title: S7D1Con

description: 10x genomics

value: Control from S7D1


title: BM1102

status: Public on Nov 30 2024

type: SRA

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

country: Germany

institute: Institute of Bioinformatics

library_source: transcriptomic

data_processing:
Accurate quantification was performed with the QuantiFluor dsDNA system (Promega).
The size range of the generated cDNA libraries was measured with the DNA 1000 chip on the Bioanalyzer 2100 (280 bp).
Amplification and sequencing of cDNA libraries were performed using the cBot and HiSeq 2000 (Illumina, SR, 1x51 bp, 8-9 gigabases, >40 mio reads per sample).
Sequence images were transformed with Illumina software BaseCaller to bcl-files, which were demultiplexed to fastq-files with CASAVA (v1.8.2).
Quality check was done via FastQC (v0.10.1, Babraham Bioinformatics).
Sequence reads were aligned with the reference genome GRCh37 using the STAR RNA-Seq alignment tool.
Gene-level abundances were estimated using the RNA-seq by expectation-maximization (RSEM) algorithm.
Assembly: hg19
Supplementary files format and content: Matrix table with RSEM gene counts for every gene and every sample.

molecule: total RNA

organism: Homo sapiens

source_name: brain metastases

growth_protocol: All brain metastases samples were obtained with informed consent as approved by the local ethics committee (24/10/05).

extract_protocol:
Total RNA was isolated with the Trizol reagent from fresh frozen tissue and RNA integrity was checked with the Bioanalyzer 2100 (Agilent Technologies).
cDNA library preparation was carried out using the TruSeq Stranded Total RNA sample preparation kit (Illumina).

treatment_protocol: Samples of brain metastases were collected from patients previously diagnosed with colorectal cancer during neurosurgical removal.

tag: tissue

value: brain metastases

tag: disease

value: primary rectal cancer

tag: treatment

value: neurosurgical removal


title: RNA-seq of cultured neurons: Tβ4-2 [P15]

city: beijin

first: Tingting

last: Zhang

address: Beijin

country: China

institute: CIBR

data_processing:
RNA-seq raw data were initially filtered with “FastQC” to obtain clean data after quality control. Clean data were aligned to the reference genome (Version: GRCm38) downloaded from Gencode by HISAT. Raw counts for each gene were calculated by FeatureCounts.
The expression level of detected genes was estimated by DESeq2.A volcano plot was generated by ggplot2 in R, with a cutoff of p-value less than 0.01 and the absolute value of log2 (Foldchange) more than 4, measured by DESeq2.
The heat map was generated by heatmap with the z-score of each gene. Gene Set Enrichment Analysis (GSEA) was performed using the ClusterProfiler package in R, with an adjusted p-value less than 0.05
Assembly: Hisat2 GRCm38
Supplementary files format and content: 20230221_cultured_neuron_withPipe_NP24vsctrl
Supplementary files format and content: 20230221_cultured_neuron_withPipe_tb10vsctrl
Supplementary files format and content: 20230221_cultured_neuron_withPipe_tb4vsctrl

organism: Mus musculus

source_name: Brain, P0

extract_protocol:
Total RNA was extracted from cultured neurons using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer's protocol
DNA library for sequencing was prepared following the protocol of SMARTer Stranded Total RNA-Seq Kit v2

value: Brain, P0

tag: cell type

value: Primary cultured neurons

tag: genotype

value: Added with Tβ4


title: E7.5 posterior mouse embryo Single Cell RNA seq

city: Westmead

first: V. Pragathi

last: Masamsetti

state: NSW

address: 214 Hawkesbury rd

department: Embryology Unit

country: Australia

institute: Children's Medical Research Institute

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
see Aryamanesh 2022, DOI: 10.1007/978-1-0716-2281-0_10
Assembly: ARC mice
Supplementary files format and content: cellranger_PE725_outs_filtered_feature_bc_matrix_barcodes.tsv.gz
Supplementary files format and content: cellranger_Pmem-E7-5_outs_filtered_feature_bc_matrix_barcodes.tsv.gz
Supplementary files format and content: cellranger_Pmem-E7-0_outs_filtered_feature_bc_matrix_barcodes.tsv.gz

source_name: Embryo

extract_protocol:
Mouse embryos were dissected at the specified stages and single cells were dissociated using Trypsin treatment and counted to load 10,000 cells into on channel of a 10X Chromium chip. One channel per sample was used. After emulsion cell lysis and RNA was extracted followed by library preparation. Libraries were sent to Novogene for sequencing. Single cell suspensions were passed through 40μm cell strainer (Corning) and concentration was adjusted to 1000 cells/μL. Suspensions were loaded in single-cell-G Chip (10X Genomics) for target output of 10,000 cells per sample. Single-cell droplet capture was performed on the Chromium Controller (10X Genomics).
cDNA library preparation was performed in accordance with the Single-Cell 3’ v 3.0 or v3.1 protocol. Libraries were evaluated for fragment size and concentration using Agilent HSD5000 ScreenTape System (Agilent).

treatment_protocol: Normal mouse embryos

value: Embryo

value: ARC mouse strain

value: Normal


title: E7.25 mouse embryo Single Cell RNA seq

description: 10X Genomics


title: sc_ID1033

city: San Francisco

first: Nadav

last: Ahituv

state: CA

department: Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics

country: USA

institute: University of California San Francisco

data_processing:
Samples were aligned to hg38 using 10x Genomics CellRanger v6.1.2
Assembly: hg38
Supplementary files format and content: zip files containing 10x mtx files with barcode, mtx, and features files

molecule: polyA RNA

source_name: human milk

extract_protocol:
Cryopreserved cells were thawed and washed with 10 ml of Mammary Epithelial Cell Growth Medium (PormoCell) and later with 2 ml of PBS+1-2% BSA.
Twenty-five thousand cells from each sample were loaded on the 10X single cell chip. Chromium Next GEM Single Cell 3ʹ Kit v3.1 was used following the manufacturers’ protocol.

value: human milk

tag: milk production

tag: days postpartum


title: sc_ID1020_165d


title: BM1084


title: E7.0 Mouse embryo Single Cell RNA seq

description: 10X Genomics


title: RNA-seq of cultured neurons: Tβ10-4 [P10]

description: 20230221_cultured_neuron_withPipe_tb10vsctrl

value: Added with Tβ10


title: BM1096

value: primary colon cancer


title: sc_ID1020_70d


title: RNA-seq of cultured neurons: Tβ10-3 [P9]


title: D1Dox_d2_rep2

data_processing:
Trimmed reads were aligned to the GRCm38/mm10 mouse reference genome using STAR aligner (Dobin, Davis et al. 2013) with the parameter `--outSAMtype BAM SortedByCoordinate` to output a coordinate-sorted BAM file for downstream processing. Transcript abundances were estimated from genome aligned sequences using featureCounts (Liao, Smyth et al. 2014) in paired-end mode keeping read pairs in which both reads aligned but excluding chimeric assignments `-p -B`. Differential expression and statistical analysis were done using the DESeq2 library (Love, Huber et al. 2014). Differentially expressed genes were identified based on the following criteria: absolute Fold change >= 2 and adjusted P-value < 0.05. Biological processes enriched in differentially expressed RNA-seq gene sets were identified using the clusterProfiler library (Yu, Wang et al. 2012).
Assembly: Trimmed reads were aligned to the GRCm38/mm10 mouse reference genome using STAR aligner (Dobin, Davis et al. 2013) with the parameter `--outSAMtype BAM SortedByCoordinate` to output a coordinate-sorted BAM file for downstream processing
Supplementary files format and content: text file

source_name: EpiSCs

extract_protocol:
Total RNA from flash frozen samples was extracted using ISOLATE II RNA Mini Kit as per manufacturer recommendations (Bioline). In short, samples were thawed on ice, lysed and passed through a column purification process and DNase treatment. Precipitated RNA was eluted into RNase-free water. RNA concentration, DNA and ethanol contamination were measured using the NanoDrop (Thermo Fisher) and adjusted using RNase-free water as required.
RNA-seq libraries were prepared from extracted RNA by Genewiz (Azenta, China) using the NEBNext Ultra II RNA Library Preparation Kit (NEB, E7770) as per manufacturer protocol and 150 bp paired-end sequenced on the HiSeq 4000 (Illumina).
150 bp paired-end reads were trimmed using Trim Galore (Felix 2021)  in paired mode `--paired` keeping reads with at least 50 bp `--length 50`.

treatment_protocol: Embryoid bodies (EB) were maintained in EB-medium consisting of Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 15% Fetal Calf Serum (Gibco), 1% Non-essential amino-acid supplement (Gibco) and 0.1 μM 2-Mercaptoethanol (Sigma). EpiSC colonies were collected after Collagenase IV (Gibco) treatment and transferred to EB-medium within non-tissue culture treated plates and placed at 37 ºC, 5% CO2 on an orbital-shaker under slight rotation to prevent single EBs from settling to the bottom of the plate or attaching to each other. Media was replenished every 48 h, unless otherwise noted. Doxycycline induction, where appropriate, was achieved by adding 1 μg/mL Doxycycline (Sigma) to the culture.

value: EpiSCs

value: +Dox


title: RNA-seq of cultured neurons: Tβ10-2 [P8]


title: sc_ID1016


title: RNA-seq of cultured neurons: Tβ10-1 [P7]


title: BM1016


title: sc_ID1029

value: Low


title: BALF,  DKO-PA

city: Ann Arbor

first: Xin

last: Yu

state: Michigan

address: 2800 Plymouth Road.

institute: University of Michigan

description: 10 x Genomics

data_processing:
Data quality analysis and mapping to ensemble gene symbols were conducted using CellRanger (10x Genomics). The cell ranger software pipeline was used to demultiplex cellular barcodes, map reads to the reference genome, and quantify gene expression.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

source_name: lung

extract_protocol:
BALF samples were collected from both WT and Padi2-/-Padi4-/- mice after PA infection and sham control. BALF samples from three mice per group were pooled to generate samples (n =3 mice/sample) for the isolation of BALF cells. The BALF samples were centrifuged for 5 minutes at 400 x g and 4°C. The cell pellet was then resuspended in 500 µL of red blood cell lysis buffer and incubated for 5 minutes at room temperature. Following this, 500 µL of cold PBS was added to dilute the RBC lysis buffer, and the mixture was centrifuged for 5 minutes at 400 x g and 4°C. The resulting single cells were resuspended in PBS containing 1% weight/volume FBS.
RNA libraries were prepared with  the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit (10x Genomics) according to the manufacture's protocol.

value: lung

tag: cell line

value: BALF cells from in vivo

value: alveolar cells

value: DKO

tag: infection

value: PA infection


title: BALF, wt-pa

description: 10 x Genomics

value: WT


title: BALF, DKO-sham

description: 10 x Genomics

value: sham control


title: RNA-seq of cultured neurons: NP24-4 [P6]

description: 20230221_cultured_neuron_withPipe_NP24vsctrl

value: Brain, P0

value: Primary cultured neurons

value: Added with NP24


title: BM1014

value: brain metastases

value: primary rectal cancer

value: neurosurgical removal


title: BALF, wt-sham

description: 10 x Genomics


title: BM1011

value: primary colon cancer


title: RNA-seq of cultured neurons: Tβ4-1 [P13]

description: 20230221_cultured_neuron_withPipe_tb4vsctrl

value: Added with Tβ4


title: sc_ID1028

value: human milk


title: 12 FUS MWM HD

city: Strasbourg

first: Anne-Laurence

last: Boutillier

address: 12 rue Goethe

department: LNCA

country: France

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using STAR v.2.5.3a
Quantification : Gene Expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 95 annotations.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: dorsal hippocampus

extract_protocol:
Dorsal hippocampi of mice were chopped on ice with a razor blade before extraction of total RNA using the RNeasy Lipid Tissue Mini Kit (Qiagen).
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: dorsal hippocampus

value: FUS delta NLS

tag: condition

value: Morris water maze


title: RNA-seq of cultured neurons: NP24-3 [P5]


title: BM1078


title: BM0007


title: 11 WT MWM HD

value: Wild-type


title: sc_ID1023

value: Low


title: sc_ID1030


title: BM0002


title: RNA-seq of cultured neurons: NP24-2 [P4]


title: sc_ID1024

value: High


title: BM0001


title: RNA-seq of cultured neurons: NP24-1 [P3]


title: sc_ID1026


title: RNA-seq of cultured neurons: Ctrl3 [C5]


title: 10 FUS MWM HD


title: 8 FUS MWM HD


title: TIG3,minusHU,H3 rep1

city: Rotterdam

first: Calvin

last: Lo

address: Doctor Molewaterplein 40

department: Molecular Genetics

country: Netherlands

institute: Erasmus MC

library_source: genomic

data_processing:
Raw reads were aligned to the human genome (hg19 assembly excluding non-canonical chromomes i.e. random, unknown and haplotype variant chromosomes) using Bowtie version 0.12.7 with default parameters except '-S -m 1', which excludes reads mapping to multiple chromosomal positions. Peak detection was performed with MACS2 version 2.0.9 (20111102) using default settings except for parameters '--broad --nomodel --shiftsize=110'. The shift size of 110 bp was calculated as the median over all Phantom Peak (Kharchenko et al. 2008)shift estimates for our H3K9me3 samples. When running differential peak detection between two H3K9me3 samples in MACS2 the additional parameter '--shift-control' was specified. Bigwig files were generated using the UCSC Kent utilities(Kent et al. 2010). We allowed only one read per chromosomal position thus eliminating potential spurious spikes, and each remaining read was extended from its 5′-end to a total length of 250 bases, before converting to bedGraph format, scaling to mapped reads per million and final convertion to bigwig format.
Assembly: hg19 assembly excluding non-canonical chromomes
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: DMEM containing 10% FBS and 1% penicillin/streptomycin, supplemented with MEM non-essential amino acid mix. 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 Bioruptor Sonicator (Diagenode).
DNA library for Illumina sequencing was prepared from 10 ng DNA, using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs) and following the manufacturer’s instructions.

value: lung

value: TIG3 cells

value: human fetal lung fibroblasts

tag: antibody


title: TIG3,minusHU,H3 rep2


title: 9 WT MWM HD


title: ID1014_Cell

data_processing:
Sequencing reads were aligned to reference human genome hg38 using STAR aligner.
Read counts were normalized to transcripts per kilobase million (TPM)
Assembly: hg38
Supplementary files format and content: Comma separated file of TPM normalized read counts

source_name: Human Milk- Cell layer

extract_protocol:
Fresh whole milk was centrifuge at 800g for 20 minutes in 4°C to pellet the cells and separate the fat layer. Fat layer was removed using a sterile spoon and mixed with RLT lysis buffer for RNA extraction using the RNeasy kit (Qiagen). Supernatant was aspirated and aliquoted and milk cells pellet was resuspended in PBS with 0.04-1% bovine serum albumin (BSA).
Total RNA samples from milk fat layer or milk cells were sequenced at Novogene Co. ltd. Libraries were generated using the SMARTetr V2 or V3 kits.  The sequencing was performed using apaired end 150bp strategyon the Illumina platform (Illumina NovaSeq 6000).

value: Human Milk- Cell layer

value: Normal


title: 7 WT MWM HD


title: ID1013_Cell


title: RNA-seq of cultured neurons: Ctrl2 [C4]

value: Brain, P0

value: Primary cultured neurons


title: sc_ID1025


title: 6 FUS HC HD

value: Home cage mice


title: RNA-seq of cultured neurons: Ctrl1 [C2]


title: RNA-seq of cultured neurons: Ctrl4 [C6]


title: TIG3,plusHU,H3 rep1

value: HU


title: ID1012_D481_Cell


title: RNA-seq of mus musculus: mouse brain SCO, SCO2-4 [SCO_8]

description: ztt_RNA seq_2.csv

data_processing:
RNA-seq raw data were initially filtered with “FastQC” to obtain clean data after quality control. Clean data were aligned to the reference genome (Version: GRCm38) downloaded from Gencode by HISAT. Raw counts for each gene were calculated by FeatureCounts.
The expression level of detected genes was estimated by DESeq2.A volcano plot was generated by ggplot2 in R, with a cutoff of p-value less than 0.01 and the absolute value of log2 (Foldchange) more than 4, measured by DESeq2.
The heat map was generated by heatmap with the z-score of each gene. Gene Set Enrichment Analysis (GSEA) was performed using the ClusterProfiler package in R, with an adjusted p-value less than 0.05
Assembly: Hisat2 GRCm38
Supplementary files format and content: Deseq2 normalized count, ztt_RNA seq_1.xlsx
Supplementary files format and content: Deseq2 normalized count, ztt_RNA seq_2.csv

source_name: brain SCO

extract_protocol:
Total RNA was extracted from SCO and hippocampus using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer's protocol
DNA library for sequencing was prepared following the protocol of TruePrep DNA Library Prep Kit V2

tag: age

value: brain SCO

tag: strain


title: TIG3,proliferating,H3 rep2


title: TIG3,plusHU,H3 rep2


title: ID1012_D469_Cell


title: RNA-seq of mus musculus: mouse brain SCO, SCO2-3 [SCO_6]

description: ztt_RNA seq_2.csv


title: 4 FUS HC HD


title: ID1014_MFG

source_name: Human Milk- Fat layer

value: Human Milk- Fat layer


title: RNA-seq of mus musculus: mouse brain SCO, SCO2-2 [SCO_3]

description: ztt_RNA seq_2.csv


title: TIG3,proliferating,H3 rep1


title: TIG3,minusHU,H3K9ME3 rep2

value: H3K9me3 (Abcam, ab8898)


title: ID1013_MFG


title: RNA-seq of mus musculus: mouse brain SCO, SCO2-1 [SCO_1]

description: ztt_RNA seq_2.csv


title: 2 FUS HC HD

value: dorsal hippocampus

value: FUS delta NLS


title: VPL131_MFG


title: 1 WT HC HD

value: Wild-type


title: TIG3,minusHU,H3K9ME3 rep1


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl2-5 [Hippo_7]

description: ztt_RNA seq_2.csv

source_name: brain hippocampus

value: brain hippocampus


title: TIG3,plusHU,H3K9ME3 rep2


title: TIG3,plusHU,H3K9ME3 rep1


title: ID1020_213D_MFG


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl2-3 [Hippo_5]

description: ztt_RNA seq_2.csv


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl2-4 [Hippo_6]

description: ztt_RNA seq_2.csv


title: 143B_shCtrl_1

city: guangzhou

first: DONGMING

last: LV

address: guangzhou,china

institute: the first affiliated hospital of sysu,guangzhou,china

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: 143B OS cells

growth_protocol: Cells were cultured in high-glucose DMEM with 10% FBS and 1% penicillin/streptomycin as well as 0.5% puromycin in an incubator at 37°C with 5% CO2.

extract_protocol:
After the total RNAs extracted from stable OS cells were separated by agarose electrophoresis and detected by Nanodrop, mRNAs were enriched with Oligo(dT) magnetic beads.
The first cDNA fragment was generated by the random primer reverse, and the second cDNA was synthesized by adding dUTP. The double-stranded cDNA ends were repaired with A tails and connected to Illumina matching adaptors, and the final library was obtained by PCR amplification. An Agilent 2100 bioanalyzer was applied for quality control, qPCR was used for library quantification, and an Illumina HiSeq 4000 instrument was used for sequencing.

treatment_protocol: Transfected with shFTO or control plasmids

value: osteosarcoma

value: control


title: 5 WT HC HD


title: 143B_shFTO_2

value: knockdown of FTO


title: ID1020_116D_MFG


title: 143B_shCtrl_2


title: TIG3,proliferating,H3K9ME3 rep2

value: lung

value: TIG3 cells

value: human fetal lung fibroblasts


title: ID1020_94D_MFG

value: Normal


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl2-2 [Hippo_3]

description: ztt_RNA seq_2.csv


title: ID1020_70D_MFG


title: 143B_shFTO_1


title: 3 WT HC HD


title: TIG3,proliferating,H3K9ME3 rep1


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl2-1 [Hippo_2]

description: ztt_RNA seq_2.csv


title: ID1016_94D_MFG


title: 143B-shCtrl-IP

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The mRNA reads were aligned to reference genome using STAR(2.5.2b)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

extract_protocol:
The extracted RNAs were separated by agarose gel electrophoresis and subjected to quality detection using a NanodropTM. Complete mRNAs were isolated with the Arraystar Seq-StarTM poly(A) mRNA Isolation Kit. The isolated mRNAs were chemically broken into fragments of approximately 100 nt.
This process mainly included immunoprecipitation reactions, cleaning and elution. The m6A mRNA and input mRNA obtained after elution were enriched to construct an RNA sequencing library. The RNA sequencing library was generated using the KAPA Stranded mRNA-seq Kit (Illumina), and an Agilent 2100 BioAnalyzer was used to detect the quality of the library obtained. The library concentration was diluted to 8 pM and a cluster was generated in the Illumina cBot using the HiSeq 3000/4000 PE Cluster Kit (#PE-410-1001, Illumina). Finally, an Illumina HiSeq 4000 was used for sequencing (HiSeq 3000/4000 SBS Kit).


title: cortex,Olig2,E15

city: SHANGHAI

first: YU

last: TIAN

state: SHANGHAI

address: 131 DONGAN ROAD

institute: FUDAN UNIVERSITY

description: Library name: scRNA-seq of Olig2-cko mouse cortex

data_processing:
High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: cortex

extract_protocol:
ScRNA-seq were performed on FACS sorted tdT+ cells from the P1 Olig2f/f;IS-reporter mice cortex which were electroporated of pCAG-Cre plasmid at E15.The cortex were immediately submerged in fresh ice-cold Hanks balanced salt solution and  was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit according to the manufacturer’s instructions.
The Chromium dropletbased sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina NovaSeq 6000 or Illumina Hiseq4000.

value: cortex

value: total RNA


title: 143B-shCtrl-Input


title: 143B-shFTO-IP


title: ID1016_68D_MFG


title: KO3

city: Changsha

first: Jie

last: Wen

address: 87 Xiangya Road, Changsha 410008, Hunan, China

institute: Xiangya Hospital of Central South University

data_processing:
The libraries were sequenced on a Illumina NovaSeq 6000 platform, and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
Geneabundance was expressed as fragments per kilobase ofexon per million  reads mapped (FPKM). Stringtie software was used to count the fragment within each gene,  and TMM algorithm was used for normalization
Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1, q value <0.05 and one group’s mean FPKM >1
Assembly: GRCm39.111
Supplementary files format and content: txt file includes raw counts and FPKM values for each Sample

source_name: liver

growth_protocol: Primary hepatocytes were cultured in MEM alpha medium supplemented with 0.1 μM dexamethasone, 10 % fetal bovine serum (FBS), 100 IU/mL penicillin and 100 mg/mL streptomycin at 37°C in a humidiﬁed incubator with 5% CO2.

extract_protocol:
Total RNAs of hepatocytes were extracted using TRIzol according to the manufacturer's protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: The primary hepatocytes were treated with PA (0.1 mM) for 24 hours to mimic the MASH model in vitro .

value: liver

value: primary hepatocytes

value: hepatocytes

value: KO

value: PA

tag: Sex

value: male


title: KO2


title: ID1029_MFG

value: Human Milk- Fat layer

value: Low


title: 143B-shFTO-Input

value: osteosarcoma


title: hLMD20 replicate 2

type: RNA

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

institute: INRA

description: Gene expression at 35g/L of CO2  produced during  wine alcoholic fermentation

hyb_protocol: Hybridization  was  performed as described previously (Rollero et al. 2016)

scan_protocol: Scanning were performed as described previously (Rollero et al. 2016) with a GenePix  4000B laser Scanner (Axon Instruments)

data_processing: data processing was performed with with the GenePix software Pro7 as described previously (Rollero et al. 2016)

organism: Saccharomyces cerevisiae

source_name: Fermenting yeast cells

label_protocol: Agilent 8 × 15 k gene expression microarrays (Design ID 038619, including 40 EC1118-specific genes, (Agilent Technologies, Santa Clara, CA, USA) were used according to the manufacturer’s instructions.

growth_protocol: Strains were cultivated overnight in YPD, washed and inoculated in synthetic grape must. Samples were collected when 35g/L of CO2 had been produced as a result of alcoholic fermentation, which corresponded to a maximum in sulfide production.

extract_protocol: Total RNA extraction was perform with Trizol reagent, and purified with RNeasy kit (Qiagen)

treatment_protocol: Fermentations were performed in triplicate, in 1.2 L bioreactor systems, in the same fermentation conditions as previous experiments in this work (i.e. SM 200 with 60 mg/L SO2, 28 °C).

tag: parental strain

value: Fermenting yeast cells

tag: replicate


title: ID1028_MFG


title: hLMD20_dZWF1_ZWF1_59A replicate 1


title: KO1


title: LOXP2

value: LOXP


title: ID1023_MFG


title: RBL-2H3 cells, WT, control

city: Hangzhou

first: Mengying

last: Chen

address: ShiLongShan

institute: Westlake University

description: WT

data_processing:
Quality inspection: fastp 0.23.0 Alignment: HISAT2 2.1.0 Reads count: HT seq 0.10.0 Difference analysis: DESeq2 1.18.1 and edegR 3.20.9
Assembly: rn6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: RBL-2H3 cells

extract_protocol:
Total RNA was isolated from each sample using the FreeZol Reagent Kit. The RNA quality and integrity were assessed using NanoDropTM One/OneC, Life Invitrogen Qubit® 3.0 fluorometer and Agilent 4200 TapeStation. 0.1-1 μg of total RNA per sample was prepared for library preparation.
The NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® UltraTM II mRNA Library Prep Kit for Illumina® were used for mRNA isolation and library construction following the manufacturers’ protocols.

value: RBL-2H3 cells

value: basophilic leukemia

value: WT


title: hLMD20_dZWF1_ZWF1_59A replicate 2


title: ID1018_MFG


title: LOXP3


title: RBL-2H3 cells, WT_E, experiment

value: incubate with IgE


title: 59A_dZWF1_ZWF1_hLMD20 replicate 2


title: sr45a-2

city: Taian

first: Kang

last: Yan

address: Daizong street 61

institute: Shandong Agricultural University

data_processing:
To get clean readings for subsequent alignment, statistics, and analysis, we used FASTP software to filter the raw data and delete reads that did not fulfill the analytical criteria. The following parameters were set for read quality filtering: minimum length of 36 bp; mean Phred quality score > 30; elimination of leading and trailing bases with base quality 3; and a sliding window of 4:15.
Assembly: Tair

organism: Arabidopsis thaliana

source_name: seedings

extract_protocol:
Two-week-old seedlings were treated with 45℃ for 3 h. Total RNA was isolated with Trizol reagen
Library preparation and RNA-Seq were performed by CapitalBio, Beijing, China, with an Illumina Novaseq 6000 with 150-bp pair-end reads and c. 30 million reads per sample. To get clean readings for subsequent alignment, statistics, and analysis, we used FASTP software to filter the raw data and delete reads that did not fulfill the analytical criteria. The following parameters were set for read quality filtering: minimum length of 36 bp; mean Phred quality score > 30; elimination of leading and trailing bases with base quality 3; and a sliding window of 4:15.

value: seedings

value: sr45a mutant


title: ID1012_D469__MFG

value: High


title: 59A replicate 3


title: ADSC, oe, rep3

city: Shanghai

first: Zhaoxi

last: Peng

address: 639 Zhizaoju Rd

department: Vascular Surgery

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm39
Supplementary files format and content: Excel file inculdes raw counts for each sample
Supplementary files format and content: Excel file inculdes RPKM values for each sample

source_name: Mesenchymal stem cells

growth_protocol: ADSCs were cultured on plates with Dulbecco’s modified Eagle medium (DMEM) containing normal glucose (5.5 mmol/L), 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 mg/mL streptomycin. 37℃ and 5% CO2

extract_protocol:
Novogeno used standard extraction methods to isolate RNA from tissues or cells, followed by strict quality control of the RNA samples. The primary quality control method involves the Agilent 2100 Bioanalyzer, which accurately assesses RNA integrity.
After completing library construction, initial quantification was performed using the Qubit 2.0 Fluorometer, and the library was diluted to 1.5 ng/μL. The insert size of the library was then assessed using the Agilent 2100 Bioanalyzer. Once the insert size met expectations, qRT-PCR was used for accurate quantification of the library's effective concentration.

treatment_protocol: ADSCs simultaneous transduced with Vla4 and Lfa1 and ADSCs transduced with empty vector were washed twice with PBS and lysed with TRIzol reagent for total RNA isolation.

value: Mesenchymal stem cells

value: overexpressing VLA-4 and LFA-1


title: ID1026_MFG


title: ID1012_D481_MFG


title: LOXP1

value: liver

value: primary hepatocytes

value: hepatocytes


title: ID1025_MFG

value: Human Milk- Fat layer


title: 59A replicate 1


title: sr45a-1


title: ADSC, oe, rep1


title: SR45a-OE3

value: SR45a-1a overexpression


title: SR45a-OE2


title: hLMD20_dZRT2_ZRT2_59A replicate 3


title: hLMD20 replicate 1


title: ID1024_MFG


title: 59A_dYLR125W_YLR125W_hLMD20 replicate 1


title: sr45a-3


title: ADSC, mock, rep3


title: hLMD20_dZWF1_ZWF1_59A replicate 3


title: ADSC, mock, rep1


title: SR45a-OE1


title: ADSC, mock, rep2


title: cell line, 5 mM glucose + 25 μM cariporide, 48hr treatment, rep1

city: Seoul

first: So Won

last: Kim

address: 88, OLYMPIC-RO 43-GIL

department: Pharmacology

country: South Korea

institute: University of Ulsan College of Medicine

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Breast, mammary gland

growth_protocol: Cells were maintained in RPMI supplemented with 10% fetal bovine serum (without antibiotics) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: 10 or 5 mM glucose medium + 0 or 25 μM cariporide, 48 hours

value: Breast, mammary gland

value: epithelial

value: wild type

value: 5 mM glucose medium + 25 μM cariporide


title: WT-Heat3


title: ADSC, oe, rep2


title: cell line, 5 mM glucose + 25 μM cariporide, 48hr treatment, rep2


title: hLMD20_dZRT2_ZRT2_59A replicate 2

value: Fermenting yeast cells


title: hLMD20_dZRT2_ZRT2_59A replicate 1


title: WT-Heat2

value: WT


title: WT-Heat1


title: F3_DCL13

city: Fuzhou

first: Zhimin

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

data_processing:
The data matrix processed by Seurat is output through R language
Assembly: mm10
Supplementary files format and content: tab delimited text file includes data value for each sample

source_name: Lung

extract_protocol:
Harvested cells at the required densities were combined with gel beads  containing the barcoded information along with a mixture of cells and  enzymes. Oil surfactant droplets in a microfluidic double-cross system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence.
The cDNA fragment was then reverse transcribed before the sample was labeled. The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200300 base pairs (bp), together with the library building process of traditional secondgeneration sequencing such as sequencing junction and primers. Finally, the DNA library was generated by PCR amplification

value: Lung

value: wide type

value: Diquat


title: cell line, 5 mM glucose, 48hr treatment, rep3

value: 5 mM glucose medium


title: F2_DCL12


title: Mouse kidney proximal tubule_D21-ovx, biological rep3

city: Kyoto

first: Yuichiro

last: Kitai

address: Yoshidakonoecho Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
The libraries were sequenced on a Nextseq 550 (Illumina) to generate 75 bp single-end reads at a read depth of at least 20 million reads per sample.
Reads were mapped to mouse (Ensembl 103; STAR version 2.6.0c) reference gene models.
The FPKM was calculated using RSEM verseion 1.3.1.
Assembly: mouse (Ensembl 103; STAR version 2.6.0c)
Supplementary files format and content: FPKM

source_name: kidney proximal tubule

growth_protocol: C57BL/6 mice were purchased from Japan SLC.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (74106; Qiagen).
The RNA-Seq library was prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions.

treatment_protocol:
The fractions of the cortex of the kidney were homogenized in DMEM-based buffer containing 10% FBS, Hepes (0.01M), using the gentleMACS Dissociator (Miltenyi Biotec). After incubation at 37°C for 30 minutes, the lysates were forced through a 40-mm filter to remove cell clumps.
The cells were washed with ice-cold sorting buffer (HBSS with 3% BSA, and 2 mM EDTA), and then incubated with anti-prominin-1 antibody (130-092-442) for 15 minutes. Cells were then washed with ice-cold sorting buffer, and passed through an MS column (Miltenyi Biotec) under the effect of a magnetic field generated by the Mini MACS Separation Unit (Miltenyi Biotec).
The prominin-1-positive cells retained inside the column were washed 3 times and then eluted once the magnetic field was removed. RNA extraction was performed from the eluted cells, as described below.

value: kidney proximal tubule

value: Female

value: ovariectomized


title: cell line, 5 mM glucose, 48hr treatment, rep2


title: 59A replicate 2


title: F1_DCL2


title: 59A_dZWF1_ZWF1_hLMD20 replicate 3


title: cell line, 5 mM glucose + 25 μM cariporide, 48hr treatment, rep3


title: F3_DVD9

description: liver-matrix-data.txt

molecule: nuclear RNA

source_name: Liver

value: Liver


title: Mouse kidney proximal tubule_D21-ovx, biological rep2


title: cell line, 5 mM glucose, 48hr treatment, rep1


title: F2_DVD8

description: liver-matrix-data.txt


title: Mouse kidney proximal tubule_D21-ovx, biological rep1


title: cell line, 10 mM glucose + 25 μM cariporide, 48hr treatment, rep3

value: 10 mM glucose medium + 25 μM cariporide


title: cell line, 10 mM glucose + 25 μM cariporide, 48hr treatment, rep2


title: hLMD20_dYLR125W_YLR125W_59A replicate 2


title: 59A_dZRT2_ZRT2_hLMD20 replicate 3


title: F1_DVD7

description: liver-matrix-data.txt


title: Mouse kidney proximal tubule_D21-s, biological rep3

value: sham-operated


title: Mouse kidney proximal tubule_D21-s, biological rep2


title: cell line, 10 mM glucose, 48hr treatment, rep3

value: 10 mM glucose medium


title: cell line, 10 mM glucose + 25 μM cariporide, 48hr treatment, rep1

value: Breast, mammary gland


title: 59A_dZWF1_ZWF1_hLMD20 replicate 1


title: 59A_dZRT2_ZRT2_hLMD20 replicate 2


title: Mouse kidney proximal tubule_M, biological rep3

value: Male


title: Mouse kidney proximal tubule_D21-s, biological rep1


title: hLMD20 replicate 3


title: 59A_dYLR125W_YLR125W_hLMD20 replicate 3


title: hLMD20_dYLR125W_YLR125W_59A replicate 3


title: D3_DV12

description: liver-matrix-data.txt


title: 59A_dYLR125W_YLR125W_hLMD20 replicate 2


title: Mouse kidney proximal tubule_M, biological rep1


title: Extracellular vesicle small RNA from TB3

city: Columbia

first: Pallav

last: Singh

state: Missouri

address: CE720 Clinical Support and Education

department: Institute for Data Science and Informatics

institute: University of Missouri

data_processing:
adapter removal done through cutadapt (v4.6)
miRge3.0 used for finding the miRNA and DESeq2 was used for differential analysis
Alignment done through Bowtie(v1.3.1) with the RNAcentral's gff3 for finding lncRNA and counts extracted using featureCounts (v2.0.6). DESeq2 used for differential analysis.
Assembly: GRCh38
Supplementary files format and content: annotated output of miRNA with raw counts values in csv file format
Supplementary files format and content: annotated output of smRNA with raw counts values in tab separated txt file format

source_name: Trophoblast

growth_protocol: iPS cells were grown for 6 days and maintained in an undifferentiated state; TB cells were grown for days, and differentiated from IPS cells to Day 6 TB cells following the BAP model; NPC stocks were maintained and experimetnal NPC cells were passaged out 24 hours prior to treatment with EVs

extract_protocol:
miRNA and mRNA were isolated with EVeryRNA EV RNA Purification System that includes the ExoQuick-TC EV Isolation (Systemic Biosciences). Samples were analyzed on the fragment analyzer at the MU Genomics Technology Core Facility, and samples were selected for sequencing based on RNA concentration.
Small RNA sequencing was provided by the Genomics Technology Core Facility at the University of Missouri.  Libraries were constructed using the manufacturer’s protocol with reagents supplied in the Takara Bio SMARTer small RNA library preparation kit(catalog number 635029).  Total RNA was first polyadenylated to provide a priming sequence for an oligo(dT) primer.  First-strand synthesis was performed with PrimeScript™ Reverse Transcriptase primed by the 3’ smRNA dT Primer.  Non-templated nucleotides are added at the 3' end of the first-strand cDNA molecule to be bound by the SMART smRNA Oligo.  The PrimeScript Reverse Transcriptase used the SMART smRNA Oligo as a template for template switching and extension. Full-length Illumina adapters containing indexes were then added by PCR amplification.  Amplified small RNA libraries were purified using the provided NucleoSpin Gel and PCR clean-up kit.  The libraries were further enriched twice using Axygen AxyPrep MAG purification beads by performing a double-sided size selection (0.8x/2.0x) to remove adapter dimers and recover the desired insert size of 18-45 bases.  The DNA fragments (libraries) were recovered by elution from the bead-bound fraction in 22 µL of 5 mM Tris Buffer. Libraries were quantified with the Qubit HS DNA kit (Invitrogen) and the fragment size analyzed by a 5200 Fragment Analyzer (Agilent). Libraries were then pooled and diluted according to the standard sequencing protocol for sequencing on a NovaSeq 6000 (Illumina).
smallRNAseq

value: Trophoblast

value: Trophoblast cells


title: E3_DVM6

description: liver-matrix-data.txt


title: OE-11-5

city: Wuhan

first: Shi

last: Lei

address: No.1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvemen

data_processing:
The obtained data underwent initial processing using the Trimmomatic v.0.36 trimming tool to eliminate adapters and low-quality reads
Trimmed and paired read files then underwent a second quality assessment through FastQC. The FastQ files were further analyzed using Kallisto v.043.1, as outlined by Bray et al. in 2016, to quantify transcript abundances via pseudoalignment to the Arabidopsis reference transcriptome (Araport11), expressed as transcripts per kilobase million (TPM).
Normalization of the quantified data was performed utilizing the sleuth package within the R environment (version 3.5.1).
Assembly: Araport11
Supplementary files format and content: FPKM

source_name: shoots

growth_protocol: Col-0 and 35S: BnaC02.TPS8 Arabidopsis plants cultivated on ½MS solid medium (comprising 1% (w/v) sucrose and 1% (w/v) agar) for ten days.

extract_protocol:
The RNeasy Plant Mini Kit (QIAGEN, Germany) was employed for RNA isolation.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: shoots

value: Overexpression line

value: Normal condition


title: Extracellular vesicle small RNA from TB2


title: D2_DV11

description: liver-matrix-data.txt

value: wide type


title: D1_DV10

description: liver-matrix-data.txt

value: Diquat


title: E2_DVM5

description: liver-matrix-data.txt


title: E1_DVM4

description: liver-matrix-data.txt


title: OE-11-3


title: C2_DVC2

description: liver-matrix-data.txt

value: Control


title: cell line, 10 mM glucose, 48hr treatment, rep1

value: epithelial

value: wild type


title: OE-11-4


title: C3_DVC3

description: liver-matrix-data.txt


title: OE-11-2


title: Y_P4

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

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 research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) 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.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) 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.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Bos grunniens, genome version: v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Bos grunniens

source_name: blood

growth_protocol: Whole blood was collected using anticoagulant ( containing EDTA ) blood vessels for transcriptome sequencing. Each tube of blood sample was 250 uL whole blood + 750 uL TRIzol LS, and the blood sample was immediately stored in liquid nitrogen after collection and processing.

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. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: Samples were immediately stored in liquid nitrogen for RNA isolation.

value: blood

value: Pregnancy period


title: Y_P5


title: Extracellular vesicle small RNA from iPSC3

source_name: iPSC

value: iPSC

value: Induced pluripotent stem cells


title: Y_P6


title: cell line, 10 mM glucose, 48hr treatment, rep2

value: 10 mM glucose medium


title: Extracellular vesicle small RNA from iPSC2


title: C1_DVC1

description: liver-matrix-data.txt

value: Liver


title: 59A_dZRT2_ZRT2_hLMD20 replicate 1

value: Fermenting yeast cells


title: OE-11-1


title: Mouse kidney proximal tubule_M, biological rep2

value: kidney proximal tubule

value: Male

value: sham-operated


title: Y_P3


title: Extracellular vesicle small RNA from iPSC1


title: F3_DCK21

description: kidney-matrix-data.txt

source_name: kidney

value: kidney


title: Y_P2


title: Col-0-5

value: shoots

value: WT

value: Normal condition


title: Extracellular vesicle small RNA from TB1

value: Trophoblast

value: Trophoblast cells


title: F2_DCK20

description: kidney-matrix-data.txt

value: wide type

value: Diquat


title: PC-3 xenograft, shVCAN_3

city: TORONTO

last: Xu

state: Ontario

address: 101 COLLEGE ST EAST TOWER 11-601D

country: Canada

institute: Princess Margaret Cancer Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to hg38 by using STAR
Read counts were generated by STAR and the differential analysis was done by DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts

source_name: PC-3 mouse xenograft

growth_protocol: PC-3 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. Male NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice (4-5 weeks) were housed under specific pathogen-free conditions.Animals were randomly assigned across three experimental groups for xenograft experiments. Lentivirus-mediated shRNAs were transduced into PC-3 cells prior to selection by 2 μg/mL puromycin. In each mouse, 1.2 million cells were injected subcutaneously in 0.1 mL 50% PBS/50% Matrigel. Tumor growth was measured using a caliper every other day for four weeks.

extract_protocol:
The total RNA was extracted from the xenograft tumors with the miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer's protocol.
RNA-Seq of the shRNA-mediated knockdown of VCAN in PC-3 derived mouse xenograft was performed by Novogene using NovaSeq 6000 S4 paired-end 150 bp.

value: PC-3 mouse xenograft

value: human prostate cancer

value: KD VCAN

value: shVCAN


title: Strain hLMD20_replaced by _YLR125W_59A replicate 1


title: Col-0-3


title: PC-3 xenograft, shVCAN_2


title: PC-3 xenograft, shGFP_3

value: KD control

value: shGFP


title: F1_DCK8

description: kidney-matrix-data.txt


title: Col-0-4


title: Y_E5

value: blood

value: Estrus period


title: Y_E6


title: Y_E4


title: E2_DCK17

description: kidney-matrix-data.txt


title: PC-3 xenograft, shGFP_2


title: D3_DVK27

description: kidney-matrix-data.txt


title: Col-0-1


title: PC-3 xenograft, shGFP_1


title: E1_DCK16

description: kidney-matrix-data.txt


title: Y_E3


title: RNA-seq of mus musculus: mouse brain SCO, SCO1-6 [X12_SCO]

city: beijin

first: Tingting

last: Zhang

address: Beijin

institute: CIBR

description: ztt_RNA seq_1.xlsx

source_name: brain SCO

value: brain SCO


title: Y_E2


title: RNA-seq of mus musculus: mouse brain SCO, SCO1-5 [X10_SCO]

description: ztt_RNA seq_1.xlsx


title: atacncrwt_clone2

first: lian

last: liu

address: No.800 Dongchuan Road,Minhang district

institute: Shanghai Jiao Tong University

data_processing:
Reads ofATAC-seq were mapped to human genome GRCh37/hg19 with bowtie2.
The peaks were called by MACS2 with default parameters.
All of the mapped Sam files were sorted and indexed by Samtools (v1.12) and normalized to RPKM by Deeptools BamCoverage function.
The BedGraph file generated from Deeptools was uploaded into USCS browser for visualizing.
Assembly: Assembly: hg19
Supplementary files format and content: Supplementary files format and content: bigWig

source_name: Uterus

extract_protocol:
Briefly, we collected 50000 cell for each experiment and lysed cells by NP-40, Tween-20 and digitoni on ice. Then, we collected the pellets and fragmented chromatin by Tn5 linked with sequence adaptor. The DNA was collected by ATAC DNA Extract Beads.
Vazyme Hyperactive ATAC-Seq Library Prep Kit for Illumina (TD711)

value: Uterus

value: endometrial carcinoma cells


title: RNA-seq of mus musculus: mouse brain SCO, SCO1-4 [X8_SCO]

description: ztt_RNA seq_1.xlsx

data_processing:
RNA-seq raw data were initially filtered with “FastQC” to obtain clean data after quality control. Clean data were aligned to the reference genome (Version: GRCm38) downloaded from Gencode by HISAT. Raw counts for each gene were calculated by FeatureCounts.
The expression level of detected genes was estimated by DESeq2.A volcano plot was generated by ggplot2 in R, with a cutoff of p-value less than 0.01 and the absolute value of log2 (Foldchange) more than 4, measured by DESeq2.
The heat map was generated by heatmap with the z-score of each gene. Gene Set Enrichment Analysis (GSEA) was performed using the ClusterProfiler package in R, with an adjusted p-value less than 0.05
Assembly: Hisat2 GRCm38
Supplementary files format and content: Deseq2 normalized count, ztt_RNA seq_1.xlsx
Supplementary files format and content: Deseq2 normalized count, ztt_RNA seq_2.csv

extract_protocol:
Total RNA was extracted from SCO and hippocampus using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer's protocol
DNA library for sequencing was prepared following the protocol of TruePrep DNA Library Prep Kit V2


title: Y_P1

value: Pregnancy period


title: Y_E1


title: atacncrwt_clone1


title: D1_DVK25

description: kidney-matrix-data.txt

value: kidney


title: E3_DCK4

description: kidney-matrix-data.txt


title: Y_A6

value: Anestrus period


title: atacNCR_clone2


title: Col-0-2

value: shoots

value: WT

value: Normal condition


title: Y_A5


title: RNA-seq of mus musculus: mouse brain SCO, SCO1-3 [X6_SCO]

description: ztt_RNA seq_1.xlsx


title: PC-3 xenograft, shVCAN_1

first: Xin

value: PC-3 mouse xenograft


title: Y_A4


title: RNA-seq of mus musculus: mouse brain SCO, SCO1-2 [X4_SCO]

description: ztt_RNA seq_1.xlsx


title: C2_DCKC18

description: kidney-matrix-data.txt

value: wide type

value: Control


title: Y_A3


title: RNA-seq of mus musculus: mouse brain SCO, SCO1-1 [X2_SCO]

description: ztt_RNA seq_1.xlsx


title: RNAseqncrwt_clone2

data_processing:
RNA-seq raw FASTQ files were aligned to GRCh37/hg19 using STAR (v2.7.3a) with the default parameters.
The bam files were feed to Cufflinks (v2.2.1) to generate expression levels of transcripts in FPKM (fragments per kilobase of exon per million fragments mapped).
Deeptools was used to convert the bam file to bedGraph file for visualizing in UCSC genome browser.
Assembly: Assembly: hg19
Supplementary files format and content: Supplementary files format and content: bigWig

extract_protocol:
About 106 cells were collected and lysed by 1 ml TRIzol Reagents (Invitrogen). After 15 mins incubation in room temperature, we add 0.2 ml chloroform and mix well. After 2 mins incubation at room temperature, we centrifuged sample at 12000 rpm for 10 mins at 4 °C. Then, we transfered supernatant to a new tube and mix with equal volume of isopropanol. After incubation at room temperature for 10 mins, we centrifuged sample at 12000 rpm for 15 mins at 4 °C to pellet RNA. Then we added 1 ml 75% ethanol to wash the RNA. Finally, we dissolved RNA pellet in nuclease-free water. We added the Oligo(dT) coupled magnetic beads (Vazyme N401) to purified total RNA to enrich the mRNA.
Libraries were constructed with the VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme NR604) according to the manual.


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl1-6 [X11_Ctrl]

description: ztt_RNA seq_1.xlsx

source_name: brain hippocampus

value: brain hippocampus


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl1-5 [X9_Ctrl]

description: ztt_RNA seq_1.xlsx


title: Y_A2


title: C3_DCKC19

description: kidney-matrix-data.txt


title: RNAseqncrwt_clone1


title: atacNCR_clone1


title: RNAseqncr_clone2


title: RNAseqncr_clone1


title: D2_DVK26

description: kidney-matrix-data.txt

value: Diquat


title: C1_DCK3

description: kidney-matrix-data.txt


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl1-4 [X7_Ctrl]

description: ztt_RNA seq_1.xlsx


title: 5m AS

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

description: 10X Genomics

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10-2020-A genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantifies using Space Ranger's default settings
Assembly: mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.mtx.gz : gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: sample.tif : images captured of the samples
Library strategy: spatial transcriptomics

extract_protocol:
Kidneys were embedded in OCT, frozen, cryosectioned at 10 um, and sections placed onto 10x Genomics Visium gene expression slides.
Spatial transcriptome sequencing libraries were prepared as per the 10x Genomics Visium Spatial Gene Expression Reagent Kit user guide.


title: Y_A1


title: Rht_D1b_NT_rep4

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

country: United Kingdom

institute: Rothamsted Research

description: Library name: Sample_24

data_processing:
Sequencing reads were trimmed for quality and adapter sequences using Trimmomatic 0.39 (Bolger, Lohse and Usadel 2014) (SLIDINGWINDOW:4:20; MINLEN:50). The trimmed reads were paired and quantified using Kallisto against the IWGSC RefSeq v1.2 annotated gene models (Consortium, Appels et al. 2018, Zhu, Wang et al. 2021). Transcript per million (TPM) values were calculated for each gene based on raw counts.
Assembly: Reads were mapped to the Triticum aestivum hexaploid wheat reference genome IWGSC v1.2
Supplementary files format and content: .csv file containing TPM values for all annotated wheat gene models in each RNA-seq library.

organism: Triticum aestivum

source_name: Leaf sheath tissue from seven-day-old seedling.

growth_protocol: Seedlings were grown in soil in a controlled environment chamber under a 16 h photoperiod (300 µmolm-2s-1) with 20 ℃/16 ℃ day/night temperatures.

extract_protocol:
Total RNA was extracted from leaf sheah tissues using the Monarch® Total RNA Miniprep Kit including a DNase treatment according to the manufacturer’s instructions (New England Biolabs, Ipswich, Massachusetts, USA). The quality of the RNA was assessed using the Agilent RNA 6000 Nano Chip and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Paired-end Illumina libraries were constructred by Novogene Bioinformatics Technology Co. Ltd. (Cambridge UK).

treatment_protocol: Seven-day-old seedlings were treated either with 100 µM GA3 (GA) or with water (NT).


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl1-3 [X5_Ctrl]

description: ztt_RNA seq_1.xlsx


title: Late treated 5m AS

description: 10X Genomics

value: hEV treatment


title: WT

description: 10X Genomics


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl1-2 [X3_Ctrl]

description: ztt_RNA seq_1.xlsx


title: Rht_D1b_NT_rep3

description: Library name: Sample_23

value: Leaf sheath tissue from seven-day-old seedling.


title: RNAseqct116wt_clone2


title: 2m AS

description: 10X Genomics


title: Rht_D1b_NT_rep2

description: Library name: Sample_22


title: RNAseqct116wt_clone1


title: RNAseqct116_clone2


title: RNA-seq of mus musculus: mouse brain hippocampus, Ctrl1-1 [X1_Ctrl]

description: ztt_RNA seq_1.xlsx


title: Early treated 5m AS

description: 10X Genomics


title: Rht_D1b_NT_rep1

description: Library name: Sample_21


title: WT Female & Hetero Female

description: 10X Genomics

value: B6C57 and B6.Cg-Col4a5tm1Yseg


title: Rht_D1b_GA_rep4

description: Library name: Sample_20


title: Colon CKO

city: Beijing

first: Jia

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 3.2.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 3000 or less than 300, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
IntegrateData function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 3.2.3). Top 40 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 3.2.3).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

source_name: murine colon infiltration immune cells

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.
10x scRNA-Seq

value: colon


title: Rht_D1b_GA_rep3

description: Library name: Sample_19


title: RNAseqcdelwt_clone1

value: Uterus


title: Rht_D1b_GA_rep2

description: Library name: Sample_18


title: Colon WT


title: Brain, Ctl-Veh12

city: Irvine

first: Mingyu

last: Du

address: 419 Physical Sciences Quad

institute: UC Irvine

hyb_protocol: The sections (10 um) were mounted onto Vizgen merslides (Vizgen #10500001) and hybridized with a specific panel of binary-coded probes that were custom-designed for 500 selected mouse genes (Vizgen #VZG0191, 40h at 37°C) after several steps of pretreatment including fixation (chilled 4% PFA in 1xPBS), permeabilization (70% ethanol), and prehybridization with formamide buffer (Vizgen).

scan_protocol: Not applicable

data_processing:
Upon completion of imaging, the MERSCOPE program automatically converted the raw imaging data into .vzg meta output files, which were then used for downstream in-depth analysis using our customized bioinformatics pipelines.
Processed data includes tables containing transcript counts for individual genes per segmented cell, with spatial information retained for downstream spatial transcriptomics analysis.

label: DAPI-polyT

source_name: A Con mice with Veh treatment

growth_protocol: Mice were maintained under standard housing conditions.

extract_protocol: Sagittal cryosections were collected from fresh-frozen OCT-embedded hemibrains of mice examined using a Leica CM1850 cryostat.

treatment_protocol: Brain samples from RT + Veh, RT + RZ, Con + Veh, and Con + RZ group mice were used for MERFISH experiments.

value: hippocampus

value: Ctl-Veh


title: Brain, Ir-Veh12

source_name: A RT  mice with Veh treatment

value: Ir-Veh


title: Gag-SRSF1_PM_rep2

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

data_processing:
BBduk from BBTools was used to processed CLIP-seq reads before mapping. 3' adapter sequences were trimmed from the raw input reads and reads that contained ambiguous nucleotides, did not contain the 3′ adapter sequence or were shorter than 10nt were discarded. The trimmed reads that remained were separated based on their 3' barcode sequences.
Reads were then aligned to the human genome (hg19) or to corresponding viral genomes, with up to 1 mismatches allowed using the Bowtie algorithm.
In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2–best–strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
SAMTools and BEDTools were used to generate various file types of mapped reads for further analysis.
Assembly: hg19 and NL4-3
Supplementary files format and content: tab-delimited files showing summarization of reads (i.e. chromosomal locations and counts).
Library strategy: CLIP-seq

source_name: cell line

growth_protocol: 293T cells grown in 10 cm dishes were transfected with 10 μg of the indicated PR- NL4-3-derived proviral plasmids using polyethylenimine (PolySciences).

extract_protocol:
UV-crosslinked cells  were fractionated via membrane flotation. Gag-RNA complexes were immunoprecipitated from the plasma membrane and Gag-bound RNA was extracted for CLIP-seq library construction.
Libraries were constructed using sequential ligations of 3' barcoded adapter followed by 5' adapter. CLIP-seq libraries were PCR amplified using primers containing Illumina adapter sequences.

treatment_protocol: For PAR-CLIP, one day following transfection and 14-16 hours before cells and virions are harvested, 100 μM 4-thiouridine (4SU) was added to the cell culture medium. Afterwards, Gag and RNAs are crosslinked via UV irradiation.

value: cell line

value: 293T cells transfected


title: Gag-SRSF5_PM_rep1

value: WT


title: Gag-SRSF4_PM_rep1


title: Rht_D1b_GA_rep1

description: Library name: Sample_17


title: RNAseqcdel_clone2

value: endometrial carcinoma cells


title: Gag-SRSF5_PM_rep2


title: Gag-SRSF4_PM_rep2


title: Brain, Ctl-Veh11


title: Brain, Ctl-Rz11

source_name: A Con mice with RZ treatment

value: Ctl-Rz


title: idd5_NT_rep4

description: Library name: Sample_16


title: Gag-SRSF1_PM_rep1


title: RNAseqcdel_clone1


title: Brain, Ir-Veh9


title: ctcfncrwt_clone2

data_processing:
Reads of ChIP-seq were mapped to human genome GRCh37/hg19 with bowtie2.
All of the mapped Sam files were sorted and indexed by Samtools (v1.12) and normalized to RPKM by Deeptools BamCoverage function.
The BedGraph file generated from Deeptools was uploaded into USCS browser for visualizing.
Assembly: Assembly: hg19
Supplementary files format and content: Supplementary files format and content: bigWig

extract_protocol:
5×106 cells are collected and crosslinked by 1% formaldehyde, quenched by 1 ml of 2 M glycine at a final concentration of 200 mM and wash by ice-cold PBS twice. Crosslinked cells were lysed twice by ChIP buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 0.15 M NaCl, and 1 × protease inhibitors (Roche)) with slow rotation at 4 °C for 10 mins. Then the nuclei were resuspended by ChIP buffer and sonicated by Bioruptor Sonicator with high energy for 30s on and 30s off for 30 times to sonicate DNA to 200-400 bp. After centrifuge 14000g for 30 min, supernatant containing sonicated DNA-protein complex was precleared by protein A/G magnetism beads (Thermo 26162). Antibody (Rad 21: abcam ab217678, CTCF : Millipore 07-729, V5 abcam ab15828) or Anti-FLAG Magnetic Beads (Sigma M8823) was added to the precleared solution to incubate at 4°C overnight with slow rotation. Protein A/G beads was added for 3h at 4 °C with slow rotation when antibody was used. ChIP buffer, high salt buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 0.4 M NaCl), no salt buffer, LiCl buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate), 10nM 10 mM Tris-HCl pH 7.5 were used to wash the bead. Elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) was used to elute ChIP DNA from bead in 65 °C for 1h with 1000rpm shaking. Then the complex was reverse crosslink at 65 °C overnight. The ChIP DNA was purified by phenol-chloroform and perciptated in 75% ethanol.
The purified DNA was used to construct libraries for deep sequencing using Universal DNA Library Prep Kit for Illumina


title: Gag-hnRNPK_PM_rep2


title: idd5_NT_rep2

description: Library name: Sample_14


title: RNAseqct116_clone1


title: Gag-hnRNPK_PM_rep1


title: RNAseqcdelwt_clone2


title: ctcfncrwt_clone1


title: ctcfncr_clone2


title: idd5_NT_rep1

description: Library name: Sample_13


title: Brain, Ir-Rz9

source_name: A RT mice with RZ treatment

value: Ir-Rz


title: Gag-hnRNPF_PM_rep2


title: idd5_GA_rep4

description: Library name: Sample_12


title: ctcfncr_clone1


title: ctcfct116wt_clone2


title: Brain, Ctl-Rz8


title: Brain, Ctl-Veh3


title: idd5_NT_rep3

description: Library name: Sample_15


title: idd5_GA_rep3

description: Library name: Sample_11


title: ctcfct116_clone2


title: ctcfct116wt_clone1


title: Brain, Ctl-Rz3


title: Gag-hnRNPA1_PM_rep2


title: Gag-hnRNPA1_PM_rep1


title: idd5_GA_rep1

description: Library name: Sample_9


title: Gag-hnRNPF_PM_rep1


title: Gag-dNC-NC_PM_rep2


title: idd5_GA_rep2

description: Library name: Sample_10


title: ctcfct116_clone1


title: Brain, Ir-Veh2

source_name: A RT mice with Veh treatment


title: Cadenza_NT_rep4

description: Library name: Sample_8


title: Gag-dNC-NC_PM_rep1


title: ctcfcdelwt_clone2


title: Cadenza_NT_rep3

description: Library name: Sample_7


title: ctcfcdelwt_clone1


title: CAdCTD_PM_rep2


title: Brain, Ctl-Veh2


title: Brain, Ir-Veh1


title: Brain, Ctl-Veh8


title: CAdCTD_PM_rep1


title: ctcfcdel_clone2


title: Brain, Ir-Rz1


title: Cadenza_NT_rep1

description: Library name: Sample_5


title: ctcfcdel_clone1


title: Cadenza_GA_rep4

description: Library name: Sample_4


title: G2A_PM_rep2


title: Cadenza_GA_rep3

description: Library name: Sample_3


title: G2A_PM_rep1


title: WT_PM_rep1


title: V663_rep2


title: CDM3

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: EquCab3
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

organism: Equus caballus

source_name: bone marrow-derived MSCs

extract_protocol:
Standard procedure of  PureLink™ RNA Mini Kit (Ambion) with DNAse treatment
Standard protocol of VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina

value: bone marrow-derived MSCs

value: Equine chondrocyte


title: VFL_rep2


title: CDM1


title: V663_rep1


title: Cadenza_GA_rep1

description: Library name: Sample_1


title: ADM3

value: Equine adipocyte


title: WT_PM_rep2


title: CDM2


title: Gag-SRSF5_virion_rep3

data_processing:
BBduk from BBTools was used to processed CLIP-seq reads before mapping.
Reads were then aligned to the human genome (hg19) or to corresponding viral genomes, with up to 1 mismatches allowed using the Bowtie algorithm.
In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2–best–strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
SAMTools was used to generate various file types of mapped reads for further analysis.
Assembly: hg19 and NL4-3
Supplementary files format and content: tab-delimited files showing summarization of reads (i.e. chromosomal locations and counts).
Library strategy: CLIP-seq

growth_protocol: 293T cells grown in 10cm dishes were transfected with 10 μg of the indicated PR- NL4-3-derived proviral plasmids using polyethylenimine (PolySciences).

extract_protocol:
UV-crosslinked cells and virions were lysed with RIPA buffer. Gag-RNA complexes were immunoprecipitated from lysates and RNA was subsequently extracted for CLIP-seq library construction.
Libraries were constructed using sequential ligations of 3' barcoded adapter followed by 5' adapter. CLIP-seq libraries were PCR amplified using primers containing Illumina adapter sequences.

treatment_protocol: For PAR-CLIP, one day following transfection and 14-16 hours before cells and virions are harvested, 100 μM 4-thiouridine (4SU) or 6-thioguanosine (6SG) was added to the cell culture medium. Afterwards, Gag and RNAs are crosslinked via UV irradiation.


title: Cadenza_NT_rep2

description: Library name: Sample_6


title: Gag-SRSF5_virion_6SG_rep1


title: Gag-SRSF5_virion_rep2


title: V637_rep1


title: V637_rep2


title: shCtrl, LX-2, Tg, replicate1, RNAseq

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt.
Trimmed reads mapped to reference genome by bowtie2 or STAR.
Peaks calling by HOMER.
Gene counts were quantified by featurecounts.
DEGs were identified by DESeq.
Assembly: hg19 for ChIP-seq, and hg38 for RNA-seq.
Supplementary files format and content: bigWig files
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts values for each Sample.

extract_protocol:
Total RNA was extracted following the protocol provided by Qiagen RNeasy Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: shRNA

value: shCtrl

value: Thapsigargin


title: ADM2

tag: tissue


title: ADM1


title: shCtrl, LX-2, TGFβ, replicate2, RNAseq

value: TGFbeta


title: Cadenza_GA_rep2

description: Library name: Sample_2

value: Leaf sheath tissue from seven-day-old seedling.


title: V611_rep2

value: Uterus


title: VFL_rep1


title: Gag-SRSF5_virion_rep1


title: shCtrl, LX-2, TGFβ, replicate1, RNAseq


title: MSC2

value: Equine MSCs


title: MSC3


title: Gag-SRSF4_virion_6SG_rep1


title: shCtrl, LX-2, Tg, replicate2, RNAseq


title: Gag-SRSF1_virion_6SG_rep1


title: shCtrl, LX-2, DMSO, replicate2, RNAseq

value: DMSO


title: shCtrl, LX-2, DMSO, replicate1, RNAseq


title: Rad21ncrwt_clone2


title: V611_rep1


title: Rad21ncr_clone2


title: ATAC-seq in sea star whole embryos at 90 hpf, replicate 2

city: Seville

first: Marta

middle: Silvia

last: Magri

address: Carretera de Utrera km1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

description: ATAC-seq

data_processing:
Alignment: reads were aligned to the reference genome using Bowtie2 software
Filtering duplicates: duplicated pairs were removed using Samtools software
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions
Visualization: bigWig files were visualized using UCSC Browser
Assembly: Patiria miniata 2020 Assembly (Pmin_1.0/GCF_015706575.1)
Supplementary files format and content: narrowPeak files with peaks called using MACS2 with q<0.01

organism: Patiria miniata

source_name: whole embryo

growth_protocol: Embryos were grown at 15°C in ASW until desired developmental stage

extract_protocol:
Wild type embryos were lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109; Magri MS et al., 2020. Front Cell Dev Biol.24;7:372. doi: 10.3389/fcell.2019.00372; Magri MS et al., 2021. Methods Mol Biol. 2219:253-265. doi: 10.1007/978-1-0716-0974-3_16

value: whole embryo

tag: time

value: 90 hpf


title: Rad21ncrwt_clone1

city: Shanghai


title: Gag-NCx3_virion_rep2

value: cell line

value: 293T cells transfected


title: MSC1


title: shCtrl, LX-2, AA_Dep, replicate2, RNAseq

tag: treatment


title: shCtrl, LX-2, AA_Dep, replicate1, RNAseq


title: Gag-NCx3_virion_rep3

tag: cell type

value: WT


title: shATF4, LX-2, Tg, replicate2, RNAseq


title: Rad21ncr_clone1

value: endometrial carcinoma cells


title: Gag-NCx2_virion_rep2

tag: genotype


title: Gag-NCx3_virion_rep1


title: ATAC-seq in sea star whole embryos at 66 hpf, replicate 2

description: ATAC-seq

value: 66 hpf


title: Rad21ct116wt_clone2


title: shATF4, LX-2, Tg, replicate1, RNAseq


title: ATAC-seq in sea star whole embryos at 66 hpf, replicate 1

description: ATAC-seq


title: Rad21ct116wt_clone1


title: Gag-NCx2_virion_rep1


title: shATF4, LX-2, TGFβ, replicate2, RNAseq


title: Rad21ct116_clone2


title: Gag-dNC-NC_virion_6SG_rep1


title: shATF4, LX-2, TGFβ, replicate1, RNAseq


title: ATAC-seq in sea star whole embryos at 24 hpf, replicate 1

description: ATAC-seq

value: 24 hpf


title: Gag-dNC-NC_virion_rep3


title: Rad21ct116_clone1


title: shATF4,LX-2, DMSO, replicate2, RNAseq


title: Gag-dNC-NC_virion_rep2


title: Rad21cdelwt_clone2


title: Rad21cdelwt_clone1


title: shATF4, LX-2, AA_Dep, replicate2, RNAseq


title: Gag-dNC-NC_virion_rep1


title: Gag-CNBP7_virion_rep3


title: Rad21cdel_clone2


title: Gag-CNBP7_virion_rep2


title: Rad21cdel_clone1


title: shCtrl, HMLE, Twist_OE, replicate2, RNAseq

source_name: HMLE

value: HMLE


title: Gag-CNBP7_virion_rep1


title: shATF4, LX-2, DMSO, replicate1, RNAseq


title: shATF4, LX-2, AA_Dep, replicate1, RNAseq


title: shCtrl, HMLE, Twist_OE, replicate1, RNAseq


title: ATAC-seq in sea star whole embryos at 24 hpf, replicate 2

description: ATAC-seq


title: 4Cncrwt_clone2

data_processing:
QHR-4C FASTQ raw reads were aligned to GRCh37/hg19 genome using bowtie2 with default parameters.
The reads per million (RPM) interaction values were calculated by r3Cseq program (v1.38.0).
The Bedgraph files generated by r3Cseq package were used for visualizing in UCSC genome browser.
Assembly: Assembly: hg19
Supplementary files format and content: Supplementary files format and content: bedGraph

extract_protocol:
106 cell were collected and crosslinked by 2% formaldehyde. Then the cell were washed twice by PBS and lysed by NP-40 and Triton X-100. SDS were added to open nucleus. Then DpnII were added to digest the chromosome overnignt. After digesting, T4 ligase were used to ligate digested DNA to perform proximity ligation. Ligated DNA were reverse-crosslinked overnight in the presence of protease K and DNA were extracted by phenol-chloroform and dissolved in water then performed linear PCR amplification using biotin-labeled primer. DNA were collected by Streptavidin Beads after linear PCR and adaptors were added to collected DNA and final PCR amplification were performed after adapter ligation. Libraries were sequence on an Illumina NovaSeq platform.
PCR
QHR-4C


title: Gag-CNBP6_virion_rep3


title: shCtrl, HMLE, Tg, replicate2, RNAseq


title: 4Cncr_clone2


title: ATAC-seq in sea star whole embryos at 90 hpf, replicate 1

description: ATAC-seq


title: shCtrl, HMLE, Tg, replicate1, RNAseq


title: 100%GG_2

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA in hybridization buffer was hybridized to 8×60 K Whole Salmon Genome Oligo Microarrays (ID 020938, Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 12.1.1.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Oncorhynchus mykiss

label_protocol: 50 ng of RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the Low Input Quick Amp protocol. Yields of cRNA and the dye-incorporation rate were measured.

growth_protocol: The study was performed with all-female rainbow trout (Störk strain) to exclude sex-related effects and thereby minimize variation. Before the experiment started, 70 rainbow trout per tank were stocked into the experimental facility and fed with a commercial feed (EFICO Enviro 920 Advance, BioMar Group, Aarhus C, Denmark). The acclimatization phase lasted eight weeks. A homogenous group of 55 fish with an average initial weight of 135.97 ± 1.71 g were randomly stocked into the different tanks (see illustration above).

extract_protocol: Fish were fasted for one day prior to sampling. To analyse weight gain (g) and growth (cm) and tissue sampling, trout were sedated with clove oil (1mL*10L-1) and samples taken at the beginning and end of the study. A pool of twenty random fish from the initial stock and a pool of five random fish from each tank at the end of the trial were sampled to perform the transcriptome analysis of the intestine. The samples were placed in cryotubes and immediately frozen in dry ice and stored at -80 °C until analysis.Individual RNA specimens were isolated from the proximal intestine of rainbow trout (tank A) fed with 100% IM GG and a control diet using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Each system had one tank being fed with the same feed, meaning that duplicates for each feed tested existed, see figure above. Ad libitum feeding by hand was conducted until satiation (excess feeding kept to a minimum) by specialists. Fish were fed with the experimental aquafeeds 3 rounds each morning from Monday to Saturday, starting at 08:30 a.m. Moreover, 2 rounds were fed every evening from Monday to Friday, starting at 3:30 p.m. Saturday evening and whole Sunday fish were fasted. To exclude tank effects, each day feeding was started with the next tank. The amount of feed fed per tank was recorded every day after the evening feeding. Between day 64 and 69 of the experiment, five fish of each tank were sampled regarding size, length and organs for transcriptomic analysis.

value: proximal gut

tag: gender

value: unknown

value: juvenile fish of ~ 136g (at the beginning of experiments)

value: Diet containing 400g insect meal + 3g Guar Gum per kg feed


title: Gag-CNBP6_virion_rep1


title: 4Cncr_clone1


title: Hi-C, Gemcitabine-resistant cells, replicate3

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

data_processing:
The raw sequenced Hi-C reads were first mapped to the human genome hg19 with BWA.
The normalization of valid mapped Hi-C reads was carried out using the HiCExplorer suite of tools (v3.6) according to the documentation provided with the software
The valid reads were used to generate raw Hi-C matrices at different resolution using hicBuildMatrix for each sample.
The application hicPlotMatrix in HiCExplorer was used to generate the heatmaps to visualize interaction frequencies.
Assembly: mm10
Supplementary files format and content: xlsx

source_name: Pancrease

extract_protocol:
3,000,000 fresh cells were collected for each Hi-C sample.
Cells were fixed with freshly made 1% formaldehyde for 10 min at room temperature for each sample. The reaction was quenched by adding 2 M glycine to a final concentration of 0.2 M for 5 min at room temperature. Fixed cells were lysed in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl and 0.2% IGEPAL CA-630 with proteinase inhibitor) for 1h at 4 °C with rotation. The supernatant was discarded and the pellet was gently resuspended in 1 × CutSmart Buffer (NEB, B7204) containing 0.1% SDS and incubated at 65°C for 10 min. Permeabilization was quenched by adding 10% Triton X-100 and incubated at 37°C for 1h. Chromatin was digested overnight at 37 °C with rotation by adding the DpnII restriction enzyme (NEB, R0543M). Digested chromatin ends were filled and marked with biotin-14-dATP (Thermo Fisher, 19524016) using a large Klenow fragment of DNA polymerase I (NEB, M0210) for 1h at 37 °C. Samples were then diluted and ligated using T4 DNA ligase (Thermo Fisher, EL0013) at 16 °C overnight. Chromatin was de-cross-linked, and proteins were removed by proteinase K, followed by phenol/chloroform extraction coupled with isopropanol precipitation using glycogen as a carrier. Biotin-14-dATP from unligated DNA ends was removed by T4 DNA polymerase (NEB, M0203) at 12 °C for 2 h. DNA was purified by phenol/chloroform and sonicated using a Covaris S220 (Covaris, USA) to approximately 300-600 bp. Biotinylated DNA fragments were then pulled down using Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher, 65001). The DNA ends were subsequently repaired and phosphorylated using T4 DNA polymerase (NEB, M0203), Klenow fragment of DNA polymerase I (NEB, M0210), and T4 Polynucleotide Kinase NK (NEB, M0201). The DNA was further prepared for sequencing using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme Biotech, ND607) and barcoded adaptors were ligated using TruePrep Index Kit V2 for Illumina (Vazyme Biotech, TD202). Each Hi-C library was indexed uniquely and amplified by 12 cycles of PCR for all samples. PCR purification and size selection was carried out using the VAHTS DNA Clean Beads (Vazyme Biotech, N411). Library quantity was assessed using a Qubit 3.0 Fluorometer (Invitrogen, USA). For each individual, the library was sequenced with 150 bp paired-end reads on the Illumina HiSeq X Ten platform.

value: Pancrease

value: primary tumor

value: Pancreatic cancer cell

value: Gemcitabine resistant

value: Gemcitabine (in DMSO)


title: shCtrl, HMLE, DMSO, replicate2, RNAseq

value: shCtrl

value: DMSO


title: Gag-CNBP5_virion_rep3

value: cell line

value: 293T cells transfected


title: Hi-C, Parental cells, replicate3

value: WT


title: 100%GG_3


title: 4Cct116wt_clone2

value: Uterus

value: endometrial carcinoma cells


title: Control_3

source_name: Control

value: Diet containing 300g soy protein concentrate per kg feed


title: 100%GG_4

value: proximal gut


title: Control_2

value: unknown


title: Hi-C, Gemcitabine-resistant cells, replicate2


title: Gag-CNBP5_virion_rep2


title: 4Cct116wt_clone1


title: Hi-C, Parental cells, replicate2


title: Gag-CNBP5_virion_rep1


title: 4Cncrwt_clone1


title: 4Cct116_clone2


title: shCtrl, HMLE, AA_Dep, replicate2, RNAseq

value: HMLE


title: Gag-CNBP6_virion_rep2


title: Hi-C, Gemcitabine-resistant cells, replicate1


title: shCtrl, HMLE, AA_Dep, replicate1, RNAseq


title: 4Cct116_clone1


title: shATF4, HMLE, Twist_OE, replicate2, RNAseq


title: Gag-CNBP4_virion_rep3


title: 4Ccdelwt_clone2


title: Gag-CNBP4_virion_rep2


title: shATF4, HMLE, Tg, replicate2, RNAseq

value: Thapsigargin


title: shCtrl, HMLE, DMSO, replicate1, RNAseq


title: 4Ccdelwt_clone1


title: Gag-CNBP3_virion_rep3


title: Gag-CNBP4_virion_rep1


title: 100%GG_1

value: juvenile fish of ~ 136g (at the beginning of experiments)

value: Diet containing 400g insect meal + 3g Guar Gum per kg feed


title: shATF4, HMLE, Twist_OE, replicate1, RNAseq


title: Hi-C, Parental cells, replicate1

value: Pancrease

value: primary tumor

value: Pancreatic cancer cell


title: shATF4, HMLE, Tg, replicate1, RNAseq


title: Control_1


title: ChIP-seq, Input, Parental cells, replicate3

data_processing:
RNA-seq data sets were trimmed and aligned to mouse genome build mm10 using STAR. All ATAC-seq and ChIP-seq data sets were trimmed and aligned to mouse genome build mm10 using Bowtie2.
Duplicate reads of all RNA-seq, ATAC-seq and ChIP-seq data were removed with SAMtools.
MACS2 was used to identify regions of ATAC-seq and ChIP-seq peaks.
The ATAC-seq and ChIP-seq peaks were used for known motif enrichment analysis of each sample, which were performed using HOMER (v4.10).
Assembly: mm10
Supplementary files format and content: The processed BigWig (.bw) coverage files were generated using deeptools bamCoverage (Version 3.3.1)

extract_protocol:
1,000,000 fresh cells were collected for each RNA-seq sample. Total RNA was extracted using the TRIzol reagent (Invitrogen, USA). 50,000 fresh cells were collected for each ATAC-seq and ChIP-seq sample. 3,000,000 fresh cells were collected for each ChIP-seq sample.
Total RNA was purified using RNeasy Mini Kit (QIAGEN, Germany) and run on an Agilent Bioanalyzer 2100 to assess RNA integrity. The RNA‐seq library preparation from 1 μg of total RNA was performed with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's instructions. For ATAC-seq fresh cells were lysed in lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630 [Sigma-Aldrich]) for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500 x g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome (DIATRE Biotech, China) and tagmentation buffer at 37 °C for 30 min. After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. PCR was performed to amplify the library for 13 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30 s; and thermocycling at 98 °C for 15 s, 60 °C for 30 s, and 72 °C for 3 min; following by 72 °C 5 min. After the PCR reaction, libraries were purified with Agencourt Ampure XP beads (Beckman, USA) to remove contaminating primer dimmers and quantitated using Qubit 2.0 Fluorimeter (Invitrogen, USA). For ChIP-seq, the following antibodies were used for ChIP experiments: FOXA1 (ab23738, Abcam, USA), H3K27ac (ab4729, Abcam, USA), H3K27me3 (9733S, CST, USA), SMC3 (ab9263, Abcam, USA), CTCF (Millipore, 07-729). For each condition, approximately 10 million fixed cells were lysed to prepare nuclear extracts. After chromatin shearing by sonication, lysates were incubated overnight at 4°C with protein A Dynabeads (Invitrogen, USA) coupled with 3-5 μg of antibody. After immunoprecipitation, the beads were recovered using a magnet and then washed. DNA was eluted and cross‐links reverted at 55°C for 4 hours then purified with QIAquick PCR Purification Kit (QIAGEN, USA). DNA was quantitated using the Qubit dsDNA HS assay and a Qubit 2.0 Fluorimeter (Invitrogen). For each ChIP-seq, 5-10 ng of purified ChIP-DNA was used to generate the sequencing library using a VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme Biotech, China).


title: Gag-CNBP3_virion_rep2


title: 4Ccdel_clone1


title: 4Ccdel_clone2


title: shATF4, HMLE, DMSO, replicate2, RNAseq


title: ChIP-seq, Input, Gemcitabine-resistant cells, replicate3

value: Gemcitabine resistant

value: Gemcitabine (in DMSO)


title: ChIP-seq, Input, Gemcitabine-resistant cells, replicate2


title: ChIP-seq, Input, Parental cells, replicate2

value: DMSO


title: Gag-CNBP3_virion_rep1

value: cell line

value: 293T cells transfected


title: shATF4, HMLE, DMSO, replicate1, RNAseq


title: Nat10_KO-3.IP_R1

city: Guangzhou

first: Ning

address: 600 Tianhe road

institute: Sun Yat-sen University

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Acetylated sites on RNAs (peaks) were identified by MACS software.
Differentially acetylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially acetylated protein coding genes,.
Assembly: hg38
Supplementary files format and content: Excel formats including Acetylated sites, Acetylated RNA, enrichment information, Annotations

extract_protocol:
RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction.
RNA libraries for IP and input samples were then constructed with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA) by following the manufacturer’s instructions.Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).

value: Human renal tubular epithelial cell

value: NAT10 knockout

value: IP


title: Gag-CNBP2_virion_rep3

value: WT


title: shATF4, HMLE, AA_Dep, replicate2, RNAseq


title: ChIP-seq, Input, Gemcitabine-resistant cells, replicate1


title: Gag-CNBP2_virion_rep2


title: ChIP-seq, Input, Parental cells, replicate1


title: Nat10_KO-2.IP_R1


title: shATF4, HMLE, AA_Dep, replicate1, RNAseq


title: ChIP-seq, Smc3, Gemcitabine-resistant cells, replicate3


title: Nat10_KO-2.Input_R1

value: input


title: Gag-CNBP2_virion_rep1


title: Thapsigargin, H3K27ac ChIP-seq

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay primarily according to the instructions of the ChIP assay kit (Cell Signaling Technology, 9003). 2х10^7 LX-2 cells for each IP.
ChIP-Seq library construction using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).

value: anti-histone H3 (acetyl K27) (Abcam, 4729)


title: Nat10_KO-1.IP_R1


title: Thapsigargin, ATF4 ChIP-seq

value: Thapsigargin

value: anti-ATF4 (Cell Signaling Technology, 11815)


title: WT_virion_rep3


title: Nat10_KO-1.Input_R1


title: ChIP-seq, Smc3, Parental cells, replicate2


title: ChIP-seq, Smc3, Gemcitabine-resistant cells, replicate1


title: WT_virion_rep1


title: Wt-3.Input_R1

value: Wild-type control


title: Nat10_KO-3.Input_R1


title: TGFβ, H3K27ac ChIP-seq

value: TGFbeta


title: ChIP-seq, Smc3, Parental cells, replicate1

value: Pancrease

value: primary tumor


title: TGFβ, ATF4 ChIP-seq


title: Gag-SRSF5_cell_6SG_rep1

data_processing:
BBduk from BBTools was used to processed CLIP-seq reads before mapping.
Reads were then aligned to the human genome (hg19) or to corresponding viral genomes, with up to 1 mismatches allowed using the Bowtie algorithm.
In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2–best–strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
SAMTools and BEDTools were used to generate various file types of mapped reads for further analysis.
Assembly: hg19 and NL4-3
Supplementary files format and content: tab-delimited files showing summarization of reads (i.e. chromosomal locations and counts).
Library strategy: CLIP-seq


title: TGFβ, ChIP-seq


title: ChIP-seq, Ctcf, Gemcitabine-resistant cells, replicate3

value: Pancreatic cancer cell

value: Gemcitabine resistant


title: Wt-2.IP_R1


title: Wt-2.Input_R1


title: Gag-SRSF5_cell_rep3


title: ChIP-seq, Smc3, Parental cells, replicate3

value: DMSO


title: ChIP-seq, Ctcf, Parental cells, replicate3


title: WT_virion_6SG_rep1

value: cell line


title: Wt-1.IP_R1


title: Gag-SRSF5_cell_rep2

value: 293T cells transfected


title: ChIP-seq, Smc3, Gemcitabine-resistant cells, replicate2

value: Gemcitabine (in DMSO)