SF3A3 RNA-Seq in HepG2

General Information


RBP	SF3A3
Cell_Line	HepG2
Method	shRNA
Exp_Name	SF3A3-BGHLV33-HepG2
ENCODE_series_ID	ENCSR415VVG
Batch_ID	BGHLV33
Pool ID	Pool-160912
Local_Set_Name	set33
ENCODE_KD_Exp_ID	ENCSR374NMJ
ENCODE_CN_Exp_ID	ENCSR691IVR
Rep1	SF3A3_BGHLV33-29
Rep2	SF3A3_BGHLV33-30
CN1	NT_BGHLV33-1
CN2	NT_BGHLV33-2
Rep1_qPCR	6.8
Rep2_qPCR	0.0
Rep1_WB	56.0
Rep2_WB	50.3
Antibody Cat#	A302-506A
Antibody Lot#	GTX118225
Antibody DCC ID	ENCAB757ZZH
Status	Released
Project	ENCODE3
ID	716

Experiment Information (Status: Released)

	BGHLV33-29	BGHLV33-30
idx	837	838
TRCN#_or_BGC#	TRCN0000000056	TRCN0000000056
shRNA_or_gRNA_sequence	CGAGACACTGAAAGGAACAAA	CGAGACACTGAAAGGAACAAA
PAM
Name	SF3A3	SF3A3
Sample_ID	BGHLV33-29	BGHLV33-30
transduction_Date	11/17/2015	11/17/2015
days
RBP_name	SF3A3	SF3A3
qPCR_result	6.8	0.0
Ave_qPCR	3.4
RT-qPCR_primer-F	catgaggtgtttgggcatc
RT-qPCR_primer-R	atttcagtttggcccacaag
protein_conc	3345	2723
WB_result	56.0	50.3
Ave_WB	53.2
WB_DONE_date	1/19/2016
MW	59kDa	WES
IP	1	1
antibody_Cat#	A302-506A	GTX118225
Antibody DCC ID	ENCAB757ZZH	ENCAB757ZZH
submitted_to_DCC_date	10/26/16
Rep1_TPM	34.2	0
Rep2_TPM	33.3	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	2926	2927

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF3A3	Product_ID: A302-506A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3A3-human

Experiment Status

	BGHLV33-29	BGHLV33-30
Sample_ID	BGHLV33-29	BGHLV33-30
Sample Name	SF3A3_BGHLV33-29	SF3A3_BGHLV33-30
Sample Name	SF3A3_BGHLV33-29	SF3A3_BGHLV33-30
RBP	SF3A3	SF3A3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1219	1220

Library-Prep
Sequencing

Library-Prep Information

	BGHLV33-29	BGHLV33-30
Sample #
Sample Name	SF3A3-BGHLV33-29	SF3A3-BGHLV33-30
Sample_Name_Alias	SF3A3_BGHLV33-29	SF3A3_BGHLV33-30
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/C1.png	DNA_Library_LV33-34-25B-32/set1/D1.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/A3.png	RNA_Library_LV32-33-34/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV33-29	BGHLV33-30
RBP	SF3A3	SF3A3
Batch_ID	BGHLV33	BGHLV33
WB_result	56.000	50.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2904	2905

Sequencing Information

	BGHLV33-29	BGHLV33-30
Sample_ID	BGHLV33-29	BGHLV33-30
Sample Name	SF3A3_BGHLV33-29	SF3A3_BGHLV33-30
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set33	set33
total_reads	131,858,438	73,869,600
total_aligned_reads	107,592,422	60,057,644
unique_aligned_reads	100,708,476	56,341,194
percent_uniqueAligned	0.76376	0.76271
correlation_replicates	0.994672	0.994672
spikein_reads	468,088	205,302
percent_spikeins	0.00355	0.00278
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1553	1554

Data Submission Information

	BGHLV33-29	BGHLV33-29
ENCODE_alias	brenton-graveley:SF3A3_BGHLV33	brenton-graveley:SF3A3-BGHLV33-HepG2
ENCODE_accession	ENCSR374NMJ	ENCSR415VVG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV33-29	BGHLV33-29
Sample Name	SF3A3_BGHLV33-29	SF3A3_BGHLV33-29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3149	6940

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
SF3A3_BGHLV33-29_GGCTAC_L001_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1553	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21428
SF3A3_BGHLV33-29_GGCTAC_L001_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1553	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21440
SF3A3_BGHLV33-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1553					GRCh38	V40	SF3A3_BGHLV33-29_GGCTAC_L001_001.R1.fastq.gz,SF3A3_BGHLV33-29_GGCTAC_L001_001.R2.fastq.gz		ENCORE2	21452
SF3A3_BGHLV33-29_Signal.Unique.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1553					GRCh38	V40	SF3A3_BGHLV33-29/Aligned.sortedByCoord.out.bam		ENCORE2	21464
SF3A3_BGHLV33-29_Signal.Unique.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1553					GRCh38	V40	SF3A3_BGHLV33-29/Aligned.sortedByCoord.out.bam		ENCORE2	21476
SF3A3_BGHLV33-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1553					GRCh38	V40	SF3A3_BGHLV33-29/Aligned.sortedByCoord.out.bam		ENCORE2	21488
SF3A3_BGHLV33-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1553					GRCh38	V40	SF3A3_BGHLV33-29/Aligned.sortedByCoord.out.bam		ENCORE2	21500
SF3A3_BGHLV33-29_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1553					GRCh38	V40	SF3A3_BGHLV33-29_GGCTAC_L001_001.R1.fastq.gz,SF3A3_BGHLV33-29_GGCTAC_L001_001.R2.fastq.gz		ENCORE2	21512
SF3A3_BGHLV33-30_CTTGTA_L001_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1554	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21429
SF3A3_BGHLV33-30_CTTGTA_L001_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1554	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21441
SF3A3_BGHLV33-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1554					GRCh38	V40	SF3A3_BGHLV33-30_CTTGTA_L001_001.R1.fastq.gz,SF3A3_BGHLV33-30_CTTGTA_L001_001.R2.fastq.gz		ENCORE2	21453
SF3A3_BGHLV33-30_Signal.Unique.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1554					GRCh38	V40	SF3A3_BGHLV33-30/Aligned.sortedByCoord.out.bam		ENCORE2	21465
SF3A3_BGHLV33-30_Signal.Unique.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1554					GRCh38	V40	SF3A3_BGHLV33-30/Aligned.sortedByCoord.out.bam		ENCORE2	21477
SF3A3_BGHLV33-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1554					GRCh38	V40	SF3A3_BGHLV33-30/Aligned.sortedByCoord.out.bam		ENCORE2	21489
SF3A3_BGHLV33-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1554					GRCh38	V40	SF3A3_BGHLV33-30/Aligned.sortedByCoord.out.bam		ENCORE2	21501
SF3A3_BGHLV33-30_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1554					GRCh38	V40	SF3A3_BGHLV33-30_CTTGTA_L001_001.R1.fastq.gz,SF3A3_BGHLV33-30_CTTGTA_L001_001.R2.fastq.gz		ENCORE2	21513