title: TS50pg
organism: Arabidopsis thaliana
description: 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.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2013-03-21T17:02:36Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-03-08T16:17:21Z
attributes.tag: External Id
attributes.value: SAMEA1713692
attributes.tag: INSDC center name
attributes.value: EMBL-EBI
attributes.tag: INSDC first public
attributes.value: 2013-03-21T17:02:36Z
attributes.tag: INSDC last update
attributes.value: 2018-03-08T16:17:21Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-1499:TS50pg
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: thale cress
attributes.tag: individual
attributes.value: TS50pg
attributes.tag: organism part
attributes.value: leaf
attributes.tag: sample name
attributes.value: E-MTAB-1499:TS50pg
attributes.tag: scientific_name
attributes.value: Arabidopsis thaliana