title: Heart [5700760021_L]

status: Public on Nov 03 2016

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadStudio was used to convert images to raw signal data.

data_processing: Using R (version 2.11.1), quality was accessed using the LUMI package PMID: 18467348). Analysis included the 21 samples listed here and GEO dataset GSE38570, which were analyzed together. Of the 36 measured samples, 4 were of a poor technical quality and removed from downstream normalization and analysis. The poor data quality samples were: 5700760018_C (Pancreas),5700760021_H (Fibroblasts), 5700760018_G (Buffy Coat), and 5700760021_J (AEC pure AT1).  Normalization was performed with VSN using LUMI  to allow for a large number of significantly differentially expressed genes. Statistical analyses were performed using LIMMA (PMID: 15297296). An unpaired T-test with Benjamini-Hochberg (BH) correction (Benjamini & Hochberg, 1995) was used to control for FDR.

organism: Rattus norvegicus

source_name: Whole Tissue RNA

label_protocol: IlluminaTotalPrep RNA kit

growth_protocol: RNA was harvested from primary rat tissue and purified AT1 cells.

extract_protocol: pure rat AT1 cells were isolated as previously described (PMC2793185). Tissues were isolated as previously described (PMID: 2440339).

treatment_protocol: Differentiating in culture over time, no extra treatments added.

tag: strain background

value: Sprague-Dawley

value: male

tag: tissue/cell type

value: Heart


title: genomic DNA from medulloblastoma_NMB186

status: Public on May 29 2017

type: genomic

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Natural Sciences

country: United Kingdom

institute: Northumbria University

description: medulloblastoma 54

hyb_protocol: According to the manufacturer’s instructions

scan_protocol: Illumina iScan System, according to the manufacturer’s instructions

data_processing: Arrays were processed using the R package minfi. Beta values were reported after functional normalisation. Intensity values were calculated without background subtraction and normalized to internal controls.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from medulloblastoma

extract_protocol: Extraction of DNA from tumor samples was carried out using Qiagen Allprep DNA/RNA/Protein Mini kit (Fresh Frozen) and Qiagen QIAamp DNA FFPE Tissue Kit (FFPE)

tag: sample type

value: medulloblastoma

tag: disease state

value: primary medulloblastoma

tag: gender

value: M

tag: age (yrs)

tag: pathology

value: CLA


title: Testis [5700760021_E]

type: RNA

city: Glendale

first: Crystal

last: Marconett

state: CA

address: 1856 Kirkby Rd

department: Translational Genomics

country: USA

institute: Keck School of Medicine

label: biotin

molecule: total RNA

value: Testis


title: genomic DNA from medulloblastoma_NMB433

description: medulloblastoma 162

label_protocol: According to the manufacturer’s instructions


title: Stomach [5700760021_F]

value: Stomach


title: Lavage [5700760021_K]

value: Lavage


title: Spleen [5700760018_K]

value: Spleen


title: RNAseq_Donor1_AT1-like_cells

type: SRA

library_source: transcriptomic

data_processing:
Image analysis and basecalling were carried out using RTA 1.13.48.0, deconvolution and fastq file generation were carried out using CASAVA_v1.7.1a5.
RNAseq fastq files were aligned to the hg19 genome using tophat2-2.0.8b. ChIPseq Fastq files were aligned to the genome using BWA0.6.2.
Genome_build: hg19
Supplementary_files_format_and_content: .fastq files are raw sequence. BigWig (bw) files are wiggle tracks designed to display the enrichment of ChIPseq regions.

source_name: Purified AT1-like cells Donor 1

extract_protocol:
RNA was isolated from in vitro differentiated AT1-like cells using the Illustra TriplePrep Kit.
RNA was isolated from 1million human AT2 or in vitro differentiated AT1-like cells using the GE TriplePrep kit (Cat# 28-9425-44, Pittsburgh PA). 2ug of RNA was made into libraries using the Illumina (Madison WI) Ribo-Zero™ Gold Magnetic Kit (MRZG 12324) and sequenced using the Illumina HiSeq2000 at the University of Southern California Epigenome Center Core. Basecalls were converted into FASTQ files and aligned to the hg19 genome using tophat2-2.0.8b.

tag: cell type

value: alveolar epithelial type 1


title: genomic DNA from medulloblastoma_NMB253

description: medulloblastoma 68


title: Skin [5700760018_E]

value: Skin


title: AEC pure AT1 [5665175063_L]

source_name: Alveolar Epithelial Cells

value: Alveolar Epithelial Cells


title: RNAseq_Donor1_AT2_cells

source_name: Purified AT2 cells Donor 1

extract_protocol:
RNA was isolated from freshly isolated primary AT2 cells using the Illustra TriplePrep Kit.
RNA was isolated from 1million human AT2 or in vitro differentiated AT1-like cells using the GE TriplePrep kit (Cat# 28-9425-44, Pittsburgh PA). 2ug of RNA was made into libraries using the Illumina (Madison WI) Ribo-Zero™ Gold Magnetic Kit (MRZG 12324) and sequenced using the Illumina HiSeq2000 at the University of Southern California Epigenome Center Core. Basecalls were converted into FASTQ files and aligned to the hg19 genome using tophat2-2.0.8b.

value: alveolar epithelial type 2


title: AEC pure AT1 [5665175063_F]


title: Duodenum [5700760018_I]

value: Duodenum


title: Brain [5700760021_G]

value: Brain


title: RNAseq_Donor2_AT1-like_cells

source_name: Purified AT1-like cells Donor 2


title: Colon [5700760018_L]

value: Sprague-Dawley

value: Colon


title: RNAseq_Donor2_AT2_cells

source_name: Purified AT2 cells Donor 2


title: Trachea [5700760021_B]

value: male

value: Trachea


title: Salivary glands [5700760018_H]

value: Salivary glands


title: Skeletal Muscle [5700760018_J]

value: Skeletal Muscle


title: FF12

status: Public on Jan 15 2016

hyb_protocol: Standard Illumina hybridization protocol.

data_processing: Data were imported into BeadStudio and raw signal data exported for analysis. Using the software R, probes were filtered using reannotation data from reMOAT, specifically filtering out probes matching to the wrong sequence, non-matching probes, and those with SNPs. Preprocessing of raw data revealed that one knockout lung sample was a technical failure, which was not used in subsequent analysis. Background correction using variance stabilizing transformation (VST) and quantile normalization were performed using the LUMI package in R. Heatmaps were generated in R by selecting the top 5% of variant probes and clustering samples, and probes with average linkage. A strict 2-fold cut-off was enforced to delineate genes with altered expression in the knockout. Pathway analysis was performed using Ingenuity Pathway Analysis (IPA) software (Ingenuity, Redwood City, CA), and pathways were ranked based on Benjamini-Hochberg (BH) corrected p-value of enrichment.

label: Biotin

organism: Mus musculus

source_name: Whole lung extract, Grp78f/f

label_protocol: Total RNA was converted into cRNA and used for Illumina MouseRef-8 v2 whole genome expression analysis (Illumina, San Diego, CA).

growth_protocol: Whole lungs were homogenized in Trizol with a Polytron.

extract_protocol: One microgram of RNA from four Grp78f/f and three cGrp78f/f whole lungs was extracted using TriZol.

tag: mixed strain background

value: C57BL/6 (major); 129S6/SvEvTac (minor); ICR (minor)

tag: age

tag: tissue

value: lung


title: KO6

source_name: Whole lung extract, cGrp78f/f


title: Illium [5700760021_C]

value: Illium


title: Liver [5700760018_B]

value: Liver


title: KO4


title: FF7-1


title: Whole trachea Scnn1b-T, PND 10, biological replicate 3

status: Public on Sep 11 2014

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 3618, 3619)

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16 hours at 45 degrees. Washing and staining was performed in the Affymetrix GeneChip Fluidics Station 450, protocol FS450_0007.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through  RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets. PND10 samples were further adjusted through Batchremoval by comparing to the rest of the samples.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Scnn1b-Tg, trachea

label_protocol: RNAs were processed for hybridization to Affymetrix Mouse Gene ST 1.0 microarrays using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit and Ambion WT Expression Kit, according to manufacturer's recommended protocol.

growth_protocol: Mouse whole trachea;  mice grown under specific-pathogen-free conditions in micro-isolator cages

extract_protocol: Whole lungs were dissected and stored in RNALater until extraction using Qiagen RNAeasy columns, followed by ethanol precipitation

treatment_protocol: Not applicable;  no treatment;  mice are either wildtype or Scnn1b-transgenic and were harvested at post natal days 0, 3, 10, and 42.

tag: strain

value: C57Bl/6N Tac

tag: genotype

tag: age (postnatal day)


title: FF7-2


title: Kidney [5700760018_D]

value: Kidney


title: Whole trachea Scnn1b-T, PND 42, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 2998, 3001)


title: KO5


title: FF2

value: C57BL/6 (major); 129S6/SvEvTac (minor); ICR (minor).


title: Whole trachea Scnn1b-T, PND 10, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 3599, 3600)


title: Whole trachea Scnn1b-T, PND 42, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 3035, 3057)


title: Whole trachea Scnn1b-T, PND 42, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 3002, 3013)


title: Whole trachea WT, PND 42, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 wild-type males (animal numbers 2999, 3033)

source_name: Wildtype, trachea

value: Wildtype


title: Whole trachea WT, PND 42, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 wild-type males (animal numbers 2996, 2997)


title: Whole trachea Scnn1b-T, PND 10, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 3589, 3597)


title: Whole trachea Scnn1b-T, PND 3, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2783, 2784, 2785)


title: Whole trachea WT, PND 3, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 wild-type males (animal numbers 2791, 2793)


title: Whole trachea WT, PND 10, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 wild-type males (animal numbers 3598, 3601)


title: Whole trachea WT, PND 42, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 wild-type males (animal numbers 3036, 3037)


title: Whole lung Scnn1b-Tg, PND 42, biological replicate 3

description: whole lung (left lobe) sample from post natal day 42 Scnn1b-transgenic male (animal number 3035)

data_processing:
CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through  RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Scnn1b-Tg, whole lung

growth_protocol: Mouse whole lung (left lobe);  mice grown under specific-pathogen-free conditions in micro-isolator cages


title: Whole trachea WT, PND 0, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively); pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2377, 2410)

value: PND 0 (<24 hrs)


title: Whole lung Scnn1b-Tg, PND 10, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 2760, 2761)


title: Whole trachea Scnn1b-T, PND 0, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2419, 2420)


title: Whole trachea Scnn1b-T, PND 3, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 Scnn1b-Tg males (animal numbers 22818, 2886, 2887, 2888)


title: Whole trachea WT, PND 3, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 wild-type males (animal numbers 2782, 2817)


title: Whole trachea WT, PND 10, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 wild-type males (animal numbers 3588, 3590)


title: Whole trachea Scnn1b-T, PND 0, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2376, 2409)


title: Whole trachea Scnn1b-T, PND 3, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2662, 2664, 2665)


title: Whole trachea Scnn1b-T, PND 0, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2369, 2377)


title: Whole lung Scnn1b-Tg, PND 3, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2664, 2665)


title: Whole trachea WT, PND 0, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2418, 2421)


title: Whole trachea WT, PND 0, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2370, 2374)


title: Whole trachea WT, PND 10, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) from a post natal day 10 wild-type male (animal number 3616)


title: Whole lung Scnn1b-Tg, PND 42, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 3013, 3034)


title: Whole lung Scnn1b-Tg, PND 10, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 2752, 2754)


title: Whole lung Scnn1b-Tg, PND 0, biological replicate 2

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2409, 2419)


title: Whole lung Scnn1b-Tg, PND 0, biological replicate 1

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2375, 2376)


title: Whole lung Scnn1b-Tg, PND 3, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2662, 2663)


title: Whole lung Scnn1b-Tg, PND 10, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 2688, 2746)


title: Whole lung WT, PND 42, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 42 wild-type males (animal numbers 3037, 3058)

source_name: Wildtype, whole lung


title: Whole lung WT, PND 0, biological replicate 3

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2418, 2421)


title: Whole lung WT, PND 3, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 3 wild-type males (animal numbers 2792, 2793)


title: Whole lung WT, PND 0, biological replicate 2

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2377, 2410)


title: Whole lung Scnn1b-Tg, PND 3, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2783, 2784)


title: Whole lung WT, PND 3, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 3 wild-type males (animal numbers 2817, 2884)


title: Whole lung Scnn1b-Tg, PND 42, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 2998, 3002)


title: Purified lung lavage macrophages WT, PND 42 germ-free, biological replicate 1

description: purified macrophages

hyb_protocol: Hybridization was performed at 48 degrees using the GeneTitan plate system.

data_processing:
CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through  RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets.
MoGene-1_1-st-v1.r4.pgf
MoGene-1_1-st-v1.r4.mps

source_name: Wildtype, macrophages, germ-free facility

label_protocol: 12 ng of RNA was used to generate cDNA using Ovation Pico WTA system V2 kig (NuGEN Technologies, CA).

growth_protocol: Mouse lung lavage macrphages purified by negative selection through from a Lys-6G column;  mice grown either under specific-pathogen-free conditions in micro-isolator cages or in a germ-free environment

extract_protocol: Magnetic activated cell sorting uas used to purify macrophages from lung lavage samples using Ant-Ly-6G MicroBeads (Miltenyi Biotec, MA).  Ly-6G negative cells (macrophages) were pelleted, snap-frozen and stored at -80 C.  Frozen macrophage pellets were lysed and homogenized in lysis buffer and QIAshedder (Qiagen).  Genomic DNA was eliminated using gDNA eliminator spin columns;  RNA was isolated using Purelink RNA mini kits (Invitrogen).

treatment_protocol: Mice are either wildtype or Scnn1b-transgenic and were harvested at post natal days 0, 3, 10, and 42.  At PND 42 macrophages were also isolated from wildtype and Scnn1b-transgenic mice grown in a germ-free environment.

tag: animal facility type

value: germ-free


title: Whole trachea WT, PND 3, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 wild-type males (animal numbers 2792, 2781)


title: Purified lung lavage macrophages WT, PND 42 germ-free, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 1

description: purified macrophages

source_name: Scnn1b-Tg, macrophages, specific pathogene free facility

value: specfic pathogen free


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 2

description: purified macrophages


title: Whole lung Scnn1b-Tg, PND 0, biological replicate 3

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2420, 2422)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 1

description: purified macrophages

source_name: Scnn1b-Tg, macrophages, germ-free facility


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 3

description: purified macrophages


title: Whole lung WT, PND 10, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 10 wild-type males (animal numbers 2683, 2684)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 2

description: purified macrophages


title: Whole lung WT, PND 42, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 42 wild-type males (animal numbers 3067, 3068)


title: Whole lung WT, PND 42, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 42 wild-type males (animal numbers 2996, 3036)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42 germ-free, biological replicate 2

description: purified macrophages

source_name: Wildtype, macrophages, germ-free free facility


title: Whole lung WT, PND 10, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 10 wild-type males (animal numbers 2745, 2753)


title: Whole lung WT, PND 0, biological replicate 1

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2370, 2374)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 4

description: purified macrophages


title: Whole lung WT, PND 10, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 10 wild-type males (animal numbers 2685, 2689)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 4

description: purified macrophages


title: Whole lung WT, PND 3, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 3 wild-type males (animal numbers 2781, 2782)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 0, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 3

description: purified macrophages

source_name: Wildtype, macrophages, specfic pathogen free facility


title: Purified lung lavage macrophages WT, PND 10, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 3, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 0, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 0, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 0, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 3, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 0, biological replicate 3

description: purified macrophages


title: CLDN18_KnockOut_3

status: Public on Apr 06 2014

description: 5388884001_D_Replicate 3

data_processing: Background correction using variance stabilizing transformation (VST) and quantile normalization were performed using the LUMI package (v.1.14.0) in R v.2.11.1 (2010-05-31).

extract_protocol: 1μg of RNA from four replicates each from wildtype and claudin-18 knockout whole lung was converted into cRNA and was used for Illumina mouseRef-8 v2 whole genome expression analysis. Expression arrays were carried out at the Southern California Genotyping Consortium (SCGC) at the University of California, Los Angeles.

treatment_protocol: No treatment

value: mixed 129S6/SvEvTac, C57BL/6J, Balb/c

tag: genotype/variation

value: 3-4 months

value: Male

value: whole lung tissue


title: WildType_2

description: 5388884001_F_Replicate 2

value: WildType


title: WildType_3

description: 5388884001_G_Replicate 3


title: AT cell D8 (AT1-like) X5626686013_L

status: Public on Apr 15 2013

description: AT cell D8 (AT1-like)

data_processing: Using R (version 2.11.1), normalization was performed with VSN using LUMI (Du et al., 2008) to allow for a large number of significantly differentially expressed genes. Statistical analyses were performed using LIMMA (Smyth, 2004). The most variant probes were selected and a linear regression model was fitted over the time-course of differentiation. Technical replicates were removed, and T-tests were performed between Day 0 samples and Day 8 samples. P-values were controlled for false-discovery using the Benjamini-Hochberg (BH) correction (Benjamini & Hochberg, 1995).

source_name: Alveolar Epithelial type 2 (AT2 cell)

growth_protocol: Remnant human transplant lungs were obtained in compliance with Institutional Review Board-approved protocols for the use of human source material in research (HS-07-00660) and processed within 3 days of death. Lung tissue was processed as previously described (Ballard et al., 2010) with inclusion of anti-EpCAM conjugated beads to select for epithelial cells.  Cells were plated in 50:50 [DMEM High glucose media (GIBCO 21063): DMEM-F12 (Sigma D6421)]. Differentiation into AT1-like cells was verified by measuring SFTPC and AQP5 expression.

extract_protocol: RNA was extracted with the Illustra TriplePrep Kit (GE LifeSciences, Piscataway, NJ).

tag: time

value: AT cell (AT1-like)

tag: Sex

value: female

tag: age (y)

tag: smoker

value: non-smoker

tag: cod

value: CVA-Stroke


title: AT cell D2 X5626686013_F

description: AT cell D2

value: AT cell

value: ICH-Stroke


title: Purified lung lavage macrophages WT, PND 3, biological replicate 2

description: purified macrophages

value: C57Bl/6N Tac


title: AT cell D4 X5626686013_J

description: AT cell D4


title: WildType_4

description: 5388884001_H_Replicate 4

tag: strain background

tag: gender


title: AT cell D6 X5626686013_E

description: AT cell D6


title: WildType_1

description: 5388884001_E_Replicate 1


title: AT cell D8 (AT1-like) X5626686013_I

description: AT cell D8 (AT1-like)


title: Purified lung lavage macrophages WT, PND 0, biological replicate 2

description: purified macrophages


title: AT cell D4 X5626686013_D

description: AT cell D4


title: Purified lung lavage macrophages WT, PND 3, biological replicate 1

description: purified macrophages


title: AT cell D6 X5626686013_B

description: AT cell D6


title: CLDN18_KnockOut_2

description: 5388884001_B_Replicate 2


title: AT cell D0 (AT2) 5626686013_A

description: AT cell D0 (AT2)

value: AT cell (AT2)


title: CLDN18_KnockOut_1

description: 5388884001_A_Replicate 1


title: AT cell D0 (AT2) X5626686013_K

description: AT cell D0 (AT2)


title: AT cell D2 X5626686013_H

description: AT cell D2


title: AT cell D6 5700760021_D

description: AT cell D6

growth_protocol: Rat AT2 cells were isolated as previously described (Zhou et al., 2008; Borok et al., 1998).

value: male


title: AT cell D8 (AT1-like) 5700760021_I

description: AT cell D8 (AT1-like)


title: Day 8 input DNA

description: Day 8 (D8)

library_source: genomic

data_processing:
ChIP products underwent Illumina GAII single-end sequencing
reads were aligned to the hg18 human genome build using the MAQ 0.7.1 aligner, performed by the USC Epigenome Center.
SICER (Zhang et al., 2009) peak calling was performed using a window size of 600 bp (H3K9/14Ac and H3K27me3) and gap size of 600 bp.  Input DNA was used for background normalization.
Differential peak occupancy was determined using the UCSC table browser.
Genome_build: hg18
Supplementary_files_format_and_content: peak calls in .bed format contain coordinates for peak occupancy

extract_protocol: ChIPseq libraries were constructed using the standard protocol from the New England Biolabs library prep kit (NEB Cat#E6200, Ipswich, MA).

treatment_protocol: Differentiating in culture over time, no extra treatments added. Chromatin immunoprecipitations for H3K9/14Ac (Millipore, #06-599) and H3K27me3 (Millipore, #07-449) were performed as previously described (Jia et al., 2003).

value: anoxia

value: in vitro diffrentiated AT1 cells

tag: chip antibody


title: AT cell D0 (AT2) X5626686013_G

description: AT cell D0 (AT2)

tag: cell type


title: AT cell D4 5665175063_K

description: AT cell D4


title: AT cell D4 X5626686013_C

description: AT cell D4


title: Day 8 H3K27me3 ChIPSeq

description: Day 8 (D8)

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: AT cell D2 5665175063_D

description: AT cell D2


title: Day 0 H3K27me3 ChIPSeq

description: Day 0 (D0)

value: Primary isolated AT2 cells


title: Day 0 H3K9/14Ac ChIPSeq

description: Day 0 (D0)


title: AT cell D8 (AT1-like) 5626686051_L

description: AT cell D8 (AT1-like)

value: Anoxia


title: Day 8 H3K9/14Ac ChIPSeq

description: Day 8 (D8)


title: AT cell D2 5665175063_C

description: AT cell D2


title: AT cell D2 5626686051_H

description: AT cell D2


title: AT cell D0 (AT2) 5626686051_F

description: AT cell D0 (AT2)


title: AT cell D6 5626686051_A

description: AT cell D6


title: AT cell D4 5626686051_C

description: AT cell D4


title: Day 0 input DNA

description: Day 0 (D0)


title: AT cell D0 (AT2) 5665175063_I

description: AT cell D0 (AT2)


title: AT cell D0 (AT2) 5700760021_A

description: AT cell D0 (AT2)


title: AT cell D8 (AT1-like) 5665175063_G

description: AT cell D8 (AT1-like)


title: AT cell D0 (AT2) 5665175063_H

description: AT cell D0 (AT2)


title: AT cell D4 5665175063_E

description: AT cell D4


title: AT cell D2 5700760018_A

description: AT cell D2


title: AT cell D8 (AT1-like) 5665175063_J

description: AT cell D8 (AT1-like)


title: AT cell D4 5700760018_F

description: AT cell D4


title: AT cell D6 5665175063_A

description: AT cell D6


title: AT cell D6 5665175063_B

description: AT cell D6