IGF2BP1      shRNA in K562      Control: Nontarget-LV11

General Information
RBPIGF2BP1
Cell_LineK562
MethodshRNA
Exp_NameIGF2BP1-BGKLV11-K562
ENCODE_series_IDENCSR002EUB
Batch_IDBGKLV11
Pool IDPool-140701
Local_Set_Nameset11
ENCODE_KD_Exp_IDENCSR629EWX
ENCODE_CN_Exp_IDENCSR129RWD
Rep1IGF2BP1-LV11-17
Rep2IGF2BP1-LV11-18
CN1Nontarget-LV11-1
CN2nontarget-LV11-2
Rep1_qPCR69.8
Rep2_qPCR74.9
Rep1_WB68.0
Rep2_WB70.2
Antibody Cat#RN007P
Antibody Lot#RN007P
Antibody DCC IDENCAB108MXA
StatusArchived
ProjectENCODE3
ID310




Experiment Information (Status: Released)
BGKLV11-17BGKLV11-18
idx8687
TRCN#_or_BGC#TRCN0000075149TRCN0000075149
shRNA_or_gRNA_sequenceGCAGTGGTGAATGTCACCTATGCAGTGGTGAATGTCACCTAT
PAM
NameIGF2BP1IGF2BP1
Sample_IDBGKLV11-17BGKLV11-18
transduction_Date5/1/20145/1/2014
days
RBP_nameIGF2BP1IGF2BP1
qPCR_result69.874.9
Ave_qPCR72.3
RT-qPCR_primer-Facagcctgctggctcagtat
RT-qPCR_primer-Rccggttggaataggtgacat
protein_conc22042232
WB_result68.070.2
Ave_WB69.1
WB_DONE_date
MW63kDa
IP0.5MB0.5MB
antibody_Cat#RN007PRN007P
Antibody DCC IDENCAB108MXAENCAB108MXA
submitted_to_DCC_date5/6/2015
Rep1_TPM35.16546680
Rep2_TPM22.6349610
ActionReadyReady
Library_start_date5/19/20145/19/2014
repeat_library
Note
ID9596




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
IGF2BP1Product_ID: RN007P
Lot_ID: 3
Source: MBLI
Target Name: IGF2BP1-human		 HepG2_MBLI_RN007P_003_IGF2BP1.png<br>Caption: IP-WB analysis of HepG2 whole cell lysate using IGF2BP1 specific antibody. Lane 1 is 1% twenty million whole cell lysate input, lane 2 is 1% of the supernatant afer IP and Lane 3 is 10% of IP enrichment using rabbit polyclonal anti-IGF2BP1 Antibody. Lane 4 is 1% ten million whole cell lysate input and lane 5 is 25% IP enrichment using rabbit normal IgG (lanes under 'IgG').
 IGF2BP1_Secondary_Western.png<br>Caption: Western blot following shRNA against IGF2BP1 in K562 and HepG2 whole cell lysate using IGF2BP1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against IGF2BP1. Lanes 5-8 follow the same pattern, but in HepG2. IGF2BP1 protein appears as the green band, Tubulin serves as a control and appears in red.
IGF2BP1_CRISPR.png<br>Caption: Western blot following CRISPR against IGF2BP1 in K562 and HepG2 whole cell lysate using IGF2BP1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against IGF2BP1. 5-8 follow the same pattern, but in HepG2. IGF2BP1 protein appears as the green band, Tubulin serves as a control and appears in red.
 K562_MBLI_RN007P_003_IGF2BP1.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using IGF2BP1 specific antibody. Lane 1 is 2.5% of five million whole cell lysate input, lane 2 is 2.5% of supernatant after immunoprecipitation and Lane 3 is 50% of IP enrichment using either rabbit polyclonal anti-IGF2BP1 antibody (lanes under 'IGF2BP1') or using rabbit normal IgG (lanes under 'IgG').
 IGF2BP1_Secondary_Western.png<br>Caption: Western blot following shRNA against IGF2BP1 in K562 and HepG2 whole cell lysate using IGF2BP1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against IGF2BP1. Lanes 5-8 follow the same pattern, but in HepG2. IGF2BP1 protein appears as the green band, Tubulin serves as a control and appears in red.
IGF2BP1_CRISPR.png<br>Caption: Western blot following CRISPR against IGF2BP1 in K562 and HepG2 whole cell lysate using IGF2BP1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against IGF2BP1. 5-8 follow the same pattern, but in HepG2. IGF2BP1 protein appears as the green band, Tubulin serves as a control and appears in red.




Experiment Status
BGKLV11-17BGKLV11-18
Sample_IDBGKLV11-17BGKLV11-18
Sample NameIGF2BP1-LV11-17IGF2BP1-LV11-18
Sample NameIGF2BP1-LV11-17IGF2BP1-LV11-18
RBPIGF2BP1IGF2BP1
Cell_LineK562K562
Exp UID
StatusReleasedReleased
Status_date2014-09-172014-09-17
ProjectENCODE3ENCODE3
Note
ID332333




Library-Prep Information
BGKLV11-17BGKLV11-18
Sample #
Sample NameIGF2BP1-BGKLV11-17IGF2BP1-BGKLV11-18
Sample_Name_AliasIGF2BP1-LV11-17IGF2BP1-LV11-18
Index Well PositionS11S12
Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
LibPrep_date2014-05-192014-05-19
Lib_IDLib-140519Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV11/set1/D2.pngDNA_Library_LV11/set1/E2.png
RIN9.19.1
libSample_RNA_WellRNA_Library_LV11/set1/C2.pngRNA_Library_LV11/set1/D2.png
SampleQC_methodTapeStationTapeStation
SampleQC_date
Sample_IDBGKLV11-17BGKLV11-18
RBPIGF2BP1IGF2BP1
Batch_IDBGKLV11BGKLV11
WB_result68.00070.200
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE3ENCODE3
ID19541955




Sequencing Information
BGKLV11-17BGKLV11-18
Sample_IDBGKLV11-17BGKLV11-18
Sample NameIGF2BP1-LV11-17IGF2BP1-LV11-18
Pool IDPool-140701Pool-140701
LocalServer_folderset11set11
total_reads67,730,00057,580,000
total_aligned_reads54,629,53847,413,634
unique_aligned_reads50,014,53443,158,782
percent_uniqueAligned0.738440.74954
correlation_replicates0.9870390.987039
spikein_reads432,846298,986
percent_spikeins0.006390.00519
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID654655




Data Submission Information
BGKLV11-17BGKLV11-17
ENCODE_aliasbrenton-graveley:IGF2BP1-LV11brenton-graveley:IGF2BP1-BGKLV11-K562
ENCODE_accessionENCSR629EWXENCSR002EUB
object_typeexperimentexperiment
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGKLV11-17BGKLV11-17
Sample NameIGF2BP1-LV11-17IGF2BP1-LV11-17
SelectedYesNo
StatusReleasedArchived
Status_Date2014-09-082022-03-01
ProjectENCODE3ENCODE3
protocol_URL
ID27156778




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
IGF2BP1-LV11-17_GGCTAC_L002_R1_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab654HiSeq2000100paired-ended1Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gzENCODE312375
IGF2BP1-LV11-17_GGCTAC_L002_R2_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab654HiSeq2000100paired-ended2Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gzENCODE312423
IGF2BP1-LV11-17_Aligned.sortedByCoord.out.bamENCODE_DATA/set11/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab654GRCh38V40IGF2BP1-LV11-17_GGCTAC_L002_R1_001.fastq.gz,IGF2BP1-LV11-17_GGCTAC_L002_R2_001.fastq.gzENCORE212471
IGF2BP1-LV11-17_Signal.Unique.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab654GRCh38V40IGF2BP1-LV11-17/Aligned.sortedByCoord.out.bamENCORE212519
IGF2BP1-LV11-17_Signal.Unique.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab654GRCh38V40IGF2BP1-LV11-17/Aligned.sortedByCoord.out.bamENCORE212567
IGF2BP1-LV11-17_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab654GRCh38V40IGF2BP1-LV11-17/Aligned.sortedByCoord.out.bamENCORE212615
IGF2BP1-LV11-17_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab654GRCh38V40IGF2BP1-LV11-17/Aligned.sortedByCoord.out.bamENCORE212663
IGF2BP1-LV11-17_quant.sfENCODE_DATA/set11/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab654GRCh38V40IGF2BP1-LV11-17_GGCTAC_L002_R1_001.fastq.gz,IGF2BP1-LV11-17_GGCTAC_L002_R2_001.fastq.gzENCORE212711
IGF2BP1-LV11-18_CTTGTA_L002_R1_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab655HiSeq2000100paired-ended1Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gzENCODE312376
IGF2BP1-LV11-18_CTTGTA_L002_R2_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab655HiSeq2000100paired-ended2Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gzENCODE312424
IGF2BP1-LV11-18_Aligned.sortedByCoord.out.bamENCODE_DATA/set11/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab655GRCh38V40IGF2BP1-LV11-18_CTTGTA_L002_R1_001.fastq.gz,IGF2BP1-LV11-18_CTTGTA_L002_R2_001.fastq.gzENCORE212472
IGF2BP1-LV11-18_Signal.Unique.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab655GRCh38V40IGF2BP1-LV11-18/Aligned.sortedByCoord.out.bamENCORE212520
IGF2BP1-LV11-18_Signal.Unique.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab655GRCh38V40IGF2BP1-LV11-18/Aligned.sortedByCoord.out.bamENCORE212568
IGF2BP1-LV11-18_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab655GRCh38V40IGF2BP1-LV11-18/Aligned.sortedByCoord.out.bamENCORE212616
IGF2BP1-LV11-18_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab655GRCh38V40IGF2BP1-LV11-18/Aligned.sortedByCoord.out.bamENCORE212664
IGF2BP1-LV11-18_quant.sfENCODE_DATA/set11/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab655GRCh38V40IGF2BP1-LV11-18_CTTGTA_L002_R1_001.fastq.gz,IGF2BP1-LV11-18_CTTGTA_L002_R2_001.fastq.gzENCORE212712