title: GF27

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

data_processing:
Raw data of fastq format were processed by in-house proprietary perl scripts at Novogene. Reads containing adapters, poly-N and low quality reads from raw data.
Hisat2 v2.0.5 software was used to map reads to the reference genome.
Stringtie v1.3.3b was used for assembly of mapped reads
featureCounts v1.5.0-p3 was sed to count the read numbers mapped to each gene and then FKPM (Fragments per Kilobase of transcript sequence per Millions base pairs sequenced) was calculated based on the length of the gene and read count mapped to each gene.
Assembly: rn6
Supplementary files format and content: Raw read counts in .txt format
Supplementary files format and content: FPKM in .txt format

organism: Rattus norvegicus

source_name: prefrontal cortex

extract_protocol:
Total RNA was isolated used the Rneasy kit from Qiagen, according to the manufacturer's protocol.
RNA sequencing was performed on four biological replicate samples per group by Novogene (Sacramento, CA). Messenger RNA was purified from total RNA using poly-T oligo-attached beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification and purification.

treatment_protocol: Adult male Sprague Dawley rats were ages 8 weeks on arrival. Animals received intraperitoneal injections of a 5% Tween-80 vehicle or 1-3mg/kg ketanserin in 5% Tween-80, followed by an injection of either a saline vehicle or 1-3mg/kg psilocybin in saline. Animals were euthanized 24 hours after the injections and prefrontal cortex collected for RNA sequencing analysis.

value: prefrontal cortex

value: Sprague-Dawley

tag: Sex

value: male

value: adult

value: vehicle, psilocybin 3mg/kg


title: EndoC-βH3 cells, Senescent cells, CTCF 2

status: Public on Jun 26 2024

type: SRA

city: Jerusalem

first: Milan

last: Patra

address: Hadassah Ein Kerem

department: Faculty of Medicine, Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

description:
processed data table contains bigwig files for each sample. Differential CTCF binding by usin DESeq2 is given.
CTCF_DESeq2.bed.gz

library_source: genomic

data_processing:
The library was demultiplexed using bcl2fastq program. The reads were aligned to human genome hg38 using Bowtie, and were sorted and indexed using Samtools.
Peak calling was done by using MACS2 for CTCF, Rb and HOMER for H3K27ac, H3K4me1, respectively. The differential binding of H3K27ac, and CTCF between non-senescent and senescent cells were analyzed using DESeq2.
The bigwig files are generated using Deeptools.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: EndoC-βH3 cells are maintained in DMEM low glucose (1 g/L) supplemented with 2% fatty acid free BSA , 10 mM nicotinamide, 5.5 µg/mL  human transferrin, 6.7 ng/mL sodium selenite, 50 µM β-mercaptoethanol, 100 U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Five million cells per sample were fixed with 1% formaldehyde, followed by quenching and cell lysis. Chromatin was sonicated using diagenode bioruptor, calibrated to yeild 200-700 bp framents.
ChIP-seq libraries were generated using the KAPA Hyper Prep kit (Roche).

treatment_protocol: Senescence induction of EndoC-βH3 cells was performed routinely by treatment with 1 mM 4-hydroxy tamoxifen (4-OHT) for 3 weeks.

tag: chip antibody

tag: cell line

tag: cell type

value: pancreatic beta cells

tag: genotype

value: WT

tag: treatment

value: Senescence induction


title: EndoC-βH3 cells, Non senescent cells, Input of CTCF 3

value: control


title: Young subject C serum treatment, CT 44

city: Philadelphia

first: Antonijo

last: Mrčela

state: Pennsylvania

address: 3400 Civic Center Boulevard

department: Institute for Translational Medicine and Therapeutics

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Raw RNA-seq reads were aligned to the GRCh38 build of the human genome by STAR version 2.7.10a.
Data were normalized and quantified at both gene and exon-intron level, using a downsampling strategy implemented in PORT (Pipeline Of RNA-seq Transformations, available athttps://github.com/itmat/Normalization), version 0.8.5f-beta_hotfix1. Both STAR and PORT were provided with gene models from release 106 of the Ensembl annotation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes PORT normalized counts for each sample.

molecule: polyA RNA

source_name: Foreskin

growth_protocol: BJ-5TA BMAL1-dLuc-GFP cells in 24-well plates (~confluent) were washed (2x) with DPBS and given serum free media (DMEM with Penn Strep) for 24hrs.

extract_protocol:
Upon sample collection wells were place on ice and rinsed with cold DPBS and then put in cold RLT buffer with 2-Mercaptoethanol (10uL/mL). Samples were frozen at -80 overnight and sent to Admera for RNA extraction and sequencing. Total RNA was extracted with RNeay mini kit (Qiagen).
Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5 ́ d(N6) 3 ́ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 40 minutes at 42°C. All remaining steps for library construction were used according to the NEBNext® UltraTM II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 430bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads per sample (20 M in each direction).

treatment_protocol: After 24hrs cells were given media with human serum (DMEM, Penn Strep, 10% human serum). Serum starvation was staggered every 12 hours over two days to allow for samples to be collected on the same day.

tag: tissue

value: Foreskin

value: Fibroblast

value: Young serum

tag: time

tag: subject

value: Young subject C


title: EndoC-βH3 cells, Non senescent cells, Input of CTCF 2


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-15

city: Seattle

first: John

middle: Kenneth

last: Mich

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

library_source: transcriptomic single cell

data_processing:
Base-calling using standard Illumina software.
Alignment with STAR (https://github.com/alexdobin/STAR)
Transformed by counts per million.
Assembly: mm10
Supplementary files format and content: Processed data in counts per million (CPM) format.

organism: Mus musculus

source_name: VISp

extract_protocol:
Single SYFP2-expressing cells from mouse brain were flow sorted into individual tubes in SMARTerv4 collection buffer.
SMARTerv4

value: VISp


title: GF3

molecule: total RNA

tag: strain

tag: age

value: ketanserin 3mg/kg, psilocybin 3mg/kg


title: EndoC-βH3 cells, Senescent cells, CTCF 1


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-14


title: GF30

value: ketanserin 1mg/kg, vehicle


title: Young subject A serum treatment, CT 44

value: Young subject A


title: EndoC-βH3 cells, Non senescent cells, CTCF 3


title: Young subject B serum treatment, CT 44

value: Young subject B


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-13


title: EndoC-βH3 cells, Non senescent cells, CTCF 2


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-12


title: GF29

value: prefrontal cortex

value: Sprague-Dawley

value: ketanserin 1mg/kg, psilocybin 1mg/kg


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-43

source_name: CBX

value: CBX


title: EndoC-βH3 cells, Senescent cells, Input of H3K4me1 2

value: pancreatic beta cells


title: Young subject D serum treatment, CT 42

value: Young subject D


title: EndoC-βH3 cells, Non senescent cells, CTCF 1

value: WT


title: GF28

value: male

value: adult


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-17


title: Young subject C serum treatment, CT 42

value: Foreskin

value: Fibroblast


title: EndoC-βH3 cells, Senescent cells, Input of H3K4me1 1

value: Senescence induction


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-41


title: Young subject B serum treatment, CT 42

value: Young serum


title: GF24

value: vehicle, psilocybin 3mg/kg


title: EndoC-βH3 cells, Non senescent cells, Input of H3K4me1 2

value: control


title: Young subject A serum treatment, CT 42

value: Young subject A


title: GF22

value: vehicle, vehicle


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-40


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-39


title: EndoC-βH3 cells, Non senescent cells, Input of H3K4me1 1


title: GF21

value: prefrontal cortex

value: ketanserin 3mg/kg, psilocybin 3mg/kg


title: Young subject C serum treatment, CT 40

value: Young subject C


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-38

value: CBX


title: Young subject D serum treatment, CT 40


title: GF20

value: Sprague-Dawley

value: ketanserin 1mg/kg, psilocybin 1mg/kg


title: EndoC-βH3 cells, Senescent cells, H3K4me1 1

description:
processed data table contains bigwig files for each sample.
Sen_enhancers.bed.gz

value: pancreatic beta cells

value: WT


title: EndoC-βH3 cells, Non senescent cells, H3K4me1 2

description:
processed data table contains bigwig files for each sample.
Nonsen_enhancers.bed.gz


title: GF19

value: male

value: adult

value: ketanserin 3mg/kg, vehicle


title: Young subject A serum treatment, CT 40

value: Foreskin

value: Fibroblast


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-37


title: Young subject B serum treatment, CT 40

value: Young serum

value: Young subject B


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-36


title: GF18


title: EndoC-βH3 cells, Non senescent cells, H3K4me1 1

value: control


title: Young subject D serum treatment, CT 38

value: Young subject D


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-42


title: GF25

value: prefrontal cortex

value: vehicle, vehicle


title: GF17

value: ketanserin 1mg/kg, vehicle


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-35

value: CBX


title: GF16

value: Sprague-Dawley


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-34


title: Young subject C serum treatment, CT 38

value: Young subject C


title: EndoC-βH3 cells, Senescent cells, Input of H3K27ac 2

value: pancreatic beta cells

value: Senescence induction


title: Young subject B serum treatment, CT 38


title: GF15

value: male


title: EndoC-βH3 cells, Senescent cells, H3K4me1 2

value: WT


title: Young subject A serum treatment, CT 38

value: Young subject A


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-33


title: EndoC-βH3 cells, Senescent cells, Input of H3K27ac 1


title: GF14

value: adult

value: ketanserin 3mg/kg, vehicle


title: Young subject D serum treatment, CT 36

value: Foreskin

value: Fibroblast

value: Young serum


title: EndoC-βH3 cells, Non senescent cells, Input of H3k27ac 3

value: control


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-32


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-31


title: EndoC-βH3 cells, Non senescent cells, Input of H3k27ac 2


title: EndoC-βH3 cells, Non senescent cells, Input of H3k27ac 1


title: GF12

value: prefrontal cortex

value: vehicle, psilocybin 3mg/kg


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-30


title: Young subject C serum treatment, CT 36


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-29


title: GF11

value: ketanserin 3mg/kg, psilocybin 3mg/kg


title: Young subject A serum treatment, CT 36


title: Young subject B serum treatment, CT 36

value: Young subject B


title: EndoC-βH3 cells, Senescent cells, H3K27ac 3

description:
processed data table contains bigwig files for each sample. Differential H3K27ac binding by usin DESeq2 is given.
Sen_enhancers.bed.gz
H3K27ac_DESeq2.bed.gz

value: H3K27ac (Active motif, #39034)


title: EndoC-βH3 cells, Senescent cells, Input of H3K27ac 3


title: GF10

value: Sprague-Dawley

value: ketanserin 1mg/kg, psilocybin 1mg/kg


title: EndoC-βH3 cells, Senescent cells, H3K27ac 2

value: pancreatic beta cells

value: Senescence induction


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-28

value: CBX


title: GF9

value: male

value: vehicle, vehicle


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-27


title: Young subject D serum treatment, CT 34

value: Young subject D


title: Young subject C serum treatment, CT 34

value: Foreskin

value: Young subject C


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-26


title: GF8

value: adult

value: vehicle, psilocybin 1mg/kg


title: EndoC-βH3 cells, Senescent cells, H3K27ac 1

value: WT


title: Young subject B serum treatment, CT 34

value: Fibroblast

value: Young serum


title: GF13

value: prefrontal cortex


title: EndoC-βH3 cells, Non senescent cells, H3K27ac 3

description:
processed data table contains bigwig files for each sample. Differential H3K27ac binding by usin DESeq2 is given.
Nonsen_enhancers.bed.gz
H3K27ac_DESeq2.bed.gz

value: H3K27ac (Active motif, #39034)

value: control


title: GF7

value: Sprague-Dawley

value: ketanserin 3mg/kg, vehicle


title: GF6

value: vehicle, psilocybin 3mg/kg


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-24

value: CBX


title: Young subject A serum treatment, CT 34

value: Young subject A


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-25


title: EndoC-βH3 cells, Non senescent cells, H3K27ac 2

value: pancreatic beta cells


title: EndoC-βH3 cells, Non senescent cells, H3K27ac 1


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-23


title: EndoC-βH3 cells, Senescent cells, ATAC-seq 3

description: processed data table contains bigwig files for each sample and DESeq2 differetial chromatin accessibility results

data_processing:
Trim galore! powered by Cutadapt was used to filtered out low quality reads. The reads were aligned to human genome hg38 using Bowtie, and were sorted and indexed using Samtools.
Picard used to remove duplicate reads. The peaks called by MACS2 used for differential chromatin accessibilty analysis using DESeq2.
The bigwig files are generated using Deeptools.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Accessible genomic DNA purified for each samples using 100000 cells and ATAC-seq kit(Active Motif).
Cells were lyzed in ice cold ATAC lysis buffer, followed by tagmentation with Tn5 tansposon in isolated nuclei. The tagmented DNA purified, indexed and paired-end sequenced in Illumina Nextseq 500.

value: Senescence induction


title: Young subject D serum treatment, CT 32

value: Foreskin

value: Young subject D


title: GF5

value: male

value: adult


title: GF4

value: ketanserin 1mg/kg, vehicle


title: EndoC-βH3 cells, Senescent cells, ATAC-seq 2

value: WT


title: Young subject C serum treatment, CT 32

value: Fibroblast

value: Young serum

value: Young subject C


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-21


title: Young subject A serum treatment, CT 32


title: EndoC-βH3 cells, Senescent cells, ATAC-seq 1


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-22


title: Young subject B serum treatment, CT 32

value: Young subject B


title: GF2

value: prefrontal cortex

value: Sprague-Dawley

value: vehicle, psilocybin 1mg/kg


title: EndoC-βH3 cells, Non senescent cells, ATAC-seq 3

value: control


title: GF1

value: vehicle, vehicle


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-20

value: CBX


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-19


title: EndoC-βH3 cells, Non senescent cells, ATAC-seq 2

value: pancreatic beta cells


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-18


title: TSP77LOF_ND11_d10

city: Nashville

first: Rebecca

middle: A

last: Ihrie

state: TN

address: 1161 21ST Avenue South

department: Cell & Developmental Biology

institute: Vanderbilt University

data_processing:
Raw data was trimmed using trim_galore. Command: trim_galore -j 8 --fastqc --fastqc_args "--outdir ${FASTQC_DIR}" --clip_R1 9 --clip_R2 9 --paired --retain_unpaired --output_dir ${TRIM_DIR} ${R1} ${R2}
Trimmed files were then mapped to the genome using the abismal (version 0.3.0) function from the methpipe package from Smith lab. Command: abismal -i ${INDEX} -o ${MAPPED_DIR}/${MAPPED}.sam -t 12 -s -v ${TRIMDIR}/${MAPPED}_val_1.fq ${TRIMDIR}/${MAPPED}_val_2.fq | samtools view -bS > ${MAPPED_DIR}/${MAPPED}.bam
Mapped files are then processed further with the methpipe package (Version 5.0.0) from Smith lab.
Assembly: hg38A
Supplementary files format and content: .meth files are files that include the methylation levels at each genomic cytosine

source_name: TSP77 TSC2 LOF/LOF (Sundberg et al., 2018)

growth_protocol: iPSCs were grown as colonies on Matrigel (Corning) coated 6 well plates in mTeSR1 medium (StemCell Tech), replaced daily, maintained at 37°C and 5% CO2, and passaged as needed with ReLSR (StemCell Tech). iPSCs were then differentiated into neural progenitor cells (NPC) following the NPC induction protocol.

extract_protocol:
NPCs were collected and pelleted at day 10 of differentiation. Pellets were stored at -80°C until all samples had been collected. All samples gDNA were extracted at the same time. gDNA was extracted following the protocol in Barnett, K.R., et al., ATAC-Me Captures Prolonged DNA Methylation of Dynamic Chromatin Accessibility Loci during Cell Fate Transitions. Mol Cell, 2020. 77(6): p. 1350-1364.e6.
Briefly, genomic DNA was extracted using phenol-chloroform extraction from 8-12 million cells. Purity and integrity of genomic DNA was confirmed using Nanodrop and Tapestation (Agilent). 50ng of genomic DNA was then incubated with Tn5 assembled with adaptor oligos(produced in-house) and reaction buffer (5x Tris-DMF) at 55C for 8 minutes. Resulting fragments were purified prior to gap repair and oligo replacement. Bisulfite conversion of repaired DNA fragments was performed using the Zymo-Gold Methylation Kit according to the manufacturer’s instructions. Libraries were amplified and purified prior to sequencing on a NovaSeq.

treatment_protocol: iPSCs were differentiated and cultured following the method described in Chambers, S.M., et al., Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nature Biotechnology, 2009. iPSCs were dissociated with Accutase into a single cell suspension for 8 minutes at 37°C. 2.5 x 10^6 cells were plated into a matrigel-coated 6 well plate well with neural maintence media supplemented with dual SMAD inhibitors and Rock inhibitor. Media was supplemented with Rock inhibitor only on the first day. Cells were cultured in this media for 10 days with media fully replaced daily at 37°C and 5% CO2.

value: day 10

value: iPSC-derived neural progenitor cells

value: TSC2 LOF/LOF

value: neural progenitor cell differentiation


title: TSP77LOF_ND13_d10

value: TSP77 TSC2 LOF/LOF (Sundberg et al., 2018)


title: p720sPT-16TUORG3PO-4_xx_rna_sr_Conrady_B_1

city: Goettingen

first: Tiago

last: De Oliveira

state: NI

address: Robert-Koch-Str. 40

department: Department of Surgery

country: Germany

institute: University Medical Center Göttingen

description: PT16 TU ORG 3PO_1

data_processing:
Alignment of the raw reads to the humane reference genome (hg19) was performed using the STAR aligner software (version 2.7.3a), in default settings
For quantification featureCounts program (version 2.0.0)34 was used
To correct for unwanted variations, the RUVs function of RUVseq software (version 3.13)35 was applied before differential gene expression was analysed by DESeq2 package (version 3.13)36.
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
The number of permutations was set to 1000. The collection “Biological Process” (c5.go.bp.v7.4.symbols.gmt.txt) contributed by Gene Ontology (Gene Ontology Consortium)39 was downloaded from the GSEA website (http://www.gsea-msigdb.org/gsea/index.jsp) as part of the Molecular Signature Database (MSigDB)40,41
Assembly: human hg19
Supplementary files format and content: log2FoldChange , GSEA enrichment score
Supplementary files format and content: txt GSEA

source_name: human colon segment

growth_protocol: patient-derived organoids were cultured in 12-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 24 hours

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
RNA-seq libraries were performed using a modified non strand-specific, massively-parallel cDNA sequencing (RNA-Seq) protocol from Illumina starting with 200 ng RNA. The TruSeq RNA Library Preparation Kit v2, Set A (48 samples, 12 indexes; Illumina) was used.The size of final cDNA libraries was determined by using the dsDNA 905 Reagent Kit (Agilent) exhibiting a sizing of 260 bp in average. Libraries were pooled and sequenced on an Illumina HiSeq 4000 (Illumina) 13 generating 50 bp single-end reads (30-40 Mio reads/sample).

treatment_protocol: organoids were treated with DMSO (Sham) or 30µM 3PO.

value: human colon segment

value: patient-derived organoids

value: colon tumor

value: 30µM 3PO


title: EndoC-βH3 cells, Non senescent cells, ATAC-seq 1

value: WT


title: p720sPT-16TUORGCtrl2-2_xx_rna_sr_Conrady_A_1

description: PT16 TU ORG Ctrl_1

value: DMSO


title: p720sPT-12TUCtrl1-13_xx_rna_sr_Conrady_G_1

description: PT12 TU ORG Ctrl_2


title: TSP77Het_ND11_d10

source_name: TSP77 TSC2 +/LOF (Sundberg et al., 2018)

value: TSC2 +/LOF


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-16


title: p720sPT-12TU3PO1-15_xx_rna_sr_Conrady_H_1

description: PT12 TU ORG 3PO_2

value: 30uM 3PO


title: TSP77Het_ND13_d10

value: TSP77 TSC2 +/LOF (Sundberg et al., 2018)


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-15


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-14


title: HT1376_DMSO/CPI-0209_Input

city: Cambridge

first: Patrick

last: Trojer

state: Massachusetts

address: 215 First Street, Suite 200

institute: Constellation Pharmaceuticals

data_processing:
sequence reads that were mapped to the genome using the BWA algorithm with default settings.
For comparative analysis, Drosophila spike-in protocols and normalization were used, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group.
Peaks were called using either the MACS or SICER algorithms (Zang et al., 2009; Zhang et al., 2008). MACS default cutoff is p-value 1e-7 for narrow peaks and 1e-1 for broad peaks, and SICER default cutoff is FDR 1e-10 with gap parameter of 600 bp.
Peak filtering was performed by removing false ChIP-Seqpeaks as defined within the ENCODE blacklist (Dunham et al., 2012).
Genome_build: hg38
Supplementary_files_format_and_content: bed file: peak location

growth_protocol: Cells were grown in MEM(Earl's Salts) + 10% FBS, 1% Non-essential AA, 1 mM NaPyruvate, 1% Pen/Strep

extract_protocol: 1x107 HT1376 cells treated with or without CPI-0209 (250 nM) for 4 and 8 days were fixed by adding formaldehyde to final concentration of 1%. Fixation was done for 10 min at room temperature. Crosslinking was stopped by adding glycine to a final concentration of 125 mM. The fixed cells were snap-frozen and shipped by Active Motif for ChIP-seq processing (Carlsbad, CA). Briefly, ChIP reactions were performed with 30 ug of extracted chromatin with antibodies to EZH2 (Active Motif #39901), H3K27Ac (Active Motif #39133) and H3K27me3 (Active Motif #39155).

treatment_protocol: Cells were treated with 250 nM of CPI-0209 for 8 days.

tag: target

value: Input


title: p720sPT-06TUMORCTRL2-30_xx_rna_sr_Conrady_R_1

description: PT06 TU ORG Ctrl_3


title: HT1376_CPI-0209_H3K27me3


title: HT1376_DMSO_H3K27me3


title: p720sPT-06TUMOR3PO1-31_xx_rna_sr_Conrady_S_1

description: PT06 TU ORG 3PO_3


title: TSP77LOF_iPSC_p51

value: day 0

value: induced pluripotent stem cells (iPSC)


title: TSP77LOF_iPSC_p43


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-18

value: VISp


title: PT33-MT Cycle 1 Day 15

data_processing:
Sequencing reads were mapped to the genome using STAR v2.7.3a with default settings
The transcript and gene read count quantification were performed using RSEM v1.3.1 with default settings
Genome_build: hg38

source_name: whole blood

extract_protocol:
Whole blood cells were collected using PAXgene blood RNA tubes. Proccessing and sequencing of patient RNA samples were performed by ALMAC. The RNA extractions were performed using PAXgene Blood RNA Kit following manufacturer’s instructions.
Library preparation proceeded with rRNA and hemoglobin depletion using KAPA RNA HyperPrep Kit with RiboErase (HMR) Globin. Paired-end 75 base pair sequencing was performed on an Illumina platform. Prior to sequencing, RNA integrity was assessed by 2100 Bioanalyser (Agilent) and concentration was assayed by Nanodrop.

treatment_protocol: The patients were from the phase 1 portion of the phase 1/2 study of CPI-0209 in patients with advanced tumors (clinicaltrials.gov identifier: NCT04104776).  Phase 1 was a 7-cohort dose escalation study in patients receiving CPI-0209 once daily at doses between 50 and 375 mg. All patients gave informed consent and the trial was conducted in accordance with the Declaration of Helsinki.

value: whole blood

tag: treatment time point

value: MT Cycle 1 Day 15

tag: dose cohort

tag: c1d1 cpi-0209 exposure

tag: patient


title: HT1376_DMSO_EZH2


title: TSP77Het_iPSC_p70


title: Sample 48: HT1376-TetOn_CPI-0209_with Dox_IgG_R1

data_processing:
Library strategy: Cut&Run
Sequence reads were mapped to the genome using the Bowtie2 algorithm with setting as “–local –very-sensitive-local –no-unal –no-mixed –no-discordant –phred 33 -I 10 -X 700”.
Duplicated reads were removed using Picard.
For comparative analysis, E.coli spike-in protocols and normalization were used, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in E.coli tags for each sample within a normalization group.
Peaks were called using the MACS2 algorithms and the signal from IgG was used as control. MACS2 default cutoff is pvalue 1e-5 for both narrow peaks and broad peaks.
Genome_build: hg38
Supplementary_files_format_and_content: bw file: bigwig; narrowPeak/broadPeak: called peaks

extract_protocol:
Cells were fixed by adding formaldehyde to final concentration of 0.1%. Fixation was done for 1 min at room temperature. Crosslinking was stopped by adding glycine to a final concentration of 125 mM. The fixed cells were snap-frozen and shipped by Epicypher (Durham, NC) for CUT&RUN processing. 0.5x106 fixed cells were washed twice in 100 uL Wash Buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Protease Inhibitors) before resuspending in 100 uL Wash Buffer and transfer to tubes containing 10 uL of activated ConA bead (Epicypher #21-1401). The ConA beads absorbed cells were resuspend in 50 uL Antibody Buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.02% Digitonin, 2 mM EDTA,  1x Protease Inhibitors) containing 0.5 ug of antibodies recognizing ARID1A (BETHYL A301-041A), SMARCA4 (BETHYL A300-813A), H3K4me3 (Epicypher #13-0041), H3K27me3 (Epicypher #13-0030), H3K27ac (Epicypher #13-0045) or IgG (Epicypher #13-0041). The beads and antibodies were incubated overnight at 4C before washing with 250 uL Digitonin Buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 1x Protease Inhibitors) twice. The beads were incubated with 50 uL cold Digitonin Buffer with 2.5 uL CUTANA pAG-MNase (Epicypher # 15-1016) for 10 min at room temperature before washing with 250 uL cold Digitonin Buffer twice. The washed beads were incubated with 50 uL Digitonin Buffer with 1 uL 100 mM CaCl2 for 2 hr at 4C.
The released DNA were purified by NEB Monarch DNA Cleanup Kit (NEB T1030S) and subjected for library preparation using NEB Ultra II Library Kit (NEB E7645S) following the manufacturer’s instructions. Prior to sequencing, library size and concentration were assessed by Agilent High Sensitivity DNA ChIP (Agilent 5067-4626) on 2100 Bioanalyser (Agilent). Sequencing was performed with an Illumina MiniSeq or NextSeq 500 platforms to generate 3-5 million paired-end reads.

treatment_protocol: HT1376-TetON control cells and a clonal HT1376-TetON-ARID1A cell line were induced with 50 ng/ml doxycycline for 24 hours and then treated for 4 days with DMSO or 250 nM CPI-0209.

value: with Dox

value: IgG

tag: repeat


title: PT33-MT Cycle 2 Day 1

value: MT Cycle 2 Day 1


title: TSP77Het_iPSC_p23


title: Sample 46: HT1376-TetOn-ARID1A_CPI-0209_without Dox_IgG_R1

value: without Dox


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-16


title: PT33-MT Cycle 1 Day 22

value: MT Cycle 1 Day 22


title: PT33-MT Cycle 1 Day 1

value: MT Cycle 1 Day 1


title: Sample 47: HT1376-TetOn_CPI-0209_with Dox_IgG_R1


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-17


title: TSP77WT_ND13_d10

source_name: TSP77 TSC2 +/+ (Sundberg et al., 2018)

value: day 10

value: TSP77 TSC2 +/+ (Sundberg et al., 2018)

value: iPSC-derived neural progenitor cells

value: neural progenitor cell differentiation


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-17

value: CBX


title: TSP77WT_iPSC_p47


title: Sample 45: HT1376-TetOn-ARID1A_DMSO_without Dox_IgG_R1

value: DMSO


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-15


title: PT33-MT Cycle 1 Day 8

value: MT Cycle 1 Day 8


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-13


title: TSP77WT_iPSC_p45

value: day 0

value: induced pluripotent stem cells (iPSC)


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-14

value: VISp


title: TSP77WT_ND11_d10


title: HT1376_CPI-0209_EZH2


title: PT31-MT Cycle 1 Day 1

value: whole blood


title: HEK293T_siLa_rep3

city: Urbana

first: Sihang

last: Zhou

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois Urbana-Champaign

data_processing:
Steady-state small RNA reads were first trimmed using TrimGalore and then mapped to the entire genome space (GRCh38) using bowtie2
Promoter-specific raw small RNA signal counts were extracted using bedtools
Differentially expressed genes were determined using edgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes log2fold change and statistics between siLA and siControl

source_name: Kidney

growth_protocol: HEK293T cells were maintained in DMEM supplied with 10% fetal bovine serum (FBS) and 1% Pen-Strep in the cell incubator with 5% CO₂ at 37°C

extract_protocol:
small RNA extraction was performed using mirVana PARIS RNA and Native Protein Purification kit according to the manufacturer’s instructions
The samples were first treated with Antarctic Phosphatase (NEB), followed by treatment with T4 Polynucleotide Kinase (NEB) according to the manufacturer’s protocol. Small RNA libraries were generated using the NEBnext small RNA library preparation kit according to instructions (New England BioLabs).

treatment_protocol: HEK293T cells were transfected with 150nM siRNA(sicontrol or siLa) using Lipofectamine® RNAi Max for 48 hours at 37 °C with 5% CO2 before collection

value: Kidney

value: epithelial

value: La knockdown


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-12


title: HEK293T_siLa_rep2


title: Sample 43: HT1376-TetOn-ARID1A_DMSO_with Dox_IgG_R1

value: with Dox

value: IgG


title: PT31-MT Cycle 1 Day 15

value: MT Cycle 1 Day 15


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-11


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-10


title: Sample 42: HT1376-TetOn_CPI-0209_with Dox_H3K4me3_R1


title: HEK293T_siControl_rep3

value: Control knockdown


title: PT31-MT Cycle 1 Day 22

value: MT Cycle 1 Day 22


title: PT31-MT Cycle 1 Day 8


title: Sample 41: HT1376-TetOn_CPI-0209_with Dox_H3K4me3_R1


title: HEK293T_siControl_rep2


title: PT30-MT Cycle 2 Day 1

value: MT Cycle 2 Day 1


title: HEK293T_siControl_rep1


title: Sample 44: HT1376-TetOn-ARID1A_DMSO_with Dox_IgG_R1


title: PT30-MT Cycle 1 Day 8


title: HEK293T_siLa_rep1


title: Sample 39: HT1376-TetOn-ARID1A_DMSO_without Dox_H3K4me3_R1

value: without Dox


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-6


title: Sample 40: HT1376-TetOn-ARID1A_CPI-0209_without Dox_H3K4me3_R1


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-8


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-7


title: Sample 38: HT1376-TetOn-ARID1A_DMSO_with Dox_H3K4me3_R1


title: Sample 37: HT1376-TetOn-ARID1A_DMSO_with Dox_H3K4me3_R1


title: PT31-MT Cycle 2 Day 1


title: Sample 36: HT1376-TetOn_CPI-0209_with Dox_H3K27me3_R1


title: PT30-MT Cycle 1 Day 15


title: Mda-mb-231, esam high population

city: Austin

first: Amy

last: Brock

state: Texas

address: 2515 Speedway

institute: The University of Texas at Austin

data_processing:
Raw FASTQ files were processed using nf-core/rnaseq (v3.14.0) using default settings. Data was aligned to GrCh38.
Bias uncorrected counts were rounded and used as recommended with DESeq2 (v1.40.2) to generate differentially expressed genes and generate normalized expression values.
Assembly: hg38
Supplementary files format and content: comma separated values with raw unnormalized counts

source_name: breast

extract_protocol:
48 hours after plating (13 days post-FACS), cells were 60-70% confluent and RNA was collected using an in-plate lysis strategy following the Qiagen RNAeasy Mini protocol.
RNA samples were quantified via Qubit, diluted, then submitted to the UT Austin Genomic Sequencing and Analysis Facility for 3’-Tag RNAseq (TagSeq) preparation

value: breast

value: breast cancer tumor


title: Mda-mb-231, esam low population


title: PT30-MT Cycle 1 Day 1

value: MT Cycle 1 Day 1


title: PT30-MT Cycle 1 Day 22


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-5


title: Mda-mb-436, bst2 high population


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-9


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-4


title: Sample 35: HT1376-TetOn_CPI-0209_with Dox_H3K27me3_R1


title: PT29-MT Cycle 2 Day 1


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-3


title: Mda-mb-436, bst2 low population


title: Sample 33: HT1376-TetOn-ARID1A_DMSO_without Dox_H3K27me3_R1

value: DMSO


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-1


title: PT29-MT Cycle 1 Day 15


title: PT29-MT Cycle 1 Day 22


title: Sample 34: HT1376-TetOn-ARID1A_CPI-0209_without Dox_H3K27me3_R1


title: BT474, Illumina, sRNA-seq, rep2

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 147, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
short RNAs (20-65nt)
sRNA_Homo_sapiens-BT474_Illumina.reps.merged.tss.txt

data_processing:
Reads were trimmed of their adapter sequences using HOMER (homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20).
Reads were subsampled using SeqKit's sample v2.5.1 to acheieve equal read depth.
Reads were aligned to the the appropriate reference genome using STAR v2.7.10a for humans and Hisat2 v2.2.1 for the livestock.
Alignment files were converted to tag directories using HOMER2 batchMakeTagDirectory.pl.
BedGraph files were generated from the tag directories using makeUCSCfile.
Peaks representing Transcription Start Regions (TSRs) for csRNA-seq and expressed small RNAs for sRNA-seq, were defined using HOMER’s findcsRNATSR.pl and findPeaks, respectively. A minimum read count of 10 per 10 million was required for regions to be considered.
Assembly: hg38, GCF_002263795.2, modified_GCA_018282365.1
Supplementary files format and content: BedGraph files (.bedGraph.gz) containing the locations that denote TSS positions.
Supplementary files format and content: Text files (.tss.txt) containing tab-delimited data on identified transcription start site clusters (TSRs).
Supplementary files format and content: Modified gtf file that underwent an ID update to achieve consistency with the fasta genome.

growth_protocol: A375 and BT474 cells were grown at 37°C with 5% CO2 in DMEM (Cellgro) supplemented with 10% FBS (Gibco), and 50 U Penicillin and 50 μg Streptomycin per mL (Gibco). Cattle and bison samples were obtained from experimental animals housed at Washington State University, Pullman, WA and University of Wyoming, Laramie WY, respectively. 2.8 ml blood was collected from healthy animals using PAXgene Blood RNA tubes (BD Bioscience) by venipuncture (jugular) and transported on ice to the laboratory for processing.

extract_protocol:
Cells were washed once with ice cold DPBS (Gibco), rested on ice for 5 minutes, washed one more time with ice cold DPBS and then lysed in 1 ml TROZOL. RNA isolated as described by the manufacturer.
csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5'-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5'-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5'dephosphorylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.


title: Aggregated cell lines (GEX), scRNA-seq

data_processing:
Single-cell data was aligned to the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) and processed using cellranger’s (version 6.1.2) multi command. The data was then aggregated using cellranger’s aggr function.
cmo ids are as follows: 1: BT474, 2: MDA-MD-453, 3: HCC388, 4: MDA-MB-231, 5: Hs548T, 6: MDA-MB-436
When loading the barcode tsv, the cmo is matched to the terminal number separated by a dash. For example, cell barcode TTTGGTTGTCGCGTCA-6 corresponds to an MDA-MB-436 cell
Assembly: hg38
Supplementary files format and content: Tab separated barcodes, features, and matrix.mtx

source_name: Breast

extract_protocol:
Cells were prepared for multiplexed scRNA-seq using the 10X Genomics 3ʹ CellPlex Kit (10X Genomics, 1000261). Briefly, MDA-MB-231 (p4), MDA-MB-436 (p4), MDA-MB-453 (p5), Hs578T (p4), BT-474 (p3), and HCC38 (p5) were gently detached, neutralized, strained through a 40 µm cell strainer, then counted. 1e6 cells from each population were added to a 2 mL tube and washed with room temperature PBS supplemented with 0.04% BSA (ThermoFisher, 15260037). Each cell line was resuspended in 100 µL of a unique cell multiplexing oligo and incubated for 5 minutes before 3 rounds of washing with cold PBS plus 1% BSA. After washing, cells were counted, and two pools were made containing equal ratios of 3 cell lines each: (Pool A) MDA-MB-231, MDA-MB-453, BT-474, and (Pool B) MDA-MB-436, Hs578T, and HCC38.
Cells were dropped off to the UT Austin Genomic Sequencing and Analysis and 15,000 cells per pool were loaded into a Chromium Next GEM Single Cell 3’ Chip following standard 10X Genomics protocols.

value: Breast

value: Human breast tumor


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-13

value: CBX


title: Sample 32: HT1376-TetOn-ARID1A_DMSO_with Dox_H3K27me3_R1


title: BrainCell_Enhancer-eHGT_380h_MouseID-614200_Cell-2

value: VISp


title: BT474, Illumina, sRNA-seq, rep1


title: PT29-MT Cycle 1 Day 8

value: whole blood

value: MT Cycle 1 Day 8


title: PT29-MT Cycle 1 Day 1


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-12


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-11


title: PT28-MT Cycle 1 Day 22


title: Sample 31: HT1376-TetOn-ARID1A_DMSO_with Dox_H3K27me3_R1

value: with Dox


title: Sample 29: HT1376-TetOn_CPI-0209_with Dox_H3K27ac_R1


title: Sample 30: HT1376-TetOn_CPI-0209_with Dox_H3K27ac_R1


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-10


title: Sample 28: HT1376-TetOn-ARID1A_CPI-0209_without Dox_H3K27ac_R1


title: PT28-MT Cycle 1 Day 1


title: BT474, Illumina, csRNA-seq, rep1

description:
short RNAs (20-65nt)
Homo_sapiens-BT474_Illumina.reps.merged.tss.txt

data_processing:
Reads were trimmed of their adapter sequences using HOMER (homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20).
Reads were subsampled using SeqKit's sample v2.5.1 to acheieve equal read depth.
Reads were aligned to the the appropriate reference genome using STAR v2.7.10a for humans and Hisat2 v2.2.1 for the livestock.
Alignment files were converted to tag directories using HOMER2 batchMakeTagDirectory.pl.
BedGraph files were generated from the tag directories using makeUCSCfile.
Peaks representing Transcription Start Regions (TSRs) for csRNA-seq and expressed small RNAs for sRNA-seq, were defined using HOMER’s findcsRNATSR.pl and findPeaks, respectively. A minimum read count of 10 per 10 million was required for regions to be considered.
Assembly: hg38, GCF_002263795.2, modified_GCA_018282365.1
Supplementary files format and content: BedGraph files (.bedGraph.gz) containing the locations that denote TSS positions.
Supplementary files format and content: Text files (.tss.txt) containing tab-delimited data on identified transcription start site clusters (TSRs).
Supplementary files format and content: Modified gtf file that underwent an ID update to achieve consistency with the fasta genome.
Library strategy: csRNA-seq


title: A375, Illumina, sRNA-seq, rep1

description:
short RNAs (20-65nt)
sRNA_Homo_sapiens-A375_Illumina.reps.merged.tss.txt


title: Aggregated cell lines (FB), scRNA-seq


title: A375, Illumina, sRNA-seq, rep2


title: Sample 27: HT1376-TetOn-ARID1A_DMSO_without Dox_H3K27ac_R1


title: Sample 26: HT1376-TetOn-ARID1A_DMSO_with Dox_H3K27ac_R1


title: A375, Illumina, csRNA-seq, rep2

description:
short RNAs (20-65nt)
Homo_sapiens-A375_Illumina.reps.merged.tss.txt


title: PT26-MT Cycle 1 Day 22


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-6


title: Sample 25: HT1376-TetOn-ARID1A_DMSO_with Dox_H3K27ac_R1


title: A375, Illumina, csRNA-seq, rep1


title: Sample 24: HT1376-TetOn_CPI-0209_with Dox_SMARCA4_R2


title: D29_500nM

city: Stanford

first: Sahin

last: Naqvi

state: CA California

address: 265 Campus Drive, Lokey Stem Cell Research Building/SIM1

institute: Stanford University

data_processing:
Adapter sequences and low-quality bases (-Q 10) were trimmed from sequencing reads using skewer v0.2.2 and aligned to the human genome (hg38) using bowtie2 v2.4.1 with the following settings: --very-sensitive, --X 2000. Read mate pair information was corrected with samtools v1.10 fixmate, PCR duplicates were removed using samtools markdup, and mitochondrial reads and low mapping quality reads (-q 20) were removed using samtools view.
Tn5 insertion counts (from shifted bed files) were counted over 151,487 reproducible peak regions (as defined by Naqvi et al 2023) using bedtools
Assembly: hg38
Supplementary files format and content: Tn5 insertion counts per reproducible peak region

source_name: H9 hESC

growth_protocol: hESCs were differentiated to cranial neural crest cells (CNCCs) using a protocol described previously (Bajpai et al., 2010; Prescott et al., 2015). Briefly, hESCs were grown for 5-6days until large colonies formed, then were disaggregated using collagenase IV and gentle pipetting. Clumps of ~200 hESCs were washed in PBS and transferred to a 10cm Petri dish in neural crest differentiation media (NDM). NDM: 1:1 ratio of DMEM-F12 and Neurobasal, 0.5x Gem21 NeuroPlex Supplement With Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF (PeproTech, 100-18B), 20ng/ml EGF (PeproTech, AF-100-15) and 5ug/ml bovine insulin (Gemini Bio-Products, 700-112P). After 7-8days, neural crest emerged from neural spheres attached to the Petri dish, and after 11days, neural crest cells were passaged onto fibronectin-coated 6-well plates (~1m cells/well) using accutase and fed with neural crest maintenance media (NMM). NMM: 1:1 ratio of DMEM-F12 and neurobasal, 0.5x Gem21 NeuroPlex Supplement with Vitamin A (Gemini, 400-160), 0.5x N2 NeuroPlex Supplement (Gemini, 400-163), 1x antibiotic/antimycotic, 0.5x Glutamax, 20ng/ml bFGF, 20ng/ml bFGF EGF and 1mg/ml BSA (Gemini). After 2-3days, neural crest cells were plated at ~1m cells/well of a 6-well plate and the following day cells were fed with neural crest long-term media. Long term media: neural crest maintenance media+ 50pg/ml BMP2 (PeproTech, 120-02)+ 3uM CHIR-99021 (Selleck Chemicals, S2924) (BCh media). After transition to BCh media, CNCCs at subsequent passages were plated at ~800,000 cells/well of a 6-well plate. CNCCs were then passaged twice to passage 4 where depletion experiments were performed

extract_protocol:
ATAC-seq was performed as described previously (Corces et al., 2017). Briefly, CNCCs were incubated with BCh media containing 200U/mL DNaseI (Worthington, LS002007) for 30 min AND harvested using accutase. Viable cells were counted using Countess Automated Cell Counter (Invitrogen), 50,000 viable cells were pelleted at 500 RCF for 5min at 4°C and resuspended in ATAC-resuspension buffer containing 0.1% NP40, 0.1% Tween20, and 0.01% Digitonin and incubated on ice for 3minutes. Following wash-out with cold ATAC-Resuspension Buffer (RSB, 10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2 in sterile water) containing 0.1% Tween20, cells were pelleted and resuspended in 50μL transposition mix (25μL 2x TD buffer, 2.5μL transposase (100nM final), 16.5μL PBS, 0.5μL 1% digitonin, 0.5μL 10% Tween20, 5μL H2O) and incubated for 30minutes at 37°C with shaking. The reaction was purified using the Zymo DNA Clean & Concentrator kit
Purified, transposed DNA was PCR-amplified with NEBNext master mix and primers as defined in Corces et al. Libraries were purified by two rounds of double-sided size selection with AMPure XP beads (Beckman Coulter, A63881), with the initial round of 0.5x sample volume of beads followed by a second round with 1.3x initial volume of beads. Library size distributions were confirmed by separation on a PAGE gel and staining with SYBRGold and pooled based on quantifications from Qubit dsDNA High Sensitivity Kit.

treatment_protocol: dTAGV-1 (Tocris, 6914) at a range of concentrations was added to BCh media, with an equivalent amount of DMSO as vehicle control, for the indicated times.

tag: differentiation batch

value: H9 hESC

value: hESC-derived P4 CNCC

tag: treatment concentration

tag: treatment time

tag: relative sox9_level


title: PT26-MT Cycle 1 Day 15

value: MT Cycle 1 Day 15


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-5

tag: genotype


title: BT474, Illumina, csRNA-seq, rep2

tag: cell line


title: PT26-MT Cycle 1 Day 8

tag: tissue


title: PT27-MT Cycle 1 Day 1


title: D29_16nM

tag: cell type

tag: treatment


title: Sample 22: HT1376-TetOn-ARID1A_CPI-0209_without Dox_SMARCA4_R2


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-3


title: D29_5nM


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-4


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-9


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-7


title: Sample 23: HT1376-TetOn_CPI-0209_with Dox_SMARCA4_R2


title: PT27-MT Cycle 1 Day 22

value: MT Cycle 1 Day 22


title: PT25-MT Cycle 1 Day 8


title: Sample 21: HT1376-TetOn-ARID1A_DMSO_without Dox_SMARCA4_R2


title: PT25-MT Cycle 1 Day 15


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-8


title: Sample 20: HT1376-TetOn-ARID1A_DMSO_with Dox_SMARCA4_R2


title: PT26-MT Cycle 1 Day 1


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-1


title: PT25-MT Cycle 2 Day 1

value: MT Cycle 2 Day 1


title: Sample 19: HT1376-TetOn-ARID1A_DMSO_with Dox_SMARCA4_R2


title: D42_500nM


title: Sample 18: HT1376-TetOn_CPI-0209_with Dox_SMARCA4_R1


title: D42_16nM


title: PT25-MT Cycle 1 Day 1


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-37


title: Sample 17: HT1376-TetOn_CPI-0209_with Dox_SMARCA4_R1


title: PT25-MT Cycle 1 Day 22


title: PT24-MT Cycle 3 Day 1

value: MT Cycle 3 Day 1


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-36


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-35


title: D42_0nM


title: D42_5nM


title: BrainCell_Enhancer-eHGT_375m_MouseID-614198_Cell-2


title: Sample 16: HT1376-TetOn-ARID1A_CPI-0209_without Dox_SMARCA4_R1

value: without Dox


title: D29_1p6nM


title: Sample 15: HT1376-TetOn-ARID1A_DMSO_without Dox_SMARCA4_R1


title: PT24-MT Cycle 1 Day 22


title: Sample 14: HT1376-TetOn-ARID1A_DMSO_with Dox_SMARCA4_R1


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-34


title: D107_500nM


title: D29_0nM


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-33


title: PT24-MT Cycle 1 Day 1


title: Sample 13: HT1376-TetOn-ARID1A_DMSO_with Dox_SMARCA4_R1


title: PT24-MT Cycle 1 Day 15


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-38


title: D107_16nM


title: Sample 12: HT1376-TetOn_DMSO_with Dox_ARDI1A_R2


title: Sample 11: HT1376-TetOn_CPI-0209_with Dox_ARDI1A_R2


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-32


title: D107_5nM


title: PT24-MT Cycle 1 Day 8


title: D42_1p6nM


title: PT24-MT Cycle 2 Day 1


title: D107_0nM


title: Sample 10: HT1376-TetOn-ARID1A_DMSO_without Dox_ARDI1A_R2


title: D107_1p6nM


title: D119_500nM


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-31


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-29


title: PT23-MT Cycle 1 Day 1


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-28


title: Sample 9: HT1376-TetOn-ARID1A_CPI-0209_without Dox_ARDI1A_R2


title: PT22-MT Cycle 1 Day 15


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-30


title: Sample 8: HT1376-TetOn-ARID1A_DMSO_with Dox_ARDI1A_R2


title: PT22-MT Cycle 1 Day 8


title: D119_5nM


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-27


title: PT23-MT Cycle 1 Day 22


title: Sample 7: HT1376-TetOn-ARID1A_CPI-0209_with Dox_ARDI1A_R2


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-26


title: PT22-MT Cycle 1 Day 22


title: D119_1p6nM


title: PT22-MT Cycle 1 Day 1


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-25


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-24


title: Sample 5: HT1376-TetOn_CPI-0209_with Dox_ARDI1A_R1


title: D119_0nM


title: PT21-MT Cycle 2 Day 1


title: D119_16nM


title: Sample 4: HT1376-TetOn-ARID1A_DMSO_without Dox_ARDI1A_R1


title: PT21-MT Cycle 1 Day 15


title: TSP77 LOF rep1

data_processing:
Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: hg37
Supplementary files format and content: txt file includes raw counts for all genes
Supplementary files format and content: txt file includes counts per million for all genes
Supplementary files format and content: txt file inclues counts per million for all transcripts
Supplementary files format and content: txt file includes raw counts for all transcripts

extract_protocol:
NPCs were collected and pelleted at day 10 of differentiation. Pellets were stored at -80°C until all samples had been collected. All samples RNA were extracted at the same time. RNA was extracted following the protocol in RNeasy Mini Kit (Qiagen). RNA extraction inlcuded treatment with DNase I following the optional portion of the RNeasy kit using the DNase I kit (Qiagen).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

tag: time

value: day 10

value: TSP77 TSC2 LOF/LOF (Sundberg et al., 2018)

value: iPSC-derived neural progenitor cells

value: TSC2 LOF/LOF

value: neural progenitor cell differentiation


title: TSP77 LOF rep2


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-23


title: PT21-MT Cycle 1 Day 8


title: TSP77 HET rep2

value: TSP77 TSC2 +/LOF (Sundberg et al., 2018)

value: TSC2 +/LOF


title: PT21-MT Cycle 1 Day 1

value: whole blood

value: MT Cycle 1 Day 1


title: Sample 3: HT1376-TetOn-ARID1A_CPI-0209_without Dox_ARDI1A_R1


title: TSP77 HET rep1


title: TSP77 WT rep2

value: TSP77 TSC2 +/+ (Sundberg et al., 2018)


title: PT21-MT Cycle 1 Day 22


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-20

value: VISp


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-19


title: Sample 6: HT1376-TetOn_DMSO_with Dox_ARDI1A_R1

value: DMSO

value: with Dox


title: spleen, challenged, predicted to die, ms34

city: Burnaby

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

data_processing:
Sequence quality was assessed using FastQC v0.11.5 and MultiQC v0.8.
The FASTQ sequence reads were aligned to the mouse genome (Ensembl GRCm38.94) using STAR v2.5 and mapped to Ensembl transcripts.
Read-counts were generated using htseq-count (HTSeq 0.6.1p1).
Assembly: Ensembl GRCm38.94
Supplementary files format and content: counts file

source_name: spleen

extract_protocol:
Total RNA was extracted from each sample using the RiboPure RNA purification kit
Poly-adenylated RNA was captured using the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalog no.: E7409L, NEB). Strand-specific cDNA libraries were generated from poly-adenylated RNA using the KAPA Stranded RNA-Seq Library Preparation Kit (cat. no.: 07277253001, Roche).

value: spleen

tag: condition

value: challenged, predicted to die


title: PT20-MT Cycle 1 Day 22

value: MT Cycle 1 Day 22


title: liver, challenged, predicted to die, ms34

source_name: liver

value: liver


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-17


title: TSC2 CR37 KO rep2

source_name: CR37 TSC2 KO (Armstrong et al., 2017)

value: day 10

value: CR37 TSC2 KO (Armstrong et al., 2017)

value: TSC2 KO


title: TSP77 WT rep1

value: iPSC-derived neural progenitor cells


title: Inflamed_basal prostate stem cells_3

city: West Lafayette

first: Majid

last: Kazemian

state: IN

address: 201 S. University Steet

department: Biochemistry and Computer Science

institute: Purdue University

description: Both_bwa.sorted.pfct.rmdup.ofst.30bp.wH.edge1.5Rdiffmerged.sorted.merged.bed

data_processing:
Raw sequencing reads were aligned to mm10 using bwa v0.7.17-r1188 with “-M” with other parameters kept as default.
Duplicate reads are removed using PicardTools v2.12.2, Properly mapped pairs were extract by samtools.
Reads were offset by using publicly available script ATAC_BAM_shifter_gappedAlign.pl. Reads with TLEN < 30bp were removed.
Tag directories were generated by makeTagDirectory from HOMER v4.8. Differential chromatin accessible regions/peaks between naive versus inflamed conditions were obtained using getDifferentialPeaksReplicates.pl from HOMER v4.8 with “-f 1.5 -edgeR -balanced”. pos2bed.pl was used to generate merged peak files from differential peaks for each sample.
makeUCSCfile was used to generate bedGraph files from tag directories. bedGraphToBigWig was used to generate bigwig files from bedGraph files with mm10 chromosome size file. findMotifsGenome.pl from HOMER v4.8 was used to find motifs enriched in the differential peaks.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: bed - differential peaks in all samples

source_name: prostate

growth_protocol: Freshly sorted cells without any in vitro culture

extract_protocol:
Minced prostate tissues from naïve or inflamed POET3 mice were digested with collagenase followed by trypsinization. Dissociated cells were passed through 20G needles and 40 µm cell strainers to eliminate aggregates, followed by removal of red blood cells by ACK buffer. Isolated cells were stained with fluorescence-conjugated specific antibodies for CD45, CD31, Sca-1 and CD49f. CD45-CD31-Sca-1+CD49f+ basal stem cells were sorted on the BD FACSAria under sterile conditions.
Nuclei were prepared by cell lysis using ice cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) before immediate transposition of DNA in 25 μl 2x TD buffer, 2.5 μl Transposase (Illumina) and 22.5 μl of nuclease free water for 30 minutes at 37 degree. Samples were then purified using Mini Elute Kit (Qiagen). PCR amplification and library prep were performed using 10 μl transposed DNA, 9.7 μl nuclease free H2O, 0.3 μL 100x SYBR Green I (Invitrogen S-7563), 25 μL NEBNext High-Fidelity 2x PCR Master Mix (New England Labs M0541), and 2.5 μl each of individual 25μM dual unique Nextera PCR primers in a 50 μl reaction.

treatment_protocol: Prostate inflammation was induced in POET3 (Prostate Ovalbumin Expressing Transgenic 3) mice by adoptive transfer of pre-activated splenocytes from OT-1 mice and was allowed to develop for 7 days before prostate harvest.

value: prostate

value: basal stem cells

value: mouse epithelial

value: inflamed


title: PT20-MT Cycle 1 Day 1

value: whole blood

value: MT Cycle 1 Day 1


title: PT19-MT Cycle 1 Day 22


title: Inflamed_basal prostate stem cells_2


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-15

value: VISp


title: Naive_basal prostate stem cells_3

value: WT

value: control


title: PT18-MT Cycle 1 Day 1


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-18


title: PT19-MT Cycle 1 Day 1


title: Sample 1: HT1376-TetOn-ARID1A_CPI-0209_with Dox_ARDI1A_R1

value: with Dox

tag: target


title: RNAPII IP, U4 AMO, repeat 3 (ChIP-seq)

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

country: China

institute: sysu

data_processing:
The NovaSeq platform was utilized for sequencing these libraries, and all ChIP-Seq data processing and analysis were carried out following the ENCODE ChIP-Seq pipeline (https://www.encodeproject.org/data-standards/chip-seq/).
Assembly: hg38
Supplementary files format and content: bw files

source_name: HeLa cells

growth_protocol: HeLa cells were obtained from ATCC and cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Thermo Scientific).

extract_protocol:
For the preparation of ChIP-Seq libraries, the ChIP-IT Express Enzymatic Shearing (Active Motif) was used to make input DNA.
For the preparation of ChIP-Seq libraries,  ChIP-Seq library preparation (Vazyme) kits were employed. The RNAPII antibodies were purchased from Santa Cruz Biotechnology (sc-47701-X)
IPed DNA library was prepared using ChIP-seq DNA library preparation kits (Vazyme)

treatment_protocol: Electroporation was performed using a Bio-Rad Gene pulser at 960 μF and 280 V. After electroporation, cells were cultured for 12 hours in 6 well plates with 2 ml DMEM.

value: HeLa cells

value: cancer cell line

value: U4 AMO treated


title: TSC2 CR37 KO rep1

value: day 10

value: neural progenitor cell differentiation


title: Inflamed_basal prostate stem cells_1


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-13

data_processing:
Base-calling using standard Illumina software.
Alignment with STAR (https://github.com/alexdobin/STAR)
Transformed by counts per million.
Assembly: mm10
Supplementary files format and content: Processed data in counts per million (CPM) format.


title: Naive_basal prostate stem cells_1


title: TSC2 CR39 WT rep2

source_name: CR39 TSC2 WT (Armstrong et al., 2017)

value: CR39 TSC2 WT (Armstrong et al., 2017)

value: TSC2 WT


title: PT18-MT Cycle 1 Day 22

tag: treatment time point

value: MT Cycle 1 Day 22


title: Naive_basal prostate stem cells_2

value: prostate

value: basal stem cells


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-16

source_name: VISp


title: TSC2 CR39 WT rep1

value: iPSC-derived neural progenitor cells


title: R4_400PPM

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description: HEMI, 400PPM, rep6

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the raw counts for each sample.

source_name: striatum

extract_protocol:
RNA was isolated using the Rneasy Plus Universal mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using standard Illumina TruSeq stranded polA+ mRNA

tag: model

value: Huntington's disease

value: HET

value: striatum

tag: strain

tag: age

value: 14 wks


title: PT17-MT Cycle 1 Day 22

value: whole blood

tag: dose cohort

tag: c1d1 cpi-0209 exposure

tag: patient


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-22

extract_protocol:
Single SYFP2-expressing cells from mouse brain were flow sorted into individual tubes in SMARTerv4 collection buffer.
SMARTerv4

value: VISp


title: PT16-MT Cycle 1 Day 22


title: RNAPII IP, negative control, repeat 3 (ChIP-seq)

value: HeLa cells

value: negative control

value: negative control AMO treated


title: R3_400PPM

description: HEMI, 400PPM, rep5


title: PT16-MT Cycle 1 Day 1

value: MT Cycle 1 Day 1


title: PT17-MT Cycle 1 Day 1


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-12


title: Sample 2: HT1376-TetOn-ARID1A_DMSO_with Dox_ARDI1A_R1

value: DMSO

value: with Dox

tag: repeat


title: input DNA, U4 AMO, repeat 3 (ChIP-seq)

value: cancer cell line

value: U4 AMO treated


title: R2_400PPM

description: HEMI, 400PPM, rep4


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-14


title: input DNA, negative control, repeat 3 (ChIP-seq)


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-10


title: RNAPII IP, U4 AMO, repeat 2 (ChIP-seq)


title: PT15-MT Cycle 1 Day 1


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-21


title: R1_400PPM

description: HEMI, 400PPM, rep3


title: N3_200PPM

description: HEMI, 200PPM, rep5


title: PT14-MT Cycle 1 Day 22

value: MT Cycle 1 Day 22


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-8


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-9


title: PT15-MT Cycle 1 Day 22


title: RNAPII IP, U4 AMO, repeat 1 (ChIP-seq)


title: PT14-MT Cycle 1 Day 1


title: RNAPII IP, negative control, repeat 1 (ChIP-seq)


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-11


title: N2_200PPM

description: HEMI, 200PPM, rep4


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-5


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-6


title: K4_CTL

description: HEMI, control, rep6

value: untreated


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-7


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-4


title: input DNA, U4 AMO, repeat 1 (ChIP-seq)


title: input DNA, negative control, repeat 2 (ChIP-seq)


title: PT13-MT Cycle 3 Day 1

value: MT Cycle 3 Day 1


title: PT13-MT Cycle 2 Day 1

value: MT Cycle 2 Day 1


title: K2_CTL

description: HEMI, control, rep4

value: Huntington's disease

value: HET


title: K3_CTL

description: HEMI, control, rep5

value: striatum

value: 14 wks


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-3

value: VISp


title: PT13-MT Cycle 1 Day 8

value: whole blood

value: MT Cycle 1 Day 8


title: I2_400PPM

description: HEMI, 400PPM, rep2


title: RNAPII IP, negative control, repeat 2 (ChIP-seq)

value: HeLa cells

value: negative control

value: negative control AMO treated


title: input DNA, negative control, repeat 1 (ChIP-seq)


title: PT13-MT Cycle 1 Day 15

value: MT Cycle 1 Day 15


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-3


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-2


title: I1_400PPM

description: HEMI, 400PPM, rep1


title: PT13-MT Cycle 1 Day 1

value: MT Cycle 1 Day 1


title: G4_200PPM

description: HEMI, 200PPM, rep3


title: PT13-MT Cycle 1 Day 22


title: HEK-293 cells, U4 AMO treated, repeat 2 (3'-Seq)

data_processing:
The downstream sequence analysis was performed utilizing our recently published pipeline, QuantifyPoly(A) (QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering. Briefings in bioinformatics22,  (2021); published online EpubNov 5 (10.1093/bib/bbab268).)
Assembly: hg38
Supplementary files format and content: bw files

source_name: HEK-293 cells

growth_protocol: HeLa and HEK293 cells were obtained from ATCC and cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Thermo Scientific).  NIH3T3, and Neuro-2a cells were obtained from iCell Bioscience Inc. (Shanghai, China) and cultured in commercially available medium (Cat. No. iCell-m041-001b; iCell-m040-001b).

extract_protocol:
Total RNA was extracted from cultured cells using the TRIzol (Thermo Scientific).
3'-Seq was conducted using the QuantSeq Rev 3ʹ mRNA-seq library prep kit (Cat. No. 016.24; Lexogen)

value: HEK-293 cells

value: cancer cell line

value: U4 AMO treated


title: HEK-293 cells, U4 AMO treated, repeat 1 (3'-Seq)


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-16


title: HEK-293 cells, U1 AMO treated, repeat 2 (3'-Seq)

value: U1 AMO treated


title: input DNA, U4 AMO, repeat 2 (ChIP-seq)


title: PT12-MT Cycle 2 Day 1

value: MT Cycle 2 Day 1


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-14


title: PT12-MT Cycle 1 Day 15


title: D2_WT

description: WT, control, rep6

value: Huntington's disease

value: WT

value: untreated


title: G3_200PPM

description: HEMI, 200PPM, rep2

value: HET

value: striatum

value: 14 wks


title: HEK-293 cells, U1 AMO treated, repeat 1 (3'-Seq)


title: HEK-293 cells, NC AMO treated, repeat 2 (3'-Seq)


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-15

value: VISp


title: PT12-MT Cycle 1 Day 8

value: whole blood

value: MT Cycle 1 Day 8


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-12


title: HEK-293 cells, NC AMO treated, repeat 1 (3'-Seq)

value: negative control

value: negative control AMO treated


title: G1_200PPM

description: HEMI, 200PPM, rep1


title: B4_WT

description: WT, control, rep4


title: D1_WT

description: WT, control, rep5


title: PT12-MT Cycle 1 Day 1

value: MT Cycle 1 Day 1


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-11


title: PT12-MT Cycle 1 Day 22

value: MT Cycle 1 Day 22


title: HeLa cells, U1 AMO treated, repeat 2 (3'-Seq)

value: HeLa cells

value: cancer cell line


title: PT11-MT Cycle 1 Day 22


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-10


title: HeLa cells, U4 AMO treated, repeat 2 (3'-Seq)

value: U4 AMO treated


title: B3_WT

description: WT, control, rep3


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-13


title: HeLa cells, U4 AMO treated, repeat 1 (3'-Seq)


title: PT11-MT Cycle 1 Day 1


title: PT10-MT Cycle 1 Day 22


title: HeLa cells, U1 AMO treated, repeat 1 (3'-Seq)

value: U1 AMO treated


title: B1_WT

description: WT, control, rep1

value: Huntington's disease


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-8


title: A1_CTL

description: HEMI, control, rep1


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-9


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-12


title: HeLa cells, NC AMO treated, repeat 1 (3'-Seq)


title: A3_CTL

description: HEMI, control, rep3


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-11


title: HeLa cells, NC AMO treated, repeat 2 (3'-Seq)


title: lib78067

city: Seattle,

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCm38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCm38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

extract_protocol:
For each TEC subset, 200 cells were sorted directly into reaction buffer using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

value: KO


title: PT10-MT Cycle 1 Day 8


title: A2_CTL

description: HEMI, control, rep2

value: untreated


title: PT10-MT Cycle 1 Day 15

value: MT Cycle 1 Day 15


title: PT10-MT Cycle 1 Day 1


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-10


title: HeLa cells, U1 AMO treated, repeat 2 (RNA-seq)

data_processing:
fastp was used to remove low quality reads; Deseq2 was used to compare the gene expression level among different groups.
Assembly: hg38
Supplementary files format and content: bw files

extract_protocol:
Total RNA was extracted from cultured cells using the TRIzol (Thermo Scientific).
mRNA-seq library preparation was carried out using standard Illumina kit TruSeq® Stranded mRNA Library Prep (https://www.illumina.com.cn/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-mrna.html)


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-7


title: HeLa cells, U4 AMO treated, repeat 1 (RNA-seq)


title: PT9-MT Cycle 1 Day 22

data_processing:
Sequencing reads were mapped to the genome using STAR v2.7.3a with default settings
The transcript and gene read count quantification were performed using RSEM v1.3.1 with default settings
Genome_build: hg38


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-9


title: HeLa cells, U1 AMO treated, repeat 1 (RNA-seq)


title: PT8-MT Cycle 1 Day 22


title: lib78065


title: lib78068


title: HeLa cells, U4 AMO treated, repeat 2 (RNA-seq)


title: lib78064


title: HeLa cells, NC AMO treated, repeat 2 (RNA-seq)


title: HeLa cells, NC AMO treated, repeat 1 (RNA-seq)


title: PT7-MT Cycle 1 Day 22


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-6


title: lib78063


title: lib78062

value: Ski flox Control


title: PT8-MT Cycle 1 Day 1


title: siP300+OGA_3

city: Hangzhou

first: Qianyu

last: Liu

address: YuhangTang Road

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: ensemble_106_homo_sapiens_GRCH38
Supplementary files format and content: excel file include FPKM values for each Sample .

growth_protocol: PXGL naïve hESC was cultured in N2B27 medium supplemented with 1 mM PD0325901, 2 mM XAV939 , 2 mM Go¨ 6983  and 10 ng/mL human LIF on the MEF layer.

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. 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 following the vendor's recommended protocol.

value: H9 hESC

value: Human embryonic stem cell

value: OGA overexpression


title: PT7-MT Cycle 1 Day 1

extract_protocol:
Whole blood cells were collected using PAXgene blood RNA tubes. Proccessing and sequencing of patient RNA samples were performed by ALMAC. The RNA extractions were performed using PAXgene Blood RNA Kit following manufacturer’s instructions.
Library preparation proceeded with rRNA and hemoglobin depletion using KAPA RNA HyperPrep Kit with RiboErase (HMR) Globin. Paired-end 75 base pair sequencing was performed on an Illumina platform. Prior to sequencing, RNA integrity was assessed by 2100 Bioanalyser (Agilent) and concentration was assayed by Nanodrop.

value: whole blood


title: lib78061


title: siP300+OGA_2


title: PT6-MT Cycle 2 Day 1

value: MT Cycle 2 Day 1


title: lib78066


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-6

value: VISp


title: PT9-MT Cycle 1 Day 1

value: MT Cycle 1 Day 1


title: siP300+OGA_1


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-5


title: PT6-MT Cycle 1 Day 8

value: MT Cycle 1 Day 8


title: lib78059


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-8


title: PT6-MT Cycle 1 Day 15


title: lib78058


title: PXGL_siP300_2

value: EP300 knockdown


title: PXGL_siP300_3


title: lib78060


title: PT6-MT Cycle 1 Day 22

value: MT Cycle 1 Day 22


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-5


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-4


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-7


title: lib78056


title: PT5-MT Cycle 2 Day 1


title: PXGL_siP300_1


title: PT6-MT Cycle 1 Day 1


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-4


title: lib78057


title: PXGL_siOGA_3

value: OGA knockdown


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-3


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-2


title: PXGL_siOGA_2


title: PXGL_siOGA_1


title: PT5-MT Cycle 3 Day 1

value: MT Cycle 3 Day 1


title: lib78054


title: PT5-MT Cycle 1 Day 8


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-3


title: lib78053

value: Control


title: PXGL_siNC_3

value: WT


title: BrainCell_Enhancer-eHGT_390m_MouseID-616740_Cell-1


title: PXGL_siNC_2


title: lib78052


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-11


title: PT5-MT Cycle 1 Day 22


title: PXGL_siNC_1


title: lib78051


title: PT5-MT Cycle 1 Day 15


title: PT5-MT Cycle 1 Day 1


title: lib78050


title: PT4-MT Cycle 1 Day 1


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-9


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-10


title: shZNF408, RNA-seq, rep3

city: Beijing

first: Chunyu

last: Yu

address: Xueyuan Road 38#

institute: Peking University

data_processing:
shCTR or shZNF408 MCF-7 cells (1 × 107) with three biological replicates were harvested, and total RNA was isolated using TRIzol reagent following the manufacturer’s protocol. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. For the quantification of high-quality reads, kallisto was employed. The reads were aligned to the transcriptome of the human reference genome (UCSC GRCh38, hg38). In this process, the gene-level counts are derived as the sum of the transcript-level counts. For the quantification and differential analysis of gene counts, the DESeq2 tool was utilized with statistical significance of p < 0.05.
Assembly: hg38
Supplementary files format and content: expression profiles for each sample

extract_protocol:
Total RNA was isolated from shCTR or shZNF408 MCF-7 cells using TRIzol reagent according to the manufacturer's instructions.
Paired-end RNA-seq libraries were prepared and sequenced on an Illumina NovaSeq 6000 following the manufacturer's recommended protocol by DIATRE Bio-tech Ltd.

value: Breast

value: human breast cancer

value: ZNF408 KD


title: PT4-MT Cycle 1 Day 22


title: lib78049


title: lib78048


title: BrainCell_Enhancer-eHGT_385m_MouseID-615515_Cell-1


title: shZNF408, RNA-seq, rep1


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-2


title: WT, RNA-seq, rep3


title: lib78055

value: KO


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-8


title: PT3-MT Cycle 1 Day 1


title: PT2-MT Cycle 1 Day 22


title: lib78046


title: WT, RNA-seq, rep2


title: PT2-MT Cycle 1 Day 1


title: lib78045


title: BrainCell_Enhancer-eHGT_391h_MouseID-617306_Cell-1


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-7


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-2


title: WT, RNA-seq, rep1


title: shZNF408, RNA-seq, rep2


title: BrainCell_Enhancer-eHGT_401h_MouseID-619575_Cell-1


title: Cuttag, SETD1A_Rep2

data_processing:
*library strategy: CUT&Tag
The raw sequencing data were examined by the Illumina NovaSeq analysis pipeline. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to the unmasked human reference genome (UCSC GRCh38, hg38) using BWA program and further analyzed by MACS2 with the p-value of 0.001 for ZNF408, SETD1A and H3K4me3. The intersection of two CUT&Tag datasets is obtained using the Bedtools intersect tool.
Assembly: hg38
Supplementary files format and content: MACS2-called peaks in BED format, and signal in bigwig format

extract_protocol:
Cells were processed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit, starting with approximately 1 × 10^5 MCF-7 cells per assay.
DNA libraries were prepared using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit as per the provided protocol.


title: PT1-MT Cycle 1 Day 1


title: lib78044


title: Cuttag, SETD1A_Rep1


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-6


title: lib78047


title: lib78042


title: PT3-MT Cycle 1 Day 22


title: Cuttag, H3K4me3


title: lib78043


title: PT1-MT Cycle 1 Day 22


title: 1205_2_resub

data_processing:
Sequencing reads were mapped to the genome using STAR v2.7.3a with default settings
The transcript and gene read count quantification were performed using RSEM v1.3.1 with default settings
Genome_build: hg38
Supplementary_files_format_and_content: txt file: raw counts

growth_protocol: The HT1376 bladder cancer cell lines was expanded in vitro under routine subculturing procedures in the medium recommended by the supplier, harvested while in the exponential growth phase, and counted for tumor inoculation. Female CB17 SCID mice at 6-8 weeks of age were used for study initiation. Each mouse was inoculated subcutaneously in the right flank with tumor cells in 0.2 ml PBS mixed with Matrigel (BD Biosciences); 5x106 cells per injection were used for HT1376 cells.

extract_protocol:
Samples were collected at indicated interim timepoints on treatment or at study endpoint for analysis at 1 hr post-dosing for pharmacokinetic (PK) and pharmacodynamic studies (PD), unless indicated otherwise. Tumors were split into two pieces (for PK and PD), snap-frozen in liquid nitrogen, then transferred to -80°C before analysis. Total RNA was extracted with Trizol, in accordance with the manufacturer’s protocol.
Sequencing libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit (v2). The resulting libraries were sequenced on an Illumina HiSeq 4000, with 9 samples multiplexed per lane.  2x150 base pair paired-end reads using the Illumina TruSeq strand specific protocol, for an expected 40 million reads per sample.

treatment_protocol: Mice were randomized and drug treatments were started 11-15 days after inoculation when tumors reached an average of 139-160 mm3; animals were distributed so that each treatment arm had a similar starting tumor size (3-21 animals per arm, depending on experiment and sampling schedule). Mice were treated with 75 mg/kg of each compound in a PO QD dosing schedule. The tumor were harvested 1hr post dosing at day 15.


title: Cuttag, ZNF408


title: BrainCell_Enhancer-eHGT_386m_MouseID-616738_Cell-1


title: ATAC-seq, WT, rep2

data_processing:
The raw sequencing data were examined by the Illumina analysis pipeline, aligned to the unmasked human reference genome (UCSC GRCh38, hg38) using Bowtie2, and further called peaks by MACS2 with p < 0.001.
Assembly: hg38
Supplementary files format and content: MACS2-called peak files and bigwig files

extract_protocol:
Approximately 5 × 10^5 MCF-7 cells were processed for ATAC-seq using the DIATRE ATAC-seq Kit for DNA purification.
DNA libraries were generated with the ATAC-seq Kit from DIATRE following the manufacturer's instructions.

value: No treatment


title: 1205_3_resub


title: BrainCell_Enhancer-eHGT_373m_MouseID-616737_Cell-1


title: lib78041


title: 1205_1


title: ATAC-seq, WT, rep1


title: 1650_1_resub


title: lib78038


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-5


title: MRC5 cells, 10 uM Ech A treated, 72H - biol rep 3 [ME_72_03]

city: Busan

first: Chaeyoung

address: 40, Jwadong-gil, Jangan-eup, Gijang-gun

country: South Korea

institute: Dongnam Institute of Rediological & Medical Sciences

data_processing:
Hisat2 v2.0.5
featureCounts v1.5.0-p3
DESeq2 v1.20.0
Assembly: hg19
Supplementary files format and content: FPKM

extract_protocol:
Total RNA was isolated using a Ribospin Kit (#304-150, GeneAll Biotechnology). 1.2 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: Human Fibroblasts

value: 10 uM Ech A


title: lib78037

first: Stephanie


title: BrainCell_Enhancer-eHGT_390m_MouseID-556485_Cell-1


title: MRC5 cells, 10 uM Ech A treated, 72H - biol rep 2 [ME_72_02]


title: lib78036


title: 1650_2


title: 7373_3

value: tazemetostat


title: 1650_3


title: MRC5 cells, 10 uM Ech A treated, 24H - biol rep 3 [ME_24_03]


title: 7373_2


title: lib78035


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-4

value: VISp


title: lib78034


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-1


title: MRC5 cells, 10 uM Ech A treated, 24H - biol rep 2 [ME_24_02]


title: lib78040


title: BrainCell_Enhancer-MBP_promoter_MouseID-638254_Cell-2


title: 0478_3


title: MRC5 cells, 10 uM Ech A treated, 24H - biol rep 1 [ME_24_01]


title: BrainCell_Enhancer-eHGT_374m_MouseID-630481_Cell-1


title: BrainCell_Enhancer-MBP_promoter_MouseID-651227_Cell-1


title: lib78039


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-3


title: lib78032


title: 0478_2


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-2


title: MRC5 cells, 10 uM Ech A treated, 72H - biol rep 1 [ME_72_01]


title: lib78031


title: MRC5 cells, untreated control, 72H - biol rep 2 [M_72_02]

value: untreated


title: 7373_1


title: lib78033


title: BrainCell_Enhancer-eHGT_376h_MouseID-614199_Cell-1


title: 0478_1


title: MRC5 cells, untreated control, 72H - biol rep 1 [M_72_01]


title: MRC5 cells, untreated control, 24H - biol rep 3 [M_24_03]


title: MRC5 cells, untreated control, 24H - biol rep 2 [M_24_02]


title: lib78028


title: lib78029


title: BrainCell_Enhancer-eHGT_405m_MouseID-601542_Cell-1


title: 0751_3

value: Valemetostat


title: 0751_2


title: MRC5 cells, untreated control, 24H - biol rep 1 [M_24_01]


title: BrainCell_Enhancer-3xCore2(390m)_MouseID-651223_Cell-1


title: 0751_1


title: BrainCell_Enhancer-eHGT_374m_MouseID-614201_Cell-1


title: lib78027


title: MRC5 cells, untreated control, 72H - biol rep 3 [M_72_03]


title: 53105 (WT)

city: Detroit

first: Kay-Uwe

last: Wagner

state: MI

address: 421 East Canfield, EL01TM

department: Department of Oncology

institute: Barbara Ann Karmanos Cancer Institute  Wayne State University School of Medicine

data_processing:
The quality of sequenced reads was evaluated using FastQC (v0.11.9).
For the differential expression analysis between parental and Jak1 knockout samples, the 75 or 150 base paired-end reads were aligned to the GRCm38/mm10 mouse reference genome (UCSC) via Rsubread (v2.0.0).
Transcript abundance was determined using the featureCounts function of the Rsburead package, and low abundance gene transcripts (cpm < 5 in more than half of the samples) were omitted in further downstream analyses.
The edgeR package was used for the paired sample differential expression analysis between wildtype parental cells and isogenic Jak1 KO cells. Genes that passed the threshold of an FDR (False Discovery Rate) below 0.05 were considered as significantly deregulated.
To visualize the differential expression of select deregulated genes, the gene counts were log2 transformed and scaled to highlight differences in isogenic cell line pairs and were subsequently plotted as a heatmap using the R-function heatmap.2 (package: gplots v3.0.3).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files that contain gene Entrez IDs and corresponding normalized or normalized and log2 transformed  values of gene counts for each sample.

growth_protocol: Mouse PDAC cells  were maintained in DMEM medium supplemented with 10% FBS, L-glutamine, and nonessential amino acids as well as 10 µg/ml penicillin/ streptomycin and 50 µg/ml gentamicin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was extracted from flash-frozen cultured cancer cells using the RNeasy Mini Kit (QIAGEN). QIAGEN's protocol was followed to extract the total RNA. The concentration of the RNA was determined on a NanoDrop spectrophotometer, and the integrity of the RNA was validated using gel electrophoresis. Quality and quantity of the total RNA was re-confirmed by Novogene. Only high quality RNA was used for library prepration.   1.3 ug of total RNA was used for the construction of sequencing libraries.
Library construction was performed by Novogene  with the following procedure: After the QC, mRNA was enriched using oligo(dT) beads. Next, the mRNA was fragmented randomly by adding fragmentation buffer, followed by cDNA was synthesis using mRNA template and random hexamer primers. Next a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. The quality of the library was confirmed via: (1) Qubit 2.0: tests the library concentration preliminarily. (2) Agilent 2100: tests the insert size. (3) Q-PCR: quantifies the library effective concentration precisely.

treatment_protocol: To generate isogenic cell lines that are deficient in JAK1, the parental lines were infected with pBabe-Cre-puro retroviral particles and selected with increasing concentrations of puromycin (2, 4, and 7 µg/ml).

value: Pancreatic Ductal Adenocarcinoma cell line

value: Wildtype


title: hiPSC-CMs, miR negative control, rep4

city: PARIS

first: Jean-Sebastien

last: Hulot

address: 56 Rue Leblanc

department: PARCC

country: France

institute: Universite Paris Cite

data_processing:
STAR was used to obtain the number of reads associated to each gene in the Gencode v31 annotation
Raw counts for each sample were imported into R statistical software. Extracted count matrix was normalized for library size and coding length of genes to compute FPKM expression levels.
The Bioconductor edgeR package was used to import raw counts into R statistical software, and compute normalized log2 CPM (counts per millions of mapped reads) using the TMM (weighted trimmed mean of M-values) as normalization procedure.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: iCell cardiomyocytes

growth_protocol: iCell cardiomyocytes were thawed according to the manufacturer’s recommendations on a 10 μg/mL fibronectin coating, and were maintained for 6 days of culture using the maintainance medium.

extract_protocol:
RNA was harvested using Nucleospin RNA kit (Macherey Nagel). 400ng total RNA was used for the construction of sequencing librairies.
RNA-seq libraries were prepared with NEBNext® Ultra™ II mRNA-Seq kit following manufacturer's protocols.

treatment_protocol: After 6 days of culture, iCell cardiomyocytes were transfected with has-miR-548v or miR negative control ( 25 nM of microRNA in OptiMEM using Lipofectine RNAimax). Medium was changed 24 hours after transfection and total RNA was extracted 3 days after transfection.

value: iCell cardiomyocytes

value: human induced pluripotent stem cells derived cardiomyocytes

value: miR negative control


title: 0209_2


title: 53105_cre (JAK1 KO)

value: JAK1 Knockout


title: lib78030


title: 0209_1


title: 0209_3


title: hiPSC-CMs, miR negative control, rep3

value: WT


title: NR3_replicate 3

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

institute: Hainan normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data (2×150 bp PE reads) were quality controlled using Trim-Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The remaining high quality Illumina reads were aligned to our previously published N. oceanica IMET1 genome (Gong, Kang, Kim, Wang, Wei, Xin, Shen, Wang, You, Lim, Jeong, Park, Oh, Pan, Poliner, Yang, Li-Beisson, Li, Hu, Poetsch, Farre, Chang, Jeong, Jeong, Xu, 2020) with STAR (Dobin, Davis, Schlesinger, Drenkow, Zaleski, Jha, Batut, Chaisson, Gingeras, 2013) with duplication marked using Picard (https://broadinstitute.github.io/picard/).
The abundance of expression was quantified using featureCounts (Liao, Smyth, Shi, 2014) and StringTie (Kovaka, Zimin, Pertea, Razaghi, Salzberg, Pertea, 2019). For each of the mRNA-Seq datasets under each experimental condition, gene expression was measured as the numbers of aligned reads to annotated genes by featureCounts (Liao, Smyth, Shi, 2014) and normalized to CPM, FPKM (fragments per kilobase of exon model per million mapped fragments) and TPM values. Besides, raw counts from featureCounts (Liao, Smyth, Shi, 2014) were used for the differential gene expression analysis with edgeR (R package)
Assembly: Nannochloropsis oceanica IMET1
Supplementary files format and content: Excel files include FPKM values for each Sample

organism: Nannochloropsis oceanica

growth_protocol: Nannochloropsis oceanica IMET1 was cultured in modified f/2 liquid medium，which was prepared with 35 g L-1 sea salt (Realocean, USA), 3.65 mg L-1 FeCl3*6H2O, 4.37 mg L-1 Na2EDTA*2H2O, 67 mg L-1 NaH2PO4*H2O, 1 g L-1 NaNO3, trace metal mix (0.01 mg L-1 CoCl2, 0.0126 mg L-1 NaMoO4*2H2O, 0.0196 mg L-1 CuSO4*5H2O, 0.044 mg L-1 ZnSO4*7H2O, and 0.36 mg L-1 MnCl2*4H2O), and vitamin mix (0.5 µg L-1 thiamine HCl, 2.5 µg L-1 VB12, and 2.5 µg L-1 biotin). The cells were initially cultivated in this medium in a 1 L column reactor with an internal diameter of 5 cm at 25 °C with continuous light (∼50 µmol photons m-2 s-1). 1.5% CO2  was used to bubble the cells.

extract_protocol:
Total microalgal RNA was extracted using Trizol reagents (Invitrogen, USA). The concentration and purity of the RNA were determined spectrophotometrically (NanoDrop-1000, Thermo Scientific, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were collected by centrifugation once they had reached the logarithmic phase of growth (OD750 = 2.5). Following three rounds of washing with axenic seawater, cell pellets were equally inoculated into f/2 medium (800 mL) and nitrogen-free f/2 medium (800 mL) in triplicate. Starting from an initial cell concentration of OD750 = 2.5, all cultures were continuously illuminated at a rate of 50 μmol m-2 s-1. After being transferred to the designated environment for 72 hours, cell samples were collected for subsequent experiments. Algal cultures were established in three replicates under the ND and NR conditions described above.

value: nitrogen repletion


title: veh_3

value: vehicle


title: hiPSC-CMs, miR negative control, rep2


title: NR2_replicate 2


title: hiPSC-CMs, miR negative control, rep1


title: ND3_replicate 3

value: nitrogen deprivation


title: ND2_replicate 2


title: veh_2


title: hiPSC-CMs, hsa-miR548v, rep4


title: veh_1


title: VMCUB_CPI-0209_R2

source_name: VMCUB

growth_protocol: Cells were grown in the individual growth medium for each cell line (varies by line). HT1197, HT1376, TCCSUP--MEM(Earl's Salts) + 10% FBS, 1% Non-essential AA, 1 mM NaPyruvate, 1% Pen/Strep; SW780, VMCUB1--DMEM +10% FBS, 1% Pen/Strep; KU1919--RPMI1640 +10% FBS, 1% Pen/Strep; 639V--DMEM + 10% FBS, 1% Pen/Strep; T24--McCoy's 5A + 10% FBS, 1% Pen/Strep.

extract_protocol:
Total RNA was extracted with Trizol, in accordance with the manufacturer’s protocol.
Sequencing libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit (v2). The resulting libraries were sequenced on an Illumina HiSeq 4000, with 9 samples multiplexed per lane.  2x150 base pair paired-end reads using the Illumina TruSeq strand specific protocol, for an expected 40 million reads per sample.

treatment_protocol: Cells were treated with 250 nM of CPI-0209 for 4 days.

value: VMCUB


title: hiPSC-CMs, hsa-miR548v, rep2


title: hiPSC-CMs, hsa-miR548v, rep3


title: VMCUB_CPI-0209_R3


title: VMCUB_CPI-0209_R1


title: ND1_replicate 1