title: Diuron_C2_12_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-36hpf, 5.16 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-36hpf, 5.16 micromol per liter


title: HSCATAC_P1170_15

status: Public on Apr 11 2019

type: SRA

city: Stanford

first: Howard

middle: Y.

last: Chang

state: CALIFORNIA

address: 269 Campus Drive, CCSR 2130

country: USA

institute: Stanford

description:
sample name:
HSCATAC_P1170_15

library_source: genomic

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters.
Paired-end reads were aligned to hg19 using bwa. Duplicates were removed using PICARD tools
Reads were subsequently filtered for alignment quality  and were required to be properly paired.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with raw counts

molecule: genomic DNA

organism: Homo sapiens

source_name: pre-leukemic HSCs

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 7 µL of harvested libraries were amplified in 50 µL PCR for an additional 17 cycles (1.25 µM custom Nextera dual-index PCR primers  in 1x NEBnext High-Fidelity PCR Master using the following PCR conditions: 72°C for 5min; 98°C for 30 s;  Mix)  using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL.  The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries  at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

tag: patient id

tag: patient diagnosis

value: acute myeloid leukemia

tag: cell type

value: pre-leukemic HSCs


title: Circumbracial nectary secretory control replicate 3 (C sec 3C Rep.1)

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

description:
C sec 3C Rep.1
Cotton_protein_counts_B.xlsx

library_source: transcriptomic

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn, normalized by upper-quartile count and reference length
Contigs aligned to cotton reference proteins
Cotton reference proteins annotated with closest Arabidopsis thaliana match
Genome_build: Cotton: UTX-JGI v1.1
Supplementary_files_format_and_content: Cotton_protein_counts_B.xls - Excel file with upper quartile and mRNA-length normalized counts

molecule: total RNA

organism: Gossypium hirsutum

extract_protocol: Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

tag: tissue

value: Near circumbracteal nectary tissue

tag: Stage

value: secretory control


title: Circumbracial nectary secretory replicate 3 (C sec 3 Rep.1)

description:
C sec 3 Rep.1
Cotton_protein_counts_B.xlsx

value: Circumbracteal nectary tissue

value: secretory


title: HSCATAC_P1170_13

description:
sample name:
HSCATAC_P1170_13


title: Blood-VitD+BPH-0min [35v2_0]

type: RNA

city: Quebec

first: Frederic

last: Guenard

address: 2440, Hochelage blvd

country: Canada

institute: Laval University

hyb_protocol: Hybridized target cRNA was stained with streptavidin phycoerythrin.

scan_protocol: Arrays were scanned on an Agilent GeneArray Scanner (Thermo Fisher Scientific Inc.) at an excitation wavelength of 488nm.

data_processing: Raw data were extracted from scanned images using Expression Console (v 1.4; Thermo Fisher Scientific Inc.). Robust Multiarray Analysis method was used to perform background correction and quantile normalization.

label: Biotin

source_name: Blood, VitD+BPH, 0 min

label_protocol: Arrays were processed at the McGill University and Genome Quebec Innovation Centre using standard Affymetrix protocols. RNA was reverse transcribed into cDNA and in-vitro transcription was performed to generate biotin-labeled cRNA.

extract_protocol: Blood samples were collected from an antecubital vein into PAXgene Blood RNA Tubes (Qiagen, Mississauga, Ontario, Canada) before and 180 min after each treatment. Total RNA was isolated and purified from blood samples using PAXgene Blood RNA Kit (Qiagen) according to the manufacturer's instructions..

tag: Sex

value: Female

value: Blood

tag: agent

value: VitD+BPH

tag: time point

value: 0 min


title: HSCATAC_P1170_12

description:
sample name:
HSCATAC_P1170_12


title: HSCATAC_P1170_11

description:
sample name:
HSCATAC_P1170_11


title: Diuron_C1_12_T

city: Koblenz

first: Andreas

last: Schüttler

address: Am Mainzer Tor 1

department: Department Biochemistry and Ecotoxicology

country: Germany

institute: German Federal Institute of Hydrology

description: whole zebrafish embryo, exposed to Diuron, 24hpf-36hpf, 2.34 micromol per liter

hyb_protocol: Agilent Gene Expression Hybridisation Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)

scan_protocol: Agilent DNA Microarray Scanner and Agilent Feature Extraction Software V11.5.1.1, according to manufacturer's protocol.

data_processing: Cyclic loess normalization between all arrays. Software for data normalization: R v3.3.1.

organism: Danio rerio

source_name: whole embryo, exposed to Diuron, 24hpf-36hpf, 2.34 micromol per liter

label_protocol: One-Color Quick Amp Labeling Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)

extract_protocol: Trizol followed by RNeasy MiniKit cleanup (Qiagen) using the manufacturers’ protocols

tag: substance

value: Diuron


title: Circumbracial nectary secretory control replicate 2 (C sec 2C Rep.1)

description:
C sec 2C Rep.1
Cotton_protein_counts_B.xlsx


title: Naproxen_C4_48_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-72hpf, 269.13 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-72hpf, 269.13 micromol per liter

value: Naproxen


title: Blood-BPH-0min [35v1_0]

source_name: Blood, BPH, 0 min

value: BPH


title: Naproxen_C5_48_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-72hpf, 309.14 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-72hpf, 309.14 micromol per liter


title: Circumbracial nectary secretory replicate 1 (C sec 1 Rep.1)

description:
C sec 1 Rep.1
Cotton_protein_counts_B.xlsx


title: Diuron_C2_12_T


title: HSCATAC_P1170_10

description:
sample name:
HSCATAC_P1170_10


title: Bracteal nectary secretory replicate 3 (B sec 3 Rep.1)

description:
B sec 3 Rep.1
Cotton_protein_counts_B.xlsx

source_name: Bracteal nectary secretory replicate 3

value: Bracteal nectary tissue


title: HSCATAC_P1164_96

description:
sample name:
HSCATAC_P1164_96


title: Naproxen_C3_48_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-72hpf, 234.29 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-72hpf, 234.29 micromol per liter


title: Blood-Placebo-180min [33v3_180]

source_name: Blood, Placebo, 180 min

value: Placebo

value: 180 min


title: Circumbracial nectary secretory control replicate 1 (C sec 1C Rep.1)

description:
C sec 1C Rep.1
Cotton_protein_counts_B.xlsx


title: Blood-VitD+BPH-0min [33v4_0]


title: Blood-BPH-180min [35v1_180]

source_name: Blood, BPH, 180 min


title: Naproxen_C3_48_T


title: Naproxen_C2_48_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-72hpf, 177.57 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-72hpf, 177.57 micromol per liter


title: Circumbracial nectary secretory replicate 2 (C sec 2 Rep.1)

description:
C sec 2 Rep.1
Cotton_protein_counts_B.xlsx


title: HSCATAC_P1164_94

description:
sample name:
HSCATAC_P1164_94


title: Bracteal nectary secretory replicate 2 (B sec 2 Rep.1)

description:
B sec 2 Rep.1
Cotton_protein_counts_B.xlsx

source_name: Bracteal nectary secretory replicate 2


title: Blood-VitD+BPH-180min [33v4_180]

source_name: Blood, VitD+BPH, 180 min


title: HSCATAC_P1164_95

description:
sample name:
HSCATAC_P1164_95


title: Bracteal nectary secretory control replicate 3 (B sec 3C Rep.1)

description:
B sec 3C Rep.1
Cotton_protein_counts_B.xlsx

value: Near bracteal nectary tissue


title: Blood-Placebo-0min [33v3_0]

source_name: Blood, Placebo, 0 min


title: Bracteal nectary secretory control replicate 2 (B sec 2C Rep.1)

description:
B sec 2C Rep.1
Cotton_protein_counts_B.xlsx


title: HSCATAC_P1164_9

description:
sample name:
HSCATAC_P1164_9

value: acute myeloid leukemia


title: Naproxen_C1_48_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-72hpf, 134.58 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-72hpf, 134.58 micromol per liter


title: HSCATAC_P1164_92

description:
sample name:
HSCATAC_P1164_92

value: pre-leukemic HSCs


title: HSCATAC_P1164_93

description:
sample name:
HSCATAC_P1164_93


title: Bracteal nectary secretory replicate 1 (B sec1 Rep.1)

description:
B sec1 Rep.1
Cotton_protein_counts_B.xlsx

source_name: Bracteal nectary secretory replicate 1


title: Bracteal nectary secretory control replicate 1 (B sec 1C Rep.1)

description:
B sec 1C Rep.1
Cotton_protein_counts_B.xlsx


title: HSCATAC_P1164_90

description:
sample name:
HSCATAC_P1164_90


title: E6_3

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

country: China

institute: Hainan University

data_processing:
paired-end sequencing on an Illumina Hiseq4000
Cutadapt  was utilized to remove reads containing undetermined bases, adaptors, and low quality bases. Then sequence quality was verified using FastQC  (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).

organism: Mus musculus

source_name: NIH/3T3 cells expressing BPV-13 E6

extract_protocol: Animal Tissue RNA Purification Kit (Product #TRK-1002; LC Sciences, Hangzhou, China).

value: embryo

tag: cell line

value: NIH/3T3 cells expressing BPV-13 E6

tag: cell passages

value: fibroblast


title: E6_2


title: HSCATAC_P1164_8

description:
sample name:
HSCATAC_P1164_8

source_name: pre-leukemic HSCs


title: Naproxen_C4_48_T


title: E6_1


title: Blood-BPH-0min [33v1_0]


title: Blood-BPH-180min [33v1_180]


title: Blood-VitD-0min [33v2_0]

source_name: Blood, VitD, 0 min

value: VitD


title: HSCATAC_P1164_89

description:
sample name:
HSCATAC_P1164_89


title: Blood-VitD-180min [32v4_180]

source_name: Blood, VitD, 180 min

value: Female


title: Naproxen_C1_48_T


title: Naproxen_Control_24_C.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-48hpf, 0 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-48hpf, 0 micromol per liter


title: HSCATAC_P1164_91

description:
sample name:
HSCATAC_P1164_91


title: Blood-VitD-0min [32v4_0]

value: Blood


title: HSCATAC_P1164_88

description:
sample name:
HSCATAC_P1164_88


title: Naproxen_Control_24_C


title: NH_GFP_2

source_name: NIH/3T3 cells expressing GFP

value: NIH/3T3 cells expressing GFP


title: HSCATAC_P1164_87

description:
sample name:
HSCATAC_P1164_87


title: Blood-BPH-180min [32v3_180]


title: Diclofenac_C3_24_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-48hpf, 6.52 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-48hpf, 6.52 micromol per liter

value: Diclofenac


title: NH_GFP_1


title: HSCATAC_P1164_86

description:
sample name:
HSCATAC_P1164_86


title: HSCATAC_P1164_85

description:
sample name:
HSCATAC_P1164_85


title: Naproxen_C5_24_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-48hpf, 309.14 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-48hpf, 309.14 micromol per liter


title: Naproxen_C3_24_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-48hpf, 234.29 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-48hpf, 234.29 micromol per liter


title: Blood-Placebo-180min [32v1_180]

source_name: Blood, Placebo, 180 min


title: P5 PDGFRa-GFP ATAC-seq

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to rn5 whole genome by Bowtie2 with default options
Peak calling was performed using Model-based analysis of MACS version 2.12 with special parameter: --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01, to call peak. And we calculated the peak_RPKM, then GSEA (v2.2.0) was used to analyze the enrichment of signature gene sets from different subtypes in E14.5 and P5 PDGFR?-GFP cells. Homer was used to generate the normalized UCSC bedgraph files (the total number of tags is normalized to 10 million) to show the genome browser tracks.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated by Homer; narrowPeak file was generated by MACS2

source_name: cerebral cortex

treatment_protocol: We isolated nuclei of 50,000 sorted cells from the cortex of PDGFRα-GFP mouse in a cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) by exclude GFP- and 7-AAD+ cells. After spinning down at 500 × g for 10 min at 4 °C, nuclei were resuspended in transposition mix containing TD (2× reaction buffer), TDE1 (Nextera Tn5 Transposase) at 37°C for 30 min. The samples were purified using a Qiagen MinElute kit. Transposed DNA fragments were subsequently amplified and purified using Qiagen MinElute PCR Purification Kit. Libraries were generated using the Ad1_noMX and Ad2.1-2.4 barcoded primers and were amplified for 11 total cycles. Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500 with 75 bp single-end reads.

tag: genotype

value: hGFAP normal

tag: developmental stage

tag: strain

value: PDGFRa-GFP in E14.5


title: Naproxen_C4_24_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-48hpf, 269.13 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-48hpf, 269.13 micromol per liter

value: Naproxen


title: E14.5 PDGFRa-GFP ATAC-seq

extract_protocol: Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500 with 75 bp single-end reads.

value: PDGFRa normal


title: Naproxen_C2_24_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-48hpf, 177.57 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-48hpf, 177.57 micromol per liter


title: HSCATAC_P1164_84

description:
sample name:
HSCATAC_P1164_84


title: GBM_dpi35

description:
total 6054
barcodes.tsv.gz;genes.tsv.gz;matrix.mtx.gz

data_processing:
Fastq files were demultiplexed, mapped to Mouse Genome (mm10) and generated filtered gene-by-cell matrics by 10x Genomics’ cellranger using default settings.
Genes-by-cells matrix market file with cell barcode and gene name tab-delimited text files

source_name: mouse glioblastoma from cerebral cortex region

extract_protocol: Libraries were prepared with 10X Genomics protocol

treatment_protocol: For single cell RNA-seq of tumor cells, the tumor tissues were digested by TryplE with collagenase Ⅰ, and single cell suspension was treated by Red Blood Cell Lysis Buffer. Cells from tumor tissues at dpi 35 were sequenced by 10x genomics. ChromiumTM Single cell 3’ User Guide A Single Cell Gel Bead kit, Single cell chip kit and Single cell library kit were used along with a 10× GemCode Single Cell Instrument, per the manufacturer's manuals.

value: GBM


title: Blood-VitD+BPH-0min [32v2_0]

source_name: Blood, VitD+BPH, 0 min

value: VitD+BPH

value: 0 min


title: HSCATAC_P1164_83

description:
sample name:
HSCATAC_P1164_83

value: acute myeloid leukemia


title: Naproxen_C1_24_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-48hpf, 134.58 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-48hpf, 134.58 micromol per liter


title: Blood-Placebo-0min [32v1_0]

source_name: Blood, Placebo, 0 min

value: Placebo


title: Naproxen_Control_3_C.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-27hpf, 0 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-27hpf, 0 micromol per liter


title: Blood-Placebo-180min [29v4_180]

value: 180 min


title: GBM_dpi25

description: total 6796

data_processing:
library strategy: Drop-seq
Raw sequence data was first filtered to remove all read pairs with a barcode base quality of less than 10. The second read (50 or 60 bp) was then trimmed at the 5’ end to remove any TSO adapter sequence,  and at the 3’ end to remove polyA tails of length 6 or greater.
Then aligned reads to mm10 reference by STAR with default settings.
Uniquely mapped reads were grouped by cell barcode. To digitally count gene transcripts, a list of UMIs in each gene, within each cell, was assembled, and UMIs within ED = 1 were merged together. The total number of distinct UMI sequences was counted, and this number was reported as the number of transcripts of that gene for a given cell.
Normalize total number of detected UMIs from each gene in each cell to 10,000
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited table of normalized UMIs

extract_protocol:
For single cell RNA-seq of tumor cells, the tumor tissues were digested by TryplE with collagenase Ⅰ, and single cell suspension was treated by Red Blood Cell Lysis Buffer (Sigma, 11814389001). Cells from tumor tissues at dpi 25 were sequenced by drop-seq.
Libraries were prepared with Drop-seq protocol

treatment_protocol: P1-P6 GFP+ pups are euthanized one the ice, decapitated, and the brain was immediately removed and submerged in fresh ice-cold HBSS-HEPES(catalog), cortices were carefully dissected and minced by blade. The tissue pieces were incubated with 3 ml of TrypLE 5X solution(catalog) for 10 min in 37 incubator following by gentle trituration through Pasteur pipettes with polished tip for ten times, filtered the suspension by 40mm strainer, centrifuge at 1300rpm to get the single cell pellet. Collect the GFP+ alive cell by excluding the population of GFP- and 7-AAD+ (catalog) death cells performed on MoFloXDP (Beckman Coulter).

value: mouse glioblastoma from cerebral cortex region


title: Naproxen_Control_3_C


title: HSCATAC_P1164_82

description:
sample name:
HSCATAC_P1164_82

source_name: pre-leukemic HSCs

value: pre-leukemic HSCs


title: Blood-VitD+BPH-0min [29v3_0]


title: Blood-BPH-180min [29v2_180]

source_name: Blood, BPH, 180 min

value: BPH


title: Blood-Placebo-0min [29v4_0]

value: Female


title: Blood-BPH-0min [29v2_0]

source_name: Blood, BPH, 0 min

value: Blood


title: HSCATAC_P1164_81

description:
sample name:
HSCATAC_P1164_81


title: Naproxen_C5_3_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-27hpf, 309.14 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-27hpf, 309.14 micromol per liter


title: Blood-VitD+BPH-180min [29v3_180]

source_name: Blood, VitD+BPH, 180 min


title: Naproxen_C3_3_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-27hpf, 234.29 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-27hpf, 234.29 micromol per liter


title: HSCATAC_P1164_80

description:
sample name:
HSCATAC_P1164_80


title: HSCATAC_P1164_7

description:
sample name:
HSCATAC_P1164_7


title: HSCATAC_P1164_79

description:
sample name:
HSCATAC_P1164_79


title: HSCATAC_P1164_78

description:
sample name:
HSCATAC_P1164_78


title: HSCATAC_P1164_77

description:
sample name:
HSCATAC_P1164_77


title: HSCATAC_P1164_76

description:
sample name:
HSCATAC_P1164_76


title: HSCATAC_P1164_75

description:
sample name:
HSCATAC_P1164_75


title: Blood-Placebo-180min [28v4_180]


title: Naproxen_C1_3_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-27hpf, 134.58 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-27hpf, 134.58 micromol per liter


title: HSCATAC_P1164_74

description:
sample name:
HSCATAC_P1164_74


title: Blood-VitD-180min [29v1_180]

source_name: Blood, VitD, 180 min

value: VitD


title: Naproxen_Control_6_C.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-30hpf, 0 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-30hpf, 0 micromol per liter


title: Blood-Placebo-0min [28v4_0]


title: Blood-BPH-180min [28v3_180]


title: Naproxen_C5_6_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-30hpf, 309.14 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-30hpf, 309.14 micromol per liter


title: Blood-VitD-0min [29v1_0]

source_name: Blood, VitD, 0 min


title: Naproxen_C5_3_T.1


title: Naproxen_C4_3_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-27hpf, 269.13 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-27hpf, 269.13 micromol per liter


title: Blood-VitD+BPH-0min [28v1_0]


title: Naproxen_C4_6_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-30hpf, 269.13 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-30hpf, 269.13 micromol per liter


title: HSCATAC_P1164_73

description:
sample name:
HSCATAC_P1164_73


title: Blood-BPH-0min [28v3_0]


title: Blood-VitD-180min [28v2_180]


title: Naproxen_C2_3_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-27hpf, 177.57 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-27hpf, 177.57 micromol per liter


title: Blood-VitD+BPH-180min [28v1_180]


title: Naproxen_C5_6_T


title: Blood-VitD-0min [28v2_0]


title: Naproxen_C1_6_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-30hpf, 134.58 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-30hpf, 134.58 micromol per liter


title: Naproxen_Control_6_C


title: Naproxen_C2_6_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-30hpf, 177.57 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-30hpf, 177.57 micromol per liter


title: Naproxen_C3_6_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-30hpf, 234.29 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-30hpf, 234.29 micromol per liter


title: HSCATAC_P1164_72

description:
sample name:
HSCATAC_P1164_72

source_name: pre-leukemic HSCs


title: HSCATAC_P1164_71

description:
sample name:
HSCATAC_P1164_71


title: HSCATAC_P1164_70

description:
sample name:
HSCATAC_P1164_70


title: Blood-BPH-180min [26v4_180]

source_name: Blood, BPH, 180 min


title: Blood-BPH-0min [26v4_0]

source_name: Blood, BPH, 0 min


title: Naproxen_Control_12_C.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-36hpf, 0 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-36hpf, 0 micromol per liter


title: HSCATAC_P1164_6

description:
sample name:
HSCATAC_P1164_6


title: HSCATAC_P1164_69

description:
sample name:
HSCATAC_P1164_69


title: HSCATAC_P1164_68

description:
sample name:
HSCATAC_P1164_68


title: Naproxen_C4_12_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-36hpf, 269.13 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-36hpf, 269.13 micromol per liter


title: Naproxen_Control_12_C


title: HSCATAC_P1164_66

description:
sample name:
HSCATAC_P1164_66


title: Blood-VitD+BPH-180min [26v3_180]

source_name: Blood, VitD+BPH, 180 min


title: Blood-VitD-180min [26v2_180]


title: Naproxen_C5_12_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-36hpf, 309.14 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-36hpf, 309.14 micromol per liter


title: HSCATAC_P1164_65

description:
sample name:
HSCATAC_P1164_65


title: HSCATAC_P1164_67

description:
sample name:
HSCATAC_P1164_67


title: HSCATAC_P1164_64

description:
sample name:
HSCATAC_P1164_64


title: Blood-VitD-180min [33v2_180]

source_name: Blood, VitD, 180 min


title: Blood-VitD+BPH-0min [26v3_0]

source_name: Blood, VitD+BPH, 0 min


title: Blood-VitD-0min [26v2_0]


title: Blood-Placebo-180min [26v1_180]

source_name: Blood, Placebo, 180 min


title: Naproxen_C3_12_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-36hpf, 234.29 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-36hpf, 234.29 micromol per liter


title: Naproxen_C2_12_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-36hpf, 177.57 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-36hpf, 177.57 micromol per liter


title: Naproxen_C1_12_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-36hpf, 134.58 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-36hpf, 134.58 micromol per liter


title: Blood-Placebo-0min [26v1_0]

source_name: Blood, Placebo, 0 min


title: miR-3679-5p_mimics_rep1

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

description: gene expression data of AGO2 bound larg RNAs

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

label: biotin

source_name: human umblical vein endothelial cells

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: HUVECs were purchased from Lonza Japan Ltd. (Tokyo, Japan) and cultured and passaged every 2 or 3 days in EBM-2 complete medium composed of EBM-2 Basal Medium (Lonza) supplemented with EGM-2 SingleQuot Kit Suppl. & Growth Factors (Lonza) and 3% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA). We sub-cultured HUVECs when they reached 80 to 90% confluence to avoid excessive floaters. HUVECs were used within passage 4 to 7 for all experiments in this work. Human monocyte cell line U937 was purchased from JCRB Cell Bank (Osaka, Japan) and grown and passaged every 2 or 3 days in RPMI1640 (Thermo Fisher Scientific) supplemented with 1% penicillin/streptomycin (Wako, Osaka, Japan) and 10% FBS. All cells were cultured at 37 ºC and 5% CO2 in a humidified incubator.

extract_protocol: RIP was performed using a RiboCluster Profiler RIP assay kit for microRNA (#RN1005; MBL) in accordance with manufacturer’s protocol. Briefly, HUVECs transfected with miR-3679-5p or negative control miRNA mimics were stimulated with TNF-α and then immunoprecipitated with magnetic Dynabeads M-280 (Thermo Fisher Scientific) coupled with anti-EIF2C2/AGO2 mouse monoclonal antibody (MBL, Aichi, Japan). A mouse IgG2a Isotype control antibody (MBL) was used as a negative control and confirmed proper functioning of the RIP assay (data not shown). Large RNAs and small RNAs were separately extracted from antibody immobilized beads-RNP complex and then the AGO2 bound large RNAs were subjected to microarray analysis.

treatment_protocol: Cells were incubated with a mixture of 100 nM miRNA mimics and Lipofectamine RNAiMax (Thermo Fisher Scientific, Waltham, MA). 80-90% confluent HUVECs plates were washed with PBS once and then serum starved in EBM-2 Basal Medium containing 0.5% FBS for 16 hrs. HUVECs were stimulated with 10 ng/ml TNF-α (Peprotech, Rocky Hill, NJ) for 4 hrs.

tag: conditions

value: miR-3679-5p mimics

tag: fraction

value: argonaute 2 (AGO2) bound large RNA


title: Naproxen_Control_72_C

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-96hpf, 0 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-96hpf, 0 micromol per liter


title: miR-3679-5p_mimics_rep2


title: Blood-BPH-0min [25v4_0]


title: HSCATAC_P1164_62

description:
sample name:
HSCATAC_P1164_62


title: Blood-BPH-180min [25v4_180]


title: Naproxen_Control_72_C.1


title: Blood-VitD-180min [25v3_180]


title: Blood-VitD-0min [25v3_0]

source_name: Blood, VitD, 0 min


title: control_miRNA_mimics_rep1

value: control miRNA mimics


title: KYNR-A-HRP3-Input-Repl1

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to human genome hg19 and hg38 using bowtie 1.0 with n = 1 as parameter
Bigwig files were created using  Galaxy/deepTools, duplicated tags were ignored
Genome_build: hg19, hg38
Supplementary_files_format_and_content: bigwig

growth_protocol: HepG2 human embryonic kidney cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS.

extract_protocol:
For ChIP-Seq samples were crosslinked using Formaldehyde, Sonicated and chromatin was extracted using the GFP or H3K36me3 antibody. DNA was purified using the AMPure XP system.
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations

treatment_protocol: Cells were infected with Lentiviral constructs expressing the respective HRP3 construct

tag: chip antibody

value: GFP (gta-20, ChromoTek)

tag: genotype/variation

value: HRP3 KYNR-A expressing cells


title: Naproxen_C5_72_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-96hpf, 309.14 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-96hpf, 309.14 micromol per liter

value: Naproxen


title: KYNR-A-HRP3-Repl2


title: KYNR-A-HRP3-Input-Repl2


title: Naproxen_C4_72_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-96hpf, 269.13 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-96hpf, 269.13 micromol per liter


title: Naproxen_C5_72_T


title: HSCATAC_P1164_61

description:
sample name:
HSCATAC_P1164_61

source_name: pre-leukemic HSCs

tag: patient id

tag: patient diagnosis


title: HSCATAC_P1164_63

description:
sample name:
HSCATAC_P1164_63

tag: cell type


title: KYNR-A-HRP3-Repl1


title: control_miRNA_mimics_rep2


title: HSCATAC_P1164_60

description:
sample name:
HSCATAC_P1164_60


title: Blood-Placebo-180min [25v2_180]

tag: tissue


title: Naproxen_C4_72_T


title: KNR-A-HRP3-Input-Repl2

value: HRP3 KNR-A expressing cells


title: Naproxen_C3_72_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-96hpf, 234.29 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-96hpf, 234.29 micromol per liter


title: HSCATAC_P1164_59

description:
sample name:
HSCATAC_P1164_59


title: HSCATAC_P1164_5

description:
sample name:
HSCATAC_P1164_5


title: Blood-Placebo-0min [25v2_0]

tag: Sex

value: 0 min


title: HSCATAC_P1164_58

description:
sample name:
HSCATAC_P1164_58

value: acute myeloid leukemia


title: Blood-VitD+BPH-0min [25v1_0]

tag: agent

value: VitD+BPH


title: KNR-A-HRP3-Repl1


title: KNR-A-HRP3-Repl2


title: HSCATAC_P1164_57

description:
sample name:
HSCATAC_P1164_57


title: HSCATAC_P1164_56

description:
sample name:
HSCATAC_P1164_56


title: pKC-rep2

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: primary keratinocyte

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

value: human neonatal epidermal keratinocytes

tag: passages


title: HSCATAC_P1164_55

description:
sample name:
HSCATAC_P1164_55


title: Naproxen_C2_72_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-96hpf, 177.57 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-96hpf, 177.57 micromol per liter

tag: substance


title: MUC-rep2

source_name: urine cells

value: urine cells

value: male


title: HSCATAC_P1164_54

description:
sample name:
HSCATAC_P1164_54

value: pre-leukemic HSCs


title: Blood-VitD+BPH-0min [18v4_0]

value: Male

tag: time point


title: Blood-VitD+BPH-180min [18v4_180]

source_name: Blood, VitD+BPH, 180 min

value: Blood

value: 180 min


title: Naproxen_C1_72_T.1

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-96hpf, 134.58 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-96hpf, 134.58 micromol per liter


title: Blood-BPH-0min [18v3_0]

source_name: Blood, BPH, 0 min

value: BPH


title: Naproxen_C5_72_R.1

description: whole zebrafish embryo, exposed to Naproxen, 309.14 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: Naproxen_C5_72_R


title: pKC-rep1


title: Blood-Placebo-180min [18v2_180]

source_name: Blood, Placebo, 180 min

value: Placebo


title: HSCATAC_P1164_53

description:
sample name:
HSCATAC_P1164_53


title: MUC-rep1


title: MiKSC-rep2

source_name: induced keratinocyte stem cell

value: urine cells-induced keratinocyte stem cell


title: Naproxen_C1_72_T


title: Naproxen_C3_72_R.1

description: whole zebrafish embryo, exposed to Naproxen, 234.29 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: HSCATAC_P1164_52

description:
sample name:
HSCATAC_P1164_52


title: HSCATAC_P1164_51

description:
sample name:
HSCATAC_P1164_51


title: MiKSC-rep1


title: Naproxen_C3_72_R


title: NH_GFP_3

source_name: NIH/3T3 cells expressing GFP

value: embryo

tag: cell line

value: NIH/3T3 cells expressing GFP

tag: cell passages

value: fibroblast


title: HSCATAC_P1164_50

description:
sample name:
HSCATAC_P1164_50


title: FUC-rep1

value: female


title: HSCATAC_P1164_4

description:
sample name:
HSCATAC_P1164_4


title: Naproxen_C4_72_R.1

description: whole zebrafish embryo, exposed to Naproxen, 269.13 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf

value: Naproxen


title: Blood-VitD-180min [18v1_180]

source_name: Blood, VitD, 180 min

value: VitD


title: Blood-BPH-180min [18v3_180]

source_name: Blood, BPH, 180 min


title: Blood-VitD-0min [18v1_0]

value: 0 min


title: Naproxen_C2_72_R.1

description: whole zebrafish embryo, exposed to Naproxen, 177.57 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: Blood-VitD+BPH-180min [25v1_180]

value: Female

value: VitD+BPH


title: Blood-Placebo-180min [14v4_180]


title: HSCATAC_P1164_49

description:
sample name:
HSCATAC_P1164_49

value: acute myeloid leukemia


title: Blood-Placebo-0min [18v2_0]

source_name: Blood, Placebo, 0 min


title: Blood-Placebo-0min [14v4_0]


title: FUC-rep2

value: urine cells


title: FiKSC-rep2


title: Naproxen_C1_72_R.1

description: whole zebrafish embryo, exposed to Naproxen, 134.58 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: HSCATAC_P1164_47

description:
sample name:
HSCATAC_P1164_47

value: pre-leukemic HSCs


title: HSCATAC_P1164_46

description:
sample name:
HSCATAC_P1164_46


title: HSCATAC_P1164_45

description:
sample name:
HSCATAC_P1164_45


title: HSCATAC_P1164_48

description:
sample name:
HSCATAC_P1164_48


title: PPCD CDDL 91 (P7)

city: Los Angeles

first: Anthony

middle: John

last: Aldave

state: California

address: 200 Stein Plaza, DS 3-143

department: Ophthalmology

institute: University of California, Los Angeles

data_processing:
The FASTQ files containing the RNA-sequencing data were aligned with CLC Biomedical Genomic Workbench to the hg38 genome.
Using CLC Biomedical Genomic Workbench, reads and read-depth were transformed to reads per kilobase per million (RPKM) values, a normalized quantity that accounts for gene size.
These data were annotated using the Ensemble 88 transcript database.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a txt file with Ensemble 88 gene symbol ID in the first column. Sample names are given on the first row with RPKM values for each gene running down the column.

source_name: ex vivo corneal endothelium

growth_protocol: Cultured cells were grown or Human Endothelial SFM.

extract_protocol:
TriReagent extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNeasy Clean-Up Kit.
Enrichment for poly(A) RNAs was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module, followed by library preparation using the PrepX Complete ILM DNA Library Kit. Libraries were prepared as per the manufacturer's instructions.

value: endothelial

tag: age

tag: disease

value: posterior polymorphous corneal dystrophy


title: Blood-VitD+BPH-180min [14v3_180]

value: Male

value: Blood

value: 180 min


title: Naproxen_C2_72_R


title: Bulk_H1_H9

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

description:
bulk_NCADpos_H1_counts.txt
bulk_NCADpos_H1_normalilzed_logcounts.txt
bulk_NCADpos_H9_counts.txt
bulk_NCADpos_H9_normalilzed_logcounts.txt

data_processing:
Sequencing outputs of the bulk and NCADpos libraries were run through CellRanger mkfastq, version 2.1.1 (10x GENOMICS).
The resulting fastq files were grouped by sample (across sequencing runs) and run through CellRanger count, version 2.1.1, to obtain bam alignment files. GRCh38 was used as a reference.
The data from bulk- and NCADpos libraries were pooled by running through CellRanger aggr, version 2.1.1 to obtain unique molecular identifiers (UMIs) matrices.
The bam files were also used to determine and annotate the sex of each cell (male-derived H1 or female-derived H9) based on the coverage of the sex chromosomes using original scripts at Princess Margaret Genomics Centre.
From the pooled UMI matrices, H1 and H9 were separated based on the annotation. To remove doublets and poor-quality cells, cells were excluded from subsequent analysis if they were outliers in terms of number of genes, number of UMIs, and percentage of mitochondrial genes using the R package scater (ver.1.8.0; nmads = 3). Normalization of cell-specific biases and removal of technical noise were performed using scran package (ver. 1.8.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files including either UMI counts or normalized logcounts for individual genes (rows) in individual cells (QCed; columns). Gene symbols and ENSEMBL gene IDs were in the first and second column, respectively. Barcodes in the first row consist of cellular barcodes and library IDs (bulk or NCADpos).

molecule: polyA RNA

source_name: H1 and H9 hESCs

growth_protocol: The cells were maintained as previously described (Sachlos et al., 2012) in feeder-free culture on Matrigel-coated plates with mouse embryonic fibroblast (MEF)-conditioned media (Xu et al., 2001) supplemented with 8 ng/ml bFGF.

extract_protocol:
The cells were encapsulated into single droplets using Chromium Controller (10x GENOMICS) according to the manufacturer's protocol.
Libraries were prepared using Chromium Single Cell 3' Reagent Kits v2 (10x GENOMICS) according to the manufacturer's protocol.

value: male and female

tag: population

value: 7-AAD negative


title: NCADpos_H1_H9

source_name: NCAD-positive H1 and H9 hESCs

value: 7-AAD negative ; PE-anti-NCAD (BD, clone 8C11) positive


title: HSCATAC_P1164_44

description:
sample name:
HSCATAC_P1164_44

source_name: pre-leukemic HSCs


title: Naproxen_Control_48_C

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-72hpf, 0 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-72hpf, 0 micromol per liter


title: Blood-VitD+BPH-0min [14v3_0]

source_name: Blood, VitD+BPH, 0 min


title: Blood-VitD-0min [14v2_0]

source_name: Blood, VitD, 0 min


title: K18G21Y22A-HRP3-Input-Repl2

description:
K18G21Y22A-Input-repl1+2-hg19.bigwig
K18G21Y22A-Input-repl1+2-hg38.bigwig

value: HRP3 K18G21Y22A expressing cells


title: Control 223 (C7)

value: Control


title: Naproxen_C1_72_R

value: Naproxen


title: H3K36me3

value: H3K36me3 (ab9050, abcam)


title: FiKSC-rep1

value: urine cells-induced keratinocyte stem cell

value: female


title: K18G21Y22A-HRP3-Input-Repl1


title: K18G21Y22A-HRP3-Repl2

description:
K18G21Y22A-repl1+2-hg19.bigwig
K18G21Y22A-repl1+2-hg38.bigwig

value: GFP (gta-20, ChromoTek)


title: HSCATAC_P1164_43

description:
sample name:
HSCATAC_P1164_43

value: acute myeloid leukemia


title: Blood-VitD-180min [14v2_180]

value: VitD


title: Blood-VitD-180min [13v4_180]


title: Naproxen_C5_48_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-72hpf, 309.14 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-72hpf, 309.14 micromol per liter


title: Blood-BPH-0min [14v1_0]

value: BPH

value: 0 min


title: Blood-BPH-180min [14v1_180]

value: Male


title: Naproxen_Control_48_C.1


title: HSCATAC_P1164_41

description:
sample name:
HSCATAC_P1164_41

value: pre-leukemic HSCs


title: K18G21Y22A-HRP3-Repl1


title: HSCATAC_P1164_3

description:
sample name:
HSCATAC_P1164_3


title: HSCATAC_P1164_40

description:
sample name:
HSCATAC_P1164_40


title: HSCATAC_P1164_42

description:
sample name:
HSCATAC_P1164_42


title: Y22A-HRP3-Input-Repl1

description:
Y22A-Input-repl1+2-hg19.bigwig
Y22A-Input-repl1+2-hg38.bigwig

value: HRP3 Y22A expressing cells


title: Y22A-HRP3-Input-Repl2


title: K18A-HRP3-Input-Repl2

description:
K18A-Input-repl1+2-hg19.bigwig
K18A-Input-repl1+2-hg38.bigwig

value: HRP3 K18A expressing cells


title: Y22A-HRP3-Repl2

description:
Y22A-repl1+2-hg19.bigwig
Y22A-repl1+2-hg38.bigwig


title: HSCATAC_P1164_37

description:
sample name:
HSCATAC_P1164_37


title: HSCATAC_P1164_39

description:
sample name:
HSCATAC_P1164_39


title: Y22A-HRP3-Repl1


title: K18A-HRP3-Input-Repl1


title: Blood-VitD-0min [13v4_0]

value: Blood


title: HSCATAC_P1164_36

description:
sample name:
HSCATAC_P1164_36


title: HSCATAC_P1164_38

description:
sample name:
HSCATAC_P1164_38


title: HSCATAC_P1164_35

description:
sample name:
HSCATAC_P1164_35


title: Blood-BPH-0min [13v3_0]


title: K18A-HRP3-Repl1

description:
K18A-repl1+2-hg19.bigwig
K18A-repl1+2-hg38.bigwig


title: K18A-HRP3-Repl2


title: HSCATAC_P1164_34

description:
sample name:
HSCATAC_P1164_34


title: Blood-Placebo-0min [13v2_0]

value: Placebo


title: Blood-Placebo-180min [13v2_180]

value: 180 min


title: Blood-VitD+BPH-180min [13v1_180]

source_name: Blood, VitD+BPH, 180 min

value: VitD+BPH


title: Blood-BPH-180min [10v4_180]


title: HSCATAC_P1164_32

description:
sample name:
HSCATAC_P1164_32


title: HSCATAC_P1164_33

description:
sample name:
HSCATAC_P1164_33


title: WT-HRP3-Input-Repl2

description:
WT-Input-repl1+2-hg19.bigwig
WT-Input-repl1+2-hg38.bigwig

value: HRP3 WT expressing cells


title: WT-HRP3-Input-Repl1


title: Blood-VitD+BPH-0min [13v1_0]


title: Blood-VitD-180min [10v3_180]


title: Blood-BPH-180min [13v3_180]


title: Blood-BPH-0min [10v4_0]


title: WT-HRP3-Repl2

description:
WT-repl1+2-hg19.bigwig
WT-repl1+2-hg38.bigwig


title: Blood-VitD-0min [10v3_0]


title: HSCATAC_P1164_2

description:
sample name:
HSCATAC_P1164_2


title: HSCATAC_P1164_30

description:
sample name:
HSCATAC_P1164_30


title: hsa-miR-1825

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NCBI Rnor_6.0  whole genome using STAR 2.7
Transcript abundance was estimated in RPKM (reads per kilobase of exon model per million mapped reads) using EdgeR function CPM (McCarthy, J. D, Chen, Yunshun, Smyth, K. G (2012). â€œDifferential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.â€ Nucleic Acids Research, 40(10))
Differentially expressed genes for a given miRNA was obtained based on fold-change in comparison to the cel-miR-67 (control) condition. For this analysis, we used a fold change cut off value of 1.3 to determine up-regulated or down-regulated genes.
Genome_build: NCBI Rnor_6.0 annotation release 106 (GCF_000001895.5)
Supplementary_files_format_and_content: Tab-separated values containing RPKM

organism: Rattus norvegicus

source_name: heart

growth_protocol: Neonatal rat cardiomyocytes were grown in the Dulbecco's modified Eagle medium 4.5 g/l glucose (DMEM, Life Technologies) supplemented with 5% FBS, 20 mg/ml vitamin B12 (Sigma) and with 100 U/ml of penicillin and 100 mg/ml of streptomycin (Sigma) at 37 Â°C in 5% CO2 and humidified atmosphere.

extract_protocol:
Total RNA was isolated from neonatal rat cardiomyocytes 72hr after reverse transfection using the DNA, RNA and protein purification kit (NucleoSpin miRNA) Macherey-Nagel (REF: 740971.50)
TruSeq mRNA protocol

treatment_protocol: Ventricular CMs were isolated from neonatal rat. Briefly, ventricles from neonatal rat (day 0) were separated from the atria, cut into pieces and then dissociated in calcium and bicarbonate-free Hanks with HEPES (CBFHH) buffer containing 1.75 mg/ml trypsin (BD Difco) and 10 mg/ml DNase II (Sigma), using a mechanical and physical stirring. Digestion was performed at room temperature in ten-min steps with collection of the surnatant to fetal bovine serum (FBS, Life Technologies) after each step. The surnatant was collected and centrifuged to pellet the cardiomyocytes, which were then resuspended in Dulbecco's modified Eagle medium 4.5 g/l glucose (DMEM, Life Technologies) supplemented with 5% FBS, 20 mg/ml vitamin B12 (Sigma) and with 100 U/ml of penicillin and 100 mg/ml of streptomycin (Sigma). The collected cells were passed through a cell strainer (40mm, BD Falcon) and then plated onto 100-mm plastic dishes for 2 hr at 37C in 5% CO2 and humidified atmosphere. Then, the surnatant, which contains mostly cardiomyocytes, was collected and counted.The cells were plated in 60-cm primary dishes at the concentration of 1,5*10^6 cells.The miRNAs  were obtained from Dharmacon, Thermo Scientific. After 24 hr miRNAs were transfected into neonatal rat CMs using a standard transfection protocol, at the final concentration of 25 nM. Briefly, the transfection reagent (Lipofectamine RNAiMAX, Life Technologies) was diluted in OPTI-MEM (Life Technologies) and added to the selected miRNAs; 30 min later, each mix, containing the transfection reagents and the miRNAs, was added to the Dulbecco's modified Eagle medium 4.5 g/l glucose (DMEM, Life Technologies) supplemented with 5% FBS and  20 mg/ml vitamin B12 (Sigma) in absence of antibiotics. Twenty-four hours after transfection, culture medium was replaced by fresh medium.

value: heart

tag: treatment

value: transfected with hsa-miR-1825

value: post natal day 0

tag: genotype

value: wild type

value: ventricular cardiomyocytes

tag: strain

value: Wistar


title: HSCATAC_P1164_29

description:
sample name:
HSCATAC_P1164_29

tag: patient id

value: acute myeloid leukemia


title: HSCATAC_P1164_31

description:
sample name:
HSCATAC_P1164_31

tag: patient diagnosis


title: hsa-miR-33b*

value: transfected with hsa-miR-33b*

tag: cell type


title: hsa-miR-302d

tag: tissue

value: transfected with hsa-miR-302d-3p


title: KNR-A-HRP3-Input-Repl1

tag: chip antibody

value: GFP (gta-20, ChromoTek)

tag: genotype/variation

value: HRP3 KNR-A expressing cells


title: Blood-VitD+BPH-0min [10v2_0]

tag: Sex

value: Male

tag: agent

value: 0 min


title: Blood-VitD+BPH-180min [10v2_180]

value: Blood

tag: time point


title: Blood-Placebo-180min [10v1_180]

value: Placebo

value: 180 min


title: HSCATAC_P1164_28

description:
sample name:
HSCATAC_P1164_28

value: pre-leukemic HSCs


title: HSCATAC_P1164_27

description:
sample name:
HSCATAC_P1164_27


title: WT-HRP3-Repl1

tag: cell line

value: HRP3 WT expressing cells


title: Blood-Placebo-0min [09v4_0]


title: Blood-Placebo-180min [09v4_180]


title: hsa-miR-373-3p

value: heart

value: transfected with hsa-miR-373-3p


title: Blood-Placebo-0min [10v1_0]


title: hsa-miR-199a-3p

value: transfected with hsa-miR-199a-3p

value: post natal day 0

value: wild type


title: HSCATAC_P1164_26

description:
sample name:
HSCATAC_P1164_26

value: acute myeloid leukemia


title: HSCATAC_P1164_25

description:
sample name:
HSCATAC_P1164_25


title: cel-miR-67

value: transfected with cel-miR-67

value: ventricular cardiomyocytes

value: Wistar


title: Blood-VitD-180min [09v3_180]

value: VitD


title: HSCATAC_P1164_24

description:
sample name:
HSCATAC_P1164_24


title: POC_snRNAseq_Lane1_MULTI

city: San Francisco

first: Christopher

middle: S

last: McGinnis

state: CA

address: 600 16th Street

department: Pharmaceutical Chemistry

institute: University of California, San Francisco

description:
MULTI-seq barcode DNA
processed data files:
POC_nuc_MULTI_matrix.csv

data_processing:
FASTQ files were generated directly from Illumina BCL files using Illumina bcl2fastq version 2.19
Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.2 with default parameters (cellranger count).
Read-depth normalization was performed (when appropriate) using 10X Genomics CellRanger version 2.2 with default parameters (cellranger aggr).
Low-quality cell barcodes were excluded as described in the paper.
MULTI-seq barcode alignment and sample classification results were performed using the deMULTIplex R package (https://github.com/chris-mcginnis-ucsf/MULTI-seq)
Genome_build: hg19 (Samples 1-3, 6-12), concatenated mm10-hg19 (Sample 13-14), concatenated mm10-hg19 pre-mRNA (Sample 4-5)
Supplementary_files_format_and_content: Expression Libraries: gene-cell matrices are provided in the format produced by CellRanger. The matrix itself is in matrix market exchange format, with the column (cell barcodes) and row (gene identities) labels given in TSV format as described in the cellranger documentation. MULTI-seq Libraries: MULTI-seq barcode-cell matrices are provided in CSV format.

organism:
Homo sapiens
Mus musculus

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C.
Library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C and using a custom MULTI-seq library preparation protocol.

value: mixture of HEK,HMECS, and Jurkats

tag: multi-seq reagent

value: LMO/CMO/None


title: HSCATAC_P1164_23

description:
sample name:
HSCATAC_P1164_23


title: HSCATAC_P1164_22

description:
sample name:
HSCATAC_P1164_22


title: G-3

city: Nanjing

first: Yucheng

last: Zhao

address: Tongjiaxiang 24

institute: China pharmaceutical unoversity

description:
Papaver somniferum leaf of G
G33

data_processing:
The low quality reads (1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed.
Illumina clean data were mapped onto our SMRT sequencing data by hisat2 v2.05
RSEM was used to identify gene expression levels and then converted into FPKM (the fragments per kb per million fragments) value to use.
DESeq R package was used to analyze differential expression 22. Foldchange ≥2 and Adjusted P-value < 0.05 were set as the thresholds for the significance of the gene expression difference between the two samples.
Genome_build: Missing
Supplementary_files_format_and_content: tab-delimited files include RPKM values of all transcripts and unigenes in different samples.

organism: Papaver somniferum

source_name: leaf

extract_protocol:
For each sample, TRizol reagent (Tiangen Biotech Co.Ltd, Beijing, China) was used to extract RNA following the protocol provided by the manufacturer.
After cDNA synthesis, samples were subjected to phosphorylation, “A” base addition and end-repair according to library construction protocol. Then sequencing adapters were added to both sizes of the cDNA fragment. After PCR amplification for cDNA fragments, the targets of 150-250 bp were clean up. And then we performed the paired-end sequencing on an Illumina HiSeq X Ten platform (Illumina Inc, CA, USA).

tag: cultivar

value: G

value: leaf

tag: developmental stage

value: Filling stage


title: Naproxen_C3_72_T

description: whole zebrafish embryo, exposed to Naproxen, 24hpf-96hpf, 234.29 micromol per liter

source_name: whole embryo, exposed to Naproxen, 24hpf-96hpf, 234.29 micromol per liter

tag: substance

value: Naproxen


title: E-6

city: Denton

first: Drew

last: Sturtevant

state: TEXAS

address: 155 Union Circle #305220

department: BioDiscovery Institute

institute: University of North Texas

description:
Endosperm6
e6

data_processing:
Data were cleaned using trimmomatic, removing adaptors, low quality bases with a sliding window of 4 and a Qscore<20, keeping reads > 25bp
Abundance measurements were done using Salmon, calling 100 bootsraps, validateMappings, and rangfactorizationbins (4)
Data were quantified using DESeq2
Genome_build: NCBI Ricinus communis Annotation Release 101
Supplementary_files_format_and_content: Salmon-coutsdata.txt, DESeq2-normalized_countstable.csv

organism: Ricinus communis

source_name: Mature Castor Seeds

growth_protocol: Plants seeds were harvested from were grown at 22C in greenhouse conditions

extract_protocol:
Total RNA was extracted using a Hot Borate RNA extraction protocol
Library was prepared using the Illumina TrueSeq library preparation
Library insert size was ~300bp. Sequencing was 2X75 on a MidOutput Cassette for an Illumina NextSeq

value: Seed

value: Baker 296

tag: Stage

value: Mature

value: Endosperm


title: Blood-BPH-0min [09v2_0]

source_name: Blood, BPH, 0 min

value: Male

value: Blood

value: BPH

value: 0 min


title: G-2

description:
Papaver somniferum leaf of G
G32


title: hsa-miR-590-3p

value: heart

tag: treatment

value: transfected with hsa-miR-590-3p

tag: age

value: post natal day 0

tag: genotype

value: wild type

value: ventricular cardiomyocytes


title: HSCATAC_P1164_21

description:
sample name:
HSCATAC_P1164_21

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters.
Paired-end reads were aligned to hg19 using bwa. Duplicates were removed using PICARD tools
Reads were subsequently filtered for alignment quality  and were required to be properly paired.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with raw counts

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 7 µL of harvested libraries were amplified in 50 µL PCR for an additional 17 cycles (1.25 µM custom Nextera dual-index PCR primers  in 1x NEBnext High-Fidelity PCR Master using the following PCR conditions: 72°C for 5min; 98°C for 30 s;  Mix)  using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL.  The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries  at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

tag: patient id

tag: patient diagnosis

value: acute myeloid leukemia

value: pre-leukemic HSCs


title: E-5

description:
Endosperm5
e5

tag: tissue


title: Blood-VitD-0min [09v3_0]

value: VitD


title: E-4

description:
Endosperm4
e4


title: HSCATAC_P1164_20

description:
sample name:
HSCATAC_P1164_20

tag: cell type


title: E-3

description:
Endosperm3
e3


title: G-1

description:
Papaver somniferum leaf of G
G31

value: G

value: leaf

value: Filling stage


title: HSCATAC_P1164_1

description:
sample name:
HSCATAC_P1164_1


title: Blood-VitD+BPH-0min [09v1_0]

value: VitD+BPH


title: HSCATAC_P1164_19

description:
sample name:
HSCATAC_P1164_19


title: Blood-BPH-180min [09v2_180]

value: 180 min


title: Z-1

description:
Papaver somniferum leaf of Z
Z31

value: Z


title: HSCATAC_P1164_18

description:
sample name:
HSCATAC_P1164_18


title: Blood-BPH-0min [07v4_0]

value: Male

value: Blood


title: T-3

description:
Papaver somniferum leaf of T
T33

value: T


title: HSCATAC_P1164_17

description:
sample name:
HSCATAC_P1164_17


title: E-1

description:
Endosperm1
e1

value: Seed

value: Baker 296

value: Mature

value: Endosperm


title: Blood-BPH-180min [07v4_180]

value: BPH


title: AC-6

description:
Embryo6
ac6

value: Embryo


title: Blood-Placebo-180min [07v3_180]

source_name: Blood, Placebo, 180 min

value: Placebo


title: Blood-Placebo-0min [07v3_0]

value: 0 min


title: Blood-VitD+BPH-180min [07v2_180]


title: Blood-VitD+BPH-180min [09v1_180]


title: HSCATAC_P1164_16

description:
sample name:
HSCATAC_P1164_16

value: acute myeloid leukemia

value: pre-leukemic HSCs


title: AC-5

description:
Embryo5
ac5


title: AC-4

description:
Embryo4
ac4


title: Z-3

description:
Papaver somniferum leaf of Z
Z33

value: leaf

value: Filling stage


title: E-2

description:
Endosperm2
e2


title: T-1

description:
Papaver somniferum leaf of T
T31


title: B2-3

description:
Papaver somniferum leaf of B2
B2-33


title: Blood-VitD-180min [07v1_180]

source_name: Blood, VitD, 180 min

value: VitD

value: 180 min


title: B2-2

description:
Papaver somniferum leaf of B2
B2-32


title: AC-3

description:
Embryo3
ac3


title: AC-2

description:
Embryo2
ac2


title: Blood-VitD-180min [05v4_180]

value: Male


title: Blood-VitD+BPH-0min [07v2_0]

value: Blood

value: VitD+BPH


title: T-2

description:
Papaver somniferum leaf of T
T32

value: T


title: Blood-VitD-0min [07v1_0]


title: HSCATAC_P1164_13

description:
sample name:
HSCATAC_P1164_13


title: Blood-VitD-0min [05v4_0]


title: Blood-VitD+BPH-180min [05v3_180]


title: B2-1

description:
Papaver somniferum leaf of B2
B2-31


title: AC-1

description:
Embryo1
ac1

value: Seed

value: Baker 296


title: HSCATAC_P1164_11

description:
sample name:
HSCATAC_P1164_11


title: florescence-3

description:
Papaver somniferum leaf in florescence stag
433

value: florescence stage


title: HSCATAC_P1164_15

description:
sample name:
HSCATAC_P1164_15


title: florescence-2

description:
Papaver somniferum leaf in florescence stag
432


title: HSCATAC_P1164_10

description:
sample name:
HSCATAC_P1164_10


title: HSCATAC_P1164_14

description:
sample name:
HSCATAC_P1164_14


title: INT_2.5_1

city: Pullman

first: Michael

middle: E

last: Konkel

state: WA

institute: Washington State University

description: Enriched mRNA

data_processing:
For files from the Illumina MiSeq instrument, MiSeq Instrument Software was used to generate fastq files. For files generated by the Ion Proton instrment, BaseCaller (Torrent Suite verision 5.0.4) was used for basecalling and demultiplexing.
Reads were aligned to the genome using bowtie2 version 2.3.2 using default options.
Reads mapping to each CDS were counted using featureCounts from the subread package, version 1.5.3 using the --largestOverlap option.
Genome_build: Genbank accession numbers for the sequences used for read mapping are as follows: C. jejuni strain 81-176  [chromosome sequence: (NC_008787), plasmid sequences: pTet (NC_008790) and pVir (NC_008770)];
Supplementary_files_format_and_content: Comma delimited text file containing counts of mapped transcripts CDS for each strain.

organism: Campylobacter jejuni

source_name: C. jejuni_co-culture with INT 407 cells

growth_protocol: C. jejuni were grown in 250 mL MH broth cultures in a microaerobic environment shaking at 220 rpm on an orbital shaker, adjusted to an OD540 of 0.3 in MEM + 1% FBS, and added to T75 flasks of cultured epithelial cells.

extract_protocol:
Bacterial pellets were collected by centrifugation and snap frozen. RNA Extraction was done using the Ambion Ribopure Bacteria kit. rRNA was depleted with 3’ biotinylated oligonucleotides that were designed to hybridize with C. jejuni 16S and 23S rRNAs.
Illumina MiSeq libraries were prepared using the KAPA stranded RNAseq kit

tag: strain

tag: culture time (hours)

tag: culture condition

value: Co-culture with INT 407 cells in MEM + 1% FBS


title: INT_2.5_2

description: Enriched mRNA


title: florescence-1

description:
Papaver somniferum leaf in florescence stag
431


title: MH_2

description: Enriched mRNA

source_name: C. jejuni

value: Mueller-Hinton Broth


title: bolting-3

description:
Papaver somniferum leaf in bolting stag
333

value: bolting stage


title: MH_1

description: Enriched mRNA


title: Blood-Placebo-180min [05v2_180]

data_processing: Raw data were extracted from scanned images using Expression Console (v 1.4; Thermo Fisher Scientific Inc.). Robust Multiarray Analysis method was used to perform background correction and quantile normalization.

extract_protocol: Blood samples were collected from an antecubital vein into PAXgene Blood RNA Tubes (Qiagen, Mississauga, Ontario, Canada) before and 180 min after each treatment. Total RNA was isolated and purified from blood samples using PAXgene Blood RNA Kit (Qiagen) according to the manufacturer's instructions..

tag: Sex

tag: agent

value: Placebo

tag: time point


title: bolting-2

description:
Papaver somniferum leaf in bolting stag
332


title: HSCATAC_P1164_12

description:
sample name:
HSCATAC_P1164_12

value: acute myeloid leukemia


title: bolting-1

description:
Papaver somniferum leaf in bolting stag
331


title: Blood-BPH-0min [05v1_0]

value: BPH

value: 0 min


title: Blood-Placebo-0min [05v2_0]

source_name: Blood, Placebo, 0 min


title: StrainB-TotalmRNA-Rep2

city: Beijing

first: Babak

last: Javid

address: Biotechnology Building Room 4302, Tsinghua University, Haidian District

department: School of medicine

institute: Tsinghua University

description:
StrainB-totalmRNA-Rep2
processed data file: StrainA-AltRibo_StrainB-AltRibo.gene.TE, StrainA-CanRibo_StrainB-CanRibo.gene.TE, StrainA-TotalRibo_StrainB-TotalRibo.gene.TE

data_processing:
For RNAseq, quality control was performed by FastQC and adaptors were trimmed by FASTX-ToolKit.
For Ribosome profiling, after quality control and adaptor removal, reads that were less than 25nt long were discareded and longer than 36nt were trimmed to 36nt.
Next, Ribosome profiling reads and RNA-seq reads that aligned to rRNAand tRNA were romoved using bowtie2.
The remaining reads were aligned to genome using bowtie2 with "sensitive-local" option.
The mapped reads were normalized to reads per kilobase million (RPKM) using total number of mapped reads.
Genome_build: ASM1500v1
Supplementary_files_format_and_content: Differential translation analysis among different groups and translation effienency of each ribosome fraction normalized by RNA-seq background in different strains. For differential translation analysis, replicates were included. X represents read count of Total Ribo, Y represents read count of experiment set (AltRibo/CanRibo), fold change, p-value were presented in the file. For translation efficiency information, left column represents translation effiency in StrainA, right column represents translation efficiency in strain B.

organism: Mycolicibacterium smegmatis

source_name: StrainB-TotalmRNA

growth_protocol: Both Mycobacterium smegmatis Strain A and Strain B were grown in sauton medium supplied with 10μM ZnSO4.

extract_protocol:
Total RNA were extracted by miRNeasy kit from bacteria lysate. For ribosome footprint library, bacteria suspension was dropped into liquid nitrogen and smashed into powder. The powder was further pulverized with beads beating 4 to 5 times with chilling in liquid nitrogen between each step. After centrifugation at 18500g for 45 min, the cleared lysate was transferred to a new tube supplied with 70U/ml MNase to digested mRNA not protected my ribosome. The pre-digested lysate was laid over a 1M sucrose cushion and centrifuged at 30,000 rpm, 4°C for 20h in Beckman 70Ti rotor. After ultracentrifugation, the ribosome pellet was washed and dissolved in polysome buffer. The dissolved ribosome solution was further digested with MNase at 4°C for 1h. The digested ribosome fraction was incubated with either Flag resin or HA resin at 4°C overnight. After washing of the bound resin, the resin was elued with 3Flag/3HA peptide to isolate the AltRibo, and the remaing flow-through was confirmed as consisting almost entirly of CanRibo. Ribosome footprints were further extracted by miRNeasy Kit.
For RNA-seq library, rRNA was romoved by Ribo-Zero rRNA Removal Kit and library was constructed by NEBNext Ultra Directional RNA Library Prep Kit for illumina. For ribosome footprint library, footprints were selected for 24-36nt by marker oligo through 15% TBE-UREA PAGE. The corresponding region was sliced and purified. RNA was further dephosphoylated and ligated with linker. The ligation products were purified again by 15% TBE-UERA PAGE. Reverse transcription was followed up as well as circularization. rRNA was depeleted by biotinylated oligo and the rRNA substracted circularized cDNA template was used for library amplification.

treatment_protocol: Bacterial cultures of both Stain A and Strain B were grown till OD600nm=1 and treated with 100μg/ml chloramphenicol for 3 mins to arreset elongating ribosomes. Bacteria were collected by centrifigation at 4500g, 4°C, 10min.

tag: strain background

value: M. smegmatis mc2 155

value: StrainB

tag: genotype/variation

value: Endogeneous AltRpsR labeled with 3HA tag; Endogeneous CanRpsR labeled with 3Flag tag

tag: molecule subtype

value: total RNA


title: TNF 4h

description: miRNA expression data of human endothelial cells through TNF-induced inflammatory signaling

hyb_protocol: Hybridization was carried out by MBL

scan_protocol: Scan was carried out by MBL

data_processing: Data processing was carried out by MBL

source_name: human umblical vein endothelial cells

label_protocol: Labing was carried out by MBL (Aichi, Japan)

extract_protocol: Total RNA including miRNA was isolated from HUVECs using miRNeasy micro Kit (Qiagen, Hilden, Germany) with DNase digestion step according to the manufactures’ instructions.

treatment_protocol: 80-90% confluent HUVECs plates were washed with PBS once and then serum starved in EBM-2 Basal Medium containing 0.5% FBS for 16 hrs. HUVECs were stimulated with or without 10 ng/ml TNF-α (Peprotech, Rocky Hill, NJ) for indicated periods thereafter.

tag: conditions

value: TNF

tag: donors

value: pooled from multiple donors


title: TNF 24h


title: jointing-3

description:
Papaver somniferum leaf in jointing stag
233

value: leaf

tag: developmental stage

value: jointing stage


title: Blood-Placebo-180min [04v4_180]

value: Male

value: Blood

value: 180 min


title: 96plexHMEC_tech.rep_Lane4

description:
polyA RNA
processed data files:
HMEC4_techrep_barcodes.tsv
HMEC4_techrep_genes.tsv
HMEC4_techrep_matrix.mtx

source_name: HMEC

value: HMEC

tag: multi-seq reagent

value: LMO


title: Blood-VitD+BPH-0min [05v3_0]

source_name: Blood, VitD+BPH, 0 min

value: VitD+BPH


title: Blood-BPH-180min [05v1_180]

source_name: Blood, BPH, 180 min


title: jointing-2

description:
Papaver somniferum leaf in jointing stag
232


title: 96plexHMEC_tech.rep_Lane3

description:
polyA RNA
processed data files:
HMEC3_techrep_barcodes.tsv
HMEC3_techep_genes.tsv
HMEC3_techrep_matrix.mtx


title: Blood-Placebo-0min [04v4_0]

value: Placebo


title: StrainB-TotalmRNA-Rep1

description:
StrainB-totalmRNA-Rep1
processed data file: StrainA-AltRibo_StrainB-AltRibo.gene.TE, StrainA-CanRibo_StrainB-CanRibo.gene.TE, StrainA-TotalRibo_StrainB-TotalRibo.gene.TE


title: StrainB-TotalRibo-Rep2

description:
TotalRibo-StrainB-Riboseq-rep2
processed data file: StrainB_AltRibo_TotalRibo.edgeR.table, StrainB_CanRibo_TotalRibo.edgeR.table

data_processing:
library strategy: Ribosome profiling
For RNAseq, quality control was performed by FastQC and adaptors were trimmed by FASTX-ToolKit.
For Ribosome profiling, after quality control and adaptor removal, reads that were less than 25nt long were discareded and longer than 36nt were trimmed to 36nt.
Next, Ribosome profiling reads and RNA-seq reads that aligned to rRNAand tRNA were romoved using bowtie2.
The remaining reads were aligned to genome using bowtie2 with "sensitive-local" option.
The mapped reads were normalized to reads per kilobase million (RPKM) using total number of mapped reads.
Genome_build: ASM1500v1
Supplementary_files_format_and_content: Differential translation analysis among different groups and translation effienency of each ribosome fraction normalized by RNA-seq background in different strains. For differential translation analysis, replicates were included. X represents read count of Total Ribo, Y represents read count of experiment set (AltRibo/CanRibo), fold change, p-value were presented in the file. For translation efficiency information, left column represents translation effiency in StrainA, right column represents translation efficiency in strain B.

source_name: StrainB-TotalRibo

value: ribosome footprints


title: no treatment 4h

value: no treatment


title: StrainB-TotalRibo-Rep1

description:
TotalRibo-StrainB-Riboseq-rep1
processed data file: StrainB_AltRibo_TotalRibo.edgeR.table, StrainB_CanRibo_TotalRibo.edgeR.table

value: M. smegmatis mc2 155


title: 96plexHMEC_tech.rep_Lane2

description:
polyA RNA
processed data files:
HMEC2_techrep_barcodes.tsv
HMEC2_techrep_genes.tsv
HMEC2_techrep_matrix.mtx


title: jointing-1

description:
Papaver somniferum leaf in jointing stag
231


title: Blood-BPH-180min [04v3_180]

value: BPH


title: StrainB-CanRibo-Rep2

description:
CanRibo-StrainB-Riboseq-rep2
processed data file: StrainB_CanRibo_TotalRibo.edgeR.table

source_name: StrainB-CanRibo

value: StrainB

value: Endogeneous AltRpsR labeled with 3HA tag; Endogeneous CanRpsR labeled with 3Flag tag


title: seedling-3

description:
Papaver somniferum leaf in seedling stag
133

value: seedling stage


title: 96plexHMEC_tech.rep_Lane1

description:
polyA RNA
processed data files:
HMEC1_techrep_barcodes.tsv
HMEC1_techrep_genes.tsv
HMEC1_techrep_matrix.mtx


title: no treatment 24h

value: pooled from multiple donors


title: StrainB-CanRibo-Rep1

description:
CanRibo-StrainB-Riboseq-rep1
processed data file: StrainB_CanRibo_TotalRibo.edgeR.table


title: StrainB-AltRibo-Rep2

description:
AltRibo-StrainB-Riboseq-rep2
processed data file: StrainB_AltRibo_TotalRibo.edgeR.table

source_name: StrainB-AltRibo


title: 96plexHMEC_original_Lane3

description:
polyA RNA
processed data files:
HMEC_orig_barcodes.tsv
HMEC_orig_genes.tsv
HMEC_orig_matrix.mtx


title: seedling-1

description:
Papaver somniferum leaf in seedling stag
131

source_name: leaf

value: leaf


title: Blood-VitD+BPH-180min [04v2_180]

source_name: Blood, VitD+BPH, 180 min


title: 96plexHMEC_original_Lane2


title: StrainB-AltRibo-Rep1

description:
AltRibo-StrainB-Riboseq-rep1
processed data file: StrainB_AltRibo_TotalRibo.edgeR.table


title: Blood-VitD+BPH-0min [04v2_0]

value: 0 min


title: leaves-3

description:
Papaver somniferum leaf in filling stag
533

value: Filling stage


title: leaves-2

description:
Papaver somniferum leaf in filling stag
532


title: StrainA-TotalmRNA-Rep2

description:
StrainA-totalmRNA-Rep2
processed data file: StrainA-AltRibo_StrainB-AltRibo.gene.TE, StrainA-CanRibo_StrainB-CanRibo.gene.TE, StrainA-TotalRibo_StrainB-TotalRibo.gene.TE

source_name: StrainA-TotalmRNA

value: StrainA

value: Endogeneous AltRpsR labeled with 3Flag tag; Endogeneous CanRpsR labeled with 3HA tag

value: total RNA


title: Caco2_4_2

description: Enriched mRNA

source_name: C. jejuni_co-culture with Caco-2 cells

value: Co-culture with Caco-2 cells in MEM + 1% FBS


title: StrainA-TotalmRNA-Rep1

description:
StrainA-totalmRNA-Rep1
processed data file: StrainA-AltRibo_StrainB-AltRibo.gene.TE, StrainA-CanRibo_StrainB-CanRibo.gene.TE, StrainA-TotalRibo_StrainB-TotalRibo.gene.TE


title: Caco2_4_1

description: Enriched mRNA


title: StrainA-TotalRibo-Rep2

description:
TotalRibo-StrainA-Riboseq-rep2
processed data file: StrainA_AltRibo_TotalRibo.edgeR.table, StrainA_CanRibo_TotalRibo.edgeR.table

source_name: StrainA-TotalRibo


title: Blood-VitD-180min [04v1_180]

source_name: Blood, VitD, 180 min

value: Male

value: Blood

value: VitD

value: 180 min


title: Caco2_2.5_2

description: Enriched mRNA


title: Blood-VitD-180min [01v4_180]


title: seedling-2

description:
Papaver somniferum leaf in seedling stag
132


title: Blood-VitD-0min [04v1_0]

source_name: Blood, VitD, 0 min


title: StrainA-TotalRibo-Rep1

description:
TotalRibo-StrainA-Riboseq-rep1
processed data file: StrainA_AltRibo_TotalRibo.edgeR.table, StrainA_CanRibo_TotalRibo.edgeR.table

value: M. smegmatis mc2 155

value: ribosome footprints


title: Caco2_2.5_1

description: Enriched mRNA


title: stem-2

description:
Papaver somniferum stem in filling stag
522

source_name: stem

value: stem


title: StrainA-CanRibo-Rep2

description:
CanRibo-StrainA-Riboseq-rep2
processed data file: StrainA_CanRibo_TotalRibo.edgeR.table

source_name: StrainA-CanRibo


title: 96plexHMEC_original_Lane1

value: HMEC

value: LMO


title: Blood-VitD-0min [01v4_0]


title: stem-1

description:
Papaver somniferum stem in filling stag
521


title: root-3

description:
Papaver somniferum root in filling stag
513

source_name: root

value: root


title: INT_4_2

description: Enriched mRNA

source_name: C. jejuni_co-culture with INT 407 cells

value: Co-culture with INT 407 cells in MEM + 1% FBS


title: Blood-VitD+BPH-180min [01v3_180]

value: VitD+BPH


title: INT_4_1

description: Enriched mRNA


title: Blood-VitD+BPH-0min [01v3_0]

value: 0 min


title: leaves-1

description:
Papaver somniferum leaf in filling stag
531

value: leaf

value: Filling stage


title: Blood-BPH-0min [01v2_0]

source_name: Blood, BPH, 0 min

value: BPH


title: StrainA-AltRibo-Rep2

description:
AltRibo-StrainA-Riboseq-rep2
processed data file: StrainA_AltRibo_TotalRibo.edgeR.table

source_name: StrainA-AltRibo

value: StrainA

value: Endogeneous AltRpsR labeled with 3Flag tag; Endogeneous CanRpsR labeled with 3HA tag


title: root-2

description:
Papaver somniferum root in filling stag
512


title: MH_4

description: Enriched mRNA

source_name: C. jejuni

value: Mueller-Hinton Broth


title: StrainA-AltRibo-Rep1

description:
AltRibo-StrainA-Riboseq-rep1
processed data file: StrainA_AltRibo_TotalRibo.edgeR.table


title: Blood-BPH-180min [01v2_180]

source_name: Blood, BPH, 180 min

value: Male

value: Blood


title: MH_3

description: Enriched mRNA


title: stem-3

description:
Papaver somniferum stem in filling stag
523


title: Blood-Placebo-180min [01v1_180]

source_name: Blood, Placebo, 180 min

value: Placebo

value: 180 min


title: KOZ1_t2-control_rep3

status: Public on Apr 10 2019

city: Aberystwyth

first: Maurice

last: Bosch

address: Gogerddan

department: Institute of Biological, Environmental & Rural Sciences

country: United Kingdom

institute: Aberystwyth University

data_processing:
Raw FASTQ data trimmed using Trim Galore (version 0.4.1 with parameters: -q 28 --phred64)
Reads mapped using Tophat2 (tophat2 version 2.1.1 and bowtie2 version 2.2.9 using parameters: --phred64-quals)
Cufflinks version 2.2.1 used for cuffmerge and cuffdiff
Genome_build: Bdistachyon_314_v3.0.fa with Bdistachyon_314_v3.1.gene.gff3 annotation
Supplementary_files_format_and_content: fpkm

organism: Brachypodium distachyon

growth_protocol: ABR4, ABR8 and KOZ1, were grown in John Innes No 1 potting compost with grit-sand at a 4:1 ratio; controlled environment conditions: 21 °C, 16 h photoperiod. Plants were well-watered and grown for 32 days after germination.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy MinElute Cleanup Kit columns (Qiagen, Valencia, CA, USA). On-column DNase I digestion (DNase-Free DNase Set, Qiagen) was performed according to manufacturer protocols to eliminate genomic DNA contamination.
BGI  performed the TruSeq library construction and sequencing with Illumina HiSeqTM 2000

treatment_protocol: After 32 days, a progressive drought treatment was applied. For each of the ecotypes, leaf tissue was harvested at three time points for RNA extraction; at the start (T0, control (C)), after 4 days (T1, both C and treatment (D)) and after 8 days (T2, both C and D).

tag: ecotype/genotype

tag: drought tolerance phenotype

value: high susceptibility to drought

tag: treatment

value: well watered

value: 8 days after treatment start

value: Leaf tissue


title: KOZ1_t2-treated_rep2

value: no watering

tag: tissue


title: KOZ1_t2-treated_rep3


title: KOZ1_t2-control_rep2


title: StrainA-CanRibo-Rep1

description:
CanRibo-StrainA-Riboseq-rep1
processed data file: StrainA_CanRibo_TotalRibo.edgeR.table

value: M. smegmatis mc2 155

tag: strain

value: ribosome footprints


title: KOZ1_t1-treated_rep2

value: 4 days after treatment start


title: KOZ1_t2-control_rep1


title: KOZ1_t1-treated_rep3


title: KOZ1_t1-control_rep3


title: Blood-Placebo-0min [01v1_0]

source_name: Blood, Placebo, 0 min

value: 0 min


title: KOZ1_t1-treated_rep1


title: ABR8_t2-treated_rep2

value: drought tolerance


title: ABR8_t2-treated_rep3


title: root-1

description:
Papaver somniferum root in filling stag
511

value: root

value: Filling stage


title: KOZ1_t0-control_rep2

value: Treatment start (day 0)


title: KOZ1_t0-control_rep3


title: ABR8_t2-control_rep2


title: ABR8_t2-control_rep1


title: ABR8_t2-treated_rep1


title: KOZ1_t2-treated_rep1


title: ABR8_t1-treated_rep2


title: ABR8_t2-control_rep3


title: KOZ1_t0-control_rep1


title: ABR8_t1-treated_rep3


title: ABR8_t1-control_rep3


title: ABR8_t1-control_rep2


title: KOZ1_t1-control_rep2


title: KOZ1_t1-control_rep1


title: ABR8_t1-treated_rep1


title: ABR8_t0-control_rep2


title: ABR4_t2-treated_rep1

value: intermediate tolerance to drought


title: ABR8_t0-control_rep1


title: ABR4_t2-treated_rep3


title: ABR8_t1-control_rep1


title: ABR4_t2-control_rep1


title: ABR4_t2-control_rep2


title: ABR4_t2-control_rep3


title: ABR8_t0-control_rep3


title: ABR4_t2-treated_rep2


title: ABR4_t1-treated_rep2


title: ABR4_t1-treated_rep3


title: ABR4_t1-treated_rep1


title: ABR4_t1-control_rep3


title: ABR4_t1-control_rep1


title: ABR4_t0-control_rep2


title: ABR4_t0-control_rep3


title: ABR4_t0-control_rep1


title: 1uM-48h-Donor1

first: Albert

last: Vallejo-Gracia

address: 1650 Owens Street

department: GIVI

institute: Gladstone Institutes

data_processing:
RNA-seq analysis was done using the Illumina RNAexpress application v 1.1.0.
Alignment of RNA-Seq reads with the STAR aligner
Assignment of aligned reads to genes
Differential gene expression with DESeq2

source_name: CD4+ T cells

growth_protocol: Isolated CD4+ T cells from PBMCS from healthy individuals cultured in RPMI+10%FBS.

extract_protocol:
RNA was prepared from CD4+ T cells using the QIAgen RNeasy Plus Kit.
The Gladstone Institutes Genomics Core carried out the downstream processing of the RNA samples.
Strand-specific cDNA libraries were prepared using the Nugen Ovation kit (Nugen) and the libraries were deep sequenced on NextSeq 500 using single-end sequencing.

treatment_protocol: Treatment with 1,000 nM AS1842856 or equivalent amount of DMSO for 48h before cell collection and RNA extraction.

tag: donor


title: ABR4_t1-control_rep2


title: DMSO-48h-Donor3

value: 48h DMSO


title: DMSO-48h-Donor1


title: 1uM-12h-Donor2


title: 1uM-12h-Donor1


title: DMSO-48h-Donor2


title: DMSO-12h-Donor1

value: 12h DMSO


title: DMSO-12h-Donor3


title: 1uM-12h-Donor3


title: Study patient _41_mind_post-intervention

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

data_processing:
RNA-seq reads were aligned to hg19 genome using STAR v2.5.1, and a raw count file was generated using STAR output
Transcipt Assembly and FPKM values were determined using cufflinks v2.2.1 and a normzlized RPKM matrix was generated using the cufflinks output
Quality Control steps tp ensure read quality were performed using rRNA STAR v2.5.1 and RseQC v2.6.2
Further differential expressions analysis was done using DEseq2 v1.1, gage v2.21, clusterprofiler 2.4.3, gostats v2.36; heatmaps were generated using complexheatmap v1.6
All analysis was performed by inputting fastq files into VIPER: https://bitbucket.org/cfce/viper/overview
Genome_build: hg19
Supplementary_files_format_and_content: Count Matrix Files

source_name: Primary Breast Cancer Tumor

extract_protocol:
Tumor samples were reviewed by a central breast pathologist, who was blinded to participant group assignment, and were macrodissected to include areas with at least 10% tumor cellularity. RNA was isolated using the RNeasy FFPE kit (Qiagen).
Capture RNA-sequencing of the transcriptome coding regions was performed using the Illumina Truseq RNA access platform.

treatment_protocol: Inactive women with newly diagnosed breast cancer were randomized to an exercise intervention or mind-body control group, and participated in the study between enrollment and surgery (mean 29.3 days). Tumor were collected at baseline and surgery.

value: Primary Breast Cancer Tumor

tag: tumor type (hr/her)

tag: tumor grade

tag: condition

value: mind-body control

tag: time

value: post-intervention


title: Study patient _44_exercise_pre-intervention

value: exercise

value: pre-intervention


title: Study patient _43_mind_post-intervention


title: Study patient _44_exercise_post-intervention


title: Z-2

description:
Papaver somniferum leaf of Z
Z32

source_name: leaf

tag: cultivar

value: Z

value: leaf


title: Study patient _41_mind_pre-intervention


title: Study patient _39_exercise_post-intervention


title: Study patient _39_exercise_pre-intervention


title: 1uM-48h-Donor3


title: 1uM-48h-Donor2


title: Study patient _35_mind_post-intervention


title: Study patient _35_mind_pre-intervention


title: Study patient _26_mind_post-intervention


title: Study patient _26_mind_pre-intervention


title: Study patient _37_exercise_post-intervention


title: Study patient _37_exercise_pre-intervention


title: DMSO-12h-Donor2


title: Study patient _36_mind_post-intervention


title: Study patient _42_exercise_post-intervention


title: Study patient _42_exercise_pre-intervention


title: Study patient _36_mind_pre-intervention


title: Study patient _43_mind_pre-intervention


title: Study patient _30_mind_post-intervention


title: Study patient _34_mind_post-intervention


title: Study patient _31_exercise_pre-intervention


title: Study patient _31_exercise_post-intervention


title: Study patient _28_mind_post-intervention


title: Study patient _30_mind_pre-intervention


title: Study patient _28_mind_pre-intervention


title: Study patient _27_exercise_post-intervention


title: Study patient _21_mind_pre-intervention


title: Study patient _21_mind_post-intervention


title: Study patient _13_exercise_post-intervention


title: Study patient _24_mind_pre-intervention


title: Study patient _24_mind_post-intervention


title: Study patient _13_exercise_pre-intervention


title: Study patient _19_mind_post-intervention


title: Study patient _19_mind_pre-intervention


title: Study patient _34_mind_pre-intervention


title: Study patient _18_exercise_post-intervention


title: Study patient _18_exercise_pre-intervention


title: Study patient _17_exercise_post-intervention


title: Study patient _17_exercise_pre-intervention


title: Study patient _16_mind_pre-intervention


title: Study patient _15_exercise_post-intervention


title: Study patient _11_exercise_post-intervention


title: Study patient _12_mind_post-intervention


title: Study patient _11_exercise_pre-intervention


title: Study patient _10_exercise_post-intervention


title: Study patient _15_exercise_pre-intervention


title: Study patient _27_exercise_pre-intervention


title: Study patient _12_mind_pre-intervention


title: Study patient _9_exercise_post-intervention


title: Blood-BPH-0min [04v3_0]

city: Quebec

first: Frederic

last: Guenard

institute: Laval University

tag: Sex

value: Male

value: Blood

tag: agent

value: BPH

tag: time point


title: Study patient _8_mind_post-intervention


title: Study patient _9_exercise_pre-intervention


title: Study patient _8_mind_pre-intervention


title: Study patient _7_mind_pre-intervention


title: Study patient _10_exercise_pre-intervention


title: Study patient _7_mind_post-intervention


title: Study patient _6_exercise_post-intervention


title: Study patient _4_exercise_post-intervention


title: Study patient _2_mind_post-intervention


title: Study patient _6_exercise_pre-intervention


title: Study patient _3_exercise_post-intervention


title: Study patient _4_exercise_pre-intervention


title: Study patient _3_exercise_pre-intervention


title: Study patient _2_mind_pre-intervention


title: Study patient _16_mind_post-intervention


title: 18_Hela_DIS3_RNAi_IppOI

city: Solna

first: Franziska

last: Bonath

state: Stockholm

address: Tomtebodavägen 23A

department: Department for Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratories

country: Sweden

institute: Stockholm University

data_processing:
adapter removal
pre-mapping to a hand-curated list of ribosomal cDNA and miRNA librarie
collapsing reads with identical sequence using an in-house pipeline allowing one mismatch and discarding reads below 18nt and with low Phred-Scores (below 20)
remapping to ribosomal RNA (custom cDNA library) using bowtie (version 1.12) with the options “-v 0 –q –k 1 –-best”
Genome_build:  the reads were mapped to a hand curated ribosomal RNA library:We curated a ribosomal RNA library based on RNA sequences retrieved from NCBI (www.ncbi.nlm.nih.gov, accessed: 2015-02-17), Silva (https://www.arb-silva.de, 23193283) and the Ensembl database (www.ensembl.org, accessed: 2015-02-17).
Supplementary_files_format_and_content: standard bowtie output format, reads mapped to ribosomal cDNA library

growth_protocol: DMEM + FBS + Pen/Strep

extract_protocol:
TRIZOL
Illumina TruSeq small RNA, input: 1μg total RNA, addition of small RNA spike-ins (EXIQON)

treatment_protocol: HeLa cells were seeded to 70 % confluence in 6-well plates the day before siRNA transfection. Then cells were transfected with siRNA using RNAiMax and incubated for 48 hrs. Finally, 2.5 micro gramms of the I-PpoI vector were transfected using Lipofectamin 3000 and the cells harvested 36 hours later.

tag: cell line

value: HeLa

tag: i-ppoi transfection

value: yes

tag: type sirna

value: Dis3 RNAi

tag: exiqon small rna spike ins

value: 1/3 of recommended amount


title: 17_Hela_DIS3_RNAi_IppOI


title: 2_Hela_control_RNAi

value: no

value: control RNAi


title: 15_Hela_EXOSC10_RNAi_IppOI

value: Exosc10 RNAi


title: 3_Hela_control_RNAi


title: 14_Hela_EXOSC10_RNAi_IppOI


title: 10_Hela_control_RNAi_IppOI


title: 11_Hela_control_RNAi_IppOI


title: 12_Hela_control_RNAi_IppOI


title: 4_Hela_EXOSC10_RNAi


title: 1_Hela_control_RNAi


title: 7_Hela_DIS3_RNAi


title: 1%_KO_RNAseq_1

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
Basecalls performed using bcl2fastq (v2.17)
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
ChIP-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc), fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen), and mapped to human genome (hg19) using bowtie2 (version 2.2.3), filtering out alignments with mapping quality less than 10. Duplicate alignments were removed using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). The ChIP-seq peaks were called using MACS2 (version 2.0.10), with a q-value threshold of 0.05 and using the random background of ChIP samples as controls.
Genome_build: hg19
Supplementary_files_format_and_content: [ChIP-Seq] Bigwig, bed
[RNA-Seq] FPKMs

source_name: MDA-MB-231 cells

growth_protocol: Cells were cultured with DMEM+10% FBS

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen). Chromatin was isolated using a SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology), sonicated to 200-300 bp in length, and subjected to immunoprecipitation overnight with respective antibodies. The ChIP DNA was eluted, decrosslinked, and purified.
mRNA-seq libraries were prepared with a TruSeq Stranded mRNA Library Prep kit (Illumina). ChIP-seq libraries were prepared with a KAPA Hyper Library Preparation kit.

treatment_protocol: Cells were exposed to 20% or 1% O2 for 24 hrs

value: MDA-MB-231 cells

tag: genotype

value: ZMYND8 knockout


title: 1%_KO_RNAseq_2

tag: treatment


title: 20%_DKO_RNAseq_2

value: HIF-1/2alpha knockout


title: 6_Hela_EXOSC10_RNAi


title: 20%_KO_RNAseq_2


title: 1%_WT_RNAseq_2

value: Parental


title: 1%_DKO_RNAseq_1


title: 5_Hela_EXOSC10_RNAi


title: 16_Hela_DIS3_RNAi_IppOI


title: 20%_DKO_RNAseq_1


title: 20%_KO_RNAseq_1


title: 20%_WT_RNAseq_2


title: 13_Hela_EXOSC10_RNAi_IppOI


title: 20%_WT_RNAseq_1


title: H3_ChIPseq_2

tag: chip antibody

value: histone H3 (Novus Biologicals, Cat.#NB500-267)


title: 8_Hela_DIS3_RNAi


title: H3_ChIPseq_1


title: H3K14ac_ChIPseq_1

value: H3K14ac (Abcam, Cat.#ab52946)


title: 1%_WT_RNAseq_1


title: HIF-1a_ChIPseq_2

value: HIF-1alpha (Bethyl Laboratories, Cat.# A300-286A)


title: HIF-1a_ChIPseq_1


title: ZMYND8_ChIPseq_2

value: ZMYND8 (Bethyl Laboratories, Cat.#A302-089A)


title: H3K14ac_ChIPseq_2


title: ZMYND8_ChIPseq_1


title: shLuc_Rep1

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

description:
SMB21 cells treated with virus coding for shRNA targeting luciferase
sample name:
Sample 13

data_processing:
A minimum of 30 million reads was generated, yielding a minimum of 26 million uniquely mapped reads.
Sequenced reads were trimmed for adaptor sequence.
Sequencing reads were aligned to the mm9 reference genome assembly and gene counts were quantified using the STAR aligner version 2.5.1b.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited processed data file contains gene counts as determined by the STAR aligner.

growth_protocol: SMB21 cells were kept in culture using DMEM/F12 mix supplemented with B-27.

extract_protocol:
Total RNA was isolated using the Rneasy Mini Kit (Qiagen).
Single-end RNA-seq libraries were prepared using Ilumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according the manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on two Illumina NextSeq 500 runs with single-end 75bp reads.

treatment_protocol: SMB21 cells were treated with the HDAC inhibitor JNJ (Quisinostat) or DMSO for indicated periods, Alternatively, SMB21 cells were treated with a virus coding for shRNA against luciferase, Hdac1 or Hdac2. Cells were selected with puromycin.

tag: cell type

value: medulloblastoma

tag: tissue

value: cell line derived from brain


title: shLuc_Rep2

description:
SMB21 cells treated with virus coding for shRNA targeting luciferase
sample name:
Sample 14


title: shLuc_Rep3

description:
SMB21 cells treated with virus coding for shRNA targeting luciferase
sample name:
Sample 15


title: JNJ_24h_Rep3

description:
SMB21 cells treated with JNJ for 24 hours
sample name:
Sample 12


title: JNJ_24h_Rep2

description:
SMB21 cells treated with JNJ for 24 hours
sample name:
Sample 11


title: shHdac2_Rep2

description:
SMB21 cells treated with virus coding for shRNA targeting Hdac2
sample name:
Sample 20


title: shHdac2_Rep3

description:
SMB21 cells treated with virus coding for shRNA targeting Hdac2
sample name:
Sample 21


title: shHdac1_Rep1

description:
SMB21 cells treated with virus coding for shRNA targeting Hdac1
sample name:
Sample 16


title: DMSO_24h_Rep1

description:
SMB21 cells DMSO control 24 hours
sample name:
Sample 7

source_name: SMB21 cells DMSO control 24 hours


title: shHdac1_Rep3

description:
SMB21 cells treated with virus coding for shRNA targeting Hdac1
sample name:
Sample 18


title: DMSO_24h_Rep2

description:
SMB21 cells DMSO control 24 hours
sample name:
Sample 8


title: JNJ_2h_Rep3

description:
SMB21 cells treated with JNJ for 2 hours
sample name:
Sample 6


title: DMSO_24h_Rep3

description:
SMB21 cells DMSO control 24 hours
sample name:
Sample 9


title: JNJ_2h_Rep1

description:
SMB21 cells treated with JNJ for 2 hours
sample name:
Sample 4


title: JNJ_2h_Rep2

description:
SMB21 cells treated with JNJ for 2 hours
sample name:
Sample 5


title: DMSO_2h_Rep2

description:
SMB21 cells DMSO control 2 hours
sample name:
Sample 2

source_name: SMB21 cells DMSO control 2 hours


title: DMSO_2h_Rep3

description:
SMB21 cells DMSO control 2 hours
sample name:
Sample 3


title: 9_Hela_DIS3_RNAi

value: HeLa


title: shHdac1_Rep2

description:
SMB21 cells treated with virus coding for shRNA targeting Hdac1
sample name:
Sample 17


title: DMSO_2h_Rep1

description:
SMB21 cells DMSO control 2 hours
sample name:
Sample 1


title: H4K16ac_mitosis_ChIPSeq_Rep1

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description:
1042
H4K16ac_Async_Mitotic_Union_Peaks.bed.gz

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters  --barcode-mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Peaks called with Sicer V1.1 using parameters mm9 1 200 150 0.74 600 0.01
Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
Genome_build: mm9
Supplementary_files_format_and_content: Bed3+2 format. Peaks were called for all  ChIP-seq replicates separately using HOMER findPeaks (v4.9.1, parameters:  -style histone) using cell-cycle-matched sequenced ChIP input. Peaks were  required to be called in at least 2 replicates, and peak sets for each  factor were merged between interphase and mitosis using BedTools merge  (v2.22.0, default parameters). For BRD4, mitosis peaks needed to be present  in at least 2 of the 6 combined nocodazole and ro3306 replicates. Peaks  were excluded if they contained >50% overlap with repeat regions and any  overlap with blacklist regions. Columns 4 and 5 are rpkm intensities  extracted from these peak regions during interphase and mitosis. All  intensities were scaled by qPCR-derived scaling factors.

source_name: G1E-ER4 cells

growth_protocol: G1E-ER4 cells are a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al., 1997) in which GATA1-ER is stably expressed. G1E-ER4 cells are induced to differentiate through the addition of estradiol to the culture medium. G1E-ER4 cells were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
Lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s ChIP-seq Sample Preparation Kit. SPRIselect (Beckman Coulter) beads were used obtain an average library target size of 338 bp (range 302-436 bp), followed by real-time qPCR quantification using the KAPA Library Quant Kit for Illumina (KAPA Biosystems catalog no. KK4835). Single-end sequencing (1x50bp or 1x75 bp) was performed on the Illumina NextSeq 500 in high-output mode using Illumina sequencing reagents according to Illumina instructions.

treatment_protocol: Cells were induced to mature with 100 nM estradiol to activate GATA1-ER. For the mitosis conditions, nocodazole (200 ng/ml) was added after 6h of estradiol induction to synchronize cells in mitosis. At 13h following the addition of E2, cells were fixed with 1% formaldehyde and used for ChIP.

tag: strain

value: G1E ER4

value: ES-derived erythroid progenitor cells

value: estradiol, nocodazole

tag: mitotic phase

value: mitosis

value: Millipore 07-370