SRSF7 RNA-Seq in HepG2

General Information


RBP	SRSF7
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SRSF7-BGHcLV03-HepG2
ENCODE_series_ID	ENCSR842FAV
Batch_ID	BGHcLV03
Pool ID	Pool-160201
Local_Set_Name	BGHcLV03
ENCODE_KD_Exp_ID	ENCSR845MNM
ENCODE_CN_Exp_ID	ENCSR105NML
Rep1	SRSF7_BGHcLV03-5
Rep2	SRSF7_BGHcLV03-6
CN1	NT_BGHcLV03-1
CN2	NT_BGHcLV03-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	81.8
Rep2_WB	84.7
Antibody Cat#	RN079PW
Antibody Lot#	RN079PW
Antibody DCC ID	ENCAB910DVS
Status	Released
Project	ENCODE3
ID	577

Experiment Information (Status: Released)

	BGHcLV03-5	BGHcLV03-6
idx	5	6
TRCN#_or_BGC#	BGC#0000003	BGC#0000003
shRNA_or_gRNA_sequence	TCGCGTTACGGGCGGTACGG	TCGCGTTACGGGCGGTACGG
PAM
Name	SRSF7-C1-A	SRSF7-C1-A
Sample_ID	BGHcLV03-5	BGHcLV03-6
transduction_Date	12/16/2015	12/16/2015
days	D6	D6
RBP_name	SRSF7	SRSF7
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gcagaagatgcagtacgagga
RT-qPCR_primer-R	ggcatgcctgtcgatagttc
protein_conc	2568	2368
WB_result	81.8	84.7
Ave_WB	83.3
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	24	0
Rep2_TPM	22	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	6146	6147

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

	BGHcLV03-5	BGHcLV03-6
Sample_ID	BGHcLV03-5	BGHcLV03-6
Sample Name	SRSF7_BGHcLV03-5	SRSF7_BGHcLV03-6
Sample Name	SRSF7_BGHcLV03-5	SRSF7_BGHcLV03-6
RBP	SRSF7	SRSF7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1107	1108

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV03-5	BGHcLV03-6
Sample #
Sample Name	SRSF7-BGHcLV03-5	SRSF7-BGHcLV03-6
Sample_Name_Alias	SRSF7_BGHcLV03-5	SRSF7_BGHcLV03-6
Index Well Position	S22	S23
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/E1.png	DNA_Library_cLV02/set1/F1.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_cLV02/set1/G2.png	RNA_Library_cLV02/set1/H2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV03-5	BGHcLV03-6
RBP	SRSF7	SRSF7
Batch_ID	BGHcLV03	BGHcLV03
WB_result	81.800	84.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2804	2805

Sequencing Information

	BGHcLV03-5	BGHcLV03-6
Sample_ID	BGHcLV03-5	BGHcLV03-6
Sample Name	SRSF7_BGHcLV03-5	SRSF7_BGHcLV03-6
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGHcLV03	BGHcLV03
total_reads	50,210,790	58,238,006
total_aligned_reads	43,682,172	50,037,428
unique_aligned_reads	41,061,152	47,045,548
percent_uniqueAligned	0.81778	0.80782
correlation_replicates	0.999636	0.999636
spikein_reads	80,976	96,090
percent_spikeins	0.00161	0.00165
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1453	1454

Data Submission Information

	BGHcLV03-5	BGHcLV03-5
ENCODE_alias	brenton-graveley:SRSF7_BGHcLV03	brenton-graveley:SRSF7-BGHcLV03-HepG2
ENCODE_accession	ENCSR845MNM	ENCSR842FAV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV03-5	BGHcLV03-5
Sample Name	SRSF7_BGHcLV03-5	SRSF7_BGHcLV03-5
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3115	6974

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_BGHcLV03-5_CGTACG_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1453	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22926
SRSF7_BGHcLV03-5_CGTACG_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1453	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22944
SRSF7_BGHcLV03-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1453					GRCh38	V40	SRSF7_BGHcLV03-5_CGTACG_L005_001.R1.fastq.gz,SRSF7_BGHcLV03-5_CGTACG_L005_001.R2.fastq.gz		ENCORE2	22962
SRSF7_BGHcLV03-5_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1453					GRCh38	V40	SRSF7_BGHcLV03-5/Aligned.sortedByCoord.out.bam		ENCORE2	22980
SRSF7_BGHcLV03-5_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1453					GRCh38	V40	SRSF7_BGHcLV03-5/Aligned.sortedByCoord.out.bam		ENCORE2	22998
SRSF7_BGHcLV03-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1453					GRCh38	V40	SRSF7_BGHcLV03-5/Aligned.sortedByCoord.out.bam		ENCORE2	23016
SRSF7_BGHcLV03-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1453					GRCh38	V40	SRSF7_BGHcLV03-5/Aligned.sortedByCoord.out.bam		ENCORE2	23034
SRSF7_BGHcLV03-5_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1453					GRCh38	V40	SRSF7_BGHcLV03-5_CGTACG_L005_001.R1.fastq.gz,SRSF7_BGHcLV03-5_CGTACG_L005_001.R2.fastq.gz		ENCORE2	23052
SRSF7_BGHcLV03-6_GAGTGG_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1454	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22927
SRSF7_BGHcLV03-6_GAGTGG_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1454	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22945
SRSF7_BGHcLV03-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1454					GRCh38	V40	SRSF7_BGHcLV03-6_GAGTGG_L005_001.R1.fastq.gz,SRSF7_BGHcLV03-6_GAGTGG_L005_001.R2.fastq.gz		ENCORE2	22963
SRSF7_BGHcLV03-6_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1454					GRCh38	V40	SRSF7_BGHcLV03-6/Aligned.sortedByCoord.out.bam		ENCORE2	22981
SRSF7_BGHcLV03-6_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1454					GRCh38	V40	SRSF7_BGHcLV03-6/Aligned.sortedByCoord.out.bam		ENCORE2	22999
SRSF7_BGHcLV03-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1454					GRCh38	V40	SRSF7_BGHcLV03-6/Aligned.sortedByCoord.out.bam		ENCORE2	23017
SRSF7_BGHcLV03-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1454					GRCh38	V40	SRSF7_BGHcLV03-6/Aligned.sortedByCoord.out.bam		ENCORE2	23035
SRSF7_BGHcLV03-6_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1454					GRCh38	V40	SRSF7_BGHcLV03-6_GAGTGG_L005_001.R1.fastq.gz,SRSF7_BGHcLV03-6_GAGTGG_L005_001.R2.fastq.gz		ENCORE2	23053