AKAP1      shRNA in K562      Batch: BGKLV08_3

Experiment Information (Status: Released)
BGKLV08-4
idx5
TRCN#_or_BGC#TRCN0000013159
shRNA_or_gRNA_sequenceGCTCAGATTCTTTCAGCACTT
PAM
NameAKAP1
Sample_IDBGKLV08-4
transduction_Date4/4/2014
days
RBP_nameAKAP1
qPCR_result86.8
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc2552
WB_result99.8
Ave_WB
WB_DONE_date
MWwes
IP1
antibody_Cat#A301-379A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM0
Rep2_TPM0
ActionReady
Library_start_date5/5/2014
repeat_library
Note
ID4




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
AKAP1Product_ID: A301-379A
Lot_ID: 1
Source: Bethyl Labs
Target Name: AKAP1-human		 HepG2_Bethyl_A301-379A_1_AKAP1.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using AKAP1 specific antibody. Lane 1 is 1% of twenty million whole cell lysate input and lane 2 is 25% of IP enrichment using rabbit normal IgG (lanes under 'IgG'). Lane 3 is 1% of twenty million whole cell lysate input and lane 4 is 10% IP enrichment using rabbit polyclonal anti-AKAP1 antibody (lanes under 'AKAP1').
 AKAP1-HEPG2.png<br>Caption: Western blot following shRNA against AKAP1 in HepG2 whole cell lysate using AKAP1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNA against AKAP1. AKAP1 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
 K562_Bethyl_A301-379A_1_AKAP1.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using AKAP1 specific antibody. Lane 1 is 1% of twenty million whole cell lysate input and lane 2 is 25% of IP enrichment using rabbit normal IgG (lanes under 'IgG'). Lane 3 is 1% of twenty million whole cell lysate input and lanes 4 and 5 are 10% IP enrichment from biological replicates using rabbit polyclonal anti-AKAP1 antibody (lanes under 'AKAP1').
 AKAP1-K562.png<br>Caption: Western blot following shRNA against AKAP1 in K562 whole cell lysate using AKAP1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against AKAP1.AKAP1 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.




Experiment Status
BGKLV08-4
Sample_IDBGKLV08-4
Sample NameAKAP1-LV08-4
Sample NameAKAP1-LV08-4
RBPAKAP1
Cell_LineK562
Exp UID
StatusReleased
Status_date2014-09-16
ProjectENCODE3
Note
ID269




Library-Prep Information
BGKLV08-4
Sample #
Sample NameAKAP1-BGKLV08-4
Sample_Name_AliasAKAP1-LV08-4
Index Well PositionS04
Index_tableIDT_TruSeqSingleIndex_24
LibPrep_date2014-05-05
Lib_IDLib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV08/set1/E1.png
RIN9.3
libSample_RNA_WellRNA_Library_LV08/set1/D1.png
SampleQC_methodTapeStation
SampleQC_date
Sample_IDBGKLV08-4
RBPAKAP1
Batch_IDBGKLV08
WB_result99.800
Library DescriptionTruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequence
ProjectENCODE3
ID1891




Sequencing Information
BGKLV08-4
Sample_IDBGKLV08-4
Sample NameAKAP1-LV08-4
Pool IDPool-140601
LocalServer_folderset10
total_reads49,730,000
total_aligned_reads42,403,288
unique_aligned_reads38,652,596
percent_uniqueAligned0.77725
correlation_replicates0.998396
spikein_reads418,872
percent_spikeins0.00842
original_ReadLength100
QC_StatusSubmitted
ID591




Data Submission Information
DCC submission information was not avaliable




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
AKAP1-LV08-4_Aligned.sortedByCoord.out.bamENCODE_DATA/set10/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab591GRCh38V40AKAP1-LV08-4_TGACCA_L001_R1_001.fastq.gz,AKAP1-LV08-4_TGACCA_L001_R2_001.fastq.gzENCORE211976
AKAP1-LV08-4_TGACCA_L001_R1_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab591HiSeq2000100paired-ended1Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gzENCODE312032
AKAP1-LV08-4_TGACCA_L001_R2_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab591HiSeq2000100paired-ended2Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gzENCODE312088
AKAP1-LV08-4_Signal.Unique.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab591GRCh38V40AKAP1-LV08-4/Aligned.sortedByCoord.out.bamENCORE212144
AKAP1-LV08-4_Signal.Unique.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab591GRCh38V40AKAP1-LV08-4/Aligned.sortedByCoord.out.bamENCORE212200
AKAP1-LV08-4_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab591GRCh38V40AKAP1-LV08-4/Aligned.sortedByCoord.out.bamENCORE212256
AKAP1-LV08-4_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab591GRCh38V40AKAP1-LV08-4/Aligned.sortedByCoord.out.bamENCORE212312
AKAP1-LV08-4_quant.sfENCODE_DATA/set10/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab591GRCh38V40AKAP1-LV08-4_TGACCA_L001_R1_001.fastq.gz,AKAP1-LV08-4_TGACCA_L001_R2_001.fastq.gzENCORE213311