title: SKBR-3_rep2

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

description: small RNA sequencing

data_processing:
FASTQ reads were subjected to adapter removal (cutadapt) per manufacturer's instructions (NEXTflex Small RNA Sequencing Kit v3). The degenerate sequences (N4) at the 5' and 3' end of the reads were removed.
Trimmed reads were mapped to the human genome (build hg38) using Bowtie2 v2.2.8.
The resulting bam file was sorted (samtools sort), converted to bed (bamToBed), and intersected with all small RNA loci annotated from TCGA-BRCA dataset (intersectBed).
The number of reads overlapping each small RNA were tallied to generate a count file.
Genome_build: hg38
Supplementary_files_format_and_content: count file for each feature
Supplementary_files_format_and_content: BED file with chromosomal coordinates for gene IDs is available on GSE114773.

growth_protocol: All cells were cultured in a 37°C, 5% CO2 humidified incubator. Cell lines MDA-MB-231, MDA-LM2, CN34-par, CN34-Lm1a, MCF7 and MDA-MB-453 were propagated in DMEM base media supplemented with 4.5 g/L glucose, 10% FBS, 4mM L-glutamine, 1mM sodium pyruvate, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin (1μg/mL). Cell lines HCC1395, ZR-75-1 and HCC38 were propagated in RPMI 1640 base media supplemented with 10% FBS, 2mM L-glutamine, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin (1μg/mL). SK-BR-3 cell line was propagated in McCoy’s 5a modified media supplemented with 10% FBS, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin (1μg/mL). HMECs were propagated in HuMEC media (Thermo Fisher Scientific cat. no. 175010).

extract_protocol:
RNA was extracted using miRNA purification kit (Norgen) per manufacturer's instructions
The libraries were constructed using the NEXTflex small RNA sequencing kit v3 for Illumina platforms (Bioo Scientific NOVA-5132-06). 15 ng of extracellular vesicle RNA and 10 ng of conditioned media RNA were used as starting material, and gel extraction was performed for all libraries.

tag: rep


title: SKBR-3_rep1

status: Public on Nov 05 2018

type: SRA

state: CA

country: USA

description: small RNA sequencing

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: MHCII_dGut_4

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
3' polyA RNA-seq
CellRanger 1.3.1
PCA (prcomp in R)
kNN-based graph clustering (R code)
Supplementary_files_format_and_content: 10X genomics CellRanger output
Genome_build: mm10
Supplementary_files_format_and_content: UMI count expression values for each gene (rows) in each cell (columns)
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

organism: Mus musculus

source_name: Inducible intestinal epithelial H2-Ab1-KO (MHCIIΔgut) mouse rep. 4 [Fig. 3C and Fig. S4C-F] [MHCII_dGut_4]

extract_protocol:
3' polyA RNA seq
Full length RNAseq (SMART-Seq2)
10X Genomics Chromium Prep

tag: cell type

value: MHCIIdelta gut mouse intestinal epithelial cells

tag: strain

tag: treatment

tag: time point

tag: genotype

value: MHCIIdelta gut


title: anti_IgG_M2_C2

source_name: Control (anti IgG) mouse rep. 2, channel 2, H. poly day 3 [Fig. 4F] [anti_IgG_M2_C2]

value: WT mouse intestinal epithelial cells

value: H. poly

value: Day 3

value: WT


title: ZR75-1_rep1

description: small RNA sequencing


title: MDA231_rep2

description: small RNA sequencing


title: anti_MHCII_M2_C2

source_name: MHCII-blocked (anti MHCII) mouse rep. 2, channel 2, H. poly day 3 [Fig. 4F] [anti_MHCII_M2_C2]


title: MDA231_rep1

description: small RNA sequencing


title: MDA453_rep1

description: small RNA sequencing


title: MDA453_rep2

description: small RNA sequencing


title: MHCII_Flox_Control_5

source_name: MHCII (H2-Ab1) flox-flox control mouse rep. 5 [Fig. 3C and Fig. S4C-F] [MHCII_Flox_Control_5]

value: MHCII flox-flox control mouse intestinal epithelial cells

value: MHCII-flox-flox


title: MHCII_dGut_2

source_name: Inducible intestinal epithelial H2-Ab1-KO (MHCIIΔgut) mouse rep. 2 [Fig. 3C and Fig. S4C-F] [MHCII_dGut_2]


title: MHCII_Flox_Control_4

source_name: MHCII (H2-Ab1) flox-flox control mouse rep. 4 [Fig. 3C and Fig. S4C-F] [MHCII_Flox_Control_4]


title: MHCII_Flox_Control_2

source_name: MHCII (H2-Ab1) flox-flox control mouse rep. 2 [Fig. 3C and Fig. S4C-F] [MHCII_Flox_Control_2]


title: MHCII_Flox_Control_3

source_name: MHCII (H2-Ab1) flox-flox control mouse rep. 3 [Fig. 3C and Fig. S4C-F] [MHCII_Flox_Control_3]


title: MCF7_rep2

description: small RNA sequencing


title: CPH2_del_mut_Rep1

city: Würzburg

first: Valentina

last: del Olmo Toledo

state: Bayern

address: Josef-Schneider-Str. 2/D15

country: Germany

institute: Institute of Molecular Infection Biology

description:
Total RNA with poly(A)+ selection.
processed data file: cph2_genes.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. albicans Build 21 transcriptome using STAR v2.5.3a with parameters --runThreadN 3 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
Raw read counts per reference feature were calculated using HTSeq v0.7.2.
Raw read counts were normalized and analysed for differentially expressed genes using DESeq2 v1.14.1.
Genome_build: Candida albicans Build 21
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw read counts for each sample.
Supplementary_files_format_and_content: *_genes.txt: Tab-delimited text files contain the mean of normalized counts, log2 fold change, log2 fold change standard error, wald statistics, p-value and adjusted p-value for each replicate pair after differential gene expression analysis sample.

organism: Candida albicans

source_name: yeast cells

growth_protocol: C. albicans reference strain and deletion mutants were grown under anaerobic conditions in Todd-Hewitt broth at 37°C for 24 h.

extract_protocol:
Total RNA was extracted using RiboPure(TM) RNA purification kit for yeast (Ambion, Life Technologies)
Library construction was carried out by GATC Biotech (Konstanz, Germany). Briefly, the protocol included poly(A)+ RNA selection, mRNA  fragmentation, random primer cDNA synthesis, adaptor ligation and Illumina (HiSeq2500) sequencing.

tag: genotype/variation

value: CPH2 deletion mutant


title: WT_Rep1

description: Total RNA with poly(A)+ selection.

value: Wildtype


title: ZR75-1_rep2

description: small RNA sequencing


title: MCF7_rep1

description: small RNA sequencing


title: 1833

city: Philadelphia

first: Caroline

middle: R

last: Bartman

state: PA

address: 34th st.

department: Department of Bioengineering

institute: University of Pennsylvania

library_source: genomic

data_processing:
used bcl2fastq to convert and demultiplex the reads
we used Bowtie to map reads to mm9 genome
used MACS to get wig files
used wigToBigWig to convert wig to bigwig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: G1E-ER4 cells

growth_protocol: cells grown in suspension in IMDM supplemented with erythropoietin

extract_protocol:
Lysates were clarified from sonicated nuclei and Pol II-DNA complexes were isolated with antibody.
use Illumina TruSeq ChIP sample preparation kit

treatment_protocol: treated with either 0 or 4 hours estradiol for GATA1-ER stabilization and differentiation

value: immortalized erythroid cell overexpressing GATA1-ER fusion

value: 4 hours estradiol

tag: chip antibody

value: RBP-1 (santa cruz sc899)


title: LM2_rep1

description: small RNA sequencing


title: 1832

value: 0 hours estradiol


title: LM2_rep2

description: small RNA sequencing


title: MHCII_Flox_Control_1

source_name: MHCII (H2-Ab1) flox-flox control mouse rep. 1 [Fig. 3C and Fig. S4C-F] [MHCII_Flox_Control_1]


title: 1831


title: LM1a_rep1

description: small RNA sequencing


title: HUMEC_rep3

description: small RNA sequencing

source_name: HUMEC

value: HUMEC


title: 1830


title: HUMEC_rep2

description: small RNA sequencing


title: CN34_rep2

description: small RNA sequencing


title: LM1a_rep2

description: small RNA sequencing


title: HCC1395_rep1

description: small RNA sequencing


title: HCC1395_rep2

description: small RNA sequencing


title: HCC38_rep2

description: small RNA sequencing


title: HCC38_rep1

description: small RNA sequencing


title: CN34_rep1

description: small RNA sequencing


title: ZR75-EV-rep2

description: small RNA sequencing

data_processing:
FASTQ reads were subjected to adapter removal (cutadapt) per manufacturer's instructions (NEXTflex Small RNA Sequencing Kit v3). The degenerate sequences (N4) at the 5    and 3    end of the reads were removed and added to the name of the read as a unique molecular identifier (UMI) using UMI tools.
Trimmed reads were mapped to the human genome (build hg38) using Bowtie2 v2.2.8.
The resulting bam file was sorted (samtools sort), converted to bed (bamToBed), and intersected with the annotated oncRNAs (intersectBed).
The number of reads overlapping each oncRNA were tallied to generate a count file.
Genome_build: hg38
Supplementary_files_format_and_content: count file for each feature

extract_protocol:
Extracellular vesicle RNA was isolated from 5mL conditioned media using the Cell Culture Media Exosome Purification Mini Kit (Norgen, cat. no. 60400).
The libraries were constructed using the NEXTflex small RNA sequencing kit v3 for Illumina platforms (Bioo Scientific NOVA-5132-06). 15 ng of extracellular vesicle RNA and 10 ng of conditioned media RNA were used as starting material, and gel extraction was performed for all libraries.

treatment_protocol: Preparation of conditioned media for isolation of RNA from extracellular vesicle and total conditioned media was carried out by seeding cells at 7x105. Twenty-four hours later, cells were washed twice with PBS and 10mL exosome-depleted media was added. Forty-eight hours later, media was harvested by spinning at 200xg for 15 minutes and taking the supernatant. Exosome-depleted media was prepared by substituting exosome-depleted FBS (Thermo Fisher Scientific cat. no. A2720803) for FBS. Exosome-depleted HuMEC media was prepared by centrifuging the bovine pituitary extract at 100,000xg, 4°C for 16 hours.

tag: compartment

value: Evs


title: HUMEC_rep1

description: small RNA sequencing


title: ZR75-EV-rep1

description: small RNA sequencing


title: CFC_3h_KO_rep3

city: Wien

first: Christoph

middle: P

last: Dotter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children’s Cancer Research Institute (St. Anna CCRI)

data_processing:
Demultiplexed raw sequencing reads were trimmed before alignment according to the guidelines provided by Lexogen, i.e. random primer sequence, adapter contamination and low quality tails were filtered using BBDuk from the BBMap package
Reads were aligned using STAR version 2.5.4 (genome: GrCm38/mm10, gene annotation: Gencode release M8). Reads that didn’t align uniquely were discarded. Parameters: --outSAMtype BAM SortedByCoordinate --alignIntronMax 1000000 --outFilterIntronMotifs RemoveNoncanonical --outFilterMultimapNmax 1 --quantMode GeneCounts
Read counts per gene were also calculated using STAR (option - quantMode GeneCounts).
Differential expression analysis was performed in R 3.5.0 employing RUVSeq. Briefly, the Bioconductor package EDASeq (version 2.14.0) was used for initial data exploration and upper quartile normalization. In the next step unwanted sources of variation were estimated using the Bioconductor package RUVSeq (version 1.14.0). All samples for one experiment (embryo or CA) were normalized together. The parameter k was set to the minimum value that yielded good separation of sample groups in the PCA plot. Differential expression analysis was performed using the EdgeR package (version 3.22.2) including the RUV variables in the design as described. Genes with FDR<=0.05 were deemed significantly differentially expressed.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Read count table STAR format (column 1: gene ID, column 2: counts for unstranded RNA-seq, column 3: counts for the 1st read strand aligned with RNA (used for quantSeq libraries), column 4: counts for the 2nd read trand aligned with RNA

molecule: polyA RNA

source_name: adult hippocampus, left CA

extract_protocol:
Whole E9.5 embryos or the left hippocampal CA region were used for RNA extraction by using 700 µL Trizol (Invitrogen) for homogenization and 140 µL chloroform (Sigma), followed by centrifugation at 12,000g for 15 min at 4°C. The upper aqueous phase was transferred to a new tube and 1.5 volumes of 100% ethanol (EtOH) were added. RNA was extracted using Zymo-Spin™ IC columns (Zymo Research). In short, the aqueous phase/ethanol mixture was loaded onto the column, washed with 400 µl 70% EtOH before being treated with RQ1 DNAseI (Promega, 5 µl + 5 µl reaction buffer + 40 µl 70% EtOH) for 15 min at RT. After two washes with 70% EtOH the sample was eluted from the column with DEPC-treated H2O. RNA concentration was measured by using the NanoDrop spectrophotometer (Thermo Scientific).
1 μg (CA) or 500 ng (E9.5) total RNA were used to generate cDNA libraries by following the manufacturer’s instructions in the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). Library quality and size distribution were assessed with the High Sensitivity DNA Analysis Kit for the Bioanalyzer 2100 (Agilent).

treatment_protocol: CFC: 120s free exploration; 3x foot-shock (0.5 mA, 2 s, 1 min interval). Mice were sacrificed upon isoflurane anesthesia 3h after training, the brain removed and immersed in ice-cold artificial cerebrospinal fluid, hippocampi removed, CA regions dissected carefully using a 30G needle, snap-frozen in liquid

tag: tissue

value: left hippocampus, CA region

tag: age

value: adult (2-3.5 months old)

value: CMV-Cre Setd5 fl/+


title: CFC_3h_KO_rep5


title: CFC_3h_KO_rep2


title: CFC_3h_KO_rep4


title: CFC_3h_KO_rep1


title: CFC_1h_KO_rep5

treatment_protocol: CFC: 120s free exploration; 3x foot-shock (0.5 mA, 2 s, 1 min interval). Mice were sacrificed upon isoflurane anesthesia 1h after training, the brain removed and immersed in ice-cold artificial cerebrospinal fluid, hippocampi removed, CA regions dissected carefully using a 30G needle, snap-frozen in liquid


title: CFC_1h_KO_rep4


title: SKBR3-EV-rep2

description: small RNA sequencing


title: MDA453-EV-rep2

description: small RNA sequencing


title: CFC_1h_KO_rep2


title: SKBR3-EV-rep1

description: small RNA sequencing


title: CFC_1h_KO_rep1


title: GSC185_shCD109

type: RNA

city: Birmingham

first: Mutsuko

last: Minata

state: Alabama

address: 1824 6th Ave. S

department: Neurosurgery

institute: University of Alabama at Birmingham

description: GSC 185 shCD109-49

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HTA-2_0
program-name = Expression Console
program-version = 1.4.1.46
program-company = Affymetrix

label: biotin

label_protocol: standard Affymetrix protocol

growth_protocol: The cell lines were cultured as tumor spheres in neural basal medium (Dulbecco's Modified Eagle Medium [DMEM]/F12 50/50 (Gibco)) containing B27 (Miltenyi), 20ng/ml EGF (Pepro Tech), and 20ng/ml FGF (Pepro Tech)

extract_protocol: Total RNA was extracted and puridied using Qiagen Rneasy mini kit

treatment_protocol: Lentiviral production was performed using vectors expressing shRNA for CD109 (Sigma) and helper plasmids (psPAX2 and pMD2G). Infection of lentivirus was performed with polybrene according to the manufactured protocol.

value: Glioma stem cells (GSCs)


title: GSC185_shNT

description: GSC 185 NT

value: shNT


title: GSC20_shCD109

description: GSC 20 shCD109-49


title: MDA231-EV-rep2

description: small RNA sequencing


title: HC_KO_rep5

treatment_protocol: Mice were sacrificed upon isoflurane anesthesia, the brain removed and immersed in ice-cold artificial cerebrospinal fluid, hippocampi removed, CA regions dissected carefully using a 30G needle, snap-frozen in liquid nitrogen, and kept at -80 °C for further processing.


title: GSC20_shNT

description: GSC 20 NT


title: MDA453-EV-rep1

description: small RNA sequencing


title: MDA231-EV-rep1

description: small RNA sequencing


title: HC_KO_rep4


title: MCF7-EV-rep1

description: small RNA sequencing


title: MCF7-EV-rep2

description: small RNA sequencing


title: HuMEC-EV-rep2

description: small RNA sequencing

source_name: HuMEC

value: HuMEC


title: HC_KO_rep2


title: CFC_3h_WT_rep5

value: wild type


title: CFC_1h_KO_rep3


title: CFC_3h_WT_rep4


title: HC_KO_rep1


title: HCC38-EV-rep2

description: small RNA sequencing


title: HCC38-EV-rep1

description: small RNA sequencing


title: CFC_3h_WT_rep2


title: HCC1395-EV-rep2

description: small RNA sequencing


title: HuMEC-EV-rep1

description: small RNA sequencing


title: CFC_3h_WT_rep3


title: CFC_3h_WT_rep1


title: LN229_shControl_H3

city: Heidelberg

first: Bernhard

last: Radlwimmer

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

institute: Deutsches Krebsforschungszentrum / German National Cancer Research Centre

description:
processed data file:
LN229_shControl_ChromHMM_18states.bed
LN229_shControl_ChromHMM_simplified_7states.bed

data_processing:
ChIP-seq datasets were processed using a custom pipeline implemented in Snakemake. Briefly, reads were trimmed using the Trimgalore tool (https://github.com/FelixKrueger/TrimGalore) and aligned using Bowtie with standard parameters. Duplicates and multi-mapping reads were removed using the samtools package and the XS flag in the bam files. Input control (WGS) and corresponding IP datasets were scaled using the SES method and converted into a bigwig track using the bamCompare tool of the deepTools2 suite. Peaks were called using the callpeak mode in MACS2 (https://github.com/taoliu/MACS) for broad and narrow peaks. In addition, SICER was used to call peaks using the gap 600 and window 200 parameters. Various QC parameters (FRiP, PCR bottleneck coefficient, cross-strand correlation) were determined according to the ENCODE guidelines. In addition, visual QC was performed using the signal profile at TSS of annotated genes and the fingerprint method from the DeepTools2 suite.
Chromatin segmentation was defined using the ChromHMM tool. ChIP-seq data (H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me3) and WGS data (input control) were binarized using ChromHMM’s “BinarizeBam” command. The Epigenome Roadmap 18-state model was used to segment the genome of each sample.  The consensus state for a subtype is defined as the state with the highest frequency in a given segment, and a minimum frequency of 50%.
The simplified 7-state model was defined by mapping the 18 states as follows: 1-4 to TSS (Tss), 5-6 to Transcription (Tx), 7-11 and 15 to Enhancer (Enh), 12-13 to Heterochromatin/Repeats (Het/Rpts), 14 to Bivalent TSS (TSSBiv), 16-17 to Polycomb Repressed (ReprPC), 18 to Quiescent (Qui).
genome build: hg19
processed data files format and content: ChromHMM results for each sample are contained in two bedfiles: the full 18-state and the reduced 7-state model. For each IPed factor, 3 files are included: a bigWig coverage file and two peak call bedfiles.

growth_protocol: The human glioblastoma cell line LN229 was obtained from ATCC (cat. CRL-2611). Cells were cultured in DMEM containing 1 g/L glucose (D5921, Sigma) supplemented with 10% tetracycline-free fetal bovine serum (Clontech), 1% penicillin and streptomycin (P/S) mix, and glutamine (0.5 mM).     The ZH487 glioblastoma spheroid primary cells were originally established at the University of Zurich Hospital.  ZH487 cells were cultured in Neurobasal medium (Cat. 12348017, NBM) supplemented with 2% B27 (cat. 12587010, retinoic acid-free, Invitrogen), EGF (20 ng/ml, AF-100-15, Peprotech), FGF (20 ng/ml, cat. 100-18B, Peprotech) and glutamine (0.5 mM).     DNA methylation array (Illumina EPIC) analysis classified the ZH487 primary tumour and derived cell line as part of the RTK I subtype.    All cell lines were cultured under 10% CO2 at 37℃ with humidity.    Cell identities were verified by the Multiplex human Cell line Authentication Test (MCA). Cells were also tested for mycoplasma contamination with the Multiplex cell test (Multiplexion GmbH, Friedrichshafen, Germany).

extract_protocol:
Cells were cross-linked with 1% methanol-free formaldehyde for 10 min. After quenching with glycine, cells were washed three times with PBS and the cell pellet was treated with 4U MNase per 1x106 cells for 15 min. MNase was stopped with 10x Covaris buffer and the chromatin was sheared for an additional 15 min with the LE220 Covaris device. The soluble chromatin was then recovered, quantified and 2µg chromatin was used in each IP with 2µl of antibody (H3: ab1791; H3K4me1, ab8895; H3K4me3, ab8580; H3K9me3, ab8898; H3K27ac, ab4729; H3K36me3, ab9050; H3K27me3, ab6002; all Abcam). After IP and washes with Covaris buffer, Li-buffer and TE, precipitated chromatin was digested with proteinase K and purified with AMPure beads.
Illumina sequencing libraries were prepared from purified DNA with the NEBNext Ultra library preparation kit (NEB) according to standard protocols.

treatment_protocol: Inducible SOX10 knockdown cells were established by infecting cells with pLKO-Tet-On non-targeting (nt) shRNA and pLKO-Tet-On SOX10 shRNA (TRCN0000018988) lentiviral particles and puromycin selection (1 µg/ml) for 7 days. shRNA expression was induced by adding 0.1 µg/ml doxycycline to the medium for at least 7 days.

value: adherent glioblastoma-derived cell line

tag: subtype

value: RTK_I cell-like line

tag: gender source

value: male

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#

tag: molecule subtype

value: genomic DNA and associated chromatin


title: ST-13_S5_R1_001

city: Kearneysville

first: Chris

last: Dardick

state: WV

address: 2217 Wiltshire Road

department: Appalachian Fruit Research Station

institute: USDA-ARS

data_processing:
Raw reads were processed and analyzed by Genewiz. Trimmed sequences were imported into CLC Genomics Workbench (version v10.0.1, Qiagen, Redwood City, CA, USA) for de novo transcriptome assembly and mapping to Solanum lycopersicum genome assembly SL 3.0 (https://www.ncbi.nlm.nih.gov/genome/?term=tomato) using the CLC Genomics Workbench v10.0.1 RNA-seq analysis tool and default parameters (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10).
Genome_build: Solanum lycopersicum assembly SL 3.0 (2018 Solanaceae Genomics Project. https://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.4/)
Supplementary_files_format_and_content: Tab-delimited text files include Gene ID-name, Region, TPM, Gene length, Unique gene reads, Total gene reads

organism: Nicotiana tabacum

source_name: Treated plantlets cultured for 10 days with MVOC exposure

growth_protocol: Premixed medium powder containing MS salts and vitamins (Murashige and Skoog, 1962, Physiol Plant 15,473) were acquired from Phytotechnology Laboratories (Cat No. M519, Overland Park, KS, USA). Culture medium was prepared by supplementing medium powder with 30 g/L sucrose with pH adjusted to 5.8 prior to autoclaving at 121°C for 20 min. Medium was distributed to Magenta GA7 vessel at 100 ml per vessel. After plants were inserted cultures were maintained at 25°C under a 16 h light and 8 h dark photocycle for 10 days prior to sample collection.

extract_protocol:
Total RNA was then extracted from 100 mg tissue powder using the RNeasyR Plant Mini Kit per manufacturer’s instructions (Qiagen, Redwood City, CA, USA). There were four biological replicates from each treatment. RNA sequencing was performed by Genewiz via Illumina HiSeq platform (100bp paired end reads) (South Plainfield, NJ, USA).
Library preparation and 50bp single-end sequencing on the Illumina HiSeq system was performed by Genewiz (South Plainfield, NJ, USA).

treatment_protocol: Tobacco seeds were surface-sterilized by immersion in 4% (w/v) sodium hypochlorite solution for 10 min followed by 3 x rinse with sterile water. Seeds were then placed on the surface of MS medium in petri dish and cultured for six days. Germinated seedlings were then transferred to Magenta GA7 vessels containing MS medium without exposure to microbial volatile organic compounds (MVOCs). There were three replicate seedling plants per vessel and four replicate vessels per treatment. After 10 days of cultivation, tissue samples including the apical meristem and 3 to 4 terminal leaves from all three seedling plants per vessel were collected, placed in a 1.5 ml microcentrifuge tube and immediately immersed in liquid nitrogen.  Samples were pulverized into a fine powder using Geno/Grinder 2010 and stored at -80°C for RNA extraction use.

tag: growth stage

value: 10 days after germination

tag: mvoc exposure

value: Yes

tag: cultivar

value: Samsun


title: HC_KO_rep3

tag: strain


title: CFC_1h_WT_rep4


title: CN34-EV-rep1

description: small RNA sequencing

tag: cell line

tag: rep


title: CFC_1h_WT_rep2

tag: genotype


title: CN34-EV-rep2

description: small RNA sequencing


title: ZR75-CM-rep2

description: small RNA sequencing

extract_protocol:
RNA was isolated from 400ul total conditioned media using the miRNeasy serum/plasma kit (Qiagen cat. no. 217184).
The libraries were constructed using the NEXTflex small RNA sequencing kit v3 for Illumina platforms (Bioo Scientific NOVA-5132-06). 15 ng of extracellular vesicle RNA and 10 ng of conditioned media RNA were used as starting material, and gel extraction was performed for all libraries.

value: conditioned media


title: HC_WT_rep5


title: CFC_1h_WT_rep3


title: CFC_1h_WT_rep1


title: HC_WT_rep3


title: SKBR3-CM-rep2

description: small RNA sequencing


title: HC_WT_rep4


title: HC_WT_rep2


title: MDA453-CM-rep2

description: small RNA sequencing


title: HC_WT_rep1


title: MDA231-CM-rep2

description: small RNA sequencing


title: MDA453-CM-rep1

description: small RNA sequencing


title: MDA231-CM-rep1

description: small RNA sequencing


title: HCC1395-EV-rep1

description: small RNA sequencing

value: Evs


title: KO_E9.5_rep2

source_name: whole embryo E9.5

treatment_protocol: Embryos were collected from pregnant females at embryonic day (E) 9.5. Mothers were briefly anesthetized with isoflurane and sacrificed by cervical dislocation. Embryos were dissected in ice cold 1x PBS, uterine tissue and yolk sack were removed and placentas were collected for genotyping.

value: whole embryo


title: MCF7-CM-rep2

description: small RNA sequencing


title: WT_E9.5_rep3


title: KO_E9.5_rep1


title: KO_E9.5_rep3


title: ZR75-CM-rep1

description: small RNA sequencing


title: WT_E9.5_rep1


title: WT_E9.5_rep2


title: HuMEC-CM-rep1

description: small RNA sequencing


title: MCF7-CM-rep1

description: small RNA sequencing


title: HuMEC-CM-rep2

description: small RNA sequencing


title: CN34-CM-rep2

description: small RNA sequencing


title: HCC1395-CM-rep2

description: small RNA sequencing


title: CN34-CM-rep1

description: small RNA sequencing


title: SKBR3-CM-rep1

description: small RNA sequencing


title: spaQ replicate 2

city: Austin

first: Enamul

last: Huq

state: TX

address: NHB 2.616, Stop A5000 100 East 24th St.

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
spaQ_2_S12_L002
processed data file: spaQ_regulated_genes.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Arabidopsis whole genome TAIR10  using bowtie2 and tophat with parameter tophat -p 5 -G reference/arabidopsis.gtf -o tophat_out/Col_1  --library-type fr-unstranded --b2-score-min L,0,-0.2 reference/arabidopsis ../fastqc_results/Col_1_S5_L002_R1_001.fastq
HTSeq package http://htseq.readthedocs.io/en/release_0.9.1/  was used for counting the mapped reads
differential gene expression was further analysed using Deseq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Genome_build: TAIR10
Supplementary_files_format_and_content:
Excel files including the cop1_regulated_genes(log2FC of cop1-4 vs WT) and spaQ_regulated_genes (log2FC of spaQ vs WT);
Text file for total counts of sequencing reads for each sample

organism: Arabidopsis thaliana

source_name: spaQ_dark-grown seedlings

growth_protocol: Total RNAs were extracted from 3 day-old dark-grown  Col-0, cop1-4 and spaQ seedlings.

extract_protocol:
Total RNA was extracted using Sigma spectrum total RNA kit (Sigma-Aldrich)
RNA libraries were prepared for sequencing using standard Illumina Truseq  protocols

treatment_protocol: Plates were kept in the dark for 3 days at 4°C to stratify. Plates were then exposed to white light for 3hrs at room temperature before being placed in the  dark for 21 hrs. Seeds were then treated with far-red light ( 2000μmolm-2) before putting back into the dark for 2 days. RNAs were extracted in Day 3.

tag: ecotype background

tag: genotype/variation

value: spaQ

value: 3 day grown

value: Seedlings


title: HCC38-CM-rep2

description: small RNA sequencing

tag: compartment


title: spaQ replicate 3

description:
spaQ_3_S13_L002
processed data file: spaQ_regulated_genes.xlsx

tag: tissue


title: spaQ replicate 1

description:
spaQ_1_S11_L002
processed data file: spaQ_regulated_genes.xlsx

tag: age


title: cop1 replicate 1

description:
cop_1_S8_L002
processed data file: cop1_regulated_genes.xlsx

source_name: cop1-4 _dark-grown seedlings


title: cop1 replicate 2

description:
cop_2_S9_L002
processed data file: cop1_regulated_genes.xlsx


title: Col-0 replicate 3

source_name: wild type_dark-grown seedlings


title: cop1 replicate 3

description:
cop_3_S10_L002
processed data file: cop1_regulated_genes.xlsx


title: Col-0 replicate 1


title: HCC1395-CM-rep1

description: small RNA sequencing


title: Col-0 replicate 2


title: ZH487_shSOX10_2

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Raw microarray .CEL files were read into R (3.4.3) and normalized using the ‘gcrma’ R package (2.50.0). Probes without an annotated gene were removed from the analysis, leaving 41941 annotated probes. R annotation package versions: hgu133plus2probe_2.18.0,  hgu133plus2cdf_2.18.0, hgu133plus2.db_3.2.3

source_name: gliomasphere patient-derived cell line

label_protocol: Affymetrix standard protocol

extract_protocol: Total RNA was isolated using the RNeasy Microkit (Qiagen) according to the manufacturer's standard protocol.

tag: cell type

value: gliomasphere patient-derived cell line

tag: subtype

value: RTK_I-like glioblastoma cell line

tag: treatment


title: ZH487_shSOX10_1

tag: gender source


title: LN229_CRISPRi_shSOX10_3

source_name: adherent glioblastoma-derived cell line


title: ZH487_mock

value: mock


title: ZH487_NT

value: NT


title: LN229_CRISPRi_NT

value: adherent glioblastoma-derived cell line


title: LN229_CRISPRi_shSOX10_2

value: male


title: HCC38-CM-rep1

description: small RNA sequencing


title: ZH487_shSOX10_3


title: LN229_CRISPRi_shSOX10_1


title: LN229_CRISPRi_mock


title: NICD-OE-HEC mLSEC biological rep5

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from primary murine liver sinusoidal endothelial cells with enhanced Notch signalling.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Notch intracellular domain overexpressing primary murine liver sinusoidal endothelial cells, biological replicate no 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Clec4g-Cre(tg/wt) mice were crossed with Rosa26-N1ICD-IRES-GFP mice to generate Clec4g-Cre(tg/wt);Rosa26-N1ICD-IRES-GFP mice (NICD-OE-HEC).

extract_protocol: Total RNA was extracted with innuPREP RNA Mini Kit (Analytik Jena).

treatment_protocol: Livers were perfused in situ through the portal vein with a collagenase/amino acid/saccharide solution (Sigma-Aldrich), dissected, mechanically disrupted, pooled from 3 mice, digested for 25 minutes at 38 °C in collagenase/Gey’s balanced salt solution (Sigma-Aldrich), and filtered through a mesh. Nonparynchymal cells were separated by a 19.3 % Nycodenz gradient. Afterward, liver sinusoidal endothelial cells (LSEC) were isolated by Magnetic-activated cell sorting (MACS) using CD146 MicroBeads (Miltenyi) according to manufacturers’ instructions.

value: Mut

value: liver

value: sinusoidal endothelial cells


title: NICD-OE-HEC mLSEC biological rep4

source_name: Notch intracellular domain overexpressing primary murine liver sinusoidal endothelial cells, biological replicate no 4


title: NICD-OE-HEC mLSEC biological rep2

source_name: Notch intracellular domain overexpressing primary murine liver sinusoidal endothelial cells, biological replicate no 2


title: NICD-OE-HEC mLSEC biological rep6

source_name: Notch intracellular domain overexpressing primary murine liver sinusoidal endothelial cells, biological replicate no 6


title: NICD-OE-HEC mLSEC biological rep3

source_name: Notch intracellular domain overexpressing primary murine liver sinusoidal endothelial cells, biological replicate no 3


title: NICD-OE-HEC mLSEC biological rep1

source_name: Notch intracellular domain overexpressing primary murine liver sinusoidal endothelial cells, biological replicate no 1


title: Control mLSEC biological rep6

description: Gene expression data from control primary murine liver sinusoidal endothelial cells

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 6

value: Ctrl


title: AK226 [tumor methylation microarray]

type: genomic

hyb_protocol: According to Illumina's protocol for methylation arrays

data_processing:
Raw signal intensities were obtained from IDAT files using the minfi Bioconductor package v.1.14.036. Each sample was individually normalized by performing a background correction (shifting of the 5% percentile of negative control probe intensities to 0) and a dye-bias correction (scaling of the mean of normalization control probe intensities to 10,000) for both colour channels. Subsequently, a correction for the type of material tissue (FFPE or frozen) was performed by fitting univariate, linear models to the log2-transformed intensity values (removeBatchEffect function, limma package v.3.24.15). Beta values were calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina).
Beta values as calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina). Due to the protected nature of this patient data, only the 358365 probes common to both 450k+EPIC platforms and that are not annotated with a SNP (IlluminaHumanMethylation450k.anno.ilmn12.hg19, dbSNP release 147) are included in the table.

source_name: adult glioblastoma tumour

extract_protocol: Tumour DNA was extracted using either the Qiagen Allprep DNA/RNA/Protein kit, or caesium chloride (CsCl) density gradient ultracentrifugation.

tag: gender

value: female

value: dead

tag: os (overall survival, month)

tag: progression

tag: pfs (progression-free survival, month)

tag: idh1 mutation status

value: wt

tag: idh2 mutation status


title: AK227 [tumor methylation microarray]

scan_protocol: According to Illumina's protocol for methylation arrays

value: alive


title: AK218 [tumor methylation microarray]

label_protocol: According to Illumina's protocol for methylation arrays


title: AK216 [tumor methylation microarray]


title: Control mLSEC biological rep5

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 5


title: AK188 [tumor methylation microarray]


title: AK236 [tumor methylation microarray]


title: AK165 [tumor methylation microarray]


title: AK205 [tumor methylation microarray]


title: AK231 [tumor methylation microarray]


title: AK167 [tumor methylation microarray]


title: AK173 [tumor methylation microarray]


title: AK149 [tumor methylation microarray]


title: Control mLSEC biological rep4

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 4


title: AK213 [tumor methylation microarray]


title: AK158 [tumor methylation microarray]


title: AK195 [tumor methylation microarray]


title: AK199 [tumor methylation microarray]


title: AK183 [tumor methylation microarray]


title: AK217 [tumor methylation microarray]


title: Control mLSEC biological rep3

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 3


title: AK185 [tumor methylation microarray]


title: AK153 [tumor methylation microarray]


title: S12

city: Gent

first: Ilias

last: Semmouri

state: Oost-Vlaanderen

address: Coupure Links 653

department: Faculty of Bio engineering

country: Belgium

institute: UGent

description:
Acute exposure
processed data file: mergedtablecounts.txt

data_processing:
Reads were trimmed using TrimGalore Version 0.4.1 (Babraham Bioinformatics, 2012).
Clean reads were then de novo assembled to form a draft transcriptome of T. longicornis, using the Trinity software (Version 2.1.1, Grabherr et. al., 2011).
The trimmed, clean paired-end reads of each sample were aligned/mapped to the de novo assembled reference transcriptome using TopHat v2.1.1.
HTSeq v0.6.1 (Anders et al. 2015) was used to calculate gene counts with the “union” model using the Htseq-count function.
Raw counts were filtered, whereby only genes with a cpm above 1 were retained.
Filtered counts were normalized using edgeR standard normalization method.
Genome_build: Mapped against assembled Temora draft transcriptome.
Supplementary_files_format_and_content: mergedtablecounts.txt: Tab-delimited text file contains raw counts.
Supplementary_files_format_and_content: Trinity.fasta: FASTA file includes de novo transcriptome assembly.

organism: Temora longicornis

source_name: whole organism

growth_protocol: Kept at dark, aerated vessels, temperature described above.

extract_protocol:
Total RNA was extracted from adult copepods using the MasterPureTM RNA Purification Kit (Epicentre®, tebu-bio NV), following the manufacturer's protocol.
An Illumina mRNA sequencing library was made from one µg total RNA of each sample using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, USA).
The size distribution, purity (absence of free adaptors) and quantity of the resulting libraries were measured using a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US). The libraries were equimolarly pooled and sequenced in three lanes of an Illumina HiSeq 3000 flow cell, generating paired-end 2x150bp reads.

value: whole body

value: switched from 14C to 17C

tag: total exposure time


title: AK139 [tumor methylation microarray]


title: AK178 [tumor methylation microarray]


title: AK133 [tumor methylation microarray]


title: S11


title: Control mLSEC biological rep2

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 2

tag: genotype


title: Control mLSEC biological rep1

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 1


title: AK156 [tumor methylation microarray]


title: S9

description:
Recovery exposure
processed data file: mergedtablecounts.txt

value: switched from 17C to 14C


title: S10


title: AK124 [tumor methylation microarray]


title: AK132 [tumor methylation microarray]


title: S8


title: AK117 [tumor methylation microarray]


title: AK123 [tumor methylation microarray]


title: AK142 [tumor methylation microarray]


title: S7


title: S6

description:
Sustained exposure
processed data file: mergedtablecounts.txt

value: kept constantly at 17C


title: S5


title: AK103 [tumor methylation microarray]


title: AK134 [tumor methylation microarray]


title: S4


title: S3

description:
Control
processed data file: mergedtablecounts.txt

value: control (constant at 14C)


title: S2


title: AK098 [tumor methylation microarray]


title: S1


title: AK081 [tumor methylation microarray]


title: AK099 [tumor methylation microarray]


title: AK088 [tumor methylation microarray]


title: AK089 [tumor methylation microarray]


title: AK085 [tumor methylation microarray]


title: AK074 [tumor methylation microarray]


title: AK091 [tumor methylation microarray]


title: AK079 [tumor methylation microarray]


title: AK006 [tumor methylation microarray]


title: AK072 [tumor methylation microarray]


title: AK071 [tumor methylation microarray]


title: AK100 [tumor methylation microarray]


title: OVCAR3_LV-CON_rep2

status: Public on Nov 04 2018

city: Shanghai

last: Liu

address: 2699 west gaoke road

department: Obstetrics and Gynecology

country: China

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

description: Biological replicate 2 of 3. Control negative vector transfected ovarian cancer OVCAR3 cells,untreated, harvested after several passages.

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

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

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

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

growth_protocol: OVCAR3 cells were cultured in RPMI-1640 medium (HyClone, USA), containing 10% fetal bovine serum (FBS, Gibco, USA), 100 units/mL penicillin, and 100 mg/mL streptomycin, at 37°C in a humidified 5% CO2 incubator.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: For overexpression of miR-200a, OVCAR3 cells were transfected with lentiviral vector with eGFP, encoding miR-200a and negative control vector (LV- miR-200a and LV-vector) by using polybrene (5.0 µg/mL). Cells were selected with medium containing 0.2 mg/mL puromycin after 48h of infection. The dysregulation of miR-200a was confirmed by using RT-PCR.

tag: cell line

value: ovarian cancer cells

tag: transfection

value: control


title: AK055 [tumor methylation microarray]


title: OVCAR3_LV-CON_rep3

description: Biological replicate 3 of 3. Control negative vector transfected ovarian cancer OVCAR3 cells,untreated, harvested after several passages.


title: 160003842T-2

city: Chongqing

first: Qingzhu

last: Jia

address: Xinqiao

department: Department of Onoclogy

institute: XinQiao Hospital

data_processing:
Illumina built-in software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Tissue 02 from patient No.024

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient

tag: diagnosis

value: non-small cell lung cancer (NSCLC)


title: AK068 [tumor methylation microarray]

value: male

tag: age


title: AK053 [tumor methylation microarray]


title: 160003842T-3

source_name: Tissue 03 from patient No.024


title: OVCAR3_LV-CON_rep1

description: Biological replicate 1 of 3. Control negative vector transfected ovarian cancer OVCAR3 cells,untreated, harvested after several passages.

tag: cell type


title: AK076 [tumor methylation microarray]


title: 160003842T-1

source_name: Tissue 01 from patient No.024


title: AK041 [tumor methylation microarray]


title: AK015 [tumor methylation microarray]


title: AK102 [tumor methylation microarray]


title: AK005 [tumor methylation microarray]


title: AK043 [tumor methylation microarray]


title: 160003830T-4

source_name: Tissue 05 from patient No.016


title: 160003830T-5

source_name: Tissue 06 from patient No.016


title: OVCAR3_LV-miR-200a_rep3

description: Biological replicate 3 of 3. Stable miR-200a-gene transfected ovarian cancer OVCAR3 cells, harvested after several passages.

value: miR-200a overexpression


title: 160003838T-1

source_name: Tissue 01 from patient No.021


title: 160003830T-3

source_name: Tissue 03 from patient No.016


title: OVCAR3_LV-miR-200a_rep1

description: Biological replicate 1 of 3. Stable miR-200a-gene transfected ovarian cancer OVCAR3 cells, harvested after several passages.


title: 160003828T-1

source_name: Tissue 01 from patient No.009


title: AK035 [tumor methylation microarray]


title: 160003828T-2

source_name: Tissue 02 from patient No.009


title: AK030 [tumor methylation microarray]


title: 160003824T-2

source_name: Tissue 02 from patient No.015


title: AK049 [tumor methylation microarray]

source_name: adult glioblastoma tumour


title: 160003824T-3

source_name: Tissue 03 from patient No.015


title: 160003824T-1

source_name: Tissue 01 from patient No.015


title: AK002 [tumor methylation microarray]


title: 160003820T-2

source_name: Tissue 02 from patient No.013


title: 160003820T-3

source_name: Tissue 03 from patient No.013


title: 160003820T-1

source_name: Tissue 01 from patient No.013


title: 160003818T-3

source_name: Tissue 03 from patient No.008


title: AK051 [tumor methylation microarray]


title: 160003818T-2

source_name: Tissue 02 from patient No.008


title: 160003814T-5

source_name: Tissue 05 from patient No.007


title: 160003814T-4

source_name: Tissue 04 from patient No.007


title: AK066 [tumor methylation microarray]


title: 160003818T-1

source_name: Tissue 01 from patient No.008


title: 160003809T-1

source_name: Tissue 01 from patient No.023


title: 160003809T-5

source_name: Tissue 05 from patient No.023


title: 160003809T-4

source_name: Tissue 04 from patient No.023


title: 160003814T-3

source_name: Tissue 03 from patient No.007


title: 160003814T-1

source_name: Tissue 01 from patient No.007


title: 160003838T-2

source_name: Tissue 02 from patient No.021


title: 160003809T-3

source_name: Tissue 03 from patient No.023


title: 160003809T-2

source_name: Tissue 02 from patient No.023


title: 160003807T-5

source_name: Tissue 05 from patient No.022


title: 160003828T-3

source_name: Tissue 03 from patient No.009


title: 160003807T-4

source_name: Tissue 04 from patient No.022


title: 160003805T-5

source_name: Tissue 05 from patient No.019


title: 160003807T-3

source_name: Tissue 03 from patient No.022


title: 160003838T-3

source_name: Tissue 03 from patient No.021


title: AK003 [tumor methylation microarray]

source_name: adult glioblastoma tumour


title: 160003805T-4

source_name: Tissue 04 from patient No.019


title: 160003807T-2

source_name: Tissue 02 from patient No.022


title: 160003805T-3

source_name: Tissue 03 from patient No.019


title: 160003805T-2

source_name: Tissue 02 from patient No.019


title: 160003803T-6

source_name: Tissue 06 from patient No.002


title: 160003807T-6

source_name: Tissue 06 from patient No.022


title: 160003803T-3

source_name: Tissue 03 from patient No.002


title: 160003803T-4

source_name: Tissue 04 from patient No.002


title: 160003803T-2

source_name: Tissue 02 from patient No.002


title: OVCAR3_LV-miR-200a_rep2

description: Biological replicate 2 of 3. Stable miR-200a-gene transfected ovarian cancer OVCAR3 cells, harvested after several passages.


title: MOLM13_dBRD9-6d_RNA-Seq_Rep2

first: Cigall

last: Kadoch

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

data_processing:
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
RNA-seq reads were aligned to UCSC hg19 using STAR version 2.5.2a Only uniquely mapping reads with at most two mismatches were retained.
RNA read counts were calculated using GFOLD
Genome_build: hg19
Supplementary_files_format_and_content: read count files for gene expression created using GFOLD

source_name: MOLM13 (AML)

growth_protocol: Malignant rhabdoid tumor cell line TTC1240 were grown in DMEM (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco).  MOLM-13 cells were grown in RPMI (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco)

extract_protocol:
RNA was collected from 2 million cells per condition, in biological duplicate, using the RNeasy Mini Kit (QIAGEN).
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

treatment_protocol: MOLM-13 and TTC1240 were treated with (1:10,000) DMSO vehicle control or 250nM dBRD9 to chemically degrade BRD9 for 6 days (MOLM-13) or 7 days (TTC1240) in biological duplicate followed by harvesting of RNA.

tag: agent


title: MOLM13_DMSO_RNA-Seq_Rep2

value: DMSO


title: MOLM13_dBRD9-6d_RNA-Seq_Rep1


title: MOLM13_DMSO_RNA-Seq_Rep1


title: TTC1240_dBRD9-7d_RNA-Seq_Rep2

source_name: TTC1240 (MRT)


title: TTC1240_dBRD9-7d_RNA-Seq_Rep1


title: 160003803T-5

source_name: Tissue 05 from patient No.002


title: 160003803T-1

source_name: Tissue 01 from patient No.002


title: TTC1240_DMSO-7d_RNA-Seq_Rep2


title: TTC1240_DMSO-7d_RNA-Seq_Rep1


title: MOLM13 (AML)_SMARCA4_dBRD9_ChIP-Seq

data_processing:
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 2.1.0, reporting only the highest scoring alignment for each sequence.
To create ChIP-seq coverage plots, bedGraph plots were created using MACS2 callpeak, sorted and then converted to bigWig format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig script downloaded from UCSC

extract_protocol:
ChIP-seq was performed using standard protocols (Millipore, Billerica, MA).  Specifically, cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 10min at 37C and quenched with 125mM glycine for 5min at 37C.   After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody.
ChIP-sequencing libraries were prepared with the Rubicon Thruplex DNAseq prep kit using standard protocols.

treatment_protocol: MOLM13 cells were treated with 250nM dBRD9 (at a 1:10,000 dilution) or DMSO control for 6 days, fixed, and then used for ChIP-seq with a SMARCA4 antibody.  Aska cells were lentivirally infected with pLKO shScramble or shSSX1, selected for two days with puromycin, and fixed for ChIP 7 days post infection.  In Aska, BRD9 antibody was used for ChIP-seq. In TTC1240, CTCF ChIP was performed on cells lentivirally infected with an empty vector, selected for 2 days with blasticidin, and fixed for ChIP 7 days post infection.  BRD9 and SMARCA4 ChIP-seq was performed in TTC1240 cells treated with either 250nM dBRD9 (1:10,000 dilution) or DMSO control for 7 days and fixed for ChIP.  Samples were spiked in with spike-in antibody (2ug) and Drosophila chromatin (15ng, Cat #53083) from Active Motif. SMARCA4 ChIP was performed in duplicate from independent samples.

tag: chip antibody

value: Abcam (EPNCIR111A)


title: Aska_BRD9_shScr_ChIP-Seq

source_name: Aska (SS)

value: Aska


title: Aska_BRD9_shSSX1_ChIP-Seq


title: TTC1240_SMARCA4_Rep2_DMSO_ChIP-Seq


title: TTC1240_SMARCA4_Rep2_dBRD9_ChIP-Seq


title: in_vitro_mix_17

city: Jerusalem

first: Joshua

last: Moss

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

description:
6% Colon cells
Multiple donors
Mix17

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing: Methylation array data were processed with the minfi package in R. For each sample analyzed on the Illumina Methylation array, CpG sites were filtered out if they were represented by less than 3 beads on the array, if the detection p-value (representing total fluorescence of the relevant probes) was greater than 0.01, or if they mapped to a sex chromosome. Background correction and normalization were performed with the preprocessIllumina function, which removes background calculated based on internal control probes and normalizes all samples to a predetermined control sample.

label: Cy5 and Cy3

source_name: in vitro mix of genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: cfDNA extraction from plasma was performed with the QIAsymphony liquid handling robot. cfDNA was treated with the Illumina Infinium FFPE  473 restoration kit. DNA from other samples was obtained as detailed in Moss et al., 2018.

tag: sample type

value: In vitro mix

tag: disease state

value: Mix


title: cfDNA_breast_cancer_1438

description:
Metastases: Brain, spinal cord, liver
pl1438

source_name: cfDNA, breast adenocarcinoma

value: cfDNA

value: Breast adenocarcinoma

tag: gender

value: Female


title: lung_epithelial_cells_rep3

description: Lung 3

source_name: lung epithelial cells

value: Lung epithelial cells

value: Normal

value: Male


title: leukocytes_1

source_name: leukocytes

value: Leukocytes


title: colon_epithelial_cells_rep3

description: Colon 3

source_name: colon epithelial cells

value: Colon epithelial cells


title: in_vitro_mix_13

description:
5% Lung cells, 3.5% Colon cells
Multiple donors
Mix13


title: in_vitro_mix_16

description:
8% Lung cells
Multiple donors
Mix16


title: TTC1240_Input_DMSO_ChIP-Seq


title: in_vitro_mix_9

description:
10% Hepatocytes, 3.5% Lung cells
Multiple donors
Mix9


title: in_vitro_mix_14

description:
10% Lung cells, 3.5% Neurons
Multiple donors
Mix14


title: in_vitro_mix_12

description:
10% Colon cells, 5% Neurons
Multiple donors
Mix12


title: in_vitro_mix_11

description:
3.5% Hepatocytes, 5% Colon cells
Multiple donors
Mix11


title: in_vitro_mix_15

description:
4% Hepatocytes
Multiple donors
Mix15


title: in_vitro_mix_10

description:
5% Hepatocytes, 10% Neurons
Multiple donors
Mix10


title: cfDNA_lung_cancer_2244

description:
Metastases: Lungs, adrenal, brain
pl2244

source_name: cfDNA, lung carcinoma

value: Small-cell lung carcinoma


title: colon_epithelial_cells_rep1

description: Colon 1


title: colon_epithelial_cells_rep2

description: Colon 2


title: cfDNA_lung_cancer_1433

description:
Metastases: Brain ,spinal cord
pl1433

value: Non-small-cell lung carcinoma


title: TTC1240_CTCF_Empty_ChIP-Seq

value: Cell Signaling Technologies (3418S)


title: cfDNA_healthy_individual_4

source_name: cfDNA, normal


title: TTC1240_BRD9_dBRD9_ChIP-Seq


title: cfDNA_lung_cancer_1478

description:
Metastases: Brain
pl1478


title: cfDNA_mix_6

description:
5% pl806, 95% HI2
Multiple donors
Mix6

source_name: cfDNA, in vitro mix

value: cfDNA In vitro mix


title: cfDNA_breast_cancer_1711

description:
Metastases: Brain, liver, adrenal
pl1711


title: cfDNA_mix_7

description:
3% pl806, 97% HI2
Multiple donors
Mix7


title: cfDNA_mix_3

description:
5% pl806, 95% HI4
Multiple donors
Mix3


title: cfDNA_breast_cancer_1040

description:
Metastases: Liver, lung, bone, brain
pl1040


title: TTC1240_dBRD9-3d_RNA-Seq_Rep2

data_processing:
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
RNA-seq reads were aligned to UCSC hg19 using STAR version 2.5.2a Only uniquely mapping reads with at most two mismatches were retained.
RNA read counts were calculated using GFOLD
Genome_build: hg19
Supplementary_files_format_and_content: read count files for gene expression created using GFOLD. Column headers are: GeneSymbol, GeneName, Read Count, Gene Exon Length, RPKM

growth_protocol: CRL7250 cells and malignant rhabdoid tumor cell line TTC1240 were grown in DMEM (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco).  Synovial sarcoma cell line SYO1 was grown in DMEM without sodium pyruvate (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco).

treatment_protocol: SYO-1 and TTC1240 were treated with (1:5,000 and 1:10,000) DMSO vehicle control or (500nM and 250nM) dBRD9 to chemically degrade BRD9 for 3 days or 6 days in biological duplicate followed by harvesting of RNA.  SYO-1 cells were also lentivirally infected in biological duplicate with pGIPZ shControl, pGIPZ shBRD9, and pGIPZ shSMARCE1 vectors to knockdown BRD9 and SMARCE1 and selected with puromycin 2 days post infection for 5 days.  RNA was harvested 7 days post infection.  CRL7250 cells were treated with either 1:10,000 DMSO vehicle control or 250nM dBRD9 for 7 days or 24hr pre-treatment with 250nM dBRD9 followed by lentiviral infection with V5-SS18-SSX1 and selected with puromycin 2 days post infection for 5 days, with RNA harvested 7 days post infection.

value: MRT

tag: condition


title: cfDNA_healthy_individual_3


title: cfDNA_colon_cancer_2010

description:
Metastases: Liver
pl2010

source_name: cfDNA, colon adenocarcinoma

value: Colon adenocarcinoma


title: TTC1240_dBRD9-3d_RNA-Seq_Rep1


title: TTC1240_DMSO-3d_RNA-Seq_Rep2

value: DMSO


title: cfDNA_mix_1

description:
5% pl806, 95% HI3
Multiple donors
Mix1


title: TTC1240_DMSO-3d_RNA-Seq_Rep1


title: SYO1_shBAF57_RNA-Seq_Rep2

source_name: SYO1 (Synovial Sarcoma)

value: Synovial Sarcoma


title: SYO1_shBAF57_RNA-Seq_Rep1


title: SYO1_shBRD9_RNA-Seq_Rep2


title: SYO1_shBRD9_RNA-Seq_Rep1


title: TTC1240_SMARCA4_Rep1_DMSO_ChIP-Seq

value: Abcam (EPNCIR111A)


title: cfDNA_healthy_individual_2

value: cfDNA


title: cfDNA_mix_5

description:
10% pl806, 90% HI2
Multiple donors
Mix5

value: Mix


title: TTC1240_SMARCA4_Rep1_dBRD9_ChIP-Seq


title: SYO1_shCtrl_RNA-Seq_Rep2

value: shCtrl


title: TTC1240_BRD9_DMSO_ChIP-Seq


title: SYO1_dBRD9-3d_RNA-Seq_Rep2


title: SYO1_shCtrl_RNA-Seq_Rep1


title: SYO1_DMSO-3d_RNA-Seq_Rep2


title: SYO1_DMSO-3d_RNA-Seq_Rep1


title: SYO1_dBRD9-6d_RNA-Seq_Rep1


title: SYO1_dBRD9-6d_RNA-Seq_Rep2


title: SYO1_DMSO-6d_RNA-Seq_Rep2


title: SYO1_dBRD9-3d_RNA-Seq_Rep1


title: cfDNA_CUP_1936_1994

description:
Metastases: Liver, brain, bones
pl1936_1994

source_name: cfDNA, CUP

value: Cancer of Unkown Primary

value: Female


title: SYO1_DMSO-6d_RNA-Seq_Rep1


title: cortical_neurons_rep3

description: Neurons 3

source_name: cortical neurons

value: Cortical neurons

value: Normal

value: Male


title: cortical_neurons_rep2

description: Neurons 2


title: hepatocytes_rep3

description: Hepatocytes 3

source_name: hepatocytes

value: Hepatocytes


title: CRL7250_dBRD9_RNA-Seq_Rep2

source_name: CRL7250 (fibroblast)

value: fibroblast


title: CRL7250_DMSO_RNA-Seq_Rep2


title: CRL7250_V5_SS18_SSX1_dBRD9_RNA-Seq_Rep1


title: cfDNA_CUP_1322

description:
Metastases: Bones, lungs
pl1322


title: TTC1240_Input_dBRD9_ChIP-Seq

source_name: TTC1240 (MRT)


title: TTC1240_BRD9_N106_Empty_ChIP-Seq

growth_protocol: HEK293T cells and malignant rhabdoid tumor cell line TTC1240 were grown in DMEM (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco).  Acute myeloid leukemia cell lines EoL-1 and MOLM-13 were grown in RPMI (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco).  Synovial sarcoma cell line SYO-1 was grown in DMEM without sodium pyruvate (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco).

treatment_protocol: EoL-1 and JURKAT cells were untreated.  MOLM-13 cells were treated with 1:10,000 DMSO for 48hr.  SYO-1 cells were lentivirally infected with either shControl or shSSX vector, selected with puromycin for 48h, and then cultured for 5 days.  Cells were harvested for ChIP-seq 7 days post infection.  TTC1240 cells were lentivirally infected with empty vector control or vector containing SMARCB1.

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

tag: antibody lot number


title: CRL7250_DMSO_RNA-Seq_Rep1


title: CRL7250_V5_SS18_SSX1_dBRD9_RNA-Seq_Rep2


title: pancreatic_beta_cells_rep4

description: Beta cells 4

source_name: pancreatic beta cells

value: Pancreatic beta cells


title: TTC1240_BRD9_N106_SMARCB1_ChIP-Seq

value: MRT


title: hepatocytes_rep2

description: Hepatocytes 2


title: CRL7250_dBRD9_RNA-Seq_Rep1


title: cfDNA_CUP_1302

description:
Metastases: Brain, lungs, bones
pl1302


title: cfDNA_pancreatic_islet_recipient_151_2_1hr_post

description:
1 hour post transplant
UB0151-Tx2-2

source_name: cfDNA, pancreatic islet transplant recipient, 1 hour post-transplant

value: Pancreatic islet transplant recipient


title: lung_epithelial_cells_rep2

description: Lung 2

value: Lung epithelial cells


title: cfDNA_pancreatic_islet_recipient_144_2_pre

description:
Pre-transplant
UB0144-Tx2-1

source_name: cfDNA, pancreatic islet transplant recipient, pre-transplant


title: JURKAT_BRD9_Naive_ChIP-Seq

source_name: JURKAT (T-ALL)

value: T-ALL

value: JURKAT


title: JURKAT_CTCF_Naive_ChIP-Seq

value: CTCF

value: CST


title: cfDNA_pancreatic_islet_recipient_151_2_2hr_post

description:
2 hours post transplant
UB0151-Tx2-3

source_name: cfDNA, pancreatic islet transplant recipient, 2 hours post-transplant

value: cfDNA


title: cfDNA_CUP_1149

description:
Metastases: Bones
pl1149

value: Cancer of Unkown Primary


title: JURKAT_Input_Naive_ChIP-Seq

value: none (Input)


title: cfDNA_pancreatic_islet_recipient_144_2_2hr_post

description:
2 hours post transplant
UB0144-Tx2-3


title: lung_epithelial_cells_rep1

description: Lung 1

source_name: lung epithelial cells


title: cfDNA_pancreatic_islet_recipient_151_2_pre

description:
Pre-transplant
UB0151-Tx2-1


title: vascular_endothelial_cells_rep2

description:
Multiple donors (2)
Vasc_endothel 2

source_name: vascular endothelial cells

value: Vascular endothelial cells


title: cfDNA_pancreatic_islet_recipient_151_1_1hr_post

description:
1 hour post transplant
UB0151-Tx1-2


title: SYO1_BRD9_shSSX_ChIP-Seq

value: Synovial Sarcoma


title: SYO1_SS18_shSSX_ChIP-Seq

value: Lot 1


title: cfDNA_pancreatic_islet_recipient_151_1_pre

description:
Pre-transplant
UB0151-Tx1-1


title: cfDNA_pancreatic_islet_recipient_151_1_2hr_post

description:
2 hours post transplant
UB0151-Tx1-3


title: SYO1_Input_shSSX_ChIP-Seq


title: SYO1_SS18_shControl_ChIP-Seq


title: cfDNA_pancreatic_islet_recipient_144_2_1hr_post

description:
1 hour post transplant
UB0144-Tx2-2


title: cfDNA_healthy_individual_1

value: Normal

value: Male


title: SYO1_BRD9_shControl_ChIP-Seq

value: Abcam


title: SYO1_CTCF_shControl_ChIP-Seq

value: Lot 3


title: SYO1_Input_shControl_ChIP-Seq


title: EOL1_H3K4me3_Naive_ChIP-Seq

source_name: EOL1 (AML)

value: AML

value: Millipore


title: EOL1_H3K4me1_Naive_ChIP-Seq


title: cfDNA_colon_cancer_806_50ng

description:
Metastases: Liver, lung, bone
pl806_cc_50

source_name: cfDNA, colon adenocarcinoma, 50 ng DNA used

value: Colon adenocarcinoma


title: MOLM13_CTCF_DMSO_ChIP-Seq

source_name: MOLM13 (AML)


title: cfDNA_colon_cancer_684

description:
Metastases: Liver
pl684_cc

source_name: cfDNA, colon adenocarcinoma

value: Female


title: cfDNA_lung_cancer_1

description:
Metastases: NA
LNG-001

source_name: cfDNA, lung carcinoma

value: Non-small-cell lung carcinoma


title: cfDNA_colon_cancer_806

description:
Metastases: Liver, lung, bone
pl806_cc_250


title: MOLM13_GLTSCR1_DMSO_ChIP-Seq

value: Santa Cruz


title: MOLM13_DPF2_DMSO_ChIP-Seq


title: MOLM13_BRD7_DMSO_ChIP-Seq

value: CST


title: MOLM13_BRD9_DMSO_ChIP-Seq


title: cfDNA_sepsis_34

description:
AST:19,AST:53,ALK:24,GGT:17,TB:22,LDH:585
SEP-034

source_name: cfDNA, sepsis

value: cfDNA

value: Sepsis


title: MOLM13_Input_DMSO_ChIP-Seq

value: none (Input)


title: MOLM13_SMARCA4_DMSO_ChIP-Seq


title: EOL1_CTCF_Naive_ChIP-Seq

value: CTCF


title: EOL1_DPF2_Naive_ChIP-Seq


title: cfDNA_sepsis_4

description:
AST:87,AST:219,ALK:71,GGT:135,TB:13,LDH:869
SEP-004


title: cfDNA_sepsis_20

description:
AST:209,AST:284,ALK:123,GGT:41,TB:3,LDH:520
SEP-020


title: cfDNA_sepsis_55

description:
AST:90,AST:20,ALK:195,GGT:178,TB:39,LDH:461
SEP-055


title: EOL1_SMARCC1_Naive_ChIP-Seq

value: homemade


title: EOL1_GLTSCR1_Naive_ChIP-Seq


title: EOL1_BRD7_Naive_ChIP-Seq


title: cfDNA_sepsis_49

description:
AST:12,AST:39,ALK:158,GGT:105,TB:40,LDH:385
SEP-049


title: cfDNA_sepsis_45

description:
AST:11,AST:8,ALK:40,GGT:27,TB:2,LDH:389
SEP-045


title: cfDNA_sepsis_31

description:
AST:11,AST:8,ALK:40,GGT:27,TB:2,LDH:389
SEP-031


title: cfDNA_sepsis_5

description:
AST:90,AST:20,ALK:195,GGT:178,TB:39,LDH:461
SEP-005


title: cfDNA_sepsis_18

description:
AST:75,AST:144,ALK:69,GGT:142,TB:15,LDH:725
SEP-018


title: cfDNA_sepsis_16

description:
AST:1082,AST:2534,ALK:63,GGT:10,TB:11,LDH:398
SEP-016


title: EOL1_BRD9_137245_Naive_ChIP-Seq


title: EOL1_SMARCA4_Naive_ChIP-Seq


title: EOL1_BRD9_66443_Naive_ChIP-Seq


title: cfDNA_sepsis_23_250ng_rep1

description:
AST:67,AST:98,ALK:144,GGT:112,TB:171,LDH:492
SEP-023_250_1


title: cfDNA_sepsis_17_250ng_rep2

description:
AST:1549,AST:3497,ALK:490,GGT:166,TB:78,LDH:4664
SEP-017_250_2


title: cfDNA_sepsis_23_50ng

description:
AST:67,AST:98,ALK:144,GGT:112,TB:171,LDH:492
SEP-023_50

source_name: cfDNA, sepsis, 50 ng DNA used


title: vascular_endothelial_cells_rep1

description:
Multiple donors (3)
Vasc_endothel 1

value: Vascular endothelial cells


title: cfDNA_sepsis_23_250ng_rep2

description:
AST:67,AST:98,ALK:144,GGT:112,TB:171,LDH:492
SEP-023_250_2


title: cfDNA_sepsis_17_250ng_rep1

description:
AST:1549,AST:3497,ALK:490,GGT:166,TB:78,LDH:4664
SEP-017_250_1


title: cfDNA_sepsis_26_100ng

description:
AST:1195,AST:3135,ALK:317,GGT:180,TB:72,LDH:4746
SEP-026_100

source_name: cfDNA, sepsis, 100 ng DNA used


title: cfDNA_sepsis_17_50ng_rep2

description:
AST:1549,AST:3497,ALK:490,GGT:166,TB:78,LDH:4664
SEP-017_50


title: EOL1_Input_Naive_ChIP-Seq


title: cfDNA_sepsis_26_250ng_rep1

description:
AST:1195,AST:3135,ALK:317,GGT:180,TB:72,LDH:4746
SEP-026_250_1


title: cfDNA_sepsis_3

description:
AST:71,AST:86,ALK:82,GGT:136,TB:8,LDH:720
SEP-003


title: MF.PC.14

status: Public on Nov 03 2018

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Peritoneal Macrophage

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Peritoneal Cavity

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

tag: strain

value: 25 weeks old

tag: sorting markers

value: live  single  F480+ ICAM2+

value: Macrophage


title: MF.PC.13

description: Peritoneal Macrophage


title: MF.PC.11

description: Peritoneal Macrophage


title: cortical_neurons_rep1

description: Neurons 1

source_name: cortical neurons

value: Cortical neurons

value: Normal

value: Male


title: adipocytes_rep3

description: Adipocytes 3

source_name: adipocytes

value: Adipocytes


title: cfDNA_post_islet_transplant_pool

description:
1 hour post transplant
Multiple donors
islet_trans_pool

source_name: cfDNA, 1 hr post pancreatic islet transplantation, pooled from multiple donors

value: Pancreatic islet transplant recipients


title: Mo.6Cp.Bl.1

description: Monocyte

source_name: Blood

value: Monocyte


title: Mo.6Cp.Bl.2

description: Monocyte


title: hepatocytes_rep1

description: Hepatocytes 1

source_name: hepatocytes

value: Hepatocytes

value: Female


title: MF.PC.12

description: Peritoneal Macrophage


title: cfDNA_old_male_pool_rep2

description:
Old males
Multiple donors
Old_M2

source_name: cfDNA of old males, pooled from multiple donors

value: cfDNA


title: cfDNA_old_female_pool_rep2

description:
Old females
Multiple donors
Old_F2

source_name: cfDNA of old females, pooled from multiple donors


title: cfDNA_sepsis_2

description:
AST:29,AST:41,ALK:193,GGT:NA,TB:138,LDH:418
SEP-002

value: Sepsis


title: cfDNA_sepsis_26_250ng_rep2

description:
AST:1195,AST:3135,ALK:317,GGT:180,TB:72,LDH:4746
SEP-026_250_2


title: adipocytes_rep2

description: Adipocytes 2


title: Mo.6Cn.Bl.2

description: Monocyte


title: Mo.6Cn.Bl.1

description: Monocyte


title: MF.PC.15

description: Peritoneal Macrophage


title: MG.SC.2

description: Microglial

source_name: Spinal Cord

value: Microglia


title: pancreatic_beta_cells_rep3

description: Beta cells 3

source_name: pancreatic beta cells

value: Pancreatic beta cells


title: MG.SC.1

description: Microglial


title: MF.SN.3

description: Macrophage

source_name: Sciatic nerve


title: pancreatic_duct_cells_rep1

description:
Multiple donors (4)
Duct 1

source_name: pancreatic duct cells

value: Pancreatic duct cells


title: cfDNA_old_male_pool_rep1

description:
Old males
Multiple donors
Old_M1


title: MF.microglia.CNS.5

description: Macrophage

source_name: Brain

value: CD45lo F4/80lo CD206lo CD11b+ CD64+


title: cfDNA_old_female_pool_rep1

description:
Old females
Multiple donors
Old_F1


title: cfDNA_young_female_pool_rep1

description:
Young females
Multiple donors
Young_F1

source_name: cfDNA of young females, pooled from multiple donors


title: adipocytes_rep1

description: Adipocytes 1


title: pancreatic_acinar_cells_rep1

description:
Multiple donors (3)
Acinar 1

source_name: pancreatic acinar cells

value: Pancreatic acinar cells


title: MF.PC.25

description: Peritoneal Macrophage

value: 25 weeks old


title: MF.PC.26

description: Peritoneal Macrophage

value: Macrophage


title: cfDNA_young_male_pool_rep2

description:
Young males
Multiple donors
Young_M2

source_name: cfDNA of young males, pooled from multiple donors


title: MG.SC.3

description: Microglial


title: MF.SN.1

description: Macrophage


title: MF.microglia.CNS.3

description: Macrophage


title: MF.microglia.CNS.2

description: Macrophage


title: pancreatic_beta_cells_rep1

description: Beta cells 1


title: pancreatic_beta_cells_rep2

description: Beta cells 2


title: MF.DRG.1

description: Macrophage

source_name: Dorsal root ganglia


title: MF.DRG.4

description: Macrophage


title: MF.alv.11cp64pSiglecFp.Lu.3

description: Alveolar Macrophage

source_name: Lung

value: CD45+ CD11blo CD64+ CD11c+ SiglecF+


title: MF.64pMerTKp11blo.Sp.2

description: Splenic Macrophage

source_name: Spleen


title: MF.64pMerTKp11blo.Sp.1

description: Splenic Macrophage


title: MF.alv.11cp64pSiglecFp.Lu.1

description: Alveolar Macrophage


title: MF.480p64pMerTKp.MAT.4

description: Mesenteric Fat Macrophage

source_name: Mesenteric Fat


title: MF.microglia.CNS.1

description: Macrophage


title: cfDNA_sepsis_26_50ng

description:
AST:1195,AST:3135,ALK:317,GGT:180,TB:72,LDH:4746
SEP-026_50

source_name: cfDNA, sepsis, 50 ng DNA used


title: MF.480p64pMerTKp.MAT.3

description: Mesenteric Fat Macrophage


title: MF.480p64pMerTKp.WAT.3

description: Inguinal Fat Macrophage

source_name: Inguinal fat


title: MF.480p64pMerTKp.MAT.1

description: Mesenteric Fat Macrophage


title: MF.480p64pLyve1p.MS.2

description: Mesenteric Sheet Macrophage

source_name: Mesenteric Sheet


title: MF.480p64pMerTKp.AT.3

description: Epididymal Fat Macrophage

source_name: Epididymal fat


title: MF.480p64pMerTKp.AT.2

description: Epididymal Fat Macrophage


title: MF.alv.11cp64pSiglecFp.Lu.2

description: Alveolar Macrophage


title: MF.480p64pLyve1p.MS.3

description: Mesenteric Sheet Macrophage


title: MF.480p64pLyve1p.MS.1

description: Mesenteric Sheet Macrophage


title: MF.480p64pMerTKp.AT.1

description: Epididymal Fat Macrophage


title: MF.480p64pMerTKp.WAT.2

description: Inguinal Fat Macrophage


title: MF.480p64pLyve1p.MS.4

description: Mesenteric Sheet Macrophage


title: MF.480p64pMerTKp.MAT.2

description: Mesenteric Fat Macrophage


title: MF.microglia.CNS.4

description: Macrophage


title: MF.226pIIp.PC.3

description: Peritoneal Macrophage

source_name: Peritoneal Cavity

value: CD11b+ CD115+ MHCII+ CD226+


title: MF.226pIIp.PC.4

description: Peritoneal Macrophage


title: MF.226pIIp480lo.PC.1

description: Peritoneal Macrophage


title: MF.480p.SP.2

description: Splenic Macrophage


title: MF.PC.40

description: Peritoneal Macrophage

value: 7 weeks old


title: MF.226pIIp.PC.1

description: Peritoneal Macrophage


title: MF.PC.23

description: Peritoneal Macrophage


title: MF.226pIIp480lo.PC.2

description: Peritoneal Macrophage

source_name: Peritoenal Cavity


title: DC.8an103p.PP.3

description: CD8- Dendritic Cell

source_name: Peyer's Patch

value: Dendritic Cell


title: DC.8an103p.PP.4

description: CD8- Dendritic Cell


title: MF.480p64pMerTKp.WAT.1

description: Inguinal Fat Macrophage


title: DC.8ap.PP.1

description: CD8+ Dendritic Cell

value: PI- (CD3/CD19/NK1.1/Ly6G)- CD11c+ MHC+ CD8a+


title: DC.8ap.PP.4

description: CD8+ Dendritic Cell


title: DC.8an103p.MLN.2

description: CD8- Dendritic Cell

source_name: Lymph Node (Mesenteric)


title: DC.8an103p.MLN.4

description: CD8- Dendritic Cell


title: DC.8ap.PP.3

description: CD8+ Dendritic Cell


title: DC.8ap.MLN.3

description: CD8+ Dendritic Cell


title: DC.8ap.MLN.4

description: CD8+ Dendritic Cell


title: MF.480p.SP.1

description: Splenic Macrophage


title: MF.PC.24

description: Peritoneal Macrophage


title: DC.8an103p.PP.1

description: CD8- Dendritic Cell


title: MF.PC.39

description: Peritoneal Macrophage


title: DC.8an103p.MLN.1

description: CD8- Dendritic Cell


title: DC.8ap.MLN.1

description: CD8+ Dendritic Cell


title: DC.8ap.MLN.2

description: CD8+ Dendritic Cell


title: Mo.6Cp.Lu.3

description: Monocytes

value: 8 weeks old

value: CD45+ Ly6G- SiglecF- F4/80+ Ly6C+ CD11b+

value: Monocyte


title: DC.8an103p.MLN.3

description: CD8- Dendritic Cell


title: Mo.6Cp.Bl.4

description: Monocytes

source_name: Blood


title: Mo.6Cp.Lu.1

description: Monocytes


title: Mo.6Cp.Bl.5

description: Monocytes


title: Mo.6Cp.Lu.2

description: Monocytes


title: Mo.6Cn.Lu.2

description: Monocytes

value: CD45+ Ly6G- SiglecF- F4/80+ Ly6C- CD11b+ Cx3cr1+


title: Mo.6Cn.Bl.3

description: Microglial


title: Mo.6Cn.Lu.1

description: Monocytes


title: MG.cortex.1

description: Microglial

source_name: Brain

value: lin- PI- CD45int CD11b+


title: MG.hippo.3

description: Microglial

value: Microglia


title: Mo.6Cn.Lu.3

description: Monocytes


title: cfDNA_young_female_pool_rep2

description:
Young females
Multiple donors
Young_F2

source_name: cfDNA of young females, pooled from multiple donors

value: cfDNA

value: Normal

value: Female


title: MG.cortex.2

description: Microglial


title: MG.cortex.3

description: Microglial


title: MG.hippo.1

description: Microglial


title: MG.hippo.2

description: Microglial


title: MF.microglia.cerebr.CNS.3

description: Macrophage

value: CD45lo CD11b+


title: MF.microglia.cerebr.CNS.2

description: Macrophage


title: MG.cerebel.1

description: Microglial


title: MF.pIC.alv.siglecFp.Lu.2

description: Macrophage

value: CD45+ SiglecF+ CD11c+


title: MG.cerebel.2

description: Microglial


title: MF.microglia.cerebr.CNS.1

description: Macrophage

value: Macrophage


title: MF.microglia.cerebel.CNS.2

description: Macrophage


title: MF.microglia.cerebel.CNS.1

description: Macrophage


title: MF.alv.6GnSigFp11cp.Lu.2

description: Alveolar Macrophage

value: CD45+ Ly6G- SiglecF+ CD11c+


title: Mo.6Cp.Bl.3

description: Monocytes


title: MG.cerebel.3

description: Microglial


title: DC.res.8p.LuLN.2

description: CD8+ Dendritic Cell

source_name: Mediastinal LN

value: CD45+ lin- PI- MHCII+ CD11chi CD8+ CD11b-


title: DC.res.8p.LuLN.3

description: CD8+ Dendritic Cell


title: DC.res.8p.LuLN.1

description: CD8+ Dendritic Cell


title: DC.res.11bp.LuLN.1

description: Dendritic Cell

value: CD45+ lin- PI- MHCII+ CD11chi CD8- CD11b+


title: DC.mig.103p.LuLN.2

description: Dendritic Cell

value: CD45+ lin- PI- MHCIIhi CD11c+ CD103+ CD11b-

value: Dendritic Cell


title: DC.mig.103p.LuLN.1

description: Dendritic Cell

value: 8 weeks old


title: DC.mig.11bp.LuLN.2

description: Dendritic Cell

value: CD45+ lin- PI- MHCIIhi CD11c+ CD103- CD11b+


title: DC.mig.11bp.LuLN.1

description: Dendritic Cell


title: DC.8p4n.Sp.1

description: CD8+ Dendritic Cell

value: CD45+ MHCII+ CD11c+ CD8+ CD4-


title: DC.8p4n.Sp.3

description: CD8+ Dendritic Cell


title: EOL1_H3K27Ac_Naive_ChIP-Seq

source_name: EOL1 (AML)

value: AML

tag: cell line

value: Abcam


title: DC.103n11bpsiglecFn.Lu.6

description: Dendritic Cell

value: CD45+ lin- PI- SiglecF- MHCII+ CD11c+ CD24+ CD103- CD11b+


title: DC.mig.103p.LuLN.3

description: Dendritic Cell


title: DC.103n11bpsiglecFn.Lu.4

description: Dendritic Cell


title: DC.103p11bnsiglecFn.Lu.5

description: Dendritic Cell

value: CD45+ lin- PI- SiglecF- MHCII+ CD11c+ CD24+ CD103+ CD11b-


title: DC.103p11bnsiglecFn.Lu.4

description: Dendritic Cell


title: DC.103n11bpsiglecFn.Lu.5

description: Dendritic Cell


title: MF.6Gn480hi.Kd.2

description: Macrophage

source_name: Kidney

value: CD45+ CD11b+ MHCII+ F4/80hi Lin- Ly6G-


title: MF.PC.01

description: Peritoneal Macrophage


title: MF.PC.02

description: Peritoneal Macrophage


title: DC.103p11bnsiglecFn.Lu.6

description: Dendritic Cell

source_name: Lung


title: MF.6Gn480hi.Kd.1

description: Macrophage


title: MF.alv.6GnSigFp11cp.Lu.1

description: Alveolar Macrophage


title: MF.6Gn480hi.Calb.8h.Kd.1

description: Ly6G- Macropage, 8h post-infection (C. albicans)


title: MF.6Gn480hi.Calb.8h.Kd.2


title: DC.res.11bp.LuLN.3

description: Dendritic Cell


title: DC.res.11bp.LuLN.2

description: Dendritic Cell


title: MF.6Gn480hi.Calb.48h.Kd.2

description: Ly6G- Macropage, 48h post-infection (C. albicans)


title: MF.6Gn480hi.Calb.48h.Kd.1


title: MF.45lo.CNS.1

description: 45lo Macrophage


title: MF.45lo.Calb.8h.CNS.2

description: 45lo Macropage, 8h post-infection (C. albicans)


title: MF.45lo.CNS.2

description: 45lo Macrophage


title: MF.45lo.Calb.48h.CNS.2

description: 45lo Macropage, 48h post-infection (C. albicans)


title: DC.8p4n.Sp.2

description: CD8+ Dendritic Cell

source_name: Spleen


title: MF.11blop64p169p.Lv.2

description: 64+ Macrophage

source_name: Liver


title: MF.11blop64p169p.Lv.1

description: 64+ Macrophage


title: MF.11blop64p169p.Calb.8h.Lv.1

description: 64+ Macropage, 8h post-infection (C. albicans)


title: MF.11blop64p169p.Calb.48h.Lv.1

description: 64+ Macropage, 48h post-infection (C. albicans)


title: MF.45lo.Calb.48h.CNS.1


title: MF.PC.08

description: Peritoneal Macrophage

value: 17 weeks old


title: MF.PC.07

description: Peritoneal Macrophage


title: MF.PC.20

description: Peritoneal Macrophage


title: MF.11blop64p169p.Calb.8h.Lv.2


title: MF.11blop64p169p.Calb.48h.Lv.2


title: Mo.64p6CpIIp.LPS.d6.Lu.2

description: 64+ Lung Monocyte in 2ug LPS 6 days

value: 10 weeks old

value: CD11b+ CD64+  Ly6C+  MHCII+

value: Monocyte


title: Mo.6Cp.Lu.4

description: Ly6C+ Monocyte


title: Mo.SSClop6Cp.LPS.d3.BAL.1

description: Broncho-alveolar lavage Macrophage in 2ug LPS 3 days

value: SSClo  F4/80+  CD11b+  Ly6C+


title: Mo.SSClop6Cp.LPS.d3.BAL.2


title: Mo.64p6CpIIp.LPS.d3.Lu.2

description: 64+ Lung Monocyte in 2ug LPS 3 days


title: Mo.64p6CpIIp.LPS.d6.Lu.1

description: 64+ Lung Monocyte in 2ug LPS 6 days


title: Mo.64p6CpIIp.LPS.d3.Lu.1

description: 64+ Lung Monocyte in 2ug LPS 3 days


title: Mo.6Cp.Lu.5

description: Ly6C+ Monocyte


title: MF.SSChipSigFn.LPS.d6.BAL.2

description: Broncho-alveolar lavage Macrophage in 2ug LPS 6 days

value: SSChi  F4/80+  CD11b+  Siglec F-

value: Macrophage


title: MF.SSChipSigFn.LPS.d6.BAL.1


title: MF.SSChipSigFn.LPS.d3.BAL.1


title: MF.SSChipSigFn.LPS.d3.BAL.2


title: MF.45lo.Calb.8h.CNS.1

value: CD45lo CD11b+


title: MF.PC.18

description: Peritoneal Macrophage


title: MF.64p6Cn206nIIp.Lu.2

description: Lung Macrophage

value: CD11b+  CD64+  Ly6C-  CD206-  MHCII+


title: MF.PC.17

description: Peritoneal Macrophage


title: MF.PC.19

description: Peritoneal Macrophage


title: MF.64p6Cn206nIIp.LPS.d6.Lu.2

description: Macrophage in 2ug LPS 6 days


title: MF.64p6Cn206nIIp.LPS.d6.Lu.1

description: Macrophage in 2ug LPS 6 days


title: MF.64p6Cn206nIIp.LPS.d3.Lu.2

description: Macrophage in 2ug LPS 3 days


title: MF.64p6Cn206pIIp.LPS.d6.Lu.1

description: Macrophage in 2ug LPS 6 days

value: CD11b+  CD64+  Ly6C-  CD206+  MHCII+


title: MF.64p6Cn206pIIp.LPS.d6.Lu.2

description: Macrophage in 2ug LPS 6 days


title: cfDNA_young_male_pool_rep1

description:
Young males
Multiple donors
Young_M1

source_name: cfDNA of young males, pooled from multiple donors

value: cfDNA

value: Normal

value: Male


title: MF.64p6Cn206pIIp.LPS.d3.Lu.1

description: Macrophage in 2ug LPS 3 days


title: MF.64p6Cn206pIIp.LPS.d3.Lu.2

description: Macrophage in 2ug LPS 3 days


title: MF.64p6Cn206pIIn.LPS.d6.Lu.2

description: Macrophage in 2ug LPS 6 days

value: CD11b+  CD64+  Ly6C-  CD206+  MHCII-


title: MF.64p6Cn206nIIp.LPS.d3.Lu.1

description: Macrophage in 2ug LPS 3 days


title: MF.64p6Cn206pIIn.Lu.2

description: Lung Macrophage


title: MF.11cpSigFp.BAL.1

description: Broncho-alveolar lavage Macrophage

value: F4/80+  CD11c+  Siglec F+


title: MF.64p6Cn206pIIn.LPS.d6.Lu.1

description: Macrophage in 2ug LPS 6 days


title: Mo.6Cint11cint.APAP.36h.Lv.3

description: Ly6C intermediate Monocyte, 36h Paracetamol treatment prior sacrificing

value: 8 weeks old

value: Ly6Cint CD11b+ CD11cint CD45+


title: Mo.6Cint11cint.APAP.36h.Lv.2


title: MF.11cpSigFp.BAL.2

description: Broncho-alveolar lavage Macrophage


title: Mo.6Cint11cint.APAP.36h.Lv.4


title: MF.11cpSigFp.LPS.d6.BAL.1


title: Mo.6Cint11cint.APAP.36h.Lv.1


title: MF.64p6Cn206pIIn.LPS.d3.Lu.1

description: Macrophage in 2ug LPS 3 days


title: MF.64p6Cn206nIIp.Lu.1

description: Lung Macrophage


title: MF.64p6Cn206pIIn.LPS.d3.Lu.2

description: Macrophage in 2ug LPS 3 days


title: Mo.6Chi11bp.PBS.Lv.2

description: Ly6C high  Monocyte PBS control

value: Ly6Chi CD11b+ CD45+


title: Mo.6Chi11bp.PBS.Lv.3

description: Ly6C high  Monocyte PBS control


title: Mo.6Chi11bp.PBS.Lv.1

description: Ly6C high  Monocyte PBS control


title: Mo.6Chi11bp.APAP.36h.Lv.4

description: Ly6C high Monocyte, 36h Paracetamol treatment prior sacrificing


title: Mo.6Chi11bp.PBS.Lv.4

description: Ly6C high  Monocyte PBS control


title: Mo.6Chi11bp.APAP.36h.Lv.3


title: Mo.6Chi11bp.APAP.12h.Lv.4

description: Ly6C high Monocyte, 12h Paracetamol treatment prior sacrificing


title: Mo.6Chi11bp.APAP.36h.Lv.1


title: MF.64p6Cn206pIIn.Lu.1

description: Lung Macrophage

value: 10 weeks old


title: Mo.6Chi11bp.APAP.12h.Lv.2


title: Mo.6Chi11bp.APAP.36h.Lv.2


title: Mo.6Chi11bp.APAP.12h.Lv.3


title: MF.KC.Clec4FpTim4p64p.PBS.Lv.3

description: Kupffer Cell/Macrophage PBS control


title: Mo.6Chi11bp.APAP.12h.Lv.1


title: MF.KC.Clec4FpTim4p64p.PBS.Lv.1

description: Kupffer Cell/Macrophage PBS control


title: MF.KC.Clec4FpTim4p64p.PBS.Lv.4

description: Kupffer Cell/Macrophage PBS control


title: MF.11cpSigFp.LPS.d6.BAL.2


title: MF.KC.Clec4FpTim4p64p.Lv.2

description: Kupffer Cell/Macrophage


title: MF.KC.Clec4FpTim4p64p.Lv.3

description: Kupffer Cell/Macrophage


title: MF.KC.Clec4FpTim4p64p.APAP.36h.Lv.2

description: Kupffer Cell/Macrophage, 36h Paracetamol treatment prior to sacrificing


title: MF.KC.Clec4FpTim4p64p.APAP.36h.Lv.4


title: MF.KC.Clec4FpTim4p64p.APAP.12h.Lv.4

description: Kupffer Cell/Macrophage, 12h Paracetamol treatment prior to sacrificing


title: DC.pDC.120g8p11cintp6Cp.Lv.1

description: preDC

value: 120g8+ CD11c(int) Ly6C+ MHCII+

value: Dendritic Cell


title: DC.pDC.120g8p11cintp6Cp.Lv.2

description: preDC


title: MF.KC.Clec4FpTim4p64p.APAP.12h.Lv.2


title: DC.cDC2.172ap.Lv.4

description: Conventional Dendritic Cells

value: CD45+ CD172a+ CD11c+ MHCII+


title: MF.KC.Clec4FpTim4p64p.APAP.36h.Lv.1


title: DC.cDC2.172ap.Lv.3

description: Conventional Dendritic Cells


title: DC.pDC.120g8p11cintp6Cp.Lv.3

description: preDC


title: DC.cDC2.172ap.Lv.2

description: Conventional Dendritic Cells


title: MF.KC.Clec4FpTim4p64p.APAP.12h.Lv.1


title: MF.KC.Clec4FpTim4p64p.APAP.36h.Lv.3


title: DC.pDC.120g8p11cintp6Cp.Lv.4

description: preDC


title: DC.cDC2.172ap.Lv.1

description: Conventional Dendritic Cells


title: DC.cDC1.XCR1p.Lv.2

description: Conventional Dendritic Cells

value: CD45+ XCR1+ CD11c+ MHCII+


title: DC.cDC1.XCR1p.Lv.1

description: Conventional Dendritic Cells


title: DC.cDC1.XCR1p.Lv.3

description: Conventional Dendritic Cells


title: MF.PC.F.Neo.2

description: Female Neonatal Peritoneal Macrophage

value: 1 weeks old

value: Macrophage


title: MF.KC.Clec4FpTim4p64p.PBS.Lv.2

description: Kupffer Cell/Macrophage PBS control


title: MF.PC.38

description: Peritoneal Macrophage

value: 6 weeks old


title: MF.PC.F.Neo.1

description: Female Neonatal Peritoneal Macrophage


title: MF.KC.Clec4FpTim4p64p.Lv.4

description: Kupffer Cell/Macrophage


title: MF.E18.5.F.PC.2

description: Female Embryonic Peritoneal Macrophages

value: 2 embryonic weeks old


title: MF.E18.5.F.PC.1

description: Female Embryonic Peritoneal Macrophages


title: MF.E14.5.F.PC.3

description: Female Embryonic Peritoneal Macrophages


title: MF.E14.5.F.PC.2

description: Female Embryonic Peritoneal Macrophages


title: MF.E14.5.F.PC.1

description: Female Embryonic Peritoneal Macrophages


title: MF.PC.37

description: Peritoneal Macrophage


title: MF.E16.5.PC.2

description: Embryonic Peritoneal Macrophages


title: MF.64p6Cn6Gn.E18.5.Thy.3

description: Embryonic Thymic Macrophages

source_name: Thymus


title: MF.64p6Cn6Gn.E18.5.Thy.2

description: Embryonic Thymic Macrophages


title: MF.64p6Cn6Gn.Kd.Neo.1

description: Neonatal Macrophages from Kidney


title: MF.64p6Cn6Gn.Lu.Neo.2

description: Neonatal Macrophages from Lung


title: MF.64p6Cn6Gn.E18.5.Sp.2

description: Embryonic Spleenic Macrophages


title: MF.64p6Cn6Gn.E18.5.Lv.2

description: Embryonic Macrophages from Liver


title: MF.64p6Cn6Gn.E18.5.PC.2

description: Embryonic Peritoneal Macrophages


title: MF.64p6Cn6Gn.E18.5.Lv.1

description: Embryonic Macrophages from Liver


title: MF.64p6Cn6Gn.Lu.Neo.1

description: Neonatal Macrophages from Lung


title: MF.E16.5.PC.1

description: Embryonic Peritoneal Macrophages


title: MF.64p6Cn6Gn.E18.5.PC.1

description: Embryonic Peritoneal Macrophages


title: MF.E18.5.F.PC.3

description: Female Embryonic Peritoneal Macrophages


title: MF.64p6Cn6Gn.E18.5.Sp.1

description: Embryonic Spleenic Macrophages


title: MF.64p6Cn6Gn.E18.5.Kd.2

description: Embryonic Macrophages from Kidney


title: MF.64p6Cn6Gn.E18.5.Thy.1

description: Embryonic Thymic Macrophages


title: MF.64p6Cn6Gn.E18.5.F.Ht.1

description: Embryonic Macrophages from Heart

source_name: Heart


title: MF.64p6Cn6Gn.E18.5.Kd.1

description: Embryonic Macrophages from Kidney


title: MF.64p6Cn6Gn.E18.5.Ep.1

description: Embryonic Macrophages from Epidermis

source_name: Epithelial Cell


title: MF.64p6Cn6Gn.E18.5.Ep.2

description: Embryonic Macrophages from Epidermis

source_name: Epithelium


title: MF.64p6Cn6Gn.E18.5.Dr.2

description: Embryonic Macrophages from Dermis

source_name: Dermis


title: MF.64p6Cn6Gn.E18.5.Dr.1

description: Embryonic Macrophages from Dermis


title: MF.64p6Cn6Gn.E18.5.F.Ht.2

description: Embryonic Macrophages from Heart


title: MF.64p6Cn6Gn.E18.5.Co.2

description: Embryonic Macrophages from Gut

source_name: Colon


title: MF.64p6Cn6Gn.E18.5.Co.3

description: Embryonic Macrophages from Gut


title: MF.64p6Cn6Gn.E18.5.Br.2

description: Embryonic Macrophages from Brain


title: MF.64p6Cn6Gn.Kd.Neo.2

description: Neonatal Macrophages from Kidney


title: MF.64p6Cn6Gn.E16.5.Lu.2

description: Embryonic Macrophages from Lung


title: MF.64p6Cn6Gn.E16.5.Lu.1

description: Embryonic Macrophages from Lung


title: MF.64p6Cn6Gn.E18.5.Br.1

description: Embryonic Macrophages from Brain


title: MF.64p6Cn6Gn.E16.5.Kd.2

description: Embryonic Macrophages from Kidney


title: MF.64p6Cn6Gn.E14.5.Lu.1

description: Embryonic Macrophages from Lung


title: MF.64p6Cn6Gn.E14.5.Kd.2

description: Embryonic Macrophages from Kidney


title: MF.64p6Cn6Gn.E14.5.Kd.3

description: Embryonic Macrophages from Kidney


title: Mo.6CpThio.8h.BI.2

description: 8h Thioglycollate Stimulated Blood Monocytes

value: Monocyte


title: Mo.6CpThio.4h.BI.2

description: 4h Thioglycollate Stimulated Blood Monocytes


title: Mo.6CpThio.8h.BI.1


title: Mo.6Cp.Thio.72h.BI.3

description: 72h Thioglycollate Stimulated Blood Monocytes


title: Mo.6CpThio.4h.BI.3


title: MF.64p6Cn6Gn.E14.5.Kd.1

description: Embryonic Macrophages from Kidney


title: Mo.6CpThio.8h.BI.3


title: MF.64p6Cn6Gn.E14.5.Lu.3

description: Embryonic Macrophages from Lung


title: Mo.6Cp.Thio.72h.BI.1


title: Mo.6Cp.Thio.72h.BI.2


title: Mo.6Cp.Bl.8

description: Blood Monocytes


title: Mo.6Cp.Bl.6

description: Blood Monocytes


title: Mo.6Cp.Thio.24h.BI.1

description: 24h Thioglycollate Stimulated Blood Monocytes


title: Mo.115pICAM2n226n6Cn.Thio.8h.PC.3

description: 8h Thioglycollate Stimulated Peritoneal Monocytes

source_name: Peritoneal Cavity


title: Mo.115pICAM2n226n6Cn.Thio.8h.PC.2


title: Mo.115pICAM2n226n6Cn.Thio.8h.PC.1


title: MF.64p6Cn6Gn.E16.5.Kd.1

description: Embryonic Macrophages from Kidney


title: Mo.6Cp.Bl.7

description: Blood Monocytes

source_name: Blood


title: Mo.6Cp.Thio.24h.BI.2


title: Mo.115pICAM2n226n6Cn.Thio.4h.PC.3

description: 4h Thioglycollate Stimulated Peritoneal Monocytes


title: Mo.115pICAM2n226n6Cn.Thio.4h.PC.1


title: Mo.115pICAM2n226n6Cn.Thio.4h.PC.2


title: MF.64p6Cn6Gn.E14.5.Lu.2

description: Embryonic Macrophages from Lung


title: Mo.115p6Cp36lopICAM2n226n.Thio.24h.PC.1

description: 24h Thioglycollate Stimulated Peritoneal Monocytes


title: Mo.115p6Cp36lopICAM2n226n.Thio.24h.PC.2


title: Mo.6Cp.Thio.24h.BI.3


title: MF.115p36p6ClopICAM2n226n.Thio.24h.PC.2

description: 24h Thioglycollate Stimulated Peritoneal Macrophage


title: MF.115p36p6ClopICAM2n226n.Thio.24h.PC.3


title: MF.115p36p6ClopICAM2n226n.Thio.24h.PC.1


title: MF.115p36p6ClopICAM2n226n.Thio.72h.PC.2

description: 72h Thioglycollate Stimulated Peritoneal Macrophage


title: MF.115p36p6ClopICAM2n226n.Thio.72h.PC.3


title: MF.115pICAM2p226n6Cn.PC.3

description: Ly6C- Peritoneal Macrophages


title: MF.115pICAM2p226n6Cn.PC.2

description: Ly6C- Peritoneal Macrophages


title: MF.115p36p6ClopICAM2n226n.Thio.72h.PC.1


title: MF.64p.Th.3

description: Thymic 64+ Macrophage


title: DC.XCR1nSIRPap.Th.4

description: Thymic 64+ Macrophage


title: MF.PC.03

description: Peritoneal Macrophage


title: MF.64p.Th.1

description: Thymic 64+ Macrophage


title: MF.PC.04

description: Peritoneal Macrophage


title: MF.115pICAM2p226n6Cn.PC.1

description: Ly6C- Peritoneal Macrophages


title: MF.64p.Th.4

description: Thymic 64+ Macrophage


title: MF.PC.05

description: Peritoneal Macrophage


title: MF.PC.06

description: Peritoneal Macrophage


title: DC.XCR1nSIRPap.Th.3

description: Thymic Dendritic Cell


title: DC.XCR1pSIRPan.Th.4

description: Thymic Dendritic Cell


title: DC.XCR1nSIRPap.Th.1

description: Thymic Dendritic Cell


title: DC.XCR1nSIRPap.Th.2

description: Thymic Dendritic Cell


title: Mo.115p6Cp36lopICAM2n226n.Thio.24h.PC.3


title: DC.XCR1pSIRPan.Th.2

description: Thymic Dendritic Cell


title: DC.XCR1pSIRPan.Th.1

description: Thymic Dendritic Cell


title: DC.SigHn.64n11chipBst2n11bp8anRFPp.Sp.3

description: Spleenic Dendritic Cell

value: SiglecHCre x RosaLSLRFP

value: Aquadead- lin- Dump- CD64- CD11c high Bst2- CD11b+ CD8a- RFP+


title: MF.PC.09

description: Peritoneal Macrophage


title: MF.PC.10

description: Peritoneal Macrophage


title: DC.SigHn.64n11chipBst2n11bp8anRFPp.Sp.2

description: Spleenic Dendritic Cell


title: DC.SigHn.64n11chipBst2n11bp8anRFPn.Sp.3

description: Spleenic Dendritic Cell

value: Aquadead- lin- Dump- CD64- CD11c high Bst2- CD11b+ CD8a- RFP-


title: MF.64p.Th.2

description: Thymic 64+ Macrophage


title: DC.24p8anXCR1n.Sp.2

description: Spleenic Dendritic Cell


title: DC.24p8anXCR1p.Sp.1

description: Spleenic Dendritic Cell


title: DC.24p8apXCR1p.Sp.2

description: Spleenic Dendritic Cell


title: DC.24p8apXCR1p.Sp.1

description: Spleenic Dendritic Cell


title: DC.SigHn.64n11chipBst2n11bp8anRFPn.Sp.2

description: Spleenic Dendritic Cell


title: DC.24p8anXCR1n.Sp.1

description: Spleenic Dendritic Cell


title: DC.24p8apXCR1n.Sp.1

description: Spleenic Dendritic Cell


title: DC.24p8apXCR1n.Sp.2

description: Spleenic Dendritic Cell


title: DC.XCR1pSIRPan.Th.3

description: Thymic Dendritic Cell


title: MF.F.PC.3

description: Female Peritoneal Macrophage


title: MF.d6.EB.1

description: Day 6 Embryonic Macrophage

source_name: Cell (Embryonic Body)


title: MF.F.PC.2

description: Female Peritoneal Macrophage


title: MF.PC.49

description: Peritoneal Macrophage


title: MF.PC.51

description: Peritoneal Macrophage


title: MF.PC.48

description: Peritoneal Macrophage


title: MF.PC.50

description: Peritoneal Macrophage


title: MF.PC.46

description: Peritoneal Macrophage

value: 15 weeks old

value: F4/80  ICAM2


title: MF.PC.45

description: Peritoneal Macrophage


title: MF.F.PC.1

description: Female Peritoneal Macrophage


title: MF.PC.44

description: Peritoneal Macrophage


title: MF.d6.EB.2

description: Day 6 Embryonic Macrophage


title: MF.PC.47

description: Peritoneal Macrophage


title: MF.64pLYVEnIIp.Ao.3

description: Aortic Macrophage

source_name: Aorta

value: CD45 CD11b CD64 MerTK LYVE-1 MHCII Dump channel


title: DC.24p8anXCR1p.Sp.2

description: Spleenic Dendritic Cell


title: MF.64pLYVEnIIp.Ao.2

description: Aortic Macrophage


title: MF.d8.EB.2

description: Day 8 Embryonic Macrophage


title: MF.PC.21

description: Spleenic Dendritic Cell

source_name: Peritoneal

value: Tnnt2-DTR  CCR2GFP  Flt3-Cre  Rosa26-tdTomato


title: MF.PC.52

description: Peritoneal Macrophage


title: MF.d8.EB.1

description: Day 8 Embryonic Macrophage


title: MF.64pLYVEpIIp.Ao.3

description: Aortic Macrophage


title: MF.64pLYVEpIIp.Ao.2

description: Aortic Macrophage


title: MF.64pLYVEnIIp.Ao.1

description: Aortic Macrophage


title: MF.64pLYVEpIIp.Ao.1

description: Aortic Macrophage


title: MF.64pLYVEpIIn.Ao.2

description: Aortic Macrophage


title: MF.64pLYVEpIIn.Ao.1

description: Aortic Macrophage