SRSF4      shRNA in K562      Control: NT_BGKLV13

General Information
RBPSRSF4
Cell_LineK562
MethodshRNA
Exp_NameSRSF4-BGKLV13-K562
ENCODE_series_ID
Batch_IDBGKLV13
Pool IDPool-140901
Local_Set_Nameset13
ENCODE_KD_Exp_IDENCSR697GLD
ENCODE_CN_Exp_IDENCSR815CVQ
Rep1SRSF4_BGKLV13_49
Rep2SRSF4_BGKLV13_50
CN1NT_BGKLV13_1
CN2NT_BGKLV13_2
Rep1_qPCR48.2
Rep2_qPCR50.3
Rep1_WB25.9
Rep2_WB11.5
Antibody Cat#A303-670A
Antibody Lot#LOT# 1
Antibody DCC IDENCAB653SNR
StatusArchived
ProjectENCODE3
ID374




Experiment Information (Status: Released)
BGKLV13-49BGKLV13-50
idx184185
TRCN#_or_BGC#TRCN0000006627TRCN0000006627
shRNA_or_gRNA_sequenceGCAGTCATTCTAAGAGTAGATGCAGTCATTCTAAGAGTAGAT
PAM
NameSRSF4SRSF4
Sample_IDBGKLV13-49BGKLV13-50
transduction_Date6/13/20146/13/2014
days
RBP_nameSRSF4SRSF4
qPCR_result48.250.3
Ave_qPCR49.3
RT-qPCR_primer-FTTGGCTGAGGACTGTCATGT
RT-qPCR_primer-RGCATCACGCAGATCATCAAA
protein_conc22292026
WB_result25.911.5
Ave_WB18.7
WB_DONE_date5/27/2015
MW
IP1MW1MW
antibody_Cat#A303-670AA303-670A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM82.88870160
Rep2_TPM58.61844710
Action
Library_start_date7/27/20147/27/2014
repeat_library
Note
ID203204




Western Blot
Western Blot info was not avaliable




Experiment Status
BGKLV13-49BGKLV13-50
Sample_IDBGKLV13-49BGKLV13-50
Sample NameSRSF4_BGKLV13_49SRSF4_BGKLV13_50
Sample NameSRSF4_BGKLV13_49SRSF4_BGKLV13_50
RBPSRSF4SRSF4
Cell_LineK562K562
Exp UID
StatusReleasedReleased
Status_date2014-10-292014-10-29
ProjectENCODE3ENCODE3
Note
ID478479




Library-Prep Information
BGKLV13-49BGKLV13-50
Sample #
Sample NameSRSF4-BGKLV13-49SRSF4-BGKLV13-50
Sample_Name_AliasSRSF4_BGKLV13_49SRSF4_BGKLV13_50
Index Well PositionS07S08
Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
LibPrep_date2014-07-272014-07-27
Lib_IDLib-140727Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV13-14/set1/H4.pngDNA_Library_LV13-14/set1/A5.png
RIN9.69.4
libSample_RNA_WellRNA_Library_LV13-14-16/set1/C1.pngRNA_Library_LV13-14-16/set1/D1.png
SampleQC_methodTapeStationTapeStation
SampleQC_date
Sample_IDBGKLV13-49BGKLV13-50
RBPSRSF4SRSF4
Batch_IDBGKLV13BGKLV13
WB_result25.90011.500
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE3ENCODE3
ID21502151




Sequencing Information
BGKLV13-49BGKLV13-50
Sample_IDBGKLV13-49BGKLV13-50
Sample NameSRSF4_BGKLV13_49SRSF4_BGKLV13_50
Pool IDPool-140901Pool-140901
LocalServer_folderset13set13
total_reads54,010,00054,310,000
total_aligned_reads50,567,61050,984,892
unique_aligned_reads46,639,26047,012,182
percent_uniqueAligned0.863530.86563
correlation_replicates0.9943740.994374
spikein_reads105,900129,806
percent_spikeins0.001960.00239
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID792793




Data Submission Information
BGKLV13-49
ENCODE_aliasbrenton-graveley:SRSF4_BGKLV13
ENCODE_accessionENCSR697GLD
object_typeexperiment
assay_typeknockdown followed by RNA-seq
Sample_IDBGKLV13-49
Sample NameSRSF4_BGKLV13_49
SelectedYes
StatusReleased
Status_Date2014-10-15
ProjectENCODE3
protocol_URL
ID2788




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
SRSF4_BGKLV13_49_CAGATC_L005_R1_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab792HiSeq2000100paired-ended1NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gzENCODE313406
SRSF4_BGKLV13_49_CAGATC_L005_R2_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab792HiSeq2000100paired-ended2NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gzENCODE313458
SRSF4_BGKLV13_49_Aligned.sortedByCoord.out.bamENCODE_DATA/set13/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab792GRCh38V40SRSF4_BGKLV13_49_CAGATC_L005_R1_001.fastq.gz,SRSF4_BGKLV13_49_CAGATC_L005_R2_001.fastq.gzENCORE213510
SRSF4_BGKLV13_49_Signal.Unique.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab792GRCh38V40SRSF4_BGKLV13_49/Aligned.sortedByCoord.out.bamENCORE213562
SRSF4_BGKLV13_49_Signal.Unique.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab792GRCh38V40SRSF4_BGKLV13_49/Aligned.sortedByCoord.out.bamENCORE213614
SRSF4_BGKLV13_49_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab792GRCh38V40SRSF4_BGKLV13_49/Aligned.sortedByCoord.out.bamENCORE213666
SRSF4_BGKLV13_49_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab792GRCh38V40SRSF4_BGKLV13_49/Aligned.sortedByCoord.out.bamENCORE213718
SRSF4_BGKLV13_49_quant.sfENCODE_DATA/set13/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab792GRCh38V40SRSF4_BGKLV13_49_CAGATC_L005_R1_001.fastq.gz,SRSF4_BGKLV13_49_CAGATC_L005_R2_001.fastq.gzENCORE213770
SRSF4_BGKLV13_50_ACTTGA_L005_R1_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab793HiSeq2000100paired-ended1NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gzENCODE313407
SRSF4_BGKLV13_50_ACTTGA_L005_R2_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab793HiSeq2000100paired-ended2NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gzENCODE313459
SRSF4_BGKLV13_50_Aligned.sortedByCoord.out.bamENCODE_DATA/set13/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab793GRCh38V40SRSF4_BGKLV13_50_ACTTGA_L005_R1_001.fastq.gz,SRSF4_BGKLV13_50_ACTTGA_L005_R2_001.fastq.gzENCORE213511
SRSF4_BGKLV13_50_Signal.Unique.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab793GRCh38V40SRSF4_BGKLV13_50/Aligned.sortedByCoord.out.bamENCORE213563
SRSF4_BGKLV13_50_Signal.Unique.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab793GRCh38V40SRSF4_BGKLV13_50/Aligned.sortedByCoord.out.bamENCORE213615
SRSF4_BGKLV13_50_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab793GRCh38V40SRSF4_BGKLV13_50/Aligned.sortedByCoord.out.bamENCORE213667
SRSF4_BGKLV13_50_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab793GRCh38V40SRSF4_BGKLV13_50/Aligned.sortedByCoord.out.bamENCORE213719
SRSF4_BGKLV13_50_quant.sfENCODE_DATA/set13/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab793GRCh38V40SRSF4_BGKLV13_50_ACTTGA_L005_R1_001.fastq.gz,SRSF4_BGKLV13_50_ACTTGA_L005_R2_001.fastq.gzENCORE213771