TS50pg
Arabidopsis thaliana
Protocols: A. thaliana total RNA was diluted using RNase-free water, and 50 pg were used for each cDNA library preparation using the SMARTer Ultra Low RNA Kit for Illumina Sequencing from Clontech according to manufacturers instructions. 24 cycles of PCR were used for library amplification, and after passing quality control, finalized cDNA libraries (6 ng - 20 ng) were fragmented with the Covaris S2 system as reported previously (Tang et al. 2010 2010 Nat Protoc 5(3): 516-535) using Covaris mircoTUBEs (#520045) and a volume of 130 ul for shearing (libraries were diluted to that volume using RNase-free water). After fragmentation, the volume was reduced to 44 ul using a SpeedVac concentrator and samples were subjected to standard Illumina library preparation using the NEBNext ChIP-Seq Sample Prep Master Mix Set 1 kit according to manufacturers instructions. Illumina PE adapters including custom-made multiplexing barcodes were ligated (amount of adapters was adjusted according to amount of input material), and Illumina PE primers (PE PCR Primer 1.0 and PE PCR Primer 2.0) were used for the PCR enrichment step (15 cycles) of the NEBNext protocol. The final purification step was performed using AMPure XP beads rather than columns and clusters were generated following the standard Illumina protocol.
ENA-FIRST-PUBLIC
2013-03-21T17:02:36Z
ENA-LAST-UPDATE
2018-03-08T16:17:21Z
External Id
SAMEA1713692
INSDC center name
EMBL-EBI
INSDC first public
2013-03-21T17:02:36Z
INSDC last update
2018-03-08T16:17:21Z
INSDC status
public
Submitter Id
E-MTAB-1499:TS50pg
broker name
ArrayExpress
common name
thale cress
individual
TS50pg
organism part
leaf
sample name
E-MTAB-1499:TS50pg
scientific_name
Arabidopsis thaliana