SRSF1      shRNA in HepG2      Control: NT-BGHLV12-93-94

General Information
RBPSRSF1
Cell_LineHepG2
MethodshRNA
Exp_NameSRSF1-BGHLV12-HepG2
ENCODE_series_IDENCSR308EYX
Batch_IDBGHLV12
Pool IDPool-140801
Local_Set_Nameset12
ENCODE_KD_Exp_IDENCSR094KBY
ENCODE_CN_Exp_IDENCSR603TCV
Rep1SRSF1-BGHLV12-75
Rep2SRSF1-BGHLV12-76
CN1NT-BGHLV12-93
CN2NT-BGHLV12-94
Rep1_qPCR50.1
Rep2_qPCR51.1
Rep1_WB80.0
Rep2_WB88.3
Antibody Cat#A302-052A
Antibody Lot#A302-052A
Antibody DCC IDENCAB962KAD
StatusReleased
ProjectENCODE3
ID355




Experiment Information (Status: Released)
BGHLV12-75BGHLV12-75BGHLV12-76BGHLV12-76
idx750760
TRCN#_or_BGC#TRCN0000001095TRCN0000001095TRCN0000001095TRCN0000001095
shRNA_or_gRNA_sequenceGAAGCAGGTGATGTATGTTATGAAGCAGGTGATGTATGTTAT
PAM
NameSRSF1SRSF1SRSF1SRSF1
Sample_IDBGHLV12-75BGHLV12-75BGHLV12-76BGHLV12-76
transduction_Date5/15/20145/15/20145/15/20145/15/2014
days
RBP_nameSRSF1SRSF1SRSF1SRSF1
qPCR_result50.150.151.151.1
Ave_qPCR50.650.6
RT-qPCR_primer-FCGGAAAGAAGATATGACCTATGCCGGAAAGAAGATATGACCTATGC
RT-qPCR_primer-RGCCCATCAACTTTAACCCGGCCCATCAACTTTAACCCG
protein_conc1221122110111011
WB_result80.093.588.394.3
Ave_WB84.293.9
WB_DONE_date6/10/20151/31/19
MW28kDa28kDa
IP11
antibody_Cat#A302-052A32-4500A302-052A
Antibody DCC IDENCAB962KADENCAB916GNL ENCAB962KADLot ID TG273235
submitted_to_DCC_date8/6/20153/11/2019
Rep1_TPM92000
Rep2_TPM88.1000
Action
Library_start_date6/12/20146/12/2014
repeat_library
Note
ID2130213221312133




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
SRSF1Product_ID: 32-4500
Lot_ID: TG273235
Source: Thermo Fisher
Target Name: SRSF1-human		 SRSF1-HepG2.png<br>Caption: Western blot following shRNA against SRSF1 in HepG2 whole cell lysate using SRSF1 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different shRNA against SRSF1. SRSF1 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 ThermoFisher_32-4500_TG273235_SRSF1.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the SRSF1 specific antibody, 32-4500. Lanes 1 and 3 are 2.5% of five million whole cell lysate input. Lanes 2 and 4 are 50% of IP enrichment from five million whole cell lysate using normal IgG antibody and the SRSF1-specific antibody, 32-4500. The same antibody was used to detect protein levels via Western blot. This antibody passes preliminary validation and will be further pursued for secondary validation. *NOTE* Protein sizes are taken from Genecards.org and are only estimates based on sequence. Actual protein size may differ based on protein characteristics and electrophoresis method used.
SRSF1Product_ID: A302-052A
Lot_ID: 1
Source: Bethyl Labs
Target Name: SRSF1-human		 HepG2_Bethyl_A302-052A_1_SRSF1.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using SRSF1 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-ASF (SRSF1) antibody (lanes under 'SRSF1').
 SRSF1_Secondary_Western.png<br>Caption: Western blot following shRNA against SRSF1 in K562 and HepG2 whole cell lysate using SRSF1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against SRSF1. Lanes 5-8 follow the same pattern, but in HepG2. SRSF1 protein appears as the green band, Tubulin serves as a control and appears in red.
 K562_Bethyl_A302-052A_1_SRSF1.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using SRSF1 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-ASF (SRSF1) antibody (lanes under 'SRSF1').
 SRSF1_Secondary_Western.png<br>Caption: Western blot following shRNA against SRSF1 in K562 and HepG2 whole cell lysate using SRSF1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against SRSF1. Lanes 5-8 follow the same pattern, but in HepG2. SRSF1 protein appears as the green band, Tubulin serves as a control and appears in red.




Experiment Status
BGHLV12-75BGHLV12-76
Sample_IDBGHLV12-75BGHLV12-76
Sample NameSRSF1-BGHLV12-75SRSF1-BGHLV12-76
Sample NameSRSF1-BGHLV12-75SRSF1-BGHLV12-76
RBPSRSF1SRSF1
Cell_LineHepG2HepG2
Exp UID
StatusReleasedReleased
Status_date2014-09-252014-09-25
ProjectENCODE3ENCODE3
Note
ID428429




Library-Prep Information
BGHLV12-75BGHLV12-76
Sample #
Sample NameSRSF1-BGHLV12-75SRSF1-BGHLV12-76
Sample_Name_AliasSRSF1-BGHLV12-75SRSF1-BGHLV12-76
Index Well PositionS09S10
Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
LibPrep_date2014-06-122014-06-12
Lib_IDLib-140612Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV12/set3/A4.pngDNA_Library_LV12/set3/B4.png
RIN9.59.4
libSample_RNA_WellRNA_Library_LV12/set1/A8.pngRNA_Library_LV12/set1/B8.png
SampleQC_methodTapeStationTapeStation
SampleQC_date
Sample_IDBGHLV12-75BGHLV12-76
RBPSRSF1SRSF1
Batch_IDBGHLV12BGHLV12
WB_result80.00088.300
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE3ENCODE3
ID20522053




Sequencing Information
BGHLV12-75BGHLV12-76
Sample_IDBGHLV12-75BGHLV12-76
Sample NameSRSF1-BGHLV12-75SRSF1-BGHLV12-76
Pool IDPool-140801Pool-140801
LocalServer_folderset12set12
total_reads62,840,00073,970,000
total_aligned_reads57,480,12467,597,748
unique_aligned_reads54,535,72664,102,954
percent_uniqueAligned0.867850.86661
correlation_replicates0.9984000.998400
spikein_reads269,706331,590
percent_spikeins0.004290.00448
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID752753




Data Submission Information
BGHLV12-75BGHLV12-75
ENCODE_aliasbrenton-graveley:SRSF1-BGHLV12brenton-graveley:SRSF1-BGHLV12-HepG2
ENCODE_accessionENCSR094KBYENCSR308EYX
object_typeexperimentgene_silencing_series
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGHLV12-75BGHLV12-75
Sample NameSRSF1-BGHLV12-75SRSF1-BGHLV12-75
SelectedYesYes
StatusReleasedReleased
Status_Date2014-09-242022-03-01
ProjectENCODE3ENCODE3
protocol_URL
ID27636966




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
SRSF1-BGHLV12-75_GATCAG_L005_R1_001.fastq.gzENCODE_DATA/set12/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab752HiSeq2000100paired-ended1NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gzENCODE312811
SRSF1-BGHLV12-75_GATCAG_L005_R2_001.fastq.gzENCODE_DATA/set12/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab752HiSeq2000100paired-ended2NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gzENCODE312880
SRSF1-BGHLV12-75_Aligned.sortedByCoord.out.bamENCODE_DATA/set12/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab752GRCh38V40SRSF1-BGHLV12-75_GATCAG_L005_R1_001.fastq.gz,SRSF1-BGHLV12-75_GATCAG_L005_R2_001.fastq.gzENCORE212950
SRSF1-BGHLV12-75_Signal.Unique.strand+.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab752GRCh38V40SRSF1-BGHLV12-75/Aligned.sortedByCoord.out.bamENCORE213020
SRSF1-BGHLV12-75_Signal.Unique.strand-.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab752GRCh38V40SRSF1-BGHLV12-75/Aligned.sortedByCoord.out.bamENCORE213090
SRSF1-BGHLV12-75_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab752GRCh38V40SRSF1-BGHLV12-75/Aligned.sortedByCoord.out.bamENCORE213160
SRSF1-BGHLV12-75_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab752GRCh38V40SRSF1-BGHLV12-75/Aligned.sortedByCoord.out.bamENCORE213230
SRSF1-BGHLV12-75_quant.sfENCODE_DATA/set12/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab752GRCh38V40SRSF1-BGHLV12-75_GATCAG_L005_R1_001.fastq.gz,SRSF1-BGHLV12-75_GATCAG_L005_R2_001.fastq.gzENCORE213300
SRSF1-BGHLV12-76_TAGCTT_L005_R1_001.fastq.gzENCODE_DATA/set12/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab753HiSeq2000100paired-ended1NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gzENCODE312812
SRSF1-BGHLV12-76_TAGCTT_L005_R2_001.fastq.gzENCODE_DATA/set12/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab753HiSeq2000100paired-ended2NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gzENCODE312881
SRSF1-BGHLV12-76_Aligned.sortedByCoord.out.bamENCODE_DATA/set12/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab753GRCh38V40SRSF1-BGHLV12-76_TAGCTT_L005_R1_001.fastq.gz,SRSF1-BGHLV12-76_TAGCTT_L005_R2_001.fastq.gzENCORE212951
SRSF1-BGHLV12-76_Signal.Unique.strand+.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab753GRCh38V40SRSF1-BGHLV12-76/Aligned.sortedByCoord.out.bamENCORE213021
SRSF1-BGHLV12-76_Signal.Unique.strand-.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab753GRCh38V40SRSF1-BGHLV12-76/Aligned.sortedByCoord.out.bamENCORE213091
SRSF1-BGHLV12-76_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab753GRCh38V40SRSF1-BGHLV12-76/Aligned.sortedByCoord.out.bamENCORE213161
SRSF1-BGHLV12-76_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab753GRCh38V40SRSF1-BGHLV12-76/Aligned.sortedByCoord.out.bamENCORE213231
SRSF1-BGHLV12-76_quant.sfENCODE_DATA/set12/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab753GRCh38V40SRSF1-BGHLV12-76_TAGCTT_L005_R1_001.fastq.gz,SRSF1-BGHLV12-76_TAGCTT_L005_R2_001.fastq.gzENCORE213301