title: MM291.9.control.input.RNA-seq.rep3

data_processing:
Library strategy: RiboTag IP-seq
Base calls were performed by the instrument control software and further processed using the Offline Base Caller (Illumina) v.1.9.4. Quality control/assessment was performed using fastqc, fastqscreen and custom scripts.
Reads were quality-trimmed with cutadapt v.1.8 using the following options: -q 20 -m 24
Expression levels of all transcripts in the UCSC RefSeq (refGene) transcript annotations and Retrogenes V6 annotations from the GRC38 (mm10) assembly were estimated using kallisto v.0.44.0 (Bray et al., 2016) with sequence-bias correction using a 31 k-mer index. These values are in *RNAseq_abundance.tsv files. See annotation file mm10_GRCm38_refGene_retrogenes_annotation.file.txt
Quantified transcripts were filtered for coding mRNAs only, and TPM values were renormalized to transcript-per-million units. These values are in *RNAseq_abundance_coding.mRNA.only.tsv files. See annotation file mm10_GRCm38_refGene_coding.mRNA.only_annotation.file.txt
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with the following fields: target_id length, eff_length, est_counts, tpm

extract_protocol:
Polysomes were immunoprecipitated from synchronized testes using the RiboTag as previously described (Sanz et al., 2009), with some modifications. Postnatal testes chemically synchronized for undifferentiated spermatogonia were homogenized at 2% w/v in polysome buffer (50 mM Tris, pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1mM DTT, 200 U/mL Promega RNasin, 1mg/mL heparin, 100 μg/mL cycloheximide, Sigma cOmplete EDTA-free protease inhibitor cocktail), first by gently pipetting, then by gently pulling through a long 26 gauge needle.  Homogenate was centrifuged at 10,000g for 10 min at 4˚C, and supernatant was transferred to a fresh tube. 35.0 μL of each sample was set aside as an input control. 2.5 μL anti-HA (BioLegend #901513; previously Covance #MMS-101R; RRID:AB_2565335) was added to 400ul of remaining lysate, and samples were gently rotated for 4 hours at 4˚C. Dynabeads Protein G (Invitrogen 10003D) were washed three times in homogenization buffer (50 mM Tris, pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40). After the final wash was removed, the lysate with antibody was added to the Dynabeads and incubated with gentle rotation overnight at 4˚C. The following day, the Dynabeads were washed three times for 10 min each with gentle rotation at 4˚C in high salt buffer (50 mM Tris, pH 7.4, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 100 μg/mL cycloheximide).    To extract the RNA, the final wash was removed from the Dynabeads and replaced with 350 μl of high salt buffer supplemented with 1% SDS and 0.25 μg/μL Proteinase K. Samples were incubated at 37˚C for 30 min with gentle mixing. Samples were then mixed with an equal volume of acid phenol:chloroform:IAA, pH 4.5, and using phase lock gel tubes, the RNA-containing aqueous phase was transferred to a new tube. RNA was ethanol-precipitated using GlycoBlue Coprecipitant, resuspended in RNase-free water, and quantified via Agilent Bioanalyzer 2100. 120-160 ng total RNA was isolated from RiboTag-positive samples while 1-3 ng total RNA was isolated from RiboTag-negative controls, and 600-1000 ng total RNA was isolated from input controls.
SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input (for 250 pg – 100 ng input) (Takara Bio) with RiboZero depletion.

treatment_protocol: Spermatogenesis was chemically synchronized and undifferentiated spermatogonia were sorted as previously described (Romer et al., 2018 Developmental Biology). Specifically, on postnatal days (PND) 2-8, ROSA26tdTomato/+; Ddx4Cre/+ male mice were injected daily subcutaneously with WIN 18,446 (Santa Cruz Biotechnology) at 0.1mg/gram body weight. On PND9, mice were euthanized to obtain testes enriched for undifferentiated spermatogonia, and testes were flash frozen. Enrichment of undifferentiated spermatogonia was verified via histological analysis of a testis biopsy.

value: Rpl22+/+; Ddx4Cre/+

tag: animal

tag: rna sample type

value: input

tag: ip type

tag: antibody


title: MM291.3.control.IP-seq.rep1

status: Public on Jul 22 2020

type: SRA

city: Cincinnati

first: Maria

middle: M.

last: Mikedis

state: OH

address: 240 Albert Sabin Way

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: undifferentiated spermatogonia-enriched postnatal testes

tag: strain

tag: genotype

value: IP

value: negative control for antibody

value: anti-HA (BioLegend #901513; previously Covance #MMS-101R; RRID:AB_2565335)

tag: tissue

value: spermatogonia


title: MM291.6.control.IP-seq.rep2


title: MM291.1.Ribotag.IP-seq.rep1

value: Rpl22HA/+; Ddx4Cre/+

value: RiboTag IP


title: MM291.6.control.input.RNA-seq.rep2


title: MM291.7.Ribotag.input.RNA-seq.rep3


title: MM291.3.control.input.RNA-seq.rep1


title: MM291.4.Ribotag.input.RNA-seq.rep2


title: DAZL iCLIP rep3

data_processing:
Base calls were performed by the instrument control software and further processed using the Offline Base Caller (Illumina) v.1.9.4. Quality control/assessment was performed using fastqc, fastqscreen and custom scripts.
Reads were quality-trimmed with cutadapt v.1.8 using the following options: -q 20 -m 24
On their 5' end, the reads contain (from 5' to 3') a 3 nt random barcode, followed by a 4 nt sample-specific barcode, followed by a 2 nt random barcode. Sample-specific barcodes are as follows: MM218_1_DAZL_CLIP, TTAG; MM218_2_IgG_CLIP, AATG; MM222_1_1_DAZL_CLIP, GGTT; MM222_1_2_IgG_CLIP, CAAT; MM222_2_1_DAZL_CLIP, AATA; MM222_2_2_IgG_CLIP, GGTC.
PCR duplicates were collapsed using the fastx_collapser tool from FASTX-Toolkit v.0.0.14
The 5'-most 3 nt random barcode was removed from the 5' end of each read with the fastx_trimmer tool from FASTX-Toolkit v.0.0.14 using the following options: -f 4
Reads were demultiplexed using the fastx_barcode_splitter.pl tool from FASTX-Toolkit v.0.0.14 using the following options: --bol
The sample-specific barcodes and remaining random barcode were removed from the 5' end of each read with the fastx_trimmer tool from FASTX-Toolkit v.0.0.14 using the following options: -f 7
Reads were mapped using STAR v.2.5.4b with 30nt overhang index and the following options: --outFilterMultimapNmax 1 --alignEndsType Extend5pOfRead1 --outFilterMismatchNmax 2 --runThreadN 8 --outSAMattributes None
Mapped reads were converted to the crosslinked site (defined as the nucleotide immediately 5' to the 5' end of the mapped read) using custom script. These crosslinked sites were deposited as bed files after bam-to-bed conversion using the bamtobed command from bedtools v.2.26.0 with default options.
Peaks were called using ASPeak v.2.0.0 using default parameters, the IgG libraries as controls, 2 RNA-seq libraries from sorted undifferentiated spermatogonia as background RNA-seq, and the following options: -gapnumber 0
The input bed files used for running ASPeak were generated from the UCSC RefSeq transcript annotations and Retrogenes V6 annotations downloaded from the UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with the following fields: Chr Strand Interval Interval_Length Tag_Count Maximum_Height Span_Size Start End RPKM Weighted_Center p-Value FDR; note: IgG files do not contain FDR field

extract_protocol:
1.5 testes from a single animal were used per iCLIP library. Tubules were dissociated in cold PBS, UV irradiated on ice at 200 mJ/cm2 at 254 nm to crosslink in vivo protein:RNA interactions, and flash frozen.  Later, samples were lysed and immunoprecipitated via anti-DAZL or IgG isotype control to extract interacting RNAs. RNA was extracted from isolated protein:RNA complexes as previously described  (Huppertz et al., 2014 Methods).
iCLIP libraries were prepared as previously described (Huppertz et al., 2014 Methods).

treatment_protocol: Spermatogenesis was chemically synchronized as previously described (Romer et al., 2018 Developmental Biology). Specifically, on postnatal days (PND) 2-8, male mice were injected daily subcutaneously with WIN 18,446 (Santa Cruz Biotechnology) at 0.1mg/gram body weight. On PND9, mice were euthanized to obtain testes enriched for undifferentiated spermatogonia. Enrichment of undifferentiated spermatogonia was verified via histological analysis of a testis biopsy.

value: wild type

value: anti-DAZL (Abcam ab34139; RRID:AB_731849)

tag: library prep batch


title: IgG iCLIP rep3

value: IgG isotype control (Santa Cruz Biotechnologies sc-2027; RRID:AB_737197


title: MM291.1.Ribotag.input.RNA-seq.rep1


title: IgG iCLIP rep2


title: Dazl ctrl1

data_processing:
Base calls were performed by the instrument control software and further processed using the Offline Base Caller (Illumina) v.1.9.4. Quality control/assessment was performed using fastqc, fastqscreen and custom scripts.
Reads were quality-trimmed with cutadapt v.1.8 using the following options: -q 20 -m 24
To quantify transcript abundance, expression levels of all transcripts in the UCSC RefSeq (refGene) transcript annotations and Retrogenes V6 annotations from the GRC38 (mm10) assembly were estimated using kallisto v.0.44.0 (Bray et al., 2016) with sequence-bias correction using a 31 k-mer index.
Quantified transcripts were filtered for refGene transcripts (excluding rRNA), and TPM values were renormalized to transcript-per-million units. These values are in *RNAseq_abundance.tsv files. See annotation file mm10_GRCm38_refGene_no.rRNA_annotation.file.txt
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with the following fields: target_id length, eff_length, est_counts, tpm

source_name: sorted Pou5f1:EGFP-positive spermatogonia from control adult male

extract_protocol:
Total RNA was isolated from freshly sorted cells using TRIzol LS Reagent (Theromo Fisher Scientific) and chloroform following the manufacturer’s protocol, precipitated via isopropanol with GlycoBlue (Thermo Fisher Scientific), and resuspended in RNase-free water.
SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) with poly(A) selection

treatment_protocol: Testes were dissected from control and Dazl conditional knockout animals carrying the fluorescent reporter Pou5f1:EGFP and washed with phosphate-buffered saline (PBS). Single cell suspensions were made by removing the tunica albuginea and digesting the tissue with trypsin and 20 μg/ml DNase (Sigma, St Louis MO) in PBS. An equal volume of cold 20% fetal bovine serum (FBS) in PBS was used to terminate digestion. Cells were washed and centrifuged at 500 g and 4˚C and resuspended in 1% v/v FBS in cold PBS with DNase. The suspension was passed through a 35 μm nylon mesh filter (Corning). Single cells were gated based on forward and side light scatter. Spermatogonia were sorted based on Pou5f1:EGFP fluorescence using a FACSAria II (BD Biosciences) and collected in PBS.

value: Dazl2L/+; Ddx4Cre/+; Pou5f1:EGFP/+

tag: age

value: 6 months

tag: facs batch


title: EoE-10.whole blood.not EoE

status: Public on Aug 22 2020

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description:
EREFS 0
lib29303_CCFMDANXX

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned using the TopHat aligner (v1.4.1)28 with the GRCh38 reference genome and gene annotations from ensembl release 77.
Gene counts were generated using HTSeq-count (v0.4.1)29. Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Genome_build: GRCh38 reference genome and gene annotations from ensembl release 77
Supplementary_files_format_and_content: Processed data (counts) are in .csv format. Each row is a gene, each column is a sample.

organism: Homo sapiens

source_name: whole blood

growth_protocol: Biopsies were collected in RNAlater (Thermo Fisher Scientific) and paired blood samples were collected in Tempus Blood RNA Tubes (Thermo Fisher) and stored at -80◦C until use.

extract_protocol:
Total RNA was isolated from adult esophageal biopsies (1-2 per subject) by homogenizing tissue in QIAzol lysis reagent (Qiagen) followed by column purification using the miRNeasy kit with on column DNA digestion (Qiagen). Whole blood RNA was extracted using MagMax for Stabilized Blood Tubes RNA Isolation Kit, followed by globin reduction using GlobinClear Human (Thermo Fisher).
Sequencing libraries were constructed from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and NexteraXT DNA sample preparation kit (Illumina) to generate Illumina- compatible barcoded libraries.
Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.

tag: study group

value: not EoE

tag: eosinophils per high-powered field


title: DAZL iCLIP rep1


title: Dazl cKO1

source_name: sorted Pou5f1:EGFP-positive spermatogonia from Dazl conditional knockout adult male

value: Dazl2L/-; Ddx4Cre/+; Pou5f1:EGFP/+


title: MM291.9.control.IP-seq.rep3


title: DAZL iCLIP rep2


title: Dazl cKO3

value: 8 months


title: RNA-seq rep1

data_processing:
Base calls were performed by the instrument control software and further processed using the Offline Base Caller (Illumina) v.1.9.4. Quality control/assessment was performed using fastqc, fastqscreen and custom scripts.
Reads were quality-trimmed with cutadapt v.1.8 using the following options: -q 20 -m 24
Libraries were mapped to the mouse genome (mm10) via STAR v.2.5.4b (Dobin et al., 2013) (options: --outFilterMultimapNmax 1 --alignEndsType Extend5pOfRead1 --outFilterMismatchNmax 2 --outSAMattributes None). All other parameters were set to default. Full mapped reads were then used as background RNA-seq for calling DAZL iCLIP peaks via ASPeak v.2.0.0
To quantify transcript abundance, expression levels of all transcripts in the UCSC RefSeq (refGene) transcript annotations and Retrogenes V6 annotations from the GRC38 (mm10) assembly were estimated using kallisto v.0.44.0 (Bray et al., 2016) with sequence-bias correction using a 31 k-mer index. These values are in *RNAseq_abundance.tsv files. See annotation file mm10_GRCm38_refGene_retrogenes_annotation.file.txt
For the comparison of biological replicates and iCLIP analysis, rRNA transcripts were removed, and TPM values were renormalized to transcript-per-million units. TPM values were summed to the gene level, with protein-coding transcripts and non-coding transcripts from the same gene summed separately. These values are in *RNAseq_no.rRNA_abundance.tsv files. See annotation file mm10_GRCm38_refGene_retrogenes_no.rRNA_annotation.file.txt
For comparison to other publically available datasets, quantified transcripts were filtered for refGene transcripts (excluding rRNA), and TPM values were renormalized to transcript-per-million units. These values are in *RNAseq_refGene.no.rRNA_abundance.tsv files. See annotation file mm10_GRCm38_refGene_no.rRNA_annotation.file.txt
For translational profiling via RIboTag IP-seq, quantified transcripts were filtered for protein-coding mRNAs only, and TPM values were renormalized to transcript-per-million units. These values are in *RNAseq_coding.mRNA.only_abundance.tsv files. See annotation file mm10_GRCm38_refGene_coding.mRNA.only_annotation.file.txt
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with the following fields: target_id length, eff_length, est_counts, tpm

extract_protocol:
Undifferentiated spermatogonia from a single chemically synchronized postnatal animal were used as one biological replicate; two biological replicates were carried out in total. RNA was extracted using Trizol LS (Thermo Fisher Scientific) and chloroform following the manufacturer’s protocol, precipitated via isopropanol with GlycoBlue (Thermo Fisher Scientific), and resuspended in RNase-free water.
TruSeq Stranded mRNA kit (Illumina) with RiboZero depletion

treatment_protocol: Spermatogenesis was chemically synchronized and undifferentiated spermatogonia were sorted as previously described (Romer et al., 2018 Developmental Biology). Specifically, on postnatal days (PND) 2-8, ROSA26tdTomato/+; Ddx4Cre/+ male mice were injected daily subcutaneously with WIN 18,446 (Santa Cruz Biotechnology) at 0.1mg/gram body weight. On PND9, mice were euthanized to obtain testes enriched for undifferentiated spermatogonia.  Testes were \biopsied for histological analysis to verify enrichment of undifferentiated spermatogonia. For the remaining testis pair, the tunica albuginea was removed, and the tissue was dissociated into a single-cell suspension using collagenase and trypsin as previously described (Romer et al., 2018) with one modification: TURBO DNAse was used in place of DNAse I. DAPI was added to cells prior to cell sorting on a FACSAria II (BD Biosciences). Single cells were gated based on forward and side light scatter, and high DAPI-positive (dead) cells were excluded. The undifferentiated spermatogonia were isolated based on tdTomato fluorescence, whose expression was activated by the germline-specific Ddx4Cre, and sorted in 1% BSA in PBS. Cells were transferred into and stored at  -80˚C in Trizol LS (Thermo Fisher Scientific).

value: ROSA26tdTomato/+; Ddx4Cre/+


title: Dazl cKO2


title: IgG iCLIP rep1


title: Aged USC rep 2 [lane5784_GAGTTAGC_A45_0d]

status: Public on Mar 02 2020

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

description:
processed data file: Raw_counts.txt
lane5784_GAGTTAGC_A45_0d_L008

data_processing:
For MeDIP-seq, Fastq data were trimmed for adaptors using Trim Galore! v0.4.4, before mapping to the Mus musculus GRCm38 genome assembly using Bowtie v2.3.2. Differentially methylated regions (DMRs) were identified by the MEDIPS package in R, using a window size of 200bp and Bonferroni p-value cut-off of 0.01. For RNA-seq, Raw FastQ data were trimmed with Trim Galore (v0.3.8, default parameters;  www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to the Mus musculus GRCm38 genome assembly using TopHat v2.0.12. Raw counts for DESeq2 analysis were generated at mRNA level using SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: For MeDIP-seq, csv file detailing location of DMR or CpG island, and RPKM quantification of relevant samples. For RNA-seq, csv file containing raw counts

source_name: Aged USC

growth_protocol: C57BL/6Babr mice were used throughout this study. Virgin females were caged in groups up to 5 until they had reached the desired age as indicated. All animal experiments were conducted in full compliance with UK Home Office regulations and with approval of the local animal welfare committee at The Babraham Institute, and with the relevant project and personal licences in place. Timed matings were set up with standard C57BL/6Babr stud males of 8-16 weeks of age, counting the morning of the vaginal plug as E0.5.

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA Mini kit (Qiagen 80204) followed by Dnase treatment using the TURBO DNA-free kit (Life Technologies AM1907)
mRNA was isolated from total DNA-free RNA (350ng) using the Dynabeads mRNA purification kit (Life Technologies 61006). Indexed, strand specific libraries were prepared using the Agilent SureSelect Strand specific Library Preparation kit (Agilent, G9691A) according to the manufacturer's instructions. Libraries were quantified/assessed using both the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent). Indexed libraries were pooled and sequenced with a 100bp single-end protocol on an Illumina HiSeq2500 sequencer.

tag: age (weeks)

tag: developmental stage

value: Uterine stromal cell (USC)


title: MM291.7.Ribotag.IP-seq.rep3


title: Aged USC rep 3 [lane5784_GATGAATC_A43_0d]

description:
processed data file: Raw_counts.txt
lane5784_GATGAATC_A43_0d_L008


title: MM291.4.Ribotag.IP-seq.rep2


title: Aged USC rep 1 [lane5784_ATTGGCTC_A42_0d]

description:
processed data file: Raw_counts.txt
lane5784_ATTGGCTC_A42_0d_L008


title: Young USC rep 1 [lane5784_AACGTGAT_Y45_0d]

description:
processed data file: Raw_counts.txt
lane5784_AACGTGAT_Y45_0d_L008

source_name: Young USC


title: Young USC rep 3 [lane5784_GACAGTGC_Y43_0d]

description:
processed data file: Raw_counts.txt
lane5784_GACAGTGC_Y43_0d_L008


title: Aged uterus rep4

description:
processed data file: MeDIPs_windows.txt
lane6311_TGGTTGTT_V8_1_L001

library_source: genomic

molecule: genomic DNA

source_name: Aged uterus

extract_protocol:
Genomic DNA was extracted from snap frozen tissue using Qiagen Allprep DNA/RNA mini kit (Qiagen, 80204), according to the manufacturers instructions.
DNA libraries were generated using the NEBNext DNA library prep master mix set for Illumina (New England BioLabs E6040L), according to the manufacturerâ€™s instructions till the end repair stage, using 1.5Âµg of sonicated DNA. Unamplified DNA libraries were subjected to methylated DNA immunoprecipitation (MeDIP) to isolate fragments of methylated DNA. Briefly, library DNA was denatured at 99oC before incubation with anti-5mC antibody (Eurogentec BI-MECY-0100) for 2 hours at 4oC, followed by a further 2 hours with pre-blocked Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112-01D). Methylated DNA was purified using the MinElute PCR purification kit (Qiagen 28104), amplified using the NEBNext DNA library prep master mix set, and size-selected for 200-800bp fragments using AMPure XP beads (Beckman Coulter A63881). Indexed libraries were pooled and sequenced on an Illumina HiSeq2500, using a 50bp paired-end protocol

value: Uterus


title: Aged uterus rep5

description:
processed data file: MeDIPs_windows.txt
lane6311_TGTACCTT_V9_1_L001


title: Aged uterus rep1

description:
processed data file: MeDIPs_windows.txt
lane6311_ATCACGTT_V1_1_L001


title: Aged uterus rep2

description:
processed data file: MeDIPs_windows.txt
lane6311_CGATGTTT_V2_1_L001


title: Dazl ctrl3

value: Dazl2L/-; Ddx4+/+; Pou5f1:EGFP/+


title: Dazl ctrl2


title: Young uterus rep1

description:
processed data file: MeDIPs_windows.txt
lane6311_ACAGTGGT_V4_1_L001

source_name: Young uterus


title: Young uterus rep2

description:
processed data file: MeDIPs_windows.txt
lane6311_TGCATAGT_V5_1_L001


title: Aged abnormal rep5

description:
processed data file: MeDIPs_windows.txt
lane6311_TTCTGTGT_A19_2D_L001

source_name: Aged abnormal_decidua

value: Decidua


title: Aged abnormal rep4

description:
processed data file: MeDIPs_windows.txt
lane6311_TTGGAGGT_A22_2D_L001


title: Aged abnormal rep3

description:
processed data file: MeDIPs_windows.txt
lane6311_TAGCTTGT_A28_8D_L001


title: Aged abnormal rep2

description:
processed data file: MeDIPs_windows.txt
lane6311_ACTTGATG_A26_2D_L001


title: Aged normal rep5

description:
processed data file: MeDIPs_windows.txt
lane6311_TCTGCTGT_A19_5D_L001

source_name: Aged normal_decidua


title: Aged normal rep3

description:
processed data file: MeDIPs_windows.txt
lane6311_GATCAGCG_A28_3D_L001


title: Aged normal rep2

description:
processed data file: MeDIPs_windows.txt
lane6311_CAGATCTG_A26_1D_L001


title: Aged normal rep1

description:
processed data file: MeDIPs_windows.txt
lane6311_TGACCACT_A23_1D_L001


title: Young  USC rep 2 [lane5784_GAATCTGA_Y44_0d]

description:
processed data file: Raw_counts.txt
lane5784_GAATCTGA_Y44_0d_L008


title: Young rep3

description:
processed data file: MeDIPs_windows.txt
lane6311_TCCGTCTT_C5_1D_L001


title: Young rep2

description:
processed data file: MeDIPs_windows.txt
lane6311_TAAGCGTT_C4_2D_L001


title: Young rep1

description:
processed data file: MeDIPs_windows.txt
lane6311_TCTCGGTT_C3_2D_L001


title: Input_CytT_MN_rep2

status: Public on Jul 31 2019

city: Dallas

first: Youn

last: Kwak

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT-Southwestern Medical Center

data_processing:
The ChIP-seq reads were aligned to the hg19 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 75 for R1 for single-end data.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: trophoblast primary culture

growth_protocol: Trophoblasts in primary culture were maintained DMEM/F12 media with 10% FBS and 1% antibiotic and antimycotic.

extract_protocol:
Trophoblasts were crosslinked with 1% formaldehyd and then either treated with Mnase or sheared to 200-500 bp by ultrasonication. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina Tru-seq protocol.

treatment_protocol: Trophoblasts were isolated from human mid-gestation placenta by treatment of DNAse I and trypsin followed by Percoll gradient. Cells were harvested either before (0h) and 18h after culture.

value: Mid-gestation placenta

tag: chip antibody

tag: shearing

value: Mnase

tag: cell culture

value: trophoblast primary culture

tag: treatment

value: Cytotrophoblast (0h)


title: H3K27me3_CytT_MN_rep2

value: H3K27me3 (CS9733, Cell Signaling)


title: Aged uterus rep3

description:
processed data file: MeDIPs_windows.txt
lane6311_TTAGGCAT_V3_1_L001


title: MM247_1_DAZL_CLIP

status: Public on Nov 22 2019

data_processing:
Base calls were performed by the instrument control software and further processed using the Offline Base Caller (Illumina) v.1.9.4. Quality control/assessment was performed using fastqc, fastqscreen and custom scripts, available on GitHub (https://github.com/mmikedis).
Reads were quality-trimmed with cutadapt v.1.8 using the following options: -q 20 -m 24
On their 5' end, the reads contain (from 5' to 3') a 3 nt random barcode, followed by a 4 nt sample-specific barcode, followed by a 2 nt random barcode. Sample-specific barcodes are as follows: MM247_1_DAZL_CLIP, TTAG; MM247_2_IgG_CLIP, AATG; MM253_1_1_DAZL_CLIP, GGTT; MM253_1_2_IgG_CLIP, CAAT; MM253_2_1_DAZL_CLIP, AATA; MM253_2_2_IgG_CLIP, GGTC.
PCR duplicates were collapsed using the fastx_collapser tool from FASTX-Toolkit v.0.0.14
The 5'-most 3 nt random barcode was removed from the 5' end of each read with the fastx_trimmer tool from FASTX-Toolkit v.0.0.14 using the following options: -f 4
Reads were demultiplexed using the fastx_barcode_splitter.pl tool from FASTX-Toolkit v.0.0.14 using the following options: --bol
The sample-specific barcodes and remaining random barcode were removed from the 5' end of each read with the fastx_trimmer tool from FASTX-Toolkit v.0.0.14 using the following options: -f 7
Reads were mapped using STAR v.2.5.4b with 30nt overhang index and the following options: --outFilterMultimapNmax 1 --alignEndsType Extend5pOfRead1 --outFilterMismatchNmax 2 --runThreadN 8 --outSAMattributes None --outReadsUnmapped Fastx
Mapped reads were converted to the crosslinked site (defined as the nucleotide immediately 5' to the 5' end of the mapped read) using custom script. These crosslinked sites were deposited as bed files after bam-to-bed conversion using the bamtobed command from bedtools v.2.26.0 with default options.
Peaks were called using the bam files of crosslinked sites for each library prep batch with ASPeak v.2.0.0 using default parameters, the IgG libraries as controls, and the following options: -gapnumber 0 -nornaseq
The input bed files used for running ASPeak were generated from the UCSC RefSeq transcript annotations and Retrogenes V6 annotations downloaded from the UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of ASPeak output with the following fields: Chr Strand Interval Interval_Length Tag_Count Maximum_Height Span_Size Start End RPKM Weighted_Center p-Value FDR; note: IgG files do not contain FDR field

source_name: leptotene-enriched postnatal testes

extract_protocol:
1.5 testes from a single animal were used per iCLIP library. Tubules were dissociated in cold PBS, UV irradiated 3x on ice at 200 mJ/cm2 at 254 nm to crosslink in vivo protein:RNA interactions, and flash frozen. Later, samples were lysed and immunoprecipitated via anti-DAZL (Abcam ab34139) or IgG isotype control (Abcam ab27478) to extract protein:RNA complexes. RNA was extracted from isolated protein:RNA complexes as previously described (Huppertz et al., 2014 Methods).
iCLIP libraries were prepared as previously described (Huppertz et al., 2014 Methods).

treatment_protocol: Spermatogenesis was chemically synchronized as prevoiusly described (Romer et al., 2018 Developmental Biology). Specifically, on postnatal days (PND) 2-8, male mice were injected daily subcutaneously with WIN 18,446 (Santa Cruz Biotechnology) at 0.1mg/gram body weight. On PND9, the mice were injected subcutaneously once with retinoic acid (RA; MilliporeSigma) at 0.0125 mg/gram body weight. Mice were euthanized 8.0 days after the RA injection to obtain testes enriched for leptotene spermatocytes. Enrichment of leptotene spermatocytes was verified via histological analysis of a testis biopsy.

value: leptotene-enriched postnatal testes

value: wild type

tag: Sex

value: male


title: MM253_1_1_DAZL_CLIP


title: MM247_2_IgG_CLIP


title: MM253_2_1_DAZL_CLIP


title: MM253_2_2_IgG_CLIP


title: Young uterus rep3

description:
processed data file: MeDIPs_windows.txt
lane6311_CTTGTACT_V6_1_L001


title: MM253_1_2_IgG_CLIP


title: H3K27me3_CytT_MN_rep1


title: H3K4me3_CytT_MN_rep2

value: H3K4me3 (39159, Active Motif)


title: H3K4me3_CytT_MN_rep1


title: Aged normal rep4

description:
processed data file: MeDIPs_windows.txt
lane6311_TCGAGCGT_A22_3D_L001


title: buccal swab 532 [201557550051_R02C01]

status: Public on Mar 26 2019

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: human buccal swab

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Control Software using standard recommended Illumina scanner setting

data_processing: Signal intensities files were extracted using the minfi Bioconductor package. Normalization was performed using the Functional Normalization function implemented in minfi

label: Cy5 and Cy3

source_name: genomic DNA from buccal swab

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from buccal swab samples, collected near term-equivalent age, using the Isohelix Buccal Swab system (Boca Scientific), quantified using the Quibit Fluorometer (Thermo Fisher, Waltham, MA, USA) and aliquoted into a standardized concentration for subsequent analyses

tag: subject status

value: infants born less than 30 weeks postmenstrual age (PMA)

tag: gender

value: Female

tag: nnns profile

tag: site

value: LAB

tag: bga

tag: outborn

value: No

tag: plate

tag: sbi

tag: inf

tag: rop

tag: class

value: Typical

tag: baycogcb

tag: bayccogcb

tag: rid

tag: rfid

tag: epi


title: buccal swab 536 [201557550051_R06C01]

description: human buccal swab

value: Male

value: Physical Risk


title: buccal swab 533 [201557550051_R03C01]

description: human buccal swab


title: buccal swab 534 [201557550051_R04C01]

description: human buccal swab

value: Yes


title: buccal swab 531 [201557550051_R01C01]

description: human buccal swab


title: buccal swab 529 [201557550012_R03C01]

description: human buccal swab


title: buccal swab 530 [201557550012_R04C01]

description: human buccal swab


title: buccal swab 528 [201557550038_R02C01]

description: human buccal swab


title: buccal swab 527 [201533530034_R08C01]

description: human buccal swab


title: Input_CytT_MN_rep1

tag: tissue

value: Mid-gestation placenta

tag: chip antibody

tag: shearing

tag: cell culture

tag: treatment


title: buccal swab 526 [201557550043_R08C01]

description: human buccal swab

tag: subject status

tag: gender

tag: nnns profile

tag: site

tag: bga


title: buccal swab 525 [201557550043_R07C01]

description: human buccal swab

tag: outborn

tag: plate

tag: sbi

tag: inf

tag: rop


title: buccal swab 524 [201533530034_R07C01]

description: human buccal swab

tag: class

tag: baycogcb

tag: bayccogcb

tag: rid

tag: rfid


title: buccal swab 523 [201557550043_R06C01]

description: human buccal swab

tag: epi


title: buccal swab 521 [201533530034_R05C01]

description: human buccal swab


title: buccal swab 519 [201533530034_R03C01]

description: human buccal swab


title: buccal swab 518 [201533530034_R02C01]

description: human buccal swab


title: buccal swab 535 [201557550051_R05C01]

description: human buccal swab


title: buccal swab 516 [201533530023_R03C01]

description: human buccal swab


title: buccal swab 517 [201533530034_R01C01]

description: human buccal swab


title: buccal swab 514 [201533530033_R06C01]

description: human buccal swab


title: buccal swab 515 [201533530033_R07C01]

description: human buccal swab


title: buccal swab 511 [201533530033_R02C01]

description: human buccal swab


title: buccal swab 512 [201533530033_R03C01]

description: human buccal swab


title: buccal swab 513 [201533530033_R05C01]

description: human buccal swab


title: buccal swab 509 [201533530032_R08C01]

description: human buccal swab


title: buccal swab 508 [201533530032_R05C01]

description: human buccal swab


title: buccal swab 504 [201533530023_R07C01]

description: human buccal swab


title: buccal swab 503 [201533530023_R06C01]

description: human buccal swab


title: buccal swab 506 [201533530032_R03C01]

description: human buccal swab

value: Psych Risk


title: buccal swab 501 [201557530011_R07C01]

description: human buccal swab


title: buccal swab 502 [201557530028_R01C01]

description: human buccal swab


title: buccal swab 507 [201533530032_R04C01]

description: human buccal swab


title: buccal swab 496 [201557530011_R01C01]

description: human buccal swab


title: buccal swab 500 [201557530011_R06C01]

description: human buccal swab


title: buccal swab 522 [201533530034_R06C01]

description: human buccal swab


title: buccal swab 495 [201533530023_R01C01]

description: human buccal swab


title: buccal swab 499 [201557530011_R05C01]

description: human buccal swab


title: buccal swab 498 [201557530011_R04C01]

description: human buccal swab


title: buccal swab 497 [201557530011_R03C01]

description: human buccal swab


title: buccal swab 494 [201557560046_R07C01]

description: human buccal swab


title: buccal swab 520 [201533530034_R04C01]

description: human buccal swab


title: buccal swab 492 [201557560046_R04C01]

description: human buccal swab


title: buccal swab 493 [201557560046_R06C01]

description: human buccal swab


title: buccal swab 510 [201533530033_R01C01]

description: human buccal swab


title: buccal swab 486 [201533530048_R01C01]

description: human buccal swab


title: buccal swab 487 [201557560042_R05C01]

description: human buccal swab


title: buccal swab 505 [201533530032_R01C01]

description: human buccal swab


title: buccal swab 485 [201557560042_R04C01]

description: human buccal swab


title: buccal swab 488 [201557560042_R06C01]

description: human buccal swab


title: buccal swab 484 [201557560042_R03C01]

description: human buccal swab


title: buccal swab 490 [201557560042_R08C01]

description: human buccal swab


title: buccal swab 483 [201557560042_R02C01]

description: human buccal swab


title: buccal swab 480 [201557560021_R07C01]

description: human buccal swab


title: buccal swab 482 [201557560042_R01C01]

description: human buccal swab


title: buccal swab 479 [201557560021_R05C01]

description: human buccal swab


title: buccal swab 476 [201557560021_R01C01]

description: human buccal swab


title: buccal swab 475 [201557560012_R08C01]

description: human buccal swab


title: buccal swab 481 [201557560021_R08C01]

description: human buccal swab


title: buccal swab 472 [201557560012_R02C01]

description: human buccal swab


title: buccal swab 474 [201557560012_R04C01]

description: human buccal swab


title: buccal swab 477 [201557560021_R03C01]

description: human buccal swab


title: buccal swab 471 [201557560012_R01C01]

description: human buccal swab


title: buccal swab 470 [201557530054_R07C01]

description: human buccal swab


title: buccal swab 467 [201557530054_R04C01]

description: human buccal swab


title: buccal swab 468 [201557530054_R05C01]

description: human buccal swab


title: buccal swab 466 [201557550043_R05C01]

description: human buccal swab

value: WFU


title: buccal swab 491 [201557560046_R02C01]

description: human buccal swab


title: buccal swab 489 [201557560042_R07C01]

description: human buccal swab


title: buccal swab 469 [201557530054_R06C01]

description: human buccal swab


title: buccal swab 473 [201557560012_R03C01]

description: human buccal swab


title: buccal swab 465 [201557550043_R04C01]

description: human buccal swab


title: buccal swab 464 [201557550015_R06C01]

description: human buccal swab


title: buccal swab 463 [201557550015_R07C01]

description: human buccal swab


title: buccal swab 462 [201557550015_R05C01]

description: human buccal swab


title: buccal swab 460 [201557550015_R04C01]

description: human buccal swab


title: buccal swab 461 [201557550043_R01C01]

description: human buccal swab


title: buccal swab 478 [201557560021_R04C01]

description: human buccal swab


title: buccal swab 458 [201557550015_R08C01]

description: human buccal swab


title: buccal swab 456 [201557550015_R03C01]

description: human buccal swab


title: buccal swab 455 [201557530054_R03C01]

description: human buccal swab


title: buccal swab 457 [201557550015_R01C01]

description: human buccal swab


title: buccal swab 452 [201557530028_R08C01]

description: human buccal swab


title: buccal swab 459 [201557550015_R02C01]

description: human buccal swab


title: buccal swab 454 [201557530054_R02C01]

description: human buccal swab


title: buccal swab 453 [201557530054_R01C01]

description: human buccal swab


title: buccal swab 451 [201557530028_R07C01]

description: human buccal swab


title: buccal swab 444 [201557530010_R06C01]

description: human buccal swab


title: buccal swab 448 [201557530028_R05C01]

description: human buccal swab


title: buccal swab 447 [201557530028_R04C01]

description: human buccal swab


title: buccal swab 446 [201557530010_R08C01]

description: human buccal swab


title: buccal swab 449 [201557530028_R06C01]

description: human buccal swab


title: buccal swab 445 [201557530010_R07C01]

description: human buccal swab


title: buccal swab 442 [201557530010_R03C01]

description: human buccal swab


title: buccal swab 440 [201557530010_R01C01]

description: human buccal swab


title: buccal swab 441 [201557530010_R02C01]

description: human buccal swab


title: buccal swab 439 [201533530056_R08C01]

description: human buccal swab


title: buccal swab 438 [201533530056_R07C01]

description: human buccal swab


title: buccal swab 437 [201533530056_R06C01]

description: human buccal swab


title: buccal swab 436 [201533530056_R05C01]

description: human buccal swab


title: buccal swab 434 [201533530056_R03C01]

description: human buccal swab


title: buccal swab 433 [201533530056_R02C01]

description: human buccal swab


title: buccal swab 432 [201533530056_R01C01]

description: human buccal swab


title: buccal swab 431 [201533530048_R07C01]

description: human buccal swab


title: buccal swab 428 [201533530048_R04C01]

description: human buccal swab


title: buccal swab 429 [201533530048_R05C01]

description: human buccal swab


title: buccal swab 427 [201533530048_R03C01]

description: human buccal swab


title: buccal swab 430 [201533530048_R06C01]

description: human buccal swab


title: buccal swab 450 [201557550014_R08C01]

description: human buccal swab


title: buccal swab 424 [201557550049_R08C01]

description: human buccal swab


title: buccal swab 426 [201533530048_R02C01]

description: human buccal swab


title: buccal swab 423 [201557550049_R07C01]

description: human buccal swab


title: buccal swab 443 [201557530010_R04C01]

description: human buccal swab


title: buccal swab 421 [201557550049_R03C01]

description: human buccal swab


title: buccal swab 420 [201557550049_R02C01]

description: human buccal swab


title: buccal swab 417 [201557550040_R07C01]

description: human buccal swab


title: buccal swab 419 [201557550049_R01C01]

description: human buccal swab


title: buccal swab 416 [201557550040_R06C01]

description: human buccal swab


title: buccal swab 415 [201557550040_R05C01]

description: human buccal swab


title: buccal swab 414 [201557550040_R04C01]

description: human buccal swab


title: buccal swab 413 [201557550040_R03C01]

description: human buccal swab


title: buccal swab 435 [201533530056_R04C01]

description: human buccal swab


title: buccal swab 412 [201557550040_R02C01]

description: human buccal swab


title: buccal swab 411 [201557550040_R01C01]

description: human buccal swab


title: buccal swab 418 [201557550040_R08C01]

description: human buccal swab


title: buccal swab 409 [201557550039_R08C01]

description: human buccal swab


title: buccal swab 410 [201557550018_R03C01]

description: human buccal swab


title: buccal swab 408 [201557550039_R07C01]

description: human buccal swab


title: buccal swab 407 [201557550039_R06C01]

description: human buccal swab


title: buccal swab 406 [201557550039_R05C01]

description: human buccal swab


title: buccal swab 422 [201557550049_R05C01]

description: human buccal swab


title: buccal swab 405 [201557550039_R04C01]

description: human buccal swab


title: buccal swab 404 [201557550018_R02C01]

description: human buccal swab


title: buccal swab 425 [201557560030_R01C01]

description: human buccal swab


title: buccal swab 403 [201533530025_R08C01]

description: human buccal swab


title: buccal swab 402 [201557560031_R05C01]

description: human buccal swab


title: buccal swab 401 [201557560031_R04C01]

description: human buccal swab


title: buccal swab 400 [201557560031_R03C01]

description: human buccal swab


title: buccal swab 399 [201533530025_R06C01]

description: human buccal swab


title: buccal swab 398 [201533530025_R05C01]

description: human buccal swab


title: buccal swab 396 [201533530025_R04C01]

description: human buccal swab


title: buccal swab 397 [201557560031_R02C01]

description: human buccal swab


title: buccal swab 393 [201557550044_R01C01]

description: human buccal swab


title: buccal swab 395 [201557550044_R03C01]

description: human buccal swab


title: buccal swab 390 [201557550041_R05C01]

description: human buccal swab


title: buccal swab 392 [201533530025_R03C01]

description: human buccal swab


title: buccal swab 394 [201557550044_R02C01]

description: human buccal swab


title: buccal swab 389 [201557550041_R03C01]

description: human buccal swab


title: buccal swab 391 [201557550041_R07C01]

description: human buccal swab


title: buccal swab 386 [201557550023_R08C01]

description: human buccal swab


title: buccal swab 382 [201557560027_R07C01]

description: human buccal swab


title: buccal swab 381 [201557560027_R06C01]

description: human buccal swab


title: buccal swab 380 [201557560027_R05C01]

description: human buccal swab


title: buccal swab 387 [201557550041_R01C01]

description: human buccal swab


title: buccal swab 384 [201557560031_R01C01]

description: human buccal swab


title: buccal swab 379 [201557530008_R01C01]

description: human buccal swab


title: buccal swab 383 [201557560027_R08C01]

description: human buccal swab


title: buccal swab 385 [201557550023_R07C01]

description: human buccal swab


title: buccal swab 376 [201557560027_R02C01]

description: human buccal swab


title: buccal swab 377 [201557560027_R03C01]

description: human buccal swab


title: buccal swab 374 [201557560022_R08C01]

description: human buccal swab


title: buccal swab 375 [201557560027_R01C01]

description: human buccal swab


title: buccal swab 371 [201557560022_R05C01]

description: human buccal swab


title: buccal swab 378 [201557560027_R04C01]

description: human buccal swab


title: buccal swab 372 [201557560022_R06C01]

description: human buccal swab


title: buccal swab 373 [201557560022_R07C01]

description: human buccal swab


title: buccal swab 369 [201557560022_R03C01]

description: human buccal swab


title: buccal swab 388 [201557550041_R02C01]

description: human buccal swab


title: buccal swab 366 [201557550042_R08C01]

description: human buccal swab


title: buccal swab 363 [201557550042_R05C01]

description: human buccal swab


title: buccal swab 370 [201557560022_R04C01]

description: human buccal swab


title: buccal swab 365 [201557550042_R07C01]

description: human buccal swab


title: buccal swab 360 [201557550042_R04C01]

description: human buccal swab


title: buccal swab 362 [201557550031_R07C01]

description: human buccal swab


title: buccal swab 361 [201557550031_R01C01]

description: human buccal swab


title: buccal swab 358 [201557550031_R03C01]

description: human buccal swab


title: buccal swab 359 [201557550031_R04C01]

description: human buccal swab


title: buccal swab 355 [201557550042_R02C01]

description: human buccal swab


title: buccal swab 356 [201557550031_R05C01]

description: human buccal swab


title: buccal swab 352 [201533530025_R02C01]

description: human buccal swab

value: CMH


title: buccal swab 354 [201557550042_R01C01]

description: human buccal swab


title: buccal swab 351 [201533530013_R07C01]

description: human buccal swab


title: buccal swab 350 [201533530013_R06C01]

description: human buccal swab


title: buccal swab 353 [201557550031_R02C01]

description: human buccal swab


title: buccal swab 348 [201533530013_R04C01]

description: human buccal swab


title: buccal swab 346 [201533530013_R02C01]

description: human buccal swab


title: buccal swab 349 [201533530013_R05C01]

description: human buccal swab


title: buccal swab 368 [201557560022_R02C01]

description: human buccal swab


title: buccal swab 367 [201557560022_R01C01]

description: human buccal swab


title: buccal swab 342 [201557560060_R06C01]

description: human buccal swab


title: buccal swab 344 [201557560060_R08C01]

description: human buccal swab


title: buccal swab 347 [201533530013_R03C01]

description: human buccal swab


title: buccal swab 345 [201533530013_R01C01]

description: human buccal swab


title: buccal swab 340 [201557560060_R04C01]

description: human buccal swab


title: buccal swab 343 [201557560060_R07C01]

description: human buccal swab


title: buccal swab 341 [201557560060_R05C01]

description: human buccal swab


title: buccal swab 339 [201557560060_R03C01]

description: human buccal swab


title: buccal swab 338 [201557560060_R02C01]

description: human buccal swab


title: buccal swab 335 [201557560058_R07C01]

description: human buccal swab


title: buccal swab 336 [201557560058_R08C01]

description: human buccal swab


title: buccal swab 337 [201557560060_R01C01]

description: human buccal swab


title: buccal swab 334 [201557560058_R06C01]

description: human buccal swab


title: buccal swab 331 [201557560058_R03C01]

description: human buccal swab


title: buccal swab 332 [201557560058_R04C01]

description: human buccal swab


title: buccal swab 330 [201557560058_R02C01]

description: human buccal swab


title: buccal swab 329 [201557560058_R01C01]

description: human buccal swab


title: buccal swab 326 [201557560057_R06C01]

description: human buccal swab


title: buccal swab 328 [201557560057_R08C01]

description: human buccal swab


title: buccal swab 325 [201557560057_R04C01]

description: human buccal swab


title: buccal swab 327 [201557560057_R07C01]

description: human buccal swab


title: buccal swab 324 [201557560057_R03C01]

description: human buccal swab


title: buccal swab 323 [201557560057_R02C01]

description: human buccal swab


title: buccal swab 322 [201557560057_R01C01]

description: human buccal swab


title: buccal swab 321 [201557560030_R08C01]

description: human buccal swab


title: buccal swab 318 [201557560030_R04C01]

description: human buccal swab


title: buccal swab 319 [201557560030_R05C01]

description: human buccal swab


title: buccal swab 320 [201557560030_R06C01]

description: human buccal swab


title: buccal swab 316 [201557560030_R02C01]

description: human buccal swab


title: buccal swab 317 [201557560030_R03C01]

description: human buccal swab


title: buccal swab 315 [201557550039_R03C01]

description: human buccal swab


title: buccal swab 314 [201557550039_R02C01]

description: human buccal swab


title: buccal swab 313 [201557530013_R06C01]

description: human buccal swab


title: buccal swab 311 [201557530013_R05C01]

description: human buccal swab


title: buccal swab 312 [201557550039_R01C01]

description: human buccal swab


title: buccal swab 310 [201557530013_R04C01]

description: human buccal swab


title: buccal swab 333 [201557560058_R05C01]

description: human buccal swab


title: buccal swab 307 [201557530007_R06C01]

description: human buccal swab


title: buccal swab 309 [201557530013_R02C01]

description: human buccal swab


title: buccal swab 306 [201557530007_R05C01]

description: human buccal swab


title: buccal swab 304 [201557530007_R03C01]

description: human buccal swab


title: buccal swab 305 [201557530007_R04C01]

description: human buccal swab


title: buccal swab 303 [201557560008_R08C01]

description: human buccal swab


title: buccal swab 302 [201557560008_R07C01]

description: human buccal swab


title: buccal swab 300 [201557560008_R04C01]

description: human buccal swab


title: buccal swab 299 [201557560008_R03C01]

description: human buccal swab


title: buccal swab 301 [201557560008_R05C01]

description: human buccal swab


title: buccal swab 297 [201557560008_R01C01]

description: human buccal swab


title: buccal swab 298 [201557560008_R02C01]

description: human buccal swab


title: buccal swab 291 [201557550044_R08C01]

description: human buccal swab


title: buccal swab 293 [201557550053_R05C01]

description: human buccal swab


title: buccal swab 296 [201557550053_R08C01]

description: human buccal swab


title: buccal swab 294 [201557550053_R06C01]

description: human buccal swab


title: buccal swab 288 [201557550044_R06C01]

description: human buccal swab


title: buccal swab 287 [201557530008_R03C01]

description: human buccal swab


title: buccal swab 289 [201557550028_R06C01]

description: human buccal swab


title: buccal swab 290 [201557550044_R07C01]

description: human buccal swab


title: buccal swab 285 [201557530008_R04C01]

description: human buccal swab


title: buccal swab 284 [201557550028_R07C01]

description: human buccal swab


title: buccal swab 308 [201557530007_R07C01]

description: human buccal swab


title: buccal swab 282 [201465940015_R08C01]

description: human buccal swab

value: KMC


title: buccal swab 283 [201557550028_R05C01]

description: human buccal swab


title: buccal swab 281 [201465940015_R07C01]

description: human buccal swab


title: buccal swab 278 [201465940015_R02C01]

description: human buccal swab


title: buccal swab 295 [201557550053_R07C01]

description: human buccal swab


title: buccal swab 276 [201557550056_R08C01]

description: human buccal swab


title: buccal swab 275 [201557550056_R07C01]

description: human buccal swab


title: buccal swab 273 [201557550056_R05C01]

description: human buccal swab


title: buccal swab 277 [201465940015_R01C01]

description: human buccal swab


title: buccal swab 271 [201557550056_R01C01]

description: human buccal swab


title: buccal swab 272 [201557550056_R04C01]

description: human buccal swab


title: buccal swab 274 [201557550056_R06C01]

description: human buccal swab


title: buccal swab 292 [201557550053_R02C01]

description: human buccal swab


title: buccal swab 270 [201557550038_R08C01]

description: human buccal swab


title: buccal swab 286 [201557550044_R05C01]

description: human buccal swab


title: buccal swab 269 [201557550038_R07C01]

description: human buccal swab


title: buccal swab 268 [201557550038_R06C01]

description: human buccal swab


title: buccal swab 266 [201557550038_R04C01]

description: human buccal swab


title: buccal swab 264 [201557550043_R03C01]

description: human buccal swab


title: buccal swab 267 [201557550038_R05C01]

description: human buccal swab


title: buccal swab 265 [201557550038_R03C01]

description: human buccal swab


title: buccal swab 262 [201557550034_R08C01]

description: human buccal swab


title: buccal swab 260 [201557550034_R05C01]

description: human buccal swab


title: buccal swab 280 [201465940015_R06C01]

description: human buccal swab


title: buccal swab 259 [201557550034_R04C01]

description: human buccal swab


title: buccal swab 257 [201557550034_R01C01]

description: human buccal swab


title: buccal swab 279 [201465940015_R04C01]

description: human buccal swab


title: buccal swab 258 [201557550034_R02C01]

description: human buccal swab


title: buccal swab 256 [201557550027_R08C01]

description: human buccal swab


title: buccal swab 254 [201557550027_R06C01]

description: human buccal swab


title: buccal swab 255 [201557550027_R07C01]

description: human buccal swab


title: buccal swab 251 [201557550027_R03C01]

description: human buccal swab


title: buccal swab 252 [201557550027_R04C01]

description: human buccal swab


title: buccal swab 250 [201557550012_R05C01]

description: human buccal swab


title: buccal swab 249 [201557550027_R01C01]

description: human buccal swab


title: buccal swab 247 [201557550026_R07C01]

description: human buccal swab


title: buccal swab 245 [201557550026_R04C01]

description: human buccal swab


title: buccal swab 246 [201557550026_R06C01]

description: human buccal swab


title: buccal swab 263 [201557550043_R02C01]

description: human buccal swab


title: buccal swab 244 [201557550026_R03C01]

description: human buccal swab


title: buccal swab 243 [201557550026_R02C01]

description: human buccal swab


title: buccal swab 261 [201557550034_R06C01]

description: human buccal swab


title: buccal swab 240 [201557550025_R06C01]

description: human buccal swab


title: buccal swab 241 [201557550025_R07C01]

description: human buccal swab


title: buccal swab 237 [201557550025_R02C01]

description: human buccal swab


title: buccal swab 236 [201557550025_R01C01]

description: human buccal swab


title: buccal swab 234 [201557550016_R07C01]

description: human buccal swab


title: buccal swab 235 [201557550016_R08C01]

description: human buccal swab


title: buccal swab 232 [201557550016_R05C01]

description: human buccal swab


title: buccal swab 231 [201557550016_R04C01]

description: human buccal swab


title: buccal swab 230 [201557550016_R03C01]

description: human buccal swab


title: buccal swab 242 [201557550026_R01C01]

description: human buccal swab


title: buccal swab 253 [201557550027_R05C01]

description: human buccal swab


title: buccal swab 248 [201557550026_R08C01]

description: human buccal swab


title: buccal swab 229 [201557550016_R02C01]

description: human buccal swab


title: buccal swab 228 [201557530019_R05C01]

description: human buccal swab


title: buccal swab 227 [201557550016_R01C01]

description: human buccal swab


title: buccal swab 225 [201557550012_R07C01]

description: human buccal swab


title: buccal swab 223 [201557550012_R06C01]

description: human buccal swab


title: buccal swab 238 [201557550025_R03C01]

description: human buccal swab


title: buccal swab 224 [201557530019_R04C01]

description: human buccal swab


title: buccal swab 239 [201557550025_R05C01]

description: human buccal swab


title: buccal swab 219 [201557560033_R06C01]

description: human buccal swab


title: buccal swab 221 [201557530019_R02C01]

description: human buccal swab


title: buccal swab 220 [201557530019_R01C01]

description: human buccal swab


title: buccal swab 217 [201557560033_R02C01]

description: human buccal swab


title: buccal swab 215 [201557530012_R07C01]

description: human buccal swab


title: buccal swab 216 [201557530012_R03C01]

description: human buccal swab


title: buccal swab 222 [201557530019_R03C01]

description: human buccal swab


title: buccal swab 233 [201557550016_R06C01]

description: human buccal swab


title: buccal swab 213 [201557550028_R03C01]

description: human buccal swab


title: buccal swab 214 [201557550028_R04C01]

description: human buccal swab


title: buccal swab 210 [201557550021_R07C01]

description: human buccal swab


title: buccal swab 212 [201557530012_R02C01]

description: human buccal swab


title: buccal swab 211 [201557550021_R01C01]

description: human buccal swab


title: buccal swab 218 [201557560033_R03C01]

description: human buccal swab


title: buccal swab 208 [201557550021_R06C01]

description: human buccal swab


title: buccal swab 209 [201557530009_R08C01]

description: human buccal swab


title: buccal swab 205 [201557550028_R01C01]

description: human buccal swab


title: buccal swab 206 [201557550021_R08C01]

description: human buccal swab


title: buccal swab 226 [201557550012_R08C01]

description: human buccal swab


title: buccal swab 204 [201557530009_R07C01]

description: human buccal swab


title: buccal swab 203 [201557530012_R04C01]

description: human buccal swab


title: buccal swab 199 [201557550028_R02C01]

description: human buccal swab


title: buccal swab 198 [201557530012_R01C01]

description: human buccal swab


title: buccal swab 195 [201557530008_R02C01]

description: human buccal swab


title: buccal swab 357 [201557550042_R03C01]

description: human buccal swab


title: buccal swab 193 [201557550014_R05C01]

description: human buccal swab

value: SHD


title: buccal swab 196 [201557530012_R06C01]

description: human buccal swab


title: buccal swab 194 [201557550014_R07C01]

description: human buccal swab


title: buccal swab 190 [201557550014_R03C01]

description: human buccal swab


title: buccal swab 191 [201557550014_R01C01]

description: human buccal swab


title: buccal swab 197 [201557530012_R08C01]

description: human buccal swab


title: buccal swab 188 [201465940037_R08C01]

description: human buccal swab


title: buccal swab 207 [201557530004_R05C01]

description: human buccal swab


title: buccal swab 186 [201465940037_R06C01]

description: human buccal swab


title: buccal swab 183 [201557550018_R08C01]

description: human buccal swab


title: buccal swab 187 [201557550014_R04C01]

description: human buccal swab


title: buccal swab 185 [201465940037_R05C01]

description: human buccal swab


title: buccal swab 184 [201465940037_R02C01]

description: human buccal swab


title: buccal swab 182 [201557550018_R01C01]

description: human buccal swab


title: buccal swab 189 [201557550014_R02C01]

description: human buccal swab


title: buccal swab 181 [201557550018_R07C01]

description: human buccal swab


title: buccal swab 202 [201557530004_R06C01]

description: human buccal swab


title: buccal swab 178 [201465940037_R07C01]

description: human buccal swab


title: buccal swab 180 [201465940037_R03C01]

description: human buccal swab


title: buccal swab 179 [201465940037_R04C01]

description: human buccal swab


title: buccal swab 177 [201557550018_R06C01]

description: human buccal swab


title: buccal swab 200 [201557550021_R05C01]

description: human buccal swab


title: buccal swab 364 [201557550042_R06C01]

description: human buccal swab


title: buccal swab 176 [201557550018_R05C01]

description: human buccal swab


title: buccal swab 201 [201557550021_R03C01]

description: human buccal swab


title: buccal swab 173 [201557550024_R05C01]

description: human buccal swab


title: buccal swab 172 [201557550024_R04C01]

description: human buccal swab


title: buccal swab 192 [201557550014_R06C01]

description: human buccal swab


title: buccal swab 175 [201557550018_R04C01]

description: human buccal swab


title: buccal swab 169 [201557550024_R01C01]

description: human buccal swab


title: buccal swab 171 [201557550024_R03C01]

description: human buccal swab


title: buccal swab 167 [201557550009_R07C01]

description: human buccal swab


title: buccal swab 170 [201557550024_R02C01]

description: human buccal swab


title: buccal swab 165 [201557550009_R05C01]

description: human buccal swab


title: buccal swab 161 [201557550009_R01C01]

description: human buccal swab


title: buccal swab 163 [201557550009_R03C01]

description: human buccal swab


title: buccal swab 164 [201557550009_R04C01]

description: human buccal swab


title: buccal swab 166 [201557550009_R06C01]

description: human buccal swab


title: buccal swab 160 [201557550008_R08C01]

description: human buccal swab


title: buccal swab 162 [201557550009_R02C01]

description: human buccal swab


title: buccal swab 159 [201557550008_R07C01]

description: human buccal swab


title: buccal swab 157 [201557550008_R05C01]

description: human buccal swab


title: buccal swab 151 [201557530044_R07C01]

description: human buccal swab


title: buccal swab 153 [201557550008_R01C01]

description: human buccal swab


title: buccal swab 152 [201557530044_R08C01]

description: human buccal swab


title: buccal swab 154 [201557550008_R02C01]

description: human buccal swab


title: buccal swab 149 [201557530044_R05C01]

description: human buccal swab


title: buccal swab 155 [201557550008_R03C01]

description: human buccal swab


title: buccal swab 148 [201557530044_R04C01]

description: human buccal swab


title: buccal swab 150 [201557530044_R06C01]

description: human buccal swab


title: buccal swab 147 [201557530044_R03C01]

description: human buccal swab


title: buccal swab 156 [201557550008_R04C01]

description: human buccal swab


title: buccal swab 146 [201557530044_R02C01]

description: human buccal swab


title: buccal swab 168 [201557550009_R08C01]

description: human buccal swab


title: buccal swab 142 [201557530026_R06C01]

description: human buccal swab


title: buccal swab 143 [201557530026_R07C01]

description: human buccal swab


title: buccal swab 174 [201465940037_R01C01]

description: human buccal swab


title: buccal swab 144 [201557530026_R08C01]

description: human buccal swab


title: buccal swab 140 [201557530026_R04C01]

description: human buccal swab


title: buccal swab 141 [201557530026_R05C01]

description: human buccal swab


title: buccal swab 158 [201557550008_R06C01]

description: human buccal swab


title: buccal swab 139 [201557530026_R03C01]

description: human buccal swab


title: buccal swab 136 [201557530025_R08C01]

description: human buccal swab


title: buccal swab 135 [201557540057_R08C01]

description: human buccal swab


title: buccal swab 133 [201557540057_R06C01]

description: human buccal swab


title: buccal swab 137 [201557530026_R01C01]

description: human buccal swab


title: buccal swab 132 [201557540057_R05C01]

description: human buccal swab


title: buccal swab 134 [201557540057_R07C01]

description: human buccal swab


title: buccal swab 124 [201557540056_R06C01]

description: human buccal swab


title: buccal swab 130 [201557540057_R03C01]

description: human buccal swab


title: buccal swab 126 [201557540056_R08C01]

description: human buccal swab


title: buccal swab 122 [201557560028_R06C01]

description: human buccal swab


title: buccal swab 128 [201557540057_R01C01]

description: human buccal swab


title: buccal swab 125 [201557540056_R07C01]

description: human buccal swab


title: buccal swab 131 [201557540057_R04C01]

description: human buccal swab


title: buccal swab 129 [201557540057_R02C01]

description: human buccal swab


title: buccal swab 121 [201557560028_R05C01]

description: human buccal swab


title: buccal swab 127 [201557560029_R02C01]

description: human buccal swab


title: buccal swab 119 [201557560028_R02C01]

description: human buccal swab


title: buccal swab 120 [201557560028_R03C01]

description: human buccal swab


title: buccal swab 118 [201557560028_R01C01]

description: human buccal swab


title: buccal swab 117 [201557560016_R08C01]

description: human buccal swab


title: buccal swab 145 [201557530044_R01C01]

description: human buccal swab


title: buccal swab 138 [201557530026_R02C01]

description: human buccal swab


title: buccal swab 114 [201557560016_R05C01]

description: human buccal swab


title: buccal swab 116 [201557560016_R07C01]

description: human buccal swab


title: buccal swab 110 [201557530025_R03C01]

description: human buccal swab


title: buccal swab 115 [201557560016_R06C01]

description: human buccal swab


title: buccal swab 111 [201557560016_R01C01]

description: human buccal swab


title: buccal swab 113 [201557560016_R04C01]

description: human buccal swab


title: buccal swab 112 [201557560016_R03C01]

description: human buccal swab


title: buccal swab 108 [201557530025_R01C01]

description: human buccal swab


title: buccal swab 123 [201557560029_R01C01]

description: human buccal swab


title: buccal swab 105 [201557530018_R06C01]

description: human buccal swab


title: buccal swab 107 [201557530018_R08C01]

description: human buccal swab


title: buccal swab 104 [201557530018_R05C01]

description: human buccal swab


title: buccal swab 103 [201557530018_R04C01]

description: human buccal swab


title: buccal swab 99 [201557530004_R04C01]

description: human buccal swab


title: buccal swab 101 [201557530018_R01C01]

description: human buccal swab


title: buccal swab 102 [201557530018_R02C01]

description: human buccal swab


title: buccal swab 100 [201557530009_R04C01]

description: human buccal swab


title: buccal swab 94 [201557540056_R05C01]

description: human buccal swab

value: WIH


title: buccal swab 95 [201557530009_R05C01]

description: human buccal swab


title: buccal swab 93 [201557540056_R04C01]

description: human buccal swab


title: buccal swab 92 [201557540056_R03C01]

description: human buccal swab


title: buccal swab 98 [201557530013_R08C01]

description: human buccal swab


title: buccal swab 91 [201557540056_R02C01]

description: human buccal swab


title: buccal swab 97 [201557530004_R03C01]

description: human buccal swab


title: buccal swab 88 [201557540048_R07C01]

description: human buccal swab


title: buccal swab 89 [201557540048_R08C01]

description: human buccal swab


title: buccal swab 109 [201557530025_R02C01]

description: human buccal swab


title: buccal swab 87 [201557540048_R06C01]

description: human buccal swab


title: buccal swab 90 [201557540056_R01C01]

description: human buccal swab


title: buccal swab 106 [201557530018_R07C01]

description: human buccal swab


title: buccal swab 86 [201557540048_R05C01]

description: human buccal swab


title: buccal swab 81 [201557540041_R08C01]

description: human buccal swab


title: buccal swab 83 [201557540048_R02C01]

description: human buccal swab


title: buccal swab 80 [201557540041_R07C01]

description: human buccal swab


title: buccal swab 78 [201557540041_R05C01]

description: human buccal swab


title: buccal swab 85 [201557540048_R04C01]

description: human buccal swab


title: buccal swab 79 [201557540041_R06C01]

description: human buccal swab


title: buccal swab 77 [201557540041_R04C01]

description: human buccal swab


title: buccal swab 84 [201557540048_R03C01]

description: human buccal swab


title: buccal swab 76 [201557540041_R03C01]

description: human buccal swab


title: buccal swab 72 [201557550033_R05C01]

description: human buccal swab


title: buccal swab 68 [201557550024_R07C01]

description: human buccal swab


title: buccal swab 64 [201557530025_R05C01]

description: human buccal swab


title: buccal swab 71 [201557550033_R04C01]

description: human buccal swab


title: buccal swab 74 [201557540041_R01C01]

description: human buccal swab


title: buccal swab 70 [201557550033_R02C01]

description: human buccal swab


title: buccal swab 66 [201557530025_R07C01]

description: human buccal swab


title: buccal swab 65 [201557530025_R06C01]

description: human buccal swab


title: buccal swab 62 [201557530006_R07C01]

description: human buccal swab


title: buccal swab 75 [201557540041_R02C01]

description: human buccal swab


title: buccal swab 69 [201557550024_R08C01]

description: human buccal swab


title: buccal swab 63 [201557530025_R04C01]

description: human buccal swab


title: buccal swab 67 [201557550024_R06C01]

description: human buccal swab


title: buccal swab 73 [201557550033_R06C01]

description: human buccal swab


title: buccal swab 59 [201557530006_R04C01]

description: human buccal swab


title: buccal swab 82 [201557540048_R01C01]

description: human buccal swab


title: buccal swab 61 [201557530006_R06C01]

description: human buccal swab


title: buccal swab 58 [201557530006_R03C01]

description: human buccal swab


title: buccal swab 60 [201557530006_R05C01]

description: human buccal swab


title: buccal swab 57 [201557530006_R02C01]

description: human buccal swab


title: buccal swab 56 [201557530006_R01C01]

description: human buccal swab


title: buccal swab 55 [201557530002_R08C01]

description: human buccal swab


title: buccal swab 52 [201557530002_R05C01]

description: human buccal swab


title: buccal swab 51 [201557550051_R07C01]

description: human buccal swab


title: buccal swab 50 [201557530002_R04C01]

description: human buccal swab


title: buccal swab 49 [201557530002_R02C01]

description: human buccal swab


title: buccal swab 48 [201557530002_R01C01]

description: human buccal swab


title: buccal swab 43 [201557560054_R03C01]

description: human buccal swab


title: buccal swab 42 [201557560054_R02C01]

description: human buccal swab


title: buccal swab 45 [201557560054_R05C01]

description: human buccal swab


title: buccal swab 47 [201557560054_R07C01]

description: human buccal swab


title: buccal swab 46 [201557560054_R06C01]

description: human buccal swab


title: buccal swab 36 [201557550023_R03C01]

description: human buccal swab


title: buccal swab 40 [201557560029_R08C01]

description: human buccal swab


title: buccal swab 37 [201557560029_R05C01]

description: human buccal swab


title: buccal swab 33 [201557550023_R02C01]

description: human buccal swab


title: buccal swab 38 [201557560029_R06C01]

description: human buccal swab


title: buccal swab 44 [201557560054_R04C01]

description: human buccal swab


title: buccal swab 32 [201557550023_R01C01]

description: human buccal swab


title: buccal swab 34 [201557560029_R03C01]

description: human buccal swab


title: buccal swab 31 [201557530021_R08C01]

description: human buccal swab


title: buccal swab 53 [201557530002_R06C01]

description: human buccal swab


title: buccal swab 39 [201557560029_R07C01]

description: human buccal swab


title: buccal swab 41 [201557560054_R01C01]

description: human buccal swab


title: buccal swab 29 [201557530021_R06C01]

description: human buccal swab


title: buccal swab 30 [201557530021_R07C01]

description: human buccal swab


title: buccal swab 28 [201557530007_R02C01]

description: human buccal swab


title: buccal swab 26 [201557550028_R08C01]

description: human buccal swab


title: buccal swab 27 [201557550023_R04C01]

description: human buccal swab


title: buccal swab 25 [201557530008_R06C01]

description: human buccal swab


title: buccal swab 35 [201557560029_R04C01]

description: human buccal swab


title: buccal swab 23 [201557530021_R05C01]

description: human buccal swab


title: buccal swab 24 [201557530007_R01C01]

description: human buccal swab


title: buccal swab 22 [201557530021_R04C01]

description: human buccal swab


title: buccal swab 21 [201557550023_R05C01]

description: human buccal swab


title: buccal swab 20 [201557530021_R03C01]

description: human buccal swab


title: buccal swab 16 [201557530021_R01C01]

description: human buccal swab


title: buccal swab 15 [201557530020_R08C01]

description: human buccal swab


title: buccal swab 13 [201557530020_R06C01]

description: human buccal swab


title: buccal swab 18 [201557530008_R07C01]

description: human buccal swab


title: buccal swab 17 [201557550023_R06C01]

description: human buccal swab


title: buccal swab 19 [201557530021_R02C01]

description: human buccal swab


title: buccal swab 4 [201557530009_R03C01]

description: human buccal swab


title: buccal swab 2 [201557530008_R08C01]

description: human buccal swab


title: buccal swab 14 [201557530020_R07C01]

description: human buccal swab


title: buccal swab 10 [201557530020_R03C01]

description: human buccal swab


title: buccal swab 12 [201557530020_R05C01]

description: human buccal swab


title: buccal swab 11 [201557530020_R04C01]

description: human buccal swab


title: buccal swab 8 [201557530020_R01C01]

description: human buccal swab


title: buccal swab 9 [201557530020_R02C01]

description: human buccal swab


title: buccal swab 5 [201557530019_R06C01]

description: human buccal swab


title: buccal swab 3 [201557530004_R01C01]

description: human buccal swab


title: buccal swab 54 [201557530002_R07C01]

description: human buccal swab


title: buccal swab 1 [201557530009_R01C01]

description: human buccal swab


title: buccal swab 6 [201557530019_R07C01]

description: human buccal swab


title: buccal swab 7 [201557530019_R08C01]

description: human buccal swab


title: buccal swab 96 [201557530009_R06C01]

description: human buccal swab


title: No primary Control for Lamin B TSA-Seq

status: Public on Apr 25 2018

city: Urbana

first: Andrew

middle: S

last: Belmont

state: IL

address: 601 S Goodwin Ave, CLSL B509

institute: University of Illinois at Urbana-Champaign

data_processing:
Library strategy: TSA-Seq
The raw .bcl files were converted into demultiplexed compressed fastq files using the bcl2fastq v1.8.2 and later v2.17.1.14 conversion software (Illumina).
Raw sequencing reads were first mapped to the human genome (UCSC hg19) using Bowtie 2 version 2.0.2 with default parameters. Chromosome Y was excluded in the reference genome to reduce mapping bias since the K562 cell line was derived from a female.
PCR duplicates reads were removed using samtools version 0.1.19 with default parameters.
We normalized and processed the TSA-Seq data using a sliding window approach as follows. The normalized SON-TSA score was calculated as the log 2 ratio of  (TSA-Seq pulldown reads in a 20 kb window divided by total mapped reads for this pulldown sample) / (input reads in the same 20 kb window divided by total mapped reads for this input). This approach can be interpreted as the fold change between the pulldown sample and the input corrected by the total number of mapped reads in each sample. The window slides on the genome with a step size of 100 bp.
We partitioned the genome into non-overlapping 20 kb bins, averaging the TSA-Seq score over the 100 bp intervals within this bin for the new TSA-Seq 20 kb score.  The values for these 20 kb bins were then smoothed by convolution using a Hanning window of length 21 (21 x 20 kb or 420 kb).  This new smoothed TSA-Seq score with 20 kb sampling was used for SON TSA-Seq decile calculations and comparisons with other genome features
Genome_build: hg19
Supplementary_files_format_and_content: normalized TSA signals were in bigWig format, and the 10 deciles are in BED format. Other data files from analyzing public datasets are in bigWig or bigBed formats.

source_name: bone marrow

growth_protocol: K562 Cells were grown according to the ENCODE protocol, in RPMI with 10% FBS (Sigma-Aldrich) and Antibiotic-antimycotic (GIBCO) at density of 0.4 x 10^6-0.75 x 10^6 /ml

extract_protocol:
Cell lysis and protease digestion were done at 55°C with constant mixing in 10mM Tris, 10mM EDTA, 0.5% SDS and 500µg/ml proteinase K (NEB) for 8-12 hrs (10^7 cells/ml).  NaCl was added for a final 0.2 M concentration and the lysate incubated 20-24 hrs at 65°C with constant mixing to reverse formaldehyde crosslinking.  DNA was extracted 2x using an equal volume of phenol (Fisher)/chloroform/isoamyl alcohol (25:24:1) and 1x with an equal volume of chloroform/isoamyl alcohol (24:1).  Tubes were kept at 55°C for 1h with the cap off to evaporate phenol residues, and then treated with 25 µg/ml RNaseA (Qiagen) at 37o C for 1hr and extracted again.  DNA was then precipitated with 1/10 volume of 3M Na Acetate, pH 5.2, and 2 volumes of 100% EtOH at -20 oC for 20 min – 2 hrs.
For each of the TSA-Seq experiment staining conditions, input and Streptavidin pull-down DNA were used to make sequencing libraries, using the Kapa Hyper Prep Kit (Kapa Biosystems).  DNA was blunt-ended, 3’-end A-tailed, and ligated to indexed adaptors with 6nt barcodes. PCR amplification selectively enriched for those fragments with adapters on both ends. Amplification was carried out for 8-16 cycles with the Kapa HiFi polymerase (Kapa Biosystems, Woburn, MA).  An Agilent bioanalyzer DNA high-sensitivity chip (Agilent, Santa Clara, CA) was used to determine library fragment sizes.  Library fragment concentrations were measured by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA) prior to pooling and sequencing.

treatment_protocol: TSA labeling was done in independent cell batches.  For each batch, cells were divided equally and stained according to four labeling protocols: “Condition 1”, “Condition 2”, “Condition 3”, and “No 1o control”.  Identical staining conditions were used except that 50% sucrose was included in the TSA staining buffer for the “Condition 2” protocol, 0.75mM DTT in addition to 50% sucrose was added in the TSA staining buffer for the “Condition 3” protocol, and the anti-SON primary antibody was omitted for the “No 1o control” protocol.  Cells were fixed by adding 10 ml of 8% paraformaldehyde (Sigma-Aldrich) freshly prepared in CMF-PBS (calcium, magnesium-free phosphate buffered saline) to 40 ml of cells in culture media, incubating for 20 min at room temperature (RT), and quenching aldehydes by addition of 5.6 ml of 1.25 M glycine (Fisher Scientific) and incubation for 5 min at RT.  All incubation steps used a rotating platform to mix the cell suspension.  Cells were then pelleted by centrifugation and resuspended in CMF-PBS buffer with 0.5% Triton-X100 (Sigma-Aldrich) for 30 min at RT.  All centrifugations were for 5 min at 100-200g.  Cells were centrifuged at RT and resuspended in 1.5% H2O2 (Fisher Scientific) in CMF-PBS for 1h at RT to quench endogenous peroxidases, followed by 3 washes at RT in PBST (0.1%Triton-X100/CMF-PBS) by repeated centrifugation and cell pellet resuspension.  Cells were resuspended in IgG Blocking Buffer (5% Normal Goat Serum (Sigma-Aldrich) in PBST) at a concentration of 10^7 cells/ml for 1 hr, followed by centrifugation and resuspension in primary antibody solution (Rabbit-anti-SON primary antibodies (Ab1, Atlas antibodies cat # HPA023535) diluted 1:1000 or 1:2000 in IgG Blocking buffer, or rabbit polyclonal-anti-SON primary antibodies (Ab2) diluted 1:2000 in IgG Blocking buffer, or mouse-anti-phosphorylated SC35 primary antibodies (Sigma-Aldrich cat # S4045) diluted 1:500 in IgG Blocking buffer, or mouse monoclonal anti-lamin A/C primary antibody (Clone 5G4) diluted 1:1000 in IgG Blocking buffer, or mouse monoclonal anti-lamin B primary antibodies (Clone 2D8) diluted 1:1000 in IgG Blocking buffer) at 10^7 cells/ml, or mouse monoclonal anti-RNA polymerase II primary antibodies (clone 4H8) (Millipore cat # 05-623) at 0.5 x 107 cells/ml and incubated 20-24 hrs at 4°C (See METHODS for more information about anti-lamin antibodies). For the no primary control, cells were incubated in IgG Blocking buffer only.  Cells were then washed 3x with PBST, resuspended in IgG Blocking buffer with secondary antibodies at 10^7 cells/ml, and incubated 20-24 hrs at 4°C.  Secondary antibodies (Jackson, ImmunoResearch) used were HRP conjugated, goat-anti-rabbit secondary antibody diluted 1:1000 or HRP conjugated goat-anti-mouse secondary antibody diluted 1:200 or 1:1000. Cells then were washed 3x in PBST and resuspended in reaction buffer A (CMF-PBS for Condition 1, or CMF-PBS with 50% sucrose for Condition 2, or CMF-PBS with 50% sucrose and 1.5mM DTT for Condition 3) at 2 x 10^7 cells/ml.  Equal volumes of buffer B (8mM tyramide-biotin stock solution diluted 1:5000 with 0.003% H2O2 in CMF-PBS for Condition 1, or CMF-PBS with 50% sucrose for Conditions 2 and 3) were then added.  Cells were incubated for 10 min and then washed 3x in PBST at RT.  Validation of TSA labeling is done by biotin immunostaining.

tag: cell line

tag: disease

value: chronic myelogenous leukemia (CML)

tag: tsa-seq target


title: Circular RNA replicate 1

status: Public on Jun 29 2017

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Dermatology

institute: Stanford University

data_processing:
Sequenced reads were collapsed for PCR duplicates and trimmed for adaptor sequence. Reads mapping to rRNA and transfected RNA were removed. Remaining reads were mapped to hg19 genome assembly whole genome using sequence aligner STAR with parameters FilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4
Reads matching each gene were calculated using HTSeq. Differential gene expression was calculated with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: counts.txt files include counts calculated by HTSeq, and DGE.txt includes fold change and p-value calculated by DESeq2.
Supplementary_files_format_and_content: MolCell2017_DNA_plasmidseq.docx includes plasmid insert sequences.

source_name: Circular RNA, HeLa

growth_protocol: Hela cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, 11995-073) supplemented with 100 units/ml penicillin-streptomycin (Gibco, 15140-163), 10% (v/v) fetal bovine serum

extract_protocol:
Total RNA was extracted using TRIzol reagent, according to manufacturer’s instructions. Total RNA was subjected to rRNA depletion with Ribo Minus Kit.
RNA sequencing libraries were prepared as decribed in Flynn et al., 2015

treatment_protocol: The RNA and Lipofectamine 2000 were diluted and mixed in Opti-MEM (Invitrogen, 31985-088), incubated for 5 min at rt, the nucleic acids and Lipofectamine 2000 were mixed together, incubated for 15 min at rt and then the nucleic acids-Lipofectamine 2000 complexes were applied to the monolayer cultures. (500 ng of nucleic acids was transfected into one well of a 24-well plate.)

value: HeLa

tag: transfection

value: Circular RNA


title: Linear RNA replicate 1

source_name: Linear RNA, HeLa

value: Linear RNA


title: Untreated replicate 1

source_name: Untreated, HeLa

value: Untreated


title: Untreated replicate 2


title: P20_XY_Meioc_wild_type_IgG-RIP-seq_2

status: Public on Mar 22 2017

data_processing:
Sequenced reads were mapped to mm10 using Tophat with parameter -g1
FPKMs were calculated using Cufflinks
For RIP-seq data, counts were obtained from HTSeq and normalized via DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks output, counts from HTSeq, or normalized counts from DESeq2

source_name: postnatal testis

extract_protocol:
For RIP-seq experiments, RNA was precleared with Dynabeads (ThermoFisher Scientific), immunoprecipitated, and isolated via phenol/chloroform extraction.
For RIP-seq experiments, Clontech SMARTer Stranded RNA-Seq Kit with rRNA depeletion was used accorindg to the manufacturer's recommendations.

tag: strain

tag: tissue

value: testis

tag: Stage

tag: genotype

value: wild-type

tag: preclearing

value: yes

tag: rip antibody

value: goat IgG (Santa Cruz Biotechnology)


title: P20_XY_Meioc_wild_type_RIP-input-RNA-seq_1


title: P20_XY_Meioc_wild_type_RIP-input-RNA-seq_2


title: No primary Control for Lamin B TSA-Seq Replicate

description: NoPrimaryCtrl_for_LaminB_TSA-Seq_Replicate.bw


title: Linear RNA replicate 2


title: 21922: E17.5 Wnt1-Cre;R26R-EYFP bowel_YFP-_rep2

status: Public on Oct 09 2018

type: RNA

city: Philadelphia

first: Robert

middle: O.

last: Heuckeroth

state: PA

address: 3615 Civic Center Blvd, Abramson Research Center, 1116i

department: Pediatrics

institute: The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania

description: Gene expression data from YFP- embryonic E17.5 Wnt1-Cre;R26R-EYFP bowel

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

label: biotin

source_name: E17.5 Wnt1-Cre;R26R-EYFP bowel

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen Ovation PicoSL WTA System V2 system from 500pg-50 ng total RNA.

growth_protocol: EYFP-positive and EYFP-negative cells from whole bowel of embyonic day 17.5 Wnt1-Cre; R26R-EYFP mice were isolated using FACS.

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

treatment_protocol: Cells were isolated into Neurobasal media, spun down, and resuspended in Trizol solution

value: Bowel

tag: age

value: Embryonic day 17.5

tag: cell type

value: non-ENCDC

tag: cell population

value: YFP-


title: 21923: E17.5 Wnt1-Cre;R26R-EYFP bowel_YFP-_rep3


title: P20_XY_Meioc_wild_type_YTHDC2-RIP-seq_2

value: anti-YTHDC2 (Santa Cruz Biotechnology sc-249370)


title: P20_XY_Meioc_wild_type_IgG-RIP-seq_1

value: rabbit IgG (Santa Cruz Biotechnology)


title: 21918: E17.5 Wnt1-Cre;R26R-EYFP bowel_YFP+_rep2

description: Gene expression data from YFP+ embryonic E17.5 Wnt1-Cre;R26R-EYFP bowel

value: ENCDC

value: YFP+


title: P15_XY_Meioc_knock-out_RIP-input-RNA-seq_2

value: Meioc knock-out


title: P15_XY_Meioc_knock-out_RIP-input-RNA-seq_1


title: 21917: E17.5 Wnt1-Cre;R26R-EYFP bowel_YFP+_rep1


title: P15_XY_Meioc_knock-out_Meioc_RIP-seq_2

value: anti-MEIOC (generated by Page lab)


title: P15_XY_Meioc_knock-out_Meioc_RIP-seq_1


title: P20_XY_Meioc_wild_type_YTHDC2-RIP-seq_1

value: anti-YTHDC2 (Bethyl Laboratories A303-026A)


title: P15_XY_Meioc_wild_type_RIP-input-RNA-seq_4


title: Circular RNA replicate 2

value: HeLa

value: Circular RNA


title: P15_XY_Meioc_wild_type_RIP-input-RNA-seq_3

value: testis


title: 21921: E17.5 Wnt1-Cre;R26R-EYFP bowel_YFP-_rep1


title: P15_XY_Meioc_wild_type_RIP-input-RNA-seq_1

value: wild-type


title: P15_XY_Meioc_wild_type_RIP-input-RNA-seq_2

value: yes


title: 21919: E17.5 Wnt1-Cre;R26R-EYFP bowel_YFP+_rep3


title: 21920: E17.5 Wnt1-Cre;R26R-EYFP bowel_YFP+_rep4


title: P15_XY_Meioc_wild_type_Meioc-RIP-seq_4


title: P15_XY_Meioc_wild_type_Meioc-RIP-seq_2


title: E14.5_XX_Meioc_het_RNA-seq_3

source_name: fetal ovary

extract_protocol:
For RNA-seq experiments, total RNA, of about 1 ug, was extracted using Trizol (Invitrogen) according to manufacturer’s instructions.
For RNA-seq experiments, TruSeq Sample Preparation kit protocol was use with poly-A selection, following the manufacturer's recommendations.

value: ovary

value: Meioc heterozygous


title: E14.5_XX_Meioc_knock-out_RNA-seq_3


title: E14.5_XX_Meioc_wild-type_RNA-seq_2


title: E14.5_XX_Meioc_knock-out_RNA-seq_1


title: P15_XY_Meioc_wild_type_IgG-RIP-seq_2


title: E14.5_XX_Meioc_knock-out_RNA-seq_2


title: P15_XY_Meioc_wild_type_IgG-RIP-seq_1


title: E14.5_XX_Meioc_wild-type_RNA-seq_1


title: Input Primed

status: Public on Jul 15 2016

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Illumina pipeline Casava 1.82
Sequenced reads were de-multiplexed to attribute each read to a DNA sample and then aligned to reference human genome hg19 with bowtie2
NGS.plot R package was used to generate the plots using the BAM files
Genome_build: hg19
Supplementary_files_format_and_content: png plots

extract_protocol:
Pellets were lysed, resuspended in 1mL of LB1 on ice for 10min (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100, protease inhibitors), then after centrifugation resuspend in LB2 on ice for 10min (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After centrifugation, resuspend in LB3 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.1% SDS and protease inhibitors) and sonicated (Covaris settings: 5% duty, 200 cycle, 140 PIP, 60 min), yielding genomic DNA fragments with a bulk size of 100-300 bp
Libraries of immunoprecipitated chromatin and total input control from ChIP were performed with single-end adaptors as previously described (Rowe et al., 2013b). Sequencing was performed on an Illumina HiSeq 2500 (Illumina), with each library sequenced in 100-bp reads run.

treatment_protocol: Cells were cross-linked for 10 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution (11% Formaldehyde Sigma 2525459, 50mM HEPES pH 7.5, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) to the growth media followed by quenching with 100 mM glycine. Cells were washed twice with PBS, then the supernatant was aspirated and the cell pellet was flash frozen in liquid nitrogen.

tag: medium

value: hESM

tag: chip antibody


title: Input Naive


title: H3K9me3 Primed lane 2

tag: antibody manufacturer and catalog number

value: Diagenode pAb-056-050


title: H3K9me3 Naive lane 2


title: H3K9me3 Primed lane 1


title: WIBR2_6i/L/A_H3K27me3

status: Public on Jul 16 2014

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 9 Cambridge Center

department: Biology

institute: MIT/Whitehead Institute

description: Chromatin IP against H3K27me3 in naive condition

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best. Seed length (-l) was set to read length for each dataset.
Genome_build: hg19
Supplementary_files_format_and_content: For all samples, aligned sequences were extended automatically by MACS and allocated into 50bp bins. Normalized read counts (Reads per million mapped reads per basepair) in 50bp are shown.

source_name: Embryonic stem cells

growth_protocol: Primed WIBR2 human ESCs were cultured on mitomycin C inactivated mouse embryonic ﬁbroblast (MEF) feeder layers in primed human ESC medium (hESM) and passaged enzymatically by treatment for 20 minutes with 1 mg/mL Collagenase Type IV (Gibco) followed by sequential sedimentation steps in human ESC medium to remove single cells. Converted naive WIBR2 human ESCs were cultured on mitomycin C-inactivated MEF feeder cells, and were passaged every 5-7 days by a brief PBS wash followed by single-cell dissociation using 3-5 minute treatment with Accutase (Gibco) and centrifugation in fibroblast medium. See the manuscript for composition of primed hESM and naive 5i/L/A and 6i/L/A culture media. Note that these WIBR2 naive human ESCs were initially converted from the primed state in 5i/L/A and supplemented with a JNK inhibitor (6i/L/A) (P18)

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: All samples were briefly washed in PBS, dissociated to single cells using trypsin, and 10 million naive or primed human ESCs were purified from GFP-labeled MEFs using the FACSAria (Beckton-Dickinson) prior to lysis and RNA extraction.

tag: antibody catalog number

value: Millipore 07-449


title: WIBR2_6i/L/A_H3K4me3

description: Chromatin IP against H3K4me3 in naive condition

value: Abcam ab8580


title: WIBR2_hESM_H3K4me3

description: Chromatin IP against H3K4me3 in primed condition


title: dicer-/-_RNAseq

status: Public on May 11 2015

city: Boston

first: Peng

last: Du

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

data_processing:
bowtie softare is used to map reads to mRNA with two mismatches permitted, and self-developed perl scripts were used to coculate the reads of each genes
For small RNA sequencing, after removal of the adaptor sequences, bowtie software was used to mapping the small RNAs into mature miRNA sequences (miRBase).
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq.txt provided a matrix table, which contained five columns including the gene's name, cDNA's name, reads number in WT, DGCR8 and Dicer samples; small RNA seq.txt provided the reads number for each miRNAs.

source_name: mESCs

growth_protocol: Mouse ESCs (V6.5, Dgcr8-/- and Dicer-/-) were cultured in DMEM with ESGRO (1000 units/mL), supplemented with 15% (v/v) FBS and antibiotics

extract_protocol:
total RNAs were extracted using Trizol reagent
200 ng polyA(+) RNA isolated as described above was used for mRNA-seq. Sample preparation was with the TruSeq Stranded mRNA Sample Prep Kits (Illumina).10ug total RNAs was used for small RNA libraries preparaion fellowing small RNA Sample Prep Kits (Illumina)

value: dicer-/- mESCs


title: WIBR2_hESM_H3K27me3

description: Chromatin IP against H3K27me3 in primed condition


title: P15_XY_Meioc_wild_type_Meioc-RIP-seq_3


title: C.reinhardtii _Fe_Long_2_hours

status: Public on Feb 20 2014

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

data_processing:
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie  in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates.
Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html)
Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium.

extract_protocol: Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA).

treatment_protocol: Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times.

tag: treatment

value: iron deprivation

tag: cultured in

value: TAP medium without Fe-EDTA for 2h


title: C.reinhardtii _Fe_Long_4_hours

value: TAP medium without Fe-EDTA for 4h


title: C.reinhardtii _Fe_Long_24_hours

value: TAP medium without Fe-EDTA for 24h


title: C.reinhardtii _Fe_Long_1_hours

value: TAP medium without Fe-EDTA for 1h


title: C.reinhardtii _Fe_Long_0.5_hours

value: TAP medium without Fe-EDTA for 0.5h


title: H3K9me3 Naive lane 1

tag: cell line


title: whole genome amplified gDNA MethDNANeg_3

status: Public on Sep 18 2013

city: Uppsala

first: Jessica

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

country: Sweden

institute: Uppsala University

description: MethDNANeg_3 Average Beta

hyb_protocol: 200ng of bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using the standard protocol from Illumina.

scan_protocol: iScan SQ instrument (Illumina)

data_processing:
Methylation Module (1.8.5) software in Genome Studio (V2010.3)
normalized (peak-based correction) Average Beta data provided

label_protocol: Cy3 and Cy5

growth_protocol: primary cells

extract_protocol: genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (QIAGEN) or the QIAamp DNA Blood Mini Kit (QIAGEN) and ~500 ng was treated with sodium bisulfite (EZ DNA methylation Gold, Zymo Research).

treatment_protocol: tumor samples: NA; fractionated blood cells: NA; remission samples: patients were treated according to the Nordic Society of Pediatric Hematology and Oncology (NOPHO) ALL92 or ALL2000 protocols

tag: disease state

value: Whole Genome Amplified gDNA

tag: immunophenotype

tag: subtype

value: normal


title: Human HCT116 DKO Methylated DNA MethDNAPos_6

description: MethDNAPos_6 Average Beta

value: Human HCT116 DKO Methylated DNA, D5014-2


title: whole genome amplified gDNA MethDNANeg_5

description: MethDNANeg_5 Average Beta