SRSF4      CRISPR in K562      Control: NT-BGKcLV04-C

General Information
RBPSRSF4
Cell_LineK562
MethodCRISPR
Exp_NameSRSF4-BGKcLV04-K562
ENCODE_series_IDENCSR901OBH
Batch_IDBGKcLV04
Pool IDPool-181119
Local_Set_Nameset41_spikeins
ENCODE_KD_Exp_IDENCSR939BTN
ENCODE_CN_Exp_IDENCSR005JBU
Rep1SRSF4-BGKcLV04-29C
Rep2SRSF4-BGKcLV04-30C
CN1NT-BGKcLV04-1C
CN2NT-BGKcLV04-2C
Rep1_qPCR43.0
Rep2_qPCR39.0
Rep1_WB66
Rep2_WB73.8
Antibody Cat#A303-670A
Antibody Lot#LOT# 1
Antibody DCC IDENCAB653SNR
StatusReleased
ProjectENCODE4
ID886




Experiment Information (Status: Released)
BGKcLV04-29BGKcLV04-30
idx7980
TRCN#_or_BGC#BGC#0000053BGC#0000053
shRNA_or_gRNA_sequenceAGGCGGCCGATGTACACCCGAGGCGGCCGATGTACACCCG
PAM
NameSRSF4_91SRSF4_91
Sample_IDBGKcLV04-29BGKcLV04-30
transduction_Date6/22/166/22/16
daysday 6day 6
RBP_nameSRSF4SRSF4
qPCR_result43.039.0
Ave_qPCR41.0
RT-qPCR_primer-FAATATGGCCCTCCTACTCGC
RT-qPCR_primer-RTCTCCTGCCTGACGCATATAAT
protein_conc21402348
WB_result6673.8
Ave_WB69.9
WB_DONE_date3/28/17
MW56 kDa
IP1MW
antibody_Cat#A303-670AA303-670A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM82.90
Rep2_TPM58.60
ActionReadyReady
Library_start_date
repeat_library5/11/175/11/17
Note
ID41774178




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
SRSF4Product_ID: A303-670A
Lot_ID: 1
Source: Bethyl Labs
Target Name: SRSF4-human		 HepG2_Bethyl_A303-670A_1_SRSF4.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using SRSF4 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-SRSF4 antibody (lanes under 'SRSF4').
 K562_Bethyl_A303-670A_1_SRSF4.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using SRSF4 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-SRSF4 antibody (lanes under 'SRSF4').
 SRSF4-K562.png<br>Caption: Western blot following CRISPR against SRSF4 in K562 whole cell lysate using SRSF4 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against SRSF4.SRSF4 protein appears as the green band, Tubulin serves as a control and appears in red.




Experiment Status
BGKcLV04-29BGKcLV04-29BGKcLV04-30BGKcLV04-30
Sample_IDBGKcLV04-29BGKcLV04-29BGKcLV04-30BGKcLV04-30
Sample NameSRSF4-BGKcLV04-29BSRSF4-BGKcLV04-30B
Sample NameSRSF4-BGKcLV04-29BSRSF4-BGKcLV04-29CSRSF4-BGKcLV04-30BSRSF4-BGKcLV04-30C
RBPSRSF4SRSF4SRSF4SRSF4
Cell_LineK562K562K562K562
Exp UID
StatusReleasedReleasedReleasedReleased
Status_date2017-11-202022-03-072017-11-202022-03-07
ProjectENCODE3ENCODE4ENCODE3ENCODE4
Note
ID134910455135010456




Library-Prep Information
BGKcLV04-29BGKcLV04-29BGKcLV04-30BGKcLV04-30
Sample #7576
Sample NameSRSF4-BGKcLV04-29CSRSF4-BGKcLV04-29DSRSF4-BGKcLV04-30CSRSF4-BGKcLV04-30D
Sample_Name_AliasSRSF4-BGKcLV04-29BSRSF4-BGKcLV04-29CSRSF4-BGKcLV04-30BSRSF4-BGKcLV04-30C
Index Well PositionS20S20S21S21
Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
LibPrep_date2017-05-112018-11-192017-05-112018-11-19
Lib_IDLib-170511Lib-181119Lib-170511Lib-181119
Tecan_Location
Tecan
Tecan_date
Size_bp301308
Peak_Molarity53.1058.10
libSampleQC_DNA_WellDNA_Library_set39/set2/C7.pngDNA_Library_set41/set1/C9.pngDNA_Library_set39/set2/D7.pngDNA_Library_set41/set1/D9.png
RIN9.69.69.49.4
libSample_RNA_WellRNA_Library_set39/set4/C1.pngRNA_Library_set39/set4/C1.pngRNA_Library_set39/set4/D1.pngRNA_Library_set39/set4/D1.png
SampleQC_methodTapeStationTapeStation
SampleQC_date2022-03-012022-03-01
Sample_IDBGKcLV04-29BGKcLV04-29BGKcLV04-30BGKcLV04-30
RBPSRSF4SRSF4SRSF4SRSF4
Batch_IDBGKcLV04BGKcLV04BGKcLV04BGKcLV04
WB_result66.00066.00073.80073.800
Library DescriptionTruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNA
Repeat_Library_SuffixCDCD
Lib_StatusSendToSequenceSendToSequenceSendToSequenceSendToSequence
ProjectENCODE3ENCODE4ENCODE3ENCODE4
ID3044325230453253




Sequencing Information
BGKcLV04-29BGKcLV04-29BGKcLV04-30BGKcLV04-30
Sample_IDBGKcLV04-29BGKcLV04-29BGKcLV04-30BGKcLV04-30
Sample NameSRSF4-BGKcLV04-29BSRSF4-BGKcLV04-29CSRSF4-BGKcLV04-30BSRSF4-BGKcLV04-30C
Pool IDPool-170911Pool-181119Pool-170911Pool-181119
LocalServer_folderset39_Kset41_spikeinsset39_Kset41_spikeins
total_reads71,457,80021,254,09673,767,02022,080,516
total_aligned_reads63,898,03621,239,43666,494,72422,119,014
unique_aligned_reads58,247,90619,411,21260,751,34820,181,614
percent_uniqueAligned0.815140.913290.823560.91400
correlation_replicates0.9984250.9987000.9984250.998700
spikein_reads8279,2341286,490
percent_spikeins0.003730.00392
original_ReadLength100100100100
QC_StatusSubmittedSubmittedSubmittedSubmitted
ID1681196516821966




Data Submission Information
BGKcLV04-29BGKcLV04-29BGKcLV04-29BGKcLV04-29BGKcLV04-29BGKcLV04-29BGKcLV04-30BGKcLV04-30
ENCODE_aliasbrenton-graveley:SRSF4-BGKcLV04-Bbrenton-graveley:SRSF4-BGKcLV04-K562_Abrenton-graveley:SRSF4-BGKcLV04-Cbrenton-graveley:L-SRSF4-BGKcLV04-29Cbrenton-graveley:SRSF4-BGKcLV04-K562brenton-graveley:SRSF4-BGKcLV04-29Bbrenton-graveley:L-SRSF4-BGKcLV04-30Cbrenton-graveley:SRSF4-BGKcLV04-30B
ENCODE_accessionENCSR905NIKENCSR506QBEENCSR939BTNENCLB044YOWENCSR901OBHENCBS217XMVENCLB818QPBENCBS578FNZ
object_typeexperimentexperimentexperimentlibrarygene_silencing_seriesbiosamplelibrarybiosample
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-seq
Sample_IDBGKcLV04-29BGKcLV04-29BGKcLV04-29BGKcLV04-29BGKcLV04-29BGKcLV04-29BGKcLV04-30BGKcLV04-30
Sample NameSRSF4-BGKcLV04-29BSRSF4-BGKcLV04-29BSRSF4-BGKcLV04-29CSRSF4-BGKcLV04-29CSRSF4-BGKcLV04-29CSRSF4-BGKcLV04-29BSRSF4-BGKcLV04-30CSRSF4-BGKcLV04-30B
SelectedYesNoYesYesYesYesYesYes
StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
Status_Date2022-03-072022-03-072022-03-072022-03-072022-03-072019-03-132022-03-072019-03-13
ProjectENCODE3ENCODE3ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
LV41_library_protocol_spikeinsLV39_biosample_protocolLV41_library_protocol_spikeinsLV39_biosample_protocol
protocol_URLL-SRSF4-BGKcLV04-29C.pdfSRSF4-BGKcLV04-29B.pdfL-SRSF4-BGKcLV04-30C.pdfSRSF4-BGKcLV04-30B.pdf
ID32146970738674067421743674077437




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
SRSF4-BGKcLV04-29B_GTGGCC_ACBE67ANXX_L003_001.R1.fastq.gzENCODE_DATA/set39_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1681HiSeq2500100paired-ended1NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R1.fastq.gzENCODE322486
SRSF4-BGKcLV04-29B_GTGGCC_ACBE67ANXX_L003_001.R2.fastq.gzENCODE_DATA/set39_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1681HiSeq2500100paired-ended2NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R2.fastq.gz,NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R2.fastq.gzENCODE322522
SRSF4-BGKcLV04-29B_Aligned.sortedByCoord.out.bamENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1681GRCh38V40SRSF4-BGKcLV04-29B_GTGGCC_ACBE67ANXX_L003_001.R1.fastq.gz,SRSF4-BGKcLV04-29B_GTGGCC_ACBE67ANXX_L003_001.R2.fastq.gzENCORE222558
SRSF4-BGKcLV04-29B_Signal.Unique.strand+.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1681GRCh38V40SRSF4-BGKcLV04-29B/Aligned.sortedByCoord.out.bamENCORE222594
SRSF4-BGKcLV04-29B_Signal.Unique.strand-.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1681GRCh38V40SRSF4-BGKcLV04-29B/Aligned.sortedByCoord.out.bamENCORE222630
SRSF4-BGKcLV04-29B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1681GRCh38V40SRSF4-BGKcLV04-29B/Aligned.sortedByCoord.out.bamENCORE222666
SRSF4-BGKcLV04-29B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1681GRCh38V40SRSF4-BGKcLV04-29B/Aligned.sortedByCoord.out.bamENCORE222702
SRSF4-BGKcLV04-29B_quant.sfENCODE_DATA/set39_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1681GRCh38V40SRSF4-BGKcLV04-29B_GTGGCC_ACBE67ANXX_L003_001.R1.fastq.gz,SRSF4-BGKcLV04-29B_GTGGCC_ACBE67ANXX_L003_001.R2.fastq.gzENCORE222738
SRSF4-BGKcLV04-30B_GTTTCG_ACBE67ANXX_L003_001.R1.fastq.gzENCODE_DATA/set39_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1682HiSeq2500100paired-ended1NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R1.fastq.gzENCODE322487
SRSF4-BGKcLV04-30B_GTTTCG_ACBE67ANXX_L003_001.R2.fastq.gzENCODE_DATA/set39_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1682HiSeq2500100paired-ended2NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R2.fastq.gz,NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R2.fastq.gzENCODE322523
SRSF4-BGKcLV04-30B_Aligned.sortedByCoord.out.bamENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1682GRCh38V40SRSF4-BGKcLV04-30B_GTTTCG_ACBE67ANXX_L003_001.R1.fastq.gz,SRSF4-BGKcLV04-30B_GTTTCG_ACBE67ANXX_L003_001.R2.fastq.gzENCORE222559
SRSF4-BGKcLV04-30B_Signal.Unique.strand+.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1682GRCh38V40SRSF4-BGKcLV04-30B/Aligned.sortedByCoord.out.bamENCORE222595
SRSF4-BGKcLV04-30B_Signal.Unique.strand-.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1682GRCh38V40SRSF4-BGKcLV04-30B/Aligned.sortedByCoord.out.bamENCORE222631
SRSF4-BGKcLV04-30B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1682GRCh38V40SRSF4-BGKcLV04-30B/Aligned.sortedByCoord.out.bamENCORE222667
SRSF4-BGKcLV04-30B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1682GRCh38V40SRSF4-BGKcLV04-30B/Aligned.sortedByCoord.out.bamENCORE222703
SRSF4-BGKcLV04-30B_quant.sfENCODE_DATA/set39_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1682GRCh38V40SRSF4-BGKcLV04-30B_GTTTCG_ACBE67ANXX_L003_001.R1.fastq.gz,SRSF4-BGKcLV04-30B_GTTTCG_ACBE67ANXX_L003_001.R2.fastq.gzENCORE222739