title: EACBEko-DP-Traj61-HTGTS-rep2

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Hi-C data process pipline. For each sample, reads were obtained following quality filtering and adapter trimming using fastp (v0.20.0). Hi-C mapping, filtering, correction, and binning were performed with Hi-C-Pro (v2.11.1). The paired-end reads were mapped to the mouse mm10 genome. Self-circle ligation, dangling ends, re-ligation, and the other dumped types were filtered out with Hi-C-Pro after mapping. We generated raw contact matrices at 10 kb, 20 kb, 50 kb, 100 kb, 500 kb, 1 Mb resolutions. For raw contact matrix correction, we used the iterative correction method (ICE). The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox hic format at fragment resolution. Heatmap, differential analysis and visualization of local interactions from Hi-C data were obtained using HiTC (v1.34.0) R package. A/B compartment analysis was performed at 100 kb resolution using a publicly available script runHiCpca.pl that performs PCA analysis with HOMER (v4.10.4). Then, we used the first principal component (PC1) to predict regions of active (A compartments) and inactive chromatin (B compartments). The TAD structure (insulation) was defined by the insulation score. The matrices which were used to calculate the insulation score were normalized by ICE method for discarding the bias of raw matrices. And then, the insulation score was computed at 10 kb resolution. The script matrix2insulation.pl was used to detect TAD boundaries, with the following options: ‘--is 100001 --ids 20001 --nt 0.3 -ss 0 --im mean’. TADs were called using normalized Hi-C matrices at 10 kb resolution with insulation2tads.pl. Chromatin loops were called using Fit-Hi-C (v2.0.7). Input files of Fit-Hi-C were created by using a publicly available script hicpro2fithic.py from Hi-C-Pro. Next, loops were called using fixed-size bin resolutions from 10 kb in all cell types. Briefly, significant interaction loops (P < 0.0001 and contact frequencies > = 5) were identified through jointly modeling the contact probability using raw contact frequencies and ICE normalization vectors with the Fit-Hi-C algorithm.
3C-HTGTS data processing for pairwise chromatin interactions. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained by splitting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exact alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph files using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph files using the CPM (Counts Per Million in cis) normalization method and visualized them on the IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6).
3C-HTGTS data processing for three-way chromatin interactions. Paired-end Illumina sequencing reads were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads were extracted from the file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged at restriction enzyme cut sites into single reads with Pear (v0.9.6), then fragments with multiple MboI cut sites were split and each fragment was aligned to the enzyme-digested mm10 reference genome by Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). We extracted concordantly exact alignments using SAMtools (v1.9). We converted the final bam files into bed files using Bedtools (v2.29.2). Self-ligation and off-targeted fragments were filtered. Subsequently, we put all fragments retrieved from the same read according to the unique ID of each read on one line, then removed the continuous fragments. To create contact matrices, we extracted the first two digested fragments after the bait fragment, or a variety of combinations of three fragments were obtained by arranging all fragments from the same read. Raw contact matrices were generated at 3 kb, 5 kb, and 10 kb resolutions. For raw contact matrices correction, these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions. Similar to a Hi-C matrix, coverage was represented in a 2-dimensional matrix where each point represented the number of interactions found between two bins meaning a specific resolution. Differential analysis and visualization of local interactions from three-way interactions were obtained using the R package GENOVA (v1.0.0). Loops seen on the IGV genome browser were called using fixed-size bin resolutions from 3 kb to 10 kb. Briefly, interaction loops (contact frequencies >= 5) were identified by using raw contact frequencies.
ATAC-Seq data process pipline. Raw sequence reads were initially processed for removing adapter sequences and poor quality reads by fastp (v0.20.0). Subsequently, the remaining reads were mapped to the human genome hg38 using Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). PCR duplicated fragments were filtered by Picard (v2.22.8). Then, we filtered the unmapped, multi-mapped reads and mapping to the reads on chrM. FRiP (Fragments Ratio in Peaks) value was calculated by using Bedtools (v2.29.2) and awk (v4.0.2). We used deepTools (v3.5.0) to generate bigWig file with CPM normalization, and these files can be visualized in IGV. SAM files were converted to BAM format using SAMtools (v1.9) and used for peak calling. MACS2 (v2.2.4) with parameters (--nomodel --shift -100 --extsize 200 -B --keep-dup all --broad --broad-cutoff 0.1) was used to call peaks.
HTGTS-VDJ data process pipline. The raw data were filtered by fastp (v0.20.0). Trimmed reads again that nested primer and adapter primer were removed were extracted from the sequence file after quality control with Cutadapt (v1.18). Contamination, and low-quality reads were also removed. T-cell receptor beta chain V, D, and J gene identification, CDR3 sequence extraction in clean reads were performed using MiXCR (v3.0.11). The corresponding germline sequences were mapped to the reference sequences derived from international ImMunoGeneTics (IMGT) information.
Assembly: mm10
Supplementary files format and content: The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format.
Supplementary files format and content: BedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample.
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.
Library strategy: HTGTS-VDJ

source_name: Thymus

growth_protocol: All experiments involving mice were performed using protocols approved by  Southern Medical University Animal Studies Committee. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol:
For Hi-C, We performed with DN thymocytes from 3-4 Rag1-/- or EACBE-/- Rag1-/- mice per experiment or 10 million CD3-stimulated DP thymocytes from Rag1-/- mice per experiment. In brief, cells were crosslinked with a final concentration of 1% formaldehyde at room temperature for 10 min and quenched with glycine (final concentration 0.125 M) on ice for 5 min. Crosslinked cells were lysed and followed by adding 150U DpnII(New England Biolabs,R0543L) to digest the chromatin overnight at 37℃ with gently shaking. DpnII was inactivated at 65℃ for 20 min, DNA fragment ends were biotinylated with biotin-dATP, and the sample was diluted, and proximity ligated for 4-6 hours at room temperature. Crosslinked DNA was reversed by addition of SDS, proteinase K, and NaCl, and allowed to incubate overnight at 68℃. DNA was purified by phenol/chloroform, followed by isopropanol precipitation, and resuspended in 100ul 10Mm Tris-HCl,pH:8.0. DNA was treated with T4 DNA polymerase to remove unligated biotinylated ends and sheared to 300-500bp by sonication subsequently, the ligated junctions were pulled down with Dynabeads MyOne Streptavidin C1 magnetic beads. End-repair, dA-tailing, adapter-ligation, and PCR amplification with P5 and P7 prime were performed on biotinylated DNA fragments bound to beads. After purification, libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
For 3C-HTGTS, mouse thymus and liver were removed, cells were filtered through nylon mech.10 million cells were cross-linked with 1% formaldehyde. Cell were lysed and digest with 200U MboI overnight at 37°C. The sample was ligated with T4 DNA ligase overnight at 16°C. Crosslinks were reversed by Proteinase K and RNase A prior to DNA extraction with 1:1 phenol-chloroform and precipitation with ethanol. The 10ug 3C DNA was sonicated to 300-500bp and was linearly amplified with a biotinylated primer. The biotin-labeled single-stranded DNA products were enriched with streptavidin C1 beads, and followed by 3’ ends ligation with the bridge adaptor. The adaptor-ligated products were amplified via nested PCR using a nested primer and an adaptor-complementary primer.The detailed primers used in this study are also listed in Supplementary information, Table S1.  And a final PCR for another 5-10 cycles with P5 and P7 was performed. After purification of the PCR products, the final libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
For ATAC-Seq, a total of 5 × 104 cell pellets were washed once with cold PBS, cells lysed on ice for 3 min in 50 μL ice-cold Lysis Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% TWEEN 20, and 0.01% Digitonin in DEPC H2O), resuspended in 1 mL ice-cold RBS-Wash (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% TWEEN 20) and pelleted at 4 °C at 500 × g for 5min. Tagmentation was performed in 1 × Tagmentation Buffer (10 mM Tris pH 7.4, 5 mM MgCl2, 10% DMF, 33% PBS, 0.1%TWEEN 20, and 0.01% Digitonin) using 100 nM Tn5 Transposase for 30 min at 37 °C. Immediately, Free DNA was purified using QIAquick PCR Purification Kit (QIAGEN, 28106, GERMANY) according to the manufacturer’s instructions. And a final PCR for 10-15 cycles of amplification with P5 and P7 primers was performed. After purification, libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
For HTGTS-VDJ, DNA was extracted by DNA Isolation Mini Kit (Vazyme, DC102) and sonicated to about 500bp on a Qsonica Bioruptor Sonicator. Sonicated DNA was linearly amplified with a biotinylated primer  that anneals to sites of interest. Biotin-labeled single stranded DNA products were enriched with streptavidin C1 beads (65001, Thermo Fisher Scientific), and followed by 3' end ligation with the bridge adapter. The adapter-ligated products were amplified through nested PCR using a nested primer and an adapter-complementary primer . The detailed primers used in this study are also listed in Supplementary information, Table S2. And a final PCR for another 10-12 cycles of amplification with P5 and P7 primers was performed. After purification, libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
Construction of libraries were described as the above extract protocol

value: Thymus

value: DP thymocytes

value: EACBE-/-


title: 32_KD_abundance_block1_input2

status: Public on Apr 27 2024

type: SRA

city: Barcelona

first: Antoni

last: Beltran

address: Dr Aiguader, 88

country: Spain

institute: CRG Barcelona

library_source: genomic

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Assembly: NA
Supplementary files format and content: Fitness scores table: Tabular format; contains the raw counts and dimsum fitness estimates per replicate and aggregated and their corresponding errors.
Supplementary files format and content: Weight tables: Tabular format; contains the MoCHI inferred 'folding' and 'activity' energies

molecule: genomic DNA

organism:
Saccharomyces cerevisiae
Homo sapiens

source_name: log phase culture

growth_protocol: BY4741 cells were transformed with the Src variant library cloned in the activity and abundance assay plasmids at a coverage of at least 20x and transferred to selective media for ~24h. The resulting cell population was transferred to input media (SC -ura-ade 2% glucose for abundance selections and SC -ura 2 % raffinose 0.1% glucose for activity selections) and grown overnight to an OD of at least 1.6. A small volume of cells was saved to inoculate outputs and the rest of cells were split in two, harvested by centrifugation, and frozen at -20C as input samples. The remainder of cells were then inoculated at an OD=0.05 in selective media (SC -ura-ade+MTX 2% glucose for abundance, and SC -ura 2% galactose 0.1% glucose for activity), and grown to an OD=1.6 at which point cells were harvested and stored as output samples as described for the inputs.

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 1 mL of DNA extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris-HCl pH8, 1mM EDTA pH8), and freeze-cracked by liquid nitrogen freezing followed by 62ºC incubation for 10 min in a water bath, twice. Subsequently, 1 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.1 mL of NaOAc 3M and 2.2 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was vacuum-dried. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (30 μL of QIAEX II beads). The samples were washed twice with PE buffer and eluted in 200 μL of 10 mM Tris-HCI buffer, pH 8.5.
Plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids. We performed 2 consecutive PCR reactions for each sample. The first PCR (PCR1) is used to amplify the amplicons for sequencing, to add a part of the Illumina sequencing adaptors to the amplicon and to increase nucleotide complexity for the sequencing reaction by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) is used to add the remainder of the Illumina adaptor and to add demultiplexing indexes (dual-indexed). The amplicon libraries were run on a 2% agarose gel for quality control and quantification, and were pooled by block and size selected on a 2% agarose gel. Bands were purified using QIAEX II Gel Extraction Kit (QIAGEN) and using 30uL of QIAEX II beads for each sample. The purified amplicons were subjected to Illumina 150bp paired-end NextSeq sequencing at the CRG Genomics Core Facility.
Amplicon-seq

treatment_protocol: abundancePCA (High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation, Levy and Michnick, 2014), activity-dependent toxicity assay (A Combined Approach Reveals a Regulatory Mechanism Coupling Src’s Kinase Activity, Localization, and Phosphotransferase-Independent Functions, Ahler et al., 2019)

tag: tissue

value: log phase culture

tag: cell line

tag: cell type


title: 37_KD_abundance_block3_input1


title: 31_KD_abundance_block1_input1


title: EACBEko-DP-Traj61-HTGTS-rep3

country: China

organism: Mus musculus

tag: strain

tag: genotype


title: 30_KD_activity_block5_output3


title: C5_output_2

description: genomic and plasmid DNA

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Assembly: NA
Supplementary files format and content: Variant growth rates table: Tabular format; contains the raw counts and dimsum fitness estimates per replicate and aggregated and their corresponding errors.
Library strategy: Amplicon-seq

organism: Saccharomyces cerevisiae

growth_protocol: BY4741 cells were transformed with the Domainome libraries cloned in the abundancePCA assay plasmid at a coverage of at least 20x and transferred to selective media for ~24h. The resulting cell population was transferred to input media (SC -ura-ade 2% glucose) and grown overnight to an OD of at least 1.6. A small volume of cells was saved to inoculate outputs and the rest of cells were split in two, harvested by centrifugation, and frozen at -20C as input samples. The remainder of cells were then inoculated at an OD=0.05 in selective media (SC -ura-ade+MTX 2% glucose), and grown to an OD=1.6 at which point cells were harvested and stored as output samples as described for the inputs.

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 1 mL of DNA extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris-HCl pH8, 1mM EDTA pH8), and freeze-cracked by liquid nitrogen freezing followed by 62ºC incubation for 10 min in a water bath, twice. Subsequently, 1 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.1 mL of NaOAc 3M and 2.2 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was vacuum-dried. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (30 μL of QIAEX II beads). The samples were washed twice with PE buffer and eluted in 200 μL of 10 mM Tris-HCI buffer, pH 8.5.
Plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids. We performed 2 consecutive PCR reactions for each sample. The first PCR (PCR1) is used to amplify the amplicons for sequencing, to add a part of the Illumina sequencing adaptors to the amplicon and to increase nucleotide complexity for the sequencing reaction by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) is used to add the remainder of the Illumina adaptor and to add demultiplexing indexes (dual-indexed). The amplicon libraries were run on a 2% agarose gel for quality control and quantification, and were pooled by block and size selected on a 2% agarose gel. Bands were purified using QIAEX II Gel Extraction Kit (QIAGEN) and using 30uL of QIAEX II beads for each sample. The purified amplicons were subjected to Illumina 150bp paired-end NextSeq sequencing at the CRG Genomics Core Facility.

treatment_protocol: abundancePCA (High-resolution mapping of protein concentration reveals principles of proteome architecture and adaptation, Levy and Michnick, 2014)


title: EACBEko-DP-Traj61-HTGTS-rep1


title: Synovium fibroblast cells of FS patient and treated with TAK715 at 5 uM_3

first: Xinhao

last: Li

address: Yanjiang street

institute: Sun Yat-sen Memorial Hospital

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for all Samples

molecule: total RNA

organism: Homo sapiens

source_name: human shoulder capsular synovium

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: human shoulder capsular synovium

value: primary human cell

value: synovium fibroblasts

value: WT

tag: treatment

value: TAK715 5uM


title: EACBEwt-DP-Traj61-HTGTS-rep3

value: EACBE+/+


title: 29_KD_activity_block5_output2


title: Synovium fibroblast cells of FS patient_3

value: PBS


title: EACBEwt-DP-Traj61-HTGTS-rep2


title: 26_KD_activity_block4_output2


title: Synovium fibroblast cells of FS patient and treated with TAK715 at 5 uM_1


title: 28_KD_activity_block5_output1


title: Synovium fibroblast cells of FS patient_2


title: EACBEwt-DP-Traj61-HTGTS-rep1


title: Synovium fibroblast cells of FS patient_1


title: 24_KD_activity_block3_output3


title: Synovium fibroblast cells of FS patient and treated with TAK715 at 5 uM_2


title: 23_KD_activity_block3_output2


title: 25_KD_activity_block4_output1


title: 22_KD_activity_block3_output1


title: EACBEko-DN-Trdj1-HTGTS-rep2

value: DN thymocytes


title: 44_KD_abundance_block5_input2


title: 21_KD_activity_block2_output3


title: 17_KD_activity_block1_output2


title: 16_KD_activity_block1_output1


title: 27_KD_activity_block4_output3


title: 15_KD_activity_block5_input3


title: EACBEwt-DN-Trdj1-HTGTS-rep1


title: 20_KD_activity_block2_output2


title: EACBEwt-Rag1ko-DP-ATAC-rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Hi-C data process pipline. For each sample, reads were obtained following quality filtering and adapter trimming using fastp (v0.20.0). Hi-C mapping, filtering, correction, and binning were performed with Hi-C-Pro (v2.11.1). The paired-end reads were mapped to the mouse mm10 genome. Self-circle ligation, dangling ends, re-ligation, and the other dumped types were filtered out with Hi-C-Pro after mapping. We generated raw contact matrices at 10 kb, 20 kb, 50 kb, 100 kb, 500 kb, 1 Mb resolutions. For raw contact matrix correction, we used the iterative correction method (ICE). The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox hic format at fragment resolution. Heatmap, differential analysis and visualization of local interactions from Hi-C data were obtained using HiTC (v1.34.0) R package. A/B compartment analysis was performed at 100 kb resolution using a publicly available script runHiCpca.pl that performs PCA analysis with HOMER (v4.10.4). Then, we used the first principal component (PC1) to predict regions of active (A compartments) and inactive chromatin (B compartments). The TAD structure (insulation) was defined by the insulation score. The matrices which were used to calculate the insulation score were normalized by ICE method for discarding the bias of raw matrices. And then, the insulation score was computed at 10 kb resolution. The script matrix2insulation.pl was used to detect TAD boundaries, with the following options: ‘--is 100001 --ids 20001 --nt 0.3 -ss 0 --im mean’. TADs were called using normalized Hi-C matrices at 10 kb resolution with insulation2tads.pl. Chromatin loops were called using Fit-Hi-C (v2.0.7). Input files of Fit-Hi-C were created by using a publicly available script hicpro2fithic.py from Hi-C-Pro. Next, loops were called using fixed-size bin resolutions from 10 kb in all cell types. Briefly, significant interaction loops (P < 0.0001 and contact frequencies > = 5) were identified through jointly modeling the contact probability using raw contact frequencies and ICE normalization vectors with the Fit-Hi-C algorithm.
3C-HTGTS data processing for pairwise chromatin interactions. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained by splitting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exact alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph files using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph files using the CPM (Counts Per Million in cis) normalization method and visualized them on the IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6).
3C-HTGTS data processing for three-way chromatin interactions. Paired-end Illumina sequencing reads were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads were extracted from the file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged at restriction enzyme cut sites into single reads with Pear (v0.9.6), then fragments with multiple MboI cut sites were split and each fragment was aligned to the enzyme-digested mm10 reference genome by Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). We extracted concordantly exact alignments using SAMtools (v1.9). We converted the final bam files into bed files using Bedtools (v2.29.2). Self-ligation and off-targeted fragments were filtered. Subsequently, we put all fragments retrieved from the same read according to the unique ID of each read on one line, then removed the continuous fragments. To create contact matrices, we extracted the first two digested fragments after the bait fragment, or a variety of combinations of three fragments were obtained by arranging all fragments from the same read. Raw contact matrices were generated at 3 kb, 5 kb, and 10 kb resolutions. For raw contact matrices correction, these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions. Similar to a Hi-C matrix, coverage was represented in a 2-dimensional matrix where each point represented the number of interactions found between two bins meaning a specific resolution. Differential analysis and visualization of local interactions from three-way interactions were obtained using the R package GENOVA (v1.0.0). Loops seen on the IGV genome browser were called using fixed-size bin resolutions from 3 kb to 10 kb. Briefly, interaction loops (contact frequencies >= 5) were identified by using raw contact frequencies.
ATAC-Seq data process pipline. Raw sequence reads were initially processed for removing adapter sequences and poor quality reads by fastp (v0.20.0). Subsequently, the remaining reads were mapped to the human genome hg38 using Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). PCR duplicated fragments were filtered by Picard (v2.22.8). Then, we filtered the unmapped, multi-mapped reads and mapping to the reads on chrM. FRiP (Fragments Ratio in Peaks) value was calculated by using Bedtools (v2.29.2) and awk (v4.0.2). We used deepTools (v3.5.0) to generate bigWig file with CPM normalization, and these files can be visualized in IGV. SAM files were converted to BAM format using SAMtools (v1.9) and used for peak calling. MACS2 (v2.2.4) with parameters (--nomodel --shift -100 --extsize 200 -B --keep-dup all --broad --broad-cutoff 0.1) was used to call peaks.
HTGTS-VDJ data process pipline. The raw data were filtered by fastp (v0.20.0). Trimmed reads again that nested primer and adapter primer were removed were extracted from the sequence file after quality control with Cutadapt (v1.18). Contamination, and low-quality reads were also removed. T-cell receptor beta chain V, D, and J gene identification, CDR3 sequence extraction in clean reads were performed using MiXCR (v3.0.11). The corresponding germline sequences were mapped to the reference sequences derived from international ImMunoGeneTics (IMGT) information.
Assembly: mm10
Supplementary files format and content: The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format.
Supplementary files format and content: BedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample.
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.


title: 14_KD_activity_block5_input2


title: 13_KD_activity_block5_input1


title: EACBEwt-Rag1ko-DP-ATAC-rep2


title: 12_KD_activity_block4_input3


title: 10_KD_activity_block4_input1


title: 11_KD_activity_block4_input2


title: EACBEwt-Rag1ko-DP-ATAC-rep1


title: 8_KD_activity_block3_input2


title: EACBEko-Rag1ko-DN-ATAC-rep2


title: EACBEko-DN-Trdj1-HTGTS-rep1


title: 19_KD_activity_block2_output1


title: 18_KD_activity_block1_output3


title: 6_KD_activity_block2_input3


title: EACBEwt-DN-Trdj1-HTGTS-rep2


title: 3_KD_activity_block1_input3


title: 7_KD_activity_block3_input1


title: EACBEwt-Rag1ko-DN-ATAC-rep2


title: 1_KD_activity_block1_input1


title: 4_KD_activity_block2_input1


title: EACBEwt-Rag1ko-DP-Trav21-3C-HTGTS-rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Hi-C data process pipline. For each sample, reads were obtained following quality filtering and adapter trimming using fastp (v0.20.0). Hi-C mapping, filtering, correction, and binning were performed with Hi-C-Pro (v2.11.1). The paired-end reads were mapped to the mouse mm10 genome. Self-circle ligation, dangling ends, re-ligation, and the other dumped types were filtered out with Hi-C-Pro after mapping. We generated raw contact matrices at 10 kb, 20 kb, 50 kb, 100 kb, 500 kb, 1 Mb resolutions. For raw contact matrix correction, we used the iterative correction method (ICE). The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox hic format at fragment resolution. Heatmap, differential analysis and visualization of local interactions from Hi-C data were obtained using HiTC (v1.34.0) R package. A/B compartment analysis was performed at 100 kb resolution using a publicly available script runHiCpca.pl that performs PCA analysis with HOMER (v4.10.4). Then, we used the first principal component (PC1) to predict regions of active (A compartments) and inactive chromatin (B compartments). The TAD structure (insulation) was defined by the insulation score. The matrices which were used to calculate the insulation score were normalized by ICE method for discarding the bias of raw matrices. And then, the insulation score was computed at 10 kb resolution. The script matrix2insulation.pl was used to detect TAD boundaries, with the following options: ‘--is 100001 --ids 20001 --nt 0.3 -ss 0 --im mean’. TADs were called using normalized Hi-C matrices at 10 kb resolution with insulation2tads.pl. Chromatin loops were called using Fit-Hi-C (v2.0.7). Input files of Fit-Hi-C were created by using a publicly available script hicpro2fithic.py from Hi-C-Pro. Next, loops were called using fixed-size bin resolutions from 10 kb in all cell types. Briefly, significant interaction loops (P < 0.0001 and contact frequencies > = 5) were identified through jointly modeling the contact probability using raw contact frequencies and ICE normalization vectors with the Fit-Hi-C algorithm.
3C-HTGTS data processing for pairwise chromatin interactions. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained by splitting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exact alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph files using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph files using the CPM (Counts Per Million in cis) normalization method and visualized them on the IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6).
3C-HTGTS data processing for three-way chromatin interactions. Paired-end Illumina sequencing reads were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads were extracted from the file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged at restriction enzyme cut sites into single reads with Pear (v0.9.6), then fragments with multiple MboI cut sites were split and each fragment was aligned to the enzyme-digested mm10 reference genome by Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). We extracted concordantly exact alignments using SAMtools (v1.9). We converted the final bam files into bed files using Bedtools (v2.29.2). Self-ligation and off-targeted fragments were filtered. Subsequently, we put all fragments retrieved from the same read according to the unique ID of each read on one line, then removed the continuous fragments. To create contact matrices, we extracted the first two digested fragments after the bait fragment, or a variety of combinations of three fragments were obtained by arranging all fragments from the same read. Raw contact matrices were generated at 3 kb, 5 kb, and 10 kb resolutions. For raw contact matrices correction, these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions. Similar to a Hi-C matrix, coverage was represented in a 2-dimensional matrix where each point represented the number of interactions found between two bins meaning a specific resolution. Differential analysis and visualization of local interactions from three-way interactions were obtained using the R package GENOVA (v1.0.0). Loops seen on the IGV genome browser were called using fixed-size bin resolutions from 3 kb to 10 kb. Briefly, interaction loops (contact frequencies >= 5) were identified by using raw contact frequencies.
ATAC-Seq data process pipline. Raw sequence reads were initially processed for removing adapter sequences and poor quality reads by fastp (v0.20.0). Subsequently, the remaining reads were mapped to the human genome hg38 using Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). PCR duplicated fragments were filtered by Picard (v2.22.8). Then, we filtered the unmapped, multi-mapped reads and mapping to the reads on chrM. FRiP (Fragments Ratio in Peaks) value was calculated by using Bedtools (v2.29.2) and awk (v4.0.2). We used deepTools (v3.5.0) to generate bigWig file with CPM normalization, and these files can be visualized in IGV. SAM files were converted to BAM format using SAMtools (v1.9) and used for peak calling. MACS2 (v2.2.4) with parameters (--nomodel --shift -100 --extsize 200 -B --keep-dup all --broad --broad-cutoff 0.1) was used to call peaks.
HTGTS-VDJ data process pipline. The raw data were filtered by fastp (v0.20.0). Trimmed reads again that nested primer and adapter primer were removed were extracted from the sequence file after quality control with Cutadapt (v1.18). Contamination, and low-quality reads were also removed. T-cell receptor beta chain V, D, and J gene identification, CDR3 sequence extraction in clean reads were performed using MiXCR (v3.0.11). The corresponding germline sequences were mapped to the reference sequences derived from international ImMunoGeneTics (IMGT) information.
Assembly: mm10
Supplementary files format and content: The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format.
Supplementary files format and content: BedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample.
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.
Library strategy: 3C-HTGTS


title: 9_KD_activity_block3_input3


title: MV+VEGFR2i PDTOs rep2

city: shanghai

first: shaoxuan

last: wang

address: 138 Yi xue yuan Road

institute: fudan university

data_processing:
The raw RNA-Seq PE reads were processed with Trim Galore v0.6.6 to remove adaptors and low-quality reads with the parameter “-q 23 --length 20 -e 0.1 --stringency 4” and then aligned to the human hg38 reference genome using STAR v2.7.10a with parameters “--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 2 -- outSJfilterReads Unique --quantMode GeneCounts”. All unmapped reads, low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.10 and Picard MarkDuplicates v2.25.0. Gene expression quantification was performed with featureCounts v2.0.3. For DGE analysis, we used DESeq2 v1.38.3 to get DGEs and then use clusterProfiler v4.6.2 and GO-Figure to do enrichment analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited raw counts file

source_name: Patient-derived tumor organoids

growth_protocol: Patient-derived tumor organoids (PDTOs) were cultured in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: PDTOs’ differentiation was induced by treatment of 10-days 2 μg/mL apatinib (Jiangsu Hengrui Medicine). PDTOs were fed with EGM-2 (Lonza) supplemented with 10% FBS and apatinib/DMSO for 10 days.

value: Patient-derived tumor organoids


title: EACBEwt-Rag1ko-DN-ATAC-rep1


title: Brain, Melanoma+Anti-PD1

city: Freiburg

first: Chintan

last: Chhatbar

address: Breisacher strasse 64

department: Department of Neuropathology

country: Germany

institute: Uniklinikum Freiburg

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing was carried out using in-built Illumina software on Next-seq 1000.
Barcode processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Processed data files individually contain the filtered matrix, features, and barcodes. The h5 file contains all three combined.

molecule: polyA RNA

source_name: Brain

extract_protocol:
After removal of CNS, tissues was flash frozen in liquid nitrogen and stroed at -80 C. For isolation of nuclei, briefly, CNS tissue was homogenized in Nuclei EZ lysis buffer (Millipore Sigma) and upon incubation was filtere through 70µm filter. The suspension was centrifuged at 600g for 5 min at 4°C. The pellet was washed with nuclei wash and resuspension buffer (1x PBS, 1.0% BSA, 0.2 U/μl RNase Inhibitor) and centrifuged at 600g for5min at 4°C.Following this, Nuclei were stained for DAPI, NeuN and Olig 2 markers and sorted by Flow cytometry. Nuclei were pre-gated on DAPI signal. NeuN and Olig2 negative nuclei were collcted and used as input for snRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Brain

value: Microglia, neuron, Oligodencrocytes


title: Brain, Melanoma+Isotype

description: 10x Genomics

value: Melanoma+Isotype (control)


title: EACBEwt-Rag1ko-DP-Trav21-3C-HTGTS-rep1


title: EACBEko-Rag1ko-DN-ATAC-rep1


title: 5_KD_activity_block2_input2


title: EACBEwt-Rag1ko-DN-ATAC-rep3


title: EACBEwt-Rag1ko-DN-Trav21-3C-HTGTS-rep2


title: 2_KD_activity_block1_input2


title: MV+DMSO PDTOs rep2

value: MV+DMSO


title: MV+DMSO PDTOs rep1


title: EACBEko-Rag1ko-DN-Trdv2-2-3C-HTGTS-rep3

value: Thymus


title: Neural stem cells_TFQA treatment_rep2

type: RNA

city: Tsukuba City

first: Hongyu

last: Lin

state: Ibaraki

address: Tennodai 1-1-1

department: Life and Earth Sciences

country: Japan

institute: University of Tsukuba

description: Gene expression data from neural stem cells of adult mice

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 h at 45 ºC on GeneChip Mouse Genome Array. Gene Chips were washed and stained in the Gene Atlas Fluidics Station 400.

scan_protocol: Gene Chips were scanned using the GeneChip Scanner 3000 (thermo Fisher Science, Japan).

data_processing:
The raw CEL data were normalized using the transcriptome analysis cosole (TAC) software ver.4.0.1 following the robust multichip average (RMA) algorithm (Thermo Fisher Scientific, Japan)
%result_name=Analysis_9
%array_type=Clariom_S_Mouse
%annotation=Clariom_S_Mouse.r1.na36.mm10.a1.transcript.csv

label: biotin

source_name: Brain of 6-8 weeks old adult male ICR mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.1 ug total RNA.

growth_protocol: 6-8 weeks old adult male ICR mice (Charles River, Japan) were used for the experiment.NSCs were isolated and collected from ICR mice brains using the adult brain dissociation kit (Miltenyi Biotec, Germany), Anti-Prominin-1 MicroBeads (Miltenyi Biotec, Germany) and the autoMACS pro separator (Miltenyi Biotec, Germany). The NSCs were cultured at 37 ℃ in a 95% air / 5% CO2 humidified Heracell™ VIOS 160i CO2 incubator (Thermo Fisher Scientific, USA). The medium was changed every three days to keep cells survival.

extract_protocol: Total RNA was extracted from neural stem cells using the ISOGEN kit (Nippon Gene Co. Ltd., Tokyo, Japan), following the manufacturer's instructions. Total RNA concentration was determined using the NanoDrop One / OneC (Thermo Fisher Scientific, USA).

treatment_protocol: Neural stem cells were randomly assigned to five group: control, 1 uM TCQA- treatment, 5 uM TCQA- treatment, 1 uM TFQA- treatment and 5 uM TFQA- treatment. The NSCs were seeded in 6-well plates (BD Falcon, USA) at the density of 100000 cells/well and were incubated at 37 ºC. NSCs were treated with differentiation medium without or with 1 and 5 μM of TCQA and TFQA respectively for 72 h.

value: Neural stem cells

value: ICR

tag: Sex

value: male

value: TFQA treatment


title: EACBEko-Rag1ko-DN-Trdv2-2-3C-HTGTS-rep2


title: Neural stem cells_TFQA treatment_rep4


title: EACBEwt-Rag1ko-DN-Trav21-3C-HTGTS-rep1


title: VEGFR2i PDTOs rep2


title: Neural stem cells_TFQA treatment_rep1


title: CM26 Unselected B

city: Seattle

first: Laura

last: Belmont

state: Washington

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.54.4 software followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v2.20.
Samples were demultiplexed using FASTX barcode splitter.
Reads were trimmed and aligned to the respective guide libraries using Bowtie v1.0.0, followed by tabulation of read counts using R.
Liu lab's CRISPR analysis tool, Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK), was used to perform differential guide analysis between various groups of interest. PMID: 25476604.
Supplementary files format and content: Tab delimited files with read counts for each guide sequence
Library strategy: CRISPR

growth_protocol: K562 cells were maintained in RPMI 1640 supplemented with Gluta-MAX , 7% fetal bovine serum, and 100 U/mL penicillin-streptomycin, at 37°C in 5% CO2

extract_protocol:
Genomic DNA was isolated using the QIAamp DNA Blood Mini Kit (Cat #51185, Qiagen), and gRNA sequences were amplified and prepared for Illumina sequencing via the NextSeq (genome-wide screen) or MiSeq (targeted screen) platforms.
Genomic DNA was amplified by a two-step PCR to amplify sgRNA sequences (genome-wide screen PCR1: 18 cycles PCR 2: 20 cycles, targeted sub-library screen PCR1: 12 cycles PCR2: 20 cycles). One thousand- or five hundred-fold coverage (for the genome-wide and targeted sub-library screens, respectively) of the sgRNAs were amplified with maximum of 2 ug of genomic DNA per reaction.  PCR1 reactions of each sample were pooled and either used directly for PCR2 (genome-wide screen) or first cleaned up with a QIAquick PCR Purification Kit (targeted sub-library screen) before PCR2, which include Illumina barcodes and adaptor sequences. PCR2 products were then pooled, run via gel electrophoresis, and bands were extracted and cleaned up using the QIAquick Gel Extraction Kit. Targeted sub-library samples were then purified by double-sided bead cleanup (AMPureXP, Beckman Coulter). Samples were quantified with a Qubit dsDNA HS Assay and pooled.

treatment_protocol: Sixty four million (GeCKO v2 library) or 32 million (custom sub-library) mutagenized cells were infected with single-round infectious dengue virus serotype 2 (DENV2-GFP) (Cat # RVP-201, Integral Molecular, Inc) at an MOI of 24 in the presence of 1.25 ug/mL anti-DENV2 mouse antibody DV2-70 (PMID: 20592088) by spinoculation. Two days later, to isolate ADE-resistant cell populations, GFP-negative cells were bulk sorted (Sony SH800 for genome-wide screen, Sony MA9000 for targeted sub-library screen) and allowed to recover and multiply for five days at 37°C prior to re-infection under the above conditions. After three total rounds of infection and bulk sorting, genomic DNA was harvested for deep sequencing.

value: Myeloid leukemia lymphoblast

tag: mutagenesis library

value: GeCKO v2 library

value: Uninfected cells


title: MV+VEGFR2i PDTOs rep1


title: VEGFR2i PDTOs rep1


title: CM26 Unselected A


title: EACBEko-Rag1ko-DN-Trdv2-2-3C-HTGTS-rep1


title: Neural stem cells_TCQA treatment_rep4

value: TCQA treatment


title: Neural stem cells_TFQA treatment_rep3


title: CM26 NoGFP B

value: DENV infected via ADE, GFP-


title: Neural stem cells_no treatment_rep2

value: no treatment


title: DMSO PDTOs rep2

value: DMSO


title: EACBEwt-Rag1ko-DP-Trdv2-2-3C-HTGTS-rep2

value: DP thymocytes


title: Neural stem cells_TCQA treatment_rep1

value: Brain


title: Neural stem cells_TCQA treatment_rep2


title: Neural stem cells_no treatment_rep3


title: CM26 NoGFP A


title: CM26 HiGFP B

value: DENV infected via ADE, highly GFP+


title: Neural stem cells_TCQA treatment_rep3


title: DMSO PDTOs rep1

value: Patient-derived tumor organoids


title: CM26 HiGFP A


title: Neural stem cells_no treatment_rep1


title: 39c_scp

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each donor.

source_name: brain (hippocampus)

extract_protocol:
Anterior hippocampus was dissected from fresh frozen postmortem human tissue. 100 micron coronal sections of hippocampus from fresh frozen postmortem human tissue were obtained by cryosectioning. Nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.
single-nucleus RNA-sequencing

value: brain (hippocampus)


title: MKN45-D3

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

description:
MKN45-D3
GSE184731_samsung_exp_batch.tsv

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using trimmomatic), then mapped to hg38 whole genome using STAR
Read count extraction were performed using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tsv

source_name: Stomach

growth_protocol: SW48, SW620 human colorectal cancer cells, MKN45, NCI-N87 human stomach cells, BT-20, BT-474 human breast cells were cultured in DMEM supplemented with 10% FBS and antibiotics (100 units/mL of penicillin, 100 μg/ml of streptomycin, and 0.25 μg/ml of Fungizone; Life Technologies Corp.) at 37°C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.  RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Colorectal cancer, breast cancer, stomach cell lines in condition with trametinib, afatinib, and palbocilib

value: stomach cancer cell line

tag: drug treatment

value: afatinib


title: EACBEwt-Rag1ko-DN-Trdv2-2-3C-HTGTS-rep3

value: Thymus

value: DN thymocytes


title: 38c_scp


title: MKN45-D2

description:
MKN45-D2
GSE184731_samsung_exp_batch.tsv


title: 37c_scp


title: EACBEwt-Rag1ko-DN-Trdv2-2-3C-HTGTS-rep2


title: MKN45-D1

description:
MKN45-D1
GSE184731_samsung_exp_batch.tsv


title: MKN45-C3

description:
MKN45-C3
GSE184731_samsung_exp_batch.tsv

value: control


title: 36c_scp


title: 33c_scp


title: EACBEko-Rag1ko-DN-INT2-3C-HTGTS-rep3


title: MKN45-C2

description:
MKN45-C2
GSE184731_samsung_exp_batch.tsv


title: DRG_C2

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DESeq2 was used for differential expression analysis between the control and treatments.
Assembly: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4_novel_gene
Supplementary files format and content: DRGvDMSO txt file containing read count, fpkm, log2 fold change, p-value
Supplementary files format and content: SCvDMSO txt file containing read count, fpkm, log2 fold change, p-value

organism: Rattus norvegicus

source_name: primary sensory neuron cultures

extract_protocol:
Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library
Total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 (Illumina Inc., CA, U.S.A). Sequencing was performed by Novogene.

treatment_protocol: Rat Primary Schwann cells (ScienCell, Catalog #R1700) were thawed using a 37°C water bath and resuspended into 8 mL of full RSC media (Schwann Cell Medium, Catalog #1701) and serologically pipetted into a poly-L-lysine coated T75 flask without centrifugation. Sixteen hours later, the media was changed to remove residual DMSO. Media was changed every three days until the culture was 70% confluent, after which media was changed every other day until passaging (at 90-95% confluency). Poly-L-lysine coated T25 flasks were prepared for exposure (density of 6-8 thousand cells per cm^2).  Culturing media was aspirated and replaced with media containing 1 mM DCA for 24 hours.  DRG from 3 adult male Sprague Dawley rats, were dissociated using a previously described method (Huang et al., 2005). Neurons were cultured in defined Hams F12 media in the presence of modified Bottensteins N2 supplement (Invitrogen). Media was supplemented with a cocktail of neurotrophic factors (0.3 ng/ml NGF, 5 ng/ml GDNF and 1 ng/ml NT-3) at concentrations that induce low levels of neurite outgrowth. DRG were plated into a six well plate. Three of the six wells were treated with 1 mM DCA while the other three wells acted as controls.

value: primary sensory neuron cultures

value: primary

value: neuronal

value: No treatment


title: DRG_C3


title: DRG_C1


title: MKN45-C1

description:
MKN45-C1
GSE184731_samsung_exp_batch.tsv


title: BT_474_D3

description:
BT_474_D3
GSE184731_samsung_exp_batch.tsv

source_name: Breast

value: breast cancer cell line


title: 32c_scp


title: EACBEwt-Rag1ko-DP-Trdv2-2-3C-HTGTS-rep1


title: EACBEko-Rag1ko-DN-INT2-3C-HTGTS-rep2


title: 27c_scp


title: EACBEko-Rag1ko-DN-INT2-3C-HTGTS-rep1


title: SC_DCA3

source_name: Schwann cells

value: Schwann cells

value: glial

value: 24 hour treatment to DCA


title: EACBEwt-Rag1ko-DN-INT2-3C-HTGTS-rep3


title: DRG_DCA3


title: DRG_DCA2


title: EACBEwt-Rag1ko-DN-INT2-3C-HTGTS-rep2


title: BT_474_D2

description:
BT_474_D2
GSE184731_samsung_exp_batch.tsv


title: 26c_scp


title: SC_DCA2


title: DRG_DCA1


title: 25c_scp


title: BT_474_D1

description:
BT_474_D1
GSE184731_samsung_exp_batch.tsv


title: EACBEwt-Rag1ko-DN-Trdv2-2-3C-HTGTS-rep1


title: SC_DCA1


title: 24c_scp


title: EACBEwt-Rag1ko-DN-INT2-3C-HTGTS-rep1


title: BT_474_C3

description:
BT_474_C3
GSE184731_samsung_exp_batch.tsv


title: EACBEko-Rag1ko-DN-Trdd2-3C-HTGTS-rep3


title: SC_C4


title: BT_20_D3

description:
BT_20_D3
GSE184731_samsung_exp_batch.tsv


title: SC_C3


title: SC_C1


title: A1_output_3

description: genomic and plasmid DNA

value: log phase culture


title: 21c_scp


title: EACBEwt-Rag1ko-DN-Trdd2-3C-HTGTS-rep3


title: 22c_scp


title: BT_20_D2

description:
BT_20_D2
GSE184731_samsung_exp_batch.tsv


title: 23c_scp


title: EACBEwt-Rag1ko-DN-Trdd2-3C-HTGTS-rep2


title: BT_20_C3

description:
BT_20_C3
GSE184731_samsung_exp_batch.tsv


title: 19c_scp


title: A1_output_1

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DN-Trdd2-3C-HTGTS-rep1


title: A1_output_2

description: genomic and plasmid DNA


title: 18c_scp


title: EACBEko-Rag1ko-DN-Trdd2-3C-HTGTS-rep1


title: BT_474_C1

description:
BT_474_C1
GSE184731_samsung_exp_batch.tsv


title: EACBEko-Rag1ko-DN-Trdv5-3C-HTGTS-rep3


title: EACBEko-Rag1ko-DN-Trdv5-3C-HTGTS-rep2


title: BT_20_C2

description:
BT_20_C2
GSE184731_samsung_exp_batch.tsv


title: A1_input_3

description: genomic and plasmid DNA


title: 17c_scp


title: EACBEko-Rag1ko-DN-Trdd2-3C-HTGTS-rep2


title: 16c_scp


title: BT_20_C1

description:
BT_20_C1
GSE184731_samsung_exp_batch.tsv


title: 15c_scp


title: A-NCl-N87-D3

description:
A-NCl-N87-D3
GSE184731_samsung_exp_batch.tsv


title: A1_input_1

description: genomic and plasmid DNA


title: EACBEko-Rag1ko-DN-Trdv5-3C-HTGTS-rep1


title: EACBEwt-Rag1ko-DN-Trdv5-3C-HTGTS-rep3


title: EACBEwt-Rag1ko-DN-Trdv5-3C-HTGTS-rep2


title: R1 Bulk tumor MycOETrp53KO

city: Amsterdam

first: Masami

last: Ando-Kuri

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

data_processing:
The paired-end reads were trimmed using SeqPurge and aligned with Burrows–Wheeler alignment (v.0.5.10) to GRCm38 (mm10). PCR duplicates were designated using MarkDuplicates.
For basecall recalibration and variant calling, the BaseRecalibrator and HaplotypeCaller functions from the genome analysis toolkit (GATK; v.4.2.6.0) were applied, respectively.  Three biological replicates were pooled at the sequencing time, hence, the sample ploidy upon calling was set to 6. Ensembl Variant Effect Predictor (VEP) was used to determine the impact of mutations on the function of the protein.
To filter out germline mutations and artefacts three identically processed WT mouse samples were used. From these WT samples the number of mutations with a high or moderate impact were determined per gene. Genes with more than 12 mutations total mutations in all three samples were excluded from analysis.
The tcgacompare function from the Maftools package was used to determine mutational burden of each sample
Assembly: mm10
Supplementary files format and content: vcf.gz: These files are the compressed "Variant Call Format". It includes a header with metadata. The columns include: CHROM (CHROMOSOME NAME)  POS ( position of the variation)     ID (identifier of the variation)      REF (reference base at the position)    ALT  (alternative alleles at the position)    QUAL (quality score)    FILTER (flag indicating which of a given set of filters the variation has failed or PASS) INFO (description of the variation)   FORMAT ( list of fields for describing the samples) SAMPLE (values are given for the fields listed in FORMAT)
Library strategy: Whole Exome Sequencing

source_name: liver

extract_protocol:
Macro-dissected HCC were weighted and equal amounts (≈1mg each)  from three different mice of intermediate- (n=3) and end-stage (n=3) HCC-bearing mice. Genomic DNA was extracted quantified on the Nanodrop 2000 (Thermofisher). A max of 2000 ng of double stranded genomic DNA were fragmented by Covaris shearing to obtain fragment sizes of 200-300 bp. Samples were purified using 2X Agencourt AMPure XP PCR Purification beads according to manufacturer’s instructions (Beckman Coulter, cat no A63881). The sheared DNA samples were quantified and qualified on a BioAnalyzer system using the DNA7500 assay kit (Agilent Technologies cat no. 5067- 1506).
With an input of maximum 1 μg sheared DNA, library preparation for Illumina sequencing was performed using the KAPA HTP Prep Kit (KAPA Biosystems, KK8234). During library amplification 4 PCR cycles were used to obtain enough yield for the exome capture. After library preparation, the libraries were cleaned up using 1X AMPure XP beads. All DNA libraries are analyzed on a BioAnalyzer system using the DNA7500 chips for determining the concentration. A single pool of six samples were created using 142ng of each indexed sample. The pool treated with Mouse COT (Invitrogen, ref 18440-016) and xGen universal Blocking Oligo’s (IDT, cat no 1075475) before being captured with a SeqCap ES Share Developer Mouse probe (Roche, ref 08333025001), following the Hypercap Target Enrichment (Roche, ref 08286370001) with the probe incubation for 20 hours. After capture the pool was amplified using 10 PCR cycles and purified with Ampure XP beads. The pool was diluted to a final concentration of 10nM and subjected to paired-end 75bp sequencing on an Illumina Nextseq 550, according to manufacturer’s instructions.

value: liver

value: Myc overexpression Trp53 knockout

tag: time

value: End-stage

tag: disease state

value: cancer


title: 14c_scp

value: brain (hippocampus)


title: A-NCl-N87-D2

description:
A-NCl-N87-D2
GSE184731_samsung_exp_batch.tsv

value: stomach cancer cell line

value: afatinib


title: R1 Bulk tumor MycOEPtenKO

value: Myc overexpression Pten knockout


title: A-NCl-N87-D1

description:
A-NCl-N87-D1
GSE184731_samsung_exp_batch.tsv


title: EACBEwt-Rag1ko-DN-Trdv5-3C-HTGTS-rep1

value: Thymus

value: DN thymocytes


title: 13c_scp


title: 12c_scp


title: R1 Bulk tumor NrasG12VPtenKO

value: NrasG12V overexpression Pten knockout


title: A-NCl-N87-C3

description:
A-NCl-N87-C3
GSE184731_samsung_exp_batch.tsv

value: control


title: A1_input_2

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DN-TEA-3C-HTGTS-rep3


title: R1 Bulk tumor NrasG12VPtenKO_int

value: Intermediate-stage


title: EACBEwt-Rag1ko-DN-TEA-3C-HTGTS-rep2


title: R1 Bulk tumor NrasG12DPtenKO

value: NrasG12D overexpression Pten knockout


title: 11c_scp


title: A-NCl-N87-C1

description:
A-NCl-N87-C1
GSE184731_samsung_exp_batch.tsv


title: 10c_scp


title: A-NCl-N87-C2

description:
A-NCl-N87-C2
GSE184731_samsung_exp_batch.tsv


title: R1 Bulk tumor NrasG12DPtenKO_int


title: 1c_scp


title: 2c_scp


title: 620t2_S17

description:
620t2_S17
GSE184731_samsung_exp_batch.tsv

source_name: Colon

value: colorectal cancer cell line

value: trametinib


title: C4_output_3

description: genomic and plasmid DNA

value: log phase culture


title: C4_output_2

description: genomic and plasmid DNA


title: PIAS1KO_TNF3

city: Rochester

first: Jessica

last: Ciesla

state: New York

address: 601 Elmwood ave

department: Biochemistry

institute: University of Rochester

data_processing:
Data was formatted with bcltofastq-2.19.1
Sequence reads were cleaned  with fastp 0.23.1
Sequence reads were mapped to the human reference genome (GRCh38 + Gencode-38 annotation) using STAR_2.7.9a.
DESeq2-1.14.1 within R-3.3.2 was used to perform data normalization and differential expression analysis with a false-discovery rate adjusted p-value threshold of 0.05 on each set of raw expression measures.
Assembly: GRCh38 + Gencode-38 annotation
Supplementary files format and content: Excel file containing gene names, transcript type, base mean, log2foldchange, stat, pvalue, and padj

growth_protocol: MRC5 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were washed 1x with 3 mL PBS then RNA harvested in 1 mL Trizol
First, 5 µg total RNA was subjected to poly(A) mRNA isolation according to the manufacturer’s protocols (NEB, #E7490). Then, 10 µL of the eluted mRNA was mixed with 1 µL 100 µM Genomic Adaptor_6N primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN-3’) and 2 µL of 5 mM AzNTP (Baseclick, #BCT-25~ -28)/dNTP mixture in a 1:35 ratio.  The mixture was then heated at 65°C/5min and snap-cooled on ice for 3min. Then, the reverse transcription was carried out using SuperScript III (ThermoFisher, #18080093). In brief, 7 µL master mix containing 4 µL 5X Superscript First Strand Buffer, 1 µL 0.1 M DTT, 1 µL RNaseOUT (ThermoFisher, #10777019), and 1 µL Superscript III was mixed with the RNA sample. Heating was performed as follows: 25°C/10 min, 50°C/40 min, and 75°C/15 min sequentially in thermocycler followed by RNase H (ThermoFisher, #AM2293) treatment using 1 U per reaction for 37°C/30 min and then 80°C/10 min. The cDNA was then purified using Sera-Mag Speedbeads (Cytiva, #65152105050250). Speedbeads working solution was made by washing 1 mL beads slurry twice in 1XTE buffer and then resuspending in 50 mL of 1XTE buffer containing 9 g PEG-8000, 1 M NaCl, and 0.05% Tween-20. Speedbeads, 1.8x reaction volume, was mixed with cDNA followed by a 5 min incubation at room temperature. The beads were then pelleted using a magnetic bead collector and the supernatant was discarded. Two washes with 80% ethanol were performed while the beads were pelleted on the magnet. The beads were then dried, and the cDNA was eluted by resuspending the beads in 22 µL 50 mM HEPES pH 7.2 for 2 min at room temperature. Then, 20 µL of the cDNA was mixed with 11 µL Click Mix and 4 µL of 5 µM UMI-click-adapter (5’-Hexynyl-NNNNNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3’, HPLC purified). To activate the reaction, 4 µL of 50 mM vitamin C and 1 µL of Click Catalyst were pre-mixed before being added into the cDNA solution for 60min room temperature incubation in the dark. Clicked cDNA was then purified in the same manner as post-RT purification except eluted in 22 µL of 10 mM Tris pH 7.4. Then, half of eluted cDNA was subjected to PCR amplification with indexing primers i5 (5’-AATGATACGGCGACCACCGAGATCTACAC[Index]ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’) and i7 (5’-CAAGCAGAAGACGGCATACGAGAT[Index]GTGACTGGAGTTCAGACGTGTGCTCTTCCGAT*C-3’). Both primers have a phosphorothioate bond added at the 3’ end (denoted as *) to increase stability. The PCR reaction was carried out in the volume of 50 µL including 25 µL 2X OneTaq Master Mix (NEB, #M0482), 2 µL of 5 µM i5 and i7 each, and cDNA in H2O with a total of 15 cycles of amplification given the 5 µg input RNA. The program was run at 94°C/4 min; 53°C/30 sec; 68°C/10 min; 15X [94°C/30 sec, 53°C/30 sec; 68°C/2 min]; 68°C/5 min; hold at 4°C. The library was then purified and size-selected with Speedbeads.  In brief, 45 µL beads (0.9X volume of PCR reaction) were mixed with the reaction to remove larger fragments. The supernatant was collected and mixed with 10 µL beads (0.2X volume of PCR reaction) to remove smaller fragments and primer dimers. Two washes with 100% ethanol were then performed while the beads were on the magnet. Beads were dried before being resuspended in 12 µL of 10 mM Tris pH 7.4. The library was then collected and subjected to quality control on Agilent 2200 TapeStation
Poly(A)-ClickSeq (PAC-seq) library preparation

treatment_protocol: Cell cycles were synchronized via serum free media for 24 hours. Cells were treated with vehicle or TNFα (3 ng/mL) for 24 hours.

value: Fibroblast

value: PIAS1-targeted sgRNAs

value: TNFa (3 ng/mL)


title: 620t1_S16

description:
620t1_S16
GSE184731_samsung_exp_batch.tsv


title: EACBEko-Rag1ko-DN-Ea-3C-HTGTS-rep1


title: C4_output_1

description: genomic and plasmid DNA


title: EACBEko-Rag1ko-DN-Ea-3C-HTGTS-rep3


title: PIAS1KO_TNF2


title: 620p3_S15

description:
620p3_S15
GSE184731_samsung_exp_batch.tsv

value: palbociclib


title: EACBEwt-Rag1ko-DN-Ea-3C-HTGTS-rep3


title: C4_input_3

description: genomic and plasmid DNA


title: PIAS1KO_TNF1


title: 620p2_S14

description:
620p2_S14
GSE184731_samsung_exp_batch.tsv


title: 620p1_S13

description:
620p1_S13
GSE184731_samsung_exp_batch.tsv


title: EACBEko-Rag1ko-DN-Ea-3C-HTGTS-rep2


title: C4_input_2

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DN-Ea-3C-HTGTS-rep2


title: PIAS1KO_vehicle3


title: EACBEwt-Rag1ko-DN-TEA-3C-HTGTS-rep1


title: EACBEwt-Rag1ko-DN-Ea-3C-HTGTS-rep1


title: C4_input_1

description: genomic and plasmid DNA


title: PIAS1KO_vehicle2


title: 620c3_S12

description:
620c3_S12
GSE184731_samsung_exp_batch.tsv


title: 620t3_S18

description:
620t3_S18
GSE184731_samsung_exp_batch.tsv


title: C3_output_3

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DP-Eb-3C-HTGTS-rep2

value: DP thymocytes


title: 620c2_S11

description:
620c2_S11
GSE184731_samsung_exp_batch.tsv


title: PIAS1KO_vehicle1


title: EACBEwt-Rag1ko-DP-Eb-3C-HTGTS-rep1


title: ntg_TNF3

value: non-targeting guide (ntg)


title: C3_output_2

description: genomic and plasmid DNA


title: 620c1_S10

description:
620c1_S10
GSE184731_samsung_exp_batch.tsv


title: C3_output_1

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DN-Eb-3C-HTGTS-rep3


title: 48t3_S9

description:
48t3_S9
GSE184731_samsung_exp_batch.tsv


title: C3_input_3

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DN-Eb-3C-HTGTS-rep1


title: C3_input_2

description: genomic and plasmid DNA


title: ntg_TNF1


title: 48t1_S7

description:
48t1_S7
GSE184731_samsung_exp_batch.tsv


title: C3_input_1

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DP-Trbv5-3C-HTGTS-rep2


title: ntg_vehicle3


title: ntg_vehicle2


title: 48p3_S6

description:
48p3_S6
GSE184731_samsung_exp_batch.tsv


title: ntg_vehicle1


title: 48p2_S5

description:
48p2_S5
GSE184731_samsung_exp_batch.tsv


title: EACBEwt-Rag1ko-DN-Trbv5-3C-HTGTS-rep2


title: C2_output_3

description: genomic and plasmid DNA


title: 48p1_S4

description:
48p1_S4
GSE184731_samsung_exp_batch.tsv


title: C2_output_2

description: genomic and plasmid DNA


title: ntg_TNF2


title: breast cancer cells, TAZ-siRNA, rep4

city: Daegu

first: HongSeok

last: Choi

address: 680, Gukchaebosang-ro, Jung-gu

department: School of medicine

institute: Kyungpook national university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes read counts for each samples
Supplementary files format and content: tab-delimited text file includes FPKM and TPM values for each samples

source_name: Breast; Mammary gland

growth_protocol: Human breast cancer cell line [MDA-MB-231 (HTB-26)] was purchased from the American Type Culture Collection (ATCC, Manassas, VA). MDA-MB-231 cells were cultured in low glucose DMEM (5.5 mM glucose) at 37℃. Medium contained 0.1% penicillin-streptomycin and 10% heat-inactivated fetal bovine serum (FBS). Cells were incubated in a humidified incubator at 37℃ and 5% CO2.

extract_protocol:
MDA-MB-231 cells were detached using trypsin/EDTA, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer’s protocols

treatment_protocol: MDA-MB-231 cells were seeded on 6-well plates and transfected with small interfering RNA (siRNA) specific for TAZ, using siGENOME human WWTR1 siRNA (M-016083-00-0010, Dharmacon; Horizon Discovery, Cambridge, UK) and DharmaFECT4 (T-2004-03, Dharmacon; Horizon Discovery, Cambridge, UK).

value: Breast; Mammary gland

value: epithelial cell

value: breast cancer

value: TAZ knockdown


title: breast cancer cells, TAZ-siRNA, rep5


title: 48c3_S3

description:
48c3_S3
GSE184731_samsung_exp_batch.tsv


title: EACBEwt-Rag1ko-DN-Trbv5-3C-HTGTS-rep1

value: Thymus

value: DN thymocytes


title: BT_474_C2

description:
BT_474_C2
GSE184731_samsung_exp_batch.tsv

value: breast cancer cell line

value: control


title: C2_output_1

description: genomic and plasmid DNA


title: 48t2_S8

description:
48t2_S8
GSE184731_samsung_exp_batch.tsv

value: colorectal cancer cell line


title: EACBEwt-Rag1ko-DP-Trbv12-2-3C-HTGTS-rep2


title: C2_input_3

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DN-Eb-3C-HTGTS-rep2


title: EACBEwt-Rag1ko-DP-Trbv5-3C-HTGTS-rep1


title: 48c2_S2

description:
48c2_S2
GSE184731_samsung_exp_batch.tsv


title: breast cancer cells, control-siRNA, rep5

value: WT


title: C2_input_2

description: genomic and plasmid DNA

value: log phase culture


title: breast cancer cells, TAZ-siRNA, rep3


title: C2_input_1

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DP-Trbv12-2-3C-HTGTS-rep1


title: breast cancer cells, control-siRNA, rep4


title: 48c1_S1

description:
48c1_S1
GSE184731_samsung_exp_batch.tsv


title: SW620_D3

growth_protocol: SW48, SW620 human colorectal cancer cells were cultured in DMEM supplemented with 10% FBS and antibiotics (100 units/mL of penicillin, 100 μg/ml of streptomycin, and 0.25 μg/ml of Fungizone; Life Technologies Corp.) at 37°C in 5% CO2.

treatment_protocol: Colorectal cancer cell lines in condition with trametinib

value: trametinib


title: C1_output_3

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DN-Trbv12-2-3C-HTGTS-rep3


title: EACBEwt-Rag1ko-DN-Trbv12-2-3C-HTGTS-rep2


title: breast cancer cells, control-siRNA, rep3


title: EACBEwt-Rag1ko-DN-Trbv12-2-3C-HTGTS-rep1


title: C1_output_2

description: genomic and plasmid DNA


title: SW620_D2


title: PH--IP (D)

city: Xi’an

first: wang

middle: gui

last: hu

address: No.157#, The West 5th Road

department: The Second Affiliated Hospital

institute: Xi'an Jiaotong University

data_processing:
Reads were aligned to Human genome (HG19) using BOWTIE software (V2.1.0).
peak detection by MACS V1.4.2 (Model-based Analysis of ChIP-Seq) software. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model (Cut-off p-value=10-3.
Contains the nearest gene annotation of the peaks using the newest UCSC RefSeq database
Read count extraction and normalization were performed using CLC genomic benchwork
Contains all the ChIP-seq signal densities in WIG format for visualizing the ChIP-seq profiles of each sample in UCSC Genome Browser (*.wig files).
Assembly: hg38
Supplementary files format and content: The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database (This data was in EXCEL format, it can be found from the Peaks_Annotation.xls file)
Supplementary files format and content: Human_ChIP-Sequencing_Summary_Report is saved in a word file

source_name: Spleen

growth_protocol: Spleen macrophages are sorted by CD11b+magnetic beads,The Chip-IP use Magna ChIP™ A/G (Catalog # 17-10085)

extract_protocol:
The sorted cells were lysed using ultrasound and broken into 150-200bp fragments，The mapped 150 bp reads represent enriched DNA fragments by ChIP experiment.  using a  Magna ChIP™ A/G (Catalog # 17-10085) reagent kit；
Sequencing Library Preparation，DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina), following the manufacturer’s instructions. ~200-1500 bp fragments were size selected using AMPure XP beads. The final size of the library was confirmed by Agilent 2100 Bioanalyzer.

value: Spleen

value: macrophage

tag: chip-antibody

tag: condition

value: Portal hypertension combined with hypersplenism (PHcH)


title: C1_output_1

description: genomic and plasmid DNA


title: PH--input (D)


title: SW620_D1


title: SW620_C3


title: C1_input_3

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DP-DpnII-HiC-rep1

description:
EACBEwt-Rag1ko-DP-DpnII-HiC.allValidPairs
EACBEwt-Rag1ko-DP-DpnII-HiC.allValidPairs.hic
bed, bedgraph, bw files containing data for all replicates are available on rep 1 sample.

value: DP thymocytes


title: Nor1--IP (A)

value: Spleen-injury


title: EACBEko-Rag1ko-DN-DpnII-HiC-rep3

description:
EACBEko-Rag1ko-DN-DpnII-HiC.allValidPairs
EACBEko-Rag1ko-DN-DpnII-HiC.allValidPairs.hic
bed, bedgraph, bw files containing data for all replicates are available on rep 1 sample.


title: C1_input_2

description: genomic and plasmid DNA


title: EACBEwt-Rag1ko-DP-DpnII-HiC-rep2


title: SW620_C1


title: SW48_D3


title: C1_input_1

description: genomic and plasmid DNA


title: EACBEko-Rag1ko-DN-DpnII-HiC-rep1


title: BM HD 2

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
scRNA-seq libraries were sequenced using a NovaSeq6000 SP 100-cycle flow cell (Illumina). scATAC-seq libraries were sequenced using a NextSeq 500 150-cycle flow cell (Illumina).
For scATAC-seq, reads were aligned to the  human genomes (hg38), and peaks were called using the cellranger-atac count pipeline. Individual samples were merged using the cellranger-atac pipeline to generate the transcription factor activity matrix.
For scRNA-seq,  raw reads were aligned to the  human genomes (hg38), and the digital expression matrix was generated using cellranger count.
Assembly: hg38
Supplementary files format and content: Transcription factor activity matrix for scATAC-seq
Supplementary files format and content: Raw count expression matrix for scRNA-seq.

source_name: Bone Marrow

extract_protocol:
BM MNCs were isolated from each sample using the standard gradient separation approach with Ficoll-Paque PLUS (GE Healthcare Lifesciences, Marlborough, MA).
For scATAC-seq, the scATAC Low Cell Input Nuclei Isolation protocol (10X Genomics) was used to isolate nuclei from FACS-purified cells. The trypan blue exclusion assay was performed to check for intact nuclei. The remaining extracted nuclei were used for the consecutive steps of the scATAC-seq library preparation protocol following 10X Genomics guidelines. Equal molar concentrations of uniquely indexed samples were pooled together. For scRNA-seq, sample preparation and sequencing were performed at MD Anderson Cancer Center’s Advanced Technology Genomics Core. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific). Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10X Genomics, Pleasanton, CA), and single cells were lysed and barcoded for reverse transcription. Equal amounts of each uniquely indexed sample library were pooled together.

value: Bone Marrow

value: BM MNCs

tag: disease

value: Healthy Control


title: BM HD 3


title: EACBEko-Rag1ko-DN-DpnII-HiC-rep2


title: SW620_C2


title: SW48_D2


title: EACBEwt-Rag1ko-DN-DpnII-HiC-rep3

description:
EACBEwt-Rag1ko-DN-DpnII-HiC.allValidPairs
EACBEwt-Rag1ko-DN-DpnII-HiC.allValidPairs.hic
bed, bedgraph, bw files containing data for all replicates are available on rep 1 sample.


title: B3_output_2

description: genomic and plasmid DNA


title: BM HD 1


title: SW48_D1


title: B3_output_1

description: genomic and plasmid DNA


title: SK-N-BE(2)_shControl_rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma cells

value: shControl


title: SW48_C3


title: SK-N-BE(2)_shControl_rep1


title: B3_input_3

description: genomic and plasmid DNA

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Assembly: NA
Supplementary files format and content: Variant growth rates table: Tabular format; contains the raw counts and dimsum fitness estimates per replicate and aggregated and their corresponding errors.
Library strategy: Amplicon-seq


title: SW48_C2


title: EACBEwt-Rag1ko-DN-DpnII-HiC-rep1

extract_protocol:
For Hi-C, We performed with DN thymocytes from 3-4 Rag1-/- or EACBE-/- Rag1-/- mice per experiment or 10 million CD3-stimulated DP thymocytes from Rag1-/- mice per experiment. In brief, cells were crosslinked with a final concentration of 1% formaldehyde at room temperature for 10 min and quenched with glycine (final concentration 0.125 M) on ice for 5 min. Crosslinked cells were lysed and followed by adding 150U DpnII(New England Biolabs,R0543L) to digest the chromatin overnight at 37℃ with gently shaking. DpnII was inactivated at 65℃ for 20 min, DNA fragment ends were biotinylated with biotin-dATP, and the sample was diluted, and proximity ligated for 4-6 hours at room temperature. Crosslinked DNA was reversed by addition of SDS, proteinase K, and NaCl, and allowed to incubate overnight at 68℃. DNA was purified by phenol/chloroform, followed by isopropanol precipitation, and resuspended in 100ul 10Mm Tris-HCl,pH:8.0. DNA was treated with T4 DNA polymerase to remove unligated biotinylated ends and sheared to 300-500bp by sonication subsequently, the ligated junctions were pulled down with Dynabeads MyOne Streptavidin C1 magnetic beads. End-repair, dA-tailing, adapter-ligation, and PCR amplification with P5 and P7 prime were performed on biotinylated DNA fragments bound to beads. After purification, libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
For 3C-HTGTS, mouse thymus and liver were removed, cells were filtered through nylon mech.10 million cells were cross-linked with 1% formaldehyde. Cell were lysed and digest with 200U MboI overnight at 37°C. The sample was ligated with T4 DNA ligase overnight at 16°C. Crosslinks were reversed by Proteinase K and RNase A prior to DNA extraction with 1:1 phenol-chloroform and precipitation with ethanol. The 10ug 3C DNA was sonicated to 300-500bp and was linearly amplified with a biotinylated primer. The biotin-labeled single-stranded DNA products were enriched with streptavidin C1 beads, and followed by 3’ ends ligation with the bridge adaptor. The adaptor-ligated products were amplified via nested PCR using a nested primer and an adaptor-complementary primer.The detailed primers used in this study are also listed in Supplementary information, Table S1.  And a final PCR for another 5-10 cycles with P5 and P7 was performed. After purification of the PCR products, the final libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
For ATAC-Seq, a total of 5 × 104 cell pellets were washed once with cold PBS, cells lysed on ice for 3 min in 50 μL ice-cold Lysis Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% TWEEN 20, and 0.01% Digitonin in DEPC H2O), resuspended in 1 mL ice-cold RBS-Wash (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% TWEEN 20) and pelleted at 4 °C at 500 × g for 5min. Tagmentation was performed in 1 × Tagmentation Buffer (10 mM Tris pH 7.4, 5 mM MgCl2, 10% DMF, 33% PBS, 0.1%TWEEN 20, and 0.01% Digitonin) using 100 nM Tn5 Transposase for 30 min at 37 °C. Immediately, Free DNA was purified using QIAquick PCR Purification Kit (QIAGEN, 28106, GERMANY) according to the manufacturer’s instructions. And a final PCR for 10-15 cycles of amplification with P5 and P7 primers was performed. After purification, libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
For HTGTS-VDJ, DNA was extracted by DNA Isolation Mini Kit (Vazyme, DC102) and sonicated to about 500bp on a Qsonica Bioruptor Sonicator. Sonicated DNA was linearly amplified with a biotinylated primer  that anneals to sites of interest. Biotin-labeled single stranded DNA products were enriched with streptavidin C1 beads (65001, Thermo Fisher Scientific), and followed by 3' end ligation with the bridge adapter. The adapter-ligated products were amplified through nested PCR using a nested primer and an adapter-complementary primer . The detailed primers used in this study are also listed in Supplementary information, Table S2. And a final PCR for another 10-12 cycles of amplification with P5 and P7 primers was performed. After purification, libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
Construction of libraries were described as the above extract protocol

value: Thymus

value: DN thymocytes


title: B3_input_2

description: genomic and plasmid DNA


title: BT_20_D1

description:
BT_20_D1
GSE184731_samsung_exp_batch.tsv

value: breast cancer cell line

value: afatinib


title: SW48_C1

value: colorectal cancer cell line

value: control


title: SK-N-BE(2)_shCDK5RAP3_rep2


title: Liver, oral, 14 days, ST_3

city: Guiyang

first: Gongzhen

last: Chen

address: Dongqing South-Road 4#

institute: Guizhou University of Traditional Chinese Medicine

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: Mus musculus
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: liver tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: liver tissue

value: water extract of Emilia sonchifolia


title: B3_input_1

description: genomic and plasmid DNA

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 1 mL of DNA extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris-HCl pH8, 1mM EDTA pH8), and freeze-cracked by liquid nitrogen freezing followed by 62ºC incubation for 10 min in a water bath, twice. Subsequently, 1 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.1 mL of NaOAc 3M and 2.2 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was vacuum-dried. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (30 μL of QIAEX II beads). The samples were washed twice with PE buffer and eluted in 200 μL of 10 mM Tris-HCI buffer, pH 8.5.
Plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids. We performed 2 consecutive PCR reactions for each sample. The first PCR (PCR1) is used to amplify the amplicons for sequencing, to add a part of the Illumina sequencing adaptors to the amplicon and to increase nucleotide complexity for the sequencing reaction by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) is used to add the remainder of the Illumina adaptor and to add demultiplexing indexes (dual-indexed). The amplicon libraries were run on a 2% agarose gel for quality control and quantification, and were pooled by block and size selected on a 2% agarose gel. Bands were purified using QIAEX II Gel Extraction Kit (QIAGEN) and using 30uL of QIAEX II beads for each sample. The purified amplicons were subjected to Illumina 150bp paired-end NextSeq sequencing at the CRG Genomics Core Facility.

value: log phase culture


title: Liver, oral, 14 days, ST_1


title: circRNA long reads sequencing

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

description:
RNase R-treated RNA
nanopore long-read sequencing, which combines rolling circular reverse transcription and nanopore sequencing

data_processing:
de novo circRNA identification and reconstruction: Raw reads were aligned with minimap2, VZV reference genomes. CIRI-long was used for circRNA calling.
Assembly: VZV pOka strain, containing GFP and luciferase coding genes
Supplementary files format and content: 1,The ID of human or VZV circRNAs, 2 The number of circRNA juction reads

source_name: SH-SY5Y cells

extract_protocol:
Cells were harvested at 24 and 48 h post-infection with TRIzol RNA Isolation Reagents (Invitrogen, USA, Catalog number: 15596026). Chloroform extraction and isopropanol precipitation methods were used to isolate RNA from samples.
Ribosome-depleted and RNase R-treated RNA samples were used for library preparation and nanopore long-read sequencing, which combines rolling circular reverse transcription and nanopore sequencing.

treatment_protocol: SH-SY5Y or ARPER-19 cells were seeded at a density of 106 in 6-well plate (Corning) 12 h prior to inoculation with log106 PFU of pOka.

value: SH-SY5Y cells

value: VZV


title: SK-N-BE(2)_shCDK5RAP3_rep1


title: DMSO_E

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DESeq2 was used for differential expression analysis between the control and treatments.
Assembly: homo_sapiens_grch38_p12_gca_000
Supplementary files format and content: BPSvDMSO excel files containing read count, fpkm, log2 fold change, p-value, BPFvDMSO excel files containing read count, fpkm, log2 fold change, p-value

source_name: neuronal

extract_protocol:
Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA samples with a measured 28S/18S > 1 and RNA integrity number (RIN) ≥ 7 were used for RNAseq library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library"
Total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 (Illumina Inc., CA, U.S.A). Sequencng was performed by Novogene.

value: neuronal


title: PANC-1 cells, shControl, biol rep 3

city: Beijing

first: Chengqi

last: Yi

address: Yiheyuan Road

department: School of Life Sciences

institute: Peking University

data_processing:
Adaptor and low-quality reads were trimmed using cutadapt
FastQC was used for quality control of the sequencing data.
Reads were aligned to the human (GRCh38) reference genome using STAR (v2.7.2b)
Mapped reads were assigned to genes using featureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for all samples

growth_protocol: H1299 and PANC-1 were maintained in DMEM(CORNING), supplemented with 10% FBS(PAN) in a 37℃ incubator with 5 % (v/v) CO2.

extract_protocol:
Total RNA was isolated from cultured cells using Trizol (Invitrogen, 10296010).
After quality check, samples were sent to library preparation using the NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530L, NEB, USA).

value: pancreatic adenocarcinoma cells

value: WT


title: DMSO_C


title: Liver, oral, 14 days, CK_3