title: Conventional CD4SP [43-1]


title: Cdk5r1_E13_control_rep5 [84999]

status: Public on Jun 30 2022

type: SRA

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

library_source: transcriptomic

data_processing:
Read processing, alignment and annotations are described elsewhere (Laukoter et al., 2020b). STAR alignment parameters: clip5pNbases 3, outFilterMultimapNmax 1, --outSAMtype BAM SortedByCoordinate and quantMode GeneCounts. Downstream analyses were performed in R (v3.6.1). Note that for Cdk5r1 samples were sequenced 3x (technical replicates) to increase read coverage. Read coverages of the deleted Cdk5r1 region (chr11:80477417-80478722, mm10) and the deleted Dab1 region (chr4:104605298-104605437, mm10) were calculated using bedtools intersect with the -split option on the aligned bam file produced by STAR. These read counts were added to the count tables produced by STAR with the gene name Cdk5r1_del and Dab1_del respectively.
Downstream analysis of read counts in genes as produced by STAR was performed in R.
We removed samples with a low percentage of uniquely aligned reads (<50%), and/or based on position in PCA plot. Two sets of samples were analysed, SetA contains control, mosaic and cKO of Cdk5r1 cells. SetB contains control and cKO samples from Cdk5r1 and Dab1. Detailed information on which samples were analysed in each set is given in Supplementary MS-Exel files.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text of read counts in genes as reported by STAR, xlsx file with alignment details and information on sample analyzed for the 2 sets (*.sample_details.xlsx) and results from differential expression analysis (DE_*.xlsx).

molecule: polyA RNA

organism: Mus musculus

source_name: MADM-11 GT/TG;Emx1-Cre

growth_protocol: All mouse colonies were maintained in accordance with protocols approved by the institutional animal care and use committee, institutional ethics committee, and the preclinical core facility (PCF) at IST Austria. Experiments were performed under a license approved by the Austrian Federal Ministry of Science and Research following the Austrian and EU animal laws (license numbers: BMWF-66.018/0007-II/3b/2012 and BMWFW-66.018/0006-WF/V/3b/2017).

extract_protocol:
Preparation of cell suspension for cell sorting was prepared as previously described (Laukoter et al., 2020b) for E13, E16, and P0 time points for RNA-seq. From the MADM samples, GFP+ cells were collected for each genotype. For RNA-sequencing, 2000 cells were sorted directly into a custom-made lysis buffer (30nM TRIS pH 8, 10nM EDTA pH 8, 1% SDS and 200 μg/μL Proteinase K). Directly after cell sorting using FACS, samples were incubated for 30min at 37°C. Total volume was filled to 250μl using RNase-free H2O (Thermo Fisher Scientific) followed by the addition of 750μl Trizol LS (Thermo Fisher Scientific). Samples were mixed by inversion (5 times). After a 5min incubation step at RT, the entire solution was transferred into a MaXtract tube (QIAGEN). 200μl chloroform (Sigma-Aldrich) was added, followed by 3 times 5sec vortexing and 2min incubation at RT. Samples were centrifuged for 2min at 12000rpm at 18°C. The supernatant was transferred to a new tube and isopropanol (Sigma-Aldrich) was added in a 1:1 ratio. For better visibility of the RNA pellet 1μl GlycoBlue (Thermo Fisher Scientific) was added and the entire solution was mixed by vortexing (3x 5sec). Samples were left for precipitation o/n at −20°C. After precipitation samples were centrifuged for 20min with 14000rpm at 4°C. The supernatant was removed and the RNA pellet was washed with 70% ethanol, followed by a 5min centrifugation step (14000rpm at 4°C). The RNA pellet was resuspended in 12,5μl RNase-free H2O. RNA quality was analyzed using RNA 6000 Pico kit (Agilent) following the manufacturer’s instructions. The RNA samples were stored at −80°C until further use.
Library preparation (SMART-Seq v2) and RNA sequencing was performed by VBCF GmbH (Vienna, Austria).

treatment_protocol: Mice with specific pathogen-free status according to FELASA recommendations (Mähler (Convenor) et al., 2014) were bred and maintained in experimental rodent facilities (room temperature 21 ± 1°C [mean ± SEM]; relative humidity 40%–55%; photoperiod 12L:12D). Food (V1126, Ssniff Spezialitäten GmbH, Soest, Germany) and tap water were available ad libitum.

tag: strain

tag: target gene

tag: deletion type

value: none/control

tag: age

tag: color

value: green


title: Cdk5r1_E13_control_rep4 [84998]


title: CVB_0m_rep2

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

data_processing:
RNAseq reads were adapter-trimmed using Cutadapt (v1.14) and mapped to human-specific repetitive elements from RepBase (version 18.05) by STAR (v2.4.0i) (Dobin et al., 2013).
Repeat-mapping reads were removed, and remaining reads were mapped to the human genome assembly (hg19) with STAR
Read counts for all genes annotated in GENCODE (hg19) were calculated using the read summarization program featureCounts (Liao et al., 2014).
Assembly: hg19
Supplementary files format and content: .txts with raw gene counts and RPKMs for each experimental group

molecule: total RNA

organism: Homo sapiens

source_name: CVB24 iPSC

growth_protocol: Cortical organoids were maintained in Neurobasal supplemented with 1% B27, 1% GlutaMax, 1% NEAA and 1% Penicillin/Strep and 20 ng/mL FGF2 (Life Technologies)  in humidified atmosphere with 5% CO2 at 37C

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 a KAPA Hyperprep total RNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: CVB24 iPSC

tag: cell type

value: induced pluripotent stem cell

tag: genotype

value: WT

tag: treatment

tag: time

value: Day 0


title: FOXP3lo Treg progenitor [42-3]

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

data_processing:
fastq files were trimmed to remove the first 3 bases from both R1 and R2 reads using trimmomatic (v0.33)
trimmed fastq files were aligned to the GRCm38 reference genome using HiSat2 (v2.1.0)
subread featureCounts (v1.4.6) was used to quantify gene expression counts using the Ensembl GTF v97 GRCm38 gtf
Assembly: GRCm38
Supplementary files format and content: subread_counts.txt is a tab delimited text file containing gene expression counts produced by subread featureCounts

organism: Mus

source_name: Thymocytes

extract_protocol:
Mechanically dissociated thymus, depleted of CD8 via negative magnetic enrichment, was sorted via flow cytometry of a BD FACSAria II to isolate each input cell population. Cells were sorted into RLT buffer with 2-mercaptoethanol.
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit

value: C57Bl/6 x Foxp3-GFP

tag: tissue

value: Thymus

value: Thymocytes

tag: cell population

tag: Sex

value: female

value: 6 week old


title: Control_6M

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 3.0.2)
MD tags were added to alignments with samtools calmd --threads 15 -rb possorted_genome_bam.bam refdata-cellranger-hg19-3.0.0/fasta/genome.fa > possorted_genome_bam_MD.bam
Reads were split based on the CB:Z tag, resulting in one BAM file per barcode.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cortical Organoids

extract_protocol: 10X Chromium Single Cell 3' polyA and feature capture v3 Chemistry

value: Cortical Organoids

value: 6 months post-differentiation


title: mouse E13.5 pancreas KO

city: BArcelona

first: Irene

last: Miguel-Escalada

address: Dr Aiguader 88

country: Spain

institute: CRG

library_source: genomic

data_processing:
none provided by the submitter
Genome_build: mm10

molecule: genomic DNA

source_name: pancreas

extract_protocol:
Dissections of E10.5 and E13.5 embryonic pancreatic tissue were dissociated to single cells and immediately used to build scRNA or to extract nuclei to build scATAC-Seq libraries.
scRNA-Seq libraries were built using Chromium Single Cell 3′ Library & Gel Bead Kit v3, 10x Genomics) and scATAC-Seq libraries were built using Chromium Single Cell ATAC Library & Gel Bead Kit, 10X Genomics)
OTHER: scRNA-Seq and scATAC-Seq

value: embryonic day 13.5


title: MPP3 WT rep 1

city: Freiburg

first: Aurelie

last: Lenaerts

address: Stübeweg 51

department: Cellular and Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Raw FASTQ files were mapped against the mm10 reference genome using the mRNA-seq module implemented in snakePipes (version 2.5.1) (Bhardwaj et al., 2019), using the --trim flag. Briefly, reads were aligned using STAR (version 2.7.3a) (Dobin et al., 2013), followed by expression count quantification with featureCounts (version 2.0.0, (Liao et al., 2014)). Data quality was assessed using Deeptools QC (version 3.3.2, (Ramírez et al., 2016)).
Genes with an average expression higher than 100 counts in any condition were selected for further analysis. Differential expression analysis was performed using DESeq2 (version 1.28.1) (Love et al., 2014) implemented in R (version 4.0.0) and ashr was used for LogFoldChange (LFC) shrinkage of results (version 2.2.47)(Stephens, 2016). Genes were considered differentially expressed at a false discovery rate (FDR) < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix of samples were generated from featureCounts (version 2.0.0).
Supplementary_files_format_and_content: Normalized count matrix of samples were generated using DESeq2 (version 1.28.1)

source_name: bone marrow

growth_protocol: Primary cells

extract_protocol:
Mouse BM cells were isolated from pooled femora, tibiae and ilia bones, by crushing them in cold-PBS-3%FCS. For progenitor cell sorting, bone marrow cells were incubated with a biotin-antibody cocktail (CD3, B220, CD11b, Gr1, Ter119), followed by magnetic depletion with streptavidin-conjugated magnetic nanobeads (BioLegend). MPP3 (LSK+ CD150- CD48+) and MPP4 (LSK+ CD150- CD48+ Flt3+) cells were sorted by a FACS Aria III or FACSymphony instrument (BD Biosciences), directly into RNA lysis buffer and harvested using Arcturus PicoPure RNA isolation kit.
RNA-seq libraries were prepared by the deep-sequencing facility (MPI-Freiburg) using NEBNext SingleCell/Low Input RNA library prep kit  (Cat#E6420), following manufacturer's recommendations. Paired-end 100 bp reads were generated using the Illumina NovaSeq 6000 system, at a depth of 50 million reads.

value: bone marrow

value: Ebf1fl/fl Tie2Cre+/+

value: 12 weeks old


title: CVB_0m_rep1


title: Microglia from naïve mice 3

city: Charlottesville

first: Tajie

last: Harris

state: VA

address: 200 Jeanette Lancaster Way

department: Neuroscience

institute: University of Virginia

description: matrix column 3

data_processing:
Fastq files were processed with Trimmomatic (Bolger et al., 2014)  to trim adapters and filter reads with a minimum quality score of 15, leading and trailing quality scores of 3, and a minimum fragment length of 36.
Quality of the reads were evaluated using FastQC, and after passing quality control (QC), were aligned to the mm10 genome (Harrow et al., 2012).
The number of reads aligning to each gene was quantified with HTSeq (Anders et al., 2015)
Raw and  normalized counts were generated in DESeq2 (Love et al., 2014), alongside a larger set of samples based on a broader experiment.
Assembly: GENCODE M13
Supplementary files format and content: .csv file containing raw counts for gene abundances

source_name: brain

growth_protocol: Age- and sex-matched mice were maintained in accordance with standard protocols of the Institutional Animal Care and Use Committee at the University of Virginia.

extract_protocol:
Immediately after sacrifice mice were perfused with 30 mL of cold 1X PBS. Brains were harvested and put into cold complete RPMI media. For serum, blood from the heart was collected and allowed to clot at 4°C overnight. Brains were minced and homogenized, digested with 0.227 mg/mL collagenase/dispase and 50 U/mL DNase (Roche) at 37°C for 45 minutes. Homogenate was passed through a 70 µm filter (Corning) and washed with cRPMI. Filtered brain homogenate was then resuspended with 20 mL of 40% Percoll and spun at 650 x g for 25 minutes. Myelin was aspirated, samples were washed with cRPMI, and then resuspended in cRPMI.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were intraperitoneally administered tamoxifen (4 mg per 20 g body weight, Sigma-Aldrich) between 4-7 weeks of age for 5 consecutive days to induce ZsGreen expression in microglia. Four weeks following tamoxifen treatment, brains were harvested for analysis.

value: brain

value: Microglia

value: CX3CR1creERT2/+ :ROSA26ZsGreen/ZsGreen

value: Tamoxifen

tag: disease state


title: Mature Tregs [40-4]


title: Conventional CD4SP [40-1]


title: Cdk5r1_E13_control_rep1 [84995]

value: none/control

value: green


title: Cdk5r1_E13_control_rep3 [84997]


title: DHRS4-AS1-BESST-KO rep3

city: Shenzhen

first: Shikuan

last: Zhang

state: Guangdong

address: Tsinghua Shenzhen International Graduate School, University Town of Shenzhen, Nanshan District

department: iBHE

country: China

institute: Tsinghua

description:
HPDE_2A9_3
KO by strategy of BESST

data_processing:
The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd (Shanghai, China).
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
The clean reads were mapped to the human genome (GRCh38) using HISAT2.
FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count.
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: FPKM_anno.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary files format and content: counts_anno.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Pancreatic duct epithelial cell line

growth_protocol: Culture in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal bovine serum in humidified incubator at 37°C with 5% carbon dioxide.

extract_protocol:
RNA was harvested using Trizol reagent.
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Knockout target sequence by CRISPR-Cas9.

value: immortalized human pancreatic duct epithelial cells

value: DHRS4-RS1 KO

tag: strategy

value: BESST


title: DM600_6M

description: 10x Genomics


title: mouse E10.5 MPCs KO 2

source_name: pancreatic multipotent progenitor cells

value: embryonic day 10.5


title: DM1200_6M

description: 10x Genomics


title: Bst2+, CD25+ and/or FOXP3+ [40-5]

value: C57Bl/6 x Foxp3-GFP

value: Thymus

value: Thymocytes

value: female

value: 6 week old


title: MECP2_WT

description: 10x Genomics

value: Cortical Organoids

value: 6 months post-differentiation


title: mouse E13.5 pancreas WT

value: embryonic day 13.5


title: Microglia from naïve mice 2

description: matrix column 2

value: brain

value: Microglia


title: MECP2_KO

description: 10x Genomics


title: FOXP3lo Treg progenitor [40-3]


title: CD25+ Treg progenitor [40-2]


title: Microglia from naïve mice 1

description: matrix column 1

value: CX3CR1creERT2/+ :ROSA26ZsGreen/ZsGreen

value: Tamoxifen


title: Conventional CD4SP [42-1]


title: mouse E10.5 MPCs WT 2


title: mouse E10.5 MPCs KO 1


title: DHRS4-AS1-BESST-KO rep2

description:
HPDE_2A9_2
KO by strategy of BESST


title: Microglia from naïve mice 4

description: matrix column 4


title: DHRS4-AS1-PE-KO rep3

description:
HPDE_027H2_3
KO by strategy of promoter-exon1


title: mouse E10.5 MPCs WT 1


title: DHRS4-AS1-PE-KO rep2

description:
HPDE_027H2_2
KO by strategy of promoter-exon1


title: CF_Pf, scRNAseq

city: Stanford

first: Carlos

last: Milla

address: 770 Welch Road

department: Pediatrics - Pulmonary Medicine

institute: Stanford University

description: 10x Genomics

data_processing:
Quality control of raw data was performed using FASTQC
reads were aligned to the GRCh38-2020 Human Reference Genome using CellRanger to generate counts
Demultiplexed data was analyzed in R using the Seurat 4.0 package
Assembly: the GRCh38-2020 Human Reference Genome
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz

source_name: Nasal Scraping

extract_protocol:
Single-cell suspensions of basal cell culture were prepared by lifting adherent cells using trypsin digestion. Dead cells were removed using the MACS Dead Cell Removal kit (Miltenyi Biotech). Cells were then washed and counted as per manufacturer’s instructions
libraries were prepared using the 10X NEXT GEM 3’ Gene Expression Library scRNA Seq v3.1 reagents and workflow (10x Genomics). Library concentration and quality was confirmed by BioAnalyzer.

value: Nasal Scraping

value: Basal Cells

value: Pf


title: A1

city: QuanZhou

first: LuJie

last: Lu

state: FuJian

address: Chenghua north road

institute: HuaQiao University

data_processing:
After the completion of library construction, the library was first preliminarily quantified by using Qubit2.0, diluted to 1ng/ul, and then the insert size of the library was detected by Agilent 2100. After the insert size met the expectation, the effective concentration of the library was accurately quantified (the effective concentration of the library > 2 nm) by using Q-PCR method to ensure the quality of the library.
Pooling different banks according to the requirement of effective concentration and the amount of data on the machine followed by sequencing of Illumina SE50
The image data of the sequenced fragments obtained by high-throughput sequencing instrument were converted into sequence data (reads) after being identified by CASAVA base, and the data were filtered to obtain clean data, which was then spliced with the transcript of Trinity, and subjected to CORSET (Nadia M Davidson, Alicia Osh Lack, 2014) hierarchical clustering, so that each cluster was defined as "Gene".
Genome_build: Sipunculus nudus

organism: Sipunculus nudus

source_name: Intestinal tract

extract_protocol:
Intestinal tissues were taken out and rapidly frozen on dry ice, RNA was extracted from the tissues using standard extraction methods, RNA samples were then subjected to stringent quality control, and a library was constructed
After passing the sample test, the library was constructed using Small RNA Sample Pre Kit

value: Intestinal tract

tag: developmental stage

value: adult


title: DHRS4-AS1-PE-KO rep1

description:
HPDE_027H2_1
KO by strategy of promoter-exon1

value: immortalized human pancreatic duct epithelial cells

value: DHRS4-RS1 KO


title: WT rep3

value: wild type


title: CF_PBS, scRNAseq

description: 10x Genomics

value: PBS


title: DHRS4-AS1-BESST-KO rep1

description:
HPDE_2A9_1
KO by strategy of BESST

value: BESST


title: WT rep2


title: 3763 HrcC  Replicate3 (Coilin-Treated) [M_16_H0211_A36]

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

description: M_16_H0211_A36_Pool_3_Arabidopsis_thaliana_GTTTCG_L003

data_processing:
Sequenced reads were trimmed using Trimmomatic 0.36 to remove all low quality reads / base pairs.
Trimmed reads were aligned to the TAIR10 genome using Tohat V2.1.1
FPKM calculation on aligned reads were done using cufflinks V2.1.1
Differential expression between two samples / condition is calculated using CuffDiff V2.1.1
Outputs were visualized using cummerbund, Venny etc.,
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel, FPKM values

organism: Arabidopsis thaliana

source_name: 3763 HrcC (Coilin-Treated)

growth_protocol: Sterilized seeds were sown on ½ MS plates containing or not SA187 (2x10^5 CFUs/mL). The seeds were stratified for 2 days at 4°C in the dark and then the plates were placed vertically to grow for 5 days.

extract_protocol: Total RNA extractions were performed using the NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's recommendations

treatment_protocol: Five -old seedlings were transferred onto ½ MS plates with or without 100 mM NaCl and let to grow for 14 days before to be rapidly frozen in liquid nitrogen.

tag: genetic background

value: Coilin

value: Treated

value: 14 days old seedlings


title: Ctrl_Pf_LPS, scRNAseq

description: 10x Genomics

value: WT


title: 3763 HrcC  Replicate1 (Coilin-Treated) [M_16_H0210_A34]

description: M_16_H0210_A34_Pool_3_Arabidopsis_thaliana_GGCTAC_L003


title: 3763 HrcC  Replicate2 (Coilin-Treated) [M_16_H0185_A35]

description: M_16_H0185_A35_Pool_1_Arabidopsis_thaliana_GTGGCC_L001


title: Lymph_ATAC

city: GuangZhou

first: Quanli

last: Yang

address: Huangpu Road

institute: Jinan University

description: gd T cells-10×scATAC-seq

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells;  The Cell Ranger ATAC software pipeline (version 1.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the BWA-MEM aligner,the unique molecular identifier (UMI) count matrix using the R package Seurat(version 3.1.5),Library size normalization was performed with NormalizeData function in Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell with RNA-Seq;  Matrix table with peaks for every peak and every cell with ATAC-Seq

source_name: gd T cells

extract_protocol:
Single cell suspensions of freshly isolated gd T cells from lymph, spleen and thymus by MACS and FACS were resuspended in PBS containing 0.04% ultra-pure BSA, and sorted gd T cells were diluted to <1000 cells/μL; Isolation, washing and counting of nuclei suspensions were performed according to the Demonstrated Protocol: Nuclei Isolation for scATAC-seq (10×Genomics).
According to the manufacturer’s protocol, single cell sequencing libraries were prepared using the Chromium Single Cell 3’ Reagent Kits v2 (10×Genomics). Indexed libraries were further sequenced using an Illumina NextSeq550 system in pair-end mode; scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits User Guide (10×Genomics; CG000168 Rev B)

value: Lymph nodes-derived gd T cells

tag: strain

value: untreated


title: Spleen_ATAC

description: gd T cells-10×scATAC-seq

value: Spleen-derived gd T cells


title: WT rep1


title: 3D standard hMSCs

type: RNA

city: Tulln

first: Vanessa

last: Dobernig

address: Konrad-Lorenz-Straße

institute: LifeTaq Analytics GmbH

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit (Affymetrix; Thermo Fisher Scientific, Inc.). It contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Fragmented and labeled sscDNA were diluted in hybridization buffer at a concentration of 23 ng/ul for a 2.3 ug total and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Clariom S was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven (60 RPM). GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software.

data_processing: R Bioconductor, RMA normalizing, no statistical analysis due to the fact that only 3 samples exist and no technical replicates were made

label: biotin

source_name: Adipose tissue human mesenchymal stem cell

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT WT Plus Kit (Affymetrix; Thermo Fisher Scientific, Inc.). With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled. All steps of the labeling protocol were performed as suggested by Affymetrix, starting from 5.5 ug of ssDNA. Each eukaryotic GeneChip® probe array contains probe sets for several B. subtilis genes that are absent in the samples analyzed (lys, phe, thr, and dap). This Poly-A RNA Control Kit contains in vitro synthesized, polyadenylated transcripts for these B. subtilis genes that are pre-mixed at staggered concentrations to allow GeneChip® probe array users to assess the overall success of the assay. Poly-A RNA Controls final concentration in each target are lys 1:100,000, phe 1:50,000, thr 1:25,000 and dap 1:6,667.

growth_protocol: DMEM/F12 media was used during cultivation process. Osteoblasts were furthermore treated with ascorbic acid, Glycerol-2-Phosphat and Dexamethasone.

extract_protocol: RNEasy Plus Mini Kit from QIAGEN

treatment_protocol: media was changed every 2 to 3 days

value: Adipose tissue

value: mesenchymal stem cell

tag: cultivation parameters

value: three dimensional mesenchymal stem cell


title: Thymus_ATAC

description: gd T cells-10×scATAC-seq

value: Thymus-derived gd T cells


title: 2D standard hMSCs

value: mesenchymal stem cell control


title: CF_LPS, scRNAseq

description: 10x Genomics

value: Nasal Scraping

value: Basal Cells

value: LPS


title: 2D osteo hMSCs

value: Osteoblasts differentiated


title: LA2-TAM

city: New Haven

first: Atreyo

last: Pal

state: CT

address: 333 Cedar St, SHMI I 120

department: Genetics

institute: Yale University

data_processing:
Basecalling was done by Illumina Pipeline software package at Yale Center for Genomic Analysis (YCGA)
Fastq files were generated from raw base calls by 10X Genomics Cell Ranger pipeline (version 5.0) by aligning to the mm10 genome
Count matrices, barcode lists and feature lists for each sample were then generated using the downstream steps of the Cell Ranger pipeline
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include barcode lists for each cell and feature lists for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: lung adenocarcinoma mouse cell line

growth_protocol: LA2 cells were grown in DMEM media supplemented with 10% FBS, pen-strep, non-essential amino acids and L-glutamine

extract_protocol:
1x10^6 LA2 cells were dissociated into a single cell suspension with 0.25% Trypsin-EDTA and resuspended ice-cold PBS + 0.04% BSA.
Library construction was performed by the Yale Center for Genomic Analysis (YCGA) according to standard 10x Genomics and Illumina recommendations

treatment_protocol: Harvested in the absence or presence of 1 mM 4-OHT, 16 h

tag: mouse model

value: KPR

value: lung

value: mock


title: CF_Pf_LPS, scRNAseq

description: 10x Genomics


title: Ctrl_Pf, scRNAseq

description: 10x Genomics

value: Pf


title: Differentiated HL-60 neutrophil-like cells processed by capsaicin for 24 hours rep-2

city: Chengdu

first: Kexin

last: Chen

state: Sichuan

address: No.37 guoxue Lane, Wuhou District, Chengdu city

department: Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China

institute: West China hospital

data_processing:
The image data of the sequencing fragments measured by the high-throughput sequencer were converted into sequence data (reads) by Illumina Casava 1.8 base recognition.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
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
Assembly: human NCBI genome build 36
Supplementary files format and content: xls file with raw gene counts for every gene and every sample

source_name: human leukemic cell line (HL-60)

growth_protocol: Differentiated HL-60 neutrophil-like cells (dHL-60) sourced from the human leukemic cell line (HL-60) (ATCC CCL-240) after the stimulation with the percent of 1.2% dimethyl sulfoxide (DMSO) in medium for 5 days. dHL-60 were maintained in the RPMI 1640 medium containing 1% penicillin and streptomycin (P/S) and 10% FBS

extract_protocol:
Total cell RNA was extracted using Trizol (Ambion, USA), every 5*10^6 cells for 1ml Trizol. Then add one-fifth of the total volume of chloroform, shake vigorously for 15 seconds, stand at room temperature for 3 minutes, and rotate at 12000 rpm for 15 minutes at 4°C. Then the upper water phase was transferred to a new centrifuge tube with equal volume of isopropyl alcohol and bottom-up to mix, and incubate at room temperature for 10 minutes. Centrifuged at 12000 rpm for 10 minutes at 4℃. Discard the up and added 1ml 75% alcohol diluted with RNase free water. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the Nanophotometer ® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations and index codes were added to the attribute sequences for each sample

treatment_protocol: Capsaicin (Sigma-Aldrich) was solved in DMSO until the final concentration reached 400uM and then added into the medium

value: 400uM capsaicin for 24 hours


title: Col0 HrcC  Replicate3 (WT-Treated) [M_16_H0193_A12]

description: M_16_H0193_A12_Pool_2_Arabidopsis_thaliana_GCCAAT_L002

source_name: Col0 HrcC (WT-Treated)

value: Treated

value: 14 days old seedlings


title: Differentiated HL-60 neutrophil-like cells processed by capsaicin for 16 hours rep-3

value: 400uM capsaicin for 16 hours


title: Col0 HrcC  Replicate2 (WT-Treated) [M_16_H0186_A11]

description: M_16_H0186_A11_Pool_1_Arabidopsis_thaliana_AGTTCC_L001


title: CD25+ Treg progenitor [42-2]

value: C57Bl/6 x Foxp3-GFP

value: Thymus

value: Thymocytes

value: female

tag: age

value: 6 week old


title: 3763 Mock  Replicate2 (Coilin-Mock) [M_16_H0201_A26]

description: M_16_H0201_A26_Pool_2_Arabidopsis_thaliana_GAGTGG_L002

source_name: 3763 Mock (Coilin-Mock)

value: Coilin

value: Mock


title: Thymus_RNA

description: gd T cells-10×scRNA-seq

value: Thymus-derived gd T cells

value: untreated


title: 4 weeks timepoint, all GFP+ cells scRNA-seq

city: Heidelberg

first: Reka

last: Toth

address: Im Neuenheimer Feld 280

institute: DKFZ

data_processing:
Alignment: Cell Ranger 3.1
Normalization, QC: R 4.0.3, Seurat 3.2.2
Exclude bad quality cells among the samples: 1000-6000 for TAM, 1000-6000 for Cas9, 1000-6000 for 2 wk-1, 2000-6000 for 2 wk-2, 1500-6000 for 4 wk-1, 2000-6000 for 4-wk GFP+, 1000-6000 for tumour
Cells with more than 10% mitochondrial genes were removed
Normalization with a scaling factor of 10000
Genome_build: mm10
Supplementary_files_format_and_content: scaled_count_data: normalized count data per gene and per cell. Metadata cells: cell barcodes and their annotations in a tab-spearated dataset

source_name: mouse lung, induced tumor

extract_protocol:
Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit V3.1
Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit V3.1

treatment_protocol: all mice were injected with tamoxifen to label the specific cell types

value: lung, induced tumor

tag: eml4-alk adenovirus

value: Yes

tag: gender

tag: age at euthanize

value: 15 weeks


title: Differentiated HL-60 neutrophil-like cells processed by capsaicin for 24 hours rep-3


title: Differentiated HL-60 neutrophil-like cells processed by capsaicin for 24 hours rep-1


title: 3763 Mock  Replicate3 (Coilin-Mock) [M_16_H0199_A27]

description: M_16_H0199_A27_Pool_2_Arabidopsis_thaliana_ACTGAT_L002


title: Lymph_RNA

description: gd T cells-10×scRNA-seq

tag: cell type

value: Lymph nodes-derived gd T cells


title: Ctrl_LPS, scRNAseq

description: 10x Genomics

value: Nasal Scraping

value: Basal Cells

tag: genotype

value: WT

tag: treatment

value: LPS


title: Ctrl_PBS, scRNAseq

description: 10x Genomics

tag: tissue

value: PBS


title: MCF10A_pLOC-MALINC1_2

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
The short-sequenced reads were mapped to the human reference genome (hg19) by the splice junction aligner Rsubread package.
We employed several R/Bioconductor packages to accurately calculate the gene expression abundance at the whole-genome level using the aligned records (BAM files) and to identify differentially expressed genes between cells stably transduced with MALINC1 and empty vector. Briefly, the number of reads mapped to each gene based on the UCSC.hg19.KnownGene database were counted, reported and annotated using the featureCounts and org.Hs.eg.db packages.
To identify differentially expressed genes (log2 fold change [FC] > ±1.5, False Discovery Rate [FDR] <0.05) between the empty vector and MALINC1 overexpressing counterparts, we utilized the edgeR Bioconductor package.
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: The processed data file contains the normalized log2 based count per million values.

source_name: MCF10A cells transduced with MALINC1 vector

growth_protocol: MCF10A cell line was obtained from the American Type Culture Collection (#CRL-10318; ATCC, VA, USA) and validated by DNA fingerprinting. MCF10A cells were cultured in Dulbecco’s Modified Eagle Medium F-12 (DMEM/F-12, Sigma-Aldrich) supplemented with 5% horse serum, 20 ng/mL epidermal growth factor (Sigma-Aldrich), 100 µg/mL hydrocortisone (Sigma-Aldrich), 10 µg/mL insulin (Sigma-Aldrich), 100 ng/mL cholera toxin (Sigma-Aldrich) and 100 U/ml penicillin - 100 μg/ml streptomycin (Sigma-Aldrich). MCF10 DCIS.COM (hereafter DCIS.COM) cells were a kind gift from Dr. Daniel Medina [30] and were maintained in DMEM/F-12 supplemented with 5% horse serum. Cell lines were maintained to 37°C with 5% CO2.

extract_protocol:
MCF10A and DCIS.COM stably transduced cells were used for RNA isolation from subconfluent plates using the RNeasy kit (Qiagen, CA, USA). RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RNA integrity values (RIN) over 8.0 were considered for subsequent analysis.
RNA-seq library construction was perfomed using the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) according to the manufacturer's protocol.
We performed 76 nt paired-end sequencing using an Illumina HiSeq2000 platform and ~20 million reads per sample were obtained.

treatment_protocol: Normal breast epithelial cell lines MCF10A and DCIS (ductal carcinoma in situ) cell line DCIS.COM were stably transduced with pLOC-MALINC1 or pLOC-empty vector (as control)  and selected with 10µg/ml blasticidin.

value: breast cell line

tag: cell line

tag: transduced with

value: MALINC1 vector


title: LA2+TAM

value: KPR

value: lung

value: 1 uM 4-OHT, 16 h


title: Col0 Mock  Replicate3 (WT-Mock) [M_16_H0183_A3]

description: M_16_H0183_A3_Pool_1_Arabidopsis_thaliana_TTAGGC_L001

source_name: Col0 Mock (WT-Mock)

value: Mock

value: 14 days old seedlings


title: DCISCOM_pLOC-MALINC1_1

source_name: DCIS.COM cells transduced with MALINC1 vector

value: DCIS


title: DCISCOM_pLOC-MALINC1_2


title: 2 weeks timepoint, rep2 scRNA-seq

value: lung, induced tumor

value: male

value: 14 weeks


title: Tumour scRNA-seq

source_name: mouse lung tumor

value: lung tumor

value: Yes

value: female

value: 23 weeks


title: Col0 HrcC  Replicate1 (WT-Treated) [M_16_H0192_A10]

description: M_16_H0192_A10_Pool_2_Arabidopsis_thaliana_TGACCA_L002

value: Treated


title: MCF10A_pLOC-MALINC1_1


title: DCISCOM_pLOC-empty_2

source_name: DCIS.COM cells transduced with empty vector

value: empty vector


title: Differentiated HL-60 neutrophil-like cells processed by capsaicin for 16 hours rep-2

value: 400uM capsaicin for 16 hours


title: Col0 Mock  Replicate1 (WT-Mock) [M_16_H0180_H1]

description: M_16_H0180_H1_Pool_1_Arabidopsis_thaliana_CGATGT_L001


title: Spleen_RNA

description: gd T cells-10×scRNA-seq

value: Spleen-derived gd T cells

value: untreated


title: 2 weeks timepoint, rep1 scRNA-seq

value: 13 weeks


title: Differentiated HL-60 neutrophil-like cells processed by capsaicin for 8 hours rep-1

value: 400uM capsaicin for 8 hours


title: Cas9 control scRNA-seq

source_name: mouse normal lung

value: normal lung

value: No

value: 27 weeks


title: MCF10A_pLOC-empty_2

source_name: MCF10A cells transduced with empty vector

value: breast cell line


title: Differentiated HL-60 neutrophil-like cells rep-3

value: control


title: DCISCOM_pLOC-empty_1

value: DCIS


title: Differentiated HL-60 neutrophil-like cells processed by capsaicin for 8 hours rep-3


title: Tamoxifen control scRNA-seq

value: male

value: 22 weeks


title: 3763 Mock  Replicate1 (Coilin-Mock) [M_16_H0195_A25]

description: M_16_H0195_A25_Pool_2_Arabidopsis_thaliana_CTTGTA_L002

value: Coilin

value: Mock

value: 14 days old seedlings


title: Differentiated HL-60 neutrophil-like cells rep-2


title: Differentiated HL-60 neutrophil-like cells processed by capsaicin for 16 hours rep-1


title: Differentiated HL-60 neutrophil-like cells processed by capsaicin for 8 hours rep-2


title: Col0 Mock  Replicate2 (WT-Mock) [M_16_H0191_A2]

description: M_16_H0191_A2_Pool_2_Arabidopsis_thaliana_CGATGT_L002


title: 4 weeks timepoint, rep1 scRNA-seq

value: lung, induced tumor

value: Yes

value: female

value: 15 weeks


title: Dopaminergic neuron precursor cells - HDF410 - Day 25

first: Jeanne

last: Loring

state: California

address: 10550 North Torrey Pines Road

department: The Center for Regenerative Medicine

institute: Scripps Research

data_processing:
nf-core-rnaseq v1.4.2 pipeline
salmon gene counts outputs were used
Transcript counts were aggregated (summed) at the gene level
Genome_build: hg38
Supplementary_files_format_and_content: .txt file containing aggregated gene-level transcript count data (rounded to integer)

source_name: Dopaminergic neuron precursor cells

growth_protocol: Sendai virus, CytoTune 2.0

extract_protocol:
mirVANA™ miRNA isolation kit (Invitrogen)
TruSeq_v2 chemistry

treatment_protocol: 3 x time durations (13, 18 and 25 days of differentiation)

value: iPSC-derived dopaminergic neuron precursor cells

tag: patient

tag: calendar days of differentiation


title: Dopaminergic neuron precursor cells - HDF411 - Day 25


title: Differentiated HL-60 neutrophil-like cells rep-1


title: Dopaminergic neuron precursor cells - HDF410 - Day 18


title: HeLa WT 2ng polyA RNA Treated rep1

city: Chicago

first: Chang

last: Ye

state: Illinois

institute: University of Chicago

data_processing:
Use the cutadapt tool (version 3.5) with customize settings to trim adapter and low-quality bases. Through this command, 6bp of UMI and 5bp of random RT tail will be removed from the sequence and appended into the reads name for downstream PCR duplicates removal. Meanwhile, low quality bases with a Phred quality less than 20 will be trimmed, and reads with a final length less than 15bp will be discarded.
Use the falco tool (version 0.3.0) to check the quality of reads after adapter trimming.
The trimmed reads are mapped to the spike-in RNA, rRNA and small RNA by the bowtie2 tool. Mapping output are filtered and sorted by the samtools (version 1.14-13). Firstly, trimmed reads are mapped to spike-in RNA sequence, and unmapped reads will be mapped to ribosomal RNA (rRNA) afterward. Similarly, unmapped reads from rRNA mapping step are mapped to the small RNA.
Mapped reads from the output of bowtie2 aligner are mapped to the human genome by STAR aligner.
Mutation calling and m6A sites filtering step can refer the GitHub repo: https://github.com/y9c/m6A-sacseq .
Assembly: GRCh38
Supplementary files format and content: tsv

source_name: HeLa Cell line

extract_protocol:
2-50 ng of poly-A enriched or ribosome RNA-depleted RNAs were fragmented and ligated, then divided in a 2:1 ratio. 2/3 of the starting materials are labeled by MjDim1, while the remaining 1/3 serve as the untreated control. After reverse transcription with HIV reverse transcriptase (Worthington Biochemical Corp), the cyclic allyl m6A sites are converted to mismatches, while unconverted m6A sites in the control group are read as A.
RNA samples were ligated to self-designed 5' and 3' adapter, RT with HIV reverse transcriptase (Worthington Biochemical Corp), and libraries were amplified with NEBNext Ultra™ II Q5 Master Mix.

tag: amount

value: 2 ng

value: Treated

tag: replicates


title: Dopaminergic neuron precursor cells - HDF411 - Day 13


title: HeLa WT 2ng polyA RNA Input rep1

value: Input


title: Dopaminergic neuron precursor cells - HDF411 - Day 18


title: rat myocardial_Thread the same position but do not ligate_reperfusion2hour [N-2]

city: JIAMUSI

first: Rao

last: Hongyu

address: 348 Dexiang Street, Jiamusi City, Heilongjiang Province, China

institute: First Affiliated Hospital of Jiamusi University

description: Gene expression 2 h after ischemia reperfusion

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar rat circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

organism: Rattus

source_name: myocardial, Ischemia-reperfusion

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Ischemia-reperfusion injury and matching non-ischemia-reperfusion injury myocardial tissue

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Rats were modeled, sampled and frozen with liquid nitrogen in time

tag: strain

value: SD

tag: Sex

tag: trreatment

tag: molecule subtype

value: circRNA


title: Dopaminergic neuron precursor cells - HDF410 - Day 13

city: La Jolla


title: wildtype(WT) cells cells for STAT5a IP

city: Nanjing

first: Zhen

last: Hua

state: Jiangsu

address: 138 Xianlin Avenue, Xianlin University Town, Nanjing

institute: Nanjing University of Chinese Medicine

data_processing:
Use the cutadapt program to remove the joint sequence in the original offline data
Use Trimmomatic program to remove low-quality sequences to get clean data
Use Fastqc program to count the amount of clean data, the ratio of q20 and q30
Use bowtie2 program to compare clean data to reference genome
Calculate the capture efficiency of the sequencing experiment and the coverage of the ChIP area and the average sequencing depth; use MACS2 to perform peak-calling on the genome; perform peak annotation; use MEME for motif detection of combined peaks; peak differences and annotations between samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Peak annotation and related analysis for each Sample ...

source_name: Multiple Myeloma cells

extract_protocol:
add 37% formaldehyde to the culture medium with at least 107 cells(final concentration of formaldehyde is 1%), shake on a shaker for 10 minutes; stop formaldehyde fixation: add glycine solution to a final concentration of 0.125mol/L, pipette and mix;Wash the cells with PBS, scrape the cells, harvest the cells, and discard the supernatant as much as possible.Combine the antibody with protein A+G magnetic beads (Magna ChIP™ 16-663);Add lysate and protease inhibitor to the cells, and sonicate in ice water bath; take 20ul as Input sample and store at 4℃;Add the sample to the protein A+G magnetic beads bound to the antibody and mix overnight; wash the magnetic column to elute the fragments bound to the protein A+G magnetic beads, and Input samples were added to ProteinaseK together and de-crosslinked at 65℃ overnight; DNA was extracted with phenol chloroform and digested with RNase.
Repair DNA fragment ends, add A base at 3'end, connect sequencing adapter; PCR amplification and fragment size selection of DNA productsm;After the library is qualified, it is sequenced through the Illumina HiSeq/NextSeq platform.

value: wildtype

value: bone marrow

tag: chip antibody


title: rat myocardial_Thread the same position but do not ligate_reperfusion2hour [N-1]

value: male


title: HeLa WT 50ng polyA RNA Treated rep2

value: 50 ng


title: MCF10A_pLOC-empty_1

value: breast cell line

value: empty vector


title: wildtype(WT) cells cells for input RNA


title: HeLa WT 50ng polyA RNA Input rep2


title: HeLa WT 50ng polyA RNA Treated rep1


title: rat myocardial_Thread the same position but do not ligate_reperfusion2hour [N-3]


title: HeLa WT 2ng polyA RNA Treated rep2


title: YTHDF2 kockdown(KD) cells for STAT5a IP

description: KD-DF2-STAT5a_Q005_peaks.narrow.annotation

value: knockdown


title: HTM-Stretch-4 [ST-10]

city: Indianapolis

first: Padmanabhan

middle: P

last: Pattabiraman

state: IN

address: Department of Ophthalmology, Room number 402, 1160 West Michigan Street

department: Ophthalmology

institute: Indiana University Purdue University Indianapolis

data_processing:
The sequence data were mapped to the human reference genome hg38 with STAR-2.5.2b
FeatureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
Genome_build: human reference genome hg38
Supplementary_files_format_and_content: excel file includeing raw counts, log2 fold change, p-values and FDR

source_name: Primary Human Trabecular Meshwork Cells

extract_protocol: KAPA mRNA Hyperprep Kit (KK8581) was ued to prepare the RNA-seq libraries.

value: Primary Human Trabecular Meshwork Cells

value: mechanical stretch


title: HeLa WT 50ng polyA RNA Input rep1


title: rat myocardial_ligature LAD 40min_reperfusion2hour [T-2]


title: rat myocardial_ligature LAD 40min_reperfusion2hour [T-1]


title: Vibrissae_PEE-PH-TA_replicate3

city: KIzugawa

first: Shun

last: Kimura

state: Kyoto

address: 6-5-4 Kunimidai

country: Japan

institute: Rohto Pharmaceutical co. ltd.

description: Gene expression after 24hr culture with 0.3% PEE, 0.015 % PH and 0.024% TA.

hyb_protocol: Then, 600 ng of each labeled cRNA sample was fragmented and hybridized to a SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k 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 withAgilent Feature Extraction ver.12.0.3.1 using default parameters.

source_name: Vibrissae, PEE-PH-TA, replicate 3

label_protocol: Isolated total RNA was amplified and biotin-labeled using a T7 promoter primer based Low Input Quick Amp Labeling Kit (Agilent, #5190-2305), and One-Color RNA Spike-In Kit (Agilent, #5188-5282), respectively.

growth_protocol: Vibrissa follicles were isolated from postnatal day 9 B6C3F1 mouse.

extract_protocol: Total mRNA was extracted using RNeasy® Micro Kit (QIAGEN, Hilden, Germany). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Vibrissa follicles were cultured in RPMI 1640 medium containing 10% fetal bovine serum and samples for 24 hour.

value: Vibrissae

tag: developmental stage

value: Post day 9


title: HeLa WT 2ng polyA RNA Input rep2


title: RNA-seq_P19_D2_MS-275-rep2

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

data_processing:
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.4.1) with default parameters. MACS (v.2.2.7.1) was used to call peaks (-q 0.01) relative to the input sample.
ATAC-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.4.1) with -X 1000 --local. MACS (v.2.2.7.1) was used to call peaks (-q 0.01).
High-quality reads of RNA-seq were quantified using Salmon (v.1.1.0) and differential gene expression analysis was conducted using DESeq2 (v1.26.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: *_Peaks.txt
Supplementary_files_format_and_content: RNA-seq_RawReadCount.txt:

source_name: NSPCs from P19 cells

growth_protocol: P19 embryonal carcinoma (EC) cells were routinely grown in proliferation medium [MEM α (Gibco) contained 10% fetal bovine serum (Gibco)]. For induced neural differentiation, P19 EC cells were treated with 1 μM retinoic acid (Sigma) for 4 days, and were dissociated and plated on poly-D-lysine coated culture dishes under neuronal differentiation medium [DMEM/F12 (Invitrogen) contained 2% B27 (Gibco)] for another 4 days.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: P19 embryonal carcinoma (EC) cells were treated with 1 μM retinoic acid (Sigma) for 2 days under proliferation medium [MEM α (Gibco) contained 10% fetal bovine serum (Gibco)]. 1 μL MS-275 (10 mM) was added as treatment after P19 EC cells treated with retinoic acid for 24 hours (Day 1).

value: Embryonal carcinoma cell


title: human TE-4-2

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

data_processing:
Raw reads from the Illumina HiSeq2000 were mapped to the hg19 genome using default parameters in BWA
Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression were filtered out, followed by quantile normalization.
Genome_build: hg19
Supplementary_files_format_and_content: human_ReadCounts.txt: matrix listing raw read counts
Supplementary_files_format_and_content: human_processed_RPKM.txt: matrix listing normalized RPKM

source_name: trophectoderm

growth_protocol: Single blastomeres were isolated by removing the zona pellucida using acidic tyrode solution (Sigma, cat. no. T1788), then separated by gentle mouth pipetting in a calcium-free medium.

extract_protocol:
RNA was isolated from single cells or single morula embryos and amplified as previously described
Library construction was performed following Illumina manufacturer suggestions.

treatment_protocol: Single cells were washed twice with 1x PBS containing 0.1% BSA before placing in lysis buffer.

tag: sample type

value: trophectoderm

tag: ethnicity

value: Han Chinese


title: human TE-4-1


title: YTHDF2 kockdown(KD) cells for input RNA

tag: genotype


title: Vibrissae_PEE-PH-TA_replicate2

source_name: Vibrissae, PEE-PH-TA, replicate 2


title: HTM-Stretch-3 [ST-6]

tag: cell type

tag: treatment


title: human TE-3-2


title: HTM-Control-4 [ST-9]

value: unstretched control


title: Vibrissae_PEE-PH-TA_replicate1

source_name: Vibrissae, PEE-PH-TA, replicate 1

tag: tissue


title: human TE-3-1


title: RNA-seq_P19_D2_DMSO-rep2

treatment_protocol: P19 embryonal carcinoma (EC) cells were treated with 1 μM retinoic acid (Sigma) for 2 days under proliferation medium [MEM α (Gibco) contained 10% fetal bovine serum (Gibco)]. 1 μL DMSO was added as control after P19 EC cells treated with retinoic acid for 24 hours (Day 1).

tag: cell line


title: human TE-2-3


title: RNA-seq_P19_D8-rep2

source_name: Neurons from P19 cells

treatment_protocol: P19 embryonal carcinoma (EC) cells were induced into neurons step by step as described in growth protocol.


title: RNA-seq_P19_D2_DMSO-rep1


title: HTM-Control-2 [ST-3]


title: RNA-seq_P19_D2_MS-275-rep1


title: HTM-Stretch-2 [ST-4]


title: HTM-Stretch-1 [ST-2]


title: RNA-seq_P19_D8-rep1


title: Vibrissae_PEE-PH_replicate3

description: Gene expression after 24hr culture with 0.3% PEE and 0.015 % PH.

source_name: Vibrissae, PEE-PH, replicate 3


title: rat myocardial_ligature LAD 40min_reperfusion2hour [T-3]

value: SD


title: Vibrissae_PEE-TA_replicate1

description: Gene expression after 24hr culture with 0.3% PEE and 0.024 % TA.

source_name: Vibrissae, PEE-TA, replicate 1


title: RNA-seq_P19_D4-rep1

treatment_protocol: P19 embryonal carcinoma (EC) cells were treated with 1 μM retinoic acid (Sigma) for 4 days under proliferation medium [MEM α (Gibco) contained 10% fetal bovine serum (Gibco)].


title: HTM-Control-1 [ST-1]


title: Vibrissae_PEE-TA_replicate3

source_name: Vibrissae, PEE-TA, replicate 3


title: Vibrissae_PEE-TA_replicate2

source_name: Vibrissae, PEE-TA, replicate 2


title: Vibrissae_PH-TA_replicate3

description: Gene expression after 24hr culture with 0.015% PH and 0.024 % TA.

source_name: Vibrissae, PH-TA, replicate 3


title: Vibrissae_PEE-PH_replicate2

source_name: Vibrissae, PEE-PH, replicate 2


title: Vibrissae_PEE-PH_replicate1

source_name: Vibrissae, PEE-PH, replicate 1


title: Vibrissae_PH-TA_replicate2

source_name: Vibrissae, PH-TA, replicate 2


title: ACHN, siControl-repeat 3

city: Shenzhen

first: Xina

last: Xie

institute: Shenzhen Second People's Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then  Fragments Per  Kilobase of transcript sequence per Millions (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: ACHN cell

extract_protocol:
After transfecting 769-P and ACHN cells with siRNA-NUF2 or siRNA-control for 48 h, total RNA from each group was extracted using Trizol and sequenced on the Illumina platform at Novogene Co. Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ACHN

value: clear cell renal cell carcinoma cells

value: treated with siRNA-control for 48 hours

value: control


title: human TE-2-2


title: RNA-seq_P19_D4-rep2


title: RNA-seq_P19_D0-rep2

source_name: P19 cells

treatment_protocol: P19 embryonal carcinoma (EC) cells were routinely grown in proliferation medium [MEM α (Gibco) contained 10% fetal bovine serum (Gibco)].


title: human TE-2-1


title: human TE-1-1


title: RNA-seq_P19_D0-rep1


title: human ICM-3-3

source_name: inner cell mass

value: inner cell mass


title: ACHN, siControl-repeat 2


title: human TE-1-2


title: Vibrissae_PH-TA_replicate1

source_name: Vibrissae, PH-TA, replicate 1


title: ATAC-seq_P19_D4_NSPCs-rep2

source_name: NSPCs from P19 cells

extract_protocol:
Tn5 enzyme was used to isolated accessible chromatin DNA.
ATAC-seq libraries were prepared according the instructions of TruePrep Index Kit V2 for Illumina (TD501, Vazyme Biotech).


title: Vibrissae_TA_replicate2

description: Gene expression after 24hr culture with 0.024% TA.

source_name: Vibrissae, TA, replicate 2


title: Vibrissae_PEE_replicate3

description: Gene expression after 24hr culture with 0.3% PEE.

source_name: Vibrissae, PEE, replicate 3


title: Vibrissae_TA_replicate1

source_name: Vibrissae, TA, replicate 1


title: ATAC-seq_P19_D4_NSPCs-rep1


title: human ICM-3-4


title: ACHN, siControl-repeat 1


title: human ICM-3-5


title: Vibrissae_PEE_replicate2

source_name: Vibrissae, PEE, replicate 2


title: ACHN, siNUF2-repeat 2

value: treated with siRNA-NUF2 for 48 hours

value: NUF2 knockdown


title: human ICM-3-2


title: ACHN, siNUF2-repeat 1


title: ChIP-seq_P19_D2_MS-275_H3K18la

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 10’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.

tag: antibody vendor

value: PTM Biolab, Hangzhou, China

tag: antibody catalog#

tag: antibody lot#


title: ChIP-seq_P19_D2_MS-275_input

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 11’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: human ICM-3-1


title: human ICM-2-2


title: ChIP-seq_P19_D2_MS-275_H3K9cr

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 9’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: Vibrissae_TA_replicate3

source_name: Vibrissae, TA, replicate 3


title: 769P, siControl-repeat 3

source_name: 769-P cell


title: ACHN, siNUF2-repeat 3


title: human ICM-2-1


title: Vibrissae_PH_replicate3

description: Gene expression after 24hr culture with 0.015% PH.

source_name: Vibrissae, PH, replicate 3


title: Vibrissae_PEE_replicate1

source_name: Vibrissae, PEE, replicate 1


title: ChIP-seq_P19_D2_MS-275_H3K9ac

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 8’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: 769P, siControl-repeat 2


title: 769P, siNUF2-repeat 3


title: human ICM-1-5


title: human ICM-1-4


title: human ICM-1-6


title: Vibrissae_PH_replicate2

source_name: Vibrissae, PH, replicate 2


title: Vibrissae_PH_replicate1

source_name: Vibrissae, PH, replicate 1


title: 769P, siControl-repeat 1


title: ChIP-seq_P19_D2_DMSO_H3K18la

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 6’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: ChIP-seq_P19_D2_DMSO_H3K9cr

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 5’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: St-4

city: Moscow

first: Maxim

last: Kozin

address: Ostrovitanova 1

country: Russia

institute: Pirogov Russian National Research Medical University

description: secondary hypertrophied left ventricle sample

data_processing:
Quality control of raw sequencing reads was assessed with FASTQC. Low quality nucleotides were trimmed from the raw fastq files using Trimmomatic (Version 0.39).
Samples were mapped on Genome primary assembly GRCh38 with the Gencode annotation using STAR (Version 2.7.6a)
Reads per gene were counted using GeneCounts option of STAR software.
DESeq2 Bioconductor package (Version 1.32.0) was used for normalization, principal component analysis, and differential gene expression analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: heart left ventricle

extract_protocol:
Myocardial samples from HCM and AS patients undergoing surgical myoectomy or aortic valve replacement, respectively, were obtained from interventricular septum in the part under the right aortic coronary leaflet. After extraction tissue samples were immediately cut into fragments up to ≤ 0.5 cm in any single dimension, submerged in 5 volumes of RNAlater solution (Thermo Fisher Scientific, USA), and stored at -20ºC for further processing.
Disruption of tissue samples was performed using the TissueLyser LT bead mill (Qiagen, USA). Total RNA was extracted from disrupted samples using RNeasy Mini Kit (Qiagen, USA)
RNA libraries were constructed from 1 μg RNA using MGIEasy RNA Library Prep Set following manufacturer instructions. Global transcriptome profiling was performed by high throughput RNA sequencing (RNA-seq) on MGISEQ-200 platform

value: heart left ventricle

tag: status

value: aortic stenosis

value: male

tag: age


title: human ICM-1-2


title: St-5

tag: Sex


title: human ICM-1-3


title: human ICM-1-1


title: 769P, siNUF2-repeat 1


title: Vibrissae_control_replicate3

description: Gene expression after 24hr culture

source_name: Vibrissae, control, replicate 3

value: Vibrissae

value: Post day 9


title: St-3

value: female


title: St-2


title: ChIP-seq_P19_D2_DMSO_H3K9ac

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 4’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.

value: Embryonal carcinoma cell


title: Vibrissae_control_replicate1

description: Gene expression after 24hr culture

source_name: Vibrissae, control, replicate 1


title: 769P, siNUF2-repeat 2


title: ChIP-seq_P19_D4_NSPCs_input-rep2

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: human 16-cell-1-6

source_name: 16-cell blastomere

value: 16-cell blastomere

value: Han Chinese


title: Vibrissae_control_replicate2

description: Gene expression after 24hr culture

source_name: Vibrissae, control, replicate 2


title: SW480 cells derived from xenograft tumor of second transplantation

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

data_processing:
CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data, then mapped to GRCh38 whole genome using Hisat2 software.
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files including fpkm values for each sample

source_name: Cells that formed neurosphere-like structures derived from xenograft tumors of the second transplantation, cultured in NDiff227 serum-free medium for 9 days at 37°C in 5% CO2.

growth_protocol: SW480 cells and tumor cells from serial transplantation were cultured in NDiff227 serum-free medium for 9 days at 37°C in 5% CO2.

extract_protocol:
Cells were collected with trypsinization and total RNA was extract with TRIzol using the protocol from the manufacturer.
Libraries were contructed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® using the protocol from the manufacturer.

value: Colorectal cancer cell line

tag: cell line source

value: Primary human colorectal adenocarcinoma

value: Not available


title: human 16-cell-1-4


title: HCT116 cell with SETDB1 knockdown

source_name: HCT116 cells infected with lentivirus carrying shRNA against SETDB1 (shSETDB1), and cultured for 5 days

growth_protocol: Control HCT116 cells and cells with SETDB1 knockdown were cultured in DMEM plus 10% FBS, at 37°C in 5% CO2 for 5 days

tag: knockdown

value: shRNA against SETDB1


title: ChIP-seq_P19_D4_NSPCs_H3K18la-rep1

source_name: NSPCs from P19 cells

tag: chip antibody


title: HCM-7

description: primary hypertrophied left ventricle sample

value: hypertrophic cardiomyopathy


title: ChIP-seq_P19_D4_NSPCs_H3K18la-rep2


title: SW480 cells

source_name: SW480 cells cultured in NDiff227 serum-free medium for 9 days at 37°C in 5% CO2.


title: ChIP-seq_P19_D4_NSPCs_H3K9cr-rep2


title: SW480 cells derived from xenograft tumor of first transplantation

source_name: Cells that formed neurosphere-like structures derived from xenograft tumors of the first transplantation, cultured in NDiff227 serum-free medium for 9 days at 37°C in 5% CO2.


title: HCM-6


title: ChIP-seq_P19_D4_NSPCs_input-rep1


title: HCM-8


title: HCM-5


title: human 16-cell-1-5


title: ChIP-seq_P19_D2_DMSO_input

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 7’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: St-1


title: SW480 cells derived from xenograft tumor of third transplantation

source_name: Cells that formed neurosphere-like structures derived from xenograft tumors of the third transplantation, cultured in NDiff227 serum-free medium for 9 days at 37°C in 5% CO2.


title: human 16-cell-1-3


title: ChIP-seq_P19_D4_NSPCs_H3K9ac-rep1


title: siSPRY4-IT1 NC_2(NC_2)

city: suzhou

first: Ji

last: Wang

address: 1055 Sanxiang Road, Gusu District

institute: Soochow University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and count values for each sample

source_name: U87 cells

growth_protocol: U87 cells were cultured in DMEM containing 10%FBS at 37 °C in a humid atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: U87 cells were transfected with SPRY4-IT1 Scramble siRNA (control) or SPRY4-IT1 siRNA

value: glioma cell line

tag: genotype/variation

value: control


title: ChIP-seq_P19_D4_NSPCs_H3K9cr-rep1

value: PTM Biolab, Hangzhou, China


title: human 16-cell-1-2

tag: sample type


title: Control HCT116 cells

source_name: HCT116 cells infected with lentivirus carrying empty shRNA knockdown vector pLKO.1, and cultured for 5 days

value: empty vector


title: RNA-seq_E13.5_rep2

data_processing:
genome_build: GRCm38
High-quality reads of RNA-seq were quantified using Salmon (v.1.1.0) and differential gene expression analysis was conducted using DESeq2(v1.26.0).

source_name: Telencephalon

tag: strain

value: ICR

value: Embronic day 13.5

value: telencephalon


title: RNA-seq_E13.5_rep1


title: HCM-3

value: heart left ventricle

value: male


title: human 16-cell-1-1

tag: ethnicity


title: siSPRY4-IT1 NC_3(NC_3)


title: HCM-4

value: female


title: siSPRY4-IT1 NC_1(NC_1)


title: HCAECs, melatonin_3

city: Shanghai

first: yuanzheng

last: Zheng

address: Dongan road 130

institute: Fudan University

data_processing:
FastQC software was used for the quality evaluation of the raw reads.
Fastp software was used for data filtering.
The spliced maping algorithm of Hisat2 software was used for reads alignment.
Stringtie software was used for calculating the counts of fragment, and the TMM（trimmed mean of M values）algorithm was used for normalization.
Supplementary_files_format_and_content: Processed Data Matrix xls. includes raw gene counts and FPKM values for every gene and every sample.

source_name: HCAEC

growth_protocol: HCAECs were cultured in flasks coated with fibronectin (2 μg/cm2) in endothelial cell medium containing 1% endothelial cell growth supplement, 5% fetal bovine serum (FBS), and 1% penicillin/streptomycin solution in a humidified atmosphere containing 5% CO2 and 95% air at 37 °C

extract_protocol:
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes to construct cDNA library which was paired-end (PE) sequenced using Illumina sequencing platforms based on Next-Generation Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCAECs were treated with 0.5nmol/L melatonin for 6h. Then, the cells were stimulated with 20 ng/ml recombinant human tumor necrosis factor-α (TNF-α, R&D Systems, USA) for 12 h.

tag: cell type

value: HCAEC

tag: treatment 1

value: 20 ng/ml TNF-α, 12 h

tag: treatment 2

value: 0.5nmol/L melatonin,6h


title: ATAC-seq_E13.5_rep2

data_processing:
genome_build: GRCm38
ATAC-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.4.1) with -X 1000 --local. MACS (v.2.2.7.1) was used to call peaks (-q 0.01).

tag: tissue


title: gStub1 #1_24h

city: Singapore

first: Simon

last: Ng

address: 8 Biomedical Grove

country: Singapore

institute: MSD

hyb_protocol: The samples were hybridized at 65 °C for 20 h and processed on the nCounter prep station.

scan_protocol: The resulting cartridge was scanned by the nCounter digital analyzer using 555 fields of view.

data_processing: Raw count data were evaluated for quality control and normalized with 19 housekeeping genes using nSolver 4.0 software. Tlk2 was excluded from the housekeeping gene due to weak expression (RNA counts <80).

label: Biotin capture probe, fluorescent barcoded reporter probe

source_name: Melanoma cell line

label_protocol: An input of 150 ng RNA from each sample was mixed with the NanoString reporter and capture probes (nCounter Mouse PanCancer IO 360, # XT-CSPS-MIO360-12).

growth_protocol: CRISPR-engineered B16-F10 cells (gControl, gStub1 #1, and gStub1 #2) were seeded separately in 12-well plate (50,000 cells per well) with DMEM + 10% FBS.

extract_protocol: Total RNA from cells were extracted with RNeasy plus mini kit (Qiagen, 74134) according to manufacturer’s protocol.

treatment_protocol: For cell treated with IFNg, the culture media were replaced with fresh media (DMEM + 10% FBS) supplemented with 0.03 ng/ml of recombinant mouse IFNg (R&D Systems, #485-MI-100).

tag: ifng treatment

value: Yes

tag: treatment length


title: RNA-seq_E16.5_rep2

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Embronic day 16.5


title: gStub1 #2_24h


title: human 16-cell-1-7

extract_protocol:
RNA was isolated from single cells or single morula embryos and amplified as previously described
Library construction was performed following Illumina manufacturer suggestions.

value: 16-cell blastomere

value: Han Chinese


title: ChIP-seq_P19_D4_NSPCs_H3K9ac-rep2

tag: cell line

value: Embryonal carcinoma cell

tag: antibody vendor

tag: antibody catalog#

tag: antibody lot#


title: human 12-cell-1-5

source_name: 12-cell blastomere

value: 12-cell blastomere


title: siSPRY4-IT1_1(siS4_IT1_1)

value: glioma cell line

value: SPRY4-IT1 knockdown


title: RNA-seq_E16.5_rep1

value: ICR

tag: age


title: siSPRY4-IT1_3(siS4_IT1_3)


title: HCAECs, melatonin_1


title: human 12-cell-1-8


title: siSPRY4-IT1_2(siS4_IT1_2)


title: human 12-cell-1-7


title: HCM-2

source_name: heart left ventricle

tag: status

value: hypertrophic cardiomyopathy

tag: Sex


title: human 12-cell-1-2


title: HCM-1


title: ChIP-seq_E16.5_input-rep2

data_processing:
genome_build: GRCm38
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.4.1) with default parameters. MACS (v.2.2.7.1) was used to call peaks (-q 0.01) relative to the input sample.

value: telencephalon

tag: antibody(vendor)

value: none (input)

tag: antibody(catalog#)

tag: antibody(lot#)


title: HCAECs, melatonin_2


title: gStub1 #2_6h

value: 6 h


title: human 12-cell-1-3

tag: sample type

tag: ethnicity


title: HCAECs, NC_3

tag: cell type

tag: treatment 1

value: control


title: human 8-cell-3-3

source_name: 8-cell blastomere

value: 8-cell blastomere


title: ATAC-seq_E13.5_rep1

extract_protocol:
Tn5 enzyme was used to isolated accessible chromatin DNA.
ATAC-seq libraries were prepared according the instructions of TruePrep Index Kit V2 for Illumina (TD501, Vazyme Biotech).

tag: strain

value: Embronic day 13.5

tag: tissue


title: HCAECs, NC_1

value: HCAEC

value: 20 ng/ml TNF-α, 12 h

tag: treatment 2


title: ChIP-seq_E16.5_H3K18la-rep2

value: Embronic day 16.5

value: PTM Biolab, Hangzhou, China


title: ChIP-seq_E16.5_input-rep1

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 10’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: gControl_24h

tag: ifng treatment

value: Yes

tag: treatment length


title: human 8-cell-3-1

value: Han Chinese


title: human 8-cell-3-4


title: HCAECs, NC_2


title: human 12-cell-1-1

value: 12-cell blastomere


title: gStub1 #2_untreated

value: No


title: gControl_6h


title: gStub1 #1_6h


title: RNA-seq of MSC transduced with EWS-ZFA7_replicate 2

city: Charlestown

first: Keith

last: Joung

state: MA

institute: MGH

description: native cells

data_processing:
RNA-seq reads were aligned to hg19 using STAR(doi: 10.1093/bioinformatics/bts635) and PCR duplicates were removed using Picard tools(http://broadinstitute.github.io/picard/). Reads aligning to ribosomal RNA were then filtered out of the alignment. Genomic coverage from filtered alignments were calculated by normalizing to sequencing depth using bedtools(https://doi.org/10.1093/bioinformatics/btq033). FPKMs were calculated using Cufflinks(https://doi.org/10.1038/nbt.1621)
ChIP-seq reads were aligned to human reference genome hg19 using Burrows-Wheeler Alignment (BWA) tool (PMC2705234). Genome-wide coverage was calculated after extending to 200 bases(approximate fragment size) and averaged over 25 bp windows using igvtools (https://doi.org/10.1093/bib/bbs017). Coverage was then normalized and scaled using RSeqC (http://rseqc.sourceforge.net/#normalize-bigwig-py)
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text files that include FPKM values for each gene
ChIP-seq: bigwig files for visualization on igv

source_name: RNA-seq of MSC transduced with EWS-ZFA7

extract_protocol:
For ChIP-seq, chromatin from 1% formaldehyde-fixed cells were fragmented to 200-500 bps by sonication for 5-6 mins using the Branson sonifer SFX250
RNA-seq:Single-end libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) and TruSeq RNA Single Indexes, pooled, and sequenced using an NextSeq500.
ChIP-seq: Sequencing libraries were prepared with 3 ng of each H3K27Ac ChIP DNA and input sample using SMARTer ThruPLEX DNA-seq kit (Takara, Cat# R400675). Libraries were sequenced with single-end (SE) 75 cycles on an Illumina Nextseq 500 system

treatment_protocol: For RNA-seq, total RNA was extracted from native cells using the NucleoSpin RNA Plus Kit (Clontech, cat# 740984.250)

value: MSC

tag: treatment

value: transduced with EWS-ZFA7


title: human 8-cell-7-1


title: RNA-seq of MSC transduced with EWS-ZFA7_replicate 1

description: native cells


title: RNA-seq of MSC transduced with EWS-FLI1_replicate 2

description: native cells

source_name: RNA-seq of MSC transduced with EWS-FLI1

value: transduced with EWS-FLI1


title: human 8-cell-6-1


title: ChIP-seq_E16.5_H3K9ac-rep2

value: ICR

value: telencephalon


title: ChIP-seq_E16.5_H3K9cr-rep1


title: gStub1 #1_untreated


title: ChIP-seq_E16.5_H3K9ac-rep1


title: human 8-cell-6-2


title: Muscle_5932_MOET

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

data_processing:
The RNAseq read pairs were mapped to the bovine reference genome (bosTau9) with STAR aligner (v. 2.7), generating the genome index with the gene Bos taurus release 102 annotation.
Read counts were estimated at gene level using HTSeq-count.
Genome_build: bosTau9
Supplementary_files_format_and_content: GeneCounts_LiverMuscle.txt: Tab-delimited text file containing raw read counts for each sample.

organism: Bos taurus

source_name: Muscle

extract_protocol:
Tissues samples were shipped in dry ice to the BGI TECH SOLUTIONS Company (Hong Kong), which performed the RNA extraction, quality control, library preparation and sequencing. All samples met the requirements for library preparation (adequate concentration and quantity, purity as OD260/280 = 1.8~2.0 and RIN > 7).
RNA sequencing (RNAseq) was run in the RNA samples through non-stranded & polyA-selected mRNA library preparation and PE100 sequencing with 5Gb clean data per sample on DNBSEQ. After library preparation and sequencing, raw data with adapter sequences or low-quality sequences were filtered to remove contamination and obtain valid data. This step was completed by the SOAPnuke software developed by BGI Company.

treatment_protocol: Holstein embryos were produced in vitro or in vivo (by ovarian superstimulation followed by AI) and transferred to synchronized recipients. Pregnancies were monitored until delivery when the birthweights of the calves were recorded. Calves were maintained in similar condition during the postnatal period until euthanasia at around 100 days of age.

tag: embryo origin

value: MOET

tag: age (days)

tag: weight at birth (kg)

tag: weight at sample collection (kg)

value: Male

value: Muscle

tag: breed

value: Holstein

tag: individual


title: human 8-cell-5-3

value: 8-cell blastomere


title: ChIP-seq_E13.5_input-rep2

tag: age

value: Embronic day 13.5

tag: antibody(vendor)

value: none (input)

tag: antibody(catalog#)

tag: antibody(lot#)


title: Muscle_5833_IVP

value: IVP

tag: Sex


title: RNA-seq of MSC transduced with EWS-FLI1_replicate 1

description: native cells

tag: cell type


title: Muscle_5841_IVP

tag: tissue


title: ChIP-seq_E16.5_H3K9cr-rep2

tag: strain

value: Embronic day 16.5

value: PTM Biolab, Hangzhou, China


title: RNA-seq of HEK293T transduced with KRAB-ZFA7_replicate 2

description: native cells

tag: cell line

value: transduced with KRAB-ZFA7


title: human 8-cell-5-2

tag: sample type

tag: ethnicity

value: Han Chinese


title: RNA-seq of HEK293T transduced with KRAB-ZFA7_replicate 1

description: native cells

tag: treatment


title: human 8-cell-6-3


title: Muscle_3218_MOET

tag: embryo origin

tag: age (days)


title: ChIP-seq_E13.5_input-rep1


title: RNA-seq of HEK293T transduced with GFP_replicate 2

description: native cells

source_name: RNA-seq of HEK293T transduced with GFP

value: transduced with GFP


title: Muscle_3217_MOET

tag: weight at birth (kg)

tag: weight at sample collection (kg)


title: human 8-cell-5-1


title: human 8-cell-4-3


title: Muscle_3213_MOET

tag: breed

tag: individual


title: ChIP-seq_E13.5_H3K18la-rep1

tag: age

tag: antibody(vendor)


title: gControl_untreated

tag: ifng treatment

value: No

tag: treatment length


title: RNA-seq of A673 transduced with KRAB-ZFA7_replicate 2

description: native cells


title: human 8-cell-4-2


title: ChIP-seq_E13.5_H3K9cr-rep2

tag: antibody(catalog#)

tag: antibody(lot#)


title: Muscle_3209_IVP

tag: Sex

tag: tissue


title: ChIP-seq_E13.5_H3K18la-rep2

tag: strain


title: human 8-cell-4-1

tag: sample type

tag: ethnicity


title: RNA-seq of A673 transduced with GFP_replicate 2

description: native cells

source_name: RNA-seq of A673 transduced with GFP

tag: cell line

tag: treatment


title: ChIP-seq_E13.5_H3K9ac-rep2


title: human 8-cell-7-2


title: ChIP-seq_E16.5_H3K18la-rep1

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 8’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: Liver_5932_MOET

source_name: Liver

tag: embryo origin

tag: age (days)

tag: weight at birth (kg)

value: Liver


title: human 8-cell-10-4


title: RNA-seq of A673 transduced with GFP_replicate 1

description: native cells


title: human 8-cell-10-5


title: ChIP-seq_E13.5_H3K9cr-rep1

value: ICR


title: HTM-Control-3 [ST-5]

source_name: Primary Human Trabecular Meshwork Cells

extract_protocol: KAPA mRNA Hyperprep Kit (KK8581) was ued to prepare the RNA-seq libraries.

tag: cell type

value: Primary Human Trabecular Meshwork Cells

value: unstretched control


title: 6w_IP-5_spleen

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20.
Filtered reads were mapped to the reference genome related to the species using the aligner TopHat v2.0.12
Gene expression level was measured with Cufflinks v2.1.1
Differential expression analysis was performed by Cuffdiff
Genome_build: UMD3.1
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: Mouse spleen

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen, Germany). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample Prep Kit

value: Spleen


title: Liver_5833_IVP

tag: weight at sample collection (kg)

value: Male

tag: breed

tag: individual


title: H929_wildtype(WT) cells cells for m6a-seq

data_processing:
Library strategy: m6A-seq
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using Bowtie2.
Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis.
Peaks of each samples and differential methylation peak were called  using the exomePeak R-package.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: fpkm

source_name: Multiple Myeloma cells

extract_protocol:
RNA fragments were incubated with anti-N6-methyladenosine (m6A) antibodies (Sigma-Aldrich, Burlington, USA) inimmunoprecipitation (IP) buffer for 2 h at 4℃. The samples were then washed with low-salt precipitation buffer and high-salt buffer thrice continuously. RNA was extracted using a phenol-chloroform lysate to obtain a purified product.
The purified RNA was collected for the generation of an RNA-seq library with NEBNext R Ultra™ RNA Library Prep Kit (New England Biolabs, MA, USA). The quality of the library was done using Bioptic Qsep100 analyzer and sequencing was done using NovaSeq's high-throughput sequencing platform

tag: genotype

value: wildtype


title: RNA-seq of HEK293T transduced with GFP_replicate 1

description: native cells


title: Liver_5841_IVP

value: Holstein


title: H929_wildtype(WT) cells cells for input RNA


title: Liver_3218_MOET

value: MOET


title: Muscle_3208_IVP

value: Muscle


title: 6w_IP-2_spleen


title: human 8-cell-10-2

value: 8-cell blastomere


title: RNA-seq of A673 transduced with KRAB-ZFA7_replicate 1

description: native cells


title: H929_YTHDF2 kockdown(KD) cells for m6a-seq

value: knockdown


title: human 8-cell-10-3


title: 6w_Oral-4_spleen


title: human 8-cell-10-1


title: H929_YTHDF2 kockdown(KD) cells for input RNA


title: ChIP-seq_E13.5_H3K9ac-rep1

tag: age

value: Embronic day 13.5

value: telencephalon

tag: antibody(vendor)

value: PTM Biolab, Hangzhou, China

tag: antibody(catalog#)


title: Liver_3213_MOET

tag: Sex

tag: tissue


title: human 8-cell-9-4

tag: sample type

value: Han Chinese


title: 6w_Oral-1_spleen

tag: strain


title: human 8-cell-9-3

tag: ethnicity


title: 6w_C-2_spleen


title: Liver_3208_IVP

value: IVP


title: ARP1_wildtype(WT) cells cells for m6a-seq


title: ARP1_YTHDF2 kockdown(KD) cells for m6a-seq


title: SPS3

city: Shenyang

first: Fang

last: Han

state: Liaoning

address: No.77 Puhe Road, Shenyang North New Area

institute: China Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel format;

organism: Rattus norvegicus

source_name: hippocampal

extract_protocol:
We extracted total RNA from the hippocampi of rats using TRIzol reagent. Ribo-Zero rRNA Removal Kits were used to remove the rRNA from total RNA. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit. Quality and quantity of the libraries were controlled by using the BioAnalyzer 2100 system. We denatured 10 pM libraries as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters, and finally sequenced for 150 cycles on an Illumina HiSeq Sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SPS rats were restricted with a plastic container for 2 hours (immobilization), then forced to swim (temperature: 24 ± 1 °C, water depth: 40 cm) for 20 minutes with a 15-minute rest. Finally, the rats were anaesthetized until they lost consciousness, and returned to their own cages. Rats in the control group remained in their home cages with no handling.

value: Sprague Dawley

value: hippocampus

tag: treatment

value: single prolonged stress (SPS)


title: human 8-cell-9-2


title: SPS2


title: 6w_C-3_spleen


title: ARP1_wildtype(WT) cells cells for input RNA


title: 6w_IP-3_MLN

source_name: Mouse mesenteric lymph node

value: Mesenteric lymph node


title: human 8-cell-9-1


title: ARP1_YTHDF2 kockdown(KD) cells for input RNA


title: SPS1


title: 6w_IP-4_MLN


title: human 4-cell-2-1

source_name: 4-cell blastomere

value: 4-cell blastomere


title: 6w_Oral-5_MLN


title: human 4-cell-2-2


title: Liver_3217_MOET

tag: embryo origin

value: Male

value: Liver


title: Liver_3209_IVP

tag: age (days)

value: Holstein


title: Control3

value: untreated


title: human 4-cell-1-3


title: procyclic form trypanosome, TRRM2 RNAi strain, tetracycline NOT added

city: hengyang

first: Logen

last: Liu

state: --- Select a state ---

address: 35. Libration Ave. the second affiliated hospital

institute: university of south china

description:
Direct RNA sequencing for poly(A) tail length evaluation
trrm2_0h

data_processing:
basecalling with Guppy, mapped to genome (release 56) with minimap2 (-ax map-ont), poly(A) tail finding and annotation with tailfindr
Assembly: trypanosoma brucei TREU927, release 56
Supplementary files format and content: CSV, poly(A) tail length of each read and its corresponding mapped mRNA ID

organism: Trypanosoma brucei

source_name: procyclic form

growth_protocol: SDM79, 10%FBS, 5% CO2, 27centigrade

extract_protocol:
Trizol
SQK-RNA002
Direct RNA sequencing of poly(A) enriched mRNA

treatment_protocol: tetrycycline induced RNAi for 48 h or not

value: procyclic form

tag: cell line

value: Lister 427, TRRM2 RNAi


title: Control2


title: human 4-cell-1-2

state: CA


title: 6w_C-3_MLN


title: procyclic form trypanosome, CPSF30 RNAi strain, tetracycline added 48h, rep1

description:
Direct RNA sequencing for poly(A) tail length evaluation when CPSF30 knockdown
cpsf30_48h

value: Lister 427, CPSF30 RNAi

tag: cell type

value: CPSF30 kncokdown

value: tetracycline


title: procyclic form trypanosome, TRRM2 RNAi strain, tetracycline added 48h

description:
Direct RNA sequencing for poly(A) tail length evaluation when TRRM2 knockdown
trrm2_48h

value: TRRM2 knockdown


title: 6w_Oral-4_MLN


title: human 4-cell-1-1

value: Han Chinese


title: 6w_C-1_MLN


title: procyclic form trypanosome, CPSF30 RNAi strain, tetracycline NOT added

description:
Direct RNA sequencing for poly(A) tail length evaluation
cpsf30_0h


title: procyclic form trypanosome, CPSF30 RNAi strain, tetracycline added 48h, rep2

description:
Direct RNA sequencing for poly(A) tail length evaluation when CPSF30 knockdown
cpsf30_48h_rep2


title: Control1


title: WT-LK-2

status: Public on Jun 29 2022

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the mm9 genome assembly using Tophat
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples.

source_name: Lin- Kit+ Bone marrow cells

growth_protocol: Total bone marrow cells were isolate from WT and Ripk3-KO mice, and sorted with Lin-, Sca1+ and Kit+ markers.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LSK and LK cells from transgenic mice without any treatment

tag: strain background

tag: genotype/variation

value: wild type

value: Bone marrow

value: Lin- Kit+ Bone marrow cells


title: Ripk3-KO-LK-2


title: WT-LK-1


title: WT-LSK-1

source_name: Lin- Sca1+ Kit+ WT-Bone marrow cells

value: Lin- Sca1+ Kit+ WT-Bone marrow cells


title: WT-LSK-2


title: Ripk3-KO-LK-1