title: Liver, TM, TREAT rep6

city: hangzhou

first: Shujie

last: Xu

address: yuhang rd 866

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 PelSin 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 pelodiscus sinensis 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: GCF_000230535.1
Supplementary_files_format_and_content: tab-delimited text file includes FPKM and count values for each Sample

organism: Pelodiscus sinensis

source_name: Liver

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

tag: treatment

value: diet supplemented with Bacillus subtilis B10

tag: Sex

value: Liver


title: C42B_ENZR_shControl

status: Public on Sep 01 2022

type: SRA

city: Spokane

first: Boyang

last: Wu

state: Washington

address: 412 E. Spokane Falls Blvd

country: USA

institute: Washington State University

library_source: transcriptomic

data_processing:
RNA-Seq was performed on an Illumina HiSeq 3000 for a single read 50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
Bowtie2 version 2.1.0 was used for mapping to the human genome hg19 transcript set.
RSEM v1.2.15 was used to calculate the count and estimate the gene expression level.
Trimmed Mean of M-values (TMM) method in the edgeR package was used for gene  expression normalization.
Assembly: hg19

molecule: total RNA

organism: Homo sapiens

source_name: Prostate

growth_protocol: C4-2B ENZR cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin and 20 µM ENZ.

extract_protocol:
The total RNA was extracted by RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stable knockdown of NRP2 in C4-2B ENZR cells were achieved by infection of lentivirus expressing a shRNA targeting the NRP2 coding region, with a non-targeting shRNA as control, followed by antibiotic selection.

tag: tissue

value: Prostate

tag: cell line

value: C4-2B ENZR

tag: cell type

value: Human prostate cancer cell line

tag: genotype

value: WT


title: C42B_ENZR_shNRP2

value: NRP2 knockdown


title: circRNA-Seq C666

city: Fuzhou

first: xiandong

last: lin

state: fujian

address: No. 420 Fuma Road, Jinan District

country: China

institute: Fujian Cancer Hospital and Fujian Medical University Cancer Hospital

description:
C666
Cell Line 1

data_processing:
Alignment to reference genome is performed using Hisat2
Transcript assembly is performed using StringTie
Cuffcompare is used to select for known circRNA, miRNA, and Mrna
circRNA identification is performed using find_circ and CIRI2
Genome_build: Homo sapiens Ensemble 97
Supplementary_files_format_and_content: contains read count for all of the samples combined

source_name: epstein-barr associated nasopharyngeal carcinoma cell line

growth_protocol: C666,NP69, CNE_2 and SUNE_1 were cultured in RPMI-1640 containing 10% (v/v) heat-inactivated fetal bovine serum (FBS) and 100 U/ ml of streptomycin/ penicillin mixture (all from Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA) in a humidified 37°C incubator supplied with 5% of CO2

extract_protocol:
Collect conventionally cultured cells in logarithmic growth phase, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human nasopharyngeal carcinoma cell line

tag: metastasized


title: sG957

city: Boston

first: VICTOR

last: BARRERA BURGOS

state: Massachusetts

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

data_processing:
BCL files were demultiplexed and fastq files were obtained using Cell Ranger (v5.0.0) mkfastq function
Filtered count data was generated using Cell Ranger (v5.0.0) count function
QC, Samples cluster structure, integration and differentially expressed genes were obtained using the Suerat package in R along with custom code
Assembly: GRCh38-v.2020-A
Supplementary files format and content: mtx files. sparse matrix format with genes on the rows and cells on the columns as output by Cell Ranger.
Supplementary files format and content: TSV files with features (genes) and barcode sequences corresponding to row and column indices, respectively.

source_name: SC-islet Graft

growth_protocol: Pagliuca et al., 2014

extract_protocol:
For graft extraction, mice were euthanized, and the transplanted kidney was removed. SC-islets graft was peeled off the kidney, was sliced into small pieces and digested in 2mg/mL collagenase D (Sigma, 11088858001) in RPMI (GIBCO, 11875-085) for 45 min in 37 °C. Additional breaking was used by pipetting and by filtering through a 40μm cell strainer. Cells were then centrifuged and resuspended in 0.5% BSA in PBS and a magnetic mouse depletion kit (Miltenyi, 130-104-694) was used to remove residual mouse cells.
All samples were loaded into Chip G per the user guide from 10x Genomics, no alterations were made at any step of the protocol (Part No. CG000315). GEMs were formed targeting 10,000 cells and reverse transcription completed immediately after. The cDNA was cleaned from the GEM reagents, amplified for a total of 11 cycles and verified via TapeStation (Agilent Technologies). Amplified cDNA was diluted and ran on the 4200 TapeStation instrument using High Sensitivity D5000 tape and reagents (Part No. 5067-5592 & 5067-5593). The amplified cDNA was fragmented, end repaired, and A-tailed followed by adaptor ligation, and PCR amplification for a total of 12 cycles with each sample receiving a unique set of dual indices (Part No. 1000215). Final libraries were diluted and ran using the High Sensitivity D5000 tape and reagents (Part No. 5067-5592 & 5067-5593) on the 4200 TapeStation (Agilent Technologies). Libraries were quantified via Kapa qPCR using the Complete Universal Kit (Part No. 07960140001, Roche Sequencing Solutions) and the CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories). Libraries were sequenced on an Illumina NovaSeq instrument using the parameters outlined in the user guide (Read1: 28 bp, i7 index: 10 bp, i5 index: 10 bp, Read2: 90 bp).
10X Chromium Single Cell 3’ Library preparation and sequencing

treatment_protocol: Sintov et al, 2022

tag: cell source

value: hESC S6

tag: immune infiltration

value: Yes

value: hPi grafts


title: Liver, CF, WT rep6

state: zhejiang

institute: Zhejiang University

value: fed with normal diet

value: female


title: DU-145 DMSO

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

data_processing:
The bcl2fastq tool was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing. Data analyses on fastq files were conducted with CLC Genomics Workbench (version 20.0.4, QIAGEN, Venlo. NL). The reads of all probes were adapter (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides max. 2).
Genome_build: Mapping was done against the Homo sapiens (hg38) (May 25, 2017) genome sequence.
Supplementary_files_format_and_content: Statistical differential expression tests were determined using the ‘Differential Expression in Two Groups’ tool (version 1.02). The resulting p-values were corrected for multiple testing by false discovery rate- (FDR) and Bonferroni-correction. A p-value of ≤0.05 was considered significant.

source_name: prostate cancer

growth_protocol: 2102EP cells were cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin); VM-CUB-1, Caki-1 and DU-145 were cultivated in RMPI medium  (10% FCS, 1% Penicillin / Streptomycin)

extract_protocol:
RNA was isolated (including DNase I digestion) using the RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manual
RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific, Meerbusch, Germany) and quality was measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA Standard Sensitivity Assay’ (Agilent Technologies Inc., Santa Clara, USA). The library preparation was performed according to the manufacturer’s protocol (‘VAHTS Stranded mRNA-Seq Library Prep Kit’). 300 ng total RNA were used for mRNA capturing, fragmentation, synthesis of cDNA, adapter ligation, and library amplification. Bead purified libraries were normalized.
RNA sequencing performed on the HiSeq 3000/4000 system (Illumina Inc., San Diego, USA) with a read setup of 1x150 basepairs (bp).

treatment_protocol: cells were treated with corresponding EC50 values of LAK31 for 16 h

value: solvent control


title: DU-145 LAK31

value: LAK31 treatment


title: Caki-1 LAK31

source_name: renal cell carcinoma


title: miRNA-Seq s307

description:
s307
Patient Sample 3

source_name: non-metastatic nasopharyngeal cariconoma patient sample

value: fresh human nasopharyngeal carcinoma tumor

value: FALSE


title: s164


title: Liver, TM, TREAT rep5

value: diet supplemented with Bacillus subtilis B10

value: male


title: Caki-1 DMSO


title: miRNA-Seq s324

description:
s324
Patient Sample 4


title: Liver, TM, TREAT rep4

value: Liver


title: Liver, TF, TREAT rep3


title: MoMac_GFP low 1

city: New York

first: Miriam

last: Merad

state: NY

address: 1470 Madison Ave, 5th Floor

department: Department of Oncological Sciences

institute: cahn School of Medicine at Mount Sinai

data_processing:
Raw bulk RNA sequencing data was processed and aligned to genome reference mm10  using  R  package  ‘Rsubread’  with  default  parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: R data file of bulk counts

organism: Mus musculus

source_name: Lung tumor associated macrophage

growth_protocol: Wyld type (c57bl/6) mice were grown in our facilities. All animals used for experiments were age and sex matched between experimental groups. All animal procedures were approved by the Institutional Animal Care and Use Committees (IACUCs) of our institution.

extract_protocol:
Lungs were perfused and processed into a since cell suspension which was immunostained with a cocktail of fluorescent antibodies. Monocyte derived macrophages were FACS sorted directly into Trizol.
RNA was extracted using the Rneasy Micro Kits (Qiagen) according to manufacturer’s instructions. RNA was quantified and quality controlled using Qbit and a Bioanalyzer. 0.5–1 ng of RNA was retrotranscribed and processed to cDNA libraries using the Smart-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio).
All samples were pooled together and loaded onto one lane. Libraries were sequenced on an Illumina NextSeq 550 system.

treatment_protocol: Wyld type mice were injected intravenously with 5*10^5 KP-GFP tumor cells and humanely sacrificed 28 days after tumor delivery

value: Monocyte derived Macrophage

tag: type of tumor

value: KP-GFP day 28

value: Lung

tag: gfp signal

value: Low


title: s162


title: s163


title: miRNA-Seq s1029

description:
s1029
Patient Sample 1

source_name: metastatic nasopharyngeal carcinoma patient sample

value: TRUE


title: Liver, TF, TREAT rep2


title: VM-CUB-1 DMSO

source_name: urothelial cacrinoma


title: s84

value: hESC S6


title: miRNA-Seq SUNE

description:
SUNE
Cell Line 4

source_name: nasopharyngeal carcinoma cell line

value: human nasopharyngeal carcinoma cell line


title: Liver, TF, TREAT rep1


title: 2102EP LAK31

source_name: non-seminoma germ cell tumor, embryonal carcinoma


title: Human PMP

city: Montréal

first: Tarik

last: Moroy

address: 110 Pine Ave W, Montreal

country: Canada

institute: IRCM

description: Platelet activation and MP release was induced by incubation with thrombin (0.1 U/ml; Sigma Aldrich, St. Louis, MO, USA) for 60 min at 37 °C under gentle agitation. Platelet activation was stopped by addition of ethylenediaminetetraacetic acid (EDTA; 20 mM final), and platelets were discarded by centrifugation at 3,200 g for 10 min. The supernatant was filtered through 0.8 μm pore filters (Corning, Troy, MI, USA) in order to avoid platelet contamination, and platelet MPs were harvested by centrifugation at 20,000 g for 90 min at 18 °C, and resuspended in Hepes-Tyrode buffer prior to total RNA extraction.

data_processing:
Adaptor were trimmed using Cutadapt V1.7.1
Quality Control was performed with fastqc V0.11.3
Identical sequences were collapsed into a single fasta sequence and were filtered to keep only those detected at least twice using a custom script
Genome_build: NA
Supplementary_files_format_and_content: Fasta files containing the aligned sequences that were detected at least twice in the dataset, separated in 2 groups based on the size (8-15nt and 16-30nt)

source_name: Human platelet microparticles (PMP) isolated from thrombin-activated human platelets isolated from venous blood collected from healthy adult volunteers

extract_protocol:
Total RNA samples were prepared using TRIzol® reagent or TRIzol LS® reagent for liquid samples (Invitrogen Life Technologies, Carlsbad, CA, USA) following the manufacturer’s recommendations. Contaminating DNA was degraded by DNase I (M0303S, New England Biolabs, MA, USA) treatment following manufacturer’s instructions. Total RNA was shipped on dry ice and analyzed by Arraystar Inc. RNA sequencing service (Rockville, MD).
The purity, quality, and concentration of total RNA samples were determined with NanoDrop ND-1000 (Thermo Fisher Scientific) and 2100 Bioanalyzer (Agilent, Santa Clara, CA). Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: (1) 3′-adapter ligation, (2) 5′-adapter ligation, (3) cDNA synthesis, (4) PCR amplification, and (5) size selection of approximately 120 to 150 bp of PCR-amplified fragments (corresponding to approximately 8 to 30 nt of small RNA). The complete libraries were quantified by Agilent 2100 Bioanalyser. Samples were diluted to a final concentration of 8 pM, denatured as single-stranded DNA, and cluster generation was performed on the Illumina cBot using TruSeq Rapid SR cluster kit (GD-402-4001, Illumina, San Diego, USA). Afterward, the clusters were sequenced for 51 cycles on Illumina HiSeq 2000 using TruSeq Rapid SBS Kits (FC-402-4002, Illumina, San Diego, USA), as per the manufacturer's instructions.

tag: sample type

value: platelet


title: VM-CUB-1 LAK31


title: Human PLT

description: Human platelets (PLT) were isolated from venous blood collected from four healthy donors and pooled, as described in Laffont et al. (2016) (https://pubmed.ncbi.nlm.nih.gov/26333874/). Platelets were isolated from venous blood harvested by centrifugation at 1,000 g for 10 minutes (min) and resuspended at 10e8 platelets/ml in Hepes-Tyrode buffer (130 mM NaCl, 3 mM KCl, 0.3 mM Na2HPO4, 12 mM NaHCO3, 20 mM HEPES, 5 mM monohydrate D-glucose, 0.5 mM MgCl2, pH 7.4), as previously described in Landry et al. (2009) (https://pubmed.ncbi.nlm.nih.gov/19668211/) prior to total RNA extraction.

source_name: Human platelets (PLT) isolated from venous blood collected from healthy adult volunteers


title: 2102EP DMSO control


title: sG953

value: Yes

value: hPi grafts


title: miRNA-Seq CNE

description:
CNE
Cell Line 2


title: miRNA-Seq s1017

description:
s1017
Patient Sample 2


title: HC_2

city: Tianjin

first: Zhao

last: Wang

address: No. 24, Fukang Road, Nankai District

department: Department of Hematology

institute: Tianjin First Central Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: peripheral blood

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumin was used with 3ug of total RNA for the construction of sequencing libraries.
following standard manufacturer’s recommendations and index codes were added to attribute sequences to each sample

tag: disease status

value: healthy controls


title: HC_3


title: RNA-Seq s324

description:
s324
Patient Sample 4


title: Liver, CF, WT rep2

value: fed with normal diet

value: female


title: Liver, CF, WT rep1


title: Control 3

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

source_name: SW480 cells

growth_protocol: The human SW480 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of SW480 cells with different treatment was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The SW480 colorectal cells were treated with TGF-β1 at a concentration of 10 ng/ml for more than 4 times, while the non-treatment cells were used as negative controls.

value: Control

value: SW480 cells

value: human colorectal cancer cells

tag: passage


title: TGFB treatment 2

value: TGFB treatment


title: TGFB treatment 3


title: TGFB treatment 1


title: miRNA-Seq C666

description:
C666
Cell Line 1


title: WT_SM_N03_FKDL210115697-1a_L1_p1

city: Bremen

first: Xun

last: Jiang

state: Bremen

address: Leobener Straße 5

department: Department of Microbe-Plant Interactions

institute: University of Bremen

data_processing:
READemption pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to AM406670.1 Azoarcus olearius strain BH72 genome by READemption
Read count extraction and normalization were performed using READemption
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Azoarcus olearius

source_name: bacterial cells

growth_protocol: cells were grown under microaerobic conditions (controlled at 0.3% dissolved O2) in 1.6 L SM medium with 0.5 g/L ammonium in a bioreactor (Minifors, Infors HT, Einsbach, Germany) at 37°C with constant stirring at 450 rpm in the presence of N2, and the pH was controlled to 6.8~7.0 by phosphoric acid addition. The cultures were harvested at an optical density (OD578) between 0.4~0.5.

extract_protocol:
The RNA was extracted from cells grown to OD578  0.4-0.5 by the hot phenol method described by Solaiyappan Mani, 2021.
The rRNA was depleted by the NEBNext rRNA Depletion Kit (Bacteria) (NEB GmbH Brüningstraße 50, Frankfurt am Main, Germany, Product NO. E7850). The cDNA library of the enriched mRNA was prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB GmbH Brüningstraße 50, Frankfurt am Main, Germany, Product NO. E7760). All the steps were performed as described by the NEB protocols. The synthesized cDNA library was frozen directly in liquid nitrogen and then kept in -80oC freezer for long time storage.

value: BH72 WT

tag: strain

value: bacterial cells

value: microaerobic conditions with additional ammonium

tag: time

value: overnight


title: HC_1


title: Liver, CM, WT rep5

source_name: Liver

value: male

value: Liver


title: RNA-Seq s1017

description:
s1017
Patient Sample 2

value: fresh human nasopharyngeal carcinoma tumor

value: TRUE


title: NO GVHD_3

value: without GVHD development


title: NO GVHD_2


title: WT_SM_N02_FKDL210115696-1a_L1_p1


title: RNA-Seq s1029

description:
s1029
Patient Sample 1


title: Control 2


title: NO GVHD_1


title: WT_SM_N01_FKDL210115695-1a_L1_p1


title: miRNA-Seq NP69

description:
NP69
Cell Line 3

source_name: non-cancerous immortalized nasopharyngeal epithelial cell line

value: immortalized human nasopharyngeal epithelial cell line


title: Liver, CM, WT rep3


title: Control 1


title: Liver, CM, WT rep4


title: RNA-Seq SUNE

description:
SUNE
Cell Line 4

value: human nasopharyngeal carcinoma cell line


title: IEL Tetramer pos scRNA

city: Cambridge

first: Damian

last: Plichta

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
Single-cell RNA sequencing data was processed with Cell Ranger (v3.1.0) as implemented in cellranger_workflow in the Terra platform (https://app.terra.bio/)
Single-cell TCR sequencing data was assembled and the clonotypes were determined using the default settings of Cell Ranger (v3.1.0) VDJ pipeline as implemented in cellranger_workflow in the Terra platform (https://app.terra.bio/)
Genome_build: mm10
Supplementary_files_format_and_content: h5 files with scRNA readout
Supplementary_files_format_and_content: csv tables with TCR contig information

source_name: IELs

growth_protocol: CD4 T cells were isolated and stained from the intraepithelial lymphocytes (IELs) and mLN of mice

extract_protocol:
Stained cells were run on a cell sorter (Sony SH700) and both tetramer positive and tetramer negative CD4+ T-cells were sorted into a tube containing FACS buffer (PBS + 2% FBS), counted and sent for sequencing
Sorted single cells were separated into droplet emulsions using the Chromium Next GEM Single Cell 5′ Solution (v1)
scRNA and TCR seq

treatment_protocol: Epithelial cells were isolated using a PBS buffer containing 2 mM EDTA, 1 mM dithiothreitol and 2% fetal bovine serum (FBS), shaking at 37°C for 30 min.

value: IELs

tag: sorted cells

value: tetramer pos


title: GVDH_4

value: with GVHD development


title: Delta3116_SM_N03_FKDL210115700-1a_L1_p1

tag: treatment


title: GVDH_3


title: RNA-Seq s307

description:
s307
Patient Sample 3

value: FALSE


title: Delta3116_SM_N02_FKDL210115699-1a_L1_p1


title: IEL Tetramer neg1 scRNA

value: tetramer neg


title: GVHD_2


title: Delta3116_SM_N01_FKDL210115698-1a_L1_p1


title: IEL Tetramer neg2 scRNA


title: RNA-Seq C666

description:
C666
Cell Line 1

source_name: epstein-barr associated nasopharyngeal carcinoma cell line


title: IEL Tetramer neg3 scRNA


title: RNA-Seq CNE

description:
CNE
Cell Line 2


title: Control [FOD9157]

city: Ann Arbor

first: Ziru

last: Li

state: MI

address: 2800 Plymouth Rd.

department: Molecular & Integrative Department

institute: University of Michigan

data_processing:
The quality of the raw reads data was checked using FastQC (v.0.11.9).
The filtered reads were aligned to reference genome (UCSC mm10) using STAR with default parameters.
All samples passed the post-alignment quality check (QualiMap (v.2.2.1).
The DEseq2 method was used for differential expression analysis.
Assembly: UCSC mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Control

growth_protocol: Mice were housed in a 12 h light/dark cycle in the Unit for Laboratory Animal Medicine at the University of Michigan, with free access to water and food.

extract_protocol:
Distal tibiae were collected by cutting through tibia/fibula junction. Whole distal tibial bones were snap-frozen, hammered into powder,  and homoginized with RNAStat60 reagent. DNA-free™ Kit was used to remove DNA before submitting for QC and RNAseq.
RNA libraries were prepared for sequencing using P_Stranded Library&Seq(PE100).

treatment_protocol: No specific treatment was applied.

value: Distal tibial bone; whole bone

tag: age

value: 24 weeks old

value: BMAd-WT

value: Ad libitum


title: mLN Tetramer pos scRNA

source_name: mLN T cells

value: mLN T cells


title: RC-K8_KO3

city: Heidelberg

first: F. Nina

last: Papavasiliou

address: Im Neuenheimer Feld 280

department: Tumor Immunology Unit

institute: German Cancer Research Center (DKFZ)

data_processing:
Total 125bp paired-end RNA-seq data from A549 and RCK8 (ADAR1 KO and WT) underwent adapter clipping (Illumina universal) from the raw reads using the tool ‘Trim Galore!’(v0.5.0). The trimmed reads were mapped to the human reference genome hg19 with STAR aligner (v2.5.3a) using the default parameters. Picard (MarkDuplicates function, v.2.18.26-SNAPSHOT) was used for removing potential PCR duplicates. Aligned data were sorted and indexed with samtools (v.1.9) RefGene from UCSC was employed for annotation to the gene level.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read-counts for each sample

source_name: B-cell lymphoma cell line (RC-K8)

growth_protocol:
RC-K8 were cultured at 37°C, 5% CO2, in RPMI with L-glutamine and sodium bicarbonate, supplemented with 15% fetal bovine serum and Penicillin/Streptomycin.
A549 cells  were cultured at 37°C, 5% CO2, in high glucose DMEM, supplemented with 10% FBS  and Penicillin/Streptomycin

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) and then treated with turbo DNase (Life technologies). RNA concentration and integrity was determined by a Qubit 4 (Thermo Fischer scientific) using the Qubit RNA BR assay kit or Qubit XR assay kit and the
A549: RNA concentration and integrity was determined by a Qubit 4 (Thermo Fischer scientific) using the Qubit RNA BR assay kit or Qubit XR assay kit and the Qubit RNA IQ kit (Thermo Fischer scientific). 1μg of RNA was processed with Kapa mRNA hyperprep Kit for illumine platforms (Kapa Biosystems, Roche) and KAPA Single-Indexed Adapter Kit for Illumina® Platforms (Kapa Biosystems, Roche). RC-K8: QC of the RNA samples was performed using a tape station. TruSeq Stranded mRNA Library Prep Kit (illumina) was used.

treatment_protocol: KO of ADAR1 was performed by CRISPR/Cas9 technology as described in the paper.

tag: tissue

value: B-cell lymphoma


title: mLN Tetramer neg1 scRNA


title: RC-K8_KO2

tag: cell line


title: mLN Tetramer neg2 scRNA

tag: cell type


title: Section (A->P)  53

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

description: GEO-seq

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
Reads were aligned to  hg38 ensembl v101 transcriptome using rsem (v1.3.1) and bowtie2 (v2.4.1) (—bowtie2—bowtie2-sensitivity-level very_sensitive— no-bam-output—estimate-rspd).
The gene expression level was calculated by using  RSEM
Genome_build: hg38

molecule: polyA RNA

source_name: UiPSM

growth_protocol: Uisomitoid elongated in an Advanced DMEM/F12 supplemented with 3uM CHIR99021 and 5uM SB431542

extract_protocol:
he mRNA content of each interval section was extracted using Geo-seq.(Jun Chen, 2017)(Peng Guangdun's group provided experimental platform )
spatial bulk RNA-seq libraries were prepared by Geo-seq(Jun Chen, 2017)(Peng Guangdun's group provided experimental platform )

treatment_protocol: UiSomitoid were forzened with liquid nitrogen after OCT embedded, and then forzen sectioned 110 slices along their anteroposterior axis

value: UiPSM


title: RNA-Seq NP69

description:
NP69
Cell Line 3


title: BMAd-DTA [FOD9135]

source_name: BMAd-DTA

tag: genotype

value: BMAd-DTA


title: Section (A->P)  52

description: GEO-seq


title: Section (A->P)  54

description: GEO-seq


title: Section (A->P)  51

description: GEO-seq


title: RC-K8_KO1


title: RC-K8_WT3

value: wild type


title: BMAd-DTA [FOD9097]


title: mLN Tetramer neg3 scRNA


title: BMAd-DTA [FOD9088]


title: RC-K8_WT2


title: Section (A->P)  50

description: GEO-seq


title: GVHD_1


title: BMAd-DTA [FOD9155]


title: Section (A->P)  49

description: GEO-seq


title: peritoneal macrophage LPS-LV-Gm26917_rep3

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

data_processing:
Raw reads were firstly processed to obtain clean reads.
Clean reads were mapped to mosue genome (mm10 version) by STAR.
FeatureCounts v1.6.3 was used to count the reads numbers mapped to each gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes read counts for Sample

source_name: peritoneal macrophage

extract_protocol:
Total RNA was obtained from cells and tissues by standard TRIzol reagent (Invitrogen, 15596-018). cDNA was synthesized from 1000 ng total RNA in a 20 μl reaction using cDNA synthesis kit (11706, Accurate Biology) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peritoneal macrophage

value: lentivirus-shRNA-Gm26917 for 72h and then LPS for 2h


title: Control [FOD9062]


title: Section (A->P)  48

description: GEO-seq


title: BMAd-DTA [FOD9058]


title: Section (A->P)  47

description: GEO-seq


title: BMAd-DTA [FOD9140]


title: peritoneal macrophage LPS-LV-Gm26917_rep2


title: peritoneal macrophage LPS-LV-NC_rep3

value: lentivirus-shRNA-NC for 72h and then LPS for 2h


title: A549_KO3

source_name: Lung carcinoma cell line (A549)

value: Lung carcinoma


title: peritoneal macrophage LPS-LV-NC_rep2


title: Section (A->P)  46

description: GEO-seq


title: peritoneal macrophage LPS-LV-Gm26917_rep1


title: A549_KO1


title: Control [FOD9041]


title: peritoneal macrophage LPS-LV-NC_rep1


title: A549_WT3


title: A549_WT2


title: liver LPS_rep3

source_name: liver

value: liver

value: LPS for 2h


title: Control [FOD9039]


title: BMAd-DTA [FOD9038]


title: Section (A->P)  44

description: GEO-seq


title: RC-K8_WT1


title: Section (A->P)  43

description: GEO-seq


title: liver LPS_rep2


title: Section (A->P)  42

description: GEO-seq


title: A549_WT1


title: A549_KO2


title: N2embB_SDC3

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

library_source: genomic

data_processing: After barcode removal or demultiplexing, 32 bp reads were aligned uniquely to the worm WS190 genome using the default settings in bowtie version 0.12.7. MACS version 1.4 was used to call peaks and create pileups using the SDC-3 ChIP as the treatment and random IgG as the control. When using MACS, all duplicate reads were kept. Because the DCC binds with great strength to relatively few sites genome-wide, duplicate reads are not due simply to PCR duplications. To account for read depth, ChIP signal was normalized to the total number of reads that uniquely aligned to the genome. To correct for non-specific binding, random IgG control signal was subtracted from treatment signal at each base pair.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: mixed stage embryos

extract_protocol: N2 worms were grown at 20°C on HB101 and mixed stage embryos were isolated from gravid adults by bleaching. Mixed-stage embryos were harvested from gravid N2 hermaphrodites and cross-linked with 2% formaldehyde for 30 min and quenched with 100 mM Tris-HCl (pH 7.5). Cross-linked embryos were resuspended in 3 ml of FA Buffer (150 mM NaCl, 50 mM HEPES-KOH (pH 7.6), 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM DTT, protease inhibitor cocktail) for every 1 gram of embryos. This mixture was frozen on liquid nitrogen, then ground under liquid nitrogen by mortar and pestle. Chromatin was sheared by the Covaris S2 (20% duty factor, power level 8, 200 cycles per burst) for a total of 30 min processing time (60 sec ON, 45 sec OFF, 30 cycles). To perform the ChIP reactions, extract containing approximately 2 mg of protein was incubated in a microfuge tube with 6.6 μg of anti-SDC-3 or random IgG antibodies (lab sticks) overnight at 4°C. A 25 μl bed volume of protein A sepharose beads was added to the ChIP for 2 hr. ChIPs were washed for 5 min at room temperature twice with FA Buffer (150 mM NaCl), once with FA Buffer (1 M NaCl), once with FA Buffer (500 mM NaCl), once with TEL buffer (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and twice with TE Buffer. Protein and DNA were eluted twice with 1% SDS, 250 mM NaCl, 1mM EDTA at 65°C for 15 min. After elution, sequencing libraries were prepared as published (Zhong et al., 2010) with minor changes: sequencing adapters were as described (Lefrancois et al., 2009) or were obtained from Bioo (NEXTflex) and adapters were ligated using NEB Quick Ligation Kit (M2200). Libraries were sequenced on the Illumina GA2 and HiSeq 2000 platforms.

value: mixed stage embryos

value: embryo


title: liver WT_rep3

value: untreated


title: Section (A->P)  41

description: GEO-seq


title: N2embB_RbIgG

data_processing:
After barcode removal or demultiplexing, 32 bp reads were aligned uniquely to the worm WS190 genome using the default settings in bowtie version 0.12.7. MACS version 1.4 was used to call peaks and create pileups using the SDC-3 ChIP as the treatment and random IgG as the control. When using MACS, all duplicate reads were kept. Because the DCC binds with great strength to relatively few sites genome-wide, duplicate reads are not due simply to PCR duplications. To account for read depth, ChIP signal was normalized to the total number of reads that uniquely aligned to the genome. To correct for non-specific binding, random IgG control signal was subtracted from treatment signal at each base pair.
genome build/assembly: e6
bed


title: Section (A->P)  45

description: GEO-seq


title: Section (A->P)  40

description: GEO-seq


title: liver WT_rep2


title: liver WT_rep1


title: Section (A->P)  39

description: GEO-seq


title: Section (A->P)  38

description: GEO-seq


title: Section (A->P)  37

description: GEO-seq


title: Section (A->P)  36

description: GEO-seq


title: R6 over R3

type: RNA

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

description:
Altered gene expression of S. suis upon exposure to sub-lethal concentrations of the human cathelicidin LL-37 at two different timepoints was determined.
S. suis grown for (R6) 30 min, in presence of 0.25 uM LL-37 vs S. suis grown for (R3) 10 min, in presence of 0.25 uM LL-37
cDNA

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5.

scan_protocol: Scanned on a ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA). Images were quantified using ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA).

data_processing:
Scanned slides were Lowess normalized using Prep (van Hijum et al., 2003); interslide scaling was performed using PostPrep (van Hijum et al., 2003).
Probe_level_data.txt: Tab-delimited text file includes the Prep/PostPrep output based on the actual array probe intensity data; background subtracted, Lowess normalized, Cy5/Cy3 ratios (no log transformation); raw (probe-level) data. The raw numbers from this analysis were multiplied by 10000, yielding the numbers that are in this file.
Array_Results.xlsx: Excel file includes all possible biological comparisons and their statistics; the normalized log2 Cy5/Cy3 ratios represent expression fold-changes of the annotated genes and ORFs of Streptococcus suis P1/7.
van Hijum SA, García de la Nava J, Trelles O, Kok J, Kuipers OP (2003). MicroPreP: a cDNA microarray data pre-processing framework. Appl Bioinformatics. 2003;2(4):241-4.

organism: Streptococcus suis

label_protocol: cDNA was synthesized with a SuperScript III Reverse Transcriptase Kit (Invitrogen) using Aminoallyl-UTP and purified with the Illustra CyScribe GFX Purification Kit (GE Healthcare). The aminoallyl-cDNA was labelled using the CyDye Post-Labelling Reactive Dye Pack (GE Healthcare).

growth_protocol: S. suis was grown in Todd-Hewitt broth (THB) (Difco) at 37°C under 5% CO2 for 18 hrs.

extract_protocol: Bacteria were incubated at 37°C for 5 or 25 min and collected by centrifugation for 5 min at 8000 x g at 30°C. Supernatant was carefully discarded and the pellets were resuspended in 2.5 mL PBS plus 5 mL RNAprotect Bacteria Reagent (Promega) by vortexing and incubated for 5 min at RT. The bacteria were collected by centrifugation and the pellet immediately frozen in liquid nitrogen and stored at -80°C until further handling. The frozen pellet was redissolved in 110 µL of TE containing protease K (1.25 µg mL-1) and lysozyme (15 µg mL-1) by thorough vortexing and incubated at RT for 10 min. Then, 700 µL RLT buffer (Promega) containing 7 µL of freshly added β-mercaptoethanol was added and the whole volume was transferred to FastPrep matrix B tubes and run for 40 sec at 6.0 m sec-1 on a FastPrep-24 (MP Biomedicals, Solon, OH) for mechanical disruption of the bacteria. Total RNA was purified from the obtained bacterial lysate using the RNeasy Mini Kit (Qiagen) following manufacturer's instructions. The quality, concentration and integrity of RNA were assessed using the Experion System (Bio-Rad) and by spectrometric analysis of the A260/A280 ratio (NanoDrop 8000 UV-Vis).

treatment_protocol: The overnight S. suis culture was diluted 1:40 in pre-warmed THB and grown for approximately 3 h until an OD600 nm of 0.25 was reached. Cells were collected by centrifugation and 2.5 mL of this cell suspension was added to 47.5 mL of pre-warmed sterile PBS, immediately followed by addition of LL-37 to a final concentration of 0.1 µM or 0.25 µM, or the addition of a similar volume of PBS as a control. Bacteria were exposed to these three conditions for 10 or 30 min prior to RNA extraction.

tag: strain/background

tag: timepoint

value: 30 min

value: 10 min


title: R2 over R5

description:
Altered gene expression of S. suis upon exposure to sub-lethal concentrations of the human cathelicidin LL-37 at two different timepoints was determined.
S. suis grown for (R2) 10 min, in presence of 0.1 uM LL-37 vs S. suis grown for (R5) 30 min, in presence of 0.1 uM LL-37
cDNA


title: R5 over R6

description:
Altered gene expression of S. suis upon exposure to sub-lethal concentrations of the human cathelicidin LL-37 at two different timepoints was determined.
S. suis grown for (R5) 30 min, in presence of 0.1 uM LL-37 vs S. suis grown for (R6) 30 min, in presence of 0.25 uM LL-37
cDNA


title: R1 over R2

description:
Altered gene expression of S. suis upon exposure to sub-lethal concentrations of the human cathelicidin LL-37 at two different timepoints was determined.
S. suis grown for (R1) 10 min, without addition of LL-37 (control) vs S. suis grown for (R2) 10 min, in presence of 0.1 uM LL-37
cDNA

source_name: (R1) 10 min, control

value: no peptide


title: R6 over R4

description:
Altered gene expression of S. suis upon exposure to sub-lethal concentrations of the human cathelicidin LL-37 at two different timepoints was determined.
S. suis grown for (R6) 30 min, in presence of 0.25 uM LL-37 vs S. suis grown for (R4) 30 min, without addition of LL-37 (control)
cDNA

source_name: (R4) 30 min, control


title: R4 over R5

description:
Altered gene expression of S. suis upon exposure to sub-lethal concentrations of the human cathelicidin LL-37 at two different timepoints was determined.
S. suis grown for (R4) 30 min, without addition of LL-37 (control) vs S. suis grown for (R5) 30 min, in presence of 0.1 uM LL-37
cDNA


title: liver LPS_rep1


title: Section (A->P)  35

description: GEO-seq


title: IgG_NOD_IMQ-9

type: protein

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description:
raw data file:
IgG_Slide2_532.gpr

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing:
8 positive controls (HIgControl1,HIgcontrol2,HIgcontrol3,H&MIgControl1,H&MIgControl2,H&MIgcontrol3,MIgControl1,MIgControl2 ) were also imprinted on the arrays as positive controls.
NFI were normalized by robust linear model using build-in Ig control with various dilutions

label: cy3-labeled anti-mouse IgG

molecule: protein

source_name: Serum

label_protocol: Not provided

extract_protocol:
Serum samples from recipients collected as per routine protocol as defined above were procured from histocompatibility lab after IRB approval. Sera of all subjects were aliquoted and stored at -80ºC.
Mouse serum samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-mouse IgG and cy5-labeled anti-mouse IgM, and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3 and 635nm for cy5 to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.

tag: slide

tag: array (block)

value: Serum

value: imiquimod (Imq)


title: IgG_PBS_2

description:
raw data file:
IgG_Slide2_532.gpr
Negative control

organism: synthetic construct

source_name: Negative control


title: R2 over R3

description:
Altered gene expression of S. suis upon exposure to sub-lethal concentrations of the human cathelicidin LL-37 at two different timepoints was determined.
S. suis grown for (R2) 10 min, in presence of 0.1 uM LL-37 vs S. suis grown for (R3) 10 min, in presence of 0.25 uM LL-37
cDNA


title: R3 over R1

description:
Altered gene expression of S. suis upon exposure to sub-lethal concentrations of the human cathelicidin LL-37 at two different timepoints was determined.
S. suis grown for (R3) 10 min, in presence of 0.25 uM LL-37, vs S. suis grown for (R1) 10 min, without addition of LL-37 (control)
cDNA


title: Section (A->P)  34

description: GEO-seq

value: UiPSM


title: IgG_NOD_IMQ-8

description:
raw data file:
IgG_Slide2_532.gpr
Bad sample


title: IgG_NOD_IMQ-7

description:
raw data file:
IgG_Slide2_532.gpr


title: Section (A->P)  31

description: GEO-seq


title: Section (A->P)  33

description: GEO-seq


title: FA_BM_MSC_2

city: Ankara

first: Ayşen

last: Özcan

address: Sihhiye

department: Department of Stem Cell Sciences

country: Turkey

institute: Hacettepe University

description: Global non-coding RNA expression profile of BM-MSCs from Fanconi anemia patient.

hyb_protocol: Samples were hybridized with GeneChip miRNA 2.0 Array (Affymetrix) and scanned by AY-KA LTD.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing:
Affymetrix GeneChip Command Console (AGCC) was used to determine the intensity value for each probe cell and to create “.CEL” file for each sample. These files were also obtained from AY-KA LTD. Quality Control (QC) was performed prior to further analysis. Initially, there were five FA preBMT and seven Donor samples, but one FA preBMT (HUSCS-FA12) and two donor samples (HUSCS-D13, HUSCS-D16) that failed QC were discarded from the study. CEL files for samples that failed QC can be found in supplementary files. Files of samples that passed QC were then RMA normalized by oligo package in R (Bioconductor version 3.13). Expression values of mature miRNAs annotated to Homo Sapiens by manufacturer were selected for further analysis.
miRNA-2_0_v2.pgf
miRNA-2_0.annotations.20101222.csv

label: biotin

source_name: Passage 3 Bone Marrow Mesenchymal Stem/Stromal Cells

label_protocol: Total RNA including small RNAs (100 ng) was used to label RNAs with biotin using Genisphere FlashTag HSR kit (Genisphere, Hatfield, PA) according to the manufacturer's instructions. All experimental services were purchased from AY-KA LTD (Ankara, Turkey).

growth_protocol: Cryopreserved bone marrow (BM)-derived mononuclear cells (BM-MNCs) from Fanconi anemia (FA) patients obtained at Hacettepe University Pediatric Hematology Bone Marrow Transplantation unit were used for isolation of BM derived mesenchymal stem/stromal cells (BM-MSCs). Patients were diagnosed by clinical manifestations and DEB treatment. BM-MSCs from allogeneic healthy donors were used as controls. BM-MSCs were maintained in expansion (DMF10) medium in a 5% CO2 incubator at 37°C. DMF10 medium consisting of 60% Dulbecco’s modified Eagle’s medium-low glucose (DMEM-LG; Gibco) and 40% MCDB-201 medium (Sigma-Aldrich) supplemented with 10% heat-inactivated fetal bovine serum (Gibco), 1% penicillin and streptomycin (Biochrom AG) and 1% L-glutamine (Biochrom AG), was changed after 3 to 4 days. Once BM-MSCs reached confluency of 70–80%, they were washed with phosphate-buffered saline (Applichem) and trypsinized in 0.25% trypsin (Invitrogen) containing 1mM EDTA (Invitrogen) solution. Passaged cells were then washed in DMF10 medium to stop the effect of trypsin enzyme, followed by centrifugation (Eppendorf, Germany) at 453 x g for 5 minutes at room temperature. BM-MSCs were then counted using Trypan Blue stain (Biological Industries) and replated. The study was approved by the Local Ethical Committee (Number 14, 24/08/2009). Informed consent was obtained from all individual participants/their parents included in the study. Characterizations of the BM-MSCs used in this study was published by Cagnan et. al. (doi:10.1007/s12015-017-9794-5).

extract_protocol: Total RNA, including small RNAs, were isolated from passage 3 BM-MSCs using miRNeasy Mini Kit (Qiagen, Germany) and treated with RNase-free DNase Digestion (Qiagen, Germany) according to the manufacturer’s instructions.

tag: pairing group

value: unpaired

tag: gender

value: Female

tag: age at the day of bone marrow transplantation

tag: mutation

value: FA-A

tag: anemia

value: Present

tag: deb test

value: Positive

tag: cytogenetic/peripheral blood dysplasia

tag: extremity anomalies

value: Absent

tag: microcephaly

tag: cardiac anomalies

tag: café au lait /hyperpigmentation

tag: renal anomalies

tag: microphthalmia/ptosis

tag: hypothyroidism

tag: g-csf intervention prior to bone marrow collection

value: Not applicable

tag: adipogenic differentiation assessed according to oro staining

value: positive

tag: osteogenic differentiation assessed according to ars staining


title: Section (A->P)  32

description: GEO-seq

tag: cell type


title: IgG_NOD_Con-6_2

tag: slide

tag: array (block)

tag: tissue

tag: strain

tag: treatment

value: control


title: FA_BM_MSC_3

value: Passage 3 Bone Marrow Mesenchymal Stem/Stromal Cells

tag: pairing group

tag: gender

value: Male

tag: age at the day of bone marrow transplantation

tag: mutation

tag: anemia

tag: deb test

tag: cytogenetic/peripheral blood dysplasia


title: FA_BM_MSC_10

value: Unknown

tag: extremity anomalies

tag: microcephaly

tag: cardiac anomalies

tag: café au lait /hyperpigmentation

tag: renal anomalies

tag: microphthalmia/ptosis

tag: hypothyroidism


title: IgG_NOD_IMQ-5

description:
raw data file:
IgG_Slide2_532.gpr

tag: slide

tag: array (block)

tag: tissue


title: Donor_BM_MSC_10

description: Global non-coding RNA expression profile of BM-MSCs from healthy individual.

tag: pairing group

value: Not Applicable

value: Not Available

tag: g-csf intervention prior to bone marrow collection

tag: adipogenic differentiation assessed according to oro staining

tag: osteogenic differentiation assessed according to ars staining


title: FA_BM_MSC_6

tag: gender

tag: age at the day of bone marrow transplantation

tag: mutation

tag: anemia

value: Negative


title: Section (A->P)  30

description: GEO-seq

tag: cell type


title: C57/BL6_liver_embryo-E18_rep2

city: Houston

first: Liuqing

last: Yang

state: Texas

address: 1515 Holcombe Blvd.

department: Molecular and Cellular Oncology

institute: The University of Texas MD Anderson Cancer Center

description:
LncRNA expression profile of mouse fetal liver
Mouse liver lncRNA_05

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
The raw intensities were first QC flag filtered before next step normalization. The probe signals were QC flagged as Present or Absent based on whether the signals are: 1) Positive and significant; 2) Uniform; 3) Above background; 4) Saturated; 5) Population outlier. The probe signals were additionally flagged as Marginal based on whether their backgrounds are: 1) Uniform; 2) Population outlier. All probes are flagged according to these rules. Probes flagged as Absent are excluded from the Fold Change analysis. Many genes on the array were filtered out primarily because many genes were not expressed across the samples and thus did not have valid intensity values, resulting in the reduced data set.
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs were identified through Fold Change filtering between two samples. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: All mice were on a C57BL/6 genetic background. Animals were housed in a controlled temperature room maintained under alternating 12 h light and dark cycles and, in between experiments, had free access to food and water

extract_protocol: Total RNAs were  isolated from mouse live tissue using TRIzol™ Plus RNA Purification Kit (ThermoFisher Scientific, Waltham, MA) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-2000 and RNA integrity was assessed by Bioanalyzer.

treatment_protocol: No treatment involved

tag: strain

tag: age

value: E18 days

tag: Sex

value: male

value: liver


title: IgG_NOD_Con-9

description:
raw data file:
IgG_Slide2_532.gpr

value: Serum

tag: treatment


title: Donor_BM_MSC_9

value: unpaired

tag: deb test

tag: cytogenetic/peripheral blood dysplasia

tag: extremity anomalies

tag: microcephaly

tag: cardiac anomalies

tag: café au lait /hyperpigmentation

tag: renal anomalies

tag: microphthalmia/ptosis

tag: hypothyroidism


title: ancestor_expression

city: Suita

first: Atsushi

last: Shibai

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description: Gene expression of the ancestral cell of UV irradiating evolution experiment

hyb_protocol: Then the cRNA of 600 ng was fragmented and hybridised to a microarray for 17 h at 65°C, rotating at 10 rpm in a hybridisation oven (Agilent Technologies).

scan_protocol: Then, the microarray was washed and scanned according to the manufacturer’s instructions.

data_processing: Microarray image analysis was performed using Feature Extraction version 10.7.3.1 (Agilent Technologies).

organism: Escherichia coli

source_name: MDS42 ancestor

label_protocol: A microarray experiment was performed using an Agilent 8× 60 K array, which was designed for the E. coli W3110 strain so that 12 probes were contained for each gene. Purified total RNA (100 ng) was labelled with Cyanine3 (Cy3) using a Low Input Quick Amp WT labelling kit (One-color; Agilent Technologies). The Cy3-labelled cRNA was checked its amount (> 5 µg) and specific activity (> 25 pmol/µg) using NanoDrop ND-2000.

growth_protocol: The cells were cultured for 16–19 h and then sampled at the time of the logarithmic growth phase (OD600 values were 0.072–0.135).

extract_protocol: RNA extraction was performed using an RNeasy mini kit with on-column DNase digestion (Qiagen), following the manufacturer’s protocols. The purified RNA was quality-controlled using an Agilent 2100 Bioanalyzer and an RNA 6000 Nano kit (Agilent Technologies).

treatment_protocol: Then, aliquots of the cells were immediately added to the same volume of ice-cold ethanol with 10% (w/v) phenol.

value: K-12 substr. MDS42

tag: day


title: C57/BL6_liver_2-months_rep3

description:
LncRNA expression profile of mouse adult liver
Mouse liver lncRNA_03

tag: tissue


title: C57/BL6_liver_2-months_rep2

description:
LncRNA expression profile of mouse adult liver
Mouse liver lncRNA_02


title: C57/BL6_liver_embryo-E18_rep3

description:
LncRNA expression profile of mouse fetal liver
Mouse liver lncRNA_06


title: C57/BL6_liver_embryo-E18_rep1

description:
LncRNA expression profile of mouse fetal liver
Mouse liver lncRNA_04


title: UVevolved_6R172_expression

description: Gene expression after 688 days of evolution under UV irradiation, lineage-6

source_name: lineage-6, 172 rounds (688 days)


title: Donor_BM_MSC_11

tag: pairing group

tag: gender

tag: age at the day of bone marrow transplantation

tag: mutation

tag: anemia

tag: g-csf intervention prior to bone marrow collection

tag: adipogenic differentiation assessed according to oro staining

tag: osteogenic differentiation assessed according to ars staining


title: Section (A->P)  29

description: GEO-seq

tag: cell type

value: UiPSM


title: UVevolved_5R172_expression

description: Gene expression after 688 days of evolution under UV irradiation, lineage-5

source_name: lineage-5, 172 rounds (688 days)

tag: strain


title: C57/BL6_liver_2-months_rep1

description:
LncRNA expression profile of mouse adult liver
Mouse liver lncRNA_01

tag: age

tag: Sex


title: Donor_BM_MSC_8

value: Absent

tag: deb test

tag: cytogenetic/peripheral blood dysplasia

tag: extremity anomalies

tag: microcephaly

tag: cardiac anomalies

tag: café au lait /hyperpigmentation

tag: renal anomalies

value: Present


title: Donor_BM_MSC_1

tag: tissue

tag: pairing group

tag: gender

value: Female

tag: age at the day of bone marrow transplantation

tag: microphthalmia/ptosis

tag: hypothyroidism

value: positive


title: FApostBMT_BM_MSC_3

data_processing:
Affymetrix GeneChip Command Console (AGCC) was used to determine the intensity value for each probe cell and to create ‘.cel’ file for each sample. These files were also obtained from AY-KA LTD. QC was performed prior to further analysis. Initially, there were 6 postBMT samples but 3 samples (HUSCS-FA02-T, HUSCS-FA04-T, HUSCS-FA10-T) that failed QC were discarded from study. CEL files for samples that failed QC can be found in supplementary files. Files of samples that passed QC were then loaded to Transcriptome Analysis Console (TAC) by Applied Biosystems, (Thermo Fisher Scientific, software version 4.0.2.15) with specifications: Analysis Type: Expression (Gene); Analysis Version: version 1; Summarization Method: RMA+DABG (All Organisms); Annotation: miRNA-2_0.annotations.20101222.csv; ANOVA Method: eBayes). Batch effect correction were applied with preBMT-Donor-postBMT grouping data as per TAC user manual. Mature miRNAs annotated to Homo Sapiens by manufacturer were selected and expression values were exported from TAC for further analysis.
miRNA-2_0_v2.pgf
miRNA-2_0.annotations.20101222.csv

label_protocol: Total RNA including small RNAs (100 ng) were used to label RNAs with biotin using Genisphere FlashTag HSR kit (Genisphere, Hatfield, PA) according to the manufacturer's instructions. All experimental services were purchased from AY-KA LTD (Ankara, Turkey)

growth_protocol: Cryopreserved bone marrow (BM)-derived mononuclear cells (BM-MNCs) from Fanconi anemia (FA) patients obtained at Hacettepe University Pediatric Hematology Bone Marrow Transplantation unit were used for isolation of BM derived mesenchymal stem/stromal cells (BM-MSCs). Patients were diagnosed by clinical manifestations and DEB treatment. BM-MSCs from allogeneic healthy donors served as controls. BM-MSCs were maintained in expansion (DMF10) medium in a 5% CO2 incubator at 37°C. DMF10 medium consisting of 60% Dulbecco’s modified Eagle’s medium-low glucose (DMEM-LG; Gibco) and 40% MCDB-201 medium (Sigma-Aldrich) supplemented with 10% heat-inactivated fetal bovine serum (Gibco), 1% penicillin and streptomycin (Biochrom AG) and 1% L-glutamine (Biochrom AG), was changed after 3 to 4 days. Once BM-MSCs reached confluency of 70–80%, they were washed with phosphate buffered saline (Applichem) and trypsinized in 0.25% trypsin (Invitrogen) containing 1mM EDTA (Invitrogen) solution. Passaged cells were then washed in DMF10 medium to stop the effect of trypsin enzyme, followed by centrifugation (Eppendorf, Germany) at 453 x g for 5 minutes at room temperature. BM-MSCs were then counted using Trypan Blue stain (Biological Industries) and replated. The study was approved by the Local Ethical Committee (Number 14, 24/08/2009). Informed consent was obtained from all individual participants/their parents included in the study. (doi:10.3906/biy-1511-93)

extract_protocol: Total RNA including small RNAs were isolated from passage 3 BM-MSCs using miRNeasy Mini Kit (Qiagen, Germany) and treated with RNase-free DNase Digestion (Qiagen, Germany) according to the manufacturer’s instructions.

value: Passage 3 Bone Marrow Mesenchymal Stem/Stromal Cells

tag: mutation

tag: anemia

value: Absent (app. one year after BMT)

tag: g-csf intervention prior to bone marrow collection

value: Not applicable

tag: adipogenic differentiation assessed according to oro staining

tag: osteogenic differentiation assessed according to ars staining


title: FApostBMT_BM_MSC_2

value: Present (app. two months after BMT)

tag: deb test

tag: cytogenetic/peripheral blood dysplasia

value: negative


title: IgG_NOD_Con-8

description:
raw data file:
IgG_Slide2_532.gpr

tag: slide

tag: array (block)

tag: strain

tag: treatment

value: control


title: IgG_NOD_Con-7

description:
raw data file:
IgG_Slide2_532.gpr

tag: tissue


title: Section (A->P)  28

description: GEO-seq

tag: cell type


title: IgG_NOD_Con-6

description:
raw data file:
IgG_Slide2_532.gpr


title: Section (A->P)  27

description: GEO-seq


title: Section (A->P)  26

description: GEO-seq


title: IgG_BL-10IMQ-6

description:
raw data file:
IgG_Slide2_532.gpr

value: imiquimod (Imq)


title: Section (A->P)  25

description: GEO-seq


title: IgG_BL-10IMQ-4

description:
raw data file:
IgG_Slide2_532.gpr


title: UVevolved_3R172_expression

description: Gene expression after 688 days of evolution under UV irradiation, lineage-3

source_name: lineage-3, 172 rounds (688 days)

tag: day


title: UVevolved_4R172_expression

description: Gene expression after 688 days of evolution under UV irradiation, lineage-4

source_name: lineage-4, 172 rounds (688 days)


title: IgG_BL-10IMQ-5

description:
raw data file:
IgG_Slide2_532.gpr


title: UVevolved_2R172_expression

description: Gene expression after 688 days of evolution under UV irradiation, lineage-2

source_name: lineage-2, 172 rounds (688 days)


title: Section (A->P)  24

description: GEO-seq

source_name: UiPSM


title: FApostBMT_BM_MSC_1

tag: pairing group

tag: gender

value: Male

tag: age at the day of bone marrow transplantation

value: FA-A

value: Not Available

tag: extremity anomalies

tag: microcephaly

tag: cardiac anomalies

tag: café au lait /hyperpigmentation

tag: renal anomalies


title: IgG_BL-10Con-6

description:
raw data file:
IgG_Slide2_532.gpr

value: Serum


title: Section (A->P)  23

description: GEO-seq


title: Section (A->P)  22

description: GEO-seq


title: UVevolved_1R172_expression

description: Gene expression after 688 days of evolution under UV irradiation, lineage-1

source_name: lineage-1, 172 rounds (688 days)

value: K-12 substr. MDS42


title: IgG_BL-10Con-5

description:
raw data file:
IgG_Slide2_532.gpr


title: IgG_BL-10Con-4

description:
raw data file:
IgG_Slide2_532.gpr


title: FA_BM_MSC_11

tag: mutation

value: Unknown

tag: anemia

tag: deb test

value: Positive

tag: microphthalmia/ptosis

tag: hypothyroidism

tag: g-csf intervention prior to bone marrow collection

tag: adipogenic differentiation assessed according to oro staining

tag: osteogenic differentiation assessed according to ars staining


title: Donor_BM_MSC_5

tag: tissue

value: Not Applicable

value: Absent

tag: cytogenetic/peripheral blood dysplasia


title: Section (A->P)  20

description: GEO-seq

tag: cell type

value: UiPSM


title: Donor_BM_MSC_7

value: Passage 3 Bone Marrow Mesenchymal Stem/Stromal Cells

tag: pairing group

tag: gender

tag: age at the day of bone marrow transplantation

value: positive


title: FA_BM_MSC_8

value: Female

value: Present

tag: extremity anomalies

tag: microcephaly

tag: cardiac anomalies

value: Not applicable


title: IgG_PBS_1

description:
raw data file:
IgG_Slide1_532.gpr
Negative control

tag: slide

tag: array (block)

tag: strain


title: IgG_NOD_IMQ-4

description:
raw data file:
IgG_Slide1_532.gpr

tag: treatment


title: Plasma Oesophageal adenocarcinoma 10

city: Bedford Park

middle: James

last: Hussey

address: Flinders Drive

country: Australia

institute: Flinders University

description: plasma from patient with Oesophageal Adenocarcinoma

data_processing:
Expression data were processed using OpenArray® Real-Time qPCR Analysis Software (BioTrove™, version 1.0.4). CSV files were generated by the software with the cycle threshold (Ct) values for each microRNA with a setting of Ct confidence value threshold of 150.
The CSV files were imported into Realtime Statminer® software (Integromics, Philadelphia, Pa., USA) for  quality checking. Data in the CSV files was then analysed using R version 3.0.2 and SPSS v19 (IBM Inc) for Mac.  Only microRNAs which amplified in every sample were analysed for further analysis.
Data were analysed in R version 3.0.2 and SPSS v19 (IBM Inc.). The relative expression of each miRNA was calculated as 2(40-Ct). miRNA ratios were generated from the relative expression values using R version 3.0.2.   Area under the curve (AUC>0.7) of Receiver Operating Characteristic curves (ROC)  were used to assess the ability of a multivariate logistic regression model using 5 microRNA ratios to discriminate Healthy controls from oesophageal adenocarcinomas.
Fold Change worksheet reports the fold difference of expression of the microRNA ratios between the indicated study groups

label: FAM

source_name: peripheral blood plasma exosomes

label_protocol: PCR assays were performed by following the protocol for TaqMan@OpenArray Human MicroRNA Panel (4461104, Life technologies). For each sample, 3μl of RNA was reverse transcribed using pre-defined RT-primers (MegaplexTM Primer Human Pool A and Pool B) and the TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). Pre-amplifications were carried out with MegaplexTM PreAmp Pools and TaqMan PreAmp Master Mix on 7.5μl cDNA/ sample for each pool. The pre-amplified products (4μl per sample) were diluted at the recommended 1:40 dilution with 156μl of RNase-free ultra pure water before loading onto the 384-well TaqMan OpenArray loading plate. PCR runs were performed on XXX.

extract_protocol: Exosomes were isolated from the serum samples using ExoquickTm (System Biosciences, EXOQ20A-1). Extraction of miRNA from exosomes was performed using an miRNeasy Serum/Plasma kit (Qiagen, #217184) with a final elution volume of 24 microlitres ultra pure water.

treatment_protocol: Peripheral blood was collected into (i)  9ml K3E K3EDTA tubes , and  (ii) 8 ml serum clot activator tubes.

tag: condition

value: locally advanced Oesophageal adenocarcinoma


title: Plasma Oesophageal adenocarcinoma 8


title: Plasma Oesophageal adenocarcinoma 9


title: Plasma Oesophageal adenocarcinoma 7


title: Plasma Oesophageal adenocarcinoma 6


title: Section (A->P)  18

description: GEO-seq


title: FA_BM_MSC_11

description: Global non-coding RNA expression profile of BM-MSCs from Fanconi anemia patient.

data_processing:
Affymetrix GeneChip Command Console (AGCC) was used to determine the intensity value for each probe cell and to create ‘.CEL’ file for each sample. These files were also obtained from AY-KA LTD. QC was performed prior to further analysis. All paired samples passed QC step. These files were then loaded to Transcriptome Analysis Console (TAC) by Applied Biosystems, (Thermo Fisher Scientific, software version 4.0.2.15) with specifications: Analysis Type: Expression (Gene); Analysis Version: version 1; Summarization Method: RMA+DABG (All Organisms); Annotation: miRNA-2_0.annotations.20101222.csv). Batch effect correction was applied with preBMT-Donor grouping data according to TAC user manual. Mature miRNAs annotated to Homo Sapiens by the manufacturer were selected and expression values were exported from TAC for further analysis.
miRNA-2_0_v2.pgf
miRNA-2_0.annotations.20101222.csv

label_protocol: Total RNA including small RNAs (100 ng) was used to label RNAs with biotin using Genisphere FlashTag HSR kit (Genisphere, Hatfield, PA) according to the manufacturer's instructions. All experimental services were purchased from AY-KA LTD (Ankara, Turkey)

growth_protocol: Cryopreserved bone marrow (BM)-derived mononuclear cells (BM-MNCs) from Fanconi anemia (FA) patients obtained at Hacettepe University Pediatric Hematology Bone Marrow Transplantation unit were used for isolation of BM derived mesenchymal stem/stromal cells (BM-MSCs). Patients were diagnosed by clinical manifestations and DEB treatment. BM-MSCs from allogeneic healthy donors  served as controls. BM-MSCs were maintained in expansion (DMF10) medium in a 5% CO2 incubator at 37°C. DMF10 medium consisting of 60% Dulbecco’s modified Eagle’s medium-low glucose (DMEM-LG; Gibco) and 40% MCDB-201 medium (Sigma-Aldrich) supplemented with 10% heat-inactivated fetal bovine serum (Gibco), 1% penicillin and streptomycin (Biochrom AG) and 1% L-glutamine (Biochrom AG), was changed after 3 to 4 days. Once BM-MSCs reached confluency of 70–80%, they were washed with phosphate buffered saline (Applichem) and trypsinized in 0.25% trypsin (Invitrogen) containing 1mM EDTA (Invitrogen) solution. Passaged cells were then washed in DMF10 medium to stop the effect of trypsin enzyme, followed by centrifugation (Eppendorf, Germany) at 453 x g for 5 minutes at room temperature. BM-MSCs were then counted using Trypan Blue stain (Biological Industries) and replated. The study was approved by the Local Ethical Committee (Number 14, 24/08/2009). Informed consent was obtained from all individual participants/their parents included in the study. Characterizations of the BM-MSCs used in this study was published by Cagnan et. al. (doi:10.1007/s12015-017-9794-5).

extract_protocol: Total RNA including small RNAs were isolated from passage three BM-MSCs using miRNeasy Mini Kit (Qiagen, Germany) and treated with RNase-free DNase Digestion (Qiagen, Germany) according to the manufacturer’s instructions.

tag: mutation

tag: anemia

tag: deb test

tag: café au lait /hyperpigmentation

tag: renal anomalies

tag: microphthalmia/ptosis

tag: hypothyroidism

tag: g-csf intervention prior to bone marrow collection

value: negative


title: Plasma Oesophageal adenocarcinoma 4


title: IgG_NOD_IMQ-3

description:
raw data file:
IgG_Slide1_532.gpr

tag: tissue

value: imiquimod (Imq)


title: Plasma Oesophageal adenocarcinoma 5


title: Section (A->P)  19

description: GEO-seq

tag: cell type


title: FA_BM_MSC_5

tag: pairing group

tag: gender

value: Male

tag: age at the day of bone marrow transplantation

value: FA-A

value: Negative

tag: cytogenetic/peripheral blood dysplasia

tag: extremity anomalies

tag: microcephaly

tag: adipogenic differentiation assessed according to oro staining

tag: osteogenic differentiation assessed according to ars staining


title: Section (A->P)  21

description: GEO-seq


title: FA_BM_MSC_9

tag: mutation

tag: anemia

tag: cardiac anomalies


title: Section (A->P)  17

description: GEO-seq


title: Plasma Oesophageal adenocarcinoma 3

tag: condition


title: IgG_NOD_IMQ-2

description:
raw data file:
IgG_Slide1_532.gpr

tag: slide

tag: array (block)

value: Serum

tag: strain

tag: treatment


title: FA_BM_MSC_8

tag: tissue

tag: deb test

tag: café au lait /hyperpigmentation

tag: renal anomalies

tag: microphthalmia/ptosis

tag: hypothyroidism

tag: g-csf intervention prior to bone marrow collection


title: FA_BM_MSC_5

tag: pairing group

tag: gender

tag: age at the day of bone marrow transplantation

tag: cytogenetic/peripheral blood dysplasia

tag: extremity anomalies

tag: microcephaly

tag: adipogenic differentiation assessed according to oro staining


title: IgG_NOD_IMQ-1

description:
raw data file:
IgG_Slide1_532.gpr

tag: slide

tag: array (block)


title: Plasma Oesophageal adenocarcinoma 2

tag: condition


title: Section (A->P)  15

description: GEO-seq

tag: cell type


title: Donor_BM_MSC_3

description: Global non-coding RNA expression profile of BM-MSCs from healthy individual.

tag: tissue

tag: mutation

tag: anemia

tag: deb test

tag: cardiac anomalies

tag: osteogenic differentiation assessed according to ars staining


title: FA_BM_MSC_7

tag: pairing group

value: FA-G

tag: café au lait /hyperpigmentation

tag: renal anomalies

tag: microphthalmia/ptosis

tag: hypothyroidism

tag: g-csf intervention prior to bone marrow collection


title: IgG_NOD_Con-5

description:
raw data file:
IgG_Slide1_532.gpr

tag: strain

tag: treatment

value: control


title: Section (A->P)  13

description: GEO-seq


title: Plasma Oesophageal adenocarcinoma 1


title: IgG_NOD_Con-3

description:
raw data file:
IgG_Slide1_532.gpr

tag: slide

tag: array (block)


title: Plasma Healthy patient 9

description: plasma from patient without Barrett's Oesophagus or Cancer


title: Plasma Healthy patient 10


title: Section (A->P)  14

description: GEO-seq

tag: cell type


title: Section (A->P)  12

description: GEO-seq


title: IgG_NOD_Con-4

description:
raw data file:
IgG_Slide1_532.gpr

tag: tissue


title: IgG_NOD_Con-2

description:
raw data file:
IgG_Slide1_532.gpr


title: IgG_NOD_Con-1

description:
raw data file:
IgG_Slide1_532.gpr


title: Section (A->P)  11

description: GEO-seq


title: Donor_BM_MSC_6

tag: gender

tag: age at the day of bone marrow transplantation

tag: mutation

value: Not Applicable

tag: cytogenetic/peripheral blood dysplasia

tag: extremity anomalies

tag: microcephaly

tag: adipogenic differentiation assessed according to oro staining


title: Donor_BM_MSC_7

tag: pairing group

tag: anemia

value: Absent

tag: deb test

tag: cardiac anomalies

tag: café au lait /hyperpigmentation

tag: renal anomalies

tag: osteogenic differentiation assessed according to ars staining


title: Plasma Healthy patient 8


title: Donor_BM_MSC_5

tag: microphthalmia/ptosis

tag: hypothyroidism

tag: g-csf intervention prior to bone marrow collection


title: FA_BM_MSC_4

tag: tissue

tag: gender

value: Positive


title: Donor_BM_MSC_4

value: Passage 3 Bone Marrow Mesenchymal Stem/Stromal Cells

tag: age at the day of bone marrow transplantation

tag: mutation


title: Section (A->P)  16

description: GEO-seq

tag: cell type

value: UiPSM


title: Plasma Healthy patient 5


title: Donor_BM_MSC_3

value: Female

tag: cytogenetic/peripheral blood dysplasia

tag: extremity anomalies

tag: microcephaly

value: positive


title: Plasma Healthy patient 6


title: Plasma Healthy patient 4


title: Section (A->P)  8

description: GEO-seq


title: IgG_BL-10IMQ-1

description:
raw data file:
IgG_Slide1_532.gpr

tag: slide

tag: array (block)

tag: strain

tag: treatment


title: IgG_BL-10Con-3

description:
raw data file:
IgG_Slide1_532.gpr


title: IgG_BL-10IMQ-2

description:
raw data file:
IgG_Slide1_532.gpr


title: IgG_BL-10Con-2

description:
raw data file:
IgG_Slide1_532.gpr


title: Section (A->P)  7

description: GEO-seq


title: Plasma Healthy patient 3


title: IgG_BL-10IMQ-3

description:
raw data file:
IgG_Slide1_532.gpr


title: Donor_BM_MSC_2

tag: pairing group

tag: anemia

tag: deb test

tag: cardiac anomalies

tag: café au lait /hyperpigmentation

tag: renal anomalies

value: Present

tag: adipogenic differentiation assessed according to oro staining


title: Section (A->P)  6

description: GEO-seq


title: N1_H_rep3

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Cy3- and Cy5-labeled RNA were hybridized to 4x44K 60mer oligonucleotide spotted microarray slides (Agilent, Mouse Whole Genome 4x44K; design ID 014868). Hybridization and subsequent washing and drying of the slides was performed following the Agilent hybridization protocol.

scan_protocol: The slides were scanned using a GenePix 4100A scanner. Images of Cy3 and Cy5 signals were analyzed using GenePix Pro 5.1 software, and calculated values for all spots were saved as GenePix results files.

data_processing: Stored data were evaluated using the R software and the limma package from BioConductor. Log mean spot signals were taken for further analysis. Signals of replicate spots (same probes) within arrays were averaged. M/A data were LOESS normalized with span=0.1 and 4 iterations.

label_protocol: Purified total RNA was amplified and Cy-labeled using the dual-color QuickAmp Kit (Agilent Technologies) according to the manufacturer’s protocol.1 μg of total RNA was used per reaction.

growth_protocol: Mice (C57BL/6J, 12-18 weeks old, Charles River Laboratories, Sulzfeld, Germany) were kept under standard labboratory conditions with unlimited access to food and water.

extract_protocol: 10µm cryo-sections of Tissue Tek-embedded (Sakura Finetek, Staufen, Germany) lungs harvested from C57BL/6J mice were mounted on PEN membrane slides (Leica Microsystems, Wetzlar, Germany). For visualization of cell nuclei, sections were stained with Hemalaun for 45 seconds, following immersion in water, 70% ethanol, 96% ethanol, and then stored in 100% ethanol until use. Intrapulmonary vessels with an outer diameter of 50–100 μm were selected and microdissected under optical control using the Laser Microdissection 6000 (Leica Microsystems). Microdissected material was collected in Eppendorf tubes, filled with RNA lysis buffer (Qiagen, Hilden, Germany) with 1% β-mercaptoethanol and finally snap-frozen in liquid nitrogen until use. Total RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Mice were exposed to chronic hypoxia (10% O2) in a ventilated chamber to induce pulmonary vascular remodeling as described in Weisel FC, Kloepping C, Pichl A, Sydykov A, Kojonazarov B, Wilhelm J, Roth M, Ridge KM, Igarashi K, Nishimura K, Maison W, Wackendorff C, Klepetko W, Jaksch P, Ghofrani HA, Grimminger F, Seeger W, Schermuly RT, Weissmann N and Kwapiszewska G. Impact of S-adenosylmethionine decarboxylase 1 on pulmonary vascular remodeling. Circulation. 2014;129:1510-23.  Briefly, animals were age-matched and randomly distributed to groups either exposed to 21 days of normobaric normoxia [inspiratory O2 fraction (FiO2) 0.21] or normobaric hypoxia [FiO2 of 0.10] with subsequent re-exposure to normoxia for 1, 3, 7 and 14 days.

value: hypoxia with subsequent re-exposure to normoxia for 1 day

tag: tissue

value: Lung vasculature

source_name: H

value: hypoxia


title: Section (A->P)  9

description: GEO-seq


title: IgG_BL-10Con-1

description:
raw data file:
IgG_Slide1_532.gpr


title: Plasma Healthy patient 1


title: Section (A->P)  4

description: GEO-seq


title: Section (A->P)  5

description: GEO-seq


title: N_H_rep4

source_name: N

value: normoxia


title: Serum Oesophageal adenocarcinoma 10

description: serum from patient with Oesophageal Adenocarcinoma

source_name: peripheral blood serum exosomes

tag: condition

value: locally advanced Oesophageal adenocarcinoma


title: Serum Oesophageal adenocarcinoma 9


title: Plasma Healthy patient 2


title: IgM_NOD_IMQ-9

description:
raw data file:
IgM_Slide2_635.gpr

label: cy5-labeled anti-mouse IgM

value: imiquimod (Imq)


title: H_N_rep4


title: Section (A->P)  2

description: GEO-seq

tag: cell type


title: N_H_rep3


title: N3_H_rep2

value: hypoxia with subsequent re-exposure to normoxia for 3 days


title: Section (A->P)  1

description: GEO-seq


title: N3_H_rep1


title: Section (A->P)  3

description: GEO-seq


title: IgM_NOD_IMQ-8

description:
raw data file:
IgM_Slide2_635.gpr
Bad sample

value: Serum


title: Serum Oesophageal adenocarcinoma 7


title: Serum Oesophageal adenocarcinoma 8


title: H_N3_rep1


title: Serum Oesophageal adenocarcinoma 6


title: Section (A->P)  0

description: GEO-seq


title: IgM_PBS_2

description:
raw data file:
IgM_Slide2_635.gpr
Negative control


title: Day9

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
We mapped single-cell sequencing data to human genome by using CellRanger 3.0.2 with setting ‘--localcores=10 --localmem=3 --mempercore=3 --maxjobs=10 --r1-length=26 --r2-length=151’.
We processed mapped data by using Seurat15. The count matrix was generated by using merge() function in Seurat and excluding low quality cells—cells with less than 200 genes and low quality genes—genes expressing less than 10 cells.
Genome_build: hg38

source_name: UiPSM reprogramming Day9

growth_protocol: UiPSM reprogrammed from Urine cell with a induction medium(DM),Advanced DMEM/F12 supplemented with 5uM EPZ5676,10ng/ml bFGF, 5ng/ml EGF and 3uM CHIR99021

extract_protocol:
Cells suspensions (500-1000 cells per microliter) were loaded on a Chromium Single Cell Controller (10x Genomics) to obtain single-cell gel beads in emulsion (GEMs) by using Single Cell 3’ Library and Gel Bead Kit V2 (10x genomics, 120237). Captured cDNAs were lysed and the released RNA were barcoded through reverse transcription in singular GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleaned by DynaBeads® MyOne Silane Beads (Invitrogen, 37002D).
Single-cell RNA-seq libraries were prepared by Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacturer’s instruction.

treatment_protocol: UiPSM cells including time-course samples were briefly washed (DPBS), dissociated (0.25% Trypsin-EDTA(Gibco)), strained (100 µm filter) twice, pelleted and resuspended in DPBS containing 0.04% BSA (Sigma) to give a final concentration of 800 cells/ul.

value: UiPSM reprogramming cell

tag: time point


title: H_N3_rep2


title: IgM_NOD_Con-6_2

value: control


title: Serum Oesophageal adenocarcinoma 5


title: IgM_NOD_IMQ-7

description:
raw data file:
IgM_Slide2_635.gpr


title: H_N7_rep1

value: hypoxia with subsequent re-exposure to normoxia for 7 days


title: IgM_NOD_IMQ-5

description:
raw data file:
IgM_Slide2_635.gpr


title: IgM_NOD_Con-9

description:
raw data file:
IgM_Slide2_635.gpr


title: Section (A->P)  10

description: GEO-seq


title: MSCs 72h (rep. 5)

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using STAR and gene abundance estimation using featurecounts
Differential gene expression computed using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated count file

source_name: Mesenchymal Stromal Cells

extract_protocol:
RNA was extracted using RNeasy Micro Kit, according to the manufacturer’s instructions and DNase treatment was performed using RNase-free DNase Set
RNA was extracted using the RNeasy micro kit (Qiagen) according to the manufacturer’s protocol. The  QC check was performed running samples on HSRNA chip (Tape Station 2100, Agilent), and only samples with RIN>7 were processed. RNA library preparation was performed following the manufacturer’s instruction using Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina).

value: Control Sample

tag: patient


title: Serum Oesophageal adenocarcinoma 4


title: IgM_NOD_Con-8

description:
raw data file:
IgM_Slide2_635.gpr

source_name: Serum


title: H_N7_rep2


title: GE-HSPCs 72h (rep. 4)

value: Gene Edited Sample


title: N7_H_rep1


title: IgM_NOD_Con-7

description:
raw data file:
IgM_Slide2_635.gpr


title: N7_H_rep2


title: Serum Oesophageal adenocarcinoma 3


title: MSCs 72h (rep. 4)


title: Serum Oesophageal adenocarcinoma 2


title: GE-HSPCs 72h (rep. 3)


title: GE-HSPCs 72h (rep. 5)


title: Serum Healthy patient 10

description: serum from patient without Barrett's Oesophagus or Cancer


title: Serum Oesophageal adenocarcinoma 1


title: MSCs 72h (rep. 3)


title: IgM_BL-10IMQ-5

description:
raw data file:
IgM_Slide2_635.gpr


title: GE-HSPCs 72h (rep. 2)


title: H_N_rep2


title: Serum Healthy patient 9


title: IgM_BL-10IMQ-4

description:
raw data file:
IgM_Slide2_635.gpr


title: Serum Healthy patient 8


title: H_N_rep3


title: Serum Healthy patient 7


title: N_H_rep1


title: MSCs 72h (rep. 2)


title: IgM_BL-10Con-6

description:
raw data file:
IgM_Slide2_635.gpr


title: N_H_rep2


title: IgM_NOD_Con-6

description:
raw data file:
IgM_Slide2_635.gpr


title: N7_N3_rep2


title: GE-HSPCs 72h (rep. 1)


title: N3_N7_rep2


title: N7_N3_rep1


title: IgM_BL-10Con-5

description:
raw data file:
IgM_Slide2_635.gpr


title: Serum Healthy patient 5


title: Serum Healthy patient 6


title: IgM_BL-10IMQ-6

description:
raw data file:
IgM_Slide2_635.gpr


title: N3_N7_rep1


title: IgM_BL-10Con-4

description:
raw data file:
IgM_Slide2_635.gpr


title: IgM_PBS_1

description:
raw data file:
IgM_Slide1_635.gpr
Negative control

source_name: Negative control


title: N3_N1_rep2


title: Serum Healthy patient 4


title: N3_N1_rep1


title: B2: Lyve1-Wnt2/9b (sub-slide 1)

type: genomic

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
SAMPLE 4
liver slide

hyb_protocol: Protocol provided and performed by resolve bioscience (https://your.resolve-biosciences.com/), with reference paper PMID: 35021063

data_processing:
Gene count per cell were identified by QuPath
File details:
Raw data files include *results.txt and *tiff.
The *results.txt file will show the gene expression at a certain location.
In the *_results.txt raw data files:
Column1: X-position
Column2: Y-position
Column3: Z-position
Column4: Gene_Name
The X, Y and Z positions are the pixel for the spatial data, indicate the X, Y and Z location on the slides.
Each row indicate a gene expression at a certain location.
The *tiff indicates the nucleus location.
The *results.txt and *tiff files are used as input for software QuPath. QuPath will outline cells based on the nucleus location and then quantify the number of genes (gene count) per cell. The output of QuPath is the *counts_measurements.csv file, a gene-by-cell matrix.
In the *counts_measurements.csv processed data files:
Column1: Gene-ID
Column2-end: single-cell columns.  Single-cell column name, for Y-position and X-position of the cell center.
Data type in the *counts_measurements.csv processed data files:  Gene count per cell for the processed data.

molecule: other

source_name: liver

growth_protocol: Mice were fed regular chow in standard caging and kept under a 12-hour light–dark cycle with no enrichment.

extract_protocol:
Frozen livers were sectioned and sent on dry ice to resolve bioscience for further processing
The RNA molecules are not extracted. It's an in-situ method to detect the gene expression. The liver section is processed directly.

treatment_protocol: For sample 2 and 3, animals were treated with four doses of FL6.13 (5mg/kg)

value: C57/BL6 background

tag: genotype

value: Lyve1-Cre; Wnt2-floxed, Wnt9b-floxed

tag: gender

value: male

tag: age

value: 8 week old

value: liver


title: Serum Healthy patient 3


title: A2: FL6.13 treatment (sub-slide 2)

description:
SAMPLE 3
liver slide

scan_protocol: Protocol provided and performed by resolve bioscience (https://your.resolve-biosciences.com/), with reference paper PMID: 35021063

tag: strain

value: Wildtype


title: IgM_NOD_IMQ-4

description:
raw data file:
IgM_Slide1_635.gpr

tag: slide

tag: array (block)

tag: treatment


title: MSCs 72h (rep. 1)


title: N1_N3_rep2

value: hypoxia with subsequent re-exposure to normoxia for 1 day

value: Lung vasculature


title: A2: FL6.13 treatment (sub-slide 1)

description:
SAMPLE 2
liver slide


title: IgM_NOD_IMQ-3

description:
raw data file:
IgM_Slide1_635.gpr


title: IgM_NOD_IMQ-2

description:
raw data file:
IgM_Slide1_635.gpr


title: A1: Wildtype

description:
SAMPLE 1
liver slide


title: SaeR

city: Melbourne

first: Tim

last: Stinear

state: Victoria

address: 792 Elizabeth St, Melbourne

institute: University of Melbourne

data_processing:
MiSeq reads from each of the five experiments (pRAB11: walRFLAG / vraRFLAG / hptRFLAG / saeRFLAG or pRAB11FLAG only) were first mapped to the S. aureus USA300 NC_007793 reference chromosome using samtools.
Read coverage plots for viewing in Artemis were created using samtools and the command %  samtools depth -aa [target_file_name].bam [subtraction_file_name].bam | cut -f3,4 | perl -nae 'use List::Util qw(max); print max(0, $F[0]-$F[1]),"\n";' > [target_peaks].userplot.
The ‘create feature from graph function’ in Artemis was then used to define sequence regions represented by the subtraction coverage plots. The resulting multi-fasta format files of these regions was the input for motif prediction using tools such as SeSiMCMC
Assembly: S. aureus USA300 NC_007793
Supplementary files format and content: userplots (Artemis)

organism: Staphylococcus aureus

growth_protocol: An overnight culture (10 ml LB in 50 ml tube) of each strain NRS384Δspa containing either pRAB11: walRFLAG / vraRFLAG / hptRFLAG / saeRFLAG or pRAB11FLAG only were grown at 37°C with shaking at 200 rpm. Overnight cultures were diluted 1:100 in fresh LB (100 ml) in a 1 L baffled flask

extract_protocol:
Bacterial cells were suspended in 1ml of lysis buffer (50 mM Tris-HCl [pH 7.4], 150 mM NaCl, 0.1% Triton X-100, 100 μg / ml lysostaphin (Ambi), 500 µg / ml RNaseA, complete mini protease inhibitor EDTA free containing 100 um zirconium beads) and incubated for 20 min at 37°C. The weakened cells were then disrupted using bead beating at 6000 rpm for 1 min and the cell lysate clarified by centrifugation (20,000xg/10min/4°C). The cation concentration of the lysate was adjusted with MgCl2 and CaCl2 to 100 mM. The DNA was sheared by the addition of a range of DNase I (NEB) concentrations (2 – 0.5 U), in a 200 uL volume, followed by incubation at 37°C for 10 min. The reaction was quenched by the addition of EDTA to 50 mM on ice. The degree of DNA fragmentation was assessed by electrophoresis of samples on a 2% (v/v) agarose TAE gel.
Samples showing maximal fragmentation at between 100-300 bp were subjected to immunoprecipitation. Lysis buffer (made up to 4 ml - omitting lysostaphin and RNaseA) containing 10 µg of M2-anti FLAG antibody was added and incubated overnight at 4°C on a rotating platform in a 15 ml tube. A 100 ul of Protein G agarose (Pierce) was added to the lysate and incubated a further 2h at room temperature. The sample was centrifuged (2,500 xg/3 min/22°C) and the agarose pellet washed three time with 4 ml of IP buffer (25mM Tris.Cl [pH 7.2}, 150mM NaCl) and finally resuspended in 200 ul of elution buffer (10mM Tris.Cl [pH 8], 1mM EDTA, 1% SDS containing 100µg of proteinase K). Crosslinks were reversed incubation for 2 h at 37°C and then 9 h at 65°C with shaking at 1400 rpm. Finally, eluted DNA was cleaned up by PCR purification (QiaQuick PCR purification kit, Qiagen). DNA libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and sequenced using an Illumina MiSeq.

treatment_protocol: Grown to an OD600nm of 0.5, induced with 100 ng/ml of anhydrotetracycline and grown for a further hour.

tag: chip antibody

value: anti-FLAG antibody

tag: culture medium

value: LB broth

tag: growth temp

value: 100 ng/ul aTc


title: HptR-all


title: Serum Healthy patient 2


title: IgM_NOD_IMQ-1

description:
raw data file:
IgM_Slide1_635.gpr

value: Serum

value: imiquimod (Imq)


title: B2: Lyve1-Wnt2/9b (sub-slide 2)

description:
SAMPLE 5
liver slide


title: VraR-all


title: Serum Healthy patient 1


title: IgM_NOD_Con-5

description:
raw data file:
IgM_Slide1_635.gpr

value: control


title: SaeR-all


title: IgM_NOD_Con-4

description:
raw data file:
IgM_Slide1_635.gpr


title: N1_N3_rep1

value: hypoxia with subsequent re-exposure to normoxia for 3 days


title: IgM_NOD_Con-3

description:
raw data file:
IgM_Slide1_635.gpr


title: N14_N7_rep1

value: hypoxia with subsequent re-exposure to normoxia for 14 days

value: hypoxia with subsequent re-exposure to normoxia for 7 days


title: N14_N7_rep2


title: N7_N14_rep2


title: IgM_NOD_Con-1

description:
raw data file:
IgM_Slide1_635.gpr


title: WalR-all


title: IgM_BL-10IMQ-3

description:
raw data file:
IgM_Slide1_635.gpr


title: WalR 10ng/ul ATc

value: 10 ng/ul aTc


title: N7_N14_rep1


title: Liver_oxaliplatin_rep4

city: Wuhan

first: xinwei

last: CHENG

state: Hubei province

address: No. 1095, Jiefang Avenue

institute: Tongji Hospital, Tongji Medical college, Huazhong University of Science and Technology

description: Gene expression in Oxaliplan-induced HSOS mice

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

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

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

source_name: mice liver,Intraperitoneal injection of oxaliplatin,qw,6w,replicate4

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: oxaliplatin injection


title: N1_N14_rep2


title: Liver_oxaliplatin_rep3

source_name: mice liver,Intraperitoneal injection of oxaliplatin,qw,6w,replicate3

value: male


title: Liver_oxaliplatin_rep2

source_name: mice liver,Intraperitoneal injection of oxaliplatin,qw,6w,replicate2


title: Liver_control_rep3

description: Gene expression for nomal mice

source_name: mice liver, normal mice,replicate3


title: WalR 50ng/ul ATc

value: 50 ng/ul aTc


title: HptR


title: WalR 100ng/ul ATc


title: WalR 0ng/ul ATc

value: 0 ng/ul aTc


title: IgM_NOD_Con-2

description:
raw data file:
IgM_Slide1_635.gpr


title: N1_H_rep2

value: hypoxia


title: N1_N14_rep1

value: hypoxia with subsequent re-exposure to normoxia for 1 day


title: IgM_BL-10IMQ-2

description:
raw data file:
IgM_Slide1_635.gpr


title: Liver_control_rep1

description: Gene expression for nomal mice

source_name: mice liver, normal mice,replicate1

value: liver


title: Liver_control_rep2

description: Gene expression for nomal mice

source_name: mice liver, normal mice,replicate2


title: N14_N1_rep1

value: Lung vasculature


title: N1_H_rep1


title: Liver_oxaliplatin_rep1

source_name: mice liver,Intraperitoneal injection of oxaliplatin,qw,6w,replicate1


title: WalR

value: anti-FLAG antibody

value: LB broth


title: IgM_BL-10IMQ-1

description:
raw data file:
IgM_Slide1_635.gpr

value: Serum


title: IgM_BL-10Con-1

description:
raw data file:
IgM_Slide1_635.gpr


title: 8rexDeletion_Hi-C

data_processing:
Libraries were sequenced with Illumina's HiSeq 4000 Platform using 100 bp paired end reads. Reads were mapped to the ce11 reference genome, binned at 50 kb, and iteratively corrected using scripts derived from those available at https://bitbucket.org/mirnylab/hiclib as in Brejc et al 2017. For genotypes with two replicates, interaction frequencies after iterative correction from the two replicates were combined. To quantify TAD boundaries, we calculated insulation scores from the Hi-C interaction data as in Crane et al 2015 using the following parameters: insulation square 500000, insulation delta span 200000, insulation mode mean, and noise threshold 0.1. To correct for experimental variation in the decay of chromatin contacts with genomic distance, we calculated Hi-C Z scores using a LOESS method (Imakaev et al 2012) with scripts available at https://github.com/dekkerlab/cworld-dekker
genome build/assembly: e11
.matrix files are tab-delimited tables of genome-wide interaction frequencies iteratively corrected and normalized for read depth as in Crane et al 2015.
.zScore.matrix files are tab-delimited tables of Z scores.
.insulation files give the insulation score and delta vector for each 50 kb bin in the genome, as defined in Crane et al 2015

source_name: mixed stage embryos

extract_protocol: Wild-type and rex site deletion and insertion worms were grown on NGM plates with HB101 bacteria, and sdc-2(y93) worms were grown on RNAi plates with HT115 bacteria carrying an sdc-2 (RNAi) plasmid. Mixed stage embryos were isolated by bleaching. We isolated nuclei, digested with DpnII restriction enzyme, filled in the restriction overhangs with biotinylated nucleotides, and ligated as in Brejc et al 2017. We purfied, sheared, and size-selected DNA and pulled down biotinylated fragments as in Brejc et al 2017. We performed end repair, A-tailing, ligation of NEXTflex DNA Barcodes, and amplification as in Brejc at al 2017.

value: mixed stage embryos

tag: cell line

value: embryo


title: 8rexDeletionPlusrex-32_Hi-C


title: IgM_BL-10Con-3

description:
raw data file:
IgM_Slide1_635.gpr

value: control


title: H_N_rep1

value: normoxia


title: VraR

value: 100 ng/ul aTc


title: H_N1_rep1


title: IgM_BL-10Con-2

description:
raw data file:
IgM_Slide1_635.gpr


title: Liver_control_rep4

description: Gene expression for nomal mice

source_name: mice liver, normal mice,replicate4


title: 8rexDeletionPlusrex-40_Hi-C


title: Plasma Healthy patient 7

source_name: peripheral blood plasma exosomes


title: H_N14_rep1

source_name: H

value: hypoxia with subsequent re-exposure to normoxia for 14 days


title: H_N14_rep3


title: 8rexDeletionPlusrex-23_Hi-C


title: H_N14_rep2