title: 06_VPC13789_ETOH_rep3

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

data_processing:
Base calling was performed using the BGISeq500 platform. The raw reads were pre-filtered by removing adaptor sequences, contamination and low-quality reads.
The high quality of the filtered reads was confirmed using the FastQC (Andrews, 2014) quality control tool.
The reads were mapped and annotated using STAR Aligner (Dobin et al., 2013) (version 2.6.1c).
The reads were counted using featureCounts (Liao, Smyth, & Shi, 2014).
Differential gene expression analysis for different treatments was performed using the DESeq2 (Love, Huber, & Anders, 2014).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: DESeq2 Differential Expression Analysis results as a Microsoft Excel Spreadsheet.

source_name: LNCaP cells

growth_protocol: LNCaP cells (6 x 10^6) were seeded in RPMI 1640 media containing 10% FBS and 1% penicillin/streptomycin. Following O/N incubation, the media was changed to RPMI 1640 containing 5% CSS and the cells were then grown for 48hrs at 37C with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol and the Qiagen RNeasy RNA Extraction Kit. Three biological replicas were collected for each condition.  The concentrations and the qualities of the RNA samples were checked by Nanodrop and tape station. All RIN values were between 9.5 and 10.
Library was constructed by BGI using library construction methods underlying the BGISEQ-500 platform.

treatment_protocol: On the day of treatment, the cells were treated with 10nM DHT and either DMSO (Control) or 1.5µM Enzalutamide, or 3µM VPC-13789. Concentration of the compound was selected based on the published IC90. Cells were treated for 6 hours before RNA isolation.

value: LNCaP


title: PLD1_16w_03

status: Public on Apr 05 2022

type: SRA

city: Tsukuba

first: Yoshiyuki

last: Nagumo

address: 1-1-1 Tennodai

department: Urology

country: Japan

institute: University of Tsukuba

library_source: transcriptomic

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 7.5.1; Qiagen, Redwood City, CA).
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: bladder tissue

extract_protocol:
Total RNA from excised whole bladders was isolated using a NucleoSpin RNA kit (TaKaRa).
For RNA sequencing, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) according to the manufacturer's instructions. Library preparation was performed using an NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

tag: tissue

value: bladder tissue

tag: strain

tag: genotype

value: PLD1 knockout

tag: treatment

value: BBN 16 weeks


title: ADSC, Donor 55, SFD culture condition

city: Seoul

first: Min Hee

last: Kang

state: Gangnam-gu

address: Dong won Building, 333

country: South Korea

institute: Xcell Therapeutics

description: RNA seq sample

data_processing:
Sequenced on an Ion Torrent S5xl machine (Thermo Fisher). Normalized method using ampliSeq RNA Plug in (ver 5.6.0.3) by Torrent Suite Software (Thermo Fisher).
Data mining and graphic visualization were performed using ExDEGA (Ebiogen Inc., Korea)
Assembly: hg19_ampliseq_transcriptome_ercc_v1
Supplementary files format and content: tab-delimited text files include expression values for each Sample

organism: Homo sapiens

source_name: adipose derived

growth_protocol: Human adipose tissue was obtained from plastic surgeries from Dr. Jung (Dacapo Dental Hospital, Seoul, Korea). ADSCs were isolated by mechanical and enzymatical treatment of the tissue as described previously [24]. In brief, adipose tissue was minced manually into small fragments and digested with 0.075% collagenase type I (Gibco, Thermo Fisher Scientific, MA, USA) in a water bath at 37C. The digested tissue was centrifuged and filtered in sequential steps to separate the ADSCs from the surrounding tissue. The isolated ADSCs were expanded in low glucose DMEM supplemented with 10% FBS and 1% penicillin/streptomycin (P/S; HyClone, Cytiva, Marlborough, MA, USA), or in serum free establishment media (CellCor establishment media, Xcell Therapeutics, Seoul, Korea). After reaching 85% confluency, cells were digested with Accutase (Gibco) and seeded (3 x 105 cells) in a T75 culture flask (Corning, Oneonta, NY, USA).

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed using Agilent 2100 bioanalyzer with the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, Netherlands). RNA was quantified using ND-2000 spectrophotometer (Thermo Fisher Scientific).
AmpliSeq libraries were constructed and sequenced on the Ion Torrent S5xl platform (Thermo Fisher) according to the manufacturer’s instructions.
For human gene analysis in cell lines, the Ion AmpliSeq Transcriptome Human Gene Expression Kit is designed for targeted amplification of over 20,000 human RefSeq genes simultaneously in a single primer pool.
A short amplicon (~ 110 base pairs (bp)) is amplified for targeted gene. For each sample, 30 ng of total RNA was used for cDNA library preparation.
Multiple libraries were multiplexed and clonally amplified using the Ion Chef System (Thermo Fisher).

treatment_protocol: Not applicable

value: adipose derived

tag: cell line

value: MSC

tag: cell type

value: ADSC

value: WT


title: 06_VPC13789_ETOH_rep2


title: 06_VPC13789_ETOH_rep1


title: PLD1_16w_01


title: MT-C rep 1 [G3_1C]

city: Blacksburg

first: Zachary

last: Johnson

state: VA

address: 1015 Life Science Cir

department: FLSI

country: USA

institute: Virginia Tech

data_processing:
library strategy: RNA bisulfite sequencing
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases
meRanGh v1.2.1 was used to map reads to C2T and G2A converted reference genomes
umi-Tools was used to identify and remove PCR duplicates
meRanCall was used to call m5C sites from mapped read files
In-house scripts using Python 3.9 and R 4.1.1 were used to further filter and process methylation calling files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited transcript abundance counts for all mitochondrial samples and all RNAseq samples
Supplementary_files_format_and_content: tab-delimited files containing methylation calling information for each called methylated site

molecule: polyA RNA

source_name: Neural stem cells

extract_protocol:
Mitochondria were isolated from NSCs cultured in medium containing 10 μmol/L folic acid using the mitochondrial isolation kit for culture cells (Abcam, ab110171) following the manufacturer's instructions. The isolated mitochondria were used for RNA extraction with DNase digestion. One round of poly(A) selection was performed to enrich mitochondrial mRNA molecules
RNA bisulfite conversion was performed as described previously with minor modifications. Briefly, poly(A) RNA was first mixed with spiked-in Xef1 unmethylated RNA at a ratio of 0.5%. The spiked-in unmethylated mRNA was transcribed from the pTRI-Xef plasmid supplied by the MEGAscript™ T7 Transcription Kit (Invitorgen), which encodes 1.85 kb Xenopus elongation factor 1α mRNA according to the manufacturer’s manual. Briefly, the linearized pTRI-Xef plasmid was in vitro transcribed in a reaction with MEGAscript T7 RNA polymerase (Ambion) at 37 °C for 4 h, followed by DNase treatment at 37 °C for 15min to remove DNA template and then purified by RNeasy Mini Kit (QIAGEN).  RNA bisulfite conversion was performed with an initial denaturation at 95°C for 1min, followed by three cycles of 70°C for 10min and 64°C for 45min using the EZ RNA methylation Kit (Zymo Research). The bisulfite converted RNA was subjected to stranded RNA-seq library construction procedure using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).

value: Neural stem cells

tag: fraction

value: Mitochondrial fraction

tag: conversion status

value: RNA BS-seq

tag: preparation condition

value: Preparation condition C:RNA fragmentation was performed first, then bisulfite conversion was performed using three cycles of 95°C for 1min, 70°C for 10min and 64°C for 45min, random primers were used for 1st strand cDNA synthesis


title: PLD1_16w_02


title: MT RNAseq rep 2 [G5_2E_RNA_seq]

data_processing:
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases
meRanGh v1.2.1 was used to map reads to C2T and G2A converted reference genomes
umi-Tools was used to identify and remove PCR duplicates
meRanCall was used to call m5C sites from mapped read files
In-house scripts using Python 3.9 and R 4.1.1 were used to further filter and process methylation calling files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited transcript abundance counts for all mitochondrial samples and all RNAseq samples
Supplementary_files_format_and_content: tab-delimited files containing methylation calling information for each called methylated site

value: RNAseq


title: tracer tRNA replicate 2

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

data_processing:
basecalling was performed by VBCF sequencing facility
Reads (if libraries were pair-end sequenced, only R1 mate was further processed) were trimmed for adapter sequences and low quality bases with q score less than 10 were removed from the 3' end using the cutadapt software. Command line: cutadapt -q 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC input.fastq > output_trimmed.fastq
Reads were further mapped to the collapsed tRNA annotation originating from https://github.com/FlorianPichot/tRNA_reference_construction . Command line:  bowtie2 --no-unal --no-1mm-upfront -D 15 -R 2 -N 0  -L 10 -i S,1,1.15 -x index -U sample.fastq -S output.sam 2> sample_mapping_report.txt
Sam files were converted to bam file, sorted and indexed using samtools (samtools view -S -b; samtools sort; samtools index)
Number of reads mapping to individual tRNA cluster was extracted by samtools idxstats. Command line samtools idxstats sample_sorted.bam > sample_idxstats.txt
Genome_build: custom collapsed human tRNA space (PMID: 33435213). FASTA available on series record and at https://github.com/FlorianPichot/tRNA_reference_construction/blob/main/Available_references/Homo_sapiens/
Supplementary_files_format_and_content: tsv files containing number of reads mapping to individual tRNA clusters

growth_protocol: HEK293 cells cultured in a humidified incubator at 37°C, 5% CO2 in standard DMEM supplemented with antibiotic/antimycotics, 2 mM L-glutamine and 10% fetal bovine serum.

extract_protocol:
Cells were collected from culture dish and solubilized in Trizol. Total RNA was extracted, and separated using UREA-PAGE. tRNAs were excised, eluted from crushed gel pieces and precipitated by isopropanol. Refolded tRNAs were further treated with recombinant angiogenin endonuclease, radiolabeled using P32-gamma-ATP and used to monitor DDX3X helicase unwinding activity
Libraries were prepared according to NEBNext small RNA cloning protocol (E7580S)

tag: enzymatic treatment

value: Cleaved with recombinant Angiogenin

tag: biochemical separation

value: Separated by native PAGE prior to library cloning

tag: molecule subtype

value: tRNA


title: MT-B rep 2 [G2_2B]

value: Preparation condition B:bisulfite conversion using three cycles of 70°C for 10min and 64°C for 45min, RNA fragmentation was performed after bisulfite conversion, random primers were used for 1st strand cDNA synthesis; B) RNA fragmentation was performed first, then bisulfite conversion was performed using three cycles of 70°C for 10min and 64°C for 45min, random primers were used for 1st strand cDNA synthesis


title: MT-B rep 1 [G2_1B]


title: PLD1_12w_03

value: BBN 12 weeks


title: tracer tRNA replicate 1


title: 05_Enzalutamide_ETOH_rep3

value: LNCaP


title: PLD1_12w_02

value: bladder tissue

value: PLD1 knockout


title: ADSC, Donor 66, FBS culture condition

description: RNA seq sample

value: adipose derived


title: 05_Enzalutamide_ETOH_rep2


title: 36-sham

city: Changsha

first: Changsheng

last: Huang

state: Hunan

address: 87 Xiangya Road

department: Department of Anesthesiology

country: China

institute: Xiangya Hospital, Central South University

data_processing:
Using seqtk to filter raw reads, we can get clean reads that can be used for data analysis. The main steps are as follows: remove the junction sequence contained in the reads; remove the base with 3 'end quality Q less than 20, that is, the base error rate is less than 0.01, where Q= - 10logerror_ Ratio; remove the reads less than 25 in length; remove the ribosome RNA reads of the species.
Using splited mapping algorithm of Hisat2（ version:2.0.4 ）to do genome mapping for clean reads,
Counting fragments of every gene by Stringtie（version:1.3.0). TMM (trimmed mean of m values) method was used to normalize, and then Fragments Per Kilobase of exon model per Million mapped reads (FPKM) value of each gene was calculated by Perl script.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Anterior Cingulate Cortex

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set(Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley

value: brain

tag: age

value: 8 weeks

value: sham


title: PLD1_12w_01


title: MT-C rep 2 [G3_2C]

value: Neural stem cells

value: Mitochondrial fraction


title: 05_Enzalutamide_ETOH_rep1


title: MT-A rep 1 [G1_1A]

value: RNA BS-seq

value: Preparation condition A:bisulfite conversion using three cycles of 70°C for 10min and 64°C for 45min, RNA fragmentation was performed after bisulfite conversion, random primers were used for 1st strand cDNA synthesis


title: 34-sham


title: 04_VPC13789_DHT_rep3

data_processing:
Base calling was performed using the BGISeq500 platform. The raw reads were pre-filtered by removing adaptor sequences, contamination and low-quality reads.
The high quality of the filtered reads was confirmed using the FastQC (Andrews, 2014) quality control tool.
The reads were mapped and annotated using STAR Aligner (Dobin et al., 2013) (version 2.6.1c).
The reads were counted using featureCounts (Liao, Smyth, & Shi, 2014).
Differential gene expression analysis for different treatments was performed using the DESeq2 (Love, Huber, & Anders, 2014).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: DESeq2 Differential Expression Analyses of DHT vs Ethanol, Enzalutamide vs DHT and 13789 vs DHT, as a Microsoft Excel Spreadsheet.

tag: agent

value: dihydrotestosterone plus VPC-13789


title: PLD1_8w_03

value: BBN 8 weeks


title: 33-sham


title: PLD1_8w_02


title: Raw264.7-VSV-input

city: Weifang

first: Panpan

last: Li

address: No.7166 Baotong West Street

institute: Shandong Second Medical University

description:
Raw264.7 macrophages with  VSV infection
total RNA removing rRNAs

data_processing:
Raw data were harvested from Illumina HiSeq4000 sequencer, and were quality controlled by Q30
adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software
clean reads were aligned to reference genome (mm10) using bowtie2 (v2.2.4) software with end-to-end mode
2'-O-methylation sites were annotated with gene information by bedtools software(v2.24) .
Genome_build: mm10
Supplementary_files_format_and_content: excel format
Supplementary_files_format_and_content: the count，coverage, ratio and fc of the methylated sites

source_name: mononuclear macrophages

extract_protocol:
Total RNA was harvested using Trizol reagent. Then total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (NEB) following the manufacturer's instructions.
RNA libraries were constructed by using a protocol from Dai Q et al., Nat Methods, 2017. with slight modification.
Nm-Seq

value: leukemia cellsin mouse macrophage

value: wild type


title: 28-CCI14d

value: CCI 14d


title: PLD1_8w_01


title: 29-CCI14d


title: Raw264.7-0h-enriched

description:
Raw264.7 macrophages without VSV infection
total RNA removing rRNAs


title: Raw264.7-0h-input


title: 04_VPC13789_DHT_rep2

value: LNCaP


title: PLD1_pre_03

value: bladder tissue


title: 27-CCI14d


title: 03_Enzalutamide_DHT_rep3

value: dihydrotestosterone plus Enzalutamide


title: 04_VPC13789_DHT_rep1


title: Raw264.7-VSV-enriched


title: PLD1_pre_01

value: PLD1 knockout


title: 03_Enzalutamide_DHT_rep2


title: PLD1_pre_02


title: 22-CCI7d

value: Sprague-Dawley

value: CCI 7d


title: MT-A rep 2 [G1_2A]


title: Fbl+/- Raw264.7 rep2

description: total RNA removing rRNAs

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the mouse reference genome (UCSC mm10) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Genome_build: mm10
Supplementary_files_format_and_content: excel format
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was harvested using Trizol reagent. Then total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (NEB) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB) according to the manufacturer's instructions.

value: Fbl+/-


title: 03_Enzalutamide_DHT_rep1


title: Fbl+/- Raw264.7 rep1

description: total RNA removing rRNAs


title: 19-CCI7d

value: brain

value: 8 weeks


title: 02_DMSO_DHT_rep3

value: dihydrotestosterone plus  DMSO


title: 18-CCI7d


title: WT Raw264.7 rep2

description: total RNA removing rRNAs


title: 02_DMSO_DHT_rep2


title: WT_16w_02

value: BBN 16 weeks


title: WT_16w_01


title: 14-CCI3d

value: CCI 3d


title: Muscle Naive ZT20 rep 4

city: Manchester

first: Polly

last: Downton

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description:
PD179
muscle_fc.txt

data_processing:
Sequencing library preparation and sequencing were performed by the University of Manchester Genomic Technologies Core Facility. Sample quality was determined using a 2200 TapeStation (Agilent Technologies). Libraries were generated using the TruSeq Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol. The multiplexed libraries were analysed by paired-end sequencing on a HiSeq 4000 instrument (76 + 76 cycles, plus indices), then demultiplexed and converted using bcl2fastq software (v2.17.1.14, Illumina).
Joint fastqs were concatenated prior to processing.
Adaptors were removed and ends trimmed using Trimmomatic (v0.36), then reads were mapped against the mouse genome (mm10/GRCm38) using STAR (v2.5.3).
Reads were counted in R using the Rsubread (v1.28.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_fc.txt: Space-delimited matrix tables with raw gene counts for every gene and every sample.

source_name: Muscle

extract_protocol:
Joint tissue was ground with liquid nitrogen using a pestle and mortar, then transferred to a Lysing Matrix D tube containing Trizol. Tissue was homogenised using a BeadMill homogeniser (3 x 4 m/s for 40s). RNA was extracted using chloroform then precipitated using isopropanol. After washing with 75% ethanol, the RNA pellet was resuspended in RNase-free water.
RNA was purified from liver samples using the SV Total RNA kit (Promega), according to the manufacturer’s instructions. Tissue was homogenised using Lysing Matrix D tubes loaded into a BeadMill homogeniser (4 m/s for 20s). RNA was eluted in RNase-free water.
RNA was purified from muscle samples using the ReliaPrep Tissue kit (Promega), following the manufacturer’s instructions for the purification of RNA from fibrous tissue. Muscle tissue was homogenised using the same protocol as for joint, and eluted in RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Male DBA/1 mice (8-10 weeks) were administered bovine type II collagen emulsified in Complete Freund’s Adjuvant (both MD Bioscience, Zurich, Switzerland) by intradermal injection under anaesthesia (2 x 50 ml of 1 mg/ml collagen in CFA). After 21 days, mice were given an intraperitoneal booster injection of collagen (200 ml of 1 mg/ml collagen in saline). Tissue collection occurred at ZT0, 4, 8, 12, 16 or 20 on day 7 after the development of disease symptoms in CIA mice, or at matched time points in naive control mice.

tag: Sex

value: Male

value: Muscle

value: Naive

tag: time


title: 01_DMSO_ETOH_rep3

value: ethanol plus DMSO


title: 01_DMSO_ETOH_rep2


title: WT_12w_03

value: wild type

value: BBN 12 weeks


title: WT_12w_02

value: bladder tissue


title: WT_12w_01


title: Muscle Naive ZT20 rep 3

description:
PD178
muscle_fc.txt


title: Muscle Naive ZT20 rep 2

description:
PD177
muscle_fc.txt


title: 01_DMSO_ETOH_rep1

value: LNCaP


title: 10-CCI1d

value: CCI 1d


title: 9-CCI1d

value: Sprague-Dawley


title: WT_8w_03

value: BBN 8 weeks


title: WT_8w_02


title: injured mutant rep2

city: Melbourne

first: Akriti

last: Varshney

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
RNA-seq reads were aligned with STAR aligner and were quantified using featuerCounts
Genome_build: GRCz10-91
Supplementary_files_format_and_content: files with raw read counts and fastq files

organism: Danio rerio

source_name: heart

extract_protocol:
For RNA Sequencing, total RNA from six pooled ventricular apices of two biological replicates was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
cDNA library was prepared using TruSeq RNA Prep Kit v2 (illumina)

value: heart

tag: nkx2.5 genotype

value: mutant

tag: Stage

value: Adult

tag: injury

value: Yes


title: Muscle Naive ZT20 rep 1

description:
PD176
muscle_fc.txt

tag: strain

tag: tissue


title: 7-CCI1d

value: brain

value: 8 weeks

tag: treatment


title: WT Raw264.7 rep1

description: total RNA removing rRNAs

value: leukemia cellsin mouse macrophage

tag: cell type

tag: genotype


title: WT_16w_03

value: BBN 16 weeks


title: 4-CCI0.5d

value: CCI 0.5d


title: injured mutant rep1


title: 02_DMSO_DHT_rep1

tag: cell line

value: dihydrotestosterone plus  DMSO


title: 15-CCI3d

value: CCI 3d


title: Muscle Naive ZT16 rep 5

description:
PD175
muscle_fc.txt

value: Male

value: Muscle

value: Naive


title: WT_8w_01

value: bladder tissue

value: wild type


title: 13-CCI3d

value: Sprague-Dawley


title: Muscle Naive ZT16 rep 4

description:
PD174
muscle_fc.txt


title: Muscle Naive ZT20 rep 5

description:
PD180
muscle_fc.txt


title: 2-CCI0.5d


title: Muscle Naive ZT16 rep 3

description:
PD173
muscle_fc.txt


title: 1-CCI0.5d


title: injured transgenic rep1

value: heart

value: transgenic


title: Muscle Naive ZT16 rep 2

description:
PD172
muscle_fc.txt


title: WT_pre_02


title: injured wildtype rep2

value: wildtype

value: Adult


title: WT_pre_01


title: injured wildtype rep1

value: Yes


title: PPARA-Wy14,643-3

city: Bethesda

first: Frank

middle: J.

last: Gonzalez

state: MD

address: 37 Convent Drive. Bldg37/Rm3106

department: National Cancer Institute

institute: National Institutes of Health

library_source: genomic

data_processing:
Base calling was perfromed by Illumina RTA 2.4.6
Demultiplexing was performed by Bcl2fasq 2.17
Adaptor and quality trimming were performed by Cutadapt 1.18
Alignment was performed by Bowtie2 2.2.6
Duplication statistics was performed by Picard 2.18.26
Integrative Genomics Viewer (IGV) to export a Bam file to a Wig file
The conditions are as follows with all standard settings;
<TDF and Count options>
Zoom Levels: 7
Window Functions: Mean
Window Size: 25
Genome_build: mm10
Supplementary_files_format_and_content: wig

molecule: genomic DNA

extract_protocol:
ChIP assays were performed using a SimpleChIP Plus Enzymatic Chromatin IP Kit-Magnetic Beads (Cell Signaling, #9005) according to the manufacturer's protocols.
Libraries were prepared according to Illumina's instructions accompanying the NextSeq 500 Kit (v1).

treatment_protocol: C57BL/6 mice were treated with Wy14,643 (50 mg/12 hour/kg for 1 day) or vehicle by oral gavage and administered either a normal diet or a 0.1% Wy14,643-chow diet for 1 day.

tag: strain background

value: 8 weeks old

value: PPARA agonist (Wy14,643)

value: liver

tag: chip antibody

value: PPARA IgG (Abcam, ab24509)


title: uninjured mutant rep2

value: mutant

value: No


title: Muscle Naive ZT12 rep 5

description:
PD170
muscle_fc.txt

value: Male


title: Muscle Naive ZT12 rep 4

description:
PD169
muscle_fc.txt

value: Muscle


title: 1 week excised atria_AMPK KO_4

type: RNA

city: New Haven

first: Lawrence

last: Young

state: CT

address: 300 George Street

department: Internal Medicine

institute: Yale University

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data were extracted using GenomeStudio (software provided by Illumina), with no background subtraction, then normalized using the “quantiles” function.  Processed data are available only as fold-change values and p-values.

label: Biotin

source_name: atria

label_protocol: Biotinylated cRNA were prepared from 250 ng of total RNA using an Illumina Totalprep RNA amplification kit according to manufacturer’s protocol.

extract_protocol: Total RNA was extracted with TRIzol Reagent followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: gender

value: male

tag: tisssue

value: atria

value: 1 week

value: Atrial AMPK KO


title: Muscle Naive ZT16 rep 1

description:
PD171
muscle_fc.txt

value: Naive


title: PPARA-Wy14,643-2

tag: age


title: injured transgenic rep2

value: heart

value: transgenic


title: uninjured mutant rep1

value: Adult


title: PPARA-Wy14,643-1


title: uninjured transgenic rep2


title: Muscle Naive ZT12 rep 3

description:
PD168
muscle_fc.txt


title: uninjured transgenic rep1


title: Muscle Naive ZT12 rep 2

description:
PD167
muscle_fc.txt


title: WT_pre_03

value: bladder tissue

value: wild type


title: PPARA-Control-3

source_name: PPARA-Control

value: 8 weeks old

value: Vehicle (Control)


title: 1 week excised atria_AMPK KO_2


title: PPARA-Control-2

value: liver

value: PPARA IgG (Abcam, ab24509)


title: uninjured wildtype rep2

value: wildtype

value: No


title: 1 week excised atria_AMPK KO_3


title: PPARA-Control-1


title: 1 week excised atria_LKB1 KO_3

value: Atrial LKB1 KO


title: uninjured wildtype rep1


title: Muscle Naive ZT12 rep 1

description:
PD166
muscle_fc.txt

value: Male

value: Muscle


title: Muscle Naive ZT8 rep 5

description:
PD165
muscle_fc.txt


title: IgG-Wy14,643-3

value: PPARA agonist (Wy14,643)

value: Normal Rabbit IgG (Cell Signaling, 2729)


title: 1 week excised atria_LKB1 KO_4

value: male

value: atria

value: 1 week


title: 1 week excised atria_AMPK KO_1

value: Atrial AMPK KO


title: c-202-1-1

city: San Francisco

first: Dawud

last: abduweli uyghurturk

state: California

address: 513 Parnassus Ave.

institute: UCSF

data_processing:
Raw data: Original image data file from high-throughput sequencing platforms is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw reads -> Remove reads containing adaptors --> Remove reads containing N > 10% --> Remove reads Qscore of over 50% bases below 5
Perform alignments with HISAT2 to the reference
The algorithm of hisat is divided into three parts: 1. The whole sequence was aligned to a single exon. 2. The sequencing sequence was piecewise aligned to two exons of the genome. 3. The sequencing sequence was segmented and aligned to more than three (including three) exons of the genome.
Supplementary files format and content: gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon. Read counts is proportional to gene expression level, gene length and sequencing depth

source_name: enamel organ

growth_protocol: Dams were Crh-IRES-Cre +/+ (11) and were paired with Ai14 tdTomato males both on a C57Bl6 background. The resulting offspring were Crh-IRES-Cre; Ai14 tdTomato.

extract_protocol:
Enamel organs from the first molars were dissected from the molars, and mRNA was extracted and purified using a Direct-zol RNA MiniPrep kit (Zymo Research).
Total RNA went through ployA caputure to remove rRNA removal), RNA was fragmented, and reverse transcription was performed to generate cDNA library.

treatment_protocol: ELA was imposed on neonatal mice using simulated poverty by limiting nesting and bedding materials in cages between P2-P12.  At P12 mice were sacrificed and mandibles of 4 P12 male control (body weight = 5.9 +/- 0.4 gm) and 5 P12 male ELA (body weight = 5.30 +/- 0.4g) mouse pups were collected.  The mandibles were immediately placed in in RNAlater Stabilization Solution (Invitrogen), and then transferred to phosphate buffered saline.

value: postnatal day 12

value: enamel organ

value: control


title: Muscle Naive ZT8 rep 4

description:
PD164
muscle_fc.txt

value: Naive


title: c-204-1-2


title: Muscle Naive ZT8 rep 3

description:
PD163
muscle_fc.txt


title: c-204-1-1


title: IgG-Wy14,643-2

value: 8 weeks old

value: liver


title: IgG-Wy14,643-1


title: IgG-Control-2

source_name: IgG-Control

value: Vehicle (Control)


title: 1 week excised atria_LKB1 KO_1


title: t-203-1-5

value: ELA treatment


title: 1 week excised atria_LKB1 KO_2

value: Atrial LKB1 KO


title: Muscle Naive ZT8 rep 2

description:
PD162
muscle_fc.txt

value: Male


title: IgG-Control-3


title: 1 week excised atria_WT_3

value: WT


title: Muscle Naive ZT4 rep 5

description:
PD160
muscle_fc.txt

value: Muscle


title: 1 week excised atria_WT_1


title: 1 week excised atria_WT_2


title: t-203-1-3


title: LK3 BMDM

city: HangZhou

first: Di

last: Wang

state: ZheJiang

address: No.866, Yuhangtang Road, Xihu District, Hangzhou

institute: ZheJiang university

data_processing:
The sequences were processed and analyzed by GENEWIZ
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1)  (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited xls files include readcount values for each Sample ...

source_name: BMDM

extract_protocol:
Bone marrow cells were flushed from tibias and femurs with cold Dulbecco’s modified Eagle’s medium (DMEM) and were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 10 ng/ml macrophage colony-stimulating factor (M-CSF, PeproTech) for 6 days to generate BMDMs. Then treated with LPS andGramicidin or KCl for 6 hours. And total RNA were extracted for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For sample C, BMDMs were cultured in complete DMEM medium for 6 hours. For group L ,BMDMs were cultured in complete DMEM medium for 6 hours in the presence of 500 ng/ml LPS.  For sample LG, BMDMs were cultured in complete DMEM medium for 6 hours in the presence of LPS (500 ng/ml) and Gramicidin (1.25 μM).  For sample LK, BMDMs were cultured in complete DMEM medium for 6 hours in the presence of LPS (500 ng/ml) and KCl (50 mM).

value: LK group

value: post natal week 8


title: LK1 BMDM


title: IgG-Control-1

value: Normal Rabbit IgG (Cell Signaling, 2729)


title: Muscle Naive ZT8 rep 1

description:
PD161
muscle_fc.txt


title: Muscle Naive ZT4 rep 3

description:
PD158
muscle_fc.txt


title: U251 LncRNA XLOC013218-overexpressing replicate 2

city: Guangzhou

first: Ningbo

last: Xu

state: Guangdong

address: NO.253 Gongye Avenue, Haizhu District

department: Department of Neurosurgery

institute: Southern Medical University

data_processing:
Raw reads were subjected to SOAPnuke (version 1.5.0)
TopHat used the Bowtie algorithm to align reads to the genome.  The transcripts were then assembled using Cufflinks (version 2.2.1)
The unigene expression was calculated using RSEM (version 1.3.1).The differentially expressed genes (DEGs) were analyzed using EdgeR software
The GO and KEGG analyses was implemented using ClusterProfiler package 3.14.0
Assembly: hg18
Supplementary files format and content: FPKMs

source_name: brain

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen). After extraction RNA underwent DNase treatment using Turbo DNAase Kit (Ambion). Poly-A selected mRNA library preparation was done using KAPPA stranded library preparation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% under optimum conditions

value: glioma cells

value: brain

value: LncRNA XLOC013218-overexpression


title: U251 LncRNA XLOC013218-overexpressing replicate 3


title: 1 week excised atria_WT_4

value: male

value: atria

value: 1 week


title: t-205-1-3

value: postnatal day 12

value: enamel organ


title: Muscle Naive ZT4 rep 2

description:
PD157
muscle_fc.txt

value: Naive


title: Muscle Naive ZT4 rep 1

description:
PD156
muscle_fc.txt


title: t-205-1-1

value: ELA treatment


title: U251 LncRNA XLOC013218-overexpressing replicate 1


title: LG1 BMDM

value: LG group


title: LG3 BMDM


title: Muscle Naive ZT0 rep 5

description:
PD155
muscle_fc.txt

value: Male


title: LG2 BMDM


title: U251 control replicate 3

value: control


title: L3 BMDM

value: L group


title: t-203-1-4


title: U251 control replicate 2


title: D9_shCTCF_Thy1-SSEA1-_rep2 [BL-Hi-C]

first: ya

middle: wei

last: song

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Raw sequence data of BL-Hi-C were subjected to trimLinker tool from ChIA-PET2 to remove linker sequences with parameters "-m 1 -k 2 -e 1 -l 15 -A ACGCGATATCTTATC -B AGTCAGATAAGATAT". The trimmed reads were processed using HiC-Pro.
The resulting valid pairs were balanced and transformed into hic format using juicer tools.
Genome_build: mm10
Supplementary_files_format_and_content: hic

source_name: Reprogramming cells, CTCF shRNA,SSEA1-Thy1- subpopulations

growth_protocol: mESCs and iPSCs were cultured in in DMEM/High glucose medium (Hyclone) supplemented with beta-mercaptoethanol (10 mM), sodium pyruvate (10 mM), non-essential amino acids (10 mM), GlutaMAX (10 mM), 15% fetal bovine serum (Gibco), 1000 U/ml leukemia inhibitory factor (LIF), 1 μM MEK inhibitor PD0325901 and 3 μM GSK3 inhibitor CH99021. MEF cells were cultured in 10% FBS medium supplemented with non-essential amino acids (10 mM) and GlutaMAX (10 mM).

extract_protocol:
The BL-Hi-C libraries were performed as previous described. Briefly, the cells were treated with 1% formaldehyde for 10 min at RT and the crosslink was quenched by adding 2.5 M glycine. Then, the cells were treated with 0.1% SDS FA lysis buffer and 1% SDS FA lysis buffer. After that, the genome was digested with enzyme HaeIII into fragments with blunt-ends, which were treated with adenine and ligated with bridge linker containing biotin for 4 hr at 16°C. The unligated DNA fragments were digested with DNA exonuclease. Next, the cells were treated with SDS and proteinase K to digest proteins, and the DNA was purified using phenol-chloroform extraction with ethanol precipitation. Then, the DNA was fragmented into 300 bp on average by sonication and the biotin-labeled DNA fragments were pulled down with streptavidin coated M280 beads.
The BL-Hi-C libraries were constructed into standard illumina libraries.

treatment_protocol: 20,000 MEFs at passage 2 were plated in a 12-well plate and then infected twice with retroviral stocks generated with Plat-E cells. 3 volumes of the supernatants of OSKM transcription factors were mixed with 1 volume of fresh MEF medium containing polybrene at a final concentration of 8 μg/ml. The infection efficiency was tested by MEFs transduced with virus of pMXs-EGFP. pMXs-CTCF and shRNAs were also transfected into OG2-MEFs by retrovirus generated from Plat-E cells. For infecting OG2-MEFs, the medium of OG2-MEFs was replaced with 2 mL of infection mixture per well in a 12-well plate. Infected cells were cultured with mESC medium containing 50 μg/ml Vitamin C (Sigma) post infection and renewed daily. For polycistronic OSKM-medaited reprogramming experiments, MEFs were transduced with 1 volume inducible lentivirus of OSKM and 2 volume rtTA retroviruses generated from HEK293T cells. Infected cells were cultured in mESC medium containing 50 μg/ml Vitamin C and 2 μg/ml doxycycline (Sigma) for 12 days to count GFP positive colonies. To ensure proper CTCF knockdown efficiency before transfecting these virus supernatants into MEFs, we concentrated virus supernatant produced from Ctcf shRNAs 4 times.

value: Reprogramming cells

tag: day of reprogramming


title: Wildtype

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: scRNA-seq

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 3.0.2, 10x Genomics, Pleasanton, CA) and the 10x mouse genome mm10 3.0.0 release as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 4.0.1)
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: kidney

growth_protocol: For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec). Lymphocytes were enriched by Percoll gradient (37% in PBS).

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 3’ v2/3 kit to generate high-quality cDNA libraries.

treatment_protocol: For pre-enrichment of murine CD4+ T cells EasySep (StemCell Technologies, Vancouver, Canada) isolation kit was used according to the manufacturers’ protocols. Renal CD45+CD3+CD4+YFP+ cells were sorted using an Aria Fusion cytometer (BD Biosciences, Franklin Lakes, New Jersey) and collected in MACS buffer containing 2% FCS.

value: kidney cells

value: 8 weeks

value: WT


title: Muscle Naive ZT0 rep 4

description:
PD154
muscle_fc.txt

tag: Sex

value: Muscle


title: LK2 BMDM

value: LK group

value: post natal week 8


title: Tbx21flox

description: scRNA-seq

value: KO


title: U251 control replicate 1

value: glioma cells

value: brain


title: Muscle Naive ZT0 rep 3

description:
PD153
muscle_fc.txt

tag: time


title: L1 BMDM


title: c-202-1-2

value: postnatal day 12

value: enamel organ


title: Muscle Naive ZT0 rep 2

description:
PD152
muscle_fc.txt

value: Naive


title: Muscle Naive ZT0 rep 1

description:
PD151
muscle_fc.txt


title: D9_shLuci_Thy1-SSEA1-_rep2 [BL-Hi-C]

source_name: Reprogramming cells, control shRNA,SSEA1-Thy1- subpopulations


title: D6_shCTCF_Thy1-SSEA1-_rep2 [BL-Hi-C]


title: Exo_KD2_3

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

data_processing:
Small RNA-seq reads were trimmed using cutadapt v1.18 (https://github.com/marcelm/cutadapt). Reads longer than 15 nucleotides were retained.
ncPRO-seq (version 1.5.1) (Chen et al., 2012) was used to map reads to the reference genome hg19 and quantitate small RNA. The miRBase v18, ACA_snoRNA and CD_snoRNA from Rfam v11.0, and tRNA from UCSC (hg19) were employed
miRNA annotation was extended in both upstream and downstream regions by using miRNA_e_+2_+2.
Principal component analysis was performed to assess the similarity between samples.
DESeq2 (Love et al., 2014) was used to identify small RNAs differentially exported from Cell to EVs in VAP-A KD compared to SC.
Genome_build: Hg19

source_name: DKs-8 colon cancer cell lines

growth_protocol: DKs-8 cells were grown in DMEM (+10% FBS) containing growth media in 37 degree C with 5% CO2. Extracellular vesicles were biochemically purified from serum-free conditioned media.

extract_protocol: RNA was extraceted from cell or extracellular vesicles pellets with QIAzol and miRNeasy mini kit (QIAGEN) following manufacturer's protocol.

value: Colon cancer derived cell lines

value: colon cancer cell lines

value: WT KRAS

tag: sample type

value: VAP-A knockdown (KD2)


title: Exo_KD2_1


title: BMDMs, LM3

description:
LMvsLPS_B.xlsx
LM3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2
Reads Per Kilo bases per Million reads (RPKM) were calculated using a protocol from Mortazavi et al., Nat. Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: readcount values for each Sample

extract_protocol:
Bone marrow cells were flushed from tibias and femurs with cold Dulbecco’s modified Eagle’s medium (DMEM) and were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 10 ng/ml macrophage colony-stimulating factor (M-CSF, PeproTech) for 6 days to generate BMDMs. Then treated with LPS and Kir2.1 inbibitor ML133 for 6 hours.And total RNA were extracted for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For sample C, BMDMs were cultured in complete DMEM medium for 6 hours. For sample L , K and LPS , BMDMs were cultured in complete DMEM medium for 6 hours in the presence of 500 ng/ml LPS.  For sample LM, BMDMs were cultured in complete DMEM medium for 6 hours in the presence of LPS (500 ng/ml) and ML133 (25 μM).

value: LM group

value: BMDMs


title: Exo_KD2_2


title: Exo_KD1_3

value: Colon

value: VAP-A knockdown (KD1)


title: BMDMs, LM1

description:
LMvsLPS_B.xlsx
LM1

value: WT


title: BMDMs, LM2

description:
LMvsLPS_B.xlsx
LM2


title: D6_shCTCF_Thy1+_rep2 [BL-Hi-C]

source_name: Reprogramming cells, CTCF shRNA,Thy1+ subpopulations

value: Reprogramming cells


title: D6_shLuci_Thy1-SSEA1-_rep2 [BL-Hi-C]


title: Muscle CIA ZT20 rep 5

description:
PD150
muscle_fc.txt

value: Male

value: Muscle

value: CIA


title: Exo_KD1_2


title: Muscle CIA ZT20 rep 4

description:
PD149
muscle_fc.txt


title: Muscle CIA ZT20 rep 3

description:
PD148
muscle_fc.txt


title: L2 BMDM

value: L group

value: post natal week 8


title: Exo_KD1_1


title: Muscle CIA ZT20 rep 2

description:
PD147
muscle_fc.txt


title: BMDMs, LPS2

description:
LMvsLPS_B.xlsx
LPS2

value: LPS_B group


title: Exo_SC_3

value: control


title: Muscle CIA ZT20 rep 1

description:
PD146
muscle_fc.txt


title: D3_shCTCF_Thy1+_rep2 [BL-Hi-C]


title: BMDMs, LPS1

description:
LMvsLPS_B.xlsx
LPS1


title: Exo_SC_2


title: D3_shLuci_Thy1+_rep2 [BL-Hi-C]

source_name: Reprogramming cells, control shRNA,Thy1+ subpopulations


title: D9_shCTCF_Thy1-SSEA1-_rep1 [BL-Hi-C]


title: BMDMs, K3

description:
KLPSvsLPS_A.txt
K3

value: kcnj2 KO

value: KLPS group


title: Muscle CIA ZT16 rep 5

description:
PD145
muscle_fc.txt


title: Muscle CIA ZT16 rep 4

description:
PD144
muscle_fc.txt


title: BMDMs, K2

description:
KLPSvsLPS_A.txt
K2


title: Exo_SC_1

value: colon cancer cell lines

value: WT KRAS


title: D9_shLuci_Thy1-SSEA1-_rep1 [BL-Hi-C]


title: BMDMs, K1

description:
KLPSvsLPS_A.txt
K1


title: BMDMs, L3

description:
KLPSvsLPS_A.txt
LPS_AvsControl.txt
L3

value: LPS_A group


title: Muscle CIA ZT16 rep 3

description:
PD143
muscle_fc.txt


title: MV_KD2_3

value: VAP-A knockdown (KD2)


title: D6_shLuci_Thy1-SSEA1-_rep1 [BL-Hi-C]


title: BMDMs, LPS3

description:
LMvsLPS_B.xlsx
LPS3

value: BMDMs


title: MV_KD2_4

value: Colon


title: Muscle CIA ZT16 rep 2

description:
PD142
muscle_fc.txt


title: D6_shLuci_Thy1+_rep2 [BL-Hi-C]


title: D6_shCTCF_Thy1-SSEA1-_rep1 [BL-Hi-C]


title: D6_shCTCF_Thy1+_rep1 [BL-Hi-C]


title: D6_shLuci_Thy1+_rep1 [BL-Hi-C]


title: Muscle CIA ZT16 rep 1

description:
PD141
muscle_fc.txt


title: BMDMs, L2

description:
KLPSvsLPS_A.txt
LPS_AvsControl.txt
L2

value: WT


title: BMDMs, L1

description:
KLPSvsLPS_A.txt
LPS_AvsControl.txt
L1


title: Muscle CIA ZT12 rep 5

description:
PD140
muscle_fc.txt


title: MV_KD1_4

value: VAP-A knockdown (KD1)


title: MV_KD1_2


title: D3_shCTCF_Thy1+_rep1 [BL-Hi-C]

value: Reprogramming cells


title: MV_KD1_1


title: D3_shLuci_Thy1+_rep1 [BL-Hi-C]


title: BMDMs, C3

description:
LPS_AvsControl.txt
C3

value: Control group


title: Muscle CIA ZT12 rep 4

description:
PD139
muscle_fc.txt

value: Male

value: Muscle

value: CIA


title: MV_SC_4


title: Muscle CIA ZT12 rep 3

description:
PD138
muscle_fc.txt


title: Muscle CIA ZT12 rep 2

description:
PD137
muscle_fc.txt


title: BMDMs, C1

description:
LPS_AvsControl.txt
C1

value: post natal week 8


title: MV_KD2_2


title: Muscle CIA ZT12 rep 1

description:
PD136
muscle_fc.txt


title: Liver tumor tissue with liver-specific double knockout of Pten and Scap 7

city: Tokyo

first: Hayato

last: Nakagawa

address: 7-3-1 Hongo Bunkyo-ku

institute: The University of Tokyo

data_processing:
Raw sequencing reads were aligned to mouse reference genome (mm39) by STAR, and gene-level read counts were calculated by RSEM.
Genome_build: mm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver tumor

extract_protocol:
RNA was extracted from tumor tissue using ISOGEN with Spin Column (Nippon Gene).
Illumina TruSeq Stranded mRNA Library Prep was used with 1 micro gram of total RNA for the construction of sequencing libraries. RNA-Seq libraries were prepared for sequencing using standard Illumina protocols.

tag: genetic modification

value: Pten-Scap double knockdown


title: MV_SC_3

value: control


title: Liver tumor tissue with liver-specific double knockout of Pten and Scap 6


title: MV_SC_2


title: Muscle CIA ZT8 rep 5

description:
PD135
muscle_fc.txt


title: Muscle CIA ZT8 rep 4

description:
PD134
muscle_fc.txt


title: cell_KD2_4


title: C2bbe1 cells, Cytoplasmic Halo, input RNA, Rep2

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

data_processing:
Adapters were removed with cutadapt 2.1
Transcripts were quantified using salmon 0.11.1 against GENCODE 28
Differentially expressed genes were quantified using DESeq2
Assembly: GENCODE 28
Supplementary files format and content: quant.sf files provide TPM expression values for all transcripts

growth_protocol: C2bbe1 cells (CRL-2102) were maintained in DMEM with 110 mg/L Sodium Pyruvate (Thermo 11995065) supplemented with 10% FBS (Atlas Biologicals F-0500-D), penicillin-streptomycin (Thermo 15140122) and 10 ug/mL human transferrin (Sigma-Aldrich T8158).

extract_protocol:
RNA was extracted using Trizol, biotinylated in vitro using click chemstry, and biotinylated RNA was enriched using streptavidin beads.
QAPA HyperPrep rRNA depletion

treatment_protocol: Cells contained transgenic Halo-tagged proteins that were either apically, basally, or cytoplasmically localized. Cells were then subjected to Halo-seq RNA proximity labeling (Engel et al, Nuc Acids Res, 2021).

value: intestinal epithelial cell

tag: localization of halo-tagged proteins

value: Cytoplasmically localized

tag: fraction

value: total input RNA


title: C2bbe1 cells, Cytoplasmic Halo, input RNA, Rep3


title: Liver tumor tissue with liver-specific double knockout of Pten and Scap 5

tag: strain


title: C2bbe1 cells, Cytoplasmic Halo, input RNA, Rep1


title: cell_KD2_3

tag: tissue

value: colon cancer cell lines

value: WT KRAS


title: C2bbe1 cells, Cytoplasmic Halo, streptavidin enriched, Rep3

tag: cell type

value: streptavidin-enriched RNA


title: Muscle CIA ZT8 rep 3

description:
PD133
muscle_fc.txt

tag: treatment


title: cell_KD2_2

value: Colon

tag: genotype

value: VAP-A knockdown (KD2)


title: Liver tumor tissue with liver-specific double knockout of Pten and Scap 4


title: BMDMs, C2

description:
LPS_AvsControl.txt
C2

value: WT

value: BMDMs


title: Liver tumor tissue with liver-specific knockout of Pten 6

value: Pten knockdown


title: Liver tumor tissue with liver-specific double knockout of Pten and Scap, crossed with Rosa26-Lox-Stop-Lox-tdTomato

value: Pten-Scap double knockdown, crossed with Rosa26-Lox-Stop-Lox-tdTomato


title: Muscle CIA ZT8 rep 2

description:
PD132
muscle_fc.txt

value: Male

value: Muscle


title: Liver tumor tissue with liver-specific knockout of Pten 3


title: cell_KD1_4

value: VAP-A knockdown (KD1)


title: Muscle CIA ZT8 rep 1

description:
PD131
muscle_fc.txt

value: CIA


title: cell_KD1_3


title: C2bbe1 cells, Cytoplasmic Halo, streptavidin enriched, Rep1

tag: cell line


title: Muscle CIA ZT4 rep 5

description:
PD130
muscle_fc.txt


title: cell_KD1_2


title: C2bbe1 cells, Basal Halo, input RNA, Rep3

value: Basally localized


title: C2bbe1 cells, Basal Halo, input RNA, Rep2

value: intestinal epithelial cell


title: Muscle CIA ZT4 rep 4

description:
PD129
muscle_fc.txt


title: cell_SC_4

value: control


title: C2bbe1 cells, Cytoplasmic Halo, streptavidin enriched, Rep2

value: Cytoplasmically localized


title: C2bbe1 cells, Basal Halo, input RNA, Rep1

value: total input RNA


title: Muscle CIA ZT4 rep 2

description:
PD127
muscle_fc.txt


title: D9_shLuci_SSEA1-Thy1- [ATAC-seq]

description:
D9_shLuci_SSEA1-Thy1-
atac_stage2_shLuc.bed.gz

data_processing:
ATAC-seq raw reads were first assessed with FastQC tool and trimmed with trim galore/cutadapt if they contained adaptors.
Reads were aligned to mm10 genome using bowtie2 with parameters "--very-sensitive --end-to-end --no-unal -X 2000". Aligned reads and high-quality (MAPQ >30) reads were extracted using samtools. Picard tools were used to remove duplicates. Peaks were called using MACS2, normalized tracks were generated during peak calling step with parameters "-B --SPMR".
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peak files were generated using MACS2, coupled to redefine_peaks() from glbase3. Bigwig files were generated from normalized bdg files using bedGraphToBigWig tool.

source_name: Reprogramming cells, control shRNA, SSEA1-Thy1- subpopulations

growth_protocol: mESCs and iPSCs were cultured in DMEM/High glucose medium (Hyclone) supplemented with beta-mercaptoethanol (10 mM), sodium pyruvate (10 mM), non-essential amino acids (10 mM), GlutaMAX (10 mM), 15% fetal bovine serum (Gibco), 1000 U/ml leukemia inhibitory factor (LIF), 1 μM MEK inhibitor PD0325901 and 3 μM GSK3 inhibitor CH99021. MEF cells were cultured in 10% FBS medium supplemented with non-essential amino acids (10 mM) and GlutaMAX (10 mM).

extract_protocol:
For ATAC-seq cells, a total of 50,000 cells were washed once with cold PBS and resuspended in 50 μl lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (10 μl TD buffer, 5 μl Tn5 transposase and 35 μl nuclease-free H2O). DNA was purified using a MinElute Kit (QIAGEN).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with AMPure XP beads.

treatment_protocol: 20,000 MEFs at passage 2 were plated in a 12-well plate and then infected twice with retroviral stocks generated with Plat-E cells. 3 volumes of the supernatants of OSKM transcription factors were mixed with 1 volume of fresh MEF medium containing polybrene at a final concentration of 8 μg/ml. The infection efficiency was tested by MEFs transduced with virus of pMXs-EGFP. pMXs-CTCF and shRNAs were also transfected into OG2-MEFs by retrovirus generated from Plat-E cells. For infecting OG2-MEFs, the medium of OG2-MEFs was replaced with 2 ml of infection mixture per well in a 12-well plate. Infected cells were cultured with mESC medium containing 50 μg/ml Vitamin C (Sigma) post infection and renewed daily. For polycistronic OSKM-mediated reprogramming experiments, MEFs were transduced with 1 volume inducible lentivirus of OSKM and 2 volume rtTA retroviruses generated from HEK293T cells. Infected cells were cultured in mESC medium containing 50 μg/ml Vitamin C and 2 μg/ml doxycycline (Sigma) for 12 days to count GFP positive colonies. To ensure proper CTCF knockdown efficiency before transfecting these virus supernatants into MEFs, we concentrated virus supernatant produced from Ctcf shRNAs.

value: Reprogramming cells


title: cell_SC_3

value: colon cancer cell lines

value: WT KRAS


title: D9_shCTCF_SSEA1-Thy1- [ATAC-seq]

description:
D9_shCTCF_SSEA1-Thy1-
atac_stage2_shCtcf.bed.gz

source_name: Reprogramming cells, CTCF shRNA, SSEA1-Thy1- subpopulations


title: C2bbe1 cells, Basal Halo, streptavidin enriched, Rep3

value: streptavidin-enriched RNA


title: cell_SC_2

value: Colon


title: D9_shCTCF_Thy1+ [ATAC-seq]

description:
D9_shCTCF_Thy1+
atac_stage1_shCtcf.bed.gz

source_name: Reprogramming cells, CTCF shRNA, Thy1+ subpopulations


title: Liver tumor tissue with liver-specific knockout of Pten 2


title: Muscle CIA ZT0 rep 5

description:
PD125
muscle_fc.txt

source_name: Muscle


title: Muscle CIA ZT0 rep 4

description:
PD124
muscle_fc.txt


title: CT1_24

city: Palo Alto

first: Haiyu

last: Zhang

state: CA

address: 300 Pasteur Dr.

institute: Stanford University

description: CT1_24_150918_LYNLEY_0500_AC7BEHACXX_L8_CAGATC_pf

data_processing:
Sequence reads, after filtering for read quality, were re-filtered by fastx (fastx_artifacts_filter) (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Reads that passed the filter were mapped to the human transcriptome hg19 (refMrna, downloaded from the UCSC genome browser, http://www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches (Guo X, 2013, PMID: 24342436).
Total numbers of sequence reads (read counts) for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix (Guo X, 2013, PMID: 24342436).
Genome_build: Human transcriptome hg19
Supplementary_files_format_and_content: The processed data files are text files (tab delimited). It contains the gene symbols in column A and the raw read counts of each gene in column B. For CT2, Nextseq generated 4 sequence files for each sample, and each of the sequence files were processed independently and then combined into one processed data file for each sample.

source_name: Peripheral blood_CT1

extract_protocol:
Blood total RNAs were extracted using columns after red blood cell lysis. Specifically, Blood Total RNA Isolation kit (Mo Bio, Carlsbad, CA) was used for samples of CT1, and QIAamp RNA Blood Mini kit (Qiagen) was used for samples of CT2.
3SEQ (3’-end sequencing for expression quantification) analyses (Beck AH, 2010, PMID: 20098735) were performed on blood RNA samples. 3SEQ is a type of RNA-seq that focuses on quantitative analysis of transcriptome by generating a directional sequencing library targeting 3’UTRs and flanking regions upstream of poly-A tail, ensuring that one read is produced and measured per transcript. 3SEQ libraries were constructed based on the previously published method (Beck AH, 2010, PMID: 20098735) with modifications. Briefly, mRNAs were enriched by poly-A selection using Dynabeads mRNA Purification kit (Thermo Fisher Scientific, Waltham, MA) and heat-fragmented to 100-200 nucleotides. First-strand cDNAs were synthesized using Superscript III reverse transcriptase with Rd2SP-oligodT primer, followed by second-strand cDNA synthesis. Adenine was added to the 3’-end of the double-stranded cDNA and then ligated to the P5-R1SP adapter. The ligated product was amplified by PCR for 15 cycles using primers P5-Rd1SP and P7-index-Rd2SP. Six Illumina indexes, each with six bases, were introduced in the P7 primers. Qualities of the libraries were examined using Agilent DNA 1000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were quantified by Qubit 2.0 fluorometer using Qubit dsDNA BR assay kit (Thermo Fisher Scientific, Waltham, MA). Six or five samples with different indexes were pooled together for next generation sequencing on HiSeq 2000 system for CT1 and on NextSeq (Illumina Inc., San Diego, CA) for CT2. Index associated 36 bp sequences from the P5 primer end, providing the 5’-end sequences of the polyA-containing mRNA fragments, were generated.

treatment_protocol: Patients were not on treatment during sample collection period except that CT2 received a platelet transfusion on day 2.

tag: subject id

value: patient 1 (CT1)

tag: disease

value: Cyclic thrombocytopenia

value: Peripheral blood


title: C2bbe1 cells, Apical Halo, input RNA, Rep3

value: Apically localized


title: CT1_23

description: CT1_23_150918_LYNLEY_0500_AC7BEHACXX_L8_ACAGTG_pf


title: C2bbe1 cells, Basal Halo, streptavidin enriched, Rep1


title: Liver tumor tissue with liver-specific knockout of Pten 1

value: Pten knockdown


title: D9_shCTCF_SSEA1+ [ATAC-seq]

description:
D9_shCTCF_SSEA1+
atac_stage3_shCtcf.bed.gz

source_name: Reprogramming cells, CTCF shRNA, SSEA1+ subpopulations


title: Muscle CIA ZT0 rep 3

description:
PD123
muscle_fc.txt

value: Male

value: Muscle


title: D9_shLuci_SSEA1+ [ATAC-seq]

description:
D9_shLuci_SSEA1+
atac_stage3_shLuc.bed.gz

source_name: Reprogramming cells, control shRNA, SSEA1+ subpopulations


title: CT1_22

description: CT1_22_150918_LYNLEY_0500_AC7BEHACXX_L8_TGACCA_pf


title: Muscle CIA ZT4 rep 3

description:
PD128
muscle_fc.txt

value: CIA


title: C2bbe1 cells, Apical Halo, input RNA, Rep2

value: intestinal epithelial cell


title: CT1_21

description: CT1_21_150918_LYNLEY_0500_AC7BEHACXX_L8_TTAGGC_pf


title: Muscle CIA ZT0 rep 2

description:
PD122
muscle_fc.txt


title: Muscle CIA ZT4 rep 1

description:
PD126
muscle_fc.txt


title: CT1_20

description: CT1_20_150918_LYNLEY_0500_AC7BEHACXX_L8_CGATGT_pf


title: C2bbe1 cells, Apical Halo, input RNA, Rep1


title: C2bbe1 cells, Apical Halo, streptavidin enriched, Rep3


title: Muscle CIA ZT0 rep 1

description:
PD121
muscle_fc.txt


title: D9_shLuci_Thy1+ [ATAC-seq]

description:
D9_shLuci_Thy1+
atac_stage1_shLuc.bed.gz

source_name: Reprogramming cells, control shRNA, Thy1+ subpopulations


title: C2bbe1 cells, Basal Halo, streptavidin enriched, Rep2

value: Basally localized


title: Joint Naive ZT20 rep 5

description:
PD120
joint_fc.txt

source_name: Joint

value: Joint

value: Naive


title: D6_shCTCF_Thy1+ [ATAC-seq]

description:
D6_shCTCF_Thy1+
atac_stage1_shCtcf.bed.gz

value: Reprogramming cells


title: CT1_19

description: CT1_19_150918_LYNLEY_0500_AC7BEHACXX_L8_ATCACG_pf


title: D6_shLuci_SSEA1-Thy1- [ATAC-seq]

description:
D6_shLuci_SSEA1-Thy1-
atac_stage2_shLuc.bed.gz


title: C2bbe1 cells, Apical Halo, streptavidin enriched, Rep2


title: C2bbe1 cells, Apical Halo, streptavidin enriched, Rep1


title: CT1_18

description: CT1_18_150918_LYNLEY_0500_AC7BEHACXX_L7_CAGATC_pf


title: D6_shLuci_Thy1+ [ATAC-seq]

description:
D6_shLuci_Thy1+
atac_stage1_shLuc.bed.gz


title: Joint Naive ZT20 rep 3

description:
PD118
joint_fc.txt


title: CT1_17

description: CT1_17_150918_LYNLEY_0500_AC7BEHACXX_L7_ACAGTG_pf


title: D6_shCTCF_SSEA1+ [ATAC-seq]

description:
D6_shCTCF_SSEA1+
atac_stage3_shCtcf.bed.gz


title: CT1_16

description: CT1_16_150918_LYNLEY_0500_AC7BEHACXX_L7_TGACCA_pf


title: D6_shCTCF_SSEA1-Thy1- [ATAC-seq]

description:
D6_shCTCF_SSEA1-Thy1-
atac_stage2_shCtcf.bed.gz


title: D6_shLuci_SSEA1+ [ATAC-seq]

description:
D6_shLuci_SSEA1+
atac_stage3_shLuc.bed.gz


title: Joint Naive ZT20 rep 2

description:
PD117
joint_fc.txt


title: P9_HP100_3h

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

institute: Medical Univrsity of Vienna

data_processing:
Quality check using FastQC
Mapping using STAR v.2.4.1a
PCR duplicates were removed using UMItools
Feature count using HTSeq-count
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Plasma

extract_protocol:
QIAGEN miRNeasy serum/plasma kit was used according to the manufacturer's instructions.
RNA-seq libraries were prepared with the Ovation SoLo RNAseq kit (NuGEN, cat# 0500-32)

treatment_protocol: Study participants received 100/200mg of either APG-157 or Placebo

tag: batch

value: Healthy control

value: Placebo

tag: concentration

tag: patient


title: P9_HP100_pre


title: CT1_15

description: CT1_15_150918_LYNLEY_0500_AC7BEHACXX_L7_TTAGGC_pf


title: D3_shCTCF_Thy1+ [ATAC-seq]

description:
D3_shCTCF_Thy1+
atac_stage1_shCtcf.bed.gz

tag: day of reprogramming


title: P9_HP100_24h


title: Joint Naive ZT20 rep 1

description:
PD116
joint_fc.txt

tag: Sex

tag: time


title: D3_shLuci_Thy1+ [ATAC-seq]

description:
D3_shLuci_Thy1+
atac_stage1_shLuc.bed.gz


title: CT1_14

description: CT1_14_150918_LYNLEY_0500_AC7BEHACXX_L7_CGATGT_pf


title: P2new_CA200_pre

value: Head and Neck Cancer

value: APG


title: Joint Naive ZT16 rep 5

description:
PD115
joint_fc.txt


title: D12_shCTCF_GFP+_rep2 [ATAC-seq]

description:
D12_shCTCF_GFP+_rep2
atac_stage4_shCtcf.bed.gz

source_name: Reprogramming cells, CTCF shRNA, GFP+ subpopulations


title: Joint Naive ZT16 rep 4

description:
PD114
joint_fc.txt


title: D12_shCTCF_GFP+_rep1 [ATAC-seq]

description:
D12_shCTCF_GFP+_rep1
atac_stage4_shCtcf.bed.gz


title: Joint Naive ZT20 rep 4

description:
PD119
joint_fc.txt


title: Muscle Naive ZT4 rep 4

description:
PD159
muscle_fc.txt


title: Joint Naive ZT16 rep 3

description:
PD113
joint_fc.txt


title: P2new_CA200_24h


title: CT1_13

description: CT1_13_150918_LYNLEY_0500_AC7BEHACXX_L7_ATCACG_pf

value: patient 1 (CT1)


title: CT1_12

description: CT1_12_150918_LYNLEY_0500_AC7BEHACXX_L4_CAGATC_pf

value: Cyclic thrombocytopenia


title: CT1_11

description: CT1_11_150918_LYNLEY_0500_AC7BEHACXX_L4_ACAGTG_pf

value: Peripheral blood


title: Joint Naive ZT16 rep 2

description:
PD112
joint_fc.txt


title: P1new_CA100_pre


title: D12_shLuci_GFP+_rep2 [ATAC-seq]

description:
D12_shLuci_GFP+_rep2
atac_stage4_shLuc.bed.gz

source_name: Reprogramming cells, control shRNA, GFP+ subpopulations


title: P1new_CA100_3h


title: Joint Naive ZT16 rep 1

description:
PD111
joint_fc.txt


title: D0_shCTCF_rep2 [ATAC-seq]

description:
D0_shCTCF_rep2
Mm_atac_shctcf_D0.bed.gz

source_name: Reprogramming cells, CTCF shRNA


title: Joint Naive ZT12 rep 5

description:
PD110
joint_fc.txt


title: CT1_9

description: CT1_9_150918_LYNLEY_0500_AC7BEHACXX_L4_TTAGGC_pf


title: P1new_CA100_24h


title: P2new_CA200_3h


title: P10_HP200_pre


title: CT1_7

description: CT1_7_150918_LYNLEY_0500_AC7BEHACXX_L4_ATCACG_pf


title: CT1_8

description: CT1_8_150918_LYNLEY_0500_AC7BEHACXX_L4_CGATGT_pf


title: D0_shCTCF_rep1 [ATAC-seq]

description:
D0_shCTCF_rep1
Mm_atac_shctcf_D0.bed.gz


title: Joint Naive ZT12 rep 4

description:
PD109
joint_fc.txt


title: D0_shLuci_rep2 [ATAC-seq]

description:
D0_shLuci_rep2
Mm_atac_shctrl_D0.bed.gz

source_name: Reprogramming cells, control shRNA


title: Joint Naive ZT12 rep 3

description:
PD108
joint_fc.txt


title: P10_HP200_3h


title: P10_HP200_24h


title: CT1_10

description: CT1_10_150918_LYNLEY_0500_AC7BEHACXX_L4_TGACCA_pf


title: CT1_6

description: CT1_6_150903_BRISCOE_0256_AC7C2MACXX_L7_CAGATC_pf


title: Joint Naive ZT12 rep 2

description:
PD107
joint_fc.txt


title: shSmarca5_D12_ATAC-rep2 [ATAC-seq]

description:
shSmarca5_D12_ATAC-rep2
Mm_atac_shsmarca5_D12.bed.gz

source_name: Reprogramming cells, Smarca5 shRNA


title: CT1_5

description: CT1_5_150903_BRISCOE_0256_AC7C2MACXX_L7_ACAGTG_pf


title: D0_shLuci_rep1 [ATAC-seq]

description:
D0_shLuci_rep1
Mm_atac_shctrl_D0.bed.gz


title: shSmarca5_D12_ATAC-rep1 [ATAC-seq]

description:
shSmarca5_D12_ATAC-rep1
Mm_atac_shsmarca5_D12.bed.gz


title: P8_CP200_pre_B


title: CT1_4

description: CT1_4_150903_BRISCOE_0256_AC7C2MACXX_L7_TGACCA_pf


title: D12_shLuci_GFP+_rep1 [ATAC-seq]

description:
D12_shLuci_GFP+_rep1
atac_stage4_shLuc.bed.gz


title: P8_CP200_pre


title: Joint Naive ZT12 rep 1

description:
PD106
joint_fc.txt


title: CT1_3

description: CT1_3_150903_BRISCOE_0256_AC7C2MACXX_L7_TTAGGC_pf


title: Joint Naive ZT8 rep 5

description:
PD105
joint_fc.txt


title: shLuci_D12_ATAC-rep2 [ATAC-seq]

description:
shLuci_D12_ATAC-rep2
Mm_atac_shctrl_D12.bed.gz


title: Joint Naive ZT8 rep 4

description:
PD104
joint_fc.txt


title: Joint Naive ZT8 rep 3

description:
PD103
joint_fc.txt


title: shLuci_D12_ATAC-rep1 [ATAC-seq]

description:
shLuci_D12_ATAC-rep1
Mm_atac_shctrl_D12.bed.gz


title: P8_CP200_3h_B


title: CT1_1

description: CT1_1_150903_BRISCOE_0256_AC7C2MACXX_L7_ATCACG_pf


title: Joint Naive ZT8 rep 2

description:
PD102
joint_fc.txt


title: P8_CP200_3h


title: D10_oeControl_rep2 [ATAC-seq]

description:
D10_oeCTRL-rep2
Mm_atac_oectrl_D10.bed.gz

source_name: Reprogramming cells, OSKM overexpress Control


title: D10_oeControl_rep1 [ATAC-seq]

description:
D10_oeCTRL-rep1
Mm_atac_oectrl_D10.bed.gz


title: Joint Naive ZT4 rep 5

description:
PD100
joint_fc.txt


title: P8_CP200_24h


title: D10_oeCTCF_shsmarca5_rep2 [ATAC-seq]

description:
D10_oeCTCF_shsmarca5-rep2
Mm_atac_oectcf_D10_shSmarca5.bed.gz

source_name: Reprogramming cells, OSKM overexpress CTCF and knockdown Smarca5


title: Joint Naive ZT4 rep 4

description:
PD99
joint_fc.txt


title: D10_oeCTCF_shsmarca5_rep1 [ATAC-seq]

description:
D10_oeCTCF_shsmarca5-rep1
Mm_atac_oectcf_D10_shSmarca5.bed.gz


title: Joint Naive ZT4 rep 3

description:
PD98
joint_fc.txt


title: CT1_2

description: CT1_2_150903_BRISCOE_0256_AC7C2MACXX_L7_CGATGT_pf


title: Joint Naive ZT4 rep 2

description:
PD97
joint_fc.txt


title: P7_CP200_pre


title: P7_CP200_pre_B


title: D10_oeCTCF_rep1 [ATAC-seq]

description:
D10_oeCTCF-rep1
Mm_atac_oectcf_D10.bed.gz

source_name: Reprogramming cells, OSKM overexpress CTCF


title: P7_CP200_3h_B


title: P7_CP200_3h


title: P7_CP200_24h_B


title: P8_CP200_24h_B


title: WD-PNEC, infected, 48, 122

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

institute: Queen's University of Belfast

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequence reads were quality checked with FastQC and pre-processed for the sequence cleaning and adapter removal using cutadapt 2.1 and TrimGalore to remove adapter contamination.
 STAR aligner version 2.7.3a using default parameters
Genes were quantified using HT-Seq v0.11.3
Assembly: GRCh38v33
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Well-differentiated primary nasal epithelial cell (WD-PNEC)

growth_protocol: Cells were passaged three times in Promocell Airway Epithelial Cell Growth Medium (C-21160 Promocell) then seeded onto collagen-coated Transwell supports (Corning) at 3x104 cells per Transwell. After 4–6 days of submersion air-liquid interface (ALI) was initiated by removing the apical medium. Cells were differentiated using Stemcell PneumaCult ALI medium (Stemcell Technologies). Complete differentiation took a minimum of 21 days. WD-PNEC cultures were only used when hallmarks of excellent differentiation were evident, including extensive apical coverage with beating cilia and obvious mucus production.

extract_protocol:
RNA was extracted at 48 and 96 h for each condition, in duplicate. Cultures were incubated with 400 µl of Lysis/Binding buffer (High Pure Isolation Kit; Roche) for 5 min at RT. Total Lysed samples were vortexed for 15 sec and transferred to a High Pure filter tube. RNA was extracted as per the manufacturer’s instructions
RNA sequencing was performed via  Kapa RNA HyperPrep with RiboErase (Roche)

treatment_protocol: WD-PNECs were infected with SARS-CoV-2 at an MOI of 0.1 by the addition of inoculum on the apical surface and incubation for 1 h at 37oC

tag: post infection time (hours)

tag: infection

value: SARS-CoV-2 infected

tag: donor

value: Female

tag: age


title: WD-PNEC, mock, 96, 311

value: Well-differentiated primary nasal epithelial cell (WD-PNEC)

value: mock infected


title: WD-PNEC, mock, 48, 311


title: Joint Naive ZT0 rep 5

description:
PD95
joint_fc.txt

data_processing:
Sequencing library preparation and sequencing were performed by the University of Manchester Genomic Technologies Core Facility. Sample quality was determined using a 2200 TapeStation (Agilent Technologies). Libraries were generated using the TruSeq Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol. The multiplexed libraries were analysed by paired-end sequencing on a HiSeq 4000 instrument (76 + 76 cycles, plus indices), then demultiplexed and converted using bcl2fastq software (v2.17.1.14, Illumina).
Joint fastqs were concatenated prior to processing.
Adaptors were removed and ends trimmed using Trimmomatic (v0.36), then reads were mapped against the mouse genome (mm10/GRCm38) using STAR (v2.5.3).
Reads were counted in R using the Rsubread (v1.28.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_fc.txt: Space-delimited matrix tables with raw gene counts for every gene and every sample.

extract_protocol:
Joint tissue was ground with liquid nitrogen using a pestle and mortar, then transferred to a Lysing Matrix D tube containing Trizol. Tissue was homogenised using a BeadMill homogeniser (3 x 4 m/s for 40s). RNA was extracted using chloroform then precipitated using isopropanol. After washing with 75% ethanol, the RNA pellet was resuspended in RNase-free water.
RNA was purified from liver samples using the SV Total RNA kit (Promega), according to the manufacturer’s instructions. Tissue was homogenised using Lysing Matrix D tubes loaded into a BeadMill homogeniser (4 m/s for 20s). RNA was eluted in RNase-free water.
RNA was purified from muscle samples using the ReliaPrep Tissue kit (Promega), following the manufacturer’s instructions for the purification of RNA from fibrous tissue. Muscle tissue was homogenised using the same protocol as for joint, and eluted in RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Male

tag: tissue


title: WD-PNEC, infected, 48, 311

tag: cell type


title: D9_shLuci_Thy1+ [BL-Hi-C]

data_processing:
Raw sequence data of BL-Hi-C were subjected to trimLinker tool from ChIA-PET2 to remove linker sequences with parameters "-m 1 -k 2 -e 1 -l 15 -A ACGCGATATCTTATC -B AGTCAGATAAGATAT". The trimmed reads were processed using HiC-Pro.
The resulting valid pairs were balanced and transformed into hic format using juicer tools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: NOT PROVIDED

extract_protocol:
The BL-Hi-C libraries were performed as previous described. Briefly, the cells were treated with 1% formaldehyde for 10 min at RT and the crosslink was quenched by adding 2.5 M glycine. Then, the cells were treated with 0.1% SDS FA lysis buffer and 1% SDS FA lysis buffer. After that, the genome was digested with enzyme HaeIII into fragments with blunt-ends, which were treated with adenine and ligated with bridge linker containing biotin for 4 hr at 16°C. The unligated DNA fragments were digested with DNA exonuclease. Next, the cells were treated with SDS and proteinase K to digest proteins, and the DNA was purified using phenol-chloroform extraction with ethanol precipitation. Then, the DNA was fragmented into 300 bp on average by sonication and the biotin-labeled DNA fragments were pulled down with streptavidin coated M280 beads.
The BL-Hi-C libraries were constructed into standard Illumina libraries.


title: WD-PNEC, mock, 96, 122


title: D9_shCTCF_Thy1+ [BL-Hi-C]

source_name: Reprogramming cells, CTCF shRNA, Thy1+ subpopulations


title: P7_CP200_24h

tag: treatment


title: WD-PNEC, infected, 96, 122


title: WD-PNEC, infected, 96, 311


title: WD-PNEC, mock, 48, 122


title: P6_HA200_pre_B


title: Joint Naive ZT8 rep 1

description:
PD101
joint_fc.txt


title: Joint Naive ZT0 rep 4

description:
PD94
joint_fc.txt


title: Joint Naive ZT0 rep 3

description:
PD93
joint_fc.txt


title: D10_oeCTCF_rep2 [ATAC-seq]

description:
D10_oeCTCF-rep2
Mm_atac_oectcf_D10.bed.gz


title: D9_shLuci_SSEA1+ [BL-Hi-C]


title: P6_HA200_pre


title: WD-PNEC, mock, 96, 43


title: Joint Naive ZT0 rep 2

description:
PD92
joint_fc.txt


title: D9_shCTCF_SSEA1+ [BL-Hi-C]


title: Joint Naive ZT4 rep 1

description:
PD96
joint_fc.txt


title: WD-PNEC, infected, 96, 43


title: P6_HA200_3h_B


title: P6_HA200_24h_B


title: WD-PNEC, infected, 48, 43


title: D6_shLuci_SSEA1+ [BL-Hi-C]


title: Joint CIA ZT20 rep 4

description:
PD89
joint_fc.txt

value: CIA


title: D6_shCTCF_SSEA1+ [BL-Hi-C]


title: WD-PNEC, infected, 96, 32


title: Joint CIA ZT20 rep 5

description:
PD90
joint_fc.txt


title: Joint Naive ZT0 rep 1

description:
PD91
joint_fc.txt


title: D0_shCTCF_rep1 [BL-Hi-C]


title: P5_HA200_pre_B


title: WD-PNEC, infected, 48, 32


title: WD-PNEC, mock, 96, 32


title: P6_HA200_3h


title: WD-PNEC, mock, 48, 32


title: D0_shCTCF_rep2 [BL-Hi-C]


title: P6_HA200_24h


title: D10_oeCTCF_CTCF_rep2 [ChIP-seq]

data_processing:
ChIP-seq raw reads were first assessed with FastQC tool and trimmed with trim galore if they contained adaptors.
Processed reads were mapped to the mm10 assembly using Bowtie2 with parameters “—very-sensitive –end-to-end –no-unal”. Any reads overlapped with mm10 blacklist regions (from ENCODE project) were filtered with bedtools, then proper-aligned and high-quality reads (MAPQ>30) were extracted with samtools, duplicated reads were removed using picard tools. Peaks were called by MACS2. Peak annotation, motif discovery, and the gene ontology analysis were performed using HOMER annotatePeaks.pl, or findMotifsGenome.pl. Differential binding sites were identified by MACS2bdgdiff tool with default parameters, or with glbase.redefine_peaks. Heatmaps from ChIP-seq was created with glbase or deeptools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peak files were generated using MACS2, coupled to redefine_peaks() from glbase3. Bigwig files were generated from normalized bdg files using bedGraphToBigWig tool.

source_name: Reprogramming cells, OSKM plus CTCF

extract_protocol:
ChIP experiments were performed as previously described. Briefly, 1×10e7 cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). Crosslinked cells were lysed in ChIP SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.0)) containing 1 X Protease Inhibitor Cocktail and PMSF, then sonicated to achieve a chromatin sized of 200-400 bp. After sonication, the supernatant was diluted with IP buffer and then co-incubated with antibodies–Dynabeads protein A/G (1:1 mixed) at 4°C overnight with rotation. Immune complexes were washed with the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 10 mM Tris-HCl (pH 8.0)) and TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for ChIP-Seq library generation. The ChIPmentation experiments were performed as previously described. Briefly, 1×10e5 cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). Crosslinked cells were lysed in lysis buffer (10 mM Tris-HCl,100 mM NaCl (pH 8.0),1 mM EDTA, 0.5 mM EGTA,0.1% NaDeoxycholate, 0.5% N-lauroylsarcosine, 1 x protease inhibitors), then sonicated to achieve a chromatin sized of 200-700 bp.Triton X-100 was added to a final concentration of 1%. After centrifuge, the supernatant was co-incubated with antibodies–Dynabeads protein A/G (1:1 mixed) at 4°C overnight with rotation. Immune complexes were washed with the following buffers: low salt wash buffer, high salt wash buffer, LiCl wash buffer, TE buffer and 10 mM Tris-HCl (pH 8.0). For tagmentation, bead bound chromatin was resuspended in 45 μl of tagmentation buffer, 5 μl of transposase (Vazyme) was added and samples were incubated at 37°C for 10 min followed by two washes with low-salt buffer. Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for ChIP-seq library generation.
ChIP-seq sequencing libraries were constructed using the VAHTSTM Universal DNA Library Prep Kit for Illumina® V2.

treatment_protocol:
20,000 MEFs at passage 2 were plated in a 12-well plate and then infected twice with retroviral stocks generated with Plat-E cells. 3 volumes of the supernatants of OSKM transcription factors were mixed with 1 volume of fresh MEF medium containing polybrene at a final concentration of 8 μg/ml. The infection efficiency was tested by MEFs transduced with virus of pMXs-EGFP. pMXs-CTCF and shRNAs were also transfected into OG2-MEFs by retrovirus generated from Plat-E cells. For infecting OG2-MEFs, the medium of OG2-MEFs was replaced with 2 ml of infection mixture per well in a 12-well plate. Infected cells were cultured with mESC medium containing 50 μg/ml Vitamin C (Sigma) post infection and renewed daily. For polycistronic OSKM-mediated reprogramming experiments, MEFs were transduced with 1 volume inducible lentivirus of OSKM and 2 volume rtTA retroviruses generated from HEK293T cells. Infected cells were cultured in mESC medium containing 50 μg/ml Vitamin C and 2 μg/ml doxycycline (Sigma) for 12 days to count GFP positive colonies. To ensure proper CTCF knockdown efficiency before transfecting these virus supernatants into MEFs, we concentrated virus supernatant produced from Ctcf shRNAs.
Lentivirus of lenti-birAV5 and pSIN-FLBio-SMARCA5 were assembled with psPAX2, pMD2.G vectors. mESCs were then infected with lenti-birAV5 lentivirus and selected with 10 μg/ ml of blastcidin for 5 days. BirAV5 overexpression was detected with anti-V5 antibody by Western blot. Then BirAV5-overexpressed cells were infected with pSIN-FLBio-Smarca5 lentivirus. Thereafter, cells were selected with 2 μg /ml of puromycin for 5 days, then single clones were picked up. Finally, in vivo biotinylation of SMARCA5 was detected with Anti-BIOTIN antibody (Cell Signaling Technology, CatLog: #7075) with a dilution ratio of 1:1000.
Three sets of oligonucleotides were cloned into an U6-sgRNA vector, separately, to create paired sgRNA target sites for SpCas9-nickase in the first or second exon of Smarca5. CRISPR/Cas9 target sites in Smarca5 (NM_053124.2) were designed by http://zifit.partners.org/ZiFiT/CSquare9Nuclease.aspx. The sequences of these three oligos were listed in Key Resources Table. Then these three sets of oligonucleotides were synthesized and inserted into the Bbs I site of the U6-gRNA vector. To generate stable Smarca5-/- mESC lines, two of the three gRNAs were used together, 2×10e6 mESCs were transfected with 20 μg of U6-sgRNA vector and 50 μg of pcDNA3.3-hCas9 plasmids. Cells were selected with 500 μg/ml of G418 (Sigma) after 24 hr of infection and were maintained in selection for 72 hr. Single clones were separated and were seeded in each well of a 48-well plate. Genotype of each colony was examined through Western blot.

tag: chip antibody

value: CTCF(Active motif Cat# 61311)


title: P2_CA200_pre


title: Joint CIA ZT20 rep 3

description:
PD88
joint_fc.txt

value: Joint


title: D0_shLuci_rep2 [BL-Hi-C]


title: P5_HA200_3h


title: Joint CIA ZT16 rep 5

description:
PD85
joint_fc.txt


title: D0_shLuci_rep1 [BL-Hi-C]


title: P5_HA200_pre


title: P2_CA200_24h


title: Joint CIA ZT20 rep 1

description:
PD86
joint_fc.txt


title: Joint CIA ZT16 rep 4

description:
PD84
joint_fc.txt


title: Input-D9-shLuci_Thy1+ [ChIP-seq]


title: WD-PNEC, mock, 48, 43


title: Joint CIA ZT16 rep 3

description:
PD83
joint_fc.txt


title: Input-D9-shCTCF_SSEA1+ [ChIP-seq]


title: Input-D9-shCTCF_Thy1+ [ChIP-seq]


title: Input-D9-shLuci_SSEA1+ [ChIP-seq]


title: Joint CIA ZT20 rep 2

description:
PD87
joint_fc.txt


title: P5_HA200_24h


title: D10_control_CTCF_rep2 [ChIP-seq]

source_name: Reprogramming cells, OSKM control


title: Joint CIA ZT16 rep 2

description:
PD82
joint_fc.txt


title: P1_CA100_pre


title: Input-D9-shCTCF_SSEA1-Thy1- [ChIP-seq]

source_name: Reprogramming cells, CTCF shRNA, SSEA1-Thy1- subpopulations


title: P2_CA200_3h


title: P4_CP100_pre_B


title: P5_HA200_3h_B


title: P4_CP100_pre


title: Joint CIA ZT16 rep 1

description:
PD81
joint_fc.txt


title: P4_CP100_3h_B


title: P1_CA100_3h


title: P1_CA100_24h


title: P4_CP100_3h


title: Joint CIA ZT12 rep 4

description:
PD79
joint_fc.txt


title: M19_CTRL_hPR

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

data_processing:
Raw sequence data quality control performed using FastQC (v0.11.8)
Whole glands were sequenced, and mouse and human reads were separated computationally 44. Raw reads were aligned to the human (hg38) and mouse genome (mm9) using HISAT2 (v2.1.0) 45, the exact parameters are: hisat2 -k 5 -p 4 --seed 42 .
Gene counts were generated using FeatureCounts (v1.6.2). Data preprocessing was done using the limma package from Bioconductor (v3.8).
Genome_build: hg38
Supplementary_files_format_and_content: counts

source_name: MCF7 Intraductal xenograft

growth_protocol: Eight to 12-week-old NSG females were injected into the cleaved teat with a blunt end Hamilton syringe with 100 000 cells. Growth was followed over 45 days through live imaging with Xenogen IVIS Imaging System 200.

extract_protocol:
Mouse mammary glands were snap-frozen, RNA extracted using TriZOL reagent (Invitrogen) total RNA was isolated with miRNeasy Mini Kit (Qiagen).
Illumina HiSeq, 2x150bp configuration

treatment_protocol: The mice were not subjected to any treatment.

tag: cell line

value: Breast cancer cell line

tag: gene

value: PGR overexpression

value: Xenografted mammary gland


title: P4_CP100_24h

city: Vienna

tag: batch

tag: disease

value: Placebo


title: M18_CTRL_hPR


title: M17_CTRL_hPR


title: Input-D9-shLuci_SSEA1-Thy1- [ChIP-seq]

source_name: Reprogramming cells, control shRNA, SSEA1-Thy1- subpopulations

value: Reprogramming cells


title: P4_CP100_24h_B

value: Head and Neck Cancer

tag: concentration

tag: patient


title: Input-D6-shCTCF_SSEA1+ [ChIP-seq]

source_name: Reprogramming cells, CTCF shRNA, SSEA1+ subpopulations

tag: day of reprogramming


title: Joint CIA ZT12 rep 3

description:
PD78
joint_fc.txt

source_name: Joint

tag: Sex

tag: time


title: Joint CIA ZT12 rep 2

description:
PD77
joint_fc.txt


title: Input-D6-shLuci_SSEA1+ [ChIP-seq]

source_name: Reprogramming cells, control shRNA, SSEA1+ subpopulations


title: P2-baseline [DD-OL-33]

city: Chicago

first: Olivia

middle: Thao

last: Ly

state: Illinois

address: 768 W Jackson Blvd, 424

department: Medicine

institute: University of Illinois in Chicago College of Medicine

description: RNA was isolated at D32 from baseline (immature) P2 iPSC-aCMs . During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates

data_processing:
Sequenced reads were aligned to Homo sapiens reference genome GRCh38 (hg38) with STAR v. 2.7.6a
mRNA expressions were quantified from the aligned reads by using STAR from option -quantMode
Gene symbols were annotated using the biomaRt R package
Principal component analysis (PCA) was performed after normalization. DEGs were identified using DESeq2, with FDR < 0.05 and absolute log2fold-change higher than 1. DEGs for each comparison were plotted using the ComplexHeatmap R package
To define the biological function significantly associated with the DEGs identified from each comparison, we performed gene set enrichment analysis suing the enrichGO function from clusterProfiler R package
Genome_build: Homo sapiens reference genome GRCh38 (hg38)
Supplementary_files_format_and_content: Processed data files are provided as .csv

growth_protocol: iPSCs were maintained on human recombinant vitronectin coated plates in mTeSR medium. iPSCs were then differentiated using the cardiomyocyte differentiation kit (Gibco), and guided into atrial subtypes using 1µmol/l all-trans retinoic acid (protocol adapted from Devalla et al., 2015). At day 10, glucose starvation metabolic selection was used to enrich the iPSC-aCM culture. For matured iPSC-aCMs, thyroid hormone, insulin-like growth factor, dexamethasone, palmitic acid, and oleic acid were added to the foundational maintenance media from day 18-32, and the cells were subjected to electrical field stimulation from day 18-25.

extract_protocol:
Cells were harvested and RNA extracted using Trizol-pheno-chloroform extraction
Strand-specific RNA-Seq libraries were prepared using a TruSEQ mRNA-SEQ library protocol (illinuma provided). Library quality and quantity was assessed using Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000.

value: iPSC-derived atrial cardiomyocytes


title: M09_CTRL_CTRL

value: Control


title: Joint CIA ZT12 rep 1

first: Polly

last: Downton

institute: University of Manchester

description:
PD76
joint_fc.txt


title: M08_CTRL_CTRL


title: Joint CIA ZT12 rep 5

description:
PD80
joint_fc.txt


title: Input-D6-shCTCF_SSEA1-Thy1- [ChIP-seq]


title: L3-3-D32 baseline [DD-OL-31]

description: RNA was isolated at D32 from baseline (immature) L3 iPSC-aCMs . This is the third biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: Joint CIA ZT8 rep 5

description:
PD75
joint_fc.txt


title: P1-baseline [DD-OL-32]

description: RNA was isolated at D32 from baseline (immature) P1 iPSC-aCMs . During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: Input-D3-shLuci-Thy1+ [ChIP-seq]

source_name: Reprogramming cells, control shRNA, Thy1+ subpopulations


title: Joint CIA ZT8 rep 3

description:
PD73
joint_fc.txt


title: Joint CIA ZT8 rep 4

description:
PD74
joint_fc.txt


title: L3-2-D32 baseline [DD-OL-30]

description: RNA was isolated at D32 from baseline (immature) L3 iPSC-aCMs . This is the second biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: Input-D6-shLuci_SSEA1-Thy1- [ChIP-seq]


title: CT2_15

source_name: Peripheral blood_CT2

tag: subject id

value: patient 2 (CT2)

value: Cyclic thrombocytopenia

value: Peripheral blood


title: L3-1-D32 baseline [DD-OL-29]

description: RNA was isolated at D32 from baseline (immature) L3 iPSC-aCMs . This is the first biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: M06_CTRL_CTRL


title: CT2_14


title: Joint CIA ZT8 rep 2

description:
PD72
joint_fc.txt


title: P2-EMM [DD-OL-28]

description: RNA was isolated at D32 from P2  iPSC-aCMs undergoing EMM. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates

source_name: D32 from P2  iPSC-aCMs undergoing EMM


title: Input-D0-shCTCF_rep1 [ChIP-seq]

source_name: Reprogramming cells, CTCF shRNA


title: Input-D0-shLuci_rep2 [ChIP-seq]

source_name: Reprogramming cells, control shRNA


title: CT2_13


title: Joint CIA ZT8 rep 1

description:
PD71
joint_fc.txt


title: Input-D0-shCTCF_rep2 [ChIP-seq]


title: Joint CIA ZT4 rep 4

description:
PD69
joint_fc.txt


title: L3-2-D32 EMM [DD-OL-25]

description: RNA was isolated at D32 from L3 iPSC-aCMs undergoing EMM. This is the second biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates

source_name: D32 from L3 iPSC-aCMs undergoing EMM


title: Input_D12_shCTCF_Oct4+_rep3 [ChIP-seq]

source_name: Reprogramming cells, CTCF shRNA, GFP+ subpopulations


title: Input-D0-shLuci_rep1 [ChIP-seq]


title: Joint CIA ZT4 rep 5

description:
PD70
joint_fc.txt


title: P1-EMM [DD-OL-27]

description: RNA was isolated at D32 from P1 iPSC-aCMs undergoing EMM.  During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates

source_name: D32 from P1 iPSC-aCMs undergoing EMM


title: Input-D3-shCTCF-Thy1+ [ChIP-seq]


title: L3-3-D32 EMM [DD-OL-26]

description: RNA was isolated at D32 from L3 iPSC-aCMs undergoing EMM. This is the third biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: CT2_11


title: Joint CIA ZT4 rep 3

description:
PD68
joint_fc.txt


title: Input_D12_shCTCF_Oct4+_rep1 [ChIP-seq]


title: L3-1-D32 EMM [DD-OL-24]

description: RNA was isolated at D32 from L3 iPSC-aCMs undergoing EMM. This is the first biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: Joint CIA ZT4 rep 1

description:
PD66
joint_fc.txt


title: CT2_9


title: Joint CIA ZT0 rep 5

description:
PD65
joint_fc.txt


title: L3-1-D25 [DD-OL-19]

description: RNA was isolated from L3 iPSC-aCMs undergoing EMM at D25. This is the first biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates

source_name: L3 iPSC-aCMs undergoing EMM at D25


title: CT2_8


title: L3-3-D25 [DD-OL-21]

description: RNA was isolated at D25 from L3 iPSC-aCMs undergoing EMM. This is the third biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates

source_name: D25 from L3 iPSC-aCMs undergoing EMM


title: Joint CIA ZT4 rep 2

description:
PD67
joint_fc.txt


title: Input_D12_shLuci_Oct4+_rep2 [ChIP-seq]

source_name: Reprogramming cells, control shRNA, GFP+ subpopulations


title: L3-2-D25 [DD-OL-20]

description: RNA was isolated at D25 from L3 iPSC-aCMs undergoing EMM. This is the second biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: CT2_12


title: CT2_4


title: Input_D12_shLuci_Oct4+_rep3 [ChIP-seq]


title: Input_D12_shLuci_Oct4+_rep1 [ChIP-seq]


title: Input_D12_shCTCF_Oct4+_rep2 [ChIP-seq]


title: CT2_3


title: CT2_6


title: CT2_7


title: CT2_5


title: Joint CIA ZT0 rep 4

description:
PD64
joint_fc.txt


title: CTCF-ChIP-D9-shCTCF_SSEA1+ [ChIP-seq]


title: P2-HAT [DD-OL-10]

description: RNA was isolated from an atrial tissue biopsy obtained during cardiac surgery of P2. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates

value: Human atrial tissue


title: Liver Naive ZT20 rep 5

description:
PD60
liver_fc.txt

source_name: Liver

value: Liver

value: Naive


title: L3-3-D15 [DD-OL-16]

description: RNA was isolated from L3 iPSC-aCMs cultured to D15. This is the third biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates

source_name: L3 iPSC-aCMs cultured to D15


title: P1-HAT [DD-OL-04]

description: RNA was isolated from an atrial tissue biopsy obtained during cardiac surgery of P1. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: L3-2-D15 [DD-OL-15]

description: RNA was isolated from L3 iPSC-aCMs cultured to D15. This is the second biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: Joint CIA ZT0 rep 3

description:
PD63
joint_fc.txt

value: Male

value: CIA


title: Liver Naive ZT20 rep 4

description:
PD59
liver_fc.txt


title: Joint CIA ZT0 rep 2

description:
PD62
joint_fc.txt

value: Joint


title: CTCF-ChIP-D9-shCTCF_Thy1+ [ChIP-seq]

source_name: Reprogramming cells, CTCF shRNA, Thy1+ subpopulations

value: CTCF(Active motif Cat# 61311)


title: CT2_2


title: L3-1-D15 [DD-OL-14]

description: RNA was isolated from L3 iPSC-aCMs cultured to D15. This is the first biological replicate. During sequencing, 2 technical replicates were performed per sample, and raw count files are compiled from both technical replicates


title: Heat denatured tracer tRNA replicate 1

first: Schaefer

last: Matthias

address: Schwarzspanierstrasse 17-I

institute: Medical University Vienna, Center for Anatomy & Cell Biology

data_processing:
basecalling was performed by VBCF sequencing facility
Reads (if libraries were pair-end sequenced, only R1 mate was further processed) were trimmed for adapter sequences and low quality bases with q score less than 10 were removed from the 3' end using the cutadapt software. Command line: cutadapt -q 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC input.fastq > output_trimmed.fastq
Reads were further mapped to the collapsed tRNA annotation originating from https://github.com/FlorianPichot/tRNA_reference_construction . Command line:  bowtie2 --no-unal --no-1mm-upfront -D 15 -R 2 -N 0  -L 10 -i S,1,1.15 -x index -U sample.fastq -S output.sam 2> sample_mapping_report.txt
Sam files were converted to bam file, sorted and indexed using samtools (samtools view -S -b; samtools sort; samtools index)
Number of reads mapping to individual tRNA cluster was extracted by samtools idxstats. Command line samtools idxstats sample_sorted.bam > sample_idxstats.txt
Genome_build: custom collapsed human tRNA space (PMID: 33435213). FASTA available on series record and at https://github.com/FlorianPichot/tRNA_reference_construction/blob/main/Available_references/Homo_sapiens/
Supplementary_files_format_and_content: tsv files containing number of reads mapping to individual tRNA clusters

extract_protocol:
Cells were collected from culture dish and solubilized in Trizol. Total RNA was extracted, and separated using UREA-PAGE. tRNAs were excised, eluted from crushed gel pieces and precipitated by isopropanol. Refolded tRNAs were further treated with recombinant angiogenin endonuclease, radiolabeled using P32-gamma-ATP and used to monitor DDX3X helicase unwinding activity
Libraries were prepared according to NEBNext small RNA cloning protocol (E7580S)

tag: enzymatic treatment

value: Cleaved with recombinant Angiogenin and heat denatured

tag: biochemical separation

value: Separated by native PAGE prior to library cloning

tag: molecule subtype

value: tRNA


title: Joint CIA ZT0 rep 1

address: Oxford Road

description:
PD61
joint_fc.txt

tag: strain

tag: tissue


title: CTCF-ChIP-D9-shLuci_Thy1+ [ChIP-seq]

tag: cell type

value: Reprogramming cells


title: CTCF-ChIP-D9-shLuci_SSEA1-Thy1- [ChIP-seq]

source_name: Reprogramming cells, control shRNA, SSEA1-Thy1- subpopulations

tag: chip antibody