title: BOTH_4_C01_batch2

city: Ann Arbor

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: Gene expression data from THDC+AZ-treated RHE cultures.

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol.

scan_protocol: The standard Affymetrix protocol was following using the GeneChip™ Scanner.

data_processing: Robust multichip average (RMA) was used to generate expression intensity estimates (R package: oligo; function: rma).

source_name: RHE tissue cultures

label_protocol: Biotinylated cDNA was prepared following the standard Affymetrix protocol using the GeneChip WT labeling kit.

growth_protocol: EpiDermFT tissues were prepared in vitro from neonatal keratinocytes and fibroblasts (Mattek, Ashland, MA). Tissue cultures were handled according to the manufacturer’s instructions.

extract_protocol: Tissues were rinsed and RNA was extracted and purified using the RNeasy Plus Mini kit (Qiagen, Germantown, MD, USA; cat. no. 74134) with QiaCube Connect robotic station. Purified total RNA was assessed at 260 and 280 nm using the NanoDrop Lite (Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: Test materials were dissolved in DMSO yielding a 20 mg/mL stock solution. Subse-quent dilutions of stock solution were performed in distilled water. Samples of test material were added at a concentration of 10 µg/cm2 to the top surface of EpiDermFT tissues. RNA extractions were then performed after 24 hours.

tag: treatment

value: THDC+AZ

tag: batch

value: Batch 2

tag: replicate

value: Replicate 5


title: THDC_2_B11_batch2

status: Public on Aug 17 2021

type: RNA

first: William

country: USA

description: Gene expression data from THDC-treated RHE cultures.

label: biotin

molecule: total RNA

organism: Homo sapiens

value: THDC


title: small RNA 15 months 15m_4

type: SRA

city: Goettingen

first: Md Rezaul

last: Islam

address: von siebold str. 3a

country: Germany

institute: DZNE

description:
15 months
small RNA

library_source: transcriptomic

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
samples were mapped to mouse genome (mm10) and microRNA counts were generated using miRDeep2
Genome_build: mm10
Supplementary_files_format_and_content: "normalized_counts.csv" contains the read counts after normalization text files contains gene counts

organism: Mus musculus

source_name: blood

extract_protocol:
Blood was collected from retro orbital sinus at every 6 weeks
Libraries were generated according to the instructions of TruSeq Small RNA Library Preparation Kit
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: Longitudinal analysis of blood small microRNAome in mice. Mice were investigated from 12 months upto 16.5 months.

tag: sample type

value: total blood


title: IRS1-555

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description: Gene expression data from m. vastus lateralis biopsies obtained with Weil-  Blakesley conchotome instrument (Agnthos, Sweden)

hyb_protocol: Fragmented and biotinylated sense-strand DNA  target (5.5 μg) were hybridized to the arrays in GeneChip Hybridization Oven 645 at 45°C for  16-18 hrs.

scan_protocol: Arrays were washed and stained in GeneChip Fluidics Station 450 prior to scanning  in Affymetrix GeneChip Scanner.

data_processing:
1) CEL files were processed with RMA algorithm from oligo R package (v1.56.0). Resulting probeset values are reported in the expression matrix.
2) Probeset IDs were matched to their corresponding ENSEMBL IDs using biomaRt R package (v2.48.2). The non-unique probesets mapping to multiple ENSEMBL IDs are filtered out.
3) The probesets with signal value below 4 in at least 24 samples (minimum Disease group size) are discarded from the analysis.
4) Remaining probeset expression values are collapsed to ENSEMBL IDs using collapseRows function from WGCNA R package (v1.70-3) with MaxMean method.
5) The resulting expression matrix with ENSEMBL IDs were used for downstream analysis. (Supplementary File: expression_ensemblLevel.tsv.gz)

source_name: Biopsy from m. vastus lateralis

label_protocol: Amplified and biotinylated sense-strand DNA targets were generated from total RNA  using the WT Plus Kit (Thermo Fisher, MA).

growth_protocol: m. vastus lateralis biopsies obtained with Weil-Blakesley conchotome instrument (Agnthos, Sweden)

extract_protocol: mirVana™ miRNA Isolation Kit (#AM1560, Invitrogen, Waltham, Massachusetts, USA)

treatment_protocol: The participants were instructed to refrain from physical exercise 48  hrs before the visit. All investigations were performed in the morning after an overnight fast.

tag: disease

value: NGT

tag: age

tag: bmi

tag: m-value

tag: lab


title: IRS1-554


title: THDC_2_B10_batch2

value: Replicate 4


title: small RNA 15 months 15m_2

description:
15 months
small RNA


title: IRS1-561


title: small RNA 15 months 15m_9

description:
15 months
small RNA


title: IRS1-551


title: small RNA 16.5 months 16.5m_1

description:
16.5 months
small RNA


title: small RNA 15 months 15m_5

description:
15 months
small RNA


title: IRS1-556


title: IRS1-558


title: IRS1-550


title: small RNA 13.5 months 13m_8

description:
13.5 months
small RNA


title: small RNA 13.5 months 13m_10

description:
13.5 months
small RNA


title: small RNA 15 months 15m_6

description:
15 months
small RNA


title: small RNA 13.5 months 13m_6

description:
13.5 months
small RNA


title: small RNA 15 months 15m_7

description:
15 months
small RNA


title: small RNA 13.5 months 13m_4

description:
13.5 months
small RNA


title: AZ_3_B05_batch2

description: Gene expression data from AZ-treated RHE cultures.

value: AZ


title: BOTH_4_B06_batch2

value: Replicate 2


title: small RNA 15 months 15m_3

description:
15 months
small RNA


title: BOTH_4_B12_batch2


title: CTL_1_B08_batch2

description: Gene expression data from CTL-treated RHE cultures.

value: CTL


title: CLA-051

value: CLA


title: small RNA 15 months 15m_1

description:
15 months
small RNA


title: IRS1-557


title: CTL_1_B09_batch2


title: IRS1-553


title: small RNA 13.5 months 13m_7

description:
13.5 months
small RNA


title: small RNA 12 months 12m_10

description:
12 months
small RNA


title: small RNA 12 months 12m_9

description:
12 months
small RNA


title: CLA-047


title: BOTH_4_B07_batch2

value: BOTH

value: Replicate 3


title: CLA-044


title: small RNA 13.5 months 13m_9

description:
13.5 months
small RNA


title: CLA-048


title: CTL_1_B02_batch2


title: small RNA 13.5 months 13m_3

description:
13.5 months
small RNA


title: small RNA 12 months 12m_6

description:
12 months
small RNA


title: CLA-052


title: CLA-034


title: IRS1-567


title: small RNA 12 months 12m_5

description:
12 months
small RNA


title: small RNA 13.5 months 13m_5

description:
13.5 months
small RNA


title: small RNA 12 months 12m_2

description:
12 months
small RNA


title: small RNA 13.5 months 13m_2

description:
13.5 months
small RNA


title: small RNA 12 months 12m_1

description:
12 months
small RNA


title: BOTH_4_A11_batch1

value: Batch 1

value: Replicate 1


title: small RNA 13.5 months 13m_1

description:
13.5 months
small RNA


title: APP anti miR-mix 6

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
were mapped to mouse genome (mm10) using STAR (v 2.5.2b)
Expression counts were enumerated using featureCounts of subread (v 1.5.1) package.
Genome_build: mm10
Supplementary_files_format_and_content: "normalized_counts.csv" contains the read counts after normalization text files contains gene counts

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
Mice were sacrificed and and CA1 hippocampal region was microdissected, snap frozen and stored at -80°c. RNA was prepared from isolated tissues using RNA clean and concentrator kit.
Libraries were generated according to the instructions of TruSeq RNA Library Prep Kit v2.
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: 7 months old APPPS1-21 and littermate control mice were treated with anti-miR-mix and corresponding controls. Lipid nanoparticles containing the anti-miR-mix and control oligonucleotides were injected into the dorsal hippocampus

value: tissue


title: APP anti miR-mix 4


title: APP anti miR-mix 5


title: AZ_3_A03_batch1


title: small RNA 12 months 12m_7

description:
12 months
small RNA


title: small RNA 12 months 12m_8

description:
12 months
small RNA


title: CLA-029


title: small RNA 12 months 12m_3

description:
12 months
small RNA


title: CTL_1_A01_batch1


title: APP anti miR-mix 3


title: AZ_3_B04_batch2


title: APP control 5


title: CLA-023


title: THDC_2_B03_batch2


title: CLA-022


title: CLA-018


title: CLA-037


title: AZ_3_A09_batch1


title: APP control 3


title: THDC_2_A08_batch1


title: LEC3

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

hyb_protocol: standard Affymetrix

scan_protocol: standard Affymetrix

data_processing: R/Bioconductor, limma rma

source_name: Tonsil

label_protocol: Obtained cell suspensions were stained for 30 min at 4°C with fluorochrome-conjugated antibodies (CD45, CD31,CD35, GP38, Helix-NP). The cells were purified by flow cytometry using a Sony S800 cell sorter 100µm nozzle.

extract_protocol: Human pediatric tonsils were obtained from pediatric tonsillectomies performing within the Amsterdam UMC or Onze Lieve Vrouwe Gasthuis hospital (Amsterdam, The Netherlands). Tonsils were digested with Colagenase D until a single cell suspension was reached.  Tonsils were processed to obtain cell suspensions as described before (Krabbendam&Nagasawa et al 2018). For ILC enrichment tonsil cell suspensions were depleted for CD3 and CD19 by MACS depletion and peripheral blood cell suspensions were depleted for CD3, CD14 and CD19 using Mojosort magnetic cell separation system (BioLegend, San Diego, CA, USA).

tag: subtype

value: Lymph endothelial cell


title: small RNA 12 months 12m_4

description:
12 months
small RNA


title: AZ_3_A10_batch1


title: CLA-016


title: APP anti miR-mix 2


title: APP control 1


title: CLA-014


title: anti-miR-mix  WT control 6


title: APP anti miR-mix 7


title: CLA-032


title: APP control 6


title: THDC_2_A02_batch1


title: LEC1


title: FRC2

value: Fibroblastic reticular cell


title: FRC3


title: CTL_1_A07_batch1


title: old anti miR-mix 7

description: old anti miR-mix 7

treatment_protocol: young (3 months) and old (16.5 months) mice were treated with anti-miR-mix and corresponding controls. Lipid nanoparticles containing the anti-miR-mix and control oligonucleotides were injected into the dorsal hippocampus


title: CLA-010


title: APP anti miR-mix 1


title: CLA-012


title: CLA-031


title: FRC1


title: OC TykNu AZA

city: Washington

first: James

last: McDonald

state: DC

address: 800 22nd St, NW, Suite 8960

institute: The George Washington University

data_processing:
Check data with FastQC.
Reads were trimmed and adapters were removed using cutadapt using the --minimum-length 1 and -q 20 flags. The adapter sequences were -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Trimmed reads were aligned to hg38 using the following flags: --sjdbOverhang 100 --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100.
TEtranscripts was run on the STAR output with the following flags: --mode multi --stranded yes. The GENCODEv21 and RepeatMasker GTF annotation files were supplied. The log2(Fold Change) values output by DESeq were used in subsequent analyses. See Jin et al. (2015) for further reference on TEtranscripts.
Telescope installation and usage instructions can be found here: https://github.com/mlbendall/telescope. Before starting, install miniconda and add the bioconda and conda-forge channels. Then create a conda environment specifically for this task: conda create -n telescope_env python=3.6 future pyyaml cython=0.29.7 numpy=1.16.3 scipy=1.2.1 pysam=0.15.2 htslib=1.9 intervaltree=3.0.2. Use the “telescope assign” command to quantify RE expression. Combine *report.tsv files as needed for processing with DESeq2. Use the log2(Fold Change) values in subsequent analysis. For further information, see Bendall et al. (2019).
Genome_build: hg38 GCA_000001405.15
Supplementary_files_format_and_content: TEtranscripts uses DESeq to output the fold changes of the repetitive elements. The *_gene_TE_analysis.txt files contain DESeq output.
Supplementary_files_format_and_content: Telescope outputs a report file. The *-telescope_report.tsv are tab-delimited text files containing this output.

source_name: cell line

growth_protocol: The A2780, Hey, and TykNu cell lines were cultured in RPMI 1640 (Corning, 10-104-CV) with 10% Fetal Bovine Serum (X&Y Cell Culture, FBS-500-HI), and 1% penicillin and streptomycin solution (Gibco, 15070063). The Kuramochi cell line was cultured in RPMI 1640 media (Corning, 10-104-CV) with 10% fetal bovine serum (X&Y Cell Culture, FBS-500-HI), 1% penicillin and streptomycin solution (Gibco, 15070063) and 1% non-essential amino acids (Gibco, 11140050). Cell lines were periodically tested for mycoplasma via the Lonza MycoAlert kit.

extract_protocol:
Following treatment, total RNA was extracted using Trizol (Thermo Scientific 15596026). Ribosomal RNA was depleted using Ribozero (Illumina).
RNA sequencing libraries were prepared using the ScriptSeq v2 RNA-seq Library Preparation kit (SSV21106). Indexed libraries were sent to the Washington University in St. Louis Center for Genome Sciences for 75 bp, paired-end sequencing.

treatment_protocol: Cells were cultured in T75 dishes (Greiner, 658170) and treated with 500 nM 5-azacytidine (Sigma-Aldrich) or PBS. Media and AZA were replaced each day for five days (Fig. 1B). The cells were then split and allowed to reattach. ITF-2357 was added at a concentration of 100 nM and treatment was continued for two days. The sequential treatment of these cells by these drugs was optimized by Topper et al. (2017).

tag: cell line

value: TykNu

value: AZA


title: APP control 4


title: CLA-026


title: anti-miR-mix  WT control 1


title: OC TykNu ITF/AZA Combined

value: ITF/AZA Combined


title: anti-miR-mix  WT control 4


title: old anti miR-mix 6

description: old anti miR-mix 6


title: anti-miR-mix  WT control 3


title: APP control 2


title: CLA-004


title: anti-miR-mix  WT control 2


title: old anti miR-mix 5

description: old anti miR-mix 5


title: old anti miR-mix 4

description: old anti miR-mix 4


title: anti-miR-mix  WT control 5


title: anti-miR-mix old control 6

description: old control 6


title: OC TykNu ITF

value: ITF


title: old anti miR-mix 3

description: old anti miR-mix 3


title: CLA-013


title: OC Kuramochi AZA

value: Kuramochi


title: old anti miR-mix 2

description: old anti miR-mix 2


title: anti-miR-mix old control 3

description: old control 3


title: anti-miR-mix old control 5

description: old control 5


title: LEC2


title: anti-miR-mix old control 4

description: old control 4


title: OC Kuramochi ITF/AZA Combined


title: old anti miR-mix 1

description: old anti miR-mix 1


title: OC TykNu Mock

value: Mock


title: anti-miR-mix old control 2

description: old control 2


title: anti-miR-mix young  6

description: young  6


title: OC Kuramochi ITF


title: anti-miR-mix old control 1

description: old control 1


title: anti-miR-mix young  5

description: young  5


title: anti-miR-mix young  4

description: young  4


title: anti-miR-mix young  3

description: young  3


title: OC Kuramochi Mock


title: FDC1

value: Follicular Dendritic Cell


title: BEC3

value: Blood endothelial cell


title: OC Hey ITF/AZA Combined

value: Hey


title: FDC2


title: FDC3


title: anti-miR-mix young  1

description: young  1


title: BEC1


title: OC Hey AZA


title: BEC2


title: 8h tetTOR C

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

description: Candida albicans Mutant  tetO-TOR1 versus Candid albicans heterozygous TOR1/tor1 strain in doxycycline for 8h

hyb_protocol: Array hybridization, washing, scanning and data extraction was carried out as described by Haran et al (PMID: 25356803)

data_processing: Data for each feature was background corrected and was expression normalised using the Lowess transformation method in GeneSpring GX13 (Agilent Technologies). Differential expression between pairs of conditions was examined by comparing relative expression ratios (Log2 values) among genes that satisfied a post-hoc test (Storey with Bootstrapping) with a corrected Q value less tahn 0.05. Gene set enrichment analysis (GSEA) was carried out as described by Haran et al PMID: 25356803.

organism: Candida albicans

source_name: Mutant  tetO-TOR1 grown to OD600nm 0.1 in YEPD at 37C

label_protocol: Total RNA (100 ng) was labelled with Cy5 or Cy3 using the Two-Color Low Input Quick Amp labelling Kit (Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Each strain was cultured for 24 h on solid YEPD containing 5 ng/ml of doxycycline. Cells were harvested from plates and washed twice in PBS and resulting cells were used to inoculate 50 ml of YEPD to an OD600nm of 0.1 in the presence or absence of doxycycline (30 µg/ml). Cells were harvested after 2 h and 8 h growth, cell pellets were flash frozen in liquid N2

extract_protocol: Total RNA was extracted using Qiagen Rnease minikit using a microdismembrator (Braun, Melsungen,Germany).

treatment_protocol: without or with Doxycycline (30 µg/ml) for 2h or 8h

tag: genotype

value: doxycycline (30 ug/ml) for 2h

source_name: Heterozygous TOR1/tor1 grown to OD600nm 0.1 in YEPD at 37C


title: miR-148a-3p mimic 6

description: mimic 6

source_name: neuon

growth_protocol: primary hippocampal neurons were cultured from E17 embryos of CD1 mice

extract_protocol:
Treated cells were dissociated in Trizol. RNA was prepared using RNA clean and concentrator kit.
Libraries were generated according to the instructions of TruSeq RNA Library Prep Kit v2.
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: At DIV10, neurons were treated with miR-148a-3p mimic and negative control for 48 hours.

tag: cell type

value: primary hippocampal neurons

tag: div

value: cells


title: 8h tetTOR B

scan_protocol: Array hybridization, washing, scanning and data extraction was carried out as described by Haran et al (PMID: 25356803)


title: miR-148a-3p mimic 4

description: mimic 4


title: miR-148a-3p mimic 3

description: mimic 3


title: miR-148a-3p mimic 5

description: mimic 5


title: anti-miR-mix young  2

description: young  2


title: miR-148a-3p mimic 2

description: mimic 2


title: OC Hey Mock


title: miR-148a-3p mimic 1

description: mimic 1


title: miR-148a-3p control 6

description: control 6


title: OC Hey ITF


title: 8h tetTOR D


title: miR-148a-3p control 5

description: control 5


title: 8h tetTOR A

description: Candida albicans Mutant  tetO-TOR1 versus Candid albicans heterozugous TOR1/tor1 strain in doxycycline for 8h


title: 2h tetTOR D

description: Candida albicans Mutant  tetO-TOR1 versus Candid albicans heterozygous TOR1/tor1 strain in doxycycline for 2h


title: 2h tetTOR C


title: miR-148a-3p control 4

description: control 4


title: OC A2780 AZA


title: 2h tetTOR B


title: OC A2780 ITF


title: miR-148a-3p control 3

description: control 3


title: miR-181a-5p mimic 4

description: mimic 4

treatment_protocol: At DIV10, neurons were treated with miR-181a mimic and negative control for 48 hours.


title: OC A2780 Mock


title: miR-148a-3p control 2

description: control 2


title: miR-181a-5p mimic 2

description: mimic 2


title: TP53 Mutant (HH23) AZA Rep 3

description:
HH23_Mut_p53-treat3_AZA.TEtranscripts.DESeq_gene_TE_analysis.txt
HH23_Mut_p53_treat3_AZA_DESeq_telescope_results.tsv

data_processing:
Check data with FastQC.
Reads were trimmed and adapters were removed using cutadapt using the --minimum-length 1 and -q 20 flags. The adapter sequences were -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Trimmed reads were aligned to hg38 using STAR with the following flags: --sjdbOverhang 100 --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100. The data from separate lanes and both runs of the same sample was combined so each sample had three biological replicates total.
TEtranscripts was run on the STAR output with the following flags: --mode multi --stranded reverse. The GENCODEv21 and RepeatMasker GTF annotation files were supplied. The log2(Fold Change) values output by DESeq2 were used in subsequent analyses. See Jin et al. (2015) for further reference on TEtranscripts.
Telescope installation and usage instructions can be found here: https://github.com/mlbendall/telescope. Before starting, install miniconda and add the bioconda and conda-forge channels. Then create a conda environment specifically for this task: conda create -n telescope_env python=3.6 future pyyaml cython=0.29.7 numpy=1.16.3 scipy=1.2.1 pysam=0.15.2 htslib=1.9 intervaltree=3.0.2. Use the “telescope assign” command to quantify RE expression. Combine *report.tsv files as needed for processing with DESeq2. Use the log2(Fold Change) values in subsequent analysis. For further information, see Bendall et al. (2019).
Genome_build: hg38 GCA_000001405.15
Supplementary_files_format_and_content: TEtranscripts uses DESeq2 to output the fold changes of the repetitive elements. The *_gene_TE_analysis.txt files contain DESeq output.
Supplementary_files_format_and_content: Telescope outputs a report file. The *-telescope_report.tsv are tab-delimited text files containing this output.

growth_protocol: The HC2 and HH23 cell lines were cultured in RPMI 1640 (Corning, 10-104-CV) with 10% Fetal Bovine Serum (X&Y Cell Culture, FBS-500-HI), and 1% penicillin and streptomycin solution (Gibco, 15070063) as was the Hey cell line from which they were derived. The cell line was periodically tested for mycoplasma via the Lonza MycoAlert kit.

extract_protocol:
Following treatment, total RNA was extracted using Trizol (Thermo Scientific 15596026). Ribosomal RNA was depleted using Ribozero (Illumina).
RNA sequencing libraries were produced from 750 ng of total RNA with a minimum RIN score of 7.0. This RNA was prepared for sequencing following the manufacturer's protocol for the Illumina TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat kit (P/N 20020596) and TruSeq RNA Single Indexes Set A and B (P/N 20020492 and 20020493). Final libraries were separated into two sets of 12 and each set was combined into an equimolar pool for sequencing on an Illumina NextSeq 500 using two High Output 150 cycle v2.5 kits (P/N 20024907) and PhiX Control v3 (P/N FC-110-3001) spike-in of 1%.

treatment_protocol: Cells were cultured in T75 dishes (Greiner, 658170) and treated with 500 nM AZA (Sigma-Aldrich) or PBS for three days and 10 uM Nutlin-3A (Cayman Chemical 18585) or DMSO for 6 hours.

value: HH23 (TP53 Mutant R1775H)


title: TP53 Mutant (HH23) Combined N3A/AZA Rep 3

description:
HH23_Mut_p53-treat4_AZA_N3A.TEtranscripts.DESeq_gene_TE_analysis.txt
HH23_Mut_p53_treat4_AZA_N3A_DESeq_telescope_results.tsv

value: N3A/AZA Combined


title: miR-181a-5p mimic 1

description: mimic 1


title: miR-181a-5p mimic 3

description: mimic 3


title: OC A2780 ITF/AZA Combined


title: miR-181a-5p mimic 5

description: mimic 5


title: miR-181a-5p control 6

description: control 6


title: 2h tetTOR A


title: miR-181a-5p control 4

description: control 4


title: miR-181a-5p control 5

description: control 5


title: Trunc 8h D

description: Candida albicans Mutant  tetO-TOR1-Del381 versus Candid albicansheterozugous TOR1/tor1 strain in doxycycline for 8h

source_name: Mutant  tetO-TOR1-Del381 grown to OD600nm 0.1 in YEPD at 37C


title: miR-181a-5p control 3

description: control 3


title: Trunc 8h B


title: TP53 Mutant (HH23) N3A Rep 3

description:
HH23_Mut_p53-treat2_N3A.TEtranscripts.DESeq_gene_TE_analysis.txt
HH23_Mut_p53_treat2_N3A_DESeq_telescope_results.tsv


title: TP53 Mutant (HH23) Mock Rep 3


title: Trunc 8h C

description: Candida albicans Mutant  tetO-TOR1-Del381 versus Candid albicansheterozygous TOR1/tor1 strain in doxycycline for 8h


title: miR-181a-5p control 2

description: control 2


title: Trunc 8h A


title: TP53 Mutant (HH23) Combined N3A/AZA Rep 2


title: Trunc 2h C

description: Candida albicans Mutant  tetO-TOR1-Del381 versus Candid albicansheterozygous TOR1/tor1 strain in doxycycline for 2h


title: Trunc 2h D

description: Candida albicans Mutant  tetO-TOR1-Del381 versus Candid albicansheterozugous TOR1/tor1 strain in doxycycline for 2h


title: miR-181a-5p control 1

description: control 1


title: TP53 Mutant (HH23) AZA Rep 2


title: RE1-SB-WT4dph

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

data_processing:
Raw files were trimmed using Trimmomatic v0.38
Trimmed fastq files were pseudoaligned to the reference rainbow trout transcriptome (GenBank Acc# GCA_002163495.1) using Kallisto
Only features with at least 5 counts per million in at least 3 samples were kept for differential expression analyses. Significance of differentially expressed genes were assessed using DESeq2 in R, with a cut-off FDR (Benjamini-Hochberg) < 0.05 and an effect size threshold |log2FC| ≥ 1
Genome_build: rainbow trout (Oncorhynchus mykiss) reference transcriptome GenBank Acc# GCA_002163495.1
Supplementary_files_format_and_content: csv - raw counts of all samples
Supplementary_files_format_and_content: tabular - differential expression results using DESeq2

organism: Oncorhynchus mykiss

source_name: pooled whole embryos 0.01% DMSO repB

growth_protocol: Rainbow trout embryo-alevins were esposed to graded concentrations (0.01% DMSO, 1.13, 1.57, 6.22, 16.3, and 55.1 ng/L) of EE2  in 9-liter tanks in a flow-through conditon (14 degrees C, 16:8 light:dark cycle)

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy plus universal mini kit following the manufacturer's protocol
Libraries were generated from 250 ng of total RNA. mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps were done using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Embryos were exposed (waterborne) from hatch to 96 hours post-hatch

tag: tissue

value: pooled whole embryos

value: 4-days post-hatch

tag: exposure compound

tag: treatment/measured concentration


title: TP53 Mutant (HH23) N3A Rep 2

tag: treatment


title: TP53 Mutant (HH23) Combined N3A/AZA Rep 1


title: miR-148a-3p control 1

description: control 1


title: RE1-3B-WT4dph

source_name: pooled whole embryos 1.57 ng/L repB

value: 1.57 ng/L 17α-ethinylestradiol


title: RE1-30C-WT4dph

source_name: pooled whole embryos 16.3 ng/L repC

value: 16.3 ng/L 17α-ethinylestradiol


title: Trunc 2h A


title: RE1-30A-WT4dph

source_name: pooled whole embryos 16.3 ng/L repA


title: RE1-3C-WT4dph

source_name: pooled whole embryos 1.57 ng/L repC


title: TP53 Mutant (HH23) AZA Rep 1

value: AZA


title: RE1-1B-WT4dph

source_name: pooled whole embryos 1.13 ng/L repB

value: 1.13 ng/L 17α-ethinylestradiol


title: Trunc 2h B


title: RE1-3A-WT4dph

source_name: pooled whole embryos 1.57 ng/L repA


title: RE1-SA-WT4dph

source_name: pooled whole embryos 0.01% DMSO repA


title: RE1-30B-WT4dph

source_name: pooled whole embryos 16.3 ng/L repB


title: het_tet2

description: Candida albicans Mutant  tetO-TOR1-Del381 versus Candid albicans totO-TOR1 strain

source_name: Mutant  tetO-TOR1-Del381 grown to OD600nm 0.8 in YEPD at 37C

source_name: Mutant  tetO-TOR1 grown to OD600nm 0.8 in YEPD at 37C


title: TP53 Mutant (HH23) N3A Rep 1


title: het_tet4


title: het_tet3


title: RE1-SC-WT4dph

source_name: pooled whole embryos 0.01% DMSO repC


title: RE1-1A-WT4dph

source_name: pooled whole embryos 1.13 ng/L repA


title: RE1-100C-WT4dph

source_name: pooled whole embryos 55.1 ng/L repC

value: 55.1 ng/L 17α-ethinylestradiol


title: RE1-1C-WT4dph

source_name: pooled whole embryos 1.13 ng/L repC


title: ArcA_8B2

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

library_source: genomic

data_processing:
Library strategy: ChIP-exo
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: the reference genome ( MG1655 = NC_000913.3 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

molecule: genomic DNA

organism: Escherichia coli K-12

source_name: bacteria cells

growth_protocol: glycerol stocks of E. coli strains were inoculated into M9 minimal media with 0.2% (w/v) acetate. The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 degree with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated TFs-DNA complexes, and then were isolated with custom anti-ArcA monoclonal antibodies.
The experiments were performed following the procedures: to identify the binding maps in vivo, we isolated the DNA bound to ArcA from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the custom anti-ArcA monoclonal antibodies that specifically recognize ArcA, and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen). ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65 degree. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation. The DNA samples incubated for primer extension were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. The experiments were performed in biological duplicate.

tag: strain

tag: myc-tagging

value: ArcA myc-tagging cells

tag: chip-exo antibody

value: custom anti-ArcA monoclonal antibody


title: het_tet1


title: RE1-10C-WT4dph

source_name: pooled whole embryos 6.22 ng/L repC

value: 6.22 ng/L 17α-ethinylestradiol


title: RE1-10B-WT4dph

source_name: pooled whole embryos 6.22 ng/L repB


title: ArcA_M4


title: S-WT-2

city: Qingdao

first: Qian

last: Wang

state: Shandong

address: Keyuanjingsi Road, Laoshan District

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
RNA-seq was performed by the Novogene using Illumina Polymerase-based sequencing-by-synthesis, obtaining a read length of 150 bp and coverage of 48 to 81 million reads per sample.
Raw reads of fastq format were firstly processed through in-house perl scripts so that all the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/edwards_et_al_2017/assembly/Nitab-v4.5_genome_Chr_Edwards2017.fasta.gz ) were downloaded from NCBI.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.05.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Pertea et al., 2015) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene and then FPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene.
DEGs of two groups were performed using the DESeq2 R package (1.20.0) and resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. ClusterProfiler R package was used to test the statistical enrichment of DEGs in KEGG pathways.
Genome_build: Nitab4.5
Supplementary_files_format_and_content: tab-delimited text files include readcount and FPKM values for each Sample ...

organism: Nicotiana tabacum

source_name: Tobacco leaf blades

growth_protocol: Salt  stress experiments were conducted in 2019 at Unifarm, Wageningen University & Research in the Netherlands. Conditions of the greenhouse were 16 h light / 8 h dark at 25/23℃ and 70% relative humidity. The shortwave radiation level was maintained in the greenhouse compartment using artificial PAR (photosynthetically active radiation) when the incoming shortwave radiation was below 200 Wm-2.  For the salt tolerance evaluations, tobacco seeds were sown in soil, and they germinated after about 8 days. About 12 days after germination (DAG), the young seedlings were transplanted in rock-wool plugs within float trays for 8 days, then they were transplanted to a circular flow hydroponic system filled with 1/2 Hoagland’s nutrient solution (500 L). The water used to prepare 1/2 Hoagland’s nutrient solution contained trace amounts of Na+ and Cl- (5.04 μg/ml and 6.72 μg/ml, respectively). After 6 days of acclimatization (at ~ 30 DAG), NaCl was added to the nutrient solution to a concentration of 50 mM on the first day to avoid salt shock, and the final NaCl concentration of 100 mM NaCl was reached the next day.

extract_protocol:
At 4 DAT, the 5th leaf blades (with main veins removed) of four individual plants under control conditions and saline conditions in the daytime were sampled and frozen immediately in liquid nitrogen. Leaf blades from four individual plants were mixed and ground to powder. RNA was isolated and purified with RNeasy Plus Mini Kit (Qiagen, Cat No./ID: 74134, the Netherlands) following the manufacturer’s protocol. RNA samples of WT and OE-2 overexpression lines from two independent salt treatment experiments were used for transcriptome sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tobacco was treated under 100 mM NaCl for 4 days

value: The 5th leaf blades (with main veins removed)

tag: developmental stage

value: About 34 days after germination

value: wild type

value: Salt (100 mM NaCl)


title: TP53 WT (HC2) Combined N3A/AZA Rep 3

description:
HC2_WT_p53-treat4_AZA_N3A.TEtranscripts.DESeq_gene_TE_analysis.txt
HC2_WT_p53_treat4_AZA_N3A_DESeq_telescope_results.tsv

source_name: cell line

value: HC2 (TP53 WT)


title: TP53 WT (HC2) N3A Rep 3

description:
HC2_WT_p53-treat2_N3A.TEtranscripts.DESeq_gene_TE_analysis.txt
HC2_WT_p53_treat2_N3A_DESeq_telescope_results.tsv


title: C-OE2-2

value: Control


title: TP53 WT (HC2) AZA Rep 3

description:
HC2_WT_p53-treat3_AZA.TEtranscripts.DESeq_gene_TE_analysis.txt
HC2_WT_p53_treat3_AZA_DESeq_telescope_results.tsv


title: C-WT-2


title: RE1-10A-WT4dph

source_name: pooled whole embryos 6.22 ng/L repA

tag: age


title: TP53 Mutant (HH23) Mock Rep 2

value: HH23 (TP53 Mutant R1775H)

value: Mock


title: ArcA_5G8


title: RE1-100B-WT4dph

source_name: pooled whole embryos 55.1 ng/L repB

value: pooled whole embryos

value: 4-days post-hatch


title: ArcA_M2


title: S-WT-1


title: S-OE2-2


title: C-OE2-1


title: ArcA_5B9


title: ArcA_7B10


title: TP53 WT (HC2) AZA Rep 2


title: TP53 WT (HC2) Mock Rep 3


title: TP53 Mutant (HH23) Mock Rep 1


title: RE1-100A-WT4dph

source_name: pooled whole embryos 55.1 ng/L repA


title: TP53 WT (HC2) Mock Rep 2


title: S-OE2-1


title: ArcA_4A3


title: TP53 WT (HC2) N3A Rep 1


title: ArcA_5B6


title: TP53 WT (HC2) Combined N3A/AZA Rep 2

value: N3A/AZA Combined


title: TP53 WT (HC2) N3A Rep 2


title: ArcA_5A10


title: ArcA_2D6


title: ArcA_5F9


title: TP53 WT (HC2) Mock Rep 1


title: ArcA_4D6


title: ArcA_4A1


title: C-WT-1


title: TP53 WT (HC2) AZA Rep 1

value: AZA


title: ArcA_2B6


title: D3_CD40L_BCR

city: Philadelphia

first: Diego

middle: A

last: Espinoza

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Data pseudo-aligned with kallisto
GENCODE index v33 used

source_name: CD3-/CD14-/CD19+ FACS sorted B cells

extract_protocol:
RNA was isolated using the Rneasy Plus Micro Kit (Qiagen) according to manufacturer's protocol. RNA quantity and quality were assessed by TapeStation and Nanodrop.
TruSeq

treatment_protocol: Post-ficoll FACS-sorted CD3-/CD14-/CD19+ human peripheral B cells were stimulated with either BCR cross-linking antibodies, CD40L, both anti-BCR and CD40L, or neither. After 18 hours, RNA was isolated.

value: CD40L and BCR

tag: culture method

value: In-vitro culture


title: ArcA_2C4

value: ArcA myc-tagging cells


title: TykNu ITF/AZA Combined

data_processing:
Check data with FastQC.
Trim adapter sequences with cutadapt using the --minimum-length 1 and -q 20 flags. The adapter sequences were -a CTGTCTCTTATACACATCT and CTGTCTCTTATACACATCT.
Trimmed reads were aligned to hg38 with Bowtie2 (2.2.9) using the -X 2000 flag.
To create input for HMMRATAC, the Bowtie2 output was converted to a BAM file, sorted, and indexed with samtools (1.3.1) view, sort, and index commands on the default settings. MACS2 callpeak (2.1.1.20160309) was used to create a peaks file on the standard settings. The bedGraph file output by MACS2 was sorted using the bash “sort -k1,1 -k2,2n“ command then converted to a bigWig with bedGraphToBigWig.
The HMMRATAC_v1.2.1 Java executable was run with the following flags: -m 75,200,400,600 --window 1250000 --bedgraph true -u 20 -l 10 -z 100. The peaks were filtered for a minimum score of 10 (i.e. at least 10 reads map to the open region). Then bedtools intersect (2.26.0) was used to remove peaks that had an 85% reciprocal overlap with peaks from the mock treated sample. These treatment specific peaks were used in subsequent analyses. For further reference, see Tarbell and Liu (2019).
Genome_build: hg38 GCA_000001405.15
Supplementary_files_format_and_content: MACS2 output was analyzed by HMMRATAC and output in gappedPeak format.

extract_protocol:
Following treatment, DNA was extracted using the Nextera DNA Library Prep Kit (FC-121-1030).
The libraries were prepared according to Corces et al. (2017). Indexed libraries were sent to the Washington University in St. Louis Center for Genome Sciences for 75 bp, paired-end sequencing on an Illumina NextSeq500.

value: TykNu

value: ITF/AZA Combined


title: TP53 WT (HC2) Combined N3A/AZA Rep 1


title: D3_BCR

value: BCR


title: D3_CD40L


title: D3_Nil


title: TykNu AZA


title: TykNu ITF

value: ITF


title: TF_6_2

data_processing:
library strategy: ChIP-exo
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: the reference genome ( MG1655 =  NC_000913.3 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

growth_protocol: glycerol stocks of E. coli myc-tagged strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 degree with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated TFs-DNA complexes, and then were isolated with myc antibody.
The experiments were performed following the procedures:  to identify each TF binding maps in vivo, we isolated the DNA bound to each TF from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen). ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65 degree. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation. The DNA samples incubated for primer extension were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. The experiments were performed in biological duplicate.

value: myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: D2_CD40L


title: Blood_depression_rep5

city: Shanghai

first: Ting

last: Zhou

address: No.6600, Nanfeng highway, Fengxian District

institute: Fengxian Hospital, Southern Medical University

description: gene ecpression in depressed patients

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Peripheral Blood,depression

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified usingPAXgeneTM  Blood RNA Kit (Cat#762174, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Ethylenediaminetetraacetic acid (EDTA)-treated whole blood samples from  depression patients and healthy volunteers were collected.

value: whole blood

tag: gender

value: male


title: D2_Nil


title: Blood_depression_rep1

description: gene ecpression in depressed patients

value: female


title: D2_BCR


title: Blood_depression_rep4

description: gene ecpression in depressed patients


title: TF_6_1


title: Blood_depression_rep6

description: gene ecpression in depressed patients


title: Kuramochi ITF/AZA Combined

value: Kuramochi


title: Blood_depression_rep3

description: gene ecpression in depressed patients


title: ArcA_2A1

value: custom anti-ArcA monoclonal antibody


title: TykNu Mock

value: Mock


title: D1_CD40L


title: Blood_healthy_rep1

description: gene ecpression in healthy people

source_name: Peripheral Blood,healthy


title: TF_5_2


title: D1_BCR


title: Kuramochi AZA


title: D1_Nil


title: Blood_healthy_rep3

description: gene ecpression in healthy people


title: D1_CD40L_BCR


title: TF_5_1


title: Blood_healthy_rep5

description: gene ecpression in healthy people


title: Blood_healthy_rep6

description: gene ecpression in healthy people


title: Blood_healthy_rep2

description: gene ecpression in healthy people


title: Blood_depression_rep2

description: gene ecpression in depressed patients


title: TykNu ITF/AZA Combined Rep3

description:
TykNu_trip_treat4_AZA_ITF.TEtranscripts.DESeq_gene_TE_analysis.txt
TykNu_trip_treat4_AZA_ITF.telescope_results.tsv

data_processing:
Check data with FastQC.
rRNA contamination was removed post-sequencing with SortMeRNA software and reads from both flow cells were combined together into one fastq file.
Reads were trimmed and adapters were removed using cutadapt using the --minimum-length 1 and -q 20 flags. The adapter sequences were -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Trimmed reads were aligned to hg38 using the following flags: --sjdbOverhang 100 --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100.
TEtranscripts was run on the STAR output with the following flags: --mode multi --stranded reverse. The GENCODEv21 and RepeatMasker GTF annotation files were supplied. The log2(Fold Change) values output by DESeq were used in subsequent analyses. See Jin et al. (2015) for further reference on TEtranscripts.
Telescope installation and usage instructions can be found here: https://github.com/mlbendall/telescope. Before starting, install miniconda and add the bioconda and conda-forge channels. Then create a conda environment specifically for this task: conda create -n telescope_env python=3.6 future pyyaml cython=0.29.7 numpy=1.16.3 scipy=1.2.1 pysam=0.15.2 htslib=1.9 intervaltree=3.0.2. Use the “telescope assign” command to quantify RE expression. Combine *report.tsv files as needed for processing with DESeq2. Use the log2(Fold Change) values in subsequent analysis. For further information, see Bendall et al. (2019).
Genome_build: hg38 GCA_000001405.15
Supplementary_files_format_and_content: TEtranscripts uses DESeq2 to output the fold changes of the repetitive elements. The *_gene_TE_analysis.txt files contain DESeq output.
Supplementary_files_format_and_content: Telescope outputs a report file. The *-telescope_report.tsv are tab-delimited text files containing this output.

growth_protocol: The TykNu cell line was cultured in RPMI 1640 (Corning, 10-104-CV) with 10% Fetal Bovine Serum (X&Y Cell Culture, FBS-500-HI), and 1% penicillin and streptomycin solution (Gibco, 15070063). The cell line was periodically tested for mycoplasma via the Lonza MycoAlert kit.

extract_protocol:
Following treatment, total RNA was extracted using Trizol (Thermo Scientific 15596026). Ribosomal RNA was depleted using Ribozero (Illumina).
RNA sequencing libraries were prepared by depleting rRNA from 1 ug of total RNA with the NEBNext rRNA Depletion Kit for Human (New England BioLabs, E6310). Libraries were then prepared by following the manufacturer’s protocol for the Illumina TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat kit (P/N 20020596). Custom 10 bp UDI TruSeq-Compatible Duplex Y Adapters from IDT were to index the libraries (IDT10_UDI_1 through IDT10_UDI_15). Final libraries were sent to the Washington University in St. Louis Center for Genome Sciences and combined into an equimolar pool for 2x150bp sequencing on an Illumina NovaSeq S4 (target read depth of 100 million). Note that each library was sequenced on two separate flow cells -- HG2LGDSXY and HHJFNDSXY -- and these data were combined and treated as a single biological replicate.


title: Blood_healthy_rep4

description: gene ecpression in healthy people


title: Kuramochi ITF


title: TykNu ITF Rep3

description:
TykNu_trip_treat2_ITF.TEtranscripts.DESeq_gene_TE_analysis.txt
TykNu_trip_treat2_ITF.telescope_results.tsv


title: TF_4_2


title: TykNu Mock Rep3


title: TF_4_1


title: TykNu AZA Rep3

description:
TykNu_trip_treat3_AZA.TEtranscripts.DESeq_gene_TE_analysis.txt
TykNu_trip_treat3_AZA.telescope_results.tsv


title: Kuramochi Mock


title: TykNu ITF/AZA Combined Rep2


title: Hey ITF/AZA Combined

value: Hey


title: TF_2_2


title: Hey ITF


title: TykNu AZA Rep1

value: AZA


title: Hey AZA


title: Hey Mock


title: A2780 ITF/AZA Combined


title: TykNu Mock Rep1


title: treat

city: wenzhou

first: Xiaohui

last: Zheng

address: Wenzhou Medical University, Chashan Street, Ouhai District, Wenzhou City, Zhejiang Province, China

department: College of Pharmacy

institute: Wenzhou Medical University

description: treated with D16

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads. And after removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64)
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)])
Genome_build: Homo sapiens
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: human breast cancer cell line, MDA-MB-231

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA). After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: MDA-MB-231 cells were incubated at 37 C in 5% CO2 and maintained in RPMI-1640 medium with 10% FBS and 100 U/mL penicillin and streptomycin.The active compound in our study is a novel chalcone named D16. The control group was cultured in nomral medium. The treated group was challenged in 24µM D16 for 48h.

value: triple negative breast cancer cells

tag: aav type

value: epithelial cell

value: treated with a novel chalcone (D16:24um) for 48h


title: TykNu Mock Rep2

value: TykNu


title: D2_CD40L_BCR

value: CD40L and BCR

value: In-vitro culture


title: TykNu ITF Rep1

value: ITF


title: TF_2_1

value: myc-tagging cells


title: TykNu AZA Rep2


title: A2780 AZA


title: TF_3_2

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: A2780 ITF


title: TF_1_2_2


title: U2OS-siTIP60 replicat 2

city: Quebec

first: Maeva

last: Devoucoux

state: Quebec

address: 9 rue MacMahon

institute: Laval University

data_processing:
For ChIP-seq, the single-end reads were mapped on the human genome build hg19 using bowtie version 2.1.6 (Langmead et al., 2009), using the pre-set sensitive parameter.
MACS version 2.0.10 (model-based analysis of ChIPseq) peak finding algorithm was used to identify regions of ChIP-seq enrichment over the background (Feng et al., 2012), using broad peaks parameters.
Unique mapped read values were normalized to library size. Peaks were annotated as per human genome EnsDb.Hspaiens.v75 - hg19
For  RNAseq, raw fast5 files were basecalled using Guppy v.4.2.2 using fast basecalling settings, and samples were demultiplexed according to barcodes with the guppy_barcoder.
The resulting FASTQ reads were aligned to the hg19 human reference with Minimap2 version 2.17-r941
Raw read counts were obtained with the featureCounts tool from the Subread package v 2.0.0, using the exon counting mode (Li, 2018; Liao et al., 2014) and normalized as Counts per Million (CPM).
Genome_build: hg19
Supplementary_files_format_and_content: MRG15_long_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the MRG15 long CHD 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: MRG15_short_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the MRG15 short CHD 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: MRGX_Flag.IgG.broad_peaks.broadPeak is a bed file containing significant MACS-called broad peaks for the MRGX 3xFlag-2xstrep ChIP sample using the IgG control sample as input sample.
Supplementary_files_format_and_content: JCote_RNAseq.DE.sig_cpm.xlsx is a tab separated excel file containing read counts for genes normalized to CPM for all RNA-seq samples.
Supplementary_files_format_and_content: Jcote_RNAseq_splicing.xlsx is a tab separated excel file containing the venn analysis between indicated samples. Fold change of 2 is used as threshold (pVal 0.01).

source_name: U2OS from ATCC

growth_protocol: DMEM, 10% FBS

extract_protocol:
Monarch Total RNA Miniprep Kit (NEB #T2010)
Libraries were prepared according to Illumina's instructions.

treatment_protocol: No treatment

value: epithelial cells from osteosarcoma

tag: growth conditions

value: normal growth conditions

tag: chip antibody

value: siTIP60, smartpool (Dharmacon)


title: U2OS-siTIP60 replicat 1

tag: cell line


title: TykNu ITF/AZA Combined Rep1

value: ITF/AZA Combined


title: control

description: without D16

value: Cultured in common medium


title: TF_1_2_1


title: U2OS-siMRGX replicat 2

tag: cell type

value: siMRGX, smartpool (Dharmacon)


title: L1824 - A2780 P53 ChIP AZA Rep 2

data_processing:
Check data with FastQC.
Trim adapter sequences with cutadapt using the -a AGATCGGAAGAGCACACGTCTGAACTCCAGT -q 20 and –minimum-length 1 flags.
Reads were aligned to the genome with Bowtie2, and the alignments were quality checked with ChIPQC.
Duplicate reads were marked with GATK MarkDuplicates (v4.0.8.0), and peaks were called with MACS2.
Peaks consistent across replicates were identified with the ENCODE IDR pipeline (https://github.com/kundajelab/idr) using an IDR cutoff of 0.05.
Genome_build: hg38 GCA_000001405.15
Supplementary_files_format_and_content: BED files generated by irreproducible discovery rate (IDR) analysis of the ChIP-seq data. IDR score is in the fifth column.

growth_protocol: The A2780 cells were cultured in RPMI 1640 (Corning, 10-104-CV) with 10% Fetal Bovine Serum (X&Y Cell Culture, FBS-500-HI), and 1% penicillin and streptomycin solution (Gibco, 15070063).

extract_protocol:
Cells were cross-linked for 10 minutes at room temperature. The samples were sheared using 2 μL MNase (NEB, M0247S) for 10 minutes, then briefly sonicated 4 cycles (30secs on/30secs off) at 4°C. Samples were then centrifuged and the supernatant was used as the input and for the downstream immunoprecipitation. The immunoprecipitation was performed following the manufacture’s protocol of the Active Motif Kit, using 4 μL of the p53 antibody (Bethyl Laboratories, A300-247A-M).
ChIP-seq library preparation was completed using the NEBNext Ultra II DNA Library Prep (NEB, E7103S) with multiplex oligos for barcoding (NEB, E7335S).

treatment_protocol: The A2780 cells were treated with 500 nM AZA (Sigma-Aldrich) or PBS for three days and 10 uM Nutlin-3A (Cayman Chemical 18585) or DMSO for 6 hours.

value: Bethyl Laboratories, A300-247A-M


title: U2OS-siMRGBP replicat 1

value: siMRGBP, smartpool (Dharmacon)


title: TF_1_3_2


title: U2OS-siLuc replicat 2

value: siLuciferase, DOYYA


title: TF_1_1_1

data_processing:
Library strategy: ChIP-exo
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: the reference genome ( MG1655 =  NC_000913.3 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

extract_protocol:
Lysates were clarified from sonicated TFs-DNA complexes, and then were isolated with myc antibody.
The experiments were performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen). ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65 degree. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation. The DNA samples incubated for primer extension were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. The experiments were performed in biological duplicate.


title: A2780 Mock

value: Mock


title: TF_1_1_2


title: TykNu ITF Rep2


title: U2OS-siMRG15 replicat 1

value: siMRG15, smartpool (Dharmacon)


title: U2OS-siMRGX replicat 1


title: ArcA_1

value: ArcA myc-tagging cells


title: L1819 - A2780 P53 ChIP N3A Rep 1


title: rpoD myc-tag 2

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: The reference genome  MG1655 =  NC_000913.2
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

treatment_protocol: For regulatory condition, M9 minimal media was supplemented with 1 mL trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2.

value: wild type cells

value: purified anti E.coli sigma factor 70, clone 2G10, BioLegend


title: S_15-023_16wpi [2H3]

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description:
Subject_023_Moderate_12w.p.i [P2H3]
Subject_023 Female Moderate 12w.p.i Total RNA

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2 and Ensembl 101
Aligned to genome using HISAT2 version 2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts per gene counts

source_name: Peripheral blood

extract_protocol:
RNA extraction and genomic DNA elimination was carried out using the PAXgene® Blood RNA kit (762164, Qiagen, Feldbachstrasse, Germany) as per the manufacturer’s instructions
Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the Nugen Universal Plus Total RNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturer’s instructions (MO1523 v2) using 12 cycles of PCR amplification for the final libraries. An Anydeplete probe mix targeting both human ribosomal and adult globin transcripts (HBA1, HBA2, HBB, HBD) was used to deplete these transcripts.
Total RNA-Seq 2x150 bp paired-end reads.

tag: Sex

value: Female

tag: disease severity

value: Moderate

tag: rin

tag: sample number

value: Peripheral blood

tag: timepoint


title: TF_3_1

tag: strain

value: myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: S_HC17_Control [2G6]

description:
HC17_Healthy_Healthy_Control [P2G6]
HC17 Female Healthy Healthy_Control Total RNA

value: Healthy

tag: tissue

value: Control


title: S_HC12_Control [2G5]

description:
HC12_Healthy_Healthy_Control [P2G5]
HC12 Female Healthy Healthy_Control Total RNA


title: L1818 - A2780 P53 ChIP Mock Rep 1

tag: treatment


title: S_15-013_16wpi [2G3]

description:
Subject_013_Mild_12w.p.i [P2G3]
Subject_013 Male Mild 12w.p.i Total RNA

value: Male

value: Mild


title: U2OS-siBRD8 replicat 2

value: epithelial cells from osteosarcoma

value: normal growth conditions

value: siBRD8, Sigma (SASI_Hs01_00131635)


title: rpoD myc-tag 1

tag: myc-tagging

tag: chip-exo antibody


title: L1816 - A2780 P53 Input AZA Rep 1

value: Bethyl Laboratories, A300-247A-M


title: S_15-041_16wpi [2G1]

description:
Subject_041_Critical_12w.p.i [P2G1]
Subject_041 Male Critical 12w.p.i Total RNA

tag: age

value: Critical


title: S_HC16_Control [2F6]

description:
HC16_Healthy_Healthy_Control [P2F6]
HC16 Female Healthy Healthy_Control Total RNA


title: U2OS-siBRD8 replicat 1


title: L1823 - A2780 P53 ChIP N3A Rep 2


title: S_HC11_Control [2F5]

description:
HC11_Healthy_Healthy_Control [P2F5]
HC11 Female Healthy Healthy_Control Total RNA


title: rpoB myc-tag 1

value: purified anti E.coli RNA polymerase β, clone NT63, catalog 663006,BioLegend


title: TF_1_3_1


title: ArcA_2

value: ArcA myc-tagging cells


title: L1815 - A2780 P53 Input N3A Rep 1


title: L1814 - A2780 P53 Input Mock Rep 1

value: Mock


title: U2OS-siMRG15 replicat 2

value: siMRG15, smartpool (Dharmacon)


title: L1822 - A2780 P53 ChIP Mock Rep 2


title: S_15-023_24wpi [2H4]

description:
Subject_023_Moderate_20w.p.i [P2H4]
Subject_023 Female Moderate 20w.p.i Total RNA

value: Female

value: Moderate


title: 4hpa_rep2

city: Hsinchu

first: Yi-Fan

last: Lin

address: 101 Sec.2, Kuang-Fu Rd.

country: Taiwan

institute: National Tsing-Hua University

data_processing:
Tophat and Cufflinks
DESeq2 Differential Analysis in R
Supplementary_files_format_and_content: raw count and normalized counts

organism: Danio rerio

source_name: larval fin fold

extract_protocol:
Fin folds were collected in cold PBS, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq RNA Library Prep Kit v2 (Illumina)

value: larval fin fold

value: 4h post amputation


title: 4hpa_rep1


title: U2OS-siLuc replicat 1

value: siLuciferase, DOYYA


title: yhjB myc-tag 2

value: YhjB myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: HUB-JP-014

first: Jens

last: Puschhof

address: Uppsalalaan 8

institute: Hubrecht Institute

description:
Single cell sequencing plate
Cells were sorted into a 384 well plate and processed for singel cell sequencing

data_processing:
Single cell data were demultiplexed, paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: hg19
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated, poisson corrected counts.

source_name: Human intestinal organoids

growth_protocol: Organoids were differentiated or grown in expansion medium for 5 days before sorting.

extract_protocol: RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.

treatment_protocol: Live cells  were sorted in 384-  well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a  24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA  kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.

tag: genotype

value: wt

value: Intestine


title: HUB-JP-012


title: S_15-047_24wpi [2F4]

description:
Subject_047_Mild_20w.p.i [P2F4]
Subject_047 Female Mild 20w.p.i Total RNA

value: Mild

value: Peripheral blood


title: Uncut fin fold_rep2

value: uncut


title: ygfI myc-tag 2

value: YgfI myc-tagging cells


title: HUB-JP-004

description:
Single cell sequencing plate
Cells were sorted into a 384 well plate and processed for singel cell sequencing; cells 193-384 contain an experimental differentiation condition and are filtered out before comparing between expansion and differentiation medium


title: S_15-013_24wpi [2G4]

description:
Subject_013_Mild_20w.p.i [P2G4]
Subject_013 Male Mild 20w.p.i Total RNA

value: Male


title: U2OS-siMRGBP replicat 2

value: epithelial cells from osteosarcoma

value: normal growth conditions

value: siMRGBP, smartpool (Dharmacon)


title: Uncut fin fold_rep1


title: S_15-056_24wpi [2E4]

description:
Subject_056_Mild_20w.p.i [P2E4]
Subject_056 Female Mild 20w.p.i Total RNA

value: Female


title: 4hpa_rep3


title: S_15-060_16wpi [2F1]

description:
Subject_060_Severe_12w.p.i [P2F1]
Subject_060 Male Severe 12w.p.i Total RNA

value: Severe


title: L1820 - A2780 P53 ChIP AZA Rep 1

value: Bethyl Laboratories, A300-247A-M


title: 11_1_Airway air liquid interface bulk

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

description:
Bulk RNA sequencing of human airway air-liquid interface cultures derived from airway organoids
Sample 11

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg38. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: hg38
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts normalized between samples.

source_name: Airway ALI culture

growth_protocol: Organoids were grown in expansion medium as previous described.

extract_protocol:
RNA from whole organoids was extracted using Trizol isolation
RNA was processed using the previously described SORT-seq technique (for bulk samples), which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.

treatment_protocol: Organoids were kept as untreated control in expansion medium or differentiated using the indicated differentiation medium as previously described. Air-liquid interface (ALI) cultures were established from airway organoids of particular sections of the airway. The ALI cultures were established as previously described and maintained at ALI for 3 weeks

value: Wildtype

value: Bronchiole

tag: culture method

value: air-liquid interface culture


title: S_HC14_Control [2E6]

description:
HC14_Healthy_Healthy_Control [P2E6]
HC14 Male Healthy Healthy_Control Total RNA

value: Healthy

value: Control


title: ypdC myc-tag 1

source_name: bacteria cells

value: YpdC myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: S_15-047_16wpi [2F3]

description:
Subject_047_Mild_12w.p.i [P2F3]
Subject_047 Female Mild 12w.p.i Total RNA

value: Mild

value: Peripheral blood


title: S_15-060_24wpi [2F2]

description:
Subject_060_Severe_20w.p.i [P2F2]
Subject_060 Male Severe 20w.p.i Total RNA


title: S_15-039_24wpi [2E2]

description:
Subject_039_Mild_20w.p.i [P2E2]
Subject_039 Male Mild 20w.p.i Total RNA


title: S_15-041_24wpi [2G2]

description:
Subject_041_Critical_20w.p.i [P2G2]
Subject_041 Male Critical 20w.p.i Total RNA

value: Critical


title: rpoB myc-tag 2

value: wild type cells

value: purified anti E.coli RNA polymerase β, clone NT63, catalog 663006,BioLegend


title: RNAseq RsmA 1

city: Dunedin

first: Peter

middle: Charles

last: Fineran

state: Otago

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

description:
countsWTvsrsmAnormalized.xlsx
RsmA1

data_processing:
Base calling with Illumina Sequencer RTA version 1.18.64
FASTQ conversion with Bcl2fastq version 2.18.0.12
FASTQ quality assesment using FASTQC v0.11.5
Trimming of the TruSeq3 sequence from FASTQ files using the ILLUMINACLIP option of Trimmomatic version 0.39
Read alignment to the Serratia geome using Bowtie2 version 2.3.5.1 using default parameters
Conversion of SAM to BAM format using Samtools version 1.9
Differential expression analysis performed using DESeq2 version 1.30.1 with FDR < 5% and fold change > 1.5
Genome_build: CP025085.1 (GenBank)
Supplementary_files_format_and_content: Processed data includes normalized counts (median of ratios method) for each locus tag and sample (wildtype and rsmaA replicates), generated using the estimateSizeFactors() function of DESeq2

organism: Prodigiosinella confusarubida

source_name: Serratia sp. ATCC 39006 cells

growth_protocol: RsmA_(NMW7) and WT control strains were grown for 12 h and 2 ml samples harvested by centrifugation. Cell pellets were resuspended in RNAlater.  RNA extracted from 12h culture.

extract_protocol:
RNA extracted from cell pellets using the Qiagen Rneasy kit, Turbo Dnase treatment was performed to remove any gDNA.
rRNA depletion using RiboCop rRNA depletion kit (Lexogen). Antisense cDNA initiated through a TruSeq adaptor, and sequencing adaptors were ligated.

treatment_protocol: No treatment applied during growth

tag: replicate

value: RsmA mutation

tag: growth phase

value: stationary phase


title: 10_1_Airway air liquid interface bulk

description:
Bulk RNA sequencing of human airway air-liquid interface cultures derived from airway organoids
Sample 10

value: Bronchus


title: ygaV myc-tag 2

value: YgaV myc-tagging cells


title: ygbI myc-tag 1

value: YgbI myc-tagging cells


title: S_HC3_Control [2E5]

description:
HC3_Healthy_Healthy_Control [P2E5]
HC3 Male Healthy Healthy_Control Total RNA

value: Male


title: 9_2_Airway air liquid interface bulk

description:
Bulk RNA sequencing of human airway air-liquid interface cultures derived from airway organoids
Sample 9_1

value: Wildtype

value: Trachea


title: HUB-JP-006

value: wt

value: Intestine


title: ygaV myc-tag 1


title: S_15-010_24wpi [2D6]

description:
Subject_010_Mild_20w.p.i [P2D6]
Subject_010 Male Mild 20w.p.i Total RNA


title: 9_1_Airway air liquid interface bulk

description:
Bulk RNA sequencing of human airway air-liquid interface cultures derived from airway organoids
Sample 9

value: air-liquid interface culture


title: ypdC myc-tag 2

value: YpdC myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: yhjB myc-tag 1

value: YhjB myc-tagging cells


title: Uncut fin fold_rep3

value: larval fin fold

value: uncut


title: 10_2_Airway air liquid interface bulk

description:
Bulk RNA sequencing of human airway air-liquid interface cultures derived from airway organoids
Sample 10_1


title: ygfI myc-tag 1

value: YgfI myc-tagging cells


title: yfjR myc-tag 2

value: YfjR myc-tagging cells


title: 8_1_Airway organoid bulk

description:
Bulk RNA sequencing of human airway organoid, in differentiation medium.
Sample 8

source_name: Airway organoids

value: Nasal epithelium

value: differentiation medium


title: RNAseq LacA 1

description:
countsWTvsrsmAnormalized.xlsx
WT1

value: WT control

value: stationary phase


title: RNAseq LacA 3

description:
countsWTvsrsmAnormalized.xlsx
WT3


title: yeeY myc-tag 1

value: YeeY myc-tagging cells


title: S_15-017_24wpi [2D4]

description:
Subject_017_Severe_20w.p.i [P2D4]
Subject_017 Male Severe 20w.p.i Total RNA

value: Male

value: Severe

value: Peripheral blood


title: S_15-056_16wpi [2E3]

description:
Subject_056_Mild_12w.p.i [P2E3]
Subject_056 Female Mild 12w.p.i Total RNA

value: Female

value: Mild


title: S_15-010_16wpi [2D5]

description:
Subject_010_Mild_12w.p.i [P2D5]
Subject_010 Male Mild 12w.p.i Total RNA


title: 11_2_Airway air liquid interface bulk

description:
Bulk RNA sequencing of human airway air-liquid interface cultures derived from airway organoids
Sample 11_1

value: Wildtype

value: Bronchiole

value: air-liquid interface culture


title: yeeY myc-tag 2

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: RNAseq RsmA 3

description:
countsWTvsrsmAnormalized.xlsx
RsmA3

value: RsmA mutation


title: S_15-039_16wpi [2E1]

description:
Subject_039_Mild_12w.p.i [P2E1]
Subject_039 Male Mild 12w.p.i Total RNA


title: S_15-024_24wpi [2D2]

description:
Subject_024_Mild_20w.p.i [P2D2]
Subject_024 Female Mild 20w.p.i Total RNA


title: RNAseq LacA 2

description:
countsWTvsrsmAnormalized.xlsx
WT2


title: yfjR myc-tag 1


title: RNAseq RsmA 2

description:
countsWTvsrsmAnormalized.xlsx
RsmA2


title: 7_2_Airway organoid bulk

description:
Bulk RNA sequencing of human airway organoid, in expansion medium.
Sample 7_1

value: expansion medium


title: 8_2_Airway organoid bulk

description:
Bulk RNA sequencing of human airway organoid, in differentiation medium.
Sample 8_1


title: ygbI myc-tag 2

value: YgbI myc-tagging cells


title: C2C12 H3K27ac (primary-Ab ChIL) at 100 cells replicate 1

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Custom demultiplexing step of mtChIL library. (1) Extracting the index reads using bcl2fastq (version. 2.2.0) with the option: --create-fastq-for-index.  (2) Run deML (version 1.1.3): deML -if1 i1.fq.gz -if2 i2.fq.gz -f r1.fq.gz -i index.txt, where the FASTQ (fq.gz) files are i1.fq.gz (index-1), i2.fq.gz (index-2) and r1.fq.gz (read-1) respectively. The index.txt is the definition of the custom dual indices of mtChIL, which consists of the tab–delimited fields of the index-1, -2 and the sample name.
Mapping: run hisat2 (version 2.1.0)  with the option "--no-spliced-alignment" using the mouse genome index (grcm38_snp).
Signal tracks: deepTools (version 3.3.1) bamCoverage with the option "-bs 100 --smoothLength 1000 --normalizeUsing CPM --minMappingQuality 60 --ignoreDuplicates" ("-bs 1000 --smoothLength 10000" for H3K27me3).
Count matrix: deepTools (version 3.3.1) multiBamSummary with the option "bins -bs 1000 --ignoreDuplicates --minMappingQuality 60"
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix: CSV (gzipped), signal tracks: bigWig

source_name: Immortal cell line

extract_protocol: Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary antibody and the ChIL probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChIL DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.

tag: cell line

tag: antibody target

tag: primary antibody

value: mouse monoclonal anti–H3K27ac (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA309)

tag: number of cells


title: C2C12 H3K27ac (primary-Ab ChIL) at 100 cells replicate 2


title: C2C12 H3K27me3 (primary-Ab ChIL) at 100 cells replicate 2

value: mouse monoclonal anti–H3K27me3 (Hayashi-Takanaka et al, Nucleic Acids Res. 2011 Aug;39(15):6475-88., CMA323)


title: S_15-017_16wpi [2D3]

description:
Subject_017_Severe_12w.p.i [P2D3]
Subject_017 Male Severe 12w.p.i Total RNA

tag: Sex

tag: disease severity

tag: rin


title: S_15-024_16wpi [2D1]

description:
Subject_024_Mild_12w.p.i [P2D1]
Subject_024 Female Mild 12w.p.i Total RNA

tag: sample number

tag: timepoint


title: yeaM myc-tag 2

tag: strain

value: YeaM myc-tagging cells


title: 6_2_Intestinal organoid bulk

description:
Bulk RNA sequencing of human intestinal organoid, in expansion medium.
Sample 6_1

source_name: Intestinal organoids

tag: tissue

value: Intestine


title: 7_1_Airway organoid bulk

description:
Bulk RNA sequencing of human airway organoid, in expansion medium.
Sample 7

value: Nasal epithelium


title: 6_1_Intestinal organoid bulk

description:
Bulk RNA sequencing of human intestinal organoid, in expansion medium.
Sample 6


title: C2C12 H3K27me3 (primary-Ab ChIL) at 100 cells replicate 1


title: S_15-025_16wpi [2C5]

description:
Subject_025_Mild_12w.p.i [P2C5]
Subject_025 Female Mild 12w.p.i Total RNA


title: S_15-057_24wpi [2C4]

description:
Subject_057_Mild_20w.p.i [P2C4]
Subject_057 Male Mild 20w.p.i Total RNA

value: Male


title: S_15-057_16wpi [2C3]

description:
Subject_057_Mild_12w.p.i [P2C3]
Subject_057 Male Mild 12w.p.i Total RNA


title: 1_2_Intestinal organoid bulk

description:
Bulk RNA sequencing of human intestinal organoid, in differentiation medium.
Sample 1_1

value: differentiation medium


title: C2C12 H3K4me3 (primary-Ab ChIL) at 100 cells replicate 2

value: mouse monoclonal anti–H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: C2C12 Pol2S2P of H3K27ac&Pol2S2P at 1k cells replicate 3

description: library strategy: mtChIL-seq

data_processing:
Custom demultiplexing step of mtChIL library. (1) Extracting the index reads using bcl2fastq (version. 2.2.0) with the option: --create-fastq-for-index.  (2) Run deML (version 1.1.3): deML -if1 i1.fq.gz -if2 i2.fq.gz -f r1.fq.gz -i index.txt, where the FASTQ (fq.gz) files are i1.fq.gz (index-1), i2.fq.gz (index-2) and r1.fq.gz (read-1) respectively. The index.txt is the definition of the custom dual indices of mtChIL, which consists of the tab–delimited fields of the index-1, -2 and the sample name.
Mapping: run hisat2 (version 2.1.0)  with the option "--no-spliced-alignment" using the mouse genome index (grcm38_snp).
Signal tracks: deepTools (version 3.3.1) bamCoverage with the option "-bs 100 --smoothLength 1000 --normalizeUsing CPM --minMappingQuality 60 --ignoreDuplicates"
Count matrix: deepTools (version 3.3.1) multiBamSummary with the option "bins -bs 1000 --ignoreDuplicates --minMappingQuality 60"
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix: CSV (gzipped), signal tracks: bigWig

value: mouse monoclonal anti–Pol2S2P (Stasevich et al., Nature. 2014;516(7530):272-275., CMA602)


title: yeaM myc-tag 1

tag: myc-tagging

tag: chip-exo antibody


title: S_15-025_24wpi [2C6]

description:
Subject_025_Mild_20w.p.i [P2C6]
Subject_025 Female Mild 20w.p.i Total RNA

tag: age

value: Female

value: Mild

value: Peripheral blood


title: 1_1_Intestinal organoid bulk

description:
Bulk RNA sequencing of human intestinal organoid, in differentiation medium.
Sample 1

tag: genotype

value: Wildtype

tag: culture method


title: ybcM myc-tag 2

value: YbcM myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: C2C12 Pol2S2P of H3K27ac&Pol2S2P at 1k cells replicate 1

description: library strategy: mtChIL-seq


title: LNCaP RES-A [scRNA-seq]

city: Tampere

first: Sinja

last: Taavitsainen

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
Raw base calls from sequencing were processed into FASTQ format using cellranger mkfastq from 10x Genomics Cell Ranger v3.0.2 (Zheng et al., 2017).
Alignment and single-cell feature count matrix generation was performed using cellranger count from 10x Genomics Cell Ranger v3.0.2 (Zheng et al., 2017). We used the Cell Ranger pre-built GRCh38 reference data v3.0.0. From the results, we utilized the filtered gene-barcode matrices, which contains the detected cellular barcodes and has been filtered for background and non-cellular barcodes.
Genome_build: hg38
Supplementary_files_format_and_content: 10x Genomics Cell Ranger filtered cell barcodes and genes (features) in TSV format and filtered gene-barcode count matrices in MTX format.

source_name: LNCaP cells

growth_protocol: LNCaP parental (ATCC), RES-A, and RES-B cells were cultured in RPMI 1640 (Sigma R0883) supplemented with 10% FBS (Sigma F7524), 2 mM Alanyl-glutamine (Sigma G8541), 1 mM sodium pyruvate (Merck TMS-005-C), 2.5 g/L glucose (Sigma G8769), and 1x Antibiotic-Antimycotic (Gibco, 15240062) in a humidified 37°C incubator with 5% CO2. RES-A and RES-B cells additionally received 10 µM enzalutamide (MedChemExpress HY-70002) with each cell splitting/feeding.

extract_protocol:
LNCaP parental (treated for 48 hours with enzalutamide or DMSO), RES-A, and, RES-B cells were harvested with 0.05% Trypsin-EDTA (Sigma T3924). After neutralization with complete medium, centrifugation (300 x g for 5 min), and resuspension in PBS/0.5% BSA, the cells were filtered through a 35 µm Cell Strainer (Corning 352235) and a single-cell suspension of living cells was acquired through sorting on a FACS Aria II cell sorter.
Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit, and Chip Kit (v3, 10x Genomics)

treatment_protocol: Cells were seeded into 5 cm culture plate dishes and allowed to settle before exposure to 10 µM enzalutamide or DMSO vehicle control (0.1%) for 48 hours.

value: LNCaP

tag: cell type

value: prostate cancer cell line

tag: enzalutamide sensitivity

value: resistant

tag: treatment

value: maintained in 10 µM enzalutamide


title: ydcR myc-tag 2

value: YdcR myc-tagging cells


title: C2C12 Pol2S2P of H3K27ac&Pol2S2P at 1k cells replicate 2

description: library strategy: mtChIL-seq

tag: cell line

tag: antibody target

tag: primary antibody


title: LNCaP DMSO [scRNA-seq]

value: sensitive

value: 0.1% DMSO for 48 hours


title: LNCaP RES-B [scRNA-seq]


title: LNCaP ENZ 48hrs  [scRNA-seq]

value: 10µM enzalutamide for 48 hours


title: C2C12 Pol2S2P of H3K27ac&Pol2S2P at 100 cells replicate 2

description: library strategy: mtChIL-seq

tag: number of cells


title: ybdO myc-tag 1

value: YbdO myc-tagging cells


title: ydcR myc-tag 1


title: C2C12 H3K4me3 (primary-Ab ChIL) at 100 cells replicate 1

value: mouse monoclonal anti–H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: ybdO myc-tag 2


title: LNCaP RES-B [scATAC-seq]

data_processing:
Raw base calls from sequencing were processed into FASTQ format using cellranger-atac mkfastq from 10x Genomics Cell Ranger ATAC v1.1.0 (Satpathy et al., 2019).
Alignment was performed using cellranger-atac count from 10x Genomics Cell Ranger ATAC v1.1.0 (Satpathy et al., 2019). The same tool was further used to generate single-cell chromatin accessibility counts from each cell in the form of a peak-barcode matrix. From the results, we utilized the filtered peak-barcode matrices, which contains the detected cellular barcodes and has been filtered for background and non-cellular barcodes.
Genome_build: hg38
Supplementary_files_format_and_content: 10X Genomics Cell Ranger ATAC filtered cell barcodes and fragment files in TSV format, filtered peak-barcode count matrices in MTX format, and peak locations in BED format.

extract_protocol:
Cell nuclei were isolated following the 10x Genomics Demonstrated Protocol for Single Cell ATAC Sequencing (CG000169-Rev C). Briefly, the cell suspension was washed once in PBS/0.04%BSA, and 2 x 105 cells were pelleted (300 x g for 5 min), resuspended in 100 µl freshly prepared Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40 Substitute, 0.01% Digitonin, 1% BSA), and incubated on ice for 4 min (LNCaP parental cells), 6 min (RES-A), or 5 min (RES-B). The lysates were diluted with 1 ml wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA), and the nuclei were pelleted (500 x g for 5 min) and resuspended in 30 µl 1x Nuclei Buffer (10x Genomics PN-2000153). Successful preparation of intact, isolated nuclei was confirmed through visual inspection in a phase-contrast microscopy, and nuclei concentration was assessed with a Countess II FL Automated Cell Counter
Single Cell ATAC sequencing using 10x Chromium, 10x Genomics library preparation and the Chromium Single Cell ATAC Reagent Kits (v1) User Guide (CG000168 Rev D).


title: C2C12 Pol2S2P of H3K27ac&Pol2S2P at 100 cells replicate 1

description: library strategy: mtChIL-seq

value: mouse monoclonal anti–Pol2S2P (Stasevich et al., Nature. 2014;516(7530):272-275., CMA602)


title: yihL myc-tag 2

value: YihL myc-tagging cells


title: C2C12 Pol2S2P of H3K27ac&Pol2S2P at 100 cells replicate 3

description: library strategy: mtChIL-seq


title: S_15-061_16wpi [2C1]

description:
Subject_061_Moderate_12w.p.i [P2C1]
Subject_061 Male Moderate 12w.p.i Total RNA

tag: Sex

value: Male

tag: disease severity

value: Moderate

tag: rin


title: S_15-040_16wpi [2B3]

description:
Subject_040_Moderate_12w.p.i [P2B3]
Subject_040 Female Moderate 12w.p.i Total RNA

value: Female

tag: sample number

value: Peripheral blood

tag: timepoint


title: ybcM myc-tag 1

tag: strain

tag: myc-tagging

value: YbcM myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: yihL myc-tag 1

tag: chip-exo antibody


title: S_15-004_24wpi [2B6]

description:
Subject_004_Mild_20w.p.i [P2B6]
Subject_004 Male Mild 20w.p.i Total RNA

tag: age

value: Mild

tag: tissue


title: S_15-037_24wpi [2A6]

description:
Subject_037_Moderate_20w.p.i [P2A6]
Subject_037 Female Moderate 20w.p.i Total RNA


title: ydiP myc-tag 2

value: YidP myc-tagging cells


title: LNCaP DMSO [scATAC-seq]

value: LNCaP

tag: cell type

value: prostate cancer cell line


title: S_15-037_16wpi [2A5]

description:
Subject_037_Moderate_12w.p.i [P2A5]
Subject_037 Female Moderate 12w.p.i Total RNA


title: S_15-040_24wpi [2B4]

description:
Subject_040_Moderate_20w.p.i [P2B4]
Subject_040 Female Moderate 20w.p.i Total RNA


title: S_15-004_16wpi [2B5]

description:
Subject_004_Mild_12w.p.i [P2B5]
Subject_004 Male Mild 12w.p.i Total RNA


title: S_15-061_24wpi [2C2]

description:
Subject_061_Moderate_20w.p.i [P2C2]
Subject_061 Male Moderate 20w.p.i Total RNA


title: C2C12 H3K27ac of H3K27ac&Pol2S2P at 1k cells replicate 2

description: library strategy: mtChIL-seq

value: mouse monoclonal anti–H3K27ac (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA309)


title: S_15-031_24wpi [2A4]

description:
Subject_031_Mild_20w.p.i [P2A4]
Subject_031 Female Mild 20w.p.i Total RNA


title: C2C12 Pol2S2P at 1k cells replicate 2

description: library strategy: mtChIL-seq


title: S_15-031_16wpi [2A3]

description:
Subject_031_Mild_12w.p.i [P2A3]
Subject_031 Female Mild 12w.p.i Total RNA


title: LNCaP ENZ 48hrs [scATAC-seq]

tag: enzalutamide sensitivity

value: sensitive


title: LNCaP RES-A [scATAC-seq]

value: resistant

tag: treatment

value: maintained in 10 µM enzalutamide


title: yjhI myc-tag 1

value: YjhI myc-tagging cells