TARDBP      shRNA in K562      Control: Nontarget-LV11

General Information
RBPTARDBP
Cell_LineK562
MethodshRNA
Exp_NameTARDBP-BGKLV11-K562
ENCODE_series_IDENCSR630HSM
Batch_IDBGKLV11
Pool IDPool-140701
Local_Set_Nameset11
ENCODE_KD_Exp_IDENCSR134JRE
ENCODE_CN_Exp_IDENCSR129RWD
Rep1TARDBP-LV11-57
Rep2TARDBP-LV11-58
CN1Nontarget-LV11-1
CN2nontarget-LV11-2
Rep1_qPCR64.3
Rep2_qPCR70.2
Rep1_WB69.3
Rep2_WB71.7
Antibody Cat#A303-223A
Antibody Lot#A303-223A
Antibody DCC IDENCAB057RGG
StatusReleased
ProjectENCODE3
ID326




Experiment Information (Status: Released)
BGKLV11-57BGKLV11-57BGKLV11-58BGKLV11-58
idx12601270
TRCN#_or_BGC#TRCN0000016038TRCN0000016038TRCN0000016038TRCN0000016038
shRNA_or_gRNA_sequenceGCTCTAATTCTGGTGCAGCAAGCTCTAATTCTGGTGCAGCAAGCTCTAATTCTGGTGCAGCAAGCTCTAATTCTGGTGCAGCAA
PAM
NameTARDBPTARDBPTARDBPTARDBP
Sample_IDBGKLV11-57BGKLV11-57BGKLV11-58BGKLV11-58
transduction_Date5/1/20145/1/20145/1/20145/1/2014
days
RBP_nameTARDBPTARDBPTARDBPTARDBP
qPCR_result64.364.370.270.2
Ave_qPCR67.367.3
RT-qPCR_primer-FGATGGACGATGGTGTGACTGGATGGACGATGGTGTGACTG
RT-qPCR_primer-RAGAACTCCCGCAGCTCATCAGAACTCCCGCAGCTCATC
protein_conc1822182219181918
WB_result69.396.771.796.7
Ave_WB70.596.7
WB_DONE_date6/24/201511/27/18
MW45kDa45kDa
IP11
antibody_Cat#A303-223A711051A303-223ALot# SI259917
Antibody DCC IDENCAB057RGGENCAB349KOVENCAB057RGG
submitted_to_DCC_date8/6/20153/11/2019
Rep1_TPM148.339946148.33994600
Rep2_TPM111.944725111.94472500
ActionReadyReadyReadyReady
Library_start_date5/19/20145/19/20145/19/20145/19/2014
repeat_library
Note
ID139141140142




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
TARDBPProduct_ID: 711051
Lot_ID: SI259917
Source: Thermo Fisher
Target Name: TARDBP-human		 ThermoFisher_711051_SI259917_TARDBP_HepG2.png<br>Caption: IP-WB analysis of HepG2 whole cell lysate using the TARDBP specific antibody, 711051. Lanes 1 and 2 are 2.5% of five million whole cell lysate input and 50% of IP enrichment using a normal IgG antibody, respectively. Lane 3 is 50% of IP enrichment from five million whole cell lysate using the TARDBP-specific antibody, 711051. 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.
 ThermoFisher_711051_SI259917_TARDBP.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the TARDBP specific antibody, 711051. 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 TARDBP-specific antibody, 711051. 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.
 TARDBP-K562.png<br>Caption: Western blot following shRNA against TARDBP in K562 whole cell lysate using TARDBP specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNA against TARDBP. TARDBP protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
TARDBPProduct_ID: A303-223A
Lot_ID: 1
Source: Bethyl Labs
Target Name: TARDBP-human		 HepG2_Bethyl_A303-223A_1_TDP43.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using TDP43 (TARDBP) specific antibody. Lane 1 is 1% of twenty million whole cell lysate input; lane 2 is 10% of IP enrichment using rabbit normal IgG (lanes under 'lgG'); Lane 3 is 1% of twenty million whole cell lysate input and lane 4 is 10% IP enrichment using rabbit polyclonal anti-TDP43 antibody (lanes under 'TDP43'). The expected molecular weight of TDP43 is 43 kDa.
 TARDBP-hepg2.png<br>Caption: Western blot following shRNA against TARDBP in HepG2 whole cell lysate using TARDBP specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against TARDBP.TARDBP protein appears as the green band, GAPDH serves as a control and appears in red.
 K562_Bethyl_A303-223A_1_TARDBP.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using TARDBP 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-TDP43 antibody (lanes under 'TARDBP').
 TARDBP_Secondary_Western.png<br>Caption: Western blot following shRNA against TARDBP in K562 whole cell lysate using TARDBP specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against TARDBP. TARDBP protein appears as the green band, GAPDH serves as a control and appears in red.




Experiment Status
BGKLV11-57BGKLV11-58
Sample_IDBGKLV11-57BGKLV11-58
Sample NameTARDBP-LV11-57TARDBP-LV11-58
Sample NameTARDBP-LV11-57TARDBP-LV11-58
RBPTARDBPTARDBP
Cell_LineK562K562
Exp UID
StatusReleasedReleased
Status_date2014-09-172014-09-17
ProjectENCODE3ENCODE3
Note
ID366367




Library-Prep Information
BGKLV11-57BGKLV11-58
Sample #
Sample NameTARDBP-BGKLV11-57TARDBP-BGKLV11-58
Sample_Name_AliasTARDBP-LV11-57TARDBP-LV11-58
Index Well PositionS20S21
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/set3/F2.pngDNA_Library_LV11/set3/G2.png
RIN9.49.3
libSample_RNA_WellRNA_Library_LV11/set1/C6.pngRNA_Library_LV11/set1/D6.png
SampleQC_methodTapeStationTapeStation
SampleQC_date
Sample_IDBGKLV11-57BGKLV11-58
RBPTARDBPTARDBP
Batch_IDBGKLV11BGKLV11
WB_result69.30071.700
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE3ENCODE3
ID19881989




Sequencing Information
BGKLV11-57BGKLV11-58
Sample_IDBGKLV11-57BGKLV11-58
Sample NameTARDBP-LV11-57TARDBP-LV11-58
Pool IDPool-140701Pool-140701
LocalServer_folderset11set11
total_reads55,400,00057,280,000
total_aligned_reads44,484,39847,979,630
unique_aligned_reads40,426,48843,710,494
percent_uniqueAligned0.729720.76310
correlation_replicates0.9947950.994795
spikein_reads218,630267,772
percent_spikeins0.003950.00467
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID688689




Data Submission Information
BGKLV11-57BGKLV11-57
ENCODE_aliasbrenton-graveley:TARDBP-LV11brenton-graveley:TARDBP-BGKLV11-K562
ENCODE_accessionENCSR134JREENCSR630HSM
object_typeexperimentgene_silencing_series
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGKLV11-57BGKLV11-57
Sample NameTARDBP-LV11-57TARDBP-LV11-57
SelectedYesYes
StatusReleasedReleased
Status_Date2014-09-082022-03-01
ProjectENCODE3ENCODE3
protocol_URL
ID27327002




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
TARDBP-LV11-57_GTGGCC_L008_R1_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab688HiSeq2000100paired-ended1Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gzENCODE312409
TARDBP-LV11-57_GTGGCC_L008_R2_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab688HiSeq2000100paired-ended2Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gzENCODE312457
TARDBP-LV11-57_Aligned.sortedByCoord.out.bamENCODE_DATA/set11/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab688GRCh38V40TARDBP-LV11-57_GTGGCC_L008_R1_001.fastq.gz,TARDBP-LV11-57_GTGGCC_L008_R2_001.fastq.gzENCORE212505
TARDBP-LV11-57_Signal.Unique.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab688GRCh38V40TARDBP-LV11-57/Aligned.sortedByCoord.out.bamENCORE212553
TARDBP-LV11-57_Signal.Unique.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab688GRCh38V40TARDBP-LV11-57/Aligned.sortedByCoord.out.bamENCORE212601
TARDBP-LV11-57_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab688GRCh38V40TARDBP-LV11-57/Aligned.sortedByCoord.out.bamENCORE212649
TARDBP-LV11-57_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab688GRCh38V40TARDBP-LV11-57/Aligned.sortedByCoord.out.bamENCORE212697
TARDBP-LV11-57_quant.sfENCODE_DATA/set11/salmon_ENCORE2_file_linkstranscript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab688GRCh38V40TARDBP-LV11-57_GTGGCC_L008_R1_001.fastq.gz,TARDBP-LV11-57_GTGGCC_L008_R2_001.fastq.gzENCORE212745
TARDBP-LV11-58_GTTTCG_L008_R1_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab689HiSeq2000100paired-ended1Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gzENCODE312410
TARDBP-LV11-58_GTTTCG_L008_R2_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab689HiSeq2000100paired-ended2Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gzENCODE312458
TARDBP-LV11-58_Aligned.sortedByCoord.out.bamENCODE_DATA/set11/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab689GRCh38V40TARDBP-LV11-58_GTTTCG_L008_R1_001.fastq.gz,TARDBP-LV11-58_GTTTCG_L008_R2_001.fastq.gzENCORE212506
TARDBP-LV11-58_Signal.Unique.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab689GRCh38V40TARDBP-LV11-58/Aligned.sortedByCoord.out.bamENCORE212554
TARDBP-LV11-58_Signal.Unique.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab689GRCh38V40TARDBP-LV11-58/Aligned.sortedByCoord.out.bamENCORE212602
TARDBP-LV11-58_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab689GRCh38V40TARDBP-LV11-58/Aligned.sortedByCoord.out.bamENCORE212650
TARDBP-LV11-58_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab689GRCh38V40TARDBP-LV11-58/Aligned.sortedByCoord.out.bamENCORE212698
TARDBP-LV11-58_quant.sfENCODE_DATA/set11/salmon_ENCORE2_file_linkstranscript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab689GRCh38V40TARDBP-LV11-58_GTTTCG_L008_R1_001.fastq.gz,TARDBP-LV11-58_GTTTCG_L008_R2_001.fastq.gzENCORE212746