title: P3--_ES_H3K27me3_D5-BMP4_Rep2

description: Library name: Sample 76


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR minus dTAG control AMO rep2

status: Public on Oct 17 2025

type: SRA

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Insitute

country: United Kingdom

institute: University of Exeter

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
Adapters removed from sequencing reads using Trim Galore 0.6.5dev (Cutadapt v2.9)
Alignment with Hisat2 v2.0.0-beta to ensembl GRCh38 (default settings)
Removal of unmapped and multimapped reads (MAPQ <30) using SAMTools v.1.13
Merge biological replicates using BamTools v2.5.1
Split reads by strand using SAMTools v1.13
Bigwig files were generated from split strand BAM files using the bamCoverage of Deeptools v3.5.0
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution RPKM bigwig coverage was generated from split strand merged replicates

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: HCT116 cell lines were maintained in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol:
Chromatin-associated RNA was extracted using Trizol reagent from fractionated nuclei
DNA-free & rRNA-free RNA libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

tag: cell line

tag: cell type

value: colorectal carcinoma

tag: genotype

tag: treatment

value: control AMO, minus dTAGv-1


title: P3--_ES_H3K27me3_D5-BMP4_Rep1

city: Paris

first: Robin

last: Rondon

address: 15 rue Hélène Brion

country: France

institute: Institut Jacques Monod / CNRS UMR7592 / Universite Paris Cite

description: Library name: Sample 74

library_source: genomic

data_processing:
ATAC:Reads in raw files were pre trimmed to 36bp using Trimmomatic (Bolger et al., 2014) (v0.39)
ATAC/CUT&Tag data: PCR duplicate removal using BBmap clumpify (Bushnell et al., 2014)(v38.87) and parameters: reorder dedupe=t k=19 passes=6 subs=(0.01 x readlength). Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using Bowtie2 (Langmead et al., 2019)(v2.4.5) for CUT&Tag using parameters: --local –very-sensitive –no-mixed –dovetail –no-discordant –phred33 -I 10 -X 700
Processed bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
RNA-Seq:PCR duplicate removal, trimming, and read alignement on mm10 genome was performed by BGI. Processed bigwig files were generated from BAM files using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
Assembly: mm10
Supplementary files format and content: Bigwig format. ATAC-Seq-CUT&Tag-RNA-Seq: CPM-normalized counts.
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
We performed CUT&Tag according with the protocol described in (Kaya-Okur et al., 2020), closely following the procedure described in “Bench top CUT&Tag V.2” (S Kaya-Okur and Henikoff, 2019). We used 500 000 per sample cells per sample and the anti-FLAG (Sigma-Aldrich F3165-5MG; 1/50) for CUT&Tag on transcription factors, or 200 000 nuclei that were previously fixed and frozen following the procedure described in(Kaya-Okur et al., 2020) with anti-H3K4me2 (Abcam ab176878; 1/100), anti-H3K27me3 (Cell Signaling 9733S; 1/100) primary antibodies. The primaries antibodies were incubated overnight at 4ºC on a rotator. Samples were then incubated with a secondary anti-rabbit IgG (ABIN6923140) or anti-mouse IgG (ABIN6923141) at room temperature on a rotator. After an incubation of 1h at room temperature with a homemade purified pA-TN5 complex, the Tn5 enzyme tagmentation reaction was performed by adding a buffer containing MgCl2 to the samples and incubating for 1h at 37°C. To stop tagmentation and solubilize DNA fragments, we added 10 μL 0.5M EDTA, 3 μL 10% SDS and 2.5 μL 20 mg/mL Proteinase K to each sample and samples were incubated at 50°C for 1h. Purified DNA was obtained by phenol/chloroform extraction and precipitated with 100% ethanol and centrifugation. The DNA pellet was washed in 80% ethanol, spun down and air-dried before being resuspended in 25µl of 1mM Tris-HCl pH8.0.
Nextera primers or indexed primers were used to perform PCR. Library quality was assessed using 4200 TapeStation system (Agilent) and paired-end, 100 bp sequencing on a DBNSEQ-G400 was performed by BGI.
All information is included as columns in the SAMPLES section above
All information is included as columns in the SAMPLES section above

value: ES cell

value: neuronal differentiation - BMP4

tag: time

value: Day 5

tag: batch


title: P3--_ES_H3K27me3_D5+BMP4_Rep2

description: Library name: Sample 75

value: neuronal differentiation + BMP4


title: MCD_T_3

city: Shanghai

first: Jingya

last: Li

address: 189 Guo Shou Jing Road

country: China

institute: Shanghai Institute of Materia Medica

data_processing:
Raw sequencing data were filtered to remove low-quality reads and adapters, and the clean data were aligned to the reference genome using HISAT2.
Gene expression levels were quantified using feature Counts and normalized to FPKM values.
Assembly: mm10
Supplementary files format and content: Excel file provided includes fpkm for each sample.

molecule: total RNA

source_name: Liver

growth_protocol: MASH livers(group of MCD_V & MCD_T) were induced by CDAA-HFD in male C57BL/6J mice.NC livers were fed with normal chow diet(group of MCD_NC).

extract_protocol:
RNA was extracted and its integrity and quantity were assessed using the Agilent 2100 bioanalyzer.
For library construction, total RNA was enriched for mRNA with poly-A tails using Oligo(dT) beads, fragmented, and used to synthesize cDNA, which was purified, end-repaired, A-tailed, and ligated with sequencing adapters. cDNA fragments of 370-420 bp were selected, PCR amplified, and purified to obtain the final library, which was quantified, diluted, and checked for insert size and concentration.

treatment_protocol: Mice of MCD_T group were treated with 30 mg/kg 326E for 6 weeks, mice of MCD_NC & MCD_V group were treated with vehicle control.

tag: tissue

value: Liver

value: WT

value: CDAA-HFD, 326E treated


title: DKO_ES_H3K27me3_D5-BMP4_Rep2

description: Library name: Sample 82

value: DKO


title: P7--_ES_H3K27me3_D5-BMP4_Rep3

description: Library name: Sample 72


title: P3--_ES_H3K27me3_D5+BMP4_Rep1

description: Library name: Sample 73


title: P7--_ES_H3K27me3_D5+BMP4_Rep3

description: Library name: Sample 71


title: HEK 293 cells, siCNOT4-2

city: Dallas

first: Yi

last: Liu

state: TX

address: 5323 HARRY HINES BLVD

department: Physiology

country: USA

institute: UT Southwestern Medical Center

data_processing:
25-35 M (100 nucleotide single-end) RNA-seq reads were mapped to the human genome (hg19 assembly).
Fastq files were quality checked using fastqc (v0.11.2). Read from each sample were mapped to the reference genome using STAR (v2.5.3a).
Read counts were generated using featureCounts.
Assembly: hg19 assembly
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: HEK 293

growth_protocol: HEK293 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion). The RNA samples were then treated with Turbo DNase (Ambion) and extracted using Acid Phenol: Chloroform (Ambion).
Poly-A RNA library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: Cells were treated with 10 nM siRNA for 72 h.

value: HEK 293

value: Human Embryonic Kidney

value: CNOT4 knockdown

value: siRNA


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR minus dTAG control AMO rep1

description: Library name: Sample 1


title: HEK 293 cells, siCNOT4-1


title: MCD_T_1


title: nucRNA-seq dTAG-EXOSC3/ZC3H4-DHFR minus TMP plus dTAG rep2

description: Library name: Sample 8

extract_protocol:
RNA was extracted using Trizol reagent from fractionated nuclei
DNA-free & rRNA-free RNA libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: plus dTAGv-1, minus TMP


title: HEK 293 cells, siControl-2


title: MCD_V_3

value: CDAA-HFD, Vehicle control


title: nucRNA-seq dTAG-EXOSC3/ZC3H4-DHFR minus TMP plus dTAG rep1

description: Library name: Sample 7


title: nucRNA-seq dTAG-EXOSC3/ZC3H4-DHFR plus TMP plus dTAG rep2

description: Library name: Sample 6

value: plus dTAGv-1, plus TMP


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR plus dTAG control AMO rep1

description: Library name: Sample 3

value: colorectal carcinoma

value: control AMO, plus dTAGv-1


title: MCD_V_1


title: P7--_ES_H3K27me3_D5-BMP4_Rep2

description: Library name: Sample 70

value: ES cell


title: P7--_ES_H3K27me3_D5+BMP4_Rep2

description: Library name: Sample 69


title: nucRNA-seq dTAG-EXOSC3/ZC3H4-DHFR plus TMP plus dTAG rep1

description: Library name: Sample 5


title: MCD_T_2


title: M-3

first: Ruizhe

last: He

address: No. 639, Zhizaoju Road

institute: Shanghai Jiao Tong University

description:
Library name: Sample14
gene_fpkm-HUVEC RNF123.txt
column name in gene_gene_fpkm-HUVEC RNF123.txt: HU-M3

data_processing:
For the animals wounds tissue, raw reads were firstly processed using fastp (v0.22.0) and the low  quality reads were removed to obtain the clean reads. The clean reads were mapped to the  reference genome using HISAT2 (v2.1.0). FPKM of each gene was calculated and the read  counts of each gene were obtained by featureCounts. PCA analysis were performed using R  (v 3.2.0) to evaluate the biological duplication of samples.                                                                     For the cell lines, the raw data was handled by Skewer and data quality was checked by FastQC (v0.11.2). Clean reads were aligned to the referance genome using STAR(2.5.3a). The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using StringTie (v1.3.1c). Differentially expression genes(DEGs) were determined by DEGseq2(v1.16.1).
Assembly: GRCh38 / mRatBN7.2
Supplementary files format and content: txt files include FPKM values for each sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the  manufacturer’s protocol.
For the animals wounds tissue, the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OBiO Technology Corp., Ltd. (Shanghai, China). Then, the libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end  reads were generated.                                                                                For the cell lines, libraries were constructed using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China), and sequencing was carried out using the Illumina NovaSeq X Plus instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: endothelial cell


title: P7--_ES_H3K27me3_D5-BMP4_Rep1

description: Library name: Sample 68

value: neuronal differentiation - BMP4

value: Day 5


title: nucRNA-seq dTAG-EXOSC3/ZC3H4-DHFR minus TMP minus dTAG rep2

description: Library name: Sample 4

value: minus dTAGv-1, minus TMP


title: M-2

description:
Library name: Sample13
gene_fpkm-HUVEC RNF123.txt
column name in gene_gene_fpkm-HUVEC RNF123.txt: HU-M2


title: P7--_ES_H3K27me3_D5+BMP4_Rep1

description: Library name: Sample 67

value: neuronal differentiation + BMP4


title: MCD_NC_2

value: Liver

value: WT

value: normal chow diet, Vehicle control


title: nucRNA-seq dTAG-EXOSC3/ZC3H4-DHFR minus TMP minus dTAG rep1

description: Library name: Sample 3


title: M-1

description:
Library name: Sample12
gene_fpkm-HUVEC RNF123.txt
column name in gene_gene_fpkm-HUVEC RNF123.txt: HU-M1


title: MCD_NC_1


title: WT_ES_H3K27me3_D5-BMP4_Rep3

description: Library name: Sample 66


title: nucRNA-seq dTAG-EXOSC3/ZC3H4-DHFR plus TMP minus dTAG rep2

description: Library name: Sample 2

value: minus dTAGv-1, plus TMP


title: W-3

description:
Library name: Sample11
gene_fpkm-HUVEC RNF123.txt
column name in gene_gene_fpkm-HUVEC RNF123.txt: HU-W3


title: MCD_V_2


title: Treat-2

data_processing:
Use Illumina Novaseq 6000 for sequencing. The sequencing strategy is PE150.
Trimmomatic software were used to remove adapter and low quality reads.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads byremoving the adaptor sequences. The clean reads were then aligned to reference genome sequencesusing the bwa program.
We calculate the fragment sizes for read pairs given a BAM file from paired-end sequencing. Severalregions are sampled depending on the size of the genome and number of processors to estimate thesummary statistics on the fragment lengths. Properly paired reads are used for computation
The bam file generated by the unique mapped reads as an input file, using macs2 software forcallpeak with cutoff qvalue < 0.05.
Assembly: mm10
Supplementary files format and content: Bigwig file was provided for each sample.

extract_protocol:
Nucleus extraction: For cell samples, refer to the method in the document "ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide" to lyse cells and obtain nuclei. For frozen tissue samples, refer to the method in the document "An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues" to extract nuclei. Transposition reaction: Take 40,000 nuclei and perform a transposition reaction with Tn5 enzyme (Illumina). The transposed DNA fragments are recovered using the MinElute PCR Purification Kit (Qiagen).
Use 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA) for PCR amplification. The amplified products are recovered using the MinElute PCR Purification Kit (Qiagen).

value: CDAA-HFD, 326E treated


title: nucRNA-seq dTAG-EXOSC3/ZC3H4-DHFR plus TMP minus dTAG rep1

description: Library name: Sample 1


title: W-2

description:
Library name: Sample10
gene_fpkm-HUVEC RNF123.txt
column name in gene_gene_fpkm-HUVEC RNF123.txt: HU-W2


title: WT_ES_H3K27me3_D5+BMP4_Rep3

description: Library name: Sample 65


title: Treat-1


title: WT_ES_H3K27me3_D5-BMP4_Rep2

description: Library name: Sample 64


title: mNET-seq ZC3H4-DHFR minus TMP rep2

description: Library name: Sample 5

data_processing:
Adapters removed from sequencing reads using Trim Galore 0.6.5dev (Cutadapt v2.9) with minimum fragment length 18 and minumum read quality 20
Alignment with Hisat2 v2.0.0-beta to ensembl GRCh38 (default settings)
Removal of unique molecular identifiers, chimeric pairs and unpaired reads using UMItools v1.2.1
Merge biological replicates using BamTools v2.5.1
Aligned fragments were reduced to the 5'-most aligned nucleotide of the second-in-pair read
Split reads by strand using SAMTools v1.13
Bigwig files were generated from split strand BAM files using the bamCoverage of Deeptools v3.5.0
Assembly: GRCh38
Supplementary files format and content: Single nucleotide resolution RPKM bigwig coverage was generated from split strand merged replicates

extract_protocol:
Chromatin isolated from fractionated nuclei was treated with MNase and RNAPII-bound RNA was captured using beads with conjugated Pol II antibody and Trizol reagent
RNA libraries were constructed using NEBNext® Small RNA Library Prep Set for Illumina

value: minus TMP


title: Veh_2


title: W-1

description:
Library name: Sample9
gene_fpkm-HUVEC RNF123.txt
column name in gene_gene_fpkm-HUVEC RNF123.txt: HU-W1


title: MCD_NC_3


title: mNET-seq ZC3H4-DHFR minus TMP rep3

description: Library name: Sample 6


title: HEK 293 cells, siCNOT4-BrU IP RNA2

description: Library name: CNOT4 KD-BrU-IP2

data_processing:
60 M (30 M each side) 150 nucleotide paired-end reads were obtained and FastQC (version v0.11.8) was applied to check the quality of raw reads.
Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting. RNA seq reads were aligned to the human genome (hg38 assembly, GRCh38) with STAR Aligner version 2.7.1a and Picard tools (version 2.20.4) was applied to mark duplicates of mapping.
The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts. The featureCounts (version 1.6.0)/HTSeq was used to count mapped reads for genomic features.
Assembly: hg38 assembly, GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each sample

extract_protocol:
Nuclear input RNA and BrU IP RNA after nuclear run-on assay was extracted using TRIzol reagent (Ambion). The RNA samples were then treated with Turbo DNase using Turbo DNA-free kit (Invitrogen).
Ribosomal RNA depletion and library preparation were done using KAPA Hyper RNA with Riboerase HMR kit following manufacturer's protocols.

value: HEK 293

value: Human Embryonic Kidney

value: CNOT4 knockdown

value: siRNA


title: Veh_1

value: CDAA-HFD, Vehicle control


title: WT_ES_H3K27me3_D5+BMP4_Rep2

description: Library name: Sample 63

value: ES cell


title: F3 DMSO female rep 5

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description:
321_F3_DMSO_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

data_processing:
Paired-end sequencing data (150 + 150) were generated by Illumina NovaSeq 6000 and processed by Hi-C Pro to obtain ICE-normalized chromatin interaction matrices.
Normalized chromatin interaction matrices were examined using Bart-3D to identify differential TAD boundaries with differential chromatin interaction scores.
Assembly: mm10
Supplementary files format and content: BED files containing start and end coordinates of TADs with differential chromatin interaction scores between TBT- and DMSO (control) group primordial germ cells.

source_name: primordial germ cells

extract_protocol:
Primordial germ cells fo F1, F2, F3 embryos were isolated by FACS and directly subjected to proximity ligation using the Arima Genome-wide Hi-C kit.
Swift Biosciences Accel-NGS 2S Plus DNA Library Kit was used with the modified protocol provided by Arima Genomics.

treatment_protocol: Pregnant F0 mothers were exposed to TBT or DMSO via drinking water.

tag: strain

value: primordial germ cells

tag: developmental stage

tag: Sex

value: female

value: F0 exposure to DMSO


title: WT_ES_H3K27me3_D5+BMP4_Rep1

description: Library name: Sample 61

value: Day 5


title: HEK 293 cells, siCNOT4-BrU IP RNA1

description: Library name: CNOT4 KD-BrU-IP1


title: WT_ES_H3K27me3_D5-BMP4_Rep1

description: Library name: Sample 62

value: neuronal differentiation - BMP4


title: mNET-seq ZC3H4-DHFR minus TMP rep1

description: Library name: Sample 4

value: colorectal carcinoma


title: mNET-seq ZC3H4-DHFR plus TMP rep3

description: Library name: Sample 3

value: plus TMP


title: HEK 293 cells, siControl-1

value: WT


title: F3 DMSO female rep 4

description:
320_F3_DMSO_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: mNET-seq ZC3H4-DHFR plus TMP rep2

description: Library name: Sample 2


title: DKO_ES_ATAC_D6+BMP4_Rep3

description: Library name: Sample 60

data_processing:
ATAC:Reads in raw files were pre trimmed to 36bp using Trimmomatic (Bolger et al., 2014) (v0.39)
ATAC/CUT&Tag data: PCR duplicate removal using BBmap clumpify (Bushnell et al., 2014)(v38.87) and parameters: reorder dedupe=t k=19 passes=6 subs=(0.01 x readlength). Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using Bowtie2 (Langmead et al., 2019)(v2.4.5) for CUT&Tag using parameters: --local –very-sensitive –no-mixed –dovetail –no-discordant –phred33 -I 10 -X 700
Processed bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
RNA-Seq:PCR duplicate removal, trimming, and read alignement on mm10 genome was performed by BGI. Processed bigwig files were generated from BAM files using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
Assembly: mm10
Supplementary files format and content: Bigwig format. ATAC-Seq-CUT&Tag-RNA-Seq: CPM-normalized counts.

extract_protocol:
ATAC-Seq was performed as in (Buenrostro et al. 2015). We used between 50 000 cells per condition, and a homemade purified pA-TN5 complex.
Nextera primers or indexed primers were used to perform PCR. Library quality was assessed using 4200 TapeStation system (Agilent) and paired-end, 100 bp sequencing on a DBNSEQ-G400 was performed by BGI.
All information is included as columns in the SAMPLES section above
All information is included as columns in the SAMPLES section above

value: DKO

value: neuronal differentiation + BMP4


title: F3 DMSO female rep 3

description:
319_F3_DMSO_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: HEK 293 cells, siControl-BrU IP RNA1

description: Library name: Control-BrU-IP1


title: DKO_ES_ATAC_D6+BMP4_Rep2

description: Library name: Sample 59


title: HEK 293 cells, siCNOT4-Input RNA2

description: Library name: CNOT4 KD-Input2


title: mNET-seq ZC3H4-DHFR plus TMP rep1

description: Library name: Sample 1


title: F3 TBT female rep 5

description:
318_F3_TBT_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to TBT


title: DKO_ES_ATAC_D6+BMP4_Rep1

description: Library name: Sample 58


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR minus TMP plus dTAG rep2

description: Library name: Sample 8

value: plus dTAGv-1, minus TMP


title: HEK 293 cells, siCNOT4-Input RNA1

description: Library name: CNOT4 KD-Input1

value: HEK 293

value: Human Embryonic Kidney


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR minus TMP plus dTAG rep1

description: Library name: Sample 7


title: HEK 293 cells, siControl-Input RNA2

description: Library name: Control-Input2

value: siRNA


title: P3--_ES_ATAC_D6+BMP4_Rep3

description: Library name: Sample 57


title: P3--_ES_ATAC_D6+BMP4_Rep2

description: Library name: Sample 56


title: F3 TBT female rep 4

description:
316_F3_TBT_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: F3 DMSO female rep 2

description:
317_F3_DMSO_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: HEK 293 cells, siControl-Input RNA1

description: Library name: Control-Input1


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR minus TMP minus dTAG rep2

description: Library name: Sample 4

value: minus dTAGv-1, minus TMP


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR plus TMP plus dTAG rep1

description: Library name: Sample 5

value: plus dTAGv-1, plus TMP


title: F3 TBT female rep 3

description:
314_F3_TBT_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells


title: P7--_ES_ATAC_D6+BMP4_Rep3

description: Library name: Sample 54

value: ES cell


title: F3 TBT female rep 2

description:
313_F3_TBT_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: female


title: WT, replicate 2

city: Iowa City

first: Damian

middle: J

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

description: Library name: Sample 11

data_processing:
Read quality was assessed using FastQC (Babraham Bioinformatics)
Each sample was mapped individually to the C. Albicans reference genome (SC5314 from FungiDB_63) with HISAT2
Raw read counts were obtained and annotated using stringtie.
DESeq2 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05 on each set of raw expression measures.
Assembly: SC5314 from FungiDB build 63
Supplementary files format and content: raw counts table, comma separated values

organism: Candida albicans

source_name: yeast cell

growth_protocol: The reference strain SN250 and the corresponding EFG1 mutant strains were subjected to hyphal induction growth conditions using RPMI + 10% bovine calf serum at 37 degrees C for 4 hrs.

extract_protocol:
Total RNA was isolated with the MasterPure yeast RNA purification kit.
RNA TruSeq Kit was used for library construction

value: yeast cell

value: WT (EFG1/EFG1)

value: RPMI, 37 degrees


title: HEK 293 cells, siControl-BrU IP RNA2

description: Library name: Control-BrU-IP2


title: WT, replicate 3

description: Library name: Sample 12


title: P3--_ES_ATAC_D6+BMP4_Rep1

description: Library name: Sample 55


title: P7--_ES_ATAC_D6+BMP4_Rep2

description: Library name: Sample 53


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR minus TMP minus dTAG rep1

description: Library name: Sample 3

value: colorectal carcinoma


title: F3 TBT female rep 1

description:
312_F3_TBT_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: efg1Δ/efg1Δ, replicate 2

description: Library name: Sample 9

value: efg1-/ efg1-


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR plus TMP minus dTAG rep2

description: Library name: Sample 2

value: minus dTAGv-1, plus TMP


title: P7--_ES_ATAC_D6+BMP4_Rep1

description: Library name: Sample 52

value: neuronal differentiation + BMP4


title: F3 DMSO male rep 5

description:
311_F3_DMSO_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: male

value: F0 exposure to DMSO


title: WT_ES_ATAC_D6+BMP4_Rep3

description: Library name: Sample 51

value: WT


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR plus TMP minus dTAG rep1

description: Library name: Sample 1


title: chrRNA-seq dTAG-INTS4/ZC3H4-DHFR plus TMP plus dTAG rep2

description: Library name: Sample 6


title: F3 DMSO female rep 1

description:
315_F3_DMSO_F
F3.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: F3 DMSO male rep 4

description:
310_F3_DMSO_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: WT, replicate 1

description: Library name: Sample 8


title: F3 DMSO male rep 3

description:
309_F3_DMSO_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: efg1Δ/efg1Δ, replicate 1

description: Library name: Sample 7


title: WT_ES_ATAC_D6+BMP4_Rep1

description: Library name: Sample 49


title: WT_ES_ATAC_D6+BMP4_Rep2

description: Library name: Sample 50


title: F3 TBT male rep 5

description:
308_F3_TBT_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to TBT


title: DE_CTNNB1+YAP_4

city: Sapporo

first: Issei

last: Kawakita

state: Hokkaido

address: N14 W5, Kita-ku

department: Graduated school of Medicine

country: Japan

institute: Hokkaido University

description: Library name: Sample16

data_processing:
Raw sequencing reads were quality controlled and adapter-trimmed (tool not specified), then aligned to the human reference genome (GRCh38) using HISAT2 (v2.0.5). Gene-level read counts were quantified using featureCounts (v1.5.0-p3). Differential gene expression analysis was performed using DESeq2 (v1.20.0) or edgeR (v3.22.5), depending on the presence of biological replicates.
Assembly: hg38
Supplementary files format and content: csv files included raw counts for each group

source_name: iPSC-derived hepatoblast

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 2 µg of total RNA was used for the construction of sequencing libraries.
RNA library preparation was performed by Novogene Co., Ltd.

value: iPSC-derived hepatoblast

value: CTNNB1+YAP overexpression


title: DE_YAP_4

description: Library name: Sample15

value: YAP overexpression


title: DKO_ES_ATAC_D6-BMP4_Rep3

description: Library name: Sample 48

value: DKO

value: neuronal differentiation - BMP4


title: DE_CTNNB1_4

description: Library name: Sample14

value: CTNNB1 overexpression


title: efg1Δ/efg1(T208A), replicate 2

description: Library name: Sample 5

value: yeast cell


title: DE_ctrl_4

description: Library name: Sample13

value: Control


title: F3 DMSO male rep 2

description:
307_F3_DMSO_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells


title: DKO_ES_ATAC_D6-BMP4_Rep2

description: Library name: Sample 47

value: ES cell


title: efg1Δ/efg1Δ, replicate 3

description: Library name: Sample 10

value: efg1-/ efg1-

value: RPMI, 37 degrees


title: efg1Δ/efg1(T208A), replicate 1

description: Library name: Sample 4


title: DKO_ES_ATAC_D6-BMP4_Rep1

description: Library name: Sample 46


title: F3 TBT male rep 4

description:
306_F3_TBT_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: DE_CTNNB1+YAP_3

description: Library name: Sample12


title: efg1Δ/EFG1, replicate 3

description: Library name: Sample 3


title: DE_YAP_3

description: Library name: Sample11


title: P3--_ES_ATAC_D6-BMP4_Rep3

description: Library name: Sample 45


title: efg1Δ/EFG1, replicate 2

description: Library name: Sample 2


title: F3 DMSO male rep 1

description:
305_F3_DMSO_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: F3 TBT male rep 3

description:
304_F3_TBT_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: F3 TBT male rep 2

description:
303_F3_TBT_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: efg1Δ/EFG1, replicate 1

description: Library name: Sample 1


title: P3--_ES_ATAC_D6-BMP4_Rep2

description: Library name: Sample 44


title: DE_ctrl_3

description: Library name: Sample9


title: P3--_ES_ATAC_D6-BMP4_Rep1

description: Library name: Sample 43


title: F3 TBT male rep 1

description:
302_F3_TBT_M
F3.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: Liver, refed GcKO, rep4

city: Davis

first: Taiyi

middle: Diana

last: Kuo

state: California

address: One Shields Ave

department: Neurobio, Physio & Behavior

institute: University of California Davis

description:
Library name: Sample 15
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK151

data_processing:
The reads were mapped to the mouse genome mm10 using STAR (v2.5.2b) algorithm with default settings.
FeatureCounts from the Subread (v1.5.2) package was used to assign concordantly aligned reads pairs to RefSeq genes. A 25-bp minimum as overlapping bases in a fragment was specified for read assignment.
Assembly: mm10
Supplementary files format and content: Gene count table for each Sample

molecule: polyA RNA

extract_protocol:
Mouse liver was harvested and we isolated total RNA with Nucleospin RNA kit (Macherey-Nagel) with DNase I treatment
Directional Poly-A RNAseq libraries were prepared and sequenced as PE100 (100-bp paired-end reads) on Illumina NextSeq 500 to a read depth of 40 million read-pairs per sample

value: Liver

value: Gc Knockout

value: Refed


title: efg1Δ/efg1(T208A), replicate 3

description: Library name: Sample 6


title: DE_CTNNB1+YAP_2

description: Library name: Sample8


title: P7--_ES_ATAC_D6-BMP4_Rep3

description: Library name: Sample 42


title: Liver, refed GcKO, rep3

description:
Library name: Sample 14
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK150

value: male


title: F2 TBT male rep 6

description:
221_F2_TBT_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to TBT


title: DE_YAP_2

description: Library name: Sample7

value: iPSC-derived hepatoblast


title: DE_CTNNB1_2

description: Library name: Sample6


title: P7--_ES_ATAC_D6-BMP4_Rep2

description: Library name: Sample 41


title: Liver, refed GcKO, rep1

description:
Library name: Sample 12
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK137


title: Liver, refed GcKO, rep2

description:
Library name: Sample 13
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK138


title: P7--_ES_ATAC_D6-BMP4_Rep1

description: Library name: Sample 40


title: DE_CTNNB1_3

description: Library name: Sample10


title: F2 DMSO female rep 5

description:
219_F2_DMSO_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: female

value: F0 exposure to DMSO


title: WT_ES_ATAC_D6-BMP4_Rep3

description: Library name: Sample 39

value: WT


title: DE_ctrl_2

description: Library name: Sample5


title: Liver, refed WT, rep3

description:
Library name: Sample 11
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK149


title: WT_ES_ATAC_D6-BMP4_Rep2

description: Library name: Sample 38

value: neuronal differentiation - BMP4


title: F2 TBT female rep 4

description:
218_F2_TBT_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: F2 DMSO female rep 4

description:
217_F2_DMSO_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: Liver, refed WT, rep1

description:
Library name: Sample 9
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK135


title: DE_YAP_1

description: Library name: Sample3

value: YAP overexpression


title: WT_ES_ATAC_D6-BMP4_Rep1

description: Library name: Sample 37


title: DKO_ES_ATAC_D5-BMP4_Rep3

description: Library name: Sample 36

value: DKO

value: Day 5


title: F2 DMSO female rep 3

description:
216_F2_DMSO_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells


title: Liver, fasted GcKO, rep5

description:
Library name: Sample 8
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK143

value: Fasted


title: F2 TBT female rep 3

description:
215_F2_TBT_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: F2 TBT female rep 5

description:
220_F2_TBT_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: DKO_ES_ATAC_D3_Rep3

description: Library name: Sample 35

value: ES cell

value: neuronal differentiation

value: Day 3


title: DE_ctrl_1

description: Library name: Sample1

value: Control


title: F2 TBT female rep 2

description:
214_F2_TBT_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: Liver, fasted GcKO, rep4

description:
Library name: Sample 7
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK140

value: Liver

value: Gc Knockout


title: DKO_ES_ATAC_D5-BMP4_Rep2

description: Library name: Sample 33


title: Liver, fasted GcKO, rep3

description:
Library name: Sample 6
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK139

value: male


title: HEK 293 cells, siCNOT4-Nuclear RNA

description: CNOT4 KD-Nuclear

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion).  Cytosolic and nuclear RNA extractions were performed following the protocol guidelines (Gagnon, K.T., et al., Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nat Protoc, 2014. 9(9): p. 2045-60.). The RNA samples were then treated with Turbo DNase (Ambion) and extracted using Acid Phenol:Chloroform (Ambion).
Ribosomal RNA depletion and library preparation of total, cytosolic and nuclear RNA were done using QIAseq FastSelect rRNA HMR and NEB ultraII Directional RNA Library Prep kits following manufacturer's protocols.

value: HEK 293

value: Human Embryonic Kidney

value: CNOT4 knockdown

value: siRNA


title: DE_CTNNB1+YAP_1

description: Library name: Sample4

value: iPSC-derived hepatoblast

value: CTNNB1+YAP overexpression


title: Liver, refed WT, rep2

description:
Library name: Sample 10
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK136

value: WT

value: Refed


title: HEK 293 cells, siCNOT4-Cytosolic RNA

description: CNOT4 KD-Cytosolic

molecule: cytoplasmic RNA


title: F2 DMSO female rep 2

description:
213_F2_DMSO_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells

value: female

value: F0 exposure to DMSO


title: HEK 293 cells, siCNOT4-Total RNA

description: CNOT4 KD-Total


title: Liver, fasted GcKO, rep2

description:
Library name: Sample 5
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK134

value: Fasted


title: Liver, fasted GcKO, rep1

description:
Library name: Sample 4
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK133


title: DKO_ES_ATAC_D3_Rep2

description: Library name: Sample 32

value: ES cell

value: DKO

value: neuronal differentiation

value: Day 3


title: F2 DMSO female rep 1

description:
212_F2_DMSO_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: DKO_ES_ATAC_D5+BMP4_Rep2

description: Library name: Sample 31

value: neuronal differentiation + BMP4

value: Day 5


title: F2 TBT female rep 1

description:
211_F2_TBT_F
F2.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to TBT


title: Liver, fasted WT, rep3

description:
Library name: Sample 3
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK145

value: Liver

value: male


title: DKO_ES_ATAC_D5-BMP4_Rep1

description: Library name: Sample 30

value: neuronal differentiation - BMP4


title: F2 TBT male rep 5

description:
210_F2_TBT_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: Liver, fasted WT, rep2

description:
Library name: Sample 2
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK132


title: DE_CTNNB1_1

description: Library name: Sample2

value: iPSC-derived hepatoblast

value: CTNNB1 overexpression


title: HEK 293 cells, siPABPN1-Cytosolic RNA

description: PABPN1 KD-Cytosolic

value: HEK 293

value: Human Embryonic Kidney

value: PABPN1 knockdown

value: siRNA


title: F2 DMSO male rep 5

description:
209_F2_DMSO_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells

value: F0 exposure to DMSO


title: DKO_ES_ATAC_D3_Rep1

description: Library name: Sample 29

value: ES cell

value: DKO


title: HEK 293 cells, siPABPN1-Total RNA

description: PABPN1 KD-Total


title: DKO_ES_ATAC_D5+BMP4_Rep3

description: Library name: Sample 34


title: Liver, fasted WT, rep1

description:
Library name: Sample 1
Column name in AK131_151_est_counts_genes_kallisto_GEO.xlsx: AK131

value: WT

value: Fasted


title: DKO_ES_ATAC_D5+BMP4_Rep1

description: Library name: Sample 28

value: neuronal differentiation + BMP4

value: Day 5


title: F2 DMSO male rep 4

description:
207_F2_DMSO_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: P3--_ES_ATAC_D5-BMP4_Rep3

description: Library name: Sample 27


title: HEK 293 cells, siZFC3H1-Cytosolic RNA

description: ZFC3H1 KD-Cytosolic

value: ZFC3H1 knockdown


title: F2 DMSO male rep 3

description:
206_F2_DMSO_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: male


title: CLK856_OdOpa1_1

city: Waltham

first: Shlesha

last: Richhariya

address: 415 South St

institute: Brandeis University/HHMI

description:
CLK856_mito_exon_umicounts.txt
Deseq2_UMI_CLK856_Opa1vCas9_OLD.csv

data_processing:
Demultiplexed libraries were mapped to the dm6 version of the Drosophila genome using STAR pipeline as part of the zUMI analysis pipeline (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007394/).
UMI counts mapping to exons of all genes were extracted for all samples using the zUMI pipeline
exon UMIcounts were used as the input for DESeq2 (https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html)
Young and Old samples were analyzed seperately. Genes with very low expression were removed. Lists of differentially expressed genes were obtained by running DESeq2 and comparing the different mutant conditions to Cas9 control.
Assembly: Drosophila melanogaster dm6
Supplementary files format and content: txt file with exonal UMI counts of all genes (CLK856_mito_exon_umicounts.txt)
Supplementary files format and content: csv file outputted from DESeq2 when young Drp1-mut samples were compared to young Cas9-control (Deseq2_UMI_CLK856_Drp1vCas9_Yng.csv)
Supplementary files format and content: csv file outputted from DESeq2 when young Marf-mut samples were compared to young Cas9-control (Deseq2_UMI_CLK856_MarfvCas9_Yng.csv)
Supplementary files format and content: csv file outputted from DESeq2 when young Opa1-mut samples were compared to young Cas9-control Deseq2_UMI_CLK856_Opa1vCas9_Yng.csv
Supplementary files format and content: csv file outputted from DESeq2 when OLD Drp1-mut samples were compared to OLD Cas9-control  (Deseq2_UMI_CLK856_Drp1vCas9_OLD.csv)
Supplementary files format and content: csv file outputted from DESeq2 when OLD Marf-mut samples were compared to OLD Cas9-control (Deseq2_UMI_CLK856_MarfvCas9_OLD.csv)
Supplementary files format and content: csv file outputted from DESeq2 when OLD Opa1-mut samples were compared to OLD Cas9-control (Deseq2_UMI_CLK856_Opa1vCas9_OLD.csv)

organism: Drosophila melanogaster

source_name: clock neurons

growth_protocol: Flies were grown on stardanrd cornmeal medium at 25°C.

extract_protocol:
Brains were dissected from male flies of the correct genotype and age at ZT14. Brains were then enzymatically digested using Collagenase+Dispase and the resulting cell suspension was loaded onto a Fluroscence-assisted cell sorter (FACS) machine and ~1000 GFP positive cells were collected per sample. FOr each genotype/condition three different sets of ~1000 cells were collected as replicates from the same cell suspension made from 80-100 brains.  Cells were sorted into ~100ul of lysis buffer (Dynabeads mRNA direct kit) and immediately frozen at -80°C.
PolyA mRNA was isolated from the frozen cell samples using the Dynabeads mRNA direct kit. Full length cDNA was generated using the smartseq3 protocol, where the 5' end was tagged with unique molecular identifier (UMI). ~750pg of cDNA was used per sample to generate sequencing libraries using Illumina Nextera XT DNA Library Preparation Kit.

treatment_protocol: Perturbations were all genetic. Genotypes as listed for the samples.

value: clock neurons

value: FACS-purified

tag: age

value: Old (~35 days)

tag: circadian timepoint


title: CLK856_OdOpa1_2


title: HEK 293 cells, siZFC3H1-Total RNA

description: ZFC3H1 KD-Total

value: HEK 293


title: HEK 293 cells, siPABPN1-Nuclear RNA

description: PABPN1 KD-Nuclear

value: Human Embryonic Kidney


title: F2 TBT male rep 3

description:
205_F2_TBT_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to TBT


title: HEK 293 cells, siControl-Nuclear RNA

description: Control-Nuclear

value: siRNA


title: CLK856_OdMarf_3


title: F2 TBT male rep 2

description:
204_F2_TBT_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells


title: P3--_ES_ATAC_D5-BMP4_Rep2

description: Library name: Sample 24

value: neuronal differentiation - BMP4


title: CLK856_OdMarf_2


title: HEK 293 cells, siControl-Cytosolic RNA

description: Control-Cytosolic


title: P3--_ES_ATAC_D3_Rep2

description: Library name: Sample 23

value: ES cell

value: neuronal differentiation

value: Day 3


title: F2 TBT male rep 4

description:
208_F2_TBT_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: HEK 293 cells, siControl-Total RNA

description: Control-Total

value: WT


title: CLK856_OdMarf_1

description:
CLK856_mito_exon_umicounts.txt
Deseq2_UMI_CLK856_MarfvCas9_OLD.csv


title: HEK 293 cells, siZFC3H1-Nuclear RNA

description: ZFC3H1 KD-Nuclear


title: F2 DMSO male rep 1

description:
202_F2_DMSO_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to DMSO


title: Panc-1, SMAP resistant cloneSMAP6G repeat3, L140-P32D

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Sequencing: Sequence-libraries of each sample were equimolarly pooled and sequenced on Illumina NovaSeq 6000 (100 bp, Single Reads, v1.5) at the VIB Nucleomics Core (www.nucleomics.be).
Preprocessing: Low-quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.40.0 (Morgan et al., 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead et al., 2012).
Mapping: The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38) (Dobin et al., 2013). Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al., 2009).
Counting: The number of reads in the alignments that overlap with gene features was counted with featureCounts 1.5.3 (Liao et al., 2014). Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id.
Assembly: Homo sapiens Ensembl GRCh38.88
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreas, duct

growth_protocol:
Panc-1 cells were cultured in 6-well plate in DMEM medium supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml Penicillin and 100 µg/ml Streptomicin
Panc-1 cells were obtained from ATCC and cultured in DMEM, 10% FCS. IC50’s were determined for 48 hour exposure to the drugs using presto blue. The values varied from 6-10 µM for SMAP2; ATUX and Sorafenib. However we found that continues exposure of naïve Panc-1 cells to 50% IC50 concentrations resulted in cell death after 1 or 2 passages. The effects on PP2A in Panc-1 manifest after longer exposure and we had to start from a lower concentration. We cultured the cells until 70-100% confluency, washed, detached with trypsine and transferred the cells to a new well at around 10% and continued this cycle. When cultures showed stability after 4-more passages, the drug concentration was increased by 25%. Cultures were kept again for 4-6 passages before the drugs were increased again.

extract_protocol:
RNA was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA). RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND8000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent).
Per sample, an amount of 500 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 1000000040498 v00 - October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library.

treatment_protocol: Over a period of 4 months we  cultures of Panc-1 cells that could grow in the presence of:  ATUX (8 µM), SMAP (8 µM), and Sorafenib (8 µM). We have used these cells (that are stable under these conditions) to develop cloned lines through serial dilution to 1 colony per well in a 96 well plate. In the first round we selected 8-10 colonies, worked from 96 well to 24 well and next to 6 well. In the end we had 4 colonies for each drug that were culture stable and could be stored in liq-N2. Samples have been collected for qRT-PCR and based on these results we want to select 2-3 cloned lines for sequencing. In addition we want to perform preform protein analysis (mass spec) and functional studies (growth rate, invasion, scratch-assay).

value: Panc-1, ATCC CRL-1469

value: Pancreas, duct

value: pancreas ductular epithelium

value: standard culture conditions supplemented with 8 µM SMAP


title: P3--_ES_ATAC_D5+BMP4_Rep2

description: Library name: Sample 22

value: neuronal differentiation + BMP4

value: Day 5


title: CLK856_OdOpa1_3

value: clock neurons

value: FACS-purified

value: Old (~35 days)

value: male


title: F2 TBT male rep 1

description:
201_F2_TBT_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells

value: F0 exposure to TBT


title: Panc-1, SMAP resistant cloneSMAP6G repeat2, L140-P32B


title: P3--_ES_ATAC_D3_Rep3

description: Library name: Sample 26

value: ES cell


title: P3--_ES_ATAC_D5-BMP4_Rep1

description: Library name: Sample 21

value: neuronal differentiation - BMP4


title: CLK856_OdDrp1_2


title: F1 TBT male rep 6

description:
184_F1_TBT_M
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: P3--_ES_ATAC_D5+BMP4_Rep3

description: Library name: Sample 25


title: P3--_ES_ATAC_D3_Rep1

description: Library name: Sample 20

value: neuronal differentiation

value: Day 3


title: Panc-1, SMAP resistant cloneSMAP6G repeat1, L140-P32A


title: CLK856_OdDrp1_1

description:
CLK856_mito_exon_umicounts.txt
Deseq2_UMI_CLK856_Drp1vCas9_OLD.csv


title: F1 TBT male rep 5

description:
183_F1_TBT_M
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: P3--_ES_ATAC_D5+BMP4_Rep1

description: Library name: Sample 19


title: CLK856_OdCas9_3

value: CLK856-Gal4>UAS-Cas9;UAS-eGFP (control)


title: Panc-1, SMAP resistant cloneSMAP9C repeat3, L140-P33D

value: Panc-1, ATCC CRL-1469


title: F1 TBT male rep 4

description:
182_F1_TBT_M
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: F2 DMSO male rep 2

description:
203_F2_DMSO_M
F2.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to DMSO


title: P7--_ES_ATAC_D5-BMP4_Rep3

description: Library name: Sample 18


title: Panc-1, SMAP resistant cloneSMAP9C repeat2, L140-P33C

value: Pancreas, duct

value: pancreas ductular epithelium


title: F1 TBT male rep 3

description:
181_F1_TBT_M
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: P7--_ES_ATAC_D3_Rep3

description: Library name: Sample 17


title: CLK856_OdDrp1_3


title: F1 TBT male rep 2

description:
180_F1_TBT_M
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: Panc-1, SMAP resistant cloneSMAP8D repeat3, L140-P34D

value: standard culture conditions supplemented with 8 µM SMAP


title: P7--_ES_ATAC_D5+BMP4_Rep3

description: Library name: Sample 16

value: neuronal differentiation + BMP4

value: Day 5


title: Panc-1, SMAP resistant cloneSMAP9C repeat1, L140-P33B


title: CLK856_YgOpa1_3

value: clock neurons

value: FACS-purified

value: Young (~15days)


title: P7--_ES_ATAC_D5-BMP4_Rep2

description: Library name: Sample 15


title: F1 TBT male rep 1

description:
179_F1_TBT_M
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells

value: male


title: CLK856_YgOpa1_2


title: Panc-1, SMAP resistant cloneSMAP8D repeat2, L140-P34B


title: P7--_ES_ATAC_D3_Rep2

description: Library name: Sample 14

value: ES cell


title: Panc-1, Sorafenib resistant clone Sor9H repeat3, L140-P27D

value: standard culture conditions supplemented with 8 µM Sorafenib


title: CLK856_YgOpa1_1

description:
CLK856_mito_exon_umicounts.txt
Deseq2_UMI_CLK856_Opa1vCas9_Yng.csv


title: Panc-1, SMAP resistant cloneSMAP8D repeat1, L140-P34A


title: CLK856_YgMarf_3


title: F1 DMSO male rep 3

description:
177_F1_DMSO_M
F1.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: P7--_ES_ATAC_D5+BMP4_Rep2

description: Library name: Sample 13


title: CLK856_YgMarf_2


title: P7--_ES_ATAC_D5-BMP4_Rep1

description: Library name: Sample 12

value: neuronal differentiation - BMP4


title: Panc-1, Sorafenib resistant clone Sor9H repeat2, L140-P27C


title: F1 DMSO male rep 2

description:
176_F1_DMSO_M
F1.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: CLK856_OdCas9_1

value: Old (~35 days)


title: P7--_ES_ATAC_D3_Rep1

description: Library name: Sample 11

value: neuronal differentiation

value: Day 3


title: Panc-1, Sorafenib resistant clone Sor9H repeat1, L140-P27B

value: Panc-1, ATCC CRL-1469


title: CLK856_OdCas9_2

value: CLK856-Gal4>UAS-Cas9;UAS-eGFP (control)


title: CLK856_YgMarf_1

description:
CLK856_mito_exon_umicounts.txt
Deseq2_UMI_CLK856_MarfvCas9_Yng.csv


title: F1 DMSO male rep 1

description:
175_F1_DMSO_M
F1.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to DMSO


title: F1 TBT female rep 5

description:
174_F1_TBT_F
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: female

value: F0 exposure to TBT


title: P7--_ES_ATAC_D5+BMP4_Rep1

description: Library name: Sample 10

value: neuronal differentiation + BMP4

value: Day 5


title: Panc-1, Sorafenib resistant clone Sor6G repeat3, L140-P30C

value: Pancreas, duct

value: pancreas ductular epithelium


title: CLK856_YgDrp1_3

value: clock neurons

value: FACS-purified

value: Young (~15days)


title: F1 DMSO male rep 4

description:
178_F1_DMSO_M
F1.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells

value: male


title: Panc-1, Sorafenib resistant clone Sor6G repeat2, L140-P30B

value: standard culture conditions supplemented with 8 µM Sorafenib


title: F1 TBT female rep 4

description:
173_F1_TBT_F
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: CLK856_YgDrp1_2


title: WT_ES_ATAC_D5-BMP4_Rep3

description: Library name: Sample 9

value: ES cell

value: WT

value: neuronal differentiation - BMP4


title: WT_ES_ATAC_D3_Rep3

description: Library name: Sample 8

value: neuronal differentiation

value: Day 3


title: F1 TBT female rep 3

description:
172_F1_TBT_F
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: female


title: Panc-1, Sorafenib resistant clone Sor6G repeat1, L140-P30A

value: Panc-1, ATCC CRL-1469


title: CLK856_YgDrp1_1

description:
CLK856_mito_exon_umicounts.txt
Deseq2_UMI_CLK856_Drp1vCas9_Yng.csv


title: WT_ES_ATAC_D5+BMP4_Rep3

description: Library name: Sample 7

value: neuronal differentiation + BMP4


title: CLK856_YgCas9_3

value: CLK856-Gal4>UAS-Cas9;UAS-eGFP (control)


title: Panc-1, ATUX resistant clone ATUX9D, repeat3, L140-P16C

value: Pancreas, duct

value: standard culture conditions supplemented with 8 µM ATUX


title: F1 TBT female rep 1

description:
170_F1_TBT_F
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to TBT


title: WT_ES_ATAC_D5-BMP4_Rep2

description: Library name: Sample 6

value: Day 5


title: F1 DMSO female rep 5

description:
169_F1_DMSO_F
F1.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: F0 exposure to DMSO


title: WT_ES_ATAC_D3_Rep2

description: Library name: Sample 5


title: Panc-1, ATUX resistant clone ATUX9D, repeat1, L140-P16A

value: pancreas ductular epithelium


title: F1 DMSO female rep 4

description:
168_F1_DMSO_F
F1.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells


title: CLK856_YgCas9_1

value: clock neurons

value: FACS-purified

value: Young (~15days)

value: male


title: WT_ES_ATAC_D5+BMP4_Rep2

description: Library name: Sample 4

value: ES cell

value: WT


title: Panc-1, ATUX resistant clone ATUX8H, repeat3, L140-P18C


title: Panc-1, ATUX resistant clone ATUX8H, repeat2, L140-P18B


title: F1 DMSO female rep 3

description:
167_F1_DMSO_F
F1.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: female


title: PBMC, Osteosarcoma patients, 19 years old, scRNAseq

city: Nanning

first: Wenyu

last: Feng

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood mononuclear cell

extract_protocol:
Firstly, PBMCs were isolated from bloods obtained from operating room by density gradient centrifugation with Ficoll-Hypaque. Then, they were washed twice with chilled Ca2+/Mg2+-free PBS, and their cell viability was measured using trypan-blue staining. Finally, the PMBCs with the cell viability above 80% were kept on ice for subsequent procedures. A notable detail that all the experiments were performed on ice.
The final single cells from each sample were loaded on a 10× Genomics Chromium Single-Cell Chip along with the single cell master mix and single cell 3’ gel beads (10× Genomics) to generate single-cell gel bead-in-emulsions (GEMs). According to the manufacturer’s instructions the samples were processed by 10× Genomics V3 barcoding chemistry kits. mRNA in drops were undergo the reverse transcription reactions and then the cDNA amplification was followed by the instructions. And the single cell libraries were sequenced on an Illumina HiSeq X Ten instrument.

tag: disease state

value: osteosarcoma

value: peripheral blood mononuclear cell

tag: histological type

value: conventional

value: 19 years old


title: WT_ES_ATAC_D5-BMP4_Rep1

description: Library name: Sample 3

value: neuronal differentiation - BMP4


title: F1 DMSO female rep 1

description:
165_F1_DMSO_F
F1.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: F1 DMSO female rep 2

description:
166_F1_DMSO_F
F1.female.20k.tbt.dmso_differential_score_after_coverageNormalization.bed


title: Panc-1, ATUX resistant clone ATUX8H, repeat1, L140-P18A

value: Panc-1, ATCC CRL-1469

value: Pancreas, duct

value: standard culture conditions supplemented with 8 µM ATUX


title: BV2_ACR rep3

status: Public on Oct 16 2025

city: Noda

first: Gaku

last: Ichihara

address: Yamazaki 2641

department: Faculty of Pharmaceutical Sciences

institute: Tokyo University of Science

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Trimommatic-v0.36 and PRINSEQ-0.20.4. Filtered reads were mapped to Refseq mouse mRNA sequences by using Bowtie2-2.2.5 with the following parameters: -t -p 11 -N 1 -D 200 -R 20 -L 20 -i S,1,0.50 --norc.
Supplementary_files_format_and_content: Excel file (.xlsx) of raw count matrix for every gene and every sample

source_name: cell line

growth_protocol: 1C11 cells were cultured in DMEM supplemented with 10% FBS, at 37℃ and 10% CO2 atmosphere. Differentiation of 1C11 cells along the noradrenergic program was initiated by treatment with 1mM Dibutyryl cAMP (Bt2cAMP), 2% Dimethyl sulfoxide (DMSO) and 0.05% 1-Methyl-1-cyclohexanecarboxylic Acid, and after 12 days 1C11 stem cells differentiated into noradrenergic 1C11NE neurons. BV-2 microglial cells were maintained in DMEM/F12 medium supplemented with 10% FBS and passaged every 2-3 days by detaching with Accutase.

extract_protocol:
After exposure, the cells were lysed in 500 μL of cold cell lysis buffer containing 1% LiDS, 100 mM Tris-HCl pH 7.5, 500 mM LiCl, 10 mM EDTA, and 5 mM DTT (Shichino et al., 2019). The cell lysates were stored at -80 °C until analyses.
Transcriptome libraries were prepared on cell lysate resolved in lysis buffer. PolyA RNAs were isolated using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) conjugated with biotin-3’ WTA-EcoP-dT25 according to the previous report with some modifications (GSE110711). 100 ng of the whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) with some modifications. The thermal cycling was performed as following condition: for 20 min at 32ºC, 30 min at 65ºC, and hold at 4ºC. Then, 1.25 μL of 1.5 μM IonA adapter was used for adapter ligation. Ligated products were purified by double size selection with 0.4× → 0.3× (final 0.7×) AmPure XP beads and eluted with 10 μL of nuclease-free water. The barcoding PCR was performed with 22.5 uL of barcoding mix [7.5 μL of the resulted eluates, 1 μM primers (IonA_[BC] and trP1), and 1× NEBNext Ultra II Q5 (New England Biolabs)], and the thermal cycling was performed as following condition: for 30 sec at 98°C, 9 cycles of 10 sec at 98°C and 75 sec at 65°C, followed by 5 min at 65°C, and hold at 4°C. Resultant products were purified twice by double size selection with 0.8× → 0.6 × (final 1.4×) AmPure XP beads and eluted with 12 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system (Shimazu) and quantified using the KAPA library quantification kit (KAPA biosystems) with appropriate dilutions. Pooled libraries were sequenced by Ion Genestudio S5 sequencer (Thermo Fisher Scientific).

treatment_protocol: Cells were treated for 24 hrs at 37℃ and 10% CO2 atmosphere.

value: BV2 microglia

value: ACR


title: PBMC, Osteosarcoma patients, 14 years old, scRNAseq

description: 10x Genomics

value: 14 years old


title: WT_ES_ATAC_D5+BMP4_Rep1

description: Library name: Sample 1

value: neuronal differentiation + BMP4

value: Day 5


title: WT_ES_ATAC_D3_Rep1

description: Library name: Sample 2

value: neuronal differentiation

value: Day 3


title: PBMC, Osteosarcoma patients, 45 years old, scRNAseq

description: 10x Genomics

value: 45 years old


title: CLK856_YgCas9_2

value: clock neurons

value: FACS-purified

value: CLK856-Gal4>UAS-Cas9;UAS-eGFP (control)

value: Young (~15days)

value: male


title: BV2_PBS rep3

value: PBS, vehicle


title: Panc-1, ATUX resistant clone ATUX9D, repeat2, L140-P16B

value: Panc-1, ATCC CRL-1469

value: pancreas ductular epithelium


title: BV2_ACR rep2


title: F1 TBT female rep 2

description:
171_F1_TBT_F
F1.male.20k.tbt.dmso_differential_score_after_coverageNormalization.bed

value: primordial germ cells

value: female

value: F0 exposure to TBT


title: BV2_ACR rep1

value: BV2 microglia

value: ACR


title: BV2_PBS rep1


title: ACR-CM rep3

value: 1C11 stem cell derived neurons

value: ACR-CM


title: ACR-CM rep2


title: BV2_PBS rep2


title: PBS-CM+ACR rep2

value: PBS-CM+ACR


title: PBS-CM+ACR rep3


title: PBS-CM rep3

value: PBS-CM


title: PBS-CM rep2


title: ACR rep2


title: PBS-CM rep1


title: ACR rep3


title: ACR rep1


title: PBS rep3


title: PBS rep1


title: PBS rep2


title: ACR-CM rep1


title: PBS-CM+ACR rep1


title: H727, lung carcinoid cells, active YAP overexpression, YAP immunoprecipitation, biol rep 1

city: Kingston

first: Neil

last: Renwick

state: ON

address: 88 Stuart St

department: Pathology and Molecular Medicine

country: Canada

institute: Queen's University

description: Library name: Active YAP H727_YAP IP_rep1

data_processing:
FASTQ sequence files were quality controlled using FastQC and adapter sequences and low-quality bases (<30) were trimmed using Trimmomatic.
Trimmed FASTQ sequence files were processed using the ENCODE Transcription Factor ChIP-seq 2 pipeline (v.2.2.0), including the following steps.
Reads were aligned to the human genome (hg38) using Bowtie2; uniquely mapped and properly paired reads were retained. PCR duplicate reads were removed using Picard Tools.
Peaks were called using MACS2 (v.2.2.7); a high-confidence peak set was selected using the IDR reproducibility framework (threshold: 0.05) to generate ChIP peak files (bed files).
ChIP-seq reads were normalized to 1% of input chromatin sequencing reads and reported in ChIP signal files (bigwig files).
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: H727 cells were cultured in ATCC-formulated RPMI-1640 medium supplemented with 10% fetal bovine essence (FBE). BON1 cells were cultured in DMEM/F12 1:1 supplemented with 10% FBE and 1% penicillin/streptomycin. Cells were maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sheared with a Sonic Dismembrator Model 100.
Sequencing libraries were generated using a KAPA Hyperprep library kit, analyzed using a Bioanalyzer High Sensitivity DNA Chip, quantified by qPCR, and sequenced (paired end) on an Illumina NovaSeq 6000 platform.

treatment_protocol: Stable cells were treated as control (-Dox) or active YAP overexpression (+Dox). Active YAP overexpression was induced with 1 µg/ml doxycycline hyclate for 48-96 h before cell collection.

value: lung carcinoid

value: active YAP overexpression

tag: chip antibody

value: YAP (Cell Signaling 14704, D8H1X)


title: H727, lung carcinoid cells, active YAP overexpression, TEAD immunoprecpitation, biol rep 1

description: Library name: Active YAP H727_TEAD IP_rep1

value: TEAD (Cell Signaling 13295, D3F7L)


title: BON1, pancreatic carcinoid cells, active YAP overexpression, TEAD immunoprecipitation, biol rep 1

description: Library name: Active YAP BON1_TEAD IP_rep1

value: pancreatic carcinoid


title: H727, lung carcinoid cells, active YAP overexpression, YAP immunoprecipitation, biol rep 2

description: Library name: Active YAP H727_YAP IP_rep2


title: H727, lung carcinoid cells, control, YAP immunoprecipitation, biol rep2

description: Library name: Control H727_YAP IP_rep2

value: control


title: H727, lung carcinoid cells, active YAP overexpression, TEAD immunoprecpitation, biol rep 2

description: Library name: Active YAP H727_TEAD IP_rep2


title: BON1, pancreatic carcinoid cells, control, YAP immunoprecipitation, biol rep 2

description: Library name: Control BON1_YAP IP_rep2


title: BON1, pancreatic carcinoid cells, control, TEAD immunoprecipitation, biol rep 2

description: Library name: Control BON1_TEAD IP_rep2


title: H727, lung carcinoid cells, control, TEAD immunoprecipitation, biol rep 2

description: Library name: Control H727_TEAD IP_rep2


title: BON1, pancreatic carcinoid cells, active YAP overexpression, TEAD immunoprecipitation, biol rep 2

description: Library name: Active YAP BON1_TEAD IP_rep2


title: BON1, pancreatic carcinoid cells, control, TEAD immunoprecipitation, biol rep 1

description: Library name: Control BON1_TEAD IP_rep1


title: H727, lung carcinoid cells, control, TEAD immunoprecipitation, biol rep 1

description: Library name: Control H727_TEAD IP_rep1


title: BON1, pancreatic carcinoid cells, active YAP overexpression, YAP immunoprecipitation, biol rep 2

description: Library name: Active YAP BON1_YAP IP_rep2


title: H727, lung carcinoid cells, control, YAP immunoprecipitation, biol rep1

description: Library name: Control H727_YAP IP_rep1


title: BON1, pancreatic carcinoid cells, active YAP overexpression, input chromatin

description: Library name: Active YAP BON1_input


title: H727, lung carcinoid cells, active YAP overexpression, input chromatin

description: Library name: Active YAP H727_input


title: H727, lung carcinoid cells, control, input chromatin

description: Library name: Control H727_input


title: BON1, pancreatic carcinoid cells, control, YAP immunoprecipitation, biol rep 1

description: Library name: Control BON1_YAP IP_rep1


title: BON1, pancreatic carcinoid cells, active YAP overexpression, biol rep 2

description: Library name: Active_YAP_BON1_rep2

data_processing:
FASTQ sequence files were quality controlled using FastQC (v.0.11.9) and adapter sequences and low-quality bases (<30) were trimmed using Trimmomatic (v.0.39).
Trimmed sequences were aligned to the human reference transcriptome GRCh38 (release 97) using Kallisto.
Assembly: human reference transcriptome GRCh38 (release 97)
Supplementary files format and content: csv files include transcripts per million (TPM) values for each sample

extract_protocol:
Total RNA was isolated from cells using TRIzol Reagent according to the manufacturer’s instructions. Total RNA was quality controlled through UV spectrophotometry using a SmartSpecTM Plus Spectrophotometer and visualization through 1% agarose gel electrophoresis.
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit and the NEBNext rRNA Depletion Kit according to the manufacturer’s instructions; RNA fragmentation was performed for 10 min. Libraries were sequenced on an Illumina NovaSeq 6000 platform.


title: BON1, pancreatic carcinoid cells, active YAP overexpression, biol rep 1

description: Library name: Active_YAP_BON1_rep1


title: BON1, pancreatic carcinoid cells, active YAP overexpression, biol rep 3

description: Library name: Active_YAP_BON1_rep3


title: BON1, pancreatic carcinoid cells, control, biol rep 2

description: Library name: Control_BON1_rep2


title: BON1, pancreatic carcinoid cells, control, biol rep 3

description: Library name: Control_BON1_rep3


title: BON1, pancreatic carcinoid cells, active YAP overexpression, YAP immunoprecipitation, biol rep 1

description: Library name: Active YAP BON1_YAP IP_rep1


title: BON1, pancreatic carcinoid cells, control, biol rep 1

description: Library name: Control_BON1_rep1


title: H727, lung carcinoid cells, active YAP overexpression, biol rep 2

description: Library name: Active_YAP_H727_rep2


title: BON1, pancreatic carcinoid cells, control, input chromatin

description: Library name: Control BON1_input


title: H727, lung carcinoid cells, control, biol rep 2

description: Library name: Control_H727_rep2


title: P191_coreD_tissue

city: Bern

first: Panagiotis

last: Chouvardas

address: Murtenstrasse 24

country: Switzerland

institute: University of Bern

description:
Library name: PCa_191_D_TS
FFPE tissue

data_processing:
The data were analyzed using the rnaseq nf-core worfklow (version 3.10)
Assembly: Hg38 human reference genome/108 version of Ensembl gene annotation.
Supplementary files format and content: Gene expression counts across all samples (csv format).

source_name: prostate

extract_protocol:
RNA from regions of interest was extracted from FFPE material using the Ambion Kit. The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) was employed for fragmentation and cDNA synthesis. Depending on RNA quality, two fragmentation conditions were used: 10 minutes at 94°C for samples with RQN ≥ 4, and 5 minutes priming at 65°C for others. Following fragmentation, cDNA synthesis took place. Quality control was subsequently conducted using Qubit to ascertain the starting concentration.
Sample preparation and hybridization capture were executed in line with the manufacturer's protocol for the SureSelectXT Low Input Target Enrichment System for Illumina Paired-End Sequencing Library (protocol v1.8, G9703-90000). For the hybridization process, Agilent SureSelectXT Human All Exon v7 Capture Library (5191-4006) baits were utilized. Clustering and sequencing using the NovaSeq6000 was performed according to manufacturer's protocols.

value: prostate


title: P214_coreD_tissue

description:
Library name: PCa_214_D_TS
FFPE tissue


title: P134_coreD_tissue

description:
Library name: PCa_134_D_TS
FFPE tissue


title: P191_coreB_tissue

description:
Library name: PCa_191_B_TS
FFPE tissue


title: P217_coreC_tissue

description:
Library name: PCa_217_C_TS
FFPE tissue


title: P191_coreC_tissue

description:
Library name: PCa_191_C_TS
FFPE tissue


title: H727, lung carcinoid cells, control, biol rep 1

description: Library name: Control_H727_rep1


title: H727, lung carcinoid cells, active YAP overexpression, biol rep 1

description: Library name: Active_YAP_H727_rep1


title: P135_coreD_tissue

description:
Library name: PCa_135_D_TS
FFPE tissue


title: P134_coreB_tissue

description:
Library name: PCa_134_B_TS
FFPE tissue


title: P133_coreC_tissue

description:
Library name: PCa_133_C_TS
FFPE tissue


title: P217_coreD_tissue

description:
Library name: PCa_217_D_TS
FFPE tissue


title: H727, lung carcinoid cells, control, biol rep 3

description: Library name: Control_H727_rep3


title: P217_coreB_tissue

description:
Library name: PCa_217_B_TS
FFPE tissue


title: P214_coreB_tissue

description:
Library name: PCa_214_B_TS
FFPE tissue


title: P191_coreA_tissue

description:
Library name: PCa_191_A_TS
FFPE tissue


title: P139_coreC_tissue

description:
Library name: PCa_139_C_TS
FFPE tissue


title: P134_coreA_tissue

description:
Library name: PCa_134_A_TS
FFPE tissue


title: P135_coreC_tissue

description:
Library name: PCa_135_C_TS
FFPE tissue


title: P134_coreC_tissue

description:
Library name: PCa_134_C_TS
FFPE tissue


title: P135_coreA_tissue

description:
Library name: PCa_135_A_TS
FFPE tissue


title: P177_coreD_tissue

description:
Library name: PCa_177_D_TS
FFPE tissue


title: P133_coreB_tissue

description:
Library name: PCa_133_B_TS
FFPE tissue


title: P195_coreD_tissue

description:
Library name: PCa_195_D_TS
FFPE tissue


title: P195_coreB_tissue

description:
Library name: PCa_195_B_TS
FFPE tissue


title: H727, lung carcinoid cells, active YAP overexpression, biol rep 3

description: Library name: Active_YAP_H727_rep3


title: P200_coreA_tissue

description:
Library name: PCa_200_A_TS
FFPE tissue


title: P177_coreA_tissue

description:
Library name: PCa_177_A_TS
FFPE tissue


title: P170_coreC_tissue

description:
Library name: PCa_170_C_TS
FFPE tissue


title: P149_coreD_tissue

description:
Library name: PCa_149_D_TS
FFPE tissue


title: pad4 ko_con_4

city: Chongqing

first: Yunjie

last: Xiong

address: 1 Youyi Street

institute: The First Affiliated Hospital of Chongqing Medical University

description: PAD4_KO_con4 FPKM

data_processing:
Clean reads were obtained by filtering the sequencing data using the filtering software SOAPnuke
Clean reads were compared to the reference genome sequence using HISAT
Clean reads are aligned to a reference sequence using Bowtie2
The expression levels of genes and transcripts were calculated using RSEM
Assembly: GRCm38
Supplementary files format and content: tab-delimited xlsx files include RPKM values for each Sample

source_name: Primary macrophage

extract_protocol:
Total RNA was extracted from PAD4-/- and WT BMDMs using Trizol (Takara), 1μg of total RNA were used for construction of  sequencing libraries.
RNA libraries for RNA-seg were prepared fowllowing BGISEQ RNA-Seq library construction protocol.

value: Primary macrophage


title: pad4 ko_con_3

description: PAD4_KO_con3 FPKM


title: P138_coreB_tissue

description:
Library name: PCa_138_B_TS
FFPE tissue


title: P233_coreD_tissue

description:
Library name: PCa_233_D_TS
FFPE tissue


title: P133_coreD_tissue

description:
Library name: PCa_133_D_TS
FFPE tissue


title: P149_coreB_tissue

description:
Library name: PCa_149_B_TS
FFPE tissue


title: P233_coreA_tissue

description:
Library name: PCa_233_A_TS
FFPE tissue


title: P133_coreA_tissue

description:
Library name: PCa_133_A_TS
FFPE tissue


title: P138_coreA_tissue

description:
Library name: PCa_138_A_TS
FFPE tissue


title: pad4 ko_con_1

description: PAD4_KO_con1 FPKM


title: P170_coreB_tissue

description:
Library name: PCa_170_B_TS
FFPE tissue


title: wt_con_4

description: WT_con4 FPKM

value: WT


title: wt_con_3

description: WT_con3 FPKM


title: P227_coreC_tissue

description:
Library name: PCa_227_C_TS
FFPE tissue


title: P227_coreB_tissue

description:
Library name: PCa_227_B_TS
FFPE tissue


title: pad4 ko_con_2

description: PAD4_KO_con2 FPKM


title: wt_con_1

description: WT_con1 FPKM


title: wt_con_2

description: WT_con2 FPKM


title: pad4 ko_con_4

data_processing:
Use the Cutadapt program to remove adapter sequences from the original sequencing data
Use the Trimmomatic program to remove low-quality sequences to obtain the clean data
Clean data was compared to the reference genome using the bowtie2
Assembly: GRCm38
Supplementary files format and content: bw files include peaks information of each sample

extract_protocol:
PAD4-/- and WT BMDMs were suffering from lysis, transposition reaction and DNA purification.
DNA libraries for ATAC-seg were prepared fowllowing BGISEQ ATAC-Seq library construction protocol.


title: P263_coreD_tissue

description:
Library name: PCa_263_D_TS
FFPE tissue


title: pad4 ko_con_3


title: pad4 ko_con_2


title: P263_coreC_tissue

description:
Library name: PCa_263_C_TS
FFPE tissue


title: P263_coreB_tissue

description:
Library name: PCa_263_B_TS
FFPE tissue


title: pad4 ko_con_1


title: P170_coreA_tissue

description:
Library name: PCa_170_A_TS
FFPE tissue


title: wt_con_4


title: P219_coreD_tissue

description:
Library name: PCa_219_D_TS
FFPE tissue


title: P219_coreA_tissue

description:
Library name: PCa_219_A_TS
FFPE tissue


title: P215_coreC_tissue

description:
Library name: PCa_215_C_TS
FFPE tissue


title: P227_coreA_tissue

description:
Library name: PCa_227_A_TS
FFPE tissue


title: Knockout Cajal-Retzius cells, postnatal day 14, scRNAseq

city: Edmotnotn

first: Qiumin

last: Tan

state: Alberta

address: 114 St and 87 Ave

department: Cell Biology

institute: University of Alberta

description:
Library name: Knockout
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
The cell suspension was prepared using the Papain Dissociation System (Worthingon Biochemical Corporation). The resulting cell pellet was resuspended in oxygenated aCSF and DAPI was added for live/dead cell discrimination. Cells were then sorted using a SONY MA900 cell sorter. Sorted DAPI- tdT+ cells suspended in aCSF were used to generate the gel-beads cell emulsion by the 10X Chromium Controller (PN-1000202).
Gene expression libraries were prepared using the Chromium Next GEM Single Cell 3' Gene Expression v3.1 (Dual Index) (PN-1000269) following the manufacturer’s protocol. Sample libraries were sequenced in Illumina NovaSeq PE150 to an average depth of ~ 50,000 reads per cell.

value: Hippocampus

value: postnatal day 14

value: Cajal-Retzius neurons

value: Knockout

value: 2 males and 2 females


title: P215_coreB_tissue

description:
Library name: PCa_215_B_TS
FFPE tissue


title: P222_coreC_tissue

description:
Library name: PCa_222_C_TS
FFPE tissue


title: P222_coreB_tissue

description:
Library name: PCa_222_B_TS
FFPE tissue


title: P219_coreB_tissue

description:
Library name: PCa_219_B_TS
FFPE tissue


title: EV_no_cre_4

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

institute: Beatson CRUK

description: Library name: EV_no_cre_4

data_processing:
Sequencing was performed with a read length of 2×150 bp using a high output kit on Illumina NextSeq 500
The quality of sequencing reads was checked using FastQC and the adaptors were trimmed using Cutadapt (Martin, 2011)
The trimmed reads were aligned to the mouse genome assembly GRCm38/mm10 using STAR
The PCR duplicates from the mapped reads were removed using Picard (Wysoker et al., 2013)
Each reads per gene was quantified using htseq (Anders et al., 2015)
Assembly: Assembly: mm10
Supplementary files format and content: Supplementary files format and content: Each reads per gene file contains a tab delimited table of reads per gene counted, the first column indicates the ensembl gene id, the second column shows the read count

source_name: embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were grown in Dulbecco's Minimum Essential Medium supplemented with 10% Fetal Bovine Serum, 100U/mL penicillin, 100µg/mL streptomycin and 0.5mg/mL G418. MEFs were cultured at 37 °C with 5 % CO2.

extract_protocol:
Total RNA was extracted using GeneJET RNA Purification Kit (ThermoFisher Scientific)
Sequencing libraries were prepared by Novogene using ribosomal RNA depletion. The libraries were sequenced by Novogene using NovaSeq 6000.

treatment_protocol: Phoenix packaging cells were transfected with pINI vectors using Lipofectamine 2000. On day 1 medium was changed and on day 2 medium was taken off the cells and after filtration (0.22μM) applied onto the MEF cells with 5μg/ml polybrene (Sigma)

value: embryonic fibroblasts

value: Cmtr1 fl/fl

value: transduced with empty vector control


title: EV_no_cre_2

description: Library name: EV_no_cre_2


title: P222_coreD_tissue

description:
Library name: PCa_222_D_TS
FFPE tissue


title: EV_no_cre_1

description: Library name: EV_no_cre_1


title: wt_con_3


title: P183_coreC_tissue

description:
Library name: PCa_183_C_TS
FFPE tissue


title: EV_no_cre_3

description: Library name: EV_no_cre_3


title: wt_con_1


title: NM-DMSO-2

city: 苏州市

first: lyp

last: l

address: 斜塘街道

institute: 苏州大学

description: Library name: Sample 8

data_processing:
Raw FASTQ files were quality-checked with FastQC (v0.11.9), and adapters/low-quality bases were trimmed using Trimmomatic (v0.39) with parameters:
Clean reads were aligned to the GRCh38 primary assembly (GENCODE v43) using STAR (v2.7.10a) with default parameters.
Gene-level counts were generated with featureCounts (v2.0.3) using paired-end mode and strand-specific counting (-s 2).
Assembly: GRCm38
Supplementary files format and content: matrix files

source_name: Cranial bone

extract_protocol:
The supernatant was removed and stored at -80°C in a refrigerator, and RNA was havested using Trizol reagent.
RNA-seq libraries were constructed by Azenta following their standard poly(A)-enriched/ribo-depleted protocol.

value: Cranial bone

value: osteoblastic cells


title: P215_coreD_tissue

description:
Library name: PCa_215_D_TS
FFPE tissue


title: P193_coreC_tissue

description:
Library name: PCa_193_C_TS
FFPE tissue


title: P263_coreA_tissue

description:
Library name: PCa_263_A_TS
FFPE tissue


title: Control Cajal-Retzius cells, postnatal day 14, scRNAseq

description:
Library name: Control
10X Genomics

source_name: Hippocampus,

value: Hippocampus,

value: Control

value: 3 males and 1 female


title: P193_coreB_tissue

description:
Library name: PCa_193_B_TS
FFPE tissue


title: P183_coreA_tissue

description:
Library name: PCa_183_A_TS
FFPE tissue


title: NM-Brdi-2

description: Library name: Sample 6


title: NM-DMSO-1

description: Library name: Sample 7


title: NM-Brdi-1

description: Library name: Sample 5


title: P193_coreA_tissue

description:
Library name: PCa_193_A_TS
FFPE tissue


title: P173_coreC_tissue

description:
Library name: PCa_173_C_TS
FFPE tissue


title: wt_con_2


title: P173_coreB_tissue

description:
Library name: PCa_173_B_TS
FFPE tissue


title: control1

description: Library name: Sample 3


title: P173_coreA_tissue

description:
Library name: PCa_173_A_TS
FFPE tissue


title: P168_coreB_tissue

description:
Library name: PCa_168_B_TS
FFPE tissue


title: Brd2

description: Library name: Sample 2


title: P234_coreA_tissue

description:
Library name: PCa_234_A_TS
FFPE tissue


title: Optic nerve, control

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

description:
Library name: C-ON
10X Genomics

data_processing:
chemistry: Single Cell 5' PE
The demultiplexing, barcode processing, gene couning and aggregation were made using cellranger-7.2.0 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
single cell data were processed using Seurat (version 5.2.1) https://satijalab.org/seurat/.
Cell quality was evaluated by number of reads, detected gene count, and percentage of mitochondrial read, followed by normalization and variance stabilization using Seruat's sctransform v2 method. To account for library chemistry, and other possible unknown differences between experiments, cells were integrated using the Seurat v5 integration method to produce batch-corrected data. PCA analysis followed by graph-based clustering using Louvain algorithm, and t-SNE/UMAP generation employing Euclidean distance, were conducted on the first 30 principal components of the integrated expression data. Differential analyses were performed using gene specific analysis (GSA).
Assembly: genome build: mm10-2020-A
Supplementary files format and content: sequences corresponding to every barcode in the matrix table
Supplementary files format and content: sequences corresponding to every feature in the matrix table
Supplementary files format and content: matrix table with the number of unique molecular identifiers for every feature by row and every barcode by column

source_name: optic nerve

extract_protocol:
Nf1-OPG optic nerves and meningeal duras were collected separately from ten 12-week old mice, and pooled to prepare a single-cell suspension. Optic nerves were collected and dissociated using the neural dissociation kit (Miltenyi Biotec, 130-095-942) followed by debris (Miltenyi Biotec, 130-107-677) and myelin (Miltenyi Biotec, 130-096-733) removal. Single cell supensions from meningeal duras were prepared as described above, stained with 7-AAD, and sorted using MoFlo. Live cells were collected and sent for scRNA sequencing with TCR V(D)J enrichment.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 5’ Reagent Kit (v2 Chemistry Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: optic nerve


title: Optic nerve, FMC new

description:
Library name: FMC_new
10X Genomics


title: Huh7,OE,SAFB2

city: Shanghai

first: Jun

last: Mi

address: 280 South Chongqing Rd.

department: Biochemistry & Molecular Cell Biology

data_processing:
Fastq files were checked with Fastqc (v. 0.11.9) for quality control. The adapters were removed from the raw reads with Cutadapt (v. 1.18) and mapped to human reference genome (hg38) with Bowtie2 (v. 2.4.2).
The alignment SAM files were sorted using Samtools (v. 1.3.1) and the possible PCR duplications were removed by Picard (v. 2.23.3).
Peak calling is a tool to identify regions which are enriched. MACS (Model-based Analysis of  ChIP-Seq) software applied in our workflow uses Dynamic Possion Distribution to calculate p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value< le-5. Thus, MACS assigns each enriched region (Peak) with set of numerical values which are the number of summits, tags, normalized p-value as well as fold enrichment information. The more enriched these regions are, the more likely they are transcription factor binding sites. The score is positively correlated to transcription factor binding intensity.
Peak-calling was performed using MACS2 (v. 2.1.1.20160309). Peak annotation and motif analysis were realized with Homer2 (v. 4.1.5).
Differential expression analysis is made using DEseq2, Data whose absolute value of log2Foldchange larger than 1 and pvalue less than 0.05 is kept for subsequent analysis. Input samples are used for removal of background noise during peak calls.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
Cells were crosslinked in 1% formaldehyde solution for 10 min followed by reaction termination in 125mM glycine. The cell pellet was washed twice with 1×PBS and then lysed in Tris-EDTA buffer (10 mM Tris, 1 mM EDTA pH8.0) at 4℃ for 15 min. The cell lysate containing nucleic acid-protein complexes was sheared by ultrasonication (Bioruptor™, Diagenode) and then centrifuged to obtain the supernatant, one-tenth of which was aliquoted as input, followed by protein removal by digestion with Proteinase K at 55℃ for 2hr.
The libraries were purified by purification beads (Vazyme, N411). Dynabeads protein A magnetic beads were eluted with PBS twice, and subjected to immunoprecipitation by adding 5μg antibody per ChIP conjugated incubated at 4℃ for 16hr. Then, followed by protein removal by digestion with Proteinase K at 55℃ for 2h. The resulting DNA fragments were purified with 1x DNA clean beads and subjected to library construction with VAHTS Universal DNA Library Prep Kit for Illumina (V3，ND607). After immunoprecipitation, beads 1x DNA clean beads were recovered using a magnet and washed DNA was eluted and cross-links reverted at 65°C for 4 hours then purified with OIAGEN Kit (MinElute PCR Purification Kit（50）Cat.No.28004) and analyzed on Agilent 2100 Bioanalyzer (Agilent) for measuring fragment size distribution (around 150 bp). The qualified libraries were sequenced on Illumina Nova Seq 6000.

value: hepatocellular carcinoma

value: SLC25A12 overexpression


title: P168_coreA_tissue

description:
Library name: PCa_168_A_TS
FFPE tissue

value: prostate


title: Brd1

description: Library name: Sample 1


title: mEER_CRT_Xevinapant_5

city: London

first: Anton

last: Patrikeev

state: London

address: Chester Beatty Laboratories, 237 Fulham Rd.

department: Targeted Therapy

institute: The Institute of Cancer Research

description: Library name: mEER_CRT_Xevinapant_5

data_processing:
Salmon quant v1.10.1 was used for transcript-level quantification against the GRCm39 mouse reference (Ensembl release 103). Transcript-level abundance estimates were aggregated to gene-level using tximport v1.34 R package. Differential gene expression analysis was performed using DESeq2 (pseudogenes were excluded and only genes with more than 10 reads in at least 5 samples were kept in the analysis).
Assembly: GRCm39 mouse reference (Ensembl release 103)
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: tumour

growth_protocol: All procedures involving animals were approved by the Animal Ethics Committee at The Institute of Cancer Research in accordance with National Home Office Regulations under the Animals (Scientific Procedures) Act 1986. 8- to 14-week-old females C57BL/6 wild-type (Charles River) were inoculated subcutaneously in the right flank with 1 × 10^6 mEER or 4 × 10^6 MOC1 cells suspended in 100 uL PBS under isoflurane anaesthesia.

extract_protocol:
RNA from tumours was extracted and purified from tumours using the RNeasy Plus Mini Kit (Qiagen, 74134) with QIAshredder (Qiagen, 79656) according to manufacturer’s protocol and stored at -80 °C.
Library preparation and sequencing were performed by Genewiz, Germany. Library preparation was strand-specific with polyA selection, with 2×150bp sequencing at 20 million paired-end reads per sample performed on an Illumina NovaSeq.

treatment_protocol: Mouse tumours were harvested 14 days after the last radiation dose, on the last day of vehicle/xevinapant treatment and snap frozen on dry ice. Tumour tissue was homogenised in 1 mL of Buffer RLT Plus (Qiagen, 1053393) with 10 uL beta-mercaptoethanol (Gibco, 21985023) within CK28 hard tissue homogenising 2 mL tubes (Precellys, 10144-494) using the Precellys Evolution Homogeniser. For all studies, mice were randomised prior to therapy for comparable tumour volumes between cohorts. In vivo treatments were commenced when tumour volumes reached approximately 20-50 mm3.  Mice were immobilised for irradiation via a single injection of ketamine 100 mg/kg (Ketavet) and 16 mg/kg xylazine (Rompun) dosed intraperitoneally (i.p.). Mice were irradiated in the prone position under lead shielding with a 15-mm diameter aperture aligned over the tumour. A total of 6 or 8 Gy × 3 fractions was delivered at a dose rate of 1.62 Gy/minute using an AGO 250 kV X-ray machine (AGO, 20090606) with dose measurement performed with a Farmer Chamber and Unidos-E Dosemeter (PTW). Following irradiation, cages were placed on heat mats and mice were monitored until full recovery.  Xevinapant powder for in vivo treatments was provided by the healthcare business of Merck KGaA, Darmstadt, Germany, and dissolved in vehicle formulated with 0.6% Malic Acid (Sigma Aldrich, 240176) (w/v) in 85 mM Sodium Acetate buffer (Calbiochem, 7610), pH 4.5. Xevinapant was administered at 100 mg/kg via oral gavage administered for five consecutive days followed by two days off, repeated twice over the course of 3 weeks.  Cisplatin powder (Sigma Aldrich, P4394) powder was diluted in 0.9% sodium chloride on the day of use and delivered by i.p. injection one hour prior to radiotherapy (if given).

value: tumour

value: mEER

value: WT

value: Xevinapant/Chemoradiotherapy


title: mEER_CRT_Xevinapant_1

description: Library name: mEER_CRT_Xevinapant_1


title: mEER_CRT_Xevinapant_3

description: Library name: mEER_CRT_Xevinapant_3


title: P234_coreB_tissue

description:
Library name: PCa_234_B_TS
FFPE tissue


title: mEER_CRT_Xevinapant_4

description: Library name: mEER_CRT_Xevinapant_4


title: mEER_RT_Xevinapant_5

description: Library name: mEER_RT_Xevinapant_5

value: Xevinapant/Radiotherapy


title: Huh7,OE,CEBPB

institute: Shanghai Jiao Tong University

value: SLC25A11 overexpression

value: C/EBP beta(invitrogen,#PA5-27244)


title: Huh7,NC,SAFB2


title: mEER_CRT_Xevinapant_2

description: Library name: mEER_CRT_Xevinapant_2


title: Huh7,NC,CEBPB


title: Huh7,OE,input

value: SLC25A10 overexpression

value: No


title: Huh7,NC,input


title: mEER_RT_Xevinapant_3

description: Library name: mEER_RT_Xevinapant_3


title: mEER_RT_Xevinapant_4

description: Library name: mEER_RT_Xevinapant_4


title: control2

description: Library name: Sample 4

value: Cranial bone

value: osteoblastic cells