title: Morulae #1 -Cell#5

description:
Sample 52
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_D5.expression.txt: hg19


title: seq-ab1191_H3K18ac_GR311521_N2_Eemb_ChIP_Rep2

status: Public on Aug 10 2013

type: SRA

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

description: ChIP DNA; Antibody information listed below: official name: ab1191-H3K18ac-GR311521;target name: H3K18ac;host: Rabbit;antigen: ?;clonal: Polyclonal;purified: Affinity;company: abcam;catalog: ab1191;short description: an affinity purified rabbit polyclonal ab raised against H3K18ac obtained from abcam (cat. #ab1191 lot #GR311521). Used for ChIP.

library_source: genomic

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

molecule: genomic DNA

organism: Caenorhabditis elegans

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/.

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.

tag: strain

tag: developmental stage

value: Early Embryo

tag: genotype

value: wild type

tag: sex type

value: mixed Male and Hermaphrodite population


title: seq-WA30834809_H3K4me2_8002_N2_Eemb_Input_Rep1

description: input DNA

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/.


title: Morulae #1 -Cell#3

city: Beijing

first: Mingyu

last: Yang

address: 5 Yiheyuan Road

country: China

institute: Peking University

description:
Sample 50
cDNAs of individual cells of preimplantation embryos

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_D3.expression.txt: hg19

molecule: total RNA

organism: Homo sapiens

source_name: Morulae #1

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 preimplantation blastomere

value: early blastomere

tag: tissue

value: human preimplantation embryos


title: Morulae #2 -Cell#2

description:
Sample 57
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_F2.expression.txt: hg19

source_name: Morulae #2


title: Morulae #1 -Cell#1

description:
Sample 48
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_D1.expression.txt: hg19


title: seq-ab1191_H3K18ac_GR311521_N2_Eemb_Input_Rep2

description: input DNA


title: seq-ab1191_H3K18ac_GR311521_N2_Eemb_Input_Rep1

description: input DNA


title: 8-cell embryo#3 -Cell#8

description:
Sample 47
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_K8.expression.txt: hg19

source_name: 8-cell embryo#3


title: 8-cell embryo#3 -Cell#7

description:
Sample 46
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_K7.expression.txt: hg19


title: seq-MP07355_H3K23ac_27133_N2_Eemb_Input_Rep2

description: input DNA


title: seq-MP07355_H3K23ac_27133_N2_Eemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: MP07355-H3K23ac-27133;target name: H3K23ac;host: Rabbit;antigen: ?;clonal: Polyclonal;purified: Crude;company: Millipore;catalog: 07355;short description: Rabbit serum raised against H3K23ac obtained from millipore (cat. #07-355 lot #27133). used for ChIP


title: seq-MP07355_H3K23ac_27133_N2_Eemb_ChIP_Rep1


title: seq-WA30834809_H3K4me2_8002_N2_Eemb_Input_Rep2

description: input DNA


title: 8-cell embryo#3 -Cell#5

description:
Sample 44
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_K5.expression.txt: hg19


title: seq-ab12181_H3K9acS10ph_873968_N2_Eemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: ab12181-H3K9acS10ph-873968;target name: H3K9acS10ph;host: Rabbit;antigen: ?;clonal: Polyclonal;purified: Affinity;company: abcam;catalog: ab12181;short description: a rabbit polyclonal antibody to H3K9acS10ph obtained from abcam (cat. #12181 lot #873968). used for ChIP


title: seq-HK00008_H3K9me2:6D11_N2_L3_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.

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 ce6   BEADS_Normalization protocol. Bias Elimination Algorithm for Deep Sequencing (BEADS): Sequence biasesin the Input and ChIP samples were normalized to remove: GC contentbiases, mappability biases, and regional biases. The originalPython/Java implementation can be accessed athttp://beads.sourceforge.net. Histone_Replicates_QC protocol. After BEADS normalization, genome wide correlation of BEADS signal was calculated in 1 kb windows, with a requirement for replicate correlation of at least 0.7. Signal tracks of biological replicates were also inspected visually for reproducibility.

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:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 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.
ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads.  The protocol uses the Illuimina TruSeq DNA Sample Prep Kit.
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


title: 8-cell embryo#3 -Cell#2

description:
Sample 41
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_K2.expression.txt: hg19


title: seq-HK00008_H3K9me2:6D11_N2_L3_Input_Rep2

description: input DNA


title: 8-cell embryo#3 -Cell#3

description:
Sample 42
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_K3.expression.txt: hg19


title: seq-ab12181_H3K9acS10ph_873968_N2_Eemb_Input_Rep1

description: input DNA


title: seq-HK00008_H3K9me2:6D11_N2_L3_Input_Rep1

description: input DNA


title: seq-ab9048_H3K36me1:206009_N2_L3_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.


title: seq-ab9048_H3K36me1:206009_N2_L3_ChIP_Rep1


title: 8-cell embryo#3 -Cell#1

description:
Sample 40
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_K1.expression.txt: hg19


title: seq-ab1191_H3K18ac_GR311521_N2_Eemb_ChIP_Rep1


title: seq-HK00008_H3K9me2:6D11_N2_L3_ChIP_Rep1


title: seq-ab12181_H3K9acS10ph_873968_N2_Eemb_ChIP_Rep2


title: 8-cell embryo#2 -Cell#8

description:
Sample 39
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_E4.expression.txt: hg19

source_name: 8-cell embryo#2


title: seq-ab9048_H3K36me1:206009_N2_L3_Input_Rep1

description: input DNA


title: seq-AB3594_H3K79me2:346021_N2_L3_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: 8-cell embryo#3 -Cell#6

description:
Sample 45
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_K6.expression.txt: hg19


title: seq-AB3594_H3K79me2:346021_N2_L3_ChIP_Rep1


title: seq-MP07355_H3K23ac_27133_N2_Eemb_Input_Rep1

description: input DNA


title: seq-ab9048_H3K36me1:206009_N2_L3_Input_Rep2

description: input DNA


title: 8-cell embryo#2 -Cell#7

description:
Sample 38
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_E3.expression.txt: hg19


title: seq-ab12181_H3K9acS10ph_873968_N2_Eemb_Input_Rep2

description: input DNA


title: 8-cell embryo#2 -Cell#6

description:
Sample 37
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_E2.expression.txt: hg19


title: 8-cell embryo#3 -Cell#4

description:
Sample 43
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_K4.expression.txt: hg19


title: 8-cell embryo#2 -Cell#5

description:
Sample 36
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_E1.expression.txt: hg19


title: seq-AB1191_H3K18ac_GR311521_N2_L3_Input_Rep2

description: input DNA


title: seq-AB1191_H3K18ac_GR311521_N2_L3_Input_Rep1

description: input DNA


title: 8-cell embryo#2 -Cell#3

description:
Sample 34
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_A7.expression.txt: hg19


title: seq-UP07449_H3K27me3:24440_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: UP07449 H3K27me3:24440;target name: H3K27me3;host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Upstate;catalog: blank;short description: An affinity purified rabbit polyclonal antibody to H3K27me3 obtained from Upstate (07-449 lot #24440). Used for ChIP.


title: 8-cell embryo#2 -Cell#1

description:
Sample 32
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_A5.expression.txt: hg19


title: 8-cell embryo#2 -Cell#2

description:
Sample 33
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_A6.expression.txt: hg19


title: seq-UP07449_H3K27me3:24440_N2_L3_ChIP_Rep1


title: seq-UP07449_H3K27me3:24440_N2_L3_Input_Rep2

description: input DNA


title: seq-UP07449_H3K27me3:24440_N2_L3_Input_Rep1

description: input DNA


title: seq-UP07448_H3K27me1:24439_N2_L3_Input_Rep2

description: input DNA


title: seq-UP07448_H3K27me1:24439_N2_L3_ChIP_Rep2

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: 8-cell embryo#2 -Cell#4

description:
Sample 35
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_A8.expression.txt: hg19


title: seq-UP07448_H3K27me1:24439_N2_L3_ChIP_Rep1


title: 8-cell embryo#1 -Cell#4

description:
Sample 31
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_A4.expression.txt: hg19

source_name: 8-cell embryo#1


title: seq-AB3594_H3K79me2:346021_N2_L3_Input_Rep2

description: input DNA


title: 8-cell embryo#1 -Cell#3

description:
Sample 30
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_A3.expression.txt: hg19


title: seq-NB211254_H3K36ac_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: H3K36ac NB211254;target name: H3K36Ac;host: Rabbit;antigen: acetylated peptide surrounding K36 of human H3.2;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Novus NB21-1254;reference: http://www.novusbio.com/Histone-H3-Antibody NB21-1254.html;short description: Affinity-purified rabbit antibody from Novus Biologicals raised against a synthetic acetylated peptide surrounding Lysine 36 of human Histone H3.2 [Swiss Prot Q71DI3].


title: seq-AB3594_H3K79me2:346021_N2_L3_Input_Rep1

description: input DNA


title: seq-NB211254_H3K36ac_N2_L3_ChIP_Rep1


title: seq-NB211254_H3K36ac_N2_L3_Input_Rep2

description: input DNA


title: 8-cell embryo#1 -Cell#2

description:
Sample 29
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_A2.expression.txt: hg19


title: seq-AB1191_H3K18ac_GR311521_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: ab1191-H3K18ac-GR311521;target name: H3K18ac;host: Rabbit;antigen: ?;clonal: Polyclonal;purified: Affinity;company: abcam;catalog: ab1191;short description: an affinity purified rabbit polyclonal ab raised against H3K18ac obtained from abcam (cat. #ab1191 lot #GR311521). 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 ce6   BEADS_Normalization protocol. Bias Elimination Algorithm for Deep Sequencing (BEADS): Sequence biasesin the Input and ChIP samples were normalized to remove: GC contentbiases, mappability biases, and regional biases. The originalPython/Java implementation can be accessed athttp://beads.sourceforge.net. Histone_Replicates_QC protocol. After BEADS normalization, genome wide correlation of BEADS signal was calculated in 1 kb windows, with a requirement for replicate correlation of at least 0.7. Signal tracks of biological replicates were also inspected visually for reproducibility.


title: seq-AB1191_H3K18ac_GR311521_N2_L3_ChIP_Rep1


title: seq-NB211254_H3K36ac_N2_L3_Input_Rep1

description: input DNA


title: seq-HK00012_H3K36me2:2C3_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HK00012 H3K36me2:2C3;target name: H3K36me2;host: Mouse;antigen: KSAPATGGV(me2-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00012;short description: A protein G purified mouse monoclonal antibody to H3K36me2 (clone 2C3) obtained from Hiroshi Kimura. Used for ChIP.


title: 8-cell embryo#1 -Cell#1

description:
Sample 28
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_A1.expression.txt: hg19


title: sigK- rep3 (K3)

city: Burlington

first: Aimee

last: Shen

state: Vermont

address: Stafford Hall rm 308, 95 Carrigan Drive

department: Microbiology and Molecular Genetics

country: USA

institute: University of Vermont

description: Sample 18

data_processing:
Illumina CASAVA 1.8.2 for basecalling
Adapters were clipped and reads were trimmed to remove the first 12 and last 11 cycles using Trimmomatic, dropping read pairs for which at least one read was less than 50 bp.
The C. difficile 630 genome sequence was modified by removing the sigK intervening (skin) element. Read pairs were aligned to the modified genome using BWA 0.6.1 with quality trimming (–q 30).
Read pairs were mapped to the modified gene annotation using the countOverlaps procedure of the R/Bioconductor IRanges package (v.1.14.4).
Hypothesis testing was based on the R (v.2.15.1)/Bioconductor package DESeq (v1.8.3)
Software name/version; R version 2.15.1, DESeq 1.8.3,  GenomicFeatures 1.8.3, GenomicRanges 1.8.13,  Iranges 1.14.4, Rsamtools 1.8.6, Rtracklayer 1.16.3, ShortRead 1.14.4
Genome_build: NC_009089.1
Supplementary_files_format_and_content: The column header description is provided in the Series supplementary 'README.txt' file

organism: Clostridioides difficile 630

source_name: sigK- cells grown on 70:30 sporulation plates

growth_protocol: Strains were transferred from BHIS agar plates onto 70:30 agar plates at time 0. The samples were grown under anaerobic conditions (85% N2, 5% CO2, 10% H2) at 37˚C for 18 hr after which the triplicate samples were harvested and processed as indicated.

extract_protocol:
Cell pellets were resuspended in RNA Pro solution and transferred to RNA Pro Blue tubes. The sample was homogenized using the FastPrep-24 automated homogenizer (MP Bio) for 30 s at setting 6.0 (homogenization was repeated a total of 3 times), and RNA was harvested according to the manufacturer's direction.
30 µg of total RNA was subjected to 2 rounds of DNase I treatment in solution, followed by one DNase I treatment using a Qiagen Rneasy kit. The samples were tested for genomic contamination using quantitative PCR for 16S rRNA and the sleC gene. 5 µg of the DNase-treated RNA was ribosomally depleted using a Ribo-Zero Gram-positive ribosomal RNA depletion kit. The enriched RNA was analyzed using a Pico kit on a Bioanalyzer. 100 ng of the enriched RNA was used to carry out cDNA synthesis using the Ovation Prokaryotic RNA-Seq cDNA Synthesis System (Nugen, 9030-08) according to the manufacturer's instructions. Libraries were prepared using the Ovation ultralow DR Library synthesis multiplex kit (Nugen, 0304/0305-32) according to the manufacturer's instructions. A PCR titration was performed, and 15 cycles of PCR amplification was used. Completed libraries were quantitated using a SYBR Fast Universal qPCR kit.

treatment_protocol: Cells were harvested from the plates and resuspended in PBS. The sample used to harvest RNA was removed from the cell suspension, pelleted and processed accordingly.

tag: parent strain

tag: genotype/variation

value: sigK- (targetron insertion in bp 230)

value: cells grown on 70:30 sporulation plates

tag: timepoint

value: 18 hr

tag: molecule subtype

value: Ribo-Zero-depleted RNA


title: seq-HK00012_H3K36me2:2C3_N2_L3_ChIP_Rep1


title: 4-cell embryo#3 -Cell#4

description:
Sample 27
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_L8.expression.txt: hg19

source_name: 4-cell embryo#3


title: sigK- rep1 (K1)

description: Sample 16


title: sigK- rep2 (K2)

description: Sample 17


title: 4-cell embryo#3 -Cell#3

description:
Sample 26
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_L7.expression.txt: hg19


title: seq-UP07448_H3K27me1:24439_N2_L3_Input_Rep1

description: input DNA


title: RNA-Seq_shSuz12

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

data_processing:
Basecalls performed using CASAVA version 1.8.
Reads were mapped on mm9 using TOPHAT v2.0.6 with the following parameters :--min-anchor=5 --min-isoform-fraction=0.01 --max-multihits=10 --bowtie1
Comparative analysis was performed using CUFFDIFF v2.0.2.
bedGraph files were generated using WIGGLES v1.2.0.
Genome_build: MGSCv37
Supplementary_files_format_and_content: bedGraph files from WIGGLES were normalized using custom script.

organism: Mus musculus

source_name: embryonic stem cells, shSuz12

extract_protocol:
Total RNA was extracted using Trizol following the manufacturer's protocol.
Library was performed using TruSeq RNA Sample Prep kit v2.

tag: cell line

value: embryonic stem cells

tag: transfection


title: 4-cell embryo#3 -Cell#2

description:
Sample 25
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_L6.expression.txt: hg19


title: seq-HK00012_H3K36me2:2C3_N2_L3_Input_Rep2

description: input DNA


title: seq-HK00012_H3K36me2:2C3_N2_L3_Input_Rep1

description: input DNA


title: RNA-Seq_shGFP

source_name: embryonic stem cells, shGFP

value: shGFP


title: 4-cell embryo#3 -Cell#1

description:
Sample 24
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_L5.expression.txt: hg19


title: sigG- rep2 (G2)

description: Sample 14

source_name: sigG- cells grown on 70:30 sporulation plates

value: sigG- (targetron insertion in bp 546)


title: seq-HK00009_H3K9me3:2F3_N2_L3_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: HK00009 H3K9me3:2F3;target name: H3K9me3;host: Mouse;antigen: ARTKQTAR(me3-K)STGGKAPRKQC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00009;short description: A protein G purified mouse monoclonal antibody to H3K9me3 (clone 2F3) obtained from Hiroshi Kimura. Used for ChIP.


title: 4-cell embryo#2 -Cell#4

description:
Sample 23
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_L4.expression.txt: hg19

source_name: 4-cell embryo#2


title: sigE- rep3 (E3)

description: Sample 12

source_name: sigE- cells grown on 70:30 sporulation plates

value: sigE- (targetron insertion in bp 119)


title: sigG- rep1 (G1)

description: Sample 13


title: seq-HK00009_H3K9me3:2F3_N2_L3_Input_Rep2

description: input DNA


title: 4-cell embryo#2 -Cell#3

description:
Sample 22
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_L3.expression.txt: hg19


title: seq-HK00009_H3K9me3:2F3_N2_L3_Input_Rep1

description: input DNA


title: 4-cell embryo#2 -Cell#2

description:
Sample 21
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_L2.expression.txt: hg19


title: 5hmC_ESC_shSuz12

data_processing:
Library strategy: GLIB-Seq
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1
Data were filtered using the following specifications: duplicate reads were filtered out
Peaks were called using MACS v1.4.1 with the following setting: --gsize=mm --nolambda --bw=300
Genome_build: mm9
Supplementary_files_format_and_content: BED files were generated from mapped SAM files using a custom script

source_name: E14 embryonic stem cells transfected with shSuz12

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen).
Genomic DNA was sonicated for 17' pulse 30"ON/30"OFF high  with Bioruptor Twin (Diagenode). GLIB precipitation was performed using Hydroxymethyl Collector (Active Motif). Libraries were generated with ChIP-seq Sample Prep Kit (Illumina) and sequenced on Illumina HiScanSQ Platform.

value: E14 transfected with shSuz12


title: 5hmC_Liver

source_name: adult liver

tag: age

value: 8 weeks


title: 5hmC_ESC_shGFP

source_name: E14 embryonic stem cells transfected with shGFP

value: E14 transfected with shGFP


title: sigE- rep2 (E2)

description: Sample 11


title: 5hmC_Brain

source_name: adult brain


title: sigE- rep1 (E1)

description: Sample 10


title: sigG- rep3 (G3)

description: Sample 15


title: 4-cell embryo#2 -Cell#1

description:
Sample 20
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_L1.expression.txt: hg19


title: sigF- rep3 (F3)

description: Sample 9

source_name: sigF- cells grown on 70:30 sporulation plates

value: sigF- (targetron insertion in bp 459)


title: 5hmC_MEF

source_name: embryonic fibroblasts

value: embryonic day 11


title: 4-cell embryo#1 -Cell#4

description:
Sample 19
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_C7.expression.txt: hg19

source_name: 4-cell embryo#1

value: human preimplantation blastomere


title: seq-HK00009_H3K9me3:2F3_N2_L3_ChIP_Rep2

value: wild type

value: mixed Male and Hermaphrodite population


title: sigF- rep2 (F2)

description: Sample 8


title: 4-cell embryo#1 -Cell#3

description:
Sample 18
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_C6.expression.txt: hg19

value: early blastomere

value: human preimplantation embryos


title: sigF- rep1 (F1)

description: Sample 7

value: cells grown on 70:30 sporulation plates


title: 5hmC_ESC

source_name: E14 embryonic stem cells


title: seq-AB8898_H3K9me3:33990_N2_L3_Input_Rep2

description: input DNA

value: L3 Larva


title: seq-AB8898_H3K9me3:33990_N2_L3_Input_Rep1

description: input DNA


title: 4-cell embryo#1 -Cell#1

description:
Sample 16
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_C4.expression.txt: hg19


title: spo0A- rep2 (S02)

description: Sample 5

source_name: spo0A- cells grown on 70:30 sporulation plates

value: spo0A- (targetron insertion in bp 178)

value: 18 hr

value: Ribo-Zero-depleted RNA


title: seq-AB2621_H3K79me3:361576_N2_L3_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: hESC passage#0 -Cell#2

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_M2.expression.txt: hg19

source_name: cDNAs of individual cell of human embryonic stem cells

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 manufacturer suggestion protocol

value: human embryonic stem cell

value: peri-implantation stem cells

value: human embryonic stem cell line


title: hESC passage#0 -Cell#1

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_M1.expression.txt: hg19


title: seq-AB8898_H3K9me3:33990_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: AB8898 H3K9ME3:339901;target name: H3K9me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1-100 of human histone H3 tri methylated at K9.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: AB8898;short description: An affinity purified rabbit polyclonal antibody to H3K9me3 (lot# 339901) obtained from Abcam. 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 ce6   BEADS_Normalization protocol. Bias Elimination Algorithm for Deep Sequencing (BEADS): Sequence biasesin the Input and ChIP samples were normalized to remove: GC contentbiases, mappability biases, and regional biases. The originalPython/Java implementation can be accessed athttp://beads.sourceforge.net. Histone_Replicates_QC protocol. After BEADS normalization, genome wide correlation of BEADS signal was calculated in 1 kb windows, with a requirement for replicate correlation of at least 0.7. Signal tracks of biological replicates were also inspected visually for reproducibility.


title: 2-cell embryo#3 -Cell#2

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_B6.expression.txt: hg19

source_name: cDNAs of individual cells of preimplantation embryos

value: human preimplantation blastomere (2-cell)


title: seq-AB2621_H3K79me3:361576_N2_L3_Input_Rep1

description: input DNA


title: seq-JA00001_HTZ1_N2_L3_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HTZ-1 JA00001;target name: HTZ-1;host: Rabbit;antigen: GAPVPGKPGAPGQGPQ;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: JA00001;short description: An Affinity purified Rabbit Polyclonal antibody to HTZ-1 obtained from Ahringer (HTZ-1 JA00001)

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 ce6   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 ce6

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 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.


title: 2-cell embryo#3 -Cell#1

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_B5.expression.txt: hg19


title: seq-AB8898_H3K9me3:33990_N2_L3_ChIP_Rep1


title: WT rep 3 (R3)

description: Sample 3

data_processing:
Illumina CASAVA 1.8.2 for basecalling
Adapters were clipped and reads were trimmed to remove the first 12 and last 11 cycles using Trimmomatic, dropping read pairs for which at least one read was less than 50 bp.
The C. difficile 630 genome sequence was modified by removing the sigK intervening (skin) element. Read pairs were aligned to the modified genome using BWA 0.6.1 with quality trimming (–q 30).
Read pairs were mapped to the modified gene annotation using the countOverlaps procedure of the R/Bioconductor IRanges package (v.1.14.4).
Hypothesis testing was based on the R (v.2.15.1)/Bioconductor package DESeq (v1.8.3)
Software name/version; R version 2.15.1, DESeq 1.8.3,  GenomicFeatures 1.8.3, GenomicRanges 1.8.13,  Iranges 1.14.4, Rsamtools 1.8.6, Rtracklayer 1.16.3, ShortRead 1.14.4
Genome_build: NC_009089.1
Supplementary_files_format_and_content: The column header description is provided in the Series supplementary 'README.txt' file

source_name: wild type cells grown on 70:30 sporulation plates


title: seq-JA00001_HTZ1_N2_L3_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 ce6   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 ce6


title: 4-cell embryo#1 -Cell#2

description:
Sample 17
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_C5.expression.txt: hg19


title: WT rep1 (R1)

description: Sample 1


title: 2-cell embryo#2 -Cell#1

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_B3.expression.txt: hg19


title: 2-cell embryo#2 -Cell#2

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_B4.expression.txt: hg19


title: seq-AB2621_H3K79me3:361576_N2_L3_ChIP_Rep2


title: 2-cell embryo#1 -Cell#2

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_B2.expression.txt: hg19


title: spo0A- rep3 (S03)

description: Sample 6


title: Zygote #2

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_C2.expression.txt: hg19

value: human preimplantation blastomere (zygote)


title: 2-cell embryo#1 -Cell#1

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_B1.expression.txt: hg19


title: seq-JA00001_HTZ1_N2_L3_Input_Rep2

description: input DNA


title: Zygote #1

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_C1.expression.txt: hg19


title: seq-JA00001_HTZ1_N2_L3_Input_Rep1

description: input DNA


title: Oocyte #3

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_M23.expression.txt: hg19

value: human preimplantation blastomere (Oocyte)


title: Zygote #3

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_C3.expression.txt: hg19


title: spo0A- rep1 (S01)

description: Sample 4


title: Oocyte #2

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) [1] to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8".  [1]. 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_M22.expression.txt: hg19


title: WT rep 2 (R2)

description: Sample 2


title: Pou5f1-Flag ChIP 512 cell stage

city: Freiburg

first: Manuel

last: Leichsenring

address: Hauptstr. 1

country: Germany

institute: Albert-Ludwigs-University Freiburg

data_processing:
Basecalls were performed using CASAVA.
Blastula Reads were trimmed to 20bps and aligned to the zv10 genome using "CLC Genomics Workbench" using the following parameters: Match Mode = Random; Sequence Masking = No; Limit = 8; Mismatch Cost = 2; Aligment = Ungapped; Global Aligment = No; Result Handling = Save; pre_MBT reads were similarly aligned but using Mode = Ignore; Using the Input Control Data as background;
Peaks were called using "CLC Genomics Workbench" using the following parameters: Analyze each reference separately = No; Filter peaks on read orientation = No; Filter peaks using Wilcoxon test = No; Shift reads based on fragment length = Yes; Fragment length = 150; Peak refinement = No; Maximum FDR = 5%; Window Size = 50
Peaks were filtered according to following criteria: Normalized read orientation difference <0.5; Wilcoxons test p-value < 0.05. Further, peaks were discarded that showed a larger than 20bp overlap with annotated repeats. Pre_MBT peaks were further filtered more stringently by allowing only peaks with FDR <2.5%
Peaks were normalized to 320 basepairs surrounding the peak center (Average peak size) for applications requiring fixed sequence length.
Genome_build: zv9
Supplementary_files_format_and_content: Filtered peak information was exported from CLC workbench. NOTE: Background peaks (Input Control) are not subtracted yet in these lists. Closest gene TSS in 5' and 3' direction were obtained using Galaxy. Processed data files include the following information: Peak ID, Position (Chromosome, Start, End), Length, False Discovery Rate, Number of total reads, Number of forward reads, Number of reverse reads, Normalized difference between forward and reverse, Wilcoxon p-value, Closest 5' and 3' gene (RefSeq ID)

organism: Danio rerio

source_name: MZspg zebrafish embryos

growth_protocol: Zebrafish were routinely kept and mated. Eggs were collected and either left untreated (Sox2) or microinjected (Pou5f1; See below). Unfertilized and dead eggs were removed. Eggs were cultivated in 0.3x Danio's at 28.5°C until the appropriate stage was reached.

extract_protocol: Embryos were homogenized and fixed with 1% PFA. Cells were lysed and nuclei purified and snap-frozen. 2*10^7 nuclei (Blastula) or 2*10^6 nuclei (preMBT) were pooled and fully lysed. Chromatin was sheared and DNA-Protein complexes were isolated with the respective antibodies and purified. ChIP-library was generated using the Illumina "ChIP-Seq DNA Sample Prep Kit" (Cat. No. IP-102-1001) according to the manufacturers instructions. Nuclei were lysed in 50mM Tris-HCl pH7.5, 10mM EDTA, 1% (w/v) SDS including protease inhibitors (Roche Complete, EDTA free).

value: 512 cell stage

value: embryo

tag: chip antibody

value: anti-FLAG® M2

tag: chip antibody vender

value: Sigma-Aldrich

tag: chip antibody catalog #

value: MZspg injected with Pou5f1-Flag mRNA