SMG7      CRISPR in K562      Control: NT-BGKcLV33

General Information
RBPSMG7
Cell_LineK562
MethodCRISPR
Exp_NameSMG7-BGKcLV33-K562
ENCODE_series_IDENCSR871SAO
Batch_IDBGKcLV33
Pool IDPool-220418
Local_Set_Nameset53
ENCODE_KD_Exp_IDENCSR157IJG
ENCODE_CN_Exp_IDENCSR271ZAB
Rep1SMG7-BGKcLV33-57
Rep2SMG7-BGKcLV33-58
CN1NT-BGKcLV33-1
CN2NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB77.8
Rep2_WB71.8
Antibody Cat#A302-210A
Antibody Lot#LOT #1
Antibody DCC ID
StatusSubmitted
ProjectENCODE4
ID910




Experiment Information (Status: Released)
BGKcLV33-53BGKcLV33-53BGKcLV33-54BGKcLV33-54
idx1155124411561245
TRCN#_or_BGC#BGC#0000872BGC#0000866BGC#0000872BGC#0000866
shRNA_or_gRNA_sequenceGAAAATGCTAGTTACCGATTACGCACTGTCCAGACAGCGTGAAAATGCTAGTTACCGATTACGCACTGTCCAGACAGCGT
PAMTGGTGGTGGTGG
NameSMG7_92SF3B3_90SMG7_92SF3B3_90
Sample_IDBGKcLV33-53BGKcLV33-53BGKcLV33-54BGKcLV33-54
transduction_Date12/7/212/22/2212/7/212/22/22
daysD6D6D6D6
RBP_nameSMG7SF3B3SMG7SF3B3
qPCR_result0.011.0
Ave_qPCR5.5
RT-qPCR_primer-Fcgttcctggccagttcttag
RT-qPCR_primer-Rccaggggagatgaaatggta
protein_conc42020194701900
WB_resultno band on the position78.469.1
Ave_WB73.7
WB_DONE_date2/1/223/7/22
MW127kd136kd
IP
antibody_Cat#A302-170AA302-508ALOT #1LOT #1
Antibody DCC IDENCAB290RUF8/4/22
submitted_to_DCC_date8/16/22
Rep1_TPM0000
Rep2_TPM0000
ActionReadyReady
Library_start_date04/13/2204/13/22
repeat_library
Note
ID5295538652965387




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
SF3B3Product_ID: A302-508A
Lot_ID: 1
Source: Bethyl Labs
Target Name: SF3B3-human
SF3B3-HEPG2-CRISPR-A302-508A.png<br>Caption: Western blot following CRISPR against SF3B3 in HepG2 whole cell lysate using SF3B3 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against SF3B3. SF3B3 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
SF3B3-K562-CRISPR-A302-508A.png<br>Caption: Western blot following CRISPR against SF3B3 in K562 whole cell lysate using SF3B3 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against SF3B3. SF3B3 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.




Experiment Status
BGKcLV33-53BGKcLV33-53BGKcLV33-54BGKcLV33-54
Sample_IDBGKcLV33-53BGKcLV33-53BGKcLV33-54BGKcLV33-54
Sample Name
Sample NameSF3B3-BGKcLV33-53SF3B3-BGKcLV33-54
RBPSF3B3SMG7SF3B3SMG7
Cell_LineK562K562K562K562
Exp UID
StatusReleasedNotSatisfiedReleasedNotSatisfied
Status_date2022-10-282022-03-302022-10-282022-03-30
ProjectENCODE4ENCODE4ENCODE4ENCODE4
Note
ID10669107391067010740




Library-Prep Information
BGKcLV33-53BGKcLV33-54
Sample #3940
Sample NameSF3B3-BGKcLV33-53SF3B3-BGKcLV33-54
Sample_Name_Alias
Index Well PositionG05H05
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2022-04-062022-04-06
Lib_IDLib-220406Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp289299
Peak_Molarity53.1057.70
libSampleQC_DNA_WellDNA_Library_set53/set1/G9.pngDNA_Library_set53/set1/H9.png
RIN9.79.6
libSample_RNA_WellRNA_Library_set53/set1/G5.pngRNA_Library_set53/set1/H5.png
SampleQC_methodTapeStation_2022TapeStation_2022
SampleQC_date2022-04-182022-04-18
Sample_IDBGKcLV33-53BGKcLV33-54
RBPSF3B3SF3B3
Batch_IDBGKcLV33BGKcLV33
WB_result78.40069.100
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE4ENCODE4
ID33003301




Sequencing Information
BGKcLV33-53BGKcLV33-54
Sample_IDBGKcLV33-53BGKcLV33-54
Sample NameSF3B3-BGKcLV33-53SF3B3-BGKcLV33-54
Pool IDPool-220418Pool-220418
LocalServer_folderset53set53
total_reads124,569,244112,717,024
total_aligned_reads112,557,122102,436,242
unique_aligned_reads103,260,86694,097,548
percent_uniqueAligned0.828940.83481
correlation_replicates0.9961800.996180
spikein_reads3,6705,392
percent_spikeins0.000030.00005
original_ReadLength101101
QC_StatusSubmittedSubmitted
ID20672068




Data Submission Information
BGKcLV33-53BGKcLV33-53BGKcLV33-53BGKcLV33-53BGKcLV33-53BGKcLV33-53BGKcLV33-54BGKcLV33-54BGKcLV33-54BGKcLV33-54
ENCODE_aliasbrenton-graveley:SF3B3-BGKcLV33brenton-graveley:SF3B3-BGKcLV33-53brenton-graveley:L-SF3B3-BGKcLV33-53brenton-graveley:SF3B3-BGKcLV33-53_S93_L002_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:SF3B3-BGKcLV33-53_S93_L002_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:SF3B3-BGKcLV33-K562brenton-graveley:SF3B3-BGKcLV33-54brenton-graveley:L-SF3B3-BGKcLV33-54brenton-graveley:SF3B3-BGKcLV33-54_S94_L002_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:SF3B3-BGKcLV33-54_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accessionENCSR034FLWENCBS586NYGENCLB153BJXENCFF172QJKENCFF919RCTENCSR497ASEENCBS612ZRNENCLB923DGLENCFF888YQJENCFF984EIX
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_IDBGKcLV33-53BGKcLV33-53BGKcLV33-53BGKcLV33-53BGKcLV33-53BGKcLV33-53BGKcLV33-54BGKcLV33-54BGKcLV33-54BGKcLV33-54
Sample NameSF3B3-BGKcLV33-53SF3B3-BGKcLV33-53SF3B3-BGKcLV33-53SF3B3-BGKcLV33-53SF3B3-BGKcLV33-53SF3B3-BGKcLV33-53SF3B3-BGKcLV33-54SF3B3-BGKcLV33-54SF3B3-BGKcLV33-54SF3B3-BGKcLV33-54
SelectedYesYesYesYesYesYesYesYesYesYes
StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
Status_Date2022-10-282022-10-282022-10-282022-10-282022-10-282022-10-282022-10-282022-10-282022-10-282022-10-28
ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
LV53_biosample_protocolLV53_library_protocolLV53_biosample_protocolLV53_library_protocol
protocol_URLSF3B3-BGKcLV33-53.pdfL-SF3B3-BGKcLV33-53.pdfSF3B3-BGKcLV33-54.pdfL-SF3B3-BGKcLV33-54.pdf
ID7489758776977809791979797588769878107920




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
SF3B3-BGKcLV33-53_S93_L002_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set53/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2067NovaSeq6000100paired-ended1NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gzENCODE46645
SF3B3-BGKcLV33-53_S93_L002_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set53/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2067NovaSeq6000100paired-ended2NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gzENCODE46701
SF3B3-BGKcLV33-53_Aligned.sortedByCoord.out.bamENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2067GRCh38V40SF3B3-BGKcLV33-53_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGKcLV33-53_S93_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE218122
SF3B3-BGKcLV33-53_Signal.Unique.strand+.bwENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2067GRCh38V40SF3B3-BGKcLV33-53/Aligned.sortedByCoord.out.bamENCORE218178
SF3B3-BGKcLV33-53_Signal.Unique.strand-.bwENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2067GRCh38V40SF3B3-BGKcLV33-53/Aligned.sortedByCoord.out.bamENCORE218234
SF3B3-BGKcLV33-53_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2067GRCh38V40SF3B3-BGKcLV33-53/Aligned.sortedByCoord.out.bamENCORE218290
SF3B3-BGKcLV33-53_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2067GRCh38V40SF3B3-BGKcLV33-53/Aligned.sortedByCoord.out.bamENCORE218346
SF3B3-BGKcLV33-53_quant.sfENCODE_DATA/set53/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2067GRCh38V40SF3B3-BGKcLV33-53_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGKcLV33-53_S93_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE218402
SF3B3-BGKcLV33-54_S94_L002_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set53/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2068NovaSeq6000100paired-ended1NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gzENCODE46646
SF3B3-BGKcLV33-54_S94_L002_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set53/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2068NovaSeq6000100paired-ended2NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gzENCODE46702
SF3B3-BGKcLV33-54_Aligned.sortedByCoord.out.bamENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2068GRCh38V40SF3B3-BGKcLV33-54_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGKcLV33-54_S94_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE218123
SF3B3-BGKcLV33-54_Signal.Unique.strand+.bwENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2068GRCh38V40SF3B3-BGKcLV33-54/Aligned.sortedByCoord.out.bamENCORE218179
SF3B3-BGKcLV33-54_Signal.Unique.strand-.bwENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2068GRCh38V40SF3B3-BGKcLV33-54/Aligned.sortedByCoord.out.bamENCORE218235
SF3B3-BGKcLV33-54_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2068GRCh38V40SF3B3-BGKcLV33-54/Aligned.sortedByCoord.out.bamENCORE218291
SF3B3-BGKcLV33-54_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2068GRCh38V40SF3B3-BGKcLV33-54/Aligned.sortedByCoord.out.bamENCORE218347
SF3B3-BGKcLV33-54_quant.sfENCODE_DATA/set53/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2068GRCh38V40SF3B3-BGKcLV33-54_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGKcLV33-54_S94_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE218403