SRSF7 RNA-Seq in K562

General Information


RBP	SRSF7
Cell_Line	K562
Method	CRISPR
Exp_Name	SRSF7-BGKcLV02-K562
ENCODE_series_ID	ENCSR941FPF
Batch_ID	BGKcLV02
Pool ID	Pool-160201
Local_Set_Name	BGKcLV02
ENCODE_KD_Exp_ID	ENCSR139LOF
ENCODE_CN_Exp_ID	ENCSR163JUC
Rep1	SRSF7_BGKcLV02-5
Rep2	SRSF7_BGKcLV02-6
CN1	NT_BGKcLV02-1
CN2	NT_BGKcLV02-2
Rep1_qPCR	11.3
Rep2_qPCR	0.0
Rep1_WB	84.3
Rep2_WB	78.7
Antibody Cat#	RN079PW
Antibody Lot#	RN079PW
Antibody DCC ID	ENCAB910DVS
Status	Released
Project	ENCODE3
ID	589

Experiment Information (Status: Released)

	BGKcLV02-5	BGKcLV02-6
idx	5	6
TRCN#_or_BGC#	BGC#0000004	BGC#0000004
shRNA_or_gRNA_sequence	TCATCATGTCGCGTTACGGG	TCATCATGTCGCGTTACGGG
PAM
Name	SRSF7-C2-A	SRSF7-C2-A
Sample_ID	BGKcLV02-5	BGKcLV02-6
transduction_Date	12/15/2015	12/15/2015
days	day 6	day 6
RBP_name	SRSF7	SRSF7
qPCR_result	11.3	0.0
Ave_qPCR	5.7
RT-qPCR_primer-F	gcagaagatgcagtacgagga
RT-qPCR_primer-R	ggcatgcctgtcgatagttc
protein_conc	3741	3581
WB_result	84.3	78.7
Ave_WB	81.5
WB_DONE_date	12/28/2015
MW	27kDa
IP	1
antibody_Cat#	RN079PW	RN079PW
Antibody DCC ID	ENCAB910DVS	ENCAB910DVS
submitted_to_DCC_date	9/28/16
Rep1_TPM	98.4	0
Rep2_TPM	65.1	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	4099	4100

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

	BGKcLV02-5	BGKcLV02-6
Sample_ID	BGKcLV02-5	BGKcLV02-6
Sample Name	SRSF7_BGKcLV02-5	SRSF7_BGKcLV02-6
Sample Name	SRSF7_BGKcLV02-5	SRSF7_BGKcLV02-6
RBP	SRSF7	SRSF7
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1095	1096

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-5	BGKcLV02-6
Sample #
Sample Name	SRSF7-BGKcLV02-5	SRSF7-BGKcLV02-6
Sample_Name_Alias	SRSF7_BGKcLV02-5	SRSF7_BGKcLV02-6
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/G3.png	DNA_Library_LV35/set1/D5.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_cLV02/set1/A5.png	RNA_Library_cLV02/set1/B5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-5	BGKcLV02-6
RBP	SRSF7	SRSF7
Batch_ID	BGKcLV02	BGKcLV02
WB_result	84.300	78.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2786	2787

Sequencing Information

	BGKcLV02-5	BGKcLV02-6
Sample_ID	BGKcLV02-5	BGKcLV02-6
Sample Name	SRSF7_BGKcLV02-5	SRSF7_BGKcLV02-6
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	61,420,092	57,017,336
total_aligned_reads	56,360,506	52,332,980
unique_aligned_reads	51,375,424	47,832,126
percent_uniqueAligned	0.83646	0.83890
correlation_replicates	0.997497	0.997497
spikein_reads	124,898	127,910
percent_spikeins	0.00203	0.00224
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1435	1436

Data Submission Information

	BGKcLV02-5	BGKcLV02-5
ENCODE_alias	brenton-graveley:SRSF7_BGKcLV02	brenton-graveley:SRSF7-BGKcLV02-K562
ENCODE_accession	ENCSR139LOF	ENCSR941FPF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV02-5	BGKcLV02-5
Sample Name	SRSF7_BGKcLV02-5	SRSF7_BGKcLV02-5
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3109	6976

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_BGKcLV02-5_ATGTCA_L007_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1435	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22768
SRSF7_BGKcLV02-5_ATGTCA_L007_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1435	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22788
SRSF7_BGKcLV02-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1435					GRCh38	V40	SRSF7_BGKcLV02-5_ATGTCA_L007_001.R1.fastq.gz,SRSF7_BGKcLV02-5_ATGTCA_L007_001.R2.fastq.gz		ENCORE2	22808
SRSF7_BGKcLV02-5_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1435					GRCh38	V40	SRSF7_BGKcLV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	22828
SRSF7_BGKcLV02-5_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1435					GRCh38	V40	SRSF7_BGKcLV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	22848
SRSF7_BGKcLV02-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1435					GRCh38	V40	SRSF7_BGKcLV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	22868
SRSF7_BGKcLV02-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1435					GRCh38	V40	SRSF7_BGKcLV02-5/Aligned.sortedByCoord.out.bam		ENCORE2	22888
SRSF7_BGKcLV02-5_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1435					GRCh38	V40	SRSF7_BGKcLV02-5_ATGTCA_L007_001.R1.fastq.gz,SRSF7_BGKcLV02-5_ATGTCA_L007_001.R2.fastq.gz		ENCORE2	22908
SRSF7_BGKcLV02-6_CCGTCC_L007_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1436	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22769
SRSF7_BGKcLV02-6_CCGTCC_L007_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1436	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22789
SRSF7_BGKcLV02-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1436					GRCh38	V40	SRSF7_BGKcLV02-6_CCGTCC_L007_001.R1.fastq.gz,SRSF7_BGKcLV02-6_CCGTCC_L007_001.R2.fastq.gz		ENCORE2	22809
SRSF7_BGKcLV02-6_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1436					GRCh38	V40	SRSF7_BGKcLV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	22829
SRSF7_BGKcLV02-6_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1436					GRCh38	V40	SRSF7_BGKcLV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	22849
SRSF7_BGKcLV02-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1436					GRCh38	V40	SRSF7_BGKcLV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	22869
SRSF7_BGKcLV02-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1436					GRCh38	V40	SRSF7_BGKcLV02-6/Aligned.sortedByCoord.out.bam		ENCORE2	22889
SRSF7_BGKcLV02-6_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1436					GRCh38	V40	SRSF7_BGKcLV02-6_CCGTCC_L007_001.R1.fastq.gz,SRSF7_BGKcLV02-6_CCGTCC_L007_001.R2.fastq.gz		ENCORE2	22909