title: Exp2_2D_LRRK050779_2


title: PHH NASH + ELA 60 µM 1

status: Public on Mar 16 2022

type: RNA

city: Brussels

first: Joost

last: Boeckmans

address: Laarbeeklaan 103

department: In Vitro Toxicology & Dermato-Cosmetology (IVTD)

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

hyb_protocol: 1) 12.5 µg fragmented aRNA was hybridized to Affymetrix Human Genome U133 plus 2.0 chips with hybridization cocktail solution.  2) Chips were incubated in an Genechip Hybridization Oven-645 (Affymetrix) (60 RPM / 45 °C /16h)  3) Chips were washed on a Genechip Fluidics Station-450 (Affymetrix)  4) Chips were stained with the Affymetrix HWS kit

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G.

data_processing: Robust Multichip Average (RMA) Express was used for normalization and summarization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: liver

label_protocol: RNA (100 ng) was amplified using the GeneChip 3' IVT PLUS Reagent Kit (Affymetrix). The amplified RNA was purified using magnetic beads and 15 µg Biotin-aRNA was treated with fragmentation reagent.

growth_protocol: Cell cultures and exposures were performed according to Rodrigues et al. (2014) (DOI: 10.1089/scd.2013.0157) and Boeckmans et al. (2020) (DOI: 10.1007/s10565-020-09544-2)

extract_protocol: Total RNA was extracted using the GenElute Mammalian Total RNA Purification Miniprep Kit (Sigma-Aldrich).

tag: treatment

value: 'NASH' triggers + elafibranor 60 µM

tag: cells

value: PHH


title: S21971_353_ctr

type: SRA

city: Milan

first: Francesco

last: Bertolini

state: I am not in the U.S. or Canada

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: European Institute of Oncology (IEO)

library_source: transcriptomic

data_processing:
FASTQ files were converted to digital gene-cell count matrices using a Singularity- dependent Snakemake pipeline (https://github.com/raveancic/scRNAaltas_TNBC_mm/tree/master/cl_crt_FASTQ2countmat) employing the Cell Ranger v4 software. As reference, the Mus musculus reference genome GENCODE vM23/Ensembl98 was used. Market Exchange Format (MEX) for sparse matrices generated from the pipeline were loaded, merged, processed and analyzed using Seurat package.
Genome_build: mm10 (GENCODE vM23/Ensembl98)
Supplementary_files_format_and_content: Market Exchange Format (MEX) for sparse matrices

molecule: polyA RNA

organism: Mus musculus

source_name: Cd45+ tumoral microenvironment

extract_protocol:
Tumours of three mice were dissociated and pooled together to generate the single cell suspension. The cell suspensions were then prepared for cell sorting with FACS Fusion sorter (BD bioscience). Only Cd45 + DAPI - (alive immune cells) were sorted and purity evaluated
10X Genomics protocol

tag: cell line

tag: condition

value: ctr

tag: 10x chemistry version


title: Exp1_3D_LRRK050779_1

city: Medford

first: Nicholas

middle: James

last: Fiore

state: MA

address: 200 College Ave

department: Biomedical Engineering

country: USA

institute: Tufts University

data_processing:
Illumina pipeline CASAVA v1.8.2 was used for base calling.
Raw sequencing data was uploaded to the Tufts University Galaxy Server for quality and adapter trimming with Trim Galore, read alignment with RNA STAR (reference human genome build 38), and read quantification with FeatureCounts using default settings.
Normalized read count tables, obtained by dividing the read counts by their size factors, were generated and extracted with the DESeq2 R package.
Genome_build: reference human genome build 38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: dopaminergic neurons

growth_protocol: On day 0, a single cell suspension of hiPSCs (maintained with mTeSR1) was seeded in 50:50 (v/v) mTeSR1:floor plate specification medium (neurobasal medium (ThermoFisher 21103049) with 1X floor plate specification supplement (ThermoFisher A3146801)) supplemented with 10 μM Y-27632 (STEMCELL Technologies 72302) at a density of 2 x 10^5 cells/cm2 on 6-well plates coated with Matrigel. The next day, cells were washed with Dulbecco’s phosphate buffered saline (DPBS, ThermoFisher) and fresh specification medium was added. Medium was carefully changed every 48 hours. On day 11, floor plate progenitors (FPPs) were split 1:2 using Accutase (Innovative Cell Technologies AT104, San Diego, CA, USA) onto new Matrigel-coated 6-well plates with FPP expansion medium (ThermoFisher A3165801) + 10 μm Y-27642. FPPs were expanded (replacing FPP expansion medium every 48 hours) until cryopreservation on day 22 with Synth-a-Freeze reagent (ThermoFisher A1254201) to establish batches of cells for experimental consistency. For each individual experiment, FPPs were thawed and plated at a density of 6.25 x 10^5 cells/cm2 in Matrigel coated 6-well plates supplemented with 10 μM Y-27642. On day 28, FPPs were differentiated to DA neurons starting with a 72 hour treatment of maturation medium (DMEM/F12 (ThermoFisher 10565018) with 1X maturation supplement (ThermoFisher A3147401)) containing 1 μM PD0325901 (MilliporeSigma PZ0162, Burlington, MA, USA) and 5 μM SU5402 (MilliporeSigma SML0443). PD0325901 and SU5402 were employed to inhibit progenitor cell proliferation and promote neurogenesis.

extract_protocol:
Total RNA was isolated from independent cultures using the RNeasy mini kit (Qiagen 74106, Hilden, Germany) utilizing the on-column DNA-digestion procedure according to manufacturer’s instructions. To improve extraction efficiency, the 2D cultures and 3D constructs were gently sonicated in the kit’s lysis buffer prior to extraction (ThermoFisher model no. FB120, 20% power, 1 second on followed by 1 second off for 10 pulses total). Sample purity and concentration was measured with a Nanodrop (ThermoFisher) spectrophotometer and 1 μg RNA per sample with a 260/280 nm reading greater than 2 were sent to Novogene for additional quality control tests, library preparation, and sequencing. First, RNA degradation and contamination were assessed on 1% agarose gels and RNA purity was checked using a NanoPhotometer spectrophotometer (Implen, Munich, Germany). RNA integrity and quantitation were assessed using the RNA Nano 6000 assay kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).
Library preparation was achieved using the NEBNext Ultra RNA library prep kit for Illumina systems following manufacturer’s recommendations (New England Biolabs, Ipswich, MA, USA) and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand complementary DNA (cDNA) was synthesized using random hexamer primer and M-MuLV reverse transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Brea, CA, USA). Then 3 μL USER Enzyme (New England Biolabs) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 minutes followed by 5 minutes at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system, Beckman Coulter) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on an Illumina Novaseq sequencer according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on the same machine and paired-end reads were generated at a read depth of 20 million reads.

treatment_protocol: On day 31, cells were pre-differentiated DA neurons were seeded into 2D and 3D culture condition

tag: cell type

value: hiPSC-derived dopaminergic neurons

tag: genotype

value: LRRK2 G2019S

tag: parkinson's disease (pd) status

value: PD

tag: culture condition

value: Three dimensional (3D)

tag: experiment number


title: Exp2_2D_LRRK050401-01_1

value: Two dimensional (2D)


title: C166_2hr_nuc_1

city: Kuopio

first: Mikko

middle: P

last: Turunen

address: Yliopistonranta 1 E

department: A. I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

data_processing:
Our data analysis pipeline is based on the Tuxedo software package, which is a combination of open-source software and implements peer-reviewed statistical methods. In addition we employ specialized software developed internally at Exiqon to interpret and improve the readability of the final results. The components of our NGS RNA seq analysis pipeline include Bowtie2 (v. 2.2.2), Tophat (v2.0.11) and Cufflinks (v2.2.1).
Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns the sequencing reads to the reference genome using the sequence aligner Bowtie2. Tophat also uses the sequence alignments to identify splice junctions for both known and novel transcripts.
Cufflinks takes the alignment results from Tophat to assemble the aligned sequences into transcripts, constructing a map or a snapshot of the transcriptome. To guide the assembly process, an existing transcript annotation is used. In addition, we perform fragment bias correction which seeks to correct for sequence bias during library preparation (see Kasper et al., 2010 and Adam et al., 2011). The Cufflinks assembles aligned reads into different transcript isoforms based on exon usage and also determines the transcriptional start sites (TSSs).
When comparing groups, Cuffdiff is used to calculate the FPKM (number of fragments per kilobase per million mapped fragments) and test for differential expression and regulation among the assembled transcripts across the submitted samples using the Cufflinks output. Cuffdiff can be used to test differential expression at different levels, from CDS and gene specific, down to the isoform and TSS transcript level. For more information on the Cuffdiff module, see Trapnell et al., (2013).
When comparing groups with paired samples, featureCounts is used to calculate the counts of mapped reads in specific genes, and generalized linear model likelihood ratio test (glmLRT) implemented by edgeR is used to test for differential expression across the submitted samples using featureCounts output. For more information on featureCounts, (see Liao Y, 2014). For more information on edgeR and glmLRT, (see McCarthy, 2012).
As a final step, CummeRbund, which is an open source R package, will be used in combination with in-house custom software for post processing of Cufflinks and Cuffdiff results. We use these tools to generate a visual representation of your sequencing results to aid the interpretation of the sequencing data and the analysis results.
Genome_build: GRCm38
Supplementary_files_format_and_content: fastq files were generated by Exiqon A/S, Vedbaek, Denmark and further processed to xlsx file by authors

molecule: nuclear RNA

source_name: C166 endothelial cell line

growth_protocol: C166 or C1.1 cells were grown on 150 mm cell culture dish in DMEM containing 10 % FBS and 1 % penicillin-streptomycin. Cells were split for experiments two days prior treatment so that they reach 80% confluency at the time of treatment.

extract_protocol:
Cells were fractionated into nuclear and cytoplasmic fractions and RNA isolated according to a protocol by Gagnon et al. (Gagnon K, Li L, Janowski BA, Corey DR. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nature Protocols 2014, vol. 9, no. 9, p.2045-60).
The library preparation was done using TruSeq® stranded total RNA sample preparation kit with rRNA depletion (Illumina inc).The starting material (300 ng) of total RNA was rRNA depleted using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal. The isolated mRNA was subsequently fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed and the double stranded cDNA was purified (AMPure XP, Beckman Coulter). The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (AMPure XP). The mRNA stranded libraries were pre-amplified with PCR and purified (AMPure XP). The libraries size distribution was validated and quality inspected on a Bioanalyzer high sensitivity DNA chip (Agilent Technologies). High quality libraries were quantified using qPCR, the concentration normalized and the samples pooled according to the project specification (number of reads). The library pool(s) were re-quantified with qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing on HiSeq2500) instrument using hiSeq v.4 reagents (51 cycles) (Illumina Inc.).(service from Exiqon A/S, Vedbaek, Denmark)

treatment_protocol: Cells were treated with hypoxia (2h or 24h) or normoxia (control). Hypoxia treatment was done using 1 % oxygen (InvivO2 Baker Ruskinn hypoxia chamber).

value: yolk sac -derived endothelial cells (ATCC:CRL-2581)

value: 2h hypoxia

tag: fraction

value: nucleus


title: PHH NASH 3

value: NASH' triggers


title: Exp2_2D_WT050176_2

value: Wild Type

value: Healthy


title: C166_2hr_nuc_2


title: Exp1_3D_LRRK05040101_2


title: C1.1_24hr_cyt_2

molecule: cytoplasmic RNA

source_name: C1.1. mutant cell line

value: yolk sac -derived endothelial cells (ATCC:CRL-2581) with CRISPR-mediated removal of mmu-miR-466c

value: 24h hypoxia

value: cytoplasm


title: Exp1_3D_LRRK05040101_1


title: PHH CTL 3

value: No treatment (vehicle)


title: S22850_400_c140

value: C140 (Cyclophosphamide)


title: C166_0hr_nuc_1

value: normoxia


title: S22851_401_c140_vino

value: C140 + V (Vinorelbine)


title: Exp1_3D_LRRK050779_2

value: hiPSC-derived dopaminergic neurons

value: LRRK2 G2019S


title: PHH NASH 1

value: PHH


title: PHH NASH 2


title: Exp1_2D_LRRK050779_1

value: PD

value: Two dimensional (2D)


title: C166_0hr_nuc_2

value: yolk sac -derived endothelial cells (ATCC:CRL-2581)


title: S22852_402_c140_vino_pd1

value: C140 + V + alphaPD-1


title: PHH CTL 2


title: S21611_320_Pd1


title: S21614_323_cispl_pd1

value: P(Cisplatin) + alphaPD-1


title: PHH CTL 1


title: C1.1_24hr_cyt_1


title: Exp1_2D_LRRK050401-01_1


title: S21613_322_doxo_pd1

value: D(Doxorubicin) + alphaPD-1


title: WGBS_HCC1954-GATA3KO_2

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

country: France

institute: IGBMC

library_source: genomic

data_processing:
WGBS reads were trimmed using trim_galore (version 0.6.4 options -q 20 --stringency 2 --clip_R2 10 --clip_R1 5) and mapped using bismark (version 0.22.1). Non-converted and duplicated reads were further filtered out using filter_non_conversion --percentage_cutoff 50 --minimum_count 5 and deduplicate_bismark. Methylation levels were extracted using bismark_methylation_extractor.
Genome_build: hg38

molecule: genomic DNA

source_name: HCC1954 cells

growth_protocol: HCC1954 cells (ATCC CRL-2328) were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin streptomycin.

extract_protocol:
One hundred nanograms of genomic DNA were fragmented to 350 bp using a Covaris E220 sonicator. DNA was bisulfite converted with the EZ DNA Methylation-Gold kit (Zymo Research).
WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) according to the manufacturer’s instructions with six or seven PCR cycles for the final amplification. The libraries were purified using Ampure XP beads (Beckman Coulter).

value: HCC1954 cells

value: GATA3 KO


title: C1.1_2hr_cyt_2

value: yolk sac -derived endothelial cells (ATCC:CRL-2581) with CRISPR-mediated removal of mmu-miR-466c

value: 2h hypoxia


title: S21612_321_c140_pd1

value: C140 + alphaPD-1


title: C1.1_2hr_cyt_3

value: cytoplasm


title: WGBS_HCC1954-GATA3KO_1


title: AZ960_1

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

country: China

institute: Sichuan University

description:
Tpm4-AZ960-1
AZ960_vs_Vehicle.xlsx

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using STAR_2.6.0a
Counts were normalized by DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files with all gene counts and DEGs

growth_protocol: The organoids sent to RNA-seq were all cultured from esophageal wild type c57BL/6 tissue. By the time of sample submission, all organoids were in the second generation after infection or treatment.

extract_protocol:
RNA was extracted with Trizol
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control and Tpm4OE organoids were wild type organoids respectively infected with vehicle construct and Tpm4 CDNA. Vehicle and AZ960 organoids were all Tpm4 overexpression and respictively treated by DMSO and JAK2 inhibitor AZ960  for 48 hours.

tag: agent

value: organoids

tag: strain

tag: genotype/variation

value: Tpm4 overexpression


title: C1.1_2hr_cyt_1


title: C1.1_0hr_cyt_3

value: normoxia


title: AZ960_3

description:
Tpm4-AZ960-3
AZ960_vs_Vehicle.xlsx


title: HepaRG NASH + ELA 60 µM 1

value: NASH' triggers + elafibranor 60 µM

value: HepaRG


title: AZ960_2

description:
Tpm4-AZ960-2
AZ960_vs_Vehicle.xlsx


title: HepaRG NASH + ELA 60 µM 2

value: 'NASH' triggers + elafibranor 60 µM


title: WGBS_HCC1954-FOXA1KO_1

value: FOXA1 KO


title: WGBS_HCC1954-GATA3WT_1

value: WT


title: vehicle_2

description:
Tpm4-vehicle-2
AZ960_vs_Vehicle.xlsx

value: DMSO


title: HepaRG NASH + ELA 60 µM 3


title: C1.1_0hr_cyt_1


title: WGBS_HCC1954-FOXA1WT_1


title: C1.1_0hr_cyt_2


title: HepaRG NASH 2

value: NASH' triggers


title: WGBS_HCC1954_1


title: C166_24hr_cyt_3

value: yolk sac -derived endothelial cells (ATCC:CRL-2581)

value: 24h hypoxia


title: vehicle_3

description:
Tpm4-vehicle-3
AZ960_vs_Vehicle.xlsx


title: S21610_319_ctr

value: ctr


title: HepaRG NASH 1


title: C1.1_24hr_cyt_3

value: yolk sac -derived endothelial cells (ATCC:CRL-2581) with CRISPR-mediated removal of mmu-miR-466c


title: Tpm4OE_3

description:
wt-Tpm4-3
TPM4_vs_control_all.xlsx

tag: infection

value: Tpm4 CDNA

value: wildtype


title: HepaRG NASH 3


title: WGBS_HCC1954-FOXA1KO_2

value: HCC1954 cells


title: C166_24hr_cyt_2

value: cytoplasm


title: Tpm4OE_1

description:
wt-Tpm4-1
TPM4_vs_control_all.xlsx

value: organoids


title: Tpm4OE_2

description:
wt-Tpm4-2
TPM4_vs_control_all.xlsx


title: C166_24hr_cyt_1


title: C166_2hr_cyt_2

value: 2h hypoxia


title: C166_2hr_cyt_3


title: Sc_All_UA_in_vitro_aposymbiotic

city: Tucson

first: Emilie

last: Lefoulon

state: AZ

address: 1117 E. Lowell Street

institute: University of Arizona

data_processing:
Illumina Casava1.8.2 software used for basecalling. Reads were trimmed and filtered using Trim Galore (version 0.6.4) and quality was assessed using FastQC (v0.11.9).
All the reads belonging to the same species were combined to performed a de novo transcriptome assembly using Trinity (v2.10). All the reads belonging to the same species were combined to performed a de novo transcriptome assembly using Trinity (v2.10). Selection of transcripts were initially identified based on similarity with a custom database of protein from the nematodes using xblast.
Open reading frames (ORFs) were identified using TransDecoder. Then, Reads from each condition were mapped back to the trancriptome assembly using Tophat (v2.1.1).
The abundances of the transcripts and the differential expression were tested using two different method: using Cufflinks (v2.2.1) and using edgeR (v 3.32.1)(parameters FDR ≤ 0.01 and p-value ≤ 0.01).
Only the transcript presenting at least 25 counts are conserved in the analysis.
Genome_build: assemblies were submitted as part of PRJNA766056
Supplementary_files_format_and_content: tab-delimited text files including raw gene counts for every transcript for the three conditions.
Supplementary_files_format_and_content: tab-delimited text files including the normalized abundance measurements and differential expression tests (logFC, logCPM, PValue and FDR) established by edgeR between the in vitro condition (colonized and aposymbiotic) and the in vivo condition.
Supplementary_files_format_and_content: tab-delimited text files including the normalized abundance measurements and differential expression tests (FPKM, log2(FPKMy/FPKMx), p-value and FDR-adjusted p-value) established by cuffdiff between the in vitro condition (colonized and aposymbiotic) and the in vivo condition.

organism: Steinernema carpocapsae

source_name: Whole worm

growth_protocol: 100 infective juveniles (IJs) was used to infect one single last instar G. mellonella larva and incubated at 25°C for 3-4 days.

extract_protocol:
A total of 10,000 IJs from each condition were grinded with an Omni tip and rotor-stator running at > 18k rpm (>30 seconds), then pelleted at high speed and the supernatant was processed using Qiagen RNeasy Mini kit.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA protocols. A total of nine samples were multiplexed.

treatment_protocol: In vivo rearing: cadavers were transferred to white trap to collect emerging IJs. In vitro rearing: eggs in liver-kidney agar (LKA) plate supplemented with 0.1% sodium pyruvate. For colonized condition: culture of native Xenorhabdus symbiont added to the LKA plate.

value: All

tag: development stage

value: Infective Juvenile

tag: tissue

value: whole worm

tag: rearing condition

value: liver-kidney agar plate without symbiont


title: Sp_Li6_UA_in_vitro_aposymbiotic

organism: Steinernema puntauvense


title: vehicle_1

description:
Tpm4-vehicle-1
AZ960_vs_Vehicle.xlsx

value: Tpm4 overexpression


title: Sp_Li6_UA_in_vitro_colonized

value: liver-kidney agar plate with cognate symbiont


title: Sp_Li6_UA_in_vivo

value: in vivo (host:Galleria mellonella)


title: WGBS_HME1_1

source_name: hTERT-HME1 cells

growth_protocol: hTERT-HME1 cells (ATCC CRL-4010) were cultured in Mammary Epithelial Cell Basal Medium (MEBM) supplemented with 4 μl/ml bovine pituitary extract, 10 ng/ml human recombinant epidermal growth factor, 5 μg/ml insulin, 0.5 μg/ml hydrocortisone.

value: hTERT-HME1 cells

value: WT


title: Control_3

description:
wt-pmig-3
TPM4_vs_control_all.xlsx

value: vehicle construct


title: Sc_All_UA_in_vivo


title: C166_0hr_cyt_3

value: yolk sac -derived endothelial cells (ATCC:CRL-2581)

tag: treatment

value: normoxia


title: C166_0hr_cyt_2


title: Mesenteric artery, WT_5K

city: Nagoya

first: Yoshiaki

last: Suzuki

address: 3-1 Tanabedori, Mizuhoku

department: Molecular and Cellular Pharmacology, Graduate School of Pharmaceutical Sciences

country: Japan

institute: Nagoya City University

description: Tissues from two mice were used to prepare the sample.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using TopHat v2.0.12. The mismatch parameter is set to two, and other parameters are set to default.
In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used. In RNA-seq, FPKM, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairssequenced, is the most common method of estimating gene expression levels, which takes into account the effects of both sequencing depth and gene length oncounting of fragments(Trapnell, Cole, et al., 2010). HTSeq software (v0.6.1) was used to analyze the gene expression levels in this experiment, using the union mode. The result files present the number of genes with different expression levels and the expression level of single genes. In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program (3.0.8) through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGseq R package (1.12.0). The P values were adjusted using the Benjamini and Hochberg methods. Corrected pvalue of 0.005 and |log2 (Fold Change)| of 1 were set as the threshold for significantly differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: Tab-delimited text file includes readcount for each Sample.

source_name: Mesenteric artery

extract_protocol:
Arteries were removed, flash frozen on liquid N2, and RNA was extracted from samples using TRIzol and PureLink RNA spin column (Thermo Fisher Scientific). Genomic DNA was digested using TURBO™ DNase (Thermo Fisher Scientific).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Mouse mesenteric arteries were treated with 60 mM K+ solution for 60min

value: Mesenteric artery

tag: age

value: 10 weeks old

value: wild type

value: 5 mM K+ solution for 60 min


title: C166_2hr_cyt_1

value: 2h hypoxia

value: cytoplasm


title: Mesenteric artery, WT_60K

value: 60 mM K+ solution for 60 min


title: Control_1

description:
wt-pmig-1
TPM4_vs_control_all.xlsx

value: organoids

value: wildtype


title: Control_2

description:
wt-pmig-2
TPM4_vs_control_all.xlsx


title: C166_0hr_cyt_1


title: Sc_All_UA_in_vitro_colonized

value: All

value: Infective Juvenile

value: whole worm


title: mRNA_ColorectalCancer_rep190

status: Public on Mar 15 2022

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

institute: Japanese Foundation Cancer Research

hyb_protocol: After fragmentation, cRNA was hybridized with Affymetrix Hybridization,Wash, and Stain Kit on Affymetrix Human Genome GeneChip U133 Plus 2.0 array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA using Affymetrix Expression Console software.

label: biotion

source_name: mRNA from fresh frozen colorectal tumor tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit  according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.

value: colorectal tumor

tag: gender

value: female


title: mRNA_ColorectalCancer_rep181

value: male


title: mRNA_ColorectalCancer_rep185


title: mRNA_ColorectalCancer_rep186


title: mRNA_ColorectalCancer_rep183


title: mRNA_ColorectalCancer_rep184


title: mRNA_ColorectalCancer_rep189


title: mRNA_ColorectalCancer_rep187


title: mRNA_ColorectalCancer_rep176


title: mRNA_ColorectalCancer_rep182


title: mRNA_ColorectalCancer_rep172


title: mRNA_ColorectalCancer_rep174


title: mRNA_ColorectalCancer_rep169


title: mRNA_ColorectalCancer_rep180


title: mRNA_ColorectalCancer_rep179


title: mRNA_ColorectalCancer_rep178


title: mRNA_ColorectalCancer_rep188


title: mRNA_ColorectalCancer_rep173


title: mRNA_ColorectalCancer_rep168


title: mRNA_ColorectalCancer_rep170


title: mRNA_ColorectalCancer_rep177


title: mRNA_ColorectalCancer_rep165


title: mRNA_ColorectalCancer_rep171


title: mRNA_ColorectalCancer_rep166


title: mRNA_ColorectalCancer_rep167


title: mRNA_ColorectalCancer_rep175


title: mRNA_ColorectalCancer_rep163


title: mRNA_ColorectalCancer_rep162


title: mRNA_ColorectalCancer_rep152


title: mRNA_ColorectalCancer_rep158


title: mRNA_ColorectalCancer_rep161


title: mRNA_ColorectalCancer_rep164


title: mRNA_ColorectalCancer_rep155


title: mRNA_ColorectalCancer_rep144


title: mRNA_ColorectalCancer_rep145


title: mRNA_ColorectalCancer_rep151


title: mRNA_ColorectalCancer_rep138


title: mRNA_ColorectalCancer_rep147


title: mRNA_ColorectalCancer_rep160


title: mRNA_ColorectalCancer_rep141


title: mRNA_ColorectalCancer_rep146


title: mRNA_ColorectalCancer_rep150


title: mRNA_ColorectalCancer_rep148


title: mRNA_ColorectalCancer_rep149


title: mRNA_ColorectalCancer_rep154


title: mRNA_ColorectalCancer_rep140


title: mRNA_ColorectalCancer_rep137


title: mRNA_ColorectalCancer_rep153


title: mRNA_ColorectalCancer_rep159


title: mRNA_ColorectalCancer_rep143


title: mRNA_ColorectalCancer_rep134


title: mRNA_ColorectalCancer_rep135


title: mRNA_ColorectalCancer_rep157


title: mRNA_ColorectalCancer_rep136


title: mRNA_ColorectalCancer_rep156


title: mRNA_ColorectalCancer_rep127


title: mRNA_ColorectalCancer_rep139


title: mRNA_ColorectalCancer_rep130


title: mRNA_ColorectalCancer_rep142


title: mRNA_ColorectalCancer_rep133


title: mRNA_ColorectalCancer_rep121


title: mRNA_ColorectalCancer_rep129


title: mRNA_ColorectalCancer_rep125


title: mRNA_ColorectalCancer_rep132


title: mRNA_ColorectalCancer_rep128


title: mRNA_ColorectalCancer_rep131


title: mRNA_ColorectalCancer_rep124


title: mRNA_ColorectalCancer_rep119


title: mRNA_ColorectalCancer_rep122


title: mRNA_ColorectalCancer_rep120


title: mRNA_ColorectalCancer_rep115


title: mRNA_ColorectalCancer_rep123


title: mRNA_ColorectalCancer_rep118


title: mRNA_ColorectalCancer_rep114


title: mRNA_ColorectalCancer_rep126


title: mRNA_ColorectalCancer_rep116


title: mRNA_ColorectalCancer_rep111


title: 28d_H3K4me3_2

city: Chengdu

first: Jing

last: Li

state: China

address: No. 211 Huimin Road, Wenjiang District

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

data_processing:
Reads were mapped to the pig genome (Sscrofa 11.1) by BWA (v 0.7.15).
Samtools (v 1.3.1) was used to remove potential PCR duplicates.
Peaks were identified with MACS2 algorithms.
Super-enhancers were defined using the standard ROSE algorithms.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Peaks file, text file

organism: Sus scrofa

source_name: Liver

extract_protocol:
Samples were washed with PBS and incubated in lysis buffer. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp). The histone-DNA complexes were isolated with H3K27ac and H3K4me3.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the Illumina TruSeq ChIP Sample Prep Set A and sequenced on Illumina HiSeq X Ten with PE150 method

treatment_protocol: Six two-years-old female pigs were fed with a high fat diet (15.12 MJ·kg-1 metabolizable energy, 11.26% crude protein, 6.8% fat and 5% lysine) for 22 weeks, compared with the pigs of  two-years-old fed with well-characterized normal diet for 22 weeks.

tag: breed

value: Bama pig

value: Liver

tag: condition

value: Developmental stage

value: postnatal day 28

tag: Sex

tag: chip antibody


title: 29d_input_2

value: none (input)


title: mRNA_ColorectalCancer_rep117


title: 110d_H3K4me3_2

value: postnatal day 110


title: E80_H3K4me3_2

value: embryonic day 80


title: HFD_RNA_replicate_5

data_processing:
Sequence reads are aligned to pig reference genome (Sscrofa 11.1) by alignment tool STAR (version 2.6.0c).
The aligned reads of these samples were assembled using Cufflinks (version 2.1.1).
Kallisto (v 0.44.0) was used to quantify gene expression and obtain TPM expression values.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: mRNA expression level (TPM), text file

extract_protocol:
liver were flash frozen in liquid nitrogen, and RNA was extracted using Trizol reagent.
rRNA depletion protocol (Ribo-Zero kit, Epicentre) and Illumina TruSeq stranded RNA-Seq library protocol are used to construct the RNA-Seq libraries. cDNA libraries were  sequenced on HiSeq X Ten (Illumina) platform to produce 150-bp paired-end raw reads.

value: High fat diet treatment


title: mRNA_ColorectalCancer_rep113


title: mRNA_ColorectalCancer_rep112


title: mRNA_ColorectalCancer_rep110


title: mRNA_ColorectalCancer_rep109


title: HFD_RNA_replicate_3


title: 0d_H3K4me3_2

value: the birth day


title: mRNA_ColorectalCancer_rep102


title: 0d_input_2


title: HFD_RNA_replicate_4


title: E38_input_2

value: embryonic day 38


title: mRNA_ColorectalCancer_rep105


title: HFD_RNA_replicate_6


title: mRNA_ColorectalCancer_rep101


title: mRNA_ColorectalCancer_rep108


title: mRNA_ColorectalCancer_rep98


title: mRNA_ColorectalCancer_rep100


title: HFD_RNA_replicate_1


title: mRNA_ColorectalCancer_rep106


title: 2y_RNA_replicate_6


title: mRNA_ColorectalCancer_rep99


title: mRNA_ColorectalCancer_rep104


title: mRNA_ColorectalCancer_rep107


title: 2y_RNA_replicate_2


title: mRNA_ColorectalCancer_rep96


title: mRNA_ColorectalCancer_rep103


title: 2y_RNA_replicate_1


title: 2y_RNA_replicate_4


title: mRNA_ColorectalCancer_rep97


title: mRNA_ColorectalCancer_rep94


title: HFD_RNA_replicate_2


title: 911E_F1

city: Greenwood

first: Vijay

last: Shankar

state: South Carolina

address: 115 Milford Pines Drive

institute: Clemson University

data_processing:
Demultiplexing: Barcoded sequence reads were demultiplexed using the Illumina pipeline v1.9.
Preprocessing: Adapter sequences were trimmed using cutadapt v1.6. Trimmed sequences were then aligned to multiple target sequence databases, using BWA v0.7.10 (MEM algorithm with parameters ‘-v 2 –t 4’): (1) all trimmed sequences were aligned against a ribosomal RNA database to filter out residual rRNA that escaped depletion during library preparation; (2) remaining sequences were then aligned against a custom database of potential microbiome component species (see below) using BWA; (3) sequences that did not align to either the rRNA or microbiome databases were aligned to all D. melanogaster sequences in RepBase.
Alignment: The remaining sequences that did not align to any of the databases above were then aligned to the D. melanogaster genome (BDGP5) and known transcriptome (FlyBase v5.57) using STAR v2.4.0e
Quantification and Normalization: Read counts for known and novel gene models were quantified using HTSeq-count with the ‘intersection-nonempty’ assignment method. Tabulated read counts for each endogenous gene present in both Baseline and ethanol-treated lines were combined and normalized across all samples using EdgeR.
Genome_build: FlyBase v5.57
Supplementary_files_format_and_content: Matrix table in tab-delimited text file contains raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: Whole fly

extract_protocol:
Briefly, total RNA was extracted with Trizol using the RNeasy Mini Kit (Qiagen, Inc.) and ribosomal RNA was depleted from 5 ug of total RNA using the Ribo-Zero™ Gold Kit (Illumina, Inc.).
Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA.  Samples were processed in batches of 48 and 16 libraries were pooled randomly into 25 pools. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM following Illumina guidance. Pooled library samples were clustered on an Illumina cBot; each pool was sequenced on one lane of an Illumina HiSeq 2500 using 125 bp single-read v4 chemistry.

value: Female

tag: line

tag: exposure

value: 10% EtOH in growth media


title: 911E_M1

value: Male


title: 900E_M2


city: Montreal

first: Rima

last: Rozen

state: Quebec

address: 1001 Decarie Blvd

department: Departments of Human Genetics and Pediatrics

country: Canada

institute: McGill University

description: cortex of P30 female whose mother was fed CD, biological replicate 3

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0.2.15) (males and females were imported separately, Affymetrix default analysis settings, SST-RMA algorithm, comparison FASD vs CD; samples from CD and FASD groups were imported separatedly, Affymetrix default analysis settings, SST-RMA algorithm, comparison Females vs Males).

source_name: P30 female cortex CD

label_protocol: biotin

growth_protocol: Animal experimentation was conducted according to the guidelines of the Canadian Council on Animal Care and approved by the Animal Care Committee of the Research Institute of the McGill University Health Center. Mice were housed in speciﬁc pathogen free facilities with 12h light/dark cycles with food and water ad libitium.

extract_protocol: Total RNA was extracted from frozen cortices of P30 pups using the AllPrep DNA/RNA/miRNA Universal Kit kit with on-column DNase I treatment (Qiagen).

treatment_protocol: At weaning, wild-type C57BL/6 female mice were placed on amino acid deﬁned Control Diet (CD) (2mg folic acid/kg diet, recommended level for rodents (TD.01369, Harlan Laboratories, Inc., Madison, WI, USA) or Folic Acid Supplemented Diet (FASD) which contained 5 times the amount of folic acid (10mg folic acid/kg diet, TD.08278, Harlan Laboratories, Inc., Madison, WI, USA). Both diets contained 2.5 g/kg choline bitrate, 3.3 g/kg L-methionine and 1% succinylsulfathiazole, an antibiotic that inhibits folate synthesis by intestinal ﬂora. Five weeks after the start of the diets, females were mated with C57BL/6 males to study offspring. Diets were maintained throughout pregnancy and lactation. We conducted several behavioral tests on offspring before sacrificing them at P30. Cerebral cortices were collected to conduct gene expression analysis by microarray.

tag: diet

value: CD


title: 911E_F2


description: cortex of P30 female whose mother was fed FASD, biological replicate 4

source_name: P30 female cortex FASD

value: FASD


title: mRNA_ColorectalCancer_rep95

value: colorectal tumor


title: mRNA_ColorectalCancer_rep92

value: male


title: 897E_F1


description: cortex of P30 male whose mother was fed FASD, biological replicate 4

source_name: P30 male cortex FASD


description: cortex of P30 female whose mother was fed CD, biological replicate 4


title: 900E_M1


title: 911E_M2


title: 897E_M2


title: 890E_M2


description: cortex of P30 female whose mother was fed FASD, biological replicate 1


title: 2y_RNA_replicate_3

value: Bama pig

value: female


description: cortex of P30 female whose mother was fed FASD, biological replicate 2


title: 897E_M1


title: 2y_RNA_replicate_5

value: Liver

value: Developmental stage


title: 890E_M1


description: cortex of P30 female whose mother was fed CD, biological replicate 2


title: mRNA_ColorectalCancer_rep93


description: cortex of P30 female whose mother was fed CD, biological replicate 1


title: 900E_F1


description: cortex of P30 male whose mother was fed CD, biological replicate 4

source_name: P30 male cortex CD


description: cortex of P30 female whose mother was fed FASD, biological replicate 3


title: 897E_F2


description: cortex of P30 male whose mother was fed FASD, biological replicate 3


title: mRNA_ColorectalCancer_rep91


title: 900E_F2


description: cortex of P30 male whose mother was fed FASD, biological replicate 1


title: 890E_F1


title: female whose mother was fed FASD, biological rep 4

data_processing: The data were analyzed with Transcriptome Analysis Console software (TAC 4.0.2.15) (males and females were imported separately, SST-RMA algorithm, comparison FASD vs CD; samples from CD and FASD groups were imported separatedly, SST-RMA algorithm, comparison Females vs Males).

source_name: E17.5 female cerebrum, FASD

growth_protocol: Animal experimentation was performed in accordance with the guidelines of the Canadian Council on Animal Care and approved by the Animal Care Committee of the Research Institute of the McGill University Health Center (AUP 3132). Mice were housed at a 12h light/dark cycle and under specific pathogen-free conditions at 18–24ºC, with ad libitum access to food and water.

extract_protocol: Total RNA was extracted from frozen cerebra of E17.5 embryos using the AllPrep DNA/RNA/miRNA Universal Kit with on-column DNase I treatment (Qiagen).

treatment_protocol: At weaning, female C57BL/6 mice were randomly fed a CD (TD.01369, Harlan Laboratories, Inc., Madison, WI, USA) or FASD (TD.08278, Harlan Laboratories, Inc., Madison, WI, USA) for 4 to 5 weeks before mating. The diets were modified from the standard amino acid-defined AIN-93G formulation, containing 2.5 g/kg choline bitrate, 3.3 g/kg L-methionine and 1% succinylsulfathiazole (to inhibit folate synthesis by intestinal ﬂora). CD contained 2 mg/kg diet of FA, the recommended amount for rodents. 5x FASD contained 10 mg/kg FA diet. The morning of discovering a vaginal plug was designated embryonic day 0.5 (E0.5). Diets were maintained until E17.5. Cerebra were collected for RNA extraction and gene expression analysis by microarray.

value: E17.5 cerebrum


description: cortex of P30 male whose mother was fed CD, biological replicate 3


description: cortex of P30 male whose mother was fed CD, biological replicate 1


title: 882E_F2


description: cortex of P30 male whose mother was fed FASD, biological replicate 2


title: female whose mother was fed FASD, biological rep 3


title: 882E_M2


title: female whose mother was fed CD, biological rep 3

source_name: E17.5 female cerebrum, CD


title: 890E_F2


description: cortex of P30 male whose mother was fed CD, biological replicate 2


title: 852E_F1


title: female whose mother was fed FASD, biological rep 2


title: 852E_M2


title: female whose mother was fed CD, biological rep 2


title: 850E_M1


title: 850E_M2


title: female whose mother was fed CD, biological rep 4


title: 882E_M1


title: male whose mother was fed FASD, biological rep 4

source_name: E17.5 male cerebrum, FASD


title: female whose mother was fed FASD, biological rep 1


title: 882E_F1


title: 852E_M1


title: 850E_F2


title: male whose mother was fed FASD, biological rep 3


title: female whose mother was fed CD, biological rep 1


title: 849E_M2


title: male whose mother was fed FASD, biological rep 1


title: 850E_F1


title: male whose mother was fed CD, biological rep 1

source_name: E17.5 male cerebrum, CD


title: 849E_M1


title: 843E_F1


title: TAM-RNA-Klf5fl/fl-rep4

city: Stony Brook

first: Jason

last: Shieh

state: NY

address: 101 Nicolls Rd.

institute: Stony Brook University

data_processing:
Quality check with FastQC
Alignment was performed with HISAT2
Raw count matrix from featureCounts
Count normalization and differential expression was performed with DESeq2
Pathway analysis was with GSEA
Genome_build: mm9
Supplementary_files_format_and_content: Raw count matrix was generated from featureCounts

source_name: Colon

growth_protocol: No growth protocol

extract_protocol:
Bulk RNA-sequencing samples were extracted with Trizol. 16s rRNA sequencing samples were collected with the Promega Maxwell RSC 48 instrument.
Libraries was performed according to Illumina's TruSeq library prep instruction (20020594).
Bulk RNA-seq and 16s rRNA sequencing

treatment_protocol: Villin-CreERT2;KLF5 fl/fl  mice were treated with corn oil or tamoxifen

tag: mouse strain

tag: mouse genotype

tag: mouse treatment

value: Tamoxifen


title: 83E_M2


title: 843E_F2


title: 83E_M1


title: male whose mother was fed CD, biological rep 4


title: 843E_M2


title: 83E_F2


title: 83E_F1


title: CO-RNA-Klf5fl/fl-rep4

value: Corn Oil


title: CO-RNA-Klf5fl/fl-rep2


title: 837E_M2


title: 837E_F2


title: healthy control 3

city: Changchun

first: Min

last: Zhao

address: Changchun

institute: Jilin University

description: molecule subtype: tiRNA and tRF

data_processing:
Illumina NextSeq 500 raw sequencing read data that passed the Illumina chastity filter were used for the following analysis. Sequencing quality was examined by FastQC software.
After that, the sequencing reads were 5’, 3’-adaptor trimmed, filtered for more than 15 nt by Cutadapt software, and for exactly aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb (http://gtrnadb.ucsc.edu/) using NovoAlign software (v2.07.11).
The tsRNA expression levels were measured and normalized as tag counts per million of total aligned tRNA reads (CPM). For each tRNA sequence-based profile, the number of tRNA sequence reads could be used to estimate expression level of each tsRNA.
Assembly: hg19

source_name: Serum

extract_protocol: Total RNAs were extracted according to the manufacturer’s instruction (Invitrogen, CA,USA). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Then we did the following treatments to remove some RNA modifications which might interfere with small RNA-sequencing library construction: 3’-aminoacyl (charged) deacylation to 3’-OH (hydroxyl group) for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH phosphorylation to 5’-P for 5’-adaptor ligation, N1-methyladenosine and N3-methylcytidine demethylation for efficient reverse transcription. All procedures were performed using rtStar tRF&tiRNA Pretreatment Kit (Arraystar) protocols.

tag: disease state

value: healthy control

value: Serum

tag: age (years)

value: M

tag: ethnicity

value: Asian


title: 843E_M1

value: 10% EtOH in growth media


title: 849E_F1

value: Female


title: male whose mother was fed CD, biological rep 2

tag: tissue

value: CD


title: TAM-RNA-Klf5fl/fl-rep2


title: TAM-RNA-Klf5fl/fl-rep1


title: male whose mother was fed FASD, biological rep 2

value: FASD


title: 849E_F2


title: CO-RNA-Klf5fl/fl-rep3


title: TAM-RNA-Klf5fl/fl-rep3


title: Sarcoidosis number 3

description: molecule subtype: tiRNA and tRF

value: Sarcoidosis


title: 837E_M1

value: Male


title: healthy control 2

description: molecule subtype: tiRNA and tRF


title: male whose mother was fed CD, biological rep 3

value: male


title: Sarcoidosis number 2

description: molecule subtype: tiRNA and tRF


title: CO-RNA-Klf5fl/fl-rep1


title: 852E_F2


title: 822E_M1


title: 822E_F2


title: 822E_F1


title: PC3M_X2_HSF2ChIP_D

city: Chicago

first: Marc

last: Mendillo

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Feinberg School of Medicine, Northwestern University

data_processing:
RNA-seq: Sequence quality was assessed with FastQC v0.11.2, Fastq files were trimmed using bbduk from BBTools v35.92 according to Lexogen QuantSeq manufacturer parameters, mapped to hg38 using STAR v2.6.0 and gene annotations from Ensembl 78. HTSeq was used to count uniquely mapped reads.
ChIP-seq: Reads were aligned to hg38 using Bowtie v0.12.9. Peaks were called relative to knockout samples using MACS v1.4.2 and annotated from Ensembl 78
Genome_build: hg38
Supplementary_files_format_and_content: htseq counts tables provide counts of uniquely mapped RNAseq reads. Bed files were generated by MACS for peaks

source_name: cancer cell line

growth_protocol: Cells were grown at 37°C and 5% CO2

extract_protocol:
KAPA HTP Library Preparation Kit
RNA was extracted using the Qiagen RNeasy kit using the Qiashredder for homogenization of cells grown in vitro and a rotor-stator homogenizer for xenograft tumors

treatment_protocol:
None
See sample section for treatment

tag: cell line

value: PC3M X2 Clone

tag: vector

tag: sirna/sgrna

tag: antibody


title: 820E_F2


title: PC3M_X2_HSF2ChIP_C


title: 822E_M2


title: 837E_F1


title: 820E_M1


title: PC3M_X1_Input_A

value: PC3M X1 Clone

value: None - Input


title: 808E_M2


title: PC3M_X2_HSF1ChIP_C


title: PC3M_X1_HSF2ChIP_B


title: 820E_M2


title: 808E_F1


title: 808E_M1


title: Sarcoidosis number 1

description: molecule subtype: tiRNA and tRF


title: 805E_M2


title: 808E_F2


title: PC3M_X2_Input_C


title: PC3M_X2_HSF1ChIP_D


title: 820E_F1


title: PC3M_sgHSF2_HSF1ChIP_D


title: healthy control 1

description: molecule subtype: tiRNA and tRF


title: 804E_M1


title: PC3M_X1_HSF2ChIP_A


title: PC3M_X1_HSF1ChIP_B


title: 804E_F1


title: 805E_F2


title: PC3M_X1_HSF1ChIP_A


title: PC3M_sgHSF2_Input_A


title: PC3M_sgHSF2_HSF1ChIP_C


title: PC3M_sgHSF2_HSF2ChIP_C


title: PC3M_sgHSF2_HSF2ChIP_D


title: 804E_F2


title: 805E_F1


title: 801E_M1


title: PC3M_sgHSF2_HSF2ChIP_B


title: PC3M_sgHSF2_HSF1ChIP_B


title: PC3M_sgHSF2_Input_B


title: 801E_M2


title: PC3M_sgHSF2_HSF2ChIP_A


title: 799E_M2


title: 805E_M1


title: PC3M_sgHSF2_HSF1ChIP_A


title: 801E_F1


title: PC3M_sgHSF1_Input_B


title: 804E_M2


title: 799E_M1


title: 801E_F2


title: PC3M_sgHSF1_HSF2ChIP_D


title: 790E_M2


title: PC3M_sgHSF1_HSF1ChIP_D


title: PC3M_sgHSF1_HSF2ChIP_C


title: PC3M_sgHSF1_HSF1ChIP_C


title: 790E_M1


title: PC3M_sgHSF1_Input_A


title: PC3M_sgHSF1_HSF2ChIP_A


title: 790E_F1


title: 787E_M2


title: 790E_F2


title: PC3M_sgHSF1_HSF2ChIP_B


title: 787E_M1


title: PC3M_sgHSF1_HSF1ChIP_B


title: 787E_F2


title: MDAMB231_WT_Input


title: MDAMB231_WT_HSF2ChIP_B


title: 786E_M1


title: 786E_M2


title: 787E_F1


title: MDAMB231_WT_HSF1ChIP_B


title: MDAMB231_WT_HSF1ChIP_A


title: 799E_F2


title: MDAMB231_sgHSF2_Input


title: 783E_M2


title: 799E_F1


title: 786E_F1


title: 786E_F2


title: MDAMB231_sgHSF2_HSF2ChIP_B


title: 783E_M1


title: 783E_F2


title: MDAMB231_sgHSF2_HSF2ChIP_A


title: PC3M_sgHSF1_HSF1ChIP_A


title: 765E_M2


title: 783E_F1


title: MDAMB231_sgHSF1_Input


title: MDAMB231_sgHSF1_HSF2ChIP_A

description: MDAMB231_sgHSF1_HSF2ChIP_merge.peaks.bed.gz


title: MDAMB231_WT_HSF2ChIP_A


title: 761E_M2


title: 765E_F1


title: MDAMB231_sgHSF1_HSF1ChIP_B


title: MDAMB231_sgHSF1_HSF1ChIP_A


title: MDAMB231_sgHSF1_HSF2ChIP_B


title: 761E_M1


title: MDAMB231_WT_HeatShock_A

extract_protocol:
Lexogen 3' QuantSeq FWD for Illumina
RNA was extracted using the Qiagen RNeasy kit using the Qiashredder for homogenization of cells grown in vitro and a rotor-stator homogenizer for xenograft tumors

treatment_protocol:
HeatShock
See sample section for treatment


title: MDAMB231_sgHSF2_HeatShock_B


title: MDAMB231_sgHSF2_HSF1ChIP_B

description: MDAMB231_sgHSF2_HSF1ChIP_merge.peaks.bed.gz


title: 75E_M2


title: 75E_M1


title: MDAMB231_sgHSF2_HeatShock_A


title: MDAMB231_WT_Control_A

treatment_protocol:
Control
See sample section for treatment


title: 761E_F2


title: MDAMB231_WT_HeatShock_B


title: MDAMB231_WT_Control_B


title: 748E_M2


title: 765E_F2


title: 761E_F1


title: MDAMB231_sgHSF2_HSF1ChIP_A


title: 748E_M1


title: MDAMB231_sgHSF2_Control_A


title: 748E_F2


title: 75E_F1


title: 75E_F2


title: 765E_M1


title: MDAMB231_sgHSF1_Control_B


title: 73E_M1


title: 73E_F2


title: MDAMB231_sgHSF2siHSF1_SS_C

treatment_protocol:
Serum Starvation
See sample section for treatment

value: sgHSF2.1 + siHSF1


title: MDAMB231_sgHSF2_Control_B


title: 73E_M2


title: 73E_F1


title: MDAMB231_sgHSF2siHSF1_SS_B


title: MDAMB231_sgHSF2siNT_SS_B

value: sgHSF2.1 + siNon-Targeting


title: 730E_M1


title: MDAMB231_sgHSF1_HeatShock_A


title: MDAMB231_sgDsiHSF1_SS_B

value: sgNon-Targeting + siHSF1


title: 727E_M2


title: 730E_F2


title: MDAMB231_sgHSF2siHSF1_SS_A


title: MDAMB231_sgDsiHSF1_SS_A


title: MDAMB231_sgHSF1_Control_A


title: 748E_F1


title: MDAMB231_sgDsiNT_SS_B

value: sgNon-Targeting + siNon-Targeting


title: 730E_F1


title: MDAMB231_sgHSF1_HeatShock_B


title: 721E_M2


title: 730E_M2


title: 727E_F2


title: MDAMB231_sgHSF2siNT_SS_A


title: 721E_M1


title: MDAMB231_sgHSF2siHSF1_CoCl2_B

treatment_protocol:
250 µM CoCl2
See sample section for treatment


title: MDAMB231_sgHSF2siNT_SS_C


title: 727E_M1


title: MDAMB231_sgDsiHSF1_SS_C


title: MDAMB231_sgHSF2siHSF1_CoCl2_A


title: MDAMB231_sgHSF2siHSF1_CoCl2_C


title: MDAMB231_sgDsiNT_SS_A


title: MDAMB231_sgDsiNT_SS_C


title: MDAMB231_sgHSF2siNT_CoCl2_B


title: 721E_F2


title: 727E_F1


title: MDAMB231_sgHSF2siNT_CoCl2_A


title: 716E_M1


title: 716E_F2


title: 721E_F1


title: 716E_M2


title: MDAMB231_sgHSF2siHSF1_2DG_C

treatment_protocol:
10 mM 2-DG
See sample section for treatment


title: MDAMB231_sgHSF2siHSF1_2DG_B


title: 716E_F1


title: MDAMB231_sgHSF2siNT_2DG_B


title: 712E_M1


title: MDAMB231_sgHSF2siNT_2DG_C


title: 712E_F1


title: MDAMB231_sgHSF2siNT_2DG_A


title: 712E_M2


title: 712E_F2


title: MDAMB231_sgHSF2siHSF1_2DG_A


title: 707E_M2


title: MDAMB231_sgHSF2siNT_Control_C

treatment_protocol:
H2O
See sample section for treatment


title: MDAMB231_sgHSF2siHSF1_Control_A


title: 705E_M2


title: 707E_F1


title: 705E_M1


title: MDAMB231_sgHSF2siNT_Control_A


title: MDAMB231_sgHSF2siHSF1_Control_B


title: MDAMB231_sgHSF2siNT_CoCl2_C


title: MDAMB231_sgHSF2siHSF1_Control_C


title: MDAMB231_sgDsiHSF1_CoCl2_C


title: MDAMB231_sgHSF2siNT_Control_B


title: 705E_F1


title: 705E_F2


title: 707E_M1


title: MDAMB231_sgDsiHSF1_CoCl2_A


title: 703E_M1


title: 703E_M2


title: 707E_F2


title: 703E_F2


title: MDAMB231_sgDsiHSF1_CoCl2_B


title: 703E_F1


title: MDAMB231_sgDsiNT_CoCl2_C


title: 94

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

hyb_protocol: Standard Illumina HT-12 beadchips hybridization protocol

scan_protocol: Illumina HiScan standard scanning protocol

data_processing:
The raw intensity values were background corrected by RMA, normalized by quantile normalization and then transformed into log2 scale in R
The non-normalized data and processed data files include gene identifiers in Array_Address_Id format.  The gene information for these IDs is availble on the GPL10558 platform record.  The file processed_data.txt includes both normalized values and detection Pvalues.

source_name: colorectal cancer tissue

label_protocol: Standard Illumina HT-12 beadchips label protocol

extract_protocol: RNA was extracted with Trizol reagent. The cDNA was synthesized from total RNA primed with T7 Oligo(dT) and amplified by an Illumina TotalPre RNA Amplification Kit (Ambion, Austin, USA).

value: Colon cancer

tag: age


title: 93


title: 88


title: 91


title: 92


title: MDAMB231_sgDsiNT_CoCl2_B


title: 59E_M2

tag: Sex


title: 85


title: 59E_M1


title: 84


title: 87


title: 86


title: MDAMB231_sgDsiNT_CoCl2_A


title: MDAMB231_sgDsiHSF1_2DG_C


title: MDAMB231_sgDsiHSF1_2DG_A


title: 59E_F1


title: MDAMB231_sgDsiHSF1_2DG_B


title: 83


title: 59E_F2


title: 78


title: 596E_M2


title: 80


title: 76


title: 596E_M1


title: 75


title: 79


title: 81


title: MDAMB231_sgDsiNT_2DG_A


title: 596E_F2


title: 82


title: 589E_M2


title: MDAMB231_sgDsiNT_2DG_B


title: 596E_F1


title: MDAMB231_sgDsiHSF1_Control_C


title: 74


title: 77


title: MDAMB231_sgDsiNT_2DG_C


title: MDAMB231_sgDsiHSF1_Control_A


title: gsCRC-069


title: 589E_M1


title: 73


title: MDAMB231_sgDsiNT_Control_B


title: 589E_F2


title: gsCRC-071


title: gsCRC-067


title: NT-16s-Klf5fl/fl-rep5

description: counts_TSV files

data_processing:
Library strategy: 16S rRNA-seq
Quality check with FastQC
Alignment was performed with HISAT2
Raw count matrix from featureCounts
Count normalization and differential expression was performed with DESeq2
Pathway analysis was with GSEA
Genome_build: mm9
Supplementary_files_format_and_content: Raw count matrix was generated from featureCounts

organism: feces metagenome

source_name: Feces


title: gsCRC-066


title: 72


title: gsCRC-062


title: NT-16s-Klf5fl/fl-rep4

description: counts_TSV files


title: 589E_F1


title: gsCRC-065


title: PC3M_CTL_C

treatment_protocol:
N/A
See sample section for treatment


title: 57E_M1


title: MDAMB231_sgDsiNT_Control_A


title: gsCRC-070


title: gsCRC-064


title: 57E_F2


title: gsCRC-056


title: gsCRC-061


title: 57E_M2


title: gsCRC-057


title: NT-16s-Klf5fl/fl-rep2

description: counts_TSV files


title: PC3M_CTL_D


title: 555E_M2


title: PC3M_sgHSF2_D


title: TAM-16s-WT-rep4

description: counts_TSV files

value: WT

value: Tamoxifen


title: NT-16s-Klf5fl/fl-rep3

description: counts_TSV files


title: 57E_F1

value: 10% EtOH in growth media


title: NT-16s-Klf5fl/fl-rep1

description: counts_TSV files


title: PC3M_CTL_A


title: PC3M_sgHSF2_B


title: gsCRC-060


title: gsCRC-054


title: gsCRC-051


title: gsCRC-055


title: PC3M_CTL_B


title: gsCRC-059


title: TAM-16s-WT-rep3

description: counts_TSV files


title: gsCRC-052


title: PC3M_sgHSF2_C


title: gsCRC-053


title: gsCRC-058


title: 530E_M1


title: PC3M_sgHSF1_D


title: TAM-16s-WT-rep1

description: counts_TSV files


title: 555E_M1


title: PC3M_sgHSF1_C


title: TAM-16s-WT-rep5

description: counts_TSV files


title: TAM-16s-WT-rep2

description: counts_TSV files


title: PC3M_sgHSF2_A


title: 530E_F1

value: Female


title: CO-16s-WT-rep5

description: counts_TSV files

value: Corn Oil


title: gsCRC-050


title: 530E_M2


title: 555E_F1


title: gsCRC-048


title: 555E_F2


title: 517E_M1


title: 517E_M2


title: MDAMB231_sgDsiNT_Control_C


title: 517E_F2


title: PC3M_sgHSF1_B


title: CO-16s-WT-rep4

description: counts_TSV files


title: MCF7_CTL_C

value: sgNon-Targeting


title: gsCRC-047


title: CO-16s-WT-rep3

description: counts_TSV files


title: 530E_F2


title: CO-16s-WT-rep2

description: counts_TSV files


title: CO-16s-WT-rep1

description: counts_TSV files


title: PC3M_sgHSF1_A


title: TAM-16s-Klf5fl/fl-rep5

description: counts_TSV files


title: 517E_F1


title: MCF7_CTL_A


title: TAM-16s-Klf5fl/fl-rep4

description: counts_TSV files


title: 513E_M2


title: gsCRC-046


title: TAM-16s-Klf5fl/fl-rep3

description: counts_TSV files


title: MCF7_sgHSF2_D


title: gsCRC-045


title: MCF7_CTL_B


title: gsCRC-049


title: MCF7_sgHSF2_C


title: gsCRC-044


title: TAM-16s-Klf5fl/fl-rep1

description: counts_TSV files


title: 513E_F2


title: gsCRC-043


title: 513E_M1


title: TAM-16s-Klf5fl/fl-rep2

description: counts_TSV files


title: gsCRC-041


title: MCF7_sgHSF2_A


title: CO-16s-Klf5fl/fl-rep5

description: counts_TSV files


title: 505E_M2


title: MCF7_sgHSF2_B


title: CO-16s-Klf5fl/fl-rep4

description: counts_TSV files


title: 513E_F1


title: CO-16s-Klf5fl/fl-rep3

description: counts_TSV files


title: MCF7_sgHSF1_B


title: MCF7_sgHSF1_C


title: gsCRC-042


title: MCF7_sgHSF1_A


title: gsCRC-040


title: 505E_F2


title: MCF7_sgHSF1_D


title: LNCaP_CTL_C

value: LNCaP


title: gsCRC-038


title: CO-16s-Klf5fl/fl-rep1

description: counts_TSV files


title: gsCRC-037


title: gsCRC-039


title: 49E_M1

value: Male


title: gsCRC-001


title: gsCRC-034


title: 505E_M1


title: LNCaP_CTL_A


title: 49E_F2


title: organoid_C_E2P4

city: Hong Kong

first: Jianlin

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to the Human genome 38 (hg38) using mapper.pl providing by miRDeep2 with -e -h -j -l 18 -m
Raw miRNA counts were generated using quantifier.pl providing by miRDeep2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw miRNA counts

source_name: endometrium

growth_protocol: Tissue samples were minced into small pieces and digested with collagenase V (1mg/ml, C-9263, Sigma, St. Louis, MO) and DNase 1 (1500U, Sigma D5025, St. Louis, MO) solution in RPMI 1640 medium (Thermo Fisher Scientific, 21875-034, San Jose, CA, USA)/10% FBS with gentle shaking at 37°C for 20-30 min. After sorting the glandular tissues through 40µm and 100 µm filters, respectively, they were washed with PBS twice and placed into a 48-well plate by 20-25µL of the Matrigel (Corning, NY, USA) suspension per well and incubated in a 37°C CO2 incubator for 30 mins. The Matrigel was overlayed with 250μl advanced DMEM/ F12 (Life Technologies, Waltham, MA) based Organoids Medium (OM) per well to maintain the culture under 37 °C.

extract_protocol:
RNA extract were using standard BGISEQ-500 platform protocols.
miRNA libraries were prepared for sequencing using standard BGISEQ-500 platform protocols

treatment_protocol: The organoids were treated with different hormones to mimic the proliferative (E2), secretory (E2+P4) and early pregnancy (E2+P4+hCG) phases (E2, 10nM, Sigma E4389, St. Louis, MO) (P4, 1uM, Sigma P7556, St. Louis, MO) (hCG, 1ug/mL, Source Bioscience ABC403, UK) for 7 days. The culture media with hormones were refreshed every 2-3 days.

tag: cell type

value: glandular epithelial cell

tag: treatment

value: estrogen and progesterone


title: organoid_C_E2P4hCG

value: estrogen, progesterone and human chorionic gonadotropin


title: organoid_C_E2

value: estrogen


title: 49E_F1

tag: line

tag: exposure


title: LNCaP_sgHSF2_D


title: CO-16s-Klf5fl/fl-rep2

description: counts_TSV files

tag: mouse strain


title: 505E_F1


title: organoid_B_E2P4hCG


title: LNCaP_sgHSF2_C


title: 49E_M2


title: LNCaP_CTL_B


title: gsCRC-033


title: gsCRC-032


title: gsCRC-035


title: 486E_M2


title: organoid_B_E2P4


title: gsCRC-031


title: gsCRC-030


title: 486E_M1


title: organoid_B_E2


title: LNCaP_sgHSF2_A


title: LNCaP_sgHSF2_B


title: organoid_A_E2P4hCG


title: LNCaP_sgHSF1_D


title: LNCaP_sgHSF1_C


title: gsCRC-029


title: organoid_A_E2P4


title: 461E_M2


title: 486E_F2


title: organoid_A_E2


title: LNCaP_sgHSF1_B


title: 461E_M1


title: 2Y_ATACseq_replicate_3

data_processing:
ATAC-seq datas was performed using trim-galore (version 0.6.4)
ATAC-seq read pairs were mapped using Bowtie2 (version 2.2.6)
Mitochondrial alignments, low-quality alignments (q<10) and PCR duplicates were removed using SAMtools (version 1.3.1)
ATAC peaks were called using MACS2
Genome_build: Susscrofa11.1
Supplementary_files_format_and_content: ATAC peak files

extract_protocol:
Chopped frozen liver tissue was resuspended in homogenization buffer, and grounded under homogeneous solution, followed by filtered with a cell strainer. Cell pellets were obtained by centrifugation.
After iodixanol density gradient centrifugation, the nuclei band was collected form the resuspended sediment. Then 50,000 nuclei were resuspended in the Tn5 transposase reaction mix with two adapters. The transposition reaction was incubated at 37°C for 30 min. The fragmented DNA was purified and amplified with a limited PCR cycle using index primers. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.

tag: breed

value: Bama pig

value: Liver


title: LNCaP_sgHSF1_A


title: 461E_F2


title: 2Y_ATACseq_replicate_2


title: gsCRC-028


title: gsCRC-027


title: 461E_F1


title: H838_CTL_D


title: 2Y_ATACseq_replicate_1


title: gsCRC-024


title: gsCRC-023


title: 45E_M2


title: H838_CTL_C


title: 486E_F1


title: E80_ATACseq_replicate_3

value: embryonic day 80


title: gsCRC-021


title: gsCRC-022


title: gsCRC-018


title: 45E_M1


title: E80_ATACseq_replicate_2


title: H838_sgHSF2_B


title: 45E_F2


title: H838_CTL_A


title: E80_ATACseq_replicate_1


title: 45E_F1


title: H838_sgHSF2_A


title: HFD_input_replicate_2

tag: condition

value: High fat diet treatment

value: female


title: 441E_M1


title: H838_CTL_B


title: gsCRC-013

value: Colon cancer


title: HFD_H3K4me3_replicate_2

tag: chip antibody


title: gsCRC-016


title: HFD_input_replicate_1


title: H838_sgHSF1_A


title: 441E_F2


title: BT20_CTL_B


title: gsCRC-025


title: 441E_F1


title: BT20_CTL_A


title: HFD_H3K27ac_replicate_2

value: H3K27ac (ab4729, Abcam)


title: gsCRC-017


title: gsCRC-015


title: 439E_M2

value: 10% EtOH in growth media


title: HFD_H3K27ac_replicate_1


title: BT20_sgHSF2_B


title: 441E_M2


title: BT20_sgHSF2_A


title: 2y_input_replicate_2

value: Developmental stage


title: H838_sgHSF1_B


title: gsCRC-026


title: gsCRC-007_2


title: gsCRC-006


title: 439E_F2

value: Female


title: BT20_sgHSF1_B


title: HFD_H3K4me3_replicate_1


title: 2y_input_replicate_1


title: 437E_M2


title: BT20_sgHSF1_A


title: 2y_H3K27ac_replicate_2


title: LNCaP_siNT_B

value: siNT


title: gsCRC-012


title: X1


title: 437E_M1


title: gsCRC-007_1


title: 2y_H3K4me3_replicate_2


title: gsCRC-002


title: 439E_M1


title: gsCRC-009


title: 2y_H3K27ac_replicate_1


title: 427E_M2


title: 2y_H3K4me3_replicate_1


title: 437E_F2


title: LNCaP_siHSF2_B

value: LNCaP


title: LNCaP_siNT_C


title: LNCaP_siNT_A


title: LNCaP_siHSF2_C


title: gsCRC-004


title: 110d_input_replicate_2

value: postnatal day 110


title: 110d_input_replicate_1


title: gsCRC-011


title: 427E_M1

value: Male


title: LNCaP_siHSF2_A


title: 110d_H3K4me3


title: 427E_F2


title: gsCRC-003


title: 110d_H3K27ac_replicate_2


title: gsCRC-005


title: 427E_F1


title: 110d_H3K27ac_replicate_1


title: LNCaP_siHSF1_C


title: 437E_F1


title: LNCaP_siHSF1_B


title: 28d_input

value: postnatal day 28


title: gsCRC-010


title: LNCaP_siHSF1_A


title: 40E_F2


title: LNCaP_siHSF1siHSF2_C

value: siHSF1 + siHSF2


title: 40E_M2


title: 28d_H3K27ac_replicate_2


title: 40E_F1


title: 28d_H3K27ac_replicate_1


title: 28d_H3K4me3


title: LNCaP_siHSF1siHSF2_B


title: LNCaP_siHSF1siHSF2_A


title: 406E_M2


title: 0d_input

value: the birth day


title: PANC1_Tumor_MNF2_REPEAT

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's HumanHT-12 V4.0 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 μm using the Illumina iScan scanner.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: Female Balb/c nude mice (aged between 6-8 weeks, weight 18-20 g) were purchased from HFK Bioscience Co., Ltd. (Beijing, China) and maintained under pathogen-free conditions with a 12-hour light/12-hour dark cycle. Animals had free access to drinking water and were fed ad libitum with normal chow. The human-derived pancreatic cancer cell line PANC-1 was purchased from ATCC (CRL-1469, Manassas, VA). Upon receipt of the cell line, cells were expanded for a few passages to enable the generation of new frozen stocks. Cells were resuscitated as needed and used for fewer than 6 months after resuscitation (no more than 12 passages). ATCC performs thorough cell line authentication utilizing Short Tandem Repeat (STR) profiling.

extract_protocol: RNA was extracted using Trizol reagent and further purified using Rneasy mini columns (QIagen, Valencia, CA) according to the manufacturer’s instructions. RNA quantity and integrity was evaluated by Nanodrop and Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

treatment_protocol: Each mouse was inoculated subcutaneously at the right flank region with PANC-1 cells (5 x 10^6) in 0.1mL of PBS for tumor development. All animals were weighed and the tumor volumes measured in two dimensions using a caliper, and the volume expressed in mm3 using the formula: V = 0.5 a × b^2, where a and b are the long and short diameters of the tumor, respectively. The treatments were started at Day 8 when the mean tumor size reached 139 +/- 34 mm^3 and the mice weighed 21.1 +/- 1.1 g. The mice were assigned into groups (n = 10) using randomized block design based on their tumor volumes. The mice received a single intraperitoneal (ip) injection 5 days per week for 3 treatment cycles of either vehicle (1% hydroxypropyl-beta-cyclodextrin) (Control) or 40 mg.kg-1 (R,S’)-MNF (MNF). The dosing volume was adjusted according to weight (10 uL/g). Tumor volumes and weights were determined at the beginning and end of each dosing cycle, while visual estimation of food and water consumption, eye/hair matting, and behavior such as mobility were determined daily. Five days after the end of the last dosing cycle (Day 33) the animals were weighed and then euthanized by cervical extension, tumors were excised, weighed, divided into three portions and snap frozen. The xenograft studies were conducted at the Crown Biosciences, Ltd. facilities and all protocols were approved by the Animal Care and Use Committee at CrownBio (AN-1407-009-164), which are based on “the Guide for the Care and Use of Laboratory Animals” (NRC 2011).

tag: cells

value: PANC-1 tumor

value: 40 mg/kg MNF

tag: host

value: Female Balb/c nude mouse


title: PANC1_Tumor_VEH2_REPEAT

value: Vehicle


title: PANC1_Tumor_VEH1_REPEAT


title: 40E_M1


title: PANC1_Tumor_MNF10


title: PANC1_Tumor_MNF1_REPEAT


title: VCaP_siNT_B

value: VCaP


title: 406E_M1


title: 439E_F1


title: gsCRC-008

tag: tissue

value: Colon cancer


title: 406E_F2


title: 0d_H3K27ac_replicate_1

value: Bama pig

value: Liver

value: female

value: H3K27ac (ab4729, Abcam)


title: 406E_F1

value: Female

value: 10% EtOH in growth media


title: VCaP_siNT_A

tag: cell line

value: siNT


title: 0d_H3K27ac_replicate_2

value: Developmental stage


title: 399E_M2

value: Male


title: E80_input_replicate_2

value: embryonic day 80


title: VCaP_siHSF2_C

tag: vector


title: 399E_M1


title: E80_input_replicate_1


title: 399E_F2


title: 0d_H3K4me3

value: the birth day


title: 399E_F1


title: VCaP_siNT_C

tag: sirna/sgrna


title: E80_H3K4me3


title: VCaP_siHSF2_A

tag: antibody


title: VCaP_siHSF1_B


title: VCaP_siHSF2_B


title: VCaP_siHSF1_C


title: 386E_M2


title: VCaP_siHSF1_A


title: E80_H3K27ac_replicate_1

tag: age


title: 386E_F2

tag: Sex


title: PANC1_Tumor_MNF9

value: PANC-1 tumor


title: E38_H3K4me3_replicate_2

value: embryonic day 38


title: VCaP_siHSF1siHSF2_B

value: siHSF1 + siHSF2


title: E80_H3K27ac_replicate_2


title: 386E_F1


title: PANC1_Tumor_MNF7

value: 40 mg/kg MNF

value: Female Balb/c nude mouse


title: PANC1_Tumor_MNF4


title: E38_H3K4me3_replicate_1


title: PANC1_Tumor_MNF6


title: 385E_M2


title: VCaP_siHSF1siHSF2_A

value: VCaP


title: PANC1_Tumor_MNF8


title: PANC1_Tumor_MNF3


title: 386E_M1


title: E38_input

value: Bama pig


title: DLDTIR1_siNT_C


title: PANC1_Tumor_MNF2


title: 385E_M1


title: PANC1_Tumor_MNF1


title: PANC1_Tumor_VEH10

value: Vehicle


title: PANC1_Tumor_MNF5


title: E38_H3K27ac_replicate_2

value: Liver

value: female


title: E38_H3K27ac_replicate_1

value: H3K27ac (ab4729, Abcam)


title: PANC1_Tumor_VEH9


title: DLDTIR1_siNT_B


title: 385E_F2

value: Female

value: 10% EtOH in growth media


title: VCaP_siHSF1siHSF2_C


title: PANC1_Tumor_VEH8


title: 110d_RNA_replicate_5

description:
110d_5
all_samples_quant_mRNA.tpm.txt

value: Developmental stage

value: postnatal day 110


title: PANC1_Tumor_VEH6


title: 383E_M2

value: Male


title: PANC1_Tumor_VEH7


title: DLDTIR1_siNT_A

value: siNT


title: 383E_M1


title: DLDTIR1_siHSF1_C


title: DLDTIR1_siHSF2_B


title: Te_rep3

city: Madison

first: Phillip

last: Newmark

state: WI

address: 330 N Orchard St

department: Howard Hughes Medical Institute, Morgridge Institute for Research

institute: University of Wisconsin-Madison

description: laser captured tissue

data_processing:
Adapters and low quality reads were trimmed from fastq sequence using defualt setting in CLC Genomics Workbench 12
Reads were mapped to a de novo assembled S. mediterranea transcriptome (Smed2014) (Robb et al., 2015) with the Smed-zfs1 transcript added with default settings in CLC Genomics Workbench 12
Normalized abundance measurements and differential gene expression were performed using default settings in CLC Genomics Workbench 12
Supplementary_files_format_and_content: tab-delimited text files include raw counts and abundance values for every gene in each sample

organism: Schmidtea mediterranea

source_name: Testis

extract_protocol:
Planarians were killed in chilled 2% HCl in PBS (RNAse-Free) and then fixed in 100% Acetone for 1 hour at -20°C. Planarians were then incubated in 10, 20, 30% sucrose in PBS (RNAse- Free) for 20 minutes each before embedding in Tissue Freezing Medium (TFM) blocks (Ted Pella). The samples were then cryosectioned at 16 μm thickness onto PEN membrane slides (Thermo Fisher). The slides were stained with 1% cresyl violet and 1% eosin Y (Sigma) in 75% ethanol (Clément-Ziza et al., 2008). The tissue samples were dissected using Veritas Laser Capture Microdissection System (Arcturus) and captured on to Capsure HS LCM Caps (Thermo Fisher). After capture, RNA was isolated using the Arcturus Picopure RNA isolation kit (Thermo Fisher).
The strand-specific RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.

tag: strain

value: Sexual

value: Testis

tag: genotype

value: wild type


title: DLDTIR1_siHSF2_C


title: 385E_F1

tag: line


title: Te_rep2

description: laser captured tissue


title: 383E_F2

tag: exposure


title: DLDTIR1_siHSF1_B


title: 110d_RNA_replicate_2

description:
110d_2
all_samples_quant_mRNA.tpm.txt

source_name: Liver


title: DLDTIR1_siHSF1_A


title: DLDTIR1_siHSF2_A


title: 28d_RNA_replicate_6

description:
28d_6
all_samples_quant_mRNA.tpm.txt

value: postnatal day 28


title: 110d_RNA_replicate_4

description:
110d_4
all_samples_quant_mRNA.tpm.txt


title: 383E_F1

source_name: Whole fly


title: 110d_RNA_replicate_1

description:
110d_1
all_samples_quant_mRNA.tpm.txt


title: 382E_M2


title: Te_rep1

description: laser captured tissue


title: 110d_RNA_replicate_3

description:
110d_3
all_samples_quant_mRNA.tpm.txt


title: 110d_RNA_replicate_6

description:
110d_6
all_samples_quant_mRNA.tpm.txt


title: PANC1_Tumor_VEH3

value: PANC-1 tumor

tag: treatment

value: Female Balb/c nude mouse


title: PANC1_Tumor_VEH4


title: 382E_M1


title: DLDTIR1_siHSF1siHSF2_C

value: siHSF1 + siHSF2


title: PANC1_Tumor_VEH1

value: Vehicle


title: 28d_RNA_replicate_5

description:
28d_5
all_samples_quant_mRNA.tpm.txt

tag: breed

value: Bama pig

value: Liver


title: PANC1_Tumor_VEH2


title: PANC1_Tumor_VEH5


title: 382E_F2


title: Ov_rep3

description: laser captured tissue

source_name: Ovary

value: Ovary


title: 28d_RNA_replicate_4

description:
28d_4
all_samples_quant_mRNA.tpm.txt

tag: condition

value: female


title: DLDTIR1_siHSF1siHSF2_B


title: Ov_rep2

description: laser captured tissue


title: Ov_rep1

description: laser captured tissue


title: Ng_rep3

description: laser captured tissue

source_name: Non-gonadal

value: Non-gonadal


title: PC3MX_siHSF2_B


title: DLDTIR1_siHSF1siHSF2_A


title: PC3MX_siHSF2_A


title: 382E_F1

value: Female

value: 10% EtOH in growth media


title: 28d_RNA_replicate_1

description:
28d_1
all_samples_quant_mRNA.tpm.txt

value: Developmental stage

tag: chip antibody


title: 28d_RNA_replicate_3

description:
28d_3
all_samples_quant_mRNA.tpm.txt


title: PC3MX_siHSF1_B


title: 380E_M2

value: Male


title: 380E_M1


title: 380E_F1


title: 0d_RNA_replicate_5

description:
0d_5
all_samples_quant_mRNA.tpm.txt

value: the birth day


title: PC3MX_siHSF1_A


title: 379E_M2


title: 0d_RNA_replicate_4

description:
0d_4
all_samples_quant_mRNA.tpm.txt


title: Retina Ythdf2 rep1

city: Shenzhen

first: Fugui

last: Niu

state: Guangdong

address: 1088 Xueyuan Avenue

department: Biology

institute: SUSTech

data_processing:
The filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5.
The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads.
The number of RNA-seq reads was further normalized to calculate FPKM.
The FPKM from RIP elute to input and any fold change greater than 2 was considered enriched.
Genome_build: GRCm38

source_name: Retina

extract_protocol:
Retinas were removed and dissociated with papain, then retinal neurons were treated following the manual of the EZ-Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore) with minor modifications.
100 ng RNA of input and elutes after RIP were used to generate the library using the TruSeq Stranded RNA Sample Preparation Kit (Illumina).

value: retina

value: post natal day 0


title: 379E_M1


title: PC3MX_siNT_B

value: siNT


title: Retina input rep2

value: wild type


title: PC3MX_siNT_A


title: Ng_rep2

description: laser captured tissue

value: Sexual


title: 0d_RNA_replicate_6

description:
0d_6
all_samples_quant_mRNA.tpm.txt


title: 379E_F2


title: 0d_RNA_replicate_2

description:
0d_2
all_samples_quant_mRNA.tpm.txt


title: 380E_F2


title: 379E_F1


title: Retina Input rep1


title: 0d_RNA_replicate_1

description:
0d_1
all_samples_quant_mRNA.tpm.txt


title: PC3MX1_siHSF2_A


title: 375E_M2


title: E80_RNA_replicate_6

description:
E80_6
all_samples_quant_mRNA.tpm.txt

value: embryonic day 80


title: Retina Ythdf2 rep2


title: E80_RNA_replicate_5

description:
E80_5
all_samples_quant_mRNA.tpm.txt


title: PC3MX1_siHSF1_A


title: PC3MX1_siHSF2_B


title: 375E_M1


title: 28d_RNA_replicate_2

description:
28d_2
all_samples_quant_mRNA.tpm.txt

value: postnatal day 28


title: 375E_F2


title: 0d_RNA_replicate_3

description:
0d_3
all_samples_quant_mRNA.tpm.txt

value: Bama pig


title: Ng_rep1

description: laser captured tissue


title: E80_RNA_replicate_4

description:
E80_4
all_samples_quant_mRNA.tpm.txt

value: Liver


title: PC3MX1_siNT_B


title: 375E_F1


title: E80_RNA_replicate_3

description:
E80_3
all_samples_quant_mRNA.tpm.txt


title: PC3MX1_siNT_A


title: normal healthy control case3

city: Nanjing

first: Pinggang

last: Ding

address: 138 Xianlin Road

department: School of Medicine

institute: Nanjing University of Chinese Medicine

description: Gene expression in normal healthy control case3

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: normal healthy control case3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using All Prep DNA/RNA Mini Kit (Cat#80204, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: RNA was extracted from whole blood from IgD multiple myeloma patient, IgG multiple myeloma patient,normal healthy volunteers

value: whole blood

tag: disease state

value: normal


title: H838_siHSF1siHSF2_B

value: siHSF1 + siHSF2


title: E80_RNA_replicate_2

description:
E80_2
all_samples_quant_mRNA.tpm.txt

value: female


title: PC3MX1_siHSF1_B


title: normal healthy control case2

description: Gene expression in normal healthy control case2

source_name: normal healthy control case2


title: normal healthy control case1

description: Gene expression in normal healthy control case1

source_name: normal healthy control case1


title: 374E_M2

value: 10% EtOH in growth media


title: 374E_M1


title: 374E_F2

value: Female


title: Ig G multiple myeloma patient case5

description: Gene expression in  IgG multiple myeloma patient case5

source_name: Ig G multiple myeloma patient case5

value: IgG multiple myeloma


title: E80_RNA_replicate_1

description:
E80_1
all_samples_quant_mRNA.tpm.txt

value: Developmental stage


title: E38_RNA_replicate_3

description:
E38_3
all_samples_quant_mRNA.tpm.txt

value: embryonic day 38


title: H838_siHSF2_B


title: H838_siHSF1siHSF2_A


title: H838_siHSF2_A


title: Ig G multiple myeloma patient case4

description: Gene expression in  IgG multiple myeloma patient case4

source_name: Ig G multiple myeloma patient case4


title: E38_RNA_replicate_2

description:
E38_2
all_samples_quant_mRNA.tpm.txt


title: H838_siHSF1_A


title: 374E_F1


title: H838_siHSF1_B


title: HFD_HiC_replicate_6

description:
HFD_6
all.samples.abindex.txt
HFD.merged.replicates.tad.txt
2y_HFD.consensus.TAD.txt
7y_HFD.Dscore.txt

data_processing:
Reads were mapped to the pig genome (Sscrofa 11.1) by BWA (v 0.7.15).
Juicer were used HiC data processing to filter duplication, low-quality alignment read pairs (MAPQ < 30) as well as intra-fragment read pairs.
High-quality reads  normalized with Knight-Ruiz [KR] algorithm and quantile  algorithm to structure contact matrixes at 20 or 100 kb resolution.
Compartments A/B were identified with A-B index as described by M Jordan Rowley. et al. Mol Cell. 2017 (PMID: 28826674).
Locations of topologically associated domains (TADs) were computed by combining  directionality index (Dixon et al. Nature. 2012 [PMID: 22495300]) and insulation index (Emily Crane et al. Nature. 2017)
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: 20 and 100 kb matrixes, hic file
A-B index, txt file
locations of TAD for each sample, merged replicates, and consensus TAD,txt file
D-score, txt file

extract_protocol:
Livers tissue was homogenized with liquid nitrogen then fixed with 4% formaldehyde solution and incubated at room temperature for 30 min. Glycine were added to a final concentration of 0.2 M to quench the fixing reaction, and incubated at room temperature for 5 min then centrifuge for 10 min at 1,000 g and 4˚C. Discarded supernatants and cells were lysed with 1M Tris-HCl, 1M NaCl, 10% CA-630 and protease inhibitors on ice for 15 min. Cell nucleus were washed twice and were permeabilized at 65˚C for 10 min with 1% SDS to a final concentration of 0.1%. To quench the SDS, added 10% TritonX-100 (0.1% final concentration) and incubated at 37˚C for 15 min. Then 200 U DpnII (a 4-cutter restriction enzyme) was added and digested chromatin at 37˚C for 90 min, 65˚C for 20 min and 25˚C for 5 min. The restriction fragment overhangs were filled and labelled by biotinylated nucleotides, then ligated in a small volume.
After crosslink reversal, ligated DNA was purified and sheared to a length of 300–500 bp, at which point ligation junctions were pulled down with magnetic beads and prepared for BGISEQ-500 sequencing.

value: High fat diet treatment

tag: restriction enzyme

value: DpnII


title: Ig G multiple myeloma patient case1

description: Gene expression in  IgG multiple myeloma patient case1

source_name: Ig G multiple myeloma patient case1

tag: tissue


title: Ig D multiple myeloma patient case5

description: Gene expression in  IgD multiple myeloma patient case5

source_name: Ig D multiple myeloma patient case5

value: IgD multiple myeloma


title: HFD_HiC_replicate_5

description:
HFD_5
all.samples.abindex.txt
HFD.merged.replicates.tad.txt
2y_HFD.consensus.TAD.txt
6y_HFD.Dscore.txt


title: 371E_F1


title: E38_RNA_replicate_1

description:
E38_1
all_samples_quant_mRNA.tpm.txt


title: Ig G multiple myeloma patient case2

description: Gene expression in  IgG multiple myeloma patient case2

source_name: Ig G multiple myeloma patient case2


title: PBMC_HC_4

city: Beijing

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

data_processing:
The Cellranger software suite (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) from 10X was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens/Info/Index) and perform UMI counting
Assembly: hg38
Supplementary files format and content: Tar files of filtered feature-barcode matrix (output of CellRanger)  and csv file of sample information

source_name: human PBMC

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics) according to the manufacturer’s instructions
RNA libraries were prepared using standard 10X genomics protocols were sequenced on Illumina NovaSeq 6000.

treatment_protocol: PBMCs were isolated from blood by density gradient centrifugation and then resuspended in PBS. Monocytes were positively isolated by CD14 MicroBeads (Miltenyi Biotec) according to the manufacturer's instructions.

tag: disease status

value: healthy control

value: male

tag: cell type

value: human PBMC


title: 370E_M1

value: Male


title: PBMC_HC_3


title: ZR751_siHSF2_A

source_name: cancer cell line

tag: cell line

tag: vector

tag: sirna/sgrna


title: 371E_F2

tag: Sex


title: 370E_M2


title: H838_siNT_A

value: siNT

tag: antibody


title: HFD_HiC_replicate_3

description:
HFD_3
all.samples.abindex.txt
HFD.merged.replicates.tad.txt
2y_HFD.consensus.TAD.txt
4y_HFD.Dscore.txt

value: Bama pig

value: Liver

tag: age


title: HFD_HiC_replicate_2

description:
HFD_2
all.samples.abindex.txt
HFD.merged.replicates.tad.txt
2y_HFD.consensus.TAD.txt
3y_HFD.Dscore.txt


title: 371E_M1

tag: line


title: Ig G multiple myeloma patient case3

description: Gene expression in  IgG multiple myeloma patient case3

source_name: Ig G multiple myeloma patient case3

value: whole blood


title: ZR751_siHSF2_B


title: ZR751_siHSF1_B


title: Ig D multiple myeloma patient case1

description: Gene expression in  IgD multiple myeloma patient case1

source_name: Ig D multiple myeloma patient case1


title: PBMC_HC_2


title: Ig D multiple myeloma patient case3

description: Gene expression in  IgD multiple myeloma patient case3

source_name: Ig D multiple myeloma patient case3


title: 370E_F1

source_name: Whole fly

tag: exposure


title: Ig D multiple myeloma patient case2

description: Gene expression in  IgD multiple myeloma patient case2

source_name: Ig D multiple myeloma patient case2


title: 371E_M2


title: H838_siNT_B


title: HFD_HiC_replicate_4

description:
HFD_4
all.samples.abindex.txt
HFD.merged.replicates.tad.txt
2y_HFD.consensus.TAD.txt
5y_HFD.Dscore.txt

source_name: Liver

value: female


title: Ig D multiple myeloma patient case4

description: Gene expression in  IgD multiple myeloma patient case4

source_name: Ig D multiple myeloma patient case4


title: ZR751_siNT_A


title: 110d_HiC_replicate_4

description:
110d_4
all.samples.abindex.txt
110d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: postnatal day 110


title: 370E_F2

value: Female

value: 10% EtOH in growth media


title: PBMC_BD_2

value: Behcet's disease (BD)


title: 110d_HiC_replicate_2

description:
110d_2
all.samples.abindex.txt
110d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: Developmental stage


title: ZR751_siHSF1_A


title: 110d_HiC_replicate_6

description:
110d_6
all.samples.abindex.txt
110d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: 110d_HiC_replicate_5

description:
110d_5
all.samples.abindex.txt
110d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: 110d_HiC_replicate_1

description:
110d_1
all.samples.abindex.txt
110d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: 367E_M2


title: 367E_M1


title: Monocyte_HC_4

source_name: human CD14+monocyte

value: human CD14+monocyte


title: PC3M_siHSF2_B


title: 28d_HiC_replicate_6

description:
28d_6
all.samples.abindex.txt
28d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: postnatal day 28

value: DpnII


title: PBMC_HC_1

value: healthy control


title: PC3M_siHSF2_A


title: Monocyte_HC_3


title: PBMC_BD_4

value: male


title: ZR751_siNT_B


title: 367E_F1


title: PC3M_siNT_B


title: HFD_HiC_replicate_1

description:
HFD_1
all.samples.abindex.txt
HFD.merged.replicates.tad.txt
2y_HFD.consensus.TAD.txt
2y_HFD.Dscore.txt

value: High fat diet treatment


title: PC3M_siNT_A


title: 28d_HiC_replicate_5

description:
28d_5
all.samples.abindex.txt
28d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: 367E_F2


title: PBMC_BD_1

value: human PBMC


title: 365E_M2

value: Male


title: PC3M_siHSF1_A


title: Monocyte_BD_4


title: PC3M_siHSF1siHSF2_B

value: siHSF1 + siHSF2


title: 365E_F2


title: BT20_siNT_B

value: siNT


title: 362E_F2


title: 110d_HiC_replicate_3

description:
110d_3
all.samples.abindex.txt
110d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: Bama pig

value: Liver


title: 365E_M1


title: PBMC_BD_3


title: Monocyte_HC_1

value: female


title: BT20_siHSF2_B


title: 28d_HiC_replicate_3

description:
28d_3
all.samples.abindex.txt
28d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: 0d_HiC_replicate_5

description:
0d_5
all.samples.abindex.txt
0d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: the birth day


title: 365E_F1

value: Female

value: 10% EtOH in growth media


title: 28d_HiC_replicate_4

description:
28d_4
all.samples.abindex.txt
28d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: Developmental stage


title: 360E_M1


title: 362E_F1


title: 28d_HiC_replicate_1

description:
28d_1
all.samples.abindex.txt
28d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: AT/RT CHLA266 TAK-228 B

first: Jeffrey

last: Rubens

state: MD

address: 1800 Orleans St

department: Oncology

institute: Johns Hopkins University

data_processing:
NOT PROVIDED; REQUESTED
Assembly: mm9
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

source_name: AT/RT cell model

growth_protocol: BT37 was grown in RPMI media while CHLA02, CHLA06, and CHLA266 were grown in EF media

extract_protocol:
Total RNA was extracted from cell pellets using Qiagen (Germantown, MD) RNeasy mini kit and column DNase treatment.
RNAseq libraries were prepared using Illumina (San Diego, CA) TruSeq stranded mRNA sample preparation kit following manufacturer’s recommended procedure with minor modifications. Briefly, mRNA was purified from 15ng of total RNA using oligo dT RNA purification magnetic beads. The purified mRNA was then fragmented at 94°C for 8 minutes, primed with random primers, and converted to double strand cDNA. The resulting cDNA was end repaired, dA tailed, and ligated to TruSeq adapter (with unique dual index barcodes). Libraries were then PCR amplified using 15 cycles. The final libraries were quality checked, quantitated, and pooled in equal molar for sequencing on NovaSeq SP 100cycle flowcells for 2X50bp sequencing.

treatment_protocol: Samples were treated with 0.1% DMSO or TAK-228 20nM x 4 hours

value: ATRT-MYC

tag: treatment

value: TAK-228 20nM x 4 hours


title: 362E_M2

data_processing:
Demultiplexing: Barcoded sequence reads were demultiplexed using the Illumina pipeline v1.9.
Preprocessing: Adapter sequences were trimmed using cutadapt v1.6. Trimmed sequences were then aligned to multiple target sequence databases, using BWA v0.7.10 (MEM algorithm with parameters ‘-v 2 –t 4’): (1) all trimmed sequences were aligned against a ribosomal RNA database to filter out residual rRNA that escaped depletion during library preparation; (2) remaining sequences were then aligned against a custom database of potential microbiome component species (see below) using BWA; (3) sequences that did not align to either the rRNA or microbiome databases were aligned to all D. melanogaster sequences in RepBase.
Alignment: The remaining sequences that did not align to any of the databases above were then aligned to the D. melanogaster genome (BDGP5) and known transcriptome (FlyBase v5.57) using STAR v2.4.0e
Quantification and Normalization: Read counts for known and novel gene models were quantified using HTSeq-count with the ‘intersection-nonempty’ assignment method. Tabulated read counts for each endogenous gene present in both Baseline and ethanol-treated lines were combined and normalized across all samples using EdgeR.
Genome_build: FlyBase v5.57
Supplementary_files_format_and_content: Matrix table in tab-delimited text file contains raw gene counts for every gene and every sample

extract_protocol:
Briefly, total RNA was extracted with Trizol using the RNeasy Mini Kit (Qiagen, Inc.) and ribosomal RNA was depleted from 5 ug of total RNA using the Ribo-Zero™ Gold Kit (Illumina, Inc.).
Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA.  Samples were processed in batches of 48 and 16 libraries were pooled randomly into 25 pools. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM following Illumina guidance. Pooled library samples were clustered on an Illumina cBot; each pool was sequenced on one lane of an Illumina HiSeq 2500 using 125 bp single-read v4 chemistry.


title: PC3M_siHSF1_B


title: 362E_M1


title: 28d_HiC_replicate_2

description:
28d_2
all.samples.abindex.txt
28d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

treatment_protocol: Six two-years-old female pigs were fed with a high fat diet (15.12 MJ·kg-1 metabolizable energy, 11.26% crude protein, 6.8% fat and 5% lysine) for 22 weeks, compared with the pigs of  two-years-old fed with well-characterized normal diet for 22 weeks.

tag: breed

value: postnatal day 28

value: DpnII


title: 0d_HiC_replicate_3

description:
0d_3
all.samples.abindex.txt
0d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

tag: condition


title: BT20_siHSF1_B


title: Monocyte_BD_2

value: Behcet's disease (BD)

value: human CD14+monocyte


title: BT20_siNT_A


title: 360E_M2


title: PC3M_siHSF1siHSF2_A


title: 0d_HiC_replicate_2

description:
0d_2
all.samples.abindex.txt
0d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

tag: chip antibody


title: BT20_siHSF1siHSF2_B


title: Monocyte_BD_1


title: 360E_F2


title: 358E_M2


title: 0d_HiC_replicate_6

description:
0d_6
all.samples.abindex.txt
0d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: AT/RT CHLA266 Control A

value: 0.1% DMSO


title: BT20_siHSF2_A


title: AT/RT CHLA266 TAK-228 C


title: 358E_F2


title: 0d_HiC_replicate_4

description:
0d_4
all.samples.abindex.txt
0d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt


title: AT/RT CHLA266 TAK-228 A


title: 358E_F1


title: 360E_F1


title: SKBR3_siNT_A


title: AT/RT CHLA266 Control C


title: 358E_M1

value: Male


title: AT/RT CHLA266 Control B


title: Monocyte_HC_2

value: healthy control


title: 355E_M2


title: E80_HiC_replicate_5

description:
E80_5
all.samples.abindex.txt
E80.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt

value: embryonic day 80