SRSF5 RNA-Seq in K562

General Information


RBP	SRSF5
Cell_Line	K562
Method	shRNA
Exp_Name	SRSF5-BGKLV11-K562
ENCODE_series_ID	ENCSR006UOZ
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR906RHU
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	SRSF5-41-LV11-51
Rep2	SRSF5-41-LV11-52
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	54.0
Rep2_qPCR	58.3
Rep1_WB	23.1
Rep2_WB	20.5
Antibody Cat#	RN082PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB038XFS
Status	Archived
Project	ENCODE3
ID	323

Experiment Information (Status: Released)

	BGKLV11-51	BGKLV11-52
idx	120	121
TRCN#_or_BGC#	TRCN0000000141	TRCN0000000141
shRNA_or_gRNA_sequence	TGGAAGAGGTAGAGGACGATA	TGGAAGAGGTAGAGGACGATA
PAM
Name	SRSF5_41	SRSF5_41
Sample_ID	BGKLV11-51	BGKLV11-52
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	SRSF5	SRSF5
qPCR_result	54.0	58.3
Ave_qPCR	56.2
RT-qPCR_primer-F	TCAAGGGATATGGACGGATAA
RT-qPCR_primer-R	CCATCAAGCTCATACACAGCA
protein_conc	2305	2294
WB_result	23.1	20.5
Ave_WB	21.8
WB_DONE_date	11/18/2015
MW	31kDa
IP	1	1
antibody_Cat#	RN082PW	RN082PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	109.786526	0
Rep2_TPM	102.440433	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	133	134

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV11-51	BGKLV11-52
Sample_ID	BGKLV11-51	BGKLV11-52
Sample Name	SRSF5-41-LV11-51	SRSF5-41-LV11-52
Sample Name	SRSF5-41-LV11-51	SRSF5-41-LV11-52
RBP	SRSF5	SRSF5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	360	361

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-51	BGKLV11-52
Sample #
Sample Name	SRSF5-BGKLV11-51	SRSF5-BGKLV11-52
Sample_Name_Alias	SRSF5-41-LV11-51	SRSF5-41-LV11-52
Index Well Position	S13	S14
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/H1.png	DNA_Library_LV11/set3/A2.png
RIN	9.3	8.9
libSample_RNA_Well	RNA_Library_LV11/set1/E5.png	RNA_Library_LV11/set1/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-51	BGKLV11-52
RBP	SRSF5	SRSF5
Batch_ID	BGKLV11	BGKLV11
WB_result	23.100	20.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1982	1983

Sequencing Information

	BGKLV11-51	BGKLV11-52
Sample_ID	BGKLV11-51	BGKLV11-52
Sample Name	SRSF5-41-LV11-51	SRSF5-41-LV11-52
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	51,270,000	57,950,000
total_aligned_reads	42,110,658	46,024,522
unique_aligned_reads	38,450,488	42,036,272
percent_uniqueAligned	0.74996	0.72539
correlation_replicates	0.991692	0.991692
spikein_reads	313,910	312,950
percent_spikeins	0.00612	0.00540
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	682	683

Data Submission Information

	BGKLV11-51	BGKLV11-51
ENCODE_alias	brenton-graveley:SRSF5-41-LV11	brenton-graveley:SRSF5-BGKLV11-K562
ENCODE_accession	ENCSR906RHU	ENCSR006UOZ
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-51	BGKLV11-51
Sample Name	SRSF5-41-LV11-51	SRSF5-41-LV11-51
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2729	6973

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
SRSF5-41-LV11-51_AGTCAA_L007_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	682	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12403
SRSF5-41-LV11-51_AGTCAA_L007_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	682	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12451
SRSF5-41-LV11-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	682					GRCh38	V40	SRSF5-41-LV11-51_AGTCAA_L007_R1_001.fastq.gz,SRSF5-41-LV11-51_AGTCAA_L007_R2_001.fastq.gz		ENCORE2	12499
SRSF5-41-LV11-51_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	682					GRCh38	V40	SRSF5-41-LV11-51/Aligned.sortedByCoord.out.bam		ENCORE2	12547
SRSF5-41-LV11-51_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	682					GRCh38	V40	SRSF5-41-LV11-51/Aligned.sortedByCoord.out.bam		ENCORE2	12595
SRSF5-41-LV11-51_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	682					GRCh38	V40	SRSF5-41-LV11-51/Aligned.sortedByCoord.out.bam		ENCORE2	12643
SRSF5-41-LV11-51_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	682					GRCh38	V40	SRSF5-41-LV11-51/Aligned.sortedByCoord.out.bam		ENCORE2	12691
SRSF5-41-LV11-51_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	682					GRCh38	V40	SRSF5-41-LV11-51_AGTCAA_L007_R1_001.fastq.gz,SRSF5-41-LV11-51_AGTCAA_L007_R2_001.fastq.gz		ENCORE2	12739
SRSF5-41-LV11-52_AGTTCC_L007_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	683	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12404
SRSF5-41-LV11-52_AGTTCC_L007_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	683	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12452
SRSF5-41-LV11-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	683					GRCh38	V40	SRSF5-41-LV11-52_AGTTCC_L007_R1_001.fastq.gz,SRSF5-41-LV11-52_AGTTCC_L007_R2_001.fastq.gz		ENCORE2	12500
SRSF5-41-LV11-52_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	683					GRCh38	V40	SRSF5-41-LV11-52/Aligned.sortedByCoord.out.bam		ENCORE2	12548
SRSF5-41-LV11-52_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	683					GRCh38	V40	SRSF5-41-LV11-52/Aligned.sortedByCoord.out.bam		ENCORE2	12596
SRSF5-41-LV11-52_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	683					GRCh38	V40	SRSF5-41-LV11-52/Aligned.sortedByCoord.out.bam		ENCORE2	12644
SRSF5-41-LV11-52_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	683					GRCh38	V40	SRSF5-41-LV11-52/Aligned.sortedByCoord.out.bam		ENCORE2	12692
SRSF5-41-LV11-52_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	683					GRCh38	V40	SRSF5-41-LV11-52_AGTTCC_L007_R1_001.fastq.gz,SRSF5-41-LV11-52_AGTTCC_L007_R2_001.fastq.gz		ENCORE2	12740