title: Experiment_2_patient_3_PBpre_TIL_Pbpost_TCR_sequencing

status: Public on Jun 03 2022

city: Munich

first: Sebastian

last: Jarosch

state: Bavaria

address: Trogerstr. 30

department: institut für Medizinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: TU Munich

data_processing:
Patient 4: Cell Ranger (version 5.0.0; 10x Genomics) was used for demultiplexing and alignment using default parameters
Patient 3: Cell Ranger (version 6.0.2; 10x Genomics) was used for demultiplexing and alignment using default parameters
Python software package SCANPY (version 1.8.0) was used for downstream analysis
Experiment_1: cells filtered out that express < 200 and >6000 genes, >40000 counts,  > 40% mitochondrial genes. Genes were filtered out that were present in < 3 cells.
Experiment_2: cells filtered out that express < 200 and >7000 genes, >50000 counts,  > 20% mitochondrial genes. Genes were filtered out that were present in < 3 cells.
Gene counts were per-cell normalized and (log+1)-transformed
Cell cycle, percent mito, n_genes and n_counts were regressed out
Assembly: human reference genome GRCh38 (Ensembl 98)
Supplementary files format and content: Output of the Cell Ranger count Analysis Pipeline (mtx and tsv files; unfiltered and unnormalized)
Supplementary files format and content: Output of the Cell Ranger VDJ Analysis Pipeline (json file for clonotype annotation)

source_name: peripheral blood

extract_protocol:
Chromium Next GEM Single Cell 5' GEM, Library & Gel Bead Kit v1.1 (10x genomics) Patient 4; Chromium Next GEM Single Cell 5' GEM, Library & Gel Bead Kit v2 (10x genomics) Patient 3
Chromium Next GEM Single Cell 5' Library Kit v1.1 (10x genomics) Chromium Single Cell V(D)J EnrichmentKit, Human T Cell (10x genomics) Chromium Single Cell 5' Feature Barcode Library Kit (10x genomics)
Paired-end, single indexing (Patient 4); dual indexing (Patient 3)

treatment_protocol: PBMCs from blood before and after TIL treatment as well as cells from the infusion product of melanoma patients were thawed and stained with CD8, multimer and TotalSeq-C anti-human antibodies prior to sorting of living multimer+CD8+ cells.

tag: subject status

value: melanoma patient

tag: cell type

value: RBM12(S->L)+CD8+ T cells

value: blood

tag: molecule subtype

value: TCR sequences


title: MG_WT_1

status: Public on Jun 15 2022

type: SRA

city: Los Angeles

first: Shaughn

last: Bell

state: CA

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

country: USA

institute: Cedars-Sinai Medical Center

library_source: transcriptomic

data_processing:
The demultiplexed raw reads were aligned to the transcriptome using STAR (version 2.5.1) with default parameters, using mouse mm10 transcriptome reference from Ensembl version 84 annotation, containing all protein coding genes, long non-coding RNA genes, and polymorphic pseudogenes. Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger software version 4.0.0 (10X Genomics). The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
Filtered digital expression matrices from the CellRanger output (filtered_feature_bc_matrix directory) were loaded into R (version 4.0.3) using the Seurat package (version 3.2.2) in Rstudio (version 1.3.1093), keeping all genes that were expressed in more than one cell. All samples were merged into a single Seurat object (30,872 cells) and filtered by removing all cells with counts, genes, or mitochondrial gene percentage outside of three standard deviations from the mean (30,065 cells).
The data were then normalized using SCTransform, regressing out the mitochondrial gene content. Dimensionality reduction was run with Principal Component Analysis (PCA) followed by Uniform Manifold Approximation and Projection (UMAP) using the default 50 principal components (PCs). After visualizing the UMAP plots, the cells appeared to cluster based on the order they were processed, the day they were processed, and the sex of the animal. Integration of the data was performed by using the Harmony R package (version 1.0.0), batch correcting for these covariates (process day, process order, and sex) resulting in a much more uniform clustering between these factors after rerunning UMAP with the Harmony-corrected PCs.
Cluster determination was performed using FindNeighbors and FindClusters with a resolution of 0.3 and resulting in an initial discovery of 19 clusters. Cluster markers were determined using FindAllMarkers with the default min.pct = 0.25 and logfc.threshold = 0.4. Investigating these markers, six distinct cell types were discovered (microglia, endothelial cells, astrocytes, granulocytes, neutrophils and lymphocytes). A seventh general cluster was positive for both monocyte and macrophage markers.
In order to investigate microglial state changes between genotypes, all non-microglia cells were removed (26,275 microglia), and the remaining cells were then normalized, centered and scaled (NormalizeData, FindVariableFeatures & ScaleData) followed by Jack Straw Analysis to determine which PCs to use for further analysis. A sharp drop-off of p-values was observed between PC 14 and 15, so 15 PCs were used for microglia analysis.
The microglia were then normalized with SCTransform regressed against mitochondrial gene content. Subsequent PCA and UMAP reductions showed similar day, order, and sex bias as the analysis with all the cells, and the microglia were again integrated with Harmony, using the same covariates as before, followed by UMAP. Using FindNeighbors and FindClusters with a resolution of 0.8 discovered 16 clusters.
Known ARM genes (Clec7a, Itgax, Apoe, and Cst7) were found to be highly expressed in Cluster 11, and known IRM genes (Ifit1, Ifit2, Ifi204, and Isg15) were found to be highly expressed in Cluster 13.  Using FindAllMarkers (min.pct = 0.25 and logfc.threshold = 0.4), 66 genes were discovered to have a positive average logfc in Cluster 11 (ARM cluster marker genes) and 86 genes were discovered to have a positive average logfc in Cluster 13 (IRM cluster marker genes).
These two gene lists were used with the AddModuleScore function to assign ARM and IRM module scores to each cell. Cells in the ARM or IRM clusters were compared across genotypes by ordinary one-way ANOVA (Dunnett’s multiple comparisons test with a single pooled variance) using GraphPad Prism (version 9.0.0 (86) for macOS).
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger 4.0 outs filtered_feature_bc_matrix (3 files per sample:  barcodes.tsv, features.tsv & matrix.mtx); excel spreadsheet with cell metadata including module scores

molecule: total RNA

organism: Mus musculus

source_name: Microglia

extract_protocol:
The meninges were removed from the mice brains of different genotypes and dissociated using the Neural Tissue dissociation kit, papain based (Miltenyi Biotech) and GentleMACSdissociator (NTDK Brain setting). The lysate was collected and passed through a 70μm strainer to obtain a single cell suspension. Next, myelin was removed fromthe cells by incubating with magnetic myelin beads (Myelin Removal Beads II, human, mouse, rat, Miltenyi Biotech) and removed using the AutoMACs. Cells were then incubated with CD11b+ magnetic beads CD11b MicroBeads, human and mouse, (Miltenyi Biotech) and sorted using the AutoMACs. After sorting, cells were counted and diluted according to the specifications in the Single Cell 3′ v3.1 Reagent Kits User Guide (10x Genomics, Pleasanton, California) to capture about 4000 cells per sample.
Single-cell RNA-Seq libraries were prepared per the Single Cell 3′ v3.1 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-RT was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA). GEMs were then harvested, and the cDNA was amplified and cleaned up with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA).  Indexed sequencing libraries were constructed usingChromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the Collibri LibraryQuantification Kit (Thermo Fisher Scientific). Libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) as per the Single Cell 3′ v3.1 Reagent Kits User Guide, with a sequencing depth of ~40,000 reads/cell.
batching protocol: To minimize batch affect, samples were processed through the GEM-RT step in batches of three on three consecutive days. We attempted to mix the genotypes over all three days, however this was not done perfectly. In addition, the order each genotype was processed on a given day was also mixed, but again not perfectly. The process day and process order value is listed in the caracteristics column of the Samples Table. After all nine samples were taken to the GEM-RT stage, all samples were taken through the rest of the library construction protocol together on the same day.
10x Genomics Single Cell 3' v3.1

tag: strain

tag: genotype

value: Wild Type

tag: age at collection

value: 12 months

tag: Sex

value: female

tag: process day

value: day 3

tag: process order


title: Experiment_2_patient_3_PBpre_TIL_Pbpost_gene expression

library_source: transcriptomic single cell

organism: Homo sapiens

tag: tissue

value: total mRNA + HTO + Surface


title: Experiment_1_patient_4_PBpre_TIL_Pbpost_TCR_sequencing

value: ENTDP4(P->L)+CD8+ T cells


title: Donor6 gRNA2 AmpSeq

status: Public on May 21 2022

city: San Francisco

first: Vivasvan

last: Vykunta

address: 513 Parnassus Avenue HSW901

institute: Gladstone-UCSF Institute of Genomic Immunology

library_source: genomic

data_processing:
Amplicons were processed with CRISPResso (Clement et al. 2019) using the CRISPRessoPooled comman in genome mode with default parameters.
Resulting amplicons were matched with gRNA sites for each sample.
Reads with potential sequencing errors detected as single mutated bases with no indels by CRISPResso alignment were eliminated.
Remaining reads were used to determine NHEJ percentage (Observed_Cutting_Percentage)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes Observed cutting percentage (%insertion or deletion) for each target site
Library strategy: Ampli-seq

molecule: genomic DNA

source_name: Bulk T

extract_protocol:
~100,000 cells per condition were resuspended in 20 μl of Quickextract DNA Extraction Solution (Epicenter) based on manufacturer recommendations.
1 μl of QE mixture was added to a two-step PCR amplicon sequencing approach using NEB Q5 2X 5 2X Master Mix Hot Start Polymerase with the manufacturer’s recommended thermocycler conditions. After amplicons of about 200 bp in length were generated, a 1.0X SPRI purification was used before samples a second PCR was then used to append P5 and P7 illumina sequencing adaptors and donor-specific barcodes to amplicons. The second PCR was following by a 1.0x SPRI purification before sequencing.
Amplicon sequencing

tag: individual

value: Bulk T


title: Experiment_1_patient_4_PBpre_TIL_Pbpost_gene expression

value: total mRNA + HTO


title: Donor5 gRNA1 AmpSeq


title: Donor4 gRNA1 AmpSeq


title: C-GAn-25

status: Public on Jul 05 2022

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
Ion Torrent S5TL XL
processed_data_mm9.txt

data_processing:
Mapping to the mouse genome was performed using the T-Map algorithm from Torrent Suite Server.
Integration sites were analyzed using the program InSiDeR. https://github.com/UppsalaGenomeCenter/InSiDeR
Assembly: mm9 or mm10
Supplementary files format and content: Tab-delimited file with integration sites together with nr of reads that supports integration.

source_name: Cell line

extract_protocol:
Genomic DNA was extracted using the MagAttract HMW DNA Kit (Qiagen), according to the manufacturer’s protocol.
Library was prepared accordingusing the Ion Xpress™ Plus protocol and the Ion Plus Library Preparation for the AB Library Builder™ System (Thermo Fisher)
Hybridization-based sequencing

tag: cell line name

tag: genotype (backgound)

value: Arf-/-

tag: reference genome

tag: mutagen

tag: successful integration

value: TRUE

tag: transgene

value: G/tv-a

tag: age

value: newborn


title: Donor3 gRNA2 AmpSeq

tag: cell type


title: 3MO_MG_WT_4

data_processing:
(RPKM generation) Raw sequencing reads were demultiplexed and FASTQ files were uploaded to the Galaxy web platform using the public server at usegalaxy.org.
(RPKM generation) FASTQ files were processed using FASTQ Groomer (Galaxy Version 1.1.1) and aligned to the mouse genome (mm10) via Tophat (Galaxy Version 2.1.1) using default settings.
(RPKM generation) BAM files were downloaded locally and annotated using Partek software v7.17.0918 to generate RPKM values for each gene.
(TPM generation) Raw sequencing reads were demultiplexed, and FASTQ files were used to generate estimated transcript counts against the mouse transcriptome (mm10) via Salmon v0.8.2.
(TPM generation)TPM values summed to the gene level were generated using the R Bioconductor package DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: comma delimited RPKM & TPM tables

extract_protocol:
The meninges were removed from the mice brains of different genotypes and dissociated using the Neural Tissue dissociation kit, papain based (Miltenyi Biotech) and GentleMACSdissociator (NTDK Brain setting). The lysate was collected and passed through a 70μm strainer to obtain a single cell suspension. Next, myelin was removed from the cells by incubating with magnetic myelin beads (Myelin Removal Beads II, human, mouse, rat, Miltenyi Biotech) and removed using the AutoMACs. Cells were then incubated with CD11b+ magnetic beads CD11b MicroBeads, human and mouse, (Miltenyi Biotech) and sorted using the AutoMACs. After sorting, cells were pelleted and stored at -80°C until further downstream application.  RNA was isolated using Qiagen RNeasy Micro Kit (Cat #74004) according to manufacturer’s instructions.
RNA-seq libraries were generated using 75ng to 180ng total RNA as input for the TruSeq Stranded mRNA Library Prep kit (Illumina) according to the manufacturer’s protocol, and samples were indexed using TruSeq RNA Single Indexes (Illumina). Library preps were analyzed via bioanalyzer (Agilent) and quantified via Qubit fluorometric quantification (Thermo Fisher). Quantified libraries were normalized, pooled, and sequenced on a NextSeq 500 sequencer (Illumina) using the single-end 75 nucleotide setting

value: 3 months

tag: total rna input


title: Donor3 gRNA1 AmpSeq


title: Donor2 gRNA1 AmpSeq


title: Donor1 gRNA1 AmpSeq


title: Donor1 gRNA2 AmpSeq


title: 25dpf testis rep4

status: Public on May 18 2022

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

data_processing:
High-throughput sequencing raw image data files were converted to reads using fqtools_plus analysis and using FastqC (v0.11.8) and sequencing report tool of MultiQC (v0.9)to evaluate the raw read quality statistics.
Reads were mapped to the corresponding reference genome (Ensembl v96) with the parameters "-- dta-x -- rna-strandness RF" and "-- known spliceset-infile" using Hisat2 (v2.0.5), and gene annotation was performed in GTF format (Ensembl 96). Hisat2 converts the data into BAM format, sorted by Samtools (v1.5), and removed duplicates using the Picard MarkDuplicates (v2.18.15) tool. HTSeq (v0.9.1) was used to read and count the parameter "-t exon-i gene_id-r pos-s reverse".
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Gonad

extract_protocol:
Gonads were removed, and RNA was extracted using RNAprep pure Micro Kit (TIANGEN).
For each sample, 5ul of RNA was used for synthesis and amplification of cDNA (Discover-sc WTA Kit,  N711, Vazyme), and 5ng of amplified cDNA was used for  construction of sequencing library using TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme TD501/TD502).

tag: strain

value: AB

value: testis

value: post fertilization day 25


title: 30dpf testis rep3

value: post fertilization day 30

tag: genotype


title: 30dpf testis rep1


title: 25dpf testis rep1


title: 25dpf testis rep2


title: 30dpf ovary rep2

value: ovary


title: 30dpf ovary rep1


title: Donor6 gRNA1 AmpSeq


title: Donor5 gRNA2 AmpSeq


title: Donor4 gRNA2 AmpSeq


title: 25dpf ovary rep1


title: 25dpf ovary rep2


title: MCF7_Input_Rad21KD_E2_2

status: Public on May 12 2022

city: Changsha

first: Jiankang

last: Wang

state: Hunan

address: Lushan

institute: School of biology

data_processing:
Sequencing reads were aligned to human reference genome (hg38) using Bowtie version 1.2.2 with “-n2 -m1” parameters
Peak calling was performed using MACS2 version 2.2.6 with default settings
Htseq version 0.11.3 was then utilized with default parameters to generate a count table
Genome_build: hg38
Supplementary_files_format_and_content: bed files of ChIP-seq peak; gene count table of RNA-seq

source_name: MCF7 cell line

growth_protocol: RPE cells and MCF-7 cells (JCRB Cell Bank) were cultured in DMEM containing 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Komata, M., et al., Chromatin immunoprecipitation protocol for mammalian cells. Methods Mol Biol, 2014. 1164: p. 33-8.).  Total RNA was extracted using TRIzol (Life Technologies) and Nucleospin RNA (Macherey-Nagel) following the manufacturers' instructions.
ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (New England BioLabs).

treatment_protocol: RPE cells were cultured in serum-free medium for 48 hours and then incubated in DMEM containing 10% FBS for 30 min. MCF-7 cells were maintained in phenol red-free medium containing charcoal-dextran stripped FBS (Life Technologies) at 70-80% confluency for 2 days before treatment with 50nM E2 ligand (SIGMA) for the indicated times.

value: MCF7 cell line

tag: antibody

value: Input

tag: treatment

value: Estrogen +

tag: sirna


title: MCF7_Input_WT_E2_2


title: MCF7_Input_WT_Ctrl_2

value: Estrogen -


title: MCF7_Input_Rad21KD_Ctrl_2


title: MCF7_Pol2ser2_Rad21KD_E2_2

value: RNA Pol2ser2


title: MCF7_Pol2ser2_WT_Ctrl_2


title: Donor2 gRNA2 AmpSeq

value: Bulk T


title: MCF7_Pol2ser2_Rad21KD_Ctrl_2


title: MCF7_Pol2_WT_E2_2

value: RNA Pol2


title: MCF7_Pol2ser2_NIPBLKD_E2_2

value: NIPBL-KD


title: MCF7_Pol2ser2_NIPBLKD_Ctrl_2


title: MCF7_Pol2_WT_Ctrl_2


title: MCF7_Pol2_Rad21KD_Ctrl_2


title: 30dpf ovary rep3


title: 30dpf testis rep2


title: MCF7_Pol2_NIPBLKD_Ctrl_2


title: RPE_Rad21_FBS-_2

source_name: RPE1 cell line

value: RPE1 cell line

value: FBS +


title: 25dpf testis rep3


title: RPE_Rad21_FBS+_2

value: FBS -


title: MCF7_Pol2_Rad21KD_E2_2


title: Patient sample 219A

status: Public on May 05 2022

first: Matthew

middle: A

last: Fischer

address: 650 Charles Young Dr

department: Anesthesiology and Perioperative Medicine

institute: University of California, Los Angeles

data_processing:
BS-Seeker2 (PMID 24206606) was used to align the reads to hg38, allowing for up to 10 mismatches, and methylation was called for CpGs and then processed using MethylKit in R as described in previous publications (PMIDs 29566149 and 26838786)
We removed from analysis CpGs with less than 10x coverage. Additionally, CpGs were removed from the cohort if they were located at SNPs with minor allele frequency greater than 1% in humans (dbSNP build 150 common SNPs: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/snp150Common.txt.gz) or not present in at least 50% of the cohort after filtering for coverage.
Genome_build: hg38
Supplementary_files_format_and_content: Each patient's methylation call file contains the chromosome and base pair location of each CpG and each CpG's coverage and percent methylation data.

source_name: Whole blood

extract_protocol:
Genomic DNA was isolated (PureLink Genomic DNA Kit, K1820-01) from whole blood (separately we biobanked buffy coat containing leukocytes and platelets at -80ºC), subjected to enzymatic digestion with MspI (NEB, R0106S) and bisulfite converted (EpiTect Fast. DNA Bisulfite Kit, Qiagen, 59824).
Libraries were prepared using Illumina TruSeq kit, size-selected for 330 bp with AMPure XP beads and subjected to 100 bp, single-end sequencing on HiSeq instruments.

tag: Sex

value: Female

tag: paroxysmal atrial fibrillation

value: No

tag: diabetes mellitus

tag: hypertension

value: Yes

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 217A

tag: Sex

value: Male

tag: age

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure


title: MCF7_Pol2ser2_WT_E2_2

tag: cell type

tag: antibody

tag: treatment

tag: sirna


title: Patient sample 209A

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition


title: Patient sample 215A

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 208A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 218A

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition


title: Patient sample 202A

tag: Sex

tag: age

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 207A

tag: hypertension

tag: congestive heart failure

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 191A

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker


title: Patient sample 193A

tag: Sex

tag: age

tag: asian

tag: black

tag: hispanic

tag: b cells composition


title: Patient sample 167A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 168A

tag: pulmonary vein isolation

tag: maze procedure

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 131A

tag: Sex

tag: age

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker


title: Patient sample 149A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: asian

tag: black

tag: hispanic

tag: b cells composition


title: Patient sample 146A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 200A

tag: Sex

tag: age

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 158A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker


title: Patient sample 130A

tag: hypertension

tag: congestive heart failure

tag: asian

tag: black

tag: hispanic

tag: b cells composition


title: MCF7_Pol2_NIPBLKD_E2_2

tag: cell type

tag: antibody

tag: treatment

tag: sirna


title: Patient sample 129A

tag: Sex

tag: age

tag: pulmonary vein isolation

tag: maze procedure

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 128A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 125A

tag: Sex

tag: age

tag: pulmonary vein isolation

tag: maze procedure

tag: hispanic

tag: b cells composition


title: Patient sample 124A

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 123AA

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 127A

tag: Sex

tag: age

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 122AA

tag: pulmonary vein isolation

tag: maze procedure

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 121AA

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 119A

tag: Sex

tag: age

tag: hypertension

tag: congestive heart failure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 120AA

tag: pulmonary vein isolation

tag: maze procedure

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 118A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 117AA

tag: Sex

tag: age

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 115A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 113A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 116AA

tag: Sex

tag: age

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 114A

tag: hypertension

tag: congestive heart failure

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 160A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 111A

tag: Sex

tag: age

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 110A

tag: hypertension

tag: congestive heart failure

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 104A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 099A

tag: Sex

tag: age

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 102A

tag: hypertension

tag: congestive heart failure

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 103A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 098A

tag: Sex

tag: age

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 097A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 105A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 107A

tag: Sex

tag: age

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 096A

tag: hypertension

tag: congestive heart failure

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 090A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 088A

tag: Sex

tag: age

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 084A

tag: hypertension

tag: congestive heart failure

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 083A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 085A

tag: Sex

tag: age

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 081A

tag: hypertension

tag: congestive heart failure

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 112A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 109A

tag: Sex

tag: age

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 078A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 076A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 077A

tag: Sex

tag: age

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 075A

tag: hypertension

tag: congestive heart failure

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 079A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 070A

tag: Sex

tag: age

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 108A

tag: hypertension

tag: congestive heart failure

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 071A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 065A

tag: Sex

tag: age

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 060A

tag: hypertension

tag: congestive heart failure

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 061A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 091A

tag: Sex

tag: age

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 063A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 066A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 062A

tag: Sex

tag: age

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 059A

tag: hypertension

tag: congestive heart failure

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 064A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 080A

tag: Sex

tag: age

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 058A

tag: hypertension

tag: congestive heart failure

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 089A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 067A

tag: Sex

tag: age

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 050A

tag: hypertension

tag: congestive heart failure

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 053A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 055A

tag: Sex

tag: age

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 051A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 047A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 056A

tag: Sex

tag: age

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 049A

tag: hypertension

tag: congestive heart failure

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 057A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 045A

tag: Sex

tag: age

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 043A

tag: hypertension

tag: congestive heart failure

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 042A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 040A

tag: Sex

tag: age

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 044A

tag: hypertension

tag: congestive heart failure

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 038A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 039A

tag: Sex

tag: age

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 029A

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: snRNA-seq_day3 [stage 4]

status: Public on Apr 09 2022

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

institute: German Federal Institute for Risk Assessment

data_processing:
Fastq files were processed with CellRanger v3.1.0 with default parameter values and using the Araport11 gene annotation
Genome_build: Araport11
Supplementary_files_format_and_content: Matrix or tsv files. Output of CellRanger

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: flower meristem

growth_protocol: pAP1:AP1-GR ap1-1 cal-1 plants were grown at 22°C under the long-day condition (16 h light, 8 h dark) on soil.

extract_protocol:
Inflorescences were gently crushed to pieces in liquid nitrogen using a mortar and a pestle and then transferred to a gentleMACS M tube. After liquid nitrogen evaporated totally, 5 ml of Honda buffer (2.5 % Ficoll 400, 5 % Dextran T40, 0.4 M sucrose, 10 mM MgCl2, 1 μM DTT, 0.5% Triton X-100, 1 tablet/50 ml cOmplete Protease Inhibitor Cocktail, 0.4 U/μl RiboLock, 25 mM Tris-HCl, pH 7.4) was added to the tube. Nuclei were released at 4 °C by homogenizing the tissue on a gentleMACS Dissociator with a running program as described previously. The resulting homogenate was filtered through a 70 μm strainer, and another 5ml Honda buffer was applied onto the filter to collect the remaining nuclei. Nuclei were then pelleted by centrifugation at 1000 g for 6 min at 4 °C and then resuspended gently in 500 μl Honda buffer. The nuclei suspension was filtered again through a 30 μm strainer, diluted by adding 500ul PBS buffer, and stained with 2 μM DAPI. Ambion RNase Inhibitor and SUPERaseIn RNase Inhibitor were added to a final concentration of 0.4 U/μl and 0.2 U/μl, respectively. 200,000 events of single nuclei were selected on DAPI signals by a BD FACS Aria Fusion into an 1.5ml tube with landing buffer (15μl 4% BSA in PBS with 80U Ambion RNase Inhibitor and 80U SUPERaseIn RNase Inhibitor). Sorted nuclei were counted in Neubauer counting chambers under a Leica DMi8 fluorescent microscope.
Single-nuclei RNA-seq library was prepared from 10,000 freshly-isolated plant nuclei with the Chromium Single Cell 3ʹ Reagent Kits v3 according to the manufacturer’s instructions. 11 PCR cycles were used for cDNA amplification, and 14 PCR cycles were used for final amplification of the constructed libraries. The average fragment size of the snRNA-seq library was checked with an Agilent High Sensitivity D1000 ScreenTape, and the concentration was measured with Qubit 1X dsDNA HS Assay Kit.

treatment_protocol: After plants bolted and reached the height of 2cm to 5cm, they were induced daily by applying the DEX-induction solution (2 μM Dexamethasone and 0.00016% Silwet L-77 in ethanol) to their main inflorescences. Around 20 inflorescences were collected and snap-frozen in liquid nitrogen on the fourth day after the first induction.

tag: developmental stage

value: stage 4 of flower development

tag: tissue

value: inflorescence

tag: background ecotype

value: Ler

tag: genotype

value: pAP1::AP1-GR ap1 cal


title: X16 AP3-domain RNA-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Araport11 whole genome using  STAR v2.7.0b with parameter values --alignIntronMax 10000 --outFilterMultimapNmax 1 --outSJfilterReads Unique and other parameters with default values
featureCounts was used to count the number of mapped reads per gene with default parameter
Next, reads mapping to genes encoded in the organelles were removed. Only genes with more than 10 reads mapped in at least 2 samples were considered in the further analyses. Read count data was analyzed with DESeq2 v1.24.0
Genome_build: Araport11
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts obtained by FeatureCounts
Supplementary_files_format_and_content: Matrix table with normalized gene counts (using DESeq2) for every gene and every sample

source_name: inflorescence stage 5

growth_protocol: Plants were grown at 22°C under long-day conditions (16 h light, 8 h dark) on soil.

extract_protocol:
Nuclei were isolated by FANS from pAP1:AP1-GR ap1-1 cal-1 transgenic plants expressing a GFP labeled nuclei envelope protein driven by tissue-specific promoters. We used AP3 promote and AG 2nd intron plus a minimal 35 s promoter element as promoters for the constructs to mark AP3 and AG expressing domains in flowers, respectively. After nuclei isolation, as described in the previous paragraph, nuclei were sorted into a 1.5 tube with 15μl of 4% BSA in PBS and 6μl of RiboLock RNase Inhibitor by a BD FACS Aria III. The GFP channel was set using pAP1:AP1-GR ap1-1 cal-1 as a negative control, and then nuclei were selected by gating on the DAPI peaks under the GFP positive events. After sorting, nuclei were pelleted at 1500 rcf for 10mins at 4°C, and the supernatant was then removed. Nuclei were lysed by vortex in 350 μl RLT buffer with 2-Mercaptoethanol, and RNA was then isolated from sorted nuclei with Qiagen RNeasy Micro Kit.
cDNA synthesis was done with SMART-Seq® v4 Ultra® Low Input RNA Kit following the manufacturer’s instructions. cDNA was sheared to 200–500 bp size by Covaris AFA system and constructed with sequencing adaptors by ThruPLEX DNA-Seq Kit.ThruPLEX DNA-Seq Kit.

treatment_protocol: After plants bolted and reached the height of 2 cm to 5 cm, they were induced daily by applying the DEX-induction solution (2 μM Dexamethasone and 0.00016% Silwet L-77) to their main inflorescences

value: stage 5 of flower development

value: pAP1::AP1-GR ap1 cal pAP3:NTF(GFP)


title: X13 AP3-domain RNA-seq


title: snRNA-seq_day4

extract_protocol:
Inflorescences were gently crushed to pieces in liquid nitrogen using a mortar and a pestle and then transferred to a gentleMACS M tube. After liquid nitrogen evaporated totally, 5 ml of Honda buffer (2.5 % Ficoll 400, 5 % Dextran T40, 0.4 M sucrose, 10 mM MgCl2, 1 μM DTT, 0.5% Triton X-100, 1 tablet/50 ml cOmplete Protease Inhibitor Cocktail, 0.4 U/μl RiboLock, 25 mM Tris-HCl, pH 7.4) was added to the tube. Nuclei were released at 4 °C by homogenizing the tissue on a gentleMACS Dissociator with a running program as described previously. The resulting homogenate was filtered through a 70 μm strainer, and another 5ml Honda buffer was applied onto the filter to collect the remaining nuclei. Nuclei were then pelleted by centrifugation at 1000 g for 6 min at 4 °C and then resuspended gently in 500 μl Honda buffer. The nuclei suspension was filtered again through a 30 μm strainer, diluted by adding 500ul PBS buffer, and stained with 2 μM DAPI. Ambion RNase Inhibitor and SUPERaseIn RNase Inhibitor were added to a final concentration of 0.4 U/μl and 0.2 U/μl, respectively. 200,000 events of single nuclei were selected on DAPI signals by a BD FACS Aria Fusion into an 1.5ml tube with landing buffer (15μl 4% BSA in PBS with 80U Ambion RNase Inhibitor and 80U SUPERaseIn RNase Inhibitor). Sorted nuclei were counted in Neubauer counting chambers under a Leica DMi8 fluorescent microscope.
Single-nuclei RNA-seq library was prepared from 10,000 freshly-isolated plant nuclei with the Chromium Single Cell 3ʹ Reagent Kits v3 according to the manufacturer’s instructions. 14 PCR cycles were used for cDNA amplification, and 13 PCR cycles were used for final amplification of the constructed libraries. The average fragment size of the snRNA-seq library was checked with an Agilent High Sensitivity D1000 ScreenTape, and the concentration was measured with Qubit 1X dsDNA HS Assay Kit.


title: X14 AG-domain RNA-seq

value: pAP1::AP1-GR ap1 cal iAG:NTF(GFP)


title: X71 AG-domain RNA-seq


title: Patient sample 037A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: Patient sample 035A

tag: Sex

tag: age

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 036A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker


title: Patient sample 034A

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition


title: donor 19, control

status: Public on Mar 29 2022

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

data_processing:
Reads alignment:  STAR
Gene level summarization:  featureCounts
Normalization:  DESeq2
Assembly: GRCh37
Supplementary files format and content: *txt, raw counts by gene and sample

source_name: post-mortem cerebellum (white matter)

extract_protocol:
Total DNAse-treated RNA was extracted using the Qiagen RNAeasy kit (Qiagen). Quality was assessed by Bioanalyzer (Agilent)
Sequencing libraries were prepared with 250 ng of total RNA using Illumina’s Truseq RNA Sample Preparation Kit v2 (Illumina, Inc.) following the manufacturer’s protocol and purifying poly-A mRNAs with poly-T oligos attached to magnetic beads. The final library was sequenced by 50 bp paired-end sequencing on a HiSeq 2500 (Illumina, Inc.)

tag: tissue

value: post-mortem cerebellum (white matter)

tag: Sex

tag: age at death

tag: post mortem interval (hours)

tag: disease state

value: control

tag: diagnosis

tag: source

value: New South Wales Brain Tissue Resource Center, Sydney, Australia


title: donor 18, control


title: Patient sample 028A

tag: age

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: donor 16, control

tag: tissue

tag: Sex

tag: age at death


title: donor 14, control

tag: post mortem interval (hours)

tag: disease state

tag: diagnosis


title: donor 17, control

tag: source


title: donor 13, control


title: donor 12, control


title: donor 11, MSA

value: Multiple system atrophy (MSA)

value: MSA-C


title: donor 8, MSA

value: MSA-P


title: donor 15, control

value: Female


title: donor 7, MSA


title: donor 6, MSA


title: donor 9, MSA


title: X74 AP3-domain RNA-seq

tag: developmental stage

tag: background ecotype

tag: genotype


title: X26 AG-domain RNA-seq


title: donor 20, control


title: donor 1, MSA


title: donor 4, MSA


title: donor 2, controls


title: donor 3, MSA


title: Small-int-Epithelium-Z000000UY

status: Public on Mar 02 2022

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

data_processing:
Paired-end FASTQ files were mapped to the human (hg19 -or- hg38), lambda, pUC19 and viral genomes using bwa-meth (V 0.2.0), with default parameters (Pedersen et al., 2014), then converted to BAM files using SAMtools (V 1.9) (Li et al., 2009).
Duplicated reads were marked by Sambamba (V 0.6.5), with parameters “-l 1 -t 16 --sort-buffer-size 16000 --overflow-list-size 10000000” (Tarasov et al., 2015).
Reads with low mapping quality, duplicated, or not mapped in a proper pair were excluded using SAMtools view with parameters -F 1796 -q 10.
Reads were stripped from non-CpG nucleotides and converted to BETA files using wgbstools (V 0.2.0) (Loyfer and Kaplan).
Genome_build: hg19
Supplementary_files_format_and_content:
beta files were generated using wgbstools (https://github.com/nloyfer/wgbs_tools) with default parameteres
bigwig files were generated from beta files using wgbstools beta2bw with default parameteres
blocks file (bed) was generated using wgbstools segment, and then compressed and indexed using tabix (samtools)

source_name: Small intestine

extract_protocol:
DNA was extracted using the DNeasy Blood and Tissue kit (#69504 Qiagen; Germantown, MD) according to the manufacturer’s instructions, and stored at -20°C for bisulfite conversion and whole genome sequencing.
Up to 75 ng of sheared gDNA was subjected to bisulfite conversion using the EZ-96 DNA Methylation Kit (Zymo Research; Irvine, CA), with liquid handling on a Hamilton MicroLab STAR (Hamilton; Reno, NV). Dual indexed sequencing libraries were prepared using Accel-NGS Methyl-Seq DNA library preparation kits (Swift BioSciences; Ann Arbor, MI) and custom liquid handling scripts executed on the Hamilton MicroLab STAR. Libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA). Four uniquely dual indexed libraries, along with 10% PhiX v3 library (Illumina; San Diego, CA), were pooled and clustered on a Illumina NovaSeq 6000 S2 flow cell followed by 150-bp paired-end sequencing.

treatment_protocol: Fresh tissue obtained at the time of surgery was trimmed to remove extraneous tissue. Cells were dispersed using enzyme-based protocols optimized for each tissue type. The resulting single-cell suspension was incubated with the relevant antibodies and FACS sorted to obtain the desired cell type. Purity of live sorted cells was determined by mRNA analysis for key known cell-type specific genes whereas purity of cells that were fixed prior to sorting was determined using previously validated cell-type specific methylation signals

value: Small intestine

tag: cell type

value: Epithelium

tag: lab

value: Had-HU

tag: age

value: F

tag: race

value: White


title: Small-int-Endocrine-Z00000436

source_name: Jejunum

value: Jejunum

value: Endocrine

value: M


title: donor 10, MSA


title: Mutant HEPs::Mutant HSCs Organoids HTO library 10

status: Public on Feb 28 2022

city: Philadelphia

first: Joshua

middle: .H

last: Rhoades

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Demultiplexed with cell ranger mkfastq
Counted with cell ranger count
Processed with Seurat package, following standard workflow with addition of demultiplexing using HTO Data.
GSEA performed with VisCello
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: fastq.gz
Supplementary_files_format_and_content: Normalized_expression.tsv: Normalized gene expression matrix, tab delimited text file
Supplementary_files_format_and_content: YJ_Lib10_2: Barcode tsv.gz
Supplementary_files_format_and_content: YJ_Lib10_2: Features tsv.gz
Supplementary_files_format_and_content: YJ_Lib10_2: Matrix tsv.gz
Supplementary_files_format_and_content: YJ_Lib9_1: Barcode tsv.gz
Supplementary_files_format_and_content: YJ_Lib9_1: Features tsv.gz
Supplementary_files_format_and_content: YJ_Lib9_1: Matrix tsv.gz
Supplementary_files_format_and_content: counts.csv: Raw gene expression counts, csv file
Supplementary_files_format_and_content: hto.txt: Hast tag counts, tab delimited file
Supplementary_files_format_and_content: Library9_YJ_1_v3_feature_ref.csv: Csv file with barcode information for demultiplexing library 9
Supplementary_files_format_and_content: Library10_YJ_2_v3_feature_ref.csv: Csv file with barcode information for demultiplexing library 10

source_name: Hepatostellate organoids

growth_protocol: Hepatoblast stage cells (HBs) at day 10 and fully differentiated HSCs were detached by Accutase and 0.05% Trypsin-EDTA, respectively. HBs and HSCs were mixed in a 5:1 ratio. These mixed cells were seeded into 96 well U bottom plate coated with Nunclon Sphera (Thermo Fisher Scientific) at a density of 3,000 per well. Organoids were cultured in Hepatocyte Culture Medium with 10 ng/mL Hepatocyte growth factor, 10 ng/mL Oncostatin M, and 0.1 mM Dexamethasone for 7 days.

extract_protocol:
Cells were encapsulated using the Chromium Controller (10x Genomics) and the Chromium Single Cell 3′ Library & Gel Bead Kit (10x Genomics) following the standard manufacturer’s protocols.
All libraries were prepared for sequencing using standard Illumina protocols.
Single-cell RNA seq with HTO

value: iPSC derived hepatic organoids

tag: cell line

value: DKC1 A353V mutant


title: Mutant HEPs::Mutant HSCs Organoids HTO library 9


title: Mutant HEPs::Mutant HSCs Organoids library 10


title: donor 5, MSA

value: post-mortem cerebellum (white matter)

value: Male


title: Mutant HEPs::Mutant HSCs Organoids library 9


title: Donor 1 pooled regions [GEX]

status: Public on Feb 21 2022

city: Durham

first: Jarrett

last: Bliton

address: 6 Davis Drive

institute: Altis Biosystems

description:
gex represents mRNA libraries
clustered_annotated_adata_k10_lr0.92_v1.7.h5ad
Donor1_filtered_feature_bc_matrix.h5
mag15

data_processing:
Read Alignment:  single-cell fastq files were aligned to reference transcriptome GRCh38 with the 10X Cell Ranger pipeline (V4.0.0),
Downstream Processing:  downstream analysis was performed with scanpy (v1.7.2).
Annotations for cell cycle phase were added following previously published methods in Moor et al 2018. Following filtering, read counts were log-transformed and normalized to the median read depth of Donor 2, which had the fewest read counts. Highly variable genes were identified with the Seurat v2 method, identifying 2777 genes that were subsequently used for principal component analysis.
Quality Filtering parameters:
Minimum genes: >500
Percent mitochondrial reads: <75%
Minimum counts: >3,000
Maximum counts: <50,000
Dimensional reduction, batch correction,  Leiden clustering, and UMAP visualization:  Mapped reads were filtered and counted by barcode and UMI and then transformed into an AnnData object using the Python implementation of scanpy (v1.7.2). Annotations for cell cycle phase were added following previously published methods78. The number of genes, number of UMIs, and percent mitochondrial expression for all cells in each sample were visualized and used to identify thresholds for high-quality cells to include in further analysis. Analysis of scRNAseq above quality control thresholds was carried out in Jupyter hub with python version 3.8 and Scanpy version 1.7179. Regional hashtag deconvolution followed published methods . Briefly, raw hashtag read counts were normalized using centered log ratio transformation followed by k-medoid clustering (k=6 medoids)19. Hashtag noise distributions were determined by removing the cluster with highest expression of a specific hashtag, then a negative binomial distribution was fit to the data of the remaining cells. Cells were considered positive for a hashtag if counts for the specific hashtag were above the distribution’s 99th percentile (p<0.01) threshold. Cells positive for multiple hashtags were excluded as likely doublets. For both single cell sequencing experiments no batch correction was performed as each dataset was analyzed separately. As each experiment was analyzed separately, no batch correction was performed, and the following steps were performed once for each dataset to generate an initial dataset. The number of genes, number of UMIs, and percent mitochondrial expression for all cells in each sample was visualized (Fig. S1F). The pp.normalize_total, pp.log1p, pp.regress_out, pp.highly_variable_genes, and pp.scale Scanpy functions were used to normalize, log-transform, regress out variation, find highly variable genes (HVGs), and scale and center the dataset at zero. HVGs were used to calculate PCs by using the tl.pca function in Scanpy (Fig. S1G). For Leiden clustering the Scanpy functions pp.neighbors, tl.leiden, and tl.paga were used to compute nearest neighbors, calculate Leiden clusters, and generate initial PAGA layouts for UMAP projections80,81. Clustering parameters used were as follows: Leiden resolution = 0.9, num_neighbors = 10, num_pcs = 40. Scoring gene lists was accomplished by using the scanpy.tl.score_genes function with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 - raw feature counts for each dataset
Supplementary_files_format_and_content: h5ad - final processed and integrated dataset for figure generation and analysis

source_name: Donor 1 pooled regions

extract_protocol:
Full human intestinal tracts (duodenum through descending colon) were received from HonorBridge (formerly Carolina Donor Services). Intestines were transported on ice in University of Wisconsin Solution, and tissue dissection began at UNC Chapel Hill within eight hours of cross-clamping. Fat and connective tissue were trimmed, and intestines were measured and regions separated, with the proximal 20 cm deemed Duodenum, Jejunum and ileum evenly splitting the remaining small intestine, and colon split into equal thirds for ascending, transverse, then descending colon. Two 3x3 cm mucosectomies were isolated from the center of each region for dissociation.   Full mucosa pieces were incubated in 10 mM NAC (Sigma-Aldrich A9165) in dPBS (Gibco 14190-144) at room temperature for 30 min to remove mucus, then tissue was moved to ice-cold Isolation Buffer consisting of 5.6 mmol/L Na2HPO4 (Sigma S7907), 8.0 mmol/L KH2PO4 (Sigma P5655), 96.2 mmol/L NaCl (Sigma S5886), 1.6 mmol/L KCl (Sigma P5405), 43.4 mmol/L Sucrose (Fisher BP 220-1), 54.9 mmol/L d-sorbitol (Fisher BP439-500), and 100 µmol/L Y27632 (Selleck Chemical, S6390) then washed several times by gently inverting the tubes. Tissues were then incubated in Isolation Buffer with 2 mmol/L EDTA (Corning 46-034-Cl) and 0.5mmol/L DTT (Fisher Scientific BP172-5), then shaken vigorously to remove crypts. Shakes were repeated several times, checking for crypts and/or villi each time. High-yield shakes were pooled for colon crypts, and small intestinal shakes were pooled to approximate 1:1 villus to crypt tissue by cell mass. Crypts and villi were dissociated to single cells using 4 mg/ml Protease VIII (Sigma P5380) in dPBS + Y-27632 on ice for ~45min with trituration via a P1000 micropipette every 10 min. Dissociation was checked on a light microscope then clumps were removed using filtration.
Single cells were washed with dPBS + Y-27632 then resuspended in Advanced DMEM/F12 (Gibco 12634-010) + 1% Bovine Serum Albumin (Fisher Scientific BP1600-1) + Y-27632 for staining with AnnexinV-APC (1:100, BioLegend 640920) and with one TotalSeq Anti-Human Hashtag Antibody per region (1:100, BioLegend B0251-B0256) to allow for tracking all six regions with a single library preparation. Cells were washed and resuspended in AdvDMEM + 1% BSA +Y-27632 for sorting on a Sony Cell Sorter SH800Z. Cells were gated using forward and backward scatter and AnnexinV to enrich for live single epithelial cells. 25k cells were collected from each separate region, then all regions were combined before sequencing. Library prep was performed with the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-100012). Sequencing was performed on an Illumina NextSeq 500.
scRNAseq

tag: individual

value: Donor 1

value: mixed sample (epithelium isolated from Duodenum, Jejunum, Ileum, Ascending Colon, Transverse Colon, and Descending Colon)


title: Donor 3 pooled regions [CSP]

description:
csp corresponds to cell surface proteins (aka hashtags (HTOs))
clustered_annotated_adata_k10_lr0.92_v1.7.h5ad
Donor3_filtered_feature_bc_matrix.h5
mag17

molecule: protein

source_name: Donor 3 pooled regions

value: Donor 3

tag: hashtag

value: mixed sample (TotalSeq-B0251 to TotalSeq-B0256)


title: Donor 3 pooled regions [GEX]

description:
gex represents mRNA libraries
clustered_annotated_adata_k10_lr0.92_v1.7.h5ad
Donor3_filtered_feature_bc_matrix.h5
mag17

tag: tissue


title: Donor 2 pooled regions [CSP]

description:
csp corresponds to cell surface proteins (aka hashtags (HTOs))
clustered_annotated_adata_k10_lr0.92_v1.7.h5ad
Donor2_filtered_feature_bc_matrix.h5
mag12

source_name: Donor 2 pooled regions

value: Donor 2


title: Donor 2 pooled regions [GEX]

description:
gex represents mRNA libraries
clustered_annotated_adata_k10_lr0.92_v1.7.h5ad
Donor2_filtered_feature_bc_matrix.h5
mag12


title: Donor 1 pooled regions [CSP]

description:
csp corresponds to cell surface proteins (aka hashtags (HTOs))
clustered_annotated_adata_k10_lr0.92_v1.7.h5ad
Donor1_filtered_feature_bc_matrix.h5
mag15


title: Trophectoderm from low-level mosaic blastocyst 26T

status: Public on Jan 31 2022

city: Valencia

first: Angel

last: Martin

address: Avenida Fernando Abril Martorell, 106 – Edificio Biopolo. Torre A, Planta 1

department: Research

country: Spain

institute: IVI Foundation-HRI La Fe

data_processing:
Pseudo-aligment and quantification were made with Salmon algorithm v1.2.1
Correlation analysis, principal component study and differential expression analysis were performed with DESeq2 package v1.24.0. Differential gene expression analyses were done using the parametric Wald test, with Benjamini-Hochberg adjustment (padj). Genes with padj <0.05 and a log2 fold change of ±2 were considered significantly differentially expressed genes (DEGs).
fgsea package v1.10.1 was used for gene set enrichment of KEGG pathways and GO terms (Biological Processes). Pathways and processes with padj<0.05 were considered significantly deregulated.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files that include TPM values and raw counts per transcript

source_name: Blastocyst fraction

extract_protocol:
SMART-Seq V4 Ultra-Low Input RNA Sequencing kit (Takara Bio, USA); AMPure XP magnetic beads (Illumina, USA)
NexteraXT DNA sample preparation (Illumina, USA)

treatment_protocol: Blastocysts were warmed and cultured for 2-4 hours at 37ºC, 6% CO2, and 5% O2 until re-expansion. An ICM biopsy and the remaining TE were separately collected for RNA extraction

value: Trophectoderm cells

tag: blastocyst biopsy (days postinsemination)

tag: reference blastocyst diagnosis (preimplantation genetic testing)

value: Low-level mosaic (1-2 chromosomes aneuploid in 30%-<50% cells); +12 (Mos), +20 (Mos)

tag: reference blastocyst grade (asebir)

value: B


title: Trophectoderm from low-level mosaic blastocyst 24T

value: Low-level mosaic (1-2 chromosomes aneuploid in 30%-<50% cells); +8 (Mos), -22 (Mos)

value: C


title: Fibroblast uninjured control replicate 2

type: RNA

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Microarray data was assessed for quality, followed by variance stabilization and quantile normalization using the Bioconductor package lumi

label: Biotin

source_name: Lung, sorted

label_protocol: High quality RNA samples were converved to cDNA and biotin-labaled

growth_protocol: Lung tissue underwent enzymatic digestion and cell sorting. We focused on the following cell populations for sorting: FoxD1-derived+/Coll-GFP– pericytes (Peri), FoxD1-derived+/Coll-GFP+ pericytes (PeriFibro), and FoxD1-derived–/Coll-GFP+ stromal fibroblasts (Fibro).

extract_protocol: Total RNA was isolated using Rneasy Micro Kit (Qiagen, Valencia, CA) and RNA integrity was confirmed with an Agilent 4200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA).

treatment_protocol: Bleomycin (0.8 U/kg mouse body weight) was administered to mice by intratracheal instillation (2 uL/g mouse body weight) or equivalent volume of saline (uninjured controls) under isoflurane anesthesia, and samples harvested at day 7.

tag: group

value: Fibroblast uninjured control

tag: gender

value: Female


title: PeriFibro bleomycin injured replicate 3

value: PeriFibro bleomycin injured


title: Fibroblast bleomycin injured replicate 3

value: Fibroblast bleomycin injured


title: PeriFibro bleomycin injured replicate 1


title: Inner cell mass from low-level mosaic blastocyst 24M

value: Inner-cell-mass cells


title: PeriFibro uninjured control replicate 1

value: PeriFibro uninjured control


title: PeriFibro uninjured control replicate 2


title: Fibroblast bleomycin injured replicate 1

value: Male


title: PeriFibro bleomycin injured replicate 2


title: Periyte uninjured control replicate 2

value: Periyte uninjured control


title: Pericyte bleomycin injured replicate 2

value: Pericyte bleomycin injured


title: Trophectoderm from high-level mosaic blastocyst 18T

value: High-level mosaic (1-2 chromosomes aneuploid in 50%-<70% cells); -20 (Mos)


title: Fibroblast uninjured control replicate 1


title: Inner cell mass from high-level mosaic blastocyst 18M


title: Trophectoderm from low-level mosaic blastocyst 16T

value: Low-level mosaic (1-2 chromosomes aneuploid in 30%-<50% cells); -22 (Mos)


title: Inner cell mass from euploid blastocyst 22M

value: Euploid (<30% of aneuploid cells)


title: Trophectoderm from euploid blastocyst 20T

value: Trophectoderm cells


title: Inner cell mass from euploid blastocyst 20M


title: Pericyte uninjured control replicate 1

value: Pericyte uninjured control


title: Trophectoderm from low-level mosaic blastocyst 19T

value: Low-level mosaic (1-2 chromosomes aneuploid in 30%-<50% cells); +4 (Mos)

value: B


title: Trophectoderm from high-level mosaic blastocyst 14T

value: High-level mosaic (1-2 chromosomes aneuploid in 50%-<70% cells); +19 (Mos)


title: Inner cell mass from low-level mosaic blastocyst 16M

value: C


title: Pericyte bleomycin injured replicate 1


title: Fibroblast bleomycin injured replicate 2


title: Trophectoderm from euploid blastocyst 13T


title: Inner cell mass from euploid blastocyst 11M


title: Trophectoderm from euploid blastocyst 11T


title: Inner cell mass from euploid blastocyst 13M


title: Trophectoderm from low-level mosaic blastocyst 4T

value: Low-level mosaic (1-2 chromosomes aneuploid in 30%-<50% cells); +6 (Mos), -7 (Mos)


title: Inner cell mass from euploid blastocyst 8M


title: Trophectoderm from high-level mosaic blastocyst 6T

value: High-level mosaic (1-2 chromosomes aneuploid in 50%-<70% cells); +8 (Mos)


title: Trophectoderm from high-level mosaic blastocyst 3T

value: High-level mosaic (1-2 chromosomes aneuploid in 50%-<70% cells); +4 (Mos)


title: Inner cell mass from low-level mosaic blastocyst 4M

value: Inner-cell-mass cells


title: Inner cell mass from high-level mosaic blastocyst 3M


title: HEC_IgA_treated_1

status: Public on Jan 20 2022

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

data_processing:
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt (https://doi.org/10.14806/ej.17.1.200) (version 1.8.1), and mapped to hg19 reference genome using star v2.5.3a with default settings.
Uniquely mapped reads were counted at gene-level byfeautreCounts (version 1.5) using Gencodev30 transcript annotations for human
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each sample

source_name: Endometrial cancer Cell line (HEC)

growth_protocol: HEC-1-A cells in culture in 2% FBS containing McCoy's 5A media

extract_protocol:
Cells were washed, trypsinized,follwed by total RNA was extraction using RNeasy Plus micro kit. Genomic DNA was removed by DNase treatment.
RNA libraries were prepared for sequencing using Ovation® Human FFPE RNA-Seq kit

treatment_protocol: Cells were treated with or without 0.5 μg/mL of antibodies or vehicle for 72 hours.

tag: cancer type

value: HEC-1-A cell line

value: Adherent cell line

tag: tag

value: Human endometrial adenocarcinoma cell line


title: HEC_IgA_treated_2


title: HEC_IgA_treated_3


title: HEC_IgG_treated_2


title: HEC_untreated_2


title: HEC_untreated_1


title: HEC_untreated_3


title: PIGR_ve_KLE_IgG_treated_3

description:
S18
processed data file: KLE_PIRG_transduction_raw_count.txt

growth_protocol: KLE cells in culture in 2% FBS containing DMEM/F12 media

tag: cancer type/cell line

value: Endometrial cancer Cell line (KLE)

tag: genotype/variation

value: PIGR transduction

tag: treatment

value: IgG


title: PIGR_ve_KLE_IgG_treated_2

description:
S17
processed data file: KLE_PIRG_transduction_raw_count.txt

tag: cell type


title: PIGR_ve_KLE_IgA_treated_2

description:
S14
processed data file: KLE_PIRG_transduction_raw_count.txt

value: IgA


title: PIGR_ve_KLE_IgG_treated_1

description:
S16
processed data file: KLE_PIRG_transduction_raw_count.txt


title: PIGR_ve_KLE_IgA_treated_3

description:
S15
processed data file: KLE_PIRG_transduction_raw_count.txt


title: Inner cell mass from high-level mosaic blastocyst 6M


title: PIGR_ve_KLE_untreated_2

description:
S11
processed data file: KLE_PIRG_transduction_raw_count.txt

value: none (untreated)


title: Inner cell mass from high-level mosaic blastocyst 14M


title: PIGR_ve_KLE_IgA_treated_1

description:
S13
processed data file: KLE_PIRG_transduction_raw_count.txt


title: Trophectoderm from euploid blastocyst 8T

value: Trophectoderm cells

value: Euploid (<30% of aneuploid cells)


title: KLE_IgG_treated_3

description:
S09
processed data file: KLE_raw_count.txt


title: PIGR_ve_KLE_untreated_1

description:
S10
processed data file: KLE_PIRG_transduction_raw_count.txt


title: KLE_IgG_treated_2

description:
S08
processed data file: KLE_raw_count.txt


title: KLE_IgA_treated_2

description:
S05
processed data file: KLE_raw_count.txt


title: HEC_IgG_treated_3


title: KLE_IgA_treated_1

description:
S04
processed data file: KLE_raw_count.txt


title: KLE_IgA_treated_3

description:
S06
processed data file: KLE_raw_count.txt


title: KLE_untreated_3

description:
S03
processed data file: KLE_raw_count.txt


title: KLE_untreated_1

description:
S01
processed data file: KLE_raw_count.txt


title: KLE_untreated_2

description:
S02
processed data file: KLE_raw_count.txt


title: heat_0.5h_40C_A

status: Public on Jan 01 2022

city: St. Louis

first: Ru

last: Zhang

state: Missouri

address: 95 N Warson Rd

institute: Donald Danforth Plant Science Center

data_processing:
Samples were quality control filtered using the JGI BBDuk and BBMap pipelines
Samples were quality assessed using FastQC
Reads were mapped to the Chlamydomonas reinhardtii v5.6 genome (Merchant et al., 2007) using STAR (Dobin and Gingeras, 2015; Dobin et al., 2013) with the maximum number of mapped loci set to 1 and the maximum mismatches per read set to 1, resulting in >92% of all reads being uniquely mapped to the Chlamydomonas reinhardtii v5.6 genome.
Reads per feature were counted via HT-seq count (Anders et al., 2014).
The dataset was filtered for genes that met minimum read count cutoffs of at least 10 mapped reads in at least 10% of the samples, resulting in 15,541 genes for downstream analyses
Differential expression modeling was performed on transcripts per million (TPM) normalized read counts using a generalized linear mixed-effect model and a negative binomial distribution. Treatment time points were compared to pre-heat controls. Significant differential expression was defined as |log2 fold-change > 1, FDR < 0.05, and |(control mean TPM) – (treatment mean TPM)| ≥ 1. FDR correction was performed using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995).
Genome_build: Chlamydomonas reinhardtii v5.6 genome
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Chlamydomonas reinhardtii

growth_protocol: Chlamydomonas reinhardtii wildtype strain (cc1690, also called 21gr, mt+) was used in all experiments. CC1690 were grown in standard Tris-acetate-phosphate (TAP) medium in 400mL photobioreactors (PBRs) (Photon System Instruments, FMT 150/400-RB). Cultures were illuminated with constant 100 µmol photons m-2 s-1 light (50% red: 50% blue), mixed by bubbling with filtered air at a flow rate of 1 L/minute. Algal growth was turbidostatically maintained using OD680 during the experiments, so the algal cultures were not limited by nutrients or light. After PBR inoculation, cultures were allowed to grow to a target cell density of 2.00x106 cells/mL corresponding to around 4.0 ug/mL chlorophyll content in log-phase growth at 25oC. The steady condition was maintained turbidostatically using OD680 for 4 days to allow cultures to adapt to steady growth conditions at 25oC before heat treatments

extract_protocol:
At each time point, approximately 4x106 cells were pelleted with Tween-20 (0.005%, v/v) by centrifugation at 1,100 x g and 4oC for 2 min. The cell pellet was flash frozen in liquid nitrogen and stored at -80oC before processing. Total RNA was extracted with the TRIzol reagent (Thermo Fisher Scientific, Cat No. 15596026) as described before with some modifications (Zones et al., 2015). RNA was purified by RNeasy mini-column (Qiagen, Cat No. 74106) after on column digestion with RNase-free DNase (Qiagen, Cat No. 79256) according to the manufacturer’s instructions. RNA was quantified with Qubit™ RNA BR Assay Kit, (Life technology, Cat No. Q10210). Total 0.4 μg RNA was reverse transcribed with oligo dT primers using SuperScript® III First-Strand Synthesis System (Life technology, Cat No. 18080-051) according to the manufacturer’s instructions. Quantitative real-time PCR (RT-qPCR) analysis was carried out using a CFX384 Real-Time System (C 1000 Touch Thermal Cycler, Bio-Rad, Hercules, California) using SensiFAST SYBR No-ROS kit (Bioline, BIO-98020). PCR was set up as follows: 2 min at 95˚C, followed by 40 cycles of 5 s at 95oC, 10 s at 60oC and 15 s at 72oC. Melting curve was checked right after all PCR cycles to make sure there are no primer dimers or unspecific PCR products. Expression of G-protein β-subunit-like polypeptide CBLP (Cre06.g278222), (Schloss, 1990) remain stable among all time points, and were used as internal controls (Xie et al., 2013). The relative expressions were calculated relative to its expression in pre-heat by the ΔΔCT method (Livak and Schmittgen, 2001b). The qPCR primers for tested genes (CBLP, HSP22A, HSP90A, and others) are listed in Supplementary Table 1. PCR efficiencies were checked and were employed to the 2−ΔΔCT method to calculate the relative expression as described previously (Livak and Schmittgen, 2001; Hellemans et al., 2007; Remans et al., 2014). Three biological replicates for each time point and treatment were conducted.
Library construction was perfored at the Department of Energy (DOE) Joint Genome Institute (JGI)

treatment_protocol: PBR temperatures were shifted to moderate or acute heat stress conditions (35oC and 40oC respectively in different PBRs) for 24 hours, then shifted back to 25oC for 48 hours for recovery.

tag: strain

value: 40C high temperature

tag: time point


title: recovery_24h_35C_C

value: recovery following 35C high temperature


title: heat_16h_40C_C


title: WM3438 - PLX4032-treated (18 h) - rep 2

status: Public on Dec 11 2021

city: Freiburg

first: Eyleen

last: Corrales

address: Breisacherstr. 153

department: Medizinische Fakultät

institute: Institut für Medizinische Bioinformatik und Systemmedizin

data_processing:
Adapter trimming and quality filtering of reads was performed with Trimmomatic, with parameters HEADCROP:3 TRAILING:20 MINLEN:35
Reads were mapped to the Ensembl GRCh37 reference genome with the STAR aligner, with parameters --twopassMode Basic --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5
Non-uniquely mapped reads were discarded.
Genes that failed to achieve a minimum of one count-per-million (CPM) in at least two of the samples were filtered out as unexpressed.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw counts

source_name: malignant melanoma

growth_protocol: The cell lines were maintained at 37°C in a humidified atmosphere of 5 % CO2 using RPMI-1640 medium supplemented with 10 % FCS, 1 % L-glutamine, and 1 % penicillin-streptomycin.

extract_protocol:
Cell pellets were collected by scrapping. Total RNA was isolated using the Universal RNA Purification Kit (Roboklon).
Libraries were prepared using standard Illumina protocols.

treatment_protocol: Pharmacological inhibition was performed with 2 µM of vemurafenib (PLX4032) or an analog volume of vehicle (0.2 % of DMSO) as control, during 4 h, 8 h, 18 h for HDF, 24 h for MaMel, and 18 h or 24 h for SBcl2 and WM3438 cell lines.

tag: cell line

value: human malignant melanoma

value: metastatic cutaneous melanoma (site not specified)

tag: tumor stage

value: metastatic

value: female

tag: genotype

value: BRAF wild-type

value: vemurafenib (PLX4032) for 18 hours


title: WM3438 - DMSO-treated (18 h) - rep 1

tag: tissue

value: DMSO (control) for 18 hours


title: WM3438 - DMSO-treated (18 h) - rep 2


title: WM3438 - PLX4032-treated (18 h) - rep 1


title: SBcl2 - DMSO-treated (18 h) - rep A

value: primary cutaneous melanoma

value: radial growth phase

value: male


title: WM3438 - PLX4032-treated (24 h) - rep 2

value: vemurafenib (PLX4032) for 24 hours


title: WM3438 - PLX4032-treated (24 h) - rep 1


title: WM3438 - DMSO-treated (24 h) - rep 2

value: DMSO (control) for 24 hours


title: SBcl2 - DMSO-treated (24 h) - rep A


title: PIGR_ve_KLE_untreated_3

description:
S12
processed data file: KLE_PIRG_transduction_raw_count.txt

value: Endometrial cancer Cell line (KLE)

value: Adherent cell line

value: PIGR transduction

value: none (untreated)


title: SBcl2 - PLX4032-treated (24 h) - rep B


title: MaMel63a - PLX4032-treated (24 h) - rep 2

value: skin metastasis

value: stage IV

value: BRAF V600E-positive


title: SBcl2 - DMSO-treated (18 h) - rep B

value: human malignant melanoma


title: WM3438 - DMSO-treated (24 h) - rep 1

value: metastatic cutaneous melanoma (site not specified)

value: metastatic

value: female


title: HEC_IgG_treated_1

value: HEC-1-A cell line

value: Human endometrial adenocarcinoma cell line


title: SBcl2 - PLX4032-treated (24 h) - rep A

value: primary cutaneous melanoma

value: radial growth phase

value: BRAF wild-type


title: SBcl2 - DMSO-treated (24 h) - rep B

value: male

value: DMSO (control) for 24 hours


title: KLE_IgG_treated_1

description:
S07
processed data file: KLE_raw_count.txt

value: Endometrial cancer Cell line (KLE)

value: Adherent cell line

value: IgG


title: MaMel21 - PLX4032-treated (24 h) - rep 1

value: skin metastasis

value: vemurafenib (PLX4032) for 24 hours


title: SBcl2 - PLX4032-treated (18 h) - rep A

value: vemurafenib (PLX4032) for 18 hours


title: SBcl2 - PLX4032-treated (18 h) - rep B

value: human malignant melanoma


title: HDF-A - PLX4032-treated (18 h) - rep 2

source_name: dermal fibroblasts

value: human dermal fibroblasts

value: juvenile foreskin


title: HDF-B - PLX4032-treated (8 h) - rep 1

value: vemurafenib (PLX4032) for 8 hours


title: MaMel21 - PLX4032-treated (24 h) - rep 2

value: stage IV

value: female

value: BRAF V600E-positive


title: MaMel63a - PLX4032-treated (24 h) - rep 1


title: HDF-B - PLX4032-treated (18 h) - rep 2


title: HDF-A - PLX4032-treated (8 h) - rep 1


title: HDF-B - PLX4032-treated (18 h) - rep 1


title: HDF-A - PLX4032-treated (8 h) - rep 2


title: HDF-B - PLX4032-treated (4 h) - rep 1

value: vemurafenib (PLX4032) for 4 hours


title: HDF-A - PLX4032-treated (4 h) - rep 2

value: BRAF wild-type


title: HDF-B - PLX4032-treated (4 h) - rep 2

value: male


title: HDF-B - DMSO-treated (18 h) - rep 2

value: DMSO (control) for 18 hours


title: HDF-B - DMSO-treated (18 h) - rep 1


title: HDF-A - PLX4032-treated (4 h) - rep 1


title: HDF-A - DMSO-treated (18 h) - rep 1


title: MaMel63a - DMSO-treated (24 h) - rep 2

value: DMSO (control) for 24 hours


title: HDF-B - DMSO-treated (8 h) - rep 2

value: DMSO (control) for 8 hours


title: HDF-A - PLX4032-treated (18 h) - rep 1


title: MaMel63a - DMSO-treated (24 h) - rep 1


title: HDF-B - DMSO-treated (4 h) - rep 1

value: DMSO (control) for 4 hours


title: MaMel21 - DMSO-treated (24 h) - rep 2

value: skin metastasis


title: HDF-A - DMSO-treated (18 h) - rep 2


title: HDF - PLX4032-treated (4 h) - rep 2

data_processing:
Adapter trimming and quality filtering of reads was performed with Trimmomatic, with parameters  TRAILING:20 MINLEN:25
Reads were mapped to the Ensembl GRCh37 reference genome using Bowtie 2, with parameters -X 2000 --very-sensitive --dovetail
Alignments with a MAPQ score bellow 30, unproperly paired, duplicates, or those mapping to the mitochondrial chromosome were discarded
Reads were shifted with deepTools alignmentSieve
Peak calling was performed on libraries down-sampled to ~53 millions reads. Peaks were collectively called from the replicates using Genrich, with parameters -v -j -r -y -e chrM -d 100 -q 0.01 -a 200. ENCODE blacklisted regions (ENCFF001TDO) were excluded from the called peaks.
Genome_build: GRCh37
Supplementary_files_format_and_content: narrowPeak

source_name: HDF - PLX4032-treated (4 h)

extract_protocol:
Cell pellets were collected by scrapping. Chromatin was isolated according to the original protocol from Buenrostro et al. (2015).
Libraries were prepared according to the original protocol from Buenrostro et al. (2015).

treatment_protocol: Pharmacological inhibition was performed with 2 µM of vemurafenib (PLX4032), or an analog volume of vehicle (0.2 % of DMSO) as control, during 4 h, 8 h, or 18 h

value: juvenil foreskin


title: HDF - PLX4032-treated (18 h) - rep 1

source_name: HDF - PLX4032-treated (18 h)

value: vemurafenib (PLX4032) for 18 hours


title: HDF-B - DMSO-treated (8 h) - rep 1


title: HDF-B - PLX4032-treated (8 h) - rep 2


title: HDF - DMSO-treated (8 h) - rep 1

source_name: HDF - DMSO-treated (8 h)


title: HDF-B - DMSO-treated (4 h) - rep 2


title: HDF-A - DMSO-treated (8 h) - rep 1


title: HDF - DMSO-treated (4 h) - rep 1

source_name: HDF - DMSO-treated (4 h)


title: HDF-A - DMSO-treated (4 h) - rep 1


title: HDF - PLX4032-treated (18 h) - rep 2


title: HDF-A - DMSO-treated (4 h) - rep 2


title: HDF-A - DMSO-treated (8 h) - rep 2


title: HDF - PLX4032-treated (8 h) - rep 2

source_name: HDF - PLX4032-treated (8 h)


title: scGOF-Seq ND donor (ND5) Dataset 2

status: Public on Nov 11 2021

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

data_processing:
For UMI (Unique Molecular Identifier) matrices (_umi.csv), demultiplexing, alignment, mapping and UMI quantification were performed using 10x Genomics Cell Ranger pipeline (v2.1.1).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file include UMI counts for each cell.
For BC (barcode) matrices (_bc.csv), fastq files were run through standard scPLATE-Seq data processing pipeline (detailed data processing pipeline described under GEO accession number GSE104493). Specifically, alignment and mapping were performed by STAR (2.5.2a) with flag --outFilterMultimapNmax 1 to exclude multi-mapping reads for accurate BC quantification.
Genome_build: Customized genome (hg38+plasmid construct sequences)
Supplementary_files_format_and_content: CSV  file include BC counts for each cell.

source_name: Non-diabetic islet cells

extract_protocol:
Standard 10x Genomics scRNA-Seq 3' V2 protocol (CG00052).
Standard Illumina HiSeq 4000 protocol.

value: Non-diabetic islet cells

tag: scgof-seq adenovirus

value: Mixed population (AFF3, BACH2, BNC2, CUX2, EBF1, FOXO1, GAS7, MYT1L, NFATC3, RARB, RFX7, TCF4, TSHZ2, ZFN385D, ZRANB3)


title: scGOF-Seq ND donor (ND5) Dataset 1

source_name: Non-diabetic islet β-cells (enriched by FAD+)

value: Non-diabetic islet Beta-cells (enriched by FAD+)


title: HDF - PLX4032-treated (4 h) - rep 1

value: human dermal fibroblasts


title: HDF - DMSO-treated (18 h) - rep 2

source_name: HDF - DMSO-treated (18 h)


title: MaMel21 - DMSO-treated (24 h) - rep 1

value: human malignant melanoma

value: stage IV


title: scGOF-Seq ND donor (ND6) ctrl Dataset 2


title: scGOF-Seq ND donor (ND6) Dataset 1


title: HDF - DMSO-treated (18 h) - rep 1


title: HDF - DMSO-treated (4 h) - rep 2


title: Perturb-Seq T2D donor (T2D7) Dataset 1

data_processing:
For UMI (Unique Molecular Identifier) matrices (_umi.csv), demultiplexing, alignment, mapping and UMI quantification were performed using 10x Genomics Cell Ranger pipeline (v2.1.1).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file include UMI counts for each cell.
For BC (barcode) matrices (_bc.csv), fastq files were run through standard scPLATE-Seq data processing pipeline (detailed data processing pipeline described under GEO accession number GSE104493). Specifically, alignment and mapping were performed by STAR (2.5.2a) with flag --outFilterMultimapNmax 1 to exclude multi-mapping reads for accurate BC quantification.
Genome_build: Customized genome (hg38+plasmid construct sequences)
Supplementary_files_format_and_content: Tab-delimited text file include BC counts for each cell.

source_name: Perturb-Seq SET

value: Islet beta-cells (enriched by FAD+)

tag: perturb-seq adenovirus

value: Mixed population (AFF3, BACH2, CNBP, CUX2, JUND, MAFA, SCAND1, SIX3, SMAD2, negative control)

tag: donor condition

value: Type 2 Diabetes (T2D)


title: blood.stbonemarrow.ststomachHP.st

status: Public on Oct 22 2021

city: Basel

first: Costanza

last: Borrelli

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zürich

data_processing:
raw FASTQ processing on the Seven Bridges Genomics platform with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: cell x read count matrix as .st data, convert to sparse matrix with function on github repository

source_name: mixed sample (non-demultiplexed)

extract_protocol:
magnetic enrichment (MACS) based on anti-SiglecF-Pe and anti-PE magnetic beads
BD Rhapsody: WTA kit and Mouse Multiplexing Kit

treatment_protocol: when indicated, mice where infected with H. pylori or C.rodentium by gavage

tag: condition

value: mixed sample (non-demultiplexed)


title: IgG replicate 3

status: Public on Jul 23 2021

data_processing:
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt (https://doi.org/10.14806/ej.17.1.200) (version 1.8.1), and mapped to mm10 reference genome using star v2.5.3a with default settings.
Uniquely mapped reads were counted at gene-level by htseq-count (version 0.6.1) using Gencode vm21 transcript annotations for mouse
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each sample

source_name: Orthotopically injected TMPRSS2-ERG+ expressing prostate tumors

extract_protocol:
Total RNA was extraction using RNeasy Plus micro kit. Genomic DNA was removed by DNase treatment.
RNA libraries were prepared for sequencing using NuGen Ovation Mouse RNA-Seq kit

value: Prostate

value: TMPRSS2-ERG+ expressing

value: IgG

tag: rin

tag: 28s/18s (height)

tag: total rna area

tag: rrna area

tag: conc. [ng/ul]


title: Lupron/anti-CSF1 replicate 3

tag: treatment

value: Lupron plus alpha-CSF1


title: HDF - DMSO-treated (8 h) - rep 2

tag: cell type

tag: gender

value: male

value: BRAF wild-type

value: DMSO (control) for 8 hours


title: Lupron replicate 3

value: Lupron


title: Perturb-Seq T2D donor (T2D7) Dataset 2

value: Islet alpha-cells (enriched by FAD-)


title: scATAC.Treg.Tconv

status: Public on Dec 07 2021

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Fastq files were generated from BCL files using bcl2fastq.
Fastq files were aligned to the mm10 genome and used to create count matrices using the cellRanger ATAC pipeline using cellranger-atac count (v1.2, 10x Genomics)
Fragments were intersected with open chromatin regions previously defined by the ImmGen consortium (Yoshida et al, Cell, 2019) to create an intial OCR x cell counts matrix. Preprocessing was done using Signac (v1.1), retaining cells with at least 4000 fragments per cell, greater than 55 percent reads in peaks, TSS enrichment score greater than 2, nucleosome signal less than 10, and ratio of blacklist-region reads less than 0.05. Putative doublets were removed using Archr (v0.9.3)
Archr (v0.9.3) was used to call cluster-specific peaks using MACS2. To create a final peak set, MACS2 peak calls were compared with OCRs defined by the ImmGen consortium in Yoshida et al. In cases where MACS2 peak calls overlapped ImmGen OCRs, the Immgen reference peak was kept. Any MACS2 peaks not overlapping OCRs in the ImmGen dataset were added to this list to create a final merged Treg-specific peak set. Immgen peaks without overlapping MACS2 calls from this dataset were not included in the final Treg peak set.
Genome_build: mm10
Supplementary_files_format_and_content: .mtx counts matrix; .tsv cell barcodes list; .tsv OCR locations; .fragments.tsv.gz fragments file; .fragments.tsv.gz.tbi fragments index file

extract_protocol:
Splenic regulatory T cells (CD4+, TCRβ+, FoxP3-IRES-GFP+) and T conventional cells (CD4+, TCRβ+, FoxP3-IRES-GFP-) were sorted from 6-8 week old B6 FoxP3-IRES-GFP mice into DMEM + 2% FCS, then resuspended in PBS + 0.04% BSA. Nuclei isolation, transposition, and GEM generation targeting capture of ~12000 cells (75% Tregs, 25% Tconv) were carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics). 0.1x lysis buffer was used for cell lysis and nuclei isolation.
Library construction was carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics).

tag: strain

value: spleen

value: wt


title: Perturb-Seq T2D donor (T2D7) ctrl Dataset 2

source_name: Perturb-Seq non-infected Ctrl SET


title: IgG replicate 2


title: anti-CSF1 replicate 2


title: scGOF-Seq ND donor (ND6) Dataset 2

value: Non-diabetic islet Beta-cells (enriched by FAD+)

tag: gof adenovirus

value: Mixed population (AFF3, BACH2, BNC2, CUX2, EBF1, FOXO1, GAS7, MYT1L, NFATC3, RARB, RFX7, TCF4, TSHZ2, ZFN385D, ZRANB3)


title: Lupron replicate 2


title: Perturb-Seq T2D donor (T2D7) ctrl Dataset 1

value: Islet beta-cells (enriched by FAD+)


title: Lupron/anti-CSF1 replicate 1


title: HDF - PLX4032-treated (8 h) - rep 1

value: human dermal fibroblasts

value: juvenil foreskin

value: vemurafenib (PLX4032) for 8 hours


title: anti-CSF1 replicate 1

value: Prostate


title: SMC 72hr replicate 3

status: Public on Jul 07 2021

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

country: Japan

institute: Kyushu University

data_processing:
Paired-end reads were mapped to the GRCh38 reference genome using hisat2 version 2.0.5 [Kim et al., 2015]. Mapped reads were assigned to all exons using featureCounts version 1.4.6 [Liao et al., 2014].
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include CPM (counts per millions) values per gene

source_name: SMC

growth_protocol: hcSMCs (Human Coronary Artery Smooth Muscle Cells) were cultured in SMGM-2 (Smooth Muscle Growth Medium-2, Lonza) at 37C. After reaching confluent, hcSMCs were washed in PBS, and the culture medium was changed to DMEM low glucose, pyruvate with 0.2% fetal bovine serum for 24 hours. After this, cholesterol was delivered to cells by changing the medium to DMEM with water-soluble cholesterol at a final concentration 1.7 μg/ml (37.5 μg/ml; cholesterol:methyl-β-cyclodextrin complexes [Chol:MβCD])). Cells were harvested at 24, 48, 72 hours after the cholesterol loading started.

extract_protocol:
Cultured hcSMCs were washed once with PBS and lysed directly with the lysis buffer in the flasks, and total RNA and DNA were extracted using RNA/DNA/Protein Purification Plus Kit (Norgen #47700). The DNA samples was quantified using Qubit® 2.0 Fluorometer (Life technologies).
RNA-seq libraries were prepared with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, E7420) and NEBNext rRNA Depletion Kit (E6310). PCR library enrichment was performed by 15 cycles of PCR with NEBNext Multiplex Oligos for Illumina (NEB #E7335). Quantification of library was performed using an Agilent 2100 Bioanalyzer and a Kapa Library Quantification Kit (Kapa Biosystems).

value: Cultured smooth muscle cells


title: SMC 72hr replicate 1


title: scGOF-Seq ND donor (ND6) ctrl Dataset 1

value: Non-diabetic islet cells


title: bloodCR.stbonemarrowCR.stcolonCR.st

value: mixed sample (non-demultiplexed)


title: Stomach.stColon.stSI.stSpleen.st


title: Lupron/anti-CSF1 replicate 2

value: TMPRSS2-ERG+ expressing

value: Lupron plus alpha-CSF1


title: SMC 48hr replicate 2


title: anti-CSF1 replicate 3


title: SMC 24hr replicate 2


title: IgG replicate 1

value: IgG


title: SMC 24hr replicate 1


title: scGOF-Seq ND donor (ND6) Dataset 1 (Technical Duplicate)


title: SMC 72hr replicate 2


title: Lupron replicate 1

value: Lupron


title: MD18239_A

status: Public on Jun 22 2021

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

data_processing:
Analysis run using Salmon 1.1.0.  Salmon index generated using GRCh38.primary_assembly.fa and the ensembl 96 release. Briefly, ensemble (cdna and ncrna) and the reference fasta were concatenated. The‘decoys.txt’ was prepared from GRCh38. Salmon index was then run on the concatenated fasta. R1 and R2 fastq files respectively concatenated for each sample, and Salmon run using auto-detect strandedness and ‘validateMappings’ active.salmon index -t entrome.fa.gz -d decoys.txt -p 6 -i ensembl_96_current
Genome_build: hg38
Supplementary_files_format_and_content: salmon output  files, transcript level. see https://salmon.readthedocs.io/en/latest/file_formats.html

source_name: rectal biopsy

extract_protocol:
After sampling normal mucosa samples were immediately placed in RNAlater and kept immersed for 24-72 hours prior to RNA extraction. RNA was then extracted from NM and PBMC samples using a TRIzol based proprietary RNA extraction kit (Ribopure kit, Applied Biosystems) according to manufacturer protocol.
Libraries were prepared from each total-RNA sample using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (#RS-122-2302) according to the provided protocol.  500ng of total-RNA was processed to deplete rRNA before being purified, fragmented and primed with random hexamers. The fragmentation time was shorten from 8 minutes to 1 minutes to allow for bigger RNA fragments. Primed RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. RNA templates were removed and a replacement strand synthesised incorporating dUTP in place of dTTP to generate ds cDNA. AMPure XP beads (Beckman Coulter, #A63881) were then used to separate the ds cDNA from the second strand reaction mix, providing blunt-ended cDNA. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to another during the subsequent adapter ligation reaction, and a corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. Multiple indexing adapters were then ligated to the ends of the ds cDNA to prepare them for hybridisation onto a flow cell, before 12 cycles of PCR were used to selectively enrich those DNA fragments that had adapter molecules on both ends and amplify the amount of DNA in the library suitable for sequencing.

treatment_protocol: Oral vitamin D (3200IU/day) supplements were administered for 12 weeks

value: pre

value: F

tag: age


title: MD18232_C

value: post


title: MD18232_A


title: MD18237_C


title: MD18231_C

value: M


title: MD18237_A


title: SMC 48hr replicate 3


title: MD18231_A


title: MD17795_C


title: SMC 48hr replicate 1


title: SMC 24hr replicate 3


title: SMC 0hr replicate 2


title: MD18239_C


title: SMC 0hr replicate 1


title: MD17477_A


title: MD17788_A


title: MD17795_A


title: MD17788_C


title: MD17468_A


title: MD17308_D


title: SMC 0hr replicate 3


title: MD17239_D


title: MD17232_C


title: MD17239_B


title: MD17232_A


title: MD17229_C


title: MD17227_C


title: MD17228_C


title: MD17228_A


title: MD17229_A


title: MD17226_A


title: MD17227_A


title: MD17226_C


title: MD17225_C


title: MD16658_D


title: MD17477_C


title: MD17138_C


title: MD16602_C


title: MD16602_A


title: MD17468_C


title: MD16658_B


title: MD16599_D


title: MD16591_D


title: MD17308_B


title: MD16591_B


title: MD16594_D


title: MD16594_B


title: MD16184_E


title: MD16184_C


title: MD17225_A


title: MD16179_B


title: MD16179_D


title: MD17138_A


title: MD14396_B


title: MD16168_C


title: MD14395_C


title: MD14392_C


title: MD14395_A2


title: MD14394_C


title: MD16599_B


title: MD14391_C


title: MD14388_C