SRSF7 RNA-Seq in HepG2

General Information


RBP	SRSF7
Cell_Line	HepG2
Method	shRNA
Exp_Name	SRSF7-BGHLV12-HepG2
ENCODE_series_ID	ENCSR328NOT
Batch_ID	BGHLV12
Pool ID	Pool-140801
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR017PRS
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	SRSF7-BGHLV12-77
Rep2	SRSF7-BGHLV12-78
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	77.0
Rep2_qPCR	73.5
Rep1_WB	72.2
Rep2_WB	80.0
Antibody Cat#	RN079PW
Antibody Lot#	RN079PW
Antibody DCC ID	ENCAB910DVS
Status	Archived
Project	ENCODE3
ID	356

Experiment Information (Status: Released)

	BGHLV12-77	BGHLV12-78
idx	77	78
TRCN#_or_BGC#	TRCN0000001142	TRCN0000001142
shRNA_or_gRNA_sequence	GAACTGTATGGATTGCGAGAA	GAACTGTATGGATTGCGAGAA
PAM
Name	SRSF7	SRSF7
Sample_ID	BGHLV12-77	BGHLV12-78
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	SRSF7	SRSF7
qPCR_result	77.0	73.5
Ave_qPCR	75.3
RT-qPCR_primer-F	gcagaagatgcagtacgagga
RT-qPCR_primer-R	ggcatgcctgtcgatagttc
protein_conc	3440	2865
WB_result	72.2	80.0
Ave_WB	76.1
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	24.2	0
Rep2_TPM	21.7	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2134	2135

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

	BGHLV12-77	BGHLV12-78
Sample_ID	BGHLV12-77	BGHLV12-78
Sample Name	SRSF7-BGHLV12-77	SRSF7-BGHLV12-78
Sample Name	SRSF7-BGHLV12-77	SRSF7-BGHLV12-78
RBP	SRSF7	SRSF7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	430	431

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-77	BGHLV12-78
Sample #
Sample Name	SRSF7-BGHLV12-77	SRSF7-BGHLV12-78
Sample_Name_Alias	SRSF7-BGHLV12-77	SRSF7-BGHLV12-78
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/C4.png	DNA_Library_LV12/set3/D4.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV12/set1/C8.png	RNA_Library_LV12/set1/D8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-77	BGHLV12-78
RBP	SRSF7	SRSF7
Batch_ID	BGHLV12	BGHLV12
WB_result	72.200	80.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2054	2055

Sequencing Information

	BGHLV12-77	BGHLV12-78
Sample_ID	BGHLV12-77	BGHLV12-78
Sample Name	SRSF7-BGHLV12-77	SRSF7-BGHLV12-78
Pool ID	Pool-140801	Pool-140801
LocalServer_folder	set12	set12
total_reads	67,330,000	62,750,000
total_aligned_reads	60,508,848	57,450,186
unique_aligned_reads	57,311,114	54,480,684
percent_uniqueAligned	0.85120	0.86822
correlation_replicates	0.993915	0.993915
spikein_reads	356,634	490,984
percent_spikeins	0.00530	0.00782
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	754	755

Data Submission Information

	BGHLV12-77	BGHLV12-77
ENCODE_alias	brenton-graveley:SRSF7-BGHLV12	brenton-graveley:SRSF7-BGHLV12-HepG2
ENCODE_accession	ENCSR017PRS	ENCSR328NOT
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-77	BGHLV12-77
Sample Name	SRSF7-BGHLV12-77	SRSF7-BGHLV12-77
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2764	6975

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-BGHLV12-77_GGCTAC_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	754	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12813
SRSF7-BGHLV12-77_GGCTAC_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	754	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12882
SRSF7-BGHLV12-77_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	754					GRCh38	V40	SRSF7-BGHLV12-77_GGCTAC_L005_R1_001.fastq.gz,SRSF7-BGHLV12-77_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	12952
SRSF7-BGHLV12-77_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	754					GRCh38	V40	SRSF7-BGHLV12-77/Aligned.sortedByCoord.out.bam		ENCORE2	13022
SRSF7-BGHLV12-77_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	754					GRCh38	V40	SRSF7-BGHLV12-77/Aligned.sortedByCoord.out.bam		ENCORE2	13092
SRSF7-BGHLV12-77_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	754					GRCh38	V40	SRSF7-BGHLV12-77/Aligned.sortedByCoord.out.bam		ENCORE2	13162
SRSF7-BGHLV12-77_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	754					GRCh38	V40	SRSF7-BGHLV12-77/Aligned.sortedByCoord.out.bam		ENCORE2	13232
SRSF7-BGHLV12-77_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	754					GRCh38	V40	SRSF7-BGHLV12-77_GGCTAC_L005_R1_001.fastq.gz,SRSF7-BGHLV12-77_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	13302
SRSF7-BGHLV12-78_CTTGTA_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	755	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12814
SRSF7-BGHLV12-78_CTTGTA_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	755	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12883
SRSF7-BGHLV12-78_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	755					GRCh38	V40	SRSF7-BGHLV12-78_CTTGTA_L005_R1_001.fastq.gz,SRSF7-BGHLV12-78_CTTGTA_L005_R2_001.fastq.gz		ENCORE2	12953
SRSF7-BGHLV12-78_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	755					GRCh38	V40	SRSF7-BGHLV12-78/Aligned.sortedByCoord.out.bam		ENCORE2	13023
SRSF7-BGHLV12-78_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	755					GRCh38	V40	SRSF7-BGHLV12-78/Aligned.sortedByCoord.out.bam		ENCORE2	13093
SRSF7-BGHLV12-78_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	755					GRCh38	V40	SRSF7-BGHLV12-78/Aligned.sortedByCoord.out.bam		ENCORE2	13163
SRSF7-BGHLV12-78_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	755					GRCh38	V40	SRSF7-BGHLV12-78/Aligned.sortedByCoord.out.bam		ENCORE2	13233
SRSF7-BGHLV12-78_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	755					GRCh38	V40	SRSF7-BGHLV12-78_CTTGTA_L005_R1_001.fastq.gz,SRSF7-BGHLV12-78_CTTGTA_L005_R2_001.fastq.gz		ENCORE2	13303