title: lung_195V-EMC1_1

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

description:
bulk polyA RNA
bulk_RNAseq_metadata.csv, bulk_RNAseq_counts.csv

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to process raw sequencing data with the GRCh38 reference for the control samples, and GRCh38 augmented by the IAV (DQ487333.1), MERS-CoV (NC_019843.3), SARS-CoV (NC_004718.3), SARS-CoV-2 (NC_045512.2) or NL63-CoV (JX504050.1) respectively
We used CellBender [17] to remove background RNA and scrublet [18] to identify doublets
Single-cell RNA sequencing data analysis was performed in R (version 3.6.3) with Seurat (version 3.2.1). Cells with at least 500 and less than 5000 detected genes and less than 10% mitochondrial content were combined from each library and library depth (total number of UMIs) was regressed out when scaling data. For organoid and ex vivo AM data we additionally regressed out cell cycle scores calculated with Seurat's CellCycleScoring function. We then integrated samples from different donors using ‘IntegrateData’ for lung explant, autopsy, organoid and ex vivo AM data separately. After automated clustering, DoubletFinder [19] was used to again identify likely cell doublets, and cluster annotation was performed with Seurat's ‘TransferData’ workflow using the Human Lung Cell Atlas reference dataset, using only epithelial cells for the organoid data [20]. We finally combined explant and autopsy data in another round of data integration.
Reads were mapped using STAR (version 2.7.3a) with lenient parameters to detect non-canonical splice junctions [15] (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --outSJfilterOverhangMin 12 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --outSJfilterCountTotalMin 1 1 1 1 --outSJfilterDistToOtherSJmin 0 0 0 0 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --scoreGapNoncan -4 --scoreGapATAC -4 --chimOutType WithinBAM HardClip --chimScoreJunctionNonGTAG 0 --alignSJstitchMismatchNmax -1 -1 -1 -1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000). Control samples were mapped against the GRCh38 genome, infected samples against GRCh38 combined with the IAV (DQ487333.1), MERS-CoV (NC_019843.3), SARS-CoV (NC_004718.3) or SARS-CoV-2 (NC_045512.2) genomes, respectively.
Gene expression was quantified with ‘feature Counts’ (version 2.0.0) using the Gencode v33 reference combined with viral transcripts extracted from the GenBank records.
Assembly: GRCh38

growth_protocol: Fresh lung explants were obtained from 25 patients suffering from lung carcinoma (1 case metastatic osteo-sarcoma), who underwent lung resection at local thoracic surgeries. Tumor-free peripheral lung tissue was dissected into small pieces by scalpel (0.5 x 0.5 x 0.5 mm, 1 - 2 mg) and incubated overnight in RPMI 1640 medium (Merck Biochrom) at 37°C with 5 % CO2 to wash off clinically applied antibiotics. Primary alveolar macrophages (AM) were isolated by repeated perfusion of the human lung tissue with HBSS as described before [4]. Injected liquid was carefully pressed out of the tissue, collected and centrifuged (340 g, 12 min, RT).  AM were infected immediately after isolation or used for Lentiviral delivery of an ACE2 expression plasmid (BPS Bioscience). Cells were seeded in 12-well plates at 0.5 x 106 cells/well in RPMI 1640 medium (supplemented with 2 % FCS).  For generation of adult stem cell-derived lung organoids, primary cells were isolated from healthy parts of distal lung tissue obtained from lung cancer patients undergoing tumor resection surgery. The tissue was chopped with scissors into small pieces and transferred to an enzyme mixture containing 500 U/mL collagenase I (Gibco), 5 U/mL dispase II (Gibco) and 1 U/mL DNase (Applichem) in HBSS supplemented with 10 µM Y-27632 dihydrochloride (Tocris). The minced tissue was incubated for 45-60 min in a shaking water bath at 37°C before being vigorously vortexed and passed through a sieve to remove undigested tissue residues. Subsequently, the cells were further filtered through 100, and 70 µm cell strainers. Cells were centrifuged (300 x g, 5 min), resuspended in red blood cell lysis buffer (Invitrogen) and incubated for 5 min at RT. Subsequently, cells were washed with ADF++ (Advanced DMEM/F12 (Invitrogen) with 10 mM HEPES (Invitrogen) and 1x GlutaMax (Invitrogen)) supplemented with 5% FCS (Capricorn Scientific).     For the generation of alveolar organoids, HTII-280+ cells were isolated using FACS. Therefore, cells were resuspended in 500 µl staining buffer (ADF++ with 1x N2 (Invitrogen), 1x B27 (Invitrogen), 5 mM nicotinamide (Sigma), 1.25 mM N-acetylcysteine (Sigma), and 10 μM Y-27632) and incubated with mouse anti-HTII-280 IgM antibody (Terrace Biotech, TB-27AHT2-280, 1:50) for 30 min on ice. Upon incubation, cells were washed with 2 ml ADF++ supplemented with 5% FCS, resuspended again in 500 µL staining buffer, and incubated for 30 min on ice with the secondary goat anti-mouse IgG (H+L) A488 antibody (Thermo Fisher, A-11017, 1:500). Control without primary but secondary antibody staining was kept in parallel. Subsequently, cells were washed with 2 ml ADF++ with 5% FCS and resuspended in DPBS (Gibco) supplemented with 10 µM Y-27632 dihydrochloride and 1x B27, before being passed through a 40 µm strainer into FACS tubes. Cell sorting was performed by the FACS Core facility using a BD FACSAriaTM II cell sorter (BD Biosciences). HTII-280 sorted cells used to generate alveolar organoids as well as unsorted cells used to generate bronchial organoids were seeded in Cultrex RGF BME (bio-techne) at a concentration of ~1000 cells/µL. After solidification of the gelatinous matrix, the following medium according to Sachs et al. [5] was added on top of the cultures to induce growth of lung organoids: ADF++ supplemented with 10 % R-spondin1 conditioned medium (produced as described previously [6] using the 293T HA Rspo1‐Fc cell line), 1x B27 supplement (Invitrogen), 1 x Primocin antibiotic mix (Invivogen), 1.25 mM N-acetylcysteine (Sigma), 5 mM nicotinamid (Sigma), 0.5 µM SB202190 (Sigma), 1 µM SB431542 (Merck), 100 ng/µl human Noggin (Peprotech), 100 ng/µl human FGF10 (Peprotech) and 25 ng/ml human FGF7 (Peprotech). For alveolar organoids, the described medium was additionally supplemented with CHIR99021 (Sigma, 3 µM). Y-27632 dihydrochloride (10 µM, Tocris) was added only in the first week of culture. Organoids were kept in an incubator at 37°C, 5 % CO2. Upon growth for 2-3 weeks, the organoids were expanded by enzymatic digestion. To do so organoids were released from Cultrex RGF BME (bio-techne) with cold ADF++, centrifuged (300 x g, 5 min), incubated in TrypLE Express Enzyme (Gibco) for ~5-6 min at 37°C and briefly vortexed. After washing with ADF++, cells were resuspended in Cultrex at a ratio of 1:4 to 1:6.     Lentiviral delivery of an ACE2 expression plasmid (BPS Bioscience) into bronchial organoids was based on a previous protocol [7]. In brief, organoids were collected with cold ADF++, pelleted and resuspended in TrypLE Express Enzyme (Gibco). After incubation for 10 min at 37°C, organoids were vortexed and passed 5-10 times through a P1000 pipette tip to completely break up the organoids.  The cells were washed with ADF++ containing 10 µM Y-27632 dihydrochloride and after centrifugation resuspended in a small volume (~50 µL) organoid medium supplemented with 8 µg/ml polybrene (Santa Cruz).  Upon transfer to a 48-well plate, virus was added to the cells (MOI 1) and the suspension mixed by pipetting. The plate was centrifuged for 60 min, 600 x g at 32°C. After incubation for another 4 h in the incubator (37°C), cells were collected in a microcentrifuge tube, pelleted, re-seeded in Cultrex and overlaid with organoid medium.

extract_protocol:
Individual human lung tissue samples were minced and placed in digestion medium (500 U/ml collagenase, 1.5 U/ml dispase and 1 U/ml DNAse) for 1 h at 37°C. Cells were then filtered through a 70 μm strainer and enzymatic reaction was stopped by cold RPMI with 10 % fetal bovine serum and 1 % L-glutamine. Cells were washed with 50 ml cold RPMI with 10 % fetal bovine serum and 1 % L-glutamine and red blood cells were lysed using red blood cell lysis solution (MiltenyiBiotec). Finally, cells were filtered using a 40 µm Flowmi® Cell Strainer (Millipore) and re-suspended in PBS supplemented with 2 % fetal bovine serum at the concentration of 10,000 cells/μl for scRNA-Seq. AM were detached using a cell scraper, washed two times with PBS and fixed with methanol. After rehydration cells were filtered using a 40 µm Flowmi® Cell Strainer (Millipore) and re-suspended in PBS supplemented with 2 % fetal bovine serum at the concentration of 10,000 cells/μl for scRNA-Seq.  Single-nuclei were isolated from snap-frozen autopsy samples as described before [16]. Briefly samples were homogenized with one stroke of “loose” pestle in citric-acid based buffer (sucrose 0.25 M, citric acid 25 mM, Hoechst 33342 1 μg/mL) using a glass dounce tissue grinder. The tissue was incubated on ice for 5 minutes and then homogenized with 5 more strokes. After further 5 minutes of incubation, tissue was homogenized with 3 strokes using the “loose” pestle and then 5 more strokes using the “tight” pestle. Homogenate was filtered through a 35-μm cell strainer and centrifuged for 5 minutes at 500 x g at 4°C. Supernatant was removed, nuclei were resuspended in of citric acid buffer and the centrifugation step was repeated. Nuclei were then resuspended in cold resuspension buffer (KCl 25 mM, MgCl2 3 mM, Tris-buffer 50 mM, RNaseIn 0.4 U/μL, DTT 1mM, SuperaseIn 0.4 U/μL, Hoechst 33342 1 μg/mL). Nuclei were counted, diluted to the desired concentration and immediately loaded on the 10X Chromium controller.
The single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 3′ V3.1 library preparation kit according to the manufacturer’s protocol (10x Genomics). Full-length cDNA along with cell-barcode identifiers were PCR-amplified and sequencing libraries were prepared.
The constructed libraries were either sequenced on the Nextseq 500 using 28 cycles for read 1.55 cycles for read 2, and 8 index cycles, or on the Novaseq 6000 S1 using 28 cycles for read 1, 64 cycles for read 2, and 8 index cycles, to a median depth of 36000 reads per cell.

treatment_protocol: Infection experiments were carried out by two independent laboratories in Berlin (Robert Koch Institute and Charité) and one external collaboration partner (Wilhelms-University in Muenster). For infection experiments with SARS-CoV-2 (Munich 929 or BavPart1) [8] and rSARS-CoV (generated in the Drosten Lab by reverse genetics based on the SARS-CoV Frankfurt-1 strain, Accession Number FJ429166.1 [9]), the isolates were propagated in Vero E6 cells. The infection experiments at the Wilhelms-University in Muenster were performed with SARS-CoV-2 FI-200 isolate strain. rMERS-CoV (generated in the Drosten Lab by reverse genetics based on the MERS-CoV strain EMC/2012, Accession Number JX869059 [10]) was propagated in Vero B4 cells. HCoV-NL63 was propagated by growing the wild-type virus on Rhesus monkey kidney epithelial cells (LLC-MK2). Infection experiments were done in RPMI 1640 medium supplemented with 10 % (or 2 % for AM) fetal bovine serum and 2 mM L-glutamine at 37°C with 5 % CO2 under biosafety level 3 conditions with enhanced respiratory personal protection equipment.     The human seasonal influenza H3N2 virus A/Panama/2007/1999 (Pan/99[H3N2]) (further referred to IAV) strain was propagated using MDCK cells as described [3, 4]. Infection experiments were done in RPMI 1640 medium supplemented with 0.3 % bovine serum albumin and 2 mM L-glutamine at 37°C with 5 % CO2.

value: lung explant tissue

value: MERS-CoV


title: 45364

status: Public on May 30 2022

type: RNA

city: Camperdown

first: Dario

last: Strbenac

state: NSW

address: City Road

department: School of Mathematics and Statistics

country: Australia

institute: University of Sydney

hyb_protocol: A thermal cycler is pre-heated to 67  C. Tagset and RNA samples are removed from a freezer and thawed at room temperature. The tubes are inverted to mix and then briefly spun down. A hybridization master mix is created by adding 70  L of hybridization buffer and 7  L of the Probe A working pool directly to the tube containing the Tagset. The solution is inverted several times to mix and spun down. 7 L of the Probe B working pool is added to the master mix. 8  L of master mix is added to each of the 12 strip tubes then 7  L of RNA sample is added to each tube. Strip tubes are inverted several times and flicked to increase mixing. The tunes are briefly spun and immediately placed in the pre-heated 67  C thermal cycler, incubated for 16 hours and then ramped down to 4  C.

scan_protocol: A high-density scan (encompassing 600 fields of view) was performed.

data_processing: Raw values.

label: Fluorescent barcode

molecule: total RNA

organism: Homo sapiens

source_name: melanoma patient

label_protocol: Batches of 12 separate samples at one time were prepared according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from 20 to 30mg of fresh frozen tissue. Tissue samples were homogenized using a high-speed agitation polytron blender (Kinematica, Luzern, Switzerland) in the presence of Trizol. The RNA was isolated and purified with an RNeasy purification kit (Qiagen RNeasy purification kit; Qiagen) with DNAse I digestion on the column. The quality of the RNA preparations was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA). RNA integrity scores were more than 8 for all the samples analysed.

tag: Sex

value: Female

tag: age at banking (years)

tag: stage at banking

value: III

tag: time since metastasis (months)

tag: recurrence-free survival (months)

tag: recurrence-free category

tag: tissue

value: melanoma


title: lung_89C-EMC2_

type: SRA

library_source: transcriptomic

molecule: polyA RNA

tag: treatment


title: 17A031059-MF

city: Shanghai

first: Jiahao

last: Wang

state: Shanghai

address: Yueyang road

department: Bioinformatisc core

country: China

institute: Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

library_source: genomic

data_processing:
Trim adapters and low-quality bases using TrimGalore version 0.6.5 with the following setting: default
Genome alignment using BSMAP version 2.90 with the following setting: -q 20 -f 5 -p 8 -r 0 -v 0.05 -s 16 -S 1 -n 0
Sorting bam file using  sambamba version 0.7.1
Extracting CpG site methylation information using MethylDackel version 0.5.0
Assembly: hg19
Supplementary files format and content: Tab-delimited text files including methylated counts and total counts for each CpG site

molecule: genomic DNA

source_name: Placenta

extract_protocol:
 Within 15 min after delivery, 5 ml of neonatal umbilical cord blood was collected using two PAXGenRNA sampling tubes (2.5 ml/tube), and collected samples were were stored at -80 ℃. The placental tissues were collected from both the maternal and fetal side. Specifically, using a clean scalpel, one full-thick placental tissue was incised 5 cm from the perimeter of the placenta (a size of about 1×1×2 cm, including maternal and fetal side). Then, the tissues were rinsed with phosphate buffer (PBS) or normal saline until no visible blood and stored at -80 ℃ in a cryopreservation tube. DNA or RNA was extracted after homogenizing the tissues together.
RRBS and RNAseq library construction protocol -- Genomic DNA of placenta and umbilical cord blood specimens were extracted by using the TIANamp genomic DNA kit (Cat. No. DP304-02, TIANGEN Biotech CO. LTD., Beijing, China) per the manufacture’s recommendations. 50-300 ng of purified genomic DNA was utilized to generate RRBS libraries as previously described (https://www.nature.com/articles/s41594-018-0046-4). Indexed RRBS libraries were pooled accordingly and sequenced in a NovaSeq 6000 sequencer (Illumina, USA) with 100-base paired-end reads. Similarly, total RNAs were isolated using a miRNeasy Mini kit (QIAGEN, Germany) according to the manufacture’s recommendations. We used the Ribo-off rRNA depletion kit (Cat. No. N406-01, Vazyme Biotech Co. Ltd, Nanjing, China) to remove ribosomal RNA from total RNAs following the manufacturer’s instructions. To generate RNA-seq libraries, 10-100 ng rRNA-depleted RNAs were utilized by using the VAHTS total RNA-seq (H/M/R) library prep kit for Illumina (Cat. No. NR603-01, Vazyme Biotech Co. Ltd, Nanjing, China) per the manufacturer’s instructions. We sequenced the RNA-seq libraries in the NovoSeq 6000 sequencer with 100-base paired-end reads. The sequencing data volume of a single sample is around 8 gigabases (Gb) and the average sequencing depth of the target region of the enzyme digestion fragment is > 30×, the coverage proportion of CpG region is > 40%, and the total data volume is 100 Gb. Similarly, transcriptome profile for each placenta and umbilical cord blood sample was also conducted. VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® based on Ribo-zero method was used to constructed transcriptome RNA library and high-throughput sequencing was performed subsequently. 10 Gb volume of transcriptome data for each sample was necessary.

tag: group

value: GDM


title: 17A031056-MF


title: 17A031057-M

source_name: Umbilical cord blood


title: 17A031057-MF


title: 17A031058-M


title: lung_663D-Panama1_1

value: IAV


title: lung_663D-S1_1


title: 17A031054-M


title: 30637 Replicate 2

value: Poor


title: 17A031054-MF


title: 31977

value: Male


title: FB00612867


title: lung_195V-S1_1


title: 17A031052-MF


title: 17A031051-MF

value: Control


title: 17A031053-M


title: 17A031052-M


title: 17A031051-M


title: 85242


title: 17A031050-MF


title: lung_663D-mock1_1

value: control


title: 17A031050-M


title: 17A031049-MF


title: lung_641D-Panama1_1


title: 17A031053-MF


title: lung_89C-mock1_1


title: 17A031056-M


title: lung_641D-EMC1_1


title: 17A031049-M


title: 17A031048-MF


title: 17A031048-M


title: 500063


title: 17A031047-MF


title: 17A031047-M


title: 17A031046-MF


title: 17A031046-M


title: 85002


title: lung_641D-S1_1


title: 17A031044-MF


title: lung_641D-mock1_1


title: 46808 Replicate 1


title: 56788


title: 46760


title: 17A031043-MF


title: 17A031044-M


title: 46666

value: Good


title: 17A031043-M


title: lung_195V-mock1_1


title: lung_663D-S2_1


title: 17A031042-M


title: 46808 Replicate 2


title: 17A020374-M


title: 17A020373-MF


title: lung_641D-S2_1


title: lung_89C-Panama1_1


title: 17A020373-M


title: 17A020371-MF


title: 17A031042-MF


title: 17A020369-MF


title: 85293


title: 30637 Replicate 1


title: lung_195V-S2_1


title: 45016 Replicate 2


title: 17A020370-MF


title: 45044


title: 17A020374-MF


title: lung_89C-S1_1


title: 84562


title: 78707


title: lung_89C-S2_1


title: 17A020370-M


title: lung_663D-EMC1_1


title: 17A020371-M


title: 17A020368-MF


title: lung_195V-Panama1_1


title: 56030


title: 503321


title: 17A020367-MF


title: 17A020368-M


title: 17A020366-MF


title: 17A020367-M


title: 45179


title: AO31_control

description:
single-cell polyA RNA
alveolar_organoids.rds

value: alveolar lung organoids


title: AO28_SCoV2


title: AO31_SCoV2


title: AO27_control


title: AO15_SCoV2

description:
single-cell polyA RNA
bronchial_organoids.rds

value: bronchial lung organoids


title: AO27_SCoV2


title: AO28_control


title: 31999


title: 31743 Replicate 2


title: 31547 Replicate 2


title: 45016 Replicate 1


title: 17A020346-M


title: 17A020363-M


title: 17A020364-M


title: 17A020363-MF


title: 30855


title: 17A020365-M


title: 17A020365-MF


title: 17A020361-MF


title: 17A020346-MF


title: 17A020345-MF


title: 17A020366-M


title: 17A020364-MF


title: 17A020361-M


title: 17A020345-M


title: AO13_SCoV2


title: 17A020344-MF


title: AO13_control


title: 31743 Replicate 1


title: 17A020344-M


title: AO15_control


title: 17A020342-M


title: 17A020343-M


title: 17A020342-MF


title: 17A020343-MF


title: lung_89C_MERS

description:
single-cell polyA RNA
lung_combined_all.rds


title: lung_89C_SCoV1


title: 17A020341-MF


title: mef2>NUAK548 muscle replicate 3

city: Manhattan

first: Erika

middle: R

last: Geisbrecht

state: KS

address: 141 Chalmers Hall, Chalmers Hall

department: Biochemistry and Molecular Biophysics

country: USA

institute: Kansas State University

description: matrix column name: NUAK548_muscle_3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36
Trimmed sequence reads were mapped using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2
Differential gene expression was determined using DESeq2 and significance was defined as p-values of <0.05.
Assembly: Drosophila melanogaster BDGP6 reference genome
Supplementary files format and content: Individual .txt files of unique gene hit counts. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.

organism: Drosophila melanogaster

source_name: L3 muscle carcass

growth_protocol: Flies were maintained on standard cornmeal-yeast-agar medium at 25 °C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.

value: L3 muscle carcass

tag: genotype

value: NUAK OE


title: mef2>NUAK550 muscle replicate 3

description: matrix column name: NUAK550_muscle_3


title: mef2>NUAK550 muscle replicate 1

description: matrix column name: NUAK550_muscle_1


title: mef2>NUAK548 muscle replicate 2

description: matrix column name: NUAK548_muscle_2


title: mef2>NUAK550 muscle replicate 2

description: matrix column name: NUAK550_muscle_2


title: lung_89C_SCoV2


title: 17A020341-M


title: mef2>NUAK548 muscle replicate 1

description: matrix column name: NUAK548_muscle_1


title: 17A020340-MF


title: 17A020340-M


title: mef2>lacZ muscle replicate 3

description: matrix column name: LacZ_muscle_3


title: mef2>lacZ muscle replicate 2

description: matrix column name: LacZ_muscle_2


title: 17A020338-MF


title: mef2>lacZ muscle replicate 1

description: matrix column name: LacZ_muscle_1


title: lung_219V_FCS

value: FCS


title: lung_89C_H3N2

value: lung explant tissue


title: 17A020338-M


title: lung_219V_SCoV1


title: mef2>NUAK550 whole replicate 3

description: matrix column name: NUAK550_whole_3

source_name: L3 whole larvae

value: L3 whole larvae


title: lung_219V_H3N2


title: lung_219V_MERS

value: MERS-CoV


title: lung_219V_BSA

value: BSA


title: 30807

value: III

value: melanoma


title: 84737 Replicate 2

value: Female


title: 45583


title: 84424


title: 500888


title: 84521

value: Poor


title: 31547 Replicate 1

value: Male


title: 29171 Replicate 2


title: 31963


title: 45177


title: 501036


title: 84737 Replicate 1


title: lung_218V_SCoV2


title: lung_700D_control


title: lung_219V_SCoV2


title: lung_700D_H3N2

value: IAV


title: mef2>NUAK550 whole replicate 2

description: matrix column name: NUAK550_whole_2


title: 142 Replicate 2


title: lung_89C_control


title: lung_218V_SCoV1


title: 84454


title: 120 Replicate 2


title: mef2>NUAK548 whole replicate 3

description: matrix column name: NUAK548_whole_3


title: mef2>NUAK548 whole replicate 1

description: matrix column name: NUAK548_whole_1


title: Dorsal E370k COs Day 60

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description:
mut.dor
mRNA
dorsal_organoids_counts.csv

data_processing:
RNA-seq reads were mapped to human genome and counted with cellranger (hg38).
Assembly: hg38
Supplementary files format and content: *_counts.csv: Comma-separated text files

source_name: Dorsal E370k COs Day 60

extract_protocol: not provided

value: Dorsal E370k COs

tag: Stage

value: 60 days old

tag: patterning protocol

value: cyclopamine A 1:500


title: Ventral Control/E370K Mosaic organoids d60 [mut20]

description:
mut20
mRNA
ventral_mosaic_counts.csv

value: Ventral Control/E370K Mosaic organoids


title: 84412 Replicate 1

value: Good


title: 84412 Replicate 2


title: mef2>NUAK550 whole replicate 1

description: matrix column name: NUAK550_whole_1

value: NUAK OE


title: 78907


title: lung_218V_control

value: FCS


title: Dorsal Control COs Day 60

description:
ctrl.dor
mRNA
dorsal_organoids_counts.csv

source_name: Dorsal Control COs Day 60

value: Dorsal Control COs


title: 56486


title: Ventral Control/E370K Mosaic organoids d60 [ctrl80]

description:
ctrl80
mRNA
ventral_mosaic_counts.csv


title: lung_218V_MERS

value: lung explant tissue


title: 17A020369-M

value: Control


title: mef2>NUAK548 whole replicate 2

description: matrix column name: NUAK548_whole_2

value: L3 whole larvae


title: lung_218V_H3N2


title: 78835

value: III


title: lung_1169Z_SCoV2


title: lung_1169Z_SCoV1


title: mef2>lacZ whole replicate 2

description: matrix column name: LacZ_whole_2

value: control


title: mef2>lacZ whole replicate 1

description: matrix column name: LacZ_whole_1


title: Ventral E370k COs Day 60

description:
mut.ven
mRNA
ventral_organoids_counts.csv

source_name: Ventral E370k COs Day 60

value: Ventral E370k COs


title: P7_ATAC

city: Toronto

first: David

last: Brooks

address: 610, University Ave

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Cellranger-arc v2.0.0 with underlying Martian v4.0.5 was used to process Chromium single cell multiome ATAC + Gene expression sequencing data
cellranger-arc was ran in count mode using GRCh38-2020-A-2.0.0
Assembly: GRCh38
Supplementary files format and content: tar archives of both data types. For ATAC data, fragment files from alignment, bed files for peaks and peak-annotations are provided. For the GEX data, the count matrix is provided in mtx format, while the features and barcodes are in a tsv file.

source_name: PBMC

extract_protocol:
Cells were DNAse treated, washed then incubated in nuclei lysis buffer (0.1% Tween, 0.1% NP-40) for 3 min as specified in the 10X protocol. Transposition was performed according to the manufacturer's protocol, targeting 10,000 cells per sample
ATAC and GEX libraries were constructed according to the manufacturer's protocol (see CG000338_Chromium_NexGEM_Multiome_ATAC-GEX_User Guide_RevE availabile on the 10X genomics website for details)

treatment_protocol: Cryopreserved PBMCs were thawed and immedaitely processed for scRNA-seq/scATAC-seq (Multiome-seq) according to the 10X multiomics protocol

tag: cell type

value: PBMC

tag: disease state

value: melanoma

tag: ifn-i response capacity

value: low


title: P6_ATAC


title: P5_ATAC


title: P4_ATAC

value: high


title: lung_1169Z_H3N2

value: IAV


title: mef2>lacZ whole replicate 3

description: matrix column name: LacZ_whole_3


title: lung_102C_SCoV2


title: Mus musculus,Lung,Control – Rep4

city: Quebec

first: Julien

last: Prunier

state: QC

address: 1030 av. de la medecine

department: Forestry

institute: Université Laval

description:
GR8-4
GR8-4

data_processing:
Raw reads were cleaned using Trimmomatics
Cleaned reads were pseudo-aligned to a composite exome made of the reference exomes of Musmusculus and Sars-Cov-2 using Kallisto
tpm and differential gene expression were obtained using the Deseq2 R package
heatmaps and volcano plots were obtained using R
Assembly: The exome assembly to which reads were aligned was built by adding Sars-Cov-2 contigs to the reference exome of mice.
Supplementary files format and content: A data table including reads counts normalized (TPM).

organism: Mus musculus

source_name: Lung

extract_protocol:
RNA from lungs of mice was extracted using the Bead Mill Tissue RNA Purification Kit and the Omni Bead Ruptor Bead Mill homogenizer (Kennesaw, GA)
NEBNext Ultra II directional RNA library and NEBNext rRNA Depletion kits

value: Lung

tag: infection


title: 502916

value: Female


title: P2_ATAC


title: 501220

value: Male


title: 29171 Replicate 1

value: Poor


title: lung_1169Z_MERS

value: MERS-CoV


title: lung_1169Z_control

value: FCS


title: lung_102C_SCoV1

value: lung explant tissue


title: 387


title: Ventral Control COs Day 60

description:
ctrl.ven
mRNA
ventral_organoids_counts.csv

source_name: Ventral Control COs Day 60

value: Ventral Control COs

value: 60 days old


title: 396

value: III

value: Good


title: Mus musculus,Lung,Control – Rep1

description:
GR8-1
GR8-1

value: Control


title: P1_ATAC

value: PBMC


title: P3_ATAC

value: melanoma


title: 31503


title: Mus musculus,Lung,Control – Rep3

description:
GR8-3
GR8-3


title: 394


title: HD2_ATAC

value: healthy


title: lung_102C_MERS


title: 351


title: Mus musculus,Lung,Delta – day5 – Rep4

description:
PROT6GR2-8
PROT6GR2-8_S205_L002

value: Delta strain


title: P8_GEX

value: low


title: Mus musculus,Lung,Control – Rep2

description:
GR8-2
GR8-2

value: Lung


title: lung_102C_FCS


title: Mus musculus,Lung,Delta – day5 – Rep5

description:
PROT6GR2-9
PROT6GR2-9_S206_L002


title: HD1_ATAC


title: lung_102C_H3N2

value: IAV


title: Mus musculus,Lung,Delta – day5 – Rep3

description:
PROT6GR2-7
PROT6GR2-7_S204_L002


title: 340

value: Male


title: lung_102C_BSA

value: BSA


title: P7_GEX


title: Mus musculus,Lung,Delta – day7 – Rep5

description:
PROT6GR2-15
PROT6GR2-15_S212_L002


title: T188-R2-prolonged

value: autopsy material

tag: condition

value: prolonged


title: P6_GEX


title: Mus musculus,Lung,Delta – day5 – Rep2

description:
PROT6GR2-6
PROT6GR2-6_S203_L002


title: Mus musculus,Lung,Delta – day7 – Rep4

description:
PROT6GR2-14
PROT6GR2-14_S211_L002


title: 334

tag: Sex

value: Female

value: Poor


title: P5_GEX


title: Mus musculus,Lung,Delta – day7 – Rep3

description:
PROT6GR2-13
PROT6GR2-13_S210_L002


title: T128-akut

value: acute


title: 350

tag: age at banking (years)

value: III


title: O325-akut


title: 278

tag: stage at banking

value: Good


title: 349

tag: time since metastasis (months)


title: BB73-control

value: control


title: 360

tag: recurrence-free survival (months)


title: Mus musculus,Lung,Delta – day7 – Rep2

description:
PROT6GR2-12
PROT6GR2-12_S209_L002


title: P3_GEX

value: PBMC

value: high


title: Mus musculus,Lung,Delta – day7 – Rep1

description:
PROT6GR2-11
PROT6GR2-11_S208_L002


title: P2_GEX

value: melanoma


title: Mus musculus,Lung,Wuhan – day7 – Rep4

description:
PROT2GR3-5
PROT2GR3-5_S202_L002

value: Wuhan strain


title: 343

tag: recurrence-free category


title: P1_GEX


title: 322

tag: tissue


title: Mus musculus,Lung,Wuhan – day7 – Rep3

description:
PROT2GR3-3
PROT2GR3-3_S200_L002

tag: treatment


title: 205


title: A344-R3-chronic

value: chronic


title: 242


title: P4_GEX


title: F2_GABA_4hr_rep2 [s30]

city: New York

last: Yan

email: linda.lee2@mssm.edu, nan.yang1@mssm.edu

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Mount Sinai

description: F2+ AD b2 2-28 4h

data_processing:
Raw reads were trimmed for base call quality (PHRED score ≥ 21) using skewer 0.2.2 (Jiang et al., 2014).
Transcript quantification was performed using combined human-mouse reference transcriptome (GENCODE v28 and vM18) and salmon 1.13.1 (Patro et al., 2017), and human reference-specific counts extrated for downstream analysis..
Count normalization and FPKM calculation were performed using DESeq2 in R.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Salmon Counts (quant.sf) transcript abundance for every gene and every sample for both mouse and human transcriptomes

source_name: NSB3188 (iPSC)

growth_protocol: hES or hiPS cell–derived neurons were routinely generated by overexpression of the transcription factors Ngn2 (Glu neurons) or Ascl1 and Dlx2 (GABA neurons). On day 1, medium was replaced by N2 media(1x N2 supplement, 1X NEAA in DMEM-F12 media) containing 2 mg/ml Doxycycline to induce TetO expression. Selection of transduced cells was achieved with N2 media containing antibiotics for 2 or 3 days, and media was replaced with N2 media containing 4 μM Cytosine β-D-arabinofuranoside hydrochloride for 2 or 3 days to inhibit cell proliferation. Induced neurons were dissociated using Accutase and replated with mouse glial cells on Geltrex-coated plates. The media used for plating was a 1:1 mix of Neurobasal medium supplemented with B27, Glutamax containing 1% FBS and glial plating media(1x Glutamax , 2mg/ml Glucose and 5% FBS) containing 2 μM Thiazovivin(TV) and 2 mg/ml Doxycycline. TV was removed from media the following day. Half of the media was changed every 2-3 days and replaced with fresh Neurobasal medium supplemented with B27, Glutamax containing 1% FBS. 7 days later, the media was replaced by Neurobasal A, B27, Glutamax containing 1% FBS and half of it was replaced every 4 days. Mature neurons were co-cultured with mouse glial cells on day in vitro 35 (DIV35) for various experiments.

extract_protocol:
DIV35 neurons were washed once with D-PBS, lifted using Accutase and RNA was extracted with TRIzol following the provider’s instructions. Following isolation, the RNA was treated with TURBO DNA-free kit. Total RNA (1μg) was used per sample for library preparation and sequencing.
Standard RNA-seq with Poly(A) mRNA selection was performed by Genewiz using Illumina NovaSeq platform and yielding 20-30 million paired-end 150 bp reads per sample.

treatment_protocol: Prior to depolarization, medium was replaced with serum free Neurobasal A/B27/Glutamax for 3 days. The neuronal culture was then silenced using 1μM of Tetrodotoxin citrate (TTX) (Labome 1069/1) and 100μM of DL-2-amino-5-phosphopentnoic acid (DL-AP5) (Abcam ab120271) for 12-16h. The neurons were then depolarized by adding depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl and 10 mM HEPES directly into the media to a final concentration of 30% of the total culture media. Neurons were collected at different time points after depolarization for experiments.

tag: cell line

value: NSB3188 (iPSC)

value: induced GABAergic neurons

value: depolarization

tag: timepoint


title: A333-chronic


title: Mus musculus,Lung,Wuhan – day7 – Rep2

description:
PROT2GR3-2
PROT2GR3-2_S199_L002

value: Lung


title: AM723D_SCoV2_ctrl_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds

value: ex-vivo infected AM cells


title: A592-prolonged

value: autopsy material

value: prolonged


title: AM723D_SCoV2_ctrl_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: HD2_GEX

value: healthy


title: Mus musculus,Lung,Delta – day5 – Rep1

description:
PROT6GR2-10
PROT6GR2-10_S207_L002

value: Delta strain


title: 61

value: Female

value: III

value: Poor


title: 149

value: Male


title: F2_GABA_45min_rep2 [s29]

description: F2+ AD b2 2-28 45'


title: 233


title: 17B-control

value: control


title: F2_GABA_0hr_rep2 [s28]

description: F2+ AD b2 2-28 0h


title: Mus musculus,Lung,Wuhan – day7 – Rep1

description:
PROT2GR3-1
PROT2GR3-1_S198_L002


title: Mus musculus,Lung,Wuhan – day7 – Rep5

description:
PROT2GR3-4
PROT2GR3-4_S201_L002


title: AM723D_SCoV2_ACE2_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: AM723D_SCoV2_ACE2_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: HD1_GEX

value: PBMC


title: Mus musculus,Lung,Wuhan – day5 – Rep4

description:
PROT2GR1-4
PROT2GR1-4_S196_L002

value: Wuhan strain


title: AM723D_NL63_ctrl_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: F2_GABA_4hr_rep1 [s27]

description: F2+ AD 2-21 4h


title: F2_GABA_45min_rep1 [s26]

description: F2+ AD 2-21 45'


title: F2_GABA_0hr_rep1 [s25]

description: F2+ AD 2-21 0h


title: Mus musculus,Lung,Wuhan – day5 – Rep3

description:
PROT2GR1-3
PROT2GR1-3_S195_L002


title: AM723D_NL63_ACE2_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: 66

value: Good

value: melanoma


title: 64


title: AM723D_NL63_ctrl_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: 142 Replicate 1


title: Mus musculus,Lung,Wuhan – day5 – Rep2

description:
PROT2GR1-2
PROT2GR1-2_S194_L002


title: F2_Glu_4hr_rep2 [s24]

description: F2 Ngn2 3/8 4h

value: NSB3188 (iPSC)

value: induced glutamatergic neurons


title: AM723D_NL63_ACE2_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: Mus musculus,Lung,Wuhan – day5 – Rep1

description:
PROT2GR1-1
PROT2GR1-1_S193_L002

value: Lung


title: 179


title: Mus musculus,Lung,Wuhan – day5 – Rep5

description:
PROT2GR1-5
PROT2GR1-5_S197_L002


title: F2_Glu_0hr_rep2 [s22]

description: F2 Ngn2 3/8 0h

value: depolarization


title: 69


title: F2_Glu_45min_rep2 [s23]

description: F2 Ngn2 3/8 45'


title: 385


title: AM723D_control_ctrl_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds

value: ex-vivo infected AM cells


title: 53


title: AM723D_control_ACE2_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: P8_ATAC

value: low


title: 74


title: J774 KO1 IFNG 4h IgG

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 Colorado Ave. JSC Biotech Bldg

department: Molecular, Cellular and Developmental Biology

institute: BioFrontiers Institute at University of Colorado Boulder

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 with arguments 'ktrim=r k=31 mink=11 hdist=1 qtrim=r trimq=10 tpe tbo' and mapped to mm10 using hisat2 v2.1.0 with options '--rna-strandness RF --no-softclip'. Aligned fragments with an alignment score less than 10 were removed with samtools v1.10. Alignment files corresponding to technical replicates (designated as "S1" and "S2") were merged, and all samples were mapped to genes in the complete refseq annotation using featureCounts v1.6.2 with options '-s 2 -t exon -g gene_id -0 -p'. For visualization aligned fragments were converted to stranded, CPM normalized bigwigs using deepTools bamCoverage v3.0.1.
Differentially expressed genes were called using DESeq2 v1.26.0 with design '~ treatment'. For the knockout differential expression analysis, normalized count data is derived from DESeq2 comparisons between KO IFNG vs WT IFNG.
Assembly: mm10
Supplementary files format and content: CPM normalized signal tracks in UCSC bigwig format
Library strategy: CUT&Tag

growth_protocol: J774 cells were routinely grown at 37C in 5% CO2 on coated plastic (Corning #430591, typically 1,000,000-2,000,000 cells in 10cm dishes) in DMEM (Gibco #10566-016) supplemented with 1X penicillin-streptomycin (Gibco #15140122) and 10% fetal bovine serum (Gibco #10437010).

extract_protocol:
DNA from J774 was extracted following CUTnTag protocol from Kaya-Okur et al 2020 and Kaya-Okur and Henikoff 2020. All DNA was stored at -20°C.
Libraries prepared according to protocol from Kaya-Okur et al 2020 and Kaya-Okur and Henikoff 2020 using barcoded i5 and i7 primers.

treatment_protocol: Cells were stimulated with 100 ng/mL mouse IFNG (R&D Systems #485-MI-100) for 4h.

tag: breed

tag: age

tag: genotype

value: B2_Mm2 knockout

value: IFNG

tag: time point


title: J774 KO1 IFNG 4h Rpb1


title: F2_Glu_45min_rep1 [s20]

description: F2 Ngn2 2/20 45'

tag: cell type


title: AM723D_control_ACE2_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: J774 KO1 IFNG 4h CTCF


title: F2_Glu_0hr_rep1 [s19]

description: F2 Ngn2 2/20 0h


title: H1_GABA_4hr_rep3 [s18]

description: H1 AD 022719 4h

source_name: WA01 (H1 ES)

value: WA01 (H1 ES)

value: induced GABAergic neurons


title: AM1212Z_SCoV2_ctrl_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: J774 KO1 IFNG 4h Anti-STAT1


title: 49

value: III


title: AM1212Z_SCoV2_ctrl_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: J774 WT IFNG 4h IgG

value: wildtype


title: H1_GABA_45min_rep3 [s17]

description: H1 AD 022719 45'


title: 37

value: Male


title: AM1212Z_SCoV2_ACE2_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: AM1212Z_SCoV2_ACE2_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: 32


title: 52

value: Female

value: Poor


title: F2_Glu_4hr_rep1 [s21]

description: F2 Ngn2 2/20 4h


title: H1_GABA_0hr_rep3 [s16]

description: H1 AD 022719 0h


title: AM723D_control_ctrl_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds

value: control


title: J774 WT IFNG 4h H3K27a


title: 119

value: melanoma


title: J774 KO1 IFNG 4h H3K27a


title: H1_GABA_4hr_rep2 [s15]

description: H1 AD b2 022219 4h


title: AM1212Z_NL63_ctrl_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: 103

value: Good


title: H1_GABA_45min_rep2 [s14]

description: H1 AD b2 022219 45'


title: J774 WT IFNG 4h Rpb1


title: 45


title: AM1212Z_NL63_ctrl_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: Aged21 PD 3

city: Kyoto

first: Hirotake

last: Tsukamoto

state: Sakyo-Ku

address: 53 Kawahara-cho Shogoin

department: Center for Cancer Immunotherapy and Immunobiology

country: Japan

institute: Kyoto University

description: Melanoma cell line, MO4 was subcutaneously inoculated into the mice.

data_processing:
bcl2fastq software version 1.8.4 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trimmomatic software, then mapped to mm10 whole genome using HISAT2.
Raw read counts and calculation of transcript per million (TPM) were preformed using featureCounts software version 1.6.3.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using deepTool version 3.5.0.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Whole lung tissue from melanoma-bearing mice

extract_protocol:
Lung tissues were minced, and total RNA was extracted using Trizol reagent. RNA samples were further purified using RNesy mini kit (Qiagen). Polyadenylated mRNA was then isolated and fragmented using NEBNext Poly(A) mRNA magnetic isolation module (NEB).
RNA sequencing cDNA libraries were prepared with reverse transcription, followed by adapter ligation at both ends of fragmented double strand cDNA, and enrichment of PCR library using NEBNext Ultra TMII directional RNA library Prep Kit (NEB).

treatment_protocol: Melanoma cell-inoculated mcie were treated with anti-PD-1 Ab or control Ab 3, 7, 11 days post melanoma inoculation.

tag: strain

value: 22 month old

value: intraperitoneal injection of anti-PD-1 Ab and anti-IL-21 receptor Ab


title: AM1212Z_NL63_ACE2_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds

tag: condition


title: AM1212Z_NL63_ACE2_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: H1_GABA_0hr_rep2 [s13]

description: H1 AD b2 022219 0h

value: depolarization


title: 120 Replicate 1

tag: Sex


title: Aged21 PD 2

value: Lung


title: H1_GABA_45min_rep1 [s11]

description: H1 AD b1 022219 45'


title: 217

tag: age at banking (years)


title: Aged21 PD 1


title: H1_GABA_0hr_rep1 [s10]

description: H1 AD b1 022219 0h


title: Aged cont 3

value: intraperitoneal injection of Isotype-matched rat control Ab


title: AM1212Z_control_ctrl_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds

value: ex-vivo infected AM cells


title: AM1212Z_control_ctrl_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: Aged cont 2


title: 30

tag: stage at banking


title: 17

tag: time since metastasis (months)


title: J774 WT IFNG 4h CTCF

value: IFNG


title: H1_Glu_4hr_rep3 [s9]

description: H1 Ngn2 b2 030519 4h

value: WA01 (H1 ES)

value: induced glutamatergic neurons


title: AM1212Z_control_ACE2_48h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: Aged cont 1


title: AM1212Z_control_ACE2_16h

description:
single-cell polyA RNA
ex_vivo_AM.rds


title: H1_Glu_0hr_rep3 [s7]

description: H1 Ngn2 b2 030519 0h


title: 125

value: III

tag: recurrence-free survival (months)


title: 16

tag: recurrence-free category


title: Young PD 3

tag: tissue

value: 2 month old

value: intraperitoneal injection of anti-PD-1 Ab


title: H1_GABA_4hr_rep1 [s12]

description: H1 AD b1 022219 4h

value: induced GABAergic neurons

tag: treatment


title: 237

value: Female

value: Poor


title: J774 WT IFNG 4h Anti-STAT1

tag: cell line

value: wildtype


title: switch_0619

first: Yoshinori

last: Yoshida

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

data_processing:
Illumina bcl2fastq (v2.17.14) 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 (v1.15) 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 (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.4.3) and its package DESeq2 (v1.18.1) were performed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 nomalized count values for each sample.

source_name: induced cardiomyocyte sorted with miRNA-switch()

growth_protocol: For iPSCs, ReproCELL supplemented with bFGF at 37 ºC in a humidified incubator with 5% CO2. For cardiomyocytes, undifferentiated iPSCs were dissociated, and then suspended in StemPro-34 media supplemented with Y-27632 and BMP4. On day 1, media, containing activin A, BMP4 and bFGF, were added. On day 4, the media were changed to differentiation media supplemented with VEGF and IWP-3. On day 7, the media were changed to StemPro-34 media supplemented with VEGF and bFGF. For the maintenance of iPSC-CMs, the culture media were exchanged every 2-3 days.

extract_protocol:
RNeasy Mini Kit
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

treatment_protocol: For purifying CMs by miRNA switch and MACS, miR-208a CD4 switch and PAC mRNA were transfected into the differentiated cells from iPSCs at day17. After 24 hours from transfection, CD4 positive cells were eliminated by CD4 micro beads and MACS. The cells were treated by puromysin subsequent 48 hours. For purifying CMs by antibodies, CD172a/b positive, CD31 negative, CD49a negative, CD90 negative, and CD140b negative cells were sorted by cell sorter at day20 fom the diffrentiation.

tag: differentiation stage

tag: sorting method

value: miRNA-switch


title: H1_Glu_45min_rep2 [s5]

description: H1 Ngn2 b1 030519 45'

tag: timepoint


title: Young PD 2

tag: age


title: SIRPA_0619

source_name: induced cardiomyocyte sorted with SIRPA(+) LIN(-)

value: Antibody


title: 15

value: Male

value: melanoma


title: H1_Glu_4hr_rep1 [s3]

description: H1 Ngn2 122018 4h

value: depolarization


title: SIRPA_0605


title: iPS_2

source_name: human iPSCs

value: iPS


title: Young PD 1

value: Lung


title: Aged PD 2

value: 22 month old


title: 196

source_name: melanoma patient


title: H1_Glu_45min_rep1 [s2]

description: H1 Ngn2 122018 45'

value: WA01 (H1 ES)


title: iPS_1


title: H1_Glu_45min_rep3 [s8]

description: H1 Ngn2 b2 030519 45'

value: induced glutamatergic neurons


title: H1_Glu_0hr_rep2 [s4]

description: H1 Ngn2 b1 030519 0h


title: H1_Glu_0hr_rep1 [s1]

description: H1 Ngn2 122018 0h


title: H1_Glu_4hr_rep2 [s6]

description: H1 Ngn2 b1 030519 4h


title: 172

value: III

value: Good


title: switch_0605


title: 288


title: 249


title: Aged PD 3

value: intraperitoneal injection of anti-PD-1 Ab


title: Fluconazole treated-Day3-replicate2 [FCZ_3_2 ]

status: Public on May 29 2022

city: London

first: Michael

last: Hallett

state: Ontario

address: 1151 Richmond St

department: Biochemistry

institute: Western University

description: R1 is UMI/CBC; R2 is transcript

library_source: transcriptomic single cell

data_processing:
Gene abundance estimation was performed using Alevin-fry pipeline to reduce the number of discarded reads and makin a gene-by-cell matrix for each sample. Cells indistinguishable from ambient RNA were excluded using EmptyDrops. Quality control and gene filtering was performed using SCANPY python library (Wolf et al 2018) and SingleCellExperiment R package(Amezquita et al 2019).
Raw reads from sequncing of the bulk sample were pre-processed with the sequence-grooming tool cutadapt (Martin 2011). Reads were mapped against C.albicans genome by STAR(Kim et al 2019). The read alignments and C. albicans genome annotation strain SC5314_A22 (haplotype A, version 22; GCF_000182965.3) were provided as input to featureCounts() from the Rsubread package (Liao, Smyth, and Shi 2019) to estimate gene abundances.
Assembly: C. albicans strain SC5314_A22 (haplotype A, version 22; GCF_000182965.3)
Supplementary files format and content: Comma-separated file containing gene raw counts per cell
Supplementary files format and content: Comma-separated file containing cell metadata
Supplementary files format and content: Comma-separated file containing gene raw counts for the bulk sample

organism: Candida albicans SC5314

source_name: Fluconazole treated

growth_protocol: Bulk and Single cell untreated: C. albicans cells were grown in YPD rich media before collecting single cell transcriptomics as untreated samples

extract_protocol:
Cells were suspended in RNAlater and stored in -20 for 2 to 3 days. After Zymolyase digestion to make spheroplasts, the transcriptomes of single cells were captured by polyT oligonucleotides attached to the surface of  specific microparticles(Chemegenes beads) in a microfluidic device. cDNAs were made and amplified for sequencing as described in Macosko et al 2015. 600pg cDNA were used for making sequencing libraries.
Sequencing libraries were prepared using Illumina protocol and samples were sequenced with Nextseq500-- 0.5 Flowcell High Output (200 M  fragments)-- 75 cycles Single-End read (maximum 1x85 nt)

treatment_protocol: Cells were grown in YPD media in presence of  different antifungals and single cell or bulk transcriptomics were done after 2, 3 or 6 days of drug treatment

tag: media

value: YPD

value: Fluconazole treated

tag: day


title: Fluconazole treated cells-Day2 [FCZ_2_bulk]

extract_protocol:
Cells were harvested after drug treatment and suspended in RNAlater and stored in -20 before RNA extraction. Total RNA were harvested using Qiagen RNeasy mini kit (cat #74104) protocol.
RNA (mRNA-Seq stranded/ Transcriptome)

tag: strain


title: Fluconazole treated-Day2-replicate2 [FCZ_2_2 ]

description: R1 is UMI/CBC; R2 is transcript


title: Fluconazole treated-Day2-replicate1 [FCZ_2_1 ]

description: R1 is UMI/CBC; R2 is transcript


title: Caspofungin treated-Day2-replicate1 [CSP_2_1 ]

description: R1 is UMI/CBC; R2 is transcript

source_name: Caspofungin treated

value: Caspofungin treated


title: Fluconazole treated-Day3-replicate3 [FCZ_3_3 ]

description: R1 is UMI/CBC; R2 is transcript


title: Fluconazole treated-Day3-replicate1 [FCZ_3_1 ]

description: R1 is UMI/CBC; R2 is transcript


title: Untreated replicate 3 [UT_0_3]

description: R1 is UMI/CBC; R2 is transcript

source_name: Untreated

value: Untreated


title: Fluconazole treated-Day6-replicate1 [FCZ_6_1 ]

description: R1 is UMI/CBC; R2 is transcript


title: Untreated replicate 2 [UT_0_2]

description: R1 is UMI/CBC; R2 is transcript


title: Rapamycin treated-Day2-replicate1 [RAPA_2_1 ]

description: R1 is UMI/CBC; R2 is transcript

source_name: Rapamycin treated

value: Rapamycin treated


title: Untreated replicate 1 [UT_0_1]

description: R1 is UMI/CBC; R2 is transcript


title: EA1_InVItro_4

city: Aurora

first: Emily

last: Kleczko

department: Medicine

institute: University of Colorado Anschutz Medical Campus

data_processing:
Reads were quality checked using FastQC.
TopHatv2 was used to align reads to the Mus musculus mm10 reference genome.
Cufflinks v2.0.2 was used to assemble aligned reads into transcripts and estimate their abundance.
Assembly: Mus musculus mm10
Supplementary files format and content: Excel files (.xlsx) include FKPM values for each sample.

growth_protocol: EA1 and EA2 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in a humidified incubator with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using RNeasy mini plus kit (Qiagen), including the genomic DNA elimination step.
Libraries were constructed using an Illumina TruSEQ stranded mRNA Sample Prep Kit (Cat# RS-122-2101). Total RNA was combined with RNA purification beads to bind PolyA RNA to oligodT magnetic beads. mRNA was eluted and converted to double stranded DNA. A-tailing, adapter ligation, and PCR amplification using 15 cycles was performed to complete the library construction.

tag: cell type

value: EML4-ALK fusion-driven murine lung cancer cell line

tag: condition

value: in vitro


title: EA1_InVivo_4

description: lung

value: in vivo


title: EA1_InVItro_5


title: EA1_InVivo_2

description: lung


title: EA1_InVivo_3

description: lung


title: EA1_InVivo_1

description: lung


title: EA1_InVivo_5

description: lung


title: EA1_InVItro_2


title: EA1_InVItro_3


title: EA1_InVItro_1


title: 36

tag: Sex

value: Female

tag: age at banking (years)

value: Poor

value: melanoma


title: PBMC aaOnepot-Seq for C donor using CD16 antibody

city: Seoul

first: Dongju

last: Shin

address: 50, Yonsei-ro

department: Chemistry

country: South Korea

institute: Yonsei University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the drop-seq pipeline
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol: Library was constructed according to the Drop-seq protocol

value: Peripheral blood

value: female


title: PBMC aaOnepot-Seq for C donor using CD3 antibody


title: PBMC aaOnepot-Seq for C donor using CD14 antibody


title: PBMC aaOnepot-Seq for C donor using CD4 antibody


title: PBMC aaOnepot-Seq for C donor using Hashtag antibody


title: Aged PD 1

value: Lung

value: 22 month old


title: PBMC aaOnepot-Seq for C donor using CD19 antibody


title: PBMC aaOnepot-Seq for A donor using Hashtag antibody replicate 1

value: male


title: H3122 0.1% spiked PBMC aaOnepot-Seq using EpCAM antibody


title: PBMC aaOnepot-Seq for A donor using CD3 antibody


title: H3122 1.0% spiked PBMC aaOnepot-Seq using EpCAM antibody


title: PBMC aaOnepot-Seq for A donor using Hashtag antibody replicate 2


title: Onepot-Seq for Pooled cell line treated with AMG-510 at 10uM dose

source_name: Mixed

value: Mixed


title: PBMC aaOnepot-Seq for B donor using Hashtag antibody


title: Onepot-Seq for SW480 control

description: Onepot-Seq for SW480 control

source_name: Colon

value: Colon


title: PBMC aaOnepot-Seq for B donor using CD8 antibody


title: PBMC aaOnepot-Seq for A donor using Hashtag antibody replicate 3


title: Onepot-Seq for Pooled cell line control

description: Onepot-Seq for Pooled cell line control


title: Onepot-Seq for H358 control

description: Onepot-Seq for H358 control

value: Age unspecified


title: Onepot-Seq for H358 treated with AMG-510 at 0.1uM dose


title: Onepot-Seq for H358 treated with AMG-510 at 10uM dose


title: Onepot-Seq for SW480 treated with AMG-510 at 0.1uM dose


title: Onepot-Seq for SW480 treated with AMG-510 at 1uM dose


title: Onepot-Seq for SW480 treated with AMG-510 at 10uM dose


title: Onepot-Seq for H358 treated with AMG-510 at 1uM dose


title: Onepot-Seq for H3122 treated with AMG-510 at 0.1uM dose


title: Onepot-Seq for Pooled cell line treated with AMG-510 at 1uM dose


title: Onepot-Seq for H3122 treated with AMG-510 at 1uM dose


title: Onepot-Seq for H3122 treated with AMG-510 at 10uM dose


title: 14-00613 ORY IgG

city: Portland

first: Theodore

middle: P

last: Braun

state: Oregon

address: 2720 S Moody Ave

institute: Oregon Health and Science University

description: CUT&Tag@home

data_processing:
Sequencing from CUT&Tag was aligned using Bowtie2
Peaks were called using gopeaks
CPM normalized bigwigs merged with UCSC bigWigMerge
Bedgraphs coverted to bigwigs with UCSC bedGraphToBigWig
Differential enrichment was assessed using DESeq2
Library strategy: CUT&Tag
Genome_build: hg38
Supplementary_files_format_and_content: peak file
Supplementary_files_format_and_content: bigwig

source_name: 14-00613 ex vivo culture

extract_protocol: Libraries were prepared according to published protocol Henikoff et al 2020

tag: time point

value: 24 hours

tag: antibody

value: IgG (CST, cat 2729, lot 9)


title: 14-00613 Ava+ORY IgG

description: CUT&Tag@home

value: 350 nM avapritinib + 12 nM ORY-1001


title: 14-00613 ORY rep 1 [Cut & Tag]

description: CUT&Tag@home


title: 14-00613 DMSO rep 1 [Cut & Tag]

description: CUT&Tag@home

value: DMSO


title: 14-00613 Ava rep 3 [Cut & Tag]

description: CUT&Tag@home

value: 350 nM avapritinib


title: Onepot-Seq for H3122 control

description: Onepot-Seq for H3122 control

source_name: Lung


title: 14-00613 DMSO IgG

description: CUT&Tag@home


title: 14-00613 Ava+ORY rep 1 [Cut & Tag]

description: CUT&Tag@home


title: S7: A549_P300_None_2

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the human genome using STAR  v2.4.2a (using options alignEndsType EndToEnd and outFilterMismatchNoverLmax set to 0.04)
Counting proceeded over genes annotated in Ensembl, using htseq-count (version 0.6.1p1)
Normalization and differential expression was performed using DESeq2 (Version 1.10.1)
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed file include raw counts and DESeq2 normalized counts.

source_name: A549 cells

growth_protocol: Human pulmonary adenocarcinoma (A549)  cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Biological Industries) supplemented with 10% fetal bovine serum (FBS, Biological Industries), 2 mM L-glutamine, 0.5 mg/mL penicillin-streptomycin and 1 mM sodium pyruvate (Biological Industries) in a humidified 37°C incubator with 5% CO2. Before treatment (EtOH or 100 nM Dexamethasone for 1 h, Sigma), cells were cultured in media containing 10% charcoal-stripped serum (CSS) (Sigma, USA).

extract_protocol:
RNA was extracted and on-column treated with DNase I with Quick-RNA Mini Prep kit (Zymo Research). Total RNA concentration and purity were measured by Nanodrop. RNA integrity was verified on 1% agarose gel and by RNA Screen Tape assay (Agilent)
Messenger RNA (mRNA) was enriched from 1 μg of total RNA by Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions. cDNA libraries were constructed using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs) following the manufacturer’s protocol. Library concentration was measured by DNA High Sensitivity Kit (Invitrogen) on a Qubit fluorometer (Invitrogen). The High Sensitivity D1000 ScreenTape assay combined with the 2200 TapeStation system (Agilent) was used to assess the quality of the libraries.

treatment_protocol: Ep300 sequence was amplified by PCR from pcDNA3.1-p300 vector (addgene 23252) and cloned in frame to EGFP located in a pFUGW-H1 based plasmid. A549 cells were transfected with 1 microgram a Ep300-GFP or GFP vector using JetPrime reagent (Polyplus-transfection company) and cultured in media supplemented with 10% CSS for 48h. Following 1h incubation with hormone (100nM Dexamethasone) or ethanol, cells were fixed in 75% ethanol and re-suspended in 5ml PBS with 0.5U/µl RNase inhibitor (Takara, #2313B). GFP expressing cells were sorted by flow cytometery (BDFACSAria III, BD Bioscience). RNA was extracted from sorted cells using E.Z.N.A. Total RNA Kit (Omega Bio-tek, # 6834-01). For qPCR analysis RNA was reverse transcribed using  qScript cDNA synthesis kit (Quanta Bioscience, #95047-100), or processed by - SMARTer Stranded Total RNA-Seq Kit v2 (Takara, 634411) for Illumina sequencing.

value: epithelial

tag: construct

value: EtOH


title: S1: A549_GFP_None_1

tag: tissue

value: GFP


title: S8: A549_P300_DEX_2

tag: treatment

value: Dex


title: S3: A549_P300_None_1

tag: cell line


title: S4: A549_P300_DEX_1


title: S5: A549_GFP_None_2


title: 14-00613 Ava rep 1 [Cut & Tag]

description: CUT&Tag@home


title: 14-00613 ORY rep 3 [Cut & Tag]

description: CUT&Tag@home


title: S6: A549_GFP_DEX_2


title: S2: A549_GFP_DEX_1


title: 14-00613 DMSO rep 3 [Cut & Tag]

description: CUT&Tag@home


title: 14-00613 ORY rep 2 [Cut & Tag]

description: CUT&Tag@home


title: 14-00613 Ava+ORY rep 3 [Cut & Tag]

description: CUT&Tag@home


title: 14-00613 Ava+ORY rep 1

description:
C1
PS14_counts.filt.txt

data_processing:
[RNA-seq]
Sequencing from Bulk RNA seq was aligned using STAR.
Differential Expression was determined using DESeq2.
[CUT&Tag]
Sequencing from CUT&Tag was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
Differential enrichment was assessed using DESeq2.
[CUT&RUN]
Sequencing from CUT&RUN was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
[ATAC-seq]
Sequencing from ATAC was aligned using BWA-MEM.
Peaks were called using MACS2.
[scRNA-seq]
Sequencing from scRNAseq libraries was aligned using Cell Ranger.
Expression matrices were processed using Seurat.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bed: peak files, bw: bigWig files, peaks.tsv: peak files.
Supplementary_files_format_and_content: barcodes.tsv: barcodes files, features.tsv: features files, matrix.mtx: matrix files.

extract_protocol: Libraries were prepared with Zymo-Seq RiboFree Total RNA Library Kit (Zymo).


title: 14-00613 Ava rep 2 [Cut & Tag]

description: CUT&Tag@home


title: 14-00613 Ava+ORY rep 2

description:
C2
PS14_counts.filt.txt


title: 14-00613 Ava+ORY rep 2 [Cut & Tag]

description: CUT&Tag@home


title: 14-00613 DMSO rep 2 [Cut & Tag]

description: CUT&Tag@home


title: S10: A549_GFP_DEX_3


title: S9: A549_GFP_None_3


title: 14-00613 ORY rep 3

description:
O3
PS14_counts.filt.txt


title: 14-00613 ORY rep 2

description:
O2
PS14_counts.filt.txt


title: 14-00613 Ava IgG

description: CUT&Tag@home


title: 14-00613 Ava+ORY rep 3

description:
C3
PS14_counts.filt.txt


title: 14-00613 DMSO rep 3

description:
D3
PS14_counts.filt.txt


title: 14-00613 Ava rep 2

description:
A2
PS14_counts.filt.txt


title: 14-00613 Ava rep 1

description:
A1
PS14_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Dox IgG

data_processing:
Library strategy: CUT&Tag
[RNA-seq]
Sequencing from Bulk RNA seq was aligned using STAR.
Differential Expression was determined using DESeq2.
[CUT&Tag]
Sequencing from CUT&Tag was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
Differential enrichment was assessed using DESeq2.
[CUT&RUN]
Sequencing from CUT&RUN was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
[ATAC-seq]
Sequencing from ATAC was aligned using BWA-MEM.
Peaks were called using MACS2.
[scRNA-seq]
Sequencing from scRNAseq libraries was aligned using Cell Ranger.
Expression matrices were processed using Seurat.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bed: peak files, bw: bigWig files, peaks.tsv: peak files.
Supplementary_files_format_and_content: barcodes.tsv: barcodes files, features.tsv: features files, matrix.mtx: matrix files.

source_name: Kasumi-1 PU.1 sh401 cells

extract_protocol: Libraries were prepared according to published protocol Henikoff et al. 2020.

value: 1 ug/ml doxycycline


title: 14-00613 Ava rep 3

description:
A3
PS14_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Ava+Dox H3K27Ac rep 3

value: 50 nM avapritinib + 1 ug/ml doxycycline


title: Kasumi-1 PU.1 sh401 Ava H3K27Ac rep 3

value: 50 nM avapritinib


title: 14-00613 DMSO rep 1

description:
D1
PS14_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Ava+Dox IgG


title: Kasumi-1 PU.1 sh401 Dox H3K27Ac rep 3


title: Kasumi-1 PU.1 sh401 Dox H3K27Ac rep 1


title: Kasumi-1 PU.1 sh401 Ava+Dox H3K27Ac rep 1


title: Kasumi-1 PU.1 sh401 Ava+Dox rep 3

description:
AVADOX3
KASUMI401_counts.filt.txt


title: 14-00613 DMSO rep 2

description:
D2
PS14_counts.filt.txt


title: Kasumi-1 PU.1 sh401 DMSO IgG


title: Kasumi-1 PU.1 sh401 DMSO H3K27Ac rep 3


title: Kasumi-1 PU.1 sh401 DMSO H3K27Ac rep 2


title: Kasumi-1 PU.1 sh401 Ava H3K27Ac rep 2


title: Kasumi-1 PU.1 sh401 Ava+Dox rep 2

description:
AVADOX2
KASUMI401_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Ava+Dox H3K27Ac rep 2


title: Kasumi-1 PU.1 sh401 Ava+Dox rep 1

description:
AVADOX1
KASUMI401_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Ava H3K27Ac rep 1


title: Kasumi-1 PU.1 sh401 Dox rep 3

description:
DOX3
KASUMI401_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Dox rep 2

description:
DOX2
KASUMI401_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Dox H3K27Ac rep 2


title: Kasumi-1 PU.1 sh401 Dox rep 1

description:
DOX1
KASUMI401_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Ava rep 3

description:
AVA3
KASUMI401_counts.filt.txt


title: 14-00613 ORY rep 1

description:
O1
PS14_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Ava IgG


title: Kasumi-1 PU.1 sh401 Ava rep 2

description:
AVA2
KASUMI401_counts.filt.txt


title: Kasumi-1 PU.1 sh401 Ava rep 1

description:
AVA1
KASUMI401_counts.filt.txt


title: Kasumi-1 PU.1 sh401 DMSO H3K27Ac rep 1


title: Kasumi-1 PU.1 sh401 DMSO rep 3

description:
DMSO3
KASUMI401_counts.filt.txt


title: Kasumi-1 PU.1 sh401 DMSO rep 2

description:
DMSO2
KASUMI401_counts.filt.txt


title: Kasumi-1 RUN GSK 24hr IgG

data_processing:
Library strategy: CUT&RUN
[RNA-seq]
Sequencing from Bulk RNA seq was aligned using STAR.
Differential Expression was determined using DESeq2.
[CUT&Tag]
Sequencing from CUT&Tag was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
Differential enrichment was assessed using DESeq2.
[CUT&RUN]
Sequencing from CUT&RUN was aligned using Bowtie2.
Peaks were called using gopeaks.
CPM normalized bigwigs merged with UCSC bigWigMerge.
Bedgraphs converted to bigwigs with UCSC bedGraphToBigWig.
[ATAC-seq]
Sequencing from ATAC was aligned using BWA-MEM.
Peaks were called using MACS2.
[scRNA-seq]
Sequencing from scRNAseq libraries was aligned using Cell Ranger.
Expression matrices were processed using Seurat.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bed: peak files, bw: bigWig files, peaks.tsv: peak files.
Supplementary_files_format_and_content: barcodes.tsv: barcodes files, features.tsv: features files, matrix.mtx: matrix files.

source_name: Kasumi-1 cells

extract_protocol: Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB).

value: 12 nM GSK-LSD1


title: Kasumi-1 PU.1 sh401 DMSO rep 1

description:
DMSO1
KASUMI401_counts.filt.txt


title: Kasumi-1 RUN DMSO 24hr IgG


title: Kasumi-1 RUN Ava+GSK 24hr IgG

value: 12 nM avapritinib + 12 nM GSK-LSD1


title: Kasumi-1 GSK PU1 rep 1

value: PU.1 (Invitrogen, cat MAS-15064, lot UE2775918)


title: Kasumi-1 Ava PU1 rep 1

value: 12 nM avapritinib


title: Kasumi-1 RUN Ava 24hr IgG


title: Kasumi-1 GSK PU1 rep 2


title: Kasumi-1 Ava+GSK PU1 rep 1


title: Kasumi-1 DMSO PU1 rep 2


title: Kasumi-1 Ava PU1 rep 2


title: Kasumi-1 Ava+GSK PU1 rep 2


title: Kasumi-1 Ava+GSK MYC rep 1

value: MYC (CST, cat 13987, lot 5)


title: Kasumi-1 Ava MYC rep 1

value: 24 hours


title: Kasumi-1 DMSO PU1 rep 1


title: Kasumi-1 DMSO MYC rep 2


title: Kasumi-1 GSK MYC rep 1


title: Kasumi-1 Ava+GSK GFI1 rep 2


title: Kasumi-1 Ava MYC rep 2


title: Kasumi-1 DMSO MYC rep 1


title: Kasumi-1 Ava+GSK GFI1 rep 1


title: Kasumi-1 GSK GFI1 rep 1


title: Kasumi-1 GSK GFI1 rep 2


title: Kasumi-1 Ava GFI1 rep 2


title: Kasumi-1 Ava GFI1 rep 1


title: Kasumi-1 DMSO GFI1 rep 1


title: Kasumi-1 Ava+GSK MYC rep 2


title: Kasumi-1 DMSO GFI1 rep 2


title: Kasumi-1 GSK MYC rep 2


title: Kasumi-1 TAG Ava 24 hr IgG

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al. 2019.

value: IgG (CST, cat 2729, lot 9)


title: Kasumi-1 TAG DMSO 24 hr IgG


title: Kasumi-1 TAG GSK 24 hr IgG


title: Kasumi-1 TAG Ava+GSK 24 hr IgG


title: Kasumi-1 GSK H3K27ac rep 2


title: Kasumi-1 Ava+GSK H3K27ac rep 1


title: Kasumi-1 DMSO H3K4me3 rep 1

value: H3K4me3 (CST, cat 9751, lot 10)


title: Kasumi-1 DMSO H3K4me3 rep 2

value: DMSO


title: Kasumi-1 Ava H3K27ac rep 2


title: Kasumi-1 DMSO H3K4me1 rep 1

value: H3K4me1 (CST, cat 5326, lot 3)


title: Kasumi-1 DMSO H3K4me1 rep 2


title: Kasumi-1 Ava H3K27ac rep 1


title: Kasumi-1 GSK H3K27ac rep 1


title: Kasumi-1 DMSO H3K27ac rep 1


title: Kasumi-1 Ava+GSK H3K27ac rep 2


title: A172

city: Tainan

first: Kwang-Yu

last: Chang

address: 367 Sheng-Li Road

country: Taiwan

institute: National Institute of Cancer Research, National Health Research Institutes

data_processing:
genes that were significantly different between parental and TMZ-resistant cells were identified by at least a 1.5-fold difference and a p-value<0.05.
The list of 1174 mitochondria-related genes was constructed according to MitoCarta2.0
Genome_build: Genome Reference Consortium Human Build 38 patch release 13
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample and annotation for mitochondria-related genes

source_name: glioblastoma

extract_protocol:
Cells RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols (VAHTS Stranded mRNA-seq Library Prep Kit for Illumina v2)

value: parental

value: without TMZ


title: A172R6

value: resistance

value: with TMZ


title: 3143_P300_DEX_2

data_processing:
Reads were aligned to the mouse genome (mm9) using the BWA algorithm (default settings)
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed
Genome_build: mm9
Supplementary_files_format_and_content: Processed file include merged peaks from all samples

source_name: 3134 cells

growth_protocol: 3134 cells were cultured in CSS for 24 h and treated with either vehicle (EtOH) or 100 nM Dex for 1h. Samples were sent to Active Motif (Carlsbad, CA) for ChIP-Seq. Active Motif prepared chromatin, performed ChIP reactions, generated libraries, sequenced the libraries and performed basic data analysis.

extract_protocol:
chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 20 ug of antibody against p300 (Santa Cruz Cat# sc-585, Lot #: B0711). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. ChIP Sequencing (Illumina)
Illumina sequencing libraries were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara).

value: RIII

value: epithelial

value: breast adenocarcinoma

tag: contruct

value: Dex


title: 3143_P300_Et1h_2

value: EtOH


title: Patient 1_Unedited_scRNA

city: SHANGHAI

first: Jiaoyang

last: Liao

address: Dongchuan Rd. 500

institute: East China Normal University

data_processing:
Raw Illumina sequencer base call files (BCLs) were processed using Cell Ranger analysis set (Version 3.1.0, https://github.com/10XGenomics/cellranger) with default parameters. Briefly, pipelines involved sample demultiplexing, barcode decoding, filtering low data, aligning to human genome version GRCh38 and gene counting. The output was a clean gene-barcode matrix composed of UMI counts for each gene. Gene-barcode matrices were processed using Seurat (version 3.2.2 https://satijalab.org/seurat/) R package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
The blood of healthy controls and patients before and after treatment was drawn, red blood cells were lysed, and then resuspended to prepare a single-cell suspension of PBMCs. Using microfluidics-based single-cell RNA sequencing (scRNAseq), we obtained in total 6 peripheral blood single-cell transcriptomes from 2 heathy donors (10X indicated data downloaded from 10 Genomics shared dataset), 1 patient sample before treatment and 2 patient samples after treatment.
The library was prepared using the Chromium Single Cell 3’ Reagent Kit v2, and sequenced with HiSeq X Ten system (Illumina).

value: blood

tag: isolate

value: PBMC

tag: time

value: unedited


title: Healthy_donor_scRNA

value: not applicable


title: Patient 2_Mo 1_scRNA

value: edited


title: Patient 2_Mo 2_scRNA


title: Patient 1_Mo 1_scRNA


title: Healthy_donor(10x)_scRNA


title: Kasumi-1 Ava+GSK RNAseq rep 3

description:
KASU_GA3
KAS_GSKAVI_counts.filt.txt

extract_protocol: Libraries were prepared by BGI.

value: 12 nM avapritinib + 12 nM GSK-LSD1

value: 12 hours


title: 3143_P300_Et1h_1


title: Kasumi-1 Ava+GSK RNAseq rep 2

description:
KASU_GA2
KAS_GSKAVI_counts.filt.txt


title: 3143_P300_DEX_1


title: Kasumi-1 DMSO H3K27ac rep 2

value: DMSO

value: 24 hours


title: sh_SC122108

city: Durham

first: Li

address: 111 T.W. Alexander Dr

institute: NIH

description: cells in each sample were either shNT or shJun, with labels in its corresponding *merged.report.csv processed data file.

data_processing:
R1 contains the cell barcode and UMI and R2 contains the biological read.
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm10 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10 for mouse
Supplementary_files_format_and_content: csv,gene expression matrix for single cell RNASeq

source_name: heart

extract_protocol:
Cell suspension was centrifuge (100 x g, 2min) three times to separate the cardiomyocytes and non-cardiomyocytes
Sequencing library was constructed according to the manufacturer’s instructions of ICELL8 TAKARA.

treatment_protocol: For Single cell RNA-Seq for four-day and seven-day mice, ventricles close to auricle and far away auricle and cardiac apex were chopped into small pieces respectively and digested with Pierce™ Primary Cardiomyocyte Isolation Kit (Thermo, 88281).For 14-day and adult mice, hearts were digested by using langendorff perfusion technique, following with heart dissociation enzyme stock solution to digest heart.

value: heart

tag: age

value: P28 Adult

tag: knockdown

value: mixed sample  (non-demultiplexed)


title: sh_SC122124


title: Kasumi-1 GSK RNAseq rep 3

description:
KASU_G3
KAS_GSKAVI_counts.filt.txt

value: 12 nM GSK-LSD1


title: Kasumi-1 Ava+GSK RNAseq rep 1

description:
KASU_GA1
KAS_GSKAVI_counts.filt.txt


title: sh_SC122111


title: sh_SC122022


title: sh_SC122112


title: P28_SC105267

value: none (wildtype)


title: Kasumi-1 GSK RNAseq rep 1

description:
KASU_G1
KAS_GSKAVI_counts.filt.txt

value: 12 nM avapritinib


title: 30D-2_S8_L001_R1_001

first: Ruohong

state: Not in US

address: 100 Haike Road, 13th building

department: IRCBC

institute: Chinese Academy of Sciences

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to human with STAR by default parameter. The read counts for each genes were calculated by HTSeq. The count files were used as input to DESeq for differential expression analysis.
Assembly: dm6
Supplementary files format and content: Counts from HTSeq output were merged into csv table with each gene in rows and each sample in columns.

source_name: head tissue

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108)
RNA libraries were prepared according to instructions of NEBNext Ultra RNA library Prep Kit for Illumina

value: head


title: 30D-1_S7_L001_R1_001


title: 30D-3_S9_L001_R1_001


title: Kasumi-1 Ava RNAseq rep 3

description:
KASU_A3
KAS_GSKAVI_counts.filt.txt


title: 3D-2_S2_L001_R1_001


title: 3D-3_S3_L001_R1_001


title: P14_SC105257


title: P28_SC105139


title: 3143_Pooled Input

value: RIII

value: epithelial

value: breast adenocarcinoma

value: pooled


title: CB Megakaryocyte day 11 DMSO #1

city: Charlottesville

first: Robert

last: Cornelison

state: VA

address: 345 Crispel Drive

department: Pathology

institute: University of Virginia School of Medicine

data_processing:
FastQC for QC check.
Compile with multiQc.
Kallisto alignment -gc bias flag paired end mode.
tximport to DESeq2 for DEG.
Assembly: GRChg38
Supplementary files format and content: count_table.csv: Comma-separated text file includes raw counts table.
Supplementary files format and content: deseq2_DEG.csv: Comma-separated text file includes DESeq2 output.

source_name: Megakaryocytes

growth_protocol: Human umbilical cord blood CD34+ cells cultured for 3 days in prestimulation medium (100 ng/ml human SCF, 100 ng/ml human TPO, 100 ng/ml FLT3 ligand and 20 ng/ml human IL-3) followed by 11 days in megakaryocytic differentiation medium (25 ng/ml human SCF, 40 ng/ml human TPO, 100 ng/ml human SDF1⍶).

extract_protocol:
RNA isolation employed the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany).
The cDNA library was constructed using an NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA).
Sequencing was conducted on an NovaSeq 6000 Sequencing System (Illumina, San Diego, CA).

treatment_protocol: Megakaryocytic cultures were treated with either solvent DMSO or Dyrk inhibitors harmine 2.5 µM.

tag: source

value: Umbilical cord blood CD34+ cells

value: Megakaryocytes


title: CB Megakaryocyte day 11 DMSO #2


title: Kasumi-1 GSK RNAseq rep 2

description:
KASU_G2
KAS_GSKAVI_counts.filt.txt


title: 3D-1_S1_L001_R1_001

city: Shanghai

last: Wang

tag: strain


title: P28_SC105117


title: P28_SC105141


title: sh_SC122106


title: P14_SC105099


title: P28_SC105124


title: Kasumi-1 Ava RNAseq rep 2

description:
KASU_A2
KAS_GSKAVI_counts.filt.txt


title: Kasumi-1 DMSO RNAseq rep 3

description:
KASU_D3
KAS_GSKAVI_counts.filt.txt


title: P28_SC105096


title: Kasumi-1 Ava RNAseq rep 1

description:
KASU_A1
KAS_GSKAVI_counts.filt.txt


title: CB Megakaryocyte day 11 Harmine #2

tag: cell type

value: Harmine 2.5 uM


title: CB Megakaryocyte day 11 Harmine #1


title: P7_SC105263


title: P4_SC105101


title: Kasumi-1 DMSO RNAseq rep 1

description:
KASU_D1
KAS_GSKAVI_counts.filt.txt

value: 12 hours


title: PolII_p7_1

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm9/mm10/rn6 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10 for mouse
Genome_build: rn6 for rat
Supplementary_files_format_and_content: txt,raw counts of RNA-seq
Supplementary_files_format_and_content: xlsx,log fold change of RNA-seq
Supplementary_files_format_and_content: bedGraph, read intensity of ChIPSeq samples

source_name: cardiomyocytes

extract_protocol:
Mouse CMs were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop fixation. Cells were harvested, and DNA was fragmented to 300–500 bp by sonication with Covaris S220 sonicator. Immunoprecipitation was performed with antibodies conjugated to Dynabeads Protein G beads (Life Technology). ChIP DNA was eluted, reverse cross-linked, extracted by phenol/chloroform, and precipitated.
Cell suspension was centrifuge (100 x g, 2min) three times to separate the cardiomyocytes and non-cardiomyocytes

value: cardiomyocytes

tag: chip antibody

value: PolII


title: P7_SC105147

value: heart


title: 9_FRAS220038443

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to the mm8 hole genome using bowtie v0.12.2 with parameters set as defaults.
Reads for kilobased of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.

source_name: Suspension cells

growth_protocol: The leukaemia cell line THP-1 used in the experiment was purchased from Wuhan Poonoses Life Co., LTD., and cultured in RPMI-1640 medium containing 10%FBS+1%PS at 37℃ and 5%CO2

extract_protocol:
Cell samples ere lyzed and harvested using Trizol reagent. THe purification of RNA was performed using protocol provided by extracting kits (Total RNA Extraction Kit, Cat. R1200, Solarbio life science, China).
RNA library were prepared for sequencnig using standard illumina protocols

treatment_protocol: RNA was extracted from THP-1 cells after 48 h treatment with lupeol

value: THP-1 cell

tag: disease state

value: Acute monocytic leukemia

value: treated with lupeol  with 80umol/L


title: PolII_p56_1


title: 8_FRAS220038442


title: P4_SC105149

value: none (wildtype)


title: PolII_p1_1


title: Inputp7_4


title: Inputp7_1


title: PolII_p21_1


title: Inputp7_2


title: Kasumi-1 DMSO RNAseq rep 2

description:
KASU_D2
KAS_GSKAVI_counts.filt.txt

value: DMSO


title: Inputp7_3


title: Inputp56_2


title: 6_FRAS220038440

value: treated with lupeol  with 50umol/L


title: 4_FRAS220038438


title: Inputp56_3


title: Inputp56_4


title: BMDC, IFN-beta-treated [R3A]

city: Grand Rapoids

first: Connie

last: Krawczyk

state: MI

address: 333 Bostwick Ave

institute: Van Andel Institute

data_processing:
Sequence reads were trimmed for adapters and low quality bases at the end of reads with trim_galore v0.6.0 and parameters -q 20.
Trimmed sequence reads were mapped to GRCm38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Reads were mapped to mm10 with STAR v2.7.8a using the basic two-pass mode algorithm and --quantmode GeneCounts.
Feature counts were extracted from the reverse strand.
Features from Gencode version M24.
Assembly: mm10 (GRCm38)
Supplementary files format and content: count_matrix_merged_samples.txt: Tab-delimited text file includes CPM values for each Sample.

source_name: bone marrow-derived dendritic cells

growth_protocol: Bone marrow was cultured in RPMI 1640 supplemented with 10% FBS, antibiotics, and beta-mercaptoethanol in the presence of GM-CSF.

extract_protocol:
RNA was isolated using TRIzol (Thermofisher Scientific). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit with RiboseErase (v2.17).

treatment_protocol: Cells were left unstimulated or stimulated with LPS or IFN-beta for 6 hours.

value: bone marrow-derived dendritic cells

tag: genotype

value: WT

value: IFN-beta


title: BMDC, LPS-activated [R2B]

value: LPS


title: Inputp56_1

tag: time point


title: BMDC, IFN-beta-treated [R3B]


title: BMDC, LPS-activated [R2C]


title: BMDC, IFN-beta-treated [R3C]


title: Inputp21_4


title: 3_FRAS220038437

description: Control

value: lupeol solvent group


title: 7_FRAS220038441


title: Inputp21_3


title: BMDC, unstimulated [R1C]

value: unstimulated


title: 5_FRAS220038439

value: treated with lupeol  with 50mol/L


title: Inputp21_2


title: Inputp21_1


title: Inputp1_4


title: Inputp1_3


title: BMDC, unstimulated [R1B]


title: Inputp1_2


title: Donor3_RASA2KO_Stim5 [P2_F2_UMI_S179]

city: San Francisco

first: Eric

last: Shifrut

state: CA

address: 513 Parnassus Ave, HSW 1033

institute: University of California, San Franscisco

data_processing:
To analyze the gene expression, reads were mapped to the human reference transcriptome (GRCh38 Ensembl release 96) using Kallisto v0.46.1 with default parameters. Genes with zero counts in more than 80% of the samples were filtered out.
Assembly: GRCh38 Ensembl release 96
Supplementary files format and content: Count matrix file with named columns as listed in "description" field.

source_name: Blood

extract_protocol:
T cells were subjected to the repeated stimulation assay in 24-well plates, transferring T cells to freshly seeded cancer cells every 48 hours. Cultured T cells were sorted after each stimulation using BD FACSAria Fusion to obtain a pure population of NY-ESO-1 multimer positive cells T cells from the co-cultures with target cancer cells, and resuspended in TRI Reagent (Sigma, Cat.# T9424). Total RNA was extracted using Direct-zol RNA MicroPrep kit (Zymo research, Cat.# R2061)
For paired-end samples, RNA-seq libraries were prepared by Oligo dT enrichment followed by a stranded Illumina library prep protocol with the KAPA mRNA HyperPrep kit (Kapa Biosystems, KK8580). Libraries were checked for quality on an AATI Fragment analyzer (Agilent, DNF-935–1000), quantified using the Illumina Quant Universal qPCR Mix (Kapa Biosystems, KK4824), and pooled evenly at 3nM. For single read samples (RASA2KO and CTRL Stim5), batch-Tag-seq protocol was used (PMID 27037501).

value: Blood

value: T cells

tag: subject id


title: Inputp21_5

value: cardiomyocytes


title: H3K4me3p7_3


title: 1_FRAS220038435

description: Control


title: BMDC, unstimulated [R1A]


title: BMDC, LPS-activated [R2A]


title: Inputp1_1


title: H3K4me3p7_2


title: BMDC, shPpargc1b, IFN-beta [894R]

growth_protocol: Bone marrow was retrovirally transduced with shRNA and cultured in RPMI 1640 supplemented with 10% FBS, antibiotics, and beta-mercaptoethanol in the presence of GM-CSF.

treatment_protocol: Cells were left unstimulated or treated with IFN-beta for 6 hours.

value: Ppargc1b KD


title: Donor3_CTRL_Stim5 [P2_E2_UMI_S178]

value: CTRL


title: Donor2_CTRL_Stim5 [P2_C2_UMI_S176]


title: BMDC, shControl, IFN-beta [892R]

value: Control


title: Donor2_RASA2KO_Stim5 [P2_D2_UMI_S177]


title: H3K4me3p7_1


title: H3K4me3p56_3


title: H3K4me3p56_1


title: H3K4me3p56_2


title: BMDC, shControl, unstimulated [891R]


title: 2_FRAS220038436

description: Control

value: THP-1 cell

value: Acute monocytic leukemia


title: Donor1_RASA2KO_Stim5 [P2_B2_UMI_S175]


title: H3K4me3p21_3


title: H3K4me3p21_4


title: BMDC, shPpargc1b, IFN-beta [890R]


title: Donor1_CTRL_Stim5 [P2_A2_UMI_S174]


title: H3K4me3p21_2


title: Donor4_CTRL_Stim1 [FB_6E_S203_L003_R1_001]


title: H3K4me3p21_1


title: BMDC, shPpargc1b, unstimulated [893R]


title: BMDC, shPpargc1b, unstimulated [889R]


title: H3K4me3p1_1


title: BMDC, shControl, IFN-beta [888R]


title: H3K4me1p7_3


title: Donor4_RASA2KO_Stim1 [FB_6D_S202_L003_R1_001]


title: H3K4me3p1_2


title: BMDC, shPpargc1b, IFN-beta [886R]


title: BMDC, shControl, unstimulated [887R]


title: Donor3_CTRL_Stim1 [FB_6C_S201_L003_R1_001]


title: H3K4me1p7_2


title: Donor3_RASA2KO_Stim1 [FB_6B_S200_L003_R1_001]


title: No Template Control

city: VANCOUVER

first: Jefferson

last: Terry

state: British Columbia

address: 4480 Oak Street, Room 2H60

institute: Anatomical Pathology

description:
NTC
No Processed Data Available

data_processing:
Data processing is performed with GeoMX-NGS Data Analysis Software, v. 2.2
Quality control is performed by excluding AOIs with <1000 raw reads, <80% aligned raw reads, sequencing saturation <50%, negative probe count geomean <10, and no template PCR control count >1000 (Sample G2-M failed QC).
Outlier probes with ≤10% of the counts for all probes to a particular gene and/or that fail the Grubbs outlier test in ≥20% of samples are expunged from all samples.
Targets with ≥10% segments and segments with ≥10% targets above the threshold of 2 or the limit of quantitation, whichever is higher, are retained.
The data is scaled to area (geometric mean) and normalized using the upper quartile (Q3) method. Background correction is performed using signal to noise ratio of the geometric mean of negative targets.
Assembly: Whole transcriptome atlas probes target 99.5% of the protein-coding genes defined in the HUGO database (23 highly expressed genes are omitted).
Supplementary files format and content: CIUE DSP JT Processed Data Matrix NS.xlsx
Library strategy: GeoMx Seq

organism: synthetic construct

extract_protocol:
A 5 micron formalin fixed paraffin embedded tissue microarray section is labeled with fluorescently labeled cytokeratin and CD68 antibodies to highlight the trophoblast, stroma, and macrophage components. GeoMX human whole transciptome atlas is hydridized and bound probe barcode oligomers cleaved and collected for further analysis using the GeoMX digital spatial profiler.
NanoString's GeoMX Human Whole Transcriptome Atlas

tag: sample type

value: No Template Control


title: Donor2_CTRL_Stim1 [FB_6A_S199_L003_R1_001]

tag: tissue


title: BMDC, shControl, IFN-beta [884R]

tag: treatment


title: BMDC, shPpargc1b, unstimulated [885R]


title: Donor2_RASA2KO_Stim1 [FB_5H_S198_L003_R1_001]


title: H3K4me1p56_5


title: Donor1_CTRL_Stim1 [FB_5G_S197_L003_R1_001]


title: EA2_InVivo_5

description: lung

data_processing:
Reads were quality checked using FastQC.
TopHatv2 was used to align reads to the Mus musculus mm10 reference genome.
Cufflinks v2.0.2 was used to assemble aligned reads into transcripts and estimate their abundance.
Assembly: Mus musculus mm10
Supplementary files format and content: Excel files (.xlsx) include FKPM values for each sample.

extract_protocol:
Total RNA was isolated using RNeasy mini plus kit (Qiagen), including the genomic DNA elimination step.
Libraries were constructed using an Illumina TruSEQ stranded mRNA Sample Prep Kit (Cat# RS-122-2101). Total RNA was combined with RNA purification beads to bind PolyA RNA to oligodT magnetic beads. mRNA was eluted and converted to double stranded DNA. A-tailing, adapter ligation, and PCR amplification using 15 cycles was performed to complete the library construction.

tag: cell line

value: EML4-ALK fusion-driven murine lung cancer cell line

tag: condition

value: in vivo


title: BMDC, shControl, unstimulated [883R]

value: bone marrow-derived dendritic cells


title: H3K4me1p56_4


title: EA2_InVivo_4

description: lung


title: Donor1_RASA2KO_Stim1 [FB_5F_S196_L003_R1_001]


title: H3K4me1p56_2


title: EA2_InVivo_3

description: lung


title: Donor4_CAR_Stim5 [FB5D_S111_L004_R1_001]

value: CAR


title: Donor2_CAR_Stim5 [FB5C_S110_L004_R1_001]


title: H3K4me1p7_1


title: Donor1_CAR_Stim5 [FB5B_S109_L004_R1_001]


title: H3K4me1p56_1


title: H3K4me1p56_6


title: EA2_InVivo_1

description: lung


title: Donor4_TCR_Stim5 [FB5A_S108_L004_R1_001]

value: TCR


title: H3K4me1p21_6


title: stimulated iNIK treated donor 47

city: Amsterdam

first: Kim

last: Jeucken

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
trimmed for adapter sequences: Trimmomatic v0.32
aligned: HISAT2 v2.1.0
counts: HTSeq, v0.11.0
quality control: FastQC, v0.11.15; dupRadar; v.1.0.0
nomalized: weigthed trimmed mean of M-values according to "Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology. 2010;11."
transformed to log2 counts per million; voom
tested for differential expression; moderated t-test, linear model framework, limma, R
data extraction; R, v3.6.3; Bioconductor, v3.10
Assembly: hg38
Supplementary files format and content: raw counts

source_name: primary HUVEC

growth_protocol: HUVEC were grown on 1% gelatin/PBS coated culture flasks in M199 supplemented with 20% FCS, L-glut, Pen/Strep, endothelial cell growth serum (Sigma) and heparin. Cells were passaged when culture flasks were 80-90% confluent and used in passage 3

extract_protocol:
RNA was lysed and isolated using Nucleospin XS (Bioké) kit according to protocol.
Kapa mRNA Hyperprep and Illumina HiSeq4000 according to protocol

treatment_protocol: 72h of stimulation with 50% Tm sup (culture supernatant of MACS sorted CD4+ T cells, cultured 72h in presence of anti-CD3 and anti-CD28) and treated with inhibitors for IKKβ or NIK. Controls: untreated unstimulated, DMSO treated unstimulated, DMSO treated stimulated

tag: stimulation

value: Tm sup stimulated

value: 2.5 uM NIK inhibitor

tag: huvec donor number


title: stimulated iIKKb treated donor 47

value: 1.0 uM IKKβ inhibitor


title: unstimulated untreated donor 47

value: unstimulated

value: untreated


title: H3K4me1p21_5

value: cardiomyocytes


title: Donor2_TCR_Stim5 [FB4H_S107_L004_R1_001]

value: Blood

value: T cells


title: unstimulated DMSO treated donor 47

value: 2.5 uM DMSO


title: EA2_InVItro_3

value: in vitro


title: EA2_InVItro_2


title: unstimulated untreated donor 46


title: H3K4me1p21_4


title: Donor1_TCR_Stim5 [FB4G_S106_L004_R1_001]


title: H3K4me1p56_3


title: EA2_InVItro_1


title: Donor4_CAR_Stim4 [FB4F_S105_L004_R1_001]


title: H3K4me1p21_3


title: EA2_InVivo_2

description: lung


title: H3K4me1p21_2


title: stimulated iIKKb treated donor 46


title: Donor2_CAR_Stim4 [FB4E_S104_L004_R1_001]


title: Donor1_CAR_Stim4 [FB4D_S103_L004_R1_001]


title: unstimulated DMSO treated donor 46


title: P.aeruginosa-infected lungs, Day 14, biological rep 4

city: Singapore

first: Hong Sheng

last: Cheng

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine,

country: Singapore

institute: Nanyang Technological University

data_processing:
Sequencing reads were mapped to the mouse genome (GRCm39) retrieved from Ensembl using Hisat2.
Gene counts of each sample were performed using featureCounts.
Assembly: GRCm39
Supplementary files format and content: A .csv file of raw gene counts of each sample.

extract_protocol:
Total RNA was extracted from frozen mouse lung tissues using TRIzol (Thermo Fisher). The integrity of the total RNA and level of DNA contamination was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) and Qubit 2.0 fluorometer (Invitrogen).
Library preparation was performed according to the mRNA-seq sample preparation kit (Illumina).

treatment_protocol: For intratracheal mouse infection experiments, 6-10 week old C57BL/6 mice were anesthetized using 80 mg/kg body weight ketamine and 10 mg/kg body weight xylazine and infected via intratracheal delivery with the Neisseria subflava (isolate SG-KL01) and Pseudomonas aeruginosa at 2 x 107 CFU in sterile phosphate-buffered saline (PBS). Mice were euthanized on Day 0, 2, 4, 7 , and 14 and the lung tissues were harvested and snap frozen in liquid nitrogen for total RNA extraction.

value: Lung

tag: time

value: Day 14

value: Wild type

value: Pseudomonas aeruginosa


title: H3K4me1p21_1


title: P.aeruginosa-infected lungs, Day 14, biological rep 3


title: H3K4me1p1_4


title: P.aeruginosa-infected lungs, Day 14, biological rep 2


title: Donor4_TCR_Stim4 [FB4C_S102_L004_R1_001]


title: stimulated DMSO treated donor 47


title: P.aeruginosa-infected lungs, Day 14, biological rep 1


title: unstimulated untreated donor 36


title: H3K4me1p1_2


title: P.aeruginosa-infected lungs, Day 7, biological rep 6

value: Day 7


title: H3K4me1p1_3


title: Donor1_TCR_Stim4 [FB4A_S100_L004_R1_001]


title: H3K4me1p1_1


title: Donor4_CAR_Stim3 [FB3H_S99_L004_R1_001]

value: CAR


title: P.aeruginosa-infected lungs, Day 7, biological rep 5


title: stimulated iIKKb treated donor 36


title: stimulated iNIK treated donor 46


title: stimulated iNIK treated donor 36


title: H3K27me3p7_2


title: P.aeruginosa-infected lungs, Day 7, biological rep 4


title: unstimulated DMSO treated donor 36


title: Donor2_CAR_Stim3 [FB3G_S98_L004_R1_001]


title: P.aeruginosa-infected lungs, Day 7, biological rep 3


title: stimulated DMSO treated donor 46


title: H3K27me3p7_1


title: Donor1_CAR_Stim3 [FB3F_S97_L004_R1_001]


title: stimulated DMSO treated donor 36


title: Donor4_TCR_Stim3 [FB3E_S96_L004_R1_001]

value: TCR


title: H3K27me3p56_3


title: unstimulated untreated donor 32


title: Donor2_TCR_Stim4 [FB4B_S101_L004_R1_001]


title: P.aeruginosa-infected lungs, Day 7, biological rep 1


title: stimulated iNIK treated donor 32

value: Tm sup stimulated


title: P.aeruginosa-infected lungs, Day 7, biological rep 2


title: H3K27me3p56_4


title: P.aeruginosa-infected lungs, Day 4, biological rep 6

value: Day 4


title: Donor1_TCR_Stim3 [FB3C_S94_L004_R1_001]


title: H3K27me3p56_2


title: stimulated iIKKb treated donor 32

value: 1.0 uM IKKβ inhibitor


title: H3K27me3p56_1


title: P.aeruginosa-infected lungs, Day 4, biological rep 5


title: P.aeruginosa-infected lungs, Day 4, biological rep 4


title: unstimulated DMSO treated donor 32

value: unstimulated


title: Donor4_CAR_Stim2 [FB3B_S93_L004_R1_001]


title: H3K27me3p21_4


title: P.aeruginosa-infected lungs, Day 4, biological rep 3


title: stimulated DMSO treated donor 32


title: Donor2_CAR_Stim2 [FB3A_S92_L004_R1_001]


title: H3K27me3p21_3


title: Donor1_CAR_Stim2 [FB2H_S91_L004_R1_001]