title: NOMEseq_MM1S_A485_32hours_Replicate2

city: South San Francisco

first: Simon

middle: J

last: Hogg

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Library strategy: Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which Trim_galore (v0.4.1) was used to remove low-quality reads and hard-trim the first 8 bases from Read 1 (R1) and 11 bases from Read 2 (R2).
The paired-end reads were then aligned as singe-end reads using Bismark (v0.18.2) to the human reference genome (Hg19) using the --non_directional parameter. Alignments in the same position in the genome that might arise during PCR amplification were removed by deduplicate_bismark.
Genomic CpG and GpC methylation calls were determined by Bismark_methylation_extractor using the –CX parameter. Coverage files were converted to bigwig files using bedGraphToBigWig which were subsequently used to produce plots using Deeptools (v3.0.0).
Genome_build: Hg19
Supplementary_files_format_and_content: bigWig

source_name: Multiple Myeloma

growth_protocol: MM1.S cells were grown under standard in vitro culture conditions.

extract_protocol:
MM1.S cells were trypsinised and collected by centrifugation at 500g for 5 minutes, then washed once in ice-cold PBS. Pellets were then resuspended in 1mL ice-cold Nuclei Extraction Buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1mM EDTA, 0.5% Igepal, plus protease inhibitors) per 5 x 106 cells and incubated on ice for 5 minutes. Nuclei were recovered by centrifugation at 500g for 5min and washed in Nuclei Wash Buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1mM EDTA, plus protease inhibitors). Freshly prepared nuclei (2.5 x 105 cells) were resuspended in 94.5uL 1X M.CviPI reaction buffer (NEB), then treated with 200 units of M.CviPI (NEB; 50,000 units/mL) in 5uL 10X reaction buffer, 45uL 1M sucrose and 1.5uL 32mM SAM. Nuclei were incubated for 7.5 minutes at 37°C then spiked with an additional 100 units of M.CviPI and 1.5uL SAM and incubated for an further 7.5 minutes. Reactions were immediately quenched by the addition of an equal volume (150uL) of Stop Solution (20nM Tris pH 7.9, 600mM NaCl, 1% SDS, 10mM EDTA, 400ug/mL Proteinase K) and incubated overnight at 55°C. DNA was purified using MicroChIP DiaPure columns (Diagenode) and conversion was performed using the EM-seq Conversion Module (NEB).
Bisulfite conversion was performed using the EZ DNA Methylation-Gold Kit (Zymo Research) after which sequencing libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit for Illumina (Swift Biosciences) and Methyl-Seq Set A Indexing Kit (Swift Biosciences). Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE150/150 run using the NovaSeq 6000 (300 cycles; Illumina). An average of 460 million paired reads was generated per sample.

treatment_protocol: MM1.S cells were treated with A-485 (1µM) or DMSO vehicle for indicated time points.

tag: cell line

tag: timepoint

value: 32 hours

tag: treatment+dose


title: NOMEseq_MM1S_A485_2hours_Replicate2

status: Public on May 11 2021

type: SRA

state: California

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: 2 hours


title: NOMEseq_MM1S_A485_6hours_Replicate1

value: 6 hours


title: NOMEseq_MM1S_A485_6hours_Replicate2


title: NOMEseq_MM1S_DMSO_Replicate2

value: DMSO


title: NOMEseq_MM1S_DMSO_Replicate1


title: Tumor+IL12-GEMy 1

city: Bethesda

first: Rosandra

middle: N

last: Kaplan

state: Maryland

address: 10 Center Drive

department: Pediatric Oncology Branch

institute: National Institute of Health

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm10 whole genome using STAR 2.7.3a built in Partek Flow
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the Partek E/M model
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: M3-9-M Tumor-Bearing_IL12-GEMy_Lung

growth_protocol: C57BL/6 mice were injected orthotopically with 5E5 M3-9-M ffluc-mCherry rhabdomyosarcoma tumor cells in the gastrocnemius muscle of the leg.

extract_protocol:
Lungs were harvested 3 days post IL12-GEMy treatment, 15 days post primary tumor inoculation. Flash frozen lungs were homogenized in TRIzol and RNA was isolated by chloroform extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with 8E6 IL12-secreting genetically engineered myeloid cells (IL12-GEMys) intravenously on day 12 post tumor inoculation.

tag: strain

tag: disease state

value: M3-9-M Tumor-Bearing

tag: treatment

tag: tissue

value: lung


title: PDX_RB_115

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

description:
Trizol
RNA
RNA-sequencing

data_processing:
Single cell RNA-seq reads from tumors and normal retina samples were aligned using the cell ranger pipeline (v3.0.2) to the hg19 reference data (v3.0.0).
RNA sequencing was aligned using STAR aligner and quantified using RSEM.
Methylation Analysis: Raw data files generated by the iScan array scanner were read and preprocessed by using “minfi” Bioconductor package.
Genome_build: hg19

source_name: O-PDX

extract_protocol:
Trizol (LifeTech #15596018) was used to extact RNA
Norrie et al. RNAseq_RSEM_TPM.xlsx

value: xenograft


title: fetal_retina_FW-18

description:
Trizol
RNA
RNA-sequencing

value: retina


title: PDX_RB_127

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_134

description:
Trizol
RNA
RNA-sequencing


title: PDX_MAST_116

description:
Trizol
RNA
RNA-sequencing


title: Tumor_RB_116

description:
Trizol
RNA
RNA-sequencing

source_name: Retinoblastoma

value: tumor


title: NOMEseq_MM1S_A485_32hours_Replicate1


title: PDX_RB_120

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_124

description:
Trizol
RNA
RNA-sequencing


title: Tumor_MAST_232

description:
Trizol
RNA
RNA-sequencing


title: PDX_MAST_216

description:
Trizol
RNA
RNA-sequencing


title: fetal_retina_FW-23

description:
Trizol
RNA
RNA-sequencing


title: Tumor_RB_115

description:
Trizol
RNA
RNA-sequencing


title: PDX_MAST_232

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_132

description:
Trizol
RNA
RNA-sequencing


title: Tumor_RB_139

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_135

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_90

description:
Trizol
RNA
RNA-sequencing


title: fetal_retina_FW-14

description:
Trizol
RNA
RNA-sequencing


title: NOMEseq_MM1S_A485_2hours_Replicate1


title: PDX_RB_154

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_157

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_152

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_150

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_149

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_147

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_148

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_144

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_143

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_139

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-4-T-A

description:
Trizol
RNA
RNA-sequencing

source_name: Retinal Organoid-Derived Retinoblastoma

extract_protocol:
Trizol (LifeTech #15596018) was used to extact RNA
Norrie et al. RB_RNAseq.xlsx

value: organoid derived tumor


title: PDX_RB_125

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-15

description:
Trizol
RNA
RNA-sequencing

source_name: induced pluripotent stem cell

extract_protocol:
Trizol (LifeTech #15596018) was used to extact RNA
Norrie et al. RNAseq_RSEM_TPM.xlsx
Norrie et al. iPSC_RNAseq.xlsx

value: iPSC line


title: SJRB-iPSC-11

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-10

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_142

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_145

description:
Trizol
RNA
RNA-sequencing


title: hESC_H9

description:
Trizol
RNA
RNA-sequencing

source_name: human embryonic stem cell

value: ESC line


title: SJRB-iPSC-8-T-B

description:
Trizol
RNA
RNA-sequencing

extract_protocol:
Trizol (LifeTech #15596018) was used to extact RNA
Norrie et al. RNAseq_RSEM_TPM.xlsx
Norrie et al. RB_RNAseq.xlsx


title: PDX_RB_136

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-3

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_140

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-12

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-1CR-T-A

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-4

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_151

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-2

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-8

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-1CR-T-A1

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-8CR-T-B

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-13

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-14

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-6

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-5

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_153

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-6CR-T-A

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-9

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-7

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-4CR_Tumor

description:
Trizol
RNA
RNA-sequencing


title: H9CR-T-D

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-1

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-4CR-T-A

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-4CR-T-D

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_128

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_129

description:
Trizol
RNA
RNA-sequencing


title: H9CR-T-A

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_122

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_116

description:
Trizol
RNA
RNA-sequencing


title: H9CR-T-C

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-8-T-A

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-8CR-T-A

description:
Trizol
RNA
RNA-sequencing


title: H9-Teratoma

description:
Trizol
RNA
RNA-sequencing

source_name: Teratoma

value: teratoma


title: SJRB-iPSC-4CR-T-A1

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-4CR-T-C 2

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-4CR-T-B

description:
Trizol
RNA
RNA-sequencing


title: Adult_Retina_Sample_2

description:
Trizol
RNA
RNA-sequencing

source_name: Human Retina


title: PDX_RB_138

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-4CR-T-C 1

description:
Trizol
RNA
RNA-sequencing

extract_protocol:
Trizol (LifeTech #15596018) was used to extact RNA
Norrie et al. RB_RNAseq.xlsx
Norrie et al. RB_RNAseq.xlsx


title: Adult_Retina_Sample_1

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_130

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-7

description:
Trizol
RNA
RNA-sequencing

source_name: Retinal Organoid

extract_protocol:
Trizol (LifeTech #15596018) was used to extact RNA
Norrie et al. RNAseq_RSEM_TPM.xlsx
Norrie et al. Organoid_RNAseq.xlsx

value: Day 45 organoid


title: D45_Organoid_SJRB-iPSC-10

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-6

description:
Trizol
RNA
RNA-sequencing


title: SJRB-iPSC-15CR_Tumor

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-14

description:
Trizol
RNA
RNA-sequencing


title: H9CR-T-B

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_121

description:
Trizol
RNA
RNA-sequencing


title: PDX_RB_133

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-5

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-9

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-11

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-3

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-15

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-13

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-4

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-1

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-2

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-12

description:
Trizol
RNA
RNA-sequencing


title: D45_Organoid_SJRB-iPSC-8

description:
Trizol
RNA
RNA-sequencing


title: RB_175

description:
10x genomics 3’ scRNA-seq
3’ RNA
single cell RNA-sequence

extract_protocol:
Tumor and xenograft samples were dissociated using an enzymatic tumor dissociation. The tumor was added to 10 mL of RPMI with 600 μl of trypsin (10 mg/ml, Sigma Cat#T9935) and incubated at 37C for 10 minutes. 600μL of each Soybean Trypsin Inhibitor (10 mg/ml) DNase I (2mg/mL) and magnesium chloride (1 M) were added and the tumor suspension was filtered through a 40 uM cell strainer and centrifuged at 500 rcf. The pellet was resuspended in 5 ml of red blood cell lysis solution (5 Prime Cat#2301310) and incubated at RT for 10 minutes. 5mL PBS -/- with 10% FBS was added and the cell suspension centrifuged at 500 rcf for 5 minutes. Supernatant was discarded and cell pellet was resuspended in RPMI. The cell suspension was then layered on top of a BSA cushion (4% BSA in REM) and centrifuged at 500g for 10 minutes. The supernatant was removed and the cells were resuspended at ~1000 cells/uL and counted.
10x genomics 3’ scRNA-seq v3.1 was used to construct the single cell library


title: SJRB-iPSC-1CR_T_A1


title: H9CR_T_A1


title: RB_174


title: D45_Organoid_H9_D45

description:
Trizol
RNA
RNA-sequencing


title: RB_166


title: RB_168


title: RB_167


title: Human_Retina_Sample_5


title: Human_Retina_Sample_3


title: RB_128_Rep_1


title: RB_129_Rep_2


title: RB_129_Rep_1


title: RB_122_Rep_2


title: RB_116_Rep_2


title: RB_116_Rep_1


title: RB_134_Rep_2


title: RB_138_Rep_1


title: RB_138_Rep_2


title: RB_169


title: RB_130_Rep_1


title: RB_130_Rep_2


title: RB_135_Rep_2


title: RB_122_Rep_1


title: RB_135_Rep_1


title: Human_Retina_Sample_2


title: RB_121_Rep_1


title: RB_121_Rep_2


title: RB_134_Rep_1


title: RB_124_Rep_1


title: Human_Retina_Sample_1


title: Human_Retina_Sample_4


title: RB_124_Rep_2


title: RB_133_Rep_1


title: RB_128_Rep_2


title: scRNAseq_MSKCLL156_6hours_DMSO_A485_Hashtag

data_processing:
For scRNA-seq, Pre-processing of scRNA-seq data was performed using Cell Ranger v4.0.0. Files were processed using the cell ranger count function mapping to the hg38 genome (arguments: --chemistry=fiveprime). Clustering was performed using Seurat V3 and cells were filtered based on nFeature_RNA greater than 200 and  less than 2500, percent of mitochondrial reads  less than 10 and nCount_RNA greater than 1000. The two samples were integrated using the standard worklow.
For scATAC-seq, Pre-processing of snATAC-seq were performed using the cell ranger v4.0.0 and reads were mapped to the hg38 genome. Cell ranger output was converted to snap files as outlined in Snaptools. Cells were filtered based on read count greater than 3000 and less than 30000 and fraction of reads in promoters greater than 20%. Samples were integrated using Harmony (Korsunsky et al., 2019) in the SnapATAC framework using binary counts in 5kb bins across the genome
For scRNA-seq,Differential gene expression between conditions was performed using the FindMarkers function (|logFC| > 0.75 and adjP < 0.05). Heatmap visualization based on normalized genes counts across cells in each condition for each cluster inferCNV of the Trinity CAT project was used to analyze large scale copy number variations (Patel et al., 2014; Tirosh et al., 2016). T-cells and myeloid cells were used as normal reference and the following parameters were used for the run function: cutoff=0.1, denoise=TRUE, HMM=TRUE.
For scATAC-seq, Visualization based on UMAP from SnapATAC pipeline and cells were colored based on label transferred from scRNA-seq using Seurat V3. Integration of scRNA-seq and snATAC-seq data was based gene activity score for snATAC-seq data and prediction score greater than or equal to 0.5. Peak calling for snATAC-seq performed using the runMACS function in SnapATAC with the following parameters: --nomodel --slocal 1000 --call-summits --qval 0.01 -B –SPMR.
Genome_build: Hg38
Supplementary_files_format_and_content: scATAC_meta_data.RDS (R Data file- scATAC-seq data)
scATAC_pmat.RDS (R Data file- peak by cell matrix for scATAC-seq data)
A485_DMSO_merged_narrow_peaks.bed (BED file of merged peaks for scATAC-seq data)
scATAC_bmat.RDS (R data file- binary 5kb bin matrix for scATAC-seq data)
scRNA_Seurat_obj.RDS (Seurat object for scRNA-seq data)

molecule: other

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: For scRNA-seq, The peripheral blood mononuclear cells (PBMC) fraction was isolated from a CLL specimen by Ficoll Paque Plus (Amersham Biosciences, Piscataway, USA). Buffy layers containing the PBMCs were removed and the red blood cells were lysed using red blood cell lysis buffer (10mM KHCO3, 150mM NH4Cl and 0.1mM EDTA, pH 8.0) for 5 minutes at 37oC followed by a wash with sterile phosphate buffer saline (PBS). Cells were then cultured in RPMI-1640 media supplemented with 10% heat inactivated bovine calf serum, 2 mM L-glutamine and 100 U/ml penicillin/streptomycin for 6 hours in the presence of A-485 (1µM) or DMSO vehicle. Following 6 hours incubation, samples for scRNA-seq were first subjected to Fc receptor blocking (using the Human TruStain FcX reagent; BioLegend) and barcoded using TotalSeq-C cell hashing antibodies (TotalSeq-C0251 for DMSO treatment and TotalSeq-C0252 for A-485 treatment; BioLegend), following the manufacturers recommendations. Samples were then pooled and resuspended at 1000 cells/µL in PBS+0.04% BSA and passed to the Integrated Genomics Operation (IGO; Memorial Sloan Kettering Cancer Center) for library preparation.

extract_protocol:
For scATAC-seq, Nuclei were incubated with transposition mix for 60 minutes at 37°C and then loaded onto Chromium Chip. GEM generation and library preparation of up to 10,000 nuclei proceeded using the Chromium Single Cell ATAC Library & Gel Bead Kit according to the manufacturer’s protocol with 11 cycles of PCR.
For scRNA-seq, the single cell suspension was loaded onto Chromium Chip A (10X Genomics PN 230027) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 6,481 cells proceeded using the Chromium Single Cell 5’ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 11 cycles and 41ng of the material was used to prepare sequencing libraries with 14 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a 28/91 paired end paired end run using the NovaSeq 6000 S1 Reagent Kit (100 cycles) (Illumina).

treatment_protocol: For scATAC-seq,The peripheral blood mononuclear cells (PBMC) fraction was isolated from a CLL specimen by Ficoll Paque Plus (Amersham Biosciences, Piscataway, USA). Buffy layers containing the PBMCs were removed and the red blood cells were lysed using red blood cell lysis buffer (10mM KHCO3, 150mM NH4Cl and 0.1mM EDTA, pH 8.0) for 5 minutes at 37oC followed by a wash with sterile phosphate buffer saline (PBS). Cells were then cultured in RPMI-1640 media supplemented with 10% heat inactivated bovine calf serum, 2 mM L-glutamine and 100 U/ml penicillin/streptomycin for 6 hours in the presence of A-485 (1µM) or DMSO vehicle. Following 6 hours incubation, samples for snATAC-seq were first subjected to nuclei isolation with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin, 1% BSA) and wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) in accordance with the 10x Genomics Nuclei Isolation for Single Cell ATAC Sequencing protocol (CG000169, Rev D). Nuclei number and quality was assessed using Trypan blue and the Countess II Automated Cell Counter (ThermoFisher). Following QC, nuclei were then resuspended at 5,000 nuclei/µL in 1X diluted nuclei buffer (10x Genomics) and used as input for the 10x Genomics Chromium Next GEM Single Cell ATAC Library Kit (PNs-1000176, 1000162, 1000212).

value: mixed samples (DMSO or A-485 (1µM))

tag: assay

value: scRNA-seq

tag: hashtag oligos

value: mixed samples (DMSO=TotalSeq-C antibody #1 (GTCAACTCTTTAGCG), A-485=TotalSeq-C antibody #2 (TGATGGCCTATTGGG))


title: scRNAseq_MSKCLL156_6hours_DMSO_A485_Gene_Expression


title: scATACAseq_MSKCLL156_6hours_DMSO

description:
scATAC_meta_data.RDS
scATAC_pmat.RDS
scATAC_bmat.RDS
A485_DMSO_merged_narrow_peaks.bed

value: scATAC-seq


title: COV-546

city: Bronx

first: Betsy

last: Herold

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

data_processing:
Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA) software.
Primary analysis was performed using Illumina's CASAVA 1.8.2 software suite.
Alignment to the human reference transcriptome was performed in Salmon using gencode v33.
Differential expression analysis was performed in DESeq2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing transcript name, length, effective length, TPM, and number of reads.

source_name: NP Swab cells

extract_protocol:
RNA was isolated from cryopreserved cells using the miRNeasy Micro kit (QIAGEN, 217084). Samples with sufficient RNA quantity and quality were used for analysis. Libraries were prepared at the Yale Center for Genome Analysis using the NEBNext rRNA Depletion kit (E6310L). Individual samples or pools from 2 patients of similar age and outcome (n = 4 pools, adults) were normalized to 1.2 nM and loaded on an Illumina NovaSeq S4 flow cell to generate 30 M read-pairs per sample.
RNA libraries were prepared for sequencing in accordance with standard Illumina library preparation protocols.

treatment_protocol: The swab was transferred to a tube containing media supplemented with 13 μM dithiothreitol to inactivate virus and then incubated in a thermomixer for 10 minutes at 37°C and 500 RPM. The cells were washed and frozen in 500 μL 90% FBS/10% DMSO.

tag: diagnosis

value: cells isolated from nasopharyngeal swabs

tag: age

tag: Sex

value: female

tag: respiratory score


title: COV-531


title: POOL 4


title: POOL 3

value: male


title: POOL 2


title: POOL 1


title: OmniC_HeLa_6hours_A485_Replicate2

data_processing:
For visualization purposes, reads were mapped to the Hg38 genome, filtered for Omni-C artifacts, duplicates marked, and valid pairs sorted following the manufacturers recommendations using the omni-c_qc.bash script (https://github.com/dovetail-genomics/).
Biological replicates were subsequently merged using Pairtools merge. To create contact matrices, the contact_map.sh script (https://github.com/dovetail-genomics/) was used to filter pairs and create a Juicer-Tools compatible file.
The resultant .hic files were loaded into Juicebox and used to create representative contact matrices (visualized at 50kb resolution).
For differential interaction  testing, the diffHic pipeline described above was followed with the following exceptions. Omni-C was treated as DNase Hi-C and FASTQ files were mapped to the Hg38 genome using an alternative iterative mapping approach to account for restriction enzyme-free proximity ligation, which is provided by the iter_map.py python script (https://github.com/LTLA/diffHic/).
Genome_build: Hg38
Supplementary_files_format_and_content: .Cool

source_name: Cervical adenocarcinoma

growth_protocol: HeLa cells were grown under standard in vitro conditions.

extract_protocol:
Samples were then processed using the Omni-C™ kit (Dovetail Genomics®) to perofrm crosslinking, in situ Nuclease digestion, proximity ligation followed by library preparation (end repair, adapter ligation, and DNA purification), and finally ligation capture and index PCR, all according to the manufactures instructions.
Pooled Omni-C™ libraries were sequenced on the NovaSeq 6000 (Ilumina) in a PE150/150 run. An average of 200-250 million paired reads was generated per sample.

treatment_protocol: HeLa cells were treated in technical duplicate with DMSO or A-485 (1µM) for 6 hours prior to being collected and washed once in ice-cold PBS and flash frozen (1e6 cells per condition).

value: HeLa

value: 6 hours


title: OmniC_HeLa_6hours_DMSO_Replicate2

value: DMSO


title: OmniC_HeLa_6hours_A485_Replicate1


title: OmniC_HeLa_6hours_DMSO_Replicate1


title: COV-543


title: COV-555


title: COV-554


title: scATACAseq_MSKCLL156_6hours_A485


title: COV-547


title: COV-549


title: COV-551


title: COV-541


title: COV-533


title: COV-526


title: 3D_N_rep3

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
hisat2
featureCounts
Deseq2
Genome_build: rheMac2
Supplementary_files_format_and_content: text file

organism: Macaca mulatta

source_name: iPSC-CM_engineered heart tissue (EHT) (3D)_normoxia

growth_protocol: Both NHP hiPSC-CM monolayer culture and EHT were cultured in RPMI+B27 insulin+

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany)
A cDNA library was prepared using the Ion Total RNA-Seq Kit v2 and sequenced by the Ion Proton method using Ion PI Hi-Q Sequencing kit.

treatment_protocol: Hypoxic treatment in anaerobic pouches for 24 hour, then 24 hour after medium refreshement

tag: cell type

value: Non-Human Primate Induced Pluripotent Stem Cell-Derived Cardiomyocytes (NHP iPSC-CMs)

tag: culture condition

value: engineered heart tissue (EHT) (3D)

tag: oxygen condition

value: normoxia


title: 3D_N_rep2


title: 3D_H_rep3

source_name: iPSC-CM_engineered heart tissue (EHT) (3D)_hypoxia

value: hypoxia


title: 3D_H_rep1


title: 3D_N_rep1


title: 2D_N_rep2

source_name: iPSC-CM_monolayer culture (2D)_normoxia

value: monolayer culture (2D)


title: COV-525


title: 2D_H_rep3

source_name: iPSC-CM_monolayer culture (2D)_hypoxia


title: COV-523


title: 2D_N_rep3


title: COV-522


title: COV-524


title: 2D_N_rep1


title: 2D_H_rep1


title: 2D_H_rep2


title: COV-532


title: 3D_H_rep2


title: Naive KOc23-2

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description:
Naive KOc23-2
ESRG knockout embryonic stem cell line clone 23 in naive condition, passage 8
70_DESeq2_normalized_counts_Naive.csv

data_processing:
Illumina bcl2fastq (v2.20.0.422) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.18) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.11.2) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.6.1) and its package DESeq2 (v1.24.0) were performed.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including DESeq2 nomalized count values for each sample.

growth_protocol: Primed human pluripotent stem cells were maintained in StemFiT media (Ajinomoto) supplemented with 100 ng/ml bFGF on Laminin 511 E8 fragment-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2.   Naive human pluripotent stem cells were cultured in NDiff227 media (Takara) supplemented with 1 μM PD325901, 10 ng/ml of recombinant human leukemia inhibitory factor, 1 μM Gö6983 and 2 μM XAV939 on mitomycin C-treated MEF feeder.

extract_protocol:
RNA was prepared using the miReasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
Illumina TruSeq Stranded Total RNA Library Prep

value: Human pluripotent stem cell line in naive condition

tag: genotype/variation

value: knockout


title: Naive KOc23-3

description:
Naive KOc23-3
ESRG knockout embryonic stem cell line clone 23 in naive condition, passage 9
70_DESeq2_normalized_counts_Naive.csv


title: COV-527


title: Naive KOc23-1

description:
Naive KOc23-1
ESRG knockout embryonic stem cell line clone 23 in naive condition, passage 7
70_DESeq2_normalized_counts_Naive.csv


title: Naive KOc18-3

description:
Naive KOc18-3
ESRG knockout embryonic stem cell line clone 18 in naive condition, passage 9
70_DESeq2_normalized_counts_Naive.csv


title: Naive WTc28-3

description:
Naive WTc28-3
ESRG wild-type embryonic stem cell line clone 28 in naive condition, passage 9
70_DESeq2_normalized_counts_Naive.csv

value: wild type


title: Naive KOc10-2

description:
Naive KOc10-2
ESRG knockout embryonic stem cell line clone 10 in naive condition, passage 8
70_DESeq2_normalized_counts_Naive.csv


title: RNA-seq_AA-I-LL-2

city: Potsdam

first: Stephan

last: Greiner

state: Branbenburg

address: Max-Planck-Institute of Molecular Plant Physiology

department: Organelle Biology, Biotechnology and Molecular Ecophysiology

country: Germany

institute: MPI for Molecular Plant Physiology

data_processing:
Ribo-seq & RNA-seq:
Fastq quality control : Quality control of Ribo-seq and RNA-seq sequencing data  was performed using FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Barcode, Adapter and UMI removal : 3' adapter trimming was applied to both data sets using Flexbar v2.5 (Dodt et al., 2012) with default parameters and the corresponding adapter-barcode-combined sequences. To remove a potential PCR bias from the Ribo-seq data set, we extracted four bases from the 3’- and 5’-unique molecular identifier (UMI) to evaluate their binding to the read identifier.
Alignment step : All Ribo-seq data, as well as RNA-seq data for computing translation efficiency, were then aligned against their respective plastome (I-johSt = AJ271079.4; II-suavG = EU262889.2) using STAR v2.7.0a with slightly  adapted indexing parameters (--genomeSAindexNbases 8, --genomeChrBinNbits 17) (Dobin et al., 2013).
Post mapping processing and filtering : Subsequently, samtools v1.10 was used to remove secondary alignments, to sort and to index them, and to generate mapping, and gene-wise count statistics (flagstat & idxstat, respectively). Conversion of transcriptomic bam  files (harboring only reads mapped to exons) to bed files was done using bamToBed from the bedtools v2.29.2 (Quinlan and Hall, 2010), adding read length as additional column. Usable reads for all follow-up analysis were defined by the following criteria : (i) removing tRNA and rRNA-associated reads as well as reads shorter than 20 bases and longer than 50 bases; (ii) read de-duplication based on chromosomal location and same UMIs (by sorting bed files on the columns scaffold_id, start/end position and both columns having the UMIs using groupBy to take only the first entry of each group identical entries (-o first); (iii) remain only reads with mapping quality equal to 255 (means unique mapped in the context of the STAR mapper). Resulting bed files were loaded into R to generate different types of plots.
Genome_build: https://ncbi.nlm.nih.gov/nuccore/AJ271079.4 and https://ncbi.nlm.nih.gov/nuccore/EU262889.2
Supplementary_files_format_and_content: Ribo-seq: Bed format; column 1= gene name, column 2= start coordinate, column 3 = end coordinate, column 4 = <4 bp 3' UMI>:<4 bp 5'UMI>, column 5 = read length, column = strand
Supplementary_files_format_and_content: RNA-seq: Bed format; column 1= gene name, column 2= start coordinate, column 3 = end coordinate, column 4 = read identifier, column 5 = mapping quality, column = strand

organism: Oenothera elata subsp. hookeri

source_name: rosette leaves, 21-30 day old

growth_protocol:
generation of plant lines: Incompatible, yellow green (AB-I) and compatible, green (AB-II) plants were obtained from F1 seeds of crosses between the wild type (AA-l) or the green chloroplast substitution line (AA-II) of johansen Standard as the seed parent and wild type line grandiflora Tuscaloosa (BB-III) as the pollen parent. Here, AA-I x BB-III yielded AB-I plants, and AA-II x BB-III produced AB-II plants. Selection against the paternally transmitted plastome III was done using appropriate makers markers.
Oenothera plants were cultivated in a glasshouse as previously described (Greiner and Köhl 2014, Front Plant Sci 5: 38).

extract_protocol:
Total RNA isolations from evening primroses were performed employing protocols specially developed for their mucilage and phenolic compound rich tissue, described in Massouh et al. 2016, Plant Cell 28: 911-929. For RNA-seq analyses, total RNA was purified from residual DNA contamination by digestion employing the Ambion® Turbo DNA-freeTM Kit.
monosome, polysome, and ribosome footprint isolation: The procedure for monosome, polysome, and ribosome footprint isolation are precisely described in Zupok et al. (2021) A photosynthesis operon in the chloroplast genome drives speciation in evening primroses. Plant Cell, in press.
Ribo-seq libraries were prepared using the NEXTflex Small RNA-Seq Kit v3.
RNA-seq libraries were prepared using the Zymo Research Zymo-Seq RiboFree Total RNA Library Kit.

treatment_protocol: AA-I, AA-II, AB-I, and AB-II plants were cultivated in soil in growth chambers using a 16-h light/8 h-darkness cycle and 24°C at low light intensities (~150 µE m-2s-1). At the beginning of the early rosette stage (cf. Greiner and Köhl 2014, Front Plant Sci 5: 38), plants were transferred to higher light intensities, i.e., 300 uE m-2s-1 (low light, LL) and 450 uE m-2s-1 (high light, HL) and then kept under the same growth regime.

value: 300 uE, low light

tag: replicate

tag: genotype

value: AA-I

tag: plant type

tag: phenotype

value: green

tag: nuclear genome type

value: AA

tag: plastome type

value: I

tag: nuclear genome

value: hjohansen Standard.hjohansen Standard

tag: chloroplast genome

value: I-johSt

tag: nucleus donor strain(s)

value: johansen Standard

tag: chloroplast donor strain

tag: barcode

value: CCATTCGA


title: RNA-seq_AA-I-LL-1

tag: treatment

value: TCGTAGTG


title: Naive KOc10-1

description:
Naive KOc10-1
ESRG knockout embryonic stem cell line clone 10 in naive condition, passage 7
70_DESeq2_normalized_counts_Naive.csv


title: RNA-seq_AA-II-HL-3

value: 450 uE, high light

value: AA-II

value: chloroplast substitution line

value: II

value: II-suavG

value: suaveolens Grado

value: GTATGTTC


title: RNA-seq_AA-II-HL-2

value: ACGCACCT


title: RNA-seq_AA-I-HL-3

value: AA-I

value: wild type

value: TTCCTGTT


title: RNA-seq_AA-I-HL-2

value: green

value: AA

value: I

value: GGAGCGTC


title: RNA-seq_AA-II-HL-1

value: hjohansen Standard.hjohansen Standard

value: johansen Standard

value: TACTCATA


title: Naive WTc28-1

description:
Naive WTc28-1
ESRG wild-type embryonic stem cell line clone 28 in naive condition, passage 7
70_DESeq2_normalized_counts_Naive.csv

value: Human pluripotent stem cell line in naive condition


title: Naive WTc21-3

description:
Naive WTc21-3
ESRG wild-type embryonic stem cell line clone 21 in naive condition, passage 9
70_DESeq2_normalized_counts_Naive.csv


title: RNA-seq_AA-I-LL-3

value: 300 uE, low light

value: I-johSt

value: TAAGTGGT


title: RNA-seq_AA-I-HL-1

value: 450 uE, high light

value: AAGATACT


title: Naive WTc21-1

description:
Naive WTc21-1
ESRG wild-type embryonic stem cell line clone 21 in naive condition, passage 7
70_DESeq2_normalized_counts_Naive.csv


title: Ribo-seq_AA-II-HL-3

data_processing:
library strategy: Ribo-seq
Ribo-seq & RNA-seq:
Fastq quality control : Quality control of Ribo-seq and RNA-seq sequencing data  was performed using FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Barcode, Adapter and UMI removal : 3' adapter trimming was applied to both data sets using Flexbar v2.5 (Dodt et al., 2012) with default parameters and the corresponding adapter-barcode-combined sequences. To remove a potential PCR bias from the Ribo-seq data set, we extracted four bases from the 3’- and 5’-unique molecular identifier (UMI) to evaluate their binding to the read identifier.
Alignment step : All Ribo-seq data, as well as RNA-seq data for computing translation efficiency, were then aligned against their respective plastome (I-johSt = AJ271079.4; II-suavG = EU262889.2) using STAR v2.7.0a with slightly  adapted indexing parameters (--genomeSAindexNbases 8, --genomeChrBinNbits 17) (Dobin et al., 2013).
Post mapping processing and filtering : Subsequently, samtools v1.10 was used to remove secondary alignments, to sort and to index them, and to generate mapping, and gene-wise count statistics (flagstat & idxstat, respectively). Conversion of transcriptomic bam  files (harboring only reads mapped to exons) to bed files was done using bamToBed from the bedtools v2.29.2 (Quinlan and Hall, 2010), adding read length as additional column. Usable reads for all follow-up analysis were defined by the following criteria : (i) removing tRNA and rRNA-associated reads as well as reads shorter than 20 bases and longer than 50 bases; (ii) read de-duplication based on chromosomal location and same UMIs (by sorting bed files on the columns scaffold_id, start/end position and both columns having the UMIs using groupBy to take only the first entry of each group identical entries (-o first); (iii) remain only reads with mapping quality equal to 255 (means unique mapped in the context of the STAR mapper). Resulting bed files were loaded into R to generate different types of plots.
Genome_build: https://ncbi.nlm.nih.gov/nuccore/AJ271079.4 and https://ncbi.nlm.nih.gov/nuccore/EU262889.2
Supplementary_files_format_and_content: Ribo-seq: Bed format; column 1= gene name, column 2= start coordinate, column 3 = end coordinate, column 4 = <4 bp 3' UMI>:<4 bp 5'UMI>, column 5 = read length, column = strand
Supplementary_files_format_and_content: RNA-seq: Bed format; column 1= gene name, column 2= start coordinate, column 3 = end coordinate, column 4 = read identifier, column 5 = mapping quality, column = strand

value: AA-II

value: chloroplast substitution line

value: II

value: II-suavG

value: suaveolens Grado

value: CGATGT


title: Naive WTc21-2

description:
Naive WTc21-2
ESRG wild-type embryonic stem cell line clone 21 in naive condition, passage 8
70_DESeq2_normalized_counts_Naive.csv

value: wild type


title: Ribo-seq_AA-I-HL-2

value: AA-I

value: green

value: AA

value: I

value: ACTGAT


title: Ribo-seq_AA-I-HL-1

value: hjohansen Standard.hjohansen Standard

value: johansen Standard

value: CGTACG


title: Naive KOc18-2

description:
Naive KOc18-2
ESRG knockout embryonic stem cell line clone 18 in naive condition, passage 8
70_DESeq2_normalized_counts_Naive.csv

value: Human pluripotent stem cell line in naive condition

value: knockout


title: Naive KOc18-1

description:
Naive KOc18-1
ESRG knockout embryonic stem cell line clone 18 in naive condition, passage 7
70_DESeq2_normalized_counts_Naive.csv


title: Naive KOc10-3

description:
Naive KOc10-3
ESRG knockout embryonic stem cell line clone 10 in naive condition, passage 9
70_DESeq2_normalized_counts_Naive.csv


title: Naive WTc1-2

description:
Naive WTc1-2
ESRG wild-type embryonic stem cell line clone 1 in naive condition, passage 8
70_DESeq2_normalized_counts_Naive.csv


title: Ribo-seq_AA-I-HL-3

value: 450 uE, high light

value: I-johSt

value: TAATCG


title: Naive WTc1-3

description:
Naive WTc1-3
ESRG wild-type embryonic stem cell line clone 1 in naive condition, passage 9
70_DESeq2_normalized_counts_Naive.csv


title: Naive WTc1-1

description:
Naive WTc1-1
ESRG wild-type embryonic stem cell line clone 1 in naive condition, passage 7
70_DESeq2_normalized_counts_Naive.csv


title: Naive WTc28-2

description:
Naive WTc28-2
ESRG wild-type embryonic stem cell line clone 28 in naive condition, passage 8
70_DESeq2_normalized_counts_Naive.csv


title: PAO1161 EV_3 RNA-seq_reused

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description: gene expression data from empty vector control

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.1 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.28.0.
Genome_build: CP032126
Supplementary_files_format_and_content: Raw counts of sequencing (FeatureCounts output summarized for all samples)(3027_Raw_counts.csv ).
A table with DE data for all genes and normalized abundance measurements (EdgeR output) (3027_norm_counts.csv). This file also includes estimated Fold Change - expression fold change comparing PA3027+ versus EV+ samples for all genes as gene information.

organism: Pseudomonas aeruginosa

source_name: empty vector

growth_protocol: The competent P. aeruginosa PAO1161 cells were prepared as described previously (Irani and Rowe, 1997) and transformed using pKKB1.11 carrying lacIQ-tacp-PA3027 and empty vector pAMB9.37 (lacIQ-tacp) to obtain PAO1161/pKKB1.11 (lacIQ-tacp-PA3027) and PAO1161/pAMB9.37 (lacIQ-tacp), respectively. Transformants were selected on L agar plates supplemented with 150 μg/ml-1 chloramphenicol and were verified by isolation of plasmid DNA and its digestion. Bacteria from single colonies were used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures with supplementation (75 g/ml-1 chloramphenicol) and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth with chloramphenicol (75 g/ml-1) and IPTG (0.05 mM) and grown with shaking at 37oC. Samples from the cultures were taken at regular intervals to measure the optical density at 600 nm (OD600). Aliquots of 2 ml from logarithmic phase cultures (OD600 0.5) were subjected to RNA extraction.

extract_protocol:
Total RNA was isolated from three independent replicates of each strain. 2 ml of cultures which reached optical density 0.5 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
Ribosomal RNA was depleted using RiboZero Bacteria kit (Illumina). Obtained mRNA was used for cDNA library construction using KAPA Stranded RNASeq kit. Library was further quality checked on 1% agarose gel and concentration was measured using qPCR KAPA Library Quantification Kit.

treatment_protocol: All cultures were incubated at 37°C in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.05 mM IPTG with shaking until reaching exponential phase of growth (OD600= 0.5).

tag: strain

value: PAO1161 carrying pAMB9.37 (lacIQ-tacp)

value: empty vector

tag: growth phase

value: logarithmic phase of liquid culture


title: PAO1161 EV_2 RNA-seq_reused


title: Primed KOc23-2

description:
Primed KOc23-2
ESRG knockout embryonic stem cell line clone 23 in primed condition, passage 49.2.9
70_DESeq2_normalized_counts_Primed.csv

tag: cell type

value: Human pluripotent stem cell line in primed condition


title: Primed KOc23-3

description:
Primed KOc23-3
ESRG knockout embryonic stem cell line clone 23 in primed condition, passage 49.2.10
70_DESeq2_normalized_counts_Primed.csv


title: Primed KOc18-3

description:
Primed KOc18-3
ESRG knockout embryonic stem cell line clone 18 in primed condition, passage 49.2.10
70_DESeq2_normalized_counts_Primed.csv


title: Primed KOc23-1

description:
Primed KOc23-1
ESRG knockout embryonic stem cell line clone 23 in primed condition, passage 49.2.8
70_DESeq2_normalized_counts_Primed.csv


title: Primed KOc18-2

description:
Primed KOc18-2
ESRG knockout embryonic stem cell line clone 18 in primed condition, passage 49.2.9
70_DESeq2_normalized_counts_Primed.csv


title: PA3027 overproducer (PA3027), biological rep2

description: gene expression data from PA3027 overproducer

source_name: PA3027 overproducer (PA3027)

value: PAO1161/pKKB1.11 (lacIQ-tacp-PA3027)

value: PA3027 overproducer, biological rep2


title: PA3027 overproducer (F-PA3027), replicate 3

description: ChIP DNA data from FLAG-PA3027 overproducer

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO1161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
Obtained *.sam files were sorted (samtools sort -n), run through samtools fixmate with the -m option, again sorted (samtools sort) and duplicates were marked with samtools markdup. Samtools ver. 1.9 was used.
The files were indexed and used to generate coverage *.bigwig files, normalized to 1× sequencing depth (RPGC), without binning and smoothing using the bamCoverage tool ver 3.3.0 included in deepTools.
PA3027 peaks were identified by comparing combined replicates of IP samples (F-PA3027) for each strain with negative control (empty vector EV-F) samples using the callpeak function of MACS2 ver 2.1.2 with default options for paired-end .BAM files, and 0.05 as false discovery rate (FDR) cut off.
Genome_build: CP032126
Supplementary_files_format_and_content: Processed files in bigwig format represent normalized coverages of individual base pairs in the P. aeruginosa PAO1161 genome.
Reference genome is enclosed in fasta format (CP032126.fa) and the annotation used is enclosed as a .bed (CP032126.bed). A modified .bed file with PAO1161 feature names changed to the names of corresponding PAO1 genes (PA… format) is included for convenience of data browsing e.g. using IGV (CP032126_PA_names.bed). These files are available on GSE163233.

source_name: PA3027 overproducer (F-PA3027)

growth_protocol: P. aeruginosa PAO1161 ΔPA3027 strain carrying pKKB1.12 (lacIQ-tacp-flag-PA3027) as well as control strain PAO1161 carrying pABB28.1 (lacIQ-tacp-flag) were obtained by conjugation of PAO1161 (leu-, r-, RifR) and E. coli S-17 donor strain carrying appropriate plasmid. Conjugants were selected on L agar plates supplemented with 300 μg/mL rifampicin and 150 μg/mL chloramphenicol. Two independent overnight cultures from each strain were inoculated from single colonies and grown overnight with shaking at 37oC. After that they were diluted 1:100 in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.05 mM IPTG to induce the expression of flag-PA3027, grown with shaking at 37oC. Bacteria were grown until reaching exponential phase of growth (OD600=0.5).

extract_protocol:
Chromatin immunoprecipitation (ChIP) protocol was based on the method described earlier (Kawalek et al, 2018; Nucleic Acids Res. 46:9, 4592-4606). Two cultures of each strain with similar OD600 were combined, formaldehyde was added from a 37% stock to a final concentration of 1%, and the cultures were kept for 10 min at room temperature with gentle inverting. Glycine was added to a final concentration of 0.5 M and the cultures were incubated for 5 min at room temperature with gentle rotation. Cells were then harvested by centrifugation (20 min, 3000 x g, 25 mL of culture in 50 mL conical tubes, 4 tubes per strain), washed twice with ice-cold Tris-buffered saline (25 mM Tris-HCl, 150 mM NaCl, pH=7.6), resuspended in 1 mL of TBS, transferred to a fresh 1.5 mL tube and centrifuged (2 min, 6000 x g). The cell pellets were frozen at -70oC. The pellets were thawed on ice, suspended in 0.5 mL of lysis buffer [10 mM Tris-HCl, 20% (w/v) sucrose, 50 mM NaCl, 10 mM ethylenediaminetetraacetic acid (EDTA), pH=8.0] supplemented with 10 µl of Protease Inhibitor Cocktail (Sigma, PA8849) and 125 µL of lysozyme (20 mg/mL) and incubated for 30 min at 37oC. Four samples for each strain were combined in 15 mL. Subsequently, 1.5 mL of IP-buffer [50 mM Tris-HCl, pH=7.5, 150 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (m/v) sodium deoxycholate], 30 µL protease inhibitor cocktail, PMSF (phenylmethanesulfonyl fluoride) to a final concentration of 2 mM, SDS (sodium dodecyl sulphate) to a final concentration of 0.1% were added to each sample. The samples were sonicated 20 times for 20 s each with 1 min break on ice using a Microson ultrasonic cell disruptor Xl2000 (Misonix) with 5-mm tip and 90% of output power to obtain DNA fragments of an average length of 250-350 bp. DNA fragmentation was checked by agarose gel electrophoresis. After sonication, samples were aliquoted (1 mL in 1.5 mL tubes) and stored at -70oC.
Sonicated lysate was thawed on ice and 150 μL of each strain variant was incubated with 20 μL of magnetic beads coupled with protein A (Dynabeads Protein A, Invitrogen, 10001D) previously separated from original suspension using Magnetic Separation Stand. Such pre-clearing step was performed for minimum 1 hour at 4oC with rotation of the mixtures. In the meantime 50 μL of magnetic beads were prepared for each reaction by separating from the suspension as above. It was then mixed with 6 μL anti-FLAG mouse antibodies [DYKDDDDK Tag polyclonal  antibodies; 1 mg/mL; PA1-985B; Invitrogen] diluted in 200 μL of PBS with 0.05% Tween-20. Mixtures of magnetic beads and antibodies were incubated for 10 minutes at 4oC with gentle rotation. Beads with bound antibodies were then separated from the supernatant, washed once with 200 μL of the PBS with 0.05% Tween-20 solution and stored on ice. Pre-cleaned lysate was separated from the beads used for pre-incubation and added to the beads coated with antibodies. Mixture containing lysate and magnetic beads with antibodies was incubated at 4oC for 20 minutes with mixing on rotator. Beads were then collected and washed. Elution was performed twice for 15 minutes in 50 μL at 65oC in thermoblock with shaking (1400 rpm). Samples from 6 parallel elutions were pooled together and 30 µL of mixture was downloaded for SDS-PAGE analysis. The pooled samples were incubated with 8 μL of RNase A (100 mg/mL, Qiagen, 19101) for 30 min at 65oC. Next, 40 μL of Proteinase K (20 mg/mL, Qiagen, 19133) was added and the samples were incubated for 1 h at 50oC followed by overnight incubation at 65oC. Subsequently, 40 μL of Proteinase K was added again and the samples were incubated for 1 h at 50oC. Then the samples were stored on ice and 24 μL of 3 M sodium acetate (pH=5) and water to the end volume 700 μL was added. DNA purification was performed using Qiaquick Qiagen PCR purification Kit according to manufacturer’s instructions. The purified DNA was stored at -20oC.

value: PA3027 overproducer (F-PA3027), replicate 2


title: empty vector control (EV-F), replicate 1

description: ChIP DNA data from empty vector control

source_name: empty vector control (EV-F)

value: PAO1161/pABB28.1 (lacIQ-tacp-flag)


title: Primed KOc18-1

description:
Primed KOc18-1
ESRG knockout embryonic stem cell line clone 18 in primed condition, passage 49.2.8
70_DESeq2_normalized_counts_Primed.csv


title: Primed KOc10-3

description:
Primed KOc10-3
ESRG knockout embryonic stem cell line clone 10 in primed condition, passage 49.2.10
70_DESeq2_normalized_counts_Primed.csv


title: PA3027 overproducer (F-PA3027), replicate 1


title: PA3027 overproducer (F-PA3027), replicate 2


title: Primed KOc10-2

description:
Primed KOc10-2
ESRG knockout embryonic stem cell line clone 10 in primed condition, passage 49.2.9
70_DESeq2_normalized_counts_Primed.csv


title: Primed KOc10-1

description:
Primed KOc10-1
ESRG knockout embryonic stem cell line clone 10 in primed condition, passage 49.2.8
70_DESeq2_normalized_counts_Primed.csv


title: Primed WTc28-2

description:
Primed WTc28-2
ESRG wild-type embryonic stem cell line clone 28 in primed condition, passage 49.8
70_DESeq2_normalized_counts_Primed.csv

value: wild type


title: Primed WTc28-1

description:
Primed WTc28-1
ESRG wild-type embryonic stem cell line clone 28 in primed condition, passage 49.7
70_DESeq2_normalized_counts_Primed.csv


title: Primed WTc21-3

description:
Primed WTc21-3
ESRG wild-type embryonic stem cell line clone 21 in primed condition, passage 49.9
70_DESeq2_normalized_counts_Primed.csv


title: Primed WTc28-3

description:
Primed WTc28-3
ESRG wild-type embryonic stem cell line clone 28 in primed condition, passage 49.9
70_DESeq2_normalized_counts_Primed.csv


title: Primed WTc21-2

description:
Primed WTc21-2
ESRG wild-type embryonic stem cell line clone 21 in primed condition, passage 49.8
70_DESeq2_normalized_counts_Primed.csv


title: SLERT_rep1_invivo_DMSO

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

data_processing:
Library strategy: SHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Analyses by Shapemapper V2.1.3
Genome_build: Target RNA sequence
Supplementary_files_format_and_content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

extract_protocol:
For SHAPE-MaP, isolated RNAs were treated with DNase I (Ambion, DNA-freeTM kit) to remove possible DNA contamination. About 50-100 ng of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for SLERT(5S rRNA was used as a spike-in control). Mn2+ was removed using G-25 micro-spin columns (GE Healthcare) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase and nested PCR was performed to further improve DNA yield.
SHAPE-MaP libraries were prepared from 1 ng of DNAs for SLERT and 5S rRNA, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina X Ten at CAS Key Laboratory of Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For SHAPE-MaP, PA1 cells were incubated with 900 uL of fresh cell culture medium and 100 μL of 10x SHAPE Chemical in DMSO with the final concentration of NAI at 200 mM for 10 minutes at 37°C.

tag: cell line

tag: type

value: cDNA

value: SLERT NAI samples modified by NAI in DMSO


title: SLERT_rep2_invivo_DC

value: SLERT DMSO samples only treated with DMSO


title: SLERT_rep2_invivo_DMSO


title: PA3027 overproducer (PA3027), biological rep1

value: PA3027 overproducer, biological rep1


title: PAO1161 EV_1 RNA-seq_reused

description: gene expression data from empty vector control


title: PA3027 overproducer (F-PA3027), input

description: INPUT ChIP DNA data from FLAG-PA3027 overproducer

value: PA3027 overproducer (F-PA3027), input


title: SLERT_rep2_invivo_NAI

value: SLERT DC samples denatured by formamide at 95degreeC


title: SLERT_rep1_invivo_NAI


title: PA3027 overproducer (PA3027), biological rep3

value: PA3027 overproducer, biological rep3


title: SLERT_rep1_invivo_DC


title: 5S_rep2_invivo_NAI

value: 5S rRNA DC samples denatured by formamide at 95degreeC


title: 5S_rep2_invivo_DC

value: 5S rRNA DMSO samples only treated with DMSO


title: 5S_rep2_invivo_DMSP

value: 5S rRNA NAI samples modified by NAI in DMSO


title: Primed WTc1-3

description:
Primed WTc1-3
ESRG wild-type embryonic stem cell line clone 1 in primed condition, passage 49.9
70_DESeq2_normalized_counts_Primed.csv

tag: genotype/variation


title: Primed WTc1-2

description:
Primed WTc1-2
ESRG wild-type embryonic stem cell line clone 1 in primed condition, passage 49.8
70_DESeq2_normalized_counts_Primed.csv


title: Primed WTc1-1

description:
Primed WTc1-1
ESRG wild-type embryonic stem cell line clone 1 in primed condition, passage 49.7
70_DESeq2_normalized_counts_Primed.csv


title: Primed WTc21-1

description:
Primed WTc21-1
ESRG wild-type embryonic stem cell line clone 21 in primed condition, passage 49.7
70_DESeq2_normalized_counts_Primed.csv


title: Sample_94_TP0001_CD4_CD45RA_Div_2_aCD3_CD28_D8

city: San Diego

first: Rashmi

last: Tippalagama

state: CA

address: 9420 Athena Cir, La Jolla

department: Peters

institute: La Jolla Institute for immunology

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_94

data_processing:
Paired-end reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human GRCh38 reference using STAR(v 2.6.1c )
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5)  and features with 0 counts across all samples were removed
Genome_build: GRCh38
Supplementary_files_format_and_content: abundance measurements as a matrix table (Transcript per million)

molecule: polyA RNA

source_name: Cryopreserved PBMC

growth_protocol: Cryopreserved PBMC were quickly thawed by incubating each cryovial at 37°C for 2 min, and cells transferred into 9 ml of cold medium HR5 (RPMI 1640 with L-Glutamin and 25 mM Hepes, supplemented with 5% human AB serum, 1% Penicillin Streptomycin and 1% Glutamax) and 20 U/mL Benzonase Nuclease. Cells were counted and re-suspended at 10 million cells per ml for CTV staining.

extract_protocol:
cells were used directly ex vivo for day 0 and harvested at day 1 and day 8 post stimulation, stained with antibodies, and 100,000 memory CD4 T cells of HLADR+ vs HLADR- and Divided vs undivied were sorted, using BD Aria 3 or BD Aria 5 cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: After thawing, PBMC were directly used for Cell Trace Violet (CTV) staining. 10μM of working stock was prepared from CellTraceTM Violet Cell Proliferation Kit (Invitrogen) according to the manufacturer’s protocol. Ten million PBMC were transferred to a 1.5ml Eppendorf tube. Cells were washed twice with 1X PBS and centrifuged at 2,500 rpm for 5 min. Cells were resuspend in 1 ml of 1X PBS and 2 μl of CTV working solution was added. Cells were gently mixed and vortexed before incubating in the dark for 10-12 min at 37°C (with occasional mixing). Cells were washed twice with 1ml of 20% FBS in 1X PBS for quenching, and resuspended at 2x106 cells/mL in HR5. Following CTV staining, cells were plated at 0.5 million cells/well in a 96-U bottom well plate and stimulated with MTB300 (Mtb specific peptide pool, PMID: 27409590) at 2 μg/mL or with an equivalent DMSO concentration (0.3% final) or with aCD3/CD28 at 1 μg/mL. Cells were incubated at 37°C for up to 8 days. Media was replaced every three to four days and was supplemented with 0.02 U/μL of IL-2.

value: PBMC

tag: day

tag: cell subset

value: Memory CD3+CD4+ Div2 T cells

tag: stimulation


title: Sample_92_TP0001_CD4_CD45RA_Div_0_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_92

value: Memory CD3+CD4+ Div0 T cells


title: 5S_rep1_invivo_DMSO


title: 5S_rep1_invivo_DC


title: 5S_rep1_invivo_NAI


title: Sample_91_TP0001_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_91

value: Memory CD3+CD4+ HLADR- T cells


title: injured telencephalic hemisphere 2 [RNA-seq]

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

data_processing:
Run was demultiplexed with bcl2fasq
Reads were mapped with STAR
Raw level of expression was computed with HTSeq
Genome_build: GRCz11
Supplementary_files_format_and_content: raw count per gene

organism: Danio rerio

source_name: telencephalic hemisphere

extract_protocol:
Total RNAs were extracted from telencephalic hemispheres with Trizol method (Invitrogen) following manufacturer's protocol.
PolyA+ RNAs were first pulled down with polydT beads. Libraries were then prepared from 1µg of polyA+ RNAs with the TrueSeq mRNA kit from Illumina and following Illumina's protocol. Quality of input RNAs and library product was assessed with a BioAnalyzer 2100.

tag: tissue

value: telencephalon

value: injury


title: injured telencephalic hemisphere 1 [RNA-seq]


title: healthy telencephalic hemisphere 3 [RNA-seq]

value: no treatment


title: Sample_87_TP0001_CD4_CD45RA_Div_0_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_87


title: healthy telencephalic hemisphere 2 [RNA-seq]


title: Sample_93_TP0001_CD4_CD45RA_Div_1_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_93

value: Memory CD3+CD4+ Div1 T cells


title: Sample_86_TP0001_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_86


title: healthy telencephalic hemisphere 1 [RNA-seq]


title: Sample_85_TP0001_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_85

value: Memory CD3+CD4+ HLADR+ T cells


title: Sample_84_TP0001_CD4_CD45RA_Div_2_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_84

value: Unstim


title: injured telencephalic hemisphere 1

data_processing:
Run was demultiplexed with bcl2fasq
Adaptor sequence was trimmed from reads with cutadapt
Reads were mapped with bwa
Raw level of expression was computed with HTSeq
Genome_build: GRCz11
Supplementary_files_format_and_content: raw count per gene

extract_protocol:
Trizol (Invitrogen)
From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions, control and injured.


title: injured telencephalic hemisphere 2


title: healthy telencephalic hemisphere 3


title: Sample_83_TP0001_CD4_CD45RA_Div_1_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_83


title: injured telencephalic hemisphere 3 [RNA-seq]


title: Sample_90_TP0001_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_90


title: Sample_89_TP0001_CD4_CD45RA_Div_2_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_89


title: Sample_82_TP0001_CD4_CD45RA_Div_0_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_82


title: Sample_81_TP0001_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_81


title: Sample_80_TP0001_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_80


title: healthy telencephalic hemisphere 1


title: Sample_78_TP0001_CD4_CD45RA_MTB_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_78

value: Memory CD3+CD4+


title: Mouse CD Organoid rep 2

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

description:
16Feb21_ZL_mOrganoids_RPKM_TMM_Annotated.csv
mCD_2

data_processing:
quality assessment: FastQC v0.11.8
adapter removal: Cutadapt 2.5
read quality trimming: Trimmomatic 0.36
alignment to Gencode m25: STAR with GeneCounts 2.7.1a
generation of RPKM and TMM: edgeR 3.28.1
Genome_build: Gencode m25 (GRCm38.p6)
Supplementary_files_format_and_content: 16Feb21_ZL_mOrganoids_RPKM_TMM_Annotated.csv

source_name: CD Organoid

extract_protocol:
QIAgen RNeasy standard protocol
Illumina TruSeq

tag: strain background

value: C57BL/6 x Swiss Webster

tag: age

value: Embryonic day 11

tag: genotype

value: Wnt11-RFP +/-

value: Kidney CD


title: Adult Mouse CD Organoid rep 1

description:
16Feb21_ZL_mOrganoids_RPKM_TMM_Annotated.csv
Adult_mCD_1

source_name: Adult CD Organoid


title: Sample_77_TP0001_CD4_CD45RA_Unstim_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_77


title: Mouse CD Organoid rep 1

description:
16Feb21_ZL_mOrganoids_RPKM_TMM_Annotated.csv
mCD_1


title: injured telencephalic hemisphere 3


title: Sample_76_TP0001_CD4_CD45RA_D0

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_76


title: Sample_88_TP0001_CD4_CD45RA_Div_1_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_88


title: Mouse UB Organoid Day 20 rep 2

description:
16Feb21_ZL_mOrganoids_RPKM_TMM_Annotated.csv
mUB_D20_2

source_name: UB Organoid Day 20

value: Kidney UB


title: Mouse UB Organoid Day 10 rep 1

data_processing:
quality assessment: FastQC v0.11.8
adapter removal: Cutadapt 2.5
read quality trimming: Trimmomatic 0.36
alignment to Gencode m22: STAR with GeneCounts 2.7.1a
generation of RPKM and TMM: edgeR 3.28.1
Genome_build: Gencode m23 (GRCm38.p6)
Supplementary_files_format_and_content: fastq format raw data

source_name: E11.5 mUB_day10


title: healthy telencephalic hemisphere 2


title: Sample_75_TU0033_CD4_CD45RA_Div_2_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_75


title: Sample_73_TU0033_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_73


title: Mouse UB Organoid Day 10 rep 2


title: Sample_74_TU0033_CD4_CD45RA_Div_0_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_74


title: Mouse UB Organoid Day 20 rep 1

description:
16Feb21_ZL_mOrganoids_RPKM_TMM_Annotated.csv
mUB_D20_1


title: Mouse UB Organoid Day 5 rep 2

source_name: E11.5 mUB_day5


title: Adult Mouse CD Organoid rep 2

description:
16Feb21_ZL_mOrganoids_RPKM_TMM_Annotated.csv
Adult_mCD_2


title: Ym1_positive_monocytes_rep3

city: Tokyo

first: Yotsumoto

last: Satoshi

address: 1432-1, Hachioji, Hachioji

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
The RNA-seq reads were aligned to a mouse reference genome (mm10/GRCm38) using Tophat software.
Duplicate reads were removed by using Picard tools (http://broadinstitute.github.io/picard).
The expression levels were quantified using Cufflinks software.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_exp.diff: Tab-delimited text file includes FPKM values for all samples.

source_name: Lung monocytes

extract_protocol:
Lung monocytes were removed by cell sorter and RNA was harvested using RNeasy Mini kit (QIAGEN). SMART-Seq v4 Ultra Low Input RNA Kit (TAKARA) and Nextera XT DNA Library Preparation Kit (Illumina) was used with 500 upg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing.

value: Lung

value: Ym1-positive monocytes

value: 8 wk


title: Ym1_positive_monocytes_rep2


title: Sample_72_TU0033_CD4_CD45RA_Div_2_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_72

value: PBMC

value: Memory CD3+CD4+ Div2 T cells


title: Mouse UB Organoid Day 5 rep 1


title: Sample_69_TU0033_CD4_CD45RA_Div_0_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_69

value: Memory CD3+CD4+ Div0 T cells


title: Sample_79_TP0001_CD4_CD45RA_aCD3_CD28_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_79


title: Sample_70_TU0033_CD4_CD45RA_Div_1_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_70


title: Sample_71_TU0033_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_71


title: Sample_68_TU0033_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_68

value: Memory CD3+CD4+ HLADR- T cells


title: Sample_67_TU0033_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_67


title: Ym1_positive_monocytes_rep1


title: Ym1_negative_monocytes_rep3

value: Ym1-negative monocytes


title: Sample_65_TU0033_CD4_CD45RA_Div_1_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_65

value: Memory CD3+CD4+ Div1 T cells


title: Ym1_negative_monocytes_rep2


title: Sample_66_TU0033_CD4_CD45RA_Div_2_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_66


title: Sample_64_TU0033_CD4_CD45RA_Div_0_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_64


title: Sample_63_TU0033_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_63


title: TAMs 208 (shSC rep 4)

city: Pittsburgh

first: Baoli

last: Hu

state: PA

address: 4401 Penn Ave

department: Neurological Surgery

institute: University of Pittsburgh School of Medicine

data_processing:
Raw sequence reads were trimmed to remove adapters and poor qualities using Trim Galore (-q 25 --phred 33 --length 36 --stringency 3).
Hisat2 was used to alignment (default settings).
Reads mapping to genes annotated in GENCODE M24 were counted using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Txt files contain raw counts of sequencing reads.

source_name: tumor-associated macrophages (TAMs)

growth_protocol: The intracranial xenograft tumor models were established by injecting 1 × 10^5 of QPP7 cells bearing shChi3l1 or shSC

extract_protocol:
Tumors were separated and homogenized for 15 min at 37°C in Collagenase IV Cocktail and red blood cells were lysed using ACK lysing buffer. Cells were Cells were incubated with 1.0 µg of TruStain fcX (BioLegend) for 10 min on ice to block Fc receptors, followed by staining with the combination of indicated antibodies and subject to FACS to sort macrophages.
First, cDNA was generated from 10ng RNA using Smart-seq ultra Low input RNA kit from Takara. Second, libraries were generated from 1ng of cDNA by using Nextera XT from Illumina

value: Glioblatoma QPP7 associated macrophages

value: QPP7 shSC


title: TAMs 206 (shSC rep 3)

description: paired with TAMs 198 (shChi3l1 rep 3) in Figure S6x


title: Sample_62_TU0033_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_62

value: Memory CD3+CD4+ HLADR+ T cells

value: Unstim


title: Sample_61_TU0033_CD4_CD45RA_aCD3_CD28_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_61

value: Memory CD3+CD4+


title: Sample_59_TU0033_CD4_CD45RA_Unstim_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_59


title: TAMs 198 (shChi3l1 rep 3)

description: paired with TAMs 206 (shSC rep 3) in Figure S6x

value: QPP7 shChi3l1


title: TAMs 200 (shSC rep 1)

description: paired with TAMs 186 (shChi3l1 rep 1) in Figure S6x


title: Sample_60_TU0033_CD4_CD45RA_MTB_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_60


title: TAMs 201 (shSC rep 2)

description: paired with TAMs 196 (shChi3l1 rep 2) in Figure S6x


title: TAMs 196 (shChi3l1 rep 2)

description: paired with TAMs 201 (shSC rep 2) in Figure S6x


title: Sample_58_TU0033_CD4_CD45RA_D0

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_58


title: Sample_54_TU0070_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_54


title: Sample_57_TU0070_CD4_CD45RA_Div_2_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_57


title: TAMs 186 (shChi3l1 rep 1)

description: paired with TAMs 200 (shSC rep 1) in Figure S6x


title: Sample_53_TU0070_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_53


title: Sample_56_TU0070_CD4_CD45RA_Div_1_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_56


title: TAC-Fat 10-ACAA2

city: Newark

first: Maha

last: Abdellatif

state: NJ

address: 185 S. Orange Ave.

department: Cell Biology and Molecular Medicine

institute: Rutgers-University

data_processing:
The 75-nt single-end (SE75 sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm (“bwa  aln/samse” with default settings)
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map  uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR  duplicates”) are removed.
Since the 5´-ends of the aligned reads (= “tags”) represent the  end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´-  ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected  library. To identify the density of fragments (extended tags) along the genome, the genome is  divided into 32-nt bins and the number of fragments in each bin is determined. This information  (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in  genome browsers (see Section VI.). bigWig files also provide the peak metrics in the Active Motif  analysis program described below.
Peak finding was performed using SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files - Binary files that can be opened in or uploaded to genome  browsers and show the fragment density for 32-nt bins along the genome (“signal map”).
Supplementary_files_format_and_content: MERGED (PEAK) REGIONS – an 'excel' file comparing peak region metrics between different samples

source_name: heart tissue

extract_protocol:
Nuclei were extracted from heart tissue, sonicated, and histone-DNA complexes were precipitated with anti-H3K9Bu or anti-H3K9ac (a pool of 3, each)
Library was constructed by Active Motif (https://www.activemotif.com/)

tag: strain and age

value: C57/Bl/6J - 12 wk-old

tag: diet

value: 10% Fat

tag: Sex

value: male

tag: surgical procedure

value: transverse aortic constriction (TAC)

tag: antibody


title: Sham-Fat 60-ACAA2

value: 60% Fat

value: Sham


title: Sham-Fat 10-ACAA2


title: Sample_55_TU0070_CD4_CD45RA_Div_0_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_55

value: PBMC


title: Input-pooled

value: pooled


title: Sample_51_TU0070_CD4_CD45RA_Div_1_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_51


title: Sample_52_TU0070_CD4_CD45RA_Div_2_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_52

value: Memory CD3+CD4+ Div2 T cells


title: TAC-Fat 60-ACAA2


title: Ym1_negative_monocytes_rep1

tag: strain

value: Lung

value: Ym1-negative monocytes

value: 8 wk


title: Sample_49_TU0070_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_49

tag: cell type

value: Memory CD3+CD4+ HLADR- T cells


title: TAC-Fat 60 (HiFat)-H3K9Bu


title: Sham-Fat 60 (HiFat)-H3K9Bu


title: TAC-Fat 60 (HiFat)-H3K9ac


title: Sham-Fat 60 (HiFat)-H3K9ac


title: Sample_48_TU0070_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_48

value: Memory CD3+CD4+ HLADR+ T cells


title: TAC-Fat 10 (control)-H3K9Bu


title: Sample_47_TU0070_CD4_CD45RA_Div_2_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_47

value: Unstim


title: Sample_46_TU0070_CD4_CD45RA_Div_1_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_46

value: Memory CD3+CD4+ Div1 T cells


title: Sham-Fat 10 (control)-H3K9Bu


title: Input-pooled 2

value: pooled DNA from sham and TAC


title: Sample_44_TU0070_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_44


title: Sample_43_TU0070_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_43


title: Sample_45_TU0070_CD4_CD45RA_Div_0_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_45

value: Memory CD3+CD4+ Div0 T cells


title: Sample_50_TU0070_CD4_CD45RA_Div_0_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_50


title: Input-pooled 1

value: C57/Bl/6J - 12 wk-old

value: 0% Fat


title: TAC-Fat 10 (control)-H3K9ac

value: 10% Fat

value: male

value: transverse aortic constriction (TAC)


title: Sham-Fat 0-H3K9Bu

value: Sham


title: Sample_40_TU0070_CD4_CD45RA_Unstim_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_40

value: PBMC

value: Memory CD3+CD4+


title: Sample_42_TU0070_CD4_CD45RA_aCD3_CD28_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_42


title: TAC-Fat 0-H3K9Bu


title: Sample_37_TU0025_CD4_CD45RA_Div_1_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_37


title: Sample_41_TU0070_CD4_CD45RA_MTB_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_41


title: Sham-Fat 0-H3K9ac


title: Sham-Fat 10 (control)-H3K9ac


title: Sample_38_TU0025_CD4_CD45RA_Div_2_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_38

value: Memory CD3+CD4+ Div2 T cells


title: Sample_36_TU0025_CD4_CD45RA_Div_0_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_36


title: pooled Input

value: pooled DNA from BaclbcJ and Balb/cByJ

value: pooled DNA from both wild type and Acads-deleted mice


title: TAC-Fat 0-H3K9ac


title: TAC-cByJ-H3K9Bu

value: Balb/cByJ

value: deletion in Acads


title: Sample_35_TU0025_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_35

value: Memory CD3+CD4+ HLADR- T cells


title: Sample_34_TU0025_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_34

value: Memory CD3+CD4+ HLADR+ T cells


title: TAC-cJ-H3K9Bu

value: Balb/cJ

value: wild type


title: TAC-cByJ-H3K9ac


title: Sham-cJ-H3K9Bu


title: Sample_32_TU0025_CD4_CD45RA_Div_1_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_32

value: Memory CD3+CD4+ Div1 T cells


title: Sample_31_TU0025_CD4_CD45RA_Div_0_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_31

value: Memory CD3+CD4+ Div0 T cells


title: TAC-cByJ-3

description:
Hearts isolated 1 week after surgery
4439Rutgers_DESeq2_results_allgenes.xlsx

data_processing:
Illumina NextSeq 500
Alignement with the genome using STAR (Spliced Transcripts Alignment to a Reference) algorithm
Read pairs that had both ends aligned were counted, and those with at least 25 bp overlapping bases in a fragment were assigned
Gene annotations were obtained from Subread package. Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930, doi:10.1093/bioinformatics/btt656 (2014).
Differential genes were detected by DESeq2 at 10%FDR (adjusted p-value). Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15, 550, doi:10.1186/s13059-014-0550-8 (2014).
Genome_build: mm10

extract_protocol:
Qiagen RNeasy Mini Kit (Qiagen, cat# 74104)
2 ug of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594)

value: Fat - 10 Kcal%

tag: surgery

value: transverse aortic constriction


title: Sample_30_TU0025_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_30


title: TAC-cByJ-1


title: Sample_25_TU0025_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_25

value: Unstim


title: Sample_26_TU0025_CD4_CD45RA_Div_0_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_26


title: Sample_39_TU0070_CD4_CD45RA_D0

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_39


title: TAC-cJ-H3K9ac

value: transverse aortic constriction (TAC)


title: Sample_33_TU0025_CD4_CD45RA_Div_2_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_33

value: PBMC


title: Sample_29_TU0025_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_29


title: Sample_27_TU0025_CD4_CD45RA_Div_1_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_27


title: Sham-cByJ-2

value: sham


title: TAC-cByJ-2


title: TAC-cJ-3


title: Sahm-cByJ-H3K9ac

value: Sham


title: Sample_23_TU0025_CD4_CD45RA_aCD3_CD28_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_23

value: Memory CD3+CD4+


title: Sample_22_TU0025_CD4_CD45RA_MTB_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_22


title: TAC-cJ-2


title: Sample_21_TU0025_CD4_CD45RA_Unstim_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_21


title: TAC-cJ-1


title: Sham-cJ-2


title: Sham-cJ-3


title: Sample_20_TU0025_CD4_CD45RA_D0

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_20


title: Sham-cJ-1


title: Sample_19_TP0004_CD4_CD45RA_Div_2_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_19

value: Memory CD3+CD4+ Div2 T cells


title: Sample_28_TU0025_CD4_CD45RA_Div_2_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_28


title: Sample_24_TU0025_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_24


title: Sample_18_TP0004_CD4_CD45RA_Div_1_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_18


title: Sham-cByJ-3

value: Balb/cByJ


title: Sample_17_TP0004_CD4_CD45RA_Div_0_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_17


title: TAC - Fat 60 - 2

description:
Hearts isolated 1 week after surgery
4242Rutgers_hiFat-DESeq2_results_allgenes.xlsx

value: C57Bl/6J - 12-wk-old

value: high-fat


title: Sample_16_TP0004_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_16

value: Memory CD3+CD4+ HLADR- T cells


title: TAC - Fat 60 - 1


title: Sham - Fat 60 - 3


title: Sample_14_TP0004_CD4_CD45RA_Div_2_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_14


title: Sham-cByJ-1

description:
Hearts isolated 1 week after surgery
4439Rutgers_DESeq2_results_allgenes.xlsx


title: Sham - Fat 60 - 2


title: TAC - Fat 60 - 3


title: Sample_13_TP0004_CD4_CD45RA_Div_1_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_13


title: Sham - Fat 60 - 1


title: TAC - Fat 0 - 3

description:
Hearts isolated 1 week after surgery
4408Rutgers_DESeq2_results_allgenes.xlsx

value: fat-free


title: TAC - Fat 0 - 2


title: Sahm-cByJ-H3K9Bu

value: deletion in Acads


title: Sample_9_TP0004_CD4_CD45RA_Div_2_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_9


title: Sample_10_TP0004_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_10

value: Memory CD3+CD4+ HLADR+ T cells


title: Sample_11_TP0004_CD4_CD45RA_HLADR_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_11


title: TAC - Fat 0 - 1


title: Sham - Fat 0 - 3


title: Sample_7_TP0004_CD4_CD45RA_Div_0_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_7

value: Memory CD3+CD4+ Div0 T cells


title: Sample_6_TP0004_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_6


title: Sham - Fat 0 - 1


title: Sample_15_TP0004_CD4_CD45RA_HLADR_aCD3_CD28_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_15


title: Sample_4_TP0004_CD4_CD45RA_aCD3_CD28_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_4


title: Sample_5_TP0004_CD4_CD45RA_HLADR_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_5


title: Sample_8_TP0004_CD4_CD45RA_Div_1_Unstim_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_8

value: Memory CD3+CD4+ Div1 T cells


title: Sham - Fat 0 - 2


title: Sham-cJ-H3K9ac

value: Balb/cJ

value: wild type


title: ATACseq_MM1S_DMSO_Control_Replicate1

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were then aligned to custom reference genome consisting the human genome (Hg19) and the Drosophila melanogaster genome (Dm3) using Bowtie2 (v2.3.3).
The resulting SAM files were converted to BAM files using Samtools (v1.4.1) using the view command, which were subsequently sorted, indexed, and potential PCR duplicates removed using the rmdup function.
BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1)
For experiments with external normalization, the reads mapping to either Hg19 or Dm3 genomes were quantified using FeatureCounts (Subread package, v1.5.0) and the percentage of mapped Dm3 reads as a total of total mapped Dm3+Hg19 reads was calculated. A scale factor was then calculated as the ratio of Dm3 reads in the control treatment condition and the treatment sample, which was then applied as the scaleFactor in the bamCoverage function.
Genome_build: HG19, Dm3
Supplementary_files_format_and_content: bigWig

source_name: Multiple Myeloma

growth_protocol: Cells were grown in vitro under standard culture conditions.

extract_protocol:
Cells were washed once in ice-cold PBS and lysed in ATAC lysis buffer (0.1% Tween-20, 0.1% NP-40, 3mM MgCl2, 10mM NaCl, 10mM Tris HCl pH 7.4). Tagmentation was performed with Tn5 transposase and 2x TD Buffer (Nextera DNA Library Prep Kit, Ilumina) for 30 minutes at 37°C.
Tagmented DNA was purified using a MinElute colum (Qiagen, 28004) and amplified for 12 cycles using 2x KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602). The amplified libraries were purified using MinElute columns (Qiagen) and sequenced on an NextSeq 500.

treatment_protocol: Cells were treated with A-485, A-241, or DMSO at indicated concentrations for indicated time-points.

tag: cell line

tag: timepoint

value: 32 hours

tag: treatment+dose

value: DMSO


title: Sample_12_TP0004_CD4_CD45RA_Div_0_MTB_D8

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_12

value: PBMC

tag: day

tag: cell subset


title: Sample_1_TP0004_CD4_CD45RA_D0

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_1

tag: stimulation

value: Unstim


title: ATACseq_MM1S_A485_32hours_Replicate2


title: XT0134_LTBI_CD4m

city: La Jolla

first: Julie

last: Burel

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample106_CD4m

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 T cells sorted using BD Aria 3 cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: No specific treatment involved

tag: disease group

value: LTBI

tag: geographic location

value: USA:San Diego

value: Memory CD3+CD4+CD8- T cells


title: ATACseq_MM1S_DMSO_Control_Replicate2


title: Sample_2_TP0004_CD4_CD45RA_Unstim_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_2

value: Memory CD3+CD4+


title: ATACseq_MM1S_A485_32hours_Replicate1


title: ATACseq_MM1S_A241_32hours_Replicate2


title: ATACseq_MM1S_A241_32hours_Replicate1


title: XT0082_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample104_CD4m

value: TBneg


title: XT0130_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample105_CD4m


title: ATACseq_MM1S_A241_6hours_Replicate1

value: 6 hours


title: ATACseq_MM1S_A241_2hours

value: 2 hours


title: TU0140_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample103_CD4m


title: ATACseq_MM1S_Control_Replicate2


title: ATACseq_MM1S_Control_Replicate1


title: Sample_3_TP0004_CD4_CD45RA_MTB_D1

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample_3


title: ATACseq_MM1S_DMSO_Replicate1


title: ATACseq_MM1S_A485_6hours_Replicate2


title: TU0137_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample102_CD4m


title: ATACseq_MM1S_DMSO_Replicate2


title: TU0110_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample99_CD4m


title: TU0084_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample97_CD4m


title: TU0081_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample96_CD4m


title: TU0085_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample98_CD4m


title: ATACseq_MM1S_A485_6hours_Replicate1


title: TU0078_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample95_CD4m


title: ATACseq_MM1S_A241_6hours_Replicate2


title: TU0070_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample92_CD4m


title: TU0075_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample94_CD4m


title: TU0071_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample93_CD4m


title: TU0063_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample90_CD4m


title: TU0113_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample100_CD4m


title: ATACseq_MM1S_A485_2hours_Replicate1


title: TTseq_MM1S_2hours_A485

data_processing:
Library strategy: TT-seq
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which QC was performed using FASTQC (v0.11.5). Sequencing reads were then aligned to custom reference genome consisting the human genome (Hg19) and the Drosophila melanogaster genome (Dm3) using Bowtie2 (v2.3.3).
The resulting SAM files were converted to BAM files using Samtools (v1.4.1) using the view command, which were subsequently sorted, indexed, and potential PCR duplicates removed using the rmdup function. BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1). For experiments with external normalization, the reads mapping to either Hg19 or Dm3 genomes were quantified using FeatureCounts (Subread package, v1.5.0) and the percentage of mapped Dm3 reads as a total of total mapped Dm3+Hg19 reads was calculated. A scale factor was then calculated as the ratio of Dm3 reads in the control treatment condition and the treatment sample, which was then applied as the scaleFactor in the bamCoverage function.
BigWig files were imported into Integrative Genomics Viewer (IGV, v2.7.0) for visualization of specific loci. Using Deeptools (v3.0.0), average profile plots and heatmaps were generated by computing read average read density (from BigWig files) across defined genomic intervals using computeMatrix, which we subsequently plot using plotProfile and plotHeatmap, respectively.
Genome_build: Hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cells were lysed in in TRIzol. Chloroform (1/5th volume) was added and samples were vortexed and centrifuged at 4°C (13000g, 15 minutes). The aqueous phase was isolated and total RNA was extracted by isopropanol precipitation at room temperature (10 minutes) followed by centrifugation at 4°C (13000g, 10 minutes). The isolated RNA pellet was washed with 70 percent ethanol followed by centrifugation at 4°C (13000g,15 minutes). The RNA pellet was dissolved in 100μL nuclease-free H2O and denatured at 65ºC for 10 minutes. 150μg total RNA per treatment condition (pl 883 us 15μg D.melanogaster S2 RNA spike-in) in 100μL final volume were sonicated in microTUBE AFA Fiber screw cap tubes (6 x 16mm, Covaris, 520096) using the Covaris S220 Focused Ultrasonicator at maximum power for 15 seconds. Thiol-specific biotinylation of fragmented RNA was performed by adding 750μL volume nuclease free water followed by incubatation with 10mM TRIS (pH 7.4), 1mM EDTA, 200 μg/mL dimethylformamide (DMF; Sigma Aldrich, 227056) and 300μg EZ-LinkTM HPDP-Biotin (ThermoFisher Scientific, 21341) at room temperature for 1.5 hours with constant rotation (1500μL final volume – ‘biotin labelling reaction’). One volume chloroform was added to the biotin-labelling reaction and the reaction was vortexed and centrifuged at 4°C (20000g, 5 minutes). The aqueous phase was isolated and the chloroform isolation was repeated twice. NaCl (to 0.5M) and one volume isopropanol was added to the aqueous phase and fragmented RNA was isolated by centrifugation at 4°C (20000g, 20 minutes). The RNA pellet was washed with 75 percent ethanol, centrifuged at 4°C (20000g, 20 minutes) and dissolved in nuclease-free water (1μL per 1μg input RNA). Fragmented RNA was denatured at 65°C for 10 minutes prior to incubation with streptavidin beads (μMACs Streptavidin Kit, Miltenyi Biotec, Bergisch Gladbach Germany, 130-074-101) at room temperature for 15 minutes with constant rotation. Biotinylated RNA was isolated using μMACs columns that had been pre-equillibrated with room temperature wash buffer (100mM Tris-HCl pH 7.4, 10mM EDTA, 1M NaCl, 0.1% v/v Tween20). Following incubation with biotinylated RNA / streptavidin beads the columns were washed with 5 times each with 0.9mL pre-warmed (65ºC) and room-temperature wash buffer. Biotinylated RNA was eluted through two additions of 100μL 100mM dithiothreitol (DTT) 3 minutes apart and collected into 700μL RLT buffer from the RNeasy MinElute Cleanup Kit (Qiagen, Hilden Germany, 74204). Biotinylated RNA was isolated using the Qiagen RNeasy MinElute Cleanup Kit using 12μL elution buffer to elute RNA. RNA was quantified using the Agilent Tapestation High Sensitivity RNA kit (Agilent, 5067-5576).
Sequencing libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: 30e6 MM1.S cells per treatment condition were incubated with 1mM 4-thiouridine (Sigma Aldrich, 877 T4509) for the final 10 minutes of A-485 or DMSO treatment (2 hours).