Illumina HiSeq 2500 sequencing; Sox2 ChIP-seq in hindbrain and spinal cord neural progenitors differentiated from mouse embryonic stem cells
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA
Attributes by original data submitter
Sample
ENA first public
2018-08-28
ENA last update
2018-01-15
ENA-CHECKLIST
ERC000011
External Id
SAMEA104469053
INSDC center alias
The Francis Crick Institute
INSDC center name
The Francis Crick Institute
INSDC first public
2018-08-28T17:03:14Z
INSDC last update
2018-01-15T13:26:26Z
INSDC status
public
Submitter Id
E-MTAB-6348:Sample 2
broker name
ArrayExpress
cell line
HM1 ESC
cell type
mouse neural progenitor cell
common name
house mouse
developmental stage
embryo
disease
normal
organism part
inner cell mass
progenitor cell type
mouse embryonic stem cell
protocol
hindbrain neural progenitor differentiation
sample name
E-MTAB-6348:Sample 2
strain
129x129
Sequenced DNA Library
library_name
Sample 2_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
To obtain neural progenitors with anterior, hindbrain or spinal cord neural identity, ESCs were differentiated as previously described (https://doi.org/10.1371/journal.pbio.1001937 Gouti et al, 2014). Briefly, ESCs were dissociated with 0.05% trypsin, and plated on gelatin-coated plates for two sequential 20 minute periods in ESC medium to separate them from their feeders. To start the differentiation, cells remaining in the supernatant were pelleted by centrifugation, washed in PBS, and pelleted again. Cells were counted and resuspended in N2B27 medium containing 10ng/ml bFGF to a concentration of 106 cells per ml, and 50,000 cells per 35mm CELLBIND dish were plated. To generate anterior neural progenitors, the cells were grown up to day 3 in N2B27 + 10ng/ml bFGF, followed by N2B27 + 500nM smoothened agonist (SAG; Calbiochem) from day 3-5. To generate hindbrain neural progenitors, cells were cultured under the same conditions as the anterior, but were additionally exposed to 100nM retinoic acid (RA; Sigma) from day 3-5. To generate spinal cord neural progenitors, cells were cultured with N2B27 + 10ng/ml bFGF until day 2, N2B27 + 10ng/ml bFGF + 5 micro M CHIR99021 until day 3, and N2B27 + 100nM RA + 500nM SAG until day 5. For all differentiations, media changes were made every 24 hours from day 2. Samples were collected as previously described (Kutejova et al., 2016). 10-30 million cells from day 5 hindbrain or day 5 spinal cord neural progenitors were collected from plates using scrapers and crosslinked in 1% formaldehyde for 20 min at 4 degrees. Chromatin was sonicated using a Diagenode Bioruptor (using a cycle of 30sec on, 30 sec off) until fragments were between 200-400bp. Samples were decrosslinked and purified using the Qiagen MinElute kit following manufacturer's instructions. Chromatin immunoprecipitation was performed as previously described in Kutejova et al., 2016. 3ug of Sox2 antibody (Santa cruz antibody SC-17320X) was incubated together with cell lysate overnight at 4°C on a rotating wheel. Immunoprecipitation of chromatin fragments were captured using Protein G-coupled Dynabeads (Life Technologies). Samples were decrosslinked and purified using the Qiagen MinElute kit as per manufacturer's instructions. To generate libraries, approximately 10ng ChIP DNA and 10ng input DNA was used for each condition. Libraries were generated by by blunt-end repair, dA-tailing, and ligation of Illumina adaptors using the KAPA Hyper Prep Kit following manufacturer's instructions. Libraries were size-selected to obtain fragments between 250-400bps using an E-Gel EX Agarose Gel. Library quality control was carried out using the Bioanalyzer High-Sensitivity DNA analysis kit as per manufacturer's instructions.