title: QBC939_PBS_rep2

first: Xiaoqiang

state: Shanghai

address: No.130 Dongan Road

department: Institutes of Biomedical Sciences

institute: Fudan University

description: Treated cell lines with PBS.

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count.
Differential expression analysis was performed using the DESeq (2012) R package. P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression.
Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed to demonstrate the expression pattern of genes in different groups and samples.
GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.count.txt: Read counts table files.

source_name: QBC939 cell line

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

tag: cell line

value: PBS

tag: replication


title: QBC939_PBS_rep3

status: Public on Dec 31 2022

type: SRA

city: Shanghai

last: Chai

country: China

description: Treated cell lines with PBS.

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment


title: ChIP_ESC_Ola_H3K27me3_IFNb_6h_Rep1

city: Heidelberg

first: Markus

last: Muckenhuber

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

library_source: genomic

data_processing:
ATAC-seq bam files: Raw reads were trimmed by Trimmomatic (v0.36) and mapped using Bowtie2 (v2.3.3.1). The mapped reads were with bedtools (v2.27.1) sorted, shifted by +4/-5bp to correct for transposase intragtion bias, duplicates and reads in blacklisted reads removed. Reads with quality score below 30 were removed.
ATAC-seq bed files: The sorted and quality filtered bam files were used for peak calling by MACS2 (v2.1.2).
ATAC Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control.
ChIP bed files: Raw reads were mapped with Bowtie (v1.2.2). The mapped reads were sorted, duplicates and reads in blacklisted regions removed with bedtools (v2.27.1).
ChIP Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control. For histon marks H3 signal was the control. For STAT ChIPs IgG_Rb_CST.
RNA-seq raw counttable: Ribosomal RNAs were removed by SortMeRNA (v2.1). Raw reads were aligned with STAR (v2.5.3a) and Aligned.sorted.ByCoord.out.bam and Aligned.to.Transcriptome.out.bam were created. STAR counted reads per genes in ReadsPerGene.out.tab files. These files were combined and the resulting raw count-table was the input for DESeq2.
RNA-seq count table TPM and FPKM: Ribosomal RNAs were removed by SortMeRNA (v2.1). Raw reads were aligned with STAR (v2.5.3a) and Aligned.sorted.ByCoord.out.bam and Aligned.to.Transcriptome.out.bam were created. The  Aligned.to.Transcriptome.out.bam files from STAR were used as input for RSEM (v1.3.0) to create TPM and FPKM values.
RNA-seq DESeq result tables: Result tables for DESeq2 (1.24.0) for the comparisons of 1h IFNb with 0h; 6h IFNb with 0h and 6h with 1h IFNb.
scATAC-seq: Raw reads were applied to CellRanger (v1.1.0), a full automatic pipeline especially for scATAC-seq data done by the 10x Chromium.
scATAC-seq: The default output counttable for downstream analysis.
scRNA-seq: Raw reads were applied to CellRanger (v1.3.1), a full automatic pipeline especially for scRNA-seq data done by the 10x Chromium.
scRNA-seq counttable: The default output folders with the counttable for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq bam files: Quality filtered mapped read files
Supplementary_files_format_and_content: ATAC-seq bed files: File containing coordinates of peaks and enrichment scores by MACS2
Supplementary_files_format_and_content: ChIP-seq bed files: File containing coordinates of peaks and enrichment scores by MACS2
Supplementary_files_format_and_content: ChIP-seq peak list for STAT1 and STAT2 by DiffBind: Peak lists for STAT1p701 and STAT2 replicates were anaylzed by DiffBind (v2.12.0) to create list of robust binding sites over replicates. Peaks at 1h and 6h of IFNb treatment were combined
Supplementary_files_format_and_content: RNA-seq raw counttable: Counttable containing ENSEMBL gene ID and the raw read counts for each gene over the replicates in ESCs, MEFs and NPCs
Supplementary_files_format_and_content: RNA-seq count table TPM and FPKM: Counttable with normalized TPM and FPKM values for each samples of ESCs, MEFs and NPCs. In addtition, the ENSEMBL gene ID, all transcript Ids and the annotated gene length.
Supplementary_files_format_and_content: RNA-seq DESeq result tables: Results table from DESeq2 of all genes for the three compariosns of 1h vs 0h, 6h vs 0h and 6h vs 1h. Each files contains the ENSEMBL gene ID, the normalized counts for all used samples, the base mean expression, the log2 fold change of the comaprison, the standard error of the log2 fold change, the Wald statistic, pvalue and adjusted pvalue.
Supplementary_files_format_and_content: scATAC: Counttable with a the coordinates of mapped fragments, the barcode of the fragment and the counts.
Supplementary_files_format_and_content: scRNA-seq: The folder contains the deault output of Cellranger. A list of detected barcodes in the sample. A List of identified genes in the sample as ENSEMBL ID and gene symbole. And a matix which is the counttable.

molecule: genomic DNA

organism: Mus musculus

growth_protocol:
Embryonic stem cells: Cultured on 0.1 % gelatinized tissue flasks in ESC media. Cells were incubated at 37 °C and 5 % CO2. Media was PowerStem ESPro1 (PAN-Biotech; P04-77510K) with self-made LIF (1:1000).
Mouse embryonic fibroblasts: Cells were incubated at 37 °C and 5 % CO2. Media was DMEM (Gibco, 11880-28), 10% FCS (PAN-Biotech; P30-3602), 1x L-Glutamine (PAN-Biotech, P04-80050), 1x PenStrep (PAN-Biotech, P06-07050).
Neural progenitor cells: ESCs were differentiated into NPCs based on the Bible-protocol Bibel et al. 2007. 4-5*10^6 cultured ESCs were split onto a T75 UltraLow-BindingPlates (Corning, 3814) in 15 ml StemPAN media (PAN-biotech, P08-50500). After 4 days 5µM retinoic acid (Sigma-Aldrich, R2625) was added. On day 8, cells were platted on plates coated with 1% Matrigel (Corning, 356230) in neuronal base medium (Gibco, 211103049), G5 supplements (Gibco, 17503012), NSC supplements (Gibco, 17502048). Experiments were performed five days after neuronal plating.

extract_protocol:
ATAC-seq: . For ESCs, the cell pellet was resuspended in 200 µl ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl2, 3 mM MgCl2, 0.1 % NP-40) and incubate for at room temperature for 2 min. 20 µl ATAC reaction buffer containing 10 µl 2x transposase buffer and 2.5 µl Tn5 enzyme (Illumina) was added and samples were incubated at 37 °C for 30 min. Samples were purified. For MEFs, the lysis buffer contained additionally 1 % digitonin.
ATAC-seq: Purified samples were directly amplifed, barcoded and purified.
ChIP-seq for histone marks in ESC: Cells were crosslinked by 1 % Formaldehyde for 10 min at room temperature and stopped with 125 mM Glycine for 5 min. Samples of around 40 million cells were treated with 40 U of MNase for 15 min at 37 °C. The samples were shared for 15 min (Burst 200; Cycle 20%; Intensity 8). Replicate 1 was shared for 30 min and no MNase treatment was performed. 4µg of antibody was used per sample and incubated for 2 hours at 4 °C. Protein G-beads were added over night. Multiple low and high salt washes were performed and the samples were eluted. Samples were reverse crosslinked and stored at -20°C.
ChIP-seq for histone marks in ESCs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)
ChIP-seq for STATs in ESCs and MEFs: The isolation of the chromatin was done with Simple ChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003)
ChIP-seq for STATs in ESCs and MEFs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)
RNA-seq: Total RNA was isolated using NucleoSpin RNA Plus Kit (Macherey-Nagel, 740984.250). Depletion of rRNA was done with Ribo-Zero rRNA Removal Kit (Illumina, 15066012) for ESCs and MEFs and with NEBNext® rRNA Depletion Kit (New England Biolabs, E6350).
RNA-seq: Libraries were prepared using NEBNext Ultra II Directional  RNA Library Prep Kit for Illumina (New England Biolabs, E7760).
scATAC-seq: The experiment was performed based on the standard manufacturer’s protocol Chromium Single Cell ATAC Reagent Kits (PN-1000110).
scRNA-seq: The experiment was performed based on the standard manufacturer’s protocol of Chromium Single Cell 3’ Reagent Kits v2 (PN-120237).

treatment_protocol: All cells were treated with 500U/ml of self-made interferon beta (16.6U/µl) for 1 hour or 6 hours

tag: strain

tag: cell type

value: Embryonic stem cells

tag: chip antibody


title: ChIP_ESC_Ola_H3K27me3_IFNb_6h_Rep3


title: ChIP_ESC_Ola_H3K4me1_IFNb_6h_Rep2


title: ChIP_ESC_Ola_H3K27me3_IFNb_1h_Rep2


title: ChIP_ESC_Ola_H3K27me3_IFNb_1h_Rep1


title: QBC939_PBS_rep1

description: Treated cell lines with PBS.


title: JH10_NHEK-Ad_lane 7

city: Rochester

first: Akhilesh

last: Pandey

state: Minnesota

address: 200 First Street SW

department: Laboratory Medicine and Pathology

country: USA

institute: Mayo Clinic

description: lane 7

data_processing:
Demultiplexed and base calling using bcl2fastq v1.8.4 of CASAVA v1.8
Alignment against hg38 using STAR-2.5.2
Alignment file processing using samtools-1.3.1
long non-coding RNA analysis using UClncR v1.0.9 (Mayo Clinic, Rochester, MN)
Genome_build: hg38
Supplementary_files_format_and_content: Read counts per gene

source_name: Epidermal Keratinocytes Adult

growth_protocol: Primary human cells were acquired from Lonza and cultured following the manufacturer’s specifications.

extract_protocol:
Ribosomal RNA depletion
TruSeq stranded mRNA library

value: Keratinocytes

tag: tissue origin

value: Skin

tag: life stage

value: Adult


title: QBC939_BF_rep3

description: Treated cell lines with BF supernatant.

value: Burkholderia fungorum


title: JH10_NHEK-Ad_lane 6

description: lane 6


title: ChIP_ESC_Ola_H3K27me3_IFNb_0h_Rep3


title: JH11_NHEK-Neo_lane 3

description: lane 3

source_name: Epidermal Keratinocytes Neonatal

value: Neonatal


title: JH10_NHEK-Ad_lane 5

description: lane 5


title: QBC939_BF_rep2

description: Treated cell lines with BF supernatant.


title: JH10_NHEK-Ad_lane 4

description: lane 4


title: ChIP_ESC_Ola_H3K27me3_IFNb_0h_Rep1


title: ChIP_ESC_Ola_H3K27ac_IFNb_6h_Rep2


title: JH11_NHEK-Neo_lane 1

description: lane 1


title: QBC939_BF_rep1

description: Treated cell lines with BF supernatant.


title: ChIP_ESC_Ola_H3K27ac_IFNb_1h_Rep2


title: ChIP_ESC_Ola_H3K27ac_IFNb_6h_Rep1


title: ChIP_ESC_Ola_H3K27ac_IFNb_1h_Rep1


title: ICC_tumor_tissue

description:
ICCT
Using our analysis method, the bacterial content of various cells in tumor tissues can be quantified. This transcriptome sequencing dataset can be used for the quantification of bacteria.

data_processing:
Raw reads were processed to generate gene expression matrices using an internal pipeline.
Reads with the same cell barcode, UMI and gene were grouped together to generate the number of UMIs per gene per cell.
Adapters and polyA tails were trimmed before aligning read two to GRCh38 with ensemble version 92 gene annotation.
The tSNE projection of the data was calculated similar to previous mentioned.
Seurat FindClusters function was applied to obtain cell clusters with resolution 0.8. Cell types were assigned based on their canonical markers.
Genome_build: human GRCh38
Supplementary_files_format_and_content: gene expression matrix

molecule: polyA RNA

source_name: ICC patient

extract_protocol:
Fresh tissue samples were collected and immediately stored in the GEXSCOPE Tissue Preservation Solution (Singleron Biotechnologies) at 2-8°C. Prior to tissue dissociation, the specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times and minced into 1–2 mm pieces. The tissue pieces were digested in 2ml GEXSCOPE Tissue Dissociation Solution (Singleron Biotechnologies) at 37°C for 15min in a 15ml centrifuge tube with continuous agitation. Following digestion, a 40-micron sterile strainer (Corning) was used to separate cells from cell debris and other impurities. The cells were centrifuged at 1000 rpm, 4°C , for 5 minutes and cell pellets were resuspended into 1ml PBS (HyClone). To remove red blood cells, 2 mL GEXSCOPE Red Blood Cell Lysis Buffer (Singleron Biotechnologies) was added to the cell suspension and incubated at 25°C for 10 minutes. The mixture was then centrifuged at 1000 rpm for 5 min and the cell pellet resuspended in PBS. Cells were counted with TC20 automated cell counter (Bio-Rad).
The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS. Single cell suspension was then loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies). The resulting single cell RNA-seq libraries were sequenced on an Illumina HiSeq X10 instrument with 150bp paired end reads.

tag: tissue

value: tumor tissue

tag: tumor type

value: intrahepatic cholangiocarcinoma

tag: tumor stage

value: II


title: JH10_NHEK-Ad_lane 2

description: lane 2


title: ICC_paracancer_tissue

description:
ICCP
Using our analysis method, the bacterial content of various cells in tumor tissues can be quantified. This transcriptome sequencing dataset can be used for the quantification of bacteria.


title: ChIP_ESC_Ola_H3K27ac_IFNb_0h_Rep1


title: ICC_plasma

description:
ICCB
Using our analysis method, the bacterial content of various cells in tumor tissues can be quantified. This transcriptome sequencing dataset can be used for the quantification of bacteria.

value: plasma


title: ChIP_ESC_Ola_H3K27me3_IFNb_0h_Rep2


title: ChIP_ESC_Ola_H3_IFNb_6h_Rep3


title: ChIP_ESC_Ola_H3_IFNb_6h_Rep1


title: H1_WT+Dox

city: Guangzhou City

first: Denghui

last: Chen

address: No. 74 Zhongshan 2nd Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

data_processing:
Sequencing quality of all high-throughput sequencing data were first comprehensively examined by FastQC. whose results were parsed using MultiQC. Next, adapter sequences and bases with sequencing quality < 20 were trimmed from raw data by TrimGalore.
Trimmed read pairs were aligned to genome with STAR.
We computed the number of mapping reads unambiguously attributed to each gene and repeat locus using the featureCounts package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Embryonic stem cells

growth_protocol: hESCs were cultured in matrigel-coated plates in the Essential 8TM hESC medium (Thermo, catalog. no. A1517001). The medium was changed daily. hESCs were treated with 0.48 mM EDTA for dissociation and then passaged onto new Matrigel -coated plates every 4–5 days.

extract_protocol:
Total RNA was extracted from  hESCs using the Trizol kit (Thermo Fisher Scientific, catalog. no. 15596018) following the manufacturer’s instructions. PolyA(+) RNA was isolated for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iCas9 or idCas9 hESC lines were generated by transfecting with PB-TRE-CAS9-PGK-puro-T2A-rtTA (50 ng) or PB-TRE-dCAS9-PGK-puro-T2A-rtTA plasmids (50 ng) plus transposase mPB.Cas9 (dCas9) was inducible by doxycycline (Dox) in these cells.

value: embryonic stem cells


title: ChIP_ESC_Ola_H3_IFNb_1h_Rep2


title: JH08_NHCF-V_lane 7

description: lane 7

source_name: Cardiac Fibroblasts

value: Fibroblasts

value: Heart


title: H1_iCas9+Dox


title: JH08_NHCF-V_lane 6

description: lane 6


title: ChIP_ESC_Ola_H3_IFNb_0h_Rep3


title: JH10_NHEK-Ad_lane 3

description: lane 3


title: ChIP_ESC_Ola_H3_IFNb_0h_Rep2


title: H9_WT


title: ChIP_ESC_Ola_H3_IFNb_0h_Rep1


title: ChIP_ESC_Ola_H3_IFNb_1h_Rep1


title: H9_WT+Dox


title: ChIP_ESC_Ola_H3_IFNb_6h_Rep2


title: JH10_NHEK-Ad_lane 1

description: lane 1


title: JH08_NHCF-V_lane 5

description: lane 5


title: JH08_NHCF-V_lane 8

description: lane 8


title: JH08_NHCF-V_lane 4

description: lane 4


title: brain503

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Read count for each Sample

source_name: brain

extract_protocol:
Total RNA was extracted using the TRIZOL following the manufacturer's instructions.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina

value: brain

tag: age

value: rGDF11 treatment 30 days


title: brain502


title: brain501


title: JH08_NHCF-V_lane 3

description: lane 3


title: brain505


title: H9_iCas9


title: blood502

source_name: blood

value: blood


title: blood503


title: JH08_NHCF-V_lane 2

description: lane 2


title: JH08_NHCF-V_lane 1

description: lane 1


title: blood501


title: H9_idCas9+Dox


title: blood504


title: ChIP_ESC_Ola_H3_IFNb_1h_Rep3


title: brainstem_502

source_name: brainstem

value: brainstem


title: JH07_NHDF-Neo_lane 7

description: lane 7

source_name: Dermal Fibroblast Neonatal


title: H9_iCas9+Dox


title: brainstem_503


title: brainstem_501


title: brain504


title: ID_3e

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: Stromal cells treated with bleomycin in culture

data_processing:
Illumina Casava1.7 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p10 using bowtie v1.1.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Transcripts Per Million fragments mapped (TPM) were calculated using a protocol from Tajnik et al. Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Research. 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text files include count and TPM values for each Sample

source_name: Primary normal prostate stromal cells_bleomycin

growth_protocol: Prostate stromal cells were routinely cultured and passaged (typically 0.5–1 × 106 cells in a T75 flask) in stroma-specific media supplemented with 10% FBS.

extract_protocol:
At the end of cell culture, media were collected and processed for sedimentation of extracellular vesicles via consecutive ultracentrigation. Final products were subject to lysis to release total RNAs. Illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101, RS-122-2102) was used with 1 ug of total RNA for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Upon 80% confluency, cells were treated with 50 μg/ml bleomycin in culture for consecutive 7-10 days, with the media changed every 2-3 days.

value: Primary normal human prostate stromal cells

tag: source

value: Derived from the prostate tisue of a human patient

value: treated with bleomycin in culture


title: brainstem_505


title: H9_idCas9


title: ID_2e


title: brainstem_504


title: ID_1e


title: JH07_NHDF-Neo_lane 6

description: lane 6

value: Skin


title: Cerebellum_501

source_name: Cerebellum

value: Cerebellum


title: Cerebellum_503


title: JH07_NHDF-Neo_lane 8

description: lane 8

value: Neonatal


title: JH07_NHDF-Neo_lane 5

description: lane 5


title: IC_3e

description: Stromal cells untreated in culture

source_name: Primary normal prostate stromal cells_untreated

value: untreated in culture


title: ChIP_ESC_Ola_H3K27ac_IFNb_0h_Rep2

value: Embryonic stem cells


title: Cerebellum_504


title: JH07_NHDF-Neo_lane 4

description: lane 4


title: Cerebellum_505


title: heart501

source_name: heart

value: heart


title: JH07_NHDF-Neo_lane 3

description: lane 3


title: heart502


title: IC_2e

description: Stromal cells untreated in culture


title: IC_1e

description: Stromal cells untreated in culture


title: JH07_NHDF-Neo_lane 2

description: lane 2


title: heart504


title: JH07_NHDF-Neo_lane 1

description: lane 1


title: TMEM43-WT_6, 19 months old

city: Wuerzburg

first: Miriam

last: Zink

address: Am Schwarzenberg

institute: University Hospital Wuerzburg

data_processing:
Sequencing was performed at 25 million reads/sample with 75 nt read length on the NextSeq 500 platform (Illumina)
Illumina reads were quality- and adapter-trimmed via Cutadapt version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded
Processed reads were subsequently mapped to the zebrafish genome (GRCz11) using STAR v2.7.2b with default parameters.
Read count were generated using featureCounts v1.6.4 from the Subread package
Assembly: GRCz11
Supplementary files format and content: Excel file including raw counts of each gene for each sample

organism: Danio rerio

growth_protocol: Zebrafish were maintained under standard condition at a constant temperature of 28 °C with a daily cycle of 14 h light/10 h dark.

extract_protocol:
RNA was harvested using Qiazol (Qiagen). 150 ng of total RNA was used for the preparation of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions

treatment_protocol:
None
None

tag: genotype

value: TMEM43-WT overexpression

tag: time

value: 19 months


title: Hippocampus501

source_name: Hippocampus

value: Hippocampus


title: Cerebellum_502


title: Hippocampus502


title: Hippocampus504


title: TMEM43-WT_4, 18 months old

value: 18 months


title: Hippocampus505


title: JH06_NHDF-Ad_lane 7

description: lane 7

source_name: Dermal Fibroblast Adult

value: Fibroblasts

value: Adult


title: JH06_NHDF-Ad_lane 8

description: lane 8


title: JH06_NHDF-Ad_lane 6

description: lane 6


title: TMEM43-p.S358L_4, 19 months old

value: TMEM43-p.S358L overexpression


title: midbrain_502

source_name: midbrain

value: midbrain

value: rGDF11 treatment 30 days


title: TMEM43-WT_5, 20 months old

value: 20 months


title: midbrain_503


title: midbrain_501


title: TMEM43-WT_1, 5 months old

value: 5 months


title: JH06_NHDF-Ad_lane 5

description: lane 5

value: Skin


title: TMEM43-p.S358L_3, 5 months old


title: heart503


title: JH06_NHDF-Ad_lane 4

description: lane 4


title: TMEM43-p.S358L_2, 5 months old


title: muscle504

source_name: muscle

value: muscle


title: muscle501


title: muscle502


title: midbrain_505


title: muscle503


title: JH06_NHDF-Ad_lane 3

description: lane 3


title: heart505


title: JH06_NHDF-Ad_lane 2

description: lane 2


title: muscle505


title: TMEM43-p.P111L_4, 19 months old

value: TMEM43-p.P111L overexpression


title: midbrain_504


title: JH06_NHDF-Ad_lane 1

description: lane 1


title: OlfactoryBulb_501

source_name: OlfactoryBulb

value: OlfactoryBulb


title: OlfactoryBulb_503


title: JH05_HMVEC-L_lane 8

description: lane 8

source_name: Lung Microvascular Endothelial Cells

value: Endothelial

value: Lung


title: TMEM43-p.P111L_2, 5 months old

value: heart


title: brain526

value: brain

value: PBS treatment 30 days


title: brain530


title: brain528


title: brain527


title: JH05_HMVEC-L_lane 6

description: lane 6


title: NTG_4, 21 months old

value: wild-type

value: 21 months


title: OlfactoryBulb_504


title: blood526

value: blood


title: blood528


title: NTG_3, 5 months old


title: TMEM43-p.S358L_1, 5 months old

value: TMEM43-p.S358L overexpression


title: JH05_HMVEC-L_lane 5

description: lane 5

value: Adult


title: NTG_2, 5 months old


title: brainstem_527

value: brainstem


title: brainstem_526


title: brainstem_528


title: brainstem_530


title: JH05_HMVEC-L_lane 4

description: lane 4


title: OlfactoryBulb_502

value: rGDF11 treatment 30 days


title: TMEM43-p.P111L_3, 20 months old

value: 20 months


title: Cerebellum_526

value: Cerebellum


title: Cerebellum_528


title: Cerebellum_527


title: JH05_HMVEC-L_lane 2

description: lane 2


title: JH05_HMVEC-L_lane 7

description: lane 7


title: Cerebellum_530


title: JH05_HMVEC-L_lane 1

description: lane 1


title: heart527


title: heart526


title: heart528


title: heart530


title: JH04_HUVEC_lane 8

description: lane 8

source_name: Umbilical Vein Endothelial Cells

value: Umbilical cord

value: Neonatal


title: JH04_HUVEC_lane 7

description: lane 7


title: Hippocampus526

value: Hippocampus


title: JH04_HUVEC_lane 6

description: lane 6

value: Endothelial


title: JH05_HMVEC-L_lane 3

description: lane 3

value: Lung


title: Hippocampus530


title: Hippocampus528


title: JH04_HUVEC_lane 5

description: lane 5


title: midbrain_526

value: midbrain


title: Ga organoid_K5C2_after

type: RNA

city: Chiba

first: Yoshitaka

last: Hippo

state: chiba

address: Nitona-cho 666-2

country: Japan

institute: Chiba Cancer Center Research Institute

description: Gene expression of subcutaneous tumor-derived organoids with KrasG12D, Trp53 loss and shCdh1 #2

hyb_protocol: Gene Expression Hybridization Kit (Agilent) were used for hybridization according to the manufacturer's instructions. After hybridization, slides were washed with Gene Expression Wash Buffer 1 and 2 (Gene Expression Wash Buffer Pack, Agilent).

scan_protocol: Scanned on Agilent G4900DA SureScan Microarray Scanner scanner (ScanRegion FullAgilentSlide, Scan resolution 3 μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction Software (version 11.0.1.1) was used for image quantification, background subtraction, and LOWESS normalization.

source_name: Subcutaneous tumor-derived organoids with KrasG12D, Trp53 loss and shCdh1 #2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low Input Quick-Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 .

growth_protocol: Gastric organoids were propagated with the serum-free media Advanced DMEM/F-12 supplemented with 50 ng/ml EGF, 250 ng/ml R-spondin1, 100 ng/ml Noggin, 10 μM Y27632, 1 μM Jagged-1 and 2.5 μM CHIR-99021, L-glutamine solution, penicillin/streptomycin, and amphotericin B suspension

extract_protocol: RNA was prepared using RNeasy Mini Kit  (Qiagen, Venlo, Netherlands) following the manufacture's recommendations.

treatment_protocol: No treatment

value: Stomach

tag: Sex

value: female

tag: histology of subcutaneous tumor

value: tumor


title: midbrain_527

value: PBS treatment 30 days


title: JH04_HUVEC_lane 4

description: lane 4


title: midbrain_530


title: JH04_HUVEC_lane 3

description: lane 3


title: muscle526

value: muscle


title: Ga organoid_K5C1_after

description: Gene expression of subcutaneous tumor-derived organoids with KrasG12D, Trp53 loss and shCdh1 #1

source_name: Subcutaneous tumor-derived organoids with KrasG12D, Trp53 loss and shCdh1 #1


title: Ga organoid_P5_after

description: Gene expression of subcutaneous tumor-derived organoids with Pik3caH1047R and Trp53 loss

source_name: Subcutaneous tumor-derived organoids with Pik3caH1047R and Trp53 loss


title: Ga organoid_K5_after

description: Gene expression of subcutaneous tumor-derived organoids with KrasG12D and Trp53 loss

source_name: Subcutaneous tumor-derived organoids with KrasG12D and Trp53 loss


title: Ga organoid_A5_after

description: Gene expression of subcutaneous tumor-derived organoids with Apc580D and Trp53 loss

source_name: Subcutaneous tumor-derived organoids with Apc580D and Trp53 loss


title: Ga organoid_5C2_after

description: Gene expression of subcutaneous tumor-derived organoids with Trp53 loss and shCdh1 #2

source_name: Subcutaneous tumor-derived organoids with Trp53 loss and shCdh1 #2


title: Ga organoid_control_before

description: Gene expression of Trp53flox/flox mice-derived Ga organoids transduced with the control vector pLKO.1 and shLuc before subcutaneous inoculation

value: pre-inoculation


title: muscle527


title: muscle528


title: JH04_HUVEC_lane 1

description: lane 1


title: muscle530


title: OlfactoryBulb526

value: OlfactoryBulb


title: JH03_NHAC-Kn_lane 8

description: lane 8

source_name: Articular Chondrocytes

value: Chondrocytes

value: Bone

value: Adult


title: OlfactoryBulb530


title: brain511

source_name: brain

value: brain

value: rGDF11 treatment 30 days


title: midbrain_528


title: OlfactoryBulb528


title: JH03_NHAC-Kn_lane 7

description: lane 7


title: brain512


title: brain514


title: JH03_NHAC-Kn_lane 6

description: lane 6


title: JH04_HUVEC_lane 2

description: lane 2

value: Umbilical cord

value: Neonatal


title: brain515


title: IQOS_6months_rep3

city: Hongo

first: Naoko

last: Nitta

state: Bunkyo-ku

department: Respiratory medicine

institute: Juntendo university

description: Gene expression after 6months exposure to IQOS aerosol in mice lung

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 8x60K Microarray (G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as feature not positive and significant or feature is not above background were excluded.

source_name: lung, IQOS, 6months, replicate3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color MicroArray-Based Gene Expression Analysis (Quick Amp Labeling Kit) . Dye incorporation and cRNA yield were checked with the NanoDrop One Spectrophotometer.

extract_protocol: Total RNA was extracted using miRNeasy mini kits (Qiagen, Hilden, Germany) following the manufacturer’s instructions.

treatment_protocol: Mice were exposed to fresh air, 3.5% IQOS aerosol, or 3.5% cigarette smoke for 6 months.

tag: gender

value: male

value: IQOS aerosol-exposed


title: blood511

source_name: blood

value: blood


title: IQOS_6months_rep1

source_name: lung, IQOS, 6months, replicate1


title: JH03_NHAC-Kn_lane 5

description: lane 5


title: CS_6months_rep2

description: Gene expression after 6months exposure to cigarette smoke in mice lung

source_name: lung, CS, 6months, replicate2

value: CS-exposed


title: CS_6months_rep3

source_name: lung, CS, 6months, replicate3


title: Ga organoid_5C1_after

description: Gene expression of subcutaneous tumor-derived organoids with Trp53 loss and shCdh1 #1

source_name: Subcutaneous tumor-derived organoids with Trp53 loss and shCdh1 #1

value: Stomach

value: female


title: IQOS_6months_rep2

source_name: lung, IQOS, 6months, replicate2


title: CS_6months_rep1

source_name: lung, CS, 6months, replicate1


title: JH03_NHAC-Kn_lane 4

description: lane 4


title: blood514


title: JH03_NHAC-Kn_lane 3

description: lane 3


title: blood515


title: brainstem_511

source_name: brainstem

value: brainstem


title: brainstem_515


title: JH03_NHAC-Kn_lane 2

description: lane 2


title: Cerebellum_511

source_name: Cerebellum

value: Cerebellum


title: brainstem_512


title: air_6months_rep3

description: Gene expression after 6months exposure to air in mice lung

source_name: lung, air, 6months, replicate3

value: air-exposed


title: JH03_NHAC-Kn_lane 1

description: lane 1


title: Cerebellum_512


title: Kc,CF,UV,No antibody, con,Rep1

city: Providence

first: Erica

last: Larschan

state: RI

address: Sidney Frank Hall 367, 185 Meeting Street

department: MCB

institute: Brown University

data_processing:
For preprocessing UMI-Tools and Cutadapt were used for Adapter, Barcode and UMI-removal.
Cutadapt (Galaxy version 3.5) was used for filtering with a custom adapter sequence  AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG. All other settings followed the Heyl et al 2020 Galaxy iCLIP-explorer workflow.
UMI-Tools Extract (Galaxy Version 1.1.2+galaxy2) was then used with a barcode pattern of NNNXXXXNN. No unpaired reads were allowed. The barcode was on the 3' end.
Je-Demultiplex (Galaxy Version 1.2.1) was then used. The barcode length was set to 4 and the barcode sequence was removed from read. No matched barcode was added at the end of the read header. The maximum mismatches (MM) was set to 1, and the minimum mismatch difference was set to 1. No extra number of bases were trimmed from right after the barcode or from the read end. The maximum base quality was set to 10.
FastQC was used for quality control.
Mapping was done by RNA STAR (Galaxy version 2.5.2b-2) using dm6. All settings were chosen based on the existing parameters from the iCLIP-explorer settings. However, we changed the following setting. We selected FALSE for the option to use end-to-end read alignments with no soft-clipping.
UMI-tools deduplicate (Galaxy version 0.5.3.0) was used to deduplicate the data following all of the existing settings except with a change in the method used to identify PCR duplicates within reads. We selected the option Reads group share the exact same UMI. Other settings followed the existing workflow with a soft clip threshold of 4, edit distance threshold of 1, only considering a random selection of the reads 1.0.
PEAKachu was used for Peak Calling to generate bed files. The PEAKachu settings were followed using the Galaxy CLIP-explorer workflow. The maximum insert size was set to 150, the minimum cluster expression fraction was set to 0.01, the minimum block overlap set to 0.5, the minimum block expression set to 0.1. The Mad Multiplier was set to 0.0, the Fold Change Threshold was set to 2.0, and the adjusted p-value threshold was set to 0.05.
Peaks were annotated using RCAS (Uyar et al. 2017) using Rstudio and R
Assembly: dm6

organism: Drosophila melanogaster

source_name: Embryonic

growth_protocol: Kc and S2 cells were maintained at 25C in Schneider's media supplemented with 10% Fetal Bovine Serum and 1.4X Antibiotic-Antimyotic. Cells were passaged every 3 days to maintain an appropriate cell density.

extract_protocol:
UV treated cells were lysed to get different cellular fractions (Cytoplasmic, Nucleoplasmic and Chromatin) according to Fr-iCLIP (fractionation-iCLIP) protocol from Brugiolo et al 2017. Each Fraction was subjected to iCLIP protocol as described in Huppertz et al 2014 using rabbit-CLAMP antibody to immuniprecipitate bound RNAs which were extracted using proteinse K and phenol:chloroform.
Custom cDNA libraries prepared according to Huppertz et al 2014 using distinct primers Rt1clip-Rt16clip for separate samples containing individual 4nt- barcode sequences that allow multiplexing of samples.
cDNA libraries for each sample amplified separetely using 31 cycles of PCR, mixed together later and sequenced using standard illumina protocols. Heyl et al. 2020 methods using the Galaxy CLIP-Explorer were followed to preprocess, perform quality control, post-process and perform peak calling.

treatment_protocol: Cells were allowed to grow to confluency and UV crosslinked using 254nm UV light in stratalinker 2400 on ice

value: Embryonic

tag: cell line

value: Kc cell

value: UV treated, No antibody


title: Kc,CF,UV,No antibody, con,Rep2

tag: treatment


title: Hippocampus527

source_name: Hippocampus

tag: strain

value: Hippocampus

value: PBS treatment 30 days


title: air_6months_rep2

source_name: lung, air, 6months, replicate2


title: Cerebellum_514

value: rGDF11 treatment 30 days


title: Kc,NF,UV,No antibody, con,Rep2


title: JH02_NHBE_lane 8

description: lane 8

source_name: Bronchial Epithelial Cells

tag: cell type

value: Epithelial

value: Lung

value: Adult


title: blood512


title: Cerebellum_515


title: Kc,NF,UV,No antibody, con,Rep1


title: Kc,ChF,UV,No antibody, con,Rep2

description: Kc_ChF.bed/ Kc_NF.bed


title: JH02_NHBE_lane 6

description: lane 6


title: heart511

source_name: heart

value: heart


title: Kc,CF,UV,CLAMPRep4

value: UV treated, IP CLAMP


title: heart514


title: heart512


title: Hippocampus511


title: JH02_NHBE_lane 7

description: lane 7


title: JH02_NHBE_lane 5

description: lane 5


title: Hippocampus512


title: heart515


title: Hippocampus514


title: JH02_NHBE_lane 4

description: lane 4


title: midbrain_511

source_name: midbrain

value: midbrain


title: air_6months_rep1

source_name: lung, air, 6months, replicate1

value: male


title: JH02_NHBE_lane 3

description: lane 3


title: brainstem_514


title: Kc,CF,UV,CLAMPRep3

value: female


title: midbrain_515


title: Kc,CF,UV,CLAMPRep2


title: midbrain_512


title: muscle511

source_name: muscle

value: muscle


title: Kc,NF,UV,CLAMPRep4


title: Kc,CF,UV,CLAMPRep1


title: Hippocampus515


title: midbrain_514


title: JH02_NHBE_lane 2

description: lane 2


title: muscle512


title: JH01_NHA_lane 8

description: lane 8

source_name: Astrocytes

value: Astrocytes

value: Brain

value: Fetus


title: muscle515


title: JH02_NHBE_lane 1

description: lane 1


title: muscle514


title: Kc,NF,UV,CLAMPRep3

value: Embryonic

value: Kc cell


title: OlfactoryBulb_511

source_name: OlfactoryBulb

value: OlfactoryBulb


title: JH01_NHA_lane 7

description: lane 7


title: Kc,NF,UV,CLAMPRep2


title: JH01_NHA_lane 6

description: lane 6


title: OlfactoryBulb_515


title: Kc,ChF,UV,CLAMPRep4


title: Kc,NF,UV,CLAMPRep1


title: brain523

source_name: brain

value: brain

value: PBS treatment 30 days


title: brain522


title: OlfactoryBulb_514

value: rGDF11 treatment 30 days


title: JH01_NHA_lane 5

description: lane 5


title: JH01_NHA_lane 4

description: lane 4


title: Kc,ChF,UV,CLAMPRep3


title: blood522

source_name: blood

value: blood


title: brain521


title: JH01_NHA_lane 3

description: lane 3


title: Kc,ChF,UV,CLAMPRep2


title: brain525


title: blood521


title: brainstem_521

value: brainstem


title: S2,CF,UV,No antibody, con,Rep2

value: S2 cell

value: UV treated, No antibody


title: JH01_NHA_lane 2

description: lane 2


title: blood525


title: OlfactoryBulb_512


title: JH01_NHA_lane 1

description: lane 1


title: brainstem_523


title: C-5-GB RNA

city: Chiba-City

first: Ariki

last: Nagashima

address: Inohana 1-8-1

department: Department of gastroenterology

institute: Graduate School of Medicine, Chiba University.

data_processing: The Deseq2 package version 1.34.0 was used for expression analysis.

source_name: Control patient 5

extract_protocol:
After the biopsy, samples were placed in a microtube containing All Protect Tissue Reagent (QIAGEN), stabilized, and stored at -80 °C. Total RNA was extracted using the miRNeasy Micro Kit (Qiagen).
RNA concentration and RNA integrity number (RIN) were measured, and micro RNA (miRNA)/messenger RNA (mRNA) sequences were performed on samples that met the criteria (total RNA >3 μg, RIN >8) for the following analysis. The extracted total RNA was sequenced for miRNA and mRNA using the Novaseq (Illumina) by GENEWIZ Japan (Tokyo, JP).

tag: phenotype

value: Control

tag: patient id

tag: biopsy site

value: GB


title: brainstem_525

tag: tissue


title: S2,CF,UV,No antibody, con,Rep1

value: male


title: S2,NF,UV,No antibody, con,Rep2


title: Cerebellum_521

value: Cerebellum


title: S2,NF,UV,No antibody, con,Rep1


title: Kc,ChF,UV,CLAMPRep1

value: female

value: UV treated, IP CLAMP


title: Cerebellum_523


title: heart521

value: heart


title: Cerebellum_525


title: C-5-LB RNA

value: LB


title: S2,ChF,UV,No antibody, con,Rep2

value: Embryonic


title: C-5-LA RNA

value: LA


title: heart523


title: heart522


title: C-4-GB RNA

source_name: Control patient 4


title: brainstem_522

source_name: brainstem


title: S2,ChF,UV,No antibody, con,Rep1


title: Hippocampus522

value: Hippocampus


title: C-4-LB RNA


title: heart525

value: PBS treatment 30 days


title: S2,CF,UV,CLAMPRep3


title: S2,CF,UV,CLAMPRep4


title: Hippocampus523


title: C-4-GA RNA

value: GA


title: midbrain_521

value: midbrain


title: Hippocampus525


title: S2,CF,UV,CLAMPRep2


title: midbrain_522


title: C-4-LA RNA


title: Cerebellum_522

source_name: Cerebellum


title: S2,CF,UV,CLAMPRep1


title: C-5-GA RNA


title: midbrain_523


title: C-3-GB RNA

source_name: Control patient 3


title: muscle521

value: muscle


title: muscle522


title: S2,NF,UV,CLAMPRep4

source_name: Embryonic

value: S2 cell


title: muscle523


title: C-3-LB RNA


title: Hippocampus521

source_name: Hippocampus


title: muscle525


title: S2,NF,UV,CLAMPRep3


title: OlfactoryBulb_521

value: OlfactoryBulb


title: S2,NF,UV,CLAMPRep2


title: C-3-GA RNA

value: Control


title: C-3-LA RNA


title: C-2-GB RNA

source_name: Control patient 2

value: GB


title: OlfactoryBulb_525


title: OlfactoryBulb_523


title: OlfactoryBulb_522


title: S2,NF,UV,CLAMPRep1

value: male


title: S2,ChF,UV,CLAMPRep4


title: C-2-LB RNA


title: C-2-GA RNA


title: S2,ChF,UV,CLAMPRep3


title: midbrain_525


title: S2,ChF,UV,CLAMPRep2


title: S2,ChF,UV,CLAMPRep1


title: MR-5-GB RNA

source_name: MR group patient 5

value: MR


title: MR-5-LB RNA


title: MR-5-GA RNA


title: MR-5-LA RNA


title: 293T plus sgRNA, no CMC treatment

first: Paul

middle: L.

last: Boutz

state: NY

address: 601 Elmwood Ave.

department: Biochemistry & Biophysics

institute: University of Rochester School of Medicine

data_processing:
Mapped using STAR aligner version 2.7.2a (Dobin et al., 2013).
Bedgraphs of 3' end counts for each sample, a separate bed graph for each strand, was generated for each sample using Bedtools genome coverage function with "-3" flag (Aaron et al 2010)
Assembly: hg38
Supplementary files format and content: bedgraphs of 3' end counts for each sample, a separate bed graph for each strand

extract_protocol:
RNA was extracted from harvested cells using the Qiagen RNAeasy kit according to manufacturor's instructions
Total RNA was harvested from HEK293T cells  transfected with sgRNA expression plasmid (psU samples), or mock transfected (wt samples),  and polyA-transcripts were selected by magnetic oligodT beads.  Two polyA selections were performed on each sample.  The selected RNA was then either treated with (CMC+) or not (CMC-), adducts other than pseudoU removed by , and the RNAs were reverse transcribed using an RT primer binding to the 3' RNA adaptor. cDNAs were again size selected to enrich for sub-full length RT products. After cleanup, a 3' DNA adaptor was ligated to the cDNA, and the resulting library PCR amplified and sequenced.

value: embryonic kidney

value: plus sgRNA

value: CMC-


title: 293T plus sgRNA, with CMC treatment

value: CMC+


title: C-1-GB RNA

source_name: Control patient 1


title: KV92: ad na resting

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
RTA 3.4.4, bcl2fastq 2.20.0.422 (Illumina)
Before alignment to reference genome each sequence in the raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using Trim Galore! wrapper tool. Reads shorter than 20 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/) with settings according to log file. Feature counts were determined using R package “Rsubread”. Only genes showing counts greater 5 at least two times across all samples were considered for further analysis (data cleansing). Gene annotation was done by R package “bioMaRt. Before starting the statistical analysis steps,  expression data was log2 transformed and TMM normalized (edgeR).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw countsfor each Sample ...
Supplementary files format and content: Matrix table with TMM-normalizedl log2CPM for every gene and every sample

growth_protocol: Neonatal and adult naive T-cells (CD4+CD45RA+CD31+) were maintained for 3 days at 37°C with 5% CO2 in RPMI 1640 containg 10% Fetal Bovine Serum, 10µg/ml streptomycin, and 10U/ml penicillin.

extract_protocol:
RNA extraction was performed with NucleoSpin RNA isolation kit (Macherey-Nagel) according to manufacturer's instructions.
The RNA library was prepared using the Collibri 3´ mRNA Library Prep Kit for Illumina Systems (Invitrogen) according to manufacturer's instructions.

treatment_protocol: A total of 5x105 cells/ml enriched naive T-cells were stimulated with B. longum-pulsed CD14+CD16+ monocytes at a ratio 2:1

value: blood

value: t-cells

value: PBS


title: C-1-LB RNA

value: LB


title: DLD1 line knocked-out for the wild type allele (expression of E545K mutated allele alone), biological rep2

city: Ioannina

first: Carol

last: Murphy

address: Panepistimioupoli

department: Biomedical reseach

country: Greece

institute: FORTH-IMBB

hyb_protocol: Following fragmentation and labeling (5.5ug of ssDNA was fragmented) (Affymetrix, #900671), 2.3 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G

data_processing: The data were analyzed using GeneSpring12.6 (Affymetrix Expression experiment type; Exon analysis type, RMA16 summarization algorithm)

label: biotin

source_name: gene expression data after serum starvation of corresponding cell line

label_protocol: Biotinylated cDNA was synthesized from 500ng of total RNA (was converted to cRNA then to ssDNA, using 10ug of cRNA for ssDNA synthesis) using Ambion WT Expression kit (#4491974)

growth_protocol: HCT116 and DLD1 colon cancer knocked-out cell lines were serum starved (0.5%FBS) in McCoy's medium for 19hrs.

extract_protocol: total RNA extraction was performed using Macherey-Nagel nucleospin RNA extraction kit (#740955.50) according to the manufacturer's instructions.

tag: genotype/variation

value: knocked-out for the wild type allele


title: DLD1 line knocked-out for the wild type allele (expression of E545K mutated allele alone), biological rep1

description: gene expression data after serum starvation

treatment_protocol: HCT116 and DLD1 colon cancer knocked-out cell lines were serum starved (0.5%FBS) in McCoy's medium for 19hrs.


title: 293T no sgRNA, with CMC treatment

value: control


title: HCT116 line knocked-out for the mutated H1047R allele (expression wild type allele alone), biological rep1


title: HCT116 line knocked-out for the wild type allele (expression of H1047R mutated allele alone), biological rep3


title: DLD1 line knocked-out for the wild type allele (expression of E545K mutated allele alone), biological rep3


title: KV92: ad na B. longum

value: B. longum


title: HCT116 line knocked-out for the mutated H1047R allele (expression wild type allele alone), biological rep2


title: DLD1 line knocked-out for the mutated E545K allele (expression wild type allele alone), biological rep1


title: 293T no sgRNA, no CMC treatment


title: C-1-GA RNA

value: GA


title: DLD1 line knocked-out for the mutated E545K allele (expression wild type allele alone), biological rep2


title: mLPS50

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

country: France

institute: University of Bordeaux

hyb_protocol: Gene expression analysis was carried out using Agilent Whole human 44K Genome Oligo Array (G4112F; Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s protocol.

scan_protocol: the scan was performed according to manufacturer’s recommendations with scanning resolution of 5µm

data_processing: For each series all microarrays were simultaneously normalized using the Quantile algorithm.

source_name: mixoid liposarcoma patient 50

label_protocol: RNA was labeled according to manufacturer’s protocol.

extract_protocol: Total RNA were extracted from frozen tumor samples using the miRNeasy® Mini Kit (Qiagen) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Frozen tissue

value: F

tag: subject status/id

value: mixoid liposarcoma patient 50

tag: metastasis

tag: os

tag: location

value: Extremities

tag: grade

tag: differentiation


title: HCT116 line knocked-out for the wild type allele (expression of H1047R mutated allele alone), biological rep1


title: KV91: ad na resting


title: mLPS46

source_name: mixoid liposarcoma patient 46

tag: Sex

tag: age

value: mixoid liposarcoma patient 46


title: HCT116 line knocked-out for the wild type allele (expression of H1047R mutated allele alone), biological rep2

tag: cell line


title: HCT116 line knocked-out for the mutated H1047R allele (expression wild type allele alone), biological rep3


title: DLD1 line knocked-out for the mutated E545K allele (expression wild type allele alone), biological rep3


title: mLPS47

source_name: mixoid liposarcoma patient 47

value: M

value: mixoid liposarcoma patient 47


title: C-1-LA RNA

value: Control

value: LA


title: C-2-LA RNA


title: mLPS43

source_name: mixoid liposarcoma patient 43

value: mixoid liposarcoma patient 43


title: KV91: ad na B. longum

value: blood

tag: treatment


title: MR-4-GB RNA

source_name: MR group patient 4

value: MR

value: GB


title: mLPS45

source_name: mixoid liposarcoma patient 45

value: mixoid liposarcoma patient 45


title: mLPS48

source_name: mixoid liposarcoma patient 48

value: mixoid liposarcoma patient 48


title: KV90: ad na resting

source_name: blood

value: t-cells

value: PBS


title: mLPS44

source_name: mixoid liposarcoma patient 44

value: mixoid liposarcoma patient 44


title: mLPS40

source_name: mixoid liposarcoma patient 40

value: F

value: mixoid liposarcoma patient 40


title: MR-4-LB RNA

value: LB


title: MR-4-GA RNA

value: GA


title: KV90: ad na B. longum

value: B. longum


title: mLPS42

source_name: mixoid liposarcoma patient 42

value: M

value: mixoid liposarcoma patient 42

value: Extremities


title: mLPS41

source_name: mixoid liposarcoma patient 41

value: mixoid liposarcoma patient 41


title: mLPS49

source_name: mixoid liposarcoma patient 49

value: mixoid liposarcoma patient 49


title: mLPS39

source_name: mixoid liposarcoma patient 39

value: mixoid liposarcoma patient 39

value: Trunk wall


title: KV89: neo resting

source_name: cord blood

value: cord blood


title: MR-4-LA RNA

value: MR

value: LA


title: KV88: neo resting

value: t-cells

value: PBS


title: KV89: neo B. longum


title: MR-3-LB RNA

source_name: MR group patient 3


title: mLPS37

source_name: mixoid liposarcoma patient 37

value: mixoid liposarcoma patient 37


title: mLPS35

source_name: mixoid liposarcoma patient 35

value: F

value: mixoid liposarcoma patient 35

value: Internal trunk


title: mLPS34

source_name: mixoid liposarcoma patient 34

value: mixoid liposarcoma patient 34


title: mLPS36

source_name: mixoid liposarcoma patient 36

value: mixoid liposarcoma patient 36


title: KV88: neo B. longum

value: B. longum


title: mLPS31

source_name: mixoid liposarcoma patient 31

value: M

value: mixoid liposarcoma patient 31

value: Extremities


title: mLPS32

source_name: mixoid liposarcoma patient 32

value: mixoid liposarcoma patient 32


title: mLPS30

source_name: mixoid liposarcoma patient 30

value: mixoid liposarcoma patient 30


title: MR-3-GA RNA

value: GA


title: mLPS28

source_name: mixoid liposarcoma patient 28

value: mixoid liposarcoma patient 28

value: Trunk wall


title: mLPS29

source_name: mixoid liposarcoma patient 29

value: mixoid liposarcoma patient 29


title: KV86: neo resting

value: cord blood

value: t-cells

value: PBS


title: mLPS33

source_name: mixoid liposarcoma patient 33

value: mixoid liposarcoma patient 33


title: KV86: neo B. longum


title: MR-2-GB RNA

source_name: MR group patient 2

value: MR

value: GB


title: MR-2-LB RNA

value: LB


title: KV85: neo resting


title: KV85: neo B. longum

value: B. longum


title: MR-2-GA RNA


title: KV84: ad na resting

source_name: blood

value: blood


title: MR-3-LA RNA

value: LA


title: MR-2-LA RNA


title: mLPS27

source_name: mixoid liposarcoma patient 27

value: F

value: mixoid liposarcoma patient 27

value: Extremities


title: mLPS26

source_name: mixoid liposarcoma patient 26

value: M

value: mixoid liposarcoma patient 26


title: mLPS21

source_name: mixoid liposarcoma patient 21

value: mixoid liposarcoma patient 21


title: mLPS20

source_name: mixoid liposarcoma patient 20

value: mixoid liposarcoma patient 20


title: mLPS25

source_name: mixoid liposarcoma patient 25

value: mixoid liposarcoma patient 25


title: mLPS22

source_name: mixoid liposarcoma patient 22

value: mixoid liposarcoma patient 22


title: mLPS24

source_name: mixoid liposarcoma patient 24

value: mixoid liposarcoma patient 24


title: MR-1-GB RNA

source_name: MR group patient 1


title: mLPS18

source_name: mixoid liposarcoma patient 18

value: mixoid liposarcoma patient 18


title: mLPS19

source_name: mixoid liposarcoma patient 19

value: mixoid liposarcoma patient 19


title: mLPS23

source_name: mixoid liposarcoma patient 23

value: mixoid liposarcoma patient 23


title: mLPS17

source_name: mixoid liposarcoma patient 17

value: mixoid liposarcoma patient 17


title: 689 H3K27Ac

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
bowtie2 alignment of paired-end reads to GRCh38 reference genome
sambamba for filtering of unmapped and duplicated reads
macs2 for calling of peaks
bedtools and bedGraphToBigWig for transforming bam files into bigwig files
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig file showing the alignment of reads to the reference genome

source_name: interneurons

growth_protocol: iPSCs were differentiated into cortical interneurons according to an established protocol (PMID: 33097921).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEBNext Ultra II DNA library Prep Kit for Illumina was used for library prep.

tag: person id

value: interneurons

tag: gender

value: Male

tag: ethnicity

value: Caucasian

tag: diagnosis

value: schizophrenia

tag: chip antibody


title: mLPS15

source_name: mixoid liposarcoma patient 15

value: mixoid liposarcoma patient 15


title: MR-1-LB RNA

tag: phenotype

value: MR

tag: patient id

tag: biopsy site

value: LB


title: MR-1-GA RNA

value: GA


title: KV84: ad na B. longum

tag: tissue

value: blood

tag: cell type

value: t-cells

value: B. longum


title: mLPS16

source_name: mixoid liposarcoma patient 16

value: M

tag: subject status/id

value: mixoid liposarcoma patient 16

tag: metastasis

tag: os

tag: location

value: Extremities


title: mLPS14

source_name: mixoid liposarcoma patient 14

tag: Sex

tag: age

value: mixoid liposarcoma patient 14

tag: grade

tag: differentiation


title: MR-1-LA RNA

value: LA


title: 292 H3K4Me1

tag: person id

tag: gender

value: Control


title: 689 H3K4Me1

value: interneurons

tag: ethnicity

tag: diagnosis


title: mLPS13

source_name: mixoid liposarcoma patient 13

value: mixoid liposarcoma patient 13


title: 292 H3K27Ac

value: Male

value: Caucasian

tag: chip antibody


title: CO58

data_processing:
Kallisto for pseudo-alignment to transcriptome of Ensembl GRCh38
DESeq2 for differential gene expression
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: A .csv file including TPM of each gene for all 9 samples

source_name: glutamatergic neurons

growth_protocol: glutamatergic neurons were generated from iPSCs according to our previously published protocols (Park et al. 2020) and were harvested for RNA preparation after 8 weeks of differentiation.

extract_protocol:
Samples were harvested using Trizol reagent (Invitrogen).
NEBNext Ultra II Directional RNA library Prep Kit for Illumina

value: iPSC-derived glutamatergic neurons

tag: disease

value: schizophrenia


title: ER+ breast cancer 43

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

data_processing:
Basecalls performed using CASAVA version 1.7
Adapter and low-quality reads were removed using Trimmomatic v0.36
Aligning was done using TopHat v2.1.1
Quantification and normalization was done using cufflinks 2.2.1
Genome_build: hg37
Supplementary_files_format_and_content: Gene expression (FPKM) values for the 44 samples. Rows are genes, columns are samples, the column header is the sample name. The 7 BMI groups considered are as follows: 18.5 – 24.99, 25.00 – 27.99, 28.00 – 29.99, 30.00 – 31.99, 32.00 – 34.00, 34.01 – 39.99, ≥ 40.

source_name: breast tissue

extract_protocol:
The Recoverall Nucleic Acid Isolation Kit for FFPE Tissue (Ambion, Austin, TX) was used to isolate RNA
Quantitation and fragmentation analysis were performed using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 and RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA). A Qubit fluorometric assay (Thermo Fisher Scientific) was used to quantitate and equalize dsDNA prepared using the Truseq RNA Access library preparation kit (Illu- mina, San Diego, CA). Libraries were randomized, indexed, multiplexed, and paired end sequenced (200 cycles total) on an Illumina Nextseq500.

value: breast

tag: cancer type

value: ER +

tag: storage type

value: FFPE

tag: treatment

value: untreated

tag: bmi group


title: CO285

tag: tissue


title: ER+ breast cancer 42


title: mLPS9

source_name: mixoid liposarcoma patient 9

tag: subject status/id

value: mixoid liposarcoma patient 9

tag: metastasis

tag: os


title: mLPS11

source_name: mixoid liposarcoma patient 11

tag: Sex

value: F

tag: age

value: mixoid liposarcoma patient 11

tag: location


title: COL8


title: ER+ breast cancer 44


title: mLPS6

source_name: mixoid liposarcoma patient 6

value: M

value: mixoid liposarcoma patient 6

value: Extremities

tag: grade

tag: differentiation


title: mLPS8

source_name: mixoid liposarcoma patient 8

value: mixoid liposarcoma patient 8


title: ER+ breast cancer 41


title: mLPS5

source_name: mixoid liposarcoma patient 5

value: mixoid liposarcoma patient 5


title: CO689


title: ER+ breast cancer 40


title: CO755


title: CO365

value: control


title: mLPS1

source_name: mixoid liposarcoma patient 1

value: mixoid liposarcoma patient 1


title: mLPS4

source_name: mixoid liposarcoma patient 4

value: mixoid liposarcoma patient 4


title: ER+ breast cancer 39


title: ER+ breast cancer 38


title: mLPS10

source_name: mixoid liposarcoma patient 10

value: mixoid liposarcoma patient 10


title: COL9

value: iPSC-derived glutamatergic neurons


title: CO107


title: ER+ breast cancer 37

value: breast


title: mLPS7

source_name: mixoid liposarcoma patient 7

value: mixoid liposarcoma patient 7


title: mLPS12

source_name: mixoid liposarcoma patient 12

value: mixoid liposarcoma patient 12


title: SarcComp87

source_name: complex sarcomas patient 87

value: complex sarcomas patient 87


title: SarcComp83

source_name: complex sarcomas patient 83

value: complex sarcomas patient 83


title: mLPS3

source_name: mixoid liposarcoma patient 3

value: mixoid liposarcoma patient 3


title: SarcComp84

source_name: complex sarcomas patient 84

value: F

value: complex sarcomas patient 84

value: Trunk wall


title: SarcComp85

source_name: complex sarcomas patient 85

value: complex sarcomas patient 85

value: Extremities


title: SarcComp82

source_name: complex sarcomas patient 82

value: complex sarcomas patient 82


title: SarcComp81

source_name: complex sarcomas patient 81

value: M

value: complex sarcomas patient 81


title: mLPS2

source_name: mixoid liposarcoma patient 2

value: mixoid liposarcoma patient 2


title: ER+ breast cancer 36

source_name: breast tissue

value: ER +

value: FFPE

value: untreated


title: COL7

source_name: glutamatergic neurons

value: iPSC-derived glutamatergic neurons

value: control


title: ER+ breast cancer 35

value: breast


title: SarcComp80

source_name: complex sarcomas patient 80

value: complex sarcomas patient 80


title: ER+ breast cancer 34


title: SarcComp79

source_name: complex sarcomas patient 79

value: complex sarcomas patient 79


title: D5_DifferentiatedEPs_CHVEGF

city: University park

first: Yuqian

last: Jiang

state: PA

address: W345 millennium science complex

institute: PSU

data_processing:
alignment, filtering, barcode counting, and UMI counting were performed using Cell Ranger from 10X Genomics
Genome_build: hg38
Supplementary_files_format_and_content: Cell Ranger output files

source_name: WA09 hPSCs

growth_protocol: hPSCs were cultured in mTeSR1 on iMatrix.

extract_protocol:
Cells were singularized and prepared using Chromium Next GEM Single Cell 3' protocol
Single cell sequencing library was constructed using Chromium Next GEM Single Cell 3' protocol and sequenced on a NextSeq High Output 150 cycle kit.
single cell RNA Seq

treatment_protocol: Cells were differentiated by treatment with 6uM CHIR for 48 hours. Two days after starting differentiation cells were replated. After replating, cells were treated with 50ng/mL VEGF in basal media until day 5. Cells were collected on day 5 for sequencing.

tag: cell line

value: WA09 hPSCs

tag: cell type

value: hPSCs differentiated to day 5 endothelial progenitors


title: SarcComp77

source_name: complex sarcomas patient 77

value: complex sarcomas patient 77


title: SarcComp78

source_name: complex sarcomas patient 78

value: F

value: complex sarcomas patient 78


title: MR-3-GB RNA

source_name: MR group patient 3

tag: phenotype

value: MR

tag: patient id

tag: biopsy site

value: GB


title: Molino_3

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome astMex_2.0 with STAR aligner (version 2.7.3a ), using Ensembl 102 gene models. TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: Astyanax mexicanus 2.0
Supplementary_files_format_and_content: TPM gene expression in text file

organism: Astyanax mexicanus

source_name: 1 year lab-reared Molino skeletal muscle

extract_protocol:
RNA from skeletal muscle was extracted using standard phenol/chloroform extraction. The subsequent RNA pellet was cleaned with the RNeasy Mini Kit (Qiagen #74104) with on-column DNAse digestion (Qiagen #79256).
Libraries were prepared according to the manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina #20020594)
The resulting libraries were quantified using a Bioanalyzer (Agilent Technologies) and Qubit fluorometer (Life Technologies). Libraries were normalized, pooled, multiplexed, and sequenced on an Illumina NextSeq 500 instrument as v2 Chemistry High Output 75bp single read runs.

value: Untreated

value: Skeletal muscle

tag: morphotype

value: Molino


title: ER+ breast cancer 33

tag: cancer type

value: ER +

tag: storage type

value: FFPE

tag: treatment


title: SarcComp76

source_name: complex sarcomas patient 76

tag: subject status/id

value: complex sarcomas patient 76

value: Extremities


title: Molino_1

tag: tissue


title: Molino_2


title: ER+ breast cancer 32

value: breast

value: untreated

tag: bmi group


title: ER+ breast cancer 31


title: Tinaja_3

source_name: 1 year lab-reared Tinaja skeletal muscle

value: Tinaja


title: SarcComp74

source_name: complex sarcomas patient 74

tag: Sex

value: M

value: complex sarcomas patient 74

tag: metastasis

tag: os


title: ER+ breast cancer 30


title: SarcComp75

source_name: complex sarcomas patient 75

tag: age

value: complex sarcomas patient 75

tag: location

value: Internal trunk

tag: grade


title: SarcComp72

source_name: complex sarcomas patient 72

value: complex sarcomas patient 72

tag: differentiation


title: Tinaja_2


title: SarcComp71

source_name: complex sarcomas patient 71

value: F

value: complex sarcomas patient 71


title: SarcComp73

source_name: complex sarcomas patient 73

value: complex sarcomas patient 73


title: SarcComp68

source_name: complex sarcomas patient 68

value: complex sarcomas patient 68

value: Trunk wall


title: SarcComp69

source_name: complex sarcomas patient 69

value: complex sarcomas patient 69


title: Tinaja_1

value: Untreated

value: Skeletal muscle


title: Wild-Surface_2

source_name: Adult wild caught surface fish skeletal muscle

value: Surface


title: ER+ breast cancer 29

source_name: breast tissue

value: breast

value: ER +

value: FFPE


title: ER+ breast cancer 28

value: untreated


title: ER+ breast cancer 27


title: ER+ breast cancer 26


title: mLPS38

source_name: mixoid liposarcoma patient 38

value: M

value: mixoid liposarcoma patient 38

value: Extremities


title: SarcComp63

source_name: complex sarcomas patient 63

value: complex sarcomas patient 63


title: SarcComp62

source_name: complex sarcomas patient 62

value: complex sarcomas patient 62


title: Wild-Pachon_3

source_name: Adult wild caught pachon skeletal muscle

value: Pachón


title: Wild-Pachon_2


title: Wild-Pachon_1


title: SarcComp86

source_name: complex sarcomas patient 86

value: complex sarcomas patient 86


title: SarcComp57

source_name: complex sarcomas patient 57

value: F

value: complex sarcomas patient 57


title: Wild-Surface_1


title: SarcComp70

source_name: complex sarcomas patient 70

value: complex sarcomas patient 70


title: SarcComp65

source_name: complex sarcomas patient 65

value: complex sarcomas patient 65

value: Trunk wall


title: Pachon_3

source_name: 1 year lab-reared pachon skeletal muscle

value: Untreated

value: Skeletal muscle


title: SarcComp61

source_name: complex sarcomas patient 61

value: complex sarcomas patient 61


title: SarcComp66

source_name: complex sarcomas patient 66

value: complex sarcomas patient 66


title: SarcComp64

source_name: complex sarcomas patient 64

value: complex sarcomas patient 64


title: SarcComp60

source_name: complex sarcomas patient 60

value: M

value: complex sarcomas patient 60


title: SarcComp67

source_name: complex sarcomas patient 67

value: complex sarcomas patient 67

value: Extremities


title: SarcComp59

source_name: complex sarcomas patient 59

value: complex sarcomas patient 59


title: SarcComp56

source_name: complex sarcomas patient 56

value: complex sarcomas patient 56


title: ER+ breast cancer 25

source_name: breast tissue

value: breast

value: ER +

value: FFPE

value: untreated


title: SarcComp58

source_name: complex sarcomas patient 58

value: complex sarcomas patient 58


title: ER+ breast cancer 22


title: SarcComp55

source_name: complex sarcomas patient 55

value: complex sarcomas patient 55


title: SarcComp53

source_name: complex sarcomas patient 53

value: complex sarcomas patient 53


title: SarcComp52

source_name: complex sarcomas patient 52

value: F

value: complex sarcomas patient 52


title: SarcComp54

source_name: complex sarcomas patient 54

value: complex sarcomas patient 54

value: Trunk wall


title: SarcComp51

source_name: complex sarcomas patient 51

value: complex sarcomas patient 51


title: Pachon_2

value: Untreated

value: Skeletal muscle

value: Pachón


title: ER+ breast cancer 24


title: ER+ breast cancer 21


title: Pachon_1


title: ER+ breast cancer 20


title: Surface_2

source_name: 1 year lab-reared surface fish skeletal muscle

value: Surface


title: ER+ breast cancer 19


title: SarcComp49

source_name: complex sarcomas patient 49

value: M

value: complex sarcomas patient 49

value: Extremities


title: Surface_3


title: ER+ breast cancer 18

value: breast

value: ER +

value: FFPE


title: Surface_1


title: ER+ breast cancer 17

value: untreated


title: SarcComp50

source_name: complex sarcomas patient 50

value: complex sarcomas patient 50


title: SarcComp48

source_name: complex sarcomas patient 48

value: complex sarcomas patient 48


title: SarcComp46

source_name: complex sarcomas patient 46

value: F

value: complex sarcomas patient 46


title: SarcComp47

source_name: complex sarcomas patient 47

value: complex sarcomas patient 47


title: ER+ breast cancer 16


title: SarcComp44

source_name: complex sarcomas patient 44

value: complex sarcomas patient 44

value: Trunk wall


title: SarcComp45

source_name: complex sarcomas patient 45

value: complex sarcomas patient 45


title: ER+ breast cancer 15


title: SarcComp43

source_name: complex sarcomas patient 43

value: complex sarcomas patient 43


title: ER+ breast cancer 14


title: ER+ breast cancer 13


title: Glandular stomach-treatment-8h-rep1

city: ZHENGZHOU CITY HENAN PROVINCE

first: Yankai

last: Chang

state: 河南

address: HENAN AGRICULTURAL UNIVERSITY, NO.15 ZHENGZHOU LONGZIHU, 河南省郑州市郑东新区龙子湖高校园区15号河南农业大学

institute: Henan Agricultural University

hyb_protocol: 0.6µg of Cy3-1abelled cRNA (specific activity > 10.0 pmol Cy3/µg cRNA) was fragmented at 60 ℃ for 30 minutes in a reaction volume of 22.5µI containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse miRNA Microarray 8 × 60 K platform for 17 hours at 65 ℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ℃ GE Wash buffer 2 (Agilent), then dried immediatel y by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array s lides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Glandular stomach, 8h, 3w, treatment group, replicate 1

label_protocol: Cyanine-3 (Cy-3) labeled cRNA was prepared from 0. 2µg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoOrop ND-1000 Spectrophotometer.

growth_protocol: Mice were maintained on a 12-hour light/dark cycles in standard cages housing three mice with ad libitum access to food and water.

extract_protocol: Frozen glandular stomach tissues were ground in liquid nitrogen and TRIzol (Invitrogen, Carlsbad, CA, USA) was extract total RNA by a conventional method, each samples were processed in individually. The quality and concentration were assessed by NanoDrop 2000 spectrophotometer (NanoDrop, Wilmington, DE, USA), and the integrity was verified using the Agilent RNA 6000 Nano Kit. All the samples passed the quality control of RIN>7.5 and 18S/28S>1.0.

treatment_protocol: The glandular stomach was collected from mice immediately euthanasia and washed with cold normal saline to remove the gastric content.

value: Glandular stomach

tag: infection

value: Cryptosporidium muris


title: Glandular stomach-treatment-8h-rep3

source_name: Glandular stomach, 8h, 3w, treatment group, replicate 3


title: Glandular stomach-treatment-8h-rep2

source_name: Glandular stomach, 8h, 3w, treatment group, replicate 2


title: ER+ breast cancer 12

source_name: breast tissue


title: SarcComp40

source_name: complex sarcomas patient 40

value: M

value: complex sarcomas patient 40


title: Glandular stomach-control-8h-rep3

source_name: Glandular stomach, 8h, 3w, control group, replicate 3

value: control


title: SarcComp42

source_name: complex sarcomas patient 42

value: complex sarcomas patient 42

value: Extremities


title: ER+ breast cancer 11

value: breast

value: ER +

value: FFPE

value: untreated


title: SarcComp37

source_name: complex sarcomas patient 37

value: complex sarcomas patient 37


title: SarcComp38

source_name: complex sarcomas patient 38

value: F

value: complex sarcomas patient 38


title: Glandular stomach-control-8h-rep2

source_name: Glandular stomach, 8h, 3w, control group, replicate 2


title: SarcComp39

source_name: complex sarcomas patient 39

value: complex sarcomas patient 39


title: SarcComp34

source_name: complex sarcomas patient 34

value: complex sarcomas patient 34


title: SarcComp35

source_name: complex sarcomas patient 35

value: complex sarcomas patient 35


title: ER+ breast cancer 10


title: SarcComp33

source_name: complex sarcomas patient 33

value: complex sarcomas patient 33


title: SarcComp32

source_name: complex sarcomas patient 32

value: complex sarcomas patient 32


title: PCOS Patient 4

city: Thiruvananthapuram

first: Malini

last: Laloraya

state: Kerala

address: Thycaud PO, Poojappura

department: Department of Molecular Reproduction,

country: India

institute: Rajiv Gandhi Centre for Biotechnology,

data_processing: RNA samples from 8 subjects, average delta CT from technical triplicates reported in data table. Standard Taqman Assay: Quantitative real-time PCR was performed using Applied Biosystems 7900HT system and universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles), FAM channel was measured.

label: FAM

source_name: PCOS Patient

label_protocol: FAM

extract_protocol: No specific treatment was performed as the study group included  blood samples collected from control and PCOS subjects.

treatment_protocol: Total RNA  with small RNAs was extracted with  QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: Female

tag: diagnosis

value: Polycystic Ovarian Syndrome (PCOS)

value: Peripheral Blood


title: SarcComp30

source_name: complex sarcomas patient 30

value: complex sarcomas patient 30

value: Trunk wall


title: SarcComp29

source_name: complex sarcomas patient 29

value: complex sarcomas patient 29

value: Internal trunk


title: SarcComp28

source_name: complex sarcomas patient 28

value: complex sarcomas patient 28


title: SarcComp27

source_name: complex sarcomas patient 27

value: M

value: complex sarcomas patient 27

value: Extremities


title: SarcComp26

source_name: complex sarcomas patient 26

value: complex sarcomas patient 26


title: SarcComp41

source_name: complex sarcomas patient 41

value: complex sarcomas patient 41


title: SarcComp36

source_name: complex sarcomas patient 36

value: complex sarcomas patient 36


title: SarcComp31

source_name: complex sarcomas patient 31

value: complex sarcomas patient 31


title: PCOS Patient 3


title: ER+ breast cancer 8

source_name: breast tissue

value: breast

value: ER +

value: FFPE

value: untreated


title: Glandular stomach-control-8h-rep1

source_name: Glandular stomach, 8h, 3w, control group, replicate 1

value: Glandular stomach

value: control


title: PCOS Patient 2

value: Female

value: Polycystic Ovarian Syndrome (PCOS)

value: Peripheral Blood


title: ER+ breast cancer 7


title: ER+ breast cancer 6


title: SarcComp24

source_name: complex sarcomas patient 24

value: complex sarcomas patient 24

value: Trunk wall


title: Healthy Individual 4

source_name: Healthy Individual

value: Healthy


title: SarcComp25

source_name: complex sarcomas patient 25

value: M

value: complex sarcomas patient 25

value: Extremities


title: ER+ breast cancer 5


title: Healthy Individual 3


title: SarcComp22

source_name: complex sarcomas patient 22

value: complex sarcomas patient 22


title: SarcComp23

source_name: complex sarcomas patient 23

value: complex sarcomas patient 23


title: SarcComp21

source_name: complex sarcomas patient 21

value: F

value: complex sarcomas patient 21

value: Internal trunk


title: ER+ breast cancer 4

value: breast

value: ER +

value: FFPE

value: untreated


title: SarcComp18

source_name: complex sarcomas patient 18

value: complex sarcomas patient 18


title: SarcComp19

source_name: complex sarcomas patient 19

value: complex sarcomas patient 19


title: PCOS Patient 1

source_name: PCOS Patient

value: Female

value: Polycystic Ovarian Syndrome (PCOS)

value: Peripheral Blood


title: SarcComp17

source_name: complex sarcomas patient 17

value: M

value: complex sarcomas patient 17


title: SarcComp15

source_name: complex sarcomas patient 15

value: complex sarcomas patient 15

value: Extremities


title: Healthy Individual 2

value: Healthy


title: SarcComp20

source_name: complex sarcomas patient 20

value: F

value: complex sarcomas patient 20


title: Healthy Individual 1


title: ER+ breast cancer 2


title: SI-ARI

city: Shanghai

first: Jie

last: Wang

address: 416 Rm., MingdaoBldg., 131 Dongan Rd., Shanghai 200032, P.R.China

institute: Fudan University

data_processing:
Basecalls performed using CASAVA
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to Human Dec.2013 (GRCh38/hg38) whole genome using Bowtie2
Peaks were called using MACS2
bw files were generated using bedGraphToBigWig,bedClip and bedtools
Genome_build: Human Dec.2013 (GRCh38/hg38)
Supplementary_files_format_and_content: bw files were generated using bedGraphToBigWig,bedClip and bedtools
Supplementary_files_format_and_content: peak files

source_name: human non-transformed breast epithelial cell

growth_protocol: MCF10A cell was cultured in DMEM/F12 media (HyClone) supplemented with 5% FBS, EGF (20 ng/mL), insulin (10 µg/mL), hydrocortisone (0.5 µg/mL), cholera toxin (100 ng/mL), 50 U/mL penicillin and 50 µg/mL streptomycin. The cells were incubated at 37°C in a humidified chamber containing 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with ARID1A antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (TruSeq® chip DNA LT Sample Prep Kit), including performing end repair, adenylating 3' ends, ligating adapters and enriching DNA Fragments. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: No extra treatment

tag: cell type

tag: cell line

tag: chip antibody

tag: genotype

value: ARID5A knockdown group


title: SarcComp13

source_name: complex sarcomas patient 13

tag: subject status/id

value: complex sarcomas patient 13

value: Trunk wall


title: ER+ breast cancer 3

tag: tissue

value: breast

tag: cancer type

value: ER +

tag: storage type

value: FFPE

tag: treatment


title: SarcComp16

source_name: complex sarcomas patient 16

tag: Sex

value: complex sarcomas patient 16

tag: metastasis

tag: os


title: SarcComp12

source_name: complex sarcomas patient 12

tag: age

value: complex sarcomas patient 12

tag: location

value: Internal trunk

tag: grade


title: SI-IgG

value: human non-transformed breast epithelial cell

value: Normal Rabbit IgG (CST #2729)

value: ARID3A knockdown group


title: SarcComp10

source_name: complex sarcomas patient 10

value: M

value: complex sarcomas patient 10

tag: differentiation


title: SI-INP

value: ARID1A knockdown group


title: SarcComp11

source_name: complex sarcomas patient 11

value: complex sarcomas patient 11


title: SarcComp14

source_name: complex sarcomas patient 14

value: complex sarcomas patient 14

value: Extremities


title: SarcComp8

source_name: complex sarcomas patient 8

value: F

value: complex sarcomas patient 8


title: SarcComp9

source_name: complex sarcomas patient 9

value: complex sarcomas patient 9


title: TA_4 h_rep2

city: Hangzhou

first: Xiangfeng

last: Chen

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang University

description: Gene expression after 4hr in TA-injected muscle

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Quadriceps muscle, 4hr, TA, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The total RNA was extracted using TRIzol reagent, and then purified with an RNeasy Mini kit (Qiagen).

treatment_protocol: Mice were intramuscularly injected in the quadriceps with 50 μg TA dissolved in 50 µL of PBS, with each mouse injected in one leg only. The corresponding contralateral quadriceps were injected with an equal volume of PBS serving as the negative control. Quadriceps muscles were collected at 4 h after injection.

value: Quadriceps muscle

tag: gender

value: female


title: ER+ breast cancer 23

source_name: breast tissue

value: breast

value: ER +

value: FFPE

value: untreated

tag: bmi group


title: SarcComp4

source_name: complex sarcomas patient 4

value: complex sarcomas patient 4

value: Internal trunk


title: NC-ARI

tag: cell type

value: human non-transformed breast epithelial cell

tag: cell line

value: control group


title: TA_4 h_rep3

source_name: Quadriceps muscle, 4hr, TA, replicate 3


title: TA_4 h_rep1

source_name: Quadriceps muscle, 4hr, TA, replicate 1


title: SarcComp6

source_name: complex sarcomas patient 6

value: complex sarcomas patient 6

value: Trunk wall


title: SarcComp1

source_name: complex sarcomas patient 1

value: M

value: complex sarcomas patient 1


title: Ctrl_4 h_rep3

description: Gene expression after 4hr in PBS-injected muscle

source_name: Quadriceps muscle, 4hr, Ctrl, replicate 3


title: SarcComp7

source_name: complex sarcomas patient 7

value: F

value: complex sarcomas patient 7

value: Extremities


title: SarcComp3

source_name: complex sarcomas patient 3

value: complex sarcomas patient 3


title: Ctrl_4 h_rep1

source_name: Quadriceps muscle, 4hr, Ctrl, replicate 1

value: Quadriceps muscle

value: female


title: SarcComp5

source_name: complex sarcomas patient 5

value: complex sarcomas patient 5


title: Ctrl_4 h_rep2

source_name: Quadriceps muscle, 4hr, Ctrl, replicate 2


title: NC-IgG

source_name: human non-transformed breast epithelial cell

tag: chip antibody

value: Normal Rabbit IgG (CST #2729)

tag: genotype


title: NC-INP


title: LMS68

data_processing:
Sequencing quality was assessed using FastQC from the Babraham Institute (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were then trimmed for adaptors using cutadapt version 1.10 with -q 30 and -m 18 parameters.
We aligned the reads with mature miRNA sequences from the miRbase Sequence database using, BWA-aln algorithm version 0.7.17 with -n 1 -o 0 -e 0 -k 1 -t 8 parameters and evaluated mapping quality using Qualimap version 2.2.2b.
We used Samtools version 1.9 to discard the reads with a mapping quality under 30 and to count mapped reads with the reference sequences (samtools idxstats)
We applied the EdgeR R package on raw counts to normalize data and define significantly differentially expressed genes with a generalized linear model fitting (glmQLFit), correcting the returned p-values using Holm’s method.
We kept as expressed any miRNAs (filterByExpr) with a summed raw count over all samples > 10 and represented by a minimum of five reads in at least one sample.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw or normalized mature miRNA counts for every samples

source_name: Primary tumor Leiomyosarcoma

extract_protocol: NEBNext Small RNA Library Prep Set for Illumina (E7330L, New England Biolabs Inc., Ipswich, MA, USA) according to the manufacturer’s recommendations.

tag: tissue

value: Primary tumor Leiomyosarcoma

value: FEMALE

value: Member

tag: lms subtype

value: hLMS

tag: molecule subtype

value: small RNA


title: LMS66

value: Internal trunk


title: LMS65

value: oLMS


title: SarcComp2

source_name: complex sarcomas patient 2

value: M

tag: subject status/id

value: complex sarcomas patient 2


title: LMS64

tag: Sex

value: MALE


title: LMS62

tag: metastasis


title: ER+ breast cancer 1

value: breast

tag: cancer type

value: ER +

tag: storage type

value: FFPE

tag: treatment

value: untreated


title: SPONT_rep6 (antimony)

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description: antimony spontaneous tumor M. musculus sample

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 GeneChip arrays (Affymetrix, Santa Clara, CA). Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Affymetrix Scanner 3000

data_processing: Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm. Data were normalized across all three groups.

source_name: lung, spontaneous tumor

label_protocol: One hundred nanograms of total RNA was amplified as directed in the Affymetrix 3′ IVT Plus kit protocol. Fifteen micrograms of amplified biotin-aRNAs was fragmented, and 12.5 μg was hybridized to each array for 16 h at 45 °C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

growth_protocol: At the start of the study, the animals were 5–6 weeks of age. The animals were housed 2 per cage. Tap water and NTP-2000 diet (Zeigler Brothers, Inc. Gardners, PA) were made available ad libitum. The care of animals on this study was according to National Institutes of Health (NIH) procedures as described in the ‘‘The U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals,’’ available from the Office of Laboratory Animal Welfare, NIH, Department of Health and Human Services, RKLI, Bethesda, MD or online at http://grants.nih.gov/grants/olaw/olaw.htm#pol.

extract_protocol: The lung was harvested and weighed, and then, a representative sections are collected and fixed in 10 % neutral buffered formalin for histology. Hematoxylin and eosin (H&E)-stained sections (5 μm) were examined by a board certified pathologist. Selected lung tumors are dissected from the remaining lung parenchyma and flash-frozen in liquid nitrogen and stored at −80 °C until RNA extraction. RNA was extracted from frozen samples using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A, Carlsbad, CA) according to the manufacturer’s protocol. RNA concentration and quality were measured on a Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples were aliquoted and stored at −80 °C until they were analyzed for gene expression studies.

treatment_protocol: Antimony trioxide was obtained from 3N International, Inc. (Akron, OH), in one lot (3N-06159) that was used in the 2-week and 2-year studies. Groups of 60 male and 60 female mice were exposed by whole body inhalation to antimony trioxide aerosol at concentrations of 0, 3, 10, or 30 mg/m3 for 6 hours plus T90 (12 minutes) per day, 5 days per week for up to 105 weeks.

tag: group

value: antimony_Spontaneous Tumor


title: Antipodal Cell, biological rep 2

city: Norman

first: Scott

middle: D

last: Russell

state: OK

address: 770 Van Vleet Oval

department: Dept of Microbiology and Plant Biology

institute: University of Oklahoma

description: Gene expression data from antipodals at anthesis

hyb_protocol: Fifteen ug of fragmented cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rice Genome oligonucleotide array. Subsequent GeneChip washing and staining steps were performed on a GeneChip Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: GCOS 2.0. Affymetrix MAS 5.0 processing, with all chips scaled to the same target value of 500.

organism: Oryza sativa Japonica Group

source_name: Greenhouse grown rice, cv Katy

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip Two-Cycle cDNA Synthesis Kit for target preparation with signal amplification according to the standard Affymetrix protocol from total RNA of three replicates each of 100 unfertilized egg cells, 100 fertilized egg cells and 100 zygotes, respectively. According to estimate of Onishi et al. 2010 (PMID: 21106719) each egg cell is estimated to contain 25 pg and zygote slightly more (with paternal contribution); total RNA is estimated to be 25 ng for each 100 cell collection.

growth_protocol: Oryza sativa ssp. japonica, cultivar Katy were grown in greenhouses of the University of Oklahoma, under long-day, disease free conditions

extract_protocol: Total RNA was purified using the RNeasy plant mini kit according to manufacturer’s instructions (Qiagen).

treatment_protocol: Synergids and antipodals were collected from anthesis florets.  Ovaries were excised and ovules bisected to remove the selected cell types from the female gametophyte using a non-enzymatic method modified from Zhang et al (2010). Synergids were isolated from the micropylar female gametophyte and antipodals from the chalazal female gametopyte.

value: Antipodal Cell

value: Wild type


title: Antipodal Cell, biological rep 1


title: Antipodal Cell, biological rep 3


title: Synergid Cell, biological rep 3

description: Gene expression data from synergids at anthesis

value: Synergid Cell


title: Synergid Cell, biological rep 1


title: SPONT_rep4 (antimony)


title: LMS61

value: Primary tumor Leiomyosarcoma

tag: os

value: FEMALE

tag: differentiation

tag: location

tag: age


title: N2 Day 5 atgl-1 RNAi [LL40]

first: Louis

last: Lapierre

address: 185 Meeting St.

institute: Brown

data_processing:
 Illumina HiSeq, 2x150bp configuration, single index, per lane
Sequences were trimmed using Trimmomatic and mapped to the Caenorhabditis elegans reference genome available on ENSEMBL  using the STAR aligner
Unique gene hit counts were calculated by using feature Counts from the Subread package. Only unique reads that fell within exon regions were counted.
Assembly: WBcel235 (Ensembl Release 67)
Supplementary files format and content: Normalized counts are TMP

organism: Caenorhabditis elegans

source_name: N2 Day 5 atgl-1 RNAi

growth_protocol: Nematodes were synchronized using hypochlorite and eggs were seeded on nematode growth media plates with E. coli OP50 and developed at 20°C

extract_protocol:
Total RNA was extracted from approximately 10-12000 worms after treatment using Trizol Reagent (Invitrogen) followed by purification using Qiagen RNeasy kit according to the manufacturers' protocols
Standard Illumina protocols were used for RNA library preparations

treatment_protocol: At Day 1 of adulthood, the nematodes were transferred onto nematode growth media plates with control bacteria or bacteria expressing dsRNA against atgl-1 and grown at 25°C for 4 days

tag: strain/genotype

value: atgl-1 RNAi 4 days 25C


title: N2 Day 5 atgl-1 RNAi [LL41]


title: SPONT_rep5 (antimony)


title: Synergid Cell, biological rep 2

tag: cell type


title: SPONT_rep3 (antimony)


title: N2 Day 5 atgl-1 RNAi [LL42]


title: N2 Day 5 Control RNAi [LL39]

source_name: N2 Day 5 Control RNAi

value: Control 4 days 25C


title: SPONT_rep2 (antimony)


title: LMS53

value: Member

value: small RNA


title: TREATED_rep6 (antimony)

description: antimony treated tumor M. musculus sample

source_name: lung, antimony treated tumor

value: antimony_Treated Tumor


title: N2 Day 5 Control RNAi [LL38]


title: Zygote (~3 hap), biological rep 2

description: Gene expression data from isolated sperm cells at pollen anthesis

data_processing: Affymetrix MAS 5.0 processing, with all chips scaled to the same target value of 500.

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip Two-Cycle cDNA Synthesis Kit for target preparation with signal amplification according to the standard Affymetrix protocol from total RNA of three replicates each of 100 unfertilized egg cells, 100 fertilized egg cells and 100 zygotes, respectively. According to estimate of Onishi et al. 2010 (PMID: 21106719) each egg cell is estimated to contain 25 pg and zygote slightly more (with paternal contribution); total RNA is estimated to be 2.5 ng for each 100 cell collection.

extract_protocol: Total RNA was purified using the RNeasy plant mini kit according to manufacturer’s instructions (Qiagen).  Yield per egg cell or zygote cell is estimated at 25 picogram (by Ohnishi et al., 2011, and our own estimates), so the total collection may represent ~2.5 ng Total RNA

treatment_protocol: Egg cells (unfertilized), egg cells (fertilized) and zygotes were collected from anthesis florets, ovaries isolated and ovules excised to remove egg and zygote cells from the micropylar female gametophyte using non-enzymatic method described in Zhang et al (2010) for isolation of rice female gametophyte cells.  Each biological technical replicate represents ~100 cells.

tag: subspecies

value: japonica

tag: cultivar

value: Katy

tag: genotype

tag: developmental stage

value: Zygote (~3 hap)


title: N2 Day 5 atgl-1 RNAi [LL36]

value: N2 (Bristol)


title: Zygote (~3 hap), biological rep 3


title: SPONT_rep1 (antimony)


title: LMS52

tag: tissue

value: Internal trunk

tag: lms subtype

value: hLMS

tag: molecule subtype


title: N2 Day 5 Control RNAi [LL37]


title: LMS51

tag: metastasis

tag: Sex

value: MALE


title: Fertilized Egg Cell (~1 hap), biological rep 1

description: Gene expression data from pollen at anthesis

value: Fertilized Egg Cell (~1 hap)


title: N2 Day 5 atgl-1 RNAi [LL35]

tag: treatment


title: Zygote (~3 hap), biological rep 1

value: Wild type


title: LMS50


title: Fertilized Egg Cell (~1 hap), biological rep 2


title: N2 Day 5 Control [LL32]

source_name: N2 Day 5 Control


title: N2 Day 5 atgl-1 RNAi [LL33]


title: TREATED_rep4 (antimony)

tag: group


title: LMS46

tag: os

value: Not evaluable


title: Unfertilized Egg Cell, biological rep 3

description: Gene expression data from whole seedlings at 3rd collar leaf stage

value: Unfertilized Egg Cell


title: TREATED_rep3 (antimony)


title: Unfertilized Egg Cell, biological rep 1