SRSF5 RNA-Seq in HepG2

General Information


RBP	SRSF5
Cell_Line	HepG2
Method	shRNA
Exp_Name	SRSF5-BGHLV23-HepG2
ENCODE_series_ID	ENCSR200UMM
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR781YNI
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	SRSF5-BGHLV23-45
Rep2	SRSF5-BGHLV23-46
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	72.6
Rep2_qPCR	77.9
Rep1_WB	67.0
Rep2_WB	74.9
Antibody Cat#	RN082PW
Antibody Lot#	RN082PW
Antibody DCC ID	ENCAB038XFS
Status	Released
Project	ENCODE3
ID	551

Experiment Information (Status: Released)

	BGHLV23-45	BGHLV23-46
idx	537	538
TRCN#_or_BGC#	TRCN0000284799	TRCN0000284799
shRNA_or_gRNA_sequence	AGTAGTCGCAGACCTCGAAAT	AGTAGTCGCAGACCTCGAAAT
PAM
Name	SRSF5_B5	SRSF5_B5
Sample_ID	BGHLV23-45	BGHLV23-46
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	SRSF5	SRSF5
qPCR_result	72.6	77.9
Ave_qPCR	75.2
RT-qPCR_primer-F	TCAAGGGATATGGACGGATAA
RT-qPCR_primer-R	CCATCAAGCTCATACACAGCA
protein_conc	3884	4482
WB_result	67.0	74.9
Ave_WB	71.0
WB_DONE_date	11/18/2015
MW	31kDa
IP	1	1
antibody_Cat#	RN082PW	RN082PW
Antibody DCC ID	ENCAB038XFS	ENCAB038XFS
submitted_to_DCC_date	12/7/2015
Rep1_TPM	263.4	0
Rep2_TPM	173.5	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2618	2619

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRSF5	Product_ID: RN082PW Lot_ID: 1 Source: MBLI Target Name: SRSF5-human

Experiment Status

	BGHLV23-45	BGHLV23-46
Sample_ID	BGHLV23-45	BGHLV23-46
Sample Name	SRSF5-BGHLV23-45	SRSF5-BGHLV23-46
Sample Name	SRSF5-BGHLV23-45	SRSF5-BGHLV23-46
RBP	SRSF5	SRSF5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	840	841

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-45	BGHLV23-46
Sample #
Sample Name	SRSF5-BGHLV23-45	SRSF5-BGHLV23-46
Sample_Name_Alias	SRSF5-BGHLV23-45	SRSF5-BGHLV23-46
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set4/E2.png	DNA_Library_LV20-22-23/set4/F2.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A8.png	RNA_Library_LV22-23-25/set1/B8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-45	BGHLV23-46
RBP	SRSF5	SRSF5
Batch_ID	BGHLV23	BGHLV23
WB_result	67.000	74.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2528	2529

Sequencing Information

	BGHLV23-45	BGHLV23-46
Sample_ID	BGHLV23-45	BGHLV23-46
Sample Name	SRSF5-BGHLV23-45	SRSF5-BGHLV23-46
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	50,460,000	56,180,000
total_aligned_reads	46,308,830	51,259,090
unique_aligned_reads	43,716,102	48,374,998
percent_uniqueAligned	0.86635	0.86107
correlation_replicates	0.998406	0.998406
spikein_reads	292,666	289,190
percent_spikeins	0.00580	0.00515
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1150	1151

Data Submission Information

	BGHLV23-45	BGHLV23-45
ENCODE_alias	brenton-graveley:SRSF5-BGHLV23	brenton-graveley:SRSF5-BGHLV23-HepG2
ENCODE_accession	ENCSR781YNI	ENCSR200UMM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-45	BGHLV23-45
Sample Name	SRSF5-BGHLV23-45	SRSF5-BGHLV23-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2952	6972

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
SRSF5-BGHLV23-45_CGTACG_L007_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1150	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16680
SRSF5-BGHLV23-45_CGTACG_L007_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1150	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16718
SRSF5-BGHLV23-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1150					GRCh38	V40	SRSF5-BGHLV23-45_CGTACG_L007_R1_001.fastq.gz,SRSF5-BGHLV23-45_CGTACG_L007_R2_001.fastq.gz		ENCORE2	16756
SRSF5-BGHLV23-45_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1150					GRCh38	V40	SRSF5-BGHLV23-45/Aligned.sortedByCoord.out.bam		ENCORE2	16794
SRSF5-BGHLV23-45_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1150					GRCh38	V40	SRSF5-BGHLV23-45/Aligned.sortedByCoord.out.bam		ENCORE2	16832
SRSF5-BGHLV23-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1150					GRCh38	V40	SRSF5-BGHLV23-45/Aligned.sortedByCoord.out.bam		ENCORE2	16870
SRSF5-BGHLV23-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1150					GRCh38	V40	SRSF5-BGHLV23-45/Aligned.sortedByCoord.out.bam		ENCORE2	16908
SRSF5-BGHLV23-45_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1150					GRCh38	V40	SRSF5-BGHLV23-45_CGTACG_L007_R1_001.fastq.gz,SRSF5-BGHLV23-45_CGTACG_L007_R2_001.fastq.gz		ENCORE2	16946
SRSF5-BGHLV23-46_GAGTGG_L008_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1151	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16681
SRSF5-BGHLV23-46_GAGTGG_L008_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1151	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16719
SRSF5-BGHLV23-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1151					GRCh38	V40	SRSF5-BGHLV23-46_GAGTGG_L008_R1_001.fastq.gz,SRSF5-BGHLV23-46_GAGTGG_L008_R2_001.fastq.gz		ENCORE2	16757
SRSF5-BGHLV23-46_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1151					GRCh38	V40	SRSF5-BGHLV23-46/Aligned.sortedByCoord.out.bam		ENCORE2	16795
SRSF5-BGHLV23-46_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1151					GRCh38	V40	SRSF5-BGHLV23-46/Aligned.sortedByCoord.out.bam		ENCORE2	16833
SRSF5-BGHLV23-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1151					GRCh38	V40	SRSF5-BGHLV23-46/Aligned.sortedByCoord.out.bam		ENCORE2	16871
SRSF5-BGHLV23-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1151					GRCh38	V40	SRSF5-BGHLV23-46/Aligned.sortedByCoord.out.bam		ENCORE2	16909
SRSF5-BGHLV23-46_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1151					GRCh38	V40	SRSF5-BGHLV23-46_GAGTGG_L008_R1_001.fastq.gz,SRSF5-BGHLV23-46_GAGTGG_L008_R2_001.fastq.gz		ENCORE2	16947