SRFBP1 RNA-Seq in K562

General Information


RBP	SRFBP1
Cell_Line	K562
Method	shRNA
Exp_Name	SRFBP1-BGKLV21-K562
ENCODE_series_ID	ENCSR895YWO
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR813NZP
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	SRFBP1_BGKLV21_59_17586
Rep2	SRFBP1_BGKLV21_60_17587
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	88.1
Rep2_qPCR	85.7
Rep1_WB	54.6
Rep2_WB	50.8
Antibody Cat#	A303-044A
Antibody Lot#	A303-044A
Antibody DCC ID	ENCAB974FYT
Status	Released
Project	ENCODE3
ID	519

Experiment Information (Status: Released)

	BGKLV21-59	BGKLV21-60
idx	330	331
TRCN#_or_BGC#	TRCN0000166862	TRCN0000166862
shRNA_or_gRNA_sequence	CCACTCTTTATCTGGATCTAA	CCACTCTTTATCTGGATCTAA
PAM
Name	SRFBP1_62	SRFBP1_62
Sample_ID	BGKLV21-59	BGKLV21-60
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	SRFBP1	SRFBP1
qPCR_result	88.1	85.7
Ave_qPCR	86.9
RT-qPCR_primer-F	aaatttcaaagaacaggctcca
RT-qPCR_primer-R	tgattcttgatctgaggctcatt
protein_conc	2869	2885
WB_result	54.6	50.8
Ave_WB	52.7
WB_DONE_date	7/11/2016
MW	49kDa
IP	1	1
antibody_Cat#	A303-044A	A303-044A
Antibody DCC ID	ENCAB974FYT	ENCAB974FYT
submitted_to_DCC_date	10/26/16
Rep1_TPM	7.53769737	0
Rep2_TPM	4.34893653	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	367	368

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SRFBP1	Product_ID: A303-044A Lot_ID: 1 Source: Bethyl Labs Target Name: SRFBP1-human

Experiment Status

	BGKLV21-59	BGKLV21-60
Sample_ID	BGKLV21-59	BGKLV21-60
Sample Name	SRFBP1_BGKLV21_59_17586	SRFBP1_BGKLV21_60_17587
Sample Name	SRFBP1_BGKLV21_59_17586	SRFBP1_BGKLV21_60_17587
RBP	SRFBP1	SRFBP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	772	773

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-59	BGKLV21-60
Sample #
Sample Name	SRFBP1-BGKLV21-59	SRFBP1-BGKLV21-60
Sample_Name_Alias	SRFBP1_BGKLV21_59_17586	SRFBP1_BGKLV21_60_17587
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/E8.png	DNA_Library_LV21-24/set1/F8.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E11.png	RNA_Library_LV19-21-24/set1/F11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-59	BGKLV21-60
RBP	SRFBP1	SRFBP1
Batch_ID	BGKLV21	BGKLV21
WB_result	54.600	50.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2458	2459

Sequencing Information

	BGKLV21-59	BGKLV21-60
Sample_ID	BGKLV21-59	BGKLV21-60
Sample Name	SRFBP1_BGKLV21_59_17586	SRFBP1_BGKLV21_60_17587
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	33,490,000	32,110,000
total_aligned_reads	30,467,382	27,137,574
unique_aligned_reads	27,915,662	24,842,496
percent_uniqueAligned	0.83355	0.77367
correlation_replicates	0.998458	0.998458
spikein_reads	190,070	129,070
percent_spikeins	0.00568	0.00402
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1064	1065

Data Submission Information

	BGKLV21-59	BGKLV21-59
ENCODE_alias	brenton-graveley:SRFBP1_BGKLV21	brenton-graveley:SRFBP1-BGKLV21-K562
ENCODE_accession	ENCSR813NZP	ENCSR895YWO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-59	BGKLV21-59
Sample Name	SRFBP1_BGKLV21_59_17586	SRFBP1_BGKLV21_59_17586
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2972	6962

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
SRFBP1_BGKLV21_59_17586_ACAGTG_L004_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1064	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15956
SRFBP1_BGKLV21_59_17586_ACAGTG_L004_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1064	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	16000
SRFBP1_BGKLV21_59_17586_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1064					GRCh38	V40	SRFBP1_BGKLV21_59_17586_ACAGTG_L004_R1_001.fastq.gz,SRFBP1_BGKLV21_59_17586_ACAGTG_L004_R2_001.fastq.gz		ENCORE2	16044
SRFBP1_BGKLV21_59_17586_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1064					GRCh38	V40	SRFBP1_BGKLV21_59_17586/Aligned.sortedByCoord.out.bam		ENCORE2	16088
SRFBP1_BGKLV21_59_17586_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1064					GRCh38	V40	SRFBP1_BGKLV21_59_17586/Aligned.sortedByCoord.out.bam		ENCORE2	16132
SRFBP1_BGKLV21_59_17586_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1064					GRCh38	V40	SRFBP1_BGKLV21_59_17586/Aligned.sortedByCoord.out.bam		ENCORE2	16176
SRFBP1_BGKLV21_59_17586_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1064					GRCh38	V40	SRFBP1_BGKLV21_59_17586/Aligned.sortedByCoord.out.bam		ENCORE2	16220
SRFBP1_BGKLV21_59_17586_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1064					GRCh38	V40	SRFBP1_BGKLV21_59_17586_ACAGTG_L004_R1_001.fastq.gz,SRFBP1_BGKLV21_59_17586_ACAGTG_L004_R2_001.fastq.gz		ENCORE2	16264
SRFBP1_BGKLV21_60_17587_GCCAAT_L004_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1065	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15957
SRFBP1_BGKLV21_60_17587_GCCAAT_L004_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1065	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	16001
SRFBP1_BGKLV21_60_17587_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1065					GRCh38	V40	SRFBP1_BGKLV21_60_17587_GCCAAT_L004_R1_001.fastq.gz,SRFBP1_BGKLV21_60_17587_GCCAAT_L004_R2_001.fastq.gz		ENCORE2	16045
SRFBP1_BGKLV21_60_17587_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1065					GRCh38	V40	SRFBP1_BGKLV21_60_17587/Aligned.sortedByCoord.out.bam		ENCORE2	16089
SRFBP1_BGKLV21_60_17587_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1065					GRCh38	V40	SRFBP1_BGKLV21_60_17587/Aligned.sortedByCoord.out.bam		ENCORE2	16133
SRFBP1_BGKLV21_60_17587_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1065					GRCh38	V40	SRFBP1_BGKLV21_60_17587/Aligned.sortedByCoord.out.bam		ENCORE2	16177
SRFBP1_BGKLV21_60_17587_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1065					GRCh38	V40	SRFBP1_BGKLV21_60_17587/Aligned.sortedByCoord.out.bam		ENCORE2	16221
SRFBP1_BGKLV21_60_17587_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1065					GRCh38	V40	SRFBP1_BGKLV21_60_17587_GCCAAT_L004_R1_001.fastq.gz,SRFBP1_BGKLV21_60_17587_GCCAAT_L004_R2_001.fastq.gz		ENCORE2	16265