STAU2      CRISPR in K562      Control: NT-BGKcLV11

General Information
RBPSTAU2
Cell_LineK562
MethodCRISPR
Exp_NameSTAU2-BGKcLV11-K562
ENCODE_series_IDENCSR486LUC
Batch_IDBGKcLV11
Pool IDPool-190423
Local_Set_Nameset42
ENCODE_KD_Exp_IDENCSR898KNS
ENCODE_CN_Exp_IDENCSR292PXV
Rep1STAU2-BGKcLV11-101
Rep2STAU2-BGKcLV11-102
CN1NT-BGKcLV11-1
CN2NT-BGKcLV11-2
Rep1_qPCR0.0
Rep2_qPCR0.0
Rep1_WB75.3
Rep2_WB61.8
Antibody Cat#RN013p
Antibody Lot#
Antibody DCC IDENCAB995HZA
StatusReleased
ProjectENCODE4
ID193




Experiment Information (Status: Released)
BGKcLV11-101BGKcLV11-102
idx417418
TRCN#_or_BGC#BGC#0000227BGC#0000227
shRNA_or_gRNA_sequenceTTCGGGGCATGTACAATCAGTTCGGGGCATGTACAATCAG
PAMAGGAGG
NameSTAU2_90STAU2_90
Sample_IDBGKcLV11-101BGKcLV11-102
transduction_Date8/3/188/3/18
daysDay 6Day 6
RBP_nameSTAU2STAU2
qPCR_result0.00.0
Ave_qPCR0.0
RT-qPCR_primer-FATCCAATCGATGGAGCAATG
RT-qPCR_primer-RCCTGGTTATTGTCCGCTTTC
protein_conc29112774
WB_result75.361.8
Ave_WB68.5
WB_DONE_date8/15/18wes
MW63kd
IP
antibody_Cat#RN013p
Antibody DCC IDENCAB995HZA
submitted_to_DCC_date2/22/19
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date03/13/1903/13/19
repeat_library
Note
ID45194520




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
STAU2Product_ID: RN013P
Lot_ID: 1
Source: MBLI
Target Name: STAU2-human		 HepG2_MBLI_RN013P_001_STAU2.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using STAU2 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-STAU2 antibody (lanes under 'STAU2').
HepG2_RN013P_001_STAU2_MassSpec.png<br>Caption: Representative image of immunoprecipitation performed on whole cell extracts from the HepG2 cell line using the STAU2-specific antibody RN013P. Lane 1: Input from IP using control IgG. Lane 2: Immunoprecipitated material using control IgG. Lane 3: Input from IP using STAU2 antibody. Lane 4: Immunoprecipitated material using STAU2 antibody. Outlined regions were excised from gel and subjected to analysis by mass spectrometry. Target molecular weight: 62.64 kDa.
 STAU2-HEPG2-CRISPR.png<br>Caption: Western blot following CRISPR against STAU2 in HepG2 whole cell lysate using STAU2 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against STAU2.STAU2 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
STAU2%20HepG2.pdf
 STAU2-K562-CRISPR.png<br>Caption: Western blot following CRISPR against STAU2 in K562 whole cell lysate using STAU2 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against STAU2. STAU2 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.




Experiment Status
BGKcLV11-101BGKcLV11-102
Sample_IDBGKcLV11-101BGKcLV11-102
Sample NameSTAU2-BGKcLV11-101STAU2-BGKcLV11-102
Sample NameSTAU2-BGKcLV11-101STAU2-BGKcLV11-102
RBPSTAU2STAU2
Cell_LineK562K562
Exp UID
StatusReleasedReleased
Status_date2020-11-062020-11-06
ProjectENCODE4ENCODE4
Note
ID26952696




Library-Prep Information
BGKcLV11-101BGKcLV11-102
Sample #2324
Sample NameSTAU2-BGKcLV11-101STAU2-BGKcLV11-102
Sample_Name_Alias
Index Well PositionG03H03
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2019-03-132019-03-13
Lib_IDLib-190313Lib-190313
Tecan_Location2-G12-H1
Tecan56.3452.18
Tecan_date2019-03-132019-03-13
Size_bp298301
Peak_Molarity116.00149.00
libSampleQC_DNA_WellDNA_Library_set42/set1/G3.pngDNA_Library_set42/set1/H3.png
RIN10.010.0
libSample_RNA_WellRNA_Library_set42/set1/G3.pngRNA_Library_set42/set1/H3.png
SampleQC_methodTapeStationTapeStation
SampleQC_date2019-03-132019-03-13
Sample_IDBGKcLV11-101BGKcLV11-102
RBPSTAU2STAU2
Batch_IDBGKcLV11BGKcLV11
WB_result75.30061.800
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE4ENCODE4
ID2324




Sequencing Information
BGKcLV11-101BGKcLV11-102
Sample_IDBGKcLV11-101BGKcLV11-102
Sample NameSTAU2-BGKcLV11-101STAU2-BGKcLV11-102
Pool IDPool-190423Pool-190423
LocalServer_folderset42set42
total_reads46,917,56448,302,272
total_aligned_reads45,675,69246,897,786
unique_aligned_reads41,671,07642,461,360
percent_uniqueAligned0.888180.87908
correlation_replicates0.9978160.997816
spikein_reads48,79040,646
percent_spikeins0.001040.00084
original_ReadLength150150
QC_StatusSubmittedSubmitted
ID7374




Data Submission Information
BGKcLV11-101BGKcLV11-101BGKcLV11-101BGKcLV11-101BGKcLV11-101BGKcLV11-101BGKcLV11-102BGKcLV11-102BGKcLV11-102BGKcLV11-102
ENCODE_aliasbrenton-graveley:STAU2-BGKcLV11brenton-graveley:STAU2-BGKcLV11-101brenton-graveley:L-STAU2-BGKcLV11-101brenton-graveley:STAU2-BGKcLV11-101_GCAGAATT+ACCGGCCA_HK3H2DSXX_S23_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:STAU2-BGKcLV11-101_GCAGAATT+ACCGGCCA_HK3H2DSXX_S23_L004_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:STAU2-BGKcLV11-K562brenton-graveley:STAU2-BGKcLV11-102brenton-graveley:L-STAU2-BGKcLV11-102brenton-graveley:STAU2-BGKcLV11-102_ATGAGGCC+GTTAATTG_HK3H2DSXX_S24_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:STAU2-BGKcLV11-102_ATGAGGCC+GTTAATTG_HK3H2DSXX_S24_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accessionENCSR898KNSENCBS185CCEENCLB213KESENCFF581ZBSENCFF892CQLENCSR486LUCENCBS029ZJFENCLB973BELENCFF999EQPENCFF748HQW
object_typeexperimentbiosamplelibraryfile_fastq1file_fastq2gene_silencing_seriesbiosamplelibraryfile_fastq1file_fastq2
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGKcLV11-101BGKcLV11-101BGKcLV11-101BGKcLV11-101BGKcLV11-101BGKcLV11-101BGKcLV11-102BGKcLV11-102BGKcLV11-102BGKcLV11-102
Sample NameSTAU2-BGKcLV11-101STAU2-BGKcLV11-101STAU2-BGKcLV11-101STAU2-BGKcLV11-101STAU2-BGKcLV11-101STAU2-BGKcLV11-101STAU2-BGKcLV11-102STAU2-BGKcLV11-102STAU2-BGKcLV11-102STAU2-BGKcLV11-102
SelectedYesYesYesYesYesYesYesYesYesYes
StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
Status_Date2020-11-202020-11-202020-11-202020-11-202020-11-202022-03-022020-11-202020-11-202020-11-202020-11-20
ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
LV42_biosample_protocolLV42_library_protocolLV42_biosample_protocolLV42_library_protocol
protocol_URLSTAU2-BGKcLV11-101.pdfL-STAU2-BGKcLV11-101.pdfSTAU2-BGKcLV11-102.pdfL-STAU2-BGKcLV11-102.pdf
ID77283992110231105734084092210241106




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
STAU2-BGKcLV11-101_GCAGAATT+ACCGGCCA_HK3H2DSXX_S23_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab73NovaSeq6000100paired-ended1NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE4405
STAU2-BGKcLV11-101_GCAGAATT+ACCGGCCA_HK3H2DSXX_S23_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab73NovaSeq6000100paired-ended2NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE4487
STAU2-BGKcLV11-101_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab73GRCh38V40STAU2-BGKcLV11-101_GCAGAATT+ACCGGCCA_HK3H2DSXX_S23_L004_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BGKcLV11-101_GCAGAATT+ACCGGCCA_HK3H2DSXX_S23_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223744
STAU2-BGKcLV11-101_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab73GRCh38V40STAU2-BGKcLV11-101/Aligned.sortedByCoord.out.bamENCORE223826
STAU2-BGKcLV11-101_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab73GRCh38V40STAU2-BGKcLV11-101/Aligned.sortedByCoord.out.bamENCORE223908
STAU2-BGKcLV11-101_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab73GRCh38V40STAU2-BGKcLV11-101/Aligned.sortedByCoord.out.bamENCORE223990
STAU2-BGKcLV11-101_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab73GRCh38V40STAU2-BGKcLV11-101/Aligned.sortedByCoord.out.bamENCORE224072
STAU2-BGKcLV11-101_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab73GRCh38V40STAU2-BGKcLV11-101_GCAGAATT+ACCGGCCA_HK3H2DSXX_S23_L004_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BGKcLV11-101_GCAGAATT+ACCGGCCA_HK3H2DSXX_S23_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224154
STAU2-BGKcLV11-102_ATGAGGCC+GTTAATTG_HK3H2DSXX_S24_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab74NovaSeq6000100paired-ended1NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE4406
STAU2-BGKcLV11-102_ATGAGGCC+GTTAATTG_HK3H2DSXX_S24_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab74NovaSeq6000100paired-ended2NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE4488
STAU2-BGKcLV11-102_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab74GRCh38V40STAU2-BGKcLV11-102_ATGAGGCC+GTTAATTG_HK3H2DSXX_S24_L004_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BGKcLV11-102_ATGAGGCC+GTTAATTG_HK3H2DSXX_S24_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223745
STAU2-BGKcLV11-102_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab74GRCh38V40STAU2-BGKcLV11-102/Aligned.sortedByCoord.out.bamENCORE223827
STAU2-BGKcLV11-102_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab74GRCh38V40STAU2-BGKcLV11-102/Aligned.sortedByCoord.out.bamENCORE223909
STAU2-BGKcLV11-102_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab74GRCh38V40STAU2-BGKcLV11-102/Aligned.sortedByCoord.out.bamENCORE223991
STAU2-BGKcLV11-102_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab74GRCh38V40STAU2-BGKcLV11-102/Aligned.sortedByCoord.out.bamENCORE224073
STAU2-BGKcLV11-102_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab74GRCh38V40STAU2-BGKcLV11-102_ATGAGGCC+GTTAATTG_HK3H2DSXX_S24_L004_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BGKcLV11-102_ATGAGGCC+GTTAATTG_HK3H2DSXX_S24_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224155