title: plasma-derived AS-exosomes Nymber 14

description:
Total RNA extracted form Plasma derived exosomes
Fataneh25

value: BASDAI 5


title: plasma-derived AS-exosomes Nymber 3

status: Public on Dec 08 2022

type: SRA

city: Toronto

first: Fataneh

last: Tavasolian

state: Ontario

address: 60 leonard Ave

country: Canada

institute: Krembil Research institute

description:
Total RNA extracted form Plasma derived exosomes
Fataneh14

library_source: transcriptomic

data_processing:
CLC Genomic Workbench20 (version 5.5.2; CLC bio)
Supplementary files format and content: tab-delimited text files

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

growth_protocol: Plasma was extracted from venous blood samples collected during clinic hours. Heparinized tubes were centrifuged at 460g (1600rpm) for 10 min before plasma was collected. Plasma aliquots, stored at -80 °C until required, underwent only one freeze-thaw cycle. With the remaining cellular layer from the heparin tubes, peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll–Paque PLUS (GE Healthcare Bioscience, ON, Canada) and were transferred to liquid N2 for storage.

extract_protocol:
RNA extraction from exosomes  The entire method for isolating RNA from exosomes with exoRNeasy Midi Kit (Qiagen) consists of two steps: exosome purification and RNA isolation. Isolating RNA from exosomes consisted of two steps: exosome purification and RNA isolation. For exosome purification, the plasma sample was mixed with buffer XBP (1:1) and centrifuged for 1 min at 500 x g to bind to an exoEasy membrane affinity spin column. The bound exosomes were washed with 3.5 ml buffer XWP after 1 min of centrifugation at 500g, and then lysed by adding 700 l QIAzol after 5 min of centrifugation at 5000g.  In the RNA extraction stage, 90 µl chloroform was added to the QIAzol eluate, which was then shaken for 15 seconds. The aqueous phase was then collected and combined with 2 volumes of 100% ethanol. Total RNA, including miRNA, attached to the spin column after 15 seconds of centrifugation at 8000 x g, was washed three times and eluted in 14 lµ RNase-free water.. All protocols were provided by Qiagen. The enzyme Bacteroides I (New England Biolabs, P0735S) and RNase Inhibitor (Enzymatic, Y9240L) were utilized after RNA extraction following the manufacturer's protocol to eliminate residual heparin potentially transferred from the heparin blood collection tubes. After incubation for 1 hr at 30C and 1 min at 99.9C, the RNA was stored at -80°C and then used as RNA templates to produce a cDNA library for sequencing.
MiRNA libraries were prepared using Qiagen’s QIAseq miRNA Library Kit with 5 μl of total RNA from each sample. This was followed by completing universal cDNA synthesis with UMI assignment, cDNA cleaning, library amplification, and library purification. The resulting libraries were quantified using the Denovix hsDNA assay, and quality was assayed using a hsDNA chip on an Agilent Bioanalyzer.

tag: tissue

value: Plasma

tag: cell line

value: Male

tag: cell type

tag: genotype

value: BASDAI 4.2

tag: disease state

value: Ankylosing Spondylitis


title: plasma-derived AS-exosomes Nymber 12

description:
Total RNA extracted form Plasma derived exosomes
Fataneh23

value: BASDAI 5.8


title: plasma-derived AS-exosomes Nymber 6

description:
Total RNA extracted form Plasma derived exosomes
Fataneh17

value: BASDAI 6.6


title: plasma-derived AS-exosomes Nymber 15

description:
Total RNA extracted form Plasma derived exosomes
Fataneh26

value: BASDAI 5.2


title: plasma-derived HC-exosomes Nymber 7

description:
Total RNA extracted form Plasma derived exosomes
Fataneh7A

value: Female

value: healthy control


title: plasma-derived HC-exosomes Nymber 9

description:
Total RNA extracted form Plasma derived exosomes
Fataneh9


title: L1_1

city: Guiyang

first: Jiao

last: Xu

address: Dongqing South Road, Huaxi District

country: China

institute: Guizhou University of traditonal Chinese Medicine

description: biol rep 1

data_processing:
The data quality control was used by FastQC
The data filtered using fastx_toolkit Version 0.0.14（http://hannonlab.cshl.edu/fastx_toolkit/）
Then all clean reads were used for de novo assembly with Trinity, (http://trinityrnaseq.sourceforge.net/).
The TPM was calculated by RSEM（http://deweylab.github.io/RSEM/ software）.

organism: Dipsacus asperoides

source_name: root

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Promega). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The roots of one-leaf stage (L1), two-leaf stage (L2), and plants that had been growing for 7 months (M7)

value: root

value: WT

tag: developmental stage

value: roots of one-leaf stage


title: plasma-derived HC-exosomes Nymber 5

description:
Total RNA extracted form Plasma derived exosomes
Fataneh5


title: plasma-derived HC-exosomes Nymber 6

description:
Total RNA extracted form Plasma derived exosomes
Fataneh6


title: plasma-derived HC-exosomes Nymber 4

description:
Total RNA extracted form Plasma derived exosomes
Fataneh4


title: plasma-derived AS-exosomes Nymber 11

description:
Total RNA extracted form Plasma derived exosomes
Fataneh22

value: BASDAI 4.5


title: L2_1

description: biol rep 1

value: roots of two-leaf stage


title: plasma-derived HC-exosomes Nymber 3

description:
Total RNA extracted form Plasma derived exosomes
Fataneh3


title: plasma-derived HC-exosomes Nymber 1

description:
Total RNA extracted form Plasma derived exosomes
Fataneh1


title: plasma-derived HC-exosomes Nymber 2

description:
Total RNA extracted form Plasma derived exosomes
Fataneh2A


title: plasma-derived HC-exosomes Nymber 8

description:
Total RNA extracted form Plasma derived exosomes
Fataneh8


title: HEM_light

city: Lund

first: Martin

last: Lauss

address: Barngatan 2B

department: Dept of Oncology

country: Sweden

institute: Lund University

data_processing:
Raw sequencing read data were demultiplexed and collated by library barcode into sample data sets.
TopHat2 was used to align reads to the human reference genome hg38 together with 104,133 transcript annotations from the UCSC knownGenes table. Cufflinks 2.1.1 was used to calculate FPKM.
Gene expression data were collapsed on 30,865 unique gene symbols by the sum of FPKM values of the individual transcripts, and 18,418 protein-coding genes were kept. The data were quantile-normalized and transformed as log2(data+1).
Cell lines from unclear sources and identified redundant cell lines from the same patient were removed. A batch effect caused by the the use of the NeoPrep system for some cell lines, was corrected using ComBat. After batch correction, negative values and original zeros were set back to zero. Further, three dabrafenib-treated and one cell line of ambiguous origin were removed, resulting in a set of 86 melanoma cell lines and three human epidermal melanocytes (ScienCell).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample, that have undergone described data processing steps.

source_name: normal skin

growth_protocol: The melanoma cell lines used in this study were purchased from ATCC or provided by the lab of Hensin Tsao and cultured according to ATCC guidelines.

extract_protocol:
RNA was extracted using AllPrep DNA RNA Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.
RNAseq strategy encompasses the performance of paired end sequencing of 75 bp reads on an Illumina NextSeq 500 instrument.

value: normal skin

tag: treatment

value: untreated


title: WM852

source_name: melanoma

value: melanoma


title: HEM_adult


title: WM608


title: HEM_medium


title: WM373


title: WM2067


title: UACC257


title: TC2139


title: WM164


title: SKMEL30


title: SKMEL1


title: D14-AM-006

city: Bunkyo-ku

first: Masanori

last: Murakami

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Raw sequencing data was analysed with the Qiagen Geneglobe Data analysis center (https://geneglobe.qiagen.com) and aligned to the miRBase v21 (http://www.mirbase.org) and piRNABank (http://pirnabank.ibab.ac.in/).
All reads assigned to a particular miRNA or piRNA were counted and the associated UMIs were aggregated to count unique molecules.
A matrix of the UMI counts of miRNA or piRNA was subjected to downstream analyses using StrandNGS 3.4 software (Agilent Technologies, Santa Clara, CA).
The UMI counts were quantified using a Trimmed Mean of M-value (TMM) method.
miRNAs were annotated against miRBase (Release 21).
Assembly: hg38, miRBase v21
Supplementary files format and content: csv files include TMM values for each Sample

source_name: plasma

extract_protocol:
RNA was harvested using miRNeasy Serum/Plasma Kit(Qiagen). 5uLof RNA was used for the construction of sequencing libraries.
Small RNA libraries for miRNA-seq were prepared using QIAseq miRNA Library Kit (QIAGEN, Valencia, CA) following manufacturer's protocols.

value: plasma

tag: phenotype

value: PBMAH


title: D08-Y116

value: CPA


title: D04-Y109

value: NFA


title: D13-Y225


title: D03-Y94


title: D05-Y26


title: D12-Y224


title: D06-Y86


title: D11-Y60


title: D01-Y73


title: Skmel_63


title: Skmel_37


title: D09-Y137


title: D10-Y221


title: WM983B


title: WM35


title: D02-Y74


title: SKMEL_3


title: Skmel_119


title: MM383


title: RVH421


title: D07-Y107


title: MGH_ST_1


title: MEL270


title: MGH_PO_1


title: MEL205


title: M14


title: MEL202


title: K4


title: IGR_1


title: HMCB

value: HMCB


title: A7


title: WM902B


title: CHL1


title: ANBU

value: ANBU


title: Gmel

value: Gmel


title: 526


title: WM9


title: HT144


title: C918


title: WM278


title: WM853_2


title: WM209


title: WM3211


title: WM239A


title: WM1158


title: WM1341D


title: UACC903


title: WM1552C


title: UACC_62


title: TC3018_1A


title: WM1361A


title: TC2823_1


title: TC1308


title: SK_MEL_39


title: SKMEL_5


title: SK_MEL_28


title: SKMEL_31


title: MGH_QU_1


title: MGH_MC_1


title: MGH_SW_1


title: SK_MEL_2


title: NAE

value: NAE


title: MGH_BA_1


title: MM455


title: MGH_BO_1


title: MGH_MEL_13


title: MGH_CH_1


title: WM1205


title: MALME3M


title: MEW0


title: MEL_H0


title: LOX

value: LOX


title: K19


title: K8


title: IGR_39


title: HS944T


title: G_361


title: COLO858


title: DM13


title: DM6


title: A375


title: RPMI_7951


title: C32


title: A2058


title: COLO783


title: IPC_298


title: 624


title: 1300


title: MEL_JUSO


title: 888


title: Patient 930 CSC

city: Atlanta

first: Michael

last: Davis

state: GA

address: 2015 Uppergate Dr

country: USA

institute: Emory University

description: Batch 1

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
10x Genomics Chromium Controller

source_name: cardiac biopsy

growth_protocol: Cells collected from the right atrial appendage of five neonatal (< 1 month) and five child (3.43 years ± 2.6 years) patients with congenital heart disease were separated for c-kit+ CSCs using magnetic cell sorting. Cells were cultured in Ham’s F-12 medium (Corning Cellgro®, Corning, NY, USA) with 10% fetal bovine serum, 1% penicillin-streptomycin, 1% L-glutamine and 0.04% human fibroblast growth factor-β. Cells were used between passage 5 and 15.

extract_protocol: Library was performed according to the manufacter’s instructions (10x Genomics).

value: cardiac biopsy

tag: patient age

value: <1 week

value: c-kit+ cardiac-derived stromal cells

tag: patient congenital_heart_disease

value: total anomalous pulmonary venous return

tag: passage


title: Patient 926 CSC

description: Batch 1

value: 14 months

value: ventricle septal defect


title: Patient 925 CSC

description: Batch 1


title: Patient 1048 CSC

description: Batch 1

value: 6 years

value: atrial septal defect


title: Patient 938 CSC

description: Batch 2

value: 5 years

value: subaortic membrane resection, mitral valve ring


title: Patient 2016 CSC

description: Batch 2

value: 1-2 weeks

value: atrial septal defect, ventricle septal defect, coarctation


title: Patient 903 CSC

description: Batch 1

value: hypoplastic left heart syndrome


title: Patient 985 CSC

description: Batch 2

value: 2 weeks

value: interrupted aortic arch


title: Patient 896 CSC

description: Batch 2

value: 12 months


title: Patient 1092 CSC

description: Batch 2


title: Sample 5

city: Xi' an

first: Xuetong

last: Chen

address: Taibai road, No. 229

institute: Northwest University

data_processing:
High quality clean reads, reads were further filtered by fastp (version 0.18.0)
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach ().
Assembly: Ensembl release-101, Mus musculus
Supplementary files format and content: tab-delimited text files include Count values for each Sample

organism: Mus musculus

source_name: C57BL/6 mouse, LLC, tumor tissue, isoleucine

growth_protocol: Mouse Lewis lung carcinoma (LLC) cells were cultured in Dulbecco’s Modified Eagle’s medium (DMEM, Gibco, United States) supplemented with 10% fetal bovine serum (FBS, JRH Bio-sciences, KS, USA) in a humidified cell incubator at 37ºC, 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
300 mg/kg of isoleucine was injected intraperitoneally every day from the third day.
For the control group, the same volume of PBS was injected.

value: LLC

value: mesenchymal stem cells

value: WT

value: isoleucine

tag: time

value: Day 18


title: Sample 4


title: Sample 6


title: Sample 1

source_name: C57BL/6 mouse, LLC, tumor tissue, control

value: PBS


title: Sample 2


title: Sample 3


title: B16_SKO_IgG_2

city: Philadelphia

first: Kathryn

last: Tsai

state: PA

address: 421 Curie Blvd

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
Adapters were trimmed with cutadapt version 1.18.
Reads were aligned to the GRCm38 genome with Bowtie2 version 2.3.4.1 using the parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 16.
Unmapped and improperly paired reads were removed (-F 1804 -f2).
For H3K27ac and H3K4me3 profiling, narrow peaks were called with macs2 using the default significance threshold of p=1e-05.
For H3K4me1 profiling, broad peaks were called using the same significance threshold.
Non-overlapping, fixed-width consensus peak sets for each histone assay were generated by combining peak calls and iteratively removing overlapping peaks (only retain the most significant peak call).
A raw count matrix was generated by counting the number of insertions in each region of the consensus peak set, and normalized count matrices were generated with DESeq2’s vst method.
Assembly: GRCm38

source_name: B16-F10 STAT1 KO

extract_protocol:
CUTNRUN libraries were extracted using standard Cell Signaling protocols.
CUTNRUN libraries were prepared for sequencing using standard Cell Signaling  protocols.

value: B16-F10 STAT1 KO

value: sorted tumor cells

value: STAT1 KO

value: no treatment


title: Res499_WT_H3K4me3_2

source_name: Res 499

value: Res 499


title: B16_WT_IgG_1


title: Res499_WT_IgG_1


title: B16_SKO_IgG_1


title: Res499_SKO_IgG_2

source_name: Res 499 STAT1 KO

value: Res 499 STAT1 KO


title: Res499_SKO_IgG_1


title: Res499_WT_H3K4me3_1


title: B16_WT_IgG_2


title: B16_WT_H3K4me3_2


title: Res499_SKO_H3K4me3_1


title: B16_WT_H3K4me3_1


title: B16_SKO_H3K4me3_1


title: Res499_SKO_H3K4me1_2


title: Res499_WT_IgG_2


title: Res499_SKO_H3K4me1_1


title: Res499_WT_H3K4me1_1


title: B16_WT_H3K4me1_2


title: B16_WT_H3K4me1_1


title: B16_SKO_H3K4me1_1


title: Res499_SKO_H3K27Ac_2


title: Res499_SKO_H3K27Ac_1


title: Res499_WT_H3K27Ac_1


title: B16_SKO_H3K4me1_2


title: Res499_WT_H3K27Ac_2


title: B16_WT_H3K27Ac_2


title: Res499_SKO_H3K4me3_2


title: B16_SKO_H3K27Ac_1


title: B16_SKO_H3K27Ac_2


title: B16_SKO_H3K4me3_2


title: R499_SKO_5_RNA

data_processing:
Adapters were trimmed with cutadapt version 1.18.
Reads were aligned to the GRCm38 genome with STAR version 2.5.2a using recommended parameter settings.
Gene-based quantification was performed with salmon version 0.13.1.
For the final count matrix, raw counts were normalized using regularized-log (rlog) transformation from DESeq2.
Assembly: GRCm38
Supplementary files format and content: Processed data files are found in RNA_counts_rlog.txt.

extract_protocol:
RNA was harvested using Direct-zol RNA kits (zymo research) with on column DNase treatment.  200,000 cells were sorted for RNA-seq.
Library was prepared using Truseq Stranded Total RNA Library Prep Gold kit.


title: R499_SKO_4_RNA


title: R499_SKO_3_RNA


title: R499_SKO_1_RNA


title: R499_cas_2_RNA


title: R499_cas_1_RNA


title: R499_SKO_2_RNA


title: Res499_WT_H3K4me1_2


title: B16_SKO_4_RNA


title: B16_SKO_3_RNA


title: B16_SKO_1_RNA


title: B16_SKO_2_RNA


title: B16_WT_H3K27Ac_1


title: B16_cas_1_RNA


title: R499_DKO_4

data_processing:
ENCODE ATAC-seq pipeline, part of the ENCODE Uniform Processing Pipelines series
Adapters were trimmed using cutadapt, and reads were aligned to the mm10 genome using Bowtie2. After alignment, duplicate reads and reads mapping to chrM were removed.
Peak calling was performed with MACS2, and high-confidence peaks were filtered using the irreproducible discovery rate (IDR).
A raw count matrix was generated by counting the number of insertions that overlapped each region in the consensus peak set. For the final count matrix, raw counts were normalized using regularized-log (rlog) transformation from DESeq2.
Assembly: mm10
Supplementary files format and content: Processed data files are found in ATAC_revisions_consensus_mat_tn5_insertion_counts_IDR_vst.txt

source_name: Res499 DKO

extract_protocol:
Extract protocol described in Buenrostro et al 2016
Library construction protocol described in Buenrostro et al 2016

value: Res499 DKO

value: DKO


title: R499_DKO_1


title: R499_IRF3KO_4

source_name: Res499 IRF3 KO

value: Res499 IRF3 KO

value: IRF3 KO


title: R499_DKO_3


title: R499_IRF3KO_3


title: R499_IRF3KO_2


title: R499_cas_4_RNA


title: B16_SKO_5_RNA


title: R499_IRF3KO_1


title: R499_SKO_5_ATAC_new


title: R499_SKO_4_ATAC_new


title: B16_cas_4_RNA


title: R499_SKO_2_ATAC_new


title: R499_cas_3_ATAC_new


title: R499_cas_4_ATAC_new


title: B16_cas_5_RNA


title: R499_cas_1_ATAC_new


title: B16_SKO_1_ATAC_new


title: B16_cas_4_ATAC_new


title: B16_SKO_4_ATAC_new


title: S70333 vs FY4

type: genomic

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: S70333 vs FY4

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2013-03-05 Scan Time : 09:50:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Extracted molecule : DNA
Extraction method : Nib and Grab

tag: species

value: S. cerevisiae

tag: strain name

value: prototroph

value: S7 evolution Pop03-day33

value: wt prototroph

tag: sex/mating type

value: diploid


title: S70433 vs FY4

description: S70433 vs FY4

label_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentDNA.pdf

value: S7 evolution Pop04-day33


title: S70533 vs FY4

description: S70533 vs FY4

value: S7 evolution Pop05-day33

value: prototroph heterozygous for ars228 deletion


title: S71133 vs FY4

description: S71133 vs FY4

scan_protocol: Pixel Size : 5 Scan Date : 2013-03-05 Scan Time : 09:09:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: S7 evolution Pop11-day33

value: prototroph homozygous for ars228 deletion


title: S70233 vs FY4

description: S70233 vs FY4

value: S7 evolution Pop02-day33


title: B16_cas_2_ATAC_new

value: sorted tumor cells

value: WT

value: no treatment


title: B16_cas_1_ATAC_new


title: R499_SKO_5_ATAC

data_processing:
ENCODE ATAC-seq pipeline, part of the ENCODE Uniform Processing Pipelines series
Adapters were trimmed using cutadapt, and reads were aligned to the mm10 genome using Bowtie2. After alignment, duplicate reads and reads mapping to chrM were removed.
Peak calling was performed with MACS2, and high-confidence peaks were filtered using the irreproducible discovery rate (IDR).
A raw count matrix was generated by counting the number of insertions that overlapped each region in the consensus peak set. For the final count matrix, raw counts were normalized using regularized-log (rlog) transformation from DESeq2.
Assembly: mm10
Supplementary files format and content: Processed data files are found in ATAC_original_consensus_mat_tn5_insertion_counts_IDR_rlog.txt

value: STAT1 KO


title: S7 evolution Pop12-day33

description: S7 evolution Pop12-day33

scan_protocol: Pixel Size : 5 Scan Date : 2013-02-28 Scan Time : 10:04:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: S7 evolution Pop12-day33


title: R499_cas_2_ATAC_new

value: Res 499


title: S7 evolution Pop09-day33

description: S7 evolution Pop09-day33

value: S. cerevisiae

value: S7 evolution Pop09-day33


title: S70733 vs FY4

description: S70733 vs FY4

scan_protocol: Pixel Size : 5 Scan Date : 2013-03-05 Scan Time : 09:34:56 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

value: prototroph

value: S7 evolution Pop07-day33


title: Tumor_Liver_replicate_4

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina Human HT12v4 Expression Bead Chips (Illumina, San Diego, CA). The arrays were then rinsed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-conjugated Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 μm using the Illumina iScan scanner.

data_processing:
Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.
ID_REF = Unique identifiers from GPL10558

label: Biotin

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: RNA was isolated from tumor and tumor-free liver samples of 5 patients using Trizol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions and further purified using RNeasy mini columns (Qiagen).

treatment_protocol: [Experimental protocol] Liver samples from 5 patients with HCC were included (3 male/ 2 female) from the tumor and from nontumorous tissue. HCC was diagnosed preoperatively by computed tomography or magnetic resonance imaging and confirmed postoperatively by histopathology. Serological markers of hepatitis B virus (HBV) and hepatitis C virus (HCV) were assessed for all patients, as well as anti-human immunodeficiency virus, which was negative for all cases. All patients were treated surgically and received the same postoperative care in the Department of Surgery, Campus Virchow Klinikum at the Charité – Universitätsmedizin Berlin. Diagnosis was confirmed by a histologist and the surrounding tumor free tissue was also evaluated by the histologist. The study was approved by the local ethics committee (Ethikommission der Charité Berlin, Germany, Approval Number EA4/080/14), and patients gave their written informed consent to participate in the study.

tag: individual

value: patient 4

value: Liver

tag: gender

value: Male

tag: age (yrs)

value: Tumor


title: S7 evolution Pop01-day33

description: S7 evolution Pop01-day33

value: S7 evolution Pop01-day33

value: wt prototroph

value: diploid


title: S70633 vs FY4

description: S70633 vs FY4

value: S7 evolution Pop06-day33

value: prototroph heterozygous for ars228 deletion


title: R499_SKO_4_ATAC

tag: cell line

value: sorted tumor cells

value: WT

value: no treatment


title: S71033 vs FY4

description: S71033 vs FY4

value: S7 evolution Pop10-day33

value: prototroph homozygous for ars228 deletion


title: Tumor_Liver_replicate_5

value: patient 5

tag: tissue

value: Female


title: R499_SKO_3_ATAC

tag: cell type

tag: genotype


title: R499_SKO_2_ATAC


title: S70833 vs FY4

description: S70833 vs FY4

value: S. cerevisiae

value: prototroph

value: S7 evolution Pop08-day33


title: Tumor_Liver_replicate_3

value: patient 3

value: Liver


title: Tumor_Liver_replicate_2

value: patient 2

value: Male

value: Tumor


title: Tumor_Liver_replicate_1

value: patient 1


title: Tumor_Liver_replicate_1_TR


title: R499_cas_1_ATAC

value: STAT1 KO


title: R499_cas_2_ATAC

value: sorted tumor cells


title: B16_SKO_5_ATAC


title: VEH6

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Gene abundance estimates were obtained for each sample using kallisto 0.44.0, with the UCSC mm10 transcriptome as the reference
The abundance levels were normalized using the DESeq between-sample normalization approach
Assembly: mm10
Supplementary files format and content: comma-separated values file includes the DESeq normalized counts for all samples

source_name: Spleen

growth_protocol: Sirt1 conditional knockout T-ALLs were injected intravenously in sub-lethally Irradiated mice.

extract_protocol:
Leukemic spleens were removed, single-cell suspensions were obtained by pressing them through a 40mm filter, and subsequently subjected to red blood cell lysis. RNA was extracted using QIAGEN QIAshredder (#79656) and Rneasy Mini (#74106) kits. 1mg of Total RNA was used for the construction of sequencing libraries by Genewiz.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were trated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection.

value: Leukemic spleen

value: Control

tag: strain


title: B16_SKO_2_ATAC

value: WT

tag: treatment

value: no treatment


title: B16_SKO_3_ATAC


title: B16_SKO_1_ATAC


title: VEH5


title: VEH4


title: B16_SKO_4_ATAC


title: VEH3


title: TMX12

value: Sirt1 deleted


title: B16_cas_4_ATAC


title: B16_cas_5_ATAC


title: TMX11


title: Non_tumor_Liver_replicate_4

value: patient 4

value: Non-tumor


title: Non_tumor_Liver_replicate_5

value: patient 5

value: Female


title: Non_tumor_Liver_replicate_3

value: patient 3


title: B16_cas_1_ATAC


title: Non_tumor_Liver_replicate_1

value: Liver


title: Non_tumor_Liver_replicate_2

value: patient 2


title: Non_tumor_Liver_replicate_1_TR

value: Male


title: R499_SKO_1_ATAC


title: R499_cas_4_ATAC


title: VEH2


title: TMX8


title: TMX10


title: SALL4 Cut & Run with Sall4 WT mESCs replicate 1

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

library_source: genomic

data_processing:
Paired-end reads were trimmed using TrimGalore (0.6.0) and CutAdapt (1.18).  Quality was assessed with Fastqc (0.11.8).
Trimmed reads were mapped with BWA MEM (0.7.17) using the mouse genome (GRCm38) as reference.
Peaks were identified using MACS  (2.1.1.20160309)  using the --call-summits  -g mm parameters.  Peak lists from each replicate were merged using R (4.1.2) to find high confidence peaks in present in both datasets.
Assembly: GRCm38/mm10
Supplementary files format and content: Coverage files in BigWig Format
Supplementary files format and content: Peak lists in NarrowPeak Format

source_name: Sall4 F/F mESC (PMID: 27471257)

growth_protocol: mESCs were cultured in 2i + LIF media.

extract_protocol:
Cells were harvested with trypsin, washed and permeabolized with 0.02% digitonin (Sigma D-141) using the published protocl (dx.doi.org/10.17504/protocols.io.zcpf2vn).
Libraries were prepared using the Kapa Hyper Prep Kit.
Cut & Run

value: Sall4 F/F mESC (PMID:27471257)

value: mouse embryonic stem cells

tag: antibody

value: SALL4 (Santa Cruz sc-101147 clone EE-30)


title: SALL4 Cut & Run with Sall4 KO mESCs replicate 2


title: IgG Cut & Run with Sall4 WT mESCs replicate 1

value: SALL4 (Santa Cruz sc-2025)


title: ES N rep2 [RNA-seq]

city: Beijing

first: Hongyao

last: Sun

address: Tsinghua street

institute: Tsinghua university

data_processing:
RNA reads were quality checked with FastQC v0.11.5 and mapped to the mouse (mm10) genome with Bowtie2 v2.3.3 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.9. On average, 80% of reads were uniquely mapped. Uniquely mapped reads were assigned to annotated genes with featureCounts v2.0.1 using default settings. Read counts were then normalized by library size and differential gene expression analysis based on a negative binomial distribution was conducted with DESeq2 packages in R language.
Assembly: mm10
Supplementary files format and content: Processed data provided as supplementary file

source_name: mouse embryonic stem cell

growth_protocol: Mouse ESCs E14Tg2a.IV, CCE lines were cultured and maintained in feeder free leukemia inhibitory factor (LIF) -supplemented medium (Keller, 1995), which 15% FBS, 100 U of Penicillin-Streptomycin, β-me, NEAA, and sodium pyruvate were also added in.Media was changed daily.

extract_protocol:
RNA of  mESCs were purified using TIANGEN kit. 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

treatment_protocol: mESCs with treatment of activin A (50ng/ml) or SB431542 (10μM) for 2 hr

value: mouse embryonic stem cell

value: untreated


title: ES AS rep1 [RNA-seq]

value: sodium arsenite treated

value: WT


title: SALL4 Cut & Run with Sall4 WT mESCs replicate 2


title: ES N rep1 [RNA-seq]


title: SALL4 Cut & Run with Sall4 KO mESCs replicate 1


title: TMX7

value: Leukemic spleen

value: Sirt1 deleted


title: PML KO rep2 [RNA-seq]

value: Pml KO


title: 12_3422.sample

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.36)
Retained reads were mapped to the reference mouse genome GRCm38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package. Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode v. M13 for the striatum tissue; Gencode v. M16 for the SVZ tissue)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: NestinTK-  PBS

extract_protocol:
SVZ and striatum were removed, flash frozen on dry ice, and RNA was harvested using Rnase Mini Kit (Qiagen Cat No./ID: 74106)
For SVZ tissue libraries were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA) performing 10 cycles of amplification, according to the manufacturer’s instructions, while for the striatum tissue libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

value: striatum

value: brain

tag: genotyping

value: wild type

value: PBS


title: PML WT rep2 [RNA-seq]


title: ES AS rep2 [RNA-seq]


title: IgG Cut & Run with Sall4 KO mESCs replicate 1


title: 11_3414.sample


title: PML KO rep1 [RNA-seq]


title: 13_3430.sample


title: 5_4013.sample

source_name: NestinTK-  GCV

value: Ganciclovir


title: 8_4051.sample


title: TRIM33 KO SB rep1 [RNA-seq]

value: SB431542 treated

value: Trim33 KO


title: TRIM33 KO AC rep2 [RNA-seq]

value: activin A treated


title: TRIM33 KO SB rep2 [RNA-seq]


title: PML WT rep1 [RNA-seq]


title: 1_3403.sample


title: 18_4041.sample

source_name: NestinTK+ PBS

value: NestinTK


title: 14_3434.sample


title: 20_4054.sample


title: TRIM33 WT SB rep2 [RNA-seq]


title: 7_4035.sample

source_name: NestinTK+ GCV


title: TRIM33 WT AC rep2 [RNA-seq]


title: TRIM33 WT AC rep1 [RNA-seq]


title: TRIM33 KO AC rep1 [RNA-seq]


title: 9_4052.sample


title: 19_4045.sample


title: 4_4003.sample


title: 3_4001.sample


title: TRIM33 WT SB rep1 [RNA-seq]


title: long-read RNA-seq P60 EpSC

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

country: Switzerland

institute: University of Zurich

description: No processed files provided for the long-read RNA-seq samples as they were not used for quantifications in our study.  However, raw files provided.

data_processing:
NANOPORE long-read RNA sequencing: Data processing by Nextflow nanoseq v1.1 (Patel et al., 2020)
Quality check by FastQC and NanoPlot (De Coster et al., 2018)
Read mapping by minimap2 and custom transcriptome reference assembly by StringTie2 (Pertea et al., 2015)
Short-read RNA sequencing and Ribosome profiling: Data processing by Nextflow rnaseq (Patel et al., 2020)
Quality check by FastQC
Quality and adapter trimming by TrimGalore
Filtering rRNA, mtRNA and tRNA by Bowtie2 v2.4.1 (Langmead et al., 2019) (Ribosome profiling only)
Read mapping by STAR v2.6.1 (Dobin et al., 2013)
Transcriptome quantifications by Salmon (Patro et al., 2017)
Genome_build: GRCm38

source_name: Mouse back skins

extract_protocol:
In vivo: CHX treatment, followed by dispase/CHX treatment to separate epidermis from dermis, trypsin/CHX to obtain single cell suspension.
NANOPORE long-read RNA sequencing according to the manufacturer's protocol of SQK-PCS109 (Oxford NANOPORE Technologies, UK). Ribosome profiling protocol as described in Ingolia et al., 2012.
long- and short-read RNA sequencing; Ribosome profiling

value: Mouse back skins

tag: age

tag: marker

value: SCA-1+ EpSCs

tag: fraction

value: total mRNA


title: long-read RNA-seq HrasG12V; Tgfbr2 KO (SCC)

source_name: Primary keratinocytes from P0 back skin

value: HrasG12V; Tgfbr2 fl/fl KO

value: Primary keratinocytes from P0 back skin

value: Passage 10-15


title: RNA-seq HrasG12V; Tgfbr2 KO (SCC) rep 1


title: RNA of PAS71 control1

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Assembly: Pseudomonas aeruginosa PAS71
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Pseudomonas aeruginosa

source_name: Transcriptome of control of P. aeruginosa PAS71

growth_protocol: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAS71, with the bacterial concentration of 1.0E8 CFU/mL.  All the three triplicate experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 180 rpm for 5 hours.

extract_protocol:
Cells of P. aeruginosa PAS71 were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction.

treatment_protocol: LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAS71 at a concentration of 1.0E8 CFU/mL. Levofloxacin were then added at a concentration of either 0 (control) or 0.125 μg/mL, respectively, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h.

tag: condition

value: native sample

value: exponential growth phase culture


title: RNA of PAS71 control3


title: RNA of PAS81 LVFX3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: Pseudomonas aeruginosa PAS81
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Transcriptome of LVFX-treated P. aeruginosa PAS81

growth_protocol: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAS81, with the bacterial concentration of 1.0E8 CFU/mL.  All the three triplicate experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 180 rpm for 5 hours.

extract_protocol:
Cells of P. aeruginosa PAS81 were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction.

treatment_protocol: LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAS81 at a concentration of 1.0E8 CFU/mL. Levofloxacin were then added at a concentration of either 0 (control) or 0.125 μg/mL, respectively, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h.

value: LVFX-treated sample

tag: Stage

value: exponential growth phase


title: RNA of PAS71 LVX1

source_name: Transcriptome of LVX-treated P. aeruginosa PAS71

value: LVX-treated sample


title: RNA-seq HrasG12V; Tgfbr2 KO (SCC) rep 2


title: RNA of PAS71 LVX3


title: S19,N,healthy

city: urumchi

first: siming

last: Tao

address: 116 Huanghe Road

institute: Xinjiang Uygur Autonomous Region Key Laboratory of Respiratory Physiology and Pathology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 15 nt or longer than 35 nt. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with Genome and known miRNAs from miRBase.
Differential expression analysis was performed using the DESeq R package (1.10.1). miRNA with |log2(FC)|>=1 and Pvalue<0.05found by DESeq were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: Files include count each Sample

source_name: peripheral blood

extract_protocol:
A 2-3-mL peripheral blood sample was collected from each participant into the PAX-gene Blood RNA Tube. After gradient cooling, the samples were stored at –80°C.
Total RNA was extracted from the blood samples using TRIzol reagent. The purity and concentration of extracted RNA were detected using Nanodrop (Optical Density (OD)260/280 ≥1.8; OD260/230 ≥ 1.0) and Qubit 2.0 (total RNA concentration ≥250 ng/µL), respectively. The integrity of the RNA sample was detected using Agilent 2100 bioanalyzer to ensure that samples qualified for sequencing (RNA integrity number of total RNA ≥8.0, 28S/18S ≥1.5; the baseline of the map was not raised; the 5S peak was normal). The high-throughput sequencing experiment of miRNA was performed by Beijing Baimaike Biotechnology Co., Ltd. through the technical service contract, which mainly included several key procedures of miRNA isolation and purification, library establishment, and sequencing.

value: peripheral blood

tag: patient diagnosis:

tag: disease progression


title: RNA of PAS71 LVX2


title: RNA of PAS81 LVFX2


title: S18,N,healthy


title: Reindeer_coculture_back_skin_R_CB

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

description: Cells loaded: 2,015 cells

data_processing:
All raw FASTQs reads were aligned to bovine (Bos taurus) genome using the STAR algorithm. The sample was quantified through the 10X Genomics Cellranger v6 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and downstream analysis.
Assembly: Bos_taurus (Downloaded from Ensembl: https://uswest.ensembl.org/Bos_taurus/Info/Index; Made cellranger compatible using cellranger-mkref pipeline; Reference Genome provided as part of the submission for GSE153095)
Supplementary files format and content: Filtered gene - barcode matrix output from CellRanger-count (transcriptome = Bos_taurus)

molecule: polyA RNA

organism: Rangifer tarandus

source_name: PBMCs from Saphenous Vein; Fibroblasts from Back skin

growth_protocol: All Reindeer (Rangifer tarandus) used for this project were housed in an outdoor enclosure at the University of Calgary Veterinary Sciences Research station in Calgary, Alberta for the entire length of the procedure. All experiments were done in accordance with guidelines set out by the University Animal Welfare Committee (UAWC), the Animal Care Committee (ACC), and with the recommendations and regulations of the Canadian Council on Animal Care and the Province of Alberta Animal Protection Act and Regulation.

extract_protocol:
Whole blood were collected 3 days post-wound from venous blood supply into EDTA tubes. Blood was spun at 300g for 10 mins and plasma was removed and stored at -80oC. Buffy coat was collected, and red blood cells were lysed with ACK buffer (1:10 ACK to blood cells) for 5 minutes and then spun at 300g for 5min and then supernatant. To liberate fibroblasts from reindeer back skin and velvet, either a 12mm circular biopsy punches (velvet) or an elliptical skin excision (back skin) was collected and dissociated to single cells by mincing the skin into 1–2 mm pieces using a pair of scalpels. Minced tissue was first submerged in dispase (2 mg/ml at 37°C for 10 minutes, Stem Cell Technologies) to remove epidermis and then in collagenase type IV (2 mg/ml at 37 for 1-3 hours with mechanical trituration at set intervals, Sigma) to digest the dermal extracellular matrix. Dissociated cell suspensions were passed through 100μm and then 70μm cell strainers, centrifuged at 1200rpm for 6 minutes to pellet the liberated cells, and resuspended in complete fibroblast culture media (DMEM + 10%FBS, 5mL of L-glutamine, penicillin-streptomycin). Fibroblasts were expanded for three days in a 37 °C 5% CO2 tissue culture incubator prior to initiating co-culture with circulating immune cells. Following co-culture incubation, immune cells cells were resuspended in 2% BSA in PBS prior to loading into the 10X controller.
The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.

value: PBMC

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3.1 NEXT GEM


title: 10_4055.sample

value: striatum

value: brain

value: Ganciclovir


title: Reindeer_coculture_antler_velvet_R_CA

description: Cells recovered: 3,169 cells

source_name: PBMCs from Saphenous Vein; Fibroblasts from Velvet


title: RNA of PAS81 LVFX1


title: Ribo-seq HrasG12V; Tgfbr2 KO (SCC)

data_processing:
Library strategy: Ribo-seq
NANOPORE long-read RNA sequencing: Data processing by Nextflow nanoseq v1.1 (Patel et al., 2020)
Quality check by FastQC and NanoPlot (De Coster et al., 2018)
Read mapping by minimap2 and custom transcriptome reference assembly by StringTie2 (Pertea et al., 2015)
Short-read RNA sequencing and Ribosome profiling: Data processing by Nextflow rnaseq (Patel et al., 2020)
Quality check by FastQC
Quality and adapter trimming by TrimGalore
Filtering rRNA, mtRNA and tRNA by Bowtie2 v2.4.1 (Langmead et al., 2019) (Ribosome profiling only)
Read mapping by STAR v2.6.1 (Dobin et al., 2013)
Transcriptome quantifications by Salmon (Patro et al., 2017)
Genome_build: GRCm38

value: Ribosome protected RNA fragments


title: Ectopic_Velvet_Graft_scRNA_6week_post-graft_4A

description: FACS sorted cells: 10,000 cells; Recovered: XXX cells

data_processing:
All raw FASTQs reads were aligned to bovine (Bos taurus) genome using the STAR algorithm. The sample was quantified through the 10X Genomics Cellranger v3 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and downstream analysis.
Genome_build: Bos_taurus (Downloaded from Ensembl: https://uswest.ensembl.org/Bos_taurus/Info/Index; Made cellranger compatible using cellranger-mkref pipeline; Reference Genome provided as part of the submission)
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger-count (transcriptome = Bos_taurus)

extract_protocol:
Following the collection of ectopic skin excision, the sample was minced and incubated in dispase (StemCell Technologies) for 10-15 minutes at 37°C to remove epidermis. Remaining dermis tissue was minced and digested using collagenase (0.2%, Sigma) in 37 degree C water bath for 1-3 hours. To further dissociate the tissue and liberate single cells, the gentleMACS™ Octo Dissociator (Miltenyi Biotec) was used for 6 minutes on a homogenization program. DNase I (1x - Sigma) was also added to the tissue for the last 30 minutes in the water bath. Single cell suspensions were resuspended in cold FACS staining buffer (1% bovine serum albumin in Hank’s Buffered Salt Solution, HBSS; Life Technologies), strained through 100 µm and 70 µm filters (Falcon) and centrifuged at 1200 rpm for 6 minutes. Cell pellets were resuspended in FACS staining buffer and quantified. Viability dye eFlour780 (eBiosciences) was used to exclude dead cells using FACSAria III (BD Biosciences). Of note, identical tissue processing steps were followed as described in GSE142854 to enable side-by-side comparisons with Day 0 Back and Day 0 Antler scRNA-Seq samples.
The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.

treatment_protocol: Animals were anesthetized using injectable anesthesia (Medetomidine, 0.07-0.15mg/kg IM with Azaperone, 0.2mg/kg IM if additional duration of anesthesia required). The animals were blindfolded, their eyes lubricated (Optixcare eye lube), and nasal insufflation of pure oxygen was administered throughout the procedure. Monitoring of anesthetic depth, hear and respiratory rate and temperature were monitored by a licenced animal health technologist with expertise in wildlife handling and anesthesia.

value: Ectopic antler velvet graft


title: RNA of PAS81 control2

source_name: Transcriptome of control of P. aeruginosa PAS81


title: S16,N,healthy


title: S17,N,healthy


title: Reindeer_fibroblast_monoculture_back_skin_R_MB

description: Cells loaded: 915 cells

source_name: Fibroblasts from Back skin

value: Fibroblast


title: RNA of PAS81 control3


title: long-read RNA-seq WT

value: R26-Sox2-IRES-eGFP fl/+

value: total mRNA


title: S15,N,healthy


title: RNA of PAS71 control2


title: RNA of PAS81 control1


title: Ectopic_Velvet_Graft_scRNA_6week_post-graft_5XD

description: FACS sorted cells: 10,000 cells; Recovered: 2,138 cells


title: DF-1, DMSO_3

city: Yangling

first: Chongyang

last: Wang

address: Xinong road

department: College of veterinary medicine

institute: Northwest Agriculture and Forestry University

description: biol rep 3

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)

organism: Gallus gallus

growth_protocol: DF-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: DF-1 cells were treated with 9-butyl-harmol or DMSO.

value: WT

value: DMSO treatment


title: DF-1, DMSO_2

description: biol rep 2


title: S14,COPD,typical rate of COPD progression

tag: patient diagnosis

value: COPD


title: DF-1, beta11_3

description: biol rep 3

tag: cell line

value: 9-butyl-harmol treatment


title: Antler_to_Back_Ectopic_Graft_ATAC_3mo_post-graft_animal_2

description: Recovered: 7,722 cells

data_processing:
All raw FASTQs reads were aligned to bovine (Bos_taurus.ARS-UCD1.2.103) genome using cellranger-atac count.
Genome_build: Bos_taurus (made cellranger compatible using cellranger-mkref pipeline; Reference Genome provided as part of the submission)
Supplementary_files_format_and_content: Filtered peak barcode matrix and filtered tf barcode matrix in hdf5 format from CellRanger-atac count (transcriptome = Bos_taurus)

extract_protocol:
Following the collection of pedicle excision, the sample was minced and incubated in dispase (StemCell Technologies) for 10-15 minutes at 37°C to remove epidermis. Remaining dermis tissue was minced and digested using collagenase (0.2%, Sigma) in 37 degree C water bath for 1-3 hours. To further dissociate the tissue and liberate single cells, the gentleMACS™ Octo Dissociator (Miltenyi Biotec) was used for 6 minutes on a homogenization program. DNase I (1x - Sigma) was also added to the tissue for the last 30 minutes in the water bath. Single cell suspensions were resuspended in cold FACS staining buffer (1% bovine serum albumin in Hank’s Buffered Salt Solution, HBSS; Life Technologies), strained through 100 µm and 70 µm filters (Falcon) and centrifuged at 1200 rpm for 6 minutes. Cell pellets were resuspended in FACS staining buffer and quantified. Viability dye eFlour780 (eBiosciences) was used to exclude dead cells using FACSAria III (BD Biosciences). Of note, identical tissue processing steps were followed as described in GSE142854 to enable side-by-side comparisons with Day 0 Back and Day 0 Antler scRNA-Seq samples.
The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.

tag: facs strategy

value: Dead cells excluded using the forward/side scatter gating and viability dye (Fixable Viability Dye eFluor™ 780)

value: 10X Genomics Chromium Next GEM Chip H version 1


title: S13,COPD,typical rate of COPD progression

tag: tissue

value: peripheral blood


title: Antler_to_Back_Ectopic_Graft_ATAC_6week_post-graft_animal_2

description: Recovered: 1,789 cells


title: Antler_to_Back_Ectopic_Graft_ATAC_6week_post-graft_animal_1

description: Recovered: 1,006 cells


title: DF-1, beta11_2

description: biol rep 2

tag: genotype


title: DF-1, beta11_1

description: biol rep 1


title: Normoxic-Side-4hr-9-30-20

city: Los Angeles

first: Megan

last: McCain

state: California

address: 1042 Downey Way

institute: University of Southern California

data_processing:
Partek Flow software was used for data processing
Sequenced reads were trimmed from both ends based on a Phred quality score of 20 and a minimum read length of 25 remaining bases
STAR alignment to the rn6 genome
noise reduction filter where the maximum ≤ 10
Genome_build: rn6
Supplementary_files_format_and_content: tab delimited text file with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: NRVMs

growth_protocol: NRVMs were generated from serial dilutions of ventricular tissue in collagenase. Microphysiological systems were seeded with 1.5 x 10^6 cells/device. Tissues formed on the device's fibronectin micropatterned surface after 72 h.

extract_protocol:
RNA was harvested using Trizol reagent. RNA isolation was performed using Qiagen miRNeasy kit and protocol.
Libraries were constructed with the Swift RNA Library Kit (Swift Biosciences, Ann Arbor, MI). Library concentration and size were measured with a Qubit fluorometer and an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA), respectively. Libraries were multiplexed and sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 75bp single-end sequencing.

treatment_protocol: 4h oxygen modulation using gas from compressed tanks interfacing with the microfluidic channels of the microphysiological system.

tag: strain

value: Sprague-Dawley

tag: time

value: 4 hours

tag: oxygen

value: gradient- normoxic side


title: S12,COPD,typical rate of COPD progression


title: Normoxic-Side-4hr-1-26-21


title: 4XE_ReindeerPBMC_Antler

description: Cells loaded: 12,000 cells

source_name: Distal Antler Velvet

extract_protocol:
PBMCs were collected from venous blood supply from saphenous vein or from distal antler velvet into EDTA tubes and briefly stored on ice.  Blood was spun at 300g for 10 min and plasma removed and stored at -80oC. Buffy coat was collected, and red blood cells were lysed with ACK buffer (1:10 ACK to blood cells) for 5 minutes and then spun at 300g for 5min and then supernatant.  Cells were washed twice with 5mL PBS, then spun at 300g 5 min.  Cells were resuspended in 2% BSA in PBS at a final concentration of 30,000 cells/100uL and run through a 40µm cell strainer, before loading into the 10X controller (~12,000 cells).
The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.

value: Distal Antler Velvet

value: 10X Genomics Single Cell RNAseq v3.1 NEXT GEM


title: Normoxic-Side-4hr-2-23-21


title: Normoxia-4hr-10-12-20

value: normoxia


title: Normoxia-4hr-12-21-20


title: S10,SLOW

value: SLOW


title: Normoxia-4hr-9-30-20


title: 4XE_ReindeerPBMC_Back

description: Cells loaded: 12,000 cells

source_name: Saphenous Vein

value: Saphenous Vein


title: 5XD_ReindeerPBMC_Antler

description: Cells loaded: 12,000 cells


title: S09,SLOW


title: Normoxia-4hr-1-25-21


title: DF-1, DMSO_1

description: biol rep 1

tag: treatment


title: 5XD_ReindeerPBMC_Back

description: Cells loaded: 12,000 cells


title: Normoxia-4hr-2-23-21


title: Hypoxic-Side-4hr-9-30-20

value: gradient- hypoxic side


title: Ectopic_Velvet_Graft_scRNA_3mo_post-graft

description: FACS sorted cells: 10,000 cells; Recovered: 6,103 cells

value: Ectopic antler velvet graft


title: S08,SLOW


title: Antler_to_Back_Ectopic_Graft_ATAC_6mo_post-graft

description: Recovered: 5,116 cells


title: Hypoxic-Side-4hr-12-21-20


title: Hypoxic-Side-4hr-1-26-21


title: Hypoxic-Side-4hr-2-23-21


title: Normoxic-Side-4hr-12-21-20


title: Hypoxia-4hr-9-30-20

value: hypoxia


title: Day_7_Back_ATAC

description: Recovered: 5,773 cells

source_name: Backskin


title: S07,SLOW


title: Day_7_Antler_ATAC

description: Recovered: 7,176 cells


title: S11,SLOW


title: Hypoxia-4hr-10-12-20


title: Hypoxia-4hr-12-21-20


title: Hypoxia-4hr-2-23-21


title: Os ChIP-Seq GLK2 Os01g13740 replicate 2

city: Hong Kong

first: Sibo

last: REN

address: Sha tin CUHK

institute: The Chinese University of Hong Kong

data_processing:
ChIP-seq reads 100 bp from 3’ end were trimmed with the bowtie2 parameter -3 100.
ChIP-seq reads were aligned to plant reference genomes (Arabidopsis thaliana TAIR10, Nicotiana benthamiana version 2.5.1, Solanum lycopersicum SL4.0, Oryza sativa MSU7.0 and Zea mays RefGen_v4) using Bowtie 2 (version 2.3.2).
The ENCODE2 ChIP-seq pipline with MACS2 (version 2.2.1) and IDR (version 2.0.4.2) were used for peak calling. Peak summit positions were retrieved by using the “--call-summits” function in MACS2. The regions +/- 75bp from the summit position with signal fold-change in NarrowPeak format were then supplied to IDR, and the regions passed the IDR 0.01 and summit signal foldchange cut-off were kept and resized back to 150bp.
BigWig files were generated using the samtools view with binsize 1bp.
Supplementary files format and content: bigWig, narrowPeak

organism: Oryza sativa Japonica Group

source_name: Leaf

extract_protocol:
The nuclei were then isolated by filtration and centrifugation, and the chromatin was sonicated to sub-kb fragments using Bioruptor.
ChIP-seq libraries were prepared using the HiSeq X Ten.

value: Leaf

tag: replicate

value: replicate 2

tag: chip antibody

value: Rabbit monoclonal anti-HA (clone C29F4), Cell Signaling Technology, Cat# 3724


title: Day_0_Antler_ATAC

description: Recovered: 17,843 cells

value: Dead cells excluded using the forward/side scatter gating and viability dye (Fixable Viability Dye eFluor™ 780)


title: Os ChIP-Seq GLK2 Os01g13740 replicate 1

value: replicate 1


title: Day_0_Back_ATAC

description: Recovered: 20,002 cells

value: 10X Genomics Chromium Next GEM Chip H version 1


title: Ectopic_Velvet_Graft_scRNA_6mo_post-graft

description:
FACS strategy: Dead cells excluded using the forward/side scatter gating and viability dye (Fixable Viability Dye eFluor™ 780).
FACS sorted cells: 10,000 cells; Recovered: 1,050 cells.
Library preparation: 10X Genomics Single Cell RNAseq v3.

data_processing:
All raw FASTQs reads were aligned to bovine (Bos taurus) genome using the STAR algorithm. The sample was quantified through the 10X Genomics Cellranger v3 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and downstream analysis.
Genome_build: Bos_taurus (Downloaded from Ensembl: https://uswest.ensembl.org/Bos_taurus/Info/Index; Made cellranger compatible using cellranger-mkref pipeline; Reference Genome provided as part of the submission).
Supplementary_files_format_and_content: R1_Ectopic_Back_scRNA_A1_filtered_feature_bc_matrix.h5: HDF5; Filtered gene - barcode matrix output from CellRanger-count (transcriptome = Bos_taurus).
Supplementary_files_format_and_content: Bos_taurus_reference_genome.tar: Tar archive includes Cellranger-compatible Bos taurus reference genome (including FASTA and GTF files).

treatment_protocol: Animals were anesthetized using injectable anesthesia (Medetomidine, 0.07-0.15mg/kg IM with Azaperone, 0.2mg/kg IM if additional duration of anesthesia required). The animals were blindfolded, their eyes lubricated (Optixcare eye lube), and nasal insufflation of pure oxygen was administered throughout the procedure. Monitoring of anesthetic depth, hear and respiratory rate and temperature were monitored by a licensed animal health technologist with expertise in wildlife handling and anesthesia.


title: Hypoxia-4hr-1-25-21

value: Sprague-Dawley


title: Os ChIP-Seq GLK1 Os06g24070 replicate 1


title: Os ChIP-Seq GLK1 Os06g24070 replicate 2


title: S04,QUICK

value: peripheral blood

value: COPD

value: QUICK


title: S01,QUICK


title: Aardvark_HiC

city: Cerdanyola del Valles

first: Lucía

last: Alvarez-Gonzalez

state: Barcelona

address: Campus de la UAB, Bellaterra

department: Dept. Biologia Cel.lular, Fisiologia i Immunologia

country: Spain

institute: Universitat Autonoma de Barcelona

data_processing:
HiC: BBDuk (version 09/2019) was used for quality check and trimming of the raw fastq sequences. HiC data processing was conducted using TADbit
ChIP-seq: Reads were trimmed using Trimmomatic (version 0.39).  Trimmed fastq files were then aligned to the reference genome using bwa-mem (version 0.7.17). Alignments with a MAPQ > 30 were extracted and used as input for MACS2 (version 2.2.7.1).
RNA-seq: BBDuk (version 09/2019) was used for quality check and trimming of the raw. Then, reads were mapped with STAR (version 2.7.10a ) using the end-to-end alignment mode and gene expression quantification was performed with featureCounts.
Assembly: Elephant (this paper); Aardvark (OryAfe1.0_HiC); Tasmanian devil (mSarHar1.11); Tammar wallaby (me-1k)
Supplementary files format and content: HiC: Mapped reads files; ChIP-seq: BedGraph coverage files;RNA-seq: tab-delimited text files include raw counts

organism: Orycteropus afer

source_name: Fibroblasts

growth_protocol: Fibroblasts cell cultures were incubated at 37°C in 10% CO2. A cell fraction of each cell line was kept for immunofluorescence analysis and quality controls (see below) and the rest were fixated with 1% formaldehyde for 10’ at RT for Hi-C and ChIP-seq

extract_protocol:
For HiC:  Fibroblasts were processed following the in situ Hi-C protocol described by Vara et. Al 2019; For CTCF ChIP-seq: Lysates were clarified from Mnase I digested nuclei and CTCF-DNA complexes were isolated with CTCF antibody (Millipore, #07-729); For H3K4me ChIP-seq: Lysates were clarified from Mnase I digested nuclei and H3K4me3-DNA complexes were isolated with H3K4me3 antibody (Abcam, #ab8580); For RNA-seq: RNA was TRIzol (Invitrogen) extracted from Tasmanian devil cultured fibroblasts according to manufactures instructions.
Libraries were prepared for sequencing using standard Illumina protocols
Hi-C
ChIP-seq
RNA-seq

tag: cell type

value: Fibroblasts


title: S02,QUICK


title: S06,QUICK


title: scRNA-Seq_Day14_Back_RNA

description: FACS sorted cells: 50,000 cells; Recovered: 2,760 cells

data_processing:
All raw FASTQs reads were aligned to bovine (Bos taurus) genome using the STAR algorithm. Samples 1-8 were quantified through the 10X Genomics Cellranger v3 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and all downstream analysis. Back and antler samples were integrated for each time point using Canonical Correlation Analysis (CCA) and Mutual Nearest Neighbor (MNM) techniques employed by Seurat v3.1.1.
Genome_build: Bos_taurus (Downloaded from Ensembl: https://uswest.ensembl.org/Bos_taurus/Info/Index Made cellranger compatible using cellranger-mkref pipeline; Reference Genome GTF file is available on series record.
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger-count (transcriptome = Bos_taurus)

extract_protocol:
Following the collection of 12mm back and velvet skin excisions, the samples were minced and incubated in dispase (StemCell Technologies) for 10-15 minutes at 37°C to remove epidermis. Remaining dermis tissue was minced and digested using collagenase (0.2%, Sigma) in 37 degree C water bath for 1-3 hours. To further dissociate the tissue and liberate single cells, the gentleMACS™ Octo Dissociator (Miltenyi Biotec) was used for 6 minutes on a homogenization program. DNase I (1x - Sigma) was also added to the tissue for the last 30 minutes in the water bath. Single cell suspensions were resuspended in cold FACS staining buffer (1% bovine serum albumin in Hank’s Buffered Salt Solution, HBSS; Life Technologies), strained through 100 µm and 70 µm filters (Falcon) and centrifuged at 1200 rpm for 6 minutes. Cell pellets were resuspended in FACS staining buffer and quantified. Viability dye eFlour780 (eBiosciences) was used to exclude dead cells using FACSAria III (BD Biosciences).
All samples were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. For all samples, sequencing was performed using a combination of Illumina NovaSeq SP and S2 Flow cells to ensure all samples received 25,000 reads/cell at minimum.

value: back skin

value: day 14

value: 10X Genomics Single Cell RNAseq v3


title: single cell RNA sequencing of patient derived organoid model 2

city: Pittsburgh

first: Kai

last: Ding

address: 204 Craft Ave

institute: University of Pittsburgh

description:
PDO2
single cell RNA
PDOs_LogCounts.txt

data_processing:
CellRanger for reads mapping, Seurat for cell filteration and data normalization.
Assembly: GRCh38
Supplementary files format and content: PDOs_LogCounts.txt: text file of normalized counts, with row as gene column as cell.
Supplementary files format and content: BoM_primary_bulkRNA.txt: text file of normalized counts, with row as gene column as sample.

source_name: in vitro organoids

extract_protocol:
10X genomic cell isolation protocol.
10X genomic single cell RNA protocol V3 3' end.

value: in vitro organoids

value: breast cancer cells


title: single cell RNA sequencing of patient derived organoid model 1

description:
PDO1
single cell RNA
PDOs_LogCounts.txt


title: Illumina.YM-155_6h.batch1

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

data_processing:
(1) Only paired end raw reads where each read was ≥ 30 bases after adaptor trimming and each base had the Phred quality score ≥ 20 were selected.  (2) Such reads were then aligned to the GRCh38/hg38 assembly of the human genome by the Tophat software, and the uniquely mapping reads were used to calculate the FPKM for each transcript annotated in UCSC Genes database and vlincRNAs by the Cufflinks software with the default parameters.
Assembly: GRCh38/hg38

growth_protocol: Human CML leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2.

extract_protocol:
Total RNA from the samples was extracted using TRNzol Universal (Tiangen, DP424) and Total RNA kit I (Omega, R6834-02) according to the manufacturer’s protocols.
The RNA samples were used for RNA-seq library construction using rRNA depletion and a strand-specific strategy. The library construction and sequencing using the Illumina NovaSeq 6000 platform with the PE150 strategy on the 10-GB scale were outsourced to Novogene Corporation (Beijing).

treatment_protocol: For drug treatments, 1.5 million cells were seeded in 3 ml of the medium without antibiotic per well in 6-well plates. After 16 hours, various drugs or DMSO/water controls were added and incubated for 3 or 6 hr. All drugs were obtained from Abmole Bioscience Inc and dissolved in DMSO (with the exception of YM-155 and cytarabine that were dissolved in water). The concentration of DMSO was kept at 0.1% in all treatments.

value: chronic myelogenous leukemia cell line

value: treated with YM-155 for 6 hours


title: TD008_after

city: 上海

first: Zhu

last: YouWei

state: Shanghai

address: 130 Dong'an Road

department: Institutes of Biomedical Sciences

institute: Fudan university

data_processing:
Raw data statistics: Perform statistical analysis on subreads to obtain information such as the number, average length and GC content of subreads sequence.
CCS analysis:Perform Circular Consensus Calling on subreads to obtain high-quality CCS reads by using pbccs software (version 3.3.0), and perform statistical analysis on CCS sequences.
barcode split: Split CCS reads according to barcode by using lima software (version 1.9.0), and statistics the split results.
Statistics of target sequences abundance:If the target area is specified, the target sequence is captured according to the 10nt of upstream and downstream of the target sequence, otherwise, the target sequence refs to the full-length sequences.
Statistics of base distribution: The CCS reads are aligned to the reference sequence by using BWA software, and the section on the alignment is extracted and mutation abundance information is counted.
Assembly: HIV-1, complete genome (GenBank: AF033819.3)
Supplementary files format and content: The target sequence is captured according to the 10nt of upstream and downstream of the HIV protease/ reverse transcriptase (PR/RT) region sequences (headers represent the date of sequencing and the sequencing number of the ccs reads)
Supplementary files format and content: The CCS reads are aligned to the reference sequence by using BWA software, and the section on the alignment is preserved to bam files

organism: Human immunodeficiency virus 1

extract_protocol:
PacBio Sequel instrument (Pacific Biosciences of California, Inc., California, USA)
For each sample, >2ug purified PCR fragments (1kb~10kb) was used for library preparation. Fragmented DNAs were treated with End Prep Enzyme Mix for end repairing, 5’Phosphorylation and 3’dA-tailing in one reaction, followed by a T-A ligation to add universal hairpin adapters to both ends. Then the SMRTbell libraries were validated by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 3.0 Fluorometer. The final SMRTbell libraries were loaded on PacBio Sequel instrument according to manufacturer’s instructions (Pacific Biosciences of California, Inc., California, USA).

value: Primary cell

value: PBMC

value: M10 CAR-T cells

tag: age

value: 36 years old

tag: gender

value: male


title: scRNA-Seq_Day7_Back_RNA

description: FACS sorted cells: 50,000 cells; Recovered: 4,112 cells

value: day 7

value: Dead cells excluded using the forward/side scatter gating and viability dye (Fixable Viability Dye eFluor™ 780)


title: TD008_before

value: peripheral blood

value: protease/ reverse transcriptase (PR/RT) region sequences


title: scRNA-Seq_Day14_Antler_RNA

description: FACS sorted cells: 50,000 cells; Recovered: 9,719 cells

value: antler velvet skin


title: scRNA-Seq_Day7_Antler_RNA

description: FACS sorted cells: 50,000 cells; Recovered: 6,520 cells


title: S05,QUICK

value: COPD

value: QUICK


title: Illumina.YM-155_3h.batch1

value: treated with YM-155 for 3 hours


title: S03,QUICK


title: scRNA-Seq_Day3_Back_RNA

description: FACS sorted cells: 50,000 cells; Recovered: 6,287 cells

value: back skin

value: day 3

value: 10X Genomics Single Cell RNAseq v3


title: H295R OE 1

city: London

first: Jack

last: Williams

state: City Of London

address: Molecular Endocrinology, William Harvey Research Institute, Charterhouse Square

country: United Kingdom

institute: Queen Mary University Of London

data_processing:
FastQC Reads Quality Control version 3.0.1 (28/10/2020)
HISAT2 version 1.03 (1/6/2017)
subread_featureCounts version 0.1.0 (21/3/2019)
DESeq2 (11/12/2017)
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files: individual txt files for each sample containing the output data generated from FeatureCounts software, displaying the counts and gene length for each individual gene.
Supplementary_files_format_and_content: TPM.xlsx: TPM values for each gene for each sample were calculated and then combined into a single spreadsheet with samples in columns and genes in rows.

source_name: H295R adrenocortical cell line

growth_protocol: H295R cells were grown in standard growth medium (1:1 DMEM/F12 basal media supplemented with 2.5% NuSerum, 1% Corning ITS Universal Premix, 1% Pen/Strep) in 6-well plates to a confluency of 80%.

extract_protocol:
RNA was extracted using the QIAGEN RNeasy kits following manufacturer's protocol. RNA was quantified using a Nanodrop spectophotometer and assessed for quality by measuring the 28S/18S ratio by agarose gel electrophoresis,
Library construction was performed by Eurofins Genomics under their NGSelect RNA on Illumina. The library construction involved purification of poly-A containing mRNA molecules, mRNA fragmentation, random pried cDNA synthesis, adaptor ligation and adapter specific PCR amplification.

treatment_protocol: No treatment

value: adrenocortical cell line

value: SGPL1 OE


title: H295R OE 3


title: H295R KO 3

value: SGPL1 KO


title: Illumina.Talazoparib_6h.batch2

value: chronic myelogenous leukemia cell line

value: treated with Talazoparib for 6 hours


title: Illumina.Talazoparib_3h.batch2

value: treated with Talazoparib for 3 hours


title: H295R KO 2


title: Tammar_wallaby__HiC

organism: Notamacropus eugenii

value: Fibroblasts


title: Illumina.SN-38_6h.batch2

value: treated with SN-38 for 6 hours


title: scRNA-Seq_Day3_Antler_RNA

description: FACS sorted cells: 50,000 cells; Recovered: 11,004 cells

value: Dead cells excluded using the forward/side scatter gating and viability dye (Fixable Viability Dye eFluor™ 780)


title: scRNA-Seq_Day0_Antler

description: FACS sorted cells: 50,000 cells; Recovered: 5,620 cells

value: day 0


title: Illumina.SN-38_3h.batch2

value: treated with SN-38 for 3 hours


title: Illumina.NU7441_6h.batch2

value: treated with NU7441 for 6 hours


title: H295R KO 1


title: scRNA-Seq_Day0_Back_RNA

description: FACS sorted cells: 50,000 cells; Recovered: 9,006 cells


title: Illumina.Selumetinib_6h.batch1

value: treated with Selumetinib for 6 hours


title: Illumina.Selumetinib_3h.batch1

value: treated with Selumetinib for 3 hours


title: H295R OE 2


title: H295R WT 3

value: WT


title: Illumina.NU7441_3h.batch2

value: treated with NU7441 for 3 hours


title: microRNA counts from adrenal gland (ENCLB994HJD)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR895SFC/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human adrenal gland
experiment encode accession: ENCSR895SFC
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB994HJD
size range: <30

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens male adult (54 years) adrenal gland tissue

label_protocol: Nanostring protocol

value: adrenal gland

value: tissue

tag: description

value: Adrenal Gland

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

value: 54 year

tag: lab

value: Barbara Wold, Caltech

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS420UOM at ENCODE; https://www.encodeproject.org/ENCBS420UOM/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: H295R WT 2

value: adrenocortical cell line

tag: genotype


title: Illumina.MK-2206_6h.batch1

value: chronic myelogenous leukemia cell line

value: treated with MK-2206 for 6 hours


title: Illumina.Nifuroxazide_6h.batch2

value: treated with Nifuroxazide for 6 hours


title: microRNA counts from adrenal gland (ENCLB011GAL)

description:
https://www.encodeproject.org/experiments/ENCSR895SFC/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human adrenal gland
experiment encode accession: ENCSR895SFC
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB011GAL
size range: <30

source_name: Homo sapiens adrenal gland tissue male adult (54 years)

value: ENCBS719AMH at ENCODE; https://www.encodeproject.org/ENCBS719AMH/

value: derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Illumina.MK-2206_3h.batch1

value: treated with MK-2206 for 3 hours


title: microRNA counts from GM23338 (ENCLB464AYR)

description:
https://www.encodeproject.org/experiments/ENCSR894GAC/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human induced pluripotent stem cell
experiment encode accession: ENCSR894GAC
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB464AYR
size range: <30

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

tag: line

value: cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: Thomas Gingeras, CSHL

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: Illumina.Mirin_6h.batch2

value: treated with Mirin for 6 hours


title: hiPSC-derived WAT sample 3

city: Boston

first: Johan

last: Spetz

state: MA

address: HSPH2, Room 229, 655 Huntington Ave.

department: JBL Center for Radiation Sciences

institute: Harvard School of Public Health

data_processing:
Sequencing output was de-multiplexed, barcodes removed, trimmed for quality, and FastQC was run on all files for quality control.
Reads were aligned to human genome assembly GRCh38 using STAR76.
Genome_build: GRCh38
Supplementary_files_format_and_content: ipsc_rnaseq_processed.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Human DiPS 1016 SeVA iPSC

growth_protocol: Human DiPS 1016 SeVA iPSC stocks (Harvard Stem Cell Institute iPS Core Facility, Harvard University) were thawed in complete StemFlex medium (Life Technologies) containing 10 µM Rho-associated, coiled-coil containing protein kinase (ROCK) inhibitor Y-27632 (Calbiochem). After 24 hours, medium was replaced with complete StemFlex free of ROCK inhibitor. Cells were detached using Accutase (StemCell Technologies) and split 1:5 to 1:10 prior to reaching confluence; cells were cultured in complete StemFlex media supplemented with ROCK inhibitor for the first 24 hours. hiPSC clones were split to 50% confluence and cultured overnight in StemFlex medium (Life Technologies) with 10 µM ROCK inhibitor. The next day (Day 1), differentiation was initiated by replacing the medium with N2B27, which consists of equal parts of Neurobasal medium and DMEM/F12 GlutaMAX (Life Technologies) supplemented with B-27 without vitamin A (Life Technologies) and N-2 supplement (Life Technologies). For the first three days 6 µM CHIR-99021 (Cayman Chemicals) and 25 ng/ml BMP4 (R&D Systems) was added daily. To generate VSMCs, media was replaced on day 4 by N2B27 supplemented with 10 ng/ml PDGF-BB (PeproTech) and 2 ng/ml Activin A (PeproTech). On Day 6, cells were split with trypsin-EDTA (Corning) into dishes coated with human fibronectin (Sigma-Aldrich) and maintained in Medium 231 (Life Technologies) supplemented with Smooth Muscle Growth Supplement (Life Technologies). To generate ECs, the same protocol was followed for the first 3 days to achieve the mesodermal lineage, but on Day 4 media was replaced with N2B27 supplemented with 200ng/ml VEGF (PeproTech) and 2µM forskolin (Sigma-Aldrich). On Day 6, cells were split and differentiated ECs were either MACS-separated using CD144 MicroBeads (Miltenyi Biotec) or flow cytometry sorted for CD144 positive cells to isolate the population expressing VE-cadherin. Endothelial lineage cells were maintained in EGM-2 Endothelial Cell Growth Medium (Lonza). Differentiation of hPSCs into adipocytes was performed as follows: hPSCs were passaged and grown in suspension culture to form embryoid bodies. After one week, the embryoid bodies were plated on tissue culture-treated plastic and grown in DMEM + 10% fetal bovine serum. The outgrowing mesenchymal progenitor cells (MPCs) were used from passage 4 through 8. For adipocyte differentiation MPCs were infected with previously described lentivirus to express the transactivator rtTA and inducible expression of PPARg2. MPCs were passaged and grown to confluence, and then exposed to 700ng/mL doxycycline for two weeks in previously established A2 medium, and then one week without doxycycline in A2 medium and used for assays. All culture media were supplemented with penicillin-streptomycin (Life Technologies) and Plasmocin (Invivogen) and changed every other day unless otherwise specified.

extract_protocol:
RNA was extracted from hiPSC-derived cells using the QIAcube and the RNeasy Plus Mini Kit (QIAGEN). RNA quality was ascertained with the TapeStation (Agilent), and only samples with a RIN>9.0 value were used for sequencing.
Sequencing libraries were made with the PrepX DNA library kit (Takara bio) using the Apollo system (Takara bio). Quality control for the libraries was performed using the KAPA library quantification kit (Roche) and the TapeStation (Agilent). Sequencing libraries were barcoded, pooled and sequenced on a HiSeq 2500 (Illumina) with single-end 150bp reads.

value: white adipose tissue


title: Illumina.Nifuroxazide_3h.batch2

value: treated with Nifuroxazide for 3 hours


title: microRNA counts from GM23338 (ENCLB779UIS)

description:
https://www.encodeproject.org/experiments/ENCSR894GAC/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human induced pluripotent stem cell
experiment encode accession: ENCSR894GAC
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB779UIS
size range: <30

value: adult

value: male

value: ENCBS373AAA at ENCODE; https://www.encodeproject.org/ENCBS373AAA/


title: Illumina.Mirin_3h.batch2

value: chronic myelogenous leukemia cell line

value: treated with Mirin for 3 hours


title: Illumina.Imatinib_6h.batch2

value: treated with Imatinib for 6 hours


title: Illumina.Imatinib_3h.batch2

value: treated with Imatinib for 3 hours


title: microRNA counts from heart left ventricle (ENCLB394KKB)

description:
https://www.encodeproject.org/experiments/ENCSR888ZAA/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human heart left ventricle
experiment encode accession: ENCSR888ZAA
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB394KKB
size range: <30

source_name: Homo sapiens heart left ventricle tissue female adult (51 year)

value: heart left ventricle

value: tissue

value: Heart - Left Ventricle

value: female

value: Barbara Wold, Caltech

value: 51 year

value: ENCBS969RHA at ENCODE; https://www.encodeproject.org/ENCBS969RHA/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: hiPSC-derived WAT sample 2

value: white adipose tissue


title: Illumina.I-BET151_3h.batch2

value: treated with I-BET151 for 3 hours


title: Illumina.I-BET151_6h.batch2

value: treated with I-BET151 for 6 hours


title: hiPSC-derived WAT sample 1


title: Illumina.Etoposide_6h.batch2

value: treated with Etoposide for 6 hours


title: microRNA counts from heart left ventricle (ENCLB369MXF)

description:
https://www.encodeproject.org/experiments/ENCSR888ZAA/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human heart left ventricle
experiment encode accession: ENCSR888ZAA
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-08-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB369MXF
size range: <30

value: adult

value: ENCBS361CPX at ENCODE; https://www.encodeproject.org/ENCBS361CPX/


title: Illumina.Etoposide_3h.batch2

value: chronic myelogenous leukemia cell line

value: treated with Etoposide for 3 hours


title: hiPSC-derived VSMC sample 2

value: vascular smooth muscle cells


title: microRNA counts from testis (ENCLB839AZA)

description:
https://www.encodeproject.org/experiments/ENCSR882QTS/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human testis
experiment encode accession: ENCSR882QTS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB839AZA
size range: <30

source_name: Homo sapiens testis tissue male adult (37 years)

value: testis

value: Testis 1-2

value: 37 year

value: male

value: ENCBS653SLC at ENCODE; https://www.encodeproject.org/ENCBS653SLC/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Illumina.DMSO_6h.batch1

value: treated with DMSO for 6 hours


title: hiPSC-derived VSMC sample 3


title: microRNA counts from testis (ENCLB640JPE)

description:
https://www.encodeproject.org/experiments/ENCSR882QTS/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human testis
experiment encode accession: ENCSR882QTS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB640JPE
size range: <30

value: tissue

value: Barbara Wold, Caltech

value: ENCBS906LAU at ENCODE; https://www.encodeproject.org/ENCBS906LAU/


title: hiPSC-derived VSMC sample 1


title: microRNA counts from thyroid gland (ENCLB257ZLM)

description:
https://www.encodeproject.org/experiments/ENCSR869POD/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human thyroid gland
experiment encode accession: ENCSR869POD
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB257ZLM
size range: <30

source_name: Homo sapiens thyroid gland tissue male adult (37 years)

value: thyroid gland

value: Thyroid

value: ENCBS018WOC at ENCODE; https://www.encodeproject.org/ENCBS018WOC/


title: Illumina.Cyclophosphamide_6h.batch2

value: treated with Cyclophosphamide for 6 hours


title: Illumina.DMSO_3h.batch2

value: chronic myelogenous leukemia cell line

value: treated with DMSO for 3 hours


title: H295R WT 1

value: adrenocortical cell line

value: WT


title: hiPSC-derived EC sample 3

value: endothelial cells


title: Illumina.BML-277_6h.batch1

value: treated with BML-277 for 6 hours


title: Illumina.Cyclophosphamide_3h.batch2

value: treated with Cyclophosphamide for 3 hours


title: Illumina.BML-277_3h.batch1

value: treated with BML-277 for 3 hours


title: microRNA counts from ovary (ENCLB409SZN)

description:
https://www.encodeproject.org/experiments/ENCSR854NNW/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human female gonad
experiment encode accession: ENCSR854NNW
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB409SZN
size range: <30

source_name: Homo sapiens ovary tissue female adult (51 year)

value: ovary

value: Ovary 4-1

value: adult

value: female

value: 51 year

value: ENCBS988BTE at ENCODE; https://www.encodeproject.org/ENCBS988BTE/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: microRNA counts from ovary (ENCLB188HVD)

description:
https://www.encodeproject.org/experiments/ENCSR854NNW/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human female gonad
experiment encode accession: ENCSR854NNW
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB188HVD
size range: <30

value: tissue

value: Ovary 4-2

value: Barbara Wold, Caltech

value: ENCBS430YCW at ENCODE; https://www.encodeproject.org/ENCBS430YCW/


title: Illumina.10074-G5_6h.batch1

value: chronic myelogenous leukemia cell line

value: treated with 10074-G5 for 6 hours


title: Illumina.10074-G5_3h.batch1

value: treated with 10074-G5 for 3 hours


title: hiPSC-derived EC sample 1

value: endothelial cells


title: hiPSC-derived EC sample 2


title: microRNA counts from body of pancreas (ENCLB876MRE)

description:
https://www.encodeproject.org/experiments/ENCSR800WFS/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human pancreas
experiment encode accession: ENCSR800WFS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB876MRE
size range: <30

source_name: Homo sapiens body of pancreas tissue male adult (54 years)

value: body of pancreas

value: Pancreas

value: 54 year

value: male

value: ENCBS213PZE at ENCODE; https://www.encodeproject.org/ENCBS213PZE/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: microRNA counts from body of pancreas (ENCLB095SXO)

description:
https://www.encodeproject.org/experiments/ENCSR800WFS/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on human pancreas
experiment encode accession: ENCSR800WFS
assay title: microRNA counts
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB095SXO
size range: <30

value: adult

value: ENCBS126RDV at ENCODE; https://www.encodeproject.org/ENCBS126RDV/


title: undifferentiated hiPSC sample 3

value: undifferentiated human induced pluripotent stem cells


title: Illumina.DMSO_6h.batch2

value: treated with DMSO for 6 hours


title: microRNA counts from lower leg skin (ENCLB747UWG)

description:
https://www.encodeproject.org/experiments/ENCSR798NKG/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on human lower leg skin
experiment encode accession: ENCSR798NKG
assay title: microRNA counts
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB747UWG
size range: <30

source_name: Homo sapiens lower leg skin tissue male adult (54 years)

value: lower leg skin

value: tissue

value: Skin - Sun Exposed (Lower leg)

value: ENCBS488XGK at ENCODE; https://www.encodeproject.org/ENCBS488XGK/