title: A4108_6: Adipose_8wks_12PM

value: Adipose


title: A4115_6: Adipose_8wks_12PM

status: Public on Apr 19 2023

type: SRA

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

library_source: transcriptomic

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the hg19 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes the raw counts for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: obese male

extract_protocol:
RNA were extracted following the protocol from Rneasy Lipid Tissue Mini kit (Qiagen) and RNA intergrity number were measured through Agilent 2200 TapeStation system
Libraries were pooled and sequenced using an Illumina HiSeq 2500 with 50-bp single-read chemistry

tag: tissue

tag: gender

value: male

tag: genotype

value: wild type


title: 11A_M_1050

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain

tag: Sex


title: PANC1-WT-1

city: beijing

first: Yanhong

last: Wang

address: Dong dan san tiao No.5

country: China

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences，School of Basic Medicine Peking Union Medical College

data_processing:
RNA-seq was performed using Illunina hiseq 6000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using a protocol from DEseq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

growth_protocol: Cells lines were plated in ultralow attachment six well plates at a density of 5000 viable cells per well. Cells were grown in spheroid medium consisting of DMEM/F12 supplemented with, 20 ng/ml basic fibroblast growth factor-2, 20 ng/ml epidermal growth factor, B27 serum-free supplement (1:50) and penicillin-streptomycin at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. VAHTS Universal V6 RNA-seq Library Prep Kit for Illuminaa was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Gemcitabine-resistant SW1990 cells were derived from original parental cell line by continuous exposure to stepwise increasing concentrations of gemcitabine. Initially, the exponentially growing cells were exposed 1 μM gemcitabine for 2-3 passages. The surviving cells were then exposed to gradually increasing concentrations of gemcitabine during every passage and this development period was persisting about 9 months. The final concentration of gemcitabine is 40 μM.

tag: cell line

tag: cell type

value: pancreatic cancer cell

tag: type

value: Wild type cell


title: 3rd instar larval imaginal discs and brains, CrolKO, Ph, rep2

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
Reads were trimmed using Trim Galore v0.6.5 and then aligned to the reference genome (dm3) using Bowtie v2.3.5 with default parameters. The PCR duplicates for each dataset were removed using the rmdup function of samtools v1.13. The data reproducibility between biological replicates was confirmed, then reads from replicates were pooled together for further analysis. Peak calling was performed with MACS v2.2.5 with parameters: -g dm -q 0.05 --nomodel --extsize 300. H3K27me3 and H3K27ac were called as broad peaks, while all other factors were called as narrow peaks. Differential binding analysis was performed using DiffBind2, with summit set as 250. Overlap of peaks were performed using the window function from BEDTools v2.29.2. ChIP-seq tracks were visualized using IGV, and heatmaps were created using DeepTools v3.5.1.
Assembly: dm3
Supplementary files format and content: narrowPeak (except for Input sample)

organism: Drosophila melanogaster

source_name: larval imaginal discs and brains

extract_protocol:
Chromatin immunoprecipitation (X-ChIP) was prepared as describe previously (Erokhin et al., BMC Biol, 2021). For each experiment, 150-200 mg of 3rd instar larvae or embryos were collected. The material was homogenized in 5 ml of buffer A1 (15 mM HEPES, pH 7.6; 60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 0.5% Triton X-100, 0.5 mM DTT, Roche cOmplete protease inhibitor) supplemented with the EDTA-free protease inhibitor cocktail (Roche, Switzerland) and formaldehyde as a crosslinking agent (final concentration 1.8%). The reaction was stopped by adding glycine (final concentration 225 mM). The homogenate was cleared by passing through 100-µm nylon cell strainer (BD Falcon) and pelleted by centrifugation at 4000 g, 4°C for 5 min. After twice washing in buffer A1 at 4°C, the pellet was treated with 0.5 ml of complete lysis buffer (15 mM HEPES, pH 7.6; 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1%Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.1% SDS, 0.5 % N-lauroylsarcosine, Roche cOmplete protease inhibitor) and sonicated to break chromatin into fragments with an average length of  200-600 bp. The material was pelleted by centrifugation at 18 000 g for 5 min, and the supernatant fluid was transferred to a new tube. The pellet was treated with the second 0.5-ml portion of lysis buffer, and the preparation was centrifuged at 18 000 g for 5 min. The two portions of the supernatant fluid were pooled, cleared by centrifuging twice at 18 000 g for 10 min, and the resultant chromatin extract (1 ml) was used for ChIP experiments. 9 ml of ChIP dilution buffer (15 mM HEPES, pH 7.6; 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1%Triton X-100, 0.5 mM DTT, Roche cOmplete protease inhibitor), was added to the sheared chromatin together with 50 ul of prewashed Protein A Sepharose beads (GE Healthcare). The samples were incubated at 4 oC for 1 hour on a rotating platform. The samples were spun at 10,000g to remove the beads and the supernatant was transferred to a fresh tube. One aliquot (1/10 volume) of chromatin extract after preincubation with Sepharose was kept as a control sample (Input).
DNA concentration of 5ul was measured using a Qubit 3.0 fluorometer (Invitrogen). 1.5ng of starting material/sample was used to make each library. ChIP-seq libraries were obtained using the NEBNext Ultra™ II DNA library preparation kit (New England Biolabs) or with the Thruplex DNA-seq and single index kits (Takara) following the manufacturer’s instructions. Samples were sequenced by 50bp or 100bp single-end sequencing with HiSeq2500 (Illumina) or with NovaSeq6000 sequencer.

tag: developmental stage

value: 3rd instar

value: larval imaginal discs and brains

value: CrolKO

tag: chip antibody

value: a gift from Donna Arndt-Jovin, Buchenau et al.,  J Cell Biol, 1998


title: A4107_6: Adipose_8wks_12PM


title: 11A_M_105


title: SW1990-WT-3


title: 3rd instar larval imaginal discs and brains, CrolKO, Ph, rep1


title: 3rd instar larval imaginal discs and brains, CrolKO, Input, rep2


title: 11A_M_1049


title: 3rd instar larval imaginal discs and brains, WT, H3K27me3, rep3

value: Wild-type

value: Millipore, 17-622


title: SW1990-WT-2


title: A4105_6: Adipose_8wks_12PM


title: SW1990-WT-1


title: 11A_M_1048


title: 3rd instar larval imaginal discs and brains, WT, H3K27me3, rep2


title: 3rd instar larval imaginal discs and brains, WT, H3K27me3, rep1


title: 11A_M_1047


title: BXPC3-2SP-3

value: Secondary  spheroid formation cells


title: A4102_6: Adipose_8wks_12PM


title: A4101_6: Adipose_8wks_12PM


title: 11A_M_1046


title: BXPC3-2SP-2


title: 3rd instar larval imaginal discs and brains, CrolKO, H3K27me3, rep3


title: 11A_M_1045


title: A4115_4: Adipose_baseline_12AM


title: 3rd instar larval imaginal discs and brains, CrolKO, H3K27me3, rep2


title: BXPC3-2SP-1


title: 11A_M_1044


title: A4114_4: Adipose_baseline_12AM


title: BXPC3-WT-3


title: A4113_4: Adipose_baseline_12AM


title: 3rd instar larval imaginal discs and brains, CrolKO, H3K27me3, rep1


title: 11A_M_1043


title: A4106_6: Adipose_8wks_12PM


title: A4112_4: Adipose_baseline_12AM


title: BXPC3-WT-2


title: 11A_M_1042


title: BXPC3-WT-1


title: A4110_4: Adipose_baseline_12AM


title: 11A_M_1041


title: 3rd instar larval imaginal discs and brains, WT, E(z), rep2

value: full length E(z)


title: 3rd instar larval imaginal discs and brains, WT, E(z), rep1


title: SW1990-GR-3

value: Gemcitabine resistant cell


title: 3rd instar larval imaginal discs and brains, CrolKO, E(z), rep2


title: A4109_4: Adipose_baseline_12AM


title: SW1990-GR-2


title: 11A_M_1040


title: 3rd instar larval imaginal discs and brains, CrolKO, E(z), rep1


title: 11A_M_104


title: SW1990-GR-1


title: A4108_4: Adipose_baseline_12AM


title: A4107_4: Adipose_baseline_12AM


title: 11A_M_1039


title: 3rd instar larval imaginal discs and brains, WT, CrolN, rep2

value: CrolN, 1-188 aa of Crol, isoform A


title: A4106_4: Adipose_baseline_12AM


title: 3rd instar larval imaginal discs and brains, WT, CrolN, rep1


title: 3rd instar larval imaginal discs and brains, WT, CrolC, rep2

value: CrolC, 726-962 aa of Crol, isoform PA


title: 11A_M_1038


title: 3rd instar larval imaginal discs and brains, WT, CrolC, rep1


title: 11A_M_1037


title: A4102_4: Adipose_baseline_12AM


title: A4105_4: Adipose_baseline_12AM


title: A4101_4: Adipose_baseline_12AM


title: 11A_M_1036


title: 11A_M_1035


title: A4115_3: Adipose_baseline_6PM


title: 11A_M_1034


title: 3rd instar whole larvae, CrolKO, RNA-seq, rep2

data_processing:
Reads were trimmed using Trim Galore v0.6.1, and then aligned to the reference genome (dm3) using STAR v2.7.3a. To identify differentially expressed genes, we first obtained the read count for each gene with the featureCount function of subread v2.0.0, then identified differentially expressed genes with FDR<0.05 and fold change>2 using DESeq2 v1.22.2. Gene ontology enrichment analysis was performed using metascape. The Transcripts Per Million (TPM) value for each gene was calculated using RSEM v1.3.2. RNA-Seq tracks were visualized using IGV.
Assembly: dm3
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

molecule: polyA RNA

source_name: whole larvae

extract_protocol:
For the extraction of RNA, the L3 larvae of wild-type (oregon) and mutant were collected in a PBS buffer (40 larvae per sample), in three biological repeats. Total RNA was extracted with the TRI reagent (Ambion).
PolyA comprising RNA fraction was isolated and prepared for sequencing with the NEBNext Ultra™ II Directional RNA Library Prep Kit. New generation sequencing was performed by Evrogen (evrogen.ru) with the Illumina NovaSeq6000 sequencer.

value: whole larvae


title: 3rd instar whole larvae, CrolKO, RNA-seq, rep1


title: 11A_M_1033


title: 3rd instar whole larvae, WT, RNA-seq, rep3


title: A4113_3: Adipose_baseline_6PM

value: Adipose


title: 11A_M_1032

value: male


title: 3rd instar whole larvae, WT, RNA-seq, rep2


title: 11A_M_1031


title: A4112_3: Adipose_baseline_6PM

value: wild type


title: 3rd instar whole larvae, WT, RNA-seq, rep1


title: 3rd instar whole larvae, CrolKO, RNA-seq, rep3


title: A4110_3: Adipose_baseline_6PM


title: neural lineages CB and VNC 105h ALH_2

city: Portugal

first: Catarina

middle: CF

last: Homem

address: Rua Campo Mártires da Pátria, 130

country: Portugal

institute: CEDOC - NMS

data_processing:
Each sequenced sample was processed with Cell Ranger Version 3.0.1 for alignment, barcode assignment and UMI counting. Samples were mapped to BDGP6 reference genome from Ensembl.
Genome_build: BDGP6
Supplementary_files_format_and_content: fastq.gz files generate with NovaSeq 6000
Supplementary_files_format_and_content: filtered gene matrices obtained after Cell Ranger processing

source_name: Neural lineages

growth_protocol: larvae raised at 18ºC and shifted to 25ºC 18h prior to dissection

extract_protocol:
larval brins were dissected, dissociated and sorted (FACS)
libraries were prepared using the 10x Genomics protocol

value: NBs, intermediate progenitors, neurons

tag: animal age

value: 105h ALH

tag: brain location

value: CB and VNC


title: A4109_3: Adipose_baseline_6PM


title: A4114_3: Adipose_baseline_6PM


title: A4108_3: Adipose_baseline_6PM


title: 11A_M_1030


title: 11A_M_1029


title: 11A_M_103


title: A4107_3: Adipose_baseline_6PM


title: 11A_M_1028


title: A4106_3: Adipose_baseline_6PM


title: S12 WGBS

city: Guangzhou

first: yuyan

last: wang

address: Zhongshan 2nd Road, Yuexiu

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports

extract_protocol:
Genome DNA were extracted using DNeasy Blood & Tissue Kit (69,506, Qiagen, Germany). The size-selected DNA fragments are treated with bisulfite.
Libraries construction was following Illumina’s standard protocol. The sequencing was performed on the Illumina HiSeq X10.

tag: treatment

value: Bisulfite conversion


title: 11A_M_1027


title: HeLa WGBS

source_name: HeLa

value: HeLa


title: A4105_3: Adipose_baseline_6PM


title: neural lineages CB and VNC 105h ALH_1


title: 11A_M_1026


title: SiHa WGBS

source_name: SiHa

value: SiHa


title: A4102_3: Adipose_baseline_6PM


title: 11A_M_1025


title: A4101_3: Adipose_baseline_6PM


title: C33A WGBS


title: SiHa Hi-C

extract_protocol:
Cells are fixed with formaldehyde and digested by the HindIII or MboI restriction enzyme. The overhangs are filled in with biotin and ligated. Finally, the ligation product with biotin maker were pulled-down with streptavidin beads and sheared.
Libraries construction was following Illumina’s standard protocol. The sequencing was performed on the Illumina HiSeq X10 platform.

value: HindIII digestion


title: 11A_M_1024


title: CaSki WGBS

source_name: CaSki

value: CaSki


title: S12 Hi-C


title: 11A_M_1023


title: A4114_2: Adipose_baseline_12PM


title: 11A_M_1022


title: HeLa Hi-C


title: 11A_M_1021


title: A4113_2: Adipose_baseline_12PM


title: 11A_M_1020


title: A4110_2: Adipose_baseline_12PM


title: C33A Hi-C


title: A4112_2: Adipose_baseline_12PM


title: genomic DNA from fresh-frozen CRC36

type: genomic

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
Signal intensities files were extracted using the minfi Bioconductor package. Normalization was performed using the Functional Normalization function implemented in minfi.
The beta value was provided calculated by normalized signals. Normalization was performed using the Functional Normalization function implemented in minfi.
Unmethylated and methylated signal intensities in Series supplementary file

label: Cy5 and Cy3

source_name: colorectal cancer

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: colorectal cancer

tag: disease state

value: early-stage CRC


title: U2OS-p53(AD/AD), p53ChIP, rep1

city: New York

first: Joshua

last: Choe

state: NY

address: 816 Fairchild Center, MC 2422

department: Department of Biological Sciences

institute: Columbia University

data_processing:
ChIP-seq reads were trimmed using Trim Galore! --quality 15 --stringency 3
Trimed reads were aligned to the UCSC hg19 genome using Bowtie2
Peaks were called uing MACS2 -q 0.01 using input as control
Unique peaks were identified by bedtools intersect
Peak annotation and motif prediction were performed by Homer software
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: Osteoblasts were cultured in osteogenic differentiation medium (α-MEM supplemented with 10% FBS, 10 mM β-glycerol phosphate, 200 μM ascorbic acid, and 0.1 μM dexamethasone). U2OS were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS) at 37°C in a humidified 5% CO2 environment.  673 bovine serum (FBS) at 37°C in a humidified 5% CO2 environment

extract_protocol:
Cells were fixed in 1% formaldehyde at room temperature for 10 min, quenched by 125mM glycine,and sonicated in ChIP lysis buffer on ice
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KK8502) according to the manufacture's instruction

value: Osteosarcoma

tag: antibody

value: p53 (Santa Cruz, sc-126)


title: PANC-1 siROR1-3

city: Kumamoto city

first: Masaya

last: Yamazaki

address: 1-1-1, Honjyo, Chuo-ku

country: Japan

institute: Kumamoto university

description:
PANC1_tpm.txt
PANC1_DESeq2.txt

data_processing:
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina).
Differential expression testing was performed with DESeq2 (version 1.28.1).
Assembly: Genome_build: GRCh37
Sequencing reads were trimmed for adaptor sequence, and aligned to human transcriptome (GRCh37) and quantified with Salmon (version 1.3.0) with default settings.
Supplementary files format and content: Tab-delimited text files include TPM values for every gene and every sample.
Supplementary files format and content: Tab-delimited text files include p-value and q-value for every genes.

source_name: Pancreas

extract_protocol:
NA was extracted from sorted ROR1high and ROR1low cells using MagMAX-96 Total RNA Isolation Kit (Thermo Fisher Scientific), and 1 ng of RNA was used for the reverse transcription reaction using SMART-seq HT (Takara).  For PANC-1 cells, RNA was harvested using ReliaPrep RNA Cell Miniprep System (Promega).
RNA-seq library was prepared using Nextera XT Library Prep Kit (Illumina). For PANC-1 cells, RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit fir Illumina (NEB) following manufacturer's protocols.

tag: tissue

value: Pancreas

value: Pancreatic adenocarcinoma

value: ROR1 knockdown

value: siRNA (against ROR1)


title: 11A_M_102

value: male


title: genomic DNA from fresh-frozen normal18

source_name: adjacent normal tissue

value: adjacent normal tissue


title: A4109_2: Adipose_baseline_12PM

value: Adipose

tag: gender

value: wild type


title: genomic DNA from fresh-frozen CRC7


title: A4115_2: Adipose_baseline_12PM

tag: genotype


title: genomic DNA from fresh-frozen CRC21

value: Recurrence


title: genomic DNA from fresh-frozen CRC17


title: genomic DNA from fresh-frozen CRC19

value: female


title: genomic DNA from fresh-frozen normal36


title: genomic DNA from fresh-frozen CRC10


title: genomic DNA from fresh-frozen CRC46


title: 11A_M_1019

tag: brain region


title: A4108_2: Adipose_baseline_12PM


title: U2OS-p53(AD/AD), p53ChIP, rep2


title: 11A_M_1018

tag: age


title: genomic DNA from fresh-frozen normal26


title: PANC-1 siROR1-1

description:
PANC1_tpm.txt
PANC1_DESeq2.txt


title: genomic DNA from fresh-frozen CRC39


title: A4107_2: Adipose_baseline_12PM


title: genomic DNA from fresh-frozen CRC34


title: genomic DNA from fresh-frozen CRC26


title: 11A_M_1017

tag: strain


title: genomic DNA from fresh-frozen normal46

tag: Sex


title: CaSki Hi-C

tag: cell line


title: genomic DNA from fresh-frozen CRC12


title: genomic DNA from fresh-frozen CRC8


title: PANC-1 siCtrl-3

description:
PANC1_tpm.txt
PANC1_DESeq2.txt

tag: cell type

value: WT

value: siRNA (control)


title: 11A_M_1016


title: genomic DNA from fresh-frozen normal4


title: 11A_M_1015


title: A4106_2: Adipose_baseline_12PM


title: genomic DNA from fresh-frozen normal22


title: A4105_2: Adipose_baseline_12PM


title: 11A_M_1014


title: PANC-1 siCtrl-2

description:
PANC1_tpm.txt
PANC1_DESeq2.txt


title: A4102_2: Adipose_baseline_12PM


title: PANC-1 siCtrl-1

description:
PANC1_tpm.txt
PANC1_DESeq2.txt


title: PANC-1 siROR1-2

description:
PANC1_tpm.txt
PANC1_DESeq2.txt


title: genomic DNA from fresh-frozen normal41


title: U2OS, input

value: p53 WT/WT


title: PDO#1_xenograft_ROR1low-3

data_processing:
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina).
Sequencing reads were trimmed for adaptor sequence, and aligned to human transcriptome (GRCh37) and quantified with Salmon (version 1.3.0) with default settings.
Differential expression testing was performed with DESeq2 (version 1.28.1).
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for every gene and every sample.
Supplementary_files_format_and_content: Tab-delimited text files include p-value and q-value for every genes.

source_name: Pancreatic adenocarcinoma

extract_protocol:
RNA was extracted from sorted ROR1high and ROR1low cells using MagMAX-96 Total RNA Isolation Kit (Thermo Fisher Scientific), and 1 ng of RNA was used for the reverse transcription reaction using SMART-seq HT (Takara).
RNA-seq library was prepared using Nextera XT Library Prep Kit (Illumina).

value: PDO#1 (human pancreatic adenocarcinoma)

tag: model

value: xenograft

tag: sorted cell


title: A4101_2: Adipose_baseline_12PM


title: genomic DNA from fresh-frozen normal42

value: early-stage CRC


title: 11A_M_1013


title: 11A_M_1012


title: PDO#1_xenograft_ROR1high-3


title: 11A_M_1011


title: 11A_M_1010


title: PDO#1_xenograft_ROR1high-2


title: A4113_1: Adipose_baseline_6AM


title: PDO#1_xenograft_ROR1low-1


title: A4112_1: Adipose_baseline_6AM


title: 11A_M_101


title: PDO#1_xenograft_ROR1high-1


title: A4115_1: Adipose_baseline_6AM


title: PDO#1_xenograft_ROR1low-2


title: genomic DNA from fresh-frozen CRC27

value: colorectal cancer


title: A4114_1: Adipose_baseline_6AM


title: A4110_1: Adipose_baseline_6AM


title: 11A_M_1009


title: A4109_1: Adipose_baseline_6AM


title: genomic DNA from fresh-frozen CRC28


title: A4108_1: Adipose_baseline_6AM


title: 11A_M_1007


title: 11A_M_1008


title: 56, GKRP-446L with 3mg/kg GKA

city: Newcastle upon Tyne

first: Loranne

last: Agius

address: Framlington Place

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

data_processing:
RNA-Seq sample quality was assessed via FastQC; all samples had quality scores > 35, no adapter contamination, and therefore none required trimming.
Transcript-level counts were obtained using Salmon (v1.4.0) run against the mouse reference transcript sequences (release M26, GRCm39) from Gencode
Assembly: gencode M26 (GRCm39)
Supplementary files format and content: tab-delimited text files include standard Salmon output (Name, Length, EffectiveLength, TPM, NumReads) for each Sample

source_name: liver

extract_protocol:
RNA was extracted mouse liver (n=56) using Trizol and purified using RNeasy kit (Qiagen #74104) with on-column DNase digestion (Qiagen #79254).
Samples were submitted to the Newcastle University Genomics Core for quality assessment and samples with a RIN value > 6 were used for sequencing.

value: liver

value: 3 mg/kg Drug

tag: diet

value: High fat, high sugar diet


title: 55, GKRP-446L with 3mg/kg GKA


title: 54, GKRP-446L with 3mg/kg GKA


title: A4106_1: Adipose_baseline_6AM


title: S2-VP10_xenograft_Chromium

data_processing:
The sequencing data were mapped against the human genome (GRCh38) and quantified using the CellRanger software package (version 6.0).
Raw gene counts were imported to R (version 4.0.2) and processed using the R package Seurat (version 4.0.4).
Cells with < 1% and > 30% mitochondrial genes mapped, < 5000 count RNA (UMIs), and < 4000 feature RNA (expressed genes) were eliminated from downstream analysis.
After filtering, UMI counts were normalized and performed principal component analysis (PCA).
Clustering analysis were obtained by the FindNeighbors and Findclusters function of Seurat with the following parameters: Findneighbors (dim = 15), Findclusters (resolution = 0.7).
The RNA velocity analysis was carried out in Velocyto.R (version 0.6) with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw UMI counts, and cell barcodes for every sample.

source_name: human pancreatic adenocarcinoma

extract_protocol: The scRNA-seq libraries were generated from sorted viable single cells (S2-VP10 xenograft) using Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) according to manufacturer’s instructions.

value: S2-VP10 (human pancreatic adenocarcinoma)


title: A4107_1: Adipose_baseline_6AM

value: male


title: 11A_M_1005


title: 53, GKRP-446L with 3mg/kg GKA


title: 11A_M_1006


title: A4105_1: Adipose_baseline_6AM


title: 52, GKRP-446L with 3mg/kg GKA


title: 11A_M_1004


title: A4102_1: Adipose_baseline_6AM


title: 11A_M_1003


title: 51, GKRP-446L with 3mg/kg GKA


title: genomic DNA from fresh-frozen normal12

value: adjacent normal tissue


title: A4101_1: Adipose_baseline_6AM

value: Adipose


title: 11A_M_1002


title: 50, GKRP-446L with 3mg/kg GKA


title: A4115_5: Adipose_8wks_6AM

value: wild type


title: 11A_M_1001


title: genomic DNA from fresh-frozen normal20

value: Recurrence


title: 48, GKRP-446L with 3mg/kg GKA


title: 49, GKRP-446L with 3mg/kg GKA


title: A4114_5: Adipose_8wks_6AM


title: genomic DNA from fresh-frozen normal25

value: female


title: A4113_5: Adipose_8wks_6AM


title: 11A_M_1000


title: A4112_5: Adipose_8wks_6AM


title: 47, GKRP-446L with 3mg/kg GKA


title: 46, GKRP-446L

value: Untreated


title: 11A_M_10


title: A4110_5: Adipose_8wks_6AM


title: 45, GKRP-446L


title: genomic DNA from fresh-frozen normal32


title: 11A_M_0


title: 44, GKRP-446L


title: genomic DNA from fresh-frozen normal2


title: genomic DNA from fresh-frozen CRC9


title: genomic DNA from fresh-frozen CRC15


title: 5F-D5-320-EV

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

data_processing:
Using the Bio-Rad SeqSense analysis software pipeline on its website (https://seqsense.bio-rad.com/), all reads for each sample were trimmed of all adapter sequences, then demultiplexed and deduplicated. Using the Galaxy instance of the TAMU HPRC (https://hprcgalaxy.tamu.edu/),  subsequent reads from the output fastq files were further trimmed of low-quality bases using Trimmomatic read trimmer software version 0.38.146. Using Trimmomatic and corresponding adapter sequence file for Illumina, reads were dropped if the read length is <15, then reads were scanned with a sliding window of 4, cutting when the average quality per base drops below 25, then trimming reads at the start and end of a read if base quality drops below 25. Resulting reads were mapped to the Mus musculus (mm39) genome assembly. Read mapping was performed using RNA STAR genomic analysis software platform version 2.7.847. Transcript-wise counts were calculated using HTSeq software version 0.9.148. Differential gene expression tests were then performed using DESeq2 software version 2.11.40.6 with a “sample type (EV vs. Cell)” x “sex (Female vs. Male)” x “treatment (0 vs. 120 vs 320 mg / dL)” experimental design.
Assembly: mm39
Supplementary files format and content: tabular text files include htseq counts for each Sample

source_name: dorsal telencephalon

growth_protocol: Young adult C57/Bl/6J nulligravid females were time-mated in- house with C57/Bl/6J males. 1-2 females in proestrous/estrous phase were placed in the male cage for a period of 90 minutes during the start of their dark cycle (7 pm), and the next morning was designated as gestational day (GD) 0.5 for pregnancyt mice. Pregnancy was confirmed when a dam exhibits daily weight gain starting from GD 8.5 after mating. Ex vivo neurosphere cultures were created from NSCs obtained from three separate pregnancies, from acutely dissociated GD 12.5 fetal mouse dorsal telencephalic neuroepithelium, which corresponds to the future isocortex, and used to model early neuronal development. At the time of collection, fetal sex was determined. Cortical neuroepithelial tissues within a single pregnancy were pooled by sex, to generate male- and female-specific cultures. Sex-specific cultures were obtained from three separate pregnancies (Pregnancy Set 3,4,5), to generate three male and three female biological replicates. Sex-specific cultures were maintained as non-adherent neurospheres in serum-free mitogenic media and passages 7 to 10 were used in this study.

extract_protocol:
Total RNA from the ultracentrifuged EV pellet was isolated using the miRNeasy micro kit (Qiagen; Catalog # 217084; Germantown, MD/USA) and total RNA from the matched cell-of-origin NSC pellets was isolated using the miRNeasy mini kit (Qiagen; Catalog # 217004).
RNA libraries for RNA-seq were prepared using SEQuoia Complete Stranded RNA Library Prep kit (Bio-Rad; Catalog # 17005726; Hercules, CA/USA) with Ribo‐Zero Plus ribosomal RNA depletion kit (Illumina; Catalog # 20040526; San Diego, CA/USA) following manufacturer's protocols.

treatment_protocol:
With four flasks defined as a single sample, dispersed single NSCs were seeded in T75 flask at a density of 4 × 10^5 cells / mL in 10 mL of culture media per flask. To model ethanol exposure levels from abstinence to the heavy exposure attainable by individuals with alcohol use disorders, each sample was randomly assigned to one of three ethanol treatment conditions: 0 mg/dL (control), 120 mg/dL (26 mM, moderate), or 320 mg/dL (70 mM, high). Ethanol (190 proof grain alcohol) was diluted into fresh culture medium and ethanol naïve media was replaced with fresh experimental media. For five days, neurosphere cultures were exposed to control or ethanol treatment conditions, with media replacement on day 3. To prevent ethanol loss in the culture medium throughout the experiment , all flasks were tightly capped with phenolic caps and sealed with parafilm. For each experiment, gas chromatography was used to verify ethanol concentrations in culture-conditioned medium. We measured the ethanol dose range, from moderate (100 – 134 mg/dL; 22 Mm – 29 mM) to high (250 – 380 mg/dL; 54 mM – 82 mM). On day 5, neurospheres and culture-conditioned medium (for the concentration and isolation of EVs) were collected.
Ultracentrifugation was used to separate and concentrate EV fractions. Cell fraction and its culture-conditioned medium were separated by centrifugation at 200 x g for 5 minutes, and the cell pellet isolated for separate RNA analysis. Next, the culture media supernatant was centrifuged at 2,000 x g at 4 °C for 10 minutes to eliminate debris and dead cells, then passed through a 0.2 µm sterile polyethersulfone membrane filter (VWR; Catalog # 28145-501; Radnor, PA/USA) to exclude debris with diameters greater than 0.2 µm. The filtered supernatant was centrifuged through a 100 kDa molecular weight cutoff (MWCO) polyethersulfone membrane (PALL; Catalog # MAP100C37; Port Washington, NY/USA) at 4,000 x g for 30 minutes to concentrate the EV-enriched supernatant while filtering out any particles below 100 kDa. The collected material on the membrane was transferred to polypropylene thick-walled centrifuge tubes (Beckman; Catalog # 355640; Brea, CA/USA), adding chilled (4 °C) 1 x PBS buffer (Thermo Fisher; Catalog # 14190144; Waltham, MA/USA) to a total volume of 7 mL per tube. This PBS-suspended material was centrifuged at 100,000 x g for 90 minutes at 4 °C in a Type 70 Ti fixed-angle titanium rotor (Beckman; Catalog # 337922; Brea, CA/USA). EV-enriched pellets were washed, by decanting the supernatant and resuspending the pellet in 1mL chilled PBS, followed by the addition of 6mL chilled PBS for centrifugation at 100,000 x g for 90 minutes at 4 °C.

value: dorsal telencephalon

value: neural stem cells

value: WT

value: alcohol

tag: alcohol dose

value: 320 mg/dL

tag: pregnancy

value: Set 5

tag: time

value: Day 5

tag: ev or_cell

value: EV


title: 43, GKRP-446L

value: liver

tag: treatment

value: High fat, high sugar diet


title: A4107_5: Adipose_8wks_6AM

tag: tissue

value: male


title: A4108_5: Adipose_8wks_6AM

tag: gender


title: genomic DNA from fresh-frozen normal5

value: adjacent normal tissue

tag: disease state

value: early-stage CRC


title: 5F-D5-120-EV

tag: genotype

value: 120 mg/dL


title: genomic DNA from fresh-frozen normal24

value: Recurrence


title: genomic DNA from fresh-frozen normal7


title: genomic DNA from fresh-frozen CRC37

value: colorectal cancer


title: A4109_5: Adipose_8wks_6AM

value: Adipose

value: wild type


title: 41, GKRP-446L

value: Untreated


title: 5F-D5-CTRL-EV

value: dorsal telencephalon

value: neural stem cells

value: WT

value: 0 mg/dL

value: female


title: A4106_5: Adipose_8wks_6AM


title: 42, GKRP-446L


title: 11A_M_100

tag: brain region

tag: age


title: 4F-D5-320-EV

tag: strain

value: alcohol

value: 320 mg/dL

value: Set 4

value: Day 5

tag: Sex

value: EV


title: A4105_5: Adipose_8wks_6AM

value: male


title: genomic DNA from fresh-frozen CRC14

value: early-stage CRC


title: genomic DNA from fresh-frozen normal28

value: adjacent normal tissue


title: genomic DNA from fresh-frozen normal44


title: A4102_5: Adipose_8wks_6AM


title: 11A_M_1


title: 4F-D5-120-EV

tag: cell type

value: 120 mg/dL


title: genomic DNA from fresh-frozen normal31

value: Recurrence


title: 40, GKRP-446L

value: liver

value: High fat, high sugar diet


title: 4F-D5-CTRL-EV

value: dorsal telencephalon


title: 38, GKRP-446L

value: Untreated


title: A4101_5: Adipose_8wks_6AM

value: Adipose

value: wild type


title: YUMMER1.7 (YR) tumor (8 days post-tumor initiation, either untreated or 24 hours post-treatment), scRNA-seq

city: New Haven

first: Miller-Jensen

last: Lab

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
24 hours post-treatment (if applicable), untreated and TTx-treated tumors for scRNA-seq were minced in RPMI with 2% FBS, then incubated with agitation at 37C, with 1 mg/mL Collagenase IV (C5138, Sigma-Aldrich) and 0.1 mg/mL DNAse I (10104159001, Roche) for 30 minutes. Tumors were then filtered through 70 µM filters into a single-cell suspension. Samples were then FACS-sorted into three populations: CD45+CD3+ (T cells), CD45+CD3- (non-T immune cells), CD45-CD3- (tumor and stroma). The populations were then recombined in a 2:1:1 ratio, and 10,000 cells from each condition (TTx-treated and control) were loaded onto the 10X Chromium System for sequencing. Antibodies used for sorting: CD45 (I3/3.2), CD3 (17A2)
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

treatment_protocol: For subcutaneous tumors, C57BL6/J mice were injected with 0.5x10^6 YUMMER1.7 cells (BrafV600E/ Pten-/-Cdkn2a -/- UV irradiated melanoma cell line). Mice were treated with 50 µg anti-CD40 (FGK4.5, BioXCell), 200 µg anti-CSF1R (m CSF1R.2 m.G1- D265A, Bristol Myers Squibb) and 200 µg anti-PD-1 (RMP1-14, BioXCell) 7 days post-tumor initation.

value: skin

value: untreated, or treated with the combination of anti-PD-1, CSF1R blockade, and agonistic CD40 (i.e., TTx) by i.p. injection 24 hours prior to collection for sequencing (treatment distinguished by metadata in labels.txt file)

value: 8 days post-tumor initiation


title: genomic DNA from fresh-frozen normal21


title: 3F-D5-320-EV

value: neural stem cells

value: WT

value: alcohol

value: 320 mg/dL

value: Set 3

value: female


title: Bone marrow immature NK Myc-/- 4

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
FASTQ files were processed using Nextflow and the nfcore/rnaseq pipeline with default values. Quantification of transcript expression on gene level was computed using Salmon and the GRCh38 reference transcriptome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Bone Marrow sample

source_name: Bone marrow

extract_protocol:
Total RNA was extracted from sorted cells with a RNeasy plus mini kit (Qiagen) according to the manufacturer’s instructions. The quantity and quality of the isolated RNA was determined with a Qubit (1.0) Fluorometer (Life Technologies) and a 4200 TapeStation System (Agilent).
Libraries were prepared following the Takara SMART-Seq v4 Ultra Low Input RNA Kit, with PolyA selection.
For the CD27SP NK cell isolated from the BM, after quantification, libraries were prepared for loading accordingly to the NovaSeq workflow with the NovaSeq6000 Reagent Kit (Illumina). Cluster generation and sequencing were performed on a NovaSeq6000 System with a run configuration of single end 100bp with a depth of around 20 Mio reads per sample. For the splenic mature NK cell, the TruSeq SR Cluster Kit HS40t00 (Illumina) was used for cluster generation of pooled normalized libraries on the cBOT.  Sequencing was performed on the Illumina HiSeq 4000 single end 125 bp using the TruSeq SBS Kit HS4000 (Illumina) with a depth of around 20 Mio reads per sample.

value: Bone marrow

tag: cell line

value: Ncr1cre Myc fl/fl

value: Immature CD27SP NK

value: Myc knock-out


title: 36, GKRP-446P/L with 3mg/kg GKA

value: liver

value: 3 mg/kg Drug

value: High fat, high sugar diet


title: Bone marrow immature NK Myc-/- 2


title: genomic DNA from fresh-frozen CRC41

value: colorectal cancer

value: male

value: early-stage CRC


title: 3F-D5-120-EV

value: dorsal telencephalon

value: 120 mg/dL

value: Day 5

value: EV


title: 35, GKRP-446P/L with 3mg/kg GKA


title: genomic DNA from fresh-frozen normal43

value: adjacent normal tissue


title: genomic DNA from fresh-frozen CRC48


title: 5M-D5-320-EV

value: neural stem cells

value: WT

value: alcohol

value: 320 mg/dL

value: Set 5


title: 34, GKRP-446P/L with 3mg/kg GKA


title: genomic DNA from fresh-frozen normal47


title: genomic DNA from fresh-frozen CRC1

value: female


title: Bone marrow immature NK Wild Type 4

value: Bone marrow

value: Ncr1cre Myc wt/wt

value: Immature CD27SP NK


title: 5M-D5-120-EV


title: Bone marrow immature NK Myc-/- 1

value: Ncr1cre Myc fl/fl

value: Myc knock-out


title: 3F-D5-CTRL-EV

value: 0 mg/dL

value: Set 3


title: 37, GKRP-446L

value: liver

value: Untreated

value: High fat, high sugar diet


title: 33, GKRP-446P/L with 3mg/kg GKA

value: 3 mg/kg Drug


title: Bone marrow immature NK Wild Type 2


title: 5M-D5-CTRL-EV

value: dorsal telencephalon

value: neural stem cells

value: Day 5

value: male

value: EV


title: 32, GKRP-446P/L with 3mg/kg GKA


title: genomic DNA from fresh-frozen normal1

value: adjacent normal tissue

value: female

value: early-stage CRC


title: 39, GKRP-446L


title: Bone marrow immature NK Wild Type 1

value: Bone marrow

value: Ncr1cre Myc wt/wt

value: Immature CD27SP NK

value: WT


title: genomic DNA from fresh-frozen CRC35

value: colorectal cancer

value: Recurrence


title: genomic DNA from fresh-frozen CRC22


title: 4M-D5-320-EV

value: alcohol

value: 320 mg/dL

value: Set 4


title: 31, GKRP-446P/L with 3mg/kg GKA

value: liver

value: 3 mg/kg Drug

value: High fat, high sugar diet


title: genomic DNA from fresh-frozen normal34


title: 4M-D5-120-EV

value: dorsal telencephalon

value: neural stem cells

value: 120 mg/dL

value: Day 5

value: male


title: 30, GKRP-446P/L with 3mg/kg GKA


title: O7c

city: Palo Alto

first: Ling

last: Liu

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (quality cutoff 20, adaptor stringency 1, final length filter 50).
Trimmed reads were mapped to mm10 mouse genome with STAR (mismatch cutoff 4% of read length, no non-canonical junction alignments).
Exonic reads uniquely mapped were summarized over genes with the featureCounts module of the Subread package.
Raw counts were analyzed with DESeq2.
Genome_build: mm10

source_name: Extensor digitorum longus muscle

extract_protocol:
Total RNA was extracted from myofibers with Qiagen Rneasy Plus Micro Kit
Reverse transcription was performed with 10ng of total RNA with Clontech SMART-SEQ v4 Ultra Low Input RNA Kit for Sequencing. Sequencing libraries were generated with Nugen Ovation Ultralow System v2.

value: 22 months

value: control

value: muscle cells


title: genomic DNA from fresh-frozen normal8

value: adjacent normal tissue

value: female

value: early-stage CRC


title: 4M-D5-CTRL-EV

value: WT

value: alcohol

value: 0 mg/dL

value: EV


title: O8c


title: O6c


title: 3M-D5-320-EV

value: 320 mg/dL

value: Set 3


title: 28, GKRP-446P/L

value: liver

value: Untreated

value: High fat, high sugar diet


title: genomic DNA from fresh-frozen normal15

value: Recurrence


title: 3M-D5-120-EV

value: dorsal telencephalon

value: neural stem cells

value: 120 mg/dL

value: Day 5

value: male


title: 27, GKRP-446P/L


title: genomic DNA from fresh-frozen normal9

value: adjacent normal tissue


title: O1e4

value: 22 months

value: 5-week voluntary wheel running

value: muscle cells


title: 3M-D5-CTRL-EV

value: WT

value: alcohol

value: 0 mg/dL


title: O5c

value: control


title: genomic DNA from fresh-frozen CRC6

value: colorectal cancer

value: early-stage CRC


title: 29, GKRP-446P/L with 3mg/kg GKA

value: liver

value: 3 mg/kg Drug

value: High fat, high sugar diet


title: 26, GKRP-446P/L

value: Untreated


title: 25, GKRP-446P/L


title: 3M-D5-CRTL-CELLS

value: dorsal telencephalon

value: neural stem cells

value: Set 3

value: Cell


title: O2ex

value: male

value: 22 months


title: 3M-D5-120-CELLS

value: 120 mg/dL

value: Day 5


title: O1ex

value: 5-week voluntary wheel running

value: muscle cells


title: O3ex


title: 3M-D5-320-CELLS

value: WT

value: alcohol

value: 320 mg/dL


title: Y8c

value: 4 months

value: control


title: 23, GKRP-446P/L

value: liver

value: High fat, high sugar diet


title: 24, GKRP-446P/L

value: Untreated


title: 22, GKRP-446P/L


title: 4M--D5-CTRL-CELLS

value: dorsal telencephalon

value: neural stem cells

value: 0 mg/dL

value: Set 4


title: Y7c

value: male


title: 21, GKRP-446P/L


title: Y6c


title: 4M-D5-120-CELLS

value: 120 mg/dL

value: Cell


title: 20, GKRP-446P with 3mg/kg GKA

value: 3 mg/kg Drug


title: genomic DNA from fresh-frozen CRC16

value: colorectal cancer

value: early-stage CRC


title: Y5c

value: muscle cells


title: genomic DNA from fresh-frozen CRC43


title: 5M-D5-CTRL-CELLS

value: WT

value: alcohol

value: Set 5

value: Day 5


title: genomic DNA from fresh-frozen CRC13

value: female


title: 19, GKRP-446P with 3mg/kg GKA

value: liver

value: High fat, high sugar diet


title: Y1e4

value: 4 months

value: 5-week voluntary wheel running


title: genomic DNA from fresh-frozen CRC33


title: 18, GKRP-446P with 3mg/kg GKA


title: 5M-D5-120-CELLS

value: dorsal telencephalon

value: neural stem cells


title: 17, GKRP-446P with 3mg/kg GKA


title: 16, GKRP-446P with 3mg/kg GKA


title: genomic DNA from fresh-frozen normal23

value: adjacent normal tissue

value: male

value: Recurrence


title: 4M-D5-320-CELLS

value: 320 mg/dL

value: Set 4

value: Cell


title: genomic DNA from fresh-frozen CRC38

value: colorectal cancer

value: early-stage CRC


title: 5M-D5-320-CELLS

value: WT

value: alcohol

value: Set 5


title: 3F-D5-CTRL-CELLS

value: 0 mg/dL

value: Set 3

value: Day 5

value: female


title: MDA-MB-231 sgAS3

city: Baltimore

first: Aikaterini

last: Kontrogianni-Konstantopoulos

state: MD

address: 108 N. Greene Street

institute: University of Maryland School of Medicine

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo Sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is used as a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated at this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed
The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values<0.01 and absolute log2 fold changes >1 were called as differentially expressed for each comparison

growth_protocol: MDA-MB-231 cells were purchased from ATCC and cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycinin. Incubated in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA extraction, library preparation, sequencing, and data analysis was conducted at Genewiz, LLC. Total RNA was extracted from frozen cell pellets using Qiagen RNeasy Plus Universal mini kit following the manufacturer’s instructions
RNA sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions

treatment_protocol: MDA-MB-231 cells were sequentially transduced with LentiMPH lentivirus and selected with hygromycin, and LentiSAM lentivirus and selected with blasticidin

value: epithelial, human breast cancer cell line

value: CRISPR-activation

value: transduced with sgAS3


title: genomic DNA from fresh-frozen CRC29


title: genomic DNA from fresh-frozen CRC5

value: male


title: MDA-MB-231 sgAS2

value: transduced with sgAS2


title: 3F-D5-120-CELLS

value: dorsal telencephalon

value: neural stem cells

value: 120 mg/dL


title: 15, GKRP-446P with 3mg/kg GKA

value: liver

value: 3 mg/kg Drug

value: High fat, high sugar diet


title: genomic DNA from fresh-frozen normal14

value: adjacent normal tissue

value: Recurrence

value: early-stage CRC


title: Y1ex

value: 4 months

value: 5-week voluntary wheel running

value: muscle cells


title: 14, GKRP-446P with 3mg/kg GKA


title: 3F-D5-320-CELLS

value: WT

value: alcohol

value: 320 mg/dL

value: Set 3

value: Day 5

value: female

value: Cell


title: MDA-MB-231 EV

value: epithelial, human breast cancer cell line

value: trandsuced with empty vector


title: genomic DNA from fresh-frozen CRC24

value: colorectal cancer

value: male


title: genomic DNA from fresh-frozen normal27

value: adjacent normal tissue


title: 4F-D5-CTRL-CELLS

value: dorsal telencephalon

value: neural stem cells

value: 0 mg/dL

value: Set 4


title: Y3ex

value: 4 months

value: 5-week voluntary wheel running

value: muscle cells


title: 4F-D5-120-CELLS

value: WT

value: alcohol

value: 120 mg/dL


title: NKYS-shScramble-3

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
sh-scramble
NKYS_ScrSh_3

data_processing:
clean fastq were obtained from Novogene after quality check removing reads containing adapters, reads with more than 10% undetermined base, low quality reads.
Sequenced reads were mapped to hg38 using STAR v2.4.2a with default parameters settings
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were computed using RSEM v1.2.25 and Gencode v35 annotation.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: NKYS

growth_protocol: Cells were grown in T25 flask in RPMI1640 supplemented with 10% FBS and 1% antibiotics

extract_protocol:
1 ug of total RNA was used for the construction of sequencing libraries, using Illumina TruSeq Stranded Total RNA Library Preparation Kit (Cat no: RS-122-2201).
Illumina TruSeq Stranded Total RNA Library Preparation Kit (Cat no: RS-122-2201) was used with 1 ug of total RNA for the construction of sequencing libraries according to manufacturer's protocol.

value: NKTCL cell line

value: NKYS

value: sh-scramble


title: 13, GKRP-446P with 3mg/kg GKA

value: liver

value: 3 mg/kg Drug

value: High fat, high sugar diet


title: Y2ex

value: male


title: genomic DNA from fresh-frozen CRC18

value: colorectal cancer

value: early-stage CRC


title: 11, GKRP-446P with 3mg/kg GKA


title: 4F-D5-320-CELLS

value: dorsal telencephalon

value: neural stem cells

value: 320 mg/dL

value: Day 5

value: female

value: Cell


title: NKYS-shScramble-2

description:
sh-scramble
NKYS_ScrSh_2


title: 5F-D5-CTRL-CELLS

value: WT

value: alcohol

value: 0 mg/dL

value: Set 5


title: 10, GKRP-446P

value: Untreated


title: genomic DNA from fresh-frozen normal30

value: adjacent normal tissue


title: genomic DNA from fresh-frozen normal48


title: 5F-D5-120-CELL

value: 120 mg/dL


title: genomic DNA from fresh-frozen CRC11

value: Recurrence


title: genomic DNA from fresh-frozen normal45

value: male


title: NKYS-shScramble-1

description:
sh-scramble
NKYS_ScrSh_1

value: NKTCL cell line

value: NKYS

value: sh-scramble


title: genomic DNA from fresh-frozen normal37

value: early-stage CRC


title: NKYS-TOX2-shRNA2-3

description:
TOX2 knockdown 2
NKYS_KD2_3


title: 5F-D5-320-CELLS

value: dorsal telencephalon

value: neural stem cells

value: 320 mg/dL


title: 12, GKRP-446P with 3mg/kg GKA

value: liver

value: 3 mg/kg Drug

value: High fat, high sugar diet


title: 8, GKRP-446P


title: NKYS-TOX2-shRNA2-1

description:
TOX2 knockdown 2
NKYS_KD2_1


title: Oc4mu

data_processing:
Sequences were demultiplexed using CellRanger version 2.0 (10x Genomics) with default parameters.
Reads were aligned to the mm10plus genome using STAR.
Gene counts were produced using HTSEQ with default parameters except “stranded” was set to false and “mode” was set to intersection-nonempty.
Genome_build: mm10plus

source_name: hindlimb muscles

extract_protocol: 10x Genomics protocol using GenCode Single-Cell 3’ Gel Bead and Library V3 kit

value: 22 months

value: control


title: genomic DNA from fresh-frozen CRC3

value: colorectal cancer

value: female


title: 7, GKRP-446P

value: Untreated


title: NKYS-TOX2-shRNA1-2

description:
TOX2 knockdown 1
NKYS_KD1_2


title: genomic DNA from fresh-frozen normal17

value: adjacent normal tissue


title: 6, GKRP-446P


title: Oc3mu

value: male


title: Oc2mu


title: genomic DNA from fresh-frozen CRC31

value: Recurrence


title: Oc1mu


title: NKYS-TOX2-shRNA1-1

description:
TOX2 knockdown 1
NKYS_KD1_1

value: NKTCL cell line

value: NKYS


title: h33 RNA seq2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

description: hot3-3 Seedling, rep2

data_processing:
Paired reads were trimmed by cutadapt v4.2 and then mapped to the Arabidopsis genome Araport11 using STAR v2.7.10b with parameters "--alignIntronMax 5000 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 10000000000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1".
Read pairs mapped to coding transcripts were counted by featureCounts v2.0.3 with parameters "-p --countReadPairs -B -C -O".
Assembly: Araport11
Supplementary files format and content: Tab-delimited txt files containing gene accession, raw read counts, and gene length.

organism: Arabidopsis thaliana

source_name: 18-day-old seedling

growth_protocol: 16 hr light/8 hr dark, 23˚C

extract_protocol:
Total RNA was isolated from 18-day-old seedlings using TRI Reagent (MRC, TR118) according to the manufacturer’s instructions. 4 ug of DNase-treated total RNA was used for the construction of sequencing libraries.
Polyadenylated RNA isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) was subjected to RNA-seq library construction with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420L).

value: 18-day-old seedling

value: somatic cells


title: 5, GKRP-446P


title: Oex4mu

value: 5-week voluntary wheel running


title: 3, GKRP-446P


title: h33 RNA seq1

description: hot3-3 Seedling, rep1


title: genomic DNA from fresh-frozen CRC47

value: early-stage CRC


title: Oex3mu


title: 2, GKRP-446P

value: liver


title: Oex2mu


title: h32 RNA seq2

description: hot3-2 Seedling, rep2


title: h32 RNA seq3

description: hot3-2 Seedling, rep3


title: 4, GKRP-446P


title: genomic DNA from fresh-frozen CRC44


title: genomic DNA from fresh-frozen CRC40


title: h32 RNA seq1

description: hot3-2 Seedling, rep1


title: Oex1mu


title: MLL4, male GKRP-446L 4

description: 14-wk M

extract_protocol:
RNA was mouse livers (n=18) using Trizol and purified using RNeasy kit (Qiagen #74104) with on-column DNase digestion (Qiagen #79254).
Samples were submitted to the Newcastle University Genomics Core for quality assessment and samples with a RIN value > 6 were used for sequencing.

value: Standard chow diet


title: genomic DNA from fresh-frozen normal11


title: 1, GKRP-446P

value: High fat, high sugar diet


title: WT RNA seq2

description: WT Seedling, rep2

value: WT


title: Yc4mu

value: 4 months

value: control


title: MLL3, male GKRP-446L 3

description: 13-wk M


title: WT RNA seq1

description: WT Seedling, rep1


title: Yc3mu


title: MLL2, male GKRP-446L 2

description: 13-wk M


title: 9, GKRP-446P


title: Yc2mu


title: KRAB, Dex 0.25microM, Rep2

city: Athens

first: Zhihua

last: Hua

state: Ohio

address: 22 Richland Ave

department: Department of Environmental and Plant Biology

institute: Ohio University

data_processing:
Adapter and low-quality sequences were removed from the raw FASTQ sequencing data using Trimmomatic (phred=33, minimum length=36; (Bolger et al., 2014)).  The resulting valid sequences were aligned to the Arabidopsis thaliana Col-0 reference genome (TAIR10; www.arabidopsis.org) using TOPHAT2 (Kim et al., 2013a) to identify accepted hits of each locus.  HTSeq was then used to calculate an absolute expression level (counts) of each locus based on the accepted hits (Anders et al., 2015).
Assembly: TAIR10
Supplementary files format and content: counts

source_name: transgenic plants

growth_protocol: Seeds harvested at the same time from plants grown under an identical environmental condition were for RNA-Seq analysis.  Dried seeds were vapor-phase surface sterilized for 3 to 5 h in the presence of 100 ml NaOCl (bleach) supplemented with 3 ml HCl.  Seeds were stratified in water at 4°C for three days in dark before being planted on half-strength Murashige-Skoog (1/2 MS) media plus 1% (w/v) sucrose supplemented with or without 0.025 and 0.025 microM Dexamethasone.  Seedlings were grown vertically for 8 days under a long day photoperiod (16-h white light (120 μmol m-2 s-1)/8-h darkness at 21°C and 19°C, respectively).

extract_protocol: RNA were isolated from whole seedlings using NucleoSpin RNA Plus kit (Macherey-Nagel) according to manufacturer's protocol.

value: whole seedlings

tag: ecotype

value: Dex (0.25 microM)


title: genomic DNA from fresh-frozen CRC32

value: colorectal cancer


title: Yc1mu

value: male


title: genomic DNA from fresh-frozen normal13

value: adjacent normal tissue

value: female


title: KRAB, Dex 0.25microM, Rep1


title: MLL1, male GKRP-446L 1

description: 13-wk M


title: Yex4mu


title: KRAB, DMSO, Rep2


title: genomic DNA from fresh-frozen normal35

value: Recurrence


title: FLL4, female GKRP-446L 4

description: 13-wk F


title: genomic DNA from fresh-frozen CRC2


title: FLL5, female GKRP-446L 5

description: 14-wk F


title: Yex3mu


title: genomic DNA from fresh-frozen CRC20


title: KRAB, DMSO, Rep1


title: FLL3, female GKRP-446L 3

description: 13-wk F


title: P1-12, Dex 0.25microM, Rep2

value: pTA7002-Dexp:KRAB U6-26p:P1


title: Yex2mu


title: FLL2, female GKRP-446L 2

description: 11-wk F


title: U2OS, p53(AD/AD), etoposide, rep3

description:
HOM_ETOPO_3
res_hom_vs_par_etopo.csv
res_hom_vs_ko_etopo.csv
normalized_expression_matrix.csv

data_processing:
Alignment of fastq files to human genome reference GRCh38.96 with kallisto using default parameters
Aggregation of RNA transcript-level counts to gene level by summing counts representing the same gene
Data were normalized by variance-stabilizing transformation using the DESeq2 R package
Assembly: hg38
Supplementary files format and content: Comma-separated value file of RPKM values for each sample
Supplementary files format and content: Comma-separated value file of differentially expressed genes (DESeq2)

growth_protocol: U2OS osteosarcoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested with TRIzol Reagent and purified using the QIAGEN RNeasy Mini Kit. RNA sample quality was assessed using the Aiglent 2100 Bioanalyzer.
RNA libraries for RNA-seq were prepared using the standard poly-A library prep protocol by BGI.

value: Osteosarcoma

value: Etoposide, 20 uM

value: 24 hr


title: P1-12, Dex 0.25microM, Rep1


title: genomic DNA from fresh-frozen CRC23

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: early-stage CRC


title: U2OS, p53(AD/AD), etoposide, rep4

description:
HOM_ETOPO_4
res_hom_vs_par_etopo.csv
res_hom_vs_ko_etopo.csv
normalized_expression_matrix.csv


title: genomic DNA from fresh-frozen normal16


title: U2OS, p53(AD/AD), etoposide, rep2

description:
HOM_ETOPO_2
res_hom_vs_par_etopo.csv
res_hom_vs_ko_etopo.csv
normalized_expression_matrix.csv


title: P1-12, Dex 0.025microM, Rep2

value: Dex (0.025 microM)


title: FLL1, female GKRP-446L 1

description: 11-wk F

value: liver

value: Standard chow diet


title: MPP4, male GKRP-446P 4

description: 14-wk M


title: U2OS, p53(AD/AD), etoposide, rep1

description:
HOM_ETOPO_1
res_hom_vs_par_etopo.csv
res_hom_vs_ko_etopo.csv
normalized_expression_matrix.csv


title: P1-12, Dex 0.025microM, Rep1


title: Oc3hsc

value: 22 months


title: MPP3, maleGKRP-446P 3

description: 14-wk M


title: Oc4hsc

value: control


title: U2OS, p53(AD/AD), DMSO, rep4

description:
HOM_DMSO_4
res_hom_vs_par_dmso.csv
res_hom_vs_ko_dmso.csv
normalized_expression_matrix.csv

value: DMSO


title: P1-12, DMSO, Rep2

value: whole seedlings


title: U2OS, p53(AD/AD), DMSO, rep3

description:
HOM_DMSO_3
res_hom_vs_par_dmso.csv
res_hom_vs_ko_dmso.csv
normalized_expression_matrix.csv


title: MPP2, male GKRP-446P 2

description: 12-wk M


title: P1-12, DMSO, Rep1


title: genomic DNA from fresh-frozen normal38


title: Oc1hsc


title: Yex1mu

value: 4 months

value: 5-week voluntary wheel running


title: genomic DNA from fresh-frozen normal6

value: adjacent normal tissue

value: male


title: U2OS, p53(AD/AD), DMSO, rep2

description:
HOM_DMSO_2
res_hom_vs_par_dmso.csv
res_hom_vs_ko_dmso.csv
normalized_expression_matrix.csv


title: genomic DNA from fresh-frozen CRC30

value: colorectal cancer

value: female


title: Tg(-8.0claudinB: lynGFP)zf106; TgBAC(cxcr4b:F-tractin-mCherry) transgenic line, scRNAseq

city: Portland

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health and Science Univ

description: 10x Genomics

data_processing:
using Cell Ranger (version 3.1.0; 10X Genomics, Pleasanton, CA. USA)
Assembly: ZebraFishGRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: zebrafish embryo

extract_protocol:
30 hpf Tg(-8.0claudinB:lynGFP)zf106/ TgBAC(cxcr4b:F-tractin-mCherry) zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube
Library was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: various

value: zebrafish embryo

value: mixed

value: 30 hours post-fertilization


title: Oc2hsc


title: FPP5, female GKRP-446P 5

description: 14-wk F


title: Oex3hsc


title: FPP4, female GKRP-446P 4

description: 12-wk F


title: MPP1, male GKRP-446P 1

description: 9-wk M


title: U2OS, p53(AD/AD), DMSO, rep1

description:
HOM_DMSO_1
res_hom_vs_par_dmso.csv
res_hom_vs_ko_dmso.csv
normalized_expression_matrix.csv

value: Osteosarcoma

value: 24 hr


title: S12-L1-hR1-1 WGS

data_processing:
RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports
Library strategy: WGS

growth_protocol: Ca Ski was maintained in RPMI-1640 supplemented with 10% fetal bovine serum (Gibco, 10270-106) and 100 U/ml penicillin and streptomycin (Invitrogen, 15140163). SiHa, HeLa, HEK293T, and C-33 A were cultured in DMEM supplemented with 10% fetal bovine serum and 100 U/ml penicillin and streptomycin (Invitrogen, 15140163). S12 and HaCaT cells were cultured in a 1:3 mixture of DMEM and Ham F-12 supplemented with 5% FBS (Gibco, 10270-106), 5 ug/ml insulin (Sigma-Aldrich, I5500), 8.4 ng/ml cholera toxin (Sigma-Aldrich, C8052), 24.3 ug/ml adenine (Solarbio, A8330), 10 ng/ml recombinant human EGF (Solarbio, P0033), and 0.5 ug/ml hydrocortisone (Solarbio, G8450) (5). All cells were cultured in a humidified 37 ℃ incubator at 5% CO2 and passaged 2-3 times weekly as recommended by ATCC.

extract_protocol:
Genome DNA were extracted using DNeasy Blood & Tissue Kit (69,506, Qiagen, Germany). The PCR reaction was conducted using Q5 Hot Start High-Fidelity 2X Master Mix (M0494S, NEW ENGLAND BioLabs, USA).
For short reads sequencing, PE100 bp read length sequencing was performed on the BGISEQ-500 sequencer after size selection by gel electrophoresis and 10 to 12 cycles of PCR. For long reads sequencing, size-select long DNA fragments used the BluePippin system and then libraries were constructed and sequenced following Nanopore standard protocol.

value: ecDNA knockout


title: FPP3, female GKRP-446P 3

description: 11-wk F

value: liver

value: Standard chow diet


title: genomic DNA from fresh-frozen normal19

data_processing:
Signal intensities files were extracted using the minfi Bioconductor package. Normalization was performed using the Functional Normalization function implemented in minfi.
The beta value was provided calculated by normalized signals. Normalization was performed using the Functional Normalization function implemented in minfi.
Unmethylated and methylated signal intensities in Series supplementary file

value: early-stage CRC


title: Oex4hsc

value: 22 months


title: HeLa-SE4-h2-3 WGS

source_name: HeLa

value: HeLa


title: Oex1hsc

value: 5-week voluntary wheel running


title: genomic DNA from fresh-frozen CRC25

value: Recurrence


title: FPP2, female GKRP-446P 2

description: 9-wk F


title: genomic DNA from fresh-frozen CRC42

value: male


title: U2OS, p53(+/AD), etoposide, rep3

description:
HET_ETOPO_3
normalized_expression_matrix.csv

value: Etoposide, 20 uM


title: Yc3hsc

value: 4 months

value: control


title: FPP1, female GKRP-446P 1

description: 9-wk F

value: female


title: U2OS, p53(+/AD), etoposide, rep2

description:
HET_ETOPO_2
normalized_expression_matrix.csv


title: HeLa-SE3-h2-5 WGS


title: GML3, hepatocyte-3 mouseGKRP-446L with GK expression

source_name: primary isolate

growth_protocol: After hepatocyte attachment (2-3h) the serum-containing MEM was replaced by serum-free MEM containing the GKRP-adenoviral vectors (human GCKR(Adv-209743; Ref-seq BC130481: 446P or 446L) and mouse Gckr transcript-1 (Ref seq XM_006503881.3: 446P or 446L); Gckr-transcript-2 (Adv:259984; BC012412: 446P or 446L) and Gckr-X1(XM_006503882); Gckr-X2 (XM_006503883: 446P) at final titres between  5x10^6 and 40x10^6  pfu/ml (corresponding to MOI 5-50 pfu/cell).

extract_protocol:
RNA was extracted hepatocyte cultures (n=36) using Trizol and purified using RNeasy kit (Qiagen #74104) with on-column DNase digestion (Qiagen #79254).
Samples were submitted to the Newcastle University Genomics Core for quality assessment and samples with a RIN value > 6 were used for sequencing.

treatment_protocol:
For the GK-adenoviral vector, a titre determined empirically to increase GK by 2-4 fold above endogenous was used.
After incubation with the vectors (4-5 h), the medium was replaced with MEM containing 10nM dexamethasone and 10nM insulin for overnight culture.

value: primary isolate

value: hepatocyte

value: Ad-mL + GK

tag: animal

value: Mouse 3


title: Oex2hsc


title: HEK293T WGS


title: Yc2hsc


title: genomic DNA from fresh-frozen normal39

value: adjacent normal tissue


title: U2OS, p53(+/AD), DMSO, rep3

description:
HET_DMSO_3
normalized_expression_matrix.csv

value: Osteosarcoma

value: DMSO

value: 24 hr


title: U2OS, p53(+/AD), DMSO, rep4

description:
HET_DMSO_4
normalized_expression_matrix.csv


title: genomic DNA from fresh-frozen normal3

value: early-stage CRC


title: Yex4hsc


title: S12-L2-hR2-1 WGS

value: ecDNA knockout


title: Yc1hsc


title: U2OS, p53(+/AD), etoposide, rep1

description:
HET_ETOPO_1
normalized_expression_matrix.csv


title: HaCaT WGS

source_name: HaCaT

value: HaCaT


title: genomic DNA from fresh-frozen normal29

value: Recurrence


title: GHL3, hepatocyte-3 human GKRP-446L with GK expression

value: Ad-hL + GK


title: S12 RCA short reads

library_source: other

data_processing:
RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports
Library strategy: RCA

molecule: other

extract_protocol:
DNA isolation by column separation（Plasmid Mini AX; A&A Biotechnology）, removal of remaining linear DNA by exonuclease（Plasmid-Safe ATP-dependent DNase; Lucigen, PacI enzyme; NEB）, and rolling-circle amplification by random hexamer.
For short-reads, DNA were fragmented by sonication. For long-reads, DNA fragments were selected by the BluePippin system. Short-reads and long-reads libraries were constructed and sequenced following MGI’s and Nanopore standard protocol, respectively.

value: Rolling circle amplification


title: U2OS, p53(+/AD), DMSO, rep1

description:
HET_DMSO_1
normalized_expression_matrix.csv


title: U2OS, p53(+/AD), DMSO, rep2

description:
HET_DMSO_2
normalized_expression_matrix.csv


title: GMP3, hepatocyte-3 mouse GKRP-446P with GK expression

value: Ad-mP + GK


title: HeLa RCA short reads

value: HeLa


title: Yex2hsc

value: male

value: 4 months

value: 5-week voluntary wheel running


title: Yex3hsc


title: GHP3, hepatocyte-3 human GKRP-446P with GK expression

value: primary isolate

value: hepatocyte

value: Ad-hP + GK


title: genomic DNA from fresh-frozen CRC45

source_name: colorectal cancer

value: colorectal cancer


title: genomic DNA from fresh-frozen normal40

source_name: adjacent normal tissue

value: adjacent normal tissue


title: genomic DNA from fresh-frozen normal33


title: Yex1hsc


title: GK6, hepatocyte-3 GK expression

value: Control + GK

value: Mouse 3


title: h32d2d4 Ribo seq2

description: hot3-2 dcl2 dcl4 Inflorescence, rep2

data_processing:
Reads were trimmed by cutadapt and then mapped to the Arabidopsis genome Araport11 using STAR.
RiboTaper was employed to determine the P-site of each read.
Assembly: Araport11
Supplementary files format and content: tab-delimited txt files containing RPF information relative to aligned transcript, including distances to START and STOP codon

source_name: inflorescence

extract_protocol:
0.2g of inflorescence tissue was ground into fine powder in liquid nitrogen and the powder was lysed in 0.45ml Buffer D, which consists of 100 mM Tris-HCl pH8.0, 40 mM KCl, 20 mM MgCl2, 2% (v/v) polyoxyethylene (10) tridecyl ether (Sigma-Aldrich, P2393), 0.5% (w/v) sodium deoxycholate (Sigma-Aldrich, D6750), 1mM dithiothreitol (Thermo-Fisher, R0861), 100 ug/ml cycloheximide (Sigma-Aldrich, C1988) and 10 U/ml DNase I (Roche, 4716728001). After 10 minutes incubation on ice, two rounds of centrifugation at 14,000 rpm for 10 minutes at 4°C were applied to generate cleared supernatant marked as total lysate. The OD260 of the cleared total lysate was measured by a NanoDrop spectrophotometer (Thermo Scientific, ND-2000), using Buffer D as the blank. Around 2,000U OD260 of the total lysate was treated with 75U RNase I (Thermo Fisher, AM2294) at 23°C for 1 hour. The reaction was stopped by adding 300U SUPERase•In RNase Inhibitor (Thermo Fisher, AM2694) and further processed with Amersham MicroSpin S-400 HR columns (Cytiva, 27514001). Ribosome protected footprints (RPFs) were isolated and purified using the RNA Clean & Concentrator-5 kit (Zymo Research, R1016). Later, rRNA depletion was performed as described before 19, using Dynabeads MyOne Streptavidin C1 (Thermo Fisher, 65001) and custom-made biotinylated DNA oligonucleotides listed in Table S1. The rRNA-depleted RPFs were concentrated by the RNA Clean & Concentrator-5 kit and fragments of 20-nt to 40-nt were selected from a 15% urea-PAGE gel. Sliced gel pieces were ground by RNase-free 1ml Olympus Premium Reach Pipet Tips (Genesee Scientific, 23-165RL). Extraction buffer (0.5M ammonium acetate, 10% SDS) was added to extract RPFs at room temperature for 2 hours. Gel debris was removed by Corning Costar Spin-X centrifuge tube filters (Sigma-Aldrich, CLS9301). RPFs were precipitated by incubation with 1ul glycogen (Thermo Fisher, R0551) and 3 volumes of 100% ethanol at -20°C overnight. End repair was performed for RPFs using T4 PNK without ATP for 30 minutes at 37°C, followed by 5’ phosphorylation with ATP for additional 30 minutes at 37°C.
RPFs recovered from the reactions were dissolved in 3ul RNase-free ddH2O and subjected to small RNA library construction using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300).
ribo-seq

value: inflorescence

value: somatic cells

value: hot3-2 dcl2 dcl4


title: genomic DNA from fresh-frozen normal10

value: early-stage CRC


title: U2OS p53 KO, etoposide, rep4

description:
KO_ETOPO_4
res_ko_vs_par_etopo.csv
normalized_expression_matrix.csv

value: Osteosarcoma

value: p53 KO

value: Etoposide, 20 uM

value: 24 hr


title: GK5, hepatocyte-3 GK expression

data_processing:
RNA-Seq sample quality was assessed via FastQC; all samples had quality scores > 35, no adapter contamination, and therefore none required trimming.
Transcript-level counts were obtained using Salmon (v1.4.0) run against the mouse reference transcript sequences (release M26, GRCm39) from Gencode
Assembly: gencode M26 (GRCm39)
Supplementary files format and content: tab-delimited text files include standard Salmon output (Name, Length, EffectiveLength, TPM, NumReads) for each Sample


title: U2OS p53 KO, etoposide, rep3

description:
KO_ETOPO_3
res_ko_vs_par_etopo.csv
normalized_expression_matrix.csv


title: h32d2d4 Ribo seq1

description: hot3-2 dcl2 dcl4 Inflorescence, rep1


title: genomic DNA from fresh-frozen CRC4

value: female

value: Recurrence


title: ML3, hepatocyte-3 mouse GKRP-446L expression

value: primary isolate

value: Ad-mL-(No GK)


title: Oc4bl

source_name: blood

value: male

value: 22 months

value: control


title: U2OS p53 KO, etoposide, rep2

description:
KO_ETOPO_2
res_ko_vs_par_etopo.csv
normalized_expression_matrix.csv


title: d2d4 Ribo seqq2

description: dcl2 dcl4 Inflorescence, rep2

value: dcl2 dcl4


title: Oc3bl


title: U2OS p53 KO, etoposide, rep1

description:
KO_ETOPO_1
res_ko_vs_par_etopo.csv
normalized_expression_matrix.csv


title: Oc2bl


title: HL3, hepatocyte-3 human GKRP-446L expression

value: hepatocyte

value: Ad-hL-(No GK)

value: Mouse 3


title: U2OS p53 KO, DMSO, rep3

description:
KO_DMSO_3
res_ko_vs_par_dmso.csv
normalized_expression_matrix.csv

value: DMSO


title: d2d4 Ribo seq1

description: dcl2 dcl4 Inflorescence, rep1

value: inflorescence

value: somatic cells


title: U2OS p53 KO, DMSO, rep4

description:
KO_DMSO_4
res_ko_vs_par_dmso.csv
normalized_expression_matrix.csv

value: Osteosarcoma

value: p53 KO


title: Oc1bl


title: HP3, hepatocyte-3 human GKRP-446P expression

value: Ad-hP-(No GK)


title: h32 Ribo seq1

description: hot3-2 Inflorescence, rep1


title: Oex4bl

value: 5-week voluntary wheel running


title: U2OS p53 KO, DMSO, rep2

description:
KO_DMSO_2
res_ko_vs_par_dmso.csv
normalized_expression_matrix.csv

value: 24 hr


title: h32 Ribo seq2

description: hot3-2 Inflorescence, rep2


title: WT Ribo seq2

description: WT Inflorescence, rep2

value: WT


title: UN6, hepatocyte-3 untreated

value: primary isolate

value: Control-(No GK)


title: U2OS p53 KO, DMSO, rep1

description:
KO_DMSO_1
res_ko_vs_par_dmso.csv
normalized_expression_matrix.csv


title: UN5, hepatocyte-3 untreated


title: WT Ribo seq1

description: WT Inflorescence, rep1


title: Oex3bl

value: male

value: 22 months


title: Oex2bl


title: GML2, hepatocyte-2 mouse GKRP-446L with GK expression

value: Ad-mL + GK

value: Mouse 2


title: U2OS, p53(+/+), etoposide, rep4

description:
PAR_ETOPO_4
res_ko_vs_par_etopo.csv
normalized_expression_matrix.csv

value: p53 WT/WT

value: Etoposide, 20 uM


title: KO d0 OCP 481

city: Boston

first: Shruti

last: Sharma

state: MA

address: 156 Harrison Ave

department: Immunology

institute: Tufts University

data_processing:
Reads from each sample were mapped to mouse mm10 reference genome using HISAT v2.0.5.
Differential expression analyses between groups were performed using Cuffdiff (Cufflinks v2.2.1).
Normalized counts of all the genes that were differentially expressed in at least one comparison group were used in downstream analyses and visualizations.
Visualization and downstream analysis was done with Qlucore Omics Explorer (v3.6).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains the FPKM values for each samples on significant genes.

source_name: Bone marrow derived

growth_protocol: Bone marrow cells were isolated from female mice between 10-12 weeks of age.  Red blood cells were lysed, and cells grown on Petri plates for 72hrs in 40ng/mL mCSF at 37°C and 5% CO2

extract_protocol: Trizol and phenol/chlorophorm

treatment_protocol: Following 72hrs of mCSF differentiation, cells were replated on tissue culture plastic at 25,000 cells/well in triplicate and cultured in RANKL (10ng/mL) and mCSF (20ng/mL) for 2, 3 or 4 days.  Remaining cells were utilized for RANKL-naive (d0 osteoclast precursors).  Half of the media were replaced at d2 with fresh mCSF and RANKL.  Triplicate well samples were pooled and RNA isolated at the indicated times.

value: Bone marrow derived

value: KO

value: Osteoclast Precursor d0


title: GMP2, hepatocyte-2 mouse GKRP-446P with GK expression

value: hepatocyte

value: Ad-mP + GK


title: U2OS, p53(+/+), etoposide, rep3

description:
PAR_ETOPO_3
res_ko_vs_par_etopo.csv
normalized_expression_matrix.csv

value: Osteosarcoma


title: KO d2 RANKL 481

value: RANKL d2


title: MP3, hepatocyte-3 mouse GKRP-446P expression

value: Ad-mP-(No GK)

value: Mouse 3


title: Oex1bl

value: 5-week voluntary wheel running


title: U2OS, p53(+/+), etoposide, rep2

description:
PAR_ETOPO_2
res_ko_vs_par_etopo.csv
normalized_expression_matrix.csv

value: 24 hr


title: GHL2, hepatocyte-2 human GKRP-446L with GK expression

value: primary isolate

value: Ad-hL + GK


title: KO d3 RANKL 481

value: RANKL d3


title: Yc4bl

value: male

value: 4 months

value: control


title: U2OS, p53(+/+), etoposide, rep1

description:
PAR_ETOPO_1
res_ko_vs_par_etopo.csv
normalized_expression_matrix.csv

value: p53 WT/WT

value: Etoposide, 20 uM


title: Yc3bl


title: HeLa-SE4-h2-2 WGS

value: HeLa

value: ecDNA knockout


title: GHP2, hepatocyte-2 human GKRP-446P with GK expression

value: hepatocyte

value: Ad-hP + GK

value: Mouse 2


title: Yc2bl


title: U2OS, p53(+/AD), etoposide, rep4

description:
HET_ETOPO_4
normalized_expression_matrix.csv

value: Osteosarcoma


title: KO d4 RANKL 481

value: Bone marrow derived

value: KO

value: RANKL d4


title: U2OS, p53(+/+), DMSO, rep4

description:
PAR_DMSO_4
res_ko_vs_par_dmso.csv
normalized_expression_matrix.csv

value: DMSO

value: 24 hr


title: WT d0 OCP 480

value: WT

value: Osteoclast Precursor d0


title: GK4, hepatocyte-2 GK expression

value: primary isolate

value: Control + GK


title: Yc1bl

value: male

value: 4 months

value: control


title: GK3, hepatocyte-2 GK expression


title: WT d2 RANKL 480

value: RANKL d2


title: Yex4bl

value: 5-week voluntary wheel running


title: ML2, hepatocyte-2 mouse GKRP-446L expression

value: hepatocyte

value: Ad-mL-(No GK)


title: WT d3 RANKL 480

value: RANKL d3


title: Yex3bl


title: U2OS, p53(+/+), DMSO, rep2

description:
PAR_DMSO_2
res_ko_vs_par_dmso.csv
normalized_expression_matrix.csv

value: Osteosarcoma

value: p53 WT/WT


title: MP2, hepatocyte-2 mouse GKRP-446P expression

value: Ad-mP-(No GK)

value: Mouse 2


title: U2OS, p53(+/+), DMSO, rep1

description:
PAR_DMSO_1
res_ko_vs_par_dmso.csv
normalized_expression_matrix.csv

value: DMSO

value: 24 hr


title: WT d4 RANKL 480

value: Bone marrow derived

value: WT

value: RANKL d4


title: Yex2bl

value: male


title: HL2, hepatocyte-2 human GKRP-446L expression

value: primary isolate

value: Ad-hL-(No GK)


title: KO d0 OCP 528

value: KO

value: Osteoclast Precursor d0


title: HP2, hepatocyte-2 human GKRP-446P expression

value: hepatocyte

value: Ad-hP-(No GK)


title: 4KO-2

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

description:
C57BL/6♂X F1 ♀
4KO

data_processing:
find feature sequence using C#
Genome_build: mm10
Supplementary_files_format_and_content: txt of format contianed efficnecy results to mm10s

source_name: embryo

extract_protocol:
Genomic DNA extracted from embryos (E6.5 to E12.5) using TIANamp Micro DNA Kit. Target sites were amplified from extracted genomic DNA using Phanta® Max Super-Fidelity DNA Polymerase (Vazyme).
PCR products were ligated with different barcodes and then pooled together. The library obtained from adapter-modified PCR and sequenced on Illumina HiSeq X Ten (2×150 PE) at Annoroad Gene Technology Corporation, Beijing, China

tag: develoment stage

value: C57BL/6 male X F1 female

value: embryos


title: Yex1bl

value: 4 months

value: 5-week voluntary wheel running


title: KO d2 RANKL 528

value: RANKL d2


title: KO d4 RANKL 528


title: WT d0 OCP 529


title: 4KO-1

description:
C57BL/6♂X F1 ♀
4KO


title: 630p1687BHI_3

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: 630 1687 plasmid C. difficile strains with 240µM Deoxycholate in BHIG medium

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
Reads were trimmed from adapters using Cutadapt 2.10
Then mapped to the Mus musculus GRCm38/mm10 genome using STAR 2.7.3a
Differential expression testing was conducted using DESeq2 library 1.24.0, scripts based on SARTools 1.7.0
Assembly: Clostridioides difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue

organism: Clostridioides difficile

growth_protocol: Strains were grown aerobically in BHISG at 37°C with 240µM of Deoxycholate

extract_protocol:
Cells were harvested at an OD of 0.6 by centrifugation for 2 min at 4°C. The cells were first broken by shaking in a Fastprep apparatus for 2 x 30 sec in the presence of one gram of 0.1-mm diameter glass Sigma beads, then treated with Trizol reagent, chloroform/ isoamylalcohol and precipitated with isopropanol. The pellet was resuspended in TE
RNA libraries were prepared for sequencing using standard Illumina protocols
Illumina stranded Total RNA prep Ligation kit with RiboZero Plus

treatment_protocol: Bacterial strains and plasmids used in this study are listed in Table S1 C. difficile strains were grown anaerobically in BHISG medium (BHI with 0.5% (w/v) yeast extract, 0.01 mg/mL cysteine and 100mM glucose)

value: wild type + 1687 plasmid


title: 630p1687BHI_2


title: 630p1687BHI_1


title: 630p1687BHI_4


title: 630pVideBHI_4

description: 630 empty plasmid C. difficile strains with 240µM Deoxycholate in BHIG medium

value: wild type + empty plasmid


title: KO d3 RANKL 528

value: Bone marrow derived

value: RANKL d3


title: 5KO-2

description:
C57BL/6♂X F1 ♀
5KO


title: UN4, hepatocyte-2 untreated

value: Control-(No GK)

value: Mouse 2


title: GML1, hepatocyte-1 mouse GKRP-446L with GK expression

value: primary isolate

value: Ad-mL + GK

value: Mouse 1


title: 5KO-1

description:
C57BL/6♂X F1 ♀
5KO


title: 630pVideBHI_3


title: U2OS, p53(+/+), DMSO, rep3

description:
PAR_DMSO_3
res_ko_vs_par_dmso.csv
normalized_expression_matrix.csv

value: Osteosarcoma

value: p53 WT/WT

value: DMSO

value: 24 hr


title: GMP1, hepatocyte-1 mouse GKRP-446P with GK expression

value: hepatocyte

value: Ad-mP + GK


title: 6KO-2

description:
C57BL/6♂X F1 ♀
6KO

value: C57BL/6 male X F1 female

value: embryos


title: WT d2 RANKL 529

value: WT

value: RANKL d2


title: 630pVideBHI_2

value: wild type + empty plasmid


title: GHL1, hepatocyte-1 human GKRP-446L with GK expression

value: Ad-hL + GK


title: WT d3 RANKL 529

value: Bone marrow derived

value: RANKL d3


title: 6KO-1

description:
C57BL/6♂X F1 ♀
6KO


title: GHP1, hepatocyte-1 human GKRP-446P with GK expression

value: primary isolate

value: Ad-hP + GK


title: Dnmt-TKO-2

description:
C57BL/6♂X F1 ♀
Dnmt-TKO


title: KO d0 OCP 532

value: KO

value: Osteoclast Precursor d0


title: 1687BHIDOC_4

description: 630 delta 1687 C. difficile strains with 240µM Deoxycholate in BHIG medium

value: CD1687 Mutant


title: Dnmt-TKO-1

description:
C57BL/6♂X F1 ♀
Dnmt-TKO


title: UN3, hepatocyte-2 untreated

value: Control-(No GK)

value: Mouse 2


title: KO d2 RANKL 532


title: Dnmt3ab-DKO-1

description:
C57BL/6♂X F1 ♀
Dnmt3ab-DKO


title: KO d4 RANKL 532

value: RANKL d4


title: Dnmt1-KO-2

description:
C57BL/6♂X F1 ♀
Dnmt1-KO


title: WT d0 OCP 531


title: 1687BHIDOC_2


title: 1687BHIDOC_3


title: 630BHIDOC_4

description: 630 C. difficile strains with 240µM Deoxycholate in BHIG medium

value: wild type


title: KO d3 RANKL 532


title: HL1, hepatocyte-1 human GKRP-446L expression

value: hepatocyte

value: Ad-hL-(No GK)

value: Mouse 1


title: ML1, hepatocyte-1 mouse GKRP-446L expression

value: Ad-mL-(No GK)


title: Dnmt1-KO-1

description:
C57BL/6♂X F1 ♀
Dnmt1-KO

value: C57BL/6 male X F1 female

value: embryos


title: 1687BHIDOC_1


title: GK1, hepatocyte-1 GK expression

value: Control + GK


title: 630BHIDOC_3


title: WT d2 RANKL 531

value: Bone marrow derived

value: WT

value: RANKL d2


title: HP1, hepatocyte-1 human GKRP-446P expression

value: primary isolate

value: Ad-hP-(No GK)


title: Tet-TKO-2

description:
C57BL/6♂X F1 ♀
Tet-TKO


title: 630BHIDOC_2


title: UN2, hepatocyte-1 untreated


title: 630pVideBHI_1

value: wild type + empty plasmid


title: WT d4 RANKL 529


title: GK2, hepatocyte-1 GK expression


title: UN1, hepatocyte-1 untreated

value: Control-(No GK)


title: Tet-TKO-1

description:
C57BL/6♂X F1 ♀
Tet-TKO


title: 630BHIDOC_1


title: WT d4 RANKL 531


title: MP1, hepatocyte-1 mouse GKRP-446P expression

value: Ad-mP-(No GK)


title: RNA-seq of mus musculus: mouse brain cell bEnd.3, Mut2

status: Public on Apr 18 2023

city: Beijing

first: Woo-ping

last: Ge

state: Beijing

address: 26 Shengming Kexue Yuan Rd

institute: Chinese Institute for Brain Research, Beijing

description: Mutation 2

data_processing:
Clean reads were mapped to the reference genome (Version: GRCm38) downloaded from Gencode by HISAT with the parameter “-5 30 -3 30”. Uniquely mapped reads were utilized to calculate the counts of each gene by feature counts with the parameter based on the GTF annotation downloaded from Gencode (Version: vm23).
Read count matrix was normalized to library size by DESeq2 with default parameters. Hierarchical clustering was performed by factoextra package in R.
Assembly: Hisat2 GRCm38
Supplementary files format and content: Deseq2 normalized count, renjian_RNA-seq_20220710

growth_protocol: The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 5 μg/ml gentamycin

extract_protocol:
Total RNA of endothelial cells was extracted with RNeasy Micro Kit (QIAGEN) as suggested by the protocol from the manufacturer.
The cDNA library was constructed using SMARTer® Stranded Total RNA-Seq Kit v2 (Takara).

value: Endothelial cell

value: MAP3K3I441M overexpression


title: Dnmt3ab-DKO-2

description:
C57BL/6♂X F1 ♀
Dnmt3ab-DKO


title: RNA-seq of mus musculus: mouse brain cell bEnd.3, Mut1

description: Mutation 1


title: RNA-seq of mus musculus: mouse brain cell bEnd.3, Ctrl3

description: Control 3


title: RNA-seq of mus musculus: mouse brain cell bEnd.3, Ctrl2

description: Control 2


title: RNA-seq of mus musculus: mouse brain cell bEnd.3, Ctrl1

description: Control 1


title: RNA-seq of mus musculus: mouse brain cell bEnd.3, Ctrl4

description: Control 4


title: RNA-seq of mus musculus: mouse brain cell bEnd.3, Ctrl5

description: Control 5


title: F1 hybrid 3, senescent

city: Novato

first: Taekyu

last: Kang

address: 8001 Redwood Blvd

institute: Buck Institute

description:
F1.4_mm_xray, F1.4_ms_xray
F1_hybrid_SEN_TPM.txt

data_processing:
Reads were mapped to their corresponding genomes via tophat v2.1.1
Reads were filtered for only those that mapped uniquely via samtools v1.3.1
Gene counts were generated using HTSeq v0.11.2
TPM counts were generated using custom R scripts.
Assembly: GRCm38.96, SPRET_EiJ_v1.96
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Mus musculus x Mus spretus

source_name: Tail

growth_protocol: All cells were cultured in DMEM with 10% FBS and 1% pen-strep in a 3% O2 and 10% CO2 humidified incubator at 37˚C.

extract_protocol:
RNA was extracted from cells using TriZol and chloroform extraction, then cleaned and treated with DNase on RNeasy columns.
Libraries were constructed in the corresponding sequencing facilities.

treatment_protocol: All senescent samples were treated with 15 Gy of ionizing radiation in a X-RAD 320 X-Ray Biological Irradiator. Senescent samples were collected 10 days or 20 days after IR treatment. 6HR samples were collected 6 hours after IR treatment.  All shRNA treated samples were infected with shRNA containing lentiviral particles with 4 µg/mL of polybrene at an MOI of 5. Cells were then cultured with 2 µg/mL of polybrene in complete medium for 10 days to select for infected cells.

value: Tail

value: Primary fibroblast

value: ionizing radiation, 15 Gy


title: C28sp_1A

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

data_processing:
Raw sequencing reads (fastq) were quality checked using SOAPnuke (v1.5.2).
Bowtie2 (v2.2.5) was applied to align the clean reads to the genomes.
The expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using DESeq2 (v1.4.5)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: C28 _monolayers_ vs_spheroid_diff

source_name: C28/I2 cell line

growth_protocol: C28/I2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin.

extract_protocol:
RNAs were extracted from culture tissues. The samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)

treatment_protocol: C28/I2 cells were treated with or without SDF-1/natural products for 48 h and then collected for bulk RNA sequencing.

value: chondrocyte

value: DMSO 0.5 percent, 48 h

value: spheroid culture


title: C28sp_3A


title: F1 hybrid 2, unirradiated control

description:
F1.2_mm_cont, F1.2_ms_cont
F1_hybrid_SEN_TPM.txt


title: F1 hybrid 2, senescent

description:
F1.2_mm_xray, F1.2_ms_xray
F1_hybrid_SEN_TPM.txt


title: F1 hybrid 1, senescent

description:
F1.1_mm_xray, F1.1_ms_xray
F1_hybrid_SEN_TPM.txt


title: C28sp_2A


title: F1 hybrid 3, unirradiated control

description:
F1.4_mm_cont, F1.4_ms_cont
F1_hybrid_SEN_TPM.txt


title: WT d3 RANKL 531

value: RANKL d3


title: 28W Kidney_L003

first: Jun

last: Deng

address: No. 25, Lane 2200, Xietu Road, Xuhui District

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
library strategy: scRNA-seq and scTCR-seq.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The CellRanger VDJ pipeline was utilized to assemble the TCR sequences and identify the CDR3 sequence and TCR genes.
The cells were filtered based on two criteria: (1) only cells annotated as T-cell clusters in the single-cell RNA sequencing data were retained, and (2) only cells that had productive T-cell receptor (TCR) α and β chains were included in the analysis.
To find out which V-J and V-D-J gene combinations are common and which are unique, we made a list of specific combinations for each sample and used the Venn Diagram package (version 1.6.20) in R software (version 3.6.1) to see how these combinations fit together.
Assembly: GRCm38 mouse reference genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
PD-1+CD44+CD8+ T cells from spleens of NZB/W F1 mice at 12 weeks or 28 weeks of age, and kidneys of 28 weeks of age were sorted for scRNA-seq.
Single-cell RNA-seq libraries were prepared with a Chromium Single Cell 5′ v2 Reagent Kit. Using primers specific to TCR constant regions, the Single-Cell V(D)J Enrichment Kit (10× Genomics) was used to enrich full-length TCR V(D)J segments from amplified cDNA from 5' libraries.

value: PD-1+CD44+CD8+ T cells

value: Kidney

value: NZB/W F1

value: 28 weeks old


title: 28W Kidney_L004

description: 10x Genomics


title: 28W Spl_L003

description: 10x Genomics

source_name: Spleen

value: Spleen

value: 12 weeks old


title: 28W Spl_L004

description: 10x Genomics


title: 28W Kidney_L002

description: 10x Genomics


title: 28W Spl_L001

description: 10x Genomics


title: 12W Spl_L004

description: 10x Genomics