title: VPR-1

type: RNA

city: changsha

first: Huaying

last: Zhou

address: Renming ROAD 139

institute: Central south university

description:
THP1 macrophage after vpr treatment
The experimental group：THP1 macrophage after vpr treatment； Control:THP1 and THP1 macrophage

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: a promonocytic cell line derived from a human acute monocytic leukemia patient

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

extract_protocol: On average, 9 samples (3 THP1, 3 THP1 macrophage, and 3 THP1 macrophage after vpr treatment) were prepared for the extraction of total RNA, RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer (Additional fees apply).

value: macrophage


title: VPR-3

status: Public on Aug 16 2022

country: China

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mR

scan_protocol: scanned with using the Agilent DNA Microarray Scanner

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: epithelium_36_13

type: SRA

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

library_source: transcriptomic

data_processing:
Trimmomatic, version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50
hisat2
htseq-count, version 0.6.0, parameters: --stranded=reverse --secondary-alignments=ignore
removal of features with less then 32 counts based on the sum of normalized counts across all samples
DESeq2, version 1.26.0, vst normalization
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized count matrix

source_name: primary nasal epithalial cells

growth_protocol: Nasal epithelial cells obtained from patients were cultured in air-liquid interface (ALI) conditions for 21 days. Macrophages and DCs were obtained from peripheral blood monocytes (PBMC) isolated from a blood sample by Lymphoprep. Monocyte derived macrophages were specialized by 20 ng/ml M-CSF  stimulation for 10 days and monocyte derived DCs by cultivation in combination of 40 ng/ml GM-CSF, 20 ng/ml IL-4 for 8 days and 50 ng/ml TNF-α and 50 ng/ml IL-1β, in 6th  day of specialization.

extract_protocol:
Total RNA were then isolated by TRIzol method and further purified on collumns. 250 ng of intact total RNA was subjected to heat fragmentation (94°C, 5 min or  85°C, 6 min for partially degraded samples) and TruSeq Unique dual index adapters (Illumina, USA) were used.
Twelve cycles of library amplification was applied. Size distribution of final libraries were validated using Agilent Bioanalyzer 2100 and High Sensitivity DNA kit (Agilent, USA). Final library concentration was determined by qPCR using Kapa Library Quantification kit (Roche, Switzerland).

treatment_protocol: Macrophages were treated with UPM (200µg/ml) into the culture medium for 24 hours before the preparation of tri-culture. Co-cultures were additionally exposed to 100 μg/ml of UPM suspension for 24 hours.

tag: disease

value: asthma

tag: culture

value: monoculture

tag: agent

value: untreated


title: PMA-2

description:
THP1 macrophage
The experimental group：THP1 macrophage after vpr treatment； Control:THP1 and THP1 macrophage


title: PMA-3


title: VPR-2


title: E14-NT

city: Camperdown

first: Pengyi

last: Yang

address: The University of Sydney

country: Australia

institute: The University of Sydney

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using STAR (v2.5.4b) with following parameters: --outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMismatchNmax 3 --alignIntronMax 1. Bowtie output were converted into Bed format.  Genome_build: mm9  Supplementary_files_format_and_content: The bed file contains chromosom name, start coordinate on the chromosome, end coordinate on the chromosome and the DNA strand orientation.
Genome_build: mm9
Supplementary_files_format_and_content: The bed file contains chromosom name, start coordinate on the chromosome, end coordinate on the chromosom and the DNA strand orientation.

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cell

growth_protocol: Embryonic stem cells were cultured at 37°C, 5% CO2, in DMEM (GIBCO) with supplemented with 15% ESC-qualified fetal bovine serum (GIBCO), 0.1 mM 2-mercaptoethanol, 1mM nonessential amino acids, and 1,000 U/ml of LIF (Millipore). For cell maintenance, ESCs were cultured in the serum-free ESGRO medium (Millipore).

extract_protocol:
Lentivirus transduced ESCs were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop the fixation. Cells were then harvested, and DNA was fragmented to 300–500 base pairs (bp) by sonication with Scientz08-III sonicator (SCIENTZ). Immunoprecipitation was performed with antibodies (Pol II, Santa Cruz, sc-47701) conjugated to Dynabeads protein A/G beads (Pierce). The ChIPped DNA was eluted, reverse-cross-linked, extracted by AMPure XP beads (Beckman).
Libraries were prepared according to the instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Briefly, DNA was end-repaired and treated with Klenow fragment to yield a protruding 3- 'A' tail for ligation of Illumina's adapters.Then, DNA was amplified with Illumina primers for 13 cycles using PCR. PCR products were purified with AMPure XP beads (Beckman). The libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: For virus production, shRNA constructs were cotransfected with the envelope plasmid pMD2.G (Addgene) and the packing vector psPAX2 (Addgene) using lipofiter reagents (Hanbio). Viruses were harvested 48 h after transfection and tittered by colony formation assay. Then, the viruses were used to transduce E14 ESCs.

value: mouse embryonic stem cell line

tag: cell line

tag: chip antibody

value: Anti-Pol II Antibody (CTD4H8):sc-47701

tag: treatment

value: nontarget shRNA Virus transduced


title: PMA-1


title: Z-138_MIGR1_Control_rep1

city: new york

first: Michael

last: Kharas

state: New York

address: 417 68th street

department: Molecular Pharmacology Program

country: USA

institute: Mamorial Sloan Kettering Cancer Center

data_processing:
The paired-end RNA-seq reads to human (hg19) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: hg19
Supplementary_files_format_and_content: Sample_MIGR1-GSK591-_vs.over_Sample_MIGR1-Control-_snp_counts_significance, Sample_MIGR1-GSK591Ro-_vs.over_Sample_MIGR1-Control-_snp_counts_significance and Sample_MIGR1-Ro-_vs.over_Sample_MIGR1-Control-_snp_counts_significance files include strand, entrez id, gene symbol, annotation, reference nucleotide, alternative nucleotide (edited nucleotide) for each RNA-seq library and p value, adjusted p value, number of edit sites per gene, fpkm in each sample for edited genes

source_name: Z-138 cells

growth_protocol: Z-138 cells (obtained from ATCC) were cultured in IMDM 10% Horse serum 1%L-Glutamine PenStrep.

extract_protocol:
0.5 million of sorted cells per sample were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform
After PicoGreen quantification and quality control by Agilent BioAnalyzer, 1ug RNA input was used for library preparation (TrueSeq Stranded mRNA LT Sample Prep Kit)

treatment_protocol: Cells were infected with virus expressing MIG (empty vector) at 1:1 ratio (v/v) cell: virus at 0.5 million and treated with 5uM Ro or GSK-591 or combination for 24h

value: Z-138 cells

value: Mantle cell lymphoma cell line

tag: overexpression

value: Overexpressing empty vector

tag: time point

value: 48hr after retrovirus transduction

value: Treated with DMSO for 24hr


title: C3

description:
THP1
The experimental group：THP1 macrophage after vpr treatment； Control:THP1 and THP1 macrophage


title: RNAseq-CkoCT442-TAF5Lsg2-7-IAA-R2-T1

status: Public on Aug 15 2022

city: Worcester

first: Anne-Laure

last: Valton

state: MA

address: 368 Plantation St

institute: University of Massachusetts Medical School

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
merged_clones_TPM_genes.tsv
genes_expression_expected_count_clones.tsv

data_processing:
RNA-seq data was mapped using a standardized pipeline in the DolphinNext environment (Yukselen O., Turkyilmaz O., Ozturk A.R., Garber M., Kucukural A. DolphinNext: a distributed data processing platform for high throughput genomics. BMC Genomics 21, 310 (2020). https://doi.org/10.1186/s12864-020-6714-x).
Reads were mapped to hg19 using STAR (Dobin et al., 2013) with default parameters to generate BAM files. RSEM was used for transcript quantification (Li and Dewey, 2011).
Differentially Expressed genes were obtained using DESeq2 on the DEBrowser interface (Kucukural et al., 2019)
Genome_build: hg19 human genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Bigwig

source_name: HAP1 cells

growth_protocol: HAP1 cells (and the derived cells lines) were cultured at 37C with 5% CO2 in IMDM GlutaMAX™ Supplement (Gibo, 31980097) with 10% FBS (Gibco, 16000069), 1% Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, 74104) with QIAshredder (Qiagen, 79654).
Total RNA was sent to the BGI Hong Kong facility (DNBseq Eukaryotic Transcriptome resequencing) for library preparation
Libraries were sequenced at the BGI Hong Kong facility on DNBseq platform (pair-ends 100bp).

treatment_protocol: For auxin treatment: 500uM auxin. For siRNA treatment: 40nM for 72H.

value: auxin

tag: genotype

value: endogenous CTCF KO, CTCF-AID, TIR1, TAF5L KO


title: RNAseq-CkoCT442-TAF5Lsg2-7-IAA-R1-T1


title: RNAseq-CkoCT442-TAF5Lsg2-3-IAA-R2-T1


title: RNAseq-CkoCT442-TAF5Lsg2-3-IAA-R1-T1


title: Z-138_MIGR1_Control_rep3


title: WT1_No

city: Kunigami-gun

first: Mohieldin

last: Youssef

state: Okinawa

address: 1919-1 Tancha

department: Cell Signal Unit

country: Japan

institute: Okinawa Institute of Science and Technology

description: WT without fear conditioing

data_processing:
fastq files were analyzed by RNA-seq analysis pipeline nf-core 2.0, alignment by STAR 2.6.1d
Counting by Htseq 0.9.0 using OmicsBox 1.4.11
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited .txt file containing raw gene counts for different time points and two genotypes (WT and Tob KO) in triplicates

source_name: Brain

extract_protocol:
Total RNA was purified from mouse hippocampi tissues using Isogen II reagent (Nippon Gene).
Intact poly(A) RNA was purified from 1 µg of total RNA using an NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA) and following the manufacturer’s protocol. Library preparation was performed using NEBNext® Ultra II Directional RNA Library Prep Kits for Illumina (New England Biolabs, USA), according to the manufacturer’s protocol with 8 PCR cycles. Library sizes were checked using microfluidic-based electrophoresis LabChip GX Touch (Perkin Elmer, USA) and concentrations were checked using Qubit 1X dsDNA HS (ThermoFisher, USA) and then pooled after concentration adjustment. 150-bp paired-end RNA sequencing was performed using a NovaSeq 6000 SP flow cell (Illumina, USA).

tag: strain

tag: tissue

value: Brain

value: WT

tag: protocol


title: RNAseq-CkoCT442-TAF5Lsg2-7-NT-R2-T1

value: non-treated


title: RNAseq-CkoCT442-TAF5Lsg2-3-NT-R1-T1


title: RNAseq-CkoCT442-DDX55sg2-7-IAA-R2-T1

value: endogenous CTCF KO, CTCF-AID, TIR1, DDX55 heterozygous KO


title: RNAseq-CkoCT442-TAF5Lsg2-3-NT-R2-T1


title: RNAseq-CkoCT442-DDX55sg2-7-IAA-R1-T1


title: RNAseq-CkoCT442-DDX55sg2-7-NT-R2-T1


title: RNAseq-CkoCT442-DDX55sg2-B-IAA-R1-T1


title: RNAseq-CkoCT442-TAF5Lsg2-7-NT-R1-T1


title: C1

value: macrophage


title: RNAseq-CkoCT442-DDX55sg2-7-NT-R1-T1


title: RNAseq-CkoCT442-DDX55sg2-B-IAA-R2-T1


title: C2


title: RNAseq-CkoCT442-DDX55sg2-B-NT-R1-T1


title: RNAseq-CkoCT442-DDX55sg2-B-NT-R2-T1


title: RNAseq-CkoCT442-AAVS1sg2-4-IAA-R1-T1

value: endogenous CTCF KO, CTCF-AID, TIR1, AAVS1 locus mutation


title: RNAseq-CkoCT442-AAVS1sg2-4-NT-R2-T1


title: RNAseq-CkoCT442-AAVS1sg2-4-IAA-R2-T1


title: RNAseq-CkoCT442-si-TAF5L-IAA-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
merged_si_TPM_genes.tsv
genes_expression_expected_count_si.tsv

value: endogenous CTCF KO, CTCF-AID, TIR1


title: RNAseq-CkoCT442-si-TAF5L-IAA-R2-T1


title: RNAseq-CkoCT442-si-DDX55-IAA-R1-T1


title: RNAseq-CkoCT442-si-TAF5L-NT-R1-T1


title: RNAseq-CkoCT442-si-CTRL-IAA-R1-T1


title: RNAseq-CkoCT442-si-DDX55-NT-R2-T1


title: RNAseq-CkoCT442-si-DDX55-NT-R1-T1


title: RNAseq-CkoCT442-si-CTRL-NT-R2-T1


title: RNAseq-CkoCT442-si-CTRL-NT-R1-T1


title: RNAseq-CkoCT442-NT-R1-T1


title: RNAseq-CkoC44-IAA-R2-T1

value: endogenous CTCF KO, CTCF-AID


title: RNAseq-CkoC44-NT-R2-T1


title: RNAseq-CkoC44-IAA-R1-T1


title: RNAseq-CkoCT442-IAA-R2-T1


title: specific pathogen free

city: Toronto

first: Derek

middle: Ka Long

last: Tsang

state: Ontario

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

data_processing:
Data is read into Seurat with 1 minimum cell and 200 minimum genes and subsequently converted in scater for quality control and filtering based on lirary size, feature size and percentage of mitochondrial genes. Furthermore, normalization steps are performed and then the normalized data is transported back to Seurat. In Seurat, data is scaled and dimesion reduction, cluster identification, PCA and tSNE are performed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix in .mtx format generated by cellranger filtered_bc_matrices, barcodes.tsv, genes.tsv

source_name: small intestine

extract_protocol:
To isolate single cells, whole epithelial segments or crypts were washed in PBS prior to adding fresh prewarmed Trypsin (Corning, USA) and incubated at 37°C for 50 minutes, with mixing every 20 minutes. Tissues were filtered through a 40 mm mesh cell strainer on ice and pelleted by centrifugation at 4°C and washed twice with ice cold regular medium to remove debris. A manually estimated 4500 single cells per sample were then subjected to 10X Genomics single cell RNA sequencing following manufacturer’s recommendations. Illumina HiSeq 3000 was used for deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small intestine epithelium

tag: microbiota state

value: specific pathogen free


title: RNAseq-CkoCT442-AAVS1sg2-4-NT-R1-T1


title: RNAseq-CkoCT442-IAA-R1-T1


title: germ free

value: germ free


title: DNA Polymerase 1 alpha_BC3_Hypoxia

city: Philadelphia

first: Erle

middle: S

last: Robertson

state: Pennsylvania

address: Johnson Pavilion, 3610 Hamilton Walk

department: Otorhinolaryngology

institute: University of Pennsylvania

data_processing:
Basecalls were performed using CLC Bio software
ChIP-seq reads were aligned with KSHV genome using CLCBio software

source_name: cell line

growth_protocol: KSHV positive BC3 cells were routinely grown in RPMI medium supplemented with 10%fetal bovine serum in a cell culture incubator at 37 degree centigrade and 5% CO2.

extract_protocol:
Cells were harvested by centrifugation and washed by resuspending them in PBS. Washed cells were lysed in hypotonic lysis buffer followed by passing through syringe and centrifugation to isolate nuclei. Isolated nuclei were resuspended in detergent containing buffer to lyse the membrane followed by sonication for fragmentation of chromatin. size of fragmented chromatin was estimated by runnig on agarose gel.
Libraries were prepared according to Illumina's instructions using ChIP sequencing sample preparation kit following the manufacturer's protocols.

treatment_protocol: Hypoxic induction was provided by growing the cells in hypoxic chamber with 1% oxygen setting. The culture medium composition remain same as that of cells grown under normoxic conditions.

value: cell line

value: Human Blood B-Cells

value: DNA Polymerase 1 alpha

value: Hypoxia


title: RNAseq-CkoCT442-si-TAF5L-NT-R2-T1


title: RTA_BC3_Normoxia

value: RTA


title: RNAseq-CkoCT442-si-CTRL-IAA-R2-T1

value: auxin


title: LANA_BC3_Normoxia

value: LANA


title: H3K27Me3_BC3_Hypoxia


title: RTA_BC3_Hypoxia


title: H3K27Me3_BC3_Normoxia


title: H3K4Me3_BC3_Hypoxia


title: H3K9Me3_BC3_Normoxia


title: H3K9Me3_BC3_Hypoxia


title: H3K4Me3_BC3_Normoxia


title: H3-Ac_BC3_Hypoxia


title: H3-Ac_BC3_Normoxia


title: RNAseq-CkoCT442-NT-R2-T1


title: RNAseq-CkoC44-NT-R1-T1


title: DNA Polymerase 1 alpha_BC3_Normoxia


title: LANA_BC3_Hypoxia


title: W854,cerebellum,dup-wt

city: Boston

first: Serkan

last: Erdin

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description:
Data Set 3-Batch 5
16p11.2_mouse_counts.txt.gz

data_processing:
Each bulk RNAseq library of mouse sample was aligned to mouse reference genome GRCm38 version 83 using STAR aligner. Expression counts for each sample was also generated by STAR aligner.
Differential expression analysis was performed by DESeq2 + SVA pipeline, whereas co-expression analysis was performed by WGCNA.
Each bulk RNAseq library of human cell line sample was aligned to human reference genome GRCh37 version 75 using STAR aligner. Expression counts for each sample was also generated by STAR aligner.
For scRNA, raw paired-end reads were aligned by Cellranger (v3.0.2) against human transcriptome GRCh38.92.
For each scRNA sample, its feature list, barcode list and count matrix were then read by Seurat (v4.0.3) into matrix. Cells with top and bottom 2.5% number of RNA molecules were filtered out.
All scRNA samples were then merged into one matrix using "merge" function in Seurat.
Assembly: single cell human reference genome GRCh38 v92; mouse reference genome for bulk RNAseq GRCm38 v83. human reference genome for bulk RNAseq GRCh37 v75.
Supplementary files format and content: "rawCounts_merged_16p_Organoid_GM08330.txt.gz" - gzipped text file for raw counts of scRNA data. Each row represents a gene while each column represents a cell. Outlier cells have been filtered out and not included.
Supplementary files format and content: "16p11.2_KCTD13_cellLines_counts.txt.gz" - gzipped tab delimited text file for raw counts of human cell line bulk RNAseq data including 16p11.2 deletion, 16p11.2 duplication and 16p11.2 wild-type NSCs and iNeurons as well as KCTD13 het del and KCTD13 wild-type iNeurons
Supplementary files format and content: "16p11.2_KCTD13_cellLines_metadata.txt" - metadata of bulk RNAseq data from human cell lines
Supplementary files format and content: "metaData_SCT_merged_16p_Organoid_GM08330.txt" - text file for scRNA meta-data.
Supplementary files format and content: "16p11.2_mouse_counts.txt.gz" - tab delimited text file for raw counts of mouse bulk RNAseq data.

molecule: polyA RNA

source_name: cerebellum

growth_protocol: NSCs were maintained in PSC Neural Expansion Medium (ThermoFisher, A1647801) in humidified atmosphere with 5% CO2 at 37C; iNs were maintained in Neural Maintenance Media (Shi et al., 2012) supplemented with BDNF and NT-3 in humidified atmosphere with 5% CO2 at 37C; cerebral organoids were maintained in organoid medium (Lancaster et al., 2014) supplemented with BDNF in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
All RNA samples were extracted with Trizol reagent according to the manufacturer’s instruction (Invitrogen).
Mouse and human cell RNASeq libraries were prepared with customized version of strand specific dUTP method and TruSeq Stranded mRNA Library Kit (Illumina); scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (PN-1000075) according to manufacturer’s instructions (CG000183) using a Chromium Single Cell B Chip (PN-1000073) for a targeted cell recovery of 5,000 cells.
RNAseq for mouse tissues and human NSCs and iNs; single-cell RNAseq for cerebral organoids

treatment_protocol: For all CRISPR lines, Passage 7 stage NSCs were dissociated for RNA-seq; iNs were dissociated for RNA-seq on Day 24 of differentiation; For single-cell suspensions of cerebral organoids, organoids at 6 months were prepared using the Worthington Papain Dissociation System (Worthington Biochemical, LK003153).

value: cerebellum

value: dup-wt

tag: Sex

value: M


title: W854,striatum,dup-wt

source_name: striatum

value: striatum


title: W853,striatum,dup-wt


title: W853,cortex,dup-wt

source_name: cortex

value: cortex


title: W852,cerebellum,dup-wt


title: W854,cortex,dup-wt


title: W852,striatum,dup-wt


title: W852,cortex,dup-wt


title: W853,cerebellum,dup-wt


title: W851,cerebellum,dup-wt


title: W851,striatum,dup-wt


title: W850,striatum,dup-wt


title: W851,cortex,dup-wt


title: W849,cerebellum,dup-wt


title: W849,cortex,dup-wt


title: W850,cortex,dup-wt


title: W850,cerebellum,dup-wt


title: W848,cortex,dup-wt


title: W848,striatum,dup-wt


title: W849,striatum,dup-wt


title: W847,striatum,dup-wt

value: F


title: W847,cortex,dup-wt


title: W847,cerebellum,dup-wt


title: W846,cortex,dup-wt


title: W846,striatum,dup-wt


title: W846,cerebellum,dup-wt


title: W845,striatum,dup-wt


title: W845,cortex,dup-wt


title: W845,cerebellum,dup-wt


title: W844,striatum,dup-wt


title: W843,cerebellum,dup-wt


title: W842,striatum,dup-wt


title: W843,cortex,dup-wt


title: W844,cortex,dup-wt


title: W844,cerebellum,dup-wt


title: W843,striatum,dup-wt


title: W842,cortex,dup-wt


title: RNAseq-CkoCT442-si-DDX55-IAA-R2-T1

value: endogenous CTCF KO, CTCF-AID, TIR1


title: W841,cortex,dup-wt


title: W841,striatum,dup-wt


title: W848,cerebellum,dup-wt


title: W840,striatum,dup-wt


title: W840,cerebellum,dup-wt


title: W842,cerebellum,dup-wt


title: W841,cerebellum,dup-wt


title: W840,cortex,dup-wt


title: W827,cortex,dup-wt


title: W826,striatum,dup-wt


title: W827,cerebellum,dup-wt


title: W826,cerebellum,dup-wt


title: W826,cortex,dup-wt


title: W827,striatum,dup-wt


title: W825,striatum,dup-wt


title: W824,striatum,dup-wt


title: W825,cerebellum,dup-wt


title: W824,cortex,dup-wt


title: W825,cortex,dup-wt


title: Dp839,striatum,dup

value: dup


title: Dp839,cortex,dup


title: W824,cerebellum,dup-wt


title: Dp839,cerebellum,dup


title: Dp838,striatum,dup


title: Dp838,cerebellum,dup


title: Dp838,cortex,dup


title: Dp837,striatum,dup


title: Dp836,striatum,dup


title: Dp837,cerebellum,dup


title: Dp837,cortex,dup


title: Dp836,cortex,dup


title: Dp835,striatum,dup


title: Dp834,cortex,dup


title: Dp835,cortex,dup


title: Dp835,cerebellum,dup


title: Dp834,cerebellum,dup


title: Dp836,cerebellum,dup


title: Dp834,striatum,dup


title: Dp833,cerebellum,dup


title: Dp832,striatum,dup


title: Dp833,cortex,dup


title: Dp831,striatum,dup


title: Dp833,striatum,dup


title: Dp831,cortex,dup


title: Dp832,cortex,dup


title: Dp830,striatum,dup


title: Dp832,cerebellum,dup


title: Dp830,cerebellum,dup


title: Dp829,striatum,dup


title: Dp829,cortex,dup


title: Dp830,cortex,dup


title: Dp829,cerebellum,dup


title: Dp828,cortex,dup


title: Dp823,cortex,dup


title: Dp822,striatum,dup


title: Dp828,striatum,dup


title: Dp828,cerebellum,dup


title: Dp823,cerebellum,dup


title: Dp822,cerebellum,dup


title: Dp822,cortex,dup


title: Dp821,cerebellum,dup


title: Dp821,cortex,dup


title: Dp820,cortex,dup


title: Dp820,cerebellum,dup


title: Dp831,cerebellum,dup


title: Dp819,striatum,dup


title: Dp819,cortex,dup


title: Dp818,cerebellum,dup


title: Dp818,striatum,dup


title: Dp817,striatum,dup


title: Dp817,cerebellum,dup


title: Dp817,cortex,dup


title: W816,striatum,del-wt

description:
Data Set 3-Batch 4
16p11.2_mouse_counts.txt.gz

value: del-wt


title: Dp823,striatum,dup


title: W816,cortex,del-wt


title: W815,striatum,del-wt


title: W816,cerebellum,del-wt


title: W814,striatum,del-wt


title: W814,cortex,del-wt


title: W815,cortex,del-wt


title: Dp821,striatum,dup


title: W814,cerebellum,del-wt


title: W815,cerebellum,del-wt


title: W813,striatum,del-wt


title: Dp820,striatum,dup


title: W808,cortex,del-wt


title: W813,cerebellum,del-wt


title: W807,cortex,del-wt


title: W807,striatum,del-wt


title: W808,cerebellum,del-wt


title: W813,cortex,del-wt


title: Dp818,cortex,dup


title: W806,striatum,del-wt


title: Dp819,cerebellum,dup


title: W808,striatum,del-wt


title: W806,cortex,del-wt


title: W807,cerebellum,del-wt


title: W805,striatum,del-wt


title: W805,cerebellum,del-wt


title: D812,striatum,del

value: del


title: W806,cerebellum,del-wt


title: D812,cortex,del


title: D811,striatum,del


title: D812,cerebellum,del


title: D811,cortex,del


title: D810,striatum,del


title: D810,cortex,del


title: D810,cerebellum,del


title: D811,cerebellum,del


title: D809,striatum,del


title: D809,cortex,del


title: D809,cerebellum,del


title: D804,cortex,del


title: D803,striatum,del


title: D802,cortex,del


title: D804,striatum,del


title: D803,cortex,del


title: D804,cerebellum,del


title: D803,cerebellum,del


title: D802,striatum,del


title: D802,cerebellum,del


title: D801,cortex,del


title: D801,cerebellum,del


title: t1994liv,liver,del

description:
Data Set 1-Batch 2
16p11.2_mouse_counts.txt.gz

source_name: liver

value: liver


title: W805,cortex,del-wt


title: t1993liv,liver,del


title: t1993bfat,brown fat,del

source_name: brown fat

value: brown fat


title: t1993wfat,white fat,del

source_name: white fat

value: white fat


title: t1992liv,liver,del


title: t1991wfat,white fat,del


title: t1992bfat,brown fat,del


title: t1991liv,liver,del


title: t1991bfat,brown fat,del


title: t1990bfat,brown fat,del-wt


title: t1990liv,liver,del-wt


title: t1989liv,liver,del-wt


title: D801,striatum,del


title: T1994wfat,white fat,del


title: t1988wfat,white fat,del-wt


title: t1989bfat,brown fat,del-wt


title: t1988liv,liver,del-wt


title: t1988bfat,brown fat,del-wt


title: t1987liv,liver,del-wt


title: t1987bfat,brown fat,del-wt


title: T1994bfat,brown fat,del


title: t1986liv,liver,dup


title: t1986bfat,brown fat,dup


title: t1985liv,liver,dup


title: t1985wfat,white fat,dup


title: t1992wfat,white fat,del


title: t1985bfat,brown fat,dup


title: t1984wfat,white fat,dup


title: t1984bfat,brown fat,dup


title: t1984liv,liver,dup


title: t1983wfat,white fat,dup


title: t1990wfat,white fat,del-wt


title: t1983liv,liver,dup


title: t1989wfat,white fat,del-wt


title: t1983bfat,brown fat,dup


title: t1982liv,liver,dup-wt


title: t1981bfat,brown fat,dup-wt


title: t1981wfat,white fat,dup-wt


title: t1986wfat,white fat,dup


title: t1982bfat,brown fat,dup-wt


title: t1980wfat,white fat,dup-wt


title: t1980liv,liver,dup-wt


title: w1516,striatum,wt

description:
Data Set 2-Batch 3
16p11.2_mouse_counts.txt.gz

value: wt


title: t1981liv,liver,dup-wt


title: t1980bfat,brown fat,dup-wt


title: t1979liv,liver,dup-wt


title: t1987wfat,white fat,del-wt


title: w1514,cortex,wt


title: w1515,cortex,wt


title: w1515,cerebellum,wt


title: w1516,cerebellum,wt


title: w1515,striatum,wt


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title: w1513,striatum,wt


title: w1514,striatum,wt


title: w1513,cortex,wt


title: w1514,cerebellum,wt


title: t1982wfat,white fat,dup-wt


title: w1513,cerebellum,wt


title: w1511,striatum,wt


title: w1511,cortex,wt


title: w1510,striatum,wt


title: w1511,cerebellum,wt


title: w1510,cortex,wt


title: w1510,cerebellum,wt


title: w1509,striatum,wt


title: t1979wfat,white fat,dup-wt


title: w1509,cerebellum,wt


title: w1509,cortex,wt


title: w1508,striatum,wt


title: t1979bfat,brown fat,dup-wt


title: w1508,cortex,wt


title: w1507,cerebellum,wt


title: w1506,striatum,wt


title: w1507,cortex,wt


title: w1506,cerebellum,wt


title: w1506,cortex,wt


title: w1504,cortex,wt


title: w1505,striatum,wt


title: w1505,cortex,wt


title: w1504,cerebellum,wt


title: w1504,striatum,wt


title: w1503,cerebellum,wt


title: w1505,cerebellum,wt


title: w1501,striatum,wt


title: w1503,cortex,wt


title: w1502,cerebellum,wt


title: w1503,striatum,wt


title: w1501,cortex,wt


title: w1502,cortex,wt


title: w1501,cerebellum,wt


title: w1216,cortex,dup-wt


title: w1215,striatum,dup-wt


title: w1216,cerebellum,dup-wt


title: w1215,cortex,dup-wt


title: w1215,cerebellum,dup-wt


title: w1216,striatum,dup-wt


title: w1508,cerebellum,wt


title: w1214,striatum,dup-wt


title: w1507,striatum,wt


title: w1214,cortex,dup-wt


title: w1213,cortex,dup-wt


title: w1213,striatum,dup-wt


title: w1213,cerebellum,dup-wt


title: w1212,cerebellum,dup-wt


title: w1212,cortex,dup-wt


title: w1212,striatum,dup-wt


title: w1502,striatum,wt


title: w1211,cerebellum,dup-wt


title: w1210,striatum,dup-wt


title: w1210,cerebellum,dup-wt


title: w1210,cortex,dup-wt


title: w1209,striatum,dup-wt


title: w1209,cerebellum,dup-wt


title: w1209,cortex,dup-wt


title: w1211,striatum,dup-wt


title: w1211,cortex,dup-wt


title: w1207,cortex,dup


title: w1207,cerebellum,dup


title: w1206,cortex,dup


title: w1206,cerebellum,dup


title: w1205,striatum,dup


title: w1205,cortex,dup


title: w1208,striatum,dup


title: w1214,cerebellum,dup-wt


title: w1205,cerebellum,dup


title: w1207,striatum,dup


title: w1208,cortex,dup


title: w1204,striatum,dup


title: w1204,cortex,dup


title: w1204,cerebellum,dup


title: w1203,striatum,dup


title: w1202,cortex,dup


title: w1203,cortex,dup


title: w1202,cerebellum,dup


title: w1201,striatum,dup


title: w1201,cortex,dup


title: w1208,cerebellum,dup


title: w1201,cerebellum,dup


title: t1994,striatum,del

description:
Data Set 1-Batch 1
16p11.2_mouse_counts.txt.gz


title: t1993,cerebellum,del


title: T1993,cortex,del


title: T1992,cortex,del


title: t1991,striatum,del


title: T1991,cortex,del


title: t1992,cerebellum,del


title: t1992,striatum,del


title: T1989,cortex,del-wt


title: T1990,cortex,del-wt


title: t1990,striatum,del-wt


title: t1989,cerebellum,del-wt


title: t1991,cerebellum,del


title: t1988,striatum,del-wt


title: w1202,striatum,dup


title: t1990,cerebellum,del-wt


title: T1988,cortex,del-wt


title: w1203,cerebellum,dup


title: T1987,cortex,del-wt


title: t1987,cerebellum,del-wt


title: t1987,striatum,del-wt


title: t1988,cerebellum,del-wt


title: T1986,cortex,dup


title: T1994,cortex,del


title: t1993,striatum,del


title: t1986,striatum,dup


title: t1985,striatum,dup


title: t1986,cerebellum,dup


title: T1985,cortex,dup


title: t1994,cerebellum,del


title: t1989,striatum,del-wt


title: t1985,cerebellum,dup


title: t1984,striatum,dup


title: T1984,cortex,dup


title: t1983,striatum,dup


title: T1982,cortex,dup-wt


title: t1982,striatum,dup-wt


title: t1981,striatum,dup-wt


title: t1984,cerebellum,dup


title: t1982,cerebellum,dup-wt


title: T1983,cortex,dup


title: t1983,cerebellum,dup


title: t1980,striatum,dup-wt


title: t1980,cerebellum,dup-wt


title: T1980,cortex,dup-wt


title: T1979,cortex,dup-wt


title: T1981,cortex,dup-wt


title: t1979,cerebellum,dup-wt


title: t1979,striatum,dup-wt


title: Vehicle_control_320

city: Chicago

first: Joshua

last: Meeks

state: Illinois

address: 302 E. Huron Street, Simpson Querrey Building, Room number: 7-500

department: Urology/BMG

institute: Northwestern University

data_processing:
Fastq files were processed using Ceto pipeline created by Dr. Elizabeth Bartom
Assembly: RNA sequence reads were aligned to reference genome using STAR (v 2.7.5). Gene expression was quantified using HTSeq and differential gene expression profiles were generated using DESeq2.
Supplementary files format and content: hg38 or mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: bladder

extract_protocol:
cells were harvested for RNA extraction. RNA was extracted using Qiagen RNeasy kit according to manufacturer instructions.
Libraries were prepared according to manufacturer’s protocol

treatment_protocol: UMUC3, UMUC9, HT1376 and 5637 cell-lines were treated with DMSO or EPZ011989 at a concentration of 5µM for 7 days.

value: bladder

value: C57BL/6 mice

value: Vehicle control


title: EZH2i_307


title: Vehicle_control_315


title: Vehicle_control_316


title: Vehicle_control_323


title: EZH2i_308


title: EZH2i_304


title: Vehicle_control_324


title: EZH2i_312


title: EZH2i_311


city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description:
FOS overexpressing isolated muscle satellite cells Hi-C Rep2
Combined_FOS_allValidPairs.hic

data_processing:
RNA-seq analysis (polyA) was performed by filtering and mapping the reads by Bowtie 2  (mm9), quantifying the transcripts by RSEM v1.2.29 . Differential gene expression was calculated using  DESeq2 by removing  genes with a gene count <10, and by using the mean value of gene-wise dispersion estimates. We defined differentially expressed genes as being changed > 0.5 log2 fold in expression with an adjusted p-value < 0.01 using the DEbrowser package (PMID: 30611200). Gene ontology (GO) analysis was performed using the FuncAssociate software version 3.0 (PMID: 19717575).
The resulting Hi-C sequencing reads were mapped (mm9), filtered, corrected and bined using the HiC-Pro software v2.8 (PMID: 26619908). There was a high eigenvector correlation among all the Hi-C biological replicates (average Pearson’s correlation R2 > 0.9), indicating the high quality and reproducibility of the datasets. Thus, we pooled all biological replicates for each condition and mapped, filtered, corrected and binned them as a single Hi-C dataset for all subsequent analyses. Genomic A/B compartments and TADs (insulation method) were defined and visualized using the cworld, HiGlass, and Juicebox toolkits (cworld toolkit codes available at: https://github.com/dekkerlab/cworld-dekker), (PMID: 27467249, 27467250, 30143029). We generated saddle plots, meta-TAD and meta-loop plots using the cooltools package (PMID: 31290943, 32003791). Compartment switching analysis was performed as previously described (PMID: 25693564). Differentially regulated looping interactions were determined using the hiccups algorithm from the juicer toolkit (PMID: 27467249).
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq gene count file (in tab-delimited txt format)
Supplementary_files_format_and_content: hic chromatin interaction file (that can be opened with juicebox (PMID:27467250)).
Supplementary_files_format_and_content: hic chromatin interaction file (that can be opened with juicebox (PMID:27467250)).

source_name: isolated muscle satellite cells

growth_protocol: Freshly isolated SCs were sorted into pre-coated, 96-well plates containing standard Growth Media (GM) consisting of 20% Donor Horse Serum (DHS), 1% Penicillin/Streptomycin, 1% GlutaMax, and  5 ng/mL of bFGF in F10 media. Plates were pre-coated for 24 hours with a solution containing Collagen Type 1 (1ug/ml final) and Laminin (10 ug/ml) in PBS. GM was refreshed every 48-72 hours, and cells were passaged by removing half the volume of GM and adding back 5 mM EDTA (to achieve a 2.5 mM final concentration), incubating for 20 minutes at 37°C, spinning at 1200 RPM, resuspending in fresh GM, counting, and seeding cells to new wells at desired densities. C2C12 cell lines (C2C12 ATCC CRL-1772) were purchased from ATCC, and cultured according to the manufacturer’s recommendations.

extract_protocol:
Total RNA was extracted from Gfp or Fos-expressing primary muscle progenitor cells using TRIzol followed by RNeasy Mini Qiagen extraction kit according to manufacturer’s protocol. In-situ Hi-C libraries were generated using the HindIII restriction enzyme (PMID: 22652625). Briefly, ~25 million cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Then, the chromatin was extracted, digested with HindIII, end-labelled with biotin-14-dCTP, followed by  in-situ ligation (EL0011, Thermo Fisher). After DNA extraction, biotin was removed from unligated ends, and the sample was sheared using a Covaris S220 instrument (100-500bp range) as previously described (PMID: 22652625). After A-tailing, biotin pull-down, and adapter ligation, we performed paired-end sequencing on Illumina’s HiSeq 2000 instrument.
RNA-seq libraries were generated using the Illumina TruSeq (version 2) kit and sequenced on the Illumina HiSeq2500 instrument.
RNA-seq libraries were prepared with polyA enrichment.

treatment_protocol: Primary muscle satellite cells (SCs) were isolated as previously reported in [12]. Briefly, hind-limb, abdominal, and tricep muscles were isolated from mice and digested in 0.2% collagenase type II (285 U/mg) in Dulbecco’s modified eagle medium (DMEM) for 90 minutes at 37°C. Single fibers were separated from digested muscle by trituration and enriched through several gravitational sedimentation steps at 37°C. Single fibers were digested in 0.0125% Collagenase type II/0.05% Dispase (1.81U/mg) in F10 for 30 minutes at 37°C to release mono-nuclear cells from the basal lamina of individual muscle fibers. The resulting cell suspension was spun (~500 rpm) to remove cellular debris, and then filtered through a 70-micron cell strainer. Cells were incubated on ice for 30 minutes with fluorescently-conjugated antibodies to detect the following antigens: anti-Ly6A/E-APC or anti-Ly6A/E-PE  (Sca-1) (1:200), anti-CD31-APC (1:200), anti-CD45-APC (1:200), CD11b-APC (Mac-1) (1:200), CD29-APC-Cy7 (β1-Integrin) (1:200), CD184-Biotin (CXCR4) (1:100). For CXCR4 detection, a secondary antibody, Streptavidin-PeCy7 (1:200), was incubated with the relevant samples for 20 minutes on ice. Stained cells were analyzed by FACS using the BD FACSAria III cell sorter. After gating on physical parameters and live cells (Propidium Iodide-negative/Calcein Blue-positive) [12], SCs were defined as the Sca1-; CD45-; CD11b-; Ter119- ; CD31- ; CD29+ (β1-Integrin); CD184+ (CXCR4) cell population.

value: FOS overexpression

value: Primary muscle satellite cells


description:
GFP overexpressing isolated muscle satellite cells Hi-C Rep2
Combined_GFP_allValidPairs.hic

value: GFP overexpression


description:
FOS overexpressing isolated muscle satellite cells Hi-C Rep1
Combined_FOS_allValidPairs.hic


title: EZH2i_303


title: t1981,cerebellum,dup-wt

value: cerebellum

value: dup-wt

value: M


description:
GFP overexpressing isolated muscle satellite cells Hi-C Rep1
Combined_GFP_allValidPairs.hic


title: LSW_89

city: London

first: Thu

middle: Hong

last: Le

address: Gower Street

country: United Kingdom

institute: UCL

data_processing:
alignment reads to the reference to generate the BAM files, using STAR
sort the raw bam files and mark duplications using Picard
assemble the GTF reference file based on your BAM files using CUFFLINK and CUFFMERGE
estimate the gene counts and then calculate the RPKMs using featureCounts and DESeq2
normalize the RPKMs of each gene and detect the significant different expression genes [using DESeq2]
Assembly: Rn6.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Liver cells

extract_protocol:
Liver tissue were dissected, and then snap-frozen. RNA was extracted using Trizol
Library preps were created using Illumina kits and run on an Illumina HiSeq 2500 to obtain 37bp paired-end reads for liver

tag: age

value: 17 weeks


title: LSW_44


title: LSW_295


title: LSW_292


title: LSW_294


title: LSW_8


title: LSW_6


title: LSW_421


title: LSW_40


title: LSW_290


title: LSW_31


title: LSW_291


title: LSW_296


title: LSW_86


title: LSW_257


title: LSW_276


title: LSW_107


title: LSW_450

tag: sample_common_id_with adipose_tissue


title: LSW_449


title: LSW_447


title: LSW_201


title: LSW_441


title: LSW_444


title: LSW_440


title: LSW_448


title: LSW_445


title: LSW_438


title: LSW_443


title: LSW_446


title: LSW_442


title: LSW_437


title: LSW_430


title: LSW_439


title: LSW_434


title: LSW_427


title: LSW_435


title: LSW_431


title: LSW_436


title: LSW_428


title: LSW_418


title: LSW_423


title: LSW_416


title: LSW_422


title: LSW_432


title: LSW_433


title: LSW_419


title: LSW_424


title: LSW_426


title: LSW_420


title: LSW_415


title: LSW_425


title: LSW_413


title: LSW_411


title: LSW_417


title: LSW_408


title: LSW_412


title: LSW_407


title: LSW_410


title: LSW_429


title: LSW_406


title: LSW_405


title: LSW_402


title: LSW_401


title: LSW_404


title: LSW_395


title: LSW_400


title: LSW_397


title: LSW_399


title: LSW_390


title: LSW_414


title: LSW_396


title: LSW_387


title: LSW_386


title: LSW_392


title: LSW_389


title: LSW_388


title: LSW_403


title: LSW_391


title: LSW_398


title: LSW_385


title: LSW_384


title: LSW_383


title: LSW_380


title: LSW_373


title: LSW_377


title: LSW_409


title: LSW_379


title: LSW_394


title: LSW_393


title: LSW_376


title: LSW_369


title: LSW_366


title: LSW_365


title: LSW_375


title: LSW_382


title: LSW_372


title: LSW_378


title: LSW_374


title: LSW_367


title: LSW_370


title: LSW_364


title: LSW_363


title: LSW_371


title: LSW_362


title: LSW_361


title: LSW_359


title: LSW_360


title: LSW_381


title: LSW_354


title: LSW_353


title: LSW_358


title: LSW_355


title: LSW_352


title: LSW_357


title: LSW_350


title: LSW_348


title: LSW_368


title: LSW_347


title: LSW_351


title: LSW_345


title: LSW_349


title: LSW_343


title: LSW_341


title: LSW_340


title: LSW_342


title: LSW_356


title: LSW_338


title: LSW_332


title: LSW_333


title: LSW_331


title: LSW_337


title: LSW_344


title: LSW_330


title: LSW_328


title: LSW_339


title: LSW_327


title: LSW_326


title: LSW_325


title: LSW_324


title: LSW_346


title: LSW_323


title: LSW_322


title: LSW_319


title: LSW_305


title: LSW_314


title: LSW_315


title: LSW_334


title: LSW_313


title: LSW_308


title: LSW_317


title: LSW_316


title: LSW_320


title: LSW_311


title: LSW_329


title: LSW_300


title: LSW_312


title: LSW_310


title: LSW_307


title: LSW_336


title: LSW_335


title: LSW_306


title: LSW_293


title: LSW_299


title: LSW_302


title: LSW_298


title: LSW_303


title: LSW_286


title: LSW_318


title: LSW_289


title: LSW_287


title: LSW_288


title: LSW_321


title: LSW_309


title: LSW_301


title: LSW_304


title: LSW_283


title: LSW_285


title: LSW_284


title: LSW_281


title: LSW_280


title: LSW_282


title: LSW_275


title: LSW_273


title: LSW_277


title: LSW_279


title: LSW_297


title: LSW_278


title: LSW_274


title: LSW_271


title: LSW_267


title: LSW_269


title: LSW_268


title: LSW_272


title: LSW_256


title: LSW_265


title: LSW_264


title: LSW_258


title: LSW_262


title: LSW_266


title: LSW_259


title: LSW_260


title: LSW_253


title: LSW_255


title: LSW_251


title: LSW_244


title: LSW_250


title: LSW_254


title: LSW_248


title: LSW_243


title: LSW_270


title: LSW_252


title: LSW_242


title: LSW_249


title: LSW_247


title: LSW_263


title: LSW_235


title: LSW_238


title: LSW_239


title: LSW_261


title: LSW_234


title: LSW_231


title: LSW_236


title: LSW_237


title: LSW_228


title: LSW_246


title: LSW_230


title: LSW_232


title: LSW_225


title: LSW_223


title: LSW_222


title: LSW_245


title: LSW_233


title: LSW_221


title: LSW_227


title: LSW_218


title: LSW_229


title: LSW_217


title: LSW_226


title: LSW_241


title: LSW_219


title: LSW_212


title: LSW_240


title: LSW_220


title: LSW_210


title: LSW_216


title: LSW_205


title: LSW_213


title: LSW_224


title: LSW_207


title: LSW_206


title: LSW_215


title: LSW_204


title: LSW_198


title: LSW_202


title: LSW_214


title: LSW_200


title: LSW_211


title: LSW_208


title: LSW_209


title: LSW_193


title: LSW_187


title: LSW_203


title: LSW_195


title: LSW_183


title: LSW_197


title: LSW_188


title: LSW_194


title: LSW_189


title: LSW_186


title: LSW_191


title: LSW_184


title: LSW_182


title: LSW_199


title: LSW_192


title: LSW_196


title: LSW_177


title: LSW_181


title: LSW_180


title: LSW_178


title: LSW_175


title: LSW_179


title: LSW_172


title: LSW_190


title: LSW_176


title: LSW_185


title: LSW_171


title: LSW_173


title: LSW_168


title: LSW_165


title: LSW_157


title: LSW_169


title: LSW_162


title: LSW_164


title: LSW_167


title: LSW_163


title: LSW_155


title: LSW_166


title: LSW_158


title: LSW_160


title: LSW_149


title: LSW_159


title: LSW_146


title: LSW_152


title: LSW_148


title: LSW_161


title: LSW_170


title: LSW_150


title: LSW_147


title: LSW_174


title: LSW_144


title: LSW_153


title: LSW_156


title: LSW_142


title: LSW_143


title: LSW_139


title: LSW_145


title: LSW_130


title: LSW_133


title: LSW_131


title: LSW_129


title: LSW_137


title: LSW_138


title: LSW_132


title: LSW_124


title: LSW_127


title: LSW_128


title: LSW_151


title: LSW_123


title: LSW_135


title: LSW_154


title: LSW_120


title: LSW_121


title: LSW_122


title: LSW_141


title: LSW_136


title: LSW_114


title: LSW_134


title: LSW_113


title: LSW_116


title: LSW_125


title: LSW_118


title: LSW_117


title: LSW_111


title: LSW_126


title: LSW_119


title: LSW_115


title: LSW_140


title: LSW_108


title: LSW_110


title: LSW_112


title: LSW_103


title: LSW_105


title: LSW_106


title: LSW_102


title: LSW_101


title: LSW_96


title: LSW_104


title: LSW_92


title: LSW_90


title: LSW_97


title: LSW_91


title: LSW_93


title: LSW_95


title: LSW_82


title: LSW_94


title: LSW_100


title: LSW_87


title: LSW_99


title: LSW_109


title: LSW_98


title: LSW_88


title: LSW_83


title: LSW_80


title: LSW_72


title: LSW_69


title: LSW_84


title: LSW_81


title: LSW_85


title: LSW_74


title: LSW_79


title: LSW_78


title: LSW_77


title: LSW_75


title: LSW_76


title: LSW_71


title: LSW_67


title: LSW_65


title: LSW_70


title: LSW_63


title: LSW_66


title: LSW_60


title: LSW_61


title: LSW_57


title: LSW_56


title: LSW_49


title: LSW_55


title: LSW_51


title: LSW_53


title: LSW_62


title: LSW_46


title: LSW_39


title: LSW_38


title: LSW_37


title: LSW_24


title: LSW_29


title: LSW_23


title: LSW_64


title: LSW_28


title: LSW_27


title: LSW_68


title: LSW_59


title: LSW_15


title: LSW_26


title: LSW_20


title: LSW_16


title: LSW_12


title: LSW_19


title: LSW_36


title: LSW_18


title: LSW_47


title: LSW_11


title: LSW_13


title: LSW_25


title: LSW_10


title: LSW_9


title: LSW_48


title: LSW_50


title: LSW_58


title: LSW_30


title: LSW_34


title: LSW_17


title: LSW_42


title: LSW_52


title: LSW_5


title: LSW_41


title: LSW_32


title: LSW_33


title: LSW_1


title: LSW_43


title: LSW_14


title: LSW_3


title: LSW_7


title: DKO_2

city: Frederick

first: Xavier

last: Bofill-De Ros

state: MD

address: 1050 Boyles St., blg 560

department: RNA Biology Laboratory

institute: National Cancer Institute

data_processing:
Adaptor removal using custom scripts. Described in Gu et al. Cell (2012)
miRNA mapping with QuagmiR. Described in Bofill-De Ros et al. Bioinformatics (2019).
Genome_build: miRBase21
Supplementary_files_format_and_content: tsv files reporting number of reads, length, 5' fidelity, trimming and tailoring events.

growth_protocol: HEK293T cells were maintained in DMEM high glucose (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Hyclone), 100 U/ml penicillin-streptomycin (Gibco) at 37℃. Cells were tested to be free of mycoplasma contamination.

extract_protocol:
Phenol-cholorphorm total RNA extraction
RNA was used to prepare small RNA-seq libraries using QIAseq miRNA Library Kit (Qiagen). Constructs were purified in a 6% (w/v) native acrylamide gel based on the expected product size and purified by ethanol precipitation.

treatment_protocol: Transfections were performed using PolyJet™ DNA Transfection Reagent (SignaGen) according to the manufacturer's instructions.

tag: cell line background

tag: genotype/replicate

tag: molecule type

value: IP RNA


title: TKO_2


title: LSW_54


title: LSW_4


title: K1_D088226_B106239_S241

city: San Francisco

first: Juliane

last: Winkler

address: 513 Parnassus Avenue

department: Department of Cell and Tissue Biology

institute: University of California, San Francisco

library_source: transcriptomic single cell

data_processing:
Sequences from the NovaSeq or NextSeq were de-multiplexed using bcl2fastq v.2.19.0.316. Reads were aligned to the gencode V30 genome using STAR v.2.5.2b with parameters TK. Gene counts were produced using HTSEQ v.0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Gene count tables were combined with the metadata variables using the Scanpy Python package version 1.8.1. We removed the genes that were not expressed in at least 5 cells. Cells with less than 5000 counts and 500 detected genes were removed. Additionally, we removed cells with more than 50% mitochondrial genes and 20% ERCC reads.  The data were then normalized using size factor normalization such that every cell has 10,000 counts and log-transformed. We selected the top 2000 genes with the highest standardized variance as the highly variable genes by using VST method from Seurat V3, which is also implemented in Scanpy. Cell-cycle regression was performed after calculating the score of S and G2M phases for each cell. The data was then scaled to a maximum value of 10. We then computed principal component (PC) analysis, neighborhood graph and clustered the data using Louvain and Leiden methods. The data was visualized using UMAP projection.
Assembly: genecode V30
Supplementary files format and content: csv
Supplementary files format and content: comma seperated values file for meta data, raw gene count matrix, and normalized and log-transformed gene count matrix

extract_protocol:
Live, LIN-/hDC298+ single breast primary tumor and metastatic cells from lung were sorted into 384 well plates followed by cDNA preparation using modified SmartSeq2.
SmartSeq2 for preparation of cDNA followed by library preparation using a homebrew adapted version.

value: patient-derived-xenograft

tag: cell type

value: tumor

value: NSG


title: K10_D088226_B106239_S250


title: J8_D088226_B106239_S224


title: K13_D088226_B106239_S253


title: K21_D088226_B106239_S261


title: LSW_2

value: liver


title: B12_D088226_B106239_S36


title: B16_D088226_B106239_S40


title: K3_D088226_B106239_S243


title: K9_D088226_B106239_S249


title: L15_D088226_B106239_S279


title: K6_D088226_B106239_S246


title: K2_D088226_B106239_S242


title: L20_D088226_B106239_S284


title: L17_D088226_B106239_S281


title: HSAEC_4T53RD_tumor_EpCAMlow/PDPN+_1

city: Tsukuba-shi

first: Shuntaro

last: Tsukamoto

state: Ibaraki

address: 5-1-3 Tokodai, Tsukuba-shi,

institute: Eisai Co., Ltd.

description: Gene expression of HSAEC_4T53RD mouse xenograft tumor

hyb_protocol: Cy3-RNAs were hybridized to a SurePrint G3 Human GE 8×60K Microarray (Agilent Technologies).

scan_protocol: Hybridization images were obtained with a DNA Microarray Scanner (Agilent Technologies).

data_processing: Scanned images were quantified by using Feature Extraction software ver. 11 (Agilent Technologies).

source_name: Mouse xenograft

label_protocol: An aliquot of total RNA (50 ng) was converted to cyanine-3-labeled cRNA by using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: Total RNA was extracted from the HSAEC_4T53RD mouse xenograft tumor by using an RNeasy Kit (QIAGEN)

value: Tumor


title: HSAEC_4T53RD_tumor_EpCAMhigh/PDPN-_2


title: HSAEC_4T53RD_tumor_EpCAMhigh/PDPN-_1


title: HSAEC_4T53RD_tumor_EpCAMlow/PDPN+_2


title: L21_D088226_B106239_S285


title: J6_D088226_B106239_S222


title: J7_D088226_B106239_S223


title: L2_D088226_B106239_S266


title: L4_D088226_B106239_S268


title: L10_D088226_B106239_S274


title: L19_D088226_B106239_S283


title: L6_D088226_B106239_S270


title: J5_D088226_B106239_S221


title: M16_D088226_B106239_S304


title: B10_D088226_B106239_S34


title: A12_D088226_B106239_S12


title: A15_D088226_B106239_S15


title: M13_D088226_B106239_S301


title: M1_D088226_B106239_S289


title: L7_D088226_B106239_S271


title: M17_D088226_B106239_S305


title: B22_D088219_B106235_S46


title: B2_D088219_B106235_S26


title: B21_D088219_B106235_S45


title: C1_D088226_B106239_S49


title: B9_D088219_B106235_S33


title: B3_D088219_B106235_S27


title: C11_D088219_B106235_S59


title: B6_D088219_B106235_S30


title: C12_D088219_B106235_S60


title: C10_D088219_B106235_S58


title: C13_D088219_B106235_S61


title: C14_D088219_B106235_S62


title: C2_D088226_B106239_S50


title: M4_D088226_B106239_S292


title: C16_D088219_B106235_S64


title: C20_D088219_B106235_S68


title: C17_D088219_B106235_S65


title: LSW_73


title: B4_D088219_B106235_S28


title: C18_D088219_B106235_S66


title: C3_D088219_B106235_S51


title: C7_D088219_B106235_S55


title: C22_D088219_B106235_S70


title: C6_D088219_B106235_S54


title: A17_D088226_B106239_S17


title: C7_D088226_B106239_S55


title: C8_D088219_B106235_S56


title: C4_D088219_B106235_S52


title: C2_D088219_B106235_S50


title: H19_D088219_B106235_S187


title: D3_D088226_B106239_S75


title: H1_D088219_B106235_S169


title: H21_D088219_B106235_S189


title: H2_D088219_B106235_S170


title: H22_D088219_B106235_S190


title: H3_D088219_B106235_S171


title: H4_D088219_B106235_S172


title: H5_D088219_B106235_S173


title: H6_D088219_B106235_S174


title: C9_D088219_B106235_S57


title: D5_D088226_B106239_S77


title: H8_D088219_B106235_S176


title: H18_D088219_B106235_S186


title: H9_D088219_B106235_S177


title: I12_D088219_B106235_S204


title: I17_D088219_B106235_S209


title: I14_D088219_B106235_S206


title: I1_D088219_B106235_S193


title: A18_D088226_B106239_S18


title: I13_D088219_B106235_S205


title: I21_D088219_B106235_S213


title: I22_D088219_B106235_S214


title: H20_D088219_B106235_S188


title: E7_D088226_B106239_S103


title: I2_D088219_B106235_S194


title: L21_D088225_B106237_S285


title: L5_D088225_B106237_S269


title: M16_D088225_B106237_S304


title: L2_D088225_B106237_S266


title: M17_D088225_B106237_S305


title: I11_D088219_B106235_S203


title: M22_D088225_B106237_S310


title: I19_D088219_B106235_S211


title: M7_D088225_B106237_S295


title: I20_D088219_B106235_S212


title: E10_D088226_B106239_S106


title: M9_D088225_B106237_S297


title: M8_D088225_B106237_S296


title: F10_D088226_B106239_S130


title: LSW_45


title: N17_D088225_B106237_S329


title: N20_D088225_B106237_S332


title: N10_D088225_B106237_S322


title: O4_D088225_B106237_S340


title: N11_D088225_B106237_S323


title: O10_D088225_B106237_S346


title: O2_D088225_B106237_S338


title: O8_D088225_B106237_S344


title: A11_B008654_B010273


title: A17_B008654_B010273


title: D1_B008654_B010273


title: D18_B008654_B010273


title: D19_B008654_B010273


title: LSW_35


title: A15_B008654_B010273


title: A16_B008654_B010273


title: D17_B008654_B010273


title: F12_D088226_B106239_S132


title: D22_B008654_B010273


title: M21_D088225_B106237_S309


title: D21_B008654_B010273


title: D6_B008654_B010273


title: D8_B008654_B010273


title: E12_B008654_B010273


title: D5_B008654_B010273


title: D2_B008654_B010273


title: D3_B008654_B010273


title: A22_D088226_B106239_S22


title: F2_D088226_B106239_S122


title: E10_B008654_B010273


title: O9_D088225_B106237_S345


title: E21_B008654_B010273


title: E14_B008654_B010273


title: E13_B008654_B010273


title: E20_B008654_B010273


title: K11_B008654_B010273


title: F9_D088226_B106239_S129


title: J9_B008654_B010273


title: J4_B008654_B010273


title: K13_B008654_B010273


title: E1_B008654_B010273


title: K15_B008654_B010273


title: K2_B008654_B010273


title: K20_B008654_B010273


title: K3_B008654_B010273


title: K5_B008654_B010273


title: K8_B008654_B010273


title: L7_B008654_B010273


title: L12_B008654_B010273


title: L14_B008654_B010273


title: L1_B008654_B010273


title: G11_D088226_B106239_S155


title: E15_B008654_B010273


title: M14_B008654_B010273


title: M18_B008654_B010273


title: L3_B008654_B010273


title: C18_B008655_B010274


title: M19_B008654_B010273


title: K10_B008654_B010273


title: C20_B008655_B010274


title: C19_B008655_B010274


title: C21_B008655_B010274


title: D11_B008655_B010274


title: D10_B008655_B010274


title: D12_B008655_B010274


title: D17_B008655_B010274


title: D14_B008655_B010274


title: G20_D088226_B106239_S164


title: D19_B008655_B010274


title: D13_B008655_B010274


title: C22_B008655_B010274


title: D18_B008655_B010274


title: D1_B008655_B010274


title: G21_D088226_B106239_S165


title: D21_B008655_B010274


title: D20_B008655_B010274


title: D3_B008655_B010274


title: B17_D088226_B106239_S41


title: M6_D088226_B106239_S294


title: D4_B008655_B010274


title: D2_B008655_B010274


title: M9_D088226_B106239_S297


title: M5_D088226_B106239_S293


title: N11_D088226_B106239_S323


title: N12_D088226_B106239_S324


title: M7_D088226_B106239_S295


title: N14_D088226_B106239_S326


title: N16_D088226_B106239_S328


title: M8_D088226_B106239_S296


title: N17_D088226_B106239_S329


title: N15_D088226_B106239_S327


title: N2_D088226_B106239_S314


title: N1_D088226_B106239_S313


title: N19_D088226_B106239_S331


title: N3_D088226_B106239_S315


title: N7_D088226_B106239_S319


title: N8_D088226_B106239_S320


title: O13_D088226_B106239_S349


title: O15_D088226_B106239_S351


title: B9_D088226_B106239_S33


title: O12_D088226_B106239_S348


title: O18_D088226_B106239_S354


title: O20_D088226_B106239_S356


title: O21_D088226_B106239_S357


title: O2_D088226_B106239_S338


title: D12_D088219_B106235_S84


title: D14_D088219_B106235_S86


title: D11_D088219_B106235_S83


title: D15_D088219_B106235_S87


title: D1_D088219_B106235_S73


title: D21_D088219_B106235_S93


title: D20_D088219_B106235_S92


title: D22_D088219_B106235_S94


title: N4_D088226_B106239_S316


title: D2_D088219_B106235_S74


title: D3_D088219_B106235_S75


title: D8_D088219_B106235_S80


title: D16_D088219_B106235_S88


title: D5_D088219_B106235_S77


title: E10_D088219_B106235_S106


title: D6_D088219_B106235_S78


title: B4_D088226_B106239_S28


title: E11_D088219_B106235_S107


title: E12_D088219_B106235_S108


title: D9_D088219_B106235_S81


title: E13_D088219_B106235_S109


title: E14_D088219_B106235_S110


title: E16_D088219_B106235_S112


title: E17_D088219_B106235_S113


title: E1_D088219_B106235_S97


title: E22_D088219_B106235_S118


title: E19_D088219_B106235_S115


title: I9_D088219_B106235_S201


title: I3_D088219_B106235_S195


title: J11_D088219_B106235_S227


title: J14_D088219_B106235_S230


title: J12_D088219_B106235_S228


title: J15_D088219_B106235_S231


title: J10_D088219_B106235_S226


title: E11_D088226_B106239_S107


title: J17_D088219_B106235_S233


title: J18_D088219_B106235_S234


title: J21_D088219_B106235_S237


title: J22_D088219_B106235_S238


title: J3_D088219_B106235_S219


title: J2_D088219_B106235_S218


title: E15_D088219_B106235_S111


title: J7_D088219_B106235_S223


title: D12_D088226_B106239_S84


title: K11_D088219_B106235_S251


title: J19_D088219_B106235_S235


title: K10_D088219_B106235_S250


title: K15_D088219_B106235_S255


title: J6_D088219_B106235_S222


title: K17_D088219_B106235_S257


title: K18_D088219_B106235_S258


title: K1_D088219_B106235_S241


title: K3_D088219_B106235_S243


title: K20_D088219_B106235_S260


title: K6_D088219_B106235_S246


title: K7_D088219_B106235_S247


title: E15_D088226_B106239_S111


title: L10_D088219_B106235_S274


title: K8_D088219_B106235_S248


title: L16_D088219_B106235_S280


title: L12_D088219_B106235_S276


title: L17_D088219_B106235_S281


title: J5_D088219_B106235_S221


title: L19_D088219_B106235_S283


title: L18_D088219_B106235_S282


title: L1_D088219_B106235_S265


title: E16_D088226_B106239_S112


title: E13_D088226_B106239_S109


title: L21_D088219_B106235_S285


title: L4_D088219_B106235_S268


title: L22_D088219_B106235_S286


title: L8_D088219_B106235_S272


title: L5_D088219_B106235_S269


title: L6_D088219_B106235_S270


title: L2_D088219_B106235_S266


title: M11_D088219_B106235_S299


title: M13_D088219_B106235_S301


title: M14_D088219_B106235_S302


title: L7_D088219_B106235_S271


title: M17_D088219_B106235_S305


title: M2_D088219_B106235_S290


title: M22_D088219_B106235_S310


title: M19_D088219_B106235_S307


title: M4_D088219_B106235_S292


title: E20_D088226_B106239_S116


title: M8_D088219_B106235_S296


title: N10_D088219_B106235_S322


title: M5_D088219_B106235_S293


title: N11_D088219_B106235_S323


title: M6_D088219_B106235_S294


title: N12_D088219_B106235_S324


title: N13_D088219_B106235_S325


title: N16_D088219_B106235_S328


title: N15_D088219_B106235_S327


title: M15_D088219_B106235_S303


title: O14_D088219_B106235_S350


title: E1_D088226_B106239_S97


title: N4_D088219_B106235_S316


title: O16_D088219_B106235_S352


title: E21_D088226_B106239_S117


title: N9_D088219_B106235_S321


title: M16_D088219_B106235_S304


title: N8_D088219_B106235_S320


title: O12_D088219_B106235_S348


title: O18_D088219_B106235_S354


title: O21_D088219_B106235_S357


title: O4_D088219_B106235_S340


title: O22_D088219_B106235_S358


title: F5_D088226_B106239_S125


title: F7_B008654_B010273


title: N21_D088219_B106235_S333


title: G15_B008654_B010273


title: G10_B008654_B010273


title: N5_D088219_B106235_S317


title: N22_D088219_B106235_S334


title: G13_B008654_B010273


title: F9_B008654_B010273


title: G16_B008654_B010273


title: G18_B008654_B010273


title: G21_B008654_B010273


title: N2_D088219_B106235_S314


title: G19_B008654_B010273


title: F6_D088226_B106239_S126


title: G6_B008654_B010273


title: G2_B008654_B010273


title: G8_B008654_B010273


title: G9_B008654_B010273


title: H10_B008654_B010273


title: G5_B008654_B010273


title: H14_B008654_B010273


title: O20_D088219_B106235_S356


title: H18_B008654_B010273


title: F7_D088226_B106239_S127


title: H22_B008654_B010273


title: H6_B008654_B010273


title: H2_B008654_B010273


title: G1_B008654_B010273


title: H8_B008654_B010273


title: H5_B008654_B010273


title: H4_B008654_B010273


title: H9_B008654_B010273


title: F8_D088226_B106239_S128


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title: E3_B008880_B106232_S99


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title: D8_B008637_B008704


title: D22_B008645_B008945


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title: F14_B008637_B008704


title: D15_B008637_B008704


title: F20_B008637_B008704


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title: E22_B008637_B008704


title: F15_B008637_B008704


title: F18_B008637_B008704


title: F3_B008637_B008704


title: D2_B008638_B010276


title: F8_B008637_B008704


title: A22_D088223_B106234_S22


title: G10_B008637_B008704


title: G12_B008637_B008704


title: G13_B008637_B008704


title: G21_B008637_B008704


title: G19_B008637_B008704


title: G20_B008637_B008704


title: D2_B008645_B008945


title: G3_B008637_B008704


title: G2_B008637_B008704


title: G9_B008637_B008704


title: D11_B008637_B008704


title: A19_B008651_B008698


title: G8_B008637_B008704


title: 84TD1394DaysLFC2 [TD139-3]

city: Cologne

first: Thomas

last: Langmann

address: Kerpener Strasse 62

department: Department of Ophthalmology

country: Germany

institute: University of Cologne

data_processing:
The analysis was carried out in Illumina BaseSpace by RNA express to determine differential gene expression.
rnaexpress.AppVersion Description: App version Content:1.1.0 ; rnaexpress.WorkflowVersion Description:App version Content:1.1.0
Trimmed sequence reads were mapped to mm10 using Illumina BaseSpace (RNA express)
Read count extraction were performed using Illumine BaseSpace (RNA express) without further changes
Assembly: mm10
Supplementary files format and content: raw counts of sequencing reads for each sample as text file (txt)

source_name: retina

extract_protocol:
Retinas were removed and RNA was harvested using Qiagen RNeasy Kit.
Library preparation and RNA-seq were carried out as described in the Illumina (Stranded mRNA Prep Ligation) reference Guide, the Illumina NextSeq 2000 Sequencing System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA).

treatment_protocol: 1h light exposure (15000lux), analysis 4days post light exposure, treatment: 15mg/kg TD139 or Vehicle

value: retina

tag: mouse line

value: Balb/cJ

tag: light exposure

value: yes

value: wt

value: TD139 treatment

tag: time


title: F13_B008637_B008704


title: 82TD1394DaysLFC2 [TD139-2]

tag: treatment


title: H20_B008637_B008704


title: H22_B008637_B008704


title: 80TD1394DaysLFC1 [TD139-1]


title: 80TD1394DaysLFC2 [TD139-1]


title: H12_B008637_B008704


title: H3_B008637_B008704


title: 78Vehicle4DaysLFC2 [Vehicle-3]

value: Vehicle treatment


title: 78Vehicle4DaysLFC1 [Vehicle-3]


title: I20_B008637_B008704


title: 82TD1394DaysLFC1 [TD139-2]


title: 76Vehicle4DaysLFC2 [Vehicle-2]


title: I2_B008637_B008704


title: 76Vehicle4DaysLFC1 [Vehicle-2]


title: H6_B008637_B008704


title: 74Vehicle4DaysLFC2 [Vehicle-1]


title: I9_B008637_B008704


title: 74Vehicle4DaysLFC1 [Vehicle-1]


title: 84TD1394DaysLFC1 [TD139-3]


title: J14_B008637_B008704


title: 72CtrlnolightLFC2 [Naive-3]

value: no

value: no treatment


title: 72CtrlnolightLFC1 [Naive-3]


title: J17_B008637_B008704


title: J19_B008637_B008704


title: H19_B008637_B008704


title: M7_B008636_B008694


title: 70CtrlnolightLFC2 [Naive-2]


title: 70CtrlnolightLFC1 [Naive-2]


title: N12_B008636_B008694


title: N13_B008636_B008694


title: 68CtrlnolightLFC1 [Naive-1]


title: D3_B008645_B008945


title: E12_B008645_B008945


title: N22_B008636_B008694


title: MOLM132R_A485_QS_R3

city: La Jolla

last: Erb

state: CA

address: 10650 N Torrey Pines Rd

department: Department of Chemistry

institute: The Scripps Research Institute

data_processing:
Sequences were aligned and count tables with CPM normaliztion were generated using SLAMdunk (https://t-neumann.github.io/slamdunk/) with the -q option.
For ERCC normalization, normalize.loess function of the affy v1.50.0 R package76 was used. Locally estimated scatterplot smoothing (LOESS) normalization was applied to all CPM values of transcripts with the model specified by the distribution of the SIRV-Set-3 spike-ins.
Assembly: hg19
Supplementary files format and content: CPM table

source_name: acute myeloid leukemia

growth_protocol: MOLM-13, MOLM-13-2R, OCI/AML-2, and MV4;11 cells were cultured in RPMI supplemented with 10% FBS, penicillin, and streptomycin. HL-60, NOMO-1, and HL-60 cells were cultured in RPMI supplemented with 20% FBS, penicillin, and streptomycin.

extract_protocol:
Total RNA was isolated with Qiagen Rneasy Mini Kit.
3' mRNA libraries were prepared with Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Cat. No. 015) according to manufacturer's instructions.

treatment_protocol: Cells were treated with 3 µM A-485 for 48h.

value: acute myeloid leukemia

tag: cell line

value: 48 hours


title: MOLM132R_DMSO_QS_R3

value: 0.1% DMSO


title: MOLM132R_A485_QS_R2


title: MOLM132R_A485_QS_R1


title: N2_B008636_B008694


title: O10_B008636_B008694


title: MOLM132R_DMSO_QS_R2


title: O14_B008636_B008694


title: MOLM13_A485_QS_R2


title: O19_B008636_B008694


title: MOLM132R_DMSO_QS_R1


title: MOLM13_A485_QS_R1


title: N6_B008636_B008694


title: J20_B008637_B008704


title: MOLM13_DMSO_QS_R1


title: N8_B008636_B008694


title: 68CtrlnolightLFC2 [Naive-1]

tag: genotype


title: O2_B008636_B008694

tag: strain


title: N14_B008636_B008694

tag: tissue


title: O16_B008636_B008694


title: MOLM13_DMSO_QS_R2


title: O1_B008636_B008694


title: OCIAML2_A485_QS_R1


title: MOLM13_A485_QS_R3


title: P20_B008636_B008694


title: OCIAML2_DMSO_QS_R1


title: P13_B008636_B008694


title: O5_B008636_B008694


title: OCIAML2_DMSO_QS_R2


title: O9_B008636_B008694


title: OCIAML2_A485_QS_R3


title: OCIAML2_DMSO_QS_R3


title: MOLM13_DMSO_QS_R3


title: D5_B008647_B008702


title: MV411_A485_QS_R3


title: D7_B008647_B008702


title: MV411_A485_QS_R2


title: E4_B008638_B010276


title: MV411_A485_QS_R1


title: E10_B008647_B008702


title: E13_B008638_B010276


title: E11_B008647_B008702


title: OCIAML2_A485_QS_R2


title: E12_B008647_B008702


title: HL60_DMSO_H3K18ac

data_processing:
Sequenced reads were aligned to hg19 and either mm9 or dm3 reference genomes with bowtie2 using default parameters except for 'k -1'.
Alignment files were sorted and indexed with Samtools -sort and -index.
Peaks were called using MACS (1.4.2) with p-val = 1e-9 cutoff used.
Bedgraphs were made from bams using Bedtools genomecov with -bg option.
Read density was calculated using Bamliquidator (v1.0, http://github.com/BradnerLab/pipeline/wiki/bamliquidator) and were normalized by dividing by the number of reads that aligned to the spike-in (mm9 or dm3) genome.
Assembly: hg19
Supplementary files format and content: bedgraph files and bed files of MACS peaks

growth_protocol: MOLM-13 cells were cultured in RPMI supplemented with 10% FBS, penicillin, and streptomycin. HL-60 cells were cultured in RPMI supplemented with 10% FBS, penicillin, and streptomycin.

extract_protocol:
Fixed numbers of mouse or drosophila cells were spiked-in to treated cells. Cells were then lysed. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared with Takara ThruPLEX® DNA-Seq Kit (Cat. No. R400674) according to manufacturer's instructions.

treatment_protocol: Cells were treated with 3 µM A-485 or DMSO for 2 hours.

tag: chip antibody

value: H3K18ac (EMD Millipore, #07-354)


title: HL60_DMSO_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: HL60_A485_H3K18ac


title: E13_B008647_B008702

value: patient-derived-xenograft

value: tumor


title: HL60_A485_H3K27ac


title: HL60_Histone_Input


title: E15_B008647_B008702

value: NSG


title: E16_B008647_B008702


title: E18_B008647_B008702