title: PBMC, R-P3, myocarditis, recovered, TCR

description: 10x Genomics, TCR


title: Pool113_RS2_Plate6-3-G18-E6

status: Public on May 04 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

molecule: genomic DNA

organism: Mus musculus

source_name: brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x1012 to 1x1013 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: tissue

value: brain

tag: source

value: AUD

tag: target

value: PTLp

tag: Sex

value: female


title: PBMC, R-P3, myocarditis, recovered, GEX

city: New Haven

first: Anis

last: Barmada

state: CT

address: 300 Cedar Street

department: Department of Immunobiology

institute: Yale University

description: 10x Genomics, GEX

library_source: transcriptomic single cell

data_processing:
The single-cell transcriptome sequencing data were aligned and processed using CellRanger v5.0.1.
Assembly: GRCh38 reference genome.
Supplementary files format and content: CellRanger output files: filtered feature-barcode matrices (filtered_feature_bc_matrix.h5) and BCR/TCR annotations (filtered_contig_annotations.csv).

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
PBMCs were first isolated by Ficoll-Paque PLUS (GE Healthcare) or Lymphoprep (STEMCELL Technologies) density gradient centrifugation. Cells were subsequently washed twice in phosphate buffered saline (PBS) and resuspended in complete RPMI 1640 (cRPMI) medium (Lonza) containing 10% fetal bovine serum (FBS), 2 mM glutamine, and 100 U/ml each of penicillin and streptomycin (Invitrogen). PBMCs were then stored at 10^6 cells/ml in 10% dimethyl sulfoxide (DMSO) in FBS and stored in -80 °C overnight before further storage in liquid nitrogen. Serum was isolated by centrifugation of serum tubes and saving the supernatant in aliquots, which were flash frozen in liquid nitrogen prior to cryopreservation in -80 °C. All patient PBMCs were processed and cryopreserved within 1-6 hours of blood draw. Cryopreserved PBMCs were thawed in a water bath at 37 °C for ~2 minutes and removed from the water bath when a tiny ice crystal remained. Cells were transferred to a 15 mL conical tube of pre-warmed growth medium. The cryovial was rinsed with additional growth medium (10% FBS in DMEM) to recover leftover cells, and the rinse medium was added to the 15 mL conical tube while gently shaking the tube. Thawed PBMCs were centrifuged at 400g for 8 minutes at RT, and the supernatant was removed without disrupting the cell pellet. The pellet was resuspended in 1X PBS with 2% FBS, and cells were filtered with a 30 μM cell strainer. Cellular concentration was adjusted to 1,000 cells/μL based on the cell count and cells were immediately loaded onto the 10x Chromium Next GEM Chip G, according to the manufacturer's user guide (Chromium Next GEM SingleCell V(D)J Reagent Kits v1.1). We aimed to obtain a yield of ~10,000 cells per lane.
cDNA libraries for gene expression and TCR/BCR sequencing were generated according to manufacturer’s instructions (Chromium Next GEM SingleCell V(D)J Reagent Kits v1.1). Each library was then sequenced on an Illumina NovaSeq 6000 platform.

value: Blood

tag: cell type

value: PBMC

tag: condition

value: Myocarditis, recovered


title: RNAseq in Nrde2d200 mES cells, replicate 1

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
RNAseq_cpm_per_gene.txt
Nrde2d200_RNAseq_r1

library_source: transcriptomic

data_processing:
Samples were pooled and sequenced on an Illumina HiSeq 2500 instrument.
BCLIP-seq and Ribo-seq samples were demultiplexed using pyBarcodeFilter.py. RNA-seq demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
BCLIP-seq preprocessed reads (collapsed and adaptor trimmed) were aligned (splicing-aware) to the mouse genome (mm10) including the transcriptome annotation of GENCODE release M23 using STAR version 2.7.0a (Dobin et al., 2013) with the parameters: --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.05
RNA-seq and Ribo-seq reads were mapped (splicing-aware) to the mouse genome (mm10) including the transcriptome annotation of GENCODE release M23 using STAR version 2.7.3a. with the parameters: --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.05 --outSAMmultNmax 1. Counts per million tables were generated using the featureCounts function from the Rsubread package with the parameters: useMetaFeatures=TRUE,allowMultiOverlap=FALSE, minOverlap=5, countMultiMappingReads=FALSE, fraction=FALSE, minMQS=255, strandSpecific=1 for Ribo and 2 for RNAseq.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools). Bed files containing peak positions were generated from the .narrowPeak output file from MACS2. HiC allValidPairs files were generated by HiC-Pro 2.9.0. 4C wig files for replicates were generated from the filtered_reads output from peak_C by adding a wiggle file header.

molecule: total RNA

source_name: embryonic stem (ES) cells

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
Total RNA was extracted using the Absolutely RNA Miniprep kit (Agilent) with on-column DNase treatment
Libraries were prepared using the TruSeq Stranded Total RNA library prep kit (Illumina 20020597) according to manufacturers instructions.

treatment_protocol: Mtrex-KO and Nrde2-KO cells were treated with 100 nM 4-hydroxytamoxifen for 3 and 4 days, respectively. Cells expressing proteins fused to FKBP12F36V degron were treated with 500 nM dTAG-13 for 24 hours. The indicated RNA-seq samples were treated with 0.1 mg/ml cycloheximide (CHX) for 4 hours.

value: embryonic stem (ES) cells

tag: genetic background

value: hybrid 129-C57BL/6

tag: genotype

value: N-terminal 200 amino acid deletion of Nrde2


title: Pool113_RS2_Plate6-3-G18-E18


title: BCLIPseq of NRDE2 in SmE-depleted mES cells, replicate 2

description: BCLIP-seq

extract_protocol:
Cells were cross-linked with 254-nm UV light for 30 seconds and lysed in a buffer containing 1 % SDS and Benzonase nuclease. Protein-RNA cross-links were tandem affinity purified on magnetic beads and RNA was extracted by Proteinase K treatment.  For a detailed protocol, see Flemr et al, 2021.
RNA was reverse transcribed with SuperScript II (ThermoFisher 18064014) in the presence of a template-switching oligo. The resulting cDNA was purified with SPRI beads and libraries were amplified using NEBNext Ultra II Q5 master mix (NEB M0544L). For a detailed protocol, see Flemr et al, 2021.

value: SmE-FKBP12F36V, 3A-tagged Nrde2

tag: antibody

value: anti FLAG (Sigma F1804), M280 Streptavidin Dynabeads (ThermoFisher 11206D)


title: BCLIPseq of NRDE2 in SmE-depleted mES cells, replicate 1

description: BCLIP-seq


title: PBMC, EYVC2, healthy, vaccinated, GEX

description: 10x Genomics, GEX

value: Healthy, vaccinated


title: Pool113_RS2_Plate6-3-G18-D6


title: BCLIPseq of EIF4A3 in wt mES cells, replicate 1

description: BCLIP-seq

value: wt, 3A-tagged Eif4a3


title: BCLIPseq of CCDC174 in wt mES cells, replicate 2

description: BCLIP-seq

value: wt, 3A-tagged Ccdc174


title: PBMC, P4, myocarditis, acute, TCR

description: 10x Genomics, TCR

value: Myocarditis, acute


title: BCLIPseq of EIF4A3 in wt mES cells, replicate 2

description: BCLIP-seq


title: PBMC, P3, myocarditis, acute, TCR

description: 10x Genomics, TCR


title: Pool113_RS2_Plate6-3-G18-D17

value: male


title: BCLIPseq of CCDC174 in wt mES cells, replicate 1

description: BCLIP-seq


title: BCLIPseq of MTREX in wt mES cells, replicate 1

description: BCLIP-seq

value: wt, 3A-tagged Mtrex


title: PBMC, P2, myocarditis, acute, TCR

description: 10x Genomics, TCR


title: Y21.KO.bH.1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for count normalization and differentail expression analysis
Assembly: mm10
Supplementary files format and content: Prosessed files contains the raw counts for each gene

source_name: YUMM2.1 cell line

extract_protocol:
All RNA samples were extracted with TRIzol Reagent (Invitrogen, Cat. #15596018) according to the manufacture's instruction and cleaned by DNA-free DNAase Treatment and Removal Reagents (Ambion, #AM1906) to get rid of DNA contamination before submission for RNA sequencing.
3' mrna-seq libraries were generated from 100ng of DNAseI treated total RNA using the quantSeq FWD Library Preparation Kit (Lexogen, Vienna, Austria)

tag: cell line

tag: arntl

value: KO

value: bHLH

tag: myh9 sirna

tag: replicate


title: BCLIPseq of NRDE2D174R in mES cells, replicate 1

description: BCLIP-seq

value: Nrde2 D174R mutation, 3A-tagged Nrde2


title: BCLIPseq of CCDC174 in Nrde2 knockout mES cells, replicate 2

description: BCLIP-seq

value: Nrde2 knockout, 3A-tagged Ccdc174


title: PBMC, P1, myocarditis, acute, TCR

description: 10x Genomics, TCR

value: Blood

value: PBMC


title: BCLIPseq of MTREX in wt mES cells, replicate 2

description: BCLIP-seq


title: BCLIPseq of NRDE2d200 in mES cells, replicate 2

description: BCLIP-seq

value: N-terminal 200 amino acid deletion of Nrde2, 3A-tagged Nrde2


title: BCLIPseq of NRDE2D174R in mES cells, replicate 2

description: BCLIP-seq

value: hybrid 129-C57BL/6


title: BCLIPseq of NRDE2d200 in mES cells, replicate 1

description: BCLIP-seq


title: Pool113_RS2_Plate6-3-G18-C18

value: brain

value: AUD

value: PTLp

value: female


title: Pool113_RS2_Plate6-3-G18-C6


title: PBMC, R-P1, myocarditis, recovered, GEX

description: 10x Genomics, GEX

value: Myocarditis, recovered


title: BCLIPseq of NRDE2 in wt mES cells, replicate 2

description: BCLIP-seq

value: wt, 3A-tagged Nrde2

value: anti FLAG (Sigma F1804), M280 Streptavidin Dynabeads (ThermoFisher 11206D)


title: BCLIPseq of NRDE2 in wt mES cells, replicate 1

description: BCLIP-seq

extract_protocol:
Cells were cross-linked with 254-nm UV light for 30 seconds and lysed in a buffer containing 1 % SDS and Benzonase nuclease. Protein-RNA cross-links were tandem affinity purified on magnetic beads. RNA was polyadenylated on beads and extracted by Proteinase K treatment.  For a detailed protocol, see Flemr et al, 2021.
RNA was reverse transcribed with SuperScript II (ThermoFisher 18064014) in the presence of a template-switching oligo. The resulting cDNA was purified with SPRI beads and libraries were amplified using NEBNext Ultra II Q5 master mix (NEB M0544L). For a detailed protocol, see Flemr et al, 2021.


title: Pool113_RS2_Plate6-3-G18-C17

value: male


title: Daudi-Cas9, ZNF217, Invitrogen

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens St

institute: UCSF Gladstone Institutes

description: CUT&RUN ZNF217 (Fisher Scientific polyclonal)

data_processing:
Bcl2fastq (version 2.19) with --minimum-trimmed-read-length 8 was run to generate fastqs
Fastqs were trimmed using cutadapt (version 1.18) prior to merging of technical replicates
Bowtie2 (version 2.2.5) was used to align the trimmed fastqs to GRCh38 and E. coli EMBL accession U00096.2
Conversion from sam to bam was performed with with samtools(version 1.9)
Conversion from bam to bed was performed with bedtools (version 2.30.0) and bedfiles were filtered to include only paired reads of less than 1000 bp distance
Normalized bedgraph files were generated using bedtools (version 2.30.0) where the scale_factor was equal to 1000000 divided by the number of aligned E. coli reads per sample
Assembly: hg38
Supplementary files format and content: normalized bedgraph scaled to the number of E.coli spike-in reads per sample
Library strategy: CUT&RUN

source_name: Lymphocytes

extract_protocol:
Nuclei were isolated with a 0.1% Triton-X extraction buffer prior to preparation following the EpiCypher CUTANA™ ChIC/CUT&RUN kit v3. Cell permeabilization was performed with 0.01% digitonin and antibodies were added at 500 ng per sample. 0.5 ng of the kit provided E. coli spike in DNA were added to each sample following chromatin cleavage.
Libraries were prepared according to the EpiCypher CUTANA™ CUT&RUN Library Prep Kit v1

value: Lymphocytes

value: B lymphoblasts

value: ZNF217 (Invitrogen polyclonal)


title: Pool113_RS2_Plate6-3-G18-D18


title: PBMC, P3, myocarditis, acute, BCR

description: 10x Genomics, BCR

value: Myocarditis, acute


title: Daudi-Cas9, IRF1, Cell Signaling Technology

description: CUT&RUN IRF1 (Cell Signaling Technology D5E4)

value: IRF1 (Cell Signaling Technology D5E4)


title: BCLIPseq of CCDC174 in Nrde2 knockout mES cells, replicate 1

description: BCLIP-seq

value: Nrde2 knockout, 3A-tagged Ccdc174


title: Pool113_RS2_Plate6-3-G18-B5


title: PBMC, P1, myocarditis, acute, BCR

description: 10x Genomics, BCR

value: Blood

value: PBMC


title: PBMC, P2, myocarditis, acute, BCR

description: 10x Genomics, BCR


title: Daudi-Cas9, IgG, EpiCypher

description: CUT&RUN IgG (Epicypher polyclonal)

value: IgG (Epicypher polyclonal)


title: Pool113_RS2_Plate6-3-G18-B6

value: brain


title: Daudi-Cas9, H3K4me3, EpiCypher

description: CUT&RUN H3K4me3 (Epicypher polyclonal)

value: H3K4me3 (Epicypher polyclonal)


title: PBMC, P4, myocarditis, acute, BCR

description: 10x Genomics, BCR


title: PBMC, P4, myocarditis, acute, GEX

description: 10x Genomics, GEX


title: HuhWT_IFNy_24h_INP

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

description: IFN gamma stimulated Huh7.5 wild type cells, 24h, input

data_processing:
After quality assessment of raw reads with FastQC, ChIPseq data was analyzed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline v3 (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters (ENCODE Project Consortium, 2012)
regionPeak files were generated using SPP with default settings, FDR threshold set to 0.01
Assembly: hg38
Supplementary files format and content: regionPeak (except for input sample). High-confidence peaks obtained after IDR evaluation between biological replicates (optimal output peak set; https://www.encodeproject.org/data-standards/terms/)

growth_protocol: Huh7.5 WT cell line was maintained in DMEM complete medium supplemented with 10% fetal bovine serum (FBS), 1% MEM NEAA and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
ChIP was carried out as previously described (Piaszyk-Borychowska et al. 2012)
ChIP-seq libraries were prepared using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (E6240, NEB) and NEBNext® Multiplex Oligos for Illumina®, according to the manufacturer's protocol. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol:
Cells were seeded in full cell culture medium, which was replaced the next day with starving medium containing 1% FBS for 8h before starting the treatment
IFNα (1000 U/ml, IF007, MERCK) or IFNγ (10 ng/ml, IF002, MERCK) was added for indicated time points

value: human hepatocellular carcinoma cells

tag: chip antibody


title: HuhWT_IFNy_72h_INP

description: IFN gamma stimulated Huh7.5 wild type cells, 72h, input


title: PBMC, P3, myocarditis, acute, GEX

description: 10x Genomics, GEX


title: Pool113_RS2_Plate6-3-G18-B18

value: AUD

value: PTLp

value: female


title: HuhWT_IFNy_0_5h_INP

description: IFN gamma stimulated Huh7.5 wild type cells, 0.5h, input


title: HuhWT_IFNa_8h_INP

description: IFN alpha stimulated Huh7.5 wild type cells, 8h, input


title: Pool113_RS2_Plate6-3-G18-B17


title: HuhWT_IFNy_4h_INP

description: IFN gamma stimulated Huh7.5 wild type cells, 4h, input


title: HuhWT_IFNa_24h_INP

description: IFN alpha stimulated Huh7.5 wild type cells, 24h, input


title: Pool113_RS2_Plate6-3-G18-A5


title: Pool113_RS2_Plate6-3-G18-A6


title: PBMC, P1, myocarditis, acute, GEX

description: 10x Genomics, GEX


title: HuhWT_IFNa_2h_INP

description: IFN alpha stimulated Huh7.5 wild type cells, 2h, input


title: HuhWT_IFNa_72h_INP

description: IFN alpha stimulated Huh7.5 wild type cells, 72h, input


title: PBMC, P2, myocarditis, acute, GEX

description: 10x Genomics, GEX


title: HuhWT_IFNa_0_5h_INP

description: IFN alpha stimulated Huh7.5 wild type cells, 0.5h, input


title: Pool113_RS2_Plate6-3-G18-A17


title: M50

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Expression counts determined by spaceranger 1.2.0 and reference genome GRCh3-2020-A.
Spots overlying samples KRP440 and KRP478 were excluded from the analysis.
The remaining processing and normalization steps described on the paper were not performed on the provided processed data
Assembly: Hg38
Supplementary files format and content: Compressed file with outputs from spaceranger in a tar.gz file, high resolution image on tiff.

source_name: Kidney

extract_protocol:
Subjects with idiopathic Calcium Oxalate stones underwent a renal papillary biopsy during a clinically indicated percutaneous nephrolithotomy for stone removal approved by the institutional review board (IRB) of Indiana University (IRB #1010002261). Human reference (non-stone former) nephrectomy papillary specimens without evidence of renal disease were obtained from the Biopsy Biobank Cohort of Indiana (IRB #1906572234).
CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics

tag: disease

value: Calcium Oxalate

tag: tissue source

value: Papillary Nephrectomy

tag: storage

value: OCT at -80C

tag: gender

value: M

tag: description

value: Single sample

tag: fraction of reads mapped to exons

tag: median genes per spot


title: HuhWT_IFNy_72h_IRF1_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 72h, IRF1

tag: cell type


title: HuhWT_IFNy_72h_IRF1_rep1


title: Pool113_RS2_Plate6-2-L17-P4

tag: tissue

tag: source

tag: target

tag: Sex


title: KRP446 (M) / KRP462 (F) / KRP475 (F)

value: pooled male and female

value: Three samples included within the fiducial zone. KRP446 refers to the sample included in the top right. KRP462 refer to the sample in the top left. KRP475 refers to the sample in the bottom right. Spots associated to each sample were separated during data processing.


title: HuhWT_IFNy_24h_IRF1_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 24h, IRF1

tag: cell line


title: HuhWT_IFNy_4h_IRF1_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 4h, IRF1


title: F59 / F63

value: F

value: Two samples included within the fiducial zone. F59 refers to Both pieces in the right. F36 refers to the piece in the left.  Spots associated to each sample were separated during data processing.


title: HuhWT_IFNy_24h_IRF1_rep1


title: Pool113_RS2_Plate6-2-L17-P3

value: male


title: HuhWT_IFNy_4h_IRF1_rep1


title: HuhWT_IFNy_0_5h_IRF1_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 0.5h, IRF1


title: Pool113_RS2_Plate6-2-L17-O4


title: mESCs,TT-FHAgo2:LIS1-GFP-OE (+Dox), FBS+LIF condition, Rep#4 - small RNA-seq

city: Rehovot

first: Orly

last: Reiner

address: 234, Herzl Street,

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Biological replicate4

data_processing:
Sequenced reads were trimmed for adaptor sequence using Cutadapt and were aligned with STAR.
Raw counts were processed with qCount, and normalized reads were obtained by DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: raw count quantification files

source_name: mouse embryonic stem cells

growth_protocol: Mouse ES cells were grown in FBS+LIF culture media.

extract_protocol:
Total RNA was extracted from cells, using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Lexogen small RNA library kit
RNAseq, size selection for small RNA was performed

tag: culture medium

value: FBS+LIF (+Dox)

tag: genotype

value: Ago1/2/3/4 -/- ; LIS1 overexpression (LIS1 GFP OE); Dox. AGO2

tag: strain

value: hybrid


title: mESCs,TT-FHAgo2:LIS1-GFP-OE (+Dox), FBS+LIF condition, Rep#2 - small RNA-seq

description: Biological replicate2


title: mESCs,TT-FHAgo2:LIS1-GFP-OE (+Dox), FBS+LIF condition, Rep#3 - small RNA-seq

description: Biological replicate3


title: S12: IBJ4, 5:1, D20

city: Cardiff

first: Karolina

last: Dec

address: Hadyn Ellis Building, Maindy Road, Cathays

department: Neuroscience and Mental Health Innovation Institute

country: United Kingdom

institute: Cardiff University

data_processing:
Data was demultiplexed using DRAGEN (v. 3.8.4) bcl data conversion
Differential Expressed Gene (DEG) analysis was performed using the DESeq2 package in R
The enrichment analysis was performed on all DEGs using the Enrichr package

extract_protocol:
RNA was extracted using RNAeasy Plus MiniKit (Qiagen)
Libraries were generated using KAPA mRNA HyperPrep Kit (Roche) and pooled in an equimolar fashion

value: hIPSCs

value: WT

tag: treatment

value: PUFA ratio 5:1


title: Pool113_RS2_Plate6-2-L17-N4

value: brain

value: AUD

value: PTLp

value: female


title: Pool113_RS2_Plate6-2-L17-O16


title: S9: IBJ4, 3:1, D20

value: PUFA ratio 3:1


title: Pool113_RS2_Plate6-2-L17-N3


title: HuhWT_IFNy_0_5h_IRF1_rep1

value: human hepatocellular carcinoma cells

tag: chip antibody


title: S11: IBJ4, 5:1, D20


title: S10: IBJ4, 5:1, D20


title: HuhWT_UN_INP

description: unstimulated Huh7.5 wild type cells, input


title: HuhWT_IFNa_72h_IRF1_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 72h, IRF1


title: Pool113_RS2_Plate6-2-L17-N15


title: S8: IBJ4, 3:1, D20


title: mESCs,TT-FHAgo2 (+Dox), FBS+LIF condition, Rep#4 - small RNA-seq

description: Biological replicate4


title: HuhWT_IFNa_72h_IRF1_rep1


title: mESCs,TT-FHAgo2 (+Dox), FBS+LIF condition, Rep#3 - small RNA-seq

description: Biological replicate3


title: S7: IBJ4, 3:1, D20


title: Pool113_RS2_Plate6-2-L17-M4


title: HuhWT_IFNa_24h_IRF1_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 24h, IRF1


title: HuhWT_IFNa_24h_IRF1_rep1


title: Pool113_RS2_Plate6-2-L17-M16


title: mESCs,TT-FHAgo2:LIS1-GFP-OE (+Dox), FBS+LIF condition, Rep#1 - small RNA-seq

description: Biological replicate1


title: S6: IBJ4, 1:3, D20

value: PUFA ratio 1:3


title: S5: IBJ4, 1:3, D20


title: mESCs,TT-FHAgo2 (+Dox), FBS+LIF condition, Rep#1 - small RNA-seq

description: Biological replicate1


title: HuhWT_IFNa_8h_IRF1_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 8h, IRF1


title: S4: IBJ4, 1:3, D20


title: mESCs,TT-FHAgo2:LIS1-GFP-OE, FBS+LIF condition, Rep#4 - small RNA-seq

description: Biological replicate4

value: FBS+LIF

value: Ago1/2/3/4 -/- ; LIS1 overexpression (LIS1 GFP OE)


title: HuhWT_IFNa_8h_IRF1_rep1


title: mESCs,TT-FHAgo2 (+Dox), FBS+LIF condition, Rep#2 - small RNA-seq

description: Biological replicate2


title: Pool113_RS2_Plate6-2-L17-M15


title: HuhWT_IFNa_2h_IRF1_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 2h, IRF1


title: HuhWT_IFNa_2h_IRF1_rep1


title: mESCs,TT-FHAgo2:LIS1-GFP-OE, FBS+LIF condition, Rep#3 - small RNA-seq

description: Biological replicate3


title: S2: IBJ4, 1:1 (control), D20

value: PUFA ratio 1:1 (control)


title: Pool113_RS2_Plate6-2-L17-L4


title: S3: IBJ4, 1:1 (control), D20


title: mESCs,TT-FHAgo2:LIS1-GFP-OE, FBS+LIF condition, Rep#2 - small RNA-seq

description: Biological replicate2


title: Pool113_RS2_Plate6-2-L17-L3

value: male


title: mESCs,TT-FHAgo2:LIS1-GFP-OE, FBS+LIF condition, Rep#1 - small RNA-seq

description: Biological replicate1


title: HuhWT_IFNa_0_5h_IRF1_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 0.5h, IRF1


title: S1: IBJ4, 1:1 (control), D20


title: mESCs,TT-FHAgo2, FBS+LIF condition, Rep#4 - small RNA-seq

description: Biological replicate4


title: Pool113_RS2_Plate6-2-L17-K15


title: Pool113_RS2_Plate6-2-L17-K16


title: Pool113_RS2_Plate6-2-L17-K4


title: mESCs,TT-FHAgo2, FBS+LIF condition, Rep#3 - small RNA-seq

description: Biological replicate3


title: week8_het6_rep1

first: Carolina

middle: C

last: Gracia-Diaz

address: 3501 Civic Center Boulevard

department: Raymond G. Perelman Center for Cellular and Molecular Therapeutics

institute: The Children's Hospital of Philadelphia

data_processing:
Raw data (raw reads) of FASTQ format were processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differentially expressed genes were called using DESeq2
Assembly: hg19
Supplementary files format and content: a tab-delimited text file include read count values for all sampes (gene names labeled)

source_name: stem cell derived neuron

extract_protocol:
On the day of RNA extraction, each well from a 6-well plate was lysed in 1ml TRIzol (15596026, Invitrogen). Addition of 0.2ml chloroform (288306, Sigma-Aldreich) followed by centrifugation was performed to separate the solution into an aqueous phase and an organic phase. Isopropyl alcohol and 75% ethanol (111000200CSPP, Pharmco) was added in sequence to precipitate and wash the RNA pellets.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: stem cell derived neuron

value: neuron

value: EZH1 +/G

value: SMAD differentiation


title: week8_het6_rep2


title: HuhWT_UN_IRF1_rep2

description: unstimulated Huh7.5 wild type cells, IRF1


title: Pool113_RS2_Plate6-2-L17-L15


title: Pool113_RS2_Plate6-2-L17-J4


title: mESCs,TT-FHAgo2, FBS+LIF condition, Rep#2 - small RNA-seq

description: Biological replicate2

value: hybrid


title: week8_het5_rep1


title: mESCs,TT-FHAgo2, FBS+LIF condition, Rep#1 - small RNA-seq

description: Biological replicate1


title: HuhWT_UN_IRF1_rep1


title: Pool113_RS2_Plate6-2-L17-J3


title: week8_het5_rep2


title: week8_16del_rep2


title: mESCs, Lis1 WT, FGF+Activin condition, Rep#1 - ATACseq

description:
Biological replicate1
b1_WT_FA_enc_atac_scalefactor_normalized.bdg

data_processing:
Paired ATAC-seq reads were first trimmed to remove adaptor sequences using cutadapt.
Trimmed reads were aligned with Bowtie2, filtering out secondary alignments, and converted to bam format.
Primary alignments were processed with qCount from QuasR package, and normalized using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Bedgraph files were generated with Deeptools and were normalized with scaleFactors. For calculating scaleFactors, reciprocals of DESeq2 size factors were estimated using calcNormFactors from edgeR Bioconductor package with RLE method.

growth_protocol: Mouse ES cells were grown in FBS+LIF, 2i+LIF and FGF+Activin culture media.

extract_protocol: ATAC-seq was performed according to the previously described protocol (Buenrostro et al., 2015) with modifications. Briefly, 50,000 cells were washed with cold PBS and resuspended in lysis buffer to extract nuclei. The nuclei were cold-centrifuged at 500 x g for 10 min. The nuclei pellet was incubated with transposition reaction buffer for 30 min. at 37 °C. The DNA was purified using the PCR Purification Kit (Qiagen).The eluted transposed DNA was submitted to the PCR using Q5 High-Fidelity Polymerase (NEB). DNA was amplified with 11-12 cycles of PCR.

value: FGF+Activin

value: Wild type


title: HuhWT_IFNy_72h_IRF9_rep1

description: IFN gamma stimulated Huh7.5 wild type cells, 72h, IRF9


title: HuhWT_IFNy_72h_IRF9_rep2


title: Pool113_RS2_Plate6-2-L17-J16

value: brain

value: AUD


title: Pool113_RS2_Plate6-2-L17-J15

value: PTLp


title: Pool113_RS2_Plate6-2-L17-I4

value: female


title: HuhWT_IFNy_24h_IRF9_rep1

description: IFN gamma stimulated Huh7.5 wild type cells, 24h, IRF9

value: human hepatocellular carcinoma cells


title: HuhWT_IFNy_24h_IRF9_rep2


title: HuhWT_IFNa_0_5h_IRF1_rep1


title: Pool113_RS2_Plate6-2-L17-I16


title: HuhWT_IFNy_4h_IRF9_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 4h, IRF9


title: week8_8del_rep1


title: week8_16del_rep1


title: HuhWT_IFNy_4h_IRF9_rep1


title: week8_WTS5_rep2


title: Pool113_RS2_Plate6-2-L17-H4


title: week8_WTS5_rep1


title: HuhWT_IFNy_0_5h_IRF9_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 0.5h, IRF9


title: mESCs, Lis1 OE, FGF+Activin condition, Rep#1 - ATACseq

description:
Biological replicate1
b1_OE_FA_enc_atac_scalefactor_normalized.bdg

value: LIS1 overexpression (LIS1 dsRED-OE)


title: mESCs, Lis1 OE, 2i+LIF condition, Rep#1 - ATACseq, technical replcate1

description:
Biological replicate1, technical replcate1
b1_OE_2IL_enc_atac_scalefactor_normalized.bdg


title: mESCs, Lis1 WT, 2i+LIF condition, Rep#1 - ATACseq, technical replcate1

description:
Biological replicate1, technical replcate1
b1_WT_2IL_enc_atac_scalefactor_normalized.bdg


title: mESCs, Lis1 F/-, FGF+Activin condition, Rep#1 - ATACseq

description:
Biological replicate1
b1_FLX_FA_enc_atac_scalefactor_normalized.bdg

value: Lis1 Floxed/- (F/-)


title: mESCs, Lis1 WT, FBS+LIF condition, Rep#1 - ATACseq

description:
Biological replicate1
b1_WT_SL_enc_atac_scalefactor_normalized.bdg

value: FBS+LIF


title: Pool113_RS2_Plate6-2-L17-H16


title: week8_H9_rep2


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#1 - ATACseq

description:
Biological replicate1
b1_FLX_SL_enc_atac_scalefactor_normalized.bdg


title: week8_H9_rep1


title: Pool113_RS2_Plate6-2-L17-G4


title: mESCs, Lis1 F/-, 2i+LIF condition, Rep#1 - ATACseq, technical replcate1

description:
Biological replicate1, technical replcate1
b1_FLX_2IL_enc_atac_scalefactor_normalized.bdg


title: mESCs, WT, FBS+LIF condition, Rep#4 - smallRNA-seq

description: Biological replicate4

extract_protocol:
Total RNA was extracted from cells, using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
TruSeq Small RNA Library Prep kit
RNAseq, size selection for small RNA was performed


title: HuhWT_IFNa_72h_IRF9_rep1

description: IFN alpha stimulated Huh7.5 wild type cells, 72h, IRF9


title: HuhWT_IFNa_72h_IRF9_rep2


title: Pool113_RS2_Plate6-2-L17-H15


title: HuhWT_IFNa_24h_IRF9_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 24h, IRF9


title: mESCs, Lis1 OE, FBS+LIF condition, Rep#1 - ATACseq

description:
Biological replicate1
b1_OE_SL_enc_atac_scalefactor_normalized.bdg


title: VCaP_siNC_2

city: Tampere

first: Tapio

last: Visakorpi

address: Kalevantie 4

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
The quality of raw RNA-seq reads was evaluated using FastQC v0.11.8 and the reads were trimmed with Trim Galore! v.0.6.5. Reads were aligned to GRCh38 using STAR v2.71a and indexed with Samtools v1.8. Quantification of protein-coding and lncRNA transcripts in the samples was performed with Kallisto v.0.46.0. The transcript counts were examined for differential expression using the DESeq2 R package.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include raw read counts and DESeq2 transcript counts for each sample

source_name: VCaP

growth_protocol: For androgen induction studies, LNCaP and VCaP cells were grown in phenol red-free RPMI 1640 medium with 10% charcoal/dextran-treated (CCS) FBS and 1% glutamine for 4 days. For AR knockdown studies, LNCaP and VCaP cells were grown in full media before reverse transfection with siRNAs.

extract_protocol:
RNA from cells was isolated using Trizol (Invitrogen, Thermo Fisher Scientific), treated with RNase-free DNase set (Qiagen), and purified by Monarch RNA Cleanup Kit (New England Biolabs) according to manufacturers’ protocols. The purified RNA was quantified by Qubit 4 Fluorometer (Invitrogen, Thermo Fisher Scientific) and Qubit RNA Broad Range Assay Kit (Invitrogen, Thermo Fisher Scientific), and its purity assessed by the 260nm/280nm ratio. RNA integrity was checked using 5300 Fragment Analyzer System (Agilent Technologies).
Library preparation was performed using standard polyA enrichment and sequenced with a Novaseq 6000 (Illumina) in Novogene for 150 bp pairedend reads.

treatment_protocol: For androgen induction studies, hormone-deprived cells were treated with 0 or 10 nM of dihydrotestosterone (DHT) for 24 hours. For AR knockdown studies, transfection reagent Lipofectamine RNAiMAX (Thermo Fisher Scientific) was used for transfecting AR or negative control siRNAs (Sigma-Aldrich) according to the manufacturer’s instructions. Cells were reverse transfected with 25 nM siRNA and grown for 48 h before RNA extraction.

value: VCaP

value: prostate cancer cells

value: negative control

value: AR silencing


title: Pool113_RS2_Plate6-2-L17-G16


title: Pool113_RS2_Plate6-2-L17-I15

value: male


title: Pool113_RS2_Plate6-2-L17-F4


title: week8_8del_rep2

value: stem cell derived neuron

value: neuron

value: SMAD differentiation


title: HuhWT_IFNa_24h_IRF9_rep1


title: VCaP_siNC_1


title: HuhWT_IFNy_0_5h_IRF9_rep1


title: mESCs, WT, FBS+LIF condition, Rep#3 - smallRNA-seq

description: Biological replicate3

value: Wild type

value: hybrid


title: Pool113_RS2_Plate6-2-L17-F3

value: brain

value: AUD


title: mESCs, WT, FBS+LIF condition, Rep#1 - smallRNA-seq

description: Biological replicate1


title: VCaP_siAR_3

value: AR knockdown


title: VCaP_siAR_2


title: HuhWT_IFNa_8h_IRF9_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 8h, IRF9

value: human hepatocellular carcinoma cells


title: VCaP_siNC_3


title: VCaP_siAR_1


title: HuhWT_IFNa_8h_IRF9_rep1


title: Pool113_RS2_Plate6-2-L17-F15

value: PTLp


title: Pool113_RS2_Plate6-2-L17-F16

value: female


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#8 - smallRNA-seq

description: Biological replicate4, clone2

value: FBS+LIF

value: LIS1 overexpression (LIS1 dsRED-OE)


title: HuhWT_IFNa_2h_IRF9_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 2h, IRF9


title: VCaP_10nM_DHT_3

value: VCaP

value: prostate cancer cells

value: DHT induction

value: androgen induction


title: HuhWT_IFNa_2h_IRF9_rep1


title: Pool113_RS2_Plate6-2-L17-E16


title: HuhWT_IFNa_0_5h_IRF9_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 0.5h, IRF9


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#6 - smallRNA-seq

description: Biological replicate2, clone2


title: Pool113_RS2_Plate6-2-L17-E15

value: male


title: VCaP_10nM_DHT_1


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#5 - smallRNA-seq

description: Biological replicate1, clone2


title: HuhWT_IFNa_0_5h_IRF9_rep1


title: mESCs, WT, FBS+LIF condition, Rep#2 - smallRNA-seq

description: Biological replicate2


title: HuhWT_UN_IRF9_rep2

description: unstimulated Huh7.5 wild type cells, IRF9


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#4 - smallRNA-seq

description: Biological replicate4, clone1


title: Pool113_RS2_Plate6-2-L17-D4


title: VCaP_0nM_DHT_3

value: hormone starved


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#3 - smallRNA-seq

description: Biological replicate3, clone1


title: Pool113_RS2_Plate6-2-L17-D3


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#2 - smallRNA-seq

description: Biological replicate2, clone1


title: HuhWT_UN_IRF9_rep1


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#7 - smallRNA-seq

description: Biological replicate3, clone2


title: VCaP_0nM_DHT_2


title: VCaP_0nM_DHT_1


title: Pool113_RS2_Plate6-2-L17-D16


title: Pool113_RS2_Plate6-2-L17-E4


title: HuhWT_IFNa_72h_pSTAT2_rep1

description: IFN alpha stimulated Huh7.5 wild type cells, 72h, phospho-STAT2 (Tyr690)

value: phospho-STAT2 (CST, #88410)


title: VCaP_10nM_DHT_2


title: Pool113_RS2_Plate6-2-L17-D15


title: Pool113_RS2_Plate6-2-L17-C4


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#8 - smallRNA-seq

description: Biological replicate4, clone2

value: Lis1 Floxed/- (F/-)


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#1 - smallRNA-seq

description: Biological replicate1, clone1

value: hybrid


title: HuhWT_IFNa_24h_pSTAT2_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 24h, phospho-STAT2 (Tyr690)


title: LNCaP_siNC_2

source_name: LNCaP

value: LNCaP

value: negative control

value: AR silencing


title: Pool113_RS2_Plate6-2-L17-C16

value: brain

value: AUD


title: HuhWT_IFNa_24h_pSTAT2_rep1

value: human hepatocellular carcinoma cells


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#7 - smallRNA-seq

description: Biological replicate3, clone2

value: FBS+LIF


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#6 - smallRNA-seq

description: Biological replicate2, clone2


title: LNCaP_siAR_3

value: AR knockdown


title: HuhWT_IFNa_8h_pSTAT2_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 8h, phospho-STAT2 (Tyr690)


title: Pool113_RS2_Plate6-2-L17-B4

value: PTLp

value: female


title: Pool113_RS2_Plate6-2-L17-B3


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#5 - smallRNA-seq

description: Biological replicate1, clone2


title: HuhWT_IFNa_72h_pSTAT2_rep2


title: LNCaP_siAR_2

value: prostate cancer cells


title: Pool113_RS2_Plate6-2-L17-B16


title: LNCaP_siNC_3


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#4 - smallRNA-seq

description: Biological replicate4, clone1


title: Pool113_RS2_Plate6-2-L17-B15


title: HuhWT_IFNa_8h_pSTAT2_rep1


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#3 - smallRNA-seq

description: Biological replicate3, clone1


title: HuhWT_IFNa_2h_pSTAT2_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 2h, phospho-STAT2 (Tyr690)


title: LNCaP_siAR_1


title: HuhWT_IFNa_2h_pSTAT2_rep1


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#2 - smallRNA-seq

description: Biological replicate2, clone1


title: Pool113_RS2_Plate6-1-C1-P2


title: LNCaP_10nM_DHT_2

value: DHT induction

value: androgen induction


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#1 - smallRNA-seq

description: Biological replicate1, clone1


title: Pool113_RS2_Plate6-1-C1-P14


title: HuhWT_IFNa_0_5h_pSTAT2_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 0.5h, phospho-STAT2 (Tyr690)


title: LNCaP_10nM_DHT_1


title: Pool113_RS2_Plate6-1-C1-P13

value: male


title: HuhWT_IFNa_0_5h_pSTAT2_rep1

value: phospho-STAT2 (CST, #88410)


title: mESCs, WT, FBS+LIF condition, Rep#4 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate4

data_processing:
Sequenced reads were trimmed for adaptor sequence using Cutadapt and were aligned with STAR.
Raw counts were processed with qCount from QuasR package, and normalized reads were obtained by DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: raw count quantification files

extract_protocol:
Total RNA was extracted from cells, using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
TruSeq Stranded Total RNA Library Prep kit

value: Wild type


title: LNCaP_siNC_1


title: HuhWT_UN_pSTAT2_rep2

description: unstimulated Huh7.5 wild type cells, phospho-STAT2 (Tyr690)


title: LNCaP_0nM_DHT_3

value: hormone starved


title: Pool113_RS2_Plate6-1-C1-P1


title: mESCs, WT, FBS+LIF condition, Rep#3 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate3

value: hybrid


title: Pool113_RS2_Plate6-1-C1-O2


title: LNCaP_0nM_DHT_2

value: LNCaP


title: LNCaP_10nM_DHT_3


title: LNCaP_0nM_DHT_1


title: Pool113_RS2_Plate6-1-C1-N2


title: HuhWT_IFNy_72h_pSTAT1_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 72h, phospho-STAT1 (Tyr701)

value: phospho-STAT1 (CST, #7649)


title: mESCs, WT, FBS+LIF condition, Rep#2 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate2


title: mESCs, WT, FBS+LIF condition, Rep#1 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate1


title: HuhWT_IFNy_24h_pSTAT1_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 24h, phospho-STAT1 (Tyr701)


title: Pool113_RS2_Plate6-1-C1-N14

value: brain


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#8 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate4, clone2

value: LIS1 overexpression (LIS1 dsRED-OE)


title: HuhWT_IFNy_24h_pSTAT1_rep1

value: human hepatocellular carcinoma cells


title: Pool113_RS2_Plate6-1-C1-M2

value: AUD


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#6 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate2, clone2

value: FBS+LIF


title: HuhWT_IFNy_72h_pSTAT1_rep1


title: Pool113_RS2_Plate6-1-C1-M14

value: PTLp


title: SC318

city: Pittsburgh

first: Tracy

last: Tabib

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

library_source: genomic single cell

data_processing:
For scRNA, FASTQ generation, demultiplexing, barcode assignment, and gene counting were performed using 10X Genomics' Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). For scATAC, FASTQ generation, demultiplexing, barcode assignment, and peak calling were performed using 10X Genomics' Cell Ranger-ATAC software v1.2.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
Downstream data analysis was performed using R packages Signac (v1.3.0) , Seurat (v4.0.3), harmony (v1.0),  and chromVAR (v1.12.0) [38]. Peak calling was performed by cluster using macs2.
Wilcoxon rank sum test with Bonferroni FDR correction was used for DEG testing.
Assembly: GRCh38 for scRNA and hg19 for scATAC
Supplementary files format and content: 10x Genomics output scRNA files: raw_feature_bc_matrix.h5
Supplementary files format and content: 10x Genomics output scATAC files: fragments.tsv.gz, fragments.tsv.gz.tbi, singlecell.csv, summary.csv, raw_peak_bc_matrix.h5, filtered_peak_bc_matrix.h5, filtered_tf_bc_matrix.h5, peaks.bed, peak_annotation.tsv

source_name: lung

extract_protocol:
Explanted subpleural peripheral lung tissue was finely diced and digested for 1 hour in a mix of either Collagenase A/DNase I or Liberase DL/DNase I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  For some lungs, CD45+ and EPCAM+ cell populations were partially depleted with Miltenyi magnetic bead separation.  For scATAC, cells were lysed according to 10X Genomics' Nuclei Isolation for Single Cell ATAC Sequencing protocol (CG000169 ).  Cells or nuclei were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed per the manufacturer’s instructions (Single Cell 3' v2, Single Cell 5' v1, scATACv1 protocols, 10x Genomics). In short, for the scRNA protocols, lung cells were added to the master mix and loaded into the chip; subsequently, gel beads and partitioning oil were added into the chip which was then loaded into the Chromium instrument, generating the gel bead-in-emulsion (GEM). Once emulsified, cells were lysed and poly-A RNA transcribed to cDNA, adding an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and 10x Barcode. Silane DynaBeads were then used to clean up the pooled and barcoded cDNA which was then amplified by PCR.  SPRIselect reagent was used to select the appropriately sized fragments for library construction. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added during the library construction protocol.  For scATAC, nuclei were incubated for one hour with the transposase then loaded into the Chromium instrument with barcoding reagents, gel beads, and partitioning oil.  Once emulsified, the P5 sequence and 10X barcode were added during the PCR GEM generation and barcoding steps.  The resulting 10x barcoded single-stranded DNA was then cleaned up with Silane Dynabeads and size selected with SPRIselect reagent.  Finally, a P7 sequence and a sample index were added during library construction via PCR.

value: lung

tag: disease state

value: IPF

tag: age

value: Male

tag: corecode

tag: samplename

value: IPF 2 ATAC

tag: lungsection

value: Lower Lobe

tag: depletions

value: 50% CD45, EPCAM depleted

tag: protocol

value: 10X Genomics scATACv1


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#5 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate1, clone2


title: Pool113_RS2_Plate6-1-C1-N13

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

tag: tissue

value: male


title: SC324

value: Normal

value: CONTROL 2 ATAC


title: SC308

value: Female

value: IPF 1 ATAC


title: SC326

value: IPF 3 ATAC


title: HuhWT_IFNy_4h_pSTAT1_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 4h, phospho-STAT1 (Tyr701)

tag: cell type

value: human hepatocellular carcinoma cells

value: phospho-STAT1 (CST, #7649)


title: HuhWT_IFNy_4h_pSTAT1_rep1


title: Pool113_RS2_Plate6-1-C1-M13

value: brain

tag: source

value: AUD

tag: target


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#4 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate4, clone1

value: FBS+LIF

value: LIS1 overexpression (LIS1 dsRED-OE)

value: hybrid


title: HuhWT_IFNy_0_5h_pSTAT1_rep2

description: IFN gamma stimulated Huh7.5 wild type cells, 0.5h, phospho-STAT1 (Tyr701)

tag: cell line


title: SC334

value: lung

tag: Sex

value: Male

value: CONTROL 5

value: 10X Genomics 5PrimeV1


title: HuhWT_UN_pSTAT2_rep1

value: phospho-STAT2 (CST, #88410)


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#3 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate3, clone1

tag: culture medium

tag: genotype


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#7 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate3, clone2

tag: strain


title: Pool113_RS2_Plate6-1-C1-M1

value: PTLp

value: male


title: HuhWT_IFNy_0_5h_pSTAT1_rep1

tag: chip antibody


title: SC333

tag: disease state

value: Normal

value: CONTROL 4

value: 50% CD45, EPCAM depleted


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#2 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate2, clone1


title: Pool113_RS2_Plate6-1-C1-L2

value: female


title: HuhWT_IFNa_72h_pSTAT1_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 72h, phospho-STAT1 (Tyr701)

value: human hepatocellular carcinoma cells

value: phospho-STAT1 (CST, #7649)


title: Pool113_RS2_Plate6-1-C1-L13

value: brain

value: AUD


title: SC316

tag: age

value: Female

value: CONTROL 1 ATAC

value: 10X Genomics scATACv1


title: mESCs, LIS1 OE, FBS+LIF condition, Rep#1 - totalRNA-seq

description:
ribosomal RNA depleted total RNA
Biological replicate1, clone1

value: FBS+LIF

value: LIS1 overexpression (LIS1 dsRED-OE)

value: hybrid


title: SC323

value: lung

value: Male

tag: corecode

value: CONTROL 2

value: 10X Genomics 5PrimeV1


title: HuhWT_IFNa_72h_pSTAT1_rep1


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#8 - totalRNA-seq

value: Lis1 Floxed/- (F/-)


title: HuhWT_IFNa_24h_pSTAT1_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 24h, phospho-STAT1 (Tyr701)


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#7 - totalRNA-seq


title: Pool113_RS2_Plate6-1-C1-K14

value: PTLp


title: Pool113_RS2_Plate6-1-C1-K2

value: female


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#6 - totalRNA-seq


title: HuhWT_IFNa_24h_pSTAT1_rep1

value: human hepatocellular carcinoma cells


title: SC313

value: Normal

tag: samplename

value: CONTROL 3

value: Lower Lobe


title: Pool113_RS2_Plate6-1-C1-K13

value: brain

value: AUD

value: male


title: HuhWT_IFNa_8h_pSTAT1_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 8h, phospho-STAT1 (Tyr701)

value: phospho-STAT1 (CST, #7649)


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#5 - totalRNA-seq

value: FBS+LIF


title: SC325

value: IPF

value: Female

value: IPF 3

tag: lungsection

value: 50% CD45, EPCAM depleted


title: HuhWT_IFNa_8h_pSTAT1_rep1


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#4 - totalRNA-seq

value: hybrid


title: EZH1, A678G, H3K27me3, R3

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 with parameters: -q --local --no-mixed --no-unal –dovetail
Uniquely aligned reads (mapping quality score >= 20) and concordant alignments were kept for downstream analysis using command: samtools -q 20 -f 0x2.
H3K27me3 peaks were called using MACS2 with parameters: --broad --keep-dup all -p 1e-5 --broad-cutoff 1e-5
ChIP-seq signal was normalized to sequencing depth using deepTools: bamCoverage --normalizeUsing CPM
ChIP-seq signal around peaks was computed and visualized using deepTools computeMatrix and plotHeatmap functions, respectively
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak

source_name: cells derived from ventral mesencephalon region of fetal brain

growth_protocol: ReNcells VM were cultured in a 1:1 ratio of N2 and B27 media supplemented with 20 ng/ml Fibroblast Growth Factor (bFGF) and 20 ng/ml Epidermal Growth Factor (bEGF). N2 media contains DMEM/F12 (Gibco #11330032), 1X N-2 neural supplement (Gibco #17502048), 5 g/ml Insulin (MilliPore Sigma #I9278), 1X GlutaMAX™ (Gibco # 35050061), 100 M MEM Non-Essential Amino Acids Solution (Gibco #11140050), 100 M -Mercaptoethanol (Gibco #21985023), 1 mM Sodium Piruvate (Gibco #11360070) and 1% Penicillin-Streptomycin (Gibco #15140122). B27 media contains Gibco Neurobasal™ medium (Gibco #21103049) supplemented with 1X B-27 neural supplement (Gibco #17504044), 1X GlutaMAX™and and 1% Penicillin-Streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature. Fixation was quenched with glycine (0.125 M). Cross-linked chromatin was fragmented by sonication carried out using a Bioruptor to generate an average fragment size of 200-500 bp.
DNA libraries were constructed with the TAKARA ThruPLEX® DNA-Seq Kit and the Illumina-compatible TAKARA DNA Single Index Kit

treatment_protocol: ReNcells were transduced to generate stable lines expressing WT or mutant EZH1 with EGFP. Cells were incubated with lentiviruses for 48 hrs, after which media was replaced with fresh ReNcell media and cells cultured for 5 days before sorting with BD FACS Aria Fusion flow cytometer

value: ReNcells VM

value: immortalized human neural progenitor line

value: EZH1 p.A678G

tag: treatment

value: anti-H3K27me3 (Cell Signaling (D5A7))


title: HuhWT_IFNa_2h_pSTAT1_rep2

description: IFN alpha stimulated Huh7.5 wild type cells, 2h, phospho-STAT1 (Tyr701)

value: human hepatocellular carcinoma cells


title: Pool113_RS2_Plate6-1-C1-J14

value: PTLp

value: female


title: Pool113_RS2_Plate6-1-C1-L1

value: brain


title: Pool113_RS2_Plate6-1-C1-J13

value: AUD


title: SC317

value: lung

value: Male

value: IPF 2

value: Lower Lobe

tag: depletions

tag: protocol

value: 10X Genomics 5PrimeV1


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#2 - totalRNA-seq

value: FBS+LIF

value: Lis1 Floxed/- (F/-)


title: mESCs, Lis1 F/-, FBS+LIF condition, Rep#3 - totalRNA-seq

value: hybrid


title: HuhWT_IFNa_2h_pSTAT1_rep1

tag: cell type

value: phospho-STAT1 (CST, #7649)


title: SC315

tag: tissue

value: Normal

value: Female

value: CONTROL 1


title: SC307

value: IPF

value: IPF 1


title: Pool113_RS2_Plate6-1-C1-J2

tag: source

tag: target

value: PTLp

value: female


title: Pool113_RS2_Plate6-1-C1-J1

value: brain

value: AUD

tag: Sex

value: male


title: HuhWT_IFNa_0_5h_pSTAT1_rep1

description: IFN alpha stimulated Huh7.5 wild type cells, 0.5h, phospho-STAT1 (Tyr701)

tag: cell line

value: human hepatocellular carcinoma cells


title: EZH1, A678G, H3K27me3, R1

value: cells derived from ventral mesencephalon region of fetal brain

value: ReNcells VM

value: immortalized human neural progenitor line

tag: genotype

value: EZH1 p.A678G

value: anti-H3K27me3 (Cell Signaling (D5A7))


title: HuhWT_UN_pSTAT1_rep2

description: unstimulated Huh7.5 wild type cells, phospho-STAT1 (Tyr701)

value: phospho-STAT1 (CST, #7649)


title: EZH1, WT, H3K27me3, R2

value: EZH1 WT


title: mESCs, FBS+LIF condition, Rep#2- seCLIPseq

description: Biological replicate2

data_processing:
seCLIP-seq analysis was performed using the eCLIP pipeline(v0.7.0+, https://github.com/YeoLab/eclip).
Reads trimmed twice with cutadapt were mapped with STAR (v2.7.7) first against a repeat element database (RepBase v25.06). Unmapped reads filtered of repeat elements were then mapped with STAR (v2.7.7) against a Mus musculus genome (mm10). PCR de-duped reads from each inline barcode were merged with samtools and peak clusters were identified with Clipper (v2.1.0) using bam files.
Normalized peak files were ranked by entropy score using merge_peaks pipeline (https://github.com/YeoLab/merge_peaks) and used as inputs to IDR (2.0.2) to determine reproducible peaks. Peaks were annotated by overlapping peak regions with gencode (vM25) annotations.
Assembly: GRCm38/mm10
Supplementary files format and content: Bedgraph files were generated and RPM normalized using Deeptools (v3.5.1).

extract_protocol: Libraries constructed according to seCLIP protocol (E. L. Van Nostrand et al. 2017 & S. Dvir et al. 2021)

value: FBS+LIF

value: Wild type (V6.5)

tag: strain

value: hybrid


title: EZH1, A678G, H3K27me3, R2


title: mESCs, FBS+LIF condition, Rep#1- seCLIPseq

description: Biological replicate1


title: EZH1, WT, H3K27me3, R1


title: Pool113_RS2_Plate6-1-C1-H14


title: mESCs, FBS+LIF condition, Rep#2 Input_B- seCLIPseq

description: Biological replicate2


title: HuhWT_UN_pSTAT1_rep1

tag: chip antibody


title: GFP, H3K27me3, R3

value: GFP


title: HuhWT_IFNa_0_5h_pSTAT1_rep2


title: Pool113_RS2_Plate6-1-C1-H13

value: PTLp


title: GFP, H3K27me3, R2


title: mESCs, FBS+LIF condition, Rep#1 Input_A- seCLIPseq

description: Biological replicate1


title: mESCs LIS1GFP-OE:F/-, 5i+LIF condition (XAV939), Rep#3, MARS-seq

description: Biological replicate3

data_processing:
Fastq files were processed using UTAP pipeline. Sequenced reads were trimmed for adaptor sequence using Cutadapt and were aligned with STAR.
Raw counts were processed with qCount, and normalized reads were obtained by DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: raw count quantification files

growth_protocol: Mouse ES cells were grown in 5i+LIF culture condtion treated with 100uM Zvad and 50uM Necrostatin-1

extract_protocol:
Total RNA was extracted from cells, using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using bulk MARS-seq protocol [Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776–9 (2014)].

tag: culture media

value: Lis1 Floxed/- (F/-):Ert2-Cre; LIS1-Overexpression (LIS1-GFP OE)


title: Pool113_RS2_Plate6-1-C1-I2

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

value: brain

value: female


title: GFP, H3K27me3, R1


title: mESCs LIS1GFP-OE:F/-, 5i+LIF condition (XAV939), Rep#4, MARS-seq

description: Biological replicate4


title: EZH1, A678G, input, R3


title: Pool113_RS2_Plate6-1-C1-G14

value: AUD


title: Pool113_RS2_Plate6-1-C1-G2


title: Pool113_RS2_Plate6-1-C1-H1

value: male


title: Pool113_RS2_Plate6-1-C1-G13


title: EZH1, WT, H3K27me3, R3

value: cells derived from ventral mesencephalon region of fetal brain


title: HuhWT_IFNy_24h_rep2

data_processing:
After quality control assessments using FastQC, fastq files were mapped to the Homo sapiens GRCh38/hg38 genome build (release-100) using STAR version 2.7.3a
Read counts were generated using FeatureCounts v1.6.2 with default parameters
Counts normalization and DEG analysis were performed using the DESeq2 v.1.30.1 package in R version 4.0.3
Assembly: hg38
Supplementary files format and content: Raw read counts in .csv format

source_name: IFN gamma stimulated Huh7.5 wild type cells, 24h

growth_protocol: Huh7.5 WT and KO cell lines were maintained in DMEM complete medium supplemented with 10% fetal bovine serum (FBS), 1% MEM NEAA and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using TRI-REAGENT (MRC) followed by a column-based Total RNA Zol-Out™ D kit (A&A Biotechnology) following the manufacturer's protocol
RNA-seq libraries were prepared in two biological replicates from 1ug of total RNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) together with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext® Multiplex Oligos for Illumina® (NEB) according to manufacturer's protocol

value: human hepatocellular carcinoma cells

value: wild type

value: IFN gamma, 10 ng/ml

tag: time


title: HuhWT_IFNy_48h_rep1

source_name: IFN gamma stimulated Huh7.5 wild type cells, 48h


title: HuhWT_IFNy_72h_rep1

source_name: IFN gamma stimulated Huh7.5 wild type cells, 72h


title: HuhWT_IFNy_48h_rep2


title: Pool113_RS2_Plate6-1-C1-I1


title: EZH1, A678G, input, R2

value: ReNcells VM

value: immortalized human neural progenitor line

value: EZH1 p.A678G


title: EZH1, A678G, input, R1


title: mESCs LIS1GFP-OE:F/-, 5i+LIF condition (XAV939), Rep#2, MARS-seq

description: Biological replicate2


title: HuhWT_IFNy_72h_rep2


title: HuhWT_IFNy_24h_rep1


title: Pool113_RS2_Plate6-1-C1-F14


title: EZH1, WT, input, R3

value: EZH1 WT


title: HuhWT_IFNy_8h_rep2

source_name: IFN gamma stimulated Huh7.5 wild type cells, 8h


title: mESCs LIS1GFP-OE:F/- (+4OHT), 5i+LIF condition, Rep#4, MARS-seq

description: Biological replicate4


title: Pool113_RS2_Plate6-1-C1-F13


title: mESCs LIS1GFP-OE:F/- (+4OHT), 5i+LIF condition, Rep#3, MARS-seq

description: Biological replicate3


title: EZH1, WT, input, R2


title: Pool113_RS2_Plate6-1-C1-E14


title: Pool113_RS2_Plate6-1-C1-E2


title: EZH1, WT, input, R1


title: mESCs LIS1GFP-OE:F/- (+4OHT), 5i+LIF condition, Rep#2, MARS-seq

description: Biological replicate2


title: HuhWT_IFNy_4h_rep2

source_name: IFN gamma stimulated Huh7.5 wild type cells, 4h


title: mESCs LIS1GFP-OE:F/-, 5i+LIF condition (XAV939), Rep#1, MARS-seq

description: Biological replicate1


title: HuhWT_IFNy_8h_rep1


title: GFP, input, R3


title: Pool113_RS2_Plate6-1-C1-E1

source_name: brain


title: mESCs LIS1GFP-OE:F/- (+4OHT), 5i+LIF condition, Rep#1, MARS-seq

description: Biological replicate1


title: GFP, input, R2


title: HuhWT_IFNy_2h_rep2

source_name: IFN gamma stimulated Huh7.5 wild type cells, 2h


title: mESCs LIS1GFP-OE:F/-, 5i+LIF condition, Rep#3, MARS-seq

description: Biological replicate3


title: HuhWT_IFNy_4h_rep1


title: GFP, input, R1


title: mESCs LIS1GFP-OE:F/-, 5i+LIF condition, Rep#2, MARS-seq

description: Biological replicate2


title: Pool113_RS2_Plate6-1-C1-D14


title: Pool113_RS2_Plate6-1-C1-D2


title: HuhWT_IFNy_2h_rep1


title: mESCs LIS1GFP-OE:F/-, 5i+LIF condition, Rep#4, MARS-seq

description: Biological replicate4


title: mESCs LIS1GFP-OE:F/-, 5i+LIF condition, Rep#1, MARS-seq

description: Biological replicate1


title: Pool113_RS2_Plate6-1-C1-D13


title: KRP449

tag: disease

value: Calcium Oxalate (KRP449) / Brushite (KRP440)

tag: tissue source

value: Papillary Nephrectomy

tag: storage

value: OCT at -80C

tag: gender

value: Female

tag: description

value: Two samples included within the fiducial zone. KRP449 refers to the sample included in the top right. KRP440 refer to the sample in the bottom left. Only spot overlying sample KRP449 were used in the conduct of this experiment.

tag: fraction of reads mapped to exons

tag: median genes per spot


title: KRP429

value: Calcium Oxalate (KRP429 and KRP478

value: pooled male and female

value: Two samples included within the fiducial zone. KRP429 refers to the sample included in the top left. KRP478 refer to the sample in the bottom. Only spot overlying sample KRP429 were used in the conduct of this experiment.


title: HuhWT_IFNa_72h_rep1

source_name: IFN alpha stimulated Huh7.5 wild type cells, 72h

tag: cell type

tag: treatment

value: IFN alpha, 1000U/ml


title: Pool113_RS2_Plate6-1-C1-C14

tag: tissue

value: brain

tag: source

value: AUD

tag: target

value: PTLp

value: female


title: mESCs F/-, 5i+LIF condition (XAV939), Rep#4, MARS-seq

description: Biological replicate4

tag: genotype

value: Lis1 Floxed/- (F/-):Ert2-Cre

value: hybrid


title: KRP428

value: Calcium Oxalate

value: Single sample


title: Pool113_RS2_Plate6-1-C1-C13

tag: Sex

value: male


title: HuhWT_IFNa_48h_rep1

source_name: IFN alpha stimulated Huh7.5 wild type cells, 48h

tag: cell line

value: human hepatocellular carcinoma cells

value: wild type


title: HuhWT_IFNa_48h_rep2


title: mESCs F/-, 5i+LIF condition (XAV939), Rep#3, MARS-seq

description: Biological replicate3

tag: culture media

tag: strain


title: 20-0034

tag: disease

value: Reference

value: Papillary Nephrectomy

value: OCT at -80C

value: Female


title: Pool113_RS2_Plate6-1-C1-C1


title: HuhWT_IFNa_72h_rep2

tag: time


title: HuhWT_IFNa_24h_rep2

source_name: IFN alpha stimulated Huh7.5 wild type cells, 24h


title: Pool113_RS2_Plate6-1-C1-B2


title: HuhWT_IFNa_8h_rep2

source_name: IFN alpha stimulated Huh7.5 wild type cells, 8h


title: Pool113_RS2_Plate6-1-C1-B14


title: pro_Tcells

city: Dolgoprudny

first: Eugene

last: Albert

address: Institutskiy Pereulok, 9

country: Russia

institute: MIPT

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0
Resuting matrix was loaded into Seurat package for filtering, cellcycle regression and subsequent clusterisation
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (cellranger count output)

growth_protocol: 12 days differentiation with growth fasctor in aMEM followed by 2 weeks differentiation by co-culturing with OP9 feeder cells  (see detailed protocol in accompanying paper)

extract_protocol:
cells were FACS sorted for the prethence of CD7, rsuspended in ice-cold PBS and processed according 10x protocol
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: CD7+ cells after 12 days differentiation with growth factors following by 10 day co-culturing with OP9 feeder cells (see detailed protocol in accompanying paper)

value: 10 days OP9 coculture


title: Tcells

description: 10x Genomics

value: CD7+ cells 12 days differentiation with growth factors following by 14 day co-culturing with OP9 feeder cells (see detailed protocol in accompanying paper)

value: 14 days OP9 coculture


title: mESCs F/- (+4OHT), 5i+LIF condition, Rep#4, MARS-seq

description: Biological replicate4

source_name: mouse embryonic stem cells


title: HuhWT_IFNa_24h_rep1

value: IFN alpha, 1000U/ml


title: mESCs F/- (+4OHT), 5i+LIF condition, Rep#3, MARS-seq

description: Biological replicate3


title: PA-Cre/Lox_SHH_48h_visium

city: Berlin

first: Ivano

last: Legnini

address: Hannoversche Strasse 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrueck Center for Molecular Medicine in the Helmholtz Association

description: 10X Visium

data_processing:
All data obtained from the BIMSB Genomics platform, after basecalling and demultiplexing
RNA-seq data processed with the PiGx pipeine (http://bioinformatics.mdc-berlin.de/pigx/), default settings; additional analyses reported in the associated publication
10X Visium processed with Spaceranger v.1.2.0 (default settings); additional analyses reported in the associated publication
Genome_build: GRCh38
Supplementary_files_format_and_content: analysis1.star.deseq_results.tsv: results from the PiGx pipeline, STAR/featurecounts/deseq2 normalized counts
Supplementary_files_format_and_content: deseq_normalized_counts.tsv: results from the PiGx pipeline, STAR/deseq2 output

source_name: HiPSC (XMO01)

growth_protocol: HEK cells were cultured 10%FBS DMEM. For the RNA-seq experiment. HiPSCs expresing a light-inducible Cre cassette and a LoxP-RFP-LoxP-SHH-NeonGreen cassette were cultured in E8 flex media on PET membranes.

extract_protocol:
RNA extraction was performed with a standard trizol protocol. No extraction was performed for the spatial transcriptimics experiment.
For RNA-seq, libraries were prepared according to the Illumina Truseq mRNA stranded kit. For the Visium, samples were treated according to the 10X Visium protocol.
RNA-seq / Other: 10X Visium

treatment_protocol: Cells were transfected with Lipofectamine 3000, with 1 microgram CasRx plasmid, 1 microgram guide RNA plasmid and 800 ng RFP reporter plasmid. Cells were harvested 36 hours post-transfection. Induced with blue light as described in the associated publication, collected after the indicated time points. Membranes were then transferred onto a Visium Slide for spatial transcriptomic profiling.

tag: stable line

value: PA-Cre/Lox, LoxP RFP LoxP SHH NG

tag: time of induction


title: mESCs F/-, 5i+LIF condition (XAV939), Rep#1, MARS-seq

description: Biological replicate1

value: Lis1 Floxed/- (F/-):Ert2-Cre


title: mESCs F/- (+4OHT), 5i+LIF condition, Rep#2, MARS-seq

description: Biological replicate2

value: hybrid


title: HuhWT_IFNa_8h_rep1


title: PA-Cre/Lox_SHH_120h_visium

description: 10X Visium


title: mESCs F/- (+4OHT), 5i+LIF condition, Rep#1, MARS-seq

description: Biological replicate1


title: PA-Cre/Lox_SHH_36h_visium

description: 10X Visium


title: mESCs F/-, 5i+LIF condition (XAV939), Rep#2, MARS-seq

description: Biological replicate2


title: Pool113_RS2_Plate6-1-C1-A2

value: brain

value: AUD

value: PTLp

value: female


title: Pool113_RS2_Plate6-1-C1-B13

value: male


title: Pool113_RS2_Plate6-1-C1-B1


title: Pool113_RS2_Plate6-1-C1-A14


title: mESCs F/-, 5i+LIF condition, Rep#4, MARS-seq

description: Biological replicate4


title: OCI-LY3 DMSO Day7 R2

city: Portland

first: Alexey

last: Danilov

state: OR

address: 3181 SW Sam Jackson Pk Rd

institute: Oregon Health and Science Univeristy

description:
PCR library sequencing
LIB200622AD_S9_L001

data_processing:
Library strategy: CRISPR screen
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches allowing no mismatches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Genome_build: Custom reference created from CRISPR library
Supplementary_files_format_and_content: Read counts per sgRNA for each sample

source_name: OCI-LY3 cells infected with library

growth_protocol: OCI-LY3 cells were grown in RPMI-1640, supplemented with 20% serum, 1%pen/strep.

extract_protocol:
30 million cells were collected for CG-806 day 7. DNA was extracted by desalting method
50 micrograms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)

treatment_protocol: Puromycin was applied at 2mg/ml concentration for 7 days. CG-806 (1 microMolar) was applied to 30 million cells in single flask

tag: genotype/variation

value: infected with CRISPR/Cas9 library

value: day 7 post puromycin selection, DMSO


title: HuhWT_IFNa_4h_rep1

source_name: IFN alpha stimulated Huh7.5 wild type cells, 4h

value: human hepatocellular carcinoma cells

value: wild type


title: PA-Cre/Lox_SHH_0h_visium

description: 10X Visium

value: non induced (0h)


title: HuhWT_IFNa_2h_rep2

source_name: IFN alpha stimulated Huh7.5 wild type cells, 2h


title: HuhWT_IFNa_4h_rep2


title: Pool113_RS2_Plate6-1-C1-A13


title: HuhWT_IFNa_2h_rep1


title: mESCs F/-, 5i+LIF condition, Rep#3, MARS-seq

description: Biological replicate3


title: OCI-LY3 CG806 Day 7 R3

description:
PCR library sequencing
LIB200622AD_S22_L002

value: day 7 post puromycin selection, CG806


title: Pool113_RS2_Plate6-1-C1-A1


title: HuhWT_UN_rep2

source_name: unstimulated Huh7.5 wild type cells

value: unstimulated


title: mESCs F/-, 5i+LIF condition, Rep#2, MARS-seq

description: Biological replicate2


title: Pool113_RS2_Plate5-6-G19-P24

value: RSP


title: HuhWT_UN_rep1


title: mESCs F/-, 5i+LIF condition, Rep#1, MARS-seq

description: Biological replicate1


title: OCI-LY3 CG806 Day 7 R1

description:
PCR library sequencing
LIB200622AD_S20_L002


title: Pool113_RS2_Plate5-6-G19-P23


title: OCI-LY3 Day0

description:
PCR library sequencing
LIB200622AD_S14_L002

value: day 0 post puromycin selection


title: Pool113_RS2_Plate5-6-G19-P12


title: HuhST2KO_IFNy_72h_rep2

source_name: IFN gamma stimulated HuhST2KO cells, 72h

value: STAT2 knockout

value: IFN gamma, 10 ng/ml


title: Lung 2

city: Hannover

first: Svenja

last: Gaedcke

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

description:
N1730-1 processed data = Alum
N1730-2 processed data = OVA
N1730-3 processed data = Tolerization protocol

data_processing:
10x Genomics CellRanger pipeline (v3.1.0)
demultiplex data with mkfastq resulting in fastq-files and 10x specific metadata
align read data to reference (10x Genomics Mus musculus reference 3.0.0, mm10) using STAR, also count HTO and ADT  tags.
HTO-A-0301 =  Alum
HTO-A-0302 = OVA
HTO-A-0303 =   Tolerization protocol
ADT-A-0825 antibody-derived tag Cleck12A
demultiplexing of samples using Seurat (v3.1.5)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table (*.mtx) with raw gene counts for every gene,  File with cell Barcodes (*_barcodes.tsv), File with Features (*_features.tsv)

source_name: Lung

extract_protocol:
Lung DC and AM were flowcytometry sorted from animals subjected to either control, asthma or tolerization protocol. The cells were labled with HTOs according to treatment and stained with tag CLEC12A. Equal Number of cells were pooled . Then they were processed into single cells and were barcoded using 10x Chromium platform.  Barcoded RNA was extracted using  Chromium Single Cell 3ʹ Reagent Kits v3 User Guide.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Lung

value: multiplexed sample (Alum, OVA, Tolerization protocol)

tag: replicate

tag: gender


title: Lung 1

description:
N1729-1 processed data = Alum
N1729-2 processed data = OVA
N1729-3 processed data = Tolerization protocol


title: OCI-LY3 DMSO Day7 R1

description:
PCR library sequencing
LIB200622AD_S10_L001


title: Pool113_RS2_Plate5-6-G19-P11

value: brain


title: OCI-AML3  processed with GTAC

city: Oxford

first: Sven

last: Turkalj

address: John Radcliffe Hospital/Headley Way, Oxford OX3 9DS

department: Radcliffe Department of Medicine

institute: WIMM

description: demultiplexed scATAC-seq data from a GTAC experiment

data_processing:
FASTQ files were trimmed and converted to BAM. BAM files were de-duplicated using Picard. De-duplicated BAM files were merged with Samtools and the provided fragment files were generated. Fragment files were used as input for analysis in ArchR.
Assembly: hg38
Supplementary files format and content: Fragment files from merged BAM files. Each fragment is linked to the single cell where it derives from.

source_name: haematopoietic

extract_protocol:
NGS library preparation and purification
GTAC

value: haematopoietic

tag: cell type

value: cell line


title: HuhST2KO_IFNy_24h_rep2

source_name: IFN gamma stimulated HuhST2KO cells, 24h

tag: treatment


title: Pool113_RS2_Plate5-6-G19-O24

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: tissue

value: PTLp

value: female


title: K562  processed with GTAC


title: HuhST2KO_IFNy_24h_rep1


title: KSHV infected, rep1

city: Seattle

last: Lagunoff

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

data_processing: Guide count files were generated and analyzed using MAGeCK (Li et al., 2014)

source_name: TIME Cells

growth_protocol: Human tert-immortalized microcascular endothelium cells (TIME cells) grown in EBM-2 media (Lonza) which was supplemented with an EGM-2 MV SingeQuot Microvascular Endothelial Cell Growth Medium Bullet Kit (Lonza)

extract_protocol:
Whole cell DNA was extracted using blood and cell culture DNA maxi kit (Qiagen)
Illumina sequencing libraries were constructed by PCR using primers from (PMID: 28333914). PCR reactions were run for 14 cycles and the resulting bands gel purified using the QIAquick gel extraction kit. Resulting purified PCR products were quantified by Qubit, diluted to 2nM and pooled.

treatment_protocol: Mock infection consisted of 8ug/ml polybrene while KSHV infection was done with 8ug/ml polybrene and BCBL-1 produced KSHV virus so that the infected population reached >90% of cells displaying latency with fewer than 5% of cells displaying markers of lytic infection.

value: TIME Cells

value: Endothelium

value: KSHV


title: HuhST2KO_IFNy_72h_rep1

value: human hepatocellular carcinoma cells


title: KSHV infected, rep2


title: JURKAT processed with GTAC

value: JURKAT


title: OCI-LY3 CG806 Day 7 R2

description:
PCR library sequencing
LIB200622AD_S21_L002

value: infected with CRISPR/Cas9 library

value: day 7 post puromycin selection, CG806


title: Mock infected, rep2

value: Mock


title: HuhST2KO_IFNy_8h_rep2

source_name: IFN gamma stimulated HuhST2KO cells, 8h

value: STAT2 knockout


title: Initial, rep2

value: Initial


title: Pool113_RS2_Plate5-6-G19-O23

city: La Jolla

source_name: brain

tag: source

value: RSP

value: male


title: Mock infected, rep1


title: HuhST2KO_IFNy_4h_rep2

source_name: IFN gamma stimulated HuhST2KO cells, 4h

value: IFN gamma, 10 ng/ml


title: Mdivi_L2C_PolII rep2

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

country: China

institute: Huazhong University of Science and Technology

data_processing:
Raw reads were processed with cutadapt v1.8.1 to remove adapters and perform quality trimming.
Trimmed reads were mapped to the UCSC mm10 assembly using Bowtie2 with default parameters.
Assembly: mm10
Supplementary files format and content: Bigwig files were generated for data visualization.

source_name: embryo

growth_protocol: Embryos were collected from ICR mice and cultured in KSOM medium.

extract_protocol:
Superovulation was performed in 6-to-8-week-old female mice by injection of 10 IU of PMSG, followed by 10 IU of hCG 48 hours later. The ovulated female mice were mated with stud males and embryos were collected from the oviduct ampulla. Cumulus cells were digested by hyaluronidase, and embryos were washed with M2 medium and cultured in KSOM medium.
ChIP-seq was performed using a Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) according to the manufacturer’s procedure

treatment_protocol: Embryos were treated with Mdivi-1.

value: embryo

value: Mdivi-1 treatment

tag: antibody

value: anti-PolII,Active Motif,39097


title: Mdivi_L2C_PolII rep1


title: Pool113_RS2_Plate5-6-G19-O11

value: brain

tag: target

value: PTLp


title: L2C_PolII rep2


title: HuhST2KO_IFNy_8h_rep1

tag: genotype


title: HuhST2KO_IFNy_4h_rep1

tag: cell line


title: L2C_PolII rep1


title: KPT, replicate 4, in vivo RNA-seq

city: Stanford

first: Laura

middle: D

last: Attardi

address: 269 Campus Drive

institute: Stanford University

description:
RNA-seq
counts_AK12_KPT

data_processing:
RNA-seq reads were aligned to the mouse genome (mm10) using HISAT2 (version 2.0.5, https://github.com/DaehwanKimLab/hisat2), sorted based on genomic location and indexed using Samtools (version 1.3.1, https://github.com/samtools/samtools), and counted and mapped to each gene using HTSeq-Count (version 0.6.1, https://github.com/simon-anders/htseq). Differentially expressed genes (DEGs) were identified using DESeq2 with a cutoff of a p-adjusted value of < 0.05 (version 1.24.0, https://github.com/mikelove/DESeq2).
Assembly: mm10
Supplementary files format and content: counts file, each column is a sample

source_name: lung

extract_protocol:
KT, KFT, and KPT mice were transduced with Ad5-SPC-Cre and harvested for cell sorting at 10 weeks post-transduction. Non-transduced lungs were used as a control. Briefly, lungs were perfused with 10 mL of ice-cold PBS and placed in a sterile dish on ice. Lungs were finely minced with sterile scissors and razor blades and resuspended in 6 mL digestion media (RPMI with 2.5 mg of Liberase TL (Sigma-Aldrich) and 25 µg/mL DNase (Sigma Aldrich)). Lungs were rotated for 45 minutes at 37ºC. Tubes were briefly cooled on ice, and then samples were passed through a 40 µM filter. 5 mL of FACS buffer (10% FBS, 2 mM EDTA, 25 µg/mL DNase in DPBS) was added and tubes were spun for 5 minutes at 300g. Cells were resuspended in ACK lysing buffer (Gibco), incubated for 1 minute on ice, and quenched with 8 mL of FACS buffer. Cells were washed 2x with FACS buffer, resuspended with biotinylated primary antibodies (CD45, BioLegend 103104 30-F11; CD31, BioLegend 102404 390; F4/80, BioLegend 123106 BM8; Ter119, BioLegend 116204 TER-119, 1:800 in FACS buffer) and incubated for 20 minutes on ice. After washing 2x, cells were resuspended in streptavidin-APC secondary antibody (BioLegend 405207, 1:800) for 20 minutes on ice. Cells were washed 2x and resuspended in FACS buffer with 1 µg/mL DAPI, filtered through a 40 µM filter, and sorted using a Sony SH800S cell sorter. Data were analyzed using the default Sony SH800S software and FCS Express (Version 7, De Novo Software).
For RNA-sequencing, 1.5x105 FACS sorted tumor cells were harvested, pelleted, and flash frozen in liquid directly after sorting. Once all samples were collected, RNA was harvested using the RNeasy Micro Kit (Qiagen). Quality and concentration of RNA was determined using a Bioanalyzer. cDNA libraries were constructed using the Trio RNA-seq library preparation kit (NuGEN) from samples with high quality RNA according to the manufacturer’s instructions. Samples were sequenced on a HiSeq4000 (Illumina).

value: lung

value: KPT


title: HuhST2KO_IFNy_2h_rep2

source_name: IFN gamma stimulated HuhST2KO cells, 2h

value: human hepatocellular carcinoma cells


title: Pool113_RS2_Plate5-6-G19-N23

tag: Sex


title: HuhST2KO_IFNa_72h_rep2

source_name: IFN alpha stimulated HuhST2KO cells, 72h

value: IFN alpha, 1000U/ml


title: Pool113_RS2_Plate5-6-G19-N12

value: female


title: HuhST2KO_IFNy_2h_rep1


title: Pool113_RS2_Plate5-6-G19-O12


title: mESC_Mdivi1_24h_PolII rep1

source_name: embryonic stem cell

growth_protocol: The mouse ESC line AB2.2 were seeded on mitotically inactivated MEF feeder cells in N2B27 medium with 2i and LIF in tissue culture dishes.

extract_protocol:
mESCs were collected and MEF cells were removed after treatment for 24h, followed by ChIP-seq library preparation.
ChIP-seq was performed using a Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) according to the manufacturer’s procedure

treatment_protocol: ESCs were treated with 50 μM Mdivi-1 for 24h.

value: embryonic stem cell


title: HuhST2KO_IFNa_72h_rep1


title: KPT, replicate 3, in vivo RNA-seq

description:
RNA-seq
counts_AK11_KPT


title: Pool113_RS2_Plate5-6-G19-M23


title: mESC_Mdivi1_24h_PolII rep2


title: Pool113_RS2_Plate5-6-G19-N24


title: Initial, rep1

value: TIME Cells

value: Endothelium


title: KPT, replicate 1, in vivo RNA-seq

description:
RNA-seq
counts_AK9_KPT


title: Pool113_RS2_Plate5-6-G19-M24


title: HuhST2KO_IFNa_24h_rep2

source_name: IFN alpha stimulated HuhST2KO cells, 24h

value: STAT2 knockout


title: mESC_Mdivi1_24h_H3K27me3 rep2

value: anti-H3K27me3, Abcam, ab6002


title: Pool113_RS2_Plate5-6-G19-M11

value: RSP

value: male


title: Pool113_RS2_Plate5-6-G19-M12


title: mESC_Mdivi1_24h_H3K4me3 rep2

value: anti-H3K4me3, CST, 9297


title: KFT, replicate 3, in vivo RNA-seq

description:
RNA-seq
counts_AK7_K5354T

value: KFT


title: KFT, replicate 4, in vivo RNA-seq

description:
RNA-seq
counts_AK8_K5354T


title: KFT, replicate 2, in vivo RNA-seq

description:
RNA-seq
counts_AK6_K5354T


title: mESC_Mdivi1_24h_H3K27me3 rep1

value: Mdivi-1 treatment


title: HuhST2KO_IFNa_24h_rep1


title: Pool113_RS2_Plate5-6-G19-L24

value: brain


title: HuhST2KO_IFNa_8h_rep2

source_name: IFN alpha stimulated HuhST2KO cells, 8h


title: KFT, replicate 1, in vivo RNA-seq

description:
RNA-seq
counts_AK5_K5354T


title: KPT, replicate 2, in vivo RNA-seq

description:
RNA-seq
counts_AK10_KPT


title: KT, replicate 3, in vivo RNA-seq

description:
RNA-seq
counts_AK4_KT

value: KT


title: mESC_WT_PolII rep2

value: anti-PolII,Active Motif,39097


title: HuhST2KO_IFNa_8h_rep1


title: mESC_WT_PolII rep1


title: mESC_WT_H3K4me3 rep2


title: mESC_Mdivi1_24h_H3K4me3 rep1


title: HuhST2KO_IFNa_4h_rep2

source_name: IFN alpha stimulated HuhST2KO cells, 4h


title: HuhST2KO_IFNa_4h_rep1


title: mESC_WT_H3K4me3 rep1


title: HuhST2KO_IFNa_2h_rep2

source_name: IFN alpha stimulated HuhST2KO cells, 2h


title: KT, replicate 1, in vivo RNA-seq

description:
RNA-seq
counts_AK1_KT

value: lung


title: Pool113_RS2_Plate5-6-G19-L11

value: PTLp


title: Pool113_RS2_Plate5-6-G19-K24


title: HuhST2KO_IFNa_2h_rep1

value: human hepatocellular carcinoma cells

value: IFN alpha, 1000U/ml


title: p53-wt-KB0081-1-Ad-Cre

extract_protocol:
For RNA-sequencing, LUAD cells were harvested, pelleted, and flash frozen in liquid directly after sorting.
Once all samples were collected, RNA was harvested and library prepared with TruSeq RNA Library Prep Kit v2 for sequencing on a HiSeq4000 (Illumina).

treatment_protocol: LUAD cell lines were maintained in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% Fetal Bovine Serum (FCS and incubated at 37°C in a carbon dioxide incubator. To reactivate p53, LUAD cell lines were treated with Ad5-CMV-Cre (University of Iowa Viral Vector Core), or cell lines were treated with Ad5-CMV-Empty (University of Iowa Viral Vector Core) to remains p53 null. Cell lines were infected at an MOI of 100. Cells were harvested for immunofluorescence, Western blotting, and RT-qPCR between 24-96 hours after infection.

value: LUAD cancer cells


title: mESC_WT_H3K27me3  rep2

value: embryonic stem cell


title: Pool113_RS2_Plate5-6-G19-L12

value: female


title: p53-wt-CB5232-Ad-Cre


title: Pool113_RS2_Plate5-6-G19-K23


title: Pool113_RS2_Plate5-6-G19-K11


title: HuhST2KO_UN_rep2

source_name: unstimulated HuhST2KO cells

value: STAT2 knockout

value: unstimulated


title: p53-wt-CB5061-1-Ad-Cre


title: KT, replicate 2, in vivo RNA-seq

description:
RNA-seq
counts_AK2_KT


title: mESC_Mdivi1_24h rep3

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
Assembly: mm10
Supplementary files format and content: DESeq result with normalized and raw gene counts for every gene and every sample

source_name: embryonic stem cells (ESCs)

extract_protocol:
For mouse ESCs, total RNA was extracted by TRIzol reagent (Invitrogen, USA) from 5×105 cells for each group.
RNA libraries were prepared for sequencing using standard RNA-seq library preparation (Truseq RNA Sample Preparation Kit, Illumina).

tag: strain

value: ESCs

value: Mdivi1 treatment


title: HuhST2KO_UN_rep1


title: Pool113_RS2_Plate5-6-G19-I24

value: RSP


title: mESC_Mdivi1_24h rep2


title: p53-null-KB0255-6-Ad-Emp


title: Pool113_RS2_Plate5-6-G19-I23

value: male


title: mESC_Mdivi1_24h rep1


title: HuhST1KO_IFNa_72h_rep2

source_name: IFN alpha stimulated HuhST1KO cells, 72h

value: STAT1 knockout


title: Pool113_RS2_Plate5-6-G19-J23

value: brain


title: HuhST1KO_IFNa_72h_rep1


title: p53-null-CB5211-Ad-Emp


title: KPT, replicate 4, ATAC-seq 2

description:
ATAC-seq
AK8

data_processing:
ATAC-seq reads were trimmed of adapter sequences using Skewer (version 0.2.2, https://github.com/relipmoc/skewer), aligned to the mouse genome (mm10) using Bowtie2 (version 2.4.0, https://github.com/BenLangmead/bowtie2), and sorted based on genomic location and indexed using Samtools (version 1.3.1, https://github.com/samtools/samtools). Peak calling and differential peak analysis were performed using the ‘ChrAccR’ package in R (version 0.9.17, https://github.com/GreenleafLab/ChrAccR) with the sorted BAM file as input using the default parameters. The setConfigElement “doPeakCalling” was used with “annotationPeakGroupAgreePerc” at 1 to generate the conserved peaks list.
Assembly: mm10
Supplementary files format and content: raw counts for all peaks for all samples

extract_protocol:
KT, KFT, and KPT mice were transduced with Ad5-SPC-Cre and harvested for cell sorting at 10 weeks post-transduction. Non-transduced lungs were used as a control. Briefly, lungs were perfused with 10 mL of ice-cold PBS and placed in a sterile dish on ice. Lungs were finely minced with sterile scissors and razor blades and resuspended in 6 mL digestion media (RPMI with 2.5 mg of Liberase TL (Sigma-Aldrich) and 25 µg/mL DNase (Sigma Aldrich)). Lungs were rotated for 45 minutes at 37ºC. Tubes were briefly cooled on ice, and then samples were passed through a 40 µM filter. 5 mL of FACS buffer (10% FBS, 2 mM EDTA, 25 µg/mL DNase in DPBS) was added and tubes were spun for 5 minutes at 300g. Cells were resuspended in ACK lysing buffer (Gibco), incubated for 1 minute on ice, and quenched with 8 mL of FACS buffer. Cells were washed 2x with FACS buffer, resuspended with biotinylated primary antibodies (CD45, BioLegend 103104 30-F11; CD31, BioLegend 102404 390; F4/80, BioLegend 123106 BM8; Ter119, BioLegend 116204 TER-119, 1:800 in FACS buffer) and incubated for 20 minutes on ice. After washing 2x, cells were resuspended in streptavidin-APC secondary antibody (BioLegend 405207, 1:800) for 20 minutes on ice. Cells were washed 2x and resuspended in FACS buffer with 1 µg/mL DAPI, filtered through a 40 µM filter, and sorted using a Sony SH800S cell sorter. Data were analyzed using the default Sony SH800S software and FCS Express (Version 7, De Novo Software).
ATAC-sequencing was performed as previously described. Two independent ATAC-sequencing experiments were performed, one with KT and KPT mice and the second with KT and KFT cells. Briefly, 5x105 cells were sorted and washed 2x in FACS buffer without DNase added. Nuclei were then isolated, lysed, and incubated with Tn5 transposase precisely as described. Transposed DNA was then isolated using the MinElute Reaction Cleanup Kit (Qiagen). Libraries were prepared by amplifying DNA for 5 cycles with NEBNext 2x MasterMix (NEB), after which qPCR was run on samples to determine the number of additional cycles needed. After any additional amplifications were performed, libraries were purified using the MinElute Reaction Cleanup Kit (Qiagen). Samples were sequenced on a HiSeq4000 (Illumina) (KT vs. KPT experiment).

value: KPT