title: RDMD

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

institute: Fred Hutch Cancer Research Center

description: MyoD ChIP-Seq in Rhabdomarcoma

data_processing:
Sequence reads were obtained using the GApipeline program (version 0.3.0).
Reads were aligned to human genome hg19 using BWA (0.5.9)
Peaks were called using an in-house peak calling algorithm
Genome_build: hg19
Supplementary_files_format_and_content: MyoD ChIP-Seq peaks in ENCODE broadPeak format

source_name: Rhabdomyosarcoma

growth_protocol: RD cells were obtained from the American Type Culture Collection (ATCC) and early passage cells were used in all experiments. RD cells were maintained in Dulbecco modified Eagle medium (DMEM) with 10% bovine calf serum and 1% penicillin-streptomycin (Gibco).

extract_protocol:
Primary myoblast samples were collected in growth medium at low density, and both primary myotubes and RD cells were collected after being cultured in differentiation medium (72 h for myotubes, 24 h for RD cells).
Libraries were generated from immunoprecipitated DNA as outlined in the  Illumina DNA Library Construction Kit protocol except that 21 rounds of PCR were performed for amplification, and DNA fragments ranging from 200-350 bp were isolated during size selection on agarose gel.

treatment_protocol: To differentiate myoblasts, cells were allowed to achieve 90% confluency prior to a shift in culture media to Dulbecco’s modified media containing 1% horse serum with insulin (10 μg/mL) and transferrin (10 μg/mL). Differentiation media was changed every 24 h for up to 5 day.

value: Rhabdomyosarcoma

tag: chip antibody

value: MyoD


title: BNST/POA Day 4 Female 3

status: Public on Aug 29 2013

type: SRA

city: Taipei

first: Pao-Yang

last: Chen

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

library_source: genomic

data_processing:
BS-seq reads were aligned to the mouse mm9 genome assembly using BS Seeker, allowing up to 10 mismatches.
Alignments with three consecutive methylated non-CG sites are removed.
If multiple alignments mapped to the same location only one is kept.
Genome_build: mouse mm9
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id (see mouse_mm9_chromosomes.txt); column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

molecule: genomic DNA

organism: Mus musculus domesticus

source_name: BNST/POA

extract_protocol:
Genomic DNA was isolated from the BNST/POA using Qiagen AllPrep DNA/RNA Mini Kit (catalog no. 80204).
Genomic DNA was digested with MspI. They were then ligated with Illumina adaptors, and size selected. Fragments from 100 to 200 bases were selected. These fragments were denatured and treated with sodium bisulfite. Libraries were sequenced using the Solexa sequencing technology (Illumna Hiseq 2000 sequencers). The reads were aligned to the reference genome (mouse mm9) using the modified bisulfite aligner, BS Seeker.

treatment_protocol: Animals were given either 15 ul of peanut oil or 100 ug testosterone on the day of birth depending on their group membership. At 21 days of age, all animals were gonadectomized. 5 mm-long Silastic capsules of testosterone were implanted in all animals at day 45.

tag: gender

value: Female

tag: strain

tag: age

value: 4 days

tag: tissue

value: BNST/POA


title: pHerd30T-LL37 induced +anaerobic

city: HANGZHOU

first: WEI

last: LIU

address: 198 SHIQIAO ROAD

country: China

institute: ZAAS

description: Sample 5

library_source: transcriptomic

data_processing:
The original image data is transfered into sequence data by base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to DH10B gene using CLC Genomics Workbench, default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench, default parameters
Genome_build: GI:170079663/NC_010473
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Escherichia coli

source_name: E.coli Top 10

growth_protocol: 37C in LB medium under aerobic and anaerobic condition

extract_protocol:
mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition.
sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000.

treatment_protocol: Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture's instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA).

value: E.coli Top 10

tag: genotype/variation

value: LL37 expression induced

tag: growth condition

value: anaerobic


title: pHerd30T-LL37 CK+ anaerobic

description: Sample 3

value: no LL37 expression (control)


title: pHerd30T-LL37 induced+aerobic

description: Sample 2

value: aerobic


title: MB135DMcon

city: Seattle

department: Human Biology

country: USA

description: preimmune control in myotube

organism: Homo sapiens

source_name: human myotube

value: myotube


title: pHerd30T CK+aerobic

description: Sample 1


title: MB135GMMD

description: MyoD ChIP-Seq in myoblast

source_name: human myoblast

value: myoblast


title: BNST/POA Day 60 Female 5

value: 60 days


title: BNST/POA Day 4 Female+T 3

tag: treatment

value: testosterone


title: BC15 PB3

status: Public on Aug 28 2013

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description: From animal bearing tumor 02

data_processing:
After demultiplexing of barcoded reads, PiggyBac transposon sequences were trimmed.
Remaining sequences were aligned to the mouse genome (GRCm38/mm10) using the Bowtie algorithm, with a seed size of 20 nucleotides, 1 allowed mismatch in the seed and any number of mismatches in the remaining read. Only the best alignment for each read was retained.
In a second step, reads were trimmed so that the resulting alignment contained at most 4 mismatches.
Reads that contained a starting position within a gamma satellite repeat element were filtered out, using annotations by RepeatMasker (www.repeatmasker.org).
Subsequently, reads were clustered according to their starting positions (corresponding to transposon insertion sites), and only starting positions and corresponding reads were retained that were supported by at least one read of a minimum size of n bases. To determine n, we used the fraction of reads from insertions that were supported by reads on both PB3 and PB5 sides as a guideline for assessing the quality of our sequence mappings. A minimum read length of n=34 was chosen for further analysis as it was the smallest cutoff value that provided for almost all samples high quality sequence mapping, while higher values of n provided no significant gain in mapping quality but lead to a decrease in the number of identified insertion sites.
Genome_build: GRCm38
Supplementary_files_format_and_content: bedGraph files were created using BEDTools version 2.16.2.

organism: Mus musculus

source_name: non-cancerous tail tip

growth_protocol: Tumors were obtained in mice that carried a constitutive expressed PiggyBac transposase allele (ROSA26-PBase) and ATP1 transposon array (ATP1-S2).

extract_protocol:
DNA was extracted from tumors and tail controls by standard DNA extraction methods with SDS lysis buffer and proteinase K digestion.
DNA was fragmented by acoustic shearing, followed by DNA end repair, A-tailing of 3'-ends, and ligation to Splinkerette adapters with 3'-T-overhang. In separate reactions, junction fragments for the 3' and 5' ends of the PiggyBac transposon (PB3 and PB5) were then amplified in two consecutive PCR rounds to generate PB3 and PB5 libraries for each sample. PCR primers contained terminal adapter sequences for Illumina solid-phase amplification and sequencing and a 6-base barcode to distinguish samples in multiplex sequencing (BC01:ATCACG, BC02:CGATGT, BC03:TTAGGC, BC04:TGACCA, BC05:ACATGT, BC06:GCCAAT, BC07:CAGATC, BC08:ACTTGA, BC09:GATCAG, BC10:TAGCTT, BC11:GGCTAG, BC12:CTTGTA, BC13:CGTGAT, BC14:ACATCG, BC15:GCCTAA, BC16:TGGTCA, BC17:CACTGT). Two pools of PB3 and PB5 libraries were sequenced on single lanes of an Illumina HiSeq 2000 device with 100 bases read length.

treatment_protocol: Tumors were obtained in mice between 59-83 weeks of age.

tag: strain/background

value: mixed 129/B6/Swiss

value: tail tip

tag: sample

value: tail 04

tag: transposon side

tag: barcode

value: GCCTAA


title: BC17 PB5

description: From animal bearing tumors 04, 10

value: tail 06

value: CACTGT


title: BC15 PB5

description: From animal bearing tumor 02


title: BC16 PB3

description: From animal bearing tumors 01, 08

value: tail 05

value: TGGTCA


title: BC16 PB5

description: From animal bearing tumors 01, 08


title: BC17 PB3

description: From animal bearing tumors 04, 10


title: BC14 PB5

description: From animal bearing tumor 03

value: tail 03

value: ACATCG


title: BC14 PB3

description: From animal bearing tumor 03


title: BC12 PB5

description: From animal bearing tumors 05, 09

value: tail 01

value: CTTGTA


title: BC12 PB3

description: From animal bearing tumors 05, 09


title: BC13 PB3

description: From animal bearing tumor 06

value: tail 02

value: CGTGAT


title: BC05 PB5

source_name: tumor, intestine

value: intestine tumor

value: tumor 11

value: ACATGT


title: MB135DMMD

description: MyoD ChIP-Seq in myotube

value: myotube

value: MyoD


title: BC11 PB5

source_name: tumor, spleen, follicular

value: mixed 129/B6/Swiss

value: spleen follicular tumor

value: tumor 10

value: GGCTAG


title: BC11 PB3


title: BC08 PB3

source_name: tumor, lung

value: lung tumor

value: tumor 08

value: ACTTGA


title: BC02 PB5

value: tumor 09

value: CGATGT


title: BC02 PB3


title: BC08 PB5


title: BC06 PB5

value: tumor 07

value: GCCAAT


title: BC03 PB3

value: tumor 06

value: TTAGGC


title: BC01 PB5

source_name: tumor, liver

value: liver tumor

value: tumor 05

value: ATCACG


title: BC01 PB3


title: BC13 PB5

description: From animal bearing tumor 06

value: tail tip

value: tail 02

value: CGTGAT


title: BC10 PB3

source_name: tumor, skin, squamous cell

value: mixed 129/B6/Swiss

value: skin squamous cell tumor

value: tumor 04

value: TAGCTT


title: BC10 PB5


title: BC07 PB3

value: tumor 01

value: CAGATC


title: BC09 PB5

value: tumor 02

value: GATCAG


title: BC07 PB5


title: BC04 PB3

value: tumor 03

value: TGACCA


title: BC09 PB3


title: CITH053_Exocrine_Input

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description: Sample name: FGC0156_s_1

data_processing:
Sequence reads and quality scores were extracted using Illumina CASAVA Pipeline v1.7
ChIP-seq reads were aligned to the human genome using ELAND, RNA-seq reads were aligned to the human genome/transcriptome using RUM
H3K4me3 ChIP-seq peak calling was performed with GLITR. H3K27me3 ChIP-seq peak calling was performed with STAR.
RNA-seq transcript quantification was performed with RUM.
Genome_build: hg18
Supplementary_files_format_and_content: Peak calls (ChIP-seq) and transcript quantification (RNA-seq), all in BED format.

source_name: FACS-sorted pancreatic islet

extract_protocol:
We performed FACS sorting on dispersed human islets using cell surface antibodies (1:20) and secondary antibodies (1:200; 115-116-075, 115-135-164, Jackson ImmunoResearch) as described before (Dorrell C, et al. Stem Cell Res 2008) to obtain cell populations highly enriched for alpha, beta, and exocrine (duct and acinar) cells. Total RNA was isolated from whole islets, and sorted alpha, beta, and exocrine cells using the Ambion mirVana miRNA Isolation Kit (AM1560) reverse transcribed to cDNA using SuperScript II reverse transcriptase (Invitrogen). ChIP and preparation of ChIP-Seq libraries was performed on individual cell sorts for each cell type and donor (H3K4me3: 8580, Abcam; H3K27me3: 07-449. Upstate).
DNA from ChIP or reverse transcription was treated by blunt end repair and ligation of sequencing adapters. Adapter-ligated fragments were size select to roughly 200bp and amplified by PCR. Final libraries were verified on an Agilent Technologies 2100 BioAnalyzer to check size, purity, and concentration of the library prior to sequencing.

value: pancreatic islets

tag: cell type

value: Exocrine

tag: donor id

tag: chip-seq antibody

value: none (input)


title: XK2367_Exocrine_Input

description: Sample name: FGC0152_s_8


title: CITH068_Exocrine_H3K4me3

description: Sample name: FGC0156_s_3


title: XK2367_Exocrine_H3K27me3

description: Sample name: FGC0152_s_7


title: CITH070_Beta_Input_r2

description: Sample name: FGC0187_s_4

value: Beta


title: BC04 PB5


title: BC06 PB3

value: lung tumor

value: tumor 07

value: GCCAAT


title: XK2367_Beta_Input

description: Sample name: FGC0152_s_5


title: XK2367_Alpha_H3K27me3

description: Sample name: FGC0152_s_4

value: Alpha


title: CITH068_Exocrine_Input

description: Sample name: FGC0156_s_2


title: CITH068_Exocrine_H3K27me3

description: Sample name: FGC0156_s_4


title: ICRH025_Exocrine_H3K27me3

description: Sample name: FGC0152_s_2


title: ICRH025_Exocrine_Input

description: Sample name: FGC0152_s_1


title: XK2367_Beta_H3K27me3

description: Sample name: FGC0152_s_6


title: BC03 PB5

value: mixed 129/B6/Swiss

value: tumor 06

value: TTAGGC


title: CITH068_Alpha_H3K27me3

description: Sample name: FGC0151_s_5


title: XK2367_Alpha_Input

description: Sample name: FGC0152_s_3


title: Case 8

status: Public on Sep 04 2013

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

data_processing:
RNA-seq reads were obtained using Bustard (Illumina Pipeline version 1.3).
Reads were quality-filtered using standard Illumina process, and a 0 (no) or 1 (yes) was used to define whether a read passed filtering or not.
The fastq files were mapped to the reference human genome (Human.B37.3) using the gene model Ensembl (release 67, May 2012). The mapping was performed with the software ArrayStudio, version 6.0 (Hu et al.) using the default parameters, allowing detection of insersions/deletions (indels).
The mapped reads were used to calculate the expression values per gene, transcript, exon and exon junction. The expression values were initially obtained in FPKM (fragment per kilobase of exon model per million of mapped read).
The Linux applications "Tophat" and 'Cufflinks' (Trapnell et al.) were used as an alternative to the ArrayStudio analysis for confirmation and comparison.
Genome_build: Human NCBI genome build 37.3
Supplementary_files_format_and_content: 8_samples_read counts.Naive.txt: Tab-delimited text file includes naive read counts for all samples.
Supplementary_files_format_and_content: 8_samples_FPKM.txt: Tab-delimited text file includes FPKM for all samples.

source_name: Lymph node, non-FOXP1 rearrangement

extract_protocol:
TRIzol LS Reagent (Invitrogen, Carlsbad, CA, USA) was used for a total RNA extraction. cDNA was synthesized from 1 μg of total RNA using reverse transcriptase Superscript II ( Invitrogen, 30 5 Carlsbad, CA, USA) and random primer (Invitrogen, Carlsbad, CA, USA).
The Illumina standard kit (Illumina ® TruSeq™ RNA Sample Preparation Kit, San Diego, CA, USA) was used for the mRNA-sequencing sample preparation according to the manufacturer's protocol. The quality of the libraries was checked by Agilent Technologies 2100 Bioanalyzer, using the Chip (Agilent 7 DNA 1000 Kit).

value: lymphoma

tag: foxp1 expression by ihc

value: positive

tag: karyotype

value: 44-48,XX, complex

tag: foxp rearrangement

value: non-FOXP1 rearrangement

tag: diagnosis

value: ABC-DLBCL


title: CITH068_Beta_H3K27me3

description: Sample name: FGC0151_s_6


title: ICRH025_Beta_Input

description: Sample name: FGC0151_s_4


title: ICRH025_Beta_H3K27me3

description: Sample name: FGC0151_s_3


title: ICRH025_Alpha_Input

description: Sample name: FGC0151_s_1


title: ICRH025_Alpha_H3K27me3

description: Sample name: FGC0151_s_2


title: XHP472_Beta_Input

description: Sample name: FGC0143_s_5


title: CITH070_Alpha_Input

description: Sample name: FGC0143_s_2


title: CITH070_Beta_Input

description: Sample name: FGC0143_s_3


title: XHP472_Beta_H3K4me3

description: Sample name: FGC0141_s_4


title: XHP472_Alpha_H3K4me3

description: Sample name: FGC0141_s_3


title: CITH053_Beta_Input

description: Sample name: FGC0138_s_8


title: XHP472_Alpha_Input

description: Sample name: FGC0143_s_4


title: CITH070_Alpha_H3K4me3

description: Sample name: FGC0141_s_1


title: CITH053_Beta_H3K4me3

description: Sample name: FGC0138_s_7


title: BSO36_PolyA

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

data_processing:
Basecalls made by standard Illumina pipleline (Bustard)
The pair end reads were aligned to the human genome build 37.1 using TopHat (1.4.0) and Bowtie (0.12.7). HTSeq (0.5.3p3) was used to perform gene counting while BEDTools (2.7.1) was used to count the reads mapping to individual exons according to RefSeq gene annotations (Feb 2009, GRCh37/hg19) with 23,113 genes.
Genome_build: hg19
Supplementary_files_format_and_content: text; gene level expression count

source_name: human mammary epithelial cell

growth_protocol: All cell lines were grown under conditions recommended by ATCC and RNA was extracted from mid log phase cultures at low passage

extract_protocol:
RNA was extracted from mid log phase cultures at low passage (P1 or P2) using Triazol kit (Invitrogen)
For Illumina libraries, 5ug total RNA were processed according to the mRNA Seq Sample Preparation Kit protocol (part number 1004898 Rev A), with the 300bp gel fragment eluted and purified for sequencing. For NuGEN libraries, 500-800pg total RNA were amplified and converted to cDNA using NuGEN’s Ovation RNA-Seq kit. Following amplification, 4.6-5.0ug cDNA was fragmented to ~200bps using Covaris S2 and the fragmentation parameters described in the NuGEN  ENCORE NGS library preparation protocol. The remainder of the library preparation followed manufacturer’s protocol as described in NGS Library System I and Multiplex System, Part no. 300.

tag: involution

value: No

value: human mammary epithelial cell

tag: rna preparation

value: Illumina PolyA


title: BSO32N_PolyA


title: CITH068_Alpha_Input

description: Sample name: FGC0138_s_2

tag: tissue

value: pancreatic islets

value: none (input)


title: BSO30_PolyA

value: Yes


title: CITH053_Alpha_Input

description: Sample name: FGC0138_s_1


title: BSO28_PolyA


title: DHF168_PolyA


title: CITH068_Beta_Input

description: Sample name: FGC0138_s_4

value: Beta


title: BSO29_PolyA


title: BSO19B_PolyA


title: BC05 PB3

value: intestine tumor

value: tumor 11

value: ACATGT


title: seq-ab817_8WG16_639746_N2_Eemb_Input_Rep1

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: input DNA

data_processing:
Illumina_DNA_Sequencing:JL:1 protocol. 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.  Processed data are obtained using following parameters: read length is 36   ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10

organism: Caenorhabditis elegans

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

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/.
Worm_ChIP-seq_ DNA_Library_Prep_vSS2. ChIP and 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, amplified by PCR, and size-selected to the 300-400 bp range. Changes: Add AMPure cleanup after ligate adapter step. During size selection, increase run time to 3 hrs and decrease voltage to 80V. Increase size selection to at least 300 bp.

tag: strain

tag: developmental stage

value: Early Embryo

tag: genotype

value: wild type

tag: sex type

value: mixed Male and Hermaphrodite population


title: seq-SDQ3927_MRG1_N2_Eemb_ChIP_Rep1

extract_protocol:
Worm_embryo_extraction_vSS5. 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 14 times in ice water bath followed by 1 minute pause at the highest setting. 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.


title: seq-SDQ3927_MRG1_N2_Eemb_ChIP_Rep2


title: CITH070_Beta_H3K4me3

description: Sample name: FGC0141_s_2


title: seq-SDQ3927_MRG1_N2_Eemb_Input_Rep2

description: input DNA


title: CITH068_Beta_H3K4me3

description: Sample name: FGC0138_s_5


title: CITH068_Alpha_H3K4me3

description: Sample name: FGC0138_s_3

value: Alpha


title: seq-SDQ3927_MRG1_N2_Eemb_Input_Rep1

description: input DNA


title: seq-SDQ3838_T26A5.5_N2_Eemb_ChIP_Rep2

growth_protocol: Worm_embryo_growth_and_harvest_vSS8. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Embryos were then washed once with PBS.  Pellets were flash frozen by adding drop-wise directly to liquid nitrogen, and stored at -80C until ready for use. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS6. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (40-48 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_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.


title: CITH053_Exocrine_H3K4me3

description: Sample name: FGC0137_s_7

value: Exocrine


title: BSO37_PolyA


title: seq-SDQ3838_T26A5.5_N2_Eemb_Input_Rep2

description: input DNA

extract_protocol:
Worm_embryo_extraction_vSS6. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (40-48 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_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/.
Worm_ChIP-seq_ DNA_Library_Prep_vSS4. ChIP and 1 ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, amplified by PCR, and size-selected to the 200-400 bp range using a Pippin prep.


title: seq-SDQ3838_T26A5.5_N2_Eemb_ChIP_Rep1


title: seq-302-32369_H3K9me2_ojIs9_YA_germline_Input_Rep2

description: input DNA

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

growth_protocol: Worm_adult_growth_and_harvest_germCW1. C. elegans were synchronized by bleaching and growth to young adult in standard S-basal media liquid culture. Young adults were collected, washed in PBS, frozen on liquid nitrogen as ?popcorn?, and stored at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_adult_purified_germline_extract_v1. Frozen worms were ground to a powder on liquid nitrogen using a Retsch mixer mill. Worm powder was dissolved into 10V NIBS buffer (25 mM HEPES pH 7.4, 118 mM NaCl, 48 mM KCl, 250 mM sucrose, 5% glycerol, 5 mM MgCl2, 0.5 mM spermine, 0.2 mM spermidine, 0.2 mM DTT, 1X protease inhibitor cocktail) and pelleted at 4000 rpm for 10 minutes at 4C. The pellet was resuspended in 2V NIBS and homogenized 10X with Potter-Elvehjem pestle. The nuclei suspension was then centrifuged once at 50 x g for 5 minutes at 4C and the supernatant was transferred to a fresh chilled tube. The nuclei suspension was then centrifuged once at 100 x g for 5 minutes at 4C and the supernatant was carefully transferred to a fresh chilled tube. This nuclei suspension was combined with prepared GFP binding nanobody-coated beads and allowed to incubate at 4C for 30 minutes. Bead nuclei complexes were then washed 2X with NIBS and fixed with NIBS + 1% formaldehyde for 5 minutes. Fixing was quenched by washing with NIBS + 125mM glycine, followed by NIBS only. Nuclei were resuspended in FA lysis buffer to lyse and sonicated using a Bioruptor XL at maximum intensity for 45 minutes (30 s on, 1 min off). The extract was then centrifuged at 15000 rpm / 15 minutes / 4C. Supernatants were pooled and assayed for quality by preparing DNA, quantifying protein by Bradford assay, and assaying germline-specific protein enrichment by western. Input and purified nuclei slide were examined for nuclei quality and enrichkment. Supernatants were aliquoted and stored at -80C. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vCW2. ~100ug (~2ug DNA) extract was used for each ChIP with 5% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 uL protein A or anti-IgG Dynabeads and washed 5 minutes with 1mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 75uL elution buffer for 15 minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transferred to 65C overnight to reverse crosslinks. DNA was cleaned up with Ampure XP beads. For a detailed protocol see http://www.modencode.org/.
Worm_ChIP-seq_ DNA_Library_Preparation_vSS2. ChIP and 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated (concentrated T4 ligase) to annealed adaptors, size-selected, and amplified by PCR.Changes: Ligate O/N at 16C. Use adapters and primer cocktail from Illumina TruSeq kit. Use AMPure cleanup in the place of Qiagne cleanup. Use Pippin prep for size selection .
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: Germline containing young adult

tag: Sex

value: Hermaphrodite


title: seq-302-32369_H3K9me2_ojIs9_YA_germline_Input_Rep1

description: input DNA


title: seq-SDQ2382_him5_fem2_AD_Input_Rep1

description: input DNA

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

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

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


title: seq-SDQ2382_him5_fem2_AD_Input_Rep2

description: input DNA

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


title: seq-SDQ4663_RPC1_N2_L3_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: SDQ4663 RPC1;target name: RPC-1;host: Rabbit;antigen: DRRHVMLLADVMTYRGEVLGITRNGLVKMKDSVLLLASFEKTMDHLFEAAFFSQRDVIHGVSECIIMGTPMTVGTGTFKLMQKYDKKAVLKQNSPIFERL;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4663 RPC1

data_processing:
Worm popcorns were grinded using a mixer mill 400 MM (Retsch) and fixed by 1% formaldehyde for 10 min at room temperature. After quenching the reaction, samples were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) supplemented with protease inhibitors, phosphatase inhibitors and 1% sarkosyl. Using a Bioruptor water-bath sonicator (Diagenode), samples were sonicated at 4 oC with the following settings: ?High? amplitude, 30 sec on/30 sec off, 15 min (including offs). After separating the supernatant from the pellet by centrifugation, the pellet was again sonicated at the same condition but in a half volume of the buffer. Supernatants from the two sonication steps were combined, aliquoted and stored at -80C. For a detailed protocol see http://www.modencode.org/.
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling_over_reps:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10

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_vKI1.doc
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: L3 Larva


title: seq-SDQ2382_him5_fem2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HIM-5 SDQ2382;target name: HIM-5;host: Rabbit;antigen: GSGISVASKPKKSVAFAPGVYEDLSTDDDLEFLNSVIVNSDRPTSQCDNPARRMCGRPPTKHRDTEQSQEITGSKKQKIFPTPHEKPAWWSFRIPKKRAQ;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2382;short description: An Affinity purified Rabbit Polyclonal antibody to HIM-5 obtained from SDI (HIM-5 SDQ2382)


title: seq-SDQ2382_him5_fem2_AD_ChIP_Rep1


title: seq-SDQ4640_SWD3_N2_Mxemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: SWD-3 SDQ4640;target name: SWD-3;host: Rabbit;antigen: MDTSENAASAAEQQPTQQIDQLTVPNAPDGGSSAPAPSTSPNSISPSNPTGTPAPGASAQTPNPNAAGASASGSANYKLMCTLEGHTKSISSAKFSPCGK;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4640;short description: An Affinity purified Rabbit Polyclonal antibody to SWD-3 obtained from SDI (SWD-3 SDQ4640)

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

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by 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.

extract_protocol:
Worm_embryo_extraction_v3. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
Solexa_Library_Prep_vKI3
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: Mixed Embryo


title: seq-SDQ4663_RPC1_N2_L3_ChIP_Rep2

data_processing:
Worm popcorns were grinded using a mixer mill 400 MM (Retsch) and fixed by 1% formaldehyde for 10 min at room temperature. After quenching the reaction, samples were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) supplemented with protease inhibitors, phosphatase inhibitors and 1% sarkosyl. Using a Bioruptor water-bath sonicator (Diagenode), samples were sonicated at 4 oC with the following settings: ?High? amplitude, 30 sec on/30 sec off, 15 min (including offs). After separating the supernatant from the pellet by centrifugation, the pellet was again sonicated at the same condition but in a half volume of the buffer. Supernatants from the two sonication steps were combined, aliquoted and stored at -80C. For a detailed protocol see http://www.modencode.org/.
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10


title: seq-SDQ4663_RPC1_N2_L3_Input_Rep1

description: input DNA


title: seq-SDQ4663_RPC1_N2_L3_Input_Rep2

description: input DNA


title: seq-SDQ4640_SWD3_N2_Mxemb_Input_Rep2

description: input DNA

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


title: CITH053_Alpha_H3K4me3

description: Sample name: FGC0138_s_6


title: seq-SDQ4585_ASH2_N2_Mxemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: ASH-2 SDQ4585;target name: ASH-2;host: Rabbit;antigen: LLGPLHEAVKLIGKRPIERENREPRHIELPPIEGPKTRGASKRRHAEAPVTGKKQKLAADYSSTAAPNGVQIDIPFSKDNYRYYLTEVDPNVPEDPAWNQ;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4585;short description: An Affinity purified Rabbit Polyclonal antibody to ASH-2 obtained from SDI (ASH-2 SDQ4585)

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


title: seq-SDQ4640_SWD3_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ4640_SWD3_N2_Mxemb_ChIP_Rep2


title: seq-SDQ3838_T26A5.5_N2_Eemb_Input_Rep1

description: input DNA


title: seq-SDQ4585_ASH2_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ4585_ASH2_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-302-32369_H3K9me2_ojIs9_YA_germline_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: WA30232369 H3K9me2;target name: H3K9me2;host: Mouse;clonal: Monoclonal;purified: Protein A/G;company: Wako;catalog: blank


title: seq-SDQ4585_ASH2_N2_Mxemb_ChIP_Rep1


title: seq-SDQ4564_DPY28_N2_Mxemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: DPY-28 SDQ4564;target name: DPY-28;host: Rabbit;antigen: QQQPTRNNDGLSGFKSITEIIAEADNNIPSEQIDKDIDSFSSYSDISDWRGIPKFFPSLSSLSRRASTYENWENRFKVVDYLVSCSGALKDSVSDYVADY;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4564;short description: An Affinity purified Rabbit Polyclonal antibody to DPY-28 obtained from SDI (DPY-28 SDQ4564)


title: seq-302-32369_H3K9me2_ojIs9_YA_germline_ChIP_Rep2


title: seq-SDQ4564_DPY28_N2_Mxemb_ChIP_Rep1


title: seq-SDQ4564_DPY28_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ4562_SMC6_N2_Mxemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: SMC-6 SDQ4562;target name: SMC-6;host: Rabbit;antigen: SYIRFADALDECFALIQLKAGEILNEQKKLKRMQEQRDLQAKLDQDRALVASFCWKLLFCKVRDYNDQIELTLKKQEAQKTLQDETKKEYAKNRAARTEV;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4562;short description: An Affinity purified Rabbit Polyclonal antibody to SMC-6 obtained from SDI (SMC-6 SDQ4562)


title: seq-SDQ4562_SMC6_N2_Mxemb_ChIP_Rep1


title: seq-SDQ0809_COH1_fem2_AD_ChIP_Rep2

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


title: seq-SDQ0809_COH1_fem2_AD_Input_Rep1

description: input DNA


title: seq-SDQ0809_COH1_fem2_AD_Input_Rep2

description: input DNA


title: seq-SDQ0809_COH1_fem2_AD_ChIP_Rep1


title: seq-SDQ4561_DPY26_N2_Mxemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: DPY-26 SDQ4561;target name: DPY-26;host: Rabbit;antigen: RVDRLHHDVRQIDSALSSGTVMRDSNGEEIHLTLESRKAKKKMAVVDGMNGMLDFLNNMDDALTTTELDADNDKNWKEDEENIAGEPRIDFKANSKDVDA;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4561;short description: An Affinity purified Rabbit Polyclonal antibody to DPY-26 obtained from SDI (DPY-26 SDQ4561)

extract_protocol:
Worm_embryo_extraction_v5. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131)+phosphatase inhibitors(Calbiochem cat#524624). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_v5. 2mg extract + 1%sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.


title: seq-SDQ4561_DPY26_N2_Mxemb_ChIP_Rep1


title: seq-SDQ4561_DPY26_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ4561_DPY26_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ3914_REC8_fem2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: REC-8 SDQ3914;target name: REC-8;host: Rabbit;antigen: IDNNSELNAIYGCVEPYLREKEITMHSTFVEGNGSNEHNKERRNDAVIADFSQLLFPEIPEITLGEKFPIDVDSRKRSAILQEEQEEALQLPKEASEIVQ;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3914;short description: An Affinity purified Rabbit Polyclonal antibody to REC-8 obtained from SDI (REC-8 SDQ3914)

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


title: seq-SDQ3914_REC8_fem2_AD_Input_Rep1

description: input DNA


title: seq-SDQ3914_REC8_fem2_AD_ChIP_Rep1


title: seq-SDQ0802_REC8_fem2_AD_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: SDQ0802-REC8;target name: REC-8;host: Rabbit;antigen: MRTEEELENVRRRQKSSLGVQFMRTDDLEEDTRRNRLFEDEERTRDAREDELFFYSSGSLLPNNRLNIHKELLNEAEARYPEWVNFNEFTADHDRKKAAT;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ0802


title: seq-SDQ0802_REC8_fem2_AD_ChIP_Rep2


title: seq-SDQ3914_REC8_fem2_AD_Input_Rep2

description: input DNA


title: seq-SDQ0802_REC8_fem2_AD_Input_Rep2

description: input DNA


title: seq-SDQ4564_DPY28_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-G0655G0656_HTP3_fem2_AD_Input_Rep2

description: input DNA


title: seq-G0655G0656_HTP3_fem2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HTP-3 G0655G0656;target name: HTP3;host: Rabbit;antigen: PTEPASPVESPVKEQPQKAPK;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: G0655G0656;short description: An Affinity purified Rabbit Polyclonal antibody to HTP3 obtained from SDI (HTP-3 G0655G0656)


title: seq-G0655G0656_HTP3_fem2_AD_ChIP_Rep1


title: seq-SDQ4562_SMC6_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ0802_REC8_fem2_AD_Input_Rep1

description: input DNA


title: seq-G0655G0656_HTP3_fem2_AD_Input_Rep1

description: input DNA


title: seq-SDQ4496_DPY26_N2_Mxemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: DPY-26 SDQ4496;target name: DPY-26;host: Rabbit;antigen: RVDRLHHDVRQIDSALSSGTVMRDSNGEEIHLTLESRKAKKKMAVVDGMNGMLDFLNNMDDALTTTELDADNDKNWKEDEENIAGEPRIDFKANSKDVDA;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4496;short description: An Affinity purified Rabbit Polyclonal antibody to DPY-26 obtained from SDI (DPY-26 SDQ4496)


title: seq-SDQ4496_DPY26_N2_Mxemb_ChIP_Rep2


title: seq-SDQ4562_SMC6_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ4496_DPY26_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ4496_DPY26_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ4493_MAU2_N2_Mxemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: MAU-2 SDQ4493;target name: MAU-2;host: Rabbit;antigen: KIHGIRWLGEPSITLLACVMNQICALVQSNTDRVEKYYHLVIKHADEIIFKSTRSPQEPGVVRCINMIKMTTLEMMACCNVLACRPQKTLHNVRDMLEWS;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4493;short description: An Affinity purified Rabbit Polyclonal antibody to MAU-2 obtained from SDI (MAU-2 SDQ4493)


title: seq-SDQ4493_MAU2_N2_Mxemb_ChIP_Rep2


title: seq-SDQ4493_MAU2_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ4493_MAU2_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ4481_PQN85_N2_Mxemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: PQN-85 SDQ4481;target name: PQN-85;host: Rabbit;antigen: QQQPVQQIQRQQPIAQPIPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERKEQEERKRKQELEEQRKRNEELKRLRIAEEKRLL;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4481;short description: An Affinity purified Rabbit Polyclonal antibody to PQN-85 obtained from SDI (PQN-85 SDQ4481)


title: seq-SDQ4481_PQN85_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ4481_PQN85_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ4154_IMB1_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ4154_IMB1_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ4154_IMB1_N2_Mxemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: SDQ4154 IMB1;target name: IMB-1;host: Rabbit;antigen: EAHFERYVGSVVPILNNAQNAAVVTDPNDDDQVDYVDRLREACLNSYTGIIQGLKAIPDTTAARNMINVFVEPIVQLITRISSMEPVPPSEALIATTAGI;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4154 IMB1


title: seq-SDQ4154_IMB1_N2_Mxemb_ChIP_Rep2


title: seq-HK00001-H3K36me3_13C9_fem2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura. Used for ChIP.

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


title: seq-HK00001-H3K36me3_13C9_fem2_AD_ChIP_Rep1


title: seq-SDQ4481_PQN85_N2_Mxemb_ChIP_Rep1


title: seq-HK00001-H3K36me3_13C9_fem2_AD_Input_Rep1

description: input DNA


title: seq-Ab6002_H3K27me3_fem2_AD_Input_Rep2

description: input DNA


title: seq-Ab6002_H3K27me3_fem2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: AB6002 H3K27me3 471901;target name: H3K27me3;host: Mouse;clonal: Monoclonal;purified: Protein A/G;company: Abcam;catalog: blank


title: seq-Ab6002_H3K27me3_fem2_AD_ChIP_Rep1


title: seq-HK00001-H3K36me3_13C9_fem2_AD_Input_Rep2

description: input DNA


title: seq-SDQ4109_TAF1_N2_Mxemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: TAF-1 SDQ4109;target name: TAF-1;host: Rabbit;antigen: NTHHHTNGYRTEKPKNEEDLEDPYANLSDFYKNHPAARNEACSSASNGGSKSVKMEPKVEKNEEFEEYIGDPVRLEDMEPFARPSLRDDAPLSSILHPDL;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ4109;short description: An Affinity purified Rabbit Polyclonal antibody to TAF-1 obtained from SDI (TAF-1 SDQ4109)


title: seq-Ab8895_H3K4me1_fem2_AD_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: ab8895 H3K4me1:733246;target name: H3K4me1;host: Rabbit;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8895;short description: A rabbit affinity purified antibody to H3K4me1 from Abcam (ab8895 lot #733246). Used for ChIP.


title: seq-Ab8895_H3K4me1_fem2_AD_Input_Rep2

description: input DNA


title: seq-SDQ4109_TAF1_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ4109_TAF1_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-Ab8895_H3K4me1_fem2_AD_ChIP_Rep1


title: seq-SDQ4109_TAF1_N2_Mxemb_ChIP_Rep2


title: seq-Ab8895_H3K4me1_fem2_AD_Input_Rep1

description: input DNA


title: seq-Ab9048_H3K36me1_fem2_AD_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_fem2_AD_Input_Rep2

description: input DNA


title: seq-Ab9048_H3K36me1_fem2_AD_ChIP_Rep1


title: seq-Ab9048_H3K36me1_fem2_AD_Input_Rep1

description: input DNA


title: seq-SDQ3892_MIX1_N2_Mxemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: MIX-1 SDQ3892;target name: MIX-1;host: Rabbit;antigen: MHIKSIHLDGFKSYQKHTDILDFSPTFNAITGYNGSGKSNILDSICFIMGINKLDNIRAKSMHELISHGGTKAIVQVRFDNTDKRCSPFGMEHLDEIVVQ;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3892;short description: An Affinity purified Rabbit Polyclonal antibody to MIX-1 obtained from SDI (MIX-1 SDQ3892)


title: seq-SDQ3892_MIX1_N2_Mxemb_ChIP_Rep2


title: seq-SDQ3892_MIX1_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ3856_SDC1_N2_Mxemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: SDC-1 SDQ3856;target name: SDC-1;host: Rabbit;antigen: VERNRHREMCKTRCEHGEYDYEKFKARQVPINPAKMKERKYLTRVVHESGPDDDVCPDEPENNIIAFSPKYENSLSDFRISAIGFREKYLADDKK;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3856;short description: An Affinity purified Rabbit Polyclonal antibody to SDC-1 obtained from SDI (SDC-1 SDQ3856)


title: seq-SDQ3892_MIX1_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ3856_SDC1_N2_Mxemb_ChIP_Rep1


title: seq-SDQ3856_SDC1_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ3582_CBP1_N2_Mxemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: SDQ3582 CBP1;target name: CBP-1;host: Rabbit;antigen: RYPYAQGGPPPGAQGMPQGYPGVSRGGPTPGQPMGRGAMMNGAMPRSGPMPTQGRPGIPPNQQAMMQPMMTDRQFMQHGQYGQQRPEFMQQYGRPGGYP;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3582 CBP1


title: seq-SDQ3856_SDC1_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ3582_CBP1_N2_Mxemb_Input_Rep2

description: input DNA


title: seq-SDQ3582_CBP1_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ3499_DPY30_N2_Mxemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: DPY-30 SDQ3499;target name: DPY-30;host: Rabbit;antigen: APAASAAAPAEAESNENTTVPSNVLSANGGQQTGNQSAPRNTSTVPTRQYLDSTVVPILLQGLGALAKDRPENPIEFLANFLLREKDRYNAENQNPAGQQ;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3499;short description: An Affinity purified Rabbit Polyclonal antibody to DPY-30 obtained from SDI (DPY-30 SDQ3499)


title: seq-SDQ3499_DPY30_N2_Mxemb_ChIP_Rep1


title: seq-SDQ3499_DPY30_N2_Mxemb_Input_Rep1

description: input DNA


title: seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: AMA-1 SDQ2358;target name: AMA-1;host: Rabbit;antigen: DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2358;short description: An Affinity purified Rabbit Polyclonal antibody to AMA-1 obtained from SDI (AMA-1 SDQ2358)

data_processing:
Worms were cultured in liquid S-medium with HB101 bacteria for 36 hrs (L3-L4 stage). Washed L3-L4 worms were transferred to new S-medium supplemented with IPTG-induced RNAi bacteria. Gravid worms were harvested and bleached to obtain embryos.
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10


title: seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_ChIP_Rep2

data_processing:
Worms were cultured in liquid S-medium with HB101 bacteria for 36 hrs (L3-L4 stage). Washed L3-L4 worms were transferred to new S-medium supplemented with IPTG-induced RNAi bacteria. Gravid worms were harvested and bleached to obtain embryos.
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling_over_reps:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10


title: seq-SDQ2357Q2358_AMA1_N2_Mxemb_EE_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: SDQ2357-AMA1;target name: AMA-1;host: Rabbit;antigen: DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2357;short description: An affinity purified rabbit polyclonal antibody to AMA-1 obtained from SDI (AMA1-Q2357)


title: seq-SDQ2357Q2358_AMA1_N2_Mxemb_EE_Input_Rep2

description: input DNA


title: seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_Input_Rep2

description: input DNA


title: seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_Input_Rep1

description: input DNA


title: seq-SDQ2357Q2358_AMA1_N2_Mxemb_EE_Input_Rep1

description: input DNA


title: seq-SDQ0839_TBP1_N2_Mxemb_EE_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: SDQ0839 TBP1;target name: TBP-1;host: Rabbit;antigen: PAHGGPNSVLGGQGPSSILTGHGPNSVMGPNSILGPGSVLNPQSIQPMQSQQMHSLQGSSMQMHSHLANSNLNLNINPASVGPDRNPGSVMHHNLDINPP;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ0839 TBP1


title: seq-SDQ0839_TBP1_N2_Mxemb_EE_ChIP_Rep2