SRSF9 RNA-Seq in HepG2

General Information


RBP	SRSF9
Cell_Line	HepG2
Method	shRNA
Exp_Name	SRSF9-BGHLV12-HepG2
ENCODE_series_ID	ENCSR128IPS
Batch_ID	BGHLV12
Pool ID	Pool-140801
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR597XHH
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	SRSF9-BGHLV12-79
Rep2	SRSF9-BGHLV12-80
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	81.1
Rep2_qPCR	84.0
Rep1_WB	34.9
Rep2_WB	60.9
Antibody Cat#	RN081PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB278ULX
Status	Archived
Project	ENCODE3
ID	357

Experiment Information (Status: Released)

	BGHLV12-79	BGHLV12-80
idx	79	80
TRCN#_or_BGC#	TRCN0000006630	TRCN0000006630
shRNA_or_gRNA_sequence	GACACCAAATTCCGCTCTCAT	GACACCAAATTCCGCTCTCAT
PAM
Name	SRSF9	SRSF9
Sample_ID	BGHLV12-79	BGHLV12-80
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	SRSF9	SRSF9
qPCR_result	81.1	84.0
Ave_qPCR	82.6
RT-qPCR_primer-F	ATATGCCCTGCGTAAACTGG
RT-qPCR_primer-R	AGCTGGTGCTTCTCTCAGGA
protein_conc	2844	3511
WB_result	34.9	60.9
Ave_WB	47.9
WB_DONE_date
MW	26kDa
IP	1	1
antibody_Cat#	RN081PW	RN081PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	77.8	0
Rep2_TPM	78.4	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2136	2137

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV12-79	BGHLV12-80
Sample_ID	BGHLV12-79	BGHLV12-80
Sample Name	SRSF9-BGHLV12-79	SRSF9-BGHLV12-80
Sample Name	SRSF9-BGHLV12-79	SRSF9-BGHLV12-80
RBP	SRSF9	SRSF9
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	432	433

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-79	BGHLV12-80
Sample #
Sample Name	SRSF9-BGHLV12-79	SRSF9-BGHLV12-80
Sample_Name_Alias	SRSF9-BGHLV12-79	SRSF9-BGHLV12-80
Index Well Position	S13	S14
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/E4.png	DNA_Library_LV12/set3/F4.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/E8.png	RNA_Library_LV12/set1/F8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-79	BGHLV12-80
RBP	SRSF9	SRSF9
Batch_ID	BGHLV12	BGHLV12
WB_result	34.900	60.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2056	2057

Sequencing Information

	BGHLV12-79	BGHLV12-80
Sample_ID	BGHLV12-79	BGHLV12-80
Sample Name	SRSF9-BGHLV12-79	SRSF9-BGHLV12-80
Pool ID	Pool-140801	Pool-140801
LocalServer_folder	set12	set12
total_reads	54,750,000	59,330,000
total_aligned_reads	50,012,812	54,711,466
unique_aligned_reads	47,489,096	51,891,956
percent_uniqueAligned	0.86738	0.87463
correlation_replicates	0.998685	0.998685
spikein_reads	358,828	218,000
percent_spikeins	0.00655	0.00367
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	756	757

Data Submission Information

	BGHLV12-79	BGHLV12-79
ENCODE_alias	brenton-graveley:SRSF9-BGHLV12	brenton-graveley:SRSF9-BGHLV12-HepG2
ENCODE_accession	ENCSR597XHH	ENCSR128IPS
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-79	BGHLV12-79
Sample Name	SRSF9-BGHLV12-79	SRSF9-BGHLV12-79
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2765	6978

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
SRSF9-BGHLV12-79_AGTCAA_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	756	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12815
SRSF9-BGHLV12-79_AGTCAA_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	756	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12884
SRSF9-BGHLV12-79_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	756					GRCh38	V40	SRSF9-BGHLV12-79_AGTCAA_L005_R1_001.fastq.gz,SRSF9-BGHLV12-79_AGTCAA_L005_R2_001.fastq.gz		ENCORE2	12954
SRSF9-BGHLV12-79_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	756					GRCh38	V40	SRSF9-BGHLV12-79/Aligned.sortedByCoord.out.bam		ENCORE2	13024
SRSF9-BGHLV12-79_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	756					GRCh38	V40	SRSF9-BGHLV12-79/Aligned.sortedByCoord.out.bam		ENCORE2	13094
SRSF9-BGHLV12-79_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	756					GRCh38	V40	SRSF9-BGHLV12-79/Aligned.sortedByCoord.out.bam		ENCORE2	13164
SRSF9-BGHLV12-79_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	756					GRCh38	V40	SRSF9-BGHLV12-79/Aligned.sortedByCoord.out.bam		ENCORE2	13234
SRSF9-BGHLV12-79_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	756					GRCh38	V40	SRSF9-BGHLV12-79_AGTCAA_L005_R1_001.fastq.gz,SRSF9-BGHLV12-79_AGTCAA_L005_R2_001.fastq.gz		ENCORE2	13304
SRSF9-BGHLV12-80_AGTTCC_L005_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	757	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12816
SRSF9-BGHLV12-80_AGTTCC_L005_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	757	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12885
SRSF9-BGHLV12-80_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	757					GRCh38	V40	SRSF9-BGHLV12-80_AGTTCC_L005_R1_001.fastq.gz,SRSF9-BGHLV12-80_AGTTCC_L005_R2_001.fastq.gz		ENCORE2	12955
SRSF9-BGHLV12-80_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	757					GRCh38	V40	SRSF9-BGHLV12-80/Aligned.sortedByCoord.out.bam		ENCORE2	13025
SRSF9-BGHLV12-80_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	757					GRCh38	V40	SRSF9-BGHLV12-80/Aligned.sortedByCoord.out.bam		ENCORE2	13095
SRSF9-BGHLV12-80_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	757					GRCh38	V40	SRSF9-BGHLV12-80/Aligned.sortedByCoord.out.bam		ENCORE2	13165
SRSF9-BGHLV12-80_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	757					GRCh38	V40	SRSF9-BGHLV12-80/Aligned.sortedByCoord.out.bam		ENCORE2	13235
SRSF9-BGHLV12-80_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	757					GRCh38	V40	SRSF9-BGHLV12-80_AGTTCC_L005_R1_001.fastq.gz,SRSF9-BGHLV12-80_AGTTCC_L005_R2_001.fastq.gz		ENCORE2	13305