title: V316C1: Input1

status: Public on Feb 27 2019

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

institute: Institut Curie

data_processing:
Reads for each replicate were mapped separately to the hg38 primary assembly with Bowtie2 v2.2.9 using a seed length of 22bp with at most 1 mismatches (-N 1 -L 22) and keeping the best scoring alignment per read.
Duplicate fragments were identified with MarkDuplicates from picard v1. Only non-duplicate, properly paired reads (same reference, inner-oriented, insert size <= 500bp; only for replicate 1) with mapping quality >= 20 were retained, using samtools v1.3. Alignment files were converted from BAM to BED/BEDPE format using bedtools bamtobed from bedtools v2.27.1.
Genome mappability was computed with gemtools v1.7.1 (--l L --m 0.04 --e 0.04 --max-big-indel-length 15 --min-matched-bases 0.80, where L is the read length). The effective genome size was then defined as m/n , where m is the number of bp with mappability score 1 and n is the genome length.
Peak calling of GFP-NLS-cGAS IP reads on hg38 chromosomes was performed with SICER v1.1 on each replicate separately, using either input or GFP-NLS IP (only for replicate 2 and 3) reads as background (redundancy threshold 1, window size 200bp, FDR 0.05, effective genome size estimated with the above procedure). The gap size was set to 600bp for replicate 1 and to 400bp for replicate 2 and 3. For replicate 1, one read for each pair was used and the fragment size was set to the average insert size computed from the alignment.
Filtered peaks were defined for each replicate i as the peaks supported by more than M ChIP reads, where M is the median across all peaks for replicate i.
The number of reads for each repeat element is computed on the annotated hg38 genome with a in-house C++ program and the cGAS enrichment over either input or GFP is retrieved for each replicate separately.
All repeat elements in the genome are ranked according to the cGAS read enrichment value and grouped into n ranking bins. The number of elements falling into each bin is computed for each repeat class R.
Genome_build: hg38
Supplementary_files_format_and_content: Bed files generated with SICER containing the peaks, which are subsequently filtered by the number of ChIP reads.
Supplementary_files_format_and_content: Tabular files containing the count and the normalized count (cpm) of the reads mapped hg38 to each annotated repeat locus

source_name: Dendritic cells

extract_protocol:
Crosslinking and lysis. 10 million cells were cross-linked in medium with 1% formaldehyde for 8 min at RT on a slow shaker, quenched with freshly prepared 0.125M glycine, incubated 5min at RT on a slow shaker, then pelleted at 400g for 5 minutes at 4°C, washed three times with 30ml of ice cold PBS and then incubated for 20 minutes rotating at 4°C in 1mL of RIPA lysis buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0 (Invitrogen), 140mM NaCl, 1% (v/v) Triton X-100 (Euromedex), 0.1% (v/v) SDS and 0.1% sodium deoxycholate (SIGMA)). Nuclei were pelleted at 1350g for 5 minutes at 4°C, washed for 10 minutes rotating with 1ml of a buffer containing 10mM Tris, 200mM NaCl, 1mM EDTA (Invitrogen), 0.5 mM EGTA (Euromedex), pelleted and lysed in buffer containing 0.4% SDS (Euromedex), 10mM EDTA (Invitrogen), 50mM Tris-HCl pH 8.0 for 30min on ice (volume of buffer = 100µl/1.6 million cells). Lysates were sonicated on a Bioruptor Pico (Diagenode) sonication devices (11cycles 30 seconds ON, 30 second OFF) to reach fragments ranging from 150 to 500bp, and then centrifuged at 10,000g for 10 minutes at 4°C to remove debris. Samples were then snap-frozen in liquid nitrogen and stored at -80°C until immunoprecipitation. All buffers contained cOmplete EDTA free Protease inhibitor cocktail (Roche).  Immunoprecipitation. Lysates were pre-cleared for 15 minutes rotating using 30µl of Binding Control magnetic agarose beads (Chromotek). Chromatin was diluted four-fold in dilution buffer containing 20mM Tris-HCl pH 8.0, 1% Triton X-100 (Euromedex), 2mM EDTA (Invitrogen), 167mM NaCl.  1% of the diluted lysate was recovered and used as input. For GFP-trap and control beads, chromatin was incubated for 5 hours in the presence of 0.1% BSA (Euromedex) (30µl of beads (GFP-Trap_MA beads (Chromotek) or Control magnetic agarose beads (Chromotek)/600µl per Eppendorf tube of the diluted lysate). Lysates were washed on a 96 well plate magnet with low salt washing buffer (140mM NaCl) (5 times), high salt washing buffer (500mM NaCl) (2 times), high LiCl washing buffer (250mM LiCl) (2 times), TE Buffer (Invitrogen) (1 time). All wash buffers were diluted in RIPA buffer 10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0 (Invitrogen), 140mM NaCl, 1% (v/v) Triton X-100 (Euromedex), 0.1% (v/v) SDS and 0.1% sodium deoxycholate (SIGMA)) and contained cOmplete EDTA free Protease inhibitor cocktail (Roche).  DNA purification. DNA was eluted in elution buffer (1% SDS, 50 mM NaHCO3) by shacking 2h at 37°C (100µl of buffer/tube) with 10 μg/mL RNaseA (Thermo Fischer), then 4h with 0.2 μg/ml proteinase K. Beads were concentrated on the magnet and take out eluate. Samples were decrosslinked overnight at 65°C. Inputs were treated like ChIP samples. DNA was purified by phenol/chloroform/isoamyl alcohol (SIGMA) followed by purification on MinElute columns (Qiagen). DNA was eluted in 50µl of H2O and DNA concentration was measured with a Qubit fluorometer (Thermo Fischer).
Traces of high molecular weight fragments were eliminated with SPRIselect beads (Beckman Coulter). Illumina TruSeqChIP library prep kit was used to prepare indexed libraries from IP and Input DNA. Libraries were pooled respecting equimolarity. Sequencing was performed on Illumina MiSeq sequencer in 150 bp paired-end reads (replicate 1 of input and GFP-NLS-cGAS IP), 100 bp single-end reads (replicates 2 and 3 of input, GFP-NLS and GFP-NLS-cGAS IP).

value: Monocyte-derived dendritic cells

tag: donor

tag: construct


title: A751C6: GFP-NLS3_ChIPSeq

type: SRA

city: Paris

country: France

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

value: pTRIP-SFFV-EGFP-NLS

tag: chip antibody

value: Chromotek GFP-Trap®_MA (cat#gtma-20)


title: M0_18h_1

status: Public on Mar 06 2019

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

country: USA

institute: Johns Hopkins University

description: mRNA

library_source: transcriptomic

data_processing:
Sequenced libraries were processed with the Galaxy platform and deepTools (Afgan et al., 2016; Ramírez et al., 2016).
STAR (Dobin et al., 2013) for trimming and mapping.
featureCounts (Liao et al., 2014) to quantify mapped reads.
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 (Love et al., 2014) to determine differentially expressed genes and generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute).
Genome_build: GRCm38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw read counts for every sample.

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow-derived macrophage

growth_protocol: Mature bone marrow-derived macrophages (BMMs) were obtained at day 7 of culture of bone marrow cells in 20 ng/mL CSF-1 (Peprotech) in RPMI medium containing 10% fetal bovine serum, 4 mM L-glutamine, 100 U/mL penicillin/streptomycin (complete RPMI) (all Gibco).

extract_protocol:
Total RNA was extracted with the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific) and quantified using Qubit 2.0 (Thermo Fisher Scientific) following the manufacturer’s instructions.
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HiSeq 3000 (Illumina).

treatment_protocol: BMMs were stimulated in complete RPMI supplemented with CSF-1 for indicated times with a combination of 20 or 100 ng/mL LPS (SIGMA), 50 ng/mL IFNg or 20 ng/mL IL-4 (all Peprotech) under 5% CO2, atmospheric oxygen, at 37°C in a humidified incubator.

tag: strain/background

tag: genotype/variation

value: Wild type

value: Bone marrow-derived macrophage

tag: treatment

value: No stimulus control 18h

tag: time point


title: LPS_1h_2

description: mRNA

value: LPS stimulation


title: M0_1h_1

description: mRNA

value: No stimulus control 1h


title: A751C4: GFP-NLS-cGAS3_ChIPSeq


title: A751C5: GFP-NLS2_ChIPSeq


title: A812C3: DC Sample 1: GFP-cGAS1_ChIPSeq

data_processing:
Raw reads were aligned to the mouse reference genome version mm10 (accession: GCA_000001305.2) with Bowtie2 v2.1.0 using a seed length of 22bp with at most 1 mismatch (--N 1 --L 22) and keeping the best scoring alignment per read.
Duplicate fragments were identified with MarkDuplicates from picard v1. Only non-duplicate, properly paired reads (same reference, inner-oriented, insert size <= 500bp; only for replicate 1) with mapping quality >= 20 were retained, using samtools v1.3. Alignment files were converted from BAM to BED/ BEDPE format using bedtools bamtobed from bedtools v2.27.1.
Genome mappability was computed with gemtools v1.7.1 (--l L --m 0.04 --e 0.04 --max-big-indel-length 15 --min-matched-bases 0.80, where L is the read length). The effective genome size was then defined as m/n , where m is the number of bp with mappability score 1 and n is the genome length.
Peak calling of GFP-cGAS IP reads on mm10 chromosomes was performed with SICER v1.1 on each replicate separately, using either input reads as background (redundancy threshold 1, window size 200bp, gap size 600bp, FDR 0.05, effective genome size estimated with the above procedure). One read for each pair was used and the fragment size was set to the average insert size computed from the alignment.
Intersection peaks between the two replicates were identified using bedtools intersect (default parameters) from bedtools v2.27.1.
Reads that failed to map to mm10 were aligned against the mouse-specific repeats from RepBase with Bowtie2 v2.1.0, using a seed length of 22bp with at most 1 mismatch, enabling soft-clipping (-N 1 -L 22 --local) and keeping the best scoring alignment per read.
The read count for each RepBase sequence was computed from the BAM files, the count per million (cpm) values were derived, and the enrichment of cGAS over either input or GFP was retrieved.
Genome_build: mm10
Supplementary_files_format_and_content: Bed file containing the genomic region corresponding to the intersection of the peaks computed on the two replicates
Supplementary_files_format_and_content: Tabular file containing the count and the normalized count (cpm) of the reads mapped to the database of mouse-specific repeats

extract_protocol:
Crosslinking and lysis. 10 million cells were cross-linked in medium with 1% formaldehyde for 8 min at RT on a slow shaker, quenched with freshly prepared 0.125M glycine, incubated 5min at RT on a slow shaker, then pelleted at 400g for 5 minutes at 4°C, washed three times with 30ml of ice cold PBS and then incubated for 20 minutes rotating at 4°C in 1mL of RIPA lysis buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0 (Invitrogen), 140mM NaCl, 1% (v/v) Triton X-100 (Euromedex), 0.1% (v/v) SDS and 0.1% sodium deoxycholate (SIGMA)). Nuclei were pelleted at 1350g for 5 minutes at 4°C, washed for 10 minutes rotating with 1ml of a buffer containing 10mM Tris, 200mM NaCl, 1mM EDTA (Invitrogen), 0.5 mM EGTA (Euromedex), pelleted and lysed in buffer containing 0.4% SDS (Euromedex), 10mM EDTA (Invitrogen), 50mM Tris-HCl pH 8.0 for 30min on ice (volume of buffer = 100µl/1.6 million cells). Lysates were sonicated on a Bioruptor Pico (Diagenode) sonication devices (11cycles 30 seconds ON, 30 second OFF) to reach fragments ranging from 150 to 500bp, and then centrifuged at 10,000g for 10 minutes at 4°C to remove debris. Samples were then snap-frozen in liquid nitrogen and stored at -80°C until immunoprecipitation. All buffers contained cOmplete EDTA free Protease inhibitor cocktail (Roche).  Immunoprecipitation. Lysates were pre-cleared for 15 minutes rotating using 30µl of Binding Control magnetic agarose beads (Chromotek). Chromatin was diluted four-fold in dilution buffer containing 20mM Tris-HCl pH 8.0, 1% Triton X-100 (Euromedex), 2mM EDTA (Invitrogen), 167mM NaCl.  1% of the diluted lysate was recovered and used as input. For GFP-trap and control beads, chromatin was incubated for 5 hours in the presence of 0.1% BSA (Euromedex) (30µl of beads (GFP-Trap_MA beads (Chromotek) or Control magnetic agarose beads (Chromotek)/600µl per Eppendorf tube of the diluted lysate). Lysates were washed on a 96 well plate magnet with low salt washing buffer (140mM NaCl) (5 times), high salt washing buffer (500mM NaCl) (2 times), high LiCl washing buffer (250mM LiCl) (2 times), TE Buffer (Invitrogen) (1 time). All wash buffers were diluted in RIPA buffer 10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0 (Invitrogen), 140mM NaCl, 1% (v/v) Triton X-100 (Euromedex), 0.1% (v/v) SDS and 0.1% sodium deoxycholate (SIGMA)) and contained cOmplete EDTA free Protease inhibitor cocktail (Roche).  DNA purification. DNA was eluted in elution buffer (1% SDS, 50 mM NaHCO3) by shacking 2h at 37°C (100µl of buffer/tube) with 10 μg/mL RNaseA (Thermo Fischer), then 4h with 0.2 μg/ml proteinase K. Beads were concentrated on the magnet and take out eluate. Samples were decrosslinked overnight at 65°C. Inputs were treated like ChIP samples. DNA was purified by phenol/chloroform/isoamyl alcohol (SIGMA) followed by purification on MinElute columns (Qiagen). DNA was eluted in 50µl of H2O and DNA concentration was measured with a Qubit fluorometer (Thermo Fischer).
Traces of high molecular weight fragments were eliminated with SPRIselect beads (Beckman Coulter). Illumina TruSeqChIP library prep kit was used to prepare indexed libraries from IP and Input DNA. Libraries were pooled respecting equimolarity. Sequencing was performed on Illumina MiSeq sequencer in 150 bp paired-end reads.

value: Bone marrow-derived dendritic cells

tag: mouse

tag: strain

tag: age

value: 6-8 weeks


title: A751C3: GFP-NLS-cGAS2_ChIPSeq


title: A812C1: DC Sample 1: GFP-cGAS_Input


title: V316C2: GFP-NLS-cGAS1_ChIPSeq


title: A751C1: Input2


title: A812C2: DC Sample 2: GFP-cGAS_Input


title: M2_val_3

status: Public on Jan 16 2019

description: IL-4 and valinomycin stimulation

data_processing:
Sequenced libraries were processed with the Galaxy platform and deepTools (Afgan et al., 2016; Ramírez et al., 2016)
STAR (Dobin et al., 2013), for trimming and mapping
featureCounts (Liao et al., 2014) to quantify mapped reads.
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 (Love et al., 2014), to determine differentially expressed genes and generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute).
Genome_build: GRCm38
Supplementary_files_format_and_content: raw read counts for every sample

source_name: bone marrow derived macrophage, IL-4 and valinomycin stimulation

growth_protocol: Mature bone marrow derived macrophages (BMMs) were obtained at day 7 of culture of bone marrow cells in 20 ng/mL CSF-1 (Peprotech) in RPMI medium containing 10% fetal bovine serum, 4 mM L-glutamine, 100 U/mL penicillin/streptomycin (complete RPMI) (all Gibco). In selected experiments BMMs were exposed to lentiviral particles containing hairpins targeting Etv1.

extract_protocol:
total RNA was extracted with the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific) and quantified using Qubit 2.0 (Thermo Fisher Scientific) following the manufacturer’s instructions.
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina)

treatment_protocol: BMMs were stimulated in complete RPMI supplemented with CSF-1 for indicated times with a combination of 20 ng/mL IL-4 (Peprotech), 10 μM PGE2 (SIGMA) or 10 nM valinomycin (SIGMA) under 5% CO2, atmospheric oxygen, at 37°C in a humidified incubator.

tag: tissue

value: bone marrow

value: bone marrow derived macrophage

tag: genotype


title: M2_val_2

description: IL-4 and valinomycin stimulation


title: LPS_18h_2

description: mRNA


title: M2_val_1

description: IL-4 and valinomycin stimulation


title: A751C2: Input3


title: M2_PGE2_3

description: IL-4 and PGE2 stimulation

source_name: bone marrow derived macrophage, IL-4 and PGE2 stimulation


title: M2_PGE2_2

description: IL-4 and PGE2 stimulation


title: A812C4: DC Sample 2: GFP-cGAS2_ChIPSeq


title: M2_PGE2_1

description: IL-4 and PGE2 stimulation


title: M2_2

description: IL-4 stimulation

source_name: bone marrow derived macrophage, IL-4 stimulation


title: M2_1

description: IL-4 stimulation


title: M2_3

description: IL-4 stimulation


title: M0_3

description: No stimulus control

source_name: bone marrow derived macrophage, No stimulus control


title: WT_M0_3

description: No stimulus control

value: Control shRNA


title: WT_M2PGE2_2

description: IL-4 and PGE2 stimulation


title: WT_M2PGE2_3

description: IL-4 and PGE2 stimulation


title: WT_M2_1

description: IL-4 stimulation


title: WT_M0_1

description: No stimulus control


title: KD_M2PGE2_3

description: IL-4 and PGE2 stimulation

value: Etv1 shRNA


title: KD_M2PGE2_2

description: IL-4 and PGE2 stimulation


title: WT_M0_2

description: No stimulus control


title: M0_2

description: No stimulus control


title: KD_M2PGE2_1

description: IL-4 and PGE2 stimulation


title: WT_M2_3

description: IL-4 stimulation


title: M0_1

description: No stimulus control


title: KD_M0_3

description: No stimulus control


title: KD_M0_2

description: No stimulus control


title: KD_M2_2

description: IL-4 stimulation


title: M2_Val.bigwig

data_processing:
Sequenced samples were trimmed with Trimmomatic (Bolger et al., 2014)
Mapped using Bowtie2 (Langmead and Salzberg, 2012)
Replicate mapped files merged with SAM tools (Li et al., 2009).
Coverage files were generated with deepTools (Ramírez et al., 2016). Open chromatin and differentially regulated chromatin was detected with MACS2 (Zhang et al., 2008) with a p value < 1x10-7 and a q value of less than 0.1 and a 2 fold enrichment threshold.
Genome_build: GRCm38
Supplementary_files_format_and_content: Coverage files in bigwig format

source_name: bone marrow derived macrophage

growth_protocol: Mature bone marrow derived macrophages (BMMs) were obtained at day 7 of culture of bone marrow cells in 20 ng/mL CSF-1 (Peprotech) in RPMI medium containing 10% fetal bovine serum, 4 mM L-glutamine, 100 U/mL penicillin/streptomycin (complete RPMI) (all Gibco).

extract_protocol:
5x10^4 BMMs treated for 6 h as described were washed in PBS and then lysed in 10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630 (all SIGMA). Nuclei were then spun down and then resuspend in 25 μl TD (2x reaction buffer), 2.5 μL TDE1 (Nextera Tn5 Transposase) and 22.5 μL nuclease-free water, incubated for 30 min at 37°C. DNA was purified with the Qiagen MinElute PCR Purification Kit (Thermo Fisher Scientific).
PCR amplification was performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs) using custom Nextera PCR Primers containing barcodes. Adaptors were removed with AMPure XP beads according to manufacturer’s protocol. Libraries were quantified with the Qubit and submitted for sequencing with a HISeq 3000 (Illumina)

tag: stimulation

value: IL-4 and PGE2


title: WT_M2_2

description: IL-4 stimulation


title: M0.bigwig

value: No stimulus control


title: M2.bigwig

value: IL-4 and Valinomycin


title: Pant_72h_rep4

status: Public on Dec 15 2018

city: Bremerhaven

first: Sara

last: Beszteri

address: Am Handelshafen 12

country: Germany

institute: Alfred Wegener Institute

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 72h (rep 4)
PA15_5

data_processing:
Basecalling for Illumina HiSeq was done by Gene Core EMBL, Heidelberg
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic (0.32), min phred quality 15 and min read length 30 bases
Reads were assembled de-novo using Trinity (2.0.4) and abundance was estimated mapped to it. The assembly is available at TSA GFUQ00000000.
Abundance estimates were determined using RSEM method at gene (not transcript/isoform) level. Abundance estimates were generated excluding sequenced stock culture to account for effective library size. Count and TMM-normalized FPKM values are provided (i.e., fragments per kilobase transcript length per million fragments mapped).
Genome_build: TSA GFUQ00000000
Supplementary_files_format_and_content: Tab-delimited text files include count and normalized abundance.
Supplementary_files_format_and_content: annotation_table.txt: Tab-delimited text file contains the functional annotation of the assembled transcripts of P. antarctica transcriptome. The supplementary dataset is derived from Trinotate's report. It includes assembled gene (i.e., contig) and transcript (i.e., isoform) IDs, GenBank ID, and, when available, best blastx hit information excluding mammalian hits (i.e., UniProt ID, e-value, and function).

organism: Phaeocystis antarctica

source_name: P. antarctica_72hr_iron-replete

growth_protocol: P. antarctica was incubated in iron-free modified f/2 growth medium after Guillard and Ryther prepared with Southern Ocean Sea Water at 16:8 light:dark cycle 40 micro-E light intensity 2+/-2 degree C temperature. Cells were harvested and total RNA was extracted. cDNA library construction and sequencing were done by Gene Core EMBL.

extract_protocol:
100+/-10 ml of each sample were filtered through 1.2_m MF-Millipore membrane filters under vacuum. Cells were resuspended in 500_l beta-mercaptoethanol/RLT buffer and preserved in liquid nitrogen at -80_ until RNA extraction. Total RNA was extracted using Rneasy Plant Mini Kit (Qiagen).
cDNA library construction and sequencing were done by Gene Core EMBL, Heidelberg

treatment_protocol: Cultures were enriched with ferric chloride after two days.

tag: time of iron supplementation

tag: culture type

value: plusFe


title: WT_M2PGE2_1

description: IL-4 and PGE2 stimulation


title: KD_M0_1

description: No stimulus control


title: Pant_72h_rep3

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 72h (rep 3)
PA15_4


title: Pant_72h_rep1

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 72h (rep 1)
PA15_2


title: KD_M2_3

description: IL-4 stimulation


title: Pant_72h_rep2

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 72h (rep 2)
PA15_3


title: Pant_14h_rep4

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 14h (rep 4)
PA13_1_5

source_name: P. antarctica_14hr_iron-replete


title: Pant_24h_rep1

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 24h (rep 1)
PA13_2_2

source_name: P. antarctica_24hr_iron-replete


title: KD_M2_1

description: IL-4 stimulation


title: Pant_24h_rep2

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 24h (rep 2)
PA13_2_3


title: Pant_0h_rep4

description:
Iron-limted culture of P. antarctica acclimated for 2 days (rep 4)
PA12_5

source_name: P. antarctica_iron-limited

value: minusFe


title: Pant_24h_rep3

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 24h (rep 3)
PA13_2_4


title: Pant_0h_rep3

description:
Iron-limted culture of P. antarctica acclimated for 2 days (rep 3)
PA12_4


title: Pant_0h_rep2

description:
Iron-limted culture of P. antarctica acclimated for 2 days (rep 2)
PA12_3


title: Pant_0h_rep1

description:
Iron-limted culture of P. antarctica acclimated for 2 days (rep 1)
PA12_2


title: M2_PGE2.bigwig


title: D35PrTzF_Via

status: Public on Dec 04 2018

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

description:
Viable cells from normal human prostate tissue transition zone
Pd_filtered_matrix.mtx
Pd_filtered_barcodes.tsv
Pd_PrF_filtered_genes.tsv

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 2.1.1 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 2.1.1 was used to generate mapped bam files using default settings
10x Genomics’ cellranger aggr version 2.1.1 was used to aggregate samples from the same patient to generate filtered gene-by-cell matrices using default settings
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix market file with cell barcode and gene name tab-delimited text files

source_name: Viable human prostate transition zone

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced R1=26cycles R2=58cycles, i7=8cycles

treatment_protocol: Populations of single-cells dissociated from health prostates from organ donors were isolated by FACS

tag: phenotype

value: TzVia

tag: facs ab profile

value: Via-


title: D35PrPzF_Via

description:
Viable cells from normal human prostate tissue peripheral zone
Pd_filtered_matrix.mtx
Pd_filtered_barcodes.tsv
Pd_PrF_filtered_genes.tsv

source_name: Viable human prostate peripheral zone

value: PzVia


title: D27PrPzF_Via


title: MEF18_Het

status: Public on Nov 29 2018

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Reads were mapped on mm10 mouse transcriptome with gencode M14 as gene annotation and quantified using RSEM v1.3.1
Read counts were normalized by calculating TPM (Transcripts Per Kilobase Million)
DESeq2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads count, TPM and FPKM for each Sample

source_name: Lztr1 +/- MEFs (murine embryonic fibroblasts)

growth_protocol: MEFs cells were routinely grown on uncoated plastic in DMEM medium (Thermofisher) supplemented with Glutamine (Thermofisher).

extract_protocol:
MEFs were trypsinized, peletted, and RNA was harvested using Nucleospjin (Macherey). 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: strain background

value: mouse embryonic fibroblasts (MEFs)

tag: passage

value: Lztr1 +/-


title: MEF12_WT

source_name: Wild Type MEFs (murine embryonic fibroblasts)

tag: cell type

value: Lztr1 +/+


title: MEF10_WT


title: MEF15_Het


title: Pant_24h_rep4

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 24h (rep 4)
PA13_2_5


title: LNCaP AR shTRIM28 regular medium

status: Public on Oct 05 2018

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

institute: Emory University

description: LNCaP AR shTRIM28 RM

data_processing:
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

source_name: Prostate cancer cell line

extract_protocol: Chromatin in nuclear fraction were sheared to 200-500bp using anCovaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antisera.  DNA was then uncrosslinked from protein, purified and sequenced using Illumina Genome Analyzers followig protocols recommended by the manufacturer. Libraries were prepared according to Illumina's instructions.

treatment_protocol: LNCaP cells were infected with shTRIM28 lentivirus for 4 days before fixation by 1% formaldehyde.

tag: cell line

value: LNCaP

value: WT

tag: antibody

value: AR

tag: vendor

value: Santa Cruz

tag: catalog number

tag: lot/batch number


title: Replicate 3

status: Public on Oct 23 2018

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Human and mouse genes were separated and then human and mouse cells were deconvolved to observe doublet rate.
Mouse cells were selected for further analysis, and barcodes with number of unique UMIs greater than a threshold (Klein et al., 2015) were selected, resulting in the processed data table.
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: colon

growth_protocol: primary cells/cell line mix

extract_protocol:
Mouse epithelial cell suspensions were obtained by EDTA extraction and Collagenase/DNAse dissociation. Viable cells were enriched with MACS. K562 cells were spiked in. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

tag: treatment

value: epithelial enrichment

tag: strain


title: Replicate 2


title: Pant_14h_rep3

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 14h (rep 3)
PA13_1_4


title: Replicate 1

organism:
Homo sapiens
Mus musculus


title: LNCaP AR LKO regular medium

description: LNCaP AR LKO RM

treatment_protocol: LNCaP cells were infected with pLKO lentivirus for 4 days before fixation by 1% formaldehyde.


title: LNCaP AR shTRIM24 regular medium

description: LNCaP AR shTRIM24 RM

treatment_protocol: LNCaP cells were infected with shTRIM24 lentivirus for 4 days before fixation by 1% formaldehyde.


title: Pant_14h_rep1

description:
Iron-limted culture of P. antarctica enriched with ferric chloride for 14h (rep 1)
PA13_1_2


title: LNCaP TRIM28 + Ethl

description: LNCaP-R TRIM28

treatment_protocol: LNCaP cells were grown in 5% charcoal-stripped FBS for 3 days before addition of ethanol for 16h. Then, cells were fixed by 1% formaldehyde.

value: Abcam


title: LNCaP HA-TRIM24 + Ethl

description: LNCaP-R HA-TRIM24

treatment_protocol: LNCaP cells stably expressing HA-TRIM24 were grown in 5% charcoal-stripped FBS for 3 days before addition of ethanol for 16h. Then, cells were fixed by 1% formaldehyde.

value: HA


title: LNCaP HA-TRIM24 + 10nM R1881

description: LNCaP+R HA-TRIM24

treatment_protocol: LNCaP cells stably expressing HA-TRIM24 were grown in 5% charcoal-stripped FBS for 3 days before addition of 10nM R1881 for 16h. Then, cells were fixed by 1% formaldehyde.


title: D27PrTzF_Via


title: BDL_Nint_r7

status: Public on Oct 04 2018

city: Pennington

first: Ron

last: Ammar

state: New Jersey

address: 311 Pennington Rocky Hill Road

institute: Bristol-Myers Squibb

data_processing:
Reads were aligned to the Rattus norvegicus Rnor_6.0 reference genome (NCBI assembly accession GCF_000001895.5) with the Omicsoft Sequence Aligner.
Gene and transcript abundance was determined with Ensembl R89 rat gene models using RSEM.
All RNA-Seq data were processed in R with Bioconductor packages.
RNA-Seq samples were TMM normalized with the edgeR package.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Tab-delimited text files of counts and log2CPM

organism: Rattus norvegicus

source_name: ex-vivo slice

extract_protocol:
Total RNA was prepared from PCLSs using the RNeasy 96 kit (Qiagen, Germany) according to the manufacturer's instructions. cDNA synthesis was performed with high capacity RNA to cDNA kit (Life Technologies, Carlsbad, CA). Real-time PCR was performed using the ViiATM7 (Life Technologies, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Liver


title: Sham_veh_r5

value: Sham


title: BDL_SB525334_r4


title: BDL_SB525334_r5


title: BDL_Sora_r4


title: LNCaP TRIM28 + 10nM R1881

description: LNCaP+R TRIM28

treatment_protocol: LNCaP cells were grown in 5% charcoal-stripped FBS for 3 days before addition of 10nM R1881 for 16h. Then, cells were fixed by 1% formaldehyde.

tag: genotype


title: BDL_veh_r9

value: BDL


title: BDL_Nint_r4


title: BDL_Nint_r10


title: BDL_Nint_r9


title: D17PrPzF_Via


title: D17PrTzF_Via


title: BDL_SB525334_r3


title: BDL_SB525334_r7


title: BDL_SB525334_r1


title: BDL_Sora_r5


title: Sham_veh_r1


title: BDL_Nint_r1


title: Sham_veh_r9


title: BDL_SB525334_r9


title: BDL_SB525334_r2


title: Sham_veh_r2


title: BDL_SB525334_r8


title: BDL_veh_r7


title: Sham_veh_r6


title: Sham_veh_r7


title: BDL_Sora_r8


title: BDL_veh_r1


title: Sham_veh_r3


title: BDL_Sora_r1


title: BDL_Sora_r3


title: Sham_veh_r4


title: BDL_Nint_r5


title: Sham_veh_r8


title: BDL_Sora_r2


title: BDL_Nint_r8


title: BDL_Nint_r6


title: BDL_veh_r5


title: BDL_veh_r4


title: BDL_Sora_r10


title: BDL_SB525334_r6


title: BDL_Nint_r2


title: BDL_Sora_r7


title: BDL_veh_r3


title: BDL_veh_r8


title: BDL_Sora_r9


title: BDL_veh_r2


title: BDL_Nint_r3


title: BDL_veh_r10


title: BDL_veh_r6


title: BDL_Sora_r6


title: K562_BG4-ChIP-rep_2c

status: Public on Jul 16 2018

city: Cambridge

first: Avazeh

middle: T

last: Ghanbarian

address: Robinson Way

department: Cancer Research UK, Cambridge Inst

country: United Kingdom

institute: University of Cambridge

data_processing:
The data was processed as described in the associated manuscript. Details about the analysis can also be found at https://github.com/sblab-bioinformatics/dna-secondary-struct-chrom-lands/blob/master/Methods.md
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at https://github.com/taoliu/MACS/. A tiled data file (TDF) file (.tdf) is a binary file that contains data that has been preprocessed  by igvtools for faster display in IGV.

source_name: K562 cell line

growth_protocol: K562 cells were cultured in RPMI-1640 medium supplemented with 10%FBS.

extract_protocol:
Chromatin was isolated from K562 cells that were cross-linked using 1% formaldehyde for 10 min at RT and prepared using a ChIP-qPCR Kit (Chromatrap, cat. no. 500117). Chromatin was sonicated using a Bioruptor Plus (Diagenode) to give a fragment distribution of 100-500 bp.
G4 ChIPed DNA was subjected to Nextera library preparation (Illumina, cat. no. FC-121-1030). For further details see methods section in the associated manuscript.


title: K562_BG4-ChIP-rep_2_input


title: K562_BG4-ChIP-rep_2b


title: K562_BG4-ChIP-rep_2a


title: K562_BG4-ChIP-rep_1c


title: K562_BG4-ChIP-rep_1_input


title: K562_BG4-ChIP-rep_1a


title: Limbs_E12_del1-13d9lac_CTCF

status: Public on Dec 22 2017

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

description: Whole forelimb and hindlimb mouse E12.5_del(1-13)d9lac_ChIP-seq

data_processing:
adapters and bad quality bases were removed with cutadapt (ref Martin et al 2011 version 1.8 options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for ChIP and -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for ChIPmentation).
Then reads were mapped using bowtie2 on the mm10 genome (ref Langmead et al. 2012 version 2.2.4 default parameters).
Bam files were merged when replicates or resequencing were done.
The peaks and the coverage were obtained as the output of MACS2 (ref Zhang et al 2008 version 2.1.1.20160309 command line: macs2 callpeak -t input.bam --call-summits -B). By default, MACS2 only kept one tag at the same location (the same coordinates and the same strand), which would remove all potential contaminants from 4C experiments.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak contains the peak calling; BedGraph contains the coverage from macs2

source_name: Whole Forelimbs and Hindlimbs

growth_protocol: Heterozygous mutant mice were crossed in order to obtain Wt and homozygous mutant embryos.

extract_protocol:
E12.5 limb tissue was micordissected from wild type or HoxD mutants embryos and used for ChIP experiments. Samples were fixed in 1% formaldehyde/PBS for 10 (CTCF, H3K27ac, RAD21) or 25 (RAD21, SMC1) minutes at room temperature, washed three times with col
For ChIP-seq, 5-10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

value: Whole Forelimbs and Hindlimbs

tag: embryonic day

value: anti-CTCF (Active motif, 61311, 61312)


title: Limbs_E12_delattP-Rel5d9lac_CTCF

description: Whole forelimb and hindlimb mouse E12.5_del(attP-Rel5)d9lac_ChIP-seq


title: Limbs_E12_del8-13rXII_CTCF

description: Whole forelimb mouse E12.5_del(8-13)rXII_ChIPmentation

data_processing:
Library strategy: ChIPmentation
adapters and bad quality bases were removed with cutadapt (ref Martin et al 2011 version 1.8 options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for ChIP and -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for ChIPmentation).
Then reads were mapped using bowtie2 on the mm10 genome (ref Langmead et al. 2012 version 2.2.4 default parameters).
Bam files were merged when replicates or resequencing were done.
The peaks and the coverage were obtained as the output of MACS2 (ref Zhang et al 2008 version 2.1.1.20160309 command line: macs2 callpeak -t input.bam --call-summits -B). By default, MACS2 only kept one tag at the same location (the same coordinates and the same strand), which would remove all potential contaminants from 4C experiments.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak contains the peak calling; BedGraph contains the coverage from macs2

source_name: Whole Forelimbs

extract_protocol: For the ChIPmentation sample, the protocol was carried out by following Schmidl et al. (Nature Methods, 2015) as well as the detailed versions in http://www.medical-epigenomics.org/papers/schmidl2015/. Forelimbs of four E12 embryos were dissected and lysed as for ChIP-seq samples. Only one fifth of the sonicated product (around 1 million cells) was used for this ChIP. Antibody (CTCF, Actif Motif) incubation was performed overnight altogether with magentic beads. Washes were performed with buffer WBI, WBIII and Tris pH8 as described in (Schmidl et al 2015). Prehetaed Tn5 transposase was added to the sample for one minute at 37ºC. Washes were done in duplicate with buffer WBI and buffer TET (Schmidl et al, 2015). Proteinase K treatment was performed overnight at 65ºC. Sample was purified with QIAGEN minielute columns in 12ul of water. qPCR test procedure was applied prior to PCR library making. For the library making, fourteen PCR amplification cycles were performed using the nextera N708 index and 3ng of final product were obtained and sent for sequencing. The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

value: Whole Forelimbs


title: Limbs_E12_del8-13rXII_RAD21

description: Whole forelimb and hindlimb mouse E12.5_del(8-13)rXII_RAD21_sequenced-twice_ChIP-seq

value: anti-RAD21 (abcam, ab992)


title: WT_ rep2 miRNA

status: Public on Jun 30 2018

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

country: China

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description: WT

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human reference genome using bowtie1 software.
For reads count, mirdeep2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files that we uploaded are reads counts of microRNAs in WT and DR8dex2 hMSCs. And, all of the processed data files are csv format.

source_name: Mesenchymal stem cell

growth_protocol: Human MSCs (hMSCs) derived from hESCs were cultured in MEMa (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific (Cat:10099-141, Lot:1616964)), 0.1 mM non-essential amino acids (Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 1 ng/mL bFGF (Joint Protein Central, JPC).

extract_protocol:
DNA was isolated using phenol-chloroform-isoamylalcohol extraction and ethanol precipitation.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: ES-derived  mesenchymal stem cell


title: DR8dex2_rep1 miRNA


title: WT_ rep1 miRNA

description: WT


title: Limbs_E12_del8-13d11lac_CTCF

description: Whole forelimb and hindlimb mouse E12.5_del(8-13)d11lac_ChIP-seq

extract_protocol:
E12.5 limb tissue was micordissected from wild type or HoxD mutants embryos and used for ChIP experiments. Samples were fixed in 1% formaldehyde/PBS for 10 (CTCF, H3K27ac, RAD21) or 25 (RAD21, SMC1) minutes at room temperature, washed three times with cold PBS containing protease inhibitor (and, for H3K27ac, deacetylase inhibitor) and stored at -80°C. For ChIP-seq samples, around, one hundred milligrams of tissue were used. Nuclei were extracted by incubating them in a cell lysis buffer provided in the ChIP IT high sensitivity kit (Active motif) during at least 10 minutes and with the aid of a Dounce homogenizer type B (Active motif). The isolated nuclei were pelleted and lysed in sonication buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH=8.0, protease inhibitor and, for the case of H3K27ac, deacetylase inhibitor) for 10 min on ice, and fragmented to a range of 200-500 bp using a Vibracell tip sonicator or a Diagenode Bioruptor pico waterbath device. DNA concentration was estimated using the Qubit ds DNA HS assay kit following manufacturer instruction and 25-30ug of chromatin were diluted ten times in ChIP dilution buffer (20mM HEPES, 150mM NaCl, 0.1% NP40) and incubated overnight at 4ºC with 4ug of anti-CTCF antibody (Active motif, 61311, 61312), anti-SMC1 (Bethyl, A300-055A), anti-RAD21 (abcam, ab992) or 2ug of anti-H3K27ac (abcam, ab4729) on a rotating platform. For ChIP-seq samples, the next day chromatin-antibody complexes were incubated with protein A/G agarose beads during 3h at 4ºC and successively washed following manufacturer instructions. Finally they were eluted and purified by phenol:chlorophorm extraction and precipitation. Between 5 to 10ng of immunoprecipitated DNA were sequenced with a 50bp single-end Illumina HiSeq flow cell.
For ChIP-seq, 5-10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.


title: DFL_E12_Wt_SMC1

description: Distal forelimb mouse E12.5_Wt_SMC1_ChIP-seq

source_name: Distal Forelimbs

value: Distal Forelimbs

value: wild type

value: anti-SMC1 (Bethyl, A300-055Al)


title: DR8dex2_rep2 miRNA


title: ChIP-seq_H3K27me3_Col_rep2

status: Public on Aug 20 2017

first: Danhua

last: Jiang

address: No.1 West Beichen Road

institute: Institute of Genetics and Developmental Biology

description: Human DNA was used to calculate the reference derived normalization factor.

data_processing:
Reads were mapped to the Arabidopsis genome (TAIR10) or human genome (hg38/GRCh38) using Bowtie2.
The number of H3K27me3 reads aligned to human genome were first normalized based on the number of input reads, and then was used to calculate reference derived normalization factor.
BedGraph files were created using the deepTools utility bamCoverage with a bin size of 10bp.
The number of reads in each bin in the bedGraphs were then scaled by the reference derived normalization factor to generate reference-adjusted reads per million (RRPM).
H3K27me3 enriched regions were identified using MACS2.
Genome_build: TAIR10 (Arabidopsis), hg38/GRCh38 (human)
Supplementary_files_format_and_content: *bigwig: Normalized coverage of H3K27me3.

organism:
Arabidopsis thaliana
Homo sapiens

source_name: Seedlings, WT, H3K27me3 ChIP

extract_protocol:
Mononucleosomes from 10-day-old Arabidopsis seedlings and human HEK293 cells generated by micrococcal nuclease (MNase) digestion were subjected to ChIP. To generate Arabidopsis mononucleosomes, nuclei were extracted from 10-day-old seedlings, and were subsequently subjected to MNase digestion in N buffer (15mM Tris pH7.5, 250mM sucrose, 60mM KCl, 15mM NaCl, 5mM MgCl2, 1mM CaCl2, 1mM DTT, 10mM ß-mercaptoethanol, protease inhibitor cocktail). EDTA and EGTA were added to a final concentration of 10mM each to stop the MNase digestion. Nuclei were lysed by adding NaCl to a final concentration of 500mM, and soluble materials containing mononucleosomes were recovered after centrifugation. To generate mononucleosomes from human HEK293 cells, nuclei were extracted by hypotonic lysis and treated with MNase in N buffer. DNA was extracted from a portion of mononucleosomes to determine the concentration of mononucleosomes. Same amount of mononucleosomes from different Arabidopsis samples were mixed with a constant amount of human mononucleosomes before immunoprecipitation with anti-H3K27me3 antibody.
Sequencing libraries were prepared using a TruSeq DNA sample prep kit (Illumina).

tag: ecotype

value: Col

tag: genotype/variation

value: wildtype

value: seedlings

tag: age

value: 10 days

tag: human cell line

tag: chip antibody

value: H3K27me3 (Millipore 07-449)


title: ChIP-seq_Input_Col_rep2

source_name: Seedlings, WT, input


title: ChIP-seq_Input_Col_rep1


title: ChIP-seq_H3K27me3_Col_rep1


title: DFL_E12_Wt_RAD21

description: Distal forelimb mouse E12.5_Wt_RAD21_ChIP-seq


title: c.elegans cells (L2 stage)

status: Public on Aug 17 2017

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: sciRNAseq with c.elegans cells (during sorting, polyploid c.elegans cells were exlcuded)

data_processing:
Base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/ 2.16.0.10 tolerating one mismatched base in barcodes (edit distance (ED) < 2)
RT barcode (10bp) and UMI (8bp) sequence in Read1 is attached to the read name of Read2. Reads not matching to the expected RT barcodes were discarded. Read2 were then adaptor clipped using trim_galore/0.4.1 with default settings.
Trimmed reads were mapped to the human reference genome (hg19), mouse reference genome (mm10), C.elegans reference genome (PRJNA13758) or a chimeric reference genome of hg19, mm10 and PRJNA13758, using STAR/v 2.5.2b (38) with default settings and gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse, WormBase PRJNA13758.WS253.canonical_gene set for C.elegans).
Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, and read 2 end-coordinate.
Mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index (ED < 2, including insertions and deletions).
To generate digital expression matrices, we calculated the number of strand-specific UMIs mapping to the exonic and intronic regions of each gene, for each cell; generally, fewer than 3% of total UMIs strand-specifically mapped to multiple genes. For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded.
Genome_build: human reference genome (hg19), mouse reference genome (mm10), C.elegans reference genome (PRJNA13758)
Supplementary_files_format_and_content: Processed data file is a sparsematrix in R: each row corresponds to genes, and each column corresponds to single cell, number in the matrix is the UMI count data.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole c.elegans (L2 stage)

growth_protocol: All cultured cell lines were cultured at 37°C with 5% CO2, and were maintained in high glucose DMEM (Gibco cat. no. 11965) supplemented with 10% FBS and 1X Pen/Strep (Gibco cat. no. 15140122; 100U/ml penicillin, 100µg/ml streptomycin).

extract_protocol:
All cell lines were trypsinized, spun down at 300xg for 5 min (4°C). and washed once in 1X PBS. L2 stage worms were disscociated with SDS-DTT solution and pronase to generate single cell suspension. Detailed protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."
library construction protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."

treatment_protocol: For c.elegans, a synchronized L2 population was obtained by two cycles of bleaching gravid adults to isolate fertilized eggs allowing the eggs to hatch in the absence of food to generate a population of starved L1 animals.

value: A C. elegans strain (RW12139 stIs11435(unc-120::H1-Wcherry;unc-119(+));unc-119(tm4063)) carrying an integrated Punc-120::mCherry gene in a wild type background was used

tag: developmental stage


title: Human SCLC H889 NEUROD1 Ctrl Input

status: Public on Jul 21 2016

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

data_processing:
All samples were ran on a Illumina GAIIX or  Illumina Hi-Seq 2000 and basecalls were performed using CASAVA
Sequence reads for each sample were mapped to the hg19 or mm9 genome assemblies as relevant with Bowtie (v1.1.1)
Duplicate reads were removed, and the remaining unique reads were normalized to 10 million reads
Peak calling was performed by HOMER (v4.2) using an FDR cutoff of 0.001, a cumulative Poisson p-value of <0.0001, and required a 4-fold enrichment of normalized sequenced reads in the treatment sample over the control/input sample
Genome_build: Human data (hg19), mouse data (mm9)

source_name: Tumor

growth_protocol: Human Cells were grown in RPMI 1640 supplemented with 5-10% FBS, or Dissected mouse tumors from lungs of Trp53;Rb1;Rbl2 triple knock out mice were pooled from an individual mouse.

extract_protocol:
For full ChIP protocol see Borromeo et al. Development. 2014. For extraction, nuclei were liberated from cells by dounce homogenization in PBS and then fixed in 1% formaldehyde for 10 minutes at room. temperature. Fixation was terminated by adding glycine to a final concentration of 0.125M. Chromatin was sheared by using a Diagenode Bioruptor for 30 minutes on high power with 30s:30s on:off cycles. 100 μg chromatin was immunoprecipitated with 5 μg affinity-purified mouse anti-ASCL1 antibody (BD Biosciences) followed by anti-mouse Dyna beads (Invitrogen).
All libraries were made according to Illumina’s or NEB (NEBNEXT) ChIP-seq DNA sample prep protocol

treatment_protocol: No treatment performed

tag: classification

value: SCLC

tag: ascl1 expression


title: Human SCLC H889 ASCL1 ChIP

tag: cell line

tag: antibody

value: mouse anti-ASCL1 antibody (BD Biosciences, cat# 556604)


title: Human SCLC H524 NEUROD1 ChIP

value: goat anti-NEUROD1 (Santa Cruz, N-19)


title: Human SCLC H524 ASCL1 Ctrl Input


title: Human SCLC H82 NEUROD1 ChIP


title: Human SCLC H2107 ASCL1 ChIP


title: Mouse Neuroendocrine lung tumor ASCL1 ChIP

value: Neuroendocrine

value: Trp53;Rb1;Rbl2 triple knockout model


title: Mouse Neuroendocrine lung tumor Input


title: Human SCLC H128 ASCL1 ChIP


title: seedling, WT in dark, biological repl1

status: Public on Dec 01 2017

type: RNA

city: Hannover

first: Thomas

last: Pflannschmidt

address: Herrenhäuser Straße 2

institute: Leibniz-Universität Hannover

description: Arabidopsis seedlings day 4 in dark; before formation of true leaves

hyb_protocol: ssDNA were hybridized on an Affymetrix Chip, Arabidopsis Gene 1.0 ST Array as described in the manual (GeneChip® WT Terminal  Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, Rev. 7, Affymetrix).

scan_protocol: Standard Affyemtrix protocol

data_processing: The data were analyzed with RobiNA (1.2.4_build656) using default analysis settings and normalization method RMA with p-value correction after Benjamini-Hochberg method.

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings day 4 in dark

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® WT Terminal  Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, Rev. 7, Affymetrix).

growth_protocol: Seeds were surface-sterilized (Ethanol) and spread on MS agar plates with 1% sucrose and powdered charcoal (4 ml / 1 l MS-medium).  The plates were kept for 72 h at 4°C in darkness and were exposed to light for 6h to induce germination. Plants grow at 21°C.

extract_protocol: Total RNA from seedlings was isolated using and RNeasy Plant Mini Kit (Qiagen) with on-column DNase I (Qiagen) treatment.

treatment_protocol: Plants grow under continuous light at 150 µmol of photons m-2 s-1 for 5 days and in darkness for 4 days respectively.

value: whole seedling

value: wildtype Col-0

value: 4 days


title: seedling, WT in light, biological repl3

description: Arabidopsis seedlings day 5 in light; before formation of true leaves

source_name: Arabidopsis seedlings day 5 in light

value: 5 days


title: seedling, pap7 in light, biological repl3

value: pap7 mutant (albino)


title: seedling, pap7 in light, biological repl2


title: seedling, WT in light, biological repl1


title: MF_brain_2

status: Public on Jul 14 2018

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

institute: VIB-University of Ghent

description: WT Microglia

hyb_protocol: All Methods listed in Scott et al.  Transcription Factor Zeb2 is required to maintain tissue-sepcific identities of macrophages. Immunity. 2018.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Bioconductor. Normalisation was done by RMA. All samples passed quality control, and the Robust Multi-array Average (RMA) procedure was used to normalize data within arrays (probeset summarization, background correction and log2-transformation) and between arrays (quantile normalization).

label: Biotin

value: Brain

tag: cell type

value: microglia


title: seedling, WT in dark, biological repl2


title: seedling, WT in dark, biological repl3


title: seedling, WT in light, biological repl2


title: MF_brain_1

description: WT Microglia

label_protocol: All Methods listed in Scott et al.  Transcription Factor Zeb2 is required to maintain tissue-sepcific identities of macrophages. Immunity. 2018.

value: wildtype


title: MF_brain_3

description: WT Microglia

extract_protocol: All Methods listed in Scott et al.  Transcription Factor Zeb2 is required to maintain tissue-sepcific identities of macrophages. Immunity. 2018.


title: EM-KCs from KC-DTR WT littermate control mouse, 30 days after DT treatment, biological replicate 2

status: Public on Nov 21 2015

description: Kupffer cells from WT DT-receptor mice, treated with DT on day 30

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
probe_group_file:  = MoGene-1_0-st-v1.r4.pgf
meta-probeset_file:  = MoGene-1_0-st-v1.r4.mps

source_name: KC_DTR_WT, DT30

label_protocol: Affymetrix WT Terminal Labeling Kit

growth_protocol: Livers were isolated from the mice between 6-12 weeks of age

extract_protocol: Livers were perfused with PBS and subsequently digested with 1mg/ml Collagenase A and 10U/ul DNase (20mins at 37oC). Kupffer cells were isolated from single cell suspensions by FACS.

treatment_protocol: Indicated KC-DTR mice received 50ng DT at the designated time prior to FACS-purification of liver Kupffer cells

value: Liver

value: DTR WT


title: EM-KCs from KC-DTR WT littermate control mouse, 30 days after DT treatment, biological replicate 1


title: RNAseq_human3_rep2

status: Public on Sep 11 2015

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

description: processed data quantified against human ENSEMBL 78 (GRCh37) gene models

data_processing:
Reads aligned to hg19 (regardless of species of origin) using default settings with Bowtie2.2.4
Wig files were generated with QuEST2.4
RNA-seq were aligned to hg19 and quantified against human ENSEMBL 78 (GRCh37) gene models using htseq-count. Variance-stabilizing transformation (VST) was applied across samples for processed data.
Genome_build: Alignments done using hg19 as reference
Supplementary_files_format_and_content: [ChIP-seq, ATAC-seq] wig
Supplementary_files_format_and_content: [RNA-seq] txt

source_name: Cranial neural crest cells

growth_protocol: hESCs/iPSCs were incubated with 2mg/ml collagenase. Once detached, clusters of 100-200 cells were plated in CNCC differentiation medium: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5× B-27 supplement with Vitamin A (50× stock, Invitrogen), 0.5× N-2 supplement (100× stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 5 μg/ml bovine insulin (Sigma-Aldrich) and 1× Glutamax-I supplement (100× stock, Invitrogen). Medium was changed every other day. After seven days of differentiation, neuroepithelial spheres attached to the dish and gave rise to migratory CNCC. Three-four days after the appearance of the first CNCC, cells were dissociated with accutase until single cells and passaged onto fibronectin-coated plates. CNCCs were then transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5× B-27 supplement with Vitamin A (50× stock, Invitrogen), 0.5× N-2 supplement (100× stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 1 mg/ml bovine serum albumin, serum replacement grade (Gemini Bio-Products # 700-104P) and 1× Glutamax-I supplement (100× stock, Invitrogen). CNCCs were passaged onto fibronectin-coated plates 1:3 every three days, and after 1-2 passages, transitioned to CNCC long term maintenance media, which is composed of CNCC early maintenance media plus 3uM ChIRON 99021 (Selleck, CHIR-99021) and 50ng/ml BMP2 (Peprotech). Cells were maintained on fibronectin with passaging every ~ 3days, and collected at passage 4 for all ChIPs and downstream assays.

extract_protocol:
ChIPs were performed using approximately 0.5-1 x 10^7 CNCCs fixed with 1% formaldehyde for 10 min at room temp. RNA was extracted using Trizol.
Sequencing libraries were prepared starting from ~30ng of ChIP DNA or oligo-dT purified mRNA using the NEBNext Multiplex Oligos for Illumina kit (Cat# E7335S).

tag: individual

value: Cranial neural crest cells (CNCCs)

tag: cnccs derived from

value: WT33 iPSC

tag: culture conditions


title: RNAseq_human1_rep2

value: H9 (ESC)


title: RNAseq_human2_rep1

value: ADRC40 iPSC


title: Input_chimp_rep1

description: processed data aligned to hg19

organism: Pan troglodytes

value: 0818 iPSC

value: none (input)


title: seedling, pap7 in light, biological repl1

tag: tissue


title: ATAC_human3_rep2

description: processed data aligned to hg19

data_processing:
Library strategy: ATAC-Seq
Reads aligned to hg19 (regardless of species of origin) using default settings with Bowtie2.2.4
Wig files were generated with QuEST2.4
RNA-seq were aligned to hg19 and quantified against human ENSEMBL 78 (GRCh37) gene models using htseq-count. Variance-stabilizing transformation (VST) was applied across samples for processed data.
Genome_build: Alignments done using hg19 as reference
Supplementary_files_format_and_content: [ChIP-seq, ATAC-seq] wig
Supplementary_files_format_and_content: [RNA-seq] txt


title: ATAC_human3_rep1

description: processed data aligned to hg19


title: RNAseq_human1_rep1


title: ATAC_human2_rep1

description: processed data aligned to hg19


title: Embryonic Kupffer cells (EM-KCs) from KC-DTR WT littermate control mouse, no DT treatment, biological replicate 1

description: Kupffer cells from WT DT-receptor mice, no treatment with DT

source_name: KC_DTR_WT, noDT

tag: genotype


title: ATAC_human1_rep1

description: processed data aligned to hg19


title: Input_human_rep1

description: processed data aligned to hg19


title: TFAP2A_human2_rep1

description: processed data aligned to hg19

value: anti-TFAP2A (Santa Cruz Biotechnology, catalog# sc-184, lot# H0911)


title: TFAP2A_human3_rep1

description: processed data aligned to hg19


title: TFAP2A_human1_rep1

description: processed data aligned to hg19


title: H3K4me3_human2_rep1

description: processed data aligned to hg19

value: anti-H3K4me3 (Active Motif, catalog# 39159, lot# 12613005)


title: H3K4me1_human3_rep1

description: processed data aligned to hg19

value: anti-H3K4me1 (Abcam, ab8895, catalog# lot# GR149140-2)


title: H3K4me3_human3_rep1

description: processed data aligned to hg19


title: p300_human3_rep1

description: processed data aligned to hg19

value: anti-p300 (Santa Cruz Biotechnology, catalog# sc-585, lot# E3113)


title: p300_human2_rep1

description: processed data aligned to hg19


title: H3K27ac_human3_rep3

description: processed data aligned to hg19

value: anti-H3K27ac (Active Motif, catalog# 39133, lot# 01613007)


title: H3K27ac_human3_rep2

description: processed data aligned to hg19


title: H3K27ac_human3_rep4

description: processed data aligned to hg19


title: H3K27ac_human3_rep1

description: processed data aligned to hg19


title: p300_human1_rep1

description: processed data aligned to hg19


title: H3K27ac_human2_rep4

description: processed data aligned to hg19


title: H3K27me3_human1_rep1

description: processed data aligned to hg19

value: anti-H3K27me3 (Active Motif, catalog# 39536, lot# 09508002)


title: H3K4me3_human1_rep1

description: processed data aligned to hg19


title: ATAC_human2_rep2

description: processed data aligned to hg19


title: H3K4me1_human1_rep1

description: processed data aligned to hg19


title: H3K27ac_human2_rep1

description: processed data aligned to hg19


title: H3K27ac_human2_rep2

description: processed data aligned to hg19


title: H3K27ac_human1_rep1

description: processed data aligned to hg19


title: H3K27ac_human1_rep2

description: processed data aligned to hg19


title: NR2F1_human3_rep1

description: processed data aligned to hg19

value: anti-NR2F1 (Perseus Proteomics, catalog# PP-H8132-00, lot# A-2)


title: ATAC_chimp2_rep2

description: processed data aligned to hg19

value: 1209 iPSC


title: RNAseq_chimp2_rep2


title: RNAseq_chimp1_rep1


title: ATAC_chimp1_rep2

description: processed data aligned to hg19


title: ATAC_chimp2_rep1

description: processed data aligned to hg19


title: p300_chimp1_rep1

description: processed data aligned to hg19


title: RNAseq_chimp2_rep1


title: ATAC_chimp1_rep1

description: processed data aligned to hg19


title: NR2F1_chimp2_rep1

description: processed data aligned to hg19


title: TFAP2A_chimp1_rep1

description: processed data aligned to hg19


title: TFAP2A_chimp2_rep1

description: processed data aligned to hg19


title: p300_chimp2_rep1

description: processed data aligned to hg19


title: H3K27me3_chimp2_rep1

description: processed data aligned to hg19


title: H3K27ac_human2_rep3

description: processed data aligned to hg19


title: H3K4me3_chimp1_rep1

description: processed data aligned to hg19


title: H3K4me3_chimp2_rep1

description: processed data aligned to hg19


title: H3K27ac_human1_rep3

description: processed data aligned to hg19


title: H3K27ac_chimp2_rep4

description: processed data aligned to hg19


title: H3K4me1_chimp1_rep1

description: processed data aligned to hg19


title: RNAseq_chimp1_rep2


title: H3K4me1_chimp2_rep1

description: processed data aligned to hg19


title: H3K27ac_chimp2_rep3

description: processed data aligned to hg19


title: H3K27ac_chimp1_rep4

description: processed data aligned to hg19


title: H3K27ac_chimp1_rep3

description: processed data aligned to hg19


title: H3K27ac_chimp1_rep2

description: processed data aligned to hg19


title: H3K27ac_chimp1_rep1

description: processed data aligned to hg19


title: H3K27ac_chimp2_rep1

description: processed data aligned to hg19


title: NR2F1_human1_rep1

description: processed data aligned to hg19


title: H3K27ac_chimp2_rep2

description: processed data aligned to hg19


title: RNAseq_human3_rep1


title: Cancer-24

status: Public on Jul 01 2015

city: Madison

first: Johan

last: den Boon

state: WI

address: 330 North Orchard Street

department: Virology

institute: Morgridge Institute for Research

description: gene expression data from epithelium

hyb_protocol: At UW-Madison Biotech Center core facilties, according to Affymetrix instructions using Affymetrix Array hybridization stations

scan_protocol: Gene Array Scanner at UW-Madison Biotech Center core facilties

data_processing: GC-RMA

source_name: cervix

label_protocol: total RNA was converted to cDNA usingT7 promoter-linked oligo-d(T), transcribed using T7 RNA polymerase, converted again to cDNA for a second round of amplification using T7 RNA polymerase in the presence of biotinylated ribonucleotides

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

tag: tissue type

value: cervical squamous epithelial cancer

tag: treatment

value: flash-frozen biopsy, cryosectioned

tag: dissection

value: laser captured


title: Cancer-27

description: gene expression data from epithelium


title: Cancer-25

description: gene expression data from epithelium


title: Cancer-14

description: gene expression data from epithelium

value: whole section


title: Cancer-12

description: gene expression data from epithelium


title: Cancer-19

description: gene expression data from epithelium


title: Cancer-23

description: gene expression data from epithelium


title: Cancer-15

description: gene expression data from epithelium


title: Cancer-07

description: gene expression data from epithelium


title: Cancer-20

description: gene expression data from epithelium


title: Cancer-13

description: gene expression data from epithelium


title: Cancer-21

description: gene expression data from epithelium


title: Cancer-26

description: gene expression data from epithelium


title: Cancer-22

description: gene expression data from epithelium


title: Cancer-09

description: gene expression data from epithelium


title: Cancer-08

description: gene expression data from epithelium


title: Cancer-28

description: gene expression data from epithelium


title: Cancer-01

description: gene expression data from epithelium


title: Cancer-18

description: gene expression data from epithelium


title: Cancer-06

description: gene expression data from epithelium


title: Cancer-16

description: gene expression data from epithelium


title: Cancer-03

description: gene expression data from epithelium


title: Cancer-02

description: gene expression data from epithelium


title: Cancer-10

description: gene expression data from epithelium


title: Cancer-17

description: gene expression data from epithelium


title: Cancer-04

description: gene expression data from epithelium


title: Cancer-11

description: gene expression data from epithelium


title: RNAseq_human2_rep2

value: Cranial neural crest cells (CNCCs)


title: CIN3-40

description: gene expression data from epithelium

value: cervical intraepithelial neoplasm, high grade lesion

value: laser-captured


title: CIN3-38

description: gene expression data from epithelium


title: CIN3-34

description: gene expression data from epithelium


title: CIN3-27

description: gene expression data from epithelium


title: CIN3-39

description: gene expression data from epithelium


title: CIN3-31

description: gene expression data from epithelium


title: CIN3-32

description: gene expression data from epithelium


title: CIN3-37

description: gene expression data from epithelium


title: CIN3-33

description: gene expression data from epithelium


title: CIN3-36

description: gene expression data from epithelium


title: CIN3-29

description: gene expression data from epithelium


title: CIN3-28

description: gene expression data from epithelium


title: CIN3-16

description: gene expression data from epithelium


title: CIN3-24

description: gene expression data from epithelium


title: CIN3-20

description: gene expression data from epithelium


title: CIN3-15

description: gene expression data from epithelium


title: CIN3-23

description: gene expression data from epithelium


title: CIN3-22

description: gene expression data from epithelium


title: CIN3-25

description: gene expression data from epithelium


title: CIN3-12

description: gene expression data from epithelium


title: CIN3-30

description: gene expression data from epithelium


title: CIN3-26

description: gene expression data from epithelium


title: CIN3-35

description: gene expression data from epithelium


title: CIN3-21

description: gene expression data from epithelium


title: CIN3-19

description: gene expression data from epithelium


title: CIN3-18

description: gene expression data from epithelium


title: CIN3-17

description: gene expression data from epithelium


title: CIN3-13

description: gene expression data from epithelium


title: CIN3-14

description: gene expression data from epithelium


title: CIN3-09

description: gene expression data from epithelium


title: CIN3-08

description: gene expression data from epithelium


title: CIN3-10

description: gene expression data from epithelium


title: CIN3-02

description: gene expression data from epithelium


title: CIN3-06

description: gene expression data from epithelium


title: CIN2-21

description: gene expression data from epithelium

value: cervical intraepithelial neoplasm, moderate grade lesion


title: CIN3-03

description: gene expression data from epithelium


title: CIN2-17

description: gene expression data from epithelium


title: CIN3-05

description: gene expression data from epithelium


title: CIN3-04

description: gene expression data from epithelium


title: CIN2-11

description: gene expression data from epithelium


title: CIN3-11

description: gene expression data from epithelium


title: CIN2-12

description: gene expression data from epithelium


title: CIN2-09

description: gene expression data from epithelium


title: CIN2-19

description: gene expression data from epithelium


title: CIN2-22

description: gene expression data from epithelium


title: CIN3-07

description: gene expression data from epithelium


title: CIN2-15

description: gene expression data from epithelium


title: CIN2-14

description: gene expression data from epithelium


title: CIN2-20

description: gene expression data from epithelium


title: CIN3-01

description: gene expression data from epithelium


title: Cancer-05

description: gene expression data from epithelium


title: CIN2-18

description: gene expression data from epithelium


title: CIN2-07

description: gene expression data from epithelium


title: CIN2-13

description: gene expression data from epithelium


title: CIN2-08

description: gene expression data from epithelium


title: CIN2-16

description: gene expression data from epithelium


title: CIN2-10

description: gene expression data from epithelium


title: CIN1-13

description: gene expression data from epithelium

value: cervical intraepithelial neoplasm, low grade lesion


title: CIN1-09

description: gene expression data from epithelium


title: CIN2-04

description: gene expression data from epithelium


title: CIN1-14

description: gene expression data from epithelium


title: CIN1-10

description: gene expression data from epithelium


title: CIN1-11

description: gene expression data from epithelium


title: CIN2-03

description: gene expression data from epithelium


title: CIN2-06

description: gene expression data from epithelium


title: CIN2-02

description: gene expression data from epithelium


title: CIN1-08

description: gene expression data from epithelium


title: Normal-22

description: gene expression data from epithelium

value: normal cervical epithelium


title: CIN1-12

description: gene expression data from epithelium


title: Normal-17

description: gene expression data from epithelium


title: CIN1-07

description: gene expression data from epithelium


title: Normal-24

description: gene expression data from epithelium


title: CIN1-04

description: gene expression data from epithelium


title: CIN1-02

description: gene expression data from epithelium


title: Normal-21

description: gene expression data from epithelium


title: CIN1-01

description: gene expression data from epithelium


title: Normal-23

description: gene expression data from epithelium


title: CIN1-03

description: gene expression data from epithelium


title: CIN1-05

description: gene expression data from epithelium


title: CIN2-01

description: gene expression data from epithelium


title: Normal-20

description: gene expression data from epithelium


title: Normal-19

description: gene expression data from epithelium


title: Normal-15

description: gene expression data from epithelium


title: Normal-18

description: gene expression data from epithelium


title: Normal-16

description: gene expression data from epithelium


title: CIN1-06

description: gene expression data from epithelium


title: CSHL_RnaSeq_Cerebellum_adult-8wks (superseded by GSE90200)

status: Public on Sep 10 2012

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
****************************
GSM1000567 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90200
****************************

source_name: Cerebellum

tag: lab

value: CSHL-m

tag: lab description

value: Gingeras - Cold Spring Harbor Laboratory

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell

value: Cerebellum

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

value: U

tag: age

tag: age description

value: Adult 8 weeks

tag: biorep

tag: labexpid

tag: readtype

tag: readtype description

value: Paired 101 nt directed reads

tag: spikeinpool

tag: strain

tag: strain description

value: A substrain of C57BL/6


title: CSHL_RnaSeq_Bladder_adult-8wks (superseded by GSE90204)

description:
****************************
GSM1000564 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90204
****************************

source_name: Bladder

tag: lab

value: Bladder

value: Urinary Bladder


title: CSHL_RnaSeq_FrontalLobe_adult-8wks (superseded by GSE90206)

description:
****************************
GSM1000562 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90206
****************************

source_name: FrontalLobe

tag: lab description

value: FrontalLobe

value: Frontal Lobe


title: Normal-03

description: gene expression data from epithelium

tag: tissue type

tag: treatment

value: flash-frozen biopsy, cryosectioned

tag: dissection

value: laser-captured


title: Normal-14

description: gene expression data from epithelium

value: normal cervical epithelium


title: CSHL_RnaSeq_Cortex_adult-8wks (superseded by GSE90205)

description:
****************************
GSM1000563 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90205
****************************

source_name: Cortex

value: CSHL-m

tag: datatype

tag: datatype description

tag: cell

value: Cortex

tag: cell organism


title: Normal-08

description: gene expression data from epithelium


title: Normal-04

description: gene expression data from epithelium


title: Normal-05

description: gene expression data from epithelium


title: Normal-10

description: gene expression data from epithelium


title: Normal-11

description: gene expression data from epithelium


title: Normal-06

description: gene expression data from epithelium


title: Normal-09

description: gene expression data from epithelium


title: Normal-01

description: gene expression data from epithelium


title: Normal-07

description: gene expression data from epithelium


title: Normal-02

description: gene expression data from epithelium


title: Normal-12

description: gene expression data from epithelium


title: CSHL_RnaSeq_Kidney_adult-8wks (superseded by GSE90179)

status: Public on Apr 02 2012

description:
****************************
GSM900194 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90179
****************************

source_name: Kidney

value: Gingeras - Cold Spring Harbor Laboratory

value: RnaSeq

value: Kidney

tag: cell description

tag: cell sex

tag: age

tag: age description

value: Paired 76 nt directed reads

tag: replicate

value: C57 black 6, the most common inbred strain of laboratory mouse


title: CIN2-05

description: gene expression data from epithelium

value: cervical intraepithelial neoplasm, moderate grade lesion


title: CSHL_RnaSeq_Heart_adult-8wks (superseded by GSE90178)

description:
****************************
GSM900199 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90178
****************************

source_name: Heart

value: Sequencing analysis of RNA expression

value: Heart

value: mouse

value: U

value: Adult 8 weeks

tag: biorep

tag: labexpid

tag: readtype

tag: readtype description

tag: spikeinpool


title: CSHL_RnaSeq_Liver_adult-8wks (superseded by GSE90180)

description:
****************************
GSM900195 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90180
****************************

source_name: Liver

tag: lab

tag: lab description

value: Liver

tag: strain

tag: strain description


title: CSHL_RnaSeq_Lung_adult-8wks (superseded by GSE90181)

description:
****************************
GSM900196 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90181
****************************

source_name: Lung

tag: datatype

tag: datatype description

value: Lung


title: CSHL_RnaSeq_Spleen_adult-8wks (superseded by GSE90182)

description:
****************************
GSM900197 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90182
****************************

source_name: Spleen

tag: cell

value: Spleen

tag: cell organism


title: Normal-13

description: gene expression data from epithelium

tag: tissue type

value: normal cervical epithelium

tag: treatment

value: flash-frozen biopsy, cryosectioned

tag: dissection

value: laser-captured


title: CSHL_RnaSeq_Colon_adult-8wks (superseded by GSE90177)

description:
****************************
GSM900198 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90177
****************************

source_name: Colon

value: CSHL-m

value: Gingeras - Cold Spring Harbor Laboratory

value: Colon

tag: cell description

tag: cell sex

tag: age

tag: age description

tag: replicate


title: CSHL_RnaSeq_Placenta_adult-8wks (superseded by GSE90203)

description:
****************************
GSM1000565 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90203
****************************

source_name: Placenta

value: RnaSeq

value: Placenta

tag: biorep

tag: labexpid

tag: readtype

tag: readtype description

value: Paired 101 nt directed reads

tag: spikeinpool

value: A substrain of C57BL/6


title: CSHL_RnaSeq_Testis_adult-8wks (superseded by GSE90184)

description:
****************************
GSM900193 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90184
****************************

source_name: Testis

tag: lab

tag: lab description

tag: datatype

value: Sequencing analysis of RNA expression

value: Testis

value: M

value: Paired 76 nt directed reads

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: CSHL_RnaSeq_Thymus_adult-8wks (superseded by GSE90183)

description:
****************************
GSM900192 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90183
****************************

source_name: Thymus

tag: datatype description

tag: cell

value: Thymus

tag: cell organism

value: mouse

value: U

value: Adult 8 weeks


title: CSHL_RnaSeq_SubcFatPad_adult-8wks (superseded by GSE90193)

description:
****************************
GSM900191 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90193
****************************

source_name: SubcFatPad

value: SubcFatPad

tag: cell description

value: Subcutaneous Adipose tissue

tag: cell sex


title: CSHL_RnaSeq_GenitalFatPad_adult-8wks (superseded by GSE90187)

description:
****************************
GSM900190 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90187
****************************

source_name: GenitalFatPad

value: CSHL-m

value: Gingeras - Cold Spring Harbor Laboratory

value: GenitalFatPad

value: Genital Adipose tissue

tag: age

tag: age description


title: CSHL_RnaSeq_LgIntestine_adult-8wks (superseded by GSE90188)

description:
****************************
GSM900189 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90188
****************************

source_name: LgIntestine

value: RnaSeq

value: LgIntestine

value: Large Intestine

tag: biorep

tag: replicate


title: CSHL_RnaSeq_SmIntestine_adult-8wks (superseded by GSE90191)

description:
****************************
GSM900186 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90191
****************************

source_name: SmIntestine

value: Sequencing analysis of RNA expression

value: SmIntestine

value: Small Intestine

tag: labexpid

tag: readtype


title: CSHL_RnaSeq_Duodenum_adult-8wks (superseded by GSE90186)

description:
****************************
GSM900187 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90186
****************************

source_name: Duodenum

value: Duodenum

tag: readtype description

value: Paired 76 nt directed reads

tag: spikeinpool

value: C57 black 6, the most common inbred strain of laboratory mouse


title: CSHL_RnaSeq_MammaryGland_adult-8wks (superseded by GSE90189)

description:
****************************
GSM900184 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90189
****************************

source_name: MammaryGland

tag: lab

tag: lab description

value: MammaryGland

value: mouse

value: Mammary Gland

value: U


title: CSHL_RnaSeq_Stomach_adult-8wks (superseded by GSE90192)

description:
****************************
GSM900185 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90192
****************************

source_name: Stomach

value: CSHL-m

tag: datatype

value: Stomach

value: Adult 8 weeks

tag: strain


title: CSHL_RnaSeq_Ovary_adult-8wks (superseded by GSE90190)

description:
****************************
GSM900183 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90190
****************************

source_name: Ovary

value: Gingeras - Cold Spring Harbor Laboratory

tag: datatype description

value: Ovary

tag: strain description


title: CSHL_RnaSeq_Adrenal_adult-8wks (superseded by GSE90185)

description:
****************************
GSM900188 record metadata submitted on Mar 23 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90185
****************************

source_name: Adrenal

value: RnaSeq

tag: cell

value: Adrenal

tag: cell organism

value: Adrenal gland


title: Cervical cancer biopsy R392ST

status: Public on Jan 31 2012

city: Mexico City

first: Mariano

last: Guardado-Estrada

state: Cuauhtémoc

address: Dr. Bálmis 148 Col. Doctores

department: Medicina Genómica

country: Mexico

institute: Hospital General de México O.D.

description: Gene expression data from Cervical cancer biopsy

hyb_protocol: Following fragmentation, ssDNA were hybridized for 16 hr at 45C and 60 rpm on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 protocol FS450_0007

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) with GeneChip Scanner 3000

data_processing: Microarrays were normalized using the RMA algorithm (Robust Multichip Average) in the Affymetrix Expression Console. The analysis was done at Gene Level Default: RMA-Sketch

source_name: Cervical cancer biopsy

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

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

tag: clinical group

value: Case

tag: haplogroup

tag: tissue

value: Cervical cancer biopsy


title: Cervical cancer biopsy R494ST


title: Cervical cancer biopsy R336ST


title: Cervical cancer biopsy R489ST


title: Cervical cancer biopsy R365ST


title: Cervical cancer biopsy R496ST


title: Cervical cancer biopsy R486ST


title: Cervical cancer biopsy R386ST


title: Cervical cancer biopsy R369ST


title: Cervical cancer biopsy R298ST


title: Cervical cancer biopsy R476ST


title: Cervical cancer biopsy R282ST


title: Cervical cancer biopsy R265ST


title: Cervical cancer biopsy R478ST


title: Cervical cancer biopsy R248ST


title: Cervical cancer biopsy R378ST


title: Cervical cancer biopsy R390ST


title: Cervical cancer biopsy R483ST


title: Cervical cancer biopsy R380ST


title: Cervical cancer biopsy R324ST


title: Cervical cancer biopsy R240ST


title: Cervical cancer biopsy R322ST


title: Cervical cancer biopsy R221ST


title: Cervical cancer biopsy R230ST


title: Cervical cancer biopsy R208ST


title: Cervical cancer biopsy R244ST


title: Cervical cancer biopsy R330ST


title: Cervical cancer biopsy R198ST


title: Cervical cancer biopsy R411ST


title: Cervical cancer biopsy R368ST


title: Cervical cancer biopsy R157ST


title: Cervical cancer biopsy R194ST


title: Cervical cancer biopsy R183ST


title: Cervical cancer biopsy R189ST


title: Cervical cancer biopsy R124ST


title: Cervical cancer biopsy R158ST


title: Cervical cancer biopsy R081ST


title: Cervical cancer biopsy R154ST


title: Cervical cancer biopsy R072ST


title: Healthy exocervix CEXO-43

description: Gene expression data from Healthy female exocervix

source_name: Healthy female exocervix

value: Control

value: Healthy female exocervix


title: Cervical cancer biopsy R121ST


title: Cervical cancer biopsy R116ST


title: Cervical cancer biopsy R075ST


title: Healthy exocervix CEXO-39


title: Healthy exocervix CEXO-24


title: Healthy exocervix CEXO-38


title: Healthy exocervix CEXO-45


title: Healthy exocervix CEXO-36


title: Healthy exocervix CEXO-20


title: Healthy exocervix CEXO-7


title: Healthy exocervix CEXO-41


title: Healthy exocervix CEXO-12


title: Healthy exocervix CEXO-19


title: Cervical cancer biopsy R087ST


title: Healthy exocervix CEXO-13


title: Cervical cancer biopsy R035ST


title: Healthy exocervix CEXO-21


title: Healthy exocervix CEXO-33


title: Healthy exocervix CEXO-5


title: Healthy exocervix CEXO-11


title: MF.Microglia.CNS#1

status: Public on Dec 28 2011

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: MF.Microglia.CNS#1, CD45low CD11b+ F480+

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: brain

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: Liberase, Percoll gradient

tag: age

value: 8 weeks

tag: genetic background

tag: phenotype markers

tag: separation method

value: dissection/trimming

tag: Sex

value: male


title: MF.RP.Sp#3

status: Public on Oct 08 2010

source_name: spleen

extract_protocol: Mechanical Dissociation

value: 6 weeks

value: F4/80hi CD11blo CD11c- autofluorescent


title: MF.II-480hi.PC#3

source_name: Peritoneal Cavity

extract_protocol: Peritoneal Lavage

value: F4/80hi CD115hi CD11b+ MHC II- CD11c-


title: MF.RP.Sp#2


title: MF.Microglia.CNS#2

description: MF.Microglia.CNS#2, CD45low CD11b+ F480+


title: MF.II-480hi.PC#1


title: MF.Lu#1

status: Public on Apr 29 2010

description: MF.Lu#1, lung macrophage

source_name: lung

extract_protocol: 15 minutes digestion with Liberase Blenzyme 3

tag: exclusion markers

value: Positive CD11c selection

value: CD11chi CD11b- CD103- MHCII- SiglecF+


title: Healthy exocervix CEXO-10


title: MF.II-480hi.PC#2


title: MF.Lu#2

description: MF.Lu#2, lung macrophage


title: MF.Lu#3

description: MF.Lu#3, lung macrophage


title: MF.Microglia.CNS#3

description: MF.Microglia.CNS#3, CD45low CD11b+ F4/80+


title: Cervical cancer_CaCx54

status: Public on Jun 04 2008

city: New York

first: Murty

last: Vundavalli

state: NY

address: 1130 St Nicholas Ave

institute: Columbia University Medical Center

description: Cervical cancer, microdissected squamous cell carcinoma

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: GCOS

source_name: Cervical cancer_CaCx54

label_protocol: Affymetrix

extract_protocol: TRIzol

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 82, HPV 16


title: Cervical cancer_CaCx28

description: Cervical cancer, microdissected sqamous cell carcinoma

source_name: Cervical cancer_CaCx28

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 53, HPV 16


title: Cervical cancer_CaCx70

source_name: Cervical cancer_CaCx70

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 48, HPV 16, HPV 31, HPV 45


title: Cervical cancer_98-04T

source_name: Cervical cancer_98-04T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 35, stage IB1, HPV 18, HPV 45


title: Cervical cancer_CaCx60

source_name: Cervical cancer_CaCx60

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 47, HPV 16


title: Cervical cancer_1907T

source_name: Cervical cancer_1907T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 33, stage IV, HPV 16


title: Cervical cancer_88-04T

source_name: Cervical cancer_88-04T

tag: Cervical cancer, squamous cell carcinoma, microdissected, stage IIB1, HPV 18, HPV 45


title: Cervical cancer_56-04T

source_name: Cervical cancer_56-04T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 45, stage IB2, HPV negative


title: MF.RP.Sp#1


title: Cervical cancer_20-04T

description: Cervical cancer, microdissected adenocarcinoma

source_name: Cervical cancer_20-04T

tag: Cervical cancer, adenocarcinoma, microdissected, age 46, stage IB2, HPV 16


title: Cervical cancer_103-04T

source_name: Cervical cancer_103-04T

tag: Cervical cancer, squamous cell carcinoma, microdissected, stage IIIA, HPV 16


title: Cervical cancer_CaCx81

source_name: Cervical cancer_CaCx81

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 32, HPV 16, HPV 31, HPV 45


title: Cervical cancer_2035T

source_name: Cervical cancer_2035T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 59, stage IIB, HPV 18


title: Cervical cancer_1900T

source_name: Cervical cancer_1900T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 57, stage IIB, HPV 18


title: Cervical cancer_1898T

source_name: Cervical cancer_1898T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 64, stage IIB, HPV 18


title: Cervical cancer_1509T

source_name: Cervical cancer_1509T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 69, stage IIB, HPV 16


title: Cervical cancer biopsy R156ST

source_name: Cervical cancer biopsy

tag: clinical group

tag: haplogroup

tag: tissue


title: Cervical cancer_CaCx83

source_name: Cervical cancer_CaCx83

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 35, HPV 16, HPV 18, HPV 31, HPV 45


title: Cervical cancer_1434T

source_name: Cervical cancer_1434T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 47, stage IIB, HPV 16


title: Cervical cacner_654T

source_name: Cervical cacner_654T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 40, stage IA, HPV 45


title: Cervical cancer_841T

source_name: Cervical cancer_841T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 58, stage IIA, HPV 16


title: Cervical cancer_1798T

source_name: Cervical cancer_1798T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 33, stage IIB, HPV 16


title: Cervical cancer_CC207

source_name: Cervical cancer_CC207

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 54, stage IIIB, HPV 16


title: Cervical cancer_1875T

source_name: Cervical cancer_1875T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 36, stage IIB, HPV 16


title: Cervical cancer_CC214

description: Cervical cacner, microdissected squamous cell carcinoma

source_name: Cervical cancer_CC214

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 43, stage IIB, HPV 16


title: Cervical cancer_CC222

source_name: Cervical cancer_CC222

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 32, stage IIIB, HPV 16


title: Cervical cancer_CC218

source_name: Cervical cancer_CC218

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 40, stage IIIB, HPV 16


title: Cervical Cancer_1981T

source_name: Cervical Cancer_1981T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 63, stage IB, HPV 16, HPV 18


title: Cervical cancer_CC126

source_name: Cervical cancer_CC126

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 28, stage IIIB, HPV 45


title: Cervical cancer_892T

description: Cervical cancer, microdissected squamoud cell carcinoma

source_name: Cervical cancer_892T


title: Normal cervix_05-1981

description: Normal cervix epithelium, microdissected

source_name: Normal cervix_05-1981

tag: Normal cervix epithelium, Age 41


title: Cervical cancer_CC205

source_name: Cervical cancer_CC205

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 45, stage IIIB, HPV 16


title: Normal cervix_05-5007

source_name: Normal cervix_05-5007

tag: Normal cervix epithelium, Age 52


title: Normal cervix_05-446

source_name: Normal cervix_05-446

tag: Normal cervix, Age 50


title: Cervical cancer_CC128

description: Cervical cancer, microdissected, squamous cell carcinoma

source_name: Cervical cancer_CC128

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 55, stage IIIB, HPV 16


title: Normal cervix epithelium_03-5419

source_name: Normal cervix epithelium_03-5419

tag: Normal cervix, microdissected epithelium, Age 45


title: Normal cervix_05-4959

source_name: Normal cervix_05-4959

tag: Normal cervix epithelium, Age 53


title: Cervical cancer_CC163

description: Cervical cancer_microdissected squamous cell carcinoma

source_name: Cervical cancer_CC163

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 62, stage IIIB, HPV 45


title: Normal cervix_05-4615

source_name: Normal cervix_05-4615

tag: Normal cervix epithelium, Age 50


title: Normal cervix_05-1352

source_name: Normal cervix_05-1352


title: Normal cervix_05-1308

source_name: Normal cervix_05-1308

tag: Normal cervix, Age 56


title: Normal cervix_05-15

source_name: Normal cervix_05-15

tag: Normal cervix epithelium, Age 64


title: Cervical cancer_1721T

source_name: Cervical cancer_1721T

tag: Cervical cancer, squamous cell carcinoma, microdissected, age 70, stage IIB, HPV negative


title: Normal cervix epithelium_03-5438

description: Normal cervix epithelium

source_name: Normal cervix epithelium_03-5438

tag: Normal Cervix, microdissected epithelium, Age 54


title: Normal cervix_03-5657

description: Normal Cervix Epithelium, micordissected

source_name: Normal cervix_03-5657

tag: Normal cervix epithelium, Age 49


title: Normal cervix_05-31

description: Normal Cervix Epithelium, microdissected

source_name: Normal cervix_05-31


title: Normal cervix_05-4602

source_name: Normal cervix_05-4602