SRSF7 RNA-Seq in K562

General Information


RBP	SRSF7
Cell_Line	K562
Method	shRNA
Exp_Name	SRSF7-BGKLV11-K562
ENCODE_series_ID	ENCSR355BTO
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR464ADT
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	SRSF7-LV11-53
Rep2	SRSF7-LV11-54
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	79.9
Rep2_qPCR	84.0
Rep1_WB	48.2
Rep2_WB	55.0
Antibody Cat#	RN079PW
Antibody Lot#	RN079PW
Antibody DCC ID	ENCAB910DVS
Status	Archived
Project	ENCODE3
ID	324

Experiment Information (Status: Released)

	BGKLV11-53	BGKLV11-54
idx	122	123
TRCN#_or_BGC#	TRCN0000001142	TRCN0000001142
shRNA_or_gRNA_sequence	GAACTGTATGGATTGCGAGAA	GAACTGTATGGATTGCGAGAA
PAM
Name	SRSF7	SRSF7
Sample_ID	BGKLV11-53	BGKLV11-54
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	SRSF7	SRSF7
qPCR_result	79.9	84.0
Ave_qPCR	81.9
RT-qPCR_primer-F	gcagaagatgcagtacgagga
RT-qPCR_primer-R	ggcatgcctgtcgatagttc
protein_conc	2193	2084
WB_result	48.2	55.0
Ave_WB	51.6
WB_DONE_date
MW	27kDa
IP	1	1
antibody_Cat#	RN079PW	RN079PW
Antibody DCC ID	ENCAB910DVS	ENCAB910DVS
submitted_to_DCC_date	4/2/2015
Rep1_TPM	98.3634636	0
Rep2_TPM	65.0514753	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	135	136

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRSF7	Product_ID: RN079PW Lot_ID: 1 Source: MBLI Target Name: SRSF7-human

Experiment Status

	BGKLV11-53	BGKLV11-54
Sample_ID	BGKLV11-53	BGKLV11-54
Sample Name	SRSF7-LV11-53	SRSF7-LV11-54
Sample Name	SRSF7-LV11-53	SRSF7-LV11-54
RBP	SRSF7	SRSF7
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	362	363

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-53	BGKLV11-54
Sample #
Sample Name	SRSF7-BGKLV11-53	SRSF7-BGKLV11-54
Sample_Name_Alias	SRSF7-LV11-53	SRSF7-LV11-54
Index Well Position	S15	S16
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/B2.png	DNA_Library_LV11/set5/B1.png
RIN	9.3	8.9
libSample_RNA_Well	RNA_Library_LV11/set1/G5.png	RNA_Library_LV11/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-53	BGKLV11-54
RBP	SRSF7	SRSF7
Batch_ID	BGKLV11	BGKLV11
WB_result	48.200	55.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1984	1985

Sequencing Information

	BGKLV11-53	BGKLV11-54
Sample_ID	BGKLV11-53	BGKLV11-54
Sample Name	SRSF7-LV11-53	SRSF7-LV11-54
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	57,040,000	60,380,000
total_aligned_reads	47,074,434	50,160,638
unique_aligned_reads	43,028,674	45,953,214
percent_uniqueAligned	0.75436	0.76107
correlation_replicates	0.995124	0.995124
spikein_reads	338,164	483,904
percent_spikeins	0.00593	0.00801
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	684	685

Data Submission Information

	BGKLV11-53	BGKLV11-53
ENCODE_alias	brenton-graveley:SRSF7-LV11	brenton-graveley:SRSF7-BGKLV11-K562
ENCODE_accession	ENCSR464ADT	ENCSR355BTO
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-53	BGKLV11-53
Sample Name	SRSF7-LV11-53	SRSF7-LV11-53
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2730	6977

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
SRSF7-LV11-53_ATGTCA_L007_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	684	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12405
SRSF7-LV11-53_ATGTCA_L007_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	684	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12453
SRSF7-LV11-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	684					GRCh38	V40	SRSF7-LV11-53_ATGTCA_L007_R1_001.fastq.gz,SRSF7-LV11-53_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	12501
SRSF7-LV11-53_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	684					GRCh38	V40	SRSF7-LV11-53/Aligned.sortedByCoord.out.bam		ENCORE2	12549
SRSF7-LV11-53_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	684					GRCh38	V40	SRSF7-LV11-53/Aligned.sortedByCoord.out.bam		ENCORE2	12597
SRSF7-LV11-53_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	684					GRCh38	V40	SRSF7-LV11-53/Aligned.sortedByCoord.out.bam		ENCORE2	12645
SRSF7-LV11-53_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	684					GRCh38	V40	SRSF7-LV11-53/Aligned.sortedByCoord.out.bam		ENCORE2	12693
SRSF7-LV11-53_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	684					GRCh38	V40	SRSF7-LV11-53_ATGTCA_L007_R1_001.fastq.gz,SRSF7-LV11-53_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	12741
SRSF7-LV11-54_CCGTCC_L007_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	685	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12406
SRSF7-LV11-54_CCGTCC_L007_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	685	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12454
SRSF7-LV11-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	685					GRCh38	V40	SRSF7-LV11-54_CCGTCC_L007_R1_001.fastq.gz,SRSF7-LV11-54_CCGTCC_L007_R2_001.fastq.gz		ENCORE2	12502
SRSF7-LV11-54_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	685					GRCh38	V40	SRSF7-LV11-54/Aligned.sortedByCoord.out.bam		ENCORE2	12550
SRSF7-LV11-54_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	685					GRCh38	V40	SRSF7-LV11-54/Aligned.sortedByCoord.out.bam		ENCORE2	12598
SRSF7-LV11-54_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	685					GRCh38	V40	SRSF7-LV11-54/Aligned.sortedByCoord.out.bam		ENCORE2	12646
SRSF7-LV11-54_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	685					GRCh38	V40	SRSF7-LV11-54/Aligned.sortedByCoord.out.bam		ENCORE2	12694
SRSF7-LV11-54_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	685					GRCh38	V40	SRSF7-LV11-54_CCGTCC_L007_R1_001.fastq.gz,SRSF7-LV11-54_CCGTCC_L007_R2_001.fastq.gz		ENCORE2	12742