title: Single-cell BCR, Subject MuSK MG-4 at 25 months

status: Public on Nov 07 2022

data_processing:
Single cell RNA-seq gene expression information from all subjects was processed using Seurat v4.1.1 in R v4.1.0.
All BCR repertoire sequence data were analyzed using the Immcantation (www.immcantation.org) framework.
Heavy and light chain BCR sequence data from 10X Genomics scRNA-seq + BCR sequencing began with the filtered V(D)J contigs from Cell Ranger version 3.1. To obtain V and J gene assignments, these contigs were aligned to the IMGT GENE-DB (v3.1.23, obtained August 3, 2019) human germline reference database using IgBlast v1.13.0. Preprocessing of NEBNext BCR sequences was performed using pRESTO v0.6.2.
Assembly: GRCh38
Supplementary files format and content: Compressed tar files contain output from CellRanger

source_name: Peripheral Blood

extract_protocol:
RNA was isolated from frozen PBMCs using the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer’s instructions.
Bulk BCR libraries were either generated using the NEBNext Immune Sequencing Kit (NEB) or the SMARTer® Human BCR IgG IgM H/K/L Profiling Kit (Takara Bio USA, Inc.) using the primers targeting IgA, IgG and IgG-sub.   Single-cell libraries were generated from sorted B cells enriched from cryopreserved PBMCs, using the Chromium Single-cell 5′ Reagent Kit (10x Genomics; V 2.0) according to manufacturer’s instructions.

value: Peripheral Blood

tag: cell type

value: B-Lymphocyte


title: Single-cell GEX, Subject MuSK MG-1 at 70 months

type: SRA

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

country: USA

institute: Yale University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Single-cell GEX, Subject MuSK MG-4 at 25 months


title: Islet28

status: Public on Mar 30 2023

city: Farmington

first: Efthymios

last: Motakis

address: 10 Farmington Drive

department: Computational Sciences

institute: The Jackson Laboratory

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads alignment with STARsolo
Estimation and removal of ambient RNA by SoupX
Genetic demultiplexing for the 12 mutiplexed libraries by Demuxlet and removal of doublets
Cluster-based cell QC: the cell clusters are generated by Seurat's processing pipeline and the cells with > 500 features & < 50% MT & >1000 UMIs are kept for further analysis
Doublet identification by Scrublet, DoubletFinder and doublet visualization in the cell clusters
Second step cluster-based cell QC: the cell clusters are re-generated with the cleaner data by Seurat's processing pipeline and the cells with > 1400 features & < 40% MT are kept for further analysis. Keep cells of particular cell types (marker-based pre-annotation) even if the do not satisfy the features criterion.
Data integration by Harmony and integrated data clustering
Visualize the estimated doublets on the integrated data clusters, remove all scrublet doublets plus while custers if they are enriched in such doublets
Keep the clean data for downstream analysis: final cell annotation, differential expression, subclustering
Assembly: HG38
Supplementary files format and content: CellRanger output files

source_name: Pancreatic islets

growth_protocol: Cultured overnight in PIM(S) [ProdoLabs] prior to dissociation and 10X Genomics single cell capture

extract_protocol:
10X Genomics standard procedures for sample dilution and single cell capture
10X Genomcis standard procedures for library construction

treatment_protocol: Islets treated with Accutase for 10 minutes at 37 degrees Celsius and gentle pipetting

value: Pancreatic islets

tag: treatment

tag: chemistry

tag: disease state

tag: Sex

value: Male

tag: bmi

tag: race

value: Hispanic

tag: age

tag: center

value: Scharp-Lacy

tag: Cause of death

value: Cerebrovascular/stroke

tag: library id


title: Single-cell BCR, Subject MuSK MG-1 at 70 months


title: Pooled bulk BCR sample (MuSK MG-1 70mo, MuSK MG-2 105mo, MuSK MG-4 25mo, MuSK MG-5 48mo)


title: Pooled bulk BCR sample (MuSK MG-4 0mo, MuSK MG-1 68mo, MuSK MG-1 70mo, MuSK MG-4 25mo)


title: Pooled bulk BCR sample (MuSK MG-1 61mo, MuSK MG-5 0mo, MuSK MG-4 0mo, MuSK MG-1 68mo)


title: Pooled bulk BCR sample (HC_A, HC_B, HC_C, HD_D)


title: Bulk BCR, Subject MuSK MG-4 at 0 months


title: Pooled bulk BCR sample (MuSK MG-1 61mo, MuSK MG-1 70mo, MuSK MG-2 105mo, MuSK MG-4 25mo)


title: Pooled bulk BCR sample (MuSK MG-5 0mo, MuSK MG-4 0mo, MuSK MG-1 68mo, MuSK MG-5 48mo)


title: CAR T cells in blood of Pt129 on day 7: TCR

status: Public on Jul 28 2022

city: Stanford

first: Zinaida

last: Good

state: California

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute, Department of Biomedical Data Science

institute: Stanford University School of Medicine

description:
pt129-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt129-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt129-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt129-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt129-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds

data_processing:
Cell Ranger count or vdj pipelines for scRNA-seq and CITE-seq, or scTCR-seq (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: An h5 file containing Cell Ranger count pipeline output for filtered cell-feature data: columns contain UMI counts across cells; rows contain features (genes for scRNA-seq or proteins for CITE-seq).
Supplementary files format and content: An HTML file containing Cell Ranger alignment summary statistics.
Supplementary files format and content: A CSV file containing Cell Ranger vdj pipeline output for all or filtered alpha-beta TCR clonotype data: columns contain cells; rows contain TCR clonotype parameters quantified.
Supplementary files format and content: seurat-day7-car-t.rds: Seurat object for all patients.
Library strategy: scTCR-seq

source_name: Live circulating CAR+ T cells

extract_protocol:
Droplet-based single-cell sequencing on 10X Genomics Chromium platform.
10X Genomics Single Cell 5' kit.

tag: patient id

tag: diagnosis

value: Large B-cell lymphoma (LBCL)

tag: time after axi-cel

value: day 7

value: CAR+ T cells

tag: library type

value: scTCR-seq


title: Bulk BCR, Subject MuSK MG-1 at 68 months


title: Pooled bulk BCR sample (HC_A, HC_B, HC_C, HC_D)


title: CAR T cells in blood of Pt116 on day 7: TCR

description:
pt116-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt116-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt116-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt116-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt116-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: Lung section derived from Gramd2:KrasG12D sample 2

status: Public on Oct 19 2022

city: Glendale

first: Crystal

last: Marconett

state: CA

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

description:
Gramd2:KrasG12D Lung 2
FFPE Visium mouse

data_processing:
Paired-end sequencing (2x100) was performed on an Illumina instrument. Sequencing data was pre-processed using the Space Ranger pipelines (10x Genomics, https://cloud.10xgenomics.com/cloud-analysis).
BCL data was demultiplexed and converted to FASTQ format using the spaceranger mkfastq pipeline.
The spaceranger count pipeline was then used for read alignment to human reference genome mm10, Unique Molecular Identifier (UMI) counting, and generation of feature-spot matrices corresponding to the microscopic tissue image. The pipeline also performs automatic tissue detection and fiducial alignment from the image.
Assembly: mm10
Supplementary files format and content: UMI count matrices

organism: Mus musculus

source_name: Lung

growth_protocol: The Sftpc-CreERT2 mouse line has been used previously to track AT2 cell fate (65, 66). Gramd2-CreERT2 mice were generated by homologous recombination insertion of a cassette including CreERT2- downstream of the endogenous Gramd2 gene stop codon within exon 12. These were separately crossed to heterozygous KrasLSL-G12D mice (Jackson laboratory, Stock: #008179). Gramd2-CreERT2 and Sftpc-CreERT2 mice were in a B6/129 mixed strain background (129 N1), while KrasLSL-G12D mice are in a B6/129S4 mixed strain background (C57BL/6 N10).

extract_protocol:
Spatial transcriptomic profiling was performed at the Molecular Genomics Core, a part of the Norris Comprehensive Cancer Center and under manufacturer’s instructions. Briefly, two biological replicates (one block for each) of Gramd2:KrasG12D and Sftpc:KrasG12D underwent initial 10μM sectioning at the Tissue Pathology Core, part of the Norris Comprehensive Cancer Center. Sections were H&E stained (as above) and underwent pathology review. Regions of Interest (ROIs) then underwent sample preparation including test slide sample sequencing using the Visium Tissue Section Test Slide (PN-2000460, 10X Genomics, Dublin, CA, USA). RNA quality assessment of test slides was determined by first extracting RNA using the Qiagen RNeasy FFPE kit (#73504, Qiagen, Hilden, Germany) and measuring RNA concentration using a Qubit fluorometer (#Q33238, ThermoFisher Scientific, Waltham, MA, USA). To determine The percentage of total fragments >200nt in length was determined by running the samples using a 4200 Tapestation (#G2991AA, Agilent, Santa Clara, CA). Once samples were determined to be of high enough quality to continue, 5μM FFPE sections were then placed in a 42C water bath and once rehydrated adhered to the Visium Spatial Gene Expression Slide (PN-2000233, 10X Genomics). Subsequently, samples were dried at 42C for 3hrs in a desiccation chamber and underwent deparrafinization using Qiagen Deparaffinization Solution (Cat # 19093) at 60C for 2 hr. Subsequently H&E staining (#MHS16, #HT110116 Millipore Sigma, Burlington MA, USA) was performed according to Visium technical parameters (CG000409) and images were captured with a Zeiss Axioscan2 microscope using a 10x objective. Decrosslinking was performed according to 10X standard protocol (CG000407) and immediately hybridized to the Visium Mouse Transcriptome probe set V1.0, which contained 20,551 genes targeted by 20,873 probes.
Post-probe extension, sequencing library construction was performed using unique sample indices using the Dual Index Kit TS, Set A (PN-1000251) for Illumina-compatible sequencing.

treatment_protocol: Tamoxifen (Sigma, CAS: 10540-29-1) powder was first dissolved in 100% ethanol (SHBJ8384, Sigma-Aldrich) and then diluted to a final concentration of 40 mg/mL with corn oil (Sigma, CAS: 8001-30-7). To ensure that tamoxifen was fully dissolved, the mixture was gently shaken in a shaking incubator (SHEL LAB, model: SSI5R; cat: #33-804R) at 55℃ for 2 hours. Six-week-old mice were injected with tamoxifen via intraperitoneal injection. For Gramd2-CreERT2; Sftpc-CreERT2, KrasLSL-G12D and WT mice, 40 mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 200 mg/Kg according to the body weight of each mouse. Tamoxifen was given three times over a period of one week. For Sftpc::KrasLSL-G12D mice, 40mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 100 mg/Kg according to the body weight of each mouse. Tamoxifen was given twice over a period of one week.

value: Lung

tag: genotype

value: C57BL/6 Gramd2-CreERT2;Kras-LSL-G12D

value: 3x 150 ug/kg Tamoxifen


title: CAR T cells in blood of Pt125 on day 7

description:
pt125-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt125-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt125-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds

data_processing:
Cell Ranger count or vdj pipelines for scRNA-seq and CITE-seq, or scTCR-seq (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: An h5 file containing Cell Ranger count pipeline output for filtered cell-feature data: columns contain UMI counts across cells; rows contain features (genes for scRNA-seq or proteins for CITE-seq).
Supplementary files format and content: An HTML file containing Cell Ranger alignment summary statistics.
Supplementary files format and content: A CSV file containing Cell Ranger vdj pipeline output for all or filtered alpha-beta TCR clonotype data: columns contain cells; rows contain TCR clonotype parameters quantified.
Supplementary files format and content: seurat-day7-car-t.rds: Seurat object for all patients.

tag: cell type

value: scRNA-seq and CITE-seq


title: CAR T cells in blood of Pt129 on day 7

description:
pt129-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt129-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt129-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: Lung section derived from Gramd2:KrasG12D sample 1

description:
Gramd2:KrasG12D Lung 1
FFPE Visium mouse

tag: tissue


title: CAR T cells in blood of Pt110 on day 7

description:
pt110-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt110-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt110-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt276 on day 7

description:
pt276-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt276-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt276-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt282 on day 7: TCR

description:
pt282-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt282-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt282-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt282-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt282-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt110 on day 7: TCR

description:
pt110-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt110-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt110-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt110-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt110-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt263 on day 7

description:
pt263-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt263-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt263-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: Bulk BCR, Subject MuSK MG-1 at 70 months


title: CAR T cells in blood of Pt125 on day 7: TCR

description:
pt125-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt125-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt125-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt125-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt125-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: Lung section derived from Sftpc:KrasG12D sample 2

description:
Sftpc:KrasG12D Lung 2
FFPE Visium mouse

value: C57BL/6 Sftpc-CreERT2;Kras-LSL-G12D

tag: treatment

value: 2x100 ug/kg Tamoxifen


title: CAR T cells in blood of Pt276 on day 7: TCR

description:
pt276-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt276-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt276-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt276-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt276-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: Bulk BCR, Subject MuSK MG-4 at 25 months

value: Peripheral Blood


title: CAR T cells in blood of Pt263 on day 7: TCR

description:
pt263-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt263-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt263-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt263-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt263-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt116 on day 7

description:
pt116-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v1
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt116-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt116-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt282 on day 7

description:
pt282-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt282-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt282-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: CAR T cells in blood of Pt253 on day 7: TCR

description:
pt253-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt253-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt253-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt253-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt253-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: Lung section derived from Sftpc:KrasG12D sample 1

description:
Sftpc:KrasG12D Lung 1
FFPE Visium mouse


title: CAR T cells in blood of Pt245 on day 7: TCR

description:
pt245-day7-car-t-tcr
abTCR CDR3 amplified RNA region
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt245-day7-car-t-filtered_feature_bc_matrix.h5
scTCR-seq clonotypes (all): pt245-day7-car-t-tcr-all_contig_annotations.csv
scTCR-seq clonotypes (filtered): pt245-day7-car-t-tcr-filtered_contig_annotations.csv
cellranger summary: pt245-day7-car-t-tcr-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: WT, HU, aux/dox [KJ30]

status: Public on Jun 15 2022

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
Sequenced paired-end 150-bp reads were mapped to the yeast genome using Juicer with default parameters.
Genome_build: Saccharomyces Genome Database (SGD), identical with sacCer3
Supplementary_files_format_and_content: hic files were generated by juicertools version 1.9.9 pre with "-r 1000" option . The total hic contact number of Hi-C samples was normalized.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WT

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose (YEPD). For arrest in G2/M, benomyl (Sigma, 381586)-containing YEPD medium was added to cells growing logarithmically for a final concentration of 80 µg ml-1. Cell cultures were then incubated for 90 minutes at 30°C achieving complete G2/M-arrest. For synchronization in S-phase, 3 μg ml-1 α-factor mating pheromone (Sigma, custom peptide WHWLQLKPGQPMY) was added every hour (a total of three additions) to cells growing logarithmically at 25°C. Upon complete G1-arrest, cells were released into medium containing 0.2 M hydroxyurea (HU) (Sigma, H8627), and S-phase was allowed to progress at 25°C. The Schizosaccharomyces pombe strain (Table S1) used for spike-in normalization in RNA-seq was grown in YES medium (0.5 % yeast extract, 3 % glucose, 150 μg ml-1 adenine, 100 μg ml-1 uracil, 100 μg ml-1 leucine, 100 μg ml-1 lysine, 100 μg ml-1 histidine) at 32°C.

extract_protocol:
Our Hi-C protocol was adapted for S. cerevisiae from ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)).  Fifty ml of cell culture (at an OD of 1.0) was fixed with 3 % formaldehyde for 20 minutes at 30°C, before the reaction was quenched by adding glycine to 0.125 M final concentration for 5 minutes at room temperature. Cells were washed once with 1 x PBS, before being resuspended in 5 ml pre-spheroplasting buffer (100mM PIPES (pH 9.4), 10mM DTT). The cells were incubated 5 minutes at room temperature and then pelleted (1500 g for 5 minutes at room temperature), before being resuspended in 5 ml spheroplasting buffer (50mM KH2PO4/K2HPO4 (pH 7.5), 1 M Sorbitol, 10 mM DTT). Twenty-five μl of 10 mg ml-1 100T Zymolyase (Nacalai Tesque, 07665-55) was added and cells were incubated for 15 minutes at 30°C. The spheroplasts were pelleted (500 g for 5 minutes at 4°C) and washed twice with ice-cold spheroplasting buffer (containing only 1 mM DTT). The spheroplasts were then resuspended in 250 μl of ice-cold Hi-C lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2 % Igepal CA630) supplemented with 50 μl 6 x Complete (Roche) and 3 μl protease inhibitor (Sigma, P8215), and incubated on ice for 15 minutes. The spheroplasts were pelleted (1500 g for 5 minutes at 4°C) and washed twice with 500 μl of ice-cold Hi-C lysis buffer. After the last wash step the supernatant was discarded and the spheroplasts were incubated for 6 minutes at 62°C. Thereafter sodium dodecyl sulphate (SDS) was added to a final concentration of 0.2 % and the reaction was immediately and thoroughly mixed by inversion, and thereafter incubated at 62°C for 10 minutes. After addition of 80 μl H2O, 25 μl 10 % Triton X-100 was added to quench the SDS. The reaction was mixed by inversion and incubated at 37°C for 15 minutes. Thereafter, 28 μl 10 x NEB DpnII buffer and 500 units of DpnII (NEB, R0543M) was added, and the chromatin was digested overnight at 37°C. At the end of the incubation, the reaction was supplemented with 250 units of DpnII and incubated for 1 hour at 37°C. Then, the restriction enzyme was inactivated at 62°C for 20 minutes. The presence of intact and individual DNA masses throughout the spheroplasting, digestion and ligation steps was confirmed by DAPI (4′,6-diamidino-2-phenylindole)-staining and microscopy.
Marking and repairing DNA ends, proximity ligation, crosslink reversal, DNA shearing, size selection, biotin pull-down, preparation for Illumina sequencing, final amplification (15 cycles) and purification was performed as in ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014).

treatment_protocol: For transcription shut-off and degradation of Scc2 and Wpl1 in G2/M-arrest, auxin (3-indoleacetic acid, Sigma, I2886) and doxycycline (Sigma, D9891) were added for 1 hour at the final concentration of 1 mM and 5 μg ml-1, respectively. For transcription shut-off and degradation of Scc2 and Wpl1 in a synchronized S-phase, auxin and doxycycline were first added to G1-arrested cells for 30 minutes, and then for an additional hour in the HU-containing release medium at the same final concentrations as above. For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes. For inactivation of RNA pol II in G2/M-arrest, temperature-sensitive rpb1-1 cells were first arrested by benomyl for 2 hours at the permissive temperature of 25°C. Thereafter, the temperature was shifted to restrictive 37°C for 2 hours.

tag: strain

value: HU-arrest, auxin, doxycycline


title: WT, HU, aux/dox [KJ31]


title: Human_paraffin-embedded_placental_tissue_Sample 85

status: Public on May 30 2022

city: Ann Arbor

first: Ashley

last: Hesson

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

data_processing:
An index of the hg38 reference genome was created and sequences were aligned to this index using the Rsubread package from the Bioconductor suite in R (Vienna, Austria)
The alignment files were subsequently summarized and associated with their respective features and meta-data.  Initial quality control was performed in MultiQC.
Read count extraction and normalization were performed using the Bioconductor suite and DESeq2 package in R
Assembly: hg38
Supplementary files format and content: counts

source_name: placenta

extract_protocol:
Placenta samples were formalin-fixed and paraffin-embedded; five 20-micron sections of each placenta sample were subjected to RNA extraction using the RNAstormTM kit (Cell Data Sciences, Fremont, CA, USA) as per the manufacturer’s instructions.
Total RNA was processed for high-throughput sequencing using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Greenland, NH, USA). Following mRNA generation, fragmentation, and cDNA synthesis, adaptor barcodes were ligated and final cDNA libraries were amplified by PCR and assessed for quality and concentration.

value: placenta

tag: gestational age

value: Preterm

tag: disease state


title: Human_paraffin-embedded_placental_tissue_Sample 74

value: Term


title: Human_paraffin-embedded_placental_tissue_Sample 57


title: Human_paraffin-embedded_placental_tissue_Sample 87

value: Preeclampsia


title: CAR T cells in blood of Pt245 on day 7

description:
pt245-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt245-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt245-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds


title: Human_paraffin-embedded_placental_tissue_Sample 50


title: Human_paraffin-embedded_placental_tissue_Sample 63


title: Human_paraffin-embedded_placental_tissue_Sample 42


title: Human_paraffin-embedded_placental_tissue_Sample 66


title: Human_paraffin-embedded_placental_tissue_Sample 48


title: Human_paraffin-embedded_placental_tissue_Sample 41


title: WT, HU [KJ20]

data_processing:
Sequenced paired-end 150-bp reads were mapped to the yeast genome using Juicer with default parameters.
Genome_build: Saccharomyces Genome Database (SGD), identical with sacCer3.
Supplementary_files_format_and_content: hic files were generated by juicertools version 1.9.9 pre with "-r 1000" option. The total hic contact number of Hi-C samples was normalized.

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose (YEPD). For arrest in G2/M, benomyl (Sigma, 381586)-containing YEPD medium was added to cells growing logarithmically for a final concentration of 80 µg ml-1. Cell cultures were then incubated for 90 minutes at 30°C achieving complete G2/M-arrest. For synchronization in S-phase, 3 μg ml-1 α-factor mating pheromone (Sigma, custom peptide WHWLQLKPGQPMY) was added every hour (a total of three additions) to cells growing logarithmically at 25°C. Upon complete G1-arrest, cells were released into medium containing 0.2 M hydroxyurea (HU) (Sigma, H8627), and S-phase was allowed to progress at 25°C. For transcription shut-off and degradation of Scc2 and Wpl1 in G2/M-arrest, auxin (3-indoleacetic acid, Sigma, I2886) and doxycycline (Sigma, D9891) were added for 1 hour at the final concentration of 1 mM and 5 μg ml-1, respectively.

extract_protocol:
Our Hi-C protocol was adapted for S. cerevisiae from ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)). Fifty ml of cell culture (at an OD of 1.0) was fixed with 3 % formaldehyde for 20 minutes at 30°C, before the reaction was quenched by adding glycine to 0.125 M final concentration for 5 minutes at room temperature. Cells were washed once with 1 x PBS, before being resuspended in 5 ml pre-spheroplasting buffer (100mM PIPES (pH 9.4), 10mM DTT). The cells were incubated 5 minutes at room temperature and then pelleted (1500 g for 5 minutes at room temperature), before being resuspended in 5 ml spheroplasting buffer (50mM KH2PO4/K2HPO4 (pH 7.5), 1 M Sorbitol, 10 mM DTT). Twenty-five μl of 10 mg ml-1 100T Zymolyase (Nacalai Tesque, 07665-55) was added and cells were incubated for 15 minutes at 30°C. The spheroplasts were pelleted (500 g for 5 minutes at 4°C) and washed twice with ice-cold spheroplasting buffer (containing only 1 mM DTT). The spheroplasts were then resuspended in 250 μl of ice-cold Hi-C lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2 % Igepal CA630) supplemented with 50 μl 6 x Complete (Roche) and 3 μl protease inhibitor (Sigma, P8215), and incubated on ice for 15 minutes. The spheroplasts were pelleted (1500 g for 5 minutes at 4°C) and washed twice with 500 μl of ice-cold Hi-C lysis buffer. After the last wash step the supernatant was discarded and the spheroplasts were incubated for 6 minutes at 62°C. Thereafter sodium dodecyl sulphate (SDS) was added to a final concentration of 0.2 % and the reaction was immediately and thoroughly mixed by inversion, and thereafter incubated at 62°C for 10 minutes. After addition of 80 μl H2O, 25 μl 10 % Triton X-100 was added to quench the SDS. The reaction was mixed by inversion and incubated at 37°C for 15 minutes. Thereafter, 28 μl 10 x NEB DpnII buffer and 500 units of DpnII (NEB, R0543M) was added, and the chromatin was digested overnight at 37°C. At the end of the incubation, the reaction was supplemented with 250 units of DpnII and incubated for 1 hour at 37°C. Then, the restriction enzyme was inactivated at 62°C for 20 minutes. The presence of intact and individual DNA masses throughout the spheroplasting, digestion and ligation steps was confirmed by DAPI (4′,6-diamidino-2-phenylindole)-staining and microscopy.
Marking and repairing DNA ends, proximity ligation, crosslink reversal, DNA shearing, size selection, biotin pull-down, preparation for Illumina sequencing, final amplification (15 cycles) and purification was performed as in ref. (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)).

treatment_protocol: For transcription shut-off and degradation of Scc2 and Wpl1 in a synchronized S-phase, auxin and doxycycline were first added to G1-arrested cells for 30 minutes, and then for an additional hour in the HU-containing release medium at the same final concentrations as above. For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes.

value: HU-arrest


title: Human_paraffin-embedded_placental_tissue_Sample 55


title: Human_paraffin-embedded_placental_tissue_Sample 64


title: Human_paraffin-embedded_placental_tissue_Sample 76


title: Human_paraffin-embedded_placental_tissue_Sample 78


title: Human_paraffin-embedded_placental_tissue_Sample 52


title: Human_paraffin-embedded_placental_tissue_Sample 69


title: CAR T cells in blood of Pt253 on day 7

description:
pt253-day7-car-t
polyA RNA, antibody DNA tag
5' kit version: v2
Data are paired-end; Read 1 contains cell barcode and UMI data (sample index is 8 bp); Read 2 contains transcript data; raw data provided as bam files per GEO specification.
cellranger results (filtered): pt253-day7-car-t-filtered_feature_bc_matrix.h5
cellranger summary: pt253-day7-car-t-web_summary.html
Seurat object for all patients: seurat-day7-car-t.rds

value: Large B-cell lymphoma (LBCL)


title: Human_paraffin-embedded_placental_tissue_Sample 83


title: Human_paraffin-embedded_placental_tissue_Sample 56


title: Human_paraffin-embedded_placental_tissue_Sample 81


title: Human_paraffin-embedded_placental_tissue_Sample 43


title: Human_paraffin-embedded_placental_tissue_Sample 39


title: Human_paraffin-embedded_placental_tissue_Sample 36


title: Human_paraffin-embedded_placental_tissue_Sample 37


title: Human_paraffin-embedded_placental_tissue_Sample 35


title: Human_paraffin-embedded_placental_tissue_Sample 40


title: Human_paraffin-embedded_placental_tissue_Sample 28


title: Human_paraffin-embedded_placental_tissue_Sample 34


title: Human_paraffin-embedded_placental_tissue_Sample 29


title: Human_paraffin-embedded_placental_tissue_Sample 32


title: Human_paraffin-embedded_placental_tissue_Sample 26


title: Human_paraffin-embedded_placental_tissue_Sample 18


title: Human_paraffin-embedded_placental_tissue_Sample 30


title: Human_paraffin-embedded_placental_tissue_Sample 27


title: Human_paraffin-embedded_placental_tissue_Sample 8

value: Control


title: Human_paraffin-embedded_placental_tissue_Sample 38


title: Human_paraffin-embedded_placental_tissue_Sample 20


title: Human_paraffin-embedded_placental_tissue_Sample 7


title: Human_paraffin-embedded_placental_tissue_Sample 6


title: Human_paraffin-embedded_placental_tissue_Sample 14


title: Human_paraffin-embedded_placental_tissue_Sample 5


title: Human_paraffin-embedded_placental_tissue_Sample 9


title: Human_paraffin-embedded_placental_tissue_Sample 3


title: Donor 1 - whole genome bisulfite sequencing- D6 (AT1-like) cells

status: Public on Oct 27 2021

data_processing:
For DNA, Fastq files were aligned to the bisulfite hg19 genome by the USC Epigenome Center core. For RNA and ChIPseq, Reads were aligned to the canonical Hg19 genome using Bowtie 2.
For DNA, Bis-SNP was used for methylation and SNPtype calling (Liu et al., Genome Biology, 2012). For RNA, TopHat2 was used to assemble transcripts using Gencode. For ChIPseq, peaks were called using SICER with gap spacing of 600 for H3K27me3 and H3K79me2, gap spacing of 200 for other marks. MACS2 was also used to call enhancer regions for ROADMAP/ENCODE comparisons.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA and ChIPseq have aligned bigwig files.
Supplementary_files_format_and_content: DNA files have peak domains in R files for processed UMR, LMR, and PMR regions.
Supplementary_files_format_and_content: UMRsLMRs.gr.D0.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D4.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D6.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: PMDs.D0dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D4dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D6dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: UMRsLMRs.D0.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D4.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D6.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D0dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D4dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D6dna.tab: partially methylated domains tab-delimited file.

source_name: In vitro differentiated AT1-like cells

growth_protocol: Primary AT2 cells were extracted as described previously and differentiated in vitro for six days (Marconett et al., PLoS Genetics, 2013).

extract_protocol:
DNA, RNA, and ChIP material were prepared as previously published (Zuber et al., JNCI, 2016).
Library construction was performed at the USC Epigenome Center core, as previously described (Zuber et al., JNCI, 2016).
WGBS Indexes were included on Donor 1 samples. Donor 1 D0 Index : TGACCA, Donor 1 D2 Index: CAGTG, Donor 1 D4 Index: GCCAAT, Donor 1 D6 Index: CAGATC. ChIPseq samples were multiplexed on Illumina HiSeq2000 lanes, the indicated adapters on FASTQ files were used to de-multiplex.

treatment_protocol: Purified DNA underwent bisulfite treatment as described previously (Zuber et al., JNCI, 2016). RNA underwent polyA selection and library preparation as previously described (Zuber at al., 2016). ChIP material underwent adapter ligation, library preparation, and multiplexed sequencing as previously described (Zuber et al., 2016).

value: In vitro differentiated AT1-like cells

tag: time point

tag: donor

tag: material type

value: WGBS:Bisulfite-treated DNA


title: Human_paraffin-embedded_placental_tissue_Sample 4


title: Donor 1 - whole genome bisulfite sequencing- D4 (AT1-like) cells


title: Human_paraffin-embedded_placental_tissue_Sample 2


title: Human_paraffin-embedded_placental_tissue_Sample 12


title: Donor 1 - whole genome bisulfite sequencing- D0 (AT2) cells

source_name: purified primary AT2 cells

value: purified primary AT2 cells


title: Donor 3 - Total RNA ribozero treated - D6 (AT1-like) cells

value: Ribozero depleted total RNA


title: Human_paraffin-embedded_placental_tissue_Sample 10


title: Donor 3 - Total RNA ribozero treated - D4 (AT1-like) cells


title: Donor 3 - Total RNA ribozero treated - D2 (AT intermediate) cells

source_name: Differentiating intermediate AT cells

value: Differentiating intermediate AT cells


title: Human_paraffin-embedded_placental_tissue_Sample 25


title: Donor 2 - Total RNA ribozero treated - D2 (AT intermediate) cells


title: Donor 3 - Total RNA ribozero treated - D0 (AT2) cells


title: Donor 1 - Total RNA ribozero treated - D4 (AT1-like) cells


title: Donor 2 - Total RNA ribozero treated - D6 (AT1-like) cells


title: Human_paraffin-embedded_placental_tissue_Sample 13


title: Donor 1 - Total RNA ribozero treated - D6 (AT1-like) cells


title: Donor 2 - ChIPseq using H3K27Ac antibody - D4 (AT1-like) cells

tag: chip antbody

value: ChIP DNA


title: Donor 2 - Total RNA ribozero treated - D4 (AT1-like) cells


title: Donor 2 - ChIPseq using H3K27Ac antibody - D0 (AT2) cells


title: Donor 2 - ChIPseq using H3K27Ac antibody - D6 (AT1-like) cells


title: Donor 1 - Total RNA ribozero treated - D0 (AT2) cells


title: Donor 1 - Total RNA ribozero treated - D2 (AT intermediate) cells


title: Donor 1 - ChIPseq using CTCF antibody - D6 (AT1-like) cells

value: CTCF


title: Donor 2 - Total RNA ribozero treated - D0 (AT2) cells


title: Donor 1 - FAIRE library - D0 (AT2) cells

data_processing:
Library strategy: FAIRE
For DNA, Fastq files were aligned to the bisulfite hg19 genome by the USC Epigenome Center core. For RNA and ChIPseq, Reads were aligned to the canonical Hg19 genome using Bowtie 2.
For DNA, Bis-SNP was used for methylation and SNPtype calling (Liu et al., Genome Biology, 2012). For RNA, TopHat2 was used to assemble transcripts using Gencode. For ChIPseq, peaks were called using SICER with gap spacing of 600 for H3K27me3 and H3K79me2, gap spacing of 200 for other marks. MACS2 was also used to call enhancer regions for ROADMAP/ENCODE comparisons.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA and ChIPseq have aligned bigwig files.
Supplementary_files_format_and_content: DNA files have peak domains in R files for processed UMR, LMR, and PMR regions.
Supplementary_files_format_and_content: UMRsLMRs.gr.D0.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D4.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D6.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: PMDs.D0dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D4dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D6dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: UMRsLMRs.D0.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D4.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D6.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D0dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D4dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D6dna.tab: partially methylated domains tab-delimited file.

value: FAIRE DNA


title: Donor 2 - ChIPseq input DNA for normalization - D0 (AT2) cells

value: ChIP INPUT DNA


title: Donor 1 - ChIPseq using CTCF antibody - D4 (AT1-like) cells


title: Donor 2 - ChIPseq input DNA for normalization - D6 (AT1-like) cells


title: Donor 2 - ChIPseq using H3K4me1 antibody - D4 (AT1-like) cells


title: Donor 1 - FAIRE library - D6 (AT1-like) cells


title: Donor 1 - FAIRE library - D4 (AT1-like) cells


title: Donor 2 - ChIPseq input DNA for normalization - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using CTCF antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K79me2 antibody - D4 (AT1-like) cells


title: Donor 2 - ChIPseq using H3K4me1 antibody - D6 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K79me2 antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K27me3 antibody - D6 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K27me3 antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K27me3 antibody - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K27Ac antibody - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K27Ac antibody - D0 (AT2) cells


title: Donor 2 - ChIPseq using H3K4me1 antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K9Ac antibody - D6 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K27Ac antibody - D6 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K9Ac antibody - D0 (AT2) cells


title: Donor 1 - ChIPseq using H3K4me1 antibody - D4 (AT1-like) cells


title: Donor 1 - ChIPseq using H3K4me1 antibody - D6 (AT1-like) cells


title: Donor 1 - ChIPseq input DNA for normalization - D6 (AT1-like) cells


title: Donor 1 - ChIPseq input DNA for normalization - D4 (AT1-like) cells


title: 965-E6_WT

status: Public on Oct 25 2021

city: Boston

first: Susan

last: Slaugenhaupt

state: Massachusetts

address: 185 Cambridge Street, CPZN-5254

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
RNASeq reads were mapped by STAR (version 2.4.2a) allowing 5% mismatch
Raw gene counts were generated by HTSeq-count (version 0.13.5)
Size factors for normalization were estimated by R package DESeq2 (version 1.28.1)
Surrogated variables (SVs) were estimated by R package sva (version 3.36.0), with full model as "~Genotype" and null model as "~1"
The uploaded processed file contains normalized counts with effects from SVs removed, meaning it only counts for expression from "pure" genotype effects
Genome_build: Ensembl GRCm38 version 83, with human ELP1 gene sequence inserted as an independent chromosome
Supplementary_files_format_and_content: Fastq format for RNASeq reads; Tab-delimited txt format for normalized expression counts

molecule: polyA RNA

source_name: mouse embryo

extract_protocol:
RNA was extracted from 8 Elp1-/-, 7 TgFD1; Elp1-/-, 6 TgFD9; Elp1-/- and 8 Elp1+/+ individual embryos at the embryonic stage of E8.5 using the QIAzol Reagent and following the manufacturer’s instructions.
RNAseq Libraries were prepared using TruSeq® Stranded mRNA Library Prep kit (Illumina 20020594), using 100 ng total RNA as input. Libraries were evaluated for final concentration and size distribution by Agilent 2200 TapeStation and/or qPCR, using Library Quantification Kit (KK4854, Kapa Biosystems), and multiplexed by pooling equimolar amounts of each library prior to sequencing.

value: embryo

value: WT


title: Donor 1 - ChIPseq using H3K79me2 antibody - D6 (AT1-like) cells


title: 965-E5_KO_FD1


title: 965-E3_KO_FD1


title: Donor 1 - ChIPseq input DNA for normalization - D0 (AT2) cells


title: 683-E7_KO

value: KO


title: 775-E2_KO_FD9


title: 682-E9_WT


title: 965-E1_WT


title: 775-E1_KO_FD9


title: 683-E1_WT


title: Donor 1 - ChIPseq using H3K9Ac antibody - D4 (AT1-like) cells


title: 682-E7_KO


title: 751-E10_KO_FD1


title: 682-E5_KO


title: 682-E6_WT


title: 604-E4_KO_FD9


title: 682-E2_WT


title: 683-E4_WT


title: 682-E1_KO


title: 682-E3_WT


title: Donor 1 - ChIPseq using H3K4me1 antibody - D0 (AT2) cells


title: 452-E8_KO_FD9


title: 365-E9_KO_FD9


title: 351-E5_KO


title: 282-E6_KO_FD1


title: 351-E4_KO_FD1


title: 351-E3_KO


title: 244-E3_KO_FD9


title: 351-E1_KO


title: 682-E4_KO


title: 840 neural progenitor [840_16.2_mirna]

status: Public on Sep 06 2021

city: Innsbruck

first: Kai

last: Kummer

address: Schoepfstrasse 41/Eg

department: Institute of Physiology

country: Austria

institute: Medical University of Innsbruck

description:
19101-0047_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv

data_processing:
miRNA only adapter trimming with flexbar
FastQC
STAR (v 020201) align, mRNA parameters: --chimSegementMin 20, --chimOutType WithinBam, --outSAMtype SortedByCoordinates, --runThreadN 16, miRNA parameters: --outFilterMismatchMax 1, --outFilterMultimapScoreRange 0, --outFilterMultimapNmax 10, --outFilterMatchNminOverLread 0, --outFilterMatchNmin 16, --alingIntronMax 1 --outWigType wiggle, --outWigStrand Stranded, --outWigNorm RPM
Htseq counting
DESeq2 LRT analysis
DESeq2 VST normalization
Normalized data were filtered for genes and miRNA with a count > 5 in at least 3 columns
Filtered normalized data were used as input for WGCNA
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: .csv

source_name: 840 neural progenitor

growth_protocol: iDNs were generated according to a modified version of the Chambers et al. (2014) protocol as described in Schoepf & Zeidler et al. (2020)

extract_protocol: High througput RNA and small RNA sequencing

tag: cell line

tag: source cell type

value: human iPSC

tag: differentiation stage

value: neural progenitor

tag: molecule subtype

value: small RNA


title: 840 late neural progenitor [840_26.3_mirna]

description:
19101-0051_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv

source_name: 840 late neural progenitor

value: late neural progenitor


title: 840 iPSC-derived nociceptor [840_36.1_mirna]

description:
19101-0052_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv

source_name: 840 iPSC-derived nociceptor

value: nociceptor


title: 245-E9_KO_FD1


title: 840 neural progenitor [840_16.1_mirna]

description:
19101-0046_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: 840 neural progenitor [840_16.3_mirna]

description:
19101-0048_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: 840 early neural progenitor [840_9.3_mirna]

description:
19101-0045_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv

source_name: 840 early neural progenitor

value: early neural progenitor


title: 840 late neural progenitor [840_26.2_mirna]

description:
19101-0050_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: 351-E7_KO_FD1


title: 840 iPSC-derived nociceptor [840_36.2_mirna]

description:
19101-0053_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: 840 late neural progenitor [840_26.1_mirna]

description:
19101-0049_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: 840 early neural progenitor [840_9.2_mirna]

description:
19101-0044_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: 840_early differentiation [840_5.1_mirna]

description:
19101-0040_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv

source_name: 840_early differentiation

value: early differentiation


title: 840 early differentiation [840_5.3_mirna]

description:
19101-0042_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv

source_name: 840 early differentiation


title: 840_iPSC [840_1.2_mirna]

description:
19101-0038_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv

value: iPSC


title: 840 iPSC-derived nociceptor [840_36.3_mirna]

description:
19101-0054_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: 840_iPSC [840_1.3_mirna]

description:
19101-0039_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: 840_iPSC [840_1.1_mirna]

description:
19101-0037_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: 840 early differentiation [840_5.2_mirna]

description:
19101-0041_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: AD2 iPSC-derived nociceptor [AD2_36.3_mirna]

description:
19101-0036_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv

source_name: AD2 iPSC-derived nociceptor


title: AD2 iPSC-derived nociceptor [AD2_36.2_mirna]

description:
19101-0035_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 iPSC-derived nociceptor [AD2_36.1_mirna]

description:
19101-0034_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 late neural progenitor [AD2_26.2_mirna]

description:
19101-0032_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv

source_name: AD2 late neural progenitor


title: AD2 neural progenitor [AD2_16.2_mirna]

description:
19101-0029_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv

source_name: AD2 neural progenitor


title: AD2 late neural progenitor [AD2_26.3_mirna]

description:
19101-0033_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 early neural progenitor [AD2_9.3_mirna]

description:
19101-0027_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv

source_name: AD2 early neural progenitor


title: 840 early neural progenitor [840_9.1_mirna]

description:
19101-0043_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_840-results-with-normalized_filtered.csv


title: AD3 iPSC-derived nociceptor [AD3_36.3_mirna]

description:
19101-0018_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv

source_name: AD3 iPSC-derived nociceptor


title: AD2 early neural progenitor [AD2_9.2_mirna]

description:
19101-0026_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 neural progenitor [AD2_16.1_mirna]

description:
19101-0028_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 early differentiation [AD2_5.1_mirna]

description:
19101-0022_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv

source_name: AD2 early differentiation


title: AD2 neural progenitor [AD2_16.3_mirna]

description:
19101-0030_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2_iPSC [AD2_1.2_mirna]

description:
19101-0020_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD3 early differentiation [AD2_5.2_mirna]

description:
19101-0023_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv

source_name: AD3 early differentiation


title: AD3 iPSC-derived nociceptor [AD3_36.2_mirna]

description:
19101-0017_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD2_iPSC [AD2_1.1_mirna]

description:
19101-0019_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2_iPSC [AD2_1.3_mirna]

description:
19101-0021_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 early differentiation [AD2_5.3_mirna]

description:
19101-0024_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD3 iPSC-derived nociceptor [AD3_36.1_mirna]

description:
19101-0016_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early neural progenitor [AD2_9.1_mirna]

description:
19101-0025_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv

source_name: AD3 early neural progenitor


title: AD3 neural progenitor [AD3_16.1_mirna]

description:
19101-0010_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv

source_name: AD3 neural progenitor


title: AD2 late neural progenitor [AD2_26.1_mirna]

description:
19101-0031_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD2-results-with-normalized_filtered.csv


title: AD3 late neural progenitor [AD3_26.3_mirna]

description:
19101-0015_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv

source_name: AD3 late neural progenitor


title: AD3 neural progenitor [AD3_16.2_mirna]

description:
19101-0011_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 late neural progenitor [AD3_26.1_mirna]

description:
19101-0013_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 neural progenitor [AD3_16.3_mirna]

description:
19101-0012_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 late neural progenitor [AD3_26.2_mirna]

description:
19101-0014_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early neural progenitor [AD3_9.3_mirna]

description:
19101-0009_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early neural progenitor [AD3_9.1_mirna]

description:
19101-0007_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early neural progenitor [AD3_9.2_mirna]

description:
19101-0008_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3_iPSC [AD3_1.3_mirna]

description:
19101-0003_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early differentiation [AD3_5.3_mirna]

description:
19101-0006_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: 840 iPSC-derived nociceptor [840_36.2]

description:
19101-0053
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: AD3 early differentiation [AD3_5.2_mirna]

description:
19101-0005_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3_iPSC [AD3_1.2_mirna]

description:
19101-0002_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: 840 iPSC-derived nociceptor [840_36.3]

description:
19101-0054
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: AD3_iPSC [AD3_1.1_mirna]

description:
19101-0001_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: 840 early neural progenitor [840_9.3]

description:
19101-0045
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 late neural progenitor [840_26.2]

description:
19101-0050
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 iPSC-derived nociceptor [840_36.1]

description:
19101-0052
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 early neural progenitor [840_9.1]

description:
19101-0043
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 late neural progenitor [840_26.3]

description:
19101-0051
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 neural progenitor [840_16.1]

description:
19101-0046
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840_early differentiation [840_5.1]

description:
19101-0040
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 late neural progenitor [840_26.1]

description:
19101-0049
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 neural progenitor [840_16.3]

description:
19101-0048
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 neural progenitor [840_16.2]

description:
19101-0047
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 early differentiation [840_5.2]

description:
19101-0041
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840 early neural progenitor [840_9.2]

description:
19101-0044
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: 840_iPSC [840_1.1]

description:
19101-0037
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: AD2 iPSC-derived nociceptor [AD2_36.2]

description:
19101-0035
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 iPSC-derived nociceptor [AD2_36.3]

description:
19101-0036
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD3 early differentiation [AD3_5.1_mirna]

description:
19101-0004_SmallRNA
processed data file: iPSC_differentiation_miRNA_only_AD3-results-with-normalized_filtered.csv


title: 840_iPSC [840_1.2]

description:
19101-0038
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: AD2 late neural progenitor [AD2_26.2]

description:
19101-0032
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 late neural progenitor [AD2_26.3]

description:
19101-0033
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: 840 early differentiation [840_5.3]

description:
19101-0042
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: AD2 neural progenitor [AD2_16.3]

description:
19101-0030
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 late neural progenitor [AD2_26.1]

description:
19101-0031
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 iPSC-derived nociceptor [AD2_36.1]

description:
19101-0034
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 neural progenitor [AD2_16.1]

description:
19101-0028
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD3 early neural progenitor [AD2_9.1]

description:
19101-0025
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 neural progenitor [AD2_16.2]

description:
19101-0029
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 early differentiation [AD2_5.3]

description:
19101-0024
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD3 early differentiation [AD2_5.2]

description:
19101-0023
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 early neural progenitor [AD2_9.2]

description:
19101-0026
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2_iPSC [AD2_1.2]

description:
19101-0020
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2_iPSC [AD2_1.3]

description:
19101-0021
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 early differentiation [AD2_5.1]

description:
19101-0022
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD2 early neural progenitor [AD2_9.3]

description:
19101-0027
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD3 iPSC-derived nociceptor [AD3_36.2]

description:
19101-0017
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 iPSC-derived nociceptor [AD3_36.3]

description:
19101-0018
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 late neural progenitor [AD3_26.3]

description:
19101-0015
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 late neural progenitor [AD3_26.2]

description:
19101-0014
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 neural progenitor [AD3_16.2]

description:
19101-0011
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 iPSC-derived nociceptor [AD3_36.1]

description:
19101-0016
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 neural progenitor [AD3_16.3]

description:
19101-0012
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early neural progenitor [AD3_9.2]

description:
19101-0008
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 neural progenitor [AD3_16.1]

description:
19101-0010
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early neural progenitor [AD3_9.3]

description:
19101-0009
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD2_iPSC [AD2_1.1]

description:
19101-0019
processed data file: iPSC_differentiation_mRNA_only_AD2-results-with-normalized_filtered.csv


title: AD3 early differentiation [AD3_5.3]

description:
19101-0006
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3_iPSC [AD3_1.3]

description:
19101-0003
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early differentiation [AD3_5.1]

description:
19101-0004
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3_iPSC [AD3_1.2]

description:
19101-0002
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early differentiation [AD3_5.2]

description:
19101-0005
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3_iPSC [AD3_1.1]

description:
19101-0001
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: PBMC sample from subject HC-9 at time point 0

status: Public on Aug 13 2021

data_processing:
Processing and analysis of bulk B cell receptor sequences was carried out using tools from the Immcantation framework as done previously (44). Preprocessing was a performed using pRESTO. Briefly, sequences with a phred score below 20 were removed and only those that  contained constant region and template switch sequences were preserved. UMI sequences were then grouped, and consensus sequences were constructed for each group and assembled into V(D)J sequences in a two-step process involving an analysis of overlapping sequences (<8 nucleotides) or alignment against the IMGT (the international ImMunoGeneTics information system®) IGHV reference (IMGT/GENE-DB v3.1.19; retrieved December 1, 2019) if no significant overlap was found. Isotypes were assigned by local alignment of the 3' end of the V(D)J sequence to constant region sequences. Duplicate sequences were removed and only V(D)J sequences reconstructed from more than 1 amplicon were preserved.
V(D)J germline genes were assigned to reconstructed V(D)J sequences using IgBLAST v.1.14.0 and also using the December 1, 2019 version of the IMGT gene database (45). V(D)J sequences with IGH associated V and J genes were then selected for further analysis and non-functional sequences were removed. Germline sequences were reconstructed for each V(D)J sequence with D segment and N/P regions masked (with Ns) using the CreateGermlines.py function within Change-O v1.0.0(46). VH gene nucleotides up to IMGT position 312 were translated from both the aligned sequence and germline reconstructed V(D)J sequence using BioPython v1.75. To quantify the frequency of N-X-S/T glycosylation motifs, matches to the regular expression pattern "N[^P][S,T]" were quantified for each  translated sequence, including for translated CDR and FWR fragments of the VH gene sequence (defined by IMGT coordinates) (4). N-X-S/T glycosylation motifs in the CDR3 and FWR4 regions were similarly quantified separately and included for CDR and FWR distribution analyses.
Genome_build: IMGT (the international ImMunoGeneTics information system®) IGHV reference (IMGT/GENE-DB v3.1.19
Supplementary_files_format_and_content: AIRR-C, a tab-delimited file format (.tsv) that defines the required and optional annotations for rearranged adaptive immune receptor sequences.

source_name: Peripheral Blood

extract_protocol:
RNA was isolated from frozen peripheral blood mononuclear cells using the RNAeasy Mini kit (Qiagen) per manufacturer’s instructions.
Bulk libraries were prepared from RNA using reagents from New England Biolabs as part of the NEBNext® Immune Sequencing Kit. cDNA was reverse-transcribed by a template-switch reaction to add a 17-nucleotide unique molecular identifier (UMI) to the 5' end with streptavidin magnetic bead purification. This was then followed by two rounds of PCR; the first round enriched for immunoglobulin sequences using IGHA, IGHD, IGHE, IGHG, and IGHM-specific 3' primers and added a 5' index primer. Libraries were purified with AMPure XP beads (Beckman) after which another round of PCR added Illumina P5 Adaptor sequences to each amplicon. The number of PCR cycles were selected based on real-time quantitative PCR to avoid the plateau phase. Libraries were then purified again with AMPure  XP beads. Libraries were pooled in equimolar libraries and sequenced by 325 cycles for read1 and 275 cycles for read 2 using paired-end sequencing with a 20% PhiX spike on the Illumina MiSeq platform according to manufacturer’s recommendations.

tag: study sample number

tag: Sex

value: Male

tag: age at time of collection

tag: antibody status

value: Peripheral Blood


title: PBMC sample from subject HC-8 at time point 0

tag: tissue


title: PBMC sample from subject HC-6 at time point 0


title: PBMC sample from subject HC-3 at time point 0


title: PBMC sample from subject HC-2 at time point 0

value: Female


title: PBMC sample from subject HC-5 at time point 0


title: PBMC sample from subject HC-1 at time point 0


title: AD3 late neural progenitor [AD3_26.1]

description:
19101-0013
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: AD3 early neural progenitor [AD3_9.1]

description:
19101-0007
processed data file: iPSC_differentiation_mRNA_only_AD3-results-with-normalized_filtered.csv


title: PBMC sample from subject HC-7 at time point 0


title: PBMC sample from subject HC-4 at time point 0


title: PBMC sample from subject AChR-12 at time point 0

value: AChR


title: PBMC sample from subject AChR-8 at time point 0


title: PBMC sample from subject AChR-9 at time point 0


title: PBMC sample from subject AChR-11 at time point 0


title: PBMC sample from subject AChR-6 at time point 0


title: PBMC sample from subject AChR-5 at time point 0


title: 840_iPSC [840_1.3]

description:
19101-0039
processed data file: iPSC_differentiation_mRNA_only_840-results-with-normalized_filtered.csv


title: PBMC sample from subject AChR-2 at time point 0


title: PBMC sample from subject AChR-1 at 4 months since first sample collection


title: PBMC sample from subject AChR-4 at time point 0


title: PBMC sample from subject MuSK-3 at time point 0

value: MuSK


title: PBMC sample from subject AChR-3 at time point 0


title: PBMC sample from subject MuSK-2 at 56 months since first sample collection


title: PBMC sample from subject MuSK-3 at 25 months since first sample collection


title: PBMC sample from subject MuSK-3 at 10 months since first sample collection


title: PBMC sample from subject MuSK-2 at time point 0


title: PBMC sample from subject MuSK-1 at 39 months since first sample collection


title: PBMC sample from subject MuSK-1 at time point 0


title: PBMC sample from subject MuSK-1 at 31 months since first sample collection


title: PBMC sample from subject MuSK-2 at 6 months since first sample collection


title: PBMC sample from subject MuSK-3 at 1 month since first sample collection


title: PBMC sample from subject MuSK-1 at 36 months since first sample collection


title: WT G1 arrest (no DSB)

status: Public on Jul 21 2021

city: PARIS

first: Helene

last: Bordelet

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

description: Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format

data_processing:
Reads were aligned and the contact data processed using Hicstuff 9. Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 in its most sensitive mode against the S. cerevisiae W303 reference genome (GCA_002163515.1). The reference was deleted for the URA3 and LYS2 genes, which are either absent or partially duplicated in our strains, respectively. Each uniquely mapped read was assigned to a restriction fragment. Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in ref. 10. PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded. Contact maps were generated with the “view” function of Hicstuff and normalized using the iterative correction and eigenvector decomposition (ICE) procedure11. Bins were set at either 1 or 2 kb for single chromosomes, or 5 kb for multiple chromosomes, log10 transformed, and rendered.
Supplementary_files_format_and_content: cool

organism: Saccharomyces cerevisiae W303

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. 2020. Quenching of formaldehyde with 300 mM glycine was performed at room temperature for 20 min. Most Hi-C experiments were performed with the Arima Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions, except those presented in Supplementary Fig. 3, performed as in Dauban et al. 2020 with a single DpnII restriction digestion.
TruSeq Nano DNA Library Prep (Illumina, cat. FC-121-9010DOC) or Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems (A38606024).

tag: treatment

value: No DSB


title: PBMC sample from subject MuSK-2 at 76 months since first sample collection


title: WT DSB t0 replicate2

tag: strain


title: 182444_EM_rash

status: Public on Jun 07 2021

data_processing:
Base calls were converted to FASTQs using Illumina’s bcl2fastq conversion software and reads were aligned to the human hg19 genome using STAR 2.7 alignment software via the Broad Institute’s dropseq_workflow pipeline (https://github.com/klarman-cell-observatory/cumulus/blob/master/workflows/drop-seq/dropseq_workflow.wdl), which also converts reads to cell-by-gene sparse count matrices.
The output was loaded into Seurat v3.1.5 for analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data for each sample is a cell-by-gene sparse count matrix, in text format and gzip compressed.

source_name: skin

extract_protocol:
Single cell suspensions were obtained from fresh human skin biopsies obtained with a Biopsy puncher using the Whole Skin Dissociation Kit (Miltenyi Biotec, San Diego, CA, 130-101-540), placed in MACS Tissue Storage Solution (Miltenyi Biotec, 130-100-008) and stored for less than 48 hrs at 4o Celsius. The tissue was washed in DMEM media (ThermoFisher Scientific, 11960).  After the enzymatic digestions, the sample was placed in the MACS Dissociator (Miltenyi Biotec, 130-093-235) and program h-skin-01 was used to isolate cells.  The cells were then washed in DMEM, filtered with a 70um filter, pelleted and resuspended in DMEM.
Single cell suspensions from skin were first counted, their viability assessed using trypan blue (Sigma, St Louis, MO) and adjusted to 50,000/ml in RPMI 1640 medium supplemented with 2 nM L-glutamine, 5 mM 462 HEPES, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.5 mM sodium pyruvate, 0.05 mM 463 nonessential amino acids, and 5% human AB serum (Gemini Bio-Products). We used the Seq-Well platform. Briefly, 10,000 single cells (200 µl of cell suspensions) were loaded into a Seq-Well array preloaded with barcoded capture beads (ChemGenes). After washing excess beads and cells, the arrays were sealed with a polycarbonate membrane and incubated for 30 minutes at 37ºC. Each cell sequestered in a nanowell with a barcoded capture bead was subject to lysis followed by transcript hybridization. The beads recovered from the entire array are washed then mixed with reverse transcriptase master mix. The resulting cDNA was amplified using KAPA HiFi PCR Mastermix (Kapa Biosystems KK2602) with 2,000 beads per 50 μL reaction volume. Generated libraries were then pooled and purified using Agencourt AMPure XP beads (Beckman Coulter, A63881) by a 0.6X SPRI followed by a 0.7X SPRI and quantified using nanodrop. Library quality was assessed using a bioanalyzer 2100 (Agilent Technologies). Single-cell barcoded paired-end sequencing libraries were produced from cDNA with the Nextera XT DNA sample Prep Kit.

value: M

tag: age

tag: ethnicity

value: Not Hispanic or Latino

tag: disease stage

value: Acute/Recent onset


title: G1 alpha-factor bloc DSB t4

value: DSB 4 hr


title: 182296_unaffected_skin

value: F


title: 182298_EM_rash


title: 182288_EM_rash


title: 182298_unaffected_skin


title: WT no HO cut site - t4


title: Subject 192566 PBMC (scTCR)

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the cellranger count subcommand.
Reconstructed V(D)J sequences from single cell sequencing were extracted using the cellranger vdj function from fastq reads.
V(D)J germline genes were re-assigned using IgBLAST v.1.6.1 also using the September 12, 2018 version of the IMGT gene database.
Following V(D)J annotation, non-functional sequences were removed from further analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files filtered_contig_annotations.csv & filtered_contig.fasta.

source_name: PBMC

extract_protocol:
PBMCs and skin infiltrating cells were isolated by Ficoll-Paque PLUS (GE Healthcare) gradient centrifugation. Red blood cells (RBCs) were lysed using ACK buffer (ThermoFisher A1049201). Single cell suspensions were obtained from fresh human skin biopsies obtained with a Biopsy puncher using the Whole Skin Dissociation Kit (Miltenyi Biotec, San Diego, CA, 130-101-540), placed in MACS Tissue Storage Solution (Miltenyi Biotec, 130-100-008) and stored for less than 48 hrs at 4o Celsius.
Single cell preparations were loaded into the Chromium Controller (10x Genomics) for emulsion generation and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol. Libraries were sequenced on the NovaSeq 6000 with 2 x150 paired end reads.


title: Subject 192567 Unaffected Skin (scTCR)


title: Subject 192565 Unaffected Lesion (scTCR)


title: Subject 192567 EM Lesion (scTCR)


title: Subject 192566 EM Lesion (scTCR)


title: Subject 192566 Unaffected Skin (scTCR)


title: 182296_EM_rash


title: Subject 192561 EM Lesion (scTCR)


title: Subject 192564 EM Lesion (scTCR)


title: Subject 192561 Unaffected Skin (scTCR)


title: Subject 192566 Unaffected Skin (scBCR)


title: Subject 192563 EM Lesion (scTCR)


title: Subject 192567 Unaffected Skin (scBCR)


title: Subject 192567 EM Lesion (scBCR)


title: Subject 192566 EM Lesion (scBCR)


title: Subject 192564 Unaffected Skin (scBCR)


title: Subject 192565 EM Lesion (scBCR)


title: Subject 192565 Unaffected Lesion (scBCR)


title: Subject 192566 PBMC (scBCR)


title: Subject 192565 EM Lesion (scTCR)


title: Subject 192561 Unaffected Skin (scBCR)


title: Subject 192561 EM Lesion (scBCR)


title: Subject 192563 EM Lesion (scBCR)


title: 192567SKN

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the cellranger count subcommand.
CellRanger output was analyzed using Seurat v.3.1.5.
Genome_build: GRCh38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files barcodes.tsv & features.tsv. The tar.gz file also contains a feature-barcode matrix file named matrix.mtx, stored in the Market Exchange Format for sparse matrices. The matrix file contains indexes to barcodes and gene/features, as well as total UMI count per cell and gene/feature combination.

source_name: Subject 192567 Unaffected Skin

extract_protocol:
PBMCs and skin infiltrating cells were isolated by Ficoll-Paque PLUS (GE Healthcare) gradient centrifugation. Red blood cells (RBCs) were lysed using ACK buffer (ThermoFisher A1049201). Single cell suspensions were obtained from fresh human skin biopsies obtained with a Biopsy puncher using the Whole Skin Dissociation Kit (Miltenyi Biotec, San Diego, CA, 130-101-540), placed in MACS Tissue Storage Solution (Miltenyi Biotec, 130-100-008) and stored for less than 48 hrs at 4o Celsius.
Single cell preparations were loaded into the Chromium Controller (10x Genomics) for emulsion generation and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol. Libraries were sequenced on the NovaSeq 6000 with 2 x100 paired end reads.

value: Acute/Recent onset Lyme Disease

value: skin


title: 192567SKL

source_name: Subject 192567 EM Lesion


title: 192565SKN

source_name: Subject 192565 Unaffected Lesion


title: 192565SKL

source_name: Subject 192565 EM Lesion


title: Subject 192564 EM Lesion (scBCR)


title: 192566

source_name: Subject 192566 PBMC

value: PBMC


title: Subject 192564 Unaffected Skin (scTCR)


title: 192561SKN

source_name: Subject 192561 Unaffected Skin


title: 192561SKL

source_name: Subject 192561 EM Lesion


title: 192564SKN

source_name: Subject 192564 Unaffected Skin


title: 192563SKL

source_name: Subject 192563 EM Lesion


title: 192566SKN

source_name: Subject 192566 Unaffected Skin


title: 192564_0_TCRB

data_processing:
Bulk repertoire data processing and analysis was carried out using tools from the Immcantation framework (http://immcantation.org).
Preprocessing was carried out using pRESTO v0.5.11 and the IMGT human germline IGHV reference database (IMGT/GENE-DB v3.1.19; retrieved May 30, 2019)
Genome_build: IMGT/GENE-DB v3.1.19
Supplementary_files_format_and_content: One annotation file in AIRR-C Rearrangement format was generated for each sample. The files are in tab-delimited format and gzip compressed.

extract_protocol:
PBMCs were isolated by Ficoll-Paque PLUS (GE Healthcare) gradient centrifugation. Red blood cells (RBCs) were lysed using ACK buffer (ThermoFisher A1049201).
RNA was prepared from frozen PBMCs using the RNAEasy Mini kit (Qiagen) per the manufacturer’s instructions. BCR and TCR RNA libraries were prepared using reagents from New England Biolabs as part of the NEBNext® Immune Sequencing Kit (a kind gift of Drs. Eileen Dimalanta and Chen Song, Ipswich, MA). These steps were performed as described previously with the inclusion of an additional set of TCRB-specific primers on the 3’ end. Libraries were sequenced by 325 cycles for read 1 and 275 cycles for read 2 base-pair paired-end sequencing with a 20% PhiX spike on the Illumina MiSeq platform according to manufacturer’s recommendations.

value: Acute/Recent onset Lyme disease


title: 192564SKL

source_name: Subject 192564 EM Lesion


title: 192561_0_TCRB


title: 192567_0_TCRB


title: 192567_PBMC

data_processing:
Bulk repertoire data processing and analysis was carried out using tools from the Immcantation framework (http://immcantation.org).
Preprocessing was carried out using pRESTO v0.5.11 and the IMGT human germline IGHV reference database (IMGT/GENE-DB v3.1.19; retrieved May 30, 2019)
BCR isotypes were assigned by local alignment of the 3’ end of each sequence to a set of constant region sequences.
Genome_build: IMGT/GENE-DB v3.1.19
Supplementary_files_format_and_content: One annotation file in AIRR-C Rearrangement format was generated for each sample. The files are in tab-delimited format and gzip compressed.

tag: isolate

value: Subject 192567

tag: assay

value: bulk BCR


title: 192563_0_TCRB


title: 192566SKL

source_name: Subject 192566 EM Lesion


title: Subject TS4 at timepoint A

status: Public on Apr 05 2021

description: single-cell RNAseq

data_processing:
Raw sequencing reads were demultiplexed using Cell Ranger mkfastq pipeline to create FASTQ files.
Cell Ranger count pipeline (v3.1) was employed in order to perform alignment (using STAR), filtering, barcode counting, and UMI counting.
Seurat v3.1 pre-processing standard protocol as defined by Satija lab.
10x cellranger count filtered output data of PBMCs from thirteen healthy controls were added to that of the eighteen Covid-19 samples. Seurat package (v3.1) was used for all downstream analysis. 10x gene expression matrices for each sample were converted and combined into one Seurat object.
Cells that had mitochondrial gene percentages higher than 12% and cells with less than 200 genes were excluded from the study to filter out dead and dying cells.
Genome_build: GRCh38 (Ensembl 93)
Supplementary_files_format_and_content: Cell Ranger filtered_gene_matrix, seurat objects

extract_protocol:
PBMCs were isolated from whole blood using density gradient centrifugation, and immediately cryopreserved. They were later thawed, DMSO was removed, cells were filtered and loaded to the 10x chromium platform
Libraries were prepared using the 10X Genomics Chromium Next GEM Chip G, according to the manufacturer’s user guide (document number CG000208, revision E, February 2020)

tag: cell type

tag: diagnosis

tag: disease severity

value: Stable

tag: tocilizumab treatment

value: Yes

tag: race

value: white

tag: bmi

tag: weight-kg

tag: height-m

value: Tocilizumab

tag: time-point

value: A

tag: chronic htn

tag: htn

tag: lung disease

value: No

tag: hospital admission

tag: icu admission

tag: outcome

value: Discharged

tag: tocilizumab dose (mg/kg)

tag: time difference between samples a and b (d)


title: 192563_PBMC

tag: Sex

value: Female

tag: age

tag: ethnicity

value: Not Hispanic or Latino

tag: disease stage

tag: isolate

value: Subject 192563

tag: assay


title: 192565_PBMC

value: Acute/Recent onset

value: Subject 192565


title: Subject TS5 at timepoint A

description: single-cell RNAseq

tag: cell type

tag: diagnosis

tag: disease severity

tag: tocilizumab treatment

value: M

tag: race

tag: bmi

tag: weight-kg

tag: treatment


title: Subject TS5 at timepoint B

description: single-cell RNAseq

value: PBMC

tag: height-m

tag: time-point

value: B

tag: chronic htn

tag: htn

tag: lung disease

tag: hospital admission

tag: icu admission

tag: outcome


title: 192564_PBMC

tag: Sex

tag: age

tag: ethnicity

tag: disease stage

tag: isolate

value: Subject 192564

tag: assay


title: 192561_PBMC

value: Subject 192561

value: bulk BCR


title: Subject TS2 at timepoint B

description: single-cell RNAseq

tag: cell type

tag: diagnosis

tag: disease severity

value: Stable

tag: tocilizumab treatment

value: Yes

tag: race

value: black

tag: bmi

tag: tocilizumab dose (mg/kg)

tag: time difference between samples a and b (d)


title: 192565_0_TCRB

tag: tissue

value: F

value: Acute/Recent onset Lyme disease


title: 192566_PBMC

value: Male

value: Subject 192566


title: Subject TP7 at timepoint A

description: single-cell RNAseq

value: Progressive

value: white

tag: weight-kg

tag: height-m

tag: treatment

value: Tocilizumab

tag: time-point

value: A

tag: chronic htn

tag: htn

tag: lung disease

tag: hospital admission

tag: icu admission

value: Expired


title: Subject TS3 at timepoint B

description: single-cell RNAseq

tag: cell type

value: PBMC

tag: diagnosis

tag: age

tag: Sex

value: No

tag: outcome

value: Discharged


title: Subject TS2 at timepoint A

description: single-cell RNAseq

tag: disease severity

tag: tocilizumab treatment

value: M

tag: race

tag: bmi

tag: tocilizumab dose (mg/kg)


title: Subject TP7 at timepoint B

description: single-cell RNAseq

tag: weight-kg

tag: height-m

tag: treatment

value: B

tag: time difference between samples a and b (d)


title: Subject TP8 at timepoint B

description: single-cell RNAseq

tag: time-point

value: B (only 1 time-point available for this patient)

tag: chronic htn

tag: htn

tag: lung disease


title: Subject TS3 at timepoint A

description: single-cell RNAseq

tag: cell type

tag: diagnosis

value: Stable

value: Yes

tag: hospital admission

tag: icu admission


title: 192566_0_TCRB

tag: tissue

tag: Sex

tag: age

tag: ethnicity

value: Not Hispanic or Latino

tag: disease stage


title: Subject TP9 at timepoint B

description: single-cell RNAseq

tag: disease severity

tag: tocilizumab treatment

tag: race

value: hispanic

tag: bmi

tag: weight-kg

tag: outcome

tag: tocilizumab dose (mg/kg)


title: Subject TP6 at timepoint B

description: single-cell RNAseq

value: black

tag: height-m

tag: treatment

tag: time-point

tag: chronic htn

tag: htn

tag: lung disease

tag: time difference between samples a and b (d)


title: CITE6_Samples TS3A, TS3B, TS4A, TS4B, TP9B

description:
single-cell RNAseq + CITEseq
Detailed sample metadata are included in the tar archive with the processed data.

data_processing:
Library strategy: CITE-seq
Raw sequencing reads were demultiplexed using Cell Ranger mkfastq pipeline to create FASTQ files.
Cell Ranger count pipeline (v3.1) was employed in order to perform alignment (using STAR), filtering, barcode counting, and UMI counting.
CITE-seq samples were demultiplexed and attributed to a biological sample
Seurat v3.1 pre-processing standard protocol as defined by Satija lab
Genome_build: GRCh38 (Ensembl 93)
Supplementary_files_format_and_content: Cell Ranger filtered_gene_matrix, seurat objects

extract_protocol:
PBMCs were isolated from whole blood using density gradient centrifugation, and immediately cryopreserved. They were later thawed, DMSO was removed, cells were filtered, antibodies were applied, and cells were loaded to the 10x chromium platform
Libraries were prepared using the 10X Genomics Chromium Next GEM Chip G, according to the manufacturer’s user guide (document number CG000208, revision E, February 2020)

tag: cell type

tag: diagnosis


title: Subject TS4 at timepoint B

description: single-cell RNAseq

tag: age

tag: Sex

tag: hospital admission

tag: icu admission


title: Subject NS0 at timepoint A

description: single-cell RNAseq

tag: disease severity

tag: tocilizumab treatment

tag: race

tag: bmi

value: No Tocilizumab


title: CITE4_Samples NS0A, NS0B, TS2A, TS2B, TP6A, TP6B


title: CITE5_Samples TS3A, TS3B, TS4A, TS4B, TP9B


title: CITE2_Samples NS1A, NS1B, TS5A, TS5B, TP7A, TP7B


title: CITE1_Samples NS1A, NS1B, TS5A, TS5B, TP7A, TP7B


title: BPN-15477-treated WT fibroblasts 3348

status: Public on Mar 29 2021

description: Cell line has been discontinued at Coriell. Here is further information on this cell line: Cellosaurus: https://web.expasy.org/cellosaurus/CVCL_7382

data_processing:
RNASeq reads were mapped against Ensembl GRCh37 (version 75) by STAR (version 2.4.2) allowing 5% mismatch
Number of reads covering splice junction was measured by STAR during alignment
Exon triplet index was built on Ensembl GRCh37 (version 75) where each triplet is a three-consecutive exons, namely exon 1, 2 and 3, according to the annotation
For each triplet, two values are measured. The first value, representing exon inclusion, is the average of number of reads connecting exon 1 and 2 and number of reads connecting exon 2 and 3. This value is an integer
The second value, representing exon exclusion, is the number of reads connecting exon 1 and 3, which is an integer as well.
Genome_build: Ensembl GRCh37 version 75
Supplementary_files_format_and_content: Fastq format for RNASeq reads; Tab-delimited txt format for splice junction counts

source_name: Human fibroblast

growth_protocol: Six different human WT fibroblast cell lines were obtained from Coriell Institute and cultured in Dulbecco's modified Eagle's medium (D-MEM, Gibco) with 10% fetal bovine serum (FBS, Sigma). Cells were counted and plated in order to achieve semi-confluence after eight days.

extract_protocol:
After seven days of treatment, cells were collected, and RNA was extracted using the TRI reagent procedure provided by the manufacturer.
RNA-Seq libraries were prepared by the Genomic and Technology Core (GTC) of MGH using strand-specific dUTP method. In brief, RNA sample quality (based on RNA Integrity Number, or RIN) and quantity was determined using the Agilent 2200 TapeStation and between 100-1000 ng of total RNA was used for library preparation. Each RNA sample was spiked with 1 µl of diluted (1:100) External RNA Controls Consortium (ERCC) RNA Spike-In Mix (4456740, ThermoFisher) alternating between mix 1 and mix 2 for each well in the batch. Samples were then enriched for mRNA using polyA capture, followed by stranded reverse transcription and chemical shearing to make appropriate stranded cDNA inserts. Libraries were finished by adding Y-adapters, with sample specific barcodes, followed by between 10-15 rounds of PCR amplification. Libraries were evaluated for final concentration and size distribution by Agilent 2200 TapeStation and/or qPCR, using Library Quantification Kit (KK4854, Kapa Biosystems), and multiplexed by pooling equimolar amounts of each library prior to sequencing.

treatment_protocol: Twenty-four hours after plating, the medium was changed and cells were treated with BPN-15477 or DMSO to a final concentration of 30 µM and 0.5%, respectively. DMSO was used as vehicle and the concentration of BPN-15477 was chosen based on our previous studies, since at this concentration BPN-15477 induces robust splicing changes.

value: fibroblast

tag: genotype

value: WT

value: BPN-15477 treated

tag: coriell accession


title: Untreated WT fibroblasts 2036

tag: treatment

value: DMSO


title: BPN-15477-treated WT fibroblasts 0041


title: Untreated WT fibroblasts 1652


title: BPN-15477-treated WT fibroblasts 8402


title: Subject NS0 at timepoint B

description: single-cell RNAseq

value: white

tag: weight-kg

tag: height-m

tag: time-point

tag: chronic htn

tag: outcome

tag: tocilizumab dose (mg/kg)


title: CITE3_Samples NS0A, NS0B, TS2A, TS2B, TP6A

tag: cell type

value: PBMC

tag: diagnosis


title: BPN-15477-treated WT fibroblasts 16409


title: Untreated WT fibroblasts 0041


title: BPN-15477-treated WT fibroblasts 2036


title: Untreated WT fibroblasts 8402


title: Subject NS1 at timepoint A

description: single-cell RNAseq

value: No

tag: age

tag: Sex

value: F

value: A

tag: htn

tag: lung disease

tag: hospital admission

tag: time difference between samples a and b (d)


title: Subject TP6 at timepoint A

description: single-cell RNAseq

tag: disease severity

value: Progressive

tag: tocilizumab treatment

value: M

tag: race

tag: bmi

value: Tocilizumab

tag: icu admission

value: Expired


title: Untreated WT fibroblasts 3348

tag: genotype

tag: treatment

tag: coriell accession


title: Complete_KO_Molt4_2 [SJTALL065786_C7]

status: Public on Mar 09 2021

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
reads were counted using htseq/0.6.1p1 with gencode.v19.annotation.gtf
htseq was used to derive the read counts with parameters -r name -a 0 -s no -m union -t exon
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: 100% KO USP7 in Molt4

extract_protocol:
Total RNA was extracted using the QIAGEN Rneasy Mini kit.
The total stranded RNA library was prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche Sequencing). RNA sequencing was performed on NovaSeq 6000 system (Illumina).

tag: cell line

value: Jurkat

value: T-ALL Cancer Cell Line

tag: genotype/varaition

value: 100% KO USP7 in Molt4

tag: molecule subtype

value: Ribo-depleted


title: Untreated WT fibroblasts 16409

tag: cell type

value: fibroblast


title: Complete_KO_Molt4_1 [SJTALL065786_C6]


title: Partial_KO_Molt4_1 [SJTALL065786_C3]

source_name: Partial KO USP7 in Molt4

value: Partial KO USP7 in Molt4


title: HSB2_USP7shRNA4058_1 [SJTALL061907_C1]

source_name: Hsb-2 cell line treated with USP7 shRNA-4058

value: USP7 shRNA-4058


title: HSB2_USP7shRNA4058_2 [SJTALL061907_C2]


title: HSB2_scrambled_2 [SJTALL061905_C2]

source_name: Hsb-2 cell line treated with scrambled siRNA

value: scrambled siRNA


title: BPN-15477-treated WT fibroblasts 1652

value: WT

value: BPN-15477 treated