title: DG038: 4WK Control Rep4

city: New York

first: GUOMEI

last: TANG

state: New York

department: Neurology

institute: Columbia University

data_processing:
Illumina software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tiphat (2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: upper half of somatosensory and parietal cortex

extract_protocol:
upper half cortex of somatosensory and parietal cortice were islolated from coronal brain sections, flash frozen on dry ice. RNA was extracted harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bl6/129S mixed background

value: cortex

tag: age

value: postnatal 4Weeks

value: mGFAPCre+ littermate control


title: DG036: 4WK Control Rep2

status: Public on Aug 31 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: genotype


title: Sample_PRO472A235_S323_L004 Naive enteric glia, rep 2

city: London

first: Vassilis

last: Pachnis

address: 1 Midland Rd

department: Development and Homeostasis of the Nervous System Laboratory

country: United Kingdom

institute: The Francis Crick Institute

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A235_S323_L004

data_processing:
Nextera adapter sequences were removed from reads using Cutadapt (version 1.18).
Reads were aligned to the Ensembl GRCm38 genome using STAR (version 2.5.2a).
Gene counts were obtained using the featureCounts program (from Subread version 1.6.4).
Quality control, normalisation and downstream analysis were performed using the software Seurat (version 3.1.1).
Cells expressing more than 2000 genes and less than 10 percent mitochondrial reads were retained for further analysis. Contaminating macrophages (n=7) were removed based on the expression of Itgam (> 10 counts), and contaminating neurons (n=95) were removed based on expression of Elavl4 (> 30 counts). Genes detected in fewer than 3 cells or with total counts < 10 were omitted from further analysis. The dimension of the final data matrix was 18643 genes by 217 cells (134 cells from naïve mice and 83 from H. poly infected mice).
Counts were normalized to ten thousand counts per cell, natural-log transformed using log1p, and scaled.
Highly variable genes were identified using Seurat, and the top 1000 used for dimensionality reduction and clustering. The first 4 principal components were selected as input for dimensionality reduction using the UMAP algorithm and Louvain clustering at a resolution of 0.1.
Genome_build: GrCM38
Supplementary_files_format_and_content: Count matrices in .tsv format. Seurat object saved as an .rds file.

source_name: Enteric glia

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
For isolation of EGCs, the longitudinal smooth muscle layer and associated myenteric plexus were peeled off the wall of the smal intestineand subjected to enzymatic digestion to prepare a single-cell suspension. Single-cell suspensions were subjected to fluorescence activated cell sorting and live EGCs were isolated based on tdT expression DAPI exclusion. 200-1000 cells were loaded into a Fluidigm C1 Single Cell Auto Prep IFC for mRNA-seq for use with the Fluidigm C1 system. After the cell load program cells were imagined using the JuliStage to identify wells that contain 1 single cell.
The SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System, IFCs was used to reverse transcribe and amplify cDNA. cDNA was quantified using the Glomax (Promega). Libraries were prepared from cDNA generated from single cells using the Nextera XT kit from Illumina. Final libraries were pooled and sequenced on the HiSeq 4000.

treatment_protocol: All mice were injected with tamoxifen 24 hours prior single cell isolation and some mice were infected with H. poly 7 days prior single cell isolation.

tag: Stage

value: Adult

tag: disease state

value: Naive


title: DG035: 4WK Control Rep1


title: EOL-1_MS9715N_replicate_1

city: DURHAM

first: Chenxi

last: Xu

state: North Carolina

address: 3 Genome Court

department: Department of Pharmacology and Cancer Biology

institute: Duke university

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed.
Raw read counts were used for differential gene expression analysis by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: matrix of RNA-seq read counts and Deseq output files

organism: Homo sapiens

source_name: EOL-1 cells

growth_protocol: EOL-1 cells were grown in the RPMI-1640 base medium plus 10% of FBS and 1% of antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit. 1 ug of total RNA for the construction of the pooled sequencing libraries.
RNA was extracted with the Qiagen RNeasy Mini Kit. 1 μg of total RNA was used for construction of the multiplexed sequencing libraries.

treatment_protocol: For compound treatment studies, EOL-1 cells were treated with 2.5 µM of either DMSO, BI-9321, MS9715 or MS9715N for 4 days and collected. For NSD3 knockout (KO), EOL-1 cell was first transduced with a doxycycline (dox)-inducible Cas9 (iCas9) and the verified iCas9-expressing EOL-1 cells then stably transduced with either empty vector (sgEV) or that with an NSD3-targeting sgRNA, followed by a four-day induction of iCas9 before cell were collected for RNA preparation.

tag: cell line

value: EOL-1 cells

tag: agent


title: Sample_PRO472A234_S322_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A234_S322_L004


title: EOL-1_BI_9321_replicate_2


title: DG033: 4WK Tsc1CKO Rep4


title: DG032: 4WK Tsc1CKO Rep3


title: Sample_PRO472A233_S321_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A233_S321_L004


title: EOL-1_BI_9321_replicate_1


title: Sample_PRO472A232_S320_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A232_S320_L004


title: DG030: 4WK Tsc1CKO Rep1


title: DG007: 15WK Control Rep2

value: postnatal 15Weeks


title: DG008: 15WK Control Rep3


title: EOL-1_MS9715_replicate_2


title: DG031: 4WK Tsc1CKO Rep2


title: DG039: 4WK Control Rep5


title: Sample_PRO472A231_S319_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A231_S319_L004


title: Sample_PRO472A230_S318_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A230_S318_L004


title: EOL-1_DMSO_replicate_2

value: DMSO


title: EOL-1_MS9715_replicate_1


title: DG004: 15WK Tsc1CKO Rep3


title: Sample_PRO472A236_S324_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A236_S324_L004


title: DG003: 15WK Tsc1CKO Rep2


title: Sample_PRO472A229_S317_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A229_S317_L004


title: DG005: 15WK Tsc1CKO Rep4


title: EOL-1_DMSO_replicate_1


title: Sample_PRO472A228_S316_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A228_S316_L004


title: DG001: 15WK Tsc1CKO Rep1


title: DG006: 15WK Control Rep1


title: Sample_PRO472A227_S315_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A227_S315_L004


title: Sample_PRO472A226_S314_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A226_S314_L004


title: Sample_PRO472A225_S313_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A225_S313_L004


title: Sample_PRO472A224_S312_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A224_S312_L004


title: HC3: Healthy Control

city: Florence

first: Paola

last: Chiarugi

state: Florence

address: Viale Morgagni 50

department: Department of Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

data_processing:
Reads were trimmed for low quality bases.  then mapped to GRCh38 whole genome using STAR v2.7.3a with default parameters
The feature count was perfomed by HTSeq (v0.11.1) with parameters --max-reads-in-buffer 80000000 -m intersection-nonempty -t gene --idattr gene_id --additional-attr gene_name -r pos -s reverse
The number of reads falling in the genes were normalized by the size of the library
Detection  of differentially expressed genes by DEseq2 (v1,26,0)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cord Blood

extract_protocol:
CD34 cells were immune magnetically isolated from Cord Blood and Bone Marrow of Calreticulin-mutated Myeloproliferative Neoplasms patients. Total RNA was extracted using Trizol Reagents. NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® was used with 1 ug of RNA for the construction od sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Healthy

tag: cell type

value: Cord Blood


title: NANOS2 KO 50 dpi rep 2

city: Pullman

first: Michael

last: Griswold

state: WA

address: Biotechnology Life Sciences

department: School of Molecular Biosciences; Center for Reproductive Biology

institute: Washington State University

description:
Sertoli cells from germ cell-deficient environment at 50 dpi
NANOS2KO_FPKM; NANOS2KO_readcounts

data_processing:
Bowtie/TopHat/Cufflinks incorporated into Ion Torrent Suite v.5.0.5.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM .xls files and raw gene counts for each sample

source_name: Testis

growth_protocol: RFPxAMH-Cre Sertoli cells were isolated from fresh testis via cell sorting of RFP-positive cells.  NANOS2 KO whole testis was harvested from animals just after euthanization.

extract_protocol:
Sorted germ cells were frozen in Trizol and total RNA was recovered using Trizol manufacturer protocol.  Whole testes were snap-frozen on dry ice then recovered using Trizol manufacturer protocol.  polyA mRNA was enriched using NEBNext poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs) according to the manufacturer's instructions.
10 ng of mRNA was used to make barcoded libraries with the Ion Total RNA-seq Kit V2 (Life Technologies).  Libraries were pooled to 75 pM before loading on Ion P1 semiconductorr chips using and Ion Chef and sequenced on and Ion Proton sequencer.

treatment_protocol: Mice were treated with WIN 18,446 for 7 days, given an RA injection the following day, then aged for 42-50 dpi.

value: CD1 background

value: Sertoli

value: NANOS2 KO

tag: treatment

value: WIN 18,446 synchrony + RA + 50 dpi


title: Sample_PRO472A223_S311_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A223_S311_L004


title: HC2: Healthy Control


title: HC1: Healthy Control


title: NANOS2 KO 50 dpi rep 1


title: Sample_PRO472A222_S310_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A222_S310_L004


title: DG037: 4WK Control Rep3


title: NANOS2 KO 49 dpi rep 1

description:
Sertoli cells from germ cell-deficient environment at 49 dpi
NANOS2KO_FPKM; NANOS2KO_readcounts

value: WIN 18,446 synchrony + RA + 49 dpi


title: NANOS2 KO 49 dpi rep 2


title: NANOS2 KO 48 dpi rep 2

description:
Sertoli cells from germ cell-deficient environment at 48 dpi
NANOS2KO_FPKM; NANOS2KO_readcounts

value: WIN 18,446 synchrony + RA + 48 dpi


title: Sample_PRO472A221_S309_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A221_S309_L004


title: NANOS2 KO 48 dpi rep 1


title: NANOS2 KO 47 dpi rep 2

description:
Sertoli cells from germ cell-deficient environment at 47 dpi
NANOS2KO_FPKM; NANOS2KO_readcounts

value: WIN 18,446 synchrony + RA + 47 dpi


title: Sample_PRO472A220_S308_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A220_S308_L004


title: NANOS2 KO 47 dpi rep 1


title: Sample_PRO472A219_S307_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A219_S307_L004


title: Leaf sheath_long-day, 2 h_rep2

type: RNA

city: Tsukuba

first: Masao

last: Iwamoto

state: Ibaraki

address: 3-1-3 Kannondai

department: Division of Crop Genome Editing

country: Japan

institute: Institute of Agrobiological Sciences, NARO

hyb_protocol: Agilent protocol G4140-90050. 825 ng of each Cy5- and Cy3-labeled cRNAs were used for hybridization.

scan_protocol: Agilent Technologies Scanner G2505C US90500268

data_processing: The scanned images were analyzed with feature extraction software (version 10.5.1.1, Agilent) to extract signal intensities.

organism: Oryza sativa

label_protocol: 400 ng RNAs were labeled by Low RNA Input Linear Amplification/Labeling Kit (Agilent).

growth_protocol: Plants were grown in soil and maintained in a growth chamber at 28ºC under long day condition (16 h light and 8 h dark).

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (Quigen), according to the manufacturer's instructions.

tag: cultivar

value: Nipponbare

tag: genotype/variation

value: RDD2 overexpressing plants (RDD2-OX)

value: leaf sheath

value: 2 weeks

value: wild type


title: Leaf blade_long-day, 2 h_rep1

value: leaf blade


title: NANOS2 KO 46 dpi rep 1

description:
Sertoli cells from germ cell-deficient environment at 46 dpi
NANOS2KO_FPKM; NANOS2KO_readcounts

value: WIN 18,446 synchrony + RA + 46 dpi


title: NANOS2 KO 46 dpi rep 2


title: Sample_PRO472A218_S306_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A218_S306_L004

value: Adult

value: Naive


title: Leaf sheath_long-day, 2 h_rep1


title: NANOS2 KO 45 dpi rep 2

description:
Sertoli cells from germ cell-deficient environment at 45 dpi
NANOS2KO_FPKM; NANOS2KO_readcounts

value: WIN 18,446 synchrony + RA + 45 dpi


title: Leaf sheath_long-day, 2 h_rep3


title: Sample_PRO472A217_S305_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A217_S305_L004


title: Leaf blade_long-day, 2 h_rep2


title: DC BM3

city: Amsterdam

first: Martijn

last: Nolte

state: Noord-Holland

address: Plesmanlaan 125

department: Molecular Hematology

country: Netherlands

institute: Sanquin Bloedvoorziening

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR (v2.5.3a). Reads that aligned to (exonic parts of) genes annotated by Ensembl (release 81) were quantified using featureCounts (v1.5.2).
Low abundant genes were removed for further analysis, genes with more than 1 CPM (counts per million) in at least 3 samples were kept.  Differentially expressed genes between BM cDC2s and spleen cDC2s were assessed with limma trend, using a paired design.
Genes with > 1.5 fold change difference and FDR-adjusted p-values < 0.05 were considered significantly differentially expressed. Pair-wise Pearson’s correlation coefficients between the samples were calculated based on log2 CPM values, and grouped by hierarchical clustering.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
Isolation of DCs from spleen or bone marrow (BM) from 8-12 wk old C57BL6 mice; for BM the femurs, tibia, pelvis, humerus and sternum was used. For each sort the DCs were enriched with CD11c microbeads from 2 mice per sample. These DC-enriched samples were sorted for CD11c+MHCII+CD11bhighCD24low cDC2
RNA was extracted with RNeasy Micro kit (Qiagen) according to the manufacturers protocol. RNA quality check, polyA RNA selection and sequencing were performed at GenomeScan BV (Leiden, The Netherlands). RNA quality and quantity was determined by a Bioanalyzer Picochip (Agilent).
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB #E7420S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Per sample, 25 ng RNA was used for library preparation and single-end, 75 nucleotide fragments were analyzed by Illumina NextSeq 500. A concentration of 1.6 pM of DNA was used.

value: Bone marrow

value: Purified DCs

value: 8-12 wk old


title: DC Spleen 1

source_name: Spleen

value: Spleen


title: DC BM2


title: DC Spleen 3


title: DC BM1


title: NANOS2 KO 45 dpi rep 1

value: CD1 background

value: Sertoli

value: NANOS2 KO


title: Sample_PRO472A216_S304_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A216_S304_L004


title: Leaf blade_long-day, 2 h_rep3

value: Nipponbare


title: DC Spleen 2


title: NANOS2 KO 44 dpi rep 2

description:
Sertoli cells from germ cell-deficient environment at 44 dpi
NANOS2KO_FPKM; NANOS2KO_readcounts

value: WIN 18,446 synchrony + RA + 44 dpi


title: Sample_PRO472A215_S303_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A215_S303_L004


title: N324545

city: Nanjing

first: Gaochao

last: Dong

address: Baiziting 42, Nanjing, P.R. China

department: Jiangsu Key Laboratory of Molecular and Translational Cancer Research

country: China

institute: The Affiliated Cancer Hospital of Nanjing Medical University,

description: Patient3 adjacent normal samples

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

source_name: Patient3 adjacent normal samples, T3N1M0

label_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated from cells and tissues using Trizol reagent (Life Technolohies, Scotland, UK) according to the manufacturer’s protocol.

treatment_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

tag: tissues

value: adjacent normal

tag: gender

value: Female


title: CD8_memory_spleen

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: Memory CD8 T cell

extract_protocol:
10x Genomics
Single-cell RNA sequencing

treatment_protocol: Six- to eight-week-old female C57BL/6 were purchased from Charles River. Mice were infected with 2 × 105 PFU/mouse LCMV-ARM by intraperitoneal injection to establish acute infection. Cells were stained with GP33 tetramer (1:100, provided by the NIH tetramer core facility) and the following antibodies against cell surface antigens for 30 min at 4 °C: anti-CD8a (clone 53-6.7, 1:200), anti-CD44 (clone 1 M7, 1:200), an-ti-CD62L (clone MEL-14, 1:200).

value: C57BL/6 mice

tag: infection

value: LCMV-Armstrong

value: spleen


title: NANOS2 KO 44 dpi rep 1


title: CD8-TRM-30

data_processing:
Reads were aligned to mouse reference genome mm10 using Star.
Genome_build: mm10
Supplementary_files_format_and_content: samples_counts.csv

extract_protocol:
Bulk RNA sequencing was performed according to a published Smart-seq2 protocol with minor modification. 1000 cells were used for each replicate. https://doi.org/10.1038/nprot.2014.006
Bulk RNA sequencing was performed according to a published Smart-seq2 protocol with minor modification. 1000 cells were used for each replicate. https://doi.org/10.1038/nprot.2014.006

treatment_protocol: Six- to eight-week-old female C57BL/6 were purchased from Charles River. Mice were infected with 2 × 105 PFU/mouse LCMV-ARM by intraperitoneal injection to establish acute infection. Cells were stained with GP33 tetramer (1:100, provided by the NIH tetramer core facility) and the following antibodies against cell surface antigens for 30 min at 4 °C: anti-CD8a (clone 53-6.7, 1:200), anti-CD44 (clone 1 M7, 1:200), an-ti-CD62L (clone MEL-14, 1:200). TEM and TCM cells are sorted from spleen, seperated by CD62L. TRM  cells are sorted from intraepithelial lymphocytes from small intestine.

value: small intestine


title: L322835

description: Patient1 metastatic lymph node

source_name: Patient1 metastatic lymph node, T2N1M0

value: metastatic lymph node

value: Male


title: L323075

description: Patient2 metastatic lymph node

source_name: Patient2 metastatic lymph node, T3N1M0


title: Sample_PRO472A214_S302_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A214_S302_L004

value: Adult

value: Naive


title: NANOS2 KO 43 dpi rep 2

description:
Sertoli cells from germ cell-deficient environment at 43 dpi
NANOS2KO_FPKM; NANOS2KO_readcounts

value: WIN 18,446 synchrony + RA + 43 dpi


title: CD8-TRM-3


title: L324545

description: Patient3 metastatic lymph node

source_name: Patient3 metastatic lymph node, T3N1M0


title: CD8_memory_IELs

value: IELs


title: N323075

description: Patient2 adjacent normal samples

source_name: Patient2 adjacent normal samples, T3N1M0


title: Sample_PRO472A212_S300_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A212_S300_L004


title: Smad4a MZ3 50% epiboly

first: Caroline

middle: S

last: Hill

address: 1 Midland Road

department: Developmental Signalling

institute: Francis Crick Institute

description:
Zebrafish
Bulk-RNAseq
mRNA

data_processing:
Basecalling with bcl2fastq v2.20.0.
Alignment and quantification with BABS-RNASeq (https://github.com/crickbabs/BABS-RNASeq) and default parameters.
Genome_build: GRCz11 Ensembl release-95
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited quantified expression from RSEM.

organism: Danio rerio

source_name: Zebrafish embryos

growth_protocol: Mutant and WT zebrafish embryos were grown in embryo media, once they reached 50% epiboly embryos were pooled for RNA extraction.

extract_protocol: RNA was isolated via TRIzol/Chloroform extraction with a DNase treatment step.

value: Tubingen (TU)

value: MZ smad4a mutant

value: Whole embryo (n=25)


title: CD8-TRM-0


title: CD8-TEM-10

value: Spleen


title: NANOS2 KO 42 dpi rep 1

description:
Sertoli cells from germ cell-deficient environment at 42 dpi
NANOS2KO_FPKM; NANOS2KO_readcounts

value: CD1 background

value: Sertoli

value: NANOS2 KO

value: WIN 18,446 synchrony + RA + 42 dpi


title: Sample_PRO472A213_S301_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A213_S301_L004


title: Sample_PRO472A211_S299_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A211_S299_L004


title: CD8-TEM-30

value: LCMV-Armstrong


title: NANOS2 KO 43 dpi rep 1


title: Sample_PRO472A210_S298_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A210_S298_L004


title: NANOS2 KO 42 dpi rep 2


title: Sample_PRO472A209_S297_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A209_S297_L004


title: Sample_PRO472A208_S296_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A208_S296_L004


title: RFPxAMH-Cre Group E rep 1

description:
Sertoli cells enriched for Stages IX-X
RFPxAMHCre_FPKM; RFPxAMHCre_readcounts

value: Derived from C57BL/6 x 129s4/SvJae

value: RFP heterozygote, Amh-Cre-positive

value: WIN 18,446 synchrony + RA + 42-50 days post-injection (dpi)


title: Smad4a MZ1 50% epiboly

description:
Zebrafish
Bulk-RNAseq
mRNA


title: CD8-TCM-10


title: RFPxAMH-Cre Group D rep 2

description:
Sertoli cells enriched for Stages VII-VIII
RFPxAMHCre_FPKM; RFPxAMHCre_readcounts


title: Smad4a WT3 50% epiboly

description:
Zebrafish
Bulk-RNAseq
mRNA

value: WT


title: Smad4a MZ2 50% epiboly

description:
Zebrafish
Bulk-RNAseq
mRNA


title: Sample_PRO472A207_S295_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A207_S295_L004

value: Adult


title: T323075

description: Patient2 ESCC tissues

source_name: Patient2 ESCC tissues, T3N1M0

value: esophageal squamous cell carcinoma (ESCC)

value: Female


title: T324545

description: Patient3 ESCC tissues

source_name: Patient3 ESCC tissues, T3N1M0


title: N322835

description: Patient1 adjacent normal samples

source_name: Patient1 adjacent normal samples, T2N1M0

value: adjacent normal

value: Male


title: CD8-TCM-30


title: T322835E

description: Patient1 ESCC tissues

source_name: Patient1 ESCC tissues, T2N1M0


title: RFPxAMH-Cre Group E rep 2


title: RFPxAMH-Cre Group D rep 1


title: Daxx F/F Pu.1 F/F 24wpi H3K27me3 2

city: Bonn

first: Paolo

last: Salomoni

address: Sigmund-Freud-Str. 27

country: Germany

institute: DZNE e.V.

description:
DaxxFFPu1FF_24wpi_H3K27me3_cov.bw
2791

library_source: genomic

data_processing:
Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against mm10 (GENCODE release M14) using STAR aligner 2.5.3 with the following options: --alignIntronMax 1 --alignMatesGapMax 1800.
Reads mapping to the the mitochondrial genome and non-uniquely were removed. In addition, read duplicates were removed and start position of reads was offset by +4 bp if mapping to the positive strand and -5 bp if mapping to the negative strand.
For peak calling the ENCODE ATAC-seq analysis pipeline 0.3.4 was used.
Peak files were sorted by coordinate and overlapping peaks were merged with bedtools merge.
Identification of differentially accessible sites using diffreps with 600 bp window size.
Genome_build: mm10
Supplementary_files_format_and_content: Bed/NarrowPeak file with merged ATAC-seq peak positions and/or tab-delimited files with differentially accessible regions identified with diffreps

molecule: genomic DNA

source_name: Hematopoietic Stem/Progenitor Cell

extract_protocol:
Primary hematopoietic stem/progenitor cells were isolated form bone marrow and Lineage-negative/c-Kit-positive (HSPCs) were enriched by MACS. Nuclei were isolated, washed and frozen in wash buffer according to the “Bench top CUT&Tag V.3” protocol (https://ww.protocols.io/view/bench-top-cut-amp-tag-bcuhiwt6).
For the actual CUT&Tag experiment, we followed the CUT&Tag-direct protocol described by Henikoff et al.74 using the CUTANA pAG-Tn5 enzyme (Epicypher). Briefly, aliquots of 30,000-45,000 native nuclei per reaction were bound to activated Concanavalin A beads. After successive incubations with primary antibody (overnight at 4°C) and secondary antibody (0.5-1 h) in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and 1x protease inhibitor), the beads were washed and resuspended in pAG-Tn5 (1:20 dilution) in 300-wash buffer (wash buffer containing 300 mM NaCl) for 1 h. Incubations were performed at room temperature, except when otherwise stated, in volumes of 25-50 ul in low-retention PCR tubes. Tagmentation was performed for 1 h in 300-wash buffer supplemented with 10 mM MgCl2. Following tagmentation, beads were washed in 50 ul TAPS buffer (10 mM TAPS pH8.5, 0.2 mM EDTA), resuspended in 5 ul SDS release buffer (0.1% SDS, 10 mM TAPS pH8.5) and incubated for 1 h at 58°C. SDS was neutralized with 15 ul of 0.67% Triton-X100, and 4 ul of dual indexed primers from the “IDT for Illumina Nextera DNA UD Indexes Set A” (Illumina) as well as 25 ul of NEBNext High-Fidelity 2x PCR Master mix (NEB) were added. Gap filling and 18 cycles of PCR were performed, followed by clean-up with 65 ul of SPRIselect beads (Beckman Coulter).
CUT&Tag

value: Bone marrow

value: Daxx F/F Pu.1 F/F Cre +/-

tag: chip antibody


title: Sample_PRO472A206_S294_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A206_S294_L004

source_name: Enteric glia

value: Naive


title: Sample_PRO472A205_S293_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A205_S293_L004


title: Smad4a WT1 50% epiboly

description:
Zebrafish
Bulk-RNAseq
mRNA

value: Tubingen (TU)

value: Whole embryo (n=25)


title: Daxx F/F Pu.1 F/F 24wpi H3K27ac 2

description:
DaxxFFPu1FF_24wpi_H3K27ac_cov.bw
2791


title: Sample_PRO472A204_S292_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A204_S292_L004


title: CD8-TCM-1

value: Spleen


title: Daxx F/F Pu.1 F/F 24wpi H3.3 2

description:
DaxxFFPu1FF_24wpi_H3.3_cov.bw
2791


title: RFPxAMH-Cre Group C rep 1

description:
Sertoli cells enriched for Stages IV-VI
RFPxAMHCre_FPKM; RFPxAMHCre_readcounts

value: Sertoli


title: Sample_PRO472A203_S291_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A203_S291_L004


title: Sample_PRO472A202_S290_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A202_S290_L004


title: Daxx F/F Pu.1 F/F 24wpi H3K9me3 1

description:
DaxxFFPu1FF_24wpi_H3K9me3_cov.bw
2485


title: Daxx F/F Pu.1 F/F 24wpi H3K27me3 1

description:
DaxxFFPu1FF_24wpi_H3K27me3_cov.bw
2485


title: RFPxAMH-Cre Group B rep 1

description:
Sertoli cells enriched for Stages I-III
RFPxAMHCre_FPKM; RFPxAMHCre_readcounts


title: Smad4a WT2 50% epiboly

description:
Zebrafish
Bulk-RNAseq
mRNA


title: Lb1

city: Lanzhou

first: Bo

last: Zhang

address: No. 1 Yingmen village, Anning District

institute: Gansu Agricultural University

data_processing:
Raw reads were first subjected to quality filtering by fastp (V0.18.0)，which removed the reads containing than 10% of unknown nucleotides (N), and low quality reads (＞50% of the bases with qvalue≤20) to generate clean reads.
Short reads alignment tool Bowtie2 (V2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.
The rRNA mapped reads were then removed, then the remaining reads were mapped to the reference genome (Sus scrofa 11.1) using HISAT2 (V2.1.0) tool and other parameters set as a default. The mapped reads from each library were assembled with Stringtie (V1.3.4).
The FPKM (fragment per kilobase of transcript per million mapped reads) was used to normalize the expression levels of genes.
Genome_build: Sus scrofa 11.1 (ncbi_GCF_000003025.6)
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

organism: Sus scrofa

extract_protocol:
All samples were immediately snap frozen in liquid nitrogen and stored at -80°C until RNA extraction, and RNA was harvested using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Landrace pig

value: testis


title: RFPxAMH-Cre Group A rep 2

description:
Sertoli cells enriched for Stages XI-XII
RFPxAMHCre_FPKM; RFPxAMHCre_readcounts

value: Derived from C57BL/6 x 129s4/SvJae

value: RFP heterozygote, Amh-Cre-positive


title: Sample_PRO472A201_S289_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A201_S289_L004


title: La3

tag: age


title: Daxx F/F Pu.1 F/F 24wpi H3K27ac 1

description:
DaxxFFPu1FF_24wpi_H3K27ac_cov.bw
2485

tag: strain


title: Lb3

tag: tissue


title: Daxx F/F Pu.1 F/F 24wpi H3K9me3 2

description:
DaxxFFPu1FF_24wpi_H3K9me3_cov.bw
2791

tag: genotype


title: RFPxAMH-Cre Group A rep 1

value: Derived from C57BL/6 x Amh-Cre background

value: WIN 18,446 synchrony + RA + 42-50 days post-injection (dpi)


title: RFPxAMH-Cre Group C rep 2


title: La2


title: Sample_PRO472A200_S288_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A200_S288_L004

tag: Stage

value: Adult


title: La1


title: Daxx F/F 24wpi H3K27me3 2

description:
DaxxFF_24wpi_H3K27me3_cov.bw
H3K27me3_DaxxFF_24wpi_noXY_diffsite.txt
2527

value: Daxx F/F Cre +/-


title: Lb2


title: RFPxAMH-Cre Group B rep 2


title: Hb3

value: Hezuo pig


title: Sample_PRO472A199_S287_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A199_S287_L004

tag: disease state


title: Sample_PRO472A198_S286_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A198_S286_L004


title: Daxx F/F 24wpi H3K9me3 2

description:
DaxxFF_24wpi_H3K9me3_cov.bw
H3K9me3_DaxxFF_24wpi_noXY_diffsite.txt
2527


title: Sample_PRO472A197_S285_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A197_S285_L004


title: Hb2


title: Sample_PRO472A196_S284_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A196_S284_L004


title: Hb1


title: Daxx F/F 24wpi H3K27ac 2

description:
DaxxFF_24wpi_H3K27ac_cov.bw
H3K27ac_DaxxFF_24wpi_noXY_diffsite.txt
2527


title: 18/5 DKO GFP HIGH 1

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
Reads were quality-trimmed using TrimGalore!; reads shorter than 15 nt were discarded.
Reads were aligned to the mouse reference genome (mm10) using bowtie with parameters "-m1 -v1 --best --strata -X 2000 --trim3 1". Duplicates were removed using Picard tools.
Reads shorter than one nucleosome length were discarded, and an offset of 4 nts was introduced.
bigWig tracks were created using deepTools bamCoverage with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks

source_name: mEpiLC

growth_protocol: Mouse ES cells were cultured in 2iL. EpiLC differentiation were performed in actinvin a, bFgf and 1% KSR medium.

extract_protocol:
50,000 cells were collected and washed with ice-cold PBS once then lysed in the buffer (10 mM Tris-HCl, pH _x000B_7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL). The nuclear pellets were collected and Tn5 tagmentation were performed with Illumina Nextera kit.  (FC-121-1030)
Library construction were performed with Illumina Nextera kit.  (FC-121-1030)

treatment_protocol: GFP high or low fraction were collected by FACS moflo.

value: mEpiLC

value: Dnmt3a3b double KO

tag: fraction

value: high


title: Sample_PRO472A195_S283_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A195_S283_L004

value: Naive


title: Daxx F/F Pu.1 F/F 24wpi H3.3 1

description:
DaxxFFPu1FF_24wpi_H3.3_cov.bw
2485

value: Bone marrow

value: Daxx F/F Pu.1 F/F Cre +/-


title: Daxx F/F 24wpi Pu.1 2

description:
DaxxFF_24wpi_Pu1_cov.bw
Pu1_DaxxFF_24wpi_noXY_diffsite.txt
2527


title: Ha3


title: Ha2


title: Sample_PRO472A194_S282_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A194_S282_L004


title: Daxx F/F 24wpi H3.3 2

description:
DaxxFF_24wpi_H3.3_cov.bw
H3.3_DaxxFF_24wpi_noXY_diffsite.txt
2527


title: Daxx F/F 24wpi H3K9me3 1

description:
DaxxFF_24wpi_H3K9me3_cov.bw
H3K9me3_DaxxFF_24wpi_noXY_diffsite.txt
2526


title: Sample_PRO472A94_S280_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A94_S280_L003


title: Sample_PRO472A93_S279_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A93_S279_L003


title: WT R2

city: Haifa

first: Serge

last: Ankri

address: Efron 1

country: Israel

institute: Technion

description: Sample 5

data_processing:
Quality control was assessed using Fastqc (v0.11.5)
reads were trimmed for adapters, low quality 3` and minimum length of 20 using CUTADAPT (v1.12). ), reads were trimmed for adapters, low quality 3` and minimum length of 20 using CUTADAPT (v1.12).
83 bp single-end reads were aligned using STAR aligner (v2.6.0a), to a Entamoeba histolytica reference genome (Entamoeba_histolytica.JCVI-ESG2- 1.0.dna.toplevel.fa) and annotation file (Entamoeba_histolytica.JCVI-ESG2-1.0.46.gff3) both downloaded from ENSEMBL (strain HM-1:IMSS, imported from the AmoebaDB, release 1.7 from 11- Jan-2012).
Genome_build: ENSEMBL (strain HM-1:IMSS, imported from the AmoebaDB, release 1.7 from 11- Jan-2012)
Supplementary_files_format_and_content: Differential expression analysis list- includes upregulated and downregulated genes with padj<0.01 in seperated tabas

organism: Entamoeba histolytica

source_name: WT

growth_protocol: Trophozoites from Entamoeba histolytica strain HM-1:IMSS were grown under axenic conditions in Diamond’s TYI S-33 medium at 37 °C

extract_protocol:
Total RNA was extracted from control trophozoites, trophozoites adapted to Auranofin (2uM) in 3 biological replicates using the TRI reagent kit, according to the manufacturer’s instructions (Sigma-Aldrich USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: E.histolytica trophozoites were exposed to 2 uM Auranofin for 24 hours

value: 3 days after splitting

value: WT

value: No treatment


title: WT R3

description: Sample 6


title: Sample_PRO472A193_S281_L004 Naive enteric glia, rep 2

description:
Naive enteric glia, rep 2
Naive 2
Sample_PRO472A193_S281_L004


title: Sample_PRO472A92_S278_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A92_S278_L003


title: WT R1

description: Sample 4


title: Daxx F/F 24wpi H3K27ac 1

description:
DaxxFF_24wpi_H3K27ac_cov.bw
H3K27ac_DaxxFF_24wpi_noXY_diffsite.txt
2526


title: Sample_PRO472A90_S277_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A90_S277_L003


title: Auranofin treated R3

description: Sample 3

source_name: Auranofin treated

value: Auranofin 2uM


title: Daxx +/+ 24wpi H3K27me3 1

description:
DaxxWtWt_24wpi_H3K27me3_cov.bw
3320

value: Daxx +/+ Cre +/-


title: Daxx F/F 24wpi H3K27me3 1

description:
DaxxFF_24wpi_H3K27me3_cov.bw
H3K27me3_DaxxFF_24wpi_noXY_diffsite.txt
2526


title: B2_FRAS202137175-2r (N0_1Y_2)

city: Yangzhou

first: Xinbo

state: jiangsu

address: 88 University South Road

department: Agricultural College

institute: yangzhou university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Chinese Spring whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using Cuffdiff.
Genome_build: Chinese Spring (IWGSC1_popseq.31)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Triticum aestivum

source_name: leaf

extract_protocol:
Wheat leaves were sampled at the anthesis stage, and than removed in ultra low temperature freezer. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Nevogene protocols

value: leaf

tag: developmental stage

value: the anthesis stage

tag: phenotype

value: 1Y, high-NUE


title: Auranofin treated R2

description: Sample 2

tag: treatment


title: genomic DNA from control 3

type: genomic

city: Beijing

first: Hang

last: Yang

state: Beijing

address: No.1 West Beichen Road,Chaoyang District

institute: CAS

description:
normal artery
control3

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and Methylation850 Beadchip using standard Illumina protocol

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

data_processing: Array data were evaluated and preprocessed using the minfi R package (version 1.32.0). The 450K and EPIC data were merged with the combineArrays function, the batch effect was corrected with sva R package (version3.34.0)

label: Cy5 and Cy3

source_name: internal mammary artery 3

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from frozen tissue specimens using the QIAamp DNA Mini Kit (Qiagen) following the manufacturer’s instructions.

value: male

tag: sample type

value: normal artery

value: normal


title: B2_FRAS202137175-3r (N0_1Y_3)


title: B2_FRAS202137175-1r (N0_1Y_1)


title: Ha1

value: Hezuo pig

value: testis


title: Daxx +/+ 24wpi H3K9me3 1

description:
DaxxWtWt_24wpi_H3K9me3_cov.bw
3320


title: Daxx +/+ 24wpi H3K27ac 1

description:
DaxxWtWt_24wpi_H3K27ac_cov.bw
3320


title: Auranofin treated R1

description: Sample 1


title: Daxx F/F 24wpi Pu.1 1

description:
DaxxFF_24wpi_Pu1_cov.bw
Pu1_DaxxFF_24wpi_noXY_diffsite.txt
2526

value: Daxx F/F Cre +/-


title: Sample_PRO472A88_S275_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A88_S275_L003

value: Adult

value: Naive


title: Sample_PRO472A87_S274_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A87_S274_L003


title: Daxx F/F 24wpi H3.3 1

description:
DaxxFF_24wpi_H3.3_cov.bw
H3.3_DaxxFF_24wpi_noXY_diffsite.txt
2526

value: Bone marrow


title: genomic DNA from control 2

description:
normal artery
control2

source_name: internal mammary artery 2


title: B1_FRAS202137174-3r (N0_1W_3)

value: 1W, low-NUE


title: Sample_PRO472A89_S276_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A89_S276_L003


title: Sample_PRO472A86_S273_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A86_S273_L003


title: M4: sir2.1_4th_1G 2

first: Akira

last: Higashibata

department: Department of Space Biology and Microgravity Sciences

institute: Japan Aerospace Exploration Agency

description: Gene expression of sir-2.1 mutant 4th generation in 1G condition

hyb_protocol: The labeled cRNA (1.65 µg/sample) was hybridized to a microarray using the Agilent Gene Expression Hybridization Kit at 65°C for 17 hours.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G49000DA) using one color scan setting for 4x44k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5.1.1
Microarray data were analyzed using Gene Spring software (Agilent Technologies). Normalized data were produced by Normalize to 75 percentile sift protocol. Arrays were filtered on expression (20-100)th percentile in raw data.

organism: Caenorhabditis elegans

source_name: C.elegans, VC199 sir-2.1 (ok434), flight 1G, 4th generation, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: The worms of each generations were cultured under microgravity at the international space station (ISS). The worms were cultured in M9 cholesterol buffer contained E. coli OP50 for 4 days from L1 larva. The cultured worms were frozen at -95 C degrees  in ISS.

extract_protocol: RNA was prepared using ISGEN (Nippon gene)following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The frozen worms were thawed and washed by M9 buffer.

tag: tag


title: B1_FRAS202137174-2r (N0_1W_2)


title: genomic DNA from unstable plaque 1

description:
unstable atherosclerotic plaque
unstable1

source_name: unstable atherosclerotic plaque 1

value: unstable atherosclerotic plaque

value: unstable lesion


title: genomic DNA from stable plaque 1

description:
stable atherosclerotic plaque
stable1

source_name: stable atherosclerotic plaque 1

value: stable atherosclerotic plaque

value: stable lesion


title: genomic DNA from control 1

description:
normal artery
control1

source_name: internal mammary artery 1


title: Sample_PRO472A85_S272_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A85_S272_L003

data_processing:
Nextera adapter sequences were removed from reads using Cutadapt (version 1.18).
Reads were aligned to the Ensembl GRCm38 genome using STAR (version 2.5.2a).
Gene counts were obtained using the featureCounts program (from Subread version 1.6.4).
Quality control, normalisation and downstream analysis were performed using the software Seurat (version 3.1.1).
Cells expressing more than 2000 genes and less than 10 percent mitochondrial reads were retained for further analysis. Contaminating macrophages (n=7) were removed based on the expression of Itgam (> 10 counts), and contaminating neurons (n=95) were removed based on expression of Elavl4 (> 30 counts). Genes detected in fewer than 3 cells or with total counts < 10 were omitted from further analysis. The dimension of the final data matrix was 18643 genes by 217 cells (134 cells from naïve mice and 83 from H. poly infected mice).
Counts were normalized to ten thousand counts per cell, natural-log transformed using log1p, and scaled.
Highly variable genes were identified using Seurat, and the top 1000 used for dimensionality reduction and clustering. The first 4 principal components were selected as input for dimensionality reduction using the UMAP algorithm and Louvain clustering at a resolution of 0.1.
Genome_build: GrCM38
Supplementary_files_format_and_content: Count matrices in .tsv format. Seurat object saved as an .rds file.

extract_protocol:
For isolation of EGCs, the longitudinal smooth muscle layer and associated myenteric plexus were peeled off the wall of the smal intestineand subjected to enzymatic digestion to prepare a single-cell suspension. Single-cell suspensions were subjected to fluorescence activated cell sorting and live EGCs were isolated based on tdT expression DAPI exclusion. 200-1000 cells were loaded into a Fluidigm C1 Single Cell Auto Prep IFC for mRNA-seq for use with the Fluidigm C1 system. After the cell load program cells were imagined using the JuliStage to identify wells that contain 1 single cell.
The SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System, IFCs was used to reverse transcribe and amplify cDNA. cDNA was quantified using the Glomax (Promega). Libraries were prepared from cDNA generated from single cells using the Nextera XT kit from Illumina. Final libraries were pooled and sequenced on the HiSeq 4000.


title: K4: hda4_4th_1G 2

description: Gene expression of hda-4 mutant 4th generation in 1G condition

source_name: C.elegans, RB756 hda-4 (ok518), flight 1G, 4th generation, replicate 2


title: Daxx +/+ 24wpi H3.3 1

description:
DaxxWtWt_24wpi_H3.3_cov.bw
3320

value: Daxx +/+ Cre +/-


title: A2_FRAS202137173-3r (N1_1Y_3)

value: leaf

value: the anthesis stage


title: Daxx F/F Pu.1 F/F 8wpi H3K9me3 1

description:
DaxxFFPu1FF_8wpi_H3K9me3_cov.bw
H3K9me3_DaxxFFPu1FFvsDaxxWtWt_8wpi_diffsite.txt
2792

value: Daxx F/F Pu.1 F/F Cre +/-


title: Daxx F/F Pu.1 F/F 8wpi H3K27me3 1

description:
DaxxFFPu1FF_8wpi_H3K27me3_cov.bw
H3K27me3_DaxxFFPu1FFvsDaxxWtWt_8wpi_diffsite.txt
2792


title: Sample_PRO472A84_S271_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A84_S271_L003


title: J4: hda4_4th_1G 1

source_name: C.elegans, RB756 hda-4 (ok518), flight 1G, 4th generation, replicate 1


title: Daxx F/F 8wpi H3K27me3 3

description:
DaxxFF_8wpi_H3K27me3_cov.bw
H3K27me3_DaxxFFvsDaxxWtWt_8wpi_diffsite.txt
2715


title: H4: N2_4th_1G2

description: Gene expression of N2 4th generation in 1G condition

source_name: C.elegans, N2, flight 1G, 4th generation, replicate 2

value: N2 wild type


title: A2_FRAS202137173-2r (N1_1Y_2)

value: 1Y, high-NUE


title: L4: sir2.1_4th_1G 1

source_name: C.elegans, VC199 sir-2.1 (ok434), flight 1G, 4th generation, replicate 1


title: Daxx F/F 8wpi H3K9me3 3

description:
DaxxFF_8wpi_H3K9me3_cov.bw
H3K9me3_DaxxFF_8wpi_diffsite.txt
2715


title: G4: N2_4th_1G1

source_name: C.elegans, N2, flight 1G, 4th generation, replicate 1


title: Sample_PRO472A83_S270_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A83_S270_L003


title: A2_FRAS202137173-1r (N1_1Y_1)


title: Sample_PRO472A82_S269_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A82_S269_L003


title: Sample_PRO472A80_S268_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A80_S268_L003


title: F4: sir2.1_4th_μG 2

description: Gene expression of sir-2.1 mutant 4th generation in µG condition

source_name: C.elegans, VC199 sir-2.1 (ok434), flight µG, 4th generation, replicate 2


title: genomic DNA from stable plaque 2

description:
stable atherosclerotic plaque
stable2

source_name: stable atherosclerotic plaque 2

value: male


title: Sample_PRO472A8_S200_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A8_S200_L003

source_name: Enteric glia


title: B1_FRAS202137174-1r (N0_1W_1)


title: A1_FRAS202137172-3r (N1_1W_3)


title: A1_FRAS202137172-2r (N1_1W_2)


title: A1_FRAS202137172-1r (N1_1W_1)


title: Sample_PRO472A79_S267_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A79_S267_L003


title: Sample_PRO472A78_S266_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A78_S266_L003


title: Male_Naive_ATACrep3 resequenced

city: Little Rock

first: Kimberly

middle: E

last: Stephens

state: AR

address: 4301 W. Markham St Slot 510

department: Neuroscience

institute: University of Arkansas for Medical Sciences

description:
Naive3b
ATAC_CCIvN_normalized_coverage.csv
ATAC_CFAvN_normalized_coverage.csv

data_processing:
Casava v1.8.2 used for base calling.
Reads trimmed for adapter sequence.
RNA-seq reads mapped to rn6 genome using HISAT2.
ATAC-seq reads mapped to rn6 genome using Bowtie2.
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: RNAseq-CountTable.csv: Count table contains raw transcript counts for each annotated gene generated using the summarizedOverlaps function of the Genomic Alignments package in R.
Supplementary_files_format_and_content: ATAC_*_normalized_coverage.csv: Align reads shifted 4 nucleotides upstream for 5' and 5 nucleotides downstream for 3' end; insertion sites identified by trimming to the 5'end. Insertion site extended in both directions by 75bp; Reads downsampled to 49million insertion sites; peaks called by MACS2; limma used to count reads for CCI versus Naive and CFA versus Naive.

organism: Rattus norvegicus

source_name: DRG

extract_protocol:
Dorsal root ganglion (L4-L6) harvested and homogenized.
RNA-seq: NEBNExt Ultra Directional RNA Library Prep Kit for Illumina and NEBNext poly(A) mRNA Isolation Module.
ATAC-seq with Illumina TDE1 enzyme after nuclei isolation.

treatment_protocol: Complete Freund's Adjuvant (CFA), Chronic Constriction Injury (CCI), Naïve groups.

tag: group

value: Dorsal root ganglia (DRG)

tag: Sex

value: Male

value: Sprague-Dawley


title: Daxx F/F 8wpi H3K9me3 1

description:
DaxxFF_8wpi_H3K9me3_cov.bw
H3K9me3_DaxxFF_8wpi_diffsite.txt
2528

source_name: Hematopoietic Stem/Progenitor Cell

value: Daxx F/F Cre +/-


title: Daxx F/F 8wpi H3K27me3 2

description:
DaxxFF_8wpi_H3K27me3_cov.bw
H3K27me3_DaxxFFvsDaxxWtWt_8wpi_diffsite.txt
2714

value: Bone marrow


title: Daxx F/F 8wpi H3K9me3 2

description:
DaxxFF_8wpi_H3K9me3_cov.bw
H3K9me3_DaxxFF_8wpi_diffsite.txt
2714


title: Daxx F/F 8wpi H3K27me3 1

description:
DaxxFF_8wpi_H3K27me3_cov.bw
H3K27me3_DaxxFFvsDaxxWtWt_8wpi_diffsite.txt
2528


title: Male_Naive_ATACrep3

description:
Naive3a
ATAC_CCIvN_normalized_coverage.csv
ATAC_CFAvN_normalized_coverage.csv

value: Naive


title: Male_Naive_ATACrep2

description:
Naive2a
ATAC_CCIvN_normalized_coverage.csv
ATAC_CFAvN_normalized_coverage.csv


title: Sample_PRO472A71_S263_L003 Naive enteric glia, rep 1

first: Vassilis

institute: The Francis Crick Institute

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A71_S263_L003

value: Adult


title: Sample_PRO472A72_S264_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A72_S264_L003


title: Sample_PRO472A69_S261_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A69_S261_L003


title: Male_Naive_ATACrep1 resequenced

description:
Naive1b
ATAC_CCIvN_normalized_coverage.csv
ATAC_CFAvN_normalized_coverage.csv


title: E4: sir2.1_4th_μG 1

source_name: C.elegans, VC199 sir-2.1 (ok434), flight µG, 4th generation, replicate 1


title: D4: hda4_4th_μG 2

description: Gene expression of hda-4 mutant 4th generation in µG condition

source_name: C.elegans, RB756 hda-4 (ok518), flight µG, 4th generation, replicate 2


title: C4: hda4_4th_μG 1

source_name: C.elegans, RB756 hda-4 (ok518), flight µG, 4th generation, replicate 1


title: B4: N2_4th_μG2

description: Gene expression of N2 4th generation in µG condition

source_name: C.elegans, N2, flight µG, 4th generation, replicate 2


title: A4: N2_4th_μG1

source_name: C.elegans, N2, flight µG, 4th generation, replicate 1


title: Male_Naive_ATACrep1

description:
Naive1a
ATAC_CCIvN_normalized_coverage.csv
ATAC_CFAvN_normalized_coverage.csv


title: Sample_PRO472A67_S259_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A67_S259_L003


title: Male_CFA_ATACrep6 resequenced

description:
CFA6b
ATAC_CFAvN_normalized_coverage.csv

value: CFA


title: Male_CFA_ATACrep6

description:
CFA6a
ATAC_CFAvN_normalized_coverage.csv


title: Male_Naive_ATACrep2 resequenced

description:
Naive2b
ATAC_CCIvN_normalized_coverage.csv
ATAC_CFAvN_normalized_coverage.csv


title: Heart CKO/CKO rep2

city: Kyiv

first: Oksana

last: Piven

address: 150 Akad. Zabolotnogo str.

department: Human Genetics

country: Ukraine

institute: Institute of Molecular Biology and Genetics

data_processing:
BCL to FASTQ file converter: bcl2fastq v2.16.0.10 Copyright (c) 2007-2015 Illumina, Inc.
RTAVersion v2.4.11
Quality control: FastQC 0.11.5
Sequence alignment: STAR aligner 2.5.3a
Conversion to reads per gene count: HTseq-count 0.6.1
Differential expression analysis: SARTools 1.6.0 [DeSeq2 1.18]
Gene enrichment analysis: Metascape.org 02.02.2018
Genome_build: Gencode Release M16 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include abundance measurements.
Supplementary_files_format_and_content: ckocko_vs_wt.txt: Tab-delimited text file includes differential expression.
Supplementary_files_format_and_content: gene_enrichment_ckocko_vs_wt.xlsx: Excel file includes gene enrichment.

source_name: Heart

extract_protocol:
Total RNA was isolated from frozen ventricles of one-day-old mice using Trizol Reagent (15596026, Invitrogen) and was purified and concentrated with RNA Clean and Concentrator-5 (R1013, ZymoResearch). 1.5 μg of total RNA was enriched for polyA+ RNA Illumina TruSeqRNA sample prep according to the manufacturer’s standard protocol. Approximately 20 ng of the polyA+ enriched RNA was then used to prepare libraries for sequencing using Kapa stranded RNA seq kit.
mRNA was enriched by oligo-dT beads from Illumina and libraries were prepared using Kapa Stranded RNA seq kit according to manufacturer protocol. NEB Next adaptors were used: #77 - > Ad. 6 (GCCAAT) and #209 -> Ad.12 (CTTGTA).

value: Ctnnb1floxP/floxP; alphaMHC-Cre+

value: (alphaMHC)-Cre mice crossed with Ctnnb1floxp/floxp mice

value: heart

value: post natal day 1


title: Daxx +/+ 3wpi Pu.1 1

description:
DaxxWtWt_3wpi_Pu1_cov.bw
Wildtype

value: Daxx +/+ Cre +/-


title: Daxx +/+ 3wpi H3.3 1

description:
DaxxWtWt_3wpi_H3.3_cov.bw
Wildtype


title: Daxx +/+ 3wpi Pu.1 2

description:
DaxxWtWt_3wpi_Pu1_cov.bw
2732


title: Daxx +/+ 3wpi H3K27ac 2

description:
DaxxWtWt_3wpi_H3K27ac_cov.bw
2732


title: Daxx +/+ 3wpi H3.3 2

description:
DaxxWtWt_3wpi_H3.3_cov.bw
2732


title: Daxx +/+ 3wpi H3K9me3 2

description:
DaxxWtWt_3wpi_H3K9me3_cov.bw
2732


title: M3: sir2.1_3rd_1G 2

description: Gene expression of sir-2.1 mutant 3rd generation in 1G condition

source_name: C.elegans, VC199 sir-2.1 (ok434), flight 1G, 3rd generation, replicate 2


title: Sample_PRO472A70_S262_L003 Naive enteric glia, rep 1

last: Pachnis

address: 1 Midland Rd

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A70_S262_L003


title: L3: sir2.1_3rd_1G 1

source_name: C.elegans, VC199 sir-2.1 (ok434), flight 1G, 3rd generation, replicate 1


title: Male_CFA_ATACrep5

description:
CFA5a
ATAC_CFAvN_normalized_coverage.csv


title: Sample_PRO472A64_S256_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A64_S256_L003


title: Sample_PRO472A63_S255_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A63_S255_L003


title: Sample_PRO472A66_S258_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A66_S258_L003


title: Male_CFA_ATACrep4 resequenced

description:
CFA4b
ATAC_CFAvN_normalized_coverage.csv


title: Heart CKO/CKO rep1


title: K3: hda4_3rd_1G 2

description: Gene expression of hda-4 mutant 3rd generation in 1G condition

source_name: C.elegans, RB756 hda-4 (ok518), flight 1G, 3rd generation, replicate 2


title: Heart WT rep1

value: Ctnnb1floxP/floxP; alphaMHC-Cre-


title: Heart WT rep2


title: Sample_PRO472A65_S257_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A65_S257_L003


title: Male_CFA_ATACrep3 resequenced

description:
CFA3b
ATAC_CFAvN_normalized_coverage.csv


title: Male_CFA_ATACrep4

description:
CFA4a
ATAC_CFAvN_normalized_coverage.csv


title: Male_CFA_ATACrep2 resequenced

description:
CFA2b
ATAC_CFAvN_normalized_coverage.csv


title: Male_CFA_ATACrep5 resequenced

description:
CFA5b
ATAC_CFAvN_normalized_coverage.csv


title: E3: sir2.1_3rd_μG 1

description: Gene expression of sir-2.1 mutant 3rd generation in µG condition

source_name: C.elegans, VC199 sir-2.1 (ok434), flight µG, 3rd generation, replicate 1


title: G3: N2_3rd_1G1

description: Gene expression of N2 3rd generation in 1G condition

source_name: C.elegans, N2, flight 1G, 3rd generation, replicate 1

value: N2 wild type


title: H3: N2_3rd_1G2

source_name: C.elegans, N2, flight 1G, 3rd generation, replicate 2


title: D3: hda4_3rd_μG 2

description: Gene expression of hda-4 mutant 3rd generation in µG condition

source_name: C.elegans, RB756 hda-4 (ok518), flight µG, 3rd generation, replicate 2


title: C3: hda4_3rd_μG 1

source_name: C.elegans, RB756 hda-4 (ok518), flight µG, 3rd generation, replicate 1


title: B3: N2_3rd_μG2

description: Gene expression of N2 3rd generation in µG condition

source_name: C.elegans, N2, flight µG, 3rd generation, replicate 2


title: J3: hda4_3rd_1G 1

source_name: C.elegans, RB756 hda-4 (ok518), flight 1G, 3rd generation, replicate 1


title: F3: sir2.1_3rd_μG 2

source_name: C.elegans, VC199 sir-2.1 (ok434), flight µG, 3rd generation, replicate 2


title: Male_CFA_ATACrep2

description:
CFA2a
ATAC_CFAvN_normalized_coverage.csv

source_name: DRG


title: Male_CFA_ATACrep1 resequenced

description:
CFA1b
ATAC_CFAvN_normalized_coverage.csv


title: Male_CFA_ATACrep1

description:
CFA1a
ATAC_CFAvN_normalized_coverage.csv


title: Male_CFA_ATACrep3

description:
CFA3a
ATAC_CFAvN_normalized_coverage.csv


title: Male_CCI_ATACrep6

description:
CCI9
ATAC_CCIvN_normalized_coverage.csv

value: CCI


title: Male_CCI_ATACrep5

description:
CCI8
ATAC_CCIvN_normalized_coverage.csv


title: Male_CCI_ATACrep3

description:
CCI6
ATAC_CCIvN_normalized_coverage.csv


title: Male_CCI_ATACrep4

description:
CCI7
ATAC_CCIvN_normalized_coverage.csv


title: Male_CCI_ATACrep2 resequenced

description:
CCI4b
ATAC_CCIvN_normalized_coverage.csv


title: H2: N2_2nd_1G2

description: Gene expression of N2 2nd generation in 1G condition

source_name: C.elegans, N2, flight 1G, 2nd generation, replicate 2


title: M2: sir2.1_2nd_1G 2

description: Gene expression of sir-2.1 mutant 2nd generation in 1G condition

source_name: C.elegans, VC199 sir-2.1 (ok434), flight 1G, 2nd generation, replicate 2


title: G2: N2_2nd_1G1

source_name: C.elegans, N2, flight 1G, 2nd generation, replicate 1


title: A3: N2_3rd_μG1

source_name: C.elegans, N2, flight µG, 3rd generation, replicate 1


title: J2: hda4_2nd_1G 1

description: Gene expression of hda-4 mutant 2nd generation in 1G condition

source_name: C.elegans, RB756 hda-4 (ok518), flight 1G, 2nd generation, replicate 1


title: K2: hda4_2nd_1G 2

source_name: C.elegans, RB756 hda-4 (ok518), flight 1G, 2nd generation, replicate 2


title: L2: sir2.1_2nd_1G 1

source_name: C.elegans, VC199 sir-2.1 (ok434), flight 1G, 2nd generation, replicate 1


title: F2: sir2.1_2nd_μG 2

description: Gene expression of sir-2.1 mutant 2nd generation in µG condition

source_name: C.elegans, VC199 sir-2.1 (ok434), flight µG, 2nd generation, replicate 2


title: Male_CCI_ATACrep2

description:
CCI4a
ATAC_CCIvN_normalized_coverage.csv


title: Sample_PRO472A44_S236_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A44_S236_L003

source_name: Enteric glia


title: Male_CCI_ATACrep1 resequenced

description:
CCI3b
ATAC_CCIvN_normalized_coverage.csv


title: D2: hda4_2nd_μG 2

description: Gene expression of hda-4 mutant 2nd generation in µG condition

source_name: C.elegans, RB756 hda-4 (ok518), flight µG, 2nd generation, replicate 2


title: E2: sir2.1_2nd_μG 1

source_name: C.elegans, VC199 sir-2.1 (ok434), flight µG, 2nd generation, replicate 1


title: Sample_PRO472A57_S249_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A57_S249_L003


title: Sample_PRO472A5_S197_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A5_S197_L003


title: Sample_PRO472A60_S252_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A60_S252_L003


title: Sample_PRO472A58_S250_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A58_S250_L003


title: Sample_PRO472A53_S245_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A53_S245_L003


title: Sample_PRO472A50_S242_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A50_S242_L003


title: Sample_PRO472A62_S254_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A62_S254_L003


title: Sample_PRO472A49_S241_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A49_S241_L003


title: Sample_PRO472A61_S253_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A61_S253_L003


title: Sample_PRO472A43_S235_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A43_S235_L003


title: Sample_PRO472A45_S237_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A45_S237_L003


title: Sample_PRO472A6_S198_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A6_S198_L003


title: Sample_PRO472A52_S244_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A52_S244_L003


title: Sample_PRO472A55_S247_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A55_S247_L003


title: B2 : N2_2nd_μG2

description: Gene expression of N2 2nd generation in µG condition

source_name: C.elegans, N2, flight µG, 2nd generation, replicate 2


title: C2: hda4_2nd_μG 1

source_name: C.elegans, RB756 hda-4 (ok518), flight µG, 2nd generation, replicate 1


title: Male_CCI_ATACrep1

description:
CCI3a
ATAC_CCIvN_normalized_coverage.csv


title: Sample_PRO472A4_S196_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A4_S196_L003


title: Sample_PRO472A40_S232_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A40_S232_L003


title: Male_CFA_RNArep2

description:
CFA2
RNAseq-CountTable_CFA.csv


title: A2: N2_2nd_μG1

source_name: C.elegans, N2, flight µG, 2nd generation, replicate 1


title: M1: sir2.1_1st_1G 2

description: Gene expression of sir-2.1 mutant 1st generation in 1G condition

source_name: C.elegans, VC199 sir-2.1 (ok434), flight 1G, 1st generation, replicate 2


title: Male_CFA_RNArep1

description:
CFA1
RNAseq-CountTable_CFA.csv


title: Sample_PRO472A38_S230_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A38_S230_L003


title: K1: hda4_1st_1G 2

description: Gene expression of hda-4 mutant 1st generation in 1G condition

source_name: C.elegans, RB756 hda-4 (ok518), flight 1G, 1st generation, replicate 2


title: L1: sir2.1_1st_1G 1

source_name: C.elegans, VC199 sir-2.1 (ok434), flight 1G, 1st generation, replicate 1


title: Sample_PRO472A33_S225_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A33_S225_L003


title: Sample_PRO472A34_S226_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A34_S226_L003


title: H1: N2_1st_1G2

description: Gene expression of N2 1st generation in 1G condition

source_name: C.elegans, N2, flight 1G, 1st generation, replicate 2


title: Sample_PRO472A36_S228_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A36_S228_L003


title: Sample_PRO472A3_S195_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A3_S195_L003


title: J1: hda4_1st_1G 1

source_name: C.elegans, RB756 hda-4 (ok518), flight 1G, 1st generation, replicate 1


title: Sample_PRO472A28_S220_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A28_S220_L003


title: Sample_PRO472A31_S223_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A31_S223_L003


title: Sample_PRO472A30_S222_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A30_S222_L003


title: F1: sir2.1_1st_μG 2

description: Gene expression of sir-2.1 mutant 1st generation in µG condition

source_name: C.elegans, VC199 sir-2.1 (ok434), flight µG, 1st generation, replicate 2


title: Sample_PRO472A25_S217_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A25_S217_L003


title: B1: N2_1st_μG2

description: Gene expression of N2 1st generation in µG condition

source_name: C.elegans, N2, flight µG, 1st generation, replicate 2


title: Sample_PRO472A27_S219_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A27_S219_L003


title: C1: hda4_1st_μG1

description: Gene expression of hda-4 mutant 1st generation in µG condition

source_name: C.elegans, RB756 hda-4 (ok518), flight µG, 1st generation, replicate 1


title: D1: hda4_1st_μG 2

source_name: C.elegans, RB756 hda-4 (ok518), flight µG, 1st generation, replicate 2


title: G1: N2_1st_1G1

source_name: C.elegans, N2, flight 1G, 1st generation, replicate 1


title: Sample_PRO472A26_S218_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A26_S218_L003


title: A1: N2_1st_μG1

source_name: C.elegans, N2, flight µG, 1st generation, replicate 1


title: Sample_PRO472A23_S215_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A23_S215_L003

source_name: Enteric glia


title: F2 Embry.63 T CM WT 378Mu

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

description:
Gene expression data from skeletal muscle of 63 dpc of F2 population basedbreed Pi and DL.
Muscle samples of foetuses (F2) derived from the F1 sows were collected and evaluated at gestational day 63. Muscle (longissimus dorsi) samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

label: biotin

source_name: Musculus longissimus dorsi tissue from 63 dpc pig

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

value: F2 based German Landrace (DL) x Pietrain (Pi)

value: Musculus longissimus dorsi

value: 63 days post conception (dpc)


title: F2 Embry.63 T CM WT 386Mu


title: F2 Embry.63 T CM WT 383Mu


title: E1: sir2.1_1st_μG1

source_name: C.elegans, VC199 sir-2.1 (ok434), flight µG, 1st generation, replicate 1


title: F2 Embry.63 T CM WT 381Mu


title: F2 Embry.63 T CM WT 385Mu


title: F2 Embry.63 T CM WT 374Mu


title: Sample_PRO472A22_S214_L003 Naive enteric glia, rep 1

city: London

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A22_S214_L003


title: F2 Embry.63 T CM WT 388Mu


title: F2 Embry.63 T CM WT 382Mu


title: F2 Embry.63 T CM WT 380Mu


title: F2 Embry.63 T CM WT 389Mu


title: F2 Embry.63 T CM WT 375Mu


title: F2 Embry.63 T CM WT 371Mu


title: F2 Embry.63 T CM WT 372Mu


title: F2 Embry.63 T CM WT 379Mu


title: F2 Embry.63 T CM WT 373Mu


title: F2 Embry.63 T CM WT 387Mu


title: Sample_PRO472A21_S213_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A21_S213_L003


title: Sample_PRO472A186_S260_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A186_S260_L003


title: Sample_PRO472A19_S211_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A19_S211_L003


title: Sample_PRO472A192_S265_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A192_S265_L003


title: Sample_PRO472A185_S251_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A185_S251_L003


title: S-Pan-2

city: Guangzhou

first: Xiaodong

last: Ma

state: Guangdong

address: Rm406,Building 29, South China Normal University

institute: South China Normal University

data_processing:
mRNA profiles were generated by deep sequencing using novaseq 6000 sequencing platform. The reads were mapped to the human reference genome (GRCh38) by STAR software (Version 2.5.1), annotation from GENCODE version vM21 was used. Differential gene expression was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample.

growth_protocol: NCI-H1688 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and Pen/Strep antibiotic at 37 °C in a balanced air humidified incubator with 5% CO2.

extract_protocol:
Total RNA was harvested using Trizol reagent. Poly(A) RNAs were purified by using the Dynabeads mRNA purification kit and Poly(A) RNAs were fragmented at 94℃ for 5 min before reverse transcribed to cDNA with random primers. cDNA fragments were blunted and ligated to sequencing adaptors.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3µl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X)Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Human SCLC cell NCI-H1688 was cultured under standard conditions and treated for 24 hours with either DMSO, or sanguinarine(1 μM), or cepharanthine(3 μM), or evodiamine(3 μM), or (+)-JQ-1(28 μM), or panobinostat(60 nM), or sanguinarine chloride(1 μM) combine with panobinostat(60 nM), or sanguinarine chloride(1 μM) combine with (+)-JQ-1(28 μM). Total RNA was collected from each treatment group and RNA sequence was performed. Biological duplicates were done and analyzed.

tag: cell line

tag: cell origin

value: Lung Carcinoma

tag: cell type

value: epithelial cell

value: treated with panobinostat(60nM) for 24 hours


title: pan2

value: treated with sanguinarine chloride(1uM) + panobinostat(60nM) for 24 hours


title: pan1


title: JQ1

value: treated with sanguinarine chloride(1uM) +  (+)-JQ-1(28uM) for 24 hours


title: Sample_PRO472A184_S248_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A184_S248_L003

value: Adult

value: Naive


title: F2 Embry.63 T CM WT 368Mu

tag: breed

tag: age


title: S-Pan-1


title: F2 Embry.63 T CM WT 364Mu

tag: tissue


title: F2 Embry.63 T CM WT 366Mu


title: F2 Embry.63 T CM WT 369Mu


title: F2 Embry.63 T CM WT 365Mu


title: F2 Embry.63 T CM WT 367Mu


title: F2 Embry.63 T CM WT 362Mu


title: Sample_PRO472A181_S243_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A181_S243_L003

tag: strain


title: F2 Embry.63 T CM WT 361Mu


title: S-JQ1-2

value: treated with (+)-JQ-1(28uM) for 24 hours


title: JQ2


title: Sample_PRO472A183_S246_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A183_S246_L003

tag: Stage


title: Sample_PRO472A176_S239_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A176_S239_L003

tag: disease state


title: Sample_PRO472A173_S238_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A173_S238_L003


title: S-JQ1-1


title: Hh-8

value: treated with evodiamine(3uM) for 24 hours


title: Ff-6

value: treated with cepharanthine(3uM) for 24 hours


title: Sample_PRO472A179_S240_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A179_S240_L003


title: Ee-5


title: F2 Embry.63 T CM WT 359Mu


title: F2 Embry.63 T CM WT 358Mu


title: Sample_PRO472A170_S234_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A170_S234_L003


title: F2 Embry.63 T CM WT 356Mu


title: ATACseq D-iPSCs-2-1 Passage25

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

data_processing:
For ATAC-seq analysis, adaptor sequences in reads were trimmed using Trim Galore (version 0.3.7.) Then trimmed reads were aligned to the mouse reference genome (mm10) build using bowtie (version 0.12.7) with default parameters. Duplicated reads were removed using samtools (version 0.1.18).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: iPS cells

extract_protocol: For ATAC-seq library, cells were lysed with a lysis buffer (10mM Tris-HCl pH7.4, 3mM MgCl2, 10mM NaCl and 0.1% IGEPAL CA-630). Yielded nuclei were suspended in the transposase reaction mix (25 µl of 2X TD Buffer (Illumina), 2.5 µl of TD Enzyme 1 (Illumina), and 22.5 µl of nuclease-free water), and incubated for 30 minutes at 37 ℃. Fragmented DNA was then purified using MinElute PCR purification kit (QIAGEN). After that, fragmented DNA was amplified by PCR to obtain ATAC-seq libraries. The libraries were paired-end sequenced with a length of 50 bp on Hiseq 1500 (Illumina).

value: iPS cells

tag: analysis method

value: ATACseq


title: ATACseq KH2 LacZ ESCs

source_name: ES cells

value: ES cells


title: ATACseq S-iPSCs-2-1 Passage4


title: ATACseq D-iPSCs-2-1 Passage4


title: F2 Embry.63 T CM WT 357Mu


title: Gg-7


title: Dd-4

value: treated with sanguinarine chloride(1uM) for 24 hours


title: Sample_PRO472A17_S209_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A17_S209_L003


title: Sample_PRO472A167_S233_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A167_S233_L003


title: Neural cell-hASC derived Protocol 1 Donor 3

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol. Normalization using ssNoob preprocessing method.

source_name: Neural cell-hASC derived

growth_protocol: hASCs were differentiated to neuronal lineage by in vitro induction using specific culture medium. Three neuronal differentiation protocols called Neu1, Neu2 and Neu3 were used. For Neu1 induction hASCs were maintained in DMEM, supplemented with 1% penicillin/streptomycin solution, 1% ciprofloxacin (Fresenius Kabi), 25 µg/ml fibroblast growth factor (FGF, Sigma-Aldrich), 0.1 mg/ml epidermal growth factor (EGF, Sigma-Aldrich) and 10 µg/ml leukemia inhibitory factor (LIF, Sigma). The medium was changed every three days during 21 days. For Neu2 induction, hASCs were maintained in HAM-F12 medium (Sigma-Aldrich), supplemented with 1% penicillin/streptomycin solution, 1% ciprofloxacin, 20 ng/ml hepatocyte growth factor (HGF, Sigma-Aldrich), 20 ng/ml vascular endothelial growth factor (VEGF, Sigma-Aldrich) and 10 ng/ml epidermal growth factor. The medium was changed every three days during 15 days. For Neu3 induction, hASCs were maintained in neuronal progenitor basal medium (NPBM, Lonza), supplemented with 1% penicillin/streptomycin solution, 1% ciprofloxacin, 10 mg/ml adenosine 3’,5’-cyclic monophosphate (AMPc, Sigma-Aldrich), 25 ng/ml nerve growth factor (NGF, Sigma-Aldrich), 2.5 µg/ml insulin (Sigma-Aldrich) and 5 µM 3-isobutyl-1-methylxanthine (IBMX, Sigma-Aldrich) changing the medium every three days during 10 days.

extract_protocol: Total DNA was isolated by standard procedures using using conventional phenol:chloroform:isoamylalcohol (Sigma) extraction

treatment_protocol: Any additional treatment from growth conditions was applied to the biological material prior DNA extraction

tag: donor

value: Donor 3

tag: protocol


title: Neural cell-hASC derived Protocol 2 Donor 3


title: KLF5KO_SCs_Dex_rep2

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

description: Dex-treated Klf5KO SCs

data_processing:
Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

source_name: primary satellite cell

growth_protocol: Mouse primary SCs were isolated from hindlimb muscles from male MCK Cre:Klf5flox/flox and control (Klf5flox/flox) mice.  After excess fat, connective tissue and tendons were removed, hindlimb muscles were minced and digested in 0.2% collagenase type II (Worthington Biochemical Corp., Freehold, NJ) for 1 h at 37℃. Mononuclear cells were stained with PE-Cy7-conjugated anti-CD31, anti-CD45 and anti-Ly6A/E as well as FITC-conjugated anti CD106 antibodies for 30 min on ice and resuspended in PBS containing 2% FBS. SCs were isolated using a FACS Aria III flow cytometer (BD Biosciences). Debris and dead cells were excluded by forward scatter, side scatter and 7-AAD gating. Data were collected using FACS Diva software and FlowJo (BD Biosciences). SCs were cultured in GlutaMax DMEM (Life Technologies, Grand Island, NY) supplemented with 10 ng/ml basic fibroblast growth factor (Cell Signaling Technology, Beverly, MA) and 1% penicillin-streptomycin at 37℃ under 5% CO2. Myogenic differentiation was induced in GlutaMax DMEM supplemented with 5% horse serum and 1% penicillin-streptomycin at 37℃ under 5% CO2.

extract_protocol: Poly-A mRNA was extracted from total RNA by using an NEBNext Poly(A) mRNA magnetic Isolation module (NEB), after which RNA-seq libraries were prepared using a NEBNext UltraII RNA Library Prep kit for Illumina (NEB) according to the manufacturer’s protocol.

treatment_protocol: For Dex treatment, 10uM of dexamethasone (Sigma-Aldrich) was added to the medium.

value: Muscle satellite cell

tag: agent

value: Dex

tag: genotype


title: F2 Embry.63 T CM WT 354Mu

value: F2 based German Landrace (DL) x Pietrain (Pi)

value: Musculus longissimus dorsi

value: 63 days post conception (dpc)


title: Neural cell-hASC derived Protocol 2 Donor 2

value: Donor 2


title: KLF5KO_SCs_Dex_rep1

description: Dex-treated Klf5KO SCs


title: Neural cell-hASC derived Protocol 1 Donor 2


title: F2 Embry.63 T CM WT 353Mu


title: Bb-2

value: Lung Carcinoma

value: epithelial cell

tag: treatment

value: untreated


title: Neural cell-hASC derived Protocol 3 Donor 3


title: F2 Embry.63 T CM WT 351Mu


title: F2 Embry.63 T CM WT 348Mu


title: Cc-3


title: F2 Embry.63 T CM WT 350Mu


title: Sample_PRO472A161_S227_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A161_S227_L003

value: Adult

value: Naive


title: Neural cell-hASC derived Protocol 2 Donor 1

value: Donor 1


title: F2 Embry.63 T CM WT 349Mu

description:
Gene expression data from skeletal muscle of 63 dpc of F2 population basedbreed Pi and DL.
Muscle samples of foetuses (F2) derived from the F1 sows were collected and evaluated at gestational day 63. Muscle (longissimus dorsi) samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.


title: Sample_PRO472A164_S231_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A164_S231_L003


title: Sample_PRO472A162_S229_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A162_S229_L003


title: KLF5KO_SCs_Veh_rep2

description: Vehicle-treated Klf5KO SCs

value: Vehicle


title: Aa-1


title: Neural cell-hASC derived Protocol 3 Donor 1

description: Neu3 -Donor1


title: Sample_PRO472A16_S208_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A16_S208_L003


title: control_SCs_Dex_rep1

description: Dex-treated control SCs

value: wildtype


title: Neural cell-hASC derived Protocol 3 Donor 2


title: KLF5KO_SCs_Veh_rep1

description: Vehicle-treated Klf5KO SCs


title: Neural cell-hASC derived Protocol 1 Donor 1


title: DG034: 4WK Tsc1CKO Rep5

city: New York

first: GUOMEI

last: TANG

department: Neurology

institute: Columbia University

data_processing:
Illumina software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tiphat (2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: upper half of somatosensory and parietal cortex

extract_protocol:
upper half cortex of somatosensory and parietal cortice were islolated from coronal brain sections, flash frozen on dry ice. RNA was extracted harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bl6/129S mixed background

value: cortex

value: postnatal 4Weeks


title: F2 Embry.63 T CM WT 345Mu


title: control_SCs_Dex_rep2

description: Dex-treated control SCs

value: Muscle satellite cell


title: SCs_Veh_rep2

description: Vehicle-treated

growth_protocol: Mouse primary SCs were isolated from hindlimb muscles from male C57BL6 mice.  After excess fat, connective tissue and tendons were removed, hindlimb muscles were minced and digested in 0.2% collagenase type II (Worthington Biochemical Corp., Freehold, NJ) for 1 h at 37℃. Mononuclear cells were stained with PE-Cy7-conjugated anti-CD31, anti-CD45 and anti-Ly6A/E as well as FITC-conjugated anti CD106 antibodies for 30 min on ice and resuspended in PBS containing 2% FBS. SCs were isolated using a FACS Aria III flow cytometer (BD Biosciences). Debris and dead cells were excluded by forward scatter, side scatter and 7-AAD gating. Data were collected using FACS Diva software and FlowJo (BD Biosciences). SCs were cultured in GlutaMax DMEM (Life Technologies, Grand Island, NY) supplemented with 10 ng/ml basic fibroblast growth factor (Cell Signaling Technology, Beverly, MA) and 1% penicillin-streptomycin at 37℃ under 5% CO2. Myogenic differentiation was induced in GlutaMax DMEM supplemented with 5% horse serum and 1% penicillin-streptomycin at 37℃ under 5% CO2.

extract_protocol: Nuclei were extracted from approximately 50,000 cells. After transposase reactions, cellular DNA was immediately purified. The DNA was amplified for 14 cycles using Nextera primer Ad1 and a unique Ad2.n barcoding primer with NEBNext High-Fidelity 2XPCR Master Mix (NEB). The resulting libraries were size selected to 175-225 bp, purified.

value: muscle satellite cell


title: Sample_PRO472A156_S216_L003 Naive enteric glia, rep 1

department: Development and Homeostasis of the Nervous System Laboratory

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A156_S216_L003


title: SCs_Veh_rep1

description: Vehicle-treated


title: Sample_PRO472A144_S207_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A144_S207_L003


title: Sample_PRO472A143_S206_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A143_S206_L003


title: Sample_PRO472A160_S224_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A160_S224_L003


title: F2 Embry.63 T CM WT 341Mu

value: F2 based German Landrace (DL) x Pietrain (Pi)


title: F2 Embry.63 T CM WT 346Mu

value: Musculus longissimus dorsi


title: D65_POU4F2_3

city: La Jolla

first: Karl

last: Wahlin

state: CA

address: 9415 Campus Point Dr., #0946

department: Ophthalmology

institute: UC San Diego

data_processing:
Adapter and quality trimming using Trimmomatic
concatenate files using Galaxy Core utilities 'concatenate datasets' and FastQC for quality assessment.
Feature counts
Reads mapped to reference genome GRCh37.13(hg19) using HISAT2 (v2.1.0)
Differential sequence analysis performed using DESeq2 (v1.22.1) and EdgeR (v3.24.1)
Genome_build: GRCh37.13(hg19)

source_name: Neural organoids

growth_protocol: Stem cells were maintained under hypoxic conditions in mTeSR1 media. Stem cells were differentiated into organoids using BE6.2-NIM (B27 + E6 at 2X concentration) (neural induction medium) consists of DMEM (#11965; Invitrogen) supplemented with 1% B27 vitamin A (-) (#12587010; Invitrogen) and 2X E6 supplement (38.8 mg/L insulin (#11376497001; Roche), +128mg/L L-ascorbic acid (#A8960; Sigma), 28μg/L selenium (#S5261; Sigma), 21.4 mg/L transferrin (#T0665; Sigma) and 38.8 mg/L NaHCO3). Osmolarity was raised +30mOsm to ~330-340mOsm) by adding 0.88 g/L NaCl (Ludwig, Bergendahl et al. 2006, Chen, Gulbranson et al. 2011). LTR (Long-Term Retina) medium was a 3:1 mix of high glucose DMEM:F12 (#11965, #11765; Invitrogen) supplemented with 1% B27 (#17504044; Invitrogen), 10% heat inactivated qualified-grade FBS (#16140071; Invitrogen), 1mM pyruvate (#11360; Invitrogen), 1xNEAA (#11140; Invitrogen), 1X Glutamax (#35050061; Invitrogen) and 1mM taurine (#T-8691; Sigma).

extract_protocol:
Organoids were harvested, stored at -80 and RNA extracted using a Zymopure RNA microprep kit
TruSeq Library Prep kit v3.0
RNA analyzed using a 4200 Tapestation System, RIN value greater than 8 used for library preparation

value: human induced pluripotent stem cell-derived organoids

tag: fluorescence

value: SIX6 GFP positive / POU4F2-Tomato positive

value: IMR90.4 SIX6-eGFP/POU4F2-tdTomato


title: control_SCs_Veh_rep2

description: Vehicle-treated control SCs


title: D65_POU4F2_4


title: F2 Embry.63 T CM WT 347Mu

value: 63 days post conception (dpc)


title: Sample_PRO472A159_S221_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A159_S221_L003


title: control_SCs_Veh_rep1

description: Vehicle-treated control SCs


title: Veh-4a2

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description:
2014_528_CAGATC_L005
Veh, fourth, Biological replicate A, Technical replicate 2

data_processing:
Illumina bcl2fastq 1.8.4 software used for demultiplexing.
The analyses were performed using the Eoulsan pipeline, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from UCSC) using Bowtie (version 0.12.9, parameters -n 2 -l 34 -e 70 -k 2 –best). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, Mus musculus (mm10) GFF3 genome annotation from UCSC database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: tab-delimited text files include gene counting for each sample

source_name: S129_Veh_Choroid plexus, 4th ventricle

extract_protocol:
RNA extracted directly from tissue with RNEasy Mini Kit (Qiagen)
Ribosomal RNA depletion was performed with the Ribo-Zero kit (Epicentre), using 0.5 (first run) or 1 µg (second run) of total RNA. Libraries were prepared using the strand specific RNA-Seq library preparation ScriptSeq V2 kit (Epicentre). Libraries were multiplexed by 6 on one flow cell lane for the first run, and by 8 on 2 flow cell lanes for the other run. A 50 bp read sequencing was performed on a HiSeq 1500 device (Illumina).

value: Veh

value: Choroid plexus, 4th ventricle


title: D65_POU4F2_2


title: F2 Embry.63 T CM WT 344Mu


title: D65_POU4F2_1


title: F2 Embry.63 T CM WT 339Mu


title: D65_SIX6_3

value: SIX6 GFP positive


title: Cre-4b2

description:
2014_525_GGCTAC_L005
Cre, fourth, Biological replicate B, Technical replicate 2

source_name: S129_Cre_Choroid plexus, 4th ventricle

value: Cre


title: SCs_Dex_rep2

description: Dex-treated

value: Dex


title: Sample_PRO472A131_S201_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A131_S201_L003

value: Adult

value: Naive


title: Sample_PRO472A12_S204_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A12_S204_L003


title: Sample_PRO472A114_S199_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A114_S199_L003


title: F2 Embry.63 T CM WT 335Mu


title: F2 Embry.63 T CM WT 343Mu


title: Cre-4a2

description:
2014_524_TAGCTT_L005
Cre, fourth, Biological replicate A, Technical replicate 2


title: D65_SIX6_2


title: Sample_PRO472A113_S194_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A113_S194_L003


title: F2 Embry.63 T CM WT 334Mu


title: F2 Embry.63 T CM WT 342Mu


title: Sample_PRO472A155_S212_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A155_S212_L003


title: Sample_PRO472A148_S210_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A148_S210_L003


title: Sample_PRO472A11_S203_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A11_S203_L003


title: Veh-4b2

description:
2014_529_CTTGTA_L005
Veh, fourth, Biological replicate B, Technical replicate 2


title: Sample_PRO472A142_S205_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A142_S205_L003


title: D65_SIX6_1


title: SCs_Dex_rep1

description: Dex-treated


title: Sample_PRO472A138_S202_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A138_S202_L003


title: F2 Embry.63 T CM WT 331Mu

description:
Gene expression data from skeletal muscle of 63 dpc of F2 population basedbreed Pi and DL.
Muscle samples of foetuses (F2) derived from the F1 sows were collected and evaluated at gestational day 63. Muscle (longissimus dorsi) samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.


title: D65_NEG2

value: SIX6 GFP negative


title: Veh-Lb2

description:
2014_527_TTAGGC_L005
Veh, lateral, Biological replicate B, Technical replicate 2

source_name: S129_Veh_Choroid plexus, lateral ventricle

value: Choroid plexus, lateral ventricle


title: F2 Embry.63 T CM WT 330Mu


title: F2 Embry.63 T CM WT 328Mu


title: F2 Embry.63 T CM WT 336Mu


title: F2 Embry.63 T CM WT 337Mu


title: I_ME79_EV_GACGAC_S35

city: Chapel Hill

first: Gregory

middle: James

last: Smith

address: 120 Mason Farm Road, 5070E Genetic Medicine Building

department: Genetics

institute: University of North Carolina

description:
pooled BALF from 3 mice
I_ME79_EV_GACGAC_S35_L003

data_processing:
Read alignment, annotation, and quantification of reads were performed with miRquant 2.0
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: RPMMM = Read counts normalized to the total number of reads mapped to all miRNA/isomiR loci multiplied by 1 million.

source_name: bronchoalveolar lavage fluid extracellular vesicles

growth_protocol: Mice were housed on alpha-dri bedding with ad libitum food/water and a standard 12 hour light cycle.

extract_protocol:
Bronchoalveolar lavage fluid extracellular vesicle RNA was isolated using a QIAGEN ExoEasy Serum/Plasma midi kit according to the manufacturers protocol.
Libraries were prepared by the University of North Carolina High Throughput Sequencing Facility using the BioOScientific NEXT FlexRNA -v3 kit. Samples were sequenced on an Illunina HS4000; 50bp single end reads; 20 million reads/sample

treatment_protocol: Mice were exposed to Filtered Air (Control), 1 or 2 ppm Ozone in a whole body inhalation exposure chamber for 3 hours.

tag: exposure

value: 2 ppm Ozone

value: 8 to 10 weeks


title: D65_NEG1


title: D65_SIX6_4


title: F2 Embry.63 T CM WT 323Mu

value: F2 based German Landrace (DL) x Pietrain (Pi)


title: Sample_PRO472A1_S193_L003 Naive enteric glia, rep 1

description:
Naive enteric glia, rep 1
Naive 1
Sample_PRO472A1_S193_L003


title: Cre-Lb2

description:
2014_523_ACTTGA_L005
Cre, lateral, Biological replicate B, Technical replicate 2

source_name: S129_Cre_Choroid plexus, lateral ventricle


title: F2 Embry.63 T CM WT 333Mu

value: Musculus longissimus dorsi


title: F2 Embry.63 T CM WT 332Mu


title: Veh-La2

description:
2014_526_ATCACG_L005
Veh, lateral, Biological replicate A, Technical replicate 2


title: Cre-La2

description:
2014_522_TGACCA_L005
Cre, lateral, Biological replicate A, Technical replicate 2


title: E_ME79_EV_GATCAG_S32

description:
pooled BALF from 4 mice
E_ME79_EV_GATCAG_S32_L003

value: bronchoalveolar lavage fluid extracellular vesicles

value: Filtered Air


title: Cre-4a1

description:
2014_524_TAGCTT_L001
Cre, fourth, Biological replicate A, Technical replicate 1


title: D65_NEG4

value: human induced pluripotent stem cell-derived organoids

value: IMR90.4 SIX6-eGFP/POU4F2-tdTomato


title: Veh-4a1

description:
2014_528_CAGATC_L001
Veh, fourth, Biological replicate A, Technical replicate 1

value: Veh


title: H_ME79_EV_GTGAAA_S37

description:
pooled BALF from 3 mice
H_ME79_EV_GTGAAA_S37_L003