SF3B1 RNA-Seq in K562

General Information


RBP	SF3B1
Cell_Line	K562
Method	shRNA
Exp_Name	SF3B1-BGKLV36-K562
ENCODE_series_ID	ENCSR406ZEB
Batch_ID	BGKLV36
Pool ID	Pool-161129
Local_Set_Name	set36
ENCODE_KD_Exp_ID	ENCSR047QHX
ENCODE_CN_Exp_ID	ENCSR424QCW
Rep1	SF3B1_BGKLV36-43
Rep2	SF3B1_BGKLV36-44
CN1	NT_BGKLV36-1
CN2	NT_BGKLV36-2
Rep1_qPCR	2.9
Rep2_qPCR	25.4
Rep1_WB	39.1
Rep2_WB	46.9
Antibody Cat#	ab66774
Antibody Lot#	GR216813-1
Antibody DCC ID	ENCAB022ALQ
Status	Archived
Project	ENCODE3
ID	749

Experiment Information (Status: Released)

	BGKLV36-43	BGKLV36-44
idx	766	767
TRCN#_or_BGC#	TRCN0000000077	TRCN0000000077
shRNA_or_gRNA_sequence	CAACTCCTTATGGTATCGAAT	CAACTCCTTATGGTATCGAAT
PAM
Name	SF3B1	SF3B1
Sample_ID	BGKLV36-43	BGKLV36-44
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	SF3B1	SF3B1
qPCR_result	2.9	25.4
Ave_qPCR	14.2
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3937	3943
WB_result	39.1	46.9
Ave_WB	43.0
WB_DONE_date	6/9/16	wes
MW	146kDa
IP
antibody_Cat#	ab66774	ab66774
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	07/28/16	07/28/16
repeat_library
Note
ID	859	860

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV36-43	BGKLV36-44
Sample_ID	BGKLV36-43	BGKLV36-44
Sample Name	SF3B1_BGKLV36-43	SF3B1_BGKLV36-44
Sample Name	SF3B1_BGKLV36-43	SF3B1_BGKLV36-44
RBP	SF3B1	SF3B1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1291	1292

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-43	BGKLV36-44
Sample #
Sample Name	SF3B1-BGKLV36-43	SF3B1-BGKLV36-44
Sample_Name_Alias	SF3B1_BGKLV36-43	SF3B1_BGKLV36-44
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-28	2016-07-28
Lib_ID	Lib-160728	Lib-160728
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV36/set1/G3.png	DNA_Library_LV36/set1/H3.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV37_38/set3/D1.png	RNA_Library_LV35_LV36/set1/B7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV36-43	BGKLV36-44
RBP	SF3B1	SF3B1
Batch_ID	BGKLV36	BGKLV36
WB_result	39.100	46.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2976	2977

Sequencing Information

	BGKLV36-43	BGKLV36-44
Sample_ID	BGKLV36-43	BGKLV36-44
Sample Name	SF3B1_BGKLV36-43	SF3B1_BGKLV36-44
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set36	set36
total_reads	68,523,458	74,001,070
total_aligned_reads	61,062,316	63,572,178
unique_aligned_reads	55,700,480	58,140,484
percent_uniqueAligned	0.81287	0.78567
correlation_replicates	0.991729	0.991729
spikein_reads	124,370	131,782
percent_spikeins	0.00181	0.00178
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1625	1626

Data Submission Information

	BGKLV36-43	BGKLV36-43
ENCODE_alias	brenton-graveley:SF3B1_BGKLV36	brenton-graveley:SF3B1-BGKLV36-K562
ENCODE_accession	ENCSR047QHX	ENCSR406ZEB
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-43	BGKLV36-43
Sample Name	SF3B1_BGKLV36-43	SF3B1_BGKLV36-43
Selected	Yes	No
Status	Released	Archived
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3185	6943

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
SF3B1_BGKLV36-43_CAGATC_L002_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1625	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21906
SF3B1_BGKLV36-43_CAGATC_L002_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1625	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21924
SF3B1_BGKLV36-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1625					GRCh38	V40	SF3B1_BGKLV36-43_CAGATC_L002_001.R1.fastq.gz,SF3B1_BGKLV36-43_CAGATC_L002_001.R2.fastq.gz		ENCORE2	21942
SF3B1_BGKLV36-43_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1625					GRCh38	V40	SF3B1_BGKLV36-43/Aligned.sortedByCoord.out.bam		ENCORE2	21960
SF3B1_BGKLV36-43_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1625					GRCh38	V40	SF3B1_BGKLV36-43/Aligned.sortedByCoord.out.bam		ENCORE2	21978
SF3B1_BGKLV36-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1625					GRCh38	V40	SF3B1_BGKLV36-43/Aligned.sortedByCoord.out.bam		ENCORE2	21996
SF3B1_BGKLV36-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1625					GRCh38	V40	SF3B1_BGKLV36-43/Aligned.sortedByCoord.out.bam		ENCORE2	22014
SF3B1_BGKLV36-43_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1625					GRCh38	V40	SF3B1_BGKLV36-43_CAGATC_L002_001.R1.fastq.gz,SF3B1_BGKLV36-43_CAGATC_L002_001.R2.fastq.gz		ENCORE2	22032
SF3B1_BGKLV36-44_ACTTGA_L002_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1626	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21907
SF3B1_BGKLV36-44_ACTTGA_L002_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1626	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21925
SF3B1_BGKLV36-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1626					GRCh38	V40	SF3B1_BGKLV36-44_ACTTGA_L002_001.R1.fastq.gz,SF3B1_BGKLV36-44_ACTTGA_L002_001.R2.fastq.gz		ENCORE2	21943
SF3B1_BGKLV36-44_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1626					GRCh38	V40	SF3B1_BGKLV36-44/Aligned.sortedByCoord.out.bam		ENCORE2	21961
SF3B1_BGKLV36-44_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1626					GRCh38	V40	SF3B1_BGKLV36-44/Aligned.sortedByCoord.out.bam		ENCORE2	21979
SF3B1_BGKLV36-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1626					GRCh38	V40	SF3B1_BGKLV36-44/Aligned.sortedByCoord.out.bam		ENCORE2	21997
SF3B1_BGKLV36-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1626					GRCh38	V40	SF3B1_BGKLV36-44/Aligned.sortedByCoord.out.bam		ENCORE2	22015
SF3B1_BGKLV36-44_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1626					GRCh38	V40	SF3B1_BGKLV36-44_ACTTGA_L002_001.R1.fastq.gz,SF3B1_BGKLV36-44_ACTTGA_L002_001.R2.fastq.gz		ENCORE2	22033