SRSF3 RNA-Seq in HepG2

General Information


RBP	SRSF3
Cell_Line	HepG2
Method	shRNA
Exp_Name	SRSF3-BGHLV35-HepG2
ENCODE_series_ID	ENCSR889URB
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR376FGR
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	SRSF3_BGHLV35-49
Rep2	SRSF3_BGHLV35-50
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	81.1
Rep2_qPCR	81.2
Rep1_WB	67.4
Rep2_WB	70.3
Antibody Cat#	RN080PW
Antibody Lot#	RN080PW
Antibody DCC ID	ENCAB701PQV
Status	Released
Project	ENCODE3
ID	740

Experiment Information (Status: Released)

	BGHLV35-49	BGHLV35-49	BGHLV35-50	BGHLV35-50
idx	905	0	906	0
TRCN#_or_BGC#	TRCN0000001224	TRCN0000001224	TRCN0000001224	TRCN0000001224
shRNA_or_gRNA_sequence	CGAGAGCTAGATGGAAGAACA		CGAGAGCTAGATGGAAGAACA
PAM
Name	SRSF3	SRSF3	SRSF3	SRSF3
Sample_ID	BGHLV35-49	BGHLV35-49	BGHLV35-50	BGHLV35-50
transduction_Date	4/29/16	4/29/16	4/29/16	4/29/16
days
RBP_name	SRSF3	SRSF3	SRSF3	SRSF3
qPCR_result	81.1	81.1	81.2	81.2
Ave_qPCR	81.1	81.1
RT-qPCR_primer-F	GTAGAAATCGTGGCCCACCT	GTAGAAATCGTGGCCCACCT
RT-qPCR_primer-R	GCAGATTCAGAGGGTGGTGA	GCAGATTCAGAGGGTGGTGA
protein_conc	2726	2726	3817	3817
WB_result	67.4	75.5	70.3	67.3
Ave_WB	68.8	71.4
WB_DONE_date	5/23/16	5/7/19
MW	20kDa	19KD
IP			FU'S
antibody_Cat#	RN080PW	33-4200	RN080PW	LOT# TE268372
Antibody DCC ID	ENCAB701PQV	ENCAB889VRL
submitted_to_DCC_date	10/26/16	4/17/19
Rep1_TPM	39.1	0	39.1	0
Rep2_TPM	34.6	0	34.6	0
Action
Library_start_date	07/18/16		07/18/16
repeat_library
Note
ID	2994	2996	2995	2997

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRSF3	Product_ID: RN080PW Lot_ID: 1 Source: MBLI Target Name: SRSF3-human
SRSF3	Product_ID: 33-4200 Lot_ID: TE268372 Source: Thermo Fisher Target Name: SRSF3-human

Experiment Status

	BGHLV35-49	BGHLV35-50
Sample_ID	BGHLV35-49	BGHLV35-50
Sample Name	SRSF3_BGHLV35-49	SRSF3_BGHLV35-50
Sample Name	SRSF3_BGHLV35-49	SRSF3_BGHLV35-50
RBP	SRSF3	SRSF3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1271	1272

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-49	BGHLV35-50
Sample #
Sample Name	SRSF3-BGHLV35-49	SRSF3-BGHLV35-50
Sample_Name_Alias	SRSF3_BGHLV35-49	SRSF3_BGHLV35-50
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set1/A4.png	DNA_Library_LV35/set1/B4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/G3.png	RNA_Library_LV35_LV36/set1/H3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-49	BGHLV35-50
RBP	SRSF3	SRSF3
Batch_ID	BGHLV35	BGHLV35
WB_result	67.400	70.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2956	2957

Sequencing Information

	BGHLV35-49	BGHLV35-50
Sample_ID	BGHLV35-49	BGHLV35-50
Sample Name	SRSF3_BGHLV35-49	SRSF3_BGHLV35-50
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	68,786,120	82,821,184
total_aligned_reads	54,566,940	65,847,918
unique_aligned_reads	51,011,238	61,529,710
percent_uniqueAligned	0.74159	0.74292
correlation_replicates	0.998651	0.998651
spikein_reads	119,414	136,300
percent_spikeins	0.00174	0.00165
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1605	1606

Data Submission Information

	BGHLV35-49	BGHLV35-49
ENCODE_alias	brenton-graveley:SRSF3_BGHLV35	brenton-graveley:SRSF3-BGHLV35-HepG2
ENCODE_accession	ENCSR376FGR	ENCSR889URB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-49	BGHLV35-49
Sample Name	SRSF3_BGHLV35-49	SRSF3_BGHLV35-49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3175	6968

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
SRSF3_BGHLV35-49_ATCACG_L007_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1605	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21704
SRSF3_BGHLV35-49_ATCACG_L007_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1605	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21730
SRSF3_BGHLV35-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1605					GRCh38	V40	SRSF3_BGHLV35-49_ATCACG_L007_001.R1.fastq.gz,SRSF3_BGHLV35-49_ATCACG_L007_001.R2.fastq.gz		ENCORE2	21756
SRSF3_BGHLV35-49_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1605					GRCh38	V40	SRSF3_BGHLV35-49/Aligned.sortedByCoord.out.bam		ENCORE2	21782
SRSF3_BGHLV35-49_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1605					GRCh38	V40	SRSF3_BGHLV35-49/Aligned.sortedByCoord.out.bam		ENCORE2	21808
SRSF3_BGHLV35-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1605					GRCh38	V40	SRSF3_BGHLV35-49/Aligned.sortedByCoord.out.bam		ENCORE2	21834
SRSF3_BGHLV35-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1605					GRCh38	V40	SRSF3_BGHLV35-49/Aligned.sortedByCoord.out.bam		ENCORE2	21860
SRSF3_BGHLV35-49_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1605					GRCh38	V40	SRSF3_BGHLV35-49_ATCACG_L007_001.R1.fastq.gz,SRSF3_BGHLV35-49_ATCACG_L007_001.R2.fastq.gz		ENCORE2	21886
SRSF3_BGHLV35-50_CGATGT_L007_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1606	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21705
SRSF3_BGHLV35-50_CGATGT_L007_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1606	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21731
SRSF3_BGHLV35-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1606					GRCh38	V40	SRSF3_BGHLV35-50_CGATGT_L007_001.R1.fastq.gz,SRSF3_BGHLV35-50_CGATGT_L007_001.R2.fastq.gz		ENCORE2	21757
SRSF3_BGHLV35-50_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1606					GRCh38	V40	SRSF3_BGHLV35-50/Aligned.sortedByCoord.out.bam		ENCORE2	21783
SRSF3_BGHLV35-50_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1606					GRCh38	V40	SRSF3_BGHLV35-50/Aligned.sortedByCoord.out.bam		ENCORE2	21809
SRSF3_BGHLV35-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1606					GRCh38	V40	SRSF3_BGHLV35-50/Aligned.sortedByCoord.out.bam		ENCORE2	21835
SRSF3_BGHLV35-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1606					GRCh38	V40	SRSF3_BGHLV35-50/Aligned.sortedByCoord.out.bam		ENCORE2	21861
SRSF3_BGHLV35-50_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1606					GRCh38	V40	SRSF3_BGHLV35-50_CGATGT_L007_001.R1.fastq.gz,SRSF3_BGHLV35-50_CGATGT_L007_001.R2.fastq.gz		ENCORE2	21887