title: 15/R57t: Fetal Ovary Early Gestation_rep6

description: RNA from whole fetal ovary

tag: gestational age [days]


title: Mid_3

status: Public on Mar 04 2022

type: SRA

city: Oxford

first: Alun

last: Vaughan-Jackson

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Raw pair-end reads (150bp) were pre-processed using fastp 0.20.1 software with following additional parameters: --trim_poly_x, --correction, --detect_adapter_for_pe
Salmon 1.3.0 selective alignment was used for transcript mapping to a full decoy-aware transcriptome using the Gencode version 34 reference human transcriptome and GRCh38 primary assembly genome. Optional parameters used: --validateMappings, --seqBias, --gcBias, --dumpEq
The counts were imported, scaled to the average transcript length over samples and the library size (‘LengthScaledTPM’), and summarised to the gene level using the tximport package (v.1.16.0)
Lowly expressed genes with length-scaled abundance estimates less than 10 in 3 samples were filtered out with the default filtering function in the edgeR package
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon quantification files (quant.sf) for each sample with transcript length , effective length , estimated abundances and TPM values

molecule: total RNA

organism: Homo sapiens

source_name: Macrophages plated at mid density, cultured in OXM

growth_protocol: Differentiation of iPSC into iPSC-Macs was carried out as previously described (Vaughan-  Jackson et al., 2021; van Wilgenburg et al., 2013) culturing in OXM medium and with the final 7 day  differentiation occurring with cells plated at stated densities.

extract_protocol:
Lysates were passed through QIAshredder columns (QIAGEN) and the total RNA extracted using a QIAGEN RNeasy Mini kit, according to the manufacturer’s protocol using on-column DNase treatment (QIAGEN). RNA samples were eluted in 50 µL of RNase-free water. The quantity and quality of RNA was measured by Nanodrop and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies), with measured RNA integrity (RIN) values ≥8.8.The mRNA fraction was selected from the total RNA for each sample before conversion to cDNA.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

tag: cell type

value: iPSC-derived macrophages

tag: batch

tag: rin

tag: density

value: mid


title: LNCAP_DMSO_rep3

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description: Transcriptional profiling (RNA sequencing)

data_processing:
The first 4 nucleotide was removed from the sequenced reads using fastx_trimmer (FASTX Toolkit 0.0.13). The low quality nucleotides from the end of each read was removed using fastq_quality_trimmer (FASTX Toolkit 0.0.13) with -Q 33 -t 20 -l 25 parameters. Only the first sequenced read form the pair end (R1) was used for the downstream analysis.
The fastq files were mapped to the hg19 genome using tophat (v2.1.0) with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene was calculated using htseq-count (0.11.2) with -s no -a 0 -t exon -m intersection-nonempty parameters and hg19 gencode.v19 annotation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HTSeq-count text files.

source_name: LNCaP human PCa cell line

growth_protocol: Cells were cultured in 5% FBS DMEM.

extract_protocol:
Total RNA was isolated using peqGOLD TriFast (Peqlab, Erlangen, Germany) according to the manufacturer’s protocol.
Sequencing library was prepared using SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian (TAKARA).

treatment_protocol: Cells were treated in DMEM for 72h with DMSO or 1nM R1881(SAL) or 1pM R1881(LAL).

tag: cell line

value: LNCaP

value: Prostate cancer cell line

tag: treatment

value: DMSO (Control)


title: Vehicle Interval exercise (VI, n = 4)

city: Matsumoto

first: Xiaoran

last: Cui

address: 3-1-1 Asahi

country: Japan

institute: Shinshu University

data_processing:
Basecalls performed using Illumina Nova6000 p150
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by fastp(Version 0.23.2)
Indexes of the reference genome was built using STAR   and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used   the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result   for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of 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,   Reads Per Kilobase of exon model per Million mapped reads, 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 (Mortazavi et al., 2008)
Genome_build: mm10
Supplementary_files_format_and_content: txt files include FPKM values for each Sample
Supplementary_files_format_and_content: txt files include rawcounts for each Sample

organism: Mus musculus

source_name: Liver

extract_protocol:
10 mg liver samples taken from each mouse and stored at -80 ̊ C were homogenized in TRIzol RNA isolation reagent (Invitrogen-Thermo Fisher, Tokyo Japan) and then pooled in 4 sample tubes (VS, VI, FS and FI groups, N = 4). The sample tubes were sent to Novogene (Nagoya, Japan) for analysis. Total RNA was extracted, and RNA purity and integrity were confirmed by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: AKR/J

tag: tissue

value: Liver

tag: age

value: post 16-week training (26-week-old)

tag: genotype

value: Apoa2c congenic mic


title: Vehicle Sedentary (VS, n = 4)


title: 15/R74t: Fetal Ovary Early Gestation_rep4

city: Adelaide

first: Katja

last: Hummitzsch

state: SA

address: Level 5, North Tce/George Street

department: Obstetrics& Gynaecology

country: Australia

institute: The University of Adelaide

description: RNA from whole fetal ovary

data_processing:
pre-alignment QA/QC and base trimming in Partek Flow, version 8
alignment using STAR 2.7.3a aligner for bovine genome ARS-UCD1.2 and Partek E/M annotation model in Partek Flow, version 8
filter counts and normalized counts were determined in Partek Flow, version 8
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each gene and each sample

molecule: polyA RNA

organism: Bos taurus

source_name: fetal ovary

extract_protocol:
Fetal ovaries were removed from fetuses, flash frozen on dry ice, and RNA was harvested using Trizol reagent (including homogenisation).
Single-end Poly A-selection mRNA libraries (~35m reads per sample) were created using the Nugen Universal Plus mRNA-Seq library kit from Tecan (Mannedorf, Switzerland) and sequenced with an Illumina Nextseq 500 using single read 75bp (v2.0) sequencing chemistry (Illumina Inc., San Diego, CA, USA). Two sequencing runs, with 10 samples per run, were performed and sample 15/R43t was used as internal control in both runs.

value: fetal ovary

tag: crown-rump-length [cm]


title: LNCAP_DMSO_rep2


title: 15/R86t: Fetal Ovary Early Gestation_rep3

description: RNA from whole fetal ovary


title: Mid_2


title: TTS

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

description: CD45+ cells sorted from heart

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.0) used for cell barcode and UMI counting
STAR (v2.7.3a) used for mouse reference genome (mm10) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Genome_build: mm10
Supplementary_files_format_and_content: tsv files include UMI counts for each cell barcode and genes

source_name: heart

extract_protocol:
hearts were harvest, minced, washed with cold PBS, digested with collagenase to get single cell suspension. The cells were stained with anti-CD45 antibody for FACS sorting. Dead cells were excluded by live-dead dye staining.
Single cells were encapsulated into emulsion droplets using Chromium controller (10X genomics). The scRNA seq libraries were prepared using the chromium single cells 3’ regent kit (V3) (10X genomics) according to the manufacturer’s protocol. scRNA-seq libraries were evaluated and quantified by Agilent Bioanalyzer using High sensitivity DNA kit and Qubit. Individual libraries were diluted and pooled for sequencing. Pooled libraries were sequenced with Illumina NovaSeq platform.
single cell RNA-seq

treatment_protocol: 200 mg/kg isoproterenol (ISO), intraperitoneal injection, 24 hours.

value: heart

tag: Sex

value: female

value: CD45+ cells


title: LNCAP_DMSO_rep1


title: 15/R85t: Fetal Ovary Early Gestation_rep2

description: RNA from whole fetal ovary


title: C42_LAL_rep3

source_name: C4-2 human PCa cell line


title: Mid_1


title: 4T1-WT_rep2

city: Seoul

first: Sean

last: Oh

address: Gwanakro

country: South Korea

institute: Seoul National University

data_processing:
Before the data analysis, the adapter sequence was removed by the Trimmomatic 0.38 program.
HISAT2 (version 2.1.0) program was used for the reference genome mapping with genomic DNA reference UCSC mm10.
Transcript assembly was performed through StringTie (version 1.3.4d) program with the reference-based aligned reads information.
Further DEG (Differentially Expressed Genes) analysis was performed with the significant DEG results selected under these conditions: |fc|>=2 & exactTest raw p-value<0.05.
With the significant gene lists, gene-set enrichment analysis (GSEA) was conducted based on KEGG database (http://www.genome.jp/kegg/).
Genome_build: UCSC mm10.
Supplementary_files_format_and_content: The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value was used for extracting expression profile.

source_name: 4T1 cell line

growth_protocol: Grow 4T1 breast cancer cell line in RPMI growth medium

extract_protocol:
Total RNA was extracted from the cells using easy-spin Total RNA Extraction Kit (#17221, iNtRON Biotechnology Inc., Seongnam, Korea).
RNA samples were proceeded for library construction according to TruSeq Stranded mRNA Sample Preparation Guide (Part #15031047 Rev. E).
For the quality of data on Illumina sequencing platforms, the libraries were quantified by qPCR according to the Illumina qPCR Quantification Protocol Guide.

treatment_protocol: 4T1 cells were treated with GPD2 gRNA and CRISPR/Cas9 containing vector.

value: BALB/c

value: breast cancer cell

value: wildtype


title: C42_LAL_rep2


title: C42_LAL_rep1


title: Low_3

source_name: Macrophages plated at low density, cultured in OXM

value: low


title: Single cell profiling from 4 stages of tomato SBR development

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

description: Sample contains 3087 cells. Barcodes are described in included readme file

data_processing:
Low quality and long polyA reads were filtered using custom scripts. zUMI pipeline was used to alignment the reads to the ITAG4 tomato genome. The 3' UTR of all genes was extended by 500bp.
Based on raw count data, cells were filltered based on the following criteria: cells with less than 800 genes or 1000 UMI or cells with 50,000 UMIs. Genes expressed in less than 50 cells were removed.
Batch correction using harmony (RunHarmony( group.by.vars = c("Stage","Batch"), reduction="pca", theta = c(0,0), sigma = 0.05, max.iter.harmony = 30, max.iter.cluster = 60, dims.use = 1:20))
Normalization was performed using Seurat 3 (NormalizeData with default parameters)
Genome_build: ITAG4
Supplementary_files_format_and_content: CSV file of expression counts following filtering and batch correction.

organism: Solanum lycopersicum

source_name: Disassociated cells from tomato internode 1

growth_protocol: Tomato seeds were germinated in soil and grown in a growth chamber under long day conditions(16h/8h light/dark cycles). Temperature was 24c in light and 18c in dark.

extract_protocol:
RNA was amplified from sorted protoplasts according to the mcSCRB-Seq protocol (Bagnoli et al., Nature Communications, 2018)
Library construction was performed using Nextera XT kit according to manufactorere instructions

tag: development stage

value: pooled 4 stages


title: HCT116_WT_Pae1_rep2

description: transcriptional profiling (RNA sequencing)

data_processing:
Fastq files quality check was performed using FastQC v0.11.5.
The fastq files were mapped to the hg9 genome using TopHat v2.1.0 with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene is calculated by HTSeq-Count 0.11.2 with -s no -a 0 -t exon -m intersection-nonempty parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Htseq-count text file

source_name: HCT116 cell line

growth_protocol: HCT116_TP53_WT, and HCT116_TP53_KO cells were cultured in RPMI (GIBCO) medium supplemented with 10% FCS, 1mM Sodium pyruvate and 1X Glutamax.

extract_protocol:
Total RNA was isolated with the use of QIAzol Lysis (Qiagen) followed by isopropanol precipitation. Then, concentration and integrity RNAestimated with the use of Fragment Analyzer (Agilent) and Qubit 4 Fluorometer (Thermo Fisher). Poly-A tail mRNA was enriched using magnetic beads.
First stand of cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher), and second strand was synthesized using the second strand master mix (TruSeq RNA Library Prep Kit V2 (Illumina)). The synthesized DNA was cleaned up with the use of AgencourtAMPure XP Beads (Beckman Coulter). After, end repair/dA-tailing, adaptors were ligated, and the library was further enriched with the use of TruSeq RNA Library Prep Kit V2 (Illumina). After determining quality and concentration, the cDNA libraries were pooled and loaded (20 pM) into the NextSeq 500 (Illumina) Sequencer with the use of NextSeq 500/550 High Output Kit v2.5(75 cycles).

treatment_protocol: For RNAseq analysis, HCT116_TP53_WT, and HCT116_TP53_KO cells (1  × 105cells/ well) were seeded in a 6-well plate. Next day, cells were treated with either aMan1 (25 μM) or Pae1 (10 μM) for 42 h.

value: TP53 wild type

value: Treated with Pae1


title: 15/R12t: Fetal Ovary Early Gestation_rep1

description: RNA from whole fetal ovary


title: Control

description: CD45+ cells sorted from heart


title: CD45Pos_eAT_SVF_WL_HTO&ADT

city: Nashville

first: Matthew

middle: A

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

country: USA

institute: Vanderbilt University Medical Center

description:
4 biological replicates pooled; 18 weeks high-fat diet, then 9 weeks low-fat diet
4808-HCF-3_FB

data_processing:
Library strategy: CITE-seq
Alignment, filtering, barcode counting, and UMI counting using 10X CellRanger Count (CellRanger V3) with default settings.
Data filtering by nFeatures_RNA > 200, nCount_RNA > 500, and %mtRNA < 5.
Normalization of RNA assay using Seurat v4.0.3 with default settings.
Normalization of CITE-seq assay using Seurat v4.0.3 with method="CLR".
Normalization of hashtag assay using Seurat v4.0.3 with method="CLR".
Hashtag demultiplexing using Seurat v4.0.3 with default settings and filtering for singlets
Data integration using Seurat v4.0.3 with reduction = 'rpca'
Genome_build: mm10
Supplementary_files_format_and_content: *counts.csv.gz: comma separated value files for matrix table with raw feature counts for every cell
Supplementary_files_format_and_content: *data.csv.gz: comma separated value files for matrix table with log10 normalized feature counts for every cell using Seurat v4.0.3 NormalizeData with default settings for GEX assay and normalization.method="CLR" for HTO and ADT (feature barcoding) assays
Supplementary_files_format_and_content: comma separated value files for matrix table with scaled feature counts for every cell using Seurat v4.0.3 with default settings
Supplementary_files_format_and_content: comma separated value file containing cell metadata
Supplementary_files_format_and_content: comma separated value files for matrix containing dimensional reduction embeddings for each cell
Supplementary_files_format_and_content: R object file containing fully integrated Seurat object

source_name: epididymal adipose tissue leukocytes

extract_protocol:
Epididymal adipose tissue was collagenase digested using Collagenase Type 2 (Worthington) for 30 minutes at 37 degrees C. Red blood cells were lysed for 3 minutes using ACK lysis buffer. The stromal vascular fraction was collected after centrifugation at 400RCF for 8 minutes. Cells were immunolabeled with anti-CD45 magnetic beads (Miltenyi) and sorted on an AutoMACs (Miltenyi) using the `possel_s` setting. The positive magnetic fraction (CD45+ cells) were sorted for viability (DAPI-) on a BD FACSAria III.
Libraries were prepared according to manufacturer's instructions for 10X Chromium Single Cell 5' Reagent Kit v2 with the 5' Feature Barcode Library Kit by the Vanderbilt Technologies for Advanced Genomics core targeting 20,000 cells/lane and sequenced on a NovaSeq 6000 targeting 50,000 reads per cell.

value: epididymal adipose tissue

tag: diet group

value: weight loss

value: leukocyte


title: Low_2

value: iPSC-derived macrophages


title: D3_cKO_3

city: Xiamen

first: Yongchao

last: Liu

address: School of life sciences, Xiamen Univesity, Xiamen, Fujian. 361102, P.R.China

country: China

institute: Xiamen University

data_processing:
The sequencing data was filtered to get clean reads with SOAPnuke (v1.5.2) and stored in FASTQ format.
HISAT2 (V2.0.4) software was applied to map the clean reads to the reference genome.
Bowtie2 (v2.2.5) software was used to align the clean reads to the reference coding gene set.
RSEM (V1.2.12) software was used to calculate the expression level of genes.
Pheatmap (v1.0.8) software was used to get the heatmap according to the gene expression.
DESeq2 (v1.4.5) software was used to perform the differential expression analysis with Q value less than or equal to 0.05.
Gene Ontology (GO) (http://geneontology.org/) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) (https://www.kegg.jp/) enrichment analysis of different expressed genes was performed by Phyper based on Hypergeometric test.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: text files include Read count for each Sample

source_name: OT-I cells

extract_protocol:
RNA was extracted from IL-2 stimulated OT-I WT and OT-I Themis cKO cells using the RNeasy Mini Kit (QIAGEN, 74104).
RNA libraries were prepared for sequencing using standard DNBSEQ-G400 protocols

treatment_protocol: Freshly enriched naïve OT-I WT and OT-I Themis cKO cells were stimulated with IL2 (1μg/ml) in vitro for 3 days.

value: OT-I

value: Spleen/LNs

value: Themis cKO


title: Low_1


title: HCT116_WT_Pae1_rep1


title: CD45Pos_eAT_SVF_Obese_HTO&ADT

description:
4 biological replicates pooled; 9 weeks low-fat diet, then 18 weeks high-fat diet
4808-HCF-2_FB

value: obese


title: Sample 16: LINC00881 knockdown rep 4

city: New York

first: Veli

middle: K

last: Topkara

state: NY

department: Cardiology

institute: Columbia University

description: Sample 16 - (VX20218)

data_processing:
Read alignment performed using the splice-aware aligner STAR v.2.7.3a
Genome_build: Gencode v38

source_name: human iPS cell derived cardiomyocytes

growth_protocol: iPSCs were maintained in RPMI 1640 with B27 supplement. Experiments were performed using cells at day 15 - 35.

extract_protocol:
Qiagen RNeasy kit was used to isolate RNA following manufacturer's guidelines. DNAse digestion on column was performed.
Sequencing libraries were constructed using the TruSeq Stranded Total RNA Library Prep Gold mRNA (Illumina, San Diego CA) with an input of 1000ng and 11 cycles final amplification.

treatment_protocol: LINC000881 knockdown was achieved by lipofectamine based transfection of antisense LNA GapmeRs designed against LINC00881 versus scrambled oligonucleotide. LINC000881 overexpression was achieved by lipofectamine based transfection of LINC00881 plasmid versus bacterial alkaline phosphatase control plasmid.

value: human induced pluripotent stem cell derived cardiomyocytes (iPSCs)

tag: genotype/variation

value: LINC00881 knockdown


title: HCT116_WT_DMSO_rep2

value: Treated with DMSO(Control)


title: CD45Pos_eAT_SVF_Lean_HTO&ADT

description:
4 biological replicates pooled; 27 weeks low-fat diet
4808-HCF-1_FB

value: lean


title: D3_cKO_2


title: High_1

source_name: Macrophages plated at high density, cultured in OXM

value: high


title: Sample 15: LINC00881 knockdown rep 3

description: Sample 15 - (VX20215)


title: HCT116_WT_DMSO_rep1


title: CD45Pos_eAT_SVF_WC_GEX

description:
4 biological replicates pooled; 9 weeks high-fat diet, then 9 weeks low-fat diet, then 9 weeks high-fat diet
4808-HCF-4

value: weight cycled


title: D3_WT_3

value: wild-type


title: Sample 14: LINC00881 knockdown rep 2

description: Sample 14 - (VX20214)


title: HCT116_WT_aMan1_rep2

value: TP53 wild type

value: Treated with aMan1


title: CD45Pos_eAT_SVF_WL_GEX

description:
4 biological replicates pooled; 18 weeks high-fat diet, then 9 weeks low-fat diet
4808-HCF-3

value: epididymal adipose tissue


title: CD45Pos_eAT_SVF_Obese_GEX

description:
4 biological replicates pooled; 9 weeks low-fat diet, then 18 weeks high-fat diet
4808-HCF-2


title: Sample 12: control knockdown rep 4

description: Sample 12 - (VX20217)

value: control knockdown


title: CD45Pos_eAT_SVF_Lean_GEX

description:
4 biological replicates pooled; 27 weeks low-fat diet
4808-HCF-1

value: leukocyte


title: Sample 13: LINC00881 knockdown rep 1

description: Sample 13 - (VX20213)


title: Sample 11: control knockdown rep 3

description: Sample 11 - (VX20216)


title: HCT116_KO_aMan1_rep1

value: TP53 knockout


title: D3_WT_1

value: OT-I


title: LR-4-Rep2

data_processing:
Reads were aligned to the tomato genome ITAG4 and expression quantified using salmon 1.3.0. As the library is 3’ biased, we extended all genes to cover 500 additional base pairs downstream. Parameters for salmons were: --noLengthCorrection --noEffectiveLengthCorrection --validateMappings
Expression data were normalized using Deseq2
Genome_build: Solanum lycopersicum ITAG4
Supplementary_files_format_and_content: Raw expression reads for all replicates

source_name: Section of primary root - lateral root stage 4

growth_protocol: Tomato M82 DR5::VENUSx3-NLS seedlings were germinated on agar plates (1/2 strengh MS, 0.5% sucrose, 0.8% agar)

extract_protocol:
For each plant lateral root stage was determine by DR5 flourescene under a stereoscope and a section of the primary root containing the lateral root primorida was microdissected and flash frozen. RNA was extracted usin QIAGEN microRNA extraction kit and treated with DNase I.
sequencing libraries prepared using Lexigen 3’ Quant-Seq kit, according to the manufacturer instructions.

value: Section of primary root containing lateral roots at Stage 4 - when the root primorida is in the middle of the cortex


title: HCT116_KO_DMSO_rep2

value: TP53 knock out


title: HCT116_KO_Pae1_rep2

value: Treated with Pae1


title: LR-5-Rep2

source_name: Section of primary root - lateral root stage 5

value: Section of primary root containing lateral roots at Stage 5 - when the root primorida reaches the epidermis, but before emergence


title: HCT116_KO_Pae1_rep1


title: CD45Pos_eAT_SVF_WC_HTO&ADT

description:
4 biological replicates pooled; 9 weeks high-fat diet, then 9 weeks low-fat diet, then 9 weeks high-fat diet
4808-HCF-4_FB


title: LR-3-Rep2

source_name: Section of primary root - lateral root stage 3

value: Section of primary root containing a lateral root at Stage 3 - primorida passes the endodermis


title: HCT116_KO_DMSO_rep1

value: Treated with DMSO(Control)


title: LR-2-Rep2

source_name: Section of primary root - lateral root stage 2

value: Section of primary root containing a lateral root at Stage 2 - first periclinal division


title: Sample 8: LINC00881 overexpression rep 4

description: Sample 8 - 881OE (16)

value: human induced pluripotent stem cell derived cardiomyocytes (iPSCs)

value: LINC00881 overexpression


title: HCT116_KO_aMan1_rep2


title: LR-1-Rep2

source_name: Section of primary root - lateral root stage 1

value: Section of primary root containing a lateral root at Stage 1 - when two cells express DR5


title: D3_cKO_1

value: Spleen/LNs

value: Themis cKO


title: Sample 21: Genomic DNA from cardiac left ventricle

type: genomic

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BMIQ normalization, batch correction, and merged on common 450K and Infinium EPIC probes

label: Cy3, Cy5

molecule: genomic DNA

source_name: cardiac left ventricle

label_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k or EPIC Beadchip using standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from Human Left Ventricle samples using Qiagen DNeasy Kit according to standard instructions

value: cardiac left ventricle

value: Unknown

tag: gender

tag: race/ethnicity

tag: hf etiology

value: Non-Failing

tag: lvad status


title: Sample 7: LINC00881 overexpression rep 3

description: Sample 7 - 881OE (15)

tag: cell type


title: HCT116_WT_aMan1_rep1

value: TP53 wild type

value: Treated with aMan1


title: Sample 6: LINC00881 overexpression rep 2

description: Sample 6 - 881OE (14)


title: LR-0-Rep2

source_name: Section of primary root - No lateral roots

value: Section of primary root from the differentiation zone with no lateral roots


title: SW48_Pae1_rep2

source_name: SW48 cell line

growth_protocol: SW48, BjhTert cells were cultured in RPMI (GIBCO) medium supplemented with 10% FCS, 1mM Sodium pyruvate and 1X Glutamax.

treatment_protocol: For RNAseq analysis, SW48, BjhTert, cell lines (1  × 105cells/ well) were seeded in a 6-well plate. Next day, cells were treated with Pae1 (10 μM) for 42 h.


title: D3_WT_2

value: OT-I

value: wild-type


title: LR-5-Rep1

value: Section of primary root containing lateral roots at Stage 5 - when the root primorida reaches the epidermis, but before emergence


title: Sample 5: LINC00881 overexpression rep 1

description: Sample 5 - 881OE (13)


title: SW48_Pae1_rep1

value: Treated with Pae1


title: LR-4-Rep1

value: Section of primary root containing lateral roots at Stage 4 - when the root primorida is in the middle of the cortex


title: Sample 4: control overexpression rep 4

description: Sample 4 - BAP (12)

value: control overexpression


title: xSW48_DMSO_rep2

value: Treated with DMSO(Control)


title: LR-3-Rep1

value: Section of primary root containing a lateral root at Stage 3 - primorida passes the endodermis


title: Sample 10: control knockdown rep 2

description: Sample 10 - (VX20212)

value: human induced pluripotent stem cell derived cardiomyocytes (iPSCs)

value: control knockdown


title: Sample 3: control overexpression rep 3

description: Sample 3 - BAP (11)


title: xSW48_DMSO_rep1


title: Sample 2: control overexpression rep 2

description: Sample 2 - BAP (10)


title: LR-2-Rep1

value: Section of primary root containing a lateral root at Stage 2 - first periclinal division


title: Sample 9: control knockdown rep 1

description: Sample 9 - (VX20211)


title: BJhTert_Pae1_rep2

source_name: BjhTERT cell line

value: BjhTERT


title: hiHep [re-analyzed]

type: RNA

city: YOKOHAMA

first: Yun-Zhong

last: NIE

state: Kanagawa

address: 3-9, Fukuura, Kanazawa-ku

department: Department of Regenerative Medicine

institute: Yokohama City University Graduate School of Medicine

description: Gene expression of D22-Hep

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for micro array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: hiHep

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: hiHep is hiPSC derived hepatocyte, and HPC is induced from hiHep with reprogrammed medium.

extract_protocol: RNA was prepared using a PureLink™ RNA Mini Kit (Invitrogen, San Diego, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: hiPSC-Hep


title: Sample 1: control overexpression rep 1

description: Sample 1 - BAP (9)


title: ePHH

description: Gene expression of 78Y-PHH

source_name: ePHH

growth_protocol: yPHH and ePHH are primary human hepatocyte, and yHPC and eHPC are induced from yPHH and ePHH, respectively.

value: PHH


title: BJhTert_Pae1_rep1


title: LR-0-Rep1


title: Reox_Control_rep2

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

institute: University of Liverool

library_source: genomic

data_processing:
Reads in fastq files were trimmed for adaptors using Cutadapt and low quality score using Sickle. Reads were aligned to the human genome version hg38 (UCSC) using Bowtie2, sorted and indexed binary alignment mapped (bam) files with mitochondrial reads removed were generated using Samtools.
Bam files were filtered to keep ‘only properly paired reads’ following ENCODE guidelines using Samtools. PCR duplicates were removed from bam files using Picard.
Library sized normalised (reads per kb per million reads (RPKM)) bigwig files were made using deepTools.
Open chromatin regions were identified using MACS2 (--nomodel --shift -100 --extsize 200 -q 0.01) and filtered to remove ENCODE DAC hg38 blacklisted regions and regions with an FDR < 1x10-15.
Genome_build: hg38
Supplementary_files_format_and_content: bed files = peak data, chr start end. bigwig files = library sized normalised alignment data

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% v/v FBS, 2 mM L-glutamine, 50 units/mL penicillin and 50 μg/mL streptomycin at 5% CO2 and 37 °C. Cells were cultured for no more than 30 passages and routinely tested for mycoplasma contamination using MycoAlert Mycoplasma Detection Kit .

extract_protocol:
Omni-ATAC protocol (Corces 2017)
Standard ATAC-seq library construction

treatment_protocol: Hypoxia treatments were performed by incubating cells in an InvivO2 300 Hypoxia Workstation (Baker Ruskinn) at 1% O2, 5% CO2 and 37 °C. Lysis of hypoxia treated samples was carried inside the hypoxia workstation to avoid reoxygenation. Reoxygenation treatments were performed by incubating cells for 24h in hypoxia followed by 1h incubation at 21% O2, 5% CO2 and 37°C. Cells were transfected with 27 nM of small interfering RNA (siRNA) oligonucleotides (Eurofins) for 48h using Interferin (Polyplus) transfection reagent according to manufacturer’s instructions.

value: Control siRNA, 24 hs 1% oxygen then 1 h 21% oxygen (reoxygenation)

value: HeLa


title: HPC

description: Gene expression of D22-pHC

source_name: HPC

value: hiPSC-Hep-pHC


title: eHPC

description: Gene expression of 78Y-pHC

source_name: eHPC

value: PHH-HPC


title: yHPC

description: Gene expression of 2M-pHC

source_name: yHPC


title: 50d-Hep

description: Gene expression of D72-Hep

growth_protocol: hiHep, 30d-Hep and 50d-Hep are hiPSC derived hepatocyte at different culture time points.


title: xBJhTert_DMSO_rep2


title: 30d-Hep

description: Gene expression of D52-Hep


title: hiHep

description: Gene expression of D22-Hep


title: SHAPE-MaP analysis of SARS-CoV (2A3 treatment)

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: In vitro refolded SARS-CoV genome, 2A3 treated

data_processing:
Library strategy: SHAPE-MaP
All the analysis steps, from reads alignment to data normalization, were performed using RNA Framework. All tools referenced in the following paragraphs are distributed as part of the RNA Framework suite (https://github.com/dincarnato/RNAFramework). The following parameters were used: rf-map (-b2 -cq5 20 -ctn -cmn 0 -mp '--very-sensitive-local'), rf-count (-m -rd), and rf-norm (-sm 3 -nm 3 -mm 1 -n 1000).
Supplementary_files_format_and_content: Additional data files are available at: http://www.incarnatolab.com/datasets/SHAPEwarp_Morandi_2022.php

organism: Severe acute respiratory syndrome-related coronavirus

source_name: SARS-CoV (2A3)

extract_protocol:
To 1 mL of infected cells in QIAzol Lysis Reagent, 200 μl of chloroform were added. The sample was vigorously vortexed for 15 sec and then incubated for 2 min at room temperature, after which it was centrifuged for 15 min at 12,500 x g (4°C). The upper aqueous phase was collected in a clean 2 mL tube, supplemented with 1 mL (~2 volumes) of 100% ethanol, and then loaded on a Monarch® RNA Cleanup Kit column (NEB, cat. T2030L). In vitro folding was carried out as previously described10,22. Briefly, ~5 μg of total RNA from infected cells was first depleted of ribosomal RNAs using the RiboMinus™ Eukaryote System v2 (ThermoFisher Scientific, cat. A15026), as per manufacturer instructions. rRNA-depled RNA in a volume of 39 μl was denatured at 95°C for 2 min, then transferred to ice for 1 min. 10 μl of ice-cold 5X RNA Folding Buffer [500 mM HEPES pH 7.9; 500 mM NaCl] supplemented with 20 U of SUPERase•In™ RNase Inhibitor (ThermoFisher Scientific, cat. AM2696) were added. RNA was then incubated for 15 min at 37°C to allow secondary structure formation. Subsequently, 1 μl of 500 mM MgCl2 (pre-warmed at 37°C) was added and RNA was further incubated for 15 min at 37°C to allow tertiary structure formation. For probing of RNA, 2A3 was added to a final concentration of 100 mM (assuming a stock concentration of 1 M). An equal volume of DMSO was added to the control samples. Samples were then incubated at 37°C for 5 min. Reactions were quenched by the addition of 1 volume DTT 1 M and then purified on Monarch® RNA Cleanup Kit columns.
SHAPE-MaP library preparation was conducted as previously described, with minor changes. Probed RNA was first fragmented to a median size of 150 nt by incubation at 94°C for 8 min in RNA Fragmentation Buffer [65 mM Tris-HCl pH 8.0; 95 mM KCl; 4 mM MgCl2], then purified on Monarch® RNA Cleanup Kit columns and eluted in 8 μl NF H2O. Eluted RNA was end repaired by treatment with 1 U of rSAP (NEB, cat. M0371L) at 37°C for 30 min, plus 5 min at 70°C to heat-inactivate the enzyme, followed by treatment with 20 U of T4 PNK (NEB, cat. M0201L), in the presence of 1 mM ATP, at 37°C for 1 hour. 50 ng of end-repaired RNA was first ligated to 10 pmol of a pre-adenylated 3’ adapter (rApp-AGATCGGAAGAGCACACGTCT-SpC3) using 200 U of T4 RNA Ligase 2 truncated KQ (NEB, cat. M0373L), in the presence of 12.5% PEG-8000, for 1 hour at 25°C. 10 pmol of a 5’ RNA adapter (CUACACGACGCUCUUCCGAUCU) was then ligated using 30 U of T4 RNA Ligase 1 (NEB, cat. M0437M), in the presence of 1 mM ATP and 8% PEG-8000, at 25°C for 1 hour. The adapter-ligated RNA was then supplemented with 10 pmol of RT primer (AGACGTGTGCTCTTCCGATCT), incubated at 70°C for 5 min and immediately transferred to ice for 1 min. Reverse transcription reactions were conducted in a final volume of 10 μl. Reactions were supplemented with 2 μl 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl], 1 μl DTT 0.1 M, 0.5 μl dNTPs 10 mM, 20 U SUPERase•In™ RNase Inhibitor and 100 U SuperScript II (Thermo Fisher Scientific, cat. 18064014). Reactions were incubated at 42°C for 2 hours. RNA was degraded by addition of 1 μl NaOH 5 N, followed by incubation at 95°C for 3 min. After purification, barcodes were introduced by PCR, using NEBNext® High-Fidelity 2X PCR Master Mix (NEB, cat. M0541L) and NEBNext® Multiplex Oligos for Illumina® Dual-Index primers (NEB, cat. E7780S).

treatment_protocol: Infection with SARS-CoV and SARS-CoV-2 was conducted as previously described. Briefly, Vero E6 cells were cultured in DMEM (Lonza, cat. 12-604F), supplemented with 8% FCS (Bodinco), 2 mM L-glutamine, 100 U/mL of penicillin and 100 µg/mL of streptomycin (Sigma Aldrich, cat. P4333-20ML). Cells were infected with either SARS-CoV or SARS-CoV-2 in EMEM (Lonza, cat. 12-611F) supplemented with 25 mM HEPES, 2% FCS, 2 mM L-glutamine, and penicillin/streptomycin. 16 h after the infection, infected cells were harvested by trypsinization, followed by resuspension in EMEM supplemented with 2% FCS, washed with 50 mL 1X PBS, and then resuspended in 1 mL of QIAzol Lysis Reagent (Qiagen, cat. 79306). All experiments with infectious SARS-CoV/SARS-CoV-2 were performed in a biosafety level 3 facility at the LUMC.


title: Reox_Control_rep1


title: xBJhTert_DMSO_rep1


title: SHAPE-MaP analysis of SARS-CoV (DMSO treatment)

description: In vitro refolded SARS-CoV genome, DMSO treated

source_name: SARS-CoV (DMSO)

value: DMSO


title: 24h_Hpx_siHIF1β_rep2

value: HIF1B siRNA, 24 hs 1% oxygen (hypoxia)


title: SW48_DMSO_rep2

treatment_protocol: For RNAseq analysis, SW48, BjhTert, cell lines (1  × 105cells/ well) were seeded in a 6-well plate. Next day, cells were treated with aMan1 (25 μM) for 42 h.


title: Of_Silk gland_rep3

city: Hangzhou

first: Lei

last: Yang

address: Shiqiao Road

institute: Zhejiang Academy of Agricultural Science

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10（https://www.ncbi.nlm.nih.gov/genome/?term=Ostrina+furnacalis） whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Ostrina+furnacalis
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Ostrinia furnacalis

extract_protocol:
Samples were collected and froze on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 3rd  instar of the Asian corn borer

value: Silk gland

value: wild type


title: SW48_DMSO_rep1

tag: cell line

value: Treated with DMSO(Control)


title: Of_Silk gland_rep2


title: SW48_aMan1_rep2

tag: treatment

value: Treated with aMan1


title: 24h_Hpx_Control_rep2

value: Control siRNA, 24 hs 1% oxygen (hypoxia)


title: Of_Silk gland_rep1


title: SW48_aMan1_rep1


title: LR-1-Rep1

value: Section of primary root containing a lateral root at Stage 1 - when two cells express DR5


title: Sample 19: Genomic DNA from cardiac left ventricle

value: cardiac left ventricle

value: Unknown

value: Non-Failing


title: Of_Fat body_rep3

value: Fat body


title: BJhTert_DMSO_rep2

value: BjhTERT


title: Of_Fat body_rep2


title: 24h_Hpx_Control_rep1

value: HeLa


title: yPHH

description: Gene expression of 2M-PHH

source_name: yPHH

value: PHH


title: Of_Fat body_rep1


title: 1h_Hpx_Control_rep2

value: Control siRNA, 1 h 1% oxygen (hypoxia)


title: Of_Midgut_rep3

value: Midgut


title: Sample 17: Genomic DNA from cardiac left ventricle


title: 1h_Hpx_Control_rep1


title: BJhTert_aMan1_rep1


title: 24h_Hpx_siHIF1β_rep1

value: HIF1B siRNA, 24 hs 1% oxygen (hypoxia)


title: Sample 14: Genomic DNA from cardiac left ventricle

value: Male

value: White

value: Ischemic

value: post-LVAD


title: Of_Midgut_rep2

value: 3rd  instar of the Asian corn borer

value: wild type


title: Sample 15: Genomic DNA from cardiac left ventricle

value: Non-Ischemic

value: pre-LVAD


title: M07e_SEKIT_Peak1_rep2

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

data_processing:
Library strategy: 4C-Seq
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie2 v2.2.6. after clipping of bait sequence
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated from alignment BAM files using Bedtools v2.26.0

source_name: 4C-seq libraries

extract_protocol:
4C experiment was performed using a modified version of Simonis et al Nat Genet. 2006 Nov;38(11):1348-54 doi: 10.1038/ng1896
Libraries were constructed using a custom protocol,  adapters and barcodes

treatment_protocol: 4C-seq using SEKIT bait GGGTAAGCAAAGGTTAGGAAAGTGAATGATC

value: M07e cell line

value: hematopoietic cells


title: Of_Midgut_rep1


title: 0h_Hpx_siHIF1β_rep1

value: HIF1B siRNA, 0 h 1% oxygen (hypoxia)


title: BJhTert_aMan1_rep2

value: BjhTERT

value: Treated with aMan1


title: M07e_SEKIT_Peak1_rep1


title: 0h_Hpx_Control_rep2

value: Control siRNA, 0 h 1% oxygen (hypoxia)

value: HeLa


title: BJhTert_DMSO_rep1

value: Treated with DMSO(Control)


title: Of_hemolymph_rep3

value: hemolymph


title: Sample 12: Genomic DNA from cardiac left ventricle

value: cardiac left ventricle

value: Male


title: Sample 18: Genomic DNA from cardiac left ventricle

value: Unknown

value: Non-Failing


title: Sample 13: Genomic DNA from cardiac left ventricle

value: White

value: Ischemic


title: Sample 11: Genomic DNA from cardiac left ventricle


title: 1h_Hpx_siHIF1β_rep2

value: HIF1B siRNA, 1 h 1% oxygen (hypoxia)


title: 1h_Hpx_siHIF1β_rep1


title: PARE-Seq_nrpd1_3

city: Cambridge

first: Satyaki

last: PRV

state: MA

address: 455 Main street, Room number 549

institute: Whitehead Institute for Biomedical Research

description: nanoPARE

data_processing:
Library strategy: nanoPARE-Seq
Sequence data were filtered for quality with “ trim_galore -q 25 --phred64 --fastqc --length 20 --stringency 5”.
Filtered reads were aligned to the TAIR10 genome using “tophat  -i 30 -I 3000 --solexa1.3-quals -p 5 -g 5 --segment-mismatches 1 --segment-length 18 --b2-very-sensitive”
Fold Change for PARE-Seq reads at each nucleotide, genome-wide, was calculated using DESeq2.  DESeq2 output and a bedgraph file with fold change at sites with statisically significant differences are provided.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: Endosperm

growth_protocol: Plants were grown in a growth-chamber with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination (DAP). Seeds were dissected at seven DAP.

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total endosperm RNA isolated using the Ambion RNAqueous Micro Kit.
Nanopare libraries were constructed from endosperm RNAusing a protocol described in Schon et al (2018) https://genome.cshlp.org/content/early/2018/10/24/gr.239202.118

treatment_protocol: no treatment

value: Ler nrpd1-/- female x  Col-0 nrpd1-/- male F1

value: 7 days after pollination

value: Endosperm


title: Sample 9: Genomic DNA from cardiac left ventricle

value: African American

value: Non-Ischemic

value: pre-LVAD


title: Sample 8: Genomic DNA from cardiac left ventricle

value: Female

value: post-LVAD


title: 0h_Hpx_siHIF1β_rep2

value: HIF1B siRNA, 0 h 1% oxygen (hypoxia)

value: HeLa


title: PARE-Seq_nrpd1_2

description: nanoPARE

value: Ler nrpd1-/- female x  Col-0 nrpd1-/- male


title: Of_hemolymph_rep1

value: 3rd  instar of the Asian corn borer

value: hemolymph

value: wild type


title: Of_hemolymph_rep2


title: VH298_rep2

data_processing:
Reads in fastq files were trimmed for adaptors using Cutadapt and low quality score using Sickle. Reads were aligned to the human genome version hg38 (UCSC) using Bowtie2, sorted and indexed binary alignment mapped (bam) files with mitochondrial reads removed were generated using Samtools.
Bam files were filtered to keep ‘only properly paired reads’ following ENCODE guidelines using Samtools. PCR duplicates were removed from bam files using Picard.
Library sized normalised (reads per kb per million reads (RPKM)) bigwig files were made using deepTools.
Open chromatin regions were identified using MACS2 (--nomodel --shift -100 --extsize 200 -q 0.01) and filtered to remove ENCODE DAC hg38 blacklisted regions and regions with an FDR < 1x10-15.
Genome_build: hg38
Supplementary_files_format_and_content: bed files = peak data, chr, start and end postions. bigwig files = library sized normalised alignment data

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% v/v FBS, 2 mM L-glutamine, 50 units/mL penicillin and 50 μg/mL streptomycin at 5% CO2 and 37 °C. Cells were cultures for no more than 30 passages and routinely tested for mycoplasma contamination using MycoAlert Mycoplasma Detection Kit .

treatment_protocol: HeLa cells were treated with 100 µM VH298 for 24 hs. DMSO treated cells were used as control.

value: 100 µM VH298 for 24 hs


title: Sample 7: Genomic DNA from cardiac left ventricle

value: cardiac left ventricle

value: White

value: Ischemic


title: Sample 6: Genomic DNA from cardiac left ventricle

value: Male


title: 0h_Hpx_Control_rep1

value: Control siRNA, 0 h 1% oxygen (hypoxia)


title: PARE-Seq_WT_1

description: nanoPARE

value: Ler female x  Col-0 male F1

value: 7 days after pollination

value: Endosperm


title: Control_rep1

value: DMSO


title: Of_Adult_rep3

value: Adult

value: The whole insect


title: PARE-Seq_nrpd1_1

description: nanoPARE

value: Ler nrpd1-/-female x  Col-0 nrpd1-/- male F1


title: Sample 10: Genomic DNA from cardiac left ventricle

value: African American

value: Non-Ischemic

value: post-LVAD


title: VH298_rep1

value: HeLa


title: Sample 16: Genomic DNA from cardiac left ventricle


title: Of_Adult_rep2

value: wild type


title: Of_Adult_rep1


title: Control_rep2


title: Of_Pupa_rep2

value: Pupa


title: mRNAseq_LCN_wildtype_1

description: mRNA-seq

data_processing:
Sequence data were filtered for quality with “ trim_galore -q 25 --phred64 --fastqc --length 20 --stringency 5”.
Filtered reads were aligned to the TAIR10 genome using “tophat  -i 30 -I 3000 --solexa1.3-quals -p 5 -g 5 --segment-mismatches 1 --segment-length 18 --b2-very-sensitive”
Cuffdiff v2.2.1 with default settings and the ARAPORT11 genome annotation to calculate changes in gene expression and their statistical significance.
Genome_build: TAIR10
Supplementary_files_format_and_content: Cuffdiff output with details of differential expression in tab delimited format
Supplementary_files_format_and_content: merged_holdouts3.bed  file indicates Col regions remaining after back-crossing the nrpd1a-4 allele into the Ler background.

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total endosperm RNA isolated using the Ambion RNAqueous Micro Kit.
DNase I-treated RNA (Invitrogen, Life Technologies Corporation, Carlsbad, CA) was used to prepare mRNA-seq libraries using the SMARTerUltralowPOLYA kit at the Whitehead Institute's Genome Technology Core.


title: HCT116 USP1GGAA REP1

first: Tony

middle: T

last: Huang

address: 450 East 29th St, Rm 807

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

data_processing:
Library strategy: Replication mapping
PE Fastq files were quality and adaptor trimmed with Trim galore 0.5.0.
Aligned with bowtie2 2.4.1 to hg19 genome, default parameters.
BAM file filtered for paired end reads with MAPQ score > 30 (samtools 1.10).
Remove duplicates with Picard 2.18.11.
Convert to bedpe (bedtools 2.27.1) and split fragments mapping to W and C strands to separate files (custom python script).
Create histogram of coverage for every 1kb for W and C reads: deeptools 3.2.1 + custom python script.
Gene lists with TSS /TTS locations downloaded from UCSC genome browser and filtered to include only protein coding genes. Duplicates dropped based on gene symbol, keeping only the first version of the gene listed.
Further details: Lui et al., Nat Protoc, 2021; DOI: 10.1038/s41596-020-00454-5
Genome_build: hg19
Supplementary_files_format_and_content: txt files representing the density of Okazaki fragment 5' ends on the Watson or Crick strand across the genome (1kb bins); csv files representing the density of Okazaki fragment 5' ends around the initiation and termination sites of annotated genes (1kb bins, - 100kb to +100kb around sites) correspond to +/- 100kb around site.

source_name: HCT116 cell line

growth_protocol: HCT116 parental and mutant cells were grown at 60-70% confluency in 15-cm dishes under standard tissue culture conditions.

extract_protocol:
Frozen cell pellets were lysed in DNA lysis buffer containing 0.5% SDS and proteinase K overnight at 50 C, and then DNA was extracted using equal volume of phenol-chloroform and precipitated with ammonium acetate and ethanol.
Okazaki fragment libraries were generated by PCR amplification and  primer dimers were  removed using SPRI beads (Beckman) before analysis by Tapestation (Agilent) and Illumina sequencing.
Replication mapping was done using paired-end 50-bp with the NovaSeq 6000 Illumina sequencing platform and SP100flowcells.

treatment_protocol: Cells were pulsed labelled with EdU for 2 min for final 25 microMolar concentration before termination.

value: cell line origin from human colon carcinoma

value: USP1 GG670/671AA biallelic knock-in mutations


title: Sample 4: Genomic DNA from cardiac left ventricle

value: cardiac left ventricle

value: Male

value: White


title: mRNAseq_nrpd1_3

description: mRNA-seq

value: 7 days after pollination


title: mRNAseq_LCN_wildtype_2

description: mRNA-seq

value: Ler female x  Col-0 male F1

value: Endosperm


title: Sample 3: Genomic DNA from cardiac left ventricle

value: pre-LVAD


title: mRNAseq_nrpd1_2

description: mRNA-seq

value: Ler nrpd1-/ -female x  Col-0 nrpd1-/- male F1


title: Of_Pupa_rep3

value: The whole insect


title: RM_antiPD-L1_rep4

city: Jette

first: Kirsten

last: De Ridder

state: Brussel

address: Laarbeeklaan 103

department: Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for 20 hours as described in the manufacturer’s protocol.

scan_protocol: Samples are loaded onto the nCounter Prep Station for further purification and immobilization onto the sample cartridge. After transfer to the Digital Analyzer (MAX Analysis System, Brightcore, VUB) absolute counts are quantified.

data_processing: For quality control the nSolver_analysis_software_4.0 was used. Raw counts were processed in R and normalized using the RUVSeq method adjusted for NanoString analysis. The DESeq R-package was used for differential expression analysis.

label: Biotin

source_name: 3rd week LLC bearing lungs

label_protocol: After RNA was converted to cDNA and amplified using target-specific primers samples were mixed with a 3′ biotinylated capture probe and a 5′ reporter probe tagged with a fluorescent barcode from the nCounter Myeloid Innate Immunity Panel.

growth_protocol: LLC-Fluc cells were maintained in DMEM+ i.e., Dulbecco’s-Modified-Eagle’s-Medium supplemented with 10% fetal bovine serum (FBS, TICO Europe), 100units/mL penicillin, 100 µg/mL streptomycin and 2 mM L-Glutamine (all Sigma-Aldrich) at 37°C, 5% CO2,21% O2 and 95% humidity level. Female 6-week-old C57BL/6 mice were injected intravenously with 5x1e5 LLC-Fluc cells dissolved in 200 µl phosphate-buffered-saline (PBS). All animals were handled according to the institutional guidelines, approved by the Ethical Committee for use of laboratory animals VUB (ECD: 18-214-1 and 18-281-9).

extract_protocol: Myeloid immune cell types were sorted by FACS with a BD FACSAriaIII. 5x1e4 cells per condition were collected and stored in Trizol at -80°C prior to RNA extraction. RNA was isolated using the chloroform-isopropanol protocol. RNA recovery was quantified using fluorimetry (Qubit, LifeTechnologies) and qualified for purity and integrity using the nanophotometer (Implen) and Bioanalyzer Labchip (Agilent Technologies), resp. Due to low RNA concentrations, samples were pre-amplified using the nCounter Low-RNA-input kit (NanoString Technologies) with five amplification cycles.

treatment_protocol: Four days after LLC-Fluc challenge, mice were treated with four intraperitoneal injections of 200µg mAb dissolved in 200 µl PBS given at 3-day intervals (days 4, 7, 10 and 13). Half was injected with rat IgG2b isotype control (IC) mAb (clone: LTF-2) , other half with rat IgG2b anti-PD-L1 mAb (clone: 10F9G2), both Biolegend.

tag: strain

tag: sorted cell type

value: Ly6Clow monocytes

value: anti-PD-L1 mAb


title: RM_antiPD-L1_rep3


title: HCT116 USP1GGAA REP2


title: Sample 5: Genomic DNA from cardiac left ventricle

source_name: cardiac left ventricle

tag: tissue

tag: age

value: African American

value: Non-Ischemic


title: HCT116 USP1C90S REP1

tag: genotype

value: USP1 C90S biallelic knock-in mutations


title: M2_antiPD-L1_rep4

value: MHC-IIlow macrophages


title: HCT116 USP1KO REP2

value: cell line origin from human colon carcinoma

value: USP1 biallelic knockout


title: Of_Pupa_rep1

value: Pupa

value: wild type


title: IM_antiPD-L1_rep3

value: Ly6Chigh monocytes


title: Of_T5th_La_rep3

value: 5th instar of the Asian corn borer


title: PARE-Seq_WT_2

description: nanoPARE

value: Ler female x  Col-0 male F1

value: 7 days after pollination


title: mRNAseq_nrpd1_1

description: mRNA-seq

value: Ler nrpd1-/- female x  Col-0 nrpd1-/- male F1

value: Endosperm


title: Of_T5th_La_rep2

value: The whole insect


title: Sample 1: Genomic DNA from cardiac left ventricle

value: cardiac left ventricle

value: Male

value: pre-LVAD


title: mRNAseq_mat_nrpd1_3

description: mRNA-seq

value: Ler nrpd1-/- female x  Col-0 male F1


title: Sample 2: Genomic DNA from cardiac left ventricle

value: African American

value: Non-Ischemic

value: post-LVAD


title: mRNAseq_mat_nrpd1_2

description: mRNA-seq


title: Of_T3rd_La_rep3

value: 3rd  instar of the Asian corn borer


title: HCT116 CONTROL

value: cell line origin from human colon carcinoma

value: parental cell strain


title: Of_T3rd_La_rep2

value: wild type


title: M2_IC_rep3

value: MHC-IIlow macrophages

value: IgG2b isotype control mAb


title: sRNA_null_nrpd1_3

description: sRNA-seq

data_processing:
Analysis of sRNA libraries began with the trimming of low-quality read ends fastq_quality_trimmer -v -t 20 -l 25; (http://hannonlab.cshl.edu/fastx_toolkit/).
Adapters were removed with  cutadapt -a TGGAATTCTCGGGTGCCAAGG  --trimmed-only --quality-base 64 -m 24 -M 40 --max-n 0.5 (https://cutadapt.readthedocs.io/en/stable/)
sRNA libraries prepared using the NEXTflex sRNA-Seq Kit v2 are appended with 4 base randomized barcodes immediately 3’ and 5’ of the sRNA read itself. These barcodes were used to remove PCR duplicates (any read of the same sRNA sequence with identical flanking barcodes on both ends) using prinseq-lite –fastq <infile> -out_format 3 –out_good <outfile> -derep 1
Filtered reads were aligned to a genome consisting of concatenated Col-0 TAIR10 and Ler pseudo-genome (Col-0 genome substituted with Ler SNPs) using Bowtie (v 1.2.2) bowtie -v 2 --best -p 8 −5 4 −3 4 --sam <index file> <infile.fq>
Aligned reads between 21 and 24nt in length were binned based on size. Bedtools was used to count reads in 300-bp windows with 200-bp overlaps and over annotated genes and TEs from Araport 11.
 DESeq2 (Love et al., 2014) was used to identify features showing differences in small RNA abundance with an adjusted p-value of 0.05 or less. One complication with using DESeq2 is that the loss of Pol IV-dependent sRNAs at most loci in nrpd1-/- null endosperm  leads to an underestimation of wild-type library size by DESeq2, which increases the proportion of false negatives and undercounts the number of Pol IV-dependent sRNA loci. To allay this effect while analyzing genes, we excluded TEs and applied differential expression analysis to just genic and miRNA loci. These non-TE loci also included Pol IV-independent sRNA loci, which provide an estimate of library size.
We separately examined TEs using genic sRNA counts to provide an estimate of library size.
Genome_build: TAIR10 and TAIR10 with Ler SNPs substituted as described in Erdmann et al (2017)
Supplementary_files_format_and_content: DESeq2 output for comparisons between different genotypes, for each size of sRNAs, for genes, transposons and 300bp sliding windows are described below in tab-delimited files with "DESEQ2" in title.
Supplementary_files_format_and_content: Presenting Shortstack output files of wild-type (LCN) small RNA data from Erdmann et al 2017 and nrpd1-/- data from here.
Supplementary_files_format_and_content: bedgraph files showing 300bp windows with 200bp overlaps with statistically significant differences in 21 and 24nt sRNA abundance between WT, nrpd1-/-, mat and pat nrpd1+/-

growth_protocol: Plants were grown in a growth-chamber with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at seven days after pollination (DAP).

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total endosperm RNA isolated using the Ambion RNAqueous Micro Kit.
The small RNA pool was separated from the larger RNA pool by sequential ethanol addition and filtering. The larger RNA pool was collected on filters after the addition of ethanol equivalent to 60% of the sample volume, and the small RNA pool was collected on filters after the addition of ethanol equivalent to 50% of the flowthrough volume from the larger RNA filter binding step.  Libraries for Illumina sequencing were constructed using the NEXTflex Small RNA-Seq Kit v3 as directed (Bioo Scientific Corporation, Austin, Texas). Final library amplification was carried out for 24 cycles and the resultant libraries were size selected (135-160bp)  with a pippin prep. 40 base single-end sequencing of sRNA libraries was performed on an Illumina HiSeq 2500 machine.

value: 7 days after pollination


title: IM_antiPD-L1_rep2

value: Ly6Chigh monocytes

value: anti-PD-L1 mAb


title: Of_T5th_La_rep1

value: 5th instar of the Asian corn borer

value: The whole insect


title: U2OS_siANKRA2_Nutlin_2_RNAseq

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Quantification and quality check of libraries were performed using the Agilent Bioanalyzer 2100 in combination with the DNA 7500 Kit. Sequence information was extracted in FastQ format using Illumina's bcl2fastq v2.20.0.422.
We utilized Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports. Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10. Potential sequencing errors were detected and corrected using Rcorrector v1.0.3.1. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1. The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.92, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option enabled (RNA-seq) or disabled (ChIP-seq). Mappings were filtered by Samtools v1.10 for uniqueness and properly aligned mate pairs. We removed duplicated reads with Picard MarkDuplicates v2.23.4.
Read quantification was performed on exon level using featureCounts v1.6.5, parametrized according to the strand specificity inferred through RSeQC v3.0.0. Differential gene expression and its statistical significance was identified using DeSeq2 v1.20.0.
Genome_build: hg38
Supplementary_files_format_and_content: .tsv DESeq2 output

extract_protocol:
Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer protocol.
Libraries were constructed from 500 ng of total RNA using NEBNext Ultra II RNA - polyA+ (mRNA) Library Preparation Kit following the manufacturer's description.

treatment_protocol: Treated for 24h with 10 µM Nutlin-3a or DMSO solvent control


title: HCT116 USP1KO REP1

value: USP1 biallelic knockout


title: mRNAseq_mat_nrpd1_1

description: mRNA-seq

value: Endosperm


title: U2OS_siANKRA2_Nutlin_3_RNAseq


title: sRNA_null_nrpd1_1

description: sRNA-seq

value: Ler nrpd1-/- female x  Col-0 nrpd1-/- male F1


title: sRNA_pat_nrpd1_3

description: sRNA-seq

value: Ler female x  Col-0 nrpd1-/- male F1


title: RM_antiPD-L1_rep2

value: Ly6Clow monocytes


title: U2OS_siANKRA2_DMSO_3_RNAseq

value: DMSO


title: Of_T3rd_La_rep1

value: 3rd  instar of the Asian corn borer


title: U2OS_siANKRA2_DMSO_2_RNAseq


title: Of_T1st_La_rep1

value: 1st instar of the Asian corn borer


title: sRNA_null_nrpd1_2

description: sRNA-seq


title: IM_IC_rep3


title: RM_IC_rep2


title: RM_IC_rep3


title: HCT116 USP1C90S REP2

value: cell line origin from human colon carcinoma

value: USP1 C90S biallelic knock-in mutations


title: Of_T1st_La_rep2

value: wild type


title: U2OS_siANKRA2_Nutlin_1_RNAseq


title: M2_IC_rep2

value: MHC-IIlow macrophages

value: IgG2b isotype control mAb


title: U2OS_siANKRA2_DMSO_1_RNAseq


title: Of_Egg_rep2

value: Egg


title: IM_IC_rep2

value: Ly6Chigh monocytes


title: U2OS_siControl_Nutlin_3_RNAseq


title: sRNA_pat_nrpd1_2

description: sRNA-seq

value: 7 days after pollination


title: Of_Egg_rep3

value: The whole insect


title: U2OS_siControl_Nutlin_2_RNAseq


title: sRNA_mat_nrpd1_2

description: sRNA-seq

value: Ler nrpd1-/- female x  Col-0 male F1


title: sRNA_mat_nrpd1_1

description: sRNA-seq

value: Endosperm


title: sRNA_mat_nrpd1_3

description: sRNA-seq


title: IM_antiPD-L1_rep1

value: anti-PD-L1 mAb


title: Of_Egg_rep1


title: RM_antiPD-L1_rep1


title: M2_antiPD-L1_rep3


title: Bisulfite-seq_pat nrpd1+/- _2

description: Bisulfite sequencing

data_processing:
Reads from Bisulfite sequencing were trimmed for quality using Trim Galore using the commands "trim_galore -q 25 --phred64  --fastqc --stringency 3 --length 25  --clip_R1 5 --clip_R2 5 --three_prime_clip_R1 10 --three_prime_clip_R2 10  --paired"
The reads were then aligned to TAIR10 using “bismark  -N 1 -L 20 --non_directional”. For this alignment, paired-end reads were treated as single reads.
Duplicate reads were removed using bismark.
Previously described Bismark methylation extractor and custom scripts (Pignatta et al., 2014, 2015) were used to determine DNA methylation/base and then methylation was calculated for 300 bp windows that overlapped by 200bp. Data from the two biological replicates for each genotype were pooled together for comparison between genotypes. To be included in analysis, windows needed to have at least three overlapping cytosines and a depth of 6 reads/cytosine. Windows that differed between genotypes by 10% CHH, 20% CHG or 30% CG DNA methylation were identified as differentially methylated. Overlapping windows with differential methylation between genotypes were merged into differentially methylated regions.
To increase the robustness of our conclusions, we added two data filtering steps. DNA methylation in the endosperm varies between maternal and paternal alleles and bisulfite sequencing is known to potentially enrich for methylated DNA (Ji et al., 2014). Since we were examining the consequences of loss of NRPD1 in either parent, we could preferentially lose DNA methylation from one set of alleles. This could lead to lower coverage of one set of parental alleles and lead to faulty measurements of DNA methylation. We therefore limited our analyses to genomic regions in which reads arising from the maternally inherited genome accounted for 67%+/- 15% of total DNA reads (based on the fact that that 2/3 of the DNA in endosperm is maternally-inherited). Next, we identified DMRs between the two replicates for each genotype to mark regions where DNA methylation was variable within the same genotype.
Genome_build: TAIR10
Supplementary_files_format_and_content: List of detected DMRs for CHH, CHG and CG methylation in comparisons between Wild-type and mat and pat nrpd1+/- in tab delimited files. Difference in methylation is described in column 4
Supplementary_files_format_and_content: Methylation level at cytosines with at least five reads is provided in bedgraph format. Methylation level was calculated using reads from both replicates for each genotype.
Supplementary_files_format_and_content: Regions with acceptable ratio of maternal and paternal reads are described in bed files labelled "percent_mat_filter".  Regions with high levels of variation in methylation levels between replicates were excluded from further analysis and are listed in bed files titled "variable"

extract_protocol:
Endosperm was hand-dissected from seeds at 7 DAP. DNA was extracted from dissected endosperm using the QiaAMP DNA microkit. Dissected tissue was incubated in ATL buffer and Proteinase K overnight. 80-100 ng of DNA obtained for each sample was subjected to bisulfite treatment using Methylcode Bisulfite conversion kit (Invitrogen).
Bisulfite-converted DNA was used to build libraries with the Pico Methyl-Seq library kit (Zymo Research, D5455). 7 cycles of amplification was used for library construction.

value: Ler female x  Col-0 nrpd1-/- male F1


title: U2OS_siControl_Nutlin_1_RNAseq


title: Of_T1st_La_rep3


title: U2OS_siControl_DMSO_3_RNAseq


title: Bisulfite-seq_pat nrpd1+/- _1

description: Bisulfite sequencing


title: RM_IC_rep1

value: Ly6Clow monocytes


title: Bisulfite-seq_mat nrpd1+/-_2

description: Bisulfite sequencing


title: U2OS_siControl_DMSO_2_RNAseq

value: DMSO


title: IM_IC_rep1


title: M2_IC_rep1


title: U2OS_siControl_DMSO_1_RNAseq


title: Bisulfite-seq_mat nrpd1+/-_1

description: Bisulfite sequencing


title: M2_antiPD-L1_rep2


title: Hepa SP LSK

city: Guangzhou

first: Mingyu

state: Guangdong

address: NO. 651 Dongfengdong Road, Yuexiu District

department: Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China

institute: Sun Yat-sen University Cancer Center

description: Raw data are available on Genome Sequence Archive, Bioproject accession number: PRJCA003519

data_processing:
Cell barcodes were filtered with fixed and adaptive thresholds, filtering out cell barcodes with unique molecular identifiers (UMIs) < 500, mitochondrial gene percentage >10%, >1% hemoglobin expression, or significant “outlyingness” based on 3 median absolute deviations (MADs) from the median value in the high-dimensional space using R packages scater and robustbase.
Data were first normalized by deconvolution using the calculateSumFactors function from R package scran.
Data integration and technical variation were performed using SCTransform command from the Seurat package (v.3.1.5). Once data were successfully integrated, we performed data dimensionality reduction with principal component analysis (PCA). The first 30 principal components were used for uniform manifold approximation and projection (UMAP) reduction and to define the cell clusters. Cluster identities were manually assigned and curated on the basis of gene expression correlation with the single-cell Mouse Cell Atlas dataset using the scMCA package and the expressed genes previously reported.
To identify cell cluster marker genes that are conserved in both BM and splenic LSK cells, we used the FindConservedMarkers function from the Seurat package. Supervised module scores for gene sets related to early myeloid differentiation and ER stress response was calculating using the AddModuleScore function from the Seurat package.
The 3D LSK cell trajectory was constructed using the Monocle 3 package. In order to place the cells in order along the trajectory, we defined a "root" node in the HSC-1 cluster, upstream the divergence of branches towards MP, DCP, and MCP. Pseudotime was estimated using the order_cells function from the Monocle 3 package.
Genome_build: mm9

source_name: Splenic lin-c-Kit+Sca1+ cells

extract_protocol:
For isolation of HSPCs, Linlow/- or c-Kit+ cells were first sorted by MACS using the Lineage Cell Depletion Kit (Miltenyi Biotec) or CD117 microbeads (Miltenyi Biotec), respectively. Then, Linlow/-Sca1+c-Kithigh (LSK) cells were purified using MoFlo XDP or MoFlo Astrios EQ flow cytometer (Beckman Coulter). FACS-sorted LSK cells from the BM or spleen of Hepa mice were washed once using PBS with 0.04% BSA, and were then resuspended to a concentration of about 700 cells/ul and loaded onto the 10x Genomics Chromium.
Library generation was performed following the Chromium Single Cell 3′ Reagents Kits version 3.1 user guide.

treatment_protocol: To establish orthotopic hepatic tumors , 7.5 × 1E5 Hepa1-6 tumor cells (purchased from ATCC) suspended in 25 µl of 50% Basement Membrane Extract (Trevigen) were injected into the left liver lobes of anesthetized mice (6–8 weeks of age).

value: Hematopoietic stem and progenitor cell

tag: tumor model

value: Hepa 1-6 orthotopic tumor


title: M2_antiPD-L1_rep1


title: Bisulfite-seq_wild-type_2

description: Bisulfite sequencing

value: Ler female x  Col male F1


title: Hepa BM LSK

source_name: Bone marrow lin-c-Kit+Sca1+ cells


title: Y_l2

status: Public on Mar 03 2022

city: Shanghai

first: Moyang

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

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. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: ASM168347v1 (https://www.ncbi.nlm.nih.gov/assembly/GCF_001683475.1) was used as the reference genome
Genome_build: a FASTA file with all transcript sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and readcounts for each Sample

organism: Chenopodium quinoa

source_name: leaf

growth_protocol: The material for this experiment was planted in the experimental field of Chengdu University (Chengdu City, Sichuan, China) under the local natural temperature, humidity and circadian cycle. Quinoa were sown in early March 2019. Samples of roots, stems, and leaves were collected in August. A total of 30 quinoa strains with the same growth rate were selected for sample collection. A mixed sample containing 10 strains was regarded as a biological replicate, and three replicates were set for quinoa.

extract_protocol:
The roots, stems, and leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The roots, stems, and leaves were collected from the same biological replicate for transcriptome sequencing samples. All of the above samples were collected from 30 plants, and the sample was thoroughly cleaned after collection, placed in liquid nitrogen and kept at -80°C.

tag: quinoa type

value: yellow bitter quinoa

value: leaf


title: Y_l3


title: Y_s2

source_name: stem

value: stem


title: Y_s1


title: Bisulfite-seq_wild-type_1

description: Bisulfite sequencing


title: Y_l1


title: PAN treated kidney organoids [UMK1_PAN_2]

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 2

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for Affymetrix Clariom S Assay Gene Expression Array

data_processing: The data were normalised using RMA normalisation from R/Bioconductor

label: biotin

source_name: PAN treated kidney organoids

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: iPSCs were cultured in mTeSR1 medium (Stem Cell). For spheroid formation, the cells were seeded in low attachment 96-well plates (Thermofisher) and grown to spheroids in mTeSR1 for 3-5 days. After this, spheroids were transferred to petri dishes and the medium was changed to advanced RPMI (Gibco) supplemented with 1% GlutaMAX, 1% non-essential amino acids and 1% Penicilin and Streptomycin. Differentiation was induced with 10 µM CHIR99021 for 4 days, followed by 3 days cultivation in non-growth factor supplemented medium, 2 days with 3 µM CHIR99021 and 50 ng/ml FGF9, 5 days with 50 ng/ml FGF9 supplementation and 6 days with 1 µM CHIR99021 supplementation. The resulting kidney organoids were kept in unsupplemented medium until further use.

extract_protocol: The RNA was extracted using QIAgen RNeasy Micro Kit following the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: Puromycin Aminonucleoside (PAN) (Sigma Aldrich) was diluted in the culture medium to a final concentration of 50 µM. Organoids were incubated for 48h with PAN and the conditioned medium was kept for secretome analyses.

tag: cell type source

value: induced pluripotent stem cells (iPSCs)-derived kidney cells

value: Puromycin aminonucleoside (PAN)


title: Y_s3


title: SHAPE-MaP analysis of SARS-CoV-2 (DMSO treatment)

description: In vitro refolded SARS-CoV-2 genome, DMSO treated

organism: Severe acute respiratory syndrome coronavirus 2

source_name: SARS-CoV-2 (DMSO)


title: kidney organoids control [UMK1_con_2]

description: replicate 2

source_name: kidney organoids control

value: control


title: spheroids [SPH_1]

description: replicate 1

source_name: spheroids

value: induced pluripotent stem cells (iPSCs)


title: Y_r2

source_name: root

value: root


title: Y_r3


title: spheroids [SPH_2]

description: replicate 2


title: PAN treated kidney organoids [UMK1_PAN_1]

description: replicate 1


title: Y_r1


title: breast cancer tissue with axillary lymph node metastasis (M1)

city: Jinan

first: Peng

last: Su

address: Wen Hua Xi Road 107

institute: Qilu Hospital of Shandong University

data_processing:
Paired-end reads were harvested from Illumina HiSeq Sequencer after quality filtering. With these reads, cloud-seq used different softwares to analyse circRNAs, LncRNAs and mRNAs.  circRNA: The reads were aligned to the reference genome/transcriptome with bowtie2 software and circRNAs were detected and identified with find_circ software. Raw junction reads for all samples were normalized by total reads number and log2 transformed. Differentially expressed circRNAs were identified by ttest between two groups, and fold change between two samples. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.  LncRNA & mRNA: After 3’ adaptor-trimming by cutadapt software (v1.9),  the high quality trimmed reads were aligned to the reference genome (UCSC hg19) guided by the Ensembl GFF gene annotation file with TopHat2 software. Then, cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: excel format

source_name: breast cancer tissue

extract_protocol:
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA).

tag: axillary lymph node metastasis

value: Yes


title: breast cancer tissue without axillary lymph node metastasis (T3)

value: No


title: breast cancer tissue without axillary lymph node metastasis (T1)


title: kidney organoids control [UMK1_con_1]

description: replicate 1


title: SHAPE-MaP analysis of SARS-CoV-2 (2A3 treatment)

description: In vitro refolded SARS-CoV-2 genome, 2A3 treated

source_name: SARS-CoV-2 (2A3)


title: TCR sequencing of T cells from breast cancer patient MR4050 (MK_02) stimulated with PIK3CA(H1047L)

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

description: RNA (enriched for VDJ transcripts)

data_processing:
Basic processing with CellRanger version 3.1.0 with vdj_GRCh38_alts_ensembl-3.1.0-3.1.0 genome version for TCR sequencing data and GRCh38-3.0.0 for scRNA-seq libraries.
Detailed QC metrics were generated and evaluated using single-cell analysis packages from Bioconductor including DropletUtils, scater, and scran. Genes detected in fewer than three cells and cells where fewer than 200 genes had nonzero counts were filtered out and excluded from subsequent analysis. Low-quality cells where more than 15% of the read counts derived from the mitochondrial genome were also discarded. For downstream analyses, only cells for which clonotype information was available were retained. To remove likely doublet or multiplet captures, cells with more than 7,000 detected genes were discarded as well as cells for which more than 2 TRA or TRB sequences were detected. Scripts and processed data can be found at https://github.com/abcwcm/Chandran2021.
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix; lists of barcodes and features; contig annotation tsv

source_name: T cells

growth_protocol: PBMCs are plated in tissue culture flasks at 1e6 cells/cm2 in complete media in the absence of cytokine for 2 hours at 37oC to separate the adherent (monocyte-containing) and non-adherent (T cell containing) fractions. To generate moDC, the adherent fraction is washed with PBS and fresh complete media supplemented with IL-4 and GM-CSF (400 IU/mL) is provided every alternate day. moDC are stimulated with LPS and IFNg for 16-24 hours prior to transfection. Naive CD8+ were enriched from the non-adherent fraction by untouched negative selection.

extract_protocol:
1e5 cells from a qPCR-positive well were harvested and cocultured with moDCs electroporated with mRNA encoding WT or Mut PIK3Ca at an E:T ratio of 1:10 for 3h. Final cell concentration was determined by cell counting on a hemocytometer, and cell concentration was adjusted to approximately 700 and 1,200 cells per microliter to maximize the likelihood of achieving the desired cell recovery target, with an initial cell viability of > 90%.
The single-cell suspension was mixed with RT Master Mix and loaded together with barcoded single-cell 5′ gel beads and partitioning oil onto Single Cell A Chip to generate GEMs using Chromium Controller. Cell lysis and barcoded reverse transcription of RNAs from single cells were finished inside each GEM. Barcoded complementary DNA (cDNA) product was recovered through post GEM-RT cleanup and PCR amplification. cDNA QC and quantification were determined by High Sensitivity D5000 DNA ScreenTape analysis (Agilent Technologies) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). Fifty nanograms of cDNA was used for 5′ Gene Expression library construction, and each sample was indexed by a Chromium i7 Sample Index Kit, which was run on an Illumina HiSeq4000 sequencer with 2 × 100 base pairs (bp) paired reads to achieve at least 30,000 read pairs per cell. Full-length V, D and J gene segments were amplified using a Chromium Single Cell V(D)J Enrichment Kit (human T cells) to generate enrichment products.
10X Chromium chemistry: Single Cell V(D)J R2-only and Single Cell 5' R2-only

treatment_protocol: MoDCs were electroporated with mRNA encoding WT or Mut PIK3Ca for 16-24h prior to coculture and plated in 24 well non-TC plates. T cells were added in at an E:T ratio of 3:1 in the presence of IL-21 (30 ng/mL)  Wells were supplemented with fresh media containing IL-7 and IL-15 (10 ng/mL each) every 3 days during the duration of the in vitro culture. Wells were screened for presence of neoantigen-reactive T cells by qPCR.

tag: antigen type

value: PIK3CA (H1047L)

value: T cells

tag: disease state

value: breast cancer


title: scRNA-seq sequencing of T cells from breast cancer patient MR4050 (MK_02) stimulated with PIK3CA(H1047L)

description: RNA


title: scRNA-seq sequencing of T cells from breast cancer patient MR4050 (MK_02) stimulated with WT PIK3CA

description: RNA

value: WT PIK3CA


title: TCR sequencing of T cells from patient 0606T1 stimulated with PIK3CA(H1047L)

description: RNA (enriched for VDJ transcripts)


title: scRNA-seq sequencing of T cells from patient 0606T1 stimulated with WT PIK3CA

description: RNA


title: scRNA-seq sequencing of T cells from patient 0606T1 stimulated with PIK3CA(H1047L)

description: RNA


title: TCR sequencing of T cells from patient 21LT2 stimulated with WT PIK3CA

description: RNA (enriched for VDJ transcripts)


title: TCR sequencing of T cells from patient 0606T1 stimulated with WT PIK3CA

description: RNA (enriched for VDJ transcripts)


title: heart rep3

city: HONG KONG

first: Dianjing

last: GUO

address: G94, South Block, Science Center, CUHK

institute: CUHK

data_processing:
Raw RNA-seq reads were trimmed to remove poor-quality base calls and adaptor contamination using Trim Galore (version 0.6.6)
Trimmed RNA-seq reads were mapped to the Araport11 transcriptome with Kallisto (v0.44.0) using default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited csv files include TPM values for each Sample

source_name: heart

growth_protocol: Plants were grown in Panasonic growth chamber (MLR-325) at 22°C with 16/8 light/dark cycle

extract_protocol:
Embryos were mannually isolated. RNA was isolated using the Dynabeads mRNA DIRECTTM Micro Kit (Life Technologies) according to the manufacturer’s instructions. cDNA synthesis and amplification were performed using a SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

tag: cell stage

value: heart


title: scRNA-seq sequencing of T cells from patient 21LT2 stimulated with PIK3CA(H1047L)

description: RNA


title: TCR sequencing of T cells from patient 21LT2 stimulated with PIK3CA(H1047L)

description: RNA (enriched for VDJ transcripts)


title: globular rep1

source_name: globular

value: globular


title: scRNA-seq sequencing of T cells from patient 21LT2 stimulated with WT PIK3CA

description: RNA


title: globular rep2


title: TCR sequencing of T cells from breast cancer patient MR4050 (MK_02) stimulated with WT PIK3CA

description: RNA (enriched for VDJ transcripts)


title: 16-cell rep3


title: 32-cell rep2


title: heart rep1


title: 32-cell rep3


title: 16-cell rep1


title: breast cancer tissue without axillary lymph node metastasis (T2)


title: 16-cell rep2


title: breast cancer tissue with axillary lymph node metastasis (M2)


title: 8-cell rep3


title: 8-cell rep2


title: 8-cell rep1


title: 2/4-cell rep3


title: 2/4-cell rep1


title: heart rep2


title: Sp180_Nm_3h

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

institute: Leibniz Institute for Natural Product Research and Infection Biology

data_processing:
quality control with FastQC (v0.11.7)
quality trimming of raw data with bbduk from the BBMap (v37.44)
read alignment STAR Aligner (v2.5.2b)
read counting with featureCounts (v1.20.6)
Genome_build: Ensembl annotation GRCh38.89
Supplementary_files_format_and_content: tab delimited text file with unnormalised read counts
Supplementary_files_format_and_content: tab delimited text file with MRN normalised read counts

source_name: monocytes

growth_protocol: CD14+ monocytes were isolated from EDTA-anticoagulated blood after Ficoll-Paque density gradient centrifugation by magnetic-activated cell sorting using human CD14 MicroBeads and the autoMACS Pro Separator system according to the manufacturer’s instructions (Miltenyi Biotec). CD14+ monocytes were resuspended in RPMI1640 with L-glutamine supplemented with 20 % heat-inactivated FBS and cultured at a density of 2.5 x 106 cells/ml. After overnight resting, monocyte viability was determined by trypan blue staining (≥85 %) prior to stimulation.

extract_protocol:
After stimulation, the cells were separated from the supernatant by centrifugation. Total RNA was purified using the AllPrep96 DNA/RNA Kit from Qiagen according to the manufacturer’s instructions.
RNA-sequencing used the QuantSeq-3’-mRNA library preparation kit (Lexogen, Vienna, Austria). Next generation sequencing (NGS) libraries were sequenced at the end of the 3' poly-A tail using a HiSeq 2500 platform (Illumina, San Diego, USA).

treatment_protocol: Monocytes were stimulated with inactivated A. fumigatus germ tubes (multiplicity of infection [MOI] =0.5), S. aureus (MOI =5), N. meningitidis (MOI =1) or media as unstimulated control for 3h or 6h

tag: Sex

value: male

tag: stimulation

value: N. meningitidis

tag: time point


title: Sp180_Nm_6h


title: Sp180_Af_6h

value: A. fumigatus


title: Sp180_K_3h

value: Control


title: Sp180_Af_3h


title: Sp180_K_6h


title: Sp179_Sa_6h

value: S. aureus


title: Sp179_Nm_6h


title: Sp179_Af_6h


title: Sp179_Sa_3h


title: Sp179_K_6h


title: Sp179_Af_3h


title: Sp179_Nm_3h


title: Sp178_Sa_6h


title: Sp179_K_3h


title: Sp178_Sa_3h


title: globular rep3


title: Sp178_Nm_6h


title: 32-cell rep1


title: Sp178_K_6h


title: Sp178_Nm_3h


title: Sp178_K_3h


title: 2/4-cell rep2


title: Sp178_Af_6h


title: Sp178_Af_3h


title: Sp177_Sa_6h


title: Sp177_Sa_3h


title: Sp177_Nm_6h


title: breast cancer tissue with axillary lymph node metastasis (M3)


title: Sp177_Af_3h


title: Sp177_Nm_3h


title: Sp177_Af_6h


title: Sp177_K_6h


title: Sp176_K_6h


title: Sp176_Sa_6h


title: Sp176_Sa_3h


title: Sp176_Nm_6h


title: Sp176_K_3h


title: Sp175_Sa_6h


title: Sp176_Nm_3h


title: Sp175_Sa_3h


title: Sp176_Af_3h


title: Sp177_K_3h


title: Sp175_Nm_3h


title: Sp176_Af_6h


title: Sp175_K_6h


title: Sp175_Nm_6h


title: Sp175_Af_6h


title: Sp175_K_3h


title: Sp174_Sa_6h


title: Sp175_Af_3h


title: Sp174_Sa_3h


title: Sp174_Nm_3h


title: Sp174_K_3h


title: Sp174_K_6h


title: Sp174_Nm_6h


title: Sp174_Af_6h


title: Sp174_Af_3h


title: Sp173_Nm_6h


title: Sp173_K_3h


title: Sp173_Sa_3h


title: Sp172_Sa_6h


title: Sp173_Af_6h


title: Sp173_Af_3h


title: Sp173_K_6h


title: Sp172_Sa_3h


title: Sp172_K_3h


title: Sp172_K_6h


title: Sp172_Af_6h


title: Sp171_Nm_6h


title: Sp172_Af_3h


title: Sp171_Sa_6h


title: Sp172_Nm_3h


title: Sp171_K_6h


title: Sp171_K_3h


title: Sp170_Sa_6h


title: Sp171_Af_3h


title: Sp171_Af_6h


title: Sp170_Sa_3h


title: Sp170_Nm_6h


title: Sp170_Nm_3h


title: Sp170_K_3h


title: Sp170_Af_6h


title: Sp170_Af_3h


title: Sp169_Sa_6h


title: Sp169_Nm_3h


title: Sp169_Nm_6h


title: Sp173_Nm_3h


title: Sp169_Af_3h


title: Sp169_K_6h


title: Sp169_Af_6h


title: Sp168_Sa_6h


title: Sp169_K_3h


title: Sp168_Sa_3h


title: Sp168_Nm_3h


title: Sp173_Sa_6h


title: Sp172_Nm_6h


title: Biliary epithelial cells - HL29 CD133+ P8 cultured in 3D

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

data_processing:
Base call data generated by Illumina NextSeq 550, NextSeq 2000
Read quality assessed using FastQC (v.0.11.9) and MultiQC (v.1.3.dev0)
Adapter and poly-G trimming with Cutadapt (v.1.16)
Read alignment with STAR (v.2.7.1a)
Read counting with featureCounts (Rsubread Bioconductor package v.2.0.1)
Differential expression computed using DESeq2 (v.1.26.0)
Genome_build: GRCh38.99
Supplementary_files_format_and_content: Tab separated matrix tables with raw gene counts for all genes and every sample

source_name: biliary epithelium

growth_protocol: Sorted hBEC were grown as organoids by plating onto low-adherence plates (Greiner) in hemispheres of growth factor reduced Matrigel (Corning) and grown in hBEC Expansion Medium: Advanced DMEMF12 +1%P/S, 1% Glut containing 10%FCS, 10 mM HEPES pH7, 10 mM Nicotinamide, 1x N2 Supplement, 1x B27 Supplement, 50 ng/ml EGF, 10 nM Gastrin, 100 ng/ml FGF-10, 25 ng/ml HGF, 500 ng/ml R-Spondin 1, 1.25 mM NAC, 5 uM A-83-01 and 10 uM Forskolin. For the first three days of culture medium was supplemented with 100 ng/ml Noggin, 100 ng/ml Wnt and 10 uM Y27632. Medium was changed every three days and cells passaged once confluent every 7 to 10 days. Cells were routinely tested for mycoplasma contamination using MycoAlert Assay Control set (Lonza).

extract_protocol:
For library preparation, 500ng of each total RNA sample was used after quality and integrity were assessed using the Agilent Bioanalyser Instrument. Poly-A containing mRNA molecules were purified from total RNA using Poly-A mRNA magnetic isolation module (NEB #E7490) following manufacturer’s protocol. cDNA was then generated from mRNA fragments using the NEBNEXT Ultra II Directional RNA Library Prep Kit (NEB) and purified using AMPure XP beads. cDNA fragments were enriched by 11 cycles of PCR with unique dual indexes to allow multiplexed sequencing (NEB, #E6440) before a final purification using AMPure XP beads.
Cryopreserved sections (or fresh samples of tissue) were defrosted at room temperature and digested for 30 min at 37°C in a solution of Collagenase (2 ug/ml, Gibco)-Dispase (1 ug/ml, Gibco)-Bovine Fetal Calf Serum (2% FCS, Gibco) in Advanced DMEMF12 (LifeTech) supplemented with 1% Penicillin/Streptomycin (P/S, Gibco) and 1% L-Glutamine (Glut, Gibco). When the intrahepatic bile ducts could be observed by microscope inspection the sample was centrifuged at 100g for 5 mins, resuspended in Versene (Thermo Fisher) and incubated at 37°C for 1 hour. Dissociated cells were filtered through a 40 um cell strainer and washed in Advanced DMEMF12. Cells were resuspended in Advanced DMEMF12 underlayered with an equal volume of 20% and 50% (v/v) Percoll (Sigma). Following centrifugation at 1800g for 30 mins at 4°C, the HPC rich fraction lying between the 20 and the 50% Percoll layers was collected, washed and re-suspended in PBS with 2% FCS and 100 mmol EDTA (Sigma) for FACS staining procedure. Cells were incubated for 1 hour with EpCAM-BV650 conjugated antibody, CD24-BV421, CD133-APC, CD45-488 and CD31-488 at the concentrations stated in Table 1. Samples were stained with SYTOX-AADvanced dead cell stain kit (ThermoFisher) prior analysis in a FACSAria Fusion (BD Biosciences). Trigger pulse width was used to exclude cell doublets from analysis and collection.

tag: cell type

value: Biliary epithelial cells of biliary origin

value: healthy

tag: passage


title: Biliary epithelial cells - HL29 CD133+ P5 cultured in 3D


title: Sp168_K_3h


title: Biliary epithelial cells - HL29 CD133+ P14 cultured in 3D


title: Sp168_Af_6h


title: Sp168_Nm_6h


title: Sp168_Af_3h


title: Biliary epithelial cells - HL29 CD133+ P2 cultured in 3D


title: Biliary epithelial cells - HL29 CD133+ P5 cultured in 2D


title: Sp167_Sa_6h


title: Biliary epithelial cells - HL29 CD133+ P3 cultured in 2D


title: Sp170_K_6h


title: Sp167_Nm_6h


title: Sp167_Sa_3h


title: Sp167_K_6h


title: Sp167_Af_6h


title: Biliary epithelial cells - HL29 CD133+ P0 cultured in 2D


title: Sp166_Sa_6h


title: Sp167_Af_3h


title: Sp169_Sa_3h


title: Testis7

first: Mengmeng

last: Jiang

address: Yuhangtang Road 866, Xihu Distric

institute: Zhejiang University

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: Danio rerio GRCz10
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

organism: Danio rerio

source_name: testis

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

tag: strain

value: Tubingen

value: testis

value: wild type


title: Swim Bladder3

source_name: swim bladder

value: swim bladder


title: Sp167_K_3h


title: Sp167_Nm_3h


title: Testis6


title: Skin5

source_name: skin

value: skin


title: Swim Bladder2


title: Skin6


title: Skin3


title: Ovary5

source_name: ovary

value: ovary


title: Sp166_Sa_3h


title: Sp166_Nm_6h


title: Sp168_K_6h


title: Ovary4


title: Biliary epithelial cells - HL29 CD133+ P0 cultured in 3D


title: Liver6

source_name: liver

value: liver


title: Sp166_K_3h


title: Sp166_Af_6h


title: Intestine7

source_name: intestinePancreas

value: intestinePancreas


title: Sp166_Af_3h


title: Biliary epithelial cells - HL29 CD133+ P1 cultured in 2D


title: Intestine6


title: Sp165_Sa_6h


title: Heart2

value: heart


title: Sp165_Sa_3h


title: Heart1


title: Sp165_Nm_6h


title: Gill3

source_name: gill

value: gill


title: Sp165_Nm_3h

value: male


title: Sp165_K_3h


title: Sp165_Af_6h


title: Gill6


title: Sp165_Af_3h


title: Sp164_Sa_6h