title: s530_Female_Young

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

data_processing:
Clustering and DNA sequencing were performed by GenomeScan BV (Leiden, Netherlands) using a NextSeq 500 sequencer (Illumina, San Diego, California, USA) with a single-read 75-cycle sequencing protocol with at least 15 million reads per sample and %Q30 > 92.58-93.75%.
Fastq files of the same sample (from mutiple sequence runs and/or lanes) were merged to 1 fastq-file/sample.
Reads of the fastq files were aligned to the human reference genome (Homo_sapiens.GRCh38.primary_assembly.GENCODE) using the Star2.5 alignment algorithm. The default mismatch rate of 2% was used (3 mismatches in a read of 150 bases). The alignment files (BAM files) were sorted and indexed with the Samtools v0.1.18 package.
Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Genome_build: Genome Reference Consortium Human Build 38 (Homo_sapiens.GRCh38.primary_assembly.GENCODE)
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample), the bottom lines contain a summary of (un-)mapped reads.

source_name: human muscle, upper leg (vastus lateralis)

growth_protocol: Study population and design  A cross-sectional study was performed between November 2016 and August 2017 among community-dwelling old and young individuals in the northern part of The Netherlands. This study was approved by the Wageningen University Medical Ethical Committee and was conducted in accordance with the principles of the Declaration of Helsinki (Fortaleza, Brazil, 2013), according to national law (WMO, The Hague, 1998), and is registered in the Dutch Trial Register (NTR6124). The old subjects (≥ 75 years) were screened for pre-frailty and frailty using the Fried criteria (e.g. weight loss, exhaustion, low physical activity, slowness and weakness)[Fried et al., J Gerontol Med Sci 2001]. Based on these criteria the old subjects were divided into two groups; fit (no frailty indicators present) and (pre-)frail (≥ 1 frailty indicator present, i.e., including pre-frail and frail subjects). As a reference group, healthy young individuals aged 20-30 years and with a healthy BMI (20-25 kg/m2) were included. The following exclusion criteria were applied: cardiac failure, COPD, anemia, dementia, cancer, neuromuscular disorders and diabetes mellitus type I and II (type II was only allowed in (pre-)frail old subjects), a significant medical event within the previous three months, and contra-indication for the dual-energy X-ray absorptiometry (DXA) scan or muscle biopsy (e.g. use of anticoagulants). In addition, use of carnitine supplements or medications that influence carnitine or energy metabolism were excluded (i.e. systemic corticosteroids, fibrates, valproic acid, emetine, zidovudine). Additional exclusion criteria were applied for the young individuals: performing sports for more than five times a week, being pregnant or nursing. After inclusion, subjects visited the Medical Centre Leeuwarden twice: on the first occasion body composition and physical performance was assessed, and on the second occasion, a blood sample and muscle biopsy was obtained. All measurements were performed by trained staff. In total, 101 subjects were included in this study. During the study, 20 subjects withdrew from the study: 5 from the young, 11 from the fit old and 4 from the (pre-)frail old group. In addition, one subject from the (pre-)frail old group was excluded from analyses due to difficulties in obtaining a muscle biopsy. Consequently, 80 subjects were used for analysis.

extract_protocol:
After an overnight fast, muscle biopsies were taken from the vastus lateralis. After local anesthesia, percutaneous needle biopsy samples (50-80 mg) were collected according to the Bergström method with suction by a trained physician [Bergström, Scand   J Clin Lab Investig 1975; Hennessey et al., Appl Physiol 1997]. Immediately after each biopsy, any visible non-muscle tissue was removed from the sample; the remaining tissue was immediately frozen in liquid nitrogen and stored at -80°C until further analyses.
Total RNA was extracted from the muscle biopsies using an RNA isolation kit with NucleoSpin columns (Macherey-Nagel, kit#740955). Total RNA concentration was determined (Nanodrop 1000, Isogen Life Science, De Meern, The Netherlands). RNA quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands). RNA was processed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina following the protocol of the supplier (NEB, #E7420S/L). Strand-specific messenger RNA sequencing libraries were generated and sequenced at GenomeScan (Leiden, The Netherlands). The libraries were multiplexed, clustered, and sequenced on an Illumina NextSeq 500 with a single-read 75-cycle sequencing protocol, 15 million reads per sample. The reference genome and annotation file of Homo_sapiens.GRCh38 was used for analysis in FastA and GTF format. The reads were aligned to the reference sequence and, based on the mapped read locations and the gene annotation, a read was mapped on the transcript region. These count data are used as input in the statistical analysis using DEseq2 pipeline [Love et al., Genome Biol 2014].
RNA was processed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina following the protocol of the supplier (NEB, #E7420S/L). Strand-specific messenger RNA sequencing libraries were generated and sequenced at GenomeScan (Leiden, The Netherlands). The libraries were multiplexed, clustered, and sequenced on an Illumina NextSeq 500 with a single-read 75-cycle sequencing protocol, 15 million reads per sample.

treatment_protocol: Body composition, dietary intake, Physical performance measuresBody weight and height of the subjects were measured to the nearest 0.1 kg and 0.1 cm, respectively. One kg was subtracted to correct for clothing. Lean body mass was measured by a DXA-scan (Hologic Discovery-A, Hologic Inc., Bedford, MA, USA).   Dietary protein and carnitine intake was measured by a 3-day food diary. Dietary intake was calculated based on the Dutch Food Composition Database [RIVM. NEVO-online. Bilthoven; 2016]. Dietary carnitine intake was calculated based on literature of the carnitine content of different food products [Demarquoy et al., Food Chem 2004; Seline & Johein, Food Chem 2007; Mitchell, Am J Clin Nutr 1978; Woollard et al., Food Chem 1999].   Physical performance and mobility were assessed by a 400-m walk, expressed as m/s [Rolland et al., J Am Geriatr Soc 2004]. The time registered for subjects unable to walk the test within the time limit (15 minutes) was 900 seconds, which corresponds to a walking speed of 0.44 m/s. The short physical performance battery (SPPB) was performed, consisting of three domains: standing balance, 4-m walking speed and repeated chair stands [Guralnik et al., J Gerontol Med Sci 1994; Guralnik et al., Gerontol Med Sci 2000]. Each domain contributes 0-4 points to the total score, which ranges from 0-12 points. Higher scores indicate higher level of physical functioning. In addition, handgrip strength was measured using a hydraulic hand dynamometer (Jamar; Patterson Medical, Nottinghamshire, UK). Handgrip strength of the dominant and non-dominant hand was measured three times to the nearest 1.0 kg with subjects sitting in an upwards position with the arm in a 90-degree angle position. The average handgrip strength of the dominant hand was reported.

value: vastus lateralis muscle

tag: age

tag: gender

value: Female

tag: group

value: Young

tag: weight

tag: bmi

tag: walktime

value: #N/A

tag: meangrip

tag: maxgrip

tag: sppb

tag: logitfitness


title: muscle tissue-2, 0 salinity

status: Public on Feb 04 2023

type: SRA

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

country: China

institute: School of Pharmaceutical Sciences, Jilin University

library_source: transcriptomic

data_processing:
Sequencing was performed on an Illumina HiSeq X Ten platform, generating 150 bp paired-end reads.
Using Trimmomatic 0.39, low-quality and poly-N reads were trimmed to obtain clean data.
For subsequent analyses, clean data were retained for each sample. The M. nipponense genome (cngb_100843) was utilized to map to the clean data by the approach of HISAT2
Bowtie2 (Langmead and Salzberg, 2012) was applied to calculate the FPKM of each gene
eXpress was used to determine the read counts of each gene.
Assembly: The M. nipponense genome (cngb_100843)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Macrobrachium nipponense

source_name: muscle

growth_protocol: The gills, hepatopancreas and muscle of 30 M. nipponense were used from the control (0 ppt) and other (7, 14, and 21 ppt) groups for long term salinity exposure

extract_protocol:
total RNA extraction
libraries were prepared for each group with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, CA, USA).

tag: tissue

value: muscle

tag: cell line

value: tissue

tag: treatment

value: different salinity exposure


title: hepatopancreas tissue-3, 14 salinity

source_name: hepatopancreas

treatment_protocol: The gills, hepatopancreas and muscle of 30 M. nipponense were used from the control (0 ppt) and other (7, 14, and 21 ppt) groups

value: hepatopancreas


title: ATAC hMSCs, Flat Surface, Growth Medium (bio rep 2)

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

country: USA

institute: Northwestern University

library_source: genomic

data_processing:
Reads trimmed using trimmomatic/0.39 using the following parameters: ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:5:20 MINLEN:30;
Reads aligned with Bowtie2  to hg38 using the following parameters: bowtie2 -X 2000 --very-sensitive -q --local and converted to BAMs using SAMtools folllowed by duplicate removal with Picard
Peaks were called on BAMs using MACS2/2.1.0 using the following parameters: macs2 callpeak -t $sortedBAM -f BAMPE -n $FILENew -g hs --nomodel --keep-dup all
Peaks were counted against BAMs using the Genomic Ranges package in R to generate a counts table
Differential accesibility analysis was carried out using DESeq2 and the counts table
Assembly: hg38
Supplementary files format and content: Tab-delimited csv count file annotated with HGNC Gene IDs/other metadata and narrowPeak files

molecule: genomic DNA

organism: Homo sapiens

source_name: hMSCs

growth_protocol: Human mesenchymal stromal cells (hMSCs, PCS-500-012) were purchased from the American Type Culture Collection (ATCC) and sub-cultured using a growth medium acquired from the same company. hMSCs (P4) were seeded onto the flat mPOC substrates and the mPOC micropillars

extract_protocol: Nextera DNA Library Prep kit (Illumina) was utilized for Tagmentation and the ATAC-Seq library preparation protocol was utilized as previoulsy published by Buenrostro et al (2015).

value: hMSCs

tag: cell type

value: mesenchymal stem cells

tag: genotype

value: WT

tag: substrate

value: growth medium

value: Day 1


title: s527_Male_Young

country: Netherlands

value: Male


title: ATAC hMSCs, Flat Surface, Growth Medium (bio rep 1)


title: ATAC hMSCs, Pillar Surface, Osteogenic Medium (bio rep 3)

value: osteogenic differentiation


title: s529_Female_Young


title: PT08DX (M28)

status: Public on Feb 05 2023

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description:
AML patient
M28

data_processing:
Cellranger 10X demultiplexing (mkfastq)
Cellranger 10X quantification (counts)
Cellranger 10X quantification (alignment possorted files)
Seurat data analysis workflow
Genome_build: refdata-cellranger-GRCh38-3.0.0
Supplementary_files_format_and_content: matrix, barcodes, features
Full_Patient_metadata.rds (Complete metadata (NPM1 annotation) - Full dataset)
AML_metadata.rds (single-cell metadata (clustering + signatures + annotation) - AML dataset)

source_name: BMMC (Bone marrow mononuclear cells)

growth_protocol: no growth

extract_protocol:
Freshly thawed BM or PB cells were sorted for population of interest as detailed for each sample. If cell recovery was > 10'000 cells then cells were washed and counted, prior to chip loading, otherwise total recovered cells were loaded on the 10x genomics chip.
Chromium(TM) Single Cell 3' Library & Gel Bead Kit v2 or v3 (10xGENOMICS) according to manufacturer’s instructions.

treatment_protocol: lineage negative transduced cells transplant

tag: disease state

value: acute myeloid leukemia (AML)

tag: patient id

tag: timepoint

value: DX (Diagnosis)

value: Live CD34+ and or CD117+ and CD3- CD19- CD235a-


title: gills tissue-3, 14 salinity

source_name: gills

value: gills


title: gills tissue-2, 21 salinity


title: gills tissue-3, 21 salinity


title: s528_Male_Young

value: vastus lateralis muscle

tag: age

tag: gender

tag: group

value: Young


title: s526_Female_Young

value: Female

tag: weight

tag: bmi

tag: walktime

value: #N/A


title: hepatopancreas tissue-1, 14 salinity

value: tissue

value: different salinity exposure


title: s524_Male_Young

tag: meangrip

tag: maxgrip

tag: sppb


title: s531_Male_Young

tag: tissue

tag: logitfitness


title: gills tissue-2, 14 salinity

tag: cell line

tag: treatment


title: hepatopancreas tissue-1, 0 salinity

value: hepatopancreas


title: s522_Female_Young


title: gills tissue-3, 7 salinity


title: gills tissue-1, 7 salinity


title: gills tissue-1, 14 salinity


title: gills tissue-2, 7 salinity


title: s521_Female_Young


title: gills tissue-3, 0 salinity


title: gills tissue-1, 21 salinity


title: gills tissue-1, 0 salinity


title: RNAseq, WT, stim Day4, rep3

city: washington dc

first: Shaoqi

last: Zhu

state: District of Columbia

address: 725 21st st nw

institute: The George Washington University

data_processing:
The sequencing quality of Cut&Run libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For Cut&Run libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Assembly: mm9

organism: Mus musculus

source_name: P14 CD8 T cells

extract_protocol:
Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Ctcf wild-type or floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4 or day 8 post infection, P14 cells were sort purified and used for RNAseq analysis.
Sort-purified cells were used for total RNA extraction using standard Qiagen RNeasy columns, and RNA libraries were prepared for sequencing using stardard Illumina protocol. The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

tag: genotype

value: wild type

value: splenocytes

tag: cell phenotype

value: GFP+ TCRbeta+ CD8+ CD45.2+

value: wildtype


title: RNAseq, WT, stim Day4, rep2


title: s512_Male_Young

value: Male


title: s513_Male_Young


title: s518_Male_Young


title: s515_Male_Young


title: s516_Female_Young


title: s511_Female_Young


title: s525_Female_Young


title: RNAseq, WT, stim Day4, rep1


title: RNAseq, CTCF KO, stim Day4, rep2

value: CTCF-floxed

value: CTCF-KO


title: s509_Male_Young


title: RNAseq, CTCF KO, stim Day4, rep1


title: s507_Female_Young


title: Day8-WT-IgG

data_processing:
The sequencing quality of Cut&Run libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Trim Galore (v0.6.7) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim low quality sequences and remove adapters.
Bowtie2 (v2.3.4.1, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For Cut&Run libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling using IgG as control. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Assembly: mm9
Library strategy: Cut&Run

source_name: CD8 T cells

extract_protocol:
Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Ctcf wild-type or floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4 or day 8 post infection, P14 cells were sort purified and used for CTCF CUT&RUN analysis in live cells along with naive cells.
The DNA segments from CTCF Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: Day4-WT-IgG


title: Tn-WT-IgG


title: s517_Female_Young


title: s504_Female_Young


title: gills tissue-2, 0 salinity


title: s502_Male_Young


title: CTCF Cut&Run, naive, rep2


title: s503_Male_Young


title: s514_Female_Young


title: CTCF Cut&Run, stim Day4, rep2


title: s440_Female_Fit

value: Fit

tag: logitgroup


title: CTCF Cut&Run, stim Day4, rep1


title: ATAC, WT naive, rep2

data_processing:
The sequencing quality of Cut&Run libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Trim Galore (v0.6.7) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim low quality sequences and remove adapters.
Bowtie2 (v2.3.4.1, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ATAC-seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Assembly: mm9
Supplementary files format and content: narrowPeak

extract_protocol:
Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Ctcf wild-type or floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4 or day 8 post infection, P14 cells were sort purified and used for ATAC-seq analysis along with naive cells.
Sort-purified cells  were treated with TN5 transposase to generate tagged DNA fragments. TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries. The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.


title: s508_Male_Young


title: ATAC, CTCF KO Day4, rep3


title: s437_Male_Fit


title: s506_Female_Young


title: s438_Male_Fit


title: ATAC, WT naive, rep1


title: s435_Male_Fit


title: ATAC, CTCF KO Day4, rep1


title: s433_Male_Fit

value: Frail


title: ATAC, WT Day4, rep2


title: s439_Male_Fit

value: vastus lateralis muscle


title: CTCF Cut&Run, naive, rep1


title: s430_Male_Fit


title: s429_Male_Fit


title: ATAC, WT Day4, rep1


title: ATAC, CTCF KO Day4, rep2


title: s436_Female_Fit


title: Dog smRNA-seq Rep #2

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
DESeq_breastCancer_normalized_counts.csv
Dog2_S7_L001_R1_001

data_processing:
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: bosTauMd3, canFam3, equCab2, rn6, susScr10, and hg19 for cow, dog, horse, rat, pig and human small RNA-seq, canFam3 and equCab2 for the dog and horse RNA-seq
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

organism: Canis lupus familiaris

source_name: mammosphere-derived epithelial cells

extract_protocol: Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

value: mammary gland

tag: cell type

value: mammosphere-derived epithelial cells

tag: breast cancer susceptibility

value: susceptible


title: s501_Male_Young

tag: age

tag: gender

value: Young

value: #N/A


title: Dog smRNA-seq Rep #3

description:
DESeq_breastCancer_normalized_counts.csv
Dog3_S14_L002_R1_001


title: s427_Male_Fit

tag: group

tag: weight


title: Dog smRNA-seq Rep #1

description:
DESeq_breastCancer_normalized_counts.csv
Dog1_S1_L001_R1_001


title: s426_Female_Fit

value: Female

tag: bmi

tag: walktime


title: s425_Female_Fit

tag: meangrip

tag: maxgrip


title: Adamts12-/-, vehicle, 7 days, replicate 5

city: Rennes

first: Vincent

last: Legagneux

address: 2 avenue du Professeur Léon Bernard, Bâtiment 5

country: France

institute: Inserm

data_processing:
FASTQ reads were aligned on the reference genome (GRCm38) using the STAR software and read counts per genes were computed using htseq-count. Read counts were normalized using the R-package DESeq2.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized read count values for each Sample

source_name: Liver

extract_protocol:
Liver samples were collected in RNAlater® and total RNA was extracted using TRIzol (Invitrogen) reagent according to the manufacturer’s instructions. RNA samples from mouse liver samples were quality controlled by RNA integrity number (RIN) measurement on a Bioanalyzer with RNA 6000 Nano assays (Agilent).
RNA-sequencing libraries were prepared from 500ng total RNA and quality-controlled on TapesStation (fragment sizes of approximately 260 bp) by the GenoBiRD facility (Nantes, France) using the TruSeq® Stranded mRNA Library Prep (96 samples) from Illumina. Multiplexed (bar-coded) libraries were randomized and sequenced on a NovaSeq 6000.

treatment_protocol: We used Adamts12−/− and wild-type mice generated and genotyped by El Hour et al. 2010 (PMID: 20208563). eight-week-old females were treated by intraperitoneal injections of CCl4 (Sigma-Aldrich, St. Louis, MO, USA) diluted at 3% v/v in olive oil. A single dose of CCl4 0.3 ml/kg of mouse body weight was administered (acute treatment) and mice were sacrificed after 4h, 12h, 24h or 7 days. Control mice were treated with the vehicle (olive oil). Liver samples were collected, weighed and treated as previously described (Kesteloot et al. 2007, PMID: 17929299).

tag: tissue

value: Liver

value: C57BL/6J - Adamts12-/-

value: vehicle

tag: time

value: 7 days


title: Adamts12-/-, vehicle, 7 days, replicate 4


title: ATAC, WT Day4, rep3

value: wild type

value: splenocytes

value: GFP+ TCRbeta+ CD8+ CD45.2+


title: s432_Male_Fit

value: Male

tag: sppb

tag: logitfitness


title: s421_Female_Fit

value: Fit


title: Adamts12-/-, vehicle, 7 days, replicate 3

tag: genotype

tag: treatment


title: s424_Female_Fit

tag: logitgroup


title: s423_Female_Fit


title: s431_Female_Fit


title: Adamts12-/-, vehicle, 7 days, replicate 2


title: Adamts12-/-, CCl4, 7 days, replicate 5


title: Adamts12-/-, vehicle, 7 days, replicate 1


title: Adamts12-/-, CCl4, 7 days, replicate 4


title: s413_Male_Fit


title: s416_Female_Fit


title: Adamts12-/-, CCl4, 7 days, replicate 3


title: s411_Male_Fit

value: Frail


title: Adamts12-/-, CCl4, 7 days, replicate 2


title: Adamts12-/-, CCl4, 7 days, replicate 1


title: s419_Female_Fit

value: vastus lateralis muscle


title: Adamts12-/-, vehicle, 24h, replicate 5


title: s406_Male_Fit


title: Adamts12-/-, vehicle, 24h, replicate 4


title: s409_Female_Fit


title: s407_Male_Fit


title: s405_Female_Fit


title: Adamts12-/-, vehicle, 24h, replicate 2


title: s404_Male_Fit


title: Adamts12-/-, vehicle, 24h, replicate 1


title: s420_Female_Fit


title: s403_Female_Fit


title: Adamts12-/-, CCl4, 24h, replicate 5


title: s401_Male_Fit


title: Adamts12-/-, CCl4, 24h, replicate 4


title: Adamts12-/-, CCl4, 24h, replicate 3


title: s331_Female_Frail


title: s329_Female_Frail


title: Adamts12-/-, CCl4, 24h, replicate 2


title: Adamts12-/-, CCl4, 24h, replicate 1


title: s330_Female_Frail


title: s328_Female_Frail


title: Adamts12-/-, vehicle, 12h, replicate 5


title: s327_Male_Frail


title: Adamts12-/-, vehicle, 12h, replicate 4


title: Adamts12-/-, vehicle, 12h, replicate 2


title: s326_Male_Frail


title: Adamts12-/-, vehicle, 12h, replicate 3


title: Adamts12-/-, CCl4, 12h, replicate 5


title: s323_Male_Frail


title: Adamts12-/-, vehicle, 24h, replicate 3


title: s320_Female_Frail


title: Adamts12-/-, CCl4, 12h, replicate 3


title: Adamts12-/-, vehicle, 12h, replicate 1


title: s325_Female_Frail


title: s322_Female_Frail


title: s319_Male_Frail


title: Adamts12-/-, CCl4, 12h, replicate 1


title: s318_Female_Frail


title: Adamts12-/-, CCl4, 12h, replicate 2


title: Adamts12-/-, vehicle, 4h, replicate 5


title: s321_Male_Frail


title: s317_Male_Frail


title: ARID4B-10

city: Monterrey

first: Fernando

last: Gonzalez-Salinas

state: Nuevo Leon

address: Morones Prieto avenue

department: Bioinformatica

country: Mexico

institute: Tecnologico de Monterrey

data_processing:
Data processing was performed using Galaxy web plattform https://usegalaxy.org
Sequence reads were trimmed  using Trimmomatic tool
Trimmed sequence reads were mapped to hg38 using HiSAT2
Read count extraction and normalization were performed using FeautureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MCF-7 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from edited and wild-type cells using the GenElute™ Mammalian Total RNA Miniprep Kit
The TruSeq Stranded mRNA Sample Preparation Kit was used to prepare the library
Transcriptome sequencing was performed using a MiSeq Reagent Kit v3 in a MiSeq Sequencer

treatment_protocol: pX459 CRISPR vector with sgRNA targeting ARID4B was transfected using XtremeGene9 and OptiMEM medium. 48 hours later, puromycin was added to de medium to select the cells. Monoclonal clones were generated through limiting dilutions.

tag: cell line

tag: cell type

value: Breast cancer cells

value: Deletion in ARID4B locus

value: CRISPR/Cas9 Edition


title: Adamts12-/-, vehicle, 4h, replicate 2


title: ARID4B-3

value: Insertion in ARID4B locus


title: Adamts12-/-, CCl4, 12h, replicate 4


title: s314_Female_Frail

tag: age


title: s316_Female_Frail

tag: gender


title: Adamts12-/-, vehicle, 4h, replicate 4


title: s312_Female_Fit

tag: group


title: Adamts12-/-, vehicle, 4h, replicate 1


title: s310_Female_Frail

tag: weight


title: Horse RNA-seq Rep #2

description:
DESeq_breastCancer_RNA_normalizedCounts.csv
8361_5515_51002_HK5FGBGX2_ML5-HB-DMSO_GGCTAC_R1

organism: Equus caballus

extract_protocol: Libraries were prepared according to the Illumina TruSeq polyA+ Sample Prep Kit protocol

value: mammary gland

value: mammosphere-derived epithelial cells

tag: breast cancer susceptibility

value: resistant


title: ARID4B-WT

value: WT


title: ARID4B-21


title: s306_Male_Frail

tag: bmi

tag: walktime


title: Adamts12-/-, CCl4, 4h, replicate 4

value: Liver

value: C57BL/6J - Adamts12-/-


title: Adamts12-/-, vehicle, 4h, replicate 3

value: vehicle


title: s315_Male_Frail

tag: meangrip

tag: maxgrip


title: Horse RNA-seq Rep #1

description:
DESeq_breastCancer_RNA_normalizedCounts.csv
8361_5515_51001_HK5FGBGX2_ML4-HN-DMSO_TAGCTT_R1

tag: tissue


title: Human smRNA-seq Rep #3

description:
DESeq_breastCancer_normalized_counts.csv
Human3_S16_L002_R1_001

value: susceptible


title: Human smRNA-seq Rep #2

description:
DESeq_breastCancer_normalized_counts.csv
Human2_S9_L001_R1_001


title: s305_Male_Frail

tag: sppb


title: Dog RNA-seq Rep #3

description:
DESeq_breastCancer_RNA_normalizedCounts.csv
8361_5515_51000_HK5FGBGX2_ML3-DM-DMSO_GATCAG_R1


title: Human smRNA-seq Rep #1

description:
DESeq_breastCancer_normalized_counts.csv
Human1_S3_L001_R1_001


title: s304_Male_Frail

tag: logitfitness


title: s303_Male_Frail


title: Adamts12-/-, CCl4, 4h, replicate 1

tag: genotype

tag: time


title: Dog RNA-seq Rep #2

description:
DESeq_breastCancer_RNA_normalizedCounts.csv
8361_5515_50999_HK5FGBGX2_ML2-DQ-DMSO_ACAGTG_R1


title: Horse RNA-seq Rep #3

description:
DESeq_breastCancer_RNA_normalizedCounts.csv
8361_5515_51003_HK5FGBGX2_ML6-HF-DMSO_ATGTCA_R1


title: L306tumor_HK1-LMP2A-W8_miRNA

type: RNA

city: Kuala Lumpur

first: Lu Ping

last: Tan

address: Jalan Pahang

department: Molecular Pathology Unit

country: Malaysia

institute: Institute for Medical Research

hyb_protocol: according to manufacturer's instructions (Agilent, USA).

data_processing: Data processed from Feature extraction was used directly without further normalization. Hence the miRNA expressions were based on equal RNA input (100ng each).

growth_protocol: 2 million cells were inoculated into nude mice and the tumors were harvested at about 6 weeks post inoculation.

extract_protocol: RNA was isolated using Trizol.

treatment_protocol: Excised tumors were snap frozen in liquid nitrogen until RNA isolation.

tag: mice tumor tag


title: Adamts12-/-, CCl4, 4h, replicate 2

tag: treatment


title: L165tumor_HK1-LMP2A-W8_miRNA

scan_protocol: according to manufacturer's instructions (Agilent, USA).

tag: cell line


title: P308tumor_HK1-pBabe-W6_miRNA

description: negative control

label_protocol: according to manufacturer's instructions (Agilent, USA).


title: P198tumor_HK1-pBabe-W6_miRNA

description: negative control


title: L199tumor_HK1-LMP2A-W8_miRNA


title: P163tumor_HK1-pBabe-W6_miRNA

description: negative control


title: Adamts12-/-, CCl4, 4h, replicate 5


title: TT

city: nanchang

first: zhao

middle: hai

last: wang

state: jaingxi

address: zhimin dadao 1101

institute: jiangxi agricultural university

description: Small RNA

data_processing:
Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
The degradome reads were matched to transcriptome to generate the degradome density file. In addition, the targeted mRNA sequences of the miRNAs were predicted using TargetFinder software (http://targetfinder.org/). The overlapped mRNAs of the predicted target mRNAs and the mRNAs in degradome density file were considered as the target genes of the miRNAs.
Assembly: ftp://ftp.ensemblgenomes.org/pub/release-44/plants/fasta/hordeum_vulgare/dna
Supplementary files format and content: excel,expression profiles
Library strategy: Degradome sequencing

organism: Oryza sativa

source_name: two-leaf seedlings

growth_protocol: Seeds were sterilized with 3% H2O2 for 30 min and rinsed three-times with deionized water, then soaked for 3 h at room temperature. A hydroponic experiment was carried out in a growth chamber at Zijingang Campus, Zhejiang University, Hangzhou, China (Hangzhou, 120.2° E, 30.5° N). After one week of germination, the uniform seedlings were selected for hydroponic incubation in 15-L black rectangular pots with aerated 1/5 Hoagland solution according to Ye et al (2017). The hydroponic solution's pH was adjusted to 5.8 using 1M HCl or NaOH, as required, and the solution was renewed every three days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Poly(A) RNA is purified from plant total RNA(20ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Because of the 3′ cleavage product of the mRNA contains a 5′-monophosphate，the 5' adapters were ligated to the 5' end of the 3′ cleavage product of the mRNA by the RNA ligase. The next step is reverse transcription to make the first strand of cDNA with a 3′-adapter random primer. and size selection was performed with AMPureXP beads.Then the cDNA were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 15cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 200-400 bp. At last, we performed the 50bp single-end sequencing on an Illumina Hiseq 2500 (LC Bio, China) following the vendor's recommended protocol.

treatment_protocol: The two-leaf-old seedlings were subjected to K treatments consisting of two levels, 0.01mM (low K) and 1mM (normally used as control).

tag: line

value: heat-tolerant line XN0437T

value: two-leaf seedlings

value: heat stress


title: Wild-type, vehicle, 7 days, replicate 5

value: C57BL/6J - wild-type

value: 7 days


title: s302_Male_Frail

value: vastus lateralis muscle

tag: age

tag: gender

value: Male

value: Frail

tag: logitgroup


title: TC

description: Small RNA

value: control


title: Wild-type, vehicle, 7 days, replicate 4


title: s301_Male_Frail

tag: group

tag: weight


title: Adamts12-/-, CCl4, 4h, replicate 3


title: SC

description: Small RNA

value: heat-sensitive line XN0437S


title: Wild-type, vehicle, 7 days, replicate 2


title: ST

description: Small RNA


title: Bos taurus smRNA-seq Rep #3

description:
DESeq_breastCancer_normalized_counts.csv
Cow3_S17_L002_R1_001

organism: Bos taurus

value: mammary gland

tag: cell type

value: mammosphere-derived epithelial cells

tag: breast cancer susceptibility


title: Wild-type, vehicle, 7 days, replicate 3


title: DIO8w12

city: Not Hispanic or Latino

first: Sheng

address: #87, Dingjiaqiao, Gulouqu

department: Biochemistry and Molecular biology

institute: Southeast University

data_processing:
Illumina Hiseq 2500 platform to get the raw data
Clean reads were generated from row reads by Trimmomatic using default parameters
The clean reads were mapped to reference genome (Ensembl Mus_musculus GRCm38.100) with Hisat2
Mapped data were assembled by Stringtie with default parameters
Group comparison by DESeq from SARTools R package was performed to estimate the differential gene expression
Enrichment analysis was then performed by Consensus PathDB
Genome_build: Ensembl Mus_musculus GRCm38.100
Supplementary_files_format_and_content: Excel file of differential expressed genes (padj<0.05)

source_name: Testis

growth_protocol: Standard animal care

extract_protocol:
50 mg testis tissue were extracted by Trizol reagent.
Strand specific RNA-Seq library were made by standard dUTP method

treatment_protocol: Normal food or high fat food feeding

tag: strain

value: Testis

tag: diet

value: high fat food for 8 weeks


title: DIO8w11

tag: tissue


title: DIO8w10


title: Wild-type, CCl4, 7 days, replicate 5

value: Liver


title: Bos taurus smRNA-seq Rep #1

description:
DESeq_breastCancer_normalized_counts.csv
Cow1_S4_L001_R1_001

value: resistant


title: Ctr8w9

value: normal food for 8 weeks


title: human induced pluripotent stem cell-derived 3D heart organoids D7

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

country: Germany

institute: Klinikum rechts der Isar – Technical University Munich

data_processing:
Cell Ranger workflow using the DropletUtils was used to generate FASTQ and bam files
Genome_build: hg19

molecule: polyA RNA

source_name: cardiac organoids

growth_protocol: Human embryonic stem cells were differentiated as described in methods of Meier et al., (2021) using a stepwise growth-factor based protocol  to direct hiPSCs towards CMs through defined developmental stages of primitive-like cells and early cardiovascular progenitor cells.

extract_protocol:
Epicardioids were dissociated with papain as described in methods of Meier et al. (2021), filtered through 40 μm filter, washed with 5 mL 1% BSA (Gibco; 15260037) in PBS-/-, centrifuged for 3 min at 200 g, and resuspended in 0.04% BSA in PBS for counting. After counting, 8 000 cells for each sample (targeted cell recovery) were processed using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10x Genomics; PN-1000092), the Chromium Chip B Single Cell Kit (10x Genomics; PN- 1000073), and the Chromium i7 Multiplex Kit v2 (10x Genomics; PN-120262) for samples d2-d15 and Chromium Next GEM Single Cell 3’ Library & Gel Bead Kit v3.1 (1000128, 10x Genomics) Chromium Single Cell G Chip Kit (1000127, 10x Genomics) and Single Index Kit T Set A (PN-1000213, 10x Genomics) for sample d30 to generate Gel Bead-In-EMulsions (GEMs) and single cell sequencing libraries.
8 000 cells for each sample (targeted cell recovery) were processed using Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10x Genomics; PN-1000092), the Chromium Chip B Single Cell Kit (10x Genomics; PN- 1000073), and the Chromium i7 Multiplex Kit v2 (10x Genomics; PN-120262) for samples d2-d15 and Chromium Next GEM Single Cell 3’ Library & Gel Bead Kit v3.1 (1000128, 10x Genomics) Chromium Single Cell G Chip Kit (1000127, 10x Genomics) and Single Index Kit T Set A (PN-1000213, 10x Genomics) for sample d30 to generate Gel Bead-In-EMulsions (GEMs) and single cell sequencing libraries. Libraries were pooled and sequenced using the NovaSeq (Ilumina; S1 flow cell) with 150bp paired end reads with 28 cycles for read1, 91 cycles for read2 8 cycles for i7 and 0 cycles for i5, and with a read depth of at least 25-30 000 pair reads per cell.

value: in vitro differentiated human induced pluriotent stem cells (hiPSC)

value: Human Pluripotent Stem Cell Registry ID:MRIi003-A

value: Day 7


title: human induced pluripotent stem cell-derived 3D heart organoids D5

value: Day 5


title: human induced pluripotent stem cell-derived 3D heart organoids D4

value: Day 4


title: Wild-type, vehicle, 7 days, replicate 1

value: C57BL/6J - wild-type

value: vehicle

value: 7 days


title: Wild-type, CCl4, 7 days, replicate 3


title: Ctr8w8


title: human induced pluripotent stem cell-derived 3D heart organoids D3

value: Day 3


title: RNA2 hMSCs, Flat Surface, Osteogenic Medium (bio rep 3)

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to hg19 using STAR
Gene counting was performed using htseq-count version 0.6 1p1
Differential expression was performed using DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited file with read counts per gene

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA quality and quantity was assessed using the Agilent bioanalyzer. RNA-Seq libraries were prepared using TruSeq mRNA RNA-Seq protocol (Illumina provided)

treatment_protocol: One-day post-seeding, an osteogenic induction medium (Lonza) was used to induce the osteogenic differentiation of hMSCs.

value: hMSCs

value: mesenchymal stem cells

value: WT

tag: substrate

value: osteogenic differentiation

tag: time point

value: Day 1


title: Bos taurus smRNA-seq Rep #2

description:
DESeq_breastCancer_normalized_counts.csv
Cow2_S11_L002_R1_001

value: mammary gland

value: mammosphere-derived epithelial cells


title: Ctr8w7

value: Testis

value: normal food for 8 weeks


title: Dog RNA-seq Rep #1

description:
DESeq_breastCancer_RNA_normalizedCounts.csv
8361_5515_50998_HK5FGBGX2_ML1-DN-DMSO_CGATGT_R1

value: susceptible


title: RNA2 hMSCs, Flat Surface, Osteogenic Medium (bio rep 2)

tag: genotype


title: Wild-type, CCl4, 7 days, replicate 4

value: Liver

tag: time


title: TT3

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles

source_name: rice

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: rice

value: heat-tolerant line

tag: molecule subtype

value: Small RNA


title: scATAC-Seq day 15

description: in vitro differentiated human iPSC into cardiovascular progenitors, cardiomyocytes and non-myocytic cardiac cell types within epicardioids D15

extract_protocol:
Epicardioids were dissociated with papain as described in methods of Meier et al. (2021), filtered through 40 μm filter, washed with 5 mL 1% BSA (Gibco; 15260037) in PBS-/-, centrifuged for 3 min at 200 g, and resuspended in 0.04% BSA in PBS for counting. Nuclei isolation was performed following the “Nuclei Isolation for Single Cell ATAC Sequencing demonstrated protocol” (10x Genomics). Briefly, ~500,000 cells from each sample were transferred to a 1.5-ml microcentrifuge tube and centrifuged at 300×g for 5 min at 4 °C. The supernatant was removed without disrupting the cell pellet, and 100 μl of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20; 0.01% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) was added and pipette-mixed 10 times. Samples were then incubated on ice for 30-120 seconds (depending on sample quality and day; optimal incubation time was optimized in advance). Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette-mixed. Nuclei were centrifuged at 500×g for 5 min at 4 °C, and the supernatant removed without disrupting the pellet, and nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration suitable for a target nuclei recovery of 8000.
8 000 cells per sample were processed using Chromium Next Single Cell ATAC Library & Gel Bead Kit v1.1 (1000175, 10x Genomics) Chromium Single Cell H Chip Kit (1000161, 10x Genomics) and Chromium  SIngle Index Kit N, Set A (PN-1000212; 10x Genomics) to generate Gel Bead-In-EMulsions (GEMs) and single cell ATAC sequencing libraries. Libraries were pooled and sequenced using the NovaSeq (Ilumina; S1 flow cell)  with 150bp paired end reads with 50 cycles for read1 and read2 8 cycles for i7 and 16 cycles for i5, and with a read depth of at least 25-30 000 pair reads per cell.

value: day 15

value: in vitro differentiated human induced pluriotent stem cells (hiPSC)

tag: cell line

value: Human Pluripotent Stem Cell Registry ID:MRIi003-A

tag: treatment


title: TT2


title: Wild-type, CCl4, 7 days, replicate 2

value: C57BL/6J - wild-type

value: 7 days


title: RNA2 hMSCs, Flat Surface, Osteogenic Medium (bio rep 1)

value: hMSCs

value: mesenchymal stem cells

value: WT


title: Wild-type, CCl4, 7 days, replicate 1


title: RNA2 hMSCs, Pillar Surface, Osteogenic Medium (bio rep 3)

value: osteogenic differentiation

value: Day 1


title: Wild-type, vehicle, 24h, replicate 5

value: vehicle


title: TT1


title: RNA2 hMSCs, Pillar Surface, Osteogenic Medium (bio rep 2)


title: scATAC-Seq day 10

description: in vitro differentiated human iPSC into cardiovascular progenitors, cardiomyocytes and non-myocytic cardiac cell types within epicardioids D10

value: day 10


title: scATAC-Seq day 7

description: in vitro differentiated human iPSC into cardiovascular progenitors, cardiomyocytes and non-myocytic cardiac cell types within epicardioids D7

value: day 7


title: TC3


title: Wild-type, vehicle, 24h, replicate 4

value: Liver


title: RNA2 hMSCs, Pillar Surface, Growth Medium (bio rep 3)

value: growth medium


title: TC2

value: rice

value: heat-tolerant line


title: Wild-type, vehicle, 24h, replicate 3


title: RNA2 hMSCs, Pillar Surface, Osteogenic Medium (bio rep 1)


title: scATAC-Seq day 5

description: in vitro differentiated human iPSC into cardiovascular progenitors, cardiomyocytes and non-myocytic cardiac cell types within epicardioids D5

value: day 5


title: human induced pluripotent stem cell-derived 3D heart organoids D2

value: in vitro differentiated human induced pluriotent stem cells (hiPSC)

value: Day 2


title: scATAC-Seq day 4

description: in vitro differentiated human iPSC into cardiovascular progenitors, cardiomyocytes and non-myocytic cardiac cell types within epicardioids D4

value: day 4

value: Human Pluripotent Stem Cell Registry ID:MRIi003-A


title: Wild-type, vehicle, 24h, replicate 2

value: C57BL/6J - wild-type


title: scATAC-Seq day 3

description: in vitro differentiated human iPSC into cardiovascular progenitors, cardiomyocytes and non-myocytic cardiac cell types within epicardioids D3

value: day 3


title: ST3

value: heat-sensitive line

value: Small RNA


title: RNA2 hMSCs, Pillar Surface, Growth Medium (bio rep 1)

value: hMSCs

value: mesenchymal stem cells

value: WT

value: Day 1


title: ST2


title: TC1


title: RNA2 hMSCs, Pillar Surface, Growth Medium (bio rep 2)


title: scATAC-Seq day 2

description: in vitro differentiated human iPSC into cardiovascular progenitors, cardiomyocytes and non-myocytic cardiac cell types within epicardioids D2

value: day 2


title: Wild-type, CCl4, 24h, replicate 5

value: Liver


title: Rat smRNA-seq Rep #3

description:
DESeq_breastCancer_normalized_counts.csv
Rat3_S15_L002_R1_001

organism: Rattus norvegicus

value: mammary gland

value: mammosphere-derived epithelial cells

value: susceptible


title: ST1

value: rice


title: RNA2 hMSCs, Flat Surface, Growth Medium (bio rep 3)

value: growth medium


title: Rat smRNA-seq Rep #2

description:
DESeq_breastCancer_normalized_counts.csv
Rat2_S8_L001_R1_001


title: Wild-type, CCl4, 24h, replicate 4


title: SC3


title: Wild-type, CCl4, 24h, replicate 3


title: RNA2 hMSCs, Flat Surface, Growth Medium (bio rep 2)


title: RNA2 hMSCs, Flat Surface, Growth Medium (bio rep 1)


title: Wild-type, CCl4, 24h, replicate 2


title: Wild-type, vehicle, 24h, replicate 1

value: vehicle


title: Rat smRNA-seq Rep #1

description:
DESeq_breastCancer_normalized_counts.csv
Rat1_S2_L001_R1_001


title: SC2


title: RNA1 hMSCs, Pillar Surface, Osteogenic Medium (bio rep 2)

value: osteogenic differentiation


title: Wild-type, CCl4, 24h, replicate 1

value: C57BL/6J - wild-type


title: Pig smRNA-seq Rep #3

description:
DESeq_breastCancer_normalized_counts.csv
Pig3_S19_L002_R1_001

organism: Sus scrofa

value: resistant


title: RNA1 hMSCs, Pillar Surface, Osteogenic Medium (bio rep 1)


title: Wild-type, vehicle, 12h, replicate 5


title: SC1

value: heat-sensitive line


title: Pig smRNA-seq Rep #2

description:
DESeq_breastCancer_normalized_counts.csv
Pig2_S13_L002_R1_001


title: RNA1 hMSCs, Flat Surface, Osteogenic Medium (bio rep 1)


title: Pig smRNA-seq Rep #1

description:
DESeq_breastCancer_normalized_counts.csv
Pig1_S6_L001_R1_001


title: Wild-type, vehicle, 12h, replicate 4


title: RNA1 hMSCs, Pillar Surface, Growth Medium (bio rep 2)


title: Wild-type, vehicle, 12h, replicate 3


title: RNA1 hMSCs, Pillar Surface, Growth Medium (bio rep 1)


title: MH05_Pup10F

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

data_processing:
bcl files were processed into fastq files with bcl2fastq v.2.17.1.14
Fastq files were processed with the manufacturer's script generate_reference.R and pete.star.script_3.0.R where tables of feature counts were generated for each samples.
Genome_build: Human TempO-Seq® whole mouse transcriptome custom probe annotation
Supplementary_files_format_and_content: table of probe counts for each sample

source_name: Whole pancreas

extract_protocol:
Whole pancreas tissue was stored in RNAlater (Qiagen) and then frozen at -80C. RNA was extracted using the Qiagen Rneasy Mini kit.
The TempO-Seq® Assay User Guide was used to build the TempO-Seq libraries for the mouse whole transcription panel. Following amplification, libraries were pooled and purified using the Macherey-Nagel NucleoSpin Gel and PCR Cleanup Kit with modifications outlined in the TempO-Seq® User Guide. Pooled, purified libraires were quantified using the KAPA Biosystemd qPCR library quantification kit and diluted to 4 nM for denaturation and dilution for sequencing.
Human TempO-Seq® mouse whole transcription panel and libraries were sequenced using an Illumina NextSeq500.

tag: Sex

value: M

tag: chemical

value: TCDD

tag: dam/pup

value: Pup

tag: species


title: Wild-type, vehicle, 12h, replicate 2


title: MH05_Pup8J


title: Wild-type, vehicle, 12h, replicate 1


title: Wild-type, CCl4, 12h, replicate 5


title: RNA1 hMSCs, Flat Surface, Osteogenic Medium (bio rep 2)

value: hMSCs

value: mesenchymal stem cells

value: WT


title: RNA1 hMSCs, Flat Surface, Growth Medium (bio rep 1)

value: Day 1


title: RNA1 hMSCs, Flat Surface, Growth Medium (bio rep 2)


title: sp p29

description: Gene expression of NPC stem-like cells.

hyb_protocol: All RNA samples were hybridized according to manufacturer's protocol.

scan_protocol: GeneChip Scanner 3000 7G.

data_processing: GeneChip Command Console software version 3.0.1.

label: biotin

source_name: SP

label_protocol: 1ug RNA from each sample was labeled according to manufacturer's protocol.

growth_protocol: HK1 were maintained in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS) while C666-1 in fibronectin coated plate in RPMI 1640 medium supplemented with 15% FCS. For sphere-forming assay, C666-1 cells were seeded at 5000 cells/ well in 6-well low attachment plate in serum-free DMEM/F12 (1:1) media supplemented with 5ug/ml Insulin-Transferrin-Selenium-A, 20ng/ml rEGF, 10ng/ml bFGF, 0.4% BSA, 1xB-27 supplement. All cell lines were maintained in 50U/ml penicillin and 50 µg/ml streptomycin at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: All RNA samples were extracted by Trizol.

tag: stem-like

value: yes

value: no


title: sp p32

description: Gene expression of NPC stem-like cells.


title: MH05_Pup6H


title: Wild-type, CCl4, 12h, replicate 4

value: Liver


title: MH05_Pup11G


title: Wild-type, CCl4, 12h, replicate 3


title: MH05_Pup10G

value: F


title: nsp p32

description: Gene expression of the counterpart for NPC stem-like cells.

source_name: NSP


title: Control6

city: Nanjing

first: Yumeng

last: Xi

address: 50 Zhongling Street

institute: Jiangsu Academy of Agricultural Sciences

description: healthy goslings renal tissues

data_processing:
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced.
We aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Anser+cygnoides
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Anser cygnoides

source_name: renal tissues

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 10 ug of total RNArepresenting a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeqsample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp)
We performed the paired-end sequencing on an IlluminaHiseq4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

treatment_protocol: The DO of the three treatment tanks was rapidly reduced to 96h-LH50 by pumping nitrogen into water from a nitrogen gas cylinder. Real-time reading with a DO meter were used to control the DO in water by adjusting oxygen intake. The sampling time was 96h.

tag: disease

value: healthy

value: renal tissues


title: Control5

description: healthy goslings renal tissues


title: Wild-type, CCl4, 12h, replicate 2


title: MH05_Pup8G


title: Control4

description: healthy goslings renal tissues


title: Control3

description: healthy goslings renal tissues


title: nsp p29


title: MH05_Pup11F


title: MH05_Pup6F


title: Wild-type, CCl4, 12h, replicate 1


title: xenoLMP2A#2

description:
Gene expression of NPC stem-like cells.
US45103080_251485045479_S02_GE2-v5_95_Feb07_1_2.txt: Cy5

scan_protocol: Scanned using GenePix 4000B

data_processing: Images from Agilent microarray were processed in Feature Extraction software. Data files from the Agilent chips were imported into GeneSpring as single color analysis and then the signal values transformed to the log base 2. Normalization was carried out with 75th percentile.

label_protocol: 200ng RNA from each sample was labeled according to manufacturer's protocol.


title: nsp p18


title: sp p18

description: Gene expression of NPC stem-like cells.


title: xenoControl#3

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485045478_S01_GE2_107_Sep09_1_4.txt: Cy5

source_name: xenoControl


title: xenoLMP2A#1

description:
Gene expression of NPC stem-like cells.
US45103080_251485045479_S02_GE2-v5_95_Feb07_1_1.txt: Cy5


title: Wild-type, vehicle, 4h, replicate 5

value: vehicle


title: xenoControl#2

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485045479_S02_GE2-v5_95_Feb07_1_2.txt: Cy3


title: Control2

description: healthy goslings renal tissues


title: Wild-type, vehicle, 4h, replicate 4

value: C57BL/6J - wild-type


title: MH05_Dam6

value: Dam


title: Wild-type, vehicle, 4h, replicate 3


title: xenoControl#1

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485045479_S02_GE2-v5_95_Feb07_1_1.txt: Cy3


title: Control1

description: healthy goslings renal tissues


title: Gout5

description: gout goslings  renal tissues

value: gout


title: Wild-type, vehicle, 4h, replicate 2


title: MH05_Dam11


title: Wild-type, vehicle, 4h, replicate 1


title: Gout4

description: gout goslings  renal tissues


title: MH05_Dam8


title: xenoLMP2A#3

description:
Gene expression of NPC stem-like cells.
US45103080_251485045478_S01_GE2_107_Sep09_1_4.txt: Cy3


title: Gout3

description: gout goslings  renal tissues


title: MH05_Pup7G

value: M

value: Control


title: Gout2

description: gout goslings  renal tissues


title: MH05_Pup2J

value: Pup


title: MH05_Pup4F


title: Gout1

description: gout goslings  renal tissues


title: Wild-type, CCl4, 4h, replicate 4


title: Wild-type, CCl4, 4h, replicate 3


title: MH05_Dam10

value: TCDD


title: Wild-type, CCl4, 4h, replicate 2


title: scProgenyProduction_highMOI_polyAseq

city: Seattle

first: Jesse

last: Bloom

state: WA

address: 1100 Fairview Ave N, room B3-123

institute: Fred Hutchinson Cancer Center

description: High MOI influenza-infected single-cell 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript and viral barcode  poly A RNA

data_processing: All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. The raw sequencing data from the single-cell RNA sequencing was aligned using STARsolo against a composite reference made up of the canine genome CanFam3.1.98 concatenated to the A/California/04/2009 influenza virus genome. Alignment produced a cell-gene matrix containing the gene expression of every canine and virus gene for each single cell.  Assembly: CanFam3.1.98, A/California/04/2009 (pdmH1N1) with the G155E cell-culture adaptation mutation

organism:
Canis lupus familiaris
Influenza A virus (A/California/04/2009(H1N1))

source_name: Single influenza-infected MDCK cell cDNA

extract_protocol: All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. Single-cell RNA sequencing was performed with the 10X Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1. The manufacturer’s standard protocol was used with the following modifications. The template-switching oligo was replaced with a modified single-stranded DNA oligo with the sequence 5’-AGAGTGTTTGGGTAGAGCAGCGTGTTGGCATGTrGrGrG-3’ at a final concentration of 45 uM in the reaction mix. This change was made to accommodate some of the barcoded influenza segments’ exogenous sequence which shares homology with the standard 10X template-switching oligo. The cDNA amplification primer mix was replaced with a pair of primers with the sequences 5’-AGAGTGTTTGGGTAGAGCAGCG-3’ (binding to the custom template-switch oligo mentioned above) and 5’-CTACACGACGCTCTTCCGATCT-3’ (binding to the standard 10X adapter sequence) at a final concentration of 1 uM in the reaction mix. The cDNA amplification PCR reaction extension time was increased to 20 seconds to encourage the formation of full-length cDNA products. The amplified cDNA product was split in half; one half was used for fragmentation and preparation of the transcriptome sequencing library while the other half was used as template for long-read sequencing of viral transcripts.  At 12 hours post-infection, the supernatant was collected and cells and debris were removed by centrifugation at 300 RCF for 3 min. The supernatant was split into 2 aliquots of 220 ul each and frozen at -80C. The cells were collected by addition of 100 ul trypsin and a single-cell suspension was generated. The trypsin digestion was stopped by addition of 400 ul of D10 medium. The cells were washed 3 times with phosphate-buffered saline supplemented with 0.8% by volume non-acetylated bovine serum albumin. The cells were counted to confirm that approximately 7,000 cells were present per well and loaded into the 10X Chromium device.

tag: sequencing target

value: Host and virus

tag: cell or_virus_type

value: Madin-Darby canine kidney cells (MDCK)-SIAT1-TMPRSS2; A/California/04/2009 (pdmH1N1)


title: pooled LMP2A

description:
Gene expression of NPC stem-like cells.
US45103080_251485038674_S01_GE2_107_Sep09_1_4.txt: Cy3


title: Control#1

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485038675_S01_GE2_107_Sep09_1_4.txt: Cy5

source_name: Control


title: Wild-type, CCl4, 4h, replicate 5


title: MH05_Pup2F


title: Wild-type, CCl4, 4h, replicate 1


title: Leaf, control, biol rep1 [BSM1]

city: Vancouver

first: Keith

middle: L.

last: Adams

state: BC

address: 3156-6270 University Blvd.

department: Botany

institute: The University of British Columbia

data_processing:
genome build/assembly: Hybrid of Brassica oleracea TO1000, Brassica rapa v3
Basecalling was performed using NovaSeq 6000's RTA3 software.
Trimmomatic v0.32 was used for adapter trimming and quality filtering, retaining reads with average quality >Q20 that exceeded 50 bases following a 6 base headcrop.
STAR v2.7 was used for alignment of trimmed reads to their respective genomes (parameters:--outFilterMultimapScoreRange 0, --outFilterMultimapNmax 1, --outSAMprimaryFlag AllBestScore).
Constitutive gene expression was quantified using featureCounts v1.5.2 from the Subread package such that only exon-spanning fragments were counted (parameters: -p)
Raw counts were normalized using edgeR v3.20.9 to perform weighted TMM normalization.
Supplementary files format and content: tab-delimited text files contain counts of exon-spanning fragments aligned to species reference.
Supplementary files format and content: tab-delimited text files contain counts of exon-spanning fragments of natural B. napus aligned to pangenomes.

organism: Brassica napus

source_name: Leaf

growth_protocol: Seeds were surface sterilized with Plant Preservative Mixture and sandwiched in distilled water-saturated Miracloth for 24 hours in the dark, then transferred to individual seed-starting pots filled with soil. Plants were grown at 20 degrees C and with 16:8 hour photoperiod (200 E/m^2/s) for three weeks prior to treatment.

extract_protocol:
RNA was extracted using the Invitrogen RNAqueous Total RNA Isolation Kit with supplementary Plant RNA Isolation Aid.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Ascospores of Sclerotinia sclerotiorum (5x10^5 spores/50 ml) were pipeted onto potato dextrose agar and incubated in low light at 20 degrees C for 48 hours. Mycelial plugs (7 mm diameter) were taken from the growing margin and brushed with 2% agar solution prior to placing the plugs on healthy leaves and securing with sterilized needles to simulate wounding. Mock-infected plants were handled similarly, but with potato dextrose agar without the the pathogen. Plants were placed in plastic bags in an 18 degree C chamber for 24 hours before tissue collection.

value: Leaf

tag: line

value: Brassica napus (resynth.)

value: resynthesized B. napus

value: Mock-infected


title: MH05_Pup4G

value: F


title: MH05_Dam2


title: Leaf, control, biol rep2 [BNM2]

data_processing:
genome build/assembly: Brassica napus v5 + pangenome
Basecalling was performed using NovaSeq 6000's RTA3 software.
Trimmomatic v0.32 was used for adapter trimming and quality filtering, retaining reads with average quality >Q20 that exceeded 50 bases following a 6 base headcrop.
STAR v2.7 was used for alignment of trimmed reads to their respective genomes (parameters:--outFilterMultimapScoreRange 0, --outFilterMultimapNmax 1, --outSAMprimaryFlag AllBestScore).
Constitutive gene expression was quantified using featureCounts v1.5.2 from the Subread package such that only exon-spanning fragments were counted (parameters: -p)
Raw counts were normalized using edgeR v3.20.9 to perform weighted TMM normalization.
Supplementary files format and content: tab-delimited text files contain counts of exon-spanning fragments aligned to species reference.
Supplementary files format and content: tab-delimited text files contain counts of exon-spanning fragments of natural B. napus aligned to pangenomes.

tag: tissue

value: Brassica napus cv. Sentry

value: natural B. napus


title: LMP2A#1

description:
Gene expression of NPC stem-like cells.
US45103080_251485038675_S01_GE2_107_Sep09_1_4.txt: Cy3

value: yes


title: K36M d8

city: Boston

first: Simona

last: Cristea

state: Massachusetts

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

library_source: transcriptomic single cell

data_processing:
sequenced reads were aligned to the mm10 reference genome using CellRanger version 3.0.2.
A first round of quality control (input: 45,751 cells) involved all cells positioned at least 3 median absolute deviations below the mean for library size (total number of reads) and  number of detected genes, above the mean for the percentage of mitochondrial genes expressed from the entire transcriptome (40,018 cells remaining).
The data was normalized using SCTransform (Hafemeister and Satija, 2019) and decomposed using PCA.
The R package monocle was used for normalization and dimensionality reduction (UMAP).
Further, 372 single cells corresponding to 3 separate clusters with low QC metrics and indicative of contamination were removed (39,646 cells remaining), and the data was normalized and clustered again. A new low quality cluster consisting of 903 single cells emerged, and was removed. The final cleaned dataset consisted of 38,743 cells.
Assembly: mm10
Supplementary files format and content: text files containing monocle-normalized expression values for each analyzed cell after QC.

source_name: reprogramming intermediates from mouse embryonic fibroblasts

growth_protocol: MEFs were cultured in DMEM 10%FBS, reprogramming was performed in AGi medium, iPSCs were passaged in S/L. Reprogramming intermediate samples for WT and K36M were harvested at days 2, 4, 6, and 8 in addition to WT samples for uninduced MEFs and passaged iPSCs.

extract_protocol:
Approx. 5000 cells per sample were encapsulated using the 10x Chromium pipeline according to manufacturer guidelines using Single Cell 3’ chemistry v3 for embedding, reverse transcription and library preparation (10x Genomics).
According to manufacturer guidelines using Single Cell 3' chemistry v3 (10x Genomics).

tag: cell type

value: cultured in Serum/LIF + 50 ug/ml ascorbic acid + 3 uM CHIR99021 (AGi condition), overexpressing Oct4, Klf4, Sox2 and c-Myc and H3.3K36M

tag: strain

tag: histone

tag: day


title: Leaf, control, biol rep1 [BNM1]

tag: genotype


title: WT d8

value: reprogramming intermediates from mouse embryonic fibroblasts

value: cultured in Serum/LIF + 50 ug/ml ascorbic acid + 3 uM CHIR99021 (AGi condition), overexpressing Oct4, Klf4, Sox2 and c-Myc and H3.3WT

value: WT


title: MH05_Dam7

value: Control

value: Dam


title: K36M d6


title: Leaf, infected, biol rep3 [BSI3]

value: Sclerotinia sclerotiorum-infected


title: Adherent#2

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485038674_S01_GE2_107_Sep09_1_2.txt: Cy5

source_name: adherent

value: no

tag: cell line


title: MH05_Pup7E

value: Pup


title: Leaf, control, biol rep2 [BSI2]

value: Leaf

tag: treatment


title: MH05_Dam4

tag: Sex


title: spheroid#3

description:
Gene expression of NPC stem-like cells.
US45103080_251485038674_S01_GE2_107_Sep09_1_3.txt: Cy5

source_name: spheroid


title: Adherent#3

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485038674_S01_GE2_107_Sep09_1_3.txt: Cy3


title: spheroid#1

description:
Gene expression of NPC stem-like cells.
US45103080_251485038674_S01_GE2_107_Sep09_1_1.txt: Cy5


title: pooled Control

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485038674_S01_GE2_107_Sep09_1_4.txt: Cy5


title: WT d6


title: Leaf, infected, biol rep3 [BNI3]


title: xenoNSP#3

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485038675_S01_GE2_107_Sep09_1_3.txt: Cy3

source_name: xenoNSP


title: Leaf, infected, biol rep2 [BNI2]


title: MH05_Dam5

tag: chemical


title: xenoSP#3

description:
Gene expression of NPC stem-like cells.
US45103080_251485038675_S01_GE2_107_Sep09_1_3.txt: Cy5

source_name: xenoSP


title: Leaf, infected, biol rep1 [BNI1]


title: Leaf, infected, biol rep1 [BSI1]

value: Brassica napus (resynth.)


title: K36M d2


title: spheroid#2

description:
Gene expression of NPC stem-like cells.
US45103080_251485038674_S01_GE2_107_Sep09_1_2.txt: Cy3


title: scProgenyProduction_highMOI_supernatant_NA_biolRep2

description:
Viral barcode sequencing: read1 file contains viral barcode and NA transcript  Supernatant (physical progeny) NA viral barcodes high MOI biological replicate 2
scProgenyProduction_trial1_filtered_progeny_viral_bc.csv.gz

library_source: other

data_processing: All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. The dms_variants package was used to parse viral barcodes from Illumina sequencing reads. Viral barcodes were corrected using UMItools directional adjacency method. Agregate counts of each viral barcode were generated for viral barcodes associated with sequenced infected cells and output in a CSV file.

molecule: other

organism: Influenza A virus (A/California/04/2009(H1N1))

source_name: Influenza supernatant, viral barcodes

extract_protocol: All code for data processing as well as detailed explanations are at https://github.com/jbloomlab/barcoded_flu_pdmH1N1. RNA was isolated from the viral supernatant or infected cell pellets using the RNeasy Mini Kit. Lysis buffer was mixed with the viral supernatant sample and 70% ethanol was added. For the infected cell pellets, the sample was mixed with lysis buffer and homogenized by vortexing at high speed for 20 seconds. The homogenized sample was processed on a gDNA eliminator spin column to remove genomic DNA. The processed sample was combined with 70% ethanol. From this point, both the viral supernatant and infected cell pellets were treated identically and followed the standard RNA purification protocol specified by the manufacturer. The RNA for each sample was eluted in 50 ul of RNase-free water. Reverse transcription was performed with a segment-specific primer targeted to the HA or NA vRNA. Two replicate reactions were performed using RNA from the viral supernatant sample, and two independent reactions were performed using RNA from the two infected cell pellet samples; these replicates provide technical duplicate measurements of both the physical progeny in the supernatant and the infectious progeny in the cell pellets. Reverse transcription was performed using the SuperScript III First-Strand Synthesis SuperMix kit according to the manufacturer protocol [46]. For the viral supernatant samples, 12 ul of each RNA sample was used as template for each 40 ul reaction. For the infected cell pellet samples–which contain much larger amounts of total RNA, due to the host RNA present in the cell–1000 ng of RNA was used as template for each 40 ul reaction. The low-concentration cDNA generated from the viral supernatant samples was purified and concentrated using 2X Ampure SPRI beads and eluted into 22 ul of elution buffer. Viral barcodes were amplified in 50 ul PCR reactions using KOD Hot-Start Master Mix. For the viral supernatant samples, 22 ul of concentrated cDNA was used as template. For the high-concentration infected cell pellet samples, 10 ul of unpurified cDNA was used as template. Segment-specific primers (Table S3) were used and reactions were run for 20 cycles. Amplicons were size-selected and purified using a double-sided AmpureXP bead cleanup. Samples were first combined with 0.8X AmpureXP beads and the supernatant was collected. The supernatant was then combined with 1.8X AmpureXP beads and the bound DNA was collected. Sequencing indices and adapters were attached in a 50 ul PCR reaction using KOD Hot-Start Master Mix. For all samples, 2 ng of purified amplicon DNA was used as template. Sample-specific index primers (Table S3) were used and reactions were run for 20 cycles. The resulting amplicons were gel-purified and pooled for sequencing. Single-end sequencing was performed on an Illumina MiSeq.  At 12 hours post-infection, the supernatant was collected and cells and debris were removed by centrifugation at 300 RCF for 3 min. The supernatant was split into 2 aliquots of 220 ul each and frozen at -80C. The cells were collected by addition of 100 ul trypsin and a single-cell suspension was generated. The trypsin digestion was stopped by addition of 400 ul of D10 medium. The cells were washed 3 times with phosphate-buffered saline supplemented with 0.8% by volume non-acetylated bovine serum albumin. The cells were counted to confirm that approximately 7,000 cells were present per well and loaded into the 10X Chromium device.

value: virus

value: A/California/04/2009 (pdmH1N1)


title: U937 cells infected with ptpA KO BCG rep1

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

institute: institution of microbology

data_processing:
The adaptors and low-quality bases assessed using FASTQC 0.11.3 were trimmed by Trimmomatic 0.39. Trimmed reads were then aligned to the ensembl 79 (GRCh38.p2) reference genome using STAR 2.4.2a (ref. 73).
HTseq (0.6.0) was subsequently employed to convert aligned short reads into read counts for each sample.
Genes with less than ten counts in two or more samples were removed.
The data were then analyzed using R 3.4.4 and DEseq2 1.18.1. Differentially expressed genes of each disease group were identified using Wald statistics test, with log2 fold-change >1.5 and Benjamini–Hochberg (BH)-adjusted P < 0.01 as compared to BCG group.
Assembly: ensembl 79 (GRCh38.p2)
Supplementary files format and content: Tab-separated count data

source_name: U937 cells infected with ptpA KO BCG

extract_protocol:
Total RNA was extracted from the U937 cells infected with BCG and delection of PtpA BCG strains according to the manual of TRIzol  (Life Technologies). The  A260/280 ratios obtained using a Nanodrop ND-2000 (Thermo Scientific) varied from 1.8 to 2.0. RNA integrity was evaluated using the Agilent 2100 TapeStation (Agilent Technologies), and quality control using RNA integrity number (RIN > 8).
RNA libraries were constructed by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and evaluated using the Agilent 2100 TapeStation and Qubit 2.0 (Life Technologies). Sequencing was conducted using the Illumina HiSeq X Ten platform (Novogene Bioinformatics Technology Co., Ltd., Beijing, China) with paired-end 150-bp reads.

treatment_protocol: U937 cells infected with BCG or ptpA KO BCG at a MOI 10 for 24 h

tag: treatment duration

value: ptptA KO BCG


title: U937 cells infected with ptpA KO BCG rep2

source_name: U938 cells infected with ptpA KO BCG


title: Adherent#1

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485038674_S01_GE2_107_Sep09_1_1.txt: Cy3


title: WT d2


title: xenoNSP#2

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485038675_S01_GE2_107_Sep09_1_2.txt: Cy5


title: xenoSP#2

description:
Gene expression of NPC stem-like cells.
US45103080_251485038675_S01_GE2_107_Sep09_1_2.txt: Cy3


title: xenoSP#1

description:
Gene expression of NPC stem-like cells.
US45103080_251485038675_S01_GE2_107_Sep09_1_1.txt: Cy5


title: xenoNSP#1

description:
Gene expression of the counterpart for NPC stem-like cells.
US45103080_251485038675_S01_GE2_107_Sep09_1_1.txt: Cy3


title: WT iPSC

source_name: passaged induced pluripotent stem cells

value: passaged induced pluripotent stem cells

value: passaged in Serum/LIF on irradiated feeders, pre-plated before harvest to remove feeder cells


title: scProgenyProduction_highMOI_supernatant_HA_biolRep2

description:
Viral barcode sequencing: read1 file contains viral barcode and HA transcript  Supernatant (physical progeny) HA viral barcodes high MOI biological replicate 2
scProgenyProduction_trial1_filtered_progeny_viral_bc.csv.gz


title: Leaf, control, biol rep2 [BSM2]

value: resynthesized B. napus

value: Mock-infected


title: scProgenyProduction_highMOI_supernatant_NA_biolRep1

description:
Viral barcode sequencing: read1 file contains viral barcode and NA transcript  Supernatant (physical progeny) NA viral barcodes high MOI biological replicate 1
scProgenyProduction_trial1_filtered_progeny_viral_bc.csv.gz


title: Leaf, control, biol rep2 [BSM3]


title: U937 cells infected with BCG rep3

source_name: U937 cells infected with BCG

value: BCG


title: WT MEF

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts

value: expanded in DMEM 10% FBS


title: scProgenyProduction_highMOI_supernatant_HA_biolRep1

description:
Viral barcode sequencing: read1 file contains viral barcode and HA transcript  Supernatant (physical progeny) HA viral barcodes high MOI biological replicate 1
scProgenyProduction_trial1_filtered_progeny_viral_bc.csv.gz


title: U937 cells infected with ptpA KO BCG rep3

source_name: U939 cells infected with ptpA KO BCG


title: K36M d4

value: reprogramming intermediates from mouse embryonic fibroblasts

value: cultured in Serum/LIF + 50 ug/ml ascorbic acid + 3 uM CHIR99021 (AGi condition), overexpressing Oct4, Klf4, Sox2 and c-Myc and H3.3K36M


title: U937 cells infected with BCG rep1


title: Leaf, control, biol rep3 [BNM3]

value: Brassica napus cv. Sentry

value: natural B. napus


title: WT d4

value: cultured in Serum/LIF + 50 ug/ml ascorbic acid + 3 uM CHIR99021 (AGi condition), overexpressing Oct4, Klf4, Sox2 and c-Myc and H3.3WT

value: WT


title: Hi-C C1_KD_br1

status: Public on Feb 03 2023

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
The in-situ Hi-C data was processed following a standard pipeline Hi-C-Pro. Briefly, the reads were aligned to reference genome (mm9) in two steps: global alignment was first performed for all pair-end reads; unaligned reads were then trimmed by restriction enzyme and aligned again.
All aligned reads were then merged together to assign to restriction fragment. In this step, invalid fragments (dangling end, self-cycle etc.) were discarded and PCR duplications were removed for each biological replicate separately.
At last, all validate pairs were merged for each condation and then normalized by read depth using HOMER followed by ICE matrix balancing to further get interaction matrix.
Assembly: mm9

source_name: Skeletal muscle

extract_protocol:
Genomic DNA was extracted by QuickExtract (Epicentre) solution.
DNA fragments containing biotin were enriched by Dynabeads MyOne Streptavidin C1 (Invitrogen 65001) for 15min at room temperature, followed by end repairing, adaptor ligation and PCR amplification

value: Quiescent muscle stem cell

tag: age

value: post natal day 38


title: Hi-C C1_KD_br3


title: Hi-C Ctrl_br2


title: Hi-C C1_KD_br2


title: Hi-C Ctrl_br1


title: Hi-C PAX7_KD_br1


title: Hi-C PAX7_KD_br2


title: U937 cells infected with BCG rep2


title: Hi-C_PAX7KO br2


title: Hi-C_Ctrl br4


title: Hi-C_PAX7KO br3


title: Hi-C_PAX7KO br1


title: Hi-C_Ctrl br2


title: Hi-C_Ctrl br3


title: Hi-C_Ctrl br1


title: FISC_CTCF_input

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie2 v2.2.3 with default parameters
Duplication reads are removed by picard with default parameters,and then merged alignment files are used to call peaks by MACS2 with p-value equal to 0.01
Assembly: mm9
Supplementary files format and content: bigWig files are generateed by homer
Supplementary files format and content: bed files are generateed by MACS2

extract_protocol:
Chromatin from Quiescent and freshly isolated muscle stem cells were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies.
ChIP-seq libraries were constructed closely according to the standard illumina pair-end or single-end ChIP-seq procedure. After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.

value: Freshly isolated muscle stem cell


title: Hi-C Ctrl_br3


title: QSC_CTCF_rep1


title: FISC_CTCF_rep1


title: FISC_CTCF_rep2


title: Hi-C_D2_br4

value: Activated muscle stem cell


title: Hi-C_D2_br3


title: Hi-C_D3_br4


title: QSC_CTCF_rep2


title: Carcinoma in situ lesion

city: Fukuoka

first: Kana

last: Hasegawa

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay human array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

source_name: carcinoma in situ lesion

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: oral squamous cell carcinoma pathological specimen

tag: tissue type

value: Carcinoma in situ lesion


title: Hi-C_D3_br3


title: Invasive carcinoma lesion

source_name: invasive carcinoma lesion

value: Invasive carcinoma lesion


title: Hi-C_D1_br7


title: Hi-C_D1_br5


title: Hi-C_D3_br2

data_processing:
The in-situ Hi-C data was processed following a standard pipeline Hi-C-Pro. Briefly, the reads were aligned to reference genome (mm9) in two steps: global alignment was first performed for all pair-end reads; unaligned reads were then trimmed by restriction enzyme and aligned again.
All aligned reads were then merged together to assign to restriction fragment. In this step, invalid fragments (dangling end, self-cycle etc.) were discarded and PCR duplications were removed for each biological replicate separately.
At last, all validate pairs were merged for each condation and then normalized by read depth using HOMER followed by ICE matrix balancing to further get interaction matrix.
Genome_build: mm9


title: Hi-C_D1_br4


title: Hi-C_D1_br6


title: Hi-C_D1_br3


title: QSC_CTCF_input


title: Hi-C_D2_br1


title: Hi-C_D3_br1


title: Non-tumor region

source_name: non-tumor region

value: Non-tumor region


title: Hi-C_D1_br2


title: Hi-C_D1_br1


title: Hi-C_FISC_br5


title: Hi-C_FISC_br6


title: Hi-C_FISC_br3


title: Hi-C_FISC_br4


title: Hi-C_D2_br2


title: Hi-C_FISC_br2


title: Hi-C_QSC_br4


title: Hi-C_QSC_br3


title: Hi-C_FISC_br1


title: RNA_FISC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic v0.36 with parameter SLIDINGWINDOW:4:15 MINLEN:50, and low-quality or duplication sequence are removed by a in-house scripts, then mapped to mm9 whole genome using tophat2 with parameters -a 8 -m 0 -I 500000 -p 20 -g 20 --library-type fr-firststrand --segment-mismatches 2 --no-coverage-search -r 50 --mate-std-dev 60
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Fresly isolated muscle stem cells were cultured in growth medium containing F10, 10% HIHS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% pen/strep for (24h)D1,(48h)D2 or 72h(D3)

extract_protocol:
RNA from freshly isolated or culture muscle stem cells was harvested using Trizol reagent.
Purified mRNAs were fragmented and the cDNA were synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added. RNA-seq libraries were constructed according to the standard illumina pair-end sequencing procedure.


title: RNA_geriatric_br3

growth_protocol: Fresly isolated muscle stem cells were cultured in growth medium containing F10, 10% HIHS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% pen/strep for (24h)D1,(48h)D2 or 72h(D3).

value: freshly isolated muscle stem cell

value: post natal month 28-32


title: Hi-C_QSC_br2


title: RNA_D2


title: RNA_D1


title: RNA_geriatric_br2


title: RNA_D3


title: Hi-C_QSC_br1


title: RNA_young_br1

value: post natal month 2


title: RNA_aged_br1

value: post natal month 23-24


title: Hi-C_geriatric_br4


title: RNA_aged_br3


title: Hi-C_geriatric_br2


title: RNA_geriatric_br1


title: Hi-C_geriatric_br1


title: Hi-C_geriatric_br3


title: Hi-C_aged_br1


title: Hi-C_young_br1


title: Hi-C_young_br2


title: Hi-C_young_br3


title: Hi-C_aged_br2


title: Hi-C_R4_br1


title: Hi-C_R4_br2


title: Hi-C_aged_br3


title: Hi-C_R3_br4


title: RNA_young_br2


title: RNA_aged_br2


title: Hi-C_R3_br3


title: Hi-C_R3_br2


title: Hi-C_R2_br5


title: WT, female #4

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Sequencing data was trimmed, aligned and normalized (reads per million mapped reads) using default settings via Partek bioinformatics software.
Supplementary files format and content: Xlsx file includes RPKM values for each Sample

source_name: Colon

growth_protocol: Mouse grown under SPF conditions

extract_protocol:
RNA from frozen colonic tissues was extracted using Qiagen RNeasy Universal kit. Integrity of the isolated RNA was analysed using the Agilent TS HS RNA Kit and TapeStation 4200
1000ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L). RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L). Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

treatment_protocol: No treatment

value: Colon

value: Whole tissue

value: Naive


title: WT, female #3


title: WT, female #6


title: WT, female #5


title: WT, female #2


title: WT, female #1


title: Hi-C_R2_br2


title: Hi-C_R2_br1


title: Hi-C_R1_br6


title: WT, male #5


title: WT, male #6


title: WT, male #4


title: Hi-C_R4_br3


title: WT, male #2


title: Hi-C_R1_br2


title: Hi-C_R1_br5


title: Hi-C_R1_br4


title: Hi-C_R2_br4


title: F121A, female #6


title: F121A, female #4


title: Hi-C_R3_br1


title: F121A, female #5


title: WT, male #1


title: Hi-C_R1_br1


title: Hi-C_Ctrl_br5


title: Hi-C_R2_br3


title: F121A, female #3


title: Hi-C_R1_br3


title: Hi-C_Ctrl_br4


title: Hi-C_Ctrl_br3


title: Chow_StructuralCell

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: matrix files

source_name: small intestine

extract_protocol:
Mice were euthanized using isoflurane (VETONE) and secondary cervical dislocation. The intestines were maintained in a moistened state, and the Peyer’s patches and the remaining mesentery/fat were excised. The small intestine from ileum to jejunum was collected and gently flushed with a syringe with ice cold 1 × Hanks' Balanced Salt Solution (HBSS) media (without Ca2+ and Mg2+) (SIGMA, Cat# H4641) to remove the feces. The intestine was cut open and dissected into 1 cm segments, which were then transferred into a 50 mL tube and gently shaken to let the tissue stretch. They were then washed twice with ice cold 1 × HBSS and the extra HBSS removed using a pipet. 20 ml pre-digestion solution (1 × HBSS with 5% FBS, 5 mM EDTA and 1 mM DTT) was added and incubated for 20 min at 37 °C with 250 rpm rotation in an incubator. The 1 × HBSS containing the epithelial cell layer was collected on ice after vortex and passed through a 100 μm cell strainer. For intraepithelial immune cell isolation, the 1 × HBSS containing the epithelial cell layer was centrifuged at 2000 rpm for 5 mins. The cell pellet was resuspended in 20 ml 40% percoll (Sigma-Aldrich, Cat# P4937) and 20 ml 70% percoll added to the bottom of each tube, spun at 2000 rpm for 20 mins (accelerate at 6 and brake at 2) at room temperature. The middle layer of cells was collected, washed, spun down with 1 × PBS, and resuspended in RPMI 1640 culture media (Corning Cellgro, Cat# 10-040-CV) (supplemented with 10% FBS (Corning, Cat# MT35015CV), 1% Penicillin-Streptomycin-Glutamine (Gibco, Cat# 10378016), 1% MEM Non-Essential Amino Acids Solution (Gibco, Cat# 11140050), 1% HEPES (Gibco, Cat# 15630056), and 1% Sodium Pyruvate (Gibco, Cat# 11360070)) for further FACS or flow cytometry analysis. For intraepithelial immune cell scRNA-seq, single cell suspensions were sorted using a FACSAria III flow cytometer to purify live hematopoietic cells (gated as DAPI-CD45.2+ cells). For IEC isolation, the epithelial cell layer in the 1 × HBSS was spun at 2000 rpm for 5 mins. The cell pellet was resuspended in RPMI 1640 culture media for further FACS. For epithelial structural cell scRNA-seq, single cell suspensions were sorted using a FACSAria III flow cytometer to purify live non- hematopoietic cells (gated as DAPI-CD45.2- cells). For lamina propria immune cell isolation, the epithelial cell layer was removed and the remaining intestine tissues washed twice with RPMI 1640 culture media. The extra media was removed and 10 ml RPMI 1640 culture media with 1mg/ml Collagenase type I (Thermo Fisher Scientific, Cat# 17100017) was added. The sample was incubated for 20 min at 37 °C with 250 rpm rotation and vigorously vortexed to allow the tissue to fully dissolve before passing through 100 μm cell strainer. Media containing the lamina propria cells was centrifuged at 2000 rpm for 5 mins and the cell pellet resuspended in 20 ml 40% percoll. 20 ml 70% percoll was added to the bottom of each tube and spun at 2000 rpm for 20 mins (accelerate at 6 and brake at 2) at room temperature. The middle layer of cells was collected, washed, spun down with 1 × PBS, and resuspended in RPMI 1640 culture media for further FACS or flow cytometry analysis. For lamina propria immune cell scRNA-seq, single cell suspensions were sorted using a FACSAria III flow cytometer to purify live hematopoietic cells (gated as DAPI-CD45.2+ cells).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Intestinal epithelial cells

value: small intestine

value: 16 weeks


title: Hi-C_Ctrl_br2

value: Quiescent muscle stem cell

value: post natal day 38


title: HFHS_LaminaPropria_2

value: Lamina propria immune cells


title: F121A, female #2


title: F121A, male #3


title: F121A, female #1


title: Hi-C_Ctrl_br1


title: F121A, male #6


title: HFHS_StructuralCell


title: F121A, male #5


title: F121A, male #2


title: F121A, male #4


title: WT, male #3


title: HFHS_LaminaPropria_1

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
4samples_barcodes.tsv.gz
4samples_features.tsv.gz
4samples_matrix.mtx.gz


title: Chow_LaminaPropria_2


title: CEA, Sample 19

city: Ashburn

first: Yuhan

last: Wang

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

data_processing:
The libraries were pooled and sequenced on an Illumina NextSeq 550 with 26 bases for read 1 and 50 bases for read 2. Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings.
Sequencing adapters were trimmed from the reads with Cutadapt v2.1.0 (Martin, 2011) prior to alignment with STAR v2.7.5c (Dobin et al., 2013) to the Mus musculus GRCm38.90 genome assembly from Ensembl (ensembl.org).
STAR alignment was performed with the following additional parameters: "--alignSJoverhangMin 8 --alignSJDBoverhangMin 8 --alignIntronMin 20 --alignIntronMax 150000 --outSAMmultNmax 20 --outSAMattributes NH HI NM MD CR CY UR UY --quantMode TranscriptomeSAM GeneCounts"
Gene counts were generated with the STARsolo v2.7.5c algorithm (github.com/alexdobin/STAR/) using the following additional parameters: “--soloType CB_UMI_Simple --soloCBwhitelist smartscrb_whitelist.txt --soloCBstart 2 --soloCBlen 8 --soloUMIstart 10 --soloUMIlen 10 -soloBarcodeReadLength 0 --soloCBmatchWLtype 1MM_multi_pseudocounts --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_Directional --soloUMIfiltering MultiGeneUMI --soloCellFilter None”.
Assembly: GRCm38.90

source_name: brain

growth_protocol: All methods for animal care and use were conducted according to National Institutes of Health guidelines for animal research and approved by the Institutional Animal Care and Use Committee (IACUC) at Janelia Research Campus.

extract_protocol:
Cells were hand-picked into PCR strip tubes containing 3 μl lysis buffer (0.2% TritonX-100 (Sigma) and 0.1 U/μl RNase inhibitor (Lucigen)) and cDNA libraries were prepared using the Smart-SCRB chemistry as described previously (Cembrowski et al., 2018; Xu et al., 2020).
600 pg cDNA from each pooled sample was used in a modified Nextera XT library preparation (Illumina) (Soumillon et al., 2014) using the P5NEXTPT5 primer and extending the tagmentation time to 15 min. The resulting libraries were purified according to the Nextera XT protocol (0.6x beads ratio) and quantified by qPCR using Kapa Library Quantification (Kapa Biosystems).

treatment_protocol: The manual single-cell sorting procedure to isolate non-fluorescent cell bodies from micro-dissected brain slices was similar to a previously described protocol (Hempel et al., 2007). Briefly, mice were deeply anesthetized with isoflurane and decapitated to collect 300 µm coronal brain slices. The CEA was manually dissected with spring scissors using the GFP signal as guidance. Two to three tissue sections from each animal were taken to cover the entire CEA and subjected to protease digestion, after which cells were dissociated. Intact neurons were manually selected into individual wells. Neurons collected from seven animals were pooled for sequencing.

value: neurons

value: 6 to 8 weeks

value: central amygdala (CEA)

tag: plate


title: Chow_LaminaPropria_1


title: Chow_IntraEpi_1

value: Intraepithelial immune cells


title: CEA, Sample 16


title: CEA, Sample 17


title: CEA, Sample 14


title: CEA, Sample 13


title: PDGFD-KO-16wk-Tdt2

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

description: 10x Genomics

data_processing:
Fastq files from each experimental group and mouse genotype were aligned to the reference genome (mm10) individually using CellRanger Software. Individual datasets were aggregated using the CellRanger aggr command without subsampling normalization. The aggregated dataset was then analyzed using the R package Seurat v4.1.1.
Assembly: Mouse genotype were aligned to the reference genome (mm10) individually using CellRanger Software (10x Genomics). Individual datasets were aggregated using the CellRanger aggr command without subsampling normalization.
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Aorta

extract_protocol:
The aortic root and ascending aorta were excised and washed three times in PBS. Collected tissues were placed into an enzymatic dissociation cocktail in Hank’s Balanced Salt Solution (HBSS)) and minced. After incubation at 37 °C for 1 h, the cell suspension was strained, pelleted by centrifugation.
Cells were loaded into a 10X Genomics microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10X Genomics Chromium controller according to the manufacturer’s instructions. Single-cell libraries were then constructed according to the manufacturer’s instructions.
Libraries from individual samples were multiplexed into one lane prior to sequencing on an Illumina platform with targeted depth of 50,000 reads per cell.

value: Aorta

value: smooth muscle cells

value: Pdgfd lacZ/lacZ, ApoE-/-, Myh11-Cre, Rosa-TdTomato

value: 16 wks High Fat Diet


title: PDGFD-KO-16wk-Tdtneg2

description: 10x Genomics


title: PDGFD-KO-16wk-Tdt3

description: 10x Genomics


title: CEA, Sample 15


title: PDGFD-KO-16wk-Tdtneg1

description: 10x Genomics


title: CEA, Sample 12


title: CEA, Sample 11


title: CEA, Sample 10