TAF15 RNA-Seq in K562

General Information


RBP	TAF15
Cell_Line	K562
Method	shRNA
Exp_Name	TAF15-BGKLV08-K562
ENCODE_series_ID	ENCSR262UQP
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR611ZAL
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	TAF15-LV08-57
Rep2	TAF15-LV08-58
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	56.3
Rep2_qPCR	56.2
Rep1_WB	74.7
Rep2_WB	66.8
Antibody Cat#	A300-307A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB410IRI
Status	Released
Project	ENCODE3
ID	302

Experiment Information (Status: Released)

	BGKLV08-57	BGKLV08-57	BGKLV08-57	BGKLV08-57	BGKLV08-58	BGKLV08-58	BGKLV08-58	BGKLV08-58
idx	58	60	62	0	59	61	63	0
TRCN#_or_BGC#	TRCN0000020143	TRCN0000020143	TRCN0000020143	TRCN0000020143	TRCN0000020143	TRCN0000020143	TRCN0000020143	TRCN0000020143
shRNA_or_gRNA_sequence	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT
PAM
Name	TAF15	TAF15	TAF15	TAF15	TAF15	TAF15	TAF15	TAF15
Sample_ID	BGKLV08-57	BGKLV08-57	BGKLV08-57	BGKLV08-57	BGKLV08-58	BGKLV08-58	BGKLV08-58	BGKLV08-58
transduction_Date	4/4/2014	4/4/2014	4/4/2014	4/4/2014	4/4/2014	4/4/2014	4/4/2014	4/4/2014
days
RBP_name	TAF15	TAF15	TAF15	TAF15	TAF15	TAF15	TAF15	TAF15
qPCR_result	56.3	56.3	56.3	56.3	56.2	56.2	56.2	56.2
Ave_qPCR	56.3	56.3	56.3	56.3
RT-qPCR_primer-F	GGGAGGCAACAGTGTCATTT	GGGAGGCAACAGTGTCATTT	GGGAGGCAACAGTGTCATTT	GGGAGGCAACAGTGTCATTT
RT-qPCR_primer-R	ACCTCCACTTCCACCTCCTC	ACCTCCACTTCCACCTCCTC	ACCTCCACTTCCACCTCCTC	ACCTCCACTTCCACCTCCTC
protein_conc	2992	2992	2992	2992	2733	2733	2733	2733
WB_result	74.7	71.9	81.6	83.2	66.8	75.4	85.1	71.9
Ave_WB	70.7	73.7	83.4	77.5
WB_DONE_date	1/22/2016	3/14/2016	2/16/2016	5/8/2019
MW	62kDa	62kDa	68KD		WES	WES	wes
IP	1	1			1	1	fu's
antibody_Cat#	A300-307A	A300-308A	ab134916	MA3-078	A300-307A	A300-308A	ab134916	LOT# SA242977
Antibody DCC ID		ENCAB249IHJ	ENCAB228JAJ	ENCAB936CXL		ENCAB249IHJ	ENCAB228JAJ
submitted_to_DCC_date		3/18/2016	3/18/2016	4/17/2019
Rep1_TPM	75.4281782	0	75.4281782	0	0	0	0	0
Rep2_TPM	68.7389156	0	68.7389156	0	0	0	0	0
Action	Ready				Ready
Library_start_date	5/9/2014				5/9/2014
repeat_library
Note
ID	61	63	65	67	62	64	66	68

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TAF15	Product_ID: ab134916 Lot_ID: YJ030723S Source: Abcam Target Name: TAF15-human
TAF15	Product_ID: MA3-078 Lot_ID: SA242977 Source: Thermo Fisher Target Name: TAF15-human

Experiment Status

	BGKLV08-57	BGKLV08-58
Sample_ID	BGKLV08-57	BGKLV08-58
Sample Name	TAF15-LV08-57	TAF15-LV08-58
Sample Name	TAF15-LV08-57	TAF15-LV08-58
RBP	TAF15	TAF15
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	316	317

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-57	BGKLV08-58
Sample #
Sample Name	TAF15-BGKLV08-57	TAF15-BGKLV08-58
Sample_Name_Alias	TAF15-LV08-57	TAF15-LV08-58
Index Well Position	S01	S02
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/set5/C1.png	DNA_Library_LV08/set5/D1.png
RIN	9.3	9.0
libSample_RNA_Well	RNA_Library_LV08/set4/C1.png	RNA_Library_LV08/set4/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-57	BGKLV08-58
RBP	TAF15	TAF15
Batch_ID	BGKLV08	BGKLV08
WB_result	74.700	66.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1936	1937

Sequencing Information

	BGKLV08-57	BGKLV08-58
Sample_ID	BGKLV08-57	BGKLV08-58
Sample Name	TAF15-LV08-57	TAF15-LV08-58
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	47,150,000	43,460,000
total_aligned_reads	44,148,526	40,050,130
unique_aligned_reads	40,824,268	36,772,642
percent_uniqueAligned	0.86584	0.84613
correlation_replicates	0.977241	0.977241
spikein_reads	285,544	378,276
percent_spikeins	0.00606	0.00870
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	636	637

Data Submission Information

	BGKLV08-57	BGKLV08-57
ENCODE_alias	brenton-graveley:TAF15-LV08	brenton-graveley:TAF15-BGKLV08-K562
ENCODE_accession	ENCSR611ZAL	ENCSR262UQP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-57	BGKLV08-57
Sample Name	TAF15-LV08-57	TAF15-LV08-57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2707	7000

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
TAF15-LV08-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	636					GRCh38	V40	TAF15-LV08-57_ATCACG_L007_R1_001.fastq.gz,TAF15-LV08-57_ATCACG_L007_R2_001.fastq.gz		ENCORE2	12023
TAF15-LV08-57_ATCACG_L007_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	636	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	12079
TAF15-LV08-57_ATCACG_L007_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	636	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	12135
TAF15-LV08-57_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	636					GRCh38	V40	TAF15-LV08-57/Aligned.sortedByCoord.out.bam		ENCORE2	12191
TAF15-LV08-57_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	636					GRCh38	V40	TAF15-LV08-57/Aligned.sortedByCoord.out.bam		ENCORE2	12247
TAF15-LV08-57_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	636					GRCh38	V40	TAF15-LV08-57/Aligned.sortedByCoord.out.bam		ENCORE2	12303
TAF15-LV08-57_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	636					GRCh38	V40	TAF15-LV08-57/Aligned.sortedByCoord.out.bam		ENCORE2	12359
TAF15-LV08-57_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	636					GRCh38	V40	TAF15-LV08-57_ATCACG_L007_R1_001.fastq.gz,TAF15-LV08-57_ATCACG_L007_R2_001.fastq.gz		ENCORE2	13358
TAF15-LV08-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	637					GRCh38	V40	TAF15-LV08-58_CGATGT_L008_R1_001.fastq.gz,TAF15-LV08-58_CGATGT_L008_R2_001.fastq.gz		ENCORE2	12024
TAF15-LV08-58_CGATGT_L008_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	637	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	12080
TAF15-LV08-58_CGATGT_L008_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	637	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	12136
TAF15-LV08-58_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	637					GRCh38	V40	TAF15-LV08-58/Aligned.sortedByCoord.out.bam		ENCORE2	12192
TAF15-LV08-58_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	637					GRCh38	V40	TAF15-LV08-58/Aligned.sortedByCoord.out.bam		ENCORE2	12248
TAF15-LV08-58_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	637					GRCh38	V40	TAF15-LV08-58/Aligned.sortedByCoord.out.bam		ENCORE2	12304
TAF15-LV08-58_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	637					GRCh38	V40	TAF15-LV08-58/Aligned.sortedByCoord.out.bam		ENCORE2	12360
TAF15-LV08-58_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	637					GRCh38	V40	TAF15-LV08-58_CGATGT_L008_R1_001.fastq.gz,TAF15-LV08-58_CGATGT_L008_R2_001.fastq.gz		ENCORE2	13359