title: E6_D8_PFHxA_2_1

address: 双清路18号林业大学北门

value: Blastocyst

value: Multiple cells differentiated from H22

value: PFHxA 10 μM


title: SU-pcGBM2

status: Public on Apr 28 2024

type: SRA

city: Utrecht

first: Konstantinos

last: Vazaios

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

library_source: transcriptomic

data_processing:
cutadapt v2.10 used for sequence trimming
Trimmed sequences were mapped to human GRCh38.p13 reference based on Burrow-Wheeler Transformation using STARv2.5.4. default settings
Mapped reads indexed and sorted into BAM with samtools v1.10
Further processing and normalization of counts was performed using EdgeR (Ensemble ids aggregated into unique Gene symbols, raw counts <10 in less than 70% or total gene counts in all samples <15 were removed before TMM normalization and CPM calculation)
Assembly: hu GRCh38.p13
Supplementary files format and content: tab-delimited text file includes log2-transformed CPMs for each sample used for the discovery of correlating genes
Supplementary files format and content: tab-delimited text file includes log2-transformed CPMs for each sample used for validation of correlating genes

molecule: polyA RNA

organism: Homo sapiens

source_name: High Grade Glioma

extract_protocol:
RNA was harvested using the miRvana™ miRNA isolation kit (Ambion)
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420S/L)

tag: cell type

value: High Grade Glioma

tag: genotype


title: JHH-DIPG-01


title: E6_D8_PFHxS_1_1

city: 北京市

first: Renjun

last: Yang

state: 北京

address: 双清路18号林业大学北门

country: China

institute: RCEES

data_processing:
BGI MGI2000
RNA concentration, RNA integrity number and 28S/18S ratio were detected with an Agilent 2100 instrument and Agilent RNA 6000 nano Reagents Part 1, to determine its quality. Qualified samples were sequenced on an MGISEQ-2000 platform. Raw reads with low-quality base ratios exceeding 20% or unknown base ratios exceeding 5% or containing sequencing adapter were removed with the SOAPnuke.
Clean reads were mapped to the reference genome and the reference coding gene set using HISAT2 and Bowtie2 respectively.
Gene expression levels were calculated with RSEM and differential expression analysis was performed with DESeq2.
Genes with fold change  greater than 2 and FDR (false discovery rate) less than or equal to 0.001 were considered to be differentially expressed genes (DEGs).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: CSV file with mRNA expression value for each sample

molecule: total RNA

source_name: Blastocyst

growth_protocol: H1 hESCs were cultured in mTeSR Plus medium. NNE differentiation was induced by repalcing homemade Essential 6 (E6) medium containing 10 ng/mL BMP4, 10 μM SB431542 and 10 μM SU5402 for 2 days, then from day 3 to day 10, the medium remained the same as on day 0, but with a decreased concentration of BMP4 (5 ng/mL) added to sustain the differentiation process. Global monolayer differentiation was initiated by supplying homemade Essential 6 (E6) medium to H1 hESCs and keeping culturing for 8 days or 16 days.

extract_protocol: Total RNA extraction was obtained with the TRNzol Reagent for all samples according to the manufacturers’ instructions. 2 μg of total RNA was used to construct RNA-seq libraries.

treatment_protocol: Add PFOA, PFHxA, PFBA, PFOS, PFHxS, and PFBS with 10 μM concentration at the very beginning of differentiation.

tag: tissue

tag: cell line

value: Multiple cells differentiated from H23

value: WT

tag: treatment

value: PFHxS 10 μM


title: PANC1PSA_PS03ULAPANC1PSAS229_TTGGCGTAC_L003_R1_001

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

country: USA

institute: Columbia University

data_processing:
The PLATE-Seq FASTQ files were pseudoaligned to the GRCh38 human transcriptome (mRNA & ncRNA) and gene expression was quantified using kallisto (version 0.44.0), tximport package (Soneson et al., 2015), and biomaRt package (Durinck et al., 2009).
The gene expression was quantified as both raw counts (i.e. sequencing fragments per genomic locus) and transcripts per million (i.e. sequencing fragments per genomic locus normalized for transcript/gene length and sample sequencing depth).
Assembly: GRCh38
Supplementary files format and content: Table containing reads count of each gene (row) in each sample (column)

source_name: PDA tumor

growth_protocol: Panc1 and Aspc1 pancreatic cancer cells were cultured in white 96-well tissue culture-treated plates at optimized density, in 100 μl of Dulbecco's Modified Eagle Medium (DMEM) media supplemented with 10% fetal bovine

extract_protocol:
After 24 h of incubation, the plates were treated with following drugs: RAF inhibitors – Sorafenib, Dabrafenib, RAF709, PLX8394, GDC-0879; MEK inhibitors – Trametinib, Cobimetinib, Binimetinib, Selumetinib, Rafametinib; and ERK inhibitors – SCH772984, Ulixertinib, AZD0364, Ravoxertinib. Each drug was dosed at the concentration at which the cells were 80% viable after 48 h of treatment. After 24 h of treatment, the medium was replaced with 100 ml of FBS supplemented with 10% DMSO and the plates were frozen at −80 °C prior to PLATE-Seq.
Detailed protocol for preparation of the automated PLATE-SEQ experiment was described by Bush et al. (Bush et al., 2017).
Samples were sequenced using PlateSeq approach

value: PDA tumor

value: Human PDA cell line

value: Binimetinib


title: PANC1PSA_PS03ULAPANC1PSAS221_TCGATATGC_L003_R1_001

value: Refametinib


title: PANC1PSA_PS03ULAPANC1PSAS220_TTCTTCCCT_L003_R1_001

value: Dabrafenib


title: CHLA-ATRT-266

source_name: Atypical teratoid/rhabdoid tumor

value: Atypical teratoid/rhabdoid tumor

value: MYC


title: E6_D8_PFHxA_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H21


title: PANC1PSA_PS03ULAPANC1PSAS228_AACGTGACG_L003_R1_001

value: DMSO


title: SU-DIPG-XXI


title: E6_D8_PFBS_2_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H20

value: PFBS 10 μM


title: VUMC-DIPGG-G


title: E6_D8_PFBS_1_1

address: 双清路18号林业大学北门

value: Blastocyst

value: Multiple cells differentiated from H19


title: E6_D8_PFBA_2_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H18

value: PFBA 10 μM


title: PANC1PSA_PS03ULAPANC1PSAS216_CAGAACCAC_L003_R1_001


title: PANC1PSA_PS03ULAPANC1PSAS219_TGTTCATCG_L003_R1_001

value: Ulixertinib


title: ATAC_U2OS_WT_SOX2_CellLine_biol rep1

city: Beijing

first: Wulan

last: Deng

address: Beijing Haidian District Yiheyuan Road #5

department: BIOPIC

institute: Peking University

library_source: genomic

data_processing: Nova-seq output paired ATAC-seq raw reads quality control performed with FastQC (version 0.10.1)  ATAC-seq raw reads were trimmed by trim_galore function with --paired mode and default parameters.  ATAC-seq reads were aligned to hg38 genome with bowtie2 v2.4.4 in the following options: bowtie2 -t -q -p 10 -N 1 -L 25 -X 700. Resulted sam files were converted to bam with samtools (v.0.1.18)  ATAC-seq bam files of the two replicates were called peaks individually using MACS2 with default parameters. For each group, peak files of the two replicates were used to call peaks by the IDR method with parameter: idr --input-file-type narrowPeak --rank p.value -soft-idr-threshold 0.1  The bigwig files of ATAC-seq data were generated using deeptools (v2.4.1) kit with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeUsing RPKM --ignoreDuplicates.  Assembly: hg38  Supplementary files format and content: Bigwig -- visualization of track information  Supplementary files format and content: NarrowPeak -- Binding Sites for ChIP-seq/ Opening Site for ATAC-seq

molecule: genomic DNA

source_name: cell line

growth_protocol: U2OS cells were cultured with 10% FBS with DMEM media

extract_protocol:
U2OS cells were seeded in 6 cm plates and treated with Doxycycline (500 ng/ml) for 4 days. 50,000 viable cells were collected by centrifugation at 500g for 10 min at 4 °C.  Cell pellets were lysed in 50 ul RSB Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin) on ice for 3 mins.  Then cells were washed with 1 ml wash buffer (0.1% Tween-20, 10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2). Nuclei were collected by centrifugation at 500g for 10 min at 4°C. The pellet was resuspended in a 50 μl transposes mix (Vazyme TD501) incubated at 37 °C for 30 min in a PCR machine, and further cleaned by a Zymo DNA purification kit.
ATAC-seq libraries were prepared using the library preparing kit (Vazyme, TD501). Transposed DNA was amplified for 10 cycles, and the library DNA was further size selected with VAHTSTM DNA Clean Beads (Vazyme, N411) to the range of 150bp - 700bp./

treatment_protocol: 500ng/ml Doxycycline for 4 days

value: cell line

value: Human Osteosarcoma


title: ATAC_U2OS_SOX2FLFOXA2CTD_day4_biol rep2

value: Tet-on SOX2FOXA2CTD

value: 500ng/ml doxycycline for 4 days


title: E6_D16_PFOS_2_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H14

value: WT

value: PFOS 10 μM


title: HSJD-DIPG-07

value: High Grade Glioma


title: VUMC-DIPG-10


title: E6_D8_PFBA_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H17


title: PANC1PSA_PS03ULAPANC1PSAS206_AAACTCCGC_L003_R1_001

value: PDA tumor

value: Human PDA cell line


title: E6_D16_PFOA_2_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H12

value: PFOA 10 μM


title: SU-DIPG-IV


title: ATAC_U2OS_WT_SOX2_CellLine_biol rep2


title: E6_D8_DMSO_2_1

address: 双清路18号林业大学北门

value: Blastocyst

value: Multiple cells differentiated from H16

value: 0.1% DMSO


title: E6_D8_DMSO_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H15


title: PANC1PSA_PS03ULAPANC1PSAS209_TGAGTCGTT_L003_R1_001

value: Ravoxertinib


title: PANC1PSA_PS03ULAPANC1PSAS208_TGAGTAGGC_L003_R1_001

value: Cobimetinib


title: PANC1PSA_PS03ULAPANC1PSAS217_AAGGACGCA_L003_R1_001


title: PANC1PSA_PS03ULAPANC1PSAS207_ACAAGAGCG_L003_R1_001

value: Trametinib


title: ATAC_U2OS_SOX2FL_day4_biol rep1

value: cell line

value: Human Osteosarcoma

value: Tet-on SOX2

value: 500ng/ml doxycycline for 4 days


title: E6_D16_PFOS_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H13

value: WT

value: PFOS 10 μM


title: PANC1PSA_PS03ULAPANC1PSAS195_TCTCTGGAG_L003_R1_001

value: PDA tumor

value: Human PDA cell line

value: Selumetinib


title: ATAC_U2OS_SOX2FL_day4_biol rep2


title: ATAC_U2OS_FOXA2dCTD_day4_biol rep2

value: Tet-on FOXA2dCTD


title: ATAC_U2OS_FOXA2FL_day4_biol rep1

value: Tet-on FOXA2


title: PANC1PSA_PS03ULAPANC1PSAS197_CCACATCCA_L003_R1_001


title: E6_D16_PFHxA_2_1

address: 双清路18号林业大学北门

value: Blastocyst

value: Multiple cells differentiated from H8

value: PFHxA 10 μM


title: ATAC_U2OS_SOX2FLFOXA2CTD_day4_biol rep1

value: Tet-on SOX2FOXA2CTD


title: ATAC_U2OS_FOXA2dCTD_day4_biol rep1


title: E6_D16_PFHxS_2_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H10

value: PFHxS 10 μM


title: ATAC_U2OS_WT_biol rep2

value: cell line

value: Human Osteosarcoma


title: U2OS_SOX2FLFOXA2CTD_day4_bio rep2

data_processing: Nova-seq output paired ChIP-seq raw reads quality control performed with FastQC (version 0.10.1).  ChIP-seq raw reads were trimmed by trim_galore function with --paired mode and default parameters.  ChIP-seq reads were aligned to hg38 genome with bowtie2 v2.4.4 in the following options: bowtie2 -t -q -p 10 -N 1 -L 25 -X 700. Resulted sam files were converted to bam with samtools (v.0.1.18).  ChIP-seq bam files of the two replicates were called peaks individually using MACS2 with default parameters. For each group, peak files of the two replicates were used to call peaks by the IDR method with parameter: idr --input-file-type narrowPeak --rank p.value -soft-idr-threshold 0.05  The bigwig files of ChIP-seq data were generated using deeptools (v.2.4.1)  with the following configurations: bamCoverage -of bigwig --binSize 50 —normalizeUsing RPKM --ignoreDuplicates.  Assembly: hg38  Supplementary files format and content: Bigwig -- visualization of track information  Supplementary files format and content: NarrowPeak -- Binding Sites for ChIP-seq/ Opening Site for ATAC-seq

extract_protocol:
Stable U2OS cell lines with Tet-on expression were induced with 500ng/ul Doxycycline for 4 days and processed with ChIP-seq protocol. 1x10^7 cells were cross-linked by 1% PFA for 10 min at room temperature and quenched by 125 mM glycine for 5 min. Pelleted cells were first lysed with NP40 buffer (50 mM Tris-HCl, pH 8.1, 150 mM NaCl, 5 mM EDTA, 0.5% NP40), and then resuspended with sonication buffer (20mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) for chromatin sonication by Bioruptor sonicator (Diagenode) at High output for 15 cycles (30s on, 30s off) at 4°C. Samples were centrifuged at 12000g for 10 min at 4°C and the supernatant was collected for IP. 4 μg ChIP-grade Flag antibody (Sigma, A01868-40) was added to the collected sample and incubated for 4 hours at 4°C with gentle shaking, followed by incubation of protein-G magnetic beads rocking at 4 °C overnight. Immunopreciated DNA was purified by Zymo DNA purification kit.  Library construction was prepared using the NextEra NEB library prep kit for illumina (NEB, e7370) following the manufacturer’s protocol. DNA was size selected at 300-700 bp by electrophoresis and the sequencing was performed on the Illumina NOVA-seq 6000 Genome Analyzer (pair-end, 150bp).
ATAC-seq libraries were prepared using the library preparing kit (Vazyme, TD501). Transposed DNA was amplified for 10 cycles, and the library DNA was further size selected with VAHTSTM DNA Clean Beads (Vazyme, N411) to the range of 150bp - 700bp./

treatment_protocol: 500ng/ml Doxycycline for  4 days

value: 500ng/ml doxycycline for 4 days


title: ATAC_U2OS_WT_biol rep1


title: E6_D16_PFBS_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H5

value: PFBS 10 μM


title: E6_D16_PFOA_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H11

value: WT

value: PFOA 10 μM


title: E6_D16_PFHxS_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H9


title: U2OS_SOX2FLFOXA2CTD_day4_bio rep1


title: E6_D16_PFBA_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H3

value: PFBA 10 μM


title: ATAC_U2OS_FOXA2FL_day4_biol rep2

value: Tet-on FOXA2


title: U2OS_SOX2FL_day4_bio rep2

value: Tet-on SOX2


title: PANC1PSA_PS03ULAPANC1PSAS193_CCTCCGATT_L003_R1_001

value: PDA tumor

value: Human PDA cell line

value: Sorafenib


title: ASPC1PSB_PS02ULAASPC1PSBS192_GCCAATTCT_L003_R1_001

value: UNTREATED


title: Normal pituitary 5

city: Gwang-ju

first: Yeongmin

last: Kim

address: Chundamguagiro

department: BMSE

country: South Korea

institute: GIST

data_processing:
Trimmomatix(Version 0.36)
STAR(Version 2.7.10) using GRCh38.109
Picards's MarkDuplicates function(Version 3.0.0)
HTseq(Version 2.0.2)
Assembly: GRCh38.109
Supplementary files format and content: counts

source_name: Pituitary gland

extract_protocol:
RNeasy mini kit
Illumina TruSeq Stranded Total RNA Library Prep Gold Kit

value: Pituitary cell

tag: disease

value: Healthy


title: E6_D16_PFHxA_1_1

address: 双清路18号林业大学北门

value: Blastocyst

value: Multiple cells differentiated from H7

value: PFHxA 10 μM


title: E6_D16_PFBS_2_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H6

value: PFBS 10 μM


title: ASPC1PSB_PS02ULAASPC1PSBS191_AGAAAGAGC_L003_R1_001

value: DMSO


title: U2OS_FOXA3dCTD_day4_biol rep2

value: cell line

value: Human Osteosarcoma

value: Tet-on FOXA3dCTD

value: 500ng/ml doxycycline for 4 days


title: ASPC1PSB_PS02ULAASPC1PSBS184_GTCTTTCGA_L003_R1_001


title: U2OS_FOXA1dCTD_day4_biol rep2

value: Tet-on FOXA1dCTD


title: PANC1PSA_PS03ULAPANC1PSAS204_CGAGGTTCA_L003_R1_001

value: PDA tumor


title: U2OS_FOXA1dCTD_day4_biol rep1


title: ASPC1PSB_PS02ULAASPC1PSBS183_AACTACCGA_L003_R1_001

value: Human PDA cell line

value: Binimetinib


title: E6_D16_PFBA_2_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H4

value: WT

value: PFBA 10 μM


title: ASPC1PSB_PS02ULAASPC1PSBS182_CCCATCTTG_L003_R1_001


title: Orange_peel_H3K4me3_aChIP-seq_rep2

city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1
Supplementary files format and content: Narrowpeak
Supplementary files format and content: \

organism: Citrus sinensis

source_name: peel

growth_protocol: For the collection of economically important plant organs, the plants were planted and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. For the collection of vegetativetissues, the plants were planted in greenhouses.

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® sequencing (New England BioLabs, E7645) and sequenced using an Illumina Novaseq 6000 platform (paired-end 150 bp reads).

value: peel

value: Rohde Red

value: peel cells

tag: chip antibody


title: ASPC1PSB_PS02ULAASPC1PSBS168_GTTCTTGCT_L003_R1_001

value: UNTREATED


title: E6_D16_DMSO_2_1

address: 双清路18号林业大学北门

value: Blastocyst

value: Multiple cells differentiated from H2

value: 0.1% DMSO


title: U2OS_FOXA3FL_day4_biol rep1

value: cell line

value: Human Osteosarcoma

value: Tet-on FOXA3


title: ASPC1PSB_PS02ULAASPC1PSBS161_TTTCATCCG_L003_R1_001

value: Trametinib


title: E6_D16_DMSO_1_1

address: 双清路18号林业大学北门

value: Multiple cells differentiated from H1


title: Orange_peel_IgG_aChIP-seq_rep1

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1,Populus:sPta717 v2
Supplementary files format and content: Narrowpeak and broadpeak
Supplementary files format and content: \

source_name: pulps

value: pulps

value: pulps cells

value: IgG


title: ASPC1PSB_PS02ULAASPC1PSBS180_GTCAAAGCC_L003_R1_001

value: PDA tumor

value: Human PDA cell line


title: Orange_peel_H3K27me3_aChIP-seq_rep2

value: peel


title: ASPC1PSB_PS02ULAASPC1PSBS179_CATCAAACG_L003_R1_001

value: DMSO


title: Orange_peel_IgG_aChIP-seq_rep2

value: Rohde Red


title: ASPC1PSB_PS02ULAASPC1PSBS173_ATCACGAAG_L003_R1_001

value: Ulixertinib


title: ASPC1PSB_PS02ULAASPC1PSBS158_AGACTCGTC_L003_R1_001

value: Ravoxertinib


title: U2OS_FOXA3dCTD_day4_biol rep1

value: Tet-on FOXA3dCTD

value: 500ng/ml doxycycline for 4 days


title: n-Sen_alkali_1

city: Minato City

first: Satoshi

last: Kawakami

address: 4-6-1 Shirokanedai

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

data_processing:
Sequenced reads were quality-controlled using fastp (v0.23.2) and aligned to mouse mm10 genome using HISAT2 (v2.1.0).
TPM values were calculated with TPMcalculator (v0.0.4), using aligned bam files and a reference gene annotation file (Ensembl 95).
Read counts for each gene features were calculated using featureCounts function in subread package (v2.0.2) and used for differential gene expression analysis using DESeq2 (v1.34.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files including read counts for each sample.

organism: Mus musculus

source_name: MEFs

growth_protocol: MEFs were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics under 37℃, 5% CO2, 3-5% O2 condition.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) and RNeasy mini kit (Qiagen).
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. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol:
Senescence was induced by nutlin3a-mediated p53 stabilization. Cells were synchronized at G2 phase by treatment with 9 mM of RO3306 for 16-20 hrs, treated with 9 mM of RO3306 and 5 mM of nutlin3a for 8 hrs, and then with 5 mM of nutlin3a for 48 hrs. After induction of cellular senescence, cells were maintained in 100 nM of BI-2536-containing media for 14 days to eliminate residual proliferating cells.
After senescence induction, cells were cultured pH-adjusted, HEPES-buffered DMEM with 10% FBS and antibiotics for 24 hrs

value: MEFs

value: Fibroblasts

value: Alkali


title: ASPC1PSB_PS02ULAASPC1PSBS171_CGCTTGATG_L003_R1_001


title: Orange_peel_input_rep2

value: peel cells


title: ASPC1PSB_PS02ULAASPC1PSBS170_GGAGTTTAG_L003_R1_001

value: Refamatinib


title: Orange_flesh_H3K4me3_aChIP-seq_rep2

value: pulps


title: Orange_peel_input_rep1


title: ASPC1PSB_PS02ULAASPC1PSBS169_CTGAGTAAC_L003_R1_001

value: Dabrafenib


title: U2OS_FOXA3FL_day4_biol rep2

value: cell line

value: Human Osteosarcoma

value: Tet-on FOXA3


title: ASPC1PSB_PS02ULAASPC1PSBS157_CGAGCAAGT_L003_R1_001

value: PDA tumor

value: Human PDA cell line

value: Cobimetinib


title: Orange_peel_H3K4me3_aChIP-seq_rep1

value: peel

value: Rohde Red


title: Orange_flesh_H3K27me3_aChIP-seq_rep2

value: pulps cells


title: U2OS_SOX2FL_day4_bio rep1

value: Tet-on SOX2

value: 500ng/ml doxycycline for 4 days


title: ASPC1PSB_PS02ULAASPC1PSBS156_GCACTTGTA_L003_R1_001

value: UNTREATED


title: ASPC1PSB_PS02ULAASPC1PSBS149_ACAGGCCAA_L003_R1_001

value: Selumetinib


title: U2OS_FOXA1FL_day4_bio rep2

value: Tet-on FOXA1


title: Orange_flesh_H3K4me3_aChIP-seq_rep1


title: n-Sen_2

value: MEFs

value: Fibroblasts

value: Senescent


title: U2OS_FOXA2dCTD_day4_biol rep1

value: cell line

value: Tet-on FOXA2dCTD


title: n-Sen_alkali_2

value: Alkali


title: ASPC1PSB_PS02ULAASPC1PSBS160_TAGCGACCT_L003_R1_001

value: PDA tumor


title: Orange_peel_H3K27me3_aChIP-seq_rep1

value: peel cells


title: U2OS_FOXA2dCTD_day4_biol rep2

value: Human Osteosarcoma


title: n-Sen_control_1

value: Control


title: n-Sen_1


title: n-Sen_control_2


title: U2OS_FOXA1FL_day4_bio rep1


title: ASPC1PSB_PS02ULAASPC1PSBS146_AAATGGCGA_L003_R1_001

value: Human PDA cell line


title: U2OS_FOXA2FL_day4_biol rep1

value: Tet-on FOXA2


title: TER 3

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

data_processing:
Demultiplexing was done with bcl2fastq v2.20.0.422. Analysis was performed using ‘nf-core/smrnaseq v2.2.0‘, against the human reference genome GRCh38. The statistical QC was performed using the FastQC tool. (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), generating the mean quality scores of all sequences, sequence duplication levels and the count of unique / duplicate reads. Counts per million were calculated by the TMM normalization method in the edgeR package
Assembly: GRCh38
Supplementary files format and content: Excel data, showing expression intensities of each analyzed microRNA. Values are averaged from 2x paired-end sequening runs performed for each sample.

source_name: non-seminoma germ cell tumor, growing teratoma

extract_protocol:
Total RNA was isolated by the TRIzol reagent according to the manual (Qiagen, Hilden, Germany). RNA concentrations and purities were measured by the Nanodrop 2000 photo-spectrometer (260 / 280 nm; 260 / 230 nm) and RIN numbers were detemrined by Fragment Analyzer measurememt.
200 ng of total RNA were used for library preparation and microRNA sequencing (microRNAseg). Library preparation (NEXTFLEX Small RNA-Seq Kit v4‘ (Revvity, Hamburg, Germany)) and microRNAseg (NovaSeq6000 SP 2 x 50 bp) has been performed at the "Institut für Klinische Molekularbiologie" (IKMB) of the University of Kiel. The quality control (QC) and identification of expressed microRNAs has been done by the IKMB.

tag: group

value: Teratoma


title: ASPC1PSB_PS02ULAASPC1PSBS147_ACGTAAGAG_L003_R1_001

value: Sorafenib


title: Orange_flesh_H3K27me3_aChIP-seq_rep1

value: pulps

value: Rohde Red

value: pulps cells


title: 48h_Rapeseed_Germinate_seed_rep2

data_processing:
The quality of the sequencing datasets was evaluated using FastQC
Fastp was used with “-l 15 -f 0 -t 0” parameters to filter out adapters and low-quality reads.
The filtered reads were aligned to the corresponding reference genome using Hisat2 with default parameters.
SAMtools with the parameter “-q 30” was used to remove low-quality mapped reads.
The normalization method employed in gene expression was EdgeR’s TMM (Trimmed Mean of M-values).
Assembly: GWHANRE00000000
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include TMM values for each Sample

organism: Brassica napus

source_name: 48h Germinate seed

extract_protocol:
Total RNA was isolated using RNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 74904).
The RNA was used for library construction using the Illumina TruSeq RNA kit, according to the manufacturer’s recommendations. The libraries were sequenced using an Illumina Novaseq 6000 system (paired-end 150 bp reads, Annoroad Gene Technology).

value: 48h Germinate seed

value: Zhongshuang 11

value: 48h Germinate seed cells


title: Proliferating_1

value: MEFs

value: Fibroblasts


title: 48h_Rapeseed_Germinate_seed_rep1


title: zs11_50d_Rapeseed_seeds_H3K27me3_rChIP-seq_nomembrane_rep2

source_name: 50DPA seeds

value: 50DPA seeds

value: 50DPA seeds cells


title: ASPC1PSB_PS02ULAASPC1PSBS144_ATGCTTCGG_L003_R1_001

value: PDA tumor

value: DMSO


title: Proliferating_2

value: Control


title: TER 2

value: non-seminoma germ cell tumor, growing teratoma


title: E6F6-B Cells sorted from Wild Type Mice, Replicate 3

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

institute: Xiamen University

description: Singleron Matrix GEXSCOPE

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, alignment, gene counting and aggregation were made using the Singleron Celescope software version 1.10.0 (https://github.com/singleron-RD/CeleScope)
The doublet were removed by using Doubletfinder R package and personal checking for conserved markers.
The R package Seurat version 4.1.1 was used for normalization, clustering and reduction. Cell type was annotated based on conserved markers.
Differential gene expression analysis and enrichment analysis were performed by using MAST and clusterProfiler R package.
Assembly: GRCm38
Supplementary files format and content: Compressed .tar.gz file containing genes, barcodes and matrix for each sample

source_name: CD45.2+ E6F6-B cells

extract_protocol:
Single-cell suspensions with 1×105 cells/mL in concentration in PBS were prepared. Single-cell suspensions were loaded into microfluidic devices and scRNA-seq libraries were constructed following the Singleron GEXSCOPER protocol by GEXSCOPER Single-Cell RNA Library Kit (Singleron Biotechnologies).
Indivaidual libraries of each sample were then dilyted to 4nM, pooled and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: CD45.2+ E6F6-B cells

value: Wild type

tag: strain


title: E6F6-B Cells sorted from Wild Type Mice, Replicate 4

description: Singleron Matrix GEXSCOPE


title: TER 1

value: Teratoma


title: ASPC1PSB_PS02ULAASPC1PSBS137_GGCGTACAT_L003_R1_001

value: Human PDA cell line


title: ASPC1PSB_PS02ULAASPC1PSBS134_CAGTGACTG_L003_R1_001


title: zs11_50d_Rapeseed_seeds_H3K27me3_rChIP-seq_nomembrane_rep1


title: E6F6-B Cells sorted from Wild Type Mice, Replicate 2

description: Singleron Matrix GEXSCOPE


title: ASPC1PSB_PS02ULAASPC1PSBS133_AAGCACGGT_L003_R1_001

value: Binimetinib


title: GTS rapid 2

value: GTS rapid


title: GTS rapid 3


title: zs11_50d_Rapeseed_seeds_H3K27me3-H3K4me3_ChIP_reChIP-seq_rep1


title: GTS rapid 1


title: ASPC1PSB_PS02ULAASPC1PSBS132_CAATAGGCG_L003_R1_001


title: E6F6-B Cells sorted from CAG-sHBs Mice, Replicate 4

description: Singleron Matrix GEXSCOPE

value: CAG-sHBs


title: ASPC1PSB_PS02ULAASPC1PSBS125_CGTATGTCC_L003_R1_001

value: Refamatinib


title: Rapeseed_14d_young_leaves_H3K9ac_aChIP-seq_rep2

source_name: 14d young leaves

value: 14d young leaves

value: Zhongshuang 11

value: 14d young leaves cells


title: E6F6-B Cells sorted from CAG-sHBs Mice, Replicate 3

description: Singleron Matrix GEXSCOPE


title: GTS slow 3

value: GTS slow


title: Rapeseed_14d_young_leaves_H3K9ac_aChIP-seq_rep1


title: ASPC1PSB_PS02ULAASPC1PSBS124_TACACTGAG_L003_R1_001

value: Dabrafenib


title: GTS slow 2


title: E6F6-B Cells sorted from CAG-sHBs Mice, Replicate 2

description: Singleron Matrix GEXSCOPE


title: Rapeseed_14d_young_leaves_H3K4me3_CUT&Tag_rep2


title: zs11_50d_Rapeseed_seeds_H3K27me3-H3K4me3_ChIP_reChIP-seq_rep2

value: 50DPA seeds

value: 50DPA seeds cells


title: E6F6-B Cells sorted from CAG-sHBs Mice, Replicate 1

description: Singleron Matrix GEXSCOPE


title: ASPC1PSB_PS02ULAASPC1PSBS121_TGGCATACC_L003_R1_001

value: PDA tumor


title: ASPC1PSB_PS02ULAASPC1PSBS123_AAGATGCTG_L003_R1_001

value: Ulixertinib


title: Rapeseed_14d_young_leaves_H3K4me3_CUT&Tag_rep1


title: Rapeseed_14d_young_leaves_H3K27me3-H3K4me3_ChIP_reChIP-seq_rep2


title: 5637 cell line 2

city: Tianjin

first: Guangming

last: Li

state: Tianjin

address: No. 22 Qixiangtai Road

department: Pathogen

institute: Tianjin Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)
The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples/groups, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method.
RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances Essentially, differential expression analysis was performed using the DESeq2 /DEGseq /edgeR /Limma /NOIseq ,DEGs with |log2 (foldchange)| ≥ 1 and P-adjust ≤ 0.05 (DESeq2/edgeR/Limma) / P-adjust ≤ 0.001 (DEGseq) / Prob > 0.8 (NOIseq) were considered to be significantly different expressed genes.

source_name: bladder

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDropTechnologies).   (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was  determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop  Technologies).
Illumina Novaseq 6000 platform was used to randomly fragment mRNA and isolate small fragments of about 300 bp by magnetic bead screening. Under the action of reverse transcriptase, random hexamers were added to synthesize one-strand cDNA using mRNA as template, followed by two-strand synthesis to form a stable double-strand structure. The cDNA structure of the double strand was A sticky End, which was made into A flat End by adding End Repair Mix, and then an "A" base was added to the 3 'End for joining the Y-shaped connector. The library was enriched and 15 cycles were amplified by PCR. Then, recover the target band by 2% agarose gel, quantify by TBS380 (Picogreen), and mix on the machine according to the proportion of data. Bridge PCR amplification was performed on cBot to generate clusters. Sequencing was performed by Illumina HiSeq xten platform (PE library, read length 2×150bp).

value: bladder

value: epithelial cell

value: WT


title: ASPC1PSB_PS02ULAASPC1PSBS120_TTCGCAACC_L003_R1_001

value: Human PDA cell line

value: DMSO


title: Negative Control, E6F6-B Cells sorted from CD45.2+ E6F6-TG Mice, Replicate 4

description: Singleron Matrix GEXSCOPE

value: CD45.2+ E6F6-B cells

value: Negative Control


title: 5637 cell line 1


title: E6F6-B Cells sorted from Wild Type Mice, Replicate 1

description: Singleron Matrix GEXSCOPE

value: Wild type


title: Dormant_rapeseed_seeds_1year_H3K27me3_rChIP-seq_nomembrane_rep2

source_name: dry seed

value: dry seed

value: dry seed cells


title: Negative Control, E6F6-B Cells sorted from CD45.2+ E6F6-TG Mice, Replicate 3

description: Singleron Matrix GEXSCOPE


title: J82 cell line 3


title: ASPC1PSB_PS02ULAASPC1PSBS112_AACGGAAGG_L003_R1_001

value: Cobimetinib


title: Dormant_rapeseed_seeds_1year_H3K27me3_rChIP-seq_nomembrane_rep1

value: Zhongshuang 11


title: Negative Control, E6F6-B Cells sorted from CD45.2+ E6F6-TG Mice, Replicate 1

description: Singleron Matrix GEXSCOPE


title: U2OS_FOXA2FL_day4_biol rep2

value: cell line

value: Human Osteosarcoma

value: Tet-on FOXA2

value: 500ng/ml doxycycline for 4 days


title: J82 cell line 2


title: GTS slow 1

value: non-seminoma germ cell tumor, growing teratoma

value: GTS slow


title: ASPC1PSB_PS02ULAASPC1PSBS111_GTACCACGA_L003_R1_001

value: PDA tumor

value: Trametinib


title: 5637 cell line 3

value: bladder

value: epithelial cell

value: WT


title: J82 cell line 1


title: ASPC1PSB_PS02ULAASPC1PSBS110_AAACGTCAG_L003_R1_001

value: Human PDA cell line


title: Dormant_rapeseed_seeds_1year_H3K9me2_aChIP-seq_rep1


title: LN-2, ATAC

city: St. Louis

first: Aaron

last: Ver Heul

state: MO

address: 660 S Euclid Ave.

department: Medicine

institute: Washington University School of Medicine

description: chromatin accessibility

data_processing:
RTA Version: v3.4.4 was used for base calls and quality scores.
The cellranger-arc-2.0.0 pipeline was used to generate FASTQ files, gene expression matrices, and ATAC fragment tables for each sample
Genome_build: Mousrefdata-cellranger-arc-mm10-2020-A-2.0.0e Ensembl GRCm38.101
Supplementary_files_format_and_content: Multiomic filtered feature barcode matrices (*.HDF5), ATAC per fragment information files (*.tsv.gz), and ATAC per fragment information indices (*.tsv.gz.tbi)

source_name: cervical skin draining lymph node

growth_protocol: Mice were maintained in standard housing conditions prior to and during the experiment

extract_protocol:
Cervical lymph nodes draining the ear skin were homogenized and ILCs were enriched by depleting T cells, B cells and granulocytes using negative magnetic-activated cell sorting with anti-CD3, CD19, and CD11b antibodies. Remaining cells were collected and frozen. Later, samples from multiple mice (3 in vehicle control, 3 in calcipotriol treatment groups) were thawed, pooled, and processed to obtain single nuclei suspensions that were further processed using the 10X Genomics multiome pipeline.
Multiome 3v3.1 GEX and ATAC libraries were prepared as recommended by the 10x Genomics ChromiumNextGEM Multiome_ATAC_GEX_User_Guide_RevD (CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevD.pdf).  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns PN-1000283, Chromium Next GEM Chip J Single Cell Kit, 48 rxns PN-1000234, Single Index Kit N Set A, 96 rxns PN-1000212 (ATAC), Dual Index Kit TT Set A, 96 rxns PN-1000215 (3v3.1 GEX), were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  GEX libraries were pooled and run over 0.05 of a NovaSeq6000 S4 flow cell using the XP workflow and running a 28x10x10x150 sequencing recipe in accordance with manufacturer’s protocol.  Target coverage was 500M reads per sample.  ATAC libraries were pooled and run over 0.167 of a NovaSeq6000 S1 flow cell using the XP workflow and running a 51x8x16x51 sequencing recipe in accordance with manufacturer’s protocol.  Target coverage was 250M reads per sample.

treatment_protocol: 8-11-week-old C57BL6 mice homozygous for a Cre-inducible dimeric red fluorescent protein allele knocked into the Rosa26 locus (lox-stop-lox-tdRFP) and also expressing transgenic Cre under control of the Rag1 promoter were treated for 7 days with 1 nmol of calcipotriol or with ethanol vehicle control on each ear

value: Rosa26(LSL-tdRFP); tg-Rag1-Cre

value: calcipotriol

tag: disease state

value: atopic dermatitis-like skin inflammation

value: cervical skin draining lymph node


title: ASPC1PSB_PS02ULAASPC1PSBS108_TGACTGGTG_L003_R1_001

value: DMSO


title: ASPC1PSB_PS02ULAASPC1PSBS113_CAGGTGGTA_L003_R1_001

value: Ravoxertinib


title: UMUC3 cell line 3


title: Dormant_rapeseed_seeds_1year_H3K9ac_aChIP-seq_rep2

value: dry seed

value: Zhongshuang 11

value: dry seed cells


title: Rapeseed_14d_young_leaves_H3K27me3-H3K4me3_ChIP_reChIP-seq_rep1

value: 14d young leaves

value: 14d young leaves cells


title: LN-2, GEX

description: gene expression


title: ASPC1PSB_PS02ULAASPC1PSBS101_GCGATCAAC_L003_R1_001

value: PDA tumor


title: UMUC3 cell line 2


title: Dormant_rapeseed_seeds_1year_H3K9ac_aChIP-seq_rep1


title: Negative Control, E6F6-B Cells sorted from CD45.2+ E6F6-TG Mice, Replicate 2

description: Singleron Matrix GEXSCOPE

value: CD45.2+ E6F6-B cells

value: Negative Control


title: ASPC1PSB_PS02ULAASPC1PSBS99_TGAATCCGA_L003_R1_001

value: Selumetinib


title: UMUC3 cell line 1

value: bladder

value: epithelial cell

value: WT


title: Dormant_rapeseed_seeds_1year_H3K4me1_aChIP-seq_rep2


title: ASPC1PSB_PS02ULAASPC1PSBS97_CCGACTAAA_L003_R1_001

value: Human PDA cell line

value: Sorafenib


title: T24 cell line 3


title: Hepatocyte_COX2_CKO_Tu_rep3

city: Chengdu

first: Yang

last: Tai

state: Sichuan

address: NO. 37, Xiang Xue Guo

institute: West China Hospital, Sichuan University

description: Primary hepatocytes from COX-2 CKO mice were treated with tunicamycin for 24 hours

data_processing:
Raw data were firstly processed through custom perl and python scripts, and were then filtered by Q20, Q30 and GC contents.
The acquired clean data were mapped to the mouse reference genome (mm10) using HISAT2 (v2.2.1).
For each sample, read counts for each gene were obtained with featureCounts (v1.5.0-p3) and were standardized as fragments per kilobase million (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with mRNA FPKM for each sample

source_name: Hepatocyte

extract_protocol:
Total RNA was extracted from hepatocytes using TRIzol reagent (Thermo Fisher Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Primary hepatocytes

value: COX-2 CKO

value: tunicamycin for 24 hours


title: Dormant_rapeseed_seeds_1year_H3K4me1_aChIP-seq_rep1

value: dry seed


title: Dormant_rapeseed_seeds_1year_H3K9me2_aChIP-seq_rep2

value: Zhongshuang 11


title: Hepatocyte_COX2_CKO_Tu_rep2


title: LN-1, ATAC

description: chromatin accessibility

value: Rosa26(LSL-tdRFP); tg-Rag1-Cre

value: ethanol

value: atopic dermatitis-like skin inflammation

value: cervical skin draining lymph node


title: Hepatocyte_COX2_CKO_Tu_rep1


title: Dormant_rapeseed_seeds_1year_H3K27me3-H3K4me3_ChIP_reChIP-seq_rep2

value: dry seed cells


title: Dormant_rapeseed_seeds_1year_H3K27me3-H3K4me3_ChIP_reChIP-seq_rep1


title: T24 cell line 2


title: ASPC1PSA_PS01ULAASPC1PSAS95_GAATCGAGA_L003_R1_001

value: PDA tumor

value: DMSO


title: T24 cell line 1

value: bladder


title: LN-1, GEX

description: gene expression


title: 50d_Rapeseed_seeds_H3K9me2_aChIP-seq_rep2

value: 50DPA seeds

value: 50DPA seeds cells


title: Hepatocyte_WT_Tu_rep2

description: Primary hepatocytes from WT mice were treated with tunicamycin for 24 hours

value: WT


title: SV-HUC-1 cell line 3

value: epithelial cell


title: 50d_Rapeseed_seeds_H3K9me2_aChIP-seq_rep1


title: Hepatocyte_WT_Tu_rep1

value: Primary hepatocytes


title: ASPC1PSA_PS01ULAASPC1PSAS88_GCATTATGC_L003_R1_001

value: Human PDA cell line


title: ASPC1PSA_PS01ULAASPC1PSAS86_AAGACGTGC_L003_R1_001


title: SV-HUC-1 cell line 2


title: ASPC1PSA_PS01ULAASPC1PSAS87_CGGTTGTAT_L003_R1_001

value: Binimetinib


title: SV-HUC-1 cell line 1


title: Hepatocyte_WT_DMSO_rep3

description: Primary hepatocytes from WT mice were treated with DMSO for 24 hours

value: DMSO for 24 hours


title: ASPC1PSA_PS01ULAASPC1PSAS84_TCTATGCGA_L003_R1_001

value: UNTREATED


title: SQLE_J82 repeat 3

value: OE-SQLE


title: 50d_Rapeseed_seeds_H3K9ac_aChIP-seq_rep2

value: Zhongshuang 11


title: 50d_Rapeseed_seeds_H3K9ac_aChIP-seq_rep1


title: ASPC1PSA_PS01ULAASPC1PSAS83_ATGTGCTGG_L003_R1_001


title: ASPC1PSA_PS01ULAASPC1PSAS96_TCCAGGTTT_L003_R1_001


title: SQLE_J82 repeat 2


title: Hepatocyte_WT_DMSO_rep2


title: Hepatocyte_WT_Tu_rep3

value: tunicamycin for 24 hours


title: SQLE_J82 repeat 1


title: 50d_Rapeseed_seeds_H3K4me1_aChIP-seq_rep2


title: ASPC1PSA_PS01ULAASPC1PSAS77_TACCTTCGT_L003_R1_001

value: Ulixertinib


title: Hepatocyte_WT_DMSO_rep1


title: Min6 cells, siSRSF2

city: 上海

first: WENJU

last: QIAN

state: 上海

address: 徐汇区岳阳路

institute: 上海中科院

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using , then mapped to mm10 whole genome using Bowtie2 v2.4.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression.xlsx

source_name: Min6 transfected with siSRSF2

extract_protocol:
Min6 transfected with negative control siRNA(siNC),siSRSF1 or siSRSF2 were collected.Then mRNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Lifetech protocol.

value: insulinoma cell line Min6

tag: transfection


title: ASPC1PSA_PS01ULAASPC1PSAS75_AATGGGCTG_L003_R1_001

source_name: PDA tumor

value: PDA tumor


title: 48h_Rapeseed_Germinate_seed_H3K9me2_aChIP-seq_rep2

value: 48h Germinate seed

value: 48h Germinate seed cells


title: NC_J82 repeat 2

value: bladder


title: ASPC1PSA_PS01ULAASPC1PSAS74_CAATGCCAC_L003_R1_001

value: Refamatinib


title: ASPC1PSA_PS01ULAASPC1PSAS73_CGATTTAGC_L003_R1_001

value: Dabrafenib


title: Min6 cells, siASF-1

source_name: Min6 transfected with siSRSF1


title: Min6 cells, siNC

description: siNC

source_name: Min6 transfected with negative control siRNA

value: siNC


title: 48h_Rapeseed_Germinate_seed_H3K9me2_aChIP-seq_rep1


title: 48h_Rapeseed_Germinate_seed_H3K9ac_aChIP-seq_rep2


title: NC_J82 repeat 1

value: epithelial cell

value: WT


title: ASPC1PSA_PS01ULAASPC1PSAS72_CATTTGGGC_L003_R1_001

value: Human PDA cell line


title: SRSF2 flox/flox Ins2-Cre

description:
sc35_ko
MappingStatistic_sc35_ko

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2 v2.4.2.
FPKM were calculated.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: All_FPKM.xlsx: Excel file includes read counts and FPKM values.
Supplementary_files_format_and_content: sc35_ff_vs_sc35_ko.DESeq.xlsx: Excel file includes DESeq results.

extract_protocol:
SRSF2 flox/flox and SRSF2 flox/flox Ins2-Cre mice pancreatic islet were collected. Then mRNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Lifetech protocol.

value: pancreatic islets

value: SRSF2 flox/flox Ins2-Cre

tag: age

value: 7 months


title: Group 3 MB D458 cells, EYA2 shRNA#8, rep 3

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC was used to assess sequence data quality.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf tool from EAutils.
FastQ Screen was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (--b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) and Bowtie2 with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools
Reads were coordinate sorted and duplicates were marked using Picard
Quality assessment of final mapped reads was performed using RSeQC
Raw gene-level count data was generated using HTSeq-count with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Assembly: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary files format and content: Tab delimited text files containing raw gene-level counts for each sample

source_name: Cell Line

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS, 1% sodium pyruvate, 1% L-glutamate, 1% pen/strep

extract_protocol:
RNeasy Plus Mini Kit (Qiagen 74136)
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

treatment_protocol: Cells were transduced with non-targeting shRNA or one of three shEYA2 constructs. Cells are selected for with 1 ug/mL puromycin for 48 hours. The top 10% of zsGreen+ (included in shRNA constructs) weree sorted for. Cells were allowed to recover for 24 hours. RNA was extracted as described below. EYA2 KD was confirmed by qRT-PCR prior to RNA-Seq.

value: Medulloblastoma

tag: replicate

value: Eya2 shRNA #8


title: ASPC1PSA_PS01ULAASPC1PSAS65_TGTGCATAC_L003_R1_001

value: Trametinib


title: 48h_Rapeseed_Germinate_seed_H3K9ac_aChIP-seq_rep1

value: Zhongshuang 11


title: SRSF2 flox/flox

description:
sc35_f/f
MappingStatistic_sc35_ff

source_name: SRSF2 flox/flox mice pancreatic islet

value: SRSF2 flox/flox


title: 48h_Rapeseed_Germinate_seed_H3K4me3_aChIP-seq_rep2

value: 48h Germinate seed


title: Group 3 MB D458 cells, EYA2 shRNA#7 rep 3

value: Eya2 shRNA #7


title: 50d_Rapeseed_seeds_H3K4me1_aChIP-seq_rep1

value: 50DPA seeds

value: 50DPA seeds cells


title: ASPC1PSA_PS01ULAASPC1PSAS64_AACGCGAAC_L003_R1_001

value: PDA tumor


title: NC_J82 repeat 3

value: bladder


title: 48h_Rapeseed_Germinate_seed_H3K4me3_aChIP-seq_rep1

value: 48h Germinate seed cells


title: Group 3 MB D458 cells, non-targeting control, rep 3

value: Control shRNA


title: Group 3 MB D425 cells, EYA2 shRNA#8, rep 3


title: Group 3 MB D425 cells, EYA2 shRNA#6, rep 3

value: Eya2 shRNA #6


title: ASPC1PSA_PS01ULAASPC1PSAS61_CGCAGTAAG_L003_R1_001

value: Human PDA cell line

value: Cobimetinib


title: 48h_Rapeseed_Germinate_seed_H3K4me1_aChIP-seq_rep2


title: 48h_Rapeseed_Germinate_seed_H3K4me1_aChIP-seq_rep1


title: ASPC1PSA_PS01ULAASPC1PSAS62_TCATGATGG_L003_R1_001

value: Ravoxertinib


title: ASPC1PSA_PS01ULAASPC1PSAS60_AGAGAGCAA_L003_R1_001

value: UNTREATED


title: Smple two of wild Eleocharis dulcis corm at its maturity stage

first: yan

last: huang

address: Wuhan East Lake New Technology Development Zone Jiufeng Road No.201

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

data_processing:
Clean reads of each tissue were mapped to the reference genome using HISAT2 v.2.0.4. The read counting of the annotated genes was performed using STRINGTIE v.2.1.6. R package ‘DESeq2’was used to analyze differential gene expression.
Assembly: SUB14033829
Supplementary files format and content: Tab-delimited text files include TPM values for each sample

organism: Eleocharis dulcis

source_name: corm

extract_protocol:
TruSeq RNA Library Kit (Illumina, NEB)
Standard DNBSEQ-T7 library preparation protocol

value: corm

tag: developmental stage

value: maturity stage


title: Group 3 MB D425 cells, non-targeting control, rep 3

value: Medulloblastoma


title: Smple one of wild Eleocharis dulcis corm at its maturity stage


title: Smple three of wild Eleocharis dulcis corm at its late swelling stage stage

value: late swelling stage stage


title: Smple three ofwild  Eleocharis dulcis corm at its maturity stage


title: Group 3 MB D458 cells, EYA2 shRNA#8, rep 2

value: Eya2 shRNA #8


title: Smple one of wild Eleocharis dulcis corm at its late swelling stage stage


title: ASPC1PSA_PS01ULAASPC1PSAS53_TTTCCGGCA_L003_R1_001

data_processing:
The PLATE-Seq FASTQ files were pseudoaligned to the GRCh38 human transcriptome (mRNA & ncRNA) and gene expression was quantified using kallisto (version 0.44.0), tximport package (Soneson et al., 2015), and biomaRt package (Durinck et al., 2009).
The gene expression was quantified as both raw counts (i.e. sequencing fragments per genomic locus) and transcripts per million (i.e. sequencing fragments per genomic locus normalized for transcript/gene length and sample sequencing depth).
Assembly: GRCh38
Supplementary files format and content: Table containing reads count of each gene (row) in each sample (column)

value: Selumetinib


title: 48h_Rapeseed_Germinate_seed_H3K27me3_aChIP-seq_rep1

value: 48h Germinate seed

value: Zhongshuang 11


title: ASPC1PSA_PS01ULAASPC1PSAS51_TACGTACGA_L003_R1_001

value: PDA tumor

value: Sorafenib


title: Group 3 MB D458 cells, non-targeting control, rep 2


title: Smple three of wild Eleocharis dulcis corm at its middle swelling stage stage

value: middle swelling stage stage


title: Group 3 MB D458 cells, EYA2 shRNA#7 rep 2

value: Eya2 shRNA #7


title: 48h_Rapeseed_Germinate_seed_H3K27me3-H3K4me3_ChIP_reChIP-seq_rep1

value: 48h Germinate seed cells


title: Smple two of wild Eleocharis dulcis corm at its imiddle swelling stage stage


title: ASPC1PSA_PS01ULAASPC1PSAS48_CGAACTCTA_L003_R1_001

value: Human PDA cell line

value: DMSO


title: 48h_Rapeseed_Germinate_seed_H3K27me3-H3K4me3_ChIP_reChIP-seq_rep2


title: U2OS_Input

source_name: cell line

value: cell line

value: Human Osteosarcoma


title: Smple two of wild Eleocharis dulcis corm at its late swelling stage stage

value: corm


title: Group 3 MB D425 cells, EYA2 shRNA#8, rep 2


title: Smple one of wild Eleocharis dulcis corm at its middle swelling stage stage


title: Group 3 MB D425 cells, EYA2 shRNA#6, rep 2

value: Eya2 shRNA #6


title: Rapeseed_dry_seeds_rep2

source_name: dry seeds

value: dry seeds

value: dry seeds cells


title: ASPC1PSA_PS01ULAASPC1PSAS41_GTCGAACCT_L003_R1_001


title: Smple three of wild Eleocharis dulcis corm at its initial swelling stage

value: initial swelling stage


title: Group 3 MB D425 cells, non-targeting control, rep 2

value: Medulloblastoma

value: Control shRNA


title: 48h_Rapeseed_Germinate_seed_H3K27me3_aChIP-seq_rep2

source_name: 48h Germinate seed

value: 48h Germinate seed

value: Zhongshuang 11


title: ASPC1PSA_PS01ULAASPC1PSAS38_CTAACGCAG_L003_R1_001

value: PDA tumor


title: Rapeseed_50 DPA_seeds_rep1

source_name: 50 DPA seeds

value: 50 DPA seeds

value: 50DPA seeds cells


title: Rapeseed_dry_seeds_rep1


title: Smple one of  wild Eleocharis dulcis corm at its initial swelling stage


title: ASPC1PSA_PS01ULAASPC1PSAS37_GCAACTTCC_L003_R1_001

value: Binimetinib


title: Group 3 MB D458 cells, EYA2 shRNA#8, rep1

value: Eya2 shRNA #8


title: ASPC1PSA_PS01ULAASPC1PSAS36_TGCTACCTT_L003_R1_001

value: Human PDA cell line

value: DMSO


title: Rapeseed_50 DPA_seeds_rep2


title: Rapeseed_young_leaves_rep2

source_name: young leaves

value: young leaves

value: young leaves cells


title: ASPC1PSA_PS01ULAASPC1PSAS50_TTGGTGAGC_L003_R1_001


title: Group 3 MB D458 cells, EYA2 shRNA#7 rep 1

value: Eya2 shRNA #7


title: ASPC1PSA_PS01ULAASPC1PSAS29_ACTGGCAAG_L003_R1_001

value: Refamatinib


title: Group 3 MB D458 cells, non-targeting control, rep 1


title: Smple three of cultivated  Eleocharis dulcis corm at its maturity stage

value: corm

value: maturity stage


title: Rapeseed_young_leaves_rep1


title: Smple two of cultivated Eleocharis dulcis corm at its maturity stage


title: Group 3 MB D425 cells, EYA2 shRNA#8, rep 1

value: Medulloblastoma


title: ASPC1PSA_PS01ULAASPC1PSAS28_GCGTCTTGA_L003_R1_001

value: Dabrafenib


title: Rapeseed_14d_young_leaves_H3K4me3_eChIP-seq_rep2

value: 14d young leaves cells


title: Smple two of wild Eleocharis dulcis corm at its initial swelling stage

value: initial swelling stage


title: Group 3 MB D425 cells, EYA2 shRNA#6, rep 1

value: Eya2 shRNA #6


title: ASPC1PSA_PS01ULAASPC1PSAS24_TTAGCCGCT_L003_R1_001

value: PDA tumor


title: ASPC1PSA_PS01ULAASPC1PSAS25_ACGCATGAT_L003_R1_001


title: Rapeseed_14d_young_leaves_H3K4me3_aChIP-seq_rep2

value: Zhongshuang 11


title: Rapeseed_14d_young_leaves_H3K4me3_eChIP-seq_rep1


title: ASPC1PSA_PS01ULAASPC1PSAS27_TGTCAGTTC_L003_R1_001

value: Ulixertinib


title: Smple two of cultivated Eleocharis dulcis corm at its late swelling stage stage

value: late swelling stage stage


title: Smple three of cultivated Eleocharis dulcis corm at its late swelling stage stage


title: Group 3 MB D425 cells, non-targeting control, rep 1

value: Control shRNA


title: Smple one of cultivated Eleocharis dulcis corm at its late swelling stage stage


title: Rapeseed_14d_young_leaves_H3K4me3_aChIP-seq_rep1


title: HK1-KD ectosome-incubated Huh7 cells_3

first: Qi-tao

last: Chen

state: Fujian Province

address: Xiang annan road

department: School of Life Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Analysis for KEGG and nmc vs ctrl, si vs nmc.txt for GSEA were generated by integrating raw count value of genes from each sample.

source_name: Huh7 cells

extract_protocol:
Ectosomes were isolated by differential centrifugation processes. LX-2 cells were cultured in DMEM medium containing 10% FBS for 36 hour. Culture medium was first collected and centrifuged (300 g, 10 min, 4℃) to remove cells. The supernatant was then centrifuged (2,000 g, 20 min, 4℃) to remove cell debris. The collected medium was centrifuged again (16,500 g, 30 min, 4℃) to obtain pellets containing the ectosomes.Huh7 cells were preincubated with different ectosomes or not for 12 hours and then  fresh medium for another 12 hours. Lastly, RNA in different groups of Huh7 cells were extracted by Trizol for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Huh7 cells

value: HK1-KD ectosome-incubated


title: HK1-KD ectosome-incubated Huh7 cells_2


title: Rapeseed_14d_young_leaves_H3K27me3_aChIP-seq_rep2


title: Rapeseed_14d_young_leaves_H3K27me3_aChIP-seq_rep1


title: Smple one of cultivated Eleocharis dulcis corm at its maturity stage


title: Smple three of cultivated Eleocharis dulcis corm at its middle swelling stage stage

value: middle swelling stage stage


title: ectosome-incubated Huh7 cells_3

value: ectosome-incubated


title: HK1-KD ectosome-incubated Huh7 cells_1


title: Smple two of cultivated Eleocharis dulcis corm at its imiddle swelling stage stage


title: Smple one of cultivated Eleocharis dulcis corm at its middle swelling stage stage


title: ASPC1PSA_PS01ULAASPC1PSAS14_CGCTAAAGT_L003_R1_001

extract_protocol:
After 24 h of incubation, the plates were treated with following drugs: RAF inhibitors – Sorafenib, Dabrafenib, RAF709, PLX8394, GDC-0879; MEK inhibitors – Trametinib, Cobimetinib, Binimetinib, Selumetinib, Rafametinib; and ERK inhibitors – SCH772984, Ulixertinib, AZD0364, Ravoxertinib. Each drug was dosed at the concentration at which the cells were 80% viable after 48 h of treatment. After 24 h of treatment, the medium was replaced with 100 ml of FBS supplemented with 10% DMSO and the plates were frozen at −80 °C prior to PLATE-Seq.
Detailed protocol for preparation of the automated PLATE-SEQ experiment was described by Bush et al. (Bush et al., 2017).
Samples were sequenced using PlateSeq approach

value: Human PDA cell line


title: Smple three of cultivated Eleocharis dulcis corm at its initial swelling stage

value: corm


title: ectosome-incubated Huh7 cells_2


title: ASPC1PSA_PS01ULAASPC1PSAS17_CTACGTCCT_L003_R1_001

value: Ravoxertinib


title: Dormant_rapeseed_seeds_1year_H3K4me3_aChIP_rep1

value: dry seed cells


title: ASPC1PSA_PS01ULAASPC1PSAS12_CAACGGAAG_L003_R1_001

value: DMSO


title: ectosome-incubated Huh7 cells_1


title: ASPC1PSA_PS01ULAASPC1PSAS5_AGCACTGGA_L003_R1_001


title: ASPC1PSA_PS01ULAASPC1PSAS16_TACGGTCAT_L003_R1_001

value: Cobimetinib


title: Smple two of cultivated Eleocharis dulcis corm at its initial swelling stage

value: initial swelling stage


title: ASPC1PSA_PS01ULAASPC1PSAS15_GTAACCCTT_L003_R1_001

value: Trametinib


title: Dormant_rapeseed_seeds_1year_H3K27me3_aChIP_rep1


title: control Huh7 cells_3

value: control


title: Dormant_rapeseed_seeds_1year_H3K4me3_aChIP_rep2

value: Zhongshuang 11


title: Dormant_rapeseed_seeds_1year_H3K27me3_aChIP_rep2


title: control Huh7 cells_2


title: 50d_Rapeseed_seeds_RNAPII_eChIP-seq_rep2

value: 50d seeds cells

value: RNAPII


title: control Huh7 cells_1


title: tumor tissues of patient 6

city: Shanghai

first: guangyong

last: zheng

address: cailun road 1200

institute: shutcm

description: 10 X  genomics

data_processing:
the demultiplexing, barcoded processing, gene counting and aggregation were conducted through the Cell Ranger Software V 3.1.0
Assembly: GRCH38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
Fresh normal mucosa and MCA tissue were washed with ice-cold PBS and minced into small pieces. Then the normal and tumor tissue pieces were digested with collagenase VIII at 0.38 mg/mL and DNase I at 0.1 mg/mL in 30% FBS for 1.0h at 37 °C. After digestion, tissue pieces were washed with PBS twice.
Library was constructed according to the manufacter's instructions (single cell 3' V2 protocol 10 X genomics)

value: colon

value: tumor tissue

value: tumor


title: Non-induced normal cells, biol rep 3

city: Toronto

first: Delphine

last: Dufour

state: Ontario

address: 124 Edward Street

country: Canada

institute: Faculty of Dentistry, University of Toronto

data_processing:
The Illumina bcl2fastq Conversion software was used for demultiplexing and to convert the base call files generated by the Illumina sequencing into FASTAQ files.
Quality of the raw data was assessed with FastQC (v0.11.9).
Removal of sequencing adapters and low-quality ends was performed using Trim Galore (v0.5.0) and the QC checks were repeated with FastQC to ensure that high-quality data was retained.
The reads were then aligned to S. Mutans UA159 complete genome (NC_004350.2) downloaded from NCBI using STAR aligner (v2.6.0c).
Assembly: NC_004350.2
Supplementary files format and content: htseq files include read counts for each sample

organism: Streptococcus mutans UA159

source_name: Non-induced normal cells

growth_protocol: S. mutans UA159 cells were grown in THYE broth at 37C with 5% CO2 for 24 hours.

extract_protocol:
RNA  was harvested using the RiboPure-Bacteria purification kit. 0.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit following manufacturer's protocols.

treatment_protocol: For the CSP induction, the CSP pheromone was added at a final concentration of 0.05µg/ml.

value: WT

value: Non-induced


title: Non-induced normal cells, biol rep 2


title: normal tissues of patient 6

description: 10 X  genomics

value: normal tissue

value: normal


title: ASPC1PSA_PS01ULAASPC1PSAS1_ACCAGTCCT_L003_R1_001

value: PDA tumor

value: Human PDA cell line

value: Sorafenib


title: 50d_Rapeseed_seeds_RNAPII_aChIP-seq_rep1

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1
Supplementary files format and content: Narrowpeak
Supplementary files format and content: \

value: 50DPA seeds cells


title: Non-induced normal cells, biol rep 1


title: 50d_Rapeseed_seeds_input_rep2


title: tumor tissues of patient 5

description: 10 X  genomics


title: normal tissues of patient 5

description: 10 X  genomics


title: ASPC1PSA_PS01ULAASPC1PSAS3_GACGTATGG_L003_R1_001

value: Selumetinib


title: Smple one of  cultivated Eleocharis dulcis corm at its initial swelling stage

value: corm

value: initial swelling stage


title: CSP-induced normal cells, biol rep 2

source_name: CSP-induced normal cells

value: CSP-induced


title: CSP-induced normal cells, biol rep 3


title: 50d_Rapeseed_seeds_input_rep1

value: Zhongshuang 11


title: 50d_Rapeseed_seeds_RNAPII_eChIP-seq_rep1

value: 50d seeds cells

value: RNAPII


title: 50d_Rapeseed_seeds_H3K4me3_aChIP-seq_rep1


title: Tomato_ripe_fruits_IgG_aChIP-seq_rep1

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : GWHANRE00000000, Solanum tuberosum L : DM v4.03, Glycine max : ZH13 v2.0, Zea mays : GCF_902167145.1, Solanum lycopersicum : GCF_000188115.4, Dianthus caryophyllus : v1, Citrus sinensis : GCF_000317415.1, Arabidopsis thaliana : TAIR10, Saccharum officinarum : AP85-441 v20190103, Cucumis melo : GCF_000313045.1, Oryza sativa : GCF_001433935.1,Populus:sPta717 v2
Supplementary files format and content: Narrowpeak and broadpeak
Supplementary files format and content: \

organism: Solanum lycopersicum

source_name: ripe fruits

value: ripe fruits

value: AC

value: ripe fruits cells

value: IgG


title: Tomato_ripe_fruits_IgG_aChIP-seq_rep2


title: 50d_Rapeseed_seeds_RNAPII_aChIP-seq_rep2


title: normal tissues of patient 4

description: 10 X  genomics

value: colon

value: normal tissue


title: tumor tissues of patient 4

description: 10 X  genomics

value: tumor tissue

value: tumor


title: 50d_Rapeseed_seeds_H3K4me3_aChIP-seq_rep2


title: 50d_Rapeseed_seeds_H3K27me3_Regular_ChIP_rep2


title: tumor tissues of patient 3

description: 10 X  genomics


title: normal tissues of patient 3

description: 10 X  genomics

value: normal


title: Tomato_ripe_fruits_input_rep2

value: fruits cells


title: 50d_Rapeseed_seeds_H3K27me3_Regular_ChIP_rep1

value: 50DPA seeds cells


title: CSP-induced normal cells, biol rep 1

value: WT


title: tumor tissues of patient 2

description: 10 X  genomics


title: Tomato_ripe_fruits_input_rep1


title: 50d_Rapeseed_seeds_H3K27me3_eChIP-seq_rep2


title: Tomato_ripe_fruits_H3K4me3_aChIP-seq_rep2


title: normal tissues of patient 2

description: 10 X  genomics


title: 50d_Rapeseed_seeds_H3K27me3_eChIP-seq_rep1


title: Tomato_ripe_fruits_H3K4me3_aChIP-seq_rep1


title: 50d_Rapeseed_seeds_H3K27me3_aChIP-seq_rep2


title: Tomato_ripe_fruits_H3K27me3_aChIP-seq_rep2


title: tumor tissues of patient 1

description: 10 X  genomics


title: normal tissues of patient 1

description: 10 X  genomics


title: 50d_Rapeseed_seeds_H3K27me3_aChIP-seq_rep1


title: Tomato_ripe_fruits_H3K27me3_aChIP-seq_rep1


title: 119_FL_abundance_block5_output2

status: Public on Apr 27 2024

city: Barcelona

first: Antoni

last: Beltran

address: Dr Aiguader, 88

country: Spain

institute: CRG Barcelona

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

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)

value: log phase culture


title: WT Encriched Infected

city: Seattle

first: Laura

last: Belmont

state: Washington

address: 1100 Fairview Ave N

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: Targeted sub-library

value: DENV infected via ADE, GFP-


title: B3Rd4 Infected


title: 117_FL_abundance_block4_output3


title: 116_FL_abundance_block4_output2


title: WT Control

value: Uninfected cells


title: B1Rd3 Infected


title: B3Rd4 Control


title: B1Rd3 Control


title: 118_FL_abundance_block5_output1


title: C7_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: C7_output_3

description: genomic and plasmid DNA


title: 113_FL_abundance_block3_output2


title: 114_FL_abundance_block3_output3


title: 112_FL_abundance_block3_output1


title: 115_FL_abundance_block4_output1


title: 111_FL_abundance_block2_output3


title: C7_output_1

description: genomic and plasmid DNA


title: 109_FL_abundance_block2_output1


title: C7_input_3

description: genomic and plasmid DNA


title: 108_FL_abundance_block1_output3


title: C7_input_1

description: genomic and plasmid DNA


title: 107_FL_abundance_block1_output2


title: C6_output_3 tech 3

description: genomic and plasmid DNA


title: 106_FL_abundance_block1_output1


title: Plant leaves, melatonin mitigation of NaCl stress, 10d, rep3

city: Kunming

first: Ling

last: Zhu

address: Southwest Forestry University, No. 300, Bailong Road, Qingyun Street, Kunming, Yunnan Province, China

institute: Southwest Forestry University

description:
nucleus
Effects of exogenous melatonin on NaCl stress in Eriobotrya japonica seedlings

data_processing:
equencing data were removed using Fastp to remove sequences with junctions at the 3' end and to remove Reads with average quality scores lower than Q20; the filtered Reads were compared to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml). Data quality was checked using FastaQC to ensure that all transcriptome data had a Q value greater than 30, resulting in high-quality Clean
Assembly: Using the Eriobotrya japonica genome as a reference genome
Supplementary files format and content: fastq

organism: Eriobotrya japonica

source_name: plant leaf

growth_protocol: Eriobotrya japonica seedling

extract_protocol:
A 0.5 g sample from each of the treatment and control groups was sent to Noemi Metabolism Ltd. for transcriptome sequencing.
Filtered Reads were compared to the reference genome using the upgraded HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml ) software for TopHat2.
HISAT2 uses an improved BWT algorithm for library construction. Default parameters are used for non-strand-specific libraries, while strand-specific libraries require the library type to be specified (i.e., use --rna-strandness RF for first, --rna-strandness FR for second).

treatment_protocol: CK was treated with water, ST was treated first with water and then with a NaCl stress concentration of 200 mmol per liter, and MTST was first root-irrigated with a screened 150 µmol per liter melatonin solution and then treated for 10 days using 200 mmol per liter NaCl stress

value: plant leaf

value: melatonin mitigation of NaCl stress


title: C6_output_2 tech 3

description: genomic and plasmid DNA


title: 102_FL_abundance_block4_input3


title: 104_FL_abundance_block5_input2


title: 103_FL_abundance_block5_input1


title: 101_FL_abundance_block4_input2


title: C6_output_1 tech 3

description: genomic and plasmid DNA


title: Plant leaves, melatonin mitigation of NaCl stress, 10d, rep1


title: 110_FL_abundance_block2_output2


title: 100_FL_abundance_block4_input1


title: Plant leaf, NaCl stress, 10d, rep3

value: water&NaCl stress


title: 99_FL_abundance_block3_input3


title: 98_FL_abundance_block3_input2


title: C7_input_2

description: genomic and plasmid DNA


title: C6_input_2 tech 3

description: genomic and plasmid DNA


title: C6_input_3 tech 3

description: genomic and plasmid DNA


title: 97_FL_abundance_block3_input1


title: 96_FL_abundance_block2_input3


title: Plant leaf, NaCl stress, 10d, rep2


title: C6_input_1 tech 3

description: genomic and plasmid DNA


title: 95_FL_abundance_block2_input2


title: Plant leaf, NaCl stress, 10d, rep1


title: C6_output_3 tech 2

description: genomic and plasmid DNA


title: 93_FL_abundance_block1_input3


title: Plant leaf, water, 10d, rep3

value: water


title: C6_output_2 tech 2

description: genomic and plasmid DNA


title: GTS slow 2

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Bead array (850k) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: Data and bioinformatic analyses were carried out using ‘GenomeStudio’ software (version 2011.1, Methylation Module v1.9) (Illumina), following an in-house pipeline at the Institute of Neuropathology (UKE).

label: Cy5 and Cy3

source_name: non-seminoma germ cell tumor, growing teratoma

label_protocol: The Infinium MethylationEPIC array BeadChip (Illumina, San Diego, CA, USA) analyses were performed at the Insitute of Neuropathology, University Hospital Hamburg-Eppendorf (UKE), Hamburg, Germany (Prof. Dr. Ulrich Schüller), following an established in-house analysis pipeline.

extract_protocol: Genomic DNA used for the Infinium MethylationEPIC BeadChip array (850k) was isolated and purified by two rounds of PCI precipitation including a RNaseA treatment. DNA concentrations were measured by the ‘Qubit 4 Fluorometer’ (Thermo Fisher Scientific).

value: growing teratoma tissue

tag: growth speed

value: GTS slow


title: Plant leaf, water, 10d, rep2


title: 90_FL_activity_block5_output3


title: C6_output_1 tech 2

description: genomic and plasmid DNA


title: 89_FL_activity_block5_output2


title: 92_FL_abundance_block1_input2


title: Plant leaf, water, 10d, rep1


title: GTS slow 4


title: 91_FL_abundance_block1_input1


title: C6_input_3 tech 2

description: genomic and plasmid DNA


title: 86_FL_activity_block4_output2


title: 88_FL_activity_block5_output1


title: C6_input_2 tech 2

description: genomic and plasmid DNA


title: 85_FL_activity_block4_output1


title: GTS medium 4

value: GTS medium


title: 84_FL_activity_block3_output3


title: GTS slow 1


title: C6_input_1 tech 2

description: genomic and plasmid DNA


title: 87_FL_activity_block4_output3


title: GTS medium 3


title: GTS rapid 2

value: GTS rapid


title: 83_FL_activity_block3_output2


title: C6_output_3

description: genomic and plasmid DNA


title: 80_FL_activity_block2_output2


title: 81_FL_activity_block2_output3


title: C6_output_2

description: genomic and plasmid DNA


title: Plant leaves, melatonin mitigation of NaCl stress, 10d, rep2


title: 79_FL_activity_block2_output1


title: C6_output_1

description: genomic and plasmid DNA


title: GTS rapid 4


title: 78_FL_activity_block1_output3


title: 94_FL_abundance_block2_input1


title: C6_input_3

description: genomic and plasmid DNA


title: 76_FL_activity_block1_output1


title: 75_FL_activity_block5_input3


title: 74_FL_activity_block5_input2


title: GTS rapid 1


title: GTS medium 1


title: C6_input_2

description: genomic and plasmid DNA


title: 71_FL_activity_block4_input2


title: C6_input_1

description: genomic and plasmid DNA


title: vzv_72h_without_RNaseR

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: without RNase R-treated RNA

data_processing: De novo circRNA identification and reconstruction: Raw reads were aligned with BWA Aligner[25] (BWA-MEM version 0.7.17-R1188) to human, VZV reference genomes: hg38, pOka strain (AB097933.1). Alignment statistics were performed with Qualimap2 (version 2.2.1). CIRI2 (version v2.0.6) vircircRNA, and find_circ were used for circRNA calling. Reconstruction of partial and full length circRNAs was performed with CIRI-full (version 2.0).

source_name: SH-SY5Y cells

extract_protocol: Ribosome-depleted and RNase R-treated RNA samples were used for library preparation and subsequently sequenced using BGISEQ platform in PE150.

treatment_protocol: SH-SY5Y cells were seeded at a density of 10^6 in 6-well plate (Corning) prior to inoculation with log106 PFU of pOka.

value: SH-SY5Y cells

value: Post pOka_WT infected 72 hours


title: 73_FL_activity_block5_input1


title: 72_FL_activity_block4_input3


title: 70_FL_activity_block4_input1


title: GTS slow 3


title: 69_FL_activity_block3_input3


title: pOka_M2_3

description: mRNA-seq

data_processing: Gene expression quantification: After removing low-quality, adapter-polluted, and high content of unknown base (N) read, the clean reads data were aligned to the human genome hg38 using STAR. The counts of mapped reads for each gene were calculated using FeatureCounts from the sorted BAM files.

source_name: ARPE-19 cells

extract_protocol: RNA samples were used for library preparation and subsequently sequenced using BGI DNBseq platform in PE150

treatment_protocol: ARPER-19 cells were seeded at a density of 10^6 in 6-well plate (Corning) prior to inoculation with VZV pOKA-WT, pOKA-M1 and pOKA-M2.

value: ARPE-19 cells

value: human retinal epithelial cells

value: pOka_M2  infected


title: 77_FL_activity_block1_output2

value: log phase culture


title: pOka_M2_2

description: mRNA-seq


title: 82_FL_activity_block3_output1


title: GTS rapid 3


title: 68_FL_activity_block3_input2


title: vzv_72h

description: RNase R-treated RNA


title: GTS medium 2


title: C5_output_2 tech 3

description: genomic and plasmid DNA


title: 67_FL_activity_block3_input1


title: pOka_M2_1

description: mRNA-seq

value: pOka_M2 infected


title: 64_FL_activity_block2_input1


title: pOka_M1_3

description: mRNA-seq

value: pOka_M1 infected


title: C5_output_1 tech 3

description: genomic and plasmid DNA


title: 66_FL_activity_block2_input3


title: 65_FL_activity_block2_input2


title: C5_input_3 tech 3

description: genomic and plasmid DNA


title: 63_FL_activity_block1_input3


title: C5_input_2 tech 3

description: genomic and plasmid DNA


title: 60_KD_abundance_block5_output3


title: 59_KD_abundance_block5_output2


title: 62_FL_activity_block1_input2


title: 61_FL_activity_block1_input1


title: C5_output_3 tech 3

description: genomic and plasmid DNA


title: pOka_M1_2

description: mRNA-seq


title: pOka_M1_1

description: mRNA-seq


title: C5_output_3 tech 2

description: genomic and plasmid DNA


title: C5_input_1 tech 3

description: genomic and plasmid DNA


title: 57_KD_abundance_block4_output3


title: 56_KD_abundance_block4_output2


title: 55_KD_abundance_block4_output1


title: pOka_WT_3

description: mRNA-seq

value: pOka_WT infected


title: pOka_WT_1

description: mRNA-seq


title: 54_KD_abundance_block3_output3


title: C5_output_1 tech 2

description: genomic and plasmid DNA


title: 53_KD_abundance_block3_output2


title: 58_KD_abundance_block5_output1


title: pOka_WT_2

description: mRNA-seq


title: vzv_48h_3

description:
circRNA-seq
RNase R-treated RNA

value: Post pOka_WT infected 48 hours


title: C5_output_2 tech 2

description: genomic and plasmid DNA


title: 52_KD_abundance_block3_output1


title: vzv_48h_2

description:
circRNA-seq
RNase R-treated RNA


title: vzv_48h_1

description:
circRNA-seq
RNase R-treated RNA


title: 50_KD_abundance_block2_output2


title: C5_input_3 tech 2

description: genomic and plasmid DNA


title: 48_KD_abundance_block1_output3


title: C5_input_2 tech 2

description: genomic and plasmid DNA


title: 49_KD_abundance_block2_output1


title: C5_input_1 tech 2

description: genomic and plasmid DNA


title: 47_KD_abundance_block1_output2


title: 46_KD_abundance_block1_output1


title: vzv_24h_3

description:
circRNA-seq
RNase R-treated RNA

value: Post pOka_WT infected 24 hours


title: C5_output_3

description: genomic and plasmid DNA


title: 45_KD_abundance_block5_input3


title: vzv_24h_2

description:
circRNA-seq
RNase R-treated RNA


title: 42_KD_abundance_block4_input3


title: vzv_24h_1

description:
circRNA-seq
RNase R-treated RNA


title: 41_KD_abundance_block4_input2


title: C5_output_1

description: genomic and plasmid DNA


title: 40_KD_abundance_block4_input1


title: mock_3

description:
circRNA-seq
RNase R-treated RNA

value: mock


title: C5_input_3

description: genomic and plasmid DNA


title: 51_KD_abundance_block2_output3


title: mock_2

description:
circRNA-seq
RNase R-treated RNA


title: 39_KD_abundance_block3_input3


title: 38_KD_abundance_block3_input2


title: mock_1

description:
circRNA-seq
RNase R-treated RNA


title: 35_KD_abundance_block2_input2


title: 36_KD_abundance_block2_input3


title: C5_input_2

description: genomic and plasmid DNA


title: 34_KD_abundance_block2_input1


title: C5_input_1

description: genomic and plasmid DNA


title: 33_KD_abundance_block1_input3


title: 43_KD_abundance_block5_input1