title: bc1008--bc1008: Pedunculate & Olfactory lobe - FLAMseq

source_name: Pedunculate & Olfactory lobe

value: Pedunculate & Olfactory lobe


title: bc1010--bc1010: Other tissues - FLAMseq

status: Public on Nov 11 2022

type: SRA

city: Berlin

first: Grygoriy

last: Zolotarov

address: Hannoversche Strasse 28

department: Berlin Institute of Medical Systems Biology

country: Germany

institute: Max Delbruck Center for Molecular Medicine

library_source: transcriptomic

data_processing:
bcl2fastq software has been used for basecalling for PolyA, total RNA and Small RNA libraries. For FLAMseq and Isoseq FLAMAnalysis and isoseq3 pipelines have been used to obtain full-length non-chimeric ( FLNC) reads.
PolyA and totalRNA sequencing data have been mapped to the genome using STAR aligner (Dobin et al. 2013) using default parameters
Iso-seq and FLAMseq FLNCs have been mapped to the genome with minimap2 (v 2.17-r941) using the parameters "--cs -ax splice:hq -uf --secondary=no -C5"
MicroRNA counts file has been generated using quantifier.pl script from miRDeep2 package and the sequences of microRNAs predicted in this study
*_clean_genomic_tail_length.txt.gz files for FLAMseq have been generated by FLAMAnalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis).
Genome_build: GCF_006345805.1_ASM634580v1
Supplementary_files_format_and_content: miRNAs_expressed_all_samples_mirgenedb.csv.gz contains raw and normalized counts for each microRNA in every tissue in the dataset
Supplementary_files_format_and_content: totalRNA_fc_221221.txt.gz, polyARNA_fc_221221.txt.gz - tab-separated file with read counts for individual genes in the genome produced with featureCounts
Supplementary_files_format_and_content: *bed files for Isoseq have been obtained by collapsing reads into individual libraries into the sets of putative isoforms using TAMA collapse (https://github.com/GenomeRIK/tama)
Supplementary_files_format_and_content: *_clean_genomic_tail_length.txt.gz files contain the poly(A) tail length, sequence and a read_ID for every read in the dataset

molecule: polyA RNA

organism: Octopus vulgaris

source_name: Other tissues

extract_protocol:
Adult specimens of O. vulgaris (body weight 800 g ± 50 g, mean ± SD) were collected from the Bay of Naples (Italy) and transferred to the Department of Biology, University of Naples Federico II (Italy). Samples (N=8) were anesthetized by isoflurane insufflation (Polese et al. 2014), and tissues were dissected under sterile conditions following institutional guidelines. The collected samples were snap frozen in liquid nitrogen and immediately put in Trizol, then stored at −80 °C. The RNA has been extracted from the tissues using Direct-zolTM RNA Miniprep (Zymo Research), following the manufacturer’s protocol. RNA has been stored at -80 C prior to sequencing, and it was transported using dry ice. The quality of RNA has been accessed with Bioanalyzer and only samples with intact RNA have been kept for library preparation.
Library construction protocols are listed in the columns of SAMPLES section above

tag: tissue

value: Non-neuronal tissues mix

value: FLAMseq

tag: strategy

value: FL cDNA

tag: basecalling

value: SMRT Link

tag: downstream analysis

value: lima, FLAMAnalysis, TAMA collapse


title: a18: Testis - FLAMseq

source_name: Testis

value: Testis


title: LNCaP Capture STARRseq Library sample 1 - mRNA

status: Public on Nov 12 2022

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

country: Canada

institute: Vancouver Prostate Centre

data_processing:
starrseq files were mapped with bwa mem (version 0.7.17) - default parameters
reads with MAPQ < 30 were removed from the bam files.
BigWig files were created with deepTools v2.0 using bamCoverage (Ramirez et al. 2016: PMID: 27079975).
Assembly: hg19
Supplementary files format and content: BigWig

molecule: total RNA

organism: Homo sapiens

source_name: Prostate Cancer Immortilized Cell line

growth_protocol: LNCaP cells were routinely grown in RPMI 1640 media with 1% Penicillin-Streptomycin and 10% FBS. After transfection and overnight recovery (recovery media contains 10% FBS only without antibiotics), the culture media was refreshed with complete media again before any treatment.

extract_protocol:
Total RNA was extracted and the mRNA was isolated using the Oligo (dT)25 Dynabeads. The isolated mRNA samples were synthesized into cDNA using the the gene-specific primer, and were PCR-amplified with the junction PCR primers. The STARRseq capture library was separately PCR-amplified with DNA specific junction PCR primers
STARRseq library was generated for sequencing by PCR amplification using standard Illumina protocols.

treatment_protocol: Approximately 24 hours after transfection, LNCaP cells transfected with STARRseq capture library were treated with 100% DMSO for 48 hours. Approximately 68 hours post transfection, 100% EtOH was further added to the culture media for 4 hours.

tag: cell line

value: LNCaP

tag: cell type

value: Prostate Cancer

tag: treatment

value: EtOH and DMSO

value: both 100%


title: Capture STARRseq Library - DNA

value: No Treatment


title: LNCaP Capture STARRseq Library sample 2 - mRNA


title: bc1009--bc1009: Frontal & Vertical lobe - FLAMseq

source_name: Frontal & Vertical lobe

value: Frontal & Vertical lobe


title: bc1003--bc1003: Stellate g. & Visceral g. - FLAMseq

source_name: Stellate g. & Visceral g.

value: Stellate g. & Visceral g.


title: bc1001--bc1001: Retina & Optic Lobe - FLAMseq

source_name: Retina & Optic Lobe

value: Retina & Optic Lobe


title: m6A-exo-seq.KO.PCIF1.ip.rep2

city: San Diego

first: Lingling

last: Wang

state: California

address: 9500 Gilman Dr

country: USA

institute: University of California San Diego

data_processing:
Library strategy: m6A-exo-seq
Single-end and paired-end sequencing data were trimmed by single-end and paired-end model of cutadapt software respectively. Reads longer than 15bp were retained for mapping.
Trimmed reads were aligned to hg38 genome assembly by hisat2 software using the default parameter for single or pair-end model
For RNA-seq, reads were counted by htseq, then gene expression was quantified by DESeq2.
For m6A-exo-seq, reads were counted by featureCount, then differential methylation sites at cap-region was detected by hypergeometric test through in-house scripts. The m6A marked genes are listed in m6Am.marked.genes.csv, with the gene names at first column, differential methylation FDR and p-value at second and third columns, change of enrichment fold in KO PCIF1 compared to KO control samples at the fourth column.
Input and IP samples bam files in m6A-exo-seq were converted to bigwig files by bamCoverage script in deepTools for visualization and analysis.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files for m6A-exo-seq coverage. m6Am.marked.genes.csv for m6Am marked genes in m6A-exo-seq. RNAseq.counts.csv for raw gene counts in RNA-seq,

source_name: HCT116 cells

growth_protocol: HCT 116 (CCL-247) cell line was purchased from ATCC. The cells were grown in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) at 37°C in 5% CO2 incubators according to ATCC’s culture methods.

extract_protocol:
After the extraction of total RNA, for RNA-seq, ribosomal RNA was depleted by RiboMinus Transcriptom Isolation Kit (life technology, K1500-02). For m6A-exo-seq, mRNA was purified using Magnetic mRNA Isolation Kit (New England Biolabs, S1550S)
For m6A-exo-seq, mRNA was fragmented with Fragmentation Reagents Kit (Invitrogen, AM8740) following the manufacturer’s protocol, then phosphorylated with T4 PNK (NEB, M0201S), and then treated with Terminator 5’-Phosphate-Dependent Exonuclease (Lucigen) to remove phosphorylation of transcripts. Lastly, Cap-Clip (CellScript) were added to remove capped transcripts. 10% uncapped 5’RNA fragments were reserved as input, the rest of fragmented RNA were proceeded to do the immunoprecipitation with anti-N6-methyladenosine (m6A) antibody (abcam, ab151230). Immunoprecipated and input RNA for m6A-exo-seq as well as ribosomal depleted and fragmented RNA for RNA-seq were both subjected to library preparation using a TruSeq mRNA library preparation kit (Illumina)
RNA-seq and m6A-exo-seq. RNA-seq was sequenced at Illumina HiSeq 4000 platform with single-end model. m6A-exo-seq was sequenced at  Illumina NovaSeq 6000 platform with paired-end model

treatment_protocol: For lentiviral producing, 293FT cells were co-transfected with packaging plasmids, including psPAX2 and pMD2.G and CRISPRV2 with the indicated sgRNA in 10 cm dishes using Lipofectamine (Life Technologies, 11668027) in Opti-MEM medium (Gibco). The media was replaced with fresh completed DMEM after 4–6 h. After 48h, supernatants were harvested and then infect the indicated cells by spin transduction.

value: colorectal cancer

tag: genotype/variation

value: FCIF1 KO

tag: antibody

value: m6A antibody (abcam, ab151230)


title: bc1008_5p--bc1008_3p: Axial Nerve Cord - Isoseq

source_name: Axial Nerve Cord

value: Axial Nerve Cord

value: Iso-seq Express 2.0

value: lima, isoseq3 cluster, TAMA collapse


title: bc1002--bc1002: Sucker - FLAMseq

source_name: Sucker

value: Sucker

value: FLAMseq

value: FL cDNA

value: SMRT Link


title: bc1006_5p--bc1006_3p: Other tissues - Isoseq

value: Non-neuronal tissues mix


title: bc1005_5p--bc1005_3p: Frontal & Vertical lobe - Isoseq


title: bc1004_5p--bc1004_3p: Pedunculate & Olfactory lobe - Isoseq

value: Pedunculate & Olfactory lobe


title: bc1003_5p--bc1003_3p: Stellate g. & Visceral g. - Isoseq


title: bc1002_5p--bc1002_3p: Sucker - Isoseq


title: NR_GZ_074: Sucker small - polyA RNA

source_name: Suckers - tip of the arm

value: Suckers - tip of the arm

value: TruSeq Stranded mRNA

value: cDNA

value: STAR 2.7.1a, featureCounts v1.6.4


title: bc1001_5p--bc1001_3p: Retina & Optic Lobe - Isoseq

value: Retina & Optic Lobe


title: NR_GZ_075: Testis - polyA RNA

value: Testis


title: NR_GZ_072: Skin - polyA RNA

source_name: Skin

value: Skin


title: NR_GZ_071: White body - polyA RNA

source_name: White body

value: White body


title: NR_GZ_070: Hepatopancreas - polyA RNA

source_name: Hepatopancreas

value: Hepatopancreas


title: NR_GZ_069: Posterior Salivary Gland - polyA RNA

source_name: Posterior salivary gland

value: Posterior salivary gland


title: NR_GZ_068: Intestine - polyA RNA

source_name: Intestine

value: Intestine


title: NR_GZ_073: Sucker big - polyA RNA

source_name: Suckers - base of the arm

value: Suckers - base of the arm


title: NR_GZ_067: Optic gland - polyA RNA

source_name: Optic gland

value: Optic gland


title: NR_GZ_066: Visceral ganglion - polyA RNA

source_name: Visceral ganglion

value: Visceral ganglion


title: NR_GZ_064: Axial Nerve Cord - polyA RNA

value: Axial Nerve Cord


title: NR_GZ_063: Pedunculate & Olfactory lobe - polyA RNA

source_name: Pedunculate & Olfactory lobe


title: NR_GZ_065: Stellate ganglion - polyA RNA

source_name: Stellage ganglion

value: Stellage ganglion


title: NR_GZ_053: Central heart - total RNAseq

source_name: Central heart

value: Central heart

value: Lexogen RiboCop rRNA Depletion,TruSeq Stranded mRNA


title: NR_GZ_056: Sucker small - totalRNAseq

value: Suckers - tip of the arm


title: NR_GZ_062: Vertical lobe - polyA RNA

source_name: Vertical lobe

value: Vertical lobe

value: TruSeq Stranded mRNA

value: cDNA


title: NR_GZ_061: Frontal lobe - polyA RNA

source_name: Frontal lobe

value: Frontal lobe

value: STAR 2.7.1a, featureCounts v1.6.4


title: NR_GZ_060: Optic Lobe - polyA RNA

source_name: Optic lobe

value: Optic lobe


title: NR_GZ_051: Hepatopancreas - total RNAseq

value: Hepatopancreas


title: NR_GZ_059: Retina - polyA RNA

source_name: Retina

value: Retina


title: NR_GZ_048: Optic gland - total RNAseq


title: NR_GZ_049: Intestine - total RNAseq

value: Intestine


title: NR_GZ_052: White body - totalRNAseq

value: White body


title: NR_GZ_054: Skin - total RNAseq

value: Skin


title: NR_GZ_055: Sucker big - totalRNAseq

value: Suckers - base of the arm


title: NR_GZ_047: Visceral ganglion - total RNAseq

value: Visceral ganglion


title: NR_GZ_046: Stellate ganglion - total RNAseq

value: Stellage ganglion


title: NR_GZ_042: Frontal lobe - total RNAseq


title: NR_GZ_043: Vertical lobe - total RNAseq


title: NR_GZ_041: Optic lobe - total RNAseq


title: NR_GZ_045: Axial nerve cord - total RNAseq

source_name: Axial Nerve Cord

value: Axial Nerve Cord


title: NR_GZ_044: Pedunculate & Olfactory lobe - total RNAseq

value: Pedunculate & Olfactory lobe

value: Lexogen RiboCop rRNA Depletion,TruSeq Stranded mRNA


title: NR_GZ_037: Stellate ganglion - smallRNA

source_name: Stellate ganglion

value: Stellate ganglion

value: TruSeq Small RNA

value: cutadapt, miRTrace 1.0.1, miRDeep2.0.1.2


title: NR_GZ_036: Posterior Salivary Gland - smallRNA

source_name: Posterior Salivary Gland

value: Posterior Salivary Gland

value: cDNA


title: NR_GZ_035: Intestine - smallRNA


title: NR_GZ_050: PSG - total RNAseq

value: Posterior salivary gland

value: STAR 2.7.1a, featureCounts v1.6.4


title: NR_GZ_033: Optic gland - smallRNA

value: Optic gland


title: NR_GZ_032: Visceral ganglion - smallRNA


title: NR_GZ_030: Sucker small - smallRNA

source_name: Sucker small

value: Sucker small


title: NR_GZ_029: White body - smallRNA

source_name: White body

value: White body


title: NR_GZ_028: Skin - smallRNA

source_name: Skin

value: Skin


title: NR_GZ_025: Retina - smallRNA

value: Retina


title: NR_GZ_026: Vertical lobe - smallRNA

value: Vertical lobe


title: NR_GZ_031: Central heart - smallRNA

value: Central heart


title: NR_GZ_022: Frontal lobe - smallRNA

value: Frontal lobe


title: NR_GZ_024: Optic Lobe - smallRNA

source_name: Optic Lobe

value: Optic Lobe


title: NR_GZ_021: Sucker big - smallRNA

source_name: Sucker big

value: Sucker big

value: SMARTer smRNA-Seq


title: NR_GZ_019: Hepatopancreas - smallRNA

source_name: Hepatopancreas

value: Hepatopancreas


title: NR_GZ_016: Stellate ganglion - smallRNA

value: Stellate ganglion

value: cutadapt, miRTrace 1.0.1, miRDeep2.0.1.2


title: NR_GZ_020: Posterior Salivary Gland - smallRNA

value: Posterior Salivary Gland

value: cDNA


title: NR_GZ_023: Pedunculate & Olfactory lobe - smallRNA

value: Pedunculate & Olfactory lobe

value: TruSeq Small RNA


title: NR_GZ_011: Frontal lobe - smallRNA


title: NR_GZ_017: Intestine - smallRNA

source_name: Intestine

value: Intestine


title: NR_GZ_039: Sucker big - smallRNA


title: NR_GZ_040: Retina - total RNA

value: Lexogen RiboCop rRNA Depletion,TruSeq Stranded mRNA

value: STAR 2.7.1a, featureCounts v1.6.4


title: NR_GZ_034: Testis - smallRNA

source_name: Testis

value: Testis


title: NR_GZ_038: Hepatopancreas - smallRNA


title: NR_GZ_027: Axial Nerve Cord - smallRNA

value: Axial Nerve Cord


title: NR_GZ_018: Optic Lobe - smallRNA


title: NR_GZ_013: Testis - smallRNA


title: NR_GZ_012: Visceral ganglion - smallRNA

source_name: Visceral ganglion

value: Visceral ganglion


title: NR_GZ_014: Optic gland - smallRNA

source_name: Optic gland

value: Optic gland


title: NR_GZ_009: Sucker small - smallRNA

value: Sucker small


title: NR_GZ_008: White body - smallRNA

value: White body


title: NR_GZ_015: Pedunculate & Olfactory lobe - smallRNA

source_name: Pedunculate & Olfactory lobe

value: SMARTer smRNA-Seq


title: D2R_hMeDIP_rep2

city: Paris

first: Jean-Antoine

last: Girault

address: 17 rue du Fer à Moulin

country: France

institute: INSERM, IFM

description:
hMeDIP, D2R, stranded
5_ACAGTG_L005
processed data file: hmedip_gene_counts.xlsx

library_source: genomic

data_processing:
library strategy: hMeDIP-seq
alignment with BWA (0.7.5) for MeDIP and hMeDIP, Tophat (2.0.10) for RNA
reads assigned to genes using Rsubread (v1.28.0)
Genome_build: mm10
Supplementary_files_format_and_content: gene counts for RNA, MeDIP and hMeDIP, xls files

molecule: genomic DNA

organism: Mus musculus

source_name: D2R striatal projection neurons

extract_protocol:
FACS-sorting of GFP nuclei, phenol/chloroform DNA extraction, fragmentation with S2 Focused-ultrasonicator (Covaris) 150bp average, Truseq adaptors ligation, DNA denaturation, IP
Illumina Truseq DNA

tag: strain

tag: mouse line

tag: males/females

value: 5-hydroxymethylcytosine monoclonal mouse antibody clone (Diagenode)


title: D2R_hMeDIP_rep3

description:
hMeDIP, D2R, stranded
7_CAGATC_L007
processed data file: hmedip_gene_counts.xlsx


title: D1R_hMeDIP_rep3

description:
hMeDIP, D1R, stranded
11_ATCACG_L007
processed data file: hmedip_gene_counts.xlsx

source_name: D1R striatal projection neurons


title: NR_GZ_005: Vertical lobe - smallRNA

source_name: Vertical lobe

value: Vertical lobe


title: D2R_hMeDIP_rep1

description:
hMeDIP, D2R, stranded
3_TTAGGC_L005
processed data file: hmedip_gene_counts.xlsx


title: D1R_hMeDIP_rep1

description:
hMeDIP, D1R, stranded
1_ATCACG_L005
processed data file: hmedip_gene_counts.xlsx


title: NR_GZ_006: Skin - smallRNA

value: Skin

value: cutadapt, miRTrace 1.0.1, miRDeep2.0.1.2


title: HEK293-4A cells +EGF rep1

city: Shirokanedai

first: Mutsuhiro

last: Takekawa

state: Minato-ku, Tokyo

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Genome_build: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample.

source_name: Embryonic kidney cells

growth_protocol: HEK293-WT and HEK293-4A cells were seeded on 100 mm dish and cultured for 18 hours.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN).
RNA libraries were prepared using 100 ng of total RNA with an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: 20 ng/ml EGF for 60 minutes

value: treated with EGF for 60 min

tag: genotype

value: Myc-tagged 4A mutant


title: NR_GZ_007: Retina - smallRNA

source_name: Retina

value: Retina

value: cDNA


title: HEK293-4A cells +EGF rep3


title: D2R_MeDIP_rep3

description:
MeDIP, D2R, stranded
MP11_TTAGGC_L004
processed data file: medip_gene_counts.xlsx

data_processing:
alignment with BWA (0.7.5) for MeDIP and hMeDIP, Tophat (2.0.10) for RNA
reads assigned to genes using Rsubread (v1.28.0)
Genome_build: mm10
Supplementary_files_format_and_content: gene counts for RNA, MeDIP and hMeDIP, xls files

value: 5-methylcytosine monoclonal mouse antibody clone 33D3 (Diagenode)


title: D2R_MeDIP_rep2

description:
MeDIP, D2R, stranded
MP7_CAGATC_L003
processed data file: medip_gene_counts.xlsx


title: D2R_MeDIP_rep1

description:
MeDIP, D2R, stranded
MP3_TTAGGC_L001
processed data file: medip_gene_counts.xlsx


title: HEK293-4A cells rep3

value: untreated


title: HEK293-WT cells +EGF rep2

value: Myc-tagged WT


title: HEK293-4A cells rep1


title: NR_GZ_010: Central heart - smallRNA

source_name: Central heart

value: Central heart


title: D1R_MeDIP_rep3

description:
MeDIP, D1R, stranded
MP9_GATCAG_L003
processed data file: medip_gene_counts.xlsx


title: D1R_MeDIP_rep1

description:
MeDIP, D1R, stranded
MP1_ATCACG_L001
processed data file: medip_gene_counts.xlsx


title: D1R_MeDIP_rep2

description:
MeDIP, D1R, stranded
MP5_ACAGTG_L001
processed data file: medip_gene_counts.xlsx


title: HEK293-WT cells +EGF rep1


title: HEK293-4A cells rep2


title: HEK293-WT cells rep3


title: HEK293-WT cells rep2


title: GP2_3

city: zhongshan

first: yongyan

last: pei

address: Long life water, wuguishan street, zhongshan city

department: School of Pharmaceutical and Chemical Engineering

country: China

institute: Guangdong Pharmaceutical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene FPKM values for every gene and every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: healthy controls whole blood

extract_protocol:
Blood samples from septic patients and healthy volunteers were centrifuged at 3000× g for 15 minutes and stored in −80℃. Total RNA was extracted using RNAprep Pure high efficiency total RNA extraction kit (TIANGen, Beijing, China). Follow the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

value: healthy control 3

value: whle blood


title: GP2_4

value: healthy control 4


title: GP2_2

value: healthy control 2


title: GP2_1

value: healthy control 1


title: D1R_hMeDIP_rep2

description:
hMeDIP, D1R, stranded
9_GATCAG_L007
processed data file: hmedip_gene_counts.xlsx

value: 5-hydroxymethylcytosine monoclonal mouse antibody clone (Diagenode)


title: HEK293-4A cells +EGF rep2


title: NR_GZ_004: Axial Nerve Cord - smallRNA

source_name: Axial Nerve Cord

value: Axial Nerve Cord

value: SMARTer smRNA-Seq


title: GP1_3

source_name: sepsis patients whole blood

value: sepsis patient 3


title: GP1_4

value: sepsis patient 4


title: HEK293-WT cells +EGF rep3

value: treated with EGF for 60 min


title: GP1_2

value: sepsis patient 2


title: HEK293-WT cells rep1


title: Alveolar organoid, -4OHT, R2

city: Philadelphia

first: Andrew

middle: E

last: Vaughan

state: PA

address: 3800 Spruce Street, Old Vet 370 E

institute: University of Pennsylvania

data_processing:
Reads were aligned to the mm10 mouse genome using Kallisto and imported into R Studio for analysis via the TxImport package.
Transcripts with low counts were filtered out if they had 1) zero reads in any sample, or 2) less than at least one count per million in at least two samples.
Data was then normalized using the trimmed mean of M values normalization method in the EdgeR package.
Mean-variance trend fitting, linear modeling, and Bayesian statistics for differential gene expression analysis were performed using the Voom, LmFit, and eBayes functions, respectively, of the Limma package, yielding differentially expressed genes between ΔNp63WT and ΔNp63KO groups.
Assembly: mm10
Supplementary files format and content: abundance.tsv files generated from Kallisto alignment and Excel files of RPKM values

source_name: Post-flu lung basal cells

growth_protocol: Post-injury basal cells were grown in either airway media for monolayers and airway organoids or in alveolar media for alveolar organoids. Media composition can be found in Methods under "Primary intrapulmonary p63+ progenitor culture and passaging".

extract_protocol:
RNA was isolated using the ReliaPrep™ RNA Cell Miniprep kit (Promega).
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina according to manufacturer's instructions

treatment_protocol:
1uM 4OHT for +4OHT (∆Np63 KO) samples or equivalent volume DMSO for -4OHT (solvent only, ∆Np63 WT) samples
Monolayers treated with DMSO or 4OHT for 48 hours, organoids for 7 days

value: Post-flu lung basal cells

value: Np63 WT

value: DMSO

tag: time

value: 7 days


title: Alveolar organoid, +4OHT, R1

value: Np63 KO

value: 1uM 4OHT


title: Alveolar organoid, +4OHT, R2


title: Alveolar organoid, -4OHT, R3


title: Alveolar organoid, +4OHT, R3


title: seedlings, pms2ab, rep1 (ATAC-seq)

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalls performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
MACS2 was used to identify accessible regions.
DiffBind was used to identify differentially accessible regions of mutants and the wide type.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long day photoperiod (23°C, 16 h light/22°C, 8 h dark).

extract_protocol:
Nucei of 12-day-old Arabidopsis seedlings were extracted and the accessible chromatin regions were fragamented and tagged with adaptor DNA sequence by Tn5.
Sequencing libraries were built for ATAC-seq (the paired-end 150-bp strategy on the Illumina Novaseq 6000 platform).

tag: seedlings

value: Arabidopsis seedlings


title: Alveolar organoid, -4OHT, R1


title: E26_tumour_CL_RNAseq

city: Edinburgh

first: Karin

last: Purshouse

address: Crewe Rd S

country: United Kingdom

institute: University of Edinburgh

data_processing:
All sequencing reads were mapped using STAR 2.7.1a
For WGS samples, STAR settings '--alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndToEnd  --outFilterMultimapNmax 1'  was used
For RNA samples, STAR settings '--outFilterMultimapNmax 1' were used
Assembly: hg38
Supplementary files format and content: Alignments were converted to bigWig files using deepTools bamCoverage with setting '--normalizeUsingRPKM'
Supplementary files format and content: AmpliconArchitect and AmpliconClassifier were used to generate AA.bed files

source_name: primary cell culture

growth_protocol: Cells cultured in serum-free basal DMEM/F12 medium (Sigma) supplemented with N2 and B27 (Life Technologies), 2 μg/mL laminin (Cultrex), and 10 ng/mL growth factors EGF and FGF-2 (Peprotech) (Pollard et al., 2009).

extract_protocol:
RNA extracted from cells using the QIAGEN RNeasy kit.
Samples prepared with KAPA mRNA Hyper prep kit with KAPA SeqCap Adapters. Fragmentation 94 deg C for 6 mins, library amplification of 12 cycles. Each library quantified with Qubit dsDNA HS assay, average fragment size calculated with Bioanalyzer DNA 1000 or DNA HS. Molarity of each library was calculated, normalized to ∼10 nM and pooled, 24 libraries per pool. Each pool quantified using Qubit dsDNA HS assay, average fragment size determined using Bioanalyzer DNA HS. Further detail at Gangoso et al, Cell, 2021.

value: primary cell culture

value: glioblastoma


title: seedlings, minu12, rep2 (ATAC-seq)


title: seedlings, minu12, rep1 (ATAC-seq)


title: E28_tumour_CL_RNAseq


title: Airway organoid, +4OHT, R3


title: seedlings, swi3d, rep2 (ATAC-seq)


title: Airway organoid, -4OHT, R3


title: Airway organoid, +4OHT, R2


title: Airway organoid, +4OHT, R1


title: CA-5M-8

city: Canterbury

first: Rebecca

middle: Anne

last: Hall

address: Giles Lane

department: School of Biosciences

institute: University of Kent

data_processing:
Evaluate sequence quality: #reads; yield(Mbases); mean quality score; % bases >=30. Per base sequence quality: FastQC. Per sequence GC content: FastQC.
Mapping sequence reads to the reference genome: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the C_albicans_SC5314 (http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/current/) or the P_aeruginosa_PAO1 (https://www.ncbi.nlm.nih.gov/nuccore/NC_002516.2) reference genomes available on ENSEMBL separately using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Extracting gene hit counts: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Differential expression was calculated using DESeq2
Genome_build: C. albicans SC5314 (http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/current/) or P. aeruginosa PAO1 (https://www.ncbi.nlm.nih.gov/nuccore/NC_002516.2)
Supplementary_files_format_and_content: Excel work books containing the DEseq2 results for the multiple comparisons performed during the analysis. Each file contains the normalised reads for each sample, p value, adjusted p value, and the log2 expression value

organism: Candida albicans

source_name: in vitro mono-species biofilm

growth_protocol: P.aeruginosa was maintained and cultured in Miller modified LB; C. albicans in YPD. Both were grown at 37°C, with aeration, at 200 rpm overnight. Cultures were washed twice in PBS and P. aeruginosa cultures diluted to OD600 of 0.2, and C. albicans cultures diluted to 1×10^6 cells/mL, in Mueller Hinton broth (MHB). 300 µl of the P. aeruginosa culture and/or 3 mL of the C. albicans culture were added to flat-bottom 6-well plates, and the total volume was made up to 6mL per well with MHB. Single- and dual-species biofilms were incubated in triplicate, statically at 37°C for 24 h.

extract_protocol:
After 4 h of treatment, the media was removed and replaced with 2 mL PBS + 50 µg/mL DNase, which had been incubated at 37°C. Sterile cell scrapers were used to detach biofilm cells and technical replicates were pooled and mixed in a 15-mL Falcon tube, on ice. The biofilm cell samples were centrifuged at 3500 rpm, at 4°C, for 5 min, to form cell pellets. The supernatant was removed, and cell pellets were snap frozen in liquid nitrogen, before being stored at -70°C. Samples were packaged on dry ice and shipped to GeneWiz®, UK, for RNA extraction, sequencing and analysis. RNA extraction was performed using the QIAGEN Rneasy Plus mini Kit.
1) Ribosomal RNA depletion, 2) RNA fragmentation and random priming, 3) first and second strand cDNA synthesis, end repair, 5' phosphorylation and dA-tailing, 4) adapter ligation, PCR enrichment and sequencing. Sequencing: Illumina HiSeq, 2x150bp configuration, single index, per lane.

treatment_protocol: After 24 h, the MHB media was replaced with MHB ± 5 μg/mL meropenem.

tag: age

value: 28-hour biofilm

value: treated with 5ug/mL meropenem at 24h, for 4h


title: seedlings, syd, rep2 (ATAC-seq)

value: syd-/-


title: CA-5M-7


title: seedlings, swi3d, rep1 (ATAC-seq)


title: Airway organoid, -4OHT, R2


title: Airway organoid, -4OHT, R1


title: GP1_1

value: sepsis patient 1

tag: tissue

value: whle blood


title: CA-0M-7

value: untreated


title: seedlings, syd, rep1 (ATAC-seq)


title: CA-5M-6


title: Monolayer, +4OHT, R3


title: CA-0M-6


title: seedlings, pms2ab, rep2 (ATAC-seq)


title: CA-5M-4


title: seedlings, brd1213, rep2 (ATAC-seq)


title: CA-0M-4


title: PACA-5M-8

organism:
Pseudomonas aeruginosa
Candida albicans

source_name: in vitro dual-species biofilm


title: Monolayer, +4OHT, R2


title: Monolayer, +4OHT, R1


title: PACA-0M-7


title: PACA-0M-8


title: seedlings, brm, rep2 (ATAC-seq)

value: brm-/-


title: PACA-5M-6


title: seedlings, brm, rep1 (ATAC-seq)


title: Monolayer, -4OHT, R2


title: PACA-0M-6


title: CA-0M-8


title: PACA-5M-4


title: Monolayer, -4OHT, R1


title: seedlings, wt, rep1 (ATAC-seq)

value: wild type


title: +4OHT KO H3K27me3 ChIP IP 3

data_processing:
Sequencing was performed using a 2 x 150bp paired-end configuration on an Illumnia® HiSeq at a read depth of ~27 million reads per sample on average.
Adapter sequences were trimmed and quality checked using Trim Galore!.
Bowtie2 was used for alignment to the built-in mm10 mouse genome index.
Trimmed and aligned files were processed using Samtools so that only properly mapped, paired, non-duplicate, non-mitochondrial, non-blacklisted reads remained.
MACS2 was used for peak calling of p63, H3K27ac, and H3K27me3 ChIP with corresponding universal 2% input controls for reference. For p63 and H3K27ac ChIP, peak calling was performed with default MACS2 settings and a FDR < 0.05. Due to difficulty in calling H3K27me3 peaks in ΔNp63KO samples, a stringent p-value cutoff of < 0.01 rather than FDR was used to identify peaks in H3K27me3 ChIP samples.
narrowpeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: BAM, BAI, narrowpeak for all samples except for 2% Inputs

growth_protocol: Post-injury basal cells were grown in airway media as monolayers. Media composition can be found in Methods under "Primary intrapulmonary p63+ progenitor culture and passaging".

extract_protocol:
ChIP was performed using the SimpleChIP® Plus Enzymatic Chromatic IP with Magnetic Beads Kit (Cell Signaling) protocol according to manufacturers instructions. In short, after 48h in either DMSO or 1μM 4OHT, media was removed and monolayers were cross-linked for 20 minutes in 1% PFA. Following fixation quenching with glycine and pelleting, nuclei were isolated, treated with micrococcal nuclease, and sonicated four times for 15 seconds each with an ultrasonic sonicator with a 1/8-inch probe on ice to shear chromatin into 150bp-900bp fragments. 5ug of cross-linked, digested chromatin was immunoprecipitated using 1ug of either rabbit anti-p63α (Cell Signaling, clone D2K8X), rabbit anti-H3K27ac (Cell Signaling, clone D5E4), or rabbit anti-H3K27me3 (Cell Signaling, clone C36B11).
ChIP-seq libraries were prepared using using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. After library cleanup, library concentrations were quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and size validated on a TapeStation (Agilent Technologies).

treatment_protocol: 1uM 4OHT for +4OHT (∆Np63 KO) samples or equivalent volume DMSO for -4OHT (solvent only, ∆Np63 WT) samples for 48 hours.

value: Post-flu lung basal cells

tag: chip antibody


title: seedlings, PMS2B-GFP, IP, rep2 (ChIP-seq)

data_processing:
Basecalls performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
MACS2 was used to identify ChIP-enriched peaks.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage.

extract_protocol:
12-day-old Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with GFP antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: seedlings

tag: expressing

value: GFP (Abcam, ab290)


title: seedlings, PMS2B-GFP, IP, rep1 (ChIP-seq)


title: seedlings, brd1213, rep1 (ATAC-seq)


title: PACA-5M-7


title: +4OHT KO H3K27me3 ChIP IP 2

value: rabbit anti-H3K27me3 (Cell Signaling, clone C36B11)


title: +4OHT KO H3K27me3 ChIP IP 1

value: Np63 KO


title: Monolayer, -4OHT, R3

value: Np63 WT

value: DMSO


title: Rujinpei

type: RNA

city: shanghai

first: he

last: sun

address: dongfang hospital

institute: east hospital

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

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

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: ARDS balf exosome

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

growth_protocol: normal balf exosome  and ARDS balf exosome

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

treatment_protocol: exosome  isolation by trizol ls

tag: exosome

value: ARDS balf exosome


title: Shijiawei


title: -4OHT WT H3K27me3 ChIP IP 3


title: PA-5M-8

organism: Pseudomonas aeruginosa


title: seedlings, PMS2B-GFP, Input (ChIP-seq)


title: seedlings, MINU2-GFP, IP, rep2 (ChIP-seq)


title: -4OHT WT H3K27me3 ChIP IP 2


title: seedlings, wt, rep2 (ATAC-seq)

value: Arabidopsis seedlings


title: PA-0M-8

value: 28-hour biofilm


title: PACA-0M-4


title: PA-5M-7

value: treated with 5ug/mL meropenem at 24h, for 4h


title: Qinwenzhen


title: seedlings, MINU2-GFP, IP, rep1 (ChIP-seq)


title: -4OHT WT H3K27me3 ChIP IP 1


title: PA-0M-7


title: PA-5M-6


title: Wuzaisheng

source_name: normal balf exosome

value: normal balf exosome


title: +4OHT KO H3K27ac ChIP IP 3

value: 1uM 4OHT

value: rabbit anti-H3K27ac (Cell Signaling, clone D5E4)


title: Chenliru


title: seedlings, MINU2-GFP, Input (ChIP-seq)


title: PA-0M-6

value: untreated


title: Sunhe


title: Wangdan


title: PA-5M-4


title: seedlings, SYS1-GFP, IP, rep2 (ChIP-seq)


title: PA-0M-4


title: E28_Blood_B_WGS

data_processing:
All sequencing reads were mapped using STAR 2.7.1a
For WGS samples, STAR settings '--alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndToEnd  --outFilterMultimapNmax 1'  was used
For RNA samples, STAR settings '--outFilterMultimapNmax 1' were used
Assembly: hg38
Supplementary files format and content: Alignments were converted to bigWig files using deepTools bamCoverage with setting '--normalizeUsingRPKM'
Supplementary files format and content: AmpliconArchitect and AmpliconClassifier were used to generate AA.bed files
Library strategy: WGS

extract_protocol:
Genomic DNA extracted from blood using QIAamp DNA blood kit
Samples were sent to BGI (Beijing Genomics) for sequencing. PE100 human WGS with normal library construction (BGI). At least 180Gb data per sample generated.  10 samples sequenced and merged.

value: primary cell culture

tag: cell line

value: glioblastoma


title: +4OHT KO H3K27ac ChIP IP 2

tag: cell type

value: Post-flu lung basal cells


title: Shimeiju


title: seedlings, SYS1-GFP, Input (ChIP-seq)

value: seedlings


title: E28_tumour_CL_WGS

extract_protocol:
Genomic DNA extracted from cells using the Qiagen DNA/RNA kit
Samples were sent to BGI (Beijing Genomics) for sequencing. PE100 human WGS with normal library construction (BGI). At least 180Gb data per sample generated.  18 samples sequenced and merged.


title: E26_Blood_B_WGS

extract_protocol:
Genomic DNA extracted from blood using QIAamp DNA blood kit
Samples were sent to BGI (Beijing Genomics) for sequencing. PE100 human WGS with normal library construction (BGI). At least 180Gb data per sample generated.  14 samples sequenced and merged.


title: seedlings, SWI3D-GFP, IP, rep2 (ChIP-seq)

value: GFP (Abcam, ab290)


title: -4OHT WT H3K27ac ChIP IP 3

tag: treatment


title: -4OHT WT H3K27ac ChIP IP 1


title: seedlings, SWI3D-GFP, IP, rep1 (ChIP-seq)


title: E26_tumour_CL_WGS

extract_protocol:
Genomic DNA extracted from cells using the Qiagen DNA/RNA kit
Samples were sent to BGI (Beijing Genomics) for sequencing. PE100 human WGS with normal library construction (BGI). At least 180Gb data per sample generated.  11 samples sequenced and merged.


title: AMM_24h, B

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

data_processing:
Illumina HiSeq v4
Reads were filtered using trimmomatic and mapped on the Cephalotrichum gorgonifer genome assembly. Mapping was performed using BWA  and reverse transcripts were counted using python script HTSeq and exons as annotation features.
Normalization and statistics were done using R/Bioconductor and the limma and edgeR packages, using mean-variance weighting (voom) and TMM normalisation
Assembly: C. gorgonifer NG_p51, PRJEB15373
Supplementary files format and content: Matrix table with RPKM values for each experiment
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Cephalotrichum gorgonifer

source_name: fungal cell

growth_protocol: 60 mL of AMM- liquid media were inoculated with 4*10^6 spores/mL. Liquid shake flask culture with in AMM-liquid media for 24/48 hours

extract_protocol: poly A enrichment, NEXTERA library prep kit

treatment_protocol: Cephalotrichum gorgonifer was grown in AMM for 24 and 48 hours

value: grown in AMM for 24 hours

tag: replicate

value: Replicate 2

value: fungal cell


title: AMM_48h, B

value: grown in AMM for 48 hours


title: seedlings, SWI3D-GFP, Input (ChIP-seq)


title: AMM_48h, A

value: Replicate 1


title: AMM_24h, A


title: seedlings, SYD-GFP, IP, rep2 (ChIP-seq)

value: SYD-GFP


title: PtrVCS2-3×FLAG overexpression plants, input_DNA, rep 3

city: Harbin

first: Xiufang

last: Dai

address: Hexing Road 26#, Xiangfang District

department: School of Forestry, State key laboratory of tree genetics and breeding

institute: Northeast Forestry University

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the P. trichocarpa genome v.3.0 genome using Bowtie2 v2.3.5 with parameter (-N 1). Only uniquely mapping reads were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 50 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=1e-05
bigWig files were generated using the Deeptools v3.5.1. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2.1.0 with default settings.
Assembly: P. trichocarpa genome v.3.0
Supplementary files format and content: bigWig (Three IP DNA biological replicates, and Three input DNA biological replicates were pooled), narrowPeak (Peak file with pooling input as control)

organism: Populus trichocarpa

source_name: cambium

extract_protocol:
Cambium tissue was cross-linked in 1% formaldehyde and used to isolate nuclei and chromatin. The chromatin was sheared into 200- to 1000-bp fragments, subjected to immunoprecipitation using Anti-FLAG antibody (Sigma, F1804), and collected with protein G magnetic beads (Invitrogen). Precipitated chromatin was de-cross-linked to release the ChIP-DNA.
Libraries were prepared using a library preparation kit (New England Biolabs) according to the manufacturer’s instructions. 20 ng of DNA was used as starting material for input and ip samples. DNA fragments around 200 bp in length were selected and amplified 9 cycles on the thermocycler.  Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: cambium

value: PtrVCS2-3XFLAG overexpression


title: -4OHT WT p63 ChIP IP 2

value: Np63 WT

value: DMSO

value: rabbit anti-p63a (Cell Signaling, clone D2K8X)


title: PtrVCS2-3×FLAG overexpression plants, input_DNA, rep 2


title: seedlings, SYD-GFP, IP, rep1 (ChIP-seq)


title: seedlings, SYS1-GFP, IP, rep1 (ChIP-seq)


title: +4OHT KO H3K27ac ChIP IP 1

value: Np63 KO

value: 1uM 4OHT

value: rabbit anti-H3K27ac (Cell Signaling, clone D5E4)


title: -4OHT WT p63 ChIP IP 1

value: Post-flu lung basal cells


title: -4OHT WT H3K27ac ChIP IP 2


title: seedlings, SYD-GFP, Input (ChIP-seq)

value: seedlings


title: PtrVCS2-3×FLAG overexpression plants, input_DNA, rep1


title: +4OHT Universal 2% Input Control


title: PtrVCS2-3×FLAG overexpression plants, IP_DNA, rep 3

value: Anti-FLAG (Sigma, F1804)


title: seedlings, SWI3C-GFP, IP, rep2 (ChIP-seq)

value: GFP (Abcam, ab290)


title: PtrVCS2-3×FLAG overexpression plants, IP_DNA, rep 2


title: -4OHT Universal 2% Input Control


title: -4OHT WT p63 ChIP IP 3


title: seedlings, SWI3C-GFP, IP, rep1 (ChIP-seq)


title: seedlings, BRD1-GFP, IP, rep2 (ChIP-seq)


title: D2R_mRNA_rep3

description:
mRNA, D2R, unstranded
mt14
processed data file: RNA_gene_counts.xlsx

source_name: D2R striatal projection neurons

extract_protocol:
mRNA purification by translating ribosome affinity purification (TRAP), RT with Nugen Ovation RNA-seq v2 kit
Illumina TruSeq RNA

tag: antibody

value: anti-GFP, clones 19F7/19C8 Memorial Sloan-Kettering Monoclonal Antibody facility New York

tag: molecule type

value: translating RNA


title: PtrVCS2-3×FLAG overexpression plants, IP_DNA, rep 1


title: seedlings, SWI3C-GFP, Input (ChIP-seq)


title: D1R_mRNA_rep3

description:
mRNA, D1R, unstranded
mt5
processed data file: RNA_gene_counts.xlsx

source_name: D1R striatal projection neurons

tag: strain

tag: mouse line

value: anti-GFP, clones 19F7/19C8 (Memorial Sloan-Kettering Monoclonal Antibody facility, New York)


title: seedlings, BRD1-GFP, Input (ChIP-seq)


title: TGF_day_12

city: Boston

last: Emili

state: MA

address: 72 East Concord St

department: Biochemistry

institute: Boston University

description: miRNA expression

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw Affymetrix CEL files (miRNA 4.0) were normalized to produce probeset-level expression values for all probesets using Expression Console (version 1.4.1.46), using the Robust Multiarray Average (RMA) and Detection Above BackGround (DABG). Each microRNA was also assigned a Present (P) or Absent (A) call in each sample, denoting whether its expression was significantly higher than that of a collection of negative control probes comprised of anti-genomic sequences of the same length and GC content. Analysis was limited to Human microRNAs interrogated by the array. All samples had similar quality metrics, including mean Relative Log Expression (RLE) values and percent Present calls (%P), indicating that all samples were of similar quality.

label: biotin

source_name: MCF10A cells treated with TGFbeta for 12 days

label_protocol: not provided

growth_protocol: Standard culture conditions for MCF10A

extract_protocol: Qiagen Rneasy kit

treatment_protocol: 10 ng/mL TGFbeta in complete growth medium for indicated time points

value: Normal breast epithelial cell line

value: TGFbeta for 12 days


title: TGF_day_8

description: miRNA expression

source_name: MCF10A cells treated with TGFbeta for 8 days

value: TGFbeta for 8 days


title: D1R_mRNA_rep1

description:
mRNA, D1R, unstranded
mt1
processed data file: RNA_gene_counts.xlsx

tag: males/females


title: D2R_mRNA_rep1

description:
mRNA, D2R, unstranded
mt7
processed data file: RNA_gene_counts.xlsx


title: seedlings, BRD1-GFP, IP, rep1 (ChIP-seq)


title: TGF_day_8 [scRNA-seq]

description:
T7
RNA_expression

library_source: transcriptomic single cell

data_processing:
Processed using BaseSpace (Illumina) with ‘hg19’ as the reference for alignment.
Assembly: hg19 (GRCh37)
Supplementary files format and content: scRNAseq_processed.tsv: umi count txt file.

growth_protocol: Standard culture conditions for MCF10A.

extract_protocol:
Qiagen RNeasy kit.
Single-cell suspensions of MCF10A were washed and resuspended in ice-cold PBS containing 0.1% BSA at a concentration of ~2500 cells/µL. Single cells were captured in the ddSEQ microfluidic system (Bio-Rad), mRNA libraries were built using the SureCell WTA 3′ Library Prep Kit (Illumina), libraries sequenced on NextSeq 500 (Illumina) using 150 cycle high output kit (Illumina). Protocols recommended by the manufacturers were followed at each stage.

treatment_protocol: 10 ng/mL TGFbeta in complete growth medium for indicated time points.


title: D1R_mRNA_rep2

description:
mRNA, D1R, unstranded
mt2
processed data file: RNA_gene_counts.xlsx


title: D2R_mRNA_rep2

description:
mRNA, D2R, unstranded
mt10
processed data file: RNA_gene_counts.xlsx


title: TGF_day_6 [scRNA-seq]

description:
T6
RNA_expression

source_name: MCF10A cells treated with TGFbeta for 6 days

value: TGFbeta for 6 days


title: adjacent non-neoplastic tissue sample 8NT

city: jinan

first: Xin

last: Qin

state: Shandong Province

address: Wenhuaxi Road

institute: Qilu hospital of Shandong University

data_processing:
RNA sequencing was carried out using Illumina HiSeq 4000 sequencer at Metware Biotechnology (Wuhan, China).
Paired-end reads were quality controlled by Q30.
Cutadapt software (v 1.9.3) was used to remove low-quality reads and 3’ adaptor-trimming
Hisat2 (v 2.0.4) was further used to align clean reads from RNA sequencing, and sequencing depth and gene length were adjusted by Fragments Per Kilobase of transcript per Million fragments mapped.
Assembly: Human NCBI genome build 36
Supplementary files format and content: text files include count values for each Sample
Supplementary files format and content: text files include FPKM values for each Sample

source_name: adjacent non-neoplastic tissue

extract_protocol:
Total RNA was extracted using Trizol reagent(Invitrogen) following the manufacturer's instructions
Sequencing libraries were generated using NEBNextR Ultra™ RNA Library Prep Kit (New England Biolabs) following manufacturer’s recommendations

treatment_protocol: Tumor specimens and their matched normal tissues were collected from these patients who underwent nephrectomy with the signed informed consent from each patient. Collected specimens were stored in nitrogen tanks until use.

value: adjacent non-neoplastic tissue

tag: Sex

value: Male

tag: tumor grade

tag: tumor stage

value: Stage I

tag: t

tag: n

tag: m

tag: tumor size


title: adjacent non-neoplastic tissue sample 9NT

tag: tissue

tag: age

value: Female


title: adjacent non-neoplastic tissue sample 10NT

value: Stage III


title: TGF_day_5

description: miRNA expression

source_name: MCF10A cells treated with TGFbeta for 5 days

tag: cell line

value: TGFbeta for 5 days


title: TGF_day_4

description: miRNA expression

source_name: MCF10A cells treated with TGFbeta for 4 days

tag: treatment

value: TGFbeta for 4 days


title: TGF_day_6

description: miRNA expression


title: TGF_day_3

description: miRNA expression

source_name: MCF10A cells treated with TGFbeta for 3 days

value: TGFbeta for 3 days


title: adjacent non-neoplastic tissue sample 7NT


title: TGF_day_5 [scRNA-seq]

description:
T5
RNA_expression

tag: cell type


title: TGF_day_2

description: miRNA expression

source_name: MCF10A cells treated with TGFbeta for 2 days

value: TGFbeta for 2 days


title: adjacent non-neoplastic tissue sample 6NT


title: adjacent non-neoplastic tissue sample 5NT


title: TGF_day_4 [scRNA-seq]

description:
T4
RNA_expression


title: TGF_day_3 [scRNA-seq]

description:
T3
RNA_expression


title: TGF_day_1

description: miRNA expression

source_name: MCF10A cells treated with TGFbeta  for 1 day

value: TGFbeta  for 1 day


title: adjacent non-neoplastic tissue sample 4NT


title: Untreated_Control

description: miRNA expression

source_name: Untreated MCF10A cells

value: Untreated


title: TGF_4_hours

description: miRNA expression

source_name: MCF10A cells treated with TGFbeta for 4 hours

value: TGFbeta for 4 hours


title: TGF_day_1 [scRNA-seq]

description:
T2
RNA_expression

source_name: MCF10A cells treated with TGFbeta for 1 day

value: TGFbeta for 1 day


title: adjacent non-neoplastic tissue sample 3NT


title: PBLD expression-PBLD-Overexpression 3

city: guangzhou

first: LU

last: HAN

state: Guangdong province

address: No.1838, baiyun avenue north, baiyun district

department: Department of gastroenterology

institute: Nanfang Hospital，southern medical university

description:
p3
microRNA expression in exosomes derived from HepG2 cells in PBLD-overexpressed group.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: All cell lines used in this study were tested by short tandem repeat analysis, validated to be free of Mycoplasma. Cells were cultured in DMEM (Gibco, USA) medium supplemented with 10% fetal bovine serum (BI, Israel), maintained at 37°C, in a 5% CO2 incubator, and used within 30 passages for all experiments.

extract_protocol: The cell culture medium was filtered with a 0.22 µm filter (Millipore, USA) and collected for exosome isolation using ExoQuick-TC® ULTRA kit (SBI, USA). 1mL of ExoQuick-TC reagent was added to 5mL of cell culture medium and maintained at 4°C overnight. Then, the exosome precipitate was harvested by centrifugation according to the manufacturer’s instructions. The isolated exosomes were resuspended by PBS and stored at -80°C for further use. The concentration of exosome suspensions was measured using the BCA method.

treatment_protocol: HCC cells were seeded in sterile cell culture dishes. When cell conﬂuency reached over 60%, the original culture medium was replaced by exosome-depleted FBS (SBI, USA) medium. After 48 h, the cell culture medium were harvested for exosome isolation.

tag: sample type

value: Exosomes

value: PBLD-upregulated


title: adjacent non-neoplastic tissue sample 2NT


title: Untreated_Control [scRNA-seq]

description:
T0
RNA_expression

value: Normal breast epithelial cell line


title: PBLD expression-PBLD-Overexpression 2

description:
p2
microRNA expression in exosomes derived from HepG2 cells in PBLD-overexpressed group.


title: TGF_4_hours [scRNA-seq]

description:
T1
RNA_expression


title: adjacent non-neoplastic tissue sample 1NT

value: Stage II


title: PBLD expression-PBLD-Overexpression 1

description:
p1
microRNA expression in exosomes derived from HepG2 cells in PBLD-overexpressed group.


title: PBLD expression-Control 3

description:
c3
microRNA expression in exosomes derived from HepG2 cells in control group.

value: Control


title: clear cell renal cell carcinoma sample 10CA

source_name: clear cell renal cell carcinoma

value: clear cell renal cell carcinoma

value: Male


title: day 36, sample 7, scRNAseq

city: Stockholm

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

description:
10x Genomics
Raw data not provided due to General Data Protection Regulation

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v3.0.1.
Assembly: Assembly: GRCh37
Supplementary files format and content: 10X Genomics .h5 file (gene expression matrices)

source_name: Human immune cells from MISTRG humanized mouse

extract_protocol:
Human myeloid cells were sort-purified as live human CD45+CD11b+HLA-DR+ cells (lacking mouse CD45) from the perfused lungs of seven different MISTRG mice that were transplanted with the same pooled batch of human CD34+ cells. Further processing of sorted lung myeloid cells (GEM generation, barcoding, cleanup, cDNA amplification) was performed with reagents and protocols from 10x Genomics Chromium Single Cell 3' Reagent kit v2.
Library construction was done according to the manufacturer’s instructions using the 10x Genomics Chromium Single Cell 3' Reagent kit v2.

value: Immune cells

value: Lung tissue

tag: host strain

value: MISTRG mice

value: 36 Days


title: PBLD expression-Control 2

description:
c2
microRNA expression in exosomes derived from HepG2 cells in control group.


title: iPS-P0-UCB-Gustav2_414

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

data_processing:
Library strategy: MethylCap-Sequencing
Sequence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with bcl2fastq v2.17.1.14
Trimming and removal of residual adapters was done with AdapterRemova
Reads were then mapped to the Ensembl GRCh38 human genome using Bowtie2
Differentially methylated regions were identified using QSEA R package
Genome_build: Human GRCh38
Supplementary_files_format_and_content: Normalized counts per gene

source_name: Umbilical cord blood

growth_protocol: Approval was obtained for human cell and tissue sample collection and genetic reprogramming from the Institutional Review Board (protocols 19–252, 18–243, 21–060, 19–284 and 415-E/1776/4-2014, Ethics Committee of the province of Salzburg). Adult samples were collected in accordance with the Declaration of Helsinki after written informed consent from healthy volunteers. Umbilical cord blood (UCB) samples were collected after written informed consent by the mother-to-be obtained prior to delivery of full-term pregnancies. MSCs from bone marrow (BM) and UCB were isolated and expanded under animal serum-free conditions using pooled human platelet lysate (pHPL) replacing fetal bovine serum and their purity, identity, and viability was characterized by flow cytometry . Clonogenicity and differentiation capacity was assessed. PBMC were isolated by density centrifugation from random donor buffy coats.   Induced pluripotent stem cells (iPSCs) were reprogrammed from primary MSCs (derived from BM or UCB) by non-integrative Sendai Viral vector kit (CytoTuneTM-iPS Sendai Reprogramming Kit encoding for Oct4, Sox2, KLF4 and c-Myc, Life Technologies Cat.No.A1378001) by the Harvard Stem Cell Institute (HSCI) iPS Core Facility (Cambridge, MA, USA). The reprogramming protocol was described by Fusaki and colleagues in 2009 and adapted by the HSCI. Human iPSCs were characterized by cytogenetic analysis of at least twenty G-banded metaphase cells per clone and teratoma formation.   Human iPSCs were initially transferred from mouse embryonic feeder layers to feeder-free conditions and thereafter maintained on a selected batch of Matrigel® (Corning) in mTeSRTM1 (STEMCELL Technologies) medium. When reaching a cell density appropriate for splitting, iPSCs were harvested using Gentle Cell Dissociation Reagent (STEMCELL Technologies). Viable cells were counted and seeded at a density of 5 x 104 cells per cm2 on Matrigel® in mTeSRTM1 containing 10 µM Y-27632 ROCK pathway inhibitor (Selleckchem).

extract_protocol:
isolated DNA was sheared using a Bioruptor device (Diagenode). Subsequently, methylated DNA was isolated and eluted in high salt elution buffer using the MethylCap kit (Diagenode) according to the manufacturer´s instructions .
Methylated DNA samples were prepared for next generation sequencing using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer´s instructions. Amplified libraries were analyzed using the Bioanalyzer 2100 device and DNA 1000 Kit (Agilent) and concentrations were determined by means of Qubit 3.0 fluorometer device and the dsDNA BR assay (ThermoFisher). Samples were sequenced using the Illumina HiSeq 1500 system (50 bp single reads) in three independent rounds.

treatment_protocol: After 24 hours, the medium was changed to STEMdiff™ Mesoderm Induction Medium (STEMCELL Technologies, defined, xeno-free medium) and the medium was replaced daily for the next consecutive 4 days. On day 5, cells were harvested using TrpLETM (Gibco) and the expression of early mesoderm markers Brachyury and CD56 was determined by flow cytometric analysis. Cells were seeded in EGMTM-2 containing hydrocortisone, hFGF-B, VEGF, R3-IGF, Ascorbic Acid, hEGF (Lonza), preservative-free heparin 10 IU/mL (Biochrom), dipeptiven (1.2 mg/ml, L-glutamin – L-arginin dipeptide, clinical grade: Fresenius Kabi), 10% pHPL and 10 µM Y-27632 at a cell density of 27,000 cells/cm2 without Matrigel® coating and cultured in humidified incubators (Binder CB210) at 37°C and 5% CO2 in ambient air. Until passage five, iPS-MSCs were passaged at a density of 27,000 cells/cm2 twice per week with addition of Y-27632. For microscopical documentation EVOS XL (Thermo Fhisher Scientific) was used. Differentiations were performed with iPS reprogrammed from MSCs derived from bone marrow (4 clones) or umbilical cord blood (3 clones).

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: day 36, sample 6, scRNAseq


title: iPS-P4-UCB-Gustav2_412


title: PBLD expression-Control 1

description:
c1
microRNA expression in exosomes derived from HepG2 cells in control group.


title: day 36, sample 5, scRNAseq


title: iPS-P8-UCB-Cornelius2_413


title: clear cell renal cell carcinoma sample 9CA

value: Female

value: Stage I


title: clear cell renal cell carcinoma sample 8CA


title: Adjacent normal biopsy from Patient 3

type: genomic

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

hyb_protocol: genomic DNA was bisulfite-converted using an EZ DNA methylation Kit (ZYMO research). DNA methylation level was measured using the Illumina Infinium HD Methylation Assay. Bisulfite converted DNA was hybridized with the Illumina HumanMethylation850 BeadChip 850K array (8 samples/chip), as described previously. (Dedeurwaerder et al, Epigenomics 2011).

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

data_processing: Raw data (uncorrected probe intensity values) from the Infinium Methylation arrays were processed as followed: Probes of low quality (detection p-value < 0.05) were first filtered out. Beta-values were then computed using the following formula: Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta-values were corrected for type I and type II bias using the peak-based correction (dedeurwaerder et al).  Then, SNP and cross-reactive probes based on the extended annotation of Mc Cartney et al. were removed. Finally, probes targeting X and Y-chromosomes were removed from the analysis.

label: Cy3 and Cy5

source_name: Breast

label_protocol: Standard Illumina Protocol

growth_protocol: HCT116 wt and double-knockout cells were maintained in McCoy's 5A medium (Gibco BRL) supplemented with 10% fetal bovine at 37°C under 5% CO2.

extract_protocol: Genomic DNA from cell lines (HCT116 WT and DKO) was extracted with the QIAamp DNA Mini Kit (Qiagen) using the recommended proteinase K and RNase A digestions, while frozen samples  genomic DNA (from breast tumour and normal biopsies) was extracted from 10-μm sections with the Qiagen DNeasy Blood and Tissue Kit according to the supplier’s instructions (Qiagen).

value: Breast biopsy

tag: condition

value: Adjacent normal

tag: cohortid


title: Adjacent normal biopsy from Patient 1


title: day 36, sample 4, scRNAseq


title: Breast tumour biopsy from Patient 7

value: Primary tumour


title: clear cell renal cell carcinoma sample 6CA


title: day 21, sample 3, scRNAseq

value: 21 days


title: Breast tumour biopsy from Patient 9


title: Breast tumour biopsy from Patient 10


title: iPS-P0-UCB-Cornelius2_410


title: day 21, sample 2, scRNAseq


title: Adjacent normal biopsy from Patient 2


title: 12X3

city: nanjing

first: ren

last: haiyan

address: No. 1 Weigang, Nanjing, China

institute: Nanjing Agricultural university

data_processing:
step1：Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
step2：Obtained clean reads were mapped to the mouse mm10 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models
step3：The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥1.5.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Spleen_ExPEC-infected group at 12 hpi

extract_protocol:
Spleens were removed, flash frozen on dry ice, and RNA was harvested using mirVana miRNA Isolation kit (AM1561, Ambion, Austin, TX, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: BALB/c

value: ExPEC-infected group at 12 hpi

value: spleen


title: 12X2


title: clear cell renal cell carcinoma sample 5CA

value: clear cell renal cell carcinoma

tag: Sex

value: Stage III


title: iPS-UCB-Gustav2_411


title: 12X1


title: iPS-P0-UCB-Cornelius1_408


title: Patient_17_pDC

city: Cambridge

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
FASTQ files were obtained by Illumina bcl2fastq2.
STAR and RSEM were used to align to GRCh38 and to calculate the raw counts for genes, respectively.
Assembly: GRCh38
Supplementary files format and content: raw counts and TPM in csv

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from the 7 cell populations using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 500 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the Hg38 human genome database and the ZIKV sequence (ZIKV strain PRVABC59, GenBank: KU501215.1).

value: peripheral blood

value: pDC

tag: phenotype

value: HD


title: DNMT1 and 3B DKO HCT116 cells repl1 (850k)

source_name: colon cell line

value: DNMT1 and 3B DKO


title: 6X2

source_name: Spleen_ExPEC-infected group at 6 hpi

value: ExPEC-infected group at 6 hpi


title: clear cell renal cell carcinoma sample 4CA

value: Male

tag: tumor grade

tag: tumor stage


title: WT HCT116 cells repl3 (850k)

value: WT


title: iPS-P4-BM-Alice1_407

source_name: Bone marrow

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: Patient_17_NK

value: NK


title: day 21, sample 1, scRNAseq

value: Immune cells

value: Lung tissue

value: MISTRG mice


title: iPS-P0-UCB-Gustav1_409


title: clear cell renal cell carcinoma sample 7CA

value: Stage I

tag: t

tag: n


title: Breast tumour biopsy from Patient 8

value: Breast biopsy

value: Primary tumour


title: clear cell renal cell carcinoma sample 3CA

value: clear cell renal cell carcinoma

value: Stage III

tag: m

tag: tumor size


title: 6X1

value: BALB/c

tag: age

tag: tissue

value: spleen


title: Breast tumour biopsy from Patient 4


title: iMSC-UBC-Gustav2_406

value: Mesenchymal stromal cells


title: Patient_17_Monocytes

value: peripheral blood

value: Monocytes

value: HD


title: 3X3

source_name: Spleen_ExPEC-infected group at 3 hpi

tag: treatment

value: ExPEC-infected group at 3 hpi


title: clear cell renal cell carcinoma sample 2CA

value: Male


title: Breast tumour biopsy from Patient 5


title: clear cell renal cell carcinoma sample 1CA

value: Female

value: Stage II


title: iPS-P4-UCB-Gustav3_405

tag: cell line

tag: cell type

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: DNMT1 and 3B DKO HCT116 cells repl2 (850k)

value: DNMT1 and 3B DKO


title: Patient_17_mDC

value: mDC


title: 3X1


title: Breast tumour biopsy from Patient 6

value: Breast biopsy

value: Primary tumour


title: PAH_3, scRNAseq

city: Graz

first: Francesco

last: Valzano

address: Neue Stiftingtalstraße 6, 8010 Graz

institute: Ludwig Boltzmann Institute for lung vascular research

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38 and mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Medium/small size pulmonary artery

extract_protocol:
Pulmonary arteries were dissected under stereomicroscope by following the branching pattern and including accompanying perivascular (adventitial) region. Arteries were minced and digested for 60 min at 37°C in phosphate-buffered saline (PBS) containing 2 mg/mL collagenase A (Roche) and DNase I (Sigma). Digest was filtered through 100 micron cell strainer into FBS and diluted with PBS. Following centrifugation, cell pellet was washed with PBS and passed through 40 micron cell strainer. The secondary, and tertiary pulmonary arteries from the left lung lobe were isolated from the lungs of 12 week old male mice kept under normobaric hypoxia (10% O2) or normoxia (21% O2) for three weeks minced and digested as described for the human counterpart.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: PA resident cells

value: Medium/small size pulmonary artery

tag: disease state

value: pulmonary arterial hypertension (PAH)


title: Patient_17_CD4


title: PAH_1, scRNAseq

description: 10x Genomics


title: PAH_2, scRNAseq

description: 10x Genomics


title: 3P3

source_name: Spleen_PBS-injected group at 3 hpi

value: BALB/c

value: PBS-injected group at 3 hpi

value: spleen


title: DNMT1 and 3B DKO HCT116 cells repl3 (850k)

tag: condition


title: 3X2


title: iPS-UCB-Cornelius3_403


title: Adjacent normal biopsy from Patient 4

value: Adjacent normal

tag: cohortid


title: iPS-P4-UCB-Cornelius1_402


title: Patient_17_B

value: peripheral blood

value: B

value: HD


title: Breast tumour biopsy from Patient 3


title: 3P2

tag: strain


title: Donor_3, scRNAseq

description: 10x Genomics

value: healthy control


title: 3P1


title: iMSC-BM-Alice2_400

value: Mesenchymal stromal cells


title: iPS-P8-UCB-Gustav2_401

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: Patient_16_pDC

value: pDC

value: nS


title: Patient_16_NK

value: NK


title: iMSC-BM-Alice1_399


title: Patient_16_Monocytes

value: Monocytes


title: iPS-BM-Betty2_398


title: WT HCT116 cells repl1 (850k)

value: WT


title: Patient_16_mDC

value: mDC


title: Breast tumour biopsy from Patient 1

value: Breast biopsy

value: Primary tumour


title: Donor_2, scRNAseq

description: 10x Genomics

value: PA resident cells

value: Medium/small size pulmonary artery


title: Breast tumour biopsy from Patient 2


title: High fat diet Tie2-Cre:RiboTAG pulldown Sample 676 IP

city: Los Angeles

first: Jason

middle: D

last: Hinman

state: CA

address: 635 Charles E. Young Dr. South, Rm 415

department: Neurology

institute: UCLA

description: High fat diet Tie2-Cre:RiboTAG pulldown

data_processing:
Reads aligned to reference genome using STAR spliced read aligner
No read trimming was performed
Fragment counts aligned to known exonic regions based on refSeq annotation were inputted into HTSeq package.
Additional QC steps assessed using PicardTools
Assembly: mm10
Supplementary files format and content: composite .csv file including FPKM values for each Sample

source_name: brain white matter

extract_protocol:
RNA samples were purified by Nucleospin miRNA kit (Machary-Nagel).
RNA libraries fro RNA-seq were prepared using Illumina Nugen Ovation Ultra Low Mass RNA kit  following manufacturer's protocol.

value: brain white matter

tag: genotype

value: 60% kCal from fat diet


title: High fat diet white matter  Sample 676 Input

description: High fat diet white matter


title: Control fat diet Tie2-Cre:RiboTAG pulldown Sample 556 IP

value: 10% kCal from fat diet


title: Patient_16_CD4

value: peripheral blood

tag: phenotype


title: Control fat diet white matter  Sample 556 Input

description: Control fat diet white matter


title: iPS-P8-BM-Alice2_396


title: iPS-P8-BM-Alice3_397


title: Donor_1, scRNAseq

description: 10x Genomics

value: healthy control


title: iMSC-UBC-Gustav1_395

value: Mesenchymal stromal cells


title: iPS-P8-BM-Betty3_394

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: Patient_15_pDC

value: pDC

value: vS


title: Control fat diet white matter  Sample 555 Input

description: Control fat diet white matter


title: Control fat diet Tie2-Cre:RiboTAG pulldown Sample 555 IP


title: Patient_15_NK

value: NK


title: High fat diet Tie2-Cre:RiboTAG pulldown Sample 517 IP

description: High fat diet Tie2-Cre:RiboTAG pulldown


title: Patient_16_CD8

value: nS


title: MPP VaviCre+Rxrabfl/fl rep2

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
Gene expression quantitation as transcript per million estimates of bulk RNA-Seq samples was obtained using the software Kallisto, using RefSeq mm10 transcript annotations, using AltAnalyze10. Gene set enrichment analyses of differentially expressed genes was performed using GO-Elite and ToppFun 11. For further gene expression analysis of WT, VavCre+Rxrabfl/fl, and VavCre+Rxrabfl/flMycfl/+ we applied the Bioconductor package NoiSeq, to correct for batch associated biases data, considering batch and genotype for LT-HSC comparisons on the Kallisto TPM values directly.12 To quantify alternative splicing differences between VaviCre+Rxrabfl/fl and Rxrabfl/fl we aligned the bulk RNA-Seq FASTQ files to the reference mouse genome (mm10) using the software STAR (version 2.6) and analyzed the associated BAM files using AltAnalyze. To adjust for batch differences prior to splicing analyses, we performed combat on the AltAnalyze produced junction count matrix, again considering both batch and genotype as covariates in the model, similar to previously described applications 13. AltAnalyze quantifies splicing events using the algorithm MultiPath-PSI and computes differential splicing events between designated sample groups, prior to predicting functional impacts (protein domain). Differential splicing events were defined based on an empirical Bayes moderated t-test p<0.05 and dPSI>0.1.
Assembly: mm10
Supplementary files format and content: Gene-level Transcript Per Million (TPM) estimates and Percent Spliced In values and annotations from MultiPath-PSI (no batch effects correction)

source_name: Bone Marrow

growth_protocol: Lineage negative cells from pulled animals were pre-flow purified using the Mouse Hematopoietic Progenitor (Stem) Cell Enrichment Set - DM (BD Bioscience). Thereafter, LT-HSC and MPP were FACS sorted in PBS 1x, 0.5 mM EDTA and 2% FCS to obtain pure populations.

extract_protocol:
After sorting, total RNA was isolated using the Arcturus® PicoPure® RNA Isolation Kit (Thermo Fisher) and RNAeasymini kit (QIAGEN) according to manufacturer's protocols.
Total RNA was extracted from sorted LT-HSCs and MPP3/MPP4 (MPPs)9 derived from each group of primary mice using Arcturus®PicoPure™ RNA Isolation Kit (Thermofisher). RNA quality and concentration were measured by Bioanalyzer 2100 using the RNA 6000 Nano Assay (Agilent Technologies). Total RNA samples (5ng) from LT-HSCs and MPPs were used for cDNA amplification using Ovation RNA-seq v2 assay kit (Tecan Genomics) to generate 2-4 microgram of double stranded cDNA. The Illumina protocol, Nextera XT DNA Library Preparation Kit was used to create DNA library templates from double stranded cDNA.
Paired-end sequencing using an Illumina NovaSeq 6000 SP Flow Cell was performed, at a target depth of 50 million paired-end reads.

value: MPP

tag: batch

value: Batch 1


title: MPP VaviCre+Rxrabfl/fl rep3


title: Patient_15_Monocytes

value: Monocytes


title: iPS-P0-UCB-Cornelius3_393


title: 6X3

value: BALB/c

value: ExPEC-infected group at 6 hpi

value: spleen


title: iPS-P4-UCB-Cornelius2_392


title: Patient_16_B

value: B


title: MPP VaviCre+Rxrabfl/fl rep1


title: MPP Rxrabfl/fl rep3


title: Patient_15_mDC

value: mDC


title: High fat diet white matter  Sample 517 Input

description: High fat diet white matter

value: brain white matter

value: 60% kCal from fat diet


title: High fat diet Tie2-Cre:RiboTAG pulldown Sample 516 IP

description: High fat diet Tie2-Cre:RiboTAG pulldown


title: iPS-P8-BM-Betty1_391


title: iPS-P0-UCB-Gustav3_389


title: Patient_15_CD4

value: peripheral blood


title: Control fat diet Tie2-Cre:RiboTAG pulldown Sample 489 IP

value: 10% kCal from fat diet


title: WT HCT116 cells repl2 (850k)

value: WT


title: MPP Rxrabfl/fl rep1


title: iPS-P8-UCB-Gustav1_388

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: Patient_15_CD8

value: vS


title: Patient_14_pDC

value: pDC


title: Patient_15_B


title: LT-HSC Vav1Cre+Rxrabfl/fl Myclfl/+ rep3

value: LT-HSC


title: LT-HSC Vav1Cre+Rxrabfl/fl Myclfl/+ rep2


title: Control fat diet white matter  Sample 489 Input

description: Control fat diet white matter


title: Patient_17_CD8

value: HD


title: High fat diet PDGFRa-Cre-ERT2:RiboTAG pulldown Sample 1325 IP

data_processing:
Reads aligned to reference genome using STAR spliced read aligner
No read trimming was performed
Fragment counts aligned to known exonic regions based on refSeq annotation were inputted into HTSeq package.
Additional QC steps assessed using PicardTools
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample


title: High fat diet white matter  Sample 516 Input

description: High fat diet white matter


title: iPS-P8-UCB-Cornelius3_387


title: iPS-BM-Betty1_386


title: Patient_14_NK

value: NK


title: iPS-P4-UCB-Gustav1_390


title: LT-HSC Vav1Cre+Rxrabfl/fl Myclfl/+ rep1


title: High fat diet PDGFRa-Cre-ERT2:RiboTAG pulldown Sample 1323 IP


title: MPP Rxrabfl/fl rep2

value: MPP

value: Batch 1


title: iPS-P4-BM-Alice2_385


title: Patient_14_Monocytes

value: Monocytes


title: LT-HSC Vav1Cre+Rxrabfl/fl rep6


title: LT-HSC Vav1Cre+Rxrabfl/fl rep5


title: High fat diet PDGFRa-Cre-ERT2:RiboTAG pulldown Sample 1322 IP


title: Patient_14_mDC


title: DNMT1 and 3B DKO HCT116 cells repl3 (450k)

hyb_protocol: genomic DNA was bisulfite-converted using an EZ DNA methylation Kit (ZYMO research). DNA methylation level was measured using the Illumina Infinium HD Methylation Assay. Bisulfite converted DNA was hybridized with the Illumina HumanMethylation450 BeadChip 450K array, as described previously. (Dedeurwaerder et al, Epigenomics 2011).

data_processing: Raw data (uncorrected probe intensity values) from the Infinium Methylation arrays were processed as followed: Probes of low quality (detection p-value < 0.05) were first filtered out. Beta-values were then computed using the following formula: Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta-values were corrected for type I and type II bias using the peak-based correction (dedeurwaerder et al).  Then, SNP and cross-reactive probes based on the extended annotation of Price et al. were removed. Finally, probes targeting X and Y-chromosomes were removed from the analysis.

extract_protocol: Genomic DNA was extracted with the QIAamp DNA Mini Kit (Qiagen) and with the recommended proteinase K and RNase A digestions.

value: DNMT1 and 3B DKO


title: iMSC-UBC-Gustav3_384

value: Mesenchymal stromal cells


title: Control fat diet PDGFRa-Cre-ERT2:RiboTAG pulldown Sample 1291 IP

value: brain white matter


title: LT-HSC Vav1Cre+Rxrabfl/fl rep4


title: Patient_14_CD8


title: Control fat diet PDGFRa-Cre-ERT2:RiboTAG pulldown Sample 1290 IP


title: DNMT1 and 3B DKO HCT116 cells repl1 (450k)


title: Patient_14_CD4


title: iPS-P4-BM-Betty3_287


title: LT-HSC VaviCre+Rxrabfl/fl rep3


title: Control fat diet PDGFRa-Cre-ERT2:RiboTAG pulldown Sample 1288 IP


title: iPS-P4-BM-Betty2_286


title: Control fat diet PDGFRa-Cre-ERT2:RiboTAG pulldown Sample 1277 IP


title: Patient_14_B

value: B


title: WT HCT116 cells repl1 (450k)


title: WT HCT116 cells repl3 (450k)


title: LT-HSC VaviCre+Rxrabfl/fl rep1


title: Patient_13_pDC

value: peripheral blood

value: nM


title: WT HCT116 cells repl2 (450k)

value: WT


title: DNMT1 and 3B DKO HCT116 cells repl2 (450k)


title: High fat diet PDGFRa-Cre-ERT2:RiboTAG pulldown Sample 1117 IP

value: 60% kCal from fat diet


title: iPS-P8-BM-Alice1_288

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: iPS-P8-BM-Betty2_284


title: iPS-P4-BM-Alice3_283


title: LT-HSC VaviCre+Rxrabfl/fl rep2


title: Hox, scRNAseq

description: 10x Genomics

source_name: Secondary, and tertiary pulmonary arteries from the left lung lobe

value: PA resident cells

value: 12 weeks

tag: mouse model

value: pulmonary hypertension (PH)


title: LT-HSC Vav1Cre+WT rep6

value: LT-HSC


title: Nox, scRNAseq

description: 10x Genomics

value: Secondary, and tertiary pulmonary arteries from the left lung lobe


title: LT-HSC Rxrabfl/fl rep3

value: Batch 1


title: Patient_13_Monocytes

value: Monocytes


title: iPS-P4-BM-Betty1_285


title: LT-HSC Vav1Cre+WT rep5


title: Patient_13_CD4


title: iPS-BM-Alice3_282


title: iPS-BM-Alice2_281


title: LT-HSC Vav1Cre+WT rep4


title: Patient_13_B


title: CM_P1_cKO_rep3

city: Milan

first: Paola

last: Cattaneo

address: Via Fantoli 16/15

department: Institute of Genetic and Biomedical Research

country: Italy

institute: National Research Council of Italy

data_processing:
The sequencing reads were processed to remove Illumina barcodes and aligned to the UCSC Mus musculus reference genome (build mm10) using STAR v.2.5.1b with default parameters.
ReadsPerGene.out.tab files were then processed with edgeR
RNA expression was calculated in reads per kilobase per million mapped reads (RPKM) considering the sum of exon length.
Differentially expressed coding genes were selected based on the following parameters: FDR ≤0.05, RPKM ≥1 in at least one biological condition, and Log Fold Change ≤ -0.5 for genes downregulated and ≥ 0.5 for genes upregulated
bigWig were generated with wigToBigWig command starting from Signal.Unique.str.out.wig file generated after STAR mapping.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: cardiomyocytes

extract_protocol:
Cardiomyocytes were isolated using collagenase enzymatic reaction and FACS sorted based on the tdTomato fluorescence driven by the XMlc2-Cre. Purified Cardiomyocytes were colleced in Tryzol and RNA extracted using Direct-zol RNA Kits (Zymo Research #R2061)
Libraries  were generated from 25ng of RNA using the TruSeq Stranded mRNA library Prep kit (Illumina# 20020594) and sequenced on HiSeq 4000 System (Illumina)

value: cardiomyocytes

value: Black Swiss

tag: developmental stage

value: postnatal day P1


title: LT-HSC Rxrabfl/fl rep2


title: Patient_13_mDC

value: mDC


title: CM_P1_Ctrl_rep3


title: ischemic muscle, Leprdb/db, praliciguat [3925]

city: Pessac

first: Marie-Ange

last: Renault

address: 1 avenue de Magellan

institute: Inserm U1034

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting counts, TPM and FPKM of genes

source_name: tibialis anterior muscle

growth_protocol: Leprdb/db male mice underwent HLI surgery and were treated orally with praliciguat or placebo. Mice were sacrificed 28 days after surgery.

extract_protocol:
RNA was isolated using Tri Reagent® as instructed by the manufacturer (Molecular Research Center Inc), from muscle tissue that had been snap-frozen in liquid nitrogen and homogenized.
Libraries were prepared from the extracted RNA using the KAPA Stranded mRNA-Seq Kit from ROCHE

treatment_protocol: Praliciguat was formulated in chow to target the maximum observed plasma concentration (Cmax) expected with an oral dose of 10 mg/kg/day. Starting on Day -3 of the experiment (i.e., 3 days before HLI surgery), mice were randomized to be given ad libitum access to a control diet containing no praliciguat (D11112201; Research Diets, New Brunswick, NJ) or a diet containing 75 ppm praliciguat (D19121105, Research Diets, New Brunswick, NJ). Animals were maintained on their assigned diet for 31 days.

value: tibialis anterior muscle

tag: Sex

value: male

value: Leprdb/db

value: Hind limb ischemia

value: praliciguat


title: CM_P1_cKO_rep1


title: CM_P1_cKO_rep2


title: Patient_13_NK

value: peripheral blood

value: NK

value: nM


title: iPS-BM-Betty3_277

value: induced Pluripotent stem cells


title: LT-HSC Rxrabfl/fl rep1

value: LT-HSC


title: iPS-BM-Alice1_280


title: Patient_12_pDC

value: pDC

value: vS


title: Patient_13_CD8


title: CM_P1_Ctrl_rep2


title: CM_P1_Ctrl_rep1


title: ischemic muscle, Leprdb/db, praliciguat [3924]


title: Patient_12_Monocytes

value: Monocytes


title: Patient_12_NK


title: iPS-UCB-Cornelius1_276


title: iPS-P0-BM-Betty3_275

value: Mesoderm Induction Medium


title: CM_E16_cKO_rep3

value: cardiomyocytes

value: Black Swiss

value: embryonic day E16.5


title: iPS-P0-BM-Alice1_278


title: CM_E16_cKO_rep2


title: ischemic muscle, Leprdb/db, praliciguat [3892]

value: tibialis anterior muscle


title: ischemic muscle, Leprdb/db, placebo [3927]

value: male

value: placebo


title: iPS-UCB-Gustav1_404


title: Patient_12_CD8


title: iPS-UCB-Cornelius2_274


title: iMSC-BM-Alice3_279

value: Mesenchymal stromal cells


title: CM_E16_cKO_rep1


title: CM_E16_Ctrl_rep3


title: ischemic muscle, Leprdb/db, placebo [3926]

value: Leprdb/db

value: Hind limb ischemia


title: iPS-P0-BM-Betty1_272


title: ischemic muscle, Leprdb/db, praliciguat [3893]

value: praliciguat


title: Patient_12_B

value: peripheral blood

value: B


title: Patient_11_pDC

value: HD


title: CM_E16_Ctrl_rep2


title: iPS-P0-BM-Alice3_271

value: induced Pluripotent stem cells


title: ischemic muscle, Leprdb/db, placebo [3896]


title: iPS-P0-BM-Alice2_270


title: Patient_11_NK

value: NK


title: iPS Gustav MIM P8+ 2

data_processing:
Quality control was conducted using FASTQC (version 0.11.7 - Bioinformatics Group at the Babraham Institute).
Trimming and removal of residual adapters was done with AdapterRemova
Reads were then mapped to the Ensembl GRCh38 human genome using Tophat2
The number of mapped reads/gene (counts) was then calculated using HTseq
Genome_build: Human GRCh38
Supplementary_files_format_and_content: Normalized counts per gene

extract_protocol:
RNASeq  RNA was isolated using Macherey&Nagel RNA isolation kit according to the manufacturers protocol. The quality of total RNA isolates was analyzed using the Agilent RNA 6000 Nano Kit.   Poly-(A)-selection was performed utilizing the NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s requirements.
mRNA libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). All libraries were analyzed with the Agilent DNA 1000 Kit and quantified using the Qubit® dsDNA BR Assay Kit (ThermoFisher). After equimolar pooling all samples were sequenced on an Illumina HiSeq 1500 system with High Output chemistry v4 (50 cycles, single-read).


title: Patient_11_Monocytes

value: Monocytes


title: iPS-P0-BM-Betty2_273

value: Mesoderm Induction Medium


title: Patient_11_mDC

value: mDC


title: mm_steroid_K

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

description: scRNA-seq

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 5.0.0, 10x Genomics, Pleasanton, CA) and the human genome hg19-1.2.0 release or mouse mm10-3.0.0 as the reference (function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 4.0.1).
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes.
Assembly: hg19-1.2.0 and mm10-3.0.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (matrix.mtx, barcodes.tsv, features.tsv).

source_name: kidney

growth_protocol: For single cell suspension kidneys were dissected and incubated for 40 min at 37°C in RPMI medium (including 0.01 M HEPES; 0.5 mL filtered FBS and 0.4µg/ mL DNase and 8 µg/ mL collagenase D). The samples were homogenized using a gentleMACS (Miltenyi Biotec).

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 3' v2 or 5' v1.1 kit to generate high-quality cDNA libraries.

value: kidney T cells

tag: disease

value: NTN induction

value: steroid

value: cGN model


title: OO-44h2

city: Liběchov

first: Matej

last: Murín

state: Central Bohemia

address: Rumburská, 89

department: Laboratory of Developmental Biology

country: Czech Republic

institute: Institute of Animal Physiology and Genetics CAS

data_processing:
Reads with lengths less than 15 nt were discarded.
Expression analysis was done using the Differential Expression in Two Groups tool in CLC Genomics Workbench v. 22.0 according to a negative binomial Generalized Linear Model function.
Data were normalized (counts per million mapped reads) and filtered (cpm > 0.5, at least two samples from each group of replicates) and expression values of read count and CPM were calculated for all of the genes.
For the normalization of data, the trimmed mean of M-values normalization method was used.
Assembly: SScrofa11.1
Supplementary files format and content: Expression Browser processed data DESeq2.xlsx; Complete list of genes after data processing and comparison of different cultivation times among themselves.

organism: Sus scrofa

source_name: oocyte

extract_protocol:
Total RNA was isolated from denuded oocytes from 4 experimental groups (each of three replicates) using an AllPRep DNA/RNA Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared using SMARTer Stranded Total RNA - v2 Kit Pico Input Mammalian (Takara Bio, Japan) according to SMARTer Stranded Total RNA - v2 kit Pico Input Mammalian protocol. After PCR amplification (15 cycles), RNA libraries were purified. Their quantity and quality were assessed using the Agilent DNA High Sensitivity Chip and Bioanalyzer 2100 instrument. Fragment length distribution was evaluated using the Agilent 2100 Expert software. After the quantification, libraries were pooled in equimolar ratios according to the quality and concentration measurements, denatured, diluted to final loading concentration (275 pM) and subsequently sequenced in NovaSeq 6000 S4 flow cell (Illumina, San Diego, CA, USA) to reach 100 M pair-end reads per sample.

value: oocyte


title: OO-44h1


title: OO-44h4


title: iPS Gustav MIM P8+ 1

source_name: Umbilical cord blood


title: Patient_12_CD4

value: vS


title: OM1

city: Durham

first: James

last: White

state: nc

address: 300 N Duke Street

institute: Duke University SOM

data_processing:
Basecalling and fastq files generated using 10X Cellranger v5.0.0 with default parameters
Alignment, counting, filtering, of single cell RNA-Seq of samples:- Y1,O1,OM1 , using 10X Cellranger v3.1.0 with default parameters.
Assembly: mm10
Supplementary files format and content: raw read counts in gene-barcode matrix (Gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes.  Gene feature info.  Barcode sequences that correspond to column indices in matrix.mtx.)

source_name: damaged muscle cell suspension from old Metrnl treated muscle

growth_protocol: Cells were not grown ex vivo or in vitro

extract_protocol:
Muscles were dissected, minced, digested, strained and washed to isolate a single cell suspension
flow cell: S1

treatment_protocol: Muscles were treated in vivo with either PBS or rMetrnl following BaCl2 induced muscle damage

value: OLD

value: METRNL

value: damaged muscle


title: iPS Cornelius MIM P8+ 2


title: Y1

source_name: damaged muscle cell suspension from young control treated muscle

value: YOUNG

value: PBS


title: O1

source_name: damaged muscle cell suspension from old control treated muscle


title: iPS Cornelius MIM P8+ 3


title: CM_E16_Ctrl_rep1

value: cardiomyocytes

value: Black Swiss

value: embryonic day E16.5


title: Patient_11_CD8

source_name: peripheral blood

value: peripheral blood

value: HD


title: ischemic muscle, Leprdb/db, placebo [3897]

value: tibialis anterior muscle

value: male

value: Leprdb/db

value: Hind limb ischemia

value: placebo


title: OO-28h3

value: oocyte


title: Patient_11_CD4


title: mm_control_K

description: scRNA-seq

value: kidney T cells

value: NTN induction

value: cGN model


title: iPS Cornelius MIM P8+ 1

value: induced Pluripotent stem cells

value: Mesoderm Induction Medium


title: Patient_10_pDC

value: pDC

value: nM


title: OO-28h2