SF3B4 RNA-Seq in K562

General Information


RBP	SF3B4
Cell_Line	K562
Method	shRNA
Exp_Name	SF3B4-BGKLV08-K562
ENCODE_series_ID	ENCSR545JRZ
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR081XRA
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	SF3B4-LV08-51
Rep2	SF3B4-LV08-52
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	64.8
Rep2_qPCR	68.5
Rep1_WB	70.6
Rep2_WB	75.6
Antibody Cat#	A303-950A
Antibody Lot#	A303-950A
Antibody DCC ID	ENCAB647CFU
Status	Released
Project	ENCODE3
ID	301

Experiment Information (Status: Released)

	BGKLV08-51	BGKLV08-52
idx	52	53
TRCN#_or_BGC#	TRCN0000000039	TRCN0000000039
shRNA_or_gRNA_sequence	CCGTCCTATCACCGTATCTTA	CCGTCCTATCACCGTATCTTA
PAM
Name	SF3B4	SF3B4
Sample_ID	BGKLV08-51	BGKLV08-52
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	SF3B4	SF3B4
qPCR_result	64.8	68.5
Ave_qPCR	66.6
RT-qPCR_primer-F	acccacatgccaaaggatag
RT-qPCR_primer-R	tggcatagtcagcatcttcc
protein_conc	2677	2710
WB_result	70.6	75.6
Ave_WB	73.1
WB_DONE_date	3/2/2016
MW	44kDa
IP	1	1
antibody_Cat#	A303-950A	A303-950A
Antibody DCC ID	ENCAB647CFU	ENCAB647CFU
submitted_to_DCC_date	3/8/2016
Rep1_TPM	18.800435	0
Rep2_TPM	12.4121784	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note
ID	55	56

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF3B4	Product_ID: A303-950A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3B4-human

Experiment Status

	BGKLV08-51	BGKLV08-52
Sample_ID	BGKLV08-51	BGKLV08-52
Sample Name	SF3B4-LV08-51	SF3B4-LV08-52
Sample Name	SF3B4-LV08-51	SF3B4-LV08-52
RBP	SF3B4	SF3B4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	314	315

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-51	BGKLV08-52
Sample #
Sample Name	SF3B4-BGKLV08-51	SF3B4-BGKLV08-52
Sample_Name_Alias	SF3B4-LV08-51	SF3B4-LV08-52
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set4/H2.png	DNA_Library_LV08/set5/B1.png
RIN	8.8	9.1
libSample_RNA_Well	RNA_Library_LV08/set4/A1.png	RNA_Library_LV08/set4/B1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-51	BGKLV08-52
RBP	SF3B4	SF3B4
Batch_ID	BGKLV08	BGKLV08
WB_result	70.600	75.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1934	1935

Sequencing Information

	BGKLV08-51	BGKLV08-52
Sample_ID	BGKLV08-51	BGKLV08-52
Sample Name	SF3B4-LV08-51	SF3B4-LV08-52
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	46,130,000	52,380,000
total_aligned_reads	41,512,578	46,397,868
unique_aligned_reads	37,882,132	42,395,254
percent_uniqueAligned	0.82120	0.80938
correlation_replicates	0.999167	0.999167
spikein_reads	291,560	366,970
percent_spikeins	0.00632	0.00701
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	634	635

Data Submission Information

	BGKLV08-51	BGKLV08-51
ENCODE_alias	brenton-graveley:SF3B4-LV08	brenton-graveley:SF3B4-BGKLV08-K562
ENCODE_accession	ENCSR081XRA	ENCSR545JRZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-51	BGKLV08-51
Sample Name	SF3B4-LV08-51	SF3B4-LV08-51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2706	6945

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
SF3B4-LV08-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	634					GRCh38	V40	SF3B4-LV08-51_ACTGAT_L007_R1_001.fastq.gz,SF3B4-LV08-51_ACTGAT_L007_R2_001.fastq.gz		ENCORE2	12021
SF3B4-LV08-51_ACTGAT_L007_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	634	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12077
SF3B4-LV08-51_ACTGAT_L007_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	634	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12133
SF3B4-LV08-51_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	634					GRCh38	V40	SF3B4-LV08-51/Aligned.sortedByCoord.out.bam		ENCORE2	12189
SF3B4-LV08-51_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	634					GRCh38	V40	SF3B4-LV08-51/Aligned.sortedByCoord.out.bam		ENCORE2	12245
SF3B4-LV08-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	634					GRCh38	V40	SF3B4-LV08-51/Aligned.sortedByCoord.out.bam		ENCORE2	12301
SF3B4-LV08-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	634					GRCh38	V40	SF3B4-LV08-51/Aligned.sortedByCoord.out.bam		ENCORE2	12357
SF3B4-LV08-51_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	634					GRCh38	V40	SF3B4-LV08-51_ACTGAT_L007_R1_001.fastq.gz,SF3B4-LV08-51_ACTGAT_L007_R2_001.fastq.gz		ENCORE2	13356
SF3B4-LV08-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	635					GRCh38	V40	SF3B4-LV08-52_ATTCCT_L007_R1_001.fastq.gz,SF3B4-LV08-52_ATTCCT_L007_R2_001.fastq.gz		ENCORE2	12022
SF3B4-LV08-52_ATTCCT_L007_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	635	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12078
SF3B4-LV08-52_ATTCCT_L007_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	635	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12134
SF3B4-LV08-52_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	635					GRCh38	V40	SF3B4-LV08-52/Aligned.sortedByCoord.out.bam		ENCORE2	12190
SF3B4-LV08-52_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	635					GRCh38	V40	SF3B4-LV08-52/Aligned.sortedByCoord.out.bam		ENCORE2	12246
SF3B4-LV08-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	635					GRCh38	V40	SF3B4-LV08-52/Aligned.sortedByCoord.out.bam		ENCORE2	12302
SF3B4-LV08-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	635					GRCh38	V40	SF3B4-LV08-52/Aligned.sortedByCoord.out.bam		ENCORE2	12358
SF3B4-LV08-52_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	635					GRCh38	V40	SF3B4-LV08-52_ATTCCT_L007_R1_001.fastq.gz,SF3B4-LV08-52_ATTCCT_L007_R2_001.fastq.gz		ENCORE2	13357