title: Caltech_ChipSeq_C2C12_H3K27me3_Control_32bp_EqS_2.0pct_60hr

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: F

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: control

tag: control description

tag: treatment

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

tag: age description


title: Caltech_ChipSeq_C2C12_H3K4me3_Control_50bp

status: Public on Apr 19 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

value: Caltech-m

value: Wold - Califonia Institute of Technology

tag: datatype description

tag: cell

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me3

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

value: This data represents a control being compared to experiments using read length of 50 bp

tag: treatment description

value: No special treatment or protocol applies

tag: age

value: immortalized

value: Immortal cells

tag: controlid

tag: labexpid

tag: labversion

value: Myoblast

tag: replicate

tag: strain

tag: strain description

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_H3K36me3_Control_50bp

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: control

tag: control description


title: Caltech_ChipSeq_C2C12_H3K27me3_Control_32bp

value: Caltech-m

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

value: F

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

value: Millipore

value: This data represents a control being compared to experiments using read length of 32 bp

tag: treatment

tag: treatment description

tag: age description


title: Caltech_ChipSeq_C2C12_H3K36me3_Control_50bp_EqS_2.0pct_60hr

tag: lab

tag: lab description

value: Wold - Califonia Institute of Technology

value: mouse

value: This data represents a control being compared to experiments using read length of 50 bp

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

tag: age

tag: controlid

tag: labexpid

tag: labversion

value: Myocyte

tag: labversion description

tag: replicate

tag: strain

tag: strain description


title: Caltech_ChipSeq_C2C12_Input_Control_50bp_EqS_2.0pct_60hr

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

tag: cell organism

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control

tag: control description

value: immortalized

value: Immortal cells

value: Strain C3H, Very related to C57BL/6


title: LICR_ChipSeq_MEL_CTCF_immortalized

source_name: MEL

tag: lab

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: Chromatin IP Sequencing

value: MEL

tag: cell description

value: Leukemia (K562 analog)

tag: cell sex

value: M

tag: antibody

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

tag: antibody vendorid

tag: age description

value: std

value: Standard input signal for most experiments.

tag: softwareversion

value: Bowtie

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


title: Caltech_ChipSeq_C2C12_H3K79me2_(ab3594)_Control_50bp

value: Caltech-m

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

value: ChipSeq

value: mouse

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: F

value: Rabbit polyclonal. Antibody Target:H3K79me2

value: H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3)

value: Abcam

value: This data represents a control being compared to experiments using read length of 50 bp

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: age

tag: controlid

tag: labexpid

tag: labversion

value: Myoblast

tag: replicate

tag: strain

tag: strain description


title: LICR_ChipSeq_Testis_Input_adult-8wks

source_name: Testis

tag: lab

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: Testis

tag: cell organism

tag: cell description

tag: cell sex

value: M

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: Adult 8 weeks

tag: control

tag: control description


title: LICR_ChipSeq_Limb_CTCF_E14.5

source_name: Limb

tag: lab description

tag: datatype

value: ChipSeq

value: Limb

value: mouse

value: U

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: age

tag: age description

value: Embryonic day 14.5

value: std

value: Standard input signal for most experiments.

tag: softwareversion

value: Bowtie

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


title: Caltech_ChipSeq_C2C12_H3K4me3_Control_50bp_EqS_2.0pct_60hr

tag: lab

value: Caltech-m

value: Wold - Califonia Institute of Technology

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: F

value: rabbit polyclonal. Antibody Target:H3K4me3

value: Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.

value: This data represents a control being compared to experiments using read length of 50 bp

tag: treatment

tag: treatment description

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

value: immortalized

value: Immortal cells

tag: controlid

tag: labexpid

tag: labversion

value: Myocyte

tag: labversion description

tag: replicate

tag: strain

tag: strain description

value: Strain C3H, Very related to C57BL/6


title: LICR_ChipSeq_Thymus_Pol2_adult-8wks

source_name: Thymus

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

value: Thymus

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

value: M

tag: antibody

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

value: Adult 8 weeks

tag: control

value: std

tag: control description


title: LICR_ChipSeq_OlfactBulb_CTCF_adult-8wks

source_name: OlfactBulb

tag: lab

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: OlfactBulb

value: Olfactory Bulb

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: antibody vendorid

tag: age

tag: age description

value: Standard input signal for most experiments.

tag: controlid

tag: softwareversion

value: Bowtie

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


title: hyl1-2_flower_8week

status: Public on Apr 25 2012

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

library_source: transcriptomic

data_processing: The raw colorspace reads containing inserts derived from 20-25nt RNAs were identified by searching for 3' matches (allowing up to two mismatches) to the sequencing adapter sequence (in colorspace); the inferred adapter sequences were then trimmed, leaving 20-25nt colorspace reads.  These data were then translated into DNA space while simultaneously discarding any reads with ambiguous (e.g., one or more "." characters) data.  The data in the Sample data tables are simple counts of each of these 20-25nt total RNAs.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: flowers and flower buds, hyl1-2

growth_protocol: 12hr light / 12hr dark, 21C.

extract_protocol: Life Tech Total RNA-seq kit, total RNA modification, per manufacturer's instructions.

tag: ecotype

tag: genotype

tag: tissue

value: flowers and flower buds


title: LICR_ChipSeq_Testis_Pol2_adult-8wks

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

value: Testis

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

value: M

tag: antibody

tag: labversion

tag: replicate

tag: strain

tag: strain description


title: LICR_ChipSeq_Spleen_CTCF_adult-8wks

source_name: Spleen

tag: lab

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: Spleen

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: age

value: Adult 8 weeks

tag: control

value: std

tag: control description


title: LICR_ChipSeq_Placenta_Input_adult-8wks

source_name: Placenta

tag: lab description

tag: datatype

value: Placenta

tag: cell organism

tag: cell description

value: F

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age description

tag: controlid

tag: softwareversion


title: LICR_ChipSeq_OlfactBulb_Pol2_adult-8wks

tag: lab

tag: datatype description

value: OlfactBulb

value: Olfactory Bulb

tag: cell sex

tag: antibody

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

value: Standard input signal for most experiments.

tag: labversion

tag: replicate

value: Bowtie

tag: strain

tag: strain description


title: LICR_ChipSeq_Limb_Pol2_E14.5

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: cell

value: Limb

value: mouse

value: U

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: age

value: Embryonic day 14.5

tag: control

tag: control description

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


title: CME-W2 (Celniker/RNA:459) extraction1_seq1 aliquote 1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

data_processing: sequence analysis protocol. 1. 3' adapter sequences starting with 'CTGTAGG' were trimmed with fastx_clipper (fastx_toolkit: http://hannonlab.cshl.edu/fastx_toolkit/). Only reads with recognized 3' adapter and longer than 18 bases were considered in further analysis.2. The trimmed sequences were mapped to genome with Bowtie. only sequences can perfectly match to genome were acceptable.  Processed data are obtained using following parameters: genome version is 5

organism: Drosophila melanogaster

source_name: CME-W2 (Celniker/RNA:459)

growth_protocol: Summary of conditions used to produce cell lines for transcriptomics group, excluding W1-Cl.8+, Kc167, S2-DRSC and DmBG3-c2, each of which have their own protocols.  For details see relevant pages at the DGRC Cell Lines page (http://dgrc.cgb.indiana.edu/cells).

extract_protocol:
Protocol for isolation of total RNA from cell cultures, which retains short RNAs.
mRNAs were purified from total RNA extracts, using standard Illumina protocol.  Briefly, 10ug total RNA was bound to oligo(dT) beads, washed twice, and eluted with 10mM Tris-HCl, using Ambion kit.
[A] Gel purification of RNA sample.  1. Spike 50 ug of total RNA with 32P-labeled 19bp and 24bp oligos (~10,000 counts per second) and load the sample in a 15% polyacrylamide/urea gel (Sequagel, National Diagnostics). Run the gel in 1x TBE at constant 10W for 1-2 hours. Expose the gel for 10 minutes in Phosphoimager.  2. Excise the band corresponding to the desired size of small RNA (~19-24 nt) into Eppendorf tubes, including the radio-labeled oligos. Add 400uL of 0.4M NaCl. Freeze rapidly in dry ice. Incubate (thaw) for 16 hours at room temperature with agitation to maximize RNA elution.  3. Spin down gel slice homogenate through micropore filter (Ultrafree-MC, 0.22um, Millipore) for 1 minute at room temperature. Add 20ug of glycogen and 2 volumes of 100% Ethanol (RNase-free). Incubate at -20oC for 4 hours.  4. Spin the sample at 4oC for 30 minutes. Wash the pellet with 70% EtOH, air dry for 2 min and resuspend in DEPC MQ water and proceed to section B. [B] 3'-linker ligation and gel purification of the ligated RNA product.  5. Ligate 50 pmol of Modban oligo (IDT:miRNA cloning linker 1) to the 3' terminus of the purified RNA sample in 1X ATP-free T4 RNA ligase buffer (50mM Tris-HCl (pH 7.5-7.6), 10mM MgCl2, 10mM DTT, 60ug/mL BSA) and 10% DMSO, with 5-10 pmol of T4 RNA ligase 2 Rnl2(1-249) (Ho et al, 2004). Incubate at room temperature for 1 hour 30 min.  6. Load the sample on a 15% polyacrylamide/urea gel as described above and expose the gel for 30 minutes.  7. Excise the band corresponding to the desired size of small RNA (~36-41 nt) into Eppendorf tubes, including the ligated radio-labeled oligos.  8. Proceed again with overnight elution and precipitation as in steps 2-4. [C] 5'-linker ligation and gel purification of the ligated RNA product.  9. Ligate 50 pmol of Solexa linker to the 5' terminus of the RNA sample in 1XT4 RNA ligase buffer (Ambion) and 10% DMSO with 5-10 Units of T4 RNA ligase (Ambion). Incubate at 37oC for 1 hour 30 min.  10. Load the sample on a 15% polyacrylamide/urea gel as described above and expose the gel for 1 hour.  11. Excise the band corresponding to the desired size of small RNA (~68-73 nt) into Eppendorf tubes, including the ligated radio-labeled oligos.  12. Proceed again with overnight elution and precipitation as in steps 2-4.  [D] Reverse transcription and cDNA amplification.  13. Reverse-transcribe the ligated RNA product by using 21 pmol of BanOne primer and 1 ul Superscript III Reverse Transcriptase (Invitrogen), for 1 hour at 50oC in 20 ul of reaction. Then, amplify 5 ul of the cDNA product with 100 pmol of primers Sol_5_SBS3 and Sol_3_Modban, and 5 Units of Taq Polymerase (New England Biolabs): [94oC 15 sec; 54oC 30 sec; 72oC 30 sec] x 5 cycles and [94oC 15 sec; 60oC 30 sec; 72oC 30 sec] x 17 cycles.  14. Clean up the PCR product with phenol:chloroform and chloroform. Precipitate the amplified cDNA with Ethanol 100%.  [E] Digestion of the spikes and gel-purification of the amplified cDNA.  15. Perform PmeI (New England Biolabs) digestion of radiolabeled oligos (spikes) for 3-4 hours at 37oC and purify the amplified cDNA in a 2% low-melt agarose gel (SeaKem).  16. Excise the ~ 120 bp DNA band and proceed to hot-phenol-based gel purification. Transfer aqueous phase to a new eppendorf tube and clean up with phenol:chloroform and chloroform. Precipitate the DNA with Ethanol 100% and resuspend it in 20uL water.  17. Perform Agilent test and dilute the sample to 10nM for Solexa sequencing.
1. cluster generation2. the length of short reads, i.e., the number of sequencing cycles, should list here. in this protocol, it is 35 cycles of sequencing.3. after each cycle, a CCD camera will scan the cells to make a image.

tag: cell line

value: CME W2

tag: tissue

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: Sex

value: Unknown


title: hyl1-2-dcl1-20_flower_8week

source_name: flowers and flower buds, hyl1-2/dcl1-20

tag: ecotype

tag: genotype

value: flowers and flower buds


title: LICR_ChipSeq_Thymus_CTCF_adult-8wks

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: Thymus

tag: cell organism

tag: cell description

tag: cell sex

value: M

tag: antibody

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: age description

value: Adult 8 weeks

value: std

tag: controlid

tag: labversion

tag: replicate

tag: softwareversion


title: LICR_ChipSeq_Heart_Input_E14.5

source_name: Heart

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

tag: cell

value: Heart

value: mouse

value: U

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age

tag: control

tag: control description

value: Standard input signal for most experiments.

value: Bowtie

tag: strain

tag: strain description


title: LICR_ChipSeq_BMDM_Pol2_adult-8wks

source_name: BMDM

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: BMDM

value: Bone marrow derived macrophage

value: F

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

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


title: CME-W2 (Celniker/RNA:461) extraction1_seq1 aliquote 1

source_name: CME-W2 (Celniker/RNA:461)

tag: cell line

value: CME W2

tag: tissue

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: Sex

value: Unknown


title: mbn2 (Celniker/RNA:47) extraction1_seq1 aliquote 1

source_name: mbn2 (Celniker/RNA:47)

value: embryonic/larval hemocyte

value: late embryonic stage

tag: genotype

value: l(2)malignant blood neoplasm


title: Caltech_ChipSeq_C2C12_H3K79me2_(ab3594)_Control_50bp_EqS_2.0pct_60hr

value: Caltech-m

value: Wold - Califonia Institute of Technology

value: ChipSeq

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: cell sex

tag: antibody

value: Rabbit polyclonal. Antibody Target:H3K79me2

value: H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3)

value: Abcam

tag: control

value: This data represents a control being compared to experiments using read length of 50 bp

tag: treatment

tag: treatment description

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

tag: labexpid

tag: labversion

value: Myocyte

tag: labversion description

tag: replicate

value: Strain C3H, Very related to C57BL/6


title: LICR_ChipSeq_BMDM_Input_adult-8wks

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

value: BMDM

value: Bone marrow derived macrophage

value: F

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: Adult 8 weeks

value: std

tag: control description

value: Standard input signal for most experiments.

tag: softwareversion

value: Bowtie

tag: strain

tag: strain description

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


title: ML-DmD8 (Celniker/RNA:207) extraction1_seq1 aliquote 1

source_name: ML-DmD8 (Celniker/RNA:207)

tag: cell line

tag: tissue

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: genotype

value: y v f mal


title: Lai_DTT-4h extraction1_seq1 aliquote 1

data_processing: sequence analysis protocol. 1. 3' adapter sequences starting with 'CTGTAGG' were mapped and trimmed, allowing 2 mismatches when starting from base 20 in a read. Only reads with recognized 3' adapter and longer than 18 bases were considered in further analysis.2. The trimmed sequences were mapped to genome by BLAT. only sequences can perfectly match to genome were acceptable.  Processed data are obtained using following parameters: genome version is 5

growth_protocol:
S2 and S2R+ cell culture:S2 (or S2R+) cells were grown in Schneider's Drosophila medium supplemented with 10% FBS, 100U/ml penicillin and 100ug/ml streptomycin at 26C in 25cm^2 or 75cm^2 flasks. Cells were harvested by centrifugation at 216g for 5 minutes in a 15ml conical tube. The pellet was resuspended in Trizol LS reagent.
cells were cultured in standard media supplemented with5 mM Dithiothreitol for 4 hours prior to RNA harvest

value: embryo-derived cell-line

value: late embryonic stage

tag: Sex

value: Male


title: S1 (Celniker/RNA:25) extraction1_seq1 aliquote 1

source_name: S1 (Celniker/RNA:25)

value: Unknown


title: LICR_ChipSeq_OlfactBulb_Input_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: OlfactBulb

tag: cell organism

value: mouse

tag: cell description

value: Olfactory Bulb

tag: cell sex

value: M

tag: antibody

tag: age

tag: age description

tag: control

tag: controlid

tag: labversion


title: LICR_ChipSeq_SmIntestine_Pol2_adult-8wks

source_name: SmIntestine

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: SmIntestine

value: Small Intestine

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

value: Adult 8 weeks

value: std

tag: control description

value: Standard input signal for most experiments.

tag: replicate

tag: softwareversion

value: Bowtie

tag: strain


title: ML-DmD20-c5 (Celniker/RNA:191) extraction1_seq1 aliquote 1

source_name: ML-DmD20-c5 (Celniker/RNA:191)

tag: cell line

tag: tissue

value: antenna disc-derived cell-line

tag: developmental stage

value: third instar larval stage

tag: genotype

value: y v f mal

tag: Sex

value: Male


title: ML-DmD16-c3 (Celniker/RNA:133) extraction1_seq1 aliquote 1

source_name: ML-DmD16-c3 (Celniker/RNA:133)

value: dorsal mesothoracic disc

value: Female


title: LICR_ChipSeq_BAT_Input_adult-24wks

source_name: BAT

tag: lab

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: BAT

tag: cell organism

value: mouse

tag: cell description

value: Brown adipocytes tissue

tag: cell sex

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age

tag: age description

value: Adult 24 weeks

tag: control

tag: controlid

tag: labversion

tag: strain description

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


title: ML-DmD20-c5 (Celniker/RNA:187) extraction1_seq1 aliquote 1

source_name: ML-DmD20-c5 (Celniker/RNA:187)

tag: cell line

tag: tissue

value: antenna disc-derived cell-line


title: ML-DmD8 (Celniker/RNA:205) extraction1_seq1 aliquote 1

source_name: ML-DmD8 (Celniker/RNA:205)

tag: developmental stage

value: third instar larval stage

tag: genotype


title: LICR_ChipSeq_MEL_Pol2_immortalized

source_name: MEL

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: MEL

value: Leukemia (K562 analog)

value: M

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

value: immortalized

value: Immortal cells

value: std

tag: control description

value: Standard input signal for most experiments.

tag: replicate

tag: softwareversion

value: Bowtie

tag: strain


title: mbn2 (Celniker/RNA:43) extraction1_seq1 aliquote 1

source_name: mbn2 (Celniker/RNA:43)

value: embryonic/larval hemocyte

value: late embryonic stage

value: l(2)malignant blood neoplasm

tag: Sex

value: Unknown


title: LICR_ChipSeq_BMDM_CTCF_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: BMDM

tag: cell organism

value: mouse

tag: cell description

value: Bone marrow derived macrophage

tag: cell sex

value: F

tag: antibody

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: age

tag: age description

value: Adult 8 weeks

tag: control

tag: controlid

tag: labversion

tag: strain description

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


title: LICR_ChipSeq_Thymus_Input_adult-8wks

source_name: Thymus

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: tissue

value: thymus

value: M

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: std

value: Standard input signal for most experiments.

value: Bowtie


title: OSC cells V144 extraction2_seq1 aliquote 1

status: Public on Apr 18 2012

source_name: OSC cells V144

tag: cell line

value: OSC

tag: tissue

value: ovary stem cells

tag: developmental stage

value: adult stage

tag: Sex

value: Female


title: CME_L1 extraction1_seq1 aliquote 1

source_name: CME_L1 cells

value: ventral prothoracic disc

value: third instar larval stage

value: Unknown


title: fGS/OSS extraction1_seq1 aliquote 1

source_name: fGS/OSS cells

value: fGS/OSS

value: ovary


title: S1 extraction1_seq1 aliquote 1

source_name: S1 cells

value: embryo-derived cell-line

value: late embryonic stage


title: OSC cells M031 extraction1_seq1 aliquote 1

source_name: OSC cells M031


title: LICR_ChipSeq_MEL_Input_immortalized

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

tag: line

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

tag: cell sex

value: M

value: immortalized

value: immortalized cell line

tag: control description

tag: replicate

tag: softwareversion

tag: strain

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


title: TEAD4

city: Kansas City

first: Byunggil

last: Yoo

state: KS

address: 3901 Rainbow Blvd

institute: KUMC

data_processing:
Basecalls performed using CASAVA 1.7
ChIP-seq reads were aligned to the mm9 genome assembly using ELANDv2 with default parameters
Two technical replicates of each sample were pooled, because each sample is sequenced twice due to insufficient read depth obtained in the first sequencing run.
Peaks are called for having both IgG and Input DNA as a control and coverages are generated using MACS 1.4 with p value cuff off set at 1e-5.  TEAD4 binding regions are Intersections of TEAD4-enriched over IgG and Input DNA
Peaks in bed file and coverage in wig file are converted to bigbed and bigwig using bedToBigBed and wigToBigWig respectively
Genome_build: mm9
Supplementary_files_format_and_content: Bigbed for TEAD4 peaks, bigwig for coverage

source_name: trophoblast stem cells

growth_protocol: Mouse Trophoblast stem cells were grown in Mouse embryonic fibroblast-conditioned media with FGF4 and heparin

extract_protocol:
Mouse trophoblast stem cells, grown in presence of FGF4, were harvested by trypsinization were used for genomic DNA preparation according to the protocol described in Ray S et al. J Biol Chem. 2009 (Context-dependent function of regulatory elements and a switch in chromatin occupancy between GATA3 and GATA2 regulate Gata2 transcription during trophoblast differentiation. J Biol Chem. 2009 Feb 20;284(8):4978-88.)
Libraries were prepared for Illumina Genome Analyzer II using TruSeq SBS kit v5-GA chemistry and for Illumina HiSeq using TruSeq SBS v2-HS chemistry.

tag: cell type

value: Blastocyst derived trophoblast stem cells

tag: chip antibody

value: TEAD4 (Abcam, Cat. No. ab58310, Lot #GR33778-1)

tag: genotype

value: wild type


title: ChIP-Seq analysis of H3K36me3 in human hippocampus middle cells; DNA_Lib 982

status: Public on Apr 17 2012

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 982
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9615
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
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: GSM916041_BI.Brain_Hippocampus_Middle.H3K36me3.150.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 982-DNA_Lib 982.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Hippocampus Middle, Donor 150, 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.12282
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,746,339
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1242
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.2081
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9358
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3703
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM916041_BI.Brain_Hippocampus_Middle.H3K36me3.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 982-DNA_Lib 982.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 150, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12329
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: BHM H3K36me3 50 82
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K36me3 Donor 150 Library DNA_Lib 982 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,746,339
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1242
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.2081
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9358
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3703
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

organism: Homo sapiens

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 982

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD present

tag: molecule

value: genomic DNA

tag: disease

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 73.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Branson


title: IgG

value: Blastocyst derived trophoblast stem cells

value: Purified IgG1 k isotype control (BD Biosciences, Cat. No. 554121, Lot #70274)

value: wild type


title: ChIP-Seq analysis of H3K4me1 in human hippocampus middle cells; DNA_Lib 980

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 980
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9613
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
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: GSM916039_BI.Brain_Hippocampus_Middle.H3K4me1.150.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 980-DNA_Lib 980.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Hippocampus Middle, Donor 150, 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.12301
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,689,857
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2575
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.3255
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9637
IROC_PERCENTILE: 57
POISSON_SCORE: 0.4969
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM916039_BI.Brain_Hippocampus_Middle.H3K4me1.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 980-DNA_Lib 980.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 150, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12348
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: BHM H3K4me1 50 80
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K4me1 Donor 150 Library DNA_Lib 980 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,689,857
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2575
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.3255
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9637
IROC_PERCENTILE: 57
POISSON_SCORE: 0.4969
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 980

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD present

value: genomic DNA

value: Hippocampus Middle

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K27me3 in human hippocampus middle cells; DNA_Lib 981

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 981
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9612
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
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: GSM916038_BI.Brain_Hippocampus_Middle.H3K27me3.150.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 981-DNA_Lib 981.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Brain Hippocampus Middle, Donor 150, 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.12291
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,890,654
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0293
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1244
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.7485
IROC_PERCENTILE: 30
POISSON_SCORE: 0.2776
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.85

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

ANALYSIS FILE NAME: GSM916038_BI.Brain_Hippocampus_Middle.H3K27me3.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 981-DNA_Lib 981.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 150, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12338
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: BHM H3K27me3 50 81
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K27me3 Donor 150 Library DNA_Lib 981 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,890,654
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0293
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1244
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.7485
IROC_PERCENTILE: 30
POISSON_SCORE: 0.2776
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.85

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 981

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 73.0 Years

value: Protein A-Sepharose 4B

value: Millipore

value: Histone H3K27me3


title: polyA RNA sequencing of H1 BMP4 Derived Mesendoderm Cells; polyA-RNA-seq_h1-mesendoderm_r2a

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 BMP4 Derived Mesendoderm Cells
Library name: polyA-RNA-seq_h1-mesendoderm_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12101
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12099
****************
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: GSM915325_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-mesendoderm_r2a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-mesendoderm_r2a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library polyA-RNA-seq_h1-mesendoderm_r2a 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.13727
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 317,296,097
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 83.72
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM915325_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-mesendoderm_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-mesendoderm_r2a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from H1 BMP4 Derived Mesendoderm Cultured Cells, Library polyA-RNA-seq_h1-mesendoderm_r2a were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13737
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-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 8
BROWSER_TRACK_NAME: HBDM mRNA 2a
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r2a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 317,296,097
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 83.72
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: H1 BMP4 Derived Mesendoderm Cultured Cell Line, biological replicate 2 (r2); polyA-RNA-seq_h1-mesendoderm_r2a

extract_protocol: Library construction protocol: Four µg of total RNA was extracted from frozen cell pellets using the RNeasy Mini Kit (Qiagen, Valencia, CA). PolyA RNA was isolated from total RNA using Dynabeads oligo(dt)25 (Invitrogen). PolyA selected RNA was eluted in 2x Superscript III buffer supplemented with 10mM DTT and was fragmented by incubation at 94°C for 4 minutes. First-strand cDNA was synthesized with the following reaction composition: 0.5 µL random hexamer, 0.5 µL RNase Out, 1 µL DTT (100 mM), 0.5 µL dNTP (25 mM), 0.5 µL SuperScript III (20 µL final). The reaction was incubated at 25°C for 10 min then 50°C for 50 min.  Single-stranded cDNA was isolated by purification with RNAClean XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing second-strand was synthesized with the following reaction: 1.5 µL NEBuffer 2 (NEB), 1 µL dNTP mix (10 mM dATP, dCTP, dGTP, and dUTP), 0.2 µL RNase H, 1 µL DNA Polymerase I (E. coli) (New England Biolabs) (15 µL final). The reaction was incubated at 16°C for 2.5 hours. The dUTP-containing cDNA was isolated by purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing cDNA was then end repaired and a 3' A base was added. TruSeq adapters (Illumina, San Diego, CA) were ligated to the dUTP-containing cDNA at 16°C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated cDNA was isolated by two rounds of purification with AMPure XP beads. The dUTP-containing strands were digested at 37°C for 30 min with uracil DNA glycosylase (Enzymatics). Adapter-ligated, single-stranded DNA molecules were enriched by 10 cycles of PCR with the following reaction composition: 5 µL TruSeq PCR Primer Cocktail (Illumina), 25 µL TruSeq PCR Master Mix (Illumina) (50 µL final). The thermocycling parameters were: 98°C 30 sec, then 10-15 cycles of 98°C 10 sec, 60°C 30 sec and 72°C 30 sec, ending with one 72°C 5 min step. The reaction products were purified using AMPure XP beads.

value: Thomson Laboratory

value: Cell Line

tag: lineage

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

tag: passage

tag: medium

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

tag: batch

value: Replicate 2

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: ChIP-Seq analysis of WCE in human hippocampus middle cells; DNA_Lib 986

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 986
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9611
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
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: GSM916037_BI.Brain_Hippocampus_Middle.Input.150.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 986-DNA_Lib 986.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Hippocampus Middle, Donor 150, 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.12311
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,947,819
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0344
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM916037_BI.Brain_Hippocampus_Middle.Input.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 986-DNA_Lib 986.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Hippocampus Middle, Donor 150, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12358
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: BHM Input 50 86
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle ChIP-Seq Input Donor 150 Library DNA_Lib 986 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,947,819
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0344
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 986

value: Brain, Hippocampus Middle

value: Post-Mortem

value: no AD present

value: genomic DNA

value: Hippocampus Middle

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 73.0 Years

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human hippocampus middle cells; DNA_Lib 985

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 985
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9608
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
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: GSM916034_BI.Brain_Hippocampus_Middle.H3K9me3.150.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 985-DNA_Lib 985.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Hippocampus Middle, Donor 150, 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.12319
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,254,064
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0295
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.1109
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.7162
IROC_PERCENTILE: 31
POISSON_SCORE: 0.2595
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM916034_BI.Brain_Hippocampus_Middle.H3K9me3.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 985-DNA_Lib 985.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 150, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12366
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: BHM H3K9me3 50 85
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K9me3 Donor 150 Library DNA_Lib 985 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,254,064
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0295
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.1109
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.7162
IROC_PERCENTILE: 31
POISSON_SCORE: 0.2595
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 985

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K9me3


title: polyA RNA sequencing of H1 cells; polyA-RNA-seq_h1_r1a

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 cells
Library name: polyA-RNA-seq_h1_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12096
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12094
****************
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: GSM915328_UCSD.H1.mRNA-Seq.polyA-RNA-seq_h1_r1a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1_r1a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the H1 Cell Line, Library polyA-RNA-seq_h1_r1a 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.13730
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 316,233,760
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 75.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM915328_UCSD.H1.mRNA-Seq.polyA-RNA-seq_h1_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1_r1a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the H1 Cell Line, Library polyA-RNA-seq_h1_r1a were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13740
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-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 8
BROWSER_TRACK_NAME: H1 mRNA 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r1a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 316,233,760
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 75.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

source_name: H1 Cell Line, biological replicate 1 (r1); polyA-RNA-seq_h1_r1a

value: H1 Cell Line

value: Thomson Laboratory

value: Cell Line

tag: line

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

tag: Sex

value: Replicate 1

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: G2 extraction1_seq1 aliquote 1

source_name: G2 cells

tag: cell line

tag: tissue

value: embryo-derived cell-line

tag: developmental stage

value: late embryonic stage

value: Unknown


title: S3 V128 (Replicate 2) extraction2_seq1 aliquote 1

source_name: S3 cells


title: ChIP-Seq analysis of H3K4me3 in human CD25int CD127+ Tmem cells; DNA_Lib 735

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 735
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9601
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9457
****************
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: GSM916027_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K4me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 735-DNA_Lib 735-DNA_Lib 735.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 62, 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.12305
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,530,545
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1445
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.2082
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9993
IROC_PERCENTILE: 55
POISSON_SCORE: 0.2243
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916027_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K4me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 735-DNA_Lib 735-DNA_Lib 735.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 62, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12352
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: CCCTmem H3K4me3 62 35
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 735 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,530,545
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1445
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.2082
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9993
IROC_PERCENTILE: 55
POISSON_SCORE: 0.2243
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 735

value: BioSam 131

value: CD4+ CD25int CD127+ Tmem Primary Cells

value: presumed normal

value: genomic DNA

tag: markers

value: CD4+ T cell

value: CD25int CD127+ Tmem

value: Primary Cell

value: Donor 62

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Branson


title: S3 V074 (Replicate 1) extraction1_seq1 aliquote 1

value: embryo-derived cell-line

value: late embryonic stage

value: mh

value: Unknown


title: ChIP-Seq analysis of H3K27ac in human CD25int CD127+ Tmem cells; DNA_Lib 734

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 734
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9600
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9457
****************
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: GSM916026_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K27ac.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 734-DNA_Lib 734-DNA_Lib 734.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 62, 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.12287
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,522,303
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.426
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4737
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9994
IROC_PERCENTILE: 100
POISSON_SCORE: 0.465
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916026_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K27ac.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 734-DNA_Lib 734-DNA_Lib 734.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 62, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12334
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: CCCTmem H3K27ac 62 34
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 734 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,522,303
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.426
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4737
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9994
IROC_PERCENTILE: 100
POISSON_SCORE: 0.465
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 734

value: BioSam 131

value: CD4+ CD25int CD127+ Tmem Primary Cells

value: presumed normal

value: genomic DNA

value: CD4+ T cell

value: Abcam

value: Histone H3K27ac


title: Input DNA

tag: cell type

value: Blastocyst derived trophoblast stem cells

value: wild type


title: ChIP-Seq analysis of H3K9me3 in human CD25int CD127+ Tmem cells; DNA_Lib 737

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 737
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9599
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9457
****************
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: GSM916025_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K9me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 737-DNA_Lib 737-DNA_Lib 737.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 62, 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.12293
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,660,585
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0169
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0973
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.3807
IROC_PERCENTILE: 8
POISSON_SCORE: 0.1642
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916025_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K9me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 737-DNA_Lib 737-DNA_Lib 737.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 62, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12340
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: CCCTmem H3K9me3 62 37
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 737 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,660,585
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0169
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0973
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.3807
IROC_PERCENTILE: 8
POISSON_SCORE: 0.1642
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 737

value: CD25int CD127+ Tmem

value: Primary Cell

value: Donor 62

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human CD25int CD127+ Tmem cells; DNA_Lib 736

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 736
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9598
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9457
****************
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: GSM916024_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K4me1.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 736-DNA_Lib 736-DNA_Lib 736.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 62, 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.12292
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,512,936
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0772
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1812
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8574
IROC_PERCENTILE: 21
POISSON_SCORE: 0.2482
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916024_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.H3K4me1.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 736-DNA_Lib 736-DNA_Lib 736.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 62, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12339
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: CCCTmem H3K4me1 62 36
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 736 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,512,936
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0772
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.1812
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8574
IROC_PERCENTILE: 21
POISSON_SCORE: 0.2482
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 736

value: BioSam 131

value: CD4+ CD25int CD127+ Tmem Primary Cells

value: presumed normal

value: Unknown

value: Histone H3K4me1

value: Branson


title: ChIP-Seq analysis of H2A.Z in human hNP r1 cells; DNA_Lib 295

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 295
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9595
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8184
****************
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: GSM916021_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H2A.Z.DNA_Lib_295.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 295-DNA_Lib 295.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H9 Derived Neuronal Progenitor Cultured Cells Histone H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2A.Z ChIP-Seq on H9 Derived Neuronal Progenitor Cultured Cells, Donor DNA_Lib 295, 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.12309
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,147,007
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.2963
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.3447
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9976
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4192
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916021_BI.H9_Derived_Neuronal_Progenitor_Cultured_Cells.H2A.Z.DNA_Lib_295.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 295-DNA_Lib 295.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Derived Neuronal Progenitor Cultured Cells Histone H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2A.Z ChIP-Seq read mappings from H9 Derived Neuronal Progenitor Cultured Cells, Donor DNA_Lib 295, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12356
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: H9DNP H2A.Z 95
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuronal Progenitor Cultured Cells Histone H2A.Z Library DNA_Lib 295 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,147,007
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.2963
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.3447
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9976
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4192
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: neuronal progenitors derived from H9 (WA09) human stem cells; DNA_Lib 295

value: genomic DNA

value: Medium:Cultured in defined proliferation medium containing AB2+ANS plus FGF2 and LIF on Matrigel-coated surfaces.

value: hNP (ES H9 derived Nuronal Progenitors)

value: Primary Cell Culture

value: ArunA Biomedical, Athens, GA

value: Upstate

value: Histone H2A.Z


title: ChIP-Seq analysis of H3K36me3 in human substantia nigra cells; DNA_Lib 554

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 554
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9589
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9444
****************
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: GSM916015_BI.Brain_Substantia_Nigra.H3K36me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 554-DNA_Lib 554-DNA_Lib 554.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Substantia Nigra Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Substantia Nigra, Donor 149, 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.12316
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,591,058
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0962
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2274
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.8711
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3739
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM916015_BI.Brain_Substantia_Nigra.H3K36me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 554-DNA_Lib 554-DNA_Lib 554.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Substantia Nigra, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12363
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: BSN H3K36me3 49 54
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K36me3 Donor 149 Library DNA_Lib 554 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,591,058
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0962
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2274
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.8711
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3739
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 554

value: Brain, Substantia Nigra

value: Post-Mortem

value: no AD evident at demise

value: Substantia Nigra

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Abcam

value: Histone H3K36me3


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: ChIP-Seq input analysis of foreskin fibroblast from skin02 (A08400) using Illumina HiSeq 2000
library name: A08400
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 114-284 bp
****************
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: GSM817247_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.Input.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08400-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Penis Foreskin Fibroblast 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.12536
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-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: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,751,358
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0013
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0008
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0084
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM817247_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.Input.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08400-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin02 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12559
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: PFF Input 02 00
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin02 Library A08400 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,751,358
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0013
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0008
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0084
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: male

tag: body site

value: Penis

tag: histological type

value: Fibroblast

tag: is tumor

value: No

value: primary cell culture

value: foreskin fibroblast