SF3A3 RNA-Seq in K562

General Information


RBP	SF3A3
Cell_Line	K562
Method	shRNA
Exp_Name	SF3A3-BGKLV34-K562
ENCODE_series_ID	ENCSR692YFS
Batch_ID	BGKLV34
Pool ID	Pool-160912
Local_Set_Name	set34
ENCODE_KD_Exp_ID	ENCSR454KYR
ENCODE_CN_Exp_ID	ENCSR174OYC
Rep1	SF3A3_BGKLV34-37
Rep2	SF3A3_BGKLV34-38
CN1	NT_BGKLV34-1
CN2	NT_BGKLV34-2
Rep1_qPCR	90.3
Rep2_qPCR	82.4
Rep1_WB	66.5
Rep2_WB	60.8
Antibody Cat#	A302-506A
Antibody Lot#	GTX118225
Antibody DCC ID	ENCAB757ZZH
Status	Released
Project	ENCODE3
ID	725

Experiment Information (Status: Released)

	BGKLV34-37	BGKLV34-38
idx	700	701
TRCN#_or_BGC#	TRCN0000000056	TRCN0000000056
shRNA_or_gRNA_sequence	CGAGACACTGAAAGGAACAAA	CGAGACACTGAAAGGAACAAA
PAM
Name	SF3A3	SF3A3
Sample_ID	BGKLV34-37	BGKLV34-38
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	SF3A3	SF3A3
qPCR_result	90.3	82.4
Ave_qPCR	86.3
RT-qPCR_primer-F	aaagccttccagcgacact
RT-qPCR_primer-R	gcaaagtgagcagtgtttgg
protein_conc	3182	3278
WB_result	66.5	60.8
Ave_WB	63.6
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	3/8/2016
Rep1_TPM	117.310203	0
Rep2_TPM	88.0886456	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	787	788

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

	BGKLV34-37	BGKLV34-38
Sample_ID	BGKLV34-37	BGKLV34-38
Sample Name	SF3A3_BGKLV34-37	SF3A3_BGKLV34-38
Sample Name	SF3A3_BGKLV34-37	SF3A3_BGKLV34-38
RBP	SF3A3	SF3A3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1239	1240

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-37	BGKLV34-38
Sample #
Sample Name	SF3A3-BGKLV34-37	SF3A3-BGKLV34-38
Sample_Name_Alias	SF3A3_BGKLV34-37	SF3A3_BGKLV34-38
Index Well Position	S07	S08
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/G3.png	DNA_Library_LV33-34-25B-32/set1/H3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/E5.png	RNA_Library_LV32-33-34/set1/F5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV34-37	BGKLV34-38
RBP	SF3A3	SF3A3
Batch_ID	BGKLV34	BGKLV34
WB_result	66.500	60.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2924	2925

Sequencing Information

	BGKLV34-37	BGKLV34-38
Sample_ID	BGKLV34-37	BGKLV34-38
Sample Name	SF3A3_BGKLV34-37	SF3A3_BGKLV34-38
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set34	set34
total_reads	76,156,960	95,964,770
total_aligned_reads	65,728,110	83,928,548
unique_aligned_reads	60,029,234	76,690,526
percent_uniqueAligned	0.78823	0.79915
correlation_replicates	0.997880	0.997880
spikein_reads	294,940	389,800
percent_spikeins	0.00387	0.00406
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1573	1574

Data Submission Information

	BGKLV34-37	BGKLV34-37
ENCODE_alias	brenton-graveley:SF3A3_BGKLV34	brenton-graveley:SF3A3-BGKLV34-K562
ENCODE_accession	ENCSR454KYR	ENCSR692YFS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-37	BGKLV34-37
Sample Name	SF3A3_BGKLV34-37	SF3A3_BGKLV34-37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3159	6941

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_BGKLV34-37_CAGATC_L003_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1573	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21532
SF3A3_BGKLV34-37_CAGATC_L003_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1573	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21552
SF3A3_BGKLV34-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1573					GRCh38	V40	SF3A3_BGKLV34-37_CAGATC_L003_001.R1.fastq.gz,SF3A3_BGKLV34-37_CAGATC_L003_001.R2.fastq.gz		ENCORE2	21572
SF3A3_BGKLV34-37_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1573					GRCh38	V40	SF3A3_BGKLV34-37/Aligned.sortedByCoord.out.bam		ENCORE2	21592
SF3A3_BGKLV34-37_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1573					GRCh38	V40	SF3A3_BGKLV34-37/Aligned.sortedByCoord.out.bam		ENCORE2	21612
SF3A3_BGKLV34-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1573					GRCh38	V40	SF3A3_BGKLV34-37/Aligned.sortedByCoord.out.bam		ENCORE2	21632
SF3A3_BGKLV34-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1573					GRCh38	V40	SF3A3_BGKLV34-37/Aligned.sortedByCoord.out.bam		ENCORE2	21652
SF3A3_BGKLV34-37_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1573					GRCh38	V40	SF3A3_BGKLV34-37_CAGATC_L003_001.R1.fastq.gz,SF3A3_BGKLV34-37_CAGATC_L003_001.R2.fastq.gz		ENCORE2	21672
SF3A3_BGKLV34-38_ACTTGA_L003_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1574	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21533
SF3A3_BGKLV34-38_ACTTGA_L003_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1574	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21553
SF3A3_BGKLV34-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1574					GRCh38	V40	SF3A3_BGKLV34-38_ACTTGA_L003_001.R1.fastq.gz,SF3A3_BGKLV34-38_ACTTGA_L003_001.R2.fastq.gz		ENCORE2	21573
SF3A3_BGKLV34-38_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1574					GRCh38	V40	SF3A3_BGKLV34-38/Aligned.sortedByCoord.out.bam		ENCORE2	21593
SF3A3_BGKLV34-38_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1574					GRCh38	V40	SF3A3_BGKLV34-38/Aligned.sortedByCoord.out.bam		ENCORE2	21613
SF3A3_BGKLV34-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1574					GRCh38	V40	SF3A3_BGKLV34-38/Aligned.sortedByCoord.out.bam		ENCORE2	21633
SF3A3_BGKLV34-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1574					GRCh38	V40	SF3A3_BGKLV34-38/Aligned.sortedByCoord.out.bam		ENCORE2	21653
SF3A3_BGKLV34-38_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1574					GRCh38	V40	SF3A3_BGKLV34-38_ACTTGA_L003_001.R1.fastq.gz,SF3A3_BGKLV34-38_ACTTGA_L003_001.R2.fastq.gz		ENCORE2	21673