title: lymph node S10000_s1095790 scRNAseq full transcriptome

description:
10X Genomics
GEX

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-3.1.0 as references
BCR comma separated cellranger output files
Assembly: GRCh38-2020-A
Supplementary files format and content: all_contig.fasta (cellranger VDJ analysis fasta output)
Supplementary files format and content: all_contig_annotations.csv (cellranger VDJ analysis annotation output)
Supplementary files format and content: GEX Tab-separated values files and matrix files
Supplementary files format and content: barcodes features matrix (cellranger GEX count table output)
Supplementary files format and content: processed PacBio csv.gz (barcode and gene aligned with read genotype)

extract_protocol:
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).
cellranger-6.0.1


title: KO_HRT_40w_rep1

status: Public on Oct 03 2024

type: SRA

city: Gainesville

first: Karyn

middle: A

last: Esser

state: Florida

address: 1345 Center Drive M5-44

department: Department of Physiology and Aging

country: USA

institute: University of Florida

library_source: transcriptomic

data_processing:
Alignment was performed by using HISAT2 software
Duplicated aligned reads were marked and removed using the Picardtools software
The gene expression count data were extracted using the HTseq software
Assembly: GRCm38 (mm10)
Supplementary files format and content: DESeq2 normalized counts are reported in normalized_counts_data.csv

molecule: total RNA

organism: Mus musculus

source_name: Heart

extract_protocol:
Samples were homogenized in TRIzol reagent and RNA was isolated using Qiagen’s RNeasy mini kit
Poly-A selected RNA-seq libraries were prepared using Illumina mRNA Prep kit following manufacturer's protocols.

tag: tissue

value: Heart

tag: Sex

value: Male

tag: age

value: 40 weeks

tag: genotype

value: KO

tag: site

value: ICBR


title: BPH-1, Mock5

city: Los Angeles

first: Joshua

middle: Andrew

last: Kochanowsky

state: California

address: 619 Charles E Young Dr E

department: Microbiology, Immunology and Molecular Genetics

institute: University of California Los Angeles

data_processing:
fastq files were aligned to version 110 of Homo sapiens reference genome (https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens) available on EnsemblDB using kallisto
Adundance.tsv files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (>1 log2FC and 5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample

organism: Homo sapiens

source_name: prostate

growth_protocol: BPH-1 cells were Human benign prostate hyperplasia 1 (BPH-1) epithelial cells were cultured at 37 degrees Celsius with 5% CO2 in RPMI 1640, L-glutamine, and HEPES media (Gibco) supplemented with 10 U/ml penicillin, 10 μg/ml streptomycin, and 10% fetal bovine serum (FBS; Gibco).

extract_protocol:
Direct-zolTM RNA Miniprep Kit (Zymo Research; Cat. #R2071) according to the manufacturer’s instructions
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: BPH-1 cells were infected with the indicated pathogens at an MOI of 1 or mock infected for 6 hours prior to RNA isolation.

value: prostate

tag: cell line

value: Wild type

tag: infection

value: Mock


title: AAV_HRT_40w_rep1

value: KO+AAV


title: HLHS_iPSC [NCH78_3]

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequences were removed, then processed with miRge3.0
Assembly: human mirna database
Supplementary files format and content: tab-delimited text files include miRNA values for each Sample

extract_protocol:
Cell-free RNA from maternal blood plasma anCell-free RNA from maternal blood plasma and supernatant from proliferating iPSC-CMs were extracted using the miRNeasy Serum/Plasma Kit (Qiagen, cat. No 217184), following the manufacturer’s protocol. The samples were then sequenced using Lexogen's small RNA sequencing service.
Library Construction was prepared by Lexogen from extracted RNA samples

value: iPSC-Derived Cardiomyocytes NCH78

tag: cell type

value: iPSC-Derived Cardiomyocytes

tag: molecule subtype

value: small RNA


title: Aged mouse Striatum, replicate 1

first: Kay

last: Linker

address: 10833 Le Conte Avenue, 53-263 CHS

department: Physiology

institute: UCLA

description: 10x Genomics

data_processing:
cellranger 4.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
scRNA-seq was performed to profile the striatum of C57BL6J mice at 18 months of age. The brain was immediately dissected out and was sectioned into 400 mm slices in ice-cold artificial cerebrospinal fluid (ACSF) oxygenated with 95% O2 and 5% CO2 and immediately transferred to an oxygenated recovery solution. The cortical, hippocampal, or striatal tissue was dissected out in ice-cold ACSF and cut into small pieces. The tissue was digested in ACSF containing 1 mg/ml pronase at 34 °C for 30 min. The digested tissue was dissociated in ice-cold oxygenated ACSF containing 1% fetal bovine serum. The dissociated cells were filtered through a 20 mm filter and washed with ice-cold ACSF. To remove myelin, the cell pellet was resuspended in PBS and processed with debris removal kit (Miltenyi Biotec). Isolated cells were diluted to 1000 cells/ml in 0.04% BSA/PBS and processed with 10X Genomics platform.  The library preparation and sequencing were performed following 10X Genomics Chromium protocols.
Single cell suspension from mouse brain tissues were prepared using 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 and v3 (10X Genomics, Pleasanton, CA) according to manufacture’s protocol. Quantity and quality of cDNA were assessed by Agilent 2100 expert High Sensitivity DNA Assay. cDNA samples were sequenced on NovaSeq 6000 or NextSeq 500 platform at UCLA Technology Center for Genomics and Bioinformatics.

value: Brain

value: 18 months

value: Glia enriched

tag: treatment


title: lymph node S8934_s1336560 scRNAseq BCR enriched_gamma_reseq

city: Leiden

first: Cornelis

last: van Bergen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
BCR comma separated cellranger output files
Supplementary files format and content: all_contig.fasta - cellranger VDJ analysis fasta output
Supplementary files format and content: all_contig_annotations.csv - cellranger VDJ analysis annotation output
GEX Tab-separated values files and matrix files
Supplementary files format and content: barcodes features matrix - cellranger GEX count table output
Assembly: GRCh38-2020-A

molecule: polyA RNA

source_name: lymph node

growth_protocol: Frozen cells were thawed, stained with CD19 and CD10, and purified by FACSariaII device prior to submission for 10X Genomics Chromium processing

extract_protocol:
cellranger-6.0.1
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-3.1.0 as references

treatment_protocol: Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).

value: lymph node

value: tissue

value: B cell

value: fresh


title: AAV_LIV_40w_rep3

source_name: Liver

value: Liver

value: Male

value: 40 weeks


title: HLHS_iPSC [NCH78_2]


title: BPH-1, Mock2

value: prostate


title: lymph node S10000_s1095790 scRNAseq BCR enriched

description:
10X Genomics
BCR

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-3.1.0 as references
BCR comma separated cellranger output files
Assembly: GRCh38-2020-A
Supplementary files format and content: all_contig.fasta (cellranger VDJ analysis fasta output)
Supplementary files format and content: all_contig_annotations.csv (cellranger VDJ analysis annotation output)
Supplementary files format and content: GEX Tab-separated values files and matrix files
Supplementary files format and content: barcodes features matrix (cellranger GEX count table output)
Supplementary files format and content: processed PacBio csv.gz (barcode and gene aligned with read genotype)
Library strategy: scBCR-seq


title: Kidney, treat-MSCs, rep3

city: Kunming

first: Shanshan

last: Wan

address: Dianmian 374 Street

department: Department of Radiology

country: China

institute: The second affiliated hospital of Kunming Medical University

description: Sample 9

data_processing:
Cutadapt was used to filter out unqualified sequences (sequencing adapters, low-quality sequences, etc.) from the raw data
Hisat2 was used for reference genome alignment
StringTie was ued to reconstruct transcripts and calculate the expressions of all genes in each sample
Assembly: Rnor 6.0 (Ensembl release 104): GCA_000001895.4
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
RNA was extracted and purified using TRIzol (Thermo Fisher, 15596018). A concentration>50ng/µL, RIN value>7.0, and total RNA>1µg are sufficient for downstream experiments. Use oligo (dT) magnetic beads (Dynabeads Oligo (dT), cat. 25-61005, Thermo Fisher, USA) to specifically capture mRNA containing PolyA (polyadenylation) through two rounds of purification. The captured mRNA was fragmented using the NEBNextR Magnesium RNA Fragmentation Module (cat. E6150S, USA) under high temperature conditions at 94 ℃ for 5-7 minutes.
cDNA was synthesized using Invitrogen SuperScriptTM II Reverse Transcriptase (cat. 1896649, CA, USA), and E Escherichia coli DNA polymerase I (NEB, cat. m0209, USA) and RNase H (NEB, cat. m0297, USA) were subjected to double stranded synthesis. The double stranded DNA was digested using UDG enzyme (NEB, cat. m0280, MA, US), and a library with fragment size of 300bp ± 50bp was formed by PCR (chain specific library)

value: Kidney

tag: strain

value: SD


title: AAV_LIV_40w_rep2

value: KO+AAV

value: ICBR


title: BPH-1, Mock1

value: Wild type

value: Mock


title: HLHS_iPSC [NCH78_1]

value: iPSC-Derived Cardiomyocytes NCH78

value: iPSC-Derived Cardiomyocytes

value: small RNA


title: Kidney, treat-MSCs, rep2

description: Sample 8


title: AAV_LIV_40w_rep1


title: HLHS_iPSC [NCH31_3]

value: iPSC-Derived Cardiomyocytes NCH31


title: Kidney, treat-MSCs, rep1

description: Sample 7


title: KO_LIV_40w_rep4

value: KO


title: Sample_6, RPE

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: 300BioTr0022-CL1-P39-LotMRPE221012-DS3-Plate22101201-T25-04

data_processing:
Azenta RNA-Seq
Sequences were trimmed for adapter sequences.
Trimmed sequences were alligned to hg38 human genome
Read counts were extracted, DE and PCA analysis was performed.
Assembly: hg38
Supplementary files format and content: Comma-seperated .csv file included raw counts for each sample

source_name: Retinal pigment epithelum

extract_protocol:
RNA was extracted from cell pellets using the TRIzol™ LS reagent (ThermoFisher Scientific). Following the manufacturer’s instructions, the extracted RNA was further purified using the Zymo RNA Clean & Concentrator™-5 kit (Zymo Research, Irvine, California). The RNA concentration was measured with a NanoDrop™ ND-1000 Spectrophotometer (ThermoFisher Scientific). To ensure the removal of any genomic DNA, the RNA samples were treated with RNase-free DNase1 (Millipore Sigma).
Complementary DNA (cDNA) was synthesized from the purified RNA using the SuperScript™ IV VILO™ Master Mix (ThermoFisher Scientific) according to the manufacturer’s protocol. After cDNA synthesis, the samples were treated with RNase at 37°C for 20 minutes to degrade any remaining RNA. The cDNA samples were then stored at -20°C until further use.

value: Retinal pigment epithelum


title: Kidney, model-Chronic kidney disease (CKD), rep3

description: Sample 6


title: HLHS_iPSC [NCH31_2]


title: Sample_5, RPE

description: 300BioTr0022-CL1-P34-LotMRPE230112-DS3-Plate23011101-T25-03


title: Sample_4, RPE

description: 300BioTr0022-CL1-P34-LotMRPE230112-DS3-Plate23011101-T25-01


title: Kidney, model-Chronic kidney disease (CKD), rep2

description: Sample 5


title: KO_LIV_40w_rep3


title: KO_LIV_40w_rep2


title: Sample_3, iPSCs

description: 300BioTr0022-CL1-P38-LotMCB221110-iPSC-Sample3

source_name: iPSC

value: iPSC


title: Control_iPSC [NCH27_3]

value: iPSC-Derived Cardiomyocytes NCH27


title: Kidney, model-Chronic kidney disease (CKD), rep1

description: Sample 4


title: KO_LIV_40w_rep1

value: Liver

value: Male


title: Sample_2, iPSCs

description: 300BioTr0022-CL1-P38-LotMCB221110-iPSC-Sample2


title: Kidney, control, rep3

description: Sample 3


title: AAV_GTN_40w_rep5

source_name: Gastrocnemius

value: Gastrocnemius

value: 40 weeks

value: Novogene


title: Control_iPSC [NCH27_2]


title: Control_iPSC [NCH27_1]


title: Sample_1, iPSCs

description: 300BioTr0022-CL1-P38-LotMCB221110-iPSC-Sample1


title: AAV_GTN_40w_rep4

value: KO+AAV


title: Kidney, control, rep2

description: Sample 2

value: Kidney

value: SD


title: AAV_GTN_40w_rep3


title: EV24

city: Liverpool

first: Richard

last: Barrett-Jolley

address: 6 West Derby Street

country: United Kingdom

institute: University of Liverpool

data_processing:
Sanger / Illumina 1.9 Paired-end sequencing.  sequencing-by-synthesis. Using NovaSeq 6000 Read depth >40 million reads per sample. Nominal read length 150.
HiSAT2
SttringTie
Assembly: GRCh38
Supplementary files format and content: comma-deliminated text file includes TPM values for each biological replicate

source_name: heart

growth_protocol: All EVs were isolated from cultured human cells using sequential centrifugation methods.  Cells were cultured using commercial EV-depleted FBS

extract_protocol:
RNA was extracted from hiPSC-CMs using a kit (Qiagen RNAeasy Micro, 217084)
Agilent SureSelect XT HS2 mRNA Library Prep Kit

treatment_protocol: There are four groups, with three samples per group: H1,H2,H3. Negative control. Healthy, normoxic iPSC-CMs D1,D2,D3. Positive control. iPSCs cultured under hypoxic (0-1% O2) for 48h with 2% v/v PBS as vehicle control EV1,EV2,EV3. Treatment 1. iPSCs cultured under hypoxic (0-1% O2) for 48h, with cardiac stromal cell derived extracellular vesicles, provided at a dose of 67ng/µl (2% v/v) EV21, EV23, EV24. Treatment 2 iPSCs cultured under hypoxic (0-1% O2) for 48h, with bone marrow mesenchymal stromal cell (BM-MSC) derived extracellular vesicles, provided at a dose of 67ng/µl (2% v/v)

value: heart

value: Induced Pluripotent Stem Cell

value: Wild Type

value: bone marrow mesenchymal stromal cell derived extracellular vesicles

tag: oxygen status

value: Hypoxia


title: Kidney, control, rep1

description: Sample 1


title: Control_iPSC [NCH25_2]

value: iPSC-Derived Cardiomyocytes NCH25

value: iPSC-Derived Cardiomyocytes

value: small RNA


title: AAV_GTN_40w_rep2


title: Control_iPSC [NCH25_1]


title: EV23


title: EV21


title: HLHS_iPSC [NCH31_1]

value: iPSC-Derived Cardiomyocytes NCH31


title: AAV_GTN_40w_rep1


title: EV3

value: cardiac stromal cell derived extracellular vesicles


title: KO_GTN_40w_rep5

value: Male

value: KO


title: HLHS_iPSC [NCH23_2]

value: iPSC-Derived Cardiomyocytes NCH23


title: KO_GTN_40w_rep4

value: Gastrocnemius

value: 40 weeks

value: Novogene


title: HLHS_iPSC [NCH23_1]


title: EV1


title: EV2


title: KO_GTN_40w_rep3


title: Control_iPSC [NCH25_3]


title: D3

value: Vehicle


title: PA_IVS_2v_iPSC [NCH013-3]

value: iPSC-Derived Cardiomyocytes NCH13


title: KO_GTN_40w_rep2


title: KO_GTN_40w_rep1


title: D1

value: heart

value: Induced Pluripotent Stem Cell


title: D2

value: Wild Type


title: WT_GTN_40w_rep5

value: WT


title: HLHS_iPSC [NCH23_3]


title: PA_IVS_1_5v_iPSC [NCH012-3]

value: iPSC-Derived Cardiomyocytes NCH12


title: H3

value: Normoxia


title: PA_IVS_1_5v_iPSC [NCH012-2]

value: iPSC-Derived Cardiomyocytes

value: small RNA


title: WT_GTN_40w_rep4


title: H2


title: WT_GTN_40w_rep3


title: H1


title: PA_IVS_1_5v_iPSC [NCH012-1]


title: A673pTERshEWS::FL1_rescue_48h_rep1

type: RNA

city: Bologna

first: Emanuela

last: Palmerini

address: via G.C.Pupilli, 1

country: Italy

institute: IRCCS Istituto Ortopedico Rizzoli

description: Gene expression of A673 transfected with the plasmid pcDNA/6TR  and pTER/shEWS::FLI1 48h after  Doxycycline removal

hyb_protocol: Hybridization was performed at 65 °C for 17 hours in a rotating oven.

scan_protocol: Images at 5 μm resolution were generated by the Agilent scanner, and Feature Extraction 10.5 software  was used to obtain the microarray raw data.

data_processing: The raw expression data from the A673pTERshEWS::FLI1 and A673pTERshCD99 were quantile normalized and log2 transformed using single-channel Agilent microarray pre-processing analysis by limma Bioconductor package

source_name: A673pTERshEWS::FL148h after removing DOX from medium replicate 1

label_protocol: Labeled cRNA was synthesized from 100 ng of total RNA using the Low Input Quick-Amp Labeling Kit, one color  in the presence of cyanine 3-CTP.

extract_protocol: total RNAs were isolated using the Trizol Reagent (Thermo Fisher Scientific) at the different time points and reverse-transcribed into cDNA using a High-Capacity cDNA Reverse Transcription Kit (ThermoFisher Scientific) according to the manufacturer’s protocols

value: A673 Ewings Sarcoma cell line


title: PA_IVS_2v_iPSC [NCH013-2]


title: WT_GTN_40w_rep2

value: Male


title: PA_IVS_1v_iPSC [NCH005-3]

value: iPSC-Derived Cardiomyocytes NCH5


title: PA_IVS_2v_iPSC [NCH013-1]


title: A673pTERshEWS::FL1_DOX+_48h_rep1

description: Gene expression of A673 transfected with the plasmid pcDNA/6TR  and pTER/shEWS::FLI1 treated with Doxycycline for 48h

source_name: A673pTERshEWS::FL1  exposed to doxycycline  for 48h replicate 1


title: PA_IVS_1v_iPSC [NCH005-2]


title: AAV_GTN_10w_rep7

value: 10 weeks

value: KO+AAV


title: PA_IVS_1v_iPSC [NCH005-1]


title: ipsc608

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Raw fastq sequencing files were aligned with human reference genome (hg38) using HISAT2
Raw counts of expressed genes were extracted using featureCounts from the Rsubread package.
Assembly: hg38
Supplementary files format and content: Samples x genes, raw counts

growth_protocol: iPSC are grown in mTeSR medium on Matrigel

extract_protocol:
Total RNA was prepared using Qiagen Rneasy kits, followed by poly(A) selection using oligo-dT magnetic beads.
Illumina TruSeq 3' RNA Library kits were used.

value: iPSC

value: LPRS


title: AAV_GTN_10w_rep6

value: Gastrocnemius

value: Novogene


title: Control_iPSC [NCH003-3]

value: iPSC-Derived Cardiomyocytes NCH3


title: ipsc399


title: ipsc929


title: A673pTERshEWS::FL1_DOX+_48h

source_name: A673pTERshEWS::FL1  exposed to doxycycline  for 48h


title: AAV_GTN_10w_rep5


title: ipsc196


title: WT_GTN_40w_rep1

value: 40 weeks


title: Control_iPSC [NCH003-2]


title: AAV_GTN_10w_rep4

value: ICBR


title: Control_iPSC [NCH003-1]


title: A673pTERshEWS::FL1_rescue_24h_rep1

description: Gene expression of A673 transfected with the plasmid pcDNA/6TR  and pTER/shEWS::FLI1 24h after  Doxycycline removal

source_name: A673pTERshEWS::FL1 24h after removing DOX from medium replicate 1


title: ipsc28


title: A673pTERshEWS::FL1_CTR_48h_rep1

description: Gene expression of A673 transfected with the plasmid pcDNA/6TR  and pTER/shEWS::FLI1

source_name: A673pTERshEWS::FL1CTR replicate 1


title: A673pTERshEWS::FL1_rescue_24h

source_name: A673pTERshEWS::FL1 24h after removing DOX from medium


title: A673pTERshCD99_rescue_48h_rep1

description: Gene expression of A673 transfected with the plasmid pcDNA/6TR  and pTER/shCD99 48h after  Doxycycline removal

source_name: A673pTERshCD99 48h after removing DOX from medium replicate 1


title: A673pTERshEWS::FL1_CTR_48h

source_name: A673pTERshEWS::FL1 CTR


title: A673pTERshCD99_rescue_24h_rep1

description: Gene expression of A673 transfected with the plasmid pcDNA/6TR  and pTER/shCD99 24h after  Doxycycline removal

source_name: A673pTERshCD99 24h after removing DOX from medium replicate 1


title: A673pTERshCD99_DOX+_48h_rep1

description: Gene expression of A673 transfected with the plasmid pcDNA/6TR  and pTER/shCD99 treated with Doxycycline for 48h

source_name: A673pTERshCD99  exposed to doxycycline  for 48h replicate 1


title: ipsc884


title: A673pTERshEWS::FL1_rescue_48h

source_name: A673pTERshEWS::FL1 48hafter removing DOX from medium


title: A673pTERshCD99_CTR_48h_rep1

description: Gene expression of A673 transfected with the plasmid pcDNA/6TR  and pTER/shCD99

source_name: A673pTERshCD99 CTR replicate 1


title: A673pTERshCD99_rescue_48h

source_name: A673pTERshCD99 48h after removing DOX from medium


title: A673pTERshCD99_CTR_48h

source_name: A673pTERshCD99 CTR


title: ipsc618


title: AAV_GTN_10w_rep3


title: Control_iPSC [NCH001-3]

value: iPSC-Derived Cardiomyocytes NCH1


title: evoCDA, plasmid, pooled, gRNA

city: Boston

first: Eric

last: Che

state: MA

address: 531 Newbury St

institute: Harvard Medical School

description: pooled, gRNA

library_source: other

data_processing:
After sequencing, the sequencing core facility performed the primary demultiplexing based on the P7 index. Subsequently, our laboratory conducted a secondary demultiplexing step using the P5 index, which is located internally within the read.
For each demultiplexed FASTQ, “raw” guide mapping was performed using CRISPR-SURF Count in base-editing mode. To identify significant regions based on the mapped guide RNA counts, we ran CRISPR-SURF Deconvolution on both the ABE8e and evoCDA datasets.
The paired-end FASTQs were also quality controlled with FastQC and MultiQC to ensure sufficient sequencing quality of our samples. Next, the paired-end FASTQs were passed into CRISPResso2 for read merging, alignment, and quantification of the edited alleles. The CRISPResso2 allele frequency tables were encoded into a feature indicator matrix containing columns for all possible REF>ALT variants across the amplicon and rows for all unique alleles. The matrices are then modeled by Millipede, a PyTorch-based Bayesian variable selection model, to generate beta coefficients and posterior inclusion probabilities for each feature (per-nucleotide).
The encoding matrix from CRISPR-Millipede, along with a design matrix describing the conditions of each sample (replicate and sorting population), was also passed into into pyDESeq2, a statistical package used to calculate differential expression of alleles between the CD19 positive and CD19 negative populations. The log fold change and adjusted p-value were plotted for the alleles observed across the cellular populations.
Assembly: N/A
Supplementary files format and content: "encoding" tsv file, produced by encoding the CRISPresso2 allele frequency tables into a feature indicator matrix, fed into CRISPR-Millipede
Supplementary files format and content: "hit_table" csv file, table of scores for hits modeled by CRISPR-Millipede

molecule: other

organism: synthetic construct

source_name: synthetic construct

growth_protocol: NALM6 cells (CVCL_0092) were cultured in RPMI 1640 (Thermo Fisher Scientific) with 10% Fetal Bovine Serum, 100U/mL Penicillin-Streptomycin and 2mM L-Glutamine (referred to as RPMI complete) at 37°C, 5% CO2.

extract_protocol:
Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen).
For sgRNA count, the sgRNA cassette was PCR amplified from genomic DNA using primers carrying partial Illumina adaptor. PCR products were then re-amplified using primers carrying sample-specific barcode combinations. The endogenous CD19 enhancer sequence was PCR-amplified and barcoded using a similar strategy.
Distributions of edits within a 346 bp fragment of the CD19 enhancer were obtained by targeted amplicon sequencing using MiSeq at PE250 and PE300 configuration. Guide RNAs were enumerated by NGS as previously reported (Seruggia et al. Mol Cell 2019).

treatment_protocol: ABE8e-SpRY and evoCDA expressing NALM-6 cell lines were produced through lentiviral transduction and and selected with 10 ug/mL Blasticidin for five days. Expression of base editors was confirmed by Western Blot using a Cas9 antibody.

tag: condition

value: plasmid


title: ABE8e, plasmid, pooled, gRNA

description: pooled, gRNA


title: ipsc838


title: BM_Mono_GCSF_2 Bulk RNA-seq

city: Philadelphia

first: Satish

last: Sati

state: Pennsylvania

address: 421 Curie Blvd, BRB 1039

department: Dermatology

institute: University of Pennsylvania

description:
Illumina
BM_Mono_GCSF_2

data_processing:
The scRNA sequencing data was mapped to the mm10 reference genome to generate gene count and cell barcode matrices using the “cellranger count” function from cellranger pipeline (version 5.0.1, 10X Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix filesfor scRNA data set. tab-delimited text files include FPKM values for each Sample for Bulk RNA-seq

source_name: Bone Marrow

extract_protocol:
The skin punch biopsies were minced into < 1 mm3 pieces, using scalpel in a serum free RPMI 1640 media with DNase I (0.2 mg/mL), 20 mM HEPES and 0.25 mg/ml Liberase TL, Roche. The suspension was incubated for 90 minutes at 37 C. The digestion was stopped by adding 100 μl FBS and 3 μl of 0.5 M EDTA and filtered through a 70-mm cell strainer. The cells were pelleted and washed twice with PBS containing 1% BSA. Finally the cells were resuspended in PBS containing 0.04% BSA and an aliquot was taken for counting.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone Marrow

value: Bone Marrow Monocytes

value: WT

value: GCSF


title: Control_iPSC [NCH001-1]

value: iPSC-Derived Cardiomyocytes

value: small RNA


title: A673pTERshCD99_rescue_24h

source_name: A673pTERshCD99 24h after removing DOX from medium

value: A673 Ewings Sarcoma cell line


title: HLHS_Blood [MBS21]

value: Maternal Blood Plasma (MBS21)

value: Maternal Blood Plasma

tag: group

value: HLHS

tag: time point

value: 24 weeks pregnant


title: Control_iPSC [NCH001-2]


title: BM_Mono_GCSF_3 Bulk RNA-seq

description:
Illumina
BM_Mono_GCSF_3


title: ipsc206

value: iPSC

value: LPRS


title: KO_GTN_10w_rep7

source_name: Gastrocnemius

value: Gastrocnemius

value: Male

value: 10 weeks

value: KO

value: Novogene


title: A673pTERshCD99_DOX+_48h

source_name: A673pTERshCD99  exposed to doxycycline  for 48h


title: ipsc92


title: BM_Mono_GCSF_1 Bulk RNA-seq

description:
Illumina
BM_Mono_GCSF_1

value: Bone Marrow

value: Bone Marrow Monocytes


title: BM_Mono_noGCSF_1 Bulk RNA-seq

description:
Illumina
BM_Mono_noGCSF_1

value: WT


title: Control_Blood [MBS18]

value: Maternal Blood Plasma (MBS18)

value: Control

value: 31 weeks pregnant


title: AAV_GTN_10w_rep2

value: KO+AAV

value: ICBR


title: ipsc260

value: HPRS


title: AAV_HRT_40w_rep2

source_name: Heart

value: Heart

value: 40 weeks


title: BM_Mono_noGCSF_2 Bulk RNA-seq

description:
Illumina
BM_Mono_noGCSF_2


title: HLHS_Blood [MBS20]

value: Maternal Blood Plasma (MBS20)

value: Maternal Blood Plasma

value: HLHS

value: 24 weeks pregnant

value: small RNA


title: KO_GTN_10w_rep6

value: Gastrocnemius

value: Male

value: 10 weeks

value: KO

value: Novogene


title: Control_Blood [MBS19]

value: Maternal Blood Plasma (MBS19)

value: Control


title: AAV_GTN_10w_rep1

value: KO+AAV


title: KO_GTN_10w_rep5


title: KO_GTN_10w_rep3

value: ICBR


title: ipsc179

value: iPSC

value: HPRS


title: ipsc864


title: ipsc528


title: KO_GTN_10w_rep2


title: hot3-2 inflorescence, normal condition, rep2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
Reads were trimmed by cutadapt and rRNA, tRNA, snRNA, snoRNA and other repeat sequences were removed. Remaining reads were then mapped to Araport11 by STAR wit parameters “–alignIntronMax 5000 –alignIntronMin 15 –outFilterMismatchNmax 2 –outFilterMultimapNmax 20 –outFilterType BySJout –alignSJoverhangMin 4 –alignSJDBoverhangMin 1 –outSAMmultNmax 1”.
Metaplots for all RPFs from 12 samples around the start and stop codons were created by ‘create_metaplots.bash’, and the P-site offset for RPFs in each length was determined accordingly.
Ribotaper.sh was called to identify TuORFs with options ‘21,22,24,25,26,27,28,29,30,31,32,33 12,13,8,9,10,11,12,13,13,15,16,17’.
Assembly: Araport11
Supplementary files format and content: BedGraph files with raw P site counts as data values.

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: growth room at 22°C under full-spectrum white fluorescent light under long-day (16 h light/8 h dark) conditions.

extract_protocol:
RNA Clean & Concentrator-5 kit (Zymo Research, R1016)
small RNA libraries using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300). The barcoded libraries were pooled for pair-end 150-bp sequencing in Illumina sequencing platform.

value: inflorescence

value: somatic


title: hot3-2 inflorescence, normal condition, rep1


title: hot3-2 inflorescence, normal condition, rep3


title: Control_Blood [MBS16]

value: Maternal Blood Plasma (MBS16)

value: Maternal Blood Plasma


title: ipsc203


title: PAIVS_Blood [MBS17]

value: Maternal Blood Plasma (MBS17)

value: PAIVS

value: 27 weeks pregnant


title: ipsc98


title: KO_GTN_10w_rep1

value: Gastrocnemius

value: Male


title: WT inflorescence, normal condition, rep3


title: WT_GTN_10w_rep6

value: 10 weeks

value: WT


title: WT_GTN_10w_rep7

value: Novogene


title: HLHS_Blood [MBS11]

value: Maternal Blood Plasma (MBS11)

value: HLHS

value: 29 weeks pregnant

value: small RNA


title: Control_Blood [MBS15]

value: Maternal Blood Plasma (MBS15)

value: Control

value: 25 weeks pregnant


title: ipsc59

value: iPSC

value: HPRS


title: WT inflorescence, normal condition, rep2

value: inflorescence

value: somatic


title: WT_GTN_10w_rep5


title: Control_Blood [MBS014]

value: Maternal Blood Plasma (MBS14)

value: Maternal Blood Plasma

value: 36 weeks pregnant


title: WT inflorescence, normal condition, rep1


title: ipsc204


title: WT_GTN_10w_rep4

value: Gastrocnemius

value: Male

value: 10 weeks

value: ICBR


title: HLHS_Blood [MBS012]

value: Maternal Blood Plasma (MBS12)

value: HLHS


title: RKO Mutant peri [RMP3]

city: Houston

first: Abigail

middle: Jones

last: Clevenger

state: Texas

address: 6500 Main Street

department: Biomedical Engineering

institute: Rice University

data_processing:
quality control using FastQC software to trim adapters and low-quality bases
Clean reads were then mapped to the Human genes GRCh38.p13 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Assembly: GRCh38.p13
Supplementary files format and content: comma-separated values file inclused normalized counts for each sample

source_name: RKO

growth_protocol: HCT116 cells were maintained in DMEM, and RKO and RKO mutant cells were maintained in EMEM, all supplemented with 10% fetal bovine serum and 1% anitbiotics-antimycotics in a humidified 5% CO2 37C incubator

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen)
RNA libraries for RNA-Seq were prepared at Azenta Life Sciences

treatment_protocol: Cells exposed to peristalsis bioreactor for 24 hours or maintained as static controls for 24 hours

value: RKO

value: colorectal cancer cells

value: KRAS mutant

value: peristalsis


title: HLHS_Blood [MBS013]

value: Maternal Blood Plasma (MBS13)

value: 24 weeks pregnant

value: small RNA


title: WT_GTN_10w_rep2

value: WT


title: RKO Mutant peri [RMP1]


title: WT_GTN_10w_rep3


title: Control_Blood [MBS009]

value: Maternal Blood Plasma (MBS9)

value: Control

value: 22 weeks pregnant


title: RKO Mutant static [RMS3]

value: static


title: hot3-2 seedling, normal condition, rep1

source_name: seedling

value: seedling

value: somatic


title: HLHS_Blood [MBS010]

value: Maternal Blood Plasma (MBS10)

value: Maternal Blood Plasma


title: RKO Mutant peri [RMP2]


title: PA_IVS_Blood [MBS008]

value: Maternal Blood Plasma (MBS8)

value: PA

value: 28 weeks pregnant


title: hot3-2seedling, normal condition, rep3


title: WT seedling, normal condition, rep3


title: hot3-2 seedling, normal condition, rep2


title: RKO Mutant static [RMS2]

value: RKO

value: colorectal cancer cells

value: KRAS mutant


title: PA_IVS_Blood [MBS007]

value: Maternal Blood Plasma (MBS7)

value: 34 weeks pregnant


title: RKO Mutant static [RMS1]


title: WT seedling, normal condition, rep2


title: WT seedling, normal condition, rep1


title: CRSwNP_NP42

city: Jinan

first: Xinyu

last: Xie

address: Wenhua West Road

institute: Shandong University

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software).
Assembly: hg38
Supplementary files format and content: Tab-separate values files and matrix files

source_name: nasal polyps

extract_protocol:
The nasal biopsies were washed in phosphate-buffered saline and were cut into approximately 0.5-mm3 pieces in RPMI-1640 medium supplemented with 1% penicillin/streptomycin, and then enzymatically digested with the Multi Tissue Dissociation Kit 2 according to the manufacturer’s instructions. The resultant cell suspension was sequentially filtered through cell strainers with pore sizes of 70 μm and 40 µm (BD).The samples were centrifuged at 300g for 10 minutes. Subsequent to the removal of the supernatant, the cells forming the pellet were reconstituted in red blood cell lysis buffer and subjected to a 2-minute incubation on ice to lyse the red blood cells. Following dual washes with PBS, the cellular pellets were re-suspended in PBS supplemented with 0.04% bovine serum albumin.
DNBelab C Series High-throughput Single-cell System (BGI-research) was utilized for scRNA-seq library preparation.

value: nasal polyps

value: chronic rhinosinusitis and nasal polyps


title: HLHS_Blood [MBS006]

value: Maternal Blood Plasma (MBS6)

value: HLHS

value: 26 weeks pregnant

value: small RNA


title: RKO peri [RP3]

value: KRAS WT

value: peristalsis


title: CRSwNP_NP41


title: Control_Blood [MBS005]

value: Maternal Blood Plasma (MBS5)

value: Maternal Blood Plasma

value: Control

value: 23 weeks pregnant


title: RKO peri [RP2]

value: RKO


title: CRSwNP_NP40


title: RNAseq_infl_h32_rep3

description: hot3-2 inflorescence, normal condition, rep2

data_processing:
Paired raw reads were trimmed with cutadapt v4.1, and then mapped to the Arabidopsis genome Araport11 (https://www.arabidopsis.org) by STAR v2.7.9a63 with parameters “–outSAMmultNmax 1 –outFilterMultimapNmax 50 –outFilterMismatchNoverLmax 0.1”.
Properly and uniquely read pairs mapped to coding transcripts were counted by featureCounts v2.0.3 with parameters "-p --countReadPairs -BCO".
Assembly: Araport11
Supplementary files format and content: Tab-delimited txt files containing gene accession, gene length, and raw read counts.

extract_protocol:
Total RNA was extracted directly from the tissue powder using TRI-reagent (MRC, TR118).
Polyadenylated RNAs isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) were subjected for RNA libraries with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420L). The barcoded libraries were pooled for pair-end 150-bp sequencing in Illumina sequencing platform.

value: inflorescence

value: somatic


title: RKO peri [RP1]

value: colorectal cancer cells


title: NCI-H292_mitoxantrone [M3]

city: 合肥

first: Defeng

last: Jiao

address: 黄山路443号

institute: USTC

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data. Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1). Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.Differential expression analysis: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis: GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways. Novel transcripts prediction: After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.  Alternative splicing analysis: Asprofile v1.0 is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. It took a GTF transcript file created by Cufflinks as its input.
Differential exon usage: By differential exon usage (DEU), we mean changes in the relative usage of exons caused by the experimental condition. The relative usage of an exon is defined as number of transcripts from the gene that contain this exonnumber of all transcripts from the gene. The basic concept can be summarized as follows. For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene. We consider the ratio of these two counts, and how it changes across conditions, to infer changes in the relative exon usage. In the case of an inner exon, a change in relative exon usage is typically due to a change in the rate with which this exon is spliced into transcripts (alternative splicing). Note, however, that DEU is a more general concept than alternative splicing, since it also includes changes in the usage of alternative transcript start sites and polyadenylation sites, which can cause differential usage of exons at the 5’ and 3’ boundary of transcripts. To analysis DEU, we used Bioconductor package DEXSeq (V 1.21.1).
Principal component analysis: This is another way to visualize sample-to-sample distances. In this ordination method, the data points (here, the samples) are projected onto the 2D plane such that they spread out in the two directions that explain most of the differences (Figure below). The x-axis is the direction that separates the data points the most. The values of the samples in this direction are written PC1. The y-axis is a direction (it must be orthogonal to the first direction) that separates the data the second most. The values of the samples in this direction are written PC2. The percent of the total variance that is contained in the direction is printed in the axis label. Note that these percentages do not add to 100%, because there are more dimensions that contain the remaining variance (although each of these remaining dimensions will explain less than the two that we see). This analysis has been dealed with R language.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).
Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. The sequences were processed and analyzed by GENEWIZ

treatment_protocol: 1*106 NCI-H292 cells were plated overningt and then treated with 1/1000 DMSO or 50 nM mitoxantrone for 48 hours

value: human lung cancer cell line

value: treated by 50 nM mitoxantrone for 48 hours


title: NCI-H292_mitoxantrone [M1]


title: RNAseq_infl_WT_rep1

description: WT inflorescence, normal condition, rep1


title: RKO static [RS3]

value: static


title: RNAseq_infl_WT_rep2

description: WT inflorescence, normal condition, rep2


title: NCI-H292_mitoxantrone [M2]


title: CRSwNP_NP36

value: nasal polyps

value: chronic rhinosinusitis and nasal polyps


title: RKO static [RS1]


title: RKO static [RS2]


title: RNAseq_infl_h32_rep2

description: hot3-2 inflorescence, normal condition, rep1


title: NCI-H292_DMSO [D3]

value: treated by 1/1000 DMSO for 48 hours


title: HCT peri [HP3]

value: KRAS mutant


title: RNAseq_sdlg_h32_rep4

description: hot3-2seedling, normal condition, rep3

value: seedling


title: RNAseq_infl_h32_rep4

description: hot3-2 inflorescence, normal condition, rep3


title: NCI-H292_DMSO [D1]


title: CRSwNP_NP43


title: CRSwNP_NP34


title: RNAseq_sdlg_h32_rep3

description: hot3-2 seedling, normal condition, rep2


title: RNAseq_sdlg_h32_rep2

description: hot3-2 seedling, normal condition, rep1


title: CRSwNP_NP39


title: A549_mitoxantrone [M2]

data_processing:
The sequences were processed and analyzed by GENEWIZ.
Quality Control:  In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.  Mapping:  Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).  Expression analysis  In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.  Differential expression analysis  Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate  data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis  GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG.  KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.  Novel transcripts prediction  After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.  Alternative splicing analysis  Asprofile v1.0 is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. It took a GTF transcript file created by Cufflinks as its input.  SNV analysis  Samtools v0.1.19 with command mpileup and Bcftools v0.1.19 were used to do SNV calling.
Differential exon usage  By differential exon usage (DEU), we mean changes in the relative usage of exons caused by the experimental condition. The relative usage of an exon is defined as number of transcripts from the gene that contain this exonnumber of all transcripts from the gene  The basic concept can be summarized as follows. For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene. We consider the ratio of these two counts, and how it changes across conditions, to infer changes in  the relative exon usage. In the case of an inner exon, a change in relative exon usage is typically due to a change in the rate with which this exon is spliced into transcripts (alternative splicing). Note, however, that DEU is a more general concept than alternative splicing, since it also includes changes in the usage of alternative transcript start sites and polyadenylation sites, which can cause differential usage of exons at the 5’ and 3’ boundary of transcripts.  To analysis DEU, we used Bioconductor package DEXSeq (V 1.21.1).
Principal component analysis  This is another way to visualize sample-to-sample distances. In this ordination method, the data points (here, the samples) are projected onto the 2D plane such that they spread out in the two directions that explain most of the differences (Figure below). The x-axis is the direction that separates the data points the most. The values of the samples in this direction are written PC1. The y-axis is a direction (it must be orthogonal to the first direction) that separates the data the second most. The values of the samples in this direction are written PC2. The percent of the total variance that is contained in the direction is printed in the axis label. Note that these percentages do not add to 100%, because there are more dimensions that contain the remaining variance (although each of these remaining dimensions will explain less than the two that we see). This analysis has been dealed with R language.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).
Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.

treatment_protocol: 1*106 A549 cells were plated overningt and then treated with 1/1000 DMSO or 50 nM mitoxantrone for 48 hours


title: RNAseq_sdlg_WT_rep3

description: WT seedling, normal condition, rep3


title: HCT static [HS3]


title: HCT peri [HP1]

value: peristalsis


title: CRSwNP_NP32


title: HCT static [HS2]


title: RNAseq_infl_WT_rep3

description: WT inflorescence, normal condition, rep3


title: A549_mitoxantrone [M1]


title: CRSwNP_NP31


title: HCT peri [HP2]


title: NCI-H292_DMSO [D2]


title: A549_DMSO [D2]


title: CRSwNP_MT27

source_name: middle turbinate

value: middle turbinate


title: HCT static [HS1]


title: RNAseq_sdlg_WT_rep2

description: WT seedling, normal condition, rep2


title: A549_DMSO [D3]


title: eCLIP_METTL3_KD1_2

city: Singapore

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

country: Singapore

institute: nuh

data_processing:
*library strategy: eCLIP-seq
eCLIP pipeline developed by Gene Yeo's lab was used to identify the peaks. The full protocol is available here: https://github.com/YeoLab/eclip
Assembly: hg19
Supplementary files format and content: The processed data file contains the peaks identified by eCLIP-Seq pipeline and the gene annotations

growth_protocol: RPMI medium 10% FBS

extract_protocol:
Cell lysate was harvested according to eCLIP protocol
Library was prepared according to pair-end eCLIP protocol

treatment_protocol: shScr control or two shDAP3 knockdown

value: human esophageal squamous carcinoma cells

value: UV crosslinking


title: A549_DMSO [D1]


title: A549_mitoxantrone [M3]


title: eCLIP_METTL3_KD2_1


title: Raw 264.7 cells, siTET3_3

city: New Haven

first: Haining

last: Lyu

state: Connecticut

address: 1145 chapel street, 401

institute: Yale

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: RAW 264.7 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using PureLink RNA Mini Kit (Ambion, 12183018A). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: For siRNA transfection in a 24-well plate scale of Raw 264.7 cells, 10 pmol of NT siRNA (AM4636, Ambion) or Tet3 siRNA (4390815/s101483, Ambion) was mixed with 100 μL of OPTI-MEM (Gibco, 31985-070) by gentle pipetting. In parallel, 3 μL of Lipofectamine RNAiMAX (Invitrogen, 13778-150) was mixed with 100 μL of OPTI-MEM by gentle pipetting. Following 5 min of incubation at RT, the two were combined and the resulting 200 μL of transfection solution was added to each well of cells. After 24 h of incubation at 370C in a 5% humidified CO2 tissue culture incubator, 300 μL of growth media was added and incubation was continued until cell harvesting. Cells were harvested 48h after transfection

value: macrophage

value: WT

value: siTET3 transfection

tag: time


title: Control Mem, biol rep 3

city: San Francisco

first: Hanson

last: Tam

state: CA

address: 513 Parnassus Ave

institute: UCSF

data_processing:
FastQC (v0.12.1) was used to examine the quality of raw sequencing reads, and cutadapt (v4.5) was used to trim adaptors and clean reads. Sequences were aligned to the mm39 genome with STAR (v2.7.11a), followed by quantification with RSEM (v1.3.3).
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: peritoneal cavity

extract_protocol:
RNA was harvested using RNeasy Micro kit (Qiagen).
The sequencing library was prepared using Ovation RNA-seq System V2 from Nugen, the KAPA Hyper prep labeling kit, and the NEXTflex DNA barcodes Adapter kit from Bioo Scientific, following manufacturers' protocols.

value: peritoneal cavity

value: MemB (IgD-IgM-)

value: Control


title: eCLIP_METTL3_KD2_2


title: Raw 264.7 cells, siTET3_2


title: KI Mem, biol rep 2

value: KI


title: eCLIP_METTL3_KD1_1


title: Control Mem, biol rep 2


title: CRSwNP_MT23


title: Raw 264.7 cells, siTET3_1


title: eCLIP_METTL3_Scr_2

value: shScr


title: Raw 264.7 cells, siCTL3


title: CRSwNP_MT22


title: Control Mem, biol rep 1


title: CRSwNP_NP44

value: nasal polyps


title: Raw 264.7 cells, siCTL2


title: eCLIP_IgG


title: Control B2, biol rep 3

value: sorted B2 (IgD+IgM+)


title: Raw 264.7 cells, siCTL1


title: CRSwNP_MT24

value: chronic rhinosinusitis and nasal polyps


title: Input_METTL3_KD2_2


title: KI Mem, biol rep 3


title: CRSwNP_IT18

source_name: inferior turbinate

value: inferior turbinate


title: FOLE_R2

city: Trondheim

first: Kristine

last: Misund

address: Prinsesse Kristinas gt 1

department: Department of Clincal and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
20 samples were sequenced on a NextSeq HO flowcell with 2 x 75 bp PE reads, giving an average output of ~28.3 M reads/sample (range 19.7 – 42.3).
Paired end FASTQ files were aligned using hisat2 v2.1.0 using pre-indexed hg37_tran (hg19) genome/transcriptome. Table with raw gene counts were generated using featureCounts v1.6.2 with Homo_sapiens.GRCh37.75.gtf (hg19) reference transcriptome, with options “’-t exon”, “-g gene_id”, “-O” (all overlapping features) and “-M --fraction” (assign multi-mapping reads using fractions).
Assembly: Hg19
Supplementary files format and content: text file includes raw gene counts for each sample

source_name: FOLE

growth_protocol: MM cell lines were maintained in their original growth medium. The cell lines were cultured in human serum (HS) or fetal calf serum (FCS) in RPMI medium with 2nmol/l L-Glutamin. Specifically, URVIN was cultivated in 10% FCS in RPMI+IL-6 sup., FOLE in 10% HS in RPMI, IH-1, OH-2 and KJON in 10% HS in RPMI+IL-6 sup., VOLIN and JJN-3 in 10% FCS in RPMI, INA-6 and ANBL-6 in 10% FCS in RPMI+IL-6 (1ng/ml). IL-6 sup: IL-6 supernatant; isolated from peripheral blood leukocytes, an activity comparable to 2ng/ml used. . Low passages of the cell lines were used in the experiments.

extract_protocol:
Total RNA were extracted using AllPrep DNA/RNA Mini prep (Qiagen).
RNA sequencing libraries were generated using 500 ng input RNA, using Lexogen SENSE mRNA-Seq library prep kit V2, according to manufacturer’s instructions (Lexogen GmbH, Vienna, Austria).

value: FOLE

value: Multiple Myeloma

tag: replicate

value: biological replicate 2


title: KI B2, biol rep 3

tag: tissue


title: Input_METTL3_KD2_1

value: human esophageal squamous carcinoma cells


title: FOLE_R1

value: biological replicate 1


title: CRSwNP_IT17


title: Control B2, biol rep 2


title: KI B2, biol rep 2


title: Input_METTL3_KD1_2

value: UV crosslinking


title: CRSwNP_IT16


title: KI Mem, biol rep 1


title: VOLIN_R1

source_name: VOLIN

value: VOLIN

value: WT


title: eCLIP_METTL3_Scr_1


title: CRSwNP_IT15


title: KI B2, biol rep 1

value: peritoneal cavity


title: Input_METTL3_Scr_2


title: CRSwNP_IT14


title: URVIN_R2

source_name: URVIN

value: URVIN


title: Input_METTL3_Scr_1


title: Control B2, biol rep 1

value: Control


title: URVIN_R1


title: CRSwNP_IT12


title: OH2_R2


title: KO_D7_1 Mice skin scRNA-seq

description: 10x Genomics

source_name: Skin

value: Skin

value: tissue

value: Cxcr2 KO


title: KO_D7_2 Mice skin scRNA-seq

description: 10x Genomics


title: RNAseq-E14-16h-rnh1OE, Spt6KD-rep3

city: Wuhan

first: Shaobo

last: Liang

state: Hubei Sheng

address: BaYi Road, LUOJIA HILL

institute: Wuhan University

description: RNAseq

data_processing:
Reads trimmed by trim_galore were mapped to genome using bowtie2 (Cut&Tag and ChIP) or STAR (RNA-seq)
Redundant reads were deduplicated by picard
Peaks determintion was performed through Macs2 callpeak command. Deeptools bamCoverage converted BAM files into bigwig files
IDR was used to combine peaks of different replicates
FeatureCounts counted the read number on  gene level for each sample
Assembly: dm6, Ecoli
Supplementary files format and content: Cut&Tag and ChIP-seq bigwig file and narrowPeak file
Supplementary files format and content: gene read count for RNA-seq

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
cut&tag：Cells were immobilized on coA beads, antibodies were bound in antibody buffer  (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.05% digitonin, 0.01% NP-40, 2 mM EDTA),  and activate Tn5-PA transposase activity in tagmentation buffer  (10 mM MgCl2, 20 mM HEPES at pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.05% digitonin) , and cells were lysed to extract library fragments by add  1.5 μl 0.5 M EDTA, 0.5 μl 10% SDS and 1 μl 20 mg/mL proteinase K (sigma).                                                                            pol2 chip-seq：Cells were fixed with 1% paraformaldehyde for 10 min, and the chromosomes were fragmented using an ultrasonic crusher after lysis of the cells.                                                                                RNA-seq: RNA was extracted using trizol. 200 ng of total RNA was used to construct sequencing libraries.
cut&tag: 1×Agencourt AMPure XP beads (Beckman Coulter, A63881) were used to purify the tagementated DNA and eluted in 10 μl 0.1% Tween-20. The eluent was mixed with 10 U Bst 2.0 WarmStart DNA polymerase (NEB, M0538) in 1× Q5 polymerase reaction buffer, incubated at 65 °C for 30 minutes and stopped by incubation at 80 °C for 20 minutes. The universal i5 primer, barcoded i7 primer and Phanta EVO Super-Fidelity DNA Polymerase (Vazyme, P503) were added to amplify the R-loop CUT&Tag library. The libraries were size-selected with 0.56-0.85* Sera-Mag carboxylate-modified magnetic beads and eluted in 20 ul RNase-free water.                                                              pol2 chip-seq:  5ng DNA was used for dsDNA library construction according to manufacturer’s instructions (Rapid Plus DNA Lib Prep Kit for Illumina V2, ABclonal, RK20255).   The library was amplified for 13 cycles on the thermocycler.                                      RNA-seq:RNA libraries for Rna-Seq was prepared using MGIEasy RNA library Prep kit following manufacturer‘s protocols.
cut&tag
pol2 chip-seq
RNA-seq

value: embryo

tag: chip antiobdy

value: rnh1-OE, Spt6-RNAi


title: KO_D3_3 Mice skin scRNA-seq

description: 10x Genomics


title: KJON_R1

source_name: KJON

value: KJON


title: KO_D3_2 Mice skin scRNA-seq

description: 10x Genomics


title: KJON_R2


title: VOLIN_R2


title: KO_D3_1 Mice skin scRNA-seq

description: 10x Genomics


title: OH2_R1


title: CRSwNP_IT11

value: inferior turbinate

value: chronic rhinosinusitis and nasal polyps


title: RNAseq-E14-16h-rnh1OE-rep3

description: RNAseq


title: Input_METTL3_KD1_1


title: JJN3_R2

value: Multiple Myeloma

value: biological replicate 2


title: RNAseq-E14-16h-rnh1OE, Spt6KD-rep2

description: RNAseq


title: RNAseq-E14-16h-rnh1OE, Spt6KD-rep1

description: RNAseq


title: JJN3_R1

value: biological replicate 1


title: Input_IgG

value: human esophageal squamous carcinoma cells

value: shScr

value: UV crosslinking


title: Structure-seq, C2C12, Dhx36-KO, NAI, Rep2

city: Hong Kong

first: Yuwei

last: ZHANG

state: Hong Kong

address: Rm503, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital, Shatin, NT, HK

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
The adapters were first removed using Cutadapt v1.15 and the reads shorter than 20nt or with quality score lower than 30 were filtered out.
The remaining reads were mapped to human or mouse transcriptome reference using Bowtie2 v2.3.3.1.
Next, the mapped reads with more than 3 mismatches or mismatch at the first base were removed, RT stops were counted and reactivity scores were calculated using StructureFold2 package.
Assembly: hg38/mm10
Supplementary files format and content: comma-delimited text file includes SHAPE/DMS reactivity score of each transcript

extract_protocol:
poly(A)-selected RNAs
Each library was prepared with 500 ng poly(A)-selected RNAs after 2 rounds of selection (Thermo Fisher Scientific, AM1922). The poly(A) RNAs were fragmented to around 300 nt length at 95°C for 1 min and purified using RNA clean and concentrator (Zymo research, R1016). The fragmented RNA was then subjected to a 5' dephosphorylation reaction at 37°C for 30 min by adding rSAP (NEB, M0371L) and PNK enzyme (NEB, M0201S) in 1× T4 PNK buffer (NEB, B0201S). Next, the 3’adapter was ligated to the dephosphorylated RNA using T4 RNA ligase 2 KQ (NEB, M0373L) at 25°C for 1 h. Excess adapters were digested and removed by adding RecJf (NEB, M0331) and 5’ deadenylase (NEB, M0331) for 30 min at 30°C followed by column purification (Zymo research, R1016). The following reverse transcription (RT) was performed in 1 X RT buffer (20 mM Tris, pH 7.5, 4 mM MgCl2, 1 mM DTT, 0.5 mM dNTPs, 150 mM LiCl) with SuperScript III enzyme (Thermo Scientific, 18080093) at 42°C for 40 min. RNA was digested by 2M NaOH and the reaction was neutralized with 1M Tris-HCl (pH 7.5) followed by column purification (Zymo research, R1016). The 5’adapter (for C2C12 libraries) or dU adapter (for HEK293T libraries) was ligated to the cDNA with Quick T4 DNA ligase (NEB, M2200L) and incubated in 37°C overnight. For the C2C12 library, the ligated product was run on the 10% denaturing urea-TBE acrylamide gel (Thermo Scientific, EC68752BOX), and the 100–400 nt region was cut and dissolved in 1X TEN250 buffer (1X TE 7.4, 0.25 M NaCl) at 80°C for 30 min followed by column purification (Zymo research, R1016). For the HEK293T libraries, the ligated product was first purified by column (Zymo research, R1016), then USER II enzyme (NEB, M5509) was added to cleave the product followed by a second column purification (Zymo research, R1016). The purified product was used for PCR cycle test and amplification with different barcoded reverse primer. PCR products with 150–400 bp were then cut and purified with 2% agarose gel and column (Zymo research, D4008).

treatment_protocol: For HEK293T cells, the WT and DHX36-KO cells were harvested in 1X PBS buffer (Thermo Fisher Scientific, 10010049) and probed with NAI (50 mM in final) or 5% DMSO as negative control for 15 min at 37°C, 500 rpm. Then DTT (200mM in final) was added immediately to quench each probing reaction. After spinning down the cells (~ 500 g) for 3 min at room temperature, total RNAs were extracted and quantified using RNeasy Plus Mini Kit (Qiagen, 74136) and Nanodrop ND-1000 Spectrophotometer. For C2C12 cells, the proliferating WT or Dhx36-KO myoblasts were harvested in 1X PBS buffer and probed with DMS (20 mM in final) or 5% DMSO as negative control for 15 min at 37°C. Then DTT (200mM in final) was added immediately to quench each probing reaction. After spinning down the cells (~ 500 g) for 3 min at room temperature, total RNAs were extracted using RNeasy Plus Mini Kit (Qiagen, 74136).

value: Dhx36 knockout

value: DMS


title: KO_D0_2 Mice skin scRNA-seq

description: 10x Genomics


title: KO_D0_3 Mice skin scRNA-seq

description: 10x Genomics


title: KO_D0_1 Mice skin scRNA-seq

description: 10x Genomics


title: Structure-seq, C2C12, Dhx36-KO, DMSO, Rep2

value: DMSO


title: RNAseq-E14-16h-rnh1OE-rep1

description: RNAseq


title: RNAseq-E14-16h-rnh1OE-rep2

description: RNAseq


title: INA6_R1

value: WT


title: RNAseq-E14-16h-Spt6KD-rep3

description: RNAseq


title: INA6_R2


title: Structure-seq, C2C12, Dhx36-KO, DMSO, Rep1


title: Structure-seq, C2C12, Dhx36-KO, NAI, Rep1


title: WT_D7_1 Mice skin scRNA-seq

description: 10x Genomics

value: Skin

value: tissue


title: RNAseq-E14-16h-Spt6KD-rep1

description: RNAseq

value: embryo


title: WT_D7_2 Mice skin scRNA-seq

description: 10x Genomics


title: IH1_R2


title: Structure-seq, C2C12, WT, DMSO, Rep1


title: RNAseq-E14-16h-Spt6KD-rep2

description: RNAseq


title: RNAseq-E14-16h-Ctrl-rep3

description: RNAseq

value: Ctrl


title: WT_D3_2 Mice skin scRNA-seq

description: 10x Genomics


title: IH1_R1


title: Structure-seq, C2C12, WT, NAI, Rep2


title: Structure-seq, C2C12, WT, DMSO, Rep2


title: ANBL6_R2


title: RNAseq-E14-16h-Ctrl-rep2

description: RNAseq


title: WT_D0_2 Mice skin scRNA-seq

description: 10x Genomics


title: Structure-seq, C2C12, WT, NAI, Rep1


title: ANBL6_R1


title: RNAseq-E14-16h-Ctrl-rep1

description: RNAseq


title: WT_D0_1 Mice skin scRNA-seq

description: 10x Genomics


title: Cattle Y-chromosome methylation profile from ONT data

status: Public on Oct 02 2024

city: Moscow

first: Brenda

last: Murdoch

state: Idaho

address: 875 Perimeter Dr.

department: Department of Animal, Veterinary & Food Sciences

institute: University of Idaho

library_source: genomic

data_processing:
Basecalling was done for the respective sequencing platform according to the manufacturer prescribed procedure using their proprietary basecallers - Dorado for ONT and Primrose for PacBio.
Assembly: GCF_002263795.3
Supplementary files format and content: methylation call in bed format
Library strategy: WGS

molecule: genomic DNA

organism: Bos taurus

source_name: Lung

extract_protocol:
DNA extraction was done on standard manufacturer suggested protocol.
The respective libraries used on the sequencing platforms were made according to the specifications of the manufacturers.

value: Lung


title: BmGATA_V

city: Hangzhou

first: Shudi

last: Zhao

address: Yuhangtang Road No.866

institute: Zhejiang University

data_processing:
Raw data was cleaned by Trim Galore (Version 0.6.6) with the parameters "-q 25 --phred33 --length 36 -e 0.1 --stringency 5" and maped to silkworm genome using Bowtie 2 (Version 2.4.4). Afterwards, the resulted SAM files were converted into BAM format using SAMtools (Version 1.12), and MACS2 (Version 2.2.7.1) was adopted for peaks calling with the parameters "-p 0.1 -f BAMPE -g 4.6e8".
Assembly: SilkBase November 2016
Supplementary files format and content: bigWig files indicating binding density for each ChIP-seq sample

organism: Bombyx mori

source_name: BmN cells

extract_protocol:
Cells were collected and cross-linked with 1% formaldehyde for 10 min at 25˚C. The reaction was then quenched by addition of glycine to a final concentration of 125 mM. Afterwards, cells were lysed and chromatin was obtained on ice. Chromatin was sheared to a mean fragment size of 200-500 base pairs. The samples were immunoprecipitated by anti-HA antibody (Abcam, 9110).
Sequencing libraries were generated using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) following the instructions.

value: BmN cells


title: BmGATA_Mock


title: Catlle CENP-A CUT&RUN to define Y-chromosome centromere locus

data_processing:
FastQC and Cutadapt for quality control
Bowtie2 for reads alignment to the reference genome
Picard tools to remove duplicates
Samtools for sorting and indexing alignment files
SEACR for peaks calling.
Assembly: Cattle reference genome ARS-UCD2.0
Supplementary files format and content: Tab-delimited file of the called peaks.
Library strategy: CUT&RUN

source_name: Cattle

extract_protocol:
The extraction was performed based on the standard antibody manufacturer recommended protocol.
The library was constructed using the GeneTex CENP-A antibody with catalog number GTX13939.

value: muscle

value: bovine satellite cells

value: CENP-A antibody


title: Negative CTL, replicate 4, snRNA-seq

city: Seoul

first: Jeongjun

last: Chae

address: Irwon-ro 115

department: SAIHST

country: South Korea

institute: Sungkyunkwan University

description: 10X Genomics

data_processing:
CellRanger mkfastq
CellRanger count
Assembly: mm10
Supplementary files format and content: CellRanger features
Supplementary files format and content: CellRanger barcodes
Supplementary files format and content: CellRanger matrix

molecule: nuclear RNA

extract_protocol:
Briefly, samples were cut into approximately 7-mm pieces, injected with 1 ml of ice-cold Nuclei EZ Lysis buffer (NUC101; MilliporeSigma) supplemented with a protease (589279100; Hoffmann-La Roche Ltd, Basel, Switzerland) and ribonuclease (RNAse, N2615; Promega Corp., Madison, WI, USA) inhibitor (250 units/ml RNasin® Plus N2615; Promega Corp., Madison, WI, USA) using a 26-gauge needle, minced into 1 to 2-mm pieces with scissors in a weigh boat with 1 ml additional supplemented lysis buffer, and then transferred to a gentleMACSTM C tube (Miltenyi Biotec, Bergisch Gladbach, Germany). The gentleMACS lung1 and lung 2 programs were run in sequence, with the latter stopped after 20 seconds. The foam was spun down for 10 seconds using a short spin. The suspension was passed through a 40-µm cell strainer and washed with 4℃ cold PBS containing 1% bovine serum albumin (BSA). Nuclei were pelleted at 500×g and resuspended in 1X PBS containing 1% BSA and 0.5 units/µl RNasin Plus before counting them by hemocytometer and diluting to 1,000 nuclei/µl.
10x Chromium libraries were prepared according to the manufacturer’s protocol
snRNA-seq

value: PBS


title: WT_D3_1 Mice skin scRNA-seq

description: 10x Genomics

data_processing:
The scRNA sequencing data was mapped to the mm10 reference genome to generate gene count and cell barcode matrices using the “cellranger count” function from cellranger pipeline (version 5.0.1, 10X Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix filesfor scRNA data set. tab-delimited text files include FPKM values for each Sample for Bulk RNA-seq

extract_protocol:
The skin punch biopsies were minced into < 1 mm3 pieces, using scalpel in a serum free RPMI 1640 media with DNase I (0.2 mg/mL), 20 mM HEPES and 0.25 mg/ml Liberase TL, Roche. The suspension was incubated for 90 minutes at 37 C. The digestion was stopped by adding 100 μl FBS and 3 μl of 0.5 M EDTA and filtered through a 70-mm cell strainer. The cells were pelleted and washed twice with PBS containing 1% BSA. Finally the cells were resuspended in PBS containing 0.04% BSA and an aliquot was taken for counting.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: Negative CTL, replicate 2, snRNA-seq

description: 10X Genomics


title: TNFi-treated, replicate 2, snRNA-seq

description: 10X Genomics

value: ZyA + anti-TNFa


title: Negative CTL, replicate 1, snRNA-seq

description: 10X Genomics


title: Negative CTL, replicate 3, snRNA-seq

description: 10X Genomics


title: TNFi-treated, replicate 4, snRNA-seq

description: 10X Genomics


title: TNFi-treated, replicate 3, snRNA-seq

description: 10X Genomics


title: TNFi-treated, replicate 1, snRNA-seq

description: 10X Genomics


title: MTX-treated, replicate 3, snRNA-seq

description: 10X Genomics

value: ZyA + MTX


title: MTX-treated, replicate 2, snRNA-seq

description: 10X Genomics


title: millet_US

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

description: small RNA

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC program, embedded in CLC
Trimming of raw reads was performed using the CLC
Removing redundant reads using CLC
Supplementary files format and content: tab-delimited counts of all unique read with its number of repeats
Assembly: as small RNAs were sequences as one read no assembly was needed

organism: Panicum miliaceum

source_name: plant leaf

extract_protocol:
Phenol-Kloroform extraction White and Karper (White, J.L.; Kaper, J.M. A simple method for detection of viral satellite rnas in small plant tissue samples. J. Virol. Methods 1989, 23, 83–93.)
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

value: plant leaf

tag: species

value: pool of 11 individual plants

value: July 2021


title: MTX-treated, replicate 1, snRNA-seq

description: 10X Genomics


title: MTX-treated, replicate 4, snRNA-seq

description: 10X Genomics


title: Positive CTL, replicate 3, snRNA-seq

description: 10X Genomics

value: ZyA + PBS


title: CGSMG1

city: Pasadena

first: Tongtong

last: Wang

address: 1200 E California Blvd

institute: California Institute of Technology

description: 10x Genomics

data_processing:
Gene-cell matrices were generated by mapping sequencing reads to mm10 based mouse pre-mRNA reference transcriptome with Cell Ranger 6.1.2
Assembly: mm10
Supplementary files format and content: Processed data files are simple gene-cell matrices (genes as rows, cell indexes as columns).

source_name: Celiac and superior mesenteric ganglia

extract_protocol:
Animals were anaesthetized with isoflurane. The celiac and superior mesenteric ganglia were dissected in ice-cold ACSF. Tissue was digested and triturated to generate single cell suspensions.
Sequencing libraries were constructed following 10x Genomics 3' v3.1 standard protocols.
3' Single-cell RNA-Seq

value: Celiac and superior mesenteric ganglia


title: CGSMG2

description: 10x Genomics


title: Positive CTL, replicate 1, snRNA-seq

description: 10X Genomics


title: T cells, TCox10-/-/Aox, IL15, rep3

city: Bethesda

first: Peter

middle: J

last: McGuire

state: MD

address: 10 Center Dr, Building 10, Room 7N260A

department: NHGRI

institute: NIH

description:
TIL15_7
gene_count_il15.txt

data_processing:
Raw read fastq files were processed by removing adapters, poly-N and low quality reads.
Paired-end reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to generate read counts mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts (from FeatureCounts) for each sample

source_name: T cells

extract_protocol:
T cells were lysed in TRIzol (Thermo Fisher). Total RNA was isolated and purified with RNeasy kit (Qiagen). Messenger RNA was purified using poly-T oligo-attached magnetitc beads.
First strand cDNA was synthesized with random hexamer primers, followed by second strand cDNA synthesis using dTTP. Libraries then underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: For bulk T cells, T cells were isolated from spleen and stimulated ex vivo for 24 hours with anti-Cd3/Cd28 before collection. For memory T cells, splenocytes were treated ex vivo for three days with OVA peptide, followed by treatment for three days with IL-15 before collection.

tag: genotype

value: T cells

value: C57Bl/6J - OT1

tag: Sex

value: male

tag: age

value: 8-12 weeks


title: Positive CTL, replicate 2, snRNA-seq

description: 10X Genomics

value: Lung


title: T cells, TCox10-/-/Aox, IL15, rep2

description:
TIL15_6
gene_count_il15.txt


title: T cells, WT, IL15, rep3

description:
TIL15_3
gene_count_il15.txt

value: WT


title: T cells, TCox10-/-/Aox, IL15, rep1

description:
TIL15_5
gene_count_il15.txt


title: millet_BA

description: small RNA

value: pool of 10 individual plants


title: T cells, WT, IL15, rep2

description:
TIL15_2
gene_count_il15.txt


title: T cells, WT, IL15, rep4

description:
TIL15_4
gene_count_il15.txt


title: T cells, WT, IL15, rep1

description:
TIL15_1
gene_count_il15.txt


title: T cells, TCox10-/-/Aox, rep6

description:
DKO6
gene_count.txt


title: T cells, TCox10-/-/Aox, rep5

description:
DKO5
gene_count.txt


title: Positive CTL, replicate 4, snRNA-seq

description: 10X Genomics


title: T cells, Aox, rep1

description:
AOX1
gene_count.txt

value: Aox


title: T cells, TCox10-/-/Aox, rep3

description:
DKO3
gene_count.txt


title: T cells, TCox10-/-/Aox, rep1

description:
DKO1
gene_count.txt


title: T cells, Aox, rep3

description:
AOX3
gene_count.txt


title: T cells, TCox10-/-/Aox, rep4

description:
DKO4
gene_count.txt


title: T cells, TCox10-/-/Aox, rep2

description:
DKO2
gene_count.txt


title: T cells, TCox10-/-, rep1

description:
COX1
gene_count.txt


title: T cells, TCox10-/-, rep3

description:
COX3
gene_count.txt


title: T cells, WT, rep2

description:
WT2
gene_count.txt


title: T cells, TCox10-/-/Aox, IL15, rep4

description:
TIL15_8
gene_count_il15.txt


title: T cells, WT, rep3

description:
WT3
gene_count.txt


title: T cells, TCox10-/-, rep2

description:
COX2
gene_count.txt


title: P130_cont2_atac

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

description:
P130_control
060222-700_K_atac

library_source: genomic single cell

data_processing:
library strategy: snATAC-seq
CellRanger ARC v2.0.2 (10X Genomics) using refdata-cellranger-arc-mm10-2020-A-2.0.0, which is mm10 reference genome 10X Genomics provided.
The CellRanger output were then processed and analyzed with Seurat (v4).
Assembly: mm10
Supplementary files format and content: a filtered / raw barcode-peak matrix (snRNA-seq)
Supplementary files format and content: a fragment file and an index file of a fragment file (snATAC-seq)

source_name: Kidney

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitor (Protector RNase Inhibitor). Samples were cut into < 1 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold lysis buffer, and incubated on ice for 5 min with an additional 1 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer and centrifuged at 500 g for 5 min at 4°C. The pellet was resuspended, washed with 3 ml of buffer, and incubated on ice for 5 min. Following centrifugation, the pellet was resuspended in Nuclei Buffer (10× Genomics, PN-2000153), filtered through a 5-μm cell strainer, and counted. All these processes were performed in a cold room at 4°C. Subsequently, nuclei suspension was diluted to target 10,000 nuclei per lane and loaded into a thermal cycler to allow transposition reaction.
Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression Reagent Kit (10X Genomics)
Single nucleus multiomics with simultaneous snRNA-seq + snATAC-seq with multiome kit [10XGenomics]

value: Kidney


title: P130_cont3_atac

description:
P130_control
071422-100_L_atac


title: P130_pkd3_atac

description:
P130_PKD
060222-200_N_atac


title: T cells, WT, rep1

description:
WT1
gene_count.txt


title: T cells, WT, rep4

description:
WT4
gene_count.txt


title: P130_pkd1_atac

description:
P130_PKD
060222-70_I_atac


title: P130_pkd2_atac

description:
P130_PKD
060222-100_M_atac


title: P130_cont1_atac

description:
P130_control
060222-400_J_atac


title: P100_cont3_atac

description:
P100_control
060122-20_O_atac


title: P100_cont2_atac

description:
P100_control
060122-7_G_atac


title: P100_cont1_atac

description:
P100_control
060122-2_E_atac


title: T cells, Aox, rep2

description:
AOX2
gene_count.txt


title: RNAseq_sdlg_WT_rep1

city: Shanghai

first: Chenjiang

last: You

address: 2005 Songhu Rd

institute: Fudan University

description: WT seedling, normal condition, rep1

data_processing:
Paired raw reads were trimmed with cutadapt v4.1, and then mapped to the Arabidopsis genome Araport11 (https://www.arabidopsis.org) by STAR v2.7.9a63 with parameters “–outSAMmultNmax 1 –outFilterMultimapNmax 50 –outFilterMismatchNoverLmax 0.1”.
Properly and uniquely read pairs mapped to coding transcripts were counted by featureCounts v2.0.3 with parameters "-p --countReadPairs -BCO".
Assembly: Araport11
Supplementary files format and content: Tab-delimited txt files containing gene accession, gene length, and raw read counts.

source_name: seedling

extract_protocol:
Total RNA was extracted directly from the tissue powder using TRI-reagent (MRC, TR118).
Polyadenylated RNAs isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) were subjected for RNA libraries with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420L). The barcoded libraries were pooled for pair-end 150-bp sequencing in Illumina sequencing platform.

value: seedling

value: somatic


title: P100_pkd3_atac

description:
P100_PKD
060122-40_P_atac


title: P66_cont2_atac

description:
P066_control
092921-2_D_atac


title: P130_cont3

description:
P130_control
071422-100_L

data_processing:
library strategy: snRNA-seq
CellRanger ARC v2.0.2 (10X Genomics) using refdata-cellranger-arc-mm10-2020-A-2.0.0, which is mm10 reference genome 10X Genomics provided.
The CellRanger output were then processed and analyzed with Seurat (v4).
Assembly: mm10
Supplementary files format and content: a filtered / raw barcode-peak matrix (snRNA-seq)
Supplementary files format and content: a fragment file and an index file of a fragment file (snATAC-seq)


title: P66_cont1_atac

description:
P066_control
092121-200_A_atac


title: P66_pkd2_atac

description:
P066_PKD
092921-1_C_atac


title: P130_cont2

description:
P130_control
060222-700_K


title: P130_pkd2

description:
P130_PKD
060222-100_M


title: P100_pkd3

description:
P100_PKD
060122-40_P


title: P100_cont3

description:
P100_control
060122-20_O


title: P66_pkd1_atac

description:
P066_PKD
092121-400_B_atac


title: P130_pkd1

description:
P130_PKD
060222-70_I


title: P100_pkd1

description:
P100_PKD
060122-4_F


title: P66_cont2

description:
P066_control
092921-2_D


title: P100_cont1

description:
P100_control
060122-2_E


title: P100_pkd2

description:
P100_PKD
060122-10_H


title: P66_pkd2

description:
P066_PKD
092921-1_C


title: P66_cont1

description:
P066_control
092121-200_A


title: P66_pkd1

description:
P066_PKD
092121-400_B


title: P100_pkd2_atac

description:
P100_PKD
060122-10_H_atac


title: MA10_mBALF_Ratac

city: New York

first: Michael

last: Bale

address: 1300 York Ave

institute: Weill Cornell

description: 10x Multiome-ATAC

data_processing:
Cell Ranger ARC 1.0.0
Assembly: mm10
Supplementary files format and content: Cell Ranger ARC filtered_feature_bc_matrix folder
Supplementary files format and content: Cell Ranger ARC ATAC_fragments and index

source_name: BALF

extract_protocol:
Cells were isolated from bronchoalveolar lavage fluid and resuspended in nuclei buffer (10X Genomics) and subsequently processed according to manufacturer's instructions.
Nuclei were proessed using Chromium Next GEM Multiome ATAC + Gene Expression Reagent Bundle following manufacturer's instructions

value: BALF

value: Airway-resident Cells


title: MA10_mBALF_Rrna

description: 10x Multiome-RNA


title: P100_pkd1_atac

description:
P100_PKD
060122-4_F_atac


title: MA10_mBALF_Nrna

description: 10x Multiome-RNA


title: MA10_mBALF_Natac

description: 10x Multiome-ATAC


title: WT, veh, iWAT, biological replicate 1, scRNAseq

city: Los Angeles

first: Xia

last: Yang

address: 2000 Terasaki Life Sciences Bldg

department: Department of Integrative Biology and Physiology

institute: University of California, Los Angeles

description: 10X Genomics

data_processing:
Data quality check was done on Illumina SAV, and data de-multiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software. The demultiplexing, barcoded processing and gene counting were all done using the Cell Ranger software version 3.0.2. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: inguinal white adipose tissue

growth_protocol: Mice were kept on a light/dark cycle with water and food ad libitum.

extract_protocol:
300mg of the white adipose tissue (eWAT or iWAT) were collected (small biopsies from several locations of the fat depot to represent tissue environment), cut into small pieces, suspended in phosphate-buffered saline (PBS) (calcium, magnesium free) (GIBCO) containing 2mg/mL of type II collagenase (Worthington), and digested for 40 minutes at 37°C with agitation (100 rpm). The resulting dissociated tissue was resuspended in DMEM (GIBCO) with 10% FBS, gently mixed, passed through 100μm strainers, and centrifuged at 150g for 8 min at 4C. Next, supernatant and floating adipocytes were removed, and pellet was resuspended in DMEM (GIBCO) with 10% FBS and centrifuged at 150g for 8 min at 4C. Red blood cells were lysed using ACK lysis buffer (GIBCO). Lysate pellets were first washed with DMEM (GIBCO) with 10% FBS, centrifuged at 150g for 8 min at 4C and then PBS with 0.04% BSA (Gemini). The resulting pellets were finally resuspended in 200uL of PBS, 0.04% BSA (Gemini), passed through 40μm tip-strainers, counted, and further used for 10X 3'GEX library preparation and sequencing.
The Chromium Single Cell Gene Expression Solution upgrades short read sequencers to deliver a scalable microfluidic platform for 3ʹ digital gene expression by profiling 500-10,000 individual cells per sample. A pool of ~3,500,000 10x Barcodes are sampled separately to index each cell’s transcriptome. It is done by partitioning thousands of cells into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated cDNA shares a common 10x Barcode. Libraries are generated and sequenced from the cDNA and 10x Barcodes are used to associate individual reads back to the individual partitions. In addition to the poly(dT) primer that enables the production of barcoded, full-length cDNA from poly-adenylated mRNA, the Single Cell 3ʹ v3.1 Gel Beads also include two additional primer sequences (Capture Sequence 1 and Capture Sequence 2), that enable capture and priming of Feature Barcoding technology compatible targets or analytes of interest. Only the poly(dT) primers are used in this protocol for generating Single Cell 3ʹ Gene Expression libraries. GEMs are generated by combining barcoded Single Cell 3ʹ v3.1 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Next GEM Chip G. To achieve single-cell resolution, cells are delivered at a limiting dilution, such that the majority (~90-99%) of generated GEMs contain no cell, while the remainder largely contains a single cell. Immediately following GEM generation, the Gel Bead is dissolved, primers are released, and any co-partitioned cell is lysed. Primer containing (1) an Illumina TruSeq Read 1 (read 1 sequencing primer), (2) 10x Barcode, (3) 12nt unique molecular identifier (UMI), and (3) 30nt poly(dT) sequence are mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents. Incubation of the GEMs produces barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs are broken, and pooled fractions are recovered. Silane magnetic beads are used to purify the first-strand cDNA from the post GEM-RT reaction mixture, which includes leftover biochemical reagents and primers. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. TruSeq Read 1 (read 1 primer sequence) is added to the molecules during GEM incubation. P5, P7, a sample index, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. A Chromium Single Cell 3’ Gene Expression library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The 10x Barcode and 12 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. Sample index sequences are incorporated as the sample index read. TruSeq Read 1 and TruSeq Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. These libraries were sequenced using Illumina’s NovaSeq6000 platform in paired end 2x100bp configuration.

treatment_protocol: To examine the effects of PPARγ agonist, C56BL/6 and Lepob/Lepob mice were given 30 mg/kg rosiglitazone (Sigma R2408), or vehicle [2.6% methylcellulose (StemCell Technologies, M3120) diluted 1:5 in Dulbecco’s modified medium (GIBCO)] by oral gavage in the morning and evening for three consecutive days.

value: inguinal white adipose tissue

value: C57BL/6J (The Jackson Laboratory #000664)

value: stromal vascular fraction

value: Vehicle


title: obob, veh, iWAT, biological replicate  2, scRNAseq

description: 10X Genomics

value: Lepob/Lepob (The Jackson Laboratory #000632)


title: P130_cont1

description:
P130_control
060222-400_J


title: WT, veh, iWAT, biological replicate  2, scRNAseq

description: 10X Genomics


title: WT, veh, eWAT, biological replicate 2, scRNAseq

description: 10X Genomics

source_name: epididymal white adipose tissue

value: epididymal white adipose tissue


title: obob, rosi, iWAT, biological replicate  2, scRNAseq

description: 10X Genomics

value: male

value: Rosiglitazone


title: obob, veh, eWAT, biological replicate  1, scRNAseq

description: 10X Genomics


title: P130_pkd3

description:
P130_PKD
060222-200_N


title: Alveolar macrophages, recovered_2_IgG

data_processing:
Trim galore
Bowtie2
Assembly: mm10
Supplementary files format and content: Bigwig norm to 1x coverage
Library strategy: CUT&RUN

source_name: alveolar macrophage

extract_protocol:
CD45+CD11c+SiglecF+ cells were sorted from bronchoalveolar lavage fluid and resuspended in PBS supplemented to contain 10% FBS and immediately processed for further analyses.
EpiCypher CUT&RUN

value: recovered

value: alveolar macrophage


title: P100_cont2

description:
P100_control
060122-7_G


title: obob, rosi, iWAT, biological replicate  1, scRNAseq

description: 10X Genomics


title: Alveolar macrophages, recovered_3_IgG


title: obob, rosi, eWAT, biological replicate 2, scRNAseq

description: 10X Genomics


title: Alveolar macrophages, recovered_3_H3K27Ac


title: obob, rosi, eWAT, biological replicate 1, scRNAseq

description: 10X Genomics


title: Alveolar macrophages, recovered_2_H3K27Ac


title: Alveolar macrophages, recovered_1_IgG


title: Alveolar macrophages, naïve_2_H3K27Ac

value: naïve


title: Alveolar macrophages, recovered_1_H3K27Ac


title: Alveolar macrophages, naïve_1_H3K27Ac


title: Alveolar macrophages, naïve_1_IgG


title: WT, veh, eWAT, biological replicate 1, scRNAseq

description: 10X Genomics


title: Alveolar macrophages, recovered_3_H3K4me3


title: Alveolar macrophages, naïve_2_H3K4me3


title: obob, veh, iWAT, biological replicate  1, scRNAseq

description: 10X Genomics


title: Alveolar macrophages, recovered_1_H3K4me3


title: obob, veh, eWAT, biological replicate 2, scRNAseq

description: 10X Genomics


title: Alveolar macrophages, recovered_2_H3K4me3


title: Alveolar macrophages, naïve_1_H3K4me3


title: Alveolar macrophages, recovered_3_H3K4me1


title: Alveolar macrophages, recovered_1_H3K4me1


title: Alveolar macrophages, recovered_2_H3K4me1


title: Alveolar macrophages, naïve_1_H3K4me1


title: Alveolar macrophages, recovered_2

data_processing:
Trim galore!
Bowtie2
Assembly: mm10
Supplementary files format and content: bigwig norm to 1x coverage
Supplementary files format and content: reads in peaks unnormalized

extract_protocol:
CD45+CD11c+SiglecF+ cells were sorted from bronchoalveolar lavage fluid and resuspended in PBS supplemented to contain 10% FBS and immediately processed for further analyses.
Omni-ATACseq


title: Alveolar macrophages, naïve_2_IgG


title: Alveolar macrophages, recovered_1


title: Alveolar macrophages, naïve_2


title: Alveolar macrophages, naïve_3


title: Alveolar macrophages, naïve_1


title: Liver, C26-TDCA_08

city: Brussels

first: Laure

last: Bindels

address: Avenue E. Mounier, 73 bte B1.73.11

department: Metabolism and Nutrition Research Group

country: Belgium

institute: Louvain Drug Research Institut

data_processing:
De-multiplexed using Illumina's bcl2fastq 2.17 software
Quality-controlled and trimming using FastQC tool and Trimmomatic version 0.40
Reads alignment to the genome was performed using Hisat2 version 2.2.1
Count matrix was produced using Featurecounts version 2.0.3
Differential expression analysis was done using DESeq2 Bioconductor package version 1.42.0
Assembly: Mus musculus GRCm38.75
Supplementary files format and content: tsv file includes raw counts for each sample

source_name: liver

extract_protocol:
Livers were removed, frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA). Excess DNA was removed by DNase I treatment (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: WT

tag: tumor

value: Yes

value: C26 cells + TDCA


title: Liver, C26-TDCA_05


title: Liver, C26-TDCA_07


title: Liver, C26-TDCA_06


title: Liver, C26-TDCA_04


title: Liver, C26-TDCA_01


title: Liver, C26-TDCA_03


title: Liver, C26_07

value: C26 cells


title: Liver, C26-TDCA_02


title: Liver, C26_05


title: Liver, C26_08


title: Liver, C26_06


title: Liver, C26_04


title: Liver, C26_02


title: Alveolar macrophages, naïve_2_H3K4me1

tag: cell type


title: Liver, C26_01


title: Liver, CT_08

value: No

value: vehicle


title: Liver, C26_03


title: Liver, CT_02


title: Liver, CT_05


title: Liver, CT_06


title: Liver, CT_07


title: Alveolar macrophages, recovered_3


title: Liver, CT_01