title: WT_2

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

institute: TIB CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Genome_build: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary_files_format_and_content: tab-delimited text files including FPKM for each sample.

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Myceliophthora thermophila ATCC 42464

growth_protocol: M. thermophila strains were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 16h. Mycelia were collected and washed three times with 1×Vogel’s salt, and then transferred into the medium with 2% Avicel as the carbon source for an additional 4 h of cultivation.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT


title: WT_1

status: Public on Jan 28 2025

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: genotype


title: P380

city: Beijing

first: Wenjie

last: Zhang

state: Not applicable

address: No. 5, Summer Palace Road, Haidian District, Beijing

department: BIOPIC

institute: Peking University

description:
10X Genomics
NSCLC_immune_scRNA_counts.mtx.gz
barcodes.csv
genes.csv
NSCLC_immune_scRNA_metadata.csv

library_source: transcriptomic single cell

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 6.1.2) against the GRCh38 human reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 6.1.2) with the manufacturer-supplied human VDJ reference genome.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.
Supplementary files format and content: UMAP_info.tar includes files with UMAP coordinates.
Supplementary files format and content: T_with_TCR_annotation.csv includes TCR annotation of T cells, only including T cells with matched TCR sequence data and RNA sequence data.

organism: Homo sapiens

source_name: lung

extract_protocol:
Fresh tumor tissues were cut into pieces of approximately 1mm3 in the RPMI-1640 medium (Gibco, 11875093) with 10% fetal bovine serum (FBS; Gibco, 10099141), and enzymatically digested with Tumor Dissociation Kit (Miltenyi, 130-095-929) for 60 minutes on a rotor at 37 °C. Dissociated cells were subsequently passed through a 100μm MACS SmartStrainers (Miltenyi, 130-110-917) and centrifuged at 300g for 8 minutes. After removing supernatant, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ, 90309-100) and incubated on ice for 5 minutes to lyse red blood cells. After washing with PBS (Gibco, 10010023), cell pellets were re-suspended in sorting buffer (PBS supplemented with 2% FBS). Single-cell suspensions were then stained with 7-AAD Viability Staining Solution (Invitrogen, 00-6993-50) and an antibody against CD235a (BioLegend, 349114) for FACS sorting on a BD Aria III instrument. Non-erythrocytic living cells were enriched by gating 7AAD−CD235a− cells. The concentration of single-cell suspensions was then adjusted to 700~1,200 cells μl–1 and single-cell suspensions with viable cell rate greater than 80% were used for single cell sequencing.
In total, ~18,000 cells for each sample were used for 10X Chromium Single cell 5′ and human TCR library construction (10X Genomics), according to the manufacturer’s instructions. All subsequent steps were performed following the standard manufacturer protocols. Purified libraries were subsequently sequenced using an Illumina NovaSeq 6000 sequencer with 150-base pair (bp) paired-end reads.

tag: tissue

value: lung

tag: disease state

value: non-small cell lung cancer


title: P423


title: P417


title: P372


title: 3D_nonCarrier_4 [DD16-7851]

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

country: USA

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Reads in FASTQ files were aligned against hg19 genome using STAR (v2,6,1a)
Raw gene counts were summarized using featureCounts (subread v1.5.2).
Assembly: hg19
Supplementary files format and content: Tab-delimited text, raw gene count

source_name: Cardiac Organoids

growth_protocol: hiPSC were generated from the PBMC isolated from the blood samples of non-carrier and D389V human subjects of South asian ethnicity. The hiPSCs from both thos genotype were then differentiated into 2D cardiomyocytes and 3D cardiac organoids. They were cultured for 30 days  and after the total RNA was isolated  for further RNAseq analysis.

extract_protocol:
Total RNA was isolated from 3D Cardiac organoids and 2D Cardiomyocytes using an RNA isolation kit (Qiagen, cat# 763134), according to the manufacturer’s instructions. Total RNA concentration and quality (A260/280 ratio ≥2.0) were evaluated using a Nanodrop spectrophotometer (ThermoFisher Scientific). The quality of total RNA was further measured using Bioanalyzer (Agilent, Santa Clara, CA)
The polyA RNA was isolated for library preparation, using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA)  with inputting good quality total RNA. The polyA RNA will be enriched using SMARTer Apollo automated NGS library prep system (Takara Bio USA, Mountain View, CA). Next, NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) will be used for library preparation under PCR cycle number of 8.

value: Cardiac Organoids

tag: cell type

value: Non-carrier

tag: treatment


title: 3D_nonCarrier_3 [DD15-7851]


title: P371


title: P368


title: P367


title: 3D_nonCarrier_1 [DD13-7851]


title: P365


title: P355


title: P349


title: 3D_mutant_4 [DD8-7851]

value: Mutant


title: 3D_mutant_2 [DD6-7851]


title: P347


title: 3D_mutant_1 [DD5-7851]


title: P346


title: 2D_nonCarrier_4 [DD12-7851]

source_name: Cardiomyocytes

value: Cardiomyocytes


title: 2D_nonCarrier_3 [DD11-7851]


title: P340


title: Mycth_90344

value: Mycth_90344 deletion mutant


title: 2D_nonCarrier_2 [DD10-7851]


title: P337


title: P329


title: 2D_mutant_3 [DD3-7851]


title: P328


title: 3D_nonCarrier_2 [DD14-7851]


title: P325


title: 2D_mutant_2 [DD2-7851]


title: P323


title: single_cell BCR seq data of patient EOMG12

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

data_processing:
Processing of sequencing data was performed with the cellranger pipeline v.6.1.1 (10X Genomics) according to the manufacturer’s instructions. Briefly, raw bcl files were de-multiplexed using the cellranger mkfastq pipeline. Subsequent read alignments and transcript counting were done individually for each sample using the cellranger count and cellranger vdj pipelines with standard parameters.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger output format
Library strategy: scBCR-seq

source_name: thymic CD45+ cells

extract_protocol:
Enrichment of CD45-positive cells was performed using CD45 (TIL) microbeads (Miltenyi Biotec., 130-118-780) according to the manufacturer’s protocol. Cell number and viability were checked before and after the enrichment to ensure that no significant cell death has been caused by the process.
CD45+ MACS-enriched single-cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1 chemistry (10x Genomics). The derived barcoded complementary DNA (cDNA) was partly used in Chromium Single Cell V(D)J Enrichment Kits (10x Genomics) for further scBCR-seq and scTCR-seq. Sample processing and library preparation were performed according to the manufacturer’s instructions using SPRIselect beads (Beckman Coulter).

tag: diagnosis

value: Early-Onset Myasthenia Gravis (EOMG)

tag: individual

value: patient EOMG12

tag: Sex

value: female

value: thymus

value: CD45+ cells


title: P322


title: 3D_mutant_3 [DD7B_7851]


title: single_cell BCR seq data of patient EOMG11

value: patient EOMG11


title: P312


title: single_cell BCR seq data of patient EOMG10

value: patient EOMG10


title: single_cell BCR seq data of patient EOMG09

value: patient EOMG09

value: male


title: P309


title: P339


title: single_cell BCR seq data of patient EOMG07

value: patient EOMG07


title: P303

value: lung


title: P304

value: non-small cell lung cancer


title: single_cell BCR seq data of patient EOMG08

value: patient EOMG08


title: single_cell BCR seq data of patient EOMG06

value: patient EOMG06


title: P334


title: 2D_mutant_4 [DD4-7851]

value: Mutant


title: P297


title: single_cell BCR seq data of patient EOMG05

value: patient EOMG05


title: 2D_nonCarrier_1 [DD9-7851]

value: Cardiomyocytes

value: Non-carrier


title: P296


title: 2D_mutant_1 [DD1-7851]


title: P293


title: single_cell BCR seq data of patient EOMG04

value: Early-Onset Myasthenia Gravis (EOMG)

value: patient EOMG04


title: single_cell BCR seq data of patient EOMG03

value: patient EOMG03

value: female

value: thymus


title: single_cell BCR seq data of patient EOMG01

value: patient EOMG01

value: CD45+ cells


title: single_cell BCR seq data of patient EOMG02

value: patient EOMG02


title: P321


title: P292


title: P291


title: P290


title: single_cell RNA seq data of patient EOMG11

data_processing:
Processing of sequencing data was performed with the cellranger pipeline v.6.1.1 (10X Genomics) according to the manufacturer’s instructions. Briefly, raw bcl files were de-multiplexed using the cellranger mkfastq pipeline. Subsequent read alignments and transcript counting were done individually for each sample using the cellranger count and cellranger vdj pipelines with standard parameters.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger output format

value: patient EOMG11


title: single_cell RNA seq data of patient EOMG12

value: patient EOMG12


title: P288

value: lung

value: non-small cell lung cancer


title: single_cell RNA seq data of patient EOMG10

value: patient EOMG10


title: single_cell RNA seq data of patient EOMG09

value: patient EOMG09

value: male


title: P287


title: P285


title: SC-islet, magnetic sorting for CD49a, positive sample

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 Euclid

institute: Washington University in St. Louis

data_processing:
Data was generated and processed by McDonnell Genome Institute (MGI) at Washington University
Sequencing files were processed with cell ranger 7.1.0
Assembly: GRCh38-2020-A
Supplementary files format and content: Processed files are in barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz

source_name: Stem cell-derived islet

growth_protocol: Stem cells were cultured, grown, and differentiated into SC-islets as described (Hogrebe et al., Nature Protocols 2021)

extract_protocol:
Cells were single cell dispersed with TrypLE, counted, and resuspended in DMEM at 1000 cells/uL
Library construction for single cell was constructed using 10X Chromium Protocol.

treatment_protocol: Cells were sorted using magnetic sorting with an anti-CD49a antibody

value: Stem cell-derived islet

tag: cell line

value: Islets of Langerhans

tag: sorting for_cd49a

value: positive sample


title: single_cell RNA seq data of patient EOMG07

value: Early-Onset Myasthenia Gravis (EOMG)

value: patient EOMG07


title: P286


title: single_cell RNA seq data of patient EOMG08

value: patient EOMG08

value: female


title: single_cell RNA seq data of patient EOMG05

value: patient EOMG05

value: thymus


title: single_cell RNA seq data of patient EOMG06

value: patient EOMG06

value: CD45+ cells


title: P281


title: P282


title: P279


title: P278


title: single_cell RNA seq data of patient EOMG02

value: patient EOMG02


title: P280

value: lung


title: single_cell RNA seq data of patient EOMG04

value: patient EOMG04


title: P277

value: non-small cell lung cancer


title: P298


title: single_cell RNA seq data of patient EOMG03

value: patient EOMG03


title: P289


title: P276


title: P273


title: F-H07_S187

city: West Lafayeete

first: Ahmed

middle: AbdelKhalek

last: Hassan

state: Indiana

address: 725 Harrison street, West Lafayette

institute: Purdue University

description:
Library name: DSP-1001660003081-F-H07_S187
Fresh frozen spatial transcriptomics sequencing

data_processing:
Following normalization, we conducted all statistical analyses and created visualizations based on the normalized Log2 counts. To determine expression correlations, we calculated the Pearson correlation coefficient (R) for paired groups, where R >0 indicated a positive correlation and R <0 as a negative correlation. We used linear mixed modeling to assess expression differences between two groups and performed one-way analysis of variance (ANOVA) for comparisons across multiple groups. For the generation of heatmaps, the normalized Log2 counts were zero-centered, and the Euclidean distance method was used to quantify distances. Average hierarchical clustering was then employed to identify expression clusters.
Assembly: Percent aligned reads segments with <80% alignment were flagged for evaluation, assessing potential contamination sources. Sequencing saturation of <50% was flagged. Negative probe count geomean (RNA-NGS) segments of negative probes <10 were flagged, likely to be influenced by slide preparation and wash steps. No template control (NTC) counts of >1000 were analyzed if the DCC file for NTC has low, even count distribution, segments do not have similar deduplicated counts as their NTC, and segments have adequate downstream gene detection. Segments with a cell number or surface area below the threshold were flagged.
Supplementary files format and content: Pathway and differential expression analyses and differential expression analysis were conducted using the GeoMx Digital Analysis Suite (DAS). The online databases Reactome (https://reactome.org/) and KEGG (https://www.genome.jp/kegg/pathway.html) databases were utilized to analyze and illustrate pathways and pathway maps. Pathways were sorted based on adjusted p-value, coverage, and normalized enrichment score (NES). Pathways with an adjusted p-value of <0.05, coverage equal to or greater than 70%, and a significant NES were prioritized. NES accounts for differences in gene set sizes and variations in enrichment scores across gene sets, providing a normalized measure of pathway enrichment. NES was considered significant if the adjusted p-value was less than 0.05.
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Intestine

extract_protocol:
Sections of paraffin embedded FFPE tissues at 5 μm thickness were placed in a positively charged slide (PathSupply, Wilmington, DE, USA). Sections were mounted on microscope slides and dried. The slides were deparaffinized in antigen retrieval solution (Thermo Fisher Scientific) at 100 °C for 20 minutes and treated with 1 µg/mL proteinase K at 37 °C for 15 minutes (Thermo). Mouse transcriptomics was visualized using the GeoMx mouse whole transcriptome atlas (WTA, NanoString, Bruker Spatial Biology, Inc,). An overnight in situ hybridization was performed with a mouse WTA probe and the next day the slides were washed twice at 37 °C for 25 minutes with 50% formamide/2X saline-sodium citrate (SSC) buffer to remove unbound probes. The slides were then incubated with morphological markers. Anti-pancytokeratin (Pan-CK) antibody at 1:200 (Thermo) tagged to Alexa Fluor 532, anti-CD45 antibody at 1:200 (CST) tagged to Alexa Fluor 594, and anti-CD3 antibody at 1:150 (OriGene) tagged to AlexaFluor 647 antibodies were used for immunostaining of slides. Nuclei were stained with Syto13 fluorescent dye (Fluorescence 532, Thermo). Stained slides were loaded onto the GeoMx Digital Spatial Profiler (DSP; NanoString) and scanned. After visual inspection using the GeoMx DSP, geometrical regions of interest (ROI) were selected for oligonucleotide collection. Photocleaved oligonucleotides from each spatially resolved ROI were sequenced with the Illumina NextSeq2000 sequencer (Illumina) and downstream analyses were performed using GeoMx Server (NanoString).
After quantifying the probes, the RNA analysis data (DCC files) were transferred to the Nanostring GeoMx platform for detailed QC, normalization, and subsequent analysis. This step facilitated a thorough quality control (QC) assessment using set criteria, the necessary normalization, and analytical procedures. Precise measurement and high-quality data of the RNA samples under study were ensured. As a quality control criterion, the raw read threshold and total number of barcodes were counted by the Illumina sequencer. Only regions with >1000 reads were used for the analysis. Percent aligned reads segments with <80% alignment were flagged for evaluation, assessing potential contamination sources. Sequencing saturation of <50% was flagged. Negative probe count geomean (RNA-NGS) segments of negative probes <10 were flagged, likely to be influenced by slide preparation and wash steps. No template control (NTC) counts of >1000 were analyzed if the DCC file for NTC has low, even count distribution, segments do not have similar deduplicated counts as their NTC, and segments have adequate downstream gene detection. Segments with a cell number or surface area below the threshold were flagged. QC values for % trimmed and % stitched were >90%. Biological QC aimed to remove low-performing probes using one specific probe per gene, focusing on negative probes. A probe was excluded if it was a high or low outlier in >20% of segments. The limit of quantification (LOQ) was defined as two standard deviations above the geometric mean of the negative probes. Segments with low signals were removed retaining segments where 5% of targets were above the expression threshold, set at LOQ below 2. Low-detected genes were removed retaining targets detected in at least 5% of segments as defined by an expression threshold. Technical effects, like segment size and tissue quality, were normalized using third quartile (Q3) normalization. The 75th percentile (Q3) of gene counts was calculated within each segment, and all gene counts were divided by this Q3 value. This step was repeated for each segment, and then all gene counts from all segments were multiplied by the geometric mean of all Q3 counts. Screening genes of interest was performed to eliminate anomalies before consolidating the data into one count per sample and target.

treatment_protocol: Six-week-old mice were adapted to the new environment for one week before oral treatment with a five-antibiotic cocktail for three days. Antibiotic treatment was then ceased for two days to allow for drug clearance before injecting the mice intraperitoneally with clindamycin. One day later, mice were orally infected with C. difficile spores. Uninfected mice were used as a control.

value: Intestine


title: P271


title: P270


title: F-H06_S186

description:
Library name: DSP-1001660003081-F-H06_S186
Fresh frozen spatial transcriptomics sequencing


title: F-H08_S188

description:
Library name: DSP-1001660003081-F-H08_S188
Fresh frozen spatial transcriptomics sequencing


title: P268


title: F-H05_S185

description:
Library name: DSP-1001660003081-F-H05_S185
Fresh frozen spatial transcriptomics sequencing


title: F-H04_S184

description:
Library name: DSP-1001660003081-F-H04_S184
Fresh frozen spatial transcriptomics sequencing


title: P266


title: F-H03_S183

description:
Library name: DSP-1001660003081-F-H03_S183
Fresh frozen spatial transcriptomics sequencing


title: P265


title: P264


title: F-H02_S182

description:
Library name: DSP-1001660003081-F-H02_S182
Fresh frozen spatial transcriptomics sequencing


title: F-H01_S181

description:
Library name: DSP-1001660003081-F-H01_S181
Fresh frozen spatial transcriptomics sequencing


title: P261


title: F-H09_S189

description:
Library name: DSP-1001660003081-F-H09_S189
Fresh frozen spatial transcriptomics sequencing


title: F-G11_S179

description:
Library name: DSP-1001660003081-F-G11_S179
Fresh frozen spatial transcriptomics sequencing


title: single_cell RNA seq data of patient EOMG01

value: patient EOMG01


title: F-G12_S180

description:
Library name: DSP-1001660003081-F-G12_S180
Fresh frozen spatial transcriptomics sequencing


title: P257


title: P259


title: F-G09_S177

description:
Library name: DSP-1001660003081-F-G09_S177
Fresh frozen spatial transcriptomics sequencing


title: P258


title: F-G10_S178

description:
Library name: DSP-1001660003081-F-G10_S178
Fresh frozen spatial transcriptomics sequencing


title: F-G08_S176

description:
Library name: DSP-1001660003081-F-G08_S176
Fresh frozen spatial transcriptomics sequencing


title: P249


title: P248


title: F-G07_S175

description:
Library name: DSP-1001660003081-F-G07_S175
Fresh frozen spatial transcriptomics sequencing


title: F-G06_S174

description:
Library name: DSP-1001660003081-F-G06_S174
Fresh frozen spatial transcriptomics sequencing


title: P247

description:
10X Genomics
NSCLC_immune_scRNA_counts.mtx.gz
barcodes.csv
genes.csv
NSCLC_immune_scRNA_metadata.csv


title: F-G05_S173

description:
Library name: DSP-1001660003081-F-G05_S173
Fresh frozen spatial transcriptomics sequencing


title: F-G04_S172

description:
Library name: DSP-1001660003081-F-G04_S172
Fresh frozen spatial transcriptomics sequencing


title: F-G03_S171

description:
Library name: DSP-1001660003081-F-G03_S171
Fresh frozen spatial transcriptomics sequencing


title: P267


title: P235


title: F-G02_S170

description:
Library name: DSP-1001660003081-F-G02_S170
Fresh frozen spatial transcriptomics sequencing


title: P226


title: F-G01_S169

description:
Library name: DSP-1001660003081-F-G01_S169
Fresh frozen spatial transcriptomics sequencing


title: P233


title: F-F12_S168

description:
Library name: DSP-1001660003081-F-F12_S168
Fresh frozen spatial transcriptomics sequencing


title: P227


title: P224


title: F-F11_S167

description:
Library name: DSP-1001660003081-F-F11_S167
Fresh frozen spatial transcriptomics sequencing


title: P223


title: P213


title: P218


title: F-F10_S166

description:
Library name: DSP-1001660003081-F-F10_S166
Fresh frozen spatial transcriptomics sequencing


title: F-F09_S165

description:
Library name: DSP-1001660003081-F-F09_S165
Fresh frozen spatial transcriptomics sequencing


title: F-F08_S164

description:
Library name: DSP-1001660003081-F-F08_S164
Fresh frozen spatial transcriptomics sequencing


title: F-F07_S163

description:
Library name: DSP-1001660003081-F-F07_S163
Fresh frozen spatial transcriptomics sequencing


title: F-F06_S162

description:
Library name: DSP-1001660003081-F-F06_S162
Fresh frozen spatial transcriptomics sequencing


title: P243


title: F-F05_S161

description:
Library name: DSP-1001660003081-F-F05_S161
Fresh frozen spatial transcriptomics sequencing


title: P209


title: P234


title: P207


title: F-F04_S160

description:
Library name: DSP-1001660003081-F-F04_S160
Fresh frozen spatial transcriptomics sequencing


title: P206


title: F-F03_S159

description:
Library name: DSP-1001660003081-F-F03_S159
Fresh frozen spatial transcriptomics sequencing


title: F-F02_S158

description:
Library name: DSP-1001660003081-F-F02_S158
Fresh frozen spatial transcriptomics sequencing


title: P205

description:
10X Genomics
NSCLC_immune_scRNA_counts.mtx.gz
barcodes.csv
genes.csv
NSCLC_immune_scRNA_metadata.csv


title: F-E12_S156

description:
Library name: DSP-1001660003081-F-E12_S156
Fresh frozen spatial transcriptomics sequencing


title: P204


title: P221


title: F-E11_S155

description:
Library name: DSP-1001660003081-F-E11_S155
Fresh frozen spatial transcriptomics sequencing


title: F-F01_S157

description:
Library name: DSP-1001660003081-F-F01_S157
Fresh frozen spatial transcriptomics sequencing


title: P201


title: P192


title: F-E10_S154

description:
Library name: DSP-1001660003081-F-E10_S154
Fresh frozen spatial transcriptomics sequencing


title: F-E09_S153

description:
Library name: DSP-1001660003081-F-E09_S153
Fresh frozen spatial transcriptomics sequencing


title: F-E08_S152

description:
Library name: DSP-1001660003081-F-E08_S152
Fresh frozen spatial transcriptomics sequencing


title: P190


title: F-E07_S151

description:
Library name: DSP-1001660003081-F-E07_S151
Fresh frozen spatial transcriptomics sequencing


title: F-E06_S150

description:
Library name: DSP-1001660003081-F-E06_S150
Fresh frozen spatial transcriptomics sequencing


title: P189


title: P185


title: P184


title: P182


title: F-E05_S149

description:
Library name: DSP-1001660003081-F-E05_S149
Fresh frozen spatial transcriptomics sequencing


title: F-E02_S146

description:
Library name: DSP-1001660003081-F-E02_S146
Fresh frozen spatial transcriptomics sequencing


title: P181


title: F-E04_S148

description:
Library name: DSP-1001660003081-F-E04_S148
Fresh frozen spatial transcriptomics sequencing


title: P180


title: F-D12_S144

description:
Library name: DSP-1001660003081-F-D12_S144
Fresh frozen spatial transcriptomics sequencing


title: F-E01_S145

description:
Library name: DSP-1001660003081-F-E01_S145
Fresh frozen spatial transcriptomics sequencing


title: P200


title: F-E03_S147

description:
Library name: DSP-1001660003081-F-E03_S147
Fresh frozen spatial transcriptomics sequencing


title: P174


title: P199


title: P179


title: P168


title: P166


title: P164


title: P161


title: F-D10_S142

description:
Library name: DSP-1001660003081-F-D10_S142
Fresh frozen spatial transcriptomics sequencing


title: P160


title: F-D09_S141

description:
Library name: DSP-1001660003081-F-D09_S141
Fresh frozen spatial transcriptomics sequencing


title: P159

description:
10X Genomics
NSCLC_immune_scRNA_counts.mtx.gz
barcodes.csv
genes.csv
NSCLC_immune_scRNA_metadata.csv


title: F-D07_S139

description:
Library name: DSP-1001660003081-F-D07_S139
Fresh frozen spatial transcriptomics sequencing


title: F-D06_S138

description:
Library name: DSP-1001660003081-F-D06_S138
Fresh frozen spatial transcriptomics sequencing


title: F-D11_S143

description:
Library name: DSP-1001660003081-F-D11_S143
Fresh frozen spatial transcriptomics sequencing


title: F-D05_S137

description:
Library name: DSP-1001660003081-F-D05_S137
Fresh frozen spatial transcriptomics sequencing


title: P158


title: P172


title: F-D04_S136

description:
Library name: DSP-1001660003081-F-D04_S136
Fresh frozen spatial transcriptomics sequencing


title: P150


title: F-D03_S135

description:
Library name: DSP-1001660003081-F-D03_S135
Fresh frozen spatial transcriptomics sequencing


title: F-D02_S134

description:
Library name: DSP-1001660003081-F-D02_S134
Fresh frozen spatial transcriptomics sequencing


title: P156


title: P146


title: F-D01_S133

description:
Library name: DSP-1001660003081-F-D01_S133
Fresh frozen spatial transcriptomics sequencing


title: P142


title: P131


title: P137


title: F-C10_S130

description:
Library name: DSP-1001660003081-F-C10_S130
Fresh frozen spatial transcriptomics sequencing


title: P130


title: F-C11_S131

description:
Library name: DSP-1001660003081-F-C11_S131
Fresh frozen spatial transcriptomics sequencing


title: F-D08_S140

description:
Library name: DSP-1001660003081-F-D08_S140
Fresh frozen spatial transcriptomics sequencing


title: F-C09_S129

description:
Library name: DSP-1001660003081-F-C09_S129
Fresh frozen spatial transcriptomics sequencing


title: F-C08_S128

description:
Library name: DSP-1001660003081-F-C08_S128
Fresh frozen spatial transcriptomics sequencing


title: P125


title: P122


title: F-C07_S127

description:
Library name: DSP-1001660003081-F-C07_S127
Fresh frozen spatial transcriptomics sequencing


title: F-C06_S126

description:
Library name: DSP-1001660003081-F-C06_S126
Fresh frozen spatial transcriptomics sequencing


title: P124


title: P120


title: F-C05_S125

description:
Library name: DSP-1001660003081-F-C05_S125
Fresh frozen spatial transcriptomics sequencing


title: F-C04_S124

description:
Library name: DSP-1001660003081-F-C04_S124
Fresh frozen spatial transcriptomics sequencing


title: P119

description:
10X Genomics
NSCLC_immune_scRNA_counts.mtx.gz
barcodes.csv
genes.csv
NSCLC_immune_scRNA_metadata.csv


title: F-C02_S122

description:
Library name: DSP-1001660003081-F-C02_S122
Fresh frozen spatial transcriptomics sequencing


title: P121


title: P118


title: P115


title: F-C03_S123

description:
Library name: DSP-1001660003081-F-C03_S123
Fresh frozen spatial transcriptomics sequencing


title: F-B12_S120

description:
Library name: DSP-1001660003081-F-B12_S120
Fresh frozen spatial transcriptomics sequencing


title: P114


title: F-C01_S121

description:
Library name: DSP-1001660003081-F-C01_S121
Fresh frozen spatial transcriptomics sequencing


title: P113


title: F-B11_S119

description:
Library name: DSP-1001660003081-F-B11_S119
Fresh frozen spatial transcriptomics sequencing


title: F-B10_S118

description:
Library name: DSP-1001660003081-F-B10_S118
Fresh frozen spatial transcriptomics sequencing


title: P127


title: P111


title: F-C12_S132

description:
Library name: DSP-1001660003081-F-C12_S132
Fresh frozen spatial transcriptomics sequencing


title: P107


title: P106


title: F-B08_S116

description:
Library name: DSP-1001660003081-F-B08_S116
Fresh frozen spatial transcriptomics sequencing


title: P105


title: F-B07_S115

description:
Library name: DSP-1001660003081-F-B07_S115
Fresh frozen spatial transcriptomics sequencing


title: P102


title: F-B05_S113

description:
Library name: DSP-1001660003081-F-B05_S113
Fresh frozen spatial transcriptomics sequencing


title: F-B06_S114

description:
Library name: DSP-1001660003081-F-B06_S114
Fresh frozen spatial transcriptomics sequencing


title: F-B04_S112

description:
Library name: DSP-1001660003081-F-B04_S112
Fresh frozen spatial transcriptomics sequencing


title: P97


title: P96


title: F-B03_S111

description:
Library name: DSP-1001660003081-F-B03_S111
Fresh frozen spatial transcriptomics sequencing


title: P94


title: F-B02_S110

description:
Library name: DSP-1001660003081-F-B02_S110
Fresh frozen spatial transcriptomics sequencing


title: P93


title: P90


title: F-A12_S108

description:
Library name: DSP-1001660003081-F-A12_S108
Fresh frozen spatial transcriptomics sequencing


title: P84


title: P92


title: F-A11_S107

description:
Library name: DSP-1001660003081-F-A11_S107
Fresh frozen spatial transcriptomics sequencing


title: F-A09_S105

description:
Library name: DSP-1001660003081-F-A09_S105
Fresh frozen spatial transcriptomics sequencing


title: P74

description:
10X Genomics
NSCLC_immune_scRNA_counts.mtx.gz
barcodes.csv
genes.csv
NSCLC_immune_scRNA_metadata.csv


title: P73


title: F-A07_S103

description:
Library name: DSP-1001660003081-F-A07_S103
Fresh frozen spatial transcriptomics sequencing


title: F-B09_S117

description:
Library name: DSP-1001660003081-F-B09_S117
Fresh frozen spatial transcriptomics sequencing


title: P70


title: P103


title: P69


title: F-A04_S100

description:
Library name: DSP-1001660003081-F-A04_S100
Fresh frozen spatial transcriptomics sequencing


title: F-A05_S101

description:
Library name: DSP-1001660003081-F-A05_S101
Fresh frozen spatial transcriptomics sequencing


title: P67


title: F-A08_S104

description:
Library name: DSP-1001660003081-F-A08_S104
Fresh frozen spatial transcriptomics sequencing


title: P71


title: E-H12_S96

description:
Library name: DSP-1001660003082-E-H12_S96
Fresh frozen spatial transcriptomics sequencing


title: P64


title: E-H11_S95

description:
Library name: DSP-1001660003082-E-H11_S95
Fresh frozen spatial transcriptomics sequencing


title: P66


title: BC776_H3K27me3

city: Manchester

first: Kiran

last: Batta

address: Paterson Building

department: Division of cancer Sciences

country: United Kingdom

institute: The University of Manchester

description: Library name: KB9_17_776_H3K27me3

library_source: genomic

data_processing:
ChIP-seq peaks were called with MACS213 (v2.1.2). For H3K27me3, broad peaks were called; for H3K27ac, H3K4me1 and H3K4me3, narrow peaks and summits were called. For ATAC-seq analysis, the flag --no-lambda was set. Intersection of peak sets and removal of blacklist regions (ENCODE annotation file set ENCFF419RSJ) was done using bedtools intersect (v2.27.1-7)14. The DAC Blacklisted Regions track was downloaded from the ENCODE project website at https://www.encodeproject.org/files/ENCFF419RSJ/. Peaks were visualised using IGV (v2.4.11). To prepare bigwig files for visualisation, scale factors were calculated as 1/(library size * fraction of reads in peaks). Bigwig files were then created using deepTools (v3.5.1) bamCoverage.  Quality control was performed with deepTools15, using computeMatrix (in reference point mode), plotHeatmap and plotFingerprint. For differential binding/accessibility analysis, DiffBind16 (v2.14; R v3.6.2) was used. DiffBind was also used to calculate fractions of reads in peaks. To annotate differentially bound regions as identified by DiffBind to genes, Homer (v 4.10) annotatePeaks.pl was used, again with the hg38 assembly of the human reference genome. Normalisation was done by fraction of reads in peaks.
Assembly: HG38
Supplementary files format and content: Bigwig

molecule: genomic DNA

source_name: PBMNCs

growth_protocol: CD14+ monocytes isolated from fresh blood were used for this experiment, at 1x106 cells per IP. Five CMML patients and three HVs were included

extract_protocol:
Cells were crosslinked with 1% formaldehyde and the reaction was quenched with glycine. Dynabeads protein G (Thermo Fisher Scientific) were washed with cold IP-100 buffer (25 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 10% v/v glycerol, 0.1% NP-40 alternative [Calbiochem, 492016-100ML], 200 µM PMSF) and incubated with antibody for 6-8h at 4°C while rotating. Cells were then sonicated in sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate, 1x EDTA-free proteinase inhibitor cocktail [PIC] [Roche], 1% v/v SDS) to a fragment size of approximately 500 bp. Sonication buffer without SDS was added to dilute SDS to 0.1% v/v. Antibody-coated beads were added to the rest of the sample, and IP was carried out O/N at 4°C while rotating. Beads were washed as follows: Twice with sonication buffer without SDS, twice with wash buffer A (50mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate, 0.1% v/v SDS, 1x PIC), twice with wash buffer B (20 mM Tris-HCl pH 8.1, 1 mM EDTA, 250 mM LiCl, 0.5% v/v IGEPAL CA-630, 0.5% w/v sodium deoxycholate, 1x PIC) and twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA), followed by addition of elution buffer (50 mM Tris-HCl pH 8.1, 1 mM EDTA, 1% v/v SDS). Samples were vortexed and incubated at 65°C, after which the first eluate was taken. The elution process was then repeated. NaCl and RNase A were added, and samples were incubated O/N at 65°C. EDTA and proteinase K were added, and samples were incubated at 42°C for 2h. Extraction with 25:24:1 phenol:chloroform:isoamyl alcohol (Sigma, P2069-400ML) was performed twice. Glycogen, sodium acetate pH 5.6 and two volumes of 100% ice-cold ethanol were added, after which DNA was precipitated at -20°C. DNA was washed and then resuspended in 10 mM Tris-HCl pH 7.5.
Cells were crosslinked with 1% formaldehyde and the reaction was quenched with glycine. Dynabeads protein G (Thermo Fisher Scientific) were washed with cold IP-100 buffer (25 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 10% v/v glycerol, 0.1% NP-40 alternative [Calbiochem, 492016-100ML], 200 µM PMSF) and incubated with antibody for 6-8h at 4°C while rotating. Cells were then sonicated in sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate, 1x EDTA-free proteinase inhibitor cocktail [PIC] [Roche], 1% v/v SDS) to a fragment size of approximately 500 bp. Sonication buffer without SDS was added to dilute SDS to 0.1% v/v. Antibody-coated beads were added to the rest of the sample, and IP was carried out O/N at 4°C while rotating. Beads were washed as follows: Twice with sonication buffer without SDS, twice with wash buffer A (50mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate, 0.1% v/v SDS, 1x PIC), twice with wash buffer B (20 mM Tris-HCl pH 8.1, 1 mM EDTA, 250 mM LiCl, 0.5% v/v IGEPAL CA-630, 0.5% w/v sodium deoxycholate, 1x PIC) and twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA), followed by addition of elution buffer (50 mM Tris-HCl pH 8.1, 1 mM EDTA, 1% v/v SDS). Samples were vortexed and incubated at 65°C, after which the first eluate was taken. The elution process was then repeated. NaCl and RNase A were added, and samples were incubated O/N at 65°C. EDTA and proteinase K were added, and samples were incubated at 42°C for 2h. Extraction with 25:24:1 phenol:chloroform:isoamyl alcohol (Sigma, P2069-400ML) was performed twice. Glycogen, sodium acetate pH 5.6 and two volumes of 100% ice-cold ethanol were added, after which DNA was precipitated at -20°C. DNA was washed and then resuspended in 10 mM Tris-HCl pH 7.5.

value: PBMNCs

value: Monocytes

value: CMML Patient

tag: chip antibody


title: F-B01_S109

description:
Library name: DSP-1001660003081-F-B01_S109
Fresh frozen spatial transcriptomics sequencing


title: P63


title: E-H10_S94

description:
Library name: DSP-1001660003082-E-H10_S94
Fresh frozen spatial transcriptomics sequencing


title: F-A06_S102

description:
Library name: DSP-1001660003081-F-A06_S102
Fresh frozen spatial transcriptomics sequencing


title: F-A10_S106

description:
Library name: DSP-1001660003081-F-A10_S106
Fresh frozen spatial transcriptomics sequencing


title: P62


title: BC776_H3K27ac

description: Library name: KB9_16_776_H3K27ac


title: P59


title: E-H09_S93

description:
Library name: DSP-1001660003082-E-H09_S93
Fresh frozen spatial transcriptomics sequencing


title: BC776_H3K4me3

description: Library name: KB9_15_776_H3K4me3


title: E-H08_S92

description:
Library name: DSP-1001660003082-E-H08_S92
Fresh frozen spatial transcriptomics sequencing


title: P58


title: P57


title: BC776_H3K4me1

description: Library name: KB9_14_776_H3K4me1


title: P53


title: E-H07_S91

description:
Library name: DSP-1001660003082-E-H07_S91
Fresh frozen spatial transcriptomics sequencing


title: P52


title: P68


title: P49


title: BC776_input

description: Library name: KB9_13_776_input

value: input


title: E-H06_S90

description:
Library name: DSP-1001660003082-E-H06_S90
Fresh frozen spatial transcriptomics sequencing


title: P47


title: P46


title: P45


title: P44


title: E-H05_S89

description:
Library name: DSP-1001660003082-E-H05_S89
Fresh frozen spatial transcriptomics sequencing


title: E-H04_S88

description:
Library name: DSP-1001660003082-E-H04_S88
Fresh frozen spatial transcriptomics sequencing


title: BC812_H3K27ac

description: Library name: KB9_11_812_H3K27ac


title: P39

description:
10X Genomics
NSCLC_immune_scRNA_counts.mtx.gz
barcodes.csv
genes.csv
NSCLC_immune_scRNA_metadata.csv


title: P36


title: BC812_H3K4me3

description: Library name: KB9_10_812_H3K4me3


title: BC812_H3K4me1

description: Library name: KB9_09_812_H3K4me1


title: P35


title: E-H03_S87

description:
Library name: DSP-1001660003082-E-H03_S87
Fresh frozen spatial transcriptomics sequencing


title: BC812_input

description: Library name: KB9_08_812_input


title: P33


title: P32


title: E-H01_S85

description:
Library name: DSP-1001660003082-E-H01_S85
Fresh frozen spatial transcriptomics sequencing


title: P31


title: E-G12_S84

description:
Library name: DSP-1001660003082-E-G12_S84
Fresh frozen spatial transcriptomics sequencing


title: BC786_H3K27ac

description: Library name: KB9_06_786_H3K27ac


title: E-H02_S86

description:
Library name: DSP-1001660003082-E-H02_S86
Fresh frozen spatial transcriptomics sequencing


title: E-G11_S83

description:
Library name: DSP-1001660003082-E-G11_S83
Fresh frozen spatial transcriptomics sequencing


title: P24


title: BC812_H3K27me3

description: Library name: KB9_12_812_H3K27me3


title: P23


title: BC786_H3K4me3

description: Library name: KB9_05_786_H3K4me3


title: P26


title: P43


title: P29


title: P22


title: E-G10_S82

description:
Library name: DSP-1001660003082-E-G10_S82
Fresh frozen spatial transcriptomics sequencing


title: BC786_H3K4me1

description: Library name: KB9_04_786_H3K4me1


title: P20


title: P18


title: E-G09_S81

description:
Library name: DSP-1001660003082-E-G09_S81
Fresh frozen spatial transcriptomics sequencing


title: P16


title: BC786_input

description: Library name: KB9_03_786_input


title: P10


title: P34


title: P9


title: E-G08_S80

description:
Library name: DSP-1001660003082-E-G08_S80
Fresh frozen spatial transcriptomics sequencing


title: BC786_H3K27me3

description: Library name: KB9_07_786_H3K27me3


title: BC796_H3K4me3

description: Library name: KB9_02_796_H3K4me3


title: E-G07_S79

description:
Library name: DSP-1001660003082-E-G07_S79
Fresh frozen spatial transcriptomics sequencing


title: P5


title: E-G06_S78

description:
Library name: DSP-1001660003082-E-G06_S78
Fresh frozen spatial transcriptomics sequencing


title: BC796_input

description: Library name: KB9_01_796_input


title: P4


title: BC830_H3K4me3

description: Library name: KB12_25_830_H3K4me3


title: E-G05_S77

description:
Library name: DSP-1001660003082-E-G05_S77
Fresh frozen spatial transcriptomics sequencing


title: P2


title: P3


title: E-G04_S76

description:
Library name: DSP-1001660003082-E-G04_S76
Fresh frozen spatial transcriptomics sequencing


title: P1


title: HV4_H3K4me3

description: Library name: KB12_23_HV4_H3K4me3

value: Healthy volunteer


title: Fibroblasts, ZIKV, 24hpi, rep4

city: Hannover

first: Karsten

last: Cirksena

state: Lower Saxony

address: Bünteweg 2

department: Institute of Biochemistry

institute: University of Veterinary Medicine Hannover

description:
N3408
ZIKV_24hpi_4

data_processing:
nfcore/rnaseq (version 1.4.2) pipeline using Nextflow
FastQ inputs, reads aligned and extensive quality-control performed
Galaxy (version 20.05) instance of the RCU Genomics, Hannover Medical School, Germany with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”).
Assembly: genome reference and annotation data were taken from GENCODE.org (Homo sapiens: GRCh38.p13; release 34)
Supplementary files format and content: tab-delimited txt file including normalised expression values

source_name: Skin

growth_protocol: Human dermal fibroblasts (hTert-immortalized(1)), a kind gift from Prof. Dusan Bogunovic, were maintained in growth media containing Dulbecco's Modified Eagle Medium (Sigma Aldrich) supplemented with 1% non-essential amino acids (Gibco, Thermo Fisher Scientific), 100U/mL penicillin & 100 µg/mL streptomycin (Gibco, Thermo Fisher Scientific) and 10% fetal bovine serum (FBS, Cytiva) at 37°C in 5% CO2.

extract_protocol:
At the time of cell harvest, media was removed, and the cells were washed twice with PBS and then lysed by the addition of lysis buffer (Macherey-Nagel, Nucleospin Viral RNA kit). The samples were stored at -80°C until RNA extraction according to the instructions from the manufacturer. For each biological replicate, three wells with cells were pooled.
Library generation was performed by Novogene using NEB Next® Ultra RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Human dermal fibroblasts (0.275 x 10^6 cells) were seeded in 6-well cell culture plates one day prior to infection in growth media supplemented with 10% FBS. The cells were infected with ZIKV or heat-inactivated ZIKV (70°C, 15 min) at a MOI of 0.1 diluted in growth media containing 2% FBS, or mock treated, for uninfected control cells, treated cells with heat inactivated virus also serves as uninfected control. The cells were incubated at 37°C and 5% CO2 for 2h before the inoculation material was removed and the cells were washed twice with PBS. New growth media containing 2% FBS was added to the cells and the incubation continued for a total duration of 10hpi (invasion stage) or 24hpi (transmission stage).

value: Skin

value: Human dermal fibroblasts (hTert-immortalized)

value: Dermal fibroblasts

value: hTert-immortalized

value: ZIKV


title: Fibroblasts, ZIKV, 24hpi, rep3

description:
N3407
ZIKV_24hpi_3


title: E-G03_S75

description:
Library name: DSP-1001660003082-E-G03_S75
Fresh frozen spatial transcriptomics sequencing


title: HV3_H3K27me3

description: Library name: KB12_24_HV3_H3K27me3


title: Fibroblasts, ZIKV, 24hpi, rep1

description:
N3405
ZIKV_24hpi_1


title: P6


title: Fibroblasts, ZIKV, 24hpi, rep2

description:
N3406
ZIKV_24hpi_2


title: Fibroblasts, Heat_Inactivated, 24hpi, rep4

description:
N3400
Heat_24hpi_4


title: E-G01_S73

description:
Library name: DSP-1001660003082-E-G01_S73
Fresh frozen spatial transcriptomics sequencing


title: Fibroblasts, Heat_Inactivated, 24hpi, rep2

description:
N3398
Heat_24hpi_2


title: Fibroblasts, Heat_Inactivated, 24hpi, rep1

description:
N3397
Heat_24hpi_1


title: E-F12_S72

description:
Library name: DSP-1001660003082-E-F12_S72
Fresh frozen spatial transcriptomics sequencing


title: Fibroblasts, Mock, 24hpi, rep2

description:
N3402
Mock_24hpi_2

value: Mock


title: E-F11_S71

description:
Library name: DSP-1001660003082-E-F11_S71
Fresh frozen spatial transcriptomics sequencing


title: HV2_H3K27me3

description: Library name: KB12_19_HV2_H3K27me3


title: Fibroblasts, Mock, 24hpi, rep1

description:
N3401
Mock_24hpi_1


title: Fibroblasts, ZIKV, 10hpi, rep4

description:
N3396
ZIKV_10hpi_4


title: E-F10_S70

description:
Library name: DSP-1001660003082-E-F10_S70
Fresh frozen spatial transcriptomics sequencing


title: Fibroblasts, ZIKV, 10hpi, rep3

description:
N3395
ZIKV_10hpi_3


title: Fibroblasts, ZIKV, 10hpi, rep2

description:
N3394
ZIKV_10hpi_2


title: E-F09_S69

description:
Library name: DSP-1001660003082-E-F09_S69
Fresh frozen spatial transcriptomics sequencing


title: Fibroblasts, Heat_Inactivated, 10hpi, rep4

description:
N3388
Heat_10hpi_4


title: HV2_H3K27ac

description: Library name: KB12_16_HV2_H3K27ac


title: Fibroblasts, ZIKV, 10hpi, rep1

description:
N3393
ZIKV_10hpi_1


title: Fibroblasts, Heat_Inactivated, 10hpi, rep3

description:
N3387
Heat_10hpi_3


title: BC932_H3K4me3

description: Library name: KB12_21_932_H3K4me3


title: HV3_input

description: Library name: KB12_22_HV3_input


title: E-G02_S74

description:
Library name: DSP-1001660003082-E-G02_S74
Fresh frozen spatial transcriptomics sequencing


title: Fibroblasts, Mock, 10hpi, rep4

description:
N3392
Mock_10hpi_4


title: Fibroblasts, Heat_Inactivated, 10hpi, rep2

description:
N3386
Heat_10hpi_2


title: BC830_H3K4me1

description: Library name: KB12_15_830_H3K4me1


title: Fibroblasts, Heat_Inactivated, 24hpi, rep3

description:
N3399
Heat_24hpi_3


title: E-F08_S68

description:
Library name: DSP-1001660003082-E-F08_S68
Fresh frozen spatial transcriptomics sequencing


title: E-F06_S66

description:
Library name: DSP-1001660003082-E-F06_S66
Fresh frozen spatial transcriptomics sequencing


title: Fibroblasts, Heat_Inactivated, 10hpi, rep1

description:
N3385
Heat_10hpi_1


title: Fibroblasts, Mock, 10hpi, rep3

description:
N3391
Mock_10hpi_3


title: Fibroblasts, Mock, 10hpi, rep1

description:
N3389
Mock_10hpi_1


title: HV3_H3K4me1

description: Library name: KB12_17_HV3_H3K4me1


title: E-F07_S67

description:
Library name: DSP-1001660003082-E-F07_S67
Fresh frozen spatial transcriptomics sequencing


title: BC932_H3K4me1

description: Library name: KB12_20_932_H3K4me1


title: E-F04_S64

description:
Library name: DSP-1001660003082-E-F04_S64
Fresh frozen spatial transcriptomics sequencing


title: HV2_H3K4me1

description: Library name: KB12_11_HV2_H3K4me1


title: Fibroblasts, Mock, 24hpi, rep4

description:
N3404
Mock_24hpi_4


title: BC830_H3K27me3

description: Library name: KB12_14_830_H3K27me3


title: HV2_H3K4me3

description: Library name: KB12_18_HV2_H3K4me3


title: HV2_input

description: Library name: KB12_13_HV2_input


title: E-F03_S63

description:
Library name: DSP-1001660003082-E-F03_S63
Fresh frozen spatial transcriptomics sequencing


title: Fibroblasts, Mock, 10hpi, rep2

description:
N3390
Mock_10hpi_2


title: E-F05_S65

description:
Library name: DSP-1001660003082-E-F05_S65
Fresh frozen spatial transcriptomics sequencing


title: HV4_input

description: Library name: KB12_10_HV4_input


title: HA_Ctrl_siRNA_rep_3

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

data_processing:
Reads were aligned to the hg38 human genome using STAR.
Aligned read files were analyzed using HOMER. Differentially expressed genes were analyzed using DESeq2.
Assembly: hg38

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Poly-A mRNA was extracted from total RNA using Oligo-dT beads in a NEBNext Poly (A) RNA Magnetic Isolation Module (New England Biolabs), after which RNA-seq libraries are prepared using a RNA-Seq library preparation kit for Illumina (New England Biolabs) according to the manufacturer’s protocols.

value: cerebral cortex

value: human astrocytes

value: primary cell

value: siRNA-transfection


title: HA_HNRNPU_siRNA_rep_1


title: E-F02_S62

description:
Library name: DSP-1001660003082-E-F02_S62
Fresh frozen spatial transcriptomics sequencing

value: Intestine


title: HV3_H3K4me3

description: Library name: KB12_12_HV3_H3K4me3


title: HA_Ctrl_siRNA_rep_1


title: HA_Ctrl_siRNA_rep_2


title: E-F01_S61

description:
Library name: DSP-1001660003082-E-F01_S61
Fresh frozen spatial transcriptomics sequencing


title: HA_HNRNPU_siRNA_rep_2


title: BC932_input

description: Library name: KB12_09_932_input


title: 710172_MONO_unstim_SS

city: Tel Aviv

first: Rachel

last: Brandes Leibovitz

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

data_processing:
MMSEQ package was used to infer gene expression levels
we mapped clean reads to reference transcripts using Bowtie2 software
we calculated the gene  expression level (FPKM) for each sample with the RSEM software
Assembly: hg19
Supplementary files format and content: FPKM normalized reads

source_name: Monocytes

extract_protocol: RNA was extracted using the RNEasy mini kit.

value: Sepsis Patient


title: E-E12_S60

description:
Library name: DSP-1001660003082-E-E12_S60
Fresh frozen spatial transcriptomics sequencing


title: 710174_MONO_unstim_SS


title: 710171_MONO_unstim_SS


title: HV4_H3K27ac

description: Library name: KB12_08_HV4_H3K27ac

value: PBMNCs


title: 710164_MONO_unstim_SS

value: Monocytes


title: HA_HNRNPU_siRNA_rep_3


title: 710163_MONO_unstim_SS


title: 710169_MONO_unstim_SS


title: E-E11_S59

description:
Library name: DSP-1001660003082-E-E11_S59
Fresh frozen spatial transcriptomics sequencing


title: BC932_H3K27me3

description: Library name: KB12_06_932_H3K27me3

value: CMML Patient


title: 710162_MONO_unstim_SS


title: 710159_MONO_unstim_SS


title: E-E10_S58

description:
Library name: DSP-1001660003082-E-E10_S58
Fresh frozen spatial transcriptomics sequencing


title: BC830_input

description: Library name: KB12_05_830_input

value: input


title: 710158_MONO_unstim_SS


title: 710157_MONO_unstim_SS


title: E-E09_S57

description:
Library name: DSP-1001660003082-E-E09_S57
Fresh frozen spatial transcriptomics sequencing


title: 710156_MONO_unstim_SS


title: E-E08_S56

description:
Library name: DSP-1001660003082-E-E08_S56
Fresh frozen spatial transcriptomics sequencing


title: HV4_H3K4me1

description: Library name: KB12_03_HV4_H3K4me1

value: Healthy volunteer


title: 710155_MONO_unstim_SS


title: 710154_MONO_unstim_SS


title: 710143_MONO_unstim_SS


title: 710142_MONO_unstim_SS


title: E-E07_S55

description:
Library name: DSP-1001660003082-E-E07_S55
Fresh frozen spatial transcriptomics sequencing


title: HV3_H3K27ac

description: Library name: KB12_01_HV3_H3K27ac


title: BC830_H3K27ac

description: Library name: KB12_02_830_H3K27ac


title: 710140_MONO_unstim_SS


title: E-E06_S54

description:
Library name: DSP-1001660003082-E-E06_S54
Fresh frozen spatial transcriptomics sequencing


title: BC932_H3K27ac

description: Library name: KB12_07_932_H3K27ac


title: HuR, irCLIPv2, HEK293T, Rep 1, Section 2

city: Stanford

first: Luca

last: Ducoli

state: CA

address: 269 Campus Drive CCSR 2150

institute: Stanford University

description: irCLIPv2 protocol

data_processing:
Custom processing scripts available at https://github.com/lducoli/irCLIP-RNP/.
Assembly: Human GRCh38 Gencode release 39 and a custom chromosome made of repetitive elements
Supplementary files format and content: Tab separated text file of RT stops counts at genomic windows as determined by htseq-clip. Scaled bigwig files using scale factors estimated from window counts using DEWSeq.
Library strategy: CLIP-seq

growth_protocol: HEK293T and A431 cells were grown in DMEM 10% FBS supplemented with 1xPS.

extract_protocol:
For irCLIPv2, immunoprecipitation (IP) followed by 3'ligation. For Re-CLIP, 1st IP, 3' ligation, IP destruction and reconstitution, 2nd IP. Then, ligated RNPs were resolved on SDS-page, transferred to nitrocellulose, and RNA was recovered after protein K digestion using streptavidin beads.
On-beads 1st strand cDNA synthesis, 3’ cDNA-tailing, 2nd strand synthesis, and amplification.

treatment_protocol: UV cross-linked at 253nm on plates. Where specified, cells were treated with 50ng/mL recombinant human EGF for the given time.

value: Human embryonic kidney cell line


title: 710133_MONO_unstim_SS


title: 710137_MONO_unstim_SS


title: 710132_MONO_unstim_SS


title: E-E05_S53

description:
Library name: DSP-1001660003082-E-E05_S53
Fresh frozen spatial transcriptomics sequencing


title: HuR, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: E-E04_S52

description:
Library name: DSP-1001660003082-E-E04_S52
Fresh frozen spatial transcriptomics sequencing


title: 710130_MONO_unstim_SS


title: E-E03_S51

description:
Library name: DSP-1001660003082-E-E03_S51
Fresh frozen spatial transcriptomics sequencing


title: 710134_MONO_unstim_SS


title: 710125_MONO_unstim_SS


title: 710124_MONO_unstim_SS


title: HuR, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: 710121_MONO_unstim_SS


title: 710126_MONO_unstim_SS


title: HV4_H3K27me3

description: Library name: KB12_04_HV4_H3K27me3


title: 710119_MONO_unstim_SS


title: E-D12_S48

description:
Library name: DSP-1001660003082-E-D12_S48
Fresh frozen spatial transcriptomics sequencing


title: HNRNPU, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: E-E01_S49

description:
Library name: DSP-1001660003082-E-E01_S49
Fresh frozen spatial transcriptomics sequencing


title: 710136_MONO_unstim_SS


title: 710122_MONO_unstim_SS


title: HNRNPU, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: 710114_MONO_unstim_SS


title: HNRNPU, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: E-D11_S47

description:
Library name: DSP-1001660003082-E-D11_S47
Fresh frozen spatial transcriptomics sequencing


title: 710115_MONO_unstim_SS


title: E-D10_S46

description:
Library name: DSP-1001660003082-E-D10_S46
Fresh frozen spatial transcriptomics sequencing


title: HNRNPU, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: 710106_MONO_unstim_SS


title: 710104_MONO_unstim_SS


title: E-D09_S45

description:
Library name: DSP-1001660003082-E-D09_S45
Fresh frozen spatial transcriptomics sequencing


title: E-E02_S50

description:
Library name: DSP-1001660003082-E-E02_S50
Fresh frozen spatial transcriptomics sequencing


title: 710102_MONO_unstim_SS


title: 710100_MONO_unstim_SS


title: HNRNPU, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: E-D07_S43

description:
Library name: DSP-1001660003082-E-D07_S43
Fresh frozen spatial transcriptomics sequencing


title: 760256_MONO_unstim_HC

value: Healthy control


title: HNRNPU, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: 760254_MONO_unstim_HC


title: 710118_MONO_unstim_SS


title: HNRNPU, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: 760252_MONO_unstim_HC


title: 760253_MONO_unstim_HC


title: E-D06_S42

description:
Library name: DSP-1001660003082-E-D06_S42
Fresh frozen spatial transcriptomics sequencing


title: E-D05_S41

description:
Library name: DSP-1001660003082-E-D05_S41
Fresh frozen spatial transcriptomics sequencing


title: E-D04_S40

description:
Library name: DSP-1001660003082-E-D04_S40
Fresh frozen spatial transcriptomics sequencing


title: HNRNPU, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: 760249_MONO_unstim_HC


title: 760251_MONO_unstim_HC


title: HNRNPC, HNRNPM, Re-CLIP, HEK293T, Rep 1

description: irCLIPv2 protocol


title: 760250_MONO_unstim_HC


title: 760248_MONO_unstim_HC


title: E-D03_S39

description:
Library name: DSP-1001660003082-E-D03_S39
Fresh frozen spatial transcriptomics sequencing


title: HNRNPC, HNRNPM, Re-CLIP, HEK293T, Rep 2

description: irCLIPv2 protocol


title: 760247_MONO_unstim_HC


title: HNRNPM, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: E-D02_S38

description:
Library name: DSP-1001660003082-E-D02_S38
Fresh frozen spatial transcriptomics sequencing


title: 760246_MONO_unstim_HC


title: 710103_MONO_unstim_SS


title: E-D08_S44

description:
Library name: DSP-1001660003082-E-D08_S44
Fresh frozen spatial transcriptomics sequencing


title: 760245_MONO_unstim_HC


title: 760244_MONO_unstim_HC


title: 760243_MONO_unstim_HC


title: E-D01_S37

description:
Library name: DSP-1001660003082-E-D01_S37
Fresh frozen spatial transcriptomics sequencing


title: 760242_MONO_unstim_HC


title: HNRNPM, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: 760255_MONO_unstim_HC


title: HNRNPM, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: E-C12_S36

description:
Library name: DSP-1001660003082-E-C12_S36
Fresh frozen spatial transcriptomics sequencing


title: 710184_PBMC_unstim_SS

source_name: PBMC

value: PBMC


title: E-C11_S35

description:
Library name: DSP-1001660003082-E-C11_S35
Fresh frozen spatial transcriptomics sequencing


title: HNRNPM, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: 710179_PBMC_unstim_SS


title: 710180_PBMC_unstim_SS


title: E-C10_S34

description:
Library name: DSP-1001660003082-E-C10_S34
Fresh frozen spatial transcriptomics sequencing


title: 710183_PBMC_unstim_SS


title: 710177_PBMC_unstim_SS


title: 710178_PBMC_unstim_SS


title: HNRNPM, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: 710176_PBMC_unstim_SS


title: HNRNPM, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: HNRNPM, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: 710173_PBMC_unstim_SS


title: E-C08_S32

description:
Library name: DSP-1001660003082-E-C08_S32
Fresh frozen spatial transcriptomics sequencing


title: E-C09_S33

description:
Library name: DSP-1001660003082-E-C09_S33
Fresh frozen spatial transcriptomics sequencing


title: 710174_PBMC_unstim_SS


title: 710172_PBMC_unstim_SS


title: 710171_PBMC_unstim_SS


title: E-C06_S30

description:
Library name: DSP-1001660003082-E-C06_S30
Fresh frozen spatial transcriptomics sequencing


title: HNRNPM, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: E-C07_S31

description:
Library name: DSP-1001660003082-E-C07_S31
Fresh frozen spatial transcriptomics sequencing


title: HNRNPFH, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: 710169_PBMC_unstim_SS


title: E-C05_S29

description:
Library name: DSP-1001660003082-E-C05_S29
Fresh frozen spatial transcriptomics sequencing


title: 710170_PBMC_unstim_SS


title: 710167_PBMC_unstim_SS


title: 710181_PBMC_unstim_SS


title: HNRNPFH, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: 710168_PBMC_unstim_SS


title: 710166_PBMC_unstim_SS


title: E-C04_S28

description:
Library name: DSP-1001660003082-E-C04_S28
Fresh frozen spatial transcriptomics sequencing


title: 710165_PBMC_unstim_SS


title: HNRNPFH, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: E-C03_S27

description:
Library name: DSP-1001660003082-E-C03_S27
Fresh frozen spatial transcriptomics sequencing


title: 710164_PBMC_unstim_SS


title: HNRNPFH, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: E-C02_S26

description:
Library name: DSP-1001660003082-E-C02_S26
Fresh frozen spatial transcriptomics sequencing


title: 710160_PBMC_unstim_SS


title: 710162_PBMC_unstim_SS


title: HNRNPFH, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: 710158_PBMC_unstim_SS


title: 710159_PBMC_unstim_SS


title: E-B12_S24

description:
Library name: DSP-1001660003082-E-B12_S24
Fresh frozen spatial transcriptomics sequencing


title: 710157_PBMC_unstim_SS


title: 710155_PBMC_unstim_SS


title: 710156_PBMC_unstim_SS


title: HNRNPFH, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: E-B10_S22

description:
Library name: DSP-1001660003082-E-B10_S22
Fresh frozen spatial transcriptomics sequencing


title: 710153_PBMC_unstim_SS


title: E-B11_S23

description:
Library name: DSP-1001660003082-E-B11_S23
Fresh frozen spatial transcriptomics sequencing


title: HNRNPC, siUPF1, irCLIPv2, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, siUPF1, irCLIPv2, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: HNRNPC, siUPF1, irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: 710154_PBMC_unstim_SS


title: 710151_PBMC_unstim_SS


title: E-B09_S21

description:
Library name: DSP-1001660003082-E-B09_S21
Fresh frozen spatial transcriptomics sequencing


title: 710163_PBMC_unstim_SS


title: E-B08_S20

description:
Library name: DSP-1001660003082-E-B08_S20
Fresh frozen spatial transcriptomics sequencing


title: 710150_PBMC_unstim_SS


title: 710152_PBMC_unstim_SS


title: HNRNPC, siUPF1, irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: 710148_PBMC_unstim_SS


title: E-C01_S25

description:
Library name: DSP-1001660003082-E-C01_S25
Fresh frozen spatial transcriptomics sequencing


title: 710147_PBMC_unstim_SS


title: E-B07_S19

description:
Library name: DSP-1001660003082-E-B07_S19
Fresh frozen spatial transcriptomics sequencing


title: HNRNPC, siRNA control,  irCLIPv2, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol


title: E-B06_S18

description:
Library name: DSP-1001660003082-E-B06_S18
Fresh frozen spatial transcriptomics sequencing


title: 710145_PBMC_unstim_SS


title: HNRNPC, siRNA control, irCLIPv2, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: 710144_PBMC_unstim_SS


title: 710146_PBMC_unstim_SS


title: 710143_PBMC_unstim_SS


title: E-B05_S17

description:
Library name: DSP-1001660003082-E-B05_S17
Fresh frozen spatial transcriptomics sequencing


title: 710142_PBMC_unstim_SS


title: 710140_PBMC_unstim_SS


title: 710141_PBMC_unstim_SS


title: HNRNPC, siRNA control, irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: 710139_PBMC_unstim_SS


title: E-B04_S16

description:
Library name: DSP-1001660003082-E-B04_S16
Fresh frozen spatial transcriptomics sequencing


title: 710149_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol


title: 710137_PBMC_unstim_SS


title: 710138_PBMC_unstim_SS


title: E-A12_S12

description:
Library name: DSP-1001660003082-E-A12_S12
Fresh frozen spatial transcriptomics sequencing


title: HNRNPC, irCLIPv2, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: E-A11_S11

description:
Library name: DSP-1001660003082-E-A11_S11
Fresh frozen spatial transcriptomics sequencing


title: 710135_PBMC_unstim_SS


title: 710134_PBMC_unstim_SS


title: 710133_PBMC_unstim_SS


title: E-A10_S10

description:
Library name: DSP-1001660003082-E-A10_S10
Fresh frozen spatial transcriptomics sequencing


title: HNRNPC, irCLIPv2, A431, 30min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 30min EGF, Rep 1

description: irCLIPv2 protocol


title: 710132_PBMC_unstim_SS


title: 710131_PBMC_unstim_SS


title: 710129_PBMC_unstim_SS


title: E-A09_S9

description:
Library name: DSP-1001660003082-E-A09_S9
Fresh frozen spatial transcriptomics sequencing


title: E-A08_S8

description:
Library name: DSP-1001660003082-E-A08_S8
Fresh frozen spatial transcriptomics sequencing


title: 710130_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, A431, 15min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, siRNA control, irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 15min EGF, Rep 1

description: irCLIPv2 protocol


title: E-B03_S15

description:
Library name: DSP-1001660003082-E-B03_S15
Fresh frozen spatial transcriptomics sequencing


title: 710128_PBMC_unstim_SS


title: 710126_PBMC_unstim_SS


title: 710127_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: E-A07_S7

description:
Library name: DSP-1001660003082-E-A07_S7
Fresh frozen spatial transcriptomics sequencing


title: E-A06_S6

description:
Library name: DSP-1001660003082-E-A06_S6
Fresh frozen spatial transcriptomics sequencing


title: 710136_PBMC_unstim_SS


title: 710125_PBMC_unstim_SS


title: E-A05_S5

description:
Library name: DSP-1001660003082-E-A05_S5
Fresh frozen spatial transcriptomics sequencing


title: 710123_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, HNRNPC, Re-CLIP, HEK293T, Rep 2

description: irCLIPv2 protocol


title: 710121_PBMC_unstim_SS


title: E-A04_S4

description:
Library name: DSP-1001660003082-E-A04_S4
Fresh frozen spatial transcriptomics sequencing


title: 710120_PBMC_unstim_SS


title: HNRNPC, HNRNPC, Re-CLIP, HEK293T, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: 710117_PBMC_unstim_SS


title: 710119_PBMC_unstim_SS


title: 710116_PBMC_unstim_SS


title: E-A01_S1

description:
Library name: DSP-1001660003082-E-A01_S1
Fresh frozen spatial transcriptomics sequencing


title: E-A02_S2

description:
Library name: DSP-1001660003082-E-A02_S2
Fresh frozen spatial transcriptomics sequencing


title: 710115_PBMC_unstim_SS


title: 710114_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: 710112_PBMC_unstim_SS


title: F-A03_S99

description:
Library name: DSP-1001660003081-F-A03_S99
Fresh frozen spatial transcriptomics sequencing


title: 710113_PBMC_unstim_SS


title: 710110_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: 710111_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: 710108_PBMC_unstim_SS


title: F-A01_S97

description:
Library name: DSP-1001660003081-F-A01_S97
Fresh frozen spatial transcriptomics sequencing


title: 710122_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: E-A03_S3

description:
Library name: DSP-1001660003082-E-A03_S3
Fresh frozen spatial transcriptomics sequencing


title: HNRNPC, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: F-A02_S98

description:
Library name: DSP-1001660003081-F-A02_S98
Fresh frozen spatial transcriptomics sequencing


title: 710124_PBMC_unstim_SS


title: 710107_PBMC_unstim_SS


title: 710118_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: 710106_PBMC_unstim_SS


title: BMDM HDAC9 delta cis regulatory element LPS treated sample 3

city: Munich

first: Rainer

last: Malik

address: Feodor-Lynen-Str. 17

department: Institute for Stroke and Dementia Research

institute: Klinikum der Universität München

data_processing:
seqPurge, STAR and edgeR
seqPurge was used to remove adapter sequences from paired-end sequencing data.
STAR was used to align reads to reference sequence and to count using quant mode
Assembly: mm39
Supplementary files format and content: tab-delimited text file with raw gene counts for each sample

source_name: BMDM

extract_protocol:
Cells were preserved in RLT buffer with β-mercaptoethanol and total RNA was later isolated with the Maxwell RSC48 instrument and miRNA Tissue Kit (Promega, Fitchburg, USA).
200 ng of total RNA were captured on oligo-dT beads and reverse transcribed directly on the beads, followed by the synthesis of the second cDNA strand after adapter ligation. The adapted cDNA was eluted and then amplified with barcoded primer. The finalized, barcoded libraries were pooled and sequenced on an Illumina NextSeq 2000 (Illumina, San Diego, CA, USA) with a read length of 60 nucleotides in paired-end mode

treatment_protocol: Cells were stimulated with LPS (100 ng/ml) for 6 hours and subsequently lysed for RNA isolation and analysis.

value: BMDM

value: HDAC9 deltaCIS

value: LPS 6hrs


title: 710105_PBMC_unstim_SS


title: BMDM HDAC9 delta cis regulatory element LPS treated sample 4


title: 710103_PBMC_unstim_SS


title: 710102_PBMC_unstim_SS


title: 710104_PBMC_unstim_SS


title: HNRNPC, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: 710101_PBMC_unstim_SS


title: FUS, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: 710098_PBMC_unstim_SS


title: BMDM HDAC9 KO LPS treated sample 4

value: HDAC9 knockout


title: 710099_PBMC_unstim_SS


title: BMDM HDAC9 delta cis regulatory element LPS treated sample 1


title: FUS, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: BMDM HDAC9 KO LPS treated sample 3


title: FUS, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: FUS, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: 710096_PBMC_unstim_SS


title: 710097_PBMC_unstim_SS


title: 710095_PBMC_unstim_SS


title: 710092_PBMC_unstim_SS


title: BMDM HDAC9 KO LPS treated sample 2


title: BMDM HDAC9 KO LPS treated sample 1


title: 710093_PBMC_unstim_SS


title: 710100_PBMC_unstim_SS


title: 710091_PBMC_unstim_SS


title: 710090_PBMC_unstim_SS


title: FUS, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: 710089_PBMC_unstim_SS


title: BMDM WT LPS treated sample 3

value: WT


title: 710088_PBMC_unstim_SS


title: 710087_PBMC_unstim_SS


title: 710094_PBMC_unstim_SS


title: BMDM HDAC9 delta cis regulatory element LPS treated sample 2


title: 710086_PBMC_unstim_SS


title: BMDM WT LPS treated sample 2


title: BMDM WT LPS treated sample1


title: RBPJ KO_Td2_rep1

city: New York

first: Baohong

last: Zhao

address: 535 E70th ST

institute: Hospital for Special Surgery

data_processing:
fastp(https://github.com/OpenGene/fastp) was used to evaluate quality of sequenced reads and trim contaminated adaptor portions of sequenced reads. RNA-seq reads were aligned to the the mouse genome (mm10) using HISAT2. HTseq was subsequently used to count reads in features and then edgeR was used to estimate the transcript abundances as CPM (counts per million) values.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for all Samples

source_name: Bone marrow macrophages

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) was used to purify poly-A+ transcripts and generate libraries with multiplexed barcode adaptors following the manufacturer’s instructions.

value: Bone marrow macrophages

value: RBPJ KO

value: TNF d2


title: RBPJ KO_d0_rep1

value: No TNF


title: 710085_PBMC_unstim_SS

value: Sepsis Patient


title: BMDM HDAC9 delta cis regulatory element sample 4


title: 710081_PBMC_unstim_SS


title: 710082_PBMC_unstim_SS


title: FUS, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: BMDM HDAC9 delta cis regulatory element sample 3


title: WT_d0_rep1


title: BMDM HDAC9 delta cis regulatory element sample 2


title: 710080_PBMC_unstim_SS


title: 710079_PBMC_unstim_SS


title: FUS, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: 710078_PBMC_unstim_SS


title: BMDM WT LPS treated sample 4


title: 710077_PBMC_unstim_SS


title: FUS, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: 710076_PBMC_unstim_SS


title: BMDM HDAC9 delta cis regulatory element sample 1


title: 710075_PBMC_unstim_SS


title: TDP-WT-Rep 5

city: Dublin

first: Jochen

middle: H. M.

last: Prehn

address: 123 St. Stephen's Green

department: Physiology and Medical Physics

country: Ireland

institute: Royal College of Surgeons in Ireland (RCSI)

data_processing:
Raw reads were first pre-processed for adapter trimming and quality check after that optical duplicate removed using Clumpify
Processed reads were mapped to the mouse genome (mm10) using STAR (V2.6) aligner
Mapped SAM files were converted into BAM files using samtools. Htseq-count was used to process the BAM files to obtain count data
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain

growth_protocol: FUS (ΔFUS(1-359)) mice on a congenic C57Bl/6 background and TDP (TDP-43A315T) mice on a congenic C57Bl/6 background (B6.Cg-Tg(Prnp-TARDBP*A315T)95Balo/J) was used in the study. Cerebral cortices were harvested from TDP and  FUS mice, along with their littermate wild-type controls, at PND 57-62 and PND 49-51 respectively.

extract_protocol:
Total RNA was extracted using TRIzol Reagent. RNA quantification was performed and quality was assessed using Agilent Bioanalyzer. cDNA libraries were prepared and sequencing was performed on Illumina HiSeq platform.
RNA libraries were prepared for sequencing using standard Illumina protocols using KAPA strandard mRNAseq Kit

treatment_protocol: Mice or tissue samples were not subjected to any kind of treatment protocol

value: Cerebral cortices

value: TDP WT


title: 710084_PBMC_unstim_SS


title: 710083_PBMC_unstim_SS


title: 710074_PBMC_unstim_SS


title: TDP-WT-Rep 4


title: 710073_PBMC_unstim_SS


title: BMDM HDAC9 KO sample 4


title: WT_Td2_rep1


title: BMDM HDAC9 KO sample 3


title: BMDM HDAC9 KO sample 2


title: 710072_PBMC_unstim_SS


title: TDP-WT-Rep 2


title: 710069_PBMC_unstim_SS


title: TDP-WT-Rep 3


title: 710071_PBMC_unstim_SS


title: TDP-WT-Rep 6


title: BMDM HDAC9 KO sample 1


title: TDP-mut-Rep 6

value: TDP mut


title: 710066_PBMC_unstim_SS


title: 710065_PBMC_unstim_SS


title: 710068_PBMC_unstim_SS


title: 710067_PBMC_unstim_SS


title: 710064_PBMC_unstim_SS


title: BMDM WT sample 4


title: BMDM WT sample 3


title: TDP-mut-Rep 5


title: TDP-WT-Rep 1


title: 710062_PBMC_unstim_SS


title: TDP-mut-Rep 4


title: BMDM WT sample 2


title: 710060_PBMC_unstim_SS


title: BMDM WT sample1


title: 710058_PBMC_unstim_SS


title: 710059_PBMC_unstim_SS


title: 710070_PBMC_unstim_SS


title: 710057_PBMC_unstim_SS


title: 710056_PBMC_unstim_SS


title: skin_slick_rep6

city: Davis

first: Anna

middle: Carolina

last: Denicol

address: 450 BIOLETTI WAY, MEYER HALL

department: Animal Science

institute: University of California Davis

description: Library name: S25827

data_processing:
R version 4.3.1
A total of 221,342,181 reads were mapped to the bovine genome (GenBank: GCA_002263795.3) with the STAR aligner (Dobin et al., 2013).
The read quality in the FASTQ files was assessed with FastQC (Andrews, 2019).
Read counts were estimated at the gene level using HTSeq-count (Anders et al., 2015).
Assembly: GCA_002263795.3
Supplementary files format and content: tab delimited text file contains raw counts for each sample

molecule: polyA RNA

organism: Bos taurus

source_name: skin

growth_protocol: Explants from each heifer were placed into an individual well of a 48-well culture plate containing 400 µL of culture medium consisting of DMEM/high glucose supplemented with ovine prolactin (50 ng/mL; cat # 22060613, Bioworld, Dublin, OH) and 5 µg/mL insulin-transferrin-selenium (5 ug/ml), hydrocortisone (0.4 µg/mL, Sigma-Aldrich, St. Louis, MO), amphotericin B (0.1 µg/mL, Sigma-Aldrich) and 1% Pen/Strep. Samples were cultured at 38.5 °C in 5% CO2 in air and saturated humidity for 36 h.

extract_protocol:
Total RNA was isolated  using the Ambion Purelink Mini Kit according to the manufacturer's instructions and eluted in 30 µL of DEPC-treated H2O and stored at -80 °C.
RNA sequencing libraries were constructed using NEBNext Ultra II RNA Library Prep by Illumina from total RNA (220-580 ng/sample) was then subjected to polyA-enriched mRNA sequencing using a Novaseq6000 sequencer (Illumina Corp) with the S4 flow cell and PE150 sequencing parameter

value: skin

value: Slick

value: ovine recombinant Prolactin


title: TDP-mut-Rep 2


title: TDP-mut-Rep 3


title: 710055_PBMC_unstim_SS

value: PBMC


title: skin_slick_rep5

description: Library name: S25821


title: skin_slick_rep4

description: Library name: S25820


title: 760765_PBMC_unstim_HC

value: Healthy control


title: 760763_PBMC_unstim_HC


title: skin_slick_rep3

description: Library name: S25816


title: 760762_PBMC_unstim_HC


title: FUS-WT-Rep 4

value: FUS WT


title: 760760_PBMC_unstim_HC


title: 760758_PBMC_unstim_HC


title: 760755_PBMC_unstim_HC


title: 710061_PBMC_unstim_SS


title: skin_slick_rep2

description: Library name: S25809


title: skin_slick_rep1

description: Library name: S25791


title: 760746_PBMC_unstim_HC


title: 760747_PBMC_unstim_HC


title: FUS-WT-Rep 1


title: FUS-WT-Rep 2


title: skin_nonslick_rep6

description: Library name: W25860

value: Wild type


title: 760745_PBMC_unstim_HC


title: 760752_PBMC_unstim_HC


title: 760744_PBMC_unstim_HC


title: 760740_PBMC_unstim_HC


title: 760743_PBMC_unstim_HC


title: FUS-mut-Rep 7

value: FUS mut


title: TDP-mut-Rep 1


title: FUS-WT-Rep 5


title: skin_nonslick_rep4

description: Library name: W25807


title: 760738_PBMC_unstim_HC


title: skin_nonslick_rep3

description: Library name: W25806


title: FUS-mut-Rep 6


title: 760737_PBMC_unstim_HC


title: FUS-WT-Rep 3


title: 760736_PBMC_unstim_HC


title: FUS-mut-Rep 5


title: 760734_PBMC_unstim_HC


title: 760733_PBMC_unstim_HC


title: FUS-mut-Rep 4


title: 760732_PBMC_unstim_HC


title: skin_nonslick_rep1

description: Library name: W25763


title: 760728_PBMC_unstim_HC


title: skin_nonslick_rep2

description: Library name: W25804


title: skin_nonslick_rep5

description: Library name: W25832


title: 760723_PBMC_unstim_HC


title: 760719_PBMC_unstim_HC


title: Imaginal wing discs, ds38k, Rep4, NovaSeq 6000

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

description:
Library name: ds38k_NovaSeq6000_R4
Column name in McNeill_ds38k_raw_gene_counts.txt: ds38k_NovaSeq6000_R4

data_processing:
Quality control of reads was performed using FastQC v.0.10.
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trimmomatic v.0.33.
Trimmed sequence reads were mapped to dm6 using Salmon v.1.80 with default parameters
Read count extraction and normalization were performed using edgeR.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

organism: Drosophila melanogaster

source_name: imaginal wing discs

extract_protocol:
RNA was harvested using ReliaPrep RNA Tissue Miniprep System (Promega). RNA-Seq libraries were prepared with 10ng of total RNA
cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq 6000 for ds^38k, using paired end reads extending 150 bases

value: imaginal wing discs


title: 760709_PBMC_unstim_HC


title: 760715_PBMC_unstim_HC


title: FUS-mut-Rep 2


title: 760707_PBMC_unstim_HC


title: FUS-mut-Rep 1


title: Imaginal wing discs, ds38k, Rep2, NovaSeq 6000

description:
Library name: ds38k_NovaSeq6000_R2
Column name in McNeill_ds38k_raw_gene_counts.txt: ds38k_NovaSeq6000_R2


title: Hq-WT Rep4

growth_protocol: Hq (B6CBACa Aw-J/A-Aifm1Hq/J) and Aifm1 (R200 del) KI mice was used in the study. Cerebral cortices were harvested from  Aifm1-KI  and Hq mutant mice and their littermate wild-type controls, at around PND180.

value: Hq-WT


title: 760705_PBMC_unstim_HC


title: Imaginal wing discs, ds38k, Rep1, NovaSeq 6000

description:
Library name: ds38k_NovaSeq6000_R1
Column name in McNeill_ds38k_raw_gene_counts.txt: ds38k_NovaSeq6000_R1


title: Imaginal wing discs, ds38k, Rep3, NovaSeq 6000

description:
Library name: ds38k_NovaSeq6000_R3
Column name in McNeill_ds38k_raw_gene_counts.txt: ds38k_NovaSeq6000_R3


title: 760706_PBMC_unstim_HC


title: 760698_PBMC_unstim_HC


title: FUS-mut-Rep 3


title: 760697_PBMC_unstim_HC


title: 760701_PBMC_unstim_HC


title: 760703_PBMC_unstim_HC


title: Hq-WT Rep3


title: Hq-WT Rep2


title: Imaginal wing discs, WT, Rep3, NovaSeq 6000.

description:
Library name: w1118.csvd111_NovaSeq6000_R3
Column name in McNeill_ds38k_raw_gene_counts.txt: w1118.csvd111_NovaSeq6000_R3

value: WT


title: Imaginal wing discs, WT, Rep2, NovaSeq 6000.

description:
Library name: w1118.csvd111_NovaSeq6000_R2
Column name in McNeill_ds38k_raw_gene_counts.txt: w1118.csvd111_NovaSeq6000_R2


title: 760700_PBMC_unstim_HC


title: Hq-mut Rep4

value: Hq-mut


title: 760695_PBMC_unstim_HC


title: Hq-WT Rep1


title: Imaginal wing discs, WT, Rep1, NovaSeq 6000.

description:
Library name: w1118.csvd111_NovaSeq6000_R1
Column name in McNeill_ds38k_raw_gene_counts.txt: w1118.csvd111_NovaSeq6000_R1


title: 760696_PBMC_unstim_HC


title: 760694_PBMC_unstim_HC


title: 760687_PBMC_unstim_HC


title: Hq-mut Rep2


title: 760686_PBMC_unstim_HC


title: Imaginal wing discs, delta F, Rep3, NovaSeq 6000

description:
Library name: deltaF_NovaSeq6000_R3
Column name in McNeill_Ft_raw_gene_counts.txt: deltaF_NovaSeq6000_R3

data_processing:
Quality control of reads was performed using FastQC v.0.10.
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trimmomatic v.0.33.
Trimmed sequence reads were mapped to dm6 using Salmon v.1.80 with default parameters
Read count extraction and normalization were performed using edgeR.
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes raw gene counts for each Sample

extract_protocol:
RNA was harvested using ReliaPrep RNA Tissue Miniprep System (Promega). RNA-Seq libraries were prepared with 10ng of total RNA
cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus for the functional domains and conserved region D, and NovaSeq 6000 for the conserved regions A, B, C, E, and F, using paired end reads extending 150 bases

value: delta F


title: Hq-mut Rep3


title: 760688_PBMC_unstim_HC


title: 760702_PBMC_unstim_HC


title: Imaginal wing discs, delta F, Rep1, NovaSeq 6000

description:
Library name: deltaF_NovaSeq6000_R1
Column name in McNeill_Ft_raw_gene_counts.txt: deltaF_NovaSeq6000_R1


title: Hq-mut Rep1


title: 760682_PBMC_unstim_HC


title: Imaginal wing discs, delta F, Rep2, NovaSeq 6000

description:
Library name: deltaF_NovaSeq6000_R2
Column name in McNeill_Ft_raw_gene_counts.txt: deltaF_NovaSeq6000_R2


title: Aifm1-WT Rep4


title: Imaginal wing discs, delta E, Rep4, NovaSeq 6000

description:
Library name: deltaE_NovaSeq6000_R4
Column name in McNeill_Ft_raw_gene_counts.txt: deltaE_NovaSeq6000_R4

value: delta E


title: 760677_PBMC_unstim_HC


title: 760679_PBMC_unstim_HC


title: Aifm1-WT Rep3

value: Cerebral cortices


title: Aifm1-WT Rep2


title: 760671_PBMC_unstim_HC


title: 760676_PBMC_unstim_HC


title: 760684_PBMC_unstim_HC


title: Imaginal wing discs, delta E, Rep2, NovaSeq 6000

description:
Library name: deltaE_NovaSeq6000_R2
Column name in McNeill_Ft_raw_gene_counts.txt: deltaE_NovaSeq6000_R2


title: 760681_PBMC_unstim_HC


title: 760691_PBMC_unstim_HC


title: Imaginal wing discs, delta E, Rep1, NovaSeq 6000

description:
Library name: deltaE_NovaSeq6000_R1
Column name in McNeill_Ft_raw_gene_counts.txt: deltaE_NovaSeq6000_R1


title: 760669_PBMC_unstim_HC


title: Aifm1-WT Rep1


title: 760670_PBMC_unstim_HC


title: 760668_PBMC_unstim_HC


title: Imaginal wing discs, delta C, Rep3, NovaSeq 6000

description:
Library name: deltaC_NovaSeq6000_R3
Column name in McNeill_Ft_raw_gene_counts.txt: deltaC_NovaSeq6000_R3

value: delta C


title: Aifm1-KI Rep4


title: 760667_PBMC_unstim_HC


title: Imaginal wing discs, delta C, Rep2, NovaSeq 6000

description:
Library name: deltaC_NovaSeq6000_R2
Column name in McNeill_Ft_raw_gene_counts.txt: deltaC_NovaSeq6000_R2


title: 760664_PBMC_unstim_HC


title: 760666_PBMC_unstim_HC


title: Aifm1-KI Rep3


title: 760663_PBMC_unstim_HC


title: Imaginal wing discs, delta C, Rep1, NovaSeq 6000

description:
Library name: deltaC_NovaSeq6000_R1
Column name in McNeill_Ft_raw_gene_counts.txt: deltaC_NovaSeq6000_R1


title: 760662_PBMC_unstim_HC


title: Imaginal wing discs, delta E, Rep3, NovaSeq 6000

description:
Library name: deltaE_NovaSeq6000_R3
Column name in McNeill_Ft_raw_gene_counts.txt: deltaE_NovaSeq6000_R3


title: Aifm1-KI Rep2


title: Aifm1-KI Rep1


title: 760644_PBMC_unstim_HC


title: Control_Tys

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
Raw reads were aligned to reference genome hg38 using BWA MEM (Li, 2013). Apparent PCR duplicates were removed using Picard MarkDuplicates (Wysoker et al., 2013). Peaks were called against the input sample using Macs2 (Zhang et al., 2008, p. 2). Peaks with a score >5 (-log10 q-value) were retained. For quantitative comparisons,  peaks were merged using bedtools merge (Quinlan and Hall, 2010). Enrichment levels for merged peak were quantified using featureCounts (Liao et al., 2014).
Assembly: hg38
Supplementary files format and content: bed, tab-delmited text

source_name: HPAEC

growth_protocol: HPAEC were grown in D150 cell culture dishes in  EGM-2 media (Lonza, CC-3162) supplemented with 10% FBS at 37°C and 5% CO2 until confluent .

extract_protocol:
Cells from 4 x D150 were pooled for each condition.Step 1 – Cross-Linking and Cell Harvesting: Cells were cross-linked with 1% formaldehyde for 10 minutes to fix protein-DNA interactions. Cross-linking reaction was stopped by adding glycine and cells were harvested, pelleted by centrifugation, and washed with cold PBS.  Step 2 – Cell Lysis and Chromatin Isolation: The cell pellets were lysed with ChIP lysis buffer and bulk chromatin was isolated by centrifugation Step 3 – Chromatin Shearing: Isolated chromatin was sheared to 150-300 bp using a cominbination of enzymatic digestion and sonication.  Step 4 – Chromatin Pre-Clearing and Antibody Incubation: Sheared chromatin was pre-cleared by incubating with Protein A/G agarose beads to reduce non-specific binding. Pre-cleared chromatin was then incubated with acetylated Histone H3K9 antibody overnight.  Step 5 – Immunoprecipitation and Washing: Protein A/G magnetic beads were added to the antibody-bound chromatin fractions to facilitate immunoprecipitation. This incubation was carried out for 2 hours. The antibody-bound chromatin was isolated from bulk chromatin with a magnetic separator. To reduce background signal,  the isolated chromatin was washed with a series of buffers containing progressively higher concentrations of salt and detergent.  Step 6 – Reverse Cross-Linking and DNA Purification: Samples were treated with RNAse to degrade RNA, Proteinase K to degrade proteins, and heat to reverse the cross-linking between proteins and DNA.  Step 7 – DNA Isolation and Storage: DNA was isolated and purified with the Qiagen QIAquick PCR Purification Kit and purified DNA samples were stored at -80°C until ready for sequencing.
Libraries were prepered by University of Chicago Core facility using Immumina Library preparation kit and sequenced on the Illumina HiSeq 4000.

treatment_protocol: 2 hours prior treatments, cell culture media was changed to 2% FBS EGM-2 and cells were treated with HK-MRSA (2.5 x10^8/ml), Tysiponate (1 μΜ), HK-MRSA +Tysiponate , or PBS (control) for 30 minutes.

value: HPAEC

value: Lung endothelial cells

value: Histone H3K9 (EMD Millipore #06-942, Temecula, CA)

value: Control


title: Imaginal wing discs, delta B, Rep3, NovaSeq 6000

description:
Library name: deltaB_NovaSeq6000_R3
Column name in McNeill_Ft_raw_gene_counts.txt: deltaB_NovaSeq6000_R3

value: delta B


title: Imaginal wing discs, delta B, Rep2, NovaSeq 6000

description:
Library name: deltaB_NovaSeq6000_R2
Column name in McNeill_Ft_raw_gene_counts.txt: deltaB_NovaSeq6000_R2


title: MRSA_Tys

value: MRSA


title: 760650_PBMC_unstim_HC

value: Healthy control

value: PBMC


title: Imaginal wing discs, delta B, Rep4, NovaSeq 6000

description:
Library name: deltaB_NovaSeq6000_R4
Column name in McNeill_Ft_raw_gene_counts.txt: deltaB_NovaSeq6000_R4


title: 760638_PBMC_unstim_HC


title: Imaginal wing discs, delta B, Rep1, NovaSeq 6000

description:
Library name: deltaB_NovaSeq6000_R1
Column name in McNeill_Ft_raw_gene_counts.txt: deltaB_NovaSeq6000_R1


title: 760637_PBMC_unstim_HC


title: Imaginal wing discs, delta A, Rep4, NovaSeq 6000

description:
Library name: deltaA_NovaSeq6000_R4
Column name in McNeill_Ft_raw_gene_counts.txt: deltaA_NovaSeq6000_R4

value: delta A


title: 760639_PBMC_unstim_HC


title: 760640_PBMC_unstim_HC


title: MRSA_no-treat


title: 760635_PBMC_unstim_HC


title: 760636_PBMC_unstim_HC


title: control_no-treat


title: 760634_PBMC_unstim_HC


title: 760630_PBMC_unstim_HC


title: 760661_PBMC_unstim_HC


title: Imaginal wing discs, delta A, Rep2, NovaSeq 6000

description:
Library name: deltaA_NovaSeq6000_R2
Column name in McNeill_Ft_raw_gene_counts.txt: deltaA_NovaSeq6000_R2

value: imaginal wing discs


title: Imaginal wing discs, delta A, Rep3, NovaSeq 6000

description:
Library name: deltaA_NovaSeq6000_R3
Column name in McNeill_Ft_raw_gene_counts.txt: deltaA_NovaSeq6000_R3


title: iPSC DET1 R26W neurons (D7) #3

city: Toronto

first: Neha

last: Rohatgi

address: Roche 7070

country: Canada

institute: Roche

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. Supplementary files use Ensemble gene IDs, counts and RPKM statistics.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: human iPSCs

extract_protocol:
Total RNA was isolated from cells and purified using RNeasy mini kits and on-column DNAse digestion per manufacturer (Qiagen) protocol. 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human iPSCs

value: DET1 R26W

tag: replicate

value: differentiated (neurons)


title: input


title: 760627_PBMC_unstim_HC


title: 760653_PBMC_unstim_HC


title: Imaginal wing discs, delta A, Rep1, NovaSeq 6000

description:
Library name: deltaA_NovaSeq6000_R1
Column name in McNeill_Ft_raw_gene_counts.txt: deltaA_NovaSeq6000_R1


title: 760626_PBMC_unstim_HC


title: 760624_PBMC_unstim_HC


title: 760623_PBMC_unstim_HC


title: Imaginal wing discs, WT, Rep3, NovaSeq 6000

description:
Library name: w1118.csvd111_NovaSeq6000_R3
Column name in McNeill_Ft_raw_gene_counts.txt: w1118.csvd111_NovaSeq6000_R3

value: WT


title: 760619_PBMC_unstim_HC


title: 760621_PBMC_unstim_HC


title: 760622_PBMC_unstim_HC


title: Imaginal wing discs, WT, Rep2, NovaSeq 6000

description:
Library name: w1118.csvd111_NovaSeq6000_R2
Column name in McNeill_Ft_raw_gene_counts.txt: w1118.csvd111_NovaSeq6000_R2


title: iPSC DET1 R26W neurons (D7) #1


title: iPSC DET1 WT neurons (D7) #3

value: DET1 WT


title: Imaginal wing discs, WT, Rep1, NovaSeq 6000

description:
Library name: w1118.csvd111_NovaSeq6000_R1
Column name in McNeill_Ft_raw_gene_counts.txt: w1118.csvd111_NovaSeq6000_R1


title: 760612_PBMC_unstim_HC


title: LN-PBS  rDC_3

first: Tracy

last: McGaha

state: Ontario

address: 610 University Ave

department: Immunology

institute: University Health Network

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

data_processing:
75b single-end reads were sequenced on a NextSeq 500 Desktop Sequencer
Reads were aligned using the STAR release102 aligner with the GRCm38 mouse genome
Count and TPM matrices were generated using RSEM v1.3.0 with the corresponding GTF file.
Raw reads were normalized using DESeq2 v1.38.3
Assembly: GRCm38, release102
Supplementary files format and content: RSEM created count and TPM matrices

source_name: Lymph node

extract_protocol:
TDLN or LN were digested and myeloid cell were sorted
Libraries were prepared using TruSeq Stranded mRNA kit (Illumina).

value: Lymph node

value: tissue

value: Resident dendritic cells

value: Wild type

value: PBS


title: 760609_PBMC_unstim_HC


title: 760629_PBMC_unstim_HC


title: 760611_PBMC_unstim_HC


title: 760610_PBMC_unstim_HC


title: iPSC DET1 WT neurons (D7) #2


title: LN-PBS  rDC_2

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: iPSC DET1 R26W iPSCs (D0) #3

value: undifferentiated (iPSCs)


title: LN-PBS  rDC_1

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: 760601_PBMC_unstim_HC


title: 760608_PBMC_unstim_HC


title: 760606_PBMC_unstim_HC


title: 760599_PBMC_unstim_HC


title: 760595_PBMC_unstim_HC


title: iPSC DET1 R26W neurons (D7) #2


title: LN-CIS  rDC_3

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

value: Cisplatin


title: iPSC DET1 R26W iPSCs (D0) #1


title: 760594_PBMC_unstim_HC


title: LN-CIS  rDC_2

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: 760591_PBMC_unstim_HC


title: 760592_PBMC_unstim_HC


title: LN-CIS  rDC_1

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: 760590_PBMC_unstim_HC


title: 760589_PBMC_unstim_HC


title: iPSC DET1 WT iPSCs (D0) #3


title: iPSC DET1 WT iPSCs (D0) #2


title: iPSC DET1 WT neurons (D7) #1


title: 760588_PBMC_unstim_HC


title: TDLN-PBS rDC_3

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

source_name: Tumor-draining lymph node

value: Tumor-draining lymph node


title: iPSC DET1 WT iPSCs (D0) #1


title: 760587_PBMC_unstim_HC

value: Healthy control


title: Flag-DET1 R26W A375 cells + Cobimetinib #3

source_name: A375 human melanoma cell line

value: A375 human melanoma cell line

value: Cobimetinib


title: TDLN-PBS rDC_1

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: iPSC DET1 R26W iPSCs (D0) #2


title: 760584_PBMC_unstim_HC

value: PBMC


title: 760585_PBMC_unstim_HC


title: 760583_PBMC_unstim_HC


title: TDLN-CIS rDC_3

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: TDLN-PBS rDC_2

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: 760582_PBMC_unstim_HC


title: 760579_PBMC_unstim_HC


title: 760581_PBMC_unstim_HC


title: Flag-DET1 R26W A375 cells + Cobimetinib #2


title: Flag-DET1 R26W A375 cells #2

value: DMSO


title: TDLN-CIS rDC_2

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: 760575_PBMC_unstim_HC


title: 760577_PBMC_unstim_HC


title: Flag-DET1 R26W A375 cells + Cobimetinib #1

value: DET1 R26W


title: TDLN-CIS rDC_1

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv


title: LN-PBS  mDC_3

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

value: Migratory dendritic cells


title: 760586_PBMC_unstim_HC


title: Flag-DET1 R26W A375 cells #1


title: Imaginal wing discs, delta D, Rep3, NovaSeq X Plus

description:
Library name: deltaD_NovaSeqXPlus_R3
Column name in McNeill_Ft_raw_gene_counts.txt: deltaD_NovaSeqXPlus_R3

value: imaginal wing discs

value: delta D


title: LN-PBS  mDC_2

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

value: Lymph node


title: Flag-DET1 A375 cells + Cobimetinib #3

value: DET1 WT


title: Imaginal wing discs, delta D, Rep2, NovaSeq X Plus

description:
Library name: deltaD_NovaSeqXPlus_R2
Column name in McNeill_Ft_raw_gene_counts.txt: deltaD_NovaSeqXPlus_R2


title: 760563_PBMC_unstim_HC


title: 760565_PBMC_unstim_HC


title: Flag-DET1 A375 cells #3


title: Flag-DET1 R26W A375 cells #3


title: Imaginal wing discs, delta D, Rep1, NovaSeq X Plus

description:
Library name: deltaD_NovaSeqXPlus_R1
Column name in McNeill_Ft_raw_gene_counts.txt: deltaD_NovaSeqXPlus_R1


title: LN-CIS  mDC_3

description:
mdc_rdc_counts.csv
mdc_rdc_tpm.csv

value: tissue


title: 760562_PBMC_unstim_HC


title: Flag-DET1 A375 cells + Cobimetinib #2