SRSF5 RNA-Seq in HepG2

General Information


RBP	SRSF5
Cell_Line	HepG2
Method	shRNA
Exp_Name	SRSF5-BGHLV14-HepG2
ENCODE_series_ID	ENCSR480QJF
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR447UCG
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	SRSF5_41_BGHLV14-55
Rep2	SRSF5_41_BGHLV14-56
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	58.1
Rep2_qPCR	52.9
Rep1_WB	see BGHLV23
Rep2_WB	see BGHLV23
Antibody Cat#	RN082PW
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB038XFS
Status	Archived
Project	ENCODE3
ID	407

Experiment Information (Status: Released)

	BGHLV14-55	BGHLV14-56
idx	151	152
TRCN#_or_BGC#	TRCN0000000141	TRCN0000000141
shRNA_or_gRNA_sequence	TGGAAGAGGTAGAGGACGATA	TGGAAGAGGTAGAGGACGATA
PAM
Name	SRSF5_41	SRSF5_41
Sample_ID	BGHLV14-55	BGHLV14-56
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	SRSF5	SRSF5
qPCR_result	58.1	52.9
Ave_qPCR	55.5
RT-qPCR_primer-F	TCAAGGGATATGGACGGATAA
RT-qPCR_primer-R	CCATCAAGCTCATACACAGCA
protein_conc	3792	3837
WB_result	see BGHLV23	see BGHLV23
Ave_WB
WB_DONE_date
MW
IP	1	1
antibody_Cat#	RN082PW	RN082PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	263.4	0
Rep2_TPM	173.5	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2216	2217

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV14-55	BGHLV14-56
Sample_ID	BGHLV14-55	BGHLV14-56
Sample Name	SRSF5_41_BGHLV14-55	SRSF5_41_BGHLV14-56
Sample Name	SRSF5_41_BGHLV14-55	SRSF5_41_BGHLV14-56
RBP	SRSF5	SRSF5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	538	539

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-55	BGHLV14-56
Sample #
Sample Name	SRSF5-BGHLV14-55	SRSF5-BGHLV14-56
Sample_Name_Alias	SRSF5_41_BGHLV14-55	SRSF5_41_BGHLV14-56
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set2/A2.png	DNA_Library_LV13-14/set2/B2.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A10.png	RNA_Library_LV13-14-16/set1/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-55	BGHLV14-56
RBP	SRSF5	SRSF5
Batch_ID	BGHLV14	BGHLV14
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2222	2223

Sequencing Information

	BGHLV14-55	BGHLV14-56
Sample_ID	BGHLV14-55	BGHLV14-56
Sample Name	SRSF5_41_BGHLV14-55	SRSF5_41_BGHLV14-56
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	64,200,000	44,520,000
total_aligned_reads	59,751,724	41,477,484
unique_aligned_reads	56,368,452	39,183,150
percent_uniqueAligned	0.87801	0.88012
correlation_replicates	0.994390	0.994390
spikein_reads	245,050	180,898
percent_spikeins	0.00382	0.00406
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	864	865

Data Submission Information

	BGHLV14-55	BGHLV14-55
ENCODE_alias	brenton-graveley:SRSF5_BGHLV14	brenton-graveley:SRSF5-BGHLV14-HepG2
ENCODE_accession	ENCSR447UCG	ENCSR480QJF
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-55	BGHLV14-55
Sample Name	SRSF5_41_BGHLV14-55	SRSF5_41_BGHLV14-55
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2818	6971

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_41_BGHLV14-55_CAGATC_L007_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	864	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13830
SRSF5_41_BGHLV14-55_CAGATC_L007_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	864	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13892
SRSF5_41_BGHLV14-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	864					GRCh38	V40	SRSF5_41_BGHLV14-55_CAGATC_L007_R1_001.fastq.gz,SRSF5_41_BGHLV14-55_CAGATC_L007_R2_001.fastq.gz		ENCORE2	13954
SRSF5_41_BGHLV14-55_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	864					GRCh38	V40	SRSF5_41_BGHLV14-55/Aligned.sortedByCoord.out.bam		ENCORE2	14016
SRSF5_41_BGHLV14-55_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	864					GRCh38	V40	SRSF5_41_BGHLV14-55/Aligned.sortedByCoord.out.bam		ENCORE2	14078
SRSF5_41_BGHLV14-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	864					GRCh38	V40	SRSF5_41_BGHLV14-55/Aligned.sortedByCoord.out.bam		ENCORE2	14140
SRSF5_41_BGHLV14-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	864					GRCh38	V40	SRSF5_41_BGHLV14-55/Aligned.sortedByCoord.out.bam		ENCORE2	14202
SRSF5_41_BGHLV14-55_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	864					GRCh38	V40	SRSF5_41_BGHLV14-55_CAGATC_L007_R1_001.fastq.gz,SRSF5_41_BGHLV14-55_CAGATC_L007_R2_001.fastq.gz		ENCORE2	14264
SRSF5_41_BGHLV14-56_ACTTGA_L007_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	865	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13831
SRSF5_41_BGHLV14-56_ACTTGA_L007_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	865	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13893
SRSF5_41_BGHLV14-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	865					GRCh38	V40	SRSF5_41_BGHLV14-56_ACTTGA_L007_R1_001.fastq.gz,SRSF5_41_BGHLV14-56_ACTTGA_L007_R2_001.fastq.gz		ENCORE2	13955
SRSF5_41_BGHLV14-56_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	865					GRCh38	V40	SRSF5_41_BGHLV14-56/Aligned.sortedByCoord.out.bam		ENCORE2	14017
SRSF5_41_BGHLV14-56_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	865					GRCh38	V40	SRSF5_41_BGHLV14-56/Aligned.sortedByCoord.out.bam		ENCORE2	14079
SRSF5_41_BGHLV14-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	865					GRCh38	V40	SRSF5_41_BGHLV14-56/Aligned.sortedByCoord.out.bam		ENCORE2	14141
SRSF5_41_BGHLV14-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	865					GRCh38	V40	SRSF5_41_BGHLV14-56/Aligned.sortedByCoord.out.bam		ENCORE2	14203
SRSF5_41_BGHLV14-56_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	865					GRCh38	V40	SRSF5_41_BGHLV14-56_ACTTGA_L007_R1_001.fastq.gz,SRSF5_41_BGHLV14-56_ACTTGA_L007_R2_001.fastq.gz		ENCORE2	14265