TBRG4      shRNA in K562      Batch: BGKLV08_59

Experiment Information (Status: Released)
BGKLV08-60
idx65
TRCN#_or_BGC#TRCN0000154962
shRNA_or_gRNA_sequenceGATGCCCACTTTCATCAACTT
PAM
NameTBRG4
Sample_IDBGKLV08-60
transduction_Date4/4/2014
days
RBP_nameTBRG4
qPCR_result47.2
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc2948
WB_result59.9
Ave_WB
WB_DONE_date
MW
IP1
antibody_Cat#A301-392A
Antibody DCC IDENCAB890JXZ
submitted_to_DCC_date
Rep1_TPM0
Rep2_TPM0
ActionReady
Library_start_date5/9/2014
repeat_library
Note
ID70




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
TBRG4Product_ID: A301-392A
Lot_ID: 1
Source: Bethyl Labs
Target Name: TBRG4-human		 HepG2_Bethyl_A301-392A_1_TBRG4.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using TBRG4 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-TBRG4 antibody (lanes under 'TBRG4').
 TBRG4-HEPG2_Secondary_Western.png<br>Caption: Western blot following shRNA against TBRG4 in HepG2 whole cell lysate using TBRG4 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against TBRG4.TBRG4 protein appears as the green band, Tubulin serves as a control and appears in red.
 K562_Bethyl_A301-392A_1_TBRG4.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using TBRG4 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-TBRG4 antibody (lanes under 'TBRG4').
 TBRG4_Secondary_Western.png<br>Caption: Western blot following shRNA against TBRG4 in K562 whole cell lysate using TBRG4 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against TBRG4. TBRG4 protein appears as the green band, Tubulin serves as a control and appears in red.




Experiment Status
BGKLV08-60
Sample_IDBGKLV08-60
Sample NameTBRG4-LV08-60
Sample NameTBRG4-LV08-60
RBPTBRG4
Cell_LineK562
Exp UID
StatusReleased
Status_date2014-09-16
ProjectENCODE3
Note
ID319




Library-Prep Information
BGKLV08-60
Sample #
Sample NameTBRG4-BGKLV08-60
Sample_Name_AliasTBRG4-LV08-60
Index Well PositionS04
Index_tableIDT_TruSeqSingleIndex_24
LibPrep_date2014-05-08
Lib_IDLib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV08/set5/F1.png
RIN9.3
libSample_RNA_WellRNA_Library_LV08/set4/F1.png
SampleQC_methodTapeStation
SampleQC_date
Sample_IDBGKLV08-60
RBPTBRG4
Batch_IDBGKLV08
WB_result59.900
Library DescriptionTruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequence
ProjectENCODE3
ID1939




Sequencing Information
BGKLV08-60
Sample_IDBGKLV08-60
Sample NameTBRG4-LV08-60
Pool IDPool-140601
LocalServer_folderset10
total_reads51,030,000
total_aligned_reads46,106,086
unique_aligned_reads41,974,792
percent_uniqueAligned0.82255
correlation_replicates0.990369
spikein_reads350,866
percent_spikeins0.00688
original_ReadLength100
QC_StatusSubmitted
ID639




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
TBRG4-LV08-60_Aligned.sortedByCoord.out.bamENCODE_DATA/set10/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab639GRCh38V40TBRG4-LV08-60_TGACCA_L008_R1_001.fastq.gz,TBRG4-LV08-60_TGACCA_L008_R2_001.fastq.gzENCORE212026
TBRG4-LV08-60_TGACCA_L008_R1_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab639HiSeq2000100paired-ended1Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gzENCODE312082
TBRG4-LV08-60_TGACCA_L008_R2_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab639HiSeq2000100paired-ended2Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gzENCODE312138
TBRG4-LV08-60_Signal.Unique.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab639GRCh38V40TBRG4-LV08-60/Aligned.sortedByCoord.out.bamENCORE212194
TBRG4-LV08-60_Signal.Unique.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab639GRCh38V40TBRG4-LV08-60/Aligned.sortedByCoord.out.bamENCORE212250
TBRG4-LV08-60_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab639GRCh38V40TBRG4-LV08-60/Aligned.sortedByCoord.out.bamENCORE212306
TBRG4-LV08-60_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab639GRCh38V40TBRG4-LV08-60/Aligned.sortedByCoord.out.bamENCORE212362
TBRG4-LV08-60_quant.sfENCODE_DATA/set10/salmon_ENCORE2_file_linkstranscript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab639GRCh38V40TBRG4-LV08-60_TGACCA_L008_R1_001.fastq.gz,TBRG4-LV08-60_TGACCA_L008_R2_001.fastq.gzENCORE213361