title: seq-SDQ3898_KLE2_FEM2_AD_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: CEC-1 SDQ2901;target name: CEC-1;host: Rabbit;antigen: MADGSELYTVESILEHRKKKGKSEFYIKWLGYDHTHNSWEPKENIVDPTLIEAFFTREAARKAEI;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2901;short description: An Affinity purified Rabbit Polyclonal antibody to CEC-1 obtained from SDI (CEC-1 SDQ2901)

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10

growth_protocol: Worm_adult_growth_and_harvest_vHP2.  Synchronized cultures of worms were grown until gravid in 400 mL batches.  Gravid adults were isolated through sucrose floatation, and frozen into pellets in liquid nitrogen with EBS (250 mM HEPES (pH 7.5), 1180 mM NaCl, 480 mM KCl, 20 mM EDTA, 5 mM EGTA, sucrose (final 340 mM) and protease/phosphatase inhibitors.  The pellets were stored at -80°C.

extract_protocol:
Worm extract was made from adult worms.  Frozen worm popcorn was ground up in a mixer mill.  Samples were then fixed with 1% formaldehyde for 10 minutes. Chromatin was then sheared by sonication in the Bioruptor, and the soluble fraction was collected and stored at -80°C for future use.
Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA.  Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay.
Worm_ChIP-seq_ DNA_Library_Preparation_vSS2. ChIP and 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, size-selected, and amplified by PCR.Changes: Ligate O/N at 16C. Use adapters and primer cocktail from Illumina TruSeq kit. Use AMPure cleanup in the place of Qiagne cleanup. Use Pippin prep for size selection .
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: Germline containing young adult

value: Hermaphrodite


title: hESC passage#10 -Cell#8

status: Public on Aug 10 2013

type: SRA

city: Beijing

first: Mingyu

last: Yang

address: 5 Yiheyuan Road

country: China

institute: Peking University

description:
Sample 127
cDNAs of individual cell of human embryonic stem cells

library_source: transcriptomic

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P13.expression.txt: hg19

molecule: total RNA

organism: Homo sapiens

source_name: hESC passage#10

growth_protocol: Donated human preplantation embryos were dissociated into individual blastmeres and were separately amplied to set up single cell cDNA libraries.

extract_protocol: Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol

tag: cell type

value: human embryonic stem cell

tag: developmental stage

value: peri-implantation stem cells

tag: tissue

value: human embryonic stem cell line


title: seq-SDQ3898_KLE2_FEM2_AD_ChIP_Rep2

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

library_source: genomic

molecule: genomic DNA

organism: Caenorhabditis elegans

tag: strain

tag: genotype

tag: Sex


title: seq-SDQ3898_KLE2_FEM2_AD_Input_Rep1

description: input DNA


title: hESC passage#10 -Cell#4

description:
Sample 123
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P7.expression.txt: hg19


title: seq-SDQ2972_HIM8_FEM2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HIM-8 SDQ2972;target name: HIM-8;host: Rabbit;antigen: RLIDHALVHCDKNFLKCKKCKHTCHTIRQMRYHYRIFHSTSKMEGFGVSGLPTKNKGFQKIMNACFADQLVEMNKRKNPPKSQNGSRRSRVKSKSKRSGI;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2972;short description: An Affinity purified Rabbit Polyclonal antibody to HIM-8 obtained from SDI (HIM-8 SDQ2972)


title: seq-SDQ2340_HPL2_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HPL-2 SDQ2340;target name: HPL-2;host: Rabbit;antigen: EDPKDNVFMVEKVLDKRTGKAGRDEFLIQWQGFPESDSSWEPRENLQCVEMLDEFEREFSKREKPIRKRHSQKPEPSEDQADPEEDKDEKKETNQNDKFS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2340;short description: An Affinity purified Rabbit Polyclonal antibody to HPL-2 obtained from SDI (HPL-2 SDQ2340)

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is wiggles are ce6, peak calls are ce10   ChIP-Seq_MACS_Peak-calling:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is wiggles are ce6, peak calls are ce10

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol:
Worms are frozen, ground, crosslinked for 20 minutes in EGS, and for an additional 10 minutes in EGS plus formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (20-30 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
DNA was incubated with an enzyme mix (Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends. The DNA fragments were ligated with appropriate adaptor (Illumina) and then amplified by PCR. The amplicon was loaded into an agarose gel, and size-selected DNA was recovered from the gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: L3 Larva

value: wild type

tag: sex type

value: mixed Male and Hermaphrodite population


title: seq-SDQ2340_HPL2_N2_L3_ChIP_Rep1


title: seq-SDQ2340_HPL2_N2_L3_Input_Rep1

description: input DNA


title: hESC passage#10 -Cell#7

description:
Sample 126
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P12.expression.txt: hg19


title: seq-SDQ2972_HIM8_FEM2_AD_Input_Rep2

description: input DNA


title: hESC passage#10 -Cell#5

description:
Sample 124
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P9.expression.txt: hg19


title: hESC passage#10 -Cell#1

description:
Sample 120
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P1.expression.txt: hg19


title: hESC passage#0 -Cell#10

description:
Sample 100
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_M10.expression.txt: hg19

source_name: hESC passage#0


title: seq-SDQ2340_HPL2_N2_L3_Input_Rep2

description: input DNA


title: hESC passage#10 -Cell#2

description:
Sample 121
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P2.expression.txt: hg19


title: hESC passage#0 -Cell#8

description:
Sample 98
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_M8.expression.txt: hg19


title: hESC passage#10 -Cell#3

description:
Sample 122
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P5.expression.txt: hg19


title: seq-SDQ2972_HIM8_FEM2_AD_Input_Rep1

description: input DNA


title: seq-SDQ1665_1666_MRG1_FEM2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: SDQ16651666-MRG1;target name: MRG-1;host: Rabbit;antigen: ALKPKKKSLAAEAPRDDRDDTPGTSKGKKAKSVTIAPVMTADDMKVELPKPLRKILIDDYDLVCRYFINIVPHEYSVDQIIEDYIKTIPVSNEQMRTVDD;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ16651666-MRG1

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10


title: seq-SDQ2972_HIM8_FEM2_AD_ChIP_Rep1


title: hESC passage#0 -Cell#7

description:
Sample 97
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_M7.expression.txt: hg19


title: seq-SDQ3898_KLE2_FEM2_AD_Input_Rep2

description: input DNA


title: seq-SDQ1665_1666_MRG1_FEM2_AD_ChIP_Rep1

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling_over_reps:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10


title: hESC passage#0 -Cell#6

description:
Sample 96
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_M6.expression.txt: hg19


title: seq-SDQ1665_1666_MRG1_FEM2_AD_Input_Rep2

description: input DNA


title: hESC passage#0 -Cell#5

description:
Sample 95
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_M5.expression.txt: hg19


title: seq-SDQ1665_1666_MRG1_FEM2_AD_Input_Rep1

description: input DNA


title: hESC passage#10 -Cell#6

description:
Sample 125
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P11.expression.txt: hg19


title: hESC passage#0 -Cell#4

description:
Sample 94
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_M4.expression.txt: hg19


title: Late blastocyst #3 -Cell#8

description:
Sample 93
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_R8.expression.txt: hg19

source_name: Late blastocyst #3

value: human preimplantation blastomere

value: early blastomere

value: human preimplantation embryos


title: seq-SDQ0821_SCC1_FEM2_AD_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: SCC-1 SDQ0821;target name: SCC-1;host: Rabbit;antigen: TPSMEAQAEPWEDLNLNEDIQEDIQAQGPAVDEFFNDVRMDDDDDRQPAQEMDFGDNFDFPQEVEHQECAPIPIQSGFAGENKENEDAEDWSDPFGSSNS;clonal: Polyclonal;purified: Crude;company: SDI;catalog: SDQ0821;short description: A Serum purified Rabbit Polyclonal antibody to SCC-1 obtained from SDI (SCC-1 SDQ0821)


title: seq-SDQ0821_SCC1_FEM2_AD_Input_Rep1

description: input DNA


title: Late blastocyst #3 -Cell#7

description:
Sample 92
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_R7.expression.txt: hg19


title: Late blastocyst #3 -Cell#6

description:
Sample 91
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_R6.expression.txt: hg19


title: seq-SDQ0812_COH1_FEM2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: COH-1 SDQ0812;target name: COH-1;host: Rabbit;antigen: RDEEKEEPETDEDNRWSKRTHALLQNIATKLENQNGQVELDEMLKKGTSRKVAAAKFYSLLCLKKNQCIDIEQKEPYGDIMIKAGPNININTI;clonal: Polyclonal;purified: Crude;company: SDI;catalog: SDQ0812;short description: A Serum purified Rabbit Polyclonal antibody to COH-1 obtained from SDI (COH-1 SDQ0812)

extract_protocol:
Worms are frozen, ground, crosslinked for 20 minutes in EGS, and for an additional 10 minutes in EGS plus formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (1 hour of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm extract from adult worms and 5 ?g of affinity purified antibody was used for ChIP. Dynal Protein A or G beads were used to recover the ChIPed DNA.  Samples were then treated with RNase A and Proteinase K, and reverse crosslinked at 65°C. ChIPed DNA was purified and then quantified using the Pico Green HS fluorescent assay.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.


title: Late blastocyst #3 -Cell#4

description:
Sample 89
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_R4.expression.txt: hg19


title: seq-SDQ0812_COH1_FEM2_AD_ChIP_Rep1


title: Late blastocyst #3 -Cell#2

description:
Sample 87
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_R2.expression.txt: hg19


title: Late blastocyst #3 -Cell#5

description:
Sample 90
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_R5.expression.txt: hg19


title: Late blastocyst #3 -Cell#3

description:
Sample 88
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_R3.expression.txt: hg19


title: seq-SDQ0812_COH1_FEM2_AD_Input_Rep2

description: input DNA


title: seq-SDQ0812_COH1_FEM2_AD_Input_Rep1

description: input DNA


title: seq-ab8896_H3K9me1_104560_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: ab8896 H3K9me1:104560;target name: H3K9me1;host: Rabbit;antigen: Synthetic peptide derived from within residues 1-100 of Histone H3;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8896;short description: An affinity purified rabbit antibody to H3K9me1 obtained from Abcam (ab8896 lot #104560). Used for ChIP.

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10

growth_protocol: Worm_embryo_growth_and_harvest_vSS5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: Early Embryo


title: Late blastocyst #2 -Cell#10

description:
Sample 85
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H10.expression.txt: hg19

source_name: Late blastocyst #2


title: seq-ab8896_H3K9me1_104560_N2_Eemb_ChIP_Rep1


title: seq-ab8896_H3K9me1_104560_N2_Eemb_Input_Rep2

description: input DNA


title: Late blastocyst #3 -Cell#1

description:
Sample 86
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_R1.expression.txt: hg19


title: Late blastocyst #2 -Cell#7

description:
Sample 82
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H7.expression.txt: hg19


title: Late blastocyst #2 -Cell#9

description:
Sample 84
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H9.expression.txt: hg19


title: seq-ab2621_H3K79me3_361576_N2_Eemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: AB2621 H3K79me3:361576;target name: H3K79me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 tri methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2621;reference: http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab2621.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide tri-methylated at K79.


title: seq-ab2621_H3K79me3_361576_N2_Eemb_ChIP_Rep2


title: Late blastocyst #2 -Cell#6

description:
Sample 81
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H6.expression.txt: hg19


title: seq-ab8896_H3K9me1_104560_N2_Eemb_Input_Rep1

description: input DNA


title: Late blastocyst #2 -Cell#8

description:
Sample 83
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H8.expression.txt: hg19


title: Late blastocyst #2 -Cell#5

description:
Sample 80
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H5.expression.txt: hg19


title: seq-ab2621_H3K79me3_361576_N2_Eemb_Input_Rep2

description: input DNA


title: Late blastocyst #2 -Cell#4

description:
Sample 79
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H4.expression.txt: hg19


title: seq-ab2621_H3K79me3_361576_N2_Eemb_Input_Rep1

description: input DNA


title: seq-ab3594_H3K79me2_346021_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: AB3594 H3K79me2:346021;target name: H3K79me2;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 di methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab3594;reference: http://www.abcam.com/Histone-H3-di-methyl-K79-antibody-ChIP-Grade-ab3594.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide di-methylated at K79.


title: seq-ab3594_H3K79me2_346021_N2_Eemb_ChIP_Rep1


title: Late blastocyst #2 -Cell#3

description:
Sample 78
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H3.expression.txt: hg19


title: seq-ab3594_H3K79me2_346021_N2_Eemb_Input_Rep2

description: input DNA


title: Late blastocyst #2 -Cell#1

description:
Sample 76
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H1.expression.txt: hg19


title: Late blastocyst #2 -Cell#2

description:
Sample 77
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_H2.expression.txt: hg19


title: seq-ab2886_H3K79me1_361912_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: AB2886 H3K79me1:361912;target name: H3K79me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 50 to the C-terminus of Human Histone H3 mono methylated at K79.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2886;reference: http://www.abcam.com/histone-h3-mono-methyl-k79-antibody-chip-grade-ab2886.html;short description: Rabbit polyclonal antibody raised against Histone H3 peptide mono-methylated at K79.


title: Late blastocyst #1 -Cell#11

description:
Sample 74
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G12.expression.txt: hg19

source_name: Late blastocyst #1


title: Late blastocyst #1 -Cell#12

description:
Sample 75
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G13.expression.txt: hg19


title: seq-ab3594_H3K79me2_346021_N2_Eemb_Input_Rep1

description: input DNA


title: Late blastocyst #1 -Cell#9

description:
Sample 72
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G10.expression.txt: hg19


title: seq-ab2886_H3K79me1_361912_N2_Eemb_ChIP_Rep1


title: seq-ab2886_H3K79me1_361912_N2_Eemb_Input_Rep2

description: input DNA


title: seq-ab9048_H3K36me1_206009_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: ab9048 H3K36me1:206009;target name: H3K36me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of homan histone H3 monomethylated at K36;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9048;short description: A rabbit affinity purified antibody to H3K36me1 from abcam (Ab9048 lot #206009). Used for ChIP.

growth_protocol: Worm_embryo_growth_and_harvest_vSS4. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.


title: seq-ab9048_H3K36me1_206009_N2_Eemb_ChIP_Rep1


title: Late blastocyst #1 -Cell#10

description:
Sample 73
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G11.expression.txt: hg19


title: seq-ab2886_H3K79me1_361912_N2_Eemb_Input_Rep1

description: input DNA


title: Late blastocyst #1 -Cell#7

description:
Sample 70
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G8.expression.txt: hg19


title: Late blastocyst #1 -Cell#5

description:
Sample 68
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G6.expression.txt: hg19


title: Late blastocyst #1 -Cell#4

description:
Sample 67
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G5.expression.txt: hg19


title: hESC passage#10 -Cell#20

description:
Sample 139
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S9.expression.txt: hg19


title: seq-ab9048_H3K36me1_206009_N2_Eemb_Input_Rep1

description: input DNA

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10


title: Late blastocyst #1 -Cell#3

description:
Sample 66
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G4.expression.txt: hg19


title: Late blastocyst #1 -Cell#6

description:
Sample 69
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G7.expression.txt: hg19


title: seq-ab9048_H3K36me1_206009_N2_Eemb_Input_Rep2

description: input DNA


title: Late blastocyst #1 -Cell#1

description:
Sample 64
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G2.expression.txt: hg19


title: Morulae #2 -Cell#8

description:
Sample 63
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_F8.expression.txt: hg19

source_name: Morulae #2


title: Morulae #2 -Cell#7

description:
Sample 62
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_F7.expression.txt: hg19


title: Late blastocyst #1 -Cell#2

description:
Sample 65
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G3.expression.txt: hg19


title: Morulae #2 -Cell#6

description:
Sample 61
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_F6.expression.txt: hg19


title: Morulae #2 -Cell#5

description:
Sample 60
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_F5.expression.txt: hg19


title: Late blastocyst #1 -Cell#8

description:
Sample 71
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_G9.expression.txt: hg19


title: seq-ab15823_H4K8ac_487128_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: ab15823-H4K8ac;target name: H4K8ac;host: Rabbit;antigen: mpdtnstinlslstrvtlaffmslvafaimlgnalvilafvvdknlrhrssyfflnlaisdffvgvisiplyiphtlfewdfgkeicvfwlttdyllcta;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: blank


title: Morulae #2 -Cell#3

description:
Sample 58
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_F3.expression.txt: hg19


title: Morulae #2 -Cell#4

description:
Sample 59
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_F4.expression.txt: hg19


title: seq-ab15823_H4K8ac_487128_N2_Eemb_Input_Rep2

description: input DNA


title: seq-ab15823_H4K8ac_487128_N2_Eemb_Input_Rep1

description: input DNA


title: seq-HK00008_H3K9me2_6D11_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HK00008 H3K9me2:6D11;target name: H3K9me2;host: Mouse;antigen: ARTKQTAR(me2-K)STGGKAPRKQC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00008;short description: A protein G purified mouse monoclonal antibody to H3K9me2 (clone 6D11) obtained from Hiroshi Kimura. Used for ChIP.


title: seq-HK00008_H3K9me2_6D11_N2_Eemb_ChIP_Rep1


title: seq-HK00008_H3K9me2_6D11_N2_Eemb_Input_Rep1

description: input DNA


title: seq-HK00008_H3K9me2_6D11_N2_Eemb_Input_Rep2

description: input DNA


title: Morulae #2 -Cell#1

description:
Sample 56
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_F1.expression.txt: hg19


title: seq-UP07448_H3K27me1_24439_N2_Eemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: UP07448 H3K27me1:24439;target name: H3K27me1;host: Rabbit;antigen: peptide including monomethyl-lysine 27 of histone H3;clonal: Polyclonal;purified: Affinity;company: Upstate/Millipore;catalog: 07-448;short description: A rabbit polyclonal antibody to H3K27me1 obtained from Upstate (07-448 lot #24439). Used for ChIP.


title: Morulae #1 -Cell#8

description:
Sample 55
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_D8.expression.txt: hg19

source_name: Morulae #1


title: seq-UP07448_H3K27me1_24439_N2_Eemb_Input_Rep1

description: input DNA


title: seq-WA30834809_H3K4me2_8002_N2_Eemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: WA30834809 H3K4me2;target name: H3K4me2;host: Mouse;antigen: ART(me2-K)QTARKSTGC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: WA30834809;short description: A protein G-purified mouse monoclonal antibody against H3K4me2.  Used for ChIP


title: Morulae #1 -Cell#6

description:
Sample 53
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_D6.expression.txt: hg19


title: seq-UP07448_H3K27me1_24439_N2_Eemb_ChIP_Rep2


title: Morulae #1 -Cell#7

description:
Sample 54
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_D7.expression.txt: hg19


title: seq-WA30834809_H3K4me2_8002_N2_Eemb_ChIP_Rep2


title: seq-UP07448_H3K27me1_24439_N2_Eemb_Input_Rep2

description: input DNA


title: Morulae #1 -Cell#4

description:
Sample 51
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_D4.expression.txt: hg19


title: seq-ab15823_H4K8ac_487128_N2_Eemb_ChIP_Rep1

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10


title: Morulae #1 -Cell#2

description:
Sample 49
cDNAs of individual cells of preimplantation embryos

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_D2.expression.txt: hg19