title: HalfHourTreatment_1a

description:
02_HalfHourTreatment_1a
Treatment


title: HalfHourControl_1

status: Public on Feb 26 2020

type: SRA

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

country: USA

institute: Medical University of South Carolina

description:
01_HalfHourControl_1
Control

library_source: transcriptomic

data_processing:
Quality check of the Fastq files using FastQC v0.11.5
Sequenced reads (fastq files) were trimmed for adaptor sequence, nucleotides with the phred score below 30 and for overrepresented sequences using cutadapt, version 1.11
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
The analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19).
genome build: Rnor_6.0
processed data files format and content: The processed data files are “.txt” tabular files, contain in as column the identifiers ensembl_gene_id, external_gene_name, description, hsapiens_homolog_ensembl_gene, hsapiens_homolog_perc_id, hgnc_symbol, Human_description, Human_entrez_geneid, ensembl_peptide_ids, ensembl_transcript_ids, with annotation for ENSEMBLE and gene symbols, the original murine gene and its orthologous genes in humans.  In the sequences we have columns with the sample names and the raw counts of the genes mentioned. The last section of the files possess 4 columns: baseMean log2FoldChange, lfcSE ,stat, pvalue, padj. Showing the results from DESeq2 analysis.

molecule: total RNA

organism: Rattus norvegicus albus

source_name: Neonatal rat ventricular myocytes

growth_protocol: All animal procedures were in accordance with the San Diego State University Animal Subjects Committee (UASC) and NIH Animal Welfare Assurance A3728-01. Neonatal rat ventricular myocytes (NRVMs) were harvested from 1-day old Harlan Sprague-Dawley Rats (Rattus norvegicus albinus) and cultured as previously described by Sprenkle et al 1995. Preplating isolated cells to remove fibroblasts yielded >98% NRVMs. Cell count was determined after preplating. Pooled NRVMs were centrifuged and resuspended in 20 ml  DMEM/F-12 (Gibco, Life Technologies, CA, USA) with 10% fetal bovine serum (Irvine Scientific, CA, USA) and quantified via hemacytometer. NRVMs were plated on Fibronectin (Gibco)- coated 35 mm dishes and incubated overnight to allow for recovery. On the following day, NRVMs were washed twice with 1:1 medium DMEM/F-12, kanamycin, ampicillin, and fungizone. NRVMs were incubated overnight in minimal medium consisting of 1:1 medium with 1 mg/ml bovine serum albumin (Sigma, MO, USA). On the third day, cells were washed two times with 1:1 medium. Minimal medium was replaced with Insulin-Transferrin-Selenium medium consisting of minimal medium, 1X Insulin-Transferrin-Selenium (Life Technologies), 0.4X MEM nonessential amino acids mixture (Sigma), and 0.1X MEM vitamins medium (Invitrogen, CA, USA).

extract_protocol:
After the appropriate exposure time, isolation of total RNA for RNA sequencing from
NRVMs was performed using RNeasy Mini Kit (Qiagen) as per the manufacturer’s protocol. RNA purity was determined by spectrophotometry using a NanoDrop 2000 (Thermo Scientific).
Library were prepared using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina (New England Biolabs Inc) and procedures were made are described by the manufacturer.

treatment_protocol: The control group was supplemented with 1% dimethyl sulfoxide (DMSO) and the experimental group was supplemented with 10 μmol/L rosiglitazone (Sigma-Aldrich) and 1% dimethyl sulfoxide (DMSO). NRVMs were exposed to control and experimental conditions for 0.5 hr, 24 hr, and 48 hr.

tag: agent

value: Control (DMSO)

tag: strain

value: Sprague-Dawley

tag: time point

value: HalfHour


title: HalfHourControl_1a

description:
01_HalfHourControl_1a
Control


title: WT-736-5

status: Public on Jan 14 2020

description:
WT_vs_KIN_deseq_132356_1508.txt
736-5

data_processing:
Quality check of the Fastq files using FastQC v0.11.5
Sequenced reads (fastq files) were trimmed for adaptor sequence, nucleotides with the phred score below 30 and for overrepresented sequences using cutadapt, version 1.11
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
The analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the moused genome (mm10).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited .txt files include the DESEQ2 output for the KO-IFT88 vs WT-IFT88. Comparison.  Columns to the right of the Base Mean column represent DEseq2 output.  WT-IR28N-3, WT-IRN272-9, KO-IR28N-6, KO-IR28N-9, KO-IRN234 contain raw count data for the two Wild-Type (NfatC1Cre(+); Ift88f/f) and three KO-IFT88 (NfatC1Cre(+), Ift88+/+)  RNAseq libraries. Symbol represent the HUGO Gene symbols for Mus musculus.  WT_vs_KIN_deseq_132356_1508.txt represents Dzip1 mutants and controls.

organism: Mus musculus

source_name: Heart Mitral leaflets

extract_protocol:
Total RNA was extracted with the RNeasy Mini kit (Qiagen, Valencia, California). All RNA were treated with DNase to ensure no DNA appeared in the results.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

tag: tissue

value: Mitral Valve tissue

tag: genotype


title: WT-736-1

description:
WT_vs_KIN_deseq_132356_1508.txt
736-1


title: WT-736-4

description:
WT_vs_KIN_deseq_132356_1508.txt
736-4


title: KIN-Mut-736-6

description:
WT_vs_KIN_deseq_132356_1508.txt
736-6


title: S33_Participant 5 Monocyte

status: Public on Mar 05 2020

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
FASTQ files were obtained by Illumina demultiplexing pipeline.
STAR and RSEM were used to align to HG38 and to calculate the raw counts for genes, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts and TPM in csv

organism: Homo sapiens

source_name: Healthy donor Monocyte

growth_protocol: Participants 1-6 without any treatment For in vitro experiment, the cells were cultured in RPMI with 10% FBS medium.

extract_protocol:
Total RNA was extracted from the 7 cell populations using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 500 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the Hg38 human genome database and the ZIKV sequence (ZIKV strain PRVABC59, GenBank: KU501215.1).

treatment_protocol: There is no treatment for participants 1-6; and for in vitro experiment, the cells were infected with ZIKV at MOI=1 for either 24h or 48h

tag: subject id

value: participant 5

tag: infection status

value: healthy donor

value: peripheral blood

tag: environment

value: ex vivo

tag: cell subtype

value: Monocyte


title: KO-IRN234 (re-analyzed)

description:
KO-IFT88_vs_WT-IFT88.txt
KO-IRN234-20

value: Knockout(NfatC1Cre(+), Ift88f/f)


title: KO-IR28N-9  (re-analyzed)

description:
KO-IFT88_vs_WT-IFT88.txt
KO-IR28N-9


title: KO-IR28N-6  (re-analyzed)

description:
KO-IFT88_vs_WT-IFT88.txt
KO-IR28N-6


title: WT-IRN272-9 (re-analyzed)

description:
KO-IFT88_vs_WT-IFT88.txt
WT-IRN272-9

value: Wild-Type(NfatC1Cre(+); Ift88+/+)


title: MSC80_AC2_RNASeq_1_4305_6

status: Public on Nov 04 2019

city: Kansas City

first: Elin

last: Grundberg

state: Missouri

address: 2401 Gillham Road

institute: CHILDREN'S MERCY HOSP (KANSAS CITY, MO)

description:
MSC80_AC2_RNASeq_1
HI.4305.006.Index_20.MSC80_AC2_RNASeq

data_processing:
Raw reads were trimmed for quality (phred33 ≥30) and length (n≥32), and Illumina adapters were clipped off using Trimmomatic v. 0.35
Filtered reads were then aligned to the GRCh38 human reference using STAR v. 2.5.3a
Raw read counts of genes were obtained using htseq-count v.0.6.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited file containing RPKM values of each sample

source_name: Mesenchymal Stem Cells

extract_protocol:
Bone-marrow derived mesenchymal stromal cells (LY-MSCs) from healthy individuals were  differentiated to adipocytes following the FRCBS previously published protocol.  In preparation for adipogenic differentiation cells at passage P3 were plated in 10 cm cell culture plates and grown in expansion media until they reached 70%-90% confluence , at which point the media was changed to adipogenic basal medium. Half of the culture plates were used as controls and maintained in the adipogenic basal medium until harvesting (AC samples). The other half was subjected to adipogenic differentiation (AD samples). More specifically the cells were first incubated for 3-4 days in adipogenic basal media (Timepoint 2), then the media was changed to the terminal differentiation cocktail. The media of all plates was changed twice a week and the differentiation was allowed to proceed for 3 weeks for Timepoint 3 or 4 weeks for Timepoint 4. For each donor samples were harvested at Timepoint 2 (AIC and AID: Adipocyte induced control without drugs in the media or differentiated with induction drugs), Timepoint 3 (AC1, AD1: Adipocyte control without drugs in the media or differentiated with drugs) and Timepoint 4 (AC2, AD2: Adipocyte control without drugs in the media or differentiated with drugs).
0.5 to 3 million cells were re-suspended in 500 uL TRIzol Reagent and total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA library preparations were carried out on 500 ng of RNA with RNA integrity number (RIN)>7 using the Illumina TruSeq Stranded Total RNA Sample preparation kit, according to manufacturer's protocol. Final libraries were analyzed on a Bioanalyzer and sequenced on the Illumina HiSeq

tag: cell type

value: Mesenchymal Stem Cells (MSCs)

value: Time Point 4

tag: control vs differentiated

value: Control


title: MSC91_ACI_RNASeq_1_4305_4

description:
MSC91_ACI_RNASeq_1
HI.4305.004.Index_15.MSC91_ACI_RNASeq

value: Time Point 2


title: WT-IR28N-3 (re-analyzed)

description:
KO-IFT88_vs_WT-IFT88.txt
WT-IR28N-3


title: MSC77_AD2_RNASeq_1_4305_3

description:
MSC77_AD2_RNASeq_1
HI.4305.003.Index_21.MSC77_AD2_RNASeq

value: Differentiated


title: MSC70_AC1_RNASeq_1_4318_2

description:
MSC70_AC1_RNASeq_1
HI.4318.002.Index_7.MSC70_AC1_RNASeq

value: Time Point 3


title: MSC77_AD1_RNASeq_1_4292_8

description:
MSC77_AD1_RNASeq_1
HI.4292.008.Index_1.MSC77_AD1_RNASeq


title: MSC91_AD1_RNASeq_1_4292_8

description:
MSC91_AD1_RNASeq_1
HI.4292.008.Index_10.MSC91_AD1_RNASeq


title: MSC74_AD1_RNASeq_1_4305_2

description:
MSC74_AD1_RNASeq_1
HI.4305.002.Index_19.MSC74_AD1_RNASeq


title: MSC83_AD2_RNASeq_1_4305_1

description:
MSC83_AD2_RNASeq_1
HI.4305.001.Index_27.MSC83_AD2_RNASeq


title: MSC80_AC1_RNASeq_1_4292_7

description:
MSC80_AC1_RNASeq_1
HI.4292.007.Index_5.MSC80_AC1_RNASeq


title: KIN-Mut-736-3

description:
WT_vs_KIN_deseq_132356_1508.txt
736-3


title: MSC83_AD1_RNASeq_1_4292_8

description:
MSC83_AD1_RNASeq_1
HI.4292.008.Index_8.MSC83_AD1_RNASeq


title: MSC80_AD1_RNASeq_1_4292_8

description:
MSC80_AD1_RNASeq_1
HI.4292.008.Index_3.MSC80_AD1_RNASeq


title: MSC77_AC1_RNASeq_1_4292_7

description:
MSC77_AC1_RNASeq_1
HI.4292.007.Index_4.MSC77_AC1_RNASeq


title: MSC83_AC1_RNASeq_1_4292_7

description:
MSC83_AC1_RNASeq_1
HI.4292.007.Index_12.MSC83_AC1_RNASeq


title: MSC77_AI_RNASeq_1_4292_6

description:
MSC77_AI_RNASeq_1
HI.4292.006.Index_7.MSC77_AI_RNASeq


title: MSC80_AI_RNASeq_1_4292_6

description:
MSC80_AI_RNASeq_1
HI.4292.006.Index_18.MSC80_AI_RNASeq


title: KIN: 3200__KIN-Mut-736-2

description:
WT_vs_KIN_deseq_132356_1508.txt
736-2


title: MSC91_AI_RNASeq_1_4292_6

description:
MSC91_AI_RNASeq_1
HI.4292.006.Index_16.MSC91_AI_RNASeq


title: MSC83_ACI_RNASeq_1_4292_5

description:
MSC83_ACI_RNASeq_1
HI.4292.005.Index_6.MSC83_ACI_RNASeq


title: MSC83_AI_RNASeq_1_4292_6

description:
MSC83_AI_RNASeq_1
HI.4292.006.Index_14.MSC83_AI_RNASeq


title: MSC80_ACI_RNASeq_1_4292_5

description:
MSC80_ACI_RNASeq_1
HI.4292.005.Index_13.MSC80_ACI_RNASeq


title: MSC83_AD1_RNASeq_1_4282_8

description:
MSC83_AD1_RNASeq_1
HI.4282.008.Index_8.MSC83_AD1_RNASeq


title: MSC77_AD1_RNASeq_1_4282_8

description:
MSC77_AD1_RNASeq_1
HI.4282.008.Index_1.MSC77_AD1_RNASeq


title: MSC80_AD1_RNASeq_1_4282_8

description:
MSC80_AD1_RNASeq_1
HI.4282.008.Index_3.MSC80_AD1_RNASeq


title: MSC91_AD1_RNASeq_1_4282_8

description:
MSC91_AD1_RNASeq_1
HI.4282.008.Index_10.MSC91_AD1_RNASeq


title: MSC80_AD1_RNASeq_1_4282_7

description:
MSC80_AD1_RNASeq_1
HI.4282.007.Index_3.MSC80_AD1_RNASeq


title: MSC83_AD1_RNASeq_1_4282_7

description:
MSC83_AD1_RNASeq_1
HI.4282.007.Index_8.MSC83_AD1_RNASeq


title: MSC77_AD1_RNASeq_1_4282_7

description:
MSC77_AD1_RNASeq_1
HI.4282.007.Index_1.MSC77_AD1_RNASeq


title: MSC91_AD1_RNASeq_1_4282_7

description:
MSC91_AD1_RNASeq_1
HI.4282.007.Index_10.MSC91_AD1_RNASeq


title: MSC80_AC1_RNASeq_1_4282_6

description:
MSC80_AC1_RNASeq_1
HI.4282.006.Index_5.MSC80_AC1_RNASeq


title: MSC80_AC1_RNASeq_1_4282_5

description:
MSC80_AC1_RNASeq_1
HI.4282.005.Index_5.MSC80_AC1_RNASeq


title: MSC91_AC1_RNASeq_1_4282_5

description:
MSC91_AC1_RNASeq_1
HI.4282.005.Index_19.MSC91_AC1_RNASeq


title: MSC83_AC1_RNASeq_1_4282_5

description:
MSC83_AC1_RNASeq_1
HI.4282.005.Index_12.MSC83_AC1_RNASeq


title: MSC77_AC1_RNASeq_1_4282_5

description:
MSC77_AC1_RNASeq_1
HI.4282.005.Index_4.MSC77_AC1_RNASeq


title: MSC77_AC1_RNASeq_1_4282_6

description:
MSC77_AC1_RNASeq_1
HI.4282.006.Index_4.MSC77_AC1_RNASeq


title: MSC77_AI_RNASeq_1_4282_4

description:
MSC77_AI_RNASeq_1
HI.4282.004.Index_7.MSC77_AI_RNASeq


title: MSC91_AC1_RNASeq_1_4292_7

description:
MSC91_AC1_RNASeq_1
HI.4292.007.Index_19.MSC91_AC1_RNASeq


title: MSC83_AC1_RNASeq_1_4282_6

description:
MSC83_AC1_RNASeq_1
HI.4282.006.Index_12.MSC83_AC1_RNASeq


title: MSC80_AI_RNASeq_1_4282_4

description:
MSC80_AI_RNASeq_1
HI.4282.004.Index_18.MSC80_AI_RNASeq


title: MSC91_AI_RNASeq_1_4282_4

description:
MSC91_AI_RNASeq_1
HI.4282.004.Index_16.MSC91_AI_RNASeq


title: MSC83_AI_RNASeq_1_4282_4

description:
MSC83_AI_RNASeq_1
HI.4282.004.Index_14.MSC83_AI_RNASeq


title: MSC77_AI_RNASeq_1_4282_3

description:
MSC77_AI_RNASeq_1
HI.4282.003.Index_7.MSC77_AI_RNASeq


title: MSC91_AI_RNASeq_1_4282_3

description:
MSC91_AI_RNASeq_1
HI.4282.003.Index_16.MSC91_AI_RNASeq


title: MSC80_AI_RNASeq_1_4282_3

description:
MSC80_AI_RNASeq_1
HI.4282.003.Index_18.MSC80_AI_RNASeq


title: MSC83_AI_RNASeq_1_4282_3

description:
MSC83_AI_RNASeq_1
HI.4282.003.Index_14.MSC83_AI_RNASeq


title: MSC83_ACI_RNASeq_1_4282_2

description:
MSC83_ACI_RNASeq_1
HI.4282.002.Index_6.MSC83_ACI_RNASeq


title: MSC80_ACI_RNASeq_1_4282_2

description:
MSC80_ACI_RNASeq_1
HI.4282.002.Index_13.MSC80_ACI_RNASeq


title: MSC83_ACI_RNASeq_1_4282_1

description:
MSC83_ACI_RNASeq_1
HI.4282.001.Index_6.MSC83_ACI_RNASeq


title: MSC80_ACI_RNASeq_1_4282_1

description:
MSC80_ACI_RNASeq_1
HI.4282.001.Index_13.MSC80_ACI_RNASeq


title: MSC74_AD2_RNASeq_1_4281_8

description:
MSC74_AD2_RNASeq_1
HI.4281.008.Index_25.MSC74_AD2_RNASeq


title: MSC91_AC1_RNASeq_1_4282_6

description:
MSC91_AC1_RNASeq_1
HI.4282.006.Index_19.MSC91_AC1_RNASeq


title: MSC73_AD2_RNASeq_1_4281_8

description:
MSC73_AD2_RNASeq_1
HI.4281.008.Index_22.MSC73_AD2_RNASeq


title: MSC73_AD2_RNASeq_1_4281_7

description:
MSC73_AD2_RNASeq_1
HI.4281.007.Index_22.MSC73_AD2_RNASeq


title: MSC74_AD2_RNASeq_1_4281_7

description:
MSC74_AD2_RNASeq_1
HI.4281.007.Index_25.MSC74_AD2_RNASeq


title: MSC72_AD2_RNASeq_1_4281_6

description:
MSC72_AD2_RNASeq_1
HI.4281.006.Index_20.MSC72_AD2_RNASeq


title: MSC70_AC2_RNASeq_1_4281_6

description:
MSC70_AC2_RNASeq_1
HI.4281.006.Index_1.MSC70_AC2_RNASeq


title: MSC70_AD2_RNASeq_1_4281_6

description:
MSC70_AD2_RNASeq_1
HI.4281.006.Index_11.MSC70_AD2_RNASeq


title: MSC72_AD2_RNASeq_1_4281_5

description:
MSC72_AD2_RNASeq_1
HI.4281.005.Index_20.MSC72_AD2_RNASeq


title: MSC74_AC2_RNASeq_1_4281_6

description:
MSC74_AC2_RNASeq_1
HI.4281.006.Index_10.MSC74_AC2_RNASeq


title: MSC74_AC2_RNASeq_1_4281_5

description:
MSC74_AC2_RNASeq_1
HI.4281.005.Index_10.MSC74_AC2_RNASeq


title: MSC74_AC1_RNASeq_1_4281_4

description:
MSC74_AC1_RNASeq_1
HI.4281.004.Index_16.MSC74_AC1_RNASeq


title: MSC72_AC1_RNASeq_1_4281_3

description:
MSC72_AC1_RNASeq_1
HI.4281.003.Index_18.MSC72_AC1_RNASeq


title: MSC72_AC1_RNASeq_1_4281_4

description:
MSC72_AC1_RNASeq_1
HI.4281.004.Index_18.MSC72_AC1_RNASeq


title: MSC73_AC2_RNASeq_1_4281_1

description:
MSC73_AC2_RNASeq_1
HI.4281.001.Index_8.MSC73_AC2_RNASeq


title: MSC70_AD2_RNASeq_1_4281_5

description:
MSC70_AD2_RNASeq_1
HI.4281.005.Index_11.MSC70_AD2_RNASeq


title: MSC70_AC2_RNASeq_1_4281_5

description:
MSC70_AC2_RNASeq_1
HI.4281.005.Index_1.MSC70_AC2_RNASeq


title: MSC74_AC1_RNASeq_1_4281_3

description:
MSC74_AC1_RNASeq_1
HI.4281.003.Index_16.MSC74_AC1_RNASeq


title: MSC91_AD2_RNASeq_1_4277_2

description:
MSC91_AD2_RNASeq_1
HI.4277.002.Index_3.MSC91_AD2_RNASeq


title: MSC73_AD1_RNASeq_1_4281_4

description:
MSC73_AD1_RNASeq_1
HI.4281.004.Index_12.MSC73_AD1_RNASeq


title: MSC80_AD2_RNASeq_1_4277_2

description:
MSC80_AD2_RNASeq_1
HI.4277.002.Index_23.MSC80_AD2_RNASeq


title: MSC91_AC2_RNASeq_1_4277_1

description:
MSC91_AC2_RNASeq_1
HI.4277.001.Index_25.MSC91_AC2_RNASeq


title: MSC91_AD2_RNASeq_1_4277_1

description:
MSC91_AD2_RNASeq_1
HI.4277.001.Index_3.MSC91_AD2_RNASeq


title: MSC83_AC2_RNASeq_1_4277_2

description:
MSC83_AC2_RNASeq_1
HI.4277.002.Index_22.MSC83_AC2_RNASeq


title: MSC91_AC2_RNASeq_1_4277_2

description:
MSC91_AC2_RNASeq_1
HI.4277.002.Index_25.MSC91_AC2_RNASeq


title: MSC83_AC2_RNASeq_1_4277_1

description:
MSC83_AC2_RNASeq_1
HI.4277.001.Index_22.MSC83_AC2_RNASeq


title: MSC73_AC1_RNASeq_1_4276_6

description:
MSC73_AC1_RNASeq_1
HI.4276.006.Index_14.MSC73_AC1_RNASeq


title: MSC80_AD2_RNASeq_1_4277_1

description:
MSC80_AD2_RNASeq_1
HI.4277.001.Index_23.MSC80_AD2_RNASeq


title: MSC72_AD1_RNASeq_1_4276_5

description:
MSC72_AD1_RNASeq_1
HI.4276.005.Index_5.MSC72_AD1_RNASeq


title: MSC72_AC2_RNASeq_1_4276_4

description:
MSC72_AC2_RNASeq_1
HI.4276.004.Index_3.MSC72_AC2_RNASeq


title: MSC77_ACI_RNASeq_1_4276_2

description:
MSC77_ACI_RNASeq_1
HI.4276.002.Index_2.MSC77_ACI_RNASeq


title: MSC70_AD1_RNASeq_1_4276_1

description:
MSC70_AD1_RNASeq_1
HI.4276.001.Index_4.MSC70_AD1_RNASeq


title: MSC77_AC2_RNASeq_1_4276_3

description:
MSC77_AC2_RNASeq_1
HI.4276.003.Index_11.MSC77_AC2_RNASeq


title: zygote-3

status: Public on Oct 29 2019

city: harbin

first: xu

last: yangx

address: mucai 59

country: China

institute: neau

data_processing:
Smart-Seq2 method was used to amplify the single cell sample. The reaction system for the first cDNA strand synthesis comprised the reverse transcription enzyme, buffer, TSO primers and oligo-dT primers with common sequence. For the second strand synthesis, added PCR amplification reagent and ISPCR primer with common sequence to the first strand products. The sample cDNA was fragmented into 300bp by Bioruptor®Sonication System (Diagenode Inc.), and then performed terminal repair, addition of A, and ligation of sequencing adapters, and amplified. The PCR amplification product with 350-450bp was extracted. Then, the concentration was measured by Qubit 2.0 Flurometer (Life Technologies, CA, USA). The integrity of the amplified products was detected by Agilent 2100 High Sensitivity DNA Assay Kit (Agilent Technologies, CA, USA). The libraries were sequenced by an Illumina HiSeq X Ten platform.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: in vivo embryo

growth_protocol: in vivo embryos

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

tag: developmental stage

value: blastomere


title: zygote-2


title: te-1

value: blastocyst-trophoblast


title: zygote-1


title: S-Bla-3

value: blastocyst


title: oocyte-4

value: MII oocyte

value: oocyte


title: MSC73_AD1_RNASeq_1_4281_3

description:
MSC73_AD1_RNASeq_1
HI.4281.003.Index_12.MSC73_AD1_RNASeq


title: M-4_6

value: morula


title: S-Bla-1


title: oocyte-2


title: M-pull


title: M-4_7


title: M-4_4


title: M-4_3


title: M-4_15


title: M-4_16


title: M-4_13


title: M-4_14


title: M-4_11


title: M-4_12


title: M-4_10


title: M-3_7


title: M-3_2


title: M-2_8


title: M-2_11


title: M-2_13


title: M-2_1


title: M-1_9


title: S34_Participant 5 NK

source_name: Healthy donor NK

growth_protocol: Participants 1-6 without any treatment. For in vitro experiment, the cells were cultured in RPMI with 10% FBS medium.

value: participant 5

value: healthy donor

value: peripheral blood

value: NK


title: M-1_7


title: M-1_6


title: M-1_11


title: M-4_2


title: icm-3

value: blastocyst-inner cell mass


title: M-1_10


title: M-1_4


title: M-1_1


title: 8cell-4_1


title: 8cell-4_8


title: 8cell-3_7


title: 8cell-3_5


title: 8cell-3_6


title: 8cell-3_2


title: 8cell-3_1


title: 8cell-2_7


title: 8cell-2_8


title: M-3_5


title: M-2_7


title: 8cell-2_6


title: 8cell-2_5


title: 8cell-2_4


title: 8cell-2_3


title: M-1_8


title: 8cell-2_1


title: 8cell-1_8


title: 8cell-1_7

source_name: in vivo oocyte


title: 8cell-1_6


title: 8cell-1_5


title: 8cell-1_4


title: 8cell-1_2


title: 8cell-1_1


title: 8cell-1_3


title: 4cell-pull


title: 8cell-3_3


title: 4cell-4_2


title: 4cell-4_4


title: 4cell-4_3


title: 4cell-4_1


title: 4cell-3_4


title: 4cell-3_3


title: 4cell-3_2


title: 4cell-3_1


title: 4cell-2_3


title: 4cell-2_4


title: 4cell-1_3


title: M-1_3


title: 4cell-1_2


title: 2cell-pull


title: 4cell-1_1


title: 2cell-5_2


title: 2cell-3_2


title: 2cell-1_1


title: Primary human fibroblasts at 6hrs after stimulation with TGFB1 Fib_41_6hr_RNA

status: Public on Oct 03 2019

city: Singapore

first: Sonia

last: Chothani

address: 8 College Road

country: Singapore

institute: Duke-NUS school of medicine

description:
Fib_41_6hr_RNA
poly(A) RNA

data_processing:
Raw sequencing data were demultiplexed with bcl2fastq V2.19.0.316 and the adaptors were trimmed using Trimmomatic45 V0.36, retaining reads longer than 20 nt post-clipping. RNA-seq reads were further clipped with FASTX Toolkit V0.0.14 to 29nt, to allow comparison directly with Ribo-seq reads. Reads were aligned using bowtie46 to known rRNA, tRNA and mt-rRNA sequences (RNACentral47, release 5.0), aligned reads were filtered out to obtain only RPFs. Alignment to the human genome (hg38) was done using STAR48. Gene expression was quantified on the CDS (coding sequence region) using uniquely mapped reads (Ensembl database release GRCh38 v86 combined with additional transcripts from RefSeq GRCh38, latest version downloaded January 2018) with feature counts49. Genes with mean transcripts per million mapped reads, TPM < 1 in either RNA-seq or Ribo-seq across all conditions were removed before downstream analysis. Ribotaper50 was used to obtain the in-frame reads around the start and stop codon. These p-sites were then visualized across samples and genes. Heatmap for the ribosome drop-off was generated using pheatmap 1.0.8 R package51. Data quality check was done using MultiQC52. Principal component analysis was carried out using prcomp function in R. Individual gene batch effect for ITGA7 was removed using limma package53 in R.
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix file consisting of genes as rows and samples as columns

molecule: polyA RNA

source_name: Patient 4

extract_protocol:
Human atrial fibroblasts were prepared and cultured as described previously12. All the experiments were carried out at low cell passage (<P4). In all experiments, cells were starved in serum-free DMEM for 16 hours prior to TGFβ1 stimulation. Stimulated fibroblasts were compared to unstimulated fibroblasts that have been grown for the same duration under the same conditions (serum-free DMEM), but without the stimuli.
Ribosome profiling was performed as previously described16. Briefly, snap-frozen cell pellets or 50-100 mg of tissue, previously powdered under liquid nitrogen, were lysed in 1ml cold lysis buffer (formulation as in TruSeq Ribosome Profile, Illumina) supplemented with 0.1mg/ml cycloheximide (CHX) to stabilize ribosomal subunits and prevent post-lysis translocation. Homogenized and cleared lysates were then footprinted with Truseq Nuclease (Illumina) according to manufacturer’s instructions. Ribosomes were purified using Illustra Sephacryl S400 columns (GE Healthcare) and the protected RNA fragments were extracted with standard phenol:chloroform:isoamylalcohol technique. Following ribosomal RNA removal (Mammalian RiboZero Magnetic Gold, Illumina), sequencing libraries were prepared out of the footprinted RNA. Ribo-seq libraries were pooled to perform multiplex sequencing on Illumina Hiseq machines. To prepare polyA+ RNA-seq libraries from primary cardiac fibroblasts, total RNA was extracted with Trizol from one 10cm dish per condition. Following cleanup with RNeasy kit (Qiagen), ~500ng of each sample were further processed with the Truseq Stranded mRNA kit (Illumina). Barcoded RNA-seq libraries were pooled and sequenced on the Illumina HiSeq platform.
The RNAseq data for the heart tissue was derived from Henig et al24. To prepare polyA+ RNA-seq libraries from primary cardiac fibroblasts, total RNA was extracted with Trizol from one 10cm dish per condition. Following cleanup with RNeasy kit (Qiagen), ~500ng of each sample were further processed with the Truseq Stranded mRNA kit (Illumina). Barcoded RNA-seq libraries were pooled and sequenced on the Illumina HiSeq platform.

value: Cardiac fibroblasts

tag: sequencing

value: RNA-seq


title: Primary human fibroblasts at 45mins after stimulation with TGFB1 Fib_41_45m_RNA

description:
Fib_41_45m_RNA
poly(A) RNA


title: Primary human fibroblasts at 6hrs after stimulation with TGFB1 Fib_27_6hr_RNA

description:
Fib_27_6hr_RNA
poly(A) RNA

source_name: Patient 2


title: Primary human fibroblasts at 45mins after stimulation with TGFB1 Fib_27_45m_RNA

description:
Fib_27_45m_RNA
poly(A) RNA


title: Primary human fibroblasts at 6hrs after stimulation with TGFB1 Fib_24_6hr_RNA

description:
Fib_24_6hr_RNA
poly(A) RNA

source_name: Patient 1


title: Primary human fibroblasts at 45mins after stimulation with TGFB1 Fib_24_45m_RNA

description:
Fib_24_45m_RNA
poly(A) RNA


title: Primary human fibroblasts at 6hrs after stimulation with TGFB1 Fib_41_6hr

description:
Fib_41_6hr
Ribosome protected fragment

value: Ribo-seq


title: Primary human fibroblasts at 6hrs after stimulation with TGFB1 Fib_34_6hr

description:
Fib_34_6hr
Ribosome protected fragment

source_name: Patient 3


title: Primary human fibroblasts at 6hrs after stimulation with TGFB1 Fib_27_6hr

description:
Fib_27_6hr
Ribosome protected fragment


title: Primary human fibroblasts at 45mins after stimulation with TGFB1 Fib_41_45m

description:
Fib_41_45m
Ribosome protected fragment


title: Primary human fibroblasts at 45mins after stimulation with TGFB1 Fib_34_45m

description:
Fib_34_45m
Ribosome protected fragment


title: Primary human fibroblasts at 45mins after stimulation with TGFB1 Fib_27_45m

description:
Fib_27_45m
Ribosome protected fragment


title: Primary human fibroblasts at 45mins after stimulation with TGFB1 Fib_24_45m

description:
Fib_24_45m
Ribosome protected fragment


title: HF_KO_3

status: Public on Aug 30 2019

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

state: IL

address: 900 E. 57th Street

institute: University of Chicago

data_processing:
Sequence reads were aligned to the mouse reference genome mm10 with STAR-2.4.2a.
featureCounts (subread-1.5.0) was used to quantify gene expression (parameters applied: "“-s 1 –Q 10")
Differential expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count for each sample.

source_name: β cell specific knockout_pancreatic islets

extract_protocol:
Qiagen RNAeasy Micro Kit
Ten nanograms of total RNA per sample were used for library preparation. cDNA was first synthesized via reverse transcription with poly-dT priming, using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.), followed by cDNA shearing with Covaris AFA sonicator (Covaris) and size selection with AMPure beads (Beckman Coulter). Barcoded cDNA library was then prepared using Ion Plus Fragment Library Kit (Life Technologies).

tag: strain background

tag: genotype/variation

value: isolated pancreatic islets


title: HF_KO_2


title: HF_KO_1


title: 2cell-5_1


title: HF_CONT_2

source_name: control_pancreatic islets

value: control


title: HF_CONT_3


title: HF_CONT_1


title: 2cell-1_2


title: 2cell-3_1


title: Primary human fibroblasts at 45mins after stimulation with TGFB1 Fib_34_45m_RNA

description:
Fib_34_45m_RNA
poly(A) RNA


title: Primary human fibroblasts at 6hrs after stimulation with TGFB1 Fib_34_6hr_RNA

description:
Fib_34_6hr_RNA
poly(A) RNA


title: DN3b_TCF1KO_2

status: Public on Aug 28 2019

city: Leiden

first: Martijn

last: Cordes

state: Zuid-Holland

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Centre

library_source: genomic

data_processing:
The reads were filtered by quality using Trim-galore tool (Krueger, 2015) (default values) and the quality control was driven by FastQC (Andrews, 2010) and MultiQC (Ewels, 2016).
The remained reads were mapped to mm10 using bowtie2 (Langmead et al, 2012) with –very-sensitive parameter. After all, before the peak calling, the read duplicates and multiple mapping reads were removed using Picard tools (http://broadinstitute.github.io/picard).
The peaks for 2 WT and 2 Tcf1 -/- samples were called using  MACS2 (Zhang et al, 2008) with the following parameters: -g mm -B –shift -100 -ext 200 –nomodel –q
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with RPKM tracks

molecule: genomic DNA

source_name: DN3b thymocytes

growth_protocol: DN thymocytes (CD8 - CD4 - ) from Tcf1-/- and wildtype littermates were sorted and subsequently crosslinked with formaldehyde (Sigma). Crosslinking was quenched with Glycine and after cell lysis chromatin was sonicated into fragments.

extract_protocol:
Sonicated chromatin was precleared and incubated with antibodies. TCF-1 (C46C7; #2206 Cell Signalling Technologies).
Nextera DNA Library Prep Kit; Illumina

value: T cells

tag: markers


title: DN3a_TCF1KO_1

source_name: DN3a thymocytes


title: DN3a_TCF1KO_2


title: DN3a_WT_1

value: WT


title: Primary human fibroblasts at 6hrs after stimulation with TGFB1 Fib_24_6hr

description:
Fib_24_6hr
Ribosome protected fragment


title: DN3a_WT_2


title: DN3b_WT_2


title: DN3b_WT_1


title: 8cell-pull

value: blastomere


title: DN3b_TCF1KO_1


title: Nor4

status: Public on Jul 01 2019

type: RNA

city: Vejle

first: Luisa

last: Matos do Canto

address: Beriderbakken 4

department: Biochemistry and Immunology

country: Denmark

institute: Vejle Hospital

description: gene expression data from rectal cancer biopsy

hyb_protocol: Performed using the Affymetrix  GeneChip® Hybridization, Wash and Stain Kit (P/N 900720) following manufacturer's instructions

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G

data_processing:
The data were extracted using the Affymetrix GeneChip Command Console (AGCC) 4.0 software and submitted to quantile normalization.
Filtering characteristics of fold-change -1.5 to 1.5 and a FDR < 0.05 were used to identify the differentially expressed genes.

label: biotin

source_name: normal rectum

label_protocol: Performed using the Affymetrix SensationPlus™ FFPE Amplification and WT Labeling Kit (P/N 902031) following manufacturer's instructions

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted using RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Invitrogen Life Technologies Inc., Carlsbad, CA, USA) according to the manufacturer’s recommendations.

treatment_protocol: Not applicable

value: Rectum

tag: disease

value: normal

tag: response

tag: trg


title: RET32

source_name: rectal cancer

value: rectal cancer

value: pIR


title: RET41

value: pCR


title: RET33


title: Nor2


title: RET28


title: RET42


title: RET34


title: Nor1


title: RET44


title: RET9


title: RET21


title: RET17


title: RET24


title: RET11


title: RET25


title: RET29


title: RET10


title: Nor3


title: RET12


title: RET30


title: RET43


title: RET20


title: RET19


title: Nor5


title: RET31


title: RET8


title: RET27


title: RET13


title: SC156NORUP

status: Public on Jun 21 2019

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

data_processing:
10X Genomics' Cell Ranger 2.0 software's mkfastq command was used for basecalling.  It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 whole genome using 10X Genomics' Cell Ranger 2.0 software's cellranger count function
Cell Ranger output of raw_gene_bc_matrices were utilized for further downstream analysis in R with the package Seurat 2.3.4, only cells expressing at least 200 genes were kept for downstream analysis.  Further filtration removed cells expressing greater than 50,000 UMI or 35% mitochondrial genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

source_name: upper lobe lung_healthy donor

extract_protocol:
10X Genomics 3 Prime V2 chemistry
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v2 User Guide

tag: subject status

value: normal/healthy donor

value: lung

tag: lung section/portion

value: upper lobe lung


title: RET6

tag: tissue


title: RET7


title: SC56NOR

source_name: mix of upper + lower lobe lung_healthy donor

value: mix of upper + lower lobe lung


title: SC59NOR


title: SC45NOR


title: SC31DNOR

extract_protocol:
10X Genomics 3 Prime V1 chemistry
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v2 User Guide


title: SC155NORLOW

source_name: lower lobe lung_healthy donor

value: lower lobe lung


title: SC31NOR


title: RET5


title: SC14NOR


title: Exp2

status: Public on Apr 02 2019

data_processing:
Quality check of the Fastq files using FastQC v0.11.5
Sequenced reads (fastq files) were trimmed for adaptor sequence, nucleotides with the phred score below 30 and for overrepresented sequences using cutadapt, version 1.11
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
The analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19).
Genome_build: GRCh37/hg19

source_name: skin tissue

growth_protocol: Normal human skin was obtained from residual tissue following plastic surgery. Subcutaneous fat tissue was removed. Skin was cut with a disposable biopsy 3 mm punch, and the pieces of tissue were cultured in medium.

extract_protocol:
Total RNA was extracted from human skin tissues using TRIZOL Lysis Reagent (Life technologies, CA, USA) and RNeasy® kit (Qiagen Inc., CA, USA)
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: Skin samples were cultured with TGFβ (10 ng/ml) or a vehicle control. Skin tissues were harvested at 48 hours.

tag: treatment

value: TGFβ (10 ng/ml)


title: Ctl3

value: vehicle


title: RET4


title: N3

status: Public on Mar 07 2019

city: chongqing

first: lei

last: bo

address: gaotan yan

institute: Army Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HiSat2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: PBMCs

growth_protocol: The study included 7 samples, of which 4 were HCC samples and 3 were normal controls.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 ml of peripheral blood was centrifuged in700x g at room temperature. Removing the plasma, then dilute it by volume with precooled PBS 1 to 1, then add it slowly to the lymphocyte isolate at room temperature, and centrifuge it in 700x g. Carefully absorb the middle layer of white membrane with straw and wash it 2 times with pre cooled PBS at room temperature.The ratio of serum and DMSO to volume ratio was 9 to 1, and suspended cells were frozen with liquid nitrogen.

value: Peripheral blood

value: Normal control


title: N2


title: N1


title: Exp1


title: Ctl1


title: Gut_3_mRNA

status: Public on Dec 26 2018

data_processing:
Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the ZEBRAFISH genome (GRCZ10) using tophat2
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited .txt files include the DESEQ2 output for the gut vs liver Comparison.  Columns to the right of the Base Mean column represent standard DEseq2 output.  Gut_1, Gut_2, Liver_1 and Liver_2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl_gene_id, external_gene_name, description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers, hsapiens_homolog_ensembl_gene, hgnc_symbol, Human_description and Human_entrez_geneid

organism: Danio rerio

source_name: Gut

extract_protocol:
Isolation of total liver RNA was performed using TRIzol reagent (Invitrogen), and the extracted RNA were further purified using the RNeasy Mini kit (Qiagen, Valencia, California). All RNA were treated with DNase to ensure no DNA appeared in the results.
To prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA), 100-200 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C, and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food (Tetra, Germany).  Fish were acclimated for one week prior to extracting the tissues, i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.

tag: Sex

value: male

value: Gut


title: Liver_1_miRNA

data_processing:
Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the ZEBRAFISH genome (GRCZ10) using tophat2
The Comprehensive Analysis Pipeline for microRNA sequencing data (CAP-miRSeq) was used for read pre-processing, alignment, mature/precursor/ novel miRNA detection and quantification, and data visualization. The miRNA-Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data, and Bowtie.
DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output. Gut_1, Gut_2, Liver_1 and Liver_2  contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol, GeneID, Description and MirBaseID represent miRNA annotation and description information.

source_name: Liver

extract_protocol:
Isolation of total liver RNA was performed using TRIzol reagent (Invitrogen), and the extracted RNA were further purified using the miRNeasy Mini kit (Qiagen, Valencia, California). All RNA were treated with DNase to ensure no DNA appeared in the results.
The miRNA-Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA

value: Liver


title: Liver_2_mRNA


title: Gut_4_mRNA


title: Gut_3_miRNA


title: Liver_1_mRNA


title: Liver_2_miRNA


title: LNCaP PDR2 PD treated replicate 3

status: Public on May 31 2018

description:
LNPDR2-PD_vs_LNPDR2Cntrl.txt
LN-PDR2-PD_vs_LN-WT-CTRL.txt
LN-PDR2-PD_vs_LN-WT-PD.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp痴 advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: human prostate cancer cells

growth_protocol: Palbociclib (PD) resistant cells (PDR) were generated from LAPC4 and LNCaP cells via sustained treatment with 0.5uM PD and kept under PD-selection to maintain the cells. Parental cells were cultured in parallel in standard growth media.

extract_protocol:
Total RNA was extracted with a RNeasy Mini Kit by Qiagen
RNA-seq from Illumina

treatment_protocol: Cells were seeded (without drugs) in standard culture media and treated for 24 hours with 0.5uM PD or vehicle control before harvesting RNA

value: immortalized cell line

value: derived from lymph node metastasis

tag: concentration

value: 0.5uM PD


title: LNCaP parental CTRL treated replicate 2

description:
LN-PDR1-CTRL_vs_LN-WT-CTRL.txt
LN-PDR2-CTRL_vs_LN-WT-CTRL.txt
LN-PDR2-PD_vs_LN-WT-CTRL.txt
LNWTPD_vs_LNWTCntrl.txt

value: vehicle control


title: LNCaP PDR2 PD treated replicate 2


title: Col0_small_RNA_rep2

status: Public on Feb 08 2019

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Illumina HiSeq

data_processing:
RNA-seq: mapping with hisat2
RNA-seq: expression estimation with HTseq-count and DESeq2
miRNA-seq: quality filtering and trimming, adapter removal
miRNA-seq: mapping with bowtie
miRNA-seq: expression estimation with HTseq-count and DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: bigwig files were generated using bedtools genomecov and bedGraphToBigWig; Scores represent reads normalized to 1e7 reads
Supplementary_files_format_and_content: miRNA-seq: bigwig files were generated using bedtools genomecov and bedGraphToBigWig; Scores represent reads normalized to 1e7 reads

organism: Arabidopsis thaliana

growth_protocol: Seeds were stratified for 2 days at 4ºC and grown on soil under a 16 h light/8 h dark (long-day) conditions.

extract_protocol:
trizol
BGI
Total plant RNA was isolated from 3-week-old plants grown using Trizol reagent (Sigma) according to manufacturer’s instructions.

value: wild type

value: 21 day old seedlings


title: LNCaP parental PD treated replicate 2

description:
LN-PDR1-PD_vs_LN-WT-PD.txt
LN-PDR2-PD_vs_LN-WT-PD.txt
LNWTPD_vs_LNWTCntrl.txt


title: Col0_small_RNA_rep1

description: Illumina HiSeq


title: Col0_small_RNA_rep3

description: Illumina HiSeq


title: LNCaP PDR2 CTRL treated replicate 3

description:
LN-PDR2-CTRL_vs_LN-WT-CTRL.txt
LNPDR2-PD_vs_LNPDR2Cntrl.txt


title: LNCaP PDR2 PD treated replicate 1


title: LNCaP PDR2 CTRL treated replicate 2


title: LNCaP PDR2 CTRL treated replicate 1


title: LNCaP parental PD treated replicate 1


title: LNCaP PDR1 PD treated replicate 3

description:
LNPDR1-PD_vs_LNPDR1Cntrl.txt
LN-PDR1-PD_vs_LN-WT-PD.txt


title: Gut_4_miRNA


title: LNCaP PDR1 CTRL treated replicate 3

description:
LN-PDR1-CTRL_vs_LN-WT-CTRL.txt
LNPDR1-PD_vs_LNPDR1Cntrl.txt


title: LNCaP PDR1 PD treated replicate 1


title: LNCaP PDR1 CTRL treated replicate 2


title: LNCaP parental PD treated replicate 3


title: LNCaP PDR1 CTRL treated replicate 1


title: LAPC4 parental PD treated replicate 2

description:
L4-PDR1-PD_vs_L4-WT-PD.txt
L4WT-PD_vs_L4WTCntrl.txt


title: LNCaP parental CTRL treated replicate 1


title: LAPC4 parental CTRL treated replicate 1

description:
L4PDR1Cntrl_vs_L4-WT-CTRL.txt
L4WT-PD_vs_L4WTCntrl.txt


title: LAPC4 parental CTRL treated replicate 3


title: LAPC4 parental PD treated replicate 1


title: LAPC4 parental PD treated replicate 3


title: LAPC4 parental CTRL treated replicate 2


title: LNCaP parental CTRL treated replicate 3


title: LAPC4 PDR1 PD treated replicate 2

description:
L4PDR1-PD_vs_L4PDR1Cntrl.txt
L4-PDR1-PD_vs_L4-WT-PD.txt


title: LAPC4 PDR1 PD treated replicate 1


title: LAPC4 PDR1 PD treated replicate 3


title: LAPC4 PDR1 CTRL treated replicate 1

description:
L4PDR1Cntrl_vs_L4-WT-CTRL.txt
L4PDR1-PD_vs_L4PDR1Cntrl.txt


title: LAPC4 PDR1 CTRL treated replicate 2


title: CL67

status: Public on Feb 13 2018

data_processing:
Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the ZEBRAFISH genome (GRCZ10) using tophat2
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl_gene_id; external_gene_name; description; hsapiens_homolog_ensembl_gene; hgnc_symbol; Human_description; Human_entrez_geneid; ensembl_peptide_ids; ensembl_transcript_ids. The baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, are all derived from DESeq2

treatment_protocol: Male zebrafish (Danio rerio) were housed in aquaria maintained at a temperature 26-29ºC with a 100 W aquarium heater, and had a light-dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial, flaked fish food (Tetra, Germany). The fish were acclimated one week before the beginning of the experiments. For both experiments, 80 L tanks were prepared for each of the experimental groups, housing 40 fish per tank. One tank contained water with 0.65 nM of 17α-ethinylestradiol (EE2), one tank contained 5.8 nM of (2-ethylhexyl) phthalate (DEHP), and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH, and stock working solutions were prepared, from which the working experimental concentrations were prepared. All exposures utilized a continuous flow-through system, and all exposures lasted for three weeks. After the end of the experimental period, the zebrafish were anaesthetized using 3-aminobenzoic acid ethyl ester (Sigma-Aldritch, St. Louis, MO; 10 g/L tap water) and sacrificed for removal of their livers, which were immediately frozen in liquid nitrogen and stored at -70ºC for molecular biology analysis.

tag: agent

value: 5.8 nM (2-ethylhexyl)-phthalate


title: LNCaP PDR1 PD treated replicate 2


title: LAPC4 PDR1 CTRL treated replicate 3


title: CL65

value: 0.65 nM Ethinylestradiol (EE2)


title: CL66


title: RNA sequencing in WT cells grown at 30C rep1

status: Public on May 08 2018

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

data_processing:
Alignment was done using Tophat.
FPKM values were calculated using cufflinks
Genome_build: asm294v2.28
Supplementary_files_format_and_content: Tab delimited text files, from cufflinks

organism: Schizosaccharomyces pombe

source_name: log. growing cells

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). For sequencing librarys from strains grown at 30°C, cultures were grown at 30˚C to OD600~0.5.  For sequencing libraries from strains grown at 18°C, cultures were first grown at 30°C to OD600~0.1-0.2 and then shifted to 18˚C for 3 days.

extract_protocol:
RNA was extracted using the MasterPure™ Yeast RNA Purification Kit (Epicentre)
ScriptSeq v2 RNA-Seq Library Preparation Kit was used according to manufacturer's recommendation.
Libraries were analyzed using the Agilent D1000 TapeStation (Agilent) and sequenced on the Illumina MiSeq platform.

treatment_protocol: Genomic deletion of AGO1, RED1, RRP6, CLR4, CCR4, and genetic mutations in CLR6 and FEP1.  Growth treatment at 30°C or 18°C.

tag: strain

value: wildtype

tag: growth temperature


title: RNA sequencing in WT cells grown at 30C rep2


title: CL68


title: C57_BMDM_ATAC_notx_rep2

status: Public on May 17 2018

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

description:
ATAC-seq
Processed data file:
peaks_C57_ATAC_notx_opt.
Processed data file available in:
ATAC-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: mm10

source_name: bone marrow derived macropages (BMDM)

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
ATAC-seq: To approximately 150k nuclei in 22.5ul GRO freezing buffer, isolated as described for GRO-seq above, 25ul DNA Tagmentation buffer was added, reaction mixed and 2.5uL DNA Tagmentation Enzyme mix (Nextera DNA Library Preparation Kit, Illumina) added. Mixture was incubated at 37°C for 30 minutes and subsequently purified using the Zymogen ChIP DNA purification kit as described by the manufacturer. DNA was amplified using the Nextera Primer Ad1 and a unique Ad2.n barcoding primers using NEBNext High-Fidelity 2X PCR MM for 10 cycles. PCR reactions were purified using 1.5 volumes of SpeedBeads in 2.5M NaCl, 20% PEG8000, size selected using PAGE/TBE gels for 160 – 280 bp and DNA eluted as described for GRO-seq.

value: bone marrow derived macropages (BMDM)

tag: culture protocol

value: 7 day cultured BMDMs

tag: ligands in culture

value: no treatment

tag: chip antibody


title: C57_BMDM_ATAC_KLA_1h_rep2

description:
ATAC-seq
Processed data file:
peaks_C57_ATAC_KLA_opt.
Processed data file available in:
ATAC-seq_processed_data_files.tar

value: KLA 1h


title: C57_BMDM_ATAC_notx_rep1


title: C57_BMDM_ATAC_KLA_1h_rep1


title: CL64

value: Control


title: RNA IP from HEK293 cells expressing sumoylation deficient La mutant  sample 2

status: Public on Nov 22 2017

description:
processed data file:
Input_sumo_ def_La_mut vs RNA_IP_sumo_def_La_mut .txt
RNA_IP_sumo_def_La_mut2

data_processing:
Sequencing was carried out on an Illumina HiSeq2500. Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the Human genome (HG19) using Tophat2
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: Tab-delimited .txt files include the DESEQ2 output for the Total RNA vs IP Comparisons.  Columns to the right of the baseMean column represent DEseq2 output.  The baseMean is a mean for the counts from the various samples. The log2FoldChange measures enrichment in the RIP sample and is reported on a logarithmic scale to base 2. The lfcSE is the standard error estimate for the log2 fold change estimate. The padj is an adjusted p value or q-value, which is a measure of false discovery rate (Benjamini and Hochberg). Columns to the left of baseMean include gene identifiers, gene symbol, Entrez Gene ID, Alias and description. The raw count data for each sample is provided.

growth_protocol: The cells were cultured in advance DMEM supplement with 2 mM L-glutamine (Life Technologies) and 9% FBS (Atlanta Biologicals).

extract_protocol:
gfp-Tagged La was immunoprecipiateted from cells using gfp-specific antibodies. RNA was extracted from the RIP pelltes by the Phenol/Cloroform method.
RIP-seq - To prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA), 100-200 ng of total or IP RNA was used following the protocol described by the manufacturer.

treatment_protocol: Stable HEK293 lines were generated by transfecting cells with gfp, gfpLaWT and gfpLaSD (LaK41/200R) using FuGENE® HD Transfection Reagent (Promega) and neomycin selection.

tag: cell line

tag: cell type

value: Human embryonic kidney cells

tag: genotype/variation

value: gfp-La sumoylation deficient (K41/200R) expressing cells

tag: passage

value: 5-10 passage

tag: molecule subtype

value: IP by gfp antibody


title: RNA IP from HEK293 cells expressing sumoylation deficient La mutant  sample 1

description:
processed data file:
Input_sumo_ def_La_mut vs RNA_IP_sumo_def_La_mut .txt
RNA_IP_sumo_def_La_mut1


title: Input RNA from HEK293 cells expressing sumoylation deficient La mutant  sample 2

description:
processed data file:
Input_sumo_ def_La_mut vs RNA_IP_sumo_def_La_mut .txt
Input_sumo_ def_La_mut2

value: Total RNA


title: Input RNA from HEK293 cells expressing gfp-La wild type sample 2

description:
processed data file:
Input_gfp-La_WT vs RNA_IP_gfp-La_WT.txt
Input_gfp-La_WT2

value: gfp-La wild type expressing cells


title: Input RNA from HEK293 cells expressing gfp-La wild type sample 1

description:
processed data file:
Input_gfp-La_WT vs RNA_IP_gfp-La_WT.txt
Input_gfp-La_WT1


title: RNA IP from HEK293 cells expressing gfp-La wild type sample 2

description:
processed data file:
Input_gfp-La_WT vs RNA_IP_gfp-La_WT.txt
RNA_IP_gfp-La_WT2


title: 72T3_Slick_3

status: Public on Nov 14 2017

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

organism: Sciaenops ocellatus

source_name: whole embryo

growth_protocol: All experiments were approved by the institutional animal care and use committee (IACUC) at the University of Texas at Austin (AUP-2014-00375). Embryonic red drum (Sciaenops ocellatus) were collected from brood stock tanks at the Texas Parks and Wildlife – CCA Marine Development Center in Corpus Christi, Texas, USA and transported under constant aeration to the University of Texas Marine Science Institute. Embryos were subsequently treated with formalin (1 ppt) for one hour with aeration to remove any bacteria. Spawns with low fertilization rates or poor egg quality were not used.

extract_protocol:
Thirty pooled embryos or larvae per replicate were homogenized with a Kontes Pellet Pestle Cordless Motor (Sigma-Aldrich, St. Louis, Missouri) in RNAzol (Molecular Research Center, Cincinnati, Ohio). 200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep kit following the protocol described by the manufacturer (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Testing was performed using two different oil types. The first was a naturally weathered oil collected from a slick in the Gulf of Mexico on June 29th, 2010 from the hold of barge number CT02404 (referred to as OFS). The second was a non-weathered source oil MASS recognized as a suitable surrogate for the DWH source oil. Both oils were delivered to the University of Texas Marine Science Institute through proper chain of custody and stored at 4 °C until used. The test was performed in an environmental control chamber set at 25 °C with a 14:10 h light: dark photoperiod. Survival was assessed daily. A minimum of 70% hatching success and 80% subsequent survival was required for the test to be valid.

value: whole embryo

tag: developmental stage


title: RNA IP from HEK293 cells expressing gfp-La wild type sample 1

description:
processed data file:
Input_gfp-La_WT vs RNA_IP_gfp-La_WT.txt
RNA_IP_gfp-La_WT1


title: 72T3_Mass_3


title: 72T2_Slick_2


title: 48T3_Slick_3


title: 48T3_Mass_3


title: 72T1_Mass_1


title: 72T2_Mass_2


title: 48T2_Slick_2


title: 48T2_Mass_2


title: 48T1_Slick_1


title: 24T3_Slick_3


title: 24T2_Slick_2


title: 24T3_Mass_3


title: 48T1_Mass_1


title: 24T1_Mass_1


title: 72C3_Mass_3


title: 24T1_Slick_1


title: 72C3_Slick_3


title: 72C2_Slick_2


title: Input RNA from HEK293 cells expressing sumoylation deficient La mutant  sample 1

description:
processed data file:
Input_sumo_ def_La_mut vs RNA_IP_sumo_def_La_mut .txt
Input_sumo_ def_La_mut1


title: 72C1_Mass_1


title: 72C2_Mass_2


title: 24T2_Mass_2


title: CL63


title: 72C1_Slick_1


title: 48C3_Mass_3


title: 48C2_Mass_2


title: 48C2_Slick_2


title: 48C1_Slick_1


title: 72T1_Slick_1


title: 48C1_Mass_1


title: 24C3_Slick_3


title: 24C2_Slick_2


title: 24C3_Mass_3


title: 24C2_Mass_2


title: 24C1_Mass_1


title: 24C1_Slick_1


title: Control_4_6

status: Public on Oct 16 2017

data_processing:
Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the ZEBRAFISH genome (GRCZ10) using tophat2
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited .txt files include the DESEQ2 output for the BPA vs Control Comparison.  Columns to the right of the Base Mean column represent DEseq2 output.  Control_1_3, Control_4_6, BPA_1_3, and BPA_4_6 contain raw count data for the two control and two BPA exposed liver RNAseq libraries. ensembl_gene_id, external_gene_name, description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers, hsapiens_homolog_ensembl_gene, hgnc_symbol, Human_description and Human_entrez_geneid

treatment_protocol: Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C, and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food (Tetra, Germany).  Fish were acclimated for one week prior to commencing the experiments. Four tanks (80 l/tank) with 20 animals each were prepared for the different experimental groups, two containing water with 100 nM BPA, and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared, from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow-through system.  Following a three-week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.

tag: exposure


title: Liver BPA 1-3

description: mIRNA

data_processing:
Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the ZEBRAFISH genome (GRCZ10) using tophat2
The Comprehensive Analysis Pipeline for microRNA sequencing data (CAP-miRSeq) was used for read pre-processing, alignment, mature/precursor/ novel miRNA detection and quantification, and data visualization. The miRNA-Seq data was aligned to GRCz10 zebrafish genome using miRDeep  a tool for miRNA identification from RNA sequencing data, and Bowtie.
DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited .txt files include the EdgeR output for the BPA vs Control Comparison.  Columns to the right of the logFC column represent EdgeR output.  CNTRL_1.3 CNTRL_4.5 Liver_BPA_1.3 Liver_BPA_4.5  contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol, GeneID, Description and MirBaseID represent miRNA annotation and description information.

value: 100 nM BPA


title: BPA_1_3


title: Liver CNTRL 1-3

description: mIRNA


title: Liver CNTRL 4-5

description: mIRNA


title: BPA_4_6


title: SFM siKLF4-siFN

status: Public on Sep 19 2017

first: Rosandra

middle: N

last: Kaplan

state: Maryland

address: 10 Center Drive

department: Pediatric Oncology Branch

institute: National Institute of Health

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm10 whole genome using STAR 2.4.1d built in Partek Flow
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the Partek E/M model
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: B16-F10 melanoma cells

growth_protocol: SMCs were plated at 5x10^5/mL and allowed to adhere overnight prior to start of the experiment, then treated with siRNA for 72 hours. Media was changed to treatment groups, and cells were cultured for an additional 72 hours. SMCs were lysed, ECM was washed, and B16-F10 cells were plated and cultured for 24 hours prior to RNA isolation

extract_protocol:
Trizol/phenol/chloroform isolation followed by clean-up using the Qiagen mini RNA isolation kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sirna

tag: media

value: SFM


title: SFM siKLF4


title: TCM siNT

value: siNT

value: TCM


title: TCM siFN

value: siFN


title: TCM siKLF4


title: TCM siKLF4-siFN


title: SFM siNT


title: SFM siFN


title: Hap1-B Hi-C

status: Public on May 03 2017

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

description:
TruSeq libraries prepared from 3C template
Hap1.validPairs

data_processing:
Library strategy: HiC-Seq
Raw sequence data was mapped and processed using HiC-Pro v2.7.7 (Servant et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation

source_name: Hap1 WT

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in IMDM (Invitrogen) supplemented with 10% FCS (Clontech), 1% Penicillin-Streptomycin (Invitrogen) and 1% Ultraglutamin (Lonza).

extract_protocol:
Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.

treatment_protocol: CRISPRs targeting WAPL (5’-CACCGCGTTCCATAGTATCCTGTA-3’) and SCC4 (5’-CACCGTACGGGCCTCGATGCGCTG-3’) were cloned into px330 (Addgene plasmid #42230). ∆WAPL and ∆SCC4 HAP1 clones were generated by insertion of a Blasticidine or Puromycin cassette respectively, as previously described (Blomen et al., 2015). ∆WAPL/∆SCC4 cells were generated by knocking out SCC4 in ∆WAPL cells.

value: WT


title: Hap1-C Hi-C


title: Hap1-A Hi-C


title: RNA-Adult-Rod_E_N-E14.5 replicate 1

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Basecalls performed using CASAVA
Transcriptome sequencing data were mapped to the mouse genome mm9 (MGSCv37) using in-house software StrongArm.
We required > 30% of exon have > 30x depth. And then classic FPKM have been calculated by cufflink package( version 2.1.1 along with default parameters and “--frag-bias-correct --multi-read-correct“) based on GENCODE annotation vM7.
For Differential Expression analysis between f-iPSC and r-iPSC, we counted reads by HTSEQ(version 0.6.1p1) and used Voom packge(R 3.23, edgeR 3.12.1, limma 3.26.9) for statical tests. CPM(counts per million) have been provided for iPSC RNA-seq
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: tab-delimited text files include FPKM or CPM values for each Sample

source_name: retina

extract_protocol:
RNA was extracted from freshly isolated retinas using RNeasy Plus Mini kit (Qiagen #74134). Technologies #Q33120)
Libraries were prepared from ~ 500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 2500 sequencers according to the manufacturer’s directions (Illumina.)

value: Wild-type

tag: age

value: embryonic day 14.5


title: Control_1_3


title: Liver BPA 4-6

description: mIRNA


title: 67 Dermatofibrosarcoma protuberans

status: Public on Apr 07 2017

city: Bologna

first: Maria Antonella

last: Laginestra

address: Via di Barbiano 1/10

department: Experimental Oncology Laboratory

country: Italy

institute: IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy

hyb_protocol: Standard 29K Whole-Genome DASL HT Assay hybridization protocol (WGDASL HT Assay Guide)

scan_protocol: Standard 29K Whole-Genome DASL HT Assay scan protocol (WGDASL HT Assay Guide)

data_processing: The data were normalized using Robust spline normalization by lumi package implemented in R Bioconductor  and log2 trasformed

source_name: FFPE

label_protocol: Standard 29K Whole-Genome DASL HT Assay label protocol (WGDASL HT Assay Guide)

extract_protocol: Total RNA was extracted started from FFPE material with RecoverAll Total Nucleic Acid Isolation. For gene expression generation was used the Illumina Whole Genome cDNA-mediated Annealing, Selection, extension, and Ligation (DASL) assay which allows to perform expression profiling of partially degraded RNA, such as commonly found in formalin-fixed, paraffin-embedded (FFPE) samples.

tag: tissue

value: Tumor

tag: disease state

value: Dermatofibrosarcoma protuberans


title: 65 Solitary fibrous

value: Solitary fibrous


title: 60 Fibroblasts

value: Normal Fibroblast

value: Normal


title: 70 FDCS

value: FDCS


title: 59 Fibroblasts


title: 58 Solitary fibrous


title: 66 Dermatofibrosarcoma protuberans


title: 57 Solitary fibrous


title: 68 Dermatofibrosarcoma protuberans


title: 61 Fibroblasts


title: 62 Solitary fibrous


title: 63 Solitary fibrous


title: 64 Solitary fibrous


title: 50 Inflammatory myofibroblastic ALK minus

value: Inflammatory myofibroblastic ALK minus


title: 49 Inflammatory myofibroblastic ALK minus


title: 51 Hemangiopericytoma

value: Hemangiopericytoma


title: 53 Hemangiopericytoma


title: 52 Hemangiopericytoma


title: 55 Solitary fibrous


title: 54 Solitary fibrous


title: 56 Solitary fibrous


title: 46 Inflammatory myofibroblastic ALK plus

value: Inflammatory myofibroblastic ALK plus


title: 45 Inflammatory myofibroblastic ALK plus


title: 47 Inflammatory myofibroblastic ALK plus


title: 41 Desmoid fibromatosis

value: Desmoid fibromatosis


title: 48 Inflammatory myofibroblastic ALK plus


title: 44 Fibromyxoid sarcoma

value: Fibromyxoid sarcoma


title: 43 Fibromyxoid sarcoma


title: 37 Dermatofibrosarcoma protuberans


title: 33 Dermatofibrosarcoma protuberans


title: 35 Dermatofibrosarcoma protuberans


title: 40 Desmoid fibromatosis


title: 39 FDCS


title: 38 Desmoid fibromatosis


title: 34 Dermatofibrosarcoma protuberans


title: 36 Dermatofibrosarcoma protuberans


title: 40 FDCS


title: 38 FDCS


title: 39 Desmoid fibromatosis


title: 37 FDCS


title: 69 FDCS


title: 35 FDCS


title: 96 FDC Castleman

value: Follicular dendritic cells microdissected

value: FDC Castleman


title: 94 FDC Castleman


title: 95 FDC Castleman


title: 41 FDCS


title: 33 FDCS


title: 21 FDCS


title: 20 FDCS


title: 19 FDCS


title: 92 FDC Castleman


title: 93 FDC Castleman


title: 18 FDCS


title: 16 FDCS


title: 15 FDCS


title: 13 FDCS


title: 14 FDCS


title: 12 FDCS


title: 11 FDCS


title: 9 FDCS


title: 7 FDCS


title: 6 FDCS


title: 10 FDCS


title: 8 FDCS


title: 2 FDCS


title: 4 FDCS


title: 3 FDCS


title: 1 FDCS


title: 48C3_Slick_3

first: Gary

last: Hardiman

address: 135 Cannon Street

institute: Medical University of South Carolina

value: whole embryo

tag: concentration


title: 5 FDCS


title: p65 ChIP-seq WT KLA1h

status: Public on Jan 04 2017

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 35

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer, Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
For ChIP-Seq (single end reads), reads were aligned to the mm9 genome (NCBI37) using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.
For RNA-Seq samples (single end reads), reads were aligned to the mm9 genome (NCBI37) using default parameter for RNA-Star. Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, then perform analyses as indicated in the study.
For ChIP-Seq, Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. UCSC Genome Browser BigWig or BigWig hub text files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), peak text files (ChIP-Seq peak data, using default HOMER parameters), and expression text files (RNA-Seq expression data, using default HOMER parameters).  All genomic coordinates are relative to mm9  (NCBI37) mouse assembly.

source_name: bone marrow derived macrophages

growth_protocol:
Peritoneal thioglycollate-elicited macrophages (TGEMs): Primary cells were isolated from 6-8 week-old C57Bl/6 (Harlan Laboratories) male mice. Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3-4 days following peritoneal injection of 2.5 ml thioglycollate. Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 1 – 24 hours. For LXR experiments cells were treated with 1uM GW3965 or 20uM Desmosterol for 24 hours.
Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 1 – 24 hours. For LXR experiments cells were treated with 1uM GW3965 or 20uM Desmosterol for 24 hours.

extract_protocol:
ChIP-Seq: Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 12-15 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles.
RNA-Seq: Sequencing libraries were prepared from polyA enriched mRNA, either as previously described (Kaikkonen M.U. et al. Molecular Cell 51, 310-325 (2013)), or as follows. Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primer (Invitrogen), 0.5 µL of Oligo dT primer (Invitrogen), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.2 µL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacture’s instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 µL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on either a Genome Analyzer II (Illumina) or Hi-Seq 2000 (Illumina) for 51 cycles.

tag: strain background

value: Srebp1 WT

value: bone marrow derived macrophages

tag: treated with

value: KLA for 1 hours

value: p65 (Vendor:Santa Cruz, cat# sc-372, lot# A0314)


title: p65 ChIP-seq WT noTx

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 34

value: none (control)


title: p65 ChIP-seq WT KLA6h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 36

value: KLA for 6 hours


title: AAE9

status: Public on Sep 15 2016

first: Yifeng

last: Xia

address: 10010 North Torrey Pines Road

department: Laboratory of Genetics

institute: Salk Insitute

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequence reads were mapped to the mm9 mouse genome build using RNA-STAR v2.3.0e.
Raw reads of each individual gene were counted and normalized to fpkm using Cuffdiff v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: genes_read_group_tracking file output from Cuffdiff.

source_name: mouse glioblastoma

growth_protocol: Mouse glioblastomas were induced by lentiviral vector expressing HrasG12V and shRNA against p53. Tumor tissues were isolated from mice reached clinical endpoints. Normal brain tissue was trimmed away from GFP+ tumor tissue using a dissecting microscope.

extract_protocol:
RNA was isolated using the Rneasy kit according to manufacturer's protocol with the addition of Dnase (Qiagen).
cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina).

value: glioblastoma


title: AAE6


title: AAE7


title: AAE5

source_name: normal mouse brain

value: brain


title: AAE8


title: BLCA_Cx_212

status: Public on Mar 13 2017

city: Lund

first: Pontus

last: Eriksson

state: Select:

address: Scheelevägen 2

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor R package Affy. Probe intensities were normalized in labeling batches of 24 using RMA. Batches were combined and RMA normalized.
The file Processed_Data_Supplement.txt contains ready-to-use median centered gene expression data for 307 tumor samples, with EntrezID and GeneSymbol. Sample order is derived from ConsensusClusterPlus, performed on the top 50% variance genes (n=7031) and matches the Sjodahl 2017 publication. Metadata: CEL Filename, GEO_SampleName, Labeling Batch, Hybridisation Number, TURB Stage, TURB Grade, Lund 2012 Taxonomy By Centroid Correlation, ConsensusClusterPlus Cluster, Sjodahl 2017 mRNA-cluster/Phenotype, Publication Heatmap Order.

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

value: bladder cancer

tag: stage and grade

value: pT2   G3

tag: labeling batch


title: BLCA_Cx_247


title: BLCA_Cx_255


title: BLCA_Cx_143


title: BLCA_Cx_280

value: pT1   G3


title: BLCA_Cx_200

value: pT2   Gx


title: BLCA_Cx_240


title: BLCA_Cx_131


title: BLCA_Cx_248


title: AAE4


title: BLCA_Cx_268


title: Filter development, replicate 2, hour 18

status: Public on Apr 21 2015

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
Sample 35
FDrep2_hr18

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names (DDB_G ids) and the second its expression. Files ending with "_raw.txt" contain raw expression values while files ending with "_nor.txt" contain normalized expression values.

organism: Dictyostelium discoideum

source_name: Cells developing on nitrocellulose filters

growth_protocol: Dictyostelium discoideum cells were grown in nutrient media (HL-5) to mid-log phase prior to collection for development.

extract_protocol:
TriZol (Life Sciences) -- Cells were scraped (filter) or pelleted (suspension) and disrupted in TriZol. Total RNA was extracted by phenol/chloroform as per manufacturer's instructions.
mRNA was enriched by 2x polyA bead selection (Ambion, Life Sciences). Multiplexed libraries were constructed as outlined in Miranda et al (2013), PMID #23494306.

tag: strain

tag: growth

tag: treatment

value: Development on 5 cm nitrocellulose filters

tag: time point (hour)

tag: replicate


title: Filter development, replicate 2, hour 20

description:
Sample 36
FDrep2_hr20


title: Filter development, replicate 2, hour 16

description:
Sample 34
FDrep2_hr16


title: Filter development, replicate 2, hour 24

description:
Sample 38
FDrep2_hr24


title: Filter development, replicate 2, hour 22

description:
Sample 37
FDrep2_hr22


title: AAE3


title: BLCA_Cx_262


title: Filter development, replicate 2, hour 12

description:
Sample 32
FDrep2_hr12


title: BLCA_Cx_256


title: Filter development, replicate 2, hour 08

description:
Sample 28
FDrep2_hr08


title: BLCA_Cx_201


title: BLCA_Cx_123


title: Filter development, replicate 2, hour 10

description:
Sample 30
FDrep2_hr10


title: Filter development, replicate 2, hour 05

description:
Sample 25
FDrep2_hr05


title: Filter development, replicate 2, hour 07

description:
Sample 27
FDrep2_hr07


title: Filter development, replicate 2, hour 06

description:
Sample 26
FDrep2_hr06


title: Filter development, replicate 2, hour 09

description:
Sample 29
FDrep2_hr09


title: Filter development, replicate 2, hour 03

description:
Sample 23
FDrep2_hr03


title: BLCA_Cx_219


title: Filter development, replicate 2, hour 04

description:
Sample 24
FDrep2_hr04


title: BLCA_Cx_101

value: pT2   G2


title: Filter development, replicate 2, hour 02

description:
Sample 22
FDrep2_hr02


title: Filter development, replicate 2, hour 11

description:
Sample 31
FDrep2_hr11


title: Filter development, replicate 2, hour 00

description:
Sample 20
FDrep2_hr00


title: Filter development, replicate 2, hour 01

description:
Sample 21
FDrep2_hr01


title: Filter development, replicate 1, hour 24

description:
Sample 19
FDrep1_hr24


title: BLCA_Cx_187


title: BLCA_Cx_156


title: Filter development, replicate 1, hour 16

description:
Sample 15
FDrep1_hr16


title: Filter development, replicate 1, hour 14

description:
Sample 14
FDrep1_hr14


title: Filter development, replicate 1, hour 18

description:
Sample 16
FDrep1_hr18


title: TGRL+LpL, biological rep1 (3 pooled replicates)

status: Public on Jan 23 2017

city: Davis

first: Hnin

middle: H

last: Aung

address: 451 E Health Science Dr., GBSF 5404

department: Internal Medicine

institute: University of California, Davis

description: Gene expression data from TGRL lipolysis products (TL).

hyb_protocol: The fragmentation of labeled aRNA samples were hybridized to Human Genome U133A 2.0 Array high-density oligonucleotide arrays. The hybridization, washing, labeling, and scanning of the GeneChips were performed as described in the Affymetrix protocols by the Microarray Core Facility in the UC Davis Genome and Biomedical Sciences Facility.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: The data were analyzed with Microarray Expression Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HBMVEC (triglyceride-rich lipoprotein lipolysis products treated)

label_protocol: Microarray experiments were performed with pooled RNA isolates from each treatment group. A 200 ng aliquot of total RNA from each pooled sample was reverse-transcribed, followed by aRNA Amplification, reverse transcription to synthesize first-strand cDNA, second-strand cDNA Synthesis, in vitro transcription to synthesize labeled aRNA, purification and fragmentation of aRNA as described in the Affymetrix 3´ IVT Express Kit protocol (Affymetrix).

growth_protocol: Human brain microvascular endothelial cells (HBMVEC) were cultured in CSC Complete Medium which includes 10% serum (4Z0-500) (Cell Systems, Kirkland, WA) under an atmosphere of 5 % CO2: 95% air at 37°C.

extract_protocol: total RNA was performed RNeasy Mini Kit (Qiagen) including the DNA digestion step as according to the manufacturer's instructions.

treatment_protocol: HBMVEC were exposed for 3 hr to the following conditions, media, TGRL (150 mg/dL =1.5 mg/mL), lipoprotein lipase (LpL) (2 U/mL), and TGRL lipolysis product (TGRL (150 mg/dL) + LpL (2 U/mL)).

tag: cell type


title: TGRL, biological rep1 (3 pooled replicates)

description: Gene expression data from triglyceride-rich lipoprotein (T).

source_name: HBMVEC (triglyceride-rich lipoprotein treated)

value: Human brain microvascular endothelial cells (HBMVEC)


title: LpL, biological rep1 (3 pooled replicates)

description: Gene expression data from lipoprotein lipase (L).

source_name: HBMVEC (lipoprotein lipase treated)


title: Filter development, replicate 1, hour 12

description:
Sample 13
FDrep1_hr12


title: Media, biological rep1 (3 pooled replicates)

description: Gene expression data from media (M).

source_name: HBMVEC (media treated)


title: Filter development, replicate 1, hour 22

description:
Sample 18
FDrep1_hr22


title: Filter development, replicate 1, hour 04

description:
Sample 5
FDrep1_hr04


title: Filter development, replicate 1, hour 07

description:
Sample 8
FDrep1_hr07


title: Filter development, replicate 1, hour 10

description:
Sample 11
FDrep1_hr10


title: Filter development, replicate 1, hour 09

description:
Sample 10
FDrep1_hr09


title: Filter development, replicate 1, hour 06

description:
Sample 7
FDrep1_hr06


title: Filter development, replicate 1, hour 01

description:
Sample 2
FDrep1_hr01


title: Filter development, replicate 1, hour 00

description:
Sample 1
FDrep1_hr00


title: Filter development, replicate 1, hour 20

description:
Sample 17
FDrep1_hr20


title: Filter development, replicate 1, hour 11

description:
Sample 12
FDrep1_hr11


title: Untreated.1

status: Public on Jul 01 2014

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description: RNA-Seq of Untreated AML3 cells

data_processing:
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to hg18 whole genome using tophat 1.4.1 with parameters –solexa-quals, -p 12, --segment-length 18, -M, -G Homo_sapiens.NCBI36.54.gtf
Aligned reads normalised by library size (number of fragments) and subsequent reads piledup and converted to bigWig format
Genome_build: hg18
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base.  bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.

growth_protocol: OCI-AML3 cells were cultured in suspension in RPMI media supplemented with FBS 20%, Penicllin 5% and L-Glutamine 5%, incubated at 37°C in humidified conditions and 5% CO2. To passage, cells were counted by haemocytometer and either centrifuged to a pellet and resuspended in fresh media or resuspended in 50% fresh media at a concentration of 0.5 x 106/ml every 2-3 days.

extract_protocol:
RNA was extracted using RNA easy mini kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AzaC was dissolved from lyophilised powder into culture-sterile DMSO to produce a 20 mM stock solution and stored as 15μl aliquots at -80°C. For each new experiment a fresh aliquot of AzaC was diluted in RPMI/20% FBS to produce a 2 mM working stock which was diluted directly onto cells in culture.

tag: cell line

value: Untreated


title: Treated.3

description: RNA-Seq of Aza treated AML3 cells

value: Aza Treated


title: Treated.2

description: RNA-Seq of Aza treated AML3 cells


title: Untreated.2

description: RNA-Seq of untreated AML3 cells


title: Untreated.3

description: RNA-Seq of Untreated AML3 cells


title: Treated.1

description: RNA-Seq of Aza treated AML3 cells


title: Filter development, replicate 1, hour 05

description:
Sample 6
FDrep1_hr05