title: MDSC 24

status: Public on Aug 07 2025

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

country: Canada

institute: Queen's University

description: Library name: DTA_rep4

data_processing:
Raw sequencing reads were base-called using Illumina RTA version 2.4.11 and demultiplexed with bcl2fastq v2.20, allowing for one index mismatch. Adapter trimming and quality filtering were carried out using Trimmomatic to remove low-quality reads and sequencing artifacts. High-quality reads were aligned to the mouse reference genome (GRCm38) using STAR version 2.5.1, which also generated gene-level read counts. These counts were imported into RStudio for normalization and differential expression analysis using the DESeq2 package. Genes with an adjusted p-value (false discovery rate) below 0.05 were considered significantly differentially expressed. All downstream statistical analyses and data visualizations were performed in R.
Assembly: GRCm38
Supplementary files format and content: Comma Separated Values File containing raw readcount for each sample

source_name: tumor

extract_protocol:
Sorted MDSCs were collected directly into 500 µL TRIzol reagent (Invitrogen 15596026) and stored at −80 °C. RNA extraction was performed according to the manufacturer’s standard TRIzol protocol. RNA integrity was assessed using an Agilent Bioanalyzer, and samples with RNA Integrity Numbers between 8.2 and 10 were used for library preparation.
Poly-A-enriched libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina. Libraries were constructed at Fulgent Genetics. Sequencing was performed on an Illumina HiSeq 4000 using 75-cycle single-end reads, generating approximately 20 million reads per sample.

value: tumor

value: FACS-purify MDSC

value: TRPV1 Cre::DTA fl/wt

value: nociceptor ablated


title: MDSC 23

type: SRA

description: Library name: DTA_rep3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: MDSC 22

description: Library name: DTA_rep2


title: MDSC 17

description: Library name: control_rep1

value: TRPV1 Cre::DTA wt/wt

value: littermate control


title: NC_HA3

status: Public on Aug 08 2025

city: hengyang

first: shishi

last: luo

state: hunan

address: 28 West Changsheng Road

department: Hengyang Medical College

country: China

institute: University of South China

description: Library name: Sample 3

data_processing:
Adapter and low-quality reads were first trimmed using Trim Galore (version 0.4.4) in paired-end mode with default parameters. Trimmed reads were then mapped to the hg38 reference genome to count mapped reads for all human transcripts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes log2normalized count values for each Sample

organism: Homo sapiens

extract_protocol:
Extraction of total RNA following the manufacturer’s instruction of the AllPrep DNA/ RNA/miRNA Universal Kit (80224, Qiagen, USA).
For library preparation, 1 mg of total RNA from each sample was depleted for rRNA using the Ribo−Zero rRNA Removal Kit (RZH1046, EPICENTRE, USA), followed by construction of sequencing library using the TruSeq RNA Sample Prep Kit v2 (RS−122, Illumina, USA).

value: the kidney of a human embryo

value: WT


title: Patient4_Cyst4I

city: Leuven

first: Jean-Paul

last: Decuypere

address: Herestraat 49

department: Cellular & Molecular Medicine

country: Belgium

institute: KU Leuven

description: Library name: GC126321

data_processing:
Quality control of raw reads was performed with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapters were filtered with ea-utils fastq-mcf v1.05 (https://github.com/ExpressionAnalysis/ea-utils). Splice-aware alignment was performed with HISAT2 (11) against the reference genome hg38 using the default parameters. Reads mapping to multiple loci in the reference genome were discarded. Resulting binary alignment map files were handled with Samtools v1.5 (12). Quantification of reads per gene was performed with HT-seq Count v0.10.0, Python v2.7.14 (13). The data were normalized by using the variance stabilisation transformation. Supplementary Table 3 shows the normalized counts of all measured transcripts.
Assembly: hg38
Supplementary files format and content: Raw counts
Supplementary files format and content: Normalized counts

source_name: PKD kidney cyst

extract_protocol:
Following RNA extraction using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol, RNA concentration and quality were determined using DropSense96 (Perkin Elemer) and Bioanalyzer (Agilent).
For RNA-Seq library preparation, the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (Bioké) was used according to the manufacturer’s protocol. After quality assessment of the obtained libraries, an equimolar pool was prepared. A qPCR was then carried out using the Kapa SYBR FAST Universal qPCR kit for Illumina (Roche).

value: PKD kidney cyst

value: PKD1 c.7589G>A, p.Gly2530Asp


title: Patient4_Cyst4J

description: Library name: GC126322


title: Healthy4

description: Library name: GC126326

source_name: Healthy kidney

value: Healthy kidney


title: MDSC 19

description: Library name: control_rep3


title: RNAseq, IMR90, Empty vector, replicate 3

city: La jolla

first: Chiara

last: Nicoletti

state: CA

address: 10901 North Torrey Pines Road

department: Development, Aging and Regeneration Program

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: RNAseq_Empty_rep3

data_processing:
For RNA-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), and aligned to the hg19 Ensembl (November 2015) version of the human genome with STAR (v 2.7.3a), using a custom genome and index to simultaneously map and quantify ERCC92 spike-in-derived reads (parameters: --runMode alignReads --runThreadN 12 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts). Counts data (from STAR output in column 4, based on library preparation strandedness: second-strand) from all conditions were filtered based on their raw count, keeping genes where the sum of the counts for all samples was higher than 10. Size factors were calculated using the R environment (v4.1.3) package DESeq2 (v1.34.0) estimateSizeFactors function - using the counts related to the spike-in transcripts as control genes, then normalized and logged with the rlog function. DESeq2 was also used to perform Principal Component Analysis (PCA) and differential gene expression analysis (significance threshold: BH FDR<0.05). Differential expression analysis results were visualized with the heatplot function (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)) from the made4 (v1.68.0) package, after expression values from the DESeq2 object were turned into a matrix of Z-scores. Gene Ontology was performed on down- and up-regulated genes separately, using the gene symbols as input in EnrichR, and gene sets repositories GO Biological Processes 2023 and Descartes Cell Types and Tissue 2021. Top10 gene ontology terms shown in figure panels were ordered by pvalue. Gene Ontology bubble plots to summarize top50 gene ontology terms, were generated with the Python (v.3.8.1) GO-Figure script (parameters: -j standard -c log10-pval -e 100 -si 0.5 -s members -g single -n bpo --font_size small -q svg). For ATAC-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (v2.3.5.1) (parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --dovetail --phred33), sorted and converted into BAM format with the SAMtools sort function. Peak calling was performed with the Macs2 (v2.2.6) callpeak function (parameters: -f BAMPE -g hs -B -q 0.05 --nomodel --shift -100 --extsize 200) and filtered for black-list regions with the BEDtools suite (v2.29.2) intersect (parameters: -v), and sorted with the sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (v2.0.3) (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. Differential chromatin accessibility analysis was carried out in R, with the DESeq2 package. The R package ChIPQC (v1.30.0), (GetGRanges function was used to import peak lists from each biological replicate, a consensus peak list was calculated for all conditions using the IRanges (v2.28.0),function reduce, keeping peaks that were called in at least two samples. Counts for each peak in each biological replicate were quantified with the Rsubread (v2.8.2) featureCounts function (parameters: isPairedEnd= T, countMultiMappingReads= F, maxFragLength= 100). Counts were normalised and logged with the DESeq2 function rlog; DESeq2 was also used to perform Principal Component Analysis (PCA), and differential chromatin accessibility analysis (significance threshold: BH FDR<0.05). Differentially Accessible Regions (DARs) at gene promoter regions were retrieved with the IRanges function promoters (parameters: TxDb.Hsapiens.UCSC.hg19.knownGene, 1000, 200; mouse genome version was: TxDb.Mmusculus.UCSC.mm10.knownGene). Promoter DARs were visualized with the made4 function heatplot (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)), after expression values from the DESeq2 object were turned into a matrix of Z-scores. Due to R visualization limits, only promoters with |log2FC|>1.5 were plotted. Motif analysis was carried out with the HOMER (v4.11), findMotifsGenome function (parameters: hg19 -size given -nomotif). For ChIP-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9) and aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (parameters: --very-sensitive-local). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs -B --nomodel --SPMR -q 0.05), using input chromatin as control. For CUT&RUN: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned either to the hg19 UCSC (January 2016) version of the human genome (for the CUT&RUN for histone marks in IMR90 and IMR90/MyoD), or to the mm10 Ensembl (November 2019) version of the mouse genome (for the CUT&RUN of AcMe and MyoD in muSC),  with Bowtie2 (parameters: --phred33 --end-to-end --no-unal --local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700 –dovetail) and converted to BAM format with the SAMtools (v1.10) function view (parameters: -bS). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs --nomodel --SPMR --call-summits -p 0.05) using input chromatin as control, and filtered for black-list regions with BEDtools intersect (parameters: -v), and sorted with the Unix sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. ChromHMM (v1.24) BinarizeBed function (parameters: -b 200 -peaks) was used to bin the genome in 200bp windows according to each IDR peak list. The BinarizeBed output was used as input to ChromHMM LearnModel (parameters: -b 200 12 hg19), to build a 12 chromatin states model based on the histone marks IDR peaks. Chromatin state numbers were converted to chromatin states names in R, based on the combination of histone marks they were enriched for. For HiChIP: Quality control of the raw data has been performed with FASTQC (v0.11.9). Alignment, filtering, normalization, and loop calling were performed with the Arima version of MAPS (v2.0) bash script (parameters: -C 0 -F 1 -M 1 -H 1 -o hg19 -f 1 -s 5000 -r 2000000 -d 2 -Q 30 -l 1000). Irreproducible Discovery Rate (IDR) was calculated with IDR2D parameters: value transformation= log additive inverse (-log(x)), ambiguity resolution method= overlap, remove non-standard chromosome, max gap= 1000, max factor= 1.5, jitter factor= 0.0001, mu= 0.1, sigma=1, rho=0.2, p=0.5, epsilon=0.001). Differential HiChIP analysis was performed with the DiffAnalysisHiChIP.r script within FitHiChIP (v7.1), and significance threshold was set to p-value<0.05.
Assembly: hg19, mm10
Supplementary files format and content: TXT raw counts files (RNA-seq)
Supplementary files format and content: BEDGRAPH pileup signal tracks, with TBI index (RNA-seq)
Supplementary files format and content: BIGWIG signal tracks (ATAC-seq data, CUT&RUN), also biological replicates average signal tracks
Supplementary files format and content: ARCPLOTS of looping interactions, with TBI index (HiChIP)

growth_protocol: IMR90 cells were cultured in EMEM supplemented with 10% FBS

extract_protocol:
For RNA-seq: IMR90 or IMR90/MyoD cells total RNA was extracted using Quick-RNA Microprep KIT (Zymo Research, R1051) following the manufacturer’s recommendation. RNA concentration was measured on Qubit (Invitrogen). For ATAC-seq: IMR90 or IMR90/MyoD cells were freshly collected directly processed for the library preparation. For ChIP-seq: IMR90 or IMR90/MyoD cells were fixed with 1% FA for 10 minutes at RT followed by quenching with glycine (final concentration 200 mM) for 15 minutes on ice. Nuclei were then extracted in hypotonic buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.05% NP-40, 1 mM PMSF and 1x protease inhibitor) and lysed in lysis buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM EDTA, pH 8.0, 0.5% SDS, 0.5% NP-40, 1 mM PMSF and 1x protease inhibitor and lysed in lysis buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM EDTA, pH 8.0, 0.5% SDS, 0.5% NP-40, 1 mM PMSF and 1x protease inhibitor). Chromatin was sheared with sonicator (S2 Covaris) to an average DNA fragment length of 200-500bp. 15µg of sonicated chromatin were diluted in 500µl RIPA Dilution Buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 0.1% Sodium Deoxycholate, 0.7% NP-40, 1 mM PMSF and 1x protease inhibitor), and precleared for 3 hours at 4°C with Protein A/G dinabeads. In parallel, 10µl of CTCF antibody (CST Cat#3418S), or 1µg of rabbit IgG (Santa Cruz #sc-2027) were prebound to Protein A/G dynabeads in 500µl of PBS containing 5 µg/ml BSA, for 3 hours at 4°C. Beads bound antibody were mixed with precleared chromatin and incubated overnight at 4°C on a rotator. Chromatin bound fraction was washed with RIPA washing buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 0.5% Sodium Deoxycholate, 1% NP-40) for 4 times, followed by LiCl washing buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, pH 8.0, 1% Sodium Deoxycholate, 1% NP-40), and TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA), each wash for 10 minutes at 4°C. Chromatin was then eluted in elution buffer (1% SDS in TE buffer) at 65°C for 6 hours 600 RPM rotation. For CUT&RUN: IMR90 or IMR90/MyoD cells or Muscle Stem Cells (MuSCs) were used as input. CUT&RUN experiments were performed using the CUT&RUN Assay Kit (CST #86652) with the following modification: cells were briefly fixed with 0.1% FA for 2 minutes at RT followed by quenching with glycine; antibody binding was performed O/N at 4C. Antibodies used: anti-MYOD (BD Bioscience, #554130), anti-H4K5/K12AcMe, anti-panAcMe, anti-H3K27ac (Active Motif #91193), anti-H3K4me3 (CST #9751), anti-H3K4me1 (Active Motif #39635), anti-H3K27me3 (Active Motif #39155), anti-H3K9me3 (Active Motif #39161). For HiChIP: IMR90 or IMR90/MyoD cells were fixed with 2%FA for 10 minutes at RT followed by quenching with STOP solution1 according to ARIMA HiC+ protocol. Digestion was performed overnight at 37C. Biotinylated enriched fragments were pulled down with anti-H3K27ac (Active Motif #91193) or anti-CTCF (Active Motif #91285). Experiments were performed using the ARIMA HiC+ kit according to manufacturer’s protocol.
For RNA-seq: Equal inputs of total RNA (10-100 ng) were used to generate stranded total RNA libraries for sequencing using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina #20040525). ERCC RNA Spike-in mix was added at the start of the protocol according to manufacturer’s instruction (Thermo Fisher Scientific #4456740). Libraries were sequenced at a depth of ~50M per library on NOVASeqS4 PE 2x100. For ATAC-seq: Freshly collected cells were subjected to ATAC-seq library preparation using the ATAC-seq Kit (Active Motif #53150) according to manufacturer’s protocol. For ChIP-seq: Precipitated chromatin and 10ng of input were used for library preparation using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21096) according to manufacturer’s protocol. Obtained libraries were sequenced at a depth of ~100M per library on NOVASeqS4 PE 2x100. For CUT&RUN: Libraries have been generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB #E7645S) according to manufacturer’s protocol. Libraries were sequenced at a depth of ~20M per library on NOVASeqS4 PE 2x100. For HiChIP: H3K27ac or CTCF enriched material was then used as input for library preparation using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences  #21096) according to ARIMA HiChIP library preparation protocol. Obtained libraries were sequenced at a depth of ~300M per library on NOVASeqS4 PE 2x100.

treatment_protocol: IMR90 cells were transfected with vector containing TET-inducible MYOD (WT or domain-deleted mutant) or EMPTY vector control, cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and collected for GM time point

value: Fetal lung fibroblasts

value: Empty


title: Healthy2

description: Library name: GC126324


title: Patient4_Cyst4G

description: Library name: GC126319


title: MDSC 21

description: Library name: DTA_rep1


title: Healthy1

description: Library name: GC126323


title: MDSC 18

description: Library name: control_rep2


title: Patient4_Cyst4E

description: Library name: GC126317


title: Patient4_Cyst4F

description: Library name: GC126318


title: Patient4_Cyst4H

description: Library name: GC126320


title: Healthy3

description: Library name: GC126325


title: Human monocytes [malaria_Pfalciparum_SPZ_vs_blood]

city: Berlin

first: Parnika

last: Mukherjee

address: Augustenburger Platz 1

country: Germany

institute: Charité Universitätsmedizin Berlin

description: Library name: malaria_Pfalciparum_SPZ_vs_blood

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0
Further quality control, donor demultiplexing, normalization, dimension reduction and clustering were done with Seurat v5
Assembly: Homo sapiens GRCh38
Assembly: Plasmodium falciparum
Supplementary files format and content: Tab-separated features and cell barcode files, UMI count matrix file, and Seurat object metadata file (cell type annotations, cell - donor pair identification etc.)

organism:
Plasmodium falciparum
Homo sapiens

source_name: Human PBMCs

extract_protocol:
GFP⁺ and GFP⁻ monocytes were sorted from human PBMCs following 4h co-culture with flow-sorted P. falciparum sporozoites or infected erythrocytes. Control monocytes were sorted from unstimulated PBMCs
Single-cell RNA sequencing data were generated using the 10x Genomics Chromium Single Cell 3’ v3.1 platform. Cell suspensions were processed immediately for library generation following manufacturer’s instructions. Sequencing was performed on an Illumina NovaSeq 6000 by the Core Unit Bioinformatics (CUBI) at the Berlin Institute of Health (BIH)

value: Human PBMCs


title: Patient4_Cyst4C

description: Library name: GC126315


title: Patient4_Cyst4A

description: Library name: GC126313


title: Patient4_Cyst4B

description: Library name: GC126314


title: Patient2_Cyst2B2

description: Library name: GC126309


title: Patient2_Cyst2G2

description: Library name: GC126311


title: Patient2_Cyst2D2

description: Library name: GC126310


title: Patient2_Cyst2I2

description: Library name: GC126312


title: RNAseq, IMR90, MyoD D102-135 vector, replicate 1

description: Library name: RNAseq_MYOD_D135_rep1

value: Myogenic transdifferentiation


title: CUTnRUN, PanAcMe, 4h post muscle injury, replicate 2

description: Library name: CUTnRUN_PanAcMe_4hpi_rep2

library_source: genomic

data_processing:
For RNA-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), and aligned to the hg19 Ensembl (November 2015) version of the human genome with STAR (v 2.7.3a), using a custom genome and index to simultaneously map and quantify ERCC92 spike-in-derived reads (parameters: --runMode alignReads --runThreadN 12 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts). Counts data (from STAR output in column 4, based on library preparation strandedness: second-strand) from all conditions were filtered based on their raw count, keeping genes where the sum of the counts for all samples was higher than 10. Size factors were calculated using the R environment (v4.1.3) package DESeq2 (v1.34.0) estimateSizeFactors function - using the counts related to the spike-in transcripts as control genes, then normalized and logged with the rlog function. DESeq2 was also used to perform Principal Component Analysis (PCA) and differential gene expression analysis (significance threshold: BH FDR<0.05). Differential expression analysis results were visualized with the heatplot function (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)) from the made4 (v1.68.0) package, after expression values from the DESeq2 object were turned into a matrix of Z-scores. Gene Ontology was performed on down- and up-regulated genes separately, using the gene symbols as input in EnrichR, and gene sets repositories GO Biological Processes 2023 and Descartes Cell Types and Tissue 2021. Top10 gene ontology terms shown in figure panels were ordered by pvalue. Gene Ontology bubble plots to summarize top50 gene ontology terms, were generated with the Python (v.3.8.1) GO-Figure script (parameters: -j standard -c log10-pval -e 100 -si 0.5 -s members -g single -n bpo --font_size small -q svg). For ATAC-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (v2.3.5.1) (parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --dovetail --phred33), sorted and converted into BAM format with the SAMtools sort function. Peak calling was performed with the Macs2 (v2.2.6) callpeak function (parameters: -f BAMPE -g hs -B -q 0.05 --nomodel --shift -100 --extsize 200) and filtered for black-list regions with the BEDtools suite (v2.29.2) intersect (parameters: -v), and sorted with the sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (v2.0.3) (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. Differential chromatin accessibility analysis was carried out in R, with the DESeq2 package. The R package ChIPQC (v1.30.0), (GetGRanges function was used to import peak lists from each biological replicate, a consensus peak list was calculated for all conditions using the IRanges (v2.28.0),function reduce, keeping peaks that were called in at least two samples. Counts for each peak in each biological replicate were quantified with the Rsubread (v2.8.2) featureCounts function (parameters: isPairedEnd= T, countMultiMappingReads= F, maxFragLength= 100). Counts were normalised and logged with the DESeq2 function rlog; DESeq2 was also used to perform Principal Component Analysis (PCA), and differential chromatin accessibility analysis (significance threshold: BH FDR<0.05). Differentially Accessible Regions (DARs) at gene promoter regions were retrieved with the IRanges function promoters (parameters: TxDb.Hsapiens.UCSC.hg19.knownGene, 1000, 200; mouse genome version was: TxDb.Mmusculus.UCSC.mm10.knownGene). Promoter DARs were visualized with the made4 function heatplot (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)), after expression values from the DESeq2 object were turned into a matrix of Z-scores. Due to R visualization limits, only promoters with |log2FC|>1.5 were plotted. Motif analysis was carried out with the HOMER (v4.11), findMotifsGenome function (parameters: hg19 -size given -nomotif). For ChIP-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9) and aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (parameters: --very-sensitive-local). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs -B --nomodel --SPMR -q 0.05), using input chromatin as control. For CUT&RUN: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned either to the hg19 UCSC (January 2016) version of the human genome (for the CUT&RUN for histone marks in IMR90 and IMR90/MyoD), or to the mm10 Ensembl (November 2019) version of the mouse genome (for the CUT&RUN of AcMe and MyoD in muSC),  with Bowtie2 (parameters: --phred33 --end-to-end --no-unal --local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700 –dovetail) and converted to BAM format with the SAMtools (v1.10) function view (parameters: -bS). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs --nomodel --SPMR --call-summits -p 0.05) using input chromatin as control, and filtered for black-list regions with BEDtools intersect (parameters: -v), and sorted with the Unix sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. ChromHMM (v1.24) BinarizeBed function (parameters: -b 200 -peaks) was used to bin the genome in 200bp windows according to each IDR peak list. The BinarizeBed output was used as input to ChromHMM LearnModel (parameters: -b 200 12 hg19), to build a 12 chromatin states model based on the histone marks IDR peaks. Chromatin state numbers were converted to chromatin states names in R, based on the combination of histone marks they were enriched for. For HiChIP: Quality control of the raw data has been performed with FASTQC (v0.11.9). Alignment, filtering, normalization, and loop calling were performed with the Arima version of MAPS (v2.0) bash script (parameters: -C 0 -F 1 -M 1 -H 1 -o hg19 -f 1 -s 5000 -r 2000000 -d 2 -Q 30 -l 1000). Irreproducible Discovery Rate (IDR) was calculated with IDR2D parameters: value transformation= log additive inverse (-log(x)), ambiguity resolution method= overlap, remove non-standard chromosome, max gap= 1000, max factor= 1.5, jitter factor= 0.0001, mu= 0.1, sigma=1, rho=0.2, p=0.5, epsilon=0.001). Differential HiChIP analysis was performed with the DiffAnalysisHiChIP.r script within FitHiChIP (v7.1), and significance threshold was set to p-value<0.05.
Assembly: hg19, mm10
Supplementary files format and content: TXT raw counts files (RNA-seq)
Supplementary files format and content: BEDGRAPH pileup signal tracks, with TBI index (RNA-seq)
Supplementary files format and content: BIGWIG signal tracks (ATAC-seq data, CUT&RUN), also biological replicates average signal tracks
Supplementary files format and content: ARCPLOTS of looping interactions, with TBI index (HiChIP)
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Skeletal muscle

value: Skeletal muscle

value: Muscle Stem Cells

value: Skeletal muscle injury


title: Patient1_Cyst 1E2

description: Library name: GC126308

value: PKD1 c.2948del, p.Asn983Metfs*14


title: Patient1_Cyst 1D2

description: Library name: GC126307


title: Patient1_Cyst 1C2

description: Library name: GC126306


title: Patient3_Cyst3I

description: Library name: GC126304

value: PKD1 c.831_849del, p.Val278Trpfs*6


title: Patient3_Cyst3G

description: Library name: GC126302


title: Patient3_Cyst3E

description: Library name: GC126300


title: Patient3_Cyst3D

description: Library name: GC126299


title: Patient3_Cyst3C

description: Library name: GC126298


title: Patient3_Cyst3F

description: Library name: GC126301


title: Patient3_Cyst3H

description: Library name: GC126303


title: Patient6_MicrocysticTissue6A

description: Library name: GC117854

source_name: PKD kidney microcystic

value: PKD kidney microcystic

value: PKD1 c.9412G>A, p.Val3138Met


title: Patient3_Cyst3B

description: Library name: GC126297


title: Patient2_Cyst2I

description: Library name: GC117851


title: Patient3_Cyst3A

description: Library name: GC126296


title: Patient5_MicrocysticTissue1

description: Library name: GC117853


title: Patient6_MicrocysticTissue6B

description: Library name: GC117855


title: Patient2_Cyst2G

description: Library name: GC117849


title: Patient2_Cyst2H

description: Library name: GC117850


title: Patient2_Cyst2F

description: Library name: GC117848


title: Patient2_Cyst2D

description: Library name: GC117846


title: Patient2_Cyst2E

description: Library name: GC117847


title: Patient2_Cyst2C

description: Library name: GC117845


title: Patient1_Cyst 1I

description: Library name: GC117839


title: Patient2_Cyst2A

description: Library name: GC117843


title: Patient1_Cyst 1J

description: Library name: GC117840


title: Patient2_Cyst2B

description: Library name: GC117844


title: Patient3_Cyst3J

description: Library name: GC126305


title: Patient1_Cyst 1G

description: Library name: GC117837


title: Patient1_Cyst 1H

description: Library name: GC117838


title: Patient1_Cyst 1F

description: Library name: GC117836


title: Patient1_Cyst 1E

description: Library name: GC117835


title: 16HBE cells, 5% patient serum 542832, 24h, rep1

city: Potomac

first: Jennifer

last: Smith

state: Maryland

address: Windsor View Dr

institute: PreCyte, Inc.

description:
48_LC10_21_16
48_LC10_21_16
542832
WB-1046663

data_processing:
Step 1: RNAseq data were processed using R packages using a custom workflow where reads were first trimmed of adapter sequence using trimmomatic (Bolger, Lohse and Usadel, 2014)
Step 2: Reference aligned to HG38 using STAR (Dobin et al., 2013)
Step 3: Transcripts were quantified at gene-level resolution using the software package featureCounts (Liao, Smyth and Shi, 2014)
Step 4: QC was performed using MultiQC, dupRadar and GATK estimate of library complexity.
Step 5:Counts were adjusted to correct GC bias using the FQN package
Step 6:Genes were filtered to remove those with low counts
Step 7: iCAP data from serum samples that exhibited signs of hemolysis data were removed (see Methods section of Berndt et al)
Step 8:Data were normalized for heteroskedasticity by variance transformation using the DESeq2 package and batch corrected using the removeBatchEffect function from the R package Limma (Ritchie et al., 2015).
Step 9: Outlier samples were identified using robust principal components analysis implemented in the rrcov package and optionally removed before generating disease models
Step 10: Differential expression analysis was performed using DESeq2 (Love, Huber and Anders, 2014).
For project Stage 3, steps 1-10 were used.  For Stage 1 and development of pilot model, step 3 included removal of read duplicates  by using –ignoreDups setting in R:featureCounts, and processing steps 5-9 were omitted.
Assembly: HG38
Supplementary files format and content: For project stage 1, feature counts table generated in step 3 is: ClassifyDataSets.rawData.010217.R1.io.Rdata  (cohorts 1-2 only) (duplicates ignored)
Supplementary files format and content: For project stage 3, feature counts tables generated in step 3 include: featureCountTable.txt (cohorts 1-2), feature_counts.csv (cohort 3)

molecule: polyA RNA

source_name: cell line

growth_protocol: 2x10E6 16HBE indicator cells were thawed and plated into a T75 flask and cultured for 2 days in complete growth medium (RPMI+10% FBS). Cells were dissociated with trypsin-EDTA (0.25%) for 10 min at 37 °C, counted and plated at 30,000 cells/cm2 in 12-well moat plates (Eppendorf) in complete medium.

extract_protocol:
At end of incubation, media was removed, lysis buffer was added, and cells were stored at -80°C for up to two weeks before RNA isolation. Total RNA was isolated by automated isolation using a MagMax mirVana kit (Invitrogen A27828) on either a KingFisher Flex or a Kingfisher Duo Prime as per the manufacturer’s recommendation. RNA was eluted in 100 µL of elution buffer, quantified using a Qubit (Qubit RNA BR Assay Kit), and stored at -80°C. For some iCAP-RNAseq experiments, total RNA was isolated manually using RNeasy Mini Kit (Qiagen).
100-650 ng of total RNA from each iCAP sample was used for automated library preparation and RNA sequencing (RNAseq) performed by Covance or Genewiz (now Azenta life sciences). Strand-specific library prep was performed with PolyA selection using TruSeq RNA library prep kit with unique dial indices (IDT) and resulting DNA was sequenced on an Illumina Hiseq 4000 with paired end 150 bp reads

treatment_protocol: 24h after growth protocol, cells were rinsed once with RPMI and 950 µL RPMI + 50µl serum was added and cells were incubated for 24 h. For a few experiments, cells were passaged an additional time before initiating experiment.

value: cell line

value: bronchial epithelial

tag: treatment group

value: benign


title: 16HBE cells, 5% patient serum 533535, 24h, rep1

description:
43_LC10_21_16
43_LC10_21_16
533535
WB-1046658

value: WT


title: Patient1_Cyst 1B

description: Library name: GC117832

value: PKD kidney cyst


title: 16HBE cells, 5% patient serum 533234, 24h, rep1

description:
39_LC10_21_16
39_LC10_21_16
533234
WB-1046654

value: malignant


title: 16HBE cells, 5% patient serum 539017, 24h, rep1

description:
45_LC10_21_16
45_LC10_21_16
539017
WB-1046660


title: 16HBE cells, 5% patient serum 535616, 24h, rep1

description:
44_LC10_21_16
44_LC10_21_16
535616
WB-1046659


title: Patient1_Cyst 1D

description: Library name: GC117834


title: 16HBE cells, 5% patient serum 530978, 24h, rep1

description:
42_LC10_21_16
42_LC10_21_16
530978
WB-1046657


title: Patient1_Cyst 1C

description: Library name: GC117833


title: 16HBE cells, 5% patient serum 539463, 24h, rep1

description:
46_LC10_21_16
46_LC10_21_16
539463
WB-1046661


title: 16HBE cells, 5% patient serum 541224, 24h, rep1

description:
47_LC10_21_16
47_LC10_21_16
541224
WB-1046662


title: 16HBE cells, 5% patient serum 530472, 24h, rep1

description:
36_LC10_21_16
36_LC10_21_16
530472
WB-1046651


title: 16HBE cells, 5% patient serum 534567, 24h, rep1

description:
38_LC10_21_16
38_LC10_21_16
534567
WB-1046653


title: Patient6_MicrocysticTissue6C

description: Library name: GC117857


title: 16HBE cells, 5% patient serum 548302, 24h, rep1

description:
37_LC10_21_16
37_LC10_21_16
548302
WB-1046652


title: 16HBE cells, 5% patient serum 526431, 24h, rep1

description:
35_LC10_21_16
35_LC10_21_16
526431
WB-1046650


title: 16HBE cells, 5% patient serum 537137, 24h, rep1

description:
41_LC10_21_16
41_LC10_21_16
537137
WB-1046656


title: Patient1_Cyst 1A

description: Library name: GC117831


title: Patient4_Cyst4D

description: Library name: GC126316

value: PKD1 c.7589G>A, p.Gly2530Asp


title: 16HBE cells, 5% patient serum 529326, 24h, rep1

description:
33_LC10_21_16
33_LC10_21_16
529326
WB-1046648


title: 16HBE cells, 5% patient serum 542293, 24h, rep1

description:
32_LC10_21_16
32_LC10_21_16
542293
WB-1046647


title: 16HBE cells, 5% serum reference control, 24h, rep14

description:
40_LC10_21_16
40_LC10_21_16
reference_14
WB-1046655

value: reference


title: 16HBE cells, 5% patient serum 541883, 24h, rep1

description:
30_LC10_21_16
30_LC10_21_16
541883
WB-1046645


title: 16HBE cells, 5% patient serum 522590, 24h, rep1

description:
31_LC10_21_16
31_LC10_21_16
522590
WB-1046646


title: 16HBE cells, 5% patient serum 529254, 24h, rep1

description:
28_LC10_21_16
28_LC10_21_16
529254
WB-1046643


title: Patient1_Cyst 1K

description: Library name: GC117841


title: 16HBE cells, 5% patient serum 531621, 24h, rep1

description:
27_LC10_21_16
27_LC10_21_16
531621
WB-1046642


title: 16HBE cells, 5% serum reference control, 24h, rep13

description:
26_LC10_21_16
26_LC10_21_16
reference_13
WB-1046641


title: 16HBE cells, 5% patient serum 567234, 24h, rep1

description:
23_LC10_21_16
23_LC10_21_16
567234
WB-1046638


title: 16HBE cells, 5% patient serum 553009, 24h, rep1

description:
25_LC10_21_16
25_LC10_21_16
553009
WB-1046640


title: 16HBE cells, 5% patient serum 522491, 24h, rep1

description:
24_LC10_21_16
24_LC10_21_16
522491
WB-1046639


title: 16HBE cells, 5% patient serum 552590, 24h, rep1

description:
22_LC10_21_16
22_LC10_21_16
552590
WB-1046637


title: 16HBE cells, 5% patient serum 556456, 24h, rep1

description:
21_LC10_21_16
21_LC10_21_16
556456
WB-1046636


title: 16HBE cells, 5% patient serum 542216, 24h, rep1

description:
19_LC10_21_16
19_LC10_21_16
542216
WB-1046634


title: 16HBE cells, 5% patient serum 549851, 24h, rep1

description:
20_LC10_21_16
20_LC10_21_16
549851
WB-1046635


title: 16HBE cells, 5% patient serum 527000, 24h, rep1

description:
18_LC10_21_16
18_LC10_21_16
527000
WB-1046633


title: 16HBE cells, 5% patient serum 530648, 24h, rep1

description:
17_LC10_21_16
17_LC10_21_16
530648
WB-1046632


title: 16HBE cells, 5% patient serum 545117, 24h, rep1

description:
16_LC10_21_16
16_LC10_21_16
545117
WB-1046631


title: 16HBE cells, 5% patient serum 562458, 24h, rep1

description:
12_LC10_21_16
12_LC10_21_16
562458
WB-1046627


title: 16HBE cells, 5% patient serum 542095, 24h, rep1

description:
11_LC10_21_16
11_LC10_21_16
542095
WB-1046626


title: 16HBE cells, 5% patient serum 528757, 24h, rep1

description:
14_LC10_21_16
14_LC10_21_16
528757
WB-1046629


title: 16HBE cells, 5% patient serum 553038, 24h, rep1

description:
13_LC10_21_16
13_LC10_21_16
553038
WB-1046628


title: 16HBE cells, 5% serum reference control, 24h, rep12

description:
15_LC10_21_16
15_LC10_21_16
reference_12
WB-1046630


title: 16HBE cells, 5% patient serum 526108, 24h, rep1

description:
34_LC10_21_16
34_LC10_21_16
526108
WB-1046649


title: 16HBE cells, 5% patient serum 535005, 24h, rep1

description:
09_LC10_21_16
09_LC10_21_16
535005
WB-1046624


title: 16HBE cells, 5% patient serum 530352, 24h, rep1

description:
07_LC10_21_16
07_LC10_21_16
530352
WB-1046622


title: 16HBE cells, 5% patient serum 552746, 24h, rep1

description:
08_LC10_21_16
08_LC10_21_16
552746
WB-1046623


title: 16HBE cells, 5% patient serum 552939, 24h, rep1

description:
10_LC10_21_16
10_LC10_21_16
552939
WB-1046625


title: 16HBE cells, 5% patient serum 540909, 24h, rep1

description:
03_LC10_21_16
03_LC10_21_16
540909
WB-1046618


title: 16HBE cells, 5% patient serum 539085, 24h, rep1

description:
06_LC10_21_16
06_LC10_21_16
539085
WB-1046621


title: 16HBE cells, 5% patient serum 550998, 24h, rep1

description:
29_LC10_21_16
29_LC10_21_16
550998
WB-1046644


title: 16HBE cells, 5% patient serum 547098, 24h, rep1

description:
04_LC10_21_16
04_LC10_21_16
547098
WB-1046619


title: 16HBE cells, 5% patient serum 521581, 24h, rep1

description:
05_LC10_21_16
05_LC10_21_16
521581
WB-1046620


title: 16HBE cells, 5% serum reference control, 24h, rep11

description:
01_LC10_21_16
01_LC10_21_16
reference_11
WB-1046616


title: 16HBE cells, 5% patient serum 554410, 24h, rep1

description:
20_LC10_28_16
20_LC10_28_16
554410
WB-1046614


title: 16HBE cells, 5% patient serum 551364, 24h, rep1

description:
18_LC10_28_16
18_LC10_28_16
551364
WB-1046612


title: 16HBE cells, 5% serum reference control, 24h, rep10

description:
16_LC10_28_16
16_LC10_28_16
reference_10
WB-1046610


title: 16HBE cells, 5% patient serum 546307, 24h, rep1

description:
17_LC10_28_16
17_LC10_28_16
546307
WB-1046611


title: 16HBE cells, 5% patient serum 544059, 24h, rep1

description:
14_LC10_28_16
14_LC10_28_16
544059
WB-1046608


title: 16HBE cells, 5% patient serum 557014, 24h, rep1

description:
15_LC10_28_16
15_LC10_28_16
557014
WB-1046609


title: 16HBE cells, 5% patient serum 546461, 24h, rep1

description:
11_LC10_28_16
11_LC10_28_16
546461
WB-1046605


title: 16HBE cells, 5% patient serum 555068, 24h, rep1

description:
13_LC10_28_16
13_LC10_28_16
555068
WB-1046607


title: 16HBE cells, 5% patient serum 550088, 24h, rep1

description:
10_LC10_28_16
10_LC10_28_16
550088
WB-1046604


title: 16HBE cells, 5% patient serum 562232, 24h, rep1

description:
12_LC10_28_16
12_LC10_28_16
562232
WB-1046606


title: 16HBE cells, 5% patient serum 554875, 24h, rep1

description:
02_LC10_28_16
02_LC10_28_16
554875
WB-1046596


title: 16HBE cells, 5% patient serum 556248, 24h, rep1

description:
09_LC10_28_16
09_LC10_28_16
556248
WB-1046603


title: 16HBE cells, 5% patient serum 554145, 24h, rep1

description:
07_LC10_28_16
07_LC10_28_16
554145
WB-1046601


title: 16HBE cells, 5% patient serum 553972, 24h, rep1

description:
08_LC10_28_16
08_LC10_28_16
553972
WB-1046602


title: 16HBE cells, 5% patient serum 564008, 24h, rep1

description:
03_LC10_28_16
03_LC10_28_16
564008
WB-1046597


title: 16HBE cells, 5% serum reference control, 24h, rep9

description:
04_LC10_28_16
04_LC10_28_16
reference_9
WB-1046598


title: 16HBE cells, 5% patient serum 558961, 24h, rep1

description:
01_LC10_28_16
01_LC10_28_16
558961
WB-1046595


title: 16HBE cells, 5% patient serum 558514, 24h, rep1

description:
05_LC10_28_16
05_LC10_28_16
558514
WB-1046599


title: 16HBE cells, 5% serum reference control, 24h, rep8

description:
24_LC10_07_16
24_LC10_07_16
reference_8
WB-1046594


title: 16HBE cells, 5% patient serum 546154, 24h, rep1

description:
06_LC10_28_16
06_LC10_28_16
546154
WB-1046600


title: 16HBE cells, 5% patient serum 520793, 24h, rep1

description:
02_LC10_21_16
02_LC10_21_16
520793
WB-1046617


title: 16HBE cells, 5% serum reference control, 24h, rep7

description:
23_LC10_07_16
23_LC10_07_16
reference_7
WB-1046593


title: 16HBE cells, 5% patient serum 559060, 24h, rep1

description:
20_LC10_07_16
20_LC10_07_16
559060
WB-1046590


title: 16HBE cells, 5% patient serum 547914, 24h, rep1

description:
22_LC10_07_16
22_LC10_07_16
547914
WB-1046592


title: 16HBE cells, 5% serum reference control, 24h, rep5

description:
19_LC10_07_16
19_LC10_07_16
reference_5
WB-1046589


title: 16HBE cells, 5% serum reference control, 24h, rep6

description:
21_LC10_07_16
21_LC10_07_16
reference_6
WB-1046591


title: 16HBE cells, 5% patient serum 533739, 24h, rep1

description:
18_LC10_07_16
18_LC10_07_16
533739
WB-1046588


title: 16HBE cells, 5% patient serum 563497, 24h, rep1

description:
17_LC10_07_16
17_LC10_07_16
563497
WB-1046587


title: 16HBE cells, 5% patient serum 553825, 24h, rep1

description:
19_LC10_28_16
19_LC10_28_16
553825
WB-1046613


title: 16HBE cells, 5% patient serum 556072, 24h, rep1

description:
15_LC10_07_16
15_LC10_07_16
556072
WB-1046585


title: 16HBE cells, 5% patient serum 563570, 24h, rep1

description:
16_LC10_07_16
16_LC10_07_16
563570
WB-1046586


title: 16HBE cells, 5% patient serum 560237, 24h, rep1

description:
14_LC10_07_16
14_LC10_07_16
560237
WB-1046584


title: 16HBE cells, 5% patient serum 565739, 24h, rep1

description:
01_LC10_07_16
01_LC10_07_16
565739
WB-1046571


title: 16HBE cells, 5% patient serum 558793, 24h, rep1

description:
09_LC10_07_16
09_LC10_07_16
558793
WB-1046579


title: 16HBE cells, 5% patient serum 530430, 24h, rep1

description:
04_LC10_07_16
04_LC10_07_16
530430
WB-1046574


title: 16HBE cells, 5% patient serum 561641, 24h, rep1

description:
13_LC10_07_16
13_LC10_07_16
561641
WB-1046583


title: 16HBE cells, 5% patient serum 519681, 24h, rep1

description:
11_LC10_07_16
11_LC10_07_16
519681
WB-1046581


title: 16HBE cells, 5% serum reference control, 24h, rep4

description:
12_LC10_07_16
12_LC10_07_16
reference_4
WB-1046582


title: 16HBE cells, 5% patient serum 532376, 24h, rep1

description:
03_LC10_07_16
03_LC10_07_16
532376
WB-1046573


title: 16HBE cells, 5% serum reference control, 24h, rep3

description:
24_LC092316
24_LC092316
reference_3
WB-1046570


title: 16HBE cells, 5% patient serum 542555, 24h, rep1

description:
23_LC092316
23_LC092316
542555
WB-1046569


title: 16HBE cells, 5% patient serum 555906, 24h, rep1

description:
21_LC092316
21_LC092316
555906
WB-1046567


title: 16HBE cells, 5% patient serum 543568, 24h, rep1

description:
18_LC092316
18_LC092316
543568
WB-1046564


title: 16HBE cells, 5% patient serum 545505, 24h, rep1

description:
22_LC092316
22_LC092316
545505
WB-1046568


title: 16HBE cells, 5% patient serum 554854, 24h, rep1

description:
17_LC092316
17_LC092316
554854
WB-1046563


title: 16HBE cells, 5% patient serum 518736, 24h, rep1

description:
16_LC092316
16_LC092316
518736
WB-1046562


title: 16HBE cells, 5% patient serum 567405, 24h, rep1

description:
19_LC092316
19_LC092316
567405
WB-1046565


title: 16HBE cells, 5% serum reference control, 24h, rep2

description:
12_LC092316
12_LC092316
reference_2
WB-1046558


title: 16HBE cells, 5% patient serum 525507, 24h, rep1

description:
14_LC092316
14_LC092316
525507
WB-1046560


title: 16HBE cells, 5% patient serum 546654, 24h, rep1

description:
11_LC092316
11_LC092316
546654
WB-1046557


title: 16HBE cells, 5% patient serum 558455, 24h, rep1

description:
09_LC092316
09_LC092316
558455
WB-1046555


title: 16HBE cells, 5% patient serum 561048, 24h, rep1

description:
15_LC092316
15_LC092316
561048
WB-1046561


title: 16HBE cells, 5% patient serum 562788, 24h, rep1

description:
10_LC092316
10_LC092316
562788
WB-1046556


title: 16HBE cells, 5% patient serum 527406, 24h, rep1

description:
06_LC10_07_16
06_LC10_07_16
527406
WB-1046576


title: 16HBE cells, 5% patient serum 549242, 24h, rep1

description:
10_LC10_07_16
10_LC10_07_16
549242
WB-1046580


title: 16HBE cells, 5% patient serum 531094, 24h, rep1

description:
07_LC10_07_16
07_LC10_07_16
531094
WB-1046577


title: 16HBE cells, 5% patient serum 529756, 24h, rep1

description:
05_LC10_07_16
05_LC10_07_16
529756
WB-1046575


title: 16HBE cells, 5% patient serum 555640, 24h, rep1

description:
08_LC092316
08_LC092316
555640
WB-1046554


title: 16HBE cells, 5% patient serum 551469, 24h, rep1

description:
08_LC10_07_16
08_LC10_07_16
551469
WB-1046578


title: 16HBE cells, 5% patient serum 556989, 24h, rep1

description:
02_LC10_07_16
02_LC10_07_16
556989
WB-1046572


title: 16HBE cells, 5% patient serum 540940, 24h, rep1

description:
03_LC092316
03_LC092316
540940
WB-1046549


title: 16HBE cells, 5% patient serum 533839, 24h, rep1

description:
02_LC092316
02_LC092316
533839
WB-1046548


title: 16HBE cells, 5% patient serum 544327, 24h, rep1

description:
04_LC092316
04_LC092316
544327
WB-1046550


title: 16HBE cells, 5% patient serum 559991, 24h, rep1

description:
01_LC092316
01_LC092316
559991
WB-1046547


title: 16HBE cells, 5% patient serum 532913, 24h, rep1

description:
07_LC092316
07_LC092316
532913
WB-1046553


title: 16HBE cells, 5% patient serum 528612, 24h, rep1

description:
32_HBE_052016
32_HBE_052016
528612
WB-1046543


title: 16HBE cells, 5% patient serum 533710, 24h, rep1

description:
31_HBE_052016
31_HBE_052016
533710
WB-1046542


title: 16HBE cells, 5% patient serum 531203, 24h, rep1

description:
13_LC092316
13_LC092316
531203
WB-1046559


title: 16HBE cells, 5% patient serum 531825, 24h, rep1

description:
33_HBE_052016
33_HBE_052016
531825
WB-1046544


title: 16HBE cells, 5% patient serum 558063, 24h, rep1

description:
20_LC092316
20_LC092316
558063
WB-1046566


title: 16HBE cells, 5% patient serum 527130, 24h, rep1

description:
13_HBE_052016
13_HBE_052016
527130
WB-1046538


title: 16HBE cells, 5% serum reference control, 24h, rep1

description:
35_HBE_052016
35_HBE_052016
reference_1
WB-1046546


title: 16HBE cells, 5% patient serum 550908, 24h, rep1

description:
06_LC092316
06_LC092316
550908
WB-1046552


title: 16HBE cells, 5% patient serum 526545, 24h, rep1

description:
12_HBE_052016
12_HBE_052016
526545
WB-1046537


title: 16HBE cells, 5% patient serum 526491, 24h, rep1

description:
10_HBE_052016
10_HBE_052016
526491
WB-1046535


title: 16HBE cells, 5% patient serum 529253, 24h, rep1

description:
34_HBE_052016
34_HBE_052016
529253
WB-1046545


title: 16HBE cells, 5% patient serum 522255, 24h, rep1

description:
09_HBE_052016
09_HBE_052016
522255
WB-1046534


title: 16HBE cells, 5% patient serum 564915, 24h, rep1

description:
20200930-60
20200930_60
564915
SCK2990


title: 16HBE cells, 5% patient serum 513175, 24h, rep1

description:
20200930-59
20200930_59
513175
SCK2989


title: 16HBE cells, 5% patient serum 561081, 24h, rep1

description:
20200930-58
20200930_58
561081
SCK2988


title: 16HBE cells, 5% patient serum 587468, 24h, rep1

description:
20200930-57
20200930_57
587468
SCK2987


title: 16HBE cells, 5% patient serum 526424, 24h, rep1

description:
11_HBE_052016
11_HBE_052016
526424
WB-1046536


title: 16HBE cells, 5% patient serum 523122, 24h, rep1

description:
20200930-56
20200930_56
523122
SCK2986


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep10

description:
20200930-55
20200930_55
20200917_pool_B10
SCK2985

value: control pool


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep10

description:
20200930-54
20200930_54
20200917_pool_M10
SCK2984

value: case pool


title: 16HBE cells, 5% patient serum 527771, 24h, rep1

description:
14_HBE_052016
14_HBE_052016
527771
WB-1046539


title: 16HBE cells, 5% patient serum 556827, 24h, rep1

description:
20200930-53
20200930_53
556827
SCK2983


title: 16HBE cells, 5% patient serum 528382, 24h, rep1

description:
05_LC092316
05_LC092316
528382
WB-1046551


title: 16HBE cells, 5% patient serum 530496, 24h, rep1

description:
15_HBE_052016
15_HBE_052016
530496
WB-1046540


title: 16HBE cells, 5% patient serum 582828, 24h, rep1

description:
20200930-47
20200930_47
582828
SCK2977


title: 16HBE cells, 5% patient serum R000020, 24h, rep1

description:
20200930-50
20200930_50
R000020
SCK2980


title: 16HBE cells, 5% patient serum 504996, 24h, rep1

description:
20200930-44
20200930_44
504996
SCK2974


title: 16HBE cells, 5% patient serum 527317, 24h, rep1

description:
16_HBE_052016
16_HBE_052016
527317
WB-1046541


title: 16HBE cells, 5% patient serum R000126, 24h, rep1

description:
20200930-48
20200930_48
R000126
SCK2978


title: 16HBE cells, 5% patient serum 519969, 24h, rep1

description:
20200930-49
20200930_49
519969
SCK2979


title: 16HBE cells, 5% patient serum 511872, 24h, rep1

description:
20200930-52
20200930_52
511872
SCK2982


title: 16HBE cells, 5% patient serum 503201, 24h, rep1

description:
20200930-51
20200930_51
503201
SCK2981


title: 16HBE cells, 5% patient serum 570964, 24h, rep1

description:
20200930-46
20200930_46
570964
SCK2976


title: 16HBE cells, 5% patient serum 548553, 24h, rep1

description:
20200930-45
20200930_45
548553
SCK2975


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep9

description:
20200930-42
20200930_42
20200917_pool_M9
SCK2972


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep9

description:
20200930-43
20200930_43
20200917_pool_B9
SCK2973


title: 16HBE cells, 5% patient serum 577653, 24h, rep1

description:
20200930-39
20200930_39
577653
SCK2969


title: 16HBE cells, 5% patient serum 505685, 24h, rep1

description:
20200930-38
20200930_38
505685
SCK2968


title: 16HBE cells, 5% patient serum 506432, 24h, rep1

description:
20200930-34
20200930_34
506432
SCK2964


title: 16HBE cells, 5% patient serum 510703, 24h, rep1

description:
20200930-36
20200930_36
510703
SCK2966


title: 16HBE cells, 5% patient serum 519888, 24h, rep1

description:
20200930-37
20200930_37
519888
SCK2967


title: 16HBE cells, 5% patient serum 505548, 24h, rep1

description:
20200930-35
20200930_35
505548
SCK2965


title: 16HBE cells, 5% patient serum 572332, 24h, rep1

description:
20200930-33
20200930_33
572332
SCK2963


title: 16HBE cells, 5% patient serum 528011, 24h, rep1

description:
20200930-28
20200930_28
528011
SCK2958


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep8

description:
20200930-31
20200930_31
20200917_pool_B8
SCK2961


title: 16HBE cells, 5% patient serum 584802, 24h, rep1

description:
20200930-27
20200930_27
584802
SCK2957


title: 16HBE cells, 5% patient serum 571663, 24h, rep1

description:
20200930-32
20200930_32
571663
SCK2962


title: 16HBE cells, 5% patient serum 560604, 24h, rep1

description:
20200930-29
20200930_29
560604
SCK2959


title: 16HBE cells, 5% patient serum 543708, 24h, rep1

description:
20200930-25
20200930_25
543708
SCK2955


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep8

description:
20200930-30
20200930_30
20200917_pool_M8
SCK2960


title: 16HBE cells, 5% patient serum 555837, 24h, rep1

description:
20200930-24
20200930_24
555837
SCK2954


title: 16HBE cells, 5% patient serum 510581, 24h, rep1

description:
20200930-22
20200930_22
510581
SCK2952


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep7

description:
20200930-19
20200930_19
20200917_pool_B7
SCK2949


title: 16HBE cells, 5% patient serum 581876, 24h, rep1

description:
20200930-26
20200930_26
581876
SCK2956


title: 16HBE cells, 5% patient serum R000402, 24h, rep1

description:
20200930-20
20200930_20
R000402
SCK2950


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep7

description:
20200930-18
20200930_18
20200917_pool_M7
SCK2948


title: 16HBE cells, 5% patient serum 525598, 24h, rep1

description:
20200930-41
20200930_41
525598
SCK2971


title: 16HBE cells, 5% patient serum 511225, 24h, rep1

description:
20200930-40
20200930_40
511225
SCK2970


title: 16HBE cells, 5% patient serum 522435, 24h, rep1

description:
20200930-16
20200930_16
522435
SCK2946


title: 16HBE cells, 5% patient serum 508643, 24h, rep1

description:
20200930-17
20200930_17
508643
SCK2947


title: 16HBE cells, 5% patient serum 596433, 24h, rep1

description:
20200930-21
20200930_21
596433
SCK2951


title: 16HBE cells, 5% patient serum 516800, 24h, rep1

description:
20200930-14
20200930_14
516800
SCK2944


title: 16HBE cells, 5% patient serum 508154, 24h, rep1

description:
20200930-11
20200930_11
508154
SCK2941


title: 16HBE cells, 5% patient serum 574112, 24h, rep1

description:
20200930-12
20200930_12
574112
SCK2942


title: 16HBE cells, 5% patient serum 520543, 24h, rep1

description:
20200930-08
20200930_08
520543
SCK2938


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep6

description:
20200930-07
20200930_07
20200917_pool_B6
SCK2937


title: 16HBE cells, 5% patient serum 507061, 24h, rep1

description:
20200930-05
20200930_05
507061
SCK2935


title: 16HBE cells, 5% patient serum 527154, 24h, rep1

description:
20200930-09
20200930_09
527154
SCK2939


title: 16HBE cells, 5% patient serum 506983, 24h, rep1

description:
20200930-04
20200930_04
506983
SCK2934


title: 16HBE cells, 5% patient serum 525097, 24h, rep1

description:
20200930-03
20200930_03
525097
SCK2933


title: 16HBE cells, 5% patient serum 513812, 24h, rep1

description:
20200930-01
20200930_01
513812
SCK2931


title: 16HBE cells, 5% patient serum 599860, 24h, rep1

description:
20200930-23
20200930_23
599860
SCK2953


title: 16HBE cells, 5% patient serum 574826, 24h, rep1

description:
20200930-02
20200930_02
574826
SCK2932


title: 16HBE cells, 5% patient serum 575089, 24h, rep1

description:
20200927-59
20200927_59
575089
SCK2929


title: 16HBE cells, 5% patient serum 511426, 24h, rep1

description:
20200927-57
20200927_57
511426
SCK2927


title: 16HBE cells, 5% patient serum 604848, 24h, rep1

description:
20200930-13
20200930_13
604848
SCK2943


title: 16HBE cells, 5% patient serum 530762, 24h, rep1

description:
20200930-15
20200930_15
530762
SCK2945


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep5

description:
20200927-55
20200927_55
20200917_pool_B5
SCK2925


title: 16HBE cells, 5% patient serum 523813, 24h, rep1

description:
20200927-51
20200927_51
523813
SCK2921


title: 16HBE cells, 5% patient serum 509284, 24h, rep1

description:
20200927-50
20200927_50
509284
SCK2920


title: 16HBE cells, 5% patient serum 531020, 24h, rep1

description:
20200927-49
20200927_49
531020
SCK2919


title: 16HBE cells, 5% patient serum 570924, 24h, rep1

description:
20200930-10
20200930_10
570924
SCK2940


title: 16HBE cells, 5% patient serum 531049, 24h, rep1

description:
20200927-52
20200927_52
531049
SCK2922


title: 16HBE cells, 5% patient serum 572241, 24h, rep1

description:
20200927-58
20200927_58
572241
SCK2928


title: 16HBE cells, 5% patient serum 514268, 24h, rep1

description:
20200927-53
20200927_53
514268
SCK2923


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep5

description:
20200927-54
20200927_54
20200917_pool_M5
SCK2924


title: 16HBE cells, 5% patient serum 582541, 24h, rep1

description:
20200927-46
20200927_46
582541
SCK2916


title: 16HBE cells, 5% patient serum 517355, 24h, rep1

description:
20200927-47
20200927_47
517355
SCK2917


title: 16HBE cells, 5% patient serum 510921, 24h, rep1

description:
20200927-45
20200927_45
510921
SCK2915


title: 16HBE cells, 5% patient serum 523702, 24h, rep1

description:
20200927-44
20200927_44
523702
SCK2914


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep6

description:
20200930-06
20200930_06
20200917_pool_M6
SCK2936


title: 16HBE cells, 5% patient serum 515076, 24h, rep1

description:
20200927-60
20200927_60
515076
SCK2930


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep4

description:
20200927-43
20200927_43
20200917_pool_B4
SCK2913


title: 16HBE cells, 5% patient serum 521271, 24h, rep1

description:
20200927-39
20200927_39
521271
SCK2909


title: 16HBE cells, 5% patient serum 670584, 24h, rep1

description:
20200927-38
20200927_38
670584
SCK2908


title: 16HBE cells, 5% patient serum 530000, 24h, rep1

description:
20200927-37
20200927_37
530000
SCK2907


title: 16HBE cells, 5% patient serum 587413, 24h, rep1

description:
20200927-36
20200927_36
587413
SCK2906


title: 16HBE cells, 5% patient serum 572112, 24h, rep1

description:
20200927-41
20200927_41
572112
SCK2911


title: 16HBE cells, 5% patient serum 512343, 24h, rep1

description:
20200927-40
20200927_40
512343
SCK2910


title: 16HBE cells, 5% patient serum 556719, 24h, rep1

description:
20200927-56
20200927_56
556719
SCK2926


title: 16HBE cells, 5% patient serum 512853, 24h, rep1

description:
20200927-34
20200927_34
512853
SCK2904


title: 16HBE cells, 5% patient serum 510431, 24h, rep1

description:
20200927-33
20200927_33
510431
SCK2903


title: 16HBE cells, 5% patient serum 516640, 24h, rep1

description:
20200927-48
20200927_48
516640
SCK2918


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep3

description:
20200927-31
20200927_31
20200917_pool_B3
SCK2901


title: 16HBE cells, 5% patient serum 579012, 24h, rep1

description:
20200927-32
20200927_32
579012
SCK2902


title: 16HBE cells, 5% patient serum 509597, 24h, rep1

description:
20200927-35
20200927_35
509597
SCK2905


title: 16HBE cells, 5% patient serum 521005, 24h, rep1

description:
20200927-29
20200927_29
521005
SCK2899


title: 16HBE cells, 5% patient serum 530132, 24h, rep1

description:
20200927-26
20200927_26
530132
SCK2896


title: 16HBE cells, 5% patient serum 579594, 24h, rep1

description:
20200927-25
20200927_25
579594
SCK2895


title: 16HBE cells, 5% patient serum 565428, 24h, rep1

description:
20200927-27
20200927_27
565428
SCK2897


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep4

description:
20200927-42
20200927_42
20200917_pool_M4
SCK2912


title: 16HBE cells, 5% patient serum R000001, 24h, rep1

description:
20200927-24
20200927_24
R000001
SCK2894


title: 16HBE cells, 5% patient serum 525167, 24h, rep1

description:
20200927-23
20200927_23
525167
SCK2893


title: 16HBE cells, 5% patient serum 531233, 24h, rep1

description:
20200927-28
20200927_28
531233
SCK2898


title: 16HBE cells, 5% patient serum 511967, 24h, rep1

description:
20200927-21
20200927_21
511967
SCK2891


title: 16HBE cells, 5% patient serum 507726, 24h, rep1

description:
20200927-22
20200927_22
507726
SCK2892


title: 16HBE cells, 5% patient serum 516417, 24h, rep1

description:
20200927-20
20200927_20
516417
SCK2890


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep2

description:
20200927-19
20200927_19
20200917_pool_B2
SCK2889


title: 16HBE cells, 5% patient serum 509905, 24h, rep1

description:
20200927-16
20200927_16
509905
SCK2886


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep2

description:
20200927-18
20200927_18
20200917_pool_M2
SCK2888


title: 16HBE cells, 5% patient serum 565175, 24h, rep1

description:
20200927-17
20200927_17
565175
SCK2887


title: 16HBE cells, 5% patient serum 508617, 24h, rep1

description:
20200927-13
20200927_13
508617
SCK2883


title: 16HBE cells, 5% patient serum 615973, 24h, rep1

description:
20200927-14
20200927_14
615973
SCK2884


title: 16HBE cells, 5% patient serum 555845, 24h, rep1

description:
20200927-15
20200927_15
555845
SCK2885


title: 16HBE cells, 5% patient serum 537495, 24h, rep1

description:
20200927-12
20200927_12
537495
SCK2882


title: 16HBE cells, 5% patient serum 581507, 24h, rep1

description:
20200927-11
20200927_11
581507
SCK2881


title: 16HBE cells, 5% patient serum 524314, 24h, rep1

description:
20200927-09
20200927_09
524314
SCK2879


title: 16HBE cells, 5% patient serum 571209, 24h, rep1

description:
20200927-08
20200927_08
571209
SCK2878


title: 16HBE cells, 5% control serum pool 20200917, 24h, rep1

description:
20200927-07
20200927_07
20200917_pool_B1
SCK2877


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep3

description:
20200927-30
20200927_30
20200917_pool_M3
SCK2900


title: 16HBE cells, 5% patient serum 517267, 24h, rep1

description:
20200927-10
20200927_10
517267
SCK2880


title: 16HBE cells, 5% case serum pool 20200917, 24h, rep1

description:
20200927-06
20200927_06
20200917_pool_M1
SCK2876


title: wt

city: San Francisco

first: Hani

last: Goodarzi

department: Department of Biochemistry and Biophysics

institute: UCSF

data_processing:
We used MISO105 for alternative splicing analysis, as this tool is known for its consistent performance and wide use 106. Specifically, RNA-seq data was processed as follows: (1) to fulfill MISO requirements (see below), the reads obtained with different sequencing lengths were truncated to 75bps with cutadapt (v.2.10) -l option, (2) the truncated reads were mapped to the human hg38 genome assembly with GENCODE v38 comprehensive gene annotation using STAR (v.2.7.9) with options --outFilterScoreMinOverLread and --outFilterMatchNminOverLread both set to 0.25 107, (3) non-unique alignments were filtered and the replicates were merged, (4) the insert size distribution was estimated for each merged bam file separately using pe_utils –compute-insert-len from MISO (v.0.5.4), constitutive exons were retrieved using exon_utils with --get-const-exons and --min-exon-size 1000 105, (5) alternative splicing events were identified using miso --run with --read-len set to 75 and --paired-end set to the previously estimated insert size parameters. Finally, only cases with non-zero numbers of exclusion and inclusion reads and sum of these reads >=10 in at least one sample are left and shown in Figure 4.
Assembly: hg38, GENOCODE v38
Supplementary files format and content: TAF15_splicing contains the MISO outputs for A3SS, A5SS, RI, SE, and MXE combined for the comparison between TAF15 and control

growth_protocol: All cells were cultured in a 37°C 5% CO2 humidified incubator. The K562 cell line was cultured in RPMI-1640 medium supplemented with 10% FBS, glucose (2 g/L), L-glutamine (2 mM), 25 mM HEPES, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco). All cell lines were routinely screened for mycoplasma with a PCR-based assay.

extract_protocol:
Total RNA for RNA-seq and RT-qPCR was isolated using the Zymo QuickRNA isolation kit with in-column DNase treatment per the manufacturer’s protocol.
RNA-seq libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara), and sequenced on Illumina NovaSeq 6000 instrument, in a PE150 (paired end 150 cycles) setting, at Novogene Corporation.

treatment_protocol: K562 cells expressing dCas9-KRAB fusion protein were constructed by lentiviral delivery of pMH0006 (Addgene #135448) and FACS isolation of BFP-positive cells. The lentiviral constructs were co-transfected with pCMV-dR8.91 and pMD2.D plasmids using TransIT-Lenti (Mirus) into 293T cells, following the manufacturer’s protocol. The virus was harvested 48 hours post-transfection and passed through a 0.45 µm filter. Target cells were then transduced overnight with the filtered virus in the presence of 8 µg/mL polybrene (Millipore). Guide RNA sequences for CRISPRi-mediated gene knockdown were cloned into pCRISPRia-v2 (Addgene #84832) via BstXI-BlpI sites. After transduction with sgRNA lentivirus, K562 cells were selected with 2 µg/mL puromycin (Gibco). Knockdown of target genes was assessed by RT-qPCR using PerfeCTa SYBR Green SuperMix (QuantaBio) per the manufacturer’s instructions. HPRT1 was used as endogenous control.

value: Lymphocyte


title: 16HBE cells, 5% patient serum R000030, 24h, rep1

description:
20200927-05
20200927_05
R000030
SCK2875


title: 16HBE cells, 5% patient serum 529706, 24h, rep1

description:
20200927-04
20200927_04
529706
SCK2874


title: 16HBE cells, 5% patient serum 517604, 24h, rep1

description:
20200927-02
20200927_02
517604
SCK2872


title: 16HBE cells, 5% patient serum 521697, 24h, rep1

description:
20200927-03
20200927_03
521697
SCK2873


title: 16HBE cells, 5% patient serum 524330, 24h, rep1

description:
20200927-01
20200927_01
524330
SCK2871


title: MV411,PU1,shRNA2,Dox,RNAseq,biol rep 2

city: Cambridge

first: Salih

last: Topal

address: 500 Technology Square Suite 700

institute: Foghorn Therapeutics

description: Library name: MV411_PU1_shRNA2_Dox_Rep2

data_processing:
Sequencing reads were aligned to version hg38 of the human genome using gencode v30 gene annotations.
Differential gene expression was calculated using limma-voom R package.
Geneset enrichment analysis and Gene ontology term overrepresentation analysis was performed using clusterProfiler and DOSE R packages.
Assembly: hg38
Supplementary files format and content: tab-delimited excel files for read counts for each gene

extract_protocol:
Total RNA was extracted from frozen cell pellets previously washed with PBS. 1 μg RNA per sample was used as input material.
. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, index codes were added to each sample. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter). Then 3 μl USER Enzyme (NEB) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

value: AML

value: Dox-inducible

value: shRNA_2 targeting PU.1


title: MV411,PU1,shRNA2,Dox,RNAseq,biol rep 1

description: Library name: MV411_PU1_shRNA2_Dox_Rep1


title: MV411,PU1,shRNA3,Dox,RNAseq,biol rep 1

description: Library name: MV411_PU1_shRNA3_Dox_Rep1

value: shRNA_3 targeting PU.1


title: MV411,PU1,shRNA1,Dox,RNAseq,biol rep 1

description: Library name: MV411_PU1_shRNA1_Dox_Rep1

value: shRNA_1 targeting PU.1


title: MV411,PU1,shRNA3,Dox,RNAseq,biol rep 2

description: Library name: MV411_PU1_shRNA3_Dox_Rep2


title: TAF15


title: MV411,PU1,shRNA2,Dox,RNAseq,biol rep 3

description: Library name: MV411_PU1_shRNA2_Dox_Rep3


title: MV411,PU1,shRNA1,Dox,RNAseq,biol rep 3

description: Library name: MV411_PU1_shRNA1_Dox_Rep3


title: MV411,PU1,NTC,NoDox,RNAseq,biol rep 1

description: Library name: MV411_PU1_NTC_NoDox_Rep1

value: Non-targeting shRNA control


title: MV411,PU1,NTC,NoDox,RNAseq,biol rep 2

description: Library name: MV411_PU1_NTC_NoDox_Rep2


title: MV411,PU1,shRNA1,Dox,RNAseq,biol rep 2

description: Library name: MV411_PU1_shRNA1_Dox_Rep2


title: THP1,Compound49,24h,RNAseq,biol rep 3

description: Library name: THP1_Compound49_24h_RNAseq_Rep3

value: Compound 49


title: THP1,Compound49,24h,RNAseq,biol rep 2

description: Library name: THP1_Compound49_24h_RNAseq_Rep2


title: MV411,FHT1015,24h,RNAseq,biol rep 3

description: Library name: MV411_FHT1015_24h_RNAseq_Rep3


title: THP1,Compound49,24h,RNAseq,biol rep 1

description: Library name: THP1_Compound49_24h_RNAseq_Rep1


title: MV411,PU1,NTC,Dox,RNAseq,biol rep 1

description: Library name: MV411_PU1_NTC_Dox_Rep1


title: THP1,DMSO,24h,RNAseq,biol rep 3

description: Library name: THP1_DMSO_24h_RNAseq_Rep3

value: negative control


title: MV411,FHT1015,24h,RNAseq,biol rep 1

description: Library name: MV411_FHT1015_24h_RNAseq_Rep1


title: MV411,DMSO,24h,RNAseq,biol rep 3

description: Library name: MV411_DMSO_24h_RNAseq_Rep3


title: THP1,DMSO,24h,RNAseq,biol rep 2

description: Library name: THP1_DMSO_24h_RNAseq_Rep2


title: MV411,PU1,shRNA3,Dox,RNAseq,biol rep 3

description: Library name: MV411_PU1_shRNA3_Dox_Rep3


title: THP1,DMSO,24h,RNAseq,biol rep 1

description: Library name: THP1_DMSO_24h_RNAseq_Rep1


title: MV411,DMSO,24h,RNAseq,biol rep 2

description: Library name: MV411_DMSO_24h_RNAseq_Rep2


title: MV411,FHT1015,24h,RNAseq,biol rep 2

description: Library name: MV411_FHT1015_24h_RNAseq_Rep2


title: MV411,DMSO,24h,RNAseq,biol rep 1

description: Library name: MV411_DMSO_24h_RNAseq_Rep1


title: lib60198

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib60198

data_processing:
Fastq files were aligned to the Ensembl version of the human genome (GRCh38) (GenBank assembly accession id GCA_000001405.15), using TopHat (version 1.4.1). The single-paired flag was set to “single,” while all other TopHat parameters were set to defaults
HTSeq-count was used to generate gene counts with mode as “Intersection (nonempty)” and minimum alignment quality set to 0 and otherwise set to default parameters
For quality control, samples were kept that had human aligned counts >250,000 and median CV coverage < 1.1. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1 in at least 10% of libraries and were classified as protein coding using BioMart. Normalized counts were transformed to log2 counts per million along with observations level weights using voomWithQualityWeights from the “limma” R package version 3.46
Assembly: GRCh38
Supplementary files format and content: counts_raw.tsv
Supplementary files format and content: hgnc_ensembl_id_mapping.tsv
Supplementary files format and content: modules_normalized_expr.tsv
Supplementary files format and content: voom_normalized_gene_expr.tsv

source_name: Nasal lavage

extract_protocol:
Cells were sorted into lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina). Single-read sequencing was carried out on a HiSeq2500 sequencer (Illumina), using a HiSeq SBS v4 Kit to generate 58-base reads, with a target of approximately 10 million reads per sample

value: Nasal lavage

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title: lib60190

description: Library name: lib60190

tag: tissue

value: Mepolizumab


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description: Library name: lib60195

value: Y


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title: MV411,PU1,NTC,NoDox,RNAseq,biol rep 3

description: Library name: MV411_PU1_NTC_NoDox_Rep3

tag: cell line

tag: cell type

tag: genotype


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value: Exacerbation


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description: Library name: lib60181

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