title: PHX-D3-2


title: PHX-D7-1

status: Public on Nov 19 2022

type: SRA

city: Shanghai

first: Meng

middle: meng

last: Jiang

address: number 3728, Jinke Road

country: China

institute: Shanghai Institute of Materia Medica

library_source: transcriptomic

data_processing:
RNA-seq data were uniquely mapped to mm10 reference genome by TopHat v1.4.1
Expression values were assigned to gene level by Cufflinks v1.3.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene id and RPKM value

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
IL6 induced hepatocytes or mouse liver were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA library for RNA-seq was prepared as flows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library

tag: tissue

value: liver

tag: genotype

value: WT

tag: treatment

value: 2/3 partial hepatectomy

tag: strain

tag: time point

value: 7 days


title: PHX-D7-3


title: PHX-D3-3

value: 3 days


title: PHX-D14-3

value: 14 days


title: PHX-D14-2


title: PHX-D14-1


title: PHX-24h-1

value: 24 hours


title: PHX-24h-3


title: PHX-24h-2


title: PHX-6h-3

value: 6 hours


title: PHX-D3-1


title: R2_Input_siP1

city: Dallas

first: Nicholas

middle: K

last: Conrad

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

country: USA

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
Single end sequenced reads were trimmed for adaptor sequence and filtered for quality with trim galore/0.6.4, and aligned to concatenated genomes of Human (GRCh38), Kaposi's sarcoma-associated herpesvirus (GQ994935.1), and Drosophila (dm6).
The aligned reads were subsequently filtered for mapping quality (MAPQ 30) and PCR duplicates by SAMtools/1.6 and Picard. Uniquely mappable reads were retained for further analysis.
Reads per million (RPM) normalizations were performed for sequencing depth normalization.
MACS2 was used for peak calling.
deeptools (3.5.0) was used for generation of Input normalized (subtracted) coverage tracks.
Assembly: concatenated genomes of human (GRCh38) and Kaposi's sarcoma-associated herpesvirus (GQ994935.1)
Supplementary files format and content: Input Normalized Bigwig files

molecule: genomic DNA

organism: Homo sapiens

source_name: iSLK cells with BAC16 WT virus latent infection

growth_protocol: All cell lines were grown at 37°C with 5% CO2, with 1X penicillin-streptomycin (Sigma), and 2mM L-glutamine (Fisher) in DMEM (Sigma) supplemented with 10% TET-free FBS (Atlanta Biologicals);

extract_protocol:
Cells were fixed with 0.5% formaldehyde at RT for 10 min then quenched with 150 mM glycine at room temperature, 5 min. Cells were harvested by scraping in cold 1X PBS and pelleted at 1000 x g, 5 min at 4°C. Harvested cells were lysed for 30 min at 4°C in Farnham lysis buffer (5 mM PIPES, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, 1X protease inhibitor cocktail (PIC)). Additional details of Dna shearing, and IP are given in Devlin et al. 2022.
For ChIP-seq library preparations, 4 ng of ChIP or input DNA was processed using the KAPA Hyper Prep Kit according to the manufacturer’s protocol (Roche KK8504).

treatment_protocol: Cells were treated with 30nM of indicated siRNA 96 hrs prior to harvesting.

tag: cell line

value: iSLK cells

value: PNUTS siRNA:siP1

tag: antibody

value: Input


title: R2_IP_siP2

value: PNUTS siRNA siP2

value: anti-Pol II IP


title: R2_IP_siP1


title: R2_IP_siNT

value: nontargeting siRNA:siNT


title: R2_Input_siNT


title: R1_IP_siP2


title: R1_IP_siP1


title: R1_Input_siP2


title: R1_Input_siP1


title: R2_Input_siP2


title: PANC1 cells, siNusap1, rep3

city: Hangzhou

first: Chen

last: Ming

state: Zhejiang

address: No. 79 Qingchun Road

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

description:
FPKM.SiNusap1_3
SiNusap1_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Solanum lycopersicum（https://solgenomics.net/ftp/genomes/Solanum_lycopersicum/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: build_3.00
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: pancreas

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: pancreas

tag: cell type

value: pancreatic ductal adenocarcinoma cells

value: Nusap1 knockdown

value: transfected with siRNA targeted with Nusap1


title: PANC1 cells, flag-Nusap1, rep3

description:
FPKM.Nusap1_3
Nusap1_3

value: Nusap1 overexpression

value: transfected overexpressed plasmid targeted with Nusap1


title: PANC1 cells, Control, rep3

description:
FPKM.Ctrl_3
Ctrl_3

value: WT

value: No


title: PANC1 cells, siNusap1, rep1

description:
FPKM.SiNusap1_1
SiNusap1_1


title: PANC1 cells, Control, rep1

description:
FPKM.Ctrl_1
Ctrl_1


title: PANC1 cells, Control, rep2

description:
FPKM.Ctrl_2
Ctrl_2


title: PANC1 cells, flag-Nusap1, rep1

description:
FPKM.Nusap1_1
Nusap1_1


title: PANC1 cells, flag-Nusap1, rep2

description:
FPKM.Nusap1_2
Nusap1_2


title: PANC1 cells, siNusap1, rep2

description:
FPKM.SiNusap1_2
SiNusap1_2


title: PHX-6h-1

value: liver

value: 2/3 partial hepatectomy


title: PHX-6h-2

value: 6 hours


title: R1_Input_siNT

value: iSLK cells


title: Rep B-IP-siP2

data_processing:
Single end sequenced reads were trimmed for adaptor sequence and filtered for quality with trim galore/0.6.4, and aligned to synthetic genome assembly (ORF59_reporter integatred into GRCh38 and dm6) using Bowtie2/2.3.2
The aligned reads were subsequently filtered for mapping quality (MAPQ 30) and PCR duplicates by SAMtools/1.6 and Picard. Uniquely mappable reads were retained for further analysis.
SpikeIN normalizations were performed after calculating scaling factor for each data set.
MACS2 was used for peak calling and generation of Input normalized (subtracted) coverage tracks.
Assembly: chimera genome assembly (ORF59_reporter integrated into chr19:55,115,766-55,121,825 of GRCh38)
Supplementary files format and content: Normalized Bigwig files

source_name: HCT116 with ORF59 reporter

growth_protocol: All cell lines were grown at 37°C with 5% CO2, with 1X penicillin-streptomycin (Sigma), and 2mM L-glutamine (Fisher) in DMEM (Sigma) supplemented with 10% FBS (Sigma);

value: HCT116 colorectal line derivative

value: PNUTS siRNA, siP2

tag: chip antibody

value: anti-RPB3 (Rabbit polyclonal, EMD Millipore, Cat#:ABE999, Lot #3764357)


title: Rep B-IP-siP1

value: PNUTS siRNA, siP1


title: R1_IP_siNT

value: nontargeting siRNA:siNT

value: anti-Pol II IP


title: Rep B-IP-siNT

value: nontargeting siRNA, siNT


title: Rep B-Input-siP2


title: WT2

status: Public on Nov 20 2022

city: Nanjing

first: Xiaoming

last: Wang

state: jiangsu

address: 101 longmian avenue jiangning district

institute: Nanjing Medical University

data_processing:
Map the sequence reads to mm10 reference genome using Bowtie2 software.
Fragments Per Kilobase per Million were calculated with Cufflinks.
A threshold of fold change > 1.2 and p < 0.05 was used to determine the differential expression of genes.
Assembly: mm10
Supplementary files format and content: *.tsv: Tab-delimited text files include count values for each Sample.

source_name: spleen

extract_protocol:
B220+ B cells were sorted from the spleen of NSD1B WT and NSD1B KO mice with a BD Aria II. Sorting efficiency was tested, and only cells with high purity (>98%) were used for RNA extraction and library construction.
Sequencing were done by BGI Co.

value: spleen

value: B220+ Bcells

value: NSD1B WT


title: Rep B-Input-siP1


title: Normal liver-3

value: Normal


title: HCM-Hepa-D7 (P0)-3

value: HCM-Hepa-D7 (P0)

value: WT


title: Normal liver-1

value: liver


title: IL6-iMHs-clone-1 (P20)-3

description: hierarchical clustering_IL6_induced_process.txt

value: IL6-iMHs-clone-1 (P20)


title: IL6-iMHs-mouse-1 (P35)-3

value: IL6-iMHs-mouse-1 (P35)


title: IL6-iMHs-mouse-2 (P10)-3

value: IL6-iMHs-mouse-2 (P10)


title: Normal liver-2


title: IL6-iMHs-clone-1 (P20)-2


title: IL6-iHPCs-D7 (P0)-3

value: IL6-iHPCs-D7 (P0)


title: IL6-iMHs-clone-1 (P20)-1


title: IL6-iMHs-mouse-1 (P35)-1


title: Primary hepatocytes-3

value: Primary-hepatocytes


title: IL6-iMHs-mouse-1 (P35)-2


title: Primary hepatocytes-2


title: HCM-Hepa-D7 (P0)-2


title: IL6-iHPCs-D7 (P0)-2


title: Primary hepatocytes-1


title: HCM-Hepa-D7 (P0)-1


title: IL6-iHPCs-D7 (P0)-1


title: Sorted-Rep3

description:
DNA-lentiviral sgRNA sequencing
These are sgRNAs sequenced from selected high-GFP expressing cells
AMD_3rep.gene_summary.txt
AMD_3rep.sgrna_summary.txt

data_processing:
The fastq files were subjected to quality check using fastqc (version 0.11.9, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and adaptors trimmed using Cutadapt version 3.3 (Martin M. et al. 2011)
The trimmed fastq files were mapped to Brunello library sequence (Doench et al. 2016; Addgene #73179), read counts generated, and median normalized using MAGeCK-VISPR version 0.5.6 (Li W. et al. 2015) disallowing any mismatches
Batch correction was performed in MAGeCK-VISPR after excluding zero count sgRNAs, considering each biological replicate as a separate batch
Positively and negatively selected sgRNA and genes were identified using the default parameters of MAGeCK-VISPR.
Assembly: n/a; seqences aligned to Brunello (Doench et al. 2016; Addgene #73179)
Supplementary files format and content: text file; output for MAGeCK

source_name: HCT116 cells with integrated reporter

growth_protocol: An HCT116-derived clonal line that expresses the ORF59-GFP reporter was grown in DMEM supplemented with 10% fetal bovine serum and 1X penicillin-streptomycin (Sigma), and 2mM L-glutamine.

extract_protocol:
DNA was extracted using phenol:chloroform:iso-amyl alcohol method. See Scarborough et al 2021 for details.
Library amplification was completed following a two-step variation of the BROAD institute protocol (BROAD Institute PCR of sgRNAs for Illumina sequencing). The two step variation of the BROAD institute protocol consists of an initial amplification step using primers flanking the P5 and P7 primers used for sequencing.
CRISPR screen

treatment_protocol: The cells were transduced with the Brunello lentiviral library (100X) and two days later puromycin was added. Seven days postinfection the hightes 8% GFP expressing cells were selected using a FACSAria cell sorter. Unselected cells were taken as a reference.

value: colorectal cancer cell

tag: library

value: Brunello lentiviral library

tag: gfp expression

value: sorted cells (those with high GFP signal)

tag: biological replicate


title: Input-Rep3

description:
DNA-lentiviral sgRNA sequencing
These were sgRNAs sequenced from unsorted cells
AMD_3rep.gene_summary.txt
AMD_3rep.sgrna_summary.txt

value: input


title: Rep B-Input-siNT

value: HCT116 colorectal line derivative

value: nontargeting siRNA, siNT


title: Rep A-IP-siNT

value: anti-RPB3 (Rabbit polyclonal, EMD Millipore, Cat#:ABE999, Lot #3764357)


title: Rep A-IP-siP1

value: PNUTS siRNA, siP1


title: Sorted-Rep2


title: Rep A-IP-siP2

value: PNUTS siRNA, siP2


title: IL6-iMHs-mouse-2 (P10)-2


title: Input-Rep2


title: IL6-iMHs-mouse-2 (P10)-1


title: Sorted-Rep1


title: IL6-iMHs-mouse-1 (P10)-3

value: IL6-iMHs-mouse-1 (P10)


title: IL6-iMHs-mouse-1 (P10)-2

value: WT


title: Input-Rep1


title: IL6-iHPCs-mouse-1 (P35)-1

value: liver

value: IL6-iHPCs-mouse-1 (P35)


title: IL6-iHPCs-mouse-1 (P35)-2


title: IL6-iHPCs-mouse-1 (P35)-3


title: Rep A-Input-P1


title: IL6-iMHs-mouse-1 (P10)-1


title: VFGp6_rep1

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

country: United Kingdom

institute: MRC Human Genetics Unit, The University Of Edinburgh

data_processing:
Fastqc for quality assessment
Cutadapt for trimming the adaptors
Bowtie 2 for aligning the reads to hg19 assembly of the genome
Homer for normalizing and calculating genome-wide coverage tracks in bigwig format
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: HUES4 cells

extract_protocol: Nextera


title: PE_rep2


title: IL6-iHPCs-clone-1 (P20)-2

value: IL6-iHPCs-clone-1 (P20)


title: Rep A-Input-siNT


title: IL6-iHPCs-mouse-2 (P10)-1

value: IL6-iHPCs-mouse-2 (P10)


title: IGF1exp-control-6h-OLA985-E14-M1-Emb4

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

country: Finland

institute: University of Helsinki

data_processing:
The RNAseq reads were evaluated and bad reads were filtered out using FastQC (version 0.11.8, Andrews et al., 2012), AfterQC (version 0.9.6, Chen et al., 2017) and Trimmomatic (version 0.39, Bolger et al., 2014), and ribosomal RNA was removed using Sortmerna (Kopylova et al., 2012). The number of remaining, good reads varied between 8.9M and 22.7M. Reads were aligned using Salmon (version 0.99.0, Patro et al., 2017) to GRCm38 (Ensembl release 100) cDNA. Deseq2 (Love et al., 2014) was used to normalise the read counts by library size and composition as well as transcript length.
Assembly: GRCm38 (Ensembl release 100) cDNA
Supplementary files format and content: Tab-delimited gene expression count values of each samples

source_name: first lower molar

growth_protocol: Embryonic day 14 (E14) mouse molars were dissected and cultured in a hanging drop culture (Närhi & Thesleff, 2010) for 6 hours pairwise so that from each embryo one tooth was treated with IGF1-containing media (750ng/ml in 1x PBS + 0.1% BSA ) or control media (same volume of 1x PBS + 0.1% BSA as was added to treatment samples). Right and left sides were balanced, n = 5 for both the treatments and controls. Tissue was stored in RNAlater (Qiagen, Düsseldorf, Germany) at −80°C for RNAseq.

extract_protocol:
Tissue was stored in RNAlater (Qiagen, Düsseldorf, Germany) at −80°C for RNAseq. For RNAseq, each tooth was handled individually. Samples were homogenized using Precellys 24 homogenizer (Bertin instruments). RNA was extracted using guanidium thiocyanate-phenol-chloroform method and purified using RNeasy Plus micro kit (Qiagen GmbH) following manufacturer's protocol. The putiry of RNA was measured using Nanodrop microvolume spectrophotometer (Thermo Fisher Scientific).
The complementary DNA (cDNA) libraries were prepared using Ovation Mouse RNAseq System (Tecan).

value: first lower molar

tag: age

value: wild type

value: media supplemented with 1x PBS + 0.1% BSA, same volume as was added to treatment samples


title: IGF1exp-control-6h-OLA985-E14-M1-Emb6

treatment_protocol: Embryonic day 14 (E14) mouse molars were dissected and cultured in a hanging drop culture (Närhi & Thesleff, 2010) for 6 hours pairwise so that from each embryo one tooth was treated with IGF1-containing media (750ng/ml in 1x PBS + 0.1% BSA ) or control media (same volume of 1x PBS + 0.1% BSA as was added to treatment samples). Right and left sides were balanced, n = 5 for both the treatments and controls. Tissue was stored in RNAlater (Qiagen, Düsseldorf, Germany) at −80°C for RNAseq.


title: IGF1exp-control-6h-OLA985-E14-M1-Emb3


title: IL6-iHPCs-mouse-2 (P10)-3


title: PE_rep1


title: IL6-iHPCs-mouse-2 (P10)-2


title: IL6-iHPCs-clone-1 (P20)-1


title: IL6-iHPCs-mouse-1 (P10)-1

value: IL6-iHPCs-mouse-1 (P10)


title: IL6-iHPCs-clone-1 (P20)-3


title: IGF1exp-control-6h-OLA985-E14-M1-Emb2


title: Rep A-Input-P2


title: VFGp3_rep2


title: VFGp6_rep2


title: IL6-iHPCs-D14 (P0)-3

value: IL6-iHPCs-D14 (P0)


title: IL6-iHPCs-mouse-1 (P10)-2


title: IL6-iHPCs-mouse-1 (P10)-3


title: VFGp3_rep1


title: IGF1exp-control-6h-OLA985-E14-M1-Emb1


title: IGF1exp-750ngIGF1-6h-OLA985-E14-M1-Emb6

value: media supplemented with mouse recombinant IGF1 protein (dissolved in 1x PBS + 0.1% BSA) for 6h


title: IL6-iHPCs-D14 (P0)-1


title: ADE_rep2


title: IL6-iHPCs-D14 (P0)-2


title: IGF1exp-750ngIGF1-6h-OLA985-E14-M1-Emb3


title: IGF1exp-750ngIGF1-6h-OLA985-E14-M1-Emb4


title: IL6-iHPCs-D3 (P0)-3

value: IL6-iHPCs-D3 (P0)


title: ADE_rep1


title: IL6-iHPCs-D3 (P0)-2


title: IL6-iHPCs-D3 (P0)-1


title: hESC_rep2


title: IGF1exp-750ngIGF1-6h-OLA985-E14-M1-Emb2


title: Hepatocytes-3

value: Hepatocytes


title: SI-SCR_C

city: Basel

first: Emanuela

last: Kerschbamer

state: Basel Stadt

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
adapters, low quality and N bases are trimmed with trim galore
transcripts are quantified with kallisto
PSI (percent spliced-in) value is calculated for each event in each sample with suppa
differential events are calculated with suppa comparing the two conditions
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include kallisto TPM abundance values for each Sample
Supplementary files format and content: tab-delimited text file including deltaPSI and pvalue of differential events comparing the two conditions

molecule: polyA RNA

growth_protocol: Human iPSC-derived NPC line GM8330-8 were cultured on poly-L-ornithine hydrobromide (20 µg/mL, Sigma)/laminin (3 µg/mL, Life Technologies) - coated plates in hiNPC medium (70% v/v DMEM (Life Technologies) completed with 30% v/v HAM F12 (Euroclone), 2% v/v B27 (Life Technologies), 1% v/v Penicillin-Streptomycin solution (Life Technologies) and 1% v/v L-Glutamine (Corning) and supplemented with EGF (20 ng/mL, Sigma), bFGF (20 ng/mL, R&D) and Heparin (5 µg/mL, Sigma)). Semi-confluent monolayers of hiNPCs were maintained in 5% CO2, 37°C humidified incubator.  Cells were cultured on poly-L-ornithine hydrobromide (20 µg/mL, Sigma)/laminin (3 µg/mL, Life Technologies) - coated plates in hiNPC medium (70% v/v DMEM (Life Technologies) completed with 30% v/v HAM F12 (Euroclone), 2% v/v B27 (Life Technologies), 1% v/v Penicillin-Streptomycin solution (Life Technologies) and 1% v/v L-Glutamine (Corning) and supplemented with EGF (20 ng/mL, Sigma), bFGF (20 ng/mL, R&D) and Heparin (5 µg/mL, Sigma)). Semi-confluent monolayers of hiNPCs were maintained in 5% CO2, 37°C humidified incubator.  Human iPSC-derived NPC line GM8330-8 (41), Sh1-CHD8, Sh2-CHD8, Sh4-CHD8 and Sh-GFP lines, previously generated by lentiviral delivery of shRNAs targeting CHD8 and GFP coding sequences respectively (11), were kindly provided by Dr. Stephen Haggarty laboratory (Massachusetts General Hospital and Harvard Medical School, Boston, MA, U.S.A.).   Cells were cultured on poly-L-ornithine hydrobromide (20 µg/mL, Sigma)/laminin (3 µg/mL, Life Technologies) - coated plates in hiNPC medium (70% v/v DMEM (Life Technologies) completed with 30% v/v HAM F12 (Euroclone), 2% v/v B27 (Life Technologies), 1% v/v Penicillin-Streptomycin solution (Life Technologies) and 1% v/v L-Glutamine (Corning) and supplemented with EGF (20 ng/mL, Sigma), bFGF (20 ng/mL, R&D) and Heparin (5 µg/mL, Sigma)). Semi-confluent monolayers of hiNPCs were maintained in 5% CO2, 37°C humidified incubator.  Human iPSC-derived NPC line GM8330-8 (41), Sh1-CHD8, Sh2-CHD8, Sh4-CHD8 and Sh-GFP lines, previously generated by lentiviral delivery of shRNAs targeting CHD8 and GFP coding sequences respectively (11), were kindly provided by Dr. Stephen Haggarty laboratory (Massachusetts General Hospital and Harvard Medical School, Boston, MA, U.S.A.).   Cells were cultured on poly-L-ornithine hydrobromide (20 µg/mL, Sigma)/laminin (3 µg/mL, Life Technologies) - coated plates in hiNPC medium (70% v/v DMEM (Life Technologies) completed with 30% v/v HAM F12 (Euroclone), 2% v/v B27 (Life Technologies), 1% v/v Penicillin-Streptomycin solution (Life Technologies) and 1% v/v L-Glutamine (Corning) and supplemented with EGF (20 ng/mL, Sigma), bFGF (20 ng/mL, R&D) and Heparin (5 µg/mL, Sigma)). Semi-confluent monolayers of hiNPCs were maintained in 5% CO2, 37°C humidified incubator.

extract_protocol:
Total RNA was extracted from iPSC-derived NPC lines using TRIZOL reagent (Invitrogen) following the manufacturer's instruction. DNA contamination was removed by treating the samples with DNase I (Invitrogen) and RNase inhibitor SUPERase (Invitrogen) for 30’ at 37°C followed by purification with RNase Mini Kit (Qiagen). RNA quality was evaluated by agarose gel electrophoretic run and Agilent 2100 Bioanalyzer.
RNA-seq libraries from hnRNPL si-RNA treated samples (si-hnRNPL-C and si-scrambled control (si-SCR) were obtained from total RNA isolated using TRIZOL (Invitrogen) and treated with DNase (AMBION)). RNA quality was assessed by Agilent bio-analyzer (RIN from 7.8 to 9.2). Selected mRNA on magnetic oligo(dT) beads were retro-transcribed using random hexamer. A second strand was generated by dUTP method. Standard Illumina paired-end (100bp) library preparation was performed with barcoded adaptors to obtain ~50-60 million reads per sample.

treatment_protocol: 3 million hiNPC cells were electroporated with 200 pM siRNA oligos using Lonza Nucleofector® 2b device and a custom-made electroporation buffer (5mM KCl, 15mM MgCl2, 10mM of glucose and 120mM K2HPO4/KH2PO4 pH 7.2). Knockdown efficiency was determined after 48-72 h from electroporation. The siRNA oligos targeting the hnRNPL gene (3 unique 27mer and 1 universal Scrambled Negative Control) were purchased by OriGene (SR302174).

value: iPSC-derived neural progenitor cells

value: wild-type

value: scrambled siRNA control

tag: time

value: 72h post treatment


title: SI-SCR_D


title: IGF1exp-750ngIGF1-6h-OLA985-E14-M1-Emb1


title: SI-SCR_B


title: mouse heart, WT-453-5

city: Augusta

first: Jianqiu

last: Zou

state: GA

address: 1460 Laney Walker Blvd

department: VBC

institute: Augusta University

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5

source_name: ventricle

extract_protocol:
Mouse ventricles were minced and treated with RNAlater (Thermo Fisher) according to the manufacturer’s protocol at -80 °C. The isolated RNA was subjected to RNA-sequencing analysis
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.

value: ventricle

value: cardiomyocyte

value: neonatal

value: wt


title: mouse heart, WT-453-3


title: Hepatocytes-2

value: liver

value: WT


title: IP-Rep2

description: RNA (human and KSHV)

data_processing:
UMIs were removed using umi_tools v0.5.1: umi_tools extract –-stdin=045IP13_S37.fastq.gz --bc-pattern=NNNNNNNNNN --log=045IP13_S37.processed.log --stdout 045IP13_S37.demultiplex.fastq.gz
Read quality was checked with Fast QC v.0.11.9: fastqc 045IP13_S37.demultiplex.fastq.gz
Reads were trimmed using two rounds of Cutadapt v3.2 to trim 3´ adaptors and to control for double ligation events: cutadapt --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a AGATCGGAAGAGCAC -a GATCGGAAGAGCACA -a ATCGGAAGAGCACAC -a TCGGAAGAGCACACG -a CGGAAGAGCACACGT -a GGAAGAGCACACGTC -a GAAGAGCACACGTCT -a AAGAGCACACGTCTG -a AGAGCACACGTCTGA -a GAGCACACGTCTGAA -a AGCACACGTCTGAAC -a GCACACGTCTGAACT -a CACACGTCTGAACTC -a ACACGTCTGAACTCC -a CACGTCTGAACTCCA -a ACGTCTGAACTCCAG -a CGTCTGAACTCCAGT -a GTCTGAACTCCAGTC -a TCTGAACTCCAGTCA -a CTGAACTCCAGTCAC -o 045IP13_S37.adapterTrim.fastq.gz 045IP13_S37.demultiplex.fastq.gz > 045IP13_S37.adapterTrim.metrics and cutadapt --match-read-wildcards --times 1 -e 0.1 -O 5  --quality-cutoff 6 -m 18 -a AGATCGGAAGAGCAC -a GATCGGAAGAGCACA -a ATCGGAAGAGCACAC -a TCGGAAGAGCACACG -a CGGAAGAGCACACGT -a GGAAGAGCACACGTC -a GAAGAGCACACGTCT -a AAGAGCACACGTCTG -a AGAGCACACGTCTGA -a GAGCACACGTCTGAA -a AGCACACGTCTGAAC -a GCACACGTCTGAACT -a CACACGTCTGAACTC -a ACACGTCTGAACTCC -a CACGTCTGAACTCCA -a ACGTCTGAACTCCAG -a CGTCTGAACTCCAGT -a GTCTGAACTCCAGTC -a TCTGAACTCCAGTCA -a CTGAACTCCAGTCAC -o  045IP13_S37.adapterTrim.round2.fastq.gz  045IP13_S37.adapterTrim.fastq.gz >  045IP13_S37.adapterTrim.round2.metrics
Repetitive elements were removed using STAR v. 2.7.7a: STAR --runMode alignReads --runThreadN 8 --genomeDir repetitive_elements/genome/ --readFilesIn 045IP13_S37.adapterTrim.round2.fastq.gz --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange --outFileNamePrefix 045IP13_S37.adapterTrim.round2.rep.bam --outSAMattributes All --readFilesCommand gunzip -c --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx  --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > 045IP13_S37.adapterTrim.round2.rep.bam
Read quality after repetitive element removal was rechecked using Fast QC v. 0.11.9: fastqc 045IP13_S37.adapterTrim.round2.rep.bamUnmapped.out.mate1
Reads were mapped using STAR V2.7.7a: STAR --runMode alignReads --runThreadN 8 --genomeDir genome/ --readFilesIn 045IP13_S37.adapterTrim.round2.rep.bamUnmapped.out.mate1 --outSAMunmapped Within --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1 --outFileNamePrefix 045IP13_S37.adapterTrim.round2.rmRep.bam --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > 045IP13_S37.adapterTrim.round2.rmRep.bam
Resulting bam files were sorted and indexed using Samtools v. 1.9: samtools sort  045IP13_S37.adapterTrim.round2.rmRep.bam -o  045IP13_S37.adapterTrim.round2.rmRep.sorted.bam and samtools index 045IP13_S37.adapterTrim.round2.rmRep.sorted.bam
PCR duplicates were removed using Umi_tools dedup v0.5.1: umi_tools dedup --method=unique -I 045IP13_S37.adapterTrim.round2.rmRep.sorted.bam --log=045IP13_S37.dedup.log -S 045IP13_S37.adapterTrim.round2.rmRep.sorted.rmDup.bam
Resulting bam files were sorted and indexed using Samtools v. 1.9: samtools sort  045IP13_S37.adapterTrim.round2.rmRep.sorted.rmDup.bam -o  045IP13_S37.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam and samtools index 045IP13_S37.adapterTrim.round2.rmRep.sorted.rmDup.sorted.bam
Assembly: UCSC version GRCh37/hg19 with GQ994935.1
Supplementary files format and content: bigwig

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: iSLK-BAC16 (WT)

growth_protocol: iSLK-BAC16 (WT) cells were grown in DMEM supplemented with 10% Tet-free FBS. Cells at ~70% confluency were treated with 1mM sodium butyrate and 1 ug/mL doxycycline for 24 hours.  Twenty million cells were harveested per sample.

extract_protocol:
Cells were lysed with eCLIP lysis  buffer (Eclipse Bio) at 20 million cells/ml, snap frozen in liquid nitrogen, and sent to Eclips Bio where the immunoprecipitation, library prep, and sequencing were performed. All folowed the methodology of van Nostrand et al. (2016; Nature Methods)
This was performed by a third party, Eclipse Bio. No modifications were made to the protocol of Van Nostrand et al (2016; Nature Methods).

treatment_protocol: Cells were treated with 400mJ/cm2

value: iSLK cells

tag: virus

value: BAC16 infectious clone

value: 1mM Sodium butyrate + 1 ug/mL doxycycline (24hr)

tag: eclip antibody

value: A300-439A-T; Bethyl labs


title: SMI-Rep2

description: RNA (human and KSHV)

value: No antibody (size-matched input)


title: mouse heart, WT-443-8


title: SI-C_D

value: siRNA-mediated hnRNPL knock-down


title: SI-C_C


title: IP-Rep1

description: RNA (human and KSHV)


title: SI-C_B


title: SI-C_A


title: mouse heart, KO-453-7

value: knockout


title: IVH-S1-110

city: Chengdu

first: Jiayidaer

last: Badai

address: No. 24, South Section 1, First Ring Road, Wuhou District

institute: Sichuan University

data_processing:
We use in-house script to perform basic statistics of raw data, and evaluate the data quality and  GC content along the sequencing cycles.
Raw FASTQ files and histology images were processed by sample with the Space Ranger (version spaceranger-1.2.0, 10X Genomics) software with  default parameters.
The filtered gene-spots matrix and the fiducial-aligned low-resolution image was used for down-streaming data analyses.
Assembly: mm10
Supplementary files format and content: The tar archive includes:
filtered_feature_bc_matrix
raw_feature_bc_matrix
spatial
filtered_feature_bc_matrix.h5
sample.web_summary.html
molecule_info.h5
raw_feature_bc_matrix.h5
Library strategy: specify

source_name: Brain

growth_protocol: Five wild-type C57/BL6 mice (weighing 25±5 g, 8 weeks old, Experimental Animal Center of Third Military Medical University, Chongqing, China) were used in this study.

extract_protocol:
RT-PCR,TRANSCRIPTOMIC.Read length for mate1(bp) is 150 and read length for mate2(bp) is 150.Sequencing was performed with a Novaseq PE150 platform according to the manufacturer’s instructions (Illumina) at an average depth of 300 million read-pairs per sample.
We collected wild-type C57/BL6 mouse brains, which were classified into the no-surgery group (control), the needle-puncture group without blood injection (sham), and the needle-puncture group with blood injection at 1st, 3rd and 7th day. Then, these brains were frozen on dry ice in OCT.Frozen brains were then sectioned coronally at 10 μm on a cryostat and mounted on 10x Genomics Visium spatial transcriptome slides. The tissue locations of the library patches started from the emergence of the lateral ventricle with 20 μm intervals and a 10 μm margin of error.

treatment_protocol: These mice were housed in a temperature-controlled room under specific-pathogen-free conditions and a standard 12-h light/dark cycle, with ad libitum access to food and water.

value: Brain

value: The needle-puncture group without blood injection (sham)

value: Sham

tag: Sex

value: male


title: hESC_rep1


title: SI-SCR_A

value: iPSC-derived neural progenitor cells

value: wild-type

value: scrambled siRNA control

value: 72h post treatment


title: IVH-S1-80

tag: tissue


title: Hepatocytes-1

value: liver

value: Hepatocytes

tag: genotype


title: IVH-S1-50

tag: treatment


title: mouse heart, KO-453-6

value: ventricle

value: cardiomyocyte

value: neonatal


title: Rep3 t48 siNT

data_processing:
Reads with Phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore (v0.4.1)
Quality-filtered reads were then aligned to the human reference genome hg19, adding KSHV GQ994935.1 as an extra chromosome and using the HISAT (v2.0.1) (13) aligner with default settings.
Duplicates were marked but retained using Sambamba (v0.6.6)
Aligned reads were quantified using featureCounts (v1.4.6) per gene ID against GENCODE GRCh37
Differential gene expression analysis was performed using the R package DEseq2 (v1.6.3)
Assembly: GENCODE GRCh37 (hg19) with GQ994935.1 (KSHV)
Supplementary files format and content: Processed data files are the DEseq2 outputs (as text files) comparing siNT with siPNUTS at each of the four time points

growth_protocol: iSLK-BAC16 (WT) cells were grown in DMEM supplemented with 10% Tet-free FBS.

extract_protocol:
RNAs were extracted using TRI-reagent (Molecualr Resarch Center Inc)
One microgram of total RNA per sample was processed with KAPA Stranded RNA-Seq kit with RiboErase (KAPA Biosystems)

treatment_protocol: Cells at 60-80% confluency were treated with 30 nM siRNA.  Twenty-four hours later, cells were split and 24 hrs after that (48 hrs post-siRNA treatment) 1mM sodium butyrate and 1 ug/mL doxycycline was added.

value: iSLK cells

value: BAC16 infectious clone

value: siNT

tag: induction

value: 1mM Sodium butyrate + 1 ug/mL doxycycline (48 hr)


title: IVH-C1-110

value: Brain

tag: strain

value: The no-surgery group (control)

value: Day 0


title: Sample_Anaerobic_CRS_006_A08

city: Minneapolis

first: Ryan

middle: C

last: Hunter

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

data_processing:
All data analysis was performed in R
The Ensembl GTF annotation file was filtered to remove annotations for non-protein-coding features
Fastq files were evenly subsampled down to a maximum of 100,000 reads per sample
Raw reads were mapped to reference Human (Homo_sapiens) genome assembly “GRCh38” using annotation from Ensembl release 98
Gene counts were generated with ‘featureCounts’ of the RSubread package
DESeq2/1.28.1 was used to estimate size factors to generate normalized count data, estimate gene-wise dispersions, shrink estimates using type=’ashr’, and perform Wald hypothesis testing
Assembly: GRCh38
Supplementary files format and content: tab delimited DESeq files comparing differentially expression of all genes between culture conditions

source_name: Calu-3 cells, mixed-oxic growth, challenged with anaerobic bacteria

growth_protocol: Calu-3 cells were cultured under normoxic or mixed oxic-anoxic conditions. For the latter, oxygen delivered basolaterally to Calu-3 cells cultured in a Coy anaerobic chamber

extract_protocol:
RNA was isolated from at least 5 separate Transwells using the RNeasy Micro Plus kit (Qiagen) according to manufacturer’s instructions
cDNA libraries were prepared using the SMARTer Universal Low Input RNA Kit (Takara Bio)

treatment_protocol: Cells were harvested after 24h of growth at ALI under each condition

value: Airway epithelium

tag: cell line

value: Non-small cell lung cancer

value: WT

value: Mixed oxic-anoxic growth, challenged with anaerobic bacteria


title: Rep3 t48 siPNUTS

value: siPNUTS


title: IVH-C1-50

value: male


title: Rep2 t48 siPNUTS


title: mouse heart, KO-443-5

value: knockout


title: SMI-Rep 1

description: RNA (human and KSHV)

value: 1mM Sodium butyrate + 1 ug/mL doxycycline (24hr)

value: No antibody (size-matched input)


title: Sample_Anaerobic_CRS_005_A09


title: mouse heart, WT-443-7

value: ventricle

value: cardiomyocyte

value: neonatal

value: wt


title: Sample_Anaerobic_CRS_005_A07


title: Sample_Anaerobic_CRS_006_A09


title: IVH-7d-2-80

value: The needle-puncture group with blood injection at 7th day

value: Day 7


title: Rep1 t48 siPNUTS

value: iSLK cells

value: BAC16 infectious clone

value: 1mM Sodium butyrate + 1 ug/mL doxycycline (48 hr)


title: Rep2 t48 siNT

value: siNT


title: M54-LV-24

city: Utrecht

first: Eva

last: van Rooij

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Reads from the Illumina sequencer were aligned to the reference genome using STAR
Reads were counted using HT-Seq
Differential expression analysis was perrfomed using DESeq
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data are raw read counts per gene

source_name: Upy-PEG_antimiR-195_left ventricle

growth_protocol: Mice were housed according to standard housing conditions

extract_protocol:
RNA isolation was performed using TRIzol according to manufacturer's instructions
Libraries were prepared by the Utrecht Sequencing Facility using TRUseq stranded mRNA kit.

treatment_protocol: Mice were euthanized by isoflurane overdose and cervical dislocation, hearts were explanted, left ventricles isolated and snap frozen .

tag: injury

value: ischemia-reperfusion

tag: vehicle

value: Upy-PEG

tag: drug

value: heart; left ventricle


title: M54-LV-26


title: Sample_Anaerobic_006_A07

source_name: Calu-3 cells untreated mixed-oxic growth

value: Airway epithelium

tag: cell type

value: Non-small cell lung cancer

value: WT

value: Mixed oxic-anoxic growth


title: IVH-3d-3-150

value: Brain

value: The needle-puncture group with blood injection at 3rd day

value: Day 3

value: male


title: mouse heart, KO-443-3

value: ventricle

value: cardiomyocyte

value: neonatal

value: knockout


title: Rep3 t24 siPNUTS

value: iSLK cells

value: BAC16 infectious clone

value: siPNUTS

value: 1mM Sodium butyrate + 1 ug/mL doxycycline (24hr)


title: M54-LV-23

value: ischemia-reperfusion

value: Upy-PEG

value: heart; left ventricle


title: Sample_Anaerobic_006_A06

value: Airway epithelium

value: Non-small cell lung cancer

value: WT


title: M54-LV-21


title: Rep1 t48 siNT

value: siNT

value: 1mM Sodium butyrate + 1 ug/mL doxycycline (48 hr)


title: Sample_Anaerobic_CRS_005_A08

value: Mixed oxic-anoxic growth, challenged with anaerobic bacteria


title: IVH-3d-3-130

value: Brain

value: The needle-puncture group with blood injection at 3rd day

value: Day 3

value: male


title: Sample_Anaerobic_006_A05

value: Mixed oxic-anoxic growth


title: M54-LV-20

source_name: Upy-PEG_left ventricle


title: IVH-7d-2-110

value: The needle-puncture group with blood injection at 7th day

value: Day 7


title: Rep3 t24 siNT

value: iSLK cells

value: BAC16 infectious clone

value: 1mM Sodium butyrate + 1 ug/mL doxycycline (24hr)


title: Sample_Anaerobic_006_A04


title: Rep2 t24 siPNUTS

value: siPNUTS


title: Sample_Anaerobic_006_A03

value: Airway epithelium


title: M54-LV-17

value: ischemia-reperfusion

value: Upy-PEG

value: heart; left ventricle


title: IVH-3d-3-110


title: Rep1 t24 siPNUTS


title: M54-LV-19


title: IVH-3d-3-50


title: IVH-3d-3-20


title: Rep2 t24 siNT

value: siNT


title: Sample_Anaerobic

value: Non-small cell lung cancer

value: WT


title: IVH-7d-2-50

value: Brain


title: M54-LV-15


title: Sample_Aerobic_006_A02

source_name: Calu-3 cells untreated normoxic growth

value: Normoxic growth


title: M51LV23


title: IVH-1d-1-150

value: The needle-puncture group with blood injection at 1st day

value: Day 1

value: male


title: Sample_Aerobic_006_A01


title: IVH-1d-1-130


title: M51LV22


title: Rep1 t24 siNT


title: Rep3 t8 siNT

value: 1mM Sodium butyrate + 1 ug/mL doxycycline (8 hr)


title: Sample_Aerobic_005_A03


title: IVH-1d-1-110


title: IVH-1d-1-80


title: M51LV21


title: Sample_Aerobic_005_A02


title: M51LV20


title: Rep3 t8 siPNUTS

value: iSLK cells


title: M51LV19


title: IVH-1d-1-50


title: M51LV18


title: IVH-1d-1-20


title: Rep2 t8 siPNUTS

value: BAC16 infectious clone


title: Rep1 t8 siNT


title: Rep3 t0 siPNUTS


title: Rep1 t8 siPNUTS


title: Rep2 t8 siNT


title: M51LV17


title: Rep3 t0 siNT


title: 2B-NNK cells,NNK treatment 3

city: Guangzhou

first: qiaoyuan

last: yang

address: Xinzao Town, Panyu District

institute: Guangzhou Medical University

data_processing:
hisat2 v 2.1.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v 1.17 (parameter- Mapped: 0.85)
Trimmed sequence reads were mapped to GRCh37 using hisat2
Read count extractionwas performed using hisat2.
Read count normalization was performed using  R package "Ballgown".
Assembly: GRCh37
Supplementary files format and content: matrix table files include FPKM values for each Sample

source_name: lung

growth_protocol: BEAS-2B and 2B-NNK cells were maintained in BEBM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using  TRIzol reagent (Invitrogen, Carlsbad, CA, USA) .   1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit(Illumina) following manufacturer's protocols.

treatment_protocol: Cells were seeded in 6-well plates containing 100 mg/L NNK and cultured for 24 h every 4 d. Finally, the total amount of NNK processed was 1mg.

value: lung

value: epithelial cell

value: NNK treatment


title: M51LV15


title: ASPC1_1_Input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: pancreatic ductal adenocarcinoma cells

tag: chip antibody


title: ASPC1_1_IP

value: NUSAP1 (proteintech, #12024-1-AP)


title: AML12 cells, AOF5

first: Yang

last: Zhen

state: China/Guangdong

address: 190 Kaiyuan Avenue, Science Park,

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

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Genome_build: GRCm39
Supplementary_files_format_and_content: tab-delimited text file includes raw gene counts and FPKM values for each Sample

source_name: hepatocyte cell line

extract_protocol:
The total RNA of each sample was isolated using TRI Reagent (MRC, USA) according to the manufacturer’s protocol. Quality and quantity of total RNA were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). The RNA from three sample within each group was mixed in equal amounts. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatocyte

value: 0.5mM free fatty acid (FFA ) for 24 hours

tag: infection

value: DKK1 lentiviruses infect AML12 cells

value: DKK1 overexpression


title: 2B-NNK cells,NNK treatment 2

value: WT


title: ALLO_rep2

city: Wuhan

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

data_processing:
Clean reads were mapped to the mm10 (UCSC) mouse genome with  subjunc (subread v1.6.4) with default parameters.
Transcripts were assembled Expression quantitation using featureCounts (subread v1.6.4) with mouse annotation (release_M20) from Gencode
Differential gene expression was calculated using the DESeq2 package (v1.30.0) package of the R (version 4.0.3) software
Genome_build: mm10
Supplementary_files_format_and_content: Comma-Separated Row counts for each sample

source_name: aortic

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI Shenzhen, China).

value: aortic


title: M51LV09

source_name: PBS_left ventricle

value: PBS

value: heart; left ventricle


title: Rep2 t0 siPNUTS

value: siPNUTS


title: 2B-NNK cells,NNK treatment 1


title: AML12 cells, AGF5

value: green fluorescent protein negative control lentiviruses infect AML12 cells

value: control


title: ALLO_rep1

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology


title: BEAS-2B cells, Control 3

value: Without treatment


title: Sample_Aerobic_005_A01

value: Airway epithelium

value: Non-small cell lung cancer

value: Normoxic growth


title: M51LV08


title: M51LV07


title: ISO_rep2


title: Rep2 t0 siNT

value: iSLK cells

value: BAC16 infectious clone

value: siNT


title: Rep1 t0 siPNUTS


title: ISO_rep1


title: M51LV05


title: BEAS-2B cells, Control 1

value: lung

value: epithelial cell


title: BEAS-2B cells, Control 2


title: Rep1 t0 siNT


title: MARCM sd 2

status: Public on Nov 18 2022

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven

data_processing:
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt (-q 15 --minmum-length 60)
Trimmed sequence reads were mapped to dm6 using STAR v2.6.1d (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: dm6
Supplementary files format and content: Tab-delimited text files with raw gene counts for every gene and every sample in a given experiment

organism: Drosophila melanogaster

source_name: eye-antennal imaginal discs

growth_protocol: All larvae were raised on standard fly food at 25°C.

extract_protocol:
Drosophila imaginal discs were dissected and transferred into RNAse-free 1xPBS on ice; a minimum of 30 discs per sample were used.
RNA was extracted immediately using the RNAeasy mini spin kit (Qiagen) and stored at -80°C.
Library preparation was performed according to the QuantSeq 3’ mRNA-Seq Library Prep kit FWD (Lexogen).

value: eye-antennal imaginal discs

value: sd47M FRT19A/tub-Gal80 FRT19A; ey-FLP Act 5C<y+<Gal4 UAS-GFP/+

tag: batch

value: seq run 1

tag: time point

value: 5 days after egg laying

tag: group

value: MARCM sd-


title: optix ctrl 2

value: w/y v; optix-Gal4/+; UAS-lucRNAi/+

value: optix ctrl


title: MARCM yki3SA 2

description:
MARCM_Counts.txt
YkiHyper_Optix_Counts.txt
YkiHyper_Counts.txt

value: FRT19A/tub-Gal80 FRT19A; ey-FLP Act 5C<y+<Gal4, UAS-GFP/+; UAS-yki3SA/+

value: MARCM yki3SA


title: MARCM yki3SA sd 3

value: sd47M FRT19A/tub-Gal80 FRT19A; ey-FLP Act 5C<y+<Gal4 UAS-GFP/+; UAS-yki3SA/+

value: MARCM yki3SA sd-


title: MARCM sd 3


title: optix yki3SA 1

value: w/y v; optix-Gal4/+; UAS-yki3SA/+

value: optix yki3SA


title: optix ctrl 3


title: MARCM yki3SA 3


title: MARCM sd 1


title: MARCM yki3SA 5


title: optix yki3SA 2


title: MARCM yki3SA 4


title: eyFLP ctrl 1

description:
YkiHyper_Optix_Counts.txt
YkiHyper_Counts.txt

value: y w eyFLP/ y w; +/+; FRT82B cl-/FRT82B

value: eyFLP ctrl


title: eyFLP ctrl 2


title: eyFLP wts KO 2

value: y w ey-FLP/y w; +/+; FRT82B cl-/FRT82B wts149

value: eyFLP wts-


title: MARCM WT 5

value: eye-antennal imaginal discs

value: FRT19A/tub-Gal80 FRT19A; ey-FLP Act 5C<y+<Gal4, UAS-GFP/+; +/+

value: MARCM ctrl


title: MARCM yki3SA sd 1

value: seq run 1

value: 5 days after egg laying


title: MARCM WT 2


title: MARCM yki3SA 1


title: MARCM WT 4


title: MARCM WT 3


title: optix ctrl 1

value: w/y v; optix-Gal4/+; UAS-lucRNAi/+


title: MARCM WT 1


title: Non-pupating larvae 11 days 2

data_processing:
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt (-q 15 --minmum-length 60)
Trimmed sequence reads were mapped to dm6 using STAR v2.6.1d (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: dm6
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample

treatment_protocol: The YPH erg2∆::TRP1 yeast strain unable to produce the hormone precursors necessary for the onset of pupation in Drosophila was cultured for 48h at 30°C, centrifuged at 4°C, 1500g for 3min, and the pellet was washed with PBS 3 times as described {Katsuyama, 2013}. The resulting yeast paste was stored at -20°C. For medium preparation, the yeast paste was boiled for 30 minutes and mixed with 10% sucrose, 1.5% agar solution and sterile water in the proportions 10:1:8:20. Nipagin and penicillin were added to prevent fungal and bacterial growth. Adult flies were left overnight to lay eggs, the medium was incubated at 25°C and the larvae were dissected on the day specified.

tag: medium

value: pupation-preventing food

value: 11 days after egg laying

value: growth completed


title: eyFLP ctrl 3


title: Non-pupating larvae 11 days 1


title: MARCM yki3SA sd 2

value: sd47M FRT19A/tub-Gal80 FRT19A; ey-FLP Act 5C<y+<Gal4 UAS-GFP/+; UAS-yki3SA/+


title: Non-pupating larvae 5 days 3

value: actively growing


title: eyFLP wts KO 1


title: Non-pupating larvae 5 days 1

value: actively growth


title: Non-pupating larvae 5 days 2


title: Lb3

city: Lanzhou

first: Bo

last: Zhang

address: No. 1 Yingmen village, Anning District

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get clean tags, raw reads were further filtered according to the following rules:  1) Removing low quality reads containing more than one low quality (Q-value≤20) base or  containing unknown nucleotides(N);  2) Removing reads without 3’adapters;  3) Removing reads containing 5’adapters;  4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them;  5) Removing reads containing ployA in small RNA fragment;  6) Removing reads shorter than 18nt (not include adapters).
All of the clean tags were aligned with small RNAs in GeneBank database(Release 209.0) to identify and remove rRNA, scRNA, snoRNA, snRNA and tRNA.Meanwhile all of the clean tags were aligned with small RNAs in Rfam database(Release 11.0) to identify and remove rRNA, scRNA, sonRNA, snRNA and tRNA.
All of the clean tags were also aligned with reference genome
All of the clean tags were then searched against miRBase database(Release 22) to identify known (Species studied) miRNAs (exist miRNAs), and according to their genome positions and hairpin structures predicted by software mirdeep2, the novel miRNA candidates were identified.
Based on all miRNA expression in each sample, the miRNA expression level was calculated and normalized to transcripts per million (TPM)
Genome_build: Sus scrofa 11.1 (ncbi_GCF_000003025.6)
Supplementary_files_format_and_content: Matrix table of TPM values of every miRNA in every sample and sequence information table of novel miRNAs

organism: Sus scrofa

source_name: testis

extract_protocol:
All samples were immediately snap frozen in liquid nitrogen and stored at -80°C until RNA extraction, and RNA was harvested using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA).
Small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Landrace pig

tag: age

value: testis


title: Non-pupating larvae 11 days 3

tag: tissue

tag: genotype


title: FLI20

city: Madison

last: Ortega

state: Wisconsin

address: 1675 Observatory Drive

department: Department of Animal and DairySciences

institute: University of Wisconsin

description: half of filamentous conceptus

data_processing:
The quality of fastq files of sequences data was checked with a FastQC tool
Illumina adapters were trimmed
Reads were mapped to the bovine reference genome using the Hisat2
Read counts were determined using FeatureCounts program
Differentially expressed genes (DEGs) between sample groups were determined by edgeR-robust
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: day 15 bovine conceptus-half

growth_protocol: in vitro embryo development

extract_protocol:
trizol/chloroform
mRNA Stranded Library Preparation (poly A enrichment)

treatment_protocol: addition of FGF2, LIF, and IGF1

tag: treatment

value: FGF2, LIF, IGF1 treatment

tag: developmental stage

value: filamentous conceptus


title: FLI50

description: half of filamentous conceptus


title: CON4M

description: half of filamentous conceptus

value: control


title: La2


title: Lb2


title: FLI3M

description: half of filamentous conceptus


title: CON20

description: half of filamentous conceptus


title: Piezo1 cKO 2

city: Shizuoka

first: Yuji

last: Hara

address: 52-1 Yada,Suruga-ku

department: Department of Integrative physiology

country: Japan

institute: School of Pharmaceutical Sciences, University of Shizuoka

data_processing:
Mapping of sequence reads to a reference genome (GRCm38.102) was done using STAR (2.7.9a).
The mapped reads were annotated by featureCounts (v.2.0.1) and counted by UMI-tools (ver.1.1.1).
Assembly: GRCm38.102
Supplementary files format and content: counts for each Sample

source_name: muscle satellite cell

growth_protocol: FACS isolated muscle satellite cells were cultured in growth medium (DMEM supplemented with 30% foetal bovine serum (Sigma), 1% chicken embryo extract (US Biological), 10 ng/mL basic fibroblast growth factor (ORIENTAL YEAST Co., Ltd.), and 1% penicillin-streptomycin (FUJIFILM Wako Pure Chemical Corporation) on culture dishes coated with Matrigel (Corning) for 3 days. 4-OH TMX (Sigma; 1 μM) was added to both control and Piezo1 cKO growth medium for freshly isolated MuSC culture.

extract_protocol:
Total RNA was obtained from cultured MuSCs using RNeasy Micro Kit (Qiagen).
To synthesize complementary DNA (cDNA), 500 pg of the total RNA were reverse transcribed with SMARTScribe Reverse Transcriptase (639536, Takara Bio) in a 15 μL reaction volume following the manufacturer’s protocol with minor modifications. Briefly, the reaction mix contained 1xFirst-Strand Buffer, 2.4 μM biotinylated LNA template-switching oligonucleotide (TSO: AAGCAGTGGTATCAACGCAGAGTACrGrG+G; Qiagen), 1.2 μM barcoded primers (SI appendix Table 3), 1 mM dNTP mix, 2 mM DTT, 11 U/μL RNase inhibitor, 1 U/μL SMARTScribe Reverse Transcriptase (639536, Takara Bio), and 0.475 x Lysis buffer (365013, Takara Bio). The reaction mix was incubated at 42C for 90 min and then 70C for 10 min. The residual primers were digested by adding 0.75 μL of exonuclease I (5 U/μL) and incubating at 37C for 30 min followed by 80C for 20 min. The synthesized cDNA was amplified by 12 cycles of PCR with SeqAmp DNA polymerase (638504, Takara Bio). The PCR product was purified with 1.0 AMPure XP (Beckman Coulter). The purified DNA samples were pooled at an equal mass concentration and 400 pg was used for constructing a sequencing library (Nextera XT DNA Library Preparation Kit, Illumina). The final product was purified with 0.6x of AMPure XP.

value: muscle satellite cell

tag: strain background

value: Piezo1 cKO

tag: time

value: Day 3


title: DEGRON 2

city: Salamanca

first: Sofía

last: Muñoz Félix

address: Campus Miguel de Unamuno

department: Cancer Research Institute (CIC)

country: Spain

institute: Universidad de Salamanca

description: nucleosomal DNA

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=25 –quality-cutoff=20”.
BWA (version 0.5.9-r16) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the yeast sacCer3 genome downloaded from the UCSC (Karolchik et al., 2004).
Alignments were filtered to remove read pairs that were discordant, mapped to different chromosomes, ambiguously mapped, had an insert size outside the range 120-200 bp, and mismatch > 4 in any reads.
Assembly: sacCer3
Supplementary files format and content: Genome-wide wig files were generated by treating each pair of reads as a single fragment, and normalising to 10 million reads.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in complete synthetic medium lacking methionine, arrested 1.5 hour with alpha-factor and treated with methionine and indole-3-acetic acid (IAA) for 30 minutes.

extract_protocol:
Preparation of mono-nucleosomal DNA was performed as described (Lantermann et al. 2009) followed by high throughput sequencing on Illumina HiSeq 4000 platform. Briefly, cells were grown under the specified conditions and then fixed with 1% formaldehide. Spheroblasts were obtained and the chromatin digested with 30u/ml of Mnase (ThermoFisher) at 37°C for 20 minutes. The samples were then treated with Proteinase K and RNase A to isolate the undigested, mono-nucleosomal DNA. The DNA was then size selected and purified in a 1.5% agarose gel.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's protocol.

treatment_protocol: Cells were cross-linked with 1% Formaldehide for 20 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.

tag: strain


title: wild type 3

value: wild type


title: Lb1


title: Piezo1 cKO 1


title: wild type 1


title: Piezo1 cKO 3


title: La1


title: La3


title: Micorwell-seq datasets of mouse_kidney_blood

first: Fang

last: Ye

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

value: BALB/c

value: Kidney

tag: Sex

value: Male


title: Micorwell-seq datasets of mouse_kidney_lymphocytes


title: Hb2

value: Hezuo pig


title: Micorwell-seq datasets of mouse_kidney_solid organ

source_name: mouse_kidney_solid organ


title: Hb3


title: FLI4M

description: half of filamentous conceptus


title: CON3M

description: half of filamentous conceptus


title: CON10

description: half of filamentous conceptus


title: wild type 2

tag: cell type


title: WT 2

description: nucleosomal DNA

value: MATa pADH1-OsTir1-Myc9::ADE2


title: Micorwell-seq datasets of mouse_liver_lymphocytes

value: Liver


title: Hb1


title: Micorwell-seq datasets of mouse_liver_solid organ

source_name: mouse_liver_solid organ


title: Micorwell-seq datasets of mouse_heart_blood

value: Heart


title: Micorwell-seq datasets of mouse_heart_lymphocytes


title: Ha3


title: Ha2


title: MARCM yki3SA batch2 1

value: eye-antennal imaginal discs

value: y w ey-FLP; FRT42D/FRT42D tub-Gal80; UAS-yki3SA/tub-Gal4 UAS-GFP

value: seq run 2

value: 5 days after egg laying

value: MARCM yki3SA


title: PGC-1beta muscle knockout, quadriceps, 24h fasted, biol rep3

first: Christoph

last: Handschin

address: Spitalstrasse 41

institute: Biozentrum, University of Basel

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41039 (399)

data_processing:
CLC Genomics Workbench v 9.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Excel file (.xlsx) with TPM values, calculated fold change and FDR

source_name: Skeletal muscle

extract_protocol:
mRNA was isolated using the Dynabeads mRNA direct kit (Ambion), and purified with the RNAeasy Mini elute Clean-up Kit 50 (Qiagen)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Mice were either fed or fasted for 24 hours

value: Skeletal muscle

value: PGC-1beta muscle-specific knockout

value: 24 hours fasted


title: MARCM yki3SA sd batch2 1

value: sd47M FRT19A/tub-Gal80 FRT19A; ey-FLP Act 5C<y+<Gal4 UAS-GFP/+; UAS-yki3SA/+

value: MARCM yki3SA sd-


title: PGC-1beta muscle knockout, quadriceps, 24h fasted, biol rep2

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41038 (398)


title: PGC-1beta muscle knockout, quadriceps, 24h fasted, biol rep5

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41041 (401)


title: MARCM sd batch2 1

value: sd47M FRT19A/tub-Gal80 FRT19A; ey-FLP Act 5C<y+<Gal4 UAS-GFP/+

value: MARCM sd-


title: MARCM yki3SA sd batch2 2


title: Wildtype, quadriceps, 24h fasted, biol rep4

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41036 (425)

value: wildtype control


title: MARCM sd batch2 2


title: PGC-1beta muscle knockout, quadriceps, 24h fasted, biol rep1

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41037 (396)


title: MARCM WT batch2 2

value: y w ey-FLP/y w; FRT42D/FRT42D tub-Gal80; +/tub-Gal4 UAS-GFP

value: MARCM ctrl


title: MARCM WT batch2 1


title: Wildtype, quadriceps, 24h fasted, biol rep2

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41034 (406)


title: Wildtype, quadriceps, 24h fasted, biol rep1

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41033 (395)


title: PGC-1beta muscle knockout, quadriceps, fed, biol rep5

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41032 (225)

value: fed


title: PGC-1beta muscle knockout, quadriceps, fed, biol rep4

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41031 (224)


title: Micorwell-seq datasets of mouse_liver_blood

value: BALB/c

value: Liver

value: Male


title: PGC-1beta muscle knockout, quadriceps, fed, biol rep3

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41030 (223)


title: C2C12 cell, Val+PA 3, VP3

city: 荆州市

first: 炳熙

last: 高

state: 湖北省

address: 湖北省荆州市荆秘路88号

department: 动物科学学院

institute: 长江大学

data_processing:
To ensure the quality and reliability of data analysis, it is necessary to remove the reads with connectors, N ratio greater than 0.002, and the reads with low-quality alkali base exceeding 50% of the length ratio of the reads in the single end reads to filter the original data (this step generates clean reads)
Use the HISAT2 software to compare the filtered clean reads to the mouse reference genome for subsequent analysis. This study uses the reference genome version: GRCm38 (Ensemble release 103).
Use featureCounts software to quantify the genes in the sample, obtain the counts expression matrix, and use the DEseq2 software package in R language to analyze the differential expression of genes. Set p.adj<0.05 and | log2FC |>1 as the criteria for screening differentially expressed genes.
Supplementary files format and content: genes_count.counts.matrix
Supplementary files format and content: genes_count.TMM.EXPR.matrix

growth_protocol: C2C12 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and 100 μg/mL antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs for all tissues and cells used in the current study, were extracted using 1 mL Trizol Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.1.0 ug of total RNA was used for the construction of sequencing
Strand-specific libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
Illumina PE150

treatment_protocol:
Sequencing samples were divided into three groups: control group (Control group), valine treatment group (Valine group), and valine palmitic acid co treatment group (Val+PA group)
Three six well plates were taken, and the OPTI-MEM medium was replaced after 12 hours of planking. After 12 hours of starvation, the cells of No. 1 plate were collected and labeled as C1-C6 as the control group for this sequencing (Control group); The second plate was added with 0.45 mM final concentration of valine to continue to culture for 36 h, labeled as V1-V6, as the valine treatment group (Valine group); Plate 3 was treated with valine with final concentration of 0.45 mM for 24 h, and the final concentration of 75 μ M Palmitic acid was treated for 12 h, labeled VP1-VP6, as the co treatment group of valine and palmitic acid (Val+PA group).
After receiving the samples, randomly select 3 samples from each group of 6 samples and send them to the company for sequencing. The client of this sequencing is Beijing Nuohe Zhiyuan

tag: cell line

value: myoblast

value: Val+PA


title: C2C12 cell, Val+PA 1, VP1

address: 湖北省荆州市荆秘路88号


title: C2C12 cell, Valine 3, V3

address: 湖北省荆州市荆秘路88号

value: Valine


title: Ha1

value: Hezuo pig

value: testis


title: C2C12 cell, Val+PA 2, VP2

address: 湖北省荆州市荆秘路88号


title: PGC-1beta muscle knockout, quadriceps, 24h fasted, biol rep4

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41040 (400)

value: Skeletal muscle

value: PGC-1beta muscle-specific knockout

value: 24 hours fasted


title: C2C12 cell, Valine 2, V2

address: 湖北省荆州市荆秘路88号


title: PGC-1beta muscle knockout, quadriceps, fed, biol rep2

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41029 (132)


title: Wildtype, quadriceps, fed, biol rep4

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41027 (259)


title: C2C12 cell, Valine 1, V1

address: 湖北省荆州市荆秘路88号


title: PGC-1beta muscle knockout, quadriceps, fed, biol rep1

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41028 (130)


title: Wildtype, quadriceps, 24h fasted, biol rep3

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41035 (424)


title: Wildtype, quadriceps, fed, biol rep3

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41026 (258)


title: C2C12 cell, Control 2, C2

address: 湖北省荆州市荆秘路88号

value: Control


title: Wildtype, quadriceps, fed, biol rep2

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41025 (237)


title: e135 caudal MNs

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
The raw Bcl output from Illumina sequencers and fastq files were processed with 10X Genomics Cell Ranger Pipeline (v2.1.11). The scRNA-seq data were demultiplexed, mapped to mouse reference genome (mm10) using STAR aligner, filtered and counted for barcode and UMI. r1-length = 26bp. Same sample from multiple sequencing runs were merged.
The generated cell barcode and gene expression matrix were further analysed using Seurat (v2.3.4). For both rostral and caudal samples, cells were retained for subsequent analysis if they displayed a number of genes between 1000 and 5300, UMI counts  <30500, as well as <10% mitochondrial counts. The digital data matrices were normalized by a global method, whereby the expression value of each gene was divided by the total expression in each cell and multiplied by a scale factor (10,000 by default). These values were then log-transformed with a pseudocount of 1. Highly variable genes across cells were selected using the FindVariableGenes function (parameters: x.low.cutoff = 0.0125, x.high.cutoff = 3, y.cutoff = 0.5). To identify cell clusters, principal component (PC) analysis was first performed using the top 34 PCs for the rostral sample and the top 31 PCs for the caudal sample, where the number of significant PCs was determined based on an elbow plot and jackstraw test. Cells were then clustered using the Louvain community dection method in the FindClusters function (resolution = 0.05) and visualized using Uniform Manifold Approximation and Projection (UMAP).
Genome_build: mm10
Supplementary_files_format_and_content: *MN_mm10.tar.gz contains tsv files containing gene feature and cell features of cells, and mtx file containing expression matrix of all cells collected, sequenced in two sequencing runs with Nextseq and Novaseq platforms

source_name: spinal cord

extract_protocol:
Spinal cordssegments were dissected in L15 medium and cells were dissociated using enzymatic (papain) and mechanical approach, following manufacturer's instruction (Neural Tissue Dissociation Kit (P) and gentleMACS dissociator, Miltenyi Biotec). Cell suspension was filtered through 70µm strainer and subjected to FACS with 85um nozzle diameter under 45 psi to enrich GFP-positive cells. Collected cells were centrifuged at 1000rpm for 5 minutes and resuspended in 1%FBS supplemented DMEM. Cells viability and concentration was determined using Countess II Automated Cell Counter. Cells were loaded into 10x Chromium Controller using Single Cell 3' v2 reagents for single cell isolation.
scRNA-seq libraries were generated following manufacturer's instruction (10X Genomics, Chromium Single Cell 3’ v2) and sequenced using a NextSeq 500 platform with pair-ended reads (PE150: Read 1: 28 bp; Read 2: 122 bp) and NovaSeq S4 150 pair-ended reads (PE150: Read 1: 75 bp; Read 2: 75 bp).

value: B6.Cg-Tg(Hlxb9-GFP)1Tmj/J MGI:J:88764

tag: tissue/cell type

value: spinal motor neurons at caudal (lumbosacral, L1 to S5) segments


title: ITDvav

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

library_source: transcriptomic single cell

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via cellranger v6.0.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Assembly: mm10
Supplementary files format and content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Lin-Kit+ cells

extract_protocol: 10x Genomics Chromium single cell preparation 3' ver3.1

value: P14 (14 days old)

value: ITDvav


title: NHD13


title: m6a immunoprecipitation

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

data_processing:
library strategy: MeRIP-seq
After quality control, clean RNA-seq data were aligned to the reference genome (UCSC mm10) with Hisat2 software v2.2.1
Peaks were called uing MACS v3.0.0a7 with the significance cut-off q-value <=0.05
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: whole uterus

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB).

value: whole uterus (GD4 uterus and GD8 uterus were pooled in equal amounts)

tag: antibody

value: anti-m6a (Synaptic Systems, #202003)


title: input control

value: whole uterus


title: RIP-Seq 8: ESC media- first replicate

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

description: ESC media- first replicate

data_processing:
Degradation assay: Raw data quality control was done using FASTQC (Version 0.11.9).
Degradation assay: Reads were aligned to reference genome (GRCm38/mm10, Dec. 2011) with STAR (Version 2.4.0.1). RIP-Seq: Raw RNA/RIP-seq reads for each condition were mapped to the reference mouse genome using TopHat program.
Degradation assay: Read normalization and differential gene expression analysis with multiple testing corrections were conducted using the R Bioconductor DESeq2 package in R Studio. RIP-Seq: TopHat results were used to run Cufflinks that generates a transcriptome assembly file for each input condition, and combined using Cuffmerge. This merged assembly was the final file used to calculate gene and transcript expression in each sample. The reads and the merged assembly provided to Cuffdiff that calculates differential expression levels as well as tests the statistical significance.
Degradation assay: TPM values were fitted to an exponential decay model (X(t) = X0*exp(-bt); b = degradation rate (1/hr)), and transcripts with minimal degradation rate (b<0.05, corresponding to a half-life of >13.86 hours) in WT cells were selected as a control set for normalization, resulting in a control set of 356 genes (Figure S4). All samples were subsequently normalized based on this control set, to a temporally constant average expression level of this control set. These normalized TPM values were fitted again to an exponential decay model, and the resulting degradation rates for each transcript were used for subsequent analysis.
Genome_build: GRCm38/mm10

source_name: ESCs

growth_protocol: Caprin1 KO and R1 cells were cultured for 4 days in ESC medium without LIF and with 1 µM RA in the medium.

extract_protocol:
Degradation assay: RNA was extracted and purified using RNA isolation kit (Qiagen). RIP-Seq: The beads were mixed with RLT buffer and samples were processed according to RNA-isolation kit (Qiagen) following manufacturer’s instruction.
Degradation assay: Indexed RNA-Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc.) according to the manufacturer’s protocol. Libraries were size-selected with SPRI beads and quantified by QuBIT (Life Technologies). Average size of 300 bp was determined by TapeStation (Agilent Technologies, USA). Libraries are then sequenced using an Illumina Nextseq500 sequencer. RIP-Seq: cDNA libraries for each sample were generated from total RNA using the Quantseq 3′ mRNA-Seq Library Prep kit for Illumina (Lexogen) following the manufacturer’s instructions. Libraries were size-selected with SPRI beads and quantified by QuBIT (Life Technologies). Average size of ∼250 bp was determined by TapeStation (Agilent Technologies, USA). Libraries are then sequenced using an Illumina Nextseq500 sequencer.

treatment_protocol: Degradation assay: On the fourth day the cells were exposed to 2 µg/ml of α-amanitin (Sigma Aldrich) and samples were harvested at different time points (0, 2, 4, 8 hrs). RIP-seq: Whole procedure of IP was performed in an ice bath. Cells were washed (X2) by re-suspending the cell pellet with 0.5 ml of ice-cold PBS buffer, centrifuged for 5 min at 2000 rpm, and the supernatant was discarded. 1 ml of pre-cooled cell lysis buffer was added to the cell pellet. Cells were incubated for 30 min on ice, vortexed for 30 sec every 5 min for 30 min. Cell lysates were centrifuged for 30 min at 20,000 g at 4oC. Supernatant was collected and used for IP (2 mg lysate was used for each IP reaction). Background was pre-cleared by incubating the supernatant with 5 µl protein A beads (Magna ChIP™ Protein A Magnetic Beads, 16-661) for 30 min. The reaction mix was placed on the magnet till supernatant became clear. Supernatants were collected. CAPRIN1 antibody (2 µg) was added along with 20 µl protein A beads to supernatants and incubated for 4 hrs. Eppendorfs were placed on the magnet till supernatants became clear. Supernatants were removed and discarded. The bead was washed 3 times with cell lysate buffer.

value: Embryonic stem cells (ESCs)

value: mouse ESC media

value: WT


title: WT


title: NHD13ITDVav


title: BL/6 AAV-Cre 3

data_processing:
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt (-q 15 --minmum-length 60, -a AGATCGGAAGAG)
Trimmed sequence reads were mapped to mm10 using STAR v2.6.1d (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50mg/kg). Livers were perfused for 5min with 40ml of perfusion medium SC-1 to remove the blood and for rapid destruction of intercellular junctions, followed by perfusion with 40ml of SC-2 medium containing 10mg collagenase for 5min to break up the supporting extracellular matrix. Each lobe was dissected off, and the tissue was disrupted inside of a beaker containing 50ml of SC-2 with 20mg collagenase (Roche) and 1ml DNase I (Sigma) followed by rotating incubation for 20min at 37°C. Cells were then filtered through a 100μm strainer and centrifuged at 50g for 2min at room temperature. Hepatocytes were washed once with 1X PBS and centrifuged again at 50g for 2min. Pellet was resuspend with 2ml of 1X PBS containing 0.04% BSA, filtered through a 70µm strainer and FACS sorted. 500,000 sorted cells were collected and lysed for RNA extraction.
RNA was extracted immediately using the RNAeasy mini spin kit (Qiagen) and stored at -80°C.
Library preparation was performed according to the QuantSeq 3’ mRNA-Seq Library Prep kit FWD (Lexogen).

treatment_protocol: Induction of hepatocyte-specific recombination of floxed alleles in Lats1flox/flox; Lats2flox/flox mice was achieved by injection of Adeno-associated virus serotype 8 (AAV8) expressing Cre recombinase under the hepatocyte specific TBG promoter which was purchased from UPenn (AAV8.TBG.PI.Cre.rBG, catalog AV-8-PV1091). Mice received 5x1011 GC (genome complements) of AAV8.TBG.PI.Cre.rBG diluted in 200μl of 1x phosphate-buffered saline (PBS) by tail vein injection. Animals were sacrificed 24 hours after AVV-Cre injection.

value: Liver

value: Hepatocyte

value: AAV8-Cre injection

tag: effective genotype

value: BL/6 AAV-Cre


title: RIP-Seq 6: arsenate (200uM/2h)- first replicate

description: arsenate (200uM/2h)- first replicate

value: arsenate (200uM/2h)


title: C2C12 cell, Control 3, C3

address: 湖北省荆州市荆秘路88号

value: myoblast


title: RIP-Seq 7: arsenate (200uM/2h)- second replicate

description: arsenate (200uM/2h)- second replicate


title: BL/6 AAV-Cre 1

tag: group


title: BL/6 AAV-Cre 2


title: RIP-Seq 4: nocodazole (10uM/8h)- first replicate

description: nocodazole (10uM/8h)- first replicate

value: nocodazole (10uM/8h)


title: RIP-Seq 5: nocodazole (10uM/8h)- second replicate

description: nocodazole (10uM/8h)- second replicate


title: BL/6 Dox 3

treatment_protocol: 0.2mg/ml doxycycline hyclate (Sigma) was diluted in filtered sterile drinking water supplemented with 2,5% sucrose and administered ad libitum. Doxycycline containing water bottles were protected from light and replaced every other day. Animals were sacrificed after 1 week of doxycyline administration.

value: doxycycline - 1 week

value: BL/6 Dox


title: C2C12 cell, Control 1, C1

address: 湖北省荆州市荆秘路88号

value: Control


title: BL/6 Dox 4


title: Wildtype, quadriceps, fed, biol rep1

description:
Run mode: NEXTSEQ_HIGH
BSSE_QGF_41024 (58)

value: Skeletal muscle

value: wildtype control

value: fed


title: RIP-Seq 1: control

description: control

value: Caprin 1 KO


title: BL/6 ctrl 4

value: BL/6 ctrl


title: BL/6 Dox 1


title: RNA-seq: WT, 8h, rep 3

description: WT, 8h, rep 3

value: Embryonic stem cells (ESCs)

value: alpha amanitin


title: RIP-Seq 2: RA- first replicate

description: RA- first replicate

value: RA

value: WT


title: RIP-Seq 9: ESC media- second replicate

description: ESC media- second replicate

value: mouse ESC media


title: e135 rostral MNs

value: B6.Cg-Tg(Hlxb9-GFP)1Tmj/J MGI:J:88764

value: spinal motor neurons at rostral (brachial and thoracic vertebral segments, from C4 to T3)


title: RNA-seq: WT, 8h, rep 4

description: WT, 8h, rep 4


title: BL/6 ctrl 3

value: Liver

value: Hepatocyte


title: BL/6 Dox 2

value: doxycycline - 1 week


title: BL/6 ctrl 2


title: BL/6 ctrl 1


title: RNA-seq: WT, 8h, rep 1

description: WT, 8h, rep 1


title: RNA-seq: Caprin1 KO clone 4 8h, rep 2

description: Caprin1 KO clone 4 8h, rep 2


title: RNA-seq: WT, 8h, rep 2

description: WT, 8h, rep 2


title: Lats1/2 KO 3

treatment_protocol: Induction of hepatocyte-specific recombination of floxed alleles in Lats1flox/flox; Lats2flox/flox mice was achieved by injection of Adeno-associated virus serotype 8 (AAV8) expressing Cre recombinase under the hepatocyte specific TBG promoter which was purchased from UPenn (AAV8.TBG.PI.Cre.rBG, catalog AV-8-PV1091). Mice received 5x1011 GC (genome complements) of AAV8.TBG.PI.Cre.rBG diluted in 200μl of 1x phosphate-buffered saline (PBS) by tail vein injection. Animals were sacrificed 1 week after AVV-Cre injection.

value: Lats1flox/flox; Lats2flox/flox

value: AAV8-Cre injection

value: Lats1/2 KO


title: Lats1/2 KO 2


title: RIP-Seq 3: RA- second replicate

description: RA- second replicate


title: Lats1/2 KO 1


title: RNA-seq: Caprin1 KO clone 2 8h, rep 2

description: Caprin1 KO clone 2 8h, rep 2


title: Lats1/2 flox ctrl 3

value: Lats1/2 flox ctrl


title: RNA-seq: Caprin1 KO clone 2 8h, rep 1

description: Caprin1 KO clone 2 8h, rep 1


title: RNA-seq: WT, 4h, rep 4

description: WT, 4h, rep 4


title: RNA-seq: WT, 4h, rep 3

description: WT, 4h, rep 3


title: Lats1/2 flox ctrl 4


title: Lats1/2 flox ctrl 2


title: RNA-seq: WT, 4h, rep 2

description: WT, 4h, rep 2


title: Lats1/2 flox ctrl 1


title: TSPC cells, NAC，7days 3

city: Chongqing

first: Kang

last: Lu

address: Gaotanyanzheng street

institute: The Second Affiliated Hospital of Chongqing Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: tendon

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: tendon

value: mesenchymal stem cells

value: tendon stem/progenitor cells

value: tenogenic differentiation


title: TSPC cells, NAC，7days 2


title: RNA-seq: Caprin1 KO clone 4 4h, rep 2

description: Caprin1 KO clone 4 4h, rep 2

value: Embryonic stem cells (ESCs)

value: alpha amanitin

value: Caprin 1 KO


title: RNA-seq: WT, 4h, rep 1

description: WT, 4h, rep 1

value: WT


title: RNA-seq: Caprin1 KO clone 4 4h, rep 1

description: Caprin1 KO clone 4 4h, rep 1


title: TSPC cells, NAC，7days 1


title: RNA-seq: Caprin1 KO clone 2 4h, rep 1

description: Caprin1 KO clone 2 4h, rep 1


title: RNA-seq: Caprin1 KO clone 2 4h, rep 2

description: Caprin1 KO clone 2 4h, rep 2


title: TSPC cells, Control，7days 3


title: ApoYap Dox 3

value: ApoE-rtTA, TRE-hYAP

value: Apo>Yap

value: ApoYap Dox


title: RNA-seq: WT, 2h, rep 4

description: WT, 2h, rep 4


title: ApoYap Dox 2

value: Liver

value: Hepatocyte


title: TSPC cells, Control，7days 2


title: RNA-seq: WT, 2h, rep 3

description: WT, 2h, rep 3


title: ApoYap Dox 1

value: doxycycline - 1 week


title: RNA-seq: WT, 2h, rep 2

description: WT, 2h, rep 2


title: RNA-seq: WT, 2h, rep 1

description: WT, 2h, rep 1


title: TSPC cells, Control，7days 1


title: RNA-seq: Caprin1 KO clone 4 2h, rep 2

description: Caprin1 KO clone 4 2h, rep 2


title: ApoYap ctrl 4

value: ApoYap ctrl


title: RNA-seq: Caprin1 KO clone 4 2h, rep 1

description: Caprin1 KO clone 4 2h, rep 1


title: RNA-seq: Caprin1 KO clone 2 2h, rep 2

description: Caprin1 KO clone 2 2h, rep 2


title: KO2

city: DALLAS

last: Yan

state: TEXAS

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Raw sequencing data was processed with Astrocyte RNASeq Analysis Workflows at UT Southwestern Bioinformatics Core Facility (https://astrocyte.biohpc.swmed.edu/workflow/12/version/324/docs) to generate Fragments Per Kilobase Million (FPKM) for each transcript.
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample

source_name: epidermis

extract_protocol:
RNeasy Mini Kit (QIAGEN, 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epidermis


title: ApoYap ctrl 3


title: KO1


title: RNA-seq: Caprin1 KO clone 2 2h, rep 1

description: Caprin1 KO clone 2 2h, rep 1


title: RNA-seq: WT, 0h, rep 4

description: WT, 0h, rep 4


title: RNA-seq: WT, 0h, rep 3

description: WT, 0h, rep 3


title: ApoYap ctrl 2


title: RNA-seq: WT, 0h, rep 2

description: WT, 0h, rep 2


title: WT2

value: Skiv2l ctl


title: RNA-seq: Caprin1 KO clone 4 0h, rep 2

description: Caprin1 KO clone 4 0h, rep 2


title: RNA-seq: Caprin1 KO clone 4 0h, rep 1

description: Caprin1 KO clone 4 0h, rep 1


title: RNA-seq: WT, 0h, rep 1

description: WT, 0h, rep 1


title: RNA-seq: Caprin1 KO clone 2 0h, rep 2

description: Caprin1 KO clone 2 0h, rep 2


title: F17_M_RNA

city: Grand Rapids

first: Ronald

middle: L

last: Chandler

state: Michigan

address: 400 Monroe Ave NW

institute: Michigan State University

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation with flag ‘--sjdbOverhang 49’ equivalent to (read length – 1), via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for unstranded (libtype), corresponding to column 2 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average). Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Assembly: mm10 indexed to GENCODE (vM16) GFF3 annotation
Supplementary files format and content: Tabular text files including gene counts (STAR output) for each sample.

source_name: Uterus

growth_protocol: 8 week old mice were placed on high-fat diet or control diet for 18 weeks. Uteri were collected after 18 weeks on diet (26 weeks of age).

extract_protocol:
Uteri were digested using Multi Tissue Dissociation Kit II (Miltenyi Biotec) and filtered using 40 micron mesh filters.Macrophages were magnetically sorted using anti-F4/80 microbeads. Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. Stroma cells were collected following removal of macrophages and epithelia. RNA was collected using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher).
Total RNA material was converted to dsDNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, v. 091817 (Takara Bio USA). The Nextera DNA flex library prep kit (Illumina) was used to generate Illumina compatible sequencing libraries.

value: Uterus

value: Macrophage

value: wild-type

value: High-fat diet


title: RNA-seq: Caprin1 KO clone 2 0h, rep 1

description: Caprin1 KO clone 2 0h, rep 1

value: Embryonic stem cells (ESCs)


title: F16_M_RNA


title: synovial tisssue, Inflamed3 (lncRNA)

first: Xiling

last: Xiao

address: No.1277, Jiefang Avenue

department: Department of Rehabilitation

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) [2]. After that, Ericscript (v0.5.5) [3]and rMATS (V3.2.5)[4] were used to detect fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 (v2.2.5) [5]was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included,then expression level of gene was calculated by RSEM (v1.2.12) [6].
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM, FPKM, TPM, read_count values for miRNAs, lncRNAs, and mRNAs

source_name: Synovial tissue

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions.. 1 ug of total RNA was used for the construction of sequencing libraries.
1.According to the manufacturer’s instructions,using target-specific oligos and RNase H maded ncRNA-Seq Library。
2.Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe).

value: Synovial tissue

tag: phenotype

value: Inflamed


title: synovial tisssue, Inflamed2 (lncRNA)