Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
lin-37

Cell type

Cell type Class
Embryo
Cell type
Late embryo
NA
NA

Attributes by original data submitter

Sample

source_name
seq-SDQ3166_LIN37_N2_LTemb_ChIP_Rep1
strain
N2
developmental stage
Late Embryos
genotype
wild type
Sex
hermaphrodite

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
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 a DiagenodeBioruptor (40 pulses of 30 seconds with 1 minute rests in between at full power). Extractsare then spun down and the 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/. Short description for UNC NimbleGen Database:Both ChIP and input DNA samples have their ends blunted and phosphorylated with KlenowDNAP, T4 DNAP, and T4 PNK. 3?-dA overhangs are then added with Klenow Fragment (3? to 5?exo minus), and Illumina adapters are subsequently ligated to the ends. Next, PCRamplification is performed using Illumina 1.1 and 2.1 primers, for a total of 18 cycles. AmplifiedDNA libraries are size-selected on a 2% agarose gel so that fragments sized between 250-350bp are obtained; gel extraction is carried out at room temperature.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

ce10

Number of total reads
27642393
Reads aligned (%)
55.6
Duplicates removed (%)
17.5
Number of peaks
2767 (qval < 1E-05)

ce11

Number of total reads
27642393
Reads aligned (%)
55.6
Duplicates removed (%)
17.5
Number of peaks
2768 (qval < 1E-05)

Base call quality data from DBCLS SRA