title: Histone-Kcr_MS-275_E13.5_NSPCs_ChIP-seq

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

data_processing:
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v. 2.3.5.1) with default parameters. MACS (v. 2.2.5) was used to call peaks (-q 0.05) relative to the IgG sample.
Genome_build: GRCm38

source_name: Neural stem/progenitor cells

growth_protocol: NSPCs isolated from the E13.5 mice forebrain were cultured with DMEM/F12 medium (Invitrogen) supplemented with 20 ng/ml epidermal growth factor and 20 ng/ml fibroblast growth factor (EGF/FGF, PeproTech), 1% penicillin/streptomycin (Invitrogen), 0.5× B27 (Invitrogen), and 0.5× N2 (Invitrogen).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA library prep kit for Illumina® (NEB) was used with 2 ug of total RNA for the construction of sequencing libraries.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Briefly, NSPCs (passage 2–3) were grown to 50–60% confluence in 10-cm plates, and were treated with DMSO (control group), 10 mM crotonate (crotonate group), or 1 μM MS-275 (MS-275 group) for 24 h.

value: E13.5 forebrain derived neural stem/progenitor cells (NSPCs)

tag: passages


title: Smoke Month1 2

status: Public on Jun 22 2021

type: SRA

city: New York City

first: Balvir

last: Kunar

state: New York

address: 1300 York Ave

department: Regenerative Medicine; Physiology, Biophysics, & Systems Biology

country: USA

institute: Weill Cornell Medical College

description:
FACS sorted
counts1month.txt
CS_2_S33_L004_R1_001

library_source: transcriptomic

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrix

molecule: polyA RNA

organism: Mus musculus

source_name: smoke month 1

extract_protocol:
Intravital labeling of VE-cadherin was performed before mice sacrificed to label the endothelial compartment.  Lung tissue was harvested and enzymatically digested into single cell suspension.  Endothelail cells were  isolated by fluorescence-activated cell sorting and subjected to RNA extraction using Trizol and RNA-easy microRNA kit from Qiagen
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: mice were treated with 1 month and  6 months of whole body smoke and compared to controls at room air

tag: tissue

value: Lung

tag: disease status

value: Smoke 1 month


title: primary mammary organoids - 1.5 uM CHIR99021 - rep2 ("CHIR_1.5uM_min")

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

data_processing:
Single-end reads (65 bp) were aligned to reference sequence GRCm38/mm10 with Tophat version 2.1 and Bowtie version 1.1.0.
Expression values were determined by HTSeq-count.
Raw gene-level count tables were processed in R using DESeq2.
Normalized values were extracted from the DESeqDataSet (dds) object
Differentially expressed genes were extracted using pairwise comparisons of different treatment conditions with padj <0.1 as a cut off for false discovery
Genome_build: Genome_build: GRCm38.77 (mm10)
Supplementary_files_format_and_content: raw counts and counts normalized to 10 million reads followed by log2 transformation

source_name: primary mammary organoids

growth_protocol: organoids were embedded in growth-factor reduced matrigel and grown in minimal media according to Ewald et al. (2008; https://doi.org/10.1016/j.devcel.2008.03.003) and Nguyen-Ngoc et al. (2015, https://doi.org/10.1007/978-1-4939-1164-6_10)

extract_protocol:
RNA was extracted using Trizol and RNA was extracted using the Qiagen RNeasy column purification kit. RNA quality was checked with a Bioanalyer (Agilent).
PolyA+ stranded RNA library preparation was performed using the Illumina TruSeq stranded RNA prep kit according to the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard Illumina protocols. RNA-sequencing was performed on a HiSeq 2500 (Illumina) System using a stranded protocol.

treatment_protocol: triplicate organoid cultures were treated with either vehicle control (DMSO) or increasing concentrations of CHIR99021 (1 uM, 1.5 uM or 3 uM) to activate WNT/CTNNB1 signaling for 7 days

tag: strain

value: FVB/N

value: mammary gland organoid

tag: developmental stage

value: 8-11 week old virgin


title: Histone-Kcr_Crotonate_E13.5_NSPCs_ChIP-seq

country: China

library_source: genomic

molecule: genomic DNA

tag: cell type


title: Air Month1 4

description:
FACS sorted
counts1month.txt
RA_4_S31_L004_R1_001

source_name: air month 1

value: Air 1 month


title: Histone-Kac_MS-275_E13.5_NSPCs_ChIP-seq


title: primary mammary organoids - 1 uM CHIR99021 - rep2 ("CHIR_1uM_min")


title: Histone-Kac_Control_E13.5_NSPCs_ChIP-seq


title: Histone-Kac_Crotonate_E13.5_NSPCs_ChIP-seq


title: Smoke Month1 1

description:
FACS sorted
counts1month.txt
CS_1_S32_L004_R1_001


title: primary mammary organoids - DMSO - rep2 ("DMSO_min")


title: IgG_E13.5_NSPCs_ChIP-seq


title: Smoke Month1 4

description:
FACS sorted
counts1month.txt
CS_4_S35_L004_R1_001


title: RL.B.RNA

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-end reads were trimmed for Illumina adaptor sequences and transposase sequences and mapped to mm9 using Bowtie2 v2.1.0 with parameters – very sensitive.
For RNA seq-Gene-level counts matrix was generated using Rsubread version 1.30.9. Count files were normalized and analyzed DESeq2 and custom R scripts. For ATAC seq number of raw reads mapped to each peak in each sample was quantified using multicov in Beltools. Peak raw counts were normalized using DESeq2.
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: matrix table with raw gene counts for every sample

molecule: total RNA

source_name: Rosa-Lipofibroblast

growth_protocol: not applicable

extract_protocol:
RNA-seq was performed on FACS-isolated mouse fibroblast subpopulations from JUN and Control mice and human cultured KO and non-KO fibroblasts resuspended in TRIzol (10k cells/1ml). The RNA-seq data was collected from ten mice and pooled into two biological replicates. Thus, each biological replicate represents 10 wounds, as each mouse has two wounds. The human RNA-seq data was collected from 4 individual patients. RNA was isolated using the Rneasy Micro Kit (Qiagen, #74004), as per the manufacturer’s instructions. ATAC-seq libraries were generated using an average of 50,000 freshly isolated fibroblasts per replicate (biological replicates for mice samples and technical replicates for human samples) as described by Buenrostro et al 2013 with the following modifications. Transposition was performed in 50 uL reaction containing in-house made 2xTD buffer, Tn5 and 1% Digitonin.
Libraries were sequenced on an Illumina HiSeq 2500 machine. KO and non-KO fibroblasts from each skin type will be prepared for RNA-seq. ATAC libraries were prepared using the protocol found in ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide by Buenrostro et al (2015).

treatment_protocol: not applicable

value: Fibroblast Cells

value: skin

tag: genotype

value: Fibroblasts


title: primary mammary organoids - 3 uM CHIR 99021 - rep1 ("CHIR_3uM_med")


title: X2_4 h

city: Guangzhou

first: Wang

last: Li

address: Wushan road, Tianhe district

institute: Guangdong Academy of Agricultural Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: PGSC v4.03

organism: Solanum tuberosum

source_name: potato

extract_protocol:
Total RNA of potato tubers was extracted from each sample using TiangenRNA extraction kit (Tiangen Biltech Co. Ltd, Beijing, China)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: potato tubers

tag: treatment

value: 4 h after cut-wounding


title: PDX413ZT4Liver

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

data_processing:
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: no

source_name: Liver

extract_protocol: The detailed protocol was published on Genome-wide mapping of nucleotide excision repair with XR-seq (Nature Protocols volume 14, pages248–282 (2019), https://www.nature.com/articles/s41596-018-0093-7).

value: cisplatin


title: RNA-Seq P53KOH9-rep2

city: Ann Arbor

first: Rajesh

middle: C

last: Rao

state: Michigan

address: 1000 Wall Street

institute: University of Michigan

data_processing:
Reads from sample 5 - 10 were aligned to the mm10 genome assembly using hisat2 version 2.0.0
Reads from sample 1-4 and sample 11-18 were aligned to the mm10 genome assembly using STAR version 2.7.3a
transcript gtf files were calculated using cufflinks version 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: transcript gtf file.

source_name: ESC

growth_protocol: Rx:GFP mESCs were maintained in 2i+LIF media and induced to differentiation with SFEBq method (5%KSR in GMEM media)

extract_protocol:
RNA isolation and DNase treatment were according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.
Single end RNA-Seq

treatment_protocol: For SFEBq differerentaton, 2% matrigel was added at EB day 1.

value: embryonic stem cell, Rx:GFP KI

value: p53 knockout clone H9

tag: agent column

value: ESC maintained in 2i+LIF


title: RNA-Seq P53KOC9-rep2

value: p53 knockout clone C9


title: PDX413ZT20Liver


title: JL.A.ATAC

source_name: Jun-Lipofibroblast


title: RNA-Seq P53KOC9-rep1


title: Histone-Kcr_Control_E13.5_NSPCs_ChIP-seq

value: E13.5 forebrain derived neural stem/progenitor cells (NSPCs)


title: RNA-Seq DKO-S91KY191F-rep2

source_name: Embryoid bodies

value: Wdr5 and p53 double knockout stably transfected with WDR5S91KY191F vector

value: ESC differeantion using SFEBq method


title: RNA-Seq DKO-S91KY191F-rep1


title: RNA-Seq DKO-EV-rep2

value: Wdr5 and p53 double knockout stably transfected with backbone vector


title: primary mammary organoids - DMSO - rep1 ("DMSO_med")

value: FVB/N

value: mammary gland organoid


title: RNA-Seq DKO-B-rep2

value: Wdr5 and p53 double knockout


title: PDX413ZT12Liver


title: RNA-Seq DKO-EV-rep1


title: RNA-Seq DKO-B-rep1


title: EDL_mdx5_6

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Demultiplex and convert to FastQ (casava 1.8.2)
Map to mm10 (Tophat 2.1.0)
Calculate RPKM (Partek 6.6)
ANOVA comparisons (Partek 6.6)
Genome_build: mm10
Supplementary_files_format_and_content: Excel RPKM and ANOVA

source_name: Extensor digitorum longus muscle

extract_protocol:
Muscles dissected, dropped inRNAse away, cleaned and extracted with Trizol. Total RNA prepared with PureLink RNA Mini kit and PureLink DNase.
mRNA isolated, fragmented and primed with NEB Next Poly (A) mRNA Magnetic Isolation Module; cDNA library preparation for RNA-Seq was performed using the Mondrian SP kit (NuGEN Technologies, San Carlos CA)

value: mdx

tag: age (months)


title: EDL_mdx5_5


title: PDX413ZT8Liver


title: RNA-Seq DKO-A-rep2


title: PDX413ZT0Liver


title: PDX119ZT20Liver


title: RNA-Seq DKO-A-rep1


title: RNA-Seq P53KOH9-rep1


title: EDL_mdx5_4


title: RNA-Seq WTEB4-rep1

value: Parental Rx:GFP


title: primary mammary organoids - 1.5 uM CHIR99021 - rep1 ("CHIR_1.5uM_med")

value: 8-11 week old virgin


title: RNA-Seq DKOS91KY191F-rep 2

description: DKOS91KY191F-rep 2

value: Wdr5 and p53 double knockout with WDR5S91KY191F rescue


title: RNA-Seq WTEB4-rep2


title: PDX119ZT16Liver


title: RNA-Seq DKOS91KY191F-rep 1

description: DKOS91KY191F-rep 1


title: PDX119ZT12Liver


title: EDL_mdx5_3


title: RNA-Seq DKOWT1-rep2

value: Wdr5 and p53 double knockout with WDR5WT rescue


title: PDX413ZT16Liver

value: cisplatin


title: SOL_mdx5_7

source_name: Soleus muscle


title: primary mammary organoids - 1 uM CHIR99021 - rep1 ("CHIR_1uM_med")


title: PDX119ZT0Liver


title: PDX119ZT08Liver


title: RNA-Seq DKOWT1-rep1

value: embryonic stem cell, Rx:GFP KI


title: ChIP-Seq WT day 2 embryoid bodies MAX Cut & Run

description: WT day 2 embryoid bodies MAX Cut & Run

data_processing:
Cut&Run sequencing reads were mapped to the mm10 genome for mouse by using Bowtie2 (v2-2.2.4) with parameters “-q --phred33  --very-sensitive -p 10”.
Then, we removed duplicated reads using SAMtools (v1.5) . BAM files of mapping results were merged for the same sample using SAMtools and converted to BED format by using BEDTools.
Peaks regions were called for each sample by using MACS2 (v 2.1.0) from ATAC mapped reads with parameters "-f BAMPE -g mm -n WTEB2P53 -B -q 0.01 --extsize 147 --keep-dup auto".  Differential peaks between groups were called by MACS2 subcommand “bdgdiff”.
Homer v4.10 was employed to perform gene annotation of peaks and differential peaks.
Genome_build: mm10
Supplementary_files_format_and_content: peak table

source_name: embryoid bodies

growth_protocol: Rx:GFP mESCs were induced to differentiation with SFEBq method (5%KSR in GMEM media)

extract_protocol:
Cut & Run experiments were performed using 2 µg anti-MAX antibody for 2X106 cells according to Cut & Run protocols.
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.
Cut&Run

treatment_protocol: 2% matrigel added at EB day 1.

value: WT EBs

value: Embryonic stem cell Rx:GFP KI


title: ChIP-Seq Wdr5 and p53 double KO day 2 embryoid bodies MAX Cut & Run

value: Wdr5 and p53 double KO EBs


title: SOL_mdx5_5


title: SOL_mdx5_6


title: PDX119ZT04Liver


title: ChIP-Seq DKOS91KY191F Input ChIP-seq

description: DKOS91KY191F Input ChIP-seq

data_processing:
Reads were aligned to the mm10 genome assembly using bwa version 0.7.17-r1188
Data were filtered using samtools with the following specifications: 1. alignments with MAPQ smaller than 10 were skipped; 2. duplicate reads were discarded using picard; 3. reads mapped to multiple locations were discarded.
Peaks were called using MACS2 version 2.1.2 with the following parameters: -p 0.01 --nomodel --shift 0 --extsize 151 --keep-dup all -B --SPMR.
Signals were normalized with MACS2 bdgcmp program over controls.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig and peaks table

source_name: ESCs

growth_protocol: Rx:GFP mESCs were maintained in 2i+LIF.

extract_protocol:
ChIP experiments were performed using anti-WDR5 or H3K4me3 antibodies for 1X108 cells according to standard protocols. Crosslinking of the cells was performed with 1% PFA for 10 minutes. ChIPed DNA was purified by Qiaquick PCR purification Kit (Qiagen).
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

value: ESC maintained in 2i+LIF

value: Wdr5 and p53 double knockout ESC rescued with WDR5S91KY191F


title: ChIP-Seq DKOS91KY191F H3K4me3 ChIP-seq

description: DKOS91KY191F H3K4me3 ChIP-seq


title: ChIP-Seq DKOS91KY191F WDR5 ChIP-seq

description: DKOS91KY191F WDR5 ChIP-seq


title: FDB_mdx5_7

source_name: Flexor digitorum brevis muscle


title: PDX057ZT20Liver


title: ChIP-Seq DKOWT H3K4me3 ChIP-seq

description: DKOWT H3K4me3 ChIP-seq

value: Wdr5 and p53 double knockout ESC rescued with WDR5WT


title: FDB_mdx5_6


title: ChIP-Seq DKOWT WDR5 ChIP-seq

description: DKOWT WDR5 ChIP-seq


title: PDX057ZT16Liver


title: ATAC-Seq Wdr5 and p53 double knockout-rep-1

description: Wdr5 and p53 double knockout-rep-1

data_processing:
Reads were aligned to the mm10 genome assembly using bowtie2 version 2.3.5
Data were filtered using samtools with the following specifications: alignments with MAPQ smaller than 10 were skipped.
Peaks were called from sample 1 to sample 12 using Genrich version 0.6 with the following parameters: -jyv -e MT.
Peaks were called from sample 13 to sample 16 using MACS2 version 2.1.2 with the following parameters: --nomodel --shift -100 --extsize 200 -B --broad -f BAMPE --keep-dup all.
Signals from different biological replicates were first merged, and then were normalized by calculating the log2 ratios over their mean DESeq2 size factors of all biological replicates.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig and peaks table

extract_protocol:
5x104 cells were used for transpoistion at 37C for 30 min using Illumina Nextera DNA Library Prep Kit.
Libraries were prepared with the Illumina Nextera DNA Library prep kit according to the manufacturer’s protocol.

value: ESC SFEBq differentiation

value: Wdr5 and p53 DKO


title: ChIP-Seq DKOWT Input ChIP-seq

description: DKOWT Input ChIP-seq


title: FDB_mdx5_5


title: PDX057ZT12Liver


title: ChIP-Seq Wdr5 KO day 2 embryoid bodies MAX Cut & Run

value: Wdr5 KO EBs


title: FDB_mdx5_4


title: ATAC-Seq Wdr5 and p53 double knockout-rep-2

description: Wdr5 and p53 double knockout-rep-2


title: ATAC-Seq WT, EB4-rep-1

description: WT, EB4-rep-1


title: ATAC-Seq WT, EB4-rep-2

description: WT, EB4-rep-2


title: PDX057ZT0Liver


title: ATAC-Seq DKOWT-rep2

value: Wdr5 and p53 DKO stably transfected with WDR5WT plasmid


title: SOL_mdx5_4

value: mdx


title: PDX057ZT04Liver


title: SOL_mdx5_3


title: PDX057ZT08Liver


title: SOL_mdx5_2


title: ATAC-Seq p53KOC9-rep2

value: p53 knockout clone C9


title: ATAC-Seq p53KOH9-rep2

value: p53 knockout clone H9


title: ATAC-Seq DKOWT-rep1


title: ATAC-Seq p53KOH9-rep1


title: SOL_mdx5_1


title: ATAC-Seq WT-rep2

value: Parental Rx:GFP


title: EDL_wt5_4

value: wt


title: ATAC-Seq DKOS91KY191F-rep1

value: Wdr5 and p53 DKO stably transfected with WDR5S91K-Y191F plasmid


title: ATAC-Seq p53KOC9-rep1


title: EDL_wt5_2


title: EDL_wt5_3


title: ATAC-Seq DKOEV-rep1

value: Wdr5 and p53 DKO stably transfected with backbone plasmid


city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

description: expression profile of splenic CD8+ T cells sorted from Cdk6-K43M mice - replicate 1

data_processing:
Alignment to genome version GRCm38 using STAR
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: raw count file (tab delimited)

source_name: splenic CD8+ T cells

growth_protocol: Splenic CD8+ T cells were sorted ex vivo and directly lysed for RNA isolation.

extract_protocol:
QIAGEN RNeasy extraction kit
RNA-seq: TruSeq Stranded mRNA LT sample preparation kit (Illumina), 50 bp single-end

treatment_protocol: no treatment was applied

value: spleen

value: CD8+ T cells

tag: gentoype


title: ATAC-Seq DKOS91KY191F-rep2

value: Embryonic stem cell Rx:GFP KI


description: expression profile of splenic CD8+ T cells sorted from Cdk6-K43M mice - replicate 2


description: expression profile of splenic CD8+ T cells sorted from Cdk6-/- (KO) mice - replicate 2


description: expression profile of splenic CD8+ T cells sorted from Cdk6-/- (KO) mice - replicate 3


description: expression profile of splenic CD8+ T cells sorted from Cdk6-K43M mice - replicate 3


description: expression profile of splenic CD8+ T cells sorted from Cdk6-/- (KO) mice - replicate 1


title: EDL_wt5_1


title: EDL_wt2_4


description: expression profile of splenic CD8+ T cells sorted from wild-type (WT) mice - replicate 3

value: WT


title: EDL_wt2_3


title: DNA Methylation_E13.5_Forebrain_WGBS

data_processing:
WGBS data were aligned to the bisulfite-converted GRCm38 reference genome using Bismark (v0.22.3). We use deduplicate_bismark script in Bismark to remove duplicate and bismark_methylation_extractor script to extract methylation status. Only CpGs with at least five reads covering them were used for downstream analysis.
Genome_build: GRCm38

source_name: E13.5 forebrain

extract_protocol: DNA was extracted from forebrain and subjected to end repair, A-tailing, adapter ligation, bisulfite conversion, amplication and sequencing according to standard Illumina protocols.

value: forebrain


title: ATAC-Seq WT-rep1

value: ESC maintained in 2i+LIF


title: Transcriptome_E13.5_Brain Explant_Crotonate-rep3_RNA-seq

data_processing:
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v. 2.3.5.1) with default parameters. MACS (v. 2.2.5) was used to call peaks (-q 0.05) relative to the IgG sample.High-quality reads of RNA-seq were quantified using Salmon (v.1.0.0) and differential gene expression analysis was conducted using DESeq2(v1.26.0).
Genome_build: GRCm38

extract_protocol: Forebrain were dissocated with trizol to obtain total RNA.RNA libraries were prepared for sequencing using standard Illumina protocols.

value: ICR


description: expression profile of splenic CD8+ T cells sorted from wild-type (WT) mice - replicate 1


title: ATAC-Seq DKOEV-rep2


title: Transcriptome_E13.5_Brain Explant_Crotonate-rep1_RNA-seq


title: EDL_wt2_1


title: Transcriptome_E13.5_Brain Explant_Control-rep3_RNA-seq


title: Brain, WT-TBI

city: San Antonio

first: Chu

state: Texas

address: 7703 Floyd Curl Dr

department: Cellular and Integrative Physiology

institute: UT Health San Antonio

description: wt-final.RDS

data_processing:
CellRanger Mkfatsq/Count Analysis
Seurat R package (v3) was used for analysis. For quality control, cell with mitochondrial content > 30% were removed. And we retained genes with a count of 1 in at least 20 cells and removed cells with < 400 or > 6000 genes per cell.
Supplementary_files_format_and_content: nko-final.rds, ako-final.rds, and wt-final.rds are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with `readRDS(“eset-final.rds”)`. It contains the gene counts, sample metadata, and feature metadata for single cells that passed quality control.
Supplementary_files_format_and_content: zip files cantain features, barcodes, and matrix files. These files can be imported in to R with "Read10X()". These files contain the raw cell count matrix exported by Cellranger software.

source_name: Brain

extract_protocol:
The brain tissue was extracted after anesthesia and single cell suspensions were prepared.
The libraries were prepared for sequencing following the manufacturer’s recommendations for the 10x Genomics 3’ Gene Expression v3 chemistry
Single-cell RNA-Seq

treatment_protocol: Three mild closed head injury once a day for three days

value: Brain

tag: age

value: 3 months

value: TBI


title: Brain, nKO-Sham

description: nko-final.RDS

value: nKO

value: Sham


title: Brain, nKO-TBI

description: nko-final.RDS


title: Brain, WT-Sham

description: wt-final.RDS


title: Brain, aKO-TBI

description: ako-final.RDS

value: aKO


title: Brain, aKO-Sham

description: ako-final.RDS


title: Transcriptome_E13.5_Brain Explant_Control-rep2_RNA-seq


title: Liver_HA.brep3_trep2

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Sequenced reads were trimmed via TrimGalore v0.4.1 using cutadapt v1.18 and FastQC v0.11.8 in paired-end mode.
Technical replicates were pooled and gene expression was quantified with Salmon v1.1.0 using the selective alignment procedure with the GENCODE vM21 gene annotation and transcript sequences on the GRCm38.p6 (GRCm38.p6 genome assembly was downloaded from the EMBL-EBI FTP site ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release _M17/GRCm38.p6.genome.fa.gz) genome sequence, adjusting for sequence and gc-content bias (-l ISR --seqBias --gcBias --validateMappings --mimicBT2).
Differential expression analysis of Mrps12ep/ep or Mrps12ha/ha mice relative to wild-type Mrps12+/+ mice was performed on a per-tissue basis (excluding mitochondrial transcripts) with DESeq2 using counts summarised by tximport and effect size estimation performed using apeglm within the lfcShrink function.
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing differential expression results and normalised counts

growth_protocol: Heterozygous mutant Mrps12+/ep and Mrps12+/ha mice were generated as described previously (10.15252/embj.2019102155). Heterozygous mutants were bred to generate homozygous mutant mice and age- and litter-mate matched wild-type (Mrps12+/+) and homozygous (Mrps12ep/ep or Mrps12ha/ha) mice were housed in standard cages (45 cm × 29 cm × 12 cm) under a 12-h light/dark schedule (lights on 7 am to 7 pm) in controlled environmental conditions of 22 ± 2 °C and 50 + 10% relative humidity.

extract_protocol:
RNA was isolated from total hearts or livers from three Mrps12+/+, Mrps12ep/ep and Mrps12ha/ha mice fed either a high-fat diet at 20 weeks, using a bead-beating RNA extraction strategy based on the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Sequencing was performed using the Illumina HiSeq platform, according to the Illumina Tru-Seq protocol.

treatment_protocol: Mic were fed a high-fat diet (19 MJ/kg, 35% of energy from carbohydrate, 42% from fat, 23% from protein; Specialty Feeds, Perth, Australia) and water was provided ad libitum.

value: Liver

value: 20 weeks


title: Liver_HA.brep3_trep3


title: EDL_mdx5_2

value: mdx


title: Transcriptome_E13.5_Brain Explant_Control-rep1_RNA-seq


title: Liver_HA.brep3_trep1


title: EDL_mdx5_1


title: EDL_mdx2_4


description: expression profile of splenic CD8+ T cells sorted from wild-type (WT) mice - replicate 2


title: cKO-4

city: beijing

first: xueyun

last: bi

address: 2 yuanmingyuan west road, haidian district, Beijing, China

institute: China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to itself assembly genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample.

source_name: mammary tumor

extract_protocol:
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: 16 weeks

tag: gender

value: female

value: mammary tumor

value: Msi1 cko


title: Liver_HA.brep2_trep3


title: EDL_wt2_2

value: wt


title: Transcriptome_E13.5_Brain Explant_Crotonate-rep2_RNA-seq

value: forebrain


title: Elastase_Day21_Replicate_2 [day21-2_S49_L006]

data_processing:
Base calling and sequencing reads de-multiplexing were performed using bcl2fastq v2.17.
Sequencing reads were checked for quality (FastQC v0.11.5), and trimmed/filtered using Trimmomatic v0.36.
Read alignment to the transcriptome sequence reference of the UCSC mm10 genome build were performed using TopHat2 v2.1.0.
Gene counts were quantified using the Python package HTSeq (v0.11.1).
Transcript abundance measures (FPKM values) were quantified using Cufflinks (v2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: Single tab-delimited data-matrix with GENE_ID, GENE_DESCRIPTION, and SAMPLE_NAMES. All numerical inputs represent FPKM values.

extract_protocol:
At least 100 ng of total RNA from both freshly harvested and cultured cells was isolated (phenol-chloroform separation of TRIzol LS) and purified using Qiagen’s RNeasy Mini Kit.
RNA library preps were prepared and multiplexed using Illumina’s TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection) and 10 nM of cDNA was used as input for high-throughput sequencing via Illumina’s HiSeq 4000 producing 51 bp paired-end reads.

treatment_protocol: All cell populations were purified via FACS. Purity mask was applied.

value: wild type

value: lung

value: endothelial cells

tag: culture status

value: freshly isolated from tissue


title: Elastase_Day21_Replicate_1 [day21-1_S48_L006]


title: Elastase_Day21_Replicate_3 [day21-3_S50_L006]


title: Elastase_Day14_Replicate_3 [day14-3_S47_L006]


title: EDL_mdx2_3


title: cKO-2


title: Elastase_Day14_Replicate_2 [day14-2_S46_L006]


title: EDL_mdx2_2


title: Elastase_Day14_Replicate_1 [day14-1_S45_L006]


title: Liver_HA.brep2_trep1


title: SOL_wt5_4


title: Ctrl-4

value: wildtype


title: Elastase_Day07_Replicate_3 [day7-3_S44_L005]


title: Ctrl-2


title: Ctrl-3


title: SOL_wt5_3


title: EDL_mdx2_1


title: Elastase_Day07_Replicate_1 [day7-1_S42_L005]


title: Liver_HA.brep1_trep1


title: Liver_HA.brep1_trep2


title: Transcriptome_E13.5_Forebrain_RNA-seq

extract_protocol:
Forebrain were dissocated with trizol to obtain total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: Elastase_Control_Replicate_2 [control-2_S40_L005]


title: Input_E13.5_Forebrain_ChIP-seq

extract_protocol:
Forebrain lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: H3K9cr_E13.5_Forebrain_ChIP-seq


title: Elastase_Control_Replicate_3 [control-3_S41_L005]


title: Liver_EP.brep3_trep3


title: SOL_wt5_1


title: SOL_wt2_4


title: Liver_EP.brep3_trep2


title: Liver_HA.brep2_trep2


title: Liver_EP.brep3_trep1


title: SOL_wt2_3


title: Elastase_Control_Replicate_1 [control-1_S39_L005]


title: cKO-1


title: H3K9ac_E13.5_Forebrain_ChIP-seq


title: Liver_EP.brep2_trep3


title: Transcriptome_E13.5_NSPCs_MS-275-rep4_RNA-seq

data_processing:
High-quality reads of RNA-seq were quantified using Salmon (v.1.0.0) and differential gene expression analysis was conducted using DESeq2(v1.26.0).
Genome_build: GRCm38

source_name: Neural stem/progenitor cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA library prep kit for Illumina® (NEB) was used with 2 ug of total RNA for the construction of sequencing libraries.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: E13.5 forebrain derived neural stem/progenitor cells (NSPCs)


title: Liver_EP.brep2_trep2


title: SOL_wt2_2


title: SOL_wt2_1


title: Liver_EP.brep2_trep1


title: SOL_mdx2_4


title: SOL_wt5_2


title: Transcriptome_E13.5_NSPCs_MS-275-rep2_RNA-seq


title: Transcriptome_E13.5_NSPCs_MS-275-rep3_RNA-seq


title: Liver_EP.brep1_trep3


title: Liver_EP.brep1_trep2


title: SOL_mdx2_2


title: SOL_mdx2_3


title: Transcriptome_E13.5_NSPCs_MS-275-rep1_RNA-seq


title: Liver_EP.brep1_trep1


title: Arc-neg_migDC_rep1

city: Hamburg

first: Manuel

middle: A

last: Friese

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

data_processing:
STAR aligment
Counting by featureCounts
DESeq2 analysis
Genome_build: mm10
Supplementary_files_format_and_content: raw ir normalized gene counts

extract_protocol:
Qiagen RNeasy Micro Kit
NEBNext UltraTM RNA Library Prep Kit for Illumina (New England Biolabs)

value: Arc/Arg3.1-eGFP mice

value: skin draining lymph nodes

value: migratory dendritic cells (migDC)

tag: cell subtype


title: Arc-pos_migDC_rep2


title: Arc-neg_migDC_rep2


title: SOL_mdx2_1


title: Liver_WT.brep3_trep3

value: Liver

value: 20 weeks


title: FDB_wt5_4


title: Transcriptome_E13.5_NSPCs_Crotonate-rep2_RNA-seq


title: FDB_wt5_3


title: Transcriptome_E13.5_NSPCs_Crotonate-rep1_RNA-seq


title: Liver_WT.brep3_trep1


title: TRAP 13-16h Input Duf replicate2

type: RNA

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

hyb_protocol: Agilent Feature Extraction Software (v 10.7.3) was used for background subtraction and LOWESS normalization.

scan_protocol: Standard Agilent protocol

data_processing: signal intensities were normalized using quantile-quantile normalization with solo2 software. Log2 fold change were computed and p-value computed using t-test

organism: Drosophila melanogaster

source_name: Drosophila embryos from stage 13-16h

label_protocol: Labelling (Low Input Quick Amp WT Labeling Kit, One-Color), hybridization and scan were done at the Genecore genomics facility at EMBL Heidelberg using agilent 8X60K arrays technology (Agilent p/n G2534-60014) starting with 10ng of purified RNA.

growth_protocol: Embryos are collected from Drosophila fly population cages grown at 25 degres for 3 hours. Plates are then collected and kept at 25 degres for 7, 10 or 13 more hours to reach desired time windows

extract_protocol: After collection, embryos are washed and lysed in order to extract and immunoprecipitate GFP-tagged polysomes and associated RNA. Trizol extraction is then performed to purify RNA

tag: origin

value: Staged collection

tag: muscle population

value: Duf


title: TRAP 13-16h Input Duf replicate3


title: Transcriptome_E13.5_NSPCs_Control-rep4_RNA-seq

tag: passages


title: Transcriptome_E13.5_NSPCs_Crotonate-rep4_RNA-seq


title: FDB_wt5_2


title: TRAP 13-16h Input Duf replicate1


title: Liver_WT.brep2_trep3

tag: tissue


title: FDB_wt5_1


title: Transcriptome_E13.5_NSPCs_Control-rep3_RNA-seq


title: Liver_WT.brep2_trep2


title: TRAP 13-16h IP Duf replicate2


title: FDB_wt2_4


title: TRAP 13-16h IP Duf replicate3


title: FDB_wt2_3


title: Transcriptome_E13.5_NSPCs_Control-rep2_RNA-seq


title: Liver_HA.brep1_trep3


title: TRAP 13-16h IP Duf replicate1


title: Transcriptome_E13.5_NSPCs_Crotonate-rep3_RNA-seq


title: Transcriptome_E13.5_NSPCs_Control-rep1_RNA-seq


title: Arc-pos_migDC_rep1


title: Liver_WT.brep3_trep2


title: Liver_WT.brep2_trep1


title: FDB_wt2_2


title: Liver_WT.brep1_trep3


title: FDB_wt2_1


title: Liver_WT.brep1_trep2


title: FDB_mdx5_3

value: mdx


title: TRAP 10-13h Input Duf replicate3

source_name: Drosophila embryos from stage 10-13h


title: TRAP 10-13h Input Duf replicate2


title: FDB_mdx5_2


title: Heart_HA.brep3_trep2

source_name: Heart

value: Heart


title: Liver_WT.brep1_trep1

source_name: Liver


title: FDB_mdx5_1


title: Heart_HA.brep3_trep1


title: Heart_HA.brep2_trep3


title: FDB_mdx2_3


title: FDB_mdx2_2


title: Heart_HA.brep2_trep2


title: FDB_mdx2_1


title: TRAP 10-13h IP Duf replicate3


title: Heart_HA.brep3_trep3


title: Heart_HA.brep2_trep1


title: TRAP 10-13h IP Duf replicate2


title: TRAP 7-10h Input Duf replicate3

source_name: Drosophila embryos from stage 7-10h

value: 7-10h AEL


title: TRAP 7-10h IP Dufreplicate3


title: TRAP 10-13h Input Duf replicate1


title: TRAP 7-10h IP Duf replicate2


title: TRAP 10-13h IP Duf replicate1


title: sgRNA1_3d_2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
FastQ files were adapter and quality trimmed with Trim Galore (v0.6.2). Trimmed sequences were then aligned to the human genome using HISAT2 (v2.1.0; no-softclipping) guided by gene models from Ensembl release 87. Aligned reads were then imported into SeqMonk (v1.47.1), and genes were quantified using the RNA-seq pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content:  table showing transcript features over mRNA. Quantitated with RNA-Seq pipeline quantitation in SeqMonk (v01.47.1) on merged transcripts counting reads over exons as raw counts. Assuming an opposing strand-specific library.

extract_protocol:
Sample collection protocol: Cells were grown in stem cell conditions (0d) and after 3 days of differentiation (3d). Then, cells were washed twice with PBS and RNA was extracted with Trizol.
Total RNA was extracted with Trizol followed by DNase treatment using TURBO DNA-free kit (Life Technologies AM1907)
RNA-seq libraries were generated from 500 ng using TruSeq Stranded mRNA library prep (Illumina, 20020594). Indexed libraries were pooled and sequenced on an Illumina HiSeq2500 sequencer in 100 bp single-end mode

value: mouse trophoblast stem cells

tag: growth media

value: TSC differentiation medium

tag: cell line

value: Bap1-overexpressing mTSCs

tag: timepoint

value: day 3


title: TRAP 7-10h Input Duf replicate1


title: sgRNA1_3d_1

tag: cell type


title: Heart_HA.brep1_trep3

tag: strain

tag: genotype


title: sgRNA1_0d_3

value: TSC complete medium

value: day 0


title: Heart_HA.brep1_trep1


title: sgRNA1_3d_3


title: TRAP 13-16h Input lms replicate2

value: lms


title: TRAP 13-16h Input lms replicate3


title: Heart_EP.brep3_trep3


title: CON-17M-2P mRNA

first: Wensi

last: Wu

address: No. 135, West Xingang Street

institute: SUN YAT-SEN UNIVERSITY

description: mRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: prefrontal cortex

growth_protocol: The Sun Yat-sen University (Guangzhou, China) provided 18-months-old male C57BL/6 mice with a weight between 45 and 50g for the experiment. The mice were randomly divided into two groups: isoflurane plus exploratory laparotomy (ISO+EL) group and control (CON) group. Each group had 13 mice. In a colony room with a temperature of 19-22°C, a humidity of 40-60%, and a light/dark cycle of 12 hours (lighting time is 07:00-19:00), 5 mice were housed in each cage with access to food and water at will. The experiments began after all the animals had adapted to the environment for two weeks.

extract_protocol:
Prefrontal cortexes were removed, flash frozen on dry ice, and RNA was harvested using miRNeasy Mini Kit (Cat# 217004, Qiagen). VAHTS Total RNA-Seq (H/M/R) Library PrepKit for Illumina (Cat#NR603-02, Vazyme) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Isoflurane anesthesia plus exploratory laparotomy has been proved to be an effective method to construct the postoperative neurocognitive disorders model. Before exploratory laparotomy, the mice were anesthetized by exposure to an oxygen chamber prefilled with 1.5% isoflurane for 30 minutes. A median incision approximately 2 centimeters in the abdomen was made to enter the abdominal cavity and explore the abdominal organs such as the liver, spleen, and intestine. Sterile 5-0 operation sutures were used to suture the peritoneum and skin. Operation was also performed under isoflurane anesthesia and lasted 30 minutes. At the end of operation and every day within 3 days after operation, 2.5% lidocaine cream was applied to the incision to alleviate the postoperative pain, and povidone iodine solution was applied to prevent infection. Mice in the control group were not treated with anesthesia or operation.

value: prefrontal cortex

value: 18 months

value: wild type

tag: treatment

value: untreated


title: CON-17M-3P mRNA

description: mRNA


title: Heart_HA.brep1_trep2

value: 20 weeks


title: Elastase_Day07_Replicate_2 [day7-2_S43_L005]

value: lung

value: endothelial cells

value: freshly isolated from tissue


title: TRAP 7-10h IP Duf  replicate1

value: Staged collection

value: Duf


title: CON-17M-1P mRNA

description: mRNA


title: TRAP 7-10h Input Duf replicate2

value: 7-10h AEL


title: Preterm birth_blood_P5617

type: genomic

city: Seoul

first: Young Ju

last: Kim

address: 1071, Anyangcheon-ro, Yangcheon-gu

country: South Korea

institute: Ewha Womans University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 BeadChip using standard Illumina protocol

scan_protocol: HiScan SQ system (Illumina)

data_processing: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Preterm birth_blood

extract_protocol: genomic DNA was extracted and purified from whole blood samples using Qiagen DNeasy Kit according to standard instructions

tag: sample group

value: Preterm birth

value: blood


title: TRAP 13-16h Input lms replicate1


title: Term birth_blood_4974_2

source_name: Term birth_blood

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 BeadChip using standard Illumina protocol

value: Term birth


title: sgRNA1_0d_1

value: mouse trophoblast stem cells

value: TSC complete medium

value: Bap1-overexpressing mTSCs


title: Heart_EP.brep3_trep2

value: Heart


title: SUr-17M-3P mRNA

description: mRNA

value: prefrontal cortex

value: 18 months

value: treated with isoflurane  anesthesia and surgery


title: sgRNA1_0d_2

value: day 0


title: TRAP 13-16h IP lms replicate3

value: lms


title: NT-sgRNA_3d_3

value: TSC differentiation medium

value: wild type  mTSCs

value: day 3


title: SUr-17M-2P mRNA

description: mRNA

value: wild type


title: SUr-17M-1P mRNA

description: mRNA


title: NT-sgRNA_3d_1


title: CON-17M-3P miRNA

description: miRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

value: untreated


title: Heart_EP.brep2_trep3

value: 20 weeks


title: Heart_EP.brep2_trep2


title: Term birth_blood_4728

value: blood


title: Term birth_blood_5023

value: Term birth


title: CON-17M-2P miRNA

description: miRNA


title: Term birth_blood_5022


title: Preterm birth_blood_4773

value: Preterm birth


title: TRAP 13-16h IP lms replicate1

value: Staged collection


title: Term birth_blood_4705


title: NT-sgRNA_3d_2

value: mouse trophoblast stem cells


title: NT-sgRNA_0d_2

value: TSC complete medium


title: Heart_EP.brep1_trep3

value: Heart


title: NT-sgRNA_0d_3


title: Heart_EP.brep2_trep1


title: Preterm birth_blood_1069


title: TRAP 10-13h Input lms replicate3


title: TRAP 13-16h IP lms replicate2


title: Preterm birth_blood_4539


title: Heart_EP.brep1_trep2


title: CON-17M-1P miRNA

description: miRNA

value: prefrontal cortex

value: 18 months


title: NT-sgRNA_0d_1

value: day 0


title: TRAP 10-13h Input lms replicate2

value: lms


title: TRAP 10-13h IP lms replicate3


title: Preterm birth_blood_4201


title: SUr-17M-3P miRNA

description: miRNA

value: treated with isoflurane  anesthesia and surgery


title: Heart_EP.brep3_trep1


title: Heart_EP.brep1_trep1


title: Heart_WT.brep3_trep3


title: SUr-17M-2P miRNA

description: miRNA


title: Heart_WT.brep3_trep2


title: Expt2: G35_4

first: Matthew

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Mus musculus retina post-natal day 49 Rs1 KO AAV8-scRS/IRBPhRS  Day 35 replicate 4

data_processing:
Fastq files were generated from reads passing chastity filter and used for further analysis. Illumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.36.
Transcript level quantitation was performed using Kallisto v0.43.0 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl ftp site. Gene level quantification was generated by summarization of the transcript level quantitation using tximport v1.2.0 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR v3.16.5.
Genome_build: GRCm38.p4 with Ensembl v84

source_name: retina

extract_protocol:
Total RNA was extracted according to QIAzol lysis based reagent  miRNA Mini Kit ( Qiagen Inc, Germantown, MD, USA). Qualitative and quantitative analysis of extracted RNA samples were carried out with a 2100 Bioanalyzer Nano Chip (Agilent Technologies Genomics, Santa Clara, CA USA). RNA Integrity Number (RIN) of extracted RNA samples applied for RNA Seq ranged between the values 8.4-9.4 and RNA samples were stored at -80°C.
Strand-specific mRNA sequencing libraries were constructed from 100 ng of total RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Self-complementary AAV8-scRS/IRBPhRS (AAV8-RS)1 delivered human retinoschisin (RS1) cDNA under control of an RS1 promoter and interphotoreceptor binding protein IRBP enhancer, produced at the Children’s Hospital of Philadelphia, Philadelphia, PA (GMP Lot # A8FP1 A1407C) (Cukras et al., 2018). Vector was diluted to 2e12 vg/ml with excipient, and 1 µl of vector (2e9 vg/eye) was injected subretinally in anesthetized Rs1-KO male mice at PND14. As negative controls, other Rs1-KO mice received 1 µl of AA8-Null vector (2e9 vg/eye). Null AAV8 vector has the AAV8 capsid, ITR from AAV2, CMV promoter, but no transgene (produced by Vector Biolabs, Malvern, PA).

value: retina

value: post-natal day 49

value: Rs1 KO

tag: day post-delivery

value: Day 35

tag: biological replicate

value: replicate 4


title: Expt2: G35_2

description: Mus musculus retina post-natal day 49 Rs1 KO AAV8-scRS/IRBPhRS  Day 35 replicate 2

tag: age

value: replicate 2


title: SUr-17M-1P miRNA

description: miRNA

value: wild type


title: Expt2: G35_1

description: Mus musculus retina post-natal day 49 Rs1 KO AAV8-scRS/IRBPhRS  Day 35 replicate 1

value: replicate 1


title: CON-17M-3P circRNA

description: circular RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include SRPBM values for each Sample

value: untreated


title: TRAP 10-13h IP lms replicate1

value: Staged collection


title: Expt2: C35_3

description: Mus musculus retina post-natal day 49 Rs1 KO AAV8-Null Day 35 replicate 3

value: replicate 3


title: Heart_WT.brep2_trep3

value: Heart

value: 20 weeks


title: CON-17M-2P circRNA

description: circular RNA

value: prefrontal cortex

value: 18 months


title: TRAP 7-10h Input lms replicate2

value: 7-10h AEL

value: lms


title: TRAP 10-13h IP lms replicate2


title: TRAP 7-10h Input lms replicate1


title: CON-17M-1P circRNA

description: circular RNA


title: Heart_WT.brep2_trep1


title: Expt2: C35_1

description: Mus musculus retina post-natal day 49 Rs1 KO AAV8-Null Day 35 replicate 1

value: retina


title: SUr-17M-3P circRNA

description: circular RNA

value: treated with isoflurane  anesthesia and surgery


title: Expt2: G35_3

description: Mus musculus retina post-natal day 49 Rs1 KO AAV8-scRS/IRBPhRS  Day 35 replicate 3

value: post-natal day 49

value: Rs1 KO


title: SUr-17M-2P circRNA

description: circular RNA


title: Heart_WT.brep1_trep3


title: Expt2: G7_4

description: Mus musculus retina post-natal day 21 Rs1 KO AAV8-scRS/IRBPhRS  Day 7 replicate 4

value: post-natal day 21

value: Day 7

value: replicate 4


title: Heart_WT.brep3_trep1


title: TRAP 7-10h IP lms replicate3


title: SUr-17M-1P circRNA

description: circular RNA

value: wild type


title: TRAP 7-10h Input lms replicate3


title: TRAP 7-10h IP lms replicate2


title: Heart_WT.brep1_trep2


title: TRAP 10-13h Input lms replicate1


title: Heart_WT.brep2_trep2


title: Expt2: G7_2

description: Mus musculus retina post-natal day 21 Rs1 KO AAV8-scRS/IRBPhRS  Day 7 replicate 2

value: replicate 2


title: Heart_WT.brep1_trep1


title: Expt2: C35_2

description: Mus musculus retina post-natal day 49 Rs1 KO AAV8-Null Day 35 replicate 2

value: Day 35


title: TRAP 13-16h Input S59 replicate3

value: Staged collection


title: Expt2: C7_4

description: Mus musculus retina post-natal day 21 Rs1 KO AAV8-Null Day 7 replicate 4


title: Expt2: C7_3

description: Mus musculus retina post-natal day 21 Rs1 KO AAV8-Null Day 7 replicate 3

value: replicate 3


title: TRAP 13-16h Input S59 replicate1


title: Expt2: G7_3

description: Mus musculus retina post-natal day 21 Rs1 KO AAV8-scRS/IRBPhRS  Day 7 replicate 3


title: Expt2: C7_1

description: Mus musculus retina post-natal day 21 Rs1 KO AAV8-Null Day 7 replicate 1

value: replicate 1


title: PCLS, high dose (D4-HD)

city: Hannover

first: Stella Marie

last: Reamon-Buettner

address: Nikolai-Fuchs Strasse1

department: Preclinical Pharmacology & In Vitro Toxicology

institute: Fraunhofer-ITEM

description: miRNA data from PCLS treated with high dose

hyb_protocol: Labeled RNA was hybridized to GeneChip Array 4.0 for 18 h at 48°C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0), using Affymetrix default settings and RMA normalization (using Summarization Method: RMA+DABG (All organisms i.e. human, mouse, rat)).

label: biotin

source_name: precision cut lung slices (PCLS)

label_protocol: Total RNA (100 ng) was  labeled with biotin using the flashtag HSR RNA labeling kit (ThermoFisher Scientific).

extract_protocol: RNA including miRNA was isolated using a modified protocol described by Niehof et al. 2017 [BMC Res Notes 10:121]. The protocol is based on a separation of lysis and precipitation steps, and a clean-up procedure with a MagMaxTM miRVana magnetic beads.

treatment_protocol: PCLS samples were exposed to low, medium, and high dose of a substance that underwent risk assessment analysis. Treatment was undertaken on three consecutive days for 1 hour each day. In between exposures, the substance was removed and the PCLS were post-incubated in the medium for 23 h.

tag: donor id

tag: gender

value: Male

value: lung

value: PCLS treated with high dose of methyl acrylate


title: Expt1: P21_KO_3

description: Mus musculus retina post-natal day 21 Rs1 KO replicate 3


title: Expt1: P21_KO_2

description: Mus musculus retina post-natal day 21 Rs1 KO replicate 2


title: TRAP 13-16h Input S59 replicate2

tag: origin


title: TRAP 13-16h IP S59 replicate2

tag: muscle population


title: SAMPLE 4_HT-29 treated with GANT61 48hr

city: NANCAHNG

first: Shiwen

last: Luo

state: JiangXi

address: 17 Yong Wai street

department: Center for experimental medicine

institute: The Frist Affiliated Hospital of Nanchang University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Each biotinylated cRNA (750 ng) was hybridized to an Illumina Human HT expression BeadChip V4 (Illumina Inc., San Diego, CA). Following standard washing steps and staining with Streotavidin-Cy3, the arrays were scanned using an Illumina BeadArray Reader.

growth_protocol: Cells were cultured as recommended by the supplier in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA from each sample was isolated by TRIzol (Invitrogen) according to the manufacturer's instructions. Double-stranded cDNA and biotin-labeled cRNA were synthesized from RNA (300 ng) using an Illumina TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX) according to the manufacturer’s protocol

treatment_protocol: HT-29 cells were treated with GANT61 (20 μM for 48 hr), Cyclopamine (20μM for 48 hr) and control vehicle DMSO, Tomatidine, respectively.

value: human colorectal adenocarcinoma cell line with epithelial morphology.

tag: cell phenotype

value: adherent

tag: treated with

value: GANT61 (20 μM for 48 hr)


title: TRAP 10-13h Input S59 replicate2


title: PCLS, medium dose (D4-MD)

description: miRNA data from PCLS treated with medium dose

tag: tissue

value: PCLS treated with medium dose of methyl acrylate


title: Expt1: P21_KO_1

description: Mus musculus retina post-natal day 21 Rs1 KO replicate 1

value: retina

value: Rs1 KO


title: Expt2: C7_2

description: Mus musculus retina post-natal day 21 Rs1 KO AAV8-Null Day 7 replicate 2

value: post-natal day 21

value: Day 7


title: TRAP 13-16h IP S59 replicate3


title: PCLS, high dose (D3-HD)

value: Female


title: TRAP 10-13h Input S59 replicate1


title: TRAP 13-16h IP S59 replicate1


title: Expt1: P21_WT_3

description: Mus musculus retina post-natal day 21 wild-type replicate 3

value: wild-type


title: TRAP 10-13h Input S59 replicate3


title: PCLS, medium dose (D3-MD)


title: PCLS, medium dose (D2-MD)


title: PCLS, high dose (D2-HD)


title: PCLS, low dose (D2-LD)

description: miRNA data from PCLS treated with low dose

value: PCLS treated with low dose of methyl acrylate


title: TRAP 7-10h IP lms replicate1

value: Staged collection

value: 7-10h AEL

value: lms


title: SAMPLE 1_HT-29 treated with DMSO 48hr

tag: cell line

value: control vehicle DMSO


title: TRAP 10-13h IP S59 replicate3


title: PCLS, low dose (D4-LD)

value: Male

value: lung


title: Expt1: P21_WT_1

description: Mus musculus retina post-natal day 21 wild-type replicate 1

value: replicate 1


title: Expt1: P12_KO_3

description: Mus musculus retina post-natal day 12 Rs1 KO replicate 3

value: post-natal day 12

value: replicate 3


title: SAMPLE 2_HT-29 treated with Cyclopamine 48hr

value: human colorectal adenocarcinoma cell line with epithelial morphology.

value: adherent

value: Cyclopamine (20μM for 48 hr)


title: Expt1: P12_KO_2

description: Mus musculus retina post-natal day 12 Rs1 KO replicate 2

value: retina

value: Rs1 KO

value: replicate 2


title: Expt1: P21_WT_2

description: Mus musculus retina post-natal day 21 wild-type replicate 2

value: post-natal day 21

value: wild-type


title: TRAP 10-13h IP S59  replicate1

value: Staged collection


title: Expt1: P12_KO_1

description: Mus musculus retina post-natal day 12 Rs1 KO replicate 1


title: SAMPLE 3_HT-29 treated with DMSO 48hr


title: KAT2A-KO2

city: Shanghai

first: Li

address: 966 Middle Huaihai Road

department: Department of Pharmacy

institute: Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University

description: Caki-2 biological replicate 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
STAR is used to align clean reads to reference genome.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: hg38
Supplementary_files_format_and_content: txt file of differentially expressed genes of  DEGseq2

source_name: Kidney

growth_protocol: The human RCC cell lines (Caki-2, SLR-21, 786-O and A498)  were derived from the American Type Culture Collection (ATCC). The cells were maintained in RPMI-1640 (Gibco, Carlsbad, CA, USA) containing 10% FBS (Gibco, Carlsbad, CA, USA) and 100 µg/ml streptomycin under 37 ℃ with 5% CO2.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment protocal: The KAT2A was knocked out via CRISPR/Cas9 method in Caki-2.

value: knockout of KAT2A

value: ccRCC


title: KAT2A-WT2

description: Caki-2 biological replicate 2

value: control


title: KAT2A-WT1

description: Caki-2 biological replicate 1


title: KAT2A-KO1

description: Caki-2 biological replicate 1


title: PCLS, medium control (H25-30)

description: miRNA data from PCLS treated with medium control

value: Female

value: PCLS treated with medium control


title: PCLS, low dose (D3-LD)

value: lung

value: PCLS treated with low dose of methyl acrylate


title: TRAP 7-10h Input S59 replicate2

value: 7-10h AEL


title: TRAP 7-10h Input S59  replicate3


title: TRAP 7-10h Input S59 replicate1


title: PCLS, medium control (H26-36)


title: hPASMC_control_rep1

city: Indianapolis

first: Robert

last: Stearman

state: IN

address: 950 W Walnut St

department: Medicine/Pulmonary

institute: Indiana Univeristy School of Medicine

data_processing:
FastQC/MultiQC v0.11.5
STAR aligner v2.5
NGSUtils/bamutils v0.5.9
subread/feature Counts v1.5.1
edgeR v3.22.5
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text file includes raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file includes Gene_Symbol, Gene_Description, FoldChange(SPHK1_OE/control), log2FoldChange(SPHK1_OE/control), p-value, q-value(FDR)

source_name: primary cell culture

growth_protocol: Human Pulmonary Artery Smooth Muscle cells (hPASMCs) were obtained from Lonza. Cells were cultured in SMGM2 containing growth supplements and 5% FBS (Lonza; complete medium) at 37°C in 5% CO2 in a humidified tissue culture incubator.

extract_protocol:
Total RNA was purified from transfected hPASMCs over-expressing SPHK1, as well as transfected vector DNA control, by using the RNeasy Plus Mini Kit (RNA > 200 nucleotides: Qiagen, Germantown, MD). Average RIN value was 9.4.
KAPA mRNA Hyperprep Kit

treatment_protocol: For transfection, 300,000 hPASMCs were cultured on 6-well plates followed by transfection of 3.75mg of plasmid using Xfect transfection reagent (Takara, Mountain View, CA) according to the manufacturer’s protocol. All experiments were performed in low passage cells (≤8). Cells were transfected in complete medium. The medium was replaced with complete medium after 4 hours, and the cells were collected after 48 hours and stored at -80 degrees C.

value: lung pulmonary artery

value: pulmonary artery smooth muscle cells

tag: genotype/variation


title: Expt1: P12_WT_3

description: Mus musculus retina post-natal day 12 wild-type replicate 3

value: post-natal day 12

value: replicate 3


title: PCLS, medium control (H17-16)


title: PCLS, medium control (H20-21)

value: Male


title: PCLS, medium control (H24-27)


title: PCLS, medium control (H11-6)


title: TRAP 7-10h IP S59 replicate2


title: HLO_OA_MGL

city: Cincinnati

first: Andrew

last: Dunn

state: Ohio

address: 3333 Burnet Ave R3.543

department: Gastroenterology

institute: Cincinnati Children's Hospital Medical Center

description: Human Liver Organoid tagged with POLYseq barcoding library

data_processing:
Base call conversion was performed using bcl2fastq v2.20.0
FASTQ files were aligned to either hg19 or mm10 v2 genomes using CellRanger v3.1.0
Read depth normalization, scailing, variable feature identification, PCA analysis, cluster identification, tSNE and UMAP clustering, and hashing demultiplexing was performed using Seurat v3.1 (HLO) / v3.2.2 (POLYseq / TotalSeq). Differential expression was performed using DESeq2 v1.28.0. Pathway analysis was performed by GAGE v2.38.3 on cell clusters normalized by the number of reads and log2 transformed. Pathway visualization was conducted through Pathview v1.28.1 using normalized, log2 transformed data.
Genome_build: hg19 / mm10 v2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene / oligo barcode of every cell.

source_name: Human liver organoid

growth_protocol: For HLOs: iPSCs were seeded into 6-well plates (Corning) in mTeSR supplemented with Y-27632 and Laminin-511. Medium was changed to mTeSR alone the following day. Medium was switched to RPMI-1640 (Life Technologies, USA) containing 100 ng/ml Activin A (R&D Systems, USA) and 50 ng/ml bone morphogenetic protein 4 (BMP4; R&D Systems) on the second day. This constitutes day 1 (D1) of differentiation. Medium was switched to RPMI-1640 + 100 ng/ml Activin A + 0.2 % KnockOut Serum Replacement (KOSR; ThermoFisher Scientific) on D2. Medium was switched to RPMI-1640 + 100 ng/ml Activin A + 2.0 % KOSR on D3. Medium was switched to Advanced DMEM/F-12 + B-27 (Gibco, USA) + N2 (Gibco, USA) + 500 ng/ml fibroblast growth factor 4 (FGF-4; R7D Systems) and 3 µM CHIR99021 (R&D Systems) for D4-6, changed daily. A single cell suspension was isolated on D7 using Accutase. Cells were washed and resuspended in growth factor Matrigel at 50,000 cells / 50 µl. Into 6-well VWR plates were plated 50 µl drops. Medium was switched to Enrichment Medium (EP): Advanced DMEM/F12 (Gibco, USA) + 2 % B-27 (Gibco, USA) + 1 % N2 (Gibco, USA) + 1 % HEPES (1 M, Gibco, USA) + 1 % Pen/Strep (ThermoFisher Scientific) + 1 % L-glutamine (ThermoFisher Scientific) + 3 µM CHIR99021 (R&D Systems) + 5 ng/ml FGF2 (R&D Systems) + 10 ng/ml VEGF (Life Technologies) + 20 ng/ml EGF (R&D Systems) + 0.5 µM A83-01 (Tocris) + 50 µg/ml ascorbic acid (Sigma-Aldrich) for D7-10, changed on D7 and D9. Medium was switched to Advanced DMEM/F12 (Gibco, USA) + 2 % B-27 (Gibco, USA) + 1 % N2 (Gibco, USA) + 1 % HEPES (1 M, Gibco, USA) + 1 % Pen/Strep (ThermoFisher Scientific) + 1 % L-glutamine (ThermoFisher Scientific) + 2 µM Retinoic acid (Sigma, USA) for D11-14, changed on D11 and D13. Medium was switched to hepatocyte culture medium (HCM; Lonza, USA) + 10 ng/ml hepatocyte growth factor (HGF; PeproTech, USA) + OSM and changed every other day. HLOs were used between D21 – D24. For cell line culture: 3T3 and B16-F10 were maintained in DMEM + GlutaMAX + 10% FBS, Mouse ES cells were maintaned feeder-free on gelatin in serum-free ES medium + 2i + LIF, ESH9 was maintained feeder-free in mTeSR, HUVECs were maintaned in Loza EGM-2, HepG2 was maintained in MEM + 10% FBS, MEG-01 was maintained in RMPI 1640 + 10% FBS.

extract_protocol:
Samples were digested using accutase / TrypLE Express into single cell suspensions, resuspended in PBS or DMEM/F-12 + 2 % FBS, and filtered by a 40 µm mesh.
Single cell suspensions were immediately run on the 10x scRNAseq platform following digestion using the Chromium Single Cell 3' v3 (HLOs) or Next GEM 3' v3.1 (POLYseq / Totalseq) kits.

treatment_protocol: HepG2 was subject ot high glucose using DMEM + GlutaMAX + 10% FBS for 3 days.

value: 500 uM Sodium Oleate + 0.5 % BSA + 200 uM Resmetirom (MGL-3196) (3 Days)


title: HLO_OA

value: 500 uM Sodium Oleate + 0.5 % BSA (3 Days)


title: PCLS, medium control (D4)


title: Expt1: P12_WT_1

description: Mus musculus retina post-natal day 12 wild-type replicate 1

value: retina

value: wild-type

value: replicate 1


title: Expt1: P12_WT_2

description: Mus musculus retina post-natal day 12 wild-type replicate 2

value: replicate 2


title: HLO

value: Untreated


title: Pan-Acetyl-H4 ChIP-seq from colorectal carcinoma cells

status: Public on Jun 21 2021

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

data_processing:
Illumina bcl2fastq version 2.17.1.14: basecalling
Mapping with bowtie2 to the hg38 genome (ENSEMBL release 87)
Conversion of bam to bigwig with bedtools
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bigWig files

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) [Invitrogen] supplemented with 10% fetal bovine serum (FBS) [Biological Industries].

extract_protocol:
ChIP protocol and DNA purification with GFX Kit [GE Healthcare Life Sciences Ref.28-9034-71]
Single-end Illumina

treatment_protocol: No treatment

tag: chip antibody

value: Acetylated H4, abcam ab177790

tag: ip or input

value: IP


title: TRAP 7-10h IP S59 replicate3

value: Staged collection


title: Ikba ChIP-seq from colorectal carcinoma cells

value: IκBα, abcam ab32518


title: NHEK-Neo cells incubated with 1 mg/ml of eESM-supplemented medium

city: Nagoya

first: Kyohei

last: Furukawa

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

hyb_protocol: 11 ug of cRNA were hybridized onto the array chip at 45 °C for 16 h and stained with streptavi-din-phycoerythrin using GeneChip™ Fluidics Station 450

scan_protocol: The image data was detected with GeneChip™ Scanner 3000.

data_processing: The data were converted to CEL file format using Affymetrix GeneChip® Command Console. The data were further normalized with Transcriptome Analysis Console.

label_protocol: The 100 ng of pooled RNA isolated from mouse skin samples were reverse-transcribed to single-strand cDNA using Genechip™ 3’ IVT Express Kit

growth_protocol: The cells were cultured at 37 °C under 95% air/5% CO2 with KGM™ Gold Keratinocyte Growth Medium BulletKit™, containing KBM™ Gold™ Basal Me-dium and KGM™ Gold™ SingleQuots™ supplements. The medium was replaced every 2 days during the experimental periods.

extract_protocol: RNA extraction from cell sample was performed using Nucleospin® RNA plus kit

treatment_protocol: One day after the Cell seeding, the medium were replaced with Control medium or  eESM (1 mg/ml) containing medium at 2 days’ interval and cultured for 4 days.

value: NHEK-Neo

tag: growth


title: YB3

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

country: Canada

institute: McGill University

description: replicate 3

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/077/395/GCA_001077395.1_ASM107739v1/GCA_001077395.1_ASM107739v1_genomic.fna.gz
Supplementary_files_format_and_content: excel, expression profiles: miRNAs shed by two D. immtitis strains, L3 and L4 stages in vitro.

organism: Dirofilaria immitis

source_name: L4 Yazoo

growth_protocol: The two D. immitis strains used were Missouri-2005 (susceptible to macrocyclic lactones) and Yazoo-2013 (resistant to macrocyclic lactones). Fresh culture media was added to well plates and L3s were added into trans-well plates and incubated in a 5 % CO2 incubator at 37 °C. Supernatant was collected every 48 h for two weeks. Supernatant collected on days 2 and 4 of culture were designated L3-derived supernatants; and those collected on days 8 and 12 were L4-derived supernatants. . In total, there were three experimental replicates per larval stage and strain.

extract_protocol:
Total RNA Norgen plasma/serum RNA purification midi kit (Cat. 56100).
Illumina Truseq Small RNA Preparation

treatment_protocol: Collected culture media were stored at -80° before RNA extraction.

tag: source

value: in vitro culture media, secretions

tag: Stage

tag: strain

value: Yazoo


title: Expt2: G7_1

city: Bethesda

description: Mus musculus retina post-natal day 21 Rs1 KO AAV8-scRS/IRBPhRS  Day 7 replicate 1

value: post-natal day 21

tag: genotype

value: Rs1 KO

tag: treatment

tag: day post-delivery

value: Day 7

tag: biological replicate


title: MB1

description: replicate 1

source_name: L4 Missouri

value: Missouri


title: MB2

description: replicate 2


title: MA1

description: replicate 1

source_name: L3 Missouri


title: MA3

description: replicate 3


title: MA2

description: replicate 2


title: PCLS, medium control (H13-10)

tag: donor id

tag: gender

value: Male

tag: age

value: lung

value: PCLS treated with medium control


title: MB3

description: replicate 3


title: PCLS, medium control (D3)

value: Female


title: YA2

description: replicate 2

source_name: L3 Yazoo


title: YA1

description: replicate 1


title: YA3

description: replicate 3


title: YB1

description: replicate 1


title: H4K12Ac ChIP-seq from colorectal carcinoma cells

value: H4K12ac, active Motif 61527


title: NHEK-Neo cells incubated with control medium

value: incubated with control medium


title: WT_Differentiated_1 [WT_1_DF]

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

institute: Francis Crick Insititue

data_processing:
The RSEM package (version 1.2.11) and Bowtie2 were used to align reads to the mouse Ensembl GRCm38 transcriptome.
Raw counts were normalised and differential expression analysis was performed with the DESeq2 package (version 1.18.1) within the R programming (version 3.4.3)
Genome_build: mouse Ensembl GRCm38
Supplementary_files_format_and_content: Tab delimited text files containing normalised data. Rows represent Ensembl mouse genes and columns represent individual samples.

extract_protocol:
Colon crypts were isloated with 2mM EDTA wash. Crypts embedded in matrigel were cultured in stem cell enrichment media containing Wnt-3A, Noggin, Rspondin-1 and EGF. Resulting organoids were allowed to differentiate in Wnt-3A free media for 3 days. RNA was extracted from stem cells and differentiated organoids.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: WT

value: Colon

tag: cell type

value: Orgnaoids

tag: culture condition

value: ENR medium


title: PCLS, medium control (D2)

tag: tissue


title: WT_Differentiated_3 [WT_3_DF]

tag: genotype/variation


title: YB2

description: replicate 2


title: WT_Differentiated_2 [WT_2_DF]


title: TRAP 7-10h IP S59 replicate1

tag: origin

value: Staged collection

value: 7-10h AEL

tag: muscle population


title: p-Ikba ChIP-seq from colorectal carcinoma cells

tag: cell line

tag: chip antibody

value: P-IκBα, cell signaling 9246

tag: ip or input

value: IP


title: WT_Stem cells_3 [WT_3_SC]

source_name: WT_Stem cells

value: WENR medium


title: Input from colorectal carcinoma cells

value: input


title: WT_Stem cells_1 [WT_1_SC]


title: AhR-/-_Differentiated_3 [AhR KO_3_DF]

value: AhR deficient


title: AhR-/-_Stem cells_3 [AhR KO_3_SC]

source_name: AhR-/-_Stem cells


title: AhR-/-_Stem cells_1 [AhR KO_1_SC]


title: AhR-/-_Differentiated_2 [AhR KO_2_DF]


title: AhR-/-_Differentiated_1 [AhR KO_1_DF]


title: AF00118

city: Los Angeles

first: Miguel

last: Quintero

institute: Cedars Sinai medical center

data_processing:
The circulating e-miRNA expression levels of the baseline blood samples of the  matched subjects were measured and processed through the workflow mentioned above
cut-off value of 500  was set as a minimal valid read counts per miRNA to eliminate the noise that had been produced in sequencing.  Expression data were further normalized using the DESeq method
Principal component analysis (PCA) was performed to reduce data dimensionality.
The principal components  (PCs) accounting for 95% of the total variance of the data were selected and calculated for each patient
The association between the PCs and recurrent ischemic events were evaluated via Mann-Whitney tests with  Bonferroni correction to determine the predictive PC for recurrent ischemic events and reduce the false discovery  rate; binary logistic model was then generated to calculate the sensitivity and specificity via a receiver operative  curve (ROC).
To further scale the contribution of each e-miRNA to the predictive PC, the absolute coefficients  of all the e-miRNAs in the PC formula were distributed in a quartile box plot, and the e-miRNAs with the coefficients  above 75% quartile were selected.
To interpret the regulatory effect of these selected e-miRNAs, functional  analysis and miRNA target analysis was carried out in Ingenuity Pathway Analysis (IPA) environment to mine  the significantly associated biological functions and downstream molecules
The up- and down-regulation of the  specific e-miRNA expression profile in the non-responders on the relevant biological functions and molecules  were predicted via a build-in Molecular Activity Predictor (MAP) tool
The networks, functional analyses, and  miRNA target analyses were generated through the use of IPA (QIAGEN Inc, https://www.qiagenbio-informatics.  com/products/ingenuity-pathway-analysis). A sensitivity analysis was conducted to address the potential impact  of including TIA in the primary endpoint
The expression levels of the relevant e-miRNAs, identified as described  above, were compared between the whole cohort and including exclusively subjects with stroke.
The statistical analyses including PCA and binary logistic regression analysis were performed in JMP (version  13). A two-tailed p value of <0.05 was considered statistically significant. The statistical significance of the  analysis in IPA environment was calculated by causal analytics algorithms which are based on a “master” network  derived from the Ingenuity Knowledge Base
Supplementary_files_format_and_content: Matrix table with raw gene counts for every miRNA and every sample for each group (responder to medical management and non responder)

source_name: Exosomal miRNA

extract_protocol:
Plasma sample with the volume of 500 μl was centrifuged at 1500 rpm for 5 min to remove residual cells and debris. The supernatant was transferred to a new 1.5 ml Eppendorf tube for exosome isolation. ExoQuick (Cat# EXOQ5A-1, System Biosciences, Palo Alto, CA) was added to the supernatant at 1:4 ratio (ExoQuick:Supernatant), mixed gently, and allowed to incubate for 30 min at 4 °C. After the incubation, the admixture was centrifuged at 1500 rpm for additional 30 min to recover the exosomes. Using ExoQuick-based precipitation techniques for exosome isolation and recovery is broadly recognized for better specific exosomal miRNAs recovery and lower intra-assay coefficients of variability (CVs) compared to other commercial exosome isolation kits, and is also backed in nearly 600 peer-review citations.
Exosomes extracted from the samples were processed for total RNA isola- tion using the SeraMir Exosome RNA Purification Column kit (Cat #RA808A-1, System Biosciences, Palo Alto, CA) according to the manufacturer’s instructions. For each sample, 1 μl of the final RNA eluate was used for meas- urement of small RNA concentration by Agilent Bioanalyzer Small RNA Assay using Bioanalyzer 2100 Expert instrument (Agilent Technologies, Santa Clara, CA). A small RNA concentration of 200 pg/ul was considers as a cutoff for subsequent library preparation.
Small RNA libraries were prepared for sequencing using standard Illumina protocols. Small Small RNA libraries were constructed with the CleanTag Small RNA Library Preparation Kit (Cat# L-3206, TriLink BioTechnologies, San Diego, CA) according to the manufacturer’s protocol
The final purified library was quanti- fied with High Sensitivity DNA Reagents (PO# G2933-85004, Agilent Technologies, Santa Clara, CA) and High Sensitivity DNA Chips (PO# 5067–4626, Agilent Technologies, Santa Clara, CA).
The libraries were pooled, and the 140 bp to 300 bp region was size selected on an 8% TBE gel (Ref# EC6215, Invitrogen by Life Technologies, Grand Island, NY). The size selected library was quantified with High Sensitivity DNA 1000 Screen Tape (PO #5067–5584, Agilent Technologies, Santa Clara, CA), High Sensitivity D1000 reagents (PO# 5067–5585, Agilent  Technologies, Santa Clara, CA), and the TailorMix HT1 qPCR assay (Cat# TM-505, SeqMatic, Union City, CA),  followed by a NextSeq High Output single-end sequencing run at SR75 using NextSeq 500/550 High Output v2  kit (Cat #FC-404-2005, Illumina, San Diego, CA) according to the manufacturer’s instructions.
Then, the open-source tools including FastqMcf, part  of the EA-utils package, and PRINSEQ were used to detect and remove N’s at the ends of reads, trim sequencing  adapters, and filter reads for quality and length. The improved set of sequence reads were mapped to the  reference genome using Bowtie and expression levels for exosomal miRNAs were calculated using R statistical  environment

tag: disease state

value: intracranial atherosclerosis

value: Serum

tag: phenotype

value: Responder to medical management


title: AF00229

value: Female


title: AF00119

value: Male


title: AF00230


title: ERSIAS0020

value: Non responder to medical management


title: ERSIAS0012


title: ERSIAS0009


title: AF00131


title: ERSIAS0018


title: AF00111


title: AF006


title: AF00120


title: ERSIAS0019


title: AF00123


title: WT_Stem cells_2 [WT_2_SC]

value: WT


title: AF00224


title: AhR-/-_Stem cells_2 [AhR KO_2_SC]

value: Colon


title: ERSIAS0004


title: AF00102


title: ALCL Primary #208_Input

city: Vienna

first: Olaf

last: Merkel

address: Spitalgasse 23

department: Department of Pathology

institute: Medical University of Vienna

data_processing:
Reads were aligned to the human genome (hg19) using bowtie with parameters –k 2 –m 2 –best and –l set to the read length. For visualization, WIG files were created from aligned ChIP-seq read positions using MACS with parameters –w –S –space=50 –nomodel –shiftsize=200 to artificially extend reads to be 200bp and to calculate their density in 50bp bins. Read counts in 50bp bins were then normalized to the millions of mapped reads, giving reads per million (rpm) values. WIG and TDF files were visualized in the IGV 2.4.6 genome browser.
Regions enriched in ChIP-seq signal were identified using MACS with corresponding control and parameters –keep-dup=auto and –p 1e-9. The distribution of peaks into other genomic features was determined by overlapping peaks with SEs, typical enhancers, promoters, and gene bodies, in this order. SEs and typical enhancers from the same cell type as the TF ChIP-seq were used. Promoters were defined as 4kb windows centered on the transcription start sites of RefSeq genes. Gene bodies were defined as the remaining portion of genes longer than 2kb from 2kb downstream of the promoter to the transcription end site.
SEs were identified using ROSE (https://bitbucket.org/young_computation/rose) algorithm with some modifications. Reads overlapping ENCODE blacklist regions were removed using bedtools intersect.  From the remaining reads, two sets of peaks of H3K27ac were identified using MACS with parameter sets –keep-dup=auto –p 1e-9 and –keep-dup=all –p 1e-9. H3K27ac peaks were stitched computationally if they were within 12500bp of each other, though peaks fully contained within +/- 2000bp from a RefSeq promoter were excluded from stitching.
These stitched enhancers were ranked by their H3K27ac signal (length * density) with input signal subtracted. SEs were defined geometrically as those enhancers above the point at which the line y=x is tangent to the curve. Stitched enhancers (typical enhancers and SEs) were assigned to the single active gene whose transcription start site is nearest the center of the stitched enhancer. Active genes were determined by taking the top two-thirds of all RefSeq promoters (+/-500 bp) ranked by their H3K27ac signal. H3K27ac signal in promoters was determined using bamToGFF (https://github.com/BradnerLab/pipeline) with parameters –e 200 –m 1 –r –d.
Genome_build: GRCh37, hg19
Supplementary_files_format_and_content: Aligned ChIP-seq read positions (WIG or bigWig files)

source_name: peripheral blood

growth_protocol: Cells were cultured in RPMI 1640 supplemented with FBS (10%) , penicillin (100 IU/ml) and streptomycin sulfate (50 mg/ml).

extract_protocol:
For each ChIP, 5 μg of antibody was conjugated to 2 mg of M-270 Epoxy Dynabeads (Thermo Fisher) and added to sonicated nuclear extract.
Library construction was performed using the Swift 2S Turbo DNA Library Kit (Swift Biosciences) as per the manufacturer’s instructions.

treatment_protocol: ChIP-seq was performed as previously described in “Lee, T., Johnstone, S. & Young, R. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729–748 (2006). https://doi.org/10.1038/nprot.2006.98"

value: anaplastic large cell lymphoma cells

tag: alk status

value: ALK+

value: − (none)

value: lymph node


title: ALCL Primary #54_H3K27ac


title: ALCL Primary #208_H3K27ac


title: ALCL Primary #54_Input


title: AF00218


title: ALK− ALCL_FE-PD_Input

value: FE-PD

value: ALK−


title: ALK− ALCL_Mac-2A_H3K27ac


title: ALK+ ALCL_SR-786_H3K27ac


title: ALK+ ALCL_SU-DHL-1_Input


title: ALK− ALCL_FE-PD_H3K27ac


title: ALK− ALCL_Mac-1_BATF3


title: ALK− ALCL_Mac-2A_Input


title: ALK+ ALCL_SUP-M2_H3K27ac


title: ALK+ ALCL_SUP-M2_Input


title: ALK+ ALCL_JB6_H3K27ac


title: ALK+ ALCL_SU-D-HL1_H3K27ac


title: ALK− ALCL_Mac-1_Input


title: ALK+ ALCL_Karpas-299_BATF3


title: ALK− ALCL_Mac-1_H3K27ac


title: ALK+ ALCL_JB6_Input


title: ALK+ ALCL_Karpas-299_H3K27ac


title: ERSIAS0001


title: ALK+ ALCL_Karpas-299_Input


title: BATF3-knockout clone #2

data_processing:
The raw fastq files were quality-checked using FastQC (v0.11.5) and low-quality ends (Phred score average of 4 consecutive bases <5) and adapters were removed using Trimmomatic (v0.36).
Alignment to the reference genome (GRCh38) with gene annotation (Ensembl v91) was performed using STAR (v2.5.3a). Post-processing was performed with Samtools (v1.4.1).
Gene counts were assessed by featureCounts (v1.5.2) and strand specificity of the sequencing was taken into account. Only uniquely aligned reads were considered. Overall statistics were continuously summarized by MultiQC (v1.4).
Differential expression calculation was performed in R (v3.4.4, http://www.R-project.org/) using DESeq2 (v1.16.1) / edgeR (v3.18.1).
Benjamini–Hochberg procedure was used to correct the P-values for multiple testing errors.
Genome_build: GRCh38, hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts and normalized abundance measurements for all samples (txt files)

extract_protocol:
RNA isolation was performed using the RNeasy Mini Kit (Qiagen) according to the manufactuer's instructions with 1 μg total RNA used for the construction of sequencing library.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) with Poly(A) selection as per the manufacturer’s instructions.

treatment_protocol: Cells were lentivirally transduced with either non-targeting (control) or BATF3 (knockout) sgRNA, followed by puromycin selection (1 μg/ml). Single clones were selected with mutations verified by Sanger sequencing and loss of protein confirmed by immunoblotting.

tag: genotype

value: BATF3 knockout


title: ALK+ ALCL_SR-786_Input


title: Non-targeting control clone #3

value: wild-type


title: Non-targeting control clone #1


title: TRAP 10-13h IP S59 replicate2

data_processing: signal intensities were normalized using quantile-quantile normalization with solo2 software. Log2 fold change were computed and p-value computed using t-test

source_name: Drosophila embryos from stage 10-13h

extract_protocol: After collection, embryos are washed and lysed in order to extract and immunoprecipitate GFP-tagged polysomes and associated RNA. Trizol extraction is then performed to purify RNA

value: Staged collection


title: Non-targeting control clone #2


title: BATF3-knockout clone #3


title: H2171-YAP Input rep1

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

institute: Mount Sinai Hospital

data_processing:
Illumina NextSeq Control Software was used for real-time base calling. The real-time base call (.bcl) files were converted to fastq files using Illumina bcl2fastq2 conversion software v2.17.
Reads were trimmed with Trimmomatic v0.32. Reads quality assessed by FastQC, and then aligned to hg19 using Bowtie2 with default parameters.
Redundant reads were removed and only uniquely mapping reads were kept before peak calling.
The Homer package version 4.10 was used for peak calling.
Peak files were converted to bed files and regions on the blacklist were removed.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Peaks in bed format with Normalized Tag Counts (number of tags found at the peak, normalized to 10 million total mapped tags).

source_name: SCLC cell line

growth_protocol: Cell lines were cultured by standard protocols as outlined by the ATCC.

extract_protocol:
Cells were crosslinked in formaldehyde, lysed and sonicated to fragment the gDNA. Clarified gDNA was immunoprecipitated with an anti-TEAD4 antibody, beads were washed then eluted and crosslinks reversed.
Libraries were prepared using the Illumina TruSeq ChIP Sample Prep Kit (cat#: IP-202-101) according to the manufacturer's protocol with 18 cycles for final PCR enrichment. Samples were size selected using PippinHT (Sage Science) with 2% gel, targeting 300 bp fragments (start at 239 bp, end at 361 bp, and tight on Range Flag).

treatment_protocol: Cells were harvested five days after transduction.

value: expressing 5SA mutant human YAP

tag: sample type

value: Input DNA


title: H2171-YAP Input rep2


title: H2171-YAP TEAD4 ChIP rep2

value: TEAD4 ChIP

value: TEAD4 (Santa Cruz sc-101184)


title: H2171-YAP TEAD4 ChIP rep1


title: H2171-Empty Input rep2

value: expressing Empty vector


title: H2171-Empty TEAD4 ChIP rep2


title: ERSIAS0008

value: intracranial atherosclerosis

value: Serum

value: Non responder to medical management

tag: gender

value: Female


title: H209-YAP TEAD4 ChIP rep1


title: H209-YAP Input rep1


title: H209-YAP Input rep2


title: H2171-Empty TEAD4 ChIP rep1


title: H209-Empty TEAD4 ChIP rep1


title: H209-Empty Input rep2


title: WERI-YAP Input rep2

source_name: retinoblastoma cell line


title: H209-Empty TEAD4 ChIP rep2


title: H209-Empty Input rep1


title: WERI-YAP TEAD4 ChIP rep2


title: WERI-YAP TEAD4 ChIP rep1


title: WERI-YAP Input rep1


title: WERI-Empty Input rep2


title: WERI-Empty Input rep1


title: WERI-Empty TEAD4 ChIP rep1


title: Y79-YAP Input rep2

value: expressing wild type human YAP


title: Y79-YAP Input rep1


title: Y79-Empty Input rep2


title: Y79-YAP TEAD4 ChIP rep2


title: H2171-Empty Input rep1


title: WERI-Empty TEAD4 ChIP rep2


title: H209-YAP TEAD4 ChIP rep2


title: Y79-YAP TEAD4 ChIP rep1


title: H2171-YAP (5SA) Rep3

description:
2x75 paired-end sequence reads
H2171_YAP_3
processed data file: gene.counts_H209_H2171_WERI.matrix

data_processing:
Illumina HiSeq Control Software (Y79 and SHP77 cells) or NextSeq Control Software (WERI, H209 and H2171 cells) was used for real-time base calling. The real-time base call (.bcl) files were converted to fastq files using CASAVA 1.8.2 (Y79 and SHP77) or Illumina bcl2fastq2 conversion software v2.17 (WERI, H209 and H2171).
Reads were adaptor trimmed. Read quality was assessed by FastQC v0.11.7 for each sample. Reads were processed for transcript quantification by using RSEM v1.3.0 with reference genome GRCh37.p13, and the resulting gene expression, as a matrix of raw counts.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: *.matrix: Tab-delimited text files with read raw counts for each gene and sample, with genes annotated by gene_id and gene_name.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy mini kit.
RNA was accessed by Fragment Analyzer, and high quality total RNA was subjected to library preparation using the Illumina TruSeq Stranded mRNA Library Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were harvested five days after transduction. Cell pellets were flash frozen and stored at -80°C until extraction.


title: Y79-Empty Input rep1


title: Y79-Empty TEAD4 ChIP rep1


title: H2171-YAP (5SA) Rep1

description:
2x75 paired-end sequence reads
H2171_YAP_1
processed data file: gene.counts_H209_H2171_WERI.matrix


title: Y79-Empty TEAD4 ChIP rep2


title: H2171-YAP (5SA) Rep2

description:
2x75 paired-end sequence reads
H2171_YAP_2
processed data file: gene.counts_H209_H2171_WERI.matrix


title: H2171-Empty Rep2

description:
2x75 paired-end sequence reads
H2171_Empty_2
processed data file: gene.counts_H209_H2171_WERI.matrix


title: H209-Empty Rep1

description:
2x75 paired-end sequence reads
H209_Empty_1
processed data file: gene.counts_H209_H2171_WERI.matrix


title: H209-Empty Rep2

description:
2x75 paired-end sequence reads
H209_Empty_2
processed data file: gene.counts_H209_H2171_WERI.matrix


title: H209-YAP (5SA) Rep1

description:
2x75 paired-end sequence reads
H209_YAP_1
processed data file: gene.counts_H209_H2171_WERI.matrix


title: H209-Empty Rep3

description:
2x75 paired-end sequence reads
H209_Empty_3
processed data file: gene.counts_H209_H2171_WERI.matrix


title: WERI-YAP (5SA) Rep3

description:
2x75 paired-end sequence reads
WERI_YAP_3
processed data file: gene.counts_H209_H2171_WERI.matrix


title: H2171-Empty Rep1

description:
2x75 paired-end sequence reads
H2171_Empty_1
processed data file: gene.counts_H209_H2171_WERI.matrix


title: H209-YAP (5SA) Rep3

description:
2x75 paired-end sequence reads
H209_YAP_3
processed data file: gene.counts_H209_H2171_WERI.matrix


title: H209-YAP (5SA) Rep2

description:
2x75 paired-end sequence reads
H209_YAP_2
processed data file: gene.counts_H209_H2171_WERI.matrix


title: WERI-YAP (5SA) Rep2

description:
2x75 paired-end sequence reads
WERI_YAP_2
processed data file: gene.counts_H209_H2171_WERI.matrix


title: WERI-YAP (5SA) Rep1

description:
2x75 paired-end sequence reads
WERI_YAP_1
processed data file: gene.counts_H209_H2171_WERI.matrix


title: WERI-Empty Rep2

description:
2x75 paired-end sequence reads
WERI_Empty_2
processed data file: gene.counts_H209_H2171_WERI.matrix


title: WERI-Empty Rep3

description:
2x75 paired-end sequence reads
WERI_Empty_3
processed data file: gene.counts_H209_H2171_WERI.matrix


title: WERI-Empty Rep1

description:
2x75 paired-end sequence reads
WERI_Empty_1
processed data file: gene.counts_H209_H2171_WERI.matrix


title: Line 47 rep.3 periderm

city: Girona

first: Olga

last: Serra

state: Girona

address: C/ Maria Aurèlia Capmany, 40

department: Biologia

institute: Universitat de Girona

description: Line 47 rep.3

data_processing:
RNA-seq data were first analysed for quality control with FastQC v0.11.2
The reads were aligned with Bowtie 2 (Langmead and Salzberg, 2012) against the S. tuberosum Group Phureja transcriptome generated from the genome assembly v4.03 (Potato Genome Sequencing Consortium et al., (2011) using the most recent version of the GFF3 genome annotation file (PGSC_DM_V403_genes.gff.zip) with the program gffread from the Cufflinks package
The quantification of transcript abundance was performed with eXpress 1.5.1
The eff_counts obtained from eXpress were passed as input to baySeq (Hardcastle et al., 2010) for the differential expression analysis. Transcripts with a likelihood ≥ 0.8 in the specified model and a False Discovery Rate (FDR) lower than 0.05 were considered as differentially expressed
Genome_build: PGSC v4.03 pseudomolecule
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: potato tuber skin (periderm)

growth_protocol: in soil under long-day conditions (12 h light/12 h dark)

extract_protocol:
Total RNA was purified by means of the PureLink® Plant RNA Reagent (Ambion) using a modification of the standard protocol by repeating twice the step four and five of the protocol and adding a KOAc 2M (pH 5.5) precipitation step to remove polysaccharides. Final RNA precipitation was performed with the GlycoBlue™ Coprecipitant (Ambion). Genomic DNA was removed using TURBO DNA-free kit (Ambion) according to the manufacturer’s instructions.
The cDNA libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina)

value: tuber periderm

value: StRIK-RNAi transgenic line 47

tag: growing conditions


title: Line 47 rep.1 periderm

description: Line 47 rep.1

value: in soil under long-day conditions (12 h light/12 h dark)


title: Line 47 rep.2 periderm

description: Line 47 rep.2


title: Line 12 rep.3 periderm

description: Line 12 rep.3

value: StRIK-RNAi transgenic line 12


title: H2171-Empty Rep3

description:
2x75 paired-end sequence reads
H2171_Empty_3
processed data file: gene.counts_H209_H2171_WERI.matrix


title: Line 9 rep.3 periderm

description: Line 9 rep.3

value: StRIK-RNAi transgenic line 9


title: Line 12 rep.1 periderm

description: Line 12 rep.1


title: Line 12 rep.2 periderm

description: Line 12 rep.2


title: Wild-type rep.3 periderm

description: Wild-type rep.3

value: Wild-type


title: Wild-type rep.1 periderm

description: Wild-type rep.1


title: Line 9 rep.1 periderm

description: Line 9 rep.1


title: Wild-type rep.2 periderm

description: Wild-type rep.2