title: DT1-1,iNeuron, KCTD13 WT

city: Boston

first: Serkan

last: Erdin

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description:
batch B
16p11.2_KCTD13_cellLines_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.

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: induced neuron

value: KCTD13 WT

value: M


title: MOLM13_3uM_A485_R3

status: Public on Aug 15 2022

type: SRA

city: La Jolla

first: Michael

last: Erb

state: CA

address: 10650 N Torrey Pines Rd

department: Department of Chemistry

country: USA

institute: The Scripps Research Institute

description: SLAMseq in MOLM-13 after 2 hour of 3 µM A-485 treatment.

library_source: transcriptomic

data_processing:
SLAMdunk (https://t-neumann.github.io/slamdunk/) was used with default settings to align reads, calculate counts per million, and calculate T to C conversion rate for each transcript.
Assembly: hg19
Supplementary files format and content: T-to-C conversion rates and CPM table.

molecule: total RNA

organism: Homo sapiens

source_name: acute myeloid leukemia

growth_protocol: MOLM-13 cells were cultured in RPMI supplemented with 10% FBS, penicillin, and streptomycin. HL-60 were cultured in RPMI supplemented with 20% FBS, penicillin, and streptomycin.

extract_protocol:
Total RNA was isolated with Qiagen Rneasy Mini Kit. SIRV-Set 3 RNA was spiked into samples.
4SU-labeled transcripts were alkylated by addition of 5 µL 100 mM iodoacetamide, 25 µL DMSO, and 5 µL of sodium phosphate buffer (0.5M, pH 8) and incubating at 50C for 15 minutes. 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 or DMSO for 2 hours. For the last hour of treatment 100 µM 4-thiouracil (4SU) was added to label newly synthesized transcripts.

tag: tissue

value: acute myeloid leukemia

tag: cell line

tag: treatment

tag: time

value: 2 hours


title: DT1-4,iNeuron, KCTD13 Het Del

state: MA

molecule: polyA RNA

tag: cell type

tag: genotype

tag: Sex


title: H16_D088224_B106233_S184

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

value: tumor

tag: strain

value: NSG


title: G15_B008640_B010275


title: H20_D088224_B106233_S188


title: DT1-5,iNeuron, KCTD13 Het Del


title: K4_D088224_B106233_S244


title: MOLM13_Day21_DMSO

library_source: genomic

data_processing:
Sequencing reads were trimmed using cutadapt (v1.7) to remove vector derived sequences.
The MaGeCK count function was used to align reads to the Brunello sgRNA library and generate read count tables for all samples.
The MaGeCK MLE function was then used with default parameters to compare sgRNA abundance changes in DMSO and A-485 samples and create gene-level beta scores.
Supplementary files format and content: MaGeCK MLE output table
Library strategy: Amplicon-seq

molecule: genomic DNA

extract_protocol:
Genomic DNA was isolated with the Quick-DNA Midiprep Plus Kit (Zymo Research, #D4075).
Illumina sequencing libraries were prepared (according to PMID: 29224076) by first amplifying the sgRNA containing vector sequences from the gDNA and then using a second PCR reaction to append sequencing adaptors.

treatment_protocol: Cells were transduced with Brunello sgRNA Library lentivirus at an MOI ~30%. Transduced cells were selected for with puromycin. Cells were then grown for 21 days in 0.1% DMSO or 300 nM A-485.

value: 0.1% DMSO

value: 21 days


title: HL60_3uM_A485_R2

description: SLAMseq in HL-60 after 2 hour of 3 µM A-485 treatment.


title: F9_B008640_B010275


title: K7_D088224_B106233_S247


title: L10_D088224_B106233_S274


title: L11_D088224_B106233_S275


title: MOLM13_DMSO_R1

description: SLAMseq in MOLM-13 after 2 hour of DMSO treatment.


title: H3_D088224_B106233_S171


title: DT1-2,iNeuron, KCTD13 WT


title: MOLM13_3uM_A485_R2


title: MOLM13_3uM_A485_R1


title: H8_D088224_B106233_S176


title: I11_D088224_B106233_S203


title: K21_D088224_B106233_S261


title: B6,iNeuron, KCTD13 Het Del

description:
batch A
16p11.2_KCTD13_cellLines_counts.txt.gz


title: K3_D088224_B106233_S243


title: D,iNeuron, KCTD13 WT


title: MOLM13_Day21_A485


title: HT1376_EZH2i_Rep2

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: bladder cancer

tag: time point

value: Day 7


title: L18_D088224_B106233_S282


title: L17_D088224_B106233_S281


title: K22_D088224_B106233_S262


title: DT1-3,iNeuron, KCTD13 WT


title: B5,iNeuron, KCTD13 Het Del


title: A4,iNeuron, KCTD13 Het Del


title: L19_D088224_B106233_S283


title: L20_D088224_B106233_S284


title: MOLM13_Day0

value: 0 days


title: F,iNeuron, KCTD13 WT


title: HT1376_DMSO_Rep3

value: DMSO


title: L13_D088224_B106233_S277


title: HT1376_EZH2i_Rep3


title: L9_D088224_B106233_S273


title: HT1376_DMSO_Rep2


title: 5974_6_A375-EV_R2_CGTACGT_S43_R1_001.fastq.gz

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

data_processing:
RNA-seq: Data  as FASTQ files, were aligned to the human hg19 genome using TopHat. SAMtools was used for file format conversions. HTSeq was used to count reads at exons of protein-coding genes. Library size normalization of read counts was done using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited .txt files containing non-normalized read counts (using HTSEQ for count of reads on gene exons) for each sample created with gencode.v19 transcript annotation file

source_name: A375 cells

growth_protocol: A375 and SKMEL28 cells were cultured in DMEM medium (Gibco), supplemented with 1% Penicillin/Streptomycin (Gibco) and 10% fetal calf serum (FCS; Hyclone).

extract_protocol:
Total RNA was isolated from A375-YAP5SA, SKMEL28-YAP5SA and respective EV control cells using Trizol (Thermo Fisher)
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (#RS-122-2101/2; Illumina) according to the manufacturer’s instructions. The generated cDNA fragments were 3’ end adenylated and ligated to Illumina paired-end sequencing adapters and subsequently amplified by 12 cycles of PCR

treatment_protocol: A375 and SKMEL28 were transduced with a lentiviral vector containing YAP5SA (YAP) or en empty vector (EV) control and selected with Blasticidin.

value: Melanoma  cancer cells

value: Control


title: E,iNeuron, KCTD13 WT

value: induced neuron


title: M14_D088224_B106233_S302


title: 5974_5_A375-EV_R1_ACTTGAA_S42_R1_001.fastq.gz


title: G18_B008640_B010275


title: M2_D088224_B106233_S290


title: 5974_3_SKMEL-YAP_R1_ATCACGA_S40_R1_001.fastq.gz

source_name: SKMEL28 cells

value: YAP1 mutant


title: M19_D088224_B106233_S307


title: G19_B008640_B010275


title: M4_D088224_B106233_S292


title: HT1376_EZH2i_Rep1


title: UMUC9_DMSO_Rep3


title: L15_D088224_B106233_S279


title: 5974_8_A375-YAP_R2_GAGTGGA_S45_R1_001.fastq.gz


title: L22_D088224_B106233_S286


title: 5974_7_A375-YAP_R1_GTTTCGG_S44_R1_001.fastq.gz


title: L6_D088224_B106233_S270


title: M10_D088224_B106233_S298


title: HT1376_DMSO_Rep1


title: M18_D088224_B106233_S306


title: D13_B008648_B008695


title: 5974_4_SKMEL-YAP_R2_TTAGGCA_S41_R1_001.fastq.gz


title: UMUC9_EZH2i_Rep2


title: UMUC3_EZH2i_Rep3


title: D18_B008648_B008695


title: M20_D088224_B106233_S308


title: UMUC9_EZH2i_Rep1


title: C5_B008648_B008695


title: M5_D088224_B106233_S293


title: 5974_1_SKMEL-EV_R1_GTCCGCA_S38_R1_001.fastq.gz


title: UMUC3_EZH2i_Rep1


title: B9_B008640_B010275


title: D3_B008648_B008695


title: UMUC9_EZH2i_Rep3


title: UMUC3_DMSO_Rep3


title: C6_B008648_B008695


title: screen-CkoCT442-T15-25uM-R1

city: Worcester

first: Anne-Laure

last: Valton

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.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_40

data_processing:
Library strategy: CRISPR screen
Reads were aligned using BOWTIE version 0.12.8 (allowing for max. 2 mismatches, ignoring qualities). Read counts for each screen library were normalized to 10 million reads total per sample.
Fold change was calculated to the T0 reference sample.
Genome_build: hg19 human genome
Supplementary_files_format_and_content: Read counts per sample

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:
Genomic DNA was extracted for T0, T6 and T15 of each triplicate of each condition using the Wizard Genomic DNA Purification kit (Promega, A1125) following manufacturer’s instructions.
Sequencing libraries were prepared by amplifying gRNA inserts via a 2-step PCR. The first PCR enriches for the gRNA regions in the genome and the second PCR adds indices by using primers that include Illumina TruSeq adaptors.
The libraries were sequence on Illumina HiSeq2500 single-end reads

treatment_protocol: For auxin treatment: 25uM and 500uM auxin.

value: endogenous CTCF KO, CTCF-AID, TIR1


title: screen-CkoCT442-T15-500uM-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_48


title: D10_B008648_B008695


title: 5974_2_SKMEL-EV_R2_GTGAAAC_S39_R1_001.fastq.gz


title: UMUC9_DMSO_Rep1


title: UMUC3_DMSO_Rep1


title: D8_B008648_B008695


title: screen-CkoCT442-T15-500uM-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_47


title: D12_B008648_B008695


title: D15_B008648_B008695


title: screen-CkoCT442-T15-500uM-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_46


title: screen-CkoCT442-T15-NT-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_34

value: non-treated


title: UMUC3_EZH2i_Rep2


title: E14_B008648_B008695


title: F8_B008640_B010275


title: UMUC9_DMSO_Rep2


title: D21_B008648_B008695


title: 5637_EZH2i_Rep2


title: screen-CkoCT442-T15-25uM-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_42


title: screen-CkoCT442-T6-500uM-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_45


title: H7_B008648_B008695


title: H8_B008648_B008695


title: D4_B008648_B008695


title: screen-CkoCT442-T15-25uM-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_41


title: C10_B008640_B010275


title: UMUC3_DMSO_Rep2


title: D2_B008648_B008695


title: D5_B008648_B008695


title: D6_B008648_B008695


title: screen-CkoCT442-T15-NT-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_36


title: D7_B008648_B008695


title: screen-CkoCT442-T6-500uM-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_43


title: I13_B008648_B008695


title: C20_B008640_B010275


title: screen-CkoCT442-T6-25uM-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_39


title: H5_B008648_B008695


title: screen-CkoCT442-T15-NT-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_35


title: D9_B008648_B008695


title: 5637_EZH2i_Rep3


title: E13_B008648_B008695


title: screen-CkoCT442-T6-25uM-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_38


title: I14_B008648_B008695


title: 5637_DMSO_Rep3


title: 5637_EZH2i_Rep1


title: I1_B008648_B008695


title: I15_B008648_B008695


title: I2_B008648_B008695


title: screen-CkoCT442-T6-500uM-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_44


title: screen-CkoCT442-T6-25uM-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_37


title: 5637_DMSO_Rep2


title: WT_TOTAL_NEB_replicate_3

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).
Assembly: 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 from Qiagen (or NEBNext® Small RNA Library Prep Set for Illumina). 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.

value: WT


title: I20_B008648_B008695

value: patient-derived-xenograft


title: I3_B008648_B008695

value: tumor


title: I19_B008648_B008695

value: NSG


title: J15_B008648_B008695


title: screen-CkoCT442-T6-NT-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_33


title: WT_IP_NEB_replicate_3


title: C21_B008640_B010275


title: screen-CkoCT442-T0

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_30


title: WT_IP_NEB_replicate_1


title: I4_B008648_B008695


title: screen-CkoCT442-T6-NT-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_32


title: J16_B008648_B008695


title: I17_B008648_B008695


title: WT_TOTAL_NEB_replicate_1


title: WT_IP_NEB_replicate_2


title: screen-CkoCT442-T6-NT-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE009-HAP1-CkoCT44.2-20180605-readcounts.txt
PACE_31


title: J12_B008648_B008695


title: J11_B008648_B008695


title: WT_TOTAL_NEB_replicate_2


title: C17_B008639_B008701


title: C18_B008639_B008701


title: WT_293T_AGO1_Endogenous_IP_replicate_2

value: Endogenous AGO1 pull-down


title: screen-CkoC44-T15-500uM-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_28

value: endogenous CTCF KO, CTCF-AID


title: WT_293T_AGO1_Endogenous_IP_replicate_1


title: I21_B008648_B008695


title: C1_B008639_B008701


title: C21_B008649_B008703


title: WT_293T_AGO2_FLAG_IP_replicate_2

value: Ectopic expression AGO2-FLAG


title: screen-CkoC44-T15-500uM-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_29


title: 5637_DMSO_Rep1

value: bladder

value: bladder cancer


title: C17_B008649_B008703


title: screen-CkoC44-T15-500uM-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_27


title: screen-CkoC44-T15-25uM-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_21


title: screen-CkoC44-T15-NT-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_17


title: C6_B008639_B008701


title: screen-CkoC44-T15-25uM-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_23


title: C6_B008649_B008703


title: WT_293T_AGO2_FLAG_IP_replicate_1


title: TKO_replicate_1

value: TKO

value: knock-out


title: b5t2,Organoid,KCTD13-HetDel

description:
10X scRNA
rawCounts_merged_16p_Organoid_GM08330.txt.gz

source_name: Cortical Organoid

value: Cortical Organoid

value: M


title: screen-CkoC44-T15-NT-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_15


title: screen-CkoC44-T15-25uM-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_22


title: WT_293T_AGO1_FLAG_IP_replicate_2

value: Ectopic expression AGO1-FLAG


title: a3t1,Organoid,16p-HetDel


title: WT_293T_AGO1_FLAG_IP_replicate_1


title: s7t1,Organoid,16p-Dup


title: C7_B008649_B008703


title: screen-CkoC44-T6-500uM-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_24


title: screen-CkoC44-T15-NT-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_16


title: TKO_replicate_2


title: b5t1,Organoid,KCTD13-HetDel


title: a3t2,Organoid,16p-HetDel


title: MV411_DMSO_QS_R3

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

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

value: 0.1% DMSO

value: 48 hours


title: screen-CkoC44-T6-500uM-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_26


title: DKO_replicate_2

value: DKO


title: RS-Growing-rep2

city: Beijing

first: Qiao

last: Song

address: No.45 Changchun Street

department: Department of Clinical laboratory

country: China

institute: Xuanwu Hospital, Capital Medical University

data_processing:
Data quality was controlled using FastQC (v.0.11.9, www.bioinformatics.babraham.ac.uk/projects/fastqc). After trimming the adaptor and removing low-quality reads, the obtained clean data were aligned to human genome hg38 by the Burrows–Wheeler Aligner tool (v.0.7.10). A peak calling analysis was conducted using MASC2 (v.2,2) with the following parameters: macs2 callpeak - nomodel - f BAMPE–keep - dup 1 - q 0.05 - B–SPMR.
Assembly: hg38

source_name: cell line

extract_protocol:
After 50,000 2BS cells were counted, Tn5 transposase was used to simultaneously cut the hierarchically folded DNA. Native nuclei were purified by MinElute PCR Purification Kit (Qiagen, 28004) and amplified by six cycles of quantitative real-time PCR. Genomic DNA of 10 ng was used as input control.
ATAC-seq libraries were sequenced on the Illumina Hiseq PE150 sequencer or BGISEQ-500 to obtain 60–130 million of 2 × 150 bp paired-end sequencing reads per sample.

value: cell line

tag: phenotype

value: Growing


title: MV411_DMSO_QS_R1


title: DKO_replicate_1


title: s7t2,Organoid,16p-Dup


title: C2_B008649_B008703

value: patient-derived-xenograft

value: tumor

value: NSG


title: p44t2,Organoid,WT

value: WT


title: PBS_biol rep3

city: Shenyang

first: li

last: bingwu

address: shenhe

institute: Shenyang Pharmaceutical University

data_processing:
Illumina NovaSeq 6000 reads were trimmed and clipped for quality control in trim_galore
Read quality was checked for each sample using FastQC
Trimmed sequence reads were mapped to GRCm39 using hisat2
Read count extraction by using
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

organism: Mus musculus

source_name: TC-1 cells

extract_protocol:
The mice were sacrificed by cervical spine removal and the tumor tissue was collected and then the total RNA was isolated using RNAiso Plus(TaKaRa).
RNA-seq library was constructed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech) according to the manufacturer's protocol

treatment_protocol: TC-1 cells (1×106) were subcutaneously injected into the waist of female C57 mice, and tumor-bearing mice were divided into two groups (n=6). When the tumor reached the size of 100-150 mm3, the mice were intratumorally injected with PBS and OMVs@P2O-Ads. The drug was given every three days for four consecutive times, the tumor volume was measured with a vernier caliper, and mice were weighed daily. On the 18th day of the efficacy experiment, the mice were sacrificed

value: TC-1 cells

value: adherent cell line

value: PBS


title: SKM1_A485_QS_R3


title: screen-CkoC44-T6-NT-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_14

value: non-treated

value: endogenous CTCF KO, CTCF-AID


title: p44t1,Organoid,WT

value: Cortical Organoid

value: M


title: TKO_TUT47

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.

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.

tag: genotype/variation


title: screen-CkoC44-T6-25uM-R3

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_20


title: TKO_mock_1


title: TKO_mock_2


title: RS-rep2

value: Senescence


title: Drug_biol rep3


title: screen-CkoC44-T6-NT-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_12


title: MV411_DMSO_QS_R2

value: acute myeloid leukemia

value: 0.1% DMSO


title: screen-CkoC44-T6-25uM-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_19


title: screen-CkoC44-T0

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_11


title: TKO_TUT4


title: TENT2KO_mock_2


title: screen-CkoC44-T6-500uM-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_25


title: PBS_biol rep2


title: TENT2KO_mock_1


title: SKM1_A485_QS_R2

value: 48 hours


title: Drug_biol rep2


title: Drug_biol rep1


title: screen-CkoC44-T6-NT-R2

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_13


title: DKO_TUT7


title: PBS_biol rep1


title: Isolated cells from meristematic root tissue at day 0 - Replicate 2

city: Raleigh

first: Lisa

last: Van den Broeck

state: NORTH CAROLINA

address: 112 Derieux Place

department: Plant and Microbial Biology

institute: North Carolina State University

description:
SCR_M_cells_D0_2
FPKM_Replicates.xlsx
complete_table.xlsx

data_processing:
ea-utils fastq-mcf for pre-processing
hisat2 for genome alignment
Cufflinks for differential expression analysis
Supplementary files format and content: FPKM_Replicates.xlsx - Excel file that contains the FPKM values of each of the replicates
Supplementary files format and content: complete_table.xlsx - Excel file that contains the expression values, log2 fold changes, and q-values

organism: Arabidopsis thaliana

extract_protocol:
To extract the RNA, 500 µl TRIzol (Thermo Scientific) was added and the cells were disrupted within the TRIzol using a mill mixer at 30 Hz for 5 minutes at room temperature. RNA was further purified using chloroform and the RNeasy Micro Kit (Qiagen).
cDNA synthesis and amplification was performed using the NEBNext® Poly(A) mRNA Magnetic Isolation Module followed by the NEBNext® Ultra™ II Directional RNA Library Prep and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1)
paired-end, 150 bp

value: Meristematic root tissue

value: day 0


title: TKO_TUT7


title: MT_5w

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

description: 10x Genomics

data_processing:
The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters. The reference genome was mm10-1.2.0
Assembly: mm10-1.2.0
Supplementary files format and content: matrix files

source_name: Testis

extract_protocol:
Fresh tesits tissue samples of about 1×1-cm size were first immersed in 15 ml PBS with vigorous shaking to remove residual blood cells. Then, tissues were cut into pieces of 1×1-mm size and enzymatically digested with 2.5 mg/ml collagenase type I (17104-019, gibco), 4 mg/ml collagenase type IV (17018029, gibco), 0.1 mg/ml neutral protease, and 2 mg/ml DNase I (#AMPD1, Sigma-Aldrich) at 37°C for 40 min. Subsequently, the cell suspension was filtered through a 40-mm nylon mesh, and the cells were sorted by MACS with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) to remove dead cells. The cells were resuspended in 0.05% BSA/PBS buffer before 10× Genomics library preparation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000094, 10× Genomics) according to the manufacturer’s instructions. Final libraries were sequenced on an Illumina NovaSeq 6000.

value: Testis

value: normal


title: SKM1_DMSO_QS_R3


title: SKM1_A485_QS_R1


title: screen-CkoC44-T6-25uM-R1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
PACE008-HAP1-CkoC44-20180605-readcounts.txt
PACE_18


title: DKO_TUT47


title: SKM1_DMSO_QS_R2


title: Isolated cells from meristematic root tissue at day 0 - Replicate 3

description:
SCR_M_cells_D0_3
FPKM_Replicates.xlsx
complete_table.xlsx


title: MT_21d

description: 10x Genomics


title: NOMO1_A485_QS_R3


title: DKO_TUT4


title: Isolated cells from meristematic root tissue at day 0 - Replicate 1

description:
SCR_M_cells_D0_1
FPKM_Replicates.xlsx
complete_table.xlsx


title: NOMO1_DMSO_QS_R2


title: NOMO1_DMSO_QS_R3


title: NOMO1_A485_QS_R2


title: DKO_GFP


title: Isolated cells from differentiated root tissue at day 0 - Replicate 3

description:
SCR_D_cells_D0_3
FPKM_Replicates.xlsx
complete_table.xlsx

value: Differentiated root tissue


title: Bioprinted constructs of meristematic root tissue at day 0 - Replicate 3

description:
SCR_M_bio_D0_3
FPKM_Replicates.xlsx
complete_table.xlsx


title: TENT2KO_GFP_3


title: NOMO1_A485_QS_R1


title: MT_25d

description: 10x Genomics


title: HL60_A485_QS_R3


title: MT_8d

description: 10x Genomics


title: TKO_TENT2_wt_2


title: Isolated cells from differentiated root tissue at day 0 - Replicate 1

description:
SCR_D_cells_D0_1
FPKM_Replicates.xlsx
complete_table.xlsx


title: DKO_mock


title: MT_6d

description: 10x Genomics


title: MT_17d

description: 10x Genomics


title: WT_GFP


title: Bioprinted constructs of meristematic root tissue at day 0 - Replicate 2

description:
SCR_M_bio_D0_2
FPKM_Replicates.xlsx
complete_table.xlsx


title: HL60_A485_QS_R2


title: HL60_A485_QS_R1


title: Bioprinted constructs of meristematic root tissue at day 0 - Replicate 1

description:
SCR_M_bio_D0_1
FPKM_Replicates.xlsx
complete_table.xlsx


title: TKO_TENT2_cd_1


title: SKM1_DMSO_QS_R1


title: HL60_DMSO_QS_R3


title: TKO_GFP_1


title: MT_14d

description: 10x Genomics


title: TKO_TENT2_cd_2


title: MT_11d

description: 10x Genomics


title: Polr_2138_7

city: Cincinnati

first: Kelly

middle: Andrew

last: Smallwood

state: OH

address: 3333 Burnet Ave, S4.200BC

department: Human Genetics

institute: Cincinnati Childrens Hospital Medical Center

data_processing:
Mouse GRCm39 cDNA from Ensembl - Mus_musculus.GRCm39.cdna.all.fa.gz
Table of filtered (<1 CPM in 2 or more samples) and normalized (TMM method) genes for each sample

source_name: Telencephalon

extract_protocol: Trizol isolation followed by ethanol and sodium acetate precipitation

value: Telencephalon

tag: polr genotype

value: missense

tag: age


title: Isolated cells from differentiated root tissue at day 0 - Replicate 2

description:
SCR_D_cells_D0_2
FPKM_Replicates.xlsx
complete_table.xlsx


title: Polr_2138_4

value: wt


title: NOMO1_DMSO_QS_R1


title: HL60_DMSO_QS_R1


title: Bioprinted constructs of differentiated root tissue at day 1 - Replicate 1

description:
SCR_D_bio_D1_1
FPKM_Replicates.xlsx
complete_table.xlsx

value: day 1


title: LINC00857 siRNA 2# 3

city: Weifang City

first: Jiaqiu

last: Li

state: 省/直辖市

address: No. 2428, Yuhe Road, Kuiwen District

institute: weifang medical university

data_processing:
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA).
After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min.
The average insert size for the final cDNA librarys were 300±50 bp.
At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Assembly: HG19
Supplementary files format and content: The Excel file contains raw counts for each gene and each sample.

source_name: HCT116 cell

growth_protocol: HCT116 was cultured in McCOY’s 5A medium supplemented with 10% bovine serum at 37ºC with 5% CO2.

extract_protocol:
After LINC00857 knockdown, total RNA was isolated using Trizol reagent. Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HCT116 cell was transfected with LINC00857 specific small interfering RNA (siRNA) using Lipofectamine RNAiMax (Invitrogen).

tag: sirna

value: LINC00857-siRNA 2


title: Polr_2138_3


title: TENT2KO_TENT2_wt_2


title: Bioprinted constructs of differentiated root tissue at day 0 - Replicate 3

description:
SCR_D_bio_D0_3
FPKM_Replicates.xlsx
complete_table.xlsx


title: Polr_2138_2


title: MT_3d

description: 10x Genomics


title: Bioprinted constructs of differentiated root tissue at day 3 - Replicate 2

description:
SCR_D_bio_D3_2
FPKM_Replicates.xlsx
complete_table.xlsx

value: day 3


title: LINC00857 siRNA 2# 2


title: TENT2KO_TENT2_wt_1


title: Polr_2138_1


title: Polr_2138_6


title: Bioprinted constructs of differentiated root tissue at day 1 - Replicate 2

description:
SCR_D_bio_D1_2
FPKM_Replicates.xlsx
complete_table.xlsx


title: Bioprinted constructs of differentiated root tissue at day 1 - Replicate 3

description:
SCR_D_bio_D1_3
FPKM_Replicates.xlsx
complete_table.xlsx


title: TENT2KO_GFP_2


title: Bioprinted constructs of differentiated root tissue at day 0 - Replicate 1

description:
SCR_D_bio_D0_1
FPKM_Replicates.xlsx
complete_table.xlsx


title: TENT2KO_TENT2_cd_2


title: TENT2KO_GFP_1


title: HL60_DMSO_QS_R2


title: TENT2KO_TENT2_cd_1


title: LINC00857 siRNA 1# 3

value: LINC00857-siRNA 1


title: TKO_1

tag: cell line background

tag: genotype/replicate

tag: molecule type

value: IP RNA


title: Polr_2048_2

tag: tissue


title: TKO_GFP_2

tag: cell line


title: Bioprinted constructs of differentiated root tissue at day 3 - Replicate 1

description:
SCR_D_bio_D3_1
FPKM_Replicates.xlsx
complete_table.xlsx


title: DKO_1


title: LINC00857 siRNA 1# 1


title: Bioprinted constructs of differentiated root tissue at day 0 - Replicate 2

description:
SCR_D_bio_D0_2
FPKM_Replicates.xlsx
complete_table.xlsx


title: LINC00857 siRNA 2# 1


title: Polr_2048_11


title: Polr_2048_3


title: NC 3

value: NC


title: Delta_12hr_2

city: Galveston

first: Steven

middle: G

last: Widen

state: Texas

address: 301 University Blvd

department: BMB

institute: University of Texas Medical Branch

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
Reads were aligned to the ENSEMBL Rnor_6 reference using STAR version 2.7.5c using the parameters recommended by the software authors for the Encode consortium
Read counts for Rnor_6 were obtained with the quantMode GeneCounts function using the ENSEMBL
Reads were aligned to the Burkholderia pseudomallei reference with Bowtie2 version 2.3.4.1 with the --local parameter
FeatureCounts software v2.0.1 was used to count reads per gene using the Burkholderia Database version 132 annotation file.
Assembly: Rnor_6
Assembly: GCF_000011545.1
Supplementary files format and content: Raw read counts for Rnor_6
Supplementary files format and content: Raw read counts for Burkholderia pseudomallei

organism: Rattus norvegicus

source_name: Primary intestinal epithelial cells

extract_protocol:
Total RNA was isolated using Direct-zol™ RNA  kit (Zymo Research) with on-column DNAse digestion according to the manufacturer’s recommendations
Ribosomal RNAs depleted with ThermoFisher RiboMinus kits, followed by Illumina TruSeq Stranded RNA kit.

tag: animal source

value: Cell biologics, inc

value: Primary intestinal epithelial cells

tag: vaccination status

tag: infection status

value: Burkholderia pseudomallei Δhcp1

tag: experiment group


title: ATAC data from re-challenged mouse

city: Pittsburgh

first: Wei

last: Chen

address: 4401 Penn Ave, Rangos Research Building 9125

institute: UPMC Children's Hospital of Pittsburgh

description: ATAC data from re-challenged mouse

data_processing:
Standard 10X Genomics Space Ranger, Cell Ranger, and Cell Ranger ATAC pipeline
Genome_build: mm10
Supplementary_files_format_and_content: For each sample, the raw UMI count matrix or raw peak count matrix is stored in a csv file with features as row names and spot barcodes or cell barcodes as column names.

source_name: Lung

extract_protocol:
For spatial transcriptomics, mouse lungs were harvested, and the left lobes were inflated with 1mL mixture of 50% sterile PBS/ 50%Tissue-Tek OCT compound (SAKURA FINETEK) followed by frozen in alcohol bath on dry ice. OCT blocks were stored in -80C until further processing. For scRNA-seq and scATAC-seq, lungs were removed and digested by Collagenase/DNase to obtain single-cell suspension. Mononuclear cells after red blood cell lysis and filtration with a 40 μM cell strainer were kept.
For spatial transcriptomics, OCT blocks were sectioned at 10μm in thickness, 6.5mm X 6.5mm in size, attached to the Visium slides, then stained with hematoxylin and eosin following 10x Genomics Visium fresh frozen tissue processing protocol. For scRNA-seq and scATAC-seq, cells were subjected to scRNA-seq and scATAC-seq library prep following the protocols by 10x Genomics using the Chromium controller.

tag: group

value: re-challenged


title: Delta_6hr_2

tag: cell type

value: 6 h


title: TKO_TENT2_wt_1


title: Delta_6hr_1


title: Spatial transcriptomics data from slice A4 (re-challenged mouse)


title: Delta_12hr_3


title: LINC00857 siRNA 1# 2


title: TENT2KO_2


title: Delta_12hr_1


title: TUT7KO_2


title: NC 1


title: Mock_2

value: Mock


title: NC 2


title: Spatial transcriptomics data from slice A3 (re-challenged mouse)


title: TUT7KO_1


title: TENT2KO_1


title: Delta_6hr3


title: Mock_3


title: Polr_2048_1


title: Spatial transcriptomics data from slice A1 (immunized mouse)

value: immunized


title: Mock_1


title: TUT4KO_1


title: TUT4KO_2


title: C1

first: Chengsheng

last: Wu

state: California

address: 2880 Torrey Pines Scenic Dr,

institute: University of California San Diego

description: 79E+EV, no LPA, repeat 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 (hg38) genome and the gencode_version37 annotation file using the STAR software package.
Reads were also aligned and counted with the STAR package.
Genome_build: GRCh38 (hg38) genome
Supplementary_files_format_and_content: Normalized_counts_for_all_samples.xlsx: Excel file includes DESeq2's median of ratios normalized counts values for each Sample.

source_name: patient-derived pancreatic cancer cells

growth_protocol: Cells were grown in charcoal-stripped Fetal bovine serum-containing media.

extract_protocol:
RNA was harvested using the RNeasy RNA purification kit (Qiagen). NEBNext Ultra RNA library prep kit (NEB) was used to generate RNA-seq libraries from 1 ug RNA per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Half million cells were grown in charcoal-stripped Fetal bovine serum-containing media overnight prior to 1 uM LPA stimulation for up to 2 hours. LPA powder was dissolved in water and sonicated at 37 'C for 15 minutes.

tag: expression

value: EV

tag: treatment

value: No LPA


title: C4

description: 79E+LPAR4, no LPA, repeat 3


title: C2

description: 79E+EV, 1uM LPA, 2 hours, repeat 3

value: 1uM LPA, 2 hours


title: C5

description: 79E+LPAR4, 1uM LPA, 2 hours, repeat 3


title: RNA data from re-challenged mouse

description: RNA data from re-challenged mouse


title: WT_293T_2


title: WT_12hr_3

value: Burkholderia pseudomallei K96243 (WT)


title: WT_12hr_2


title: WT_293T_1


title: B5

description: 79E+LPAR4, 1uM LPA, 2 hours, repeat 2


title: NPC sc-seq Nrg4 KO-1

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

data_processing:
FastQC was used to assess the sequencing quality on fastq files.
STAR was used for alignment to generate bam files.
The reads aligned to each gene feature were counted by Rsubread package (version 2.0.1).
R package DESeq2 was used for differential expression analysis.
Single-cell RNA seq data was processed by Seurat package (version 3.1.2).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from bulk RNA-seq, UMI count matrices from single cell RNA-seq.

source_name: liver

extract_protocol:
Perfusion collagenase and pronase (0.4mg/ml) from portal vein into mouse liver was performed after euthanasia. Hepatocyte was removed from total cell suspension by gradient centrifugation. The NPCs were suspended in 1ml 10% FBS DMEM.
RNA libraries were prepared for sequencing using standard Illumina and 10X genomics Chromium single cell protocols

treatment_protocol: mice were fed on NASH diet (D09100301, Research Diets) for 36 weeks

tag: strain

value: liver non-parenchymal cells

tag: phenotype

value: NASH

tag: genotype


title: NPC sc-seq Nrg4 KO-2

extract_protocol:
Perfusion collagenase and pronase (0.4mg/ml) from portal vein into mouse liver was performed after euthanasia. Hepatocyte was removed from total cell suspension by gradient centrifugation. The NPCs were suspended in 1ml 2% FBS DMEM at a density of 106 cell/ml.
RNA libraries were prepared for sequencing using standard Illumina and 10X genomics Chromium single cell protocols


title: WT_12hr_1


title: Spatial transcriptomics data from slice A2 (immunized mouse)


title: B4

description: 79E+LPAR4, no LPA, repeat 2


title: B2

description: 79E+EV, 1uM LPA, 2 hours, repeat 2


title: tetraploid S288C 4N_02

type: RNA

city: Kaiserslautern

first: Zuzana

last: Storchova

state: Rhineland Palatinate

address: Paul Ehrlich Straße 24

department: Molecular Genetics

country: Germany

institute: Technical University Kaiserslautern

hyb_protocol: Samples were hybridized to GeneChip Yeast Genome 2.0 microarrays following the instructions from the supplier (Affymetrix)

scan_protocol: Following the instructions from the supplier (Affymetrix).

data_processing:
Analysis of cDTA data was carried out as described {Sun, 2012 #47} using R/Bioconductor and the DTA package
Matrix table includes median value of mRNA abundance

label: biotin

organism: Saccharomyces cerevisiae S288C

source_name: tetraploid saccharomyces cerevisiae

label_protocol: Labeling of samples for array analysis was performed using the GeneChip 3′IVT labeling assay (Affymetrix) with 100 ng input RNA

growth_protocol: S. cerevisiae cells were grown in SD medium overnight, diluted to an OD600 of 0.1 the next day and grown up to a mid‐log phase (OD600 of 0.8)

extract_protocol: Total RNA was extracted with the RiboPure‐Yeast Kit (Ambion/Applied Biosystems), following the manufacturer's protocol

tag: ploidy

value: tetraploid


title: NPC sc-seq WT-2

value: WT


title: WT_6hr_3


title: tetraploid S288C 4N_03


title: NPC sc-seq WT-1


title: WT_6hr_2


title: B1

description: 79E+EV, no LPA, repeat 2


title: tetraploid S288C 4N_01


title: Normal_nasopha_RNAseq_3

city: Chengdu, Cihna

first: zhang

last: lu

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
Sequenced reads were mapped to mm10 reference using STAR
Counts were normalized and measured by Transcript per million (TPM).
Differential gene expression was analyzed by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: csv files with gene counts,TPM,DESeq  results

source_name: Nasopharyngeal organoids

growth_protocol: The tumors was developed on recipient mice after orthotopical nasopharynx transplantation.

extract_protocol:
RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The tumor organoids (primary/metastasized) estalished from TMP( Trp53-/-;Myc;sgCdkn2a ) and TMPL(Trp53-/-;Myc;sgCdkn2a; LMP1) mice

value: untreated


title: WT_6hr_1


title: A5

city: La Jolla

description: 79E+LPAR4, 1uM LPA, 2 hours, repeat 1


title: A2

description: 79E+EV, 1uM LPA, 2 hours, repeat 1


title: tetraploid S288C 4N_04


title: Normal_nasopha_RNAseq_2


title: OSC_Lint-O KD RNA-seq rep 2

city: Yayoi, Bunkyo-ku

first: Hitomi

last: Yamamoto-Matsuda

state: Tokyo

department: Dept. Biol. Sci.

country: Japan

institute: the University of Tokyo

data_processing:
Basecalls were performed by illumina Hiseq
trim down the base to first 50 bp from 150 bp using seqkit
Reads were alighed to the dm6 genome assembly using HISAT2
only unique reads were extracted
read count by using HTseq
Genome_build: dm6
Supplementary_files_format_and_content: txt file(count data)

organism: Drosophila melanogaster

source_name: OSCs

growth_protocol: OSCs were cultured in Shields and Sang M3 Insect Medium(Sigma). The medium included extra-added 0.6 mg/ml glutathione, 10% FBS, 10mU/mL insulin and 10% fly extract(Saito et al., 2009)

extract_protocol:
RNAs were extracted according to NipponGene's instructions accompanying RNA extraction kit(311-07361).
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit. Poly-A selected mRNAs were brought to library preparation.

treatment_protocol: RNAi treated for 48 hours

value: cultured ovarian somatic cells [OSCs]

value: RNAi treatment for 48 hours, Lint-O KD


title: OSC_Lint-O KD RNA-seq rep 3


title: Normal_lung_RNAseq_3

source_name: Lung organoids


title: A4

description: 79E+LPAR4, no LPA, repeat 1


title: Normal_lung_RNAseq_2


title: Normal_nasopha_RNAseq_1


title: triploid S288C 3N_08

source_name: triploid saccharomyces cerevisiae

value: triploid


title: triploid S288C 3N_07


title: OSC_Lint-O KD RNA-seq rep 1


title: triploid S288C 3N_05


title: triploid S288C 3N_06


title: A1

description: 79E+EV, no LPA, repeat 1


title: DO0_4

city: tianjin

first: Qiangqiang

last: Liu

state: State...

address: weijin road94

institute: Nankai University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequenced reads were then mapped to GRH38 whole genome using Hisat2 with default parameters
Samtools were used to get sorted bam files and featurecounts were used to get raw counts.
Homo sapiens
Genome_build: GRH38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Breast

extract_protocol:
RNA of MDA-MB-231 cells was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Lung-LMP1_RNAseq_3

description: Trp53-/-;Myc;sgCdkn2a; LMP1(TMPL),metastasis

source_name: organoids


title: triploid S288C 3N_04


title: Normal_lung_RNAseq_1


title: OSC_L(3)mbt KD RNA-seq rep 3

value: RNAi treatment for 48 hours, L(3)mbt KD


title: OSC_L(3)mbt KD RNA-seq rep 2


title: DO0_3


title: Lung-LMP1_RNAseq_2


title: triploid S288C 3N_03


title: DO0_2


title: OSC_L(3)mbt KD RNA-seq rep 1


title: triploid S288C 3N_01


title: OSC_EGFP KD RNA-seq rep 3

value: RNAi treatment for 48 hours, EGFP KD


title: Lung-LMP1_RNAseq_1


title: triploid S288C 3N_02


title: Lung-Ctr_RNAseq_2


title: WT24_4

value: treated with hypoxia for 24 hours

value: wild type


title: diploid S288C 2N_08

source_name: diploid saccharomyces cerevisiae

value: diploid


title: OSC_EGFP KD RNA-seq rep 1


title: diploid S288C 2N_06


title: OSC_input genome rep 2

data_processing:
Basecalls were performed by illumina Hiseq
trim down the base to first 50 bp from 150 bp using seqkit
Reads were alighed to the dm6 genome assembly using bowtie2
only unique reads were extracted
dupicate reads were removed with picard tool
Genome_build: dm6
Supplementary_files_format_and_content: wig

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA-protein complexes were immunoprecipitated with antibody
Libraries were prepared according to illumina's instructions accompanying NEBNext Ultra 2 FS DNA Library Prep Kit (E7805). In the adaptor ligation step, the original adaptor reagent was diluted to 10 times. After adapter ligation DNA was purified with AMPure XP beads(Beckman Coulter) for size selection. Then DNA was PCR amplified with Illumina primers for 13~16 cycles and library fragments of ~325 bp (insert plus adaptor and PCR primer sequences) were purified with AMPure XP beads(Beckman Coulter). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.


title: OSC_EGFP KD RNA-seq rep 2


title: WT24_2


title: LMP1_RNAseq_2


title: Lung-Ctr_RNAseq_1


title: WT24_1


title: LMP1_RNAseq_1


title: OSC_Lint-O-ChIP-seq rep 2

value: Lint-O antibody


title: WT0_4


title: Ctr_RNAseq_3


title: WT0_3


title: Ctr_RNAseq_2


title: diploid S288C 2N_03


title: OSC_Lint-O-ChIP-seq rep 1


title: OSC_input genome rep 1


title: diploid S288C 2N_05


title: WT0_2


title: OSC_L(3)mbt-ChIP-seq rep 2

value: L(3)mbt antibody produced in our lab


title: diploid S288C 2N_02


title: WT24_3


title: WT0_1


title: diploid S288C 2N_07


title: Ctr_RNAseq_1


title: OSC_L(3)mbt-ChIP-seq rep 1


title: DO0_1


title: diploid S288C 2N_01


title: haploid S288C 1N_04

source_name: haploid saccharomyces cerevisiae

value: haploid


title: Mixed samples (A,B,C) Day 5_scRNA-Seq

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

description: A: Mouse 1-4, collagen; B: Mouse 1-4, matrigel, C: 4T1

data_processing:
base-calling and alignment to GRCm38 reference v3.1.0 using cellranger v3.0.2 to filter cells based on count depth and umi rank knee plot and to generate gene count matrix
cell to sample barcode matrix generated from barcode fastq files using kite workflow of kb_python v0.24.4 and demultiplexed using deMULTIplex v1.2.0
filtering done with scanpy v1.4.4 to remove cells with less than 200 genes detected and mitocondrial gene content more than 10%, and remove genes detected in less than 3 cells
Genome_build: mm10
Supplementary_files_format_and_content: mtx file containing gene counts

source_name: A,B:C3(1)-Tag primary breast cancer cells, C:4T1 (ATCC® CRL-2539™)

extract_protocol:
[media]  A: Cells were removed from collagen matrix by a 10 min incubation on a benchtop shaker at 180 r.p.m. (37 °C) with 2 mg ml−1 collagenase in PBS, B:For Matrigel matrix, gels were washed once with ice-cold PBS without Ca2+ and Mg2+ followed by a 30 min incubation on ice with 10 mM EDTA (Sigma, EDS)
[dissociation into single cells]  A,B:After two washes in PBS, organoids were dissociated into single cells by incubating with 10X TryplE (Thermo Fischer, A1217701), 10 min on a benchtop shaker at 180 r.p.m. (37 °C). After centrifugation at 400g for 10 min, 2 U μl−1 DNase (Sigma, D4263) were added in DMEM-F12 and incubated for 5 min at room temperature. Cells were resuspended in PBS and filtered through a 40-μm filter to remove the undigested organoids;C:4T1 cells were trypsinized using trypsin-EDTA 0.25 % (Thermo Fisher, 25200056). Detached cells were resuspended in culture media and centrifuged at 400g, 5 min at room temperature.
[barcoding protocol]  Cells were barcoded by condition with MultiSeq (McGinnis et al., 2019) and flow sorted for live cells using Propidium iodide (Thermo Fisher, P3566).
Multi-seq library was prepared following 10X single cell controller protocol and Multi-Seq specific protocol. Library construction from the single cell suspensions were performed using the 10X Genomics Chromium Single Cell 3' Reagent Kit v2, following manufacturer's instructions.Briefly, Multi-Seq barcoded and pooled single cell suspension were counted using Countess II (Thermal Fisher) to determine cell concentration and viability. The cell volume to use was calculated based on the cell concentration and the targeted cell number. The cell suspension was brought to 46.6 µl with molecular biology water and then mixed with 33.4 µl premade single cell master mix containing RT reagent, template switch oligo, reducing reagent, and RT enzyme.  75 µl of the resulting cell/master mix solution were loaded to 10X single cell A Chip row 1. The gel beads were vortexed for 30 seconds and 40 µl were loaded to 10X single cell A Chip row 2.  280 µl partition oil were loaded to 10X single cell A Chip row 3. The unused lanes were filled on the Chip with 50% Glycerol. 10X provided gasket was attached to the chip, then the chip was loaded into 10X single cell controller and the cell partitioning program was run. After the program completes, 100 µl of GEM were removed from the recovery well and slowly dispensed into pre-chilled PCR plate. The plate was sealed and incubated at 53°C for 45 min, 80°C for 5 min and then chill to 4°C. The recovery reagent was then added to the GEM-RT reaction to break up the single cell emulsion and the cDNA was purified using Thermal fisher Dynabeads MyOne Saline magnetic beads and amplified by PCR using 10X provided reagents and Multi-Seq primer. The amplified cDNA was purified using Beckman Coulter SPRI magnetic beads and the endogenous transcript cDNA and Multi-Seq barcode cDNA were separated. The purified cDNA was quantitated using Thermal Fisher Qubit high sensitivity dsDNA assay and ran on Agilent Bioanalyzer High sensitivity DNA chip for quality control. The transcript cDNA library was prepared following standard Illumina library preparation using 10X provided reagents, i.e., fragmentation, end repair and dA tailing, adapter ligation, and PCR amplification. The Multi-Seq barcode cDNA library was prepared by PCR amplification using universal i5 primer and RPI index primer. After library qc and quantitation, the transcript library and the Muti-Seq barcode library were pooled in 95:5 ration and sequenced together on NovaSeq.

treatment_protocol: A,B: DMEM/F12, ITS 1% vol/vol, PS 1% vol/vol, 2.5 nM FGF2;C: RPMI-1640 10% FBS, PS 1% vol/vol

tag: time

value: day 5

tag: batch

tag: passage

value: A,B:0 (freshly isolated tissue), C:2

tag: age

value: A,B:Between 25-30 weeks (primary tumor:20mm)

tag: culture condition

value: A:Organoids plated in collagen I for 5 days, B:Clusters plated in Matrigel for 5 days, C:Cells cultivated on plastic


title: TC71-EF-KD-NKX2-2-rep1

city: Columbus

first: Iftekhar

middle: Ahmed

last: Showpnil

address: 700 Childrens Drive

department: CCCBD

institute: Nationwide Children's Hospital

data_processing:
Demultiplexing reads to retain only reads containing the reading primer identifying the viewpoint (region of interest) using pipe4C, version 1.0.0. Only R1 files were used for processing
Trimming of reads was performed to extract the capture sequence (loci interacting with the region of interest) between the two restriction sites
Read alignment using Bowtie2
in silico fragment end library generation using the Bioconductor BSgenome.Hsapiens.UCSC.hg19 R package
reads mapping uniquely to the reference genome with the capture length were counted, normalized for sequencing depth, and tored in rds files
Genome_build: hg19
Supplementary_files_format_and_content: RDS files containing normalized read counts and quality metrics were generated using pipe4C; RDS files were used in peakC R package to identify significant interactions

source_name: TC71 Ewing sarcoma cells

growth_protocol: A673 cells were cultured in DMEM with L-Glutamine, supplemented with 10% FBS, 1% PSQ, 1% sodium pyruvate for 2-3 days, followed by selection in the same media supplemented with 2μg/mL puromycin, and 150μg/mL hygromycin B at 37ºC and 5% CO2. TC71 cells were cultured in RPMI 1640 without L-Glutamine, supplemented with 10% FBS and 1% PSQ at 37ºC and 5% CO2 for 2 days, followed by selection in the same media supplemented with 2μg/mL puromycin.

extract_protocol:
PCR purification followed by AMPure XP bead extraction
4C (circular chromosome conformation capture)

treatment_protocol: EWS/FLI knock-down with RNAi followed by rescue of EWS/FLI expression with a 3XFLAG tagged EWS/FLI cDNA construct

tag: transduced shrna

value: iEF + empty cDNA

tag: replicate

tag: sample condition

value: EF-KD


title: haploid S288C 1N_03


title: Mixed samples (A,B,C) Day 0_scRNA-Seq

value: day 0

value: A:Organoids plated in collagen I for 12 hours, B:Clusters plated in Matrigel for 12 hours, C:Cells cultivated on plastic


title: Mixed samples (A,B,C) Day 3_scRNA-Seq

value: day 3

value: A:Organoids plated in collagen I for 3 days, B:Clusters plated in Matrigel for 3 days, C:Cells cultivated on plastic


title: diploid S288C 2N_04


title: TC71-EF-KD-NKX2-2-rep2


title: TC71-EF-Endo-NKX2-2-rep2

value: iLuc + empty cDNA

value: EF-Endo


title: haploid S288C 1N_02


title: RNA-seq Fc-Nrg4-6

description: Mouse liver was harvested and immediately frozen into liquid nitrogen. RNA was extract by TRIzol. Sequencing library was constructed from more than 400ng of total RNA by BGI sequencing service.

data_processing:
Fastp (version 0.12.4) was used to assess the sequencing quality on fastq files.
STAR (version 2.5.3a) was used for alignment to generate bam files.
The reads aligned to each gene feature were counted by HTseq (version 0.11.3)
R package DESeq2 was used for differential expression analysis.
Assembly: mm39
Supplementary files format and content: Processed data files contain DESeq2-normalized read counts, log2FoldChange, pvalue and padj from bulk RNA-seq

extract_protocol:
please see samples description
RNA libraries were prepared for sequencing using standard Illumina

treatment_protocol: male mice were put on NASH diet  (D09100301, Research Diets) for two weeks before a single tail vein injection of the AAV-oncogene cocktail (AAV8-cMyc + AAV8-nRAS-V12 each at 6X109 genome copies/mouse). Two weeks after tumor induction, mice received weekly treatments of Fc or hNRG4-Fc at a dose of 2.5 mg/kg for four weeks before sample collection

tag: tissue

value: whole liver


title: MhcGal4PtxRNAi2_sample1

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA version 1.7
Sequences derived from total RNA paired-end 100-bp sequences were mapped to the mouse mm9 genome with the STRONGARM pipeline, which uses BWA and STAR aligner.
Transcript-level data were counted with HTSEQ
Genome_build: dm5
Supplementary_files_format_and_content: txt

source_name: Ptx1 RNAi in skeletal muscle

extract_protocol:
RNA was isolated from total cell lysates with the RNeasy Plus Mini kit (Qiagen)
total RNA, paired 100 bp; RNA was prepared for RNA-seq with the TruSeq stranded mRNA library preparation kit (Illumina)

treatment_protocol: RNAi treated skeletal muscle

value: Pitx RNAi

value: skeletal muscle

value: 10 days old

tag: Sex

value: male


title: A673-EF-Rescue-NKX2-2-rep2

source_name: A673 Ewing sarcoma cells

value: iEF + 3XFLAG-EWS/FLI

value: EF-Rescue


title: haploid S288C 1N_01

value: haploid


title: RNA-seq Fc-Nrg4-5


title: RNA-seq Fc-3

value: Fc


title: ATC#4

city: Amsterdam

first: Linda

last: Smit

address: De Boelelaan 1117

department: Hematology

institute: Amsterdam UMC

description:
ATC4
diffexp_ATCs_Parental.txt

data_processing:
A mixture of 10 pM libraries were pooled equimolar and the resulting DNA was clustered onto a V3 flow cell lane using a c-Bot cluster station and subsequently sequenced in single read fashion for 50bp using a TruSeq SBS v3-Kit and HiSeq2000 Sequencing System (Illumina).
Sequence reads were aligned to the human reference genome (GRCh38)
The R package DEGseq was used to determine differentially expressed genes between purified samples.
For interpretation of gene expression data, functional pathway analysis was performed using DAVID (v6.8), protein-protein interaction was performed using String, and gene-set enrichment analysis was performed using Broad Institute Software (v4.1.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited tekst files include raw read count values and log2 fold change value (calculted with the R package DEGseq) per gene for each sample

source_name: cell line

growth_protocol: K562 cells were purchased from the American Type Culture Collection (ATCC) and cultured in Roswell Park Memorial Institute-1640 (RPMI1640; ThermoFisher Scientific) medium with 10% fetal calf serum (FCS).

extract_protocol:
Total RNA was extracted with TRIzol (ThermoFisher Scientific) according to manufacturer's protocol. Quality of RNA was measured on a 2100 Bioanalyzer (Agilent).
Sequencing libraries, each with individual Illumina indexes, were constructed using the TruSeq™ Stranded mRNA procedure (Sample Prep Kit v2; Illumina).

treatment_protocol: For making doxorubicin tolerant cells, 5x 96 well plates (Corning) were seeded with 10.000 cells/well (480 wells in total). Two days post seeding, treatment with 100 ng/ml doxorubicin was started. After 3 days, part of the cells was passaged to new 96 well plates containing 225 ng/ml doxorubicin. Four weeks later, 21 wells containing viable cells that survived chemotherapy treatment were transferred to new wells in a 96 well plates containing 225 ng/ml doxorubicin. Subsequently, cells from 4 wells could be maintained in culture in the presence of 225 ng/ml doxorubicin. To compare gene expression profiling, parental cells were shortly treated with 225 ng/ml doxorubicin for 48 hours.

value: cell line

tag: cell line

tag: cell type

value: chronic myelogenous leukemia

value: anthracycline-tolerant clone

value: 225 ng/ml doxorubicine

value: maintained in culture in presence of drug


title: A673-EF-Rescue-NKX2-2-rep1


title: MhcGal4PtxRNAi2_sample2


title: RNA-seq Fc-2

tag: treatment


title: ATC#2

description:
ATC2
diffexp_ATCs_Parental.txt


title: A673-EF-KD-NKX2-2-rep2

value: iEF + empty cDNA

value: EF-KD


title: ATC#3

description:
ATC3
diffexp_ATCs_Parental.txt


title: MhcGal4PtxRNAi2_sample3


title: RNA-seq Fc-1

tag: strain


title: A673-EF-KD-NKX2-2-rep1


title: RNA-seq Nrg4 KO-3

extract_protocol:
Mouse liver was harvested and immediately frozen into liquid nitrogen. RNA was extract by TRIzol. Sequencing library was constructed from more than 400ng of total RNA by BGI sequencing service.
RNA libraries were prepared for sequencing using standard Illumina and 10X genomics Chromium single cell protocols

tag: phenotype

value: NASH


title: siRBAP48-DHT rep1

city: Wuhan

first: Ge

last: Sun

state: Hubei

address: Shizi Mountain Street No.1

institute: Huazhong Argriculture University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38

source_name: Oral squamous cell carcinoma

growth_protocol: Cells were cucltured into DMEM medium with 10% FBS

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Oral squamous cell carcinoma

value: Oral squamous  carcinoma

value: CAL-27 cell

tag: genotype

value: RBAP48 knockdown

value: DHT


title: ATC#1

description:
ATC1
diffexp_ATCs_Parental.txt


title: siRBAP48-DHT rep2


title: siRBAP48-EtOH rep3


title: siRBAP48-EtOH rep2


title: siRBAP48-EtOH rep1


title: A673-EF-Endo-NKX2-2-rep2

value: iLuc + empty cDNA

value: EF-Endo


title: siCtrl-DHT rep3

value: wild type

value: EtOH


title: TC71-EF-Endo-NKX2-2-rep1


title: siRBAP48-DHT rep3


title: RNA-seq Nrg4 KO-2

value: whole liver


title: siCtrl-DHT rep2


title: K562 parental cells + 225 ng/ml doxo

description:
Parental_Doxo
diffexp_Parental.txt

value: cell line

value: chronic myelogenous leukemia

value: WT

value: 48 hours


title: RNA-seq Nrg4 KO-1


title: L3 NotDissociated ATAC Rep2

first: Elizabeth

last: Fogarty

address: 1105 N. University Ave

data_processing:
Adaptors and low-quality bases trimmed with cutadapt version 1.18, -q 20, -m 25
Alignment to Wolbachia genome ASM802v1, --local --very-sensitive -X 1000
Alignment to Drosophila genome dm6, --local --very-sensitive -X 1000
PCR duplicates marked with Picard version 2.8.1 MarkDuplicates
Bam file generation, sub-nucleosomal fragments selected, downsampling, sorting, and indexing with samtools version 1.5
Bigwig file generation with Deeptools bamCoverage --binsize 10 --extendreads --normalizeUsing CPM --ignoreForNormalization chrM
Peaks called using macs2 verison 2.1.2 callpeak
Read coverage in peaks quantified by subread version 1.6.0 featurecounts
Assembly: dm6
Supplementary files format and content: BigWig

source_name: wing disc

growth_protocol: Animals were raised at 25°C on Bloomington Cornmeal media without malt extract

extract_protocol:
Dissect 10 larval wing discs or pupal wings per sample in Wash+ solution (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.1% BSA, 0.5 mM Spermidine and Roche complete Protease Inhibitor Tablet: 1 tablet per 50 mL). Pipet 100ul of dissected tissues in Wash+ solution directly into 100µL 2X Collagenase/Dispase solution. Incubate at 23C for 30 minutes, shaking at 500 rpm. Vortex for 10 seconds at 60% max speed on a benchtop vortexer. Incubate another 10 minutes at 23C, shaking at 500 rpm. Vortex again for 10 seconds at 60% speed. From here, we use the Omni-ATAC Protocol (Corces et al., 2017). Spin down at 800 x g, 5 minutes, at 4C. Remove supernatant and wash in 200 µL 1X PBS. Repeat 4C spin and remove supernatant. Resuspend cell pellet in 50 µl cold ATAC-RSB (10mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2) supplemented with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Pipette up and down 3 times. Incubate on ice 3 minutes. Add 1 mL cold ATAC-RSB containing 0.1% Tween-20 without NP40 or Digitonin. Invert tube 3 times. Spin down at 800 x g for 10 minutes, 4°C. Discard supernatant and resuspend nuclei in 50 µL transposition reaction mix: 25 µl 2x TDE1 Buffer, 3.5 µl Tn5 Enzyme, 16.5 µl PBS, 0.5 µL 1% Digitonin, 0.5 µL 10% Tween-20, 5 µL water. Incubate at 37°C for 30 minutes shaking at 1000 rpm.Purify using a Qiagen MinElute kit according to manufacturer’s protocol. Elute in 21 µl Elution Buffer (10 mM Tris buffer pH 8.0).
Library amplification was performed with NEBNext High-Fidelity 2X PCR Master Mix, according to cycling conditions described in Corces et al., 2017, and qPCR side reactions to optimize the number of PCR cycles for each sample. Libraries were assessed on an Agilent Bioanalyzer prior to sequencing

treatment_protocol: Larval samples were dissected from wandering larvae isolated from uncrowded vials. Vials with more than ~100 larvae were diluted into fresh vials to keep larvae uncrowded. Pupa were collected from vials at the White Pre-pupa stage (WPP) as described (Flegel et al., 2013), which was taken as 0h After Puparium Formation (APF) and reared on damp Kimwipes at 25°C to the indicated hours APF.

value: wing disc

value: y,w,hsflp/w ; + ; +

value: female

value: Not Dissociated


title: UMUC9-Chipseq_H3K27me3

city: Chicago

first: Joshua

last: Meeks

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

institute: Northwestern University

data_processing:
Chip-seq reads were trimmed from the 3' end using Trimmomatic.
Peaks were called using SICER version 1.1, with a window size of 200, fragment size of 150 and effective genome fraction of 0.8
Peaks were determined relative to input control.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Cells were fixed with freshly prepared 1% formaldehyde for 10 minutes, quenched with 0.125Mglycine for 10 minutes at room temperature. Next, chromatin was sonicated using E220 focused ultra-sonicator (Covaris).
ChIP-seq libraries were prepared with 10ng DNA as input using KAPA HTP Library preparation kit complemented with NEXTFLex DNA barcode from Bioo Scientific and validated using Agilent High Sensitivity DNA kit.

value: bladder cancer

tag: antibody

value: anti-H3K27me3, #9733 Cell Signaling Technology, Lot# 19


title: K562 parental cells

description:
Parental_1, Parental_2
diffexp_Parental.txt
diffexp_ATCs_Parental.txt

tag: time


title: siCtrl-EtOH rep3

value: Oral squamous cell carcinoma

value: Oral squamous  carcinoma

value: CAL-27 cell


title: HT1376-Chipseq_H3K27me3


title: siCtrl-DHT rep1


title: L3 Dissociated ATAC Rep1

value: Dissociated


title: UMUC9_Chipseq_input


title: A673-EF-Endo-NKX2-2-rep1

value: iLuc + empty cDNA

value: EF-Endo


title: L3 Dissociated ATAC Rep2


title: siCtrl-EtOH rep2

value: wild type

value: EtOH


title: DT-40 and mitotic Hela S3 treated with RGFP966 cells (1:3 ratio) - H3K9ac_rep1

status: Public on Aug 14 2022

city: Jerusalem

first: Itamar

last: Simon

state: Israel

address: Hebrew University Medical School

department: Microbiology and Molecular Genetics

country: Israel

institute: The Hebrew University

description: STC synchronized; RGFP966 treatment

data_processing:
ChIP-Seq reads were aligned to the human genome (hg38) using Bowtie2 version 2.3.4.3, suppressing unpaired and discordant read pairs.
Duplicate alignments were removed with Picard Tools MarkDuplicates.
Peak detection on merged replicates (with WCE dataset as a control) was done using MACS2 using p-value of 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: All files are in BED format. The peaks file include all H3K9ac peaks in unsynchronized cells.

organism:
Gallus gallus
Homo sapiens

source_name: DT-40 and Hela S3

growth_protocol: HeLa-S3 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin-streptomycin, L-glutamine, sodium pyruvate, and 0.1% Pluronic F-68. Cells were incubated at 37°C and 5% CO2. DT-40 cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 1% chicken serum, 10 mM HEPES and 1% penicillin-streptomycin mixture at39.5 °C with 5% CO2

extract_protocol:
Hela S3 cells (unsynchronized or STC synchronized with or without the indicated treatments) and unsynchronized and untreated DT-40 cells were cross-linked and mixed. The cell mixture was lysed and sonicated. Immunoprecipitation, using anti-H3K9ac (C5B11, Cell Signalling Technology), was carried out with inverting at 4°C for 14–16 h. Antibody-chromatin complexes were pulled-down using Protein A/G magnetic beads (Dy-10001D and Dy-10003D, Invitrogen), washed and then eluted. After cross-link reversal and Proteinase K treatment, immunoprecipitated DNA was extracted with 1.8x Agencourt AMPure XP beads (BCA63881, Beckman Coulter).
ChIP DNA (or unenriched whole cell extract) were prepared for Illumina sequencing as described (Yehuda, Blumenfeld et al., 2018). Briefly, DNA was subjected to a 50 μl end repair reaction, cleaned by 1.8× Ampure XP beads, followed by a 50μl A-tail reaction. The products were cleaned and ligated to 0.75 μM illumina compatible forked indexed adapters. Ligation products were size selected in order to remove free adaptors. Ligation products were amplified with 15 (Input DNA) or 18 PCR cycles (ChIP DNA). Amplified DNA was size selected for 300–700 bp fragments using Ampure XP beads. The final quality of the library was assessed by Qubit and TapeStation. Libraries were pooled and sequenced on NextSeq (Illumina), using a paired-end protocol

treatment_protocol: Mitotic arrested cells were pre-synchronized in G1/S by addition of 2 mM thymidine for 16 h, washed with PBS, released for 3 h in fresh medium, and arrested with 10uM S-trityl-L-cysteine (STC) (164739, Sigma) for 12 h. HDACs inhibitors (10uM RGFP966, 1uM MS-275, 1uMCAY10683 and 5nM EX-527) were added for the last 9 hours.

value: treated with RGFP966 for 9 hours

tag: chip antibody


title: DT-40 and mitotic Hela S3 treated with RGFP966 cells (1:3 ratio) - H3K9ac_rep2

description: STC synchronized; RGFP966 treatment

value: anti-H3K9ac (C5B11, Cell Signalling Technology)


title: HT1376_Chipseq_input


title: DT-40 and mitotic Hela S3 cells (1:3 ratio) - H3K9ac_rep3

description: STC synchronized; No-treatment

value: untreated


title: DT-40 and mitotic Hela S3 treated with CAY10683 cells (1:3 ratio) - H3K9ac_rep2

data_processing:
ChIP-Seq reads were aligned to the human genome (hg38) using Bowtie2 version 2.3.4.3, suppressing unpaired and discordant read pairs.
Duplicate alignments were removed with Picard Tools MarkDuplicates.
Peak detection on merged replicates (with WCE dataset as a control) was done using MACS2 using p-value of 0.05.
bedtools coverage was used to report the coverage of the inhibitors in H3K9ac peaks. The coverage was normalized to the number of mapped reads multiplied by the chicken factor (10^6 / number_of_mapped_reads * chicken_factor)
edgeR package was used to identify differential peaks between the inhibitors using all the replicates. Peaks with FDR < 0.05 were considered as differential.
Genome_build: hg38
Supplementary_files_format_and_content: All files are in BED format. The peaks file include all H3K9ac peaks in unsynchronized cells.

source_name: STC synchronized; CAY10683 treatment

value: Hela S3 and DT-40

value: treated with CAY10683 for 9 hours


title: DT-40 and mitotic Hela S3 cells (1:3 ratio) - H3K9ac_rep2

description: STC synchronized; No-treatment

data_processing:
ChIP-Seq reads were aligned to the human genome (hg38) using Bowtie2 version 2.3.4.3, suppressing unpaired and discordant read pairs.
Duplicate alignments were removed with Picard Tools MarkDuplicates.
Peak detection on merged replicates (with WCE dataset as a control) was done using MACS2 using p-value of 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: BED format. The peaks file include all H3K9ac peaks in unsynchronized cells.


title: DT-40 and mitotic Hela S3 treated with EX-527 cells (1:3 ratio) - H3K9ac_rep2

source_name: STC synchronized; EX-527 treatment

value: treated with EX-527 for 9 hours


title: DT-40 and Hela S3 cells (1:3 ratio) - input DNA (WCE)

description: WCE

source_name: Unsyncronized; No-treatement


title: DT-40 and mitotic Hela S3 treated with MS-275 cells (1:3 ratio) - H3K9ac_rep1

source_name: STC synchronized; MS-275 treatment

value: treated with  MS-275  for 9 hours


title: RNA-seq WT-3

data_processing:
FastQC was used to assess the sequencing quality on fastq files.
STAR was used for alignment to generate bam files.
The reads aligned to each gene feature were counted by Rsubread package (version 2.0.1).
R package DESeq2 was used for differential expression analysis.
Single-cell RNA seq data was processed by Seurat package (version 3.1.2).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from bulk RNA-seq, UMI count matrices from single cell RNA-seq.

source_name: liver

value: whole liver

value: NASH

value: WT


title: DT-40 and mitotic Hela S3 treated with MS-275 cells (1:3 ratio) - H3K9ac_rep2

data_processing:
ChIP-Seq reads were aligned to the human genome (hg38) using Bowtie2 version 2.3.4.3, suppressing unpaired and discordant read pairs.
Duplicate alignments were removed with Picard Tools MarkDuplicates.
Genome_build: hg38
Supplementary_files_format_and_content: All files are in BED format. The peaks file include all H3K9ac peaks in unsynchronized cells.


title: DT-40 and mitotic Hela S3 treated with CAY10683 cells (1:3 ratio) - H3K9ac_rep1


title: DT-40 and Hela S3 cells (1:3 ratio) - H3K9ac_rep2


title: DT-40 and mitotic Hela S3 cells (1:3 ratio) - H3K9ac_rep1

source_name: STC synchronized; No-treatment


title: L3 NotDissociated ATAC Rep1

value: wing disc

value: y,w,hsflp/w ; + ; +

value: female

value: Not Dissociated


title: DT-40 and mitotic Hela S3 treated with EX-527 cells (1:3 ratio) - H3K9ac_rep1


title: 24h APF wings, IgG, 20 wings, supernatant

description: 24h IgG 20 wings

data_processing:
library strategy: CUT&RUN
Raw sequencing files assessed using FastQC
Trimmomatic-0.39 used to trim adaptors and low-quality bases
Reads aligned to dm6 genome using Bowtie2.4.1 with --local --very-sensitive parameters. Max fragment size set to 1000.
Duplicates marked using picard-tools2.8.1 MarkDuplicates, and BAM files generated using samtools1.5.
Peaks called using macs2 version 2.1.2. Bigwigs and heatmaps generated using DeepTools.
Assembly: dm6
Supplementary files format and content: BigWig

source_name: pupa wing

extract_protocol:
Tissues were dissected in CUT&RUN wash buffer, then dissociated in collagenase/dispase solution for 40 minutes
Libraries were prepared using Takara ThruPLEX DNA-seq and Dual Index kits. Libraries were amplified using 14-19 PCR cycles, then cleaned up using AMPure XP beads from Beckman Coulter. Library quality was assessed using an Agilent Tape Station.

value: pupa wing

tag: cut&run antibody

value: Rabbit Anti-Mouse IgG, Abcam,Cat#Ab46540


title: siCtrl-EtOH rep1

value: Oral squamous cell carcinoma

value: Oral squamous  carcinoma

value: CAL-27 cell

value: wild type

value: EtOH


title: RNA-seq WT-2


title: 24h APF wing, H3K27me3, 20 wings, supernatant

description: 24h H3K27me3 20 wings

value: Rabbit Anti-H3K27me3, Cell Signaling, cat#9733


title: RNA-seq WT-1


title: DT-40 and Hela S3 cells (1:3 ratio) - H3K9ac_rep1

value: Hela S3 and DT-40

value: untreated

value: anti-H3K9ac (C5B11, Cell Signalling Technology)


title: plas_71

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue D'ulm

country: France

institute: Institut Curie

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore software (v0.6.2)
STAR-2.5.3a with two-pass mode was used to alignment the reads
STAR-2.5.3a with  --quantMode GeneCounts
Assembly: hg19 (Ensembl)
Supplementary files format and content: tab-delimited text files include raw counts (from STAR) for each Sample

source_name: lung

extract_protocol:
kit from Qiagen “allprep DNA/RNA/miRNA Universal kit” (ref. 80224) was used. Before extraction, samples were cut with cryostat to obtain around 200µm of thickness of tissue.  The homogenization step with lysis buffer were done with tissue lyzer system
Stranded mRNA prep Ligation-Illumina

value: lung

value: tumos sample, NSCL


title: plas_72


title: plas_63


title: plas_65


title: plas_66


title: plas_69


title: plas_54


title: plas_75


title: plas_55


title: plas_50


title: plas_52


title: plas_61


title: plas_53


title: plas_62


title: plas_49


title: plas_47


title: plas_45


title: plas_42


title: plas_40


title: plas_38


title: plas_34


title: plas_36


title: plas_20


title: plas_30


title: plas_28


title: plas_25


title: plas_56


title: plas_57


title: plas_19


title: plas_14


title: plas_06


title: plas_73


title: plas_03


title: plas_76


title: plas_80


title: plas_60


title: plas_51


title: plas_58


title: plas_77


title: plas_79


title: plas_67


title: plas_78


title: plas_48


title: plas_39


title: plas_27


title: plas_11


title: plas_22


title: plas_15


title: plas_16


title: plas_26


title: plas_74


title: plas_29


title: plas_23


title: plas_21


title: plas_17


title: plas_41


title: plas_13


title: plas_12


title: plas_32


title: plas_10


title: plas_07


title: plas_08


title: plas_31


title: plas_05


title: plas_02


title: plas_01


title: Y19F_03

city: Houston

first: YU YI

last: CHU

address: 6565 MD Anderson Blvd

department: Molecular and Cellular Oncology

institute: MD Anderson Cancer Center

description: expressing Y19F-CDK9

data_processing:
raw data was transformed to raw reads by CASAVA and stored in FASTQ files
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Transcript quantification was performed using featureCounts v1.5.0-p3
Genome_build: Homo sapiens (GRCh38/hg38)
Supplementary_files_format_and_content: A xlsx file of gene expression level (read counts) of all samples.

source_name: ovarain cancer cell line

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic mixture containing 100 units/mL penicillin and 100 mg/ml streptomycin (P/S).

extract_protocol:
Total RNA was extracted from SKOV3 cells using the RNeasy Mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: under basal condtion or ALK inhibitor treatment for 24 hours

value: expressing Y19F-CDK9


title: Ai_01

description: expressing WT CDK9 treated with an ALK inhibitor


title: WT_03

description: expressing WT-CDK9

value: expressing WT-CDK9


title: Y19F_01

description: expressing Y19F-CDK9


title: Ai_02

value: expressing WT CDK9 treated with an ALK inhibitor


title: WT_01

description: expressing WT-CDK9


title: WT_02

description: expressing WT-CDK9


title: SCVI-111_hiPSC_CM_Reporter_1182

city: Stanford

first: Francisco

middle: Xavier

last: Galdos

state: CA

address: 265 Campus Dr.

department: Cardiovascular Institute

institute: Stanford University

description:
Human induced pluripotent stem cells containing a TBX5-lineage tracing system consisting of a TBX5-Cre and CMV Drive lox-stop-lox-TurboGFP construct were differentiated to day 15 hiPSC cardiomyocytes. Cells were dissociated and processed for scRNA-seq using the ICELL8 system.
111_ICELL8_D15_barcodes.tsv.gz
111_ICELL8_D15_features.tsv.gz
111_ICELL8_D15_matrix.mtx.gz

data_processing:
All single cell ibraries were sequenced with the Illumina NovaSeq 6000 platform.
Droplet Based Sequencing: Data generated using the 10X Genomics 3' scRNA-seq v3.1 kit  were processed using CellRanger v6.0.0 (10X Genomics). Default parameters were used for alignment. The reference genomes used were refdata-gex-GRCh38-2020-A  for Human alignment and refdata-gex-mm10-2020-A for mouse data. References were obtained from the 10X Genomics website.
Samples (SCVI-111_hiPSC-Derived Cardiomyocytes_Day7-30) were multiplexed using the 10X Genomics CellPlex kit were demultiplexed using the CellRanger multi configuration. 10X Genomics cell multiplexing oligos used for each individual sample were as follow: Day7-CMO306, Day11-CMO307, Day13-CMO308, Day15-CMO309, Day30-CMO310.
Smartseq2 Based Sequencing: Data generated using the ICELL8 Takara Smartseq2 kit were processed using STARSolo aligner v2.7.9a software developed by Alexander Dobin. Reference genome used was a custom reference from GRCh38-2020-A (10X Genomics) containing added TurboGFP sequence. Parameters used were:  --soloType SmartSeq --soloStrand Unstranded.
GRCh38 (for Human) and mm10 (for Mouse)
Genome_build: Samples containing tab-delimited files contain output from CellRanger or STARSolo containing file with gene ensembl ID and gene symbols, cell barcodes, and matrix file containing raw counts.

source_name: hiPSC-derived Cardiomyocytes

extract_protocol:
Droplet based extraction: HiPSC-derived cardiomyocyte or mouse embryonic heart derived single cells were dissociated and captured and lysed using 10X Genomics Chromium Next GEM Single Cell 3' v3.1 Kit. mRNA was reverse transcribed to cDNA, and cDNA pre-amplification was conducted following manufacturer's protocol.    Smart-seq2 based extraction: HiPSC-derived cardiomyocytes were dissociated into single cell suspensions and captured using the ICELL8 Smartseq2 TAKARA system. mRNA was reverse transcribed to cDNA and cDNA pre-amplification was conducted per manufacturer’s protocol on an ICELL8 nanowell chip.
Droplet based library construction: Libraries for samples processed using 10X Genomics Single Cell 3' v3.1 kit were prepared from pre-amplified cDNA according to manufactrer's protocol. Gene expression libraries were generated for all 10X samples, and CellPlex multiplexing libraries were generated for running hiPSC-CM samples (Day 7, 11, 13,15, 30). Individual library index primers were used for multiplexing libraries on flow cell during sequencing.     Smart-seq2 library construction: Following Takara Smartseq2 ICELL8 protocol, pre-amplified and tagmented cDNA from individual single cells in ICELL8 nanowells received individual index sequencing barcodes for demultiplexing cells during downstream analysis.

value: hiPSC-derived cardiomyocytes

tag: developmental stage

value: Day 15

value: SCVI-111 TBX5-Lineage Reporter Line


title: SCVI-111_hiPSC_CM_Reporter_1183


title: SCVI-111_hiPSC_CM_Reporter_1181


title: SCVI-111_hiPSC_CM_Reporter_1179


title: SCVI-111_hiPSC_CM_Reporter_1180


title: SCVI-111_hiPSC_CM_Reporter_1176


title: SCVI-111_hiPSC_CM_Reporter_1175


title: SCVI-111_hiPSC_CM_Reporter_1177


title: SCVI-111_hiPSC_CM_Reporter_1174


title: Ai_03


title: Y19F_02

description: expressing Y19F-CDK9


title: SCVI-111_hiPSC_CM_Reporter_1170


title: SCVI-111_hiPSC_CM_Reporter_1172


title: SCVI-111_hiPSC_CM_Reporter_1169


title: SCVI-111_hiPSC_CM_Reporter_1173


title: SCVI-111_hiPSC_CM_Reporter_1167


title: SCVI-111_hiPSC_CM_Reporter_1164


title: SCVI-111_hiPSC_CM_Reporter_1165


title: SCVI-111_hiPSC_CM_Reporter_1178


title: SCVI-111_hiPSC_CM_Reporter_1161


title: SCVI-111_hiPSC_CM_Reporter_1157


title: SCVI-111_hiPSC_CM_Reporter_1168


title: SCVI-111_hiPSC_CM_Reporter_1160


title: SCVI-111_hiPSC_CM_Reporter_1159


title: SCVI-111_hiPSC_CM_Reporter_1166


title: SCVI-111_hiPSC_CM_Reporter_1163


title: SCVI-111_hiPSC_CM_Reporter_1158


title: SCVI-111_hiPSC_CM_Reporter_1156


title: SCVI-111_hiPSC_CM_Reporter_1155


title: SCVI-111_hiPSC_CM_Reporter_1162


title: SCVI-111_hiPSC_CM_Reporter_1171


title: SCVI-111_hiPSC_CM_Reporter_1154


title: plas_43


title: SCVI-111_hiPSC_CM_Reporter_1150


title: SCVI-111_hiPSC_CM_Reporter_1149


title: SCVI-111_hiPSC_CM_Reporter_1151


title: SCVI-111_hiPSC_CM_Reporter_1146


title: SCVI-111_hiPSC_CM_Reporter_1147


title: SCVI-111_hiPSC_CM_Reporter_1148


title: SCVI-111_hiPSC_CM_Reporter_1144


title: SCVI-111_hiPSC_CM_Reporter_1143


title: SCVI-111_hiPSC_CM_Reporter_1142


title: SCVI-111_hiPSC_CM_Reporter_1152


title: SCVI-111_hiPSC_CM_Reporter_1153


title: SCVI-111_hiPSC_CM_Reporter_1135


title: SCVI-111_hiPSC_CM_Reporter_1139


title: SCVI-111_hiPSC_CM_Reporter_1138


title: SCVI-111_hiPSC_CM_Reporter_1131


title: SCVI-111_hiPSC_CM_Reporter_1137


title: SCVI-111_hiPSC_CM_Reporter_1136


title: SCVI-111_hiPSC_CM_Reporter_1133


title: SCVI-111_hiPSC_CM_Reporter_1129


title: SCVI-111_hiPSC_CM_Reporter_1132


title: SCVI-111_hiPSC_CM_Reporter_1134


title: SCVI-111_hiPSC_CM_Reporter_1141


title: SCVI-111_hiPSC_CM_Reporter_1130


title: SCVI-111_hiPSC_CM_Reporter_1124


title: SCVI-111_hiPSC_CM_Reporter_1128


title: SCVI-111_hiPSC_CM_Reporter_1126


title: SCVI-111_hiPSC_CM_Reporter_1125


title: SCVI-111_hiPSC_CM_Reporter_1127


title: SCVI-111_hiPSC_CM_Reporter_1145


title: SCVI-111_hiPSC_CM_Reporter_1123


title: SCVI-111_hiPSC_CM_Reporter_1121


title: SCVI-111_hiPSC_CM_Reporter_1122


title: SCVI-111_hiPSC_CM_Reporter_1140


title: SCVI-111_hiPSC_CM_Reporter_1120


title: SCVI-111_hiPSC_CM_Reporter_1119


title: SCVI-111_hiPSC_CM_Reporter_1118


title: SCVI-111_hiPSC_CM_Reporter_1117


title: SCVI-111_hiPSC_CM_Reporter_1116


title: SCVI-111_hiPSC_CM_Reporter_1115


title: SCVI-111_hiPSC_CM_Reporter_1114


title: SCVI-111_hiPSC_CM_Reporter_1113


title: SCVI-111_hiPSC_CM_Reporter_1111


title: SCVI-111_hiPSC_CM_Reporter_1112


title: SCVI-111_hiPSC_CM_Reporter_1110


title: SCVI-111_hiPSC_CM_Reporter_1107


title: SCVI-111_hiPSC_CM_Reporter_1105


title: SCVI-111_hiPSC_CM_Reporter_1108


title: SCVI-111_hiPSC_CM_Reporter_1106


title: SCVI-111_hiPSC_CM_Reporter_1099


title: SCVI-111_hiPSC_CM_Reporter_1101


title: SCVI-111_hiPSC_CM_Reporter_1102


title: SCVI-111_hiPSC_CM_Reporter_1098


title: SCVI-111_hiPSC_CM_Reporter_1095


title: SCVI-111_hiPSC_CM_Reporter_1096


title: SCVI-111_hiPSC_CM_Reporter_1097


title: SCVI-111_hiPSC_CM_Reporter_1094


title: SCVI-111_hiPSC_CM_Reporter_1090


title: SCVI-111_hiPSC_CM_Reporter_1092


title: SCVI-111_hiPSC_CM_Reporter_1100


title: SCVI-111_hiPSC_CM_Reporter_1089


title: SCVI-111_hiPSC_CM_Reporter_1093


title: SCVI-111_hiPSC_CM_Reporter_1091


title: SCVI-111_hiPSC_CM_Reporter_1088


title: SCVI-111_hiPSC_CM_Reporter_1087


title: SCVI-111_hiPSC_CM_Reporter_1104


title: SCVI-111_hiPSC_CM_Reporter_1109


title: SCVI-111_hiPSC_CM_Reporter_1103


title: SCVI-111_hiPSC_CM_Reporter_1085


title: SCVI-111_hiPSC_CM_Reporter_1084


title: SCVI-111_hiPSC_CM_Reporter_1082


title: SCVI-111_hiPSC_CM_Reporter_1081


title: SCVI-111_hiPSC_CM_Reporter_1080


title: SCVI-111_hiPSC_CM_Reporter_1083


title: SCVI-111_hiPSC_CM_Reporter_1076


title: SCVI-111_hiPSC_CM_Reporter_1078


title: SCVI-111_hiPSC_CM_Reporter_1079


title: SCVI-111_hiPSC_CM_Reporter_1075


title: SCVI-111_hiPSC_CM_Reporter_1077


title: SCVI-111_hiPSC_CM_Reporter_1074


title: SCVI-111_hiPSC_CM_Reporter_1072


title: SCVI-111_hiPSC_CM_Reporter_1070


title: SCVI-111_hiPSC_CM_Reporter_1073


title: SCVI-111_hiPSC_CM_Reporter_1071


title: SCVI-111_hiPSC_CM_Reporter_1086


title: SCVI-111_hiPSC_CM_Reporter_1069


title: SCVI-111_hiPSC_CM_Reporter_1063


title: SCVI-111_hiPSC_CM_Reporter_1068


title: SCVI-111_hiPSC_CM_Reporter_1066


title: SCVI-111_hiPSC_CM_Reporter_1064


title: SCVI-111_hiPSC_CM_Reporter_1065


title: SCVI-111_hiPSC_CM_Reporter_1061


title: SCVI-111_hiPSC_CM_Reporter_1060


title: SCVI-111_hiPSC_CM_Reporter_1062


title: SCVI-111_hiPSC_CM_Reporter_1067


title: SCVI-111_hiPSC_CM_Reporter_1059


title: SCVI-111_hiPSC_CM_Reporter_1055


title: SCVI-111_hiPSC_CM_Reporter_1058


title: SCVI-111_hiPSC_CM_Reporter_1056


title: SCVI-111_hiPSC_CM_Reporter_1054


title: SCVI-111_hiPSC_CM_Reporter_1053


title: SCVI-111_hiPSC_CM_Reporter_1052


title: SCVI-111_hiPSC_CM_Reporter_1051


title: SCVI-111_hiPSC_CM_Reporter_1049


title: SCVI-111_hiPSC_CM_Reporter_1057


title: SCVI-111_hiPSC_CM_Reporter_1048


title: SCVI-111_hiPSC_CM_Reporter_1047


title: SCVI-111_hiPSC_CM_Reporter_1050


title: SCVI-111_hiPSC_CM_Reporter_1045


title: SCVI-111_hiPSC_CM_Reporter_1046


title: SCVI-111_hiPSC_CM_Reporter_1043


title: SCVI-111_hiPSC_CM_Reporter_1041


title: SCVI-111_hiPSC_CM_Reporter_1042


title: SCVI-111_hiPSC_CM_Reporter_1044


title: SCVI-111_hiPSC_CM_Reporter_1039


title: SCVI-111_hiPSC_CM_Reporter_1040


title: SCVI-111_hiPSC_CM_Reporter_1038


title: SCVI-111_hiPSC_CM_Reporter_1035


title: SCVI-111_hiPSC_CM_Reporter_1037


title: SCVI-111_hiPSC_CM_Reporter_1034


title: SCVI-111_hiPSC_CM_Reporter_1029


title: SCVI-111_hiPSC_CM_Reporter_1033


title: SCVI-111_hiPSC_CM_Reporter_1030


title: SCVI-111_hiPSC_CM_Reporter_1031


title: SCVI-111_hiPSC_CM_Reporter_1032


title: SCVI-111_hiPSC_CM_Reporter_1028


title: SCVI-111_hiPSC_CM_Reporter_1027


title: SCVI-111_hiPSC_CM_Reporter_1025


title: SCVI-111_hiPSC_CM_Reporter_1026


title: SCVI-111_hiPSC_CM_Reporter_1024


title: SCVI-111_hiPSC_CM_Reporter_1023


title: SCVI-111_hiPSC_CM_Reporter_1022


title: SCVI-111_hiPSC_CM_Reporter_1021


title: SCVI-111_hiPSC_CM_Reporter_1020


title: SCVI-111_hiPSC_CM_Reporter_1019


title: SCVI-111_hiPSC_CM_Reporter_1018


title: SCVI-111_hiPSC_CM_Reporter_1012