title: PBMCs, mixed sample, batch B, sublibrary 8

city: Oxford

first: Matt

last: Jackson-Wood

address: 9400 Business Park, Garsington Road

country: United Kingdom

institute: Gilead Sciences

description:
Library name: batchB_Sublibrary_8
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.

data_processing:
The Parse pipeline (v1.2.1) was used for demultiplexing pooled Parse Evercode libraries using the sample loading table and well assignments, followed by trimming, filtering and alignment of reads to the GRCh38 reference genome; assignment of reads to cell barcodes; per-sample QC and filtering of cells vs. ambient RNA; and output of filtered count matrices for downstream analyses.
Quality control filtering was applied in Seurat to remove low‑quality cells (>15% mitochondrial UMIs or ≤0.8 log10 genes per UMI) and potential multiplets based on standard single‑cell RNA‑seq metrics.
Datasets from multiple donors, conditions and experimental batches were integrated using RPCA in Seurat.
Cell types were annotated based on canonical marker gene expression.
Assembly: Human reference genome GRCh38 with GENCODE annotation.
Supplementary files format and content: A processed R Seurat single-cell object (seurat_v5_object.rds) is provided in .rds format. This file contains expression data and cell type metadata used for downstream analyses.
Supplementary files format and content: sample_metadata.tsv: tab-delimited metadata file linking GEO sample identifiers to original Parse sample loading table identifiers and well assignments. The file records donor, stimulation condition, experimental batch, and the well assignment(s) used for each biological sample prior to combinatorial barcoding and pooled sub-library sequencing.

organism: Homo sapiens

source_name: Blood

growth_protocol: Blood cones were processed to obtain PBMCs using density gradient centrifugation. Briefly, diluted blood cone cells were layered over Ficoll-Paque PLUS Media (Cytiva) in a 50 mL Leucosep tube (Greiner Bio-One GmbH). The resulting cells were seeded into tissue culture treated Biolite 24-well plates (Thermo Fisher Scientific) at a density of 1 × 10^5 cells/cm^2 in a final volume of 1 mL RPMI (Gibco), supplemented with Penicillin-Streptomycin-Neomycin (Gibco), 10% foetal bovine serum (Gibco) and L-Glutamine (Gibco).

extract_protocol:
Harvested cells from the in vitro stimulation were fixed using the Evercode™ cell fixation kit v2 (Parse Biosciences) according to the manufacturer’s protocol.
Single‑cell RNA‑seq libraries were generated using Evercode™ WT 100k Whole Transcriptome Kit v2 (Parse Biosciences) according to the manufacturer’s instructions. Cells from multiple biological samples were combinatorially barcoded and pooled, such that each sequencing sub-library contained multiplexed material rather than a one-biological-sample-to-one-library relationship. In batch A, some biological samples were loaded across two wells in the sample loading plate, whereas others were loaded into a single well; in batch B, biological samples were loaded into one well each. After barcoding, eight sub-libraries were prepared per batch, each containing ~10,000 cells. The final libraries underwent standard library QC and quantification followed by sequencing on NovaSeq X Plus (Illumina) 25B 300-cycle flow cell lanes in 150 bp paired-end mode. Detailed sample-to-well assignments are provided in sample_metadata.tsv.

treatment_protocol: Isolated PBMCs were treated in vitro with a panel of immunomodulatory stimuli for 48 hours prior to single‑cell capture. Unstimulated control samples were processed in parallel. A total of 12 separate donors were used, with stimulations carried out across two batches, each comprising six donors and a baseline condition. The stimulation conditions used were 1 ng/mL Ultra-LEAF Purified anti-human CD3 antibody, 10 ng/mL human TGF-β1, 1 ng/mL GMP Human IL-1β, 10 ng/mL human IL-4 GMP, 10 ng/mL human TNF-α GMP, 10 ng/mL human IL-2 GMP, 10 ng/mL human IL-10 GMP, IFN-α (BioLegend), 100 ng/mL lipopolysaccharide (LPS) solution (eBiosciences), 20 µL/mL CytoStim™ human (Miltenyi Biotec), and B cell stimulator cells (BCS; 8:1 PBMC:BCS) together with 100 ng/mL IL-21 (BioLegend).

value: Blood

value: PBMCs

value: mixed sample

value: B


title: Liver, HFD, TOFA, rep1

status: Public on Jul 06 2026

type: SRA

city: Berkeley

first: Chi

last: Zhu

state: CA California

address: Morgan Hall, Rm238

department: Department of Nutritional Sciences & Toxicology

country: USA

institute: University of California, Berkeley

description: Library name: WT_HFD_TOFA_liver_1

library_source: transcriptomic

data_processing:
Transcriptome mapping was performed with STAR using the Ensembl annotation of the mm10 reference genome.
Read counts for individual genes were generated using HTSeq. Only genes with CPM > 1 for at least one sample were included in the analyses.
Analysis of differential expression was performed using only genes with normalized counts (CPM) >=1 for at least one sample
Assembly: mm10
Supplementary files format and content: Table with FPKM values in log2 for all samples

molecule: polyA RNA

organism: Mus musculus

source_name: liver

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq

treatment_protocol: C57BL/6J mice were exposed to a 60% high fat diet for seven weeks followed by an oral dosing regimen of vehicle control or TOFA (one week of loading dose of 125 mg/kg followed by maintenance dosing 62.5 mg/kg, BID) for a total of three weeks

tag: tissue

value: liver

tag: strain

tag: treatment

value: TOFA


title: PA1761-1

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1761.xlsx

data_processing:
RNA-seq reads were mapped to the Pseudomonas aeruginosa (NC_002516.2) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Assembly: Pseudomonas aeruginosa (NC_002516.2)
Supplementary files format and content: xlsx files were generated from RNA-seq, containing the differential expressional genes.

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1

growth_protocol: RNA-seq(LB)

extract_protocol:
The Pseudomonas aeruginosa PAO1 wild type strain and the HP mutants were inoculated into LB with corresponding antibiotics overnight cultured at 37 °C. Then the strains were one hundred times diluted into fresh LB. Before harvested, the P. aeruginosa strains were cultured for 3 h until OD600 to 0.6, at 37 °C with 220 rpm shaking. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4 °C). RNA extraction was performed by using the TianGen RNA extraction kit with the recommended DNase digestion. After removing rRNA by following the RiboRid protocol, mRNA was used to construct the cDNA library according to the NEBNext Ultra II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina).
NEBNext UltraTM II RNA Library Prep Kit protocol

treatment_protocol: grow until mid-log phase

value: Pseudomonas aeruginosa PAO1

tag: genotype

value: PA1761 mutant

value: grow until mid-log phase in LB


title: PA1123-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1123.xlsx

value: PA1123 mutant


title: Liver, HFD, ctrl, rep4

description: Library name: WT_HFD_ctrl_liver_4

value: control


title: PBMCs, mixed sample, batch B, sublibrary 7

description:
Library name: batchB_Sublibrary_7
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.

library_source: transcriptomic single cell

molecule: total RNA

tag: cell type

tag: batch


title: Col-0_mock_mRNA_R3

city: Shanghai

first: qi

last: Tang

state: Shanghai

address: 复旦大学江湾校区生命科学学院

country: China

institute: Fudan University

description: Library name: Col-0_mock_mRNA_R3

data_processing:
For sRNA-seq, raw reads was filtered by TrimGalore (version 0.4.1) to trim adaptors and remove low-quality sequences. Alignment was performed with the shortstack using TAIR10 reference genome from Ensembl Plants with default parameters.
For lariat RNA-seq, raw reads was filtered by using Fastp (v0.23.2) to remove adapter and low-quality reads with parameters “-z 4 -q 20 -n 10 -c -t 1”. Alignment was performed with the HISAT2 (v2.2.1) using TAIR10 reference genome from Ensembl Plants with default parameters, and duplicates were removed by Samtools markdup (v1.14). Subread featureCounts was used to obtain counts for intron and loop region with parameters “-p -C -O -M - -fraction - -fracOverlap 1”, tail region with parameters “-p -C -O -M - -fraction - -minOverlap 10”. To normalize expression, FPKM of loop region was calculated with custom R script, and those transcripts with FPKM≥5 and the ratio of loop/tail ((loop reads/loop length)/(tail reads/tail length))>2 in all three replicates were identified as lariat RNAs.
For mRNA-seq analysis, FPKM of parent genes was calculated by StringTie (v2.2.1) with parameters “-e -G”.
Assembly: Ensembl
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Arabidopsis tissue (0.4 g) was ground in liquid nitrogen with 1.25 ml cold PEB buffer (200 mM Tris-HCl, pH 9.0; 200 mM KCl; 35 mM MgCl2; 25 mM Na2EDTA; 5 mM DTT; 1 % Brij-35 ; 1 % IGEPAL® CA-630; 1 % Tween 20; 1 % Triton X-100; 1 % polyoxyethylene 10 tridecyl ether; 1 % DOC; 0.5 x Cocktail; 1 mM PMSF; 100 μg/ml CHX; 100 μg/ml Chl; 0.5 U / ml RRI, and 10 units/mL DNase I [Invitrogen AM2238]) and incubated on ice for 20 mins. After centrifugation twice at 16,000 g for 15 mins at 4 °C, lysate contains mainly monosomes which were layered onto a 12 ml 15 % to 60 % sucrose gradient, and centrifuged at 4 °C in a Beckman SW41Ti rotor at 35,000 r.p.m. for 7 h. Samples were peak fractionated by A260 absorption using the gradient station (Biocomp). polysome fractions were collected and subjected to RNA extraction with Trizol LS.
For sRNA sequencing (sRNA-seq),we prepared sRNA libraries using the NEBNext Small RNA Library Prep Set for Illumina.For lariat RNA-seq, 20 μg of total RNA were incubated at 37°C for 1 h in 50 μL reactions with RNase R (Epicentre, USA) at a final concentration of 1 U RNase R per μg total RNA. Then, RNAs were purified using the RNA Clean & Concentrator-5 (Zymo Research) following the manufacturer’s instructions. A Ribo-off kit (Vazyme, Nanjing, China) was used to remove rRNA from the above RNase Rtreated RNAs. 50 ng of RNA for each sample was fragmented with Frag/Prime Buffer (Vazyme) at 80°C for 1 min and used as the starting material for strand-specific RNA-seq library preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme). For lncRNAseq, 5 μg of total RNA for each sample was treated by the Ribo-off kit to remove rRNA and RNA. 50 ng of RNA for each sample was fragmentated at 94°C for 5 min for strand-specific RNA-seq library preparation using the above kit. For Ribo-seq,the ribosome footprint fragments were repaired via T4 PNK (NEB M0201S) in the absence of ATP and rRNA depletion was performed using Ribo-off kit (Yeason 12254ES). RNA 3' ligation, 5' ligation, reverse transcription and Library Amplification were performed using The QIAseq miRNA Library Kit (QIAGEN 331595). The PCR amplified cDNA construct was purified using a Monarch PCR & DNA Kit (NEB T1030S). The cDNA was separated via 6% (w/v) TBE-PAGE 10-well gel and and the library of the expected size (~180 bp) was selected and recovered.

value: seedlings

tag: sample group


title: in vitro fertilization 18 days, sample 2

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

description:
Library name: 2_IVF_18d
IVF18_02:Counts

data_processing:
Quality control of raw reads (fastq files) was carried out using FastQC (v0.11.9)
Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! (v0.6.6)
Trimmed reads were aligned to the reference genome using STAR (v2.6.1d)
BAM file filtering and indexing was carried out using SAMtools (v1.9)
Duplicate reads were marked using Picard tools (v2.23.9)
Reads overlapping with exons were assigned to genes using featureCounts (v2.0.1)
Differential gene expression analysis was completed using DESeq2 (Galaxy Version 2.11.40.7+galaxy1)
Assembly: Bos taurus - assembly ARS-UCD1.2
Supplementary files format and content: tabular file include raw counts for each Sample

organism: Bos taurus

source_name: extracellular vesicles

growth_protocol: Non-lactating Nelore cows (Bos taurus indicus) with an average body condition score (BCS) of 3.0 ± 0.04 were selected and synchronized using a timed-AI protocol with estradiol benzoate. Artificial insemination (AI) and in vitro embryo production (IVF) were performed using semen from a single Angus bull (Bos taurus taurus).

extract_protocol:
Total RNA was extracted using the miRVana kit from Thermo Fisher Scientific Co.
Total RNA-Seq libraries were constructed from 150 ng of total RNA, using Zymo-Seq RiboFree Total RNA Library Kit according to manufacturer’s instructions.

treatment_protocol: On day 0, cows in the AI group were inseminated, while embryos were transferred to the IVF group on day 6.5. Slaughter took place on days 18 and 32 after AI and on days 12 and 26 post-embryo transfer (IVF group), representing key periods for maternal recognition (18 days) and early placental attachment (32 days). After slaughter, the reproductive tracts were immediately removed and kept on ice. On day 18, uterine horns were flushed with a saline solution to confirm pregnancy by embryo presence; on day 32, pregnancy was diagnosed via ultrasonography one day prior. Uterine fluid from 16 cows was collected and centrifuged to isolate extracellular vesicles, classified by size and concentration for AI and IVF on days 18 and 32. Samples from day 18 of the estrous cycle served as controls.

value: extracellular vesicles

value: in vitro fertilization


title: Col-0_mock_lariats_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_lariats_R1


title: Col-0_TuMV_mRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_mRNA_R1


title: Muscle, HFD, ctrl, rep4

description: Library name: WT_HFD_ctrl_muscle_4

source_name: skeletal muscle

value: skeletal muscle


title: PA1123-1


title: PBMCs, mixed sample, batch B, sublibrary 6

description:
Library name: batchB_Sublibrary_6
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.


title: Liver, HFD, ctrl, rep3

description: Library name: WT_HFD_ctrl_liver_3


title: artificial insemination 32 days, sample 2

description:
Library name: 2_AI_32d
AI32_02:Counts

value: artificial insemination


title: PA1075-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1075.xlsx

value: PA1075 mutant


title: Liver, HFD, ctrl, rep2

description: Library name: WT_HFD_ctrl_liver_2


title: PBMCs, mixed sample, batch B, sublibrary 5

description:
Library name: batchB_Sublibrary_5
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.

value: Blood


title: Col-0_mock_mRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_mRNA_R2


title: Col-0_mock_mRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_mRNA_R1


title: PA1075-1


title: PBMCs, mixed sample, batch B, sublibrary 4

description:
Library name: batchB_Sublibrary_4
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.

value: PBMCs


title: dbr1-2_mock_mRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_mRNA_R3


title: Liver, HFD, ctrl, rep1

description: Library name: WT_HFD_ctrl_liver_1


title: PA1050-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1050.xlsx

value: PA1050 mutant


title: PBMCs, mixed sample, batch B, sublibrary 3

description:
Library name: batchB_Sublibrary_3
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.

value: mixed sample

value: B


title: PA1050-1


title: Bhlhe40 ko_TL1A 3

city: New York

first: Wei

last: Yang

state: NY

address: Belfer Research Building,Room 760B,413 E. 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing.  After trimming the adaptors with cutadapt (version1.18) (https://cutadapt.readthedocs.io/en/v1.18/), RNA reads were aligned and mapped to the GRCm38 mouse reference genome by STAR (Version2.5.2) (https://github.com/alexdobin/STAR). and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/).  The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM)
Assembly: GRCm38 mouse reference genome
Supplementary files format and content: excel file includes normalized counts for each sample

source_name: Intestine

extract_protocol:
RNA was extracted and purified using RNeasy Plus Micro Kit (Qiagen)
libraries were generated using SMART-Seq® v4 Ultra® Low Input RNA Kit

value: Intestine

value: Bhlhe40 ko


title: PBMCs, mixed sample, batch B, sublibrary 2

description:
Library name: batchB_Sublibrary_2
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.


title: dbr1-2_TuMV_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_sRNA_R2


title: Bhlhe40 ko_TL1A 2


title: dbr1-2_TuMV_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_sRNA_R1


title: PA0990-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0990.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA0990 mutant


title: PBMCs, mixed sample, batch B, sublibrary 1

description:
Library name: batchB_Sublibrary_1
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.


title: Bhlhe40 ko_TL1A 1


title: dbr1-2_mock_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_sRNA_R3


title: PA0990-1

value: grow until mid-log phase in LB


title: Bhlhe40 het_TL1A 3

value: Bhlhe40 het


title: PBMCs, mixed sample, batch A, sublibrary 8

description:
Library name: batchA_Sublibrary8
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.

value: A


title: artificial insemination 18 days, sample 1

description:
Library name: 1_AI_18d
AI18_01:Counts

value: extracellular vesicles


title: PA1126-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1126.xlsx

value: PA1126 mutant


title: dbr1-2_mock_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_sRNA_R2

value: seedlings


title: PA0937-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0937.xlsx

value: PA0937 mutant


title: PBMCs, mixed sample, batch A, sublibrary 7

description:
Library name: batchA_Sublibrary7
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.


title: Bhlhe40 het_TL1A 2


title: PA0937-1


title: PBMCs, mixed sample, batch A, sublibrary 6

description:
Library name: batchA_Sublibrary6
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.


title: Bhlhe40 het_TL1A 1


title: dbr1-2_mock_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_sRNA_R1


title: Col-0_TuMV_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_sRNA_R3


title: Bhlhe40 ko_un3

value: un


title: PA0833-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0833.xlsx

value: PA0833 mutant


title: PBMCs, mixed sample, batch A, sublibrary 5

description:
Library name: batchA_Sublibrary5
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.

value: Blood

value: PBMCs


title: Col-0_TuMV_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_sRNA_R2


title: PA0833-1


title: PBMCs, mixed sample, batch A, sublibrary 4

description:
Library name: batchA_Sublibrary4
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.

value: mixed sample


title: Bhlhe40 ko_un2


title: Col-0_TuMV_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_sRNA_R1


title: PBMCs, mixed sample, batch A, sublibrary 3

description:
Library name: batchA_Sublibrary3
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.


title: PA0818-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0818.xlsx

value: PA0818 mutant


title: Bhlhe40 ko_un1

value: Intestine


title: PBMCs, mixed sample, batch A, sublibrary 2

description:
Library name: batchA_Sublibrary2
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.


title: Col-0_mock_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_sRNA_R3


title: Bhlhe40 het_un 3


title: Col-0_mock_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_sRNA_R2


title: PA0818-1


title: PBMCs, mixed sample, batch A, sublibrary 1

description:
Library name: batchA_Sublibrary1
Pooled Parse Evercode sublibrary containing multiplexed PBMC samples from multiple donors and stimulation conditions; sample identities were assigned computationally during demultiplexing using the Parse sample loading table and well assignments. Detailed sample-to-well mapping is provided in sample_metadata.tsv.


title: Bhlhe40 het_un 2


title: PA0793-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0793.xlsx

value: PA0793 mutant


title: Col-0_mock_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_sRNA_R1


title: PA0793-1

value: Pseudomonas aeruginosa PAO1


title: Bhlhe40 het_un 1


title: PA0695-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0695.xlsx

value: PA0695 mutant


title: kifunensine treatment, replicate3

city: HangZhou

first: Hua

last: Jiang

state: Zhejiang

address: Hangzhou, Zhejiang province, China

institute: Westlake University

description: Library name: kif_3

data_processing:
Rawdata (raw reads) of fastq format were firstly processed through fastp software. 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 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file to create splice-aware alignments, providing better alignment accuracy compared to other non-splice alignment tools.
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: csv file include FPKM values for each sample

source_name: cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing library.
Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

value: cell line

tag: cell line

value: TALL cell

value: WT

value: Kifuenensine


title: dbr1-2_dcl4-2_polysome_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_polysome_sRNA_R3


title: dbr1-2_dcl4-2_polysome_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_polysome_sRNA_R2


title: SKOV3 Cell line, shNC-3

city: Zhenjiang

first: Lumeng

last: Rui

address: NO.301 Xuefu Road

institute: Jiangsu University

description: Library name: sample 6

data_processing:
Comprehensive analyses were performed utilizing Trinity (v2.11.0), RSEM (v1.3.3), DESeq2 (v1.26.0), and edgeR (v3.32.1).
Assembly: The filtered transcriptomic sequences were aligned to the reference genome using STAR (version 2.7.9a) with default parameters, and the alignment statistics were subsequently generated.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: ovary

extract_protocol:
Total RNA was extracted from JUP-knockdown SKOV3 cells and control (shNC) SKOV3 cells from three independent biological replicates. RNA high-throughput sequencing was performed by Wuhan Benagen Tech Solutions Company Limited (Wuhan, China). Fragments per kilobase of exon per million fragments mapped (FPKM) values were calculated as the expression profiles of mRNAs using Cuffdiff software.
Enrich mRNA using oligo(dT) magnetic beads. Add fragmentation reagents to the enriched mRNA to fragment it. Synthesize first-strand and second-strand cDNA from the fragmented mRNA according to the standard procedures. Then, complete the entire library preparation through steps including end repair, A-tailing, adapter ligation, purification, PCR amplification, and product circularization. After the library passes quality control, perform sequencing using the BGI high-throughput sequencing platform DNBSEQ.

value: ovary

value: human ovarian cancer cell


title: PA0695-1

value: grow until mid-log phase in LB


title: kifunensine treatment, replicate2

description: Library name: kif_2


title: kifunensine treatment, replicate1

description: Library name: kif_1


title: SKOV3 Cell line, shNC-2

description: Library name: sample 5


title: dbr1-2_TuMV_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_sRNA_R3

value: seedlings


title: dbr1-2_dcl4-2_polysome_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_polysome_sRNA_R1


title: PA0659-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0659.xlsx

value: PA0659 mutant


title: SKOV3 Cell line, shNC-1

description: Library name: sample 4


title: dbz treatment, replicate3

description: Library name: dbz_3

value: dbz


title: dbr1-2_polysome_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_polysome_sRNA_R3


title: dbz treatment, replicate2

description: Library name: dbz_2


title: PA0659-1


title: dbr1-2_polysome_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_polysome_sRNA_R2


title: PA0269-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0269.xlsx

value: PA0269 mutant


title: dbz treatment, replicate1

description: Library name: dbz_1


title: SKOV3 Cell line, shJUP-2

description: Library name: sample 2

value: JUP knockdown


title: SKOV3 Cell line, shJUP-3

description: Library name: sample 3


title: dbr1-2_polysome_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_polysome_sRNA_R1


title: PA0269-1


title: DOCK2 KO, replicate3

description: Library name: KO_3

value: DOCK4 KO


title: SKOV3 Cell line, shJUP-1

description: Library name: sample 1


title: Col-0_polysome_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_polysome_sRNA_R3


title: PA0239-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0239.xlsx

value: PA0239 mutant


title: PA0239-1


title: White Leghorn chicken male gonadal PGC line IP6 with non-adherent capture of MEF feeder layer, CF1 MitC-treated

first: Matthew

middle: T

last: Biegler

address: 1230 York Ave

institute: The Rockefeller University

description:
Library name: cN150
White Leghorn chicken male gonadal PGC line IP6 with non-adherent capture of Mouse Embryonic Fibroblast feeder layer, CF1 MitC-treated
10X genomics

data_processing:
Quality control analysis was performed using similar approaches in our previous study28. Briefly, raw sequencing data, was aligned to either the zebra finch, chicken, or mouse reference genome (depending on the sample) using CellRanger (v6.0.1). The DIV150 chicken dataset was also aligned to a concatenated chicken and mouse assembly for competitive mapping. Subsequent processing steps (quality controls and barcode trimming) were performed using R (v4.4.1) with soupX (v1.5.2), Seurat (v5.1.0), and DoubletFinder (v2.0.4).
Metadata for each cell barcode passing quality controls may be found in Table S2 of the associated study.
Assembly: Zebra Finch - bTaeGut1.4.pri: GCF_003957565.2 with custom GTF Chicken - Galgal6a: GCF000002315.6 with custom GTF Mouse - mm10_2020_A (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz)
Supplementary files format and content: barcodes.tsv.gz is a standard cellranger output denoting the cellbarcodes identified in the dataset
Supplementary files format and content: features.tsv.gz is a standard cellranger output denoting the gene IDs identified in the dataset
Supplementary files format and content: matrix.tsv.gz is a standard cellranger output denoting the gene counts per cell barcode identified in the dataset

organism: Gallus gallus

growth_protocol: Gonadal cultures from HH28 zebra finch and chicken embryos were generated as previously described9,27, incubated at 37°C and 5% CO2 in a Heracell VIOS 160i incubator (Thermo Scientific). Cell culture media recipes used are available in Table S16 of the associated manuscript.  For each primary culture pool, forty embryos (unsexed male and female) were pooled and dissociated at 37°C with 0.05% trypsin (zebra finch: 5min; chicken: 15min) and equally split across multiple wells of a 12-well plate (zebra finch = 8 wells; chicken = 12 wells). For the non-adherent fraction, the supernatant was collected from all wells after briefly swirling the plate and pelleted at 300xg for 5min. For the adherent cells, wells were washed twice with HBSS and dissociated with 0.05% trypsin for 5min, neutralized in PGC media, and pelleted at 300xg for 5min. For each fraction, half of the pellets were taken for DIV3 samples, while the remaining cells were resuspended in fresh PGC media and incubated in 4-6 wells until DIV6.  To generate a long-term chicken PGC line, gonads from single embryos were cultured as in the short-term gonadal cultures for more than one month before transfer to wells with a feeder layer of CF1 MitC-treated MEFs (Gibco, Cat. #A34959) in the same chicken PGC media conditions. One male chicken PGC line, designated IP6, proliferated for multiple months. At DIV150, we purified the cultures through dead-cell removal by MACS (Miltenyi Biotec, Cat. #130-090-101) and stored cryopreserved cells in a 5:4:1 mix of chicken PGC culture media (Table S16), FBS, and DMSO.

extract_protocol:
Pelleted and FACS-sorted samples were immediately processed for scRNAseq, as previously reported28. For the DIV150 chicken cells, a cryovial was thawed and cultured for at least one week prior to collecting the cell suspension. Appropriate volumes of water and cell suspension to yield approximately 7,000 cells per sample, following the manufacturer’s instructions for Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit (v3). The droplet emulsion was reverse transcribed at 53˚C for 45 min before heat deactivation at 85˚C for 5 min and cDNA amplification. cDNA was measured on a Qubit Fluorometer (ThermoFisher #Q33238) and validated for size and purity on an Agilent Fragment Analyzer (#M5310AA) using the High Sensitivity NGS Kit (Agilent, Cat. #DNF-474-0500).
cDNA samples were normalized (zebra finch: 100ng/sample; chicken: 50ng/sample) for Illumina sequencing library preparation following the 10x Genomics protocol (Chromium Single Cell 3’ Reagent Kit v3). Illumina libraries were quantified using a Qubit Fluorometer (Thermo, Cat. #Q33238) and visualized using an Agilent Fragment Analyzer (#M5310AA, DNF-474-0500). Libraries were labeled using the Chromium i7 Multiplex Kit (10X Genomics, Cat. #PN-120262) and sequenced on a NovaSeq S4 (pair-ended with read lengths of 150bp).

treatment_protocol: Non-adherent cells were pelleted at 250xg for 3min and resuspended in 0.05% trypsin-EDTA at 37˚C (zebra finch: 10min; chicken: 3.5min). Trypsin was inactivated with an equal volume of PGC media before pelleting and resuspension in Sorting Buffer (Table S16). Following non-adherent cell aspiration, the adherent cell layer was dissociated with Accutase (Sigma, Cat. #A6964) for 10min. Cells were dislodged by gentle tapping, pelleted at 250xg for 3min, and resuspended in Sorting Buffer. All cell suspensions were filtered through a 40µm cell strainer (Bel-Art, Cat. #03-421-228) immediately before sorting on a BD FACSAria™ II at The Rockefeller University Flow Cytometry Resource Center (RRID:SCR_017694) for dead cell and debris exclusion using DAPI.

tag: Sex

value: Male

tag: days in_vitro

value: 150 days in vitro

value: White Leghorn male PGCs cultured on MEF feeder layer


title: Col-0_polysome_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_polysome_sRNA_R2


title: DOCK2 KO, replicate2

description: Library name: KO_2

value: cell line

value: DOCK3 KO


title: PA1789-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1789.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA1789 mutant


title: Col-0_polysome_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_polysome_sRNA_R1


title: Chicken gonadal cultures DIV6, batch B, non-adherent fraction

description:
Library name: cN6B
10X genomics

source_name: primary cell culture

value: pooled male and female

value: primary cell culture

value: 6 days in vitro

value: embryonic gonadal cell cultures (HH28)

value: B


title: DOCK2 KO, replicate1

description: Library name: KO_1

value: TALL cell

value: DOCK2 KO


title: PA0238-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0238.xlsx

value: PA0238 mutant

value: grow until mid-log phase in LB


title: WT, replicate3

description: Library name: WT_3

value: WT


title: Chicken gonadal cultures DIV3, batch B, adherent fraction

description:
Library name: cA3B
10X genomics

value: 3 days in vitro


title: PA0238-1


title: WT, replicate2

description: Library name: WT_2


title: PA0068-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0068.xlsx

value: PA0068 mutant


title: dbr1-2_AGO1_IP_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_AGO1_IP_sRNA_R2

source_name: Inflorescence

value: Inflorescence


title: WT, replicate1

description: Library name: WT_1

value: cell line


title: dbr1-2_AGO1_IP_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_AGO1_IP_sRNA_R3


title: Chicken gonadal cultures DIV3, batch B, non-adherent fraction

description:
Library name: cN3B
10X genomics


title: in vitro fertilization 32 days, sample 1

description:
Library name: 1_IVF_32d
IVF32_01:Counts

value: extracellular vesicles

value: in vitro fertilization


title: dbr1-2_AGO1_IP_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_AGO1_IP_sRNA_R1


title: PA0068-1

value: Pseudomonas aeruginosa PAO1


title: Chicken gonadal cultures DIV3, batch A, non-adherent fraction

description:
Library name: cN3A
10X genomics

value: pooled male and female

value: A


title: SmartSeq_batch2

city: Bethesda

first: Chaim

middle: A

last: Schramm

state: MD

address: 40 Convent Dr

department: Vaccine Research Center

institute: NIAID, NIH

description:
Library name: SmartSeq_batch2
polyA RNA via SmartSeq

data_processing:
SmartSeq: Sequencing reads were demultiplexed and V(D)J sequences were assembled using BALDR. Sequences were then filtered using a custom script (https://github.com/scharch/filterBALDR) to remove incomplete sequences. Filtered sequences were annotated with SONAR v4.2. The OGRDB database was used to identify and annotate V, D, and J genes using IMGT nomenclature
10x: For sequences generated from 10x Chromium, reads from the hashing libraries were analyzed with Cell Ranger (10x Genomics). The resulting count matrix was loaded into Seurat for downstream analysis, and sample identities were assigned using the HTODemux function.  For the V(D)J libraries, paired-end reads were subjected to preprocessing, merging, and annotation in SONAR under single-cell mode with UMI detection enabled, using default settings. For all analyses, we discarded any nonproductive rearrangements and cells with multiple heavy or light chains. To assemble lineage trees, sequences were analyzed using SONAR v4 in single cell mode.
Assembly: OGRDB Homo Sapiens Germline Reference Set
Supplementary files format and content: AIRR-formated VDJ sequences recovered from B cells
Supplementary files format and content: tab-delimited HTO assignments for each cell
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: PBMC

extract_protocol:
RNA was extracted from single B cells using RNA clean XP beads (Beckman Coulter) and 5’ RACE was performed to synthesize and amplify cDNA. A second round of PCR was performed to amplify DNA for IgG, IgA, IgK, and IgL sequences.
SmartSeq: Ig enrichment products were prepared into DNA libraries using the Illumina Nextera XT library preparation kit (Illumina). The Illumina-ready libraries were sequenced on a Nextseq 2000 (Illumina) using a P1 300 cycle kit (Illumina) for paired end 2x150 base pair reads to obtain V(D)J sequences;10x:To analyze the V(D)J repertoires sorted single B cells, a cell suspension was loaded on the 10x Genomics Chromium Instrument with reagents from the Next GEM Single Cell 5’ Kit v2 (10x Genomics P/N 1000263) to generate gel bead-in emulsions. Following the manufacturer’s protocol, GEM-RT was performed followed by purification and amplification of the total cDNA. Heavy and light chains were amplified using Ig-specific 3’ primers with the addition of Illumina sequences. The Illumina-ready libraries were sequenced on a Nextseq 2000 (Illumina) using a P1 600 cycle kit for paired end 2x 300 base pair reads. For hashing data, the 10x Genomics protocol for sequencing of surface DNA was followed.

value: PBMC

value: Memory B cells

tag: time

value: Pre and Post XBB

tag: tags


title: Col-0_mock_lariats_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_lariats_R2

value: seedlings


title: mesenteric lymph nodes single cells from Bhlhe40 ko mice treated with agonist DR3

description: Library name: scBhlhe40-KO-aDR3

data_processing:
Reads were aligned to the mm10-2020-A reference genome with Cell Ranger 9.0.0 (10x Genomics), and raw count matrices were imported into Seurat v5. Cells from all conditions were merged into a single Seurat object with uniquely prefixed barcodes to retain sample identity. Cells with 200–7,500 detected genes and <5% mitochondrial transcripts were retained for downstream analysis.
Assembly: Mouse mm10 (10x Genomics reference package mm10-2020-A).
Supplementary files format and content: Processed data include: (1) per-sample 10x Genomics sparse matrices (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz) containing gene-by-cell UMI counts; (2) an integrated Seurat v5 .rds object containing merged runs with integrated embeddings, clustering, and annotations; and (3) a .csv table with one row per cell barcode containing run/sample identifiers, QC metrics, cluster IDs, and cell-type annotations.

source_name: mesenteric lymph nodes

extract_protocol:
Mesenteric lymph nodes(MLNs) were enzymatically digested in R10 media containing 100U/ml type VIII collagenase and 150ug/ml DNase I for 30 min at 37°C.CD45+MHCII+Lineage- cells were isolated from the MLNs.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell platform according to the manufacturer’s instructions.

value: mesenteric lymph nodes

value: KO

value: agonist DR3


title: dbr1-2_rdr126_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_rdr126_sRNA_R3


title: Muscle_Day14_immobilisation [20171208-0063]

type: genomic

city: Robina

first: Paul

last: Dunn

state: QLD

address: 14 University Dr

country: Australia

institute: Bond University

description: bisulfite conveted DNAextracted fromMuscle_Day14_immobilisation

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to human infium methylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
Channel intensities in IDAT files were analysed using MINIFI 1.28.0. Methylation distribution range was assessed using a beta density plot to check for probe type bias. Filtering was performed based on P-value detection (>0.01), beadcount (<3 in at least  5% samples), non-CpG probes, cross-reactive probes, and probes containing SNPs.
Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

source_name: vastus lateralis muscle

label_protocol: Standard Illumina protocol

extract_protocol: DNA was bound to the AllPrep DNA Mini spin column (Qiagen) and oncolumn digestion performed with Proteinase K. 250ng of each DNA sample underwent bisulfite conversion using the EZ DNA  Methylation Kit (Zymo Research, Irine, CA, USA)

value: vastus lateralis muscle

value: Day 14


title: SmartSeq_batch1

description:
Library name: SmartSeq_batch1
polyA RNA via SmartSeq


title: mesenteric lymph nodes single cells from Bhlhe40 ko mice

description: Library name: scBhlhe40-KO


title: dbr1-2_rdr126_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_rdr126_sRNA_R2


title: Muscle_Day14_immobilisation [20171208-0062]


title: mesenteric lymph nodes single cells from Bhlhe40 het mice treaed with agonist DR3

description: Library name: scBhlhe40-Het-aDR3

value: Het


title: dbr1-2_rdr126_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_rdr126_sRNA_R1

value: Inflorescence


title: Muscle_Day14_immobilisation [20171208-0061]


title: 10xHTO_batch2

description:
Library name: 10xHTO_batch2
Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: other

value: Pre and Post KP.2

value: COVEND.041_PreKP.2/totalseq-C0251; COVEND.041_PostKP.2/totalseq-C0252; COVEND.045_PreKP.2/totalseq-C0253; COVEND.045_PostKP.2/totalseq-C0254; COVEND.046_PreKP.2/totalseq-C0255; COVEND.046_PostKP.2/totalseq-C0256; COVEND.049_PreKP.2/totalseq-C0257; COVEND.049_PostKP.2/totalseq-C0258; COVEND.052_PreKP.2/totalseq-C0259; COVEND.052_PostKP.2/totalseq-C0260; COVEND.053_PreKP.2/totalseq-C0261; COVEND.053_PostKP.2/totalseq-C0262; COVEND.060_PreKP.2/totalseq-C0263; COVEND.060_PostKP.2/totalseq-C0264


title: 10xVDJ_batch2

description:
Library name: 10xVDJ_batch2
IGG/IGA/IGK/IGL enriched from polyA RNA via 10x Chromimum


title: dbr1-2_dcl4-2_Ribo_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_Ribo_R2

data_processing:
For sRNA-seq, raw reads was filtered by TrimGalore (version 0.4.1) to trim adaptors and remove low-quality sequences. Alignment was performed with the shortstack using TAIR10 reference genome from Ensembl Plants with default parameters.
For lariat RNA-seq, raw reads was filtered by using Fastp (v0.23.2) to remove adapter and low-quality reads with parameters “-z 4 -q 20 -n 10 -c -t 1”. Alignment was performed with the HISAT2 (v2.2.1) using TAIR10 reference genome from Ensembl Plants with default parameters, and duplicates were removed by Samtools markdup (v1.14). Subread featureCounts was used to obtain counts for intron and loop region with parameters “-p -C -O -M - -fraction - -fracOverlap 1”, tail region with parameters “-p -C -O -M - -fraction - -minOverlap 10”. To normalize expression, FPKM of loop region was calculated with custom R script, and those transcripts with FPKM≥5 and the ratio of loop/tail ((loop reads/loop length)/(tail reads/tail length))>2 in all three replicates were identified as lariat RNAs.
For mRNA-seq analysis, FPKM of parent genes was calculated by StringTie (v2.2.1) with parameters “-e -G”.
For Ribo-seq, raw reads was filtered by TrimGalore (version 0.4.1) to trim adaptors and remove low-quality sequences. We first built a Bowtie2 (v. 2.3.4.1) index with the bowtie2-build function for removing unwanted contaminating sequences such as those from rRNAs, tRNAs, snRNAs, and snoRNAs. We mapped the remaining Ribo-seq reads from Step 2 with STAR aligner using the following options: --alignIntronMax 5000, --alignIntronMin 15, --outFilterMismatchNmax 1, --outFilterMultimapNmax 20, --outFilterType BySJout, --alignSJoverhangMin 8, --alignSJDBoverhangMin 2, --outSAMtype BAM SortedByCoordinate, --quantMode TranscriptomeSAM, --outSAMmultNmax 1, --outMultimapperOrder Random.
Assembly: Ensembl
Supplementary files format and content: bigWig
Library strategy: Ribo-Seq

extract_protocol:
Arabidopsis tissue (0.4 g) was ground in liquid nitrogen with 1.25 ml cold PEB buffer (200 mM Tris-HCl, pH 9.0; 200 mM KCl; 35 mM MgCl2; 25 mM Na2EDTA; 5 mM DTT; 1 % Brij-35 ; 1 % IGEPAL® CA-630; 1 % Tween 20; 1 % Triton X-100; 1 % polyoxyethylene 10 tridecyl ether; 1 % DOC; 0.5 x Cocktail; 1 mM PMSF; 100 μg/ml CHX; 100 μg/ml Chl; 0.5 U / ml RRI, and 10 units/mL DNase I [Invitrogen AM2238]) and incubated on ice for 20 mins. After centrifugation twice at 16,000 g for 15 mins at 4 °C, 1.2 mL of the clarified lysate were incubated with 5 μl of RNase T1 (Thermo EN0541, 1.25 µl /per 0.1g plant materials) for 1 h at room temperature with gentle rotation to degrade mRNA regions that are not covered and protected by translating ribosomes. The ribonuclease-treated lysate contains mainly monosomes which were layered onto a 12 ml 15 % to 60 % sucrose gradient, and centrifuged at 4 °C in a Beckman SW41Ti rotor at 35,000 r.p.m. for 7 h. Samples were peak fractionated by A260 absorption using the gradient station (Biocomp). Monosome fractions were collected and subjected to RNA extraction with Trizol LS. The purified RNA was separated via 17% (w/v) TBE-urea PAGE gel, and gel slices corresponding to 26–34 nt were excised. Ribosome footprint fragments were recovered and used for library construction.
For sRNA sequencing (sRNA-seq),we prepared sRNA libraries using the NEBNext Small RNA Library Prep Set for Illumina.For lariat RNA-seq, 20 μg of total RNA were incubated at 37°C for 1 h in 50 μL reactions with RNase R (Epicentre, USA) at a final concentration of 1 U RNase R per μg total RNA. Then, RNAs were purified using the RNA Clean & Concentrator-5 (Zymo Research) following the manufacturer’s instructions. A Ribo-off kit (Vazyme, Nanjing, China) was used to remove rRNA from the above RNase Rtreated RNAs. 50 ng of RNA for each sample was fragmented with Frag/Prime Buffer (Vazyme) at 80°C for 1 min and used as the starting material for strand-specific RNA-seq library preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme). For lncRNAseq, 5 μg of total RNA for each sample was treated by the Ribo-off kit to remove rRNA and RNA. 50 ng of RNA for each sample was fragmentated at 94°C for 5 min for strand-specific RNA-seq library preparation using the above kit. For Ribo-seq,the ribosome footprint fragments were repaired via T4 PNK (NEB M0201S) in the absence of ATP and rRNA depletion was performed using Ribo-off kit (Yeason 12254ES). RNA 3' ligation, 5' ligation, reverse transcription and Library Amplification were performed using The QIAseq miRNA Library Kit (QIAGEN 331595). The PCR amplified cDNA construct was purified using a Monarch PCR & DNA Kit (NEB T1030S). The cDNA was separated via 6% (w/v) TBE-PAGE 10-well gel and and the library of the expected size (~180 bp) was selected and recovered.


title: Muscle_Day14_immobilisation [20171208-0060]


title: mesenteric lymph nodes single cells from Bhlhe40 het mice

description: Library name: scBhlhe40-Het


title: dbr1-2_dcl4-2_Ribo_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_Ribo_R1


title: pre-aged HSC Selp_low 3 (ATAC-seq)

city: Tianjin

first: Chong

state: Tianjin

address: 288 Nanjing Rd, Tianjin 300020, China.

institute: Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: L3

library_source: genomic

data_processing:
Raw reads were processed using fastp (v0.20.0) to obtain clean reads by removing adapters, poly-N sequences, and low-quality reads (base quality < 15 for > 40% of the read; length < 18 bp).
Clean reads were aligned to the reference genome using BWA-mem (v0.7.12). Alignments were filtered to remove mitochondrial and chloroplast DNA, improperly paired reads, and PCR duplicates.
Peaks were called using MACS2 (v2.1.0) with a q-value threshold of 0.05.
Motif discovery was performed on 500 bp regions centered on peak summits using HOMER (v4.9.1). Peak annotation and assignment to nearest genes were performed with ChIPseeker, followed by KEGG pathway analysis using KOBAS. Differential peaks between groups were identified by merging peaks with bedtools, calculating mean RPM, and selecting peaks with |log2 fold change| >1; associated genes were annotated using ChIPseeker.
Assembly: mm39
Supplementary files format and content: ATAC-seq signal tracks were generated as normalized genome-wide coverage files in bedGraph format using the mm39 reference genome assembly. For each sample (H1, H2, H3, L1, L2, L3, Y1, Y2, Y3), files were split by chromosome and provided as compressed .bedGraph.gz files. Each file contains chromosome coordinates and quantitative accessibility signal values.

source_name: Bone marrow

extract_protocol:
Nuclei were isolated from bone marrow cells using the lysis reagents provided in the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme).
ATAC-seq libraries were prepared using the Hyperactive ATAC-Seq Library Prep Kit for Illumina and TruePrep Index Kit V2 for Illumina (Vazyme), following the manufacturer’s instructions. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). The library preparations were sequenced on an Illumina NovaSeq platform at Tianjin Novogene Bioinformatic Technology Co., Ltd, generating 150 bp paired-end reads.

value: Bone marrow


title: 10xHTO_batch1

description:
Library name: 10xHTO_batch1
Hashtag-derived oligonucleotide (HTO)

value: COVEND.001_PreKP.2/totalseq-C0251; COVEND.001_PostKP.2/totalseq-C0252; COVEND.004_PreKP.2/totalseq-C0253; COVEND.004_PostKP.2/totalseq-C0254; COVEND.009_PreKP.2/totalseq-C0255; COVEND.009_PostKP.2/totalseq-C0256; COVEND.011_PreKP.2/totalseq-C0257; COVEND.011_PostKP.2/totalseq-C0258; COVEND.015_PreKP.2/totalseq-C0259; COVEND.015_PostKP.2/totalseq-C0260; COVEND.033_PreKP.2/totalseq-C0261; COVEND.033_PostKP.2/totalseq-C0262; COVEND.037_PreKP.2/totalseq-C0263; COVEND.037_PostKP.2/totalseq-C0264


title: Muscle_Day14_immobilisation [20171208-0059]


title: 10xVDJ_batch1

description:
Library name: 10xVDJ_batch1
IGG/IGA/IGK/IGL enriched from polyA RNA via 10x Chromimum


title: Muscle_Day14_immobilisation [20171208-0057]


title: Muscle_Day14_immobilisation [20171208-0058]


title: A portion of gall bladder2

city: Valhalla

first: Ravi

last: Sachidanandam

address: 15 Dana Road

institute: NYMC

description:
Library name: T0160
50nt Forward & 72nt Reverse

data_processing:
Kraken2
Assembly: Kraken2_db_uhgg_v2.0.2
Supplementary files format and content: kraken_all.tsv

source_name: Gallbladder 3

extract_protocol:
Trizol method was used for RNA extraction from dissected tissue samples from human
NEXTFLEX® Small RNA-Seq https://resources.revvity.com/pdfs/man-nova-5132-XX-mn-nextflex-small-rna-seq-kit-v4-with-udis.pdf

value: Gallbladder 3


title: dbr1-2_Ribo_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_Ribo_R1


title: dbr1-2_Ribo_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_Ribo_R2


title: pre-aged HSC Selp_low 1 (ATAC-seq)

description: Library name: L1


title: pre-aged HSC Selp_low 2 (ATAC-seq)

description: Library name: L2


title: Col-0_Ribo_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_Ribo_R2


title: A portion of gall bladder1

description:
Library name: T0140
50nt Forward & 72nt Reverse

source_name: Gallbladder 2

value: Gallbladder 2


title: Muscle_Day14_immobilisation [20171208-0056]


title: pre-aged HSC Selp_high 3 (ATAC-seq)

description: Library name: H3


title: Half of Polypoid nodule of gallbladder

description:
Library name: T0130
50nt Forward & 72nt Reverse

source_name: Gallbladder 1

value: Gallbladder 1


title: Col-0_Ribo_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_Ribo_R1


title: pre-aged HSC Selp_high 2 (ATAC-seq)

description: Library name: H2


title: Muscle_Day14_immobilisation [20171208-0055]


title: A portion of stomach2

description:
Library name: T0120
50nt Forward & 72nt Reverse

source_name: Stomach 2

value: Stomach 2


title: dbr1-2_dcl4-2_mRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_mRNA_R3

data_processing:
For sRNA-seq, raw reads was filtered by TrimGalore (version 0.4.1) to trim adaptors and remove low-quality sequences. Alignment was performed with the shortstack using TAIR10 reference genome from Ensembl Plants with default parameters.
For lariat RNA-seq, raw reads was filtered by using Fastp (v0.23.2) to remove adapter and low-quality reads with parameters “-z 4 -q 20 -n 10 -c -t 1”. Alignment was performed with the HISAT2 (v2.2.1) using TAIR10 reference genome from Ensembl Plants with default parameters, and duplicates were removed by Samtools markdup (v1.14). Subread featureCounts was used to obtain counts for intron and loop region with parameters “-p -C -O -M - -fraction - -fracOverlap 1”, tail region with parameters “-p -C -O -M - -fraction - -minOverlap 10”. To normalize expression, FPKM of loop region was calculated with custom R script, and those transcripts with FPKM≥5 and the ratio of loop/tail ((loop reads/loop length)/(tail reads/tail length))>2 in all three replicates were identified as lariat RNAs.
For mRNA-seq analysis, FPKM of parent genes was calculated by StringTie (v2.2.1) with parameters “-e -G”.
For Ribo-seq, raw reads was filtered by TrimGalore (version 0.4.1) to trim adaptors and remove low-quality sequences. We first built a Bowtie2 (v. 2.3.4.1) index with the bowtie2-build function for removing unwanted contaminating sequences such as those from rRNAs, tRNAs, snRNAs, and snoRNAs. We mapped the remaining Ribo-seq reads from Step 2 with STAR aligner using the following options: --alignIntronMax 5000, --alignIntronMin 15, --outFilterMismatchNmax 1, --outFilterMultimapNmax 20, --outFilterType BySJout, --alignSJoverhangMin 8, --alignSJDBoverhangMin 2, --outSAMtype BAM SortedByCoordinate, --quantMode TranscriptomeSAM, --outSAMmultNmax 1, --outMultimapperOrder Random.
Assembly: Ensembl
Supplementary files format and content: bigWig


title: Muscle_Day14_immobilisation [20171208-0054]


title: A portion of stomach1

description:
Library name: T0110
50nt Forward & 72nt Reverse

source_name: Stomach 1

value: Stomach 1


title: Muscle_Day14_immobilisation [20171208-0053]


title: dbr1-2_dcl4-2_mRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_mRNA_R2

source_name: seedlings

value: seedlings


title: pre-aged HSC Selp_high 1 (ATAC-seq)

description: Library name: H1


title: A large solid nodule of ovary

description:
Library name: T0040
50nt Forward & 72nt Reverse

source_name: Ovary

value: Ovary


title: young HSC 3 (ATAC-seq)

description: Library name: Y3


title: dbr1-2_dcl4-2_mRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_mRNA_R1


title: young HSC 2 (ATAC-seq)

description: Library name: Y2


title: A mass near the left ventricular apex of Heart

description:
Library name: T0030
50nt Forward & 72nt Reverse

source_name: Heart

value: Heart


title: Muscle_Day14_immobilisation [20171208-0052]


title: dbr1-2_mRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mRNA_R3


title: young HSC 1 (ATAC-seq)

description: Library name: Y1


title: A portion of placenta

description:
Library name: T0020
50nt Forward & 72nt Reverse

source_name: Placenta

value: Placenta


title: pre-aged HSC Selp_low 3 (RNA-seq)

description: Library name: L3

data_processing:
Illumina Casava 1.8 software used for basecalling.
Raw data (raw reads) in FASTQ format were first processed. In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data. Meanwhile, the Q20, Q30, and GC content of the clean data were calculated. All subsequent analyses were based on the high-quality clean data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.2.1 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.2.1.
FeatureCounts v2.0.6 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.42.0).
Assembly: mm39
Supplementary files format and content: Tab-delimited text file containing raw gene counts for each sample

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
cDNA was synthesized using the SMARTer® Ultra® Low RNA Kit for Illumina® (Takara Bio/Clontech) following the manufacturer’s instructions. Libraries were constructed using TruePrep DNA Library Prep Kit V2 for Illumina (TD503-02) following manufacturer's protocols.


title: Muscle_Day14_immobilisation [20171208-0050]

value: vastus lateralis muscle


title: dbr1-2_mRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mRNA_R2


title: pre-aged HSC Selp_low 2 (RNA-seq)

description: Library name: L2


title: Muscle_Day14_immobilisation [20171208-0049]

value: Day 14


title: dbr1-2_mRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mRNA_R1


title: Muscle_Day14_immobilisation [20171208-0051]


city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: DZNE Göttingen

description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_4_L003

data_processing:
Raw BCL files were demultiplexed (using cellranger mkfastq), mapped and counts files were generated using cellranger count (cellranger-6.1.0), using default settings.
Assembly: hg38 pre-mRNA
Supplementary files format and content: The processed data files include unfiltered (raw) and filtered feature-barcode matrices in the MEX (Market Exchange) file format ouput by CellRanger.

source_name: innervated engineered human myocardium (iEHM)

extract_protocol:
Frozen iEHMs were used to isolate nuclei, adapted from Sakib et. al. [PMID: 33554149] with modifications. In brief, 500 µL EZ prep nuclei lysis buffer (Sigma, #NUC101) were added to the frozen samples and dounce homogenized for 40-60 strokes (until not big tissue chunks were seen) using plastic pestles in a 1.5 mL DNA low bind tube. Lysates were transferred into a 2 mL DNA low bind tube and additional lysis buffer were supplemented to fill up to 2 mL mark. Samples were incubated for 5 minutes on ice and later centrifuged for 500 xg for 5 minutes at 4 °C. Supernatants were discarded and the nuclei pellets were resuspended into 2 mL lysis buffer, and incubated on ice for 5 minutes. After centrifugation (500 xg, 5 minutes, 4 °C), the pellet was resuspended into Nuclei Suspension buffer, NSB (0.5% OmniPur BSA (Merck Millipore, #2905), 1:200 RNasin® Ribonuclease Inhibitor (Promega, #N2615), 1x cOmplete™, EDTA-free Protease Inhibitor Cocktail (Roche, #04693132001), dissolved in 1x PBS (RNAse free, Invitrogen, #AM9624). Filtered through 0.22 µm Syringe Filter Unit (Millipore, #SLGVR33RB)). It was centrifuged again for 500 xg, 5 minutes at 4 °C, and resuspended into 500 µL NSB. The lysate was strained through 40 µM Flowmi® Cell Strainers (Sigma, #BAH136800040) into a FACS tube. 1:500 of 7-AAD (Invitrogen, #00-6993-50) nuclei staining solution was added and nuclei were gated from the debris (Supplementary Figure 8) and sorted with a BD FACSaria III with 85 µM Nozzle, in a 15 mL falcon tube, coated with and containing 1 mL NSB. Around 200,000 nuclei were sorted per sample.
Sorted iEHM nuclei were immediately taken to process for single nuclei barcoding using 10X Genomics Chromium Single Cell 3' Reagent Kits (v3 Chemistry). 5000 nuclei were subjected to GEM generation and barcoding using Chromium Controller, according to the manufacturer’s protocol. For cDNA amplification, 14 PCR cycles were used. Indexed cDNA libraries were pooled into a single pool and sequenced 4 times in Illumina NextSeq 550 to achieve >50,000 reads/nuclei.


title: pre-aged HSC Selp_low 1 (RNA-seq)

description: Library name: L1


title: Col-0_mRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mRNA_R3


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_4_L004

value: innervated engineered human myocardium (iEHM)


title: pre-aged HSC Selp_high 3 (RNA-seq)

description: Library name: H3


title: Col-0_mRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mRNA_R2


title: Muscle_Day14_immobilisation [20171208-0048]


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_4_L002


title: Muscle_Day14_immobilisation [20171208-0047]

description: bisulfite conveted DNAextracted fromMuscle_Day14_immobilisation


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_4_L001


title: pre-aged HSC Selp_high 2 (RNA-seq)

description: Library name: H2


title: Col-0_mRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mRNA_R1


title: pre-aged HSC Selp_high 1 (RNA-seq)

description: Library name: H1


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_3_L004


title: Muscle_Day14_immobilisation [20171208-0046]


title: dbr1-2_lariats_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_lariats_R3


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_3_L003


title: young HSC 3 (RNA-seq)

description: Library name: Y3


title: Muscle_Day14_immobilisation [20171208-0045]


title: dbr1-2_lariats_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_lariats_R2


title: Muscle_Day14_immobilisation [20171208-0044]


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_3_L002


title: dbr1-2_lariats_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_lariats_R1


title: young HSC 2 (RNA-seq)

description: Library name: Y2


title: Muscle_Day14_immobilisation [20171208-0043]


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_3_L001


title: young HSC 1 (RNA-seq)

description: Library name: Y1


title: Col-0_lariats_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_lariats_R3


title: Bhlhe40 ko_IL23 3

description: Library name: Sample 21

source_name: Intestine

value: Intestine

value: Bhlhe40 ko


title: Col-0_lariats_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_lariats_R2


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_2_L004


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_2_L003


title: Muscle_Day3_Immobilisation [20171208-0041]

description: bisulfite conveted DNAextracted fromMuscle_Day3_Immobilisation

value: Day 3


title: Muscle_Day3_Immobilisation [20171208-0042]


title: Col-0_lariats_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_lariats_R1


title: Muscle_Day3_Immobilisation [20171208-0040]


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_2_L002


title: Bhlhe40 ko_IL23 2

description: Library name: Sample 20


title: Bhlhe40 ko_IL23 1

description: Library name: Sample 19


title: dbr1-2_dcl4-2_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_sRNA_R3


title: Muscle_Day3_Immobilisation [20171208-0039]


title: Bhlhe40 het_IL23 3

description: Library name: Sample 15

value: Bhlhe40 het


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_2_L001


title: dbr1-2_dcl4-2_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_sRNA_R2


title: Muscle_Day3_Immobilisation [20171208-0038]


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_1_L004


title: Bhlhe40 het_IL23 2

description: Library name: Sample 14


title: Muscle_Day3_Immobilisation [20171208-0037]


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_1_L003


title: dbr1-2_dcl234_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl234_sRNA_R3

value: Inflorescence


title: Bhlhe40 het_IL23 1

description: Library name: Sample 13


title: dbr1-2_dcl4-2_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl4-2_sRNA_R1


title: Muscle_Day3_Immobilisation [20171208-0036]


title: Brain, CapTrap-seq SS500

city: Poznan

first: Barbara

last: Uszczyńska-Ratajczak

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry, Polish Academy of Sciences

description: Library name: Sample2

data_processing:
Base-calling: Guppy basecaller Version 6.5.7+ca6d6af
Data processing: LyRic v1.0.4
Assembly: GRCz11
Supplementary files format and content: gff3 annotation

organism: Danio rerio

source_name: brain

growth_protocol: Zebrafish wild-type lines from the AB background were maintained at the zebrafish core facility of the International Institute of Molecular and Cell Biology in Warsaw, Poland (License No. PL14656251), in accordance with institutional and national ethical guidelines for animal welfare. Zebrafish embryos obtained from group spawning of adult AB wild-type individuales were incubated at 28°C in egg water (1.5 ml sea salt stock/L distilled water, 60 μg/ml) until desired developmental stage, 2–4 cell stage or 28 hpf.

extract_protocol:
Adult AB wild-type zebrafish (> 3 months old) were first anesthetized and subsequently euthanized using Tricaine methanesulfonate (MS-222) (Sigma Aldrich, Catalog No. A5040-25G) solution before being used for heart and testis dissection. Heart and testis tissues, as well as zebrafish embryos at the desired developmental stages, were washed in 1× PBS to remove contaminants and then homogenized in TRIzol reagent. RNA was extracted via isopropanol precipitation, followed by treatment with RNase-Free DNase (Qiagen, Cat. No. 79254) to eliminate genomic DNA contamination, and subsequently purified using Agencourt RNAClean XP beads (Beckman Coulter, Cat. No. A63987).  RNA samples (RIN ≥ 8.5) were pooled from 1,000 embryos per developmental stage, from 50 adult zebrafish (25 females and 25 males) for heart tissue, and from 50 males for testis tissue. The pooled RNA was concentrated using sodium acetate–ethanol precipitation. RNA concentration and purity were assessed using a Quantus Fluorometer (Promega) and a Nanodrop Spectrophotometer (Thermo Fisher Scientific), respectively, while RNA integrity was verified using the 2200 TapeStation system (Agilent Technologies). Potential genomic DNA contamination was evaluated by PCR amplification, and the RNA samples were stored at –80°C until further use.
The CapTrap-seq cDNA libraries for the 2–4 cell stage, 28 hpf, heart, and testis were size-selected using the ProNex® Size-Selective Purification System (Promega, Catalog No. NG2001) to enrich for cDNA fragments longer than 500 bp. For each sample, 2 µg of the cDNA library was mixed with ProNex beads at a 1:1.1 ratio to selectively retain cDNA molecules exceeding 500 bp, followed by purification and elution according to the manufacturer’s protocol.The size-selected fraction was assessed for quality using an Agilent 2100 Bioanalyzer and quantified with a Qubit fluorometer. Samples for Oxford Nanopore Technologies (ONT) MinION long-read sequencing were prepared using the Nanopore Ligation Sequencing Kit (SQK-LSK109), following the manufacturer’s protocol (version ACDE_9064_v109_revG_23May2018). To achieve optimal loading concentrations for MinION sequencing, 500 ng of each cDNA library was used as input material. A total of 150 fmol of each Nanopore sequencing library was loaded onto separate R9.4.1 flow cells (FLO-MIN106D) and sequenced for at least 72 hours.

tag: developmental stage

tag: biosample type

value: tissue

value: brain

value: WT


title: dbr1-2_dcl234_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl234_sRNA_R2

source_name: Inflorescence


title: Muscle_Day3_Immobilisation [20171208-0035]


title: Shield, CapTrap-seq SS500

description: Library name: Sample1

source_name: shield

value: shield


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_1_L001


title: dbr1-2_dcl234_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl234_sRNA_R1


title: Muscle_Day3_Immobilisation [20171208-0034]


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_4_L004


title: Testis, CapTrap-seq SS500

description: Library name: Sample12

source_name: testis

extract_protocol:
Adult AB wild-type zebrafish (> 3 months old) were first anesthetized and subsequently euthanized using Tricaine methanesulfonate (MS-222) (Sigma Aldrich, Catalog No. A5040-25G) solution before being used for heart and testis dissection. Heart and testis tissues, as well as zebrafish embryos at the desired developmental stages, were washed in 1× PBS to remove contaminants and then homogenized in TRIzol reagent. RNA was extracted via isopropanol precipitation, followed by treatment with RNase-Free DNase (Qiagen, Cat. No. 79254) to eliminate genomic DNA contamination, and subsequently purified using Agencourt RNAClean XP beads (Beckman Coulter, Cat. No. A63987).  RNA samples (RIN ≥ 8.5) were pooled from 1,000 embryos per developmental stage, from 50 adult zebrafish (25 females and 25 males) for heart tissue, and from 50 males for testis tissue. The pooled RNA was concentrated using sodium acetate–ethanol precipitation. RNA concentration and purity were assessed using a Quantus Fluorometer (Promega) and a Nanodrop Spectrophotometer (Thermo Fisher Scientific), respectively, while RNA integrity was verified using the 2200 TapeStation system (Agilent Technologies). Potential genomic DNA contamination was evaluated by PCR amplification, and the RNA samples were stored at –80°C until further use.
Template Switching Oligo (TSO): 5 μg of total RNA per sample (heart, testis, 2–4 cell, 28 hpf) was combined with 3 μl of a 1:100-diluted, pre-5′-capped SIRV-Set 4 (Lexogen) and processed for rRNA depletion using the riboPOOL kit for Danio rerio (SiTools, Cat. No. 27DP-K012-000010) following the manufacturer's protocol (riboPOOLKitManual_v6). After rRNA depletion, RNA was purified using Agencourt RNAClean XP beads (1.8× ratio) according to the manufacturer’s recommendations.For cDNA synthesis, 4 μL of ribo-depleted RNA per reaction (performed in duplicates) was used for first-strand cDNA synthesis with Template Switching RT Enzyme Mix (NEB, Cat. No. M0466) and anchored oligo-dT, following the manufacturer’s protocol. The resulting single-stranded cDNA underwent second-strand synthesis and long-range PCR (LA-PCR) using TaKaRa LA Taq (Takara, Cat. No. RR002M) with 9 PCR cycles. To minimize PCR duplicates, cDNA was split into two independent PCR reactions. PCR replicates were pooled, purified using AMPure XP beads (1× ratio), and resuspended in RNase-free water. Samples were quantified using a Qubit 4 Fluorometer and assessed for quality using an Agilent 2100 Bioanalyzer. For Oxford Nanopore Technologies (ONT) MinION long-read sequencing, libraries were prepared using the Nanopore Ligation Sequencing Kit (SQK-LSK109), following the manufacturer’s protocol (version ACDE_9064_v109_revG_23May2018). To achieve optimal loading concentrations for MinION sequencing, 500 ng of each cDNA library was used as input material. A total of 150 fmol of each Nanopore sequencing library was loaded onto separate R9.4.1 flow cells (FLO-MIN106D) and sequenced for at least 72 hours.
CapTrap-seq: CapTrap‐seq cDNA libraries were prepared as described (Carbonell-Sala et al., 2024). 5 μg of total RNA per sample (2-4Cell, 28hpf, heart and testis) was combined with 3 μl of a 1:100-diluted, pre-5′-capped SIRV-Set 4 (Lexogen) and reverse-transcribed using PrimeScript II RTase (200 U/μl) and an anchored oligo(dT) primer. Full-length, 5′-capped transcripts were enriched via the captrapper method. Briefly, the 5′ cap structure was oxidized to introduce aldehyde groups, which were then biotinylated to enable selective enrichment of capped RNA molecules with streptavidin-coated magnetic beads. Then specific adaptors were ligated to both cDNA ends to facilitate amplification, sequencing, and further enrichment of full-length molecules. The cDNA was converted into double-stranded form using 2× HiFi KAPA mix (Kapa, Cat. No. 7958927001-KK2601) and amplified by LA-PCR with TaKaRa LA Taq (Cat. No. RR002M, Takara) with 16 PCR cycles. Libraries were quantified using a Qubit 4 Fluorometer and quality-checked with an Agilent 2100 Bioanalyzer. For Oxford Nanopore MinION sequencing, libraries were prepared using the Nanopore Ligation Sequencing Kit (SQK-LSK109) following the manufacturer's protocol (version ACDE_9064_v109_revG_23May2018). To achieve optimal loading, 500 ng of each cDNA library was used as input, and 150 fmol was loaded onto separate R.9.4.1 flow cells (FLO-MIN106D) for a minimum of 72 hours of sequencing.
CapTrap-seq SS500: The CapTrap-seq cDNA libraries for the 2–4 cell stage, 28 hpf, heart, and testis were size-selected using the ProNex® Size-Selective Purification System (Promega, Catalog No. NG2001) to enrich for cDNA fragments longer than 500 bp. For each sample, 2 µg of the cDNA library was mixed with ProNex beads at a 1:1.1 ratio to selectively retain cDNA molecules exceeding 500 bp, followed by purification and elution according to the manufacturer’s protocol.The size-selected fraction was assessed for quality using an Agilent 2100 Bioanalyzer and quantified with a Qubit fluorometer. Samples for Oxford Nanopore Technologies (ONT) MinION long-read sequencing were prepared using the Nanopore Ligation Sequencing Kit (SQK-LSK109), following the manufacturer’s protocol (version ACDE_9064_v109_revG_23May2018). To achieve optimal loading concentrations for MinION sequencing, 500 ng of each cDNA library was used as input material. A total of 150 fmol of each Nanopore sequencing library was loaded onto separate R9.4.1 flow cells (FLO-MIN106D) and sequenced for at least 72 hours.

value: testis


title: dbr1-2_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_sRNA_R3


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_4_L003


title: Testis, CapTrap-seq

description: Library name: Sample11


title: Muscle_Day3_Immobilisation [20171208-0032]

source_name: vastus lateralis muscle


title: Muscle_Day3_Immobilisation [20171208-0033]


title: dbr1-2_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_sRNA_R2


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_4_L002


title: dbr1-2_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_sRNA_R1


title: Muscle_Day3_Immobilisation [20171208-0031]


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_4_L001


title: Testis, TSO

description: Library name: Sample10


title: Muscle_Day3_Immobilisation [20171208-0030]


title: Heart, CapTrap-seq SS500

description: Library name: Sample9

source_name: heart

value: heart


title: Col-0_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_sRNA_R3


title: Heart, CapTrap-seq

description: Library name: Sample8


title: Muscle_Day3_Immobilisation [20171208-0029]


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_3_L004


title: Col-0_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_sRNA_R2


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_3_L003


title: Heart, TSO

description: Library name: Sample7


title: Col-0_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_sRNA_R1


title: Muscle_Day3_Immobilisation [20171208-0028]


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_3_L002


title: 28hpf, CapTrap-seq SS500

description: Library name: Sample6

source_name: early embryonic cell

value: whole organism

value: early embryonic cell


title: Muscle_Day3_Immobilisation [20171208-0027]


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_3_L001


title: Zebra finch gonadal cultures DIV6, batch B, adherent fraction

description:
Library name: zA6B
10X genomics

organism: Taeniopygia guttata

source_name: primary cell culture

value: pooled male and female

value: primary cell culture

value: 6 days in vitro

value: embryonic gonadal cell cultures (HH28)

value: B


title: 28hpf, CapTrap-seq

description: Library name: Sample5


title: Muscle_Day3_Immobilisation [20171208-0026]

value: vastus lateralis muscle


title: Zebra finch gonadal cultures DIV6, batch B, non-adherent fraction

description:
Library name: zN6B
10X genomics


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_2_L004

value: innervated engineered human myocardium (iEHM)


title: Zebra finch gonadal cultures DIV3, batch B, adherent fraction

description:
Library name: zA3B
10X genomics

value: 3 days in vitro


title: Muscle_Day3_Immobilisation [20171208-0025]

value: Day 3


title: 2-4Cell, CapTrap-seq SS500

description: Library name: Sample3


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_2_L003


title: Zebra finch gonadal cultures DIV3B, non-adherent fraction

description:
Library name: zN3B
10X genomics


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_2_L002


title: Muscle_Day3_Immobilisation [20171208-0023]

description: bisulfite conveted DNAextracted fromMuscle_Day3_Immobilisation


title: Zebra finch gonadal cultures DIV3, batch A, non-adherent fraction

description:
Library name: zN3A
10X genomics

value: A


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_2_L001


title: 2-4Cell, TSO

description: Library name: Sample1


title: Brain, Slide 4

type: RNA

city: Leiden

first: Qirong

last: Mao

state: South Holland

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: A total of 298 panel including 248 probes Xenium Mouse Brain Gene Expression panel and 50 probes in custom panel. All probes hybridized to their target RNAs, were ligated to form circular DNA, and enzymatically amplified to generate multiple copies of gene-specific barcodes for each transcript. Background autofluorescence was quenched, and nuclei were counterstained with DAPI, following the manufacturer’s protocol (10x Genomics, CG000582).

scan_protocol: Samples were processed and analyzed following the standard 10x Genomics Xenium protocol for fresh frozen tissues (10x Genomics, Protocol: CG000579).

data_processing: Raw data were processed using Xenium Ranger (v1.7.1). Cell segmentation was based on DAPI-stained nuclei with a 15 μm expansion. Low-quality transcript signals (q < 20) were excluded from downstream analysis. Cells were assigned manually to corresponding samples using Xenium Explorer (v3.0).

label: Xenium probe set

source_name: Brain

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Tissue sections were cut at a thickness of 10 μm onto Xenium slides followed by fixation and premeablization

value: Brain

tag: tissue preservation method

value: Fresh Frozen


title: Muscle_Day3_Immobilisation [20171208-0022]


title: 3D fibrillar collagen 50k cells/matrix, rep 3

city: Dallas

first: Kara

last: Poole

state: TX

address: 5323 Harry Hines Blvd

department: Ophthalmology

institute: UT Southwestern Medical Center

description: Library name: E7SF_3DF_50

data_processing:
Standard bioinformatics analyses were conducted by Novogene Co.
Assembly: OryCun2
Supplementary files format and content: txt file includes raw counts for each sample
Supplementary files format and content: txt file includes FPKM values for each sample

organism: Oryctolagus cuniculus

source_name: keratocyte

growth_protocol: Primary keratocytes were maintained in defined serum-free media in a humidified incubator maintained at 5% CO2 and 37C.

extract_protocol:
Total RNA was extracted using the BioRad Aurum Total RNA Mini Kit according to the manufacturer's instructions, quantified by NanoDrop, and stored at -80C for later shipping to Novogene for bulk RNA-seq.
Preparation of cDNA libraries was conducted by Novogene Co.

treatment_protocol: First passage keratocytes were plated with serum-free media on collagen-coated substrates, on top of fibrillar collagen matrices, or embedded within fibrillar collagen matrices (day 0). Cells were cultured for a total of 6 days, with serum-free media swaps on days 2 and 5.

value: keratocyte

tag: culture condition

value: 3D fibrillar collagen 50k cells/matrix


title: Muscle_Baseline [20171208-0021]

description: bisulfite conveted DNAextracted fromMuscle_Baseline

value: Day 0


title: Brain, Slide 3


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_1_L003


title: 3D fibrillar collagen 50k cells/matrix, rep 2

description: Library name: E5SF_3DF_50


title: Brain, Slide 2


title: Muscle_Baseline [20171208-0020]


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_1_L002


title: Brain, Slide 1


title: Muscle_Baseline [20171208-0019]


title: 3D fibrillar collagen, 50k cells/matrix, rep 1

description: Library name: E3SF_3DF_50

value: 3D fibrillar collagen, 50k cells/matrix


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_1_L001


description: Library name: LennyiEHM2innervatedheartmuscle5KSakib_H_1_L002


title: 3D fibrillar collagen, 100k cells/matrix, rep 3

description: Library name: E8SF_3DF_100


title: Tg（mpx:eGFP), treated with znf711 MO,Day2,biol rep3

first: Shuiyi

last: Tan

address: 197 Rui-Jin Road II, Shanghai, China

institute: CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics

description: Library name: Sample6

data_processing:
Raw sequencing reads were quality controlled using in-house scripts and Trimmomatic to remove adapters and low-quality bases. Clean reads were aligned to the Zebrafish  reference genome(GRCz11) using HISAT2 v2.0.5. Gene-level read counts were generated using HTSeq-count, and expression levels were calculated as FPKM. Differential expression analysis was performed using DESeq2 or edgeR depending on the presence of biological replicates.
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 and trimming low qulity base with Trimmomatic. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Htseq-count was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned adifferentially expressed.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: hematopoietic cells

extract_protocol:
RNA was harvested using DP451 kit (Tiangen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TIANSeq Fast RNA Library Kit following manufacturer's protocols.

value: hematopoietic cells

value: mpx+

value: neutrophil

value: znf711 knockdown

value: znf711 MO


title: Muscle_Baseline [20171208-0018]


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_4_L004


title: 3D fibrillar collagen, 100k cells/matrix, rep 2

description: Library name: E7SF_3DF_100


title: Tg（mpx:eGFP), treated with znf711 MO,Day2,biol rep2

description: Library name: Sample5


title: Muscle_Baseline [20171208-0017]


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_4_L003


title: 3D fibrillar collagen, 100k cells/matrix, rep 1

description: Library name: E6SF_3DF_100


title: Muscle_Baseline [20171208-0016]


title: Tg（mpx:eGFP), treated with znf711 MO,Day2,biol rep1

description: Library name: Sample4


title: 2D fibrillar collagen, rep 3

description: Library name: E10SF_2DF

value: 2D fibrillar collagen


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_4_L002


title: Tg（mpx:eGFP),control,Day2,biol rep3

description: Library name: Sample3

value: WT

value: control


title: Muscle_Baseline [20171208-0015]

value: vastus lateralis muscle


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_4_L001

value: innervated engineered human myocardium (iEHM)


title: 2D fibrillar collagen, rep 2

description: Library name: E9SF_2DF


title: Tg（mpx:eGFP),control,Day2,biol rep2

description: Library name: Sample2


title: Muscle_Baseline [20171208-0014]


title: Tg（mpx:eGFP),control,Day2,biol rep1

description: Library name: Sample1


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_3_L004


title: 2D fibrillar collagen, rep 1

description: Library name: E5SF_2DF


title: Muscle_Baseline [20171208-0013]


title: 2D collagen-coated, lysis control, rep 3

description: Library name: E7SF_CML

value: 2D collagen-coated, lysis control


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_3_L003


title: Penile tissue, case, RNA-seq, rep3

city: beijing

first: Jingmin

last: Zhang

address: Yabao Road

institute: CMU

description: Library name: RNA_case-3

data_processing:
Raw sequencing reads were subjected to quality assessment and adaptor trimming.
Clean reads were aligned to the Rattus norvegicus reference genome (Rnor_6.0) using HISAT2.
Gene expression levels were quantified using featureCounts.
Differential gene expression analysis was performed using standard R/Bioconductor packages.
Assembly: Rnor_6.0
Supplementary files format and content: Microsoft Excel spreadsheet containing raw gene count matrices for all RNA-seq samples.

organism: Rattus norvegicus

source_name: penile tissue

growth_protocol: Timed-pregnant Sprague–Dawley (SD) rats were maintained under specific pathogen-free conditions with a 12 h light/12 h dark cycle and free access to food and water. The day of vaginal plug detection was designated as gestational day 0 (GD0).

extract_protocol:
Total RNA was extracted from fetal penile tissues using TRIzol Reagent (Invitrogen) according to the manufacturer's instructions. RNA concentration and purity were determined using a NanoDrop spectrophotometer, and RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
RNA sequencing libraries were prepared according to the manufacturer's instructions and sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing.

treatment_protocol: Pregnant rats were randomly assigned to either the DEHP-treated group or the corn oil vehicle control group. DEHP was administered by oral gavage once daily from gestational day 12 (GD12) to GD19. Control animals received an equal volume of corn oil. Fetuses were collected by cesarean section on GD19.5.

value: penile tissue


title: Muscle_Baseline [20171208-0012]


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_3_L002


title: 2D collagen-coated, lysis control, rep 2

description: Library name: E3SF_CML


title: Penile tissue, case, RNA-seq, rep2

description: Library name: RNA_case-2


title: Muscle_Baseline [20171208-0011]


title: Penile tissue, case, RNA-seq, rep1

description: Library name: RNA_case-1


title: 2D collagen-coated, lysis control, rep 1

description: Library name: E2SF_CML


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_3_L001


title: 28hpf, TSO

description: Library name: Sample4

value: whole organism

value: early embryonic cell


title: Muscle_Baseline [20171208-0010]


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_2_L004


title: 2D collagen-coated, rep 3

description: Library name: E6SF_CMC

value: keratocyte

value: 2D collagen-coated


title: Muscle_Day3_Immobilisation [20171208-0024]

value: Day 3


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_2_L003


title: 2D collagen-coated, rep 2

description: Library name: E3SF_CMC


title: 2-4Cell, CapTrap-seq

description: Library name: Sample2


title: Penile tissue, control, RNA-seq, rep2

description: Library name: RNA_control-2


title: Muscle_Baseline [20171208-0008]

value: Day 0


description: Library name: LennyiEHM1innervatedheartmuscle5KSakib_G_1_L004


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_2_L002


title: Muscle_Baseline [20171208-0007]

description: bisulfite conveted DNAextracted fromMuscle_Baseline


title: Penile tissue, control, RNA-seq, rep1

description: Library name: RNA_control-1


title: 2D collagen-coated, rep 1

description: Library name: E2SF_CMC


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_2_L001


title: Penile tissue, case, MeRIP-seq, rep3

description: Library name: MeRIP_case-3

data_processing:
Raw sequencing reads were subjected to quality assessment and adaptor trimming.
Clean reads were aligned to the Rattus norvegicus reference genome (Rnor_6.0) using HISAT2.
m6A peaks were identified using exomePeak2.
Differential m6A methylation analysis was performed using exomePeak2 and downstream analyses were conducted using R/Bioconductor packages.
Differential gene expression and differential m6A methylation analyses were performed using standard R/Bioconductor packages.
Assembly: Rnor_6.0
Supplementary files format and content: Microsoft Excel spreadsheet containing transcriptome-wide m6A peak coordinates and peak annotation information.

extract_protocol:
Total RNA was extracted from fetal penile tissues using TRIzol Reagent (Invitrogen) according to the manufacturer's instructions. RNA concentration and purity were determined using a NanoDrop spectrophotometer, and RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
Total RNA was fragmented and subjected to methylated RNA immunoprecipitation using an anti-m6A antibody. Both input RNA and immunoprecipitated RNA were used for library preparation according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing.


title: Muscle_Baseline [20171208-0009]


title: Muscle_Baseline [20171208-0006]


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_1_L004


title: 20240809_Yosuke7_AJ-CCR5-CG_12

city: Cleveland

first: Karen

last: Keslar

state: OH

address: 9500 Euclid Avenue NB30

institute: Cleveland Clinic

description: transplanted kidney

hyb_protocol: RNA was hybridized to the mouse Fibrosis panel following manufacturer's instructions

data_processing: Data was processed using the online Rosalind platform

source_name: kidney

extract_protocol: RNA was isolated with Qiagen RNeasy mini kit

value: kidney

tag: treatment group

value: AJ CCR5 CG unt d19


title: 20240809_Yosuke7_AJ-CCR5-CG_11

description: transplanted kidney

tag: tissue

value: AJ CCR5 CG unt d18


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_1_L003


title: Penile tissue, case, MeRIP-seq, rep1

description: Library name: MeRIP_case-1


title: Penile tissue, control, RNA-seq, rep3

description: Library name: RNA_control-3


title: 20240809_Yosuke7_AJ-CCR5-CG_10

description: transplanted kidney

value: AJ CCR5 CG unt d17


title: Muscle_Baseline [20171208-0004]


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_1_L002


title: Muscle_Baseline [20171208-0003]


title: Penile tissue, control, MeRIP-seq, rep3

description: Library name: MeRIP_control-3


title: 20240809_Yosuke7_AJ-CCR5_09

description: transplanted kidney

value: AJ CCR5 unt d17


description: Library name: PatapiaiEHM1innervatedheartmuscle5KSakib_I_1_L001


title: Muscle_Baseline [20171208-0002]


title: Penile tissue, control, MeRIP-seq, rep2

description: Library name: MeRIP_control-2


title: 20240809_Yosuke7_AJ-CCR5_08

description: transplanted kidney


title: Penile tissue, control, MeRIP-seq, rep1

description: Library name: MeRIP_control-1


title: Muscle_Baseline [20171208-0001]