title: 5578

description: Library name: ZT23.LL.female.5578


title: THP-1 control 1

status: Public on Feb 08 2025

type: SRA

city: Wuhan

first: Chunjiang

last: He

state: Hubei

address: Donghu Road 185

country: China

institute: Wuhan University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to genome(hg38) using STAR/bowtie2/BWA
circRNAs were identified by CIRI2/CIRCexplorer2/circRNA_cinder/find_circ
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count

molecule: total RNA

organism: Homo sapiens

extract_protocol:
For PBMC, total RNA was extracted and treated with the RiboZero rRNA Removal Kit. Then, the RNA was fragmented and synthesized cDNA with random primer. Purified the PCR amplification products of cDNA, then the libraries were quality controlled and sequenced.For cell lines, total RNA was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: treatment


title: Prostate epithelial tissues (PN2) [RNA-Seq]

first: Zezhong

last: Xiong

address: 1095 Jiefang Ave. Wuhan, P.R.China

institute: Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were mapped to the reference genome of Homo sapiens (Homo_sapiens.GRCh38;ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/） using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the deseq2 package (version 3.12.1).
Assembly: hg38
Supplementary files format and content: csv

source_name: normal prostate

extract_protocol:
Total RNAs were extracted from prostate cancer and adjacent normal tissues using TRIzol (Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

tag: tissue

value: normal prostate

tag: gender

value: male

tag: age


title: Prostate epithelial tissues (PN6) [RNA-Seq]


title: Prostate epithelial tissues (PN7) [RNA-Seq]


title: 5575

city: Philadelphia

first: Thomas

middle: G

last: Brooks

address: 3400 Civic Center Blvd

department: ITMAT

country: USA

institute: University of Pennsylvania

description: Library name: ZT23.LL.female.5575

data_processing:
RNA-seq reads were quantified using Salmon v1.9.0to the GRCm38 genome with Ensembl v102 annotation. Quantifications were imported with the tximeta package v1.20.3] for use with DESeq2 v1.42.0 and aggregated to gene level quantifications.
Assembly: GRCm38
Supplementary files format and content: salmon.genes.TPM.txt is a tab-separated file containing gene-level transcripts-per-million (TPM) values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

growth_protocol: Specific pathogen-free 8-12 week-old C57bl/6J mice were placed in circadian cabinets on reverse light-dark cycle. This allowed us to simultaneously infect mice or harvest tissues across all experimental groups. After 4-6 weeks of acclimatization in these cabinets, mice were anesthetized lightly with isoflurane prior to being infected intranasally (i.n.) with mouse-adapted influenza virus (PR8 ). Given the use of circadian cabinets, mice were simultaneously infected at either ZT23 or ZT11 and maintained in 12 hr light-dark cycle. The dose chosen was likely to cause >50% mortality when mice were infected at ZT11. On day four p.i. a subset of ZT23-LD mice were moved to constant light (LL) until the end of the study.

extract_protocol:
TRIzol (Life Technologies) was used to extract and isolate RNA from the inferior lobe of the mouse lung. The RNeasy Mini Elute Clean Up Kit (Qiagen) was used to further purify the RNA as per the manufacturer’s protocol. The NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc) was used to assess the quality and quantity of the extracted RNA. Only samples with RINS>7 after QC were sent for sequencing to Azenta Life Sciences.
Strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, the enriched RNAs were fragmented for 8 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

value: Lung

tag: Sex

value: female

tag: time

tag: condition

value: LL


title: whole worm, CDK12as-Starved-DMSO-1

city: Genève

first: François-Xavier

last: Stubbe

state: Genève

address: 30, quai Ernest-Ansermet

department: MOCEL

country: Switzerland

institute: University of Geneva

data_processing:
Basecalls were performed using bcl2fastq for NovaSeq output
RNA-seq reads were aligned to WBCel235 genome using hisat2 (with parameters –no-discordant –min-intronlen 20 –max-intronlen 5000)
Read Count extraction was performed using FeatureCount
DGE analysis was performed usig DESEQ2
Assembly: WBCel235
Supplementary files format and content: FeatureCount matrix: tab-delimited text files includes raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: L1 were synchornized by hypochlorite treatment and hatched over night

extract_protocol:
RNA was harvested using TriZol reagent. DNA was removed Ambion Turbo DNAse and cleaned by phenol/cloroform extraction
RNA-seq libraries were made following the Illumina TRUESeq protocol

treatment_protocol: 100k L1s were grown in liquid in presence or absence of food and in presence or absence of 3MB-PP1

tag: developmental stage

value: whole worm

tag: genotype

tag: feeding time

value: Staved

value: DMSO


title: RLKO1 Xenium

type: RNA

city: Balitmore

first: Charles

middle: Scott

last: Kirby

state: Maryland

address: 1551 Orleans Street, Koch CRBII Suite 216

institute: Johns Hopkins

description: RLKO1_output-XETG00089__0025300__Region_1__20240426__181527

data_processing:
Output files were generated by the Xenium Onboard Analysis pipeline to generate gene transcript by cell and transcript by tissue location data matrices.
cell_boundaries.csv.gz: compressed dimensions of cell boundaries
experiment.xenium: executable file to open data in Xenium Explorer
features.tsv.gz: gene expression feature names
matrix.mtx.gz: gene expression matrix
barcodes.tsv.gz: cell barcode names
gene_panel.json: gene panel list
cell_feature_matrix.h5: compressed cell expression data
cell_feature_matrix.zarr.zip: compressed cell expression data
cells.csv.gz: compressed cell locations
transcripts.csv.gz: zcompressed transcripts

source_name: SD0 Wounded back skin

label_protocol: Spatial transcriptome sequencing libraries were prepared with 10X Xenium spatial gene expression slides & reagent kit according to manufacturer's construction

extract_protocol: Wound samples were formalin-fixed and paraffin-embedded (FFPE) then underwent sectioning, and H&E staining. Samples were then trimmed to match Xenium slides, then analyzed according to manufacturers protocols. Post xenium H&E staining was then performed.

treatment_protocol: Using surgical scissors  approximately 1.26 cm2 X 1.25cm2 of skin was excised creating wounds deep into the fascia

tag: strain

value: Formalin-fixed and paraffin-embedded (FFPE) wounded back skin at SD0


title: whole worm, CDK12as-Starved-DMSO-2

value: Starved


title: Prostate cancer tissues (PC19) [RNA-Seq]

source_name: prostate cancer

value: prostate cancer


title: 5189

description: Library name: ZT23.LD.female.5189

value: LD


title: whole worm, E22K-Fed-DMSO-3


title: 5

description: Library name: ZT23.LD.female.5


title: whole worm, cdk-12as;ssup-72[E22K],3

library_source: other

data_processing:
Basecalls were performed using bcl2fastq for NEstSeq output
GRO-seq reads were trimmed from adapater sequence (TGGAATTCTCGGGTGCCAAGG) and tetramers (5'&3') with cutadapt
GRO-seq reads were aligned to WBCel235 genome using bowtie2
Read Count extraction was performed using featurecount and DGE analysis was performed using DESEQ2
BigWig files were generated with Deeptools using DESEQ2 sizefactor as normalizator
Assembly: WBCel235
Supplementary files format and content: BigWig
Supplementary files format and content: FeatureCount matrix: tab-delimited text files includes raw counts for each sample
Library strategy: GRO-seq

molecule: other

growth_protocol: L1 were synchornized by hypochlorite treatment and hatched overnight.

extract_protocol:
L1 nuclei were extracted, RUN-On was performed and RNA was extracted using TRIzol-LS
Quarato et al., 2021

treatment_protocol: 400K were cultured in liquid with HB101 and 2 uM 3MB-PP1 for 4H

tag: sample type

value: nuclei

value: Double

value: 3MB-PP1 (2 uM)


title: Prostate epithelial tissues (PN1) [RNA-Seq]


title: whole worm, E22K-Fed-DMSO-1


title: whole worm, ssup-72[E22K], 3


title: 4999

description: Library name: ZT23.LD.female.4999


title: whole worm, E22K-Fed-DMSO-2


title: 4717

description: Library name: ZT23.LL.female.4717


title: whole worm, cdk-12as, 3


title: whole worm, N2, 3


title: Prostate cancer tissues (PC20) [RNA-Seq]


title: Prostate cancer tissues (PC18) [RNA-Seq]


title: 5576

description: Library name: ZT23.LD.female.5576


title: 5001

description: Library name: ZT23.LD.female.5001


title: Prostate cancer tissues (PC17) [RNA-Seq]


title: Prostate cancer tissues (PC16) [RNA-Seq]


title: whole worm, cdk-12as;ssup-72[E22K],2


title: whole worm, N2-Fed-DMSO3


title: whole worm, ssup-72[E22K], 2


title: whole worm, N2-Fed-DMSO-2


title: Prostate cancer tissues (PC15) [RNA-Seq]


title: whole worm, cdk-12as, 2


title: P14D AVNM_3

city: Jatani

first: Uday

last: Pandey

address: NISER, Jatani, Odisha

department: Biological Sciences

country: India

institute: National Institute of Science Education and research

data_processing:
1. Quality Assessment Paired-end raw sequence reads were assessed for base quality and contamination by sequencing artefacts. 2. Trimming & Filtering Trimming of adapters and poor quality sequences was performed for paired sequence reads with Trim Galore. 3. Reference Alignment Trimmed sequence reads was mapped to reference with splice aware alignment tool STAR. 4. Expression Estimation Feature specific expression counts were estimated by using the Rsubread R package. 5. Low Expression Filter Detection and removal of low count features across samples was performed NOISeq R package. 6. Normalization Expression counts normalization was performed with TMM method from NOISeq R package. 7. Differential Analysis Estimation of significant differential features was performed with NOISeq R package which simulates technical replicates for data without biological replicates. 8. Functional Annotation Enrichment of functional annotation was performed with R package gprofiler2. Gene ontology summarization and treemap plot was generated with R package rrvgo
Assembly: mm39, GRCm39 (GCA_000001635.9), Jun. 2020
Supplementary files format and content: tab-delimited text files includes raw count for each sample
Supplementary files format and content: tab-delimited text files includes normalized count for each sample

source_name: Small intestine (Ileum)

extract_protocol:
RNA was extracted using a Direct-zol RNA Miniprep kit as per the manufacturer's protocol.
RNA library was prepared using the KAPA RNA hyper prep kit following manufacurer's protocol.

treatment_protocol: PBS and AVNM treatment daily once by oral gavaging from P3D to P14D.

value: Small intestine (Ileum)

value: Wild type (C57BL/6j)

value: AVNM


title: whole worm, N2-Fed-DMSO-1


title: Prostate cancer tissues (PC14) [RNA-Seq]

value: male


title: whole worm, N2, 2


title: whole worm, ssup-72(0), reseq, 2

data_processing:
Basecalls were performed using bcl2fastq for NovaSeq output
RNA-seq reads were aligned to WBCel235 genome using hisat2 (with parameters –no-discordant –min-intronlen 20 –max-intronlen 5000)
Read Count extraction was performed using FeatureCount
DGE analysis was performed usig DESEQ2
BigWig files were generated with Deeptools using DESEQ2 sizefactor as normalizator
Assembly: WBCel235
Supplementary files format and content: FeatureCount matrix: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: Bigwig

treatment_protocol: 100k L1s were grown in liquid, with food, for 4H

tag: sequencing batch


title: Prostate cancer tissues (PC13) [RNA-Seq]


title: whole worm, cdk-12as, 1


title: whole worm, ssup-72[E22K], 1


title: P14D control_3

value: PBS


title: Prostate cancer tissues (PC12) [RNA-Seq]


title: Prostate cancer tissues (PC11) [RNA-Seq]


title: whole worm, ssup-72(0), reseq, 1


title: P14D control_2


title: whole worm, N2, 1


title: whole worm, N2, reseq, 1


title: P14D control_1


title: Prostate cancer tissues (PC10) [RNA-Seq]


title: whole worm, pinn-1(0), 3


title: qing3

city: Jiangsu Lianyungang

first: xu

middle: xin

last: yu

state: Lianyun District

address: Jiangning industrial city,Economic and Technological Development Zone

department: Drug screening research department

institute: Jiangsu Kanion Pharmaceutical Co.,Ltd.

data_processing:
Genomics Workbench
Nextseq 2000 was used for sequencing. The principle of sequencing is to sequence while synthesizing. Filter the original data, including removing the reads with connectors; Remove reads containing N; Remove low quality reads.
Compare clean reads to the reference genome, use hisat2 software to compare clean reads with the reference genome, filter out the reads with a comparison quality value of less than 10, and compare the reads with multiple regions of the genome.
The "deseq2" R software package was used to screen the differentially expressed genes (DEGs) between koa samples and normal samples. The screening conditions were p<0.05, 𞓜 log2fc|>2.
The featurecounts tool in subread software is used for analysis.
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include p values for DEG

organism: Rattus norvegicus

source_name: synovium

extract_protocol:
RNA was isolated using TaKaRa MiniBEST Universal RNA Extraction Kit(Takara). 800ng of total RNA was used for the construction libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) folowing manufacturer's protocols

treatment_protocol:
SD rats were randomly divided into control group, model group, Jingu Zhitong Gel high, medium, and low dose groups, Votalin ointment group, and Qingpeng ointment group, with 10 rats in each group. TheKOAmodel of rats was conducted, 50μL of MIA solution was injected into the lateral side of the patella. Rats in the control group were injected with 50μL of sterile physiological saline. The intervention was initiated on day 1 of model establishment and administered twice a day for 14 days.
Synovial tissues were fixed in 4% polyformaldehyde for 24 hours, then dehydrated, paraffin embedded, sectioned, dewaxed with xylene and gradient ethanol treatment, and then stained with hematoxylin-eosin (HE), dehydrated and sealed for observation under the microscope.

value: synovium

value: qing(positive control)


title: whole worm, pinn-1(0), 2

value: whole worm


title: whole worm, cdk-12as;ssup-72[E22K],1


title: tRNA ShTRMT6 rep 3

city: Shanghai

first: En-Wei

last: Tao

address: 145 Middle Shandong Road

institute: Shanghai Jiao Tong University

data_processing:
For tRNA-seq data analysis, sequencing quality was examined by FastQC software, and trimmed reads (pass Illumina quality filter, trimmed 3’-adaptor bases by cutadapt) were aligned to the cytoplasmic mature-tRNA sequence getting from GtRNAdb and the mitochondrial mature-tRNA sequences getting from mitotRNAdb using BWA software.
For tRNA alignment, the maximum mismatch was 2.
The tRNAs expression profiling was calculated based on uniquely mapped reads.
Assembly: GtRNAdb, mitotRNAdb

source_name: RKO

extract_protocol:
Total RNA samples were extracted with the TRIzol reagent (Takara, #9109) according to the manufacturer’s instructions, and over 2µg total RNA was resolved on urea-polyacrylamide gels and recovered within a size window of 60-100 nt for tRNA
The partially hydrolyzed tRNA fragments were converted to barcoded small RNA sequencing libraries using NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs, #E7330L).

value: RKO

value: Colorectal cancer cells

tag: cell type

value: TRMT6 knockdown


title: P14D AVNM_2


title: P14D AVNM_1


title: whole worm, ssup-72(0), reseq, 3


title: Prostate cancer tissues (PC9) [RNA-Seq]


title: tRNA ShTRMT6 rep 2


title: qing1


title: whole worm, pinn-1(0), 1


title: tRNA ShTRMT6 rep 1


title: Prostate cancer tissues (PC7) [RNA-Seq]


title: fu3

value: fu(positive control)


title: tRNA ShControl rep 3

value: WT


title: Prostate cancer tissues (PC6) [RNA-Seq]

value: prostate cancer


title: qing2


title: whole worm, ssup-72[S39A], 2


title: tRNA ShControl rep 2


title: Prostate cancer tissues (PC5) [RNA-Seq]


title: fu2


title: whole worm, ssup-72[S39A], 3


title: whole worm, ssup-72[S39A], 1


title: tRNA ShControl rep 1


title: low3

value: low


title: Prostate cancer tissues (PC3) [RNA-Seq]


title: Ribo ShTRMT6 rep 3

data_processing:
low-quality reads were filtered by fastp, and reads with lengths between 20-40 bp were retained for subsequent analysis.
Processed RNA-seq reads were aligned to the genome using whole genome alignment by STAR, and three-nucleotide periodicity was plotted using the riboWaltz R package
Reads counts in the open reading frame of coding genes were calculated by software RSEM, and the gene expression level was normalized by using the FPKM method.
Assembly: ensembl_release104
Library strategy: Ribo-seq

extract_protocol:
To prepare ribosome-protected mRNA fragments, 10 μl of RNase I and 6 μl of DNase I were added to the supernatant and incubated at room temperature for 45 min, followed using 10 μl RNase inhibitor (Thermo Scientific, #AM2694) to stop the nuclease digestion. Size exclusion columns (GE Healthcare, #27-5140-01) were equilibrated with 3 ml of polysome buffer, and digested RNAs were added to the column and centrifuged at 600 g for 2 min. Next, 10 μl 10% SDS was added to the elution, and the ribosome-protected mRNA fragments with a size greater than 17 nt were isolated according to the RNA Clean and Concentrator-25 kit (Zymo Research, #R1017) and further purified using magnet beads (Vazyme, #N412-01).
Ribo-seq libraries were constructed using NEBNext® Multiple Small RNA Library Prep Set for Illumina® (New England Biolabs, #E7300L)


title: low2


title: Prostate cancer tissues (PC2) [RNA-Seq]


title: whole worm, ssup-72[S39E], 2


title: Ribo ShTRMT6 rep 2


title: low1


title: Ribo ShTRMT6 rep 1


title: whole worm, ssup-72[S39E], 1


title: Prostate cancer tissues (PC4) [RNA-Seq]


title: Prostate cancer tissues (PC1) [RNA-Seq]


title: medium3

value: medium


title: whole worm, ssup-72[E22K], 3


title: medium2


title: Ribo ShControl rep 3


title: fu1


title: Ribo ShControl rep 2


title: medium1


title: Ribo ShControl rep 1


title: high3

value: high


title: whole worm, ssup-72[S39E], 3


title: Inv-Xi-CA12-H3K27me3-CUTandRUN

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description:
Library name: XiInv1, H3K27me3 CUTandRUN
H3K27me3 CUT&RUN experiment in a Patski cell line (Inv-Xi-CA12) with a Xi-inversion of a CTCF boundary upstream of Car5b

library_source: genomic

data_processing:
Paired-end reads were mapped using SNPsplit to an N-masked C57BL6/J reference genome (mm10) where the M. spretus SNP locus was substituted with an N to reduce mapping bias. SNPs were based on Sanger data for mouse species M. spretus compared to the mm10 B6 reference assembly.
Uniquely mapped paired-end reads were  segregated to its parental allele of origin (genome 1 for BL6 and genome 2 for spretus) if either end of the read pair contained at least one SNP particular to one of the parental strains. Enrichment profiles were produced using allelic reads.
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&Run

molecule: genomic DNA

organism:
Mus musculus
Mus spretus

source_name: embryonic kidney

growth_protocol: Dulbecco's Modified Eagle's Medium (DMEM) with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
CUT&RUN was performed using Patski cells as described in Skene and Henikorff, 2017. In brief, permeabilized Patski cells are incubated with specific antibody, followed by binding of a Protein A-Micrococcal Nuclease (pA/MNase) fusion protein. Upon activation of tethered MNase, the bound complex is excised and released into the supernatant for DNA extraction and sequencing
Sequencing libraries were prepared using the Illumina Truseq ChIP sample prep kit. Size selection of the library was done by two-step Ampure bead purification and purification of DNA in the 200-600bp range.

value: embryonic kidney

value: Patski cells

value: Fibroblasts derived from hybrid embryonic kidney


title: Inv-Xi_CA12-CTCF-CUTandRUN

description:
Library name: XiInv1, CTCF CUTandRUN
CTCF CUT&RUN experiment in a Patski cell line (Inv-Xi-CA12) with a Xi-inversion of a CTCF boundary upstream of Car5b


title: whole worm, ssup-72[C13S], 3


title: N3,Healthy control

source_name: PBMC

tag: disease state

value: Normal

value: PBMC


title: high2

value: synovium

value: male


title: Del-Xi_CA5-H3K27me3-CUTandRUN

description:
Library name: XiDel2, H3K27me3 CUTandRUN
H3K27me3 CUT&RUN experiment in a Patski cell line (Del-Xi-CA5) with a Xi-deletion of a CTCF boundary upstream of Car5b


title: N2,Healthy control


title: whole worm, ssup-72[C13S], 2

value: whole worm


title: high1


title: Del-Xi_CA5-H3K27ac-CUTandRUN

description:
Library name: XiDel2, H3K27ac CUTandRUN
H3K27ac CUT&RUN experiment in a Patski cell line (Del-Xi-CA5) with a Xi-deletion of a CTCF boundary upstream of Car5b


title: whole worm, ssup-72[C13S], 1


title: Del-Xi_CA5-CTCF-CUTandRUN

description:
Library name: XiDel2, CTCF CUTandRUN
CTCF CUT&RUN experiment in a Patski cell line (Del-Xi-CA5) with a Xi-deletion of a CTCF boundary upstream of Car5b


title: whole worm, ssup-72[E22K], 2


title: whole worm, ssup-72[E22K], 6


title: N1,Healthy control


title: Inv-Xi_CA12-H3K27ac-CUTandRUN

description:
Library name: XiInv1, H3K27ac CUTandRUN
H3K27ac CUT&RUN experiment in a Patski cell line (Inv-Xi-CA12) with a Xi-inversion of a CTCF boundary upstream of Car5b


title: Del-Xi_c11.8-H3K27me3-CUTandRUN

description:
Library name: XiDel1, H3K27me3 CUTandRUN
H3K27me3 CUT&RUN experiment in a Patski cell line (Del-Xi-c11.8) with a Xi-deletion of a CTCF boundary upstream of Car5b


title: model2

value: model


title: whole worm, ssup-72[E22K], 5


title: C5,BCR3,AML

value: AML


title: C6,MLL/AF4,AML


title: whole worm, ssup-72[E22K], 1


title: whole worm, ssup-72[E22K], 4


title: Del-Xi_c11.8-H3K27ac-CUTandRUN

description:
Library name: XiDel1, H3K27ac CUTandRUN
H3K27ac CUT&RUN experiment in a Patski cell line (Del-Xi-c11.8) with a Xi-deletion of a CTCF boundary upstream of Car5b


title: C4,AML1/ETO,AML


title: Del-Xi_c11.8-CTCF-CUTandRUN

description:
Library name: XiDel1, CTCF CUTandRUN
CTCF CUT&RUN experiment in a Patski cell line (Del-Xi-c11.8) with a Xi-deletion of a CTCF boundary upstream of Car5b


title: model1


title: whole worm, N2, 3


title: ctrl3

value: ctrl


title: C3,CBFB/MHY11,AML


title: model3


title: whole worm, N2, 2


title: Del-Xa_b1-H3K27me3-CUTandRUN

description:
Library name: XaDel1, H3K27me3 CUTandRUN
H3K27me3 CUT&RUN experiment in a Patski cell line (Del-Xa-b1) with a Xa-deletion of a CTCF boundary upstream of Car5b


title: ctrl2


title: ctrl1


title: C2,BCR1,AML


title: Del-Xa_b1-H3K27ac-CUTandRUN

description:
Library name: XaDel1, H3K27ac CUTandRUN
H3K27ac CUT&RUN experiment in a Patski cell line (Del-Xa-b1) with a Xa-deletion of a CTCF boundary upstream of Car5b


title: whole worm, N2, 1


title: Del-Xa_b1-CTCF-CUTandRUN

description:
Library name: XaDel1, CTCF CUTandRUN
CTCF CUT&RUN experiment in a Patski cell line (Del-Xa-b1) with a Xa-deletion of a CTCF boundary upstream of Car5b


title: C1,MLL/AF9,AML


title: 4H4 Dioxin-exposed 8-cell stage blastomere

status: Public on Feb 07 2025

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: Dioxin-exposed 8-cell stage blastomere

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using STAR
number of reads was calculated for each Symbol, Entrez gene
differential expression analysis was performed using edgeR, zero-inflated model, non-parmetric tests
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Mouse preimplantation embryo

growth_protocol: Two-cell, 4-cell, 8-cell, and blastocyst stage embryos were collected from superovulated naïve Ahr+/+and Ahr-/- females that were mated at E-0.5 with males of the corresponding genotype and exposed to control oil vehicle or TCDD at 46-, 55-, 70-, and 97-hour post-hCG time into M2 media respectively.

extract_protocol:
Messenger RNAs obtained from single blastomeres were converted into full-length cDNA directly following SMART-seq v4 ultra low input RNA manufacture’s protocol with some modifications.  A 1.5-ul volume of 1X PBS containing 0.4% of BSA and one single blastomere was transferred into PCR tubes containing lysis buffer and 10X RNase inhibitor provided by the kit.  cDNA of each single blastomere was prepared by first-strand-cDNA conversion from polyA-RNA followed by 18 cycles of full-length amplification.
150-ug of amplified cDNA were subjected to library preparation using a Nextera XT DNA library preparation kit.

treatment_protocol: Embryos were exposed to 1-ug/ml TCDD and equivalent volume of corn oil for vehicle control via oral gavage at gestation days E-0.5 and E2.5.

value: Blastomere

value: Through Dam exposed to 1-ug/kg TCDD

value: 8-cell stage blastomere


title: 4H2 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4H1 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4G6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere

value: Untreated


title: 4H6 Positive control

description: Positive control


title: 4H3 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4G5 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: Prostate cancer tissues (PC3)

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with FastUniq（version 1.1）to eliminate duplication.
Deduplicated reads were mapped to the reference genome of Homo sapiens (Homo_sapiens.GRCh38;https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip） from using bowtie2 software (version 2.2.6) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis. The insert length was counted by Collect Insert Size Metrics tools from picard software (version 2.8.2).
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
ATAC assay was performed on prostate cancer and normal prostate tissues by SeqHealth (Wuhan, China). 10000-50000 cells were treated with cell lysis buffer and nucleus was collected by centrifuging for 5min at 500g(500mg tissue was frozen in liquid nitrogen, and grinded by tissue lyser；The grinded powder was treated with cell lysis buffer and nucleus was collected by centrifuging for 5min at 2000g).
Transposition and high-throughput DNA sequencing library were carried out by TruePrep DNA Library Prep Kit V2 for Illumina kit（Catalog NO. TD501, Vazyme）.

value: prostate cancer


title: 4H5 Negative control

description: Negative control


title: Prostate cancer tissues (PC8) [RNA-Seq]


title: RLKO3 Xenium

description: RLKO3_output-XETG00089__0025300__Region_3__20240426__181528

value: Formalin-fixed and paraffin-embedded (FFPE) wounded back skin at SD0


title: 4F6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 4G2 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4G1 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4F5 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4F1 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4F4 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4E6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 4G4 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4F3 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4E4 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4E3 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4E2 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4G3 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4F2 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4E1 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4D6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 4D5 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4D4 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4D3 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4D1 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4C5 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4C4 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4C3 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4C2 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4E5 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4B6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 4B2 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4B4 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4A4 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4B5 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4B1 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4B3 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4A3 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3H7 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3H6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 4A6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3H5 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 4A5 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3H4 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3H9 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere

value: Through Dam exposed to corn oil

value: 4-cell stage blastomere


title: 4D2 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: X2536N

city: Guangzhou

first: Jinlong

last: Lin

address: Dongfeng dong road

institute: Sun Yat-sen university cancer center

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: hg19
Supplementary files format and content: all.gene.FPKM.mRNA_processed.txt: Tab-delimited text file includes all FPKM values for each Sample.

source_name: normal colorectal tissue1

extract_protocol:
RNA was harvested using Trizol.
Select the corresponding testing methods for quality inspection according to the requirements of samples and products. A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. The PCR reaction system and program are configured and set up to amplify the product. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: normal colorectal tissue1


title: 4C6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3H3 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 4C1 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3H1 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3H12 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3H11 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3G9 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3H10 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4A2 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 4A1 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3G6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3G8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3G3 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3G5 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3H8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3G1 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3G11 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3G7 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3G4 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3G2 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3G12 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3F9 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3F7 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3F4 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3F6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3F8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3H2 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3F1 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3F3 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3E8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3F2 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3F11 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3E7 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3F10 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3E9 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3F12 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3G10 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3E4 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3E6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3E5 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3E3 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3E1 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3E10 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3E12 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3E11 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3F5 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3D9 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3D8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3D5 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3D7 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3D3 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3D4 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3D12 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3D2 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3D10 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3C9 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3C6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3C7 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3C4 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3C5 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3E2 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3C3 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3C8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3C11 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3C1 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3B8 Negative control

description: Negative control


title: 3D6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3C12 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3B7 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3C10 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3B6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3D1 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3B5 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3B1 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3B3 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3D11 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3B10 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3B4 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3C2 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3A9 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3B2 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3B12 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3B11 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3A8 Positive control

description: Positive control


title: 3A7 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3A6 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3A5 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3A3 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3A4 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3B9 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 3A1 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3A2 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 3A12 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 3A11 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 2H9 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2H8 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2H7 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2H6 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2H5 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2H3 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 3A10 Dioxin-exposed 8-cell stage blastomere

description: Dioxin-exposed 8-cell stage blastomere


title: 2H1 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2H12 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2H11 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2G9 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2G4 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2G5 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2G7 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2H10 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2G3 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2H2 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2F9 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2G10 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2G2 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2G8 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2F7 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2F8 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2F6 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2G1 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2F2 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2F5 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2H4 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2F12 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2F1 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2F3 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2F11 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2E9 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2E8 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2E6 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2E7 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2E2 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2E4 Ahr-knockout 8-cell stage blastomere

description: Ahr-knockout 8-cell stage blastomere


title: 2E1 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2G6 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2F10 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2G12 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2E3 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2E10 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2D9 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2G11 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2D7 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2D6 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2D8 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2D4 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2E12 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2D1 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2D11 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2D12 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2C9 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2D5 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2C7 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2C6 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2C5 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2D3 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2C1 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2C2 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2C4 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2E11 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2C11 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2C10 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2E5 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2B7 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2B8 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2B6 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2B5 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2B4 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2D2 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2B9 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2B2 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2B1 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2B12 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2C8 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 2B11 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 2B10 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2A9 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2A7 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2B3 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2A8 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 2C12 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2A5 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 2A6 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 2A4 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2A3 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2A1 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2A2 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 2A11 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 1H8 Negative control

description: Negative control


title: 2A12 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 1H9 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1H6 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere

value: 2-cell stage blastomere


title: 1H2 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1H5 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1H7 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1H4 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1H3 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1H1 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1H11 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1H10 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1H12 Positive control

description: Positive control


title: 1G8 Positive control

description: Positive control


title: 1G7 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1G9 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1G6 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1G1 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1G2 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1G3 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 2A10 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1G12 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1G4 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1G10 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1F7 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 2D10 Wild-type 8-cell stage blastomere

description: Wild-type 8-cell stage blastomere


title: 1F5 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1F4 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1F3 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1F2 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1G11 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1F10 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1E9 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1G5 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1F11 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1F1 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1E8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1E7 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 2F4 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere


title: 1E4 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1E2 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1E1 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1E3 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1E11 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1E12 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1F9 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1E10 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1D9 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1F8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1F6 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1D8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1E5 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1D6 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1D5 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1D7 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1D4 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1D3 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1D12 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1D2 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1D11 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1D1 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1D10 Positive control

description: Positive control


title: 1C8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1C9 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1C6 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1E6 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1C7 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1F12 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1C12 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1C2 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1C10 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1B7 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1B8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: 1C3 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1C11 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1B9 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: n1n2_P_2

city: Beijing

first: Ba

middle: Xin

last: Wei

address: No.1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology CAS

description: Library name: n1n2_P_2

data_processing:
Low-quality reads were removed with fastp (version 0.20.0), thus resulting in more than 6 Gigabytes of clean reads per library.
The paired-end clean reads were then aligned by STAR (version 2.4.2a) to the tomato reference genome (SL2.5), which was downloaded from the Solanaceae (SOL) Genomics Network (http://solgenomics. net/).
The gene expression levels were calculated as fragments per kilobase of transcript per million fragments(FPKM).
Differential gene expression analyses were performed using the R (version 3.3.1) package DESeq (version 1.26.0) with the absolute value of log2 fold change >1 and P value <0.05
Assembly: tomato reference genome (SL2.5)
Supplementary files format and content: tab_delimited text file includes raw counts for each Sample
Supplementary files format and content: tab_delimited text file includes FPKM values for each Sample

organism: Solanum lycopersicum

source_name: Roots

extract_protocol:
The plant total RNA was extracted using a TRIzol kit (Invitrogen) according to the manufacturer’s instructions. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.the libraries were sequenced on the DNBSEQ-T7 ，150 pair-end.

value: Roots

value: phosphate


title: 1B6 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1B5 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: n1n2_P_3

description: Library name: n1n2_P_3


title: n1_P_3

description: Library name: n1_P_3


title: 1C5 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: 1B4 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: n1n2_P_1

description: Library name: n1n2_P_1


title: 1B3 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1C1 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1C4 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1B2 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: WT_P_3

description: Library name: WT_P_3

value: WT


title: WT_P_2

description: Library name: WT_P_2


title: n1_P_1

description: Library name: n1_P_1


title: WT_P_1

description: Library name: WT_P_1


title: 1B1 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1B12 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1B11 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: n1n2_PF_2

description: Library name: n1n2_PF_2

value: phosphate free


title: 1B10 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: n1n2_PF_3

description: Library name: n1n2_PF_3


title: 1A9 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: n1n2_PF_1

description: Library name: n1n2_PF_1


title: 1A8 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: n1_PF_3

description: Library name: n1_PF_3


title: 1A7 Wild-type 4-cell stage blastomere

description: Wild-type 4-cell stage blastomere


title: n1_PF_2

description: Library name: n1_PF_2


title: 1A6 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: n1_P_2

description: Library name: n1_P_2


title: 1A5 Ahr-knockout 2-cell stage blastomere

description: Ahr-knockout 2-cell stage blastomere


title: WT_PF_3

description: Library name: WT_PF_3


title: 1A4 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: 1A3 Dioxin-exposed 2-cell stage blastomere

description: Dioxin-exposed 2-cell stage blastomere


title: WT_PF_1

description: Library name: WT_PF_1


title: 1A2 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: 1A1 Wild-type 2-cell stage blastomere

description: Wild-type 2-cell stage blastomere


title: WT_PF_2

description: Library name: WT_PF_2


title: 1A12 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: 1A11 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: Hepatoblastoma sample 31

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

description:
Library name: H1226
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)

data_processing:
Raw sequencing data was demultiplexed and aligned to the human reference genome GRCh38-2020-A with Space Ranger 2.0.1 (Visium v1) and Space Ranger 2.1.1 (Visium v2) using spaceranger mkfastq and spaceranger count with default parameters. Fiducial alignment was repeated manually for samples H1156, H1190, H1192, and H1225 using Loupe Browser (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv: list of genes and their spatial enrichment
Supplementary files format and content: cytassist_image.tif: hi-res image of tissue from CytAssist machine
Supplementary files format and content: loupe_alignment.json: manual fiducial alignment in json format
Library strategy: Spatial Transcriptomics

extract_protocol:
Ten tissue sections with a maximum area of 6.5 x 6.5 mm2 were cut from ten distinct HB FFPE tissue bocks, placed on the mRNA capture areas of Visium Gene Expression slides for FFPE (10x Genomics, Visium v1), deparaffinized, and H&E stained according to the respective user guide (CG000409 Rev C, 10x Genomics). Twelve additional samples were processed using a CytAssist machine (10x Genomics, Visium v2), which transfers the transcriptomic probes from standard glass slides to spatially barcoded Visium slides, enabling more efficient capture of whole gene expression. For all samples, brightfield histology images were taken using a 4x or 10x objective on a Nikon Eclipse Ni. Raw images were stitched together using NIS-Elements (Nikon) and exported as TIFF files with high-resolution settings.
Libraries were prepared following the manufacturer’s user guide (G000407 Rev D, 10x Genomics).


title: Hepatoblastoma sample 32

description:
Library name: H1227
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: Hepatoblastoma sample 29

description:
Library name: H1192
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: Hepatoblastoma sample 30

description:
Library name: H1225
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: Hepatoblastoma sample 28

description:
Library name: H1191
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: KO_striatum_3

city: strasbourg

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

country: France

institute: CNRS

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Assembly: mm10
Supplementary files format and content: STRIATUM_KO.csv

source_name: Striatum

extract_protocol:
total RNA was extracted from a single striatum of mice using the RNeasy Plus Kit according to manufacturer’s instructions.
RNA-Seq libraries were generated from 1000 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94°C for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Striatum

value: Dclk3 knock out


title: KO_striatum_2


title: Hepatoblastoma sample 27

description:
Library name: H1190
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: Hepatoblastoma sample 25

description:
Library name: H1180
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: Hepatoblastoma sample 26

description:
Library name: H1189
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: KO_striatum_1


title: n1_PF_1

description: Library name: n1_PF_1


title: WT_KO-control_striatum_4


title: WT_KO-control_striatum_3


title: WT_KO-control_striatum_2


title: Hepatoblastoma sample 22

description:
Library name: H1155
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: WT_KO-control_striatum_1


title: 1A10 Dioxin-exposed 4-cell stage blastomere

description: Dioxin-exposed 4-cell stage blastomere


title: THP1_Huh6_iMDK_10µM_1

description: Library name: Sample 50

data_processing:
Alignment of raw FASTQ files to the human reference genome GRCh38 was performed using STAR v2.7.3a followed by generation of BAM files, sorting, and indexing using SAMtools v1.16.1 (mapping quality for uniquely mapping reads set to 255) and extracting read counts for all genes using featureCounts() from Rsubread v2.14.2. Raw counts were RLE (relative log expression) normalized and counts per million wer calculated as implemented in edgeR v3.36. Genes with zero counts in all samples were filtered out.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RLE normalized counts of filtered genes for each sample

growth_protocol: HepG2 and Huh6 cell lines were cultured in RPMI-1640 cell culture medium with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells were subcultured roughly once per week using 0.25% Trypsin/EDTA for detachment. THP-1 cells were maintained in culture and expanded, prior to differentiation, in RPMI-1640 supplemented with 10% FBS, 1% penicillin/streptomycin, 1% L-glutamine, and 1% pyruvate. To induce their differentiation into macrophages, THP-1 cells were cultured in the presence of 80 ng/ml (130 nM) of phorbol 12-myristate 13-acetate (PMA) for 48 hours, followed by 48 hours of resting phase in control medium without PMA.

extract_protocol:
RNA isolation was performed using the RNeasy Mini Kit (Qiagen, # 74104) including DNase treatment following the corresponding instructions.
Libraries were prepared using NEBNext Poly(A) enrichment and Ultra II Directional RNA (New England Biolabs) using 1 µg total RNA. Library quality was controlled using D1000 ScreenTape assays (Agilent Technologies, Inc.).

treatment_protocol: HepG2 and Huh6 cells were seeded into 6-well plates at roughly 5.5 x 10^5 and 2.5 x 10^5 cells per well, respectively. After letting the cells attach and grow for 48 hours, cell culture medium was exchanged for inhibitor- or vehicle-containing medium. Cells were kept in culture for another 48 hours followed by RNA isolation. For co-cultures, the tumor cells were added directly to the differentiated THP-1 cells after 24 hours of MDK inhibition. After an additional 24 hours of co-culture, THP-1 cells were sorted followed by RNA isolation.

value: co-culture with Huh6, iMDK, 10 µM


title: KO_rep3

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Assembly: mm10
Supplementary files format and content: HIPPO_KO.csv

source_name: hippocampus

extract_protocol:
total RNA was extracted from a single hippocampus of mice using the RNeasy Plus Kit according to manufacturer’s instructions.
RNA-Seq libraries were generated from 1000 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94°C for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: hippocampus


title: THP1_Huh6_iMDK_10µM_3

description: Library name: Sample 52


title: Hepatoblastoma sample 21

description:
Library name: H691
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: THP1_Huh6_iMDK_5µM_3

description: Library name: Sample 49

value: co-culture with Huh6, iMDK, 5 µM


title: KO_striatum_4


title: KO_rep4


title: KO_rep1


title: KO_rep2


title: THP1_Huh6_iMDK_10µM_2

description: Library name: Sample 51


title: WT_KO-control_rep4


title: THP1_Huh6_ctrl_2

description: Library name: Sample 45

value: co-culture with Huh6 untreated


title: WT_KO-control_rep2


title: THP1_Huh6_ctrl_3

description: Library name: Sample 46


title: WT_KO-control_rep1


title: Hepatoblastoma sample 23

description:
Library name: H1156
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: WT_cKO-control_rep5

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Assembly: mm10
Supplementary files format and content: HIPPO_cKO.csv

source_name: Hippocampus

value: Hippocampus


title: THP1_Huh6_iMDK_5µM_2

description: Library name: Sample 48


title: THP1_Huh6_ctrl_1

description: Library name: Sample 44


title: 2C3 Ahr-knockout 4-cell stage blastomere

description: Ahr-knockout 4-cell stage blastomere

value: Blastomere

value: Untreated


title: THP1_HepG2_iMDK_10µM_2

description: Library name: Sample 42

value: co-culture with HepG2, iMDK, 10 µM


title: THP1_HepG2_iMDK_10µM_3

description: Library name: Sample 43


title: WT_cKO-control_rep4


title: Hepatoblastoma sample 24

description:
Library name: H1157
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)


title: WT_cKO-control_rep3


title: THP1_HepG2_iMDK_10µM_1

description: Library name: Sample 41


title: THP1_HepG2_iMDK_5µM_3

description: Library name: Sample 40

value: co-culture with HepG2, iMDK, 5 µM


title: WT_cKO-control_rep1


title: THP1_HepG2_iMDK_5µM_1

description: Library name: Sample 38


title: THP1_HepG2_ctrl_2

description: Library name: Sample 36

value: co-culture with HepG2 untreated


title: THP1_HepG2_ctrl_3

description: Library name: Sample 37


title: THP1_Huh6_iMDK_5µM_1

description: Library name: Sample 47


title: cKO_rep5

value: Conditional Dclk3 knock out


title: WT_KO-control_rep3


title: cKO_rep3


title: THP1_ctrl_3

description: Library name: Sample 34

value: monoculture


title: THP1_HepG2_ctrl_1

description: Library name: Sample 35


title: THP1_HepG2_iMDK_5µM_2

description: Library name: Sample 39


title: THP1_ctrl_2

description: Library name: Sample 33


title: cKO_rep1


title: giaSC, mGC from individual 6, UC-MSC from person 1, passage 7, replicate 2

city: Stanford

first: Jingxue

last: Xin

state: California

address: JAMES CLARK CENTER E100A

institute: Stanford University

data_processing:
The raw RNA sequencing reads for all samples were aligned to the human reference genome hg19 using the STAR program with standard input parameters. Gene expression levels were quantified by calculating FPKM values (fragments per kilobase of transcript per million fragments mapped) using RSEM software, and the gene annotation reference was GENCODE hg19.
The single-cell RNA-seq data for m-GCs was processed using 10x Genomics Cell Ranger 3.1.0 to handle the raw fastq files. For alignment and gene annotation, the human reference genome used was hg19, in conjunction with Ensembl 87
Assembly: hg19
Supplementary files format and content: Count and FPKM matrix text file, feature barcode matrix text file.

source_name: a new cell type generated from cell-cell communication between m-GC and UC-MSC

growth_protocol: Human unmobilized peripheral blood samples were collected from healthy donors. Immediately after collection, majority of the red blood cells were removed using lysis buffer and majority of lymphocytes were removed by high-speed centrifugation. The supernatant was removed and the cell pellet was gently rinsed with 1xPBS (pH 7.4) which contains pre-GC.

extract_protocol:
Total RNA were extracted using TRI Reagent protocol (Sigma-Aldrich). Residual DNA contamination was digested by using PerfeCTa DNase I (RNase-free, Quantabio).
RNA-seq libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs (NEB), E7770). Single cell RNA-seq library was constructed using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000268).

treatment_protocol: The cell pellet was gently resuspended in 19 mL hepatic-conditioned medium to activate pre-GCs. The cell suspension was seeded in 100 mm diameter treated culture dishes (Corning, 430293) at 3,000,000 to 5,000,000 cells per dish, and incubated for 14-18 days in a CO2 (5%) incubator at 37oC. The hepatic-conditioned medium was changed every other day. Aggregation of granules near the center of the cells indicates maturation (m-GCs). Co-culture of m-GC and human umbilical cord-derived mesenchymal stromal cells (UC-MSC) at the ratio of 10:1 give rise to giaSC in the presence of hepatic-conditioned medium.


title: THP1_ctrl_1

description: Library name: Sample 32


title: giaSC, mGC from individual 5, UC-MSC from person 1, passage 3, replicate 3

value: a new cell type generated from cell-cell communication between m-GC and UC-MSC


title: cKO_rep2


title: Hepatoblastoma sample 20

description:
H392
10x Genomics Visium FFPE spatial transcriptomics

data_processing:
Raw sequencing data was demultiplexed and aligned to the human reference genome GRCh38-2020-A with Space Ranger 2.0.1 using spaceranger mkfastq and spaceranger count with default parameters.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv: list of genes and their spatial enrichment
Library strategy: spatial transcriptomics

extract_protocol:
Ten tissue sections with a maximum area of 6.5 x 6.5 mm2 were cut from ten distinct HB FFPE tissue bocks, placed on the mRNA capture areas of Visium Gene Expression slides for FFPE (10x Genomics), fixed in methanol, and H&E stained according to the respective user guide (CG000409 Rev C, 10x Genomics). Brightfield histology images were taken using a 4x or 10x objective on a Nikon Eclipse Ni. Raw images were stitched together using NIS-Elements (Nikon) and exported as TIFF files with high-resolution settings.
Libraries were prepared following the manufacturer’s user guide (G000407 Rev D, 10x Genomics).


title: WT_cKO-control_rep2

value: WT


title: giaSC, mGC from individual 6, UC-MSC from person 1, passage 7, replicate 1


title: giaSC, mGC from individual 5, UC-MSC from person 1, passage 3, replicate 1


title: Hepatoblastoma sample 19

description:
H391
10x Genomics Visium FFPE spatial transcriptomics


title: Hepatoblastoma sample 18

description:
H389
10x Genomics Visium FFPE spatial transcriptomics


title: cKO_rep6


title: Hepatoblastoma sample 17

description:
H388
10x Genomics Visium FFPE spatial transcriptomics


title: Hepatoblastoma sample 16

description:
H387
10x Genomics Visium FFPE spatial transcriptomics


title: m-GC, individual 4, replicate 1

source_name: mature Guide Cells activated from dormant pre-GC


title: Hepatoblastoma sample 14

description:
H289
10x Genomics Visium FFPE spatial transcriptomics


title: cKO_rep4


title: m-GC, individual 3, replicate 2

value: mature Guide Cells activated from dormant pre-GC


title: pre-GC, individual 2, replicate 3

source_name: dormant cells isolated from human peripheral blood


title: Hepatoblastoma sample 12

description:
H287
10x Genomics Visium FFPE spatial transcriptomics


title: Hepatoblastoma sample 13

description:
H288
10x Genomics Visium FFPE spatial transcriptomics


title: m-GC, individual 3, replicate 3


title: m-GC, individual 4, replicate 2


title: pre-GC, individual 2, replicate 2

value: dormant cells isolated from human peripheral blood


title: Hepatoblastoma sample 9

description:
H133
10x Genomics scRNA-seq

library_source: transcriptomic single cell

data_processing:
Binary Base Call (BCL) files were demultiplexed and aligned to the human reference genome GRCh38-2020-A with Cell Ranger v3.0.2 and v6.0.2 using cellranger mkfastq and cellranger count with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Fresh hepatoblastoma tissue

extract_protocol:
Ten fresh tumor samples from five patients were obtained for single-cell dissociation. Using scalpels, samples were minced into pieces 1-2 mm3 in size, followed by digestion in a papain solution containing papain (Worthington) in pre-warmed DMEM/F12 (Thermo Fisher) and 32.4 µg/ml DNAse (Worthington). After digestion, samples were passed through a 40 µm cell strainer (Corning) followed by red blood cell lysis using ACK lysing buffer (Thermo Fisher). Resulting single-cell suspensions were cryopreserved.
After sorting for vital cells using 7-aminoactinomycin D (7-AAD, eBioscience) staining in flow cytometry with a BD FACSAria II Cell Sorter (BD Biosciences), single-cell suspensions were processed using Chromium Single Cell 3’ Gel Bead Kit v3.1 (10x Genomics) and a Chromium Next GEM Chip G Single Cell Kit (10x Genomics) according to the manufacturer’s protocol.

value: Fresh hepatoblastoma tissue


title: Hepatoblastoma sample 11

description:
H286
10x Genomics Visium FFPE spatial transcriptomics


title: pre-GC, individual 2, replicate 1


title: pre-GC, individual 1, replicate 3


title: m-GC, individual 3, replicate 1


title: giaSC, mGC from individual 5, UC-MSC from person 1, passage 3, replicate 2


title: Hepatoblastoma sample 7

description:
H128
10x Genomics scRNA-seq


title: pre-GC, individual 1, replicate 2


title: Hepatoblastoma sample 8

description:
H132
10x Genomics scRNA-seq


title: Hepatoblastoma sample 6

description:
H121
10x Genomics scRNA-seq


title: Hepatoblastoma sample 15

description:
H386
10x Genomics Visium FFPE spatial transcriptomics


title: pre-GC, individual 1, replicate 1


title: SL470905

city: Ann Arbor

first: Elaine

last: Hebda-Bauer

state: Michigan

address: 205 Zina Pitcher Place

department: Michigan Neuroscience Institute

institute: University of Michigan

data_processing:
Alignment: STAR: 2.7.3a
Quantification of gene-level counts: Subread version 2.0.0
Quality control and filtering: Rstudio (v.1.4.1717, R v. 4.1.1)
Differential expression analysis: limma v.3.48.3
Assembly: Rnor6, annotation: Ensembl v.103
Supplementary files format and content: Filtered log(2) cpm per Ensembl-annotated gene for each F2 hippocampal sample

growth_protocol: Selectively breeding rats for a high or low propensity to explore a novel environment produced the bHR and bLR lines, respectively, at the University of Michigan (Stead et al., 2006). After 37 generations, an initial set (“F0”) of bHRs and bLRs were chosen from 24 distinct families (12 bHR, 12 bLR) to cross-breed for creating 12 intercross families. Their “F1” offspring were screened for novelty-induced locomotion, and individuals with similarly high or low LocoScores were bred with each other to produce a re-emergence of diverse behavioral phenotypes in the “F2” generation. These 48 F2 litters generated 540 rats, 323 of which were phenotyped as young adults (2-4 months old). Our current study used a subset of these animals (F0: n=24, n=6/phenotype per sex; F2: n=250, n=125/sex) that overlapped with those in previous genetic studies (Chitre et al., 2022; Z. Zhou et al., 2019a) but was distinct from those included in our previous male-only RNA-Seq meta-analysis (Birt et al., 2021).  All procedures were conducted in accordance with the National Institutes of Health Guide for the Care and Use of Animals and approved by the Institutional Animal Care and Use Committee at the University of Michigan.

extract_protocol:
Adults (postnatal days 113-132) were decapitated without anesthesia and brains extracted within two minutes. For the F0s, whole HPC was immediately dissected and flash frozen. For the F2s, whole brains were flash frozen, and then later hole punches from the dorsal and ventral HPC were pooled from four hemisected coronal slabs (-2.12 to -6.04 mm Bregma; (Paxinos & Watson, 2013)) for each animal. RNA was extracted using the Qiagen RNeasy Plus Mini Kit.
A Ribogreen Assay was performed using 2 ml of a 7X dilution to measure RNA concentration and total RNA amount. To measure RNA quality, 2 ml of various dilutions were loaded onto a HS RNA Fragment Analyzer chip. The samples were then normalized to 500ng input into 50ml volume for use in Poly A RNA-seq library reactions that were completed through Second Strand Synthesis and Purification. Diluted samples were used for a PicoGreen assay and loaded onto a HS Caliper chip for quality analysis of the cDNA libraries. Following Kapa qPCR, samples were sequenced on a NovaSeq S4 101PE flowcell targeting an average of 25 million reads.

treatment_protocol: Behavioral data analysis: All F0 and F2 rats were tested for locomotor activity in a novel environment (“LocoScore,” protocol: (Stead et al., 2006)). Exploratory and anxiety-related behaviors were measured on an Elevated Plus Maze (protocol: (Chitre et al., 2022)), including distance traveled (cm), time immobile (sec), and percent time in the open arms. A subset of F2s (n=209) was subsequently tested for Sign Tracking vs. Goal Tracking behavior during the last two days of a week-long Pavlovian Conditioned Approach task (protocol: (Meyer et al., 2012)) using a combined score (“PavCA Index”) summarizing behaviors indicating preference for the conditioned stimuli (lever) vs. unconditioned stimuli (food magazine).

tag: hippocampal siide used

value: right

value: Male

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: Hepatoblastoma sample 3

description:
H095
10x Genomics scRNA-seq

tag: tissue


title: SL470903

value: hippocampus

tag: hippocampal siide used

tag: Sex

value: Female

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm


title: Hepatoblastoma sample 4

description:
H096
10x Genomics scRNA-seq

tag: tissue


title: Hepatoblastoma sample 1

description:
H020
10x Genomics scRNA-seq


title: AdultSample57_Saliva

type: genomic

city: University Park

first: Idan

last: Shalev

state: PA

address: 219 Biobehavioral Health Building

institute: The Pennsylvania State University

description: Processed data file column header: 574

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the human Infinium MethylationEPICv2 BeadChip (Illumina) using standard Illumina protocols.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard Illumina scanner settings.

data_processing:
IDAT files were read into R statistical software using the read.metharray.exp function in the minfi package. Samples with probe detection p-values greater than 0.05 for more than 5% of probes or with bisulfite conversion rates of less than 80% were excluded from the current data (no IDAT files or processed data are included for these samples). CpG probes with a bead count of less than 3 in 5% or more samples or with an average detection p-value of > 0.05 across all samples were excluded. All samples were normalized using the beta-mixture quantile normalization (BMIQ) method. In order to remove duplicate probes in the EPIC v2 chip, we used the R package ENmix (using v1.36.08 or newer). This package has a function called rm.cgsuffix. This function both removes the suffix on EPIC v2 probe names (i.e., removes “_BC11” from “cg25324105_BC11”) and collapses duplicate probes by taking their averages.
Processed data files includes: Average Beta

label: Cy3 and Cy5

source_name: Cell-free DNA from Saliva tissue

label_protocol: Standard Illumina protocol.

extract_protocol: To minimize the impact of DNA extraction procedures, DNA was extracted from all tissue samples using the Gentra Puregene DNA Extraction Kit according to factory guidelines (Qiagen). Extracted DNA was stored at -80°C in Qiagen DNA Hydration Solution.

value: Saliva

tag: Sex

tag: age


title: Hepatoblastoma sample 5

description:
H118
10x Genomics scRNA-seq


title: AdultSample57_Buccal

description: Processed data file column header: 573

source_name: Cell-free DNA from Buccal tissue

value: Buccal


title: HepG2_iMDK_10µM_2

growth_protocol: HepG2 and Huh6 cell lines were cultured in RPMI-1640 cell culture medium with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were subcultured roughly once per week using 0.25% Trypsin/EDTA for detachment.

treatment_protocol: HepG2 and Huh6 cells were seeded into 6-well plates at roughly 5.5 x 10^5 and 2.5 x 10^5 cells per well, respectively. After letting the cells attach and grow for 48 hours, cell culture medium was exchanged for inhibitor- or vehicle-containing medium. Cells were kept in culture for another 48 hours followed by RNA isolation.

tag: cell line

tag: treatment

value: iMDK, 10 uM


title: Hepatoblastoma sample 2

description:
H063
10x Genomics scRNA-seq


title: HepG2_iMDK_10µM_3


title: Hepatoblastoma sample 10

description:
H134
10x Genomics scRNA-seq


title: SL470904

tag: hippocampal siide used

value: left

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: epm distancetraveled

tag: epm time_immobile

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: SL470902

tag: tissue

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli


title: SL470906

tag: tissue

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: ribosomeperc

tag: mrnaperc

tag: epm distancetraveled

tag: epm time_immobile

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod