title: DIO_3

description: Library name: SAMPLES6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
E exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPM values for each Sample ...

source_name: plasma extracellular vesicles

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: plasma extracellular vesicles

value: high-fat diet


title: Peripheral CD8+ T cells, siDUSP2 transfected, healthy donor 1

status: Public on Jul 31 2026

type: SRA

city: Rochester

first: Emilia

middle: R

last: Dellacecca

state: MN

address: 200 First Street SW, Kellen Building 02-102

department: Immunology

country: USA

institute: Mayo Clinic

description:
Library name: 39M siDUSP2 BL
Human RNA-seq Baseline counts and FPKM.txt

library_source: transcriptomic

data_processing:
Raw RNA sequencing paired-end reads were processed through Mayo RNA-Seq bioinformatics pipeline, MAP-Rseq (v3.1.4) to align to genome build hg38.
Variants were called using the RVBoost module from MAPR-seq.
Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (FPKM) reads.
FASTQC, MultiQC, and RSEQC tools were used for comprehensive quality control assessment of the aliqned reads.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including raw counts and FPKM for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: CD8+ T cells were maintained in RPMI 1640 + 10% fetal bovine serum, 20 mM HEPES buffer, and 1X penicillin/streptomycin at 37 degrees Celsius with 5% CO2.

extract_protocol:
Total RNA was isolated with TRIzol Reagent (Invitrogen), prior to inclusion in spin-column based isolation (Zymo Research). 250 ng of total RNA was used for construction of cDNA libraies.
Libraries were prepared with Illumina TruSeq Stranded mRNA Prep kit following manufacturer's instructions. The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation's D1000 ScreenTape and Qubit fluorometry.

treatment_protocol: CD8+ T cells were transfected with DUSP2-targeting siRNA (Horizon Discovery, Dharmacon) or negative control siRNA (Horizon DIscovery, Dharmacon) by nucleofection (Lonza) and activated with anti-CD3/CD28 soluble antibodies (STEMCELL Technologies) for 24-hours, rested cells were maintained under the same conditions without addition of activating antibodies.

tag: individual

value: healthy donor 1

tag: tissue

value: Peripheral blood

tag: cell type

value: CD8+ T cells

tag: genotype

tag: treatment

value: not activated

tag: Sex

value: Male

tag: age

value: 39 years


title: NC_1

city: Nanjing

first: Huichen

last: Song

state: Jiangsu

address: Qixia District, Xianlin Road No.163

country: China

institute: Nanjing university

description: Library name: SAMPLES1

data_processing:
Illumina Casava1.7 software used for basecalling.
The remaining reads that passed all the filtering steps was counted  as clean reads and all subsequent analyses were based on this. Finally, we  used FastQC to perform basic statistics on the quality of the clean data reads
Bismark software was used to  perform alignments of bisulfite-treated reads to a reference genome . The reference genome was firstly transformed into bisulfiteconverted version (C-to-T and G-to-A converted) and then indexed using bowtie2. Clean reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to- A converted) before being aligned to the similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) were then compared to the normal genomic sequence and the methylation state of all cytosine positions was inferred.
Assembly: GRCm38_Ensembl_104
Supplementary files format and content: Methylated sites were identified with a binomial test using the methylated counts (mC), totols counts (mC+umC) and the non-conversion rate (r)

organism: Mus musculus

source_name: liver

extract_protocol:
After samples DNA testing, positive control DNAs were added into the DNAs,  Next, ssDNA fragements were Bisulfite treated. After BS treatment, unmethylated Cytosine will change into Uracil, while methylated Cytosine will stay unchanged. Then, methylation sequencing adapters ligation, size selection and PCR amplification steps were performed to the DNA fragmentszol reagent. I
llumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: liver

value: injected with extracellular vesicles rich in NC


title: P3, pNeuroD cell population, PolyI:C treatment, rep 2

city: Paris

first: Tabitha

last: Rücker

address: 25, rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Adapter trimming was performed with cutadapt v. 3.1 (parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA x.fastq). Trimmed sequences were aligned using RNA STAR aligner (v. 2.7.8a) against the GRCm38/mm10 reference. For Gap-aware read counting featureCounts (v. 2.0.1) was applied.
Read counts were normalized by rlog transformation with DESeq2 and subjected to downstream analyses.
Assembly: mm10
Supplementary files format and content: comma-separated value file includes raw counts for each sample (countTable_RNAseq.csv).
Supplementary files format and content: comma-separated value file includes normalized counts of each sample (rld_transformed_counts.csv).

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted from frozen aliquots of 10,000 sorted cells using the RNeasy® Micro Kit (Qiagen, #74004).
From total RNA cDNA was synthesized, PolyA enriched and amplified using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories, # 634891). cDNA was then further processed with the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1096).

value: cerebral cortex

value: neuronal cells

tag: transgene constructs

value: pNeuroD-eGFP/pCAG-tDimer

value: 3 days old puppy (P3)

tag: harvest mode


title: C57_BrainStem_KO_Male1

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

description:
Library name: C57_BrainStem_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Transcripts were quantified with Salmon (v1.10.3) in quasi-mapping-based mode.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

molecule: polyA RNA

source_name: BrainStem

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: BrainStem

value: Mecp2 KO

tag: strain

value: 7 weeks

tag: mouse id


title: DIO_1

description: Library name: SAMPLES4

value: plasma extracellular vesicles

value: Female

tag: group


title: intercept2025A

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

institute: Institut Necker Enfants Malades, INSERM U1151

description:
Library name: intercept2025A
BD Rhapsody

library_source: transcriptomic single cell

data_processing:
For scRNA-seq, data were processed using the BD Rhapsody™ pipeline to generate digital gene expression matrices for downstream analysis.
Assembly: Human reference genome (GRCh38.p13, Ensembl release 110)

source_name: Blood

extract_protocol:
PBMCs were isolated from fresh human blood by Ficoll-Paque density-gradient centrifugation
Single-cell RNA sequencing was performed on the BD Rhapsody™ platform, with libraries sequenced on Illumina NovaSeq or NextSeq instruments.

value: Blood

value: PBMCs


title: P3, pNeuroD cell population, PBS treatment, rep 4

value: PBS


title: intercept2024D

description:
Library name: intercept2024D
BD Rhapsody


title: P3, pNeuroD cell population, PBS treatment, rep 3


title: Con_3

description: Library name: SAMPLES3

value: control


title: C57_BrainStem_KO_Female2

description:
Library name: C57_BrainStem_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: C57_BrainStem_KO_Female1

description:
Library name: C57_BrainStem_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: intercept2024C

description:
Library name: intercept2024C
BD Rhapsody


title: Con_2

description: Library name: SAMPLES2


title: intercept2024B

description:
Library name: intercept2024B
BD Rhapsody


title: Con_1

description: Library name: SAMPLES1


title: P3, pNeuroD cell population, PBS treatment, rep 2


title: C57_BoneMarrow_WT_Male5

description:
Library name: C57_BoneMarrow_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: BoneMarrow

value: BoneMarrow

value: WT

value: Male

value: 8 weeks


title: P3, pNeuroD cell population, PBS treatment, rep 1

value: cerebral cortex

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer


title: C57_BoneMarrow_WT_Male3

description:
Library name: C57_BoneMarrow_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: intercept2024A

description:
Library name: intercept2024A
BD Rhapsody


title: P3, pNeuroD cell population, w/o treatment, rep 6

value: 3 days old puppy (P3)

value: w/o


title: C57_BoneMarrow_WT_Male2

description:
Library name: C57_BoneMarrow_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: E13.5 LK Ddx21-cKO_RNAseq_Rep2

city: Shatin

first: Hoi-Hung

middle: Hoi Hung

last: Cheung

state: NT

address: Rm.707, School of Biomedical Sciences, Area 39, The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: E13.5 LK Ddx21-cKO_RNAseq_Rep2

data_processing:
Reads were aligned to UCSC mm10 or hg38 using STAR aligner:  --outFilterMultimapNmax 20 \         --alignSJoverhangMin 8 \         --alignSJDBoverhangMin 1 \         --outFilterMismatchNmax 999 \         --outFilterMismatchNoverReadLmax 0.04 \         --alignIntronMin 20 \         --alignIntronMax 1000000 \         --alignMatesGapMax 1000000 \         --sjdbScore 1 \
Raw count matrix produced by counting exons with featureCounts
Only genes where 2 or more samples have CPM >1 where retained
RLE normalization was performed using DEseq2
Assembly: mm10 and hg38
Supplementary files format and content: Raw count matrix
Supplementary files format and content: DEseq2-RLE normalized count matrix with Log2 fold change of inidvidual samples after normalization

source_name: Fetal liver

growth_protocol: HSC differentiation from H1 hESC with performed with STEMdiff™ Hematopoietic Kit (Stemcell Tech)

extract_protocol:
Dissected fetal livers were washed twice with PBS and kept in fetal liver juice (2%FBS/1mM EDTA/10mMGlucose/PBS) on ice. Cell suspension was obtained by trituration and strained with a sterile 70um cell strainer. Cells were first stained with lineage-biotin antibodies (Gr1, Cd11b, CD3, B220, Ter119) and fixable viability stain 450, washed and subsequently stained with (cKit-APC and streptavidin-APC/Cy7). Live lineage- cKit+ cells were sorted with BD FACSDiscover™ S8 Cell Sorter. Cells were kept on ice or 4oC throughout harvest and sorting. For H1 differntiated HSC (CD34+, CD45+, CD43+, shRNA+) cells, live cells were sorted by BD FACSDiscover™ S8 Cell Sorter 2 days post transduction after staining with surface antibodies and fixable viability stain 450.
Total RNA was extracted with microprep RNA kit (Zymo). mRNA-enriched cDNA library was prepared using mRNA-seq Lib Prep Module for Illumina (abclonal).

treatment_protocol: HSC derived from H1 hESC was transduced with shRNA-mCherry lentivirus

value: Fetal liver

value: LK (Lineage- Kit+) Hematopoietic progenitor cell

value: Vav-Cre; Ddx21f/f


title: P3, pNeuroD cell population, w/o treatment, rep 5


title: ESCC cell line-3

city: SHANTOU

first: Dajia

last: Li

address: No. 22 Xinling Road

institute: Shantou University Medical College

description: Library name: TE1

library_source: genomic

data_processing:
The default parameters of Trimmomatic were applied for the removal of adapter from Illumina platform FASTQ sequences and the trimming of sequence files according to the base quality values. This process generated clean raw data, which was then suitable for further analysis.
For each sample, quality assessment was performed using the FastQC and MultiQC procedures.
Bowtie2 was employed to align the reads derived from ATAC-seq sequencing data to the corresponding human reference genome, with the default parameters utilized in the analysis.
To ensure unbiased signal detection, repetitive sequences generated by PCR amplification were removed using the Picard. MACS2 callpeak was used for the purpose of identifying and confirming open regions of chromatin.
The mainstream tool HOMER performs motif analysis of accessible chromatin regions of interest, facilitating the identification of potential regulatory factor binding sites within these regions.
Assembly: hg38
Supplementary files format and content: BigWig

molecule: genomic DNA

extract_protocol:
For fibroblasts and ESCC cell lines,cells were digested and counted, and 5 × 10^5  cells were used directly for ATAC-seq experiment. For ESCC tissues, nuclei were isolated by cryogenic grinding (LUKYM, 80 Hz, 20 seconds). Following isolation and counting, 5 × 10^5 nuclei were used for subsequent experiments. The ATAC-seq assay followed the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711).
The DNA was purified with VAHTS DNA Clean Beads (Vazyme, N411-01) and amplified with barcode primers using the TruePrep DNA Library Prep Kit (Vazyme, TD501-01). Finally, all ATAC-seq libraries were sequenced using the Illumina NovaSeq 6000 platform (Novogene).

tag: cell line

value: ESCC cell line

tag: disease state

value: esophageal squamous cell carcinoma


title: C57_BoneMarrow_WT_Female2

description:
Library name: C57_BoneMarrow_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: P3, pNeuroD cell population, w/o treatment, rep 4


title: E13.5 LK WT_RNAseq_Rep3

description: Library name: E13.5 LK WT_RNAseq_Rep3


title: E13.5 LK Ddx21-cKO_RNAseq_Rep1

description: Library name: E13.5 LK Ddx21-cKO_RNAseq_Rep1


title: C57_BoneMarrow_WT_Female1

description:
Library name: C57_BoneMarrow_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BoneMarrow


title: ESCC cell line-1

description: Library name: KYSE150


title: P3, pNeuroD cell population, w/o treatment, rep 3


title: E13.5 LK WT_RNAseq_Rep2

description: Library name: E13.5 LK WT_RNAseq_Rep2


title: C57_BoneMarrow_KO_Male5

description:
Library name: C57_BoneMarrow_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: ESCC cancer associated fibroblast-4

description: Library name: 169260CF

source_name: Human Tissue

value: Human Tissue

value: Cancer-associated fibroblasts


title: E13.5 LK WT_RNAseq_Rep1

description: Library name: E13.5 LK WT_RNAseq_Rep1


title: P3, pNeuroD cell population, w/o treatment, rep 2

value: cerebral cortex

value: neuronal cells


title: C57_BoneMarrow_KO_Male4

description:
Library name: C57_BoneMarrow_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 8 weeks


title: ESCC cancer associated fibroblast-3

description: Library name: 9128CF


title: P3, pNeuroD cell population, w/o treatment, rep 1

value: pNeuroD-eGFP/pCAG-tDimer

value: 3 days old puppy (P3)

value: w/o


title: Optic cup, P347S, P60, biol replicate 1

city: Pozzuoli

first: Santiago

last: Negueruela

address: Via Campi Flegrei, 34

department: Genetic Medicie

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

description:
Library name: P347S_P60
10X Genomics

data_processing:
10x Genomics Cell Ranger v7.0.0
Assembly: mm10 [refdata version 2020-A from Cell Ranger]
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Optic cup

growth_protocol: Maintenance of the mice was on a regular 12/12-h light/dark cycle, temperature of 20–24°C, and humidity of 54–65%, with ad libitum access to food and water.

extract_protocol:
Eye samples were dissociated using the Worthington Papain Dissociation System, according to the manufacturer's instructions.
Single Cell 3′ Library and Gel Bead Kit V3.1 (10x Genomics)

value: Optic cup

tag: time point

tag: batch


title: C57_BoneMarrow_KO_Male3

description:
Library name: C57_BoneMarrow_KO_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: P3, mixed brain cell population, w/o treatment, rep 6

value: mixed population of brain cells

value: pCAG-tDimer


title: ESCC cancer associated fibroblast-2

description: Library name: 27CF

value: esophageal squamous cell carcinoma


title: Optic cup, WT, P60, biol replicate 2

description:
Library name: WT_P60_2
10X Genomics

value: WT


title: Optic cup, WT, P60, biol replicate 1

description:
Library name: WT_P60
10X Genomics


title: C57_BoneMarrow_KO_Male1

description:
Library name: C57_BoneMarrow_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BoneMarrow


title: P3, mixed brain cell population, w/o treatment, rep 5


title: P3, mixed brain cell population, w/o treatment, rep 4


title: C57_BoneMarrow_KO_Female3

description:
Library name: C57_BoneMarrow_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: Female

value: 7.5 months


title: ESCC Tumor tissue-3

description: Library name: 275T

value: Human Tissue


title: C57_BoneMarrow_KO_Female2

description:
Library name: C57_BoneMarrow_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: ESCC Tumor tissue-2

description: Library name: 272T


title: intercept2025B

description:
Library name: intercept2025B
BD Rhapsody

value: Blood

value: PBMCs


title: DIO_2

description: Library name: SAMPLES5

value: plasma extracellular vesicles

value: high-fat diet


title: P3, mixed brain cell population, w/o treatment, rep 2

value: cerebral cortex

value: 3 days old puppy (P3)


title: Optic cup, WT, P30, biol replicate 2

description:
Library name: WT_P30_2
10X Genomics

value: Optic cup


title: P3, pNeuroD cell population, PolyI:C treatment, rep 1

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer


title: C57_Bladder_WT_Male5

description:
Library name: C57_Bladder_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Bladder

value: Bladder

value: Male

value: 8 weeks


title: C57_BrainStem_KO_Female3

description:
Library name: C57_BrainStem_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BrainStem

value: Mecp2 KO


title: ESCC Tumor tissue-1

description: Library name: 271T

value: esophageal squamous cell carcinoma


title: Primary PCa, patient with no bone metastasis, donor NR_12

city: Melbourne

first: xin

last: liu

address: 305 Graattan St

country: Australia

institute: Peter mac

description: Library name: NR_12_RARP

data_processing:
RNA-seq analysis was performed in R (v4.1.0). Clean reads (no adapter contamination, < 20% undecided bases, > 50% high quality bases) were aligned using the RSubread package (v2.8.1). An index was built using the Ensembl Homo sapiens GRCh38 primary assembly genome file and alignment was performed using subjunc with default settings.
Gene counts were obtained using featureCounts using the Ensembl Homo sapiens GRCm38 version 105 GTF annotation file, with isPairedEnd = TRUE, useMetaFeatures = TRUE and strandSpecific = 0.
Ensembl gene IDs were annotated using the biomaRt package (v2.50.1) and a DGEList object was created with the counts and gene annotation using the edgeR package (v3.36.0). A design matrix was constructed incorporating the sample group (NBmRC, BmRC, LN or Bone met).
Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method. Counts were transformed using the voom method and a linear model was fit using the edgeR voomLmFit function, incorporating sample weights and using donor as a blocking factor.
Differential gene expression analyses were performed using the limma (v3.50.0) package. Groups were compared using the contrasts.fit function and moderated t-statistics were calculated using the treat function with a 1.2-fold cut-off. Differentially expressed genes were determined using a false discovery rate-adjusted (FDR) p-value < 0.05.
Assembly: hg38
Supplementary files format and content: PCa_Met_processed.xlsx contains processed counts (tab 1) and voom-transformed expression values (tab 2).

source_name: Primary adenocarcinoma

extract_protocol:
Total RNA was extracted from fresh frozen tissue (n = 50) using the AllPrep DNA/RNA Mini kit (Qiagen, Maryland U.S.A) according to manufacturer’s instructions. RNA yield was quantified using the Qubit RNA High Sensitivity Assay (Invitrogen) with the Qubit 2.0 Fluorometer. RNA quality was assessed using the RNA 6000 Pico Kit on the Agilent 2100 Bioanalyzer.
One microgram of total RNA (RIN > 6.5) was used as input into the TruSeq RNA Sample Preparation Kit v2 (Illumina). cDNA fragments were end repaired, adenylated, adaptors-ligated, purified and PCR enriched. Two samples did not pass pre-sequencing QC (RC_02_RARP, RC_17_RARP). Sequencing (n = 48) was performed on the Illumina HiSeq3000 (PE-150, 20 million paired reads per sample) by Novogene Bioinformatics (Hong Kong).

value: Primary adenocarcinoma

tag: donor

tag: cancer type

value: Prostate cancer

value: NBmRC

tag: group description

value: NBmRC denotes non-metastatic primary tumor tissue

tag: age at_diagnosis

tag: path ggs

tag: clinical tumor_stage


title: P3, mixed brain cell population, w/o treatment, rep 1

tag: tissue

tag: cell type

value: mixed population of brain cells

value: pCAG-tDimer

tag: treatment

value: w/o


title: C57_Bladder_WT_Male4

description:
Library name: C57_Bladder_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

tag: genotype

value: WT

tag: Sex

tag: age


title: E19_P, pNeuroD cell population, PolyI:C treatment, rep 4

value: cerebral cortex

tag: transgene constructs

value: 19 days old embryo (E19)

tag: harvest mode


title: Optic cup, rd10, P18, biol replicate 1

description:
Library name: rd10_P18
10X Genomics

value: Optic cup


title: C57_Bladder_WT_Male3

description:
Library name: C57_Bladder_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Bladder

tag: strain

tag: mouse id


title: E19_P, pNeuroD cell population, PolyI:C treatment, rep 3

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer


title: Primary PCa, patient with no bone metastasis, donor NR_07

description: Library name: NR_07_RARP

tag: group


title: Optic cup, WT, P30, biol replicate 1

description:
Library name: WT_P30
10X Genomics

tag: time point

tag: batch


title: C57_Bladder_WT_Male2

description:
Library name: C57_Bladder_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 10 weeks


title: DU 145 cells, DMOS 48h, rep1

city: shang hai

first: Yi

last: Jiayan

address: pujian road

institute: SHANG HAI JIAO TONG UNIVERSITY

description: Library name: sample4

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software8-9. The analysis waswww.oebiotech.com used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: prostate

extract_protocol:
Total RNA was extracted using the TRIzol Reagent (Ambion, 15596026) according to the manufacturer’s protocol.l. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: prostate

tag: cell line

value: epithelial cell


title: E19_P, pNeuroD cell population, PolyI:C treatment, rep 2


title: Optic cup, P347S, P10, biol replicate 2

description:
Library name: P347S_P10_2
10X Genomics


title: C57_Bladder_WT_Female3

description:
Library name: C57_Bladder_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: DU 145 cells, talazoparib 48h,rep3

description: Library name: sample3


title: umbilical cord plasma, Gen3G, PubM2562

city: Sherbrooke

first: Luigi

last: Bouchard

country: Canada

institute: Université de Shebrooke

description: Library name: Gen3G_UCP_PubM2562

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with the FASTX-Toolkit integrated in the exceRpt pipeline. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using the STAR alignment algorithm version 2.4.2a.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple samples (PMID : 30956140).
Assembly: GRCh37
Supplementary files format and content: Comma-seperated value file, include non-normalized read counts for each microRNA detected in each samples.

source_name: umilical cord plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from up to 500 μL of UCP (130 µL to 500 µL, based on availability) kept at -80 °C until extraction. Prior to extraction, a volume of miRNeasy Serum/Plasma  Caenorhabditis elegans cel-miR-39-3p mimic Spike-In Control (Qiagen, catalog # 219610) was added to each sample, folowing a 1 μL for each 250 μL of plasma ratio. Elution of total RNA was performed in 75 µL of nuclease-free water, and 70 µL of this RNA eluate was then precipitated, dried and resuspended in 5 μL of nuclease-free water as previously described (PMID: 35246451). The whole volume was used for library preparation.
Samples were randomized before library preparation. The libraries were created using the the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) following  the standard procedure adapted to samples of low RNA concentration by Burgos et al (PMID: 23525801). To maintain an optimal reaction ratio, half of the reagents volumes were used for RNA ligation with adapters at 3′ and 5′ ends, reverse transcription, barcoding (index 1-48: one index per sample) and PCR amplification (15 cycles). Libraries were purified by migration in a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, Waltham, United States, catalog #EC265BOX). Fragments between 145 and 160 bp were excised and eluted from the gel with 300 µL of nuclease-free water at room temperature, during an overnight incubation at 500 RPM on a microplate shaker (VWR, ON, Canada, catalog #12620-930). Libraries were concentrated by precipitation following manufacturer's instructions, briefly with a 30 minutes incubation at -80°C, and resuspended in 25 µL of 10 mM Tris-HCl pH 8.5 buffer. Libraries sequencing, including quality control and sample pooling, was performed at the Centre d’expertise et de services Génome Québec (Montréal, Canada). The Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) was used to assess the quality of each library (i.e., concentration, library length and primer dimers absence).  Librairies were pooled equimolarly (200 pM final molarity; 48 libraries with different indexes per lane), denatured and clustered on an Illumina NovaSeq S1 flowcell following the Xp protocol from manufacturer’s recommendations. The sequencing run was performed for 100 cycles in single-end mode, on a NovaSeq 6000 platform.

value: umilical cord plasma

tag: fetal sex

value: female

tag: gestational age_at_birth_(weeks)

tag: delivery type

value: vaginal

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: E19_P, pNeuroD cell population, PolyI:C treatment, rep 1

tag: tissue

tag: cell type

tag: transgene constructs

tag: age

tag: treatment

tag: harvest mode


title: DU 145 cells, talazoparib 48h,rep2

description: Library name: sample2

tag: cell line


title: E19_P, mixed brain cell population, PolyI:C treatment, rep 1

value: mixed population of brain cells

value: pCAG-tDimer


title: umbilical cord plasma, Gen3G, PubM2084

description: Library name: Gen3G_UCP_PubM2084

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: z-score birth_weight


title: C57_Bladder_WT_Female1

description:
Library name: C57_Bladder_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

tag: genotype

value: WT

tag: strain

tag: Sex

value: 8 weeks

tag: mouse id


title: E19_E, pNeuroD cell population, PolyI:C treatment, rep 4

value: cerebral cortex

value: 19 days old embryo (E19)


title: DU 145 cells, talazoparib 48h,rep1

description: Library name: sample1


title: kidney biopsies, severe AAV

first: Yucheng

last: Tang

address: No. 639, Longmian Avenue

institute: China Pharmaceutical University

description:
Library name: Group3
fresh frozing spatial transcriptome sequencing, aav2

data_processing:
Raw sequencing data were processed using Space Ranger pipeline (10X Genomics) to generate FASTQ files
Spatial transcriptomics data were aligned using Space Ranger pipeline (10x Genomics) with the GRCh38 human reference genome.
Gene expression level of Refseq coding genes were quantified using SpaceRanger's default settings.
Assembly: GRCh38
Supplementary files format and content: barcode.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: integrated_AAV.rds.gz: integrated datasets of control, mild and severe AAV groups
Library strategy: Spatial Transcriptomics

source_name: kidney cortex_severe AAV

extract_protocol:
Frozen sections (10 µm thick) were obtained from OCT-embedded fresh frozen tissues.
Human kidney biopsy samples were mounted onto slides, stained, and imaged following the protocols outlined in the Visium Spatial Protocols – Tissue Preparation Guide (10x Genomics, CG000240). Subsequent processing was conducted using the Visium Spatial Tissue Optimization Reagents Kit (10x Genomics, CG000238) and the Gene Expression Reagent Kit (10x Genomics, CG000239), as per the manufacturer’s guidelines.

value: kidney cortex_severe AAV


title: miR-29a-3p_3

description: Library name: miR-29a-3p_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver


title: C57_Bladder_KO_Male4

description:
Library name: C57_Bladder_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Bladder

value: Mecp2 KO

value: Male


title: E19_E, pNeuroD cell population, PolyI:C treatment, rep 3

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer


title: Optic cup, P347S, P30, biol replicate 1

description:
Library name: P347S_P30
10X Genomics

value: Optic cup

tag: time point

tag: batch


title: ESCC Tumor tissue-4

description: Library name: 278T

tag: tissue

value: Human Tissue

tag: disease state

value: esophageal squamous cell carcinoma


title: Kidney biopsies, mild AAV

description:
Library name: Group2
fresh frozing spatial transcriptome sequencing, aav1

source_name: kidney cortex_mild AAV

value: kidney cortex_mild AAV


title: E19_E, pNeuroD cell population, PolyI:C treatment, rep 2

tag: cell type

tag: transgene constructs

tag: age


title: P3, mixed brain cell population, w/o treatment, rep 3

value: mixed population of brain cells

value: 3 days old puppy (P3)

tag: treatment

value: w/o

tag: harvest mode


title: Optic cup, rd10, P30, biol replicate 1

description:
Library name: rd10_P30
10X Genomics


title: C57_Bladder_KO_Male2

description:
Library name: C57_Bladder_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: miR-29a-3p_1

description: Library name: miR-29a-3p_1


title: Kidney biopsies, control

description:
Library name: Group1
fresh frozing spatial transcriptome sequencing, ctrl

source_name: kidney cortex_control

value: kidney cortex_control


title: C57_Bladder_KO_Male1

description:
Library name: C57_Bladder_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: E19_E, mixed brain cell population, PolyI:C treatment, rep 1

value: cerebral cortex

value: pCAG-tDimer

value: 19 days old embryo (E19)


title: Surface stain of NK cells from Peripheral Blood donor NP6 and Placenta donor P5

first: Shihan

state: Victoria

address: 792 Elizabeth Street

institute: Peter Doherty Institute, University of Melbourne

description: Library name: run6_PROT

library_source: other

data_processing:
Raw sequencing data were processed with Cell Ranger v7.1.0 (10x Genomics). Donors were demultiplexed based on differences in single nucleotide polymorphisms using cellsnp-lite v1.2.2 and vireo v0.2.3. Gene expression (GEX) and Feature Barcode (CITE-seq) matrices were analysed with the Seurat package v4.3.0.1
Assembly: GRCh38
Supplementary files format and content: Tab separated values and matrix count files
Supplementary files format and content: metadata of donor ids in comma separated format
Library strategy: CITE-seq

molecule: protein

source_name: PBMC and Placenta

extract_protocol:
Sorted NK cells were encapsulated in gel beads in emulsion (GEMs) using a 10x Genomics Chromium Controller iX. Reverse transcription and cDNA amplification according to the 10x Genomics protocol CG000330: Chromium Next GEM Single Cell 5-v2 Cell Surface Protein UserGuide RevD.
Gene expression and Feature Barcode libraries were prepared according to 10x Genomics protocol CG000330: Chromium Next GEM Single Cell 5-v2 Cell Surface Protein UserGuide RevD

value: PBMC and Placenta

value: NK cells

tag: hto

tag: adt

value: See feature_reference.csv

tag: library type

value: ADT and HTO


title: E19_P, pNeuroD cell population, PBS treatment, rep 4

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: PBS


title: NC_2

description: Library name: NC_2

value: liver


title: C57_Bladder_KO_Female2

description:
Library name: C57_Bladder_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Bladder

value: Mecp2 KO

value: Female

value: 8 months


title: E19_P, pNeuroD cell population, PBS treatment, rep 3


title: NC_1

description: Library name: NC_1


title: Surface stain of NK cells from Peripheral Blood donor P7 and Placenta donors P7 and P8

description: Library name: run4_PROT

value: C0253(Placenta P7),C0256(Blood P7),C0254(Placenta P8)


title: C57_Bladder_KO_Female1

description:
Library name: C57_Bladder_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: C57_AdrenalGland_WT_Male5

description:
Library name: C57_AdrenalGland_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: AdrenalGland

value: AdrenalGland

value: WT

value: Male

value: 8 weeks


title: E19_P, pNeuroD cell population, PBS treatment, rep 1

value: cerebral cortex

value: 19 days old embryo (E19)


title: D4PP_TPR_Rep1

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

description: Library name: D4PP_TPR_Rep1

data_processing:
Reads were trimmed using fastp with default settings.
Reads were aligned to the mm10 genome using STAR version 2.7a at default settings
ChIP-seq bedGraphs were generated using bamCompare (from Deeptools) with bam files with normalizeUsing CPM, binSize 1, skipNAs, and normalized to input
Peaks were called using MACS2 with a cutoff of p < 0.05 (TPR; narrowPeak) and normalized to input
Assembly: mm10
Supplementary files format and content: narrowPeak or bedGraph (linked to the corresponding rep1 sample records, if generated from both replicates)
Supplementary files format and content: bedGraph

source_name: Myometrium

extract_protocol:
Frozen, crushed mouse myometrium tissue was fixed with formaldehyde for 10 minutes.  After quenching the reaction with glycine for 15 minutes, tissue was lysed with three lysis buffers at 4 degrees and sonicated using a probe sonicator. Lysates were incubated overnight with 5ug of the TPR antibody (Invitrogen SP2 Antibody: MA5-14505), proceeded with an overnight incubation with Dynabeads (protein A). Lysates were reverse crosslinked overnight at 65 degrees and then extracted via phenol-chloroform.
ChIP seq  libraries were prepared for sequencing using standard Illumina HiSeq 2500 protocols
DNA samples were quantified using Qubit High Sensitivity Assay. 3 ng of DNA was used as input for library preparation using the NEB Ultra II DNA Library Prep Kit following the manufacturer’s recommended protocol. In brief, DNA was end-repaired, A-tailed and ligated with Illumina-compatible adapters. Bead size-selection was performed to keep all fragments <700bp, and fragments were enriched with PCR using dual-indexed primers. Final libraries were validated on the Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size and absence of primer dimers, and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). Validated libraries were pooled in equimolar quantities and paired-end sequenced on the Illumina Novaseq platform following Illumina’s recommended protocol to generate paired-end reads of 150-bases in length.

value: Myometrium

value: postpartum (D4PP)

tag: antibody

value: TPR antibody (Invitrogen SP2 Antibody:MA5-14505)


title: C57_AdrenalGland_WT_Male4

description:
Library name: C57_AdrenalGland_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

tag: genotype


title: Surface stain of NK cells from Peripheral Blood donor P6

description: Library name: run2_PROT

source_name: PBMC

value: PBMC

value: NK cells

value: See feature_reference.csv

value: ADT and HTO


title: E19_P, mixed brain cell population, PBS treatment, rep 1

source_name: cerebral cortex

value: mixed population of brain cells

value: pCAG-tDimer

value: PBS


title: D4PP_Input

description: Library name: D4PP_Input


title: C57_AdrenalGland_WT_Male3

description:
Library name: C57_AdrenalGland_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

tag: strain


title: Surface stain of NK cells from Peripheral Blood donor P5

description: Library name: run1_PROT


title: Surface stain of NK cells from Peripheral Blood donor NP5

description: Library name: run3_PROT


title: D4PP_TPR_Rep2

description: Library name: D4PP_TPR_Rep2


title: E19_E, pNeuroD cell population, PBS treatment, rep 4

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer


title: LAB_TPR_Rep2

description: Library name: LAB_TPR_Rep2

value: term labour (LAB)


title: C57_AdrenalGland_WT_Male2

description:
Library name: C57_AdrenalGland_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: AdrenalGland

value: WT

tag: Sex

value: Male

value: 10 weeks


title: GEX of NK cells from Peripheral Blood donor NP7

description: Library name: run7_GEX

value: GEX


title: E19_E, pNeuroD cell population, PBS treatment, rep 3

value: cerebral cortex

value: 19 days old embryo (E19)


title: LAB_TPR_Rep1

description: Library name: LAB_TPR_Rep1

value: Myometrium

value: TPR antibody (Invitrogen SP2 Antibody:MA5-14505)


title: C57_AdrenalGland_WT_Female3

description:
Library name: C57_AdrenalGland_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months

tag: mouse id


title: GEX of NK cells from Peripheral Blood donor NP6 and Placenta donor P5

description: Library name: run6_GEX

value: PBMC and Placenta

value: NK cells


title: E19_E, pNeuroD cell population, PBS treatment, rep 2

value: PBS


title: LAB_Input

description: Library name: LAB_Input

tag: time point


title: C57_AdrenalGland_WT_Female2

description:
Library name: C57_AdrenalGland_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: GEX of NK cells from Peripheral Blood donors P7 and P8 and Placenta donor P6

description: Library name: run5_GEX


title: E19_E, pNeuroD cell population, PBS treatment, rep 1

value: neuronal cells


title: PL_TPR_Rep2

description: Library name: PL_TPR_Rep2

value: prelabour (PL)

tag: batch


title: C57_AdrenalGland_WT_Female1

description:
Library name: C57_AdrenalGland_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

tag: tissue

value: 8 weeks


title: E19_P, pNeuroD cell population, w/o treatment, rep 9

value: pNeuroD-eGFP/pCAG-tDimer

value: w/o


title: GEX of NK cells from Peripheral Blood donor P7 and Placenta donors P7 and P8

description: Library name: run4_GEX


title: PL_TPR_Rep1

description: Library name: PL_TPR_Rep1


title: C57_AdrenalGland_KO_Male5

description:
Library name: C57_AdrenalGland_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: AdrenalGland

value: Mecp2 KO

value: Male

value: 7 weeks


title: GEX of NK cells from Peripheral Blood donor NP5

description: Library name: run3_GEX

value: PBMC

value: GEX


title: E19_P, pNeuroD cell population, w/o treatment, rep 8

value: cerebral cortex

value: 19 days old embryo (E19)


title: PL_Input

description: Library name: PL_Input

value: Myometrium


title: C57_AdrenalGland_KO_Male4

description:
Library name: C57_AdrenalGland_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: GEX of NK cells from Peripheral Blood donor P6

description: Library name: run2_GEX


title: E19_P, pNeuroD cell population, w/o treatment, rep 7


title: D17_TPR_Rep2

description: Library name: D17_TPR_Rep2

value: gestational day 17 (D17)

value: TPR antibody (Invitrogen SP2 Antibody:MA5-14505)


title: C57_Epididymis_WT_Male4

description:
Library name: C57_Epididymis_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Epididymis

value: Epididymis

value: WT


title: C57_AdrenalGland_KO_Male2

description:
Library name: C57_AdrenalGland_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: C57_BoneMarrow_KO_Male2

description:
Library name: C57_BoneMarrow_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: BoneMarrow

value: BoneMarrow


title: GEX of NK cells from Peripheral Blood donor P5

description: Library name: run1_GEX

value: NK cells


title: ESCC cancer associated fibroblast-1

description: Library name: 13CF

value: Human Tissue

value: Cancer-associated fibroblasts

tag: disease state

value: esophageal squamous cell carcinoma


title: E19_P, pNeuroD cell population, w/o treatment, rep 6

tag: cell type

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: w/o


title: D17_TPR_Rep1

description: Library name: D17_TPR_Rep1


title: 19-044N1_Lung

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description:
Library name: 19-044N1_Lung
19-044N1_Lung

data_processing:
Amplified, target-enriched libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), employing a 2x 100-cycle paired-end sequencing strategy
FASTQ files were generated using Illumina’s bclconvert v3.10.5 and trimmed with Agilent Locatit v3.0
The RNA sequencing reads were aligned to the Gencode GRCh38.primary_assembly reference genome using STAR29 (v2.7.7a).
Gene-level quantification was conducted with HTSeq30 (v0.11.0) using Gencode V22 primary assembly annotations.
Counts per million ( cpm) reads were calculated using the cpm() function from R package, edgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts per million (cpm) values for each Sample.

source_name: Lung

growth_protocol: Total RNA was extracted from flash-frozen tissue samples using the Maxwell RSC RNA FFPE Kit (Promega, Madison, WI, USA) on the automated Maxwell RSC 48 instrument (Promega)

extract_protocol:
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
RNA-seq libraries were pooled (70-plex) and clustered onto an P2-100 flow cell.

treatment_protocol: untreated

value: Lung

value: Metastatic

value: Flash-frozen


title: E19_P, pNeuroD cell population, w/o treatment, rep 5

value: cerebral cortex

tag: transgene constructs

value: 19 days old embryo (E19)


title: C57_AdrenalGland_KO_Male1

description:
Library name: C57_AdrenalGland_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: AdrenalGland

value: Mecp2 KO

value: Male

tag: age

value: 7 weeks


title: D17_Input

description: Library name: D17_Input

value: Myometrium

value: gestational day 17 (D17)


title: C57_AdrenalGland_KO_Female2

description:
Library name: C57_AdrenalGland_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 8 months


title: 19-044K3_LN

description:
Library name: 19-044K3_LN
19-044K3_LN

source_name: LN

value: LN

tag: treatment


title: X3

first: Yifei

last: Sun

address: West Wenyi Road, 1369

institute: Liangzhu Laboratory

description:
Library name: SAMPLE9
Column name in gene_FPKM.xlsx: X3

data_processing:
The PCR products were subsequently purified, and the quality of the library was evaluated using an Agilent Bioanalyzer 4150. Sequencing was conducted on Illumina NovaSeq 6000 and MGISEQ-T7 (BGI Group), followed by bioinformatics analysis.
Assembly: Hisat2
Supplementary files format and content: gene_FPKM file includes FPKM values for each sample

source_name: Kidney

growth_protocol: Ten-week-old male C57BL/6 mice, 22-25 g, were procured from GemPharmatech Co., Ltd (Nanjing, China). All mice were housed in a pathogen-free environment with a 12-hour light/12-hour dark cycle.

extract_protocol:
Total RNA was extracted from the mouse renal cortex utilizing TRIzol. 1 µg of RNA was utilized as the input material for each sample.
Paired-end libraries were constructed in accordance with the protocols in the mRNA-seq Lib Prep Kit (#RK20350, Abclonal Technology).

treatment_protocol: The mice in the bIRI + Vehicle group and the bIRI + TJ0113 group were received oral gavage daily for 3 days before bIRI surgery. Briefly, after anesthesia, a 1 cm incision was made on both sides of the back of each mouse to expose the kidneys, and bilateral renal pedicles were clamped for 30 minutes using microarterial clamps in a sterile environment. After confirming renal reperfusion, the incisions were sutured. During the ischemia and recovery periods, mice were placed on heating pads to maintain their body temperature at approximately 36 °C to 38 °C. The Sham group as a control for bIRI mice underwent the same surgical procedures without clamping the renal artery. The mice in the bIRI + Vehicle group and the bIRI + TJ0113 group were administered on the day of bIRI surgery and oral gavage daily until the mice were sacrificed on the 14th days after surgery.

value: Kidney

value: male

value: WT

value: bIRI sugery with TJ013 treatment


title: C57_AdrenalGland_KO_Female1

description:
Library name: C57_AdrenalGland_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: E19_P, pNeuroD cell population, w/o treatment, rep 4

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: w/o

tag: harvest mode


title: 19-044J3_Pelvic

description:
Library name: 19-044J3_Pelvic
19-044J3_Pelvic

source_name: Pelvic

value: Pelvic

value: Metastatic

value: Flash-frozen


title: KO79_indexG4

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Reads aligned to MesAur1.0 genome assembly using Ensembl GTF file and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Assembly: Mesocricetus Auratus MesAur1.0
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)
Supplementary files format and content: .csv files show the read count for individual base calls compared to the viral reference sequence

organism: Mesocricetus auratus

source_name: G.I., SARS-CoV-2, I.N., 3dpi, 1

growth_protocol: Golden hamstsers were housed in pairs in the ABSL3 facility of NYU-Langone/Mount Sinai Hospital, under 12 hour light/dark cycle. Water and Food (PicoLab Rodent Diet 20 5053) was provided ad libitum.

extract_protocol: RNA was extracted using Trizol reagent and following manufacturer's instructions. 100 ng of RNA were used for the construction ofn libraries.

treatment_protocol: Dexamethasone was prepared fresh each day at a dose of 1 mg/kg in 0.5 mL of 20% DMSO/60% PEG400/20% 2-hydroxypropyl-beta-cyclodextrin in water (w/w), and administered via subcutaneous injection.

tag: time

value: 3 dpi

value: 1000 PFU SARSCOV2 IN


title: Microbiota of stool EG26 –  PAE female

city: Florence

first: Sara

last: Bertorello

address: Viale Gaetano Pieraccini 6

institute: University of Florence

description:
Library name: EG26
16s rRNA v3-v4 sequencing of mice stool

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 –verbose
qiime demux summarize  --i-data trim-seqs.qza --o-visualization quality.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 224 --p-trunc-len-r 218 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x INDEXED_mouse_GRCm39_BOWTIE2/GRCm39  -U dna-sequences.fasta --un filtered.fasta
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R software for further analysis
Supplementary files format and content: filtered.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: otu_table.csv: CSV text file containing the abundance table
Supplementary files format and content: tax.csv: CSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: 16S rRNA-seq

source_name: Stool

extract_protocol:
Total DNA was extracted from stools, amplified to collect amplicons of variable V3–V4 region of the bacterial 16S rRNA gene were sequenced in paired-end mode (2 × 250 cycles) with Illumina Novaseq.
For detailed library preparation please contact IGA Technology Services (Udine, Italy)

value: Stool

tag: group

value: PAE

value: female


title: E19_P, mixed brain cell population, w/o treatment, rep 9

data_processing:
Adapter trimming was performed with cutadapt v. 3.1 (parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA x.fastq). Trimmed sequences were aligned using RNA STAR aligner (v. 2.7.8a) against the GRCm38/mm10 reference. For Gap-aware read counting featureCounts (v. 2.0.1) was applied.
Read counts were normalized by rlog transformation with DESeq2 and subjected to downstream analyses.
Assembly: mm10
Supplementary files format and content: comma-separated value file includes raw counts for each sample (countTable_RNAseq.csv).
Supplementary files format and content: comma-separated value file includes normalized counts of each sample (rld_transformed_counts.csv).

extract_protocol:
Total RNA was extracted from frozen aliquots of 10,000 sorted cells using the RNeasy® Micro Kit (Qiagen, #74004).
From total RNA cDNA was synthesized, PolyA enriched and amplified using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories, # 634891). cDNA was then further processed with the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1096).

value: cerebral cortex

value: mixed population of brain cells

value: pCAG-tDimer

value: 19 days old embryo (E19)


title: X2

description:
Library name: SAMPLE8
Column name in gene_FPKM.xlsx: X2

value: Kidney

value: male

value: WT

value: bIRI sugery with TJ013 treatment


title: H9C2_0_3 input

city: Fuzhou

first: Yiyang

last: Chen

address: No. 1 Xueyuan Road, Shangjie Town, Minhou County, Fuzhou City, Fujian Province

institute: Fujian Medical University

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: rn6
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.

organism: Rattus norvegicus

source_name: myocardium

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: myocardium

tag: cell line

value: rat myocardial cell line

value: myoblast

value: Wild type

value: Control


title: 19-044I3_Liver2

description:
Library name: 19-044I3_Liver2
19-044I3_Liver2

source_name: Liver

value: Liver

value: Metastatic

value: Flash-frozen


title: X1

description:
Library name: SAMPLE7
Column name in gene_FPKM.xlsx: X1


title: E19_P, mixed brain cell population, w/o treatment, rep 8

first: Tabitha

institute: Institut Pasteur

value: w/o


title: 19-044G2_Liver1

description:
Library name: 19-044G2_Liver1
19-044G2_Liver1


title: H9C2_0_2 input


title: E19_P, mixed brain cell population, w/o treatment, rep 7

value: cerebral cortex


title: S3

description:
Library name: SAMPLE6
Column name in gene_FPKM.xlsx: S3

value: Sham operation


title: H9C2_0_1 input


title: 19-037P3_Perinephritic

description:
Library name: 19-037P3_Perinephritic
19-037P3_Perinephritic

source_name: Perinephritic

value: Perinephritic


title: S2

description:
Library name: SAMPLE5
Column name in gene_FPKM.xlsx: S2


title: H9C2_Pe_3 input

value: treat with periplocin


title: E19_P, mixed brain cell population, w/o treatment, rep 6

value: mixed population of brain cells

value: pCAG-tDimer

value: 19 days old embryo (E19)


title: 19-037L2_Pancreas

description:
Library name: 19-037L2_Pancreas
19-037L2_Pancreas

source_name: Pancreas

value: Pancreas


title: PCa bone metastases, donor RC_02

description: Library name: RC_02_MET

source_name: Bone metastases

value: Bone metastases

tag: donor

tag: cancer type

value: Prostate cancer

tag: group description

value: Bone met denotes tissue from PCa bone metastases

tag: age at_diagnosis

tag: path ggs

tag: clinical tumor_stage


title: cDC1, Clec1a KO5_n1_ifn

city: Nantes

first: Elise

last: Chiffoleau

address: 30 Bd jean Monnet CHU

description:
Library name: Sample 162
TO241_DGEseq.unq.refseq.umi.dat

data_processing:
An average of 5 million 75 bp single-end reads were obtained for each sample.
Samples were demultiplexed and aligned to the GRCm38 (mm10) genome using the DGE bioinformatics pipeline.
Post-sequencing, data demultiplexing was performed using Illumina bcl2fastq.
The resulting FASTQ files were analyzed using the 3’ Sequencing RNA Profiling (SRP) pipeline
Assembly: mm10
Supplementary files format and content: Digital gene expression (DGE) profiles were generated by counting the number of unique UMIs associated with each RefSeq gene for each sample and expressed in .dat format

source_name: spleen

extract_protocol:
5,000 cells were incubated in lysis buffer containing 0.16uL 10% Triton X-100, 0.08 uL RNAse Out (40U/µL, Invitrogen) and 3.75 µL RNAse DNAse free water
Lyzed cells were loaded on a 96-plate using an OT-2 library prep robot (Opentrons). 1uL barcoded RT-primers with universal adapters, well-specific barcodes, and unique molecular identifiers were then added to the wells and incubated at 72°C for 3 min before reverse transcription. Barcoded complementary DNAs from multiple samples were then pooled, amplified, and tagmented using a transposon fragmentation approach which enriches for 3′ ends of complementary DNA.

treatment_protocol: Spleen from WT and Clec1a KO mice were recovered, minced and incubated with collagenase IV for 45 minutes at 37°C (Roche, cat: 11088882001). The resulting cell suspension was then enriched in cDC1s by incubation with a DC isolation kit (Milteny, cat: 130-091-169) and sorted with an AutoMACS separator. The resulting cell suspension was then stained with fluorochrome-conjugated antibodies and purified cDC1s were sorted by FACS (based on the expression of CD11c, MHC-II and XCR1) using a Cytek Aurora spectral flow cytometer. Purified cDC1s were then plated in flat-bottom 96-well plates and stimulated with E. coli (MOI = 10), MCA-OVA UV-treated cells (ratio 1:10) or recombinant mouse IFNβ (1000 U/ml, BioTechne R&D Systems cat: 8234-MB-010) for 6h. Then, cells were extensively washed and harvested for RNAseq experiments.

value: spleen

tag: strain

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

tag: genotype

value: Clec1a KO

value: stimulated with type I IFN


title: E19_P, mixed brain cell population, w/o treatment, rep 5

last: Rücker

address: 25, rue du Docteur Roux

tag: tissue

value: cerebral cortex

value: w/o


title: S1

description:
Library name: SAMPLE4
Column name in gene_FPKM.xlsx: S1

value: Kidney

tag: Sex

value: male

value: WT

value: Sham operation


title: Optic cup, WT, P10, biol replicate 1

description:
Library name: WT_P10
10X Genomics

source_name: Optic cup

value: Optic cup

tag: time point

tag: batch


title: 19-037K9_LN

description:
Library name: 19-037K9_LN
19-037K9_LN

value: LN

value: Metastatic

tag: treatment

value: Flash-frozen


title: H9C2_Pe_2 input

value: myocardium

value: rat myocardial cell line

tag: cell type

value: myoblast

value: Wild type

value: treat with periplocin


title: E19_P, mixed brain cell population, w/o treatment, rep 4

value: mixed population of brain cells

tag: transgene constructs

value: pCAG-tDimer

tag: age

value: 19 days old embryo (E19)

tag: harvest mode


title: C3

description:
Library name: SAMPLE3
Column name in gene_FPKM.xlsx: C3

value: bIRI sugery with Vehicle treatment


title: H9C2_Pe_1 input

tag: cell line


title: 19-037I2_Liver2

description:
Library name: 19-037I2_Liver2
19-037I2_Liver2

value: Liver


title: E19_E, pNeuroD cell population, w/o treatment, rep 9

value: cerebral cortex

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: w/o


title: C2

description:
Library name: SAMPLE2
Column name in gene_FPKM.xlsx: C2

value: Kidney

value: male

value: WT


title: 19-037G3_Liver1

description:
Library name: 19-037G3_Liver1
19-037G3_Liver1

value: Metastatic

value: Flash-frozen


title: H9C2_Bu_3 input

value: myocardium

value: rat myocardial cell line

value: myoblast

value: treat with bufalin


title: E19_E, pNeuroD cell population, w/o treatment, rep 8


title: H9C2_Bu_2 input

value: Wild type


title: C1

description:
Library name: SAMPLE1
Column name in gene_FPKM.xlsx: C1


title: Optic cup, AAV2.8-Sponge.mir181

description: 10X Genomics

data_processing:
10x Genomics Cell Ranger v7.0.0
Assembly: mm10 [refdata version 2020-A]
Supplementary files format and content: Tab-separated values files and matrix files

treatment_protocol: Retinal injection of viral vectors

value: Optic cup

value: 4 months old


title: H9C2_Bu_1 input


title: E19_E, pNeuroD cell population, w/o treatment, rep 7

value: 19 days old embryo (E19)


title: 19-022H1_Adrenal

description:
Library name: 19-022H1_Adrenal
19-022H1_Adrenal

source_name: Adrenal

value: Adrenal


title: E19_E, pNeuroD cell population, w/o treatment, rep 6

source_name: cerebral cortex

value: cerebral cortex

value: neuronal cells


title: 19-022N2_Lung

description:
Library name: 19-022N2_Lung
19-022N2_Lung

value: Lung


title: Optic cup, AAV2.8-GFP

description: 10X Genomics


title: 19-022I1_Liver

description:
Library name: 19-022I1_Liver
19-022I1_Liver

value: Liver


title: H9C2_0_3 IP

value: Control


title: E19_E, pNeuroD cell population, w/o treatment, rep 5

value: pNeuroD-eGFP/pCAG-tDimer

value: w/o


title: dCLNs,sCLNs,iLNs,WT,5xFAD,scRNAseq [vdj_t]

city: Rehovot

first: Michal

last: Schwartz

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

description: 10x Genomics

data_processing:
Samples were demultiplexed using mkfastq, and gene expression count matrices were created using multi from the 10x Genomics Cell Ranger Software Suite (version 6.0.1). UMI counts were uploaded into the R environment with the read10x function and converted into a Seurat object using CreateSeuratObject function. Demultiplexing with hashtag oligos (HTOs also called cell hashing) was performed using the Seurat R package, as previously described (Stoeckius, M. et al. Genome Biol. 19, 224. 2018).  Downstream analysis was performed using the Seurat R package (version 4.1.0).
Quality control was performed by including cells expressing less than 3009 genes and less than 10129.5 UMIs.  Cells with more than 443 genes, more than 744 UMIs and less than 7.4% mitochondrial genes were also included.  Cells expressing hemoglobin genes (Hbb-bt, Hbb-bs, Hbb-bh1, Hbb-bh2, Hbb-y, Hba-x, Hba-a1, Hba-a2, Hbq1b, Hbq1a) were removed. Cells having UMI counts higher than 5000 and expressing a combination of either Cd3e and Cd79a or Cd3e and Ms4a1, were also removed, since they represent potential doublets. The lincRNA genes AY036118 and Gm42418 were removed from the analysis since they represent rRNA contamination75. Normalization, scaling, and selection of variable genes out of the expression matrix were performed using SCTransform. Principal Component Analysis was performed, and the first 30 principal components were chosen based on the heatmap and elbow plots for downstream analysis. A KNN graph depicting the Euclidian distance of cells in PCA space was constructed using FindNeighbors and then the Louvain algorithm was implemented to group cells together using the function FindClusters (selected resolution was 1.2). Clusters were given a general annotation of either T-cells or B-cells based on the expression of canonical gene markers Cd3e, Cd4, Cd8a (T cells) and CD79a, CD79b (B cells). T cell and B cell clusters were sub-clustered for separate analysis using the same clustering parameters as the original dataset. Clusters were then merged based on the gene expression pattern resulting in 9 clusters for both T cells and B cells compartments. T cells clusters were annotated based on the expression of gene markers manually, while B cells clusters were given a generic annotation based on the cluster separation. Analysis of differentially expressed genes between conditions was performed using the FindMarkerGenes function.
For BCRs and TCRs analysis, samples were demultiplexed using mkfastq, and reads were aligned to the reference genome to assemble BCRs and TCRs followed by creation of expression count matrices using multi from the 10x Genomics Cell Ranger Software Suite (version 6.0.1). Downstream analysis was performed following the Immcantation framework recommendations.
IgBLAST was used to perform germline V(D)J annotation utilizing Ig reference specific for C57BL/6 strain of Mus musculus. IgBLAST results are parsed into AIRR format for downstream analysis. Productive BCR heavy chain sequences were subsetted, and then only cells with one heavy chain sequence paired with at least one light chain sequence were kept. TCRs were selected for having one TRB chain, and the TRA chain with the highest UMI count was kept in cells with multiple TRA chains.
BCRs and TCRs with two or more identical CDR3 regions in one sample were considered clonally expanded. Information about BCR and TCR clonality was added to the Seurat gene expression analysis by adjusting the metadata. After pre-processing there were 15019 cells with paired heavy and light BCR chains of which 13726 had matching gene expression data. There were 8776 cells with paired TRA and TRB chains for TCRs of which 7788 had matching gene expression data.
Assembly: Mouse (mm10) 2020-A (from 10x Genomics)
Supplementary files format and content: Filtered contig igblast db passed output

source_name: deep cervical lymph node, SUPERFICIAL CERVICAL LYMPH NODE, INGUINAL LYMPH NODE

extract_protocol:
Females 10–11-month-old mice were i.p. administered a lethal dose of ketamine (100 mg/mL)/xylazine (10 mg/mL), intracardially injected with 10 µl of heparin sodium and transcardially perfused with ice-cold 1x PBS. The dCLNs, sCLNs and iLNs were harvested and placed into a 0.4 ml enzymatic mix [100 µg/ml Liberase TL (Roche) and 20 µg/ml DNase I (Roche) in sterile freshly opened IMDM (Sigma)] in a 24-well plate on ice. The tissues were mechanically dissociated using sterile 1 ml syringe plungers on ice and incubated at 37°C for 10 minutes with frequent agitation. The enzymatic reaction was stopped by placing the plate on ice and adding ice-cold RPMI (Biological Industries) supplemented with 10% FBS (Gibco) and 2 mM EDTA (Biological Industries). Samples were then filtered through a 100 µm filter and centrifuged at 450 x g for 6 minutes. The supernatant was aspirated and BioLegend cell staining buffer was used to wash and resuspend the cells. Cell count was evaluated using an automated cell counter (TC20, Bio-Rad). From each sample, 2*106 cells were transferred into new tubes and washed with 1 ml of BioLegend cell staining buffer. After aspiration of the supernatant, the residual contents of each sample were resuspended and incubated with 0.5 µl TruStain FcX PLUS (anti-mouse CD16/32, BioLegend) blocking reagent at 4°C for 10 minutes. Cell hashing was performed by incubating at 4°C for 30 minutes 0.5 µg of anti-mouse Totalseq-C 001, 002, 003 or 004 hashtags (oligo-tagged antibodies from BioLegend). Next, three washes with 3.5 ml of BioLegend cell staining buffer were performed. The cells were then resuspended with 1x PBS supplemented with 1% bovine serum albumin (BSA, Sigma), and cell viability was evaluated using Trypan blue and an automated cell counter (TC20, Bio-Rad). Only samples with cellular viability higher than 87% were used. The single cell suspension from the different tubes were finally combined into composite samples containing an equal number of cells from each original sample.
Up to 17,500 cells from each composite sample (final concentration ~1000 cells/μl) were loaded onto a 10x Genomics Chromium platform for gel beads-in-emulsion (GEM) partitioning and cDNA generation. Gene Expression (GEX), V(D)J (TCR and BCR) and Cell Surface Protein library from the same samples were then constructed using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein and Immune Receptor Mapping. Libraries were sequenced on the NovaSeq 6000 (Illumina), achieving library depths of ~22,200-36,800 mean reads per cell for GEX, ~13,100-26,400 reads per cell for TCR, ~10,900-26,500 mean reads per cell for BCR, and ~4,400-8,400 mean reads per cell for feature barcodes (cell hashing).

value: immune cells


title: 19-007K3_LN3

description:
Library name: 19-007K3_LN3
19-007K3_LN3

value: LN

value: Metastatic

value: Flash-frozen


title: H9C2_0_2 IP

value: myocardium

value: rat myocardial cell line

value: myoblast


title: E19_E, pNeuroD cell population, w/o treatment, rep 4


title: iLNs,5xFAD,scRNAseq [vdj_t]

description: 10x Genomics

source_name: inguinal lymph node

value: inguinal lymph node


title: 19-007J1_LN2

description:
Library name: 19-007J1_LN2
19-007J1_LN2


title: H9C2_0_1 IP

value: Wild type


title: iLNs,WT,scRNAseq [vdj_t]

description: 10x Genomics

value: WT


title: Surface stain of NK cells from Peripheral Blood donors P7 and P8 and Placenta donor P6

description: Library name: run5_PROT

source_name: PBMC and Placenta

value: PBMC and Placenta

value: NK cells

tag: hto

value: C0251(Blood P7),C0252(Blood P8),C0254(Placenta P6)

tag: adt

value: See feature_reference.csv

tag: library type

value: ADT and HTO


title: E19_E, mixed brain cell population, w/o treatment, rep 9

value: cerebral cortex

value: mixed population of brain cells

value: pCAG-tDimer

value: 19 days old embryo (E19)


title: 19-007H2_LN1

description:
Library name: 19-007H2_LN1
19-007H2_LN1

source_name: LN

value: LN

value: Metastatic


title: E19_E, mixed brain cell population, w/o treatment, rep 8

value: w/o


title: H9C2_Pe_3 IP

value: myocardium

value: rat myocardial cell line

value: treat with periplocin


title: sCLNs,5xFAD,scRNAseq [vdj_t]

description: 10x Genomics

source_name: superficial cervical lymph node

value: superficial cervical lymph node

value: immune cells


title: H9C2_Pe_2 IP

value: myoblast

value: Wild type


title: 19-004L1_Lung

description:
Library name: 19-004L1_Lung
19-004L1_Lung

source_name: Lung

value: Lung

value: Flash-frozen


title: sCLNs,WT,scRNAseq [vdj_t]

description: 10x Genomics

value: WT


title: E19_E, mixed brain cell population, w/o treatment, rep 7

value: cerebral cortex


title: H9C2_Pe_1 IP


title: 19-004J1_LN

description:
Library name: 19-004J1_LN
19-004J1_LN


title: E19_E, mixed brain cell population, w/o treatment, rep 6

value: mixed population of brain cells


title: H9C2_Bu_3 IP

value: treat with bufalin


title: dCLNs,5xFAD,scRNAseq [vdj_t]

description: 10x Genomics

source_name: deep cervical lymph node

value: deep cervical lymph node


title: 19-004I1_Adrenal

description:
Library name: 19-004I1_Adrenal
19-004I1_Adrenal

value: Adrenal


title: E19_E, mixed brain cell population, w/o treatment, rep 5

value: pCAG-tDimer

value: 19 days old embryo (E19)


title: 19-004G3_Liver

description:
Library name: 19-004G3_Liver
19-004G3_Liver

value: Liver

value: Metastatic


title: H9C2_Bu_2 IP

value: myocardium

value: rat myocardial cell line


title: dCLNs,WT,scRNAseq [vdj_t]

description: 10x Genomics

value: immune cells


title: E19_E, mixed brain cell population, w/o treatment, rep 4

value: w/o


title: dCLNs,sCLNs,iLNs,WT,5xFAD,scRNAseq [vdj_b]

description: 10x Genomics

value: deep cervical lymph node, SUPERFICIAL CERVICAL LYMPH NODE, INGUINAL LYMPH NODE


title: H9C2_Bu_1 IP

value: myoblast

value: Wild type


title: 19-001L1_LN

description:
Library name: 19-001L1_LN
19-001L1_LN

value: LN

value: Flash-frozen


title: E19, pNeuroD cell population, w/o treatment, rep 3

value: cerebral cortex

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: both


title: iLNs,5xFAD,scRNAseq [vdj_b]

description: 10x Genomics

value: inguinal lymph node


title: E19, pNeuroD cell population, w/o treatment, rep 2

value: 19 days old embryo (E19)


title: Old_PM_3

city: Daejeon

first: You Mee

last: Ahn

address: Yuseong-daero, Yuseong-gu

country: South Korea

institute: KOREA INSTITUTE OF ORIENTAL MEDICINE

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Kidney

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Male

value: Kidney

value: WT

value: Old+PM


title: 19-001J4_Liver2

description:
Library name: 19-001J4_Liver2
19-001J4_Liver2

value: Liver

value: Metastatic


title: iLNs,WT,scRNAseq [vdj_b]

description: 10x Genomics

value: immune cells


title: Old_PM_2


title: 19-001G4_Liver1

description:
Library name: 19-001G4_Liver1
19-001G4_Liver1


title: E19, pNeuroD cell population, w/o treatment, rep 1

value: w/o


title: sCLNs,5xFAD,scRNAseq [vdj_b]

description: 10x Genomics

value: superficial cervical lymph node


title: Old_PM_1


title: 18-120L1_LN3

description:
Library name: 18-120L1_LN3
18-120L1_LN3

value: LN


title: E19, mixed brain cell population, w/o treatment, rep 3

value: mixed population of brain cells

value: pCAG-tDimer


title: 18-120J1_LN2

description:
Library name: 18-120J1_LN2
18-120J1_LN2

value: Flash-frozen


title: sCLNs,WT,scRNAseq [vdj_b]

description: 10x Genomics


title: E19, mixed brain cell population, w/o treatment, rep 2

value: cerebral cortex


title: Old_YM_3

value: Old+YM


title: dCLNs,5xFAD,scRNAseq [vdj_b]

description: 10x Genomics

value: deep cervical lymph node


title: Old_YM_2


title: E19, mixed brain cell population, w/o treatment, rep 1

value: 19 days old embryo (E19)

value: both


title: 18-120H1_LN1

description:
Library name: 18-120H1_LN1
18-120H1_LN1


title: dCLNs,WT,scRNAseq [vdj_b]

description: 10x Genomics


title: Old_YM_1

value: Male

value: Kidney


title: 18-101K2_Liver2

description:
Library name: 18-101K2_Liver2
18-101K2_Liver2


title: E18, pNeuroD cell population, PolyI:C treatment, rep 4

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: 18 days old embryo (E18)


title: 18-101G1_Liver1

description:
Library name: 18-101G1_Liver1
18-101G1_Liver1

value: Liver

value: Metastatic


title: iLNs,5xFAD,scRNAseq [GEX]

description: 10x Genomics

data_processing:
Samples were demultiplexed using mkfastq, and gene expression count matrices were created using multi from the 10x Genomics Cell Ranger Software Suite (version 6.0.1). UMI counts were uploaded into the R environment with the read10x function and converted into a Seurat object using CreateSeuratObject function. Demultiplexing with hashtag oligos (HTOs also called cell hashing) was performed using the Seurat R package, as previously described (Stoeckius, M. et al. Genome Biol. 19, 224. 2018).  Downstream analysis was performed using the Seurat R package (version 4.1.0).
Quality control was performed by including cells expressing less than 3009 genes and less than 10129.5 UMIs.  Cells with more than 443 genes, more than 744 UMIs and less than 7.4% mitochondrial genes were also included.  Cells expressing hemoglobin genes (Hbb-bt, Hbb-bs, Hbb-bh1, Hbb-bh2, Hbb-y, Hba-x, Hba-a1, Hba-a2, Hbq1b, Hbq1a) were removed. Cells having UMI counts higher than 5000 and expressing a combination of either Cd3e and Cd79a or Cd3e and Ms4a1, were also removed, since they represent potential doublets. The lincRNA genes AY036118 and Gm42418 were removed from the analysis since they represent rRNA contamination75. Normalization, scaling, and selection of variable genes out of the expression matrix were performed using SCTransform. Principal Component Analysis was performed, and the first 30 principal components were chosen based on the heatmap and elbow plots for downstream analysis. A KNN graph depicting the Euclidian distance of cells in PCA space was constructed using FindNeighbors and then the Louvain algorithm was implemented to group cells together using the function FindClusters (selected resolution was 1.2). Clusters were given a general annotation of either T-cells or B-cells based on the expression of canonical gene markers Cd3e, Cd4, Cd8a (T cells) and CD79a, CD79b (B cells). T cell and B cell clusters were sub-clustered for separate analysis using the same clustering parameters as the original dataset. Clusters were then merged based on the gene expression pattern resulting in 9 clusters for both T cells and B cells compartments. T cells clusters were annotated based on the expression of gene markers manually, while B cells clusters were given a generic annotation based on the cluster separation. Analysis of differentially expressed genes between conditions was performed using the FindMarkerGenes function.
For BCRs and TCRs analysis, samples were demultiplexed using mkfastq, and reads were aligned to the reference genome to assemble BCRs and TCRs followed by creation of expression count matrices using multi from the 10x Genomics Cell Ranger Software Suite (version 6.0.1). Downstream analysis was performed following the Immcantation framework recommendations.
IgBLAST was used to perform germline V(D)J annotation utilizing Ig reference specific for C57BL/6 strain of Mus musculus. IgBLAST results are parsed into AIRR format for downstream analysis. Productive BCR heavy chain sequences were subsetted, and then only cells with one heavy chain sequence paired with at least one light chain sequence were kept. TCRs were selected for having one TRB chain, and the TRA chain with the highest UMI count was kept in cells with multiple TRA chains.
BCRs and TCRs with two or more identical CDR3 regions in one sample were considered clonally expanded. Information about BCR and TCR clonality was added to the Seurat gene expression analysis by adjusting the metadata. After pre-processing there were 15019 cells with paired heavy and light BCR chains of which 13726 had matching gene expression data. There were 8776 cells with paired TRA and TRB chains for TCRs of which 7788 had matching gene expression data.
Assembly: Mouse (mm10) 2020-A (from 10x Genomics)
Supplementary files format and content: Barcodes (tsv.gz), features (tsv.gz) and matrix (mtx.gz) gzipped files, which logically make up the count matrix

value: inguinal lymph node

value: immune cells


title: Old_5

value: WT

value: Old control


title: dCLNs,sCLNs,iLNs,WT,5xFAD,scRNAseq [GEX]

description: 10x Genomics

value: deep cervical lymph node, SUPERFICIAL CERVICAL LYMPH NODE, INGUINAL LYMPH NODE


title: E18, pNeuroD cell population, PolyI:C treatment, rep 3

value: cerebral cortex


title: Old_4


title: E18, pNeuroD cell population, PolyI:C treatment, rep 2


title: iLNs,WT,scRNAseq [GEX]

description: 10x Genomics


title: 18-065I1_LN

description:
Library name: 18-065I1_LN
18-065I1_LN

value: LN

value: Flash-frozen


title: Old_3


title: E18, pNeuroD cell population, PolyI:C treatment, rep 1


title: 18-065G1_Uterus-Cervical

description:
Library name: 18-065G1_Uterus-Cervical
18-065G1_Uterus-Cervical

source_name: Uterus

value: Uterus


title: Old_2


title: E18, mixed brain cell population, PolyI:C treatment, rep 4

value: mixed population of brain cells

value: pCAG-tDimer


title: sCLNs,5xFAD,scRNAseq [GEX]

description: 10x Genomics

value: superficial cervical lymph node


title: 17-071P4_Mesentric2

description:
Library name: 17-071P4_Mesentric2
17-071P4_Mesentric2

source_name: Mesentric

value: Mesentric


title: sCLNs,WT,scRNAseq [GEX]

description: 10x Genomics


title: Old_1

value: Male

value: Kidney


title: 17-071I1_Omentum

description:
Library name: 17-071I1_Omentum
17-071I1_Omentum

source_name: Omentum

value: Omentum


title: dCLNs,5xFAD,scRNAseq [GEX]

description: 10x Genomics

value: deep cervical lymph node


title: Young_5

value: Young control


title: E18, mixed brain cell population, PolyI:C treatment, rep 2

value: 18 days old embryo (E18)


title: 17-071G6_Mesenteric1

description:
Library name: 17-071G6_Mesenteric1
17-071G6_Mesenteric1

value: Metastatic


title: E18, mixed brain cell population, PolyI:C treatment, rep 3


title: dCLNs,WT,scRNAseq [GEX]

description: 10x Genomics

value: immune cells

value: WT


title: 17-047I5_At-ao-ar-me

description:
Library name: 17-047I5_At-ao-ar-me
17-047I5_At-ao-ar-me

source_name: Atrial aortic

value: Atrial aortic


title: Young_4


title: E18, mixed brain cell population, PolyI:C treatment, rep 1

value: cerebral cortex


title: 17-047G5_Lung-LN

description:
Library name: 17-047G5_Lung-LN
17-047G5_Lung-LN

value: Lung

value: Flash-frozen


title: iLNs,5xFAD,scRNAseq

description: 10x Genomics

value: inguinal lymph node


title: dCLNs,sCLNs,iLNs,WT,5xFAD,scRNAseq

description: 10x Genomics

value: deep cervical lymph node, SUPERFICIAL CERVICAL LYMPH NODE, INGUINAL LYMPH NODE


title: Young_3


title: 17-030L1_Pericolonic-met

description:
Library name: 17-030L1_Pericolonic-met
17-030L1_Pericolonic-met

source_name: Pericolonic

value: Pericolonic


title: E18, pNeuroD cell population, PBS treatment, rep 4

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: PBS


title: Young_2

value: Male

value: Kidney


title: E18, pNeuroD cell population, PBS treatment, rep 3


title: iLNs,WT,scRNAseq

description: 10x Genomics


title: Young_1

value: Young control


title: 17-030I1_L-ab-wall-met

description:
Library name: 17-030I1_L-ab-wall-met
17-030I1_L-ab-wall-met

source_name: adbdominal wall

value: adbdominal wall


title: E18, pNeuroD cell population, PBS treatment, rep 2

value: 18 days old embryo (E18)


title: mpeg1.1 mCherry+ cells, ALK5 inhibitor, 6 dpf

city: Bronx

first: Teresa

last: Bowman

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: Library name: 6dpf_ALK5

data_processing:
For all samples, CellRanger 9.0.1 was used. The standard count function in Cell Ranger was used for all samples.
Assembly: Danie rerio GRCz11
Supplementary files format and content: Matrix files (CellRanger output filtered_feature_bc_matrix)

organism: Danio rerio

source_name: larval zebrafish

growth_protocol: Zebrafish embryos were maintained in embryo E3 medium at 28 °C until 5dpf. Thereafter, they were moved into the Fish Facility system and maintenaid according to Institutional Animal Care and Use Committee (IACUC)-approved protocols (#1636) in accordance with the Albert Einstein College of Medicine research guidelines.

extract_protocol:
Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 10 min at 37°C. FBS was used to inactivate the liberase. Cells were filtered once before isolating via FACS.  The gata2b and mCherry expressing cells were isolated using FACS.
Libraries were prepared according to manufacturer's instructions of the kits. For all samples, the Chromium Next GEM Single Cell 3' Kit v4 was used.

treatment_protocol: Zebrafish embryos were treated with DMSO vs TGF-β receptor I (ALK5) inhibitor SB431542 (Selekchem- S1067) drug at a concentration of 20 μM. Embryos were first dechorionated. ALK5 inhibitor or DMSO were added to embryo E3 medium in 6-well plates with 40-50 30hpf-embryos per well. Treatment was stopped at 50hpf.

value: larval zebrafish

value: Hematopoietic & Immune Cells

tag: sorted cells

value: mpeg1.1 mCherry+ cells

value: AKL5 inhibitor SB431542

tag: developmental stage

value: 6 dpf


title: E18, pNeuroD cell population, PBS treatment, rep 1

city: Paris

value: cerebral cortex


title: 17-030H1_Adrenal

description:
Library name: 17-030H1_Adrenal
17-030H1_Adrenal

source_name: Adrenal

value: Adrenal

value: Metastatic

value: Flash-frozen


title: E18, mixed brain cell population, PBS treatment, rep 2

source_name: cerebral cortex

value: mixed population of brain cells

value: pCAG-tDimer


title: mpeg1.1 mCherry+ cells, Control DMSO, 6 dpf

description: Library name: 6dpf_DMSO

value: DMSO


title: 17-030G1_Liver

description:
Library name: 17-030G1_Liver
17-030G1_Liver

source_name: Liver

value: Liver


title: sCLNs,WT,scRNAseq

description: 10x Genomics

value: superficial cervical lymph node

value: immune cells

value: WT


title: sCLNs,5xFAD,scRNAseq

description: 10x Genomics


title: dCLNs,5xFAD,scRNAseq

description: 10x Genomics

value: deep cervical lymph node


title: gata2b GFP+ cells, ALK5 inhibitor, 3 dpf

description: Library name: 3dpf_ALK5

value: larval zebrafish

value: gata2b GFP+ cells

value: 3 dpf


title: 17-026N2_Small-bowel

description:
Library name: 17-026N2_Small-bowel
17-026N2_Small-bowel

source_name: Small Bowel

value: Small Bowel


title: E18, mixed brain cell population, PBS treatment, rep 1

value: 18 days old embryo (E18)

value: PBS


title: dCLNs,WT,scRNAseq

description: 10x Genomics


title: gata2b GFP+ cells, Control DMSO, 3 dpf

description: Library name: 3dpf_DMSO

value: Hematopoietic & Immune Cells


title: 17-026J3_Omentum2

description:
Library name: 17-026J3_Omentum2
17-026J3_Omentum2

value: Omentum

value: Metastatic


title: E18, pNeuroD cell population, w/o treatment, rep 6

value: cerebral cortex

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: w/o


title: RNA_TTX_AP5_shNup153_2_Replicate3

city: Dresden

first: Abhinav

last: Soni

state: Saxony

address: Tatzberg 41

department: Nuclear architecture in neural plasticity and aging

country: Germany

institute: German Center for Neurodegenerative Diseases, Dresden

description: RNA sequencing sample collected from pre-silenced primary cortical neurons treated with AAV-shControl from DIV8 to DIV13.Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.

data_processing:
FastQC was used to perform basic quality control of the sequencing data. Fragments were aligned to the mouse reference (mm10) with support of the Ensembl 98 splice sites using the gsnap aligner (v2020-12-16) . Fragments per gene and sample were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl gene annotation using featureCounts (v2.0.1) .
Assembly: mm10
Supplementary files format and content: Processed data file 'CountData_Basalstate_RNASeq.txt' & 'CountData_TTX_AP5_RNASeq.txt'  includes matrix of count per genes for RNA-Sequencing dataset in basal state PCNs and TTX-AP5 treated PCNs respectively.

source_name: Primary cortical neurons

growth_protocol: Embryonic cortices (embryonic day 17.5-19.5) (C57/BL6 mice) from one litter were dissected and pooled together to be processed as a single biological replicate. Dissociated primary cortical neurons were plated in Poly-Dl-Ornithine Hydrobromide coated plates. Cells were maintained in incubators at 37°C with a CO2 concentration of 5%. 30% medium was replaced at DIV4 and DIV8 with Brain Phys Neuronal Culture Medium (STEMCELL Tec), supplemented with 2% SM1-NC (STEMCELL Tec).

extract_protocol:
poly-dT enrichment from total RNA, followed by strand specific RNA-seq library preparation (Ultra II Directional RNA Library Prep, NEB). Purified libraries were quantified on a Fragment analyser (Agilent) and sequenced on an IlluminaNovaSeq 6000 in 100bp paired-end mode to a depth of 30-55 million fragments per library.
Samples confirmed to have sufficient Nup153 knockdown were further processed for RNA sequencing. To remove any contaminating DNA, samples were treated with TURBO DNAase (Life Technologies), and RNA integrity was checked by Bioanalyzer (Agilent). Only samples with RIN number greater than 8 were used for further processing. A total of 3-4 biological replicates were used for each condition analyzed in the study, with one biological replicate being primary neurons derived from pooled cortical tissue from embryos of one litter.
mRNA was isolated from an average of 150-300 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). Ligation was performed using the NEBNext Adapter of the NEBNext Multiplex Oligos for Illumina Kit. After ligation, the adapters were depleted by XP bead purification (Beckman Coulter). Unique dual indexing was used during the subsequent PCR enrichment (12 cycles) with amplification primers carrying the same sequence for i7 and i5 indices (primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After purification, libraries were quantified on a Fragment Analyzer (Agilent). Libraries were sequenced on an Illumina NovaSeq 6000 in 100 bp paired-end mode to a depth of 30-55 million fragments per library.

value: Primary cortical neurons

value: AAV treatment from DIV8 to DIV13. Pre-silencing of neuronal activity using tetrodotoxin (TTX, 1-2 µM, hellobio) at DIV12 for 24 hours, and D-AP5(100 µM, Tocris) for six hours before collection.

tag: owner

value: Abhinav Soni & Tomohisa Toda


title: 17-026I1_Liver

description:
Library name: 17-026I1_Liver
17-026I1_Liver

value: Liver

tag: genotype

value: Flash-frozen


title: Rars2_48hpf

city: Chengdu

first: Xing

last: Wei

state: --- Select One ---

address: No. 20, Section 3, Renmin South Road

institute: West China Second University Hospital

description:
Library name: Rars2
Single-cell RNA sequencing of rars2 mutant zebrafish embryos at 48 hpf

data_processing:
Raw sequencing data were processed using Cell Ranger (v6.0.1) with the zebrafish reference genome (GRCz11). Gene expression matrices were generated and analyzed using Seurat (v4.1.0).
Assembly: GRCz11
Supplementary files format and content: Processed data include gene expression matrices in Matrix Market format (matrix.mtx.gz), cell barcodes (barcodes.tsv.gz), and gene features (features.tsv.gz).

source_name: whole embryo

growth_protocol: Zebrafish embryos were maintained under standard laboratory conditions at 28.5°C and staged according to hours post fertilization (hpf).

extract_protocol:
Zebrafish embryos at 48 hpf were dissociated into single-cell suspensions using enzymatic digestion and mechanical trituration. Cells were filtered and counted prior to library preparation.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3’ Reagent Kit (v3.1) according to the manufacturer’s instructions.

treatment_protocol: No chemical or environmental treatment was applied. Samples were collected from wild-type and rars2 mutant zebrafish embryos.

tag: tissue

value: whole embryo

value: single cells


title: E18, pNeuroD cell population, w/o treatment, rep 5


title: RNA_TTX_AP5_shNup153_2_Replicate2


title: 17-026H2_Omentum1

description:
Library name: 17-026H2_Omentum1
17-026H2_Omentum1


title: Control_1_48hpf

description:
Library name: Control_1
Single-cell RNA sequencing of wild-type zebrafish embryos at 48 hpf

value: wild-type (WT)


title: E18, pNeuroD cell population, w/o treatment, rep 4

value: 18 days old embryo (E18)


title: RNA_TTX_AP5_shNup153_2_Replicate1


title: znf804a-light,hom,rep4

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

description: Library name: Sample 24

data_processing:
Paired-end and single-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28).
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
To analyze splicing and produce the sample_#.isoforms.results.gz files, rsem-calculate-expression from the 1.3.3 version was run with the following commands:   --paired-end \   --bam \   --calc-pme \   --num-threads 4 \
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.
Supplementary files format and content: Isoform quantification from RSEM

source_name: 6 dpf head with eyes, 4 heads combined

extract_protocol:
RNA was extracted using the MicroElute Total RNA Kit (Omega Bio-Tek R6834-02), with a 15-min incubation with Dnase I.
Libraries were constructed using an in-house protocol based on SMART-Seq2, followed by Nextera XT Library Preparation (FC-131-1096).

value: 6 dpf head with eyes, 4 heads combined

value: znf804a homozygous mutant

tag: sample group


title: E18, pNeuroD cell population, w/o treatment, rep 3


title: 17-020K1_Pleura

description:
Library name: 17-020K1_Pleura
17-020K1_Pleura

source_name: Pleura

value: Pleura


title: RNA_TTX_AP5_shControl_Replicate3


title: znf804a-light,hom,rep3

description: Library name: Sample 23


title: 17-020H4_Lung

description:
Library name: 17-020H4_Lung
17-020H4_Lung

source_name: Lung

value: Lung

value: Metastatic


title: E18, pNeuroD cell population, w/o treatment, rep 2

value: cerebral cortex

value: neuronal cells


title: RNA_TTX_AP5_shControl_Replicate2


title: 16-097K2_Liver2

description:
Library name: 16-097K2_Liver2
16-097K2_Liver2


title: znf804a-light,hom,rep2

description: Library name: Sample 22


title: E18, pNeuroD cell population, w/o treatment, rep 1

value: pNeuroD-eGFP/pCAG-tDimer

value: w/o