title: NatBiom-1 : Exposure to Tenacibaculum finnmarkense, culture 5

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing:
Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed
Processeed data: Lowess normalized signal minus background

organism: Salmo salar

source_name: Scale explant

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Scales were picked from salmon reared in cages or tanks with sea water and placed in wells containing L15 medium with 5% FBS, 1% antibiotic antimycotic solution and 10mM HEPES.

extract_protocol: RNA lysis buffer was added directly to wells and RNA was extracted using the Quick-RNA™ Miniprep Kit (Zymo Research) .

treatment_protocol: Explant cultures were exposed to media with bacteria for 2h. Next, media with bacteria were replaced with fresh media with antibiotics, and cells were harvested in 24h.

value: scale explant


title: NatBiom-1 : Exposure to Tenacibaculum finnmarkense, culture 6

status: Public on Mar 30 2025

type: RNA

molecule: total RNA

tag: tissue


title: Black PtenΔ/+ control skin, replicate 3, scRNAseq

type: SRA

city: Irvine

first: Anand

middle: K

last: Ganesan

state: CA

address: 839 Health Science Rd

department: Dermatology

country: USA

institute: University of California, Irvine

library_source: transcriptomic single cell

data_processing:
FASTQ files were generated from Illumina’s binary base call raw output with Cell Ranger’s (v2.1.0; RRID:SCR_017344) ‘cellranger mkfastq’ command and the count matrix for each sample was produced with ‘cellranger count‘.
Downstream bioinformatic analysis was conducted using Seurat78. For quality control, cells with fewer than 200 detected genes and genes detected in less than 3 cells were discarded. We calculated the percent mitochondrial gene expression and kept cells with less than 15% mitochondrial gene expression, and cells with fewer than 4000 genes per cell.
Assembly: mm10
Supplementary files format and content: normalized count matrix, barcodes, and genes for two merged Seurat Objects ( whole skin tumor and skin in Fig2B, and NC-derived subset of transplanted tumors in Fig 3B)

organism: Mus musculus

source_name: skin

extract_protocol:
The mice were euthanized, shaved, and depilated. For non-tumor bearing samples, a 2 by 3 cm section of the back skin was retrieved, and the fat scraped off from the underside. For melanoma-bearing samples, the skin sample on top of the tumor piece was also collected, with the mouse-matched adjacent skin next to the tumor (termed “tumor-adjacent skin”) as sample-matched control. The tumor or skin sample was then physically minced, and suspended in a gentle-macs C-tube dissociation buffer (5mL of RPMI, 50 µL  of liberase 0.25 mg/mL, 116 µL of Hepes 23.2 mM, 116 µL of Sodium Pyruvate 2.32 mM, 500 µL of Collagenase :Dispase 1 mg/mL) for 50 min at 37°C incubation with gentle agitation at a speed of 85-90rpm. After initial 50 minute digestion i, 10 µL of DNaseI (23 µL was added for another 10 min of 37°C agitated incubation and then inactivated with 400 µL of fetal bovine serum and 10 µL of EDTA (1 mM). The tissue suspension was further dissociated mechanically with GentleMACS by running the setting m_imptumor_04.01 twice. The digested suspensions were filtered twice through a 70 mm strainer and dead cells removed by centrifugation at 300 x g for 15 min. The live cells were washed with 0.04% UltraPure BSA:PBS buffer, gently re-suspended in the same buffer, and counted using trypan blue and cell counter.
Libraries were prepared using the Chromium Single Cell 3’ v2 protocol (10X Genomics). Briefly, individual cells and gel beads were encapsulated in oil droplets where cells were lysed and mRNA was reverse transcribed to 10X barcoded cDNA. Adapters were ligated to the cDNA followed by the addition of the sample index. Prepared libraries were sequenced using paired end 100 cycles chemistry for the Illumina HiSeq 4000.

treatment_protocol: Conditional allele BrafCA, Tyr::CreER, and/or Ptenlox4-5/+ mice (RRID:MGI:5902125, from Dr. Martin McMahon) were backcrossed with C57BL/6J (JAX 000664) for greater than 5 generations. Conditional allele BrafCA, Tyr::CreER, and/or Ptenlox4-5/+ congenic C57BL/6J mice were then crossed with Albino B6(Cg)-Tyrc-2J/J (JAX 000058) to create albino BrafCA/+ melanoma and nevi bearing mice. Topical 4-hydroxytamoxifen (4-OHT; 25 mg/mL or 75 mg/mL in DMSO; 98% Z-isomer, Sigma-Aldrich) was administered to pups on their back at ages P2-P4. Mice were euthanized if the volume of their tumors exceeded 10% of total body volume, if tumors were significantly ulcerated, if mice were moribund, if they lost weight, if they were lethargic, or if they were unable to ambulate. All mouse procedures were approved by UCI’s IACUC.

value: skin

tag: sample location

value: mouse depilated back

tag: gender

value: Female

tag: genotype

value: Cre+; mTmG+

tag: coat color

value: black


title: NatBiom-1 : Exposure to Tenacibaculum finnmarkense, culture 3


title: Group3 medulloblatoma rep2

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

library_source: transcriptomic

data_processing:
The row reads were trimmed to remove adaptor sequences using Skewer (v0.2.2).
The reads were mapped to the mm10 genome using STAR (v.2.7.8a).
The mapped reads were then counted using featureCounts (v.2.0.10).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: primary

extract_protocol:
Total RNAs extracted with RNeasy Plus Mini Kit (74134, QIAGEN) were used for RNA-seq differential expression analysis in some experiments.
For RNA sequencing, 450-700 ng of the RNA was used to prepare each library using the SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara, 634874), according to the provided guidelines.

value: primary

tag: cell type

value: medulloblastoma

tag: treatment


title: Black PtenΔ/+ control skin, replicate 1, scRNAseq


title: NatBiom-1 : Exposure to mixture of  probioticbacteria, culture 2


title: BioAct: Control (mock exposure), culture 6


title: NatBiom-1 : Exposure to mixture of  probioticbacteria, culture 6


title: NatBiom-1 : Exposure to mixture of  probioticbacteria, culture 4


title: NatBiom-1 : Exposure to mixture of  probioticbacteria, culture 5


title: sgPtch1-sgChd7 tumors rep1


title: Black BrafCA/+; PtenΔ/+ tumor, replicate 3, scRNAseq

source_name: tumor

value: tumor

value: BrafCA/+; Ptendelta/+; Cre+; mTmG+


title: Black BrafCA/+; PtenΔ/+ tumor, replicate 2, scRNAseq


title: Black BrafCA/+; PtenΔ/+ tumor-adjacent skin, replicate 4, scRNAseq


title: BioAct: Control (mock exposure), culture 4


title: NatBiom-1 : Exposure to mixture of  probioticbacteria, culture 3


title: Black BrafCA/+; PtenΔ/+ tumor, replicate 1, scRNAseq


title: Black BrafCA/+; PtenΔ/+ tumor-adjacent skin, replicate 3, scRNAseq


title: Black BrafCA/+; PtenΔ/+ tumor-adjacent skin, replicate 1, scRNAseq


title: BioAct: Control (mock exposure), culture 5


title: Black BrafCA/+; PtenΔ/+ p50 nevus skin, replicate 3, scRNAseq

value: Male

value: BrafCA/+; Cre+


title: Black BrafCA/+; PtenΔ/+ p50 nevus skin, replicate 1, scRNAseq


title: BioAct: Control (mock exposure), culture 1-13


title: Black BrafCA/+; PtenΔ/+ p50 nevus skin, replicate 2, scRNAseq


title: Black BrafCA/+; PtenΔ/+ tumor, replicate 4, scRNAseq


title: Black PtenΔ/+ control skin, replicate 2, scRNAseq


title: BioAct: Control (mock exposure), culture 1


title: 278_22_Apc_Myc2_540_null

city: Stockholm

first: Inderpreet

last: Sur

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
Library name: Sample 14
10x Genomics

data_processing:
For adult samples the demultiplexing, barcoded processing, gene counting and aggregation was done using Cell Ranger software v6.0.1.
For fetal samples from 3D cultures, Cell Ranger (v7.2.0)  and Cell Ranger multi pipeline was used.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Crypt enriched Intestinal fraction

extract_protocol:
For adult- crypt enriched fractions were used to make single-cell suspensions, FACS sorted and run on 10x Controller. For fetal 3D cultures- single cell suspensions were fixed and processed using 10x Genomics Flex technology. The samples were run on a Chromium X instrument.
For samples from adult mice, library construction was according to the manufacturer's protocol (single cell 3´v3.1 protocol, 10x Genomics).  Libraries from fixed fetal cells from 3D cultures were prepared using Next GEM single cell fixed RNA hybridization and library kit (catalog nr: 1000415) and according to manufacturer’s protocol (10x Genomics).

treatment_protocol: For mice treated with gamma Irradiation- a total body radiation of 12 Gy was given in two doses of 6 Gy (6hr apart) and intestines were harvested at 2 days post irradiation (2dpi).

value: Crypt enriched Intestinal fraction

value: Apc-Min/+; Myc2-540_null


title: NatBiom-1 : Exposure to Tenacibaculum finnmarkense, culture 2


title: NatBiom-1 : Exposure to Tenacibaculum finnmarkense, culture 4


title: Black Wildtype p50 control skin, replicate 3, scRNAseq

value: Cre+


title: NatBiom-1 : Exposure to Tenacibaculum finnmarkense, culture 1


title: NatBiom-1 : Exposure to mixture of  probioticbacteria, culture 1


title: NatBiom-1 : Exposure to Moritella viscosa, culture 6


title: NatBiom-1 : Exposure to Moritella viscosa, culture 3


title: NatBiom-1 : Exposure to Moritella viscosa, culture 5


title: Black Wildtype p50 control skin, replicate 2, scRNAseq


title: NatBiom-1 : Exposure to Moritella viscosa, culture 4


title: Black Wildtype p50 control skin, replicate 1, scRNAseq


title: NatBiom-1 : Exposure to Moritella viscosa, culture 2


title: 142_22_1_WT1_fetal_3D_culture

description:
Library name: Sample 12
10x Genomics (Flex)

source_name: E16.5 intestinal 3D cultures

value: E16.5 intestinal 3D cultures

value: WT


title: 141_22_null_fetal_3D_culture

description:
Library name: Sample 11
10x Genomics (Flex)


title: Black BrafCA/+; PtenΔ/+ p30 nevus skin, replicate 2, scRNAseq


title: BioAct: Control (mock exposure), culture 2

value: scale explant


title: BioAct: Exposure to Tenacibaculum finnmarkense, culture 5


title: Black BrafCA/+; PtenΔ/+ tumor-adjacent skin, replicate 2, scRNAseq

value: skin


title: BioAct: Exposure to Tenacibaculum finnmarkense, culture 2


title: Black BrafCA/+; PtenΔ/+ p30 nevus skin, replicate 1, scRNAseq

value: mouse depilated back


title: 61_22_Apc_Myc2_540_null

description:
Library name: Sample 9
10x Genomics


title: BioAct: Exposure to Tenacibaculum finnmarkense, culture 1-13


title: Black Wildtype p30 control skin, replicate 2, scRNAseq


title: Black Wildtype p30 control skin, replicate 1, scRNAseq


title: AlgOil : Control (mock exposure), culture 6


title: AlgOil : Control (mock exposure), culture 5


title: 22_63_Apc

description:
Library name: Sample 8
10x Genomics

value: Apc-Min/+


title: Albino BrafCA/+ Transplanted tumor (round 1), replicate 2, scRNAseq

value: Female

value: NSG

value: albino


title: NatBiom-1 : Exposure to Moritella viscosa, culture 1


title: 142_22_2_WT2_fetal_3D_culture

description:
Library name: Sample 13
10x Genomics (Flex)


title: AlgOil : Control (mock exposure), culture 4


title: 107_22_null_fetal_3D_culture

description:
Library name: Sample 10
10x Genomics (Flex)


title: BioAct: Exposure to Tenacibaculum finnmarkense, culture 4


title: BioAct: Exposure to Tenacibaculum finnmarkense, culture 1


title: AlgOil : Control (mock exposure), culture 63


title: 276_21, Null2, scRNA-seq

description: 10x Genomics


title: Black BrafCA/+; PtenΔ/+ Transplanted tumor (round 1), replicate 2, scRNAseq


title: AlgOil : Control (mock exposure), culture 1


title: 69_70_22, Null, scRNA-seq

description: 10x Genomics

value: Irradiated, 2dpi


title: 62_22, Wildtype2, scRNA-seq

description: 10x Genomics

value: Wildtype


title: AlgOil : Exposure to Moritella viscosa, full strength, culture 5


title: AlgOil : Exposure to Moritella viscosa, full strength, culture 3


title: AlgOil : Exposure to Moritella viscosa, full strength, culture 6


title: BioAct: Exposure to Tenacibaculum finnmarkense, culture 6


title: AlgOil : Exposure to Moritella viscosa, full strength, culture 4


title: AlgOil : Exposure to Moritella viscosa, dilution 1:100, culture 2-6


title: D185 human fetal retina derived retinosphere, periphery

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

description:
Library name: Periphery
10x Genomics

data_processing:
Raw sequencing files were demultiplexed using cellranger mkfastqs, and fastqs were aligned to the GRCh38 reference genome using cellranger count to generate gene expression matrices. Cellranger 7.0.0 was used.
Seurat analysis was performed in R using Seurat v5.0.3, UMAP (Becht et al., 2018)20, ggplot2, and dplyr. The raw counts were normalized, scaled, and variable features were identified. Datasets combined in Seurat were integrated by performing CCA on the combined datasets, and reduced into a lower dimensional space using dimensional reduction (Butler et al., 2018)19. Clustering resolution for all datasets were set so clusters matched well with known cell type markers (Fig. S2A). Cell types were assigned to clusters in the merged objects.
Assembly: GRCh38
Supplementary files format and content: Processed data files are zipped filtered_feature_matrices generated from cellranger count.

organism: Homo sapiens

source_name: Periphery

growth_protocol: Fetal retina was dissected into 300–400-micron pieces with dissecting scissors. These were then maintained in RDM (Retinal differentiation medium, 46% DMEM, 46% DMEM/F12, 2% B27, 1% Pen Strep, 2% NEAA, and 5% FBS) in low-adhesion 6 well plates or 10cm dishes.

extract_protocol:
The CMZ was dissected from the retinospheres or peripheral retinospheres were isolated and dissociated using Accutase and DNAse for 20-30 minutes on a nutator at 37C, with gentile pipetting to break up cells every 7 minutes. Cell pellets were resuspended in PBS containing 0.04% bovine serum albumin and filtered through a 35µm cell strainer (Fisher, 08-771-23) to remove cell clumps.
Cells were then counted with a hemocytometer. 8,000-10,000 cells of the sample were then used as input into the 10X protocol. GEM generation, reverse transcription, cDNA amplification, and library construction steps were performed according to the standard 10x workflow for Single Cell 3 v3.1 Dual Index Gene Expression kit according to the manufacturers instructions.

value: Retina

tag: age

value: 137 days gestation + 48 days in vitro culture

tag: Sex


title: Black BrafCA/+; PtenΔ/+ Transplanted tumor (round 1), replicate 1, scRNAseq

value: tumor

value: Male


title: AlgOil : Exposure to Moritella viscosa, dilution 1:100, culture 2-5


title: AlgOil : Control (mock exposure), culture 3


title: AlgOil : Exposure to Moritella viscosa, dilution 1:100, culture 2-4


title: AlgOil : Control (mock exposure), culture 64


title: Albino BrafCA/+ Transplanted tumor (round 1), replicate 1, scRNAseq


title: AlgOil : Exposure to Moritella viscosa, dilution 1:100, culture 2-3


title: Albino BrafCA/+ tumor, replicate 3, scRNAseq

value: BrafCA/+; Cre+; mTmG-; Fucci+


title: 67_68_22, Wildtype, scRNA-seq

description: 10x Genomics

value: Crypt enriched Intestinal fraction


title: IDHwt_unt_rnaseq

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Read sequences were aligned to mm10 mouse reference genome using BWA mem v.0.7.6a and default parameters
Custom java program (BAM2WIG) was used to generate wig files for downstream analysis and visualization in genome browser. Reads with BWA mapping quality scores <5 were discarded and reads that aligned to the same genomic coordinate were counted only once in the profile generation.
Duplicate reads were marked using Picard Tools MarkDuplicates v1.92
Genome_build: mm10
Supplementary_files_format_and_content: BED files from hmeDIP-seq generated using MACS2 v.2.1.0
Supplementary_files_format_and_content: Wig files from meDIP-seq generated using a custom java program (BAM2WIG)
Supplementary_files_format_and_content: bigWig files from hmeDIP-seq and meDIP-seq generated using Deeptools v2.5.0.1
Supplementary_files_format_and_content: Text files with RPKM values where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)

source_name: HoxA9 IDH1-wt

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (Stem Cell Technologies, Vancouver, BC, Canada) supplemented with 15% heat-inactivated fetal bovine serum (Life Technologies, Burlington, ON, Canada) and 6 ng/mL murine interleukin-3, 10 ng/mL human interleukin-6, 20 ng/mL murine stem cell factor (Peprotech, Hamburg, Germany), and antibiotics (penicillin/streptomycin).

extract_protocol:
Frozen pellets were treated with 1% 2-mercaptoethanol in Qiagen Buffer RLT Plus to lyse the cells. DNA was separated using the Qiagen AllPrep DNA spin columns, and the flow-through was used for RNA purification. DNA extraction was completed using the Qiagen DNeasy kit. RNA was purified as per the mirVana miRNA isolation kit (ThermoFisher AM1560).
We constructed RNA-seq, meDIP-seq, and hmeDIP-seq libraries as described previously (Mingay et al., 2017).  Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

treatment_protocol: Vitamin C (L-ascorbic acid 2-phosphate sesqui-magnesium salt hydrate) (Sigma-Aldrich) was added to culture medium daily at a concentration of 100µg/mL (0.345mM). Cells were taken out for DNA/RNA extraction for hmeDIP-seq, meDIP-seq, and RNA-seq at 15hrs and 72hrs after the initial vitamin C treatment.

tag: cell line

value: HoxA9 IDH1-wt

value: Tetwt

value: Untreated for 72hr

tag: librarystrategy

value: RNA-seq


title: 72hr_DKO_vitc_rnaseq

source_name: HoxA9 IDH1-R132H

value: HoxA9 IDH1-R132H

value: Vitamin C for 72hr


title: Albino BrafCA/+ tumor-adjacent skin, replicate 3, scRNAseq

value: skin

value: mouse depilated back

value: Female


title: D185 human fetal retina derived retinosphere, CMZ

description:
Library name: CMZ
10x Genomics

source_name: CMZ


title: AlgOil : Exposure to Moritella viscosa, dilution 1:100, culture 2-1

value: scale explant


title: AlgOil : Exposure to Moritella viscosa, dilution 1:100, culture 2


title: 72hr_DKO_unt_rnaseq


title: Black BrafCA/+; PtenΔ/+ Transplanted tumor (round 2), replicate 2, scRNAseq

value: NSG

value: albino


title: Albino Wildtype control skin for the Albino BrafCA/+ cohort, replicate 3, scRNAseq

value: Cre+; mTmG-; Fucci+


title: Black BrafCA/+; PtenΔ/+ Transplanted tumor (round 2), replicate 1, scRNAseq

value: tumor


title: 72hr_TET3KO_vitc_rnaseq


title: AlgOil : Exposure to Moritella viscosa, dilution 1:10,, culture 1-4


title: AlgOil : Exposure to Moritella viscosa, dilution 1:10,, culture 1-3


title: Albino Wildtype control skin for the Albino BrafCA/+ cohort, replicate 2, scRNAseq

value: Male


title: AlgOil : Exposure to Moritella viscosa, dilution 1:100, culture 2-2


title: AlgOil : Exposure to Moritella viscosa, dilution 1:10,, culture 1-5


title: 72hr_TET3KO_unt_rnaseq


title: 72hr_TET2KO_vitc_rnaseq


title: AlgOil : Exposure to Moritella viscosa, dilution 1:10,, culture 1-6


title: Albino BrafCA/+ tumor, replicate 2, scRNAseq

value: BrafCA/+; Cre+; mTmG+; Fucci+


title: Albino BrafCA/+ tumor-adjacent skin, replicate 2, scRNAseq


title: AlgOil : Exposure to Moritella viscosa, dilution 1:10, culture 1


title: AlgOil : Exposure to Moritella viscosa, dilution 1:10,, culture 1-1


title: AlgOil : Exposure to Moritella viscosa, dilution 1:10,, culture 1-2


title: NatBiom-1 : Control (mock exposure), culture 6


title: Albino Wildtype control skin for the Albino BrafCA/+ cohort, replicate 1, scRNAseq

value: Cre+; mTmG+


title: 72hr_TET2KO_unt_rnaseq


title: 72hr_R132H_vitc_rnaseq


title: Albino BrafCA/+ tumor, replicate 1, scRNAseq

value: BrafCA/+; Cre+; mTmG-


title: NatBiom-1 : Control (mock exposure), culture 5


title: NatBiom-1 : Control (mock exposure), culture 4


title: NatBiom-1 : Control (mock exposure), culture 2


title: NatBiom-1 : Control (mock exposure), culture 1


title: NatBiom-2 : Exposure to Psychrobacter  spp., culture 6


title: Albino BrafCA/+ tumor-adjacent skin, replicate 1, scRNAseq


title: 72hr_R132H_unt_rnaseq

value: Tetwt


title: NatBiom-2 : Exposure to Psychrobacter  spp., culture 5


title: Albino Wildtype control skin for the Albino BrafCA/+; PtenΔ/+ cohort, replicate 2, scRNAseq


title: 15hr_DKO_vitc_rnaseq

value: Vitamin C for 15hr


title: NatBiom-2 : Exposure to Psychrobacter  spp., culture 2


title: NatBiom-2 : Exposure to Psychrobacter  spp., culture 4


title: NatBiom-2 : Exposure to Psychrobacter  spp., culture 1


title: 15hr_DKO_unt_rnaseq

value: Untreated for 15hr

value: RNA-seq


title: 15hr_TET3KO_vitc_rnaseq

value: HoxA9 IDH1-R132H


title: Albino BrafCA/+ nevus skin, replicate 4, scRNAseq

value: skin

value: BrafCA/+; Cre+; mTmG+


title: NatBiom-2 : Exposure to Pseudomonas spp., culture 5


title: Albino Wildtype control skin for the Albino BrafCA/+; PtenΔ/+ cohort, replicate 1, scRNAseq

value: mouse depilated back


title: NatBiom-2 : Exposure to Pseudomonas spp., culture 4

value: scale explant


title: Albino BrafCA/+ nevus skin, replicate 3, scRNAseq


title: NatBiom-2 : Exposure to Pseudomonas spp., culture 3


title: NatBiom-2 : Exposure to Pseudomonas spp., culture 2


title: NatBiom-2 : Exposure to Pseudomonas spp., culture 1


title: Albino BrafCA/+ nevus skin, replicate 2, scRNAseq

value: Female


title: 15hr_TET2KO_vitc_rnaseq


title: NatBiom-2 : Exposure to mixture of bacteria, culture 6


title: 15hr_TET2KO_unt_rnaseq


title: Albino BrafCA/+ nevus skin, replicate 1, scRNAseq

value: albino


title: NatBiom-2 : Exposure to mixture of bacteria, culture 4


title: NatBiom-1 : Control (mock exposure), culture 3


title: NatBiom-2 : Exposure to mixture of bacteria, culture 5


title: Albino PtenΔ/+ control skin, replicate 2, scRNAseq

value: Ptendelta/+; Cre+; mTmG+


title: 15hr_R132H_vitc_rnaseq


title: NatBiom-2 : Control (mock exposure), culture 5


title: NatBiom-2 : Control (mock exposure), culture 4


title: Albino BrafCA/+; PtenΔ/+ tumor, replicate 4, scRNAseq

value: tumor

value: BrafCA/+; Ptendelta/+; Cre+; mTmG+


title: NatBiom-2 : Exposure to mixture of bacteria, culture 2


title: NatBiom-2 : Exposure to mixture of bacteria, culture 3


title: Albino BrafCA/+; PtenΔ/+ tumor-adjacent skin, replicate 4, scRNAseq

value: Male


title: 72hr_DKO_unt_medip

library_source: genomic

molecule: genomic DNA

value: Untreated for 72hr

tag: antibody

value: Anti-5mC (Eurogenentec BI-MECY-0100)

value: meDIP-seq


title: NatBiom-2 : Control (mock exposure), culture 3


title: 15hr_R132H_unt_rnaseq

value: Tetwt


title: 72hr_DKO_vitc_medip

value: Vitamin C for 72hr


title: NatBiom-2 : Control (mock exposure), culture 2


title: Albino PtenΔ/+ control skin, replicate 1, scRNAseq


title: 15hr_TET3KO_unt_rnaseq

value: Untreated for 15hr

value: RNA-seq


title: NatBiom-2 : Control (mock exposure), culture 1


title: NatBiom-2 : Exposure to Aliivibrio spp., culture 6


title: NatBiom-2 : Exposure to Aliivibrio spp., culture 5


title: NatBiom-2 : Exposure to Aliivibrio spp., culture 4


title: 72hr_TET3KO_vitc_medip

value: HoxA9 IDH1-R132H


title: Albino BrafCA/+; PtenΔ/+ tumor, replicate 3, scRNAseq


title: 72hr_TET3KO_unt_medip


title: NatBiom-2 : Exposure to Aliivibrio spp., culture 2


title: NatBiom-2 : Exposure to Aliivibrio spp., culture 1


title: 72hr_TET2KO_vitc_medip


title: Albino BrafCA/+; PtenΔ/+ tumor-adjacent skin, replicate 3, scRNAseq

value: skin


title: Albino BrafCA/+; PtenΔ/+ tumor, replicate 2, scRNAseq

value: mouse depilated back


title: 72hr_TET2KO_unt_medip


title: 19_132_Apc

description:
Library name: Sample 7
10x Genomics

value: Crypt enriched Intestinal fraction

value: Apc-Min/+


title: Albino BrafCA/+; PtenΔ/+ tumor-adjacent skin, replicate 2, scRNAseq

value: albino


title: Atria, CUG960 no dox, biol rep 3

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S. Moody Avenue

institute: OREGON HEALTH & SCIENCE UNIVERSITY

description: Library name: TC-56280

data_processing:
Sequence reads were mapped to mm10 using STAR_2.7.10b.
Read counts extraction and normalization were performed using RSEM_v1.3.1.
Assembly: GENCODE vM25
Supplementary files format and content: .txt (Raw counts and TPM)

source_name: Atria

extract_protocol:
Protocol from Rnwasy Fibrous Tissue Mini Kit (QIAGEN)
The Genomic and RNA Profiling Core (GARP) at BCM conducted sample quality checks using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100. The samples passing the following criteria were used for RNA-Seq: RNA integrity number (RIN) ≥ 8.0, A260nm/A280nm ≥ 1.9, A260nm/A230nm ≥ 1, and r28S/16S ≥ 1.5. The Illumina TruSeq Stranded mRNA library preparation protocol was then used to generate cDNA libraries starting with 250 ng of total RNA. The resulting libraries were quantitated using the NanoDrop spectrophotometer and fragment size assessed with the Agilent Bioanalyzer. The pooled libraries were loaded onto a NovaSeq 6000 S4 flow cell and sequenced to a depth of approximately 100 million read pairs/sample. A paired-end 150 cycle run was used to sequence the flowcell on a NovaSeq 6000 sequencing system.

treatment_protocol: For all cohorts except no dox cohort, CUG960 mice were put on dox since post-natal day 1. The three experimental cohorts received AAV9 through tail vein injection at 9 weeks of age and remained on dox as the on dox cohort till last time point (21 weeks of age). For the on/off dox cohort, the mice were taken off dox feed at 9 weeks of age and remained on normal chow till last time point.

value: Atria

value: TREDT960I (Hom)/ MHCrtTA (Hem)

value: no dox


title: Atria, CUG960 no dox, biol rep 2

description: Library name: TC-53763


title: 72hr_R132H_vitc_medip


title: Albino BrafCA/+; PtenΔ/+ tumor, replicate 1, scRNAseq

value: tumor

value: Male

value: BrafCA/+; Ptendelta/+; Cre+; mTmG+


title: Atria, CUG960 on/off dox, biol rep 3

description: Library name: TC-56274

value: on/off dox


title: Albino BrafCA/+; PtenΔ/+ tumor-adjacent skin, replicate 1, scRNAseq


title: Atria, CUG960 on/off dox, biol rep 2

description: Library name: TC-53759


title: 15hr_DKO_vitc_medip

value: Vitamin C for 15hr

value: Anti-5mC (Eurogenentec BI-MECY-0100)

value: meDIP-seq


title: Atria, CUG960 no dox, biol rep 1

description: Library name: TC-53762


title: Atria, CUG960 on/off dox, biol rep 1

description: Library name: TC-53758


title: 15hr_DKO_unt_medip

value: Untreated for 15hr


title: 72hr_R132H_unt_medip

value: HoxA9 IDH1-R132H

value: Tetwt

value: Untreated for 72hr


title: Atria, CUG960 on dox with 3XFLAG-MBNL1 and 3XMYC-MBNL2, biol rep 1

description: Library name: TC-56266

value: on dox; AAV9-3XFLAG-MBNL1 and AAV9-3XMYC-MBNL2


title: Atria, CUG960 on dox with 3XMYC-MBNL2, biol rep 2

description: Library name: TC-53751

value: on dox; AAV9-3XMYC-MBNL2


title: Atria, CUG960 on dox with 3XFLAG-MBNL1 and 3XMYC-MBNL2, biol rep 2

description: Library name: TC-56267


title: Atria, CUG960 on dox with 3XFLAG-MBNL1 and 3XMYC-MBNL2, biol rep 3

description: Library name: TC-56268


title: 15hr_TET3KO_unt_medip


title: mPFC, Vehicle 2

city: Sendai

first: Hajime

last: Yamamoto

address: 2-1-1 Katahira, Aoba-ku

institute: Tohoku university

description: Library name: Sample_vivo_Cnt_biol_rep2

data_processing:
The quality control process was performed with fastp (v0.23.4), followed by the alignment of the processed data to mouse genome (mm39) with the Salmon (v1.8.0).
Assembly: mm39
Supplementary files format and content: sf files for each sample

source_name: brain

growth_protocol: Cortical neurons were cultured onto poly-L-lysine coated plates. The cultures were maintained in Neurobasal Medium supplemented with B27 Plus supplement, Gultamax-I, and penicillin-streptomycin at 37°C under 5% CO2. Mice were maintained individually in clear plastic cages in a temperature- and humidity-controlled room with a 12-h light/dark cycle and could access standard food and water ad libitum.

extract_protocol:
Total RNAs were purified from the specimen by thiocyanate-phenol-chloroform extraction method.
The process of mRNA purification from total RNA involved the use of poly-T oligo-attached magnetic beads. Subsequent to this, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was subsequently prepared by performing end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Those process were following manufacturer's protocols.

treatment_protocol: Cultured neurons at 14 div were treated with the SSRIs (10 µM fluoxetine, 2.5 µM sertraline, and 4 µM citalopram) for 24 hours. The SSRIs were diluted in water containing 1% saccharin to mask their taste and administered to mice. The final concentrations were 18 mg/kg/day for fluoxetine, 10 mg/kg/day for sertraline, and 15 mg/kg/day for citalopram. Mice received the diluted solutions by drinking ad libitum for 2 weeks.

value: brain

value: Vehicle

tag: time

value: 2 weeks


title: 15hr_TET3KO_vitc_medip


title: mPFC, Vehicle 1

description: Library name: Sample_vivo_Cnt_biol_rep1


title: Atria, CUG960 on dox with 3XFLAG-MBNL1, biol rep 3

description: Library name: TC-56256

value: Atria

value: TREDT960I (Hom)/ MHCrtTA (Hem)

value: on dox; AAV9-3XFLAG-MBNL1


title: Atria, CUG960 on dox with 3XMYC-MBNL2, biol rep 1

description: Library name: TC-53750


title: 15hr_TET2KO_vitc_medip


title: Atria, CUG960 on dox with 3XMYC-MBNL2, biol rep 3

description: Library name: TC-56262


title: mPFC, Vehicle 3

description: Library name: Sample_vivo_Cnt_biol_rep3

value: Male


title: mPFC, Citalopram 2

description: Library name: Sample_vivo_Cit_biol_rep2

value: Citalopram


title: Atria, CUG960 on dox, biol rep 2

description: Library name: TC-53743

value: on dox


title: mPFC, Citalopram 3

description: Library name: Sample_vivo_Cit_biol_rep3


title: Atria, CUG960 on dox with 3XFLAG-MBNL1, biol rep 1

description: Library name: TC-53746


title: Atria, CUG960 on dox with 3XFLAG-MBNL1, biol rep 2

description: Library name: TC-53747


title: 15hr_TET2KO_unt_medip

value: Anti-5mC (Eurogenentec BI-MECY-0100)


title: mPFC, Citalopram 1

description: Library name: Sample_vivo_Cit_biol_rep1


title: Atria, CUG960 on dox, biol rep 1

description: Library name: TC-53742


title: mPFC, Sertraline 3

description: Library name: Sample_vivo_Ser_biol_rep3

value: Sertraline


title: Ventricle, CUG960 no dox, biol rep 1

description: Library name: TC-53760

source_name: Left ventricle

value: Left ventricle

value: no dox


title: 15hr_R132H_unt_medip

value: HoxA9 IDH1-R132H

value: Tetwt

value: Untreated for 15hr

value: meDIP-seq


title: 15hr_R132H_vitc_medip

value: Vitamin C for 15hr


title: Ventricle, CUG960 no dox, biol rep 2

description: Library name: TC-53761


title: mPFC, Sertraline 2

description: Library name: Sample_vivo_Ser_biol_rep2

value: brain


title: Ventricle, CUG960 no dox, biol rep 3

description: Library name: TC-56277


title: Ventricle, CUG960 on/off dox, biol rep 3

description: Library name: TC-56271

value: on/off dox


title: 72hr_DKO_vitc_hmedip

data_processing:
Library strategy: hmeDIP-seq
Read sequences were aligned to mm10 mouse reference genome using BWA mem v.0.7.6a and default parameters
Custom java program (BAM2WIG) was used to generate wig files for downstream analysis and visualization in genome browser. Reads with BWA mapping quality scores <5 were discarded and reads that aligned to the same genomic coordinate were counted only once in the profile generation.
Duplicate reads were marked using Picard Tools MarkDuplicates v1.92
Genome_build: mm10
Supplementary_files_format_and_content: BED files from hmeDIP-seq generated using MACS2 v.2.1.0
Supplementary_files_format_and_content: Wig files from meDIP-seq generated using a custom java program (BAM2WIG)
Supplementary_files_format_and_content: bigWig files from hmeDIP-seq and meDIP-seq generated using Deeptools v2.5.0.1
Supplementary_files_format_and_content: Text files with RPKM values where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)

value: Vitamin C for 72hr

value: Anti-5hmC (Eurogenetec BI-HMCY-0100)

value: hmeDIP-seq


title: Ventricle, CUG960 on/off dox, biol rep 2

description: Library name: TC-53757

value: TREDT960I (Hom)/ MHCrtTA (Hem)


title: mPFC, Sertraline 1

description: Library name: Sample_vivo_Ser_biol_rep1

value: Male

value: 2 weeks


title: 72hr_DKO_unt_hmedip

value: Untreated for 72hr


title: Ventricle, CUG960 on dox with 3XFLAG-MBNL1 and 3XMYC-MBNL2, biol rep 2

description: Library name: TC-56264

value: on dox; AAV9-3XFLAG-MBNL1 and AAV9-3XMYC-MBNL2


title: mPFC, Fluoxetine 3

description: Library name: Sample_vivo_Flu_biol_rep3

value: Fluoxetine


title: Ventricle, CUG960 on dox with 3XFLAG-MBNL1 and 3XMYC-MBNL2, biol rep 1

description: Library name: TC-56263

value: Left ventricle


title: Atria, CUG960 on dox, biol rep 3

description: Library name: TC-56250

value: Atria

value: on dox


title: Ventricle, CUG960 on dox with 3XMYC-MBNL2, biol rep 3

description: Library name: TC-56259

value: on dox; AAV9-3XMYC-MBNL2


title: 72hr_TET3KO_unt_hmedip

value: HoxA9 IDH1-R132H


title: Ventricle, CUG960 on dox with 3XMYC-MBNL2, biol rep 2

description: Library name: TC-53749


title: 72hr_TET3KO_vitc_hmedip


title: mPFC, Fluoxetine 1

description: Library name: Sample_vivo_Flu_biol_rep1


title: mPFC, Fluoxetine 2

description: Library name: Sample_vivo_Flu_biol_rep2


title: 72hr_TET2KO_vitc_hmedip


title: Ventricle, CUG960 on dox with 3XFLAG-MBNL1, biol rep 3

description: Library name: TC-56253

value: on dox; AAV9-3XFLAG-MBNL1


title: Cortical cultures, Vehicle 3

description: Library name: Sample_vitro_Cnt_biol_rep3

source_name: Cortical neurons

value: Cortical neurons

value: Pooled male and female

tag: developmental stage

value: Vehicle

value: 24 hours


title: Ventricle, CUG960 on dox with 3XMYC-MBNL2, biol rep 1

description: Library name: TC-53748


title: Ventricle, CUG960 on dox with 3XFLAG-MBNL1, biol rep 2

description: Library name: TC-53745


title: 72hr_TET2KO_unt_hmedip

value: Anti-5hmC (Eurogenetec BI-HMCY-0100)

value: hmeDIP-seq


title: Cortical cultures, Vehicle 1

description: Library name: Sample_vitro_Cnt_biol_rep1


title: Ventricle, CUG960 on dox, biol rep 1

description: Library name: TC-53740

value: TREDT960I (Hom)/ MHCrtTA (Hem)


title: Cortical cultures, Vehicle 2

description: Library name: Sample_vitro_Cnt_biol_rep2


title: Ventricle, CUG960 on dox with 3XFLAG-MBNL1, biol rep 1

description: Library name: TC-53744


title: 72hr_R132H_vitc_hmedip

value: Tetwt

value: Vitamin C for 72hr


title: Ventricle, CUG960 on dox, biol rep 3

description: Library name: TC-56247


title: Ventricle, CUG960 on dox, biol rep 2

description: Library name: TC-53741


title: Ventricle, CUG960 on dox with 3XFLAG-MBNL1 and 3XMYC-MBNL2, biol rep 3

description: Library name: TC-56265

value: on dox; AAV9-3XFLAG-MBNL1 and AAV9-3XMYC-MBNL2


title: Ventricle, CUG960 on/off dox, biol rep 1

description: Library name: TC-53756

value: on/off dox


title: 48_19, Null1, scRNA-seq

description: 10x Genomics

value: Crypt enriched Intestinal fraction


title: 72hr_R132H_unt_hmedip

value: Untreated for 72hr


title: Cortical cultures, Citalopram 3

description: Library name: Sample_vitro_Cit_biol_rep3

value: Citalopram


title: amonafide_sample_5

city: Amsterdam

first: Man

middle: Iman

last: Hu

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

country: Netherlands

institute: Amsterdam UMC Location University of Amsterdam

description: N2 worms treated with amonafide sample-5

data_processing:
Reads were subjected to quality control FastQC and trimmed using fastp (version 0.23.2) and aligned to the C. elegans genome obtained from Ensembl (wbcel235), using STAR2 (version 2.5.4)
Assembly: Ensembl (wbcel235)
Supplementary files format and content: table delimited raw counts

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: N2 worms were synchronized by hypochlorite treatment, then plated on NGM plates containing DMSO or 50 µM amonafide. The worms were fed E. coli bacteria.

extract_protocol:
Total RNA was extracted as described above in the “RNA Isolation” section. Contaminating genomic DNA was removed using RNaseFree DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands). The qualities of RNA samples were checked with TapeStation (Agilent, CA, USA).
Sequencing libraries were constructed by using KAPA mRNA HyperPrep Kit (Roche, Switzerland)

value: Whole body

value: Amonafide


title: 47_19, Wildtype1, scRNA-seq

description: 10x Genomics

value: Wildtype


title: 15hr_DKO_unt_hmedip

value: HoxA9 IDH1-R132H

value: Untreated for 15hr


title: 15hr_DKO_vitc_hmedip

value: Vitamin C for 15hr


title: amonafide_sample_4

description: N2 worms treated with amonafide sample-4


title: amonafide_sample_2

description: N2 worms treated with amonafide sample-2


title: 15hr_TET3KO_vitc_hmedip


title: Cortical cultures, Citalopram 2

description: Library name: Sample_vitro_Cit_biol_rep2

value: Cortical neurons

value: Pooled male and female

value: 24 hours


title: 15hr_TET3KO_unt_hmedip

value: Anti-5hmC (Eurogenetec BI-HMCY-0100)

value: hmeDIP-seq


title: amonafide_sample_3

description: N2 worms treated with amonafide sample-3


title: Cortical cultures, Sertraline 3

description: Library name: Sample_vitro_Ser_biol_rep3

value: Sertraline


title: Cortical cultures, Citalopram 1

description: Library name: Sample_vitro_Cit_biol_rep1


title: MCF10A, PTBP1KD, 3

city: Sheffield

first: Pei Li

last: Tseng

state: Sheffield

address: Western Bank

country: United Kingdom

institute: University of Sheffield

data_processing:
Assembly: Poly(A) mRNA was enriched from total RNA using poly-T oligo-attached magnetic beads. The enriched RNA was fragmented, followed by first-strand and second-strand cDNA synthesis. After adapter ligation and PCR amplification, the libraries were sequenced on an Illumina platform to generate paired-end reads (150 bp).
Raw data (raw reads) of fastq format were firstly processed by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 (v2.0.5). Read counts for each gene were calculated using feature Counts (v1.5.0-p3).
Differential alternative splicing events (DASs) were identified using the rMATS tool (v4.1.0)
Splicing events across the transcriptome was identified using StringTie's output files.
Supplementary files format and content: tab-delimited xls file containing raw counts for each sample
Supplementary files format and content: tab-delimited xls file containing fpkm for each sample

growth_protocol: MCF10A (ATCC) were cultured with DMEM/F12 media (Gibco) supplemented with 5% Horse Serum (Gibco), 20 ng/ml EGF (Sigma-Aldrich), 500 μg/ml hydrocortisone (Sigma-Aldrich), 10 μg/ml insulin (Thermo Fisher Scientific)) and 1 % penicillin/streptomycin (Gibco).

extract_protocol:
Total RNA was harvested using RNeasy Mini Kit (QIAGEN) according to manufacturer protocol.
RNA samples were sent to Novogene Co., Ltd, where mRNA was converted into sequencing libraries.

treatment_protocol: MCF10A was transfected with PTBP1 siRNA (PTBP1 KD) or control siRNA (NC) for 96 h before the total RNA was isolated.

value: Human breast epithelial cells

value: PTBP1 KD


title: MCF10A, PTBP1KD, 2


title: vehicle_sample_5

description: N2 worms treated with DMSO sample-5

value: DMSO


title: amonafide_sample_1

description: N2 worms treated with amonafide sample-1


title: 15hr_TET2KO_vitc_hmedip


title: Cortical cultures, Sertraline 2

description: Library name: Sample_vitro_Ser_biol_rep2


title: Cortical cultures, Sertraline 1

description: Library name: Sample_vitro_Ser_biol_rep1


title: MCF10A, PTBP1KD, 1


title: 15hr_TET2KO_unt_hmedip


title: vehicle_sample_3

description: N2 worms treated with DMSO sample-3


title: MCF10A, control, 2

value: WT


title: MCF10A, control, 3


title: vehicle_sample_1

description: N2 worms treated with DMSO sample-1


title: 15hr_R132H_unt_hmedip

value: Tetwt


title: 15hr_R132H_vitc_hmedip


title: Cortical cultures, Fluoxetine 3

description: Library name: Sample_vitro_Flu_biol_rep3

value: Fluoxetine


title: Cortical cultures, Fluoxetine 1

description: Library name: Sample_vitro_Flu_biol_rep1


title: MCF10A, control, 1


title: As3mtd2d3_tg, P60, replicate3, snRNA-seq

status: Public on Mar 29 2025

city: Pohang-si

first: Dahun

last: Um

address: 77 Cheongam-Ro. Nam-Gu. Pohang. Gyeongbuk. Korea 37673

department: Life science

country: South Korea

institute: Pohang University of Science and Technology(POSTECH)

description: 10x genomics

data_processing:
Alignment and gene counting were made Cell Ranger software v5.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Isocortex

extract_protocol:
For E15, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) embryos were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Single cell isolation was performed by incubation of tissue with digestion buffer (0.1% DNase I + 0.25% Trypsin) in 37°C  incubator for 10 min. Added neurobasal media with 10mM HEPES and passed through the Pasteur pipette several times. Stored in ice before the library generation step. For P60, freshly collected isocortex from AS3MTd2d3-Tg (mCherry) or littermate (no signal) mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free) to remove debris. Transferred the tissues to MACS® Tissue Storage Solution in ice before the automated nuclei isolation was performed by Singulater 100.
For E15.5 scRNA-seq and P60 snRNA-seq, we used 'Chromium Single Cell 3p RNA library v3' kit. Library construction was performed following 'Chromium Single Cell 3' Reagent Kit User Guide v3'.

value: Isocortex

tag: strain

value: Postnatal day 60


title: vehicle_sample_4

description: N2 worms treated with DMSO sample-4

value: Whole body


title: het-WT-rep1

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

description: Library name: het-WT-rep1

data_processing:
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) using TopHat (v2.1.1) with default parameters. Only uniquely mapped reads were kept for downstream analysis. The RNA abundance of each gene was quantified using Cufflinks (v2.2.1).
genome build/assembly: mm9

molecule: polyA RNA

source_name: Treg cells

growth_protocol: CD4+YFP+ Treg cells from Foxp3cre and Foxp3cre Cxxc1fl/fl mice were enriched by the MojoSort™ Mouse CD4 T Cell Isolation Kit (Biolegend, 480005) and then sorted by BD Aria II flow cytometer.

extract_protocol:
Total RNA was extracted from sorted CD4+YFP+ Treg cells using the RNeasy Plus Mini Kit (Qiagen, #74134), following the manufacturer’s protocol.
RNA-Seq libraries were constructed and sequenced by Haplox (Nanchang, China), using an Illumina platform with paired-end reads of 150 bp.

value: Treg cells

value: Wild type


title: het-KO-rep2

description: Library name: het-KO-rep2

value: Cxxc1 hetKO


title: Treg-H3K4me3-rep2

description: Library name: Treg-H3K4me3-rep2

data_processing:
CUT&Tag reads were trimmed to 50 bp and aligned against the mouse genome build mm9 using Bowtie2(v2.3.4.1) with default parameters. All PCR duplicates and unmapped reads were removed. Peak calling was performed using MACS2(v2.1.1.20160309) and signal tracks for each sample were generated using the ‘wigToBigWig’ utility of UCSC.
genome build/assembly: mm9

extract_protocol:
In brief, approximately 1x105 single cells were carefully pipetted twice into a wash buffer. The pelleted cells were resuspended in wash buffer and activated concanavalin (Bangs Laboratories, BP531) and incubated for 15 minutes at room temperature. Cells bound to the beads were resuspended in a Dig-Wash Buffer and a 1:50 dilution of the primary antibody (rabbit anti-H3K4me3, Active Motif,39016; rabbit anti-Cxxc1, abcam, ab198977; normal IgG, Cell Signaling, 2729), and incubated at 4℃ overnight. The beads were then incubated with a secondary antibody (goat anti-rabbit IgG, SAB3700883, Sigma-Aldrish) diluted 1:100 in Dig-Wash buffer for 60 minutes at room temperature. Cells were treated with Hyperactive pG-Tn5 Transposase for CUT&Tag (Vazyme, S602) diluted in Dig-300 Buffer for 1 hour at room temperature. The cells were then resuspended in Tagmentation buffer (10mM MgCl2 in Dig-300 Buffer) and incubated at 37℃ for 1h. To stop tagmentation, 10l was spiked with 0.5M EDTA, 3l with 10%SDS, and 3l with 20mg/ml Proteinase K and incubated at 55℃ for 1h.
DNA library amplification was performed according to the instructions and purified using VAHTS DNA Clean Beads (Vazyme, N411). Libraries were sequenced on an Illumina NovaSeq platform from Annoroad Gene Technology.


title: Tcon-H3K4me3-rep1

description: Library name: Tcon-H3K4me3-rep1

source_name: Tcon cells

value: Tcon cells


title: Foxp3cre-Cxxc1fl-Foxp3-rep2

description: Library name: Foxp3cre-Cxxc1fl-Foxp3-rep2

value: Cxxc1 KO


title: het-KO-rep1

description: Library name: het-KO-rep1


title: Foxp3cre-Cxxc1fl-Foxp3-rep1

description: Library name: Foxp3cre-Cxxc1fl-Foxp3-rep1


title: Foxp3cre-WT-Foxp3-rep2

description: Library name: Foxp3cre-WT-Foxp3-rep2


title: Tcon-H3K4me3-rep2

description: Library name: Tcon-H3K4me3-rep2


title: het-WT-rep2

description: Library name: het-WT-rep2


title: Treg-H3K4me3-rep1

description: Library name: Treg-H3K4me3-rep1


title: Foxp3cre-WT-Foxp3-rep1

description: Library name: Foxp3cre-WT-Foxp3-rep1


title: As3mtd2d3_tg, P60, replicate4, snRNA-seq

description: 10x genomics


title: As3mtd2d3_tg, P60, replicate2, snRNA-seq

description: 10x genomics


title: Control, P60, replicate4, snRNA-seq

description: 10x genomics


title: Cortical cultures, Fluoxetine 2

description: Library name: Sample_vitro_Flu_biol_rep2

value: Cortical neurons

value: Pooled male and female

value: 24 hours


title: Control, P60, replicate3, snRNA-seq

description: 10x genomics


title: As3mtd2d3_tg, P60, replicate1, snRNA-seq

description: 10x genomics


title: Control, P60, replicate2, snRNA-seq

description: 10x genomics


title: Control, P60, replicate1, snRNA-seq

description: 10x genomics


title: As3mtd2d3_tg, E15.5, replicate2, scRNA-seq

description: 10x genomics

value: Embryonic day 15.5


title: WT_MII_2

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

description: Ribo-lite

data_processing:
The adapter and pA on raw reads were removed by using cutadapt (v1.14)
The rRNA were removed by using Bowtie2 (v2.2.2)
The remaining reads were mapped to mouse genome (mm10) using STAR (v2.5.3a)
The gene expression levels were calculated by featueCounts
Assembly: mm10
Supplementary files format and content: Raw fastq and fpkm file
Library strategy: Ribo-lite

source_name: Ovary

extract_protocol:
Ribo-lite experiments were improved according to published procedure. Briefly, 500 oocytes were gathered in 1.5 ml Eppendorf LoBind microcentrifuge tubes and lysed with lab-made cell lysis buffer with CHX added. After digesting by RNase I, the pellet ribosome with ribosome-binding fragments (RPF) were centrifuged by Beckman Optima MAX-IP ultracentrifuge. Then the RPF were purified by electrophoresis, and the cDNA library were constructed with Dplex-Small-RNA-seq Kit (DIAGENODE, c05030001).
The purified RPF were dephpsphorylated and tailed. After hybrided with RT primer and TSO, the RPF were RT into cDNA. Then the primer with barcode and index were added for ligation and amplification.

value: Ovary

value: Oocyte

value: Control


title: Control, E15.5, replicate1, scRNA-seq

description: 10x genomics


title: As3mtd2d3_tg, E15.5, replicate1, scRNA-seq

description: 10x genomics


title: Control, E15.5, replicate2, scRNA-seq

description: 10x genomics


title: Treat_MII_2

description: Ribo-lite

value: WT

value: Treat


title: Treat_MII_1

description: Ribo-lite


title: WT_MII_1

description: Ribo-lite


title: WT_FGO_2

description: Ribo-lite


title: WT_FGO_1

description: Ribo-lite


title: KO-H3K4me3-rep2

data_processing:
CUT&Tag reads were trimmed to 50 bp and aligned against the mouse genome build mm9 using Bowtie2(v2.3.4.1) with default parameters. All PCR duplicates and unmapped reads were removed. Peak calling was performed using MACS2(v2.1.1.20160309) and signal tracks for each sample were generated using the ‘wigToBigWig’ utility of UCSC.
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: CUT&Tag


title: KO-H3K4me3-rep1


title: WT-H3K4me1-rep1


title: WT-H3K4me3-rep2


title: KO-H3K4me1-rep2


title: T2Day9

city: Hong Kong

first: Yimeng

last: Li

address: 21 Sassoon Road, Pokfulam Hong Kong

institute: The university of Hong Kong

description:
Library name: Sample 2
10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: Filtered feature-barcode matrices (features.tsv, barcodes.tsv, matrix.mtx).

source_name: human endometrial organoid-stromal cell co-culture

extract_protocol:
Endometrial organoids were harvested using cell recovery solution, incubated on ice for 30 minutes, and centrifuged at 400 ×g for 3 minutes to remove supernatant. The organoids were digested with a mixture of 10% DNase and TrypLE Express at 37°C for 5 minutes, followed by termination with 10% FBS. After filtering the cell suspension through a 35 µm strainer (Falcon, 352235) to remove aggregates, dead cells were selectively removed using Dead Cell Removal Beads (Miltenyi, 130-090-101) and MACS separation with a LS Column and MACS Separator (Miltenyi, 130-090-312). Viable cells were resuspended in 4°C PBS. Samples meeting viability (>80%) and density criteria (1000-5000 cells, 500 cells/μl at 0.5×10⁶ cells/ml) were submitted for sequencing analysis at the Centre for PanorOmic Sciences, HKU.
Library preparation and Illumina sequencing (Pair-End sequencing of 150 bp) were conducted at the Genomics Core, Centre for PanorOmic Sciences (CPOS), LKS Faculty of Medicine, the University of Hong Kong. Cells will be encapsulated into Gel Beads-in-emulsion (GEMs) by the 10X Chromium iX, followed by reverse transcription and library preparation to become a pool of cDNA libraries. Transcripts from the same cell will be identified by a 10X barcode, while each of these transcripts will be discernible from one another by a Unique Molecular Identifier (UMI).

tag: time point


title: WT-Cxxc1-rep2


title: KO-H3K4me1-rep1


title: T2Day1

description:
Library name: Sample 1
10× Genomics

value: human endometrial organoid-stromal cell co-culture


title: U2OS SUMO2 Rescue Rep1

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

description: Library name: SUMO2 Rescue Rep1

data_processing:
Preprocessing Using the TopHat2 software, the sequencing reads were processed by trimming and mapping them to the human hg38 reference genome (Kim, Pertea et al. 2013). The maximum insertion and deletion length was set to 2 base pairs and default parameters were used for the remaining settings. In addition, only reads that were uniquely mapped, excluding any 'mixed' or 'discordant' reads from the results, were retained. Differential expression analysis Read counts for each gene were calculated using GENCODE v38 annotation with the HTSeq software, and the statistics of differential expression using the DESeq2 package with default parameters (Love, Huber et al. 2014, Anders, Pyl et al. 2015). Differentially expressed genes were defined as adjusted p-values < 0.05 (Table S1).
Assembly: hg38
Supplementary files format and content: tsv files include raw counts for each sample

growth_protocol: U2OS WT, S1KO, S2KO, and S2R cell lines have been previously described and were grown at 37°C, 5% CO2 in DMEM (Gibco, 11965118) supplemented with 10% fetal bovine serum (Sigma-Aldrich, F2442) (Bouchard, Wang et al. 2021).

extract_protocol:
Total RNA isolation was performed using the Sigma-Aldrich GenElute Mammalian Total RNA Miniprep kit (RTN70).
Total RNA from three biological replicates was sent to Novogene for ribo-minus selection and RNA sequencing.


title: U2OS SUMO2 Rescue Rep2

description: Library name: SUMO2 Rescue Rep2


title: WT-IgG


title: HAF EPCAM condition - replicate 3

city: Planegg

first: Anna

last: Danese

address: Grosshaderner strasse 9

country: Germany

institute: Ludwig Maximilians University

description: Library name: Sample_24L018303

data_processing:
Sequencing primers are trimmed with trimmomatic v0.39
The reference genome (GRCh38 v47 from gencode) and alignment are done using STAR v2.7.10b
Reads are sorted and PCR duplicates are removed using samtools v1.6
the count matrices are built using htseq v0.11.3
Assembly: GRCh38 (gencode v47)
Supplementary files format and content: tab delimited file containing the raw counts for each samples

source_name: Skin

extract_protocol:
RNAs with RIN > 7 were selected for mRNA sequencing (poly-A selected). Libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit with an input of 1000 ng following to the kit instructions.
After a final QC, the libraries were sequenced in paired-end mode (2x100 bases) on the NovaseqX+ sequencer (Illumina) at a depth of ≥ 30 million reads per sample.

value: Skin

value: NHDF-Ad

value: Human Dermal Fibroblasts, Adult (HAF)

value: EPCAM condition

tag: batch


title: MV4;11.TDI-11055.5uM.24h_batch2_C

city: Philadelphia

first: Liling

last: Wan

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

description: Library name: MV4;11.TDI-11055.5uM.24h_C

data_processing:
RNA-seq samples were sequenced using Illumina NextSeq 2000.
Raw reads were mapped to the human reference genome (hg19) and transcriptome using HISAT2 v 2.2.1 with default parameters.
Unmapped reads from hg19 alignment were mapped to the Spike-In ERCC control transcriptome using Kallisto v 0.46.2 as Spike-In control.
Lowly expressed genes with raw counts less than 10 in any individual sample were filtered before downstream analysis.
The size factor of Spike-In control was estimated using estimateSizeFactors from R Bioconductor DESeq2 v1.28.1 package
Then the size factor was assigned to the RNAseq result using the assignment function sizeFactors<-.
Differentially expressed genes between conditions were statistically determined using R Bioconductor DESeq2 v1.28.1 package
Gene-specific normalization factors for each sample was provided using pre-generated sizeFactors from Spike-In control, which preempts sizeFactors in DESeq2 calculations.
Assembly: hg19
Supplementary files format and content: TPM values for individual human genes.

extract_protocol:
RNeasy plus mini kit (Qiagen, #74136) was used to extract total RNA and remove genomic DNA.
1000ng total RNA was used for library preparation using polyA mRNA magnetic Isolation module (NEB, #E7490) and RNA library prep kit (NEB, #7770) following manufacturer’s instructions. The library quality was assessed on an Agilent Bioanalyzer DNA chip ( Agilent, #5067-1504). RNA-seq samples were sequenced using Illumina NextSeq 2000.

treatment_protocol: Human leukemia cells were treated with DMSO or 5 uM TDI-055 for 24 hour

value: Leukemia cells


title: MV4;11.DMSO.24h_batch2_D

description: Library name: MV4;11.DMSO.24h_D

value: DMSO


title: MV4;11.DMSO.24h_batch2_B

description: Library name: MV4;11.DMSO.24h_B


title: MV4;11.TDI-11055.5uM.24h_batch2_A

description:
Library name: MV4;11.TDI-11055.5uM.24h_A
Leukemia cells


title: MV4;11.TDI-11055.5uM.24h_batch2_B

description: Library name: MV4;11.TDI-11055.5uM.24h_B


title: MV4;11.DMSO.24h_batch2_C

description: Library name: MV4;11.DMSO.24h_C


title: WT-Cxxc1-rep1

value: Treg cells

value: Wild type


title: MV4;11.TDI-11055.5uM.24h_batch2_D

description: Library name: MV4;11.TDI-11055.5uM.24h_D


title: MV4;11.DMSO.24h_batch2_A

description: Library name: MV4;11.DMSO.24h_A


title: U2OS SUMO2 KO Rep1

description: Library name: SUMO2 KO Rep1


title: U2OS SUMO2 KO Rep3

description: Library name: SUMO2 KO Rep3


title: WT-H3K4me1-rep2


title: U2OS SUMO2 Rescue Rep3

description: Library name: SUMO2 Rescue Rep3


title: HAF Control condition - replicate 3

description: Library name: Sample_24L018301

tag: tissue


title: WT-H3K4me3-rep1


title: Foxp3Cre-WGBS

data_processing:
Raw reads were trimmed using TrimGalore (v0.4.4) with default parameters. Subsequently, the reads were mapped against the mm9 reference genome using Bismark v0.19.0 with parameters ‘--bowtie2’. PCR duplicates were removed and the methylation levels were calculated using ‘bismark_methylation_extractor’.
Assembly: mm9
Supplementary files format and content: bigwig

extract_protocol:
Sorted CD4+YFP+ Treg cells(3ⅹ106) were placed inll cell lysis buffer . The bisulfite-treated DNA were used to prepare the sequencing library.
DNA librarie was transferred to the Illumina Platform for sequencing using 150 bp paired-end reads.


title: U2OS SUMO1 KO Rep3

description: Library name: SUMO1 KO Rep3


title: U2OS SUMO2 KO Rep2

description: Library name: SUMO2 KO Rep2


title: HAF EPCAM condition - replicate 2

description: Library name: Sample_24L018300


title: HAF Control condition - replicate 2

description: Library name: Sample_24L018298


title: U2OS SUMO1 KO Rep2

description: Library name: SUMO1 KO Rep2


title: U2OS WT Rep3

description: Library name: WT Rep3


title: WT,replicate1,scRNAseq；WT,replicate2,scRNAseq;cKO,replicate1,scRNAseq;Cko,replicate2,scRNAseq (tag)

city: zhangzhou

first: xiaoyu

last: meng

address: Institute of Immunology Zhejiang University School of Medicine Medical Research Building A812 388 Yuhang Tang Road, Hangzhou

institute: mxy

description: BD Rhapsody;WT,replicate1,Sample Tag1;WT,replicate2,Sample Tag2;cKO,replicate1,Sample Tag3;cKO,replicate2,Sample Tag4

data_processing:
The FASTQ files were processed using the BD Rhapsody Targeted analysis pipeline  on v2.0 the Seven Bridges platform (https://www.sevenbridges.com).
Assembly: mm10
Supplementary files format and content: Tab-seperatated values files and matrix files

source_name: peripheral lymph node

extract_protocol:
Single cells were extracted using a chromium controller (BD platform, BD Bioscience) according to product directions and as previously described.
RNA fragments of singe cells were captured by Singleron Matrix system, and further applied to retrieved transcription. Acquired cDNA was used to produce amplification and index labelling.

value: peripheral lymph node

value: CD4+YFP+Treg cell

value: WT,Foxp3cre;Cko,Foxp3Cre Cxxc1fl/fl


title: Foxp3Cre-Cxxc1fl-WGBS

value: Cxxc1 KO


title: U2OS WT Rep2

description: Library name: WT Rep2


title: 612-L1

city: Atlanta

first: Mac

last: Mao

state: GA

address: 101 Woodruff Cir

institute: Emory University

data_processing:
Data were initially QCed via FastQC v0.11.4 and MultiQC v1.12. Data were trimmed only to remove Illumina adapters via trimmomatic v0.36. Data were aligned via STAR aligner v2.5.2 to the mm10 reference genome, and counts were pulled per sample into a counts matrix with the  mm10 annotations via HTseq-count v0.13.5.
Assembly: mm10
Supplementary files format and content: count

source_name: lung

extract_protocol:
Lung samples were extracted with Trizol reagent and RNA was purified using  standard protocols.
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: Irradiated or mock irradiated at the NASA space radiation laboratory.

tag: ear tag

tag: radiation dose

value: 0 Gy

tag: radiation type

value: mock

tag: group

value: L

tag: counter measure

value: yes

value: M


title: HAF Control condition - replicate 1

description: Library name: Sample_24L018295

value: Skin

tag: cell type

tag: treatment

value: Control


title: crp_2

city: Wrocław

first: Michał

last: Śmiga

address: Fryderyka Joliot-Curie 14a

country: Poland

institute: Faculty of Biotechnology, University of Wrocław

description: ΔcrpPg mutant strain generated in A7436 wild-type strain

data_processing:
data processing was performed by Novogene (Cambridge, United Kingdom) according to the company standard protocols.
Assembly: GCF_001263815.1
Supplementary files format and content: gene count.txt
Supplementary files format and content: tab-delimited text file include raw counts for each sample

organism: Porphyromonas gingivalis

source_name: bacteria cells

growth_protocol: Porphyromonas gingivalis was cultured in 37°C in anaerobic conditions

extract_protocol:
RNA was isolated from the bacteria pellet received from 1 ml of the culture (OD600 = 0.5-0.6). RNA isolation was performed by Novogene (Cambridge, United Kingdom) according to the company standard protocols.
RNA libraries were constructed by Novogene (Cambridge, United Kingdom) according to the company standard protocols.

treatment_protocol: Porphyromonas gingivalis was cultured in heme and iron-rich conditions (Basal medium supplemented with 7.7 µM heme; Hm) until the mid-exponential growth phase (OD600 = 0.5-0.6).

value: bacteria cells

tag: genotype

value: crp{delta}Emr

value: heme and iron rich conditions

tag: optical density_at_600_nm


title: 610-L1

tag: Sex


title: crp_1

tag: cell line


title: 608-L1


title: U2OS WT Rep1

description: Library name: WT Rep1


title: 609-L1


title: ST88-14, Control, replicate 2

city: San Francisco

first: Iowis

last: Zhu

address: 1450 3rd Street, HD449

institute: University of California, San Francisco

description:
Library name: ST88-14_ctrl_-2
NormalizedCounts_ST88_RT.txt

data_processing:
Following quality control of FASTQ files with FASTQC, trimming of adapter sequences, reads were filtered to remove bases that did not have an average quality score of 20 within a sliding window across 4 bases (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was performed prior to mapping. Reads were mapped to the appropriate reference genome (hg19) using HISAT2 with default parameters.
Transcript abundance estimation in transcripts per million (TPM) and differential expression analysis were performed using DESeq2.
Principal component analysis was performed in R using the prcomp function. Differentially expressed transcripts with an adjusted p-value<0.1 were identified and filtered based on an expression cutoff (TPM>1) and a fold change threshold (log2FC>1) to prioritize biologically relevant gene sets.
Assembly: hg38
Supplementary files format and content: Normalized counts for genes organized by ENTREZ ID

source_name: tumor

growth_protocol: Plexiform neurofibroma line NF955.1b and MPNST cell line ST88-14 were grown in Dulbecco’s Modified Eagle Medium (#11960069, Life Technologies) with 10% FBS and 1X Pen-Strep (#15140122, Life Technologies) in a cell culture incubator at 37oC and 5% CO2.

extract_protocol:
Library preparation was performed using the TruSeq RNA Library Prep Kit v2 (#RS-122- 2001, Illumina).
50 bp single end reads were sequenced on an Illumina HiSeq 2500 to a minimum depth of 25M reads per sample at Medgenome, Inc.

value: tumor

value: MPNST

tag: treatment/time point


title: ST88-14, Control, replicate 1

description:
Library name: ST88-14_ctrl_-1
NormalizedCounts_ST88_RT.txt


title: crp_3


title: ST88-14, 5 days post radiation, replicate 2

description:
Library name: 88-14_5d_RT-2
NormalizedCounts_ST88_RT.txt

value: 5 days post radiation


title: 547-K2

value: K

value: no

value: F


title: 548-K2


title: Bemisia tabaci feeding on Nicotiana tabacum

first: fan

last: xiaoping

state: zhejiang

address: Hangzhou, China

institute: LC-Bio Technology Co.

description:
Library name: Bemisia_tabaci
Column name in Table5_All_Expressed_miRNA.txt:Bemisia_tabaci

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: http://www.whiteflygenomics.org/ftp/MEAM1/v1.2/
Supplementary files format and content: txt,expression profiles

organism: Bemisia tabaci

source_name: Intact insect body tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare one small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Intact insect body tissue

value: Intact insect body tissue


title: lateTLN-6W, S26

first: Xin

middle: Yuan

last: Guan

state: -- Country other than USA or Canada --

address: Room L10-56, 10/F, Laboratory Block, 21 Sassoon Road, Hong Kong

department: Department of Clinical Oncology

institute: The University of Hong Kong

description:
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Starting from raw base call (BCL) files generated by the Illumina HiSeq X Ten system, the BCL files were demultiplexed using the CellRanger-4.0.0 package with the “cellranger mkfastq” command to generate raw FASTQs. Using the “cellranger count” command, raw FASTQ files were aligned, filtered, and barcoded, and the UMI was counted to generate single-cell gene expression profiles. To remove the bias, the “cellranger aggr” command was used to aggregate the gene expression counts of all samples and normalize those counts to the same sequencing depth and then to recalculate the feature-barcode single-cell gene expression matrix.
The R Seurat package (version 4.0.1) was used to convert the output of “cellranger aggr” into a Seurat object for downstream analysis.
The inference and removal of cell doublets were performed by using Single-Cell Remover of Doubelts (Scrublet) with the default parameters.
Based on the various metric distributions of our data, we applied the following thresholds: nGene >= 2500 and mitoRatio < 0.2 to remove low-quality cells.
To avoid low average cell expression due to genes that were counted as zero or expressed in only a few cells, we retained only genes that were expressed in 10 or more cells. To account for differences in per-cell sequencing depth for each sample, the remaining expression matrix was normalized by using the “NormalizeData” function in the Seurat package. To eliminate cell cycle and mitochondrial effects, the normalized matrix was further scaled to produce a final single-cell gene expression matrix with high quality by regressing out cell cycle phase (S, G2/M) scores and mitochondrial expression with the CellCycleScoring and SCTransform functions in the Seurat package.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.  In barcodes.tsv.gz, BC-1 corresponds to sample PT-6W, BC-2 corresponds to sample LNM-6W, BC-3 corresponds to sample lateTLN-6W.

source_name: Macro-metastatic lymph node site of esophageal carcinoma

extract_protocol:
Tumor tissues or lymph nodes from mice were collected and minced in sterile PBS solution. Subsequently, each sample was digested with 0.1 mg/ml Liberase and 0.1 mg/mL DNAse I in PBS for 5-30 min at 37 °C with manual vortexing. The dissociation was terminated with DMEM containing 10% fetal bovine serum, and the samples were filtered successively through a 70-μm and 40-μm cell strainer to collect a suspension of single cells. The filtrate was centrifuged at 300×g for 5 min at 4 °C and washed twice with medium. Cells were stained for viability using Trypan Blue. In some experiments, primary cells were then plated in tissue culture flasks in medium containing puromycin to select tumor cells derived from primary tumor tissues and metastatic lymph nodes. The selected tumor cells were expanded ex vivo into sublines of PTs (derived from the primary tumors) or LNMs (derived from LNs with micrometastases) and then subjected to molecular and functional analysis.
The single tumor cells were rinsed with DPBS on ice before loading into the Gel Bead & Multiplex Kit and Chip Kit (10× Genomics, Pleasanton, CA, USA) for the construction of a chromium single-cell 3′-library according to the manufacturer’s instructions. Libraries were sequenced on an HiSeq X Ten system and mapped to the human reference genome (build GRCh38) using CellRanger-4.0.0 (10× Genomics).

value: Esophageal Carcinoma

value: No


title: ST88-14, 5 days post radiation, replicate 1

description:
Library name: 88-14_5d_RT-1
NormalizedCounts_ST88_RT.txt


title: lateTLN-6W, S6

value: Macro-metastatic lymph node site of esophageal carcinoma


title: HAF EPCAM condition - replicate 1

description: Library name: Sample_24L018297

value: NHDF-Ad

value: Human Dermal Fibroblasts, Adult (HAF)

value: EPCAM condition


title: WT,replicate1,scRNAseq；WT,replicate2,scRNAseq;cKO,replicate1,scRNAseq;Cko,replicate2,scRNAseq (target)

value: peripheral lymph node

value: CD4+YFP+Treg cell

value: WT,Foxp3cre;Cko,Foxp3Cre Cxxc1fl/fl


title: ST88-14, 14 days post radiation, replicate 2

description:
Library name: 88-14_14d_RT-2
NormalizedCounts_ST88_RT.txt

value: 14 days post radiation


title: WT,replicate1,scRNAseq；WT,replicate2,scRNAseq;cKO,replicate1,scRNAseq;Cko,replicate2,scRNAseq (TCR)


title: LNM-6W, S5

source_name: Micro-metastatic lymph node site of esophageal carcinoma


title: U2OS SUMO1 KO Rep1

description: Library name: SUMO1 KO Rep1


title: ST88-14, 14 days post radiation, replicate 1

description:
Library name: 88-14_14d_RT_-1
NormalizedCounts_ST88_RT.txt

value: tumor


title: 556-L2

value: 0 Gy

value: mock

value: L

value: yes


title: 602-K1

value: K

value: no

value: M


title: 601-K1


title: NF95.11b, 5 days post radiation, replicate 2

description:
Library name: 11b_5d_RT-2
NormalizedCounts_11b_RT.txt

value: plexiform neurofibroma

value: 5 days post radiation


title: NF95.11b, 5 days post radiation, replicate 1

description:
Library name: 11b_5d_RT-1
NormalizedCounts_11b_RT.txt


title: 599-K1


title: NF95.11b, 14 days post radiation, replicate 2

description:
Library name: 11b_14d_RT-2
NormalizedCounts_11b_RT.txt


title: 600-K1


title: NF95.11b, 14 days post radiation, replicate 1

description:
Library name: 11b_14d_RT-1
NormalizedCounts_11b_RT.txt


title: RNA_IFNg_Tofa_2

city: Cheongju-si

first: Geunho

last: Kwon

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu, 310, S1-5

institute: Chungbuk National University

data_processing:
RNA-seq data were mapped to the hg38 genome using STAR aligner (v2.7.3a) with default parameters.
HOMER (v4.11.1) was used to convert aligned reads into ‘‘Tag Directory’’ for further analysis.
To annotate aligned reads, we used “hg38.ncbiRefSeq.gtf” files provided by USCS.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Blood

growth_protocol: Human THP-1 cells were obtained from Korean Cell Line Bank (KCLB40202) and were cultured in RPMI-1640 (Gibco, 11875-119) supplemented with 10% Fetal Bovine Serum (Gibco, 16000-044) and 1% Penicillin/streptomycin (Gibco, 15070-063). The THP-1 cell line was routinely cultured in a humidified 5% CO2 incubator at 37 °C.

extract_protocol:
Total RNA was extracted from THP-1-monocyte-derived macrophages using RibospinTM II (GeneAll Biotechnology, 314-150).
RNA libraries for sequencing were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: THP-1 monocytes were differentiated into macrophages by incubation with 100 ng/ml Phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich, P1585) for 24 h. THP-1-monocyte-derived IFN-γ-primed macrophages were induced by co-stimulation with PMA and 100 U/ml human IFN-γ (Roche, 11040596001) for 24 h. Following priming, the macrophages were treated with JAK inhibitors (Tofacitinib) (Sigma-Aldrich, PZ0017) at up to 1 μM for a maximum of 6 h.

value: Blood

value: Monocytic leukemia

value: WT

tag: differentiation

value: Phorbol 12-myristate 13-acetate

tag: priming

value: IFN-γ

value: Tofacitinib


title: 693-H2

tag: strain

value: 137-Cs gamma rays

value: H

value: F


title: Pkd1 null MEK cells  repeat 3

city: Rochester

first: Xinyue

state: Minnesota

address: 150 3rd St SW

department: Nephrology and Hypertension

institute: Mayo Clinic

description:
Library name: Sample9
Column name in raw_counts_All samples.txt: null_3

data_processing:
CLC Genomics Workbench v 11.0.1
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library Prep Kit following manufacture's protocols.
Sequence reads were limited for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameter-mismath cost 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
mm10
Assembly: HISAT2 software was used to map all clean reads to the mouse genome, and mapped reads were assembled and quantified using StringTie software.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Pkd1 null MEK cells

growth_protocol: Pkd1 WT MEK and Pkd1 null MEK cells were maintained at 33 °C in 5% CO2 in DMEM/F-12 supplemented with 2% FBS.

extract_protocol:
Libraries were prepared using the Illumina TruSeq Stranded Total RNA (Cat. # RS-122-2301) or mRNA (Cat. # RS-122-2101) kit according to the manufacturer’s protocol starting with 1 μg total RNA. Briefly, the data processing step is rRNA-depleted RNAs (Total RNA kit) or purified mRNAs (mRNA kit) were fragmented and converted to cDNA with reverse transcriptase. The resulting cDNAs were converted to double stranded cDNAs and subjected to end-repair, A-tailing, and adapter ligation. The constructed libraries were amplified using 8 cycles of PCR.
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN).

treatment_protocol: Pkd1 WT MEK and Pkd1 null MEK cells were treated with D-gal (40g/l) for 48 hours.

value: Pkd1 null MEK cells

value: collect ducts

value: Pkd1 gene mutant type

tag: batch


title: RNA_IFNg_Ctrl_2

tag: tissue

value: Untreated


title: Pkd1 null MEK cells+D-gal  repeat 1

description:
Library name: Sample10
Column name in raw_counts_All samples.txt: null+D-gal_1

value: D-gal


title: Pkd1 null MEK cells  repeat 2

description:
Library name: Sample8
Column name in raw_counts_All samples.txt: null_2

value: no


title: Pkd1 null MEK cells  repeat 1

description:
Library name: Sample7
Column name in raw_counts_All samples.txt: null_1


title: PT-6W

source_name: Primary tumor site of esophageal carcinoma xenografts

value: Esophageal Carcinoma

value: No


title: 651-H1

tag: ear tag

value: M


title: RNA_IFNg_Ctrl_1

value: Blood

value: Monocytic leukemia


title: RNA_Resting_Tofa_2

value: WT

value: Phorbol 12-myristate 13-acetate


title: Pkd1 WT MEK cells+D-gal  repeat 3

description:
Library name: Sample6
Column name in raw_counts_All samples.txt: WT+D-gal_3

source_name: Pkd1 WT MEK cells

value: Pkd1 WT MEK cells

value: Pkd1 gene wild type


title: LNM-6W, S25

value: Micro-metastatic lymph node site of esophageal carcinoma


title: 365-1-E2

tag: radiation dose

value: 5-ion simulated GCR

value: E

value: F


title: Pkd1 WT MEK cells+D-gal  repeat 2

description:
Library name: Sample5
Column name in raw_counts_All samples.txt: WT+D-gal_2

value: collect ducts


title: Pkd1 WT MEK cells+D-gal  repeat 1

description:
Library name: Samole4
Column name in raw_counts_All samples.txt: WT+D-gal_1


title: Pkd1 null MEK cells+D-gal  repeat 3

description:
Library name: Sample12
Column name in raw_counts_All samples.txt: null+D-gal_3

value: Pkd1 null MEK cells

value: Pkd1 gene mutant type


title: Pkd1 null MEK cells+D-gal  repeat 2

description:
Library name: Sample11
Column name in raw_counts_All samples.txt: null+D-gal_2

value: D-gal


title: 694-H2

tag: radiation type

value: 137-Cs gamma rays

value: H

value: no


title: RNA_IFNg_Tofa_1

value: Blood

value: IFN-γ

value: Tofacitinib


title: 0056-E2

tag: group


title: ATAC_IFNg_Tofa_2

data_processing:
ATAC-seq data were mapped to the hg38 genome using Bowtie2 with the parameters "--very-sensitive --no-discordant -X 2000".
The quality check of ATAC-seq was performed with ATACseqQC (v1.12.5)
HOMER (v4.11.1) was used to convert aligned reads into ‘‘Tag Directory’’ for further analysis.
To identify peaks in ATAC-seq, we used the “findPeaks” command in HOMER software.
The bigWig file was created using the "bamCoverage" deepTools (v3.5.0) command, with the "--binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2913022398" parameter.
Assembly: hg38
Supplementary files format and content: bigWig; [Sample]_ATAC_[Condition].BlacklistV1.removed.bw files were processed using ENCODE blacklist version 1; [Sample]_ATAC_[Condition].BlacklistV2.removed.bw files were processed using ENCODE blacklist version 2.

extract_protocol:
THP-1 monocyte-derived macrophages (50,000 cells) were treated with Deoxyribonuclease I (Worthington, LS002004) at 200 U/ml for 30 minutes to digest free-floating and dead cell DNA. After washing with Dulbecco's phosphate-buffered saline, cells were harvested using TrypLE (Gibco, 12604013). The cell pellet was then resuspended in ATAC-seq RSB (RSB; 10 mM Tris-HCl pH 7.5 (Invitrogen™, 15567-027), 10 mM NaCl (Invitrogen™, AM9759), and 3 mM MgCl2 (Invitrogen™, AM9530G) in Nuclease-Free Water (QIAGEN, 981103)) containing agents like NP40 (Roche, 11332473001), Tween-20 (Roche, 11332465001), and Digitonin (Promega, G9441), and incubated on ice for lysis. Following lysis, cells were washed in ATAC-seq RSB with Tween-20 and then centrifuged to isolate nuclei.
The isolated nuclei were subjected to a transposition process using a specific mix (25 μl TD Tagment DNA Buffer (Illumina, 15027866), 2.5 μl TDE1 Tagment DNA Enzyme (Illumina, 15027865), 16.5 μl DPBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl Nuclease-Free Water) and incubated at 37°C with shaking for 30 minutes. The DNA was then cleaned using the MinElute Reaction Cleanup Kit (QIAGEN, 28206). This was followed by a PCR amplification step using the NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0541L) with adapter primers. After determining and executing any additional amplification cycles, the library was purified using AMPure XP beads (Beckman, A63880) and stored at -80°C for future ATAC-seq analysis.

value: Monocytic leukemia

value: WT

value: Phorbol 12-myristate 13-acetate


title: 645-H1

tag: counter measure

value: M


title: Pkd1 WT MEK cells  repeat 1

description:
Library name: Sample1
Column name in raw_counts_All samples.txt: WT_1

value: Pkd1 WT MEK cells

tag: cell type

value: Pkd1 gene wild type


title: 0053-E2

value: 5-ion simulated GCR

value: E

value: F


title: 0740-E1


title: ATAC_IFNg_Tofa_1

tag: treatment


title: 0733-E1


title: S8_SJ2_LSK1

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

description: sample obtained from a Specific Pathogen Free mouse

data_processing:
Reads were processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce fastq files
Fastq files were aligned to mm10 and cuantified using RSEM v1.3.1.
Counts at gene level were normalized using limma’s voom
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include CPM values for each Sample

source_name: Endogenous LSK_2

extract_protocol:
BM LSK were FACS sorted from parabiotic mice using Lineage, Sca-1 and C-kit and DAPI labelling, with typical purities > 95%%. RNA was extracted using the Pico Pure RNA Isolation Kit
cDNA from LSK cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina).

value: Lineage- Sca-1+ c-Kit+ (LSK sorted cells)

value: Bone Marrow

value: B6SJL CD45.1


title: S9_SJ3_LSK1

source_name: Endogenous LSK_3


title: 0732-E1


title: ATAC_IFNg_Ctrl_1

tag: genotype

value: Untreated


title: S7_SJ1_LSK1

source_name: Endogenous LSK_1


title: RNA_Resting_Tofa_1


title: ATAC_IFNg_Ctrl_2


title: 598-K1

value: 0 Gy

value: mock

value: K

value: no


title: S6_DD3_LSK2

source_name: Irradiated LSK_3


title: 515-D2

value: 300 MeV/U Si  ion

value: D

value: yes


title: ATAC_Resting_Tofa_2

value: Blood

value: Monocytic leukemia

value: WT

value: Phorbol 12-myristate 13-acetate

value: Tofacitinib


title: 0057-E2

value: 5-ion simulated GCR

value: E

value: F


title: 655-H1

value: 137-Cs gamma rays

value: H

value: M


title: RNA_Resting_Ctrl_2

value: Untreated


title: 513-D2


title: Pkd1 WT MEK cells  repeat 3

description:
Library name: Sample3
Column name in raw_counts_All samples.txt: WT_3

value: Pkd1 WT MEK cells

value: collect ducts

value: Pkd1 gene wild type


title: S5_DD2_LSK2

source_name: Irradiated LSK_2

value: Lineage- Sca-1+ c-Kit+ (LSK sorted cells)

value: Bone Marrow


title: 862-D1

value: 300 MeV/U Si  ion

value: D

value: yes


title: Pkd1 WT MEK cells  repeat 2

description:
Library name: Sample2
Column name in raw_counts_All samples.txt: WT_2

value: no


title: S4_DD1_LSK2

source_name: Irradiated LSK_1


title: ATAC_Resting_Ctrl_2

value: Blood

value: Monocytic leukemia

value: WT

value: Phorbol 12-myristate 13-acetate


title: ATAC_Resting_Tofa_1

value: Tofacitinib


title: RNA_Resting_Ctrl_1


title: S3_DD3_LSK1

source_name: Circulating LSK_3


title: 570-D1

source_name: lung


title: ATAC_Resting_Ctrl_1


title: Mild par2a mutant Enew

city: Singapore

first: Tom

middle: James

last: Carney

address: 59 Nanyang Drive

department: Cancer Discovery & Regenerative Medicine Programme

country: Singapore

institute: Lee Kong Chian School of Medicine

description:
Library name: Mild par2a mutant 3
Column name in all.fpkm_anno.xls: ENew_count

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Assembly: Zebrafish Genome assembly GRCz11
Supplementary files format and content: all.fpkm_anno.xls -  Excel file with all samples raw counts and FPKM in alternating columns

organism: Danio rerio

growth_protocol: Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour after egg laying and maternal RNA extracted

extract_protocol:
RNA was extracted using TRI-Zol (Invitrogen) and precipitated by isopropanol. polyA mRNA isolated by Oligo(dT) beads
mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: par2a mutant Mild

value: biol rep 3


title: S1_DD1_LSK1

source_name: Circulating LSK_1


title: Mild par2a mutant Dnew

description:
Library name: Mild par2a mutant 2
Column name in all.fpkm_anno.xls: DNew_count

value: biol rep 2


title: 569-D1

value: M


title: 506-B2

value: B

value: F


title: 861-D1


title: Mild par2a mutant D2

description:
Library name: Mild par2a mutant 1
Column name in all.fpkm_anno.xls: D2_count

value: biol rep 1


title: Severe par2a mutant Cnew

description:
Library name: Severe par2a mutant 3
Column name in all.fpkm_anno.xls: CNew_count

value: par2a mutant Severe


title: 505-B2

value: 300 MeV/U Si  ion


title: MCF-7 NTC knockout_48 hours hypoxia

city: Zürich

first: Małgorzata

last: Wilk

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

description: Library name: 2-48Hx

data_processing:
Alignment + quantification carried out using BeeNet v1.1.2
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited transcript counts per barcode

extract_protocol:
Cells were extracted and prepared for sequencing according to HIVE kit producer Honeycomb Biotechnologies. Cells were treated for 48 hours in normoxia or hypoxia, and afterward, they were prepared as single-cell suspensions with the use of 0.5mg/ml porcine trypsin in 0.5 mM EDTA (pH 8.0).  A total of 20,000 cells were seeded under the same oxygen conditions on HIVE Collectors (Honeycomb Biotechnologies). The HIVE devices, allow individual cells to settle into picowells that contain barcoded mRNA-capture beads. Picowells were sealed to isolate each cell-bead pair, and cells were lysed to release mRNA, which then binds to the barcoded beads. Beads were extracted from the HIVE and the captured mRNA was amplified to generate sequencing-ready libraries. Pooling the libraries from multiple samples and performing the sequencing with custom sequencing primers.
The libraries were prepared according to the Honeycomb Biotechnologies protocol. A lysis solution from the kit was used to release RNA from the cells, then a provided hybridization solution was used to facilitate mRNA capture onto barcoded beads within the HIVE. The hybridization solution was removed and barcoded beads that contained captured mRNA were retrieved, then the beads were transferred to a filter plate and washed using bead recovery solution. Afterward, the specific enzymes and buffers from the HIVE kit were used for the first-strand synthesis reaction - synthesizing complementary DNA (cDNA) from the captured mRNA. Then second-strand synthesis to generate double-stranded cDNA was performed. Next, the full-length cDNA was amplified using PCR (oligos and enzymes provided in the HIVE kit). With the use of SPRI magnetic beads amplified cDNA was purified. Next, unique index sequences to each sample were assigned using provided by the company indexed PCR primers, and the libraries were amplified. Then a final SPRI bead purification to remove unwanted PCR byproducts was done and the final sequencing-ready libraries were eluted. Next, library quality and concentration were checked using Qubit and fragment analysis tools.

value: 48 hours hypoxia (0.2% oxygen)


title: Severe par2a mutant Bnew

description:
Library name: Severe par2a mutant 2
Column name in all.fpkm_anno.xls: BNew_count


title: MCF-7 NTC knockout_48 hours normoxia

description: Library name: 1-48Nx

value: 48 hours normoxia


title: MCF-7 HIF-1α knockout_48 hours hypoxia

description: Library name: 2-KO_HIF-1a_Hx


title: 502-B2

value: no


title: Severe par2a mutant B3

description:
Library name: Severe par2a mutant 1
Column name in all.fpkm_anno.xls: B3_count


title: 622-B1


title: MCF-7 HIF-1α knockout_48 hours normoxia

description: Library name: 1-KO_HIF-1a_Nx


title: Sibling3 S3_New

description:
Library name: Sibling3
Column name in all.fpkm_anno.xls: S3New_count

value: Sibling


title: 620-B1


title: MCF-7 HIF-2α knockout_48 hours hypoxia

description: Library name: 2-KO_HIF-2a_Hx


title: MCF-7 HIF-2α knockout_48 hours normoxia

description: Library name: 1-KO_HIF-2a_Nx


title: 618_B1


title: Sibling2 S2_New

description:
Library name: Sibling2
Column name in all.fpkm_anno.xls: S2New_count


title: S2_DD2_LSK1

source_name: Circulating LSK_2

value: Lineage- Sca-1+ c-Kit+ (LSK sorted cells)

value: Bone Marrow


title: Sibling1 S1_New

description:
Library name: Sibling1
Column name in all.fpkm_anno.xls: S1New_count


title: LX-A2003 168h rep4

status: Public on Mar 28 2025

city: Fujisawa

first: Shinya

last: Asano

state: Kanagawa

address: Muraoka-Higashi 2-chome

institute: Axcelead Drug Discovery Partners, Inc.

description: Library name: Sample 36

data_processing:
Base calling, quality filtering, read mapping and gene expression quantification were performed by the Ion Torrent Browser plugin.
Assembly: AmpliSeq Mouse Transcriptome V1 Reference
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver

extract_protocol:
RNA extraction from tissues were according to manufacturer instructions following beads homogenization using Tissue Lyser II (Qiagen) in TriPure isolation reagent (Roche).
Sequence library was prepared using the Ion AmpliSeq Transcriptome Mouse Gene Expression Kit (Thermo Fisher Scientific) according to the manufactures' instruments.

value: liver


title: LX-A3928 168h rep4

description: Library name: Sample 48


title: LX-A2003 72h rep2

description: Library name: Sample 30


title: LX-A3928 72h rep2

description: Library name: Sample 42


title: LX-A1656 168h rep4

description: Library name: Sample 24


title: LX-A1656 72h rep2

description: Library name: Sample 18


title: PBS 72h rep2

description: Library name: Sample 6


title: LX-A3928 168h rep3

description: Library name: Sample 47


title: LX-A3928 72h rep1

description: Library name: Sample 41


title: LX-A2003 72h rep1

description: Library name: Sample 29


title: 504-B2


title: LX-A2003 168h rep3

description: Library name: Sample 35


title: PBS 168h rep4

description: Library name: Sample 12


title: PBS 168h rep3

description: Library name: Sample 11


title: PBS 72h rep1

description: Library name: Sample 5


title: LX-A1656 72h rep1

description: Library name: Sample 17


title: LX-A1656 168h rep3

description: Library name: Sample 23


title: LX-A3928 24h rep4

description: Library name: Sample 40


title: LX-A3928 168h rep2

description: Library name: Sample 46


title: LX-A2003 168h rep2

description: Library name: Sample 34


title: LX-A1656 168h rep2

description: Library name: Sample 22


title: LX-A2003 24h rep4

description: Library name: Sample 28


title: LX-A1656 24h rep4

description: Library name: Sample 16


title: PBS 168h rep2

description: Library name: Sample 10


title: PBS 24h rep4

description: Library name: Sample 4


title: LX-A1656 168h rep1

description: Library name: Sample 21


title: LX-A2003 168h rep1

description: Library name: Sample 33


title: LX-A3928 168h rep1

description: Library name: Sample 45


title: LX-A2003 24h rep3

description: Library name: Sample 27


title: LX-A3928 24h rep3

description: Library name: Sample 39


title: PBS 24h rep3

description: Library name: Sample 3


title: PBS 168h rep1

description: Library name: Sample 9


title: LX-A1656 24h rep3

description: Library name: Sample 15


title: LX-A3928 24h rep2

description: Library name: Sample 38


title: LX-A3928 72h rep4

description: Library name: Sample 44


title: LX-A2003 72h rep4

description: Library name: Sample 32


title: LX-A3928 24h rep1

description: Library name: Sample 37


title: PBS 72h rep4

description: Library name: Sample 8


title: LX-A2003 24h rep1

description: Library name: Sample 25


title: PBS 24h rep2

description: Library name: Sample 2


title: LX-A2003 72h rep3

description: Library name: Sample 31


title: LX-A1656 72h rep4

description: Library name: Sample 20


title: LX-A1656 24h rep2

description: Library name: Sample 14


title: LX-A3928 72h rep3

description: Library name: Sample 43


title: LX-A2003 24h rep2

description: Library name: Sample 26


title: LX-A1656 24h rep1

description: Library name: Sample 13


title: LX-A1656 72h rep3

description: Library name: Sample 19


title: PBS 72h rep3

description: Library name: Sample 7


title: PBS 24h rep1

description: Library name: Sample 1


title: DNA from PD54838a

type: genomic

city: Saffron Walden

first: Sam

last: Behjati

address: Hinxton

institute: Wellcome Sanger Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Human Infinium MethylationEPIC v1.0 Beadchip (Illumina) using the standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina IScan using the standard recommended scanner settings

data_processing:
Minfi in R, with funnorn normalisation method
Average Beta

label: Cy3 and Cy5

source_name: Kidney

label_protocol: Standard Illumina protocol

extract_protocol: Tumour and normal kidney DNA/RNA were extracted by standard methods using the Qiagen Allprep kit/QIAmp DNA kit/RNeasy kit. Blood germline DNA was extracted with the QIAamp DNA Blood Midi Kit (Qiagen).

value: Kidney


title: DNA from PD53970c

value: Blood


title: DNA from PD54840a


title: DNA from PD54838b


title: DNA from PD54840b


title: DNA from PD53970a


title: DNA from PD53970b


title: DNA from PD53969a


title: DNA from PD53968c


title: DNA from PD53968b


title: DNA from PD53969b


title: DNA from PD53968a


title: DNA from PD53964d


title: DNA from PD53964b


title: DNA from PD53964c


title: DNA from PD53964a


title: DNA from PD53658a


title: DNA from PD53658c


title: DNA from PD53654c


title: DNA from PD53654d


title: DNA from PD53654b


title: DNA from PD53658b


title: DNA from PD53654a


title: DNA from PD53651f


title: DNA from PD53651b


title: DNA from PD53647h


title: DNA from PD53651d


title: DNA from PD53651a


title: DNA from PD53647e


title: DNA from PD53647b


title: DNA from PD53647d


title: DNA from PD53643c


title: DNA from PD53643b


title: DNA from PD53643d


title: DNA from PD53641d


title: DNA from PD53641c


title: DNA from PD53647c


title: DNA from PD53641a


title: DNA from PD53640d


title: DNA from PD53640c


title: DNA from PD53641b


title: DNA from PD53640a


title: DNA from PD53640b


title: DNA from PD53619d


title: DNA from PD53658d


title: DNA from PD52241d


title: DNA from PD53619b


title: DNA from PD52241b


title: DNA from PD53619a


title: DNA from PD52239i


title: DNA from PD52241f


title: DNA from PD52239d


title: DNA from PD52239c


title: DNA from PD52239a


title: DNA from PD52236c


title: DNA from PD52236d


title: DNA from PD52236b


title: DNA from PD52236a


title: DNA from PD52230f


title: DNA from PD52235b


title: DNA from PD52230d


title: DNA from PD52235c


title: DNA from PD53619c


title: DNA from PD52235d


title: DNA from PD52228a


title: DNA from PD52230b


title: DNA from PD52227d


title: DNA from PD52239b


title: DNA from PD52227b


title: DNA from PD52228b


title: DNA from PD52227a


title: DNA from PD52230e


title: DNA from PD52222c


title: DNA from PD52241a


title: DNA from PD52222b


title: DNA from PD52221c


title: DNA from PD52221a


title: DNA from PD52221b


title: DNA from PD52220c


title: DNA from PD52222a


title: DNA from PD52220b


title: DNA from PD52219e


title: DNA from PD52220a


title: DNA from PD52227c


title: DNA from PD52219c


title: DNA from PD52219b


title: DNA from PD52218f


title: DNA from PD52218b


title: DNA from PD52219a


title: DNA from PD52218g


title: DNA from PD52219d


title: DNA from PD52211g


title: DNA from PD52211e


title: DNA from PD52215f


title: DNA from PD52211b


title: DNA from PD52210c


title: DNA from PD52209e


title: DNA from PD52210b


title: DNA from PD52215b


title: DNA from PD52209c


title: DNA from PD52209b


title: DNA from PD52221d


title: DNA from PD52210a


title: DNA from PD52209a


title: DNA from PD52205f


title: DNA from PD52205d


title: DNA from PD52205a


title: DNA from PD52202d


title: DNA from PD52205c


title: DNA from PD52202c