title: Input pool, technical replicate 2

status: Public on Nov 04 2024

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description:
PCR
vector2
SuppTableS1_revision.xlsx

data_processing:
*library strategy: Amplicon-seq
2FAST2Q v 2.6 was used to extract and quantify the protospacer abundance in each sample (parameters: Phred score 30, no mismatches allowed).
Count data were analyzed using R version 4.0.5 and the Bioconductor package DESeq2 version 1.30.1 with default parameters (alpha 0.05, log2FCtest 1).  Pairwise comparison was performed for WT and Delta CovR samples (2 biological replicates), and raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and protospacer with an adjusted p-value lower than 0.05 were considered differentially distributed. (2 biological replicates). Sequencing data from the vectors (input pool) have been used for normalisation.
Supplementary files format and content: 2fast2q output and DESeq 2 output matrix

molecule: other

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Input pools in E. coli were grown in LB supplemented with 25 µg/ml kanamycin. Ouput pools in GBS were selected on THY supplemented with 500 µg/ml kanamycin.

extract_protocol:
Plasmid purification were done with QIEprep Spin Miniprep (Qiagen) following instructions for large vector (>10kb).
PCR amplification (25 cycles) were done with Phusion+ high fidelity polymerase (NEB). PCR products were gel purified (QIAquick PCR, Qiagen). Illumina adaptaters were added (PCR-free) following provider workflow (Novogen).

value: bacterial cell


title: Output pool, ∆covR ∆P2cas, Replicate 1

type: SRA

description:
PCR
Deltadeltap2_Rep1
SuppTableS1_revision.xlsx

library_source: other

organism: Streptococcus agalactiae

tag: cell type

tag: genotype

value: {delta}covR {delta}P2cas


title: Normoxia_CD45

status: Public on Dec 03 2024

city: New Haven

first: Jean-Leon

last: Thomas

state: CT

address: 800 Howard Ave

country: USA

institute: Yale University

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing and gene quantififcation were performed with CellRanger v2.1.1
After generation of gene expression matrices using CellRanger (10x Genomics), processing and analysis of the data were performed using the Seurat R-package (v4)
First, quality control steps filtered out genes that were expressed in less than 10 cells and cells that expressed fewer than 100 genes. Lastly, only cells which had fewer than 60000 counts, between 500 and 7500 genes and less than 20% of the unique molecular identifiers (UMIs) originating from mitochondrial genes were retained for further analysis.
For clustering and visualization, individual samples were normalized using the SCTransform function. Seurat SCTransform dataset integration was performed to merge P17 Control and Anti-Robo1/2 datasets to correct for batch effects. Dimensional reduction was performed using Uniform Manifold Approximation and Projection (UMAP) as implemented in the RunUMAP function, where 15 dimensions were used for the dims parameter and all other settings were default
Assembly: mm10
Supplementary files format and content: h5Seurat files with counts and scaled data

molecule: total RNA

organism: Mus musculus

source_name: Retina

growth_protocol: For the induction of OIR, the mother and P7 pups were placed in 75% O2 until P12. Upon return to room air, the pups were placed for adoption with a nursing mother and treated. Eyes were collected at P17.

extract_protocol:
Briefly, 8 retinas per group were dissected and dissociated with the Neural Tissue Dissociation kit (P) (Miltenyi Biotec, Cat#130- 092-628). The digestion was stopped by adding BSA (5% final) and the cells were immediately filtered through a 70 mm cell strainer. After centrifugation (600g for 5 min), cells were resuspended in PBS supplemented with 2mM EDTA and 0.5% BSA. The single cell suspension was enriched for ECs and immune cells using CD31 and CD45 MicroBeads (Miltenyi Biotec) according to the manufacturer’s instructions.
Single cell suspensions of retinal cells were resuspended in PBS containing 0.04% ultra-pure BSA. scRNA-seq  libraries were prepared using the Chromium Single Cell 30 Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions. The target cell recovery for each library was 10,000. Generated libraries were sequenced on an Illumina HiSeq4000.

treatment_protocol: For antibody treatment, 10mg/kg of antibodies or isotype control IgG were diluted in 200uL of sterile 0.9% NaCl and given i.p. at P12, P14 and P16. For IPI-549 treatment, 15mg/kg of the inhibitor was diluted in 200uL of sterile vehicle (0.9% NaCl 2%DMSO) and given i.p. daily from P12 to P16; and control mice were treated i.p. with 200uL of vehicle.

tag: tissue

value: Retina

value: Immune cell

tag: treatment


title: Output pool, ∆covR, Biological Replicate 2

description:
PCR
DcovR_Rep2
SuppTableS1_revision.xlsx

value: {delta}covR


title: Input pool, technical replicate 1

description:
PCR
vector1
SuppTableS1_revision.xlsx


title: Output pool, BM110 WT, Biological Replicate 2

description:
PCR
WT_Rep2
SuppTableS1_revision.xlsx

value: WT


title: Output pool, BM110 WT, Biological Replicate 1

description:
PCR
WT_Rep1
SuppTableS1_revision.xlsx


title: Output pool, ∆covR, Biological Replicate 1

description:
PCR
DcovR_Rep1
SuppTableS1_revision.xlsx


title: CRSwNP_NP33

status: Public on Oct 03 2024

city: Jinan

first: Xinyu

last: Xie

address: Wenhua West Road

country: China

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

organism: Homo sapiens

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

tag: condition

value: chronic rhinosinusitis and nasal polyps


title: Input pool, technical replicate 3

description:
PCR
vector3
SuppTableS1_revision.xlsx


title: CaSki_16E6E7

status: Public on Aug 25 2024

type: RNA

city: Tsukuba

first: Takeo

last: Minaguchi

state: Ibaraki

address: 1-1-1 Tennoudai

country: Japan

institute: University of Tsukuba

hyb_protocol: 600 ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K Microarrays. The slides were incubated for 17 h at 65°C in an Agilent hybridization oven, and then washed at room temperature.

scan_protocol: The hybridized array was scanned with an Agilent Microarray Scanner D.

data_processing: Quantile normalization was done using BRB-ArrayTools.

source_name: CaSki cells transfected with si-16E6E7

label_protocol: 100 ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-2000.

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum and 1 U/ml Penicillin-Streptomycin-Amphotericin B Suspension at 37˚C with 5% CO2.

extract_protocol: Total RNAs were extracted using TRIzol reagent (Thermo Fisher Scientific) from cells transfected with the siRNAs.

treatment_protocol: Cells were transfected with siRNAs at a concentration of 10 nM (HeLa) or 40 nM (CaSki) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer’s instructions.

tag: cell line

value: CaSki

value: cervical cancer


title: HeLa_NC

source_name: HeLa cells transfected with si-NC

value: HeLa

value: si-NC


title: CaSki_NC

source_name: CaSki cells transfected with si-NC


title: CaSki_mock

source_name: CaSki cells with mock transfection

value: mock


title: PAN only, rep1

status: Public on Dec 01 2024

city: Columbus

first: Julie

middle: A

last: Dougherty

state: OH

address: 700 Children's Dr, Research Building 2

department: Research

institute: Nationwide Children's Hospital, Columbus, Ohio

library_source: transcriptomic

data_processing:
.  Sequencing adapters matching at least 6 bases were then removed from the reads, as well as low-quality bases (<10) using v1.10 of cutadapt  (https://cutadapt.readthedocs.io/en/stable/index.html)
An alignment report was also generated, using custom scripts, and manually reviewed to ensure that at least ~80% of reads aligned to the expected reference, and that at least ~50% of the reads aligned to features annotated as protein coding
Each sample was aligned to the Rnor_6.0 assembly of the Rattus norvegicus reference from the National Center for Biotechnology Information (NCBI) using version 2.5.0c of the RNA-Seq aligner STAR (http://bioinformatics.oxfordjournals.org/content/29/1/15)
Transcript features were identified from the general feature format (GFF) file that came with the assembly from the NCBI. Feature coverage counts were calculated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
raw RNA-Seq gene expression data were normalized, and post-alignment statistical analyses and figure generation were performed using DESeq2 (http://genomebiology.com/2014/15/12/550) and custom analysis scripts written in R.
Comparisons of gene expression and associated statistical analyses were made between different conditions of interest using the normalized read counts. All fold-change values were expressed as test condition / control condition, where values <1 were denoted as the negative of its inverse (note that there will be no fold change values between –1 and 1, and that the fold changes of “1” and “-1” represent the same value)
Transcripts were considered significantly differentially expressed using a 10% false discovery rate (DESeq2 adjusted P value < 0.1). Genes were removed from comparisons if they were not expressed above a background threshold (0.5 reads per million) for most samples within each group
Assembly: Rnor_6.0 assembly
Supplementary files format and content: htseq.cov files contain waw counts of reads per gene generated by HTSeq v0.6.1p1.
Supplementary files format and content: AllData_160322_RNASeq_Smoyer_Results_iScience.xlsx contains DESeq2 normalized counts per gene for all samples.

organism: Rattus norvegicus

source_name: kidney, glomeruli

growth_protocol: ad libitum water and standard chow, 12h/12h light/dark cycle, temperature/humidty controlled environment

extract_protocol:
Total RNA from the isolated glomeruli was extracted using the RNeasy Mini Kit #74104, Qiagen
350 ng total RNA was prepared to libraries with TruSeq Standard total RNA with Ribo-Zero Globin Complete kit, Illumina
To generate directional signals in RNA seq data, libraries were constructed from first strand cDNA using TruSeq Standard total RNA with Ribo-Zero Globin Complete kit from Epicentre Biotechnologies

treatment_protocol: day 0 tail vein injection of 50 mg/kg PAN, treatment thereafter 15mg/kg MP IP injection or 10mg/kg Pio PO daily. Healthy and disease controls received vehicle PO daily.

value: kidney, glomeruli

value: PAN only


title: Hela_18E6E7

source_name: HeLa cells transfected with si-18E6E7


title: CaSki_16E6

source_name: CaSki cells transfected eith si-16E6


title: Ace2 KO mouse corneal rim 3

status: Public on Jul 15 2024

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

data_processing:
follow the protocol from 10X genomics
Assembly: GRCm38.91
Supplementary files format and content: matrix file

organism: Mus

source_name: cornea/limbus

extract_protocol:
Whole eyes were harvested . The lens, retina, iris, and trabecular network were removed leaving the entire ocular anterior segment, from which most of the conjunctiva was carefully dissected and discarded. The corneal rims were subsequently digested at 37°C for 2 hours with 2 ml of 1 mg/mL collagenase A (Sigma-Aldrich) in DMEM containing 10% FBS, 50 μg/mL gentamicin, and 1.25 μg/mL amphotericin B.  After 2hr incubation, the corneal rims were rinsed once with PBS without Ca2+-Mg2+. Clusters were further digested with 0.25% trypsin and 1 mM EDTA at 37°C for 20 minutes with intermediate gentle pipetting to yield single cells. After trypsin digestion, cells were rinsed once with DMEM+10% FCS media to deactivate and remove trypsin. The cells were rinsed twice with sterile PBS containing 0.04% BSA. After final centrifugation, cells were resuspended in 60ul of PBS containing 0.04% BSA to achieve 700-1200 cells/ul, and filtered into an Eppendorf tube by using Flowmi Cell Strainer (Fisher Scientific). Cell viability was checked and accepted with at least an 80% viability score. Such cells were processed for scRNA-seq using 10XGenomics pipeline in the Northwestern University NUseq Core.
follow the instructions from 10XGenomics

value: cornea/limbus


title: Ace2 KO mouse corneal rim 2


title: wild type mouse corneal rim 3

value: wt


title: Ace2 KO mouse corneal rim 1


title: wild type mouse corneal rim 2


title: wild type mouse corneal rim 1


title: PAN + MP, rep1

value: PAN + MP


title: RPMI-RomiMS-H3K27ac

status: Public on Jul 01 2024

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

library_source: genomic

data_processing:
cleaning fastq files with fastq-mcf, quality control with fastQC
mapping to reference genome with Bowtie2, processing with SAMtools
spike-in (dm6) normalization with deepTools
peak calling with MACS2
Assembly: Homo Sapiens (hg38)
Supplementary files format and content: bigwig files were generated using the deepTools software package (with spike-in normalization)
Supplementary files format and content: narrowPeak files were generated with the MACS2 peak calling algorithm (FDR<0.01)

molecule: genomic DNA

extract_protocol:
ChIP-sequencing (ChIPmentation) was performed as described in Vanden Bempt, M., Demeyer, S. et al, Cancer Cell, 2018.
all libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody

value: H3K27ac (Active Motif Cat #39133)


title: RPMI-input


title: RPMI-Romidepsin-H3K27ac

value: Romidepsin


title: RPMI-Taz5-72h-2

data_processing:
cleaning with fastq-mcf
quality control with FastQC
mapping with HISAT2, further processing with SAMTools
counting abundances with htseq-count
Assembly: Homo Sapiens (hg38)
Supplementary files format and content: tab-delimited text file includes raw count values for each gene

extract_protocol:
RNA extraction was performed using a Promega Maxwell, using the Maxwell RSC simplyRNA Cells Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tazemetostat


title: RPMI-DMSO-H3K27ac

value: DMSO


title: RPMI-DMSO-72h-3


title: RPMI-Taz5-72h-3


title: HeLa_mock

source_name: HeLa cells with mock transfection


title: RPMI-DMSO-72h-1


title: RPMI_Romi_25-01


title: RPMI-DMSO-72h-2


title: RPMI_Romi_10-05


title: RPMI-Taz5-72h-1


title: RPMI_Romi_05-05


title: RPMI_Romi_+_MS_25-01


title: ATAC MA29

city: South San Francisco

first: Xin

last: Luo

state: CA

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

description: paired single nucleus RNA + assay for transposable accessible chromatin, ATAC

data_processing:
Raw fastq files were aligned to the human GRCh38 reference genome (v) using CellRanger ARC (10x Genomics, v6.1).
ArchR (https://www.archrproject.com) was used to process the ATAC fragments and Seurat was used to process RNA.
Assembly: GRCh38
Supplementary files format and content: metadata.csv contains metainformation of all samples with cells in rows and labels in columns. For each sample, the CellRanger ARC output filtered matrix files including  barcodes.tsv, features.tsv and matrix.mtx were included as processed data files as well.

molecule: nuclear RNA

source_name: Heart

extract_protocol:
Nuclei were isolated according to 10x Genomics protocol (CG00375; Nuclei Isolation Complex Sample for ATAC GEX Sequencing RevB) and flow cytometry for 7-AAD positive nuclei was used for sorting.
Protocol CG000338 from 10x Genomics was used for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. Briefly, following nuclei isolation, permeabilization was performed, followed by transposition, GEM generation and barcoding using ChipJ (10x Genomics; PN1000234), post-GEM clean up, pre-amplification PCR, cDNA amplification, library construction, and sequencing. Gene expression and ATAC libraires were sequenced to a read depth of 50,000 and 25,000 respectively.
snRNA-Seq; snATAC-Seq

value: Heart

tag: disease state

value: Donor


title: RPMI_Romi_+_MS_10-05


title: RPMI_Romi_+_MS_05-05


title: RPMI_MS1943_25-01


title: HeLa_18E6

source_name: HeLa cells transfected with si-18E6


title: RPMI_MS1943_10-05


title: RPMI_MS1943_05-05


title: RPMI_DMSO_10-05


title: RPMI_DMSO_05-05


title: GEX MA29


title: RPMI-MS1943-H3K27ac


title: RPMI_DMSO_25-01


title: MT2_scRNAseq_Day3_Benz

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description:
SingleCell_Day1_Day3_count_matrix.csv
SingleCell_Day1_Day3_sample_metadata.csv

data_processing:
Bulk RNA-seq:  Quantification was done using Salmon (v 0.13.0) to the mouse reference genome GRCm38. Transcript expression were merged to the gene-level based on tximeta package
Single-cell RNA-seq: Raw sequencing reads were processed using CellRanger v3.0.0. To the mouse reference genome mm10, Ensembl  version 93. Totalseq sample barcodes were demultiplexed using CITE-seq-Count  (v 1.4.2)
Chip-seq: Raw sequencing reads were aligned to mouse genome (mm10) using Bowtie2. Aligned reads were elongated in silico using the DNA fragment size inferred from paired-reads using R pipeline named PASHA. These elongated reads were then used to calculate the number of fragments that overlapped at a given nucleotide thus representing an enrichment score for each nucleotide in the genome.
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix: Gene-by-sample matrix containing raw counts for each sample.
sample_metadata: Gene-by-sample matrix containing raw counts for each sample.
WIG file: Enrichment score of the ChIP-seq experiments in wiggle format

molecule: polyA RNA

source_name: Ty1.MOZ-TIF2 cell line

extract_protocol:
All RNA was extracted using Qiagen's RNeasy kit following manufacturer's protocol.   DNA was isolated by phenol:chloroform: isoamylalcohol (25:24:1 pH 8) extraction followed by Qiaquick PCR purification.
At least 1ng of ChIP DNA was used to prepare sequencing library with NEBUltra ChIP Sample Library Prep Kit (New England Biolabs).    For bulk RNA-seq Indexed polyA libraries were prepared using 200 ng of total RNA and 14-15 cycles of amplification with the Agilent SureSelect Automated Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing (G9691B) on an Agilent NGS Workstation Option B liquid handling platform (G5522A).    For scRNA-seq, amplified cDNA was prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics, PN-120237) with 9-13 cycles of amplification according to manufacturer’s instructions with modifications specified in “TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v2” protocol (BioLegend). Sequencing libraries were prepared from the cDNA fraction according to the 10x Genomics protocol using 11 cycles of amplification. The HTO sequencing library was prepared from the remaining fraction according to the TotalSeq-A protocol using 8 cycles of amplification.

tag: process

value: scRNA seq

value: Ty1.MOZ-TIF2 cell line

tag: cell type origin

value: c-Kit+ HSPCs from C57Bl/6 bone marrow retrovirally transduced with Ty1.MOZ-TIF2

tag: selection

value: FACS sorting GFP+ cells and serial replating in methylcellulose

value: 5uM Benzarone for 3 days


title: MT2_scRNAseq_Day1_DMSO

value: DMSO for 1 day


title: MT2_scRNAseq_Day1_Benz

value: 5uM Benzarone for 1 day


title: MT2_Ty1_ChIP_rep1

value: MOZ-TIF2 ChIPseq

value: C15200054 (Diagenode)


title: MT2_scRNAseq_Day5_DMSO_Benz

value: DMSO or 5uM Benzarone for 5 days


title: ckit_RNAseq_replicate2

source_name: c-Kit+ HSPCs

value: RNA Seq

value: c-Kit+ HSPCs

value: c-Kit+ HSPCs from C57Bl/6 bone marrow

value: Freshly isolated


title: Input_ChIP_MT2

value: Input DNA


title: H3K9-14A_ckitDiff

source_name: Differentiated c-Kit+ HSPCs

value: H3K9/14ac ChIPseq

value: Differentiated c-Kit+ HSPCs

value: c-Kit+ HSPCs from C57Bl/6 bone marrow retrovirally transduced with empty vector

value: FACS sorting for GFP+ cells and culturing in cytokine supplemented medium for 4 days

value: C15410005 (Diagenode)


title: ckit_RNAseq_replicate1


title: H3K9-14A_ckit


title: ckitDiff_RNAseq_replicate1


title: H3K9-14A_MT2

value: Ty1.MOZ-TIF2 cell line

value: c-Kit+ HSPCs from C57Bl/6 bone marrow retrovirally transduced with Ty1.MOZ-TIF2


title: ckitDiff_RNAseq_replicate2


title: MT2_RNAseq_replicate1


title: MT2_RNAseq_replicate2


title: Hoxa9_RNAseq_replicate3_BENZ

source_name: HOXA9 cell line

value: HOXA9 cell line

value: c-Kit+ HSPCs from C57Bl/6 bone marrow retrovirally transduced with HOXA9

value: FACS sorting GFP+ cells and serial replating in methylcellulose for 4 rounds

value: 5uM Benzarone for 72 hours


title: Hoxa9_RNAseq_replicate2_BENZ


title: Hoxa9_RNAseq_replicate2_DMSO

value: DMSO for 72 hours


title: Hoxa9_RNAseq_replicate1_DMSO

value: RNA Seq


title: Hoxa9_RNAseq_replicate3_DMSO


title: Hoxa9_RNAseq_replicate1_BENZ


title: Eya1_Hoxa9_RNAseq_replicate3_DMSO

source_name: EYA1_HOXA9 cell line

value: EYA1_HOXA9 cell line

value: c-Kit+ HSPCs from C57Bl/6 bone marrow retrovirally transduced with EYA1 and HOXA9

value: FACS sorting GFP+ and dTomato+ cells and serial replating in methylcellulose for 4 rounds


title: Eya1_Hoxa9_RNAseq_replicate3_BENZ


title: MT2_Ty1_ChIP_rep2

value: MOZ-TIF2 ChIPseq

value: FACS sorting GFP+ cells and serial replating in methylcellulose


title: Eya1_Hoxa9_RNAseq_replicate2_BENZ


title: Eya1_Hoxa9_RNAseq_replicate2_DMSO


title: Eya1_Hoxa9_RNAseq_replicate1_BENZ


title: Pro-T_Cas9_TLX3+FLT3-ITD+gLuc_R2

status: Public on Jun 17 2024

data_processing:
cleaning with fastq-mcf
quality control with FastQC
mapping with HISAT2, further processing with SAMTools
counting abundances with htseq-count
Assembly: Mus Musculus (mm10)
Supplementary files format and content: tab-delimited text file includes raw count values for each gene

source_name: Pro-T cell line

value: Pro-T cell line


title: Pro-T_Cas9_TLX3+FLT3-ITD+TLE4_R2


title: Pro-T_Cas9_TLX3+FLT3-ITD+TLE4_R3


title: Pro-T_Cas9_TLX3+FLT3-ITD+gLuc_R3


title: Pro-T_Cas9_TLX3+FLT3-ITD+gLuc_R1


title: Eya1_Hoxa9_RNAseq_replicate1_DMSO


title: Pro-T_Cas9_TLX3+EV+gLuc_R1


title: Pro-T_Cas9_TLX3+EV+gLuc_R2


title: Pro-T_Cas9_TLX3+EV+TLE4_R1


title: Pro-T_Cas9_TLX3+EV+TLE4_R3


title: Pro-T_Cas9_EV+FLT3-ITD+gLuc_R3


title: Pro-T_Cas9_TLX3+FLT3-ITD+TLE4_R1


title: Pro-T_Cas9_TLX3+EV+TLE4_R2


title: Pro-T_Cas9_EV+FLT3-ITD+gLuc_R2


title: Pro-T_Cas9_EV+EV+gLuc_R3

value: EV+EV+gLuc


title: Pro-T_Cas9_EV+EV+gLuc_R2


title: Pro-T_Cas9_EV+EV+gLuc_R1


title: Pro-T_Cas9_EV+EV+TLE4_R1


title: Pro-T_Cas9_EV+EV+TLE4_R2


title: Cat_22-007 VDJ

status: Public on May 17 2024

city: Davis

first: Stefan

middle: Matthias

last: Keller

state: California

address: One Shields Avenue

department: Pathology, Immunology, Microbiology

institute: University of California, Davis

data_processing:
Cell Ranger version 7.1
Seurat v5 & custom R scripts
Assembly: Felis_catus_9.0
Supplementary files format and content: Cell Ranger GEX output: raw_feature_bc_matrix and filtered_feature_bc_matrix
Supplementary files format and content: Cell Ranger VDJ output: all_contig_annotations.csv (one each for AB & GD libraries)
Supplementary files format and content: Excel file links the cell barcodes to the clusters or cell types

organism: Felis catus

source_name: Blood leukocytes

extract_protocol: Chromium Next GEM Single Cell 5’ Kit v2 (10x Genomics) - separate amplification of TRA/TRB and TRG/TRD receptor chains

tag: breed

value: Domestic shorthair

tag: age

value: 6 months

tag: Sex

value: female

value: Blood leukocytes

value: healthy


title: Cat_22-007 GEX


title: Cat_21-005 VDJ

value: 1 year


title: Cat_21-005 GEX


title: Cat_18-003 VDJ

value: 4 years


title: Cat_18-003 GEX


title: Cat_13-101 GEX

value: 9 years


title: MSE371

status: Public on May 01 2024

city: Pittsburgh

first: Sharon Ann

last: George

state: PA

address: 200 Lothrop Street W1355

institute: University of Pittsburgh

description: Male, Sedentary

data_processing:
After evaluating sequence quality, sequence reads were trimmed to remove possible adapter sequences using Trimmomatic v.0.36.
Trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using STAR aligner v.2.5.2b, and BAM files were generated.
Hit counts were calculated using featureCounts from the Subread package v.1.5.2, summarized and reported using gene_id feature in the annotation file.
Assembly: GRCm38
Supplementary files format and content: .bam files containing aligned sequences.

extract_protocol:
Hearts were fixed in RNA later and shipped to Genewiz by Azenta Life Sciences for RNA sequencing.
RNA libraries were prepared by Genewiz by Azenta Lifesciences.

treatment_protocol: Exercise mice were run on a treadmill at 1km/hr for 45 mins/day, 5 days/week for 6 weeks and hearts were havested at the end of the protocol. Sedentary age-matched mice were not exercised and remained in their cage over th e6 week duration.

value: Heart

value: Bulk tissue

value: WT

value: Sedentary


title: Cat_13-101 VDJ


title: MSE369

description: Male, Sedentary


title: MEX365

description: Male, Exercise

value: Exercise


title: Pro-T_Cas9_TLX3+EV+gLuc_R3


title: MEX364

description: Male, Exercise


title: Pro-T_Cas9_EV+FLT3-ITD+gLuc_R1


title: MEX363

description: Male, Exercise


title: FSE368

description: Female, Sedentary


title: FEX362

description: Female, Exercise


title: MSE370

description: Male, Sedentary


title: FSE367

description: Female, Sedentary


title: FEX360

description: Female, Exercise


title: iTEC_10day_Coculture_1

status: Public on Apr 22 2024

city: Nashville

first: Seung Woo

last: Kang

state: TN

address: MRBIV 10475, 2215 Garland Avenue

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

description: 10X genomics

data_processing:
Demultiplexed with CellRanger v.7.
Downstream analyses were done with Seurat v.4 (Hao* & Hao* et al., 2021).
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Murine embryonic fibroblasts

growth_protocol: Primary iFoxn1/+ MEFs were thawed then cultured in DMEM containing 15% fetal calf serum, 2 mM sodium pyruvate, 4 mM glutamine, 50 µg/ml streptomycin and 50 U/ml penicillin (DMEM/FCS).

extract_protocol:
MEFs, and iTECs of various treatments were trypsinised with 0.25% trypsin in 37'C and washed with media 2 times to remove residual EDTA.
Library was constructed according to the manufacturer's instructions (single cell 3', 10X genomics).

value: Murine embryonic fibroblasts

value: iTECs

value: Cocultured with E16.5 thymocytes


title: Pro-T_Cas9_EV+EV+TLE4_R3

value: Pro-T cell line


title: iTEC_12day_DAPT_1

description: 10X genomics

value: DAPT for 7 days


title: FEX361

description: Female, Exercise


title: iTEC_12day_DMSO_1

description: 10X genomics

value: DMSO for 7 days


title: iTEC_12day_DAPT_2

description: 10X genomics


title: iTEC_12day_1

description: 10X genomics

value: No


title: FSE366

description: Female, Sedentary


title: Fetal_TEC_Control_1

data_processing:
Bulk RNA sequencing was performed in Georgia genomics and bioinformatics core (GGBC) using an Illumina NextSeq 500 sequencing platform to generate single end sequencing data. Raw reads were pre-processed with sequencing grooming tools FASTQC, Trimmomatic and then further assembled by Hisat2, SAMtools, and StringTie. Differential gene expression analysis between samples and graphical display (including count matrix plot, PCA, heatmap and other plots) were performed using DEseq2 and R package ggplot2. Gene ontology enrichment analysis was performed using online EnrichR program (Chen et al.; Kuleshov et al.).
Assembly: mm10
Supplementary files format and content: Csv file containing a gene count matrix of all of the samples combined.

source_name: Mouse thymic epithelial cells

extract_protocol:
RNA was prepared using the RNAeasy mini kit (Qiagen) according to the manufacturer’s instructions. All samples were DNaseI treated during the preparation.
RNA was frozen in -80'C freezer until the libraries could be constructed with UGA GGBC.

treatment_protocol: Primary iFoxn1/+ MEFs for Nucleofection experiment were passaged no more than 5 times for all analyses in this research. Nucleofection experiments were performed following the manufactures’ protocol for mouse embryonic fibroblasts: free program N-024 (Amaxa™ Nucleofector™, Lonza). To induce iFoxn1 expression, pPGK-Cre-bpA (Addgene # 11543) was used in the transfection according to the manufacturer’s protocol. After Nucleofection, cells were further cultured for 48 hours until sorted by flow cytometry.

value: Mouse thymic epithelial cells

value: TECs

value: No treatment, E15.5


title: Fetal_TEC_Control_2


title: iTEC_12day_2

description: 10X genomics


title: iTEC_12day_Epcam+_1

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts

value: Cre-induced, 12 days


title: MEF_control_1

description: 10X genomics

value: MEFs


title: iTEC_10day_3

value: Cre-induced, 10 days


title: iTEC_10day_1


title: iTEC_12day_Epcam+_2


title: iTEC_2day_2

value: Cre-induced, 2 days


title: iTEC_10day_2


title: MEF_Control_2

value: No treatment, E13.5


title: iTEC_10day_DAPT_1

description: 10X genomics

value: DAPT for 5 days


title: Resilient

status: Public on Feb 09 2024

city: Beijing

first: TING

last: WANG

address: Haidian District, Beijing

institute: Beijing Institute of Basic Medical Sciences

description: 10x Genomics

data_processing:
Spatial Transcriptomics
bcl2fastq command line tool was used for base calling  Sequence reads were trimmed for adapter sequence and polyA homopolymers using cutadapt
Reads were mapped, annotated and demultiplexed using the spaceranger v1.0.0 command line tool
Annotated reads were quantified and mapped to the Hematoxylin and Eosin image using the spaceranger v1.0.0 command line tool
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: raw.zip include matrix with raw counts for every gene and every spot and spatial informations
Library strategy: Spatial Transcriptomics (Visium)

source_name: brain

extract_protocol:
The brains were coronally cryosectioned at a thickness of 10 μm by Cryostat Microtome (Leica CM1950, Germany). Then 5-10 sections were selected to be stained with HE, photographed and tested for RNA integrity number (RIN) value
RNA libraries were prepared for sequencing following the 10x Genomics Visium protocol

value: brain

tag: strain

value: male

value: 8 weeks

tag: sample group

value: Resilient


title: BM1

status: Public on Feb 26 2024

city: London

first: Hector

last: Huerga Encabo

address: The Francis Crick Institute, 1 Midland Rd

institute: The Francis Crick Institute

description: 10x Genomics

data_processing:
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina)
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, aligning to the mm10 transcriptome + eGFP sequence using STAR (v.2.5.1b)
All subsequent analyses were performed in R v.3.6.1  using the Seurat (v3) package
Assembly: GRCh38
Supplementary files format and content: Tab-separated barcodes ID's, features files and count files

source_name: Bone marrow

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Bone marrow

value: Heterogenous. Enriched by FACS-sorting for DCs and progeniotors before sequencing.


title: Susceptible

description: 10x Genomics

value: Susceptible


title: Control

description: 10x Genomics

value: Control


title: P133

status: Public on Jan 24 2024

city: Novosibirsk

first: Nikita

last: Torgunakov

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics

description: Chromatin fragmentation by S1. Raw data not provided due to patient privacy concerns

data_processing:
merged_nodups.txt files were obtained using modified version of the Juicer 1.6 (https://github.com/genomech/juicer1.6_compact)
Assembly: hg19
Supplementary files format and content: merged_nodups.txt.gz files containing valid Hi-C pairs (described as "Long format" in Juicer documentation here: https://github.com/aidenlab/juicer/wiki/Pre#long-format), modified to remove fields <cigar1> <sequence1> <cigar2> <sequence2> <readname1> <readname2> due to patient privacy concerns. Fields <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> remain.

source_name: blood

extract_protocol:
Extraction protocol was performed as described in Gridina. et. al 2021 (PMID: 33743768).
Exo-C protocol includes a 3C part followed by exome enrichment. The 3C part was performed either following DNase I protocol as described in Gridina. et. al 2021 (PMID: 33743768), or S1 as described in Gridina. et. al 2023 (PMID: 38072950).

value: blood

value: Lymphocytes


title: iTEC_2day_1

value: Mouse embryonic fibroblasts

value: iTECs


title: P137


title: P136


title: P131


title: P135


title: P132


title: iTEC_3day_1

description: 10X genomics

value: Murine embryonic fibroblasts

value: No


title: iTEC_12day_Epcam-_1

value: Cre-induced, 12 days


title: P125


title: iTEC_12day_Epcam-_2


title: P124


title: P123


title: P115


title: P92


title: P71

description: Chromatin fragmentation by DNase I. Raw data not provided due to patient privacy concerns


title: P78


title: MEF_Control_1

value: MEFs

value: No treatment, E13.5


title: P70


title: P69


title: P53


title: P63


title: P57


title: P58


title: P45


title: P44


title: P54


title: P51


title: P119


title: P122


title: P49


title: P46


title: P43


title: P48


title: P42


title: P10


title: TAF9

source_name: skin fibroblasts

value: skin fibroblasts

value: Fibroblasts


title: TAF4


title: K562

description: Chromatin fragmentation by DNase I


title: P39


title: P52


title: P62


title: TAF3


title: P40


title: P47


title: P38


title: P55


title: P37


title: P35


title: P32


title: P31


title: P50


title: ChIP-DND41_TLX3

status: Public on Jan 23 2024

tag: antibody


title: ChIP-DND41_input


title: P26

tag: cell type


title: P.UTA.01.1

status: Public on Dec 04 2023

city: Gaithersburg

first: Prabha

last: Chandrasekaran

state: Maryland

address: 8348 Hawkins Creamery Rd

institute: ehealth&Informatics, LLC

description: PIDTC Cohort

data_processing:
Raw sequence reads in fastq files were analyzed using the QIIME2 (Quantitative Insights Into Microbial Ecology version 2), to obtain the taxonomic profiles. Sequence quality analysis was also carried out using FastQC. The QIIME2 plugin, DADA2 v1.10 [57] was used for quality-score based filtering.
The alpha rarefaction maximum depth was 127,928 sequences. The sequences were clustered into Operational Taxonomic Units (OTUs) using an open-reference OTU picking workflow against the SILVA v132 database. For all analyses, feature tables were filtered requiring a microbial feature to have at least 0.01% relative abundance. The Alpha diversity was calculated using the estimate richness function in phyloseq [58] using 4 different indices (observed species, Chao1, Shannon and Fisher) and compared using the Kruskal-Wallis test. Beta diversity was evaluated by principal coordinate analyses (PCoA) based on the weighted UniFrac distance method, and significance was determined by Permutational MANOVA (PERMANOVA, 9999 permutations).
The differential abundance analyses from the OTU count table were performed using the EdgeR package [59]. Predictive functional profiling of the microbial communities based on 16S rRNA sequencing was performed using PICRUSt2 [60]. The heat tree analysis depicting taxonomic differences between the groups utilizes the quantitative median abundance value and the non-parametric Wilcoxon Rank Sum test to leverage the hierarchical structure of taxonomic classifications. Heat tree analyses were performed using the Metacoder R package [61]. The OTU correlation analysis between the NIH and PIDTC cohorts and the network generation were performed using the spearman rank correlation method at the genus level setting a p-value threshold of p<0.05 and the r value threshold of 0.3 through the SparCC method incorporation using sparse network assumptions and 100 iterations [62].
The Python package MICOM (for microbial communities) was utilized to calculate the growth rates, niche and the imports and exports of metabolites at the genus level (performed by COSMOSIDÒ [cosmosid.com])[63]. The microbiome biomarkers in the dataset were identified using Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis performed in lefser R package version 1.8.0 [64]. For further accurate prediction of biomarkers or predictive features, the machine learning algorithm of Random Forest was used. This method is an ensemble of decision trees, that implements Breiman's random forest algorithm (based on Breiman and Cutler's original Fortran code) for classification and regression. The randomForest package in R was utilized by averaging 1000 decision trees [65]. Multiple factor analysis was performed to identify the metadata variables contributing to the diversity of the microbiome using FactoMineR package in R. The resulting Factor analysis of mixed data (FAMD) plots were generated with the principal component method for quantitative variables and multiple correspondence analysis (MCA) for the qualitative variables [66]. All diversity trends and community composition visualizations were created using the ggplot2 package in R. This work utilized the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov) and the Nephele platform from the NIAID Office of Cyber Infrastructure and Computational Biology (OCICB) (http://nephele.niaid.nih.gov, Bethesda, MD).
Supplementary files format and content: Biom Format File: NIH_PIDTC_combined_feature-table.biom

source_name: humanstool

extract_protocol:
DNA was extracted from stool samples using PowerSoil® DNA Isolation Kit (MO BIO Laboratories, #12888-100) as per manufacturer’s instructions (available online at https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf), with the following 2 modifications: 1) Prior to bead beating, proteinase K (20μL) (Qiagen, #19131) was added to each sample, and samples were incubated for 10 minutes at 65C° using a heating block, and 2) the bead beating step was completed using a TissueLyser II (Qiagen) at 30 Hz for 2 minutes. DNA was eluted in UltraClean® PCR Water (MoBio Laboratories, #17000-10).
The stool microbiome was characterized by amplicon sequencing of the 16S rRNA gene’s V4 hypervariable region amplified using the following primers (515F = GTGCCAGCAGCCGCGGTAA and 806R = GGACTACCAGGGTATCTAAT) that were modified to include a linker sequence, a 12 bp index sequence and a heterogeneity spacer as described in [56]. The PCR conditions were: sample DNA (2.5μL), 10X PCR Buffer (2.5μL), dNTP Mix (4μL), Takara LA Taq Polymerase (0.25μL) (Takara Bio USA, #RR013A), PCR Water (13.75μL) (Qiagen, #17000-10), and 1μL of each primer (515F (10μM) and 806R (10μM)). Reactions were performed in duplicate according to the following conditions: 98C° for 30 seconds, 30 cycles (98C° for 15 seconds, 58C° for 15 seconds, 72C° for 15 seconds), and 72C° for 60 seconds. Libraries were combined, cleaned up with the Agencourt AMPure XP Kit (Beckman Coulter, #A63880) and quantified using the Quant-IT dsDNA High-Sensitivity Assay Kit (Invitrogen, #Q33120) as above. Normalized libraries were then pooled, purified using a Qiagen MinElute column (Qiagen, #28004), and sequenced using a 250-bp paired-end sequencing protocol on the Illumina MiSeq platform (Illumina Inc.) at the NIH Intramural Sequencing Center (NISC, NIH, Rockville, MD).
OTHER: 16S rRNA sequencing

value: humanstool

tag: sample type

value: 16s rRNA

tag: genotype

value: UNKNOWN

value: CGD


title: P.STJ.11.1

description: PIDTC Cohort

tag: tissue

tag: treatment


title: P.STJ.03.1

description: PIDTC Cohort


title: P.STJ.02.1

description: PIDTC Cohort


title: P.STJ.10.1

description: PIDTC Cohort


title: P.STJ.01.1

description: PIDTC Cohort


title: P.SC.07.1

description: PIDTC Cohort


title: P.SC.06.1

description: PIDTC Cohort


title: P139


title: P.SC.04.1

description: PIDTC Cohort


title: P.SC.03.1

description: PIDTC Cohort


title: P.SC.01.1

description: PIDTC Cohort


title: P.MCW.01.1

description: PIDTC Cohort


title: P.Duke.09.1

description: PIDTC Cohort


title: P.Duke.06.1

description: PIDTC Cohort


title: P.SC.02.1

description: PIDTC Cohort


title: P73


title: P.Duke.03.1

description: PIDTC Cohort


title: P.Duke.02.1

description: PIDTC Cohort


title: P.CHP.03.1

description: PIDTC Cohort


title: P.CIN.01.1

description: PIDTC Cohort


title: P.CHP.02.1

description: PIDTC Cohort


title: P.CHOP.07.1

description: PIDTC Cohort


title: P.CHOP.08.1

description: PIDTC Cohort


title: P.STJ.05.1

description: PIDTC Cohort


title: P.STJ.04.1

description: PIDTC Cohort


title: P.CHOP.01.1

description: PIDTC Cohort


title: P.CHLA.07.1

description: PIDTC Cohort


title: P.CHLA.04.1

description: PIDTC Cohort


title: P.CHLA.05.1

description: PIDTC Cohort


title: P.BC.02.1

description: PIDTC Cohort


title: P.ACH.01.1

description: PIDTC Cohort


title: P.ACH.02.1

description: PIDTC Cohort


title: P.BC.01.1

description: PIDTC Cohort


title: SGD.01.1

description: NIH Cohort

value: HealthyPPX

value: Healthy


title: p67.02.1

description: NIH Cohort


title: P.CHLA.03.1

description: PIDTC Cohort


title: P.Duke.10.1

description: PIDTC Cohort


title: p47.23.1

description: NIH Cohort


title: p47.21.1

description: NIH Cohort


title: p47.19.1

description: NIH Cohort


title: p47.20.1

description: NIH Cohort


title: p47.17.1

description: NIH Cohort


title: p47.18.1

description: NIH Cohort


title: P.CHP.01.1

description: PIDTC Cohort


title: p67.01.1

description: NIH Cohort


title: p47.13.1

description: NIH Cohort


title: P.CHOP.06.1

description: PIDTC Cohort


title: p47.14.1

description: NIH Cohort


title: p47.11.1

description: NIH Cohort


title: p47.10.1

description: NIH Cohort


title: p47.09.1

description: NIH Cohort


title: p47.08.1

description: NIH Cohort


title: p47.15.1

description: NIH Cohort


title: p47.06.1

description: NIH Cohort


title: p47.07.1

description: NIH Cohort


title: p47.05.1

description: NIH Cohort


title: p47.03.1

description: NIH Cohort


title: p47.04.1

description: NIH Cohort


title: p47.02.1

description: NIH Cohort


title: p47.01.1

description: NIH Cohort


title: p22.01.1

description: NIH Cohort


title: p22.02.1

description: NIH Cohort


title: p22.04.1

description: NIH Cohort


title: p22.03.1

description: NIH Cohort


title: P.NIH.10.1

description: NIH Cohort


title: P.NIH.05.1

description: NIH Cohort


title: P.NIH.09.1

description: NIH Cohort


title: P.NIH.01.1

description: NIH Cohort


title: P.NIH.03.1

description: NIH Cohort


title: P.NIH.02.1

description: NIH Cohort


title: HV.17.1

description: NIH Cohort


title: p47.12.1

description: NIH Cohort


title: P.NIH.04.1

description: NIH Cohort


title: HV.16.1

description: NIH Cohort


title: HV.14.1

description: NIH Cohort


title: HV.11.1

description: NIH Cohort


title: HV.10.1

description: NIH Cohort


title: HV.09.1

description: NIH Cohort


title: HV.13.1

description: NIH Cohort


title: HV.08.1

description: NIH Cohort


title: HV.04.1

description: NIH Cohort


title: HV.06.1

description: NIH Cohort


title: HV.07.1

description: NIH Cohort


title: HV.02.1

description: NIH Cohort


title: HV.01.1

description: NIH Cohort


title: HABX.01.1

description: NIH Cohort


title: gp91CA.04.1

description: NIH Cohort

value: Carrier

value: CARRIER


title: gp91CA.03.1

description: NIH Cohort


title: gp91.50.1

description: NIH Cohort


title: gp91CA.02.1

description: NIH Cohort

value: HLCARRIER


title: gp91.49.1

description: NIH Cohort


title: gp91.47.1

description: NIH Cohort


title: HV.15.1

description: NIH Cohort


title: gp91.46.1

description: NIH Cohort


title: gp91.48.1

description: NIH Cohort


title: gp91.45.1

description: NIH Cohort


title: gp91.44.1

description: NIH Cohort


title: gp91.42.1

description: NIH Cohort


title: gp91.39.1

description: NIH Cohort


title: gp91.38.1

description: NIH Cohort


title: gp91.41.1

description: NIH Cohort


title: gp91.40.1

description: NIH Cohort


title: HV.05.1

description: NIH Cohort


title: gp91.35.1

description: NIH Cohort


title: gp91.34.1

description: NIH Cohort


title: gp91.33.1

description: NIH Cohort


title: HV.03.1

description: NIH Cohort


title: gp91.32.1

description: NIH Cohort


title: gp91.31.1

description: NIH Cohort


title: gp91.30.1

description: NIH Cohort


title: gp91.29.1

description: NIH Cohort


title: gp91.51.1

description: NIH Cohort


title: gp91.27.1

description: NIH Cohort


title: gp91.25.1

description: NIH Cohort


title: gp91.28.1

description: NIH Cohort


title: gp91CA.01.1

description: NIH Cohort


title: gp91.23.1

description: NIH Cohort


title: gp91.24.1

description: NIH Cohort


title: gp91.22.1

description: NIH Cohort


title: gp91.14.1

description: NIH Cohort


title: gp91.15.1

description: NIH Cohort


title: gp91.16.1

description: NIH Cohort


title: gp91.37.1

description: NIH Cohort


title: gp91.13.1

description: NIH Cohort


title: gp91.19.1

description: NIH Cohort


title: gp91.17.1

description: NIH Cohort


title: gp91.20.1

description: NIH Cohort


title: gp91.07.1

description: NIH Cohort


title: gp91.08.1

description: NIH Cohort


title: gp91.11.1

description: NIH Cohort


title: gp91.12.1

description: NIH Cohort


title: gp91.10.1

description: NIH Cohort


title: gp91.04.1

description: NIH Cohort


title: gp91.03.1

description: NIH Cohort


title: gp91.02.1

description: NIH Cohort


title: gp91.01.1

description: NIH Cohort


title: gp91.26.1

description: NIH Cohort


title: DUOX.01.2

description: NIH Cohort

value: DUOX


title: DUOX.02.1

description: NIH Cohort


title: DUOX.01.1

description: NIH Cohort


title: CGD.08.1

description: NIH Cohort


title: CGD.02.1

description: NIH Cohort


title: BEE0D0, 1_ATAC

status: Public on Oct 17 2023

city: Durham

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

description:
library name:
ICU-58

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cells with > 5% of reads mapping to the mitochondrial genome or > 2,500 genes detected were removed from the analysis. Counts were log-normalized, and the top 2,000 variable features were identified. Principal component analysis was performed using these variable genes, and the top 20 principal components were used for downstream analysis. UMAP dimensionality reduction was performed using the top 20 principal components identified using the Harmony package. Graph-based clustering was performed with resolution = 0.5. Cell types were inferred by using the DatabaseImmuneCellExpressionData() function from the SingleR package. Labels were confirmed by identification of differentially expressed genes using the FindAllMarkers() function from Seurat. For scRNA-seq and scATAC-seq integration, fragment file outputs generated using CellRanger ATAC count were analyzed using ArchR following the standard workflow and with default parameters unless otherwise specified. Cells with a transcription start site enrichment score < 4, cells with fewer than 1000 detected fragments, and putative doublets were removed from downstream analysis. Dimensionality reduction was computed using iterative latent semantic indexing (LSI), and batch effect correction was applied using Harmony. Graph-based clustering was performed using the FindClusters() method from Seurat 3 with resolution = 0.8. UMAP embeddings were calculated with the top 30 principal components from either LSI or Harmony. scRNA-seq cell type annotations were directly transferred to label the scATAC-seq data. Pseudo-scRNA-seq gene expression profiles were estimated for each cell type using the addGeneIntegrationMatrix() function from ArchR during the constrained label transfer procedure.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood mononuclear cells

extract_protocol:
Cryopreserved PBMCs were washed and counted using Countess II FL Automated Cell Counter (ThermoFisher). Nuclei were prepared from 600,000 cells by incubation and wash with chilled Lysis Buffer (10 mM Tris-HCl, pH 7.4 with 10mM NaCl, 3mM MgCl2, 0.01% Tween-20, 0.1% NP-40m 0.01% Digitonin, 1% BSA, 1mM DTT, and 1U/ul RNase inhibitor). Intact nuclei were collected by centrifugation, resuspended in 1X Diluted Nuclei Buffer (10X Genomics) with 1mM DTT and 1U/uL RNase inhibitor, and nuclei concentration and viability determined using Countess II FL with trypan blue.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: peripheral blood mononuclear cells

tag: time

value: FEMALE

tag: cohort

value: Worsening


title: CGD.01.1

description: NIH Cohort


title: 293747, 1_ATAC

description:
library name:
ICU-51

value: MALE


title: 293747, 1_GEX

description:
library name:
ICU-51


title: BEE0D0, 1_GEX

description:
library name:
ICU-58


title: A3674E, 1_ATAC

description:
library name:
ICU-34


title: A3674E, 1_GEX

description:
library name:
ICU-34


title: 36EA16, 1_ATAC

description:
library name:
ICU-18


title: 3E8E37, 0_ATAC

description:
library name:
60036


title: 3E8E37, 0_GEX

description:
library name:
60036


title: gp91.06.1

description: NIH Cohort


title: BEE0D0, 3_GEX

description:
library name:
66518


title: 36EA16, 1_GEX

description:
library name:
ICU-18


title: 293747, 0_GEX

description:
library name:
56915


title: BEE0D0, 3_ATAC

description:
library name:
66518


title: 293747, 0_ATAC

description:
library name:
56915


title: DUOX.02.2

description: NIH Cohort


title: 5717ED, 0_GEX

description:
library name:
56114


title: E1D5C6, 3_ATAC

description:
library name:
5584

value: Control


title: A4423D, 3_ATAC

description:
library name:
56849


title: A4423D, 3_GEX

description:
library name:
56849


title: E6D451, 0_ATAC

description:
library name:
5493


title: 5717ED, 0_ATAC

description:
library name:
56114


title: 96179A, 0_GEX

description:
library name:
54349


title: E1D5C6, 3_GEX

description:
library name:
5584


title: 96179A, 0_ATAC

description:
library name:
54349


title: 2F0D5E, 0_ATAC

description:
library name:
44596


title: 2F0D5E, 0_GEX

description:
library name:
44596


title: E6D451, 0_GEX

description:
library name:
5493


title: A3674E, 0_GEX

description:
library name:
38259


title: A3674E, 0_ATAC

description:
library name:
38259


title: BCCE50, 0_ATAC

description:
library name:
29509


title: BCCE50, 0_GEX

description:
library name:
29509


title: DD170B, 0_ATAC

description:
library name:
16503


title: D99C78, 0_GEX

description:
library name:
19829


title: D99C78, 0_ATAC

description:
library name:
19829


title: DD170B, 0_GEX

description:
library name:
16503


title: 226F26, 0_ATAC

description:
library name:
10152


title: 12B6DB, 0_ATAC

description:
library name:
15192


title: C31FF9, 0_GEX

description:
library name:
39800


title: 0FF381, 0_ATAC

description:
library name:
3737


title: 12B6DB, 0_GEX

description:
library name:
15192


title: 226F26, 0_GEX

description:
library name:
10152


title: animal17007_kidney_RNA

status: Public on Oct 14 2023

city: Basel

first: Remi

last: Terranova

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis Biomedical Research

description:
kidney, F0-treated/F1-control/F2-control, olive oil, 39 days
kidney_RNA_counts.csv
kidney_RNA_avgTxLength.csv

data_processing:
liver: 1x library pool on 2 runs of NovaSeq 6000, S1-100 with 2x50 bp paired-end reads; kidney: 1x library pool on 1 run of NovaSeq 6000, S2-100 with 2x50 bp paired end reads
NovaSeq Control Software 1.7.0 (liver), NovaSeq Control Software 1.7.5 (kidney); RTA v3.4.4; bcl2fastq2.20 v2.20.0.422
Salmon (version 0.14.0) was used to quantify gene expression from fastq files. Each sample was quantified independently, providing fastq files from all sequencing runs if present for the sample, and the following parameters: -l ISR --validateMappings --gcBias.
The quantification results were loaded in R (version 3.5.0) using tximport (1.10.1) to summarize quantification results by gene.
Differential gene expression analysis was performed with DESeq2
Assembly: The index was generated from Rattus norvegicus Ensembl release 100 with parameter -k 31
Supplementary files format and content: The csv files contains gene counts for each sample

source_name: kidney

extract_protocol:
Tissue grinding in liquid nitrogen, RNA extraction with Qiagen RNeasy kit
RNA-seq (polyA mRNA capture); Illumina TruSeq® Stranded mRNA Library Prep with TruSeq UD-indexing

treatment_protocol: Treatment of F0 and F1 with either 100% olive oil or 50% (v/v) CCl4 in olive oil via oral gavage three times a week for 6 weeks followed by 2 weeks recovery before mating. Treatment of F2 with either 100% olive oil, 8% (v/v) CCl4 in olive oil or 50% (v/v) CCl4 in olive oil via oral gavage three times a week for 6 weeks; sampling of liver after 39 days

value: kidney

value: Sprague Dawley

value: male

tag: treatment name

value: olive oil

tag: treatment frequency

value: 3 times per week

tag: treatment administration

value: oral gavage

tag: treatment duration_[days]

tag: treatment dose_[%_v/v]

value: 100 % olive oil

tag: dose volume_[ml/kg]


title: animal20009_kidney_RNA

description:
kidney, F0-treated/F1-treated/F2-control, olive oil, 39 days
kidney_RNA_counts.csv
kidney_RNA_avgTxLength.csv

tag: Sex


title: animal20004_kidney_RNA

tag: strain


title: animal20005_kidney_RNA


title: animal17001_kidney_RNA


title: animal17004_kidney_RNA


title: animal17010_kidney_RNA


title: animal20007_kidney_RNA


title: animal20010_kidney_RNA


title: animal17009_kidney_RNA


title: animal20001_kidney_RNA


title: C31FF9, 0_ATAC

description:
library name:
39800

tag: age


title: animal14010_kidney_RNA

description:
kidney, F0-control/F1-treated/F2-control, olive oil, 39 days
kidney_RNA_counts.csv
kidney_RNA_avgTxLength.csv


title: animal17002_kidney_RNA


title: animal20002_kidney_RNA


title: animal14007_kidney_RNA


title: animal14009_kidney_RNA


title: animal14005_kidney_RNA


title: animal14001_kidney_RNA


title: 0FF381, 0_GEX

description:
library name:
3737


title: animal11009_kidney_RNA

description:
kidney, F0-control/F1-control/F2-control, olive oil, 39 days
kidney_RNA_counts.csv
kidney_RNA_avgTxLength.csv


title: animal11010_kidney_RNA


title: animal11007_kidney_RNA


title: animal11004_kidney_RNA


title: animal11002_kidney_RNA


title: animal11005_kidney_RNA


title: animal11001_kidney_RNA


title: MuSC IP77, 100 ng/ml BMP6 (solved in 4 mM HCl containing 0.1% BSA) for 1 hour, replicate 2

status: Public on Oct 01 2023

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP77_B
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP77_B

data_processing:
FASTQ files were aligned to the mouse genome: GeneCode M32 (GRCm39) using STAR v2.7.11a with the following settings: --runThreadN 36 --outReadsUnmapped Fastx --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --seedSearchStartLmax 25 --alignSoftClipAtReferenceEnds No --outSAMattrIHstart 0 --alignEndsType EndToEnd --twopassMode Basic. The resulting *.bam file was sorted and indexed using samtools v1.17.
The sorted *.bam file was passed to StringTie v2.2.1 with the following settings: -u -p 36. The resulting *.gtf files were merged using stringtie merge and normalized read counts (TPM and FPKM) were generated using stringtie ballgown. The read counts of all experimental samples were then concatenated into a single table: output.tpm.csv and output.fpkm.csv.
Genome_build: GeneCode M32 (GRCm39)
Supplementary_files_format_and_content: Stringtie ballgown output files: *.cov.refs.ballgown.gtf => contains details of the transcripts that StringTie assembles from RNA-Seq data in the GTF format; *.gene_abund.ballgown.tab => contains gene abundance counts as normalized FPKM and TPM values as a CSV table; *.out.ballgown.gtf => This is a file listing all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
Supplementary_files_format_and_content: FPKM_joined.tab, FPKM_joined.csv, TPM_joined.tab, TPM_joined.csv => fused tables with all the samples of the experiment in CSV and EXCEL format provided as TPM and FPK values.

source_name: muscle

growth_protocol: Muscle stem cells were isolated from muscle of female 6-8-week-old mice, cultured on Matrigel® for expansion over 2 days. In order to limit the effect of BMPs in the culture medium (e.g. from serum supplements), cells were cultured prior to the BMP stimulation for 6 h in serum-free medium containing BMP soluble receptor (recombinant mouse BMPR-IA/ALK3-Fc Chimera, R&D Systems, 437-MR) in a concentration of 200 ng/ml.

extract_protocol:
Cells were lysed directly in their dish, homogenized, and stored at -80°C for subsequent RNA isolation. Lysis (RLT buffer+10% beta-ME), homogenization (QIAshredder, Qiagen), and total RNA extraction were done according to the manual of the RNeasy Micro kit (Qiagen, Hilden, Germany). The RNA concentration was measured using the NanoDrop2000 photometer and aliquots of 1-2 µg RNA were snap-frozen in liquid nitrogen and stored at -80°C.
The construction of the eukaryotic strand-specific transcriptome library was performed according to the ?SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing Kit (Illumina). Briefly, 500 ng total RNA was enriched for polyA-carrying molecules using oligo-dT beads. The RNA was then fragmented and the first cDNA strand was synthesized using random primers. Second strand cDNA was synthesized and the resulting cDNA was subjected to end repair and 3' adenylation. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments, which were then amplified by PCR.
The library was then sequenced on a Illumina HiSeq 4000 machine as 50 bp single-end reads with an intended sequencing depth of >40 Mio reads. After removing of the sequencing adapters, the resulting FASTQ files were finally filtered for the desired length of 50 bp and for quality scores of Phred+33.

treatment_protocol: Cells were stimulated with a one-hour pulse with 100 ng/ml BMP4 or BMP6 or only with vehicle used for reconstitution of BMP in the case of controls.

value: 100 ng/ml BMP6

value: muscle stem cells

value: wildtype (C57BL/6J)

tag: biological replicate


title: MuSC IP54, 100 ng/ml BMP4 (solved in 4 mM HCl containing 0.1% BSA) for 1 hour, replicate 2

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP54_B
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP54_B

value: 100 ng/ml BMP4

tag: cell type


title: CRISPR guide library 1 - timepoint 3 (day 14)

status: Public on Sep 30 2023

description: 10x Genomics

data_processing:
Sequencing data was processed with the CellRanger software.
Further processing was performed with the R package Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: annotated h5ad file

source_name: bone marrow

growth_protocol: ProT cells were grown in presence of Dll4, Scf and Il7

extract_protocol:
RNA and CRISPR guides were extracted at 3 timepoint: 3, 7 and 14 days after transduction
Library was performed according to the manufacter’s instructions ( 10x Genomics 3' end scRNA with feature barcoding).
scRNA-seq with feature barcoding for the gRNAs

treatment_protocol: Cells were transduced with a CRISPR guide library targeting respectively 17 and 42 genes (5 gRNAs per gene) together with positive and negative controls. The retroviral vector contains a capture sequence that can be recognized by the feature barcoding of 10x Genomics.

value: bone marrow

tag: cell line

value: ProT

value: transduced with CRISPR library


title: MuSC IP48, Vehicle (4 mM HCl containing 0.1% BSA) for 1 hour, replicate 1

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP48_A
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP48_A

value: vehicle (control)

tag: genotype


title: MuSC IP75, Vehicle (4 mM HCl containing 0.1% BSA) for 1 hour, replicate 1

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP75_A
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP75_A


title: MuSC IP77, Vehicle (4 mM HCl containing 0.1% BSA) for 1 hour, replicate 2

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP77_A
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP77_A


title: animal14004_kidney_RNA

tag: tissue


title: CRISPR guide library 2 - timepoint 2 (day 7)

description: 10x Genomics

tag: treatment


title: TLX1-48h-3

status: Public on Sep 16 2023

data_processing:
cleaning with fastq-mcf
quality control with FastQC
mapping with HISAT2, further processing with SAMTools
counting abundances with htseq-count
Assembly: mm10
Supplementary files format and content: tab delimited text file with raw counts

source_name: ProT CreER

tag: agent

value: tamoxifen

tag: time point

value: ProT CreER


title: MuSC IP75, 100 ng/ml BMP6 (solved in 4 mM HCl containing 0.1% BSA) for 1 hour, replicate 1

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP75_B
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP75_B


title: MuSC IP54, Vehicle (4 mM HCl containing 0.1% BSA) for 1 hour, replicate 2

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP54_A
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP54_A


title: CRISPR guide library 2 - timepoint 3 (day 14)

description: 10x Genomics


title: HCFs, non-targeting control siRNA, 48 hrs, rep2

status: Public on Sep 22 2023

city: Rochester

first: Duan

last: Liu

email: liud25@gmail.com, liu.duan@mayo.edu

state: MN

address: 200 1st ST SW

department: MPET

institute: Mayo Clinic

data_processing:
RNA sequencing quality was determined with FastQC.
Sequencing reads were aligned to human genome using STAR.
Raw counts were generated with featureCounts.
Differential expression analysis was conducted with the EdgeR package using R
Assembly: hg38
Supplementary files format and content: tab-delimited text files  which is a matrix table with raw gene counts for every gene and every sample.

source_name: Primary HCF

growth_protocol: Cryopreserved adult human cardiac fibroblasts (HCFs) were purchased from Cell Applications, Inc. (Cat#:306V-05a, San Diego, CA). Cell culture and subculture were performed following the manufacturer’s Instructions for HCF Culture.

extract_protocol:
Total RNA was extracted with TRIzol® Reagent (ThermoFisher) and the miRNAeasy kit (QIAGEN) per the manufacturer’s instructions.
RNA-seq libraries were generated using the Illumina TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA) following the manufacturer’s protocol.

value: Primary HCF

value: cardiac fibroblast


title: MuSC IP48, 100 ng/ml BMP4 (solved in 4 mM HCl containing 0.1% BSA) for 1 hour, replicate 1

description:
GSE159594_TPM_joined.tab: TPM_BGI_1_IP48_B
GSE159594_FPKM_joined.tab: FPKM_BGI_1_IP48_B


title: TLX1-48h-1


title: CRISPR guide library 1 - timepoint 2 (day 7)

description: 10x Genomics


title: TLX1-24h-3


title: animal14002_kidney_RNA

value: kidney

value: Sprague Dawley

value: male

tag: treatment name


title: TLX3-48h-3


title: TLX1-48h-2


title: TLX1-24h-2


title: TLX3-48h-2


title: TLX1-24h-1


title: TLX3-48h-1


title: TLX3-24h-2


title: TLX3-24h-1


title: DMSO-48h-3

value: DMSO


title: HCFs, non-targeting control siRNA, 48 hrs, rep1


title: CRISPR guide library 2 - timepoint 1 (day 3)

description: 10x Genomics


title: CRISPR guide library 1 - timepoint 1 (day3)

description: 10x Genomics


title: DMSO-24h-3


title: DMSO-48h-1


title: DMSO-48h-2


title: DMSO-24h-1


title: TLX3-tam-24h-2


title: TLX3-tam-6h-2


title: TLX3-tam-0h-3


title: ProT-FL3-TLX3-V5-3


title: TLX3-24h-3


title: TLX3-tam-6h-3


title: ProT-CreER-1


title: TLX3-tam-6h-1


title: animal22010_liver_RNA

status: Public on Sep 06 2023

data_processing:
1x library pool on 2 runs of NovaSeq 6000, S1-100 with 2x50 bp paired-end reads
NovaSeq Control Software 1.7.0; RTA v3.4.4; bcl2fastq2.20 v2.20.0.422
Salmon (version 0.14.0) was used to quantify gene expression from fastq files. Each sample was quantified independently, providing fastq files from all sequencing runs if present for the sample, and the following parameters: -l ISR --validateMappings --gcBias.
The quantification results were loaded in R (version 3.5.0) using tximport (1.10.1) to summarize quantification results by gene.
Differential gene expression analysis was performed with DESeq2
Assembly: The index was generated from Rattus norvegicus Ensembl release 100 with parameter -k 31
Supplementary files format and content: The csv files contains gene counts for each sample

source_name: liver, F0-treated/F1-treated/F2-treated, 50% CCl4, 39 days

extract_protocol:
Tissue grinding in liquid nitrogen, RNA extraction with Qiagen RNeasy kit
Illumina TruSeq® Stranded mRNA Library Prep with TruSeq UD-indexing

value: liver

value: CCl4, high dose

tag: treatment frequency

value: 3 times per week

value: oral gavage

value: 50 % CCl4 in olive oil


title: TLX3-tam-24h-3

extract_protocol:
RNA extraction was performed using a Promega Maxwell, using the Maxwell RSC simplyRNA Cells Kit
RNA libraries were prepared for sequencing using standard Illumina protocols


title: animal22007_liver_RNA

tag: treatment administration


title: DMSO-24h-2


title: animal22005_liver_RNA

tag: treatment duration_[days]


title: ProT-CreER-3


title: animal22009_liver_RNA

tag: treatment dose_[%_v/v]


title: TLX3-tam-0h-2


title: ProT-FL3-TLX3-V5-1


title: animal22004_liver_RNA

tag: dose volume_[ml/kg]


title: animal22001_liver_RNA

tag: Sex


title: animal22002_liver_RNA

tag: strain


title: animal21009_liver_RNA

source_name: liver, F0-treated/F1-treated/F2-treated, 8% CCl4, 39 days

value: CCl4, low dose

value: 8 % CCl4 in olive oil


title: animal21010_liver_RNA


title: animal21005_liver_RNA


title: TLX3-tam-24h-1


title: TLX3-tam-0h-1


title: animal21007_liver_RNA


title: ProT-FL3-TLX3-V5-2


title: ProT-CreER-2


title: animal21001_liver_RNA


title: animal21004_liver_RNA


title: animal20009_liver_RNA

source_name: liver, F0-treated/F1-treated/F2-control, olive oil, 39 days

value: olive oil

value: 100 % olive oil


title: animal20007_liver_RNA


title: animal21002_liver_RNA


title: animal20004_liver_RNA


title: animal20001_liver_RNA


title: animal20002_liver_RNA


title: animal19010_liver_RNA

source_name: liver, F0-treated/F1-control/F2-treated, 50% CCl4, 39 days


title: animal20005_liver_RNA


title: animal19009_liver_RNA


title: animal19005_liver_RNA


title: animal19007_liver_RNA


title: animal19004_liver_RNA


title: animal19002_liver_RNA


title: animal18008_liver_RNA

source_name: liver, F0-treated/F1-control/F2-treated, 8% CCl4, 39 days


title: animal19001_liver_RNA


title: animal18006_liver_RNA


title: animal18003_liver_RNA


title: animal18004_liver_RNA


title: animal18001_liver_RNA


title: animal17010_liver_RNA

source_name: liver, F0-treated/F1-control/F2-control, olive oil, 39 days


title: animal17009_liver_RNA


title: animal17007_liver_RNA


title: animal18002_liver_RNA


title: animal20010_liver_RNA


title: animal17002_liver_RNA


title: animal17001_liver_RNA


title: animal16005_liver_RNA

source_name: liver, F0-control/F1-treated/F2-treated, 50% CCl4, 39 days


title: animal16002_liver_RNA


title: animal16010_liver_RNA


title: animal16007_liver_RNA


title: animal16004_liver_RNA


title: animal15007_liver_RNA

source_name: liver, F0-control/F1-treated/F2-treated, 8% CCl4, 39 days


title: animal15005_liver_RNA


title: animal16001_liver_RNA


title: animal15010_liver_RNA


title: animal18010_liver_RNA


title: animal15001_liver_RNA


title: animal15009_liver_RNA


title: animal15002_liver_RNA


title: animal14005_liver_RNA

source_name: liver, F0-control/F1-treated/F2-control, olive oil, 39 days


title: animal14010_liver_RNA


title: animal14009_liver_RNA


title: animal14007_liver_RNA


title: animal14004_liver_RNA


title: animal14002_liver_RNA


title: animal17004_liver_RNA


title: animal14001_liver_RNA


title: animal13009_liver_RNA

source_name: liver, F0-control/F1-control/F2-treated, 50% CCl4, 39 days


title: animal13007_liver_RNA


title: animal16009_liver_RNA


title: animal13002_liver_RNA


title: animal13004_liver_RNA


title: animal12010_liver_RNA

source_name: liver, F0-control/F1-control/F2-treated, 8% CCl4, 39 days


title: animal12009_liver_RNA


title: animal12004_liver_RNA


title: animal12005_liver_RNA


title: animal12002_liver_RNA


title: animal12001_liver_RNA


title: animal13001_liver_RNA


title: animal11010_liver_RNA

source_name: liver, F0-control/F1-control/F2-control, olive oil, 39 days


title: animal11009_liver_RNA


title: animal11007_liver_RNA


title: animal13005_liver_RNA


title: animal11001_liver_RNA


title: animal11005_liver_RNA


title: animal11002_liver_RNA


title: animal15004_liver_RNA


title: STUDY, replicate 2, scRNAseq

status: Public on Jun 01 2023

first: Lillian

last: Tran

state: Pennsylvania

address: 200 Lothrop Street

department: Surgery

description:
10x Genomics
DCREG_STUDY 002

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Filtered gene-barcode matrices generated using the 10X Genomics Cell Ranger analysis pipeline were pre-processed and analyzed with the R package Seurat version 4.0
Cells with detected gene number between 500 and 6000, mitochondrial gene percentage < 35%, and hemoglobin gene percentage < 0.5% were kept for further downstream analysis
Assembly: Hg38
Supplementary files format and content: matrix files

source_name: Liver allograft

extract_protocol:
Freshly collected 18g core biopsy of liver allograft tissue obtained 12 months post-transplant from 4 STUDY and 4 SOC living donor liver transplant patients was minced into small pieces and incubated with 1 mg/ml collagenase digestion solution at 37 °C for 8 minutes. The isolated liver cell suspensions were resuspended in 20%∆ FCS, 2mM EDTA, 1XPBS solution. Cells were washed and re-suspended in 4% Ultrapure BSA/1x DPBS
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: non-parenchymal, parenchymal

value: Liver allograft

value: Regulatory dendritic cell therapy

tag: time

value: 12 months post-transplant


title: FLC NML tumor RNA-seq sample #6

status: Public on May 27 2023

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

state: NY

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

description:
FLC and non-malignant liver samples were collected from female and male FLC patients.
RNA-seq. Gene expression was analyzed in FLC and non-malignant liver (NML) samples.
NML_FLC26_ICBQ

data_processing:
Sequencing was aligned and quantified using STAR/Salmon (RNA-seq).
RNA-seq data was normalized using DESeq2.
Assembly: Paired end RNA sequencing results were aligned to the human genome (hg38) using STAR (v2.4.2a) and quantified using Salmon (v0.8).
Supplementary files format and content: Normalized counts

source_name: FLC tumor samples

extract_protocol:
Libraries were prepared using the NEBNext Ultra II Directional Library Prep Kit following PolyA enrichment at the Cornell Transcriptional Regulation and Expression Facility (Cornell University, Ithaca, NY).
RNA was isolated from the new cohort using the Total RNA Purification Kit (Norgen Biotek).

value: FLC tumor samples

tag: Stage

value: tumor stage


title: animal13010_liver_RNA

value: Sprague Dawley

value: male


title: Old_LinNeg_ATAC

status: Public on Mar 28 2023

city: Cambridge

first: Jason

last: Buenrostro

state: MA

address: 7 Divinity Ave

institute: Harvard University

description:
Old_LinNeg.fragments.tsv.gz
mouse_HSC_aging_peaks.bed.gz
mouse_HSC_aging_ATAC_cell_meta.txt.gz
mouse_HSC_aging_ATAC_count_matrix.txt.gz

data_processing:
Data processing was performed using CellRanger pipeline
Assembly: mm10
Supplementary files format and content: Old_HSC.fragments.tsv.gz, Old_LinNeg.fragments.tsv.gz, Young_HSC.fragments.tsv.gz, Young_LinNeg.fragments.tsv.gz
Supplementary files format and content: mouse_HSC_aging_peaks.bed.gz
Supplementary files format and content: mouse_HSC_aging_ATAC_cell_meta.txt.gz
Supplementary files format and content: mouse_HSC_aging_ATAC_count_matrix.txt.gz
Supplementary files format and content: File for ATAC fragments. Tab-delimited table with 4 columns: Chromosome, start coordinate, end coordinate, cell barcode.
Supplementary files format and content: Bed file for ATAC peak ranges. Tab-delimited table with 3 columns: Chromosome, start coordinate, end coordinate.
Supplementary files format and content: Tab-delimited text file of cell metadata. Each row corresponds to a cell and each column is a metadata feature.
Supplementary files format and content: Tab-delimited text file of single cell ATAC read counts. Each row corresponds to an ATAC peak and each column is a cell.

source_name: Bone marrow

growth_protocol: Mouse experiments were approved and performed in compliance with Harvard University’s Institutional Animal Care and Use Committee. C57BL6 mice were obtained from either Jackson Laboratory or the National Institute on Aging Aged Rodent Colony (Charles River Laboratory), and housed at a density of 2-5 mice per cage in standard ventilated racks and provided food and water ad libitum in a pathogen-specific free facility accredited by the Association and Accreditation of Laboratory Animal Committee (AALAC). Mouse cages contained Anderson’s Bed o Cob bedding (The Anderson, Inc), two nestlets (Ancare, 2x2” compressed cotton square), and a red mouse hut (Bioserv)

extract_protocol: 10x Multiomic sequencing

treatment_protocol: For HSC isolation and flow cytometry. Cells from the bone marrow of long bones (2 femurs and 2 tibias per mouse) from young (n=10; 11 weeks old) and aged (n=5; 24 mo. old) male C57BL/6 mice were flushed with a 21-gauge needle into staining media (HBSS/2% fetal bovine serum), pelleted, and resuspended in ACK lysis buffer for 5 min on ice. Cells were then washed with staining media, filtered through a 40mm cell strainer, pelleted, and incubated with the following cocktail of  rat anti-mouse, biotin conjugated lineage antibodies on ice for 30 min: CD3 clone C145-2c11 (Biolegend, 1000304; 1:100), CD4 clone GK15 (Biolegend, 1000404; 1:400), CD5 clone 53-7.3 (eBioscience, 13-0051-85; 1:400), CD8 clone 53-6.7 (Biolegend, 100704; 1:400), CD19 clone 6D5 (Biolgend, 115504; 1:400), B220 clone RA3-6B2 (Biolegend, 103204; 1:200), GR1 (Ly6-G/Ly6-C) clone RB6-8C5 (eBioscience, 13-5931-82; 1:400), Mac1/CD11b clone M1/70 (Biolegend, 101204; 1:800), and Terr119 clone TERR-119 (Biolegend, 116204; 1:100). Cells were then washed in staining media, with a small aliquot reserved for each sample to serve as a non-depleted control, and lineage depleted using sheep anti-rat Dynabeads (Invitrogen, 1135) on a magnet. Cells were washed, pelleted, and incubated with the following cocktail of anti-mouse antibodies on ice for 45 min. to identify hematopoietic stem cells (HSC): Pacific Orange Streptavidin (Invitrogen, S32365; 1:500), PE/Cy7 Sca1(Ly-6a/E) clone D7 (eBioscience, 25-5981-82; 1:200), APC cKit clone 2B8 (BD Pharmingen, 553356; 1:200), FITC CD48 clone HM48-1 (Biolegend, 103403; 1:200), and PE CD150 clone Tc15-12F12.2 (Biolegend, 115904; 1:200). Following incubation, cells were washed and resuspended in staining media, and 7-AAD (BD Pharmingen, 559925; 1:50) added immediately prior to flow cytometry. Cell sorting of HSCs (Live Lin- Sca1+ cKit+ CD48- CD150+) was performed on a BD FACS Aria II, and data analysis performed using BD FACS Diva and FlowJo software

value: Bone marrow

tag: cell type

value: Hematopoietic progenitors

tag: age

value: 24 weeks


title: Old_HSC_ATAC

description:
Old_HSC.fragments.tsv.gz
mouse_HSC_aging_peaks.bed.gz
mouse_HSC_aging_ATAC_cell_meta.txt.gz
mouse_HSC_aging_ATAC_count_matrix.txt.gz

value: Hematopoietic stem cells


title: Young_LinNeg_ATAC

description:
Young_LinNeg.fragments.tsv.gz
mouse_HSC_aging_peaks.bed.gz
mouse_HSC_aging_ATAC_cell_meta.txt.gz
mouse_HSC_aging_ATAC_count_matrix.txt.gz

value: 11 months


title: RIP N PGC-1α-KD MB + FLAG-RIP N PGC-1α(CBM5mut), rep #3

status: Public on Jan 19 2023

first: Lynne

last: Maquat

state: New York

address: 601 Elmwood Ave # 712

institute: University of Rochester

data_processing:
Adapter sequences are trimmed using fastp v0.20.0
Processed reads are aligned to the mouse reference genome GRCm38 using STAR v2.7.2c
Parameters outFilterScoreMinOverLread and outFilterMatchNminOverLread are set to 0.5
Genome_build: GRCm38v23

source_name: C2C12 myoblasts stably expressing a PGC-1α-mRNA-targeting shRNA

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco) containing 15% fetal bovine serum (VWR), 1% penicillin/streptomycin (Gibco), and 1 µg/ml puromycin (Gibco)

extract_protocol:
Total RNA was extracted using TRIzolTM reagent, purified by ethanol precipitation
"Lysates of cells were subjected to IP using anti-FLAG as previously described (Cho et al., 2018) with the following modifications. IPs utilized Anti-FLAG® M2 Magnetic Beads (Millipore), immunoprecipitates were washed twice with NET2 Buffer supplemented to 150 mM NaCl, twice with NET2 Buffer supplemented to 300 mM NaCl, and once with NET2 Buffer supplemented to 150 mM NaCl.  For native RIP-seq, contaminating genomic DNA was degraded using RQ1 RNase-free DNase in the presence of 0.4 U/µl of RNase OUT, and RNA was purified by phenol extraction and precipitated using ethanol. cDNA libraries were prepared using a TruSeq RNA Library Prep Kit v2 (Illumina) with the following modification: 20 ng of immunoprecipitated RNA was not subjected to poly(A)+ enrichment but rather directly fragmented, shortening the fragmentation time to 4 min.

treatment_protocol: Cells were transiently transfected per 6-cm diameter dish with 2 µg of plasmid DNA using 10 µl of LipofectamineTM 2000 (Invitrogen), and harvested ~48h post-transfection.

tag: cell lines

value: PGC-1a-KD MB

tag: transfection

tag: ip antibody

value: anti-FLAG (M2)


title: RIP N PGC-1α-KD MB + FLAG-RIP N PGC-1α(CBM5mut), rep #2


title: RIP N PGC-1α-KD MB + FLAG-RIP N PGC-1α(CBM5mut), rep #1


title: RIP N PGC-1α-KD MB + FLAG-RIP N PGC-1α(WT), rep #3


title: RIP N PGC-1α-KD MB + FLAG-RIP N PGC-1α(WT), rep #1


title: RIP N PGC-1α-KD MB + FLAG, rep #3


title: RIP N PGC-1α-KD MB + FLAG-RIP N PGC-1α(WT), rep #2


title: RIP N PGC-1α-KD MB + FLAG, rep #2


title: RIP N PGC-1α-KD MB + FLAG, rep #1


title: PRO PGC-1α-KD MB + FLAG, rep #2

description:
KD_FLAG_F._normD1.37.bw
KD_FLAG_R._normD1.37.bw

data_processing:
Library strategy: PRO-seq
Dual, 6nt UMIs extracted from FASTQs and subsequently used to deduplicate mapped reads, both using UMI-tools 1.1.1
Low-quality bases trimmed from 3’ ends with a cutoff score of 10, followed by adapter removal using cutadapt 1.14. Read pairs with either trimmed read falling shorter than 20nt filtered.
Read pairs mapped to combined mm10/dm6 index using BWA-MEM 0.7.17 (-L 100,5) and separated according to primary/spike genome using samtools 1.3.1
PROseq strand-specific bedGraphs generated using custom scripts based on 3' mapping location of end 1 reads only, with all replicates combined
Genome_build: mm10
Supplementary_files_format_and_content: bigwig containing combined count of end 1 3' mapping locations for all replicates for a given treatment

growth_protocol: Cells  were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco) containing 15% fetal bovine serum (VWR), 1% penicillin/streptomycin (Gibco), and 1 µg/ml puromycin (Gibco)

extract_protocol:
nascent biotin-labeled RNA was isolated from permeabilized cells, essentially as described in Elrod et al., Mol. Cell, 2019
PRO-seq libraries, essentially as described in Reimer et al., Mol. Cell, 2021


title: PRO PGC-1α-KD MB + FLAG, rep #1


title: STUDY, replicate 3, scRNAseq

description:
10x Genomics
DCREG_STUDY 003

tag: tissue

tag: treatment


title: PRO PGC-1α-KD MB + FLAG-PGC-1α(CBM5mut), rep #1

description:
KD_5mut_F._normD1.00.bw
KD_5mut_R._normD1.00.bw

value: pcDNA3xFLAG- PGC-1a(CBM5mut)


title: PRO PGC-1α-KD MB + FLAG-PGC-1α(WT), rep #2

description:
KD_WT_F._normD1.20.bw
KD_WT_R._normD1.20.bw

value: pcDNA3xFLAG- PGC-1a(WT)


title: PRO PGC-1α-KD MB + FLAG-PGC-1α(CBM5mut), rep #2


title: PRO CTL MBs + FLAG, rep #1

description:
WT_FLAG_F._normD1.23.bw
WT_FLAG_R._normD1.23.bw

source_name: C2C12 myoblasts stably expressing a control GFP-mRNA-targeting shRNA

value: CTL C2C12 MBs


title: RNA PGC-1α-KD MB + FLAG-RNA PGC-1α(CBM5mut), rep #2

data_processing:
Adapter sequences are trimmed using fastp v0.20.0
Processed reads are aligned to the mouse reference genome GRCm38 using STAR v2.7.2c
Parameters outFilterScoreMinOverLread and outFilterMatchNminOverLread are set to 0.3
Genome_build: GRCm38v23
Supplementary_files_format_and_content: bigWig containing normalized coverage for a given treatment and replicate

extract_protocol:
Total RNA was extracted using TRIzolTM reagent, purified by ethanol precipitation
Purified total cell-RNA was diluted in 2× Alkaline Fragmentation Solution (12 mM Na2CO3, 88 mM NaHCO3), incubated for 2−5-minutes at 95°C to generate ~20−100-nucleotide RNA fragments, and precipitated using ethanol. Contaminating genomic DNA was degraded using RQ1 RNase-free DNase (Promega) in the presence of 0.4 U/µl of RNase OUT (Invitrogen). RNA was purified by phenol extraction and precipitated using ethanol. DNA-free RNA (500 ng) was decapped using RNA 5´ pyrophosphohydrolase (RppH; New England Biolabs), purified using TRIzol extraction, and precipitated overnight at 4°C using isopropanol. RNA 5´ and 3´ ends were dephosphorylated using recombinant Shrimp Alkaline Phosphatase (rSAP) (New England Biolabs), rSAP was heat-inactivated, and RNA 5´ends were re-phosphorylated using T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of RNase OUT. RNA with repaired ends was purified using Monarch® RNA Cleanup Kit (New England Biolabs). cDNA libraries were prepared using a NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, Version 8.0_10/20 protocol). PCR products of 140–300-bp were size-selected using Pippin HT (Sage Science).


title: animal11004_liver_RNA

value: liver

tag: treatment name

value: olive oil

value: 3 times per week

value: oral gavage

value: 100 % olive oil


title: PRO CTL MBs + FLAG, rep #2


title: RNA PGC-1α-KD MB + FLAG-RNA PGC-1α(CBM5mut), rep #1


title: RNA PGC-1α-KD MB + FLAG-RNA PGC-1α(WT), rep #3


title: RNA PGC-1α-KD MB + FLAG-RNA PGC-1α(WT), rep #2


title: Young_HSC_ATAC

description:
Young_HSC.fragments.tsv.gz
mouse_HSC_aging_peaks.bed.gz
mouse_HSC_aging_ATAC_cell_meta.txt.gz
mouse_HSC_aging_ATAC_count_matrix.txt.gz


title: RNA PGC-1α-KD MB + FLAG-RNA PGC-1α(WT), rep #1


title: RNA PGC-1α-KD MB + FLAG-RNA PGC-1α(CBM5mut), rep #3


title: RIP FP PGC-1α-KD MB + FLAG-RIP FP PGC-1α(CBM5mut), rep #2

extract_protocol:
Total RNA was extracted using TRIzolTM reagent, purified by ethanol precipitation
Lysates of cells were subjected to IP using anti-FLAG as previously described (Cho et al., 2018) with the following modifications. IPs utilized Anti-FLAG® M2 Magnetic Beads (Millipore), immunoprecipitates were washed twice with NET2 Buffer supplemented to 150 mM NaCl, twice with NET2 Buffer supplemented to 300 mM NaCl, and once with NET2 Buffer supplemented to 150 mM NaCl.  For RIP-seq footprinting, washed immunoprecipitates were digested on-bead using 2 U/μL RNase I for 30 minutes at 4°C so as to generate ~20−100-nucleotide RNP fragments, i.e. PGC-1α or control RNA footprints. Immunoprecipitated RNA fragments were purified using TRIzol and precipitated using ethanol. Contaminating genomic DNA was degraded using RQ1 RNase-free DNase (Promega) in the presence of 0.4 U/µl of RNase OUT (Invitrogen). RNA was purified by phenol extraction and precipitated using ethanol. DNA-free RNA (500 ng) was decapped using RNA 5´ pyrophosphohydrolase (RppH; New England Biolabs), purified using TRIzol extraction, and precipitated overnight at 4°C using isopropanol. RNA 5´ and 3´ ends were dephosphorylated using recombinant Shrimp Alkaline Phosphatase (rSAP) (New England Biolabs), rSAP was heat-inactivated, and RNA 5´ends were re-phosphorylated using T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of RNase OUT. RNA with repaired ends was purified using Monarch® RNA Cleanup Kit (New England Biolabs). cDNA libraries were prepared using a NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, Version 8.0_10/20 protocol). PCR products of 140–300-bp were size-selected using Pippin HT (Sage Science).


title: animal12007_liver_RNA

value: Sprague Dawley

value: CCl4, low dose

tag: treatment frequency

value: 8 % CCl4 in olive oil


title: RNA PGC-1α-KD MB + FLAG, rep #2


title: RIP FP PGC-1α-KD MB + FLAG-RIP FP PGC-1α(WT), rep #2


title: PRO PGC-1α-KD MB + FLAG-PGC-1α(WT), rep #1


title: RIP FP PGC-1α-KD MB + FLAG-RIP FP PGC-1α(WT), rep #1


title: RIP FP PGC-1α-KD MB + FLAG, rep #1


title: MV411.PolIIS2P.TDI-055.2h [ChIP-Seq]

status: Public on Oct 05 2022

city: Philadelphia

first: Liling

last: Wan

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Basecalls performed using CASAVA version 1.4
Raw reads were aligned to the UCSC hg-19 genome sequence build from the Bsgenome.Hsapiens.UCSC.hg19 Bioconductor package using the Rsubread v 2.26 package's align function
Aligned BAM files were sorted using function sortBam from Rsubread v 2.2.6. Secondary alignments, unmapped reads, and duplicate reads in the sorted bam files were filtered out using sambamba v 0.7.1. The filtered and sorted bam files were then indexed using function indexBam from Rsubread v 2.2.6.
peaks were called using MACS v 2.2.7.1, peaks were called at P ≤ 1 × 10−8.
filtered, sorted, indexed BAM files were converted to bigwig files using bamCoverage from deeptools v3.5.0
Assembly: hg19
Supplementary files format and content: bigWig files are in an indexed binary format

source_name: MV411 cells

growth_protocol: Human leukaemia cell lines were maintained in RPMI 1640 (Fisher scientific, #MT10040CV) supplemented with 10% FBS (HyClone, #SH30910.03) and 100 U ml−1 penicillin/streptomycin  (Fisher scientific, #15-140-122).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq sample libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, #E7645L) following the manufacturer's instructions.  After adapter ligation, DNA was PCR amplified with Illumina primers for indicated cycles and the DNA size distribution was quantified on an Agilent Bioanalyzer DNA chip ( Agilent, #5067-1504). Then samples were sequenced using Illumina NextSeq500 or NextSeq2000.

treatment_protocol: Human leukemia cells were treated with DMSO or 5 uM TDI-055 for 0.5 or 2 hour

value: Leukemia cell line

tag: chip antibody

value: Pol II S2P antibody

tag: cell line


title: First tarsal segment, male, 30h APF, scRNA-seq

status: Public on Oct 13 2022

first: Ben

last: Hopkins

department: Evolution & Ecology

institute: UC Davis

description: 10x Genomics

data_processing:
The alignment, barcode assignment, and UMI counting of the two 10x leg samples were performed using the ‘count’ function in CellRanger (v4.0.0). The reference index was built using the ‘mkref’ function in CellRanger (v3.1.0) and the Ensembl BDGP6.28 Drosophila melanogaster genome. The GTF was filtered to remove non-polyA transcripts that overlap with protein-coding gene models, as recommended in the CellRanger tutorial (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr).
Assembly: Ensembl BDGP6.28
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: First tarsal segment

extract_protocol:
White P1 prepupae (0-1 hour After Puparium Formation, APF) from the DGRP line RAL-517 (Mackay et al., 2012) were collected and sexed based on the presence of testes. Males were transferred to a folded kimwipe, wet with 500µl of water and held inside of a petri dish in an incubator maintained at 25°C on a 12:12 cycle. 1h before the desired age was reached (e.g. 23h after collection for the 24h sample), pupae were removed from puparia using forceps and placed on top of a water-soaked kimwipe. When the desired age was reached, pupae were placed ventral side up on tape. The base of the abdomen was pierced to release some of the fluid pressure and the foreleg removed at the tibia/tarsal joint. The dissected leg was then placed on tape, covered in a drop of 1X Dulbecco’s PBS (DPBS, Sigma, D8537), and a scalpel was used to sever at approximately the mid-point of the second tarsal segment. The first tarsal segment was then eased out of the pupal cuticle and transferred to a glass well on ice containing 100µl of 1X DPBS using a BSA-coated tip. We separately prepared two single cell suspensions, each composed of 67 first tarsal segments collected following the procedures described above: one from 24h APF male pupae, the other from 30h APF male pupae. For a given timepoint, once 67 first tarsal segments had been collected, the DPBS was removed from the well and replaced with 100µl of dissociation buffer, which consisted of 10X TrypLE (Thermo Fisher Scientific, A12177-01) with a final concentration of 2µl/mL of collagenase (Sigma, C0130). The well was sealed and submerged in a metal bead bath in an incubator at 37°C for 35 minutes. The dissociation buffer was then removed from the well and replaced with 50µl of room temperature DPBS before the tissues were subjected to mechanical dissociation. For this, the solution was pipetted up and down 20 times using a 200µl, widebore, low bind, freshly BSA coated tip on a 50µl pipette set to 40µl. The tip was fully submerged to avoid bringing air into the suspension. The solution was then pipetted up and down a further 20x using a flame-rounded, BSA-coated 200µl tip, again on a 50µl pipette set to 40µl. Next, the solution was pipetted up and down slowly 3 times using the same flame-rounded tip before 40µl was taken up and transferred to a 2mL, low-bind, wide-bottomed tube on ice. 20µl of DPBS was then slowly dripped around the edges of the well using a different tip to flush the cells into the center. This was then pipetted up and down 3 times using the original flame-rounded 200µl tip and added to the tube. Cell concentration and viability was assayed using an acridine orange/propidium iodide stain and measured using a LUNA-FL Fluorescent Cell Counter averaged across 2 x 5µl aliquots (24h APF sample: 1990 cells/µl, 98% viability; 30h APF sample: 967 cells/µl, 98% viability).
Barcoded 3’ single cell libraries were prepared from single cell suspensions using the Chromium Next GEM Single Cell 3’ kit v3.1 (10X Genomics, Pleasanton, California) for sequencing according to the recommendations of the manufacturer.  The cDNA and library fragment size distribution were verified on a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA) and by qPCR with a Kapa Library Quant kit (Kapa Biosystems-Roche) prior to sequencing. The libraries were sequenced on a NovaSeq 6000 sequencer (Illumina, San Diego, CA) with paired-end 150 bp reads.

value: First tarsal segment

value: Male

value: 30h APF


title: MV411.DOT1L.DMSO [ChIP-Seq]

value: DOT1L antibody

value: DMSO control


title: MV411.DOT1L.TDI-055.0.5h [ChIP-Seq]


title: MV411.AFF1.DMSO [ChIP-Seq]

value: AFF1 antibody


title: MV411.HA-ENL.DMSO [ChIP-Seq]

value: HA antibody


title: MOLM13.FlagENL.input [ChIP-Seq]

data_processing:
Basecalls performed using CASAVA version 1.4
Raw reads were aligned to the UCSC Hg-19 genome sequence build from the Bsgenome.Hsapiens.UCSC.hg19 Bioconductor package using the Rsubread v 2.26 package's align function
Aligned BAM files were sorted using function sortBam from Rsubread v 2.2.6. Secondary alignments, unmapped reads, and duplicate reads in the sorted bam files were filtered out using sambamba v 0.7.1. The filtered and sorted bam files were then indexed using function indexBam from Rsubread v 2.2.6.
peaks were called using MACS v 2.2.7.1, peaks were called at P ≤ 1 × 10−8.
filtered, sorted, indexed BAM files were converted to bigwig files using bamCoverage from deeptools v3.5.0
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are in an indexed binary format
Supplementary_files_format_and_content: tab-delimited text files included chromosome number, start, end, width peak number, pvalue,annotation, distancetotss, symbol and genename for each peaks

source_name: MOLM13 cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq sample libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, #E7645L) following the manufacturer's instructions.  After adapter ligation, DNA was PCR amplified with Illumina primers for indicated cycles and the DNA size distribution was quantified on an Agilent Bioanalyzer DNA chip ( Agilent, #5067-1504). Then samples were sequenced using Illumina NextSeq 500.

treatment_protocol: Human leukemia cells were treated with DMSO or 5 uM TDI-055 for 24 hour

value: input


title: MV411.PAF1.TDI-055.24h [ChIP-Seq]

value: PAF1 antibody


title: RIP FP PGC-1α-KD MB + FLAG-RIP FP PGC-1α(CBM5mut), rep #1

value: PGC-1a-KD MB

value: anti-FLAG (M2)


title: RNA PGC-1α-KD MB + FLAG, rep #1


title: RIP FP PGC-1α-KD MB + FLAG-RIP FP PGC-1α(CBM5mut), rep #3


title: RIP FP PGC-1α-KD MB + FLAG, rep #2


title: MV411.input.DMSO [ChIP-Seq]


title: MV411.AFF1.TDI-055.0.5h [ChIP-Seq]


title: RIP FP PGC-1α-KD MB + FLAG, rep #3


title: First tarsal segment, male, 24h APF, scRNA-seq

description: 10x Genomics

value: 24h APF


title: MV411.HA-ENL.TDI-055.0.5h [ChIP-Seq]


title: RIP FP PGC-1α-KD MB + FLAG-RIP FP PGC-1α(WT), rep #3


title: MOLM13.FlagENL.TDI-055 [ChIP-Seq]

value: Flag antibody


title: MV411.PolIIS2P.DMSO [ChIP-Seq]


title: MV411.DOT1L.DMSO.24h [ChIP-Seq]


title: RNA PGC-1α-KD MB + FLAG, rep #3