dNTP mix (10 mM dATP, dCTP, dGTP, and dUTP), 0.2 µL RNase H, 1 µL DNA Polymerase I (E. coli) (New England Biolabs) (15 µL final). The reaction was incubated at 16°C for 2.5 hours. The dUTP-containing cDNA was isolated by purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing cDNA was then end repaired and a 3’ A base was added. TruSeq adapters (Illumina, San Diego, CA) were ligated to the dUTP-containing cDNA at 16°C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated cDNA was isolated by two rounds of purification with AMPure XP beads. The dUTP-containing strands were digested at 37°C for 30 min with uracil DNA glycosylase (Enzymatics). Adapter-ligated, single-stranded DNA molecules were enriched by 10 cycles of PCR with the following reaction composition: 5 µL TruSeq PCR Primer Cocktail (Illumina), 25 µL TruSeq PCR Master Mix (Illumina) (50 µL final). The thermocycling parameters were: 98°C 30 sec, then 10-15 cycles of 98°C 10 sec, 60°C 30 sec and 72°C 30 sec, ending with one 72°C 5 min step. The reaction products were purified using AMPure XP beads.

tag: sample alias

tag: sample common name

value: Adult Liver

tag: molecule

value: genomic DNA

tag: disease

value: coronary artery disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Liver

value: Autopsy

value: coronary artery disease. No history of hypertension or diabetes.

value: Male

value: Caucasian

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: E16.5 TGFβ3-KO BioRep1 Lane006

description: T3 G1

tag: strain

value: Palatal shelves

value: Embryonic day 16.5

tag: genotype

value: TGF-beta3 -/-


title: RNASeq_polyA_DauerExit_N2_5hr

value: 5 hours post-dauer

value: Dauer-exit


title: E16.5 TGFβ3-KO BioRep1 Lane007

description: T3 G1


title: brain_control_sampleid_mr283

status: Public on Jul 27 2007

city: Cambridge

first: Sabine

last: Bahn

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridised to Affymetrix Human Genome 133A GeneChips for 16 hours at 45oC with constant rotation at 60rpm. Chips were washed and stained according to manufacturer's instructions using the Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Affymetrix HG-U133A GeneChips were scanned with the Agilent GeneArray Scanner

data_processing: The raw data (CEL files) were read into R statistical package and normalised using the robust multi-chip average (RMA) method (Irizarray et al, 'Exploration, normalization and summaries of high density oligonucleotide array probe level data', Biostatistics, 2003).

label: Biotin

source_name: human post-mortem brain tissue, healthy control

label_protocol: Double-stranded cDNA was synthesised from 5 micrograms of total RNA using Superscript II double-stranded cDNA synthesis kit (Invitrogen, USA), purified, then in-vitro transcribed and labelled using BioArray HighYield RNA transcript Labeling Kit (Enzo Life Sciences, USA)

extract_protocol: Total RNA was isolated from human postmortem brain tissue using Trizol (Invitrogen, USA) or Tri reagent (Sigma, UK) total RNA isolation kits according to the manufacturer's instructions.

value: Healthy control

tag: Age (years)

tag: Gender

value: Male

tag: Post mortem interval (hours)

tag: Braak stage

value: Unknown

tag: Cause of death

value: Cardiac


title: brain_Down_syndrome_sampleid_jg1734

source_name: human post-mortem brain tissue, Down syndrome

value: Down syndrome

value: Female

value: VI


title: brain_Down_syndrome_sampleid_jg1737


title: brain_healthy_control_sampleid_jg1744

value: II

value: Aortic aneurysm


title: brain_control_sampleid_mr523


title: brain_control_sampleid_mr284


title: brain_Down_syndrome_sampleid_jg1741


title: brain_healthy_control_sampleid_jg1745

value: Lung cancer


title: brain_Down_syndrome_sampleid_jg1739

value: Bronchopnuemonia


title: brain_control_sampleid_mr275


title: brain_control_sampleid_mr276


title: brain_Down_syndrome_sampleid_jg1740


title: brain_Down_syndrome_sampleid_jg1742


title: brain_control_sampleid_mr951


title: brain_Down_syndrome_sampleid_jg1738


title: HA69770_HA1

description: HA ChIP in HA-SutA expressing strain, replicate 1

value: delta-sutA carrying pMQ72_HASutA

tag: growth phase

value: late statiAonary

tag: medium

value: minimal medium plus 40mM sodium pyruvate, 20mM arabinose and 100 µg/ml gentamicin