title: GE42.male_4023_PRE_novice

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

institute: University of California San Diego

description: Library name: GE42.M_4023_PRE_N

data_processing:
Sequencing read data were converted to FASTQ format for bioinformatic processing using Lonestar6 supercomputer at the Texas Advanced Computing Center (University of Texas at Austin). Trimming of flanking forward (TGG AAT TCT CGG GTG CCA AGG) and reverse (AGA TCG GAA GAG CGT CGT GTA GGG AAA GA) adapter sequences prior to alignment was accomplished using Cutadapt (https://cutadapt.readthedocs.io). Paired reads larger than 16 nucleotides with quality scores above 20 were mapped to the human genome primary assembly (Release 47, GRCh38.p14). Reads-to-genome alignment was conducted using STAR aligner. Mapping quality was assessed using MultiQC tool.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file includes non-normalized STAR aligner counts.
Supplementary files format and content: Columns: ID — ENSEMBL gene identifiers; Colimns include non-normalized counts for each sample

source_name: whole-plasma-isolated exosome

extract_protocol:
Exosomes were isolated from human plasma samples (300-500 µl) by centrifugation at 300 x g for 10 min at 4°C to remove cell debris. Supernatants were transferred to microcentrifuge tubes, filled with 1x PBS, balanced for mass, placed in a pre-cooled Beckman Coulter Type 70.1 rotor, and centrifuged at 10,000 × g for 30 min at 4°C with maximum acceleration and gradual deceleration. Supernatants were transferred to new tubes, and exosome pellets were resuspended in 100 µl 1x PBS. Samples underwent another round of ultracentrifugation at 100,000 × g for 2 hrs. at 4°C to wash the exosome pellet. The final exosome pellets were resuspended in 150 µl 1x PBS, analyzed by nanoparticle tracking using the same protocol as with whole plasma, and stored at -80°C.
Total RNAs were purified from exosome pellets using Direct Zol RNA mini kit (Zymo Research). RNAs were eluted in 20 µl of RNAse-free water and concentrated to 5 µl using SpeedVac Vacuum Concentrator (Thermo Fisher Scientific). A total of 44 to 523 ng of exosome-specific extracellular small RNAs (exRNAs) were obtained from 28 human plasma samples. exRNA quantity and integrity were determined using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA), respectively. Small exRNA libraries were generated using NEXTFlex Small RNA-seq Kit v4 with UDIs (Revvity Inc, Waltham, MA, USA) according to modified manufacturer’s protocol to account for low exRNA concentrations in exosome samples. The strategy for small RNA libraries aimed at a range of 16-120 nucleotide (nt)-long RNA of transcripts for accurate identification and quantification of exosome-specific extracellular microRNAs, ncRNAs, and protein-coding RNAs. NEXTFLEX® 3’ Adenylated Adapter v4 was ligated at 25°C for 1h. Following 3’ Adenylated Adapter inactivation, NEXTFLEX 5’ Adapter v4 was ligated at 20°C for 1h. Reverse Transcription-First Strand Synthesis from 5’ and 3’ NEXTFLEX® Adapter Ligated RNA templates was conducted at 50°C for 1h, followed by inactivation at 90°C for 5 min. First Strand Synthesis products were purified using NEXTFLEX Cleanup Beads by two washes in 80% ethanol. RNA templates were combined with NEXTFLEX UDI Barcoded Primer Mixes v4 diluted 1:4 and amplified by PCR for 24 cycles. PCR products size selection and cleanup were done using NEXTFLEX Cleanup Beads. Small exRNA libraries were eluted from beads in 15 µl and concentrations were determined using Qubit dsDNA HS Assay (Life Technologies). DNA fragment profile in small exRNA libraries was analyzed on the Bioanalyzer 2100. RNA-seq was conducted on the NovaSeq X Plus Short-Read Sequencer (Illumina, San Diego, CA) at the Genomics Research and Technology Hub, University of California Irvine.

treatment_protocol: Whole plasma isolated from centrifugation after venous puncture phlebotomy before and after a 6-day mind-body intensive retreat featuring meditation, reconceptualization, and open label placebo healing ritual. Plasma was isolated by centrifugation at 3000 RPM for 15 min in an E8 Touch tabletop centrifuge (LW Scientific, Lawrenceville, GA), aliquoted into 1.5 mL Eppendorf tubes, and immediately frozen on dry ice. At the end of the retreat, samples were shipped to UC San Diego and stored at -80 ºC.

value: whole-plasma-isolated exosome

value: male

value: pre


title: GE42.male_4099_POST_advanced

status: Public on Dec 04 2025

type: SRA

state: CA

department: Anesthesiology

country: USA

description: Library name: GE42.M_4099_POST_E

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: Sex

tag: treatment

value: post


title: mouse sperm head, 90-week, traditional sncRNA-seq, rep1

city: Salt Lake City

first: Qi

last: Chen

state: Utah

department: Department of Human Genetics

institute: university of utah

data_processing:
The raw reads were trimmed by performing SPORTS1.1.1 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse), hg38 (for human)
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

organism: Mus musculus

source_name: sperm head

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: sperm head

tag: age

value: 90 weeks

value: The 15-50nt RNAs were sequenced with standard protocols.


title: NP15_PDDM

city: Yangsan

first: Haeseul

last: Lee

address: 49 Busandaehak-ro

country: South Korea

institute: Pusan National University

description:
Library name: NP 15
Plasma exosomal RNA from PDDM subject

data_processing:
Sequencing adapters were trimmed, and quality control was performed using standard pipelines. Reads were aligned to the human reference genome (GRCh38) using a suitable aligner, and miRNAs were annotated based on miRBase v22.1 and RNAcentral v14.0.
Assembly: GRCh38
Supplementary files format and content: The processed data files are provided in CSV format and contain RPM-normalized expression values for each small RNA species across all samples. Separate files are included for different RNA types, including miRNA, piRNA, scRNA, snoRNA, snRNA, tRNA, vaultRNA, and YRNA. Each file includes RNA identifiers and sample-wise RPM values generated from the same sequencing dataset using a consistent analysis pipeline.

source_name: plasma

extract_protocol:
Total RNA was extracted from isolated plasma exosomes using the miRNeasy Kit (Qiagen, Hilden, Germany), following the manufacturer's instructions.
Small RNA libraries were constructed using the SMARTer smRNA-Seq Kit for Illumina (Takara Bio, Shiga, Japan), according to the manufacturer’s protocol.

value: plasma


title: AB_7, Tumor_chemo_controldiet

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Avenue

department: Laboratory Medicine and Pathology

country: Canada

institute: University of Alberta

data_processing:
The TruSeq Stranded Total RNA with Ribo-ZeroTM Human/Mouse/Rat kit was used to make RNA-seq libraries, which were prepared according to the manufacturer's instructions. All samples were sequenced on an Illumina NextSeq 500 with high throughput 2x150 nt (paired-end sequencing) run.
Illumina CASAVA 1.9 with default parameters was used for base-calling and de-multiplexing. Trim Galore v.0.4.1 was used to trim the adapters. FastQC v.0.11.4 was used to check the quality of the sequenced reads. Tophat 2.0.10 and Bowtie2 were used to match the trimmed sequences to the rat reference genome. The rat genome (Rnor 6, Ensembl) was used as a reference genome and was downloaded from the iGENOME website. Sequences that were aligned were saved as .sam files, which were subsequently transformed to .bam files and used for further data processing.
Assembly: rnor6.0
Supplementary files format and content: tab-delimited file includes the raw counts for each sample

organism: Rattus norvegicus

source_name: Skeletal muscle tissue

extract_protocol:
The MagMax-96 total RNA isolation Kit (Ambion, Austin, TX, USA) was used to extract total RNA from gastrocnemius muscle (10 mg / n>5 per group) according to the manufacturer's protocol. The quantity and quality of extracted RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA Integrity Number (RIN) from Bioanalyzer were >9.0, indicating high quality of RNA isolated from muscle biopsies, and these were subjected to NGS analysis.
The TruSeq Stranded Total RNA with Ribo-ZeroTM Human/Mouse/Rat kit was used to make RNA-seq libraries, which were prepared according to the manufacturer's instructions.

tag: strain

value: Fischer 344

value: Gastrocnemius

value: Skeletal muscle tissue

value: chemo

tag: diet

value: control

value: female


title: GE42.male_4023_POST_novice

description: Library name: GE42.M_4023_POST_N


title: mouse sperm head, 70-week, traditional sncRNA-seq, rep4

value: 70 weeks


title: Splenic CD11b+ cells, M2

city: Shanghai

first: Youming

last: Zhang

address: Jimo Road 150, Shanghai 200120, PR China

country: China

institute: Shanghai East Hospitol

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ ). Clean reads were aligned to the Ensembl GRCm39 using STAR.
Assembly: Ensembl GRCm39
Supplementary files format and content: csv file includes raw counts for each sample

source_name: spleen

extract_protocol:
Total RNA was isolated from each sample using the RNAmini kit (Qiagen, Germany).
Strand-specific libraries were constructed using the TruSeq RNAsample preparation kit (Illumina, USA), and sequencing was carriedout using the Illumina Novaseq 6000 instrument.

value: spleen

tag: cell line

value: primary cells

tag: cell type

value: splenic CD11b+ cells

tag: genotype

value: WT

value: MI


title: AB_6, Tumor_chemo_controldiet


title: NP22_PD

description:
Library name: NP22
Plasma exosomal RNA from PD subject


title: AB_5, Tumor_chemo_controldiet


title: mouse sperm head, 70-week, traditional sncRNA-seq, rep3


title: NID2_PDDM

description:
Library name: NID 2
Plasma exosomal RNA from PDDM subject


title: GE42.male_4022_POST_novice

description: Library name: GE42.M_4022_POST_N

value: whole-plasma-isolated exosome

value: male

value: post


title: NP19_PD

description:
Library name: NP19
Plasma exosomal RNA from PD subject


title: NP16_PD

description:
Library name: NP16
Plasma exosomal RNA from PD subject


title: GE42.male_4099_PRE_advanced

description: Library name: GE42.M_4099_PRE_E

value: pre


title: NPDM10_PDDM

description:
Library name: NPDM 10
Plasma exosomal RNA from PDDM subject

value: plasma


title: mouse sperm head, 70-week, traditional sncRNA-seq, rep1

value: sperm head

value: The 15-50nt RNAs were sequenced with standard protocols.


title: NP24_PDDM

description:
Library name: NP 24
Plasma exosomal RNA from PDDM subject


title: GE42.male_4020_POST_advanced

description: Library name: GE42.M_4020_POST_E


title: mouse sperm head, 70-week, traditional sncRNA-seq, rep2


title: AB_3, Tumor_chemo_controldiet

value: Fischer 344

value: Gastrocnemius

value: Skeletal muscle tissue


title: GE42.male_4020_PRE_advanced

description: Library name: GE42.M_4020_PRE_E


title: AB_2, Tumor_chemo_controldiet

value: chemo

value: control

value: female


title: GE42.male_4014_PRE_advanced

description: Library name: GE42.M_4014_PRE_E


title: PY8_PD

description:
Library name: PY 8
Plasma exosomal RNA from PD subject


title: GE42.male_4022_PRE_novice

description: Library name: GE42.M_4022_PRE_N


title: GE42.male_4014_POST_advanced

description: Library name: GE42.M_4014_POST_E


title: mouse sperm head, 50-week, traditional sncRNA-seq, rep3

value: 50 weeks


title: PY7_PD

description:
Library name: PY 7
Plasma exosomal RNA from PD subject


title: PY6_PD

description:
Library name: PY 6
Plasma exosomal RNA from PD subject


title: mouse sperm head, 50-week, traditional sncRNA-seq, rep2


title: Gallbladder tumour, patient 8

city: Parktown, Johannesburg

first: Ekene

last: Nweke

state: Gauteng

address: 7 York Road

department: Surgery

country: South Africa

institute: University of the Witwatersrand

description:
Library name: Sample 10
EN-Tu12_S8_L001

data_processing:
To perform differential expression analysis, the Nextflow nf-rnaSeqCount pipeline (https://github.com/phelelani/nf-rnaSeqCount)  was used to obtain a matrix of raw read counts from the RNA-Seq data. The nf-rnaSeqCount pipeline offers a fast and efficient method for mapping raw RNA-seq reads to a reference genome and quantifying the abundance of genomic features for differential gene expression analysis 34. The resulting read count matrix (N), where Nᵢⱼ represents the number of reads assigned to gene i in sequencing experiment j 35, can be analyzed using tools such as DESeq2 36 and edgeR 37 for differential expression analysis. In this study, the read count matrix generated by the nf-rnaSeqCount pipeline was analyzed using DESeq2 (version 1.44.0) in R (version 4.4.0) to identify DEGs.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited txt file includes raw count for each sample

source_name: Gallbladder

extract_protocol:
Total RNA was extracted by following the steps described in the RNeasy mini kit (Qiagen Cat No: 74104). Total RNA underwent DNASE I (Cat No: AMPD1-1KT St. Louis, Missouri, United States) digestion to eradicate genomic DNA contamination.
RNA underwent a ribosomal RNA (rRNA) depletion step using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (Cat No: E6310S NEB Ipswich, Massachusetts, United States) as per the manufacturer’s protocol. The resulting rRNA-depleted RNA was converted to double-stranded cDNA, using the Ultra RNA Library Prep kit (NEB Cat No: 7530L).

value: Gallbladder


title: AB_1, Tumor_chemo_controldiet


title: GE42.male_1960_PRE_advanced

description: Library name: GE42.M_1960_PRE_E


title: PY3_PD

description:
Library name: PY 3
Plasma exosomal RNA from PD subject


title: AB_4, Tumor_chemo_controldiet


title: PY5_PD

description:
Library name: PY 5
Plasma exosomal RNA from PD subject


title: mouse sperm head, 50-week, traditional sncRNA-seq, rep1


title: GE42.male_1960_POST_advanced

description: Library name: GE42.M_1960_POST_E


title: GE42.female_4027_PRE_novice

description: Library name: GE42.F_4027_PRE_N


title: PY2_PD

description:
Library name: PY 2
Plasma exosomal RNA from PD subject


title: mouse sperm head, 30-week, traditional sncRNA-seq, rep3

value: 30 weeks


title: Gallbladder tumour, patient 7

description:
Library name: Sample 9
EN-Tu11_S7_L001


title: Gallbladder tumour, patient 5

description:
Library name: Sample 7
EN-Tu09_S5_L001


title: PY18_PD

description:
Library name: PY 18
Plasma exosomal RNA from PD subject


title: Gallbladder tumour, patient 4

description:
Library name: Sample 6
EN-Tu08_S4_L001


title: mouse sperm head, 50-week, traditional sncRNA-seq, rep4


title: Gallbladder tumour, patient 6

description:
Library name: Sample 8
EN-Tu10_S6_L001


title: GE42.female_4027_POST_novice

description: Library name: GE42.F_4027_POST_N


title: GE42.female_4026_PRE_novice

description: Library name: GE42.F_4026_PRE_N


title: mouse sperm head, 30-week, traditional sncRNA-seq, rep1


title: mouse sperm head, 30-week, traditional sncRNA-seq, rep2


title: Gallbladder tumour, patient 3

description:
Library name: Sample 5
EN-Tu07_S3_L001


title: pre-YHH-1_PD

description:
Library name: pre-YHH-1
Plasma exosomal RNA from PD subject


title: pre-SCA5-5_PD

description:
Library name: pre-SCA5-5
Plasma exosomal RNA from PD subject


title: GE42.female_4026_POST_novice

description: Library name: GE42.F_4026_POST_N


title: mouse sperm head, 10-week, traditional sncRNA-seq, rep4

value: 10 weeks


title: GE42.female_4021_PRE_advanced

description: Library name: GE42.F_4021_PRE_E

value: whole-plasma-isolated exosome


title: Gallbladder tumour, patient 2

description:
Library name: Sample 4
EN-Tu06_S2_L001


title: mouse sperm head, 30-week, traditional sncRNA-seq, rep4


title: SCA3-pre-4-B_PD

description:
Library name: SCA3-pre-4-B
Plasma exosomal RNA from PD subject


title: GE42.female_4021_POST_advanced

description: Library name: GE42.F_4021_POST_E


title: mouse sperm head, 10-week, traditional sncRNA-seq, rep2


title: GE42.female_4019_PRE_advanced

description: Library name: GE42.F_4019_PRE_E


title: mouse sperm head, 10-week, traditional sncRNA-seq, rep1


title: A8_normal

description:
Library name: A8
Plasma exosomal RNA from normal subject


title: A7_normal

description:
Library name: A7
Plasma exosomal RNA from normal subject


title: Normal Gallbladder tissue, patient 2

description:
Library name: Sample 2
EN-GB02_S10_L001


title: Normal Gallbladder tissue, patient 1

description:
Library name: Sample 1
EN-GB01_S9_L001


title: GE42.female_4019_POST_advanced

description: Library name: GE42.F_4019_POST_E


title: mouse sperm head, 90-week, PANDORA-seq, rep3

value: 90 weeks

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: GE42.female_4018_PRE_advanced

description: Library name: GE42.F_4018_PRE_E

value: pre


title: mouse sperm head, 90-week, PANDORA-seq, rep2


title: GE42.female_4018_POST_advanced

description: Library name: GE42.F_4018_POST_E

value: post


title: Microbiota of stool DM43 - Healthy control

city: Florence

first: Sara

last: Bertorello

address: Viale Gaetano Pieraccini 6

country: Italy

institute: University of Florence

description:
Library name: DM43
16s rRNA v3-v4 sequencing of human stool

library_source: genomic

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 –verbose
qiime demux summarize  --i-data trim-seqs.qza --o-visualization quality.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 230 --p-trunc-len-r 215 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x INDEXED_GRCh38_analysis_set_BOWTIE2/GRCh38_noalt_as  -U dna-sequences.fasta --un filtered.fasta
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R software for further analysis
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: otu_table.csv: CSV text file containing the abundance table
Supplementary files format and content: tax_table.csv: CSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: 16S rRNA-seq

molecule: genomic DNA

source_name: Stool

extract_protocol:
Total DNA was extracted from stools and brain biopsis, amplified to collect amplicons of variable V3–V4 region of the bacterial 16S rRNA gene were sequenced in paired-end mode (2 × 300 cycles) with Illumina Miseq.
For detailed library preparation please contact IGA Technology Services (Udine, Italy)

value: Stool

tag: sample group

value: Healthy control


title: A5_normal

description:
Library name: A5
Plasma exosomal RNA from normal subject

value: plasma


title: mouse sperm head, 90-week, PANDORA-seq, rep1

value: sperm head


title: Microbiota of stool DM44 - Healthy control

description:
Library name: DM44
16s rRNA v3-v4 sequencing of human stool


title: A4_normal

description:
Library name: A4
Plasma exosomal RNA from normal subject


title: SCA4-pre-3-B_PD

description:
Library name: SCA4-pre-3-B
Plasma exosomal RNA from PD subject


title: mouse sperm head, 10-week, traditional sncRNA-seq, rep3

value: The 15-50nt RNAs were sequenced with standard protocols.


title: GE42.female_2119_PRE_novice

description: Library name: GE42.F_2119_PRE_N


title: GE42.female_2119_POST_novice

description: Library name: GE42.F_2119_POST_N


title: mouse sperm head, 70-week, PANDORA-seq, rep3

value: 70 weeks


title: A3_normal

description:
Library name: A3
Plasma exosomal RNA from normal subject


title: mouse sperm head, 70-week, PANDORA-seq, rep4


title: Microbiota of stool DM40 - Healthy control

description:
Library name: DM40
16s rRNA v3-v4 sequencing of human stool


title: GE42.female_1580_PRE_advanced

description: Library name: GE42.F_1580_PRE_E


title: mouse sperm head, 70-week, PANDORA-seq, rep2


title: A6_normal

description:
Library name: A6
Plasma exosomal RNA from normal subject


title: A2_normal

description:
Library name: A2
Plasma exosomal RNA from normal subject


title: mouse sperm head, 70-week, PANDORA-seq, rep1


title: A1_normal

description:
Library name: A1
Plasma exosomal RNA from normal subject


title: Microbiota of stool DM38 - Healthy control

description:
Library name: DM38
16s rRNA v3-v4 sequencing of human stool


title: NAB8_normal

description:
Library name: NAB 8
Plasma exosomal RNA from normal subject


title: Gallbladder tumour, patient 1

description:
Library name: Sample 3
EN-Tu05_S1_L001


title: mouse sperm head, 50-week, PANDORA-seq, rep4


title: PAOA

first: Liang

last: Li

state: Shanghai

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
Hi-C reads were aligned to the hg38 genome using HiCpro .
tadlist were generated using the Rpackage GENOVA, TADs were called using Rpackage GENOVA.
Assembly: hg38
Supplementary files format and content: csv

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Hi-C assays were performed by Shanghai Jiayin Biotechnology Co., Ltd, according to the standard Hi-C protocol with modifications.
The Hi-C library was prepared using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: HepG2 cell lines were treated with 1% BSA (fatty acid-free) DMEM cell culture medium containing 120 μM palmitic acid and 240 μM oleic acid (for PA+OA group) or v/v 1/1000 DMSO (for mock group) for 48 hrs

value: Liver cancer cell


title: NAB42_normal

description:
Library name: NAB 42
Plasma exosomal RNA from normal subject


title: Microbiota of stool DM42 - Healthy control

description:
Library name: DM42
16s rRNA v3-v4 sequencing of human stool


title: Microbiota of stool DM36 - Healthy control

description:
Library name: DM36
16s rRNA v3-v4 sequencing of human stool


title: Microbiota of stool DM37 - Healthy control

description:
Library name: DM37
16s rRNA v3-v4 sequencing of human stool


title: DMSO


title: NAB4_normal

description:
Library name: NAB 4
Plasma exosomal RNA from normal subject


title: Microbiota of stool DM41 - Healthy control

description:
Library name: DM41
16s rRNA v3-v4 sequencing of human stool


title: mouse sperm head, 50-week, PANDORA-seq, rep3


title: Mbovis-0.5_2

city: Seattle

first: Hazem

last: Abdelaal

state: WA

address: 1900 9th street

institute: Seattle Children's Researcch Institute

description: Library name: Sample 12

data_processing:
Raw reads underwent quality control with FastQC and adapter and quality trimming with Trimmomatic. Reads were aligned to the M. bovis AF2122/97 reference using HISAT2. Gene level quantitation used reads per kilobase per million. Normalization used the median of ratios method in DESeq2. Differential expression was assessed in R with DESeq2 with Benjamini and Hochberg adjustment and a false discovery rate threshold p less than zero point zero five, with genes under five counts removed prior to testing. Variance stabilized counts were used for weighted gene co expression network analysis.
Assembly: M. bovis AF2122/97 reference
Supplementary files format and content: gene level quantitation values, normalized counts, and differential expression results that include log base two fold change and adjusted p values. The study also generated variance stabilized counts for network analysis modules. At minimum, provide for GEO: a gene by sample count matrix, the corresponding normalized count matrix, and a differential expression results table with log base two fold change, Wald or likelihood ratio statistic as applicable, raw p and adjusted p values. If available, include RPKM values used for visualization

organism: Mycobacterium

source_name: prokayotic

extract_protocol:
For in vitro samples: pellets from frozen cultures were processed with TRIzol reagent. Pellets were resuspended in TRIzol with one percent polyacryl carrier, transferred to screw cap tubes with zirconia or silica beads, and disrupted in a bead beater. Total RNA was isolated per manufacturer instructions and treated with DNase I, followed by TURBO DNase until PCR negative. For murine lung tissues: lungs were homogenized in TRIzol, centrifuged three thousand g for five minutes at four Celsius, and RNA purified as above
non

value: prokayotic

value: Mycobacterium bovis

tag: batch

value: non


title: NAB18_normal

description:
Library name: NAB 18
Plasma exosomal RNA from normal subject


title: mouse sperm head, 50-week, PANDORA-seq, rep1

value: 50 weeks


title: Mbovis-0.5_1

description: Library name: Sample 11


title: Microbiota of stool DM34 - Healthy control

description:
Library name: DM34
16s rRNA v3-v4 sequencing of human stool


title: Microbiota of stool DM39 - Healthy control

description:
Library name: DM39
16s rRNA v3-v4 sequencing of human stool


title: mouse sperm head, 50-week, PANDORA-seq, rep2


title: GE42.female_1580_POST_advanced

description: Library name: GE42.F_1580_POST_E

value: female


title: NAB13_normal

description:
Library name: NAB 13
Plasma exosomal RNA from normal subject


title: Mbovis-2_2

description: Library name: Sample 10


title: Microbiota of stool DM35 - Healthy control

description:
Library name: DM35
16s rRNA v3-v4 sequencing of human stool


title: Microbiota of stool DM33 - Healthy control

description:
Library name: DM33
16s rRNA v3-v4 sequencing of human stool


title: mouse sperm head, 30-week, PANDORA-seq, rep4

value: 30 weeks


title: Mbovis-2_1

description: Library name: Sample 9


title: SCA-normal-2_normal

description:
Library name: SCA-normal-2
Plasma exosomal RNA from normal subject


title: mouse sperm head, 30-week, PANDORA-seq, rep3


title: Microbiota of stool DM32 - Malignant tumor

description:
Library name: DM32
16s rRNA v3-v4 sequencing of human stool

value: Malignant tumor


title: Mbovis-1_2

description: Library name: Sample 8


title: Microbiota of stool DM31 - Malignant tumor

description:
Library name: DM31
16s rRNA v3-v4 sequencing of human stool


title: mouse sperm head, 30-week, PANDORA-seq, rep2

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: Mbovis-1_1

description: Library name: Sample 7


title: mouse sperm head, 30-week, PANDORA-seq, rep1


title: Microbiota of stool DM30 - Benign tumor

description:
Library name: DM30
16s rRNA v3-v4 sequencing of human stool

value: Benign tumor


title: BCG-0.5_2

description: Library name: Sample 6

value: Mycobacterium bovis BCG


title: SCA-cont5-5_normal

description:
Library name: SCA-cont5-5
Plasma exosomal RNA from normal subject


title: Microbiota of stool DM29 - Malignant tumor

description:
Library name: DM29
16s rRNA v3-v4 sequencing of human stool

value: Stool


title: BCG-0.5_1

description: Library name: Sample 5


title: GATA2_bio_rep3

city: L'Hospitalet de Llobregat

first: Alessandra

last: Giorgetti

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: PCMRC

country: Spain

institute: IDIBELL

data_processing:
Analysis of data was conducted using the nf-core/atacseq (10.5281/zenodo.2634132) pipeline implemented in Nextflow (34556866). This pipeline integrates various software tools for quality control, read alignment, peak calling, and differential accessibility analysis. Raw sequencing reads were pre-processed by adapter trimming using Trim Galore!(https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-quality bases. Subsequently, read mapping to the hg38 reference genome was performed with BWA (19451168). SAMtools (19505943) was employed for sorting, indexing, and filtering of aligned reads. Normalized coverage tracks were generated using BEDTools (20110278) and bedGraphToBigWig (20639541). Peak calling was performed using MACS2 (18798982), and annotation relative to gene features was conducted with HOMER (20513432). Consensus peak sets were created using BEDTools. Quantification of reads was achieved using featureCounts (24227677), and quality control assessment was performed using MultiQC (27312411) and FastQC (27312411). Differential accessibility analysis was conducted with DESeq2 (25516281) within the R programming environment. Tornado plots were generated using Deeptools (27079975) computeMatrix and plotHeatmaps tools. An adjusted P value ≤0.05 was used as the significance threshold for the identification of differentially accessible regions.
Assembly: hg38
Supplementary files format and content: bigWig files containing peak calling results

source_name: Cord blood hematopoietic stem cells

growth_protocol: Cells were cultured on SFM StemPro-34 + 1%P/S + 1%Glu supplemented with early hematopoietic cytokines (100 ng/ml SCF , 100ng/ml FLT3L, 20ng/ml IL-3,  20ng/ml IL-6, 100ng/ml TPO

extract_protocol:
we spun 50,000 cells at 500 × g for 5 minutes, followed by a wash using 50 μL of cold 1x PBS and centrifugation at 500 × g for 5 minutes. Cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 × g for 10 minutes using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed angle centrifuge and carefully pipetted away from the pellet after centrifugations. Transpose and purify: Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Qiagen Minelute kit
Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 (see table below), using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. To reduce GC and size bias in our PCR we monitored the PCR reaction using qPCR in order to stop amplification prior to saturation. To do this, we amplified the full libraries for 5 cycles, after 5 cycles we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6x. We ran this reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles

value: Cord blood hematopoietic stem cells


title: Microbiota of stool DM28 - Benign tumor

description:
Library name: DM28
16s rRNA v3-v4 sequencing of human stool


title: BCG-2_2

description: Library name: Sample 4


title: mouse sperm head, 10-week, PANDORA-seq, rep2

value: 10 weeks


title: GATA2_bio_rep1


title: Microbiota of stool DM27 - Malignant tumor

description:
Library name: DM27
16s rRNA v3-v4 sequencing of human stool


title: GATA2_bio_rep2


title: BCG-2_1

description: Library name: Sample 3


title: CTRL_bio_rep3

value: WT


title: mouse sperm, 90-week, traditional sncRNA-seq, rep4

source_name: sperm

value: sperm

value: 90 weeks

value: The 15-50nt RNAs were sequenced with standard protocols.


title: Microbiota of stool DM26 - Malignant tumor

description:
Library name: DM26
16s rRNA v3-v4 sequencing of human stool


title: CTRL_bio_rep2


title: Microbiota of stool DM25 - Malignant tumor

description:
Library name: DM25
16s rRNA v3-v4 sequencing of human stool


title: BCG-1_2

description: Library name: Sample 2

value: prokayotic


title: SCA-normal-1-K_normal

description:
Library name: SCA-normal-1-K
Plasma exosomal RNA from normal subject

value: plasma


title: mouse sperm head, 10-week, PANDORA-seq, rep1

value: sperm head


title: mouse sperm head, 10-week, PANDORA-seq, rep4


title: Microbiota of stool DM24 - Benign tumor

description:
Library name: DM24
16s rRNA v3-v4 sequencing of human stool


title: CTRL_bio_rep1


title: mouse sperm, 90-week, traditional sncRNA-seq, rep2


title: AML_day12_Rep4, CAGE-seq

city: Huddinge

first: Anna

last: Palau

address: Hälsovägen 9

country: Sweden

institute: Karolinska Institutet

data_processing:
1. Extracting read1 reads by using read2 "LQ-ssCAGE" barcode sequence. (home made script). 2. Adapter trimming by using fastx software. 3. Filtering rRNA reads by using rRNAdust software. 4. Alignment reads to genome reference (GRCh38) by using STAR.    5. Counting cage transcript start-site "CTSS" from bam file by using home made script.
Assembly: GRCh38
Supplementary files format and content: .ctss.bed files
Library strategy: CAGE-seq

extract_protocol:
Total RNA was extracted from cells using miRNeasy Micro Kit (Qiagen).
LQ-ssCAGE(Low Quantity single strand CAGE protocol) library. https://www.protocols.io/view/low-quantity-single-strand-cage-protocol-5jyl8md29g2w/v1 https://link.springer.com/protocol/10.1007/978-1-0716-1597-3_4

value: differentiated HSPC from iPSC

tag: time

tag: fraction

value: capped RNAs


city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description:
Library name: EBNA1-2
HEK293 cells transfected with Flag-EBNA1 vector for 48 hours, sample 2

data_processing:
In order to ensure the reliability of information analysis results, the original sequencing data needs to be filtered so as to obtain clean reads, which are stored in the FASTQ format.
NanoFilt is used to filter the original fastq data to obtain valid data for subsequent analysis, and SeqKit is used to conduct data statistics.
The filtered full-length sequences are aligned with the reference genes by minimap2, and the alignment results are statistically analyzed using samtools.
The transcriptome sequencing reads are aligned with the human genome sequence and visualized using the Integrative Genomics Viewer (IGV).
Assembly: human genome GRCh38
Supplementary files format and content: The data alignment result files for each sample after processing are usually in BAM format.

source_name: human embryonic kidney

growth_protocol: The human HEK293 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum.

extract_protocol:
For RNA-seq, mRNA was enriched by polyA(+) selection.
Total RNA was qualitatively examined using Nanodrop and Agilent 2000. The construction of long-read sequencing for cDNA libraries was performed using the Oxford Nanopore Technologies PCR-amplified cDNA kit (SQK-PCS109) at Benagene Company (Wuhan, China). Specifically, full-length cDNA libraries were constructed from poly(A)+ mRNA using the cDNA-PCR Sequencing kit. Subsequently, the cDNA was PCR-amplified for 13–14 cycles with barcoded adapters from the Oxford Nanopore PCR Barcoding kit (SQK-PBK004).
Then the cell RNA was sequenced by a PromethION platform (P48-seq, the third generation sequencing).
the 1D sequencing adapter was ligated to the cDNA before loading onto an R9.4.1 FLO PRO002 flow cell for sequencing on a PromethION platform. The raw data of Nanopore sequencing downstream data are quality controlled, and the obtained sequences are filtered for low-quality data to obtain effective data. Based on the filtered data, the high-quality full-length sequences are obtained. The full-length sequences are compared with the reference genome sequences for visualization.

treatment_protocol: HEK293 cells were transfected with either Flag-EBNA1 vector or empty vector (NC)  for 48 hours.

value: human embryonic kidney

value: epithelial cells

value: Transfected with EBNA1

value: transfeced for 48 h


title: mouse sperm, 90-week, traditional sncRNA-seq, rep3


description:
Library name: EBNA1-1
HEK293 cells transfected with Flag-EBNA1 vector for 48 hours, sample 1


title: Microbiota of stool DM23 - Malignant tumor

description:
Library name: DM23
16s rRNA v3-v4 sequencing of human stool

value: Malignant tumor


title: BCG-1_1

description: Library name: Sample 1

value: Mycobacterium bovis BCG

value: non


title: mouse sperm head, 10-week, PANDORA-seq, rep3

value: 10 weeks

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


description:
Library name: NC-2
HEK293 cells transfected with empty vector (NC) for 48 hours, sample 2

value: Negative control


title: mouse sperm, 90-week, traditional sncRNA-seq, rep1

value: sperm

value: 90 weeks


title: AML_day10_Rep4, CAGE-seq


title: ctrl_day12_Rep4, CAGE-seq


title: Microbiota of stool DM22 - Malignant tumor

description:
Library name: DM22
16s rRNA v3-v4 sequencing of human stool

value: Stool


title: Microbiota of stool DM21 - Benign tumor

description:
Library name: DM21
16s rRNA v3-v4 sequencing of human stool

value: Benign tumor


title: mouse sperm, 70-week, traditional sncRNA-seq, rep4

value: 70 weeks

value: The 15-50nt RNAs were sequenced with standard protocols.


title: mouse sperm, 70-week, traditional sncRNA-seq, rep3


title: Microbiota of brain DM9 - Benign tumor

description:
Library name: DM9
16s  rRNA v3-v4 sequencing of human brain

source_name: Brain

value: Brain


title: AML_day8_Rep4, CAGE-seq

value: differentiated HSPC from iPSC

value: capped RNAs


title: mouse sperm, 70-week, traditional sncRNA-seq, rep2


title: RAT-FIA-3_S84

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

institute: Texas A&M University

description:
Library name: RAT-FIA-3_S84
normcounts_rat.csv
qc_hash_rat.csv

data_processing:
The gene count matrices were generated from paired-end reads with 2 lanes per sample with ~150 base pairs (bp).
The reads from the 2 lanes for each sample were combined to generate a single fastq file.
Reads were quality trimmed using fastp (version 0.23.2) with the following steps: (1) automatic detection of adapter sequences for paired-end reads, (2) trimming of homopolymer stretches, and (3) removal of bases with Phred quality scores below 20 (Chen et al., 2018).
Reads were aligned to the species-specific genome assembly using STAR version 2.7.10b (Dobin et al. 2013). Aligned reads were sorted with SAMtools version 1.14 (Danecek et al. 2021), and gene-level counts were generated using HTSeq version 2.0.1 (Anders et al. 2014).
Samples with fewer than 1 million total counts or with uniquely mapped reads below 50% were excluded from further analysis. For transcript-level quality control, transcripts that were not expressed across the entire sample set for each species were removed. The Bioconductor package DESeq2 (Love et al., 2014) was used to perform within-species normalization and differential expression analysis across all experimental conditions.
Assembly: Reads from dog, monkey, human, and rat were mapped to the ROS_Cfam_1.0, Macaca_fascicularis_6.0, GRCh38, and mRatBN7 genome assemblies, respectively, using STAR. Gene annotations from Ensembl GTF files corresponding to each assembly were used for quantification.
Supplementary files format and content: normcounts_* files contain normalized count data using DESeq2 R package (Love et al., 2014) for each species
Supplementary files format and content: qc_hash* files contain meta data of the qc-passed samples for each species

source_name: hepatocytes

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) and the Direct-zol RNA Miniprep (Zymo, USA) following the manufacturer’s protocol with slight modifications detailed here. MPS Scaffolds from each experiment were preserved in RNAlater at -80°C until RNA extraction. On the day of extraction, samples were thawed at room temperature, and each scaffold was cut into two pieces before transferring to a 1.5 mL microcentrifuge tube. Next, 700 µL of TRIzol reagent was added to the samples, which were then incubated at room temperature for 20 minutes. During incubation, the samples were vortexed for 30 seconds every 5 minutes to ensure complete lysis. The scaffolds were removed from the microcentrifuge and the RNA was precipitated using equal volume of 100% molecular grade ethanol, then transferred to a Zymo-Spin™ IICR column. The remainder of the extraction was performed according to the standard protocol. RNA was eluted in 60 uL of DNAase/RNAse free water.
mRNA was isolated from 150ng total RNA using a Nextflex Poly-A Selection kit. Unique dual indexed cDNA libraries were prepared on a Sciclone NGSx liquid handler, using a Nextflex Rapid Directional RNA 2.0 kit miniaturized to 2/5 reaction volume. Optimal PCR cycle count was empirically determined to be 17 by cycling a pool of samples to the plateau phase on a real-time PCR machine. The concentration of libraries was determined using a Molecular Devices (San Jose, CA) Spectramax M2 fluorescent plate reader and Thermo Fisher Scientific (Waltham, MA) Picogreen Assay. Libraries were then pooled by equal mass using a Janus Mini liquid handler. The libraries were pooled by equal mass. The pool was sequenced on a Illumina (San Diego, CA) NovaSeq X+ 1.5B flowcell using the 2x150 bp recipe.

value: hepatocytes

value: fialuridine


title: Microbiota of brain DM8 - Benign tumor

description:
Library name: DM8
16s  rRNA v3-v4 sequencing of human brain


title: ctrl_day8_Rep4, CAGE-seq


title: Primary human and mouse cerebellar NEPs neurosphere cultures

city: Cambridge

first: Jens

middle: Bager

last: Christensen

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
Library name: primary_NEP_cultures
CellPlex-IDs (see protocols): CMO301-CMO310 human, CMO311-CMO312 mouse

library_source: transcriptomic single cell

data_processing:
The data was aligned using CellRanger (v8.0.1) multi, aligning to both GRCm39 and GRCh38. Each CellRanger output is available as processed data.
Assembly: GRCm39 and GRCh38.
Supplementary files format and content: Default CellRanger output containing barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz and the assignment_confidence_table.csv. Aligned to GRCm39 (Mm_) and GRCh38 (Hs_)

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: Primary nestin-expressing progenitor neuosphere cultures establised from developing mouse or human cerebella

growth_protocol: Neural stem cell media with EGF and FGF in suspension

extract_protocol:
Primary NEP neurospheres were establised from postnatal day 1 old Nes-Cfp/+ or Swiss webster mouse cerebella, or fetal human cerebella obtained from HDRB and BRC (see details for the manuscript). Briefly, the this tissue was dissociated using Accutase (ThermoFisher, #A1110501) for 10-20 minutes at 37°C.Cells were filtered with a 40 µM nylon filter (Merck, #CLS352340) after dissociation to remove debris. Once a single cell suspension was obtained, cells were washed with NSC media (Neurobasal (ThermoFisher, #10888022) with 1X B27 (ThermoFisher, #A3353501), 1X N2 (ThermoFisher, #11520536), 2mM L-glutamine (ThermoFisher, #A2916801), 1X non-essential amino acids (ThermoFisher, 11140035) and 100 U/mL penicillin-streptomycin (ThermoFisher, #15140122)) and plated onto ultra-low attachment plates ~100,000 cells/mL density. Cultures were maintained with 20 ng/mL of EGF (Fisher Scientific, #PMG8041) and FGF2 (Qkine, #Qk042-0500) (or human EGF (QKINE, #Qk011-0100) and FGF2 (QKINE, #Qk027-0100) for human cultures). Growth factors were supplemented every other day and media was changed weekly.  For scRNA-seq analysis, the primary neurosphere cultres (passages <20) were dissociated  with Accutase and washed once in NSC media. The cell suspensions were filtered (Corning, #352235) and pelleted at 500g for 5 minutes at room temperature followed by a washed with 1x PBS + 0.04% bovine serum albumin. The single cell RNA-sequencing was performed on Chromium X/iX (10X Genomics) with the Next-GEM 3′ v3.1 abd CellPlex multiplexing (10X Genomics). A final amount of ~2000cells/sample were aimed when loading based on manufacturer's instructions. Below is a list of the samples and the CellPlex Oligos used for multiplexing.  Sample  Age     ID BRC_2584        9w      CMO301 BRC_2583        9w 4d   CMO302 BRC_2591        10w 5d  CMO303 BRC_2593        12w     CMO304 HDBR_18265      12w     CMO305 HDBR_18294      12w     CMO306 HDBR_18267      13w     CMO307 HDBR_18285      13w     CMO308 HDBR_18290      15w     CMO309 HDBR_18275      17w     CMO3010 SW   P1      CMO311 Nes-Cfp      P1      CMO312
cDNA amplification and library preparation was performed according to manufacturer’s guidelines (10X Genomics Next-GEM 3' 3.1v) by Cambridge Stem Cell Institute NGS core. 28 base paired-end sequencing was performed on a NovaSeq X at Cancer Research UK Cambridge Institute.


title: RAT-FIA-2_S83

description:
Library name: RAT-FIA-2_S83
normcounts_rat.csv
qc_hash_rat.csv


title: Microbiota of brain DM7 - Malignant tumor

description:
Library name: DM7
16s  rRNA v3-v4 sequencing of human brain

value: Malignant tumor


title: mouse sperm, 50-week, traditional sncRNA-seq, rep4

value: 50 weeks


title: AML_day0_Rep4, CAGE-seq

value: iPSC


description:
Library name: NC-1
HEK293 cells transfected with empty vector (NC) for 48 hours, sample 1

value: human embryonic kidney

value: epithelial cells

value: transfeced for 48 h


title: Microbiota of brain DM6 - Malignant tumor

description:
Library name: DM6
16s  rRNA v3-v4 sequencing of human brain


title: Microbiota of brain DM5 - Benign tumor

description:
Library name: DM5
16s  rRNA v3-v4 sequencing of human brain


title: AML_day12_Rep3, CAGE-seq


title: RAT-D8-2_S32

description:
Library name: RAT-D8-2_S32
normcounts_rat.csv
qc_hash_rat.csv


title: mouse sperm, 50-week, traditional sncRNA-seq, rep3

value: sperm


title: Microbiota of brain DM4 - Benign tumor

description:
Library name: DM4
16s  rRNA v3-v4 sequencing of human brain


title: Microbiota of brain DM3 - Benign tumor

description:
Library name: DM3
16s  rRNA v3-v4 sequencing of human brain


title: mouse sperm, 50-week, traditional sncRNA-seq, rep1


title: RAT-D8-1_S31

description:
Library name: RAT-D8-1_S31
normcounts_rat.csv
qc_hash_rat.csv


title: AML_day10_Rep3, CAGE-seq


title: ctrl_day10_Rep4, CAGE-seq


title: mouse sperm, 70-week, traditional sncRNA-seq, rep1


title: ctrl_day12_Rep3, CAGE-seq


title: mouse sperm, 30-week, traditional sncRNA-seq, rep3

value: 30 weeks


title: Microbiota of brain DM2 - Benign tumor

description:
Library name: DM2
16s  rRNA v3-v4 sequencing of human brain


title: RAT-D4-2_S29

description:
Library name: RAT-D4-2_S29
normcounts_rat.csv
qc_hash_rat.csv


title: RAT-D4-3_S30

description:
Library name: RAT-D4-3_S30
normcounts_rat.csv
qc_hash_rat.csv


title: Microbiota of brain DM15 - Malignant tumor

description:
Library name: DM15
16s  rRNA v3-v4 sequencing of human brain


title: ctrl_day10_Rep3, CAGE-seq


title: mouse sperm, 30-week, traditional sncRNA-seq, rep2


title: RAT-D8-3_S33

description:
Library name: RAT-D8-3_S33
normcounts_rat.csv
qc_hash_rat.csv


title: Microbiota of brain DM14 - Malignant tumor

description:
Library name: DM14
16s  rRNA v3-v4 sequencing of human brain


title: AML_day8_Rep3, CAGE-seq


title: ctrl_day0_Rep4, CAGE-seq


title: Microbiota of brain  DM13 - Malignant tumor

description:
Library name: DM13
16s  rRNA v3-v4 sequencing of human brain


title: mouse sperm, 50-week, traditional sncRNA-seq, rep2


title: RAT-D14-3_S36

description:
Library name: RAT-D14-3_S36
normcounts_rat.csv
qc_hash_rat.csv


title: mouse sperm, 10-week, traditional sncRNA-seq, rep4

value: 10 weeks


title: RAT-FIA-1_S82

description:
Library name: RAT-FIA-1_S82
normcounts_rat.csv
qc_hash_rat.csv


title: ctrl_day8_Rep3, CAGE-seq


title: AML_day0_Rep3, CAGE-seq


title: RAT-D4-1_S28

description:
Library name: RAT-D4-1_S28
normcounts_rat.csv
qc_hash_rat.csv


title: RAT-D14-2_S35

description:
Library name: RAT-D14-2_S35
normcounts_rat.csv
qc_hash_rat.csv


title: Microbiota of brain DM12 - Benign tumor

description:
Library name: DM12
16s  rRNA v3-v4 sequencing of human brain

value: Benign tumor


title: mouse sperm, 30-week, traditional sncRNA-seq, rep4


title: mouse sperm, 10-week, traditional sncRNA-seq, rep3


title: Microbiota of brain DM11 - Benign tumor

description:
Library name: DM11
16s  rRNA v3-v4 sequencing of human brain


title: ctrl_day0_Rep3, CAGE-seq


title: RAT-D14-1_S34

description:
Library name: RAT-D14-1_S34
normcounts_rat.csv
qc_hash_rat.csv


title: mouse sperm, 10-week, traditional sncRNA-seq, rep2


title: RAT-D0-3_S27

description:
Library name: RAT-D0-3_S27
normcounts_rat.csv
qc_hash_rat.csv


title: mouse sperm, 10-week, traditional sncRNA-seq, rep1


title: mouse sperm, 30-week, traditional sncRNA-seq, rep1


title: Microbiota of brain DM1 - Benign tumor

description:
Library name: DM1
16s rRNA v3-v4 sequencing of human brain


title: AML_day12_Rep2, CAGE-seq


title: RAT-D0-2_S26

description:
Library name: RAT-D0-2_S26
normcounts_rat.csv
qc_hash_rat.csv


title: Microbiota of brain DM10 - Benign tumor

description:
Library name: DM10
16s rRNA v3-v4 sequencing of human brain


title: ctrl_day12_Rep2, CAGE-seq


title: RAT-D0-1_S25

description:
Library name: RAT-D0-1_S25
normcounts_rat.csv
qc_hash_rat.csv


title: mouse sperm, 90-week, PANDORA-seq, rep3

value: 90 weeks

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: Fetus chorionic villus sample CMA-20250719

type: genomic

city: Hefei

state: Anhui

address: No. 15, Yimin Street, Shushan District, Hefei City, Anhui Province

institute: Anhui Women and Children's medical center

description: Hybridized to CytoScan 750K array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were washed and stained on an Affymetrix Fluidics Station 450Dx using the appropriate protocols and then scanned using the Affymetrix GeneChip Scanner 3000 Dx v.2 system. The scanning process was controlled by the Affymetrix GeneChip Command Console (AGCC) software to acquire fluorescent signal intensities from the array probes.

data_processing:
Raw CEL files were processed using the Chromosome Analysis Suite (ChAS) software (version 4.4.0.63) from Thermo Fisher Scientific with reference to the GRCh37 (hg19) genome assembly. Copy number variants (CNVs) were called with the following thresholds: gains required a minimum of 25 markers and a size of 50 kbp; losses required a minimum of 25 markers and a size of 25 kbp. The overlap setting for both was set to 100%. LOH (Loss of Heterozygosity) regions were also analyzed using the software's default algorithm. All analysis was performed using the settings for the CytoScan 750K array.
Genotype Call (SNP call): AA, AB, BB, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Fetus chorionic villus

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from chorionic villus samples using the TIANamp micro DNA Kit (catalog #DP316) according to the manufacturer's instructions. DNA concentration and quality were assessed using a Nanodrop spectrophotometer and agarose gel electrophoresis.

tag: group

value: Ultrasound abnormalities


title: Fetus chorionic villus sample CMA-20251119

description: Hybridized to CytoScan 750K array


title: RAT-CPZ-3_S78

description:
Library name: RAT-CPZ-3_S78
normcounts_rat.csv
qc_hash_rat.csv

value: chlorpromazine


title: Fetus chorionic villus sample CMA-20250718

description: Hybridized to CytoScan 750K array

value: history of complicated obstetrics


title: AML_day8_Rep2, CAGE-seq

value: differentiated HSPC from iPSC

value: capped RNAs


title: mouse sperm, 90-week, PANDORA-seq, rep2


title: mouse sperm, 90-week, PANDORA-seq, rep1


title: ctrl_day10_Rep2, CAGE-seq


title: RAT-CON-3_S75

description:
Library name: RAT-CON-3_S75
normcounts_rat.csv
qc_hash_rat.csv

value: hepatocytes

value: DMSO control


title: Fetus chorionic villus sample CMA-20250070

description: Hybridized to CytoScan 750K array


title: Fetus chorionic villus sample CMA-20250023

description: Hybridized to CytoScan 750K array

value: high-risk first trimester serum screening test results


title: RAT-CON-1_S73

description:
Library name: RAT-CON-1_S73
normcounts_rat.csv
qc_hash_rat.csv


title: AML_day0_Rep2, CAGE-seq

value: iPSC


title: mouse sperm, 70-week, PANDORA-seq, rep4

value: 70 weeks


title: Fetus chorionic villus sample CMA-20242918

description: Hybridized to CytoScan 750K array


title: RAT-BOS-3_S81

description:
Library name: RAT-BOS-3_S81
normcounts_rat.csv
qc_hash_rat.csv

value: bosentan


title: ctrl_day0_Rep2, CAGE-seq


title: mouse sperm, 90-week, PANDORA-seq, rep4

value: sperm


title: mouse sperm, 70-week, PANDORA-seq, rep3


title: AML_day12_Rep1, CAGE-seq


title: RAT-BOS-2_S80

description:
Library name: RAT-BOS-2_S80
normcounts_rat.csv
qc_hash_rat.csv


title: mouse sperm, 70-week, PANDORA-seq, rep2


title: AML_day10_Rep2, CAGE-seq


title: Fetus chorionic villus sample CMA-20242660

description: Hybridized to CytoScan 750K array


title: Fetus chorionic villus sample CMA-20242418

description: Hybridized to CytoScan 750K array


title: RAT-BOS-1_S79

description:
Library name: RAT-BOS-1_S79
normcounts_rat.csv
qc_hash_rat.csv


title: AML_day10_Rep1, CAGE-seq


title: ctrl_day8_Rep2, CAGE-seq


title: mouse sperm, 50-week, PANDORA-seq, rep4

value: 50 weeks


title: mouse sperm, 50-week, PANDORA-seq, rep3


title: Fetus chorionic villus sample CMA-20242492

description: Hybridized to CytoScan 750K array


title: mouse sperm, 70-week, PANDORA-seq, rep1


title: Fetus chorionic villus sample CMA-20242343

description: Hybridized to CytoScan 750K array


title: mouse sperm, 50-week, PANDORA-seq, rep2


title: AML_day8_Rep1, CAGE-seq


title: ctrl_day12_Rep1, CAGE-seq


title: P5 Smad4 Mut 2

city: New Orleans

first: Styder

last: Meadows

state: LA

address: 6400 Freret St, 2000 Stern

department: Cell and Molecular Biology

institute: Tulane University

description:
Library name: Sample 5
Column name in P5_Smad4_iLEC_combined counts.csv: P5_lit14_2_mut

data_processing:
The libraries were sequenced using the NextSeq 500/550 High Output Kit v2.5 (Illumina, 20024907) on a NextSeq 550 System (Illumina, SY-415-1002). Sequenced reads were aligned to the mouse (mm10) reference genome with Illumina Basespace RNA-Seq alignment tool (version 2.0.1). Data was analyzed using Illumina Basespace RNA-seq Differential Expression (version 1.0.1), which utilizes DESeq2. Gene expression was normalized in DESeq2 using median of ratios (counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene).
Assembly: Sequenced reads were aligned to the mouse (mm10) reference genome with Illumina Basespace RNA-Seq alignment tool (version 2.0.1).
Supplementary files format and content: csv file combined for normalized counts from DeSeq2

source_name: lung

extract_protocol:
P5 lungs from Smad4 f/f and Smad4 f/f;Cdh5-CreERT2 pups were dissected, minced, and digested in collagenase I (Thermo Fisher Scientific,17-100-17)/dispase (Corning, 354235) buffer at 37·C for 30 minutes under constant rotation. The digested tissue was triturated 10 times through an 18G needle to dissociate the clumps and filtered using 70 µm nylon mesh (VWR, 10199-656) to remove any cell debris. The cell suspension was centrifuged at 250g at 4°C for 5 minutes. Single-cell suspensions were incubated with sheep anti–rat IgG dynabeads (Invitrogen,11035) coated with CD31 antibody (BD Pharmingen, 553370) at room temperature for 20 minutes with agitation. CD31+ cells were isolated using a magnetic rack separator and quantified using Qubit RNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32852). RNA integrity was determined using the Bioanalyzer RNA 6000 Nano assay kit (Agilent, 5067-1511).
RNA (0.5 μg per sample) was used for RNA library construction with a TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) as per the manufacturer'r instructions; independent biological samples from HHTf/f and HHTiECKO mice were used to create individual RNA-Seq libraries. The quality and quantity of mRNA library was determined by Qubit dsDNA High Sensitivity Assay Kit (Thermo, Q32851) and Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505), respectively.

value: lung

value: Endothelial cells

value: Smad4 iECKO mutant


title: P5 Smad4 Mut 3

description:
Library name: Sample 6
Column name in P5_Smad4_iLEC_combined counts.csv: P5_lit14_9_mut


title: ctrl_day10_Rep1, CAGE-seq


title: RAT-CON-2_S74

description:
Library name: RAT-CON-2_S74
normcounts_rat.csv
qc_hash_rat.csv


title: Fetus chorionic villus sample CMA-20241858

description: Hybridized to CytoScan 750K array


title: mouse sperm, 50-week, PANDORA-seq, rep1

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: Fetus chorionic villus sample CMA-20241833

description: Hybridized to CytoScan 750K array

value: Ultrasound abnormalities


title: ctrl_day8_Rep1, CAGE-seq


title: mouse sperm, 30-week, PANDORA-seq, rep4

value: 30 weeks


title: AML_day0_Rep1, CAGE-seq


title: P5 Smad4 WT 3

description:
Library name: Sample 3
Column name in P5_Smad4_iLEC_combined counts.csv: P5_lit14_8_wt

value: Wildtype


title: Fetus chorionic villus sample CMA-20241543

description: Hybridized to CytoScan 750K array


title: mouse sperm, 30-week, PANDORA-seq, rep3


title: P5 Smad4 WT 1

description:
Library name: Sample 1
Column name in P5_Smad4_iLEC_combined counts.csv: P5_lit14_6_wt


title: ctrl_day0_Rep1, CAGE-seq


title: mouse sperm, 30-week, PANDORA-seq, rep2


title: P5 Smad4 WT 2

description:
Library name: Sample 2
Column name in P5_Smad4_iLEC_combined counts.csv: P5_lit14_7_wt


title: Fetus chorionic villus sample CMA-20241764

description: Hybridized to CytoScan 750K array


title: Fetus chorionic villus sample CMA-20241377

description: Hybridized to CytoScan 750K array


title: Fetus chorionic villus sample CMA-20241417

description: Hybridized to CytoScan 750K array


title: V453_ST2

city: Vienna

first: Andreas

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

data_processing:
adapter trimming; bbduk
UMI extraction, UMItools
alignment; STAR (2.7.3c)
UMI collapsing; UMItools
Read count; htseq (version 0.11.2)
Assembly: GENCODE V38
Supplementary files format and content: count table of each submitted sample

source_name: placenta

extract_protocol:
RNA extraction was carried out using RNeasy mini/micro and DNAse I kit (all from QIAGEN) according to the manufacturer’s instruction. RNA quantification was carried out by Nanodrop (ThermoFisher) or RNA broad range QUBIT assay kit (ThermoFisher, Q10211).
Libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina - Dual Indexing, 96 UDI (Workflow B), Set B1 (Lexogen) following the manufacturer’s instructions.

value: placenta

value: ST

value: WT


title: V453_ST3


title: P5 Smad4 Mut 1

description:
Library name: Sample 4
Column name in P5_Smad4_iLEC_combined counts.csv: P5_lit14_1_mut


title: Fetus chorionic villus sample CMA-20241326

description: Hybridized to CytoScan 750K array

value: history of complicated obstetrics


title: Metastasis_M3_PLX

city: Stockholm

first: Martin

last: Bergö

address: Hälsovägen 7C (Neo building)

department: Department of Biosciences and Nutrition

institute: Karolinska Institute

description:
Library name: Sample 12
RNASeq

data_processing:
Alignment using START aligner
Assembly: GRCm38
Supplementary files format and content: readcounts

source_name: Metastasis derived

growth_protocol: Cells were cultured in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma-Aldrich) supplemented with 10% fetal bovine serum (10270-106, Thermo Fisher Scientific), non-essential amino acids, and antibiotics (Sigma-Aldrich).

extract_protocol:
RNA was isolated from cells using RNAesy Plus Mini Kit (74134, Qiagen).
TruSeq Stranded Total RNA Sample Preparation Kit with RiboZero Gold

treatment_protocol: Cells were incubated with 2 μM PLX4720 or DMSO for 48 hours, followed by RNA extraction and analysis.

value: Metastasis derived

value: HCC Lymph node metastasis

value: BRAFV600E; p53 KO


title: Metastasis_M3_DMSO

description:
Library name: Sample 11
RNASeq

value: DMSO


title: Metastasis_M2_PLX

description:
Library name: Sample 10
RNASeq


title: mouse sperm, 10-week, PANDORA-seq, rep4

institute: university of utah

data_processing:
The raw reads were trimmed by performing SPORTS1.1.1 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse), hg38 (for human)
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: sperm

value: 10 weeks


title: mouse sperm, 10-week, PANDORA-seq, rep2


title: mouse sperm, 30-week, PANDORA-seq, rep1


title: mouse sperm, 10-week, PANDORA-seq, rep3


title: V453_SR2

value: hTSC


title: Fetus chorionic villus sample CMA-20240904

description: Hybridized to CytoScan 750K array

value: high-risk first trimester serum screening test results


title: Fetus chorionic villus sample CMA-20241014

description: Hybridized to CytoScan 750K array


title: Metastasis_M1_PLX

description:
Library name: Sample 8
RNASeq


title: Metastasis_M2_DMSO

description:
Library name: Sample 9
RNASeq


title: V453_ST1


title: V453_SR3


title: V453_SR1


title: pLSEC,Stiff+HP

city: Beijing

first: Yi

last: Long

address: Jinchun Road

institute: Tsinghua university

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool,BMKCloud(www.biocloud.net) online platform
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high qualit
Clean reads were mapped to GRCm38 using Hisat2.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include fpkm values for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted by using Trizol reagent. Around 1000 ng of total RNA was used for the construction of sequencing libraries according to standard Illumina protocols.
RNA libraires for RNA-seq were prepared using VAHTS Universal V6 RNAseq Library Prep Kit for Illumina ® (NR604-01/02).

value: Liver

value: Primary LSEC

value: Endothelial cell

value: Stiff+HP


title: Fetus chorionic villus sample CMA-20240880

first: Qi

description: Hybridized to CytoScan 750K array

value: Ultrasound abnormalities


title: Primary Tumor_T3_PLX

description:
Library name: Sample 6
RNASeq

source_name: liver tumors

value: liver tumors

value: Primary Tumor_T3

value: HCC liver tumor


title: Fetus chorionic villus sample CMA-20241169

description: Hybridized to CytoScan 750K array


title: Metastasis_M1_DMSO

description:
Library name: Sample 7
RNASeq


title: V452_ST3

value: placenta

value: ST

value: WT


title: mouse sperm, 10-week, PANDORA-seq, rep1

city: Salt Lake City

last: Chen

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: Primary Tumor_T3_DMSO

description:
Library name: Sample 5
RNASeq

value: BRAFV600E; p53 KO

value: DMSO


title: V452_ST1


title: V452_SR3


title: Primary Tumor_T2_PLX

description:
Library name: Sample 4
RNASeq

value: Primary Tumor_T2


title: pLSEC, 12W

value: CCl4 treat 12 weeks


title: pLSEC,Soft+LP

value: Soft+LP


title: V452_ST2


title: Fetus chorionic villus sample CMA-20240207

description: Hybridized to CytoScan 750K array


title: Fetus chorionic villus sample CMA-20240228

description: Hybridized to CytoScan 750K array

value: history of complicated obstetrics


title: pLSEC, NC

description: NC

value: Liver

value: Primary LSEC

value: NC

value: Healthy


title: pLSEC,4W

value: Endothelial cell

value: CCl4 treat 4 weeks


title: Fetus chorionic villus sample CMA-20240157

description: Hybridized to CytoScan 750K array

value: Ultrasound abnormalities


title: KO3

value: KO

value: GPR116 conditional knock out in endothelial cell


title: Primary Tumor_T2_DMSO

description:
Library name: Sample 3
RNASeq

value: liver tumors

value: HCC liver tumor


title: Primary Tumor_T1_DMSO

description:
Library name: Sample 1
RNASeq

value: Primary Tumor_T1

value: BRAFV600E; p53 KO


title: Fetus chorionic villus sample CMA-20240152

description: Hybridized to CytoScan 750K array


title: LG_RNA_40L4

city: La Jolla

first: Helen

last: Makarenkova

address: 10550 N Torrey Pines Rd, MB-218

department: Molecular Medicine

institute: The Scripps Research Institute

data_processing:
Fastq files generated by sequencing were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt (Martin 2011). Quality scores were assessed using FastQC.
Reads were aligned to the Mus musculus genome build mm10 using STAR (Dobin, Davis et al. 2013).
Individual sample reads were quantified using HTseq (Anders, Pyl et al. 2015) and normalized via Relative Log Expression (RLE) using DESeq2 R library (Love, Huber et al. 2014).
Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC(Wang, Wang et al. 2012).
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: Lacrimal Gland

extract_protocol:
LGs were harvested, and total RNA was isolated using a QIAGEN RNeasy Plus Mini RNA isolation kit (Qiagen; Hilden, Germany) following the manufacturer's protocol.
Libraries were prepared with the Lexogen QuantSeq 3` mRNA-seq FWD kit with Lexogen 12 nt Unique Dual Indexes.

value: Lacrimal Gland

value: 10/11 Months

value: Female

value: Calorie Restriction 40%

tag: treatment duration

value: 4 Months


title: Fetus chorionic villus sample CMA-20232015

description: Hybridized to CytoScan 750K array


title: Fetus chorionic villus sample CMA-20240435

description: Hybridized to CytoScan 750K array


title: WT3

value: Liver

value: Primary LSEC

value: WT

value: Control


title: V451_ST1

value: placenta

value: ST

value: shBRM


title: V451_ST2


title: NCM460-siRNA-KLK1-3

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg19
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
RNA was harvested using RNAiso Plus (TAKARA)
RNA libraries for RNA-Seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

value: Epithelial cells


title: WT2

value: Endothelial cell


title: Fetus chorionic villus sample CMA-20240050

last: Zhang

description: Hybridized to CytoScan 750K array

value: Ultrasound abnormalities


title: LG_RNA_40L2


title: NCM460-siRNA-KLK1-2


title: LG_RNA_40L1


title: V452_SR2

value: hTSC


title: V451_SR3


title: V451_SR2


title: V452_SR1


title: Primary Tumor_T1_PLX

description:
Library name: Sample 2
RNASeq

value: liver tumors

value: Primary Tumor_T1

value: HCC liver tumor

value: BRAFV600E; p53 KO


title: PBS_input_rep3

city: Tokyo

first: Ryuta

last: Koyama

address: 7-3-1 Hongo Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: University of Tokyo

data_processing:
Trimmed sequence reads were aligned to mm10 using STAR spliced read aligner
Reads were counted with featureCounts
Normalization with TMM and FPKM was performed using the Bioconductor packages edgeR and limmaVoom. Genes with FPKM greater than 1 in all compared samples were included in the following analysis.
Differentially expressed genes (>=2-fold and <5% false discovery rate) were identified by edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each sample
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: brain

extract_protocol:
RNA was extracted from the input and IP samples using the RNeasy plus mini kit (QIAGEN).
Multiplexed libraries were prepared from RNA extracted from input and IP samples using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770; New England Biolabs).

value: brain

value: hippocampal astrocyte

tag: intrahippocampal injection

value: PBS

tag: rna sample_type

value: input


title: NCM460-siRNA-NC-3


title: PBS_input_rep2

tag: tissue

value: WT


title: V450_V451_ST3


title: V451_SR1


title: LG_RNA_AL3

value: Lacrimal Gland

value: 10/11 Months

tag: Sex

value: Female

value: Ad libitum diet

value: 4 Months


title: NCM460-siRNA-KLK1-1

value: Epithelial cells


title: KO2

value: Liver

value: Primary LSEC

value: Endothelial cell

value: KO

tag: treatment

value: GPR116 conditional knock out in endothelial cell


title: KO1


title: NCM460-siRNA-NC-2


title: PBS_input_rep1


title: V450_V451_ST2

value: placenta

value: ST


title: LG_RNA_AL1

tag: age


title: NCM460-siRNA-NC-1


title: tdTom3

city: Cleveland

first: Sujata

last: Rao

state: OH

address: 2022 E 105th St i building

institute: Cole eye, Cleveland Clinic foundation

description: Library name: Sample 6

data_processing:
Fastq files were subject to quality control (FastQC).
Sequences were trimmed using trimmomatic tool for adapter/ low quality sequences.
Trimmed sequence was mapped to reference Ensembl GRCm38/mm10.
read counts and extraction was done using the featurecounts.
Normalization and differential expression analysis was performed using Deseq2.
Assembly: mm10
Supplementary files format and content: Jidigam_RNAseq_reads.csv

source_name: Retina

extract_protocol:
RNA extraction was done using Rneasy micro kit (Qiagen). Total of around 500pg-1ng of RNA was used for amplification. Amplification was performed using smart v4kit.
The libraries were made using Nextera XT Library Preparation kit by following the manufacture protocol. Libraries were subject to high throughput sequencing for poly A RNAs by NGS facility (Novogene).

treatment_protocol: Freshly isolated retinas were collected and dissected in ice cold DMEM from P7.5 mouse pups. Retinal dissociation was done in DMEM containing 10mg/ml of collagenase A and 3U/ml of DNase1at 37 degree C for 20 minutes with pipetting every 10 min. Cells were passed through the cell strainer and centrifuged for 8 min at 3000 rpm. After PBS washes cells were reconstituted in PBS containing 1mM EDTA. TO-PRO or DAPI  were used for identification of dead cells. Both GFP and tomato double positive population were FACS sorted and collected as enriched VECs.

value: Retina

value: Endotheal cells

value: Control 3

value: Tamoxifen inj. P0.5-P2.5


title: V450_V451_ST1

value: WT


title: Mouse lung_LPS_12h_4

city: Munich

first: Lianyong

last: Han

state: Bavaria

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)

data_processing:
Scanpy (v1.8.0)
Assembly: mm39
Supplementary files format and content: .h5ad, processed data contains all treatmentas, ready to use

extract_protocol:
Lung single-cell suspensions for Dropseq were generated from right lung lobes. Briefly, right lung lobes were removed and minced before undergoing enzymatic digestion in a mix of dispase, collagenase, elastase and DNase for 20-30 min at 37°C with agitation. Following straining of cell suspension through a 40 micron mesh filter, cells were centrifuged and counted in PBS with 10% FCS. For Dropseq, cell aliquots in PBS supplemented with 0.04% of bovine serum albumin were prepared with a cell density of 100 cells/µl.
The library protocol was described in published paper in detail (https://doi.org/10.1038/s41467-020-17358-3)

value: lung

value: C57BL/6, WT

value: Instillation


title: tdTom2

description: Library name: Sample 5

value: Control 2


title: V450_V451_SR2

value: hTSC


title: AAV-Control_input_rep1

value: brain

value: hippocampal astrocyte

value: input


title: AAV-Control_input_rep2


title: tdTom1

description: Library name: Sample 4

value: Control 1


title: V450_V451_SR3


title: LG_RNA_40L3

value: Lacrimal Gland

value: 10/11 Months

value: Female

value: Calorie Restriction 40%

value: 4 Months


title: Mouse lung_LPS_12h_2


title: KA_input_rep2

value: kainic acid


title: KA_input_rep3


title: Mouse lung_LPS_12h_1


title: V450_ST3

value: placenta

value: ST


title: WT1

value: Liver

value: Primary LSEC

value: Endothelial cell

value: WT

value: Control


title: LG_RNA_AL2

value: Ad libitum diet


title: V450_V451_SR1

value: hTSC


title: Bmal 1

description: Library name: Sample 1

value: Retina

value: Endotheal cells

value: Mutant 1

value: Tamoxifen inj. P0.5-P2.5


title: Mouse lung_DWCNT_12h_4

value: lung

value: C57BL/6, WT

value: Instillation


title: Mouse lung_DWCNT_12h_3


title: V450_ST2


title: Bmal 2

description: Library name: Sample 2

value: Mutant 2


title: PBS_IP_rep3

value: brain

value: hippocampal astrocyte

value: PBS

value: GFP IP


title: V451_ST3

value: placenta

value: ST

value: shBRM


title: Mouse lung_LPS_12h_3


title: V450_ST1

value: WT


title: KO-2-B-CELL

city: Shenzhen

first: Yuxing

last: Li

address: No. 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
Bcl2fastq (v2.17.1.14) were used for basecalling.
Sequence reads were filtrated using Cutadapt (V1.9.1)
Clean reads were mapped to the reference genome sequences (GRCm38.98) using Hisat2 (V2.0.1).
Gene expression level was calculated using Htseq software (V0.6.1)
Assembly: GRCm38.98
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: spleen

growth_protocol: B cells were cultured 24 hours at the concentration of 2 million cells per ml in DMEM medium supplemented with 10% FBS, 1% penicillin/streptomycin, 1% non-essential amino acids and 20 μg/ml LPS at 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and poly(A) mRNA was isolated with the poly(A) mRNA Magnetic Isolation Module (NEB).
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: B cells were stimulated with 20 μg/ml LPS

value: spleen

value: B cell

value: Wac cKO

value: Cultured 24 hours with 20 ug/mL LPS


title: Mouse lung_DWCNT_12h_2


title: Mouse lung_DWCNT_12h_1


title: PBS_IP_rep1


title: KO-3-B-CELL


title: PBS_IP_rep2


title: V450_SR3

value: hTSC


title: WT-3-B-CELL

value: wild type


title: Mouse lung_MWCNT_12h_4

value: lung

value: C57BL/6, WT


title: Mouse lung_MWCNT_12h_3

value: Instillation


title: KO-1-B-CELL


title: AAV-Control_input_rep3

value: brain

value: input


title: AAV-Control_IP_rep2

value: hippocampal astrocyte


title: LG_RNA_AL4

value: Lacrimal Gland

value: 10/11 Months

value: Female

value: Ad libitum diet

value: 4 Months


title: KA_input_rep1

value: WT

value: kainic acid


title: V188_ST3

value: placenta

value: ST

value: shNeg


title: WT-2-B-CELL

value: spleen

value: B cell

value: wild type

value: Cultured 24 hours with 20 ug/mL LPS


title: Bmal 3

description: Library name: Sample 3

value: Retina

value: Endotheal cells

value: Mutant 3

value: Tamoxifen inj. P0.5-P2.5


title: WT-1-B-CELL


title: Mouse lung_MWCNT_12h_1

value: lung

value: C57BL/6, WT

value: Instillation


title: V188_ST2


title: Mouse lung_MWCNT_12h_2


title: KA_IP_rep3

value: brain

value: hippocampal astrocyte

value: GFP IP


title: NH32619D16_CITE

city: Minneapolis

first: David

last: Masopust

address: 2101 6th St. SE

institute: University of Minnesota

data_processing:
Sequence libraries were sequenced using Illumina chemistry, on either Novaseq or HiSeq instruments (Illumina). The resulting sequence data were processed using cell ranger software (10x Genomics). Data were aligned to the MMul_10 genome build (release 98, assembly ID GCA_003339765.3), using Ensembl gene annotations (Build 10.98). The raw count matrix was imported directly into R and analyzed using the Seurat software package, version 4.168. Briefly, the EmptyDrops algorithm was used to select droplets containing viable transcriptomes 69, followed by filtering on UMI count (discarding cells >20,000), feature count (discarding cells with <200 or >5000). Passing cells were merged across samples and normalized using Seurat’s “LogNormalize” method. Feature counts are divided by the total counts for that cell, multiplied by a scale factor, and natural-log transformed using log1p. The top 3,000 variable features were selected using Seurat’s FindVariableFeatures function, using the “vst” method. Dimensionality reduction was performed with PCA followed by UMAP on the first 15 components. Differential expression was performed using FindMarkers, using a Wilcoxon Rank Sum test, and then filtered using adjusted p-value <0.001 and average log fold-change > 0.5. Data were visualized using the pheatmap R package (1.0.12).
Assembly: Mmul_10
Supplementary files format and content: barcodes, features, and matrix for gene expression (GEX) and CITE-seq files
Library strategy: CITE-seq

organism: Macaca mulatta

source_name: pooled cervix and vagina

extract_protocol:
Single-cell suspensions of unsorted and sorted leukocytes were stained with a cocktail of BioLegend TotalSeq-C nucleotide-labeled antibodies (Table S4). Cells to be sorted were additionally stained with fixable viability dye and Mamu*01/CM9-PE tetramers, FITC anti-CD45 (clone D058–1283), and anti-CD3 (clone SP34-2) BV650 antibodies. To isolate leukocytes, live single cells were sorted on a FACS Aria sorter. Pilot studies had shown that recovery of CD3- (non-T cell) leukocytes was poor in the CITE-seq data. Hence, for analysis of all leukocytes, reproductive tract cells were sorted as CD45+CD3+ T cells or CD45+CD3− cells and mixed at a 2:3 ratio respectively for 10x capture. Sorted and unsorted cells were normalized to a concentration of 1000 cells/µL in chilled media, loaded into a 10x Genomics Chromium instrument and processed using the Single Cell 5' kit Version 1.1 following the manufacturer’s protocol.
Generation of gene expression and VDJ-enriched libraries was performed using manufacturer’s instructions, except that macaque-specific TCR C region primers were used in place of human-specific TCR enrichment primers, as previously published66. Enrichment was performed using two nested PCR reactions. The first enrichment PCR used 5′- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3′ as the forward primer at a stock concentration of 1 µM, with reverse primers targeted the α and β constant regions: 5′- GTCTGCTGGAATAACGCTGTCC-3′ (1 µM stock concentration) and 5′- GCGCTGATCTTTTGGGTGATGG-3′ (0.5 μM stock concentration). The forward primer 5′-AATGATACGGCGACCACCGAGATCT-3′ (1 μM stock concentration) was used for the nested PCR and reverse primers targeted the α and β constant regions: 5′-ATGCACGTCAGAATCCTTGC-3′ (1 μM stock concentration) and 5′-CAGAAGGTGGCCGAGACC-3′ (0.5 μM stock concentration). In both cases, the concentration of the α C region primer was increased relative to the β primer to improve capture. PCR conditions for both reactions were as follows: lid temperature 105°C; 98°C for 45 s; 12 cycles of 98°C for 20 s, 60°C for 30 s, and 72°C for 1 min; followed by 72°C for 1 min and 4°C hold. B-cell receptor enrichment was performed using the primers adapted for Rhesus macaque67. The same PCR program was used, with the exception that 16 cycles of amplification were performed instead of 12.

value: pooled cervix and vagina

value: all reproductive tract cells

value: female

tag: haplotype

tag: vaccination

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag

value: 20mg intravaginal CM9 peptide

tag: library type

value: ADT


title: AAV-Control_IP_rep1

tag: cell type

value: WT


title: Mouse lung_CNP_12h_4

tag: genotype


title: KA_IP_rep2

value: kainic acid


title: V188_ST1

value: placenta

tag: cell line

value: ST

value: shNeg


title: V450_SR2

value: hTSC


title: V450_SR1


title: V188_SR3


title: AAV-Control_IP_rep3


title: Mouse lung_CNP_12h_3

value: lung

value: C57BL/6, WT


title: NH32619D16_GEX

value: GEX


title: NH31674D13_CITE


title: V188_SR2


title: KO2_IP

data_processing:
Sequencing data was filtered by Trimmomatic (version 0.36).
Sequencing data was mapped to the reference genome (GRCm38.101) using STAR (version 2.5.3a).
Peak calling was performed using MACS2 (Version 2.1.1).
Peaks annotation and peak distribution analyzed by bedtools (Version 2.25.0).
Differentially peaks were identified by a python (Version 3.10) using fisher test.
Assembly: GRCm38.101
Supplementary files format and content: bigWig

growth_protocol: B cells were cultured 24 hours at the concentration of 2 million cells per ml in DMEM medium supplemented with 10% FBS, 1% penicillin/streptomycin, 1% non-essential amino acids and 20 μg/ml LPS at 37℃ in 5% CO2.

extract_protocol:
cell was crosslinked in 1% formaldehyde for 10 min at room temperature. The crosslinking reaction was terminated by 0.125 M glycine for 5 min at room temperature. Then the nucleus was extracted form lysates by centrifuging at 2000g for 5min and lysed and sonicated to fragment chromatin DNA. The sonicated chromatin was incubated with anti-ubH2B antibody.
The DNA fragment was extracted by phenol-chloroform method. The sequencing libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607).

value: spleen

value: B cell

value: Wac cKO

value: Cultured 24 hours with 20 ug/mL LPS

tag: chip antibody


title: Mouse lung_CNP_12h_2

value: Instillation


title: Mouse lung_CNP_12h_1


title: V188_SR1


title: NH31674D13_GEX

value: pooled cervix and vagina

value: all reproductive tract cells

value: female

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag


title: KO1_IP


title: sample 12_stage 14 day 12 circRNA biol rep 3

city: Singapore

first: Jun Wei

last: Pek

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description:
Library name: sample 12
Sample7-12_cirR12_vs_cirR2.circRNAs.xlsx

data_processing:
For linear RNA sequencing, rRNA-depletion was performed using the Ribo-Zero kit, followed by library construction and sequencing (Illumina). After quality control, the reads were mapped using HISAT 2 software (Kim et al., 2015). The mapped reads were assembled by StringTie and ballgrown was used to detect differential expressed transcripts (p<0.05) (Pertea et al., 2016). For circRNA sequencing, additional RNase R treatment to digest linear RNA was performed. The sequencing libraries were generated by NEBNext UltraTM Directional RNA Library Prep Kit for Illumina following the manufacturer’s protocol. Reads were mapped using the Spliced Transcripts Alignment to a Reference (STAR) software, and circRNAs identified using CIRCexplorer2 (Dong et al., 2019). Differential expression analysis was done using DESeq2.
Assembly: dm6
Supplementary files format and content: Sample1-6_lncR12_vs_lncR2.xlsx
Supplementary files format and content: Sample7-12_cirR12_vs_cirR2.circRNAs.xlsx

organism: Drosophila melanogaster

source_name: Ovaries

extract_protocol:
RNA was extraction in accordance to Trizol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ovaries

tag: time point

value: stage 14 day 12

value: Oregon R


title: NH28700D3_CITE

value: ADT


title: NH28700D3_GEX


title: Mouse lung_Sham_12h_4


title: sample 11_stage 14 day 12 circRNA biol rep 2

description:
Library name: sample 11
Sample7-12_cirR12_vs_cirR2.circRNAs.xlsx


title: WT2_IP

value: wild type


title: Mouse lung_Sham_12h_3

value: lung


title: WT1_IP


title: Mouse lung_Sham_12h_2

value: C57BL/6, WT


title: sample 10_stage 14 day 12 circRNA biol rep 1

description:
Library name: sample 10
Sample7-12_cirR12_vs_cirR2.circRNAs.xlsx


title: D8989 - OCAplus DNA

city: Graz

first: Kristijan

last: Skok

address: Neue Stiftingtalstraße 6

department: Diagnostic and Research Institute of Pathology

institute: Medical University of Graz

description: Library name: D8989-3

data_processing:
Oncomine Comprehensive Plus Workflow 2.3, IonReporter 5.18.4.0
Assembly: hg19
Supplementary files format and content: VCF file containing Variants called by the OCAPlus Pipeline

source_name: Thermo Fisher Oncomine Comprehensive Assay Plus

extract_protocol:
Maxwell FFPE Plus DNA Kit
Ion AmpliSeq Library Kit v2

value: tumor

tag: gender

value: male


title: sample 9_stage 14 day 2 circRNA biol rep 3

description:
Library name: sample 9
Sample7-12_cirR12_vs_cirR2.circRNAs.xlsx

value: stage 14 day 2


title: NH28752D4_CITE


title: KA_IP_rep1

value: brain

value: hippocampal astrocyte

value: WT

value: kainic acid

value: GFP IP


title: Mouse lung_Sham_12h_1

value: Instillation


title: sample 8_stage 14 day 2 circRNA biol rep 2

description:
Library name: sample 8
Sample7-12_cirR12_vs_cirR2.circRNAs.xlsx


title: AB/Tub larvae, 0.000410 uM TPP GBT, Rep 3

city: Saskatoon

first: Morgan

middle: W

last: Kirzinger

state: Saskatchewan

address: 110 Gymnasium Place

institute: National Research Council Canada

description:
Library name: Sample 36
TPP_GBT_10m4_C

data_processing:
raw sequence files were trimmed for adapter seqeunce/low quality sequences using cutadapt
trimmed reads were aligned to the GRCz11 reference genome using STAR (default parameters)
raw read per gene counts from STAR were formatted into a matrix and imported into DESeq2 for differential gene expression analysis and pair wise comparison - results were filtered using p-value = 0.05
corrected, normalized DEseq2 data tables were input directly into BMDexpress
Assembly: GRCz11
Supplementary files format and content: BMDExpress_TPP_ZET.tsv
Supplementary files format and content: BMDExpress_TPP_GBT.tsv

organism: Danio rerio

source_name: 20 Whole larvae

growth_protocol: For ZET assays, 6 hpf larvae were placed in 96-well plates in HEPES buffered E3 medium and 10X concentrations of test substance were added. Plates were sealed and incubated at 28 degrees C until 120 hpf, where they were removed and flash frozen prior to RNA extraction.

extract_protocol:
Total RNA was extracted from each sample of 20 larvae using the Norgen BioTek Corp Total RNA Purification kit (Norgen Cat#17200, Thorold, ON, Canada) with the optional RNase-Free DNase I kit (Norgen Cat#25710, Thorold, ON, Canada).
Sequencing libraries were prepared using the Illumina Truseq Stranded mRNA kit using 1ug of total RNA.

treatment_protocol: Prior to treatment, GBT larvae were reared in nursery baskets on a recirculating system. At 72 hpf larvae were placed in 96-well plates in HEPES buffered E3 medium and 10X concentrations of test substance were added. Plates were sealed and incubated at 28 degrees C until 120 hpf, where they were removed and flash frozen prior to RNA extraction.

value: 20 Whole larvae

value: AB/Tub

value: 72-120 hours post-fertilization


title: D8989 - Archer Solid v2

description: Library name: D8989-5

data_processing:
Analysis was performed in Archer Analysis Pipeline Version: 7.1.0-14
Assembly: hg19
Supplementary files format and content: Text file in VCF format containing all variants called by the Archer Pipeline

source_name: IDT Archer FUSIONPlex Pan Solid Tumor v2

extract_protocol:
Maxwell RSC RNA FFPE Kit
ITD Archer FUSIONPlex Protocol for Ion Torrent


title: colitis associate cancer(CAC5),scRNA-seq

description:
10x Genomics
C5

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
After the tumor was removed, it was digested into single cell suspension with tumor tissue dissociation kit on ice, and 10x-RNA reagents were added
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cell suspension were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: colon

value: Intestinal tissue single cell suspension

value: Tumor cells,Stromal cells,Immune cells

value: AOM/DSS

tag: disease state

value: colitis associate cancer


title: sample 6_stage 14 day 12 mRNA biol rep 3

description:
Library name: sample 6
Sample1-6_lncR12_vs_lncR2.xlsx

value: Ovaries

value: stage 14 day 12

value: Oregon R


title: colitis associate cancer(CAC4),scRNA-seq

description:
10x Genomics
C4


title: AB/Tub larvae, 0.000410 uM TPP GBT, Rep 2

description:
Library name: Sample 35
TPP_GBT_10m4_B


title: H32619D16_GEX

value: pooled cervix and vagina

value: leukocytes

value: female

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag

value: 20mg intravaginal CM9 peptide

value: GEX


title: colitis associate cancer(CAC3),scRNA-seq

description:
10x Genomics
C3


title: sample 5_stage 14 day 12 mRNA biol rep 2

description:
Library name: sample 5
Sample1-6_lncR12_vs_lncR2.xlsx


title: AB/Tub larvae, 0.000410 uM TPP GBT, Rep 1

description:
Library name: Sample 34
TPP_GBT_10m4_A

value: 20 Whole larvae


title: AB/Tub larvae, 0.00410 uM TPP GBT, Rep 3

description:
Library name: Sample 33
TPP_GBT_10m3_C

value: AB/Tub


title: H31674D13_GEX


title: sample 4_stage 14 day 12 mRNA biol rep 1

description:
Library name: sample 4
Sample1-6_lncR12_vs_lncR2.xlsx


title: colitis associate cancer(CAC1),scRNA-seq

description:
10x Genomics
C1


title: colitis associate cancer(CAC2),scRNA-seq

description:
10x Genomics
C2


title: sample 3_stage 14 day 2 mRNA biol rep 3

description:
Library name: sample 3
Sample1-6_lncR12_vs_lncR2.xlsx

value: stage 14 day 2


title: H28700D3_CITE

value: ADT


title: colitis 4,scRNA-seq

description:
10x Genomics
A4

value: colon

value: Intestinal tissue single cell suspension

value: DSS

value: colitis


title: H28700D3_GEX


title: sample 2_stage 14 day 2 mRNA biol rep 2

description:
Library name: sample 2
Sample1-6_lncR12_vs_lncR2.xlsx

value: Ovaries


title: H32619D16_CITE


title: sample 7_stage 14 day 2 circRNA biol rep 1

description:
Library name: sample 7
Sample7-12_cirR12_vs_cirR2.circRNAs.xlsx


title: NH28752D4_GEX

value: all reproductive tract cells


title: colitis 3,scRNA-seq

description:
10x Genomics
A3

value: Tumor cells,Stromal cells,Immune cells


title: H28752D4_CITE

value: pooled cervix and vagina


title: sample 1_stage 14 day 2 mRNA biol rep 1

description:
Library name: sample 1
Sample1-6_lncR12_vs_lncR2.xlsx

value: Oregon R


title: AB/Tub larvae, 0.0410 uM TPP GBT, Rep 3

description:
Library name: Sample 30
TPP_GBT_10m2_C

value: 72-120 hours post-fertilization


title: colitis 2,scRNA-seq

description:
10x Genomics
A2


title: AB/Tub larvae, 0.0410 uM TPP GBT, Rep 2

description:
Library name: Sample 29
TPP_GBT_10m2_B


title: AB/Tub larvae, 0.00410 uM TPP GBT, Rep 1

description:
Library name: Sample 31
TPP_GBT_10m3_A


title: H28752D4_GEX

value: leukocytes

value: female

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag


title: TCRβ+ CD8αα+ DN 2

first: Lukasz

last: Wojciech

address: 5 Science Drive 2 Blk MD4

institute: Nus

description:
Library name: TCRB+ CD8alphaalpha+ DN 2
TCRβ CD8αα DN.txt

data_processing:
The raw reads were aligned using MiXCR
VDJtool was used to analyse TCR repertoires
Assembly: mm10
Supplementary files format and content: Tab-deliminated file include raw counts of TCR for each population
Library strategy: TCR-seq

source_name: small intestine

extract_protocol:
total RNA was extracted from sorted TCRβ CD8αα+ Ly49+, TCRβ+ CD8αα+ Bmp7+, TCRβ+ CD8αα+ DN IEL. using RNAeasy isolation KIT
Synthesis of TCR libraries was performed using reverse transcriptase reaction employing template-switching primers with the sequence TAAGAGACAGCAACTACTACTGCrGrGrGr

treatment_protocol: Adoptive transfer of T cell into Rag -/- lymphopenic host

value: small intestine

value: IEL

value: intraepithelial T lymphocyte

value: WT

value: SPF mouse


title: colitis 1,scRNA-seq

description:
10x Genomics
A1

value: colon

value: Intestinal tissue single cell suspension


title: AB/Tub larvae, 0.0410 uM TPP GBT, Rep 1

description:
Library name: Sample 28
TPP_GBT_10m2_A

value: 20 Whole larvae

value: AB/Tub


title: TCRβ+ CD8αα+ DN 1

description:
Library name: TCRB+ CD8alphaalpha+ DN 1
TCRβ CD8αα DN.txt


title: Fetal liver, treated 3

city: Corvallis

first: Daniella

last: Hasan

state: OR

address: Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

description: Library name: Fetal_Liver_T3

data_processing:
Trimmed using fastp
rRNA removal using SortMeRNA
Aligned using STAR
Quantified using Salmon
Assembly: Cavia porcellus Broad/cavPor3 (Feb 2008)
Supplementary files format and content: Fetal_and_Maternal_Liver_Data.xlsx; proceced maternal and fetal data provided on separate sheets

organism: Cavia porcellus

source_name: Fetal liver

extract_protocol:
TRIzol-chloroform separation followed by purification with the Qiagen Rneasy Mini Kit
Libraries were prepared from high-quality RNA (RIN > 7.7) using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit following the manufacturer's protocol and sequenced as 100 bp single-end reads on an Illumina NextSeq 2000.

value: Fetal liver

value: Dimethyl Fumarate


title: Normal 5,scRNAseq

description:
10x Genomics
N5

value: Tumor cells,Stromal cells,Immune cells

value: water

value: normal


title: Maternal liver, treated 3

description: Library name: Maternal_Liver_T3

source_name: Maternal liver

value: Maternal liver


title: Fetal liver, treated 2

description: Library name: Fetal_Liver_T2


title: AB/Tub larvae, 0.00410 uM TPP GBT, Rep 2

description:
Library name: Sample 32
TPP_GBT_10m3_B

value: 72-120 hours post-fertilization


title: TCRβ+ CD8αα+ Bmp7+ 3

description:
Library name: TCRB+ CD8alphaalpha+ Bmp7+ 3
TCRβ CD8αα Bmp7.txt


title: Normal 4,scRNAseq

description:
10x Genomics
N4


title: AB/Tub larvae, 0.410 uM TPP GBT, Rep 3

description:
Library name: Sample 27
TPP_GBT_10m1_C


title: AB/Tub larvae, 0.410 uM TPP GBT, Rep 2

description:
Library name: Sample 26
TPP_GBT_10m1_B


title: TCRβ+ CD8αα+ Bmp7+ 2

description:
Library name: TCRB+ CD8alphaalpha+ Bmp7+ 2
TCRβ CD8αα Bmp7.txt


title: TCRβ+ CD8αα+ Bmp7+ 1

description:
Library name: TCRB+ CD8alphaalpha+ Bmp7+ 1
TCRβ CD8αα Bmp7.txt


title: Normal 2,scRNAseq

description:
10x Genomics
N2


title: H31674D13_CITE

value: pooled cervix and vagina

value: leukocytes

value: female

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag

value: 20mg intravaginal CM9 peptide

value: ADT


title: AB/Tub larvae, 0.410 uM TPP GBT, Rep 1

description:
Library name: Sample 25
TPP_GBT_10m1_A


title: Maternal liver, treated 1

description: Library name: Maternal_Liver_T1


title: Fetal liver, treated 1

description: Library name: Fetal_Liver_T1


title: AB/Tub larvae, 4.10 uM TPP GBT, Rep 3

description:
Library name: Sample 24
TPP_GBT_EC20_C


title: Normal 1,scRNAseq

description:
10x Genomics
N1

value: colon


title: TCRβ CD8αα+ Ly49+ 2

description:
Library name: TCRB CD8alphaalpha+ Ly49+ 2
TCRβ CD8αα Ly49 .txt

value: small intestine

value: IEL

value: intraepithelial T lymphocyte

value: WT

value: SPF mouse