SF3B1      CRISPR in K562      Control: NT-BGKcLV11

General Information
RBPSF3B1
Cell_LineK562
MethodCRISPR
Exp_NameSF3B1-BGKcLV11-K562
ENCODE_series_IDENCSR787FNM
Batch_IDBGKcLV11
Pool IDPool-190423
Local_Set_Nameset42
ENCODE_KD_Exp_IDENCSR544ZCR
ENCODE_CN_Exp_IDENCSR292PXV
Rep1SF3B1-BGKcLV11-93
Rep2SF3B1-BGKcLV11-94
CN1NT-BGKcLV11-1
CN2NT-BGKcLV11-2
Rep1_qPCR93.6
Rep2_qPCR97.3
Rep1_WB61.9
Rep2_WB64.8
Antibody Cat#ab66774
Antibody Lot#
Antibody DCC IDENCAB022ALQ
StatusReleased
ProjectENCODE4
ID190




Experiment Information (Status: Released)
BGKcLV11-93BGKcLV11-94
idx409410
TRCN#_or_BGC#BGC#0000283BGC#0000283
shRNA_or_gRNA_sequenceTCCCGGTCTGCAATCTTTGGTCCCGGTCTGCAATCTTTGG
PAMaggagg
NameSF3B1_87SF3B1_87
Sample_IDBGKcLV11-93BGKcLV11-94
transduction_Date8/3/188/3/18
daysDay 6Day 6
RBP_nameSF3B1SF3B1
qPCR_result93.697.3
Ave_qPCR95.5
RT-qPCR_primer-FATCAAGTTGGGATCAGGCAG
RT-qPCR_primer-RCAGGAGTCTCGCTTCCCTTT
protein_conc29192691
WB_result61.964.8
Ave_WB63.3
WB_DONE_date8/22/18wes
MW146kDa
IP
antibody_Cat#ab66774
Antibody DCC IDENCAB022ALQ
submitted_to_DCC_date2/22/19
Rep1_TPM00
Rep2_TPM00
ActionReadyReady
Library_start_date03/13/1903/13/19
repeat_library
Note
ID45114512




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
SF3B1Product_ID: ab66774
Lot_ID: GR216813-1
Source: Abcam
Target Name: SF3B1-human		 SF3B1-HEPG2.png<br>Caption: Western blot following shRNA against SF3B1 in HepG2 whole cell lysate using SF3B1 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against SF3B1.SF3B1 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
 K562_Abcam_ab66774_GR216813-1_SF3B1.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using SF3B1 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-SF3B1 antibody (lanes under 'SF3B1').
 SF3B1-K562-CRISPR.png<br>Caption: Western blot following CRISPR against SF3B1 in K562 whole cell lysate using SF3B1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against SF3B1.SF3B1 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.




Experiment Status
BGKcLV11-93BGKcLV11-94
Sample_IDBGKcLV11-93BGKcLV11-94
Sample NameSF3B1-BGKcLV11-93SF3B1-BGKcLV11-94
Sample NameSF3B1-BGKcLV11-93SF3B1-BGKcLV11-94
RBPSF3B1SF3B1
Cell_LineK562K562
Exp UID
StatusReleasedReleased
Status_date2020-11-062020-11-06
ProjectENCODE4ENCODE4
Note
ID26912692




Library-Prep Information
BGKcLV11-93BGKcLV11-94
Sample #1920
Sample NameSF3B1-BGKcLV11-93SF3B1-BGKcLV11-94
Sample_Name_Alias
Index Well PositionC03D03
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2019-03-132019-03-13
Lib_IDLib-190313Lib-190313
Tecan_Location2-C12-D1
Tecan40.6452.20
Tecan_date2019-03-132019-03-13
Size_bp298293
Peak_Molarity203.0091.70
libSampleQC_DNA_WellDNA_Library_set42/set1/C3.pngDNA_Library_set42/set2/B1.png
RIN9.59.5
libSample_RNA_WellRNA_Library_set42/set1/C3.pngRNA_Library_set42/set1/D3.png
SampleQC_methodTapeStationTapeStation
SampleQC_date2019-03-132019-03-13
Sample_IDBGKcLV11-93BGKcLV11-94
RBPSF3B1SF3B1
Batch_IDBGKcLV11BGKcLV11
WB_result61.90064.800
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE4ENCODE4
ID1920




Sequencing Information
BGKcLV11-93BGKcLV11-94
Sample_IDBGKcLV11-93BGKcLV11-94
Sample NameSF3B1-BGKcLV11-93SF3B1-BGKcLV11-94
Pool IDPool-190423Pool-190423
LocalServer_folderset42set42
total_reads152,079,53894,902,736
total_aligned_reads143,977,19090,743,124
unique_aligned_reads130,723,87482,517,756
percent_uniqueAligned0.859580.86950
correlation_replicates0.9979900.997990
spikein_reads307,700139,914
percent_spikeins0.002020.00147
original_ReadLength150150
QC_StatusSubmittedSubmitted
ID6768




Data Submission Information
BGKcLV11-93BGKcLV11-93BGKcLV11-93BGKcLV11-93BGKcLV11-93BGKcLV11-93BGKcLV11-94BGKcLV11-94BGKcLV11-94BGKcLV11-94
ENCODE_aliasbrenton-graveley:SF3B1-BGKcLV11brenton-graveley:SF3B1-BGKcLV11-93brenton-graveley:L-SF3B1-BGKcLV11-93brenton-graveley:SF3B1-BGKcLV11-93_ATGTAAGT+ACTCTATG_HK3H2DSXX_S19_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:SF3B1-BGKcLV11-93_ATGTAAGT+ACTCTATG_HK3H2DSXX_S19_L004_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:SF3B1-BGKcLV11-K562brenton-graveley:SF3B1-BGKcLV11-94brenton-graveley:L-SF3B1-BGKcLV11-94brenton-graveley:SF3B1-BGKcLV11-94_GCACGGAC+GTCTCGCA_HK3H2DSXX_S20_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:SF3B1-BGKcLV11-94_GCACGGAC+GTCTCGCA_HK3H2DSXX_S20_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accessionENCSR544ZCRENCBS919IYAENCLB072KVWENCFF350YOGENCFF273HWHENCSR787FNMENCBS623CLMENCLB682HHAENCFF325MKSENCFF224YEZ
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_IDBGKcLV11-93BGKcLV11-93BGKcLV11-93BGKcLV11-93BGKcLV11-93BGKcLV11-93BGKcLV11-94BGKcLV11-94BGKcLV11-94BGKcLV11-94
Sample NameSF3B1-BGKcLV11-93SF3B1-BGKcLV11-93SF3B1-BGKcLV11-93SF3B1-BGKcLV11-93SF3B1-BGKcLV11-93SF3B1-BGKcLV11-93SF3B1-BGKcLV11-94SF3B1-BGKcLV11-94SF3B1-BGKcLV11-94SF3B1-BGKcLV11-94
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_URLSF3B1-BGKcLV11-93.pdfL-SF3B1-BGKcLV11-93.pdfSF3B1-BGKcLV11-94.pdfL-SF3B1-BGKcLV11-94.pdf
ID77083591710171099732483691810181100




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
SF3B1-BGKcLV11-93_ATGTAAGT+ACTCTATG_HK3H2DSXX_S19_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab67NovaSeq6000100paired-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.gzENCODE4399
SF3B1-BGKcLV11-93_ATGTAAGT+ACTCTATG_HK3H2DSXX_S19_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab67NovaSeq6000100paired-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.gzENCODE4481
SF3B1-BGKcLV11-93_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab67GRCh38V40SF3B1-BGKcLV11-93_ATGTAAGT+ACTCTATG_HK3H2DSXX_S19_L004_R1_001.filtered.trimmed.paired.fastq.gz,SF3B1-BGKcLV11-93_ATGTAAGT+ACTCTATG_HK3H2DSXX_S19_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223738
SF3B1-BGKcLV11-93_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab67GRCh38V40SF3B1-BGKcLV11-93/Aligned.sortedByCoord.out.bamENCORE223820
SF3B1-BGKcLV11-93_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab67GRCh38V40SF3B1-BGKcLV11-93/Aligned.sortedByCoord.out.bamENCORE223902
SF3B1-BGKcLV11-93_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab67GRCh38V40SF3B1-BGKcLV11-93/Aligned.sortedByCoord.out.bamENCORE223984
SF3B1-BGKcLV11-93_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab67GRCh38V40SF3B1-BGKcLV11-93/Aligned.sortedByCoord.out.bamENCORE224066
SF3B1-BGKcLV11-93_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab67GRCh38V40SF3B1-BGKcLV11-93_ATGTAAGT+ACTCTATG_HK3H2DSXX_S19_L004_R1_001.filtered.trimmed.paired.fastq.gz,SF3B1-BGKcLV11-93_ATGTAAGT+ACTCTATG_HK3H2DSXX_S19_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224148
SF3B1-BGKcLV11-94_GCACGGAC+GTCTCGCA_HK3H2DSXX_S20_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab68NovaSeq6000100paired-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.gzENCODE4400
SF3B1-BGKcLV11-94_GCACGGAC+GTCTCGCA_HK3H2DSXX_S20_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab68NovaSeq6000100paired-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.gzENCODE4482
SF3B1-BGKcLV11-94_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab68GRCh38V40SF3B1-BGKcLV11-94_GCACGGAC+GTCTCGCA_HK3H2DSXX_S20_L004_R1_001.filtered.trimmed.paired.fastq.gz,SF3B1-BGKcLV11-94_GCACGGAC+GTCTCGCA_HK3H2DSXX_S20_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223739
SF3B1-BGKcLV11-94_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab68GRCh38V40SF3B1-BGKcLV11-94/Aligned.sortedByCoord.out.bamENCORE223821
SF3B1-BGKcLV11-94_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab68GRCh38V40SF3B1-BGKcLV11-94/Aligned.sortedByCoord.out.bamENCORE223903
SF3B1-BGKcLV11-94_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab68GRCh38V40SF3B1-BGKcLV11-94/Aligned.sortedByCoord.out.bamENCORE223985
SF3B1-BGKcLV11-94_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab68GRCh38V40SF3B1-BGKcLV11-94/Aligned.sortedByCoord.out.bamENCORE224067
SF3B1-BGKcLV11-94_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab68GRCh38V40SF3B1-BGKcLV11-94_GCACGGAC+GTCTCGCA_HK3H2DSXX_S20_L004_R1_001.filtered.trimmed.paired.fastq.gz,SF3B1-BGKcLV11-94_GCACGGAC+GTCTCGCA_HK3H2DSXX_S20_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224149