GTF2F1      shRNA in K562      Batch: BGKLV13_39

Experiment Information (Status: Released)
BGKLV13-40
idx175
TRCN#_or_BGC#TRCN0000020836
shRNA_or_gRNA_sequenceGCGCAAGATGATCAACGACAA
PAM
NameGTF2F1
Sample_IDBGKLV13-40
transduction_Date6/13/2014
days
RBP_nameGTF2F1
qPCR_result92.3
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc2271
WB_result88.6
Ave_WB
WB_DONE_date
MW
IP1
antibody_Cat#GTX114455
Antibody DCC IDENCAB108WPN
submitted_to_DCC_date
Rep1_TPM0
Rep2_TPM0
Action
Library_start_date7/27/2014
repeat_library
Note
ID194




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
GTF2F1Product_ID: GTX114455
Lot_ID: 40723
Source: GeneTex
Target Name: GTF2F1-human		 HepG2_Genetex_GTX114455_40723_GTF2F1.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using GTF2F1 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-GTF2F1 antibody (lanes under 'GTF2F1').
 GTF2F1_Secondary_Western.png<br>Caption: Western blot following shRNA against GTF2F1 in K562 and HepG2 whole cell lysate using GTF2F1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against GTF2F1. Lanes 5-8 follow the same pattern, but in HepG2. GTF2F1 protein appears as the green band, Tubulin serves as a control and appears in red.
 K562_Genetex_GTX114455_40723_GTF2F1.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using GTF2F1 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-GTF2F1 antibody (lanes under 'GTF2F1').
 GTF2F1_Secondary_Western.png<br>Caption: Western blot following shRNA against GTF2F1 in K562 and HepG2 whole cell lysate using GTF2F1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against GTF2F1. Lanes 5-8 follow the same pattern, but in HepG2. GTF2F1 protein appears as the green band, Tubulin serves as a control and appears in red.




Experiment Status
BGKLV13-40
Sample_IDBGKLV13-40
Sample NameGTF2F1_BGKLV13_40
Sample NameGTF2F1_BGKLV13_40
RBPGTF2F1
Cell_LineK562
Exp UID
StatusReleased
Status_date2014-10-29
ProjectENCODE3
Note
ID455




Library-Prep Information
BGKLV13-40
Sample #
Sample NameGTF2F1-BGKLV13-40
Sample_Name_AliasGTF2F1_BGKLV13_40
Index Well PositionS02
Index_tableIDT_TruSeqSingleIndex_24
LibPrep_date2014-07-27
Lib_IDLib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV13-14/set1/C4.png
RIN9.7
libSample_RNA_WellRNA_Library_LV12/set1/F12.png
SampleQC_methodTapeStation
SampleQC_date
Sample_IDBGKLV13-40
RBPGTF2F1
Batch_IDBGKLV13
WB_result88.600
Library DescriptionTruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequence
ProjectENCODE3
ID2145




Sequencing Information
BGKLV13-40
Sample_IDBGKLV13-40
Sample NameGTF2F1_BGKLV13_40
Pool IDPool-140901
LocalServer_folderset13
total_reads45,750,000
total_aligned_reads42,396,638
unique_aligned_reads38,892,636
percent_uniqueAligned0.85011
correlation_replicates0.984422
spikein_reads293,540
percent_spikeins0.00642
original_ReadLength100
QC_StatusSubmitted
ID787




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
GTF2F1_BGKLV13_40_CGATGT_L004_R1_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab787HiSeq2000100paired-ended1NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gzENCODE313383
GTF2F1_BGKLV13_40_CGATGT_L004_R2_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab787HiSeq2000100paired-ended2NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gzENCODE313435
GTF2F1_BGKLV13_40_Aligned.sortedByCoord.out.bamENCODE_DATA/set13/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab787GRCh38V40GTF2F1_BGKLV13_40_CGATGT_L004_R1_001.fastq.gz,GTF2F1_BGKLV13_40_CGATGT_L004_R2_001.fastq.gzENCORE213487
GTF2F1_BGKLV13_40_Signal.Unique.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab787GRCh38V40GTF2F1_BGKLV13_40/Aligned.sortedByCoord.out.bamENCORE213539
GTF2F1_BGKLV13_40_Signal.Unique.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab787GRCh38V40GTF2F1_BGKLV13_40/Aligned.sortedByCoord.out.bamENCORE213591
GTF2F1_BGKLV13_40_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab787GRCh38V40GTF2F1_BGKLV13_40/Aligned.sortedByCoord.out.bamENCORE213643
GTF2F1_BGKLV13_40_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab787GRCh38V40GTF2F1_BGKLV13_40/Aligned.sortedByCoord.out.bamENCORE213695
GTF2F1_BGKLV13_40_quant.sfENCODE_DATA/set13/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab787GRCh38V40GTF2F1_BGKLV13_40_CGATGT_L004_R1_001.fastq.gz,GTF2F1_BGKLV13_40_CGATGT_L004_R2_001.fastq.gzENCORE213747