HNRNPK      shRNA in K562      Control: Nontarget-LV11

General Information
RBPHNRNPK
Cell_LineK562
MethodshRNA
Exp_NameHNRNPK-BGKLV11-K562
ENCODE_series_IDENCSR208JOG
Batch_IDBGKLV11
Pool IDPool-140701
Local_Set_Nameset11
ENCODE_KD_Exp_IDENCSR529JNJ
ENCODE_CN_Exp_IDENCSR129RWD
Rep1HNRNPK-LV11-15
Rep2HNRNPK-LV11-16
CN1Nontarget-LV11-1
CN2nontarget-LV11-2
Rep1_qPCR71.0
Rep2_qPCR67.3
Rep1_WB47.9
Rep2_WB61.0
Antibody Cat#RN019P
Antibody Lot#RN019P
Antibody DCC IDENCAB000BFN
StatusReleased
ProjectENCODE3
ID309




Experiment Information (Status: Released)
BGKLV11-15BGKLV11-15BGKLV11-15BGKLV11-16BGKLV11-16BGKLV11-16
idx84008500
TRCN#_or_BGC#TRCN0000062455TRCN0000062455TRCN0000062455TRCN0000062455TRCN0000062455TRCN0000062455
shRNA_or_gRNA_sequenceGCCAGTGTTTCAGTCCCAGACGCCAGTGTTTCAGTCCCAGACCTCGAGGTCTGGGACTGAAACANTGNGCCAGTGTTTCAGTCCCAGACCTCGAGGTCTGGGACTGAAACANTGNGCCAGTGTTTCAGTCCCAGACGCCAGTGTTTCAGTCCCAGACCTCGAGGTCTGGGACTGAAACANTGNGCCAGTGTTTCAGTCCCAGACCTCGAGGTCTGGGACTGAAACANTGN
PAM
NameHNRNPKHNRNPKHNRNPKHNRNPKHNRNPKHNRNPK
Sample_IDBGKLV11-15BGKLV11-15BGKLV11-15BGKLV11-16BGKLV11-16BGKLV11-16
transduction_Date5/1/20145/1/20145/1/20145/1/20145/1/20145/1/2014
days
RBP_nameHNRNPKHNRNPKHNRNPKHNRNPKHNRNPKHNRNPK
qPCR_result71.071.071.067.367.367.3
Ave_qPCR69.269.269.2
RT-qPCR_primer-FCCATTACAGGAACACAGGACCCCATTACAGGAACACAGGACCCCATTACAGGAACACAGGACC
RT-qPCR_primer-RTCTTGCATTAGAATCCTTCAACATCTTGCATTAGAATCCTTCAACATCTTGCATTAGAATCCTTCAACA
protein_conc201220122012204120412041
WB_result47.980.292.661.084.492.6
Ave_WB54.582.392.6
WB_DONE_date6/27/20141/24/196/14/23
MW51kDa51kDa51kDanew ABNO MORE SAMPLES
IP11
antibody_Cat#RN019PMA1-0879081SRN019PLOT #SA246066LOT# 1
Antibody DCC IDENCAB000BFNENCAB309WNL no IDENCAB000BFN10/18/23
submitted_to_DCC_date5/4/20153/11/19
Rep1_TPM121.3073500000
Rep2_TPM103.40286200000
ActionReadyReady
Library_start_date5/19/20145/19/2014
repeat_library
Note
ID899193909294




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
HNRNPKProduct_ID: MA1-087
Lot_ID: SA246066
Source: Thermo Fisher
Target Name: HNRNPK-human		 ThermoFisher_MA1-087_SA246066_HNRNPK.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the HNRNPK specific antibody, MA1-087. Lanes 1 and 3 are 2.5% of five million whole cell lysate input. Lanes 2 and 4 are 50% of IP enrichment from five million whole cell lysate using normal IgG antibody and the HNRNPK-specific antibody, MA1-087. The same antibody was used to detect protein levels via Western blot. This antibody passes preliminary validation and will be further pursued for secondary validation. *NOTE* Protein sizes are taken from Genecards.org and are only estimates based on sequence. Actual protein size may differ based on protein characteristics and electrophoresis method used.
 HNRNPK-K562.png<br>Caption: Western blot following shRNA against HNRNPK in K562 whole cell lysate using HNRNPK specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNA against HNRNPK. HNRNPK protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
HNRNPKProduct_ID: RN019P
Lot_ID: 1
Source: MBLI
Target Name: HNRNPK-human		 HEPG2_MBL_RN019P_1_HNRNPK.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using HNRNPK specific antibody. Lane 1 is 1% of twenty million whole cell lysate input and lane 2 is 10% 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-HNRNPK antibody (lanes under 'HNRNPK').
 HNRNPK_Secondary_Western.png<br>Caption: Western blot following shRNA against HNRNPK in K562 and HepG2 whole cell lysate using HNRNPK specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against HNRNPK. Lanes 5-7 follow the same pattern, but in HepG2. HNRNPK protein appears as the green band, GAPDH serves as a control and appears in red.
 MBLI_RN019P_001_HNRNPK_K562.png<br>Caption: IP-WB characterization of HNRNPK specific antibody in K562 cell line . Lane 1 is 2.5% of five million K562 whole cell lysate Input, lane 2 is 2.5% of supernatant after immunoprecipitation and Lane 3 is 50% of IP enrichment using rabbit polyclonal Anti-HNRNPK(Human)pAb. This antibody passes preliminary validation and will be further pursued for primary and secondary validation.
 HNRNPK_Secondary_Western.png<br>Caption: Western blot following shRNA against HNRNPK in K562 and HepG2 whole cell lysate using HNRNPK specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against HNRNPK. Lanes 5-7 follow the same pattern, but in HepG2. HNRNPK protein appears as the green band, GAPDH serves as a control and appears in red.
HNRNPKProduct_ID: 9081S
Lot_ID: 1
Source: Cell Signaling Technology
Target Name: HNRNPK-human		 CST_9081S_1_HNRNPK.png<br>Caption: IP-WB analysis of 9081S whole cell lysate using the HNRNPK specific antibody, 9081S. Lanes 1 and 2 are 2.5% of five million whole cell lysate input and 50% of IP enrichment, respectively, using a normal IgG antibody. Lane 3 is 50% of IP enrichment from five million whole cell lysate using the HNRNPK-specific antibody, 9081S. The same antibody was used to detect protein levels via Western blot. This antibody passes preliminary validation and will be further pursued for secondary validation. *NOTE* Protein sizes are taken from Genecards.org and are only estimates based on sequence. Actual protein size may differ based on protein characteristics and electrophoresis method used.
 HNRNPK-K562-9081S.png<br>Caption: Western blot following shRNA against HNRNPK in K562 whole cell lysate using HNRNPK specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNA against HNRNPK. HNRNPK protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGKLV11-15BGKLV11-16
Sample_IDBGKLV11-15BGKLV11-16
Sample NameHNRNPK-LV11-15HNRNPK-LV11-16
Sample NameHNRNPK-LV11-15HNRNPK-LV11-16
RBPHNRNPKHNRNPK
Cell_LineK562K562
Exp UID
StatusReleasedReleased
Status_date2014-09-172014-09-17
ProjectENCODE3ENCODE3
Note
ID330331




Library-Prep Information
BGKLV11-15BGKLV11-16
Sample #
Sample NameHNRNPK-BGKLV11-15HNRNPK-BGKLV11-16
Sample_Name_AliasHNRNPK-LV11-15HNRNPK-LV11-16
Index Well PositionS09S10
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/B2.pngDNA_Library_LV11/set1/C2.png
RIN9.19.2
libSample_RNA_WellRNA_Library_LV11/set1/A2.pngRNA_Library_LV11/set1/B2.png
SampleQC_methodTapeStationTapeStation
SampleQC_date
Sample_IDBGKLV11-15BGKLV11-16
RBPHNRNPKHNRNPK
Batch_IDBGKLV11BGKLV11
WB_result47.90061.000
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE3ENCODE3
ID19521953




Sequencing Information
BGKLV11-15BGKLV11-16
Sample_IDBGKLV11-15BGKLV11-16
Sample NameHNRNPK-LV11-15HNRNPK-LV11-16
Pool IDPool-140701Pool-140701
LocalServer_folderset11set11
total_reads61,130,00069,680,000
total_aligned_reads50,317,88455,155,720
unique_aligned_reads46,097,79050,563,676
percent_uniqueAligned0.754090.72566
correlation_replicates0.9958990.995899
spikein_reads446,352358,396
percent_spikeins0.007300.00514
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID652653




Data Submission Information
BGKLV11-15BGKLV11-15
ENCODE_aliasbrenton-graveley:HNRNPK-LV11brenton-graveley:HNRNPK-BGKLV11-K562
ENCODE_accessionENCSR529JNJENCSR208JOG
object_typeexperimentgene_silencing_series
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGKLV11-15BGKLV11-15
Sample NameHNRNPK-LV11-15HNRNPK-LV11-15
SelectedYesYes
StatusReleasedReleased
Status_Date2014-09-082022-03-01
ProjectENCODE3ENCODE3
protocol_URL
ID27146763




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
HNRNPK-LV11-15_GATCAG_L002_R1_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab652HiSeq2000100paired-ended1Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gzENCODE312373
HNRNPK-LV11-15_GATCAG_L002_R2_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab652HiSeq2000100paired-ended2Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gzENCODE312421
HNRNPK-LV11-15_Aligned.sortedByCoord.out.bamENCODE_DATA/set11/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab652GRCh38V40HNRNPK-LV11-15_GATCAG_L002_R1_001.fastq.gz,HNRNPK-LV11-15_GATCAG_L002_R2_001.fastq.gzENCORE212469
HNRNPK-LV11-15_Signal.Unique.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab652GRCh38V40HNRNPK-LV11-15/Aligned.sortedByCoord.out.bamENCORE212517
HNRNPK-LV11-15_Signal.Unique.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab652GRCh38V40HNRNPK-LV11-15/Aligned.sortedByCoord.out.bamENCORE212565
HNRNPK-LV11-15_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab652GRCh38V40HNRNPK-LV11-15/Aligned.sortedByCoord.out.bamENCORE212613
HNRNPK-LV11-15_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab652GRCh38V40HNRNPK-LV11-15/Aligned.sortedByCoord.out.bamENCORE212661
HNRNPK-LV11-15_quant.sfENCODE_DATA/set11/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab652GRCh38V40HNRNPK-LV11-15_GATCAG_L002_R1_001.fastq.gz,HNRNPK-LV11-15_GATCAG_L002_R2_001.fastq.gzENCORE212709
HNRNPK-LV11-16_TAGCTT_L002_R1_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab653HiSeq2000100paired-ended1Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gzENCODE312374
HNRNPK-LV11-16_TAGCTT_L002_R2_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab653HiSeq2000100paired-ended2Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gzENCODE312422
HNRNPK-LV11-16_Aligned.sortedByCoord.out.bamENCODE_DATA/set11/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab653GRCh38V40HNRNPK-LV11-16_TAGCTT_L002_R1_001.fastq.gz,HNRNPK-LV11-16_TAGCTT_L002_R2_001.fastq.gzENCORE212470
HNRNPK-LV11-16_Signal.Unique.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab653GRCh38V40HNRNPK-LV11-16/Aligned.sortedByCoord.out.bamENCORE212518
HNRNPK-LV11-16_Signal.Unique.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab653GRCh38V40HNRNPK-LV11-16/Aligned.sortedByCoord.out.bamENCORE212566
HNRNPK-LV11-16_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab653GRCh38V40HNRNPK-LV11-16/Aligned.sortedByCoord.out.bamENCORE212614
HNRNPK-LV11-16_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab653GRCh38V40HNRNPK-LV11-16/Aligned.sortedByCoord.out.bamENCORE212662
HNRNPK-LV11-16_quant.sfENCODE_DATA/set11/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab653GRCh38V40HNRNPK-LV11-16_TAGCTT_L002_R1_001.fastq.gz,HNRNPK-LV11-16_TAGCTT_L002_R2_001.fastq.gzENCORE212710