title: liver_1105

description:
CGNP_1105
10466_11196_90485_HLWKLBGX9_1105_CGNP_CGATGT

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349122


title: N03

status: Public on Jan 01 2024

type: SRA

city: Shanghai

first: bo

last: tian

address: No.168, changhai road

country: China

institute: changhai hospital

description: 150 bp paired-end

library_source: transcriptomic

data_processing:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
About xxxxx raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
Then about xxxxxx clean reads for each sample were retained for subsequent analyses.The clean reads were mapped to the reference genome using HISAT22
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: paracancerous

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

tag: patient

value: patient 3

tag: tissue

value: paracancerous

tag: treatment


title: N01

description: 150 bp paired-end

value: patient 1


title: NR_1479

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

country: USA

institute: Cornell University

description:
CCNR_1479
10465_11196_90484_HM2TYBGX9_1479_CCNR_CTTGTA

data_processing:
library strategy: Length extension chromatin run-on sequencing (leChRO-seq)
ChRO-seq mapping was performed with an established pipeline (Chu, Wang, Chou, & Danko, 2019).  Briefly, read quality was assessed using FastQC.  PCR deduplication was performed by collapsing UMIs using PRINSEQ lite 0.20.2.
Adapters were trimmed from the 3’ end of remaining reads using cutadapt 1.16 with a maximum 10% error rate, minimum 2 bp overlap, and minimum 20 quality score.
Processed reads with a minimum length of 15 bp were mapped to the genome using Burrows-Wheeler Aligner (BWA).
The resulting bigwig files were processed using dREG (Chu et al., 2019; Z. Wang, Chu, Choate, & Danko, 2019) to call peaks of active transcriptional regulatory elements.
Read counts of gene loci (hg38 GENCODE v33 coordinates) as well as the defined transcriptioinal regulatory elements were quantified using the R package bigwig (https://github.com/andrelmartins/bigWig).
Genome_build: hg38 plus a single copy of the Pol I ribosomal RNA transcription unit (GenBank U13369.1)
Supplementary_files_format_and_content: a tab-delimited text file of raw count matrix for gene loci; a tab-delimited text file of raw count matrix for transcriptional regulatory elements

molecule: nuclear RNA

source_name: primary tissues

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349121

tag: subject status

value: NASH resistance (NR)

value: liver


title: T11

description: 150 bp paired-end

source_name: esophageal squamous cell carcinoma

value: patient 11

value: esophageal squamous cell carcinoma


title: UPFL_369_Primary

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

description: scRNAseq

library_source: transcriptomic single cell

data_processing:
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the mouse reference genome using STAR
Transcript abundance estimates for each sample were performed using SALMON
Raw SALMON read counts for all RNAseq samples were normalized by DESeq2
Illumina Novaseq_6000 for scRNAseq base calling
Transcript abundance estimates for cell were performed using cell ranger
Supplementary files format and content: Tab-delimited text files include Normalized count values for each sample
Supplementary files format and content: H5 format files of cell ranger output for each scRNAseq samples
Assembly: mm10

molecule: total RNA

organism: Mus musculus

source_name: bladder tumor

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
scRNAseq libraries were prepared using Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry)

tag: strain

value: bladder tumor

tag: tissue type

value: primary UPFL control

value: untreated


title: SKH04

type: RNA

city: Tsukiji, Chuo-ku

first: Chihiro

last: Takeuchi

state: Tokyo

department: Division of Epigenomics

country: Japan

institute: National Cancer Center Research Institute

hyb_protocol: Samples were hybridized according to the Agilent One-Colour Microarray-based Gene Expression Analysis Protocol.

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263.

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software(v11.0.1.1).

source_name: Gastric mucosa

label_protocol: Amplified double-stranded cDNA was labelled with Cy3 using the Agilent’s Quick Amp Labeling Kit.

extract_protocol: Total RNA was extracted (miRNeasy Mini kit, Qiagen) from tissue samples, and its integrity was verified by Nanodrop 1000 spectrometer.

value: Gastric mucosa with H. pylori-associated gastritis

tag: gender

value: Female


title: Young_Sham, single cell sample from the contralateral brain tissues of young mice received PBS as sham control

city: Chicago

first: April

last: Bell

state: IL

address: 2053 N Mozart St Apt 3F

institute: Northwestern University

data_processing:
Raw sequencing data was converted into FASTQ files using Cell Ranger mkfastq (version 3.0.2)
FASTQ files were aligned to the mm10 genome (downloaded from the 10X Genomics website) using Cell Ranger count (version 3.0.2)
Cell Ranger output was analyzed using Seurat (version 2.3.4)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: contralaterall brain tissue

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: contralaterall brain tissue

tag: age

value: young

value: received PBS as sham control


title: T10

description: 150 bp paired-end

value: patient 10


title: SKH03


title: NR_2094

description:
CGNR_2094
10465_11196_90483_HM2TYBGX9_2094_CGNR_ACAGTG

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349120


title: UPFL_517_Erdafitinib_Primary

description: scRNAseq

value: Erdafitinib-treated primary UPFL tumor

value: Erdafitinib


title: Young_GBM, single cell sample from contralateral brain tissues of young mice engrafted with CT2A tumor cells

value: engrafted with CT2A tumor cells


title: Old_Sham, single cell sample from contralateral brain tisssues from old mice received PBS as sham control

value: old


title: SKH05

value: Male


title: TDA09

value: Gastric mucosa with autoimmune gastritis


title: NR_2690

description:
CCNR_2690
10465_11196_90481_HM2TYBGX9_2690_CCNR_TTAGGC

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349118

value: NASH resistance (NR)

value: liver


title: SKH02


title: TSA01


title: NP_2695

description:
CGNP_2695
10464_11196_90480_HW7F7BGX9_2695_CGNP_GGCTAC

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349117

value: NASH prone (NP)


title: liver_2109

description:
CCNP_2109
10465_11196_90482_HM2TYBGX9_2109_CCNP_TGACCA

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349119


title: Old_GBM, single cell sample from contralaterall brain tissues from old mice engrafted with CT2A tumor cells


title: T09

description: 150 bp paired-end

value: patient 9

value: esophageal squamous cell carcinoma


title: liver_2288

description:
CCNR_2288
10464_11196_90479_HW7F7BGX9_2288_CCNR_GATCAG

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349116


title: TDA06


title: T06

description: 150 bp paired-end

value: patient 6


title: NP_1398

description:
CGNP_1398
10464_11196_90478_HW7F7BGX9_1398_CGNP_GCCAAT

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349115


title: T05

description: 150 bp paired-end

value: patient 5


title: TDA08


title: T04

description: 150 bp paired-end

value: patient 4


title: TDA05

value: Female


title: NR_2111

description:
CGNR_2111
10464_11196_90477_HW7F7BGX9_2111_CGNR_ATCACG

extract_protocol: Library were prepared according to T Chu et al., Nature Genetics (2018) PMID: 30349114


title: SC61_3290

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
cellranger V4.0.0 mkfastq.
cellranger V4.0.0 count.
Reads are mapped to GRCm38.
UMI counts are summarized are gene expression levels.
Assembly: GRCm38
Supplementary files format and content: .tar archives include filtered feature matrix (matrix.mtx), barcodes (barcodes.tsv), and features (features.tsv) files.

source_name: breast adenocarcinoma

growth_protocol: Spontaneous breast tumors.

extract_protocol:
Cells were processed according to the manufacturer's protocol.
Libraries were constructed following standard Illumina protocols for scRNA sequencing in a sequencing and microarray core facility.

treatment_protocol: Breast tumors were treated with AAV on day 0, 3, and harvest on day 6. Tumors were dissociated into single cells and prepared for 10x Genomics Chromium Controller single cell separation.

value: breast tumor

tag: genotype

value: K14-Cre, Trp53wm-R245W/fl and Rosa26LSL CAS9-P2A-EGFP/+


title: TDA04


title: T08

description: 150 bp paired-end

value: patient 8


title: TDA02


title: TDA01


title: T07

description: 150 bp paired-end

value: patient 7


title: SC61_3923


title: SC61_3629


title: NRSF/REST_ChIPseq_Cf_Input

city: IRVINE

first: Shan

last: Jiang

address: 2300E Biological Sciences III

institute: UNIVERSITY OF CALIFORNIA, IRVINE

library_source: genomic

data_processing:
ChIP and input sequencing reads were aligned using Bowtie v.0.12.8
After alignment, peaks were detected using MACS v.1.4.2, retaining all statistically enriched regions ( p<10-4.5). Binding regions were considered reproducible when they were identified in both replicates. Consensus binding regions were then merged and called subpeaks using PeakSplitter_Cpp v.1.0. Subpeaks in 50bp were merged. Peaks having (1) higher signal in control than ChIP replicates in each species or (2) signal in control is higher than 1.4 RPM in each species or (3) in Blacklist (ENCODE Project Consortium. 2012) in human and mouse were filtered out as artificially high signal peaks.
Genome_build: GRCh37/hg19,GRCm38/mm10, CanFam3.1, EquCab2.0
Supplementary_files_format_and_content: peak calling results for each species in .txt format. (chromosome, start, end)

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Myelomonocytic leukemia cells

growth_protocol: Mouse macrophage cells (RAW264.7, ATCC, Manassas, VA) were grown in DMEM medium (30-2002, ATCC, Manassas, VA) supplemented with 10% FBS (VWR, Radnor, PA) and penicillin/streptomycin (Life Technologies). Dog myelomonocytic leukemia cells (ML2, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with 1000 mM Hepes, 10mM MEM NEAA, 100mM Sodium pyruvate, 55mM β- mercaptoethanol, 10% FBS and penicillin/streptomycin. Horse skin fibroblast (E.Derm, ATCC, Manassas, VA) were grown in EMEM(30-2003, ATCC, Manassas, VA) supplemented with 10% FBS and penicillin/streptomycin. Trypan Blue (VWR) staining was performed before harvesting the cells for each assay to make sure that at least 90% of the cells were viable.

extract_protocol:
We cross-linked about 20 million cells with 1% formaldehyde for each replicate. Cross-linked chromatin was sonicated into 200-300bp fragments. DNA fragments were incubated with Dynabeads protein G (Thermo Fisher Scientific) bound by NRSF monoclonal antibody (Caltech Protein Expression Center, Pasadena, CA, USA, 12C11-1B11) overnight to perform immunoprecipitation. Then chromatin was reverse cross-linked to extract NRSF-bound DNA.
DNA fragments recovered from ChIPs were end-repaired, ligated to adapters, size selected (200 to 300bp) and PCR-amplified to make the libraries for sequencing. The libraries were made based on Myers Lab protocol v042211 (http://myers.hudsonalpha.org/documents/Myers%20Lab%20ChIP-seq%20Protocol%20v042211.pdf).

tag: cell type

value: Myelomonocytic leukemia cells

tag: passages

tag: chip antibody


title: SKA06


title: SC059_2912


title: T03

description: 150 bp paired-end

value: patient 3


title: NRSF/REST_ChIPseq_Cf_R1

description: NRSF/REST.peaks.Cf.txt

value: NRSF monoclonal antibody (Caltech Protein Expression Center, Pasadena, CA, USA, 12C11-1B11)


title: SC67_3174

value: AAV-Control


title: SC048_2832


title: T02

description: 150 bp paired-end

value: patient 2


title: A2

city: tianjin

first: congjuan

last: xu

address: weijin load

institute: nankai university

data_processing:
After sequencing by sequencer, raw data were obtained. Q30 was first used as a standard for performing QC. Use cutadap software (v1.9.3) to de-join and remove low quality reads to get high quality reads.
High-quality reads were aligned to rRNA sequences using bowtie to obtain unaligned clean reads. alignment to the reference genome was performed using Tophat2 software. Raw counts were then obtained using HTSeq software (v0.9.1).
Differentially expressed genes were screened using edgeR for normalisation and calculation of fold change and p-value between the two sets of sample
GO analysis and KEGG pathway analysis using differentially expressed genes
Supplementary files format and content: excel/gene expression profiling

organism: Pseudomonas aeruginosa

source_name: bacteria

extract_protocol:
Cycloheximide-treated cells were lysed with lysis buffer and then digested with nuclease. Digested samples were passed through a size exclusion column to isolate single ribosomes. RNA fragments protected by ribosomes were subjected to fragment selection by polyacrylamide gel electrophoresis, followed by removal of rRNA from them.
Purified RNA ends were repaired with junctions and converted by reverse transcription to cDNA. cDNA was purified by polyacrylamide gel electrophoresis and amplified by PCR after cyclisation.
Ribo-seq

value: bacteria

value: 16 mg/L azithromycin treated


title: SC61_3592


title: NRSF/REST_ChIPseq_Cf_R2

description: NRSF/REST.peaks.Cf.txt


title: LncR-3363 Ctrl rep4

first: Wenju

last: Liu

address: 1239  siping road

institute: University of Tongji

data_processing:
Illumina NovaSeq 6000 System was used for basecalling and 150 bp paired-end reads were generated.
Sequenced reads were trimed for adaptor and low-quality sequence using cutadapt v1.18 and then mapped to GRCm38 whole genome using HISAT2 v2.1.0 with parameters "--rna-strandness RF --dta-cufflinks --no-discordant"
gene expression levels were quantified as FPKM by stringtie V1.3.4d with parameters “-e --rf”. Genes with FPKM <0.1 in all samples were filtered, and FPKM values of replicates were averaged.
Differences in expression were determined using Cuffdiff V2.2.1.
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include FPKM values for each Sample

source_name: embryo

growth_protocol: For in vitro fertilization, sperm collected from the cauda epididymides of adult male BDF1 mice were incubated in G-IVF™ PLUS medium for 20–30 min at 37 °C under 5% CO2 to induce sperm swim-up. The zona pellucida of each MII oocyte was punched to make a small hole using a Piezo-drill micromanipulator. Oocytes were then placed in the prepared sperm suspension in G-IVF™ PLUS medium. At 5 h post fertilization (hpf), these embryos were washed and cultured in G-IVF™ PLUS medium. The fertilized oocyte embryos were thoroughly washed and cultured in G-1 PLUS medium at 37 °C under 5% CO2

extract_protocol:
Total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions.
TruSeq Stranded Total RNA kit(illumine) was used to construct library of early embryonic development stage following the manufacturer’s instructions, each sample need approximately 150-200 embryos. In briefly, Ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with beads, and cleaved RNA fragments were copied into cDNA using reverse transcriptase and random primers. cDNA subjected to 12–15 cycles of PCR amplification. For small amount total RNA-Seq, we used a SMARTer Stranded Total RNA-Seq Kit version 2(Takara) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina NovaSeq 6000 platform with paired ends and 150-bp read lengths at Berry Genomics.

treatment_protocol: The RNA for microinjection, MT2-Mm sgRNA was diluted to 150 ng/μL, Cas9 mRNA was diluted to 100 ng/μL, and ASO was diluted to 20uM before injection. For MII oocytes microinjection, the oocytes were treated with hyaluronidase, and then they were injected with 5 to 10 pL of sample per oocyte.

tag: developmental stage

value: embryo

value: wild type


title: LncR-3363 Ctrl rep3


title: SKA01

value: Gastric mucosa with autoimmune gastritis

value: Male


title: A1


title: KD3

description: 150 bp paired-end

data_processing:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
About xxxxx raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
Then about xxxxxx clean reads for each sample were retained for subsequent analyses.The clean reads were mapped to the reference genome using HISAT22
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

tag: cell line

value: esophageal cancer cell line

value: ShHNRNPC


title: KD4

description: 150 bp paired-end


title: KD2

description: 150 bp paired-end


title: NRA02


title: WT2

value: no treatment


title: JSA01


title: WT1


title: LncR-3363 Ctrl rep2


title: T01

description: 150 bp paired-end

value: patient 1

value: esophageal squamous cell carcinoma


title: KD1

description: 150 bp paired-end


title: LncR-3363 Ctrl rep1


title: CHMm_rep1

city: Seoul

first: Je-Yoel

last: Cho

address: 1, Gwanak-ro, Gwanak-gu

department: Biochemistry

country: South Korea

institute: Seoul National University

data_processing:
To remove adaptors with low-quality reads and extract miRNA-specific sequence, cutadapt was used with options (--quality-base 33 -u 4 -m 22 -M 30 -f fastq -q 20 -O 6 -j 23 -a adapter-sequence
Before and after the trimming step, quality of sequenced reads was estimated using FastQC.
For known and novel miRNA analysis, miRDeep2 package was used. First, all filtered reads data were merged into one file for novel miRNA analysis. The merged data were converted to collapsed fasta-formatted file and aligned to reference genome using mapper.pl script with options (-e -h -j -m -p). Second, novel miRNAs were identified using miRDeep2.pl script. The identified mature and hairpin forms of novel miRNAs were extracted and combined with known forms of miRBase prepared previously. Finally, the expression values of known and novel miRNAs were calculated using the quantifier.pl script. The CPM (counts per million), which is counts scaled by total number of reads, was used for further analysis. To estimate data reproducibility between replicate samples, Pearson correlation values were calculated and visualized using correlation function in R.
Assembly: canFam3.1
Supplementary files format and content: text

source_name: CHMm

growth_protocol: Canine mammary gland adenocarcinoma cell lines (CHMp and CHMm) was grown in RPMI 1640 medium (Hyclone) containing 10% fetal bovine serum (FBS, Gibco) and gentamicin (50ug/ml).

extract_protocol:
Exosomes were purified from cells cultured under serum-free conditions using a combined method of ultrafiltration and ultracentrifuge. First, the culture supernatant was subjected to a differential centrifuge to eliminate cells, dead cells, and cell debris and sequential filtered with 0.45 and 0.22 μm. The filtered supernatant was concentrated using 10K Amicon-Ultra 15 Centrifugal Filter Units (Merck). Filtered units were ultracentrifuged for 80 min and washed with PBS. Exosomes for RNA isolation were lysed with Qiazol (Qiagen) and miRNeasy mini plus kit (Qiagen). Isolated small RNA fracation was directly performed small RNA sequencing.
Small RNA library was prepared using NEXTflex™ Small RNA-Seq Kit v3 following manufacturer's instructions.

treatment_protocol: At 70~80% confluency in 100mm culture dishes, cell were washed with PBS two times and RPMI media without FBS and antibiotics was replaced.

value: CHMm


title: SKA05


title: LncR-3363 KD-2cell rep1

value: LncR-3363 KD


title: CHMp_rep1

source_name: CHMp

value: CHMp


title: NRA01

value: Female


title: NC3

description: 150 bp paired-end

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: Control


title: LncR-3363 KD-1cell rep4


title: UCMSC, exosome, rep3

city: Hanoi

first: Quang

middle: Minh

last: Dang

address: 458 Minh Khai Street

country: Viet Nam

institute: Vinmec-VinUni Institute of Immunology

data_processing:
Nextera adapter sequences, low-quality base calls (Phred score < 15), and short reads (read length < 20 base pairs) were trimmed using Trim Galore v0.6.2
FASTQ paired-end reads were aligned using HISAT2 v2.2.1 32 to human GRCh38 genome build from Ensembl
BAM files were sorted by read name and chromosome position using Samtools v1.8
Transcripts were quantified via the FeatureCounts function of the Bioconductor R package Rsubread v1.6.4 35, counting non-strand-specific fragments instead of reads.
Assembly: hg38
Supplementary files format and content: Comma-delimited file includes raw counts for each sample
Supplementary files format and content: Comma-delimited file includes raw counts for each sample, aggregated into a single count matrix

source_name: primary cells

growth_protocol: The primary umbilical cord-derived mesenchymal stem cells (UCMSCs) at passage 3 (P3) were supplied by the EV group (Vinmec Hi-Tech Center) and expanded to P5 in DMEM/F12 (Gibco, Massachusetts, USA) supplemented with 10 % FBS (Gibco, Massachusetts, USA) (v/v) at 5 % CO2 and 37 oC.

extract_protocol:
Total RNAs from EXs and secreting UCMSCs were extracted using Trizol method.  An amount of 50 ng total RNA was used for subsequent library preparation.
RNA was used for reversed transcription using random hexamer primers to synthesize the first cDNA strand. The second cDNA strand was synthesized by DNA polymerase using the first cDNA strand as a template. The cDNA fragments were then end-repaired and A-tailed to generate the 5’ overhangs for indexing adapter ligation. The A-tailed cDNA fragments were ligated with an indexing adapter, followed by amplification with i5 and i7 indexing primers for sample multiplexing. The indexed libraries were pooled and hybridized with the Illumina exome sequencing panel (Illumina, USA). The library was diluted to 4 nM using the resuspension buffer (RSB), followed by a denaturing step in the presence of NaOH 0.2 N by ration 1:1 (v/v). The denatured library was diluted with denaturing buffer HT1 to achieve a 20 pM denatured library solution. The denatured library was then diluted to the final concentration of 1.3 pM in a total volume of 1.3 mL for sequencing. Sequencing was done on the Nextseq 500/550 system using Nextseq High Output v2.5 (300 cycles) (Illumina, USA).

treatment_protocol:
At P5, UCMSCs were seeded in T75 flask (5000 cell/cm2) with EV-depleted culture media (DMEM/F12 supplemented with 10 % EV-depleted FBS).
After four or five days of incubation, when UCMSCs reached 80 % confluency, the conditioned medium was collected for EV isolation.
Conditioned media collected from cell culture were centrifuged 300 x g / 10 minutes / 4 °C to remove cell debris, then apoptotic bodies and microvesicles (MV) were removed using sequential centrifugations at 2,000 × g / 20 min / 4 °C and 16,500 × g / 30 min / 4 °C, respectively.
The remained supernatant was collected and centrifuged at 100,000 × g / 90 min / 4 °C for EXs (Optima XPN-100 Ultracentrifuge, Beckman Coulter, California, USA).
All EXs were resuspended in PBS and stored at −80 °C for further use.

value: primary cells

value: mesenchymal stem cells

value: exosome isolation


title: NC2

description: 150 bp paired-end


title: LncR-3363 KD-1cell rep2

value: embryo


title: LncR-3363 KD-1cell rep3


title: ST486_ZDHHC11_all_sh2_1

city: Groningen

first: Lotteke

last: Ziel-Swier

state: Groningen

address: Hanzeplein 1

department: Department of Pathology and Medical Biology

country: Netherlands

institute: University Medical Center Groningen

description: mRNA and lncRNA expression analysis

hyb_protocol: According to the manufacturers instructions

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 10.7.3.1.

data_processing: GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: ST486 cell line with ZDHHC11_all shRNA

growth_protocol: RPMI-1640 medium supplemented with 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM glutamine and 20 % Fetal Calf Serum; 37⁰C, 5 % CO2.

extract_protocol: miRNeasy Micro/Mini Kit (Qiagen)

treatment_protocol: Cells were transduced with lentiviral miRZip vector containing shRNAs against the ZDHHC11 transcripts or control shRNA. RFP+ cells were sorted and RNA was isolated.

value: Burkitt lymphoma cell line

value: Transduced with ZDHHC11_all shRNA 2


title: Brain, CLCF1 05

city: Jinan

first: Xudong

last: Zhou

address: 4655 University Road, University Science and Technology Park, Changqing District, Jinan City, Shandong Province, China

department: First Clinical College

institute: Shandong University of Traditional Chinese Medicine

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

organism: Rattus norvegicus

source_name: Brain

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

value: Brain

value: Inhaled carbon monoxide


title: UCMSC, rep3


title: ST486_ZDHHC11_all_sh2_2

description: mRNA and lncRNA expression analysis

label_protocol: According to the manufacturers instructions


title: NC4

description: 150 bp paired-end

value: esophageal cancer cell line


title: ST486_ZDHHC11_all_sh1_1

description: mRNA and lncRNA expression analysis

value: Transduced with ZDHHC11_all shRNA 1


title: UCMSC, exosome, rep2


title: ST486_ZDHHC11_all_sh1_2

description: mRNA and lncRNA expression analysis


title: ST486_NT1_1

description: mRNA and lncRNA expression analysis

source_name: ST486 cell line with control shRNA

value: Transduced with control shRNA


title: Brain, CLCF1 04


title: UCMSC, rep2

value: no treatment


title: KD3

description: 150 bp paired-end


title: Brain, CLCF1 06


title: Brain, CLCF1 03


title: ST486_NT1_2

description: mRNA and lncRNA expression analysis


title: KD4

description: 150 bp paired-end


title: Brain, CLCF1 02


title: UCMSC, exosome, rep1


title: KD2

description: 150 bp paired-end


title: KD1

description: 150 bp paired-end


title: After-fertilize-20h rep1_add

value: wild type


title: NC1

description: 150 bp paired-end


title: Brain, CLCF1 01


title: After-fertilize-20h rep2


title: UCMSC, rep1


title: HepaRG cells_Replicate-4_FL

city: Regensburg

first: James

middle: A.

last: Hutchinson

department: Surgery

country: Germany

institute: UKR

data_processing:
Quality control and read mapping to the human reference genome (GRCh38, Gencode release 29) was performed using an adapted version of the SnakePipes18 analysis pipeline (v1.2.2 including rDNA removal by Bowtie2 (v2.3.5) mediated mapping).
Transcript counts from Salmon (v0.13.1)20 were imported by tximport20 and summarized to gene-level (“original counts and offset”) and prefiltered with edgeR:filterByExpr.
Quality control of the count matrix and DE-Gene calling was performed with DESeq2 (fdr=0.1).
Genome_build: GRCh38, Gencode release 29
Supplementary_files_format_and_content: .Rdata

growth_protocol: HepaRG cells were cultured for 2 weeks in 12-well plates (3.9 cm^2; TPP) at 2.5x10^4 cells/cm^2 in HepaRG growth medium (William's E medium supplemented with 10% FCS, 1% Pen-Strep, 1% Glutamine, 0.023 IE/ml insulin, 4.7 ug/ml hydrocortisone plus 80 ug/ml gentamycin). HepaRG cells were then cultured for a further 2 weeks in HepaRG growth medium containing 1.8% DMSO to promote differentiation into hepatocyte-like cells.

extract_protocol:
RNA was isolated from UL- and FL-HepaRG cells was done using the RNeasy Mini Kit (Qiagen - Cat. 74106) and a DNA cleanup was performed using the RNase-Free DNase Set (Qiagen-Cat. 79254).
Equimolar amounts of each library were single-end sequenced (75bp) on a NextSeq 550 instrument (Illumina, bcl2fastq software v2.20.0.422) using the NextSeq Control Software (NCS v2.2.0) and Real Time Analysis Software (RTA, v2.4.11).

treatment_protocol: Differentiated HepaRG cells (ie. after 4 weeks of growth protocol) were cultured for 24 hours in serum-free HepaRG growth medium and then treated with (i) bovine serum albumin (BSA)-conjugated palmitic and oleic acid (1:2 - 0.5 mM) isopropanol for a further 24 hours for fat-loading, or (ii) treated with isopropanol (solvent) alone.

tag: cells

tag: state

value: Differentiated

value: BSA-conjugated palmitic and oleic acid in isopropanol


title: Brain, CO 06

value: WT


title: After-fertilize-20h rep1


title: LncR-3363 KD-1cell rep1

value: LncR-3363 KD


title: After-fertilize-20h rep2_add


title: HepaRG cells_Replicate-4_UL

value: Isopropanol (solvent) control


title: Brain, CO 05


title: HepaRG cells_Replicate-3_FL


title: NC4

description: 150 bp paired-end

value: Control


title: HepaRG cells_Replicate-3_UL


title: NC3

description: 150 bp paired-end


title: NC2

description: 150 bp paired-end


title: After-fertilize-17h rep2_add


title: Brain, CO 03


title: HepaRG cells_Replicate-2_UL


title: NC1

description: 150 bp paired-end


title: HepaRG cells_Replicate-2_FL


title: GM12878_met80

city: Guangzhou

first: Yicong

last: Xu

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

description: The 80% methanol-fixed cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

data_processing:
The adapter sequences and low-quality reads were removed using fastp.
The processed reads were aligned to the genome using STAR.
The duplicate reads with identical sequences were removed using Picard.
The transcripts were assembled and quantified using HTSeq.
Assembly: hg38;mm10
Supplementary files format and content: Tab-separated matrix files of counts for bulk samples
Supplementary files format and content: HDF5 matrix files of counts for the single-cell samples

source_name: Cell line

growth_protocol: The cells were cultured in RPMI 1640 medium or DMEM supplemented with 10% fatal bovine serum and 1% penicillin–streptomycin. Adherent cells were detached by 0.25% Trypsin-EDTA at 37℃ for 3min and quenched with growth medium. All the cells were maintained in 37℃ with 5% CO2.

extract_protocol:
The methanol fixed cells were kept in -20℃ for 30min and pelleted at 500×g for 5min at 4℃. After two further washes with 1ml of ice-cold wash-resuspension buffer I, permeabilized cells were resuspended in 20ul of ice-cold wash-resuspension buffer II.
The cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

treatment_protocol: The cultured cells were washed twice with 1ml of ice-cold PBS and resuspended in 200ul of ice-cold PBS, 800ul of methanol were added dropwise and gently mixed.

value: Cell line

value: B-Lymphocyte

value: Fixed by 80% methanol


title: Brain, CO 04


title: GM12878_met60

description: The 60% methanol-fixed cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

value: Fixed by 60% methanol


title: After-fertilize-17h rep1_add


title: Brain, CO 02

value: Brain


title: After-fertilize-17h rep1


title: 293T_met50

description: The 50% methanol-fixed cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

value: Embryonic kidney cells

value: Fixed by 50% methanol


title: Brain, NC 05


title: After-fertilize-14h rep2


title: HepaRG cells_Replicate-1_FL


title: Brain, NC 06


title: Brain, CO 01

value: Inhaled carbon monoxide


title: After-fertilize-14h rep2_add


title: GM12878_met40

description: The 40% methanol-fixed cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

value: Fixed by 40% methanol


title: After-fertilize-14h rep1_add


title: After-fertilize-14h rep1


title: 293T_met40


title: HepaRG cells_Replicate-1_UL


title: Brain, NC 04


title: Brain, NC 03


title: Blastocyst rep2_add

value: Blastocyst


title: Brain, NC 02


title: Brain, NC 01


title: PBMCs_TAB_AS2311_AS1830

city: Oxford

first: Feng

state: Oxfordshire

address: Botnar Research Centre, Windmill Road, Headingtong

country: United Kingdom

institute: University of Oxford

description: 10x Genomics

data_processing:
Paired reads were mapped to the reference genome of hg38 to generate gene expression matrixes using CellRanger v7.0.0.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMCs

extract_protocol:
1x106 PBMC were cultured in 200 μl medium in non-tissue culture treated 96-well round bottom plates (Corning) and left unstimulated or treated with 200 ng/ml LPS (Enzo Bioscience) or anti-CD2/CD3/CD28-coated T-cell activation/expansion beads (Miltenyi Biotec) for 16 h before being prepared for sequencing. After cell culture, cells were harvested and washed in PBS with 0.1% BSA. 20,000 cells from each condition were put into a channel of Chromium Next GEM Chip K of 10x Genomics platform.
Single cell RNA-sequencing libraries were generated using Chromium Next GEM Single Cell 5' Kit v2 kit according to the manufacturer’s instruction.

value: PBMCs

value: T cell activation beads for 16h


title: PBMCs_Unsti_AS2311_AS1830

description: 10x Genomics

value: Unsti for 16h


title: Blastocyst rep1_add

value: wild type


title: PBMCs_LPS_AS2311_AS1830

description: 10x Genomics

value: LPS for 16h


title: SN SREBP1, Input

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
FastQ files were generated by bcl2fastq v2.20.0.422.
FastQ files were mapped to reference genome rn5 using Bowtie2
BAM files were filtered for mapped reads using BamTools (Quinlan and Hall, 2010; Barnett et al., 2011) and sorted into called peaks using MACS2 (Zhang et al., 2008; Feng et al., 2012; Liu, 2014).
BedTools bamCoverage generated bedgraphs of ChIP-seq samples. Data processing was performed in a cloud-based manner through GalaxyBiostars (Afgan, 2018).
Assembly: Rn5

source_name: sciatic nerve

growth_protocol: S16 Schwann cellswere cultured in 10 cm plates and supplemented with Corning DMEM containing 4.5 g/L glucose and L-glutamine without sodium pyruvate (#10-017-CV).

extract_protocol:
Plates were washed with PBS containing protease inhibitor cocktail, then washed with nuclear extraction buffer (20mM HEPES pH 7.9, 10mM KCl, 1.5mM MgCl2, 0.5mM Spermidine, 10% Glycerol, 0.3% Triton X-100) to isolate nuclei. Cell nuclei were bound to Concanavalin A beads using the Cut&Run assay kit (Cell Signaling Technology #86652). Nuclei were permeabilized with digitonin, then incubated with protein AG-micrococcal nuclease (PAG MNase). The following antibodies were used for the IP: Nr2f2 (Perseus Proteomics PP-H7147-00), RxRG (Developmental Studies Hybridoma Bank PRCP-RXRG-5H4), and TEAD1 (BD Biosciences 610923). Other antibodies used were: YY1 Active Motif (AM-61980), and H3K27ac  Active Motif (AM-39133), and a SREBP1 antibody provided Tim Osborne PMID: 19666523.  After removal of Concanavalin-bound nuclei, DNA was purified from the remaining solution using the Cell Signaling DNA purification kit (Cat# 14209S). Cut&Run samples were processed using the Illumina NovaSeq6000 system and NEBNext Cut&Run library prep. ChIP-seq was performed as described in Srinivasan et al. PMID: 22492709.
NEBNext Cut&Run library prep.

value: sciatic nerve

value: Schwann

value: postnatal day 15

tag: antibody


title: Blastocyst rep1


title: Blastocyst rep2


title: SN SREBP1, IP

value: SREBP1 antibody provided Tim Osborne PMID:19666523


title: PBMCs_TAB_AS1802

description: 10x Genomics


title: Morula rep2_add

value: Morula


title: 293T_met30

description: The 30% methanol-fixed cells were mixed with 1ul 10mM dNTP and 1ul 100M oligo-dT30VN and incubated at 55C for 5min, then placed on ice immediately for 2min to facilitate RNA denaturation. Next, reverse transcription was performed by adding 6ul RT mix. Full-length transcriptome amplification and quality control. After reverse transcription, cells were further lysed by adding 5ul Proteinase K and incubating at 56C for 60 min and 95C 10 min. Then, the PCR reaction was performed after added 25ul PCR buffer. PCR product was purified by DNA Clean & ConcentratorTM-5 kit.

value: Cell line

value: WT

value: Fixed by 30% methanol


title: S16 TEAD1 CR

data_processing:
FastQ files were generated by bcl2fastq v2.20.0.422.
FastQ files were mapped to reference genome rn5 using Bowtie2
BAM files were filtered for mapped reads using BamTools (Quinlan and Hall, 2010; Barnett et al., 2011) and sorted into called peaks using MACS2 (Zhang et al., 2008; Feng et al., 2012; Liu, 2014).
BedTools bamCoverage generated bedgraphs of ChIP-seq samples. Data processing was performed in a cloud-based manner through GalaxyBiostars (Afgan, 2018).
Assembly: Rn5
Library strategy: CUT&RUN

value: TEAD1 (BD Biosciences 610923)


title: Morula rep1_add


title: PBMCs_LPS_AS1802

description: 10x Genomics


title: PBMCs_Unsti_AS1802

description: 10x Genomics


title: S16 RXRG CR

value: RxRG (Developmental Studies Hybridoma Bank PRCP-RXRG-5H4)


title: Morula rep2


title: PBMCs,  septic shock secondary to AC, scRNAseq, B3

city: Hefei

first: He

middle: Ms.

last: Zhang

address: Jixi Road 218

institute: Anhui medical university

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCh38
Supplementary files format and content: tar archives of barcodes , genes, matrix files

source_name: peripheral blood mononuclear cells

extract_protocol:
The PBMCs were immediately separated from the samples by a density gradient cen-trifugation making use of Ficoll-Paque Plus medium (GE healthcare). To remove erythrocytes, 2 ml GEXSCOPE ® red blood cell lysis buﬀer (Singleron) was added to the solution for 10 min at 25°C. The liquid solution was then centrifuged at 500g for 5 min, and the solution was suspended in phosphate buffered saline. Blood specimens were isolated by centrifuge at 400 g at 4°C for 5 min, and the supernatant was dis-carded. The PBMCs were centrifuged at 400 g at 4°C for 10 min, and the supernatant was discarded. To obtain a single-cell suspension, PBMCs were resuspended using phosphate buffered saline. Finally, the trypan blue staining method was used to stain the samples and evaluate cell viability under a microscope.
We used GEXSCOPETM Single Cell RNA Library Kit  to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a Nova-seq 6000 platform with 150 bp paired-end reads.

value: peripheral blood mononuclear cells

tag: disease state

value: septic shock secondary to acute cholangitis


title: Liver - Male_CD_CAS - Rep6

city: Toulouse

first: Laurence

last: Gamet-Payrastre

address: 180 chemin de Tournefeuille

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 52 out of 64 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 38363  spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 35356 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Following euthanasia by cervical dislocation, liver was collected, weighted and snap-frozen in liquid nitrogen and stored at −80°C.  Total RNA was extracted using TRI Reagent® (Molecular Research Center, Cincinnati, Ohio, USA). RNAs were quantified using Nanodrop

tag: Sex

value: Male

tag: diet

value: CD

tag: source

value: CAS

tag: washbatch


title: Liver - Female_WD_AA - Rep7

value: Female

value: WD

value: AA


title: Liver - Male_WD_AA - Rep7


title: PBMCs,  septic shock secondary to AC, scRNAseq, B2


title: S16 H3K27ac

value: Schwann

tag: treatment

value: H3K27ac  Active Motif (AM-39133)


title: Liver - Male_WD_CAS - Rep8


title: 8-cell rep2_add

city: Shanghai

tag: strain

value: wild type


title: Liver - Female_CD_CAS - Rep8


title: PBMCs,  septic shock secondary to AC, scRNAseq, B1


title: S16 NR2F2 CR

value: Nr2f2 (Perseus Proteomics PP-H7147-00)


title: 8-cell rep1_add


title: Liver - Female_WD_CAS - Rep8


title: 8-cell rep2


title: Liver - Female_CD_AA - Rep8


title: PBMCs,  AC, scRNAseq, A2

value: acute cholangitis


title: 915 72hr biol rep 3

first: Weiyi

address: One Baylor Plaza, 441E

department: Department of Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Reads were aligned with STAR version 2.5.1a
Gene counts were derived using Subread:featureCount version 1.4.6-p5
Assembly: Rat Ensembl Rnor_6.0.101
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes CPM values for each sample

source_name: NRVM

extract_protocol:
Total RNA was extracted using Qiagen miRNeasy kit according to the manufacturer's instructions.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000

treatment_protocol:
NRVM were isolated from rat pups (P3) as described in PMID:28878135. Following overnight incubation in 0.05% trypsin EDTA at 4°C, cardiomyocytes were dissociated with type 2 collagenase (Worthington, LS004176) in HBSS and neutralized with 10% FBS in DMEM. The cell suspension was further incubated in a tissue culture-treated plastic dish for 90 min to allow fibroblast attachment. Typically, NRVMs were seeded at 50-70% confluence in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin and 100μM bromodeoxyuridine. 2 days after seeding, the medium was changed to DMEM supplemented with insulin/transferrin/selenium (Sigma-Aldrich, I3146) and cultures were used within 5 days.
For treatment with 915 or vehicle, cells were treated with 10uM 915 or equivalent volume of vehicle (DMSO) for 72h.

value: NRVM

value: cardiomyocyte

value: WT


title: 915 72hr biol rep 2


title: PBMCs,  AC, scRNAseq, A3


title: Liver - Male_CD_AA - Rep8


title: 8-cell rep1


title: S16 YY1 CR

value: YY1 Active Motif (AM-61980)


title: Morula rep1

value: Morula


title: B2S10.m6A (Islets, T1D)

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads were trimmed for adapters and polyX tails, and filtered by sequencing Phred quality (>= Q15) using fastp.
Adapter-trimmed reads to the human genome using STAR aligner with the two-pass option.
Alignments were assigned to genomic features by using featureCounts. Multi-mapping reads were counted as fractions.
Assembly: hg38
Supplementary files format and content: CSV file includes gene counts for each Sample

source_name: Islets

extract_protocol:
High-quality total RNA (>200nt) was extracted using standard Trizol reagent (Invitrogen) according to manufacturer instructions and the resultant aqueous phase was mixed (1:1) with 70% RNA-free ethanol and added to Qiagen Rneasy mini kit columns (Qiagen) and the kit protocol was followed with DNA digestion on column step performed.
RNA libraries for RNA-seq were prepared Takara Pico-Input Strand-Specific Total RNA-seq for Illumina v2 Kit following manufacturer's protocols.

tag: tissue

value: Islets

tag: disease

tag: gender

value: M

tag: age

tag: clone

tag: bmi

tag: batch


title: 915 72hr biol rep 1

tag: cell line

tag: cell type

tag: genotype


title: Liver - Male_WD_AA - Rep5

value: Male


title: 4-cell rep2_add

tag: developmental stage


title: 4-cell rep1_add


title: DMSO 72hr biol rep 3

value: DMSO


title: B2S9.m6A (Islets, T1D)


title: Liver - Female_CD_CAS - Rep3

tag: Sex

value: Female

value: CD

value: CAS


title: Liver - Male_WD_CAS - Rep3

tag: diet

value: WD


title: DMSO 72hr biol rep 2


title: 4-cell rep2


title: Liver - Female_WD_AA - Rep4

tag: source

value: AA


title: Liver - Female_CD_AA - Rep6

tag: washbatch


title: Liver - Female_WD_CAS - Rep1


title: Liver - Male_CD_AA - Rep5


title: B2S6.m6A (Islets, T1D)

tag: treatment


title: Liver - Male_CD_CAS - Rep8


title: B2S8.m6A (Islets, T1D)


title: B2S7.m6A (Islets, T1D)

value: F


title: 4-cell rep1

tag: strain

value: wild type


title: DMSO 72hr biol rep 1


title: LPS-HuRi 4

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

data_processing:
All read mapping and analysis was performed using the CLC Genomics Workbench v20.0.2 (CLC Bio-Qiagen).
Reads were mapped using the following parameters:  min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Expression value= Transcripts per million (TPM).
Assembly: Rnor_6.0
Supplementary files format and content: Processed data file is an excel sheet containing expression value in Transcripts per million (TPM) for each gene

source_name: Neonatal rat ventricular myocytes (NRVMs)

growth_protocol: NRVMs were isolated using collagenase digestion and adhesion differential from fibroblasts. Sprague Dawley neonatal rats (1-3 days old, Charles River) were decapitated, and the hearts were isolated. Following removal of the atria, the ventricles were cut into small pieces and digested first in 0.05% trypsin/EDTA (Corning) overnight. The next day trypsin was aspirated, and hearts were placed in collagenase II (Gibco) for 15 minutes in a 37°C water bath followed by 15 minutes of incubation at 37°C, 5% CO2. Cells were manually dissociated by trituration and the supernatant passed through a 40um strainer.  Cells were then spun at 100 × g followed by a 40-minute pre-plating process on non-treated plates to allow for fibroblasts adherence. The non-adherent NRVMs were then transferred to gelatin (0.1%) coated culture-treated dishes in MEM alpha media (Gibco) with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
RNA was isolated using the Macherey-Nagel NucleoSpin RNA kit. RNA quantity and quality was assessed by optical density at 260 nm and optical density ratios of 260/280 nm and 260/230 nm ratios, respectively. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NRVMs were treated with lipopolysaccharide (LPS) at a concentration of 1 ug/ml and inhibition of HuR was achieved via 10 uM KH3.

value: Sprague-Dawley

value: 1 ug/ml LPS + 10 uM KH-3


title: L2-cell rep1


title: LPS-HuRi 3

value: Neonatal rat ventricular myocytes (NRVMs)


title: B2S5.m6A (Islets, CTRL patients)

tag: tissue

value: CTRL


title: LPS 4

value: 1 ug/ml LPS


title: LPS-HuRi 2


title: PBMCs,  AC, scRNAseq, A1

value: peripheral blood mononuclear cells

tag: disease state

value: acute cholangitis


title: LPS 3


title: B2S4.m6A (Islets, CTRL patients)

value: Islets

tag: disease

tag: gender

value: M


title: E2-cell rep1


title: Liver - Male_WD_AA - Rep4

value: Male


title: B2S3.m6A (Islets, CTRL patients)

tag: age

tag: clone


title: Zygote rep2

value: Zygote


title: L2-cell rep2


title: Liver - Male_CD_AA - Rep6

value: CD


title: B2S2.m6A (Islets, CTRL patients)

tag: bmi

tag: batch


title: E2-cell rep2


title: Zygote rep1


title: MII rep2

value: MII


title: B2S1.m6A (Islets, CTRL patients)

tag: cell line

tag: cell type


title: LPS 2


title: Vehicle 4

value: Vehicle Control


title: After-fertilize-17h rep2

tag: developmental stage

tag: genotype


title: Liver - Male_WD_CAS - Rep2

tag: Sex

tag: diet

value: WD

value: CAS


title: Liver - Male_CD_CAS - Rep2

tag: source

tag: washbatch


title: Liver - Female_WD_AA - Rep5

value: Female

value: AA


title: Vehicle 3

tag: strain

value: Sprague-Dawley

tag: treatment


title: B2S9.input (Islets, T1D)

tag: tissue


title: MII rep1

value: wild type


title: Liver - Female_WD_CAS - Rep5


title: Vehicle 2

value: Neonatal rat ventricular myocytes (NRVMs)


title: Liver - Female_CD_AA - Rep4


title: FR_3

city: Chongqing

first: Cong

last: Yu

address: No. 426 Songshi North Road, Yubei District

department: Anesthesiology

institute: The stomatology hospital affiliated chongqing medical university

description: Treatment

data_processing: FPKM data

source_name: RVM

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: RVM

value: CFA


title: B2S8.input (Islets, T1D)

tag: disease


title: DKO-B-4

first: Bo

last: Meng

address: 3663 Zhongshan Rd(N.)

institute: East China Normal Univeristy

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCm38.p6 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.

value: brain

value: PS1/PS2 DKO

value: water


title: Liver - Female_CD_CAS - Rep1


title: FR_2

description: Treatment


title: DKO-B-2


title: B2S10.input (Islets, T1D)

value: Islets

tag: gender

value: M


title: Liver - Female_CD_CAS - Rep5

value: CD


title: B2S6.input (Islets, T1D)

tag: age


title: B2S5.input (Islets, CTRL patients)

value: CTRL

tag: clone


title: FR_1

description: Treatment


title: DKO-B-1


title: Liver - Female_CD_AA - Rep2


title: CR_3

description: Control


title: CR_2

description: Control


title: DKO-N-2

value: nicotine


title: DKO-B-3


title: B2S3.input (Islets, CTRL patients)

tag: bmi


title: CR_1

description: Control


title: B2S7.input (Islets, T1D)

value: F

tag: batch


title: Liver - Female_WD_CAS - Rep2

value: WD

value: CAS


title: B2S2.input (Islets, CTRL patients)

tag: cell line


title: FQ_3

description: Treatment

source_name: thalamus

value: thalamus


title: WT-B-4

value: wildtype C57BL6/J


title: Liver - Female_WD_AA - Rep6

value: Female

value: AA


title: B2S1.input (Islets, CTRL patients)

tag: cell type


title: Liver - Male_CD_AA - Rep4

value: Male


title: FQ_2

description: Treatment

value: CFA


title: Liver - Male_CD_CAS - Rep1


title: WT-B-3

value: brain


title: DKO-N-3

value: PS1/PS2 DKO


title: B2S4.input (Islets, CTRL patients)


title: B1T1D_patient3.m6A (Islets, T1D)


title: B1T1D_patient3.input (Islets, T1D)


title: FQ_1

description: Treatment


title: Liver - Male_WD_CAS - Rep1


title: CQ_3

description: Control


title: DKO-N-1


title: WT-B-1

value: water


title: B1T1D_patient1.m6A (Islets, T1D)

value: Islets


title: Liver - Male_WD_AA - Rep1


title: CQ_2

description: Control


title: WT-N-4


title: CQ_1

description: Control


title: Liver - Male_WD_CAS - Rep5


title: WT-N-3


title: B1S9A.m6A (Islets, cytokine-treated)

value: cytokine-treated

value: M


title: Liver - Male_CD_AA - Rep2

value: CD


title: SD, liver, EW_Leu3

city: Harbin

first: Yuchen

last: Sun

state: Heilongjiang

address: Changjiang Street No. 600

institute: Northeast Agricultural University

description:
genes_fpkm_expression 2
Early weaning with leucine supplement d211

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

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Agilent Bioanalyzer 2100
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: SD

value: Liver


title: WT-N-2

value: nicotine


title: SD, liver, EW_Leu2

value: Early weaning with leucine supplement d211


title: WT-B-2


title: Liver - Male_CD_CAS - Rep3

value: CAS


title: WT-N-1

value: wildtype C57BL6/J


title: B1S9.m6A (Islets, CTRL)

value: CTRL


title: SD, liver, EW_Leu1


title: WT_Vehicle MZnLib_227

city: South San Francisco

first: Russell

last: Bainer

state: CA

address: 171 Oyster Point Blvd

department: Data Sciences

institute: Maze Therapeutics

data_processing:
After demultiplexing, indvidual fastq files were aligned via kallisto with the command:
Pseudoaligning reads were summarized across all transcripts annotated to each gene. Lowly expressed genes were removed, and then size factors were calculated for the resulting count matrix via edgeR and data were normalized by limma/voom with scaling normalization.
Assembly: GRCh38.96-cdna
Supplementary files format and content: tab-delimited text files include raw counts or normalized log2 CPM for each Sample

source_name: WT

extract_protocol:
RNA was harvested using Rneasy mini plus kit by Seqmatic following the manufacturer's instructions
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA prep Library Prep Kit by Seqmatic following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
mice were provided with chow formulated with vehicle (veh.), MZ-101 (SRT), or alglucosidase alfa 20mg/kg biweekly (ERT) for 12 weeks

tag: sample

tag: group

value: WT

value: Vehicle

tag: treatment type

tag: dob

tag: animal number

tag: seqmatic sample_id

tag: rin

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: B1T1D_patient1.input (Islets, T1D)

tag: tissue

tag: treatment

tag: disease

tag: gender

tag: age


title: B1S9.input (Islets, CTRL)

tag: cell line

tag: cell type

tag: clone

tag: bmi

tag: batch


title: SD, liver, Ew3

description:
genes_fpkm_expression 2
Early weaning d211

tag: strain

value: Early weaning d211


title: WT_Vehicle MZnLib_226

tag: sample

tag: group

tag: treatment type

tag: dob

tag: animal number

tag: seqmatic sample_id


title: Liver - Female_CD_CAS - Rep6

tag: Sex

value: Female

tag: diet

tag: source

tag: washbatch


title: WT_Vehicle MZnLib_225

tag: treatment

tag: rin

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: SD, liver, Ew2

tag: strain

tag: tissue


title: B1S8A.m6A (Islets, cytokine-treated)

tag: cell line

tag: cell type

tag: disease

tag: gender

tag: age

tag: clone

tag: bmi

tag: batch


title: B1S9A.input (Islets, cytokine-treated)


title: WT_Vehicle MZnLib_224

tag: sample

tag: group

tag: treatment type

tag: dob

tag: animal number

tag: seqmatic sample_id


title: Liver - Female_WD_AA - Rep8

tag: Sex

tag: diet

value: WD

tag: source

value: AA

tag: washbatch


title: B1S8.m6A (Islets, CTRL)

tag: tissue

value: Islets

tag: cell line

tag: cell type

tag: treatment


title: Liver - Female_CD_AA - Rep3


title: WT_Vehicle MZnLib_223

tag: strain

tag: rin

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: Liver - Female_WD_CAS - Rep7


title: B1S8.input (Islets, CTRL)

tag: disease

tag: gender

tag: age

tag: clone

tag: bmi

tag: batch


title: Liver - Female_WD_CAS - Rep4

tag: Sex

tag: diet

tag: source

tag: washbatch


title: SD, liver, Con2

description:
genes_fpkm_expression 2
Control d211

tag: tissue

tag: treatment

value: Control d211


title: Pompe_Combo MZnLib_222

source_name: Pompe

tag: sample

tag: group

tag: strain

value: Pompe

value: Combo

tag: treatment type

value: ERT + SRT

tag: dob

tag: animal number

tag: seqmatic sample_id

tag: rin


title: Liver - Female_CD_CAS - Rep4

value: CD


title: B1S7A.m6A (Islets, cytokine-treated)

tag: cell line

tag: cell type

value: cytokine-treated

tag: disease

tag: gender

value: M

tag: age

tag: clone


title: Liver - Female_CD_AA - Rep5

tag: Sex

tag: diet

tag: source

tag: washbatch


title: SD, liver, Con1

description:
genes_fpkm_expression 2
Control d211

value: SD

tag: tissue

value: Liver

tag: treatment


title: Liver - Male_WD_AA - Rep3

value: Male


title: Liver - Male_WD_CAS - Rep7

value: CAS


title: B1S7A.input (Islets, cytokine-treated)

value: CTRL

tag: bmi

tag: batch


title: B1S8A.input (Islets, cytokine-treated)


title: Pompe_Combo MZnLib_221

tag: sample

tag: group

tag: strain

tag: treatment type

tag: dob

tag: animal number

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: Liver - Female_WD_AA - Rep1

tag: Sex

tag: diet


title: B1S7.m6A (Islets, CTRL)

tag: cell line

tag: cell type

tag: disease

tag: gender

tag: age

tag: clone


title: Wistar, liver, EH2

description:
genes_fpkm_expression 1
Early weaning d63

value: Wistar

tag: tissue

tag: treatment

value: Early weaning d63


title: Wistar, liver, EH3

tag: strain


title: Pompe_Combo MZnLib_220

tag: sample

tag: group

tag: treatment type

tag: dob

tag: seqmatic sample_id

tag: rin


title: SD, liver, Ew1

value: Early weaning d211


title: SD, liver, Con3

description:
genes_fpkm_expression 2
Control d211


title: Pompe_Combo MZnLib_219

tag: animal number

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: Wistar, liver, EH1


title: Pompe_Combo MZnLib_218


title: B1S7.input (Islets, CTRL)

tag: cell line

tag: cell type

tag: disease

tag: gender

tag: bmi

tag: batch


title: B1S6A.m6A (Islets, cytokine-treated)

tag: tissue

tag: treatment

value: F

tag: age

tag: clone


title: Pompe_MZ1447581 MZnLib_217

tag: sample

tag: group

tag: strain

tag: treatment type

value: SRT

tag: dob

tag: seqmatic sample_id


title: Liver - Female_CD_CAS - Rep7

tag: Sex

value: Female

tag: diet

tag: source

tag: washbatch


title: B1S6A.input (Islets, cytokine-treated)

value: Islets

tag: cell line

tag: cell type

tag: disease

tag: gender


title: Liver - Male_CD_CAS - Rep5


title: Pompe_MZ1447581 MZnLib_216

value: Pompe

tag: treatment

tag: animal number

tag: rin

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: Pompe_MZ1447581 MZnLib_215

tag: sample

tag: group

tag: strain

tag: treatment type

tag: dob


title: Liver - Male_CD_AA - Rep1

tag: Sex

tag: diet

tag: source

value: AA

tag: washbatch


title: B1S6.input (Islets, CTRL)

tag: tissue

tag: cell line

tag: cell type

tag: disease

tag: gender

tag: age

tag: clone

tag: bmi

tag: batch


title: Wistar, liver, EW3

description:
genes_fpkm_expression 1
Early weaning d23

tag: treatment

value: Early weaning d23


title: B1S6.m6A (Islets, CTRL)


title: Wistar, liver, CH3

description:
genes_fpkm_expression 1
Control d63

tag: strain

value: Control d63


title: B1S5A.m6A (Islets, cytokine-treated)

value: cytokine-treated

value: M


title: Pompe_MZ1447581 MZnLib_213

tag: sample

tag: group

tag: treatment type

tag: animal number

tag: seqmatic sample_id

tag: rin

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: Liver - Male_WD_CAS - Rep6

tag: Sex

tag: diet

value: WD

tag: source

tag: washbatch


title: Wistar, liver, EW2

tag: tissue

value: Liver


title: Wistar, liver, EW1

tag: treatment


title: Liver - Male_CD_AA - Rep7

value: Male

value: CD


title: Pompe_Lumizyme MZnLib_212

tag: strain

value: Lumizyme

value: ERT

tag: dob


title: B1S5.m6A (Islets, CTRL)

tag: cell line

tag: cell type

value: CTRL

tag: disease

tag: gender

tag: age

tag: clone

tag: bmi

tag: batch


title: Liver - Male_CD_CAS - Rep7

value: CAS


title: Liver - Male_WD_AA - Rep8


title: Wistar, liver, CH2

description:
genes_fpkm_expression 1
Control d63

value: Wistar


title: Pompe_Lumizyme MZnLib_211

tag: sample

tag: group

tag: treatment type

tag: animal number

tag: seqmatic sample_id

tag: rin

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: Wistar, liver, CH1

description:
genes_fpkm_expression 1
Control d63

tag: strain

tag: tissue

tag: treatment


title: Liver - Female_CD_AA - Rep7

tag: Sex

value: Female

tag: diet

tag: source

tag: washbatch


title: Wistar, liver, CON2

description:
genes_fpkm_expression 1
Control d23

value: Control d23


title: Pompe_MZ1447581 MZnLib_214

tag: sample

value: Pompe

value: SRT

tag: dob


title: Wistar, liver, CON3

description:
genes_fpkm_expression 1
Control d23


title: B1S5A.input (Islets, cytokine-treated)

value: Islets

tag: cell line

tag: cell type

tag: disease

tag: gender

tag: age

tag: clone

tag: bmi

tag: batch


title: B1S4A.m6A (Islets, cytokine-treated)


title: Wistar, liver, CON1

description:
genes_fpkm_expression 1
Control d23

tag: strain


title: B1S4A.input (Islets, cytokine-treated)

tag: tissue


title: Liver - Female_WD_AA - Rep2

value: AA


title: Liver - Female_WD_CAS - Rep6


title: Pompe_Lumizyme MZnLib_209

tag: group

tag: treatment

tag: treatment type

tag: animal number

tag: seqmatic sample_id

tag: rin

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: Patch rep4

city: hangzhou

first: sibo

last: jiang

address: zhejiang

institute: zju

data_processing:
The files were first converted to fastq format using fastq-dump command. Then, belowFastp was used to generate clean data by removing low-quality reads, poly-N reads, and adapter sequences. Then, the clean data of rat were aligned to their respective reference genomes (rat genome version 6.0.104) using Hisat2 tool.
The samtools was employed to transform the aligned data to sorted bam files, which were counted by featureCounts function from Rsubread package.
DESeq2 was utilized to normalize these data.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
RNA was harvested using TRIZOL method. 1 ug of total RNA was used for the construction of sequencing libraries.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: heart

value: Sprague Dawley

tag: genotype

value: WT

value: the patches were sutured on 1 and 3 or 4 points on the edge of the infarcts with 6-0 silk threads.


title: Pompe_Lumizyme MZnLib_208

tag: sample

tag: dob


title: Patch rep3


title: Pompe_Vehicle MZnLib_207

value: Vehicle


title: B1S4.m6A (Islets, CTRL)

tag: cell line

tag: cell type

tag: disease

tag: gender

value: M

tag: age

tag: clone

tag: bmi


title: B1S5.input (Islets, CTRL)

tag: tissue

tag: treatment

tag: batch


title: Liver - Female_WD_CAS - Rep3

tag: Sex

tag: diet

value: WD

tag: source

tag: washbatch


title: B1S4.input (Islets, CTRL)


title: Patch rep2

tag: strain

tag: genotype


title: Liver - Female_WD_AA - Rep3


title: Pompe_Vehicle MZnLib_206

tag: sample

tag: group

tag: treatment type

tag: dob

tag: animal number

tag: seqmatic sample_id

tag: rin

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: B1S3A.m6A (Islets, cytokine-treated)

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: cytokine-treated

tag: disease

tag: gender

tag: age

tag: clone

tag: bmi

tag: batch


title: Patch rep1

tag: strain

tag: genotype


title: Pompe_Lumizyme MZnLib_210

tag: sample

tag: group

value: Lumizyme

tag: treatment type

value: ERT

tag: dob

tag: animal number

tag: seqmatic sample_id

tag: rin


title: B1S3A.input (Islets, cytokine-treated)

tag: tissue

tag: cell line

tag: cell type

value: CTRL


title: Liver - Female_CD_CAS - Rep2

tag: Sex

value: Female

tag: diet

value: CD

tag: source

value: CAS

tag: washbatch


title: B1S3.m6A (Islets, CTRL)

tag: treatment

tag: disease

tag: gender

tag: age

tag: clone

tag: bmi

tag: batch


title: Pompe_Vehicle MZnLib_204

tag: sample

tag: group

tag: strain

value: Pompe

tag: treatment type

tag: dob

tag: animal number

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: MI rep3

tag: tissue

tag: genotype

tag: treatment

value: MI operation


title: Pompe_Vehicle MZnLib_203

tag: seqmatic sample_id

tag: rin


title: B1S3.input (Islets, CTRL)

value: Islets

tag: cell line

tag: cell type

tag: disease

tag: gender

tag: age

tag: clone

tag: bmi


title: Liver - Male_WD_CAS - Rep4

tag: Sex

value: Male

tag: diet

tag: source

tag: washbatch


title: Liver - Female_CD_AA - Rep1

value: AA


title: MI rep1

value: heart

tag: strain

value: Sprague Dawley

value: WT


title: ESCs-derived differentiated cells, MF rep3

city: Nanjing

first: ZHAOYUAN

last: GUO

address: XuanWuqu

institute: Nanjing Agricultural University

data_processing:
The clean reads were mapped to the Mus musculus mm10 reference genome, which was performed using HISAT2 v2.0.5
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using featureCounts.
Fragments Per Kilobase per Million is calculated to represent the gene expression level
Functional enrichment (GO annotation, KEGG) of gene sets with different expression patterns was performed using clusterProfiler.
Assembly: mm10
Supplementary files format and content: tab-delimited files include FPKM and count values

source_name: mouse ESCs-derived differentiated cells

growth_protocol: For normal culture condition, ESCs were cultured under 5% CO2 at 37 °C in ES cell culture medium consisting of knockout DMEM supplemented with 20% fetal bovine serum (FBS, ES quality, Hyclone), 1,000 U/ml leukemia inhibitory factor (LIF)(ESGRO, Chemicon), 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 2 mM L-glutamine, and penicillin (100 U/ml) and streptomycin (100 µg/ml). For static magnetic field condition, cells were stimulated by static magnetic fields. ESCs were induced to differentiate into cardiomyocytes using the hanging drop method. Cells were digested and diluted to a certain concentration, dropped on a culture dish and cultured in inverted suspension, and EB was formed after 3 days.

extract_protocol:
Total RNA was extracted using the trizol method ,according to the manufacturer's instructions.
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Then the selected RNA was fragmented and copied into first strand cDNA, which was followed by second strand cDNA synthesis. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR amplification. PCR yield was quantified and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: ESCs-derived differentiated cells were washed by PBS and trypsinized to single cells, and then were committed to RNA extraction.

value: J1 ESCs-derived differentiated cells

tag: culture condition

value: static magnetic field incubator


title: B1S2A.m6A (Islets, cytokine-treated)

tag: tissue

value: cytokine-treated

value: M

tag: batch


title: MI rep4

tag: genotype

tag: treatment


title: Liver - Male_CD_AA - Rep3


title: B1S2A.input (Islets, cytokine-treated)

tag: cell line


title: ESCs-derived differentiated cells, MF rep2

tag: cell type


title: Pompe_Vehicle MZnLib_205

tag: sample

tag: group

value: Vehicle

tag: treatment type

tag: dob

tag: animal number

tag: seqmatic sample_id

tag: rin

tag: concentration ng_ul

tag: r

tag: mapped pct

tag: lib size


title: Liver - Male_WD_AA - Rep2

tag: Sex

tag: diet

value: WD

tag: source

tag: washbatch


title: Liver - Male_CD_CAS - Rep4


title: MI rep2

tag: tissue

tag: strain

tag: genotype

tag: treatment


title: ESCs-derived differentiated cells, MF rep1

tag: cell line

tag: cell type

tag: culture condition


title: B1S21A.m6A (EndoC_bH1, cytokine-treated)

source_name: EndoC_bH1 cells

value: beta cells

tag: disease

tag: gender

value: F

tag: age

tag: clone

tag: bmi

tag: batch


title: sham rep3

value: sham operation


title: sham rep4


title: ESCs-derived differentiated cells, NC rep3

value: conventional incubator


title: B1S21A.input (EndoC_bH1, cytokine-treated)


title: ESCs-derived differentiated cells, NC rep2


title: B1S21.m6A (EndoC_bH1, CTRL)

value: CTRL


title: sham rep1


title: PEL 1d 3

first: Mingfeng

state: Guangdong Province

address: No.1838 Guangzhou Avenue North

department: Department of Neurosurgery

institute: Nanfang Hospital, Southern Medical University

description: 1 days after PEL surgery

data_processing:
Illumina Casava1.7 software used for basecalling.
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq2 R package (1.16.1)
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias  was corrected.
Genome_build: ensemble97
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hypothalamic median eminence (ME)

extract_protocol:
Hypothalamic ME tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina Hiseq Platform was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain

value: S-D

value: Hypothalamic median eminence (ME)

value: PEL


title: Replicate 2 of G4P ChIP-seq in HCT116, ChIP enriched reads

city: Changsha

first: Ke-wei

last: Zheng

address: Lushan Road (S), Yuelu District

department: School of Medical Sciences

institute: Hunan University

data_processing:
We used fastp to preprocess our raw paired-end G4P ChIP-seq reads, which are allegedly trimmed. Fastp automatically filtered out low quality reads and detected adapter by complementing the paired sequences, which reported that all adapters were successfully trimmed beforehand (Command: --detect_adapter_for_pe). We also allowed it to correct low quality mismatch in the complement region of paired reads. (Command: --correction)
We utilized Bowtie 2 to align all G4P ChIP-seq reads to the primary assembly GRCh38 genome sequence downloaded from GENCODE, whose FM index was built by Bowtie 2 itself (Command: bowtie2-build). We used default parameters in the alignment process. The output “.sam” files were later converted to “.bam” format with SAMtools (Command: sort). These binary files were subsequently sent to BamTools for filtering out whose mapping quality was lower than 20 (Command: filter -mapQuality ">=20") and indexed with SAMtools (Command: index).
We entrusted deepTools to generate “.bigwig” files from “.bam” files. For G4P ChIP-seq data, we ignored all duplicative reads, and normalized the reads per genomic content (RPGC) to 1. We also extended these paired-end reads to match the fragment size. (Command: bamCoverage –ignoreDuplicates --normalizeUsing RPGC --extendReads)
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: colon cancer tissue

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1 × penicillin-streptomycin

extract_protocol:
Approximately 0.5–1 × 108 transiently or stably transfected cells expressing G4P were crosslinked with 1% formaldehyde for 20 min at room temperature. Fixation was quenched by 0.125 M glycine for 15 min. The fixed cells were washed twice with PBS, suspended in NP-40 buffer (10mM Tris–HCl pH 7.4, 150 mM NaCl, 0.5% NP-40 and 2 mM AEBSF) and incubated on ice for 10 min. After centrifugation at 800×g for 5 min, the cell pellet was resuspended in a CHAPS buffer (20mM Tris-HCl pH 7.4, 0.5mMEGTA, 50 mM NaCl, 0.5% CHAPS, 10% glycerol and 2mM AEBSF). The suspension was incubated on ice for 30 min and centrifuged at 800×g for 5 min. The pellet was resuspended in 1 mL 1× dsDNase digestion buffer supplied with 50 μL dsDNase (Invitrogen, EN0771) and incubated at 37 ℃ for 20 min with constant agitation. A final concentration of 20 mM EDTA was added to terminate the reaction. The samples were pelleted by centrifugation at 15 000×g at 4 ℃ and the resulting supernatant was collected and incubated on ice. The pellet was resuspended in 500 μL wash buffer (150 mM NaCl, 10 mM Tris–HCl, pH 7.4, 0.1 mM EDTA, 0.5% Triton X-100) and sonicated for 30–60 s in an ice-cold water bath. After centrifugation at 15 000×g for 5 min, the supernatant of chromatin fragment was collected and combined with the supernatant from the previous step.
For library preparation, 50 μL of anti-FLAG M2 magnetic beads (Sigma-Aldrich) were washed with washing buffer (10 mM Tris–HCl, pH 8.0, 150 mM NaCl and 0.5% Triton X-100) and blocked in the same buffer containing 75 μg/mL single-stranded sperm DNA and 1 mg/mL BSA. 1% chromatin fragment was saved as input and the remaining was incubated with blocked anti-FLAGmagnetic beads in rotation at 4 ℃ for 3 h. The beads were sequentially washed ten times with washing buffer and transferred to new tubes three times. The chromatin was eluted with 300 g/mL 3xFLAG peptide (Sigma-Aldrich) at 4 ℃ for 1 h. The eluted chromatin and the input sampleswere incubated with proteinase K at 65 ℃ overnight. After sequential RNase A and proteinase K digestion, DNA fragment was cleaned by extraction with phenol:chloroform:isoamyl alcohol, followed by ethanol precipitation. Libraries were constructed from the recovered DNA fragment using the NEBNext Ultra II DNA LibraryPrep Kit from Illumina (NEB) according to the manufacturer’s instructions. The next-generation sequencing was performed with Illumina HiSeq X Ten by Genewiz (Suzhou, China).

value: colon cancer tissue

value: untreated

tag: group

value: experiment group

tag: target

value: G-quadruplex (G4P)

tag: methodology

value: ChIP-seq

tag: replicate


title: BC132

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
Data-no_QC-counts.tsv
Data-counts.tsv
Data-normed.tsv

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were alligned using Kallisto, and transcript level tpm values were summed up to gene level tpm values
Genome_build: GRCm38 version 95
Supplementary_files_format_and_content: tpm.tsv contains the transcript per million levels of each gene within each cell, in a tab deliminated matrix. Counts.tsv contains the kallisto, aligned pseudocounts of each gene within each cell, in a tab. deliminated matrix. no-QC-counts.tsv contains the same information as counts.tsv, but including cells that failed quality control

source_name: MGE derived interneuron within the dorsal CA1 pyramidal cell layer

growth_protocol: Pups were housed under standard conditions with parents until post-natal day 4.

extract_protocol:
Cell contents including mRNA were aspirated within a patch pipette from acute slices.
Nextera XT

treatment_protocol: No treatment.

value: MGE derived interneuron

tag: condition

value: Mut female

tag: Sex

value: female

value: Mut

tag: contamination

value: No

value: Post natal day 4 (p4)


title: cells_card9-/- mice_rep3

city: nanjing

first: zhen

last: xu

address: hankou street 22

institute: nanjing university

description: gene expression in peritoneal macrophage

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: peritoneal macrophages,4hr,card9-/-  mice,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Isolation of peritoneal macrophages from mice with thioglycolate injected are succeeded. After the intraperitoneal injection with 1 ml of 3% thioglycolate (Sigma, B2551) to the mice, their ascites gathered 4 d afterwards subjects to centrifugation for the receipt of cell pellet. Pellets collected from 4 or 5 mice each group are subject to resuspension in red blood cell lysis buffer and subsequently the cells are subject to seeding in the DMEM medium. 3 h later, after the removal of cells unseparated, the adherent cells are washed twice only with medium before adding fresh culture medium.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Mice in WT and Card9-/- group were intraperitoneally treated with zymosan 500 mg/kg for 4 hours.

tag: tissue

value: peritoneal macrophages

tag: genotype

tag: treatment

value: zymosan


title: BC131

tag: cell type


title: B1S21.input (EndoC_bH1, CTRL)

tag: cell line

value: beta cells

value: CTRL

tag: disease

tag: gender

value: F


title: ESCs-derived differentiated cells, NC rep1

value: J1 ESCs-derived differentiated cells

tag: strain

tag: culture condition

value: conventional incubator


title: B1S20A.m6A (EndoC_bH1, cytokine-treated)

value: cytokine-treated

tag: age

tag: clone

tag: bmi

tag: batch


title: PEL 1d 2

last: Zhou

description: 1 days after PEL surgery

tag: stain

value: S-D

value: Hypothalamic median eminence (ME)

value: PEL


title: cells_card9-/- mice_rep4

source_name: peritoneal macrophages,4hr,card9-/-  mice,replicate 4


title: cells_card9-/- mice_rep1

source_name: peritoneal macrophages,4hr,card9-/-  mice,replicate 1


title: PEL 1d 1

description: 1 days after PEL surgery


title: BC130

value: MGE derived interneuron

tag: condition


title: B1S20A.input (EndoC_bH1, cytokine-treated)


title: cells_card9-/- mice_rep2

source_name: peritoneal macrophages,4hr,card9-/-  mice,replicate 2


title: Replicate 1 of G4P ChIP-seq in HCT116, ChIP enriched reads

value: colon cancer tissue

value: untreated

tag: group

value: experiment group

tag: target

value: G-quadruplex (G4P)

tag: methodology

value: ChIP-seq

tag: replicate


title: B1S20.m6A (EndoC_bH1, CTRL)

tag: tissue

tag: treatment


title: BC129

tag: cell type

value: Mut female

tag: Sex

value: female

tag: genotype

value: Mut

tag: contamination

value: No

value: Post natal day 4 (p4)


title: Control 3

value: Control


title: Replicate 1 of G4P ChIP-seq in HCT116, input reads

tag: cell line

value: control group


title: sham rep2

value: heart

tag: strain

value: Sprague Dawley

value: WT

value: sham operation


title: cells_wt mice_rep3

source_name: peritoneal macrophages,4hr,wt mice,replicate 3

value: peritoneal macrophages

value: wt

value: zymosan


title: B1S20.input (EndoC_bH1, CTRL)

value: beta cells

value: CTRL

tag: disease

tag: gender

value: F

tag: age

tag: clone


title: cells_wt mice_rep4

source_name: peritoneal macrophages,4hr,wt mice,replicate 4


title: cells_wt mice_rep1

source_name: peritoneal macrophages,4hr,wt mice,replicate 1


title: Replicate 2 of G4P ChIP-seq in HCT116, input reads

value: colon cancer tissue

value: untreated

value: G-quadruplex (G4P)

value: ChIP-seq


title: Liver - Male_WD_AA - Rep6

source_name: Liver

value: Male

tag: diet

value: WD

tag: source

value: AA

tag: washbatch


title: Control 2

tag: stain

value: S-D

value: Hypothalamic median eminence (ME)

value: Control


title: cells_wt mice_rep2

source_name: peritoneal macrophages,4hr,wt mice,replicate 2


title: early erythroid cells, EZH2-shRNA, day 7, rep3

city: zhengzhou

first: li

last: mengjia

address: Science Road 100, Zhengzhou, Henan, 450001, P.R.

institute: zhengzhou university

data_processing:
HTSeq6 was used to read the counts for each gene in each sample, and then FPKM (Fragments Per Kilobase Million Mapped Reads) was calculated to evaluate the expression leve
DEseq2 version 1.6.3 software7 (https://bioconductor.org/packages/3.0/bioc/html/DESeq2.html) and edgeR version 3.26.8 software8 (https://bioconductor.org/packages/3.9/bioc/html/edgeR.html) were used to identify differentially expressed genes from the data.
The GO and KEGG databases were used for the functional enrichment analysis.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA version 4.1.0 software9 (http://www.gsea-msigdb.org/gsea/downloads.jsp).
The original data were filtered and compared with the reference genome hg19.l.
Assembly: hg19
Supplementary files format and content: include RPKM values for each Sample

source_name: early erythroid cells

growth_protocol: CD34+ cells were purified from cord blood by using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’s instructions. The purity of isolated CD34+ cells was 95% to 98%. The cell culture procedure was comprised of 3 phases, Composition of the base culture medium was Iscove’s Modified Dulbecco’s Medium, 2% human peripheral blood plasma, 3% human AB serum, 200 mg/mL Holohuman transferrin, 3 IU/mL heparin, and 10 mg/mL insulin. In the first phase (day 0 to day 6), CD34+ cells at a concentration of 105 /mL were cultured in the presence of 10 ng/mL stem cell factor, 1 ng/mL IL-3, and 3 IU/mL erythropoietin. In the second phase (day 7 to day 11), IL-3 does not need to be added into the culture medium. In the third phase that lasted until day 21, the cell concentration was adjusted to 106 /mL on day 11 and to 5×106/mL on day 15, respectively, the medium for this phase was the base medium plus 3 IU/mL erythropoietin, and the concentration of transferrin was adjusted to 1 mg/mL. The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NovaSeq 5000/6000 S4 Reagent Kit (#A00358, Illumina) and sequenced on an Illumina X-ten (E00487, Illumina)following manufacturer's protocols.

treatment_protocol: The day of getting CD34+ cells was recorded as day 0. Lentivirus human CD34+ transduction at day 2. During the early stage erythroid development, we used an shRNA-mediated approach by using a tetracycline-inducible-GFP expression system, which can be induced by adding doxycycline (DOX) at day 3. During the terminal erythroid development, we added DOX at day 7 .

value: early erythroid cells

value: EZH2 knockdown

value: erythropoiesis


title: Control 1

city: Guangzhou


title: BC127

value: MGE derived interneuron

tag: condition

value: Mut female

value: female

value: Mut

value: No

value: Post natal day 4 (p4)


title: B1S2.m6A (Islets, CTRL)

source_name: Islets

tag: tissue

value: Islets

value: CTRL

value: M

tag: bmi

tag: batch


title: early erythroid cells, EZH2-shRNA, day 7, rep2

tag: cell type

tag: treatment


title: B1S2.input (Islets, CTRL)


title: early erythroid cells, EZH2-shRNA, day 7, rep1

tag: genotype


title: B1S1A.m6A (Islets, cytokine-treated)

tag: cell line

value: cytokine-treated

value: F


title: BC126

value: Mut male

tag: Sex

value: male

tag: contamination


title: PEL_1d_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
Genome_build: ensemble97
Supplementary_files_format_and_content: PEL_1d_vs_PEL_7d_vs_Control_read_count.txt: Matrix table with raw gene counts for every gene and every sample

source_name: Hypothalamic SON+PVN

extract_protocol:
Hypothalamic SON and PVN tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina NovaSeq Platform was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: S-D

value: Hypothalamic SON+PVN

value: PEL

tag: time point

value: 1 days after PEL surgery


title: PEL_1d_2

description: PEL_1d_vs_PEL_7d_vs_Control_read_count.txt


title: B1S19A.m6A (EndoC_bH1, cytokine-treated)

value: beta cells

tag: disease

tag: gender

tag: age

tag: clone


title: BC124

value: MGE derived interneuron


title: PEL_1d_3


title: early erythroid cells, Scramble-shRNA, day 7, rep2

value: early erythroid cells

value: Control

value: erythropoiesis


title: BC125

value: Mut

value: No

value: Post natal day 4 (p4)


title: early erythroid cells, Scramble-shRNA, day 7, rep3


title: early erythroid cells, Scramble-shRNA, day 7, rep1


title: B1S1A.input (Islets, cytokine-treated)

value: Islets

value: CTRL


title: BC123


title: BC128

value: Mut female

value: female


title: PEL_7d_2

value: 7 days after PEL surgery


title: PEL_7d_3

value: S-D


title: BC122

value: WT female with contaminants

value: WT

value: WT female

value: Yes


title: B1S19.m6A (EndoC_bH1, CTRL)

value: beta cells

value: F