SRSF1 RNA-Seq in K562

General Information


RBP	SRSF1
Cell_Line	K562
Method	shRNA
Exp_Name	SRSF1-BGKLV11-K562
ENCODE_series_ID	ENCSR374CDY
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR066VOO
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	SRSF1-LV11-49
Rep2	SRSF1-LV11-50
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	77.5
Rep2_qPCR	82.5
Rep1_WB	89.9
Rep2_WB	84.1
Antibody Cat#	A302-052A
Antibody Lot#	A302-052A
Antibody DCC ID	ENCAB962KAD
Status	Released
Project	ENCODE3
ID	322

Experiment Information (Status: Released)

	BGKLV11-49	BGKLV11-50
idx	118	119
TRCN#_or_BGC#	TRCN0000001095	TRCN0000001095
shRNA_or_gRNA_sequence	GAAGCAGGTGATGTATGTTAT	GAAGCAGGTGATGTATGTTAT
PAM
Name	SRSF1	SRSF1
Sample_ID	BGKLV11-49	BGKLV11-50
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	SRSF1	SRSF1
qPCR_result	77.5	82.5
Ave_qPCR	80.0
RT-qPCR_primer-F	CGGAAAGAAGATATGACCTATGC
RT-qPCR_primer-R	GCCCATCAACTTTAACCCG
protein_conc	1614	1748
WB_result	89.9	84.1
Ave_WB	87.0
WB_DONE_date	6/10/2015
MW	28kDa
IP	1	1
antibody_Cat#	A302-052A	A302-052A
Antibody DCC ID	ENCAB962KAD	ENCAB962KAD
submitted_to_DCC_date	8/6/2015
Rep1_TPM	99.9233326	0
Rep2_TPM	62.7704982	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	131	132

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRSF1	Product_ID: A302-052A Lot_ID: 1 Source: Bethyl Labs Target Name: SRSF1-human

Experiment Status

	BGKLV11-49	BGKLV11-50
Sample_ID	BGKLV11-49	BGKLV11-50
Sample Name	SRSF1-LV11-49	SRSF1-LV11-50
Sample Name	SRSF1-LV11-49	SRSF1-LV11-50
RBP	SRSF1	SRSF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	358	359

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-49	BGKLV11-50
Sample #
Sample Name	SRSF1-BGKLV11-49	SRSF1-BGKLV11-50
Sample_Name_Alias	SRSF1-LV11-49	SRSF1-LV11-50
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set3/F1.png	DNA_Library_LV11/set3/G1.png
RIN	9.2	9.2
libSample_RNA_Well	RNA_Library_LV11/set1/C5.png	RNA_Library_LV11/set1/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-49	BGKLV11-50
RBP	SRSF1	SRSF1
Batch_ID	BGKLV11	BGKLV11
WB_result	89.900	84.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1980	1981

Sequencing Information

	BGKLV11-49	BGKLV11-50
Sample_ID	BGKLV11-49	BGKLV11-50
Sample Name	SRSF1-LV11-49	SRSF1-LV11-50
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	61,370,000	52,170,000
total_aligned_reads	48,814,616	42,981,760
unique_aligned_reads	45,034,374	39,589,190
percent_uniqueAligned	0.73382	0.75885
correlation_replicates	0.997631	0.997631
spikein_reads	347,392	258,778
percent_spikeins	0.00566	0.00496
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	680	681

Data Submission Information

	BGKLV11-49	BGKLV11-49
ENCODE_alias	brenton-graveley:SRSF1-LV11	brenton-graveley:SRSF1-BGKLV11-K562
ENCODE_accession	ENCSR066VOO	ENCSR374CDY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-49	BGKLV11-49
Sample Name	SRSF1-LV11-49	SRSF1-LV11-49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2728	6967

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
SRSF1-LV11-49_GGCTAC_L006_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	680	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12401
SRSF1-LV11-49_GGCTAC_L006_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	680	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12449
SRSF1-LV11-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	680					GRCh38	V40	SRSF1-LV11-49_GGCTAC_L006_R1_001.fastq.gz,SRSF1-LV11-49_GGCTAC_L006_R2_001.fastq.gz		ENCORE2	12497
SRSF1-LV11-49_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	680					GRCh38	V40	SRSF1-LV11-49/Aligned.sortedByCoord.out.bam		ENCORE2	12545
SRSF1-LV11-49_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	680					GRCh38	V40	SRSF1-LV11-49/Aligned.sortedByCoord.out.bam		ENCORE2	12593
SRSF1-LV11-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	680					GRCh38	V40	SRSF1-LV11-49/Aligned.sortedByCoord.out.bam		ENCORE2	12641
SRSF1-LV11-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	680					GRCh38	V40	SRSF1-LV11-49/Aligned.sortedByCoord.out.bam		ENCORE2	12689
SRSF1-LV11-49_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	680					GRCh38	V40	SRSF1-LV11-49_GGCTAC_L006_R1_001.fastq.gz,SRSF1-LV11-49_GGCTAC_L006_R2_001.fastq.gz		ENCORE2	12737
SRSF1-LV11-50_CTTGTA_L006_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	681	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12402
SRSF1-LV11-50_CTTGTA_L006_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	681	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12450
SRSF1-LV11-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	681					GRCh38	V40	SRSF1-LV11-50_CTTGTA_L006_R1_001.fastq.gz,SRSF1-LV11-50_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	12498
SRSF1-LV11-50_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	681					GRCh38	V40	SRSF1-LV11-50/Aligned.sortedByCoord.out.bam		ENCORE2	12546
SRSF1-LV11-50_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	681					GRCh38	V40	SRSF1-LV11-50/Aligned.sortedByCoord.out.bam		ENCORE2	12594
SRSF1-LV11-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	681					GRCh38	V40	SRSF1-LV11-50/Aligned.sortedByCoord.out.bam		ENCORE2	12642
SRSF1-LV11-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	681					GRCh38	V40	SRSF1-LV11-50/Aligned.sortedByCoord.out.bam		ENCORE2	12690
SRSF1-LV11-50_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	681					GRCh38	V40	SRSF1-LV11-50_CTTGTA_L006_R1_001.fastq.gz,SRSF1-LV11-50_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	12738