title: nchip_Mash1CreER_Ngn1GFPbright_H3K9me3_r2

source_name: TdTomato + GFP +(bright) cells from the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato + cells were isolated with FAC-sorting

value: immediate neuronal progenitors (INP)


title: AD_1_LS

status: Public on Jun 14 2023

type: SRA

city: Davos Wolfgang

first: Yasutaka

last: Mitamura

state: Graubünden

address: Herman-Bruchard-Strasse 9

department: Immunology

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research

library_source: transcriptomic

data_processing:
Bcl files were processed in Space Ranger v.1.2.0 (10X Genomics) and demultiplexed using "spaceranger mkfastq". The resulting fastq files were mapped to the human genome build GRCh38.p13 and annotated using the GENCODE gene annotation release 32 with "spaceranger count" to produce feature-barcode count matrices. Fiducial alignment and tissue assignment was done manually by providing a json file generated in Loupe Browser (10X Genomics) to the "spaceranger count" command.
Genome_build: hg38 (GRCh38.p13)
annotation: GENCODE release 32
Supplementary_files_format_and_content: Tar archive containing an hdf5 file (filtered_feature_bc_matrix.h5), as well as two tsv files (barcodes.tsv.gz and features.tsv.gz) and a mtx file (matrix.mtx.gz). Furthermore, a spatial directory is included which contains two jpg files (aligned_fiducials.jpg and detected_tissue_image.jpg), two png files (tissue_hires_image.png and tissue_lowres_image.png), a json file (scalefactors_json.json), and a csv file (tissue_positions_list.csv). All processed data files are filtered, i.e. containing only spot barcodes. Processed data for sample AD_4_NL is missing due to bad library quality.

molecule: polyA RNA

organism: Homo sapiens

source_name: Atopic dermatitis lesional skin

extract_protocol:
Human skin biopsy samples were snap-frozen in liquid nitrogen-cooled isopentane and placed in a –80 °C freezer for long-term storage. To prepare tissues for cryosectioning, fresh-frozen tissue samples were embedded in ice-cold optimal cutting temperature (OCT) compound (Tissue-Tek, Sakura Finetek, USA) and frozen on powdered dry ice. After solidification, the OCT embedded tissue block was used immediately for cryosectioning. Block was equilibrated in a cryostat for 30 min with a cryostat chamber temperature adjusted to –20 °C and specimen stage temperature set to –15 °C. Embedded tissues were cryosectioned at 12 μm thickness and transferred onto a Visium optimization slide or a gene expression slide (10X Genomics, USA). Slides were kept in chilled slide mailers on dry ice and transferred to the –80 °C freezer.
Visium Spatial Gene Expression Slide with cryosectioned tissue sections were dried for 1 min at 37 °C, fixed in chilled 100% methanol for 20 min and stained with hematoxylin and eosin for 7 min and 1 min, respectively. Brightfield images for the spatial gene expression slides were captured using an Axio Z1 slide scanner (Zeiss, Germany). Gene expression samples were prepared by permeabilization of tissues for 18 minutes, as optimally determined using the Tissue Optimization Kit. Gene expression libraries were constructed according to the Visium Spatial Gene Expression Reagent Kits User Guide (Rev D, 10X Genomics).

tag: individual

tag: disease state

value: Atopic dermatitis

tag: tissue

value: Atopic dermatitis lesional skin


title: M-PC3-3

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All bisulfite sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads that passed quality control were mapped to human reference genome (version: hg19) or mouse reference genome (version: mm9) using bismark (version: 0.7.6) in single-end alignment mode.
Assembly: hg19 (human); mm9 (mouse)
Supplementary files format and content: bigWig (1 if a methylated CpG, 0 if an unmethylated CpG, no value otherwise)

molecule: genomic DNA

source_name: ATCC cell line cells

extract_protocol:
Single cell were either manully picked or sorted into the scBS lysis buffer by FACS, and DNA was released after proteinase treatment at 50C and then bisulfite converted.
After bislfite purification, DNA was complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

tag: cell type

value: ATCC cell line cells

tag: patient donor/cell_line

tag: genome build

tag: cpg coverage

tag: bisulfite conversion_rate

tag: qc

value: pass


title: M_22Rv1_batch2_7


title: nchip_Ngn1GFPdim_H3K79me3_r2

city: New York

first: Elizaveta

last: Bashkirova

state: NY

address: 3227 Broadway

department: Biochemistry

institute: Columbia University

data_processing:
For RNA-seq, native ChIP-seq, omni ATAC-seq and CUT&RUN adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). The RNAseq libraries that were sequenced 75PE were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20, single cell RNA-seq were aligned with the Drop-seq pipeline (http://mccarrolllab.org/dropseq/). Native ChIP-seq, omni-ATAC-seq, and CUT&RUN  reads were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000).  HiC data was aligned with the distiller pipeline (https://github.com/mirnylab/distiller-nf). Dip-c data was aligned according to the Dip-C pipeline (https://github.com/tanlongzhi/dip-c).
Filtering:  We filtered out unmapped reads and reads with a mapping quality below q30 with Samtools for RNA-seq, native ChIP-seq, omni-ATAC-seq, Cut&RUN and HiC and below q255 for single cell RNA-seq
For RNA-seq, native ChiP-seq, omni-ATAC-seq and Cut&RUN  BigWig files were generated using HOMER. For single cell RNA-seq digital expression matrices (DGE) were generated with drop-seq. For HiC ".cool" contact matixes were generated with cooler.
genome build: mm10
processed data files format and content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

organism: Mus musculus

source_name: TdTomato - GFP +(dim) cells from the olfactory epithelium

growth_protocol: Newborn mice (P2-P4) were injected  IP with tamoxifen. 48 hours later mice were sacrificed and cells were collected

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K9me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(dim) tdTomato - cells were isolated with FAC-sorting

tag: genotype/variation

tag: tissue/cell type

value: mature olfactory sensory neurons (mOSN)


title: RNASeq_E8.5 Whole Embryo_WT_M_Sample 3

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

country: Canada

institute: McGill University

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
J_7444_3_WT

data_processing:
Reads were trimmed using Trimmomatic (v0.34)
Trimmed reads wre then mapped to the GRCm38/mm10 genome using STAR (v2.7.8a) using default parameters
Picard (v2.9.0) was used to sort, mark and remove duplicates.
Raw and normalized counts were quanitified using HTSeq-counts and the StringTie suite(v1.3.5)
Differential expression analysis was then measured using DESeq2 and EdgeR
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimted text file showing raw and normalized read counts
Supplementary files format and content: tab-delimted text file showing RPKM of samples

molecule: total RNA

source_name: Whole Embryo

extract_protocol:
Total RNA was isolated using a Rneasy Micro Kit (Qiagen, 74084) or AllPrep DNA/RNA Micro Kit (Qiagen, 82084)
Sequencing libraries were prepared by the Genome Quebec Innovation Center using the NEB mRNA stranded library preperation kit

tag: developmental stage

value: Whole Embryo

tag: strain

tag: Sex

value: Male

tag: genotype

value: Wild-Type


title: RNASeq_E8.5 Whole Embryo_WT_M_Sample 1

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
H2121_5


title: AD_3_LS


title: M_22Rv1_batch2_6


title: M-PC3-2


title: omniATACseq_Z1_Ngn1GFPbright_r2

source_name: TdTomato - GFP +(bright) cells from zone1 of the olfactory epithelium

extract_protocol:
Cells were permeabilized in RSB buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin), nuclei were pelleted and transposed with Tn5.
omniATAC-seq libraries were prepared by amplifying transposed DNA fragments with 2x NEBNext MasterMix using adaptors with unique barcodes in the primers.

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone 1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato - cells were isolated with FAC-sorting.

value: immature olfactory sensory neurons (iOSN)


title: M_22Rv1_batch2_8


title: WT, scRNAseq [1086A]

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole kidney

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: WT

value: whole kidney

tag: age


title: M_22Rv1_batch2_3


title: M_22Rv1_batch2_2


title: omniATACseq_Z1_Ngn1GFPbright_r1


title: RNAseq_Zone2_Ngn1GFPdim_r2

source_name: TdTomato - GFP +(dim) cells from zone2 of the olfactory epithelium

extract_protocol:
Cells were lysed in Trizol (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
RNA: RNA-seq libraries were prepared using Ovation RNA-Seq System 1-16 for Model Organisms (Nugen 0348)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The middle segments (zone2/3) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(dim) tdTomato - cells were isolated with FAC-sorting

value: mature olfactory sensory neurons (mOSN), mature olfactory sensory neurons (mOSN)


title: M_22Rv1_batch2_1


title: Huh-7 transfected with miR-122 inhibitors, Pool3 Rep2

type: RNA

city: Dusseldorf

first: Mirco

last: Castoldi

state: No allergies

address: Moorenstr. 5

country: Germany

institute: University Hospital Dusseldorf

description: Gene expression data from RNA isolated from the polyribosomal fractions of miR-122 inhibitor transfected Huh-7 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Gene Chip Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with AltaAnalyze using Affymetrix default analysis settings and Robust Multiarray Averaging (RMA) as normalization method.

label: biotin

source_name: RNA from Huh-7, with inhibited miR-122 Pool3, light polyribosomes, Rep02

label_protocol: biotinylated cRNA from the P1, P2 and P3 RNA pools were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Huh7-hepatoma cells were cultured in DMEM supplemented with 10%FCS and Penicillin and Streptomycin.

extract_protocol: Polyribosomes were isolated from Huh-7 cells transfected with miR 122 mimic or miR 122 inhibitor for 48 h. for this, cells were lysed in presence of 200 µg/mL cycloheximide. Following cell nuclei removal supernatant was layered on top of a linear sucrose gradient (10–50% sucrose) and ultracentrifuged. Sucrose gradients were eluted into a BR-188 density gradient fractionation system and nucleic acids passing through a UV recorder were detected at a wavelength of λ = 254 nm. Fractions of approximately 800 µL were collected and RNAs were recovered from each fraction by using phenol-chloroform-isoamyl alcohol. The resulting RNAs were quantified by Qubit and 2100 agilent Pico Chip, and then were combined to create polyribosomal pools of decreasing densities [i.e., P1 = Heavy (fractions A1-A4), P2 = Middle (fractions A5-A8), and P3 = Light (fractions A9-A12)

treatment_protocol: Huh7-7 cells were transfected with miR-122 mimics or miR-122 inhibitors by using Lipofectamine RNAiMAX and incubated for 48h in incubator, 27C, 5% CO2

tag: cells

value: Hepatoma cell line

tag: transfection

value: miR-122 antagomiRs


title: omniATACseq_Z5_Ngn1GFPbright_r2

source_name: TdTomato - GFP +(bright) cells from zone5 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zone 4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato - cells were isolated with FAC-sorting.


title: RNASeq_E8.5 Whole Embryo_WT_M_Sample 2

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
H2408_4


title: RNAseq_Zone2_Ngn1GFPdim_r1


title: Huh-7 transfected with miR-122 inhibitors, Pool3 Rep1

source_name: RNA from Huh-7, with inhibited miR-122 Pool3, light polyribosomes, Rep01


title: WT, scRNAseq [JP1353]

description: 10x Genomics


title: Huh-7 transfected with miR-122 inhibitors, Pool2 Rep2

source_name: RNA from Huh-7, with inhibited miR-122 Pool2, middle polyribosomes, Rep02


title: omniATACseq_Z5_Ngn1GFPbright_r1


title: Huh-7 transfected with miR-122 inhibitor, Pool1 Rep2

source_name: RNA from Huh-7, with inhibited miR-122 Pool1, heavy polyribosomes, Rep02


title: Huh-7 transfected with miR-122 inhibitors, Pool2 Rep1

source_name: RNA from Huh-7, with inhibited miR-122 Pool2, middle polyribosomes, Rep01


title: WT, scRNAseq [1563F]

description: 10x Genomics


title: RNAseq_Zone2_Ngn1GFPbright_r2

source_name: TdTomato - GFP +(bright) cells from zone2 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The middle segments (zone2/3) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato- cells were isolated with FAC-sorting


title: WT, scRNAseq [JP1296]

description: 10x Genomics


title: Huh-7 transfected with miR-122 inhibitor, Pool1 Rep1

source_name: RNA from Huh-7, with inhibited miR-122 Pool1, heavy polyribosomes, Rep01


title: RNAseq_Zone2_Ngn1GFPbright_r1


title: M-LNCap-2

value: LNCap


title: WT, scRNAseq [JP1295]

description: 10x Genomics


title: M-LNCap-1


title: Placode2

city: Helsinki

first: Marja

middle: L

last: Mikkola

address: P.O.B 56 (Viikinkaari 5)

country: Finland

institute: University of Helsinki

data_processing:
10x genomics “cellranger” and R package “Seurat” were used to process the data.
mm10
Supplementary files format and content: Tab-delimited gene expression count values of each cell
Supplementary files format and content: Tab-delimited gene expression count values of each cell

source_name: Dorsal skin

extract_protocol:
Epithelium and mesenchyme of dorsal skins were enzymatically separated using Dispase II (Roche, Tokyo, Japan). Epithelial sheets of embryos from the same litter were pooled (3-4 embryos per sample) and dissociated to single cell suspension by TrypLE Select Enzyme (Life Technologies/Gibco). Cell were stained with rat anti-MAdCAM-1 (BD Pharmingen), followed by anti-rat Alexa Fluor 488 - conjugated antibody (Life Technologies). Live total epithelium cells or placode-enriched (MAdCAM-1 positive) cells were sorted on BD Influx Cell Sorter (BD Biosciences) with 100 µm nozzle to PBS + 0.04% BSA.
Single-cell cDNA libraries were prepared using the 10X Genomics Chromium Single Cell 3’ reagent v2 chemistry in accordance with manufacturer’s recommendations.

value: Dorsal skin

value: Epithelial Cells


title: RNAseq_Zone2_Mash1CreER_Ngn1GFPbright_r2

source_name: TdTomato + GFP +(bright) cells from zone2 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The middle segments (zone2/3) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato + cells were isolated with FAC-sorting

value: immediate neuronal progenitors (INP)


title: WT, scRNAseq [1737A]

description: 10x Genomics


title: Huh-7 transfected with miR-122 mimcs, Pool2 Rep2

description: Gene expression data from RNA isolated from the polyribosomal fractions of Huh-7 cells overexpressing miR-126

source_name: RNA from Huh-7, overexpressing miR-122 Pool2, middle polyribosomes, Rep02

value: miR-122 mimics


title: M_GURa15_171220_CTC9

source_name: Single prostate CTCs

value: Single prostate CTCs


title: Placode1


title: Huh-7 transfected with miR-122 mimc, Pool1 Rep2

description: Gene expression data from RNA isolated from the polyribosomal fractions of Huh-7 cells overexpressing miR-125

source_name: RNA from Huh-7, overexpressing miR-122 Pool1, heavy polyribosomes, Rep02


title: Huh-7 transfected with miR-122 mimcs, Pool3 Rep2

description: Gene expression data from RNA isolated from the polyribosomal fractions of Huh-7 cells overexpressing miR-127

source_name: RNA from Huh-7, overexpressing miR-122 Pool3, light polyribosomes, Rep02


title: RNAseq_Zone2_Mash1CreER_Ngn1GFPbright_r1


title: M-LNCap-3

source_name: ATCC cell line cells

value: ATCC cell line cells

value: pass


title: M_GURa15_171220_CTC8


title: Epithelium


title: M_GURa15_171220_CTC7

value: fail


title: RNAseq_Zone2_Mash1CreER_r2

source_name: TdTomato + GFP- cells from zone2 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The middle segments (zone2/3) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP- tdTomato + cells were isolated with FAC-sorting

value: globose basal cells (GBC)


title: RNAseq_Zone2_Mash1CreER_r1


title: Huh-7 transfected with miR-122 mimcs, Pool3 Rep1

description: Gene expression data from RNA isolated from the polyribosomal fractions of Huh-7 cells overexpressing miR-124

source_name: RNA from Huh-7, overexpressing miR-122 Pool3, light polyribosomes, Rep01


title: M_GURa15_171220_CTC6


title: M_GURa15_171220_CTC4


title: RNAseq_Zone5_Ngn1GFPdim_r3

source_name: TdTomato - GFP +(dim) cells from zone5 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zones 4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(dim) tdTomato - cells were isolated with FAC-sorting

value: mature olfactory sensory neurons (mOSN)


title: DM1000 3dpi [D8_CRRA200000249-1a_HT7GVDSXX_L3_1]

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

data_processing:
Star
Data QC
Quantification
DeSeq2
Cluster analysis
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Partek_quantification_annotation.tar: Tar archive includes raw counts and annotation.
Supplementary_files_format_and_content: DeSeq2-Rs-7-7-2020.txt: DESeq2 results

source_name: corneas

extract_protocol:
Corneas were collected, and total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Performed by NOVAGene NGS services.

treatment_protocol: Corneas from normal and diabetic mice were gently scratched with 26‐gauge needles, followed by topical inoculation of Pseudomonas Aeruginosa (PA).

tag: disease

value: Diabetic

value: Corneas

tag: treatment

value: infection with 1000 CFU of PA

tag: time point


title: DM1000 3dpi [D9_CRRA200000250-1a_HT7GVDSXX_L3_1]

tag: tissue


title: M_GURa15_171220_CTC2

tag: cell type

tag: patient donor/cell_line

tag: genome build


title: A012_27-7-3IFE

data_processing:
Illumina bcl2fastq2 v2.17.1.14 for basecalling
The quality control of the rna-seq reads were done by AfterQC, Trimmomatic , MultiQC and FastQC
The ribosomal rRNA were filtered out using SortMeRna
The reads where aligned to mouse genome using STAR (1.5) with default parameters (GRCm38/mm10/Ensembl release 79 - March 2015) )
The gene expression was measured by counting the corresponding reads of the exons. This step was performed by htseq-count with parameters (-s reverse -t exon -i gene_id)
Assembly: mm10
Supplementary files format and content: Tab-delimited gene expression count values of each samples

extract_protocol:
Epithelium and mesenchyme of dorsal skins were enzymatically separated using Dispase II (Roche, Tokyo, Japan). Epithelial sheets of embryos from the same litter were pooled (3-4 embryos per sample) and dissociated to single cell suspension by TrypLE Select Enzyme (Life Technologies/Gibco). Cell were stained with rat anti-MAdCAM-1 (BD Pharmingen), followed by anti-rat Alexa Fluor 488 - conjugated antibody (Life Technologies). Live placode-enriched (MAdCAM-1 positive) and IFE (MAdCAM-1 negative) cells were sorted on BD Influx Cell Sorter (BD Biosciences) with 100 µm nozzle directly to TRI Reagent® RT – Liquid Samples (Molecular Research Center, Inc. Cincinnati, OH). Total RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research, Irvine, CA), including DNase treatment, according manufacturer’s instructions.
cDNA libraries were prepared with Ovation SoLo RNA-seq System (NuGen/Tecan Genomics), according to manufacturer's instructions

value: WT

tag: sample type

value: interfollicular epithelium


title: A011_27-7-3P

value: placode-enriched


title: RNAseq_Zone5_Mash1CreER_Ngn1GFPbright_r3

source_name: TdTomato + GFP +(bright) cells from zone5 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zones 4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato + cells were isolated with FAC-sorting

tag: genotype/variation


title: DM750 3dpi [D6_CRRA200000247-1a_HT7GVDSXX_L3_1]

value: infection with 750 CFU of PA


title: M_GU216_180809_CTC3

tag: cpg coverage

tag: bisulfite conversion_rate

tag: qc


title: A010_27-7-2IFE

value: Dorsal skin

tag: strain


title: DM750 3dpi [D5_CRRA200000246-1a_HT7GVDSXX_L3_1]


title: RNAseq_Zone1_Ngn1GFPdim_r3

source_name: TdTomato - GFP +(dim) cells from zone1 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone 1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(dim) tdTomato - cells were isolated with FAC-sorting

tag: tissue/cell type


title: Huh-7 transfected with miR-122 mimcs, Pool2 Rep1

description: Gene expression data from RNA isolated from the polyribosomal fractions of Huh-7 cells overexpressing miR-123

source_name: RNA from Huh-7, overexpressing miR-122 Pool2, middle polyribosomes, Rep01

value: Hepatoma cell line


title: Huh-7 transfected with miR-122 mimc, Pool1 Rep1

description: Gene expression data from RNA isolated from the polyribosomal fractions of Huh-7 cells overexpressing miR-122

source_name: RNA from Huh-7, overexpressing miR-122 Pool1, heavy polyribosomes, Rep01


title: A014_27-7-4IFE

value: Epithelial Cells

tag: genotype

tag: age


title: A009_27-7-2P


title: M_GU216_180809_CTC2


title: RNAseq_Zone1_Ngn1GFPbright_r3

source_name: TdTomato - GFP +(bright) cells from zone1 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone 1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato- cells were isolated with FAC-sorting

value: immature olfactory sensory neurons (iOSN)


title: A008_1-6-3IFE


title: A013_27-7-4P


title: M_GU216_180809_CTC1

value: Single prostate CTCs


title: DM750 3dpi [D4_CRRA200000245-1a_HT7GVDSXX_L3_1]


title: RNAseq_Zone5_Ngn1GFPbright_r3

source_name: TdTomato - GFP +(bright) cells from zone5 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zones 4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato- cells were isolated with FAC-sorting


title: DM1000 3dpi [D7_CRRA200000248-1a_HT7GVDSXX_L3_1]


title: NL 3dpi [D3_CRRA200000244-1a_HT7GVDSXX_L3_1]

value: Normal

value: infection with 10000 CFU of PA


title: A007_1-6-3P

source_name: Dorsal skin


title: NL 3dpi [D2_CRRA200000243-1a_HT7GVDSXX_L3_1]


title: RNAseq_NfiABXko_OMPCre_rep3

data_processing:
Adapter sequences were trimmed with Cutadapt (--nextseq-trim=20 --minimum-length 18)
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Filtered out unmapped reads and reads with a mapping quality below q30 with Samtools
BigWig files were generated using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: TdTomato + cells from the olfactory epithelium

growth_protocol: Olfactory epithelium was dissected from adult mice.

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. Olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then tdTomato +cells were isolated with FAC-sorting.

value: NfiAfl/fl; NfiBfl/fl; NfiXfl/fl;  OMPCre*/+; Rosa-CAG-tdtomfl/fl

value: mature olfactory sensory neurons


title: M_GU216_180705_CTC7

value: pass


title: A006_18-5-IFE


title: M_GU216_180705_CTC6


title: RNAseq_NfiABXko_OMPCre_rep2


title: M_GU216_180705_CTC4


title: RNAseq_NfiABXko_OMPCre_rep1


title: A005_18-5-P


title: A004_17-5-IFE


title: RNAseq_wt_OMPCre_rep3

value: OMPCre*/+; Rosa-CAG-tdtomfl/fl


title: DM 1dpi [C6_CRRA200000241-1a_HT7GVDSXX_L3_1]

value: Diabetic

value: Corneas

value: infection with 2000 CFU of PA


title: M_GU181_CTC8_180102


title: DM 1dpi [C5_CRRA200000240-1a_HT7GVDSXX_L3_1]


title: RNAseq_Zone1_Mash1CreER_Ngn1GFPbright_r3

source_name: TdTomato + GFP +(bright) cells from zone1 of the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone 1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato + cells were isolated with FAC-sorting

value: immediate neuronal progenitors (INP)


title: RNAseq_wt_OMPCre_rep2


title: A003_17-5-P

value: WT

value: placode-enriched


title: nchip_Ngn1GFPbright_H3K9me3_r2

source_name: TdTomato - GFP +(bright) cells from the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato- cells were isolated with FAC-sorting


title: A002_11-5-2IFE

value: Dorsal skin

value: interfollicular epithelium


title: RNAseq_wt_OMPCre_rep1


title: DM 1dpi [C4_CRRA200000239-1a_HT7GVDSXX_L3_1]


title: M_GU181_CTC6_180130

source_name: Single prostate CTCs


title: M_GU181_CTC6_180102


title: NL 1dpi [C3_CRRA200000238-1a_HT7GVDSXX_L3_1]


title: A001_11-5-2P

value: Epithelial Cells


title: M_GU181_CTC2_180102


title: NL 1dpi [C2_CRRA200000237-1a_HT7GVDSXX_L3_1]


title: RNAseq_NfiABXko_K5CreER_rep2

source_name: TdTomato +/dim cells from the olfactory epithelium

growth_protocol: Adult mice were injected 3x IP with tamoxifen (24 hours apart), 10 days following the first injection olfactory epithelium was ablated with an IP injection of methimazole. Then olfactory epithelium was regenerated for 40 days.

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. Olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+ tdTomato +(dim) cells were isolated with FAC-sorting.

value: NfiAfl/fl; NfiBfl/fl; NfiXfl/fl;  K5CreER*/+; Rosa-CAG-tdtomfl/fl

value: tdTomato +(dim) cells from the olfactory epithelium


title: RNAseq_NfiABXko_K5CreER_rep1


title: M_GU216_180705_CTC1

value: Single prostate CTCs


title: NL 1dpi [C1_CRRA200000236-1a_HT7GVDSXX_L3_1]

value: Normal

value: infection with 10000 CFU of PA


title: M_GU181_CTC2_171107


title: NL 3dpi [D1_CRRA200000242-1a_HT7GVDSXX_L3_1]


title: CRE- 2_GEX

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Sequencing files were processed with STARsolo (STAR version 2.7.10a) to perform sample and cell demultiplexing, and alignment of reads to the mouse genome (mm10; supplemented with the Cre, tdTomato eGFP construct sequences) and UMI counting on gene models from Ensembl 102. The options “--outFilterType=BySJout --outFilterMultimapNmax=10 --outSAMmultNmax=1 --outFilterScoreMin=30 --soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts --soloUMIlen=10 --soloUMIfiltering=MultiGeneUMI_CR --soloUMIdedup=1MM_CR --soloCellFilter=None --clipAdapterType=False --soloType=CB_UMI_Simple –soloStrand=Reverse –soloMultiMappers=EM” were used for STARsolo.
For each sample, empty droplets were detected and removed using the emptyDrops() function from the Bioconductor DropletUtils package (version 1.14.2; using 5000 iterations, the option test.ambient=TRUE, a lower threshold of 100 UMIs and an FDR threshold of 0.1%)
Filtering for high-quality cells was done using the cells library sizes, the number of detected genes and the percentage of reads mapping to mitochondrial genes, based on the distribution observed across cells. After hierarchical clustering, clusters gathering low-quality cells were additionally removed. After final quality filtering, the resulting dataset consisted of 28,644 cells derived from the 7 samples. The filtered UMI counts matrix for these genes and cells is provided in file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the scran, and scater Bioconductor packages (Bioconductor release 3.15), mostly following the steps of the OSCA book workflow (https://bioconductor.org/books/3.15/OSCA/).
Assembly: mm10
Supplementary files format and content: UMIsMatrix.txt.gz: TSV file (tab separated values) with UMI counts for Ensembl release 102 gene models in cells retained after QC; columns correspond to: 1. Ensembl gene ID, remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample name separated by a dash (e.g., "BSSE_QGF_174485-AAACCTGAGCCAGAAC")
Supplementary files format and content: colData.txt: TSV file (tab separated values) with metadata for retained good quality cells; columns correspond to: 1. Cell barcode sequence and sample name as used in UMIsMatrix.txt.gz; 2. Sample ID; 3. Sample name; 4. Inferred cell cycle phase; 5. Cell type annotation; 6. Number of detected genes; 7. Percent of reads originating from the mitochondria; 8. Percent of reads originating from the ribosomal genes; 9. and 10. tSNE coordinates

source_name: Sorted immune compartment from CT-2A glioma-bearing Siglecefl/fl mice

growth_protocol: Sall1CreERT2 x Siglecefl/fl (B6;129-Sall1<tm5(cre/ERT2)Ryn> x B6.129P2-Siglece<tm1Bcgen>) mice were used for intracranial tumor engraftment at age 8–12 weeks. Mice were being anesthetized with 2.5% isoflurane in an induction chamber. Anesthesia was maintained at 1.5% isoflurane delivered through a nose adaptor on the stereotactic frame. A midline incision was made and a burr hole was drilled at 1 mm posterior to the Bregma, and 2 mm lateral from the midline to the right. Stereotactic injection of tumor cells was done using a Hamilton 10 μL syringe (#80300, 701N, 26s/2”/2, Hamilton) at a depth of 3mm below the dura surface. A microinjection pump was used to inject 5 x 104 CT-2A glioma cells in 3 μL PBS + 2% FBS total volume at 1 μL/min injection speed. One minute after injection ended, the needle was slowly retracted to avoid reflux of the cell suspension. The scalp wound was closed with sutures (5-0, Polypropylene suture, #8661H, Ethicon, USA).

extract_protocol:
Mice were euthanized by CO2-suffocation at endpoint or indicated time points and tumor-bearing cerebral hemisphere without cerebellum was harvested into ice-cold HBSS. On ice, brain tissue was manually minced using razor blades and enzymatically dissociated at 37°C for 30 minutes. The suspension was filtered through a 70 μm strainer and subjected to a density gradient centrifugation using debris removal solution (#130-109-398, Miltenyi Biotec, Germany) according to manufacturer’s protocol to remove myelin and cell debris. Following ACK-lysis, the remaining myelin- and erythrocytes-depleted tumor cells were resuspended in Bambanker and frozen in liquid nitrogen. At the time of analysis, cell suspensions were thawed, stained with Zombie fixable viability dye, Fc-receptor blocked and stained with CD45 and CD11b. Live, CD45+ and/or CD11b+ immune cells were sorted into ice-cold PBS with 0.4% BSA. Cells were kept on ice and brought to the Genomics Facility Basel at the Department of Biosystems Science and Engineering.
Cell suspensions from each sample were loaded each into a single well of a 10× Genomics Chromium Single Cell Controller for a targeted recovery of 10,000 cells. Single-cell capture and cDNA and library preparation were at the D-BSSE Genomics facility, Basel, with a Chromium Single Cell 5’ Reagent Kit v2 (10× Genomics) according to manufacturer’s instructions.
Libraires were prepared following the 10x Genomics protocol for 5′ GEX profiling (CG000331) and cDNA or library quality was assessed using a Bioanalyzer instrument. A total of seven libraries were prepared and sequenced using an Illumina NovaSeq 6000 instrument aiming to obtain 50,000 reads per cell.

treatment_protocol: Tamoxifen (#T5648-5G, Sigma-Aldrich, USA) was dissolved in corn oil (#C8267, Sigma-Aldrich, USA) and 2.5 mg were administered i.p. per mouse and injection, starting from d 7 post tumor injection daily until d 21 and from d 21 onwards, every other day throughout the duration of the experiment. Cre+ and Cre- mice were treated with Tamoxifen.


title: CRE- 3_GEX


title: M_GU181_CTC11_180130


title: CRE- 1_GEX


title: RNAseq_wt_K5CreER_rep1

value: K5CreER*/+; Rosa-CAG-tdtomfl/fl


title: CRE+ 4_GEX

source_name: Sorted immune compartment from CT-2A glioma-bearing Sall1CreERT2 x Siglecefl/fl mice

value: Siglece KO


title: DM 6hpi [B5_CRRA200000234-1a_HT7GVDSXX_L3_1]


title: RNAseq_Zone5_NfiXko_K5CreER_OMPgfp_rep2

source_name: GFP+ TdTomato +/dim cells from zone5 of the olfactory epithelium

extract_protocol:
Cells were lysed in Trizol (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
RNA: RNA-seq libraries were prepared using Universal RNA-Seq with NuQuant (Nugen 0531-32)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segment (zone 5) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+ tdTomato +(dim) cells were isolated with FAC-sorting.

value: NfiXfl/fl;  K5CreER*/+; Rosa-CAG-tdtomfl/fl; OMPgfp

value: mature olfactory sensory neurons


title: M_GU181_CTC10_180130

value: pass


title: DM 6hpi [B4_CRRA200000233-1a_HT7GVDSXX_L3_1]

value: Diabetic

value: Corneas


title: CRE+ 3_GEX


title: M_GU181_171219_CTC9


title: NL 6hpi [B3_CRRA200000232-1a_HT7GVDSXX_L3_1]


title: RNAseq_Zone5_NfiXko_K5CreER_OMPgfp_rep1


title: M_GU181_171219_CTC8

value: fail


title: CRE+ 2_GEX


title: RNAseq_Zone5_NfiABXko_K5CreER_OMPgfp_rep3

value: NfiAfl/fl; NfiBfl/fl; NfiXfl/fl;  K5CreER*/+; Rosa-CAG-tdtomfl/fl; OMPgfp


title: NL 6hpi [B2_CRRA200000231-1a_HT7GVDSXX_L3_1]


title: CRE+ 1_GEX


title: M_GU181_171219_CTC7


title: NL 6hpi [B1_CRRA200000230-1a_HT7GVDSXX_L3_1]


title: RNAseq_Zone5_NfiABXko_K5CreER_OMPgfp_rep2


title: M_GU181_171219_CTC6


title: RNAseq_wt_K5CreER_rep2


title: DM 6hpi [B6_CRRA200000235-1a_HT7GVDSXX_L3_1]


title: DM [A6_CRRA200000229-1a_HT7GVDSXX_L3_1]

value: no treatment


title: RNAseq_Zone5_NfiABXko_K5CreER_OMPgfp_rep1


title: M_GU181_171219_CTC4


title: RNAseq_Zone5_NfiABko_K5CreER_OMPgfp_rep2

value: NfiAfl/fl; NfiBfl/fl; K5CreER*/+; Rosa-CAG-tdtomfl/fl; OMPgfp


title: ST_pIpC3

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

institute: ETH ZURICH / University of Zurich

data_processing:
RNA-seq reads were aligned with STAR-aligner using the genome build GENCODE GRCm38.p6 Release_M23.
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GENCODE GRCm38.p6 Release_M23
Supplementary files format and content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

source_name: bone marrow

extract_protocol:
After isolation of the bone marrow and FACS sorting of the hematopoietic subpopulations, the RNA was extracted using the Rneasy Micro Kit (Qiagen). The samples were then treated with DNAse I on the column and collected in 12µl of RNAse-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: short-term hematopoietic stem cells

value: pIpC


title: ST_pIpC2


title: DM [A5_CRRA200000228-1a_HT7GVDSXX_L3_1]

source_name: corneas


title: DM [A4_CRRA200000227-1a_HT7GVDSXX_L3_1]


title: RNAseq_Zone5_NfiABko_K5CreER_OMPgfp_rep1


title: ST_pIpC1


title: M_GU181_171219_CTC3


title: M_GU181_171219_CTC2


title: NL [A3_CRRA200000226-1a_HT7GVDSXX_L3_1]


title: ST_PBS3

value: untreated


title: M_GU181_171219_CTC13

value: Single prostate CTCs


title: ST_PBS2


title: RNAseq_Zone5_wt_K5CreER_OMPgfp_rep2

value: K5CreER*/+; Rosa-CAG-tdtomfl/fl; OMPgfp


title: NL [A2_CRRA200000225-1a_HT7GVDSXX_L3_1]

value: Normal


title: M_GU181_171219_CTC12


title: ST_PBS1


title: RNAseq_Zone5_wt_K5CreER_OMPgfp_rep1


title: NL [A1_CRRA200000224-1a_HT7GVDSXX_L3_1]


title: M_GU181_171219_CTC11


title: M_22Rv1_batch2_4

source_name: ATCC cell line cells

value: ATCC cell line cells


title: M_GU181_171219_CTC10


title: MPP_pIpC2

value: multipotent progenitor cells


title: MPP_pIpC3


title: M_GU181_171128_CTC9


title: week 10 WT-DES uterus

city: RTP

first: Yin

last: Li

state: NC

address: 111 TW alexander Drive

institute: NIEHS

data_processing:
The raw ChIP-Seq reads were initially processed by filtering with average quality scores greater than 20.
Then the reads were aligned to the mouse reference genome (mm10; Genome Reference Consortium Mouse Build 38 from December 2011) using Bowtie version 1.1.2 with unique mapping and up to 2 mismatches for each read (-m 1 -v 2)
The duplicated reads with the same sequence were discarded
Genome_build: mm10
Supplementary_files_format_and_content: biWig files were generated from normalized bedgraph files using bedGraphToBigWig; Scores represent normalized mapped read coverage

source_name: week 10 WT mouse uterus DES group

growth_protocol: The mouse SV or uterus tissues were colleclted from WT and aERKO mice in the control and DES groups.

extract_protocol:
Pooled genomic DNA samples were sent to ACTIVE MOTIF for the assay
It was performed at ACTIVE MOTIF fllowing their protocol

treatment_protocol: For neonatal treatment, male or female pups were treated by subcutaneous injection with DES (Sigma Aldrich), dissolved in corn oil at 2 µg/pup/day on days 1-5 (day of birth = 1) (DES group) or an equal volume of corn oil (control group).

value: uterus

value: wt

value: DES

value: week 10

tag: antibody


title: MPP_pIpC1


title: RNAseq_Zone5_wt_K5CreER_OMPgfp_rep3

value: mature olfactory sensory neurons


title: M_GU181_171128_CTC8

value: pass


title: MPP_PBS3


title: M_GU181_171128_CTC7


title: mtOGG1_M_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Purified RNA was hybridized for 16 to 24 hours at 65°C  in nCounter hybridization buffer with NanoString Reporter and Capture probes, using 8 μL Master Mix, 5 µL sample, and 2 µL Capture ProbeSet per sample.

scan_protocol: Once the hybridization reactions have been removed from the thermal cycler, proceed immediately to an nCounter Prep Station. This step can process up to 12 samples per run in approximately 2.5 to 3 hours. Next, the nCounter Digital Analyzer which is a multi-channel epifluorescence scanner collects raw data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the results are exported as a.csv file.

data_processing: The raw data as RCC files format were analyzed via the NanoString nCounter nSolver 4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10,030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04). Both positive control and housekeeping normalization were used to normalize all sources of variation associated with the platform.

label_protocol: Per manufacturer recommendations, https://nanostring.com/products/ncounter-assays-panels/oncology/metabolic-pathways/.The purified RNA is diluted in nuclease-free water to 20 ng/uL.  RNA (~100 ng) added for hybridization assay.

extract_protocol: The hippocampus tissue were used for the extraction of total RNA using PureLink™ RNA Mini Kit (Thermo Fisher Scientific, #12183018A) according to the manufacturer’s protocol.

treatment_protocol: Mice were treated according to animal study protocol 361-OSD-2023. Mice were group housed and fed ad libitum.

value: brain

tag: brain region

value: hippocampus

tag: Sex

value: M

tag: age (months)

tag: background strain


title: mtOGG1_M_2

tag: tissue


title: Con_M_3

value: Control


title: mtOGG1_M_1


title: M_GU181_171128_CTC6

tag: cell type

tag: patient donor/cell_line


title: MPP_PBS1

tag: treatment


title: M_GU181_171128_CTC5

tag: genome build


title: week 10 WT-DES seminal vesicles

source_name: week 10 WT mouse SVs DES group

value: seminal vesicles


title: LT_pIpC3

value: long-term hematopoietic stem cells

value: pIpC


title: Con_M_2


title: week 10 aERKO-DES seminal vesicles

source_name: week 10 aERKO mouse SVs DES group

value: aERKO


title: week 10 WT-veh uterus

source_name: week 10 WT mouse uterus control group

value: control


title: M_GU181_171128_CTC3

value: Single prostate CTCs

tag: cpg coverage


title: LT_pIpC2


title: nchip_Mash1CreER_Ngn1GFPbright_H3K79me3_r2

source_name: TdTomato + GFP +(bright) cells from the olfactory epithelium

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K79me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato + cells were isolated with FAC-sorting

tag: genotype/variation

value: immediate neuronal progenitors (INP)


title: Con_M_1


title: week 10 WT-veh seminal vesicles

source_name: week 10 WT mouse SVs control group


title: week 5 aERKO-DES seminal vesicles

source_name: week 5 aERKO mouse SVs DES group

value: week 5


title: Pooled_Input

source_name: Pooled samples

value: input


title: M_GU181_171128_CTC2

tag: bisulfite conversion_rate

tag: qc


title: MPP_PBS2

value: multipotent progenitor cells

tag: strain

value: untreated


title: M_GU181_171128_CTC13


title: LT_pIpC1


title: mtOGG1_F_2

tag: genotype

value: F


title: week 5 aERKO-veh seminal vesicles

source_name: week 5 aERKO mouse SVs control group

tag: age


title: LT_PBS3


title: week 5 WT-DES seminal vesicles

source_name: week 5 WT mouse SVs DES group

value: wt

value: DES

tag: antibody


title: M_GU181_171128_CTC12

source_name: Single prostate CTCs

value: pass


title: LT_PBS2


title: week 10 aERKO-veh seminal vesicles

source_name: week 10 aERKO mouse SVs control group

value: week 10


title: mtOGG1_F_1

value: brain

tag: brain region

value: hippocampus


title: week 5 WT-veh seminal vesicles

source_name: week 5 WT mouse SVs control group

value: seminal vesicles


title: Con_F_3

value: Control

tag: Sex


title: LT_PBS1

value: long-term hematopoietic stem cells


title: M_GU181_171128_CTC11

value: fail


title: mtOGG1_F_3

tag: age (months)


title: week 5 aERKO-DES4 seminal vesicles

data_processing:
The raw RNA-Seq reads were initially processed by filtering with average quality scores greater than 20.
The reads passing the initial processing were aligned to the mouse reference genome (mm10; Genome Reference Consortium Mouse Build 38 from December 2011) using TopHat version 2.0.4. The FPKM was calculated with Cufflinks version 2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: biWig files were generated from normalized bedgraph files using bedGraphToBigWig; Scores represent normalized mapped read coverage

extract_protocol: Trizol/ extraction of total RNA was perforemd accoding to the manufacture's instructions. RNA-Seq was performed at NISC/NIH for each group which includes four samples. The RNA libraries were sequenced with a HiSeq 2000 system [Illumina]

value: aERKO


title: Con_F_2

tag: background strain


title: M_GU181_171128_CTC1

extract_protocol:
Single cell were either manully picked or sorted into the scBS lysis buffer by FACS, and DNA was released after proteinase treatment at 50C and then bisulfite converted.
After bislfite purification, DNA was complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

value: Single prostate CTCs


title: Lin_pIpC3

value: lineage positive cells

value: pIpC


title: P_Q5A_37_P2

first: Sasha

middle: Leilani

last: Fulton

data_processing:
fastq files were aligned to ensembl rat reference genome rn6 using HISAT2 (Version 2.1.0).
BAM files resulting from the alignments were summarized to genes using the featureCounts (Version 2.0.1) algorithm against Ensembl v90 annotation
Expression data was normalized using DESEQ2 (Version 1.6.3)
Differentially expressed genes (10% false discovery rate) were identified using DESEQ2 based on a model using the negative binomial distribution
Supplementary files format and content: featurecounts output filtered for count >10

organism: Rattus norvegicus

source_name: mPFC

extract_protocol:
RNA was isolated using trizol-chloroform extraction followed by cleanup on the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the Illumina Truseq RNA Library Prep Kit V2 , according to the manufacturer’s instructions.

tag: tissue

value: mPFC

value: Sprague-Dawley

value: Male

value: Young Adult (200-250g)

tag: virus

value: Extended Access Cocaine Self Administration


title: Con_F_1

value: F


title: P_Q5A_34_P2


title: Lin_pIpC2

source_name: bone marrow

tag: cell type


title: week 5 aERKO-DES3 seminal vesicles

tag: treatment

value: DES

value: week 5


title: week 5 aERKO-DES2 seminal vesicles


title: M_GU159_CTC4_171025

tag: patient donor/cell_line

tag: genome build


title: Lin_pIpC1


title: P_Q5A_15_P2


title: M_GU114_180710_CTC5

tag: cpg coverage

value: pass


title: week 5 aERKO-veh4 seminal vesicles

value: seminal vesicles

value: control


title: P_Q5A_14_P2


title: Lin_PBS3

value: untreated


title: P_WT_36_P2


title: Lin_PBS2


title: M_GU114_180710_CTC2

tag: bisulfite conversion_rate


title: week 5 aERKO-veh3 seminal vesicles


title: MCAO-brain, scRNAseq

city: Shanghai

first: Yueman

last: Zhang

address: 160 Pujian Rd

country: China

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

description: BD Rhapsody

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 30%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: TXT file contain counts and barcodes for each sample

source_name: Brain

growth_protocol: Male C57/BL6 mice were purchased from Shanghai SLAC Laboratory Animals and were housed under standard laboratory conditions (22°C and a 12‐hour light‐dark cycle with free access to food and water).

extract_protocol:
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice treated middle cerebral artery occlusion (MCAO) means they were anesthetized with 3% isoflurane in 67%:30% N2O/ O2 (induction), until they were unresponsive to the tail pinch test and were then fitted with a nose cone providing 1.5% isoflurane for anesthesia maintenance. A monofilament was introduced into the common carotid artery, advanced to the origin of the middle cerebral artery, and left in position for 60 minutes until reperfusion.Sham-operated animals underwent the same anesthesia and surgical procedures except MCAO.

value: Brain

value: MCAO


title: P_WT_35_P2


title: M-CTC2_GU70_170906

value: Single prostate CTCs

tag: qc

value: fail


title: P_WT_21_P2

tag: strain


title: week 5 aERKO-veh1 seminal vesicles

tag: genotype

value: aERKO


title: week 5 aERKO-veh2 seminal vesicles

tag: age


title: M_GU114_180710_CTC1


title: Lung cells mCherry-negative (2)

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality control was peformed using fastQC ( v0.11.8) and multiQC (v 1.9)
Alignment, filtering and gene quantification was performed using 10x cellranger v5.0.0; the alignment was perfomed against the MMus reference genome mm10 (GENCODE vM23/Ensebl 98) provided by 10x genomics.
Normalization of expression was levels was performed with SCTransform (Hafemeister and Satija, 2019)
Clustering was performed using Louvain algorithm from the FindClusters function from Seurat (Satija, 2021)
Differential Expression was perfored using the Wilcoxon Rank Sum test  from FindMarkers function from Seurat (Satija, 2021)
Assembly: mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: Seurat object including processed count data, normalised count data, and meta data for all samples. Provided as an R object (.rds file).

source_name: FACS isolated cells from tumourigenic KrasG12D/+; p16FDR/+; Rosa26loxP-STOP-loxP-YFP/+ lungs

extract_protocol:
Tumour bearing lungs from KrasG12D/+; p16FDR/+; Rosa26loxP-STOP-loxP-YFP/+ mice were dissected into 1 mm3 pieces and dissociated in a solution of 0.5% w/v collagenase type 2 (Lorne Laboratories Ltd.), 0.1x Trypsin (Gibco), 50 μg/ml DNaseI (Worthington) and 2.5 μg/ml fungizone (Gibco) in Hank’s Balanced Salt Solution (HBSS (Gibco) for 45 minutes at 37°C. Tissue fragments were further dissociated into single cells through mechanical trituration using a pipette and filtration through a 70 μm filter. Single cells were washed in HBSS and suspended in FACS media (PBS supplemented with 1% foetal calf serum (PAA), 25 mM HEPES and 10 μg/ml of 4′,6-diamidino-2-phenylindole (DAPI, BD Pharmingen) for live/dead cell discrimination) before being analysed using a BD FACS AriaIII Flow Cytometer. Cells were collected into 4°C FACS media for 10X single cells RNA-sequencing analysis.
Flow-sorted cells were centrifuged and resuspended in complete DMEM to a concentration of 700-1000 cells per microlitre. Cells were partitioned and barcoded using the 10X Genomics Chromium Controller and associated v3 kit components, according to manufacturer’s instructions. Harvested cDNA was assessed and quantified using the Agilent 2100 Bioanalyser and library construction performed using the 10X Single Cell 3' Library Kit v3. Libraries were quality controlled by performing a MiSeq Nano PE100 run followed by deeper sequencing on the HiSeq2500 v4 system.

value: Lung

tag: timepoint

value: 8 weeks post tumour induction


title: M_GU159_CTC2_171025

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All bisulfite sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads that passed quality control were mapped to human reference genome (version: hg19) or mouse reference genome (version: mm9) using bismark (version: 0.7.6) in single-end alignment mode.
Assembly: hg19 (human); mm9 (mouse)
Supplementary files format and content: bigWig (1 if a methylated CpG, 0 if an unmethylated CpG, no value otherwise)


title: Lin_PBS1

value: lineage positive cells


title: week 5 aERKO-DES1 seminal vesicles


title: week 5 WT-DES4 seminal vesicles

value: WT


title: P_Q5A_5_P1

value: mPFC

value: Sprague-Dawley

value: Male

value: Young Adult (200-250g)

value: Extended Access Cocaine Self Administration


title: week 5 WT-DES3 seminal vesicles

value: seminal vesicles

value: DES

value: week 5


title: P_Q5A_4_P1


title: P_Q5A_2_P1


title: sham-brain,  scRNAseq

description: BD Rhapsody

value: Brain

value: sham surgey


title: M-CTC1_GU169_170928

value: Single prostate CTCs

value: pass


title: Lung cells mCherry-negative (1)


title: Lung cells mCherry-positive (1)


title: P_WT_13_P1


title: M_GU114_180710_CTC4


title: week 5 WT-DES1 seminal vesicles


title: week 5 WT-DES2 seminal vesicles


title: UUO2

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v3.1.0 using default parameters to obtain the gene expression matrices
Assembly: mm10
Supplementary files format and content: mtx matrix files

source_name: UUO - Unilateral Ureteral Obstruction

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: Adult

tag: condition

value: Unilateral Ureteral Obstruction (UUO)

value: kidney


title: P_WT_11_P1

tag: Sex


title: week 5 WT-veh4 seminal vesicles

value: control


title: UUO1


title: UUO


title: P_WT_6_P1


title: week 5 WT-veh3 seminal vesicles

value: WT


title: P_WT_3_P1

value: mPFC


title: week 5 WT-veh1 seminal vesicles


title: N_Q5A_28_P2

source_name: NAc

value: NAc

value: Sprague-Dawley


title: week 5 WT-veh2 seminal vesicles


title: UIR1

source_name: UIR - Unilateral Ischemia-Reperfusion

value: Unilateral Ischemia-Reperfusion (UIR)


title: UIR


title: hSC_IL13_3_1

city: Henan

first: Wenhao

address: 开封

institute: Henan University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. SOAPnuke(Version v1.5.2)  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these
Supplementary files format and content: fpkm, tpm, read counts

source_name: Human schwann cell

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

extract_protocol:
Remove the upper medium and wash it twice with cold PBS, frozen on ice, and RNA was harvested using Trizol reagent.The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Shenzhen, China)

treatment_protocol: HSC were treated with IL-13(100 ng/ml) for 6h

value: Human schwann cell

value: IL-13 activated


title: AN2

source_name: AN - Additional Normal

value: Control


title: N_Q5A_22_P2

value: Male

value: Young Adult (200-250g)

value: Extended Access Cocaine Self Administration


title: hSC_IL13_2_1


title: N_Q5A_19_P2


title: SVGP12_TELO2OE_01

city: Taipei

first: Yi-Lin

last: Chiu

address: No.161, Minquan E. Road 6th Sec., Neihu dist.,

country: Taiwan

institute: National Defense Medical Center

hyb_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, AM1753) to generate amino-allyl antisense RNA(aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridization. Purified coupled aRNA was quantified using NanoDrop ND-1000; pass criteria for CyDye incorporation efficiency at > 15 dye molecular/1000nt.

scan_protocol: The scanner used for the OneArray® chip is the Agilent Microarray Scanner (G2505C). Two scans are performed with the scanner's XDR function using PMT 100% and 10% at 10um resolution. The GenePix™ 4 was then used to acquire the image data and obtain two primary data format gpr files. The signal strength of the two gpr data files was then converted using a control probe on the OneArray chip and combined into one gpr data file for subsequent data analysis.

data_processing: A GPR file is generated when a wafer is scanned with a wafer scanner and a wafer probe information file is loaded into the GenePix software to convert the image into the corresponding probe signal value file (GPR file). The data from the same sample are technically duplicated and corrected for median scaling, and the average of the duplicated data from the same probe is taken as the representative signal for that probe. The data were normalized using Rosetta Resolver® System (Rosetta Biosoftware). The value in the normalized data of the data analysis file is the value of this calculation

source_name: SVGP12 cell line

label_protocol: Add the sample to the fluorescent calibration reaction in the ratio recommended by kit instruction, followed by complete dry drying by vacuum drying. Add RNAse free H2O and Cy5-NHS to each tube and mix well. After preparation, the reaction was completely mixed and centrifuged for 30 min at room temperature and protected from light to complete the calibration reaction.  Add 350 ul of RNA binding buffer to the finished sample in order and mix well. Add the above mixture to the RNA binding column, centrifuge at 10,000g for 10 sec and discard the liquid from the bottom of the centrifuge tube. Repeat the above procedure, add the liquid underneath the centrifuge tube to the RNA binding column and centrifuge for 10,000g for 10 sec. Discard the liquid under the centrifuge tube. Add 500 ul wash buffer 2 to the RNA binding column and centrifuge for 10,000g for 10 sec. Repeat the above steps once, add 500 ul wash buffer 2 to the RNA binding column, centrifuge at 10,000g for 10 sec and discard the liquid under the centrifuge tube.  Place the column in the centrifuge and centrifuge at 10,000g for 1 min.  Transfer the RNA binding column to a new collection tube. Add 50 ul of preheated Nuclease-free water at 55°C to the RNA binding column and leave at 55°C for 2 minutes, centrifuge at 10,000g for 2 minutes. Store at -20°C for further use.

growth_protocol: NHA (normal human astrocyte) cells were maintained in 4.5g/mL glucose Dulbecco’s modified Eagle’s medium (DMEM; Corning, NY, USA) containing 1% N-2 Supplement (Thermo Fisher Scientific, MA, USA). SVGp12 (simian virus 40-immortalized human fetal astrocyte) cells were cultured in Eagle’s Minimum Essential media (Thermo Fisher Scientific). GBM8401 (glio-blastoma multiforme) cells were cultured in 4.5g/mL glucose DMEM. All culture media were supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and penicil-lin-streptomycin (Thermo Fisher Scientific). The cells were incubated at 37°C under 5% CO2 and 95% air.

extract_protocol: Parental, TELO2-overexpressed, or siRNA-interfered cell lines were pretreated, and total RNA was extracted using TRIzol RNA Isolation Reagent according to the manufacturer's instruc-tions. The obtained total RNA was sent to Phalanx Biotech Group (Hsinchu, Taiwan) for gene expression profiling service using HOA OneArray method and HmiOA v5. The amount and pu-rity of RNA were assessed by NanoDrop ND-1000 (ThermoFisher Scientific Inc., MA, USA), and the passing criteria were determined to be A260/A280 ≥ 1.8 and A260/A230 ≥ 1.5, indicating ac-ceptable purity of RNA. RNA integrity values (RIN) were determined using an Agilent RNA 6000 Nano detector (Agilent Technologies, Waldbronn, Germany), and the qualifying criterion for RIN values was determined to be ≥6, indicating acceptable RNA integrity. Data analysis was processed by the Rosetta Resolver® system (Rosetta Biosoftware).

treatment_protocol: TELO2 siRNA and siScramble were purchased from Dharmacon (CO, USA). The full-length PCR fragment of human TELO2 was amplified, cut with EcoRI/XhoI, and cloned into the pSG5.HA expression vector. pSG5.HA-TELO2 fusion expression clones were successfully ob-tained. Cells were seeded and incubated at 37 °C under 5% CO2 for 24 hr. On the following day, the transfection of cells was performed using DharmaFECT 1 transfection reagent (Dharmacon) in accordance with the manufacturer's instructions, with either 25 nM siTELO2 or siScramble used for knockdown or 0.5 µg pSG5.HA-TELO2 or empty vector for overexpression.


title: N_Q5A_18_P2


title: hSC_IL13_1_1


title: AN1


title: N_WT_23_P2


title: UIR2


title: hSC_Control_3_1

value: Vehicle


title: N_WT_21_P2


title: N2

source_name: N - Normal


title: N1


title: hSC_Control_1_1


title: N_WT_20_P2


title: SVGP12_TELO2OE_02


title: NHA_TELO2OE_01

source_name: NHA cell line


title: Ctrl

source_name: Ctrl - Control


title: N_Q5A_7_P1


title: SVGP12_Parental_01

value: Parental


title: TP, IgG

city: Birmingham

first: Ryan

last: Miller

state: AL

address: 1824 Sixth Ave S

department: Pathology

institute: UAB

data_processing:
Base calls were performed using bcl2fastq2 for NextSeq output
ChIP-seq reads were trimmed from 3' end to remove Illumina adapters using CutAdapt
ChIP-seq reads were aligned to the UCSC hg38 genome using Bwa-mem2. Only uniquely mapping reads were retained.
PCR duplicates were removed using Picard MarkDuplicates
Spike-in normalized BigWig files were produced using deepTools bamCoverage with a scaling factor derived by dividing E. coli read counts by total read counts and normalizing to the smallest number for each CUT&RUN mark
Alignment files were converted to BEDPE format using bedtools bamtobed and extended to the full fragment length. Scaled bedgraphs were generated using bedtools genomecoverage and the E. coli spike in normalization factor. Peaks were called with SEACR in stringent mode using these bedgraphs as input. Peaks were merged and reported in BED file format.
Assembly: hg38
Supplementary files format and content: BigWig

source_name: TP iDMG

growth_protocol: DMEM/F12, 1xB27, heparin, EGF, bFGF grown on Matrigel or Cultrex basement membrane

extract_protocol:
Adherent cells were detached with Accutase and processed using the EpiCypher CUTANA CUT&RUN kit according to manufacturer instructions. 0.5 ng E. coli spike-in DNA was added for normalization.
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs). Libraries were size selected using Ampure XP bead from Beckman Coulter to retain fragments >150 bp. Libraries were amplified using 14 cycles on the thermocycler and validated using the Agilent High Sensitivity D1000 Tapestation Kit. All libraries were pooled and sequenced on a 150 cycle Mid Output v2.5 Illumina kit.

tag: cell line

value: TP iDMG

value: iPSC-derived high grade glioma model tumor cells

tag: cut&run antibody

value: IgG (EpiCypher, 13-0042)


title: THP, IgG

source_name: THP iDMG

value: THP iDMG


title: TP, H3K27me3, rep 2

value: H3K27me3 (Cell Signaling Technology, 9733)


title: cKO1_2

first: Jianlong

last: Wang

department: Department of Medicine

institute: Columbia University Irving Medical Center

data_processing:
Expression matrix was generated using Cell Ranger (V4.0.0)
Cells were filtered using Seurat (V4.0.5) to exclude cells with fewer than 200 genes expressed and >50% of total expression from mitochondrial genes.
To remove batch effect, the top 2000 highly variable genes were used for canonical correlation analysis implemented in Seurat (V4.0.5).
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx file format, feature, barcode, and gene expression matrix

source_name: Cells pooled from testis of two conditional knockout mice

growth_protocol: Cells were isloated from testis of adult mice

extract_protocol:
Testicular tissues were digested with collagenase type IV, and filtered with 70 μm (Falcon cat #352350) and 40 μm (Falcon cat #352340) cell strainer to get single cell suspension.
Libraries were prepared using 10x Genomics Chromium Single Cell 3' Reagent Kits v3.1 Chemistry with Dual Indexing.

treatment_protocol: Both wildtype and conditional mice were used

tag: tissue

value: testis

value: conditional Tex10 knockout


title: NHA_TELO2OE_02


title: SVGP12_Parental_02


title: WT2

source_name: Cells from testis of one wildtype mouse #2

value: wildtype


title: hSC_Control_2_1


title: NHA_Parental_02


title: GBM8401_siTELO2_02

source_name: GBM8401 cell line


title: NHA_Parental_01


title: HF-ESTR 4

city: Los Angeles

first: Mansoureh

last: Eghbali

state: CA

address: 10833 Le Conte Ave

institute: UCLA David Geffen School of Medicine

hyb_protocol: Labeled LMW RNA samples were hybridized to the MicroRNA microarrays according to conditions recommended in the Flash Tag RNA labeling Kit manual.

scan_protocol: The microarrays were scanned on an Axon GenePix 4000B scanner, and data was extracted from images using GenePix V4.1 software.

data_processing: Raw data was background-subtracted, Log2-untransformed, and normalized. Intensity for each oligo probe is based on averaging of triplicate spots. Normalized threshold is calculated based on: log2(5* stdev of negative controls) + trim mean (log2-transformed negative control probe signals). Normalized Factor is the averge value of 20% Trim MeanNormalized TPT95 is calculated based on 95th percentile of negative control probe signal

label: Oyster-550 fluorescent dye

source_name: cardiac left ventricle

label_protocol: The total RNA was DNase digested and low-molecular weight (LMW) RNA was isolated by ultrafiltration through YM-100 columns (Millipore) and subsequent purification using the RNeasy MinElute Clean-Up Kit (Qiagen). The LMW RNA samples were 3’-end labeled with Oyster-550 fluorescent dye using the Flash Tag RNA labeling Kit (Genisphere).

extract_protocol: For RNA extraction, hearts were powdered with a mortar and pestle on dry ice, suspended in Trizol (Invitrogen), and homogenized with a Polytron (Kinematica). Total RNA was isolated using Trizol according to manufacturer instructions. Quality control of the total RNA samples was assessed using gel electrophoresis. The samples sent to Ocean Ridge Biosciences were checked for quality by Bioanalyzer on Agilent 2100 Bioanalyzer RNA 6000 Pico Chip(s).

treatment_protocol: Healthy mice with an ejection fraction of ˜60% were randomly subjected to sham or transaortic constriction (TAC) surgery as described previously. HF was achieved 6 to 8 weeks after the TAC surgery with an ejection fraction of ˜35%. Once TAC mice reached HF, mice were randomly euthanized (HF group), or were assigned to treatment of estradiol (E2) via a subcutaneous 10-day continuous-release pellet of 0.03 mg E2/kg per day (Innovative Research of America, )

value: 3-4 months

value: Transverse aortic constriction + 10‐day continuous‐release pellet of 0.03 mg Estradiol/kg per day


title: WT1

source_name: Cells from testis of one wildtype mouse #1


title: GBM8401_siScramble_01

value: siScramble


title: GBM8401_siScramble_02


title: GBM8401_siTELO2_01


title: N_Q5A_2_P1

institute: Columbia University

value: NAc

value: Sprague-Dawley

tag: virus


title: TP, H3K27ac, rep 2

tag: cell type

value: H3K27ac (Cell Signaling Technology, 8173)


title: N_WT_14_P1

value: Male

value: Young Adult (200-250g)

tag: treatment

value: Extended Access Cocaine Self Administration


title: APC-FT-LM

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

description: APC-FT-MR

data_processing:
Demultiplexed FASTQ files (paired-end,Read 1: 30bp, Read 2:100bp) were generated using the CellRanger mkfastq command. The primary data analyses which included alignment, filtering, barcode counting and UMI quantification, quality control, clustering and statistical analysis were performed using CellRanger count command. Gene positions were annotated using Ensembl build 93 and filtered for biotype. Raw gene expression matrices were imported into R (version 4.0.2) and converted to a Seurat object using the Seurat R package (version 4.0.0). To remove dead cells and doublets, the total number of UMIs and genes and the percentage of UMIs derived from the mitochondrial genome for each cell were counted.  The upper and lower bounds were defined as the mean +/- two standard deviations for both the total UMIs and genes, respectively. Cells which had over 10% UMIs derived from mitochondrial genome were discarded. Finally, cells with total UMIs or genes outside of the upper and lower bounds were removed. For the remaining  cells, gene expression matrices were normalized to the total cellular read count and to mitochondrial read count. Highly variably genes (HVG) were selected from the normalized data using Seurat SCTransform function. The top 3000 HVGs were used as features for dimensionality reduction and clustering. The Seurat RunPCA and JackStraw functions were performed to calculate and to select significant (P-value <0.05) principal components (PCs), respectively.  The RunUMAP function was then applied to plot the selected significant PCs. The FindNeighbors constructed a Shared Nearest Neighbor (SNN) Graph, and FindClusters function with “resolution = 0.1” parameter was carried out to cluster cells into different groups.
Genome_build: mm10
Supplementary_files_format_and_content: hd5 file, data matrix from cell ranger exprot

source_name: Small intestine

growth_protocol: None, immune cells were directly isolated from mice.

extract_protocol:
Single cell libraries were prepared on a 10x Genomics Chromium controller (10x Genomics, Pleasanton, CA) using the version 3 reagent kit according to the manufacturer’s instructions. The reagent mixture was calculated for capturing 6000 cells. The libraries were sequenced on a NovaSeq (Illumina, San Diego, CA) by the NIEHS Epigenomics core laboratory. Raw read processing was carried out using the Cell Ranger Single-Cell Software Suite (version 6.0.1, 10X Genomics).
scRNA-seq

treatment_protocol: B6 donor mice were fed with a control diet or MR diet for a total of 3-4 weeks. Apc<min+/-> Fecal recipient mice were fed with an antibiotic cocktail (1 g/L Ampicillin and 0.575 g/L Enrofloxacin) in drinking water for 1 week, then inoculated daily by oral gavage for 7 days with 100 ul/mouse of fresh fecal solution prepared from donor C57BL/6J mice (1:1 dilution of feces with PBS). Apc<min+/-> mice were then maintained with sterile RO/DI water and chow diet during fecal transplantation and afterward and the small intestinal tissues were harvested for purification of small intesttinal CD45+ cells 3-4 weeks after the fecal transplantation.

value: total CD45+ immune cells from the small intestine

value: Small intestine

value: 2-3 month

tag: dignosis

value: intestinal tumors

tag: gender

value: male

value: Transplanted with feces from MR diet fed C57BL/6J mice daily for 1 week after depletion of own gut microbiota by antibiotics


title: N_WT_12_P1

address: 3227 Broadway


title: N_Q5A_3_P1


title: TP, H3K27ac, rep 1

value: TP iDMG

value: iPSC-derived high grade glioma model tumor cells


title: APC-FT-HM

description: APC-FT-CTRL

value: Transplanted with feces from control diet fed C57BL/6J mice daily for 1 week after depletion of own gut microbiota by antibiotics


title: HF-ESTR 3

value: 3-4 months

value: Transverse aortic constriction + 10‐day continuous‐release pellet of 0.03 mg Estradiol/kg per day


title: N_WT_8_P1

value: NAc


title: TP, H3K4me3, rep 2

value: H3K4me3 (EpiCypher, 13-0041)


title: TP, H3K4me3, rep1


title: TP, H3K27me3, rep 1

value: H3K27me3 (Cell Signaling Technology, 9733)


title: RPKM_4h-L-A-PH5_5_rep2

city: GwangJu

first: JongHee

last: Lee

address: kimchi ro86

country: South Korea

institute: World Institute of Kimchi

data_processing:
Illumina bcl2fastq software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends
Sequenced reads were mapped to Lactobacillus_plantarum_WCFS1 (GCF_000203855.3). whole genome by using bowtie v1.1.1 with parameter -I 0 –X 250 -m 1 --chunkmbs 500
The expression level of each cds region was calculated using the reads per kilobase per million mapped reads (RPKM) method.
Assembly: The sequence data for the reference genome was retrieved from the NCBI database (GCF_000203855.3, Lactobacillus plantarum WCFS1).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Lactiplantibacillus plantarum

source_name: bacterial cells

growth_protocol: Bacteria was cultivated in MRS, MRS media

extract_protocol:
Total RNA was extracted using RNeasy Mini kits. 1ug of total RNA was used for the construction of sequencing libraries.
Libraries for Illumina sequencing were made with the TruSeq RNA Library prep kit (Illumina, USA) following the manufacturer’s protocol.

treatment_protocol: The bacteria was incubated at 30℃ for 4h in MRS media pH 5.5 adjusted pH with HCl or lactic acid

value: bacterial cells

value: MRS pH 5.5 (with Lactic acid)


title: B6-HM

value: normal, tumor-free

value: Fed with a control diet containing 0.86% methionine for 3-4 weeks


title: HF-ESTR 2

value: Male


title: N_WT_17_P2

city: New York

source_name: NAc

value: Sprague-Dawley

value: Young Adult (200-250g)

value: Extended Access Cocaine Self Administration


title: RPKM_4h-L-A-PH5_5_rep1


title: HF 5

value: Transverse aortic constriction


title: HF-ESTR 1


title: THP, H3K27me3, rep 2

value: THP iDMG


title: HF-ESTR 5


title: HF 4


title: RPKM_4h-HC1-PH5_5_rep2

value: MRS pH 5.5 (with HCl)


title: THP, H3K27me3, rep 1

value: iPSC-derived high grade glioma model tumor cells


title: THP, H3K27ac, rep 2

value: H3K27ac (Cell Signaling Technology, 8173)


title: RPKM_4h-HC1-PH5_5_rep1


title: B6-LM

value: total CD45+ immune cells from the small intestine

value: Small intestine

value: 2-3 month

value: male

value: Fed with a MR diet containing 0.172% methionine for 3-4 weeks


title: THP, H3K27ac, rep 1


title: RPKM_4h-con_rep2

value: bacterial cells

value: MRS


title: HF 3

value: 3-4 months


title: THP, H3K4me3, rep 2

value: H3K4me3 (EpiCypher, 13-0041)


title: HF 2

value: Male


title: HF 1


title: Control 4

value: sham


title: RPKM_4h-con_rep1


title: THP, H3K4me3, rep1


title: Paraffin control

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: PC

data_processing:
[demultiplexing}  from raw data to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
[pair merging}  micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 3
[primer check and trimming}  micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
[quality check}  micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
[reads merging}  micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
[abundance table creation}  micca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
[taxonomic assignment (RDP)}  micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
[further analyses and figure production}  R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2022breast)
Supplementary files format and content: otutable.txt, taxa.txt, otus.fasta

organism: other sequences

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

tag: individual

value: not applicable

tag: disease state


title: Control 3


title: priB_Repliseq_WT_late_rep2

status: Public on Jun 13 2023

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description:
Repli-Seq
priB_Repliseq_WT_RT_5kb_loess.bw
priB_Repliseq_WT_RT_20kb_loess.bw
priB_Repliseq_WT_RT_5kb_loess.bedGraph
priB_Repliseq_WT_RT_20kb_loess.bedGraph
priB_Repliseq_WT_RT_domains.bed

data_processing:
library strategy: Repli-seq
All RepliSeq analysis was wrapped into the reproducible Nextflow workflow repliseq-nf available at https://github.com/t-neumann/repliseq-nf loosely following the steps previously described in Marchal et al., 2018:
Raw reads from  replicates of early (E) and late (L) fractions were trimmed with trim_galore v0.6.5 and aligned to the mouse mm9 reference sequence using bwa mem v0.7.17  and unmapped reads, secondary alignments and multimapping reads were filtered with samtools v1.9.
Replicates were merged using samtools and read duplicates were filtered using picardTools MarkDuplicates.
E/L log2 ratios were calculated in 5kb and 20kb windows using deeptools bamCompare v3.4.1.
Loess smoothing was performed with bedtools v2.29.2 and a custom R script using the preprocessCore package v1.46.0 with a span size of 300 kb and bigwig tracks were produced using kent_tools v377.
The correlation between replicates was assessed with deepTools multiBamSummary.
RT domains were called with hmm_bigwigs v1.3
Assembly: NCBI mm9
Supplementary files format and content: bigWig of loess smoothed E/L log2 ratios.
Supplementary files format and content: bed file of hmm assigned RT domains

source_name: priB

growth_protocol: CH12 cells cultured in complete RPMI medium wit IL4/CD40/TGF beta stimulation.

extract_protocol:
BrdU labled DNA was extracted via phenol, phenol-chlorophorm extraction and subjected to immunoprecipitation
Libraries were prepared following standard Illumina protocols
Repli-seq was performed as previously described (Marchal C, 2018). In brief,  Cells were fixed and incubated with a mix of RNase A  and propidium iodide  . For each sample, three fractions were sorted: G1 phase, early S phase and late S phase cells, 50 000 cells per fraction Sorted cells were lysed . Extracted DNA was sonicated for 9 min in a Diagenode Bioruptor resulting in 100-500 bp DNA fragments . Sonicated DNA was subjected to end-repair and adapter ligation using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB) following the NEB protocol. Adapter-ligated DNA was incubated with 25 mg/ml of anti-BrdU antibody (BD Pharmingen) for 4h with rotation followed by incubation with 40 μg of anti-mouse IgG antibody (Sigma) for 1h with rotation (light protected) which was followed by DNA purification

treatment_protocol: Two million asynchronously dividing cells were seeded and incubated with 100mM BrdU for 2h in a light protected environment to maintain BrdU stability.

value: primary B cells

tag: sample group


title: priB_Repliseq_Rif1KO_Het_late_rep2

description:
Repli-Seq
priB_Repliseq_Rif1Het_RT_5kb_loess.bw
priB_Repliseq_Rif1Het_RT_20kb_loess.bw
priB_Repliseq_Rif1Het_RT_5kb_loess.bedGraph
priB_Repliseq_Rif1Het_RT_20kb_loess.bedGraph


title: priB_Repliseq_Rif1KO_Het_late_rep4


title: priB_Repliseq_Rif1KO_Het_late_rep1


title: shCIRC-RKO-3

city: Jinan

first: Ya'nan

last: Zhen

state: Shandong

address: No.38 Wuyinshan Road

department: Department of Gastrointestinal Surgery

institute: The Third Affiliated Hospital of Shandong First Medical University

description:
E10162-3
KD-3

hyb_protocol: GeneChip Hybridization Oven 645 and GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data was analyzed using GeneChip GCOS 1.4 software (Affymetrix, USA)

source_name: shCIRC group

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: The cells were grown in dulbecco's modified eagle medium (DMEM) (Gibco, Waltham, MA, USA) with 10% fetal bovine serum (FBS) (Gibco, Waltham, MA, USA), 100 U/ml penicillin G, and 100 μg/ml streptomycin (Sigma, Shanghai, China) at 37°C in a humid incubator with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Short hairpin RNA targets for hsa_circ_0064559 (shCIRC) and empty vectors (shEV) were synthesized by GeneChem Co.Ltd. (Shanghai, China). The sequence of shCIRC (short hairpin circular RNA) was 5'-TTTATTATAGCCTGCCACAGC-3' and the nonsense shRNA was 5'-TTCTCCGAACGTGTCACGT-3'. Lipofectamine 2000 (Invitrogen, Shanghai, China) was used for transfection in accordance with the manufacturer's instructions.

value: RKO

value: shCIRC


title: Control 1

tag: strain


title: Control 2


title: shCIRC-RKO-1

description:
E10162-1
KD-1

tag: genotype


title: priB_Repliseq_WT_early_rep2


title: priB_Repliseq_WT_late_rep1


title: shCIRC-RKO-2

description:
E10162-2
KD-2


title: shEV1-RKO-3

description:
E10161-3
NC-3

source_name: shEV group

value: shEV


title: priB_Repliseq_WT_early_rep1


title: shEV1-RKO-2

description:
E10161-2
NC-2


title: shEV1-RKO-1

description:
E10161-1
NC-1


title: priB_Repliseq_Rif1KO_Het_early_rep2


title: priB_Repliseq_Rif1KO_Het_early_rep1


title: priB_Repliseq_Rif1KO_double_late_rep4

description:
Repli-Seq
priB_Repliseq_Rif1KO_RT_5kb_loess.bw
priB_Repliseq_Rif1KO_RT_20kb_loess.bw
priB_Repliseq_Rif1KO_RT_5kb_loess.bedGraph
priB_Repliseq_Rif1KO_RT_20kb_loess.bedGraph


title: priB_Repliseq_Rif1KO_double_late_rep1


title: priB_Repliseq_Rif1KO_double_early_rep3


title: priB_Repliseq_Rif1KO_double_early_rep4


title: priB_Repliseq_Rif1KO_double_late_rep2


title: priB_Repliseq_Rif1KO_Het_late_rep3


title: CH12_Repliseq_shMcm6_late_rep1

description:
Repli-Seq
CH12_Repliseq_shMcm6_RT_5kb_loess.bw
CH12_Repliseq_shMcm6_RT_20kb_loess.bw
CH12_Repliseq_shMcm6_RT_5kb_loess.bedGraph
CH12_Repliseq_shMcm6_RT_20kb_loess.bedGraph


title: CH12_Repliseq_shMcm6_late_rep2


title: priB_Repliseq_Rif1KO_double_early_rep1


title: priB_Repliseq_Rif1KO_Het_early_rep4


title: CH12_Repliseq_shMcm6_early_rep2


title: CH12_Repliseq_shMcm6_early_rep1


title: priB_Repliseq_Rif1KO_Het_early_rep3


title: CH12_Repliseq_shLacZ_late_rep1

description:
Repli-Seq
CH12_Repliseq_shLacZ_RT_5kb_loess.bw
CH12_Repliseq_shLacZ_RT_20kb_loess.bw
CH12_Repliseq_shLacZ_RT_5kb_loess.bedGraph
CH12_Repliseq_shLacZ_RT_20kb_loess.bedGraph
CH12_Repliseq_shLacZ_RT_domains.bed


title: CH12_Repliseq_Rif1KO_shMcm6_late_rep1

description:
Repli-Seq
CH12_Repliseq_Rif1KO_shMcm6_RT_5kb_loess.bw
CH12_Repliseq_Rif1KO_shMcm6_RT_20kb_loess.bw
CH12_Repliseq_Rif1KO_shMcm6_RT_5kb_loess.bedGraph
CH12_Repliseq_Rif1KO_shMcm6_RT_20kb_loess.bedGraph


title: CH12_Repliseq_shLacZ_early_rep1


title: CH12_Repliseq_Rif1KO_shMcm6_early_rep2


title: CH12_Repliseq_Rif1KO_shMcm6_late_rep2


title: CH12_Repliseq_shLacZ_early_rep2


title: CH12_Repliseq_Rif1KO_shLacZ_early_rep2

description:
Repli-Seq
CH12_Repliseq_Rif1KO_shLacZ_RT_5kb_loess.bw
CH12_Repliseq_Rif1KO_shLacZ_RT_20kb_loess.bw
CH12_Repliseq_Rif1KO_shLacZ_RT_5kb_loess.bedGraph
CH12_Repliseq_Rif1KO_shLacZ_RT_20kb_loess.bedGraph


title: CH12_Repliseq_Rif1KO_shLacZ_late_rep1


title: CH12_Repliseq_Rif1KO_shLacZ_late_rep2


title: WT cells, 48h activated in vitro; IL-12 + BRM014, Input

city: San Diego

first: Bryan

last: McDonald

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Single-end 75-bp reads were aligned to the M. musculus mm10 genome using STAR (Dobin et al., 2013) with default parameters.
ChIP-seq peaks were called using findPeaks within HOMER using -style factor and an -i input control. Differential ChIP peaks were called using getDiffExpression.pl with fold change ≥ 1.5 or ≤ 1.5, Poisson P value < 0.0001. ChIP-seq peaks were annotated by mapping to the nearest transcription start site (TSS) using the annotatePeaks.pl program.
Metaplots were generated using annotatePeaks.pl with parameters -size 2000 and -hist 10. Heatmaps showing overlap of binding sites were generated using mergePeaks in HOMER with flag -matrix, which outputs hypergeometric P values of overlap and the observed/expected ratio of overlap. Peaks sets were annotated with HOMER, and visualizations were created using deepTools.
bigWig files were generated using makeUCSCfile program in HOMER using -style chipseq and an -i input control
Assembly: mm10
Supplementary files format and content: bigWig (except for Input sample)

source_name: WT

extract_protocol:
Cells were cross linked in 3 mM disuccinimidyl glutarate for 30 min then in 1% formaldehyde for 10 min at room temperature. After quenching with 125 mM glycine, the cells were washed in 1× PBS, pelleted, flash frozen in liquid nitrogen, and stored at 80 °C. Cell pellets were thawed on ice and incubated in lysis solution (50 mM Hepes KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min. The isolated nuclei were washed (10 mM TrisHCl pH 8, 1 mM EDTA, 0.5 mM EGTA, and 200 mM NaCl) and sheared in (0.1% SDS, 1 mM EDTA, and 10 mM TrisHCl pH 8) with the Covaris E229 sonicator for 10 min. After centrifugation, chromatin was immunoprecipitated overnight at 4 °C with 1:50 T-bet/TBX21 (Cell Signaling Technology, mAb #97135S). The next day, the antibody-bound DNA was incubated with Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM Hepes KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS), washed, and treated with Proteinase K and RNase A and reverse cross linked.
Purified ChIP DNA was used for library generation (NEBNext Ultra II DNA Library Prep Kit for Illumina) according to manufacturer’s instructions

value: WT

value: CD8+ T cell

tag: chip antibody


title: CH12_Repliseq_Rif1KO_shLacZ_early_rep1


title: WT cells, 48h activated in vitro; IL-12 + ACBI1, Input

value: IL-12 + ACBI1


title: WT cells, 48h activated in vitro; Untreated, Input

value: Untreated


title: priB_Repliseq_Rif1KO_double_late_rep3


title: WT cells, 48h activated in vitro; IL-12, Input


title: priB_Repliseq_Rif1KO_double_early_rep2


title: WT cells, 48h activated in vitro; IL-12 + BRM014, ChIP

value: T-bet


title: WT cells, 48h activated in vitro; Untreated, ChIP


title: CH12_Repliseq_shLacZ_late_rep2


title: CH12_Repliseq_Rif1KO_shMcm6_early_rep1