title: H3K27me3_ChIPSeq_Control

value: H3K27me3 (Millipore, 07-449)


title: H3K27me3_ChIPSeq_Nickel

status: Public on Sep 24 2014

type: SRA

city: Duarte

first: Dustin

middle: E

last: Schones

state: CA

address: 1500 Duarte Rd

department: Cancer Biology

country: USA

institute: City of Hope

library_source: genomic

data_processing:
basecalling have been done by CASAVA-1.8.2
Histone modification ChIP-seq data have been aligned to human hg19 by bowtie ( version 1.0.0 "–strata –best –n 1 –m 1 -3 10" for sequence by Illumina HiSeq 2500 because Fastqc checked last 10 bases are not good in quality, otherwise "–strata –best –n 1 –m 1"). CTCF ChIP-seq data have been aligned to human hg19 by bowtie ( version 1.0.0 –strata –best –n 1 –m 1 )
H3K4me3, H3K9ac, CTCF peaks have been called by MACS (1.4.2 version 20120305, default parameters) take correspond input sequence as control.
H3K9me2 and H3K27me3 domains have been called by RSEG (version 0.4.8-rc) with binsize 10kb and 5kb respectively
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: BEAS-2B cells

growth_protocol: Immortalized human Bronchial Epithelial Cells (Beas-2B) were cultured in Dulbecco’s Modified Eagle’s Medium (Cellgro) supplemented with 1% Penicillin Streptomycin and 10% Fetal Bovine Serum (Atlanta Biologicals) at 37° C and 5 % CO2.

extract_protocol:
For ChIP, untreated and NiCl2 exposed BEAS-2B cells were crosslinked with 1% formaldehyde for 10 minutes at 25°C and sonicated to obtain 200-500 base pair fragments. ChIP was performed using ChIP grade antibodies against H3K9me2 (Abcam, ab1220), H3K27me3 (Millipore, 07-449), H3K4me3 (Millipore, 07-473), H3K9ac (Abcam, ab4441) and CTCF (Active Motif, 61311).
ChIP-Seq libraries were prepared using Illumina TruSeq ChIP sample preparation Kit (IP-202-1024), according to manufacturer’s protocol.

treatment_protocol: For exposing cells to nickel, NiCl2  (Sigma N6136) was added to the media at a concentration of 500 mM and the cells were cultured for 72 hours.

tag: treatment

tag: time point (hours)

tag: chip antibody


title: H3K9me2_ChIPSeq_Nickel

value: H3K9me2 (Abcam, ab1220)


title: H3K9me2_ChIPSeq_Control


title: Namalwa DNAse-Seq

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
Base-calling (Illumina)
DNAse-seq reads were aligned to the hg18 genome assembly using Bowtie 1.00 to SAM output using standard parameters
Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011.
Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011
Peaks were called using CoCAS
Genome_build: hg18
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Peaks were called using CoCAS

source_name: Burkitt's lymphoma cell line

growth_protocol: Cells lines from Hodgkin's lymphoma (L1236, L428 and L519), Pro-B lymphoblastic leukemia (Reh) and Burkitt's lymphoma (Namalwa) were grown in IMDM medium containint 10% FCS, penicillin 100 U/mL, and streptomycin 50 pg/mL and incubated at 37C in a humidified atmosphere containing 5% CO2, with cell densities kept under 5x105 per ml

extract_protocol: DNaseI-Seq samples were generated from a size selection of DNaseI-digested DNA fragments comprised within a range of 100 to 600 bp and subjected to library preparation as per manufacturer´s instruction (Illumina)

treatment_protocol: To perform DNaseI accessibility assays with HRS and NH cell lines, the optimal cell number and DNaseI (DPFF DNaseI, Worthington Biochemical Corporation) concentration was titrated for each cell line. The DNA digestion extent was comparable in all the generated samples as measured by RT-PCR (5). Briefly, nuclei were isolated from 1-5 x 106 cells by detergent lysis and immediately digested for 3 min at 33 °C with DNaseI at 1-10 U/ml in a 1 mM CaCl2 supplemented buffer. The nuclei were lysed, the nuclear proteins digested with 1 mg/ml Proteinase K overnight at 37 °C

tag: cell line

value: Namalwa

tag: lymphoma type

value: non-Hodgkin's Lymphoma cell line

tag: passages

tag: dnasei origin

value: Worthington

tag: dnasei units (u/ml)


title: H3K4me3_ChIPSeq_Nickel

value: H3K4me3 (Millipore, 07-473)


title: NonDorm030411

city: Erie

first: Michael

middle: A

last: Campbell

state: PA

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

library_source: transcriptomic

data_processing:
Illumina software used for basecalling.
Sequence reads were trimmed for adaptor sequences and filtered using Galaxy with 100% of all reads having a minimum phred score of 20
Reads were mapped t  double monoploid DM1-3 516 R44 (DM1-3), Solanum tuberosum Grp. Phureja line (2n=24)
Reference genome was PGSC_DM_v3_2.1.11
Supplementary_files_format_and_content: tab delimited text file with FPKM values

molecule: total RNA

organism: Solanum tuberosum

source_name: Meristems excised from nondormant potato tubers in spring 2011

growth_protocol: Plants were field grown in the Red River Valley in North Dakota. Tubers were mechanically harvested.

extract_protocol:
Meristems were excised with a micro curette, frozen in liquid N2. RNA was isolated using an Ambion RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dormant tubers mersitems were harvested approximately two weeks after harvest. Nondormant tubers mmeristesm were harvested from tubers stored at 4 C until peeping.

tag: cultivar

value: Russet Burbank

tag: tissue

value: Non-dormant meristem


title: H3K4me3_ChIPSeq_Control


title: Kasumi1_siRE_ATGTCA_rep3

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Quality of reads was verified using FASTQC analysis and reads aligned to the hg19 human genome build using TopHat
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values for each gene were extracted and differentially expressed genes were extracted using  using Cufflinks and limma R package. All genes with p-value ≤ 0.1 were considered
The reads in the resulting alignment files were used to generate density maps using genomeCoverageBed function from bedtools (Quinlan and Hall, 2010)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: RNA_seq replicate 3 from Kasumi1 cells after RUNX1/ETO knockdown

extract_protocol:
Kasumi-1 cells were transfected with 200 nM siRNA using a Fischer EPI 3500 electroporator (Fischer, Heidelberg, Germany). RNA samples from three experimental replicates per condition were processed using the Tru-seq RNA Sample Prep Kit v2 from Illumina according to manufacturer’s protocol.
Libraries were run in 4x multiplex on an Illumina Hiseq 2000 sequencer generating ~90 million paired-end reads per sample

tag: genotype

value: siRE

value: transfection with RUNX1-ETO siRNA


title: Foxp2hum/hum DLS

city: Martinsried

first: Cemil

last: Kerimoglu

address: Grosshaderner Strasse 2

institute: Ludwig-Maximilians University Munich

data_processing:
Basecalls were performed using Ibis.
Sequenced reads were mapped to mm9 whole genome using TopHat 1.4.1.
Mapped reads were counted by Bedtools.
Differential gene expression was analyzed by multifactor model of DESeq package (Anders and Huber, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: The Excel file includes normalized reads computed by DESeq for each detected gene in every sample used.

organism: Mus musculus

source_name: Dorsolateral striatum (DLS)

extract_protocol:
Brains from 8-week old mice were isolated and flash-frozen in isopentane (-20°C). Samples from dorsomedial and dorsolateral striatum were collected with laser capture microdissection. RNA was isolated with RNeasy Micro kit from Qiagen.
Enrichment for mRNA, RNA fragmentation and cDNA synthesis were performed using an in-house protocol modified from Illumina TruSeq protocol in order to be suitable for small RNA amounts (15 ng of total RNA/sample).

tag: strain

value: dorsolateral striatum

tag: age

value: 8 weeks


title: Foxp2hum/hum DMS

source_name: Dorsomedial striatum (DMS)

value: dorsomedial striatum


title: Kasumi1_siRE_TGACCA_rep2

source_name: RNA_seq replicate 2 from Kasumi1 cells after RUNX1/ETO knockdown


title: NonDorm032210

source_name: Meristems excised from nondormant potato tubers in spring 2010


title: NonDorm031308

source_name: Meristems excised from nondormant potato tubers in spring 2008


title: Kasumi1_siMM_TAGCTT_rep2

source_name: RNA_seq replicate 2 from Kasumi1 cells

value: siMM

value: transfection with scrambled siRNA


title: Kasumi1_siMM_ACTTGA_rep3

source_name: RNA_seq replicate 3 from Kasumi1 cells


title: Kasumi1_siRE_AGTCAA_rep1

source_name: RNA_seq replicate 1 from Kasumi1 cells after RUNX1/ETO knockdown


title: NonDorm022406

source_name: Meristems excised from nondormant potato tubers in spring 2006


title: Dorm112009

source_name: Meristems excised from potato tubers harvested in fall 2009

value: dormant meristem


title: Kasumi1_siMM_GTCCGC_rep1

source_name: RNA_seq replicate 1 from Kasumi1 cells


title: Dorm113005

source_name: Meristems excised from potato tubers harvested in fall 2005


title: Dorm102207

source_name: Meristems excised from potato tubers harvested in fall 2007


title: RNASeq_Nickel

description: Sample 2

data_processing:
basecalling have been done by CASAVA-1.8.2
RNA-seq raw sequence data have been aligned to human hg19 by tophat (version 2.0.8 beta default parameters) with known reference annotation gtf file download from GENCODE website (v16). The gtf file have been modified to be compatible to tophat that only records denoted as “CDS,exon,start_codon,stop_codon,UTR” have been kept. Records annotated as "miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,rRNA" have been export to another mask gtf file for further usage.
To estimate the FPKM values, cuffdiff from cufflinks package (version 2.1.1 default parameters with --multi-read-correct and --frag-bias-correct) have been used with mask gtf file that 15836 genes have been estimated as expressed in control( Fragments Per Kilobase of exon per Million fragments mapped (FPKM) > 1).
Genome_build: hg19

source_name: BEAS-2B cells

extract_protocol:
Total RNA was isolated from untreated and nickel treated cells using RNeasy kit (Qiagen, 74104) according to manufacturer’s instructions.
RNA-Seq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002), according to manufacturer’s protocol.


title: RNASeq_Control

description: Sample 1


title: CTCF_ChIPSeq_Nickel

value: CTCF (Active Motif, 61311)


title: H3K9ac_ChIPSeq_Nickel

value: H2K9ac (Abcam, ab4441)


title: H3K9ac_ChIPSeq_Control


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: miRNA-Seq analysis of placenta (basal plate and villi) tissue from CTL04 (m09076) using Illumina HiSeq 2000
library name: m09076
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 5.6
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.326 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127165_UCSF-UBC.Placenta_Basal_Plate.smRNA-Seq.CTL04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09076-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Basal Plate smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Basal Plate, Donor CTL04 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19965
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,405,787
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.43
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1127165_UCSF-UBC.Placenta_Basal_Plate.smRNA-Seq.CTL04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09076-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Basal Plate smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Basal Plate, Donor CTL04 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19988
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PBP smRNA 04 76
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Basal Plate smRNA-Seq Donor CTL04 Library m09076 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,405,787
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.43
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1127165_UCSF-UBC.Placenta_Basal_Plate.smRNA-Seq.CTL04.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09076-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Basal Plate smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Basal Plate, Donor CTL04 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20011
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,405,787
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.43
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

extract_protocol: library construction protocol: Refer to document 'miRNA3 - Plate Format miRNA Library Construction' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Placenta

tag: histological type

value: Basal plate tissue

tag: is tumor

value: No

value: primary tissue

value: placenta (basal plate and villi) tissue


title: Dorm1126210

source_name: Meristems excised from potato tubers harvested in fall 2010

value: Russet Burbank


description:
design description: miRNA-Seq analysis of peripheral mononuclear cell from TC017 (m09079) using Illumina HiSeq 2000
library name: m09079
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 5.7
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 0.8168 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127163_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.smRNA-Seq.TC017.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09079-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC017 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19973
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,739,694
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 68.95
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.073

**********************************************************************

ANALYSIS FILE NAME: GSM1127163_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.smRNA-Seq.TC017.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09079-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC017 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19996
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PBM smRNA 17 79
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells smRNA-Seq Donor TC017 Library m09079 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,739,694
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 68.95
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.073

**********************************************************************

ANALYSIS FILE NAME: GSM1127163_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.smRNA-Seq.TC017.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09079-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Peripheral Blood Mononuclear Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC017 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20019
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,739,694
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 68.95
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.073

**********************************************************************

value: Blood

value: Peripheral blood mononuclear cell

value: primary cell


description:
design description: miRNA-Seq analysis of foreskin melanocyte from skin03 (m09089) using Illumina HiSeq 2000
library name: m09089
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 9.2
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.584 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127159_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.smRNA-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09089-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19966
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,312,920
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 88.07
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.366

**********************************************************************

ANALYSIS FILE NAME: GSM1127159_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.smRNA-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09089-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19989
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFM smRNA 03 89
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells smRNA-Seq Donor skin03 Library m09089 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,312,920
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 88.07
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.366

**********************************************************************

ANALYSIS FILE NAME: GSM1127159_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.smRNA-Seq.skin03.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09089-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Penis Foreskin Melanocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20012
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,312,920
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 88.07
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.366

**********************************************************************

value: Penis

value: Melanocyte

value: primary cell culture

tag: cell type

value: foreskin melanocyte


description:
design description: miRNA-Seq analysis of foreskin melanocyte from skin02 (m09088) using Illumina HiSeq 2000
library name: m09088
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 8.1
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.704 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127164_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.smRNA-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09088-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19964
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,905,842
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 85.17
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.24

**********************************************************************

ANALYSIS FILE NAME: GSM1127164_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.smRNA-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09088-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19987
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFM smRNA 02 88
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells smRNA-Seq Donor skin02 Library m09088 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,905,842
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 85.17
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.24

**********************************************************************

ANALYSIS FILE NAME: GSM1127164_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.smRNA-Seq.skin02.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09088-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Penis Foreskin Melanocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin02 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20010
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,905,842
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 85.17
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.24

**********************************************************************


description:
design description: miRNA-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL02 (m09068) using Illumina HiSeq 2000
library name: m09068
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 3.1
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 0.4648 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127162_UCSF-UBC.Placenta_Chorion_Smooth.smRNA-Seq.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09068-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Chorion Smooth, Donor CTL02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19967
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,943,484
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.75
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.529

**********************************************************************

ANALYSIS FILE NAME: GSM1127162_UCSF-UBC.Placenta_Chorion_Smooth.smRNA-Seq.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09068-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Chorion Smooth, Donor CTL02 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19990
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PCS smRNA 02 68
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth smRNA-Seq Donor CTL02 Library m09068 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,943,484
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.75
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.529

**********************************************************************

ANALYSIS FILE NAME: GSM1127162_UCSF-UBC.Placenta_Chorion_Smooth.smRNA-Seq.CTL02.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09068-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Chorion Smooth smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Chorion Smooth, Donor CTL02 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20013
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,943,484
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.75
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.529

**********************************************************************

value: Chorion smooth tissue


description:
design description: miRNA-Seq analysis of placenta (villi) tissue from CTL04 (m09075) using Illumina HiSeq 2000
library name: m09075
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 4.8
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.9239 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127166_UCSF-UBC.Placenta_Villi.smRNA-Seq.CTL04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09075-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Villi smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Villi, Donor CTL04 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19974
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,336,896
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.93
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1127166_UCSF-UBC.Placenta_Villi.smRNA-Seq.CTL04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09075-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Villi smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Villi, Donor CTL04 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19997
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PV smRNA 04 75
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Villi smRNA-Seq Donor CTL04 Library m09075 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,336,896
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.93
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1127166_UCSF-UBC.Placenta_Villi.smRNA-Seq.CTL04.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09075-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Villi smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Villi, Donor CTL04 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20020
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,336,896
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.93
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

value: Villi tissue

value: placenta (villi) tissue


description:
design description: miRNA-Seq analysis of placenta (trophoblast) tissue from CTL05 (m09078) using Illumina HiSeq 2000
library name: m09078
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 6.9
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.3887 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127160_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.smRNA-Seq.CTL05.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09078-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Trophoblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Trophoblast Primary Cells, Donor CTL05 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19982
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,945,993
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 91.43
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.457

**********************************************************************

ANALYSIS FILE NAME: GSM1127160_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.smRNA-Seq.CTL05.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09078-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Trophoblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Trophoblast Primary Cells, Donor CTL05 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20005
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PT smRNA 05 78
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Trophoblast Primary Cells smRNA-Seq Donor CTL05 Library m09078 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,945,993
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 91.43
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.457

**********************************************************************

ANALYSIS FILE NAME: GSM1127160_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.smRNA-Seq.CTL05.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09078-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Trophoblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Trophoblast Primary Cells, Donor CTL05 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20028
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,945,993
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 91.43
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.457

**********************************************************************

value: Trophoblast

value: placenta (trophoblast) tissue


description:
design description: miRNA-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL03 (m09071) using Illumina HiSeq 2000
library name: m09071
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 4.8
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 0.8778 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127158_UCSF-UBC.Placenta_Chorion_Smooth.smRNA-Seq.CTL03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09071-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Chorion Smooth, Donor CTL03 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19968
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,474,335
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 84.44
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.487

**********************************************************************

ANALYSIS FILE NAME: GSM1127158_UCSF-UBC.Placenta_Chorion_Smooth.smRNA-Seq.CTL03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09071-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Chorion Smooth, Donor CTL03 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19991
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PCS smRNA 03 71
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth smRNA-Seq Donor CTL03 Library m09071 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,474,335
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 84.44
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.487

**********************************************************************

ANALYSIS FILE NAME: GSM1127158_UCSF-UBC.Placenta_Chorion_Smooth.smRNA-Seq.CTL03.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09071-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Chorion Smooth smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Chorion Smooth, Donor CTL03 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20014
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,474,335
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 84.44
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.487

**********************************************************************

value: Placenta


description:
design description: miRNA-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (m09072) using Illumina HiSeq 2000
library name: m09072
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 4.6
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 0.7787 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127161_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM02.m09072.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01586-1-m09072-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Germinal Matrix smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Brain Germinal Matrix, Donor HuFGM02 Library m09072 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19961
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,355,098
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 89.1
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1127161_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM02.m09072.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01586-1-m09072-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 Library m09072 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19984
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BGM smRNA 02 86
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix smRNA-Seq Donor HuFGM02 Library M01586 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,355,098
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 89.1
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1127161_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM02.m09072.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01586-1-m09072-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Brain Germinal Matrix smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Brain Germinal Matrix, Donor HuFGM02 Library m09072 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20007
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,355,098
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 89.1
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

value: male

value: Brain

value: Germinal matrix tissue

value: No

value: brain (germinal matrix) tissue


description:
design description: miRNA-Seq analysis of placenta (trophoblast) tissue from CTL04 (m09077) using Illumina HiSeq 2000
library name: m09077
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 6.4
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.1273 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127156_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.smRNA-Seq.CTL04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09077-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Trophoblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Trophoblast Primary Cells, Donor CTL04 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19980
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,924,251
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 89.36
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.457

**********************************************************************

ANALYSIS FILE NAME: GSM1127156_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.smRNA-Seq.CTL04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09077-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Trophoblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Trophoblast Primary Cells, Donor CTL04 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20003
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PT smRNA 04 77
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Trophoblast Primary Cells smRNA-Seq Donor CTL04 Library m09077 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,924,251
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 89.36
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.457

**********************************************************************

ANALYSIS FILE NAME: GSM1127156_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.smRNA-Seq.CTL04.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09077-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Trophoblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Trophoblast Primary Cells, Donor CTL04 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20026
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,924,251
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 89.36
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.457

**********************************************************************

value: primary tissue


description:
design description: miRNA-Seq analysis of placenta (amniotic membrane) tissue from CTL02 (m09069) using Illumina HiSeq 2000
library name: m09069
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN N/A
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: N/A ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127154_UCSF-UBC.Placenta_Amnion.smRNA-Seq.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09069-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Amnion, Donor CTL02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19975
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,866,675
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.6
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1127154_UCSF-UBC.Placenta_Amnion.smRNA-Seq.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09069-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Amnion, Donor CTL02 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19998
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PA smRNA 02 69
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion smRNA-Seq Donor CTL02 Library m09069 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,866,675
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.6
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1127154_UCSF-UBC.Placenta_Amnion.smRNA-Seq.CTL02.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09069-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Amnion smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Amnion, Donor CTL02 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20021
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,866,675
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.6
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

value: Amnion tissue

value: placenta (amniotic membrane) tissue


description:
design description: miRNA-Seq analysis of placenta (villi) tissue from CTL02 (m09067) using Illumina HiSeq 2000
library name: m09067
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RQS 4.3
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.2178 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1127157_UCSF-UBC.Placenta_Villi.smRNA-Seq.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09067-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Villi smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Villi, Donor CTL02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19969
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,268,906
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.5
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.461

**********************************************************************

ANALYSIS FILE NAME: GSM1127157_UCSF-UBC.Placenta_Villi.smRNA-Seq.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09067-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Villi smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Villi, Donor CTL02 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.19992
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PV smRNA 02 67
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Villi smRNA-Seq Donor CTL02 Library m09067 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,268,906
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.5
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.461

**********************************************************************

ANALYSIS FILE NAME: GSM1127157_UCSF-UBC.Placenta_Villi.smRNA-Seq.CTL02.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09067-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Villi smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Villi, Donor CTL02 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.20015
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,268,906
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.5
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.461

**********************************************************************