SRSF9 RNA-Seq in K562

General Information


RBP	SRSF9
Cell_Line	K562
Method	shRNA
Exp_Name	SRSF9-BGKLV11-K562
ENCODE_series_ID
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR113HRG
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	SRSF9-LV11-55
Rep2	SRSF9-LV11-56
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	53.1
Rep2_qPCR	53.9
Rep1_WB	25.6
Rep2_WB	22.9
Antibody Cat#	RN081PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB278ULX
Status	Archived
Project	ENCODE3
ID	325

Experiment Information (Status: Released)

	BGKLV11-55	BGKLV11-56
idx	124	125
TRCN#_or_BGC#	TRCN0000006630	TRCN0000006630
shRNA_or_gRNA_sequence	GACACCAAATTCCGCTCTCAT	GACACCAAATTCCGCTCTCAT
PAM
Name	SRSF9	SRSF9
Sample_ID	BGKLV11-55	BGKLV11-56
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	SRSF9	SRSF9
qPCR_result	53.1	53.9
Ave_qPCR	53.5
RT-qPCR_primer-F	ATATGCCCTGCGTAAACTGG
RT-qPCR_primer-R	AGCTGGTGCTTCTCTCAGGA
protein_conc	2038	2025
WB_result	25.6	22.9
Ave_WB	24.3
WB_DONE_date
MW
IP	1	1
antibody_Cat#	RN081PW	RN081PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	102.807709	0
Rep2_TPM	79.0699497	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	137	138

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV11-55	BGKLV11-56
Sample_ID	BGKLV11-55	BGKLV11-56
Sample Name	SRSF9-LV11-55	SRSF9-LV11-56
Sample Name	SRSF9-LV11-55	SRSF9-LV11-56
RBP	SRSF9	SRSF9
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	364	365

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-55	BGKLV11-56
Sample #
Sample Name	SRSF9-BGKLV11-55	SRSF9-BGKLV11-56
Sample_Name_Alias	SRSF9-LV11-55	SRSF9-LV11-56
Index Well Position	S18	S19
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/D2.png	DNA_Library_LV11/set3/E2.png
RIN	8.7	8.8
libSample_RNA_Well	RNA_Library_LV11/set1/A6.png	RNA_Library_LV11/set1/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-55	BGKLV11-56
RBP	SRSF9	SRSF9
Batch_ID	BGKLV11	BGKLV11
WB_result	25.600	22.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1986	1987

Sequencing Information

	BGKLV11-55	BGKLV11-56
Sample_ID	BGKLV11-55	BGKLV11-56
Sample Name	SRSF9-LV11-55	SRSF9-LV11-56
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	63,470,000	61,600,000
total_aligned_reads	51,251,750	48,671,694
unique_aligned_reads	46,906,314	44,538,788
percent_uniqueAligned	0.73903	0.72303
correlation_replicates	0.997164	0.997164
spikein_reads	398,992	283,866
percent_spikeins	0.00629	0.00461
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	686	687

Data Submission Information

	BGKLV11-55
ENCODE_alias	brenton-graveley:SRSF9-LV11
ENCODE_accession	ENCSR113HRG
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGKLV11-55
Sample Name	SRSF9-LV11-55
Selected	Yes
Status	Released
Status_Date	2014-09-08
Project	ENCODE3

protocol_URL
ID	2731

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
SRSF9-LV11-55_GTCCGC_L007_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	686	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12407
SRSF9-LV11-55_GTCCGC_L007_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	686	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12455
SRSF9-LV11-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	686					GRCh38	V40	SRSF9-LV11-55_GTCCGC_L007_R1_001.fastq.gz,SRSF9-LV11-55_GTCCGC_L007_R2_001.fastq.gz		ENCORE2	12503
SRSF9-LV11-55_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	686					GRCh38	V40	SRSF9-LV11-55/Aligned.sortedByCoord.out.bam		ENCORE2	12551
SRSF9-LV11-55_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	686					GRCh38	V40	SRSF9-LV11-55/Aligned.sortedByCoord.out.bam		ENCORE2	12599
SRSF9-LV11-55_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	686					GRCh38	V40	SRSF9-LV11-55/Aligned.sortedByCoord.out.bam		ENCORE2	12647
SRSF9-LV11-55_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	686					GRCh38	V40	SRSF9-LV11-55/Aligned.sortedByCoord.out.bam		ENCORE2	12695
SRSF9-LV11-55_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	686					GRCh38	V40	SRSF9-LV11-55_GTCCGC_L007_R1_001.fastq.gz,SRSF9-LV11-55_GTCCGC_L007_R2_001.fastq.gz		ENCORE2	12743
SRSF9-LV11-56_GTGAAA_L007_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	687	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12408
SRSF9-LV11-56_GTGAAA_L007_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	687	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12456
SRSF9-LV11-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	687					GRCh38	V40	SRSF9-LV11-56_GTGAAA_L007_R1_001.fastq.gz,SRSF9-LV11-56_GTGAAA_L007_R2_001.fastq.gz		ENCORE2	12504
SRSF9-LV11-56_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	687					GRCh38	V40	SRSF9-LV11-56/Aligned.sortedByCoord.out.bam		ENCORE2	12552
SRSF9-LV11-56_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	687					GRCh38	V40	SRSF9-LV11-56/Aligned.sortedByCoord.out.bam		ENCORE2	12600
SRSF9-LV11-56_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	687					GRCh38	V40	SRSF9-LV11-56/Aligned.sortedByCoord.out.bam		ENCORE2	12648
SRSF9-LV11-56_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	687					GRCh38	V40	SRSF9-LV11-56/Aligned.sortedByCoord.out.bam		ENCORE2	12696
SRSF9-LV11-56_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	687					GRCh38	V40	SRSF9-LV11-56_GTGAAA_L007_R1_001.fastq.gz,SRSF9-LV11-56_GTGAAA_L007_R2_001.fastq.gz		ENCORE2	12744