characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-09-06T00:18:36Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-09-06T00:18:36Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110403740
characteristics.characteristic: External Id
characteristics.text: Institute of Human Genetics Polish Academy of Sciences
characteristics.characteristic: INSDC center name
characteristics.text: 2022-09-06T00:18:36Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-09-06T00:18:36Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12501930
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11987:IG3_T-444.1
characteristics.characteristic: Submitter Id
characteristics.text: 29
characteristics.unit: year
characteristics.characteristic: age
characteristics.text: Batch3
characteristics.characteristic: batch
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: aged 15 to 39 at time of diagnosis
characteristics.characteristic: clinical history
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: T-cell acute lymphoblastic leukemia cells were obtained from bone marrow samples collected at diagnosis, by isolation of mononuclear cells, using density gradient centrifugation, followed by mmunomagnetic separation (Human T Lymphocyte Enrichment Set-DM, Becton Dickinson) in case of samples with low blast count. Thymocyte CD4+CD8+ and CD34+ samples were obtained from children undergoing cardiac surgery. Immature CD34+ thymocytes were purified based on MACS purification using CD34 microbeads (Miltenyi Biotec) without lineage depletion, while CD4 and CD8 labeling was used to sort the CD4+CD8+ double positive subset by a FACSAriaIII (BDBiosciences). Total RNA was isolated using miRCURY RNA Isolation Kit Cell & Plant (Exiqon) or Trizol reagent. RNA isolates were DNase treated and purified with use of RNA Clean and Concentrator Kit (Zymo Research). The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 100 ng RNA was converted into microRNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (16 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation QC was performed using Bioanalyzer 2100 (Agilent). Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: T-cell acute lymphoblastic leukemia
characteristics.characteristic: disease
characteristics.text: EGIL_I_pro
characteristics.characteristic: disease staging
characteristics.text: ETP
characteristics.characteristic: immunophenotype
characteristics.text: 444.1
characteristics.characteristic: individual
characteristics.text: no
characteristics.characteristic: inter-batch control
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: bone marrow
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: IG3_T-444.1
characteristics.characteristic: title