title: Alox12b fl/fl biological rep.2

description: Gene expression data from mouse epidermis control (unaffected Alox12b)

source_name: epidermis,  tamoxifen-treated control, biological rep.2

label_protocol: Biotin-labeled single-stranded cRNA was generated from 100 ng of total RNA isolated from epidermal sheets by using the Affymetrix Gene Chip 3´IVT PLUS Reagent kit. 11 ng of fragmented and labeled cRNA were hybridized for 17 hours at 45°C on Affymetrix GeneChip® Mouse Genome U430 2.0 arrays.

growth_protocol: Mice with a tamoxifen-inducible epidermis-specific inactivation of Alox12b (Alox12bfl/fl/K14Cre; genotype: p/p +/Cre) were generated by crossing mice homozygous for a LoxP-flanked Alox12b allele (Alox12bfl/fl; genotype: p/p +/+) with mice that express the tamoxifen-dependent Cre-ERT2 recombinase driven by the cytokeratin K14 promoter. The mice were backcrossed into the hairless SKH1 background for 5 generations. For the experiment Alox12bfl/fl/K14Cr and Alox12bfl/fl mice as controls were grown to the age of 8 weeks.

extract_protocol: Skin of sacrificed animals was extended on paper and immediately frozen in liquid nitrogen. The epidermis was separated from the dermis by scratching. Total RNA samples were extracted from epidermal sheets using Precellys Lysing kits and RNeasy Mini kits.

treatment_protocol: Alox12b inactivation was induced in Alox12bfl/fl/K14Cre mice by three intraperitoneal injections of 1 mg tamoxifen in 100 µl sunflower seed oil per injection. Homozygous floxed littermates (Alox12bfl/fl) treated in parallel served as controls.

tag: genotype

tag: phenotype

value: control


title: macrophage_CpG ODN1826 stimulated_16h

status: Public on Mar 01 2019

type: RNA

city: Changsha

first: ying

last: zheng

state: Hunan

address: 139 Renmin Middle Rd

country: China

institute: The second Xiangya Hospital of Central South University

description: lncRNAs and mRNAs expression at 16h following stimulation of CpG ODN1826 in RAW264.7

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

molecule: total RNA

organism: Mus musculus

source_name: RAW264.7_CpG ODN1826 stimulated_16h

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The mouse macrophage cell line RAW264.7 was cultured in Dulbeccco’s modified Eagles’ Dedium (DMEM) (Gibco Laboratories, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA), at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop.

treatment_protocol: The RAW264.7 cells were treated with 1 μM ODN1826. At oh, 4h, 8h, or 16h after stimulation of CpG ODN, the cells were harvested for RNA isolation.

tag: cell line

tag: cell type

value: mouse macrophage cell line

tag: treatment

value: 1 μM ODN1826

tag: time point

value: 16h after stimulation


title: Alox12b fl/fl biological rep.3

city: Heidelberg

first: Thomas

last: Hielscher

address: INF 280

department: Biostatistics

country: Germany

institute: German Cancer Research Center

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The data were analyzed with R/Bioncoductor, using rma (affy package) as normalization method with default settings. Control probes were removed.

label: biotin

source_name: epidermis,  tamoxifen-treated control, biological rep.3


title: macrophage_CpG ODN1826 stimulated_4h

description: lncRNAs and mRNAs expression at 4h following stimulation of CpG ODN1826 in RAW264.7

source_name: RAW264.7_CpG ODN1826 stimulated_4h

value: 4h after stimulation


title: SCC Replicate 4

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: The RNA was extracted from the whole lung tumor.

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using OmicSoft Array Studio (Version 9.0) software.

source_name: lung tumor

label_protocol: Starting with 400ng of total RNA, Cy3 labeled cRNA was produced following the manufacturer’s protocol.

growth_protocol: The mice wre bred in mouse facility following animal protocol approved by NIEHS and Baylor College of Medicine

extract_protocol: Total RNAs were isolated from mouse lungs or lung tumors using TRIzol reagent (Invitrogen) and cleaned by RNeasy kit (QIAGEN, 74104).

treatment_protocol: There is no special treatment for these mice.

tag: strain

tag: age

value: 13 months

tag: genotype/variation


title: Alox12b fl/fl biological rep.4

source_name: epidermis,  tamoxifen-treated control, biological rep.4


title: WHIM2 Liver Metastasis from mouse 100091

type: SRA

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

country: USA

institute: Virginia Commonwealth University

description:
Tissue from liver metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Liver.Met.100091

library_source: transcriptomic

data_processing:
Alignment: STAR v2.5.2b was used for alignment with the following settings: --outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1
Read Counting: Salmon v0.8.2 was used for counting reads with the "quant" algorithm and library type set to "IU" using the transcriptome output of STAR.
TPM Calculations: TPM values were calculated using a custom in-house script from the raw read counts and transcript lengths provided by Salmon.  TPM values are raw and have not been log2 transformed or further processed in any way.
Genome_build: A custom reference genome was built by concatenating the following three genome builds: GRCh38 human genome from the Genomic Data Commons (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files), GRCm38 M12 Gencode release of the Mouse genome (http://www.gencodegenes.org/mouse_releases/12.html), and the Xenotropic murine leukemia virus accession JF274252.1 (https://www.ncbi.nlm.nih.gov/nuccore/JF274252.1).  Prior to concatenation, human chromosomes were concatenated with "HUMAN_" and mouse chromosomes were concatenated with "MOUSE_".
Supplementary_files_format_and_content: The processed data files contain the output from Salmon and include Salmon calculated TPM, gene lengths, and raw counts for the human and mouse genomes.

organism:
Homo sapiens
Mus musculus

source_name: Liver, Human xenograft, Mus musculus

growth_protocol: PDX cells were grown in various organs in NSG mice

extract_protocol:
RNA was harvested from tissue/cell samples using the Qiagen Rneasy Mini Kit.
KAPA Stranded mRNA-Seq Kit was used for library preparation.

treatment_protocol: All samples are untreated and all tissues flash frozen during extraction

tag: histologic subtype

value: Liver metastasis

tag: intrinsic subtype

tag: model type

value: Patient-derived xenograft

tag: pdx model


title: macrophage_CpG ODN1826 stimulated_8h

description: lncRNAs and mRNAs expression at 8h following stimulation of CpG ODN1826 in RAW264.7

source_name: RAW264.7_CpG ODN1826 stimulated_8h

value: 8h after stimulation


title: WHIM2 Liver Metastasis from mouse 100086

description:
Tissue from liver metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Liver.Met.100086


title: SCC Replicate 2


title: WHIM2 Liver Metastasis from mouse 100084

description:
Tissue from liver metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Liver.Met.100084


title: UCD52 Mammary Gland Tumor from Liver Metastasis from mouse 102042

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.MGT.FromLiverMet.102042

source_name: Mammary Gland, Human xenograft, Mus musculus

value: Mammary gland tumor grown from liver metastasis

value: Basal


title: UCD52 Mammary Gland Tumor from Liver Metastasis from mouse 102046

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.MGT.FromLiverMet.102046


title: SCC Replicate 1


title: UCD52 Mammary Gland Tumor from mouse 100916

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.MGT.100916

value: Mammary gland tumor


title: Alox12b fl/fl Cre biological rep.5

description: Gene expression data from mouse epidermis upon tamoxifen-induced Alox12b inactivation

source_name: epidermis, upon tamoxifen-induced Alox12b inactivation, biological rep.5

value: p/p +/cre

value: diseased


title: Alox12b fl/fl biological rep.1

source_name: epidermis,  tamoxifen-treated control, biological rep.1


title: Alox12b fl/fl Cre biological rep.4

source_name: epidermis, upon tamoxifen-induced Alox12b inactivation, biological rep.4


title: Alox12b fl/fl Cre biological rep.3

source_name: epidermis, upon tamoxifen-induced Alox12b inactivation, biological rep.3


title: UCD52 Mammary Gland Tumor from Liver Metastasis from mouse 102043

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.MGT.FromLiverMet.102043


title: UCD52 Mammary Gland Tumor from mouse 100775

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.MGT.100775


title: WT Replicate 4

description: The RNA was extracted from the whole lung.

source_name: Lung

value: wild type (Lkb1f/f)


title: SCC Replicate 3


title: macrophage_CpG ODN1826 stimulated_0h

description: lncRNAs and mRNAs expression at 0h following stimulation of CpG ODN1826 in RAW264.7

source_name: RAW264.7_CpG ODN1826 stimulated_0h

value: 0h after stimulation


title: UCD52 Mammary Gland Tumor from mouse 100304

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.MGT.100304


title: UCD52 Mammary Gland Tumor from mouse 100302

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.MGT.100302


title: BM_54-31+_Rep2

city: Marseille

first: Stéphane

middle: JC

last: Mancini

address: 27 Boulevard Lei Roure

department: Centre de Recherche en Cancérologie de Marseille

country: France

institute: INSERM

hyb_protocol: cDNAs were hybridized for 16 hours at 45°C on GeneChip Mouse Gene 430 2.0 arrays (Affymetrix). The chips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Chips were scanned with the GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm

data_processing: The data were processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms.

source_name: bone marrow

label_protocol: Biotinylated double strand cDNA targets were prepared starting from total RNA (unknown quantity from 1800 to 10 000 sorted cells), using the Ambion MessageAmp II aRNA amplification kit

extract_protocol: mRNA extraction was performed using the RNeasy plus micro kit (Qiagen)

value: wild type

value: young adults

value: bone marrow endothelial cells


title: WT Replicate 1


title: WT Replicate 5


title: Alox12b fl/fl Cre biological rep.2

source_name: epidermis, upon tamoxifen-induced Alox12b inactivation, biological rep.2


title: UCD52 Mammary Gland Tumor from mouse 100303

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.MGT.100303


title: UCD52 Mammary Gland Tumor from mouse 100917

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.MGT.100917


title: WT Replicate 3


title: UCD52 Liver Metastasis from mouse 100889

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.Liver.Met.100889


title: BM_54-31+_Rep1


title: UCD52 Liver Metastasis from mouse 100888

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.Liver.Met.100888


title: UCD52 Liver Metastasis from mouse 100887

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.Liver.Met.100887


title: UCD52 Liver Metastasis from mouse 100425

description:
Tissue from liver metastasis from Cardiac Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.Liver.Met.100425


title: 3152086_Bone Marrow_TimePoint5

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
E06M99FGMmKnXXBM_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E06M99FGMmKnXXBM_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v2.7.7) with default parameters. Illumina bcl2fastq v2.17.1.14 was used for demultiplexing. FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
Reads were mapped to a composite reference assembly consisting of host, parasite, and ERCC control references with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues).  The MacaM assembly and annotation has been deposited in GenBank under BioProject accession  PRJNA214746. Parasite: Plasmodium knowlesi PK1 (A+) Malayan H strain  genome assembly and annotation was used. The assembly has been deposited in GenBank under the BioProject accession PRJNA377737.
Supplementary_files_format_and_content: Excel files contain raw counts at the gene level, for each individual. Raw counts are further classified by experimental Time Point and Specimen Type.    Note that in addition to raw counts, normalized data are available as supplementary files as described in the supplementary file E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt.  Normalized results contain data from from 2 experiments, this one (E06) and another known within MaHPIC as 'E30'.  See http://plasmodb.org/plasmo/mahpic.jsp for details on E30, which is also available in GEO and SRA.
Supplementary_files_format_and_content: Host and Parasite Raw Read Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Sample Identifier / Raw file list / Abundances': The raw file names and sample identifers both contain information regarding Specimen Type, NHP ID, and Time Point.  Abundances measures are from the raw files listed.     Example Notes:  There are 12 columns representing 2 animals for Time Points T01-T05 and Necropsy.    There is a read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0.

organism:
Plasmodium knowlesi
Macaca mulatta

source_name: Bone Marrow

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
RNASeq data for this experiment was produced across three specimen types: venous whole blood (WB), bone marrow (BM), and spleen tissue (SP).  Samples were collected using RNAlater (SP), and PAXgene (WB, BM) sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq3000 at the Yerkes Genomics Core, aiming for 50 million paired-end 100 base pair (bp) reads per library.
RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples."

treatment_protocol: Telemetry devices (DSI, model L11) with blood pressure sensors and electrocardiogram (ECG) leads were surgically implanted in four malaria-naive male rhesus macaques (Macaca mulatta), approximately five years of age.  After a resting period of two weeks, physiological data that include activity, temperature, ECG, and blood pressure were continuously collected. Two weeks after activation of the telemetry implant, the macaques were inoculated intravenously with cryopreserved P. knowlesi Malayan strain salivary gland sporozoites, obtained from Anopheles dirus infected with parasites from the Pk1A+ clone and previously tested in E30 for their infectivity of macaques. The sporozoite stocks used were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention, and then stored at Yerkes. After inoculation, the macaques were profiled longitudinally for clinical, hematological, parasitological, immunological, functional genomic, proteomic, and metabolomic measurements. The experiment was designed with pathology studies and thus terminal necropsies, which were scheduled at the log phase of the infections or at the peak of parasitemias. Capillary blood samples were collected daily for the measurement of complete blood counts, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomics analyses. Venous blood and bone marrow samples were collected at five timepoints for functional genomic, targeted proteomic, targeted metabolomics, and immunological analyses. Physiological data noted above were continuously captured via the implanted telemetry devices.  Within the MaHPIC, this project is known as ‘Experiment 06’. This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel, and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from E06 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp.  This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and the MRMC Office of Research Protection Animal Care and Use Review Office (ACURO).     During the 55-day period subjects experienced log phase infection.     Samples were collected either daily for select specimen types or on clinically determiend time point days. Time points were planned based on the expected progression of infection.  Sample collection at time points was planned to coincide with this expected clinical progression.  However, because of individual variations in the clinical progression of infection for each NHP the clinically defined stage of infection may differ between NHPs at the same time point.  For this reason it is imortant for anyone consuming these data to be aware of any differences between the 'Idealized' and 'Actual' disease progression for each NHP and the corresponding clinical stage of each NHP at each time point when samples were collected.  For this reason the supplementary file E06M99MEMmKnXXZZ_Supporting-Clinical-Information_MULTIPL.pdf is provided to clarify both the 'Idealized' or planned collection of time point samples and the clinically-defined 'Actual' disease progression for each NHP.  Anyone consuming these data should use this information to ensure they are aware of the clinical state of each NHP at each time point and be aware of differences between NHPs.  Time Point 1 = Baseline 1 (Pre-implant) - Pre-telemetry device implantation baseline control. Served as control and a comparison for the rest of the experiment. NHPs had not undergone surgery for telemetry implantation and were not infected with P. knowlesi.        Time Point 2 = Baseline 2 (Post-implant) - Post-telemetry device implantation baseline control. TP2 occurred 20 days after telemetry device implantation and device activation. NHPs were not yet infected with P. knowlesi.     Time Point 3 = Post-inoculation / Early infection - Post-inoculation with cryopreserved sporozoites. TP3 occurred 3 days after inoculation.  Time point was representative of the liver stage infection.         Time Point 4 = Log I - Log phase/ pre-peak phase. This time point was intended to examine responses prior to the peak of parasitemia. Activation at cellular and immune levels as well as differential telemetry results compared to baseline readings was expected.  Parasitemia of ~100-10,000/ul was expected.        Time Point 5 = Log II - This time point was intended to examine the response of the immune system and metabolism of the host during the peak of infection when the NHP was experiencing clinical signs of the disease that should be severe in rhesus macaques infected with P. knowlesi.          Necropsy - Terminal endpoint. Necropsy dates were staggered following either timepoint 4 or timepoint 5.     Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt

tag: collection time point (#) or necropsy

tag: gender

value: Male

tag: non human primate individual id

tag: tissue

value: Bone Marrow


title: Alox12b fl/fl Cre biological rep.1

source_name: epidermis, upon tamoxifen-induced Alox12b inactivation, biological rep.1

tag: genotype


title: BM_54+31-BP1+_Rep3

value: bone marrow stromal cells


title: UCD52 Liver Metastasis from mouse 100422

description:
Tissue from liver metastasis from Cardiac Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.Liver.Met.100422


title: BM_54-31+_Rep3


title: UCD52 Liver Metastasis from mouse 100420

description:
Tissue from liver metastasis from Cardiac Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.Liver.Met.100420


title: UCD52 Brain Metastasis from mouse 100422

description:
Tissue from brain metastasis from Cardiac Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD52.Brain.Met.100422

source_name: Brain, Human xenograft, Mus musculus

value: Brain metastasis


title: 3152068_Whole blood_TimePoint5

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
E06M99FGMmKnXXWB_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E06M99FGMmKnXXWB_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

source_name: Whole blood

value: Whole blood


title: UCD18 Mammary Gland Tumor from mouse 102009

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
UCD18.MGT.102009

value: Patient-derived xenograft


title: 3151980_Bone Marrow_TimePoint5


title: WT Replicate 2

value: 13 months


title: BM_54+31-BP1+_Rep4


title: BM_54+31-BP1+_Rep2


title: BM_54+31-BP1+_Rep1


title: HCI16 Mammary Gland Tumor from mouse 100358

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI16.MGT.100358


title: 3151538_Spleen_Necropsy

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
E06M99FGMmKnXXSP_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E06M99FGMmKnXXSP_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

source_name: Spleen

value: Necropsy

value: Spleen


title: 3151962_Whole blood_TimePoint5


title: 3151409_Whole blood_Necropsy


title: HCI13 Mammary Gland Tumor from mouse 100822

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI13.MGT.100822

value: Mammary gland tumor

value: LumB


title: HCI10 Mammary Gland Tumor from Liver Metastasis from mouse 100574

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.MGT.FromLiverMet.100574

value: Mammary gland tumor grown from liver metastasis

value: Basal


title: 3151212_Spleen_Necropsy


title: 3151426_Bone Marrow_Necropsy


title: 3151083_Whole blood_Necropsy


title: 3150886_Spleen_Necropsy


title: HCI10 Mammary Gland Tumor from mouse 100277

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.MGT.100277


title: HCI10 Mammary Gland Tumor from mouse 100276

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.MGT.100276


title: 3150774_Bone Marrow_Necropsy


title: HCI10 Lung Metastasis from mouse 100281

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.Lung.Met.100281

source_name: Lung, Human xenograft, Mus musculus

value: Lung metastasis


title: HCI10 Liver Metastasis from mouse 100282

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.Liver.Met.100282

source_name: Liver, Human xenograft, Mus musculus

value: Liver metastasis


title: 3150757_Whole blood_Necropsy


title: 3150560_Spleen_Necropsy


title: 3150448_Bone Marrow_Necropsy


title: 3150431_Whole blood_Necropsy


title: HCI10 Liver Metastasis from mouse 100276

description:
Tissue from liver metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.Liver.Met.100276


title: HCI10 Liver Metastasis from mouse 100281

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.Liver.Met.100281


title: 3148910_Bone Marrow_TimePoint4


title: HCI10 Liver Metastasis from mouse 100208

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.Liver.Met.100208


title: HCI10 Brain Metastasis from mouse 100282

description:
Tissue from brain metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.Brain.Met.100282


title: sample57: post+WO+dex

type: genomic

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: HPC treated with dex at post+WO

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalize the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 25% of the samples.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: HPC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

value: dex

value: post+WO

tag: cell vial


title: 3148892_Whole blood_TimePoint4

value: Male


title: 3148804_Bone Marrow_TimePoint4

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
E06M99FGMmKnXXBM_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E06M99FGMmKnXXBM_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

value: Bone Marrow


title: sample55: post+WO+dex

description: HPC treated with dex at post+WO


title: HCI10 Brain Metastasis from mouse 100208

description:
Tissue from brain metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI10.Brain.Met.100208


title: sample50: pro-diff+dex

description: HPC treated with dex at pro-diff

value: pro-diff


title: sample59: post+WO+veh

description: HPC treated with veh at post+WO

value: veh


title: sample60: post+WO+dex

description: HPC treated with dex at post+WO


title: HCI09 Mammary Gland Tumor from Liver Metastasis from mouse 102018

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.MGT.FromLiverMet.102018

source_name: Mammary Gland, Human xenograft, Mus musculus


title: 3148786_Whole blood_TimePoint4

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
E06M99FGMmKnXXWB_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E06M99FGMmKnXXWB_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

value: Whole blood


title: HCI09 Mammary Gland Tumor from Liver Metastasis from mouse 102016

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.MGT.FromLiverMet.102016

value: Patient-derived xenograft


title: sample53: post+WO+veh

description: HPC treated with veh at post+WO


title: 3148680_Whole blood_TimePoint4


title: sample54: pro+vehs

description: HPC treated with vehs at pro

value: vehs

value: pro


title: sample58: pro+vehs

description: HPC treated with vehs at pro


title: HCI09 Mammary Gland Tumor from mouse 100512

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.MGT.100512


title: HCI09 Mammary Gland Tumor from Liver Metastasis from mouse 102015

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.MGT.FromLiverMet.102015


title: 3148698_Bone Marrow_TimePoint4


title: sample51: pro-diff+dex

description: HPC treated with dex at pro-diff


title: sample52: pro+vehs

description: HPC treated with vehs at pro


title: sample48: pro-diff+veh

description: HPC treated with veh at pro-diff


title: 3148592_Bone Marrow_TimePoint4


title: sample45: pro-diff+veh

description: HPC treated with veh at pro-diff

tag: cell line

value: immortalized, multipotent human fetal HPC line HPC03A/07


title: 3148574_Whole blood_TimePoint4


title: 3139445_Bone Marrow_TimePoint3


title: HCI09 Mammary Gland Tumor from mouse 100511

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.MGT.100511

value: Mammary gland tumor

value: LumA


title: sample49: pro-diff+veh

description: HPC treated with veh at pro-diff


title: HCI09 Mammary Gland Tumor from mouse 100241

description:
Tissue from mammary tumors grown in mice (post FACS)
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.MGT.100241

value: LumB


title: 3139427_Whole blood_TimePoint3


title: HCI09 Lung Metastasis from mouse 100453

description:
Tissue from lung metastasis from Liver Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Lung.Met.100453


title: HCI09 Mammary Gland Tumor from mouse 100508

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.MGT.100508


title: 3139339_Bone Marrow_TimePoint3


title: sample47: pro-diff+dex

description: HPC treated with dex at pro-diff


title: sample46: pro-diff+dex

description: HPC treated with dex at pro-diff


title: sample56: post+WO+veh

description: HPC treated with veh at post+WO


title: HCI09 Lung Metastasis from mouse 100359

description:
Tissue from lung metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Lung.Met.100359


title: sample43: pro-diff+dex

description: HPC treated with dex at pro-diff


title: 3139233_Bone Marrow_TimePoint3


title: sample44: pro-diff+veh

description: HPC treated with veh at pro-diff


title: HCI09 Lung Metastasis from mouse 100212

description:
Tissue from lung metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Lung.Met.100212


title: 3139215_Whole blood_TimePoint3


title: sample41: pro-diff+veh

description: HPC treated with veh at pro-diff


title: sample42: pro-diff+dex

description: HPC treated with dex at pro-diff


title: HCI09 Liver Metastasis from mouse 100714

description:
Tissue from liver metastasis from portal vein injection
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Liver.Met.100714


title: sample40: pro-diff+veh

description: HPC treated with veh at pro-diff


title: HCI09 Liver Metastasis from mouse 100696

description:
Tissue from liver metastasis from portal vein injection
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Liver.Met.100696


title: 3139127_Bone Marrow_TimePoint3


title: sample37: pro+dexs

description: HPC treated with dexs at pro

value: dexs


title: sample38: pro+dexs

description: HPC treated with dexs at pro


title: sample36: pro+dexs

description: HPC treated with dexs at pro


title: HCI09 Liver Metastasis from mouse 100489

description:
Tissue from liver metastasis from portal vein injection
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Liver.Met.100489


title: sample39: pro+dexs

description: HPC treated with dexs at pro


title: HCI09 Liver Metastasis from mouse 100455

description:
Tissue from liver metastasis from liver injection
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Liver.Met.100455


title: HCI09 Liver Metastasis from mouse 100454

description:
Tissue from liver metastasis from liver injection
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Liver.Met.100454


title: 3118576_Whole blood_TimePoint2


title: HCI09 Liver Metastasis from mouse 100453

description:
Tissue from liver metastasis from liver injection
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Liver.Met.100453


title: 3139109_Whole blood_TimePoint3


title: 3118594_Bone Marrow_TimePoint2

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
E06M99FGMmKnXXBM_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E06M99FGMmKnXXBM_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx


title: HCI09 Brain Metastasis from mouse 100503

description:
Tissue from brain metastasis from Cardiac Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI09.Brain.Met.100503

value: Brain metastasis


title: 3118470_Whole blood_TimePoint2

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
E06M99FGMmKnXXWB_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E06M99FGMmKnXXWB_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx


title: sample35: pro+dexs

description: HPC treated with dexs at pro


title: 3118488_Bone Marrow_TimePoint2


title: HCI08 Mammary Gland Tumor from mouse 100879

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI08.MGT.100879


title: 3118382_Bone Marrow_TimePoint2


title: 22Rv1_siOCT1_DHT

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

description: Gene expression data from 22Rv1 cells  treated with DHT 10 nM after trasfected with siOCT1

hyb_protocol: The samples were hybridized to Human Clariom S-arrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: prostate cancer

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: 22Rv1 cells were cultures in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with each siRNA 48 h before hormone treatment. Cells were treated with vehicle or dihydrotestosterone (DHT) (10 nM) for 24 h.

tag: sirna

tag: ligand

value: DHT 10 nM


title: sample31: pro+vehs

description: HPC treated with vehs at pro

tag: treatment

tag: time point


title: HCI04 Mammary Gland Tumor from mouse 100763

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI04.MGT.100763

value: Basal


title: sample29: pro-diff+WO+dex

description: HPC treated with dex at pro-diff+WO

value: dex

value: pro-diff+WO


title: 3118364_Whole blood_TimePoint2

value: Male


title: 3107395_Bone Marrow_TimePoint1

value: Bone Marrow


title: HCI03 Mammary Gland Tumor from mouse 102031

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI03.MGT.102031


title: HCI02 Mammary Gland Tumor from mouse 100948

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI02.MGT.100948


title: 22Rv1_siControl_Veh

description: Gene expression data from 22Rv1 cells treated with vehicle (ethanol) after transfected with siControl

value: siControl

value: Vehicle


title: 22Rv1_siOCT1_Veh

description: Gene expression data from 22Rv1 cells treated with vehicle (ethanol) after trasfected with siOCT1


title: 22Rv1_siControl_DHT

description: Gene expression data from 22Rv1 cells treated with DHT 10 nM after transfected with siControl


title: 3118682_Whole blood_TimePoint2

value: Whole blood


title: sample28: pro-diff+WO+veh

description: HPC treated with veh at pro-diff+WO

value: veh


title: HCI02 Mammary Gland Tumor from mouse 100945

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI02.MGT.100945

value: Patient-derived xenograft


title: HCI02 Mammary Gland Tumor from mouse 100946

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI02.MGT.100946


title: 3107298_Bone Marrow_TimePoint1


title: sample32: pro+vehs

description: HPC treated with vehs at pro

value: immortalized, multipotent human fetal HPC line HPC03A/07

value: vehs

value: pro


title: sample30: pro-diff+WO+dex

description: HPC treated with dex at pro-diff+WO


title: siERK3 3

city: Dayton

first: Michael

last: Markey

state: OH

address: 3640 Colonel Glenn Hwy.

department: Biochemistry and Molecular Biology

institute: Wright State Unviersity

hyb_protocol: Samples were hybridized with Human Clariom S microarrays (Affymetrix) and scanned at the WSU Center for Genomics Research Core Facility.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 according to the manufacturer's instruction (Affymetrix).

data_processing: The array CEL files were acquired using Affymetrix Command Console (AGCC version 4.1). CHP files were generated using Affymetrix Transcriptome Analysis Software v4.0.

source_name: A375 cell line

label_protocol: As per manufacturer (Afftmetrix)

growth_protocol: A375 cells were maintained in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics penicillin-streptomycin.

extract_protocol: Total RNA of each cell line was extracted using Trizol® reagent (Ambion).

treatment_protocol: DharmaFECT Transfection Reagent (Dharmacon) was used to transiently knock down  mRNA following the manufacturer’s instructions. siRNA used were:  siERK3 (Ambion Silencer® Select Pre-Designed siRNA);  and Ambion® Silencer® Select Negative Control siRNA).

value: melanoma

tag: sirna target


title: HCI02 Lung Metastasis from mouse 100664

description:
Lung metastasis from mammary tumor
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI02.Lung.Met.100664

value: Lung metastasis

value: Normal


title: 3107280_Whole blood_TimePoint1


title: 3107377_Whole blood_TimePoint1


title: siERK3 2


title: sample21: pro-diff+WO+dex

description: HPC treated with dex at pro-diff+WO


title: sample33: pro+vehs

description: HPC treated with vehs at pro


title: sample25: pro-diff+WO+dex

description: HPC treated with dex at pro-diff+WO


title: HCI02 Lung Metastasis from mouse 100567

description:
Lung metastasis from mammary tumor
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI02.Lung.Met.100567


title: 3107183_Whole blood_TimePoint1


title: 3107201_Bone Marrow_TimePoint1


title: sample20: pro-diff+WO+veh

description: HPC treated with veh at pro-diff+WO


title: HCI02 Lung Metastasis from mouse 100554

description:
Lung metastasis from mammary tumor
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI02.Lung.Met.100554


title: 3107104_Bone Marrow_TimePoint1


title: HCI02 Liver Metastasis from mouse 102021

description:
Liver metatasis from portal vein
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI02.Liver.Met.102021

value: Liver metastasis


title: sample22: pro-diff+WO+dex

description: HPC treated with dex at pro-diff+WO


title: sample24: pro-diff+WO+veh

description: HPC treated with veh at pro-diff+WO


title: sample34: pro+dexs

description: HPC treated with dexs at pro

value: dexs


title: RhpRS-MM-2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
RhpR_and_RhpRS_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas savastanoi pv. phaseolicola 1448A ΔrhpRS in MM

data_processing:
ChIP-seq results were mapped to the Pseudomonas savastanoi pv. phaseolicola 1448A genome (NC_005773.3) by using Bowild-typeie (Version 1.2.1.1).   Only the uniquely mapped reads were kept for the subsequent analyses. Binding peaks (P < 1e-5) were identified using MACS software (version 2.1.0).
Bacterial RNA-seq reads were mapped to the Pseudomonas savastanoi pv. phaseolicola 1448A genome (NC_005773.3) by using STAR, Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0)
Genome_build: Pseudomonas savastanoi pv. phaseolicola 1448A
Supplementary_files_format_and_content: xlsx file containing comparisons between RhpR/RhpR-D70A and control ;xlsx file containing comparisons between  ΔrhpS /ΔrhpRS and wild-type

source_name: liquid culture in minimal medium

growth_protocol: ChIP-(KB or MM with Rif and Spec) ; RNA-seq(KB or MM with Rif)

extract_protocol:
The wild-type, ΔrhpS and ΔrhpRS strains were cultured in KB medium until the OD600 = 0.6 before transferring to MM liquid medium for 6 hours. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4℃). RNA purification was conducted by an RNeasy mini kit (Qiagen). After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext UltraTM II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial RNA-seq reads were mapped to the Pseudomonas savastanoi pv. phaseolicola 1448A genome (NC_005773.3) by using STAR, Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0) . GO enrichment analyses were conducted on all differentially transcribed genes using DAVID .
TruSeq RNA sample prep kit protocol (Illumina)
ChIP-seq:  An empty pHM2, pHM2-rhpRpsph-HA or pHM2-rhpRpsph(D70A)-HA plasmid was transformed into the wild-type or ΔrhpS strain, then cultured in KB medium until the OD600 = 0.6 before transferring to MM liquid medium for 6 hours. The strains were treated with 1% formaldehyde for 10 min at 37℃. Cross-linking was stopped by the addition of 125 mM glycine. The bacteria were centrifugated and the pellets were washed twice with Tris-buffer (20 mM Tris-HCl [pH 7.5], 150 mM NaCl), and then resuspended in 500 μl IP buffer (50 mM HEPES-KOH [pH 7.5], 1 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail). Next, the DNA was subjected to sonication to produce 100 to 300 bp DNA fragments. The insoluble cellular debris was removed by centrifugation at 4℃, and the supernatant was saved as the input sample in the IP experiments. Both the control and IP samples were washed by protein A beads (General Electric) and mixed with 50 μl agarose conjugated anti-HA antibodies (Sigma) in IP buffer. The following washing, crosslink reversal and purification of ChIP-DNA were conducted as previously described. DNA fragments (150 to 250 bp) were selected for library construction, and libraries were constructed by using the NEXTflexTM ChIP-Seq Kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). ChIP-seq results were mapped to the Pseudomonas savastanoi pv. phaseolicola 1448A genome (NC_005773.3) by using Bowild-typeie (Version 1.2.1.1). Only the uniquely mapped reads were kept for the subsequent analyses. Binding peaks (P < 1e-5) were identified using MACS software (version 2.1.0). All the experiments have two repeats and the reported peaks are found in both experiments
RNA-seq:The wild-type, ΔrhpS and ΔrhpRS strains were cultured in KB medium until the OD600 = 0.6 before transferring to MM liquid medium for 6 hours. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4℃). RNA purification was conducted by an RNeasy mini kit (Qiagen). After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext UltraTM II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial RNA-seq reads were mapped to the Pseudomonas savastanoi pv. phaseolicola 1448A genome (NC_005773.3) by using STAR, Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0) . GO enrichment analyses were conducted on all differentially transcribed genes using DAVID .
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)  and TruSeq RNA sample prep kit protocol (Illumina)

treatment_protocol: grow until mid-log phase

value: delta-rhpRS

value: grow until mid-log phase in KB, then transfer to MM for 6 h


title: HCI02 Liver Metastasis from mouse 100664

description:
Liver metatasis from tail vein
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI02.Liver.Met.100664


title: 3107086_Whole blood_TimePoint1

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
E06M99FGMmKnXXWB_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E06M99FGMmKnXXWB_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

value: Male


title: 3151100_Bone Marrow_Necropsy

description:
Please note that the RNASeq data for this experiment was produced across three specimen types (venous whole blood (WB), bone marrow (BM), and spleen tissue (SP)) using RNAlater and PAXgene sample collection and storage technologies.  Please carefully review the two  README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt  E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt
E06M99FGMmKnXXBM_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx, E06M99FGMmKnXXBM_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx

value: Necropsy

value: Bone Marrow


title: RhpRS-MM-1

organism: Pseudomonas savastanoi pv. phaseolicola 1448A


title: sample17: pro-diff+WO+veh

description: HPC treated with veh at pro-diff+WO

value: pro-diff+WO


title: RhpRS-KB-2

description:
RhpR_and_RhpRS_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas savastanoi pv. phaseolicola 1448A ΔrhpRS in KB

source_name: liquid culture in King's B medium

value: grow until mid-log phase in KB


title: sample16: pro-diff+WO+dex

description: HPC treated with dex at pro-diff+WO

value: dex


title: HCI01 Mammary Gland Tumor from Liver Metastasis from mouse 102049

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.MGT.FromLiverMet.102049

value: Mammary gland tumor grown from liver metastasis

value: Basal

value: Patient-derived xenograft


title: siCon 1

value: Control


title: sample23: pro-diff+WO+veh

description: HPC treated with veh at pro-diff+WO

value: immortalized, multipotent human fetal HPC line HPC03A/07

value: veh


title: 3118700_Bone Marrow_2


title: sample27: pro-diff+WO+veh

description: HPC treated with veh at pro-diff+WO


title: HCI01 Mammary Gland Tumor from Liver Metastasis from mouse 102048

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.MGT.FromLiverMet.102048


title: sample26: pro-diff+WO+dex

description: HPC treated with dex at pro-diff+WO


title: HCI01 Mammary Gland Tumor from Liver Metastasis from mouse 102047

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.MGT.FromLiverMet.102047


title: sample18: pro-diff+WO+dex

description: HPC treated with dex at pro-diff+WO


title: RhpS-MM-2

description:
RhpR_and_RhpRS_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas savastanoi pv. phaseolicola 1448A ΔrhpS in MM

value: delta-rhpS


title: HCI01 Mammary Gland Tumor from mouse 101022

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.MGT.101022

value: Mammary gland tumor


title: HCI01 Mammary Gland Tumor from mouse 101021

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.MGT.101021


title: sample15: pro-diff+WO+veh

description: HPC treated with veh at pro-diff+WO


title: siCon 3

value: melanoma


title: RhpS-MM-1


title: siERK3 1


title: RhpS-KB-1

description:
RhpR_and_RhpRS_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas savastanoi pv. phaseolicola 1448A ΔrhpS in KB


title: RhpS-KB-2


title: Kras IKKa low cell, biological rep3

city: Frederick

first: NA-YOUNG

last: SONG

state: MD

address: 1050 Boyles Street

institute: NCI

hyb_protocol: 15 ug of biotinylated cRNA were fragmented and hybridized for 16 hr at 45C on mouse Clariom S Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450,  were scanned using the Affymetrix GeneChip scanner 3000 with AutoLoader.

data_processing:
Data were collected using Affymetrix AGCC software and analyzed using Affymetrix Expression Console.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_S_Mouse
program-name = Expression Console
program-version = 1.4.1.46

source_name: WT C57BL/6 mice injected with Kras IKKa low cells

label_protocol: RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix GeneChip 3'IVT Plus Reagent Kit following manufacturer’s protocol.

growth_protocol: All mice used in this study were cared for in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) of the National Institute of Health (NIH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The mice were intratracheally treated with adeno virus containing cre recombinase. At 4 months post injection, the mice were euthnized and lung tissues were collected.

tag: strain

tag: injected with

value: Kras IKKa low cells

value: 1.5 months after cell injection

value: lung

tag: cell type

value: lung adenocarcinoma-associated CD4+ cells


title: HCI01 Mammary Gland Tumor from mouse 101020

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.MGT.101020

tag: histologic subtype

tag: intrinsic subtype

tag: model type


title: HCI01 Lung Metastasis from mouse 100517

description:
Lung metastasis from mammary tumor
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.Lung.Met.100517

value: Lung metastasis

tag: pdx model


title: Kras IKKa low cell, biological rep2


title: CK-MM-2

description:
RhpR_and_RhpRS_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas savastanoi pv. phaseolicola 1448A wild-type in MM

value: WT

value: grow until mid-log phase in KB, then transfer to MM for 6 h


title: sample19: pro-diff+WO+veh

description: HPC treated with veh at pro-diff+WO

value: pro-diff+WO


title: siCon 2


title: HCI01 Lung Metastasis from mouse 100514

description:
Lung metastasis from mammary tumor
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.Lung.Met.100514


title: CK-MM-1


title: Kras CL cell, biological rep 3

source_name: WT C57BL/6 mice injected with Kras CL cells

value: Kras-CL cells


title: Kras CL cell, biological rep 2


title: Kras IKKa low cell, biological rep1


title: CK-KB-2

description:
RhpR_and_RhpRS_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas savastanoi pv. phaseolicola 1448A wild-type in KB

value: grow until mid-log phase in KB


title: sample11: post+WO+dex

description: HPC treated with dex at post+WO

value: dex

value: post+WO


title: HCI01 Lung Metastasis from mouse 100288

description:
Lung metastasis from mammary tumor
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.Lung.Met.100288

value: Basal

value: Patient-derived xenograft


title: HCI01 Liver Metastasis from mouse 100794

description:
Liver metatasis from portal vein
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.Liver.Met.100794

value: Liver metastasis


title: sample10: post+WO+veh

description: HPC treated with veh at post+WO

value: immortalized, multipotent human fetal HPC line HPC03A/07

value: veh


title: Kras CL cell, biological rep 1


title: RhpR-70A in ΔrhpS-MM-2

library_source: genomic

extract_protocol:
An empty pHM2, pHM2-rhpRpsph-HA or pHM2-rhpRpsph(D70A)-HA plasmid was transformed into the wild-type or ΔrhpS strain, then cultured in KB medium until the OD600 = 0.6 before transferring to MM liquid medium for 6 hours. The strains were treated with 1% formaldehyde for 10 min at 37℃. Cross-linking was stopped by the addition of 125 mM glycine. The bacteria were centrifugated and the pellets were washed twice with Tris-buffer (20 mM Tris-HCl [pH 7.5], 150 mM NaCl), and then resuspended in 500 μl IP buffer (50 mM HEPES-KOH [pH 7.5], 1 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail). Next, the DNA was subjected to sonication to produce 100 to 300 bp DNA fragments. The insoluble cellular debris was removed by centrifugation at 4℃, and the supernatant was saved as the input sample in the IP experiments. Both the control and IP samples were washed by protein A beads (General Electric) and mixed with 50 μl agarose conjugated anti-HA antibodies (Sigma) in IP buffer. The following washing, crosslink reversal and purification of ChIP-DNA were conducted as previously described. DNA fragments (150 to 250 bp) were selected for library construction, and libraries were constructed by using the NEXTflexTM ChIP-Seq Kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). ChIP-seq results were mapped to the Pseudomonas savastanoi pv. phaseolicola 1448A genome (NC_005773.3) by using Bowild-typeie (Version 1.2.1.1). Only the uniquely mapped reads were kept for the subsequent analyses. Binding peaks (P < 1e-5) were identified using MACS software (version 2.1.0). All the experiments have two repeats and the reported peaks are found in both experiments.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)
ChIP-seq:  An empty pHM2, pHM2-rhpRpsph-HA or pHM2-rhpRpsph(D70A)-HA plasmid was transformed into the wild-type or ΔrhpS strain, then cultured in KB medium until the OD600 = 0.6 before transferring to MM liquid medium for 6 hours. The strains were treated with 1% formaldehyde for 10 min at 37℃. Cross-linking was stopped by the addition of 125 mM glycine. The bacteria were centrifugated and the pellets were washed twice with Tris-buffer (20 mM Tris-HCl [pH 7.5], 150 mM NaCl), and then resuspended in 500 μl IP buffer (50 mM HEPES-KOH [pH 7.5], 1 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail). Next, the DNA was subjected to sonication to produce 100 to 300 bp DNA fragments. The insoluble cellular debris was removed by centrifugation at 4℃, and the supernatant was saved as the input sample in the IP experiments. Both the control and IP samples were washed by protein A beads (General Electric) and mixed with 50 μl agarose conjugated anti-HA antibodies (Sigma) in IP buffer. The following washing, crosslink reversal and purification of ChIP-DNA were conducted as previously described. DNA fragments (150 to 250 bp) were selected for library construction, and libraries were constructed by using the NEXTflexTM ChIP-Seq Kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). ChIP-seq results were mapped to the Pseudomonas savastanoi pv. phaseolicola 1448A genome (NC_005773.3) by using Bowild-typeie (Version 1.2.1.1). Only the uniquely mapped reads were kept for the subsequent analyses. Binding peaks (P < 1e-5) were identified using MACS software (version 2.1.0). All the experiments have two repeats and the reported peaks are found in both experiments
RNA-seq:The wild-type, ΔrhpS and ΔrhpRS strains were cultured in KB medium until the OD600 = 0.6 before transferring to MM liquid medium for 6 hours. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4℃). RNA purification was conducted by an RNeasy mini kit (Qiagen). After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext UltraTM II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial RNA-seq reads were mapped to the Pseudomonas savastanoi pv. phaseolicola 1448A genome (NC_005773.3) by using STAR, Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0) . GO enrichment analyses were conducted on all differentially transcribed genes using DAVID .
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)  and TruSeq RNA sample prep kit protocol (Illumina)


title: RhpRS-KB-1

value: delta-rhpRS


title: HCI01 Liver Metastasis from mouse 100757

description:
Liver metatasis from portal vein
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.Liver.Met.100757


title: sample12: post+WO+dex

description: HPC treated with dex at post+WO


title: HCI01 Liver Metastasis from mouse 100672

description:
Liver metatasis from portal vein
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
HCI01.Liver.Met.100672


title: CK-KB-1


title: IMR90 tPBAT Library, NovaSeq

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

description:
IMR90_tPBAT
lung, fibroblast-like cell, 16 week embryo

data_processing:
Reads were mapped on mixed reference of human genome hg19 and lambda phage genome using in-house program BMap.
Alignments exported from BMap were summarized into a binary file in graph format using in-house program MPTC.
The methylation levels and coverage were exported from the file in graph format using in-hose program MethExport.
Genome_build: hg19 (GRCh37) and lambda genome
Supplementary_files_format_and_content: bedGraph

source_name: IMR-90 cell

growth_protocol: Cultured in MEM+10%FBS.

extract_protocol:
Genomic DNA was purified using QIAAmp Mini Kit.
Genomic DNA was treated with bisulfite using Methyl Easy Gold Kit from Zymo Research, then adaptor tagging was performed with tPBAT protocol.

treatment_protocol: Cells were removed from culture flask with Trypsin-EDTA and collected by centrifugation.


title: breast cancer lung metastasis cell line

city: Nanjing

first: shouyu

last: wang

address: 22 Hankou Road

institute: Nanjing university medical school

description: circRNA expression in breast cancer lung metastasis cell line

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 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA 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 using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: Breast tissue, fresh frozen

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). 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 cells cultured in DMEM medium. The media were supplemented with 10% fetal bovine serum (FBS). Cultures were incubated at 37°C in a humidified chamber with 5% CO2.

extract_protocol: Total RNA from each sample using the TRIzol® Plus RNA Purification Kit (Life Technologies, Grand Island NY) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-2000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.


title: breast cancer bone metastasis cell line

description: circRNA expression in breast cancer bone metastasis cell line


title: CTCL-HTO

city: New York

first: Eleni

last: Mimitou

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
antibody oligos
processed data file:
CTCL-HTO-count.csv.gz
CTCL-HTO-count.csv.gz includes: raw counts for 12 bases HTO

data_processing:
Library strategy: ECCITE-seq
10x data were processed using cellranger and cellranger vdj pipeline
R1 includes cell barcode, UMI read
R2 is the  biological read
ADT data were mapped to a 12 bases or a 15 bases reference ADT list separately using CITE-seq-count
HTO data were mapped to a 12 bases reference HTO list using CITE-seq-count
GDO data were mapped to a 19 bases reference GDO list using CITE-seq-count
ADT, HTO and GDO sequence lists are available at: https://www.biorxiv.org/content/10.1101/466466v1
Genome_build: hg19 for human only samples
Genome_build: samples with both human and mouse cells were mapped to the hg19-mm10 concatenated reference as provided by cell-ranger
Supplementary_files_format_and_content: tab-delimited text file for 10x data; comma-delimited file for ADT, HTO, GDO and clonotype mapping

molecule: polyA RNA

source_name: Peripheral blood mononuclear cells

extract_protocol:
‘Stained’ and washed cells were loaded into 10x Genomics single cell 5’ system and processed according to manufacturer’s instructions, and the CITE-seq protocols (Stoeckius et al, 2017). For sgRNA capture a custom RT primer was spiked in during the RT reaction.
library construction was performed with the 10x Genomics single cell 5' (VDJ) product.

treatment_protocol: K562, NIH-3T3 and peripheral blood mononuclear cells (PBMCs) were stained as described for CITE-seq (Stoeckius et al, 2017)

value: Peripheral blood mononuclear cells

tag: antibodies/tag

value: 12 bases tag:hashtag_3, hashtag_4


title: parental cell line

description: circRNA expression in parental cell line


description: circRNA expression in breast cancer brain metastasis cell line


title: sample8: post+WO+dex

description: HPC treated with dex at post+WO


title: RhpR in ΔrhpS- MM-1


title: RhpR in ΔrhpS- MM-2


title: RhpR-70A in ΔrhpS-MM-1


title: CAL_62_THZ1_rep2

city: Tianjin

first: Xinyi

last: Cao

state: Tianjin

address: Tianjin Medical University No.22 Qixiangtai Road

institute: Collaborative Innovation Center of Tianjin for Medical Epigenetics

data_processing:
Low quality reads was filtered using internal software SOAPnuke
Clean reads were mapped to reference using Bowtie2. Only unique mapped reads were used in further analysis.
DEGs (differential expressed genes) between samples were generated by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Anaplastic thyroid carcinoma cells

growth_protocol: BCPAP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. CAL-62 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) medium supplemented with 20% fetal bovine serum (FBS). All cells were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from cultured cells were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

treatment_protocol: BCPAP cells and CAL-62 cells were treated with 100 nM THZ1 for 6 h

tag: tissue

value: Thyroid

tag: tissue type

value: Anaplastic thyroid carcinoma


title: CAL_62_THZ1_rep1


title: sample14: pro-diff+dex

description: HPC treated with dex at pro-diff

value: pro-diff

tag: cell vial


title: CTCL-cDNA

description:
polyA mRNA
processed data file:
CTCL-cDNA.txt.gz
CTCL-cDNA.txt.gz includes: raw counts for RNA
raw data submitted to dbGaP


title: CTCL-ADT

description:
antibody oligos
processed data file:
CTCL-ADT-count.csv.gz
CTCL-ADT-count.csv.gz includes: raw counts for 15 bases ADT

value: 15 bases tag:CD3,CD4,CD8,TCRb,TCRg,CD44,CD62L,Ox40 (CD134), PD1 (CD279), PD-L1,EpCAM (CD326),CD66b,MHCII (HLA-DR),CD45,CD19,B220 (CD45R),CD11c,CD14,CD34,CD56,CD16,CD2,CD5,CD45RA,CD45RO,CCR7,CD11b,CD1a,CD27,CD69,PECAM (CD31),CD138,CD24,Siglec-8,LAMP1,C-kit (CD117),IL7Ralpha (CD127),CTLA4,HLA-A,B,C,CD77,CD366, CD223, CD28, CD7,CD26 (Adenosine), PD-1 (CD279), PD-L1 (CD274), IgG1,IgG2a


title: RhpR-70A  in ΔrhpS-KB-2

tag: genotype


title: ctrl-HTO

description:
antibody oligos
processed data file:
ctrl-HTO-count.csv.gz
ctrl-HTO-count.csv.gz includes: raw counts for 12 bases HTO

value: 12 bases tag:hashtag_3, hashtag_4, hashtag_5, hashtag_6


title: RhpR-70A  in ΔrhpS-KB-1


title: RhpR-HA in ΔrhpS-KB-2


title: sample9: post+WO+veh

description: HPC treated with veh at post+WO

tag: cell line


title: sample6: post+WO+veh

description: HPC treated with veh at post+WO


title: ctrl-ADT

description:
antibody oligos
processed data file:
ctrl-ADT-count.csv.gz
ctrl-ADT-count.csv.gz includes: raw counts for 15 bases ADT


title: BCPAP_THZ1_rep1

value: BCPAP


title: CAL_62_DMSO_rep1

value: DMSO


title: ctrl-cDNA

description:
polyA mRNA
processed data file:
ctrl-cDNA.txt.gz
ctrl-cDNA.txt.gz includes: raw counts for RNA
raw data submitted to dbGaP


title: RhpR-MM-2

value: grow until mid-log phase in KB, then transfer to MM for 6 h


title: sample7: post+WO+dex

description: HPC treated with dex at post+WO

value: dex

value: post+WO


title: RhpR-HA in ΔrhpS-KB-1

value: grow until mid-log phase in KB


title: BCPAP_DMSO_rep2


title: BCPAP_DMSO_rep1


title: RhpR-MM-1


title: sample4: post+WO+dex

description: HPC treated with dex at post+WO


title: Kminus-cDNA

description:
polyA mRNA
processed data file:
Kminus-cDNA.txt
Kminus-cDNA.txt.gz includes: raw counts for RNA


title: K-GDO

description:
sgRNAs
processed data file:
K-GDO-count.csv.gz
K-GDO-count.csv.gz includes: raw counts for 19 bases GDO


title: RhpR-KB-2


title: BCPAP_H3K27ac

data_processing:
ChIP-seq data were mapped to human reference genome (GRCh37/hg19) by SOAPaligner/SOAP2
ChIP-Seq peaks were generated using peak finding algorithm MACS (Model-based Analysis for ChIP -Seq, version: MACS-1.4.2)
Reads mapped only once at locus were allowed for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated by MACS-1.4.2.

growth_protocol: BCPAP  cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. CAL-62 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) medium supplemented with 20% fetal bovine serum (FBS). All cells were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
BCPAP and CAL-62 cells were cross-linked with 1% formaldehyde for 10 min at RT. The crosslink was stopped by adding 1/20 volume of 2.5 M glycine. Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed with H3K27ac antibody (Abcam cat# ab4729). After elution and reversal cross-linking, DNA was purified and sequenced on BGISEQ-500.
Construction of ChIP-seq library was completed by BGI company (Shenzhen,China).

tag: chip antibody

value: H3K27ac (Abcam cat# ab4728)


title: sample2: post+WO+veh

description: HPC treated with veh at post+WO

value: immortalized, multipotent human fetal HPC line HPC03A/07

tag: treatment


title: K-HTO

description:
antibody oligos
processed data file:
K-HTO-count.csv.gz
K-HTO-count.csv.gz includes: raw counts for 12 bases HTO

value: 12 bases tag:hashtag_3, hashtag_5, hashtag_6


title: K-ADT

description:
antibody oligos
processed data file:
K-ADT-count.csv.gz
K-ADT-count.csv.gz includes: raw counts for 12 bases ADT

value: 12 bases tag:hCD29, hCD46


title: RhpR-KB-1


title: sample3: post+WO+dex

description: HPC treated with dex at post+WO

tag: time point


title: sample5: post+WO+veh

description: HPC treated with veh at post+WO

value: veh


title: CK-HA-2


title: CK-HA-1


title: CAL_62_H3K27ac


title: CAL_62_Input


title: WT

status: Public on Feb 28 2019

city: Boston

first: Niklas

last: Krupka

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine - Gastroenterology

institute: Brigham and Women's Hospital

data_processing:
Illumina RTA software was used for basecalling.
Cellranger mkfast (v2.2.0, 10X genomics) was used for demultiplexing the Illumina base call files (BCLs).
Cellranger count (v2.2.0, 10X genomics) was used to generate single cell feature counts for each sample.
Cellranger aggr (v2.2.0, 10X genomics) was used to aggregate samples.
Potential doublets were filtered out using DoubletFinder.
Seurat v2.3.0 was used for clustering analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Three processed data files are provided for each sample (output of cellranger count function): barcodes.tsv (filtered barcode sequences and their corresponding GEM groups), genes.tsv (gene ID and gene names), matrix.mtx (feature-barcode matrix in Market Exchange Format).

source_name: Peritoneal cavity cells

extract_protocol:
For each sample, equal cell numbers of 4 male mice of the same genotype were pooled. 8700 cells of each pooled sample were encapsulated into droplets using Chromium Controller (10X Genomics).
Libraries were prepared using Chromium Single Cell 3′ Library Kits v2 (10x Genomics) according to the manufacturer’s protocol. Equal quantities of each library were pooled and sequenced over two lanes of a HiSeq 2500 Rapid Run Flow Cell (Illumina) using custom parameters: Read 1, 26 cycles; i7, 8 cycles; i5, 0 cycles; Read 2, 98 cycles.

tag: condition

value: germ-free

value: WT


title: e9.5_placenta_rep2

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

data_processing:
ATAC-seq reads were aligned to the mm9 genome using Bowtie2 versions 2.3.1 using the very-sensitive, maxins 2000, no-discordant option.
Reads with mapping quality < 20, those mapping to the mitochondrial genome, those with > 2 mismatches, and duplicates were removed.
Reads were offset to account for the transposon dimer as explained in Adey et al. (2010).
Fragments of length <= 140bp  that mapped within 500bp of a TSS were used for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using pybedtools bam_to_bigwig.

extract_protocol:
Placenta were microdissected from e9.5 timed-pregnant mice and collected in cold dPBS
We performed tissue homogenization and cell lysis, following the transposition and purification steps as described previously by Buenrostro et al.( 2015). We amplified the purified DNA with adapters from the Nextera index kit (Illumina). PCR purification was performed using AMpure XP beads (Beckman Coulter) in order to remove large fragments and remaining primers. Library quality was assessed using the Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) to check for proper periodicity, and the DNA concentrations were estimated using the Qubit and Bioanalyzer. Libraries were sequenced by Elim Biopharmaceuticals, Inc. using the Illumina HiSeq 2500 Rapid run platform with 50bp paired-end sequencing.

tag: strain

tag: developmental stage

value: Embryonic day 9.5

value: whole placenta


title: K-cDNA

description:
polyA mRNA
processed data file:
K-cDNA.txt.gz
K-cDNA.txt.gz includes: raw counts for RNA

tag: cell type


title: Xbp1dIEC


title: e9.5_placenta_rep3


title: BCPAP_Input

value: Thyroid

value: Anaplastic thyroid carcinoma


title: BM5-34p

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

description:
Single cell RNA-seq data for BM5-34p
Single cell annotations for BM5-34p

data_processing:
Data procesing was performed in three main steps:
1) Cell barcodes were extracted from sequencing reads prior to alignment.
2) Reads were aligned to the human genome using STAR guided by RefSeq gene annoations, producing both genome and pseudo-transcriptome alignments.
3) For each cell barcode, reads mapping uniquely to a gene were collapsed by their unique molecular identifier (UMI).
4) For each gene and cell barcode the number of UMIs was used to generate a digital expression matrix (DEM).
Genome_build: Hg38
Supplementary_files_format_and_content: Processed data is provided as tab-delimited text files. There are two files per sample. The first file contains a number of annotations (columns) for each cell (rows). The second file contains a digital expression matrix containing the number of UMIs for each gene (rows) and cell (columns).

source_name: Bone marrow aspirate from healthy donor

growth_protocol: Not applicable, material from human subjects

extract_protocol:
Bone marrow aspirates were viably frozen after using density gradient centrifugation to isolate mononuclear cells.
Single-cell transcriptome analysis was performed using the Seq-Well method.
Bone marrow aspirates were viably frozen after using density gradient centrifugation to isolate mononuclear cells.
Single-cell transcriptome analysis was performed using the Seq-Well method.

tag: gender

value: M

tag: age


title: BM5-34p38n

description:
Single cell RNA-seq data for BM5-34p38n
Single cell annotations for BM5-34p38n

treatment_protocol: Not applicable, material from human subjects


title: MUTZ3

description:
Single cell RNA-seq data for MUTZ3
Single cell annotations for MUTZ3

source_name: AML cell line


title: OCI-AML3

description:
Single cell RNA-seq data for OCI-AML3
Single cell annotations for OCI-AML3


title: BM4-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for BM4

data_processing:
Data procesing was performed in three main steps:
1) Cell barcodes were extracted from sequencing reads prior to alignment.
2) Reads were aligned to the human genome using STAR guided by RefSeq gene annoations, producing both genome and pseudo-transcriptome alignments.
3) For each cell barcode, reads mapping uniquely to a gene were collapsed by their unique molecular identifier (UMI).
4) For each gene and cell barcode the number of UMIs was used to generate a digital expression matrix (DEM).
Single-cell genotyping analysis was performed by assigning reads to the expected mutant or wild-type allele, and collapsing reads by their UMI and cell barcode.
Genome_build: Hg38
Supplementary_files_format_and_content: Processed data is provided as tab-delimited text files. There are two files per sample. The first file contains a number of annotations (columns) for each cell (rows). The second file contains a digital expression matrix containing the number of UMIs for each gene (rows) and cell (columns).


title: sample1: post+WO+veh

description: HPC treated with veh at post+WO


title: e9.5_placenta_rep1


title: BM3-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for BM3


title: BM3

description: Single cell RNA-seq data for BM3


title: sample13: pro-diff+veh

description: HPC treated with veh at pro-diff

value: pro-diff


title: AML997-D35

description: Single cell RNA-seq data for AML997-D35

source_name: Bone marrow aspirate from AML patient


title: BM1

description:
Single cell RNA-seq data for BM1
Single cell annotations for BM1


title: BM4

description: Single cell RNA-seq data for BM4


title: AML997-D35-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML997-D35


title: AML997-D0

description: Single cell RNA-seq data for AML997-D0


title: AML921A-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML921A-D0


title: AML916-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML916-D0

value: F


title: AML921A-D0

description: Single cell RNA-seq data for AML921A-D0


title: AML916-D0

description: Single cell RNA-seq data for AML916-D0


title: AML870-D14-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML870-D14


title: AML870-D14

description: Single cell RNA-seq data for AML870-D14


title: AML722B-D49

description: Single cell RNA-seq data for AML722B-D49


title: AML722B-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML722B-D0


title: AML722B-D49-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML722B-D49


title: AML870-D0

description: Single cell RNA-seq data for AML870-D0


title: AML707B-D97

description: Single cell RNA-seq data for AML707B-D97


title: AML707B-D18

description: Single cell RNA-seq data for AML707B-D18


title: AML722B-D0

description: Single cell RNA-seq data for AML722B-D0


title: AML707B-D41

description: Single cell RNA-seq data for AML707B-D41


title: AML707B-D18-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML707B-D18


title: AML707B-D41-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML707B-D41


title: AML707B-D97-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML707B-D97


title: AML707B-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML707B-D0


title: BM2

description:
Single cell RNA-seq data for BM2
Single cell annotations for BM2


title: AML556-D31-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML556-D31


title: AML556-D31

description: Single cell RNA-seq data for AML556-D31


title: AML997-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML997-D0


title: AML707B-D113

description: Single cell RNA-seq data for AML707B-D113


title: AML707B-D113-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML707B-D113


title: AML707B-D0

description: Single cell RNA-seq data for AML707B-D0


title: AML556-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML556-D0


title: AML870-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML870-D0


title: AML475-D29

description: Single cell RNA-seq data for AML475-D29


title: AML475-D29-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML475-D29


title: AML556-D15-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML556-D15


title: AML475-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML475-D0


title: AML475-D0

description: Single cell RNA-seq data for AML475-D0


title: CAL_62_DMSO_rep2

value: DMSO


title: AML329-D37

description: Single cell RNA-seq data for AML329-D37


title: AML420B-D0

description: Single cell RNA-seq data for AML420B-D0


title: AML329-D0

description: Single cell RNA-seq data for AML329-D0


title: BCPAP_THZ1_rep2

value: BCPAP


title: AML420B-D35

description: Single cell RNA-seq data for AML420B-D35


title: AML420B-D14

description: Single cell RNA-seq data for AML420B-D14


title: AML419A-D0

description: Single cell RNA-seq data for AML419A-D0


title: AML314-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML314-D0


title: AML210A-D0

description: Single cell RNA-seq data for AML210A-D0


title: AML420B-D14-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML420B-D14


title: AML1012-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML1012-D0


title: AML1012-D0

description: Single cell RNA-seq data for AML1012-D0


title: AML314-D0

description: Single cell RNA-seq data for AML314-D0


title: conventional CD4 T cell Lef1 ChIP-Seq

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

data_processing:
The sequencing quality of ChIP-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.3.4.1, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm10 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ChIP-Seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a P value of < 1E-4  as identified Lef1 binding peaks.
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: conventional CD4+ T cells

extract_protocol:
Conventional CD4+ T cells were sort-purified from WT C57BL/6 mice, and the Lef1-deficient CD4+ T cells were sorted from CD4-Cre+ Lef1 fl/fl mice. The cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with an anti-Lef1 antibody (C18A7, Cell Signaling Technology), which were then properly washed and immunoprecipitated DNA extracted.
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: wild type

value: naive CD4 T cells

tag: cell phenotype

value: TCRb+, CD4+, CD25-


title: AML210A-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML210A-D0


title: Xbp1dIEC rep7

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore! v0.4.4, then mapped to the NCBI GRCm38.p5 mouse genome using STAR v2.5.2b with standard parameters.
Reads per gene were counted using STAR’s “quantMode GeneCounts” function and the Ensembl annotation release 91.
Differentialy expressed genes were determined using DESeq2 v1.18.1
Genome_build: NCBI GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited text file with raw counts of sequencing reads per gene for each sample. Column 1: gene ID; Column 2: counts for unstranded RNA-seq; Columns 3 and 4: counts for the 1st/2nd read strand aligned with RNA (not used)

source_name: Peritoneal B1b cells

extract_protocol:
For each sample 6000 live peritoneal B1b cells (CD19+CD23-CD5-CD3-F4/80-) were isolated by FACS. RNA was isolated using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara)


title: WT rep5


title: AML314-D31

description: Single cell RNA-seq data for AML314-D31


title: Xbp1dIEC rep6


title: AML556-D15

description: Single cell RNA-seq data for AML556-D15


title: AML556-D0

description: Single cell RNA-seq data for AML556-D0


title: AML420B-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML420B-D0


title: AML371-D0

description: Single cell RNA-seq data for AML371-D0


title: AML419A-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML419A-D0


title: AML329-D37-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML329-D37


title: AML371-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML371-D0


title: AML329-D20-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML329-D20


title: AML329-D20

description: Single cell RNA-seq data for AML329-D20


title: AML420B-D35-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML420B-D35


title: AML371-D34

description: Single cell RNA-seq data for AML371-D34


title: AML329-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML329-D0


title: AML328-D171-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML328-D171


title: WT rep4


title: Xbp1dIEC rep3


title: Xbp1dIEC rep1


title: AML328-D171

description: Single cell RNA-seq data for AML328-D171


title: WT rep3


title: Xbp1dIEC rep5


title: AML707B-nanopore

description: Single cell nanopore data for AML707B


title: AML328-D113-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML328-D113


title: AML328-D29

description: Single cell RNA-seq data for AML328-D29


title: Xbp1dIEC rep4


title: AML328-D29-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML328-D29


title: AML328-D113

description: Single cell RNA-seq data for AML328-D113


title: AML328-D0-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML328-D0


title: PDD1KO_C10_totalRNAs-rep3

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
All RNA-seq data were mapped to theTetrahymena thermophila 2016 genome using Tophat2 (2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed, but not single-end data by SAMtools (v1.5).
For RNA-seq, the bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from BAM files by using “bamCoverage” from deepTools with parameters “--ignoreDuplicates --normalizeUsingRPKM --skipNonCoveredRegions --binSize 50”.
Genome_build: Tetrahymena thermophila micronuclear genome 2016 (http://159.226.67.237/sun/TetBLAST/blast/db/T_thermophila_Mic_Supercontig_id.fa)
Supplementary_files_format_and_content: bigwig

organism: Tetrahymena thermophila

growth_protocol: Tetrahymena cells were grown at 30 oC in SPP medium (Sweet and Allis 1998).

extract_protocol:
Total RNA was extracted from Tetrahymena cells using the RNeasy Protect Cell Mini Kit (Qiagen), as described (TetraFGD: http://tfgd.ihb.ac.cn/index/smphelp). Polyadenylated transcripts were enriched using the Sera‐Mag magnetic oligo (dT) beads (GE).
First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101).

treatment_protocol: To initiate conjugation, log-phase growing cells (~2×105 /ml) of two different mating types were washed, starved, and mixed in 10 mM Tris (pH 7.4) or Dryl’s buffer (2 mM sodium citrate, 1 mM NaH2PO4, 1 mM Na2HPO4, 1.5 mM CaCl2, pH 6.8) at 30°C.

tag: strain background

value: Tetrahymena wildtype strains CU427 and CU428

tag: genotype/variation

value: C10 (10 hours post-mixing)


title: EZL1KO_C10-rep4


title: WT rep2


title: PDD1KO_C10_totalRNAs-rep4


title: EZL1KO_C10-rep3


title: DCL1KO_C10-rep3


title: Xbp1dIEC rep2


title: AML371-D34-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML371-D34


title: WT_C10-rep4


title: AML328-D0

description: Single cell RNA-seq data for AML328-D0


title: DCL1KO_C10-rep2


title: AML328-nanopore

description: Single cell nanopore data for AML328


title: EZL1KO_C10-rep2


title: WT rep1


title: AML419A-nanopore

description: Single cell nanopore data for AML419A


title: PDD1KO_C10_totalRNAs-rep2


title: EZL1KO_C10_totalRNAs-rep1


title: PDD1KO_C10_totalRNAs-rep1


title: WT_C10_totalRNAs-rep1

value: wild-type


title: DCL1KO_C10_totalRNAs-rep1


title: EZL1KO_C6-rep2

value: C6 (6 hours post-mixing)


title: PDD1KO_C6_totalRNAs-rep1


title: DCL1KO_C10_totalRNAs-rep4


title: PDD1KO_C6_totalRNAs-rep2


title: WT_C10-rep3

value: WT


title: EZL1KO_C6-rep1


title: PDD1KO_C3_totalRNAs-rep2

value: C3 (3 hours post-mixing)


title: WT_C6-rep1


title: WT_C6-rep2


title: PDD1KO_C3_totalRNAs-rep1


title: DCL1KO_C6-rep2


title: DCL1KO_C6-rep1


title: AML314-D31-anno

description:
single-cell genotyping by targeted PCR.
Single cell annotations for AML314-D31


title: WT_C10-rep2


title: WT_C3-rep2


title: WT_C3-rep1


title: DCL1KO_C3-rep2