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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 26, 2018 |
| Title |
MV411_sgZFP64e5.1_Rep1 |
| Sample type |
SRA |
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| Source name |
acute myeloid leukemia
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MV4-11
treatment: day4 after sgZFP64e5.1 guide RNA infection
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| Treatment protocol |
Cells were lentivirally infected with sgRNA for knockout
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| Growth protocol |
MOLM13, NOMO1, MV4-11, THP1, RN2 were cultured in RPMI with 1XP/S and 10% FBS, OCIAML3 cells were cultured in a-MEM plus 10% FBS and 1XP/S, MLL-AF9/NrasG12D cells were cultured in IMDM with 20%FBS and 1XP/S.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
RNA_seq_MV411_ZFP64_Rep1.txt
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| Data processing |
Sequencing reads were mapped into reference human genome hg38 or mouse genome mm10 using TopHat2
Differentially expressed genes were analyzed using a Cufflinks tool, Cuffdiff, by masking structural RNAs
normalized to total mapped reads
RNA-seq files of two sgRNAs for each target gene were treated as replicates
Genome_build: hg38, mm10
Supplementary_files_format_and_content: txt, normalized RPKM. Processed data files are included in a tar archive on the series record.
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| Submission date |
Jun 01, 2018 |
| Last update date |
Oct 26, 2018 |
| Contact name |
Olaf Klingbeil |
| E-mail(s) |
klingbe@cshl.edu
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| Organization name |
Cold Spring Harbor Laboratory
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| Street address |
1 Bungtown Road
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| City |
Cold Spring Harbor |
| State/province |
New York |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE115237 |
A transcription factor addiction imposed by an oncogene promoter sequence [RNA-seq] |
| GSE115238 |
A transcription factor addiction imposed by an oncogene promoter sequence |
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| Relations |
| BioSample |
SAMN09294552 |
| SRA |
SRX4154163 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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