title: ark1ark2_doublemutant_rep7


title: ark1ark2_doublemutant_rep8

status: Public on Jun 01 2021

type: SRA

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

country: Germany

institute: Max Planck Institute for Plant Breeding Research

library_source: transcriptomic

data_processing:
RNAseq reads of FASTQ format were processed to remove low quality reads and reads containing adapter and poly-N sequences. Q20, Q30 and GC content of the clean data were calculated
The quality of the FASTQ files were validated with FastQC (v0.11.8)
The resulting reads from the raw fastq data were quality controlled and and mapped to the O. sativa reference genome Os-Nipponbare-Reference-IRGSP-1.0 using STAR (2.7.3a)
The raw counts and FPKM (Fragments per kilobase per million mapped reads) values were calculated with featureCounts in R package Rsubread (2.0.0)
The TPM (Transcripts per million) values were calculated by custom python script using the raw counts file
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: tab separated files with the corresponding expression values

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: whole root

growth_protocol: Plants were watered every second day, the first two weeks with reverse osmosis water (R-O H2O) followed by low Pi fertilization every other watering day with half-strength Hoagland solution containing 25 μM KH2PO4.

extract_protocol:
RNA was extracted using the TRIzol method
1 μg RNA per sample was used for library preparation generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Hitchin, United Kingdom) following manufacturer’s instructions. Library quality was monitored on the Agilent Bioanalyzer 2100 system

treatment_protocol: The AM fungal model species R. irregularis (DAOM197198) was employed for all inoculation assays. Spores extracted from Agrobacterium rhizogenes transformed carrot hairy root cultures (Bécard and Fortin, 1988) were used. Aliquoted inoculum was applied onto the substrate of half-filled cones (12 cm depth, 2.5 cm diameter), after which sand substrate was replenished and germinated seedlings transferred to the containers.

tag: cultivar

value: Nipponbare

tag: inoculum

value: R. irregularis (DAOM197198)

tag: genotype

value: ark1ark2 double mutant

tag: tissue

value: whole root


title: ark1ark2_doublemutant_rep9


title: wildtype_control_rep3

value: wild type


title: ark1ark2_doublemutant_rep6


title: ark1ark2_doublemutant_rep5


title: ark1ark2_doublemutant_rep1


title: ark2_mutant_rep9

value: ark2 mutant


title: ark1ark2_doublemutant_rep2


title: ark2_mutant_rep10


title: ark1ark2_doublemutant_rep3


title: ark2_mutant_rep7


title: ark2_mutant_rep6


title: ark2_mutant_rep8


title: ark1ark2_doublemutant_rep4


title: T1.RNA-seq.AD

city: Shenzhen,Guangdong Province,China

first: Yayan

last: Feng

state: --- Select a state ---

address: No. 7 pengfei road, dapeng new district, shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
SOAPnuke was used for trimming adapters and filtering on length and quality of the raw sequencing reads, with the following paramaters: -q 0.5 -d -Q 2 --sanger -l 20
Clean reads were mapped to respective reference genome using hisat2 with default settings
The levels of gene expression were quantified using Cufflinks (v2.2.1) with RPKM (reads per kilobase million).
Differentially expressed genes were estimated by Cuffdiff (v2.2.1) with default paramaters
Genes with a threshold false discovery rate (FDR) ≤ 0.05 and the absolute value of log2Ratio ≥ 1 or ≤ -1 were considered significantly differentially expressed
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: rpkm Bed format

molecule: polyA RNA

organism: Trichinella spiralis

source_name: T. spiralis

extract_protocol:
Total RNA of T. spiralis (Ad, NBL and ML) was purified using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
To degrade any possible DNA contamination, the total RNA samples were dissolved in diethylpyrocarbonate (DEPC)-treated water and treated with DNaseI. NanoDrop 2000 (Thermo Scientific CA, USA) was then used to assess the quantity and quality of the total mRNA enriched using oligo (dT) magnetic beads. Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform following the Illumina’s protocols.

tag: strain

tag: passages

value: Adult


title: ark2_mutant_rep4


title: T1.RNA-seq.NBL

value: Newborn larvae


title: ark2_mutant_rep2


title: T1.WGBS.AD

library_source: genomic

data_processing:
Raw sequencing reads with more than 30% ‘N’s in over 10% of the sequences or smaller than 30 bp were discarded
Clean reads were aligned to the corresponding reference genome using BSMAP (v2.73) with a of maximal four mismatches and gap size up to 2 nucleotides
Methylation level of each cytosine was calculated as the number of reads ascertained methylated to the total number of reads for each covered CpG sites.
To accurately investigate the methylation levels in each sample, we used CpG sites with a minimal 5× sequencing depth per strand.
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: cout, bed format

molecule: genomic DNA

extract_protocol:
DNA was extracted using the phenol chloroform extraction method
Genomic DNA extracted from three life stages of all Trichinella species were selected for libraries construction of WGBS. Briefly, approx. two to five micrograms of gDNA were first fragmented by Covaris to an average size of ~200-300 bp. End-repair, A-tailing and ligation were conducted as the Illumina PE genomic DNA sample prep kit protocol, except that ligation was performed using methylated cytosine PE adapters provided by Illumina previously. Ligation products were purified and bisulfited converted using the EZ DNA Methylation-Gold KitTM (ZYMO) according to the manufacturer’s instructions. The libraries were sequenced using Illumina HiSeq 2,500 platform.

tag: tag


title: T1.WGBS.NBL


title: ark2_mutant_rep5


title: Human_brain_ONT_cDNA

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
short-read RNA-seq: Sequencing data were quality controlled and adapter trimmed using Trim Galore
short-read RNA-seq: Filtered data were mapped to the relevant genome using TopHat2
short-read RNA-seq: CircRNA detection was performed using primarily using CIRI2 and secondarily using find_circ.
ONT_DNA: Nanopore data was basecalled using Guppy (v 3.4.5)
ONT_DNA: Basecalled fastq files were mapped to the relevant genome using FLAIR v1.4
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: For short-read RNA-seq: Tab-delimited text files list all detected circRNAs, including genomic coordinates, number of reads spanning backsplice junction (BSJ), host gene that circRNAs originates from and circRNA ID from circBase, circAtlas and CIRCpedia. For ONT cDNA: bigWig files show genome mapping of reads

organism: Homo sapiens

source_name: Human cortex

extract_protocol:
Total human brain RNA was derived from post mortem cortex and provided by Agilent (Agilent Technologies, cat: 540143). For the preparation of mouse brain RNA, a male mouse (strain 129S2/SV) was sacrificed, and the entire brain was harvested and grained in Trizol (Thermo Fisher Scientific). Total RNA was obtained according to the manufacture’s protocol.
ONT cDNA sequencing libraries were prepared according to the protocol, SQK-PCS108, version PCS_9035_v108_revF_26Jun2017

tag: source

value: Agilent Technologies, cat:540143

value: cortex

tag: age

value: 25 and 50 years mix


title: ark2_mutant_rep1


title: circPanel-LRS_SH-SY5Y

data_processing:
Nanopore data was basecalled using Guppy (v 3.4.5)
filtered using NanoFilt (v 2.6.0) allowing only reads with average base quality of 7 or more and a read length of 250 bp or more
mapped to the human genome (hg19) or mouse genome (mm10) using a parallelized version of  Blat
Detetion of circular RNA (circRNA) using custom scripts
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Tab-delimited text files list all detected circRNAs, including genomic coordinates, number of reads spanning backsplice junction (BSJ), host gene that circRNAs originates from and circRNA ID from circBase, circAtlas and CIRCpedia.

source_name: SH-SY5Y cell line

extract_protocol:
Total human brain RNA was derived from post mortem cortex and provided by Agilent (Agilent Technologies, cat: 540143). For the preparation of mouse brain RNA, a male mouse (strain 129S2/SV) was sacrificed, and the entire brain was harvested and grained in Trizol (Thermo Fisher Scientific). Total RNA was obtained according to the manufacture’s protocol.
After rRNA and linear RNA depletion the enriched circRNA linearized and polyadenylated. Later, the protocol, SQK-PCS108, version PCS_9035_v108_revF_26Jun2017, provided by ONT was applied to prepare  the library and run it on the MinION flow cells.
Sequencing of circular RNA

tag: cell line

tag: molecule subtype

value: enriched circRNA


title: ark1-2_mutant_rep9

value: ark1-2 mutant


title: T1.RNA-seq.ML

value: Muscle larvae


title: ark2_mutant_rep3


title: ark1-2_mutant_rep10


title: circNick-LRS_human_brain


title: ark1-2_mutant_rep8


title: circPanel-LRS_human_brain


title: T1.WGBS.ML


title: ark1-2_mutant_rep7


title: ark1-2_mutant_rep6


title: ark1-2_mutant_rep5


title: T9.WGS

data_processing:
Library strategy: WGS
FastQC (v0.11.7) was used to assess the quality of sequence reads.
Adapters and low-quality reads were removed from raw sequencing reads by Trimmomatic (v0.36) using following paramaters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:75
Clean reads from each species were mapped to respective reference genome after quality control, and then conduct SNP calling using GATK workflow.
MUMmer (v3.0) was used to examine all the single nucleotide polymorphism (SNPs) between reference genomes of T. pseudospiralis and other eleven Trichinella species. SNPs from uniquely aligned regions and with homozygous genotypes constituted the final set of SNVs.
Genome_build: The genomic data resources of the twelve Trichinella species were downloaded from NCBI BioProject database with the following accession codes: PRJNA12603 for T. spiralis,  PRJNA451013 for T. pseudospiralis, and PRJNA257433 for other ten Trichinella species.

organism: Trichinella sp. T9

extract_protocol:
DNA was extracted using the phenol chloroform extraction method.
High molecular DNA from 12 Trichinella genotypes were extracted from freshly collected muscle larvae. Qubit Fluorometer dsDNA HS Kit (Invitrogen) was used to determine total DNA amounts, followed by measurement of integrity by by agarose gel electrophoresis and using a BioAnalyzer (2100, Agilent). Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform, according to instructions provided by Illumina.


title: T8.WGS

organism: Trichinella sp. T8


title: T7.WGS

organism: Trichinella nelsoni

source_name: T. nelsoni


title: mSCLC_OE_YAP5SA_21D_NO2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
Sequencing reads were mapped to the mouse genome (mm10) with STAR v.2.4.2. The mapped reads were subjected to featureCounts with the reference annotation (Refseq) to calculate the counts of each gene.
Genome_build: mm10
Supplementary_files_format_and_content: the processed data files contain the count number of genes at each sample

organism: Mus musculus

source_name: This mouse small cell lung cancer cell line was obtained from CGRPCreER/+;Rbf/f;P53f/f;Ptenf/f;Rosa26rtTA;Tet-onYAP5SA mouse which was injected with TM after 2 months

growth_protocol: This mouse small cell lung cancer cell line was obtained from CGRPCreER/+;Rbf/f;P53f/f;Ptenf/f;mouse and grown in Hites medium

extract_protocol:
Total RNA was extracted from Msclc celllines using Trizol (Takara, Japan) according to manual instruction. Cells were ground into powder by liquid nitrogen in a 1.5 mL tube, followed by being homogenized for 5 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 10 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 12,000 rpm for 10 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed with 1 mL 75% ethanol, then the mix was centrifuged at 12,000 rpm for 5 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Mixed

value: lung tumor

tag: Stage

value: adult

tag: amount

tag: cell type

value: small cell lung cancer


title: ark1-2_mutant_rep4

value: Nipponbare

value: R. irregularis (DAOM197198)


title: mSCLC_OE_YAP5SA_21D_NO1


title: mSCLC_OE_YAP5SA_7D_NO2


title: mSCLC_OE_YAP5SA_7D_NO1


title: T6.WGS

organism: Trichinella sp. T6


title: mSCLC_OE_YAP5SA_3D_NO2


title: ark1-2_mutant_rep3

value: whole root


title: ark1-2_mutant_rep2


title: PF179TCAF-shGR-1_Dox+Dex_rep2

type: RNA

city: Innsbruck

first: Martin

last: Puhr

address: Anichstrasse 35

department: Department of Urology

country: Austria

institute: Medical University of Innsbruck

description: gene expression profiling of treated CAFs

hyb_protocol: The generated target RNA was loaded onto the Affymetrix Clariom D human array cartridge and hybridized for 16 hours at 45°C using GeneTitan Hybridization modul.

scan_protocol: Array were scanned in the GeneChip Scanner 7G. The image files were imported into the Affymetrix Expression Console software.

data_processing: Preprocessing were performed with Affymetrix Expression Console software and RMA was used for background modeling, quantile normalization, and probe summarization. Analysis were performed on the gene level (with Refseq annotation) and differentially expressed genes were identified using moderated t-test with limma R package.

label: biotin

source_name: Immortalized primary human prostate cancer associated fibroblasts (PF179TCAF) w/ shGR treated with Dox+Dex

label_protocol: A target preparation of 150 ng RNA was used for cDNA synthesis, in vitro transcription and terminal labeling utilizing the WT PLUS reagent kit (Affymetrix).

growth_protocol: PF179TCAF-shGR-1 were grown in minimum essential medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 1 mM sodium pyruvate and antibiotics. Cells were maintained in a humidified incubator at 37°C and 5% CO2.

extract_protocol: Total RNA from cell lines was isolated with the EXTRACTOME TOTAL RNA KIT (DNA-Gdansk) according to manufacturer’s instructions. Quality and amount of isolated RNA were determined on a Nanodrop2000 system (ThermoFisher Scientific).

treatment_protocol: 5 Mio stromal PF179TCAF-shGR-1 were seeded into T175 tissue flasks. On the next day specific treatments were performed as followed. Stromal cells: Group 1: vehicle Ctrl was treated with DMSO for 24h. Group 2: 100 nM dexamethasone for 24h. Group 3: 100 nM dexamethasone and 1µg/ml doxycycline treatment for 24 hours. Group 4: 100 nM dexamethasone and 12µM RU486 treatment for 24 hours.

tag: treatment

value: Doxycycline+Dexamethasone

tag: concentration

value: 1ug/ml (Dox)+100nM(Dex)


title: PF179TCAF-shGR-1_Dex_rep1

source_name: Immortalized primary human prostate cancer associated fibroblasts (PF179TCAF) w/ shGR treated with Dex

value: Dexamethasone

value: 100nM (Dex)


title: PF179TCAF-shGR-1_DMSO_rep2

source_name: Immortalized primary human prostate cancer associated fibroblasts (PF179TCAF) w/ shGR treated with DMSO

value: DMSO

value: Control


title: PF179TCAF-shGR-1_RU486+Dex_rep2

source_name: Immortalized primary human prostate cancer associated fibroblasts (PF179TCAF) w/ shGR treated with RU486+Dex


title: PF179TCAF-shGR-1_Dex_rep2


title: Mouse_brain_short_read_total-RNA

source_name: Mouse total brain

extract_protocol:
Total human brain RNA was derived from post mortem cortex and provided by Agilent (Agilent Technologies, cat: 540143). For the preparation of mouse brain RNA, a male mouse (strain 129S2/SV) was sacrificed, and the entire brain was harvested and grained in Trizol (Thermo Fisher Scientific). Total RNA was obtained according to the manufacture’s protocol.
After rRNA depletetion, sequencing was performed using DNA nanoball sequencing technology, BGISEQ-500

value: total brain

value: wild type

value: 8 weeks


title: mSCLC_OE_YAP5SA_0D_NO2


title: mSCLC_OE_YAP5SA_3D_NO1


title: ark1-2_mutant_rep1

value: ark1-2 mutant


title: mSCLC_OE_YAP5SA_0D_NO1

source_name: This mouse small cell lung cancer cell line was obtained from CGRPCreER/+;Rbf/f;P53f/f;Ptenf/f;mouse which was injected with TM after 2 months

value: Mixed


title: PF179TCAF-shGR-1_RU486+Dex_rep1


title: PF179TCAF-shGR-1_DMSO_rep1


title: PF179TCAF-shGR-1_Dex_rep3


title: PF179TCAF-shGR-1_DMSO_rep3


title: mSCLC_Non_NE3

value: lung tumor


title: PF179TCAF-shGR-1_Dox+Dex_rep1


title: PF179TCAF-shGR-1_Dox+Dex_rep3


title: PF179TCAF-shGR-1_RU486+Dex_rep3


title: mSCLC_Non_NE2

value: adult


title: T12.RNA-seq.NBL

organism: Trichinella patagoniensis

source_name: T. patagoniensis

value: Newborn larvae


title: mSCLC_Non_NE1

value: small cell lung cancer


title: mSCLC_NE3


title: T12.RNA-seq.ML

value: Muscle larvae


title: mSCLC_NE1


title: 20180327.A-Olga_NullN1_R1

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the H111 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: H111 genome sequence (accession no. HG938370, HG938371, and HG938372)
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample

organism: Burkholderia cenocepacia H111

source_name: Bc H111 null planktonic cells

growth_protocol: LB medium, OD600 equal 1

extract_protocol:
Cells were flash frozen on dry ice. The RNA was obtained using a hot phenol protocol (Pessi et al 2007). The cDNA was prepared and NuGen libraries obtained.
RNA libraries were prepared using Ovation Complete Prokaryotic RNA-Seq DR Muliplex System
NuGen

value: null mutant (enzymes that methylate and cut DNA)


title: 20180327.A-Olga_WTH3_R1

source_name: Bc H111 wt planktonic cells


title: T12.RNA-seq.AD

value: Adult


title: T12.WGBS.NBL


title: P20IECs_dist_AB_rep3

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

hyb_protocol: Fragmented cDNA was hybridized on mouse Clariom D pico assay platform following standard hybridisation protocol (Thermofisher)

scan_protocol: Gene Titan instrument

data_processing: Data were analysed using Affimetrix expression console, RMA as normalization method

source_name: sorted EpCAM intestinal epithelial cells from P20 distal small intestine, daily oral gavage with antibiotic mix started at P10

label_protocol: 400ng RNA was amplified and labelled using 3’ IVT pico kit Affymetrix RNA amplification kit (Nugene) according to manufacturer’s protocol.

growth_protocol: Pregnant females were individually housed and received AIN-93G diet (Triple A Trading/Altromin). Mice were kept in innovive disposable mice cages, enriched with corncob bedding and carton house, with tissue as nesting material, under a strict 7am to 7pm dark-light cycle, controlled temperature and humidity, with food and water given ad libitum. Pups were monitored daily, weighted every other day from P10 onwards and kept with the mothers throughout the experiment.

extract_protocol: Small intestine of P20 pups was cut open and proximal and distal parts were separated, cut into pieces and washed with ice-cold PBS. As the intestine of P20 pups is still small, Pthe parts of four different small intestines were combined in one sample, in order to obtain enough material for transcriptome profile analysis. Crypts were dissociated after incubation with 2 mM EDTA for 30 minutes at 4°C and filtered through a 70 µm cell strainer. Single cells were obtained by incubating crypts with TrypLE Express. Cells were kept in PBS 2% FCS Rho-kinase inhibitor and RNase inhibitor solution and stained with EpCAM-FITC antibody (1:50, BioLegend, 324204) for 30 minutes on ice. RNA was extracted from EpCAM-positive cells using phenol-chloroform method. RNA quality was measured on an Agilent 2100 Bioanalyzer.

treatment_protocol: From P10 to P20 pups were oral gavaged daily with 30ul of either PBS (control group) or antibiotic mix (treatment group) consisting of 25mg/kg/day amoxicillin, 50mg/kg/day metronidazole, and 50mg/kg/day vancomycin

value: Distal small intestine

value: Postnatal day (P) 20


title: 20180327.A-Olga_WTH2_R1


title: P20IECs_dist_AB_rep4


title: P20IECs__prox_AB_rep4

source_name: sorted EpCAM intestinal epithelial cells from P20 proximal small intestine, daily oral gavage with antibiotic mix started at P10

value: Proximal small intestine


title: T12.WGBS.ML


title: mSCLC_NE2


title: Human_brain_short_read_total-RNA

value: Agilent Technologies, cat:540143

value: cortex

value: 25 and 50 years mix


title: P20IECs_dist_AB_rep2


title: T12.WGBS.AD


title: P20IECs__prox_AB_rep3


title: T10.RNA-seq.NBL

organism: Trichinella papuae

source_name: T. papuae


title: 20180327.A-Olga_NullN2_R1


title: T10.RNA-seq.ML


title: T10.RNA-seq.AD


title: T10.WGBS.NBL


title: T10.WGBS.ML


title: P20IECs__prox_AB_rep2


title: P20IECs_dist_control_rep4

source_name: sorted EpCAM intestinal epithelial cells from P20 distal small intestine, daily oral gavage with PBS started at P10


title: A10-Amerchol 10%

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

country: France

institute: AltraBio

hyb_protocol: Labeled material was hybridized to Affymetrix GeneChip Human PrimeView arrays as described in the Affymetrix GeneChip 3’ IVT Express Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA)

scan_protocol: Scanning was performed using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix CEL files were analyzed in R using the Bioconductor suite of packages. Raw probe signals were background-corrected using the maximum likelihood estimation of the normal-exponential mixture model and normalized using the variance stabilization normalization followed by a quantile normalization. For summarization, probe signals for each probe set of each sample were summarized into a single value using the summarization step of the Robust Multichip Average (RMA) approach

source_name: Biopsy from previously positive skin treated with amerchol 10%

label_protocol: Total RNA from each sample was labeled as described in the Affymetrix GeneChip 3’ IVT Express Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted from skin biopsies using Qiagen RNeasy Mini Kit (Courtaboeuf, France) and contaminating DNA was removed using  DNA-FreeTM DNA Removal kit (Invitrogen, Cergy-Pontoise, France)

tag: donor

tag: compound

value: Amerchol 10%

tag: reaction grade


title: P20IECs_prox_control_rep4

source_name: sorted EpCAM intestinal epithelial cells from P20 proximal small intestine, daily oral gavage with PBS started at P10


title: A10-Petrolatum

source_name: Biopsy from previously positive skin treated with petrolatum

value: Petrolatum


title: P20IECs_dist_control_rep3


title: A10-Amerchol 100%

source_name: Biopsy from previously positive skin treated with amerchol 100%

value: Amerchol 100%


title: A5-Petrolatum


title: T10.WGBS.AD


title: A5-Amerchol 50%

source_name: Biopsy from previously positive skin treated with amerchol 50%

value: Amerchol 50%


title: A10-Amerchol 30%

source_name: Biopsy from previously positive skin treated with amerchol 30%

value: Amerchol 30%


title: A5-Amerchol 100%


title: P20IECs__prox_AB_rep1


title: P20IECs_dist_AB_rep1


title: A5-Amerchol 10%


title: CD73- AD-MSCs of mice rep2

status: Public on Jun 02 2021

city: Xinxiang

first: Huifang

last: Hou

address: 601 Jinsui Avenue

institute: Xinxiang Medical University

description: CD73- AD-MSCs were isolated using flow cytometry and then cultured.

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on PrimeView Human Gene Expression Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: CD73 negative adipose derived mesenchymal stem cells of the C57BL/6 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured with low sugar DMEM(Dulbecco’s modified Eagle’s medium) containing 10% FBS (Fetal bovine serum; Hyclone, USA).

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000.

treatment_protocol: The same number of cells were digested and centrifuged, and then the cells were collected in RNA enzyme free Ep tubes.

value: AD-MSCs were isolated from adipose tissues surrounding the groin of mice


title: A5-Amerchol 30%


title: A10-Amerchol 50%


title: P20IECs_dist_control_rep2


title: C4-Amerchol 100%

source_name: Biopsy from previously negative skin treated with amerchol 100%


title: A2-Amerchol 10%


title: P20IECs_prox_control_rep2


title: A2-Petrolatum


title: P20IECs_prox_control_rep3


title: A2-Amerchol 30%


title: C4-Petrolatum

source_name: Biopsy from previously negative skin treated with petrolatum


title: T2.RNA-seq.ML

organism: Trichinella nativa

source_name: T. nativa


title: T2.RNA-seq.AD


title: T2.WGBS.NBL

value: Newborn larvae


title: T2.RNA-seq.NBL


title: T2.WGBS.ML


title: 028-19

city: Frederiksberg

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

department: Department of Veterinary and Animal Sciences

institute: University of Copenhagen

data_processing:
Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Binoinformatics).
The remaining clean reads were aligned to the porcine genome (Sscrofa11.1) using Tophat.
The annotated gene information of porcine genome was downloaded from Ensembl (release 91).
The script htseq-count was used to generate gene count matrix.
The gene count was normalized using DESeq2.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Raw counts of sequencing reads for each gene (Ensembl gene IDs) generated from htseq-count.

organism: Sus scrofa

extract_protocol:
Total RNA was isolated with MagMax 96 blood RNA isolation kit (Thermo Fisher, USA).
RNA-seq libraries were constructed using 500 ng RNA and VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, China). The libraries were sequenced on the Illumina Hiseq X Ten platform (Illumina, USA) to generate 150 bp paired-end reads.

tag: batch

tag: Sex

value: M

tag: group

value: CON

tag: severity

value: Con

value: Blood


title: 049-19

value: F

tag: tissue


title: 023-19


title: T2.WGBS.AD

tag: tag

value: Adult


title: P20IECs_dist_control_rep1

value: Distal small intestine

tag: age

value: Postnatal day (P) 20


title: C3-Petrolatum


title: A1-Amerchol 30%


title: s1_2_pbmc_10x_esat

city: Ithaca

first: Gerlinde

last: Van de Walle

state: NY

address: 235 Hungerford Hill Road

department: Microbiology and Immunology

country: USA

institute: Cornell University

data_processing:
fastq files were aligned to version 95 of the horse genome reference (with manually annotated immunoglobulins (adapted from Wagner B. Immunoglobulins and immunoglobulin genes of the horse. Developmental & Comparative Immunology. 2006;30: 155–164. doi:10.1016/j.dci.2005.06.008)) from ensembl using the count function in the cellranger suite (10X Genomics, v3.0.1)
Intermediate BAM files were extracted and modified by appending cell barcode and unique molecular identifiers to their read names
The End Sequence Analysis Toolkit(v0.1.1) was applied on the resulting BAM files to obtain gene-cell barcode expression matrices (Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, et al. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res. 2016;26: 1397–1410. doi:10.1101/gr.207902.116)
Custom script was applied to identify duplicated genes and scale their expression proportionally
Genome_build: EquCab3.0
Supplementary_files_format_and_content: gene-cell barcode matrices

organism: Equus caballus

source_name: Peripheral blood mononuclear cells

extract_protocol:
Periperal blood mononuclear cells were isolated by Ficoll gradient separation
Libraries were prepared in accordance to the 10X Genomics 3' end single cell RNA sequencing library prepration protocol, version 2

value: Male

tag: breed

value: Warmblood

tag: time-point

value: Peak-viremia

value: Peripheral blood mononuclear cells


title: A8-Petrolatum

value: Petrolatum


title: C3-Amerchol 100%

value: Amerchol 100%


title: P20IECs__prox_control_rep1

value: Proximal small intestine


title: A2-Amerchol 50%

value: Amerchol 50%


title: A1-Amerchol 50%


title: A1-Amerchol 10%

value: Amerchol 10%


title: A2-Amerchol 100%


title: A1-Petrolatum


title: A8-Amerchol 10%


title: 047-19

value: NEC

value: Mild


title: 056-19

value: M

value: CON

value: Con


title: A1-Amerchol 100%


title: A8-Amerchol 100%


title: 043-19

value: Blood


title: Heart-1_C01

city: Beijing

first: Shuxian

last: Li

address: No.5 Yiheyuan Road Haidian District

institute: Institute of Molecular Medicine，Peking University

description: heart.uniq.sorted.bw

data_processing:
ROI (Reads-Of-Insert) reads were extracted and primer sequences flanking ROI reads were then trimmed
Primer-trimmed reads were further processed to scan the PA tail and trimmed to get PA-trimmed reads which represents reads with a PA tail trimmed.
PA-trimmed reads were then mapped to the reference genome (rheMac8) by GMAP and the low-quality reads were filtered to get the final processed alignments.
Genome_build: rheMac8
Supplementary_files_format_and_content: BigWig files were generated using Iso-seq reads alignment; scores represented Iso-seq reads coverage.

organism: Macaca mulatta

source_name: Heart

extract_protocol:
Total RNAs were extracted using the Trizol Reagent (Invitrogen, catalog #15596018) and analyzed on an Agilent 2100 Bioanalyzer to access the quality. The quantity of total RNA was measured by Qubit. cDNA was synthesized using the SMARTer PCR cDNA Synthesis Kit (Clotech, catalog #634925) and PrimeSTAR GXL DNA Polymerase (Clontech, catalog #R050B).
SMRT bell libraries were generated by using SMRTbellTM Template prep kit 1.0-SPv3 (PN 100-991-900)

value: Heart


title: 039-19


title: Heart-1_E03

description: heart.uniq.sorted.bw


title: A8-Amerchol 50%


title: C5-Amerchol 100%


title: A7-Petrolatum


title: C5-Petrolatum


title: 038-19


title: s1_pbmc_10x_esat (reanalysis)

description: Re-analysis of GSM4468651

value: Pre-infection


title: Heart-1_B03

description: heart.uniq.sorted.bw


title: A7-Amerchol 10%


title: 037-19

value: F


title: Heart-1_B01

description: heart.uniq.sorted.bw


title: A8-Amerchol 30%

value: Amerchol 30%


title: Testis-1_A01_180202

description: testis.uniq.sorted.bw

source_name: Testis

value: Testis


title: 036-19


title: 035-19

value: Severe


title: Testis-1_A01_181224

description: testis.uniq.sorted.bw


title: A7-Amerchol 30%


title: 034-19


title: C2-Petrolatum

value: Petrolatum


title: Testis-1_A01_180130

description: testis.uniq.sorted.bw


title: A7-Amerchol 50%


title: A7-Amerchol 100%

value: Amerchol 100%


title: Testis-2_C02

description: testis.uniq.sorted.bw


title: 046-19


title: Testis-1_G02

description: testis.uniq.sorted.bw


title: 026-19


title: C2-Amerchol 100%


title: FrontalCortex-4_E01

description: brain.uniq.sorted.bw

source_name: Brain

value: FrontalCortex


title: A4-Amerchol 10%


title: C1-Petrolatum


title: FrontalCortex-3_D01

description: brain.uniq.sorted.bw


title: A4-Petrolatum


title: C1-Amerchol 100%


title: A4-Amerchol 30%


title: A4-Amerchol 100%


title: 033-19


title: A4-Amerchol 50%

value: Amerchol 50%


title: A3-Petrolatum


title: 655-18


title: A3-Amerchol 10%

value: Amerchol 10%


title: 651-18

value: NEC


title: 656-18


title: A3-Amerchol 50%


title: A3-Amerchol 30%


title: FrontalCortex-2_F03

description: brain.uniq.sorted.bw


title: FrontalCortex-2_C03

description: brain.uniq.sorted.bw


title: 030-19

value: Mild


title: A9-Petrolatum


title: A3-Amerchol 100%


title: A9-Amerchol 10%


title: 649-18


title: A9-Amerchol 30%


title: A9-Amerchol 50%


title: A6-Petrolatum


title: L_AsPA5

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Sus Scrofa (ss11.1) using HISAT
DEG assessed using DeSeq2
Genome_build: ss11.1
Supplementary_files_format_and_content: excel file with count data for each sample.

source_name: Lung tissue

growth_protocol: Pigs (aged 10 weeks) were infected with 5000 A. summ eggs or left as controls, and killed 14 days post-infection. Dietary treatments were for 28 days, 14 days pre- and 14 days post-infection

extract_protocol:
Tissue was collected at euthanasia. Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard Illumina

value: Danish Landrace x yorkshire

value: lung

tag: infection status

value: infected with Ascaris suum

tag: diet

value: control diet supplemented with 1 % PAC


title: 647-18

value: M

value: CON

value: Con

value: Blood


title: L_AsPA3


title: L_AsPA4


title: L_AsPA2


title: 644-18


title: A6-Amerchol 10%


title: 643-18


title: 642-18


title: L_AsPA1


title: 641-18


title: L_As6

value: control


title: CCMV infected 96h, replicate 1

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al., doi: 10.1038/s41587-019-0201-4)
Sequencing reads were aligned to the hg19 version of the human genome, using standard parameter, using the Refseq gtf file downloaded from the UCSC genome browser, or the CCMV genome.
Reads were then quantified using quasR (Gaidatzis et al., doi: 10.1038/nbt.3269) and the above mentioned gtf file, or the CCMV annotation (accession number NC_003521).
Genome_build: hg19
Genome_build: CCMV NC_003521
Supplementary_files_format_and_content: readcounts

organism:
Homo sapiens
Panine betaherpesvirus 2

source_name: Primary human lung fibroblasts (Fi301)

growth_protocol: Primary human lung fibroblasts (Fi301) cells were maintained in EMEM supplemented with 10% FCS, 2 mM Ultraglutamine, 0.15% sodium bicarbonate, 1 mM sodium pyruvate, 1x non-essential amino acids, 45 µg/ml gentamycine. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
For RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New Engand Biolabs)
adapter sequence:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

treatment_protocol: CCMV BAC virus was added to the cells in a MOI of 5 and incubated in a humidified 5% CO2 incubator at 37°C for 30 minutes. After incubation, fresh medium was added, plates were centrifuged at 1000 rcf for 30 minutes at 34°C and infection mix was subsequently replaced by fresh medium. Infected cells were harvested at the 6, 24, 48, 72 and 96 hours post infection.

tag: infection

value: CMV

tag: host cell type

value: Primary human lung fibroblasts (Fi301)

tag: harvesting timepoint


title: CCMV infected 72h, replicate 3


title: CCMV infected 48h, replicate 3


title: CCMV infected 48h, replicate 1


title: CCMV infected 72h, replicate 2


title: L_As5


title: A9-Amerchol 100%

tag: donor

value: Amerchol 100%


title: A6-Amerchol 100%

tag: compound


title: A6-Amerchol 50%

tag: reaction grade


title: 113-17

tag: batch

value: F


title: CCMV infected 72h, replicate 1


title: CCMV infected 96h, replicate 2


title: CCMV infected 24h, replicate 3


title: A6-Amerchol 30%

value: Amerchol 30%


title: 535-16

tag: Sex


title: CCMV infected 24h, replicate 2


title: CCMV infected 96h, replicate 3


title: L_As4


title: CCMV infected 24h, replicate 1


title: L_As2


title: 536-16

tag: group


title: untreated, replicate 3

value: no CMV infection


title: 537-16

tag: severity


title: 516-16

tag: tissue


title: untreated, replicate 2


title: CCMV infected 48h, replicate 2


title: untreated, replicate 1


title: L_As1


title: 518-16

value: NEC

value: Severe


title: L_PA6

value: Danish Landrace x yorkshire

value: uninfected


title: 538-16

value: Mild


title: L_PA4

value: lung

value: control diet supplemented with 1 % PAC


title: 533-16

value: M

value: CON


title: L_PA5


title: low BHB  [2260]

city: quebec

first: ying

last: zhang

address: 735 Ave.Neree tremblay

country: Canada

institute: UNIVERSITY LAVAL

data_processing:
Adapter-removal and quality trimming of the libraries were performed with TRIMMOMATIC. BISMARK was then used to align the bisulfite-converted libraries to a synthetic converted bovine genome (ARS-UCD1.2,  bosTau9)
The Bioconductor package BSseq was then used to perform methylation smoothing and identification of differentially methylated cytosines and differentially methylated regions.
The MethylKit package was also used for cytosine methylation analysis and searching of hypermethylated and hypomethylated regions with an adjusted p value.
Genome_build: bosTau9
Supplementary_files_format_and_content: tab-delimited text files include corrected p value for DMR identification

organism: Bos taurus

source_name: low BHB_blood

extract_protocol:
Genomic DNA was extracted with the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA).
Genomic DNA from calf blood underwent bisulfite conversion and the libraries were constructed with the Pico Methyl-SeqTMLibrary Prep Kit (Catalog Nos.D5455).

tag: cell type

value: low BHB

value: blood cell

tag: birthdate

tag: gender

value: female


title: low BHB  [8761]


title: high BHB [2275]

source_name: high BHB_blood

value: high BHB


title: high BHB [2258]


title: low BHB  [2262]


title: 534-16

value: Con

value: Blood


title: high BHB [2268]


title: L_PA2

tag: breed


title: high BHB [2267]


title: L_PA3

tag: infection status


title: L_As3

value: infected with Ascaris suum

tag: diet

value: control


title: low BHB [2261]


title: OVCAR3, 09/20, 23

city: Atlanta

first: Katherine

middle: Monnet

last: Young

state: GA

address: 315 Ferst Dr. NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

description:
Test
ThermoFisher Human Single Genomechanics PCR Array

data_processing: Raw data was exported from the Fluidigm Real-Time PCR Analysis Software. Custom R code was used to calculate Rn values at each cycle number for each sample and assay combination by taking the ratio of the difference between the raw and background EvaGreen fluorescence readings and the difference between the raw and background ROX fluorescence readings. These Rn values were then analyzed using LinRegPCR (https://www.medischebiologie.nl/files/) to determine the efficiency of each amplicon and the threshold value for each amplicon to identify a Ct for each sample-assay pair. We transformed this Ct value by subtracting it from 45 resulting in a metric where high values corresponded with high expression and low values corresponded with low expression. Additionally, we identified GAPDH and RPL32 as stable housekeeping genes in our 3 cell types and removed single cell samples where either of these housekeeping genes did not amplify. The transformed Ct values were normalized to the geometric mean of the GAPDH and RPL32 expression and cells where the normalized GAPDH expression was lower than 0.8 were also removed.

label: SYBR Green

source_name: OVCAR3 cell line

label_protocol: We followed the advanced development protocol from Fluidigm for investigating single cell gene expression using SsoFast EvaGreen with Low ROX on the BioMark system (Fluidigm, ADP 41).

growth_protocol: The mesenchymal ovarian cancer cell line HEY and its derivative cell line HEY A8 were cultured in RPMI-1640 media (Sigma-Aldrich) supplemented with 10% fetal bovine serum (Atlanta Biologicals) and 1% penicillin-streptomycin (Sigma-Aldrich). The epithelial ovarian cancer cell line OVCAR3 was cultured in RPMI-1640 media supplemented with 20% fetal bovine serum and 1% penicillin-streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol: After AFM measurements for each cell, the coverslip with the cells attached was moved to a micropipette rig for aspiration. Due to the sensitivity of single cell gene expression techniques, caution was exercised in the decontamination of the system along with the removal of all RNAse and DNAse enzymes. Using micromanipulators (Scientifica) to control the x-y-z position of the micropipette, the micropipette tip was located with a 40x objective light microscope and lowered to each cell of interest. Once together, 345 to 500 mbar of negative pressure was applied for 0.2 to 2 seconds to aspirate the cell of interest into the micropipette. The micropipette was then removed from the cell media bath and 1000 mbar of positive pressure was applied for 3 seconds to displace the aspirated cell into an individual PCR tube containing 5 μL of CellsDirect One-Step qRT-PCR 2x reaction mix (Invitrogen) with 1 U/ μL of SUPERase-In, a RNAse inhibitor (Ambion). These individual cells were stored at -80°C.

tag: date collected

tag: young's modulus

tag: slow viscous time constant

tag: fast viscous time constant

tag: cell area

tag: major axis length

tag: minor axis length

tag: circularity

tag: aspect ratio

tag: roundness

tag: solidity


title: OVCAR3, 09/20, 22


title: L_PA1

tag: tissue


title: 530-16

tag: batch

tag: Sex

value: F

tag: group

value: NEC

tag: severity


title: OVCAR3, 09/20, 19


title: OVCAR3, 09/20, 18


title: 514-16

value: Severe


title: 114-17


title: L_Con5

tag: breed

value: Danish Landrace x yorkshire

tag: infection status

value: uninfected

tag: diet


title: 511-16


title: L_Con6

value: lung


title: L_Con3


title: OVCAR3, 09/20, 16

tag: date collected

tag: young's modulus

tag: slow viscous time constant


title: L_Con2


title: 112-17


title: L_Con4


title: OVCAR3, 09/20, 15

tag: fast viscous time constant

tag: cell area

tag: major axis length


title: L_Con1


title: OVCAR3, 09/20, 20

tag: minor axis length

tag: circularity

tag: aspect ratio


title: OVCAR3, 09/20, 13

tag: roundness

tag: solidity


title: OVCAR3, 09/20, 11


title: OVCAR3, 09/20, 12


title: gumB rep4

city: Pittsburgh

first: Robert

middle: MQ

last: Shanks

state: PA

address: EEI 1020, 203 Lothrop st.

department: Ophthalmology

institute: University of Pittsburgh

description: corneas were harvested 24 h post-injection

hyb_protocol: standard nCounter methods

scan_protocol: standard nCounter methods

data_processing: nSolver software

label: nanostring

organism: Oryctolagus cuniculus

source_name: infected rabbit cornea

label_protocol: standard nCounter methods

growth_protocol: ~500 CFU of Serratia marcescens in 25 microliters of PBS or 25 microliters of PBS without bacteria were injected into juvenile female New Zealand White rabbits and corneas were havested after 24 hours

extract_protocol: Extracted according to protocol of Xu, et al Methods Mol Biol 2016 (1361:57-65) Pathogen gene expression profiling during infection using a nanoString nCounter platform

treatment_protocol: n/z

value: NZW

tag: gender

tag: treatment

value: Serratia marcescens (isogenic gumB mutant )

tag: tissue

value: corneas


title: gumB rep2

tag: breed


title: OVCAR3, 09/20, 07


title: OVCAR3, 09/20, 06


title: gumB rep3


title: WT scTCR

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description: WT t cell receptor sequences

data_processing:
Library strategy: TCR-seq
GEX fastq files were processed using cellranger count pipeline
TCR fastq files were processed using cellranger vdj pipeline
Genome_build: mm10

source_name: mouse pancreatic islets

growth_protocol: cells were isolated from 8-10 week old nondiabetic mice

extract_protocol:
CD45+ cells were isolated by flow cytometry
gene expression and t cell receptor libraries were constructed based on protocols from 10X genomics

value: pancreatic islets

tag: genotype

value: WT

tag: cell type

value: sorted CD45+


title: gumB rep1

value: female


title: WT-K904 rep5

value: Serratia marcescens (wild-type keratitis isolate strain K904)


title: OVCAR3, 09/20, 17

tag: date collected


title: OVCAR3, 09/20, 14

tag: young's modulus


title: OVCAR3, 09/20, 03

tag: slow viscous time constant


title: OVCAR3, 09/20, 10

tag: fast viscous time constant


title: OVCAR3, 09/20, 09

tag: cell area


title: WT-K904 rep4


title: WT scRNA

description: WT single cell gene expression

data_processing:
GEX fastq files were processed using cellranger count pipeline
TCR fastq files were processed using cellranger vdj pipeline
Genome_build: mm10


title: K392R scRNA

description: K392R single cell gene expression

value: STAT3 +/K392R


title: OVCAR3, 09/18, 40

tag: major axis length


title: OVCAR3, 09/18, 41

tag: minor axis length


title: WT-K904 rep3


title: OVCAR3, 09/18, 37

tag: circularity


title: OVCAR3, 09/20, 04

tag: aspect ratio


title: WT scATAC

description: WT single cell ATAC

data_processing:
fastq files were processed using cellranger count-atac pipeline
Genome_build: mm10
Supplementary_files_format_and_content: fragments files representing processed paired end reads

extract_protocol:
CD45+ cells were isolated by flow cytometry
scATAC-seq libraries were constructed based on protocols from 10X genomics


title: OVCAR3, 09/18, 35

tag: roundness


title: K392R scATAC

description: K392R single cell ATAC


title: OVCAR3, 09/18, 34

tag: solidity


title: OVCAR3, 09/18, 33


title: OVCAR3, 09/18, 29


title: OVCAR3, 09/18, 28


title: WT_6L_CT_22_S134

city: Tampere

first: Nemanja

last: Milicevic

address: Arvo Ylpon katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: RPE from 1 eye

data_processing:
Trimmed using Trimmomatic v0.32 for adapter sequences.
Aligned using HISAT2 (v2.1.0) (default parameters; -p 4 --dta-cufflinks --rna-strandness R)
Gene level counts were obtained using HTSeq (v0.11) with default parameters except --stranded=reverse and the mouse GTF from Ensembl (release 93)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited file contains raw count data as obtained using HTSeq; rownames contain the Ensemble gene identifier; one column per sample.

growth_protocol: 6 week old male mice were used

extract_protocol:
The total RNA was extracted using the Qiagen RNeasy Micro Kit
Libraries were constructed using the KAPA mRNA HyperPrep kit (Illumina platforms) as specified by manufacturer's instructions.

treatment_protocol: Eyes were enucleated at time-points before, during and after the peak in phagocytosis of photoreceptor outer segments. Eyes were snap-frozen and retinal pigment epithelium was laser capture microdissected from each eye.

value: microdissected retinal pigment epithelium

tag: time-point

tag: strain

value: C57BL/6/J x 129 SvEvBrd

tag: gender

value: male


title: K392R scTCR

description: K392R t cell receptor sequences

tag: tissue


title: OVCAR3, 09/18, 42


title: OVCAR3, 09/18, 26


title: PBS - no bacteria rep3

source_name: rabbit cornea

tag: breed

tag: treatment

value: no bacteria control


title: WT-K904 rep2


title: WT-K904 rep1


title: OVCAR3, 09/18, 25

tag: date collected


title: OVCAR3, 09/18, 24

tag: young's modulus


title: WT_5L_CT1_S133

description: RPE from 1 eye

tag: genotype


title: WT_4L_CT_19_S132

description: RPE from 1 eye


title: OVCAR3, 09/18, 23

tag: slow viscous time constant

tag: fast viscous time constant


title: OVCAR3, 09/18, 22

tag: cell area

tag: major axis length


title: PBS - no bacteria rep1


title: WT_4L_CT_10_S131

description: RPE from 1 eye


title: OVCAR3, 09/18, 21

tag: minor axis length

tag: circularity


title: C12

description: bacteria grown in LB

organism: Serratia marcescens

source_name: bacterial culture

growth_protocol: LB medium with shaking, grown to OD600=1.0, treated with RNA-protect, frozen at -80 until RNA extraction

extract_protocol: RNA was prepared according to Shedlovskiy, et al RNA Biology 2017 Vol 14, pages 1722-26, followed by Dnase treatment and concentration using New England Biolabs Monarch column

treatment_protocol: mutant versus wild type

value: eepR


title: OVCAR3, 09/18, 09

organism: Homo sapiens

tag: aspect ratio

tag: roundness


title: C11

description: bacteria grown in LB


title: OVCAR3, 09/18, 14

tag: solidity


title: OVCAR3, 09/18, 10


title: OVCAR3, 09/18, 11


title: WT_3L_and_6L_CT1_S129

description: RPE from 2 eyes was pooled

tag: time-point

tag: strain


title: C10

description: bacteria grown in LB


title: WT_2L_CT_19_S128

description: RPE from 1 eye

tag: tissue

tag: gender


title: PBS - no bacteria rep2

tag: breed

tag: treatment


title: OVCAR3, 09/18, 07

tag: date collected

tag: young's modulus


title: C9

description: bacteria grown in LB

tag: genotype


title: OVCAR3, 09/18, 05

tag: slow viscous time constant

tag: fast viscous time constant


title: OVCAR3, 09/18, 01

tag: cell area

tag: major axis length


title: OVCAR3, 09/18, 03

tag: minor axis length

tag: circularity


title: C8

description: bacteria grown in LB


title: WT_2L_CT_10_S127

description: RPE from 1 eye


title: OVCAR3, 09/18, 30

tag: aspect ratio

tag: roundness


title: WT_3L_CT_22_S130

description: RPE from 1 eye

tag: time-point


title: OVCAR3, 09/18, 04

tag: solidity


title: OVCAR3, 09/15, 34


title: WT_1L_CT_22_S125

description: RPE from 1 eye

tag: tissue

tag: strain


title: OVCAR3, 09/15, 33


title: C5

description: bacteria grown in LB

value: gumB


title: OVCAR3, 09/15, 31


title: OVCAR3, 09/15, 28


title: OVCAR3, 09/15, 27


title: WT_1L_CT_19__S124

description: RPE from 1 eye

tag: gender


title: C6

description: bacteria grown in LB


title: OVCAR3, 09/15, 26


title: WT_1L_CT_10_S123

description: RPE from 1 eye


title: OVCAR3, 09/15, 21


title: OVCAR3, 09/15, 22


title: C4

description: bacteria grown in LB


title: C7

description: bacteria grown in LB


title: OVCAR3, 09/15, 24


title: C3

description: bacteria grown in LB


title: KO_5L_CT_1_S122

description: RPE from 1 eye


title: OVCAR3, 09/15, 17


title: OVCAR3, 09/15, 18


title: OVCAR3, 09/15, 16


title: C2

description: bacteria grown in LB


title: KO_4_and_6L_CT_1_S119

description: RPE from 2 eyes was pooled


title: KO_4L_CT_10_S120

description: RPE from 1 eye


title: KO_3_and_5L_CT_19_S117

description: RPE from 2 eyes was pooled


title: B10

description: bacteria grown in LB


title: KO_3L_CT_22_S118

description: RPE from 1 eye


title: OVCAR3, 09/15, 07


title: B11

description: bacteria grown in LB


title: OVCAR3, 09/15, 12


title: OVCAR3, 09/15, 14


title: OVCAR3, 09/15, 13


title: OVCAR3, 09/15, 02


title: C1

description: bacteria grown in LB


title: OVCAR3, 09/15, 05


title: OVCAR3, 09/15, 10


title: B9

description: bacteria grown in LB


title: KO_3_and_5_L_CT_10_S116

description: RPE from 2 eyes was pooled


title: KO_2L_CT_22_S115

description: RPE from 1 eye


title: OVCAR3, 09/15, 01


title: OVCAR3, 09/13, 28


title: OVCAR3, 09/13, 29


title: B8

description: bacteria grown in LB


title: KO_2L_CT_19_S114

description: RPE from 1 eye


title: B7

description: bacteria grown in LB


title: OVCAR3, 09/13, 25


title: KO_4L_CT_19_S121

description: RPE from 1 eye


title: OVCAR3, 09/15, 11


title: B12

description: bacteria grown in LB


title: OVCAR3, 09/13, 23


title: KO_2L_CT_10_S113

description: RPE from 1 eye


title: KO_1L_CT_1_S112

description: RPE from 1 eye


title: OVCAR3, 09/13, 24


title: B6

description: bacteria grown in LB


title: OVCAR3, 09/13, 27


title: B5

description: bacteria grown in LB


title: OVCAR3, 09/13, 20


title: B4

description: bacteria grown in LB


title: KO_1_and_4L_CT_22_S111

description: RPE from 2 eyes was pooled


title: WT_2L_CT1_S126

description: RPE from 1 eye


title: OVCAR3, 09/13, 19


title: OVCAR3, 09/13, 16


title: OVCAR3, 09/13, 18


title: s9_WT2LCT19

treatment_protocol: Eyes were enucleated at time-points before, during and after the peak in phagocytosis of photoreceptor outer segments. Eyes were snap-frozen and photoreceptors were laser capture microdissected from each eye.

value: microdissected photoreceptors


title: s8_KO2LCT10


title: OVCAR3, 09/13, 26


title: B2

description: bacteria grown in LB


title: OVCAR3, 09/13, 14


title: OVCAR3, 09/13, 15


title: OVCAR3, 09/13, 13


title: B3

description: bacteria grown in LB


title: B1

description: bacteria grown in LB


title: OVCAR3, 09/13, 12


title: OVCAR3, 09/13, 07


title: as-ssn3  + DMSO 3h rep 3

city: Hanover

first: Deborah

middle: Ann

last: Hogan

institute: Geisel School of Medicine

data_processing:
Basecalls - Illumina native app
Trimming - Illumina native app to trim adapter sequences
Quality Control CLC Genomics Workbench: quality score = 0.05, ambiguous bases = 2, auto adapter trim = NO, trim bases 5' and 3', filter length above =  NO,  filter length below = NO
Allignment to Ca genome - CLC Workbench: mismatched cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, strands = both, max # hits per read = 10, global allignment = NO
CGD Assembly22
Supplementary_files_format_and_content: Counts per million (CPM) for all samples in a .csv file

organism: Candida albicans

source_name: single species liquid culture

growth_protocol: C. albicans ssn3-AS was grown as a YPD for 16 hours at 30℃, washed once, then inoculated into room temperature YNB medium.

extract_protocol:
Cell pellets were dissolved in Trizol and cells were lysed by bead beating. Lysate was phase separated by centrifugation and from the aqueous phase RNA was precipitated by linear acrylimide. Centrifugation collected the RNA into a pellet that was, after supernatent removal, washed with ethanol and resuspended into deionized, nuclease-free water.
RNA was treated with Dnase using the Rneasy MinElute protocol and ribo-depletion using RiboZero (bacteria). Library prep was done as the Illumina TrueSeq Stranded RNAseq.

treatment_protocol: 3-MB-PP1 was added 5 minutes prior to transfter to hypha-formation permissive medium.

tag: treatment

value: DMSO

tag: time point (hours)


title: OVCAR3, 09/13, 05

tag: date collected

tag: young's modulus


title: OVCAR3, 09/13, 17

tag: slow viscous time constant


title: as-ssn3  + DMSO 3h rep 2

tag: genotype


title: s4_KO3LCT22


title: s5_WT5LCT1_6LCT1


title: as-ssn3 + 3-MB-PP1 3h rep 3


title: OVCAR3, 09/13, 04

tag: fast viscous time constant

tag: cell area


title: as-ssn3  + DMSO 3h rep 1


title: OVCAR3, 09/13, 03

tag: major axis length

tag: minor axis length


title: HEY, 08/07, 31

source_name: HEY cell line

tag: circularity

tag: aspect ratio


title: OVCAR3, 09/13, 02

tag: roundness


title: s7_WT5RCT10

tag: time-point


title: OVCAR3, 09/13, 01

tag: solidity


title: OVCAR3, 09/13, 11


title: s31_WT2LCT10

tag: tissue

tag: strain


title: HEY, 08/07, 30


title: s30_KO5LCT1

tag: gender


title: as-ssn3 + 3-MB-PP1 3h rep 1

tag: treatment

tag: time point (hours)


title: HEY, 08/07, 27

tag: date collected

tag: young's modulus


title: HEY, 08/07, 29

tag: slow viscous time constant


title: Wild type + DMSO 3h rep 3

tag: genotype

value: wild type


title: HEY, 08/07, 28

tag: fast viscous time constant

tag: cell area


title: s3_WT2LCT22


title: HEY, 08/07, 26

tag: major axis length

tag: minor axis length


title: s6_KO6LCT1


title: HEY, 08/07, 18

tag: circularity

tag: aspect ratio


title: HEY, 08/07, 17

tag: roundness


title: HEY, 08/07, 15

tag: solidity


title: Wild type + DMSO 3h rep 2


title: s29_WT3LCT1

tag: tissue

tag: time-point


title: s32_KO4LCT10

tag: strain

tag: gender


title: as-ssn3 + 3-MB-PP1 3h rep 2

tag: treatment

tag: time point (hours)


title: Wild type + DMSO 3h rep 1


title: s28_KO2LCT22


title: HEY, 08/07, 14

tag: date collected

tag: young's modulus


title: Wild type + 3-MB-PP1 3h rep 3

tag: genotype


title: s27_WT3LCT22


title: Wild type + 3-MB-PP1 3h rep 2


title: HEY, 08/07, 12

tag: slow viscous time constant

tag: fast viscous time constant


title: Wild type + 3-MB-PP1 3h rep 1


title: HEY, 08/07, 07

tag: cell area

tag: major axis length


title: HEY, 08/07, 06

tag: minor axis length

tag: circularity


title: HEY, 08/07, 11

tag: aspect ratio

tag: roundness


title: s26_KO3LCT19

tag: tissue


title: s25_WT4LCT19

tag: time-point


title: as-ssn3  + DMSO 0h rep 3

tag: strain


title: HEY, 08/07, 01

tag: solidity


title: HEY, 08/07, 05


title: HEY, 08/07, 04


title: HEY, 08/02, 28


title: s24_KO3LCT10

tag: gender


title: HEY, 08/07, 03


title: HEY, 08/07, 02


title: as-ssn3  + DMSO 0h rep 2

tag: treatment

tag: time point (hours)


title: as-ssn3  + DMSO 0h rep 1


title: s23_WT1LCT10


title: HEY, 08/02, 26

tag: date collected

tag: young's modulus


title: HEY, 08/02, 25

tag: slow viscous time constant


title: HEY, 08/02, 24

tag: fast viscous time constant


title: s22_KO1LCT1

tag: genotype


title: as-ssn3 + 3-MB-PP1 0h rep 3


title: s21_WT4LCT1


title: HEY, 08/02, 21

tag: cell area

tag: major axis length


title: as-ssn3 + 3-MB-PP1 0h rep 2


title: s20_KO4LCT22


title: as-ssn3 + 3-MB-PP1 0h rep 1


title: HEY, 08/02, 19

tag: minor axis length

tag: circularity


title: s2_KO4LCT19


title: HEY, 08/02, 20

tag: aspect ratio

tag: roundness


title: HEY, 08/02, 29


title: HEY, 08/02, 17


title: Wild type + DMSO 0h rep 3


title: HEY, 08/02, 23


title: s19_WT1LCT22

tag: tissue

tag: time-point


title: HEY, 08/02, 15

tag: solidity


title: HEY, 08/02, 16


title: s17_WT1LCT19

tag: strain

tag: gender


title: HEY, 08/02, 18


title: HEY, 08/02, 09


title: HEY, 08/02, 13


title: Wild type + DMSO 0h rep 2

tag: treatment

tag: time point (hours)


title: Wild type + DMSO 0h rep 1


title: HEY, 08/02, 11

tag: date collected

tag: young's modulus


title: s18_KO5LCT19


title: HEY, 08/02, 10

tag: slow viscous time constant

tag: fast viscous time constant


title: Wild type + 3-MB-PP1 0h rep 2

tag: genotype


title: s16_KO5LCT10


title: HEY, 08/02, 06

tag: cell area

tag: major axis length


title: s15_WT4LCT10


title: HEY, 08/02, 04

tag: minor axis length

tag: circularity


title: Wild type + 3-MB-PP1 0h rep 1


title: Wild type + 3-MB-PP1 0h rep 3


title: s14_KO4LCT1


title: HEY, 08/02, 05

tag: aspect ratio

tag: roundness


title: HEY, 08/01, 27


title: HEY, 08/01, 26


title: HEY, 08/01, 23


title: HEY, 08/02, 08


title: HEY, 08/01, 21


title: HEY, 08/01, 22


title: HEY, 08/01, 19


title: s12_KO1LCT22

tag: tissue

tag: time-point


title: HEY, 08/01, 17

tag: solidity


title: HEY, 08/01, 16


title: HEY, 08/01, 15


title: s1_WT3LCT19

tag: strain

tag: gender


title: s10_KO2LCT19


title: s11_WT6LCT22


title: HEY, 08/01, 13


title: HEY, 08/01, 14


title: s13_WT1LCT1


title: HEY, 08/01, 11


title: HEY, 08/01, 08


title: HEY, 08/01, 07


title: HEY, 08/01, 12


title: HEY, 08/01, 06


title: KO Br male rep1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression data from male rest of brain (whole brain minus the cerebellum)

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the TAC 4.0 Software using the MAS5 algorithm to generate .CHP files.

source_name: KO male rest of brain

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Plus kit protocol.

growth_protocol: Animals were maintained under regular housing conditions prior to sampling

extract_protocol: RNA was extracted using Trizol from 50-100 mg of tissue

treatment_protocol: mice were sacrificed and their brains removed immediately afterwards; while fresh, extracted brains were manually cleaned of brain stem tissue remnants by gross dissection, and split into cerebellum and rest-of-brain.  Each sample was then placed inside an individual 15-ml conical, put dry-ice to snap-freeze, and archived in -80degC.  To prevent cross-contamination and tissue degradation due to delayed processing, mice were dissected one at a time with a single-use scalpel blade each.


title: KO Br male rep2


title: HEY, 08/01, 05


title: KO Br female rep1

description: gene expression data from female rest of brain (whole brain minus the cerebellum)

source_name: KO female rest of brain


title: KO Br female rep2


title: HEY, 08/01, 02


title: HEY, 08/01, 04


title: HEY, 07/31, 25


title: HEY, 08/01, 01


title: KO cb female rep1

description: gene expression data from female cerebellum

source_name: KO female cerebellum


title: HEY, 07/31, 21


title: HEY, 07/31, 20


title: HEY, 07/31, 23


title: HEY, 07/31, 19


title: HEY, 07/31, 16


title: HEY, 07/31, 10


title: KO cb female rep2


title: HEY, 07/31, 17


title: HEY, 07/31, 08


title: HEY, 07/31, 05


title: HEY, 07/31, 07


title: HEY, 07/31, 06


title: HEY, 07/31, 24


title: KO cb male rep1

description: gene expression data from male cerebellum

source_name: KO male cerebellum


title: HEY, 07/31, 04


title: KO cb male rep2


title: HEY, 07/31, 02


title: WT Br male rep2

source_name: wild type male rest of brain


title: WT Br female rep2

source_name: wild type female rest of brain


title: HEY, 07/31, 18


title: WT Br female rep1


title: HEY, 07/31, 01


title: WT cb male rep1

source_name: wild type male cerebellum


title: WT cb male rep2


title: HEY, 06/21, 13


title: HEY, 06/21, 14


title: WT cb female rep2

source_name: wild type female cerebellum


title: HEY, 07/31, 03


title: Wnt6_Ko_infected_Rep3

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

institute: Research Center Borstel - Leibniz Lung Center

hyb_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

data_processing: Data has been log-transformed and normalized (percentile shift) within the Agilent GeneSpring V13 software

source_name: bone-marrow derived macrophages

growth_protocol: 24h at 37°C and 5%CO2

extract_protocol: Trizol lysis followed by DirectZol® RNA MiniPrep

treatment_protocol: Mycobacterium tuberculosis MOI 3:1

value: NMRI

tag: infection

value: Mtb


title: WT cb female rep1


title: HEY, 06/21, 07

tag: date collected


title: HEY, 06/21, 08

tag: young's modulus


title: HEY, 06/21, 01

tag: slow viscous time constant


title: HEY, 06/21, 03

tag: fast viscous time constant


title: WT Br male rep1


title: HEY, 06/21, 06


title: HEY, 06/07, 15


title: 2812_STC1_A

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

description: ChIP-DNA

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using a snakemake based pipeline https://github.com/crazyhottommy/pyflow-ChIPseq. Briefly, raw reads were first processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and uniquely mapped reads were aligned to the hg19 reference genome using Bowtie version 1.1.2 (Langmead et al., 2009). Duplicate reads were removed using SAMBLASTER (Faust and Hall, 2014) before compression to bam files. To directly compare ChIP-seq samples uniquely mapped reads for each mark were downsampled per condition to 18 million, sorted and indexed using samtools version 1.5 (Li et al., 2009). To visualize ChIP-seq libraries on the IGV genome browser, we used deepTools version 2.4.0 (Ramirez et al., 2014) to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Super ChIP-seq tracks were generated by merging bam files from each cancer type, sorting and indexing using samtools and scaling to RPKM using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: Cell Line

growth_protocol: Melanoma tumors were obtained from the Melcore tumor bank at MD Anderson Cancer Center. Tissue was disassociated (50 mg of tissue; ~8 mg per histone modification antibody) manually in 2 mL of Hanks' Balanced Salt Solution (HBSS) using a sterile razor blade. Mince the tissue into 3 to 4 mm pieces for approximately 5 min in a sterile tissue culture dish. Transfer the tissue and HBSS solution into a dissociator tube and add another 8 mL of HBSS. Further disassociate the tissue using a dissociator until homogenized. For melanoma tumors, place the tubes in a dissociator and run the following cycles each one time in this order: h_tumor_01.01, h_tumor_02.01, h_tumor_03.01 and m_heart_02.01.

extract_protocol:
ChIP assays were performed as described previously in Terranova et al (An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues; JoVE 2018). Briefly, 50mg of tissue or 20million cells were harvested via cross-linking with 1% (wt/ vol) formaldehyde for 10 min at 37 °C with shaking. After quenching with 150 mM glycine for 10 min at 37 °C with shaking, cells were washed twice with ice-cold PBS and frozen at −80 °C for further processing. Cross-linked pellets were thawed and lysed on ice for 30 min in ChIP harvest buffer (12 mM Tris-Cl, 1 × PBS, 6 mM EDTA, 0.5% SDS) with protease inhibitors (Sigma). Lysed cells were sonicated with a Bioruptor (Diagenode) to obtain chromatin fragments (~200–500 bp) and centrifuged at 15,000 × g for 15 min to obtain a soluble chromatin fraction. In parallel with cellular lysis and sonication, antibodies (5 μg/3 × 106 cells) were coupled with 30 μl of magnetic protein G beads in binding/blocking buffer (PBS + 0.1% Tween + 0.2% BSA) for 2 h at 4 °C with rotation. Soluble chromatin was diluted five times using ChIP dilution buffer (10 mM Tris-Cl, 140 mM NaCl, 0.1% DOC, 1% Triton X, 1 mM EDTA) with protease inhibitors and added to the antibody-coupled beads with rotation at 4 °C overnight. After washing, samples were treated with elution buffer (10 mM Tris-Cl, pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS), RNase A, and Proteinase K, and cross-links were reversed overnight at 37. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). ChIP DNA was purified using AMPure XP beads (Agencourt) and quantified using the Qubit 2000 (Invitrogen) and Bioanalyzer 1000 (Agilent). Libraries for Illumina sequencing were generated following the New England BioLabs (NEB) Next Ultra DNA Library Prep Kit protocol. A total of 10 cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments (~200–500 bp) and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing. Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

tag: chip-antibody

tag: cell type

value: melanoma short-term patient culture cell line

tag: cell genotype

value: BRAF mutation


title: HEY, 06/07, 14

tag: cell area

tag: major axis length

tag: minor axis length


title: HEY, 06/07, 12

tag: circularity

tag: aspect ratio

tag: roundness


title: Wt_infected_Rep3

scan_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

tag: genotype

value: Wt


title: HEY, 06/21, 12

tag: solidity


title: HEY, 06/07, 11


title: Wt_infected_Rep2

label_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

tag: strain


title: 2792_STC1_A

description: ChIP-DNA


title: 2765_STC1_A

description: ChIP-DNA


title: Wnt6_Ko_infected_Rep2

tag: infection


title: HEY, 06/07, 08

tag: date collected


title: Wt_infected_Rep1


title: 2698_STC1_A

description: ChIP-DNA


title: HEY, 06/21, 11

tag: young's modulus


title: 2761_STC1_A

description: ChIP-DNA


title: Wnt6_Ko_infected_Rep1


title: HEY, 06/07, 07

tag: slow viscous time constant


title: HEY, 06/07, 04

tag: fast viscous time constant


title: HEY A8, 08/31, 04

source_name: HEY A8 cell line


title: HEY A8, 08/31, 33


title: 2549_STC1_A

description: ChIP-DNA

tag: chip-antibody


title: 2559_STC1_A

description: ChIP-DNA

tag: cell type


title: 2379_STC1_A

description: ChIP-DNA

tag: cell genotype


title: 2357_STC1_A

description: ChIP-DNA


title: HEY A8, 08/31, 31

tag: cell area


title: HEY A8, 08/31, 32

tag: major axis length


title: HEY, 06/07, 10

tag: minor axis length


title: HEY A8, 08/31, 03

tag: circularity


title: HEY A8, 08/31, 25

tag: aspect ratio


title: HEY A8, 08/31, 26

tag: roundness


title: HEY A8, 08/31, 27


title: HEY A8, 08/31, 20


title: HEY A8, 08/31, 08


title: HEY A8, 08/31, 21


title: M-WM793B_A

description: ChIP-DNA

value: melanoma cell line from Cancer Cell Line Encyclopedia


title: M-PNPN_E

description: ChIP-DNA

value: isogenic melanocytes harboring an NRAS mutation

value: NRAS mutation


title: M-PNPN_G

description: Input-DNA


title: HEY A8, 08/31, 24


title: M-PNPN_F

description: ChIP-DNA


title: HEY A8, 08/31, 14


title: HEY A8, 08/29, 30


title: HEY A8, 08/29, 09


title: HEY A8, 08/31, 02


title: HEY A8, 08/31, 13


title: HEY A8, 08/29, 29


title: HEY A8, 08/31, 30


title: M-WM266_A

description: ChIP-DNA


title: HEY A8, 08/29, 28


title: HEY A8, 08/29, 22


title: M-WM165_A

description: ChIP-DNA


title: 2173_STC1_A

description: ChIP-DNA


title: HEY A8, 08/29, 20


title: M-WM115_A

description: ChIP-DNA


title: M-HS934_A

description: ChIP-DNA


title: HEY A8, 08/29, 15


title: HEY A8, 08/29, 19


title: HEY A8, 08/29, 14


title: HEY A8, 08/22, 09


title: M-G361_A

description: ChIP-DNA


title: M-A2058_A

description: ChIP-DNA


title: HEY A8, 08/22, 08


title: HEY A8, 08/22, 06


title: M-96_A

description: ChIP-DNA


title: HEY A8, 08/22, 07


title: HEY A8, 08/22, 05


title: M-940_A

description: ChIP-DNA


title: HEY A8, 08/29, 21


title: HEY A8, 08/22, 23


title: HEY A8, 08/22, 22


title: M-84_A

description: ChIP-DNA


title: HEY A8, 08/22, 21


title: HEY A8, 08/22, 25


title: M-61_A

description: ChIP-DNA


title: HEY A8, 08/22, 17


title: M-57_A

description: ChIP-DNA


title: HEY A8, 08/29, 17


title: HEY A8, 08/22, 16


title: HEY A8, 08/22, 15


title: HEY A8, 08/22, 13


title: M-48_A

description: ChIP-DNA


title: HEY A8, 08/22, 12


title: HEY A8, 08/22, 11


title: HEY A8, 08/22, 10


title: M-22_A

description: ChIP-DNA


title: HEY A8, 08/22, 01


title: HEY A8, 08/22, 24


title: M-12_A

description: ChIP-DNA


title: HEY A8, 08/22, 18


title: HEY A8, 08/08, 09


title: HEY A8, 08/08, 07


title: HEY A8, 08/08, 39


title: HEY A8, 08/08, 06


title: HEY A8, 08/08, 38


title: HEY A8, 08/08, 37


title: HEY A8, 08/08, 35


title: M-52_A

description: ChIP-DNA


title: HEY A8, 08/08, 34


title: HEY A8, 08/08, 33


title: HEY A8, 08/08, 31


title: HEY A8, 08/08, 32


title: HEY A8, 08/08, 30


title: B7 [miRNA-seq]

city: Kunming, Yunnan, China

first: Danqi

last: Deng

address: 374 Dianmian Road, Wuhua District

institute: The Second Affiliated Hospital of Kunming Medical University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

source_name: Tibetan health control

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

tag: subject status

value: Tibetan health control

tag: subject age

value: adults

value: Peripheral Blood Mononuclear Cell

tag: molecule subtype

value: small RNA


title: B8 [miRNA-seq]


title: B10 [miRNA-seq]


title: A14 [miRNA-seq]

source_name: Tibetan SLE patients

value: Tibetan SLE patients


title: B9 [miRNA-seq]


title: B12 [miRNA-seq]


title: A12 [miRNA-seq]


title: A11 [miRNA-seq]


title: HEY A8, 08/08, 08

tag: solidity


title: HEY A8, 08/08, 28

tag: date collected


title: HEY A8, 08/08, 26

tag: young's modulus


title: HEY A8, 08/08, 25

tag: slow viscous time constant


title: HEY A8, 08/08, 24

tag: fast viscous time constant


title: A8 [miRNA-seq]


title: HEY A8, 08/08, 23


title: A5 [miRNA-seq]


title: HEY A8, 08/08, 22


title: HEY A8, 08/08, 20


title: B10

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: B12


title: B9


title: HEY A8, 08/08, 15


title: HEY A8, 08/08, 17


title: HEY A8, 08/08, 18


title: B8


title: B7


title: HEY A8, 08/08, 03


title: HEY A8, 08/08, 16


title: A14


title: HEY A8, 08/08, 11


title: HEY A8, 07/17, 06


title: HEY A8, 07/17, 09


title: HEY A8, 07/17, 08


title: A12


title: HEY A8, 08/08, 10


title: HEY A8, 07/17, 05


title: HEY A8, 08/08, 21


title: HEY A8, 07/17, 04


title: HEY A8, 07/17, 03


title: HEY A8, 07/17, 02


title: HEY A8, 08/08, 02


title: A8


title: A11


title: HEY A8, 08/08, 19


title: HEY A8, 07/17, 15


title: HEY A8, 07/17, 13


title: HEY A8, 07/17, 12


title: HEY A8, 08/08, 14


title: GBM22AR_R1

city: New York

first: Markus

last: Siegelin

state: New York

department: Pathology and Cell Biology

institute: Columbia University

description: CHIP sequencing

data_processing:
GBM22-Fig4I and GBM22AR-Fig4I were generated by using Galaxy software (https://usegalaxy.org/)
GBM22-FigS8C and GBM22AR-FigS8C were generated by using basepair software (https://www.basepairtech.com/)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: GBM22 glioblastoma cell line

growth_protocol: DMEM+10%FBS+primocin+ 1µM Alisertib

extract_protocol:
DNA was extracted using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 from Cell Signalling.
next generation sequencing (NGS) from Genewiz, New Jersey

value: Glioblastoma cell

tag: treatment

value: Alisertib

tag: cell line

tag: chip antibody

value: H3K27ac (Cell Signalling, 8173)


title: HEY A8, 07/17, 11

tag: cell area


title: GBM22_R1

description: CHIP sequencing

tag: cell type

value: DMSO


title: HEY A8, 07/17, 10

tag: major axis length

tag: minor axis length


title: GBM22AR-2

description: ATAC sequencing

data_processing:
data was generated by using basepair software (https://www.basepairtech.com/)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

growth_protocol: DMEM+10%FBS+primocin+1µM Alisertib

extract_protocol:
DNA was extracted using the ATAC-Seq Kit ( #53150) from Active Motif.
next generation sequencing (NGS) from Genewiz, New Jersey


title: GBM22-2

description: ATAC sequencing


title: GBM22AR-1

description: ATAC sequencing


title: HEY A8, 07/17, 01

tag: circularity

tag: aspect ratio


title: GBM22-1

description: ATAC sequencing


title: HEY A8, 07/17, 14

tag: roundness


title: EBL24_LS-Patient_30

first: Eduardo

last: Vilar-Sanchez

state: Texas

address: 1515 Holcombe Blvd, Unit 1360

institute: UT MD Anderson Cancer Center

description: colon mucosa from patient with Lynch Syndrome (LS)

data_processing:
Sequencing reads quality check - FastQC
Alignment: patient samples - STAR
Expression quantification - rsem-calculate-expression
Genome_build: patient samples - UCSC hg19;  mouse model samples - NCBI mm10
Supplementary_files_format_and_content: tab-delimited output with raw read counts

source_name: NORMAL

extract_protocol:
Intestinal (small) crypts from mice were isolated and prepared as single cells. Stem and non stem cells were FACS sorted. Total RNA and total cell extracts (proteins) were generated from a pool of cells.
Total RNA was sequenced on Illumina Hi-seq instrument using 78 base pairs paired end reads. For TCE, tryptic peptides were individually analyzed by nano-LC coupled Synapt G2-si ion-mobility mass spectrometry in HDMSE mode using Waters Masslynx (version 4.1, SCN 851).

tag: tissue

value: NORMAL

tag: localization

value: COLON

tag: pathology

value: UM

tag: batch

tag: mmr status

value: HET


title: A5

tag: subject status


title: Primary-CI1123 II

city: Madurai

first: Divya

last: Arunachalam

state: Tamil Nadu

address: No 1 Anna Nagar

department: Proteomics

country: India

institute: Aravind Medical Research Foundation

hyb_protocol: 100ng of total RNA was probed with nCounter® Human Immunology Panel (XT-CSO-HIM2-12) using NanoString gene expression protocol. Hybridization was carried out at 65 Deg Centigrade for 18 hours and ramped to 4 Degree Centrigad, kept for 15 mins  before loading on to the cartridge.

scan_protocol: Hybridized molecules are loaded to Nanostring sprint catridge and loaded onto nCounter SPRINT machine for scanning the barcodes. Raw counts data was retrieved from the machine after the scanning completes.

data_processing: Raw data were normalized using nSolver 4.0 software. Normalization were carried out using Positive controls probes and house keeping genes.

source_name: Primary corneal epithlial cells

label_protocol: NanoString uses combination of oligonucleotide based barcodes. Each probe hybridising the mRNAs will be unique with combination of color and position barcodes.

growth_protocol: Corneal epithelial cells were cultured in 6-well culture plate till it reaches 80-90% confluence at 37ºC, 5% CO2 incubator

extract_protocol: After infection, the total RNA was isolated from control and infected samples using Qiagen Rneasy mini kit as per manufacturer's protocol (74104).

treatment_protocol: Cell line and primary cultures were infected with clinical isolates of A. flavus CI1698 and CI1123 for 6h at one in ten multiplicity of infection.

value: Corneal tissue from cadaveric eyes

value: A .flavus CI1123


title: RCB2280-CI1123 II

source_name: SV40 immortalized cell line

value: Corneal epithelial cell line


title: EBL21_LS-Patient_29


title: Primary-CI1698 I

value: A .flavus CI1698


title: Primary-CI1698 II


title: Primary-control I

value: Control


title: Primary-CI1123 I


title: RCB2280-CI1123 I


title: Rhein_MCE_RNAinput

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

data_processing:
Trim Galore (v.0.6.5) was initially used to trim the low quality sequences and retain paired reads under -length 100 -paired parameters.
The paired-end reads were aligned to mouse genome (GRCm38) with HISAT2 aligner (v2.1.0) with default parameters and Ensemble genes (GRCm38.102) transcriptome annotation.
Then gene expression were quantified using stringtie (v2.1.4), and differentially expressed genes were identifified using DESeq2 (v1.30.1). The FoldChange > 2 or < 0.5 and p-value < 0.05 genes were considered as differentially expressed genes.
Quality control of MeRIP-seq data was performed using FastQC (v.0.11.9). Low-quality bases and adaptor contamination were removed by Trim Galore Remaining reads were aligned to mouse genome version mm10 with HISAT2 aligner with default parameters.
The mapped reads were filtered with Picard (v2.23.5) to remove PCR duplicates and SAMtools (v1.9) to remove the reads with mapping quality below.
m6A peaks were identified using exomePeak2 R package with default parameters. Peaks were annotated by R package ChIPseeker (v.1.26).
The distribution of m6A peaks was plotted by R package Guitar (v.2.6.0). Motif finding on m6A was performed using HOMER (v.4.11) findMotifs.pl with parameters -rna -p 10 -len 5,6,7,8 -S 10.
The final bam files were transformed to bigwig format by using Deeptools (v3.5.0) with --normalizeUsing BPM parameters. IGV (Integrative genomics viewer, v2.94) was used to visualize the aligned data.
Genome_build: mm10
Supplementary_files_format_and_content: peak csv files
Supplementary_files_format_and_content: bigwig files

growth_protocol: Cells were seeded and cultured until a confluency of 100% was reached. Two days after complete confluency, cells were fed with MDI induction media. Three days later, cells were replenished with media supplied with 10% FBS, 1% PS and 10 μg/ml insulin every 2-3 days until fully diffenretiated adipocyte-like cells were obtained.

extract_protocol:
Total RNA was extracted using TRIzol Reagent and MeRIP-seq samples were immunoprecipitated by m6A antibody.
Samples were first dephosporylated and 40-60nt region was selected according to 15% polyacrylamide TBE-urea gel separation. Desired RNA species were excised and soaked overnight followed by ethanol precipitation. the purified RNA was processed for Poly-(A) tailing reaction and reverse transcription afterwards. Eventually, PCR amplification was proceeded using Phusion High-Fidelity DNA Polymerase.
MeRIP-seq

treatment_protocol: One sample was treated by 20 μM Rhein and DMSO from DAY0 to DAY3.

tag: m6a antibody

value: preadipocytes at the mitotic clonal expansion stage

value: Rhein

tag: merip antibody


title: Rhein_MCE_IP

value: anti-m6A antibody (Abcam ab151230)

tag: treatment


title: RCB2280-CI1698 I


title: RCB2280-control I


title: RCB2280-control II


title: Rhein_Diff_IP

value: mature adipocytes


title: Rhein_Diff_RNAinput


title: EBL27_LS-Patient_27


title: EBL19_LS-Patient_26


title: RCB2280-CI1698 II


title: Primary-control II


title: DMSO_Pre_RNAinput

value: preadipocytes


title: EBL14_LS-Patient_25


title: DMSO_Pre_IP


title: DMSO_MCE_IP


title: EBL12_LS-Patient_24


title: DMSO_Diff_IP


title: HE3

city: Shanghai

first: Huihui

last: Wang

state: Shanghai

address: No. 845, Lingshan Road, Pudong New District, Shanghai

department: Center for Reproductive Medicine

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to mm10 whole genome using Tophat2 with default parameters.
Coding and non-coding transcripts were distinguished by Coding Potential Calculator (CPC), Coding-Non-Coding Index (CNCI), and Pfam-scan (PFAM). Non-coding RNAs with length >200 nt and exon number ≥ 2 were considered to be lncRNAs. Expression values were expressed as Reads Per Kilo base per Million reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with RPKM and read count for every gene and every sample

source_name: Neural stem cells

extract_protocol:
The first-passage NSCs were harvested, each group contained samples of 2 mice.RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Illumina, USA) was used  for the construction of sequencing libraries.The libraries were size-selected by agarose gel electrophoresis, PCR-amplified, and sequenced by HiSeq x Ten.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 mice at 8 wks pregnant received 100 μg/kg/d estradiol valerate (high estradiol [HE] group) or an equal amount of blank solvent (corn oil; control [NC] group) via gavage from E5.5 to E11.5. Mice were euthanized at E14.5 and the male fetuses extracted and decapitated to isolate NSCs. The hypothalami were fragmented in Neurobasal-A (Gibco), digested with TrypLE (Gibco) in 37℃ for 15 min, and gently triturated into single cells with tips. The cells were then washed twice in Neurobasal-A and suspended in a proliferation medium containing Neurobasal-A, 2% B27 (Gibco), 10 ng/mL EGF (Peprotech), 10 ng/mL bFGF (Peprotech), and 1% Glutamax (Gibco), seeded in ultralow adhesion 6-well plates and incubated in 5% CO2 at 37℃.

tag: strain

value: hypothalamus

value: neural stem cells (NSCs)

tag: age

value: embryonic day 14.5

value: prenatal high estradiol exposure


title: EBL10_LS-Patient_23

value: NORMAL

value: COLON


title: HE2

tag: cell type


title: HE1


title: NC1

value: untreated


title: EBL8_LS-Patient_22

value: UM

value: HET


title: NC3


title: NC2


title: lps_pc#4

first: Junhao

last: Hu

address: No.26, Qiuyue Rd., Pudong District

department: Interdisciplinary Research Center of Biology and Chemistry

institute: Chinese Academy of Sciences

data_processing:
Reads cleaning: raw FASTQ files were quality checked using FASTQC . Then fastp was used to quality trim FASTQ files by both read quality and length (Q30 > 20, length > 36).
Alignment: clean reads were processed to pseudo-align to mouse transcriptome GRCm38 using salmon.
Quantification: transcriptional level expression was aggregated to gene level expression using tximport. Ensembl release 95 was used to annotate genes.
Quality check: sample clustering was performed with principle component analysis analysis and sample to sample distance correlation analysis.
DEGs analysis: differential expressed genes were defined by DESeq2 with foldchange > 1.5 and adjusted p-value < 0.05. DEGs based hypergeometric test and gene set enrichment analysis were produced by clusterProfiler.
Genome_build: GRCm38

source_name: Lung pericytes

extract_protocol: standard smartSeq2 protocol

treatment_protocol: Mice were given PBS or LPS trachea instillation and sacrificed after 24 hours

value: PC

value: LPS


title: EBL4_LS-Patient_20


title: EBL6_LS-Patient_21


title: DMSO_Diff_RNAinput

value: DMSO


title: lps_pc#3


title: lps_pc#6


title: mRNA_Negtive Control-4

city: Kunming

first: Jing

last: Sun

state: Yunnan

address: NO. 935,JIAO LIN ROAD

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Sample 16

data_processing:
RNA-seq reads from paired-end libraries.
The sequencing data was filtered with SOAPnuke (v1.5.2)
The clean reads were mapped to the mm9 genome using HISAT2 (v2.0.4).
Then expression level of gene was calculated by STRING TIE(v1.2.3).
Differntal miRNA expression was analyzed using the DESeq(v.1.12.1)
Genome_build: mm9

source_name: splenocyte

growth_protocol: Mice splenocytes were  were cultured in 1640 containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 U/mL streptomycin

extract_protocol:
Total RNA was extracted using the RNAfast200 kit according to the manufacturer’s protocol.
The strand-specific RNA-seq libraries were prepared using a NEBNext® Ultra™ I RNA Library Prep Kit for Illumina (NEB, MA, USA) following the manufacturer’s instructions.

treatment_protocol: Mice splenocytes were harvested and washed two times with PBS containing 2% BSA. Cells were then adjusted to the concentration of 1×106/ml and incubated for 12 h at 37℃ and 5% CO2 with Kynurenine  (40μg/ml).

value: spleen

value: Balb/C

value: 6 weeks


title: DMSO_MCE_RNAinput

value: preadipocytes at the mitotic clonal expansion stage


title: lps_pc#2


title: mRNA_Negtive Control-2

description: Sample 14


title: EBL2_LS-Patient_19


title: mRNA_Kynurenine stimulated -3

description: Sample 3

value: treat with the Kynurenine


title: mRNA_Kynurenine stimulated -4

description: Sample 4


title: H_G62_FAP-Patient_17

description: colon mucosa from patient with Familial Adenomatous Polyposis  (FAP)

value: WT


title: lps_pc#1


title: mRNA_Kynurenine stimulated -2

description: Sample 2


title: H_G60_FAP-Patient_16


title: mRNA_Kynurenine stimulated -1

description: Sample 1


title: lps_pc#5


title: pbs_pc#6

value: PBS


title: mRNA_Negtive Control-3

description: Sample 15


title: mRNA_Negtive Control-1

description: Sample 13


title: H_G49_FAP-Patient_15


title: H_G26_FAP-Patient_12


title: PD-replicate1

city: Guangzhou

first: Zhen

last: Xiong

address: No.7 Jinsui Road

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
Sequenced raw reads were mapped to mouse mm10 reference genome using STAR (v2.4.2a).
RSEM (V1.2.29) was used to generate FPKM values for known gene models
Genome_build: mm10
Supplementary_files_format_and_content: Excel file contains a matrix table with FPKM values for every gene and every sample

source_name: RPE-choroids

extract_protocol:
RPE-Choroid complex was quickly dissected and put into the reagent(QIAGEN, cat: 74104) for RNA isolation.mRNA was extracted from total RNA using magnetic beads with oligo-dT then were fragmented randomly.
RNA libraries were prepared for sequencing according to Illumina's standard protocols.Briefly,The first strand of cDNA and the second strand are synthesized using reverse transcriptase. The reverse transcription product is subjected to terminal repair, followed by addition of an A base at the 3' end. Subsequently, the fragments were ligated with a Illumina universal adapter. After PCR amplified, the ligation products were purified in order to remove the incompletely ligated fragment and the self-ligated adapter. Library sizes were detected using an Agilent 2100 Bioanalyzer and library concentrations were detected using Qubit 2.0.

treatment_protocol: Subretinal AAV injection after 4 weeks

value: RPE-choroids

tag: genotype/variation

value: AAV-PDGF-D


title: GFP-replicate1

value: AAV-GFP


title: GFP-replicate3


title: PD-replicate2


title: GFP-replicate2


title: H_G40_FAP-Patient_14

value: NORMAL

value: COLON


title: PD-replicate3


title: pbs_pc#3


title: pbs_pc#5


title: pbs_pc#4


title: H_G31_FAP-Patient_13

value: UM


title: Disn-/-_(-/- x -/-)_rep3

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

description:
from crosses between homozygote parents
KO3(-/- x -/-)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat v2.1.1 with parameters -p 8 -r 50
Fragments Per Kilobase of exon model per Million mapped fragments were calculated using Cufflinks software (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: mouse brain

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

value: brain

tag: genotype

value: untreated


title: Disn-/-_(-/- x -/-)_rep2

description:
from crosses between homozygote parents
KO2(-/- x -/-)


title: pbs_pc#2

value: PC