title: CBL0137 replicate 2 [Nascent RNA-Seq]

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequencing adatper was removed by cutadpt program
Nascent RNA reads are mapped to human reference genome hg19 using bwa mem with default parameters
raw count of reads for RefGene are generated using FeatureCount command of the Subread package
bigWig files are generated from bamCoverage of deeptools package
Genome_build: hg19
Supplementary_files_format_and_content: raw read count of RefGene and bigWig file

growth_protocol: standard DMEM + 5% FBS

extract_protocol:
Click-iT™ Nascent RNA Capture Kit (Invitrogen, cat#C10365)
Nascent RNA capture and 1st strand cDNA synthesis were performed using the Click-iT Nascent RNA Capture Kit (Molecular Probes).  2nd strand cDNA synthesis was performed using Illumina Second Strand Mix, which incorporates dUTP to preserve strand data.  Full length ds cDNA was purified using AmpureXP beads (Beckman Coulter) and sheared using a Covaris S220 (Covaris Inc) to a final size of 150-200bp.  KAPA Hyper Prep (KAPA Biosystems) reagents were used to make final libraries following the kit instructions for end repair, A tailing, ligation of Illumina TruSeq Stranded RNA indexes, and PCR amplification.  Amplified final libraries were purified using AmpureXP beads, quantitated using qPCR (KAPA Biosystems), and pooled in an equimolar fashion.  Pooled libraries are loaded to an individual lane of a HiSeq High Output v3 flow cell, using an Illumina cBot, for 50cycle SR sequencing on a HiSeq2500 sequencer according to the manufacturer's recommended protocol (Illumina Inc.).

treatment_protocol: CBL0137 for 1 hour at 1uM. EU was added for the last 15 minutes.

value: 1uM CBL0137 for 1hr


title: control replicate 2

status: Public on Mar 13 2018

type: SRA

city: Buffalo

first: Katerina

last: Gurova

state: NY

address: Elm and Carlton Str

department: Cell Stress Biology

country: USA

institute: Roswell Park Cancer Institute

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.9
ChIP-seq reads were aligned to the hg19 genome assembly using bwa sampe with default parameters
Broad peaks were called using MACS2 with default parameters
BigWig files and heatmap/profiles are generated using deeptools
Genome_build: hg19
Supplementary_files_format_and_content: Bed files with peak calling results from MACS2, bigWig files from deeptools using RPKM normalization.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: DMEM 5% FBS

extract_protocol:
ChIP-with SSRP1 antibody
20ng of Chromatin-immunoprecipitated (ChIP) DNA is used to generate a library for Next generation sequencing using the ThruPLEX DNA seq kit (Rubicon Genomics, Inc.) as per manufacturer’s instructions.  ThruPLEX uses stem-loop adapters to construct high quality libraries in a fast and efficient workflow. In the first step, Template Preparation, the DNA is repaired and yields molecules with blunt ends. Next, stem-loop adaptors with blocked 5’ ends are ligated with high efficiency to the 5’ end of the genomic DNA, leaving a nick at the 3’ end.  In the final step, the 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. The library is quantitated using quantitative PCR (KAPA Biosystems), normalized, and pooled in an equimolar fashion.  Pooled libraries are loaded to an individual lane of a HiSeq High Output v3 flow cell, using an Illumina cBot, for 2 x 100 PE sequencing on a HiSeq2500 sequencer according to the manufacturer's recommended protocol (Illumina Inc.).

treatment_protocol: 1.5 hours, 3uM of CBL0137, 0.3uM of CBL0100 or 3uM of aclacinomycin A

tag: cell line

tag: treated with

value: none (control)

tag: time of treatment

tag: chip antibody

value: SSRP1 antibody

tag: chip antibody vendor

value: BioLegend

tag: chip antibody clone

tag: chip antibody cat#


title: MM1.S control 2nd replicate

status: Public on Jul 25 2018

type: RNA

description:
Replicate 2
SAMPLE 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were summarized and quantile normalized by using  GenomeStudio 1.9.0

label: biotin

molecule: total RNA

source_name: MM1.S control

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: standard, DMEM + 5% FBS + antibiotics

extract_protocol: TRIZOL reagent

treatment_protocol: 6 hours of CBL0137, 0, 0.3, 1 and 3 microM for MM1.S; 0 and 3microM for HeLa, controls - plain medium


title: Aclacinomycin A (AclA) replicate 1

source_name: HT1080_Aclacinomycin A (AclA)

value: Aclacinomycin A

tag: concentration


title: MM1.S CBL0137 1uM  2nd replicate

description:
Replicate 2
SAMPLE 6

source_name: MM1.S CBL0137 1uM


title: Control replicate 2 [Nascent RNA-Seq]

library_source: transcriptomic


title: MM1.S CBL0137 0.3uM  1st replicate

description:
replicate 1
SAMPLE 3


title: CBL0137 replicate 1


title: Control replicate 1 [Nascent RNA-Seq]


title: CBL0137 replicate 1 [Nascent RNA-Seq]


title: HeLaS3 CBL0137 3uM 1st replicate

description:
Replicate 2
SAMPLE 12

source_name: HeLaS3 CBL0137 3uM

value: HeLa S3


title: MM1.S control 1st replicate

description:
replicate 1
SAMPLE 1


title: MM1.S CBL0137 3uM  1st replicate

description:
replicate 1
SAMPLE 7

source_name: MM1.S CBL0137 3uM


title: HeLaS3 CBL0137 3uM 2nd replicate

description:
replicate 1
SAMPLE 11


title: MM1.S CBL0137 0.3uM  2nd replicate

description:
Replicate 2
SAMPLE 4


title: MM1.S CBL0137 1uM  1st replicate

description:
replicate 1
SAMPLE 5


title: MM1.S CBL0137 3uM  2nd replicate

description:
Replicate 2
SAMPLE 8


title: dsLuc_PAPI-RIP-seq

status: Public on Mar 01 2018

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

description: RNA (immunoprecipitated)

data_processing:
Adapter sequences were removed from the obtained reads, and the reads were mapped to the silkworm reference genome using Bowtie, allowing no mismatches. Genome mapped reads were extracted and aligned to B. mori transposon consensus sequences (Kind gift from Dr. S. Kawaoka) using Bowtie, allowing up to two mismatches.
Genome_build: silkworm reference genome (downloaded from the Silkworm Genome Research Program Database; http://sgp.dna.affrc.go.jp/data/integretedseq.txt.gz).
Supplementary_files_format_and_content: space-delimited text files include count of reads mapped to each transposable element (TE) consensus sequence in sense and antisense direction.

organism: Bombyx mori

source_name: BmN4 cells

growth_protocol: BmN4 cells were grown at 27 degrees on Ex-Cell medium

extract_protocol:
RIP-seq: RNAs were eluted from the PAPI immunoprecipitates by phenol-chloroform after protease K treatment and precipitated with ethanol. RNAs were resolved by denaturing PAGE, and 65- to 100-nt-long RNAs were eluted from gels.
smRNA-seq: Immunoprecipitation of Flag-Siwi and Flag-Ago3 was carried out as described previously (Nishida et al., 2015). RNAs were eluted from the immunoprecipitates by phenol-chloroform after protease K treatment, and precipitated with ethanol. RNAs of 23–35 nts in length were eluted from the gels and used to generate small RNA libraries.
The libraries were generated with NEBNext Small RNA Library Sample Prep Set (New England BioLabs (NEB), E7330), as described previously (Nishida et al., 2015).

treatment_protocol:
RNAi-KD: BmN4 cells were transfected with 2 µg of dsRNAs (per 3 × 10^5 cells) using FuGENE HD (Promega).
Flag-Siwi/Ago3 expression: To exogenously express proteins in BmN4 cells, the cells were transfected with 2 µg of plasmids (per 6 × 10^5 cells) using FuGENE HD.

value: BmN4 cells

tag: antibody

value: anti-PAPI (generated in this study)


title: ctl1_3

status: Public on Feb 26 2018

city: Montreal

first: Jeremy

middle: Michael

last: Van Raamsdonk

state: QC

address: 1001 Decarie Boulevard

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

data_processing:
Libraries were sequenced using 1x75 bp sequencing on the Illumina NextSeq 500 platform at the Van Andel Research Institute.  Data were demultplexed using bcl2fastq v 2.18.
Read quality was assessed using FASTQC v. 0.11.5 and aligned first to the E. coli K-12 genome to assess contamination, then one-pass aligned to WBcel235 C. elegans genome using STAR v. 2.5.2b with default parameters and --outReadsUnmapped None. The STAR genome index was generated with the corresponding Ensembl WBcel235 build 89 GTF annotations integrated.
Transcript abundances were quantified using the --quantMode GeneCounts option enabled during alignment. Differential gene expression analysis was performed using the quasi-likelihood framework in edgeR package v. 3.20.1 in R v. 3.4.1. Gene names, gene IDs, and predicted function annotations were downloaded using the biomaRt package v. 2.34.0.
CPM files were filtered keeping genes that had CPM > 2 in at least 3 samples.
Genome_build: WBcel235
Supplementary_files_format_and_content: Text file containing filtered gene counts per million matrix (CPM) from all samples.

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: NGM plates, 20 degrees Celsius, OP50 bacteria

extract_protocol:
See Schaar et al. 2015 PLoS Genetics for RNA isolation protocol
Sequencing libraries were prepared using the Kapa Biosystems stranded mRNA-Seq kit for the Illumina platform.

tag: developmental stage

value: prefertile young adult

tag: genotype


title: prdx2_1


title: sod1_3


title: prdx2_2


title: ctl1_2


title: ctl1_1


title: sod1_1


title: daf2_5


title: daf2_3


title: daf2_4


title: daf2_2


title: daf2_1


title: prdx2_3


title: isp1_3


title: isp1_1


title: nuo6_6


title: nuo6_5


title: isp1_4


title: isp1_5


title: nuo6_1


title: isp1_2


title: isp1_6


title: clk1_6


title: nuo6_4


title: nuo6_2


title: nuo6_3


title: clk1_5


title: clk1_4


title: sod1_2


title: daf2_6


title: clk1_2


title: WT_10

value: wildtype


title: WT_11


title: clk1_1


title: WT_8


title: WT_7


title: WT_9


title: sod-2_1

data_processing:
Libraries were sequenced using 1x75 bp sequencing on the Illumina NextSeq 500 platform at the Van Andel Research Institute.  Data were demultplexed using bcl2fastq v 2.18.
Read quality was assessed using FASTQC v. 0.11.5 and aligned first to the E. coli K-12 genome to assess contamination, then one-pass aligned to WBcel235 C. elegans genome using STAR v. 2.5.2b with default parameters and --outReadsUnmapped None. The STAR genome index was generated with the corresponding Ensembl WBcel235 build 89 GTF annotations integrated.
Transcript abundances were quantified using the --quantMode GeneCounts option enabled during alignment. Differential gene expression analysis was performed using the quasi-likelihood framework in edgeR package v. 3.20.1 in R v. 3.4.1. Gene names, gene IDs, and predicted function annotations were downloaded using the biomaRt package v. 2.34.0.
CPM files were filtered keeping genes that had CPM > 2 in at least 3 samples.
genome build: WBcel235
Supplementary_files_format_and_content: Text file containing filtered gene counts per million matrix (CPM) from all samples.


title: sod-2_2


title: WT_6


title: sod-2_5


title: sod-2_3


title: clk1_3


title: WT_5


title: sod-2_4


title: sod-2_6


title: WT_12


title: WT_3


title: Aecia_replicate 1

status: Public on Jan 15 2018

city: Champenoux

first: Sebastien

last: Duplessis

address: INRA Centre Grand Est - Nancy

department: UMR 1136 IAM

country: France

institute: INRA

description: This sample is from Melampsora larici-populina_Larix decidua. It is the first of three biological replicates used in this experiment.

data_processing:
Data acquisition was performed in Beckman Coulter Genomics facilities according to standard Illumina’s procedures.
All reads per sample were mapped onto the 16,399 M. larici-populina transcripts using the RNAseq analysis tool of the CLC Genomics Workbench  8.0.1 (QIAgen) using default parameters except for the similarity fraction, which was set at 90% across 90% of the read length.
The count of unique reads mapped per transcript was recorded for each sample and R packages DESeq2 (v1.10.1) and edgeR (3.12.0) were used to conduct differential expression analysis of M. larici-populina transcripts.
genome build: Melampsora larici-populina 98AG31 transcripts (Mlaricis_populina.FrozenGeneCatalog_20110215.CDS.fasta) available from https://genome.jgi.doe.gov/Mellp1/Mellp1.home.html)
processed data files format and content: tab-delimited text files include for each sample the number of unique mapped reads and the normalized count from DESeq2

organism: Melampsora laricis-populina

growth_protocol: Basidia (BSD) were collected from rust-infected dead poplar leaves. Living poplar leaves were inoculated on previous autumn by M. larici-populina isolate 98AG31 urediniospores and let standoutside in grid bags for proper telia and basidia differentiation in natural conditions. Samples consisted of a mix of dead poplar leaf tissue, remains of overwintered telia, basidia and basidiospores.  Pycnia (PYC) were collected from rust-infected larch needles one week after inoculation with M. larici-populina isolate 98AG31 basidiospores.  Aecia (AEC) were collected from rust-infected larch needles two weeks after inoculation with M. larici-populina isolate 98AG31 basidiospores. PYC and AEC samples consisted of larch needle tissues and various in planta infection fungal cell types.

extract_protocol:
Total RNA from BSD samples were isolated with the QIAgen RNeasy Plant Minikit from  several rounds of RNA isolation using low inputs of material (10 to 20mg). Total RNA from PYC and AEC samples were isolated from 100mg infected larch needles using a protocol adapted to RNA isolation from conifers (Chang et al 1993 Plant Mol Biol doi: 10.1007/BF02670468).
cDNA synthesis and RNA-Seq library construction were performed by Beckman Coulter Genomics using the Illumina TruSEQ RNA seq kit

tag: host organism

value: Larix decidua

tag: host tissue

value: rust-infected larch needles

tag: sexual stage

value: aecia

tag: strain


title: Pyncia_replicate 1

value: pycnia


title: Pyncia_replicate 3

description: This sample is from Melampsora larici-populina_Larix decidua. It is the third of three biological replicates used in this experiment.


title: Aecia_replicate 2

description: This sample is from Melampsora larici-populina_Larix decidua. It is the second of three biological replicates used in this experiment.


title: WT_4


title: Aecia_replicate 3


title: WT_1


title: WT_2


title: Pyncia_replicate 2


title: bESC_B_P46

status: Public on Feb 11 2018

city: Davis

first: Pablo

last: Ross

state: CA

address: 1 Shields Ave

institute: University of California, Davis

data_processing:
Libraries were sequenced on an Illumina HiSeq 2500 platform
Sequence reads were mapped to the bovine UMD3.1 genome assembly and Ensembl 78 genebuild annotation using CLC Genomics Workbench 7.0 (CLCbio, Aarhus, Denmark).
Reads per million mapped reads per kilobase of exon model (RPKM) values were calculated for each gene and the levels of expression compared among groups using EdgeR with FDR correction for multiple testing.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: tab-delimited text file including RPKM values for each gene and sample.

organism: Bos taurus

source_name: bESC

growth_protocol: bESC were grown in CTFR medium [a custom basal medium similar to mTeSR medium (STEMCELL Technologies)] that is completely devoid of growth factors FGF2 and TGFb and contains low fatty acid BSA (MP Biomedicals NZ), similar to basal medium in the published recipe (Ludwig TE, et al. (2006) Feeder-independent culture of human embryonic stem cells. Nat Methods 3:637–646), and supplemented with 20 ng/mL human FGF2 and 2.5 μM IWR1, and were incubated at 37 °C and 5% CO2 (Wu J, et al. (2015) An alternative pluripotent state confers interspecies chimaeric competency. Nature 521:316–321) in wells containing MEFs and were passaged every 4–5 d at a 1:10 split ratio.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit and then was reverse-transcribed using iScript RT Supermix (Bio-Rad).
Libraries were constructed using the TruSeq RNA Sample Prep Kit (Illumina)

tag: cell type

value: BL-derived ESC

tag: passage number


title: bESC_A_P45


title: invivo_BL_A

source_name: Blastocyst

value: Blastocyst stage embryo


title: Basidia_replicate 2

description: This sample is from Melampsora larici-populina_Populus trichocarpa. It is the second of three biological replicates used in this experiment.

value: Populus trichocarpa

value: rust-infected dead poplar leaves

value: basidia


title: Basidia_replicate 1

description: This sample is from Melampsora larici-populina_Populus trichocarpa. It is the first of three biological replicates used in this experiment.


title: isp-1sod-3_1

status: Public on Aug 30 2017

data_processing:
Libraries were sequenced using 1x75 bp sequencing on the Illumina NextSeq 500 platform at the Van Andel Research Institute.  Data were demultplexed using bcl2fastq v 2.17.1.14.
Read quality was assessed using FASTQC v. 0.11.3 and aligned first to the E. coli K-12 genome to assess contamination, then aligned to the WBcel235 C. elegans genome assembly using Subread v. 1.5.0 with default parameters.
Transcript abundances were quantified using featureCounts v. 1.4.6 with strand specific read counting.
Differential gene expression analysis was performed using the edgeR package v. 3.14.0 in R v. 3.3.0.
Genome_build: WBcel235
Supplementary_files_format_and_content: Text file containing raw counts per million matrix (CPM) from WT, isp-1, isp-1;sod-3, and isp-1;sod-5 samples.

source_name: isp-1;sod-3 double mutant_whole worm

tag: genotype/variation

value: isp-1;sod-3 double mutant

tag: pooling

tag: tissue

value: whole worm


title: isp-1sod-5_1

source_name: isp-1;sod-5 double mutant_whole worm

value: isp-1;sod-5 double mutant


title: isp-1sod-3_3


title: isp-1sod-3_2


title: isp-1_3

source_name: isp-1 mutant_whole worm

value: isp-1 mutant


title: WT_3

source_name: wild type_whole worm

value: wild type


title: isp-1_1


title: WT_2


title: WT_1


title: Basidia_replicate 3

description: This sample is from Melampsora larici-populina_Populus trichocarpa. It is the third of three biological replicates used in this experiment.


title: isp-1sod-5_2


title: isp-1sod-5_3


title: Sample_RS-01708829

status: Public on Aug 18 2017

description: Lung from NIH Swiss mice, female 7 weeks old treated with one dose of 60mg/kg CBL0137, IV, 24 hrs before organ collection

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were  mapped to mm910 whole genome and ENSEMBL gene annotation database GRCm38.71) using Tophat 2.0.9 with  parameters -g 1 -p 10
Raw count data are generated by HTSeq using intersection-strict mode
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count  values for each sample

organism: Mus musculus

source_name: whole lung

growth_protocol: DMEM, 10% FBS

extract_protocol:
TRIzol followed by RNA-Clean columns
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CBL0137, 1uM (cells), 60mg/kg IV (mice) 24 hrs

value: NIH Swiss

tag: treatment

value: CBL0137, 60mg/kg IV, 24 hrs


title: Sample_RS-01708830

description: MEF from Trp53tm1Tyj (p53-/-) mice, untreated

source_name: mouse embryo fibroblasts

value: untreated


title: Sample_RS-01708831

description: MEF from Trp53tm1Tyj (p53-/-) mice, treated with 1microM of CBL0137 for 24 hrs


title: Sample_RS-01708819

description: MEF from C57BL/6J mice, treated with 1microM of CBL0137 for 24 hrs


title: Sample_RS-01708827

description: Lung from NIH Swiss mice, female 7 weeks old treated with one dose of vehicle (5% dextrose) IV, 24 hrs before organ collection

value: vehicle


title: Sample_RS-01708826


title: Sample_RS-01708828


title: isp-1_2

value: prefertile young adult


title: Sample_RS-01708816

description: MEF from C57BL/6J mice, untreated


title: C Lung #2

description:
Lung from NIH Swiss male mice, 7 weeks old, treated with one IV dose of vehicle (5% dextrose 24 hrs before organ collection)
SAMPLE 26

data_processing: The data were normalized using quantile normalization using GenomeStudio

extract_protocol: TRIzol

treatment_protocol: CBL0137, IV, 30, 60 or 90 mg/kg, 24 hrs before organ collection


title: 90 Lung #1

description:
Lung from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 90mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 31

value: CBL0137 90mg/kg


title: 90 Lung #2

description:
Lung from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 90mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 32


title: C Lung #1

description:
Lung from NIH Swiss male mice, 7 weeks old, treated with one IV dose of vehicle (5% dextrose 24 hrs before organ collection)
SAMPLE 25


title: 30 Lung #2

description:
Lung from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 30mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 28

value: CBL0137 30mg/kg


title: 60 Liver #1

description:
Liver from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 60mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 21

source_name: whole liver

value: CBL0137 60mg/kg


title: 90 Liver #1

description:
Liver from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 90mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 23


title: 60 Liver #2

description:
Liver from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 60mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 22


title: Sample_RS-01708818


title: 30 Lung #1

description:
Lung from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 30mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 27


title: 60 Lung #1

description:
Lung from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 60mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 29


title: 90 Liver #2

description:
Liver from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 90mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 24


title: C Liver #1

description:
Liver from NIH Swiss male mice, 7 weeks old, treated with one IV dose of vehicle (5% dextrose 24 hrs before organ collection)
SAMPLE 17


title: C Liver #2

description:
Liver from NIH Swiss male mice, 7 weeks old, treated with one IV dose of vehicle (5% dextrose 24 hrs before organ collection)
SAMPLE 18


title: 60 Lung #2

description:
Lung from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 60mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 30


title: 30 Liver #2

description:
Liver from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 30mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 20


title: 90 Spleen #1

description:
Spleen from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 90mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 15

source_name: whole spleen


title: 90 Spleen #2

description:
Spleen from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 90mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 16


title: 30 Liver #1

description:
Liver from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 30mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 19


title: 60 Spleen #1

description:
Spleen from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 60mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 13


title: 60 Spleen #2

description:
Spleen from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 60mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 14


title: 30 Spleen #2

description:
Spleen from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 30mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 12


title: 60 Testis #2

description:
Testis from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 60mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 6

source_name: whole testis


title: C Spleen #2

description:
Spleen from NIH Swiss male mice, 7 weeks old, treated with one IV dose of vehicle (5% dextrose 24 hrs before organ collection)
SAMPLE 10


title: 30 Spleen #1

description:
Spleen from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 30mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 11


title: 90 Testis #1

description:
Testis from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 90mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 7


title: Sample_RS-01708817

description: MEF from C57BL/6J mice, untreated


title: 90 Testis #2

description:
Testis from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 90mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 8


title: C Spleen #1

description:
Spleen from NIH Swiss male mice, 7 weeks old, treated with one IV dose of vehicle (5% dextrose 24 hrs before organ collection)
SAMPLE 9


title: PIWIL1-IP small RNA-seq rep2

status: Public on May 25 2017

description:
RNA (immunoprecipitated)
PIWIL1_smRNA-seq_smRNAreads.txt

data_processing:
PIWIL1-IP-seq: Adapter sequences were removed from obtained reads, and mapped to the mouse reference genome (mm10) using Bowtie (Langmead et al., 2009). Annotation of the reads was determined according to UCSC genome browser (Meyer et al., 2013) and Ensembl databases (Yates et al., 2016).
RNA-seq: Reads were mapped to the mouse reference genome (mm10) using STAR (Dobin et al., 2013) with default parameters. Expression of each transcript was determined by calculating the number of reads that map to the transcript sequence of each CDS in Ensembl fasta file (Yates et al., 2016). These mapped reads were normalized by the length of each transcript and the total number of genome mapped reads to calculate Reads pre Kilobase per Million mapped reads (RPKM).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include small RNA sequence and read counts for PIWIL1-IP small RNA-seq samples for two replicate samples (PIWIL1_smRNAseq_smRNAreads.txt); tab-delimited text files include Ensembl gene ID with RPKM values for RNA-seq samples from Piwil1 +/- and -/- mice (RNAseq_RPKM.txt).

source_name: Testes

extract_protocol:
Testes were dissected and frozen. For PIWIL1-IP samples, immunopurification of PIWIL1 was performed using testis lysates followed by RNA isolation, and the size fractionation was obtained by gel-purification. RNA-seq samples were prepared by total RNA isolation using Isogen (Nippongene).
Small RNA-seq libraries were prepared using NEBNext Small RNA Library Sample Prep Set (New England BioLabs), and RNA-seq libraries were prepared with the directional mRNA-seq library prep protocol using TruSeq Standard mRNA Sample Prep Kit (Illumina). rRNAs were removed by Ribo-zero Magnetic Gold Kit (Illumina).

value: Testes

tag: age

value: WT (C57BL/6J)


title: directional RNA-seq from Piwil1+/-

description:
total RNA
RNA-seq_RPKM.txt

value: post-natal day 23


title: PIWIL1-IP small RNA-seq rep1


title: directional RNA-seq from Piwil1-/-

description:
total RNA
RNA-seq_RPKM.txt


title: 60 Testis #1

description:
Testis from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 60mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 5


title: C Testis #1

description:
Testis from NIH Swiss male mice, 7 weeks old, treated with one IV dose of vehicle (5% dextrose 24 hrs before organ collection)
SAMPLE 1


title: 30 Testis #1

description:
Testis from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 30mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 3


title: C Testis #2

description:
Testis from NIH Swiss male mice, 7 weeks old, treated with one IV dose of vehicle (5% dextrose 24 hrs before organ collection)
SAMPLE 2


title: Genomic DNA from human placenta 341

status: Public on Jul 01 2016

type: genomic

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

institute: Rollins School of Public Health at Emory University

description: normal infant placenta tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Human placenta

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: infant gender

value: Male

tag: maternal age

tag: birth weight (grams)

tag: gestational age

tag: placental as levels

tag: post-partum maternal toenail as

tag: urinary as

value: No

tag: bmi

tag: parity

tag: maternal race

value: White

value: Any post-grad


title: 30 Testis #2

description:
Testis from NIH Swiss male mice, 7 weeks old, treated with one IV dose of 30mg/kg of CBL0137 24 hrs before organ collection
SAMPLE 4


title: Genomic DNA from human placenta 334

description: normal infant placenta tissue

value: Female

value: Other/Unknown

value: College graduate


title: Genomic DNA from human placenta 336

description: normal infant placenta tissue


title: Genomic DNA from human placenta 332

description: normal infant placenta tissue


title: Genomic DNA from human placenta 342

description: normal infant placenta tissue


title: Genomic DNA from human placenta 333

description: normal infant placenta tissue

value: Yes

value: HS grad


title: Genomic DNA from human placenta 331

description: normal infant placenta tissue


title: Genomic DNA from human placenta 319

description: normal infant placenta tissue


title: Genomic DNA from human placenta 337

description: normal infant placenta tissue


title: Genomic DNA from human placenta 327

description: normal infant placenta tissue

value: Jr College/technical school


title: Genomic DNA from human placenta 343

description: normal infant placenta tissue


title: Genomic DNA from human placenta 323

description: normal infant placenta tissue


title: Genomic DNA from human placenta 339

description: normal infant placenta tissue


title: Genomic DNA from human placenta 340

description: normal infant placenta tissue


title: Genomic DNA from human placenta 326

description: normal infant placenta tissue


title: Genomic DNA from human placenta 325

description: normal infant placenta tissue


title: Genomic DNA from human placenta 335

description: normal infant placenta tissue


title: Genomic DNA from human placenta 338

description: normal infant placenta tissue


title: Genomic DNA from human placenta 324

description: normal infant placenta tissue


title: Genomic DNA from human placenta 329

description: normal infant placenta tissue


title: Genomic DNA from human placenta 322

description: normal infant placenta tissue


title: Genomic DNA from human placenta 328

description: normal infant placenta tissue


title: Genomic DNA from human placenta 318

description: normal infant placenta tissue


title: Genomic DNA from human placenta 320

description: normal infant placenta tissue


title: Genomic DNA from human placenta 330

description: normal infant placenta tissue


title: Genomic DNA from human placenta 321

description: normal infant placenta tissue


title: Genomic DNA from human placenta 317

description: normal infant placenta tissue


title: Genomic DNA from human placenta 316

description: normal infant placenta tissue


title: Genomic DNA from human placenta 314

description: normal infant placenta tissue


title: Genomic DNA from human placenta 315

description: normal infant placenta tissue


title: Genomic DNA from human placenta 311

description: normal infant placenta tissue


title: Genomic DNA from human placenta 312

description: normal infant placenta tissue


title: Genomic DNA from human placenta 310

description: normal infant placenta tissue


title: Genomic DNA from human placenta 313

description: normal infant placenta tissue


title: Genomic DNA from human placenta 304

description: normal infant placenta tissue


title: Genomic DNA from human placenta 305

description: normal infant placenta tissue


title: Genomic DNA from human placenta 297

description: normal infant placenta tissue


title: Genomic DNA from human placenta 295

description: normal infant placenta tissue


title: Genomic DNA from human placenta 308

description: normal infant placenta tissue


title: Genomic DNA from human placenta 298

description: normal infant placenta tissue


title: Genomic DNA from human placenta 306

description: normal infant placenta tissue


title: Genomic DNA from human placenta 296

description: normal infant placenta tissue


title: Genomic DNA from human placenta 309

description: normal infant placenta tissue


title: Genomic DNA from human placenta 300

description: normal infant placenta tissue


title: Genomic DNA from human placenta 303

description: normal infant placenta tissue


title: Genomic DNA from human placenta 302

description: normal infant placenta tissue


title: Genomic DNA from human placenta 291

description: normal infant placenta tissue


title: Genomic DNA from human placenta 301

description: normal infant placenta tissue


title: Genomic DNA from human placenta 294

description: normal infant placenta tissue


title: Genomic DNA from human placenta 287

description: normal infant placenta tissue


title: Genomic DNA from human placenta 289

description: normal infant placenta tissue


title: Genomic DNA from human placenta 284

description: normal infant placenta tissue


title: Genomic DNA from human placenta 288

description: normal infant placenta tissue


title: Genomic DNA from human placenta 307

description: normal infant placenta tissue


title: Genomic DNA from human placenta 281

description: normal infant placenta tissue

tag: bmi:


title: Genomic DNA from human placenta 290

description: normal infant placenta tissue


title: Genomic DNA from human placenta 293

description: normal infant placenta tissue


title: Genomic DNA from human placenta 292

description: normal infant placenta tissue


title: Genomic DNA from human placenta 280

description: normal infant placenta tissue


title: Genomic DNA from human placenta 283

description: normal infant placenta tissue


title: Genomic DNA from human placenta 299

description: normal infant placenta tissue


title: Genomic DNA from human placenta 278

description: normal infant placenta tissue


title: Genomic DNA from human placenta 282

description: normal infant placenta tissue


title: Genomic DNA from human placenta 275

description: normal infant placenta tissue


title: Genomic DNA from human placenta 273

description: normal infant placenta tissue


title: Genomic DNA from human placenta 276

description: normal infant placenta tissue


title: Genomic DNA from human placenta 274

description: normal infant placenta tissue


title: Genomic DNA from human placenta 271

description: normal infant placenta tissue


title: Genomic DNA from human placenta 286

description: normal infant placenta tissue


title: Genomic DNA from human placenta 268

description: normal infant placenta tissue


title: Genomic DNA from human placenta 285

description: normal infant placenta tissue


title: Genomic DNA from human placenta 270

description: normal infant placenta tissue


title: Genomic DNA from human placenta 267

description: normal infant placenta tissue


title: Genomic DNA from human placenta 279

description: normal infant placenta tissue


title: Genomic DNA from human placenta 269

description: normal infant placenta tissue


title: Genomic DNA from human placenta 256

description: normal infant placenta tissue


title: Genomic DNA from human placenta 272

description: normal infant placenta tissue


title: Genomic DNA from human placenta 263

description: normal infant placenta tissue


title: Genomic DNA from human placenta 266

description: normal infant placenta tissue


title: Genomic DNA from human placenta 259

description: normal infant placenta tissue


title: Genomic DNA from human placenta 261

description: normal infant placenta tissue


title: Genomic DNA from human placenta 257

description: normal infant placenta tissue


title: Genomic DNA from human placenta 254

description: normal infant placenta tissue


title: Genomic DNA from human placenta 265

description: normal infant placenta tissue


title: Genomic DNA from human placenta 277

description: normal infant placenta tissue


title: Genomic DNA from human placenta 264

description: normal infant placenta tissue


title: Genomic DNA from human placenta 262

description: normal infant placenta tissue


title: Genomic DNA from human placenta 251

description: normal infant placenta tissue


title: Genomic DNA from human placenta 249

description: normal infant placenta tissue


title: Genomic DNA from human placenta 260

description: normal infant placenta tissue


title: Genomic DNA from human placenta 246

description: normal infant placenta tissue


title: Genomic DNA from human placenta 250

description: normal infant placenta tissue


title: Genomic DNA from human placenta 252

description: normal infant placenta tissue


title: Genomic DNA from human placenta 248

description: normal infant placenta tissue


title: Genomic DNA from human placenta 245

description: normal infant placenta tissue


title: Genomic DNA from human placenta 241

description: normal infant placenta tissue


title: Genomic DNA from human placenta 244

description: normal infant placenta tissue

value: <11th grade


title: Genomic DNA from human placenta 233

description: normal infant placenta tissue


title: Genomic DNA from human placenta 238

description: normal infant placenta tissue


title: Genomic DNA from human placenta 243

description: normal infant placenta tissue


title: Genomic DNA from human placenta 229

description: normal infant placenta tissue


title: Genomic DNA from human placenta 237

description: normal infant placenta tissue


title: Genomic DNA from human placenta 234

description: normal infant placenta tissue


title: Genomic DNA from human placenta 247

description: normal infant placenta tissue


title: Genomic DNA from human placenta 228

description: normal infant placenta tissue


title: Genomic DNA from human placenta 231

description: normal infant placenta tissue


title: Genomic DNA from human placenta 253

description: normal infant placenta tissue


title: Genomic DNA from human placenta 230

description: normal infant placenta tissue


title: Genomic DNA from human placenta 227

description: normal infant placenta tissue


title: Genomic DNA from human placenta 224

description: normal infant placenta tissue


title: Genomic DNA from human placenta 258

description: normal infant placenta tissue


title: Genomic DNA from human placenta 232

description: normal infant placenta tissue


title: Genomic DNA from human placenta 240

description: normal infant placenta tissue


title: Genomic DNA from human placenta 223

description: normal infant placenta tissue


title: Genomic DNA from human placenta 239

description: normal infant placenta tissue


title: Genomic DNA from human placenta 225

description: normal infant placenta tissue


title: Genomic DNA from human placenta 221

description: normal infant placenta tissue


title: Genomic DNA from human placenta 226

description: normal infant placenta tissue


title: Genomic DNA from human placenta 235

description: normal infant placenta tissue


title: Genomic DNA from human placenta 219

description: normal infant placenta tissue


title: Genomic DNA from human placenta 236

description: normal infant placenta tissue


title: Genomic DNA from human placenta 220

description: normal infant placenta tissue


title: Genomic DNA from human placenta 255

description: normal infant placenta tissue


title: Genomic DNA from human placenta 216

description: normal infant placenta tissue


title: Genomic DNA from human placenta 218

description: normal infant placenta tissue


title: Genomic DNA from human placenta 242

description: normal infant placenta tissue


title: Genomic DNA from human placenta 215

description: normal infant placenta tissue


title: Genomic DNA from human placenta 211

description: normal infant placenta tissue


title: Genomic DNA from human placenta 213

description: normal infant placenta tissue


title: Genomic DNA from human placenta 214

description: normal infant placenta tissue


title: Genomic DNA from human placenta 222

description: normal infant placenta tissue


title: Genomic DNA from human placenta 212

description: normal infant placenta tissue


title: Genomic DNA from human placenta 208

description: normal infant placenta tissue


title: Genomic DNA from human placenta 207

description: normal infant placenta tissue


title: Genomic DNA from human placenta 210

description: normal infant placenta tissue


title: Genomic DNA from human placenta 201

description: normal infant placenta tissue


title: Genomic DNA from human placenta 202

description: normal infant placenta tissue


title: Genomic DNA from human placenta 206

description: normal infant placenta tissue


title: Genomic DNA from human placenta 198

description: normal infant placenta tissue


title: Genomic DNA from human placenta 197

description: normal infant placenta tissue


title: Genomic DNA from human placenta 203

description: normal infant placenta tissue


title: Genomic DNA from human placenta 193

description: normal infant placenta tissue


title: Genomic DNA from human placenta 204

description: normal infant placenta tissue


title: Genomic DNA from human placenta 200

description: normal infant placenta tissue


title: Genomic DNA from human placenta 194

description: normal infant placenta tissue


title: Genomic DNA from human placenta 195

description: normal infant placenta tissue


title: Genomic DNA from human placenta 190

description: normal infant placenta tissue


title: Genomic DNA from human placenta 209

description: normal infant placenta tissue


title: Genomic DNA from human placenta 196

description: normal infant placenta tissue


title: Genomic DNA from human placenta 191

description: normal infant placenta tissue


title: Genomic DNA from human placenta 217

description: normal infant placenta tissue


title: Genomic DNA from human placenta 185

description: normal infant placenta tissue


title: Genomic DNA from human placenta 187

description: normal infant placenta tissue


title: Genomic DNA from human placenta 199

description: normal infant placenta tissue


title: Genomic DNA from human placenta 189

description: normal infant placenta tissue


title: Genomic DNA from human placenta 188

description: normal infant placenta tissue


title: Genomic DNA from human placenta 184

description: normal infant placenta tissue


title: Genomic DNA from human placenta 180

description: normal infant placenta tissue


title: Genomic DNA from human placenta 179

description: normal infant placenta tissue


title: Genomic DNA from human placenta 178

description: normal infant placenta tissue


title: Genomic DNA from human placenta 183

description: normal infant placenta tissue


title: Genomic DNA from human placenta 205

description: normal infant placenta tissue


title: Genomic DNA from human placenta 182

description: normal infant placenta tissue


title: Genomic DNA from human placenta 192

description: normal infant placenta tissue


title: Genomic DNA from human placenta 171

description: normal infant placenta tissue


title: Genomic DNA from human placenta 173

description: normal infant placenta tissue


title: Genomic DNA from human placenta 174

description: normal infant placenta tissue


title: Genomic DNA from human placenta 177

description: normal infant placenta tissue


title: Genomic DNA from human placenta 175

description: normal infant placenta tissue


title: Genomic DNA from human placenta 167

description: normal infant placenta tissue


title: Genomic DNA from human placenta 169

description: normal infant placenta tissue


title: Genomic DNA from human placenta 176

description: normal infant placenta tissue


title: Genomic DNA from human placenta 166

description: normal infant placenta tissue


title: Genomic DNA from human placenta 186

description: normal infant placenta tissue


title: Genomic DNA from human placenta 168

description: normal infant placenta tissue


title: Genomic DNA from human placenta 165

description: normal infant placenta tissue


title: Genomic DNA from human placenta 161

description: normal infant placenta tissue


title: Genomic DNA from human placenta 154

description: normal infant placenta tissue


title: Genomic DNA from human placenta 158

description: normal infant placenta tissue


title: Genomic DNA from human placenta 164

description: normal infant placenta tissue


title: Genomic DNA from human placenta 172

description: normal infant placenta tissue


title: Genomic DNA from human placenta 155

description: normal infant placenta tissue


title: Genomic DNA from human placenta 157

description: normal infant placenta tissue


title: Genomic DNA from human placenta 162

description: normal infant placenta tissue


title: Genomic DNA from human placenta 156

description: normal infant placenta tissue

tag: parity:


title: Genomic DNA from human placenta 160

description: normal infant placenta tissue


title: Genomic DNA from human placenta 163

description: normal infant placenta tissue


title: Genomic DNA from human placenta 153

description: normal infant placenta tissue


title: Genomic DNA from human placenta 151

description: normal infant placenta tissue


title: Genomic DNA from human placenta 147

description: normal infant placenta tissue


title: Genomic DNA from human placenta 170

description: normal infant placenta tissue


title: Genomic DNA from human placenta 159

description: normal infant placenta tissue


title: Genomic DNA from human placenta 148

description: normal infant placenta tissue


title: Genomic DNA from human placenta 149

description: normal infant placenta tissue


title: Genomic DNA from human placenta 145

description: normal infant placenta tissue


title: Genomic DNA from human placenta 142

description: normal infant placenta tissue


title: Genomic DNA from human placenta 152

description: normal infant placenta tissue


title: Genomic DNA from human placenta 146

description: normal infant placenta tissue


title: Genomic DNA from human placenta 143

description: normal infant placenta tissue


title: Genomic DNA from human placenta 144

description: normal infant placenta tissue


title: Genomic DNA from human placenta 150

description: normal infant placenta tissue


title: Genomic DNA from human placenta 138

description: normal infant placenta tissue


title: Genomic DNA from human placenta 140

description: normal infant placenta tissue


title: Genomic DNA from human placenta 181

description: normal infant placenta tissue


title: Genomic DNA from human placenta 127

description: normal infant placenta tissue


title: Genomic DNA from human placenta 136

description: normal infant placenta tissue


title: Genomic DNA from human placenta 135

description: normal infant placenta tissue


title: Genomic DNA from human placenta 128

description: normal infant placenta tissue


title: Genomic DNA from human placenta 129

description: normal infant placenta tissue


title: Genomic DNA from human placenta 124

description: normal infant placenta tissue


title: Genomic DNA from human placenta 132

description: normal infant placenta tissue


title: Genomic DNA from human placenta 139

description: normal infant placenta tissue


title: Genomic DNA from human placenta 141

description: normal infant placenta tissue


title: Genomic DNA from human placenta 123

description: normal infant placenta tissue


title: Genomic DNA from human placenta 134

description: normal infant placenta tissue


title: Genomic DNA from human placenta 137

description: normal infant placenta tissue


title: Genomic DNA from human placenta 117

description: normal infant placenta tissue


title: Genomic DNA from human placenta 130

description: normal infant placenta tissue


title: Genomic DNA from human placenta 126

description: normal infant placenta tissue


title: Genomic DNA from human placenta 125

description: normal infant placenta tissue


title: Genomic DNA from human placenta 131

description: normal infant placenta tissue


title: Genomic DNA from human placenta 120

description: normal infant placenta tissue


title: Genomic DNA from human placenta 119

description: normal infant placenta tissue


title: Genomic DNA from human placenta 122

description: normal infant placenta tissue


title: Genomic DNA from human placenta 133

description: normal infant placenta tissue


title: Genomic DNA from human placenta 118

description: normal infant placenta tissue


title: Genomic DNA from human placenta 121

description: normal infant placenta tissue


title: Genomic DNA from human placenta 116

description: normal infant placenta tissue


title: Genomic DNA from human placenta 115

description: normal infant placenta tissue


title: Genomic DNA from human placenta 107

description: normal infant placenta tissue


title: Genomic DNA from human placenta 114

description: normal infant placenta tissue


title: Genomic DNA from human placenta 108

description: normal infant placenta tissue


title: Genomic DNA from human placenta 110

description: normal infant placenta tissue


title: Genomic DNA from human placenta 109

description: normal infant placenta tissue


title: Genomic DNA from human placenta 106

description: normal infant placenta tissue


title: Genomic DNA from human placenta 101

description: normal infant placenta tissue


title: Genomic DNA from human placenta 112

description: normal infant placenta tissue


title: Genomic DNA from human placenta 95

description: normal infant placenta tissue


title: Genomic DNA from human placenta 94

description: normal infant placenta tissue


title: Genomic DNA from human placenta 88

description: normal infant placenta tissue


title: Genomic DNA from human placenta 100

description: normal infant placenta tissue


title: Genomic DNA from human placenta 87

description: normal infant placenta tissue


title: Genomic DNA from human placenta 92

description: normal infant placenta tissue


title: Genomic DNA from human placenta 93

description: normal infant placenta tissue


title: Genomic DNA from human placenta 103

description: normal infant placenta tissue


title: Genomic DNA from human placenta 90

description: normal infant placenta tissue


title: Genomic DNA from human placenta 104

description: normal infant placenta tissue


title: Genomic DNA from human placenta 97

description: normal infant placenta tissue


title: Genomic DNA from human placenta 86

description: normal infant placenta tissue


title: Genomic DNA from human placenta 102

description: normal infant placenta tissue


title: Genomic DNA from human placenta 91

description: normal infant placenta tissue


title: Genomic DNA from human placenta 89

description: normal infant placenta tissue


title: Genomic DNA from human placenta 113

description: normal infant placenta tissue


title: Genomic DNA from human placenta 105

description: normal infant placenta tissue


title: Genomic DNA from human placenta 99

description: normal infant placenta tissue


title: Genomic DNA from human placenta 111

description: normal infant placenta tissue


title: Genomic DNA from human placenta 98

description: normal infant placenta tissue


title: Genomic DNA from human placenta 81

description: normal infant placenta tissue


title: Genomic DNA from human placenta 96

description: normal infant placenta tissue


title: Genomic DNA from human placenta 82

description: normal infant placenta tissue


title: Genomic DNA from human placenta 83

description: normal infant placenta tissue


title: Genomic DNA from human placenta 85

description: normal infant placenta tissue


title: Genomic DNA from human placenta 84

description: normal infant placenta tissue


title: Genomic DNA from human placenta 79

description: normal infant placenta tissue


title: Genomic DNA from human placenta 80

description: normal infant placenta tissue


title: Genomic DNA from human placenta 78

description: normal infant placenta tissue


title: Genomic DNA from human placenta 77

description: normal infant placenta tissue


title: Genomic DNA from human placenta 76

description: normal infant placenta tissue


title: Genomic DNA from human placenta 72

description: normal infant placenta tissue


title: Genomic DNA from human placenta 70

description: normal infant placenta tissue


title: Genomic DNA from human placenta 73

description: normal infant placenta tissue


title: Genomic DNA from human placenta 75

description: normal infant placenta tissue


title: Genomic DNA from human placenta 62

description: normal infant placenta tissue


title: Genomic DNA from human placenta 71

description: normal infant placenta tissue


title: Genomic DNA from human placenta 68

description: normal infant placenta tissue


title: Genomic DNA from human placenta 56

description: normal infant placenta tissue


title: Genomic DNA from human placenta 66

description: normal infant placenta tissue


title: Genomic DNA from human placenta 64

description: normal infant placenta tissue


title: Genomic DNA from human placenta 74

description: normal infant placenta tissue


title: Genomic DNA from human placenta 58

description: normal infant placenta tissue


title: Genomic DNA from human placenta 54

description: normal infant placenta tissue


title: Genomic DNA from human placenta 53

description: normal infant placenta tissue


title: Genomic DNA from human placenta 48

description: normal infant placenta tissue


title: Genomic DNA from human placenta 57

description: normal infant placenta tissue


title: Genomic DNA from human placenta 59

description: normal infant placenta tissue


title: Genomic DNA from human placenta 60

description: normal infant placenta tissue


title: Genomic DNA from human placenta 50

description: normal infant placenta tissue


title: Genomic DNA from human placenta 67

description: normal infant placenta tissue


title: Genomic DNA from human placenta 63

description: normal infant placenta tissue


title: Genomic DNA from human placenta 61

description: normal infant placenta tissue


title: Genomic DNA from human placenta 55

description: normal infant placenta tissue


title: Genomic DNA from human placenta 49

description: normal infant placenta tissue


title: Genomic DNA from human placenta 51

description: normal infant placenta tissue


title: Genomic DNA from human placenta 46

description: normal infant placenta tissue


title: Genomic DNA from human placenta 47

description: normal infant placenta tissue


title: Genomic DNA from human placenta 52

description: normal infant placenta tissue


title: Genomic DNA from human placenta 44

description: normal infant placenta tissue


title: Genomic DNA from human placenta 69

description: normal infant placenta tissue


title: Genomic DNA from human placenta 43

description: normal infant placenta tissue


title: Genomic DNA from human placenta 40

description: normal infant placenta tissue


title: Genomic DNA from human placenta 42

description: normal infant placenta tissue


title: Genomic DNA from human placenta 38

description: normal infant placenta tissue


title: Genomic DNA from human placenta 41

description: normal infant placenta tissue


title: Genomic DNA from human placenta 34

description: normal infant placenta tissue


title: Genomic DNA from human placenta 36

description: normal infant placenta tissue


title: Genomic DNA from human placenta 45

description: normal infant placenta tissue


title: Genomic DNA from human placenta 65

description: normal infant placenta tissue


title: Genomic DNA from human placenta 32

description: normal infant placenta tissue


title: Genomic DNA from human placenta 39

description: normal infant placenta tissue


title: Genomic DNA from human placenta 37

description: normal infant placenta tissue


title: Genomic DNA from human placenta 31

description: normal infant placenta tissue


title: Genomic DNA from human placenta 35

description: normal infant placenta tissue


title: Genomic DNA from human placenta 19

description: normal infant placenta tissue


title: Genomic DNA from human placenta 28

description: normal infant placenta tissue


title: Genomic DNA from human placenta 29

description: normal infant placenta tissue


title: Genomic DNA from human placenta 27

description: normal infant placenta tissue


title: Genomic DNA from human placenta 33

description: normal infant placenta tissue


title: Genomic DNA from human placenta 25

description: normal infant placenta tissue


title: Genomic DNA from human placenta 17

description: normal infant placenta tissue


title: Genomic DNA from human placenta 21

description: normal infant placenta tissue


title: Genomic DNA from human placenta 26

description: normal infant placenta tissue


title: RNA-seq from Piwi-KD

status: Public on Jun 30 2016

data_processing:
RNA-seq analysis was performed as previously described (Ohtani et al., 2013) with slight modifications. Briefly, Cutadapt was used to remove adapter sequences from RNA-seq reads. Reads shorter than 20 nt were removed. Bowtie 2.0.6 (Langmead and Salzberg, 2012) was used with default parameters to map sequences to the Drosophila genome (dm3). Reads mapped to the genome were then mapped to the Drosophila melanogaster transposon consensus sequence from Repbase (Jurka, 1998), extracting those that were uniquely mapped. Expression levels (RPKM) of transposons were calculated using transposon consensus sequence mapped reads. Expression levels (RPKM) of Pol II-regulated genes were calculated using TopHat 2.0.7 (Trapnell et al., 2009) and cufflinks 2.1.1. (Trapnell et al., 2010).
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).

organism: Drosophila melanogaster

source_name: Piwi-KD OSC

growth_protocol: Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium).

extract_protocol:
Total RNAs were isolated with the Isogen reagent (NipponGene). Poly(A)+ RNAs were obtained using Oligo-dT beads.
Poly(A)+ RNA libraries were prepared as described (Ohtani et al., 2013).

treatment_protocol: Transfection of siRNAs was performed using Cell Line 96-well Nucleofector Kit SF and 96-well Shuttle Device (Lonza).

tag: cell type

value: Ovarian Somatic Cells (OSC)

tag: variation

value: RNAi Piwi


title: RNA-seq from H1-KD

source_name: H1-KD OSC

value: RNAi H1


title: RNA-seq from Control-KD

source_name: EGFP-KD OSC

value: RNAi EGFP


title: Genomic DNA from human placenta 18

description: normal infant placenta tissue


title: Genomic DNA from human placenta 22

description: normal infant placenta tissue


title: ATAC-seq from HP1a-KD rep2

data_processing:
Library strategy: ATAC-Seq
ATAC-seq analysis was performed as previously described (Buenrostro et al., 2013) with some modifications. Adaptors were removed using Cutadapt software, and reads with lengths shorter than 50 bp were removed. Reads were first aligned to dm3 genome using Bowtie2.0.6 (Langmead and Salzberg, 2012) with the parameter –X 4000, to allow fragments up to 4 kbp long. MACS2 (Zhang et al., 2008) was used for peak calling with the parameters –g dm –nomodel –nolambda –extsize 239 –keep-dup all. MACS2 bdgdiff was used to compare samples, and CEAS (Shin et al., 2009) was used to annotate the peaks. To analyze the ATAC-seq reads mapped to transposons, reads mapped to the genome concordantly were extracted and mapped to Repbase transposon consensus sequences (Jurka, 1998) using the same parameters as for genome mapping.
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).

source_name: HP1a-KD OSC

extract_protocol:
ATAC-seq samples were extracted as described (Buenrostro et al., 2013; Buenrostro et al., 2015).
ATAC-seq libraries were constructed as described (Buenrostro et al., 2013; Buenrostro et al., 2015).

value: RNAi HP1a


title: Genomic DNA from human placenta 10

description: normal infant placenta tissue


title: Genomic DNA from human placenta 24

description: normal infant placenta tissue


title: Genomic DNA from human placenta 23

description: normal infant placenta tissue


title: Piwi-IP smRNA-seq from H1-KD

data_processing:
Piwi associated small RNA sequencing data was analyzed as described previously (Sato et al., 2015) with slight modifications. Briefly, adapters were removed using Cutadapt to remove the reads without adapter sequences. The reads were mapped to the Drosophila genome (dm3) using Bowtie 1.0.1 (Langmead et al., 2009), with –n 1 option. Length distribution was calculated using genome-mapped reads, and reads in the range of 24-30 nt were used for further analysis. The genome-mapped reads were mapped to Drosophila melanogaster transposon consensus sequences obtained from Repbase (Jurka, 1998), and reads mapped uniquely to the transposon consensus sequence were used to calculate the frequency of piRNAs obtained from each transposon.
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).

extract_protocol:
Piwi was immunoprecipitated from confluent OSCs in 9-cm dishes, and Piwi-associated RNA was isolated from the immunopurified complex by phenol-chloroform extraction and ethanol precipitation.
Libraries were prepared using NEBNext Small RNA Library Sample Prep Set (New England BioLabs), according to the manufacturer’s instructions.


title: ATAC-seq from Piwi-KD rep2


title: Genomic DNA from human placenta 16

description: normal infant placenta tissue


title: Genomic DNA from human placenta 14

description: normal infant placenta tissue


title: Genomic DNA from human placenta 15

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3

description: normal infant placenta tissue


title: ATAC-seq from HP1a-KD rep1


title: Genomic DNA from human placenta 7

description: normal infant placenta tissue


title: Piwi-IP smRNA-seq from Control-KD

source_name: Control-KD OSC


title: Genomic DNA from human placenta 8

description: normal infant placenta tissue


title: Genomic DNA from human placenta 4

description: normal infant placenta tissue


title: Genomic DNA from human placenta 13

description: normal infant placenta tissue


title: Genomic DNA from human placenta 9

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5

description: normal infant placenta tissue


title: ChIP-seq input from HP1a-KD sample3

data_processing:
Adapters were removed from the ChIP-seq reads using Cutadapt, and subsequent reads shorter than 50 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm3) using Bowtie 1.0.1 (Langmead et al., 2009), using --M 1 --best --strata parameters. Reads mapped to the genome were extracted and mapped to Drosophila melanogaster transposon consensus sequences from Repbase (Jurka, 1998), permitting up to three mismatches and extracting those that mapped uniquely to the transposon consensus sequence.
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).

extract_protocol:
OSC cells were fixed, lysed, and their nuclei isolated using truChIP Chromatin Shearing Kits (Covaris) according to the manufacturer’s instructions. DNA was sonicated to ~300 bases using Bioruptor (Cosmobio), then diluted with ChIP buffer. IP was performed using 3 μg of antibodies on Dynabeads-Protein G beads. Samples were reverse cross-linked, treated with RNase and Proteinase K, and DNA was extracted.
DNA fragments from the ChIP experiment were sheared to ~200 bases using Covaris S220 (Covaris), and were used for library preparation with the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.


title: Genomic DNA from human placenta 12

description: normal infant placenta tissue


title: ATAC-seq from H1-KD rep1


title: H1 ChIP-seq from HP1a-KD sample3

tag: chip antibody

value: anti-H1 antibody (generated in this study)


title: H1 ChIP-seq from Control-KD sample3


title: ATAC-seq from Control-KD rep1


title: Genomic DNA from human placenta 2

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6

description: normal infant placenta tissue

value: Male


title: H1 ChIP-seq from Mael-KD sample2

source_name: Mael-KD OSC

value: RNAi Mael


title: ChIP-seq input from Control-KD sample3


title: H1 ChIP-seq from Control-KD sample2


title: Genomic DNA from human placenta 30

description: normal infant placenta tissue

value: No

value: White


title: ChIP-seq input from Control-KD sample2


title: Genomic DNA from human placenta 20

description: normal infant placenta tissue


title: HP1a ChIP-seq from Piwi-KD sample1

value: anti-HP1a antibody (C1A9, DSHB)


title: HP1a ChIP-seq from H1-KD sample1


title: HP1a ChIP-seq from Control-KD sample1


title: H3K9me3 ChIP-seq from H1-KD sample1

value: anti-H3K9me3 antibody (61013, Active motif)


title: ChIP-seq input from Mael-KD sample2


title: H3K9me3 ChIP-seq from Piwi-KD sample1

data_processing:
ChIP-seq analysis: Adapters were removed from the ChIP-seq reads using Cutadapt, and subsequent reads shorter than 50 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm3) using Bowtie 1.0.1 (Langmead et al., 2009), using --M 1 --best --strata parameters. Reads mapped to the genome were extracted and mapped to Drosophila melanogaster transposon consensus sequences from Repbase (Jurka, 1998), permitting up to three mismatches and extracting those that mapped uniquely to the transposon consensus sequence.
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).


title: Genomic DNA from human placenta 11

description: normal infant placenta tissue


title: H3K9me3 ChIP-seq from Control-KD sample1


title: H1 ChIP-seq from Piwi-KD sample1


title: ATAC-seq from Mael-KD rep2


title: H1 ChIP-seq from Control-KD sample1


title: ChIP-seq input from Piwi-KD sample1


title: ATAC-seq from Mael-KD rep1


title: ATAC-seq from Control-KD rep2


title: ATAC-seq from Piwi-KD rep1


title: ChIP-seq input from H1-KD sample1


title: ChIP-seq input from Control-KD sample1


title: ATAC-seq from H1-KD rep2


title: Genomic DNA from human placenta 1

description: normal infant placenta tissue

value: Female

value: College graduate


title: Genomic DNA from human placenta 3999997114 _ R02C01

status: Public on Jun 01 2016

description: normal infant placenta tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylatio450k Beadchip using standard Illumina protocol

source_name: Term placenta

extract_protocol: genomic DNA was extracted and purified from Placental samples using Qiagen DNeasy Kit according to standard instructions

tag: job1 nightshift

tag: prepreg smoke

tag: maternal age yrs

tag: arousal

tag: lethargy

tag: subfertility

value: Any post graduate schooling

tag: maternalrace


title: Genomic DNA from human placenta 3999997080 _ R03C01

description: normal infant placenta tissue

tag: gestational age

tag: ivf

tag: infant gender


title: Genomic DNA from human placenta 3999997093 _ R01C02

description: normal infant placenta tissue

value: Yes

tag: bmi


title: Genomic DNA from human placenta 3999997072 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997093 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R06C02

description: normal infant placenta tissue

tag: batch

tag: birth weight group

value: LGA

tag: attention

tag: quality of movement


title: Genomic DNA from human placenta 3999997077 _ R02C02

description: normal infant placenta tissue

value: Junior college graduate or equivalent

value: Asian


title: Genomic DNA from human placenta 3999997114 _ R05C01

description: normal infant placenta tissue

value: AGA


title: Genomic DNA from human placenta 3999997076 _ R04C01

description: normal infant placenta tissue

value: Other


title: Genomic DNA from human placenta 3999997093 _ R06C02

description: normal infant placenta tissue

value: Less than 11th grade

value: Black


title: Genomic DNA from human placenta 3999997114 _ R06C02

description: normal infant placenta tissue

value: Male


title: Genomic DNA from human placenta 3999997080 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997072 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997093 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997080 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997093 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997093 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R02C01

description: normal infant placenta tissue

value: High school graduate


title: Genomic DNA from human placenta 3999997080 _ R06C01

description: normal infant placenta tissue

value: No


title: Genomic DNA from human placenta 3999997114 _ R03C02

description: normal infant placenta tissue

value: White


title: Genomic DNA from human placenta 3999997114 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997072 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997072 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997080 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997080 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997091 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997072 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997091 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997093 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997091 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997114 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997091 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997080 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997072 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R04C02

description: normal infant placenta tissue

value: SGA


title: Genomic DNA from human placenta 3999997051 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997114 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997091 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997080 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997114 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997072 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R04C01

description: normal infant placenta tissue

tag: gender


title: Genomic DNA from human placenta 3999997072 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997091 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997080 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997114 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R04C02

description: normal infant placenta tissue

value: Unknown/Not Reported


title: Genomic DNA from human placenta 3999997091 _ R04C01

description: normal infant placenta tissue

value: Female


title: Genomic DNA from human placenta 3999997091 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R05C01

description: normal infant placenta tissue

value: College graduate


title: Genomic DNA from human placenta 3999997110 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997072 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R04C01

description: normal infant placenta tissue

value: Any post graduate schooling


title: Genomic DNA from human placenta 3999997080 _ R05C02

description: normal infant placenta tissue

value: Yes


title: Genomic DNA from human placenta 3999997091 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997093 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997114 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R04C02

description: normal infant placenta tissue

value: LGA

value: More than one


title: Genomic DNA from human placenta 3999997093 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R06C01

description: normal infant placenta tissue

value: Junior college graduate or equivalent


title: Genomic DNA from human placenta 3999997091 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997072 _ R05C02

description: normal infant placenta tissue

value: AGA


title: Genomic DNA from human placenta 3999997074 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R01C02

description: normal infant placenta tissue

value: Other


title: Genomic DNA from human placenta 3999997093 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997072 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997093 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997077 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997074 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997100 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997091 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997080 _ R03C02

description: normal infant placenta tissue

value: Indian


title: Genomic DNA from human placenta 3999997091 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417064 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417023 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417045 _ R04C02

description: normal infant placenta tissue

value: Black


title: Genomic DNA from human placenta 5806417081 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997051 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417023 _ R01C02

description: normal infant placenta tissue

value: Male


title: Genomic DNA from human placenta 5806417023 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417023 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417009 _ R02C01

description: normal infant placenta tissue

value: High school graduate


title: Genomic DNA from human placenta 5806636063 _ R04C02

description: normal infant placenta tissue

value: No


title: Genomic DNA from human placenta 6190781088 _ R06C02

description: normal infant placenta tissue

value: White


title: Genomic DNA from human placenta 5806417081 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636061 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6190781088 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417081 _ R02C02

description: normal infant placenta tissue

value: Asian


title: Genomic DNA from human placenta 5806417023 _ R01C01

description: normal infant placenta tissue

value: Less than 11th grade


title: Genomic DNA from human placenta 5806417077 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417064 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636063 _ R03C01

description: normal infant placenta tissue

value: Female


title: Genomic DNA from human placenta 5806417077 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417023 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636051 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417009 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417023 _ R03C01

description: normal infant placenta tissue

value: College graduate


title: Genomic DNA from human placenta 5806417064 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417081 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636083 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417064 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636051 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417009 _ R02C02

description: normal infant placenta tissue

value: Any post graduate schooling


title: Genomic DNA from human placenta 5859720011 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636019 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997110 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417081 _ R06C01

description: normal infant placenta tissue

value: Yes


title: Genomic DNA from human placenta 6008581005 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581028 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417077 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636061 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417064 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594006 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594028 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636079 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636062 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417077 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720025 _ R04C01

description: normal infant placenta tissue

value: SGA


title: Genomic DNA from human placenta 5806636062 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6190781088 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636037 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417076 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636026 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581009 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594025 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581026 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997051 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636030 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636036 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417076 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417023 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636029 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581003 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417064 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636042 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636079 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636036 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581028 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636020 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720012 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636063 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720011 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581026 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636079 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636028 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636042 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594006 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636029 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417045 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636027 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636020 _ R05C02

description: normal infant placenta tissue

value: LGA


title: Genomic DNA from human placenta 5859594028 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636079 _ R03C01

description: normal infant placenta tissue

value: Junior college graduate or equivalent


title: Genomic DNA from human placenta 5806636085 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720012 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720011 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581026 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636027 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581008 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636051 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581005 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636030 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636030 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636034 _ R03C01

description: normal infant placenta tissue

value: AGA

value: More than one


title: Genomic DNA from human placenta 5806417076 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581005 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636034 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581009 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636026 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581014 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636020 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720011 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581026 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636035 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581028 _ R06C01

description: normal infant placenta tissue

value: Other


title: Genomic DNA from human placenta 5806636035 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636086 _ R01C02

description: normal infant placenta tissue

value: Black


title: Genomic DNA from human placenta 5806636036 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636020 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417009 _ R06C02

description: normal infant placenta tissue

value: Male


title: Genomic DNA from human placenta 5806636030 _ R04C01

description: normal infant placenta tissue

value: High school graduate


title: Genomic DNA from human placenta 5806636030 _ R05C01

description: normal infant placenta tissue

value: No


title: Genomic DNA from human placenta 5806636063 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417045 _ R06C02

description: normal infant placenta tissue

value: White


title: Genomic DNA from human placenta 5806636085 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636090 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636020 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720025 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417081 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636063 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636059 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636085 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636063 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581028 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720025 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636030 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581003 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594009 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720025 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636086 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636019 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636039 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594028 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581028 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581008 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581009 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594025 _ R01C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636029 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 3999997076 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581009 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636030 _ R02C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581008 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720012 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417081 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636035 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859594028 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636030 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636090 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636034 _ R06C01

description: normal infant placenta tissue

value: Indian


title: Genomic DNA from human placenta 6008581008 _ R03C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636085 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636059 _ R02C02

description: normal infant placenta tissue

value: Asian


title: Genomic DNA from human placenta 5806636037 _ R05C01

description: normal infant placenta tissue

value: Female


title: Genomic DNA from human placenta 6190781088 _ R04C01

description: normal infant placenta tissue

value: College graduate


title: Genomic DNA from human placenta 5806417076 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5859720029 _ R05C02

description: normal infant placenta tissue

value: Any post graduate schooling


title: Genomic DNA from human placenta 5859720012 _ R01C02

description: normal infant placenta tissue

value: Yes


title: Genomic DNA from human placenta 5806417064 _ R01C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636030 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636039 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636059 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636085 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581009 _ R04C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636038 _ R05C01

description: normal infant placenta tissue

value: SGA

value: Less than 11th grade


title: Genomic DNA from human placenta 5806636086 _ R02C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417077 _ R02C01

description: normal infant placenta tissue

value: Junior college graduate or equivalent


title: Genomic DNA from human placenta 6008581009 _ R04C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581008 _ R06C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6008581003 _ R04C01

description: normal infant placenta tissue

value: AGA


title: Genomic DNA from human placenta 5859594009 _ R05C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 6190781088 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636039 _ R06C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636042 _ R03C01

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806417045 _ R04C01

description: normal infant placenta tissue

value: More than one


title: Genomic DNA from human placenta 5806636026 _ R05C02

description: normal infant placenta tissue


title: Genomic DNA from human placenta 5806636086 _ R03C01

description: normal infant placenta tissue

value: LGA