title: WT-AC rep2


title: HMCES-KO1-SB

status: Public on Sep 14 2022

type: SRA

city: Beijing

first: Qiaoran

last: Xi

address: Haidian District

country: China

institute: School of Life Sciences, Tsinghua University

library_source: transcriptomic

data_processing:
RNA reads were quality checked with FastQC v0.11.5 and mapped to the mouse (mm10) genome with Bowtie2 v2.3.3 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.9. On average, 80% of reads were uniquely mapped. Uniquely mapped reads were assigned to annotated genes with featureCounts v2.0.1 using default settings. Read counts were then normalized by library size and differential gene expression analysis based on a negative binomial distribution was conducted with DESeq2 packages in R language.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data provided as supplementary file

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic stem cell (mESC)

growth_protocol: ESCs were cultured on gelatin coated plates with 15% serum ESC culture medium

extract_protocol:
RNA of non-treated or activin, SB431542, BMP4, LDN193189 treated WT or HMCES-KO mESCs were purified using TIANGEN kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment. Or activin A (50 ng/ml, R&D Systems), SB431542 (10 μM), BMP4 (10ng/ml),  or LDN193189 (50nM) treated for 2h

tag: cell type

value: mouse embryonic stem cell (mESC)

tag: strain

tag: genotype

value: HMCES-KO

tag: treatment


title: CRC01603

city: Taoyuan City

first: Hsuan

last: Liu

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

description: mCRC98_NR-gene row.txt

data_processing:
sequencing data were assessed for quality and trimmed of the primer-adaptor sequences by the Partek® Flow® Genomic Analysis Software (Partek)
Reads were alignment to the human reference genome (hg38) (by bowtie 2)
annotation of known miRNA based on miRBase
The number of reads for each miRNA was normalized to reads per million (RPM+0.0001) and quantified across all samples
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized miRNA counts(RPM+0.0001) for every miRNA and every sample

organism: Homo sapiens

source_name: CRC

extract_protocol:
Circulating small EVs were isolated from 1 mL of pre-filtered plasma using a procedure described in the exoEasy Plasma Handbook (QIAGENE). Briefly, plasma was mixed with binding buffer (XBP) and added to the exoEasy membrane affinity column for binding. After centrifugation, the flow-through was discarded and wash buffer (XWP) was added to the column to wash off nonspecifically retained materials. After EVs were bound on the exoEasy membrane affinity column as described in the isolation procedure above, the vesicles were lysed by adding QIAzol to the spin column and further collected by centrifugation (exoRNeasy, QIAGEN). Following chloroform extraction, samples were thoroughly mixed and centrifuged to separate organic and aqueous phases. The aqueous phase was recovered and mixed with ethanol. The sample-ethanol mixture was added to a RNeasy MinElute spin column and centrifuged. The column was washed once with buffer RWT and then twice with buffer RPE followed by elution of RNA in water. The RNA concentration, purity, and integrity were assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
Prior to sequencing experiments, RNA concentration, purity, and integrity were assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA). Illumina sequencing libraries were prepared using the NEXTflexTM small RNA-seq kit v3 Guide (Bioo Scientific, 5132-05), according to the manufacturer’s instructions. For each library, 60 ng of purified small EV RNA were ligated to 3’ and 5’ adaptors and then reverse transcribed to cDNA using adaptor-specific primers. After purification and PCR amplification using universal and specific barcode primers, the miRNA library was resolved and recovered from the 6% TBE-PAGE gel based on the corresponding size for miRNA distribution. The yield and size distribution of the small RNA libraries were assessed using the Agilent 2100 Bioanalyzer instrument with the High-Sensitivity DNA Assay (Agilent Technologies). Equal concentration of each library was sequenced on a NextSeq 500 (Illumina) platform.

tag: disease state

value: CRC

tag: tissue

value: plasma small extracellular vesicles

tag: Stage

tag: sampling time points

tag: patient id

tag: molecule subtype

value: miRNA


title: HMCES-KO2 rep1

value: no treatment


title: S2_Dora_1_mRNA_sequence

city: Cambridge

first: David

last: Bartel

state: MA

address: 455 Main St

country: USA

institute: Whitehead Institute, MIT

description:
RNAseq from WT and dora S2 cells
S2_WTDora_mRNA_rawreads.csv

data_processing:
Sequencing reads for sRNAseq libraries were processed and counted as previously described (Kingston and Bartel, 2021)
RNAseq reads were aligned to the genome (UCSC dm6.08 reference assembly) using STAR (V2.4, with the paramaters “--alignIntronMax 1 --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated –outSJfilterReads”) (Dobin et al., 2013), and alignments to all chromosomal genes were counted using htseq-count (with the parameters “-m union -s reverse") (Anders et al., 2015). TPM values were determined by dividing these htseq-determined counts for each gene by the median length for all isoforms of that gene, and then normalizing these values for library depth.
Genome_build: dm6
Supplementary_files_format_and_content: All processed .csv files contain non-normalized miRNA or mRNA counts for the indicated samples

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Drosophila S2 cells were grown at 26°C in Schneider’s Drosophila Medium (Life Technologies) supplemented with 10% heat-inactivated FBS (Life Technologies). Cells were passaged 1:5 every 3–5 days.

extract_protocol:
RNA-seq libraries were prepared using the NEXTflex Rapid Directional RNA-seq Kit (Bioo Scientific) following enrichment of polyadenylated mRNAs with NEXTflex Poly(A) Beads (Bioo Scientific). Libraries were sequenced on an Illumina HiSeq platform with 50-nt single-end reads.
RNA was extracted with TRI Reagent (Life Technologies), according to the manufacturer’s protocol. Briefly, samples were homogenized in TRI reagent, and RNA was phase-separated by the addition of chloroform (J.T. Baker Analytical) at a ratio of 250 µL per 1 mL TRI Reagent. RNA was then precipitated with isopropanol, with GlycoBlue (Life Technologies) added as a co-precipitant when necessary, and pellets were washed twice with 70% ethanol prior to resuspension in water.

value: dora

tag: ip target


title: HMCES-KO2-AC

value: activin A


title: CRC01606

description: mCRC98_NR-gene row.txt


title: HMCES-KO1 rep1


title: S2_Dora_3_sRNA_sequence

description:
sRNAseq to verify candidate triggers
S2_kah_ago1_rawreads.csv

extract_protocol:
sRNA-seq libraries were constructed as described in the step-by-step protocol found at http://bartellab.wi.mit.edu/protocols.html, with some alterations. Briefly, between 1 and 5 ug of total RNA was mixed with size-selection markers (18- and 32-nt, 5′-radiolabeled RNAs) and 1 uL of quantitative standards (cel-lsy-6 and xtr-427) (ratios of total RNA:quantitative standards for each sample listed in Table S7). This mixture was size-selected on a denaturing gel, and then 2S rRNA was depleted by subtractive hybridization (Seitz et al., 2008). 3′ and 5′ adapters (each containing 4 random-sequence nucleotides at their ligation junctions) were then sequentially ligated using RNL2 truncated K227Q (NEB) and RNLI (NEB), respectively, in the presence of 10% polyethylene glycol (PEG 8000, NEB) and Superasin (Thermo Fischer Scientific), with gel purification following each ligation step. Purified RNA was reverse transcribed using SuperScript III (Thermo Fischer Scientific) and amplified using Kapa HiFi HotStart Ready Mix (Roche Diagnostics). Libraries were sequenced on an Illumina HiSeq platform with 50-nt single-end reads.
RNA was extracted with TRI Reagent (Life Technologies), according to the manufacturer’s protocol. Briefly, samples were homogenized in TRI reagent, and RNA was phase-separated by the addition of chloroform (J.T. Baker Analytical) at a ratio of 250 µL per 1 mL TRI Reagent. RNA was then precipitated with isopropanol, with GlycoBlue (Life Technologies) added as a co-precipitant when necessary, and pellets were washed twice with 70% ethanol prior to resuspension in water.


title: WT-SB rep2

value: wild type


title: WT-AC rep1


title: CRC01511

description: mCRC98_NR-gene row.txt


title: S2_WT_2_sRNA_sequence

value: WT


title: S2_Dora_2_sRNA_sequence


title: WT-BMP4 rep2


title: HMCES-KO2 rep2


title: CRC01513

description: mCRC98_NR-gene row.txt


title: S2_WT_1_sRNA_sequence


title: S2_kah_3_sRNA_sequence

value: kah


title: HMCES-KO1 rep2


title: CRC01512

description: mCRC98_NR-gene row.txt


title: WT rep2


title: WT rep1


title: STko_H3T6p

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

library_source: genomic

data_processing:
Reads were adapter stripped (CutAdapt),
mapped to Mm10 (bowtie2)
and duplicates removed (Picard).
Bedgraph files were created from the first read using HTSEQ.
Enriched regions were called against NS using HOMER (-fragLength 200 findPeaks -style histone –F 2 –size 600 –tagThreshold 20  –minDist 1200) and then filtered so that each region had at least 11.5 normalised reads
Genome_build: Mm10
Supplementary_files_format_and_content: bedgraph files show tag densities and bed files show enriched regions.

molecule: genomic DNA

source_name: B lymphocyte

growth_protocol: Spleens, thymi and lymph nodes were harvested from mice and single cell suspensions were prepared by sieving through a 70 µm nylon mesh filter. Cells were stained for sorting into B cell populations with antibodies APC Rat Anti-Mouse CD45R/B220 (BD Pharmingen, Cat no.: 553092.)

extract_protocol:
Briefly, cells were cross-linked with formaldehyde (1%, 10 min) then quenched with glycine (125mM). Fixed cells were lysed in SDS lysis buffer and chromatin-bound DNA sheared by sonication with a Misonix Sonicator S-4000. ChIP samples were incubated overnight at 4°C with Protein A Magnetic Beads (Millipore) and 5 μg of H3T6p (Abcam, AB141012)  antibodies. Protein-DNA cross-links were reversed by incubating overnight at 65°C and purified with the Zymo-SpinTM I kit (Zymo Research).
Libraries were prepared from  ChIP DNA (10ng) using the NEBNext®  ChIP-Seq Library for Illumina (New England Biolabs) and Ampure XP Bead clean-up.

treatment_protocol: Primary mouse B cells were stimulated with 10ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1µM calcium ionophore (I; Sigma-Aldrich, A23187) for 1 hour.

tag: strain background

tag: genotype/variation

value: C57BL/6 Tilcara (Til), a PKCbeta mutant mice model

value: Spleens, thymi and lymph nodes

value: B lymphocyte

value: 10ng/mL of phorbol 12-myristate 13-acetate and 1µM calcium ionophore for 1 h

tag: antibody


title: CRC01507

description: mCRC98_NR-gene row.txt


title: S2_kah_1_sRNA_sequence


title: CRC01510

description: mCRC98_NR-gene row.txt


title: ST_H3T6p


title: CRC01601

description: mCRC98_NR-gene row.txt

value: 1 (treatment naive)


title: S2_WT_3_sRNA_sequence


title: S2_ago1_3_sRNA_sequence


title: CRC01509

description: mCRC98_NR-gene row.txt


title: NS_H3T6p


title: S2_Dora_1_sRNA_sequence


title: CRC01508

description: mCRC98_NR-gene row.txt


title: S2_kah_2_sRNA_sequence


title: CRC01506

description: mCRC98_NR-gene row.txt


title: CRC01505

description: mCRC98_NR-gene row.txt


title: S2_ago1_2_sRNA_sequence


title: CRC01504

description: mCRC98_NR-gene row.txt


title: T_656_4

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to bumblebee genome using STAR (Dobin et al., 2013)  v2.7.2b with default parameters based on RefSeq annotation version 102 for GCF_000214255.1/Bter_1.0
Calculation of read counts on exon level summarized for each gene with gene_biotype protein_coding (RefSeq annotation release 102 for Bter_1.0) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O –fraction).
Assembly: GCF_000214255.1/Bter_1.0 (primary assembly)
Supplementary files format and content: Character (TAB) separated value file containing mRNA abundance measurements

organism: Bombus lucorum

source_name: thorax and abdomen tissues

extract_protocol:
Head and gut of the bumbleebees were disected in the field and afterwards the thorax and abdomen was frozen at -80°C. RNA was extracted using the RNeasy Mini Kit according to manufactur protocol.
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for the samples was from 2,7 – 9,0. DNA libraries suitable for sequencing were prepared from 400 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (½ volume, 4 samples: full volume). After 15 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~285 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.

value: Thorax and abdomen

tag: altidue of sampling

tag: ave. temperature of sampling site

tag: plant richness at sampling site

tag: plant cover at sampling site

tag: year of sampling

tag: sampling site

value: sampling site T3, valley, Berchtesgarden, German Alps


title: germ-free, veh, liver, 3

type: RNA

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

country: Switzerland

institute: École polytechnique fédérale de Lausanne

description: Gene expression data

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: The MTA1.0 arrays were scanned on Affymetrix GSC3000 7G Scanner

data_processing: Microarray data was normalized with RMA-sketch method using the Affymetrix Expression console.

label: biotin

source_name: Liver from germ-free mouse treated with vehicle

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (Part Number 4411974) according to manufactures protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

extract_protocol: Total RNA was isolated from flash-frozen and powdered liver and kidney aliquots using TRIzol (Life Technologies) according to the manufacturer's instructions.

treatment_protocol: Male 9 weeks-old C57BL/6J mice were treated for 16 days with 500 mg/kg/day doxycycline hyclate (Sigma) in drinking water and sacrified afterwards. Organs were directly flashfrozen in liquid nitrogen after recovery.

tag: Sex

value: male

tag: genotype

value: Liver

tag: age

tag: treatment

value: Vehicle


title: Dora_B_1620_sRNA_rep1_sequence

description:
dora[B] embryonic timecourse
mutB_timecourse_sRNA_rawreads.csv

source_name: 16-20 h embryos

value: dora[B]


title: germ-free, veh, kidney, 3

description: Gene expression data

source_name: Kidney from germ-free mouse treated with vehicle

tag: tissue

value: Kidney


title: germ-free, dox, kidney, 3

description: Gene expression data

source_name: Kidney from germ-free mouse treated with Doxycycline 500mpdk

value: Doxycycline 500mpkd


title: Dora_B_1620_mRNA_rep2_sequence

description:
dora[B] embryonic timecourse
mutB_timecourse_mRNA_rawreads.csv


title: germ-free, veh, liver, 1

description: Gene expression data


title: germ-free, dox, kidney, 2

description: Gene expression data


title: CRC01501

description: mCRC98_NR-gene row.txt

tag: disease state

value: CRC

value: plasma small extracellular vesicles

tag: Stage

tag: sampling time points

tag: patient id

value: miRNA


title: H_1808_8

value: sampling site H6, hintersee, Berchtesgarden, German Alps


title: germ-free, dox, liver, 2

description: Gene expression data

source_name: Liver from germ-free mouse treated with Doxycycline 500mpdk


title: CRC01403

description: mCRC98_NR-gene row.txt

tag: molecule subtype


title: germ-free, dox, liver, 3

description: Gene expression data


title: germ-free, veh, liver, 2

description: Gene expression data


title: germ-free, dox, kidney, 1

description: Gene expression data


title: germ-free, dox, liver, 1

description: Gene expression data


title: germ-free, veh, kidney, 1

description: Gene expression data


title: Dora_B_1620_mRNA_rep1_sequence

tag: ip target


title: Dora_B_1620_sRNA_rep2_sequence


title: CRC01503

description: mCRC98_NR-gene row.txt


title: H_1808_7

tag: altidue of sampling


title: T_656_3

tag: ave. temperature of sampling site


title: S2_ago1_1_sRNA_sequence


title: CRC01502

description: mCRC98_NR-gene row.txt


title: H_1808_5

tag: plant richness at sampling site


title: T_656_2

tag: plant cover at sampling site


title: H_1808_9

tag: year of sampling


title: T_656_1

tag: sampling site


title: CRC01402

description: mCRC98_NR-gene row.txt


title: Dora_B_1216_sRNA_rep2_sequence

source_name: 12-16 h embryos


title: H_1808_4


title: H_1808_3


title: Dora_B_1216_mRNA_rep2_sequence


title: H_1808_6


title: germ-free, veh, kidney, 2

description: Gene expression data

tag: Sex


title: Dora_B_1216_sRNA_rep1_sequence

tag: genotype


title: Dora_B_1216_mRNA_rep1_sequence


title: H_1579_3

value: sampling site H5, hintersee, Berchtesgarden, German Alps


title: H_1579_2


title: H_1579_4


title: H_1579_5


title: CRC01303

description: mCRC98_NR-gene row.txt


title: CRC01304

description: mCRC98_NR-gene row.txt


title: Dora_B_812_sRNA_rep2_sequence

source_name: 8-12 h embryos


title: H_1579_1


title: CRC01401

description: mCRC98_NR-gene row.txt


title: CRC01302

description: mCRC98_NR-gene row.txt


title: H_1330_5

value: sampling site H4, hintersee, Berchtesgarden, German Alps


title: Dora_B_812_sRNA_rep1_sequence


title: H_1808_1


title: CRC01203

description: mCRC98_NR-gene row.txt


title: H_1330_3


title: CRC01301

description: mCRC98_NR-gene row.txt


title: Dora_B_812_mRNA_rep2_sequence


title: H_1330_4


title: H_1330_2


title: Dora_B_812_mRNA_rep1_sequence


title: H_1330_1


title: CRC01201

description: mCRC98_NR-gene row.txt


title: H_1808_2


title: H_987_5

value: sampling site H2, hintersee, Berchtesgarden, German Alps


title: CRC01108

description: mCRC98_NR-gene row.txt


title: H_987_3


title: H_987_4


title: H_987_2


title: CRC01107

description: mCRC98_NR-gene row.txt


title: Dora_A_1620_sRNA_rep1_sequence

description:
dora[A] embryonic timecourse
mutA_timecourse_sRNA_rawreads.csv

value: dora[A]


title: Dora_A_1620_sRNA_rep2_sequence


title: WM_1813_1

value: sampling site Wmb5, watzmann, Berchtesgarden, German Alps


title: H_987_1

value: Thorax and abdomen


title: CRC01106

description: mCRC98_NR-gene row.txt


title: CRC01105

description: mCRC98_NR-gene row.txt


title: Dora_A_1620_mRNA_rep1_sequence

description:
dora[A] embryonic timecourse
mutA_timecourse_mRNA_rawreads.csv


title: WM_1813_2


title: WM_1655_5

value: sampling site Wmb4, watzmann, Berchtesgarden, German Alps


title: WM_1655_3


title: WM_1655_1


title: WM_1655_4


title: CRC01104

description: mCRC98_NR-gene row.txt


title: WM_1420_4

value: sampling site Wmb3, watzmann, Berchtesgarden, German Alps


title: WM_1655_2


title: CRC01101

description: mCRC98_NR-gene row.txt

value: 1 (treatment naive)


title: CRC01102

description: mCRC98_NR-gene row.txt


title: CRC01003

description: mCRC98_NR-gene row.txt


title: Dora_A_1216_sRNA_rep1_sequence


title: Dora_A_1216_mRNA_rep1_sequence


title: WM_1420_5


title: WM_1420_1


title: WM_1420_2


title: WM_1140_3

value: sampling site Wmb2, watzmann, Berchtesgarden, German Alps


title: CRC01001

description: mCRC98_NR-gene row.txt


title: Dora_A_1620_mRNA_rep2_sequence


title: CRC00901

description: mCRC98_NR-gene row.txt


title: CRC01002

description: mCRC98_NR-gene row.txt


title: Dora_A_812_sRNA_rep1_sequence


title: WM_1140_2


title: WM_1140_5


title: WM_1140_4


title: Dora_A_1216_sRNA_rep2_sequence


title: Dora_A_812_sRNA_rep2_sequence


title: Dora_A_812_mRNA_rep2_sequence


title: WM_1420_3


title: WM_960_5

value: sampling site Wmb1, watzmann, Berchtesgarden, German Alps


title: WM_960_1


title: WM_960_2


title: CRC00704

description: mCRC98_NR-gene row.txt


title: WM_1140_1


title: CRC00705

description: mCRC98_NR-gene row.txt


title: CRC00801

description: mCRC98_NR-gene row.txt


title: WM_960_4


title: Dora_A_812_mRNA_rep1_sequence


title: Dora_A_1216_mRNA_rep2_sequence


title: CR43432_mut_16_20_mRNA_line2_sequence

description:
CR43432 embryonic timecourse
CR43432_mRNA_rawreads.csv


title: WM_1423_2

value: sampling site Wma3, watzmann, Berchtesgarden, German Alps


title: WM_1423_5


title: CR43432_mut_12_16_mRNA_line2_sequence


title: CR43432_mut_12_16_mRNA_line1_sequence


title: WM_1423_3


title: CRC00701

description: mCRC98_NR-gene row.txt


title: WM_1245_3

value: sampling site Wma2, watzmann, Berchtesgarden, German Alps


title: WM_1423_1


title: WM_1245_1


title: CRC00604

description: mCRC98_NR-gene row.txt

value: CRC


title: CR43432_WT_12_16_mRNA_line2_sequence

description:
Paired WT samples for CR43432 embryonic timecourse
CR43432_mRNA_rawreads.csv

value: WT


title: CRC00606

description: mCRC98_NR-gene row.txt

value: plasma small extracellular vesicles

value: miRNA


title: CRC00603

description: mCRC98_NR-gene row.txt


title: CR43432_mut_8_12_mRNA_line2_sequence


title: WM_1245_2


title: WM_766_3

value: sampling site Wma1, watzmann, Berchtesgarden, German Alps


title: CR43432_WT_16_20_mRNA_line2_sequence


title: WM_766_2


title: WM_766_5


title: CR43432_WT_8_12_mRNA_line2_sequence


title: WM_766_4


title: CR43432_WT_12_16_mRNA_line1_sequence


title: CRC00702

description: mCRC98_NR-gene row.txt


title: WM_1423_4


title: CRC00602

description: mCRC98_NR-gene row.txt


title: WM_1245_4


title: WM_766_1


title: CRC00511

description: mCRC98_NR-gene row.txt


title: CRC00509

description: mCRC98_NR-gene row.txt


title: WM_1930_1

value: sampling site Wma6, watzmann, Berchtesgarden, German Alps


title: WM_1930_4


title: CR43432_WT_2_4_mRNA_line1_sequence

source_name: 2-4 h embryos


title: WM_1245_5


title: CR43432_WT_8_12_mRNA_line1_sequence


title: WM_1930_3


title: CR43432_mut_8_12_mRNA_line1_sequence


title: CRC00601

description: mCRC98_NR-gene row.txt


title: WM_1930_5


title: T_746_1

value: sampling site T5, valley, Berchtesgarden, German Alps


title: CR43432_WT_2_4_mRNA_line2_sequence


title: CR43432_WT_0_2_mRNA_line1_sequence

source_name: 0-2 h embryos


title: CRC00605

description: mCRC98_NR-gene row.txt


title: CR43432_WT_0_2_mRNA_line2_sequence


title: WM_1930_2


title: T_746_4


title: T_641_4

value: sampling site T4, valley, Berchtesgarden, German Alps


title: T_641_5


title: CRC00506

description: mCRC98_NR-gene row.txt


title: CRC00508

description: mCRC98_NR-gene row.txt


title: WM_960_3


title: CRC00507

description: mCRC98_NR-gene row.txt


title: CR43432_WT_16_20_sRNA_line2_sequence

description:
Paired WT samples for CR43432 embryonic timecourse
CR43432_Line2_sRNA_rawreads.csv


title: T_641_1


title: CR43432_WT_12_16_sRNA_line2_sequence


title: T_641_3


title: CR43432_WT_12_16_sRNA_line1_sequence

description:
Paired WT samples for CR43432 embryonic timecourse
CR43432_Line1_sRNA_rawreads.csv


title: CRC00503

description: mCRC98_NR-gene row.txt


title: CRC00505

description: mCRC98_NR-gene row.txt


title: CR43432_WT_16_20_sRNA_line1_sequence


title: T_746_5


title: CRC00504

description: mCRC98_NR-gene row.txt


title: Brd7_AID_Ctrl_1_STARRseq

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

data_processing:
Library strategy: STARR-seq
paired end reads were trimmed with cutadapt v1.18 and mapped to dm3 genome using bowtie 1.2.2 allowing 1 mismatch and reporting best alignment and collapsed based on unique start and end positions.
Coverage was calculated using genomeCoverageBed from bedtools 2.27.1, and then converted to bigWig using KentUtils wigToBigWig
Genome_build: dm3
Supplementary_files_format_and_content: bigWig files containing STARRseq coverage
Supplementary_files_format_and_content: Tab delimited files include enhancer positions and annotation based of Zabidi et al 2015, and raw counts from sequencing experiments at enhancers.

growth_protocol: Per replicate, 1000*10^6 cells were grown at no more than 70% confluency.

extract_protocol:
After 24 hours, cells were harvested and total RNA isolated using the Qiagen Rneasy MaxiPrep.
A nested PCR strategy on the reporter cDNA was used used to prepare libraries as previously described (Neumayr et al 2019 Current Protocols).

treatment_protocol: Cells were harvested and transfected using a Maxcyte Electroporation with mixed genome-wide STARRseq library. After recovery, half the cells were treated with H20 (mock) and the other half with 500uM Auxin.

tag: cell line

tag: protocol

value: STARR-seq

value: STARR-seq Reporter


title: T_746_3

tag: tissue

value: Thorax and abdomen


title: T_746_2


title: T_656_5

value: sampling site T3, valley, Berchtesgarden, German Alps


title: Brd7_AID_Ctrl_2_STARRseq


title: Brd7_AID_Auxin_1_STARRseq


title: Brd7_AID_Auxin_2_STARRseq


title: CR43432_WT_8_12_sRNA_line1_sequence


title: Snr1_AID_Ctrl_1_STARRseq


title: CR43432_WT_4_8_sRNA_line2_sequence

source_name: 4-8 h embryos


title: CR43432_WT_8_12_sRNA_line2_sequence


title: S2_OsTir1_Ctrl_2_STARRseq


title: CRC00502

description: mCRC98_NR-gene row.txt

tag: disease state


title: Snr1_AID_Ctrl_2_STARRseq


title: Snr1_AID_Auxin_1_STARRseq


title: CRC00501

description: mCRC98_NR-gene row.txt

tag: Stage

value: 1 (treatment naive)


title: CRC00311

description: mCRC98_NR-gene row.txt

tag: sampling time points


title: CRC00312

description: mCRC98_NR-gene row.txt

tag: patient id


title: CR43432_WT_2_4_sRNA_line2_sequence


title: S2_OsTir1_Ctrl_1_STARRseq

tag: molecule subtype


title: S2_OsTir1_Auxin_2_STARRseq


title: Snr1_AID_Auxin_2_STARRseq


title: Iswi_AID_antiFLAG_2_CUT&RUN

data_processing:
Library strategy: CUT&RUN
paired end reads were trimmed with cutadapt v1.18 and mapped to dm3 genome using bowtie 1.2.2 allowing 1 mismatch and reporting best alignment and collapsed based on unique position.
Coverage was calculated using genomeCoverageBed from bedtools 2.27.1, and then converted to bigWig using KentUtils wigToBigWig
Genome_build: dm3
Supplementary_files_format_and_content: bigWig, STARRseq.enhancers.mixed.tsv (S2 Enhancer annotation)

growth_protocol: S2 cells were grown to 70% confluency in a 75mm2 dish

extract_protocol:
Cells were permeabilized and incubated with anti-FLAG M2 antibody, followed by pAG-Mnase. pAG-Mnase digestion was activated by addition of CaCl2 to 2mM for 2 hours at 4C.
Soluble DNA fragments were cloned using NEBNext  Ultra II DNA Library Prep Kit

tag: treatment

value: anti-FLAG CUT&RUN


title: Iswi_AID_antiFLAG_1_CUT&RUN


title: CR43432_WT_2_4_sRNA_line1_sequence

tag: ip target


title: CRC00309

description: mCRC98_NR-gene row.txt


title: Snr1_AID_antiFLAG_2_CUT&RUN


title: CRC00313

description: mCRC98_NR-gene row.txt


title: S2_OsTir1_Auxin_1_STARRseq


title: CRC00310

description: mCRC98_NR-gene row.txt


title: CR43432_WT_0_2_sRNA_line2_sequence


title: Snr1_AID_antiFLAG_1_CUT&RUN


title: S2T6_antiFLAG_2_CUT&RUN


title: CR43432_WT_0_2_sRNA_line1_sequence


title: S2T6_antiFLAG_1_CUT&RUN


title: Ino80_AID_Auxin_2_Mnaseseq

data_processing:
paired end reads were trimmed with cutadapt v1.18 and mapped to dm3 genome using bowtie 1.2.2 allowing 1 mismatch and reporting best alignment and collapsed based on unique position.
Coverage was calculated using genomeCoverageBed from bedtools 2.27.1, and then converted to bigWig using KentUtils wigToBigWig
Genome_build: dm3
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cells were washed and permeabilized with .75% NP-40 solution, and Mnase digest on nuclei was performed for 25 minutes at 37C. The DNA was size selected on a gel for mono-nucleosomal fragments.
Purified DNA fragments were cloned using NEBNext  Ultra II DNA Library Prep Kit

treatment_protocol: Cells were either treated with H20 (Ctrl) or 500uM auxin (IAA) for 12 hours.

value: Auxin


title: CR43432_WT_4_8_sRNA_line1_sequence


title: CRC00306

description: mCRC98_NR-gene row.txt


title: Ino80_AID_Auxin_1_Mnaseseq


title: Ino80_AID_Ctrl_2_Mnaseseq

value: Mock


title: CR43432_mut_16_20_sRNA_line2_sequence

description:
CR43432 embryonic timecourse samples
CR43432_Line2_sRNA_rawreads.csv


title: CRC00305

description: mCRC98_NR-gene row.txt


title: CRC00308

description: mCRC98_NR-gene row.txt


title: Ino80_AID_Ctrl_1_Mnaseseq


title: CR43432_mut_16_20_sRNA_line1_sequence

description:
CR43432 embryonic timecourse samples
CR43432_Line1_sRNA_rawreads.csv


title: Iswi_AID_Auxin_2_Mnaseseq


title: CRC00304

description: mCRC98_NR-gene row.txt


title: CR43432_mut_12_16_sRNA_line2_sequence


title: Iswi_AID_Ctrl_2_Mnaseseq


title: Iswi_AID_Auxin_1_Mnaseseq


title: CRC00302

description: mCRC98_NR-gene row.txt


title: CRC00303

description: mCRC98_NR-gene row.txt


title: CR43432_mut_8_12_sRNA_line2_sequence


title: CRC00301

description: mCRC98_NR-gene row.txt


title: Iswi_AID_Ctrl_1_Mnaseseq


title: Snr1_AID_Ctrl_2_Mnaseseq


title: Snr1_AID_Auxin_1_Mnaseseq


title: CR43432_mut_12_16_sRNA_line1_sequence


title: Chd1_AID_Auxin_2_PROseq

data_processing:
Library strategy: PRO-seq
UMI removal and adapter trimming: Sequenced reads consist of a 8nt long UMI (for counting unique RNA molecules), followed by PolII active site-associated RNA sequence and potentially a part of the Illumina sequencing adapter (in cases where RNA was shorter than 42nt). Prior to mapping, the UMI sequence (8nt at the 5' end of the read) was removed and noted for later counting. Illumina adapter was trimmed off with cutadapt v1.18.
Read alignment: All reads longer than 15nt after adapter trimming were mapped to dm3 genome using Bowtie version 0.12.9 allowing 1 mis-match. Reads mapping to multiple positions were randomly assigned to one mapping position.
Genomic coverage:  5' ends of mapped reads (the last nucleotide transcribed by PolII) were counted per genomic position taking into account only unique UMIs. Coverage was generated separately for positive and negative strands. Coverage was normalized to tags per million. Coverage was generated with GenomicRanges v1.34.0 package in R and exported into bigWig format with rtracklayer v1.42.2.
Quantification and differential analysis:  5' ends of mapped, UMI-collapsed reads overlapping promoter+pause region (from +1 to +150bp downstream of the TSS) were counted for each individual sample/replicate. Annotated TSSs were corrected to nearest CAGE-defined TSS from FANTOM5 collection. Provided raw counts were used for downstream differential analysis between different conditions with DEseq2 v1.22.2.
Genome_build: dm3
Supplementary_files_format_and_content: BigWig files contain normalized genome-wide coverage of 5' ends of PRO-seq reads, separately for positive and negative strands (the values for negative strand are shown as negative). Tab delimited files include genomic coordinates of a reference set of Transcription Start Sites (TSSs) with gene/transcript IDS, TSS positions corrected by CAGE, motif scoring, and cluster assignment. Raw read counts from each sequencing experiment at the TSS +150bp are included in PROseq.tss.counts.tsv.

extract_protocol:
After treatment cells were harvested and nuclei were isolated; Spike in cels (5% total human HCT116 cells) were added at the level of nuclei permeabilization.
3’ RNA adapters were ligated to isolated RNA and second biotin RNA enrichment followed by RNA 5’ cap modification via TAP (Biozym #187005) treatment was performed. Furthermore, 5’ hydroxyl repair via PNK (NEB #M0201S) treatment and subsequent 5’ adapter ligation was carried out. Afterwards, cDNA was generated from enriched RNA via reverse transcription (Super Script III Reverse Transcriptase, Invitrogen #18080-044). 10µl of the cDNA library was amplified via KAPA Amplification reaction (Roche #7959028001) on a qPCR machine (Biorad CFX Connect RealTime System). KAPA reaction: 10µl cDNA, 1µl forward primer 35µM (RP1-RP20), 1µl of reverse primer 35µM (RP1: 5’-AATGATACGGCGACCACCGAGATCTACAGTTCAGAGTTCTACAGTCCGA-3’), 25µl 2x KAPA SYBER master mix, 13µl water. PCR program: 98°C - 45 sec, 98°C - 15 sec, 60°C - 30 sec, 72°C - 30 sec, 72°C - 10 sec. Samples were removed from the qPCR machine after 12-15 cycles and cleaned with Ampure beads (Beckman #A63881) in a 1:1.4 (DNA:beads) ratio. DNA bound to the beads was eluted in 11µl of water and subjected to single-end deep sequencing.

treatment_protocol: S2 cells were grown to 70% confluency in a 75mm2 dish, and eather treated with H20 (Ctrl) or 500uM auxin (IAA) for 6 hours.

value: Nascent RNA


title: Snr1_AID_Ctrl_1_Mnaseseq


title: CR43432_mut_8_12_sRNA_line1_sequence


title: Snr1_AID_Auxin_2_Mnaseseq


title: CR43432_mut_4_8_sRNA_line2_sequence


title: CR43432_mut_4_8_sRNA_line1_sequence


title: CRC00202

description: mCRC98_NR-gene row.txt

value: CRC


title: Chd1_AID_Ctrl_1_PROseq


title: Chd1_AID_Auxin_1_PROseq


title: Chd1_AID_Ctrl_2_PROseq


title: Ino80_AID_Auxin_3_PROseq


title: CR43432_mut_2_4_sRNA_line2_sequence


title: CRC00201

description: mCRC98_NR-gene row.txt


title: Ino80_AID_Ctrl_3_PROseq


title: Ino80_AID_Auxin_2_PROseq


title: CRC00108

description: mCRC98_NR-gene row.txt


title: CRC00107

description: mCRC98_NR-gene row.txt


title: T_641_2

tag: altidue of sampling

tag: ave. temperature of sampling site


title: CR43432_mut_2_4_sRNA_line1_sequence


title: CRC00106

description: mCRC98_NR-gene row.txt


title: WT mESCs, MNase, replicate 2

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

country: Spain

institute: CBMSO(CSIC/UAM)

data_processing:
Alignment against mm10 genome using Bowtie2 (Langmead and Salzberg, 2012) and standard parameters.
BigWig files were generated with bamCoverage function from depTools.
Assembly: mm10
Supplementary files format and content: bigwig for browser compatible tracks.
Supplementary files format and content: fastq for raw reads

source_name: mESCs

growth_protocol: Mouse embryonic stem cells were grown in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Biosera), 1x non-essential aminoacids (Gibco), 1mM sodium piruvate (Gibco), 2mM L-glutamine (Gibco), 50 uM B-mercaptoethanol (Gibco), 103 U/mL LIF (ESGRO), 100 U/mL penicillin (Invitrogen) and 100 ug/mL streptomycin (Invitrogen), at 37ºC and 5% CO2

extract_protocol: 0, 5, 15 or 45 min after DRB removal, cells were lysed with 5 ml of TRIzol (Invitrogen), and total RNA was isolated and sonicated. 100 μg of RNA per cell line and condition were biotinylated using EZ-Link HPDP-Biotin dissolved in dimethylformamide (DMF) and labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) for 2h with rotation at RT. Unbound Biotin-HPDP was removed by chloroform/isoamylalcohol (24:1) extraction in MaXtract tubes (Qiagen) and RNA was precipitated with 5M NaCl/isopropanol (10:1). RNA pellets were washed in 80% ethanol, dried and resuspended in 100 μL RNase-free water. Biotinylated RNA was purified using Macs Streptavidin kit, eluted twice using 100 mM DTT and recovered using Rneasy MinElute Cleanup column (Qiagen). cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) following manufacturer’s instructions. Libraries were pooled and sequenced by 2x75 paired-end reads at Fundación Parque Científico de Madrid.

treatment_protocol: Cells growing at 80% confluency were treated with 100 μM 5,6-dichlorobenzimidazole 1-b-d-ribofuranoside (DRB) (Sigma) for 3h. 1 mM of 4-thiouridine (4sU) was added to the medium 10 min before harvest.

tag: cell type

value: mESCs

value: WT


title: Brd7_AID_Auxin_2_PROseq


title: H1-TKO mESCs, MNase, replicate 2


title: H1-TKO mESCs, MNase, replicate 1


title: CRC00105

description: mCRC98_NR-gene row.txt

value: plasma small extracellular vesicles

value: miRNA


title: Ino80_AID_Auxin_1_PROseq


title: Ino80_AID_Ctrl_1_PROseq


title: Ino80_AID_Ctrl_2_PROseq


title: CRC00203

description: mCRC98_NR-gene row.txt


title: WT mESCs, MNase, replicate 1


title: CRC00104

description: mCRC98_NR-gene row.txt


title: TKO mESCs, 4sU-DRB 5 min, replicate 2, high throughput

data_processing:
Alignment against mm10 genome using Bowtie2 (Langmead and Salzberg, 2012) and standard parameters.
BigWig files were generated with bamCoverage function from depTools.
Assembly: mm10
Supplementary files format and content: bigwig for browser compatible tracks.
Supplementary files format and content: fastq for raw reads
Library strategy: 4sU-DRB-seq

value: TKO

tag: time point

value: 5 min


title: Brd7_AID_Ctrl_1_PROseq


title: CRC00103

description: mCRC98_NR-gene row.txt


title: S2_OsTir1_Auxin_2_PROseq


title: S2_OsTir1_Ctrl_2_PROseq


title: TKO mESCs, 4sU-DRB 5 min, replicate 1, high throughput


title: Iswi_AID_Auxin_2_PROseq


title: TKO mESCs, 4sU-DRB 0 min, replicate 2, high throughput

value: 0 min


title: CRC00102

description: mCRC98_NR-gene row.txt


title: S2_OsTir1_Auxin_1_PROseq


title: Iswi_AID_Ctrl_2_PROseq


title: CRC00101

description: mCRC98_NR-gene row.txt


title: S2_OsTir1_Ctrl_1_PROseq


title: Iswi_AID_Auxin_1_PROseq


title: Brd7_AID_Ctrl_2_PROseq


title: Brd7_AID_Auxin_1_PROseq


title: NGSC059

description: CRC192-exomiR NR-gene row.txt

source_name: healthy


title: Iswi_AID_Ctrl_1_PROseq


title: NGSC049

description: CRC192-exomiR NR-gene row.txt

value: healthy


title: WT mESCs, 4sU-DRB 5 min, replicate 1, high throughput


title: Snr1_AID_Auxin_1_PROseq


title: WT mESCs, 4sU-DRB 0 min, replicate 2, high throughput


title: WT mESCs, 4sU-DRB 0 min, replicate 1, high throughput


title: Snr1_AID_Auxin_2_PROseq


title: WT mESCs, 4sU-DRB 5 min, replicate 2, high throughput


title: NGSC043

description: CRC192-exomiR NR-gene row.txt


title: Snr1_AID_Ctrl_2_PROseq


title: NGSB102

description: CRC192-exomiR NR-gene row.txt


title: NGSB100

description: CRC192-exomiR NR-gene row.txt


title: MM233

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

data_processing:
The sequenced data were processed into expression matrices with the Cell Ranger Single Cell software suite v3.0.1 by 10x Genomics.
Raw base-call files from HiSeq2500 sequencer were demultiplexed into library-specific FASTQ files using Cell Ranger mkfastq option.
Sequencing reads were mapped to the GRCh38 (version 3.0.0) reference
Cell barcodes and unique molecular identifiers underwent filtering and correction. Reads associated with the retained barcodes were quantified using Cell Ranger count option and used to build a transcript count table.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 format: Contains the per molecule read information from Cell Ranger. The instructions to read the matrix in hdf5 format can be found here: https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices

source_name: bone marrow mononuclear cells

extract_protocol:
Bone marrow aspirate samples were collected at baseline prior to the induction treatment of VMP or VTD. BM aspirates were subjected to a Ficolle-Paque PLUS gradient, and isolated mononuclear cells were cryopreserved in freezing medium before the experiments.
The single-cell library preparation relied on a commercially available droplet method, the 10x Genomic Chromium System (10x Genomic Inc., San Francisco, CA), with 10x Genomics Single Cell 3’ v3 Reagent kit according to the manufacturer’s protocol. In brief, dissociated cells were counted by hemocytometer (ThermoFisher) and 16,000 cells per sample were added to each channel. The cells were then partitioned into gel beads in emulsion (GEMs) in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred. cDNA was synthesized and amplified for 14 cycles. cDNA clean-up was performed using a SPRIselect Reagent Kit (Beckman Coulter, Brea, CA). 50 ng of the amplified cDNA were used for each sample to construct indexed sequencing libraries.

value: bortezomib-melphalan-prednisolone

value: Bone marrow

value: Multiple myeloma


title: TKO mESCs, 4sU-DRB 15 min, replicate 2, mid throughput

value: 15 min


title: Snr1_AID_Ctrl_1_PROseq


title: TKO mESCs, 4sU-DRB 45 min, replicate 1, mid throughput

value: 45 min


title: TKO mESCs, 4sU-DRB 0 min, replicate 1, high throughput


title: H295R_DMSO_24_Rep2

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
Salmon (Patro et al. 2017) was used for quantifying transcript levels from all libraries using Gencode v26 (parameters -l A --allowDovetail --validateMappings).
Assembly: Gencode GRCh38 v26
Supplementary files format and content: Comma separated text files with raw transcript counts quantified using salmon

molecule: polyA RNA

growth_protocol: H295R cells were cultured in complete media (DMEM/F12 media, 10% Cosmic Calf Serum, 1% Insulin-Transferrin-Selenium) at 37°C, 5% CO2. For all ELISA assays, cells were cultured in low sera media (DMEM/F12 media, 0.1% Cosmic Calf Serum, 1% Insulin-Transferrin-Selenium).

extract_protocol:
Cells were collected in TRIzol and RNA was isolated using DirectZol Miniprep Plus kit (ZYMO) with on-column DNase I digestion. Isolated total RNA was quantified using the Qubit RNA Broad Range assay kit (Invitrogen) with the Qubit 3.0 fluorometer.
Poly(A) RNA was enriched from 1ug of total RNA using the NEBNext poly(A) mRNA magnetic isolation module (New England Biolab). At the final elution step of polyA selection, the RNA-bound beads were resuspended into 1X Fragment, Primer, Elute (FPE) buffer from the KAPA RNA Hyper Prep kit (Roche), heated at 85°C for 6 minutes for fragmentation. The resulting RNA was used as input into library preparation at the first strand synthesis step using the KAPA RNA Hyper Prep Kit (Roche). Libraries were sequenced to a depth of 20 million paired-end 2x150bp reads each on the NovaSeq 6000 (Illumina) at University of Colorado Genomics and Microarray Core.

treatment_protocol: H295R cells (500,000 cells per well) were plated in complete media. After 24 hours, complete media was removed and replaced with low sera media for an additional 24 hours. Cells were then stimulated with 10nM AngII and treated with DMSO control or 5 uM Ro. Cells were harvested at 0, 4, 8, 12, 16, 24 hours post-stimulation.

value: DMSO

tag: time (hours)


title: MM226


title: NGSB098

description: CRC192-exomiR NR-gene row.txt

value: 1 (treatment naive)


title: TKO mESCs, 4sU-DRB 15 min, replicate 1, mid throughput


title: H295R_DMSO_24_Rep1


title: MM220


title: NGSC044

description: CRC192-exomiR NR-gene row.txt


title: NGSB097

description: CRC192-exomiR NR-gene row.txt


title: TKO mESCs, 4sU-DRB 5 min, replicate 2, mid throughput


title: H295R_Ro_24_Rep2

value: Ro


title: H295R_Ro_24_Rep1


title: NGSB095

description: CRC192-exomiR NR-gene row.txt


title: TKO mESCs, 4sU-DRB 0 min, replicate 2, mid throughput


title: MM209


title: TKO mESCs, 4sU-DRB 5 min, replicate 1, mid throughput


title: TKO mESCs, 4sU-DRB 45 min, replicate 2, mid throughput


title: MM203


title: NGSB099

description: CRC192-exomiR NR-gene row.txt


title: NGSB096

description: CRC192-exomiR NR-gene row.txt


title: MM174


title: MM188


title: NGSB094

description: CRC192-exomiR NR-gene row.txt


title: H295R_DMSO_16_Rep2


title: TKO mESCs, 4sU-DRB 0 min, replicate 1, mid throughput


title: H295R_DMSO_16_Rep1


title: H295R_Ro_16_Rep2


title: WT mESCs, 4sU-DRB 45 min, replicate 1, mid throughput


title: WT mESCs, 4sU-DRB 45 min, replicate 2, mid throughput


title: H295R_Ro_16_Rep1


title: NGSB087

description: CRC192-exomiR NR-gene row.txt


title: WT mESCs, 4sU-DRB 15 min, replicate 2, mid throughput


title: NGSB084

description: CRC192-exomiR NR-gene row.txt


title: H295R_DMSO_12_Rep2


title: MM158


title: WT mESCs, 4sU-DRB 15 min, replicate 1, mid throughput


title: NGSB083

description: CRC192-exomiR NR-gene row.txt


title: MM098


title: NGSB079

description: CRC192-exomiR NR-gene row.txt


title: MM089


title: NGSB090

description: CRC192-exomiR NR-gene row.txt


title: WT mESCs, 4sU-DRB 5 min, replicate 1, mid throughput


title: MM173


title: H295R_Ro_12_Rep1


title: H295R_DMSO_12_Rep1


title: WT mESCs, 4sU-DRB 5 min, replicate 2, mid throughput


title: NGSB073

description: CRC192-exomiR NR-gene row.txt


title: WT mESCs, 4sU-DRB 0 min, replicate 1, mid throughput


title: NGSB075

description: CRC192-exomiR NR-gene row.txt


title: MM068


title: MM088


title: NGSB074

description: CRC192-exomiR NR-gene row.txt


title: H295R_DMSO_08_Rep2


title: WT mESCs, 4sU-DRB 0 min, replicate 2, mid throughput


title: MM043


title: MM163


title: H295R_Ro_08_Rep2


title: NGSB072

description: CRC192-exomiR NR-gene row.txt


title: MM042


title: MB_lac_2

city: Schwerzenbach

first: Ferdinand

last: von Meyenn

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

data_processing:
FastQC v0.11.0 used for quality control
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
HISAT2 v2.2.1 used for read mapping
subread v2.0.1 used for gene expression quantification
Assembly: mm10
Supplementary files format and content: tab delimited raw counts

source_name: Mouse primary myoblasts treated with 10 mM lactate

growth_protocol: MBs were cultured in growth medium (1:1 ratio of DMEM (ThermoFisher Scientific, 12320032) and Ham’s F-10 (1×) nutrient mix (ThermoFisher Scientific, 22390058) supplemented with 10% horse serum (ThermoFisher Scientific, 16050-122), 20% FBS and 10 ng/ml basic-FGF (ThermoFisher Scientific, PHG0266) on dishes coated with Matrigel Basement Membrane Matrix (Corning, #356237, 1/25 dilution). When cells reached 80% confluency, growth medium was switched to differentiation medium containing DMEM, 2% HS and 1% P/S. MBs were fully differentiated into MTs after 3 days of differentiation. Cells were cultured in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA from myoblasts and myotubes incubated with various overnight conditions was isolated using TRIzol extraction. Purification of extracted RNA was performed using Zymo RNA Clean and Concentrator Kit with DNase (Zymo Research, Irvine, CA, cat. #R1018) according to the manufacturers’ instructions.
Quantification of total RNA was performed using a nanodrop system. 5 ng of RNA was used as an input for the Smart-seq2 protocol as described in Picelli et al. (61,62) including cDNA synthesis, pre-amplification, tagmentation, and enrichment steps.
Smart-seq2

treatment_protocol: For lactate treatment, the cell medium was supplemented with 10 mM sodium-L-lactate dissolved in PBS before read-out of the experiment. Control cells were treated with the same amount of PBS.

tag: biological replicate

tag: strain


title: MB_lac_1


title: NGSB071

description: CRC192-exomiR NR-gene row.txt


title: H295R_Ro_08_Rep1

tag: cell line


title: MM023


title: H295R_Ro_12_Rep2


title: MB_ctrl_2

source_name: Mouse primary myoblasts


title: NGSB069

description: CRC192-exomiR NR-gene row.txt


title: H295R_DMSO_04_Rep2


title: H295R_DMSO_08_Rep1


title: NGSB068

description: CRC192-exomiR NR-gene row.txt


title: MM012


title: NGSB066

description: CRC192-exomiR NR-gene row.txt


title: H295R_DMSO_04_Rep1


title: NGSB067

description: CRC192-exomiR NR-gene row.txt


title: MT_ctrl_2

source_name: Mouse primary myotubes


title: MB_ctrl_1


title: H295R_Untreated_00_Rep3

value: untreated


title: H295R_Untreated_00_Rep4


title: ADIPO_H3K27ac_1

description:
DNA marked by H3K27ac and cut by Tn5
ADIPO_H3K27ac_peaks.bed

data_processing:
Library strategy: Cut&Tag
FastQC v0.11.0 used for quality control
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
bedtools v2.30 used for merging replicate specific bedgraph files for each sample
SEACR v1.3 used for calling peaks
Assembly: mm10
Supplementary files format and content: tab delimited called peak regions

source_name: Mouse white adipocytes

extract_protocol:
ESC were processed exactly as per the original CUT&Tag protocol for whole cells. All other samples were processed as per the CUT&Tag protocol for nuclei. Muscle samples were thawed and sliced in small pieces on ice. Subsequently, the pieces were transferred to an ice-cold dounce homogenizer (7 mL) and 3 mL of nucleus extraction buffer (1× prelysis buffer from the EpiQuick Total Histone Extraction Kit (EpiGentek)) was added before douncing, on ice, 10× with pestle A and 10× with pestle B. Nuclei from PIM was obtained through resuspension of centrifuged and washed cell pellets in the same nucleus extraction buffer. Nuclei from adipocytes were isolated using a Kimble 7 ml glass douncer using ice-cold nuclei isolation buffer (10 mM Tris-HCl pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1 % Igepal-CA630, 1x protease inhibitor). To all samples: to stop the lysis reaction, of PBS+1%BSA was added in a 1:1 volume. After 5’ centrifugation at 4˚C, 500 rpm, the supernatant was removed, the nuclei were resuspended in PBS+1%BSA and a sample was visually inspected for viability, purity and abundance of nuclei under the microscope. CUT&Tag was performed according to the published CUT&Tag sequencing protocol for nuclei.All buffers were supplemented with 5 mM sodium-butyrate and 1X complete protease inhibitor (Merck, 1187358000). Protein lo-bind tubes (Eppendorf, EP0030108116) were used to reduce sample loss.  Antibodies against H3K18la (PTM-Bio, PTM-1406), H3K4me3 (Abcam, ab8580), H3K27me3 (Cell Signaling Technology, C36B11), H3K27ac (Abcam, ab4729) and H3K9me3 (Abcam, ab8898) were used in this study.
PCR was performed with 21 μL DNA + 2 μL Universal i5 primer (10 μM) + 2 μL uniquely barcoded i7 primers (10 μM) in a thin-wall 0.5 ml PCR tube, using a different barcode for each sample. *Nextera primers or indexed primers described by Buenrostro, J.D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523:486 (2015).To this mixture,  25 μL NEBNext HiFi 2x PCR Master mix was added. The samples were mixed, quick spinned and placed in  a thermocycler with heated lid. The following program was used: Cycle 1: 72 °C for 5 min (gap filling) Cycle 2: 98 °C for 30 sec.Cycle 3: 98 °C for 10 sec.Cycle 4: 63 °C for 10 sec.Repeat Cycles 3-4 13 times 72°C for 1 min and hold at 8 °C.

treatment_protocol: control

tag: histone


title: H295R_Ro_04_Rep2


title: H295R_Ro_04_Rep1


title: NGSB062

description: CRC192-exomiR NR-gene row.txt

tag: tissue


title: MT_ctrl_1


title: ADIPO_H3K27ac_2


title: NGSB064

description: CRC192-exomiR NR-gene row.txt

tag: disease state


title: NGSB055

description: CRC192-exomiR NR-gene row.txt

tag: Stage


title: H295R_Untreated_00_Rep2


title: ADIPO_H3K18la_1

description:
DNA marked by H3K18la and cut by Tn5
ADIPO_H3K18la_peaks.bed


title: H295R_Untreated_00_Rep1


title: ADIPO_H3K18la_2


title: NGSB048

description: CRC192-exomiR NR-gene row.txt

tag: sampling time points


title: PIM_H3K27ac_1

description:
DNA marked by H3K27ac and cut by Tn5
PIM_H3K27ac_peaks.bed

source_name: Mouse post-ischemia macrophages


title: NGSB047

description: CRC192-exomiR NR-gene row.txt

tag: patient id


title: GAS_H3K27ac_2

description:
DNA marked by H3K27ac and cut by Tn5
GAS_H3K27ac_peaks.bed

source_name: Mouse gastrocnemius muscle


title: NGSB042

description: CRC192-exomiR NR-gene row.txt

tag: molecule subtype


title: H1975_PDL1s

city: Milano

first: Matteo

last: Cereda

address: Via Celoria, 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
Basecalling performed by Illumina NovaSeq6000.
RNA sequencing reads were aligned to the human genome reference GENCODE GRCh37 version 28 using STAR (v. 2.7.3a) in two-pass mode with parameters: --alignInsertionFlush Right  --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --peOverlapNbasesMin 20 --peOverlapMMp 0.25 --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --outFilterIntronStrands RemoveInconsistentStrands --outFilterMultimapNmax 1 --bamRemoveDuplicatesType UniqueIdentical.
Gene level read counts were estimated using featureCounts (Subread v. 2.0.0) with parameters: -O --primary -Q 1 -J -s 2 -p -B.
Assembly: hg19
Supplementary files format and content: One tab-delimeted text file for each sample obtained with featureCounts including gene raw counts.

source_name: lung

extract_protocol:
RNA was extracted from NSCLC pneumospheres by Maxwell® RSC Instrument, according to Maxwell® RSC RNA tissue Kit manufacturer instructions.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus following manufacturer's protocols.

value: lung

value: adenocarcinoma

tag: treatment


title: H1975_untreated


title: GAS_H3K27ac_1


title: H820_PDL1s


title: NGSB030

description: CRC192-exomiR NR-gene row.txt

value: plasma small extracellular vesicles


title: ESC-ser_H3K27ac_1

description:
DNA marked by H3K27ac and cut by Tn5
ESC-ser_H3K27ac_peaks.bed

source_name: Mouse serum-lif embyonic stem cells

tag: growth medium

value: serum-lif


title: ESC-2i_H3K4me3_2

description:
DNA marked by H3K4me3 and cut by Tn5
ESC-2i_H3K4me3_peaks.bed

source_name: Mouse 2i-lif embryonic stem cells


title: H820_untreated


title: NGSB026

description: CRC192-exomiR NR-gene row.txt

value: miRNA


title: EBC1_untreated

value: squamous cell carcinoma


title: ESC-2i_H3K4me3_1


title: ESC-2i_H3K27me3_2

description:
DNA marked by H3K27me3 and cut by Tn5
ESC-2i_H3K27me3_peaks.bed


title: H23_untreated


title: ESC-2i_H3K27me3_1


title: NGSB017

description: CRC192-exomiR NR-gene row.txt


title: H23_PDL1s


title: NGSB041

description: CRC192-exomiR NR-gene row.txt


title: ESC-2i_H3K18la_1

description:
DNA marked by H3K18la and cut by Tn5
ESC-2i_H3K18la_peaks.bed


title: NGSB014

description: CRC192-exomiR NR-gene row.txt


title: NGSB013

description: CRC192-exomiR NR-gene row.txt


title: EBC1_PDL1s


title: MT_NHEK2

city: Hangzhou

first: Yebei

last: Hu

address: West Lake Road 38

institute: Hangzhou Third People's Hospital

data_processing:
cutadapt-1.9
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
Assembly: GRCh38
Supplementary files format and content: perform expression level for mRNAs by calculating FPKM

source_name: skin

growth_protocol: NHEK cells were grown in Keratinocyte Growth Medium with SupplementMix in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's procedure.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

treatment_protocol: Co-incubating with melanocores for 24h, then treated by Tranexamic acid (Abcam, Cambridge, UK) for 24h

value: skin

value: NHEK

value: normal human epidermal keratinocytes (NHEK)

value: co-incubating with melanocores for 24h, then treated by Tranexamic acid for 24h


title: MT_NHEK3


title: NGSB015

description: CRC192-exomiR NR-gene row.txt

data_processing:
sequencing data were assessed for quality and trimmed of the primer-adaptor sequences by the Partek® Flow® Genomic Analysis Software (Partek)
Reads were alignment to the human reference genome (hg38) (by bowtie 2)
annotation of known miRNA based on miRBase
The number of reads for each miRNA was normalized to reads per million (RPM+0.0001) and quantified across all samples
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized miRNA counts(RPM+0.0001) for every miRNA and every sample

extract_protocol:
Circulating small EVs were isolated from 1 mL of pre-filtered plasma using a procedure described in the exoEasy Plasma Handbook (QIAGENE). Briefly, plasma was mixed with binding buffer (XBP) and added to the exoEasy membrane affinity column for binding. After centrifugation, the flow-through was discarded and wash buffer (XWP) was added to the column to wash off nonspecifically retained materials. After EVs were bound on the exoEasy membrane affinity column as described in the isolation procedure above, the vesicles were lysed by adding QIAzol to the spin column and further collected by centrifugation (exoRNeasy, QIAGEN). Following chloroform extraction, samples were thoroughly mixed and centrifuged to separate organic and aqueous phases. The aqueous phase was recovered and mixed with ethanol. The sample-ethanol mixture was added to a RNeasy MinElute spin column and centrifuged. The column was washed once with buffer RWT and then twice with buffer RPE followed by elution of RNA in water. The RNA concentration, purity, and integrity were assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
Prior to sequencing experiments, RNA concentration, purity, and integrity were assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA). Illumina sequencing libraries were prepared using the NEXTflexTM small RNA-seq kit v3 Guide (Bioo Scientific, 5132-05), according to the manufacturer’s instructions. For each library, 60 ng of purified small EV RNA were ligated to 3’ and 5’ adaptors and then reverse transcribed to cDNA using adaptor-specific primers. After purification and PCR amplification using universal and specific barcode primers, the miRNA library was resolved and recovered from the 6% TBE-PAGE gel based on the corresponding size for miRNA distribution. The yield and size distribution of the small RNA libraries were assessed using the Agilent 2100 Bioanalyzer instrument with the High-Sensitivity DNA Assay (Agilent Technologies). Equal concentration of each library was sequenced on a NextSeq 500 (Illumina) platform.

value: healthy


title: NGSB023

description: CRC192-exomiR NR-gene row.txt


title: AJ5_16

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Bioinformatic analysis of the resulting reads contained two parts: removing duplicates using  UMIs and implementing the CCseqBasicS pipeline. First, the beginning eight base pairs on the  forward and reverse reads respectively were extracted using fgbio toolkit as UMIs (v0.5.0a,  https://github.com/fulcrumgenomics/fgbio), which we later used for PCR duplication removal.  Reads were then aligned to reference genome (mm10) using BWA MEM (v0.7.17) and default  parameters. Only properly paired, primary alignments were kept for downstream analysis. Read  pairs aligned to the same location and have the same UMI were removed as PCR duplicates  using Picard (v2.18.15).
The successfully aligned, non-duplicated read pairs were reverted to  FASTQ format for Capture-C analysis using the CCseqBasicS (VS1.0.8) pipeline. FLASH  (v1.2.11) was first used to merge paired-end reads from the same fragment, allowing the reads  to overlap to a maximum of 250 bp (‘-M 150’). Fragments were digested with DpnII using the  Python script implemented by the CCseqBasicS pipeline and mapped to mm10 reference  genome using Bowtie(Langmead, 2010) (version 2.3.4.3) using default parameters and the  maximum allowed insert size of 2000bp. Blacklist regions provided by the CCseqBasicS  pipeline were excluded from the alignment file using bedtools toolkit (v.2.17.0).
CCseqBasic tool  (vCC5) was implemented with default settings (“--ampliconSize 2000 --noTrim -w 200 -i 20”) to  acquire reporter reads of each designed captured probe in each sample. The tool was run in  both non-SNP-specific as well as SNP-specific configurations (we designed probes so that they  have B6/JF1 SNPs nearby to be sequenced; the list of used SNPs is available in Supp. Table  3). The final read counts for each probe region for each SNP are provided in Supp. Table 3.
Bigwig files were generated for each sample and each probe by piling up all reads, B6 reads and JF1 reads separately, and then normalized to 10K  reporter reads per designed probe for track visualization. We pooled reads from alleles in the same experimental group (WT-maternal, WT-paternal, mKO-maternal and pKO-paternal) together for contact site calling and visualization.
For each of them and for each probe, contact sites were defined as peaks called using MACS2 (v2.1.1) with parameters “--nomodel --extsize 700 --qvalue 1e-100 --broad --nolambda --broad-cutoff 1e-100 --minsize 5000”. The corresponding contact site visualization, for each group and each probe, was defined by fourSig(Williams et al., 2014) with parameters “window.size=1, iterations=100, fdr=0.001, fdr.prob=0.05” and normalized to 100K  reporter reads per designed probe for track visualization. Signal for each  contact site was quantified on each bigwig file generated from the pipeline using bwtool  (v1.0)(Pohl and Beato, 2014). Differential analysis between experiment groups was then  performed using DESeq2 R package (FDR 0.05). Figures were generated using .bw and  .longinteraction files and visualized on WashU Epigenome Browser.
Assembly: mm10
Supplementary files format and content: normalized bigwig files for each probe in on maternal, paternal and both (non-SNP-specific) strands
Library strategy: Capture-C

source_name: heart

extract_protocol:
Briefly, heart and muscle tissues were obtained from wildtype neonate hearts of reciprocal F1 C57BL/6 (B6) and Japanese Fancy [J11] F1 hybrid mice, and J[11] JF1 mice bred to male or female CBR2.3/ mice to generate maternal- and paternal-specific CBR2.3 KO F1 hybrids (CBR2.3/+ mKO and CBR2.3+/ pKO).
3C libraries were generated from nuclei using standard methods and DnpII as the primary restriction enzyme. Before oligonucleotide capture, 3C libraries were fragmented to 200-1000 bp sizes using a second digestion with two spike-ins of NlaIII overnight and in the morning for library prep and sequencing. The xGen Prism DNA library kit with primers (IDT 10006202 & 10005975) and adapters with unique molecular identifier (UMI) sequences were incorporated during adapter ligation to minimize sequence errors and reduce PCR duplication rates (IDT, 10006914). 1 ug of indexed samples were pooled before oligonucleotide capture using biotinylated oligonucleotides designed for the Grb10 and Ddc promoters, CTCF binding sites and putative enhancer sequences using IDT Discovery Pool technology. Probe sequences are provided in Supplementary Table 2. The first hybridization reaction included 5 pools of 4 samples (one of each genotype was included in each pool), with each hybridization pool set up using Mouse-COT DNA and 1.5 pM of Discovery Probes using reagents provided by the xGen Hybridization and Wash Kit according to the manufacturer’s instructions (IDT, 1080577). After a 16-hour hybridization step, streptavidin bead pulldown (IDT, 1080577) and multiple bead washes using IDT xGen Hybridization and Wash Kit, PCR amplification of the captured material was performed using KAPA HiFi HotStart Readymix Kit (KAPA Biosystems, KR0370) and library amplification primer (IDT, 1077676) for 14 cycles. A second capture was performed as above, with the exception that it was carried out with one-half of the Mouse-COT DNA and probe concentration used in the first capture. The material was sequenced using the Illumina NOVA-Seq platform with 250-bp paired end reads.

value: heart

tag: genotype

value: mKO


title: M_NHEK3

value: co-incubating with melanocores for 24h


title: MT_NHEK1


title: NGSB012

description: CRC192-exomiR NR-gene row.txt

value: 1 (treatment naive)


title: AJ5_15

value: WT


title: AJ5_14

source_name: muscle

value: muscle

value: pKO


title: NGSB011

description: CRC192-exomiR NR-gene row.txt


title: NGSB016

description: CRC192-exomiR NR-gene row.txt


title: M_NHEK2


title: NGSB008

description: CRC192-exomiR NR-gene row.txt


title: AJ4_13


title: M_NHEK1


title: IPSC – Replicate 5 – IFNa – 24h

city: Anderlecht

first: Florian

last: Szymczak

state: Brussels

address: Route de Lennik 808 - CP618

department: Faculty of Medicine

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Raw RNA-seq data was quality checked with fastp to remove reads with poor quality and trim remaining adapters.
The quality control (QC) of the passing reads was assessed with FastQC (Babraham Bioinformatics).
Gene expression was quantified in TPM (Transcripts per Millions) using Salmon v1.4  with additional parameters “--seqBias --gcBias --validateMappings”.
We used GENCODE v35  as the reference genome and indexed it with default k-mer values. Differential Gene Expression (DGE) analysis was performed with DESeq2 v1.30.1
Assembly: GENCODE v35 (GRCh38.p13)
Supplementary files format and content: Tab Separated Values (TSV) file containing TPM values at the gene level

extract_protocol:
Total RNA was extracted from at least 200.000 cells collected at the end of dead cell removal step, using a RNeasy Plus mini kit according to the manufacturer’s instructions (Germantown). Total RNA was eluted in 30 µL RNA-free water. Genomic DNA was removed by using DNAse I (Thermo Fisher Scientific) and the purified RNA was recovered using SurePrep RNA Cleanup and Concentration Kit, according to the manufacturer’s instructions (Fisher Scientific). The genomic DNA removal and clean-up step was repeated a second time.
The purity of the finally obtained total RNA was evaluated using a Bioanalyzer. RNA-seq was performed on a NovaSeq 6000  (Genomics Core, Indiana University School of Medicine).

value: induced pluripotent stem cell

tag: karyotype

value: XY

value: IFNa (Interferon Alpha)


title: AJ4_12


title: NGSB007

description: CRC192-exomiR NR-gene row.txt

value: plasma small extracellular vesicles

value: miRNA


title: ESC-2i_H3K18la_2


title: IPSC – Replicate 4 – IFNa – 24h

tag: cell type


title: AJ3_8


title: AJ3_9


title: IPSC – Replicate 3 – IFNa – 24h


title: IPSC – Replicate 2 – IFNa – 24h


title: NGSA103

description: CRC192-exomiR NR-gene row.txt


title: NGSB004

description: CRC192-exomiR NR-gene row.txt


title: AJ3_10


title: IPSC – Replicate 1 – IFNa – 24h


title: NGSA102

description: CRC192-exomiR NR-gene row.txt


title: IPSC – Replicate 5 – Untreated – 24h

value: Untreated


title: NGSA100

description: CRC192-exomiR NR-gene row.txt


title: IPSC – Replicate 4 – Untreated – 24h


title: AJ2_6


title: NGSA098

description: CRC192-exomiR NR-gene row.txt


title: IPSC – Replicate 3 – Untreated – 24h


title: AJ2_5


title: AJ1_4


title: IPSC – Replicate 2 – Untreated – 24h


title: NGSB006

description: CRC192-exomiR NR-gene row.txt


title: NGSA096

description: CRC192-exomiR NR-gene row.txt


title: NGSA091

description: CRC192-exomiR NR-gene row.txt


title: AJ1_3


title: NGSB005

description: CRC192-exomiR NR-gene row.txt


title: AJ3_11


title: IPSC – Replicate 1 – Untreated – 24h


title: AJ2_7


title: AJ1_1


title: AJ1_2


title: NGSA087

description: CRC192-exomiR NR-gene row.txt


title: PSCHYPx3

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: Sample name: Sample_2847-KL-12

data_processing:
Alignment with STAR (v2.6.1b).
Assigned count estimates to genes with RSEM (v1.3.1).
Assembly: GRCm38
Supplementary files format and content: gene_expected_count_PSC.txt: Tab-delimited text file includes raw counts.

source_name: Primary mouse pancreatic stellate cells

extract_protocol:
Total RNA was isolated from cells using the RNeasy mini kit (#74104, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: PSCs cocultured with mT3 PDAC

value: 1% oxygen for 48 hours


title: NGSA086

description: CRC192-exomiR NR-gene row.txt


title: PSCNORx3

description: Sample name: Sample_2847-KL-10

value: 21% oxygen for 48 hours


title: Replicate 1– IFNa – 24h

library_source: transcriptomic single cell

data_processing:
Raw scRNA sequencing data (fastq) was aligned with Cellranger v6.0 on the human genome GRCh38 in accordance with the instructions provided by 10X Genomics.
Filtered counts by Cellranger were aggregated using Seurat with default parameters and exported as h5 files for Seurat and Scanpy.
Assembly: GRCh38
Supplementary files format and content: h5 files containing the expression matrix of all samples

extract_protocol:
Cells were filtered using a 30 µm cell strainer (Corning) and resuspended in 200 µL Dead Cell Removal MicroBeads (Dead Cell Removal kit, Miltenyi Biotec). The dead cells were removed according to the manufacturer’s instructions, using LS columns and MidiMACS separator (Miltenyi Biotec).
The final cell suspension was centrifuged at 300 rcf for 3 min and resuspended into 1 ml of PBS + 5% BSA. The cell count and the cell viability were determined using a Countess II Automated Cell Counter and trypan blue solution (Thermo Fisher Scientific).
The single cell gene expression analysis was conducted using a 10X Chromium single cell system (10X Genomics, Inc) and a NovaSeq 6000 sequencer (Illumina, Inc). Around 10,000 targeted cell recovery per sample has been applied to a single cell master mix with lysis buffer and reverse transcription reagents, following the Chromium NextGEM Single Cell 3’ Reagent Kits User Guide, CG000204 Rev D (10X Genomics, Inc). Along with the single cell gel beads and partitioning oil, the single cell master mixture containing the single cell suspension was dispensed onto a Single Cell Chip G in separate wells, and the chip loaded to the Chromium Controller for GEM generation and barcoding, followed by cDNA synthesis and library preparation. At each step, the quality of cDNA and library has been examined by Bioanalyzer and Qubit. The resulting library has been sequenced in a custom program for 28b plus 91b paired-end sequencing on Illumina NovaSeq 6000.

value: IFNa (Interferon alpha)


title: Replicate 3– IFNa – 24h


title: Replicate 5– IFNa – 24h


title: PSCNORx2

description: Sample name: Sample_2847-KL-6


title: Replicate 4 – IFNa - 24h


title: PSCHYPx1

description: Sample name: Sample_2847-KL-4


title: NGSA083

description: CRC192-exomiR NR-gene row.txt

value: healthy


title: Replicate 3 – Untreated – 24h


title: NGSA074

description: CRC192-exomiR NR-gene row.txt


title: Replicate 2 – Untreated – 24h


title: NGSA090

description: CRC192-exomiR NR-gene row.txt


title: PSCNORx1

description: Sample name: Sample_2847-KL-2


title: s12_TBL1XR_M

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

country: Netherlands

institute: Amsterdam University Medical Centers

data_processing:
Trimmed using Trimmomatic v0.36 for adapter sequences.
Aligned using HISAT2 (v2.1.0) (default parameters; -p 4 --dta-cufflinks --rna-strandness RF)
Gene level counts were obtained using HTSeq (v0.11) with default parameters except "-stranded = reverse" and the mouse GTF from Ensembl (release 93)
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited file contains raw count data as obtained using HTSeq; rownames contain the Ensemble gene identifier; one column per sample.

growth_protocol: 12 week old mice were used

extract_protocol:
Total RNA was extracted from WAT of 12 mice using TriReagent (Sigma) and the ISOLATE II RNA Mini Kit (BIOLINE). (six Tbl1xr1Y446C/Y446C mice and six wild-type mice; three males and three females of each genotype).
In order to create cDNA libraries, samples were prepared using the Kapa mRNA Hyperprep kit (Roche, Basel, Switserland). Concentration of the library samples was measured using the Quant-it DNA HS assay (Thermo Fisher Scientific, Waltham, MA, USA). Libraries were equimolar pooled and the pool was checked on Tapestation using DNA1000 ScreenTape (Agilent Technologies, Santa Clara, CA, USA). The libraries were sequenced on the NovaSeq6000 PE150 sequencer (Illumina, San Diego, CA, USA), producing at least 40M 150-bp paired-end reads per library.

treatment_protocol: Male and female mice at the age of 12 weeks were killed by exsanguination.White adipose tissue (WAT) was removed, immediately frozen on dry ice and stored at -80 °C until further processing

tag: gender

value: Male

tag: age

value: 12 weeks

value: white adipose tissue (WAT)


title: NGSA072

description: CRC192-exomiR NR-gene row.txt

value: 1 (treatment naive)


title: NGSA089

description: CRC192-exomiR NR-gene row.txt


title: Replicate 4 – Untreated – 24h


title: Replicate 1 – Untreated - 24h


title: NGSA068

description: CRC192-exomiR NR-gene row.txt


title: Replicate 2– IFNa – 24h


title: s11_WT_M

value: wild type


title: NGSA065

description: CRC192-exomiR NR-gene row.txt


title: PSCHYPx2

description: Sample name: Sample_2847-KL-8


title: NGSA085

description: CRC192-exomiR NR-gene row.txt


title: Replicate 5 – Untreated – 24h


title: NGSA057

description: CRC192-exomiR NR-gene row.txt


title: NGSA060

description: CRC192-exomiR NR-gene row.txt


title: EndoC-βH1, NT 8h, siNLRC5 (exp185)

data_processing:
Raw RNA-seq data (2x150bp paired-end with a depth >200M reads) was quality checked with fastp to remove reads with poor quality and trim remaining adapters.
The quality control (QC) of the passing reads was assessed with FastQC (Babraham Bioinformatics). One paired experiment for the IFNα treatment at 24h did not pass our QC (insufficient read quality) and was removed from the subsequent analyses.
Gene expression was quantified in TPM (Transcripts per Millions) using Salmon v1.4  with additional parameters “--seqBias --gcBias --validateMappings”.
We used GENCODE v35  as the reference genome and indexed it with default k-mer values. Differential Gene Expression (DGE) analysis was performed with DESeq2 v1.30.1
Assembly: GENCODE v35 (GRCh38.p13)
Supplementary files format and content: Tab Separated Values (TSV) file containing TPM values at the gene level

growth_protocol: The EndoC-βH1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 5.6 mmol/L glucose (Gibco, Thermo Fisher Scientific), 2% fatty acid-free BSA fraction V, 50 μmol/L 2-mercaptoethanol (Gibco, Thermo-Fisher Scientific), 10 mmol/L nicotinamide (Sigma-Aldrich), 5.5 μg/mL transferrin (Sigma-Aldrich), 6.7 ng/mL selenite (Sigma-Aldrich), 100 U/mL penicillin + 100 μg/mL streptomycin in matrigel–fibronectin–coated plates (60).

extract_protocol:
Total RNA was isolated from EndoC-βH1 samples using the RNeasy Plus Micro kit (Qiagen) and quantified using a Nanodrop (NanoDrop ND-1000; Thermo Fisher Scientific).
A minimum of 500ng of high-quality RNA with RNA integrity number > 9 (as determined by Agilent Bioanalyzer) per sample and replicate was used for library preparation. RNA-seq was performed on a NovaSeq 6000 (Eurofins).

treatment_protocol: NLRC5 gene expression was silenced using two independent siRNA (Thermo Fisher Scientific; siNL#1 (siRNA HSS130675): 5’-GGACACCUGGCAGUCUUUCAUUCAU-3’; siNL#2 (siRNA HSS130676): 5’-GCAGUUGGCAGAGUCUCUCGUUCUU-3’). Allstars Negative Control siRNA (siCTL) (Qiagen) was used as a negative control; the siRNA control does not interfere with β-cell gene expression, function, or viability. Cells were transfected using the Lipofectamine RNAiMAX lipid reagent (Invitrogen, Life Technologies) in OptiMEM (Gibco, Thermo Fisher Scientific) reduced serum medium, according to the manufacturer's instructions. EndoC- βH1 were transfected using 30 nmol/L of each siRNA, overnight. Dispersed human islets and iPSC-derived β-like cells were transfected with 60 nmol/L of each siRNA, also during an overnight incubation period. After transfection, EndoC-βH1  were kept in culture for a 48h recovery period and subsequently exposed or not to human IFNα (2,000 U/mL; PeproTech) for 8 or 24h.

tag: knock-down (kd)

tag: time


title: EndoC-βH1, NT 8h, siNLRC5 (exp182)

tag: cell line


title: EndoC-βH1, NT 8h, siNLRC5 (exp179)


title: NGSA081

description: CRC192-exomiR NR-gene row.txt


title: NGSA056

description: CRC192-exomiR NR-gene row.txt


title: s7_TBL1XR_M

tag: strain


title: s9_TBL1XR_M

tag: tissue


title: EndoC-βH1, NT 8h, siNLRC5 (exp175)


title: EndoC-βH1, NT 8h, siNLRC5 (exp166)


title: EndoC-βH1, NT 8h, siNLRC5 (exp169)


title: s10_WT_M


title: NGSA054

description: CRC192-exomiR NR-gene row.txt

tag: disease state


title: s3_TBL1XR_F

value: Female


title: s5_WT_F


title: s4_WT_F


title: EndoC-βH1, NT 8h, siCT (exp185)

value: siCT


title: NGSA053

description: CRC192-exomiR NR-gene row.txt

tag: Stage


title: s8_WT_M


title: EndoC-βH1, NT 8h, siCT (exp182)


title: s2_WT_F


title: EndoC-βH1, NT 8h, siCT (exp179)


title: s1_TBL1XR_F


title: NGSA049

description: CRC192-exomiR NR-gene row.txt

tag: sampling time points


title: NGSA046

description: CRC192-exomiR NR-gene row.txt

tag: patient id


title: NGSA048

description: CRC192-exomiR NR-gene row.txt

tag: molecule subtype


title: Epithelial 4

city: PHILADELPHIA

first: Andrew

last: Vaughan

state: United States

address: 3800 Spruce Street

data_processing:
Kallisto ( pseudoalignment)
Limma (differential expression)
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv with RPKM values

source_name: mouse lung post-flu

extract_protocol:
cells sorted straight into lysis buffer and cDNA amplification performed with Takara SMART-Seq HT
illumina nextera xt

value: post-influenza tuft cells

tag: sorted cells


title: EndoC-βH1, NT 8h, siCT (exp175)

tag: treatment


title: EndoC-βH1, NT 8h, siCT (exp169)


title: Tuft 4


title: NGSA044

city: Taoyuan City

first: Hsuan

last: Liu

address: No.259, Wenhua 1st Rd., Guishan Dist.

description: CRC192-exomiR NR-gene row.txt


title: EndoC-βH1, NT 8h, siCT (exp166)


title: s6_TBL1XR_F

tag: genotype


title: Epithelial 3


title: NGSA038

description: CRC192-exomiR NR-gene row.txt


title: WID2D_0046_U

description: Influenza H1N1 PR8 H1N1 PR8 virus infected

data_processing:
FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles FASTA_FILE.fa --sjdbGTFfile GTF_FILE.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 $R2 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
The RUV R package was used to remove batch effects.
A threshold of 1 log2 absolute fold change and p-value larger than 0.05 were considered when identifying the differentially expressed genes.
The clusterProfiler (version 3.10.1) package was then used to perform various Enrichment Analysis on the obtained results.
Genome_build: rnm10
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

source_name: Lungs

growth_protocol: We subjected 8 week-old female BALB/cN mice to either mock  or intranasal inoculation with 175 PFU of the IFV H1N1 PR8 strain

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen) and then extracted and cleaned using Direct-zol-96 RNA kit (Zymo Research). 1 ug of total RNA was used for the construction of sequencing libraries.
Transcriptome Library construction Protocol

treatment_protocol: The 3 infected groups were given vehicle, Tet1 (at 40 mpkd) or Tet2 (at 1 mpkd) by daily intraperitoneal injection (mock group respectively injected with vehicule as well).

value: BALB/C

tag: age (weeks)

tag: tratment

value: Dox at 40mpkd


title: EndoC-βH1, NT 24h, siNLRC5 (exp185)


title: NGSA051

description: CRC192-exomiR NR-gene row.txt

source_name: healthy

value: plasma small extracellular vesicles

value: miRNA


title: WID2D_0030_U


title: Tuft 3

tag: cell type


title: EndoC-βH1, NT 24h, siNLRC5 (exp182)

value: Untreated


title: WID2D_0029_U


title: NGSA037

description: CRC192-exomiR NR-gene row.txt


title: NGSA036

description: CRC192-exomiR NR-gene row.txt


title: Epithelial 2


title: EndoC-βH1, NT 24h, siNLRC5 (exp179)


title: NGSA035

description: CRC192-exomiR NR-gene row.txt


title: Tuft 2


title: EndoC-βH1, NT 24h, siNLRC5 (exp175)


title: Epithelial 1


title: NGSA041

description: CRC192-exomiR NR-gene row.txt


title: WID2D_0027_U


title: WID2D_0026_U


title: NGSA031

description: CRC192-exomiR NR-gene row.txt


title: Tuft 1


title: EndoC-βH1, NT 24h, siNLRC5 (exp169)


title: NGSA028

description: CRC192-exomiR NR-gene row.txt


title: EndoC-βH1, NT 24h, siNLRC5 (exp166)


title: WID2D_0028_U


title: GAS_3

data_processing:
FastQC v0.11.0 used for quality control
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
HISAT2 v2.2.1 used for read mapping
subread v2.0.1 used for gene expression quantification
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts

extract_protocol:
To each GAS sample, 1 stainless steel bead together with 1ml of ice-cold TRIzol (15596018, Thermo Fisher Scientific, Rockford U.S.A.) was added. The mixtures were homogenized for 7 minutes using a bead mill at 50 rpm (TissueLyzer LT, 85600, Qiagen, Hilden Germany). The beads were removed using a forceps cleaned with RNAzap (AM9780/AM9782, Thermo Fisher Scientific, Rockford U.S.A.) after each transfer to avoid carryover of RNA. Addition of 200 μl of chloroform (22711.324, VWR international, Radnor U.S.A.) was followed by vigorous shaking for 15-20 sec and a centrifugation step of 15 min at 14,000 rcf at 4°C. The aqueous phase was transferred into a new vial and mixed with an equal amount of 100% ethanol (10821.365, VWR international, Radnor U.S.A.). RNA was then extracted using the RNA Clean & ConcentratorTM-25 Kit (R1017 & R1018, Zymo Research, Irvine USA). The whole volume was transferred to a Zymo-SpinTM IICR-column in a collection tube, spun down for 30 sec at 10000 rpm and the flow-through discarded. Next, a mixture of 5 μl of DNAse and 75 μl of DNA digestion buffer was added to the column and incubated for 15 min at room temperature. 400 μl of RNA Prep buffer was added directly on top of the DNase solution and the samples were spun down for 30 sec (4°C, 10,000 rpm). This process was repeated twice from the addition of 700 μl of RNA Wash buffer, spinning down for 30 sec at 4°C (10,000 rpm) and removal of flow through, followed by the addition of 400 μl of RNA wash buffer and a 2 min centrifugation step with the same settings. After the final removal of flow through, 30 μl of DNase/RNase-Free Water was added directly onto the colum matrix. The colum was placed in a fresh vial and once again spun down for 30 seconds (4°C, 10000 rpm).
The RNA quality was measured with a Fragment Analyzer (Agilent, Santa Clara, California, USA) and only those samples with a 28S/18S ratio over 1.9 were used for library construction which was outsourced to Novogene. Total mRNA was sequenced PE150 on a Novaseq.

tag: biological replicate


title: WID2T_0045_U

value: 9TB at 1mpkd


title: NGSA024

description: CRC192-exomiR NR-gene row.txt


title: GAS_2


title: EndoC-βH1, NT 24h, siCT (exp185)

tag: knock-down (kd)


title: NGSA020

description: CRC192-exomiR NR-gene row.txt


title: WID2T_0025_U


title: EndoC-βH1, NT 24h, siCT (exp182)

tag: time


title: WID2T_0024_U


title: NGSA018

description: CRC192-exomiR NR-gene row.txt


title: EndoC-βH1, NT 24h, siCT (exp179)

tag: cell line


title: NGSA016

description: CRC192-exomiR NR-gene row.txt


title: PIM_H3K4me3_2

description:
DNA marked by H3K4me3 and cut by Tn5
PIM_H3K4me3_peaks.bed

data_processing:
Library strategy: Cut&Tag
FastQC v0.11.0 used for quality control
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
bedtools v2.30 used for merging replicate specific bedgraph files for each sample
SEACR v1.3 used for calling peaks
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited called peak regions

extract_protocol:
ESC were processed exactly as per the original CUT&Tag protocol for whole cells. All other samples were processed as per the CUT&Tag protocol for nuclei. Muscle samples were thawed and sliced in small pieces on ice. Subsequently, the pieces were transferred to an ice-cold dounce homogenizer (7 mL) and 3 mL of nucleus extraction buffer (1× prelysis buffer from the EpiQuick Total Histone Extraction Kit (EpiGentek)) was added before douncing, on ice, 10× with pestle A and 10× with pestle B. Nuclei from macrophages, myoblasts and myotubes were obtained through resuspension of centrifuged and washed cell pellets in the same nucleus extraction buffer. To all samples: to stop the lysis reaction, of PBS+1%BSA was added in a 1:1 volume. After 5’ centrifugation at 4˚C, 500 rpm, the supernatant was removed, the nuclei were resuspended in PBS+1%BSA and a sample was visually inspected for viability, purity and abundance of nuclei under the microscope. CUT&Tag was performed according to the published CUT&Tag sequencing protocol for nuclei.All buffers were supplemented with 5 mM sodium-butyrate and 1X complete protease inhibitor (Merck, 1187358000). Protein lo-bind tubes (Eppendorf, EP0030108116) were used to reduce sample loss.  Antibodies against H3K18la (PTM-Bio, PTM-1406), H3K4me3 (Abcam, ab8580), H3K27me3 (Cell Signaling Technology, C36B11), H3K27ac (Abcam, ab4729) and H3K9me3 (Abcam, ab8898) were used in this study.
PCR was performed with 21 μL DNA + 2 μL Universal i5 primer (10 μM) + 2 μL uniquely barcoded i7 primers (10 μM) in a thin-wall 0.5 ml PCR tube, using a different barcode for each sample. *Nextera primers or indexed primers described by Buenrostro, J.D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523:486 (2015).To this mixture,  25 μL NEBNext HiFi 2x PCR Master mix was added. The samples were mixed, quick spinned and placed in  a thermocycler with heated lid. The following program was used: Cycle 1: 72 °C for 5 min (gap filling) Cycle 2: 98 °C for 30 sec.Cycle 3: 98 °C for 10 sec.Cycle 4: 63 °C for 10 sec.Repeat Cycles 3-4 13 times 72°C for 1 min and hold at 8 °C.

tag: antibody

tag: growth medium

tag: strain


title: WID2T_0023_U


title: PIM_H3K4me3_1


title: WID2T_0022_U


title: NGSA009

description: CRC192-exomiR NR-gene row.txt

tag: disease state

tag: tissue

tag: Stage


title: EndoC-βH1, NT 24h, siCT (exp169)


title: WID2T_0021_U


title: GAS_1


title: PIM_H3K27me3_2

description:
DNA marked by H3K27me3 and cut by Tn5
PIM_H3K27me3_peaks.bed


title: NGSA006

description: CRC192-exomiR NR-gene row.txt

tag: sampling time points

tag: patient id

tag: molecule subtype


title: EndoC-βH1, NT 24h, siCT (exp166)

tag: treatment


title: PIM_H3K27me3_1


title: WID2V_0042_U

tag: age (weeks)

value: Vehicule


title: WID2V_0010_U

tag: tratment


title: NGSA003

description: CRC192-exomiR NR-gene row.txt


title: NGSA004

description: CRC192-exomiR NR-gene row.txt


title: PIM_H3K18la_2

description:
DNA marked by H3K18la and cut by Tn5
PIM_H3K18la_peaks.bed


title: EndoC-βH1, IFNa 8h, siNLRC5 (exp185)

value: IFNa (Interferon Alpha)


title: WID2V_0009_U


title: EndoC-βH1, IFNa 8h, siNLRC5 (exp182)


title: PIM_H3K18la_1


title: MT_H3K27me3_2

description:
DNA marked by H3K27me3 and cut by Tn5
MT_H3K27me3_peaks.bed

value: DMEM

value: primary


title: EndoC-βH1, IFNa 8h, siNLRC5 (exp179)


title: Sirt1 control 6

city: Raleigh

first: Xiaoqiu

last: Wang

address: 120 W Broughton Dr.

institute: NC State University

data_processing:
Raw fastq data were mapped to the Mus musculus GRCm38 genome assembly using HISAT2 v2.2.0
Data were quantitated at a protein-coding mRNA level using Partek Flow bioinformatics software
Data were normalized according to total read count (reads per kilobase of transcript per million mapped reads, RPKM), and 75% distribution.
Differential expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: excel

source_name: uterus

extract_protocol:
Total RNA was extracted using Trizol reagent.
1 ug of total RNA  was used for the construction of sequencing libraries with Illumina Stranded TruSeq kit and Ribo-Zero.

treatment_protocol: Uteri were harvested from Sirt1d/d and Sirt1f/f female mice at day 3.5 of pregnancy

tag: age

value: 6-8 weeks old


title: EndoC-βH1, NT 24h, siCT (exp175)


title: Sirt1 control 5


title: MT_H3K27me3_1

tag: biological replicate


title: Sirt1 control 4


title: EndoC-βH1, IFNa 8h, siNLRC5 (exp175)

tag: knock-down (kd)


title: EndoC-βH1, IFNa 8h, siNLRC5 (exp169)

tag: time


title: MT_H3K18la_2

description:
DNA marked by H3K18la and cut by Tn5
MT_H3K18la_peaks.bed

tag: cell line


title: WID2V_0007_U


title: Sirt1 control 3


title: WID2C_0041_U

description: Influenza H1N1 PR8 H1N1 PR8 virus uninfected

value: Control


title: EndoC-βH1, IFNa 8h, siNLRC5 (exp166)


title: Sirt1 control 2


title: MB_H3K27me3_1

description:
DNA marked by H3K27me3 and cut by Tn5
MB_H3K27me3_peaks.bed

tag: antibody


title: EndoC-βH1, IFNa 8h, siCT (exp185)


title: WID2C_0005_U


title: MB_H3K18la_1

description:
DNA marked by H3K18la and cut by Tn5
MB_H3K18la_peaks.bed

tag: growth medium


title: WID2V_0008_U

tag: strain


title: WID2C_0004_U


title: WID2C_0003_U


title: GAS_H3K4me3_2

description:
DNA marked by H3K4me3 and cut by Tn5
GAS_H3K4me3_peaks.bed


title: Sirt1 control 1


title: Sirt1-KO 6


title: EndoC-βH1, IFNa 8h, siCT (exp179)


title: Sirt1-KO 5


title: WID2C_0002_U


title: Sirt1-KO 4


title: EndoC-βH1, IFNa 8h, siCT (exp169)


title: GAS_H3K4me3_1


title: GAS_H3K27me3_2

description:
DNA marked by H3K27me3 and cut by Tn5
GAS_H3K27me3_peaks.bed


title: Sirt1-KO 3


title: WID2V_0006_U


title: EndoC-βH1, IFNa 8h, siCT (exp166)


title: WID2D_0046_K

source_name: Kidney


title: WID2D_0030_K


title: GAS_H3K27me3_1


title: MT_H3K18la_1


title: EndoC-βH1, IFNa 8h, siCT (exp182)


title: EndoC-βH1, IFNa 24h, siNLRC5 (exp185)


title: WID2D_0029_K


title: GAS_H3K18la_2

description:
DNA marked by H3K18la and cut by Tn5
GAS_H3K18la_peaks.bed


title: Sirt1-KO 2


title: Sirt1-KO 1


title: EndoC-βH1, IFNa 8h, siCT (exp175)


title: GAS_H3K18la_1


title: WID2D_0028_K


title: ESC-ser_H3K4me3_2

description:
DNA marked by H3K4me3 and cut by Tn5
ESC-ser_H3K4me3_peaks.bed

value: serum-lif


title: EndoC-βH1, IFNa 24h, siNLRC5 (exp179)


title: WID2D_0027_K


title: 16_WT_H2O2

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

data_processing:
Illumina software RTA 2.4.11 was used for basecalling.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Mouse_mm10) and the annotated transcripts using  STAR and RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts and  RPKM values for each Sample

extract_protocol:
Cells with/without 1uM H2O2 treatement were lysed with RLT lysis buffer containing 1% beta mercaptoethanol after 24 hours and RNA was harvased using QIAcube as per Rneasy kit from Qiagen.
RNA libraries were prepared for sequencing using llumina TruSeq Stranded mRNA Library Prep.
The mRNA-Seq samples were sequenced on NextSeq using paired-end sequencing.

tag: strain background

tag: cell type

value: mammary cancer cell line

tag: genotype/variation

value: wildtype cells

value: treated with 1uM H2O2


title: EndoC-βH1, IFNa 24h, siNLRC5 (exp175)


title: 15_WT_H2O2


title: ESC-ser_H3K4me3_1


title: EndoC-βH1, IFNa 24h, siNLRC5 (exp169)


title: 14_WT_H2O2


title: WID2D_0026_K


title: WID2T_0045_K


title: 13_WT_H2O2


title: ESC-ser_H3K27me3_2

description:
DNA marked by H3K27me3 and cut by Tn5
ESC-ser_H3K27me3_peaks.bed


title: ESC-ser_H3K27me3_1


title: EndoC-βH1, IFNa 24h, siNLRC5 (exp166)


title: WID2T_0024_K


title: ESC-ser_H3K18la_2

description:
DNA marked by H3K18la and cut by Tn5
ESC_H3K18la_peaks.bed


title: WID2T_0025_K


title: EndoC-βH1, IFNa 24h, siCT (exp185)

value: siCT


title: 11_WT_NT

value: untreated


title: EndoC-βH1, IFNa 24h, siNLRC5 (exp182)


title: ESC-ser_H3K18la_1


title: WID2T_0023_K

value: BALB/C


title: EndoC-βH1, IFNa 24h, siCT (exp182)


title: EndoC-βH1, IFNa 24h, siCT (exp179)


title: WID2T_0021_K


title: 10_WT_NT


title: BMDM_H3K27me3_1

description:
DNA marked by H3K27me3 and cut by Tn5
BMDM_H3K27me3_peaks.bed

source_name: Mouse bone marrow-derived macrophages


title: 9_WT_NT


title: BMDM_H3K27ac_1

description:
DNA marked by H3K27ac and cut by Tn5
BMDM_H3K27ac_peaks.bed


title: 8_KO_H2O2


title: WID2V_0010_K

description: Influenza H1N1 PR8 H1N1 PR8 virus infected


title: EndoC-βH1, IFNa 24h, siCT (exp169)


title: 7_KO_H2O2


title: BMDM_H3K18la_1

description:
DNA marked by H3K18la and cut by Tn5
BMDM_H3K18la_peaks.bed


title: 12_WT_NT