title: PDAC_140694

city: Toronto

first: Faiyaz

last: Notta

address: 101 College Street

department: Research

institute: University Health Network

description: Fresh frozen spatial transcriptomic sequencing

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger pipeline to generate FASTQ files
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count data along with tissue position list, barcodes, and features in a h5 format
Library strategy: Spatial Transcriptomics

source_name: Primary resected tumor from pancreatic ductal adenocarcinoma stage II B

extract_protocol:
Fresh samples were obtained at diagnosis and were embedded in optimal cutting temperature compound. The regions of interest for capture areas (6.5 mm)  were selected, targeting tumor areas with representative subtype glandular and non-glandular morphologies.
Library preparation was performed according to manufacturer's instructions (10X Genomics. Part number: 1000200, Protocol : CG000160 RevB, CG000239 RevD).


title: 6day lung, knockout, RNA-seq, rep 3

status: Public on Mar 16 2025

type: SRA

city: Houston

first: Maria

middle: Elisa

last: Ruiz Echartea

state: Texas

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

description: Library name: 6_6d_knockout

library_source: transcriptomic

data_processing:
The FASTQ files underwent quality control metrics (trimming), read mapping, and gene annotation with default parameters with the RNA-seq Alignment v2.0.2 pipeline (BaseSpace, Illumina).
The RNA-Seq Differential Expression v1.0.1 workflow (BaseSpace, Illumina) was used with default parameters to extract gene counts and to obtain differentially expressed genes with an adjusted p value (FDR) < 0.05 between control and knockout samples.
Assembly: GRCm38
Supplementary files format and content: csv files contain TPM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Approximately 800 ng of total RNA was used for construction of sequencing libraries.
Nonstrand-specific, polyA+ -selected RNA-seq libraries were generated using the Illumina TruSeq protocol.

treatment_protocol: Treatment protocol is as described in associated paper.

tag: tissue

value: lung

tag: cell type

value: whole lung

tag: genotype

value: let7afd-/-;Sftpc-CreER/+; R26-tdT/+

tag: treatment

value: tamoxifen


title: Ube2iF/F HA_GFP

city: Iowa City

first: Zhijie

last: Li

state: IA

address: 285 Newton Road

institute: University of Iowa

library_source: genomic

data_processing:
Libraries were pooled to equimolar concentrations and sequenced with paired-end 150 bp reads on a NovoSeq HiSeq X instrument.
The sequencing reads were mapped with BWA-MEM to mouse reference genome mm10 with default parameters, and peak calling was performed by MACS2. Annotation of CUT&RUN peaks was using GREAT (version 4, mouse) with a gene regulatory domain defined as nearest gene within 100kb. Heatmap and density plot were generated using DeepTools, and CUT&RUN tracks were visualized by Integrative Genomics Viewer (IGV) for co-alignment of peaks. Motif enrichment analysis was performed by HOMER Motif Analysis (-findMotifsGenome).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: Ube2iF/F cells with exogenous expression of HA-tagged Etv1 were maintained at 37 ℃ and 5% CO2 in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin.

extract_protocol:
Cells in log-phase culture (60-80% confluent) were harvested by cell scraping, centrifuged at 300 g and washed twice in calcium-free wash-buffer ((20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine and protease inhibitor cocktail, cOmplete Mini, EDTA-free Roche). Cells were counted and 500,000 cells per antibody per condition were used for CUT&RUN. Preactivated Concanavalin A-coated magnetic beads (Bangs Laboratories Inc) were added to cell suspension and incubated at 4°C for 10 minutes. Antibody buffer (wash buffer with 2mM EDTA and 0.025% digitonin) containing anti-HA-tag (#3724, Cell Signaling Technology) was added and cells were incubated overnight at 4°C on nutator. The following day, cells were washed in dig-wash buffer (wash buffer containing 0.03% digitonin) and pAG-MNase was added at a concentration of 500 μg/mL. The pAG-MNase reactions were quenched with 2X Stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 100 μg/mL RNAse A, 50 μg/mL Glycogen, and 2 pg/mL sonicated yeast spike-in control). Released DNA fragments were Phosphatase K (1 μL/mL, Thermo Fisher Scientific) treated for 1 hr at 50°C and purified by phenol/chloroform-extracted and ethanol-precipitated. CUT&RUN experiments were performed in parallel as positive control and fragment sizes analyzed using an 2100 Bioanalyzer (Agilent).
CUT&RUN libraries were prepared using the KAPA Hyper Prep Kit (Roche). Quality control post-library amplification was conducted using the 2100 Bioanalyzer for fragment analysis.

treatment_protocol: Ube2iF/F cells with exogenous expression of HA-tagged Etv1 were seeded 1 day before adenovirus transduction at about 50% confluency. Ad5CMVeGFP or Ad5CMVCre-eGFP was diluted with serum-free Opti-MEM before adding into cells. Multiplicity of infection (MOI) was calculated based on PFU/ml. Virus solutions were incubated overnight and replaced with complete culture medium.

tag: cell line

value: basal and luminal epithelial cells

value: UBE2I knockout

tag: chip antibody


title: WT, Biuds, MS, rep3

city: Waterloo

first: Benjamin

middle: Jean-Marie

last: Tremblay

state: Ontario

address: 200 University Ave W

department: Department of Biology

country: Canada

institute: University of Waterloo

description: Library name: wm3_FRDM190664684-1a_HLL3MDSXX

data_processing:
Reads were quality filtered and adapter-trimmed using Trim Galore! with default parameters.
Reads were mapped onto the TAIR10 genome assembly, deduplicated, and cytosine methylation calls performed using Bismark with default parameters.
Assembly: TAIR10
Supplementary files format and content: bedGraph files include fraction of methylated cytosines in CG, CHG or CHH contexts.

organism: Arabidopsis thaliana

source_name: Unopened flower buds

growth_protocol: Arabidopsis thaliana (Col-0) seeds were surface sterilized using chlorine gas and stratified in the dark at 4 ˚C for 72 h before sowing on half-strength MS medium with 0.8% agarose and 1% (w/v) sucrose. Seedlings were grown in a tissue culture chamber at 22 ˚C with continuous 100 µmol m-2 s-1 photosynthetically active radiation (PAR) for 14 d. Plants to be grown to maturity were transplanted to soil in individual pots and moved to a growth chamber with 150 µmol m-2 s-1 PAR in long day conditions.

extract_protocol:
DNA was extracted from approximately 50 mg samples of pooled frozen ground unopened bud tissue using the DNeasy Plant Mini Kit (Qiagen).
Whole-genome bisulfite treatment and library preparation were performed by Novogene (Beijing, China).

treatment_protocol: Spermidine treatments were performed by supplementing MS medium with 100 µM spermidine.

value: Unopened flower buds

value: wild-type

value: mock


title: PDAC_64630

molecule: total RNA

organism: Homo sapiens

value: Primary resected tumor from pancreatic ductal adenocarcinoma stage II B


title: 6day lung, knockout, RNA-seq, rep 2

description: Library name: 5_6d_knockout


title: WT, Buds, MS, rep2

description: Library name: wm2_FRDM190633199-1a_HKYWCDSXX


title: mixed_samples_DSC_from HE and from LE (non-demultiplexed)

city: Yokohama

first: Yumiko

last: Ishimatsu-Tsuji

address: Nishi-ku

country: Japan

institute: Shiseido

data_processing:
Sequencing was performed by the DNBSEQ-G400.
The GRCh38 genome was aligned with Cell Ranger 6.1.2 as a reference. In total, of 5264 uniquely tagged cells were detected from the 6,746 initial cell outputs from Cell Ranger.
For quality control, cells with less than 1200 and 3800 counts, cells with mitochondrial genes expressed in excess of 10%, and cells expressing more than 32,000, 40,000 and 50,000 counts in HE, LE1 and LE2, respectively, were removed. In total, 3620 cells were used for the final analysis.
Assembly: GRCh38-2020-A
Supplementary files format and content: Cell Ranger output

source_name: dermal sheath cup cells

growth_protocol: Freshly isolated dermal sheath cups from clinical trial volunteers were transferred into culture plates and were incubated at 37°C and 5% CO2 in the culture medium for cell expansion.

extract_protocol:
Cell suspension samples were labeled separately with TotalSeq™-B0252, 0253 and 0254 anti-human Hashtag Antibody (Biolegend, San Diego, CA, USA), mixed, and subjected to single-cell barcoding using Chromium Next GEM Single Cell 3ʹ Reagent Kits (10x Genomics, Pleasanton, CA, USA) for library preparation.
RNA libraries were prepared for sequencing using standard Chromium Next GEM Single Cell 3ʹ Reagent Kits protocols

value: dermal sheath cup

tag: clinical response

value: responder, non-responder


title: 6day lung, knockout, RNA-seq, rep 1

description: Library name: 4_6d_knockout


title: WT, Buds, MS, rep1

description: Library name: wm1_FRDM190633198-1a_HKYWCDSXX


title: npp-214∆ mip-1∆, replicate 2 (smallRNAseq)

city: Baltimore

first: Geraldine

last: Seydoux

address: 725 N Wolfe Street

department: HHMI and Department of Molecular Biology and Genetics

description: Library name: Sample_5

data_processing:
Reads shorter than 18nt and longer than 30nt were discarded, and 5’ Illumina adaptor sequences were removed using the default settings of Cutadapt (Martin 2011). Libraries were aligned to the reference genome ce11 (WormBase version WS289) using STAR (Dobin et al. 2013). Reads mapping to genomic features were counted using modified scripts based on previously described methods (Seroussi et al., 2023) and differential expression analysis was performed using DESeq2.
Assembly: ce11/WS289
Supplementary files format and content: bigWig files normalized by total reads

organism: Caenorhabditis elegans

source_name: whole organism

extract_protocol:
Staged adult C. elegans (72 hours after L1 synchronization at 20°C) were collected, snap-frozen, and total RNA was extracted using TRIzol (Thermo Fisher cat # 15596026) and chloroform, using standard protocols.
5µg of total RNA was treated with 5’ polyphosphatase. 1µg of purified, treated RNA was inputted into the Illumina TruSeq small RNA library prep kit (cat # RS-200-0012) according to manufacturer’s instructions. Libraries were size selected, purified, and sequenced on a NovaSeq6000 system at the Johns Hopkins University School of Medicine Genetic Resources Core Facility.

value: whole organism


title: SPholdSW_bio rep 2

city: Tromsø

first: Alexander

middle: Christopher

last: West

state: Troms

address: Framstredet 39, Tromsø

department: Arctic Chronobiology and Physiology

country: Norway

institute: Universitetet i Tromsø

description:
Library name: Sample 12
name, length, effective length, TPM, num reads

data_processing:
Cutadapt was next used to remove sequencing adapters, trim low quality bases and remove short sequencing reads under the parameters -q 20 -O 8—minimum-length 40
Transcripts from single-end RNAseq data were quantified based on the Atlantic salmon reference transcriptome version 3 by using Salmon (v 1.1.0.) on mapping-mode using the flags --keepDuplicates for indexing. The flags –validateMappings, --gcBias and –numBootstraps 100 were used during quantification
Assembly: Ssal_v3.1, GCA_905237065.2
Supplementary files format and content: tab delimited raw counts

organism: Salmo salar

source_name: Saccus vasculosus

extract_protocol:
SV tissue was disrupted using a TissueLyser II (QIAgen, Germany) and RNA extracted using a RNeasy micro kit (QIAgen, Germany).
Sequencing libraries were generated using TruSeq Stranded mRNA HS kit (Illumina). Library concentration was measured using a QUBIT BR kit (Thermo Scientific) and mean length was measured using a 2100 Bioanalyzer and DNA 1000 kit (Agilent Technologies). Individual samples were then barcoded using Illumina HiSeq indexes and single-end 100bp sequencing of the samples were performed using an Illumina HiSeq 2500 at the Norwegian Sequencing Centre (University of Oslo, Norway).

value: Saccus vasculosus

value: Aquagen, commercial strain

value: 16 weeks short photoperiod collected after 24h in seawater. Bio rep 2


title: SPholdSW_bio rep 3

description:
Library name: Sample 13
name, length, effective length, TPM, num reads

value: 16 weeks short photoperiod collected after 24h in seawater. Bio rep 3


title: npp-214∆ mip-1∆, replicate 1 (smallRNAseq)

institute: Johns Hopkins University School of Medicine

description: Library name: Sample_4


title: 6day lung, control, RNA-seq, rep 3

description: Library name: 3_6d_control

value: lung

value: Sftpc-CreER/+; R26-tdT/+


title: mtn1-1mtn2-1, Buds, Spd, rep2

description: Library name: ms2_FRDM190664683-1a_HLL3MDSXX

value: 100 µM Spermidine


title: N2, replicate 3 (smallRNAseq)

description: Library name: Sample_3


title: SPholdSW_bio rep 1

description:
Library name: Sample 11
name, length, effective length, TPM, num reads

value: 16 weeks short photoperiod collected after 24h in seawater. Bio rep 1


title: 6day lung, control, RNA-seq, rep 2

description: Library name: 2_6d_control

value: whole lung

value: tamoxifen


title: SPholdFW_bio rep 4

description:
Library name: Sample 10
name, length, effective length, TPM, num reads

value: 16 weeks short photoperiod collected in freshwater. Bio rep 4


title: WT, Buds, Spd, rep1

description: Library name: ws1_FRDM190633201-1a_HKYWCDSXX

value: Unopened flower buds

value: wild-type


title: 6day lung, control, RNA-seq, rep 1

description: Library name: 1_6d_control


title: mtn1-1mtn2-1, Buds, MS, rep3

description: Library name: mm3_FRDM190633206-1a_HKYWTDSXX

value: mock


title: N2, replicate 2 (smallRNAseq)

description: Library name: Sample_2


title: mA3R CAR T cells- Unstimulated

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Sample9
KS.R23

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (mm10])
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: mm10
Supplementary files format and content: count file generated by featureCounts

source_name: T cells

extract_protocol:
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

value: T cells

value: mA3R transduced CAR

value: Unstimulated


title: N2, replicate 1 (smallRNAseq)

description: Library name: Sample_1

value: whole organism


title: SPholdFW_bio rep 2

description:
Library name: Sample 8
name, length, effective length, TPM, num reads

value: Saccus vasculosus

value: Aquagen, commercial strain

value: 16 weeks short photoperiod collected in freshwater. Bio rep 2


title: npp-214∆ mip-1∆, replicate 3 (smallRNAseq)

description: Library name: Sample_6


title: mA1R CAR T cells- Unstimulated

description:
Library name: Sample8
KS.R22

value: mA1R transduced CAR


title: mtn1-1mtn2-1, Buds, MS, rep1

description: Library name: mm1_FRDM190633204-1a_HKYWCDSXX


title: mtn1-1mtn2-1, Buds, MS, rep2

description: Library name: mm2_FRDM190633205-1a_HKYWTDSXX


title: Control CAR T cells- Unstimulated

description:
Library name: Sample7
KS.R21

value: Control CAR


title: npp-214∆ mip-1∆, replicate 1 (RNAseq)

description: Library name: Sample_7

data_processing:
Read quality of all libraries was assessed using fastQC (v0.11.9). Raw sequencing reads were aligned to the C. elegans reference genome ce 11 (WormBase version WS289) using STAR (Dobin et al. 2013). Total counts for each genomic feature were used for differential expression analysis using DESeq2 (Love et al. 2014).
Assembly: ce11/WS289
Supplementary files format and content: bigWig files normalized by RPKM

extract_protocol:
Staged adult C. elegans (72 hours after L1 synchronization at 20°C) were collected, snap-frozen, and total RNA was extracted using TRIzol (Thermo Fisher cat # 15596026) and chloroform, using standard protocols.
Total RNA was hybridized to anti-sense oligonucleotides (ASO) against C. elegans ribosomal RNA. Annealed ASO-rRNA hybrids were digested using Rnase H, as previously described (Duan et al. 2020). RNA sequencing libraries were prepared from 10ng of rRNA depleted RNA, from two independent biological replicates for each genotype, using the Illumina Stranded Total RNA kit (cat # 20040529) following the manufacturer’s instructions and sequenced on a NovaSeq6000 system at the Johns Hopkins University School of Medicine Genetic Resources Core Facility.


title: SPLLSW_bio rep 4

description:
Library name: Sample 6
name, length, effective length, TPM, num reads

value: 8 weeks short photoperiod, 8 weeks constant light collected after 24h in seawater. Bio rep 4


title: mA3R CAR T cells- Tumor Stimulated rep 2

description:
Library name: Sample6
KS.R12

value: Tumor stimulated


title: mip-1∆, replicate 2 (RNAseq)

description: Library name: Sample_6


title: mtn1-1mtn2-1, Buds, Spd, rep1

description: Library name: ms1_FRDM190633207-1a_HKYWTDSXX

value: 100 µM Spermidine


title: SPLLSW_bio rep 3

description:
Library name: Sample 5
name, length, effective length, TPM, num reads

value: 8 weeks short photoperiod, 8 weeks constant light collected after 24h in seawater. Bio rep 3


title: G3, Buds, Spd, rep3

description: Library name: gs3_FRDM190644884-1a_HKYWTDSXX


title: mtn1-1mtn2-1, Buds, Spd, rep3

description: Library name: ms3_FRDM190633209-1a_HKYWTDSXX


title: SPholdFW_bio rep 1

description:
Library name: Sample 7
name, length, effective length, TPM, num reads

value: 16 weeks short photoperiod collected in freshwater. Bio rep 1


title: npp-214∆ mip-1∆, replicate 2 (RNAseq)

description: Library name: Sample_8


title: mA3R CAR T cells- Tumor Stimulated rep 1

description:
Library name: Sample5
KS.R11


title: SPLLSW_bio rep 2

description:
Library name: Sample 4
name, length, effective length, TPM, num reads

value: 8 weeks short photoperiod, 8 weeks constant light collected after 24h in seawater. Bio rep 2


title: mip-1∆, replicate 1 (RNAseq)

description: Library name: Sample_5


title: mA1R CAR T cells- Tumor Stimulated rep 2

description:
Library name: Sample4
KS.R8


title: G3, Buds, Spd, rep1

description: Library name: gs1_FRDM190633213-1a_HKYWTDSXX

value: Unopened flower buds


title: npp-214∆, replicate 2 (RNAseq)

description: Library name: Sample_4


title: SPholdFW_bio rep 3

description:
Library name: Sample 9
name, length, effective length, TPM, num reads

value: 16 weeks short photoperiod collected in freshwater. Bio rep 3


title: SPLLSW_bio rep 1

description:
Library name: Sample 3
name, length, effective length, TPM, num reads

value: 8 weeks short photoperiod, 8 weeks constant light collected after 24h in seawater. Bio rep 1


title: npp-214∆, replicate 1 (RNAseq)

description: Library name: Sample_3


title: SPLLFW_bio rep 2

description:
Library name: Sample 2
name, length, effective length, TPM, num reads

value: 8 weeks short photoperiod, 8 weeks constant light collected in freshwater. Bio rep 2


title: G3, Buds, MS, rep3

description: Library name: gm3_FRDM190633212-1a_HKYWTDSXX

value: mock


title: mA1R CAR T cells- Tumor Stimulated rep 1

description:
Library name: Sample3
KS.R7

value: T cells


title: Control CAR T cells- Tumor Stimulated rep 2

description:
Library name: Sample2
KS.R4


title: N2, replicate 2 (RNAseq)

description: Library name: Sample_2

value: whole organism


title: G3, Buds, MS, rep2

description: Library name: gm2_FRDM190633211-1a_HKYWTDSXX


title: G3, Buds, MS, rep1

description: Library name: gm1_FRDM190633210-1a_HKYWTDSXX


title: SPLLFW_bio rep 1

description:
Library name: Sample 1
name, length, effective length, TPM, num reads

value: Saccus vasculosus

value: Aquagen, commercial strain

value: 8 weeks short photoperiod, 8 weeks constant light collected in freshwater. Bio rep 1


title: N2, replicate 1 (RNAseq)

description: Library name: Sample_1


title: WT mouse cortical neuron, DIV7, Brg1 CUTANDRUN, rep 2

status: Public on Mar 15 2025

city: Stanford

first: Sai

last: Gourisankar

state: CA

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

description: Library name: CR_24

data_processing:
The data quality was checked using fastq (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The raw reads were trimmed from adapters with cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
The raw reads were aligned to mm10 mouse genome assembly using bowtie2 (parameters: --local --maxins 1000).
Low quality reads, duplicated reads and reads with multiple alignments were removed using samtools and Picard (https://broadinstitute.github.io/picard/).
deepTools was used to generate coverage densities across multiple experimental conditions (deeptools computeMatrix and deeptools plotProfile) and to generate bigwig files (deeptools bamCoverage), where reads mapping to ENCODE blacklist regions were excluded.
Assembly: mm10
Supplementary files format and content: Depth-normalized coverage as bigwig files
Library strategy: CUT&Run

source_name: E16.5 cortex

growth_protocol: Primary Neuron Culture Coating plates: Culture plates (Corning #353003) were coated overnight at room temperature by flooding with poly-D-lysine (Sigma #P6407) at 0.1 mg/mL in borate buffer (1.55 g boric acid/2.4 g sodium tetraborate in 500 mL sterile water). Plates were washed 3x with water and 1x with PBS before plating neurons. Dissection and culture: Cortical neurons were dissected and cultured following established protocols (PMID 32312822, PMID 26139371). Brefly, embryonic cortical neurons were harvested from embryonic day 16.5 (E16.5) mice using sterile tools. Pregnant female mice were anesthetized with isoflurane and euthanized by cervical dislocation on E16.5. A 4 cm long, V-shaped incision was made through the derma and muscle layers of the lower abdomen just above the vaginal opening of the euthanized mouse. After pulling back skin and muscle, the uterus was carefully disconnected and the string of embryos gently pulled from the abdomen and placed in a dish of sterile PBS on ice. Fetuses were removed from the amniotic sac using forceps and baby scissors and placed in a second dish of fresh PBS on ice. From this point onwards, the cortex from each embryo was considered a biological replicate. Individual embryos were transferred on sterile filter paper in ice cold PBS and stabilized from behind the neck using a curved forcep. Using a sharp pair of forceps, two incisions were made: above the olfactory bulbs between the eyes and upwards between the hemispheres skimming along the underside of the skull. The flat side of a curved forcep was then used to apply gentle pressure from the brainstem to the eyes to push the brain out of the skull. The brain was scooped up and placed in a fresh dish of sterile PBS on ice. The brain was anchored vertically under a dissecting microscope by grasping near the brainstem using forceps. The meninges and remaining olfactory bulb were removed by gently tugging along the length of the tissue. Using forceps, each hemisphere was gently lifted, avoiding the hippocampus, striatum and basal ganglia, and transferred to a 15 mL sterile Falcon tube of ice-cold PBS and allowed to settle. Then, cortices were enzymatically dissociated to single neurons with Neural Tissue Dissociation Kit (P) (Miltenyi Biotech #130-092-628). Neurons were resuspended in plating media [DMEM (Life Technologies #11960-077), 10% FBS (Omega #FB-01), 1x penicillin-streptomycin (ThermoFisher #15140122)], counted, and plated at a density of 25-30M neurons per 15 cm plate, 6-10M per 10 cm plate, 1M per well of a 6-well plate, 0.5M per well of a 12-well plate, or 0.1M per well of a 24-well plate. After incubation for 1 hour at 37 ºC/5% CO2, neurons were attached to the plates and media was changed to neuron maintenance media [Neurobasal Medium (Life Technologies #21103049), 2.5% B27 (ThermoFisher #17504044), 1% penicillin-streptomycin (Life Technologies #15070-063), 0.25% GlutaMax (Life Technologies #35050061)]. On day in vitro 2 (DIV2), ara-c (Sigma #C1768) was added to a final concentration of 0.5 µM to inhibit proliferation of any contaminating glial cells. Beginning on DIV3, half the media was exchanged for fresh neuron maintenance media every three days. Cultures were kept at 37 ºC/5% CO2.

extract_protocol:
CUT&RUN was performed as previously described (PMCID 6598765, PMID 29651053)  with modifications. Briefly, neurons were plated at 1M/6-well of a 6-well plate and harvested by scraping in 1 mL PBS supplemented with protease and phosphatase inhibitors and pelleting for 3 mins at 1,200g at 4 °C. Cells were resuspended in 1 mL nuclear extraction buffer (NE: 20mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100 (v/v), 20% glycerol (v/v), 0.5 mM spermidine, 1X cOmplete protease inhibitors (Roche 11836153001), 1 phosphatase inhibitor tablet/10 mL (PhosSTOP, Roche #4906837001), pelleted at 1,700g for 3 mins at 4 °C, and washed twice more. Nuclei were resuspended in NE, charged with paramagnetic-bead conjugated activated Concanavalin A coated beads (EpiCypher 21-1411), and rotated for 1 hr at 4 °C. 250,000 nuclei were counted and incubated with primary antibodies at 1:50 dilution (v:v) (anti-Brg1: Santa Cruz H-10; anti-Smarcc2: Santa Cruz E-6) in antibody buffer (20mM HEPES pH 7.9, 150 mM NaCl, 0.5mM spermidine, protease and phosphatase inhibitors, 0.025% digitonin, 2 mM EDTA). Incubation proceeded for 1 hr under shaking at 1,500 rpm at 4 °C; nuclei were resuspended gently every 30 minutes. Primary antibodies were washed with wash buffer (20mM HEPES pH 7.9, 150 mM NaCl, 0.5mM spermidine, protease and phosphatase inhibitors, 0.025% digitonin) and rabbit anti-mouse IgG secondary antibodies (EMD Millipore 06-371) were added at 1:100 (v:v) dilution in antibody buffer. Incubation proceeded for 1 hr under shaking at 900 rpm at 4 °C; nuclei were resuspended gently every 30 minutes. Secondary antibodies were washed using wash buffer twice and resuspended in wash buffer charged with 1:50 (v:v) dilution of pA-MNase (a kind gift from Steve Henikoff). Incubation proceeded for 1 hr under shaking at 800 rpm at 4 °C; nuclei were resuspended gently every 30 minutes. Nuclei were washed twice with wash buffer, washed once with low salt rinse buffer (3.5 mM HEPES pH 7.9, 0.5 mM spermidine, 0.025% digitonin). After incubation in ice-cold water for 1-5 minutes to allow the temperature to reach 0 °C, digestion commenced upon addition of 10 mM CaCl2 (final). Digestion proceeded for 5 minutes before termination by addition of stop buffer at 1:3 dilution (v:v) (4X stop buffer: 680 mM NaCl, 40 mM EDTA, 80 mM EGTA, 0.04% digitonin, 0.1 µg/µL RNaseA, 0.1 µg/µL glycogen) and incubation at 37 °C for 30 minutes to release digested DNA. The sample was centrifuged at 5,000g for 5 minutes at 4 °C and supernatant containing DNA collected. DNA was purified by phenol:chloroform extraction and size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067).
Libraries were prepared following described protocol to make libraries from small DNA fragments (https://dx.doi.org/10.17504/protocols.io.wvgfe3w); briefly: Paired-end sequencing libraries were constructed using an NEBNext Ultra II DNA kit (E7645S) and indexed (NEB E7335). Libraries were size-selected using Ampure XP beads (Beckman A63882). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067) and concentrations determined by qPCR. Equimolar pooled libraries were sequenced on an Illumina HiSeq with 2 x 150 bp cycles.

value: E16.5 cortex

value: primary neuron


title: WT mouse cortical neuron, DIV7, Smarcc2 CUTANDRUN, rep 1

description: Library name: CR_34


title: WT mouse cortical neuron, DIV7, Smarcc2 CUTANDRUN, rep 2

description: Library name: CR_36


title: G3, Buds, Spd, rep2

description: Library name: gs2_FRDM190670915-1a_HLKMYDSXX


title: Smarcc2 knockout + addback of Smarcc2(S586A) mouse cortical neuron DIV18, 30 min depolarized, rep 2

description: Library name: SG15

data_processing:
Raw reads were checked for quality using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were trimmed from adapters using cutadapt using parameters cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -b AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --nextseq-trim=20 --minimum-length 1.
Transcripts were quantified using kallisto against a mouse Gencode vM24 indexed transcriptome and annotations.
Assembly: Gencode vM24
Supplementary files format and content: abundance.tsv containing transcripts counts quantified by kallisto, used for downstream differential gene analyses

extract_protocol:
Cells were harvested in TRIsure (Bioline #38033). RNA was extracted using Direct-zol RNA MicroPrep columns (Zymo #R2062) treated with DNAseI.
For sequencing library preparation, rRNA was depleted (NEB #E7400) and prepared into paired-end libraries (NEB #E7760). For naïve (WT) DIV7 neuron RNA-seq, polyA-enriched mRNAs were isolated (NEB #E7490). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067) and concentrations determined by qPCR. Equimolar pooled libraries were sequenced on an Illumina NextSeq or HiSeq.

treatment_protocol: Membrane Depolarization by KCl Stimulation in Neurons At the designated DIV, neurons were silenced overnight with 1 µM tetrodotoxin (Tocris #1069) and 100 µM D-AP5 (Tocris #79055-68-8) to reflect the resting state and then depolarized with 50 mM KCl for indicated time points as described (PMID 26139371, PMID 27830782, PMID 2498163). Briefly, to avoid excitotoxic death, depolarization proceeded as follows: 3/10th of neuronal media was reserved and charged with 170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, and 10 mM HEPES pH 7.9 by adding 69.72 µL/1 mL reserved media of concentrated isotonic stimulation buffer (2.44M KCl, 28.7 mM CaCl2, 14.4 mM MgCl2, and 143.4 mM HEPES pH 7.9). At this point, the reserved media contains 3x the final concentration for the neuron. Control wells underwent media removal without addition of any components. The mix was restored to each well and gently swirled for 3 seconds, then the plate was placed back in the incubator for the appropriate incubation time. The excitotoxicity-induced gene Clca1 was verified not to be upregulated in our RNA-seq datasets, excluding toxic reaction. Neurons were then immediately moved to ice, media was then immediately exchanged to ice-cold PBS and harvested for downstream assays. Other Pharmacological Treatments in Neurons: Neurons were treated with 0.1% DMSO during depolarization or before harvesting (unstimulated) for the indicated times (30 mins or less).

value: 50 mM KCl (30 min)


title: Smarcc2 knockout + addback of WT Smarcc2 mouse cortical neuron DIV18, 30 min depolarized, rep 2

description: Library name: SG10


title: Smarcc2 knockout + addback of WT Smarcc2 mouse cortical neuron DIV18, 30 min depolarized, rep 1

description: Library name: SG8


title: Smarcc2 knockout + addback of Smarcc2(S586A) mouse cortical neuron DIV18, 30 min depolarized, rep 1

description: Library name: SG13


title: Smarcc2 knockout + addback of WT Smarcc2 mouse cortical neuron DIV18, 30 min depolarized, rep 3

description: Library name: SG11


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, 30 min depolarized, rep 2

description: Library name: SG4


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, 30 min depolarized, rep 1

description: Library name: SG2


title: Non-targeting gRNA mouse cortical neuron DIV18, 30 min depolarized, rep 1

description: Library name: SG22


title: Smarcc2 knockout + addback of Smarcc2(S586E) mouse cortical neuron DIV18, unstimulated, rep 2

description: Library name: SG18


title: Smarcc2 knockout + addback of Smarcc2(S586E) mouse cortical neuron DIV18, unstimulated, rep 1

description: Library name: SG16


title: Smarcc2 knockout + addback of WT Smarcc2 mouse cortical neuron DIV18, unstimulated, rep 2

description: Library name: SG9


title: Smarcc2 knockout + addback of WT Smarcc2 mouse cortical neuron DIV18, unstimulated, rep 1

description: Library name: SG7


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, unstimulated, rep 1

description: Library name: SG1


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, unstimulated, rep 3

description: Library name: SG5


title: Non-targeting gRNA mouse cortical neuron DIV18, unstimulated, rep 2

description: Library name: SG23


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, unstimulated, rep 2

description: Library name: SG3


title: Control CAR T cells- Tumor Stimulated rep 1

description:
Library name: Sample1
KS.R3

value: Control CAR

value: Tumor stimulated


title: Non-targeting gRNA mouse cortical neuron DIV18, unstimulated, rep 1

description: Library name: SG21


title: WT mouse cortical neuron, DIV7, Brg1 CUTANDRUN, rep 1

description: Library name: CR_22


title: Smarcc2 knockout + vector mouse cortical neuron DIV18, 30 min depolarized, rep 3

description: Library name: SG6


title: Non-targeting gRNA mouse cortical neuron DIV18, 30 min depolarized, rep 2

description: Library name: SG24


title: Smarcc2 knockout + addback of Smarcc2(S586E) mouse cortical neuron DIV18, unstimulated, rep 3

description: Library name: SG20


title: VP38b

type: RNA

first: Nicholas

last: Mitsiades

department: Medicine-Hematology & Oncology

description: SAMPLE 20

hyb_protocol: The aRNA was prepared for direct hybridization by diluting to the appropriate concentration following the Whole-Genome Gene Expression Direct Hybridization (Illumina, Inc.; San Diego, CA) assay guide. The biotin-labeled samples were loaded onto Beadchip arrays which contain complementary gene-specific sequences and incubated at 58°C for approximately 18 hrs. The arrays were removed from overnight incubation and washed as per the manufacturer’s recommendation.

scan_protocol: Cy3-Streptavidin was added to introduce fluorescent and differential detection of the signal to the analytical probes that have been hybridized to the array by the use of the Illumina iScan (Illumina, Inc.; San Diego, CA). An internal laser was utilized to excite the fluorophore product on the array allowing light emissions to be recorded in high-resolution imagery. The GenomeStudio (V2011.1) Gene Expression Analysis Module (v1.9.0) was applied to the scanned microarray images where preliminary quality control data was assessed.

data_processing:
Raw data were imported to the R environment and processed using the Illumina-specific package lumi. Background Correction (bgAdjust), Variance-stabilizing transformation (VST), and quantile normalization were applied.
Gene expression differences were derived utilizing the t-test and imposing a fold change exceeding 4/3x (p<0.05), using the R statistical system. Enriched pathways were inferred using the Gene Set Enrichment Analysis (GSEA) method1, and the Molecular Signature Database (MSigDB) pathway collection2. Gene sets with a nominal P value <0.05 and FDR < 0.25 were defined as significantly enriched.

label: biotin

source_name: Mel202_48 hr 9-cis-retinoic acid 100 nM

label_protocol: RNA samples were put through the Illumina TotalPrep RNA Amplification Kit (Ambion by Life Technologies; Carlsbad, CA) to generate biotinylated, amplified RNA (aRNA) for downstream processing. In summary, a reverse transcriptase with an oligo(dT) primer was utilized in first strand synthesis to produce cDNA containing a T7 promoter sequence.  Second strand synthesis followed, whereby the product became the template for in vitro transcription with T7 RNA polymerase along with biotin-UTP.  After purification of the aRNA, the samples were subjected to quantitation utilizing the spectrometric Quant-iT RiboGreen assay (Invitrogen, Ltd.; Eugene, OR).

growth_protocol: The Mel202 cell line (carrying both a GNAQ Q209L and a GNAQ R210K mutations) was established from a previously irradiated, locally recurrent primary uveal melanoma by Dr. B.R. Ksander (Schepens Eye Research Institute, Boston, USA) and was generously provided by Dr. Demetrios Vavvas, Massachusetts Eye and Ear Infirmary and Schepens Eye Research Institute, Harvard Medical School, Boston, MA. Cells were confirmed to be BRAF-wt. Cells were grown in DMEM/F12 (Invitrogen, Carlsbad, CA) with 100 units/ml penicillin, 100 μg/ml streptomycin, and 10% FBS (in a 37C incubator in a humid environment with 5% CO2) and were passaged for <6 months.

extract_protocol: Following treatment, cells were harvested in RNAlater (Qiagen; Germantown, MD) and RNA was isolated using the RNeasy Micro Kit (Qiagen). Briefly, an equal number of cells were centrifuged at high speeds to remove RNAlater. Buffer RLT with 1% beta-mercaptoethanol was utilized for cell lysis followed by homogenization using a QIAshredder spin column.  RNA was precipitated with 70% EtOH and transferred to the RNeasy MinElute spin column.  Samples were treated with DNase, washed, and eluted as per the manufacturer’s instructions. The RNA integrity for each sample was assessed with a RNA 6000 Nano chip on a 2100 Bioanalyzer (Agilent; Santa Clara, CA). RNA integrity score (RIN) for all samples was at least 9.7.

treatment_protocol: All-trans-Retinoic acid and 9-cis-Retinoic acid were purchased from Sigma-Aldrich (St. Louis, MO). GNAQ-mutant Mel202 uveal melanoma cells with treated, in their regular medium, with all-trans-retinoic acid (100 nM) or 9-cis-retinoic acid (100 nM) (dissolved in EtOH) or EtOH control for 24h or 48h in 6-well plates.

value: uveal melanoma line

value: 48 Hr. 9-cis-retinoic acid 100 nM


title: VP34

description: SAMPLE 16

source_name: Mel202_48 hr all-trans-Retinoic acid 100 nM

value: 48 Hr. all-trans-Retinoic acid 100 nM


title: VP23

description: SAMPLE 11

source_name: Mel202_48 hr EtOH Control

value: 48 Hr. EtOH Control


title: VP24a

description: SAMPLE 12


title: VP38a

description: SAMPLE 19


title: VP24b

description: SAMPLE 13


title: VP17

description: SAMPLE 8

source_name: Mel202_24 hr 9-cis-retinoic acid 100 nM

value: 24 Hr. 9-cis-retinoic acid 100 nM


title: VP19b

description: SAMPLE 10


title: VP33b

description: SAMPLE 15


title: VP36

description: SAMPLE 17


title: VP19a

description: SAMPLE 9


title: VP15

description: SAMPLE 6

source_name: Mel202_24 hr all-trans-Retinoic acid 100 nM

value: 24 Hr. all-trans-Retinoic acid 100 nM


title: VP37

description: SAMPLE 18


title: VP13b

description: SAMPLE 5


title: VP33a

description: SAMPLE 14


title: VP13a

description: SAMPLE 4


title: VP04a

description: SAMPLE 2

source_name: Mel202_24 hr EtOH Control

value: 24 Hr. EtOH Control


title: VP03

description: SAMPLE 1


title: VP04b

description: SAMPLE 3


title: siSRC1-1

state: TX

address: One Baylor Plaza, Suite R407

department: Medicine and Molecular and Cellular Biology

description: SAMPLE 7

hyb_protocol: The aRNA was prepared for direct hybridization by diluting to the appropriate concentration following the Whole-Genome Gene Expression Direct Hybridization (Illumina, Inc.; San Diego, CA) assay guide.  The biotin-labeled samples were loaded onto Beadchip arrays which contain complementary gene-specific sequences and incubated at 58°C for approximately 18 hrs.  The arrays were removed from overnight incubation and washed as per the manufacturer’s recommendation.

scan_protocol: Cy3-Streptavidin was added to introduce fluorescent and differential detection of the signal to the analytical probes that have been hybridized to the array by the use of the Illumina iScan (Illumina, Inc.; San Diego, CA).  An internal laser was utilized to excite the fluorophore product on the array allowing light emissions to be recorded in high-resolution imagery. The GenomeStudio (V2011.1) Gene Expression Analysis Module (v1.9.0) was applied to the scanned microarray images where preliminary quality control data was assessed.

source_name: prostate cancer cell line

growth_protocol: LNCaP-abl cells were generated and generously provided by Dr. Zoran Culig, Innsbruck Medical University, Inssbruck, Austria (Culig et al., 1999) and cultured in phenol-red free RPMI-1640 media (Gibco), supplemented with 10% charcoal-stripped serum (CSS) and 100units/mL of penicillin/streptomycin (P/S; 100units/mL; Gibco).

extract_protocol: RNA was extracted 72h post-transfection using Trizol (LifeTechnologies) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with 25 nM of Stealth siRNA against Wnt5a (clone: HSS111355, Life Technologies) or SRC1 (clone: SASI_Hs01_00177579, Sigma) or non-targeting control (siNT). Transfections were performed using Lipofectamine RNAiMax (LifeTechnologies) according to the manufacturer’s instructions and as previously described (He et al., PNAS 2014).

value: Abl


title: siNT-3

description: SAMPLE 2

value: siNT


title: siWnt5A-2

description: SAMPLE 5


title: M-AR-4

description: SAMPLE 6

data_processing: Raw data were imported to the R environment and processed using the Illumina-specific package lumi. Background Correction (bgAdjust), Variance-stabilizing transformation (VST), and quantile normalization were applied.

growth_protocol: LNCaP MDV-3100/enzalutamide-resistant (MDV-R) cells were generated by continually culturing parental LNCaP cells in RPMI-1640 (Gibco (ThermoFisher), Waltham, MA) supplemented with 10% fetal bovine serum (Gibco) and penicillin/streptomycin (P/S; 100units/mL; Gibco), with the addition of 25 microM MDV-3100 (enzalutamide), for more than a year (enzalutamide concentration was decreased to maintenance of 10 microM during experiments).

extract_protocol: RNA was extracted 72h post-transfection using Trizol (LifeTechnologies) according to the manufacturer’s instructions.  The RNA integrity (RIN) for each sample was assessed with a RNA 6000 Nano chip on a 2100 Bioanalyzer (Agilent; Santa Clara, CA) where the average RIN score was 9.0.

treatment_protocol: Cells were transfected with 25 nM of Stealth siRNA against AR (clone: HSS100619, LifeTechnologies, ThermoFisher Scientific, Waltham, MA) or non-targeting control (siNT). Transfections were performed using Lipofectamine RNAiMax (LifeTechnologies) according to the manufacturer’s instructions and as previously described (He et al., PNAS 2014).

value: MDVR

value: siAR


title: siWnt5A-3

description: SAMPLE 6


title: siWnt5A-1

description: SAMPLE 4


title: siNT-2

description: SAMPLE 1


title: siNT-4

description: SAMPLE 3


title: siSRC1-2

description: SAMPLE 8


title: M-G2-3

description: SAMPLE 12

growth_protocol: LNCaP-abl cells were generated and generously provided by Dr. Zoran Culig, Innsbruck Medical University, Inssbruck, Austria (Culig et al., 1999) and cultured in phenol-red free RPMI-1640 media (Gibco), supplemented with 10% charcoal-stripped serum (CSS) and 100units/mL of penicillin/streptomycin (P/S; 100units/mL; Gibco). LNCaP MDV-3100/enzalutamide-resistant (MDV-R) cells were generated by continually culturing parental LNCaP cells in RPMI-1640 (Gibco (ThermoFisher), Waltham, MA) supplemented with 10% fetal bovine serum (Gibco) and penicillin/streptomycin (P/S; 100units/mL; Gibco), with the addition of 25 microM MDV-3100 (enzalutamide), for more than a year (enzalutamide concentration was decreased to maintenance of 10 microM during experiments).

extract_protocol: RNA was extracted 72h post-transfection using Trizol (LifeTechnologies) according to the manufacturer’s instructions.  The RNA integrity (RIN) for each sample was assessed with a RNA 6000 Nano chip on a 2100 Bioanalyzer (Agilent; Santa Clara, CA) where the average RIN score was 9.9.

treatment_protocol: Cells were transfected with 25 nM of Stealth siRNA against GATA2 (clone: HSS104003, LifeTechnologies, ThermoFisher Scientific, Waltham, MA) or non-targeting control (siNT). Transfections were performed using Lipofectamine RNAiMax (LifeTechnologies) according to the manufacturer’s instructions and as previously described (He et al., PNAS 2014).


title: M-NT-4

description: SAMPLE 9


title: M-G2-1

description: SAMPLE 10


title: VP16

description: SAMPLE 7


title: M-AR-1

description: SAMPLE 4


title: M-NT-2

description: SAMPLE 7


title: M-AR-2

description: SAMPLE 5


title: M-G2-2

description: SAMPLE 11


title: CF_H_1

description:
MDVR.H2O
SAMPLE 1

hyb_protocol: Standard Illumina Hybridization protocol (Human HT-12, Direct Hyb Gene Expression array)

scan_protocol: Illumina iScan.

label_protocol: Illumina TotalPrep 96 RNA Amplification Kit is a complete system for generating biotinylated, amplified RNA for hybridization with Illumina sentrix arrays.

growth_protocol: LNCaP MDV-3100/enzalutamide-resistant (MDV-R) cells were generated by continually culturing parental LNCaP cells as previously described, with the addition of 25 microM MDV-3100 (enzalutamide), for more than a year (enzalutamide concentration was decreased to maintenance of 10 microM during experiments).

extract_protocol: Total RNA was extracted using Trizol (Life Technologies) and purified with the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Cells were treated with 50 µM dilazep (Santa Cruz Biotechnologies, Dallas, TX) or control for 48h.


title: A-G2-3

description: SAMPLE 5


title: A-NT-2

description: SAMPLE 2


title: A-G2-4

description: SAMPLE 6


title: A-NT-1

description: SAMPLE 1


title: CF_H_2

description:
MDVR.H2O
SAMPLE 2


title: CF_Di_3

description:
MDVR.Dilazep
SAMPLE 5

value: Dilazep (50 microM)


title: CF_Di_2

description:
MDVR.Dilazep
SAMPLE 4


title: M-NT-3

description: SAMPLE 8


title: A-NT-3

description: SAMPLE 3


title: CF_K_2

description:
MDVR.K11706
SAMPLE 4

treatment_protocol: LNCaP MDV-3100/enzalutamide-resistant (MDV-R) cells were treated with 1 µM K-11706 or vehicle (DMSO) for 48h.

value: MDVR cells


title: A-G2-2

description: SAMPLE 4


title: CF_Di_1

description:
MDVR.Dilazep
SAMPLE 3


title: CF-Bu-1

description: SAMPLE 3

treatment_protocol: Cells were treated with 10 nM bufalin (Santa Cruz Biotechnologies, Dallas, TX) or control for 48h.

value: Bufalin (10 nM)


title: CF_K_3

description:
MDVR.K11706
SAMPLE 5


title: CF_K_1

description:
MDVR.K11706
SAMPLE 3


title: CF_DM_3

description: SAMPLE 2

value: DMSO


title: CF_DM_1

description: SAMPLE 1


title: ABD_2

scan_protocol: Illumina iScan

label_protocol: Illumina TotalPrep 96 RNA Amplification Kit: is a complete system for generating biotinylated, amplified RNA for hybridization with Illumina sentrix arrays

growth_protocol: LNCaP cells (American Type Culture Collection (ATCC), Manassas, VA) were cultured in RPMI-1640 (Gibco (ThermoFisher), Waltham, MA) supplemented with 10% fetal bovine serum (Gibco) and penicillin/streptomycin (P/S; 100units/mL; Gibco). LNCaP-abl cells were generated and generously provided by Dr. Zoran Culig, Innsbruck Medical University, Inssbruck, Austria (Culig et al., 1999) and cultured in phenol-red free RPMI-1640 media (Gibco), supplemented with 10% charcoal-stripped serum (CSS) and 100units/mL of penicillin/streptomycin (P/S; 100units/mL; Gibco).

value: LNCaP-abl

value: prostate cancer cell line


title: CF-Bu-2

description: SAMPLE 4


title: siSRC1-3

description: SAMPLE 9


title: ABD_3


title: LND_2

value: LNCaP


title: AK_3

description: SAMPLE 13

treatment_protocol: LNCaP cells and LNCaP-abl (Abl) cells were treated with 1 µM K-11706 or vehicle (DMSO) or H2O for 48h.

value: K-11706 (1 microM for 48h)


title: AK_1

description: SAMPLE 9


title: LK_4

description: SAMPLE 6


title: LND_1


title: AB_1

description: SAMPLE 11


title: LK_1

description: SAMPLE 2


title: AH_3

description: SAMPLE 8


title: LND_4


title: ABD_1


title: AK_2

description: SAMPLE 11


title: LB_2

description: SAMPLE 5


title: AD_3

description: SAMPLE 10


title: AD_1

description: SAMPLE 9


title: LB_3

description: SAMPLE 6


title: AB_3

description: SAMPLE 12


title: ACLY_WT_survival_3

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Gene abundance estimates were obtained for each sample using kallisto 0.44.0, with the Ensemble GRCm38 transcriptome as the reference
The abundance levels were normalized using the DESeq between-sample normalization approach
Assembly: GRCm38
Supplementary files format and content: comma-separated values file includes the DESeq normalized counts

source_name: Spleen

growth_protocol: Acly conditional knockout T-ALLs were injected intravenously in sub-lethally Irradiated mice.

extract_protocol:
Leukemic spleens were removed, single-cell suspensions were obtained by pressing them through a 40μm filter, and subsequently subjected to red blood cell lysis. RNA was extracted using QIAGEN QIAshredder (#79656) and Rneasy Mini (#74106) kits. 1μg of Total RNA was used for the construction of sequencing libraries by Genewiz.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For acute experiments, mice were allowed to become overtly leukemic and then treated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection, and leukemic spleens were collected 48h later. For surival experiments, 48h upon transplantation with Acly conditional knockout leukemic cells, mice were treated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection, and their surivival was monitored afterwards. Samples were collected at the time of humane endpoint.

value: Leukemic spleen

value: Control

tag: strain


title: ACLY_WT_acute_3


title: ACLY_WT_survival_2


title: ACLY_WT_survival_4


title: LK_3

description: SAMPLE 4


title: ACLY_WT_acute_1


title: LD_2

description: SAMPLE 3


title: AH_2

description: SAMPLE 7


title: ACLY_WT_survival_1


title: ACLY_KO_survival_second_wave_3

value: Acly deleted


title: LD_3

description: SAMPLE 4


title: ACLY_KO_survival_second_wave_1


title: ACLY_KO_survival_first_wave_2


title: ACLY_KO_survival_first_wave_1


title: ACLY_KO_acute_1


title: NaB_3

city: Shanghai

first: Xiaotong

last: Yang

address: 160 Pujian Rd, Shanghai

country: China

institute: Shanghai Jiaotong University

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity sequence, then mapped to mm10 whole genome.
Reads Per Kilobase of exon per Megabase of library size were calculated using a protocol from Chepeleve et al., Nucleic Acids Research, 2009.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

source_name: tumor cell

extract_protocol:
Briefly, tumor cell were generated and collected after 24 hours of stimulation.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: tumor cell

value: NaB


title: ACLY_KO_acute_2


title: ACLY_WT_acute_2


title: LH_1

description: SAMPLE 1


title: LH_3

description: SAMPLE 2


title: NaB_1


title: Con_1

value: Con


title: Con_3


title: split ePE3 with untethered MMLV-RT_delta_RH at EMX1 loci - Repeat2 -I11

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

description:
Library name: split_ePE3-unRT.R2.I11
Rep 2 -I11
vitro_processed_ePE3.xlsx

data_processing:
*library strategy: Amplicon Sequencing
Traget site and protential off-target sites were amplified by PCR using the primer sequences, then sequenced on an Illumina NovaSeq system. Deep sequencing data analysis was processed using CRISPResso2 and untreated cells were used as negative controls to exclude PCR amplification and sequencing errors. Reads were align to the amplicon sequence by crispresso2 using --max_paired_end_reads_overlap 140 --min_paired_end_reads_overlap     10 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0.2
On-target editing efficiencies, which are greater than 0.1%, were quantified as a percentage of (number of on-target reads) / (number of total reads).
Assembly: sequence.txt
Supplementary files format and content: xlsx files, percentage of total sequencing reads with on-target editing or off-target editing for all libraries, percentage of total sequencing reads with indels.

source_name: HEK293T cell

growth_protocol: HEK293T cell and Hepa1-6 cell were grown in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gemini #900-108) and 1% GlutaMAX (Thermo #35050061). Cells were passaged every 2-3 days. After one day post-transduction, the medium was changed. Cells were harvested at 72 hours post-transduction.

extract_protocol:
Genomic DNA (gDNA) was isolated using TIANamp Genomic DNA Kit (TIANGEN #DP304) according to the manufacturer’s protocol.
The region that integrated with genomic DNA including RT template was PCR amplified from genomic DNA for HTS. For the first round of PCR, genomic sites of interest were amplified from 150 ng of genomic DNA using Q5 PCR Master Mix (New England Biolabs #M0544S) with the primers containing Illumina forward and reverse adapters. 50 uL of PCR 1 reaction was performed with forward and reverse primers each at 0.25 uM, ~1 uL of genomic DNA extract, and 25 uL of Q5 PCR Master Mix. To add a unique sequencing index, 50 uL of a given PCR 2 contained 2.5 uL of previous step unpurified PCR product; a unique forward or reverse primer pair, each at 0.25 uM; and 25 uL of Q5 PCR Master Mix. Primers are listed in Table S1. PCR 2 products were purified by DNA AMPure XP beads (Beckman Coulter #A63882) and eluted with 25 uL of water. DNA concentration was quantified by Nanodrop One (Thermo Fisher Scientific).

treatment_protocol: Cells were transfected at 60%-70% confluency using 3 uL of Lipofectamine 3000 (Thermo Fisher) with 1500 ng each half of the Split-PE. Three days post transfection, cells were collected. All animal experiments were conducted under the protocol approved by Institutional Animal Care and Use Committee (IACUC) of the Westlake University. C57BL/6 male mice were purchased and housed in the Laboratory Animal Resource Center (LARC) at the Westlake University. The LARC is a certified pathogen-free and environmental-control facility (21 ± 2°C, 55 ± 15% humidity and 12:12-h light: dark cycle). AAV were injected into the tail vein of six-week-old male C57BL/6 mice.

value: HEK293T cell

value: human embryonic kidney cells

value: WT


title: split ePE3 with untethered MMLV-RT_delta_RH at EMX1 loci - Repeat2 -I7

description:
Library name: split_ePE3-unRT.R2.I7
Rep 2 -I7
vitro_processed_ePE3.xlsx


title: split ePE3 with untethered MMLV-RT_delta_RH at EMX1 loci - Repeat2 -I5

description:
Library name: split_ePE3-unRT.R2.I5
Rep 2 -I5
vitro_processed_ePE3.xlsx


title: split ePE3 with untethered MMLV-RT_delta_RH at EMX1 loci - Repeat2 -I9

description:
Library name: split_ePE3-unRT.R2.I9
Rep 2 -I9
vitro_processed_ePE3.xlsx


title: split ePE3 with untethered MMLV-RT_delta_RH at EMX1 loci - Repeat2 -I3

description:
Library name: split_ePE3-unRT.R2.I3
Rep 2 -I3
vitro_processed_ePE3.xlsx


title: split ePE3 with untethered MMLV-RT_delta_RH at EMX1 loci - Repeat2 -I1

description:
Library name: split_ePE3-unRT.R2.I1
Rep 2 -I1
vitro_processed_ePE3.xlsx


title: ACLY_KO_survival_second_wave_2


title: split PE2 at EMX1- Repeat 2- I5

description:
Library name: split_PE2-EMX1.R2.I5
Rep 2- I5
vitro_processed_ePE3.xlsx

value: split PE2 at EMX1


title: split PE2 at EMX1- Repeat 2- I7

description:
Library name: split_PE2-EMX1.R2.I7
Rep 2- I7
vitro_processed_ePE3.xlsx


title: split PE2 at EMX1- Repeat 2- I9

description:
Library name: split_PE2-EMX1.R2.I9
Rep 2- I9
vitro_processed_ePE3.xlsx


title: ACLY_KO_survival_first_wave_3


title: split PE2 at EMX1- Repeat 2- I3

description:
Library name: split_PE2-EMX1.R2.I3
Rep 2- I3
vitro_processed_ePE3.xlsx


title: split PE2 at EMX1- Repeat 2- I1

description:
Library name: split_PE2-EMX1.R2.I1
Rep 2- I1
vitro_processed_ePE3.xlsx


title: ACLY_KO_acute_4


title: ACLY_KO_acute_3


title: NaB_2


title: split ePE3 with untethered MMLV-RT_RH at EMX1 loci - Repeat1 -I9

description:
Library name: split_ePE3-unRT.R1.I9
Rep 1 -I9
vitro_processed_ePE3.xlsx


title: split PE2 at EMX1- Repeat 1- I3

description:
Library name: split_PE2-EMX1.R1.I3
Rep 1- I3
vitro_processed_ePE3.xlsx


title: split ePE3 with untethered MMLV-RT_RH at EMX1 loci - Repeat1 -I11

description:
Library name: split_ePE3-unRT.R1.I11
Rep 1 -I11
vitro_processed_ePE3.xlsx


title: split ePE3 with untethered MMLV-RT_RH at EMX1 loci - Repeat1 -I7

description:
Library name: split_ePE3-unRT.R1.I7
Rep 1 -I7
vitro_processed_ePE3.xlsx


title: Con_2


title: split ePE3 with untethered MMLV-RT_RH at EMX1 loci - Repeat1 -I5

description:
Library name: split_ePE3-unRT.R1.I5
Rep 1 -I5
vitro_processed_ePE3.xlsx


title: split ePE3 with untethered MMLV-RT_RH at EMX1 loci - Repeat1 -I3

description:
Library name: split_ePE3-unRT.R1.I3
Rep 1 -I3
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I54

description:
Library name: split_ePE3-multi.R3.I54
Rep 3- I54
vitro_processed_ePE3.xlsx

value: split ePE3 at multiple endogenous sites


title: split ePE3 with untethered MMLV-RT_RH at EMX1 loci - Repeat1 -I1

description:
Library name: split_ePE3-unRT.R1.I1
Rep 1 -I1
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I52

description:
Library name: split_ePE3-multi.R3.I52
Rep 3- I52
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I51

description:
Library name: split_ePE3-multi.R3.I51
Rep 3- I51
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I50

description:
Library name: split_ePE3-multi.R3.I50
Rep 3- I50
vitro_processed_ePE3.xlsx


title: split PE2 at EMX1- Repeat 1- I9

description:
Library name: split_PE2-EMX1.R1.I9
Rep 1- I9
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I49

description:
Library name: split_ePE3-multi.R3.I49
Rep 3- I49
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I47

description:
Library name: split_ePE3-multi.R3.I47
Rep 3- I47
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I46

description:
Library name: split_ePE3-multi.R3.I46
Rep 3- I46
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I44

description:
Library name: split_ePE3-multi.R3.I44
Rep 3- I44
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I40

description:
Library name: split_ePE3-multi.R3.I40
Rep 3- I40
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I41

description:
Library name: split_ePE3-multi.R3.I41
Rep 3- I41
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I48

description:
Library name: split_ePE3-multi.R3.I48
Rep 3- I48
vitro_processed_ePE3.xlsx


title: split PE2 at EMX1- Repeat 1- I7

description:
Library name: split_PE2-EMX1.R1.I7
Rep 1- I7
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I42

description:
Library name: split_ePE3-multi.R3.I42
Rep 3- I42
vitro_processed_ePE3.xlsx


title: split PE2 at EMX1- Repeat 1- I5

description:
Library name: split_PE2-EMX1.R1.I5
Rep 1- I5
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I53

description:
Library name: split_ePE3-multi.R3.I53
Rep 3- I53
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I45

description:
Library name: split_ePE3-multi.R3.I45
Rep 3- I45
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I39

description:
Library name: split_ePE3-multi.R3.I39
Rep 3- I39
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I38

description:
Library name: split_ePE3-multi.R3.I38
Rep 3- I38
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I36

description:
Library name: split_ePE3-multi.R3.I36
Rep 3- I36
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I35

description:
Library name: split_ePE3-multi.R3.I35
Rep 3- I35
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I37

description:
Library name: split_ePE3-multi.R3.I37
Rep 3- I37
vitro_processed_ePE3.xlsx


title: split PE2 at EMX1- Repeat 1- I1

description:
Library name: split_PE2-EMX1.R1.I1
Rep 1- I1
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I34

description:
Library name: split_ePE3-multi.R3.I34
Rep 3- I34
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I55

description:
Library name: split_ePE3-multi.R3.I55
Rep 3- I55
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I33

description:
Library name: split_ePE3-multi.R3.I33
Rep 3- I33
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I30

description:
Library name: split_ePE3-multi.R3.I30
Rep 3- I30
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I31

description:
Library name: split_ePE3-multi.R3.I31
Rep 3- I31
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I32

description:
Library name: split_ePE3-multi.R3.I32
Rep 3- I32
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I29

description:
Library name: split_ePE3-multi.R3.I29
Rep 3- I29
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I28

description:
Library name: split_ePE3-multi.R3.I28
Rep 3- I28
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I43

description:
Library name: split_ePE3-multi.R3.I43
Rep 3- I43
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I27

description:
Library name: split_ePE3-multi.R3.I27
Rep 3- I27
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I24

description:
Library name: split_ePE3-multi.R3.I24
Rep 3- I24
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I26

description:
Library name: split_ePE3-multi.R3.I26
Rep 3- I26
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I23

description:
Library name: split_ePE3-multi.R3.I23
Rep 3- I23
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I25

description:
Library name: split_ePE3-multi.R3.I25
Rep 3- I25
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I22

description:
Library name: split_ePE3-multi.R3.I22
Rep 3- I22
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I21

description:
Library name: split_ePE3-multi.R3.I21
Rep 3- I21
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I20

description:
Library name: split_ePE3-multi.R3.I20
Rep 3- I20
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I18

description:
Library name: split_ePE3-multi.R3.I18
Rep 3- I18
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I19

description:
Library name: split_ePE3-multi.R3.I19
Rep 3- I19
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I14

description:
Library name: split_ePE3-multi.R3.I14
Rep 3- I14
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I16

description:
Library name: split_ePE3-multi.R3.I16
Rep 3- I16
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I17

description:
Library name: split_ePE3-multi.R3.I17
Rep 3- I17
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I13

description:
Library name: split_ePE3-multi.R3.I13
Rep 3- I13
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I12

description:
Library name: split_ePE3-multi.R3.I12
Rep 3- I12
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I11

description:
Library name: split_ePE3-multi.R3.I11
Rep 3- I11
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I9

description:
Library name: split_ePE3-multi.R3.I9
Rep 3- I9
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I7

description:
Library name: split_ePE3-multi.R3.I7
Rep 3- I7
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I8

description:
Library name: split_ePE3-multi.R3.I8
Rep 3- I8
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I6

description:
Library name: split_ePE3-multi.R3.I6
Rep 3- I6
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I5

description:
Library name: split_ePE3-multi.R3.I5
Rep 3- I5
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I3

description:
Library name: split_ePE3-multi.R3.I3
Rep 3- I3
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I1

description:
Library name: split_ePE3-multi.R3.I1
Rep 3- I1
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I55

description:
Library name: split_ePE3-multi.R2.I55
Rep 2- I55
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I54

description:
Library name: split_ePE3-multi.R2.I54
Rep 2- I54
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I53

description:
Library name: split_ePE3-multi.R2.I53
Rep 2- I53
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I52

description:
Library name: split_ePE3-multi.R2.I52
Rep 2- I52
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I50

description:
Library name: split_ePE3-multi.R2.I50
Rep 2- I50
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I51

description:
Library name: split_ePE3-multi.R2.I51
Rep 2- I51
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I48

description:
Library name: split_ePE3-multi.R2.I48
Rep 2- I48
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I49

description:
Library name: split_ePE3-multi.R2.I49
Rep 2- I49
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I15

description:
Library name: split_ePE3-multi.R3.I15
Rep 3- I15
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I46

description:
Library name: split_ePE3-multi.R2.I46
Rep 2- I46
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I47

description:
Library name: split_ePE3-multi.R2.I47
Rep 2- I47
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I10

description:
Library name: split_ePE3-multi.R3.I10
Rep 3- I10
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I44

description:
Library name: split_ePE3-multi.R2.I44
Rep 2- I44
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I42

description:
Library name: split_ePE3-multi.R2.I42
Rep 2- I42
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I41

description:
Library name: split_ePE3-multi.R2.I41
Rep 2- I41
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I43

description:
Library name: split_ePE3-multi.R2.I43
Rep 2- I43
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I39

description:
Library name: split_ePE3-multi.R2.I39
Rep 2- I39
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I45

description:
Library name: split_ePE3-multi.R2.I45
Rep 2- I45
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I40

description:
Library name: split_ePE3-multi.R2.I40
Rep 2- I40
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I38

description:
Library name: split_ePE3-multi.R2.I38
Rep 2- I38
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I2

description:
Library name: split_ePE3-multi.R3.I2
Rep 3- I2
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I36

description:
Library name: split_ePE3-multi.R2.I36
Rep 2- I36
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I33

description:
Library name: split_ePE3-multi.R2.I33
Rep 2- I33
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I34

description:
Library name: split_ePE3-multi.R2.I34
Rep 2- I34
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 3- I4

description:
Library name: split_ePE3-multi.R3.I4
Rep 3- I4
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I32

description:
Library name: split_ePE3-multi.R2.I32
Rep 2- I32
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I31

description:
Library name: split_ePE3-multi.R2.I31
Rep 2- I31
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I37

description:
Library name: split_ePE3-multi.R2.I37
Rep 2- I37
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I30

description:
Library name: split_ePE3-multi.R2.I30
Rep 2- I30
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I35

description:
Library name: split_ePE3-multi.R2.I35
Rep 2- I35
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I28

description:
Library name: split_ePE3-multi.R2.I28
Rep 2- I28
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I29

description:
Library name: split_ePE3-multi.R2.I29
Rep 2- I29
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I27

description:
Library name: split_ePE3-multi.R2.I27
Rep 2- I27
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I26

description:
Library name: split_ePE3-multi.R2.I26
Rep 2- I26
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I25

description:
Library name: split_ePE3-multi.R2.I25
Rep 2- I25
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I24

description:
Library name: split_ePE3-multi.R2.I24
Rep 2- I24
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I23

description:
Library name: split_ePE3-multi.R2.I23
Rep 2- I23
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I22

description:
Library name: split_ePE3-multi.R2.I22
Rep 2- I22
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I19

description:
Library name: split_ePE3-multi.R2.I19
Rep 2- I19
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I20

description:
Library name: split_ePE3-multi.R2.I20
Rep 2- I20
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I21

description:
Library name: split_ePE3-multi.R2.I21
Rep 2- I21
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I18

description:
Library name: split_ePE3-multi.R2.I18
Rep 2- I18
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I17

description:
Library name: split_ePE3-multi.R2.I17
Rep 2- I17
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I16

description:
Library name: split_ePE3-multi.R2.I16
Rep 2- I16
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I15

description:
Library name: split_ePE3-multi.R2.I15
Rep 2- I15
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I13

description:
Library name: split_ePE3-multi.R2.I13
Rep 2- I13
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I14

description:
Library name: split_ePE3-multi.R2.I14
Rep 2- I14
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I11

description:
Library name: split_ePE3-multi.R2.I11
Rep 2- I11
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I10

description:
Library name: split_ePE3-multi.R2.I10
Rep 2- I10
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I9

description:
Library name: split_ePE3-multi.R2.I9
Rep 2- I9
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I8

description:
Library name: split_ePE3-multi.R2.I8
Rep 2- I8
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I12

description:
Library name: split_ePE3-multi.R2.I12
Rep 2- I12
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I7

description:
Library name: split_ePE3-multi.R2.I7
Rep 2- I7
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I5

description:
Library name: split_ePE3-multi.R2.I5
Rep 2- I5
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I2

description:
Library name: split_ePE3-multi.R2.I2
Rep 2- I2
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I6

description:
Library name: split_ePE3-multi.R2.I6
Rep 2- I6
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I3

description:
Library name: split_ePE3-multi.R2.I3
Rep 2- I3
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I51

description:
Library name: split_ePE3-multi.R1.I51
Rep 1- I51
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I50

description:
Library name: split_ePE3-multi.R1.I50
Rep 1- I50
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I49

description:
Library name: split_ePE3-multi.R1.I49
Rep 1- I49
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I54

description:
Library name: split_ePE3-multi.R1.I54
Rep 1- I54
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I53

description:
Library name: split_ePE3-multi.R1.I53
Rep 1- I53
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 2- I1

description:
Library name: split_ePE3-multi.R2.I1
Rep 2- I1
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I55

description:
Library name: split_ePE3-multi.R1.I55
Rep 1- I55
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I48

description:
Library name: split_ePE3-multi.R1.I48
Rep 1- I48
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I46

description:
Library name: split_ePE3-multi.R1.I46
Rep 1- I46
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I45

description:
Library name: split_ePE3-multi.R1.I45
Rep 1- I45
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I44

description:
Library name: split_ePE3-multi.R1.I44
Rep 1- I44
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I43

description:
Library name: split_ePE3-multi.R1.I43
Rep 1- I43
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I52

description:
Library name: split_ePE3-multi.R1.I52
Rep 1- I52
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I47

description:
Library name: split_ePE3-multi.R1.I47
Rep 1- I47
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I41

description:
Library name: split_ePE3-multi.R1.I41
Rep 1- I41
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I42

description:
Library name: split_ePE3-multi.R1.I42
Rep 1- I42
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I39

description:
Library name: split_ePE3-multi.R1.I39
Rep 1- I39
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I40

description:
Library name: split_ePE3-multi.R1.I40
Rep 1- I40
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I37

description:
Library name: split_ePE3-multi.R1.I37
Rep 1- I37
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I34

description:
Library name: split_ePE3-multi.R1.I34
Rep 1- I34
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I32

description:
Library name: split_ePE3-multi.R1.I32
Rep 1- I32
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I36

description:
Library name: split_ePE3-multi.R1.I36
Rep 1- I36
vitro_processed_ePE3.xlsx


title: ACLY_WT_acute_4


title: split ePE3 at multiple endogenous sites- Repeat 2- I4

description:
Library name: split_ePE3-multi.R2.I4
Rep 2- I4
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I33

description:
Library name: split_ePE3-multi.R1.I33
Rep 1- I33
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I38

description:
Library name: split_ePE3-multi.R1.I38
Rep 1- I38
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I31

description:
Library name: split_ePE3-multi.R1.I31
Rep 1- I31
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I30

description:
Library name: split_ePE3-multi.R1.I30
Rep 1- I30
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I26

description:
Library name: split_ePE3-multi.R1.I26
Rep 1- I26
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I27

description:
Library name: split_ePE3-multi.R1.I27
Rep 1- I27
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I25

description:
Library name: split_ePE3-multi.R1.I25
Rep 1- I25
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I28

description:
Library name: split_ePE3-multi.R1.I28
Rep 1- I28
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I23

description:
Library name: split_ePE3-multi.R1.I23
Rep 1- I23
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I24

description:
Library name: split_ePE3-multi.R1.I24
Rep 1- I24
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I21

description:
Library name: split_ePE3-multi.R1.I21
Rep 1- I21
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I20

description:
Library name: split_ePE3-multi.R1.I20
Rep 1- I20
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I17

description:
Library name: split_ePE3-multi.R1.I17
Rep 1- I17
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I19

description:
Library name: split_ePE3-multi.R1.I19
Rep 1- I19
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I18

description:
Library name: split_ePE3-multi.R1.I18
Rep 1- I18
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I35

description:
Library name: split_ePE3-multi.R1.I35
Rep 1- I35
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I16

description:
Library name: split_ePE3-multi.R1.I16
Rep 1- I16
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I15

description:
Library name: split_ePE3-multi.R1.I15
Rep 1- I15
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I14

description:
Library name: split_ePE3-multi.R1.I14
Rep 1- I14
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I13

description:
Library name: split_ePE3-multi.R1.I13
Rep 1- I13
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I11

description:
Library name: split_ePE3-multi.R1.I11
Rep 1- I11
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I10

description:
Library name: split_ePE3-multi.R1.I10
Rep 1- I10
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I12

description:
Library name: split_ePE3-multi.R1.I12
Rep 1- I12
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I9

description:
Library name: split_ePE3-multi.R1.I9
Rep 1- I9
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I6

description:
Library name: split_ePE3-multi.R1.I6
Rep 1- I6
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I7

description:
Library name: split_ePE3-multi.R1.I7
Rep 1- I7
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I5

description:
Library name: split_ePE3-multi.R1.I5
Rep 1- I5
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I4

description:
Library name: split_ePE3-multi.R1.I4
Rep 1- I4
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I29

description:
Library name: split_ePE3-multi.R1.I29
Rep 1- I29
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I1

description:
Library name: split_ePE3-multi.R1.I1
Rep 1- I1
vitro_processed_ePE3.xlsx


title: split ePE3 at multiple endogenous sites- Repeat 1- I22

description:
Library name: split_ePE3-multi.R1.I22
Rep 1- I22
vitro_processed_ePE3.xlsx


title: VM_biol_rep_1

city: Rochester

first: Atta

last: Behfar

state: MN

address: 200 1st St SW

department: Cardiovascular Diseases

institute: Mayo Clinic

description:
Library name: VM1
column name in Processed data files: VM1

data_processing:
Secondary analysis performed by Mayo Clinic Bioinformatics core, according to Map-Rseq workflow
Assembly: hg38
Supplementary files format and content: .txt tab-delimitted file contains raw counts for all samples
Supplementary files format and content: .csv file includes FPKM's for all samples
Supplementary files format and content: .xlsx file includes differential gene expression of PF versus EC and VM specimens using DESeq2 analysis software

source_name: cardiac

extract_protocol:
Total RNA was extracted from ≈30 mg tissue by TissueRuptor II (Qiagen, 9002755) homogenization, following RNeasy Fibrous Tissue Kit instructions (Qiagen, 74704).
Library preparation and primary mRNA sequencing analysis was conducted by the Mayo Clinic Genome Analysis core, according to Map-Rseq: Mayo Analysis Pipeline for RNA Seq. Briefly, mRNA was selected from total RNA specimens with RIN values ≥7 (n = 10 VM, 16 PF, and 5 EC) by poly-A tail capture on oligo-dT magnetic beads, and used to prepare cDNA libraries according to Illumina TruSeq RNA Library Prep Kit v2 instructions (RS-122-2001).

value: cardiac

value: ventricular myocardium

tag: Sex

value: female

value: healthy

tag: age

value: 62 yro


title: PF_biol_rep_16

description:
Library name: PF16
column name in Processed data files: PF16

value: cardiac Purkinje fiber

value: 36 yro


title: VM_biol_rep_9

description:
Library name: VM9
column name in Processed data files: VM9


title: VM_biol_rep_7

description:
Library name: VM7
column name in Processed data files: VM7

value: 32 yro


title: VM_biol_rep_3

description:
Library name: VM3
column name in Processed data files: VM3

value: 46 yro


title: VM_biol_rep_4

description:
Library name: VM4
column name in Processed data files: VM4

value: 64 yro


title: PF_biol_rep_12

description:
Library name: PF12
column name in Processed data files: PF12

value: 53 yro


title: PF_biol_rep_9

description:
Library name: PF9
column name in Processed data files: PF9


title: PF_biol_rep_15

description:
Library name: PF15
column name in Processed data files: PF15


title: PF_biol_rep_10

description:
Library name: PF10
column name in Processed data files: PF10


title: PF_biol_rep_13

description:
Library name: PF13
column name in Processed data files: PF13


title: VM_biol_rep_8

description:
Library name: VM8
column name in Processed data files: VM8

value: 58 yro


title: VM_biol_rep_6

description:
Library name: VM6
column name in Processed data files: VM6


title: split ePE3 at multiple endogenous sites- Repeat 1- I3

description:
Library name: split_ePE3-multi.R1.I3
Rep 1- I3
vitro_processed_ePE3.xlsx

value: HEK293T cell


title: PF_biol_rep_7

description:
Library name: PF7
column name in Processed data files: PF7


title: PF_biol_rep_14

description:
Library name: PF14
column name in Processed data files: PF14

value: 66 yro


title: PF_biol_rep_4

description:
Library name: PF4
column name in Processed data files: PF4


title: PF_biol_rep_3

description:
Library name: PF3
column name in Processed data files: PF3


title: PF_biol_rep_6

description:
Library name: PF6
column name in Processed data files: PF6


title: PF_biol_rep_8

description:
Library name: PF8
column name in Processed data files: PF8


title: PF_biol_rep_5

description:
Library name: PF5
column name in Processed data files: PF5


title: VM_biol_rep_2

description:
Library name: VM2
column name in Processed data files: VM2


title: PF_biol_rep_1

description:
Library name: PF1
column name in Processed data files: PF1


title: split ePE3 at multiple endogenous sites- Repeat 1- I8

description:
Library name: split_ePE3-multi.R1.I8
Rep 1- I8
vitro_processed_ePE3.xlsx

value: human embryonic kidney cells

value: WT


title: VM_biol_rep_10

description:
Library name: VM10
column name in Processed data files: VM10

value: 51 yro


title: EC_biol_rep_5

description:
Library name: EC5
column name in Processed data files: EC5

value: cardiac

value: endocardium


title: VM_biol_rep_5

description:
Library name: VM5
column name in Processed data files: VM5

value: ventricular myocardium

value: female


title: PF_biol_rep_2

description:
Library name: PF2
column name in Processed data files: PF2

value: healthy


title: PF_biol_rep_11

description:
Library name: PF11
column name in Processed data files: PF11

value: cardiac Purkinje fiber


title: EC_biol_rep_4

description:
Library name: EC4
column name in Processed data files: EC4


title: Subject5_Day7_PBMC

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

state: Gelderland

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

description: Peripheral blood mononuclear cells were isolated one week (7 days) after in vivo LPS challenge (LPS-induced systemic inflammation) and scRNA-seq libraries were prepared using 10X single cell 3' (v3.1) method.

library_source: transcriptomic single cell

data_processing:
Sequencing data were mapped to hg38 reference genome and gene/cell count matrix was generated using cellRanger software with default parameters.
Assembly: hg38
Supplementary files format and content: tar.gz, Gene/single-cell Count Matrix obtained from CellRanger

source_name: Peripheral Blood

growth_protocol: Bone marrow and peripheral blood mononuclear cells were isolated from bone marrow aspirates and peripheral blood and cryopreserved until library preparation step.

extract_protocol: Single-cell RNA-seq libraries were prepared using Chromium (10X) single cell 3' V3 kit following manufacturer's protocol.

treatment_protocol: No treatment

value: Peripheral Blood

value: Peripheral Blood Mononuclear Cells (PBMC)


title: EC_biol_rep_1

description:
Library name: EC1
column name in Processed data files: EC1


title: Subject4_Day7_PBMC


title: EC_biol_rep_2

description:
Library name: EC2
column name in Processed data files: EC2

value: 46 yro


title: Subject1_Day0_PBMC

description: Peripheral blood mononuclear cells were isolated from healthy volunteer on day 0, before in vivo LPS challenge (LPS-induced systemic inflammation) and scRNA-seq libraries were prepared using 10X single cell 3' (v3.1) method.


title: Subject4_4h_PBMC

description: Peripheral blood mononuclear cells were isolated 4 hours after in vivo LPS challenge (LPS-induced systemic inflammation) and scRNA-seq libraries were prepared using 10X single cell 3' (v3.1) method.


title: Subject1_Day7_PBMC


title: Subject4_Day0_PBMC


title: Subject5_Day0_PBMC


title: Patient 11, lymph node tumor

city: Durham

first: Katherine

middle: Ismei

last: Zhou

state: NC

address: 2301 Erwin Rd

institute: Duke University

data_processing:
RNA-seq reads for clinical patient were mapped to the human genome (build hg38) using STAR (v2.7.11b)  (PMCID:PMC3530905)  to generate bam files.
Samtools (v1.9a) (PMCID: PMC2723002) were used to sort the bam files.
Assembly: build hg38 (Ensembl)
Supplementary files format and content: quant.sf (read count)

source_name: lymph node

extract_protocol:
Total RNA was extracted from 10 mg of snap-frozen tissue on a KingFisher Flex instrument (Thermo Scientific, 5400610) using the MagMAX mirVana total RNA isolation kit (Applied Biosystems, A27828).
Nucleic acid quantification was performed on a Qubit Flex Fluorometer (Thermo Scientific, Q33327) using the Qubit RNA broad range assay (Invitrogen, Q10211), and RNA quality was evaluated on a TapeStation 4200 instrument (Agilent, G2991AA) by RNA ScreenTape Analysis (Agilent, 5067-5576). Libraries were prepared from 1 µg of total RNA on a Hamilton NGS STAR instrument using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, 20020599). Library quantification was performed on a Qubit 3.0 Fluorometer (Thermo Scientific, Q33216) using the Qubit 1X dsDNA broad range assay (Invitrogen, Q33266). Library quality was evaluated on a TapeStation 4200 instrument (Agilent, G2991AA) by DNA ScreenTape Analysis (Agilent, 5067-5582).

tag: subject

value: Patient 11

value: lymph node


title: EC_biol_rep_3

description:
Library name: EC3
column name in Processed data files: EC3


title: Patient 22, breast tumor

source_name: breast tumor

value: Patient 22

value: breast tumor


title: Patient 25, lymph node tumor

value: Patient 25


title: Patient 2, lymph node tumor

value: Patient 2


title: Subject5_4h_PBMC


title: Subject1_4h_PBMC


title: Patient 24, breast tumor

value: Patient 24


title: Patient 14, breast tumor

value: Patient 14


title: Patient 29, lymph node tumor

value: Patient 29


title: Patient 17, lymph node tumor

value: Patient 17


title: Patient 23, breast tumor

value: Patient 23


title: Patient 28, lymph node tumor

value: Patient 28


title: Patient 4, lymph node tumor

value: Patient 4


title: Patient 22, lymph node tumor


title: Patient 9, lymph node tumor

value: Patient 9


title: Patient 16, lymph node tumor

value: Patient 16


title: Patient 27, breast tumor

value: Patient 27


title: Patient 16, breast tumor


title: Patient 21, lymph node tumor

value: Patient 21


title: Patient 25, breast tumor


title: Patient 5, lymph node tumor

value: Patient 5


title: Patient 19, breast tumor

value: Patient 19


title: Patient 18, lymph node tumor

value: Patient 18

value: lymph node


title: Patient 20, breast tumor

value: Patient 20

value: breast tumor


title: Patient 29, breast tumor


title: Patient 20, lymph node tumor


title: Patient 24, lymph node tumor

value: Patient 24


title: Patient 14, lymph node tumor

value: Patient 14


title: Patient 3, breast tumor

value: Patient 3


title: Patient 2, breast tumor

value: Patient 2


title: Patient 12, lymph node tumor

value: Patient 12


title: Patient 5, breast tumor


title: Patient 11, breast tumor

value: Patient 11


title: Patient 1, breast tumor

value: Patient 1


title: Patient 8, breast tumor

value: Patient 8


title: Patient 4, breast tumor

value: Patient 4


title: Patient 15, lymph node tumor

value: Patient 15


title: split ePE3 at multiple endogenous sites- Repeat 1- I2

description:
Library name: split_ePE3-multi.R1.I2
Rep 1- I2
vitro_processed_ePE3.xlsx

value: HEK293T cell

value: human embryonic kidney cells

value: WT

value: split ePE3 at multiple endogenous sites


title: Patient 12, breast tumor


title: Patient 3, lymph node tumor

value: lymph node


title: Patient 18, breast tumor

value: Patient 18


title: Patient 21, breast tumor

value: Patient 21

value: breast tumor


title: Patient 8, lymph node tumor