title: NF2 (Non-painful)_set1_N2

extract_protocol:
Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer’s instructions.
Libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit from 500ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer’s recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: spinal (L4)

value: N2 or NP2


title: DOS-66

status: Public on May 01 2020

type: SRA

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

country: USA

institute: University of Minnesota

description:
DNA methylation
canine_MethValues_allSamples_crossSpecies.txt

library_source: genomic

data_processing:
Illumina specific adapter sequences and low quality sequences were removed from raw sequencing data using Trimmomatic50. Reads were aligned to a bisulfite converted human (hg19) or canine (canfam3.1) genome using WALT51. Duplicate sequences were removed from alignment data using MethPipe52 duplicate-remover and bisulfite conversion rates were estimated for each sample using bsrate. All samples had conversion efficiencies > 99%. Sequencing depths for each sample were such that an average of 88.3% and 81.3% of targeted CpGs were sequenced at a 10X depth or higher. MethPipe methcounts was used to calculate methylation levels and read coverage at individual CpGs in each sample. A custom perl script was used to isolate CpGs with a read depth of 10 or greater and MethPipe roimethstats was used to summarize methylation levels in 500 bp windows, generated by BEDtools53 windowBed, along the capture targets in each genome.  CpG methylation levels were expressed as a value between 0 and 1.
USCS utility liftOver with the appropriate genome wide alignment file was used to convert the canine genomic coordinates for each 500bp window from CanFam3.1 to hg19. and the human genomic coordinates for each 500bp window to GRCh38. Converting both sets of coordinates to GRCh38 resulted in the highest number of 500bp windows being conserved between the two species. Genomic regions were considered homologs if the converted GRCh38 coordinates were within 1,000bp of each other as calculated by BEDtools closest.
Genome_build: hg19, canfam3.1

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: primary osteosarcoma

extract_protocol: Tumor tissues were removed from -86℃ and sectioned to avoid areas of necrosis. Thirty mg of tissue were placed in 80 µL of phosphate buffered saline (PBS) solution and pulverized in a tissue homogenizer. Isolation of genomic DNA was done according to the manufacturer’s protocol using the QIAamp DNA Mini Kit from Qiagen.Illumina library preparation, bisulfited converted and bead capture was performed as specified in the Roch SeqCap Epi protocol outlined in Li et al (doi: 10.1093/nar/gkv244)

tag: tissue

value: osteosarcoma


title: 201516240034_R06C01_Smoker

type: genomic

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 East Cornwallis Road

institute: RTI International

description: postmortem nucleus accumbens from a smoker

hyb_protocol: DNA was profiled with the Infinium MethylationEPIC BeadChip array using the manufacturer's protocol.

scan_protocol: The Illumina MethylationEPIC array hybridization and scanning were performed at the Lieber Institute for Brain Development.

data_processing: Raw data resulted from GenomeStudio software (Illumina)

label: Cy5, Cy3

organism: Homo sapiens

source_name: nucleus accumbens

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from dissected postmortem nucleus accumbens tissue using the Qiagen AllPrep DNA/RNA Mini Kit (Cat No./ID: 80204).

tag: current smoking status

value: Smoker

tag: age at death

tag: sex (m, male; f, female)

value: M

tag: ancestry (cauc, caucasian; aa, african american)

value: AA


title: NF2 (Non-painful)_set1_N6

city: Boston

first: Gary

last: Brenner

state: MA

address: 15 Parkman Street

department: Anesthesia Critical Care and Pain Medicine

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
Illumina Bcl2fastq v2.17 was used to demultiplex raw bcl files and generate fastq files
Transcriptome mapping was performed with SALMON (PMID:28263959) using the Ensembl annotation of hg19 reference genome
Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: hg19
Supplementary_files_format_and_content: TPM, NumReads

molecule: total RNA

source_name: Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue block from human NF2 patient

value: Neurofibromatosis II (NF2) tumor sample

tag: site of tumor extracted (location)

value: spinal (cervical)

tag: sample id in rnaseq analysis

value: N6 or NP6

tag: patient tumor related pain status

value: Non-Painful


title: DOS-64


title: Ctrl_Input_H3K27me3_rep2

city: Beijing

first: Qiu

last: Xie

state: Beijing

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

country: China

institute: Peking Union Medical College Hospital

data_processing:
Raw data were trimmed using TrimGalore version 0.6.0.
RNA-seq reads were aligned to the mm10 genome assembly using Tophat2 version 2.1.1. ChIP-seq for histone modifications and ATAC-seq reads were aligned to the mm10 genome assembly using STAR version 2.7.0d. ChIP-seq for CTCF were aligned to the mm10 genome assembly using Bowtie2
Gene expression was calculated using Cufflinks version 2.2.1 and differentially expressed genes were called using Cuffdiff version 2.2.1.
Peaks were called using MACS version 1.4.2 with the following setting: -p 1-6, --keep-dup auto, -w -S, --space 50, --nolambda, --nomodel.
Genome_build: mm10
Supplementary_files_format_and_content: peaks.bed were generated using MACS version 1.4.2 with the following setting: -p 1-6, --keep-dup auto, -w -S, --space 50, --nolambda, --nomodel.

organism: Mus musculus

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells Sv/129 (mESCs) were kindly provided by Xuanwu Hospital (Beijing, China). The cells were cultured as previously described 15. Briefly, mESCs were maintained on mitotically inactivated primary mouse embryonic fibroblasts prior to cultivation under feeder-free conditions. The cells were kept at 37°C in a humidified atmosphere with 5% CO2, and passaged every 2–3 days. A split ratio of 1:4 to 1:7 was performed.

extract_protocol:
For RNA isolation, total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s recommendations. reverse transcription was carried out using the TransScript First-Strand cDNA Synthesis SuperMix (TransGen Biotech, Beijing, China). For ChIP, In accordance with the manufacturer’s protocol, a SimpleChIP™ Enzymatic Chromatin IP Kit (CST) was used for the ChIP assays. Briefly, formaldehyde cross-linked chromatin was obtained from about 2×107 mESCs. Cross-linked chromatin was immunoprecipitated with antibodies to H3K4me1, H3K4me3, H3K27me3, H3K27ac, H3K9me3, gamma-phosphorylated H2AX and CTCF. Non-specific mouse IgG and H3 were used for negative and positive controls, respectively.
For RNA-seq, briefly, total RNA was treated with the Epicentre Ribo-Zero kit to remove the all the rRNAs. The remaining RNAs were processed using the TruSeq RNA Sample Prep Kit according to the Illumina protocol. Then, RT-PCR was performed with Phusion High-Fidelity DNA polymerase, Index (X) Primer, and Universal PCR primers. Finally, the products were purified using the AMPure XP system, and library quality was evaluated on an Agilent Bioanalyzer 2100 system. The RNA library was sequenced on an Illumina Hiseq 4000 platform, and 150 bp paired-end reads were generated. For ChIP-seq, DNA libraries of H3K4me1,H3K27ac, H3K4me3, H3K27me3, H3K9me3, phospho S139 gamma H2A.X and CTCF were prepared for HiSeq 4000 sequencing as previously before.

treatment_protocol: 0.12 μM Methotrexate (MTX, Sigma) were treated at 24 h against mESCs as MTX treatment. Other drugs refer to Etoposide (Sigma) was at 5 μM, NU7026 (Calbiochem) was at 5mM.

tag: cell type

value: normal mESC

tag: strain

tag: chip antibody


title: 201516260055_R02C01_Smoker

value: F

value: CAUC


title: DOS-69


title: DOS-60


title: NF2 (Non-painful)_set1_N8

value: right vestibular

value: N8 or NP8


title: DOS-55


title: DOS-54


title: DOS-52


title: Ctrl_Input_H3K27me3_rep1


title: NF2 (Non-painful)_set1_N7

value: right femoral

value: N7 or NP7


title: DOS-39


title: 201516260019_R05C01_Smoker


title: 201516280060_R02C01_Smoker


title: Mtx_H3K27me3_rep1

value: MTX-treated mESC


title: 201516250042_R04C01_Smoker


title: DOS-24


title: 201516280040_R06C01_Smoker


title: DOS-29


title: NF2 (Non-painful)_set1_N9

value: right nasal

value: N9 or NP9


title: DOS-32-2

value: osteosarcoma


title: 201516260028_R07C01_Smoker

value: Smoker


title: DOS-121


title: 201516260008_R01C01_Smoker

value: AA


title: Ctrl_H3K27me3_rep2


title: DOS-120


title: Ctrl_H3K27me3_rep1


title: NF2 (Non-painful)_set1_N3

value: Neurofibromatosis II (NF2) tumor sample

value: left neck

value: N3 or NP3


title: DOS-11


title: 201516250045_R04C01_Smoker

value: M


title: DOS-114


title: DOS-110


title: Mtx_Input_H3K4me3_H3K27ac


title: DOS-108


title: NF2 (Non-painful)_set1_N1

value: spinal (T12)

value: N1 or NP1

value: Non-Painful


title: DOS-105


title: NF2 (painful)_set1_Y2

value: left peroneal

value: Y2 or P2

value: Painful


title: Ctrl_Input_H3K4me3_H3K27ac

value: normal mESC


title: Mtx_H3K27ac

value: MTX-treated mESC


title: DOS-103


title: 201516250030_R06C01_Smoker

value: CAUC


title: DOS-104


title: NF2 (painful)_set1_Y3

value: left forearm

value: Y3 or P3


title: NF2 (painful)_set1_Y5

value: right hand

value: Y5 or P5


title: Ctrl_H3K27ac


title: DOS-09

value: osteosarcoma


title: Mtx_H3K27me3_rep2


title: NF2 (Non-painful)_set1_N4

value: Neurofibromatosis II (NF2) tumor sample

value: left brachial

value: N4 or NP4


title: Mtx_Input_H3K27me3_rep1


title: 201516280040_R07C01_Smoker

value: Smoker

value: M


title: DOS-0956


title: DOS-0951


title: DOS-0945


title: Mtx_H3K4me3


title: Midbrain organoids carrying the LRRK2-G2019S mutation differentiated for 35 days

city: Maastricht

first: Silvia

last: Bolognin

state: -- None selected --

address: Universiteitssingel 40,

country: Netherlands

institute: Maastricht University

description:
org4Mu35_S2_DGE
scRNA-Seq
mRNA

data_processing:
Bcl2fastq ver 2.0 was used for the base calling.
Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Drop-seq implementation (Macosko et al., 2015), the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCh38 using STAR genome aligner - with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts.

source_name: IPSC

growth_protocol: As described in Smits et al., NPJ Parkinsons Dis doi: 10.1038/s41531-019-0078-4

extract_protocol:
Single cell RNA seq using Drop-seq - 3' bead based enrichment technique, using SMART synthesis (Macosko et al., 2015 doi: 10.1016/j.cell.2015.05.002).
Libraries were prepared according to Drop-seq methods (Macosko et al., 2015 doi: 10.1016/j.cell.2015.05.002). After cDNA tagmentation, PCR amplification was performed using Illumina primers (N701, N702, A501). The purified cDNA fragments of ~600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: No treatment was performed.

value: Midbrain organoids

tag: genotype/variation

tag: differentiation time

value: 35 days

value: Astrocytes


title: Ctrl_H3K4me3


title: DOS-0942


title: Midbrain organoids LRRK2-WT differentiated for 35 days

description:
org3wt35_S1_DGE
scRNA-Seq
mRNA


title: DOS-0941


title: DOS-0939


title: DOS-0944


title: DOS-0940


title: Ctrl-Input_gH2AX_H3K4me1


title: HEK-293t, siNF90 Rep3 (smallRNA-seq)

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

data_processing:
Raw data were processed using the Subread package (version 1.6.0). The mapping was performed using the following parameters: -t 1 -n 50 -m 4 -M 4 -I 0 -P 3 --multiMapping -B 10
Measure gene expression from alignment files with FeatureCounts (version 1.6.3)
Differential expression analysis performed with DESeq2 (2.11.40.2)
Genome_build: GRCh38.96, reference annotation from miRbase (release 22.1)
Supplementary_files_format_and_content: [HEK-293t_miRprofiling_results.xlsx] tabular file in .xlsx format containing results of differential expression analysis (siNF90 vs siScr).
[.tsv] Counts file

growth_protocol: Human HEK-293t cell line was grown in Dulbecco’s Modified Eagle’s medium – high glucose-HEPES modification, supplemented with 10% fetal bovine serum , 1% penicillin-streptomicin (v/v) and 1% L-glutamine (v/v). Cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol according to the manufacturer’s instructions
Libraries were prepared by FASTERIS, Standard Library preparation - Protocol small RNA Illumina
Standard Library preparation - Protocol small RNA Illumina

treatment_protocol: HEK-293t cells were transfected with control and NF90 siRNAs (30 nM final concentration) using INTERFERin® transfection reagent according to the manufacturer’s instructions. Two rounds of transfection were performed. Cells were collected for RNA extraction after 10 days.

value: Human Embryonic Kidney

tag: cell line

tag: treatment


title: Midbrain organoids LRRK2-WT differentiated for 70 days

description:
org1wt70II_S1_DGE
scRNA-Seq
mRNA

value: 70 days


title: DOS-0931


title: Mtx_gH2AX

value: MTX-treated mESC


title: DOS-0932


title: HEK-293t, siNF90 Rep2 (smallRNA-seq)


title: DOS-0930


title: Ctrl_gH2AX

value: normal mESC


title: HEK-293t, siNF90 Rep1 (smallRNA-seq)


title: DOS-0828


title: Mtx_H3K4me1


title: DOS-04


title: DOS-0934


title: HEK-293t, siScr Rep3 (smallRNA-seq)

value: siScr


title: Mtx-Input_gH2AX_H3K4me1


title: DOS-02


title: 201516260055_R05C01_Smoker

value: CAUC


title: Ctrl H3K4me1


title: DOS-00


title: 201516260029_R03C01_Smoker


title: DOS-0829


title: HEK-293t, siScr Rep2 (smallRNA-seq)


title: Genomic input

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

data_processing:
ChIP-seq reads were aligned to the Saccharomyces cerevisiae genome build 3 (sacCer3) using Burrows-Wheeler Alignment ( BWA) with default parameters in bwa aln and bwa samse
2M reads of each sample were random selected for peak calling, peaks were called using MACS version 2 with the following settings: -B -nomodel -extsize 200 -q 0.01 -g 12157105
MACS2 bdgcmp was used to generate fold-enrichment and logLR track with parameters -m FE and -m logLR -p 0.00001
Genome_build: sacCer3
Supplementary_files_format_and_content: [.narrowPeak] file reports peaks with FDR q <0.01

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Strains were grown at 30C in YPD (1% yeast extract, 2% peptone, 2% glucose) until early log phase of growth

extract_protocol:
Cells were lysed by vortexing with glass beads in the presence of protease inhibitors. The samples were then sonicated four times for 10 seconds to shear the DNA. Samples were pre-cleared using protein A agarose beads for 30 minutes with rotation at 4C. Samples were then incubated at 4C overnight with 5µL of anti-HA (Sigma H6908). Sir2-HA and Hst1-HA were pulled down using protein A agarose beads. The DNA was eluted from the beads and crosslinking was reversed at 65C overnight. The DNA was extracted with phenol chloroform. The DNA was resuspended in 25 uM tris.
ChIP samples were sent for ChIP-seq library preparation and 50 cycle single read sequencing on an Illumina HiSeq2500 at The University at Buffalo Genomics and Sequencing Core.

treatment_protocol: Chromatin IPs were performed by harvesting 50 OD of cells at the early log phase of growth. The cells were washed twice with PBS, resuspended in DMA (10mM dimethyl adipimidate, 0.1% DMSO, 1X PBS) and rocked at room temperature for 1 hour. Cells were then washed again in PBS and resuspended in formaldehyde (1% final concentration formaldehyde, 1X PBS) and rocked at room temperature for 1 hour.

value: early log phase

value: Parental Strain


title: HEK-293t, siScr Rep1 (smallRNA-seq)


title: Hst1_ChIPSeq

value: Hst1 Ha tagged strain

value: anti-HA (Sigma, catalog# H6908, lot# 072M4847)


title: Mtx-ATAC-rep3


title: Sir2_ChIPSeq

value: Sir2 Ha tagged strain


title: Mtx-ATAC-rep1


title: 201516250010_R06C01_Smoker

value: F

value: AA


title: Mtx-ATAC-rep2


title: FL [72143]

city: Toronto

first: Laurie

last: Ailles

state: ON

address: 101 College St.

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
The reads were mapped using STAR/2.5.2 to the hg38 reference genome
Read counts per gene were obtained through htseq-count v.0.6.1.
Genome_build: hg38
Supplementary_files_format_and_content: read counts per gene

extract_protocol: RNA was extracted using the Rneasy Plus Micro kit (Qiagen). 4 ng of RNA were used to prepare RNA libraries using the SMARTer Stranded Total RNA-seq Kit – Pico Input Mammalian (Takara Bio USA Inc.). The samples were sequenced using a paired-end 75 cycle sequencing run to achieve a minimum of ~40M reads per sample on NextSeq 500 system.

treatment_protocol: Sorted populations were washed with PBS

tag: subject id

value: high-grade serous ovarian cancer (HGSOC)

value: fibroblast

tag: caf subtype

value: FL


title: pmk-1(km25) total mRNA Replicate 2

city: Dallas

first: Benjamin

last: Weaver

address: 6001 Forest Park Rd

department: Pharmacology

institute: University of Texas Southwestern Medical Center

description:
mRNA
P1T2

data_processing:
Adaptors were removed using SeqPurge
rRNA reads were removed using bowtie2
Reads were mapped to the C. elegans genome using STAR
Mapped reads were counted using HTSeq
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files includeraw count values for each Sample using HTSeq...

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: C elegans strains were cultured on solid agar plates with OP50 bacteria lawn.

extract_protocol:
The ribosomal profiling protocol and total mRNA isolation were modified based on a published protocol (Aeschimann et al., 2015) and the TruSeq® Ribo Profile Protocol (Illumina).
TruSeq® Ribo Profile Protocol (Illumina).
RNA-seq and Ribosome profilling

treatment_protocol: Synchronized day 1 young adult wild type (N2), ced-3(n717) and pmk-1(km25) worms were bleached and then the eggs were incubated in M9 for 24 hours to obtain synchronized L1s. L1s were plated on OP50 for 18hrs at 20°C until >90% of wild type worms reached L3 stage

tag: Stage

tag: genotype


title: pmk-1(km25)RPF Replicate 2

description:
ribosomal protected fragments (RPFs) are derived from the same sample as total mRNA
P1R9


title: 201516260029_R01C01_Smoker

tag: current smoking status

value: Smoker

tag: age at death

value: M


title: 201516240041_R02C01_Smoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)


title: 201516250050_R07C01_Smoker


title: mock IP


title: FH [72143]

tag: tissue

value: FH


title: FL [72130]


title: pmk-1(km25) total mRNA Replicate 1

description:
mRNA
P1T7


title: ced-3(n717)RPF Replicate 2

description:
ribosomal protected fragments (RPFs) are derived from the same sample as total mRNA
C3R10


title: ced-3(n717) total mRNA Replicate 2

description:
mRNA
C3T3


title: Ctrl_ATAC_rep2


title: FH [71853]


title: Ctrl_ATAC_rep3


title: 201516250045_R01C01_Smoker


title: ced-3(n717)RPF Replicate 1

description:
ribosomal protected fragments (RPFs) are derived from the same sample as total mRNA
C3R12


title: ced-3(n717) total mRNA Replicate 1

description:
mRNA
C3T8


title: WT RPF Replicate 2

description:
ribosomal protected fragments (RPFs) are derived from the same sample as total mRNA
N2R5

value: wild type


title: Mtx_RNA-seq_rep3

value: MTX-treated mESC


title: Ctrl_ATAC_rep1

value: normal mESC


title: FL [71423]


title: FH [71423]


title: WT total mRNA Replicate 2

description:
mRNA
N2T1


title: WT RPF Replicate 1

description:
ribosomal protected fragments (RPFs) are derived from the same sample as total mRNA
N2R6


title: Mtx_RNA-seq_rep2


title: FH [70924]


title: WT total mRNA Replicate 1

description:
mRNA
N2T4


title: Mtx_RNA-seq_rep1


title: FL [70535]


title: pmk-1(km25)RPF Replicate 1

description:
ribosomal protected fragments (RPFs) are derived from the same sample as total mRNA
P1R11


title: FH [70535]


title: WT_2

city: Smithville

first: Jianqiang

last: Bao

state: Texas

address: 1808 Park Road 1C (P.O. Box 389), Smithville  TX 78957

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version 3.3.76).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on July 17, 2015) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the cpm (count per million) value for each gene was calculated by R/Bioconductor package edgeR (version 3.8.6).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are cpm values (estimated by edgeR) for all the samples.

source_name: testis

growth_protocol: Freshly isolated testis tissue

extract_protocol:
Trizol reagent
The libraries were prepared using the Illumina TruSeq stranded mRNA-seq kit according to the manufacturer’s protocol.

treatment_protocol: Dnase I treatment

value: WT

value: germ cells

value: FVB


title: WT_1


title: MUT_2

value: lrrc8a MUT


title: 1M

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

data_processing:
Cell ranger (Version 3.0.2, https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger) was used to demultiplex reads, followed by extraction of cell barcode and unique molecular identifiers (UMIs). The cDNA insert was aligned to a modified reference mouse genome (mm10).
Doublets or cells with poor quality (genes>6000, genes<200, or >5% genes mapping to mitochondrial genome) were excluded. Expression was natural log transformed and normalized for scaling the sequencing depth to a total of 1x104 molecules per cell, followed by regressing out the number of UMIs and percent mitochondrial genes using Seurat V2 8.
Genome_build: modified mm10 with sequence of tomato
Supplementary_files_format_and_content: txt files of raw UMI counts per sample

source_name: endosteal bone marrow

extract_protocol:
Endosteal bone marrow cells were harvested as described, the outer surfaces of long bones were scraped and digested to remove the periosteum. After cutting off the epiphyses and flushing out the central bone marrow, metaphyseal bone fragments were longitudinally cut into two halves and digested by proteases to collect endosteal bone marrow cells. Freshly isolated endosteal bone marrow cells were resuspended into FACS buffer containing 25 mM HEPES (Thermofisher scientific) and 2% FBS in PBS and sorted for top 1% Td+ cells if a Td peak was not obvious or Td+ cells if a Td peak was obvious using Influx B (BD Biosciences, San Jose, CA) or Aria B (BD Biosciences, San Jose, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

tag: age

value: 1 month


title: 3M

value: 3 month


title: Bifido

city: Shanghai

first: Xue

last: Fang

address: No.168, Changhai Road,Yangpu District 200433

department: Department of Gastroenterology

institute: Changhai Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Enteroid incubated with B.longum

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: primary cultured enteroid

value: 8 weeks

tag: location

value: Department of Gastroenterology of Changhai hospital


title: 1.5M

tag: strain

value: 1.5 month


title: Ctrl_RNA-seq_rep2

tag: cell type


title: 106886_acapsular +HKARB25

city: Ann Arbor

first: Jaime

middle: Joel

last: Fuentes

state: MI

address: 1150 West Medical Center Drive, 6751 Medical Science BLDG II

department: Microbiology and Immunology

institute: University of Michigan

description:
rRNA-depleted, mRNA
Bt Acaps ARB25 in vitro.xlsx

data_processing:
Data was analyzed using Arraystar software (DNASTAR, Inc.)
DEseq2 normalization with default parameters
Gene expression in ribose was compared to gene expression in heat-killed phage treated reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >5-fold and with at least 2/3 biological replicates with a normalized expression level >1%
Genome_build: NC_004663.1
Supplementary_files_format_and_content: xslx files include DEseq2 values for each sample

organism: Bacteroides thetaiotaomicron VPI-5482

source_name: acapsular +HKARB25

growth_protocol: For in vitro samples: Bacteroides thetaiotaomicron cells were grown overnight in Bacteroides phage recovery media (BPRM) then diluted 1:100 in fresh BPRM, and 5x10^6 PFU/mL of heat-killed (HK) or live phage was added to 100ul of culture in a 96 well plate. Cells were then grown until mid-log phase (absorbance between 0.4-0.5); For in vivo samples: Germ-Free swiss webster mice were monocolonized with either WT (tdk) or acapsular (cps) and gavaged with ARB25 phage 7 days later.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit buffers (Qiagen) and purified on RNA-binding spin columns (Epoch), treated with DNase I (NEB) after elution and purified again using a second RNeasy mini kit isolation column. Total RNA was then rRNA depleted using the Ribo-Zero Bacterial rRNA Removal Kit (Illumina Inc.) and concentrated with the RNA Clean and Concentrator-5 kit (Zymo Research Corp, Irvine, CA).
Samples were multiplexed for sequencing on the Illumina NextSeq 500 platform at the University of Michigan Sequencing Core.

treatment_protocol: Two volumes of RNA Protect (Qiagen) were added to cells and frozen at -80C until RNA was extracted

value: Bt acapsular

tag: culture method

value: in vitro, BPRM culture

tag: growth phase

value: Mid-Log, exponential growth

value: Heat-killed ARB25 phage treated


title: 106885_acapsular +HKARB25


title: Ctrl_RNA-seq_rep1


title: control

source_name: Enteroid


title: 106884_acapsular +HKARB25


title: liver, K5

city: shanghai

first: Lu

last: Yifei

address: Pudong New area

institute: Shanghai University of traditional Chinese Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, counts

source_name: liver

extract_protocol:
RNA extraction protocol
library construction protocol

treatment_protocol: fed with high fat diet (60.9% fat, 21.8% carbohydrate, and 18.3% protein; D12492, Research Diets) for 24 weeks and treated with kaempferol (20mg/kg/day) through By intragastric administration in the last 4 weeks

value: liver

value: six-week-old

value: fed with high fat diet and treated with kaempferol


title: liver, K4


title: 106883_acapsular +ARB25

source_name: acapsular +ARB25

value: ARB25 phage treated


title: 106882_acapsular +ARB25


title: Ctrl_RNA-seq_rep3

value: normal mESC


title: T07_Regen_Day3_2

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

description: Single cell RNA-Seq (10x)

data_processing:
3' RNAseq (10x kit V2 or V3 chemistry)
Demultiplexing is run using Cell Ranger mkfastq.
Cell-ranger count is run using cell-ranger v3.1 on firecoud.
R package dropletUtils is used to exclude chimeric reads and identify and exclude empty droplets
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matriece are in the HDF5 Feature Barcode Matrix Format used by 10x, and metadata files are comma-delimited text.
mmProstate10x_full_sample_final.tsv: BatchID, cell-type, csv file
mmProstate10x_timecourse_rawCount.h5: hdf5 10x feature barcode matrix format, raw post-QC filtering cells
mmProstate10x_timecourse_log2TP10k.h5: hdf5 10x feature barcode matrix format, post-QC filtering cells, log2 transcripts per 10,000.

source_name: Mouse prostate regeneration day 3

growth_protocol: FVB/NJ mice were purchased from Taconic. Prostates used for scRNA-seq, histology and cell seeding experiments were derived from FVB/NJ mice.

extract_protocol:
Prostates were harvested and subsequently digested with Collagenase Type II (Gibco) for two hours at 37oC, followed by TryplE (Gibco) digestion at 37oC until a single cell suspension was obtained. Digestions were supplemented with Y-27632 (10 μM) to inhibit anoikis. Cells were filtered and checked for viability using trypan blue staining. All experiments were done with a minimum of 80% viable cells.
scRNA-Seq for dissociated mouse tissues was performed using 10X genomics Chromium Single Cell 3’ Library & Gel bead Kit V2 according to the manufacturer’s protocol (CG00052 Rev E). Briefly, samples containing approximately 6,000 FACS-sorted cells (mean viability 78%) were encapsulated in microfluidic droplets resulting in ~3,200 recovered single-transcriptomes per sample with a multiplet rate of ~3.7%. After the RT step, emulsion droplets were broken and barcoded-cDNA was purified with DynaBeads, followed by 12-cycles of PCR-amplification (98 °C for 180 s; [98 °C for 15 s, 67 °C for 20 s, 72 °C for 60 s] x 12-cycles; 72 °C for 60 s). The 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, DNA library was ligated to the sequencing adapter followed by indexing PCR (98 °C for 45 s; [98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s] x 10 cycles; 72 °C for 60 s). The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NextSeq using HO-SE75 kit or on HiSeq2500 platform using PE50 kit
3' RNAseq (10x kit V2 or V3 chemistry)

treatment_protocol: Mice were castrated at 8-12 weeks of age. For castration time points, tissue was harvested 1 day, 7 days, 14 days, and 28 days post castration. Dihydrotestosterone (DHT) pellets were implanted subcutaneously 4 weeks post castration. For regeneration, tissue was harvested at 1 day, 2 days, 3 days, 7 days, 14 days and 28 days post DHT Pellet implantation.

tag: background strain

value: FVB/NJ

value: Prostate

tag: androgen status

value: DHTpellet

tag: day


title: 106881_acapsular +ARB25

tag: treatment


title: 104702_wild-type +HKARB25

description:
rRNA-depleted, mRNA
Bt WT ARB25 in vitro.xlsx

source_name: wild-type +HKARB25

value: Bt Wild-type


title: 16M

value: bone marrow

value: 16 month


title: liver, K2


title: T07_Regen_Day3_1

description: Single cell RNA-Seq (10x)


title: liver, K3


title: T08_Regen_Day7_2

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate regeneration day 7


title: 104701_wild-type +HKARB25


title: liver, K1


title: MUT_1

value: lrrc8a MUT

value: germ cells

value: FVB


title: T06_Regen_Day2_2

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate regeneration day 2


title: 104700_wild-type +ARB25

source_name: wild-type +ARB25

value: in vitro, BPRM culture


title: T09_Regen_Day14_1

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate regeneration day 14


title: liver, M5

treatment_protocol: fed with high fat diet (60.9% fat, 21.8% carbohydrate, and 18.3% protein; D12492, Research Diets) for 24 weeks

value: fed with high fat diet


title: 104698_wild-type +ARB25

value: Mid-Log, exponential growth


title: T06_Regen_Day2_1

description: Single cell RNA-Seq (10x)


title: T03_Cast_Day14_2

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate castrate day 14

value: Castrate


title: liver, M3

value: liver

value: six-week-old


title: T03_Cast_Day14_1

description: Single cell RNA-Seq (10x)


title: liver, M2


title: liver, M4


title: 104703_wild-type +HKARB25

value: Heat-killed ARB25 phage treated


title: liver, N5

treatment_protocol: fed with control diet for 24 weeks

value: control


title: Ishikawa_DMSO_O16

type: RNA

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

description: vehicle

hyb_protocol: PCR amplicon of each gene is hybridized to barcoded Luminex beads. The barcode incorporated in each amplicon is complementary to a barcode on a Luminex bead, ensuring that each gene from the original lysate mRNA is represented by an amplicon bound to a specific bead.

scan_protocol: Luminex scanners detect individual beads by color, then measure the fluorescent intensity of the SAPE molecules attached to the biotin label on each amplicon-bound bead

data_processing: Raw intensity measurements are deconvoluted to provide intensity values for each landmark gene (the 978 directly measured features). Data is then normalized using a calibration curve based on invariant gene sets, and then quantile normalized.

label: biotin

source_name: Ishikawa

label_protocol: mRNA is reverse transcribed and the cDNA product PCR amplified using primers that contain contiguous sequence (barcode) complementary to each L1000 gene; in addition, the upstream primer is biotinylated to enable identification of amplicon-bound beads.

growth_protocol: MCF7, A549 and HepG2 cells were grown in phenol red free DMEM, supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin and maintained at 37°C in an atmosphere of 5% CO2. The Ishikawa cells were routinely maintained in DMEM/F12 supplemented with 10% FBS and antibiotic/antimycotic solution containing 100 units/ml penicillin-G, 100 ug/ml streptomycin and 0.25 ug/ml amphotericin B in a 37oC incubator at 5% CO2.

extract_protocol: Cells were lysed with cell lysis buffer (100 µL per well), and stored at -80⁰C

treatment_protocol: Cells were treated with compounds for 6h at 37oC

value: human endometrial adenocarcinoma

tag: cell line

value: Ishikawa

value: DMSO


title: HepG2_DMSO_P15

description: vehicle

value: human hepatocellular carcinoma


title: T02_Cast_Day7_1

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate castrate day 7

value: FVB/NJ

value: Prostate


title: MCF7_DMSO_O15

description: vehicle

value: human breast adenocarcinoma


title: T02_Cast_Day7_2

description: Single cell RNA-Seq (10x)


title: liver, M1


title: T00_intact_2

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate intact (control)

value: Intact


title: A549_DMSO_P16

description: vehicle

value: human lung adenocarcinoma


title: 104699_wild-type +ARB25

tag: genotype

value: Bt Wild-type

value: in vitro, BPRM culture

value: ARB25 phage treated


title: A549_St. John's Wort_N06

description: test

value: St. John's Wort_2.5 mcg/ml


title: A549_DMSO_N08

description: vehicle


title: HepG2_St. John's Wort_N09

description: test


title: HepG2_DMSO_N07

description: vehicle


title: A549_St. John's Wort_N10

description: test


title: liver, N4

value: liver


title: T00_intact_1

description: Single cell RNA-Seq (10x)


title: HepG2_St. John's Wort_N05

description: test


title: liver, N3

value: six-week-old


title: HepG2_St. John's Wort_N01

description: test

value: St. John's Wort_25 mcg/ml


title: A549_St. John's Wort_N04

description: test


title: A549_St. John's Wort_N02

description: test


title: liver, N1

value: control


title: Ishikawa_St. John's Wort_M10

description: test

value: human endometrial adenocarcinoma


title: HepG2_St. John's Wort_N03

description: test


title: Ishikawa_DMSO_M08

description: vehicle

value: Ishikawa


title: MCF7_St. John's Wort_M09

description: test


title: E6.5 Mut 2

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

country: United Kingdom

institute: Oxford University

data_processing:
Paired-end reads were aligned against the mm10 genome using the STAR RNA-seq aligner in Galaxy with default parameters outputting bam files
BAM files were imported imported into Seqmonk 1.45.4. (https://www.bioinformatics.babraham.ac.uk/projects/download.html#seqmonk) and analysed using the RNA-seq quantitation pipeline
Differentially expressed genes between groups were identified using DESeq2 with FDR > 0.05 based on raw counts generated using opposing strand, paired end and merge transcripts options.
Genome_build: mm10
Supplementary_files_format_and_content: [.txt] Read Counts and DESeq2 Results from SeqMonk

source_name: E6.5 whole decidua

extract_protocol:
Total RNA was extracted using an RNeasy Mini kit (Qiagen Cat#74104) with on column DNase treatment according manufacturer’s protocol.
RNA was normalized to 800ng per sample followed by depletion of cytoplasmic and mitochondrial ribosomal RNA sequences (Ribo-Zero Gold rRNA Removal Kit (H/M/R), Cat: #MRZG12324). Subsequent library preparation was completed using the Illumina TruSeq Stranded Total RNA Library Prep kit (H/M/R) (Cat: #20020597). Followed by sequencing on an Illumina HiSeq4000 (75bp paired end).

treatment_protocol: WT and Blimp1 mutant (Prdm1 BEH/CA ;PRCre) females were mated with C57BL6/J studs. For staging purposes, E0.5 was defined as midday on the day of vaginal plug. Whole decidua minus the overlying myometrium were harvested at E5.5 and E6.5.

value: Prdm1 BEH/CA ;PRCre

value: Blimp1 mutant

tag: gender

value: Female

tag: developmental stage

value: whole decidua


title: E6.5 Mut 4


title: E6.5 Mut 3


title: E6.5 WT 3

value: Prdm1 CA/WT

value: WT


title: E6.5 Mut 1


title: LPS_mouse_Tet2F/F;VavCre_3

city: Cincinnati

first: Kwangmin

last: Choi

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Sample name: s318
DKO-LPS
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv
Tet2-LPS
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv

data_processing:
Paired-end fastq files were aligned to hg38 (human) or mm10 (mouse) genomes using HISAT2 (CD34Mir146aKO-LPS, Tet2-LSK datasets)  and Tophat (VavTRAF6-LPS dataset)
Raw counts were calculated using featureCounts.
Genome_build: hg38 (human) or mm10 (mouse)
Supplementary_files_format_and_content: raw counts

source_name: Mouse Lineage-Sac1+cKit+ BM

growth_protocol: Cells were cultured in StemSpan containing SCF and TPO

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen) following manufacturer's protocol
RNA libraries were prepared according to the Illumina protocol (Nextera 817 XT DNA Sample Preparation Kit).

treatment_protocol: Cells were treated with PBS or LPS (1µg/mL) for 90 minutes

value: Lineage-Sac1+cKit+ BM

tag: tumor stage

value: Normal

value: LPS


title: MCF7_DMSO_M07

description: vehicle

value: human breast adenocarcinoma

value: DMSO


title: MCF7_St. John's Wort_M05

description: test

value: St. John's Wort_2.5 mcg/ml


title: Ishikawa_St. John's Wort_M06

description: test


title: A549_St. John's Wort_L24

description: test

value: human lung adenocarcinoma


title: E6.5 WT 2


title: MCF7_St. John's Wort_M03

description: test


title: LPS_mouse_Tet2F/F;VavCre_2

description:
Sample name: s317
DKO-LPS
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv
Tet2-LPS
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv


title: HepG2_St. John's Wort_L23

description: test

value: human hepatocellular carcinoma

value: St. John's Wort_25 mcg/ml


title: Ishikawa_St. John's Wort_M02

description: test

value: human endometrial adenocarcinoma


title: liver, N2

value: liver

value: six-week-old

value: control


title: MCF7_St. John's Wort_M01

description: test


title: A549_DMSO_L18

description: vehicle


title: A549_St. John's Wort_L22

description: test


title: HepG2_DMSO_L17

description: vehicle


title: HepG2_St. John's Wort_L21

description: test


title: E6.5 WT 1

value: Female


title: PBS_mouse_Tet2F/F;VavCre_3

description:
Sample name: s300
DKO-media
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv
Tet2-ctrl
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv

value: PBS


title: Ishikawa_St. John's Wort_M04

description: test

value: Ishikawa


title: A549_St. John's Wort_L16

description: test

value: St. John's Wort_250 mcg/ml


title: A549_St. John's Wort_L14

description: test


title: PBS_mouse_Tet2F/F;VavCre_2

description:
Sample name: s299
DKO-media
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv
Tet2-ctrl
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv

value: Lineage-Sac1+cKit+ BM


title: HepG2_St. John's Wort_L15

description: test


title: PBS_mouse_Tet2F/F;VavCre_1

description:
Sample name: s298
DKO-media
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv
Tet2-ctrl
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv

value: Normal


title: LPS_mouse_Tet2F/F_3

description:
Sample name: WT-LPS-3
WT-LPS
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv

value: LPS


title: E5.5 Mut 3

source_name: E5.5 whole decidua

value: Prdm1 BEH/CA ;PRCre

value: Blimp1 mutant

value: whole decidua


title: E5.5 Mut 2


title: LPS_mouse_Tet2F/F_2

description:
Sample name: WT-LPS-2
WT-LPS
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv


title: A549_St. John's Wort_L12

description: test

value: human lung adenocarcinoma


title: E5.5 Mut 1


title: HepG2_St. John's Wort_L11

description: test

value: human hepatocellular carcinoma


title: E5.5 WT 4

value: Prdm1 CA/WT

value: WT


title: LPS_mouse_Tet2F/F;VavCre_1

description:
Sample name: s316
DKO-LPS
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv
Tet2-LPS
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv


title: Ishikawa_St. John's Wort_K24

description: test

value: human endometrial adenocarcinoma

value: St. John's Wort_25 mcg/ml


title: PBS_mouse_Tet2F/F_3

description:
Sample name: WT-Ctl-3
WT-ctrl
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv


title: MCF7_St. John's Wort_K23

description: test

value: human breast adenocarcinoma


title: LPS_mouse_Tet2F/F_1

description:
Sample name: WT-LPS-1
WT-LPS
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv


title: Ishikawa_St. John's Wort_K22

description: test


title: E5.5 WT 3

value: Female


title: MCF7_St. John's Wort_K21

description: test


title: E5.5 Mut 4


title: E5.5 WT 2


title: HepG2_St. John's Wort_L13

description: test


title: Ishikawa_St. John's Wort_K16

description: test


title: MCF7_DMSO_K17

description: vehicle

value: DMSO


title: Ishikawa_DMSO_K18

description: vehicle

value: Ishikawa


title: PBS_mouse_Tet2F/F_1

description:
Sample name: WT-Ctl-1
WT-ctrl
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv

value: PBS


title: MCF7_St. John's Wort_K15

description: test

value: St. John's Wort_250 mcg/ml


title: HepG2_DMSO_L01

description: vehicle


title: Ishikawa_St. John's Wort_K14

description: test


title: A549_DMSO_L02

description: vehicle


title: MCF7_St. John's Wort_K13

description: test


title: LPS_mouse_VavTRAF6_3

description:
Sample name: s315
vT6-LPS
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv

value: Lineage-Sac1+cKit+ BM

value: Normal


title: ChIP_EGFP_BLIMP1_2

data_processing:
Paired-end sequence reads were mapped to the mm10 genome using bwa-MEM (0.7.15-r1140)
PCR duplicates were removed using Samtools 1.9 (Li et al., 2009).
Peaks were called against input DNA using MACS 2.1.2 (Zhang et al., 2008) with default parameters.
Bigwig files were generated using Deeptools2 (Ramirez et al., 2016)
Genome_build: mm10
Supplementary_files_format_and_content: [.bw] bigWig represent genome coverage generated using Deeptools2.

source_name: E6.5 decidua

extract_protocol:
Multiple pools of freshly dissected decidua (E6.5) from mice expressing an endogenous N-terminal EGFP tagged Blimp1 protein (Mitani et al., 2017) and WT mice were minced using a razor blade in a drop of culture media (RPMI-1640, 10% FCS, 0.0004% β-mercaptoethanol, 1x Pen/Strep, 2mM glutamine) and cross-linked in 1% formaldehyde in culture media for 20 min at ambient temperature.  After quenching in 0.125 M glycine for 5 min, cells were washed in PBS and processed for ChIP using 6 micrograms of rabbit anti-GFP antibody (Ab290, Abcam). Triplicate test (GFP ChIP of Prdm1NEG/NEG) and duplicate control (GFP ChIP of WT) decidual samples, and their respective input samples were analysed.
DNA was multiplexed and paired end sequencing was performed over two lanes of Illumina HiSeq4000 platform.

treatment_protocol: WT and homozygous EGFP-Blimp1 females were mated with C57BL6/J studs. For staging purposes, E0.5 was defined as midday on the day of vaginal plug. Whole decidua minus the overlying myometrium were harvested at E6.5.

value: Homozygous EGFP-BLIMP1

value: whole decidua minus myometrium


title: ChIP_EGFP_BLIMP1_3


title: Ishikawa_St. John's Wort_K12

description: test


title: LPS_mouse_VavTRAF6_2

description:
Sample name: s314
vT6-LPS
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv

value: LPS


title: Ishikawa_DMSO_K02

description: vehicle


title: Input_EGFP_BLIMP1_3


title: A549_Kava_J14

description: test

value: human lung adenocarcinoma

value: Kava_2.5 mcg/ml


title: MCF7_DMSO_K01

description: vehicle


title: LPS_mouse_VavTRAF6_1

description:
Sample name: s313
vT6-LPS
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: ChIP_EGFP_BLIMP1_1


title: HepG2_Kava_J13

description: test

value: human hepatocellular carcinoma


title: Input_EGFP_BLIMP1_2


title: PBS_mouse_Tet2F/F_2

description:
Sample name: WT-Ctl-2
WT-ctrl
Tet2-LSK__rawCounts_for_GEO.csv
Tet2-LSK__metadata_for_GEO.csv


title: PBS_mouse_VavTRAF6_2

description:
Sample name: s296
vT6-media
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: E5.5 WT 1

value: Prdm1 CA/WT

value: WT

value: whole decidua


title: PBS_mouse_VavTRAF6_3

description:
Sample name: s297
vT6-media
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: A549_DMSO_J10

description: vehicle


title: HepG2_DMSO_J09

description: vehicle


title: A549_Kava_J12

description: test


title: HepG2_Kava_J11

description: test


title: PBS_mouse_VavTRAF6_1

description:
Sample name: s295
vT6-media
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: MCF7_St. John's Wort_K11

description: test

value: human breast adenocarcinoma


title: A549_Kava_J08

description: test


title: ChIP_WT_3


title: LPS_mouse_WT_3

description:
Sample name: s312
WT-LPS
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: ChIP_WT_2


title: A549_Kava_J06

description: test

value: Kava_25 mcg/ml


title: HepG2_Kava_J05

description: test


title: HepG2_Kava_J07

description: test


title: LPS_mouse_WT_2

description:
Sample name: s311
WT-LPS
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: ChIP_WT_1


title: LPS_mouse_WT_1

description:
Sample name: s310
WT-LPS
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: A549_Kava_J04

description: test


title: Input_WT_3


title: PBS_mouse_WT_3

description:
Sample name: s294
WT-media
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: Input_EGFP_BLIMP1_1


title: MCF7_Kava_I13

description: test


title: Ishikawa_Kava_I14

description: test

value: human endometrial adenocarcinoma


title: A549_Kava_J02

description: test


title: HepG2_Kava_J01

description: test


title: Input_WT_2


title: PBS_mouse_WT_2

description:
Sample name: s293
WT-media
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: Input_WT_1


title: PBS_mouse_WT_1

description:
Sample name: s292
WT-media
VavTRAF6-LPS__rawCounts_for_GEO.csv
VavTRAF6-LPS__metadata_for_GEO.csv


title: Ishikawa_Kava_I12

description: test

value: Ishikawa


title: Ishikawa_DMSO_I10

description: vehicle

value: DMSO


title: MCF7_Kava_I11

description: test


title: MCF7_DMSO_I09

description: vehicle


title: NIH3T3+MDA-MB-231 EV rep2

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Sequences were aligned to hg19 using Tophat2 with default settings
Gene expression level of Refseq coding genes were quantified using in-house R scripts
Count data were normalized using "edgeR"
Genome_build: hg19
Supplementary_files_format_and_content: edgeR normalized counts

source_name: NIH3T3 fibroblast cell line

growth_protocol: NIH3T3 cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum.

extract_protocol:
TRIZOL reagent (Invitrogen) was used to extract total RNA from cells following the manufacturer’s protocols.  RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
Kapa mRNA stranded protocol

treatment_protocol: For 1.25x10e5 recipient NIH3T3 cells, 1x10e8 of EVs resuspended in PBS was added.  RNA was extracted after 48 h.

value: fibroblast cell line

tag: passage

value: MDA-MB-231 EV


title: ChIP_mouse_WT_MCMVD35_5_H3K4me3_input

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

description: pkLstAssign_oneFeatGene_H3K4me3_Ly49Hpos_WTtimecourse.bed

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated from BAM files by using either bedtools (v.2.26.0)  and UCSC’s bedGraphToBigWig (v4), or by using the bamCoverage function from deepTools (v3.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are unscaled pileups of reads aligned to the genome. BED files are genomic ranges that represent the reference peak atlas used for analysis, with names representing unique peak IDs for each atlas.

source_name: splenic NK cells

extract_protocol:
DNA and proteins from sorted NK cells were cross-linked for 8 minutes at room temperature using 1% formaldehyde. Cross-linked cells incubated in cell lysis buffer (25 mM HEPES, 1.5 mM MgCl2, 10mM KCl, 0.1% NP-40, 1mM DTT, 1x proteinase inhibitor) and nuclei were isolated by centrifugation at 5400 rpm for 5.5 minutes. ChIP was performed using 1.5 μg of rabbit polyclonal anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473) or 8 µg anti-Stat5 (#AF2168, R&D Systems) and Dynabeads Protein G (Invitrogen).
Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Whenever possible, fragments between 100 and 600 bp were size selected using aMPure XP beads (Beckman Coulter catalog # A63882) and Illumina libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions with up to 10ng input DNA and 8-11 cycles of PCR. Barcoded libraries were run on a HiSeq 2500 in Rapid or High Output mode or a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq Rapid SBS Kit v2, HiSeq SBS Kit v4, or HiSeq 3000/4000 SBS Kit, respectively (Illumina). An average of 46 million paired reads were generated per sample.

value: ex-vivo NK cells

tag: condition

tag: replicate

tag: chip antibody

value: none (H3K4me3 input)

tag: experimentid


title: ChIP_mouse_WT_MCMVD35_5_H3K4me3_IP

tag: cell type

value: anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473)


title: HepG2_Kava_J03

description: test

tag: tissue


title: NIH3T3+MDA-MB-231 EV rep1


title: ChIP_mouse_WT_MCMVD35_4_H3K4me3_IP


title: Ishikawa_Kava_I08

description: test


title: MCF7_Kava_I07

description: test


title: NIH3T3+MCF10A EV rep2

value: MCF10A EV


title: Ishikawa_Kava_I06

description: test


title: ChIP_mouse_WT_MCMVD35_4_H3K4me3_input


title: Ishikawa_Kava_I04

description: test


title: MCF7_Kava_I05

description: test


title: MCF7_Kava_I03

description: test


title: Ishikawa_Kava_I02

description: test


title: NIH3T3+PBS rep2

value: PBS


title: NIH3T3+MCF10A EV rep1


title: A549_Kava_H24

description: test

value: human lung adenocarcinoma

value: Kava_250 mcg/ml


title: HepG2_Kava_H23

description: test

value: human hepatocellular carcinoma


title: A549_Kava_H22

description: test


title: ChIP_mouse_WT_MCMVD7_3_H3K4me3_input

value: WT


title: NIH3T3+PBS rep1


title: ChIP_mouse_WT_MCMVD7_3_H3K4me3_IP


title: HepG2_Kava_H21

description: test


title: A549_DMSO_H20

description: vehicle


title: HepG2_DMSO_H19

description: vehicle


title: ChIP_mouse_WT_MCMVD7_2_H3K4me3_input


title: ChIP_mouse_WT_MCMVD7_2_H3K4me3_IP


title: A549_Kava_H18

description: test


title: ChIP_mouse_WT_IL12IL18_1_H3K4me3_input

description: pkLstAssign_oneFeatGene_H3K4me3_CytokineCombos_dropped.bed


title: ChIP_mouse_WT_IL12IL18_1_H3K4me3_IP


title: ChIP_mouse_WT_IFNA_3_H3K4me3_IP

description:
pkLstAssign_oneFeatGene_H3K4me3_CytokineCombos_dropped.bed
pkLstAssign_oneFeatGene_H3K4me3_STAT1KOplus_kg9.bed

value: IFNA


title: ChIP_mouse_WT_MCMVD4_4_H3K4me3_input


title: ChIP_mouse_WT_MCMVD4_4_H3K4me3_IP


title: HepG2_Ginger_H15

description: test

value: Ginger_0.1 mcg/ml


title: A549_Ginger_H16

description: test


title: ChIP_mouse_WT_IFNA_3_H3K4me3_input


title: MCF7_Kava_I01

description: test

value: human breast adenocarcinoma

value: Kava_25 mcg/ml


title: ChIP_mouse_WT_MCMVD4_3_H3K4me3_IP


title: ChIP_mouse_WT_MCMVD4_3_H3K4me3_input


title: A549_Ginger_H14

description: test


title: ChIP_mouse_WT_UNSTIM_3_H3K4me3_IP

value: UNSTIM


title: ChIP_mouse_WT_UNSTIM_3_H3K4me3_input


title: A549_Ginger_H12

description: test


title: HepG2_Ginger_H11

description: test


title: ChIP_mouse_WT_MCMVD4_2_H3K4me3_IP


title: HepG2_Ginger_H09

description: test

value: Ginger_1 mcg/ml


title: ChIP_mouse_WT_MCMVD4_2_H3K4me3_input


title: HepG2_Kava_H17

description: test


title: HepG2_Ginger_H07

description: test


title: A549_Ginger_H08

description: test


title: ChIP_mouse_WT_MCMVD2_3_H3K4me3_IP


title: A549_Ginger_H06

description: test


title: HepG2_Ginger_H05

description: test


title: HepG2_Ginger_H13

description: test


title: Arginase 2 knockout mouse -hypoxia ( ARG2KO_HYP_4)

city: Chicago

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

description: RNA-seq data files

data_processing:
RNA-seq reads were subjected to low quality read and adapter trimming using Trim Galore.
RNA-seq reads were mapped to the University of California Santa Cruz mm10 Mus musculus genome assembly using TopHat2.
Raw read counts were generated using HTseq.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: Tab-delimted text file of raw (non-normalized) mapped reads.

source_name: Lung

extract_protocol:
Total RNA was extracted from frozen lung tissues using Trizol reagent (Invitrogen), solubilized in UltraPure RNase/DNase-free water, and quantified by using NanoDrop ND-1000 spectrophotometer (Marshall Scientific, Hampton, NH).
For RNA-seq analyses, 1 µg total RNA was used as starting material. First,ribosomal RNAs were depleted using a NEBNext rRNA Depletion Kit (New England Biolabs, Ipswich, MA), according to the manufacture’s recommendations. The RNA library was prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, RNA was fragmented, and cDNA was synthesized using random primers. The resulting double-strand cDNA was then subject to end-repair, adapter ligation, and PCR amplification to generate each library.

treatment_protocol: Both male and female adult Arg2+/+ and Arg2-/- mice (8-10 weeks-old) were exposed to hypoxia by placing the animal’s cage in a Plexiglas® chamber with a constant flow of 10%O2 (hypoxia) in nitrogen at 1-3 LPM or of 21%O2 (normoxia) for 28 d. The animals exposed to hypoxia were immediately placed in a hypoxic gas mixture upon removal from the exposure chamber to maintain hypoxic exposure until sacrifice. Age-matched normoxic controls were housed in similar conditions. Following exposure, the mice were anesthetized with ketamine/xylazine (4.5/90 mg/kg). After a median sternotomy, the lungs were removed, rinsed in ice-cold PBS, pH 7.4, blotted dry, and snap frozen in liquid N2

tag: strain

value: Lung

tag: genotype/variation


title: HepG2_DMSO_H03

description: vehicle

value: DMSO


title: HepG2_Ginger_H01

description: test

value: Ginger_10 mcg/ml


title: A549_Ginger_H02

description: test


title: Arginase 2 knockout mouse -hypoxia ( ARG2KO_HYP_3)

description: RNA-seq data files


title: Ishikawa_Kava_G24

description: test

value: human endometrial adenocarcinoma

value: Ishikawa


title: A549_Ginger_H10

description: test


title: ChIP_mouse_WT_MCMVD2_2_H3K4me3_input

value: ex-vivo NK cells

value: none (H3K4me3 input)


title: ChIP_mouse_WT_MCMVD2_2_H3K4me3_IP

value: anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473)


title: MCF7_Kava_G23

description: test

value: Kava_250 mcg/ml


title: Arginase 2 knockout mouse -hypoxia ( ARG2KO_HYP_1)

description: RNA-seq data files


title: Ishikawa_Kava_G22

description: test


title: ChIP_mouse_WT_MCMVD2_1_H3K4me3_IP


title: ChIP_mouse_WT_UNSTIM_1_H3K4me3_input


title: Ishikawa_DMSO_G20

description: vehicle


title: Arginase 2 knockout mouse -room air ( ARG2KO_RA_4B)

description: RNA-seq data files


title: ChIP_mouse_WT_MCMVD2_1_H3K4me3_input


title: ChIP_mouse_WT_UNSTIM_1_H3K4me3_IP


title: MCF7_Kava_G21

description: test


title: MCF7_DMSO_G19

description: vehicle


title: ChIP_mouse_WT_MCMVD2_3_H3K4me3_input


title: Arginase 2 knockout mouse -room air ( ARG2KO_RA_4A)

description: RNA-seq data files


title: A549_DMSO_H04

description: vehicle

value: human lung adenocarcinoma


title: ChIP_mouse_WT_MCMVD0_4_H3K4me3_IP

value: WT


title: Arginase 2 knockout mouse -hypoxia ( ARG2KO_HYP_2)

description: RNA-seq data files


title: Arginase 2 knockout mouse -room air ( ARG2KO_RA_3)

description: RNA-seq data files


title: MCF7_Kava_G17

description: test


title: ChIP_mouse_WT_MCMVD0_4_H3K4me3_input


title: Ishikawa_Kava_G18

description: test


title: Arginase 2 knockout mouse -room air ( ARG2KO_RA_2B)

description: RNA-seq data files


title: Ishikawa_Ginger_G16

description: test


title: ChIP_mouse_WT_MCMVD0_2_H3K4me3_IP


title: MCF7_Ginger_G13

description: test


title: Ishikawa_Ginger_G14

description: test


title: MCF7_Ginger_G15

description: test


title: ChIP_mouse_WT_MCMVD0_2_H3K4me3_input


title: Arginase 2 knockout mouse -room air ( ARG2KO_RA_2A)

description: RNA-seq data files


title: Ishikawa_Ginger_G12

description: test


title: MCF7_Ginger_G11

description: test


title: Ishikawa_Ginger_G10

description: test


title: MCF7_Ginger_G09

description: test


title: Ishikawa_Ginger_G08

description: test


title: ChIP_mouse_WT_IL2IL15IL12IL18IFNA_8_H3K4me3_IP


title: Arginase 2 wildtype mouse  - hypoxia ( WT_HYP_4)

description: RNA-seq data files

value: Wildtype


title: ChIP_mouse_WT_IL2IL15IL12IL18IFNA_8_H3K4me3_input


title: MCF7_Ginger_G07

description: test


title: ChIP_mouse_WT_IL2IL15IL12IL18IFNA_7_H3K4me3_IP


title: MCF7_Ginger_G05

description: test


title: ChIP_mouse_WT_IL2IL15IL12IL18IFNA_7_H3K4me3_input


title: ChIP_mouse_WT_IL2IL15_1_STAT5_IP

description: pkLstAssign_oneFeatGene_Chip_Stat5_OShea_IDR_peaks.bed

value: anti-Stat5 (#AF2168, R&D Systems)


title: Arginase 2 wildtype mouse - hypoxia ( WT_HYP_1)

description: RNA-seq data files


title: Arginase 2 wildtype mouse - hypoxia ( WT_HYP_2)

description: RNA-seq data files


title: Ishikawa_Ginger_G06

description: test


title: Arginase 2 wildtype mouse - hypoxia ( WT_HYP_3)

description: RNA-seq data files


title: Ishikawa_DMSO_G04

description: vehicle


title: Arginase 2 wildtype mouse  - room air ( WT_RA_4)

description: RNA-seq data files


title: Arginase 2 wildtype mouse - room air ( WT_RA_3B)

description: RNA-seq data files


title: ChIP_mouse_WT_IL2IL15_1_STAT5_input

value: none (STAT5 input)


title: Ishikawa_Ginger_G02

description: test


title: MCF7_DMSO_G03

description: vehicle

value: human breast adenocarcinoma


title: MCF7_Ginger_G01

description: test


title: ChIP_mouse_WT_IL2IL15_8_H3K4me3_IP


title: Arginase 2 wildtype mouse - room air ( WT_RA_3A)

description: RNA-seq data files


title: HepG2_Ginger_F21

description: test

value: human hepatocellular carcinoma


title: Arginase 2 knockout mouse -room air ( ARG2KO_RA_1)

description: RNA-seq data files


title: A549_Chaste tree_F20

description: test

value: Chaste tree_10 mcg/ml


title: ChIP_mouse_WT_IL2IL15_8_H3K4me3_input


title: HepG2_Chaste tree_F19

description: test


title: HepG2_Ginger_F23

description: test


title: Arginase 2 wildtype mouse - room air ( WT_RA_2B)

description: RNA-seq data files

value: Lung


title: A549_Ginger_F22

description: test


title: ChIP_mouse_WT_IL2IL15_7_H3K4me3_IP


title: A549_Chaste tree_F18

description: test


title: HepG2_Chaste tree_F17

description: test


title: Arginase 2 wildtype mouse - room air ( WT_RA_2A)

description: RNA-seq data files


title: A549_Chaste tree_F16

description: test


title: ChIP_mouse_WT_IL2IL15_7_H3K4me3_input


title: Arginase 2 wildtype mouse - room air ( WT_RA_1)

description: RNA-seq data files


title: A549_Ginger_F24

description: test


title: ChIP_mouse_WT_IL2IL15_4_H3K4me3_IP


title: E9.5 mEC ETV2 Pos 2

city: New York

first: Brisa

last: Palikuqi

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
RNA-seq reads were aligned using STAR version 2.6.0c.  The STAR index was made with the GENCODE GRCh38.p12 or GENCODE GRCm38.p6 primary assembly and corresponding GENCODE annotation file --sjdbGTFfile gencode.v28.annotation.gtf or  --sjdbGTFfile gencode.vM17.annotation.gtf, respectively.
Fragments mapping uniquely to genes in the GENCODE v28 (for human samples) or GENCODE vM17 (for mouse samples) main GTF were counted using featureCounts version v1.6.2.
Genome_build: GRCh38.p12 (human), GRCm38.p6 (mouse)
Supplementary_files_format_and_content: featureCount output files

source_name: mouse endothelial cells E9.5 (whole embryo)

extract_protocol: RNA libraries were prepared for sequencing using Illumina's TruSeq RNA Library Preparation Kit v2

tag: growth protocol

value: sorted mouse EC CD31+ ETV2 positive

tag: treatment protocol

value: freshly isolated from Venus reporter mice CD31+, Venus positive

tag: extraction protocol

value: qiagen


title: A549_Chaste tree_F12

description: test

tag: cell line

tag: treatment

value: Chaste tree_100 mcg/ml


title: HepG2_DMSO_F13

description: vehicle

value: DMSO


title: HepG2_Chaste tree_F11

description: test


title: A549_DMSO_F14

description: vehicle


title: ChIP_mouse_WT_IL2IL15_4_H3K4me3_input

tag: genotype

value: ex-vivo NK cells

value: none (H3K4me3 input)


title: E9.5 mEC ETV2 Pos 1


title: ChIP_mouse_WT_IL12IL18_8_H3K4me3_IP

value: anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473)


title: E9.5 mEC ETV2 Neg 2

value: sorted mouse EC CD31+ ETV2 negative

value: freshly isolated from Venus reporter mice CD31+, Venus neg


title: A549_Chaste tree_F10

description: test

value: human lung adenocarcinoma


title: ChIP_mouse_WT_IL12IL18_8_H3K4me3_input

value: WT


title: E9.5 mEC ETV2 Neg 1


title: ChIP_mouse_WT_IL12IL18_7_H3K4me3_IP


title: HepG2_Chaste tree_F09

description: test


title: HepG2_Chaste tree_F05

description: test

value: Chaste tree_1000 mcg/ml


title: RNA-seq Rcor2cko_Rep2

city: Bronx

first: Mark

middle: F

last: Mehler

address: 1300 Morris Park Ave.

department: Neuroscience

institute: Albert Einstein College of Medicine

description:
Processed RNA-seq DATA.txt
normalizedcount.D64.CKO

data_processing:
ChIP-seq base calling performed using Model-based Analysis for ChIP-seq (MACS).  RNA-seq aligned using HISAT2 v2.1.0 software
RNA-seq adapters and low quality reads were trimmed using trim galore website
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files for ChIP-seq include peak calls, peak enrichment compared to ChIP IgG and total input, gene region location, and gene name.
Supplementary_files_format_and_content: peaks
Supplementary_files_format_and_content: Normalized Count and fold change

source_name: Cortical Midline

extract_protocol:
Midline corticies were dissected in cold PBS.  For ChIP-seq samples, tissue was fixed in ethylene glycolbis (succinimidyl succinate) (EGS) then Formaldehyde; quenched in Glycine, and sonicated to 500bp fragments.  Sonicated was immunoprecipitated with appropriate antibody overnight and pulled down with magnetic Dynabeads (Invitrogen).  Immunoprecipitated DNA was reverse-crosslinked and purified. NEBNEXT Ultra II DNA Library Prep kit (New England Biolabs) was used to construct multiplex libraries using 5ng of DNA.  For RNA-seq RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). RNA libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit with 20ng RNA per sample.
Libraries for ChIP-seq and RNA-seq were prepared according to standard Illumina protocols

tag: age

value: Embryonic day 14.5


title: HepG2_Chaste tree_F15

description: test

value: human hepatocellular carcinoma


title: HepG2_Chaste tree_F03

description: test


title: A549_Chaste tree_F04

description: test


title: A549_Chaste tree_F08

description: test


title: A549_Chaste tree_F06

description: test


title: ChIP_mouse_WT_IL12IL18_7_H3K4me3_input


title: RNA-seq Rcor2cko_Rep1

description:
Processed RNA-seq DATA.txt
normalizedcount.D62.CKO


title: ChIP_mouse_WT_IFNA_9_H3K4me3_IP

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 (v2.3.4).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated from BAM files by using either bedtools (v.2.26.0)  and UCSC’s bedGraphToBigWig (v4), or by using the bamCoverage function from deepTools (v3.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are unscaled pileups of reads aligned to the genome. BED files are genomic ranges that represent the reference peak atlas used for analysis, with names representing unique peak IDs for each atlas.

value: IFNA


title: RNA-seq CTL_Rep2

description:
Processed RNA-seq DATA.txt
normalizedcount.D65.WT

value: Rcor2f/f (CTL)


title: HepG2_Chaste tree_F01

description: test


title: RNA-seq CTL_Rep1

description:
Processed RNA-seq DATA.txt
normalizedcount.D63.WT


title: ChIP_mouse_WT_IFNA_9_H3K4me3_input


title: MCF7_Ginger_E23

description: test

value: human breast adenocarcinoma

value: Ginger_10 mcg/ml


title: HepG2_Chaste tree_F07

description: test


title: Ishikawa_Ginger_E22

description: test

value: human endometrial adenocarcinoma

value: Ishikawa


title: MCF7_Ginger_E21

description: test


title: ChIP_mouse_WT_IFNA_8_H3K4me3_input


title: ChIP-seq Total Input_rep1

description: Processed ChIP-seq DATA.txt

value: wild type


title: ChIP_mouse_WT_IFNA_7_H3K4me3_IP

value: ex-vivo NK cells


title: Ishikawa_Chaste tree_E18

description: test

value: Chaste tree_10 mcg/ml


title: Ishikawa_Chaste tree_E20

description: test


title: MCF7_Chaste tree_E19

description: test


title: A549_Chaste tree_F02

description: test


title: ChIP-seq anti-Rb IgG_rep2

description: Processed ChIP-seq DATA.txt

value: Cell Signalling Technologies (ca# 2729)


title: MCF7_Chaste tree_E17

description: test


title: ChIP-seq anti-Rb IgG_rep1

description: Processed ChIP-seq DATA.txt


title: ChIP_mouse_WT_IFNA_7_H3K4me3_input

value: none (H3K4me3 input)


title: ChIP_mouse_WT_IFNA_6_H3K4me3_IP

value: anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473)


title: Ishikawa_Chaste tree_E16

description: test


title: Ishikawa_Ginger_E24

description: test


title: ChIP-seq anti-Rcor2_rep2

description: Processed ChIP-seq DATA.txt

value: ProteinTech (ca# 23969-1-AP)


title: ChIP_mouse_WT_IFNA_6_H3K4me3_input

value: WT


title: ChIP_mouse_WT_IFNA_8_H3K4me3_IP


title: MCF7_DMSO_E13

description: vehicle

value: DMSO


title: Ishikawa_Chaste tree_E12

description: test

value: Chaste tree_100 mcg/ml


title: Ishikawa_DMSO_E14

description: vehicle


title: ChIP-seq Total Input_rep2

description: Processed ChIP-seq DATA.txt

value: Embryonic day 14.5


title: MCF7_Chaste tree_E11

description: test


title: ChIP-seq anti-Rcor2_rep1

description: Processed ChIP-seq DATA.txt


title: Ishikawa_Chaste tree_E10

description: test


title: ChIP_mouse_WT_UNSTIM_1_STAT5_IP

value: UNSTIM

value: anti-Stat5 (#AF2168, R&D Systems)


title: ChIP_mouse_WT_UNSTIM_1_STAT5_input

value: none (STAT5 input)


title: Ishikawa_Chaste tree_E08

description: test


title: MCF7_Chaste tree_E15

description: test

value: human breast adenocarcinoma


title: MCF7_Chaste tree_E09

description: test


title: MCF7_Chaste tree_E07

description: test


title: Ishikawa_Chaste tree_E06

description: test

value: human endometrial adenocarcinoma

value: Chaste tree_1000 mcg/ml


title: ChIP_mouse_WT_UNSTIM_9_H3K4me3_IP


title: MCF7_Chaste tree_E05

description: test


title: ChIP_mouse_WT_UNSTIM_9_H3K4me3_input


title: Ishikawa_Chaste tree_E04

description: test

value: Ishikawa


title: MCF7_Chaste tree_E03

description: test


title: MCF7_Chaste tree_E01

description: test


title: Ishikawa_Chaste tree_E02

description: test


title: A549_DMSO_D24

description: vehicle

value: human lung adenocarcinoma


title: ChIP_mouse_WT_UNSTIM_8_H3K4me3_IP

value: ex-vivo NK cells


title: ChIP_mouse_WT_UNSTIM_8_H3K4me3_input


title: A549_Ashwagandha_D22

description: test

value: Ashwagandha_1.25 mcg/ml


title: A549_Ashwagandha_D20

description: test


title: ChIP_mouse_WT_UNSTIM_7_H3K4me3_IP


title: HepG2_DMSO_D23

description: vehicle

value: human hepatocellular carcinoma


title: HepG2_Ashwagandha_D21

description: test


title: HepG2_Ashwagandha_D19

description: test


title: ChIP_mouse_WT_UNSTIM_7_H3K4me3_input

value: none (H3K4me3 input)


title: A549_Ashwagandha_D18

description: test


title: ChIP_mouse_WT_UNSTIM_6_H3K4me3_IP

value: anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473)


title: HepG2_Ashwagandha_D17

description: test


title: A549_Ashwagandha_D16

description: test

value: Ashwagandha_12.5 mcg/ml


title: ChIP_mouse_WT_UNSTIM_6_H3K4me3_input

value: WT


title: ChIP_mouse_WT_UNSTIM_4_H3K4me3_IP


title: 119 Casp8 fl/fl

city: Cologne

first: Manolis

last: Pasparakis

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Institute for Genetics

country: Germany

institute: University of Cologne

description: gene expression data from mouse colon tissue at 11 weeks of age

hyb_protocol: accoring to GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays protocol(thermo Fisher, 2017) for 16h at 45°C, hybridization was performed in a GeneChip Hybridization Oven 645

scan_protocol: Gene chips were scanned using the GeneChip Scanner 7G

data_processing: Array analysis was performed using Affymetrix Expression Console and Transcriptome Analysis Console Software (TAC).

source_name: mouse colon tissue at week 10-61

label_protocol: labelled ssc-DNA was prepared according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays protocol(thermo Fisher, 2017) from 100 ng total RNA

growth_protocol: Mice were maintained at an SPF animal facility uner a 12h light cycle and given a regular chow diet

extract_protocol: Colon tissues were disrupted using a Precellys 24 (Bertin technologies) and total RNA was extracted using a Nucelospin RNA kit (Macherey-Nagel) according to manufacturer's instructions. rDNAse treatment was increased to 45 minutes.

treatment_protocol: Colon tissues were frozen on dry ice immeadiately after collection.

value: Casp8 fl/fl


title: 91 Casp8 fl/fl

source_name: mouse colon tissue at week 10-58


title: 105 Casp8 fl/fl

source_name: mouse colon tissue at week 10-60


title: 98 Casp8 fl/fl

source_name: mouse colon tissue at week 10-59


title: A549_Ashwagandha_D14

description: test


title: HepG2_Ashwagandha_D13

description: test


title: HepG2_Ashwagandha_D15

description: test


title: 123 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse colon tissue at week 10-56

value: FADD IEC-KO RIPK3 IEC-KO


title: 86 Casp8 fl/fl

source_name: mouse colon tissue at week 10-57


title: ChIP_mouse_WT_UNSTIM_4_H3K4me3_input

value: UNSTIM


title: A549_Ashwagandha_D10

description: test


title: HepG2_DMSO_D11

description: vehicle

value: DMSO


title: A549_DMSO_D12

description: vehicle


title: 113 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse colon tissue at week 10-55


title: A549_Ashwagandha_D08

description: test

value: Ashwagandha_125 mcg/ml


title: ChIP_mouse_STAT1KO_IFNA_9a_H3K4me3_input

description: pkLstAssign_oneFeatGene_H3K4me3_STAT1KOplus_kg9.bed

value: IFNA


title: A549_Ashwagandha_D06

description: test


title: HepG2_Ashwagandha_D07

description: test


title: 112 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse colon tissue at week 10-54


title: 93 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse colon tissue at week 10-53


title: 15 FADD IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-51

value: FADD IEC-KO Mlkl -/-


title: 13 FADD IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-49


title: ChIP_mouse_STAT1KO_IFNA_9_H3K4me3_IP


title: 88 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse colon tissue at week 10-52


title: ChIP_mouse_STAT1KO_IFNA_9_H3K4me3_input


title: HepG2_Ashwagandha_D05

description: test


title: ChIP_mouse_STAT1KO_IFNA_6_H3K4me3_IP


title: 14 FADD IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-50


title: MCF7_DMSO_C23

description: vehicle

value: human breast adenocarcinoma


title: ChIP_mouse_STAT1KO_IFNA_6_H3K4me3_input

source_name: splenic NK cells


title: 12 FADD IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-48


title: Sacromatoid Mesothelioma 2

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

description: Obtained from the same tumor analyzed in our previously submitted experiment: GSM402909

hyb_protocol: According to the manufacturer’s protocol (miRNA Microarray System with miRNA Complete Labeling and Hyb Kit, Protocol version 2.1).

scan_protocol: According to the manufacturer’s protocol (miRNA Microarray System with miRNA Complete Labeling and Hyb Kit, Protocol version 2.1, Agilent C Scanner Settings).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The data set from the scanned microarrays were analyzed with GeneSpring software 13.1 (Agilent). The parameter settings for importing the data into GeneSpring were as follows: Threshold, 1.0; Logbase, 2; Technology, Agilent.miRNA.19159; Normalization: Shift to 90 percentile, Baseline Transformation, None.

organism: Rattus norvegicus

extract_protocol: The total RNA including miRNA was extracted by using miRNeasy Mini Kit (QIAGEN).

treatment_protocol: The intraperitoneal injection of iron saccharate was started at 4 weeks of age. Ferric saccarate (5 mgFe/kg body weight) was injected 5 days a week for 12 weeks.Nitrilotriacetate (NTA) (80 mg/kg body weight) was injected separetely 5 days a week for 20 weeks. The experiment was terminated at 26.7 months.of age.

value: F1 hybrid rats between Fischer344 and Brown-Norway strains

value: Sacroma


title: 11 FADD IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-47


title: ChIP_mouse_STAT1KO_UNSTIM_9_H3K4me3_input

value: ex-vivo NK cells


title: 08 CASP8 IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-44

value: CASP8 IEC-KO Mlkl -/-


title: HepG2_Ashwagandha_D03

description: test

value: human hepatocellular carcinoma


title: ChIP_mouse_STAT1KO_UNSTIM_9_H3K4me3_IP


title: 10 CASP8 IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-46


title: A549_Ashwagandha_D04

description: test

value: human lung adenocarcinoma


title: ChIP_mouse_STAT1KO_UNSTIM_6_H3K4me3_IP

value: anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473)


title: Ishikawa_DMSO_C24

description: vehicle

source_name: Ishikawa

value: human endometrial adenocarcinoma

value: Ishikawa


title: Epithelioid Mesothelioma 3

description: Obtained from the same tumor analyzed in our previously submitted experiment: GSM402905

label_protocol: According to the manufacturer’s protocol (miRNA Microarray System with miRNA Complete Labeling and Hyb Kit, Protocol version 2.1).

value: Epithelioid Mesothelioma


title: Epithelioid Mesothelioma 2

description: Obtained from the same tumor analyzed in our previously submitted experiment: GSM402903


title: Ishikawa_Ashwagandha_C20

description: test

value: Ashwagandha_1.25 mcg/ml


title: Sacromatoid Mesothelioma 1

description: Obtained from the same tumor analyzed in our previously submitted experiment: GSM402908


title: ChIP_mouse_STAT1KO_UNSTIM_6_H3K4me3_input

value: UNSTIM

value: none (H3K4me3 input)


title: 09 CASP8 IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-45


title: Ishikawa_Ashwagandha_C22

description: test


title: Epithelioid Mesothelioma 4

description: Obtained from the same tumor analyzed in our previously submitted experiment: GSM402906


title: 06 CASP8 IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-42


title: 07 CASP8 IEC-KO Mlkl -/-

source_name: mouse colon tissue at week 10-43


title: Rat Mesothelial Tissue Collection (MTC)

source_name: Rat MTC

value: Mesothelial Tissue Collection (MTC)


title: MCF7_Ashwagandha_C21

description: test


title: Ishikawa_Ashwagandha_C18

description: test


title: HepG2_Ashwagandha_D09

description: test

value: Ashwagandha_12.5 mcg/ml


title: MCF7_Ashwagandha_C17

description: test


title: MCF7_Ashwagandha_C19

description: test


title: 05 FADD IEC-KO Zbp1 -/-

source_name: mouse colon tissue at week 10-41

value: FADD IEC-KO Zbp1 -/-


title: Rat Peritoneal Mesothelial Cell (RPMC)

source_name: RPMC

value: Peritoneal Mesothelial Cell (RPMC)


title: Epithelioid Mesothelioma 1

description: Obtained from the same tumor analyzed in our previously submitted experiment: GSM402902

value: F1 hybrid rats between Fischer344 and Brown-Norway strains


title: Ishikawa_Ashwagandha_C14

description: test


title: Ishikawa_Ashwagandha_C16

description: test


title: Ishikawa_DMSO_C12

description: vehicle

value: DMSO


title: MCF7_Ashwagandha_C13

description: test

value: human breast adenocarcinoma


title: MCF7_DMSO_C11

description: vehicle


title: Ras[V12]+Dph5IR_2

city: Bunkyo-ku, Tokyo

first: Miura

last: Masayuki

address: 7-3-1 Hongo

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent GE blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 custom microarray 8x60K for Drosophila for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner using AgilentG3_GX_1Color_HighSensitivity.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 040871_D_F_20120511) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. If the probes scored low values in Evaluation Metrics, the probes were removed (filtered).GeneSpring (Agilent), a microarray analysis software was used for normalizing the data.

organism: Drosophila melanogaster

source_name: adult male whole gut expressing transgenes under the control of esg[ts]-Gal4, 2days at 29 degree

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000c Spectrophotometer.

growth_protocol: Flies were kept on standard diet at 18℃ for 8-14 days .

extract_protocol: Total RNA was extracted from 15 whole guts of adult males by using QIAzol Lysis Reagent (QIAGEN#79306), followed by purification using RNeasy Plus Micro Kit (QIAGEN#74034).

treatment_protocol: They were further incubated for two days at 29℃ to inactivate Gal80ts and allow regulation of gene expression by Gal4/UAS system.

value: esg[ts]-Gal4>GFP, Ras[V12], Dph5IR

value: whole gut

tag: Sex

value: male


title: 03 FADD IEC-KO Zbp1 -/-

source_name: mouse colon tissue at week 10-39


title: 124 FADD IEC-KO

source_name: mouse colon tissue at week 10-36

value: FADD IEC-KO


title: Ishikawa_Ashwagandha_C10

description: test

value: human endometrial adenocarcinoma


title: MCF7_Ashwagandha_C09

description: test


title: 01 FADD IEC-KO Zbp1 -/-

source_name: mouse colon tissue at week 10-37


title: 04 FADD IEC-KO Zbp1 -/-

source_name: mouse colon tissue at week 10-40


title: 120 FADD IEC-KO

source_name: mouse colon tissue at week 10-35


title: MCF7_Ashwagandha_C15

description: test


title: Ras[V12]+Dph5IR_3


title: 02 FADD IEC-KO Zbp1 -/-

source_name: mouse colon tissue at week 10-38


title: 117 FADD IEC-KO

source_name: mouse colon tissue at week 10-34


title: Ras[V12]+LacZIR_4

value: esg[ts]-Gal4>GFP, Ras[V12], lacZIR


title: Ras[V12]+Dph5IR_1


title: Ishikawa_Ashwagandha_C08

description: test

value: Ishikawa

value: Ashwagandha_125 mcg/ml


title: MCF7_Ashwagandha_C07

description: test


title: Ras[V12]+LacZIR_2


title: Ishikawa_Ashwagandha_C06

description: test


title: 25 FADD IEC-KO

source_name: mouse colon tissue at week 10-31


title: Ras[V12]+LacZIR_3


title: 95 FADD IEC-KO

source_name: mouse colon tissue at week 10-33


title: Ras[V12]+Dph5IR_4


title: 89 FADD IEC-KO

source_name: mouse colon tissue at week 10-32


title: Dph5IR_3

value: esg[ts]-Gal4>GFP, Dph5IR


title: 24 FADD IEC-KO

source_name: mouse colon tissue at week 10-30


title: Dph5IR_4


title: Ras[V12]+LacZIR_1


title: MCF7_Ashwagandha_C03

description: test


title: MCF7_Ashwagandha_C05

description: test


title: 23 FADD IEC-KO

source_name: mouse colon tissue at week 10-29


title: Dph5IR_2


title: A549_DMSO_B22

description: vehicle

value: human lung adenocarcinoma


title: Ishikawa_Ashwagandha_C04

description: test

source_name: Ishikawa


title: VPA_OCA6

city: Zürich

first: Evelin

last: Krajnc

address: Rämistrasse 100

department: Department of Clinical Pharmacology and Toxicology

country: Switzerland

institute: University Hospital Zürich

data_processing:
Analysis: NGS two group analysis with EdgeR . Feature level: gene. Data Column Used: est_counts.
Method: glm using secondary factor. Statistical Model: used provided second factor. Comparison: VPA_OCA-over-VPA.
Normalization: TMM. Differential expression test: QL. Log2 signal treshold: 4.322. Linear signal treshold: 20.
Genome_build: GRCm38.p5 (Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26)
Supplementary_files_format_and_content: tab-delimited text files include normalized count and FPKM (Fragments Per Kilobase Million) for each Sample

source_name: liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA standard kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver

value: 16 weeks


title: VPA_OCA5


title: VPA_OCA4


title: 22 FADD IEC-KO

source_name: mouse colon tissue at week 10-28


title: HepG2_DMSO_B21

description: vehicle

value: human hepatocellular carcinoma


title: Dph5IR_1


title: A549_DMSO_B06

description: vehicle


title: 30 Fadd fl/fl

source_name: mouse colon tissue at week 10-26

value: Fadd fl/fl


title: 29 Fadd fl/fl

source_name: mouse colon tissue at week 10-25


title: VPA_OCA3


title: LacZIR_2

source_name: adult male whole gut expressing transgenes under the control of esg[ts]-Gal4, 2days at 29 degree

value: esg[ts]-Gal4>GFP, lacZIR


title: HepG2_DMSO_B05

description: vehicle

value: DMSO


title: Car1-GFP+ bone marrow cells

city: Newark

middle: C.

last: Siracusa

state: NJ

address: Cancer Center 1226, 205 South Orange Avenue

department: Medicine

institute: Rutgers New Jersey Medical School

data_processing:
Basecalling and fastq conversion performed via cellranger v2.1
Raw reads were aligned to the mm10 genome and deconvoluted along cell barcodes and unique molecular identifiers via cellranger v2.1
Digital gene expression matrices were analyzed via Seurat (v2) in R studio (v3.4.2)
Genome_build: mm10
Supplementary_files_format_and_content: digital gene expression matrices per samples. Deconvoluted read counts per cell per gene

source_name: naïve Car1-GFP reporter mouse

extract_protocol:
scRNA-seq libraries were prepared using standard 10X Genomics library preparations (v2 chemistry)
Droplet based scRNA-seq using 10X Genomics

tag: strain background

value: Car1-GFP reporter mouse

value: bone marrow

tag: cell population

value: CD45+ Car1-GFP-expressing cells


title: LacZIR_1

value: whole gut

value: male


title: 28 Fadd fl/fl

source_name: mouse colon tissue at week 10-24


title: 21 FADD IEC-KO

source_name: mouse colon tissue at week 10-27

value: FADD IEC-KO


title: 26 Fadd fl/fl

source_name: mouse colon tissue at week 10-22


title: 27 Fadd fl/fl

source_name: mouse colon tissue at week 10-23


title: Ishikawa_DMSO_A22

description: vehicle

value: human endometrial adenocarcinoma


title: VPA_OCA1


title: 20MC

city: Philadelphia

first: Song-Jun

last: Xu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Sequences were aligned to Rat Genome assembly (Rnor_6.0) using STAR-2.5.2a(26). rRNA reads were filtered using Bedtools intersectBed and rRNA annotation from Biomart.
Gene read counts generated by HTseq-count were used to compute fold changes and significance of expression differences using DESeq
DEGs were assessed through a generalized linear model implemented in limma, with phenotype (VS vs. control) and sex (male vs. female) as main factors for every brain region. The log expression values for each gene were averaged over each treatment group, and the log2 fold change was computed.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

source_name: nucleus basalis of Meynert

extract_protocol:
RNA was extracted as detailed in SI methods. RNA quality was assessed using Qubit RNA HS assay and Bioanalyzer RNA 6000 Nano assay.
Libraries were prepared using NuGen Ovation RNA-Seq System v2 from total RNA.
Samples were barcoded for multiplexing and sequenced at 75 bp paired-end on Illumina HiSeq4000. Samples were pooled 16 per lane and sequenced at a depth of 130 million reads per sample.

value: Long Evans

value: Brain

value: 70+ days

value: ChAT::Cre rats

value: Male

tag: group

value: Control


title: Bone marrow-resident progenitor cells

source_name: naïve C57BL/6 mice

value: CD45+ CD3- Ly6G- cells


title: VPA_OCA2

value: liver

value: 16 weeks


title: 18MC


title: MCF7_DMSO_A21

description: vehicle

value: human breast adenocarcinoma

value: DMSO


title: VPA6


title: Ishikawa_DMSO_A06

description: vehicle

value: Ishikawa


title: 104 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-20

value: CASP8 IEC-KO


title: VPA5


title: 17MC


title: 16MC


title: VPA4


title: MCF7_DMSO_A05

description: vehicle


title: drug_64cell-5-rep

city: Shanghai

first: Tengjiao

last: Zhang

state: Shanghai

address: 1239 Siping Road

department: School of life science and technology

institute: Tongji University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Drop-seq software (James Nemesh, McCarroll Lab) were used for data de-multiplexing, reads alignment and cellular molecular barcodes processing. Barcodes (9-16bp of read1) and UMI (17-25bp of read1) extracted from read1 were added to read2 as tags. Ploy(A) tail sequence and template switch oligo (TSO) sequence were trimmed. Only read2 were mapped to C.sav genome (CSAV2.0; ensembl). Gene exon were then labeled and attached to mapping output file. Genes of used exact barcodes were counted to get the final expression matrix.
Normalization of read count was performed in each cell by a scale factor estimated by DESeq2 (Anders and Huber 2010).
We considered a gene a differentially expressed gene (DEG) if its read count across all cells does not conform to a Poisson distribution. To remove batch effect of embryo, we excluded genes that have greater than two fold change on average expression between any pair of embryos at the same developmental stage.
Dimension reduction was implemented by t-distributed stochastic neighbor embedding (t-SNE) in Seurat (Macosko et al. 2015) to visualize and cluster cells at each stage using DEGs. Cell types were identified by the specific expression of tissue marker (Imai et al. 2006) on the clusters of t-SNE map at each stage.
Genome_build: CSAV 2.0
Supplementary_files_format_and_content: txt files include the raw count values of genes; xlsx files include barcode information of samples.

molecule: polyA RNA

organism: Ciona savignyi

source_name: 64-cell embryo

growth_protocol: Fecund C. sav animals were collected from the Jiaozhou Bay in Qingdao, Shandong and kept in 18c circulation sea water tank. Fertilization, dechorination and embryo cultures were done. For FGF drug inhibitor experiments, embryos were grown in sea water containing 2ug/ml U0126. C. sav embryo in situ experiments were done according to previous published methods.

extract_protocol:
All blastomeres from a single embryo were transferred to a new dish of fresh sea water at 4c. After that, cells were individually transferred using a glass capillary needle attached to mouth pippet to PCR tubes containing lysis buffer the same as smart-seq2 except that barcoded primer were used. Reverse transcription and pre-amplification were processed as smart-seq2 protocol. We use 12, 13, 14, 15, 16 and 17 cycles respectively for the amplification of 1/2-cell, 4-cell, 8-cell, 16-cell, 32-cell and 64/110-cell samples.
Equal amount of cDNA of the same stage and different barcodes were pooled together for Nextera XT sequencing library construction. 500 pg cDNA of each pooled sample was fragmented, tagged, and amplified according to the manufacturer’s instructions except that P5 and N7-index primers were used. Fragments were purified twice using 0.6x AMPure XP beads and once with 1x AMPure XP beads.

treatment_protocol: Staged embryos were transferred to Ca2+/Mg2+ free artificial sea water containing freshly prepared 0.1% trypsin (MP). Single embryos were gently pippeted using a mouth pippet until all blastomeres dissociate.

value: embryo

tag: developmental stage

value: 64-cell embryo U0126


title: drug_64cell-6-rep


title: 108 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-21


title: 100 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-19


title: drug_64cell-4-rep


title: 92 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-18


title: 13MS

value: Stress


title: 20 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-16


title: 87 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-17


title: VPA2

source_name: liver


title: drug_64cell-3-rep


title: VPA1


title: drug_64cell-2-rep


title: 11MS


title: 5hmC-hMeDIP-seq-ko

city: Beijing

first: Lin

address: 10 You’anmen Outer West 1st Street

institute: Capital Medical University

description: hMeDIP

data_processing:
Library strategy: hMeDIP
ChIP-seq and hMeDIP reads quality control performed using FastQC v0.11.5 and  cutadapt v1.8.3
ChIP-seq and hMeDIP reads were aligned to the mm10 genome assembly using Bowtie2 v2.2.5
ChIP-seq and hMeDIP peaks were called using macs2 v2.1.1.20160309
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq and hMeDIP bw files were generated using bamCoverage

source_name: pituitary tissues of Foxk2 knockout mice

growth_protocol: Pituitary tissues of wild-type or Foxk2 knockout mice

extract_protocol:
At least 100ng fragmented genomic DNA from pituitary tissues were performed for hMeDIP reactions. The DNA precipitated by polyclonal antibodies against 5hmC. The DNA samples were purified with the Active Motif's Chromatin IP DNA Purification Kit before in-depth whole genome DNA sequencing was performed by BGI (Wu Han, China). The process were validated by the instructions from Active Motif Kit. cat#55010
The raw sequencing image data were examined by the Illumina analysis pipeline, aligned to the unmasked mouse reference genome (mm10) using Bowtie2, and further analyzed by MACS.

value: pituitary tissue

tag: gender

value: female

value: Foxk2 Knockout

tag: antibodies

value: 5hmC using antibodies in hMeDIP kit:Active Motif, cat#55010


title: ChIP_mouse_STAT1KO_IFNA_9a_H3K4me3_IP

source_name: splenic NK cells

tag: cell type

value: ex-vivo NK cells

tag: condition

value: IFNA

tag: replicate

tag: chip antibody

value: anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473)

tag: experimentid


title: 19 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-15


title: drug_64cell-1-rep

tag: tissue


title: 10FC

tag: strain

value: Long Evans

value: Brain

value: 70+ days

value: ChAT::Cre rats

value: Female

value: Control


title: 14MS

value: Male


title: VPA3

value: liver

value: 16 weeks


title: Input DNA-hMeDIP-seq-pituitary-ko

description: hMeDIP


title: 18 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-14

value: CASP8 IEC-KO


title: 32cell-4-rep

source_name: 32-cell embryo

value: embryo

value: 32-cell embryo


title: 16 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-12


title: 17 CASP8 IEC-KO

source_name: mouse colon tissue at week 10-13