title: Human monocytes, unconditioned, rep3

status: Public on Aug 20 2024

city: Bethesda

first: Sasisekhar

last: Bennuru

state: MD

address: 10 Center Dr, Bldg 10, Rm 11N208

department: LPD

institute: NIH/NIAID

data_processing:
The mRNA sequencing data was processed using default parameter with RNA-seek workflow (https://github.com/OpenOmics/RNA-seek).
This included preprocessing of the raw sequencing reads to remove low quality bases, adapters, and shorter reads using Cutadapt v1.18, followed by alignment to human hg38 reference genome (GRCh38, Gencode Release 30) using STAR (v.2.7.6a) aligner in two-pass mapping mode.
The gene expression counts estimated from number of reads mapping to each annotated gene using RSEM (v.1.3.0).
Assembly: GRCh38, Gencode Release 30
Supplementary files format and content: tab-delimited text file inlcudes RSEM expected gene counts for all samples

source_name: Donor PBMC

growth_protocol: Donor PBMC samples were collected from the NIH Clinical Center Blood Bank. Human monocyte cells were isolated from 4 donors using magnetic beads (Pan Monocyte Isolation Kit, human, Miltenyi).

extract_protocol:
RNA was extracted from DCs using the Total RNA and Protein Isolation Kit (Thermo Fisher Scientific). The mRNA was purified from total RNA using the RNeasy Pure mRNA Bead Kit (Qiagen) according to manufacturer instructions. Samples with RIN values above 8.0 were prepared for library preparation.
Indexed RNA sequencing (RNA-seq) libraries were constructed from 1 µg total RNA using a TruSeq Stranded mRNA Library Prep (Illumina). The mRNA-Seq libraries were sequenced in paired-end mode (2x151 bp) on Illumina NextSeq sequencer.

treatment_protocol: The monocyte cells (1x10^6/mL) from 4 different donors and exposed to media (unconditioned), 50,000 live microfilariae (Mf), Mf-derived EVs (normalized using 10ug of protein content), 10uL of Mf E/S, or 10uL of Mf supernatant depleted of EVs for 48hrs at 37°C in 5% CO2.

tag: cell line

value: Donor PBMC

value: Monocytes

value: unconditioned


title: Human monocytes, unconditioned, rep1

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: Human monocytes, Mf-derived extracellular vesicles (EVs), rep3

value: Mf-derived extracellular vesicles (EVs)


title: PBS, scRNA-seq

status: Public on Aug 28 2024

city: Beijing

first: Yuanhanyu

last: Luo

state: Beijing

address: No.7, Science Park Road, Zhongguancun Life Science Park, Beijing

country: China

institute: National Institute of Biological Sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Downstream pre-processing steps were performed using Cell Ranger (v.7.0.0) for sample demultiplexing, barcode processing, alignment, filtering and UMI counting.
For the first step of quality control, cells with less than 300 genes or more than 6,000 genes detected were removed. After this exclusion, cells with greater than 10% mitochondrial gene content were excluded.
scDblFinder (v.1.16.0) was utilized to detect and remove possible multiple cells captured within the same droplet (also called doublets/multiplets), yielding an expression matrix of 12,984 cells.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: annotated_Version20250711_PBS.rds: This file contains a set of repeated PBS (control) group Seurat objects, intended to help readers explore the expression of ALPK1 and TIFA across different cell lines under baseline (unstimulated) conditions.

molecule: total RNA

organism: Mus musculus

source_name: Tumour-infiltrating immune cells

extract_protocol:
On day 19, three tumours from each experimental group were excised for further analysis. Tumour-infiltrating immune cells were isolated according to the methodology outlined in the section "Flow cytometry analysis of immune cells in tumours and dLNs". These cells were then subjected to staining with PE-anti-mouse CD45 antibody (clone 30-F11, BioLegend). The CD45+ immune cell population was subsequently enriched utilizing a BD FACSAria Fusion flow cytometer. Real-time monitoring of cell viability was conducted during the preparation of the single CD45+ immune-cell suspension.
Subsequently, ten thousand cells (approximately 1,000 single cells per microlitre) from each experimental group were barcoded and pooled using the 10x Genomics device. Sample preparation was carried out in accordance with the manufacturer's protocol, and sequencing was performed on an Illumina NextSeq sequencer.

treatment_protocol: Mice were administered subcutaneous injections of 1×106 B16F10-OVA cells, with subsequent injections of either PBS or UDSP-Hep on days 10, 12, 14, and 16 of the experimental timeline

value: Tumour-infiltrating immune cells

value: subsequent injections of PBS


title: Human monocytes, Mf-derived extracellular vesicles (EVs), rep2


title: Lung, Saline, Rep 2

status: Public on Sep 27 2024

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description: library name: 18578

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.7.0f with default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

source_name: Lung

extract_protocol:
The inferior lobe was dissected, homogenised in lysis buffer and RNA was isolated using the NucleoSpin® Kit (MACHEREY-NAGEL).
cDNA libraries were prepared using the NEBNext® Ultra II Directional RNA library prep kit for illumina (New England Biolabs) and sequenced on NextSeq 500 (Illumina) with the NextSeq 500/550 High Output kit V2 (#75 CYS, Illumina)

treatment_protocol: 12–14-week-old mice received a single intratracheal instillation of bleomycin sulphate. Untreated mice served as healthy controls (CTRL). Only animals that showed a mild to moderate body weight loss (≥-5% and ≤-17%) at day 6 post-administration were randomized into study groups. Animals were terminated on day 7, 14, 21, 28, 35, or 42 after BLEO administration

tag: tissue

value: Lung

value: Saline


title: Human monocytes, Mf-derived excretory/secretory (E/S) products, rep2


title: Human monocytes, Mf-derived extracellular vesicles (EVs), rep1


title: Human monocytes, Mf-derived excretory/secretory (E/S) products, rep1


title: Human monocytes, Mf live, rep2

value: Live Mf


title: Human monocytes, Mf live, rep1


title: Human monocytes, Mf live, rep3


title: Human monocytes, EV depleted E/S, rep2

value: EV depleted E/S


title: Mono-derived DC, unconditioned, rep3

data_processing:
The mRNA sequencing data was processed using default parameter with RNA-seek workflow (https://github.com/OpenOmics/RNA-seek).
This included preprocessing of the raw sequencing reads to remove low quality bases, adapters, and shorter reads using Cutadapt v1.18, followed by alignment to human hg38 reference genome (GRCh38, Gencode Release 30) using STAR (v.2.7.6a) aligner in two-pass mapping mode.
The gene expression counts estimated from number of reads mapping to each annotated gene using RSEM (v.1.3.0).
The expression data were transformed to log2-counts per million (logCPM) and then filtered to remove genes with <1 CPM that are expressed in less than 4 samples. The filtered gene expression count was normalized using TMM (Trimmed Mean of M-values) method.
Assembly: GRCh38, Gencode Release 30
Supplementary files format and content: single tab-delimited text file inlcudes RSEM expected gene counts for all samples
Supplementary files format and content: single tab-delimited text file inlcudes TMM normalized gene counts for all samples

growth_protocol: Donor PBMC samples were collected from the NIH Clinical Center Blood Bank. Human monocyte cells were isolated from 4 donors using magnetic beads (Pan Monocyte Isolation Kit, human, Miltenyi). 12x10^6 human monocyte cells were cultured for 6 days with addition of GM-CSF and IL-4 to differentiate monocyte-derived DCs.

treatment_protocol: The dendritic cells (1x10^6/mL) from 4 different donors and exposed to media (unconditioned), 50,000 live microfilariae (Mf), Mf-derived EVs (normalized using 10ug of protein content), 10uL of Mf E/S, or 10uL of Mf supernatant depleted of EVs for 48hrs at 37°C in 5% CO2.

value: Monocyte-derived dendritic cells


title: Mono-derived DC, unconditioned, rep4


title: Human monocytes, EV depleted E/S, rep3


title: Mono-derived DC, unconditioned, rep2


title: Mono-derived DC, unconditioned, rep1


title: Mono-derived DC, Mf-derived extracellular vesicles (EVs), rep4


title: Mono-derived DC, Mf-derived extracellular vesicles (EVs), rep3


title: Human monocytes, Mf-derived excretory/secretory (E/S) products, rep3


title: Mono-derived DC, Mf-derived excretory/secretory (E/S) products, rep3


title: Mono-derived DC, Mf-derived extracellular vesicles (EVs), rep2


title: Human monocytes, EV depleted E/S, rep1


title: Mono-derived DC, Mf-derived excretory/secretory (E/S) products, rep4


title: Mono-derived DC, Mf-derived excretory/secretory (E/S) products, rep1


title: Mono-derived DC, Mf live, rep3


title: Mono-derived DC, Mf live, rep2


title: Mono-derived DC, Mf-derived extracellular vesicles (EVs), rep1


title: Mono-derived DC, Mf-derived excretory/secretory (E/S) products, rep2


title: Mono-derived DC, EV depleted E/S, rep4


title: Mono-derived DC, EV depleted E/S, rep1


title: Mono-derived DC, Mf live, rep1


title: Mono-derived DC, EV depleted E/S, rep3


title: HMGA2 fibroid (HMGA2F), patient MP458

status: Public on Aug 14 2024

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

data_processing:
Reads were trimmed for quality and adapters using TrimGalore (version 0.6.5)
Trimmed reads were mapped to Homo sapiens (human) using STAR (version 2.7.9a)
Overlapping Ensembl annotations (version 99)
Analysis was performed using edgeR-robust
Assembly: GRCh38 (hg38)
Supplementary files format and content: txt file with the raw cout per gene

source_name: Fibroid

growth_protocol: Cells were cultured in DMEM/F12 with 10% FBS

extract_protocol:
RNA from cell was extracted using colums from the Qiagen RNAeasy kit. RNA from tissue was isolated using trizol.
paired-end (2 × 100 bp) RNA-sequencing on an Illumina NextSeq 6000
RNA-seq - Kapa RNA HyperPrep kit with ribosomal re-duction, pooled, and sequenced on flowcells to yield approximately 50–60 million reads/sample.

value: Fibroid

tag: genotype

value: HMGA2 Fibroid

tag: age

tag: passage


title: HMGA2 fibroid (HMGA2F), patient MP548


title: HMGA2 fibroid (HMGA2F), patient MP521


title: HMGA2 fibroid (HMGA2F), patient MP301


title: HMGA2 fibroid (HMGA2F), patient MP498


title: HMGA2 fibroid (HMGA2F), patient MP302


title: HMGA2 fibroid (HMGA2F), patient MP293


title: HMGA2 fibroid (HMGA2F), patient MP277


title: HMGA2 fibroid (HMGA2F), patient MP275


title: HMGA2 fibroid (HMGA2F), patient MP228


title: HMGA2 fibroid (HMGA2F), patient MP261


title: Mono-derived DC, Mf live, rep4


title: HMGA2 fibroid (HMGA2F), patient MP172


title: HMGA2 fibroid (HMGA2F), patient MP173


title: HMGA2 fibroid (HMGA2F), patient MP171


title: HMGA2 fibroid (HMGA2F), patient MP098


title: HMGA2 fibroid (HMGA2F), patient HF020


title: HMGA2 fibroid (HMGA2F), patient MP406


title: Myometrium from fibroid-free patient (MyoN), patient MP516

source_name: myometrium

value: myometrium

value: Control myometrium


title: Myometrium from fibroid-free patient (MyoN), patient MP502


title: Myometrium from fibroid-free patient (MyoN), patient MP537


title: HMGA2 fibroid (HMGA2F), patient MP096


title: Mono-derived DC, EV depleted E/S, rep2


title: Myometrium from fibroid-free patient (MyoN), patient MP500


title: Myometrium from fibroid-free patient (MyoN), patient MP499


title: Myometrium from fibroid-free patient (MyoN), patient MP497


title: HMGA2 fibroid (HMGA2F), patient MP299


title: Myometrium from fibroid-free patient (MyoN), patient MP485


title: Myometrium from fibroid-free patient (MyoN), patient MP495


title: Myometrium from fibroid-free patient (MyoN), patient MP479


title: Myometrium from fibroid-free patient (MyoN), patient MP478


title: Myometrium from fibroid-free patient (MyoN), patient MP484


title: HMGA2 fibroid (HMGA2F), patient MP184


title: Myometrium from fibroid-free patient (MyoN), patient MP460


title: Myometrium from fibroid-free patient (MyoN), patient MP472


title: Myometrium from fibroid-free patient (MyoN), patient MP473


title: Myometrium from fibroid-free patient (MyoN), patient MP459


title: Myometrium from fibroid-free patient (MyoN), patient MP452


title: Myometrium from fibroid-free patient (MyoN), patient MP451


title: Myometrium from fibroid-free patient (MyoN), patient MP450


title: Myometrium from fibroid-free patient (MyoN), patient MP408


title: Myometrium from fibroid-free patient (MyoN), patient MP407


title: Myometrium from fibroid-free patient (MyoN), patient MP402


title: Myometrium from fibroid-free patient (MyoN), patient MP399


title: Myometrium from fibroid-free patient (MyoN), patient MP398


title: Myometrium from fibroid-free patient (MyoN), patient MP361


title: Myometrium from fibroid-free patient (MyoN), patient MP365


title: Myometrium from fibroid-free patient (MyoN), patient MP397


title: Myometrium from fibroid-free patient (MyoN), patient MP362


title: Myometrium from fibroid-free patient (MyoN), patient MP363


title: Myometrium from fibroid-free patient (MyoN), patient MP358


title: Myometrium from fibroid-free patient (MyoN), patient MP496


title: Myometrium from fibroid-free patient (MyoN), patient MP490


title: TERT immortalized myometrium cells depleted for CRIP1 transduced with an HMGA2 lentivirus passage 6

value: CRIP1 negative

value: HMGA2 lentivirus


title: TERT immortalized myometrium cells depleted for CRIP1 transduced with a control lentivirus passage 6

value: Control lentivirus


title: TERT immortalized myometrium cells depleted for CRIP1 transduced with an HMGA2 lentivirus passage 5


title: HMGA2 fibroid (HMGA2F), patient MP314


title: TERT immortalized myometrium cells depleted for CRIP1 transduced with a control lentivirus passage 5


title: HMGA2 fibroid (HMGA2F), patient MP120


title: TERT immortalized myometrium cells depleted for CRIP1 transduced with a control lentivirus passage 4


title: HMGA2 fibroid (HMGA2F), patient MP111


title: BALF cells, WT, replicate 2, scRNAseq

status: Public on Jul 29 2024

first: Stewart

middle: J

last: Levine

state: Maryland

address: Bldg 10, Room 6D03, MSC 1590

department: Cardiovascular & Pulmonary Branch

institute: NHLBI, NIH

description: 10x Genomics

data_processing:
FASTQ data was generated from raw (.bcl) files from NovaSeq sequencing runs using the CellRanger software package, version 5.0.1 (10x Genomics).
Reads from each sample were aligned to mouse (mm10) reference transcriptome, feature barcode matrices were generated, and gene expression analyses was performed using default parameters in CellRanger version 6.0.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BALF cells

extract_protocol:
BALF cells in every sample were pooled from three Apoa1-/- and three Apoa1+/+ mice, respectively.
10X Gene Expression libraries were generated using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (catalogue number: PN-1000121) (10x Genomics, Pleasanton, CA).
Library quality was assessed by sequencing them on Illumina MiSeq sequencer (Illumina, San Diego, CA). Post-quality assessment libraries were sequenced using the Illumina Novaseq 6000 instrument (lllumina, San Diego, CA).

value: BALF cells

tag: strain

value: 7 to 8 weeks old

tag: Sex

value: female

value: LPS+house dust mite, 3 days


title: BALF cells, WT, replicate 1, scRNAseq

description: 10x Genomics


title: BALF cells, KO, replicate 1, scRNAseq

description: 10x Genomics


title: A673,IC90,48h,Rep3

status: Public on Jun 12 2024

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

description: IC90_48h_A673vsDMSO_48h_A673.complete.txt

data_processing:
Low quality and adapter sequences were trimmed using Trim_galore
Trimmed sequences were mapped to hg38 using STAR with 2-pass approach
Reads were assigned to features using featureCounts
Normalization, differential analysis and statistical reports were done using DESeq2 and SARTools
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw and normalized counts for each sample generated by DESeq2
Supplementary files format and content: tab-delimited text file include log2FoldChange, p-values adjusted and other the statistics generated by DESeq2 for each sample

growth_protocol: A673 cells were grown in DMEM + 10% FBS + PSQ + 1% Sodium Pyruvate. TTC466, 402-91, 1765-92, SUCCS1 and DTC1 cells were grown in RPMI-1640 + 10% FBS + PSQ. DL221 cells were grown in DMEM + 10% FBS + PSQ. JN-DSRCT and BER cells were grown in DMEM/F12 + 10% FBS + PSQ.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen). 300ng of total RNA was used for library prep.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were seeded at 30% confluency and left to adhere overnight. After 24 hours, cells were dosed with DMSO or Seclidemstat equating calculated IC90 for that cell line. Cells were harvested for RNA extraction after 48 hours.

value: Ewing sarcoma

value: wildtype

tag: time

tag: replicate


title: A673,IC90,48h,Rep2


title: A673,DMSO,48h,Rep3

value: DMSO


title: Myometrium from fibroid-free patient (MyoN), patient MP356


title: A673,DMSO,48h,Rep2


title: P32, negative, TCR

status: Public on Jun 01 2024

city: Seoul

first: Junha

last: Cha

address: Yonsei-Ro 50

department: Department of Biotechnology

country: South Korea

institute: Yonsei University

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh 1.2.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Oropharynx, HNSCC

extract_protocol:
We collected fresh tumor tissues which was mechanically and enzymatically dissociated using a gentleMACS dissociator (Miltenyi Biotec, Gladbach Bergisch, Germany, Cat#130-093-235) and the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat#130-095-929) following the manufacturer's instructions. After incubation for 1 h at 37℃, the resuspended samples were filtered through a 70-µm MACS SmartStrainer (Miltenyi Biotec, Cat# 130-098-462) into RPMI-1640 medium (Corning, Inc. Corning, NY, USA) supplemented with 10% fetal bovine serum (Biowest, Riverside, MO, USA) and centrifuged at 300 ×g for 10 min.
Libraries were prepared using the Chromium controller according to the 10x Chromium Next GEM Single Cell 5-v2_CellSurfaceProtein_UserGuide (CG000330). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 5′ Gel Beads and Partitioning Oil into a Next GEM Chip K. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and enriched with PCR. The amplified cDNA are separated by size selection for 5ʹ Gene Expression libraries, V(D)J Enriched Libraries and Cell Surface Protein libraries

value: Oropharynx, HNSCC

value: M

tag: tumor stage

value: IVA

tag: hpv state


title: P30, negative, TCR

description: 10x Genomics

value: F

value: IVB


title: P28, negative, TCR

description: 10x Genomics

value: III


title: P27, negative, TCR

description: 10x Genomics


title: P23, positive, TCR

description: 10x Genomics

value: II


title: P20, positive, TCR

description: 10x Genomics


title: A673,DMSO,48h,Rep1


title: P25, positive, TCR

description: 10x Genomics


title: P29, positive, TCR

description: 10x Genomics


title: P18, positive, TCR

description: 10x Genomics


title: TERT immortalized myometrium cells depleted for CRIP1 transduced with an HMGA2 lentivirus passage 4

value: myometrium

value: CRIP1 negative


title: P32, negative

description: 10x Genomics


title: BALF cells, KO, replicate 2, scRNAseq

description: 10x Genomics


title: P27, positive

description: 10x Genomics


title: P30, negative

description: 10x Genomics


title: P28, positive

description: 10x Genomics


title: A673,IC90,48h,Rep1


title: P23, positive

description: 10x Genomics


title: P25, positive

description: 10x Genomics


title: P29, positive

description: 10x Genomics


title: P18, positive

description: 10x Genomics


title: HPV10, negative

description: 10x Genomics


title: HPV09, negative

description: 10x Genomics


title: P31, positive, TCR

description: 10x Genomics


title: HPV04, positive

description: 10x Genomics


title: HPV07, negative

description: 10x Genomics


title: HPV03, positive

description: 10x Genomics

value: I


title: HPV02, positive

description: 10x Genomics

value: IV


title: HPV01, positive

description: 10x Genomics


title: HPV06, negative

description: 10x Genomics


title: Large_C

status: Public on May 24 2024

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: Roslin Institute, University of Edinburgh

library_source: other

data_processing:
Trimming for adapters was performed using Cutadapt v1.11
UMI correction
Mapping was performed using Bowtie 2.2.2
Assembly: Sscrofa10.2
Supplementary files format and content: raw_counts: comma separated values containing raw reads, and miRNA names with associated sequence for each sample

molecule: other

organism: Sus scrofa

source_name: Semitendinosus muscle

extract_protocol:
Muscle samples (30 mg) from porcine foetal pairs (IUGR and NW, n=4 litters) were homogenized in RNABee (AMS Biotechnology, Abingdon, UK) in Lysing Matrix D tubes (MP Biomedicals, Illkirch, France), and extracted according to manufacturer's instructions followed by transfer to a RNeasy Mini Spin column and treatment with RNase-free DNase (Qiagen, Manchester, UK). RNA concentration and quality, as defined by RNA Integrity Number equivalent (RINe) were determined by Tapestation 2200 (Agilent Technologies, Edinburgh, UK). All samples used for sequencing had RINe values >8.5.
QIAseq miRNA Library Prep kit (QIAGEN) following manufacturer's instructions

value: Semitendinosus muscle

tag: phenotype

value: Large

tag: litter

value: C


title: HPV05, positive

description: 10x Genomics


title: P31, positive

description: 10x Genomics


title: Small_D

value: Small

value: D


title: Small_C


title: Large_D


title: Small_B

value: B


title: Large_B


title: IgG, ChIP, PS312, J2,, rep2

status: Public on May 21 2024

city: New York

first: Avrami

last: Aharonoff

state: NY

address: 29 Washington Place

department: Biology

institute: New York University

library_source: genomic

data_processing:
Adapters were trimmed when necessary with trimmomatic (version 0.39). Reads were aligned with bowtie2 (version 2.4.2) using the default parameters. Sam files were converted to bam files, sorted and indexed using samtools (version 1.11). Bam files were used to generate bigwig files with the bamCoverage tool in deeptools (version 3.5.0) with the following parameters: --binsize 10 --minMappingQuality 20 --extendReads 200 --ignoreDuplicates --normalizeUsing CPM --exactScaling --ignoreForNormalization chrM.
Assembly: PRJNA982879 (S. hermaphroditum), this paper (P. pacificus), PRJNA644888 (O. tipulae)
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Pristionchus pacificus

growth_protocol: S. hermaphroditum early stage mixed larvae were isolated by filtering mixed stage worms through a 30 micron nylon mesh filter, and collecting the flow through. Pristionchus pacificus J2-J3 larvae were isolated by filtering mixed stage worms through a 20 micron nylon mesh, and collecting the flow through. Oscheius tipulae early stage synchronized larvae were isolated by bleaching mixed stage worms (0.5 M NaOH, 1% sodium hypochlorite for 2 minutes), hatching embryos in M9, and growing synchronized L1 larvae on NGM plates supplemented with agarose at 22˚C for 24 hours.

extract_protocol:
Around 100-150 µL of pelleted larvae was removed from -80 ˚C and washed in FA Buffer (final concentrations of 50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate, 150 mM NaCl, filter sterilized) with 0.1% sarkosyl, 1 mM PMSF, and 1X protease inhibitors (protease inhibitor cocktail set I – Calbiochem, catalog # 539131) added fresh. Larvae were then dounced 30 times in a glass dounce tissue grinder (VWR, catalog number 22877-280) with pestle type B. Sonication was performed in a Biopruptor ® Pico (catalog # B01060010) to obtain fragments between 200 and 800 bp in length (30 seconds on, 30 seconds off, 10-15 cycles). Protein concentration was determined using the Bradford assay (Bio-Rad, catalog # 500-0006). For chromatin immunoprecipitation, 1-2 mg of extract and 3-5 µg of antibody were used (see supplemental file 1), and allowed to rotate overnight at 4 ˚C. nProtein A Sepharose beads (Cytiva, catalog # 17528001) were added and incubation was allowed to continue for 2 hours. Beads were washed with FA buffer, FA buffer – 1 M NaCl, FA buffer – 500 mM NaCl, TEL buffer (final concentrations of 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.0, filter sterilized), and TE, respectively. Immunocomplexes were eluted twice with ChIP elution buffer (final concentrations of 1% SDS, 250 mM NaCl, 10 mM Tris, pH 8.0, 1 mM EDTA) at 65 ˚C for 15 min at 1400 rpm. The eluate was then treated with 2 µL of 10 mg/mL proteinase K for 1 hour at 50 ˚C, and reverse crosslinked overnight in a 65 ˚C waterbath. DNA was purified the next morning with Qiagen MinElute PCR Purification Kit (catalog # 28006), and fragment size was checked by agarose gel electrophoresis or TapeStation. The remaining DNA was stored at -20 ˚C.
Library preparation was performed as follows. To perform end repair, we used half the ChIP DNA and 10-30 ng of input DNA, T4 DNA Ligase Reaction Buffer (NEB, catalog #  B0202S), 0.4 mM dNTPs, 20 U PNK (Fisher, catalog # FEREK0032), 0.7 U Large Klenow Fragment (NEB, catalog # M0210S), and 6 U T4 DNA Polymerase (Fisher, catalog # FEREP0062) (total volume 33 µL). The reaction was incubated at 20 ˚C for 30 minutes, and was cleaned with Qiagen MinElute PCR Purification Kit (eluted in 21 µL). To perform A-tailing, NEBuffer 2 (catalog # B7002S), 0.2 mM dATP, and 7.5 U of Klenow Fragment (3’ → 5’ exo-) (NEB, catalog # M0212L) were added to the cleaned DNA (total volume of 25 µL), and incubated for an hour in a 37 ˚C water bath. The reaction was cleaned with Qiagen MinElute PCR Purification Kit (eluted in 17 µL). To perform adapter ligation, Quick Ligation Buffer, Illumina Truseq Adapters (see supplemental file 1), and 2 µL of Quick Ligase (NEB, catalog # M2200L) were added to cleaned DNA (total volume of 40 µL), and incubated for 20 minutes at 23 ˚C. The reaction was size selected and cleaned with Ampure XP beads (Beckman Coulter, catalog # A63881). The eluate was amplified by PCR with Phusion HF Reaction Buffer, 0.5 µM TruSeq forward and reverse primers (see supplemental file 1), 0.2 mM dNTP, and 1 U Phusion High-Fidelity DNA Polymerase (Fisher, catalog F-530L) for a total reaction volume of 50 µL under the following parameters: 98 ˚C for 1 min, 98 ˚C for 30 seconds, 60 ˚C for 30 seconds, 72 ˚C for 30 seconds, repeat steps 2-4 14 times, 72 ˚C for 5 min, 8 ˚C forever. 10 µL of 3 M sodium acetate (pH 5.2) was added to reaction, and the reaction was cleaned with Qiagen MinElute PCR Purification Kit, (eluted in 11 µL). The eluate was gel purified (1.5% agarose gel) to obtain fragments between 250-600 bp using the Qiagen MinElute Gel Extraction Kit (catalog # 28606). Library concentration was determined with the KAPA Library Quantification Kit (catalog # KK4824). Single-end (75 bp) sequencing was performed at the Genomics Core at the Center for Systems and Genome Biology, New York University using the Illumina NextSeq 500 platform.

treatment_protocol: Larvae were treated with 2% formaldehyde for 30 minutes, washed with M9 (PBS was used for S. hermaphroditum), collected by centrifugation, flash frozen in liquid nitrogen, and stored at -80˚C until extract preparation

tag: source

value: whole worm

value: hermaphrodite

tag: developmental stage

tag: antibody (target)

value: IgG

tag: antibody (vendor,_catalog_number)

value: Abcam, ab46540

tag: antibody (host,_clonality)

value: rabbit, polylconal

tag: matching input

value: input AA76, PS312, J2


title: IgG, ChIP, PS312, J2, rep1

value: input AA66, PS312, J2


title: P20, positive

description: 10x Genomics

tag: tissue

value: Oropharynx, HNSCC

value: M

value: II


title: Small_A

value: A


title: input AA76, PS312, J2


title: input AA66, PS312, J2


title: H3K4me3, ChIP, PS312, J2, rep 1

value: Abcam, ab8580


title: HPV08, positive

description: 10x Genomics

tag: age


title: input AA77, CEW1, early stage synchronized larvae

organism: Oscheius tipulae

value: early stage synchronized larvae


title: input AA85, CEW1, early stage synchronized larvae


title: IgG, ChIP, CEW1, early stage synchronized larvae, rep 2

value: input AA85, CEW1, early stage synchronized larvae


title: H4K20me1, ChIP, CEW1, early stage synchronized larvae, rep 1

value: Abcam, ab9051

value: input AA77, CEW1, early stage synchronized larvae


title: IgG, ChIP, CEW1, early stage synchronized larvae, rep 1


title: H4K20me1, ChIP, CEW1, early stage synchronized larvae, rep 2


title: H3K4me3, ChIP, CEW1, early stage synchronized larvae,  rep 2


title: SLCL_AMS5_3

status: Public on Apr 04 2024

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Sequenced reads were aligned using RSEM along with STAR against the human genome (version: hg19)
DESeq2 was used to normalize the reads and obtain the differentially expressed genes

source_name: blood

extract_protocol: Lexogen Quantseq

value: blood

tag: cell type

value: spontaneous lymphoblastoid cell lines

tag: condition

value: Multiple Sclerosis_Active

tag: batch


title: SLCL_AMS5_1


title: SLCL_SMS6_3

value: Multiple Sclerosis_Stable


title: SLCL_SMS6_2


title: SLCL_SMS6_1


title: H4K20me1, ChIP, PS312, J2, rep2

value: whole worm

tag: Sex

value: hermaphrodite

tag: strain


title: SLCL_SMS5_3


title: SLCL_SMS5_2


title: H4K20me1, ChIP, PS312, J2, rep1

value: rabbit, polylconal


title: Large_A

value: Semitendinosus muscle

value: Large


title: H3K4me3, ChIP, PS312, J2, rep 2

value: input AA76, PS312, J2


title: SLCL_SMS4_2


title: SLCL_SMS4_1


title: SLCL_SMS4_3


title: SLCL_HC4_3

value: Healthy


title: SLCL_SMS5_1


title: SLCL_HC4_2


title: SLCL_HC4_1


title: SLCL_HC3_3


title: SLCL_HC3_2


title: DFif3CW3

status: Public on Mar 13 2024

city: Qingdao 266237

first: Ma kexuan

last: Qin yuqi

state: China

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

institute: Shandong University

description: DFif3CW3 FPKM

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: All_samples.GeneExpression.FPKM.txt

organism: Penicillium oxalicum

source_name: fungal cell

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 1% bran + 1% microcrystalline cellulose as carbon resources for 18h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fungal cell

tag: genotype

value: FaiR deletion strain

tag: treatment

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: DFif3CW2

description: DFif3CW2 FPKM


title: DFif3CW1

description: DFif3CW1 FPKM


title: p23162.s052_NB.16.118.Week.6

status: Public on Feb 14 2024

city: Boston

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

description:
2207.rawdata.csv
2207.normdata.csv

data_processing:
The quality of the raw reads was assessed using multiQC. Raw demultiplexed fastq paired-end read files were trimmed of adapters and filtered using the program skewer to discard those with an average phred quality score of less than 30 or a length of less than 36.
Human-sequenced data were aligned to the Homo Sapiens NCBI reference genome assembly version GRCh38, and the rhesus macaques data were aligned to the Mmul10-100 and the MacaM assemblies and annotations of the Indian rhesus macaque genome using STAR version 2.7.3a, and transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
DESeq2 was used for normalization, producing both a raw and normalized read count table.
Supplementary files format and content: 2207.rawdata.csv (Raw count matrix )
Supplementary files format and content: 2207.normdata.csv (Normalized count matrix)

organism: Macaca mulatta

source_name: BAL

extract_protocol:
RNA quality was assessed using a TapeStation 4200 (Agilent) and then one microgram of total RNA was subjected to globin transcript depletion using the GLOBINclear Kit, human (ThermoFisher Scientific).
Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina).
Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with SR100 reads on an Illumina NovaSeq 6000, yielding ~25 million reads per sample on average.

tag: vaccine administered

value: Bivalent Ad26

tag: route administered

value: No Boost

value: BAL

tag: time

value: week 6


title: SLCL_AMS5_2

value: blood

value: spontaneous lymphoblastoid cell lines


title: p23162.s050_NB.16.086.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s051_NB.16.104.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: H3K4me3, ChIP, CEW1, early stage synchronized larvae, rep 1

tag: source

tag: developmental stage

value: early stage synchronized larvae

value: Abcam, ab8580

value: input AA77, CEW1, early stage synchronized larvae


title: Human monocytes, unconditioned, rep2

tag: cell line

value: Donor PBMC

value: Monocytes

value: unconditioned


title: p23162.s049_NB.16.032.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s045_Intratracheal.16.144.Week.6

description:
2207.rawdata.csv
2207.normdata.csv

value: Intratracheal


title: p23162.s046_Intratracheal.BH31.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s043_Intratracheal.16.036.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s042_Intratracheal.15.193.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s041_Intratracheal.15.150.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s039_Intranasal.16.051.Week.6

description:
2207.rawdata.csv
2207.normdata.csv

value: Intranasal


title: p23162.s038_Intranasal.16.040.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s037_Intranasal.16.037.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s032_Intramuscular.16.041.Week.6

description:
2207.rawdata.csv
2207.normdata.csv

value: Intramuscular


title: p23162.s040_Intranasal.16.138.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s030_Intramuscular.15.119.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s047_NB.15.133.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s029_Intramuscular.15.001.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s035_Intranasal.15.129.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s031_Intramuscular.16.013.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s033_Intramuscular.99C225.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s028_NB.16.118.Week.1

description:
2207.rawdata.csv
2207.normdata.csv

value: week 1


title: p23162.s048_NB.15.147.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: SLCL_HC3_1

value: Healthy


title: p23162.s027_NB.16.104.Week.1

description:
2207.rawdata.csv
2207.normdata.csv

value: Bivalent Ad26


title: p23162.s025_NB.16.032.Week.1

description:
2207.rawdata.csv
2207.normdata.csv

value: No Boost


title: p23162.s026_NB.16.086.Week.1

description:
2207.rawdata.csv
2207.normdata.csv

value: BAL


title: p23162.s024_NB.15.147.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s023_NB.15.133.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s022_Intratracheal.BH31.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s021_Intratracheal.16.144.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s020_Intratracheal.16.090.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s019_Intratracheal.16.036.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s018_Intratracheal.15.193.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s017_Intratracheal.15.150.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s016_Intranasal.16.138.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s015_Intranasal.16.051.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s014_Intranasal.16.040.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s034_Intramuscular.AJ08.Week.6

description:
2207.rawdata.csv
2207.normdata.csv

value: week 6


title: p23162.s013_Intranasal.16.037.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s012_Intranasal.15.195.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s011_Intranasal.15.129.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s009_Intramuscular.99C225.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s010_Intramuscular.AJ08.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s008_Intramuscular.16.041.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s044_Intratracheal.16.090.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s006_Intramuscular.15.119.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s003_Intramuscular.BS32.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s007_Intramuscular.16.013.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s005_Intramuscular.15.001.Week.1

description:
2207.rawdata.csv
2207.normdata.csv


title: p23162.s004_Intranasal.AJ49.Week.6

description:
2207.rawdata.csv
2207.normdata.csv


title: Br1508, DLPFC, AUD Case [D14988]

status: Public on Feb 01 2024

type: genomic

city: Research Triangle Park

first: Melyssa

last: Minto

state: NC

address: 3040 E. Cornwallis Road

institute: RTI International

hyb_protocol: Bisulfite converted genomic DNA, performed with the EZ DNA methylation kit (Zymo Research), was amplified, fragmented and hybridized to Infinium HumanMethylation EPIC BeadChips (Illumina) assessed for methylation using standard Illumina protocols

scan_protocol: The Illumina MethylationEPIC array hybridization and scanning were performed at the Lieber Institute for Brain Development

data_processing:
Raw data resulted from GenomeStudio software (Illumina)
matrix processed value definition: Averaged beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: DLPFC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted with the phenol chloroform method

tag: dsm-5 aud status

value: Case

value: M

tag: agedeath

tag: dsm-5 major depression diagnosis

value: Yes

tag: current smoker at death

tag: manner of death

value: NotNatural

tag: postmortem ethanol toxicology

value: Negative

tag: pmi

tag: sample plate

tag: sample well

tag: manner of death (detailed)

value: Suicide


title: p23162.s001_Intramuscular.BS32.Week.1

description:
2207.rawdata.csv
2207.normdata.csv

tag: cell type


title: p23162.s002_Intranasal.AJ49.Week.1

description:
2207.rawdata.csv
2207.normdata.csv

tag: vaccine administered


title: Br1489, DLPFC, AUD Case [D14987]

tag: Sex

value: Control


title: Br1446, DLPFC, AUD Control [D14985]

value: No

value: Natural


title: Br1402, DLPFC, AUD Case [D14983]

value: F


title: Br1426, DLPFC, AUD Control [D14984]


title: Br1387, DLPFC, AUD Case [D14982]

value: Positive


title: Br1475, DLPFC, AUD Case [D14986]


title: Br1378, DLPFC, AUD Control [D14981]


title: Br1373, DLPFC, AUD Control [D14979]


title: Br8663, Nucleus Accumbens, AUD Case

data_processing:
Raw data resulted from GenomeStudio software (Illumina)
Averaged beta

source_name: Nucleus Accumbens

value: Accident


title: Br8569, Nucleus Accumbens, AUD Case


title: Br1355, DLPFC, AUD Control [D14978]


title: Br8660, Nucleus Accumbens, AUD Case


title: Br8548, Nucleus Accumbens, AUD Case


title: Br8473, Nucleus Accumbens, AUD Control


title: Br8408, Nucleus Accumbens, AUD Case


title: Br8404, Nucleus Accumbens, AUD Case


title: Br8452, Nucleus Accumbens, AUD Control


title: Br8392, Nucleus Accumbens, AUD Case


title: Br8382, Nucleus Accumbens, AUD Control


title: Br8357, Nucleus Accumbens, AUD Case


title: Br8262, Nucleus Accumbens, AUD Control


title: Br8338, Nucleus Accumbens, AUD Case


title: Br8290, Nucleus Accumbens, AUD Case


title: Br1474, DLPFC, AUD Control [D15054]

value: Homicide


title: Br8140, Nucleus Accumbens, AUD Case


title: Br8128, Nucleus Accumbens, AUD Control


title: Br8125, Nucleus Accumbens, AUD Control


title: Br8137, Nucleus Accumbens, AUD Case


title: Br8313, Nucleus Accumbens, AUD Control


title: Br8035, Nucleus Accumbens, AUD Control


title: Br8037, Nucleus Accumbens, AUD Case


title: Br6565, Nucleus Accumbens, AUD Case


title: Br8090, Nucleus Accumbens, AUD Case


title: Br6441, Nucleus Accumbens, AUD Control


title: Br6492, Nucleus Accumbens, AUD Control


title: Br8168, Nucleus Accumbens, AUD Case


title: Br6436, Nucleus Accumbens, AUD Control


title: Br6423, Nucleus Accumbens, AUD Control


title: Br6320, Nucleus Accumbens, AUD Case


title: Br1374, DLPFC, AUD Case [D14980]


title: Br6393, Nucleus Accumbens, AUD Case


title: Br6265, Nucleus Accumbens, AUD Control


title: Br6026, Nucleus Accumbens, AUD Control


title: Br6150, Nucleus Accumbens, AUD Control


title: Br6023, Nucleus Accumbens, AUD Control


title: Br5946, Nucleus Accumbens, AUD Case


title: Br5931, Nucleus Accumbens, AUD Control


title: Br8252, Nucleus Accumbens, AUD Case


title: Br5899, Nucleus Accumbens, AUD Case


title: Br5910, Nucleus Accumbens, AUD Case


title: Br5884, Nucleus Accumbens, AUD Control


title: Br5879, Nucleus Accumbens, AUD Control


title: Br8066, Nucleus Accumbens, AUD Case


title: Br5840, Nucleus Accumbens, AUD Control


title: Br5829, Nucleus Accumbens, AUD Control


title: Br5864, Nucleus Accumbens, AUD Control


title: Br5759, Nucleus Accumbens, AUD Control


title: p23162.s036_Intranasal.15.195.Week.6

description:
2207.rawdata.csv
2207.normdata.csv

value: Bivalent Ad26

tag: route administered

value: Intranasal

tag: time


title: Br5754, Nucleus Accumbens, AUD Control


title: Br5796, Nucleus Accumbens, AUD Control


title: Br5726, Nucleus Accumbens, AUD Case

value: Undetermined


title: Br5673, Nucleus Accumbens, AUD Control


title: Br5695, Nucleus Accumbens, AUD Control


title: Br5703, Nucleus Accumbens, AUD Control


title: Br5657, Nucleus Accumbens, AUD Case


title: Br5639, Nucleus Accumbens, AUD Control


title: Br5643, Nucleus Accumbens, AUD Case


title: Br5540, Nucleus Accumbens, AUD Case


title: Br5600, Nucleus Accumbens, AUD Case


title: Br5459, Nucleus Accumbens, AUD Control


title: Br5598, Nucleus Accumbens, AUD Control


title: Br5526, Nucleus Accumbens, AUD Control


title: Br5531, Nucleus Accumbens, AUD Case


title: Br5454, Nucleus Accumbens, AUD Control


title: Br5885, Nucleus Accumbens, AUD Case


title: Br5441, Nucleus Accumbens, AUD Case


title: Br5368, Nucleus Accumbens, AUD Control


title: Br5326, Nucleus Accumbens, AUD Case


title: Br5276, Nucleus Accumbens, AUD Control


title: Br5293, Nucleus Accumbens, AUD Case


title: Br5262, Nucleus Accumbens, AUD Control


title: Br5211, Nucleus Accumbens, AUD Case


title: Br5148, Nucleus Accumbens, AUD Case


title: Br5163, Nucleus Accumbens, AUD Case


title: Br5025, Nucleus Accumbens, AUD Case


title: Br5455, Nucleus Accumbens, AUD Case


title: Br3953, Nucleus Accumbens, AUD Case


title: Br5060, Nucleus Accumbens, AUD Case


title: Br5400, Nucleus Accumbens, AUD Control


title: Br3925, Nucleus Accumbens, AUD Case


title: Br4000, Nucleus Accumbens, AUD Case


title: Br3870, Nucleus Accumbens, AUD Case


title: Br3878, Nucleus Accumbens, AUD Case


title: Br3874, Nucleus Accumbens, AUD Control


title: Br2727, Nucleus Accumbens, AUD Case


title: Br2726, Nucleus Accumbens, AUD Case


title: Br3877, Nucleus Accumbens, AUD Case


title: Br2724, Nucleus Accumbens, AUD Control


title: Br2709, Nucleus Accumbens, AUD Case


title: Br2715, Nucleus Accumbens, AUD Control


title: Br2638, Nucleus Accumbens, AUD Control


title: Br1998, Nucleus Accumbens, AUD Control


title: Br2483, Nucleus Accumbens, AUD Control


title: Br1916, Nucleus Accumbens, AUD Case


title: Br2015, Nucleus Accumbens, AUD Control


title: Br1995, Nucleus Accumbens, AUD Control


title: Br1903, Nucleus Accumbens, AUD Control


title: Br1735, Nucleus Accumbens, AUD Control


title: Br1635, Nucleus Accumbens, AUD Case


title: Br1600, Nucleus Accumbens, AUD Control


title: Br1559, Nucleus Accumbens, AUD Control


title: Br1620, Nucleus Accumbens, AUD Control


title: Br1551, Nucleus Accumbens, AUD Control


title: Br1514, Nucleus Accumbens, AUD Control


title: Br1530, Nucleus Accumbens, AUD Case


title: Br1475, Nucleus Accumbens, AUD Case


title: Br1474, Nucleus Accumbens, AUD Control


title: Br1446, Nucleus Accumbens, AUD Control


title: Br1387, Nucleus Accumbens, AUD Case


title: Br1378, Nucleus Accumbens, AUD Control


title: Br1402, Nucleus Accumbens, AUD Case


title: Br1373, Nucleus Accumbens, AUD Control


title: Br1355, Nucleus Accumbens, AUD Control


title: Br1374, Nucleus Accumbens, AUD Case


title: Br8663, DLPFC, AUD Case [D15066]

status: Public on Jan 18 2024


title: Br8569, DLPFC, AUD Case [D15064]


title: Br8548, DLPFC, AUD Case [D15063]


title: Br8473, DLPFC, AUD Control [D15062]


title: Br8660, DLPFC, AUD Case [D15065]


title: Br8404, DLPFC, AUD Case [D15059]


title: Br8408, DLPFC, AUD Case [D15060]


title: Br8392, DLPFC, AUD Case [D15049]


title: Br8382, DLPFC, AUD Control [D15048]


title: Br1581, Nucleus Accumbens, AUD Control


title: Br8313, DLPFC, AUD Control [D15030]


title: Br8290, DLPFC, AUD Case [D15029]


title: Br1508, Nucleus Accumbens, AUD Case


title: Br8338, DLPFC, AUD Case [D15046]


title: Br8090, DLPFC, AUD Case [D10533]


title: Br8128, DLPFC, AUD Control [D15034_2]


title: Br8252, DLPFC, AUD Case [D15032]


title: Br8262, DLPFC, AUD Control [D15031]


title: Br8037, DLPFC, AUD Case [D10478]


title: Br6565, DLPFC, AUD Case [D15067]


title: Br1426, Nucleus Accumbens, AUD Control


title: Br6492, DLPFC, AUD Control [D15053]


title: Br8168, DLPFC, AUD Case [D15033]


title: Br8066, DLPFC, AUD Case [D10522]


title: Br8035, DLPFC, AUD Control [D15023]


title: Br8452, DLPFC, AUD Control [D15061]


title: Br8017, DLPFC, AUD Control [D10434]


title: Br6423, DLPFC, AUD Control [D15050]


title: Br6436, DLPFC, AUD Control [D15051]


title: Br6441, DLPFC, AUD Control [D15052]


title: Br6393, DLPFC, AUD Case [D15058]


title: Br6320, DLPFC, AUD Case [D15035]


title: Br8357, DLPFC, AUD Case [D15047]


title: Br8137, DLPFC, AUD Case [D15024]


title: Br6265, DLPFC, AUD Control [D15036]


title: Br8140, DLPFC, AUD Case [D15025]


title: Br8125, DLPFC, AUD Control [D15026]


title: Br6026, DLPFC, AUD Control [D10247]


title: Br6150, DLPFC, AUD Control [D10379]


title: Br5946, DLPFC, AUD Case [D10106]


title: Br5899, DLPFC, AUD Case [D15016]


title: Br5910, DLPFC, AUD Case [D15015]


title: Br6023, DLPFC, AUD Control [D10277]


title: Br5885, DLPFC, AUD Case [D10019]


title: Br5864, DLPFC, AUD Control [D10200]


title: Br5884, DLPFC, AUD Control [D10009]


title: Br5879, DLPFC, AUD Control [D15013]


title: Br5726, DLPFC, AUD Case [D15012]


title: Br5796, DLPFC, AUD Control [D10122]


title: Br5840, DLPFC, AUD Control [D15019]


title: Br5703, DLPFC, AUD Control [D15011]


title: Br5829, DLPFC, AUD Control [D9368]


title: Br5643, DLPFC, AUD Case [D15007]


title: Br5657, DLPFC, AUD Case [D15008]


title: Br5600, DLPFC, AUD Case [D15006]


title: Br5673, DLPFC, AUD Control [D15009]


title: Br5598, DLPFC, AUD Control [D15005]


title: Br5540, DLPFC, AUD Case [D15037]


title: Br5531, DLPFC, AUD Case [D15004]


title: Br5526, DLPFC, AUD Control [D9646]


title: Br5454, DLPFC, AUD Control [D15003]


title: Br5455, DLPFC, AUD Case [D9628]


title: Br5931, DLPFC, AUD Control [D10234]


title: Br5368, DLPFC, AUD Control [D9366]


title: Br5326, DLPFC, AUD Case [D9353]


title: Br5441, DLPFC, AUD Case [D9623]


title: Br5759, DLPFC, AUD Control [D15018]


title: Br5314, DLPFC, AUD Control [D9343]


title: Br5276, DLPFC, AUD Control [D9444]


title: Br5293, DLPFC, AUD Case [D9347]


title: Br5400, DLPFC, AUD Control [D9465]


title: Br5262, DLPFC, AUD Control [D9339]


title: Br5148, DLPFC, AUD Case [D9272]


title: Br5060, DLPFC, AUD Case [D9265]


title: Br5163, DLPFC, AUD Case [D9274]


title: Br5695, DLPFC, AUD Control [D15010]


title: Br4000, DLPFC, AUD Case [D15057]


title: Br3925, DLPFC, AUD Case [D15055]


title: Br3953, DLPFC, AUD Case [D15056]


title: Br5025, DLPFC, AUD Case [D15000]


title: Br5459, DLPFC, AUD Control [D9468]


title: Br3877, DLPFC, AUD Case [D15039_2]


title: Br5639, DLPFC, AUD Control [D9514]


title: Br2727, DLPFC, AUD Case [D15045]


title: Br2724, DLPFC, AUD Control [D15043]


title: Br2726, DLPFC, AUD Case [D15044]


title: Br2715, DLPFC, AUD Control [D15041]


title: Br5444, DLPFC, AUD Case [D9625]


title: Br2709, DLPFC, AUD Case [D15042]


title: Br2483, DLPFC, AUD Control [D15002]


title: Br2638, DLPFC, AUD Control [D9742]


title: Br3874, DLPFC, AUD Control [D15040]


title: Br1998, DLPFC, AUD Control [D15022]


title: Br2015, DLPFC, AUD Control [D15001]


title: Br1995, DLPFC, AUD Control [D15021]


title: Br1735, DLPFC, AUD Control [D14998]


title: Br1916, DLPFC, AUD Case [D15020]


title: Br1635, DLPFC, AUD Case [D14997]


title: Br1600, DLPFC, AUD Control [D14994]


title: Br1620, DLPFC, AUD Control [D14995]


title: Br1551, DLPFC, AUD Control [D14991]


title: Br3878, DLPFC, AUD Case [D15038]


title: Br3870, DLPFC, AUD Case [D15027]


title: Br1514, DLPFC, AUD Control [D14989]


title: Human, H. pylori-positive moderate intestinal metaplasia, scRNAseq, IM-HP-P_3_zhouyoulan

status: Public on Dec 11 2023

city: Nanchang

first: Pan

last: Zheng

address: 17 of Yongwaizhengjie Street

institute: The Affiliated Hospital of Nanchang University

description:
10x genomics
sample18

data_processing:
The raw reads were processed to gene expression matrices using Cell Ranger (10×genomics). The Seurat software package was used for further quality control. To remove low quality cells and likely multiple captures, the following quality control steps: the cells with gene numbers less than 200, UMI less than 1000 and log10Genes Per UMI less than 0.7 were filtered out. Furthermore, the cells where ＞20% of the counts belonged to mitochondrial genes and 5% of the counts belonged to hemoglobin genes were removed. Additionally, the DoubletFinder package (version 2.0.2) was used to identify potential doublet. Finally, 124528 cells (Median: 5319 cells/patient) were obtained for the downstream analysis. We obtained 1717 genes and 5763 UMIs per cell on average
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: stomach

extract_protocol:
The tissue samples were removed from patients and quickly immersed in Dulbecco’s modified eagle medium (DMEM; Cat#11995065, Gibco) containing 10% fetal bovine serum (FBS; Cat#10091148, Gibco). Samples were minced into about 0.5 mm3 pieces and enzymatically digested in digestion medium DMEM supplemented with trypsin (Cat#15090046, Gibco), collagenase I (Cat# 17018029, Gibco), collagenase II (Cat# 17101015, Gibco) and collagenase IV (Cat# 17104019, Gibco). The samples were incubated and digested at 37℃ for approximately 60 min and then filtered using a 100μm strainer (Corning). Following centrifugation (300g) at 4℃ for 5 min, the cells were resuspended with medium containing red cell lysate (Cat#130094183, MACS). After standing 10min at 4℃, the single-cell suspension was centrifuged at 300g for 5min and resuspended in 100μl medium. Cell concentration and viability were detected under Luna Cell Counter.
The suspensions were then converted to separate barcoded scRNA-seq libraries using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Cat#1000268, 10×genomics) according to the manufacturer’s instruction. Libraries were sequenced on an Illumina Nova 6000 PE150

tag: tissue

value: stomach

value: epithelial cells, endothelial cells, fibroblasts, smooth muscle cells, T cells, B cells, myeloid cells, plasma cells, mast cells


title: Human, H. pylori-positive moderate intestinal metaplasia, scRNAseq, IM-HP-P_2_wuxiaole

description:
10x genomics
sample17


title: Human, H. pylori-negative severe intestinal metaplasia, scRNAseq, IM-HP-N_2_chengjugen

description:
10x genomics
sample14


title: Human, H. pylori-negative mild intestinal metaplasia, scRNAseq, IM-HP-N_1_yanglinsheng

description:
10x genomics
sample13


title: Human, H. pylori-negative moderate intestinal metaplasia, scRNAseq, IM-HP-N_3_meipingqing

description:
10x genomics
sample15


title: Human, H. pylori-positive moderate intestinal metaplasia, scRNAseq

description:
10x genomics
sample16


title: Human, H. pylori-positive non-atrophic gastritis, scRNAseq, GS-HP-P_3_zengdexing

description:
10x genomics
sample12


title: Human, H. pylori-positive non-atrophic gastritis, scRNAseq, GS-HP-P_2_liuyanlan

description:
10x genomics
sample11


title: Human, H. pylori-positive non-atrophic gastritis, scRNAseq, GS-HP-P_1_yangyuxiang

description:
10x genomics
sample10


title: Human, H. pylori-negative non-atrophic gastritis, scRNAseq, GS-HP-N_3_liujian

description:
10x genomics
sample9


title: Human, H. pylori-negative non-atrophic gastritis, scRNAseq, GS-HP-N_2_quelujing

description:
10x genomics
sample8


title: Human, H. pylori-positive Gastric adenocarcinoma, scRNAseq, GC-HP-P_3_zhongshanlin

description:
10x genomics
sample6


title: Human, H. pylori-negative non-atrophic gastritis, scRNAseq,GS-HP-N_1_liuxiaoju

description:
10x genomics
sample7


title: Br1903, DLPFC, AUD Control [D15017]

value: M


title: Human, H. pylori-negative Gastric adenocarcinoma, scRNAseq, GC-HP-N_3_chenyingxian

description:
10x genomics
sample3


title: Human, H. pylori-positive Gastric adenocarcinoma, scRNAseq, GC-HP-P_1_huwenming

description:
10x genomics
sample4


title: Human, H. pylori-negative Gastric adenocarcinoma, scRNAseq, GC-HP-N_2_wanghailong

description:
10x genomics
sample2


title: Br1559, DLPFC, AUD Control [D14992]

value: Yes


title: WT_Gen0_rep2

status: Public on Nov 13 2023

city: Klosterneuburg

first: Daniel

last: Zilberman

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria

data_processing:
Assembly: Araport 11
GFF files containing C/T counts for cytosines in the CG context

organism: Arabidopsis thaliana

source_name: leaf tissue

extract_protocol:
Genomic DNA (gDNA) was extracted from 1-month-old Arabidopsis thaliana rosette leaves with the DNeasy plant mini kit (Qiagen, cat. no. 69104) per the manufacturer’s instructions.
Libraries were produced with the Ultra II DNA Library prep kit according to manufacturer’s instructions (New England Biolabs, cat. no. E7645L). Bisulfite conversion of DNA was carried out according to manufacturer’s protocol (Zymo, EZ DNA Methylation Lightning Kit, cat. no. D5046). DNA was converted twice to ensure complete bisulfite conversion of unmethylated cytosine.

value: leaf tissue

tag: generation

tag: genotype

value: WT


title: cmt3_Gen0_rep2


title: cmt3_Gen0_rep1


title: WT_Gen0_rep1


title: BI-442

status: Public on Oct 13 2023

data_processing:
The quality of the raw reads was assessed using multiQC. Raw demultiplexed fastq paired-end read files were trimmed of adapters and filtered using the program skewer to discard those with an average phred quality score of less than 30 or a length of less than 36.
Human-sequenced data were aligned to the Homo Sapiens NCBI reference genome assembly version GRCh38, and the rhesus macaques data were aligned to the Mmul10-100 and the MacaM assemblies and annotations of the Indian rhesus macaque genome using STAR version 2.7.3a, and transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
DESeq2 was used for normalization, producing both a raw and normalized read count table.
Assembly: GRCh38
Supplementary files format and content: CSV file (normalized read count matrix), GSE220659_sep25_mrnavax_log2cpm_counts.csv
Supplementary files format and content: CSV file (raw read count matrix), GSE220659_sep25_mrnavax_rawCounts.csv

source_name: PBMC

extract_protocol:
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific). RNA quality was assessed using a TapeStation 4200 (Agilent) and then one microgram of total RNA was subjected to globin transcript depletion using the GLOBINclear Kit, human (ThermoFisher Scientific).
Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina).
Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with SR100 reads on an Illumina NovaSeq 6000, yielding ~25 million reads per sample on average.

value: PBMC

tag: visit number

value: Visit 1

tag: vaccine


title: Br1530, DLPFC, AUD Case [D14990]

tag: dsm-5 aud status

value: Case

tag: agedeath

tag: dsm-5 major depression diagnosis

tag: current smoker at death

value: Control

value: Negative


title: BI-445 v2

value: Visit 2


title: BI-445 v1


title: Human, H. pylori-negative Gastric adenocarcinoma, scRNAseq, GC-HP-N_1_tongchunxia

description:
10x genomics
sample1


title: BI-333

value: ModernaBoost


title: BI-330


title: BI-305


title: BI-197


title: BI-313


title: BI-362


title: Human, H. pylori-positive Gastric adenocarcinoma, scRNAseq, GC-HP-P_2_liufugui

description:
10x genomics
sample5


title: BI-344 v1


title: BI-171 v2


title: BI-164 v2


title: BI-188


title: CWRU006437

description:
Cov001_cpmCounts.csv
rCov001_rawCounts.csv

data_processing:
The quality of the raw reads was assessed using multiQC. Raw demultiplexed fastq paired-end read files were trimmed of adapters and filtered using the program skewer to discard those with an average phred quality score of less than 30 or a length of less than 36.
Human-sequenced data were aligned to the Homo Sapiens NCBI reference genome assembly version GRCh38, and the rhesus macaques data were aligned to the Mmul10-100 and the MacaM assemblies and annotations of the Indian rhesus macaque genome using STAR version 2.7.3a, and transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
DESeq2 was used for normalization, producing both a raw and normalized read count table.
Assembly: GRCh38
Supplementary files format and content: CSV file (raw read count matrix), rCov001_rawCounts.csv
Supplementary files format and content: CSV file (normalized read count matrix), Cov001_cpmCounts.csv

source_name: Blood

value: Blood

value: PBMCs


title: BI-164 v1


title: BI-160


title: CWRU006436


title: CWRU006435


title: CWRU006434


title: BI-345


title: CWRU006432


title: BI-344 v2


title: CWRU006431


title: CWRU006430


title: CWRU006427


title: CWRU006429


title: CWRU006428


title: CWRU006424


title: CWRU006422


title: CWRU006426


title: CWRU006425


title: CWRU006421


title: CWRU006423


title: BI-171 v1


title: CWRU006419


title: CWRU006417


title: CWRU006418


title: CWRU006416


title: CWRU006415


title: CWRU006414


title: CWRU006413


title: CWRU006433


title: CWRU006411


title: CWRU006412


title: CWRU006410


title: CWRU006409


title: CWRU006408


title: CWRU006405


title: CWRU006406


title: CWRU006407


title: CWRU006404


title: CWRU006401


title: CWRU006402


title: CWRU006403


title: CWRU006400


title: CWRU006399


title: CWRU006420


title: CWRU006397


title: CWRU006398


title: CWRU006396


title: CWRU006395


title: CWRU006394


title: CWRU006391


title: CWRU006392


title: CWRU006393


title: BI-312


title: CWRU006390


title: CWRU006389


title: CWRU006385


title: CWRU006383


title: CWRU006384


title: CWRU006386


title: CWRU006387


title: CWRU006378


title: CWRU006381


title: CWRU006388


title: CWRU006377


title: CWRU006380


title: CWRU006379


title: CWRU006376


title: CWRU006375


title: CWRU006374


title: CWRU006372


title: CWRU006370


title: CWRU006371


title: CWRU006369


title: CWRU006368


title: CWRU006373


title: CWRU006367


title: CWRU006366


title: CWRU006364


title: CWRU006365


title: CWRU006361


title: CWRU006362


title: CWRU006382


title: CWRU006359


title: CWRU006360


title: CWRU006358


title: CWRU006357


title: CWRU006356


title: CWRU006355


title: CWRU006354


title: CWRU006351


title: CWRU006349


title: CWRU006352


title: CWRU006353


title: CWRU006348


title: CWRU006347


title: CWRU006346


title: CWRU006345


title: CWRU006341


title: CWRU006340


title: CWRU006344


title: CWRU006343


title: Br5211, DLPFC, AUD Case [D9281]

tag: manner of death

value: NotNatural

tag: postmortem ethanol toxicology

value: Positive

tag: pmi

tag: sample plate

value: Accident


title: CWRU006338

tag: cell type


title: CWRU006337


title: CWRU006339


title: CWRU006333


title: CWRU006335


title: CWRU006332


title: CWRU006334


title: CWRU006331


title: CWRU006330


title: CWRU006363


title: CWRU006328


title: CWRU006327


title: CWRU006350


title: CWRU006325


title: CWRU006323


title: CWRU006324


title: CWRU006322


title: CWRU006342


title: CWRU006319


title: CWRU006321


title: CWRU006320


title: CWRU006316


title: CWRU006314


title: CWRU006318


title: CWRU006336


title: CWRU006317


title: CWRU006326


title: CWRU006315


title: CWRU006312


title: CWRU006313


title: CWRU006311


title: CWRU006310


title: CWRU006309


title: CWRU006308


title: CWRU006305


title: CWRU006329


title: CWRU006306


title: CWRU006307


title: CWRU006304


title: CWRU006303


title: CWRU006301


title: CWRU006302


title: CWRU006300


title: CWRU006299


title: CWRU006297


title: CWRU006296


title: CWRU006298


title: CWRU006293


title: CWRU006292


title: CWRU006295


title: CWRU006294


title: CWRU006291


title: p20185.s158_20.14_15.183_D7

data_processing:
The quality of the raw reads was assessed using multiQC. Raw demultiplexed fastq paired-end read files were trimmed of adapters and filtered using the program skewer to discard those with an average phred quality score of less than 30 or a length of less than 36.
Human-sequenced data were aligned to the Homo Sapiens NCBI reference genome assembly version GRCh38, and the rhesus macaques data were aligned to the Mmul10-100 and the MacaM assemblies and annotations of the Indian rhesus macaque genome using STAR version 2.7.3a, and transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
DESeq2 was used for normalization, producing both a raw and normalized read count table.
Assembly: Mmul_10 (GCA_003339765.3)
Supplementary files format and content: CSV file (read count matrix), 2014.forGeo.csv

tag: time point

tag: vaccine dose

value: sham


title: p20185.s108_20.14_15.183_D1


title: p20185.s183_20.14_15.183_D14


title: p20185.s133_20.14_15.183_D3


title: p20185.s208_20.14_15.183_D28


title: CWRU006290


title: p20185.s157_20.14_15.179_D7


title: p20185.s083_20.14_15.183_D0


title: p20185.s182_20.14_15.179_D14


title: p20185.s181_20.14_15.175_D14


title: p20185.s131_20.14_15.175_D3


title: p20185.s082_20.14_15.179_D0


title: p20185.s206_20.14_15.175_D28


title: p20185.s106_20.14_15.175_D1


title: p20185.s132_20.14_15.179_D3


title: p20185.s203_20.14_15.173_D28


title: p20185.s178_20.14_15.173_D14


title: p20185.s153_20.14_15.173_D7


title: p20185.s081_20.14_15.175_D0


title: p20185.s103_20.14_15.173_D1


title: p20185.s078_20.14_15.173_D0


title: p20185.s128_20.14_15.173_D3


title: p20185.s207_20.14_15.179_D28


title: p20185.s202_20.14_15.171_D28


title: p20185.s177_20.14_15.171_D14


title: p20185.s077_20.14_15.171_D0


title: p20185.s127_20.14_15.171_D3


title: p20185.s152_20.14_15.171_D7


title: p20185.s176_20.14_15.169_D14


title: p20185.s101_20.14_15.169_D1


title: p20185.s107_20.14_15.179_D1


title: p20185.s156_20.14_15.175_D7


title: p20185.s198_20.14_15.161_D28


title: p20185.s173_20.14_15.161_D14


title: p20185.s148_20.14_15.161_D7


title: p20185.s123_20.14_15.161_D3


title: p20185.s098_20.14_15.161_D1


title: p20185.s197_20.14_15.159_D28


title: p20185.s172_20.14_15.159_D14


title: p20185.s073_20.14_15.161_D0


title: p20185.s147_20.14_15.159_D7


title: p20185.s122_20.14_15.159_D3


title: p20185.s097_20.14_15.159_D1


title: p20185.s072_20.14_15.159_D0


title: p20185.s196_20.14_15.157_D28


title: p20185.s102_20.14_15.171_D1


title: p20185.s171_20.14_15.157_D14


title: p20185.s201_20.14_15.169_D28


title: p20185.s146_20.14_15.157_D7


title: p20185.s126_20.14_15.169_D3


title: p20185.s151_20.14_15.169_D7


title: p20185.s096_20.14_15.157_D1


title: p20185.s121_20.14_15.157_D3


title: p20185.s071_20.14_15.157_D0


title: p20185.s076_20.14_15.169_D0


title: p20185.s085_20.14_15.148_D0


title: p20185.s160_20.14_15.148_D7


title: p20185.s110_20.14_15.148_D1


title: p20185.s209_20.14_15.146_D28


title: p20185.s185_20.14_15.148_D14


title: p20185.s210_20.14_15.148_D28


title: p20185.s135_20.14_15.148_D3


title: p20185.s184_20.14_15.146_D14


title: p20185.s134_20.14_15.146_D3


title: p20185.s084_20.14_15.146_D0


title: p20185.s143_20.14_15.145_D7


title: p20185.s193_20.14_15.145_D28


title: p20185.s109_20.14_15.146_D1


title: p20185.s168_20.14_15.145_D14


title: p20185.s068_20.14_15.145_D0


title: p20185.s093_20.14_15.145_D1


title: p20185.s118_20.14_15.145_D3


title: p20185.s192_20.14_15.143_D28


title: p20185.s142_20.14_15.143_D7


title: p20185.s167_20.14_15.143_D14


title: p20185.s067_20.14_15.143_D0


title: p20185.s092_20.14_15.143_D1


title: p20185.s205_20.14_15.140_D28


title: p20185.s180_20.14_15.140_D14


title: p20185.s130_20.14_15.140_D3


title: p20185.s105_20.14_15.140_D1


title: p20185.s080_20.14_15.140_D0


title: p20185.s191_20.14_15.139_D28


title: p20185.s166_20.14_15.139_D14


title: p20185.s141_20.14_15.139_D7


title: p20185.s159_20.14_15.146_D7


title: p20185.s091_20.14_15.139_D1


title: p20185.s116_20.14_15.139_D3


title: p20185.s163_20.14_15.131_D14


title: p20185.s188_20.14_15.131_D28


title: p20185.s088_20.14_15.131_D1


title: p20185.s204_20.14_15.118_D28


title: p20185.s179_20.14_15.118_D14


title: p20185.s063_20.14_15.131_D0


title: p20185.s104_20.14_15.118_D1


title: p20185.s117_20.14_15.143_D3


title: p20185.s129_20.14_15.118_D3


title: p20185.s155_20.14_15.140_D7


title: p20185.s079_20.14_15.118_D0


title: p20185.s162_20.14_15.117_D14


title: p20185.s137_20.14_15.117_D7


title: p20185.s062_20.14_15.117_D0


title: p20185.s187_20.14_15.117_D28


title: p20185.s087_20.14_15.117_D1


title: p20185.s112_20.14_15.117_D3


title: p20185.s186_20.14_15.115_D28


title: p20185.s066_20.14_15.139_D0


title: p20185.s161_20.14_15.115_D14


title: p20185.s136_20.14_15.115_D7


title: p20185.s111_20.14_15.115_D3


title: p20185.s138_20.14_15.131_D7


title: p20185.s200_20.14_15.114_D28


title: p20185.s150_20.14_15.114_D7


title: p20185.s113_20.14_15.131_D3


title: p20185.s125_20.14_15.114_D3


title: p20185.s061_20.14_15.115_D0


title: p20185.s086_20.14_15.115_D1


title: p20185.s100_20.14_15.114_D1


title: p20185.s149_20.14_15.108_D7


title: p20185.s174_20.14_15.108_D14


title: p20185.s154_20.14_15.118_D7


title: p20185.s075_20.14_15.114_D0


title: p20185.s124_20.14_15.108_D3


title: p20185.s099_20.14_15.108_D1


title: p20185.s074_20.14_15.108_D0


title: p20185.s195_20.14_15.104_D28


title: p20185.s145_20.14_15.104_D7


title: p20185.s070_20.14_15.104_D0


title: p20185.s169_20.14_15.086_D14


title: p20185.s095_20.14_15.104_D1


title: p20185.s194_20.14_15.086_D28


title: p20185.s144_20.14_15.086_D7


title: p20185.s175_20.14_15.114_D14


title: p20185.s120_20.14_15.104_D3


title: p20185.s119_20.14_15.086_D3


title: p20185.s165_20.14_15.084_D14


title: p20185.s140_20.14_15.084_D7


title: p20185.s090_20.14_15.084_D1


title: p20185.s115_20.14_15.084_D3


title: p20185.s189_20.14_15.072_D28


title: p20185.s069_20.14_15.086_D0


title: p20185.s190_20.14_15.084_D28


title: p20185.s065_20.14_15.084_D0


title: p20185.s139_20.14_15.072_D7


title: p20185.s089_20.14_15.072_D1


title: p20185.s114_20.14_15.072_D3


title: p20185.s064_20.14_15.072_D0


title: 18-KTD-M80-35-L

city: OSLO

first: Knut

middle: Tomas

last: Dalen

state: OSLO

address: Sognsvannsveien 9

department: Department of Nutriton

country: Norway

institute: University of Oslo

data_processing:
50 bp paired end reads were sequenced on an Illumina Novaseq 600 intrument
BBDuk (BBMap v34.56) was used to remove/trim low-quality reads and adapter sequences
Reads were  mapped to a human reference genome/transcriptome (ENSEMBL release 101, GRCh38.101) using HiSat2 v.1.2.1
Read counting was done with FeatureCounts v1.4.6-p1
Assembly: GRCh38.101
Supplementary files format and content: Normalized_gene_counts_TPM.csv is a csv file that containes normalised counts (TPM), for all samples, annotated to ensembl/entrez/hgnc. Unnormalised_feature_counts.csv is a csv file containing unnormalised counts for all samples, annotated to ensembl, generated in HiSat2 v.1.2.1

source_name: Liver tissue

growth_protocol: Female 15-week old Plin2+/+ and Plin2-/- mice on C57BL/6N background fed chow or fasted for 24h.

extract_protocol:
RNA was isolated with a NucleoSpin RNA mini kit (Machery-Nagel), according to the manufacturer’s instructions.
Strand-Specific TruSeqTM mRNA-seq library preparation

tag: sample group

value: Fasted

tag: strain

tag: timepoint

value: 15-week old


title: 19-KTD-M80-38-L


title: 17-KTD-M80-33-L


title: p20185.s170_20.14_15.104_D14

tag: tissue


title: p20185.s199_20.14_15.108_D28


title: p20185.s164_20.14_15.072_D14


title: 16-KTD-M80-32-L


title: 20-KTD-M80-39-L


title: p20185.s094_20.14_15.086_D1


title: 13-KTD-M80-25-L

value: Fed


title: 14-KTD-M80-26-L


title: 11-KTD-M80-22-L


title: 10-KTD-M80-20-L

value: Plin2+/+ Fasted


title: 7-KTD-M80-15-L


title: 12-KTD-M80-24-L


title: 5-KTD-M80-8-L

value: Plin2+/+ Fed


title: 6-KTD-M80-14-L


title: 2-KTD-M80-3-L


title: 1-KTD-M80-2-L


title: 4-KTD-M80-6-L


title: 9-KTD-M80-17-L


title: T451F-wk4d31

status: Public on Sep 29 2023

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s267_T451F.wk4d31_S193

data_processing:
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing are suitable for further analysis.
Adapter sequences, other contaminant sequences such as polyA tails and low-quality sequences with PHRED quality scores less than five were trimmed from reads using atropos (https://github.com/jdidion/atropos).
Trimmed reads were aligned to the Macaca mulatta genome using STAR. Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap and other custom tools.
Transcript abundance estimates was calculated internal to the STAR aligner using the algorithm of htseq-count as described previously.
DESeq2 was used for normalization, producing both a raw and normalized read count table. Normalized expression counts were used for visualizations purposes using PCA and heatmaps where indicated.
Assembly: New Rhesus Genome (MacaM version 7.6) (https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome)
Supplementary files format and content: raw_counts_p22321.csv
Supplementary files format and content: normalized_counts_p22321.csv

source_name: Whole blood

extract_protocol:
Whole-blood was collected from PAXgene tubes at pre and post-challenge timepoints, including necropsy. Whole-blood RNA was extracted and sequenced on an Illumina NovaSeq 6000.
Total RNA was extracted from these samples and libraries were prepared for Next-Gen Sequencing Paired-End 75bp (PE75).
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).

value: Whole blood


title: T451F-Group-VI-Necropsy

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s269_T451F.Group.VI.Necropsy_S195


title: 15-KTD-M80-27-L


title: T451F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s264_T451F.wk3_S190


title: T451F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s263_T451F.wk.1_S189


title: T451F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s266_T451F.wk4d29_S192


title: T451F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s265_T451F.wk4d28_S191


title: T465M-Day-2-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s262_T465M.Day.2.Terminal_S188


title: 8-KTD-M80-16-L


title: T465M-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s261_T465M.wk6_S187


title: 3-KTD-M80-4-L


title: T465M-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s260_T465M.wk5d38_S186


title: T465M-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s259_T465M.wk5d35_S185


title: T465M-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s257_T465M.wk4d29_S183


title: T465M-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s258_T465M.wk4d31_S184


title: T465M-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s256_T465M.wk4d28_S182


title: T465M-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s255_T465M.wk3_S181


title: T465M-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s254_T465M.wk2_S180


title: T465M-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s253_T465M.wk1d10_S179


title: T465M-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s251_T465M.wk0d3_S177


title: T465M-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s250_T465M.wk0d1_S176


title: T451F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s268_T451F.wk5d35_S194


title: T465M-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s249_T465M.wk.1_S175


title: T443F-Day-1-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s248_T443F.Day.1.Terminal_S174


title: T443F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s247_T443F.wk6_S173


title: T443F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s246_T443F.wk5d38_S172


title: T443F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s241_T443F.wk3_S167


title: T443F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s244_T443F.wk4d31_S170


title: T443F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s242_T443F.wk4d28_S168


title: T443F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s240_T443F.wk2_S166


title: T443F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s237_T443F.wk0d3_S163


title: T443F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s239_T443F.wk1d10_S165


title: T443F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s235_T443F.wk.1_S161


title: T443F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s238_T443F.wk1d7_S164


title: T443F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s236_T443F.wk0d1_S162


title: T465M-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s252_T465M.wk1d7_S178


title: T462M-Day-2-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s234_T462M.Day.2.Terminal_S160


title: T443F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s245_T443F.wk5d35_S171


title: T462M-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s231_T462M.wk5d35_S157


title: T462M-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s230_T462M.wk4d31_S156


title: T443F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s243_T443F.wk4d29_S169


title: T462M-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s232_T462M.wk5d38_S158


title: T462M-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s229_T462M.wk4d29_S155


title: T462M-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s228_T462M.wk4d28_S154


title: T462M-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s227_T462M.wk3_S153


title: MuSC BMP6 treated, biological rep. 1

status: Public on Oct 01 2023

type: RNA

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description: Gene expression data from BMP6 treated MuSC

hyb_protocol: Biotinylated cDNA was hybridized to the array at 45°C, 60 rpm for 16 h. The hybridized array was stained with streptavidin phycoerythrin conjugate using the Affymetrix GeneChip® Fluidics Station 450. Hybridization and staining steps were done with the Affymetrix GeneChip® Hybridization, Wash, and Stain Kit.

scan_protocol: The arrays were scanned with the Affymetrix GeneChip® Scanner 3000 G7.

data_processing: Microarray data were analyzed with the R packages "affy" and "oligo" of the Bioconductor suite. Data quality control was carried out by creating pseudo images for each array using the "oligo" package and visually inspecting them for the presence of artifacts. The raw count *.CEL files were normalized using Robust Multichip Averaging (RMA) with quantile normalization, background correction, and annotation (using the MG 1.0 ST Chip Description File "mogene10stv1cdf" from Bioconductor).

label: biotin

source_name: MuSC from mouse #1 treated with 100 ng/ml BMP6

label_protocol: Affymetrix GeneChip™ WT PLUS Reagent Kit was used to generate sense-strand target (ST) cDNA. Briefly, first-cycle cDNA was generated from total RNA using a reverse transcription priming method that specifically primes non-ribosomal RNA from the sample, including both poly(A) and nonpoly(A) mRNA. This was then used to generate antisense cRNA by in vitro transcription. The second-cycle ST cDNA was synthesized from cRNA using random primers resulting in a product that contained dUTP at a fixed ratio relative to dTTP. Uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) were then used to recognize and fragment the cDNA at the unnatural dUTP residues. Fragmented cDNA was then biotinylated by terminal deoxynucleotidyl transferase (TdT). Fragmentation and biotinylation were done with the Affymetrix GeneChip® WT Terminal Labeling Kit.

growth_protocol: Muscle stem cells were isolated from muscle of female 6-8-week-old mice, cultured on Matrigel® for expansion over 2 days. In order to limit the effct of BMPs in the culture medium (e.g. from serum supplements), cells were cultured prior to the BMP stimulation for 6 h in serum-free medium containing BMP soluble receptor (recombinant mouse BMPR-IA/ALK3-Fc Chimera, R&D Systems, 437-MR) in a concentration of 200 ng/ml. Cells were then stimulated for 1 h with a pulse of of 100 ng/ml BMP4 or BMP6 or only with vehicle used for reconstitution of BMP in the case of controls.

extract_protocol: Total RNA was extracted. Cells were lysed directly in their dish, homogenized, and stored at -80 deg C for subsequent RNA isolation. Lysis (RLT buffer+10% βME), homogenization (QIAshredder, Qiagen), and total RNA extraction were done according to the manual of the RNeasy Micro kit (Qiagen).

treatment_protocol: Cells were stimulated with a pulse of 1 h duration with 100 ng/ml BMP6 or only with vehicle used for reconstitution of BMP in case of controls.

tag: treatment

value: BMP6 [100 ng/ml]

value: adult muscle stem cells

tag: mouse strain


title: T462M-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s233_T462M.wk6_S159


title: MuSC vehicle treated, biological rep. 2

description: Gene expression data from control treated MuSC

source_name: MuSC from mouse #2 treated with vehicle

value: control


title: T462M-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s226_T462M.wk2_S152


title: T462M-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s223_T462M.wk0d3_S149


title: T462M-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s224_T462M.wk1d7_S150


title: T462M-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s225_T462M.wk1d10_S151


title: MuSC BMP6 treated, biological rep. 3

source_name: MuSC from mouse #3 treated with 100 ng/ml BMP6


title: T462M-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s222_T462M.wk0d1_S148


title: T437F-Day-1-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s220_T437F.Day.1.Terminal_S146


title: MuSC BMP6 treated, biological rep. 2

source_name: MuSC from mouse #2 treated with 100 ng/ml BMP6


title: T437F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s219_T437F.wk6_S145


title: MuSC vehicle treated, biological rep. 1

source_name: MuSC from mouse #1 treated with vehicle


title: T462M-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s221_T462M.wk.1_S147


title: MuSC vehilce treated, biological rep. 3


title: T437F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s218_T437F.wk5d38_S144


title: T437F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s217_T437F.wk5d35_S143


title: T437F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s216_T437F.wk4d31_S142


title: T437F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s215_T437F.wk4d29_S141


title: T437F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s213_T437F.wk3_S139


title: T437F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s208_T437F.wk0d1_S134


title: T437F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s210_T437F.wk1d7_S136


title: T437F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s214_T437F.wk4d28_S140


title: T437F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s207_T437F.wk.1_S133


title: T437F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s212_T437F.wk2_S138


title: T445F-Day-2-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s206_T445F.Day.2.Terminal_S132


title: T437F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s211_T437F.wk1d10_S137


title: T437F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s209_T437F.wk0d3_S135


title: T445F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s202_T445F.wk4d31_S130


title: T445F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s203_T445F.wk5d35_S131


title: T445F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s201_T445F.wk4d29_S129


title: T445F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s199_T445F.wk3_S127


title: T445F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s200_T445F.wk4d28_S128


title: T445F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s198_T445F.wk2_S126


title: T445F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s194_T445F.wk0d1_S122


title: T409F-Day-1-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s192_T409F.Day.1.Terminal_S120


title: T445F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s193_T445F.wk.1_S121


title: T409F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s190_T409F.wk5d38_S118


title: T445F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s197_T445F.wk1d10_S125


title: T409F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s188_T409F.wk4d31_S116


title: T409F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s187_T409F.wk4d29_S115


title: T409F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s184_T409F.wk2_S112


title: T409F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s189_T409F.wk5d35_S117


title: T409F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s186_T409F.wk4d28_S114


title: T409F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s185_T409F.wk3_S113


title: T409F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s182_T409F.wk1d7_S110


title: T466M-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s177_T466M.wk5d35_S90


title: T409F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s180_T409F.wk0d1_S108


title: T466M-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s176_T466M.wk4d31_S89


title: T466M-Group-VI-Necropsy

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s178_T466M.Group.VI.Necropsy_S91


title: T409F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s183_T409F.wk1d10_S111


title: T466M-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s174_T466M.wk4d28_S87


title: T466M-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s173_T466M.wk3_S86


title: T409F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s181_T409F.wk0d3_S109


title: T409F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s179_T409F.wk.1_S107


title: T466M-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s172_T466M.wk.1_S85


title: T409F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s191_T409F.wk6_S119


title: T466M-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s175_T466M.wk4d29_S88


title: T441F-Day-1-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s171_T441F.Day.1.Terminal_S84


title: T441F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s170_T441F.wk6_S83


title: T441F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s169_T441F.wk5d38_S82


title: T445F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s195_T445F.wk0d3_S123


title: T441F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s166_T441F.wk4d29_S79


title: T441F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s162_T441F.wk1d10_S75


title: T441F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s163_T441F.wk2_S76


title: T448F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s152_T448F.wk4d29_S65


title: T445F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s196_T445F.wk1d7_S124


title: T448F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s145_T448F.wk0d1_S58


title: T448F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s148_T448F.wk1d10_S61


title: T444F-Day-2-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s143_T444F.Day.2.Terminal_S56


title: T441F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s161_T441F.wk1d7_S74


title: T441F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s160_T441F.wk0d3_S73


title: T448F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s155_T448F.wk5d38_S68


title: T448F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s149_T448F.wk2_S62


title: T448F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s156_T448F.wk6_S69


title: T448F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s150_T448F.wk3_S63


title: T444F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s141_T444F.wk5d38_S54


title: T448F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s147_T448F.wk1d7_S60


title: T441F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s158_T441F.wk.1_S71


title: T448F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s154_T448F.wk5d35_S67


title: T448F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s153_T448F.wk4d31_S66


title: T448F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s146_T448F.wk0d3_S59


title: T441F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s159_T441F.wk0d1_S72


title: T441F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s165_T441F.wk4d28_S78


title: T448F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s151_T448F.wk4d28_S64


title: T441F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s167_T441F.wk4d31_S80


title: T444F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s142_T444F.wk6_S55


title: T444F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s139_T444F.wk4d31_S52


title: T444F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s140_T444F.wk5d35_S53


title: T444F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s137_T444F.wk4d28_S50


title: T448F-Day-2-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s157_T448F.Day.2.Terminal_S70


title: T444F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s138_T444F.wk4d29_S51


title: T448F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s144_T448F.wk.1_S57


title: T444F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s134_T444F.wk1d10_S47


title: T444F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s136_T444F.wk3_S49


title: T444F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s133_T444F.wk1d7_S46


title: T444F-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s135_T444F.wk2_S48


title: T444F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s132_T444F.wk0d3_S45


title: T461M-Day-2-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s129_T461M.Day.2.Terminal_S42


title: T441F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s168_T441F.wk5d35_S81


title: T444F-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s131_T444F.wk0d1_S44


title: T461M-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s126_T461M.wk5d35_S39


title: T441F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s164_T441F.wk3_S77


title: T461M-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s128_T461M.wk6_S41


title: T461M-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s124_T461M.wk4d29_S37


title: T461M-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s125_T461M.wk4d31_S38


title: T461M-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s123_T461M.wk4d28_S36


title: T461M-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s127_T461M.wk5d38_S40


title: T461M-wk2

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s121_T461M.wk2_S34


title: T461M-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s119_T461M.wk1d7_S32


title: T461M-wk0d1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s117_T461M.wk0d1_S30


title: T461M-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s120_T461M.wk1d10_S33


title: T461M-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s118_T461M.wk0d3_S31


title: T461M-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s122_T461M.wk3_S35


title: T438F-Day-1-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s115_T438F.Day.1.Terminal_S28


title: T438F-wk4d31

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s111_T438F.wk4d31_S24


title: T438F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s110_T438F.wk4d29_S23


title: T438F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s112_T438F.wk5d35_S25


title: T438F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s113_T438F.wk5d38_S26


title: T461M-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s116_T461M.wk.1_S29


title: T438F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s114_T438F.wk6_S27


title: T438F-wk4d28

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s109_T438F.wk4d28_S22


title: T444F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s130_T444F.wk.1_S43


title: T438F-wk3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s108_T438F.wk3_S21


title: T438F-wk-1

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s102_T438F.wk.1_S15


title: T438F-wk1d7

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s105_T438F.wk1d7_S18


title: T438F-wk0d3

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s104_T438F.wk0d3_S17


title: T438F-wk1d10

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s106_T438F.wk1d10_S19


title: T433F-wk6

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s100_T433F.wk6_S13


title: T433F-Day-1-Terminal

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s101_T433F.Day.1.Terminal_S14


title: T433F-wk5d38

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s099_T433F.wk5d38_S12


title: T433F-wk5d35

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s098_T433F.wk5d35_S11


title: T433F-wk4d29

description:
raw_counts_p22321.csv
normalized_counts_p22321.csv
p22321.s096_T433F.wk4d29_S9