title: Tanzisertib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Tanzisertib followed by 2h IL4 10ng/mL


title: Telatinib_IL4_4h

status: Public on Apr 16 2024

type: SRA

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: ChIPseq

library_source: genomic

data_processing:
Reads were quality filtered according to the illumina pipeline
Single end reads were mapped to the mouse mm10 genome (Illumina's iGenomes reference annotation downloaded from UCSC http://support.illumina.com/sequencing/sequencing_software/igenome.html) by exploiting the mapping steps of ShortStack (Johnson et al. 2016).Briefly, ShortStack exploits bowtie to identify all best-matched alignments for each read. It will compute a probability for each alignment to different loci in the genome. To do so the frequency of uniquely aligned reads mapping within the vicinity of multi-mapping reads is used to redistribute multi-mapping reads accordingly.
Mapped reads were filtered in order to remove randomly placed multi-mappers and unmapped reads using SAMtools standard procedure (version 1.9)(Li et al. 2009).
In order to identify high confidence genome wide site of enrichment per antibody we implemented three strategies accordingly to the type of signal distribution evaluated after visual inspection of bigwig tracks on IGV (Robinson et al. 2011):   For H2K27ac we used peaks identified in ATACseq samples (see below) expanding the ATAC peaks by 1.5 kb on both sides.
Read counts per samples at the identified loci were retrieved using the R/Bioconductor package GenomicRanges and GenomicAlignment (Lawrence et al. 2013). Sample normalization was achieved by selecting invariant peaks across samples (Gualdrini et al. 2016). Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.
Assembly: mm10
Supplementary files format and content: .bw are BigWig normalised files

molecule: genomic DNA

organism: Mus musculus

source_name: mouse bone marrow derived macrophages

extract_protocol:
genomic DNA
ChIPseq was carried out as previously described (XXXXXXX). Briefly, 2 x 106 BMDM cells were fixed with 1% of formaldehyde (Merck cod. 252549) for 10 min at RT and lysed to prepare nuclear extracts. After chromatin shearing by sonication with a Bioruptor® Pico, lysates were incubated overnight at 4°C with protein G Dynabeads (Invitrogen, cod.10009D) previously coupled with 2 μg of H3K27ac antibody (ab4729). After immunoprecipitation, beads were recovered using a magnetic stand and washed six times with FA/SDS buffer (50mM Hepes pH 8, 1% Triton-X, 0.1% Na-deoxycholate, 0.1% SDS, 1mM EDTA, 650mM Nacl), four times with Wash buffer (10mM Tris pH 8, 0.25M LiC, 1mM EDTA, 0.5% NP40, 0.5% Na-deoxycholate), followed by two washes with TEbuffer plus 50mM NaCl. Immunoprecipitated chromatin was eluted and cross-link reverted overnight at 65°C. DNA was purified with QIAquick PCR Purification Kit (QIAGEN) and then quantified with QuantiFluor (Cod.E2670, Promega. DNA libraries were prepared for NextSeq500 sequencing as described (Gualdrini et al 2022). The purified DNA libraries were quantified with the Quantifluor reagent (Cod.E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the High Sensitivity Assay HD5000 (Agilent cod.5067-5592). Library DNA were diluted to a working concentration of 4 nM and Single Reads (76bp) sequenced on an Illumina NextSeq500 platform.

treatment_protocol: Individual samples have been pre-treated with each compound separately for 1h before stimulating the cells with either LPS (10ng/mL) or IL4 (10 ng/mL) for 30minutes, 1h, 2h or 4h.

tag: cell type

value: BMDM

tag: treatment

value: 1h pre-treatment with Telatinib followed by 4h IL4 10ng/mL

tag: genotype

value: wild type

tag: antibody


title: Tanzisertib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Tanzisertib followed by 30 IL4 10ng/mL


title: lib79917

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

library_source: transcriptomic

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the human GRCh38 release 91 reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count (v0.4.1). Quality control and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCh38 release 91
Supplementary files format and content: counts.csv: Gene count matrix in text file

molecule: total RNA

organism: Homo sapiens

source_name: Islet TMR+ CD8 T cells

growth_protocol: Cryopreserved PBMC were thawed and rested at 37C for 3h in RPMI with 10% commercial human serum. After resting PBMC were cultures with overlapping peptide libraries (20 aa in length, 12 aa overlap) from the islet proteins GAD65, IGRP, ZnT8, and preproinsulin in the presence of anti-CD40 antibody for 14h.

extract_protocol:
Sorted cells were lysed, followed by reverse transcription (SMART-Seq v1 Ultra Low Input RNA Kit; Takara, Mountain View, CA).
Sequencing libraries were prepared using Nextera XT DNA kits (Illumina, San Diego, CA).

treatment_protocol: After 14h cutlture CD154+ activated T cells were enriched by magnetic bead enrichment and single cell sorted to isolate CD4+CD154+CD69+ T cells. Cells were sorted directly into wells of a 96 w plate containing SMART-seq v1 Ultra Low Input RNA buffer and then processed for library preparation.

value: Islet TMR+ CD8 T cells

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides

tag: donorid

tag: project number

tag: study group


title: Tanzisertib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Tanzisertib followed by 30 LPS 10ng/mL


title: Talmapimod_UT_0h

description: ChIPseq

value: 1h pre-treatment with Talmapimod followed by 4h UT


title: lib79918


title: lib79915


title: Tanzisertib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Tanzisertib followed by 2h LPS 10ng/mL


title: Tanzisertib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Tanzisertib followed by 1h IL4 10ng/mL


title: lib79919


title: lib79916


title: Talmapimod_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Talmapimod followed by 4h LPS 10ng/mL


title: lib79912


title: Talmapimod_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Talmapimod followed by 2h LPS 10ng/mL


title: Talmapimod_LPS_30

description: ChIPseq

value: 1h pre-treatment with Talmapimod followed by 30 LPS 10ng/mL


title: Talmapimod_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Talmapimod followed by 1h LPS 10ng/mL


title: lib79913


title: Talmapimod_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Talmapimod followed by 2h IL4 10ng/mL


title: lib79921


title: Talmapimod_IL4_30

description: ChIPseq

value: 1h pre-treatment with Talmapimod followed by 30 IL4 10ng/mL


title: lib79911


title: Talmapimod_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Talmapimod followed by 1h IL4 10ng/mL


title: lib79909


title: lib79914


title: lib79910


title: SNS314_UT_0h_b

description: ChIPseq

value: BMDM

value: 1h pre-treatment with SNS314 followed by 4h UT


title: SNS314_UT_0h

description: ChIPseq

value: wild type


title: lib79908


title: SNS314_LPS_4h

description: ChIPseq

value: 1h pre-treatment with SNS314 followed by 4h LPS 10ng/mL


title: SNS314_LPS_30

description: ChIPseq

value: 1h pre-treatment with SNS314 followed by 30 LPS 10ng/mL


title: lib79906

value: Islet TMR+ CD8 T cells

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib79905


title: SNS314_LPS_30_b

description: ChIPseq


title: lib79904


title: lib79907


title: lib79902


title: SNS314_IL4_30

description: ChIPseq

value: 1h pre-treatment with SNS314 followed by 30 IL4 10ng/mL


title: lib79901


title: lib79899

source_name: CD154+CD69+ CD4 T cells

value: CD154+CD69+ CD4 T cells


title: SNS314_LPS_2h

description: ChIPseq

value: 1h pre-treatment with SNS314 followed by 2h LPS 10ng/mL


title: SNS314_IL4_2h

description: ChIPseq

value: 1h pre-treatment with SNS314 followed by 2h IL4 10ng/mL


title: SNS314_IL4_1h

description: ChIPseq

value: 1h pre-treatment with SNS314 followed by 1h IL4 10ng/mL


title: lib79898


title: lib79897


title: SNS314_IL4_4h

description: ChIPseq

value: 1h pre-treatment with SNS314 followed by 4h IL4 10ng/mL


title: Silmitasertib_UT_0h_b

description: ChIPseq

value: 1h pre-treatment with Silmitasertib followed by 4h UT


title: Silmitasertib_UT_0h

description: ChIPseq


title: lib79896


title: SNS314_LPS_1h_b

description: ChIPseq

value: 1h pre-treatment with SNS314 followed by 1h LPS 10ng/mL


title: lib79894


title: Silmitasertib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Silmitasertib followed by 4h LPS 10ng/mL


title: Silmitasertib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Silmitasertib followed by 2h LPS 10ng/mL


title: Silmitasertib_LPS_30

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Silmitasertib followed by 30 LPS 10ng/mL


title: lib79900


title: lib79893


title: Silmitasertib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Silmitasertib followed by 4h IL4 10ng/mL

value: wild type


title: Silmitasertib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Silmitasertib followed by 30 IL4 10ng/mL


title: lib79890


title: Silmitasertib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Silmitasertib followed by 1h LPS 10ng/mL


title: lib79891

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib79962

value: Islet TMR+ CD8 T cells


title: lib79888

value: CD154+CD69+ CD4 T cells


title: Silmitasertib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Silmitasertib followed by 2h IL4 10ng/mL


title: Silmitasertib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Silmitasertib followed by 1h IL4 10ng/mL


title: lib79889


title: lib79887


title: lib79886


title: SGX523_LPS_4h

description: ChIPseq

value: 1h pre-treatment with SGX523 followed by 4h LPS 10ng/mL


title: lib79940


title: SGX523_UT_0h

description: ChIPseq

value: 1h pre-treatment with SGX523 followed by 4h UT


title: lib79895


title: lib79884


title: SGX523_LPS_4h_b

description: ChIPseq


title: SGX523_LPS_1h

description: ChIPseq

value: 1h pre-treatment with SGX523 followed by 1h LPS 10ng/mL


title: lib79882


title: SGX523_LPS_30

description: ChIPseq

value: 1h pre-treatment with SGX523 followed by 30 LPS 10ng/mL


title: lib79892


title: lib79883


title: lib79880


title: Patient B1, Spatial Transcriptomics (Visium)

city: Montpellier

first: Andrei

last: Turtoi

address: 208 Avenue des Apothicaires

country: France

institute: Institut de Recherche en Cancérologie de Montpellier

description: 10X Genomics

data_processing:
Sequencing of the libraries was done by DNBSEQ-G400 (MGI Tech) with a DNBSEQ-G400RS High-throughput Sequencing Set (App-A FCL PE100) following the manufacturer’s instructions.
The raw fastq files were processed with the SpaceRanger software 1.0 (10x Genomics) using the human genome reference set GRCh38-3.0.0 and default parameters.
The gene spatial expression analysis mainly relied on our library BulkSignalR and project-specific R scripts. Count matrices were filtered for non-expressed genes by imposing a minimum read count of 1 in at least 1% of the Visium spots. Subsequently, normalization was achieved by total count. Cell population-specific gene signatures were retrieved from sequence data for BC general cell populations (PMID: 34493872) and for CAFs (PMID: 32434947), from previously published studies.
Assembly: Hg 38
Supplementary files format and content: *_filtered_feature_bc_matrix.zip contains gene expression matrices produced by spaceranger : barcodes.tsv, features.tsv and matrix.tsv.
Supplementary files format and content: *_spatial.zip contains mainly images : aligned_fiducials, detected_tissue_image, scalefactors_json.json, tissue_hires_image, tissue_lowres_image and tissue_positions_list.
Supplementary files format and content: *_filtered_feature_bc_matrix.h5 is a compressed binary format file to access gene expression matrices produced by spaceranger.
Library strategy: Spatial Transcriptomics

source_name: Breast cancer lesion

extract_protocol:
Fresh frozen samples were cut and deposited on the 10x Visium slides.
Libraries were prepared using 10x Genomics kit (CG000239, 10x Genomics).

tag: tissue

value: Breast cancer lesion

tag: age

tag: tumor subtype

value: Triple negqtive

tag: tumor stage

value: ⅡA


title: Patient C1, Spatial Transcriptomics (Visium)

description: 10X Genomics

value: Ⅰ


title: lib79885


title: lib79878


title: SGX523_IL4_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with SGX523 followed by 4h IL4 10ng/mL


title: lib79881


title: SGX523_IL4_30

description: ChIPseq

value: 1h pre-treatment with SGX523 followed by 30 IL4 10ng/mL

value: wild type


title: lib79877

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: Patient D1, Spatial Transcriptomics (Visium)

description: 10X Genomics

value: Luminal

value: ⅡB


title: lib79879

value: CD154+CD69+ CD4 T cells


title: SGX523_IL4_2h

description: ChIPseq

value: 1h pre-treatment with SGX523 followed by 2h IL4 10ng/mL


title: lib79875


title: lib79874


title: Patient A1, Spatial Transcriptomics (Visium)

description: 10X Genomics

value: ⅢC


title: SGX523_IL4_1h

description: ChIPseq

value: 1h pre-treatment with SGX523 followed by 1h IL4 10ng/mL


title: lib79872


title: SGI1776_UT_0h

description: ChIPseq

value: 1h pre-treatment with SGI1776 followed by 4h UT


title: lib79871


title: lib79870


title: lib79868


title: lib79876


title: SGI1776_LPS_4h

description: ChIPseq

value: 1h pre-treatment with SGI1776 followed by 4h LPS 10ng/mL


title: lib79866


title: SGI1776_LPS_30_b

description: ChIPseq

value: 1h pre-treatment with SGI1776 followed by 30 LPS 10ng/mL


title: lib79867


title: lib79865


title: lib79864


title: SGI1776_LPS_30

description: ChIPseq


title: SGI1776_LPS_2h

description: ChIPseq

value: 1h pre-treatment with SGI1776 followed by 2h LPS 10ng/mL


title: lib79873


title: lib79863


title: SGI1776_LPS_2h_b

description: ChIPseq


title: lib79862


title: lib79860


title: lib79861


title: lib79869


title: lib79859


title: SGI1776_LPS_1h

description: ChIPseq

value: 1h pre-treatment with SGI1776 followed by 1h LPS 10ng/mL


title: SGI1776_IL4_4h

description: ChIPseq

value: 1h pre-treatment with SGI1776 followed by 4h IL4 10ng/mL


title: lib79858


title: lib79857


title: lib79856


title: lib79854


title: lib79853


title: lib79855


title: SGI1776_IL4_30

description: ChIPseq

value: BMDM

value: 1h pre-treatment with SGI1776 followed by 30 IL4 10ng/mL


title: SGI1776_IL4_2h

description: ChIPseq

value: 1h pre-treatment with SGI1776 followed by 2h IL4 10ng/mL


title: lib79852


title: lib79850


title: lib79849


title: lib79851


title: lib79903

value: Islet TMR+ CD8 T cells


title: SNS314_LPS_1h

description: ChIPseq

value: 1h pre-treatment with SNS314 followed by 1h LPS 10ng/mL

value: wild type


title: SGI1776_IL4_1h

description: ChIPseq

value: 1h pre-treatment with SGI1776 followed by 1h IL4 10ng/mL


title: Selumetinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Selumetinib followed by 4h UT


title: lib79844

value: CD154+CD69+ CD4 T cells

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: SGI1776_IL4_2h_b

description: ChIPseq


title: Selumetinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Selumetinib followed by 30 LPS 10ng/mL


title: lib79846


title: Selumetinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Selumetinib followed by 4h LPS 10ng/mL


title: lib79848


title: lib79845


title: lib79842


title: Selumetinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Selumetinib followed by 2h LPS 10ng/mL


title: Selumetinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Selumetinib followed by 1h LPS 10ng/mL


title: lib79847


title: lib79839


title: lib79840


title: lib79838


title: Selumetinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Selumetinib followed by 4h IL4 10ng/mL


title: 393_Q

type: genomic

city: Beijing

first: Jie

last: Yan

address: Xi'anmen Street

country: China

institute: Peking University First Hospital

description: genomic DNA from cord blood

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: cord blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from 2 ml of whole blood from each sample using Blood DNA Midi Kit (Omega).

value: cord blood

tag: condition

value: control


title: 315_T

description: genomic DNA from maternal blood

source_name: maternal blood 3 trimester

value: maternal blood


title: 398_Q

description: genomic DNA from cord blood


title: 315_Q

description: genomic DNA from cord blood


title: lib79836


title: 315_F

description: genomic DNA from maternal blood

source_name: maternal blood 1 trimester


title: lib79835


title: lib79834


title: Selumetinib_IL4_2h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Selumetinib followed by 2h IL4 10ng/mL


title: 398_S

description: genomic DNA from maternal blood

source_name: maternal blood 2 trimester


title: lib79833


title: 315_S

description: genomic DNA from maternal blood


title: 398_T

description: genomic DNA from maternal blood


title: 393_T

description: genomic DNA from maternal blood


title: 398_F

description: genomic DNA from maternal blood


title: Selumetinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Selumetinib followed by 1h IL4 10ng/mL


title: 386_Q

description: genomic DNA from cord blood


title: lib79832


title: lib79830


title: lib79831


title: 393_S

description: genomic DNA from maternal blood


title: 375_T

description: genomic DNA from maternal blood


title: lib79837


title: lib79841


title: lib79829


title: Ruxolitinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Ruxolitinib followed by 4h UT


title: lib79827


title: 393_F

description: genomic DNA from maternal blood


title: 386_T

description: genomic DNA from maternal blood


title: lib79826


title: Ruxolitinib_UT_0h_b

description: ChIPseq

value: wild type


title: 375_Q

description: genomic DNA from cord blood


title: Ruxolitinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Ruxolitinib followed by 4h LPS 10ng/mL


title: lib79825


title: 386_F

description: genomic DNA from maternal blood


title: lib79824


title: lib79828


title: Ruxolitinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Ruxolitinib followed by 30 LPS 10ng/mL


title: lib79823

value: CD154+CD69+ CD4 T cells


title: 386_S

description: genomic DNA from maternal blood


title: Ruxolitinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Ruxolitinib followed by 2h LPS 10ng/mL


title: lib79821

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: 375_S

description: genomic DNA from maternal blood


title: Ruxolitinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Ruxolitinib followed by 1h LPS 10ng/mL


title: lib79819


title: lib79818


title: lib79817


title: Ruxolitinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Ruxolitinib followed by 4h IL4 10ng/mL


title: 375_F

description: genomic DNA from maternal blood


title: lib79085

value: Islet TMR+ CD8 T cells

value: Aab negative


title: Ruxolitinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Ruxolitinib followed by 30 IL4 10ng/mL


title: lib79822


title: lib79820


title: Selumetinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Selumetinib followed by 30 IL4 10ng/mL


title: 366_T

description: genomic DNA from maternal blood

value: maternal blood

value: control


title: Ruxolitinib_IL4_2h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Ruxolitinib followed by 2h IL4 10ng/mL


title: lib79082


title: 366_Q

description: genomic DNA from cord blood

value: cord blood


title: lib79843


title: lib79078


title: lib79079


title: lib79077


title: lib79081


title: Ruxolitinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Ruxolitinib followed by 1h IL4 10ng/mL

value: wild type


title: 364_Q

description: genomic DNA from cord blood


title: 366_S

description: genomic DNA from maternal blood


title: Refametinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Refametinib followed by 30 LPS 10ng/mL


title: lib79080


title: Refametinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Refametinib followed by 4h UT


title: lib79072


title: Refametinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Refametinib followed by 4h LPS 10ng/mL


title: lib79076

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib79071


title: lib79074


title: lib79073


title: 364_T

description: genomic DNA from maternal blood


title: Refametinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Refametinib followed by 1h LPS 10ng/mL


title: Refametinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Refametinib followed by 2h LPS 10ng/mL


title: 366_F

description: genomic DNA from maternal blood


title: lib79075

value: Islet TMR+ CD8 T cells


title: lib79068

value: Aab negative


title: lib79069


title: Refametinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Refametinib followed by 4h IL4 10ng/mL


title: Refametinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Refametinib followed by 2h IL4 10ng/mL


title: lib79064


title: Refametinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Refametinib followed by 1h IL4 10ng/mL


title: Refametinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Refametinib followed by 30 IL4 10ng/mL


title: 358_S

description: genomic DNA from maternal blood

value: maternal blood

value: control


title: lib79062


title: lib79063


title: 358_F

description: genomic DNA from maternal blood


title: 358_Q

description: genomic DNA from cord blood

value: cord blood


title: 364_S

description: genomic DNA from maternal blood


title: lib79059


title: 356_Q

description: genomic DNA from cord blood


title: lib79060


title: lib79061


title: Poziotinib_UT_0h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Poziotinib followed by 4h UT


title: 356_T

description: genomic DNA from maternal blood


title: lib79058


title: lib79057


title: Poziotinib_UT_0h_b

description: ChIPseq

value: wild type


title: Poziotinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Poziotinib followed by 4h LPS 10ng/mL


title: 356_S

description: genomic DNA from maternal blood


title: lib79067


title: lib79083


title: lib79084


title: lib79065


title: lib79066


title: lib79055


title: lib79070


title: lib79056


title: 358_T

description: genomic DNA from maternal blood


title: lib79054


title: Poziotinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Poziotinib followed by 30 LPS 10ng/mL


title: Poziotinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Poziotinib followed by 2h LPS 10ng/mL


title: lib79051

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: 364_F

description: genomic DNA from maternal blood


title: lib79052


title: lib79053


title: Poziotinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Poziotinib followed by 4h IL4 10ng/mL


title: 312_Q

description: genomic DNA from cord blood


title: lib79048

value: Islet TMR+ CD8 T cells


title: lib79050

value: Aab negative


title: Poziotinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Poziotinib followed by 1h LPS 10ng/mL


title: 356_F

description: genomic DNA from maternal blood


title: Poziotinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Poziotinib followed by 30 IL4 10ng/mL


title: lib79046


title: lib79045


title: Poziotinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Poziotinib followed by 2h IL4 10ng/mL


title: lib79044


title: lib79043


title: Poziotinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Poziotinib followed by 1h IL4 10ng/mL


title: 307_T

description: genomic DNA from maternal blood

value: maternal blood


title: lib79040


title: lib79039


title: 312_T

description: genomic DNA from maternal blood

value: control


title: lib79041


title: lib79038


title: 312_F

description: genomic DNA from maternal blood


title: 307_F

description: genomic DNA from maternal blood


title: lib79037


title: lib79042


title: Pimasertib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Pimasertib followed by 30 LPS 10ng/mL


title: lib79036


title: 312_S

description: genomic DNA from maternal blood


title: Pimasertib_LPS_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Pimasertib followed by 4h LPS 10ng/mL


title: lib79035


title: Pimasertib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Pimasertib followed by 2h LPS 10ng/mL

value: wild type


title: 307_Q

description: genomic DNA from cord blood

value: cord blood


title: lib79034


title: Pimasertib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Pimasertib followed by 1h LPS 10ng/mL


title: lib79033

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib79049


title: lib79032


title: lib79031


title: 134_Q

description: genomic DNA from cord blood

value: exercise


title: Pimasertib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Pimasertib followed by 4h IL4 10ng/mL


title: lib79030

value: Islet TMR+ CD8 T cells

value: Aab negative


title: lib79029


title: lib79047


title: lib79028


title: Pimasertib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Pimasertib followed by 30 IL4 10ng/mL


title: 307_S

description: genomic DNA from maternal blood


title: 302_S

description: genomic DNA from maternal blood


title: 302_T

description: genomic DNA from maternal blood


title: 302_Q

description: genomic DNA from cord blood


title: 302_F

description: genomic DNA from maternal blood


title: lib79026


title: Pimasertib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Pimasertib followed by 2h IL4 10ng/mL


title: lib79027


title: lib79025


title: Pimasertib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Pimasertib followed by 1h IL4 10ng/mL


title: lib79024


title: lib79023


title: Pimasertib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Pimasertib followed by 4h UT


title: lib79022


title: PH797804_UT_0h

description: ChIPseq

value: 1h pre-treatment with PH797804 followed by 4h UT


title: 134_T

description: genomic DNA from maternal blood

value: maternal blood


title: lib79021


title: PH797804_LPS_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with PH797804 followed by 4h LPS 10ng/mL


title: lib79019


title: PH797804_LPS_30

description: ChIPseq

value: 1h pre-treatment with PH797804 followed by 30 LPS 10ng/mL


title: lib79017


title: 114_S

description: genomic DNA from maternal blood


title: PH797804_LPS_2h

description: ChIPseq

value: 1h pre-treatment with PH797804 followed by 2h LPS 10ng/mL

value: wild type


title: lib79020


title: 134_S

description: genomic DNA from maternal blood


title: 114_T

description: genomic DNA from maternal blood


title: lib79015


title: lib79016


title: lib79018


title: PH797804_LPS_1h

description: ChIPseq

value: 1h pre-treatment with PH797804 followed by 1h LPS 10ng/mL


title: lib79014

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib79013


title: PH797804_IL4_4h

description: ChIPseq

value: 1h pre-treatment with PH797804 followed by 4h IL4 10ng/mL


title: lib79012


title: 134_F

description: genomic DNA from maternal blood

value: exercise


title: PH797804_IL4_30

description: ChIPseq

value: 1h pre-treatment with PH797804 followed by 30 IL4 10ng/mL


title: 113_Q

description: genomic DNA from cord blood

value: cord blood


title: lib79007

value: Islet TMR+ CD8 T cells

value: Aab negative


title: lib79011


title: lib79010


title: lib79006


title: lib79009


title: PH797804_IL4_2h

description: ChIPseq

value: 1h pre-treatment with PH797804 followed by 2h IL4 10ng/mL


title: PF04691502_UT_0h

description: ChIPseq

value: 1h pre-treatment with PF04691502 followed by 4h UT


title: lib79004


title: 113_T

description: genomic DNA from maternal blood


title: lib79003


title: lib79005


title: 114_F

description: genomic DNA from maternal blood


title: PF04691502_LPS_4h

description: ChIPseq

value: 1h pre-treatment with PF04691502 followed by 4h LPS 10ng/mL


title: lib79001


title: lib79000


title: PF04691502_LPS_30

description: ChIPseq

value: 1h pre-treatment with PF04691502 followed by 30 LPS 10ng/mL


title: lib79002


title: PH797804_IL4_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with PH797804 followed by 1h IL4 10ng/mL


title: lib78999


title: PF04691502_LPS_2h

description: ChIPseq

value: 1h pre-treatment with PF04691502 followed by 2h LPS 10ng/mL


title: lib78998


title: 114_Q

description: genomic DNA from cord blood


title: lib78997


title: 113_F

description: genomic DNA from maternal blood

value: maternal blood


title: lib78996


title: lib79008


title: 110_S

description: genomic DNA from maternal blood


title: lib78994


title: PF04691502_IL4_4h

description: ChIPseq

value: 1h pre-treatment with PF04691502 followed by 4h IL4 10ng/mL

value: wild type


title: PF04691502_LPS_1h

description: ChIPseq

value: 1h pre-treatment with PF04691502 followed by 1h LPS 10ng/mL


title: lib78993

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: 105_T

description: genomic DNA from maternal blood

value: exercise


title: 110_F

description: genomic DNA from maternal blood


title: PF04691502_IL4_30

description: ChIPseq

value: 1h pre-treatment with PF04691502 followed by 30 IL4 10ng/mL


title: PF04691502_IL4_30_b

description: ChIPseq


title: 113_S

description: genomic DNA from maternal blood


title: lib78990


title: lib78992


title: 88_Q

description: genomic DNA from cord blood

value: cord blood


title: lib78989

value: CD154+CD69+ CD4 T cells


title: lib78988

value: Aab negative


title: lib78991

value: Islet TMR+ CD8 T cells


title: 105_Q

description: genomic DNA from cord blood


title: 110_Q

description: genomic DNA from cord blood


title: lib78987


title: PF04691502_IL4_2h

description: ChIPseq

value: 1h pre-treatment with PF04691502 followed by 2h IL4 10ng/mL


title: lib78986


title: 105_S

description: genomic DNA from maternal blood


title: lib78983


title: lib78984


title: lib78985


title: lib78982


title: 110_T

description: genomic DNA from maternal blood


title: Pacritinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Pacritinib followed by 4h UT


title: lib78995


title: Pacritinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Pacritinib followed by 30 LPS 10ng/mL


title: lib78979


title: 105_F

description: genomic DNA from maternal blood


title: 88_S

description: genomic DNA from maternal blood


title: Pacritinib_LPS_2h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Pacritinib followed by 2h LPS 10ng/mL


title: lib78978


title: lib78977


title: lib78976


title: Pacritinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Pacritinib followed by 4h LPS 10ng/mL


title: lib78975


title: Pacritinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Pacritinib followed by 4h IL4 10ng/mL


title: 62_Q

description: genomic DNA from cord blood


title: lib78974


title: lib78973


title: Pacritinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Pacritinib followed by 30 IL4 10ng/mL


title: 67_F

description: genomic DNA from maternal blood

value: maternal blood


title: 88_F

description: genomic DNA from maternal blood


title: 67_S

description: genomic DNA from maternal blood


title: 67_Q

description: genomic DNA from cord blood


title: 88_T

description: genomic DNA from maternal blood


title: 62_F

description: genomic DNA from maternal blood


title: lib78971


title: Pacritinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Pacritinib followed by 2h IL4 10ng/mL

value: wild type


title: lib78970

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib78972


title: lib78969


title: Pacritinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Pacritinib followed by 1h IL4 10ng/mL


title: PF04691502_IL4_1h

description: ChIPseq

value: 1h pre-treatment with PF04691502 followed by 1h IL4 10ng/mL


title: 62_S

description: genomic DNA from maternal blood

value: exercise


title: lib78968

value: CD154+CD69+ CD4 T cells


title: lib78967


title: lib78966


title: OSI930_LPS_4h

description: ChIPseq

value: 1h pre-treatment with OSI930 followed by 4h LPS 10ng/mL


title: lib78963


title: lib78980

value: Aab negative


title: 59_F

description: genomic DNA from maternal blood


title: lib78981


title: Pacritinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Pacritinib followed by 1h LPS 10ng/mL


title: lib78962


title: 59_T

description: genomic DNA from maternal blood


title: lib78961


title: OSI930_LPS_2h

description: ChIPseq

value: 1h pre-treatment with OSI930 followed by 2h LPS 10ng/mL


title: lib78960


title: 59_Q

description: genomic DNA from cord blood

value: cord blood


title: lib78959


title: OSI930_LPS_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with OSI930 followed by 1h LPS 10ng/mL


title: lib78964


title: lib78958


title: 59_S

description: genomic DNA from maternal blood


title: 58_Q

description: genomic DNA from cord blood


title: lib78956


title: 58_T

description: genomic DNA from maternal blood


title: lib78955


title: BioD_rep3

city: Beachwood

first: Trailhead

last: Biosystems

state: Ohio

address: 23215 Commerce Park Rd

institute: Trailhead Biosystems Inc

data_processing:
processed the raw data with nextflow nf-core/rnaseq (v 3.6) pipeline, with default parameters. Netxflow version 22.05.0-edge.5704.
Trim Galore (v.0.6.7) was used for adaptor trimming and quality control
STAR (v 2.6.1) was used for alignment and counting within nf-core/rnaseq pipeline
Assembly: GRCh38
Supplementary files format and content: Tab delimited raw count files for each sample

source_name: hiPSC

growth_protocol: Cells were maintained in E8 medium on vitronectin coated 6 well plate and dissociated with TrypLE to be seeded in bioreactors for a 4 day growth protocol. The control bioreactor had E8 medium and the treated bioreactor had E8 medium + PEG + Heparin

extract_protocol:
RNA was qualified using Qubit™ RNA BR Assay Kit. Isolated RNA's quality validated with 4200 TapeStation System.
Library preparation done with Illumina Stranded mRNA Prep.

treatment_protocol: Single cells (hiPSCs) seeded in E8 plus (0.1 µg/ml) Heparin and (10 mg/ml PEG). 50% of the media was replaced on the second day following seeding. No other changes were made the following days of the growth assay

value: hiPSC

tag: cell line

value: Pluripotent Stem Cells

value: Wild Type

value: Control


title: OSI930_IL4_4h

description: ChIPseq

value: 1h pre-treatment with OSI930 followed by 4h IL4 10ng/mL

value: wild type


title: 58_S

description: genomic DNA from maternal blood

value: maternal blood


title: lib78953

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: OSI930_IL4_2h

description: ChIPseq

value: 1h pre-treatment with OSI930 followed by 2h IL4 10ng/mL


title: lib78952

value: CD154+CD69+ CD4 T cells


title: OSI930_IL4_30

description: ChIPseq

value: 1h pre-treatment with OSI930 followed by 30 IL4 10ng/mL


title: OSI930_IL4_1h

description: ChIPseq

value: 1h pre-treatment with OSI930 followed by 1h IL4 10ng/mL


title: lib78951


title: 67_T

description: genomic DNA from maternal blood

value: exercise


title: lib78950


title: BioD_rep1


title: BioD_rep2


title: 54_Q

description: genomic DNA from cord blood


title: ONO4059analogue_UT_0h

description: ChIPseq

value: 1h pre-treatment with ONO4059analogue followed by 4h UT


title: BioC_rep3

value: PEG and HS


title: lib78948


title: lib78946


title: BioC_rep2


title: lib78945


title: BioC_rep1


title: lib78943


title: lib78947


title: lib78949


title: OSI930_LPS_30

description: ChIPseq

value: BMDM

value: 1h pre-treatment with OSI930 followed by 30 LPS 10ng/mL


title: lib78944


title: lib78942


title: 54_T

description: genomic DNA from maternal blood


title: ONO4059analogue_LPS_30

description: ChIPseq

value: 1h pre-treatment with ONO4059analogue followed by 30 LPS 10ng/mL


title: lib78957


title: 54_S

description: genomic DNA from maternal blood


title: MPS, ScRNA-seq

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

institute: Sichuan University

library_source: transcriptomic single cell

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene_x0002_expression/software/pipelines/latest/what-is-cell-ranger) using default parameters
Assembly: mm10
Supplementary files format and content: Tab-separaed value files and matrix files

source_name: Metaphysis of distal femur and proximal tibia

extract_protocol:
Removing the femoral distal epiphysis and the tibial proximal epiphysis gently, and about 5 mm long the metaphysis region was dissected and crushed with mortar and pestle in FACS buffer (10%FBS in PBS). The isolated metaphysis was cut into small pieces with scissors and was digested with 3mg/ml collagenase type I  in α-MEM for 30 minutes at 37℃ with gentle shaking. Cells were filtered through a 70 μm cell strainer and centrifuged to obtain the cell pellet, then re-suspended with FACS buffer to receive the cell suspension. The Gli1+ progenitors were sorted using a BD Arial III according to the presence or absence of PE signal using a C57BL/6J mouse as a negtive control.
Sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics) according to the manufacturer’s instructions.

value: Primary cells

value: Metaphyseal mesenchymal progenitors

value: Gli1-CreERT2; tdTomato

value: The one-month-old Gli1-CreERT2; tdTomato mice were treated with tamoxifen for three days and injected with methylprednisolone for three days


title: ONO4059analogue_LPS_1h

description: ChIPseq

value: 1h pre-treatment with ONO4059analogue followed by 1h LPS 10ng/mL

value: wild type


title: lib78940

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: 58_F

description: genomic DNA from maternal blood

value: maternal blood


title: ONO4059analogue_LPS_2h

description: ChIPseq

value: 1h pre-treatment with ONO4059analogue followed by 2h LPS 10ng/mL


title: 54_F

description: genomic DNA from maternal blood


title: 32_Q

description: genomic DNA from cord blood

value: cord blood


title: ONO4059analogue_LPS_4h

description: ChIPseq

value: 1h pre-treatment with ONO4059analogue followed by 4h LPS 10ng/mL


title: male chicken embryonic gonad

city: New York

first: Wei

last: Wang

state: New York

address: 1230 York Ave.

department: Bioinformatics Resource Center

institute: The Rockefeller University

description: 10X genomics

data_processing:
Sequenced reads were mapped to lab maintained ant genome assembly using cellranger version 6.0.1
Assembly: GCF_003957565.2
Assembly: GCF_000002315.6
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Gallus gallus

source_name: early embryonic gonad (HH28)

extract_protocol:
single cell extraction protocol
10X Genomics 3' v3 kit

tag: Sex

value: Male

value: early embryonic gonad (HH28)


title: lib78939

value: CD154+CD69+ CD4 T cells


title: elipsa mutant, clutch 4

city: Trondheim

first: Nathalie

last: Jurisch-Yaksi

address: Erling Skjalgsons gate 1

country: Norway

institute: NTNU

data_processing:
Standard processing by BGI.p
HISAT to align the clean reads to the reference genome.
Bowtie2 to align the clean reads to the reference genes.
Assembly: GCF_000002035.6_GRCz11
Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized, and log transformed using the voom algorithm from the limma package of Bioconductor.
Supplementary files format and content: excel file containing fold changes

organism: Danio rerio

source_name: whole larvae

extract_protocol:
To isolate RNA for sequencing, 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples, 500μL trizol was added and the euthanized larvae were homogenized through a 27-gauge needle until the mixture looked uniform. After adding another 500μL trizol, the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform, and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. After centrifugation, the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column (Qiagen) and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme (Qiagen) in RDD buffer (10μL Dnase+ 70μL RDD buffer per tube) for 45 minutes at room temperature. After incubation, 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice, and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column, 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI.
standard procedure performed by BGI

value: whole larvae

value: no treatment


title: ONO4059analogue_IL4_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with ONO4059analogue followed by 4h IL4 10ng/mL


title: ONO4059analogue_IL4_30

description: ChIPseq

value: 1h pre-treatment with ONO4059analogue followed by 30 IL4 10ng/mL


title: 32_F

description: genomic DNA from maternal blood

value: exercise


title: female chicken embryonic gonad

description: 10X genomics

value: Female


title: lib78936

value: Islet TMR+ CD8 T cells

value: >1 Aab+ any age


title: lib78935

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: 32_T

description: genomic DNA from maternal blood

value: maternal blood


title: lib78937


title: ONO4059analogue_IL4_1h

description: ChIPseq

value: 1h pre-treatment with ONO4059analogue followed by 1h IL4 10ng/mL

value: wild type


title: lib78932


title: lib78931


title: ONO4059analogue_IL4_2h

description: ChIPseq

value: 1h pre-treatment with ONO4059analogue followed by 2h IL4 10ng/mL


title: lib78934


title: lib78930


title: 32_S

description: genomic DNA from maternal blood


title: elipsa mutant, clutch 1

data_processing:
Standard processing by BGI.
HISAT to align the clean reads to the reference genome.
Bowtie2 to align the clean reads to the reference genes.
Assembly: GCF_000002035.6_GRCz11
Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized, and log transformed using the voom algorithm from the limma package of Bioconductor.
Supplementary files format and content: excel file containing fold changes


title: lib78928


title: elipsa mutant, clutch 2


title: Omipalisib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Omipalisib followed by 4h UT


title: lib78941


title: 62_T

description: genomic DNA from maternal blood


title: lib78927


title: lib78954


title: elipsa mutant, clutch 3


title: lib78926


title: lib78933


title: Omipalisib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Omipalisib followed by 30 LPS 10ng/mL


title: lib78929


title: lib78925


title: lib78924


title: elipsa control, clutch 3

value: mixture wt and +/-


title: Omipalisib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Omipalisib followed by 2h LPS 10ng/mL


title: Omipalisib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Omipalisib followed by 4h LPS 10ng/mL


title: elipsa control, clutch 2

value: whole larvae

value: no treatment


title: lib78922


title: lib78921


title: elipsa control, clutch 1


title: lib78919


title: Omipalisib_IL4_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Omipalisib followed by 4h IL4 10ng/mL


title: Omipalisib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Omipalisib followed by 1h LPS 10ng/mL


title: lib78918

value: Islet TMR+ CD8 T cells


title: elipsa control, clutch 4


title: Omipalisib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Omipalisib followed by 30 IL4 10ng/mL


title: lib78917

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides

value: >1 Aab+ any age


title: DIPG4 cells, AZD4573, radiation, 6 hours, replicate 3, RNAseq

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
The quality of the fastq files was accessed using FastQC  (v.0.11.8), FastQ Screen (v.0.13.0) and MultiQC (v.1.8).
Illumina adapters and low-quality reads were filtered out using BBDuk (v. 38.87).
Trimmed fastqc files were aligned to the hg38 human reference genome and aligned counts per gene were quantified using STAR (v.2.7.9a).
Differential gene expression analysis was performed using the DESeq2 package.
Assembly: hg38
Supplementary files format and content: Raw count matrix

growth_protocol: SU-DIPG4 cells were cultured in tumor stem media (TSM) consisting of Neurobasal(-A) (Invitrogen), human-basic FGF (20 ng/mL; Shenandoah Biotech), human-EGF (20 ng/mL; Shenandoah Biotech), human PDGF-AB (20 ng/mL; Shenandoah Biotech), B27(-A) (Invitrogen), and heparin (10 ng/mL). HSJD-DIPG007 cells were maintained in TSM media as above with 10% fetal bovine serum (FBS)(Atlanta Biologicals). SF8628 cells were maintained in Dulbecco’s modified eagle medium (DMEM)(Gibco/ThermoFisher) and supplemented with 10% FBS, MEM non-essential amino acids (Gibco/ThermoFisher) and antibiotic/antimicotic (Gibco/ThermoFisher). Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
Cells were collected in Qiazol and RNA extraction was performed using Rneasy Plus Mini Kit (Qiagen)
RNA purity, quantity and integrity was determined with NanoDrop (ThermoFisher Scientific) and TapeStation 4200 (Agilent) analysis prior to RNA-seq library preparation.  The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan) with an input of 200ng of total RNA to generate RNA-Seq libraries.  Paired-end sequencing reads of 150bp was generated on NovaSeq 6000 (Illumina) sequencer at a target depth of 80 million paired-end reads per sample.  Raw sequencing reads were de-multiplexed using bcl2fastq.

treatment_protocol: Cells were treated with DMSO or 40nM AZD4573. After 2 hrs, cells were irradiated at 6 Gy and collected after an additional 4 hrs.

value: Diffuse intrinsic pontine glioma

value: AZD4573+6Gy radiation

tag: dosage

tag: timepoint

value: 8 hours


title: DIPG4 cells, AZD4573, radiation, 6 hours, replicate 2, RNAseq


title: lib78916


title: lib78915


title: DIPG4 cells, AZD4573, radiation, 6 hours, replicate 1, RNAseq


title: Omipalisib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Omipalisib followed by 2h IL4 10ng/mL

value: wild type


title: lib78914


title: Omipalisib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Omipalisib followed by 1h IL4 10ng/mL


title: lib78913


title: lib78912


title: lib78923


title: NMS1286937_UT_0h

description: ChIPseq

value: 1h pre-treatment with NMS1286937 followed by 4h UT


title: DIPG4 cells, DMSO, radiation, 6 hours, replicate 2, RNAseq

value: DMSO+6Gy radiatio


title: lib78920


title: lib78910


title: NMS1286937_LPS_4h

description: ChIPseq

value: 1h pre-treatment with NMS1286937 followed by 4h LPS 10ng/mL


title: lib78909


title: DIPG4 cells, DMSO, radiation, 6 hours, replicate 1, RNAseq


title: lib78907


title: lib78908


title: NMS1286937_LPS_30

description: ChIPseq

value: 1h pre-treatment with NMS1286937 followed by 30 LPS 10ng/mL


title: DIPG4 cells, DMSO, 6 hours, replicate 3, RNAseq

value: DMOS


title: lib78906


title: lib78905


title: DIPG4 cells, DMSO, 6 hours, replicate 2, RNAseq

value: DMSO


title: NMS1286937_LPS_2h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with NMS1286937 followed by 2h LPS 10ng/mL


title: OSI930_UT_0h

description: ChIPseq

value: 1h pre-treatment with OSI930 followed by 4h UT


title: lib78965

value: CD154+CD69+ CD4 T cells

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib78903

value: Islet TMR+ CD8 T cells

value: >1 Aab+ any age


title: NMS1286937_LPS_1h

description: ChIPseq

value: 1h pre-treatment with NMS1286937 followed by 1h LPS 10ng/mL


title: lib78902


title: DIPG4 cells, DMSO, radiation, 6 hours, replicate 3, RNAseq

value: Diffuse intrinsic pontine glioma

value: 8 hours


title: DIPG4 cells, DMSO, 6 hours, replicate 1, RNAseq


title: lib78904


title: NMS1286937_IL4_4h

description: ChIPseq

value: 1h pre-treatment with NMS1286937 followed by 4h IL4 10ng/mL

value: wild type


title: lib78901


title: lib78911


title: lib78900


title: Stroma-Slide_4-ROI_004

city: Grand Rapids

first: Gregory

last: Burns

state: MI

address: 400 Monroe Ave NW

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: (v1.0) Human NGS Whole Transcriptome Atlas RNA

library_source: other

data_processing:
Base calling was done by Illumina RTA3 and output was demultiplexed and converted to fastq format with bcl2fastq v1.9.0.
Fastq files were converted to digital count conversion (DCC) files using GeoMx NGS Pipeline v2.3.3.10. Sample annotation, PKC configuration, and DCC files were imported with GeomxTools (v3.2.0) in R to generate a NanoStringGeoMxSet object.
Assembly: hg38
Supplementary files format and content: dcc

molecule: other

source_name: endometriotic lesion

extract_protocol:
Tissue sections were cut at 5 μm thickness and mounted on charged slides. Slides were baked at 60°C for one hour and stored at 4°C in a vacuum-sealed container containing desiccant for up to two weeks. All subsequent steps were performed under RNase-free conditions with DEPC-treated water. Slides were deparaffinized with three sequential five-minute washes in xylenes, followed by two washes in 100% ethanol for five minutes, one wash in 95% ethanol, and one wash in 1X PBS. Antigen retrieval was performed in target retrieval reagent (EDTA, pH 9.0) diluted to 1X in the BioGenex EZ-Retriever System for 10 minutes at 95°C. Slides were then washed with 1X PBS for five minutes. Slides were then incubated in 1 μg/mL proteinase K 10 minutes at 37°C and washed in 1X PBS for five minutes at room temperature. Slides were fixed for five minutes in 10% neutral buffered formalin followed by two washes in NBF stop buffer, for five minutes each, and one wash in 1X PBS for five minutes. Slides were then incubated with UV-photocleavable Human Whole Transcriptome Atlas hybridization probes diluted in buffer R (GeoMx RNA Slide Prep FFPE-PCLN kit) in a hybridization oven at 37°C for 16-20 hours. Following probe incubation, slides were washed with stringent buffer (1:1, formamide:4X SSC buffer) at 37°C twice for 25 minutes each. Then slides were washed twice in 2X SSC buffer. Slides were blocked in 200 μL buffer W (GeoMx RNA Slide Prep FFPE-PCLN kit) for 30 minutes and incubated at 4ºC overnight with SYTO 13 nucleic acid stain (500 nM) and antibodies for pan-cytokeratin (panCK; 1 µg/mL), smooth muscle actin (ACTA2; 1.25 µg/mL), and CD68 (0.5 µg/mL) diluted in buffer W. Slides were washed four times in 2X SSC buffer for 3 minutes each and placed in the nanoString GeoMx DSP instrument. Duplicate 500 µm2 regions of interest (ROI) were selected for each based on fluorescent imaging on the GeoMx DSP instrument (NanoString Technologies). ROI were drawn in the central portion of the endometrium stratum functionalis, to include glandular and not luminal epithelium, for eutopic uterine tissue and in lesions areas with defined epithelium. ROIs were then segmented in order of macrophages (CD68+), epithelium (panCK+), and stroma (ACTA2-) areas of illumination (AOI) for individual collection. AOI were processed sequentially on the instrument using UV light focused through each AOI that released the photocleavable oligos into wells of a 96 well plate.
After AOI collection, indexing primers were hybridized during NanoString library preparation. Quality and quantity of the finished library pools were assessed using a combination of Agilent DNA High Sensitivity chips and the QuantiFluor dsDNA System.
Spatial Transcriptomics

treatment_protocol: Superficial peritoneal endometriotic lesions and matched eutopic uterine tissues from 10 patients were obtained as archived deidentified formalin-fixed paraffin-embedded (FFPE) tissue blocks. All protocols involving tissue collection were approved by the institutional review board (IRB) Committee of Ponce Health Sciences University, School of Medicine (PHSU).

value: endometriotic lesion

tag: sampleID

value: Stroma


title: NMS1286937_IL4_30

description: ChIPseq

tag: cell type

value: 1h pre-treatment with NMS1286937 followed by 30 IL4 10ng/mL


title: lib78899

tag: treatment


title: lib78898


title: Epithelium-Slide_4-ROI_004

value: Epithelium


title: NMS1286937_IL4_2h

description: ChIPseq

value: 1h pre-treatment with NMS1286937 followed by 2h IL4 10ng/mL

tag: genotype


title: Macrophages-Slide_4-ROI_004

value: Macrophages


title: lib78897


title: NMS1286937_IL4_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with NMS1286937 followed by 1h IL4 10ng/mL

tag: antibody


title: lib78893

tag: donorid


title: lib78895

tag: project number


title: lib78894

tag: study group


title: Neratinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Neratinib followed by 4h UT


title: Neratinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Neratinib followed by 4h LPS 10ng/mL


title: Macrophages-Slide_4-ROI_003

tag: tissue


title: Stroma-Slide_4-ROI_003


title: lib78892

value: Islet TMR+ CD8 T cells

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: Epithelium-Slide_4-ROI_003


title: lib78890

value: >1 Aab+ any age


title: lib78891


title: lib78889


title: Neratinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Neratinib followed by 30 LPS 10ng/mL


title: lib78888


title: Neratinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Neratinib followed by 2h LPS 10ng/mL


title: Epithelium-Slide_4-ROI_002

source_name: eutopic endometrium

value: eutopic endometrium


title: lib78887


title: Neratinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Neratinib followed by 1h LPS 10ng/mL

value: wild type


title: Stroma-Slide_4-ROI_002

value: Stroma


title: lib78886


title: Macrophages-Slide_4-ROI_002


title: lib78884


title: Neratinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Neratinib followed by 4h IL4 10ng/mL


title: lib78896


title: lib78883


title: lib78885


title: Stroma-Slide_4-ROI_001


title: Neratinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Neratinib followed by 30 IL4 10ng/mL


title: Epithelium-Slide_4-ROI_001

value: Epithelium


title: lib78881


title: lib78882


title: lib78880


title: Neratinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Neratinib followed by 2h IL4 10ng/mL


title: lib78879


title: lib78878


title: Macrophages-Slide_4-ROI_001

value: Macrophages


title: lib78877


title: lib78876


title: Neratinib_IL4_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Neratinib followed by 1h IL4 10ng/mL


title: lib78875


title: Macrophages-Slide_3-ROI_009

value: endometriotic lesion


title: lib78874

value: Islet TMR+ CD8 T cells


title: lib78873

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: Mubritinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Mubritinib followed by 4h LPS 10ng/mL


title: Mubritinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Mubritinib followed by 30 LPS 10ng/mL


title: lib78872

value: >1 Aab+ any age


title: lib78870


title: Epithelium-Slide_3-ROI_008


title: lib78871


title: Mubritinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Mubritinib followed by 2h LPS 10ng/mL


title: lib78869


title: Stroma-Slide_3-ROI_007


title: lib78868


title: Mubritinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Mubritinib followed by 1h LPS 10ng/mL


title: lib78867


title: lib78866


title: lib78865


title: lib78864


title: Mubritinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Mubritinib followed by 4h IL4 10ng/mL

value: wild type


title: Stroma-Slide_3-ROI_006

value: eutopic endometrium

value: Stroma


title: Macrophages-Slide_3-ROI_010


title: Mubritinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Mubritinib followed by 4h UT


title: Epithelium-Slide_3-ROI_007

value: Epithelium


title: Mubritinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Mubritinib followed by 30 IL4 10ng/mL


title: lib78863


title: lib78861


title: Epithelium-Slide_3-ROI_006


title: Stroma-Slide_3-ROI_008


title: Mubritinib_IL4_2h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Mubritinib followed by 2h IL4 10ng/mL


title: lib78860


title: Macrophages-Slide_3-ROI_006

value: Macrophages


title: Stroma-Slide_3-ROI_005


title: lib78862

value: Islet TMR+ CD8 T cells


title: lib78858

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: Mubritinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Mubritinib followed by 1h IL4 10ng/mL


title: lib78856


title: Epithelium-Slide_3-ROI_005


title: Momelotinib_UT_0h_b

description: ChIPseq

value: 1h pre-treatment with Momelotinib followed by 4h UT


title: Momelotinib_UT_0h

description: ChIPseq


title: lib78855

value: >1 Aab+ any age


title: lib78854


title: Momelotinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Momelotinib followed by 4h LPS 10ng/mL


title: lib78853


title: lib78852


title: lib78851


title: Stroma-Slide_3-ROI_004

value: endometriotic lesion


title: lib78850


title: Epithelium-Slide_3-ROI_004


title: Momelotinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Momelotinib followed by 2h LPS 10ng/mL


title: Momelotinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Momelotinib followed by 30 LPS 10ng/mL

value: wild type


title: Macrophages-Slide_3-ROI_004


title: lib78849


title: lib78848


title: lib78859


title: lib78847


title: Momelotinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Momelotinib followed by 4h IL4 10ng/mL


title: Stroma-Slide_3-ROI_003

value: Stroma


title: Momelotinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Momelotinib followed by 1h LPS 10ng/mL


title: lib78857


title: lib78845


title: Epithelium-Slide_3-ROI_003

value: Epithelium


title: lib78844


title: Momelotinib_IL4_30

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Momelotinib followed by 30 IL4 10ng/mL


title: Macrophages-Slide_3-ROI_005

value: eutopic endometrium

value: Macrophages


title: lib78843

value: Islet TMR+ CD8 T cells

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: Momelotinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Momelotinib followed by 2h IL4 10ng/mL


title: lib78841

value: CD154+CD69+ CD4 T cells

value: >1 Aab+ any age


title: Macrophages-Slide_3-ROI_003

value: endometriotic lesion


title: lib78842


title: Stroma-Slide_3-ROI_002


title: lib78840


title: lib78839


title: Momelotinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Momelotinib followed by 1h IL4 10ng/mL


title: lib78837


title: lib78838


title: Epithelium-Slide_3-ROI_002


title: MK5108_UT_0h

description: ChIPseq

value: 1h pre-treatment with MK5108 followed by 4h UT


title: lib78846


title: lib78836


title: MK5108_LPS_4h

description: ChIPseq

value: 1h pre-treatment with MK5108 followed by 4h LPS 10ng/mL

value: wild type


title: lib78835


title: Stroma-Slide_3-ROI_001

value: Stroma


title: lib78834


title: lib78832


title: lib78831


title: MK5108_LPS_30

description: ChIPseq

value: 1h pre-treatment with MK5108 followed by 30 LPS 10ng/mL


title: Macrophages-Slide_3-ROI_001


title: MK5108_LPS_2h

description: ChIPseq

value: 1h pre-treatment with MK5108 followed by 2h LPS 10ng/mL


title: Stroma-Slide_1-ROI_008


title: MK5108_LPS_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with MK5108 followed by 1h LPS 10ng/mL


title: lib78828


title: lib78830


title: MK5108_IL4_4h

description: ChIPseq

value: 1h pre-treatment with MK5108 followed by 4h IL4 10ng/mL


title: lib78829


title: lib78827


title: Epithelium-Slide_1-ROI_008

value: Epithelium


title: MK5108_IL4_30

description: ChIPseq

value: 1h pre-treatment with MK5108 followed by 30 IL4 10ng/mL


title: lib78826

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib78824


title: lib78823


title: Macrophages-Slide_3-ROI_002

value: eutopic endometrium

value: Macrophages


title: Stroma-Slide_1-ROI_007


title: MK5108_IL4_1h

description: ChIPseq

value: 1h pre-treatment with MK5108 followed by 1h IL4 10ng/mL


title: lib78833

value: CD154+CD69+ CD4 T cells

value: >1 Aab+ any age


title: lib78822


title: Epithelium-Slide_3-ROI_001


title: lib78821


title: lib78819


title: Epithelium-Slide_1-ROI_007

value: endometriotic lesion


title: MK2461_LPS_4h

description: ChIPseq

value: 1h pre-treatment with MK2461 followed by 4h LPS 10ng/mL


title: lib78817


title: Macrophages-Slide_1-ROI_007


title: lib78818


title: MK2461_UT_0h

description: ChIPseq

value: 1h pre-treatment with MK2461 followed by 4h UT

value: wild type


title: MK2461_LPS_30

description: ChIPseq

value: 1h pre-treatment with MK2461 followed by 30 LPS 10ng/mL


title: lib78814


title: lib78825


title: MK2461_LPS_2h

description: ChIPseq

value: 1h pre-treatment with MK2461 followed by 2h LPS 10ng/mL


title: lib78813


title: Macrophages-Slide_1-ROI_008


title: lib78812


title: MK2461_LPS_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with MK2461 followed by 1h LPS 10ng/mL


title: MK5108_IL4_2h

description: ChIPseq

value: 1h pre-treatment with MK5108 followed by 2h IL4 10ng/mL


title: Stroma-Slide_1-ROI_005

value: Stroma


title: lib78810


title: lib78811


title: lib78820


title: lib78809


title: MK2461_IL4_4h

description: ChIPseq

value: 1h pre-treatment with MK2461 followed by 4h IL4 10ng/mL


title: lib78808

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: Epithelium-Slide_1-ROI_006

value: eutopic endometrium

value: Epithelium


title: Epithelium-Slide_1-ROI_005


title: lib78807


title: Macrophages-Slide_1-ROI_005

value: Macrophages


title: Macrophages-Slide_1-ROI_006


title: lib78815

value: CD154+CD69+ CD4 T cells


title: Stroma-Slide_1-ROI_006


title: lib78805

value: >1 Aab+ any age


title: MK2461_IL4_2h

description: ChIPseq

value: 1h pre-treatment with MK2461 followed by 2h IL4 10ng/mL


title: lib78804


title: lib78816


title: MK2461_IL4_1h

description: ChIPseq

value: 1h pre-treatment with MK2461 followed by 1h IL4 10ng/mL


title: Stroma-Slide_1-ROI_004

value: endometriotic lesion


title: lib78803


title: lib78802


title: MK2206_UT_0h

description: ChIPseq

value: 1h pre-treatment with MK2206 followed by 4h UT

value: wild type


title: Epithelium-Slide_1-ROI_004


title: Macrophages-Slide_1-ROI_004


title: lib78801


title: lib78799


title: lib78800


title: MK2206_LPS_30

description: ChIPseq

value: 1h pre-treatment with MK2206 followed by 30 LPS 10ng/mL


title: lib78798


title: lib78797


title: Stroma-Slide_1-ROI_003


title: MK2206_LPS_2h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with MK2206 followed by 2h LPS 10ng/mL


title: lib78796


title: Epithelium-Slide_1-ROI_003


title: lib78806


title: lib78795


title: MK2206_IL4_4h

description: ChIPseq

value: 1h pre-treatment with MK2206 followed by 4h IL4 10ng/mL


title: lib78793


title: lib78792


title: Stroma-Slide_1-ROI_002

value: Stroma


title: lib78791


title: lib78794


title: Epithelium-Slide_1-ROI_002


title: MK2206_IL4_30

description: ChIPseq

value: 1h pre-treatment with MK2206 followed by 30 IL4 10ng/mL


title: lib78788

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: MK2206_IL4_2h

description: ChIPseq

value: 1h pre-treatment with MK2206 followed by 2h IL4 10ng/mL


title: lib78789


title: Macrophages-Slide_1-ROI_002

value: eutopic endometrium


title: MK2206_IL4_1h

description: ChIPseq

value: 1h pre-treatment with MK2206 followed by 1h IL4 10ng/mL


title: lib78790

value: CD154+CD69+ CD4 T cells


title: lib78787

value: >1 Aab+ any age


title: lib78786


title: lib78785


title: Stroma-Slide_1-ROI_001


title: Midostaurin_UT_0h

description: ChIPseq

value: 1h pre-treatment with Midostaurin followed by 4h UT


title: lib78784

value: Aab negative


title: Macrophages-Slide_1-ROI_003

value: endometriotic lesion

value: Macrophages


title: MK2206_LPS_1h

description: ChIPseq

value: 1h pre-treatment with MK2206 followed by 1h LPS 10ng/mL

value: wild type


title: lib78783


title: Macrophages-Slide_1-ROI_001


title: Midostaurin_LPS_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Midostaurin followed by 4h LPS 10ng/mL


title: lib78781


title: Midostaurin_LPS_30

description: ChIPseq

value: 1h pre-treatment with Midostaurin followed by 30 LPS 10ng/mL


title: lib78780


title: Midostaurin_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Midostaurin followed by 2h LPS 10ng/mL


title: lib78779


title: lib78778


title: lib56165

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the human GRCh38 release 91 reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count (v0.4.1). Quality control and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCh38 release 91
Supplementary files format and content: counts.txt: Gene count matrix in text file
Supplementary files format and content: tcrs.txt: tab-delimited text file of TCR sequences and accompanying metadata

source_name: ISLET TMR+ CD8 T cells

value: ISLET TMR+ CD8 T cells

value: islet peptide library


title: Midostaurin_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Midostaurin followed by 1h LPS 10ng/mL


title: lib78777

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: Midostaurin_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Midostaurin followed by 4h IL4 10ng/mL


title: lib56164


title: Epithelium-Slide_1-ROI_001

value: eutopic endometrium

value: Epithelium


title: Midostaurin_IL4_30

description: ChIPseq

value: 1h pre-treatment with Midostaurin followed by 30 IL4 10ng/mL


title: lib56161


title: lib56162


title: Midostaurin_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Midostaurin followed by 2h IL4 10ng/mL


title: lib56163


title: H3K27ac_replicate 2

city: Beer Sheva

first: Idan

last: Cohen

address: David Ben Gurion Blvd 1

department: Microbiology, Immunology and Genetics

country: Israel

institute: Ben-Gurion University

data_processing:
*library strategy: CUT&RUN
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. Cut &Run-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trim Galore v0.4.5, discarding reads left with < 25 bp.  Duplicates Cut &Run-seq reads  were removed using Samtools v1.6.
Cut &Run reads were aligned to the UCSC hg38 genome and  using BWA-Mapper version 0.7.17. Reads  from off-chromosome locations were removed with uscs-bedclip v377 .
To create Cut &Run coverage plots, bin size was set to 10 and the mapped reads were re-normalized (to reads per kilobase per million, RPKM). and reformatted to bigWig file format by BamCoverage, deepTools v1.5.9.1. bigWig files were generated using bedGraphToBigWig by deepTools v1.5.9.1. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Peaks were called using MACS v3.0.0 with the top broad-cutoff value <0.1. Peaks were called using SEACR v1.3 in 'stringent' mode with the significance broad-cutoff value set to 0.01.
Peaks found by both MACS and SEACR were determined and merged (-d = 100 bp) with Bedtools v2.30.0 . Peaks were annotated with Homer v4.11 annotatePeaks.pl script
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Normal Human Epidermal Keratinocytes (NHEK)

growth_protocol: Primary neonatal human epidermal keratinocytes were cultured in KGM-Gold media (Lonza).  To induce epidermal differentiation, growth media was supplemented with 1.4mM CaCl2 and cells were grown for six days.

extract_protocol:
Cells were then dissociated by warm 0.25% Trypsin for 10 min at 37°C. Cells were then centrifuged at 200 g for 4 min at 4°C, washed twice with 1x PBS. Nuclei were isolated according the manufacture's protocol and processed using the CUTANA CUT&RUN assay (Epichypher).
CUT&RUN libraries were prepared using the CUTANA CUT&RUN Library Prep Kit (Epicypher).  Post amplification libraries were size selected at 200-700bp in length using SPRIselect beads. The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed  libraries were sequenced on the Illumina NovaSeq X  platform, obtaining 150-nucleotide paired-end reads.

value: Neonatal keratinocytes

value: Epidermal


title: lib56160


title: lib56159


title: lib78782

value: CD154+CD69+ CD4 T cells

value: Aab negative


title: Losmapimod_UT_0h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Losmapimod followed by 4h UT

value: wild type


title: H3K27ac

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. Cut &Run-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trim Galore v0.4.5, discarding reads left with < 25 bp.  Duplicates Cut &Run-seq reads  were removed using Samtools v1.6.
Cut &Run reads were aligned to the UCSC hg38 genome and  using BWA-Mapper version 0.7.17. Reads  from off-chromosome locations were removed with uscs-bedclip v377 .
To create Cut &Run coverage plots, bin size was set to 10 and the mapped reads were re-normalized (to reads per kilobase per million, RPKM). and reformatted to bigWig file format by BamCoverage, deepTools v1.5.9.1. bigWig files were generated using bedGraphToBigWig by deepTools v1.5.9.1. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Peaks were called using MACS v3.0.0 with the top broad-cutoff value <0.1. Peaks were called using SEACR v1.3 in 'stringent' mode with the significance broad-cutoff value set to 0.01.
Peaks found by both MACS and SEACR were determined and merged (-d = 100 bp) with Bedtools v2.30.0 . Peaks were annotated with Homer v4.11 annotatePeaks.pl script
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

value: Normal Human Epidermal Keratinocytes (NHEK)


title: Losmapimod_UT_0h_b

description: ChIPseq


title: lib56155

value: ISLET TMR+ CD8 T cells


title: lib56157

value: islet peptide library


title: lib56156


title: lib56154


title: Midostaurin_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Midostaurin followed by 1h IL4 10ng/mL


title: H3K4me3


title: lib56158


title: Losmapimod_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Losmapimod followed by 4h LPS 10ng/mL


title: lib56153


title: lib56152


title: CASZ1_replicate 2


title: CASZ1_replicate 1


title: lib56151


title: lib56150


title: lib56149


title: Losmapimod_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Losmapimod followed by 1h LPS 10ng/mL


title: lib56146


title: lib56148


title: lib56147


title: lib56145


title: lib56144


title: Losmapimod_IL4_30

description: ChIPseq

value: 1h pre-treatment with Losmapimod followed by 30 IL4 10ng/mL


title: lib56143


title: Losmapimod_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Losmapimod followed by 1h IL4 10ng/mL


title: lib56142


title: lib56141


title: lib56139


title: lib56140


title: Lenvatinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Lenvatinib followed by 4h UT


title: Lenvatinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Lenvatinib followed by 4h LPS 10ng/mL


title: lib56138


title: lib56137


title: lib56136


title: lib56135


title: Losmapimod_LPS_30

description: ChIPseq

value: 1h pre-treatment with Losmapimod followed by 30 LPS 10ng/mL


title: lib56134


title: lib56133


title: Lenvatinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Lenvatinib followed by 2h LPS 10ng/mL


title: Losmapimod_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Losmapimod followed by 4h IL4 10ng/mL


title: lib56132


title: lib56131


title: Lenvatinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Lenvatinib followed by 1h LPS 10ng/mL


title: Lenvatinib_IL4_30

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Lenvatinib followed by 30 IL4 10ng/mL


title: nonSMA24

city: Albuquerque

first: Douglas

middle: Jay

last: Perkins

state: NM

address: MSC10 5550, 1 University of New Mexico

department: Center for Global Health

institute: University of New Mexico

data_processing:
Raw data were quality-controlled and filtered using fastp
Sequences were aligned to the human reference genome (GRCh38.p13) using the STAR sofware version 2.5
HTSeq v0.6.1 was used to generate read counts mapped to each gene.
Differential expression analysis of the two clinical conditions (non-SMA vs SMA) was performed using EdgeR (3.16.5) package, utilizing a negative binomial (NB) based statistical model
Assembly: GRCh38.p13
Supplementary files format and content: excel files includes Mapped reads stats for each sample
Supplementary files format and content: excel  files includes raw read counts for each sample
Supplementary files format and content: excel  files includes Quality control summary for each sample

source_name: blood

extract_protocol:
Total RNA was batch-isolated using E.Z.N.A® Total RNA Kit (Omega Bio-Tek Inc.), treated with RNase-free DNase I (New England Biolabs Inc.), and further processed using RNA Clean & Concentrator (ZYMO Research Corp.).
Only samples with RNA integrity number (RIN) >8 were used for library preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: blood

value: FEMALE

tag: genetic variants

value: HbAA

tag: time

value: Day 0


title: lib56129

value: ISLET TMR+ CD8 T cells

value: islet peptide library


title: Lenvatinib_IL4_2h

description: ChIPseq

source_name: mouse bone marrow derived macrophages

value: 1h pre-treatment with Lenvatinib followed by 2h IL4 10ng/mL

value: wild type


title: IgG

value: Normal Human Epidermal Keratinocytes (NHEK)

value: Neonatal keratinocytes

value: Epidermal

value: IgG


title: lib56128


title: lib56127


title: Lenvatinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Lenvatinib followed by 1h IL4 10ng/mL


title: lib56126


title: lib56125


title: Lenvatinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Lenvatinib followed by 30 LPS 10ng/mL


title: Lapatinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Lapatinib followed by 4h UT


title: lib56121


title: Lapatinib_LPS_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Lapatinib followed by 4h LPS 10ng/mL


title: lib56122


title: lib56124


title: lib56123


title: Lapatinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Lapatinib followed by 30 LPS 10ng/mL


title: lib56120


title: lib56130


title: Lapatinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Lapatinib followed by 2h LPS 10ng/mL


title: lib56119


title: lib56117


title: lib56116


title: Lapatinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Lapatinib followed by 1h LPS 10ng/mL


title: Lapatinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Lapatinib followed by 4h IL4 10ng/mL


title: lib56016

source_name: CD154+CD69+CD4 T cells

value: CD154+CD69+CD4 T cells


title: lib56015

value: islet peptide library


title: Lapatinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Lapatinib followed by 30 IL4 10ng/mL


title: Lapatinib_LPS_1h_b

description: ChIPseq

value: wild type


title: lib56017


title: lib56014


title: Lapatinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Lapatinib followed by 2h IL4 10ng/mL


title: lib56018


title: lib56011


title: lib56115

value: ISLET TMR+ CD8 T cells


title: lib56012


title: lib56007


title: lib56013


title: IMD0354_UT_0h

description: ChIPseq

value: 1h pre-treatment with IMD0354 followed by 4h UT


title: Lapatinib_IL4_30_b

description: ChIPseq


title: MK2461_IL4_30

description: ChIPseq

value: 1h pre-treatment with MK2461 followed by 30 IL4 10ng/mL


title: Lapatinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Lapatinib followed by 1h IL4 10ng/mL


title: lib56008


title: lib56006


title: lib56010


title: lib56005


title: IMD0354_LPS_4h

description: ChIPseq

value: 1h pre-treatment with IMD0354 followed by 4h LPS 10ng/mL


title: lib56004


title: lib56009


title: lib56003


title: lib56118


title: IMD0354_LPS_30

description: ChIPseq

value: 1h pre-treatment with IMD0354 followed by 30 LPS 10ng/mL


title: lib56002


title: lib55722


title: lib56001


title: lib55723


title: lib55999


title: lib56000


title: IMD0354_LPS_2h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with IMD0354 followed by 2h LPS 10ng/mL


title: lib55720


title: lib55718


title: lib55716


title: lib55721


title: lib55717


title: IMD0354_LPS_2h_b

description: ChIPseq


title: IMD0354_LPS_1h

description: ChIPseq

value: 1h pre-treatment with IMD0354 followed by 1h LPS 10ng/mL


title: lib55715


title: lib55714


title: lib55719


title: IMD0354_IL4_30

description: ChIPseq

value: 1h pre-treatment with IMD0354 followed by 30 IL4 10ng/mL


title: lib55711


title: IMD0354_IL4_2h

description: ChIPseq

value: 1h pre-treatment with IMD0354 followed by 2h IL4 10ng/mL


title: IMD0354_IL4_1h

description: ChIPseq

value: 1h pre-treatment with IMD0354 followed by 1h IL4 10ng/mL


title: IMD0354_IL4_4h

description: ChIPseq

value: 1h pre-treatment with IMD0354 followed by 4h IL4 10ng/mL


title: lib55709

value: islet peptide library


title: lib55712


title: lib55710


title: GSK461364_UT_0h

description: ChIPseq

value: 1h pre-treatment with GSK461364 followed by 4h UT


title: lib55708


title: GSK461364_LPS_4h

description: ChIPseq

value: 1h pre-treatment with GSK461364 followed by 4h LPS 10ng/mL

value: wild type


title: IMD0354_LPS_1h_b

description: ChIPseq


title: lib55713

value: ISLET TMR+ CD8 T cells


title: lib55705


title: lib55706


title: GSK461364_LPS_2h

description: ChIPseq

value: 1h pre-treatment with GSK461364 followed by 2h LPS 10ng/mL


title: GSK461364_LPS_30

description: ChIPseq

value: 1h pre-treatment with GSK461364 followed by 30 LPS 10ng/mL


title: lib55700


title: lib55707


title: lib55704


title: lib55702


title: lib55699


title: GSK461364_IL4_30

description: ChIPseq

value: 1h pre-treatment with GSK461364 followed by 30 IL4 10ng/mL


title: lib55703


title: lib55695


title: lib55698


title: GSK461364_LPS_1h

description: ChIPseq

value: 1h pre-treatment with GSK461364 followed by 1h LPS 10ng/mL


title: lib55694


title: lib55701


title: GSK461364_IL4_1h

description: ChIPseq

value: 1h pre-treatment with GSK461364 followed by 1h IL4 10ng/mL


title: lib55693


title: GSK461364_IL4_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with GSK461364 followed by 4h IL4 10ng/mL


title: GSK461364_IL4_2h

description: ChIPseq

value: 1h pre-treatment with GSK461364 followed by 2h IL4 10ng/mL


title: lib55697


title: lib55690


title: GSK2110183_UT_0h

description: ChIPseq

value: 1h pre-treatment with GSK2110183 followed by 4h UT


title: lib55691


title: lib55692


title: GSK2110183_LPS_4h

description: ChIPseq

value: 1h pre-treatment with GSK2110183 followed by 4h LPS 10ng/mL


title: lib55688


title: GSK2110183_LPS_30

description: ChIPseq

value: 1h pre-treatment with GSK2110183 followed by 30 LPS 10ng/mL


title: lib55687


title: lib55696


title: lib55684


title: GSK2110183_LPS_2h

description: ChIPseq

value: 1h pre-treatment with GSK2110183 followed by 2h LPS 10ng/mL


title: GSK2110183_LPS_2h_b

description: ChIPseq


title: lib55683

value: islet peptide library


title: lib55682


title: lib55679


title: GSK2110183_LPS_1h

description: ChIPseq

value: 1h pre-treatment with GSK2110183 followed by 1h LPS 10ng/mL


title: lib55678


title: lib55676


title: lib55673


title: lib55674


title: lib55675


title: lib55680


title: lib55677


title: lib55671


title: lib55672


title: lib55670


title: lib55689


title: lib55686


title: lib55685


title: GDC0994_UT_0h

description: ChIPseq

value: 1h pre-treatment with GDC0994 followed by 4h UT


title: GSK2110183_IL4_30

description: ChIPseq

value: 1h pre-treatment with GSK2110183 followed by 30 IL4 10ng/mL

value: wild type


title: GDC0994_UT_0h_b

description: ChIPseq


title: GSK2110183_IL4_1h

description: ChIPseq

value: 1h pre-treatment with GSK2110183 followed by 1h IL4 10ng/mL


title: GSK2110183_IL4_4h

description: ChIPseq

value: 1h pre-treatment with GSK2110183 followed by 4h IL4 10ng/mL


title: lib55669

value: ISLET TMR+ CD8 T cells


title: lib55681


title: lib55666


title: GDC0994_LPS_4h

description: ChIPseq

value: 1h pre-treatment with GDC0994 followed by 4h LPS 10ng/mL


title: GSK2110183_IL4_2h

description: ChIPseq

value: 1h pre-treatment with GSK2110183 followed by 2h IL4 10ng/mL


title: lib55668


title: GDC0994_LPS_30

description: ChIPseq

value: BMDM

value: 1h pre-treatment with GDC0994 followed by 30 LPS 10ng/mL


title: lib55667


title: GDC0994_LPS_2h

description: ChIPseq

value: 1h pre-treatment with GDC0994 followed by 2h LPS 10ng/mL


title: lib55664


title: lib55662


title: GDC0994_LPS_1h

description: ChIPseq

value: 1h pre-treatment with GDC0994 followed by 1h LPS 10ng/mL


title: lib55663


title: lib55660


title: GDC0994_IL4_4h

description: ChIPseq

value: 1h pre-treatment with GDC0994 followed by 4h IL4 10ng/mL


title: lib55656


title: lib55659


title: lib55658


title: lib55661


title: GDC0994_IL4_30

description: ChIPseq

value: 1h pre-treatment with GDC0994 followed by 30 IL4 10ng/mL


title: lib55655


title: GDC0994_IL4_2h

description: ChIPseq

value: 1h pre-treatment with GDC0994 followed by 2h IL4 10ng/mL


title: lib55654

value: islet peptide library


title: GDC0994_IL4_1h

description: ChIPseq

value: 1h pre-treatment with GDC0994 followed by 1h IL4 10ng/mL


title: lib55652


title: lib55665


title: lib55651


title: lib55653


title: lib55650


title: lib55648


title: lib55647


title: Filgotinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Filgotinib followed by 4h LPS 10ng/mL


title: Filgotinib_UT_0h_b

description: ChIPseq

value: 1h pre-treatment with Filgotinib followed by 4h UT


title: lib55644


title: lib55645


title: lib55646


title: lib55642


title: Filgotinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Filgotinib followed by 30 LPS 10ng/mL

value: wild type


title: lib55657


title: PBMC, HIV Exposed Infected (HEI), CP18M, BCR

city: Miami

first: Akshay

last: Iyer

state: FL

institute: University of Miami

data_processing:
Cell Ranger v6 count and aggr funtions to aggregate reads across sequencing lanes.
filtered_feature_bc_matrix.h5 consists of barcode matrix/counts after read alignment, barcode counting, UMI counting and filtering
Downstream processing, integration and analysis was performed in R with packages such as Seurat
Assembly: GRCh38 (hg38)
Supplementary files format and content: CellRanger output files (mRNA+ADT output): raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files (VDJ Output): TCR_filtered_contig_annotations.csv, BCR_filtered_contig_annotations.csv
Library strategy: BCR-seq

source_name: Blood

growth_protocol: Thaw cryopreserved PBMC and rest for 16-18 hr at 37C 5% C02

extract_protocol:
10x 5' V2.0 chemistry
cDNA amplification and library preparation for gene expression profiling and V(D)J sequencing were carried out according to manufacturer’s instructions without modification (10x Genomics PN: 1000263, 1000286, 1000250, 1000215, 1000252,1000253, 1000190, 1000541)

value: Blood

value: PBMC

value: HIV Exposed Infected (HEI)

tag: library type

value: BCR


title: lib55641

value: ISLET TMR+ CD8 T cells


title: PBMC, HIV Exposed Infected (HEI), CP18M, TCR

data_processing:
Cell Ranger v6 count and aggr funtions to aggregate reads across sequencing lanes.
filtered_feature_bc_matrix.h5 consists of barcode matrix/counts after read alignment, barcode counting, UMI counting and filtering
Downstream processing, integration and analysis was performed in R with packages such as Seurat
Assembly: GRCh38 (hg38)
Supplementary files format and content: CellRanger output files (mRNA+ADT output): raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files (VDJ Output): TCR_filtered_contig_annotations.csv, BCR_filtered_contig_annotations.csv
Library strategy: TCR-seq

value: TCR


title: lib55640


title: Filgotinib_IL4_4h

description: ChIPseq

data_processing:
Reads were quality filtered according to the illumina pipeline
Single end reads were mapped to the mouse mm10 genome (Illumina's iGenomes reference annotation downloaded from UCSC http://support.illumina.com/sequencing/sequencing_software/igenome.html) by exploiting the mapping steps of ShortStack (Johnson et al. 2016).Briefly, ShortStack exploits bowtie to identify all best-matched alignments for each read. It will compute a probability for each alignment to different loci in the genome. To do so the frequency of uniquely aligned reads mapping within the vicinity of multi-mapping reads is used to redistribute multi-mapping reads accordingly.
Mapped reads were filtered in order to remove randomly placed multi-mappers and unmapped reads using SAMtools standard procedure (version 1.9)(Li et al. 2009).
In order to identify high confidence genome wide site of enrichment per antibody we implemented three strategies accordingly to the type of signal distribution evaluated after visual inspection of bigwig tracks on IGV (Robinson et al. 2011):   For H2K27ac we used peaks identified in ATACseq samples (see below) expanding the ATAC peaks by 1.5 kb on both sides.
Read counts per samples at the identified loci were retrieved using the R/Bioconductor package GenomicRanges and GenomicAlignment (Lawrence et al. 2013). Sample normalization was achieved by selecting invariant peaks across samples (Gualdrini et al. 2016). Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.
Assembly: mm10
Supplementary files format and content: .bw are BigWig normalised files

value: BMDM

value: 1h pre-treatment with Filgotinib followed by 4h IL4 10ng/mL


title: Filgotinib_UT_0h

description: ChIPseq


title: PBMC, HIV Exposed Infected (HEI), CP18M, Feature Barcode/Antibody Derived Tag (FB/ADT)

description: see GEX sample for processed data; ADT antibodies - TotalSeq-C Human Universal Cocktail (Biolegend, Cat# 399905)

data_processing:
Cell Ranger v6 count and aggr funtions to aggregate reads across sequencing lanes.
filtered_feature_bc_matrix.h5 consists of barcode matrix/counts after read alignment, barcode counting, UMI counting and filtering
Downstream processing, integration and analysis was performed in R with packages such as Seurat
Assembly: GRCh38 (hg38)
Supplementary files format and content: CellRanger output files (mRNA+ADT output): raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files (VDJ Output): TCR_filtered_contig_annotations.csv, BCR_filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

value: ADT


title: lib55638


title: lib55649


title: lib55637


title: Filgotinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Filgotinib followed by 30 IL4 10ng/mL


title: lib55636


title: Filgotinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Filgotinib followed by 2h IL4 10ng/mL


title: PBMC, HIV Exposed Infected (HEI), CP6M, BCR


title: PBMC, HIV Exposed Infected (HEI), CP18M, Gene Expression (GEX)

data_processing:
Cell Ranger v6 count and aggr funtions to aggregate reads across sequencing lanes.
filtered_feature_bc_matrix.h5 consists of barcode matrix/counts after read alignment, barcode counting, UMI counting and filtering
Downstream processing, integration and analysis was performed in R with packages such as Seurat
Assembly: GRCh38 (hg38)
Supplementary files format and content: CellRanger output files (mRNA+ADT output): raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files (VDJ Output): TCR_filtered_contig_annotations.csv, BCR_filtered_contig_annotations.csv

value: mRNA


title: Filgotinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Filgotinib followed by 1h IL4 10ng/mL


title: lib55633

value: islet peptide library


title: lib55643


title: Filgotinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Filgotinib followed by 1h LPS 10ng/mL


title: PBMC, HIV Exposed Infected (HEI), CP6M, TCR


title: Filgotinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Filgotinib followed by 2h LPS 10ng/mL


title: lib55634


title: lib55631


title: PBMC, HIV Exposed Infected (HEI), CP6M, Feature Barcode/Antibody Derived Tag (FB/ADT)


title: Encorafenib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Encorafenib followed by 4h UT

value: wild type


title: lib55629


title: lib55639


title: lib55630


title: lib55628


title: PBMC, HIV Exposed Infected (HEI), CP6M, Gene Expression (GEX)

value: Blood

value: PBMC


title: Encorafenib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Encorafenib followed by 30 LPS 10ng/mL


title: lib55635

value: ISLET TMR+ CD8 T cells


title: Encorafenib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Encorafenib followed by 2h LPS 10ng/mL


title: lib55626

value: CD154+CD69+CD4 T cells


title: PBMC, HIV Exposed Infected (HEI), CP3M, BCR

value: HIV Exposed Infected (HEI)

value: BCR


title: Encorafenib_LPS_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Encorafenib followed by 1h LPS 10ng/mL


title: lib55625


title: PBMC, HIV Exposed Infected (HEI), CP3M, TCR

value: TCR


title: Encorafenib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Encorafenib followed by 4h IL4 10ng/mL


title: lib55632

value: islet peptide library


title: lib55624


title: Encorafenib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Encorafenib followed by 30 IL4 10ng/mL


title: lib55623


title: PBMC, HIV Exposed Infected (HEI), CP2M, BCR


title: lib55622


title: lib55619


title: lib55620


title: PBMC, HIV Exposed Infected (HEI), CP3M, Feature Barcode/Antibody Derived Tag (FB/ADT)

value: ADT


title: Encorafenib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Encorafenib followed by 2h IL4 10ng/mL


title: lib55621


title: lib55627


title: PBMC, HIV Exposed Infected (HEI), CP2M, TCR


title: lib55616


title: lib55617


title: DMSO_UT_0h_R2

description: ChIPseq

value: 1h pre-treatment with DMSO followed by 4h UT

value: wild type


title: lib55618


title: lib55615


title: lib55614


title: PBMC, HIV Exposed Infected (HEI), CP2M, Feature Barcode/Antibody Derived Tag (FB/ADT)

value: Blood

value: PBMC


title: PBMC, HIV Exposed Infected (HEI), CP3M, Gene Expression (GEX)

value: mRNA


title: DMSO_UT_0h_R1

description: ChIPseq


title: lib55612


title: PBMC, HIV Exposed Infected (HEI), CP2M, Gene Expression (GEX)


title: DMSO_LPS_4h_R2

description: ChIPseq

value: 1h pre-treatment with DMSO followed by 4h LPS 10ng/mL


title: lib55611

value: CD154+CD69+CD4 T cells


title: PBMC, HIV Exposed Uninfected (HEU), CE37M, BCR

value: HIV Exposed Uninfected (HEU)


title: lib55610


title: Encorafenib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Encorafenib followed by 1h IL4 10ng/mL


title: lib55609


title: DMSO_LPS_4h_R1

description: ChIPseq

value: BMDM


title: lib55608


title: DMSO_LPS_30_R2

description: ChIPseq

value: 1h pre-treatment with DMSO followed by 30 LPS 10ng/mL


title: lib55607


title: PBMC, HIV Exposed Uninfected (HEU), CE37M, Feature Barcode/Antibody Derived Tag (FB/ADT)


title: lib55606


title: lib55604


title: lib55605


title: lib55603


title: PBMC, HIV Exposed Uninfected (HEU), CE37M, Gene Expression (GEX)


title: DMSO_LPS_30_R1

description: ChIPseq


title: lib55602


title: DMSO_LPS_2h_R2

description: ChIPseq

value: 1h pre-treatment with DMSO followed by 2h LPS 10ng/mL


title: lib55601


title: PBMC, HIV Exposed Uninfected (HEU), CE25M, TCR

value: TCR


title: lib55613

value: islet peptide library


title: lib55600


title: DMSO_LPS_1h_R2

description: ChIPseq

value: 1h pre-treatment with DMSO followed by 1h LPS 10ng/mL


title: DMSO_LPS_2h_R1

description: ChIPseq


title: lib55599


title: PBMC, HIV Exposed Uninfected (HEU), CE25M, Feature Barcode/Antibody Derived Tag (FB/ADT)

value: ADT


title: lib55598


title: lib55597


title: PBMC, HIV Exposed Uninfected (HEU), CE37M, TCR


title: DMSO_LPS_1h_R1

description: ChIPseq


title: PBMC, HIV Exposed Uninfected (HEU), CE25M, Gene Expression (GEX)


title: PBMC, HIV Exposed Uninfected (HEU), CE21M, BCR

value: BCR


title: lib55596


title: lib55595


title: DMSO_IL4_4h_R2

description: ChIPseq

value: 1h pre-treatment with DMSO followed by 4h IL4 10ng/mL


title: lib55594


title: PBMC, HIV Exposed Uninfected (HEU), CE25M, BCR


title: DMSO_IL4_4h_R1

description: ChIPseq

value: wild type


title: lib55593


title: DMSO_IL4_30_R2

description: ChIPseq

value: 1h pre-treatment with DMSO followed by 30 IL4 10ng/mL


title: lib55590


title: PBMC, HIV Exposed Uninfected (HEU), CE21M, Feature Barcode/Antibody Derived Tag (FB/ADT)

value: Blood

value: PBMC


title: PBMC, HIV Exposed Uninfected (HEU), CE21M, Gene Expression (GEX)

value: mRNA


title: lib55589

value: CD154+CD69+CD4 T cells


title: lib55592


title: DMSO_IL4_30_R1

description: ChIPseq


title: lib55591


title: lib55587


title: DMSO_IL4_2h_R2

description: ChIPseq

value: 1h pre-treatment with DMSO followed by 2h IL4 10ng/mL


title: PBMC, HIV Exposed Uninfected (HEU), CE21M, TCR

value: HIV Exposed Uninfected (HEU)


title: DMSO_IL4_2h_R1

description: ChIPseq

value: BMDM


title: JJN3-NS-2

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

description:
BNS
counts.strict.txt

data_processing:
OneStopRNAseq server
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to hg38 using STAR
Read count extraction was performed using featureCounts
Assembly: hg38
Supplementary files format and content: counts.strict.txt

growth_protocol: JJN3 cells were cultured in 40% DMEM 40% IMDM, and 20% FBS in 37°C supplemented with 10% CO2

extract_protocol:
Trizol following manufacturer's protocol
Novogene

treatment_protocol: Cells were transduced with NS or WNK1 shRNA

value: multiple myeloma cell line

value: NS


title: lib55588


title: lib55585


title: JJN3-NS-1

description:
ANS
counts.strict.txt


title: lib55586


title: lib55584


title: DMSO_IL4_1h_R2

description: ChIPseq

value: 1h pre-treatment with DMSO followed by 1h IL4 10ng/mL


title: JJN3-shNWK1-2

description:
B46
counts.strict.txt


title: lib55583

value: islet peptide library


title: lib55581


title: DMSO_IL4_1h_R1

description: ChIPseq


title: lib55580


title: JJN3-shWNK1-1

description:
A46
counts.strict.txt


title: lib55579


title: Capmatinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Capmatinib followed by 4h UT


title: JJN3-WNK463-6h-2

description:
B6
counts.strict.txt

treatment_protocol: Cells were treated with DMSO or WNK463 (5μM) for 2/6 h

value: WT


title: lib55578


title: Capmatinib_UT_0h_b

description: ChIPseq


title: lib55577


title: lib55575


title: JJN3-WNK463-2h-2

description:
B2
counts.strict.txt


title: lib55574