title: MK886-PMCs-2-H01_2018-7-11


title: MK886-PMCs-2-C09_2018-7-11

status: Public on Jun 01 2022

type: SRA

city: Boston

first: Cynthia

middle: A.

last: Bradham

state: MA

address: 24 Cummington Mall

department: Biology

country: USA

institute: Boston University

description:
cell collection protocol: t 18 hours post-fertilization, embryos were collected and disaggregated into single cells. Embryos were exposed to pronase, washed in calcium-free sea water, incubated in hyaline extraction medium (0.3 M glycine, 0.3 M NaCl, 10 mM KCl, 10 mM MgS04, 10 mM Tris, 2 mM EGTA), washed in calcium free-sea water, then triturated with a pipette to separate cells.
FACS protocol: PMC-specific antibody 6a9 (1:5) and anti-mouse alexa Fluor 488 (Invitrogen, 1:500) in BSA-ASW block was added to the cell suspension for 5 min, then washed out. SYTOX dead stain (1:1000) was added. Cells were gated to exclude doublets and dead cells and sorted into RNA lysis buffer.

library_source: transcriptomic

data_processing:
Read concatentation: Reads sequenced across multiple lanes were concatenated together for single cells using the “cat” command in a linux terminal
Quality control: Reads and bases in reads were filtered and quality controlled using fastp (version 0.20.0) with specified parameters “-y -Y 30” and default parameters otherwise
GFF conversion: The GFF annotation file was converted to a GTF file using gffread with default parameters
Genome Alignment: Reads were aligned for to the most recent L. variegatus genome using STAR (version 2.7.1a). The index was built with specified parameter “--sjdbOverhang 151” and default otherwise. Alignment was run using default parameters.
Alignment Quantification: Read quantification was performed using featureCounts (v1.6.4) with the fragment specification option “-p” enabled, and default parameters otherwise
Count Normalization: Prior to normalization, cells with fewer that 50,000 feature counts, and genes with total counts less than 0.5 cpm were filtered out. Counts were normalized per batch for downstream analysis using the “computeSumFactors” function in the scran library (version 1.12.1) in R (version 3.6.2). Normalized counts were subsequently batch corrected using the function “multiBatchNorm” function in the scran library.
Genome_build: L. variegatus genome (Li et al., 2020)
Supplementary_files_format_and_content: Comma-separated text files containing raw and normalized count matrices for all cells used in the analysis, their associated metadata, and genome annotation information.

molecule: total RNA

organism: Lytechinus variegatus

source_name: Primary Mesenchyme Cells

growth_protocol: Sea urchin gametes were collected from wild-caught Lytechinus variegatus. Eggs were fertilized in artificial sea water at room temperature and embryos were cultured in artificial sea water at 23°C.

extract_protocol:
Individual PMCs were sorted directly into RNA lysis buffer supplemented with 1% β-mercaptoethanol.
Transcripts were purified, reverse-transcribed, and amplified according to the SMART-Seq2 protocol (Tombetta et al., Curr Protoc Mol Biol, 2014). Libraries were prepared using the Nextera XT kit (Illumina) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq 500 using 100bp paired end reads.

treatment_protocol: MK-886 in DMSO was added to embryo cultures at 12 hours post-fertilization to a final concentration 1.5µM.  Chlorate in ASW was added to embryo cultures at 12 hpf to a total concentration of 30 mM. Volume-matched DMSO was added to DMSO control samples.

tag: tissue

value: primary mesenchyme

tag: developmental stage

value: 18 hours post-fertilization

tag: treatment

value: MK-886 (1.5uM final)


title: TIC96

city: Chaoyang District

first: Tiejun

last: Liu

state: Beijing

address: Panjiayuan

country: China

institute: Chinese Academy of Medical Science

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Trimmed Mean of M-values (TMM) were calculated using edgeR in Rstudio.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Trimmed Mean of M-values (TMM) for each Sample …

organism: Homo sapiens

source_name: platelet

extract_protocol:
Frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted from isolated platelets frozen in 5 ml PBS using Trizol Reagent and Qiagen RNeasy minElute spin column as described in the manufacturer's instructions. The integrity of the total RNA was determined using an Agilent 2100 Bioanalyzer and RNA was quantified using a Thermo Scientific NanoDrop.

tag: disease state

value: Healthy Control

value: platelet


title: VE1

value: ESCC


title: MK886-PMCs-3-D01_2018-7-11


title: ASW-PMCs-2-H01_2018-7-11


title: TIC94


title: TIC92


title: ASW-PMCs-2-E06_2018-7-11


title: MK886-PMCs-3-F01_2018-7-11


title: MK886-PMCs-3-G06_2018-7-11


title: TIC90


title: MK886-PMCs-2-E08_2018-7-11


title: MK886-PMCs-2-C02_2018-7-11


title: TIC83


title: MK886-PMCs-3-F08_2018-7-11


title: Chlorate-PMCs-1-A10_2018-7-11

value: Chlorate (30mM final)


title: Chlorate-PMCs-2-G06_2018-7-11


title: TIC81


title: TIC76


title: Chlorate-PMCs-2-A12_2018-7-11


title: DMSO-PMCs-1-D08_2018-7-11

value: DMSO


title: MK886-PMCs-2-C06_2018-7-11


title: DMSO-PMCs-1-H07_2018-7-11


title: TIC75


title: TE70


title: ASW-PMCs-2-D01_2018-7-11


title: Chlorate-PMCs-1-C11_2018-7-11


title: ASW-PMCs-2-H09_2018-7-11


title: TE67


title: MK886-PMCs-2-E01_2018-7-11


title: Chlorate-PMCs-2-E02_2018-7-11


title: TE69


title: Chlorate-PMCs-1-E04_2018-7-11


title: Chlorate-PMCs-1-C09_2018-7-11


title: Chlorate-PMCs-1-D11_2018-7-11


title: DMSO-PMCs-1-G12_2018-7-11


title: MK886-PMCs-3-B02_2018-7-11


title: MK886-PMCs-3-C02_2018-7-11


title: MK886-PMCs-3-A02_2018-7-11


title: TE62


title: MK886-PMCs-2-A11_2018-7-11


title: TE60


title: Chlorate-PMCs-2-E11_2018-7-11


title: TE57


title: MK886-PMCs-2-C05_2018-7-11


title: MK886-PMCs-3-D05_2018-7-11


title: Chlorate-PMCs-1-D07_2018-7-11


title: TE55


title: Chlorate-PMCs-1-H06_2018-7-11


title: TE43


title: Chlorate-PMCs-2-C01_2018-7-11

description:
NOTE: This cell filtered out of analysis for quality reasons
cell collection protocol: t 18 hours post-fertilization, embryos were collected and disaggregated into single cells. Embryos were exposed to pronase, washed in calcium-free sea water, incubated in hyaline extraction medium (0.3 M glycine, 0.3 M NaCl, 10 mM KCl, 10 mM MgS04, 10 mM Tris, 2 mM EGTA), washed in calcium free-sea water, then triturated with a pipette to separate cells.
FACS protocol: PMC-specific antibody 6a9 (1:5) and anti-mouse alexa Fluor 488 (Invitrogen, 1:500) in BSA-ASW block was added to the cell suspension for 5 min, then washed out. SYTOX dead stain (1:1000) was added. Cells were gated to exclude doublets and dead cells and sorted into RNA lysis buffer.


title: TE49


title: Chlorate-PMCs-2-G11_2018-7-11


title: TE50


title: DMSO-PMCs-1-G05_2018-7-11


title: ASW-PMCs-2-B05_2018-7-11


title: ASW-PMCs-2-B10_2018-7-11


title: DMSO-PMCs-1-D09_2018-7-11


title: Chlorate-PMCs-2-H08_2018-7-11


title: MK886-PMCs-2-H12_2018-7-11


title: MK886-PMCs-3-C01_2018-7-11


title: Chlorate-PMCs-2-B05_2018-7-11


title: MK886-PMCs-3-B08_2018-7-11


title: ASW-PMCs-2-E09_2018-7-11


title: TE37


title: ASW-PMCs-2-H08_2018-7-11


title: TE38


title: TE3


title: TE52


title: Chlorate-PMCs-1-D01_2018-7-11


title: Chlorate-PMCs-1-D04_2018-7-11


title: Chlorate-PMCs-1-B07_2018-7-11


title: MK886-PMCs-2-C12_2018-7-11


title: Chlorate-PMCs-2-D01_2018-7-11


title: TE35


title: ASW-PMCs-2-B06_2018-7-11


title: ASW-PMCs-2-D02_2018-7-11


title: TE27


title: TE29


title: ASW-PMCs-2-F08_2018-7-11


title: MK886-PMCs-2-H06_2018-7-11


title: TE20


title: TE40


title: Chlorate-PMCs-1-E09_2018-7-11


title: Chlorate-PMCs-2-H10_2018-7-11


title: MK886-PMCs-3-G03_2018-7-11


title: TE2


title: Chlorate-PMCs-1-F03_2018-7-11


title: DMSO-PMCs-1-G02_2018-7-11


title: Chlorate-PMCs-1-B09_2018-7-11


title: RW01016: SCC-25_EVI1_rep4

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Department of Medicine I

country: Austria

institute: Medical University of Vienna

data_processing:
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403).
Reads were trimmed and filtered using cutadapt (1) version 1.15 to trim polyA tails and remove reads with N’s.
Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode.
Raw reads per gene were counted by STAR.
Differential gene expression was calculated using DESeq2 (5) version 1.22.2.
Genome_build: GRCh38 human reference genome downloaded from NCBI (2018-09-27)
Supplementary_files_format_and_content: Text file, ";"-delimited. Matrix table with raw gene counts for every gene and every sample

source_name: HNSCC cell line

extract_protocol:
RNA was extracted from cell lines using TRIzol®. RNA quality was checked on a Bioanalyzer 2100 (Agilent Technologies).
RNA-seq library preparation was performed using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen) according to the manufacturer’s instructions. In order to avoid distortions of gene expression values due to over-cycling, the optimal numbers  of PCR cycles for library preparation were determined by qPCR according to the library preparation manual. Library quality was checked on a Bioanalyzer 2100 using a High Sensitivity DNA Kit for correct insert size and dsDNA was quantified using Qubit dsDNA HS Assay (Thermo Fisher Scientific).

tag: cell line

tag: cell type

value: head and neck squamous cell carcinoma (HNSCC)

tag: subline

value: EVI1 over-expression


title: ASW-PMCs-2-B07_2018-7-11


title: TE15


title: Chlorate-PMCs-1-D08_2018-7-11


title: ASW-PMCs-2-C05_2018-7-11


title: ASW-PMCs-2-H05_2018-7-11


title: MK886-PMCs-2-D03_2018-7-11


title: RW01015: SCC-25_EVI1_rep3


title: Chlorate-PMCs-2-F03_2018-7-11


title: DMSO-PMCs-1-F01_2018-7-11


title: MK886-PMCs-3-A06_2018-7-11


title: RW01014: SCC-25_EVI1_rep2


title: Chlorate-PMCs-2-E09_2018-7-11


title: ASW-PMCs-2-E08_2018-7-11


title: Chlorate-PMCs-2-C11_2018-7-11


title: Chlorate-PMCs-2-G12_2018-7-11


title: TE19


title: RW01011: SCC-25_vec_rep3

value: empty vector control


title: DMSO-PMCs-1-F10_2018-7-11


title: RW01012: SCC-25_vec_rep4


title: Chlorate-PMCs-1-G07_2018-7-11


title: DMSO-PMCs-1-H03_2018-7-11


title: DMSO-PMCs-1-H05_2018-7-11


title: TE16


title: MK886-PMCs-3-D07_2018-7-11


title: ASW-PMCs-2-A02_2018-7-11


title: ASW-PMCs-2-H04_2018-7-11


title: RW01013: SCC-25_EVI1_rep1


title: MK886-PMCs-3-H01_2018-7-11


title: RW01009: SCC-25_vec_rep1


title: Chlorate-PMCs-2-A10_2018-7-11


title: RW01007: CAL-33_EVI1_rep3


title: Chlorate-PMCs-1-A03_2018-7-11


title: RW01008: CAL-33_EVI1_rep4


title: Chlorate-PMCs-1-G03_2018-7-11


title: RW01006: CAL-33_EVI1_rep2


title: DMSO-PMCs-1-E06_2018-7-11


title: MK886-PMCs-2-D11_2018-7-11


title: ASW-PMCs-2-H12_2018-7-11


title: MK886-PMCs-3-A10_2018-7-11


title: DMSO-PMCs-1-H02_2018-7-11


title: RW01004: CAL-33_vec_rep4


title: Chlorate-PMCs-2-C07_2018-7-11


title: MK886-PMCs-3-F03_2018-7-11


title: MK886-PMCs-2-A03_2018-7-11


title: DMSO-PMCs-1-E07_2018-7-11


title: RW01010: SCC-25_vec_rep2


title: RW01002: CAL-33_vec_rep2


title: Chlorate-PMCs-2-G07_2018-7-11


title: RW01005: CAL-33_EVI1_rep1


title: RW01001: CAL-33_vec_rep1


title: ASW-PMCs-2-C01_2018-7-11


title: MK886-PMCs-3-D04_2018-7-11


title: MK886-PMCs-2-E05_2018-7-11


title: MK886-PMCs-2-F04_2018-7-11


title: 9_1_2

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: FFPE block sections

data_processing:
Bulk mRNA-Seq libraries were aligned to the hg38 genome using STAR. The alignment  profile was determined by Picard Tools v1.64 (http://broadinstitute.github.io/picard/). Transcript  abundance estimates for each sample were performed using Salmon
Genome_build: hg38
Supplementary_files_format_and_content: Normlaized and log-transformed data

source_name: DCIS

extract_protocol:
For bulk RNAseq; FFPE block sections were used and RNA was isolated using the RNeasy FFPE Kit (Cat. No. / ID: 73504, Qiagen) according to manufacturer protocol.
Libraries were made using the Illumina Total RNA (Ribo Zero Gold) kit following the TruSeq Stranded Total RNA Sample Preparation Guide 15031048 E
For bulk mRNA-Seq Paired end (2 50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer

tag: histologic annotation

value: DCIS

tag: pam50 molecular subtype

value: Luminal A

tag: paired or unpaired info


title: 9_2_1

description: FFPE block sections

source_name: invasive

value: invasive


title: MK886-PMCs-3-G12_2018-7-11


title: ASW-PMCs-2-A06_2018-7-11


title: MK886-PMCs-3-C04_2018-7-11


title: Chlorate-PMCs-2-D12_2018-7-11


title: ASW-PMCs-2-E07_2018-7-11


title: 8_1_1

description: FFPE block sections


title: Chlorate-PMCs-2-D10_2018-7-11


title: MK886-PMCs-3-D11_2018-7-11


title: ASW-PMCs-2-F10_2018-7-11


title: 6_1_2

description: FFPE block sections

value: LumADCIS_5 (Unpaired; No tumor component available)


title: Chlorate-PMCs-1-C06_2018-7-11


title: DMSO-PMCs-1-C08_2018-7-11


title: MK886-PMCs-3-A12_2018-7-11


title: MK886-PMCs-3-F02_2018-7-11


title: Chlorate-PMCs-1-A04_2018-7-11


title: 7_1_1

description: FFPE block sections


title: Chlorate-PMCs-2-E12_2018-7-11


title: 8_1_2

description: FFPE block sections


title: 5_1_1

description: FFPE block sections

value: LumATumor_5 (Unpaired; No DCIS component available)


title: 4_1_1

description: FFPE block sections

value: Basal


title: 3_1_2

description: FFPE block sections

value: BasalDCIS_4 (Unpaired; No tumor component available)


title: ASW-PMCs-2-H07_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization


title: MK886-PMCs-3-C03_2018-7-11

value: MK-886 (1.5uM final)


title: 4_1_2

description: FFPE block sections


title: MK886-PMCs-3-H08_2018-7-11


title: MK886-PMCs-2-E03_2018-7-11


title: MK886-PMCs-2-D01_2018-7-11


title: RW01003: CAL-33_vec_rep3


title: Chlorate-PMCs-2-E10_2018-7-11


title: ASW-PMCs-2-C07_2018-7-11


title: MK886-PMCs-3-H10_2018-7-11


title: 7_2_2

description: FFPE block sections


title: 2_2_2

description: FFPE block sections


title: ASW-PMCs-2-B12_2018-7-11


title: MK886-PMCs-2-B06_2018-7-11


title: 2_1_1

description: FFPE block sections


title: Chlorate-PMCs-1-H04_2018-7-11


title: 11_1_2

description: FFPE block sections


title: MK886-PMCs-3-D02_2018-7-11


title: MK886-PMCs-3-C08_2018-7-11


title: MK886-PMCs-2-F09_2018-7-11


title: 11_1_1

description: FFPE block sections


title: ASW-PMCs-2-F04_2018-7-11


title: Chlorate-PMCs-2-A09_2018-7-11


title: 1_1_2

description: FFPE block sections


title: INS-1 line 19-4 (PWS 3) [ncRNA-Seq]

city: Pittsburgh

first: Erik

last: Koppes

state: PA

address: 204 Craft Ave

department: MWRI

institute: University of Pittsburgh

data_processing:
UMI Extraction / de-duplication UMI-Tools v1.0.0
Adapter Trimming Cutadapt v1.18
Genomic Alignement Bowtie2 v2.3.4.2
Feature Counts HTSeq v0.11.2 (with --mode combined with either union --nonunique all or --nonunique none)
Differential Expression DESeq2
Genome_build: Ensembl Rnor 6.0 v99
.csv of all detected smallRNA genes
https://github.com/KoppesEA/INS-1_PWS_RNA-Seq/
Supplementary_files_format_and_content: .csv of all detected smallRNAs with PWS vs Control differential expression using --nonunique all HTSeq option
Supplementary_files_format_and_content: .csv of all detected smallRNAs with PWS vs Control differential expression using --nonunique none HTSeq option

organism: Rattus norvegicus

growth_protocol: RPMI INS-1 media 7.5mM Glucose

extract_protocol:
Trizol; Qiagen miRNeasy
QIAseq miRNA NGS  (adapted for <200nt smallRNAs)

tag: genotype

value: PWS


title: INS-1 line 19-1 (PWS 2) [ncRNA-Seq]


title: MK886-PMCs-2-H03_2018-7-11


title: MK886-PMCs-2-F02_2018-7-11


title: 10_1_2

description: FFPE block sections

value: LumADCIS_6 (Unpaired; No tumor component available)


title: HeLa-Exo

city: Delhi

first: Alok

middle: Chandra

last: Bharti

state: New Delhi

address: North campus, Chhatra Marg

department: Zoology Department

country: India

institute: University of Delhi

description: Exosome sequencing data

data_processing:
The sequence data was generated using Illumina HiSeq
Data quality was checked using FastQC and MultiQC software
Raw sequence reads were processed to remove adapter sequences and low quality bases using fastp
The QC passed reads were mapped onto the indexed combined reference genome of Human (GRCh38.p7), Human Papillomavirus 16 (HPV16) and Human Papillomavirus 18 (HPV18) using STAR v2 aligner
Uniquely mapped reads were used for transcripts assembly using StringTie software with default parameters.
Assembled transcripts of all the samples are merged into a single gtf file using the StringTie merge option and merged gtf files were compared and annotated with reference gff using gffcompare software
Differential expression analysis was carried out using the DESeq2 package
Enrichment analysis for Biological process, Molecular function, Cellular component and KEGG Pathway was performed using ClusterProfiler R package
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: xls

molecule: polyA RNA

source_name: Cervical epithelium

growth_protocol: The cervical cancer cell lines were cultured in growth medium DMEM/MEM supplemented with 10% fetal bovine serum and 1X antibiotic and antimycotic solution.

extract_protocol: Exosomes were isolated from these cervical cancer cells using exosome isolation kit(Exocan Healthare Pvt.Ltd., Pune,India) and then RNA was isolated using Trizol reagent and sent for NGS

treatment_protocol: There was no treatment given to the cell lines

value: Cervical epithelium

tag: type of cancer

value: Cervical cancer

tag: presence of hpv

value: HPV-positive


title: 1_1_1

description: FFPE block sections


title: SiHa-Exo

description: Exosome sequencing data


title: INS-1 line 16 (Control 3) [ncRNA-Seq]

value: Control


title: INS-1 line 3 (PWS 1) [ncRNA-Seq]


title: INS-1 line 2 (Control 2) [ncRNA-Seq]


title: Chlorate-PMCs-1-E01_2018-7-11

value: Chlorate (30mM final)


title: C33a-Exo

description: Exosome sequencing data

value: HPV-negative


title: Chlorate-PMCs-1-G05_2018-7-11


title: RS180

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC.
Reads were trimmed with SolexaQA++ dynamic trim [54] and the aligned to GRCh38 with STAR.
Counts were normalized to transcripts per million (TPM) and then log + 1 transformed for all visualizations.
Differential expression was calculated using the software edgeR (v3.26.8) [56]. Raw counts were formatted into a DGE list and filtered for genes with counts > 1 in at least 3 samples. In order to capture all gene expression changes in response to VPA all genes with counts > 0 in at least 1 sample were used. Counts were then normalized with the TMM method. Dispersion was estimated in three steps. First common dispersion was calculated with the conditional maximum likelihood method, followed by tagwise dispersion as a moving average, and then trended dispersion calculated as a spline. These dispersions were then used to calculate differential expression between the relevant two groups. P-values were then adjusted for multiple-testing using the p.adjust function in R (v3.6.1) with the fdr method. To identify the number of genes differentially expressed we used an FDR < 0.05 with no minimum logFC. In the case where differences in expression were calculated as a function of time, these were calculated using the edgeR GLM function with expression as a function of time + disease status. For bulk analyses, days 8-42 were combined and tested as a function of disease status using the described exact test functions. Results were reported as volcano plots with fold change transformed using base 2 and raw p-values transformed using base exp(1).
Functional enrichment analysis was performed using DAVID bioinformatics (v6.8) [57, 58]. All genes with FDR < 0.05 for a given differential expression test were uploaded as a gene list in official gene symbol format and corrected against the Homo sapiens background. A functional annotation chart was then calculated from the results.
Principal component analysis was performed on TPM values using the package pcaMethods (v1.76.0) with the svd algorithm.
LEF1 predicted downstream targets were identified using the Transfac database (gene id = 51176).
Genome_build: hg38
Supplementary_files_format_and_content: Transcripts Per Million normalized expression table as a tab-separated text file

source_name: neurons

growth_protocol: NPCs were differentiated to dentate gyrus-like neurons in N2B27 media supplemented with 200 nM ascorbic acid (STEMCELL Technologies), 500 μg/ml cyclic AMP (Tocris Bioscience), 20 ng/ml brain-derived neurotrophic factor (BDNF, PeproTech), 20 ng/ml Wnt3a (R&D Systems) and 5 μg/ml laminin for 3 weeks. Media was changed three times a week and Wnt3a was removed after 3 weeks.

extract_protocol:
 Cells (~5x106 cells) were collected in RNA-Bee solution (Tel-Test, Inc) and total RNA was extracted using the DNA-Free RNA Kit (Zymo Research) according to the manufacturer’s instructions.
Stranded mRNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions. All libraries were then quantified, pooled and sequenced at single-end 50 bp reads on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing (NGS) Core at a depth of approximately 40 million reads per library.
stranded mRNA

treatment_protocol: 24h treatment with 1 mM LiCl, 1 mM valproic acid, vehicle (water)

tag: cohort

value: iPSC-derived ("Kelsoe cohort")

value: Bipolar Disorder, Lithium Non-responsive

tag: sorted/bulk

value: Bulk

value: 4 week of induction

tag: clone

tag: passage number


title: MK886-PMCs-3-F05_2018-7-11

tag: tissue


title: INS-1 line 5-9 (Control 1) [ncRNA-Seq]


title: INS-1 line 19-1 (PWS 2)

data_processing:
QC with FastQC v0.11.5 and adapter trimming with CutAdapt using wrapper in TrimGalor v0.4.5
Splice-aware genome alignement using STAR v2.7.0e
Gene-level feature counts with HTSeq v0.11.2 (with --mode union combined with --nonunique all or with --nonunique none ) or with RSEM v.1.3.1
Differential gene expression with DEseq2 v.3.9
Genome_build: Ensembl Rnor6.0 v98 + custom transgene and annotation tracks (see github.com/KoppesEA/INS-1_PWS_RNA-Seq for more information)
https://github.com/KoppesEA/INS-1_PWS_RNA-Seq/
Supplementary_files_format_and_content: .csv files for expression all rat genes in PWS vs Control samples; .txt files for custom annoation
Supplementary_files_format_and_content: .csv STAR/HTSeq/DESeq2 output
Supplementary_files_format_and_content: .csv STAR/HTSeq/DESeq2 output
Supplementary_files_format_and_content: .csv STAR/RSEM/DESeq2 output
Supplementary_files_format_and_content: .gtf of additional custom annotations
Supplementary_files_format_and_content: .fa sequence of mINS2-mCherryCP transgene
Supplementary_files_format_and_content: .fa sequence of hINS-NeoR transgene

extract_protocol:
Trizol; Qiagen miRNeasy
Illumina Next-seq
rRNA depletion (Total RNA-Seq)


title: INS-1 line 19-4 (PWS 3)


title: RS179

value: 2 week of induction


title: MK886-PMCs-2-F11_2018-7-11

tag: developmental stage


title: ASW-PMCs-2-G10_2018-7-11

tag: treatment


title: INS-1 line 16 (Control 3)


title: RS178

tag: disease state

value: 1 week of induction


title: RS177

source_name: neuronal progenitor cells

tag: cell line

value: Neural Progenitor Cells (NPC)


title: Chlorate-PMCs-2-B07_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization


title: INS-1 line 2 (Control 2)


title: MK886-PMCs-2-C10_2018-7-11

value: MK-886 (1.5uM final)


title: INS-1 line 5-9 (Control 1)


title: RS135

value: Sorted

value: VPA


title: RS134

value: Li


title: Rat Gastroc KO17

city: Baton Rouge

first: Jaycob

middle: D

last: Warfel

state: Louisiana

address: 6400 Perkins Road

department: RNA Homeostasis

institute: PBRC

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

source_name: Gastrocnemius Muscle Tissue

extract_protocol:
Total RNA was prepared using Trizol, RNA concentration was determined usign a nanodrop UV spectrophotometer, and 500ng RNA per sample was given for sequencing library construction.
Lexogen Quant-Seq
indexed and pooled samples, 50bp forward read

treatment_protocol: Gastrocnemius muscles were dissected from 7 male wild-type and 9 male UCP1 knockout rats before and after 2 weeks of 4 Celsisus cold exposure at 20 weeks of age.

value: Gastrocnemius Muscle Tissue

value: UCP1 KO

tag: temperature

value: RT Exposed


title: Chlorate-PMCs-2-B08_2018-7-11

value: Chlorate (30mM final)


title: RS133

value: iPSC-derived ("Kelsoe cohort")

value: CTRL


title: Chlorate-PMCs-2-F02_2018-7-11


title: Rat Gastroc KO16


title: Rat Gastroc KO14


title: ASW-PMCs-2-D10_2018-7-11


title: RS152

value: Bipolar Disorder, Lithium Non-responsive

value: Bulk

value: C5 <Jun>


title: RS119


title: Chlorate-PMCs-1-C04_2018-7-11


title: Chlorate-PMCs-1-D10_2018-7-11


title: MK886-PMCs-3-D12_2018-7-11


title: RS120


title: MK886-PMCs-3-A11_2018-7-11


title: INS-1 line 3 (PWS 1)

value: PWS


title: RS118


title: Rat Gastroc KO13


title: Rat Gastroc KO11


title: RS145

value: 4 week of induction

value: C1 <Jun>


title: Rat Gastroc KO10


title: RS144

value: 2 week of induction


title: Rat Gastroc KO8


title: Rat Gastroc KO15


title: RS143

value: 1 week of induction


title: Chlorate-PMCs-1-H07_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization


title: Chlorate-PMCs-2-E08_2018-7-11


title: Chlorate-PMCs-1-G10_2018-7-11


title: RS142

value: Neural Progenitor Cells (NPC)


title: rat gastroc RT wt7

value: Gastrocnemius Muscle Tissue

value: Control


title: ASW-PMCs-2-F06_2018-7-11


title: RS113

value: Sorted

value: VPA


title: Chlorate-PMCs-1-G06_2018-7-11

value: Chlorate (30mM final)


title: RS114

value: iPSC-derived ("Kelsoe cohort")

value: Li


title: ASW-PMCs-2-A10_2018-7-11


title: rat gastroc RT wt4

value: RT Exposed


title: ASW-PMCs-2-G01_2018-7-11


title: RS171

value: Bipolar Disorder, Lithium Responsive

value: Bulk

value: 6 week of induction


title: RS170

value: 4 week of induction


title: rat gastroc RT wt3


title: rat gastroc RT wt5


title: RS169

value: 2 week of induction


title: rat gastroc RT wt6


title: MK886-PMCs-2-G04_2018-7-11

value: MK-886 (1.5uM final)


title: RS168

value: 1 week of induction


title: MK886-PMCs-2-G11_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization


title: RS112

value: Bipolar Disorder, Lithium Non-responsive

value: CTRL

value: C1 <Jun>


title: rat gastroc RT wt1

value: Gastrocnemius Muscle Tissue

value: Control


title: rat gastroc CC ko9

value: UCP1 KO

value: 4C Exposed


title: Chlorate-PMCs-1-A02_2018-7-11

value: Chlorate (30mM final)


title: rat gastroc RT wt2

value: RT Exposed


title: rat gastroc CC ko8


title: RS167

value: iPSC-derived ("Kelsoe cohort")

value: Bipolar Disorder, Lithium Responsive

value: Bulk

value: Neural Progenitor Cells (NPC)


title: rat gastroc CC ko7


title: RS128

value: Sorted

value: VPA


title: ASW-PMCs-2-A05_2018-7-11

value: primary mesenchyme


title: MK886-PMCs-3-G08_2018-7-11

value: 18 hours post-fertilization

value: MK-886 (1.5uM final)


title: rat gastroc CC ko6


title: DMSO-PMCs-1-H09_2018-7-11

value: DMSO


title: rat gastroc CC ko5


title: RS151

value: 6 week of induction

value: C6 <Jun>


title: RS127

value: CTRL


title: rat gastroc CC ko4

value: Gastrocnemius Muscle Tissue

value: UCP1 KO


title: rat gastroc CC ko3

value: 4C Exposed


title: RS150

value: 4 week of induction


title: ASW-PMCs-2-D05_2018-7-11


title: MK886-PMCs-2-H04_2018-7-11


title: MK886-PMCs-2-E04_2018-7-11


title: MK886-PMCs-2-C03_2018-7-11


title: Chlorate-PMCs-1-B10_2018-7-11

value: Chlorate (30mM final)


title: RS148

value: iPSC-derived ("Kelsoe cohort")

value: Bipolar Disorder, Lithium Responsive

value: 1 week of induction


title: rat gastroc CC ko1


title: MK886-PMCs-3-B10_2018-7-11


title: rat gastroc CC wt7

value: Control


title: Chlorate-PMCs-1-C07_2018-7-11


title: RS116

value: Sorted

value: VPA


title: rat gastroc CC wt6


title: RS129

value: Li


title: RS117


title: rat gastroc CC wt5


title: RS115


title: RS149

value: Bulk

value: 2 week of induction


title: Chlorate-PMCs-2-A08_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization


title: rat gastroc CC ko2


title: Chlorate-PMCs-1-B06_2018-7-11


title: Chlorate-PMCs-2-B09_2018-7-11


title: RS147

value: Neural Progenitor Cells (NPC)

value: C6 <Jun>


title: Chlorate-PMCs-1-G04_2018-7-11


title: rat gastroc CC wt4

value: Gastrocnemius Muscle Tissue


title: RS163


title: RS164


title: MK886-PMCs-2-B11_2018-7-11

value: MK-886 (1.5uM final)


title: rat gastroc CC wt3

value: 4C Exposed


title: RS165

value: 4 week of induction


title: MK886-PMCs-2-E09_2018-7-11


title: RS166

value: iPSC-derived ("Kelsoe cohort")

value: 6 week of induction


title: rat gastroc CC wt2


title: RS162

value: Bipolar Disorder, Lithium Responsive


title: S26-sh-GOLIM4-L

city: Guangzhou

first: Jin-Xin

last: Bei

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guanzhou, P.R. China

institute: Sun Yat-sen University Cancer Center

description: S26 cells infected with GOLIM4-L shRNA lentivirus

data_processing:
Illumina-implemented software bcl2fastq (version v2.19.0.316) was used for basecalling.
Sequenced reads were trimed for adapter sequence and removed low-complexity and low quality reads.
Clean reads were mapped to human rRNA sequence to remove rRNA reads using Bowtie2.0
Then reads were mapped to hg19 genome using HISAT2.0
TPM (Transcripts Per Kilobase Million) were calculated by HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: Each sample was represented by tab-delimited text files include TPM (Transcripts Per Kilobase Million) value of each gene.

source_name: Nasopharyngeal carcinoma cell line

extract_protocol:
For whole-transcriptome sequencing, total RNA was extracted from tumor specimens by using RNeasy Mini Kit (Qiagen), and 1 μg total RNA was subjected for the depletion of ribosomal RNAs by using Ribo-Zero Magnetic Kit (Illumina), followed by library preparation according to the manufacturer’s instructions as in the TruSeq RNA Library  Prep Kit (Illumina).
Library was processed with high-throughput sequencing for pair-end of 150 bp, using Hiseq X Ten sequencer (Illumina, USA). High-quality pair-end reads were mapped using Bowtie 2. After filtering out ribosomal RNAs, reads counts of each gene were then quantitated using HTseq.

treatment_protocol: Total RNA were extracted with S26 cells, which were infected with shRNA lentivirus and selected with puromycine.

value: Nasopharyngeal carcinoma

tag: shRNA


title: rat gastroc CC wt1

value: Control


title: S26-sh-RBFOX2

description: S26 cells infected with RBFOX2 shRNA lentivirus


title: S26-sh-Luci

description: S26 cells infected with control shRNA lentivirus

value: sh-Luci


title: ASW-PMCs-2-C03_2018-7-11


title: MK886-PMCs-3-A03_2018-7-11


title: RS126

value: Sorted

value: Li


title: Chlorate-PMCs-2-D08_2018-7-11

value: Chlorate (30mM final)


title: RS124

value: CTRL


title: MK886-PMCs-2-B08_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization


title: 5-8F-si-hnRNPM

description: 5-8F cells transfected with hnRNPM siRNA

extract_protocol:
For whole-transcriptome sequencing, total RNA was extracted from tumor specimens by using RNeasy Mini Kit (Qiagen), and 1 μg total RNA was subjected for the depletion of ribosomal RNAs by using Ribo-Zero Magnetic Kit (Illumina), followed by library preparation according to the manufacturer’s instructions as in the TruSeq RNA Library  Prep Kit (Illumina).
Library was processed with high-throughput sequencing for pair-end of 150 bp, using Hiseq X  Ten sequencer (Illumina, USA). High-quality pair-end reads were mapped using Bowtie 2. After filtering out ribosomal RNAs, reads counts of each gene were then quantitated using HTseq.

treatment_protocol: Total RNA were extracted with S26 and 5-8F cells  transfected with siRNAs for 48h.

value: Nasopharyngeal carcinoma cell line

tag: transfection

value: sihnRNPM


title: RS125

value: VPA


title: 5-8F-si-RBM47

description: 5-8F cells transfected with RBM47 siRNA


title: DMSO-PMCs-1-D10_2018-7-11

value: DMSO


title: 5-8F-si-NC

description: 5-8F cells transfected with control siRNA

value: siNC


title: Chlorate-PMCs-1-C12_2018-7-11


title: RS185

value: iPSC-derived ("Kelsoe cohort")

value: Bulk

value: 4 week of induction


title: RS184

value: 2 week of induction


title: S26-si-NC

description: S26 cells transfected with control siRNA


title: MK886-PMCs-2-D12_2018-7-11

value: MK-886 (1.5uM final)


title: MK886-PMCs-3-C05_2018-7-11


title: GSC1517_YY1_KD_rep2_Hi-C

city: Shanghai

first: Zhixin

last: Qiu

address: Dongan Road

institute: Fudan University

library_source: genomic

data_processing:
The ChIA-PET2 v0.9.3 software was used for quality control, mapping to hg19 genome and identification of chromatin interactions with the following parameter setting: -A ACGCGATATCTTATC -B AGTCAGATAAGATAT -s 1 -m 1 -t 24 -k 2 -e 1 -l 15 -S 500 -M “-q 0.05.”
HiC-Pro hicpro2juicebox.sh utility was used to generate hic file for further visualization of interaction matrix.
Genome_build: hg19
Supplementary_files_format_and_content: The hic files containing contact matrices

molecule: genomic DNA

source_name: patient-derived cells

extract_protocol:
BL-Hi-C library construction were performed as described previously (Liang et al., 2017).
PCR products between 300–700 bp were purified as BL-Hi-C library using Ampure XP beads and subjected to Illumina HiSeq X10 for paired end 150 bp sequencing.

value: glioblastoma stem cells

tag: cell type


title: RS182

value: Control

value: Neural Progenitor Cells (NPC)


title: GSC1517_YY1_KD_rep1_Hi-C


title: ASW-PMCs-2-B09_2018-7-11


title: RS138

value: Sorted


title: GSC1517_Control_KD_rep2_Hi-C

value: shCONT


title: MK886-PMCs-2-H10_2018-7-11

value: primary mesenchyme


title: Chlorate-PMCs-1-F02_2018-7-11

value: 18 hours post-fertilization

value: Chlorate (30mM final)


title: RS183

value: 1 week of induction


title: RS137

value: Li


title: MK886-PMCs-3-H04_2018-7-11


title: ASW-PMCs-2-G08_2018-7-11


title: RS186

value: 6 week of induction


title: GSC1517_Control_KD_rep1_Hi-C


title: MK886-PMCs-2-D10_2018-7-11


title: Rat Gastroc KO9

value: Gastrocnemius Muscle Tissue

value: UCP1 KO

value: RT Exposed


title: RS136

value: iPSC-derived ("Kelsoe cohort")

value: CTRL


title: RS175

value: Bulk

value: 4 week of induction


title: RS176

value: Control


title: GBM22 0.5-0.5-10 2

type: RNA

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

description: Gene expression data from GBM22 cells grown in 0.5 mM glucose, 0.5 mM glutamate, 10 mM L-lactate.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.61.0), using R version 3.6.0 and the Brainarray hugene20sthsentrezgcdf R package (version 24.0.0).

label: biotin

source_name: GBM22 cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Cells were initially grown in DMEM+10%FBS+primocin.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Cat No./ID: 217004) from Qiagen.

treatment_protocol: Cells were starved in empty DMEM+1.5%FBS+primocin + glucose (0.5mM), glutamine (0.5mM), and lactate (0mM or 10mM).

value: glioblastoma

tag: medium


title: GBM22 0.5-0.5-10 1

value: 0.5 mM glucose, 0.5 mM glutamate, 10 mM L-lactate


title: RS174

value: 2 week of induction


title: Chlorate-PMCs-2-B03_2018-7-11

value: primary mesenchyme


title: MK886-PMCs-2-C11_2018-7-11

value: 18 hours post-fertilization

value: MK-886 (1.5uM final)


title: RS172

value: Neural Progenitor Cells (NPC)


title: GBM22 0.5-0.5-0 2

description: Gene expression data from GBM22 cells grown in 0.5 mM glucose, 0.5 mM glutamate, 0 mM L-lactate.


title: GBM22 0.5-0.5-0 1

value: 0.5 mM glucose, 0.5 mM glutamate, 0 mM L-lactate


title: GBM43 0.5-0.5-10 2

description: Gene expression data from GBM43 cells grown in 0.5 mM glucose, 0.5 mM glutamate, 10 mM L-lactate.

source_name: GBM43 cells


title: PDX_CTRL_rep2

type: genomic

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

hyb_protocol: 600ng of genomic DNA was bisulfite converted using EZ DNA Methylation Kit (Zymo) following manufacturer’s protocol. 4uL of bisulfite-converted DNA were hybridized to Infinium HumanMethylationEPIC BeadChip following Illumina Infinium HD Methylation protocol

scan_protocol: Chip analysis was performed using Illumina HiScan SQ fluorescent scanner and the intensities of the images were extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software

data_processing: Quality control, background correction and quantile normalization across arrays was performed with functions from Minfi R/Bioconductor package

label: Cy5 and Cy3

source_name: Cell line, PDX

label_protocol: Standard Illumina labelling protocol.

growth_protocol: Cells were maintained in Iscove’s Modified Dulbecco’s Medium (EBC2072L, IMDM, Euroclone, Milan, Italy) supplemented with 10% heat-inactivated FBS (ECS01180L, Euroclone), penicillin (20U/mL) and streptomycin (100microgr/mL) (ECB3001D, Euroclone) in a 37C humidified at 5% CO2.

extract_protocol: DNA was extracted from cell pellets by PureLink genomic DNA kit (K182001, Thermo Fisher Scientific)

treatment_protocol: 2-5x10⁵ cells were plated in 6-wells dishes and treated 24h with the indicated drugs for 72h, roughly equivivalent to at least two doubling times of each cell lines


title: GBM43 0.5-0.5-10 1


title: S26-si-RBM47

description: S26 cells transfected with RBM47 siRNA

value: Nasopharyngeal carcinoma cell line


title: PDX_CTRL_rep3


title: GBM43 0.5-0.5-0 2

description: Gene expression data from GBM43 cells grown in 0.5 mM glucose, 0.5 mM glutamate, 0 mM L-lactate.


title: PDX_MC3343_72h_rep2


title: Chlorate-PMCs-2-C04_2018-7-11

value: Chlorate (30mM final)


title: Chlorate-PMCs-1-A05_2018-7-11


title: RS132

value: Sorted

value: Li


title: RS130

value: iPSC-derived ("Kelsoe cohort")


title: DMSO-PMCs-1-C05_2018-7-11

value: DMSO


title: PDX_5AzadC_72h_rep2


title: PDX_MC3343_72h_rep3


title: A673_5AzadC_72h_rep3

source_name: Cell line, A673


title: A673_CTRL_rep2

value: CTRL


title: A673_MC3343_72h_rep3


title: MK886-PMCs-2-A04_2018-7-11


title: RS189

value: Bulk


title: RS173

value: Control

value: 1 week of induction


title: TC-71_5AzadC_72h_rep2

source_name: Cell line, TC-71


title: RS190

value: 4 week of induction


title: GBM43 0.5-0.5-0 1

value: glioblastoma


title: RS131

value: VPA


title: TC-71_MC3343_72h_rep3


title: A673_5AzadC_72h_rep2


title: 0.5-0.5-10 1

description: Gene expression data from KNS42 cells treated with 0.5 mM glucose, 0.5 mM glutamate, 10 mM L-lactate.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

source_name: KNS42 cells


title: PDX_5AzadC_72h_rep1


title: 0.5-0.5-10 2

value: 0.5 mM glucose, 0.5 mM glutamate, 10 mM L-lactate


title: A673_MC3343_72h_rep2


title: 0.5-0.5-0 2

description: Gene expression data from KNS42 cells treated with 0.5 mM glucose, 0.5 mM glutamate, 0 mM L-lactate.


title: 0.5-0.5-0 1


title: APEX-seq APEX2DDX3Y woArs rep2

city: philadelphia

first: Fange

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

data_processing:
The high throughput sequencing reads were adaptor and quality trimmed using Trimmomatic with following command: trimmomatc SE -phred33 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:25 TRAILING:25 SLIDINGWINDOW:4:20 MINLEN:30.
Then, the reads were aligned to the GRCh38 human genome reference using HISAT2. Parameters used were: --no-unal (not report the unaligned reads), --known-splicesite-file (generated from the Ensembl hg38 annotation file) and –k 1 (report one alignment).
Aligned reads were quantified using featureCounts
The DEseq2 package was uded to analysis the differential enriched genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: table with raw gene counts for every gene and every sample

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM + GlutaMAX (GIBCO, 11995065) with 10% FBS (GIBCO, 26140-079) and 1% Pen/Strep (Corning, 30-002-CI) in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
After the cellular labeling, total RNA was purified using TRIzol per the manufacturer’s instruction. To enrich biotinylated RNAs, Pierce streptavidin magnetic beads (Thermo Fisher) were used (20 μL beads per 50 μg RNA). The beads were washed 3 times with 500 μL B&W buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl, and 0.1% TWEEN 20), followed by 2 times of 500 μL solution A (0.1 M NaOH and 50 mM NaCl), and 1 time of 500 μL solution B (100 mM NaCl). The beads were then suspended in 125 μL solution B. 50 μg RNA diluted in 125 μL water was mixed with the beads and incubated at 4 °C for 2 hrs with rotation. Then, the beads were placed on a magnetic stand to remove the solution and washed 3 times with 500 μL B&W buffer. Finally, the beads were resuspended in 54 μL water. To release the biotinylated RNA, 33 μL proteinase buffer (3 x PBS, 6% N-Lauryl sarcosine sodium solution (Sigma-Aldrich), 30 μM EDTA, and 15 μM DTT) was added to the beads with 10 μL proteinase K (Thermo Fisher) and 5 μL RNase inhibitor. The beads were then incubated at 42 °C for 1 hr and 55 °C for 1 hr on a shaker at 600 rpm. The RNA was then purified using the RNA clean and concentrator 5 kit (Zymo Research) following the manufacturer’s instruction. The resulted RNA was then used for RNA-seq library construction.
Libraries were constructed according to TruSeq Stranded mRNA Kit (Illumina) protocol. The concentrations for all the libraries were determined by KAPA Library Quantification Kit (KAPA Biosystems) following the manufacturer’s protocol, and subjected to Next-generation high-throughput sequewncing using an illumina NextSeq 550 with a single-end 75-bp read length.

treatment_protocol: To enable APEX labeling in mammalian cells, prewarmed 5 mL of biotin-phenol (at 500 mM final concentration)-containing DMEM media was added to the cells in 10 cm plate for 30 minutes prior to the start of the experiment. H2O2 (Sigma-Aldrich) was added to each dish at 1 mM final concentration for a total labeling time of exactly 1 minute with gentle agitation. To stop labeling after 1 min treatment, the culture media was removed, and the quenching solution (10 mM sodium ascorbate, 10 mM sodium azide, and 5 mM Trolox in PBS) was immediately used to wash the cells for three times.  Finally, 1 mL quenching solution was applied to cover the cells. Cells were then collected with cell scraper.

tag: genotype/variation


title: MK886-PMCs-3-B09_2018-7-11

source_name: Primary Mesenchyme Cells

value: primary mesenchyme

value: 18 hours post-fertilization

value: MK-886 (1.5uM final)


title: APEX-seq APEX2DDX3Y woArs rep1


title: TC-71_CTRL_rep2


title: ASW-PMCs-2-G12_2018-7-11


title: RS188


title: RS140


title: TC-71_MC3343_72h_rep2


title: PDX_MC3343_72h_rep1


title: PDX_CTRL_72h_rep1


title: A673_CTRL_rep3


title: DMSO-PMCs-1-H10_2018-7-11


title: RS187

value: Neural Progenitor Cells (NPC)


title: MK886-PMCs-3-E07_2018-7-11


title: RS139


title: APEX-seq APEX2DDX3X woArs rep2


title: MK886-PMCs-3-E02_2018-7-11


title: ASW-PMCs-2-A01_2018-7-11


title: RS191

value: 6 week of induction


title: APEX-seq APEX2DDX3X woArs rep1


title: MK886-PMCs-2-C04_2018-7-11


title: DMSO-PMCs-1-F08_2018-7-11


title: Chlorate-PMCs-2-C12_2018-7-11

value: Chlorate (30mM final)


title: A673_5AzadC_72h_rep1


title: APEX-seq APEX2EGFP woArs rep1


title: APEX-seq APEX2EGFP woArs rep2


title: TC-71_CTRL_rep3


title: ANON3006 May Pf III (classical) [15010]

city: Hamilton

first: Sarah

last: Anzick

state: MT

address: 903 South 4th Street

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

data_processing:
Reads were processed using fastx toolkit to trim for adapter and low quality bases and filter for low quality reads.
Processed reads were mapped to GRCh38 reference genome using HISAT2, version 2.1.0.
Reads mapping to genes were counted using htseq-count, version 0.9.1
Gene normalization and differential expression analysis were performed using Deseq2, version 1.18.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.

source_name: PBMC

extract_protocol:
direct lysate
Cells were sorted directly into Takara lysis buffer and a volume of lysate corresponding to 4 or fewer cells was used as input for cDNA synthesis and library construction using the SMART-Seq V4 Ultra Low Input RNA kit (Takara) and SMARTer ThruPLEX DNA-Seq kit, respectively.  Libraries were sequenced as 2 X 150 bp reads

treatment_protocol: flow cytometry and B cell selection

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: Pf+ classical

tag: season

value: May


title: RS123

tag: cohort

value: iPSC-derived ("Kelsoe cohort")

tag: sorted/bulk

value: Sorted

value: Li

tag: clone

value: C4 <Jun>


title: MK886-PMCs-3-H09_2018-7-11

tag: tissue

tag: developmental stage


title: RS157

tag: disease state

value: Control

value: Bulk

tag: treatment

tag: passage number


title: Chlorate-PMCs-2-E06_2018-7-11


title: RS122

tag: cell line

value: VPA


title: ANON3006 May HA III (classical) [15007]

value: HA+ classical


title: Chlorate-PMCs-2-E01_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization


title: RS121

value: CTRL


title: ANON3006 May Pf I (atypical) [15008]

value: Pf+ atypical


title: DMSO-PMCs-1-G08_2018-7-11

value: DMSO


title: RS82

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Non-responsive

value: 2 week of induction


title: TC-71_5AzadC_72h_rep1


title: DMSO-PMCs-1-G07_2018-7-11


title: A673_MC3343_72h_rep1


title: RS83

value: 4 week of induction


title: ANON3006 May HA I (atypical) [15005]

value: primary B cells

value: female

value: HA+ atypical

value: May


title: TC-71_5AzadC_72h_rep3


title: DMSO-PMCs-1-A06_2018-7-11


title: ANON3006 Conv HA I (atypical) [14999]

value: Convalescence


title: RS40

value: Sorted


title: RS80

value: Bulk

value: Neural Progenitor Cells (NPC)


title: RS41

value: Li


title: ANON3001 May Pf I (atypical) [14996]


title: ANON3001 May Pf III (classical) [14998]

value: Pf+ classical


title: RS81

value: 1 week of induction


title: ASW-PMCs-2-F11_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization


title: MK886-PMCs-2-A05_2018-7-11

value: MK-886 (1.5uM final)


title: TC-71_MC3343_72h_rep1


title: ANON3001 May HA III (classical) [14995]

value: HA+ classical


title: DMSO-PMCs-1-G09_2018-7-11

value: DMSO


title: ANON3001 May HA II (activated) [14994]

value: HA+ activated


title: ANON3001 May Pf II (activated) [14997]

value: primary B cells

value: Pf+ activated


title: ANON3001 May HA I (atypical) [14993]

value: female

value: HA+ atypical


title: Chlorate-PMCs-1-F07_2018-7-11

value: Chlorate (30mM final)


title: RS74

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Non-responsive

value: 6 week of induction


title: TC-71_CTRL_rep1

value: CTRL


title: Colon_propionate_HFD_rep4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.24.0).

organism: Mus musculus

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium propionate, high fat background diet, replicate 4

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Male C57Bl/6J mice (Charles River, Maastricht, the Netherlands), 8 weeks of age, were individually housed in a light- and temperature-controlled facility (lights on 23:00  to 11:00, 21 °C). Mice were fed a standard laboratory chow (RMH-B, Arie Blok, Woerden, the Netherlands), and had free access to drinking water.

extract_protocol: Total RNA was prepared from scrapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: After 2 weeks mice were switched to semi-synthetic diets, either containing 10 en% of fat (low fat diet; LFD) or 45 en% of fat (high fat diet; HFD). Diets were based on Research Diets formulas D12450B/D12451, with adaptations regarding type of fat (palm oil instead of lard) and carbohydrates to mimic the fatty acid and carbohydrate composition of the average human diet in Western societies. Diets were prepared by Research Diet Services (Wijk bij Duurstede, The Netherlands). After 2 weeks on either the LFD or HFD, the infusion period started. Mice were assigned to one of 4 treatment groups: Control, Acetate, Propionate or Butyrate. On 6 consecutive days, mice were mildly sedated with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%) 2h before the start of the dark phase, where after they received a rectal infusion of the test solutions. At time of infusion, mice were kept under sedation. Mice received an 80 µL saline solution (Control; n = 6 per diet group), or an 80 µL saline solution containing 100 mM sodium acetate (Acetate; n = 6), 100 mM sodium propionate (Propionate; n = 6) or 100 mM sodium butyrate (Butyrate; n = 6). All solutions had a pH of 6.5 and were isotonic. The solutions were administered by inserting a gel loading tip 3 cm into the rectum and slowly pipetting the solution out of the tip. 4 h after the last (6th) infusion, mice were anaesthetized with isoflurane where after the colon was excised. The adhering fat around the colon was carefully removed, and the colon was cut open longitudinally. The intestinal content was removed and the tissue was rinsed with phosphate buffered saline. Subsequently, the epithelial lining of the colon was scraped, snap frozen, and stored at -80 °C for RNA isolation.

tag: strain

value: male

value: 13 weeks

value: colonic scrapings


title: P39-DEC-R (methylome)

city: Pokfulam

first: Rita

middle: Lok Hay

last: Yim

address: Room 311, 3rd Floor, Professorial Block, Queen Mary Hospital,

department: Department of Medicine

country: Hong Kong

institute: Hong Kong University

hyb_protocol: Standard hybridization

scan_protocol: Scanning on iScan system with default setting

data_processing: Standard analysis on Genome studio, no normalization is done

label: Cy5 & Cy3

source_name: Bone Marrow Cell Line

label_protocol: Standard labelling

growth_protocol: RPMI-1640 GlutaMAX supplemented with 10% fetal bovine serum (FBS)

extract_protocol: Qiagen RNAeasy mini kit

treatment_protocol: Parental P39 sensitive to HMA were treated with 1µM of AZA or DEC for 48 hours, namely P39-AZA-S, P39-DEC-S. To establish derivative cell lines resistant to AZA or DEC, both cell lines were continuously exposed to AZA or DEC starting at a concentration of 5nM. P39 resistant to at least 10µM of AZA or DEC was established as P39-AZA-R and P39-DEC-R

value: DEC, continuously exposed

tag: phenotype

value: HMA resistant


title: ANON3001 Conv Pf II (activated) [14991]

tag: cell type

value: Convalescence


title: RS39

value: Sorted


title: MK886-PMCs-2-G12_2018-7-11

data_processing:
Read concatentation: Reads sequenced across multiple lanes were concatenated together for single cells using the “cat” command in a linux terminal
Quality control: Reads and bases in reads were filtered and quality controlled using fastp (version 0.20.0) with specified parameters “-y -Y 30” and default parameters otherwise
GFF conversion: The GFF annotation file was converted to a GTF file using gffread with default parameters
Genome Alignment: Reads were aligned for to the most recent L. variegatus genome using STAR (version 2.7.1a). The index was built with specified parameter “--sjdbOverhang 151” and default otherwise. Alignment was run using default parameters.
Alignment Quantification: Read quantification was performed using featureCounts (v1.6.4) with the fragment specification option “-p” enabled, and default parameters otherwise
Count Normalization: Prior to normalization, cells with fewer that 50,000 feature counts, and genes with total counts less than 0.5 cpm were filtered out. Counts were normalized per batch for downstream analysis using the “computeSumFactors” function in the scran library (version 1.12.1) in R (version 3.6.2). Normalized counts were subsequently batch corrected using the function “multiBatchNorm” function in the scran library.
Genome_build: L. variegatus genome (Li et al., 2020)
Supplementary_files_format_and_content: Comma-separated text files containing raw and normalized count matrices for all cells used in the analysis, their associated metadata, and genome annotation information.

extract_protocol:
Individual PMCs were sorted directly into RNA lysis buffer supplemented with 1% β-mercaptoethanol.
Transcripts were purified, reverse-transcribed, and amplified according to the SMART-Seq2 protocol (Tombetta et al., Curr Protoc Mol Biol, 2014). Libraries were prepared using the Nextera XT kit (Illumina) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq 500 using 100bp paired end reads.

value: primary mesenchyme

value: 18 hours post-fertilization

value: MK-886 (1.5uM final)


title: Chlorate-PMCs-2-C02_2018-7-11


title: RS141

value: iPSC-derived ("Kelsoe cohort")

value: Control

value: VPA


title: ASW-PMCs-2-C09_2018-7-11


title: Colon_propionate_LFD_rep4

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium propionate, low fat background diet, replicate 4


title: ANON3001 Conv Pf III (classical) [14992]

value: primary B cells

value: female

value: Pf+ classical


title: Chlorate-PMCs-1-E05_2018-7-11

value: Chlorate (30mM final)


title: Colon_control_HFD_rep4

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of isotonic control solution (saline), high fat background diet, replicate 4

value: male


title: MK886-PMCs-2-D02_2018-7-11


title: ANON3001 Conv HA II (activated) [14988]

value: HA+ activated


title: RS73

source_name: neurons

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Non-responsive

value: Bulk

value: 4 week of induction


title: ANON3001 Conv HA I (atypical) [14987]

value: HA+ atypical

value: Convalescence


title: P39-DEC-S (methylome)

value: DEC, 48 hours

value: HMA sensitive


title: ANON3001 Conv HA III (classical) [14989]

value: HA+ classical


title: Chlorate-PMCs-2-G08_2018-7-11

value: primary mesenchyme

value: 18 hours post-fertilization


title: P39-AZA-R (methylome)

value: AZA, continuously exposed

value: HMA resistant


title: RS72

value: 2 week of induction


title: A673_CTRL_rep1

value: CTRL


title: RS35

value: Sorted

value: Li


title: P39-AZA-S (methylome)

value: AZA, 48 hours


title: RS71

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Non-responsive

value: 1 week of induction


title: Colon_butyrate_LFD_rep4

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium butyrate, low fat background diet, replicate 4

value: male

value: 13 weeks

value: colonic scrapings


title: ANON3002 May Pf II (activated) [14985]

value: primary B cells

value: Pf+ activated

value: May


title: RS104

value: Bulk

value: 6 week of induction


title: Fetal fibroblasts-donor,FFB3-huiwa

city: kaifeng

first: haoqiang

last: ma

state: henan

address: Jinming Revenue

institute: henan university

data_processing:
The raw data obtained by sequencing needed to be filtered, and we removed the reads containing adapter sequences, single-ended sequencing reads with undetected bases (represented by N) that exceeded the length of the reads by 10%, and single-ended sequencing reads that contained low-quality bases that exceeded the length ratio of the reads by 50%, finally producing clean reads.
Then, a quality evaluation of the clean reads was conducted, including assessments of the production statistics of our sequencing data, the distribution of the sequence base content and quality, and the distribution of GC content in the sequencing data, to ensure that the obtained data were of high quality.
The quality-controlled sequences were aligned to the reference genome sequence using HISAT2 and to the reference transcript sequence using Bowtie2 for subsequent differential expression analysis.
Assembly: bosTau9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Bos taurus

source_name: ear

growth_protocol: One-month-old ear tissues from live surviving cloned cattle waswere soaked in 70% alcohol for 30 s. Several pieces of epidermal tissue were cut from the tissue with sterile scissors and placed in basic medium containing 10% FBS (DMEM + NEAA). These tissues were thoroughly minced in 60 mm sterile culture dishes, placed in T25 culture flasks containing 5 ml of 10% FBS basic medium in batches, and cultured in a 37°C 5% CO2 incubator .

extract_protocol:
RNA was extracted from the above six cell lines using the TRIzol method, and the concentration and purity were determined using a NanoDrop 2000 microspectrophotometer.
20 μg of high-quality RNA was used to synthesize cDNA, which was subsequently sheared using an ultrasonic apparatus with the size controlled to 300–500 bp. After purification, amplification was carried out to complete library construction, and these libraries were then sequenced using an Illumina HiSeq system.

value: ear

value: huiwa

tag: genotype

value: Fetal fibroblasts-donor


title: RS103

value: 4 week of induction


title: RS70

source_name: neuronal progenitor cells

value: Neural Progenitor Cells (NPC)


title: MK886-PMCs-3-B01_2018-7-11

first: Cynthia

address: 24 Cummington Mall

value: primary mesenchyme

value: 18 hours post-fertilization

value: MK-886 (1.5uM final)


title: RS34

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Non-responsive

value: Sorted

value: VPA


title: ANON3002 May Pf III (classical) [14986]

value: primary B cells

tag: gender

value: male

value: Pf+ classical


title: MK886-PMCs-3-C11_2018-7-11


title: Colon_butyrate_LFD_rep3

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium butyrate, low fat background diet, replicate 3

tag: age

value: 13 weeks

value: colonic scrapings


title: Colon_butyrate_HFD_rep4

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium butyrate, high fat background diet, replicate 4


title: RS84

value: Bulk

value: 6 week of induction


title: Fetal fibroblasts-donor,FFB1-xingwa

value: ear

value: xingwa

value: Fetal fibroblasts-donor


title: ASW-PMCs-2-C02_2018-7-11

value: primary mesenchyme


title: RS33

value: CTRL


title: ANON3002 May HA II (activated) [14982]

tag: subset

value: HA+ activated

value: May


title: RS52

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Non-responsive


title: Chlorate-PMCs-2-B12_2018-7-11

value: 18 hours post-fertilization

value: Chlorate (30mM final)


title: Fetal oviduct epithelial cell-donor,FOV2-S1232

value: Fetal oviduct epithelial cell-donor


title: ANON3002 May HA I (atypical) [14981]

value: primary B cells

value: male

value: HA+ atypical

tag: season


title: RS102

tag: cohort

value: Bulk

value: 2 week of induction


title: Fetal fibroblasts-donor,FFB2-longwa

value: ear

value: longwa


title: Colon_acetate_HFD_rep4

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium acetate, high fat background diet, replicate 4

value: 13 weeks

value: colonic scrapings


title: ANON3002 Conv Pf III (classical) [14980]

value: Pf+ classical

value: Convalescence


title: Colon_control_HFD_rep3

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of isotonic control solution (saline), high fat background diet, replicate 3


title: Colon_acetate_HFD_rep3

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium acetate, high fat background diet, replicate 3


title: Colon_propionate_HFD_rep3

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium propionate, high fat background diet, replicate 3


title: RS101

tag: sorted/bulk

value: 1 week of induction


title: ANON3002 May HA III (classical) [14983]

value: HA+ classical

value: May


title: ANON3002 Conv Pf II (activated) [14979]

value: Pf+ activated


title: Colon_acetate_LFD_rep3

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium acetate, low fat background diet, replicate 3


title: Fetal oviduct epithelial cell-donor,FOV3-S1253


title: Colon_butyrate_HFD_rep3

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium butyrate, high fat background diet, replicate 3


title: RS51

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Non-responsive

value: Sorted

value: CTRL

tag: clone


title: Colon_propionate_LFD_rep3

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium propionate, low fat background diet, replicate 3

value: male

tag: tissue


title: RS100

value: Bulk

value: Neural Progenitor Cells (NPC)


title: ANON3002 Conv Pf I (atypical) [14978]

source_name: PBMC

value: primary B cells

value: Pf+ atypical


title: ANON3002 Conv HA I (atypical) [14975]

value: HA+ atypical


title: Fetal oviduct epithelial cell-donor,FOV1-S1231

value: ear

value: Fetal oviduct epithelial cell-donor


title: ANON3002 Conv HA III (classical) [14977]

value: Convalescence


title: RS99

value: Bipolar Disorder, Lithium Responsive

value: 6 week of induction


title: ANON3007 May Pf III (classical) [14974]

value: Pf+ classical

value: May


title: Control_2

first: Yongjie

last: Cai

address: 56 Ling Yuan Xi Road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by  Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base  quality less than or equal to 5) is more than 20%
Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored  in FASTQ format. The clean reads were mapped to the reference genome using HISAT2  (v2.0.4)
Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
The heatmap was drawn by pheatmap (v1.0.8) [5] according to the gene expression in different samples.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimted text files include FPKM values for each Sample

source_name: macrophages

growth_protocol: The RAW264.7 cells were cultured in alpha-minimum essential medium supplemented with 10% fetal bovine serum  at 37 °C under an atmosphere with 5% CO2

extract_protocol:
Total RNA was first extracted with RNAzol
Limited RNA more than 200pg, high-quality was amplified with oligo-dT and dNTPs, incubated at 72 and immediately put back on ice, then reverse transcribed to cDNA based on polyA tail. The template was switched to the 5' end of the RNA and the full-length cDNA was generated by PCR. Agilent 2100 bioanalyzer instrument (Thermo Fisher Scientific, MA, USA) was used to determine the average molecule length of PCR product. Purified cDNA from previous steps was fragmented into small pieces with fragment buffer by PCR, and the product was purified and selected by the Agencourt AMPure XP-Medium kit (Thermo Fisher Scientific, USA). cDNA was quantified by Agilent Technologies 2100 bioanalyzer. The double stranded PCR product undergo QC step was heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was quantitated in two ways in order to ensure the high quality of the sequencing data: Determined the average molecule length used the Agilent 2100 bioanalyzer instrument, quantified library used real-time quantitative PCR (qPCR).The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) 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: RAW264.7 cells were treated with e.coli LPS for 12h

value: RAW264.7 mouse macrophage cell line

value: transfected with nonspecific shRNA


title: RS98

value: iPSC-derived ("Alda cohort")

value: 4 week of induction


title: ANON3007 May HA I (atypical) [14969]

value: male


title: Control_1


title: ANON3002 Conv HA II (activated) [14976]

value: HA+ activated


title: Colon_control_LFD_rep4

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of isotonic control solution (saline), low fat background diet, replicate 4

value: 13 weeks

value: colonic scrapings


title: shMettl3_2

value: transfected with METTL4 shRNA


title: ANON3007 Conv Pf III (classical) [14968]

value: primary B cells


title: leukocytes - spleen - first stimulus with β-Glucan, 3 days after second stimulus with E. piscicida infection

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

data_processing:
Processing of sequencing data was performed with the cellranger pipeline.
Clustering of cells and DEGs analysis was performed using the Seurat R package.
For trajectory analysis using Monocle
Genome_build: Turbot ensembl v98
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Scophthalmus maximus

source_name: spleen

growth_protocol: Turbots were acclimatized in a recirculating tank system with 17 ℃ seawater for two weeks. Edwardsiella piscicida EIB202 was resuscitated with tryptic broth medium and then grown for 12 h in 30°C

extract_protocol:
Leukocytes were obtained by gradient density centrifugation. mRNA was extracted according to to Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (CG000204 Rev B)
Library preparation was performed with all samples using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (CG000204 Rev B)
scRNA-Seq

treatment_protocol: Turbots were intraperitoneally injected with 50 μl β-glucan as first stimulus, 7 days after were immersed with 2×10e8 CFU/ml E. piscicida for 1 h

value: first stimulus with β-Glucan

tag: infection

value: Edwardsilella piscicida EIB202

tag: sampling time

value: 3 days after infection

value: spleen


title: Colon_butyrate_LFD_rep2

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium butyrate, low fat background diet, replicate 2


title: Colon_propionate_LFD_rep2

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium propionate, low fat background diet, replicate 2


title: ANON3007 Conv Pf II (activated) [14967]

value: Pf+ activated

value: Convalescence


title: leukocytes - spleen - first stimulus with PBS, 3 days after second stimulus with E. piscicida infection

tag: treatment

value: first stimulus with PBS


title: shMettl3_1

value: RAW264.7 mouse macrophage cell line

value: transfected with METTL3 shRNA


title: RS97

source_name: neurons

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Bipolar Disorder, Lithium Responsive

value: Bulk

value: 2 week of induction

tag: passage number


title: RS53

value: Bipolar Disorder, Lithium Non-responsive

tag: cell line

value: Sorted

value: Li


title: Colon_butyrate_HFD_rep2

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium butyrate, high fat background diet, replicate 2

tag: strain

value: male

value: 13 weeks

value: colonic scrapings


title: RS96

value: 1 week of induction


title: RS95

source_name: neuronal progenitor cells

value: Neural Progenitor Cells (NPC)


title: ANON3007 Conv HA II (activated) [14964]

tag: cell type

value: primary B cells

value: HA+ activated


title: RS50


title: RS48

value: CTRL


title: leukocytes - spleen - 7 days after first stimulus with β-Glucan

value: first stimulus with β-Glucan

value: mock

value: 7 days after first stimulus

value: spleen


title: leukocytes - head kidney - first stimulus with β-Glucan, 3 days after second stimulus with E. piscicida infection

source_name: head kidney

value: Edwardsilella piscicida EIB202

value: 3 days after infection

value: head kidney


title: leukocytes - head kidney - first stimulus with PBS, 3 days after second stimulus with E. piscicida infection

value: first stimulus with PBS


title: Colon_acetate_LFD_rep2

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium acetate, low fat background diet, replicate 2


title: Colon_control_HFD_rep2

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of isotonic control solution (saline), high fat background diet, replicate 2


title: ANON3008 May Pf III (classical) [14962]

value: female

value: Pf+ classical

value: May


title: Colon_control_LFD_rep2

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of isotonic control solution (saline), low fat background diet, replicate 2

value: male

value: 13 weeks

value: colonic scrapings


title: Colon_butyrate_LFD_rep1

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium butyrate, low fat background diet, replicate 1


title: Colon_propionate_LFD_rep1

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium propionate, low fat background diet, replicate 1


title: leukocytes - spleen - 7 days after first stimulus with PBS


title: ANON3008 May HA III (classical) [14959]

value: primary B cells

value: HA+ classical


title: Colon_acetate_HFD_rep2

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium acetate, high fat background diet, replicate 2


title: ANON3008 May HA II (activated) [14958]

value: HA+ activated


title: ANON3008 May HA I (atypical) [14957]

value: HA+ atypical


title: leukocytes - head kidney - 7 days after first stimulus with PBS

value: mock


title: RS93

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Responsive

value: Bulk

value: 4 week of induction


title: ANON3008 Conv Pf III (classical) [14956]

value: Convalescence


title: ANON3008 May Pf I (atypical) [14960]

value: Pf+ atypical


title: RS91

value: 1 week of induction


title: RS49

value: Sorted

value: VPA


title: RS90

value: Neural Progenitor Cells (NPC)


title: RS94

value: 6 week of induction


title: CHOtige

first: Dawei

last: Wang

address: 197 Ruijin Road II

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
HISAT2 (v2.1.0) software was used for sequence aligment.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CriGri-PICR whole genome using Bowtie2 v2.3.5.
Transcripts Per Million reads (TPM) were calculated using RSEM tool (v1.3.1) from Bo Li et al., BMC Bioinformatics, 2011.
Assembly: Chinese hamster PICR (Cricetulus griseus)
Supplementary files format and content: Matrix table file with abundance measurements for every gene and every sample.

organism: Cricetulus griseus

source_name: cell line

extract_protocol:
The total RNA of CHO cells was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The CHO cells treated with tigecycline (0 mg/ml and 0.2 mg/ml) for 48 h.

value: CHO

value: tigecycline treatment (0.2 mg/ml) for 48 h


title: CHOctrl

value: untreated


title: Colon_acetate_LFD_rep1

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium acetate, low fat background diet, replicate 1

value: male

value: 13 weeks

value: colonic scrapings


title: Colon_butyrate_HFD_rep1

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium butyrate, high fat background diet, replicate 1


title: Colon_acetate_HFD_rep1

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium acetate, high fat background diet, replicate 1


title: RS46

extract_protocol:
 Cells (~5x106 cells) were collected in RNA-Bee solution (Tel-Test, Inc) and total RNA was extracted using the DNA-Free RNA Kit (Zymo Research) according to the manufacturer’s instructions.
Stranded mRNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions. All libraries were then quantified, pooled and sequenced at single-end 50 bp reads on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing (NGS) Core at a depth of approximately 40 million reads per library.
stranded mRNA

value: iPSC-derived ("Alda cohort")


title: Colon_control_LFD_rep1

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of isotonic control solution (saline), low fat background diet, replicate 1


title: leukocytes - head kidney - 7 days after first stimulus with β-Glucan

value: first stimulus with β-Glucan

value: mock

value: 7 days after first stimulus

value: head kidney


title: ANON3008 Conv HA III (classical) [14953]

source_name: PBMC

value: primary B cells

value: female

value: HA+ classical

value: Convalescence


title: RS47

value: Bipolar Disorder, Lithium Responsive

value: Sorted

value: Li


title: ANON3008 Conv Pf I (atypical) [14954]

value: Pf+ atypical


title: GL261, input, IR

city: Fuzhou

first: Fei

last: Huang

address: No 20 Chazhong Road

institute: First Affiliated Hospital, Fujian Medical University

data_processing:
After trimmed to get the clean daya by the software fastq, reads were were aligned to the mouse genome (mm10) using the BWA algorithm.
The resulting histograms (genomic ‘‘signal maps’’) were stored in bigWig files.
The signals in the 2KB region upstream and downstream of transcription initiation site (TSS) were counted by using the computematrix module of deeptools software.
The data was visualized and analyzed using Integrative Genomics Viewer (IGV) genome browser.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sonicated using a sonicator.
The resulting lysates, in which DNA fragments with the requested sizes (300-500bp), were pre-incubated with protein A Agarose beads for 30 min at 4 °C. Later, 10 μg indicated antibodies were used to incubate the lysates overnight at 4 °C. At the second day, protein A Agarose beads were added to bind antibodies and targeted proteins for two or three hours at 4 °C.  The bound DNA and protein immunocomplexes were eluted with elution buffer (25 mM Tris, pH 8.0, 10 mM EDTA, 0.5% SDS) at 65 °C with occasional vortex for 15 min after washed four times sequentially with salt buffers. Then the products gotten were reversed crosslinking by 1mg/mL protease K overnight at 65 °C. Then immunoprecipitated DNAs and input DNAs were finally purified by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation.
The sequencing library preparation was carried out by Novogene (Beijing, China). ChIP libraries were sequenced using Illumina HiSeq or NovaSeq at 150 bp PE reads.

value: Mice glioblastoma

tag: chip antibody


title: WT_2

city: Beijing

first: Wang

middle: Zhi

last: rong

address: 2#, Yuanmingyuan West Road,100193 Beijing, China

institute: China Agricultural University

data_processing:
Illumina Novaseq 6000 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SL4.0 whole genome.
Transcripts Per Million reads of library size were calculated.
Genome_build: SL4.0
Supplementary_files_format_and_content: tab-delimited text files include tpm values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Solanum lycopersicum

source_name: leaf

extract_protocol:
Total RNA was isolated from the tomato samples with the RNAeasy Plant Kit (Huayueyang Company) . RNA-seq was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the fourth leaf of three-week-old WT, slwrky37-CR and SlWRKY37-OE plants were individually collected with three biological replicates for RNA-seq

value: leaf

tag: tag

value: wild type (Micro Tom)

value: three-week


title: WT_3

tag: age


title: WRKY37_OE_3

value: WRKY37 overexpressed line


title: RS92

first: April

address: 10010 N Torrey Pines Rd

data_processing:
Sequenced reads were quality-tested using FASTQC.
Reads were trimmed with SolexaQA++ dynamic trim [54] and the aligned to GRCh38 with STAR.
Counts were normalized to transcripts per million (TPM) and then log + 1 transformed for all visualizations.
Differential expression was calculated using the software edgeR (v3.26.8) [56]. Raw counts were formatted into a DGE list and filtered for genes with counts > 1 in at least 3 samples. In order to capture all gene expression changes in response to VPA all genes with counts > 0 in at least 1 sample were used. Counts were then normalized with the TMM method. Dispersion was estimated in three steps. First common dispersion was calculated with the conditional maximum likelihood method, followed by tagwise dispersion as a moving average, and then trended dispersion calculated as a spline. These dispersions were then used to calculate differential expression between the relevant two groups. P-values were then adjusted for multiple-testing using the p.adjust function in R (v3.6.1) with the fdr method. To identify the number of genes differentially expressed we used an FDR < 0.05 with no minimum logFC. In the case where differences in expression were calculated as a function of time, these were calculated using the edgeR GLM function with expression as a function of time + disease status. For bulk analyses, days 8-42 were combined and tested as a function of disease status using the described exact test functions. Results were reported as volcano plots with fold change transformed using base 2 and raw p-values transformed using base exp(1).
Functional enrichment analysis was performed using DAVID bioinformatics (v6.8) [57, 58]. All genes with FDR < 0.05 for a given differential expression test were uploaded as a gene list in official gene symbol format and corrected against the Homo sapiens background. A functional annotation chart was then calculated from the results.
Principal component analysis was performed on TPM values using the package pcaMethods (v1.76.0) with the svd algorithm.
LEF1 predicted downstream targets were identified using the Transfac database (gene id = 51176).
Genome_build: hg38
Supplementary_files_format_and_content: Transcripts Per Million normalized expression table as a tab-separated text file

source_name: neurons

value: iPSC-derived ("Alda cohort")

value: Bulk

value: 2 week of induction


title: WT_1


title: ANON3008 Conv HA II (activated) [14952]

tag: gender

tag: subset

value: HA+ activated


title: RS69

tag: cohort

value: 6 week of induction


title: Colon_propionate_HFD_rep2

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium propionate, high fat background diet, replicate 2

value: male

value: 13 weeks

value: colonic scrapings


title: Colon_control_HFD_rep1

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of isotonic control solution (saline), high fat background diet, replicate 1


title: Colon_control_LFD_rep3

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of isotonic control solution (saline), low fat background diet, replicate 3


title: ANON3003 May Pf III (classical) [14950]

value: primary B cells

value: female

value: Pf+ classical

tag: season

value: May


title: ANON3008 Conv Pf II (activated) [14955]

value: Pf+ activated

value: Convalescence


title: ANON3003 May Pf I (atypical) [14948]

value: Pf+ atypical


title: WRKY37_OE_1

value: leaf

value: three-week


title: WRKY37_OE_2

value: WRKY37 overexpressed line


title: RS45

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Responsive

tag: sorted/bulk

value: Sorted

value: CTRL

tag: clone


title: Total lung RNA isolated from TGFalpha mice on Dox for 6weeks treated pirfenidone [VS12]

city: Cincinnati

first: Anil

last: Jegga

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics

institute: Cincinnati Children's

description:
BT Dox + Pirfenidone 3
TGFalpha mice on Dox for 6weeks treated Pirfenidone

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Assembly: mm10
Supplementary files format and content: tab delimited raw counts with genes in rows and samples in columns

source_name: Lungs

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: Dox for 6weeks treated Pirfenidone

tag: genotype

value: TGFalpha


title: ANON3003 May HA I (atypical) [14945]

value: HA+ atypical


title: Colon_propionate_HFD_rep1

source_name: colonic scrapings, 4 hrs after last infusion with 80 ul of 100mM  isotonic solution of sodium propionate, high fat background diet, replicate 1

value: male

value: 13 weeks

tag: tissue

value: colonic scrapings


title: ANON3008 Conv HA I (atypical) [14951]

value: primary B cells

value: female


title: RS68

tag: disease state

value: Bulk

tag: treatment

value: 4 week of induction


title: RS66

tag: cell line

value: 1 week of induction

tag: passage number


title: Total lung RNA isolated from TGFalpha mice on Dox for 6weeks treated vehicle [VS6]

description:
BT Dox 3
TGFalpha mice on Dox for 6weeks treated vehicle

value: Dox for 6weeks treated vehicle


title: ANON3003 Conv Pf III (classical) [14944]

tag: cell type

value: Pf+ classical

value: Convalescence


title: GL261, H3K27me3, Con

value: Mice glioblastoma

tag: chip antibody


title: Total lung RNA isolated from TGFalpha mice on Dox for 6weeks treated pirfenidone [VS11]

description:
BT Dox + Pirfenidone 2
TGFalpha mice on Dox for 6weeks treated Pirfenidone


title: Total lung RNA isolated from TGFalpha mice on Dox for 6weeks treated pirfenidone [VS10]

description:
BT Dox + Pirfenidone 1
TGFalpha mice on Dox for 6weeks treated Pirfenidone


title: RS65

source_name: neuronal progenitor cells

value: iPSC-derived ("Alda cohort")

value: Bipolar Disorder, Lithium Responsive

value: Neural Progenitor Cells (NPC)


title: WRKY37_CR_1

value: leaf

tag: tag

value: WRKY37 mutant

value: three-week


title: ANON3003 Conv Pf II (activated) [14943]

tag: age

value: Pf+ activated


title: GL261, input, Con


title: ANON3003 Conv Pf I (atypical) [14942]

tag: gender

value: Pf+ atypical


title: RS31

value: Sorted

value: VPA


title: RS67

value: Bulk

value: 2 week of induction


title: RS32

value: Li


title: Total lung RNA isolated from TGFalpha mice on Dox for 6weeks treated vehicle [VS5]

description:
BT Dox 2
TGFalpha mice on Dox for 6weeks treated vehicle

value: Dox for 6weeks treated vehicle

value: TGFalpha


title: ANON3003 Conv HA III (classical) [14941]

value: primary B cells

value: female

tag: subset

value: HA+ classical

value: Convalescence


title: RS64

tag: cohort

value: iPSC-derived ("Alda cohort")

value: Control

value: 6 week of induction


title: Total lung RNA isolated from control mice treated with vehicle [VS3]

description:
ST3 Normal 3
Control mice treated with vehicle

value: vehicle


title: WRKY37_CR_2

value: leaf

value: WRKY37 mutant

value: three-week


title: 961276

city: Durham

first: Wendell

last: Jones

address: 2400 Ellis Rd

institute: Q2 Solutions

hyb_protocol: Samples were hybed (capture probes) based on the typical NanoString protocol

scan_protocol: Samples were scanned based on the typical NanoString protocol on the nCounter instrument

data_processing: Samples were normalized between batches using common samples that had sufficient detection.  Some samples have more than 1 NanoString cartridge.  The cartridge with the highest level of detection was brought forward.  Genes were then separated into cancer-related and immune related genes.  Immune genes were scaled to a common log2 value of 8 across samples using the entire NanoString sample profile(immune and cancer gene expression).  Cancer genes were normalized separately to attempt to estimate the relative expression in non-immune cells as samples varied widely in tumor purity.  Cancer genes were also normalized to a common log2 value of 8 but only using the sample profile of the cancer (non-immune) genes.

source_name: uterine serous cancer

label_protocol: Isolated RNA was assessed by sample source using TapeStation for the percentage of fragments (fragmentation score) between 50 and 300 nt.  Based on a linear function that increased input for higher fragmentation scores, the input level for samples ranged from 100 ng to 1000 ng in proportion to the fragmentation score (higher scores implied higher levels of fragmentation which led to higher input levels to the assay).  After the first round of testing, all 60 samples were evaluated for provenance and consistency between paired samples.  Several samples were repeated at the same or higher input levels to potentially boost detection rates for some samples that initially had low detection rates.  Analysis went forward with the best of the two runs for each sample based on detection rates. A small subset of samples (patient ID #1 Met, patient ID #9 Met and Primary, patient ID #12 Met, patient ID #20 Distant Met, and patient ID#28, Primary) yielded unacceptable NanoString results from either run.

extract_protocol: Archived formalin-fixed paraffin-embedded tumor blocks of paired primary and metastatic tumor from 29 patients with complete clinical treatment/response information were used to obtain 5-8 unstained slides sectioned at 10-micron thickness. The unstained tissue sections were used for extraction of RNA and DNA.  We used Qiagen’s Allprep DNA/RNA FFPE kit to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections.  DNA and RNA were released sequentially by differential solubilization of the same FFPE sample.  FFPE tissue sections were first deparaffinized using xylene.  The tissue was then digested with proteinase K to enable cell lysis and release of the RNA into the supernatant while the DNA and other insoluble material are precipitated.  The sample was then centrifuged to separate the RNA containing supernatant from the DNA containing pellet.  The RNA containing supernatant was heated to partially reverse formalin crosslinks before application to a RNeasy Mini spin column where the total RNA was bound to the membrane.  An on-column DNase digestion was performed to ensure purification of DNA-free RNA.  Following DNase digestion, contaminants were removed through column washing and total RNA was eluted in Nuclease-free water.

value: metastatic USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:M

tag: wes data (small variants/cn) (x if present)

value: X

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

tag: plk3 est. cn

tag: plk3 cna call

value: Gain+

tag: tp53 cna call

value: Gain

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: GL261, H3K27me3, IR

tag: cell line

tag: cell type

value: Mice glioblastoma

tag: chip antibody


title: ANON3003 May HA III (classical) [14947]

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: HA+ classical

tag: season

value: May


title: ANON3003 Conv HA II (activated) [14940]

value: HA+ activated

value: Convalescence


title: RS30

last: Williams

institute: Salk Institute for Biological Studies

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

value: Bipolar Disorder, Lithium Responsive

tag: sorted/bulk

value: Sorted

tag: treatment

value: CTRL

tag: clone

tag: passage number


title: 961277

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: plk3 est. cn

tag: plk3 cna call

tag: tp53 cna call

value: Loss

tag: log2 ratio plk3 locus


title: Total lung RNA isolated from control mice treated with vehicle [VS2]

description:
ST2 Normal 2
Control mice treated with vehicle

tag: agent

value: vehicle

tag: genotype

value: Control


title: ANON3003 Conv HA I (atypical) [14939]

tag: cell type

value: primary B cells

tag: gender

value: female

tag: age

tag: subset

value: HA+ atypical

tag: season


title: 961275

description:
USC34P
Censored data (time=outcome)

tag: tissue

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

value: PtS-NED

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

tag: ethnicity (self-reported)

tag: tumor stage

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

value: LN

tag: site of recurrence

value: X

value: Gain

tag: plk3 adj. est. cn (for tumor purity)

tag: tp53 adj. est cn (for tumor purity)

tag: tcellextrect (est tcell proportion)-dna


title: RS110

tag: cohort

value: iPSC-derived ("Alda cohort")

tag: disease state

tag: cell line

tag: sorted/bulk

value: Bulk

tag: treatment

value: 4 week of induction

tag: clone

tag: passage number


title: Total lung RNA isolated from control mice treated with vehicle [VS1]

description:
ST1 Normal 1
Control mice treated with vehicle

tag: agent

tag: genotype


title: ANON3005 May Pf III (classical) [14938]

tag: cell type

tag: gender

tag: age

tag: subset

value: Pf+ classical

tag: season

value: May


title: RS62

value: 2 week of induction


title: ANON3005 May Pf I (atypical) [14936]

value: Pf+ atypical


title: Total lung RNA isolated from TGFalpha mice on Dox for 6weeks treated vehicle [VS4]

description:
BT Dox 1
TGFalpha mice on Dox for 6weeks treated vehicle

value: Dox for 6weeks treated vehicle

value: TGFalpha


title: 961273

description:
USC33P
Censored data (time=outcome)

tag: tissue

value: primary USC

tag: clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease)

tag: age of patient at time of surgery

tag: population group  or ancestry (genomic analysis)

value: Afr

tag: ethnicity (self-reported)

value: AA

tag: tumor stage

value: IIIC

tag: date of last chemo- therapy

tag: date of recurrence

tag: date of death

tag: time to recurrence (ttr in months) \

tag: overall survival (os in months)

tag: time to recurrence (months) - censored data - 1 implies censored

tag: overall survival (months) - censored data - 1 implies censored

tag: site of metastasis

tag: site of recurrence

tag: sample_name (matched primary-met)

tag: tumor type

value: M-Metastatic,   D-Distant,   P-Primary:P

tag: wes data (small variants/cn) (x if present)

tag: nanostring io 360 expression data (x if present)

tag: tumor purity estimate from wes analysis

tag: favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable

tag: plk3 est. cn

tag: plk3 cna call

value: Normal

tag: tp53 cna call

tag: log2 ratio plk3 locus

tag: plk3 adj. est. cn (for tumor purity)


title: RS61

tag: cohort

tag: disease state

value: Control

tag: cell line

tag: sorted/bulk

tag: treatment

value: 1 week of induction

tag: clone

tag: passage number