title: Sample173 rat GH3 RNA

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

data_processing:
Paired end data was trimmed with fastp(v0.23.2) software to retain reads with average quality of at least 20 (Phred score) and minimum read length of 100 base pairs.
Ribosomal RNA (rRNA) read alignment and removal was performed with SortMeRNA.
Quality and rRNA filtered reads were further quasi-mapped and quantified using Salmon(v1.6.0) against the GENCODE(v38) Homo sapiens genome for tissue and pituisphere samples  while simultaneously performing GC bias, sequence level bias and positional bias correction to increase the number of high quality mappings. Tissue samples with quasi-mapping rate of at least 45% were selected for differential expression analysis.
Quality and rRNA filtered reads were further quasi-mapped and quantified using Salmon(v1.6.0) against Ensembl(v105) Rattus Norvegicus genome for the GH3 cell lines while simultaneously performing GC bias, sequence level bias and positional bias correction to increase the number of high quality mappings.
The quantified transcripts were imported in the R software and summarized to gene level counts using the tximeta package. Differential expression analysis was performed by DESeq2. Quantified read counts were filtered by frequency setting the count threshold at 10 and the sample frequency threshold as 33% of the smallest comparison group contrast size.  Parametric dispersion fit type was chosen to model the counts, after also checking the fit of mean and local fits. Euclidean distances between samples and PCA graphs of 500 most variable genes were used to check for unforeseen variability within the comparison groups and possible batch effects. Subsequently Wald test was performed to determine expression differences both in PitNET type and SSA/DA therapy contrasts.   The default independent filtering function was replaced with independent hypotheses weighing from the IHW package.  Adjustment p values based on the mean expression level of each gene which was followed with multiple testing correction using the Benjamini-Hochberg adjustment.
Assembly: GENCODE v38 GRCh38
Assembly: Ensembl 105 mRatBN7.2
Supplementary files format and content: raw counts

organism: Rattus norvegicus

source_name: GH3 cells

growth_protocol: Within 12 hours after surgery, PitNET tissue samples were processed for propagation. Tissue material was mechanically sliced into small pieces and washed in DMEM with 1x Antibiotic-Antimycotic solution (Thermo Fisher Scientific, USA). Enzymatic dissociation using Accutase solution (Thermo Fisher Scientific, USA) was carried out on a rotating platform for 20 min at 37°C in a humidified environment with 5% CO2. The cells were centrifuged for 5 min at 360 x g after the incubation period to obtain cell pellets. The cell pellet was treated with a red blood cell lysis solution (154 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA, pH 7.4) for 10 min to reduce contamination with red blood cells. To remove red blood cell debris, the sample was centrifuged and the cell pellet was washed twice. The obtained pellet was split into two portions. To obtain PitNET tissue-derived free-floating spheres, cells were grown in DMEM-F12 (Thermo Fisher Scientific, USA), containing 1x penicillin/streptomycin solution, 20 ng/ml epidermal growth factor (EGF) (Sigma-Aldrich, Germany), 10 ng/ml basic fibroblast growth factor (bFGF) (Sigma-Aldrich, Germany), and 1x B27 supplement (GIBCO, USA).  To obtain MSC, culture cells were grown in DMEM-F12, supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Fisher Scientific, USA), 1% ITS (Corning, USA), and 100 µg/ml primocin (InvivoGen, USA) until confluent, then propagated and passaged 2–6 times. All cell culture cultivations and incubations were performed at 37°C, 95% air, and 5% CO2.

extract_protocol:
Total RNA for transcriptome sequencing was extracted using AllPrep DNA/RNA/miRNA universal kit (Qiagen, Germany) according to manufacturer’s instructions from tumor tissue samples stored in RNAlater Tissue Storage Reagent (Sigma-Aldrich, USA). The concentrations of extracted RNA were measured using Qubit 2.0 with Qubit RNA HS kit (Thermo Fisher, USA). The quality of extracted RNA was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Following this the RIN and DV200 values were calculated to calculate the RNA input amounts for RNA-seq compatible library preparation.
Prior to the library preparation rRNA removal was performed using MGIEasy rRNA Depletion kit (MGI, China). After the rRNA depletion reverse transcription, second strand synthesis, and cDNA library preparation for NGS were carried out using MGIEasy RNA Directional Library Prep Set (MGI, China). The libraries were sequenced on DNBSEQ-G400 platform (MGI, China) with 35 M reads per sample and with 2 x 150 bp read length.

treatment_protocol:
To obtain PitNET tissue-derived free-floating spheres, cells were grown in DMEM-F12 (Thermo Fisher Scientific, USA), containing 1x penicillin/streptomycin solution, 20 ng/ml epidermal growth factor (EGF) (Sigma-Aldrich, Germany), 10 ng/ml basic fibroblast growth factor (bFGF) (Sigma-Aldrich, Germany), and 1x B27 supplement (GIBCO, USA). Cell culture cultivation and incubation was performed at 37°C, 95% air, and 5% CO2. For the gene expression experiments, pituispheres were grown on a 6-well plate and treated with 10 μM octreotide or 10 μM cabergoline for 4, 8, 24, 48, and 72 h.
The GH3 cells were maintained in F12-K medium containing 15% horse serum, 2.5% FBS and  1x penicillin/streptomycin solution. For studying the effects of PitNET drugs on gene expression, the cells were incubated for  4, 8, 24, 48, and 72 h with 10 μM octreotide and 10 μM cabergoline. Cell culture cultivation and incubation was performed at 37°C, 95% air, and 5% CO2.
To obtain MSC cells were grown in DMEM-F12, supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Fisher Scientific, USA), 1% ITS (Corning, USA), and 100 µg/ml primocin (InvivoGen, USA) until confluent, then propagated and passaged 2–6 times. Cell culture cultivation and incubation was performed at 37°C, 95% air, and 5% CO2.

tag: tumor functional type

tag: therapy


title: Blood sample from individual 16

status: Public on Apr 08 2022

type: genomic

city: Darlinghurst

first: Joseph

middle: E

last: Powell

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: Sample ID: 16

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Genomic DNA extracted from blood was genotyped using the Infinium Global Screening Array-24 v1.0 BeadChip (Illumina).
Primary assessment and SNP call rate quality control of SNP intensity output files were performed using GenomeStudio software (Illumina).
Genotype: AA,AB,BB,or NC (no call)
Processed data file onek1k_genotype_matrix.txt.gz is linked as supplementary file at the foot of the Series record.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood sample

label_protocol: Standard Illumina label protocol

extract_protocol: DNA was extracted from blood stored in EDTA tubes using the QIAamp Blood Mini kit.

tag: individual id

tag: gender

value: Female

tag: tissue

value: Blood

tag: disease state

value: No active inflammatory disease


title: Blood sample from individual 17

description: Sample ID: 17

value: Male


title: Adrenal Cortex, PBS, 13R

type: SRA

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

country: Germany

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

library_source: transcriptomic

data_processing:
Low quality nucleotides were removed Illumina fastq filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner  using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENC
HTSeq-0.6.1p1  was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read
Assembly: mm10
Supplementary files format and content: Tab-Delimited Gene-Wise Raw read counts text file

molecule: total RNA

organism: Mus musculus

source_name: Adrenal Cortex

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

value: Adrenal Cortex

tag: treatment

value: PBS


title: pHUVEC - Negative_1

city: Toronto

first: Dakota

last: Gustafson

address: 101 College Street, 3-309

country: Canada

institute: University Health Network

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Negative_1

data_processing:
Sequencing quality was examined using fastqc (v0.11.2), and adaptors were subsequently trimmed with trimmomatic (v0.36).
One sample was removed on the basis of abnormal read duplication rates (n=1 ambulatory disease, sample Mild_4). Gene quantification was performed using salmon (v1.3.0) using adaptor-trimmed reads.
Salmon index was built using the entire hg38 genome (obtained from UCSC) as the decoy sequence with Gencode transcript annotation (V31).
Genes were quantified by Salmon with command "salmon quant" with the following parameters: "-l A --gcBias --validateMappings". Read counts were imported into R using R package tximport (v 1.18.0) with argument (countsFromAbundance="lengthScaledTPM").
Read counts were first normalized by DESeq2 (v 1.26.0), with the svaseq() function (from "sva" package, v 3.34.0) being used to subsequently estimate hidden batch effects with n.sv=4.
Sva-normalized read counts were obtained by regressing out covariates using the cleaning function. Differential gene expression analysis was performed with DESeq2 with sva-estimated surrogate variables added to the design matrix.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include Salmon quantification results for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Pooled human umbilical vein endothelial cells (pHUVEC)

growth_protocol: Pool human umbilical vein endothelial cells (pHUVEC, Lonza, Basel, Switzerland) were cultured in Endothelial Cell Growth Basal Medium-2 (Lonza, Basel, Switzerland) containing the complete Endothelial Cell Growth Medium BulletKitTM (Lonza, Basel, Switzerland) at 37°C in a 5% CO2 humidified incubator. Cells were maintained on 10 cm tissue culture plates (Corning, Costar, New York, NY, USA) coated with 0.1% (v/v) gelatin attachment factor (ThermoFisher, Waltham, MA, USA) and passaged every 2-4 days at 70%-80% confluency. For experimentation, pHUVECs at passages 3-7 were used. Source cell vials were monitored and subsequently tested negative for the presence of mycoplasma contamination (ThermoFisher, Waltham, MA, USA).

extract_protocol:
Isolation of RNA was facilitated using a Qiagen RNeasy Plus Micro Kit (Cat#: 74004) only after washing twice with ice-cold Dulbecco's Phosphate Buffered Saline (PBS) without magnesium and calcium.
RNA quantities and quality were assessed using the Agilent 2100 Bioanalyzer with all samples passing a quality control threshold (RIN ≥ 7.0) to proceed to library preparations and RNA-seq. A total amount of 20 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μL USER Enzyme was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 minutes followed by five minutes at 95 °C before PCR. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. The resulting PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Sequencing was carried out on an Illumina NovaSeq® 6000 (Illumina, San Diego, California, United States), using paired end 2×150 bp chemistry at a depth of 20 million reads per sample.

treatment_protocol: Once the cells reached the peak of log phase, 20% v/v plasma (differing severties) or PBS was added, and the cells co-incubated at 37°C in a 5% CO2 atmosphere for six hours.

tag: passage

tag: cell type

value: HUVEC

value: SARS-CoV-2 Negative Plasma


title: Blood sample from individual 12

description: Sample ID: 12


title: pHUVEC - PBS_1

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA)
Control_2


title: 1656-A029869

data_processing:
The sequencing data on miRNA expression of target genes were imported into HTG EdgeSeq Parser software.
Post-sequencing QC metrics (QC0, QC1, and QC2) detect three different sample failure modes (1 - Degraded RNA or poor quality of sample, Pos% >- 14% as failure; 2 - Insufficient read depth, Read Deapth <= 500 K as failure; 3 - Minimal expression variability, RSD >= 0.08 as failure).
The HTG EdgeSeq Reveal Application was utilized to quality check and normalize data which utilizes DeSeq.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files including raw counts and processed data; DeSeq Normalized Count Data

source_name: EDTA Platelet Depleted Plasma_Severe

growth_protocol: Whole blood was colleced via cubital vein into EDTA tubes and spun down at 2,500xg for 25 minutes according to CLIA protocols for the reduction of platelets. Upon separation plasma was frozen at -80 degrees Celsuis for downstream use. When isolating miRNA, samples were thawed on ice until sample homogeny was verified. Hemoylsis was examed at 414nm using a spectrophotometer to confirm absense of erythrocyte lysis and subsequent contamination.

extract_protocol:
A total of 30uL of thawed plasma was co-incubated with 1:1 volumes of HTG Plasma Lysis buffer (pre-warmed to 50 degrees celsius) and 1/10th v/v proteinase K for three hours at 50 degrees celsius with shaking (200prm).
The lysed sample was transferred to a standard 96-well micro-titer plate, referred to as the sample plate. Target capture was done by the HTG EdgeSeq chemistry. Briefly, the nuclease protection probes (NPPs) were added to the lysed samples in the sample plate in excess amount and hybridized to the target miRNA. Then S1 nuclease was added to digest non-hybridized mRNA and excess NPPs, thus producing a stoichiometric amount of target miRNA NPP duplexes. After the S1 digestion was completed, the processed sample was transferred to a new 96-well micro-titer plate with a v-bottom, referred to as the stop plate, and S1 digestion was terminated by the addition of termination solution followed by heat denaturation of S1 enzyme. Each processed sample from the stop plate was used as   template to set up PCR reactions with specially designed primers, referred to as tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode that is used for sample identification and multiplexing. HTG has developed 12 forward and eight reverse primer tags; therefore, up to 96 samples can be analyzed simultaneously on an Illumina sequencing platform. Clean-up procedures were performed according using AMPure cleanup protocols for Illumina Sequencing Libraries. The library was quantified in accordance with the HTG EdgeSeq KAPA Library Quantification kit for Illumina Sequencing. All samples and controls were quantified in triplicate. No Template Control (NTC) reactions were made for each master mix used (using the same master mix as for samples) during the qPCR process. NTCs serve as a test for qPCR reagent contamination. Molecular-grade water is used in place of test sample in the NTC reactions using the same volume as the template.

tag: grouping

value: Severe

tag: tissue/sample type

value: EDTA Platelet Depleted Plasma

tag: molecule subtype

value: microRNA


title: ISM-Cre.Vehicle_rep6

city: Wauwatosa

first: Shi

last: Fang

state: Wisconsin

address: 8701 W Watertown Plank Rd.

department: Physiology

country: USA

institute: The Medical College of Wisconsin

data_processing:
Data was trimmed and quality assessed with FastQC and RSeQC
Reads were aligned to the mouse reference Gencode vM23 (based on Ensembl v98) using the STAR aligner and MAPR-Seq workflow v3.0
Differential gene expression was processed through EdgeR utilizing both the pairwise and generalized linear model statistics with the cutoffs set at an FDR <0.05 and log 2 fold change ≥1 or ≤-1.
Genome_build: Gencode vM23 (GRCm38.p6)
Supplementary_files_format_and_content: GeneCount,RPKM

source_name: aorta

extract_protocol:
Aortae were disscted, cleaned and snap frozen in liquid nitrogen. Tissue were lysed in Trizol using a bead mill homogenizer. Total RNA were extracted following the instructions provided by the Invitrogen Purelink kit.
RNA was quantifed by fluorimetirc methods (Qubit, Invitrogen) and quality assessed by Fragment Analysis (Agilent).  Library preparation was initiated with 500ng of RNA and completed following manufacture's recommendations for the TruSeq stranded mRNA kit (Illumina).  Final libraries were quantified by qPCR (Kapa Library Quantification Kit, Kapa Biosystems) and fragment size observed with high sensitivity DNA fragment analysis (Agilent).  Paired end sequencing was completed on the NovaSeq 6000 at 2x100bp reads, targeting 50 million reads per sample.

treatment_protocol: Mice were first implanted with osmotic mini pumps that releases either vehicle or Ang-II continously for 6 weeks. Two weeks after the implantation, five daily tamoxifen injections were used to activate the transgene. Tissue were collected two weeks after the completion of the tamoxifen injections.

tag: genotype

value: smooth muscle-specific, tamoxifen inducible Cre

value: vehicle


title: Adrenal Cortex, PBS, 14R


title: Sample172 rat GH3 RNA


title: Sample171 rat GH3 RNA


title: Adrenal Cortex, LPS, 3R

value: LPS


title: ISM-Cre.Vehicle_rep3


title: ISM-Cre.Vehicle_rep5


title: Adrenal Cortex, PBS, 11R


title: Sample170 rat GH3 RNA


title: ISM-Cre.Vehicle_rep8


title: Blood sample from individual 13

description: Sample ID: 13


title: Sample169 rat GH3 RNA


title: 1656-A029859


title: ISM-Cre.Vehicle_rep4


title: Blood sample from individual 14

description: Sample ID: 14


title: Blood sample from individual 10

description: Sample ID: 10


title: Blood sample from individual 9

description: Sample ID: 9


title: Adrenal Cortex, LPS, 1R


title: Sample168 rat GH3 RNA


title: ISM-Cre.Vehicle_rep1


title: Blood sample from individual 11

description: Sample ID: 11


title: Sample167 rat GH3 RNA


title: Blood sample from individual 8

description: Sample ID: 8


title: Sample166 rat GH3 RNA


title: single cell ATO DLL4 derived BM cells Sample3_10x_ATO

city: Pasadena

first: Wen

last: Zhou

state: California

address: 1200 E California Blvd, Mail Code 250-86

department: BBE

institute: California Institute of Technology

description:
single cell ATO DLL4 derived BM cells
10x Chromium v2

data_processing:
Base calls were performed with RTA 1.13.48.0
conversion to FASTQ with bcl2fastq 1.8.4
FASTQ files were mapped onto the mouse genome build GRCm38(mm10) with STAR (v2.4.0) (Dobin et al., 2013) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings ?--output-genome-bam --sampling-for-bam? was added to rsem-calculate-expression.
STAR and RSEM reference libraries were created from genome build GRCm38(mm10) together with the Ensembl gene model file Mus_musculus.GRCm38.gtf.The resulting bam-files were used to create HOMER (Heinz et al., 2010) tag directories (makeTagDirectory with ?keepAll setting).
For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the ?noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson et al., 2010).
single cell data was processed with Cellranger 2.0 is run on the FASTQ files to generate matrix
Genome_build: GRCm38(mm10)

molecule: polyA RNA

source_name: Bone Marrow

growth_protocol: Lineage purified bone marrow cells (Lin-) were cultured with stromal cells (OP9 or MS5) following the previously published conditions and recommended setups.(T. M. Schmitt, J. C. Zúñiga-Pflücker, Induction of T cell development from hematopoietic progenitor cells by Delta-like-1 in vitro. Immunity. 17, 749–756 (2002). A. Montel-Hagen, V. Sun, D. Casero, S. Tsai, A. Zampieri, N. Jackson, S. Li, S. Lopez, Y. Zhu, B. Chick, C. He, S. C. de Barros, C. S. Seet, G. M. Crooks, In Vitro Recapitulation of Murine Thymopoiesis from Single Hematopoietic Stem Cells. Cell Rep. 33, 108320 (2020)). The cells were cultured for 4-6 days, purified through FACS sorting as described.

extract_protocol:
RNAeasy MicroKit (Qiagen) for bulk RNA-seq
NEBNext Ultra RNA

tag: strain

value: WT

tag: facs purification gate

value: Lin- 7AAD- CD44+ Kit+


title: ISM-Cre.Vehicle_rep2


title: GLUTag replicate 5

city: Oxford

first: Thomas

last: Monfeuga

address: Innovation Building, Old Road Campus, Roosevelt Drive

country: United Kingdom

institute: Novo Nordisk Research Centre Oxford

data_processing:
Adaptor trimming with Trim Galore! (v. 0.6.4_dev)
Alignement with Salmon (v. 1.5.1) (with --noLengthCorrection argument)
Abundance data imported with Tximeta (v. 1.10) (with countsFromAbundance = "no" argument)
Genome_build: GRCm38, release M23
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt

source_name: GLUTag

growth_protocol: GLUTag cells were cultured in low glucose (1g/L) DMEM supplemented with GlutaMAX and 10% in-house heat inactivated FBS. Cells were seeded at 1e6 cells/well in 6-well dishes coated with 0.4% Matrigel and grown for 48hrs until the cell harvest.

extract_protocol:
Dynabeads mRNA DIRECT Kit
QuantSeq 3’mRNA-Seq Library Prep Kit-FWD

tag: cell line

value: GLUTag

value: enteroendocrine cells

tag: plate


title: GLUTag replicate 4


title: Blood sample from individual 6

description: Sample ID: 6

value: Female

value: Blood


title: Sample165 rat GH3 RNA

tag: tumor functional type


title: Adrenal Cortex, LPS, 2R


title: Blood sample from individual 7

description: Sample ID: 7

value: No active inflammatory disease


title: GLUTag replicate 3


title: mesenteric LN adult

city: Milan

first: Andrea

last: Brendolan

address: via Olgettina 60

department: Experimental Oncology

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v 4.0.0).
The counts were obtained with CellRanger v 4.0.0 using cellranger count
Genome_build: CellRanger transcriptome from mm10 (GRCm38)[refdata-gex-mm10-2020]
Supplementary_files_format_and_content: Tab separated matrix files of raw counts; gene names in rows and cell barcodes in columns. One file per sample, gzipped (.gz).

source_name: lymph node CD45-/CD31+/GP38+ and GP38-

extract_protocol:
For the scRNAseq performed on E17.5 LNs:  Brachial, inguinal and mesenteric lymph nodes were harvested from E17.5 C57BL6/N wild-type embryos into RPMI (Fisher Scientific) with 2% FBS (EuroClone), 20mM HEPES (Fisher Scientific). Tissue were transferred to room temperature digestion buffer (0,8mg/ml Collagenase/Dispase (Roche) + 100ug/ml DNAse I (Roche) in RPMI with 2% FBS and 20mM Hepes) and incubated at 37°C for 30 minutes at 900rpm in thermomixer. Every 10 minutes, tissues were placed on ice, large pieces were settled and supernatant were transferred into a new tube with MACS buffer; next larger fragments were pipetted with fresh digestion mix and placed into thermomixer for the remaining time. The digested cell suspension was centrifugated, then cells were counted and stained with anti-CD45, anti-VCAM1 and anti-ICAM1 for sorting. Sorted cells CD45-/VCAMhi/ICAMhi cells were spun down and immediately run on the 10X Chromium (10X Genomics) and then processed through library preparation following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit (v2 Chemistry, 10X Genomics).
For the scRNAseq performed on adult LNs: Brachial, inguinal and mesenteric lymph nodes were harvested from C57BL6/N wild-type mice at 2 months of age into RPMI (Fisher Scientific) with 2% FBS (EuroClone), 20mM HEPES (Fisher Scientific). Tissue were transferred to room temperature digestion buffer (0,2mg/ml Collagenase (Roche) + 0,45mg/ml Liberase (Roche) + 100ug/ml DNAseI (Roche) in RPMI with 2% FBS and 20mM Hepes) and incubated at 37°C for 30 minutes at 900rpm in thermomixer. Every 10 minutes, tissues were placed on ice, large pieces were settled and supernatant were transferred into a new tube with MACS buffer; next larger fragments were pipetted with fresh digestion mix and placed into thermomixer for the remaining time. The digested cell suspension was centrifugated, cells were counted and resuspended in MACS buffer with anti-CD45-APC antibody + anti-APC MACS microbeads (Miltenyi) to deplete CD45+ cells. Eluted CD45- cells were spun down, counted and stained for anti-CD45, anti-CD31 and anti-GP38 for sorting. Sorted stromal cells (CD45-/GP38+) and endothelial cells (CD45-/CD31+ and CD45-/GP38+/CD31+) were spun down and immediately run on the 10X Chromium (10X Genomics) and then processed through library preparation following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit (v2 Chemistry, 10X Genomics).
Chromium Single Cell 3’ Reagent Kit (v2 Chemistry, 10X Genomics)

value: brachial lymph node pooled from 5 adult mice

tag: age

value: adult P60

value: wild-type


title: Sample157 rat GH3 RNA

tag: therapy


title: inguinal LN adult


title: Blood sample from individual 5

description: Sample ID: 5

tag: individual id

tag: gender


title: Sample164 rat GH3 RNA


title: GLUTag replicate 6


title: GLUTag replicate 2


title: Blood sample from individual 4

description: Sample ID: 4

tag: tissue

tag: disease state


title: mesenteric LN E17.5

source_name: lymph node CD45-/ICAMhiVCAMhi

value: brachial lymph node pooled from 30 embryos

value: embryonic day E17.5


title: Sample155 rat GH3 RNA


title: Blood sample from individual 3

description: Sample ID: 3


title: Sample156 rat GH3 RNA


title: GLUTag replicate 1

tag: passage


title: Blood sample from individual 1

description: Sample ID: 1


title: Blood sample from individual 2

description: Sample ID: 2


title: brachial LN

data_processing:
FASTQ files were demultiplexed from raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v 2.1.1).
The whitelist of cell barcodes was identified with 'umi_tools whitelist --set-cell-number 5000 --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNN' (umi_tools v0.5.4).
Reads of the whitelisted cells were extracted with 'umi_tools extract --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNN --filter-cell-barcode --whitelist=whitelist.txt' (umi_tools v0.5.4).
Extracted reads were aligned with STAR aligner (v2.5.3a) to the primary assembly of mouse genome (GRCm38) with parameter '--outFilterMultimapNmax 1' (to exclude multi-mapping reads).
Mapped reads were assigned to gene_name attributes from GENCODE basic annotation for GRCm38 (version M16) using Subread featureCounts (v1.6.2). Results were saved in BAM files with option 'featureCounts -R BAM' and successively sorted and indexed with samtools (v1.4).
Per gene counts were summarized for each cell using 'umi_tools count --per-gene --gene-tag=XT --assigned-status-tag=XS --per-cell --wide-format-cell-counts' (umi_tools v0.5.5).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-separated matrix files of raw counts; with gene names in rows and cell barcodes in columns. One file per sample, gzipped (.gz).

source_name: lymph node CD45- cells

extract_protocol:
Brachial, inguinal and mesenteric lymph nodes were harvested from Islet-CRE:Rosa-EYFP P2 pups into RPMI (Fisher Scientific) with 2% FBS (EuroClone), 10mM HEPES (Fisher Scientific). Tissue were transferred to room temperature digestion buffer (0,45mg/ml LiberaseTM (Roche) in FBS) and incubated at 37oC for 10 minutes at 900rpm in thermomixer. Tissue was pipetted 30 times with P1000 and incubated another 10 minutes. The digested cell suspension was resuspended in complete RPMI medium and centrifugated, then cells were resuspended in MACS buffer with anti-CD45 MACS microbeads (Miltenyi) to deplete CD45+ cells. The remaining cell suspension was spun down and immediately run on the 10X Chromium (10X Genomics) and then processed through library preparation following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit (v2 Chemistry, 10X Genomics).
Libraries were run on the NextSeq 500 for Illumina sequencing.

value: brachial lymph node pooled from 14 pups

value: postnatal day 2


title: brachial LN E17.5


title: inguinal LN

data_processing:
FASTQ files were demultiplexed from raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v 2.1.1).
The whitelist of cell barcodes was identified with 'umi_tools whitelist --set-cell-number 5000 --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNN' (umi_tools v0.5.4).
Reads of the whitelisted cells were extracted with 'umi_tools extract --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNN --filter-cell-barcode --whitelist=whitelist.txt' (umi_tools v0.5.4).
Extracted reads were aligned with STAR aligner (v2.5.3a) to the primary assembly of mouse genome (GRCm38) with parameter '--outFilterMultimapNmax 1' (to exclude multi-mapping reads).
Mapped reads were assigned to gene_name attributes from GENCODE basic annotation for GRCm38 (version M16) using Subread featureCounts (v1.6.2). Results were saved in BAM files with option 'featureCounts -R BAM' and successively sorted and indexed with samtools (v1.4).
Per gene counts were summarized for each cell using 'umi_tools count --per-gene --gene-tag=XT --assigned-status-tag=XS --per-cell --wide-format-cell-counts' (umi_tools v0.5.5).
Genome_build: mm10 (GRCm38).
Supplementary_files_format_and_content: Tab-separated matrix files of raw counts; with gene names in rows and cell barcodes in columns. One file per sample, gzipped (.gz).

value: inguinal lymph node pooled from 14 pups


title: sibling rep1

status: Public on Apr 07 2022

city: Wuhan

first: Yuexia

last: Lv

state: Hubei

address: Hubei, Wuhan, Hongshan district, Luoyu Road, Huazhong University of Science and Technology

department: College of Life Science and Technology

country: China

data_processing:
Illumina Casava 1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each gene and each sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene and each sample

organism: Danio rerio

source_name: zebrafish embryos except the heads region

growth_protocol: Zebrafish embryos were bred from male and female prpf31+/- parents and raised in an incubator under a photoperiod of 14/10 hours light/dark cycle at 28.5℃.

extract_protocol:
Total RNA was isolated from dissected tails including the AGM and CHT of zebrafish using RNA isolater Total RNA Extraction Reagent (Vazyme, R401-01).NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB #E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos, which were bred from male and female prpf31+/- parents, were collected at 36 hpf. The heads were dissected for genotyping, the residual dissected tails (including the AGM and CHT) of similar genotype were used for RNA extraction.

value: AB*

value: 36 hours post fertilization


title: scRNA-seq library of BM derived T cells from WT and Bcl11b KO animals run1

description:
polyA RNA
single cell droplet performed with 10x Chromium v3
scRNA_Bcl11b_run1.h5

data_processing: Single-cell RNA-seq data were processed using 10X Cellranger 3.0.0 software. Standard cellranger-mm10-3.0.0 reference annotations were loaded to the pipeline for read mapping and gene quantification.

extract_protocol: Purified LSK precursors from different animals were cultured in mouse artificial thymic organoids with MS5-mDLL4 stromal cells for 10 days. Samples from different animal origins were stained for surface markers and barcoded cell hashing antibodies separately, sorted through FACS, and pooled for scRNA-seq

value: Bone Marrow

value: Vav1-iCre/+ or +/+ ,and Bcl11b wt/wt or Bcl11b flx/flx.

tag: cell type

value: CD45+ Lin- 7AAD- CD25+


title: sibling rep2

institute: Huazhong University of Science and Technology

value: zebrafish embryos except the heads region


title: prpf31-/- rep2


title: prpf31-/- rep3


title: prpf31-/- rep1


title: brachial LN adult


title: antimir501 3

city: Goettingen

first: Md Rezaul

last: Islam

address: von siebold str. 3a

institute: DZNE

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
were mapped to mouse genome (mm10) using STAR (v 2.5.2b)
Expression counts were enumerated using featureCounts of subread (v 1.5.1) package.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: "differential_expression_409_5p_inhibition.csv" file contains the normalized counts and statistical details for the analysis of anti-miR-409-5p treatment compared to control samples.
Supplementary_files_format_and_content: "differential_expression_501_3p_inhibition.csv" file contains the normalized counts and statistical details for the analysis of anti-miR-501-3p treatment compared to control samples.

source_name: primary hippocampal neuronal culture

extract_protocol:
RNA was isolated tissues using RNA clean and concentrator kit.
Libraries were generated according to the instructions of TruSeq RNA Library Prep Kit v2.
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: primary neuronal cultures were treated with lipid nano particles packaged with either scramble RNA or anti-miRs for 48 hours, followed by RNA isolation.

value: primary neurons

tag: div

tag: treatment

tag: sample type

value: cell culture


title: antimir501 4


title: antimir409 4


title: sibling rep3

tag: genotype


title: inguinal LN E17.5

tag: strain


title: antimir409 3


title: antimir501 2


title: mesenteric LN

extract_protocol:
Brachial, inguinal and mesenteric lymph nodes were harvested from Islet-CRE:Rosa-EYFP P2 pups into RPMI (Fisher Scientific) with 2% FBS (EuroClone), 10mM HEPES (Fisher Scientific). Tissue were transferred to room temperature digestion buffer (0,45mg/ml LiberaseTM (Roche) in FBS) and incubated at 37oC for 10 minutes at 900rpm in thermomixer. Tissue was pipetted 30 times with P1000 and incubated another 10 minutes. The digested cell suspension was resuspended in complete RPMI medium and centrifugated, then cells were resuspended in MACS buffer with anti-CD45 MACS microbeads (Miltenyi) to deplete CD45+ cells.
The remaining cell suspension was spun down and immediately run on the 10X Chromium (10X Genomics) and then processed through library preparation following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit (v2 Chemistry, 10X Genomics).
Libraries were run on the NextSeq 500 for Illumina sequencing.

value: mesenteric lymph node pooled from 14 pups


title: antimir409 1


title: antimir409 2


title: Sample154 rat GH3 RNA


title: control 1

value: control


title: control 2


title: LFE7

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
Reads were trimmed using Trimmomatic v 0.39 to remove adapter content and low-confidence base calls
Trimmed reads were aligned to the bovine reference using HISAT2 v 2.2.1
Raw read counts were generated using the R/Bioconductor package Genomic Alignments v 1.26.0
Normalized counts, FPKM values, and log2 fold changes were computed using DESeq2 v 1.30.1
Gene Set Enrichment Analysis (GSEA) was used to compare fold changes to Reactome Pathways, using the R/Biocopnductor package fgsea v 1.16.0
Genome_build: Bos_taurus.ARS-UCD1.2
Supplementary_files_format_and_content: raw_counts.csv contains raw read counts per gene per sample, as calculated by the GenomicAlignments R/Bioconductor package, in comma-separated value format
Supplementary_files_format_and_content: normalized_counts.csv contains read counts per gene per sample, normalized by sample using DESeq2 v 1.20.0 with default settings, in comma-separated value format
Supplementary_files_format_and_content: fpkm.csv  contains FPKM values as computed by DESeq2 v 1.30.1, in comma-separated value format

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was extracted from the composited samples using RNeasy Protect Animal Blood kit (Cat. No. 73224; Qiagen) following the manufacturer’s instructions.
Libraries were prepared from 100 – 250 ng of total RNA per sample using the KAPA RNA HyperPrep Kit with RiboErase (Human, Mouse, Rat) Globin Reduction method in the WVU Genomics Core according to the kit manufacturer’s instructions.

tag: residual food intake

value: Low

value: Whole blood


title: LFE8


title: LFE5


title: LFE4


title: antimir501 1


title: LFE2


title: LFE3


title: HFE15

value: High


title: HFE9


title: HFE13


title: HFE16


title: HFE14


title: LFE1


title: HFE12


title: HFE10


title: Left ventricle_none stimulation

type: RNA

city: Tokyo

first: Shuheng

last: Wen

address: 1-5-45 Yushima

department: Forensic Science

country: Japan

institute: Tokyo Medical and Dental University

description: gene expression data extracted from left ventricle without stiumulation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rattus norvegicus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: left ventricle, none stimulation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: male

value: Left ventricle

value: SD


title: HFE11


title: non-CF, untreated [E12_B-37-19_Phil]

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

description: non-CF, untreated

data_processing:
Raw fastq files were aligned to a hybrid genome consisting of human genome assembly GRCh38.p13 and lentivirus genome sequence. Filtering, barcode counting, and UMI counting were performed with 10x CellRanger software version 3.0.2 with the argument --expect-cells=5000.
Assembly: GRCh38.p13
Supplementary files format and content: HDF5 format file containing counts for each gene (row) and cell barcode (column)

source_name: lung

extract_protocol:
Cultured cells were rinsed in PBS -/- and lifted in TrypLE for 45 min at 37C. Cells were centrifuged for 5 min at 200xrcf, supernatent was removed, and cells were resuspended in Phenol red-free DMEM:F12 with 0.04% non-acetylated BSA and counted.
10x Genomics Chromium Single Cell 3’ Reagent Kits v3 system

value: untreated

tag: subject id

value: lung

tag: disease

value: non-CF


title: CF, untreated [CFB-16-19_Phil]

description: CF, untreated

value: CF


title: CF, untreated [E6_CFB-15-19_Phil]

description: CF, untreated


title: WT2-2

city: Hangzhou

first: Lijiang

last: Fei

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Unmapped paired bam
Base-calls were performed with MGI software
Sequenced reads were trimmed for adaptor sequence. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. For experiments sequenced with MGISEQ-2000, we used the 150bp paired-end sequencing mode for the read1 (R1) and the read2 (R2). The cell barcode consists of three sequences, which are located at positions 1-6, 22-27, 43-48bp of R1. The UMI barcode is at position 49-54bp of R1. For experiments sequenced with MGI DNBSEQ-T7, we took a dark reaction for R1, where R1 measured 24bp and R2 measured 150bp. The cell barcode is at position 1-18 of R1, and the UMI barcode is at position 19-24 of R1.
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: *.csv: Comma-separated text files of digital expression matrix (dge) based on raw UMI counts, columns are cells, and rows are genes.
Supplementary_files_format_and_content: Cell_info.csv: Comma-separated text file provides information for every cell used.

extract_protocol:
Tissue dissociation and single-cell lysate
Library preparations were performed with the Microwell-seq protocol

value: E12.5 embryo

value: wild type


title: Left ventricle_cocaine_14 days

description: gene expression data extracted from left ventricle after 14 days cocaine administration

source_name: left ventricle, cocaine, 14 days

value: cocaine


title: LFE6


title: non-CF, untreated [B-23-19_Phil]

description: non-CF, untreated


title: WT2-1


title: WT1-2


title: U3 Control

city: Guangzhou

first: Ruihui

last: Xie

state: Guangdong

address: 107 Yan Jiang West Road

institute: Sun Yat-sen Memorial Hospital, SYSU

description: UUCUCCGAACGUGUCACGUTT

data_processing:
Base-calling bcl2fastq2 v2.19.1
Data filtering  in house
Read alignment hisat2 v2.1.0
transcript assemble htseq-count v0.6.1
Assembly: hg19
Supplementary files format and content: excel files include normalize values for each Sample

source_name: bladder cancer cell line UM-UC-3

growth_protocol: UM-UC-3 was cultured in DMEM (Gibco), T24 was cultured in 1640 (Gibco), supplemented with 10% FBS (Shanghai ExCell Biology, China) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life technologies) following manufacturer's instructions.

tag: sirna

value: Negetive control


title: U3 Control acinput

description: UUCUCCGAACGUGUCACGUTT


title: U3 NAT10-si

description: CCAUCUCUCGCAUCUAUUUTT

value: siRNA targeting NAT10 was transfected in the cell


title: U3 NAT10-si acIP

description: CCAUCUCUCGCAUCUAUUUTT


title: WT1-1

tag: age


title: U3 Control acIP

description: UUCUCCGAACGUGUCACGUTT


title: T24 NAT10-si

description: CCAUCUCUCGCAUCUAUUUTT

source_name: bladder cancer cell line T24


title: U3 NAT10-si acinput

description: CCAUCUCUCGCAUCUAUUUTT


title: E12.5 embryo, WT4-4

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol


title: E12.5 embryo, WT4-3


title: E12.5 embryo, WT4-1


title: E12.5 embryo, WT4-2


title: E12.5 embryo, WT3-3


title: E12.5 embryo, WT3-2


title: MCF7 shBRCA1+E2 yH2AX ChIP-seq rep2

city: Guanghzou

first: Zeng

last: Pengguihang

address: No.74, Zhongshan 2nd Road, Guangzhou, Guangdong

institute: Sun Yat-Sen University

library_source: genomic

data_processing:
Raw fastq files were under adapter trimming and quality control by Trim Galore 0.4.4_dev, using default parameters.
Trimmed reads were mapped to hg19 genome assembly by STAR2 020201 and Bowtie2 2.3.4.1, using default parameters.
Mapped RNA-seq reads were counted by HTSeq-count 0.9.1, using default parameters.
Mapped ChIP-seq reads peakcalling were performed by macs2 2.1.1.20160309, using default parameters.
Bigwig files were converted from uniquely mapped reads by deeptools 3.1.1 bamCoverage tool.
Assembly: hg19
Supplementary files format and content: Bigwig files, matrix table with raw gene counts for every gene and every sample

source_name: breast cancer MCF7 cells

growth_protocol: MCF7 were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) (VISTECH) and 1% penicillin-streptomycin (Hyclone).

extract_protocol:
For RNA-seq: Total RNA was extracted from cell pellets using RNAzol reagent. For ChIP-seq: 1% formaldehyde in PBS was used to crosslink the cells. Antibody enrich DNA fragments overnight from Sonicated lysates.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each sample is treated with E2/DRB/ETOH for 12h. The concentration of treatment: E2(10nM); DRB(5μM)

tag: cell line

value: breast cancer MCF7 cells

value: treated with E2

tag: RNAi

value: BRCA1 knockdown

tag: chip antibody


title: MCF7 shBRCA1+E2 ER ChIP-seq rep1

value: anti-ER


title: MCF7 shBRCA1+E2 yH2AX ChIP-seq rep1


title: MCF7 shBRCA1+E2+DRB yH2AX ChIP-seq rep1

value: treated with E2 and DRB


title: E12.5 embryo, KO5-4

value: knock out


title: T24 Control

description: UUCUCCGAACGUGUCACGUTT


title: MCF7 shBRCA1 yH2AX ChIP-seq rep2

value: treated with ETOH


title: MCF7 shBRCA1+E2+DRB yH2AX ChIP-seq rep2


title: MCF7 shBRCA1+E2 ER ChIP-seq rep2


title: E12.5 embryo, WT3-1


title: E12.5 embryo, KO5-3


title: MCF7 shBRCA1 yH2AX ChIP-seq rep1


title: MCF7 shBRCA1 ER ChIP-seq rep2


title: E12.5 embryo, KO5-1


title: E12.5 embryo, KO4-3


title: MCF7 shBRCA1 Input ChIP-seq rep1

value: none (input)


title: MCF7 shBRCA1 Input ChIP-seq rep2


title: E12.5 embryo, KO4-1


title: E12.5 embryo, KO4-2


title: MCF7 shEV+E2 yH2AX ChIP-seq rep1

value: EV


title: MCF7 shEV+E2 yH2AX ChIP-seq rep2


title: MCF7 shEV+E2 ER ChIP-seq rep2


title: E12.5 embryo, KO3-4


title: MCF7 shEV+E2 Input ChIP-seq rep2


title: MCF7 shBRCA1 ER ChIP-seq rep1


title: E12.5 embryo, KO3-1


title: E12.5 embryo, KO2-2


title: E12.5 embryo, KO2-1


title: E12.5 embryo, KO1-2


title: E12.5 embryo, KO1-3


title: MCF7 shEV+E2 Input ChIP-seq rep1


title: MCF7 shBRCA1+E2 RNA-seq rep1


title: E12.5 embryo, KO5-2


title: E12.5 embryo, KO1-1


title: MCF7 shBRCA1+E2 RNA-seq rep2


title: Wt-Female-Sal, 3 (Bisulfite-seq)

city: North Chicago

first: Johnny

last: He

state: IL

address: 3333 Green Bay Road, Basic Science Building 2.300

department: Microbiology and Immunology

institute: Rosalind Franklin University

data_processing:
A bioinformatics analysis pipeline nf-core/methylseq (Ewels et al., 2020) was used to process the methylation (Bisulfite) sequencing data.
In the pipeline, FASTQC (v 0.11.9) was chosen for quality control and Trim Galore! (v0.6.5) for adapter sequence trimming with default parameters.
Trimmed sequences were then mapped to the Mus musculus assembly (GRCm38/mm10) from Genome Reference Consortium, using Bismark 0.22.3 with the alignment tool Bowtie2 2.4.2.
Sequence duplicates were further removed by command “deduplicate_bismark” and context-dependent methylation (CpG and CpH) were extracted by command “bismark_methylation_extractor”.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited plain text. for each sample and for each cytosine context (CpG, CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, methylation level (#methylated cytosines sequenced/#total cytosines sequenced), #methylated cytosines sequenced, #unmethylated cytosines sequenced, and ID(concatenating chromsome and start coordinate with underscore)

source_name: Brain hippocampus

extract_protocol:
Genomic DNA was isolated from one HIP hemisphere by DNeasy Blood & Tissue Kit, the DNA quality was first confirmed by Nanodrop, with 260/280 ratio at 1.95-2.0 (in 10 mM Tris·Cl, pH 7.5 solution) and then verified by 1% agarose gel analysis to make sure no DNA degradation and RNA contamination.
Genomic DNA libraries were prepared genomic DNA (10 ng) using a Pico Methyl-Seq Library Prep Kit. MQ beads, were used in place of the column purification system in the library kit for higher DNA recovery

tag: tissue

value: Brain hippocampus

value: WT

value: Saline i.p.

tag: Sex

value: Female


title: MCF7 shEV+E2 RNA-seq rep1


title: MCF7 shEV RNA-seq rep2


title: MCF7 shEV+E2 RNA-seq rep2


title: MCF7 shBRCA1 RNA-seq rep2


title: Wt-Female-Sal, 2 (Bisulfite-seq)


title: E12.5 embryo, KO3-3

value: E12.5 embryo


title: MCF7 shEV+E2 ER ChIP-seq rep1


title: MCF7 shEV RNA-seq rep1


title: Wt-Female-Coc, 2 (Bisulfite-seq)

value: Cocaine i.p.


title: Wt-Female-Coc, 3 (Bisulfite-seq)


title: JCP_Patient_53_SLIT_pre_VDJ

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

data_processing:
Basecalls and mapping performed using Cell Ranger ver 6.0
Assembly: GRCh38
Supplementary files format and content: TCR VDJ, barcodes, features and matrix tsv files

source_name: PBMC

extract_protocol:
Cultured PBMCs were immediately processed in TRIzol reagent (Invitrogen, Carlsbad, CA). For comparison of good responder and poor responders, 25 ng/ml of phorbol-12-myristate-13-acetate and 1 µg/ml of ionomycin (Sigma-Aldrich) were added at the last 4 h of culture because the number of cells available was small.
Singel cell RNA-seq, Single cell TCR V(D)J segments (scVDJ-seq)
Libraries were prepared using Chromium Single Cell 5’ Reagent Kits v1.1 and Single-Cell V(D)J Enrichment Kit for Human T Cells according to manufacturer’s protocol (10X Genomics).

treatment_protocol: PBMC samples from seven out-patients suffering from JCP, which were obtained both before and at one-year after initiating SLIT administration. PBMCs were purified from whole blood using the Ficoll-Hypaque technique and cultured as previously described16. RPMI 1640 (Sigma-Aldrich), supplemented with fetal calf serum (10%), L-glutamine (2 μM), penicillin (100 U/ml), streptomycin (100 μg/ml), HEPES (10 mM), 2-mercaptoethanol (55 μM), nonessential amino acids (1%), and sodium pyruvate (1 mM) (all from Gibco BRL, Grand Island, NY), was used as the culture medium. PBMCs obtained from patients were pre-cultured (1 × 106 cells/ml) at 37°C overnight and cells were stimulated with Sugi (Japanese cedar in Japanese) basic protein (SBP; 2 µg/ml; HAYASHIBARA, Okayama, Japan) in the presence of rhIL-2 (1 U/ml; Kyowa, Tokyo, Japan) for 5 days. SBP is composed of major Japanese cedar pollen allergen Cry j 1 and Cry j 2.

tag: method

tag: patient

tag: treat

value: pre

value: male

tag: curative effect

value: high


title: JCP_Patient_46_SLIT_post_VDJ-2

value: post


title: JCP_Patient_46_SLIT_post_VDJ


title: JCP_Patient_53_SLIT_post_VDJ


title: Wt-Female-Coc, 1 (Bisulfite-seq)

tag: treatment


title: Wt-Male-Sal, 3 (Bisulfite-seq)

tag: genotype

value: Male


title: MCF7 shBRCA1 RNA-seq rep1

tag: cell type

value: breast cancer MCF7 cells

value: BRCA1 knockdown


title: JCP_Patient_46_SLIT_pre_VDJ


title: Wt-Male-Sal, 2 (Bisulfite-seq)

tag: strain


title: JCP_Patient_44_SLIT_pre_VDJ


title: Wt-Male-Coc, 3 (Bisulfite-seq)


title: Wt-Male-Sal, 1 (Bisulfite-seq)


title: Wt-Male-Coc, 2 (Bisulfite-seq)


title: JCP_Patient_25_SLIT_post_VDJ


title: JCP_Patient_44_SLIT_post_VDJ


title: iTat-Female-Sal, 2 (Bisulfite-seq)

value: iTat


title: Wt-Male-Coc, 1 (Bisulfite-seq)


title: JCP_Patient_25_SLIT_pre_VDJ


title: JCP_Patient_50_SLIT_post_VDJ

value: low


title: iTat-Female-Sal, 3 (Bisulfite-seq)


title: iTat-Female-Sal, 1 (Bisulfite-seq)


title: Wt-Female-Sal, 1 (Bisulfite-seq)


title: JCP_Patient_48_SLIT_post_VDJ


title: JCP_Patient_20_SLIT_post_VDJ


title: iTat-Female-Coc, 3 (Bisulfite-seq)


title: JCP_Patient_48_SLIT_pre_VDJ


title: iTat-Male-Sal, 3 (Bisulfite-seq)


title: iTat-Female-Coc, 1 (Bisulfite-seq)


title: JCP_Patient_53_SLIT_pre_expression

value: Expression


title: JCP_Patient_20_SLIT_pre_VDJ


title: JCP_Patient_53_SLIT_post_expression


title: iTat-Female-Coc, 2 (Bisulfite-seq)


title: JCP_Patient_46_SLIT_post_expression-2


title: iTat-Male-Coc, 2 (Bisulfite-seq)


title: JCP_Patient_46_SLIT_post_expression


title: JCP_Patient_50_SLIT_pre_VDJ


title: iTat-Male-Coc, 1 (Bisulfite-seq)


title: iTat-Male-Sal, 2 (Bisulfite-seq)


title: iTat-Male-Sal, 1 (Bisulfite-seq)


title: JCP_Patient_44_SLIT_pre_expression


title: JCP_Patient_25_SLIT_post_expression


title: iTat-Male-Coc, 3 (Bisulfite-seq)


title: Untreated, replicate 4, 10x chip 2 lane 8, pooled from 2 mice, scRNAseq

city: Cambridge

first: Chiaowen

middle: Joyce

last: Hsiao

state: MA

address: 200 Technology square

institute: Moderna Therapeutics

description:
10x Genomics
LIB000033805

library_source: transcriptomic single cell

data_processing:
bustools v0.39.3 was used to map sequencing reads to the mm10genome and also to perform demultiplexing, barcoded processing and gene counting.
DropletUtils v1.14.2 EmptyDrops function was used to distinguish droplets containing cells and droplets containing cell-free RNA (FDR threshold < .01, niter=100,000 for the Monte Carlo p-value calculation).
Filtering cells:  Cells were further excluded if they were associated with low number of molecules (< 500 total molecules) or low number of genes detected (< 500 genes)
Low count gene exclusion: Low count genes were excluded to retain genes detected in > 0.01% of the cells.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Spleens were collected from C57BL/6 female mice dosed with HSA-IL2wt or HSA-IL2m at 0.05mpk at 2 days and 4 days post injection (n = 3 mice each condition and timepoints) and from untreated mice for baseline comparison (n = 2). Each spleen was homogenized by mechanical disruption and CD4 T cells were isolated using a negative selection magnetic enrichment kit (StemCell). CD4 T cells collected from each treatment condition were pooled across individual mice, resulting in five single-cell suspensions. For each sample, the purity exceeded 98% purity and viability exceeded 99%. Each sample was diluted to a 1 million cells per mL.
10x Genomics 3’ Library and Gel Bead Kit (Chromium Next GEM v3.1 516 1000128, 1000157, 1000213) and Single Cell Chip G kit (Chromium Next GEM 1000127) were used to prepare libraries using the 10x Genomics Chromium Controller according to the manufacture’s guidelines (CG00052 Rev D). Two chips were used with a target 10,000 cells collected in each lane. The five pooled samples were each split into technical replicates and distributed to the two chips as follows: The untreated pooled sample was split into four technical replicates with two replicates distributed to each chip. For the treated conditions, each pooled sample was split into three technical replicates, with one replicate from Day 2 and two replicates from Day 4 on Chip 1, and two replicates from Day 2 and one replicate from day 4 on Chip 2.

value: Untreated

value: CD4 T

value: Spleen

value: 8wk old

tag: weight


title: JCP_Patient_25_SLIT_pre_expression

value: Female


title: HSA-ILm, day 4, replicate 3, 10x chip 2 lane 7, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033804

value: HSA-ILm, day 4


title: HSA-ILm, day 2, replicate 2, 10x chip 2 lane 5, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033802

value: HSA-ILm, day 2


title: HSA-ILm, day 2, replicate 3, 10x chip 2 lane 6, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033803


title: JCP_Patient_44_SLIT_post_expression


title: JCP_Patient_46_SLIT_pre_expression

value: pre


title: JCP_Patient_50_SLIT_post_expression


title: JCP_Patient_48_SLIT_pre_expression


title: JCP_Patient_48_SLIT_post_expression


title: Untreated, replicate 2, 10x chip 1 lane 8, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033797


title: HSA-ILwt, day 4, replicate 3, 10x chip 2 lane 4, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033801

value: HSA-ILwt, day 4


title: JCP_Patient_50_SLIT_pre_expression


title: JCP_Patient_20_SLIT_pre_expression

value: male


title: HSA-ILwt, day 2, replicate 3, 10x chip 2 lane 3, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033800

value: HSA-ILwt, day 2


title: HSA-ILwt, day 4, replicate 2, 10x chip 1 lane 6, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033795


title: HSA-ILwt, day 2, replicate 2, 10x chip 2 lane 2, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033799


title: HSA-ILwt, day 2, replicate 1, 10x chip 1 lane 7, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033796


title: eGFP+2

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: flow sorted eGFP positive cells at 150 days post neural retina induction

data_processing:
Reads obtained from the sequencing machines were further filtered by fastp (Chen et al., 2018) (version 0.18.0).
Short reads alignment tool Bowtie2 (Langmead and Salzberg, 2012)(version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed.
Paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 (Kim et al., 2015) with “-rna-strandness RF” and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 (Pertea et al., 2016; Pertea et al., 2015) in a reference-based approach.
For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM (Li and Dewey, 2011) software.
RNAs differential expression analysis was performed by DESeq2 (Love et al., 2014) software between two different groups (and by edgeR (Robinson et al., 2010) between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 was considered differentially expressed genes/transcripts.
Genome_build: Ensembl_release100
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: hiPSCs derived retinal organoids

growth_protocol: The BC1 hiPSC line was a gift from Professor Linzhao Cheng (University of Science and Technology of China) (Chou et al., 2011).HiPSCs were cultured in mTeSR1 medium (Stemcell Technologies) on Matrigel (Corning) coated 6-well plates, and passaged every 5-7 days at about 80% confluence according to our previously published protocol (Guan et al., 2021).

extract_protocol:
The differentiation of RCVRN-eGFP hiPSCs into ROs was performed according to our previously published protocol (Guan et al., 2021). Briefly, hiPSCs were dissociated and cultured in suspension at day (D) 0 to formed embryoid bodies (EBs). On D1 to D3, EBs were gradually switched in Neural induction medium (NIM) mixed with DMEM/F12 (1:1) (GIBCO), 1% N2 supplement (GIBCO), 1% minimum essential media Non-Essential Amino Acids (MEM NEAA, GIBCO) and 2 mg/ml heparin (Sigma-Aldrich). During D5 to D7, EBs were seeded on Matrigel-coated dishes and changed to retinal differentiation medium (RDM) mixed with DMEM/F12 (3:1), 2% B27 (without vitamin A, GIBCO), 1% MEM NEAA and 1% Antibiotic-Antimycotic (GIBCO). Typical optical vesicles (OVs) appeared around D25 with adjacent pigmented retinal epithelium cells (RPEs). After D28, OVs were mechanically detached and formed 3D ROs in suspension culture. Then, ROs were maintained in suspension culture to further development and maturation. Retinal culture medium 1 (RC1) supplemented with 10% fetal bovine serum (FBS, Natocor), 100 μM Taurine (Sigma-Aldrich), and 2 mM GlutaMAX (GIBCO) was used since D42. For long-term culture, Retinal culture medium 2 (RC2) was used and replaced B27 with 1% N2 since D90. ROs derived from RCVRN-eGFP reporter line were collected at D150 and mechanically separated into small pieces by a needle with 1 mL syringe. Then the clumps were dissociated into single cells by papain dissociation system (Worthington Biochemical). Cell suspensions were resuspended in sorting buffer (PBS containing 1 mM EDTA (GIBCO), 2% [vol/vol] FBS). Cells were sorted at 4℃ by BD FACSAria III Cytometer (BD Biosciences). Both eGFP positive (eGFP+) and negative (eGFP-) cells were separately collected in collecting buffer (RC1 medium (Guan et al., 2021) plus 50% [vol/vol] FBS). FSC-A and SSC-A, FSC-A and FSC-H were examined for all cells to obtain live single eGFP+ cells. Retinal cells derived from BC1-hiPSCs were used to determine gate for sorting. Then，ROs and purified cells were collected in Trizol reagent. Total RNA was extracted using Trizol reagent kit and the quality of RNA was assessed by an Agilent 2100 Bioanalyzer and checked using RNase free agarose gel electrophoresis.
The enriched mRNA was subjected to RNA-seq library construction from each two independent samples of three groups: unsorted (ROs), eGFP+ (FASC-sorted RCVRN-eGFP positive cells) and eGFP- (FASC-sorted RCVRN-eGFP negative cells).Briefly，Oligo (dT) beads were used to isolate the poly mRNA from the total RNA. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen), end repaired, Abaseadded, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq 6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: tissues/cell types

value: cell type:eGFP positive retinal cells derived from RCVRN-eGFP reporter hiPSCs

tag: day of induction

value: day post induction:Day 150


title: eGFP-2

description: flow sorted eGFP negative cells at 150 days post neural retina induction

value: cell type:eGFP negetive retinal cells derived from RCVRN-eGFP reporter hiPSCs


title: JCP_Patient_20_SLIT_post_expression

value: post


title: eGFP+1


title: eGFP-1


title: HSA-ILm, day 2, replicate 1, 10x chip 1 lane 4, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033793

tag: age


title: HSA-ILwt, day 4, replicate 1, 10x chip 1 lane 5, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033794


title: HSA-ILm, day 4, replicate 1, 10x chip 1 lane 2, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033791


title: Untreated, replicate 1, 10x chip 1 lane 1, pooled from 2 mice, scRNAseq

description:
10x Genomics
LIB000033790


title: Untreated, replicate 3, 10x chip 2, lane 1, pooled from 2 mice, scRNAseq

description:
10x Genomics
LIB000033798


title: CellLine_KP_rep2

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

data_processing:
Raw sequences files’ quality was checked via FastQC (v0.11.9, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads alignment to the mouse reference genome using Salmon tool (v1.4.0)
Salmon outputs were analysed using R’s package DESeq2 (v1.32.0)
Assembly: Mus musculus GRCm39 DNA primary assembly, transcript version GRCm39.103

source_name: KP cells

extract_protocol:
Lungs were digested using collagenase and total RNA was extracted using TriPure (Roche) accordingly to manifacturer guidelines. Extraction was followed by Qiagen Rneasy column clean-up accordingly to manifacturer instructions.RNA was amplified using the Nugen protocol before hybridization.
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: Mice were injected with 100.000 KP cells in the tail vein. Lungs were harvested 28 days after challenge.

value: KP cell line


title: unsorted2

description: RCVRN-eGFP reporter hiPSCs-derived retinal organoids at 150 days post neural retina induction

value: retinal organoids:derived from RCVRN-eGFP reporter hiPSCs


title: HSA-ILm, day 4, replicate 2, 10x chip 1 lane 3, pooled from 3 mice, scRNAseq

description:
10x Genomics
LIB000033792


title: CellLine_KP_rep1


title: Lung_KP_rep3

source_name: Lung tissues  injected with KP cells

value: lung


title: non_responder_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: BALF derived from non-responders

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000 systems, with 101 bp single-end reads obtained.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: BALF derived from non-responders

extract_protocol:
RNA was extracted from BALF cells stored in RNAlater. An miRNeasy Mini Kit (Qiagen) was utilized for total RNA extraction.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio). An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina) according to the SMARTer Kit instructions.

tag: cell line

value: bronchoalveolar lavage fluid


title: unsorted1


title: non_responder_rep2

description: BALF derived from non-responders


title: Lung_KP_rep1


title: responder_rep1

description: BALF derived from responders

source_name: BALF derived from responders


title: responder_rep3

description: BALF derived from responders


title: P21_V2_LV

city: Shanghai

first: Yuqing

last: Hu

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias  wascorrected.We used clusterProfiler R package to test the  statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were  filtered with GATK standard filter method and other parameters (cluster:3;  WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to  annotation for the Variablesite.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1).
Alternative Splicing is an important mechanism for regulate the expression of   genes and the variable of protein. rMATS(3.2.5) software was used to analysis the AS  event.
PPI analysis of differentially expressed genes was based on the STRING  database, which known and predicted Protein-Protein Interactions.
WGCNA (Weighted correlation network analysis) was used to describe the gene association modes among different samples.
Genome_build: GRCm38(mm10)
Supplementary_files_format_and_content: FPKM

source_name: LV free wall myocardium_volume overload(AVF)

extract_protocol:
Myocardium of LV free wall was rapidly removed from executed mice and flash frozen in liquid nitrogen , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: myocardium

tag: treatment method

value: volume overload(AVF)

tag: treatment  age

value: postnatal day 7

tag: test age

value: postnatal day 21


title: P21_V3_LV

tag: tissue


title: CellLine_KP_rep3


title: SCI_woMSC_4w_2

city: GuangZhou

first: Mangmang

last: Weiping

address: 1838 Guangzhou North Ave

department: Department of Cell Biology

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean data was obtained by using Trim Galore (v0.5.0) to remove reads containing adapter, ploy-N and low quality reads (Q < 30). The remaining reads were then mapped to reference genome using Hisat2 (v2.1.0).
To filter out the reads that might generate from the residual hUC-MSCs in rat spinal cord, the clean reads were firstly map to the human reference genome (GRCh38).
Then, the filtered non-human reads were further aligned to the rat reference genome (Rnor6) to obtain the data generated from rat spinal cord. Using Samtools (v1.9) with the parameter –f 2, reads mapped in proper pair were extracted.
featureCounts (v1.6.4) was used to count the reads numbers
Genome_build: Rnor6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Merged Matrix table with raw gene counts for all samples

source_name: Rat spinal cord

extract_protocol:
Total RNA was extracted with 1ml of Trizol reagent (Takara, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The compression injury was applied to 250 g adult female Sprague-Dawley rats at T10 level of spinal cord for 1 min using an aneurysm clip with clamping force of 60 g. At 7 days post-injury, human umbilical cord mesenchymal stem cells (hUC-MSCs) were injected intrathecally. 5mm segments of spinal cord centered at the lesion site were collected from rats treated with or without hUC-MSCs at 0, 1, 2, 4 weeks post transplantation.

value: Sprague-Dawley rats

value: spinal cord

value: post natal day 70

value: wild type

value: SCI_without MSC_4w


title: Thapsigargin_9h_siUPF1LL_1

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

data_processing:
Reads were trimmed using fastp software, with options --detect_adapter_for_pe and --trim_poly_g.
Trimmed reads were aligned with Hisat2, using default parameters and the hg19/grch37 combined genome and transcriptome index provided by the authors.
Bam files from Hisat2 mapping were used for quantification with featureCounts, using Ensembl GRCh37 release 75 gene annotations.
Differential gene expression analysis was performed using limma/voom, implemented by degust.erc.monash.edu.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file contains counts and normalized CPM values for all samples and log2 expression changes and statistics from limma/voom analysis of the indicated comparisons.

source_name: HEK-293 cells

growth_protocol: HEK-293 cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml L-glutamine at 37°C and 5% CO2.

extract_protocol:
Qiagen RNeasy Plus Mini RNA isolation kit
2 μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq Stranded RNA Library Preparation Kit (Illumina).

treatment_protocol: HEK-293 cells were reverse-transfected with 40 nM of the indicated siRNA using Lipofectamine RNAiMAX. Forty-eight hours post-siRNA transfection, cells were replated at a density of 5x105 cells per well of a 6-well plate. The next day, cells were treated with vehicle control, 25, 50, or 100 µg/mL puromycin (Sigma) for 4 hours, or 1 µM thapsigargin for 6 hours.

tag: agent

value: 1  microM thapsigargin

tag: sirna

value: UPF1LL-specific siRNA


title: responder_rep2

description: BALF derived from responders


title: SCI_woMSC_4w_3


title: Thapsigargin_9h_siUPF1LL_2


title: DMSO_9h_siUPF1LL_3

value: vehicle control


title: P21_S3_LV

source_name: LV free wall myocardium_operated-sham

value: operated-sham


title: Thapsigargin_9h_siUPF1LL_3


title: Lung_KP_rep2


title: SCI_woMSC_2w_1

value: SCI_without MSC_2w


title: SCI_woMSC_1w_3

value: SCI_without MSC_1w


title: SCI_woMSC_4w_4


title: P21_S2_LV


title: P21_V1_LV


title: SCI_woMSC_1w_1


title: SCI_woMSC_2w_2


title: SCI_woMSC_4w_1


title: P14_V3_LV

value: postnatal day 14


title: DMSO_9h_siUPF1LL_2


title: Thapsigargin_9h_siNT_2

value: non-targeting siRNA


title: non_responder_rep1

description: BALF derived from non-responders

value: bronchoalveolar lavage fluid


title: P14_V1_LV

value: myocardium

value: volume overload(AVF)


title: P14_S3_LV

value: postnatal day 7


title: Thapsigargin_9h_siNT_1


title: P21_S1_LV

value: postnatal day 21


title: SCI_woMSC_1w_2

value: Sprague-Dawley rats

value: spinal cord


title: SCI_wMSC_2w_2

value: post natal day 70

value: wild type

value: SCI_with MSC_2w


title: DMSO_9h_siUPF1LL_1

value: UPF1LL-specific siRNA


title: Thapsigargin_9h_siNT_3

value: 1  microM thapsigargin


title: P14_S2_LV

value: operated-sham


title: SCI_wMSC_4w_3

value: SCI_with MSC_4w


title: SCI_wMSC_4w_4


title: SCI_wMSC_4w_1


title: P14_S1_LV


title: SCI_wMSC_2w_3


title: SCI_1

value: SCI


title: SCI_wMSC_1w_3

value: SCI_with MSC_1w


title: DMSO_9h_siNT_3

value: vehicle control

value: non-targeting siRNA


title: SCI_wMSC_1w_2


title: SCI_wMSC_1w_1


title: DMSO_9h_siNT_2


title: Intact_1

value: untreated


title: NUP133-Mutant-1 repl.-3

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

institute: University Medical Center Freiburg

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using fastp v0.20.1
Reads were mapped to hg38 whole genome using HISAT2 v2.2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v2.0.1 and DESeq2 v2.11.40.6 were applied for differential expression analysis
Genome_build: Human Dec. 2013 (GRCh38/hg38) (hg38)
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for all Sample

source_name: human immortalized podocyte (AB8/13)

growth_protocol: Podocytes were cultured in RPMI 1640 cell growth medium supplemented with Glutamine (Thermo Fisher Scientific, #61870036), 10 % FCS (Merck, #S0615), 10 µg/ml ITS (Merck, #11074547001), 5 mM HEPES (Thermo Fisher Scientific, #15630-056), non-essential amino acids (MEM NEAA, Thermo Fisher Scientific, #11140050) 1:1000, 0.1 mM Sodium-Pyruvate (Thermo Fisher Scientific, #11360-039) and Penicillin-Streptomycin (Thermo Fisher Scientific, #15140122) at 33°C, 95% air and 5% CO2.

extract_protocol:
Cell were washed in PBS, scraped into PBS and pelleted by centrifugation. RNA was isolated from cell pellets using the Monarch Total RNA Miniprep Kit (T2010S, New England Biolabs) including gDNA depletion by gDNA binding columns and on column DNase-1 digest according to the supplier instructions. RNA quality number (RQN) was measured as 10.0 for all samples using an Agilent Fragment Analyzer system.
RNA libraries were prepared for sequencing using the NEBnext ultra II RNA kit. Libraries were sequenced on the Illumina NovaSeq 6000 sequencer following the manufacturer's protocols.

treatment_protocol: Podocytes were cultured on Collagen IV (C5533, Merck) precoated cell culture plates for 24 hours.

tag: background

value: NUP133 KO-1

value: podocyte


title: SCI_3


title: SCI_wMSC_2w_1


title: SCI_wMSC_4w_2


title: DMSO_9h_siNT_1


title: SCI_2


title: Mouse treated with PM2.5+melatonin, biological rep5 [MP8_Clariom_S_Mouse]

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description:
MP8_(Clariom_S_Mouse)
Mouse treated with PM2.5 and melatonin for 4 weeks

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Clariom_S_Mouse or Affymetrix miRNA-4_0 arrays. Arrays were washed and stained.

scan_protocol: Arrays were scanned.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse treated with PM2.5+melatonin

label_protocol: Biotinylated cRNA were prepared.

growth_protocol: Mice treated with PM2.5 for 4 weeks.

treatment_protocol: Mice in the experimental group were given melatonin orally (20 mg/kg•bw) every day for 28 days and PM2.5 (5 mg/kg•bw) via intratracheal instillation twice a week for 4 weeks. Mice in control group were intragastrically given equal volume of sterile water containing 0.5% ethanol, and intratracheal instillation with corresponding volume of blank filters eluted with saline.

value: liver

value: PM2.5 and melatonin for 4 weeks


title: NUP133-Mutant-2 repl.-3


title: Intact_4

value: Sprague-Dawley rats

value: spinal cord


title: NUP133-Mutant-2 repl.-2


title: Intact_3

value: post natal day 70

value: wild type


title: Intact_2


title: NUP133-Mutant-1 repl.-2


title: NUP133-Mutant-1 repl.-1


title: NUP133-WT repl.-2

value: NUP133 WT

value: WT


title: NUP133-WT repl.-1


title: UDP-treated HSC, treated in culture for 24h [PSR25]

city: NEW YORK

first: Robert

middle: F

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

description:
PSR25
Primary mouse HSC, cultured for 24h in the presence of UDP-glucose (10uM).
Bulk RNA-seq
tpm_values_genes_kallisto-PSR.txt

data_processing:
Bulk RNA-seq:
20M paired-end 100bp sequencing was performed using the Illumina NovaSeq 6000.
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index was created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Differentially expressed genes were tested using DESeq2. Normalization was done internally using DESeq2's specialized algorithm and normalization to compare across samples, was performed using the TPM (transcripts per million) method.
scRNA-seq:
10x Genomics' cellranger pipeline was used to process the data (v2.1.1).
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bulk RNA-seq: Text files include TPM values for each Sample.
Supplementary_files_format_and_content: scRNA-seq: Raw counts in MatrixMarket (mtx) format, barcodes.tsv, genes.tsv.

source_name: liver

growth_protocol:
HSC were obtained perfusing and digesting the liver, followed by gradient centrifugation (Mederacke et al., Nat Protocol 2015).
For experiments evaluating effects of UDP-glucose, primary mouse HSC were plated and cultured in DMEM +10%FBS for 5h followed by change to medium containing 0.1% FBS.

extract_protocol:
Total RNA was column purified (Qiagen mini).
Construct libraries using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: Following the change of medium containing DMEM 0.1% FBS, HSC were treated with UDP-glucose (10uM) for 24h.

value: Balbc

tag: liver damage

value: HSC

value: UDP-glucose


title: All cell types from a normal untreated liver [RS007]

description:
RS007
scRNA-seq (10x) on fresh isolated liver cells.
scRNA-seq

growth_protocol: For single cell RNA-seq of the whole liver, hepatic cell populations were obtained by perfusing and digesting the liver.

extract_protocol: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s instructions, 12 cycles of cDNA amplification and 12 cycles of library amplification were performed, and samples were sequenced on an Illumina HiSeq and NovaSeq 6000 sequencing system instrument at the JP Sulzberger Columbia Genome Center.

value: All liver cell types


title: OLs_3-5

city: Seoul

first: Macrogen

last: Inc.

address: 12F, World Meridian Venture Center #254 Beotkkot-ro, Geumcheon-gu

country: South Korea

institute: Macrogen Inc.

description: Oligodendrocyte differentiated condition

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic 0.38 is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2.
Raw read count and normalized values were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -e for each sample.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Raw read count and Normalized values for each sample.

source_name: Rat oligodendrocytes

growth_protocol: Rat oligodendrocyte precursors are cultured in standard Raff medium and grown.

extract_protocol:
RNA was harvested using ISOGEN reagent. QIAGEN Rneasy MinElute Cleanup Kit (Cat#74204) was used to purify and concentrate RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols, TruSeq Stranded Total RNA Sample Prep Guide, Part #15031048 Rev. E.

treatment_protocol: Rat oligodendrocyte presursors are cultured in Raff medium and allowed to be differentiated in standard growth factor changes.

value: Rat oligodendrocytes

value: SD rat

tag: condition

value: Differentiated condition (after differentiation)


title: Day0-2

description: Oligodendrocyte control condition

source_name: Rat oligodendrocyte precursors

value: Rat oligodendrocyte precursors

value: Control condition (before differentiation)


title: OLs_0-5

description: Oligodendrocyte control condition


title: Day3-2


title: Day3-1


title: NUP133-WT repl.-3

value: NUP133 KO-1

value: podocyte

tag: genotype


title: UDP-treated HSC, treated in culture for 24h [PSR24]

description:
PSR24
Primary mouse HSC, cultured for 24h in the presence of UDP-glucose (10uM).
Bulk RNA-seq
tpm_values_genes_kallisto-PSR.txt

tag: cell type

tag: treatment


title: Control HSC, cultured for 24h [PSR22]

description:
PSR22
Primary mouse HSC, cultured for 24h on plastic.
Bulk RNA-seq
tpm_values_genes_kallisto-PSR.txt

tag: strain


title: Day0-1

description: Oligodendrocyte control condition


title: CF, untreated [CFB_14_19_Phil_lane4]

first: Alejandro

last: Pezzulo

address: 6316 Pappajohn Biomedical Discovery Building

institute: Universty of Iowa

description: CF, untreated

data_processing:
Raw fastq files were aligned to a hybrid genome consisting of human genome assembly GRCh38.p13 and lentivirus genome sequence. Filtering, barcode counting, and UMI counting were performed with 10x CellRanger software version 3.0.2 with the argument --expect-cells=5000.
Assembly: GRCh38.p13
Supplementary files format and content: HDF5 format file containing counts for each gene (row) and cell barcode (column)

source_name: lung

extract_protocol:
Cultured cells were rinsed in PBS -/- and lifted in TrypLE for 45 min at 37C. Cells were centrifuged for 5 min at 200xrcf, supernatent was removed, and cells were resuspended in Phenol red-free DMEM:F12 with 0.04% non-acetylated BSA and counted.
10x Genomics Chromium Single Cell 3’ Reagent Kits v3 system

value: untreated

tag: subject id

value: lung

tag: disease

value: CF


title: P14_V2_LV

value: myocardium

value: volume overload(AVF)

value: postnatal day 7

value: postnatal day 14


title: UDP-treated HSC, treated in culture for 24h [PSR23]

description:
PSR23
Primary mouse HSC, cultured for 24h in the presence of UDP-glucose (10uM).
Bulk RNA-seq
tpm_values_genes_kallisto-PSR.txt

value: Balbc

value: HSC


title: NUP133 KO-2 repl.-2

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using Cutadapt v1.16
Reads were mapped to hg38 whole genome using HISAT2 v2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v1.6.4 and DESeq2 v2.11.40.6 were applied for differential expression analysis
Genome_build: Human Dec. 2013 (GRCh38/hg38) (hg38)
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for all Sample

extract_protocol:
Cell were washed in PBS, scraped into PBS and pelleted by centrifugation. RNA was isolated from cell pellets using the Monarch Total RNA Miniprep Kit (T2010S, New England Biolabs) including gDNA depletion by gDNA binding columns and on column DNase-1 digest according to the supplier instructions. RNA quality number (RQN) was measured as 10.0 for all samples using an Agilent Fragment Analyzer system.
RNA libraries were prepared for sequencing using the NEBnext ultra II RNA directional kit. Libraries were sequenced on the Illumina NovaSeq 6000 sequencer following the manufacturer's protocols.

tag: monoclonal background

value: NUP133 KO

tag: genotype&monoclonal background

value: NUP133 KO-2


title: Mouse treated with PM2.5+melatonin, biological rep1 [MP1_Clariom_S_Mouse]

description:
MP1_(Clariom_S_Mouse)
Mouse treated with PM2.5 and melatonin for 4 weeks

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: liver

value: PM2.5 and melatonin for 4 weeks


title: Mouse treated with PM2.5+melatonin, biological rep4 [MP4_Clariom_S_Mouse]

description:
MP4_(Clariom_S_Mouse)
Mouse treated with PM2.5 and melatonin for 4 weeks


title: Mouse treated with PM2.5+melatonin, biological rep2 [MP2_Clariom_S_Mouse]

description:
MP2_(Clariom_S_Mouse)
Mouse treated with PM2.5 and melatonin for 4 weeks


title: Mouse treated with PM2.5, biological rep3 [P14_Clariom_S_Mouse]

description:
P14_(Clariom_S_Mouse)
Mouse treated with PM2.5 for 4 weeks

source_name: mouse treated with PM2.5

value: PM2.5 for 4 weeks


title: Mouse treated with PM2.5, biological rep5 [P17_Clariom_S_Mouse]

description:
P17_(Clariom_S_Mouse)
Mouse treated with PM2.5 for 4 weeks


title: Mouse treated with PM2.5+melatonin, biological rep3 [MP3_Clariom_S_Mouse]

description:
MP3_(Clariom_S_Mouse)
Mouse treated with PM2.5 and melatonin for 4 weeks


title: NUP133 KO-2 repl.-1


title: CF, untreated [CFB_13_19_Phil]

description: CF, untreated


title: NUP133 WT-2 repl.-2

value: NUP133 WT

value: NUP133 WT-2


title: non-CF, untreated [B_20_19_Phil_lane8]

description: non-CF, untreated

value: non-CF


title: Mouse treated with PM2.5, biological rep2 [P12_Clariom_S_Mouse]

description:
P12_(Clariom_S_Mouse)
Mouse treated with PM2.5 for 4 weeks


title: Mouse treated with PM2.5, biological rep1 [P10_Clariom_S_Mouse]

description:
P10_(Clariom_S_Mouse)
Mouse treated with PM2.5 for 4 weeks


title: non-CF, untreated [B_18_19_Phil]

description: non-CF, untreated

value: untreated


title: Mouse treated with PM2.5, biological rep4 [P15_Clariom_S_Mouse]

description:
P15_(Clariom_S_Mouse)
Mouse treated with PM2.5 for 4 weeks


title: Mouse treated with melatonin, biological rep5 [M35_Clariom_S_Mouse]

description:
M35_(Clariom_S_Mouse)
Mouse treated with melatonin for 4 weeks

source_name: mouse treated with melatonin

value: melatonin for 4 weeks


title: Control HSC, cultured for 24h [PSR21]

description:
PSR21
Primary mouse HSC, cultured for 24h on plastic.
Bulk RNA-seq
tpm_values_genes_kallisto-PSR.txt


title: NUP133 KO-1 repl.-1

value: podocyte

value: NUP133 KO-1


title: NUP133 WT-2 repl.-1


title: NUP133 WT-1 repl.-2

value: NUP133 WT-1


title: Control HSC, cultured for 24h [PSR20]

description:
PSR20
Primary mouse HSC, cultured for 24h on plastic.
Bulk RNA-seq
tpm_values_genes_kallisto-PSR.txt


title: NUP133 KO-1 repl.-2


title: Mouse treated with melatonin, biological rep3 [M33_Clariom_S_Mouse]

description:
M33_(Clariom_S_Mouse)
Mouse treated with melatonin for 4 weeks


title: Unplated quiescent HSC [RSB22]

description:
RSB22
Isolated HSC from uninjured liver.
Bulk RNA-seq
tpm_values_genes_kallisto_RSB19_to_RSB22.txt

growth_protocol:
HSC were obtained perfusing and digesting the liver, followed by gradient centrifugation (Mederacke et al., Nat Protocol 2015).
For HSC that were not treated by UDP-glucose, further purification was achieved by FACS sorting for VitA and LratCre-induced TdTom and then centrifuged for RNA extraction.

value: LratCre+, TdTom+ in C57BL/6J


title: Mouse treated with melatonin, biological rep4 [M34_Clariom_S_Mouse]

description:
M34_(Clariom_S_Mouse)
Mouse treated with melatonin for 4 weeks


title: NUP133 WT-1 repl.-1


title: 7042: HLHS-Poor outcome scRNA-seq

city: Pittsburgh

first: Cecilia

middle: Wenya

last: Lo

state: United States

address: 530 45th St. 8120 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

description: single cell total RNA

data_processing:
Reads were processed using the Cell Ranger (version 3.1.0) count pipeline using the human reference genome GRCh38 and annotations from Ensembl (version 93).
Filtered data was read into a SingleCellExperiment object using the read10XCounts function of the R package DropletUtils [10.1186/s13059-019-1662-y] (v1.6.1). Quality control and filtering were performed using the R packages and scater [10.1093/bioinformatics/btw777] (v1.14.6). For each sample, cells with library size less than 500 and number of detected genes less than 300 or greater than 6,000 were excluded. Additionally, we used the automated outlier detection of scater to exclude cells with high mitochondrial percentage (greater than 3 times the median absolute deviation (MAD) from the median value).
Processed data files include the filtered feature barcode matrices for each sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: H5

source_name: induced pluripotent stem cell derived cardiomyocytes (iPSC-CM)

growth_protocol: Human fibroblasts or lymphoblastoid cells are transfected with four episomal plasmids71 (Addgene: 27077 (pCXLE-hOCT3/4-shp53-F), 27078 (pCXLE-hSK), 27080 (pCXLE-Hul), 27082 (pCXLE-EGFP)) using electroporation. After 7 days electroporated cells are switched to a 6-well plate with mTESR1 media and transferred to hypoxic conditions. After 21-40 days, islands of expanded iPSC clones were stained with Alkaline phosphatase, and positive colonies isolated onto 24well dishes.Isolated colonies are expanded in 24 well plates coated with feeder cells or BD Matrigel with mTESR1 media. After >15 passages, stable iPSC cells were seed on BD Matrigel pre-coated plates for 2-3 days under mTESR1 media then switched to CDM3 media consisting of RPMI 1640, BSA, 213 ug/ml Vitamin C and 6 uM CHIR9902172. After 2 days the media was replaced with CDM3 Media containing RPMI 1640, BSA, 10 uM XAV939, 213 ug/lm Vitamin C, and BSA. Finally,  beating cells were assayed by single cell RNAseq (Day20).

extract_protocol:
The iPSC-CMs were disaggregated using cold active protease [10 mg/ml Bacillus Licheniformis protease; Creative Enzymes NATE0633) and 125 U/ml DNAse (Applichem, A3778) incubated on ice with trituration for 5-7 minutes. Then 5% bovine serum albumin (BSA) was added, and cells were filtered through a 100 μm strainer and cetrifuged to pellet the cells and then re-suspended in 200ul PBS/5% BSA. Trypan blue exclusion was used to quantify cell viability, and the volume was adjusted to 200,000 cells/ml for 10X chromium single-cell RNA-seq.
Paired-end library preparation was carried out using the V3 version (10X Genomics). Single-cell droplet libraries from ~10K cells from each suspension were generated using the 10X Genomics Chromium controller with the Chromium Single Cell 3’ GEM Library and Gel Bead Kit v.3 and the Chromium Chip B Single Cell kit (1 GEMs per sample, expected recovery ~6k cells per GEM). All samples were barcoded with the Chromium i7 Multiplex Kit. All libraries were pooled and sequenced across two lanes of a HiSeq4000, 150bp paired-end reads with a target coverage of 20k fragments per cell.

treatment_protocol: The iPSC-CM from three patients and one control was prepared for single cell RNAseq.

tag: day after differentation

tag: clinical outcome

value: HLHS-Poor outcome


title: 1053: Healthy scRNA-seq

description: single cell total RNA

value: induced pluripotent stem cell derived cardiomyocytes (iPSC-CM)

value: Healthy


title: 7464: HLHS-Good outcome scRNA-seq

description: single cell total RNA

value: HLHS-Good outcome


title: Unplated quiescent HSC [RSB20]

description:
RSB20
Isolated HSC from uninjured liver.
Bulk RNA-seq
tpm_values_genes_kallisto_RSB19_to_RSB22.txt

value: HSC


title: Mouse treated with melatonin, biological rep2 [M31_Clariom_S_Mouse]

description:
M31_(Clariom_S_Mouse)
Mouse treated with melatonin for 4 weeks

value: liver


title: Unplated quiescent HSC [RSB19]

description:
RSB19
Isolated HSC from uninjured liver.
Bulk RNA-seq
tpm_values_genes_kallisto_RSB19_to_RSB22.txt


title: Mouse treated with melatonin, biological rep1 [M28_Clariom_S_Mouse]

description:
M28_(Clariom_S_Mouse)
Mouse treated with melatonin for 4 weeks