title: ESCC E1270T

description:
ESCC E1270T
Hybridized to SNP6.0

source_name: ESCC E1270T


title: CD14_TGF(-)_TNFD6_rep1

status: Public on Mar 22 2022

type: SRA

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

country: USA

institute: HOSPITAL FOR SPECIAL SURGERY

library_source: transcriptomic

data_processing:
fastp(https://github.com/OpenGene/fastp) was used to evaluate quality of sequenced reads and trim contaminated adaptor portions of sequenced reads.  RNA-seq reads were aligned to the human genome (hg38) using HISAT2. HTseq was subsequently used to count reads in features and then edgeR was used to estimate the transcript abundances as CPM (counts per million) values.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Primary human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll  and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in MEMa (Invitrogen) supplemented with 10% heat-inactivated defined FBS, penicillin/streptomycin, L-glutamine, and 20 ng/mL human macrophage colony-stimulating factor (M-CSF) with or without TGFb(10 ng/mL).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) was used to purify poly-A+ transcripts and generate libraries with multiplexed barcode adaptors following the manufacturer’s instructions.

treatment_protocol: CD14+ cells cultured in M-CSF (20ng/ml)  with or without TGFb (10 ng/ml) for 3 days and then stimulated with TNFa (40 ng/ml) for various time points(day0, day1, day6)

tag: cell type

value: CD14+ monocyte

tag: tissue

value: peripheral blood

tag: treatment


title: HC-F-71

city: Groningen

first: Rosanne

last: Reitsema

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

description:
filtered_counts_barcodes.tsv.gz
filtered_counts_data.mtx.gz
filtered_counts_genes.tsv.gz
metadata_percell.csv

data_processing:
BCL files resulting from sequencing were transformed to FASTQ files with 10x Genomics Cell Ranger mkfastq.
FASTQ files were mapped with Cell Ranger count. During sequencing, 28 bp read 1 were used for identification of the Illumina library barcode, cell barcode and UMI. Read 2 was used to map to the reference transcriptome GRCh38. Filtering of empty barcodes was done in Cell Ranger.
The data from all samples were loaded in R (R version 3.6.2) and processed using the Seurat package (version 3.2.0)3. Cells with at least 2000 UMI’s per cell and less than 20% mitochondrial gene content were retained for analysis. The data of all 10X libraries was merged and processed together. The merged dataset was normalized for sequencing depth per cell and log-transformed using a scaling factor of 10,000. The patient-effect was corrected using the integration function of Seurat. The most variable genes in the dataset were identified and the top 2000 was used for dimensionality reduction and clustering. Principal component analysis was performed on the 2000 variable genes to identify the dimensionality in the dataset and the first 10 principal components were selected for downstream analysis. Cells were clustered using graph-based clustering as implemented in Seurat. The original Louvain algorithm was utilized for modularity optimization. The top differentially expressed genes per cluster were used to identify cell types. The B cell population was selected and clustered separately to identify cell types. To evaluate the differences between samples and clusters, differential expression analysis was performed using the Wilcoxon rank sum test.
Assembly: Human: Hg38
Supplementary files format and content: filtered_counts_data.mtx.gz; final dataset containing the expression counts for all genes across filtered cells
Supplementary files format and content: filtered_counts_barcodes.tsv.gz; cell-associated barcodes corresponding to the column indices of filtered_counts_data.mtx
Supplementary files format and content: filtered_counts_genes.tsv.gz; feature names corresponding to the row indices of filtered_counts_data.mtx
Supplementary files format and content: metadata_percell.csv; file containing metadata per single cell
Supplementary files format and content: matrix.mtx.gz; barcodes.tsv.gz, features.tsv.gz; cell ranger output for each 10X library

source_name: PBMCs

growth_protocol: Human PBMCs were isolated from whole heparin blood by density gradient centrifugation using Lymphoprep. PBMCs were cultured at 1 x 107/mL in RPMI 1640 containing 10% heat-inactivated fetal calf serum and 10% DMSO. Samples were stored in liquid nitrogen prior to use.

extract_protocol:
Cryopreserved PBMCs were thawed by adding 10 mL warm RPMI containing 10% FCS. Next, samples were washed twice with warm RPMI+10% FCS to remove DMSO.
Single-cell mRNA sequencing was performed at Single Cell Discoveries according to standard 10x Genomics 3’ V3.1 chemistry protocol. Cryopreserved cells were thawed and counted to assess cell integrity and concentration prior to loading on the 10X Genomics controller. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol.

treatment_protocol: Not applicable to this study.

tag: disease state

value: Healthy controls

tag: gender

value: F

tag: age


title: ESCC E1241T

type: genomic

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description:
ESCC E1241T
Hybridized to SNP6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

source_name: ESCC E1241T

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Germline DNA from whole blood was extracted and purified using the standard phenol/chloroform method. DNA was extracted from tumor by using the Allprep kit (Qiagen). DNA quality and quantity were determined using NanoDrop 2000 (Thermo Scientific).

value: Esophageal squamous cell carcinoma (ESCC)

value: Tumor

tag: individual id


title: LX2_3

city: Beijing

first: Yanan

last: Ma

state: Beijing

address: No.8, Youanmen wai St

department: Department of Gastroenterology and Hepatology

country: China

institute: Beijing You’an Hospital affiliated with Capital Medical University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

extract_protocol:
RNA was extracted with Trizol reagent. The RNA quantification and qualification were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatocellar carcinoma cells

value: liver

value: HepG2 cells co-cultured with LX-2 cells


title: ESCC E1187T

description:
ESCC E1187T
Hybridized to SNP6.0

source_name: ESCC E1187T


title: CD14_TGF(+)_D0_rep1

value: TGF-priming


title: H2S_3

value: HepG2 cells treated with NaHS


title: LX2_2


title: LX2_1


title: ESCC E0948T-repeat

description:
ESCC E0948T-repeat
Hybridized to SNP6.0

source_name: ESCC E0948T


title: Naive CD115+ rep2

city: Seoul

first: Yunyun

last: Zou

address: 103 Daehak-ro, Jongno-gu,

country: South Korea

institute: Seoul National Universiry

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Mus musculus (mm10) using HISAT v2.0.5 [Nature methods 12.4 (2015): 357]. HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2. Because of its use of these efficient data structures and algorithms, HISAT generates spliced alignments several times faster than Bowtie and BWA widely used. The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from the UCSC table browser (http://genome.uscs.edu). Transcript assemble and abundance estimation using StringTie v1.3.3b [Nature biotechnology 33.3 (2015): 290, Nature protocols 11.9 (2016): 1650]. After alignment, StringTie was used to assemble aligned reads into transcripts and to estimate their abundance.
The relative abundances of gene were measured in read count using StringTie v1.3.3b. We performed the statistical analysis to find differentially expressed genes using the estimates of abundances for each gene in samples. Genes with one more than zeroed read count values in the samples were excluded. Filtered data were log2-transformed and subjected to RLE Normalization. Statistical significance of the differential expression data was determined using DESeq2 nbinomWaldTest [Genome biology 15.12 (2014): 550] and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm. For DEG set, hierarchical clustering analysis was performed using complete linkage and Euclidean distance as a measure of similarity. Gene-enrichment analysis for DEGs was also performed based on Gene Ontology (http://geneontology.org/) database.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
CD115- monocytes and CD115+ monocytes were sorted by flow cytomentry seperatly. Total RNA was extracted from cells using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) and residual DNA was removed with a DNA-free Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. Samples were loaded onto a 1% agarose gel before electrophoresis. DNA-free conditions were confirmed by SYBR Gold staining (Invitrogen). The quantity and the quality of RNA was evaluated by Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) and bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). RNA-Seq libraries were prepared with 1 μg of total RNA from two biological replicates of each group using TruSeq Stranded mRNA LT Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Bone marrow

value: tumor free

tag: genotype

value: wild type

tag: population


title: Naive CD115- rep2


title: H2S_1


title: ESCC E0891T

description:
ESCC E0891T
Hybridized to SNP6.0

source_name: ESCC E0891T


title: ESCC E0892T

description:
ESCC E0892T
Hybridized to SNP6.0

source_name: ESCC E0892T


title: ESCC E0863T-repeat2

description:
ESCC E0863T-repeat2
Hybridized to SNP6.0

source_name: ESCC E0863T


title: C3

value: control


title: H2S_2


title: ESCC E0848T

description:
ESCC E0848T
Hybridized to SNP6.0

source_name: ESCC E0848T


title: Naive CD115+ rep1


title: EL4 CD115+ rep2

value: post tumor inoculation day 21


title: ESCC E0842T

description:
ESCC E0842T
Hybridized to SNP6.0

source_name: ESCC E0842T


title: EL4 CD115+ rep1


title: HC-F-63


title: C1


title: CD14_TGF(+)_TNFD1_rep1


title: Naive CD115- rep1


title: ESCC E0379T

description:
ESCC E0379T
Hybridized to SNP6.0

source_name: ESCC E0379T


title: EL4 CD115- rep2


title: CD14_TGF(-)_TNFD1_rep1


title: SEZ-F4: SEZ aNSPCs 4 +CAG-FoxG1-IRES-GFP

city: Erlangen

first: Dieter

middle: Chichung

last: Lie

address: Fahrstr. 17

department: Institut für Biochemie

country: Germany

data_processing:
quality filtering with FASTQ Trimmer
alignment of the reads to the mouse reference genome Ensembl GRCm39, release 104
read counts per gene were obtained using htseq-count and Ensembl gff3 annotation file
differential expression analysis via DESeq2
Genome_build: GRCm39
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample seperated by treatment

source_name: adult neural stem/progenitor cells derived from Subependymal Zone (SEZ)

growth_protocol: Adult neural stem/progenitor cells (NSPC)  from 8-week old female C57BL/6J mice were isolated from the DG or SEZ with the MACS neural tissue dissociation kit according to manufacturer’s protocol (MACS Miltenyi Biotec, Cat# 130-092-628). NSPCs were kept under proliferative conditions in DMEM F12 Glutamax (GIBCO, Cat# 10565018) medium with 1xNeurobrew-21 (MACS Miltenyi Biotec, Cat# 130-093-566), 1xPSF (GIBCO, Cat# 15240062), 8mM HEPES, 10ng/ml EGF (Peprotech, Cat# AF-100-15) and 10ng/ml FGF (Peprotech, Cat# AF-100-18B).

extract_protocol:
Adult NSPCs were harvested via centrifugation, washed once with ice-cold PBS and total RNA was isolated using TRIZOL/Rneasy Mini Kit from Quiagen
Library preparation, Illumina, RNA with PolyA selection

treatment_protocol: Adult NSPCs, dissociated into single cells, were seeded onto tissue culture plates or glass cover slips coated with PDL/Laminin. 24 hours later, adherent NSPCs were transduced with a GFP encoding control MML-retrovirus or an MML-retrovirus bi-cistronically encoding for FoxG1 and GFP.

value: postnatal day 56


title: CD14_TGF(-)_D0_rep1

value: CD14+ monocyte

value: untreatment


title: EL4 CD115- rep1


title: W6_2

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

country: Japan

institute: Kobe University

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) and mapped to Refseq transcripts by Strand NGS software using default parameters.
All aligned reads were normalized using Transcripts Per Kilobase Million (TPM).
TPM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol, gene ID and TPM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: Gastric organoids at week6

extract_protocol:
Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacture's instruction.
RNA libraries were prepared using SMARTer Stranded RNA kit.

value: Gastric organoids at week6


title: SEZ-F2: SEZ aNSPCs 2 +CAG-FoxG1-IRES-GFP

value: adult neural stem/progenitor cells derived from Subependymal Zone (SEZ)


title: Ythdc2_E332Q-4 [RR1125; RNA]

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description: gene expression profiling

data_processing:
For gene expression profiling the reads were sorted into individual libraries based on the barcodes and mapped to the mouse genome (Ensembl release 102) either using salmon v1.3.0 (salmon quant with options -l A  --validateMappings --gcBias)(Patro et al., 2017) or kallisto (quant v0.46.2 with options --plaintext)(Bray et al., 2016). The DESeq function of DESeq2_1.25.10 bioconductor package (Love et al., 2014) was used to obtain log2 fold changes of gene expression between wild-type and knock-in/mutant samples and the adjusted p-values. Log2 fold change of 1.5 and adjusted p-value 0.05 was used as a threshold for statistical significance. The individual mouse tissues were analyzed separately.
The whole single-cell RNAseq (scRNA-seq) analysis strategy was based on a previously published approach (Luecken and Theis, 2019). Demultiplexed raw sequencing data were processed by cellranger pipeline (v3.0.2) developed by 10x Genomics. Reads were aligned to the custom mm10 reference by cellranger count. Cell count matrix, gene and barcode tables were taken as final output for further processing. Scanpy scRNA-seq toolkit (v1.4.5) was mainly used to integrate, normalize, and process the data. Once integrated, scRNA-seq dataset was filtered based on the following criteria: 1) transcript counts per cell (cells containing less than 1500 or more than 40000 transcripts were discarded) using filter_cells function; 2) genes expressed per cell (cells with less than 2000 genes expressed were discarded) using filter_cells function; 3) mitochondrial gene fraction (cells with more that 20% of mt genes per total number of genes expressed were discarded); 4) gene occurrence (genes which were found in less than 20 cells were discarded) with filter_genes function. Ythdc2+/+ sample was removed from the analysis because of very low sequencing quality, only Ythdc2+/- and Ythdc2-/- samples were processed. Finally, 4528 cells were retained for further analysis. Scran bioconductor package was used for the normalization with default parameters on count matrices before constructing single-cell maps. To reduce the dimentionality of the data and construct single-cell maps UMAP algorithm was applied to the normalized count matrices based on 3000 highly variable genes identified. Batch correction was done by MNN algorithm with mnnpy package. Leiden clustering algorithm (leiden function of the scanpy package) was used to identify cell populations. MAST algorithm  was used to perform differential gene expression analysis (diffxpy.api python package). Pseudotime variable for the developmental trajectory analyses was inferred with the Slingshot software (v1.4.0).
Reads were QC-checked with FastQC (v0.11.5) and adapters were removed with Flexbar (v3.5.0, SeqAn v2.4.0). Trimmed reads were aligned to the mouse genome reference (GRCm38) by STAR (v2.7.9a) with the following iCLIP-specific parameters: --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --alignEndsType Extend5pOfRead1. BAM files were further deduplicated with umi_tools dedup (v1.1.1). The 2 replicas were merged together with samtools merge (v1.7). PureCLIP was used to identify binding sites from the merged library.
Genome_build: Ensembl release 102
Supplementary_files_format_and_content: ScRNA-seq files contain either gene expression matrix per cell, or cell-related parameters (mitochondrial gene fraction per cell, cell type annotated, etc.), or gene-related parameters (highly variable gene label, total gene expression counts in cells, etc.). YTH mutant RNA-seq supplementary file contains tables with DESeq2-specific differential gene expression parameters (baseMean, log2 fold change, adjusted p-value, etc.), as well as DESeq2-normalized gene counts per replica per condition both for 2N and for 4N cells. Ythdc2 cat-dead mutant RNA-seq supplementary file contains DESeq2-specific differential gene expression parameters table (baseMean, log2 fold change, adjusted p-value, etc.), as well as DESeq2-normalized gene counts matrix per replica per condition. ICLIP supplementary file contains a summary table with the total number of filtered binding sites (0<log2(BS coverage)<4.5) per 5’UTR, CDS, and 3’UTR of the YTHDC2 binding target, a table of the ubiquitination pathway genes, as well as a BED file of all the PureCLIP-defined and annotated binding sites.

source_name: Testes

growth_protocol: Mutant mice were generated at the Transgenic Mouse Facility, University of Geneva. The mice were bred in the Animal Facility of Sciences III, University of Geneva. The generation of Ythdc2 knockout mouse line is described previously (Wojtas et al., 2017). The exon 7 encodes for parts of the N-terminal RecA domain of the RNA helicase module in YTHDC2, and specifically the ATPase motif DEVH. YTH domain is encoded in exon 27-29. We targeted the endogenous Ythdc2 locus in mouse embryos of the hybrid background B6D2F1 (50% C57BL/6 and 50% DBA/2) with specific guide RNAs and homology repair templates to create Ythdc2 mutant lines inactivating the RNA helicase domain and the m6A-binding capacity of the YTH domain.

extract_protocol:
RNA extract: Total RNA was isolated using the Trizol reagent (ThermoFisher Scientific; Cat. No. 15596026) from the required mouse testes samples (whole testes or FACS purified germ cells). Biological replicates were used. RNA concentration was measured with a Qubit fluorimeter (Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
RNA-seq library: The TruSeq Stranded Total RNA kit with Ribo-Zero Gold was used for library preparation with 500 ng of total RNA as input. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were diluted at 2 nM and pooled before the clustering process on a HiSeq 4000 Single Read flow cell. Reads of 50 bases were generated using the TruSeq SBS reagents on the Illumina HiSeq 4000 sequencer (iGE3 Genomics Platform, University of Geneva).

value: Testes

value: Mut

tag: experiment

value: gene expression profiling


title: W3_2

source_name: Derivatives at week3 during gastric induction from hiPSC


title: Ythdc2_E332Q-3 [RR1124; RNA]

description: gene expression profiling


title: SEZ-F3: SEZ aNSPCs 3 +CAG-FoxG1-IRES-GFP


title: Ythdc2_E332Q-2 [RR1123; RNA]

description: gene expression profiling


title: SEZ-F1: SEZ aNSPCs 1 +CAG-FoxG1-IRES-GFP


title: DG-F4: DG aNSPCs 4 +CAG-FoxG1-IRES-GFP

source_name: adult neural stem/progenitor cells derived from Dentate Gyrus (DG)


title: W1_2

source_name: Derivatives at week1 during gastric induction from hiPSC


title: Ythdc2_E332Q-1 [RR1122; RNA]

description: gene expression profiling


title: DG-F3: DG aNSPCs 3 +CAG-FoxG1-IRES-GFP

value: adult neural stem/progenitor cells derived from Dentate Gyrus (DG)


title: DG-F2: DG aNSPCs 2 +CAG-FoxG1-IRES-GFP


title: Ythdc2_wt-4 [RR1121; RNA]

description: gene expression profiling

value: WT


title: DG-F1: DG aNSPCs 1 +CAG-FoxG1-IRES-GFP


title: Ythdc2_wt-3 [RR1120; RNA]

description: gene expression profiling


title: Stomach_2

source_name: Stomach

value: normal stomach tissue


title: Ythdc2_wt-2 [RR1119; RNA]

description: gene expression profiling


title: SEZ-G2: SEZ aNSPCs  2 + CAG-GFP


title: Ythdc2YTHmut/YTHmut_4N_rep2 [RR963; RNA]

description: gene expression profiling

source_name: 4N cells

value: 4N cells

value: adult (P60)

value: KI


title: SEZ-G4: SEZ aNSPCs  4 + CAG-GFP


title: W8_2

source_name: Gastric organoids at week8

value: Gastric organoids at week8


title: CD14_TGF(-)_TNFD1_H3K27ac_rep1

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Cut and Run-seq reads were aligned to the human genome (hg38) using Bowtie2. MACS2 to identify peaks of CUT&RUN-seq enrichment over background.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file

source_name: Primary human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in MEMa (Invitrogen) supplemented with 10% heat-inactivated defined FBS, penicillin/streptomycin, L-glutamine, and 20 ng/mL human macrophage colony-stimulating factor (M-CSF) with or without TGFb(10 ng/mL).

extract_protocol:
nuclei from 500,000 cells were extracted and subjected to CUT&RUN protocol using the indicated antibody.
NEB Next Ultra II FS DNA Library Kit

treatment_protocol: CD14+ cells cultured in M-CSF (20ng/ml) with or without TGFb (10 ng/ml) for 3 days and then stimulated with TNFa (40 ng/ml) for various time points(day0, day1, day6)

value: peripheral blood

tag: antibody

value: H3K27ac(Abcam ab4729)


title: Ythdc2YTHmut/YTHmut_4N_rep1 [RR960; RNA]

description: gene expression profiling


title: SEZ-G3: SEZ aNSPCs  3 + CAG-GFP

value: postnatal day 56


title: DG-G3: DG aNSPCs 3 +CAG-GFP


title: cKO_3

city: Urbana

first: Jenny

last: Drnevich

state: IL

address: 1206 W. Gregory Dr.

institute: University of Illinois

data_processing:
The libraries were pooled; quantitated by qPCR and sequenced on one SP lane for 101 cycles from one end of the fragments on a NovaSeq 6000.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina). Adaptors were trimmed from the 3'-end of the reads.
Salmon (v 1.2.0) was used to quasi-map reads to the transcriptome and quantify the abundance of each transcript. The transcriptome was first indexed using the decoy-aware method in Salmon with the entire genome as the decoy sequence. Then quasi-mapping was performed to map reads to transcriptome with additional arguments --seqBias and --gcBias to correct sequence-specific and GC content biases, --numBootstraps=30 to compute bootstrap transcript abundance estimates and --validateMappings and --recoverOrphans to help improve the accuracy of mappings.
Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package (v 1.18.0) in R 4.0.4.
TMM-normalized logCPM values were calculated using edgeR (3.32.1) and 22,342 genes without logCPM > log2 (0.5) in at least 3 samples were filtered out, leaving 16,911 genes to be analyzed for differential expression. TMM-values logCPM were re-calculated then analyzed using the limma-trend method from the limma package (v 3.46.0) using a statistical model of treatment + batch
Genome_build: NCBI GRCm39, Annotation 109
Supplementary_files_format_and_content: Reddi_rawCounts_cKO_2021-05-25.xlsx contains estimated gene-level counts, some gene annotation information and a column indicating which genes passed the filtering thresholds. Reddi_TMMnormValues_cKO_2021-05-25.xlsx contains TMM-normalized log2 count per million expression values for genes that passed filtering thresholds.

source_name: Testis

extract_protocol:
Testes were dissected out and flash frozen in liquid nitrogen, then stored at -80 until extraction of total RNA using Qiagen RNA extraction kit
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

value: conditional Tardbp knock-out

value: postnatal day 12

tag: batch


title: hiPSC_2

source_name: hiPSC

value: hiPSC


title: Ythdc2YTHmut/YTHmut_2N_rep2 [RR957; RNA]

description: gene expression profiling

source_name: 2N cells

value: 2N cells


title: Ythdc2_wt-1 [RR1118; RNA]

description: gene expression profiling

value: Testes


title: Ythdc2+/YTHmut_2N_rep3 [RR956; RNA]

description: gene expression profiling

value: HET


title: C2

value: hepatocellar carcinoma cells

value: liver

value: control


title: cKO_1


title: Ythdc2+/YTHmut_4N_rep3 [RR962; RNA]

description: gene expression profiling

value: gene expression profiling


title: SEZ-G1: SEZ aNSPCs  1 + CAG-GFP

value: adult neural stem/progenitor cells derived from Subependymal Zone (SEZ)


title: Ythdc2+/YTHmut_4N_rep2 [RR961; RNA]

description: gene expression profiling

value: 4N cells

value: adult (P60)


title: Ythdc2YTHmut/YTHmut_2N_rep3 [RR958; RNA]

description: gene expression profiling

value: KI


title: DG-G4: DG aNSPCs 4 +CAG-GFP

value: adult neural stem/progenitor cells derived from Dentate Gyrus (DG)


title: Ythdc2+/YTHmut_4N_rep1 [RR959; RNA]

description: gene expression profiling


title: WT_2

value: wild type


title: WT_1


title: CD14_TGF(+)_D0_H3K27me3_rep1

value: CD14+ monocyte

value: peripheral blood

value: TGF-priming

value: H3K27me3(Millipore 07-449)


title: CD14_TGF(-)_D0_H3K27me3_rep1

value: no treatment


title: CD14_TGF(+)_TNFD1_H3K27ac_rep1

value: H3K27ac(Abcam ab4729)


title: Ythdc2_KO1_P10_embryo [RR797; scRNA]

description: Single-cell RNA sequencing

value: KO

value: Single-cell RNA sequencing


title: Ythdc2_KO_P10_embryo [RR798; scRNA]

description: Single-cell RNA sequencing


title: Ythdc2+/YTHmut_2N_rep1 [RR953; RNA]

description: gene expression profiling

value: 2N cells

value: HET


title: DG-G1: DG aNSPCs 1 +CAG-GFP

value: postnatal day 56


title: Ythdc2+/YTHmut_2N_rep2 [RR955; RNA]

description: gene expression profiling

value: gene expression profiling


title: cKO_2

value: conditional Tardbp knock-out

value: postnatal day 12


title: WT_3


title: CD14_TGF(-)_TNFD1_H3K4me3_rep1

value: H3K4me3(Millipore 07-473)


title: CD14_TGF(+)_D0_H3K27ac_rep1


title: CD14_TGF(+)_D0_H3K4me3_rep1


title: Ythdc2YTHmut/YTHmut_4N_rep3 [RR964; RNA]

description: gene expression profiling

value: 4N cells

value: adult (P60)

value: KI


title: CD14_TGF(-)_D0_H3K27ac_rep1

value: CD14+ monocyte

value: peripheral blood


title: CD14_TGF(-)_TNFD1_H3K27me3_rep1

value: H3K27me3(Millipore 07-449)


title: CD14_TGF(+)_TNFD1_H3K27me3_rep1


title: Pancreas_KNGC_rep3

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with STAR 2.6.0a  to the reference genome UCSC mm10 using 2-pass mode with default parameters.
Gene level counts were obtained using featureCounts  with gene models from corresponding UCSC annotation mm10.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in tab-delimited text file

source_name: Pancreas

extract_protocol:
Pancreatic total RNA was isolated using Trizol and further purified with an RNeasy Mini Kit (Qiagen, Valencia, CA). The average RNA integrity number values were then measured by an Agilent Bioanalyzer.
Individual transcriptome sequencing (RNA-Seq) libraries were prepared from each mouse using an Illumina TruSeq v2 kit. 100 base pairs reads were collected with an Illumina HiSeq 4000 instrument.

value: Pancreas

value: 4 weeks


title: Ythdc2YTHmut/YTHmut_2N_rep1 [RR954; RNA]

description: gene expression profiling


title: siFBXO7_MDAMB231

city: La Jolla

first: Zhixin

last: Qiu

state: CA

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

data_processing:
Raw FASTQ reads were trimmed using Trim Galore and transcript quantification was performed using Salmon in the quasi-mapping mode.
Salmon “quant” files were converted using Tximport function to obtain gene expression matrix.
Genome_build: hg19
Supplementary_files_format_and_content: RNA abundance (FPKM) matrix at the gene level.

source_name: breast cancer cell line

extract_protocol:
PolyA+ RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module
Libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).


title: DG-G2: DG aNSPCs 2 +CAG-GFP

value: adult neural stem/progenitor cells derived from Dentate Gyrus (DG)


title: Pancreas_KNGC_rep1


title: 3_KO814

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

description:
R1 read: Cell barcodes (position 1, 16nt) + UMIs (position 17, 12nt)
R2 read: Biological read (cDNA) (91nt)
UMIsMatrix.txt.gz

data_processing:
Cell barcode demultiplexing, pseudo-alignment of reads to the mouse transcriptome (Ensembl release 97), and generation of the table of UMI counts were performed using Kallisto (version 0.46.0) and BUStools (version 0.39.2).
Further processing of the UMI counts table was performed by using R 4.0 and Bioconductor 3.11 packages, notably DropletUtils (version 1.8.0), scran (version 1.16.0) and scater (version 1.16.2), following mostly the steps illustrated in the Bioconductor OSCA book (https://osca.bioconductor.org/).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CellAnnotation.txt.gz: TSV file (tab separated values) with sample of origin, condition, cluster membership and cell type annotation for each cell.
Supplementary_files_format_and_content: UMIsMatrix.txt.gz: TSV file (tab separated values) with UMI counts for ensembl release 97 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dot (e.g., "AAACCCATCATCCTAT.1_KO707").

source_name: colon epithelial cells from Gpr35 KO mouse

growth_protocol: Gpr35[flox/flox] mice were generated using CRISPR/Cas9 by Biocytogen (Wakefiled, USA). Villin Cre mice were kindly provided by Claudia Cavelti, Department of Biomedicine, University of Basel. All mice were kept in the animal facility of the Department of Biomedecine, University of Basel, Switzerland, under SPF conditions.

extract_protocol:
We isolated proximal colon epithelial cells from 4 Gpr35flfl-Vilcre+ and 4 Gpr35flfl-Vilcre- female littermates at a steady state. Crypts were dissociated to single-cell suspensions.
Single-cell suspensions were stained with Epcam+ (BioLegend #118213), CD45- (eBioscience #64-0451-82) and CD31- (BioLegend #102414) and sorted into an Eppendorf tube containing 50 μL of 1X PBS with 0.4% BSA and 5% FBS.
Sorted cell suspensions from each mouse were loaded into a single well of a 10X Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v3 Reagent Kit (10X Genomics) according to manufacturer’s instructions.

value: colon epithelium

value: Gpr35[flox/flox Vil+]

tag: Sex

value: female

value: 7 weeks


title: CD14_TGF(+)_TNFD1_H3K4me3_rep1


title: 7_WT815

source_name: colon epithelial cells from WT mouse

value: Gpr35[flox/flox Vil-]


title: 8_WT816


title: 6_WT813


title: 5_WT709


title: Pancreas_KNGC_rep2


title: KNGC

data_processing:
10X Genomics cellranger v3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: feature-barcode matrix file

growth_protocol: Normal Chow Diet in animal facility

extract_protocol:
Collagenase digestion
up to 6000 cells were loaded per lane on an 10X Genomics Chromium system. Single-cell capture, barcoding, and library preparation were performed using the 10X Genomics Chromium system according to the manufacturer’s protocol.

treatment_protocol: No treatment

tag: tumor stage

value: Low-grade IPMN


title: 2_KO708


title: 1_KO707


title: 4_KO817


title: Ythdc2_WT_P10_embryo [RR796; scRNA]

description: Single-cell RNA sequencing

value: WT

value: Single-cell RNA sequencing


title: CD14_TGF(-)_D0_H3K4me3_rep1

value: no treatment

value: H3K4me3(Millipore 07-473)


title: EYA2chip_siFBXO7

data_processing:
Raw FASTQ files were trimmed using TrimGalore and aligned to the hg19 human genome using Bowtie2.
SamTools was used to sort and index the BAM files.
The bigwig files were generated using the DeepTools “bamCoverage”
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
ChIP was performed using Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (MilliporeSigma, 17-10085) according to the manufacturer’s instructions
Library was constructed using NEB NEBNext® Ultra™ DNA Library Prep Kit for Illumina for sequencing

value: Flag antibody (Cell signaling 14793)

tag: cell line


title: Stomach

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) and mapped to Refseq transcripts by Strand NGS software using default parameters.
All aligned reads were normalized using Transcripts per million (TPM).
TPM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol, gene ID and TPM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: gastric tissue

value: gastric tissue


title: Pancreas_KC_rep2


title: Melan-a_siScr_48h_rep3

type: RNA

city: ORSAY Cedex

first: Juliette

last: BERTRAND

address: Bat 110, Centre universitaire

department: CNRS UMR3347, INSERM  U1021

country: France

institute: Institut Curie

hyb_protocol: The biotin-labelled RNA was hybridized to miRNA 4.0 microarrays (Affymetrix) for 16 h at 48°C.

scan_protocol: Affymetrix reagents were used to wash and Streptavidin-Phycoerythrin stain the microarrays and they were scanned using a GeneChip Scanner 3000 7G System (Affymetrix, Santa Clara, CA, United States).

data_processing: Microarray analysis was performed by Genosplice Technology. Quality controls were performed using Expression Console metrics (Affymetrix). Data were normalized with Expression Console using the “RMA+DABG” normalization method. A miRNA in one sample was considered to be expressed in this sample if the corresponding DABG p-value was ≤ 0.05, and not expressed otherwise. A miRNA was considered expressed in one condition if miRNA was expressed in at least 75% of the samples of this condition. A paired Student t-test was applied on expressed miRNA.

label: biotin

source_name: Melan-a cells, siScr, 48h

label_protocol: Sample preparation and hybridization were performed by the Genomic platform of the Institut Curie. The flashTag Biotin HSR RNA labelling kit (Affymetrix) was used to label 100 ng total RNA according to the manufacturer’s protocol. Briefly, RNA was tailed with poly(A) and then ligated to a biotin labelling molecule.

growth_protocol: The mouse melanocyte Melan-a cell line was provided by D. Bennett (Bennett et al, 1987) and cultured in F12 medium (Gibco 21765) supplemented with 10% fetal bovine serum (Eurobio CVFSVF00-01), 1% penicillin/streptomycin (Gibco 15140-122), and 200 nM TPA (Sigma P8139). For transfection experiements, 150 000 Melan-a cells were seeded in a well of 12-well plate 24 hours before transfection. Cells were grown at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA from Melan-a cells was extracted using the miRNeasy Kit (Qiagen, #217004).

treatment_protocol: Melan-a cells were transfected with siDicer or siScr using lipofectamin (Invitrogen 11668019) and magnetofectamin (OZ bioscience CM20200) following manufacturer instructions. For each well, 2 ul of lipofectamin, 1 ul of magnetofectamin and 50 pmol of siRNA diluted in  100 ul Optimem (Gibco) and 900 ul F12 medium (Gibco 21765) without antiboitics were added to the cells. Plates were incubated at 37°C on a magnetic plate which was remove 20 minutes later. Six hours later, medium was replaced by complete F12 medium. Cell lysates were collected 24 hours later by scratching in Qiazol reagent as indicated in miRNeasy Kit (Qiagen, #217004) protocol.

value: Melan-a cells

tag: sirna

value: siScr

tag: rin

tag: passage


title: Pancreas_NGC_rep2

tag: tissue

value: Pancreas


title: Day56

source_name: hiPSC-derived gastric organoid at day56

tag: cell type

value: hiPSC-derived gastric organoids at day 56


title: Ex117SB_Posi

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) and mapped to Refseq transcripts by Strand NGS software using default parameters.
All aligned reads were normalized using Trimmed mean of M values (TMM).
TMM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol, gene ID and TMM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: hiPSC-derived gastric organoids treated with SB431542

value: hiPSC-derived gastric organoids

tag: treatment


title: VTA_GH1_S21

city: Buffalo

first: Fengwei

last: Yang

address: 955 Main St

institute: University at Buffalo

data_processing:
Illumina Casava1.7 software used for basecalling.
Strand-specific RNA libraries from 1 μg purified RNA using TruSeq stranded total RNA plus Ribo-zero kits (Illumina)
Reads were first trimmed using Cutadapt to remove the 3’ end adapters and trailing sequences, followed by aligning to mouse RefSeq mRNAs using TopHat2 with default.
Transcript counts were estimated using HTSeq
Assembly: mm10
Supplementary files format and content: Matrix table with raw counts for every gene and every sample

source_name: cerebrum

extract_protocol:
Brain punches were collected, and RNA was harvested using Trizol reagent. TruSeq stranded total RNA plus Ribo-zero kits was used with 1 ug of purified RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cerebrum

value: Group housed


title: Pancreas_NGC_rep1

tag: age

value: 4 weeks


title: Melan-a_siScr_48h_rep1

value: female


title: VTA_GH3_S23


title: Melan-a_siScr_48h_rep2


title: VTA_GH2_S22


title: Pancreas_WT_rep3


title: Pancreas_KC_rep3


title: Day20

source_name: hiPSC-derived gastric organoid at day20

value: hiPSC-derivedgastric organoids at day 20


title: Pancreas_NGC_rep3


title: Pancreas_WT_rep2


title: EYA2chip_siCONT


title: Pancreas_KC_rep1


title: siControl_MDAMB231

value: siControl


title: VTA_ESI1_S25

value: Early social isolated


title: Day43

source_name: hiPSC-derived gastric organoid at day43

value: hiPSC-derived gastric organoids at day 43


title: Melan-a_siDicer_48h_rep1

source_name: Melan-a cells, siDicer, 48h

value: siDicer


title: Melan-a_siDicer_48h_rep3


title: Ex117SB_Nega

source_name: hiPSC-derived gastric organoids treated with vehicle

value: vehicle


title: VTA_ESI3_S26


title: Melan-a_siScr_24h_rep3

source_name: Melan-a cells, siScr, 24h


title: Melan-a_siDicer_48h_rep2


title: Day7

source_name: hiPSC-derived gastric organoid at day7

value: hiPSC-derivedgastric organoids at day 7


title: Melan-a_siScr_24h_rep2


title: Pancreas_WT_rep1


title: HCT_WT_rep2

first: Jimin

last: Hwang

address: 52, Ewhayeodae-gil, Seodaemun-gu

institute: Ewha Womans University

data_processing:
bcl2fastq2 (Version 2.20) was used for basecalling.
Sequenced reads were trimmed for quality control (QS>20).
STAR-RSEM pipeline was applied for read alignment to the hg19 reference genome and for expression quantification at the gene level.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes TPM values for each Sample

source_name: colon cancer cell line

growth_protocol: MDA-MB-231 and HCT116 cells were cultured in DMEM and MyCoy 5a media respectively, supplemented with 10% (v/v) FBS.

extract_protocol:
Cells were havested and lysed with RLT lysis buffer provided from Qiagen Rneasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 100 microM H2O2 for 8 hours at 37 oC.

value: colon cancer

value: IgG


title: VTA_ESI2_S24


title: BLA_GH3_S33


title: BLA_GH2_S32


title: BLA_ESI3_S36


title: BLA_GH1_S31


title: HCT_H2O2_HSP60N_rep2


title: HCT_H2O2_rep2


title: HCT_H2O2_rep1


title: HCT_H2O2_HSP60N_rep1


title: rat vascular smooth muscle cell - cholesterol plus DAPT2

city: Xiamen

first: Wei

last: Shen

state: Fujian

address: 2999 Jinshan Rd, Huli District

institute: Xiamen University

data_processing:
Fastq reads were mapped to genome by using hisat2
Genes reads were calculated by using htseq-count
Genome_build: Rnor_6.0, hg38
Supplementary_files_format_and_content: Counts files were generated using htseq-count; Scores represent reads number assigned to each gene

organism: Rattus norvegicus

source_name: rat vascular smooth muscle cell

growth_protocol: VSMCs were cultured with DMEM supplemented with 10% PBS and 1% penicillin and streptomycin.

extract_protocol:
Total RNA was extracted by using TRIzol Reagent (Invitrogen 15596018) following manufacture’s instruction.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: VSMCs were cultured with water soluble cholesterol (Chol:MβCD) or NOTCH inhibitor DAPT or both for 48 hours.

value: primary aortic vascular smooth muscle cell

value: Sprague-Dawley

tag: agent

value: cholesterol plus DAPT


title: Melan-a_siScr_24h_rep1

value: Melan-a cells

tag: strain

value: siScr


title: ALS_Colgalt2_SOD_TRAP_IP_rep4

city: New York

first: Eric

middle: F

last: Schmidt

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Sequence and transcript coordinates for mouse mm10 UCSC genome and gene models were retrieved from the Bioconductor Bsgenome.Mmusculus.UCSC.mm10 (version 1.4.0) and TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.0) Bioconductor libraries respectively.
RNA-seq reads are aligned to the genome using Rsubread's subjunc method (version 1.30.6)
BigWigs normalised to reads per million were exported using the rtracklayer package (version 1.40.6).
Counts in genes were generated using featureCounts within the Rsubread package(version 1.30.6) with default settings and the TxDb.Mmusculus.UCSC.mm10.knownGenegene models.
Differential expression was calculated by DESeq2 v1.26.0 using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: CSV format; Data output from DESeq2 on all genes for each sample in the analysis including: gene symbol, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, isSig, normalized counts for each sample.

source_name: TRAP IP RNA from M1 cortex of Colgalt2-bacTRAP::SOD1*G93A mouse

extract_protocol:
Motor cortex (or whole cortex for samples 15-21) was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol. Total RNA from "input" samples was purified from the pre-IP tissue homogentates using the Agilent Nanoprep kit.
15 ng total RNA from TRAP IP or input was amplified using the NuGEN Ovation RNA-Seq System V2 and libraries were prepared from 10 ug amplified cDNA using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocols.

treatment_protocol: EGFP-L10a transgene was expressed in lower layer 5b pyramidal cells in cortex of Gprin3-bacTRAP mice and upper layer 5b pyramidal cells in Colgalt2-bacTRAP mice. For ALS experiments, both bacTRAP lines were crossed to SOD1*G93A mice. TRAP was performed in adult (8-17 week old) animals.

tag: brain region

value: Whole Cortex

value: Upper L5b pyramidal cells

tag: genotype

value: SOD+

tag: rna

value: TRAP IP


title: Melan-a_siScr_48hrs_rep3

hyb_protocol: Affymetrix GeneChip® Mouse ClariomD microarrays were hybridized with 4.7 µg labelled DNA.

scan_protocol: The microarrays were scanned using a GeneChip Scanner 3000 7G System (Affymetrix, Santa Clara, CA, United States)

data_processing: Microarray analysis was performed by Genosplice Technology. Quality controls were performed using Expression Console metrics (Affymetrix). Further analysis and visualization were performed with EASANA (GenoSplice Technology, www.genosplice.com), using FAST DB 2016_1 annotations as already described {Tury, 2018 #3315;Sharma, 2017 #3316;Schaller, 2017 #3317}. Data were normalized by quantile normalization. Background corrections were made with antigenomic probes selected as previously described. Only probes targeting exons annotated from FAST DB transcripts were selected to ensure that we focused on well-annotated genes for which mRNA sequences were present in public databases. Low-quality probes (e.g., probes labeled by Affymetrix as “cross-hybridizing”) and those with a low signal intensity (relative to antigenomic background probes with the same GC content) were removed from the analysis. Only probes with a detection above background (DABG), p ≤ 0.05, in at least half the arrays were considered for statistical analysis. Only genes expressed in at least one of the compared conditions compared were analyzed. Expression was defined as a DABG p ≤ 0.05 for at least half of the gene probes. A paired Student’s t-test was used to compare gene-expression intensities between the various biological replicates.

label_protocol: Sample preparation and hybridization were performed by the Genomic platform of the Institut Curie. Mouse ClariomD arrays were hybridized according the recommendations of Affymetrix (Santa Clara, CA, United States) using the WT PLUS protocol and labelling and hybridization kits from Affymetrix. Total RNA (100 ng) was processed in parallel with an external Universal Mouse Reference RNA to verify the robustness of the data. The mean yield of labelled DNA was 9.75 µg (min: 8.15 µg; max: 11.65 µg).

value: female


title: Melan-a_siDicer_24h_rep1

source_name: Melan-a cells, siDicer, 24h


title: Melan-a_siDicer_24h_rep3


title: Melan-a_siDicer_24h_rep2


title: Melan-a_siDicer_48hrs_rep3


title: BLA_ESI2_S35

value: cerebrum

value: Early social isolated


title: Melan-a_siDicer_48hrs_rep2

value: siDicer


title: MDA_H2O2_HSP60N_rep2

source_name: breast cancer cell line

value: breast cancer


title: BLA_ESI1_S34


title: Melan-a_siScr_24hrs_rep3

treatment_protocol: Melan-a cells were transfected with siDicer or siScr using lipofectamin (Invitrogen 11668019) and magnetofectamin (OZ bioscience CM20200) following manufacturer instructions. For each well, 2 ul of lipofectamin, 1 ul of magnetofectamin and 50 pmol of siRNA diluted in 100 ul Optimem (Gibco) and 900 ul F12 medium (Gibco 21765) without antibiotics were added to the cells. Plates were incubated at 37°C on a magnetic plate which was remove 20 minutes later. Six hours later, medium was replaced by complete F12 medium. Cell lysates were collected 24 hours later by scratching in Qiazol reagent as indicated in miRNeasy Kit (Qiagen, #217004) protocol.


title: Melan-a_siScr_48hrs_rep1


title: ALS_Colgalt2_SOD_TRAP_IP_rep2


title: MDA_H2O2_rep2


title: rat vascular smooth muscle cell - DAPT1

value: DAPT


title: HCT_WT_rep1

value: colon cancer


title: Melan-a_siDicer_48hrs_rep1


title: hiPSC

source_name: human induced pluripotent stem cells

value: hiPSC


title: ALS_Colgalt2_SOD_TRAP_IP_rep1


title: ALS_Colgalt2_SOD_TRAP_IP_rep3


title: MDA_H2O2_HSP60N_rep1


title: rat vascular smooth muscle cell - cholesterol1

value: primary aortic vascular smooth muscle cell

value: cholesterol


title: ALS_Colgalt2_WT_TRAP_IP_rep1

source_name: TRAP IP RNA from M1 cortex of wildtype littermate of Colgalt2-bacTRAP::SOD1*G93A mice

value: SOD-


title: rat vascular smooth muscle cell - DMSO2

value: Sprague-Dawley

value: DSMO


title: rat vascular smooth muscle cell - cholesterol2


title: PRRSV NSP1a-2

status: Public on Mar 21 2022

first: In byung

last: Park

address: 145, Anam-ro, Seongbuk-gu, Seoul

institute: Korea University

description: processed data file: data3_PRRSV_Nsp1a_vs_mock_fc2 & raw.p

data_processing:
The raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Sus scrofa (GCF_000003025.6_Sscrofa11.1) using HISAT v2.1.0
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2
Transcript assembly and abundance estimation using StringTie version 1.3.4d. After alignment, StringTie v1.3.4d was used to assemble aligned reads into transcripts and to estimate their abundance.
It provides the relative abundance estimates as FPKM values (Fragments Per Kilobase of exon per Million fragments mapped) of transcript and gene expressed in each sample.
Genes with one more than zeroed FPKM values in the samples were excluded. To facilitate log2 transformation, 1 was added to each FPKM value of filtered genes
Genome_build: GCF_000003025.6_Sscrofa11.1
Supplementary_files_format_and_content: Excel spreadsheet format which includes contents; 1) Gene_symbol, 2) NCBI Protein accession ID, 3) Product, 4) Fold change, 5) Volume, 6) KEGG stat, 7) KEGG genes, 8) DAVID chart

organism: Sus scrofa

source_name: 3D4/31_PRRSV NSP1a

extract_protocol:
Total RNA was isolated from 3D4/31 cells using TRIzol reagent according to the manufacturer's instructions.
In order to construct cDNA libraries with the TruSeq mRNA LT library kit (Illumina, USA), 1 ug of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina NovaSeq 6000

value: macrophage cell line

tag: tissue source

value: lung

tag: genotype/variation

value: PRRSV NSP1 alpha-pBabepuro (PRRSV NSP1a)


title: PRRSV NSP1b-2

description: processed data file: data3_PRRSV_Nsp1b_vs_mock_fc2 & raw.p

source_name: 3D4/31_PRRSV NSP1b

value: PRRSV NSP1 beta-pBabepuro (PRRSV NSP1b)


title: ALS_Colgalt2_WT_TRAP_IP_rep3

value: Whole Cortex

value: Upper L5b pyramidal cells

value: TRAP IP


title: PRRSV NSP1-2

description: processed data file: data3_PRRSV_Nsp1_vs_mock_fc2 & raw.p

source_name: 3D4/31_PRRSV NSP1

value: PRRSV NSP1-pBabepuro (PRRSV NSP1)


title: PRRSV NSP1b-1


title: Melan-a_siScr_48hrs_rep2

source_name: Melan-a cells, siScr, 48h

value: Melan-a cells

value: siScr

tag: Sex

value: female


title: MDA_H2O2_rep1

value: breast cancer


title: PRRSV NSP1-3


title: Melan-a_siDicer_24hrs_rep3

value: siDicer


title: Melan-a_siScr_24hrs_rep2


title: ALS_Colgalt2_WT_TRAP_IP_rep2


title: Melan-a_siScr_24hrs_rep1


title: hemogenATACKORep2

city: bethesda

first: Xiang

last: Guo

address: 50 south drive, blg50

department: NIDDK

institute: NIH

data_processing:
ATAC-seq reads were aligned to  mouse GENCODE release 18 using Bowtie2 v2.3.5
Multimapping reads removed with samtools v1.9 using “view” subcommand and the additional argument “-q 20”, duplicated reads were removed with Picard v2.21.4
peaks were called using  MACS2 version 2.2.7.1
Genome_build: mouse GENCODE release 18
Supplementary_files_format_and_content: bed files were generated using MACS2 version 2.2.7.1

source_name: fetal livers

growth_protocol: Hemogen WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol: E14.5 fetal liver cells (~50,000) were treated according to the Omni-ATAC-seq protocol of the Kaestner Lab (https://www.med.upenn.edu/kaestnerlab/protocols.html).

value: Embryonic day 14.5

value: hemogen KO

value: fetal livers


title: MDA_WT_rep1

value: IgG


title: PRRSV NSP1-1

value: macrophage cell line


title: PRRSV NSP1b-3

value: lung


title: PRRSV NSP1a-1

value: PRRSV NSP1 alpha-pBabepuro (PRRSV NSP1a)


title: rat vascular smooth muscle cell - DMSO1

value: primary aortic vascular smooth muscle cell

value: Sprague-Dawley

value: DSMO


title: rat vascular smooth muscle cell - cholesterol plus DAPT1

value: cholesterol plus DAPT


title: hemogenATACWTRep1

value: WT


title: Melan-a_siDicer_24hrs_rep2

value: Melan-a cells


title: Melan-a_siDicer_24hrs_rep1


title: MDA_WT_rep2


title: Mock-2

description: processed data file: data3_PRRSV_Nsp*_vs_mock_fc2 & raw.p

value: pBabepuro (Mock)


title: Peripheral blood [A584_106 card A ]

city: Oslo

first: Sjur

last: Reppe

address: Kirkeveien 166

department: Medical biochemistry

country: Norway

institute: OSLO UNIVERSITY HOSPITAL

data_processing:
The data were analyzed using SDS 2.3 software (Applied Biosystems, Foster City, CA, USA) and the comparative threshold cycle (ΔΔCt) method.
We used a restricted mean of expressed miRNAs, and normalized between two plates with the same sample and performed a normalization across samples.

label: FAM

source_name: Peripheral blood

label_protocol: Total RNA (45 ng) was reverse-transcribed using Megaplex TM reverse transcription (RT) primersets A and B (Applied Biosystems, Foster City, CA, USA). TaqMan miRNA LDA Arrays A and B (Applied Biosystems) were used for profiling 758 different ncRNAs.

growth_protocol: Not applicable

extract_protocol: RNA from whole blood was isolated according to the PAXgene Blood RNA Kit manufacturer (BD, Franklin Lakes, NJ, USA), including the optional on-column DNase digestion according to manufacturer’s instructions.

treatment_protocol: Not applicable

tag: age (years)

tag: tag

value: Postmenopausal women


title: Peripheral blood [A584_100-2 card A ]


title: Mock-1

tag: cell line


title: Peripheral blood [A584_097 card A ]


title: rat vascular smooth muscle cell - DAPT2

value: DAPT


title: Peripheral blood [A584_104 card A ]


title: Peripheral blood [A584_094 card A ]


title: hemogenATACWTRep2


title: Peripheral blood [A584_107 card A ]


title: Peripheral blood [A584_099-2 card A ]


title: Peripheral blood [A584_101 card A ]


title: Peripheral blood [A584_098-2 card A ]


title: Peripheral blood [A584_102 card A ]


title: PRRSV NSP1a-3


title: hemogenATACKORep1


title: Peripheral blood [A584_091 card A ]


title: Peripheral blood [A584_096 card A ]


title: Peripheral blood [A584_103-2 card A ]


title: Peripheral blood [A584_087 card A ]


title: Peripheral blood [A584_085 card A ]


title: Mock-3


title: Peripheral blood [A584_092 card A ]


title: Peripheral blood [A584_081 card A ]


title: Peripheral blood [A584_089 card A ]


title: Peripheral blood [A584_088 card A ]


title: Peripheral blood [A584_078 card A ]


title: Peripheral blood [A584_084 card A ]


title: Peripheral blood [A584_083 card A ]


title: Peripheral blood [A584_082 card A ]


title: Peripheral blood [A584_086 card A ]


title: Peripheral blood [A584_074 card A ]


title: Peripheral blood [A584_080 card A ]


title: Peripheral blood [A584_072 card A ]


title: Peripheral blood [A584_095 card A ]


title: Peripheral blood [A584_079 card A ]


title: Peripheral blood [A584_069 card A ]


title: Peripheral blood [A584_065 card A ]


title: Peripheral blood [A584_077 card A ]


title: Peripheral blood [A584_064 card A ]


title: Peripheral blood [A584_063 card A ]


title: Peripheral blood [A584_073 card A ]


title: Peripheral blood [A584_090 card A ]


title: Peripheral blood [A584_060 card A ]


title: Peripheral blood [A584_067 card A ]


title: Peripheral blood [A584_061 card A ]


title: Peripheral blood [A584_071 card A ]


title: Peripheral blood [A584_058 card A ]


title: Peripheral blood [A584_056-2 card A ]


title: Peripheral blood [A584_054 card A ]


title: Peripheral blood [A584_068 card A ]


title: Peripheral blood [A584_053 card A ]


title: Peripheral blood [A584_075 card A ]


title: Peripheral blood [A584_093 card A ]


title: Peripheral blood [A584_050 card A ]


title: Peripheral blood [A584_070 card A ]


title: Peripheral blood [A584_062 card A ]


title: Peripheral blood [A584_076 card A ]


title: Peripheral blood [A584_048 card A ]


title: Peripheral blood [A584_055-2 card A ]


title: Peripheral blood [A584_044 card A ]


title: Peripheral blood [A584_059 card A ]


title: Peripheral blood [A584_066 card A ]


title: Peripheral blood [A584_040-2 card A ]


title: Peripheral blood [A584_051 card A ]


title: Peripheral blood [A584_046 card A ]


title: Peripheral blood [A584_047 card A ]


title: Peripheral blood [A584_057 card A ]


title: Peripheral blood [A584_038-2 card A ]


title: Peripheral blood [A584_045 card A ]


title: Peripheral blood [A584_052 card A ]


title: Peripheral blood [A584_049 card A ]


title: Peripheral blood [A584_041 card A ]


title: Peripheral blood [A584_042 card A ]


title: Peripheral blood [A584_037-2 card A ]


title: Peripheral blood [A584_043 card A ]


title: Peripheral blood [A584_036-2 card A ]


title: Peripheral blood [A584_033 card A ]


title: Peripheral blood [A584_032 card A ]


title: Peripheral blood [A584_039-2 card A ]


title: Peripheral blood [A584_035-2 card A ]


title: Peripheral blood [A584_031 card A ]


title: Peripheral blood [A584_030 card A ]


title: Peripheral blood [A584_029 card A ]


title: Peripheral blood [A584_025 card A ]


title: Peripheral blood [A584_021 card A ]


title: Peripheral blood [A584_022 card A ]


title: Peripheral blood [A584_023 card A ]


title: Peripheral blood [A584_020 card A ]


title: Peripheral blood [A584_019 card A ]


title: Peripheral blood [A584_018 card A ]


title: Peripheral blood [A584_016 card A ]


title: Peripheral blood [A584_015 card A ]


title: Peripheral blood [A584_014 card A ]


title: Peripheral blood [A584_017 card A ]


title: Peripheral blood [A584_013 card A ]


title: Peripheral blood [A584_009 card A ]


title: Peripheral blood [A584_011 card A ]


title: Peripheral blood [A584_010 card A ]


title: Peripheral blood [A584_008 card A ]


title: Peripheral blood [A584_007 card A ]


title: Peripheral blood [A584_006 card A ]


title: Peripheral blood [A584_003 card A ]


title: Peripheral blood [A584_002 card A ]


title: Peripheral blood [A584_001 card A ]


title: Peripheral blood [A584_034 card A ]


title: E14.5 placental labyrinth - antibiotic-treated rep3

city: Los Angeles

first: Geoffrey

last: Pronovost

address: 610 Charles E Young Drive South, Hsiao Lab MSB 3560

institute: UCLA

data_processing:
UMI sequences for each read was added to the read identifier using Lexogen's BlueBee QuantSeq pipeline.
Sequences were trimmed with the Bbduk from the bbmap suite trimming feature in Lexogen's BlueBee QuantSeq pipeline; trimming criteria include low quality tails, poly(A) read-through and adapter contamination
Sequences were aligned using the START Aligner with modified ENCODE settings using Lexogen's BlueBee QuantSeq pipeline; reads with identical mapping coordinates and UMI sequences were collapsed to remove PCR duplicates
Gene read counting was performed using HTSeq-count with QuantSeq FWD-specific options in Lexogen's Bluebee pipeline
Differential expression was determined using the DESeq2 pipeline within Lexogen's BlueBee QuantSeq pipeline
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

molecule: polyA RNA

source_name: E14.5 placental labyrinth

extract_protocol:
2 randomly selected placentas were removed from each litter and the placental labyrinths were microdissected and then pooled in ice-cold RNAlater; RNA was isolated using Trizol reagent and the Qiagen Rneasy mini kit (#74104) following standard protocols. 1 ug of RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Antibiotic-treated mice were orally gavaged with neomycin, vancomycin and metronidazole while maintained on ampicillin-supplemented water for 1-week; following initial microbiota clearance by gavage, dams were maintained on sterile water supplemented neomycin, vancomycin and ampicillin during breeding and throughout gestation until sacrificed at E14.5

value: placental labyrinth

value: treated with antibiotics prior to and during gestation

tag: gestational age


title: E14.5 placental labyrinth - antibiotic-treated rep2


title: E14.5 placental labyrinth - antibiotic-treated rep1


title: Peripheral blood [A584_027 card A ]


title: E14.5 placental labyrinth - germ-free rep3

value: germ-free


title: E14.5 placental labyrinth - germ-free rep2


title: 2023Bulk TCR sequencing

city: New Haven

first: Jack

middle: Anthony

last: Collora

state: CT

address: 295 Congress Ave

department: Microbial Pathogenesis

institute: Yale University

data_processing:
Library strategy: TCR-seq
RTA3 was used for basecalling.
Cellranger count (3.0)
Cellranger vdj (3.1)
Seurat (4.0.3)
VDJ results further processed using Presto(0.6.2) and Changeo (1.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq counts sparse matricies from cellranger, unfiltered, scTCRs - fasta and csv/tsv annotation files, Bulk TCR - tsv annotation files ( Adaptive Immune Receptor Repertoire (AIRR) fromat)

source_name: CD4+ T cells

growth_protocol: Isolated resting CD4+ T cells by negative selection: no growth conditions ; antigen stimulated CD4+ T cells: RPMI with 10% human serum for 9h after antigen stimulation

extract_protocol:
10X was used for all single cell experiements following the 5' v1.1 immune profiling with feature barcoding protocol. For the bulk TCR, CD4+ T cells were isolated by negative selection, and total RNA was extracted using the Zymo Directzol RNA kit.
10X Immune Profiling V1.1. Briefly, after cDNA amplification, cDNA is separated into high molecular weight (HMW) and low molecular weight (LMW) fractions. The LMW fraction is library prepped to generate CITE-seq libraries of surface protein expression. The HMW is sheered enzymatically, end repaired, and adapters are ligated on to generate the transcriptome library. In parallel, targetted amplification of TCR sequences occurs on the HMW fraction.

treatment_protocol: Isolated resting CD4+ T cells by negative selection: no treatment protocol ; antigen stimulated CD4+ T cells: treated with antigen peptide pools for 9h in the presence of T20 fusion inhibitor, sorted using FACS ARIA for AIM+

tag: cell state

value: Isolated unstimulated CD4+ T cells by negative selection

tag: hiv-1 infection status

value: Uninfected


title: Peripheral blood [A584_024 card A ]


title: 2022BulkTime2 TCR sequencing


title: 2022BulkTime1 TCR sequencing


title: E14.5 placental labyrinth - germ-free rep1

tag: tissue


title: 2004BulkTime2 TCR sequencing


title: E14.5 placental labyrinth - specific pathogen-free rep1

tag: treatment

value: conventionally colonized


title: E14.5 placental labyrinth - specific pathogen-free rep2


title: E14.5 placental labyrinth - specific pathogen-free rep3


title: 2004BulkTime1 TCR sequencing


title: DS910Bulk TCR sequencing

value: Suppressed


title: E14.5KOinput-2

data_processing:
ChIP-seq reads were aligned to the GENCODE release 25 genome assembly or mouse GENCODE release 18 using Bowtie2 v2.3.5
Multimapping reads removed with samtools v1.9 using “view” subcommand and the additional argument “-q 20”, duplicated reads were removed with Picard v2.21.4
peaks were called using  MACS2 version 2.2.7.1
IDR analysis was performed by IDR Filter v1.2
Genome_build: GENCODE release 25 and mouse GENCODE release 18
Supplementary_files_format_and_content: bed files were generated using MACS2 version 2.2.7.1

growth_protocol: Human K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum. Hemogen WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol:
Briefly, 30X106 K562 cells were fixed with 1% formaldehyde, sonicated and immunoprecipitated with antibodies against H3K27ac, HA and BRG1 . Chromatin was pulled down using Dynabeads Protein G, washed twice with RIPA-LS, RIPA-HS, LiCL washing buffer, followed by one wash with 10mM TrisHCl pH8.0. Precipitated DNA was reverse cross link and eluted for ChIP or was tagmentated (ChIPmentation)on magnetic beads with 0.2ul of tagmentation enzyme (Nextera XT DNA Library Preparation Kit, Illumina # FC-131-1024) for 10 minutes at 37 degree while shaking. The beads with tagementated DNA were washed twice with RIPA-LS and TE buffers. The DNA was eluted and de-crosslinked in ChIP elution buffer (20 mM Tris, pH 7.5, 5 mM EDTA, pH 8.0, 50 mM NaCl, 1% SDS, and 50 μg/mL proteinase K) for 1 hour at 55 degree and incubated at degree  overnight.
ChIP-mentation Libraries were prepared using Nextera XT DNA Library Preparation Kit, Illumina # FC-131-1024. Eluted DNA was purified using SRI beads (1.8x) and PCR amplified with Nextera primers. Libraries were purified (1.8x) and size selected (0.65x/ 0.15x) with SRI beads. ChIP Libaries were processing followed manufacturer’s protocol (Takara Bio, R400675)

tag: chip antibody

tag: age

value: Embryonic day 14.5

value: hemogen KO

value: fetal livers


title: DV910Bulk TCR sequencing

value: Viremic


title: DV799Bulk TCR sequencing


title: E14.5KOBRG1IP-2


title: E14.5KOBRG1IP-1


title: E14.5KOinput-1


title: DS739Bulk TCR sequencing


title: DS799Bulk TCR sequencing


title: DV739Bulk TCR sequencing


title: Peripheral blood [A584_012 card A ]


title: E14.5WTBRG1IP-1


title: E14.5WTBRG1IP-2


title: Peripheral blood [A584_004 card A ]


title: Peripheral blood [A584_005 card A ]


title: E14.5WTH3K27acIP-2


title: IV829Bulk TCR sequencing


title: IV640Bulk TCR sequencing


title: IS829Bulk TCR sequencing


title: IV236Bulk TCR sequencing


title: IS236Bulk TCR sequencing


title: E14.5WThemogenIP-2


title: E14.5WTinput-2


title: Peripheral blood [A584_107 card B ]


title: E14.5WTinput-1


title: E14.5WTH3K27acIP-1


title: fetal liver hemogen KO-4, RNA-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg38 and mm10  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.20.0
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample ...

source_name: Fetal livers

growth_protocol: Primary CD34+ umbilical cord cells (Lonza, cat. 2C-101) were cultured as described (Wilber et al., 2010). HUDEP2 cells was cultured in SFEM medium and induced in DMEM medium as described (Vinjamur and Bauer, 2018). K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum.Hemogen WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit
RNA sequencing libraries were generating from 100ng-1 ug of RNA using Illumina TruSeq Stranded mRNA Library Preparation kit (20020594) following manufacturer’s protocol.

tag: strain

value: Fetal livers

value: embryonic day 14.5


title: Peripheral blood [A584_026 card A ]


title: Peripheral blood [A584_104 card B ]


title: Peripheral blood [A584_102 card B ]


title: Peripheral blood [A584_100-2 card B ]


title: Peripheral blood [A584_103-2 card B ]


title: 3a1KO_Neuron nuclei_RNA_1

city: Houston

first: Tianpeng

last: Gu

address: Cambridge steet

institute: Baylor College of Medicine

description: 3a1KO_Neuron nuclei_RNA_1

data_processing:
STAR v2.5.4a was used to map to the genome. Gencode.mouse.v1.annotation.gtf was used for gene annotation.
2-pass strategy of STAR was used, see https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ for more details.
htseq/0.11.0 was used to calculate the raw read counts for each gene. htseq-count -m intersection-nonempty -i gene_id -s reverse -r pos -f bam
Genome_build: mm9

source_name: Cortical neuron nuclei

extract_protocol:
Cortical neuron nuclei were isolated by douncing the cerebral cortex tissue in a dounce homogenizer and sorted with an anti-NEUN antibody. Genomic DNA and total RNA were purified from the same materials with AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-Seq libraries were prepared with TruSeq® Stranded mRNA Library Prep (illumina)

value: Cortical neuron nuclei

tag: developmental stage

value: postnatal day 21


title: fetal liver hemogen KO-3, RNA-seq

tag: genotype


title: Peripheral blood [A584_097 card B ]

value: Postmenopausal women


title: WT_Neuron nuclei_RNA_2

description: WT_Neuron nuclei_RNA_2

value: Wild type


title: fetal liver hemogen KO-2, RNA-seq


title: IS640Bulk TCR sequencing


title: MC4RTB/TB mouse primary BM-derived macrophages

city: Chuo

first: Kentaro

last: Mori

address: 1110, Shimokato

institute: Yamanashi University

description: RMA expression value derived from GeneChipTM Command Console

hyb_protocol: Prepared for 73μL Hybridization Master Mix and 2.3μg Fragmented and Labeled cDNA, then incubate array at 45° for 16 hours (60rpm) according to Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific, Inc., cat.# 900720) protocol with GeneChipTM Hybridization Oven 645. Wash the array according to the kit protocol by using GeneChipTM Fluidics Station 450.

scan_protocol: sanned according to GeneChipTM Command Console (AGCC) 4.0 User Manual by using GeneChipTM Scanner 3000 7G.

data_processing: Data were processed using Expression Console™ Software  (Thermo Fisher Scientific, Inc.). Nomalization was done with SST-RMA.

label_protocol: Samples were enzymatically fragmented and biotinylated using GeneChipTM WT PLUS Reagent Kit (Thermo Fisher Scientific, Inc., cat.# 902281).

growth_protocol: BM was flushed out with 10-mL phosphate-buffered saline (PBS) through a 23-gage needle. The clumps were gently disaggregated using a needle-less syringe and passed through a 70- cell strainer. The cell suspension was centrifuged at 250 g at room temperature for 5 min to pellet the cells. The supernatant was discarded, and the cells were resuspended in Dulbecco’s Modified Eagle Medium (DMEM; Invitrogen, St. Louis, MO, USA) supplied with 10% fetal bovine serum (FBS) and 1% L-glutamine (Invitrogen). M-CSF was added at 25 ng/mL on days 0 and 3, and then, the following experiment started from day 5.

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

treatment_protocol: not applicable

value: bone marrow

tag: cell type

value: BM-derived macrophages


title: Peripheral blood [A584_099-2 card B ]


title: WT_Neuron nuclei_RNA_1

description: WT_Neuron nuclei_RNA_1


title: Peripheral blood [A584_094 card B ]


title: fetal liver hemogen KO-1, RNA-seq


title: E14.5WThemogenIP-1

value: WT


title: Peripheral blood [A584_093 card B ]


title: Peripheral blood [A584_098-2 card B ]


title: Peripheral blood [A584_096 card B ]


title: Peripheral blood [A584_091 card B ]


title: Peripheral blood [A584_090 card B ]


title: Peripheral blood [A584_101 card B ]


title: Peripheral blood [A584_095 card B ]


title: WT_Neuron nuclei_H2AK119ub

description: WT_Neuron nuclei_H2AK119ub

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA v0.7.17 with configurations: bwa mem -t 8 -c 1
Duplicates were removed using Samtools v1.10
Coverage tracks were generated by deepTools normalizing to 1*depth: bamCoverage --bam $samplename --effectiveGenomeSize 2150570000 --normalizeUsing RPGC --extendReads 200 --binSize 30
Genome_build: mm9

extract_protocol:
Cortical neuron nuclei were isolated and cross-linked by douncing the cerebral cortex tissue in Nuclei extraction buffer containing 1% formaldehyde in a dounce homogenizer, and then sorted with an anti-NEUN antibody.
ChIP-Seq Libraries were prepared with ThruPLEX® DNA-seq 48D Kit (Rubicon Genomics).

value: Dnmt3a-FLAG knock-in


title: 3a1KO_Neuron nuclei_RNA_2

description: 3a1KO_Neuron nuclei_RNA_2


title: fetal liver wt-3, RNA-seq


title: Peripheral blood [A584_106 card B ]


title: WT_Neuron nuclei_H3K27ac

description: WT_Neuron nuclei_H3K27ac


title: Peripheral blood [A584_089 card B ]


title: WT_Neuron nuclei_H3K27me3

description: WT_Neuron nuclei_H3K27me3


title: LysM (+);MC4RTB/TB mouse primary BM-derived macrophages

value: LysM (+);MC4RTB/TB


title: WT_Neuron nuclei_H3K4me1

description: WT_Neuron nuclei_H3K4me1


title: Peripheral blood [A584_092 card B ]


title: Peripheral blood [A584_086 card B ]


title: CamKII-Cre RosaIL2  [S7_TG_blood]

city: Cambridge

first: Adrian

last: Liston

address: Babraham Research Campus

country: United Kingdom

institute: The Babraham Institute

data_processing:
Step1: cellranger mkfastq (Cell Ranger V.3.1, 10x Genomics)
Step2: cellranger count (Cell Ranger V.3.1, 10x Genomics)
Step 3: Quality control in each sample (keeping genes expressed in ≥5 cells and cells with gene count ≥200). Further quality control (keeping cells with UMI counts≥500 and mitochondrial genes<20%) after merging all samples into one object using Seurat V3.1.4.
Genome_build: mm10
Supplementary_files_format_and_content: A matrix of raw UMI counts for each feature (i.e. gene; row) that are detected in each cell (column)  in each sample

source_name: Blood

growth_protocol: mice were kept in SPF cages for 12 weeks prior to use

extract_protocol:
CD4+CD45+CD11b- and CD45+CD11b+ cells were sorted using FACS Aria III
Library was ferformed using 10x Genomics Chromium Single Cell 3'kit, v2

treatment_protocol: mice were treated with tamoxifen with 4 weeks age

value: treated with Tamoxifen 5 days


title: WT_Neuron nuclei_H3K4me3

description: WT_Neuron nuclei_H3K4me3


title: Peripheral blood [A584_084 card B ]


title: fetal liver wt-1, RNA-seq


title: WT_Neuron nuclei_input

description: WT_Neuron nuclei_input


title: Wildtype [S8_WT_blood]


title: Peripheral blood [A584_087 card B ]


title: Peripheral blood [A584_082 card B ]


title: CamKII-Cre RosaIL2  [S5_TG_blood]


title: fetal liver wt-4, RNA-seq


title: Peripheral blood [A584_081 card B ]


title: Peripheral blood [A584_078 card B ]


title: Wildtype [S6_WT_blood]


title: Peripheral blood [A584_076 card B ]


title: 3AKO_ES_DNMT3A1_Mut2

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells were culture on 0.1% gelatin-coated dishes in DMEM supplemented with 15% Fetal Bovine Serum, 1×Non-Essential Amino Acids, 1×Sodium pyruvate, 1×GlutaMAX, 1 μM 2-Mercaptoethanol, 1×Penicillin/Streptomycin and 1000 U/ml LIF.

extract_protocol:
Cells were cross-linked in 1% formaldehyde, and chromatin was sheared with a Bioruptor sonicator. Protein-DNA complexes were immunoprecipitated with indicated antibody.
ChIP-Seq Libraries were prepared with ThruPLEX® DNA-seq 48D Kit (Rubicon Genomics).

value: Embryonic stem cells

value: Dnmt3a-/-, DNMT3A1-Mut2 over-expressed

value: anti-FLAG


title: Peripheral blood [A584_083 card B ]


title: Peripheral blood [A584_075 card B ]


title: fetal liver wt-2, RNA-seq


title: 3a1dN_Cortex_DNMT3A

source_name: Cerebral cortex

extract_protocol:
The cerebral cortex was isolated, crushed and homogenized briefly by pipetting. Tissues were cross-linked in 1% formaldehyde and sheared with a Covaris M220 Ultrasonicator.
ChIP-Seq Libraries were prepared with ThruPLEX® DNA-seq 48D Kit (Rubicon Genomics).

value: Cerebral cortex


title: WT_J1ES_RING1B/RNF2


title: Wildtype [S4_WT_brain]

source_name: Brain


title: Peripheral blood [A584_079 card B ]


title: Peripheral blood [A584_077 card B ]


title: CamKII-Cre RosaIL2  [S3_TG_brain]


title: Wildtype [S2_WT_brain]


title: LowRep6

city: Milwaukee

first: Rebecca

middle: D.

last: Klaper

state: WI

address: 600 E Greenfield Ave

department: School of Freshwater Sciences

institute: University of Wisconsin - Milwaukee

data_processing:
quality-assessment of sequence data using FastQC v0.11.5, no base-calling errors to be removed
primers clipped using Cutadapt v1.18
pseudoalignment of quality-controlled data
quality-controlled data sample-quantified against GRCz11 Ensemble zebrafish reference transcriptome release using Kallisto v0.45.0
Genome_build: assembled transcriptome
Supplementary_files_format_and_content: estimated counts, text (tsv)

organism: Danio rerio

source_name: larvae

growth_protocol: Starting day 5, larvae fed with golden pearl larval food powder (50 microns)

extract_protocol:
Larvae flash frozen in liquid nitrogen prior to RNA extraction and purification with Direct-zol MiniPrep (Zymo Research)
Standard Illumina protocols followed for preparing RNA libraries for sequencing

treatment_protocol: Larvae exposed for 48 hours to 1 or 10 mg/L LCO, or Ions

value: wild type

value: whole larvae

value: LCO 1 mg/l

value: 10 days post fertilization

tag: exposure

value: 48 hours


title: WT_Cortex_DNMT3A

value: postnatal day 21


title: Peripheral blood [A584_070 card B ]

value: Postmenopausal women


title: Peripheral blood [A584_088 card B ]


title: WT_J1ES_H2AK119ub

value: Wild type


title: 3AKO_ES_DNMT3A1

value: Dnmt3a-/-, DNMT3A1 over-expressed


title: Peripheral blood [A584_072 card B ]


title: LowRep3

value: WT


title: Peripheral blood [A584_068 card B ]


title: Peripheral blood [A584_066 card B ]


title: Peripheral blood [A584_065 card B ]


title: ASM35_3

city: ATHENS

first: Aaron

middle: P

last: Mitchell

state: GA

address: 120 EAST GREEN STREET

department: Microbiology

institute: University of Georgia

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina)
Library preparations were sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were generated.
Paired-end clean reads were aligned to the reference genome using HISAT2.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.14.1)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Candida albicans

source_name: Candida albicans clinical isolate SC5314

growth_protocol: C. albicans cells were culturered in RPMI+%10 SERUM at 37°C for 4 hours

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy mini kit (Cat#74104) following manufacturer's instructions.
Library was constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA), following manufacturer's instructions.

value: hgc1 mutant 5C5314

tag: culture condition

value: RPMI +10% SERUM, 37°C-4HRS


title: CamKII-Cre RosaIL2  [S1_TG_brain]

value: treated with Tamoxifen 5 days


title: LowRep1


title: Peripheral blood [A584_071 card B ]


title: Peripheral blood [A584_062 card B ]


title: Peripheral blood [A584_085 card B ]


title: Peripheral blood [A584_073 card B ]


title: ASM33_3

source_name: Candida albicans clinical isolate P57055

value: hgc1 mutant P57055


title: LowRep5


title: Peripheral blood [A584_074 card B ]


title: Peripheral blood [A584_060 card B ]


title: Peripheral blood [A584_061 card B ]


title: IonRep3

value: Ion


title: WT_J1ES_input

value: Embryonic stem cells


title: Peripheral blood [A584_069 card B ]


title: Peripheral blood [A584_080 card B ]


title: Peripheral blood [A584_067 card B ]


title: LowRep2


title: Peripheral blood [A584_054 card B ]


title: Peripheral blood [A584_053 card B ]


title: HighRep6

value: LCO 10 mg/l


title: HighRep4

value: wild type


title: Peripheral blood [A584_051 card B ]


title: ASM35_2


title: Peripheral blood [A584_050 card B ]


title: ASM33_2


title: Peripheral blood [A584_064 card B ]


title: Peripheral blood [A584_063 card B ]


title: ASM1_3

value: SC5314 WT


title: ASM35_1


title: Peripheral blood [A584_049 card B ]


title: HighRep3

value: whole larvae


title: IonRep6

value: 10 days post fertilization


title: ASM33_1


title: IonRep4

value: 48 hours


title: Peripheral blood [A584_059 card B ]


title: Peripheral blood [A584_058 card B ]


title: Peripheral blood [A584_057 card B ]


title: HighRep2


title: IonRep2


title: Peripheral blood [A584_056-2 card B ]


title: Peripheral blood [A584_045 card B ]


title: Peripheral blood [A584_055-2 card B ]


title: ASM3_3


title: IonRep1


title: ASM3_2


title: Peripheral blood [A584_052 card B ]


title: F3-2

city: Blacksburg

first: Guillaume

last: Pilot

state: VA

address: 220 Ag Quad Lane

department: School of Plant and Environmental Sciences

institute: Virginia Tech

description:
BiolRep2
gdu1-1D_Cuffdiff_genes.fpkm_tracking

data_processing:
Tophat2 was used for read mapping
Cufflinks for transcript assembly
Cuffdiff2 was used for abundance estimation and identification of significant change in mRNA contents
Comparisons: DEX 7 h vs. 4c-S7 7 h; DEX 25 h vs. 4c-S7 25 h; gdu1-1D vs. Col
Comparisons: GDU2 vs. Col-7, GDU4 vs. Col-7, GDU5 vs. Col-7,  GDU6 vs. Col
Assembly: TAIR 10
Supplementary files format and content: cuffdiff output: genes.fpkm_tracking

organism: Arabidopsis thaliana

source_name: gdu1-1D mutant

growth_protocol: Plants were grown for 23 days on soil, in a growth chamber (16h/8h light dark), 22C, 120 uE

extract_protocol:
RNA were extracted using the Qiagen Plant RNeasy kit from all leaves from 4 to 6 plants.
Performed by the GeneWiz company in 2013

treatment_protocol: 100 µM dexamethasone + 300 ppm silwet L-77  at 11 am - 5 h after dawn - keeping a humidity dome for 7 h, for inducible (183B7) and control (4c-S7) lines. Not treatment for the constitutuve over-expressors and wild type

value: Leaves

tag: ecotype

value: Columbia

tag: trangenic

value: Constitutive


title: Peripheral blood [A584_041 card B ]

tag: age (years)

tag: tag

value: Postmenopausal women


title: ASM3_1


title: ControlRep4

value: WT

value: untreated


title: Peripheral blood [A584_039-2 card B ]


title: Peripheral blood [A584_038-2 card B ]


title: ControlRep2


title: DE5-1

description:
BiolRep1
GDU6_Cuffdiff_genes.fpkm_tracking

source_name: GDU6 over-expressor


title: Peripheral blood [A584_034 card B ]


title: Peripheral blood [A584_035-2 card B ]


title: ControlRep1


title: ControlRep5


title: Peripheral blood [A584_032 card B ]


title: Peripheral blood [A584_048 card B ]


title: CRS_16

city: Rochester

first: Chantal

last: McCabe

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
We aligned the reads to the human reference genome (hg38) using MAPRSeq 3.1.4 which utilizes the aligner STAR-2.6.1
Gene counts were generated using featureCounts from subread package 1.5.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: Ethmoidal tissue

extract_protocol:
The tissue was formalin-fixed, paraffin-embedded (FFPE) and RNA access, a capture-based strategy was used to assess the transcriptome
Illumina TruSeq Stranded mRNA library prep protocol

treatment_protocol: Ethmoidal or inferior turbinate tissue was obtained from patients who underwent endoscopic skull base surgery or septoplasty and did not have sinonasal disease.

value: Ethmoidal tissue

tag: clinical diagnosis

value: CRSwNP

tag: count


title: CRS_15

value: CRSsNP

value: Over 10 EOS/HPF


title: Peripheral blood [A584_030 card B ]


title: DE5-2

description:
BiolRep2
GDU6_Cuffdiff_genes.fpkm_tracking


title: Peripheral blood [A584_047 card B ]


title: Peripheral blood [A584_029 card B ]


title: HighRep1


title: ASM1_1

value: RPMI +10% SERUM, 37°C-4HRS


title: Peripheral blood [A584_027 card B ]


title: CRS_14


title: DC5-1

description:
BiolRep1
GDU4_cuffdiff_genes.fpkm_tracking

source_name: GDU4 over-expressor


title: CRS_13


title: DB6

description:
BiolRep
not processed

source_name: GDU3 over-expressor


title: Peripheral blood [A584_044 card B ]

source_name: Peripheral blood


title: Peripheral blood [A584_043 card B ]


title: Peripheral blood [A584_042 card B ]


title: F3-3

description:
BiolRep3
gdu1-1D_Cuffdiff_genes.fpkm_tracking


title: Peripheral blood [A584_040-2 card B ]


title: Peripheral blood [A584_024 card B ]


title: Peripheral blood [A584_023 card B ]


title: F3-1

description:
BiolRep1
gdu1-1D_Cuffdiff_genes.fpkm_tracking


title: CRS_12


title: Peripheral blood [A584_037-2 card B ]


title: ControlRep3


title: Peripheral blood [A584_036-2 card B ]


title: Peripheral blood [A584_046 card B ]


title: ASM1_2


title: Peripheral blood [A584_033 card B ]


title: DD6-2

description:
BiolRep2
GDU5_cuffdiff_genes.fpkm_tracking

source_name: GDU5 over-expressor


title: Peripheral blood [A584_031 card B ]


title: DD6-1

description:
BiolRep1
GDU5_cuffdiff_genes.fpkm_tracking


title: Peripheral blood [A584_019 card B ]


title: Peripheral blood [A584_018 card B ]


title: Peripheral blood [A584_016 card B ]


title: Peripheral blood [A584_015 card B ]


title: DC5-2

description:
BiolRep2
GDU4_cuffdiff_genes.fpkm_tracking


title: Peripheral blood [A584_014 card B ]


title: Peripheral blood [A584_013 card B ]


title: Peripheral blood [A584_026 card B ]


title: Peripheral blood [A584_025 card B ]


title: Peripheral blood [A584_011 card B ]


title: 4C-S7-7h3

description:
BiolRep3
DEX7_cuffdiff_genes.fpkm_tracking

source_name: Control line treated by DEX. Analyzed 7 h post-treatment

value: Inducible

value: Dexamethasone


title: Peripheral blood [A584_009 card B ]


title: CRS_5

value: Under 10 EOS/HPF


title: 4C-S7-7h2

description:
BiolRep2
DEX7_cuffdiff_genes.fpkm_tracking


title: DA6-2

description:
BiolRep2
GDU2_cuffdiff_genes.fpkm_tracking

source_name: GDU2 over-expressor


title: 4C-S7-7h1

description:
BiolRep1
DEX7_cuffdiff_genes.fpkm_tracking


title: CRS_3


title: Peripheral blood [A584_022 card B ]


title: CRS_11


title: Peripheral blood [A584_004 card B ]


title: Peripheral blood [A584_003 card B ]


title: Peripheral blood [A584_021 card B ]


title: 4C-S7-25h3

description:
BiolRep3
DEX25_cuffdiff_genes.fpkm_tracking

source_name: Control line treated by DEX. Analyzed 25 h post-treatment


title: Peripheral blood [A584_002 card B ]


title: Peripheral blood [A584_007 card B ]


title: DA6-1

description:
BiolRep1
GDU2_cuffdiff_genes.fpkm_tracking


title: Peripheral blood [A584_020 card B ]


title: Peripheral blood [A584_005 card B ]


title: CRS_1


title: Peripheral blood [A584_001 card B ]


title: CRS_10


title: CRS_9


title: CZ6

description:
BiolRep
not processed

source_name: GDU1 over-expressor


title: Peripheral blood [A584_017 card B ]


title: Col-7-2

description:
BiolRep2
control of constitutive transgenics

source_name: Wild type control

value: Wild type


title: CRS_8


title: CRS_7


title: Peripheral blood [A584_012 card B ]


title: 4C-S7-7h4

description:
BiolRep4
DEX7_cuffdiff_genes.fpkm_tracking


title: Col-7-1

description:
BiolRep1
control of constitutive transgenics


title: CRS_6


title: Peripheral blood [A584_010 card B ]


title: Control_3

source_name: inferior turbinate tissue

value: inferior turbinate tissue

value: Non CRS


title: 183B7-7h4

source_name: Inducible line treated by DEX. Analyzed 7 h post-treatment

value: Leaves


title: Peripheral blood [A584_008 card B ]


title: Control_2


title: Peripheral blood [A584_006 card B ]


title: CRS_4


title: Control_1


title: Peripheral blood RNA [A584_107]

hyb_protocol: Labeled and fragmented single stranded cDNAs were hybridized to Human Exon 1.0 ST  Arrays (Affymetrix, GPL28228). The arrays were washed and stained using FS-450 fluidics station (Affymetrix).

scan_protocol: Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA, USA). The scanned images were processed using AGCC (AffymetrixGeneChip Command Console) software.

data_processing: For statistical analysis the Affymetrix.CEL files (containing probe intensities) were imported into Partek Genomics Suite software (Partek, Inc. MO, USA). Robust microarray analysis (RMA) yielding normalized log2 transformed signal intensities were applied for normalization (http://bip.weizmann.ac.il/toolbox/overview/Partek_Users_Guide.pdf).

source_name: Postmenopausal woman

label_protocol: 100 ng of total RNA from each sample was subjected to GeneChip WT Reagent Kit and WT Labeling Kit, following the manufacturer’s protocol for whole genome gene expression analysis (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Not Applicable


title: V72

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

institute: Hopitaux universitaires de Geneve

data_processing:
Raw reads were trimmed by fastp (version 0.20.0)
Cleaned reads were then aligned onto the human reference genome (assembly GRCh-38) using the ultrafast STAR program (version 2.5.2b)
Gene quantification was carried out using Salmon (version 0.14.1)
Assembly: GRCh-38
Supplementary files format and content: tab delimited text file with normalized transcripts per million for each sample by column and genes by row

source_name: Melanoma cell culture

growth_protocol: Melanoma cells were grown in RPMI 1640 with 10% FCS, 5 mM glutamine, and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted with the QIAGEN RNeasy Mini kit
RNA-seq-poly-A

tag: mutation

value: BRAF

value: melanoma


title: 4C-S7-25h4

description:
BiolRep4
DEX25_cuffdiff_genes.fpkm_tracking

tag: tissue

value: Columbia


title: Peripheral blood RNA [A584_104]


title: Peripheral blood RNA [A584_103-2]


title: Peripheral blood RNA [A584_100-2]


title: 4C-S7-25h2

description:
BiolRep2
DEX25_cuffdiff_genes.fpkm_tracking

tag: treatment


title: Peripheral blood RNA [A584_101]


title: V71

value: During Targeted Therapy


title: CRS_2


title: Control_4


title: Peripheral blood RNA [A584_096]


title: 183B7-25h1

description:
BiolRep1
DEX25_cuffdiff_genes.fpkm_tracking

source_name: Inducible line treated by DEX. Analyzed 25 h post-treatment


title: V69

value: After Immunotherapy


title: 183B7-7h2


title: 183B7-7h1


title: V67


title: EB  rep3

city: Shijiazhuang

first: Yanmin

last: Zou

state: Hebei

address: 286 Huaizhong Road

department: Center for Agricultural Resources Research

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: 7-day-old seedlings

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Bowtie v2.2.3 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We  selected TopHat as the mapping tool for that TopHat can generate a database of splice  junctions based on the gene model annotation file and thus a better mapping result than  other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0).
Assembly: Arabidopsis thaliana
Supplementary files format and content: tab-delimited text files include reads and FPKM values for each Sample ...

source_name: seedling

growth_protocol: Seeds were surface-sterilized with 50% (v/v) bleach for 5 min and washed at least four times with sterile water. Sterile seeds were germinated and grown on 1/2 Murashige and Skoog (MS)

extract_protocol:
Total RNA for transcriptome sequencing was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: 7-d-old plants grown in1/2 Murashige and Skoog (MS) medium and then treated with H2O, Dox or EtBr were collected.

value: Total seedling

value: wild type (Col-0)

value: seedling treated with EtBr


title: EB  rep1

description: 7-day-old seedlings


title: 4C-S7-25h1