TRA2A RNA-Seq in K562

General Information


RBP	TRA2A
Cell_Line	K562
Method	shRNA
Exp_Name	TRA2A-BGKLV11-K562
ENCODE_series_ID	ENCSR352VCT
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR916WOI
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	TRA2A-LV11-63
Rep2	TRA2A-LV11-64
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	53.2
Rep2_qPCR	61.8
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	A303-779A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB683DWW
Status	Archived
Project	ENCODE3
ID	328

Experiment Information (Status: Released)

	BGKLV11-63	BGKLV11-64
idx	132	133
TRCN#_or_BGC#	TRCN0000074548	TRCN0000074548
shRNA_or_gRNA_sequence	CCCAATGTTATGTTATGCTTT	CCCAATGTTATGTTATGCTTT
PAM
Name	TRA2A	TRA2A
Sample_ID	BGKLV11-63	BGKLV11-64
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	TRA2A	TRA2A
qPCR_result	53.2	61.8
Ave_qPCR	57.5
RT-qPCR_primer-F	CGATCACCTTCTCCTTATTATAGTCG
RT-qPCR_primer-R	TCCTTAATTGCAACCATTCC
protein_conc	2020	2083
WB_result	0.0	0.0
Ave_WB	0.0
WB_DONE_date	5/27/2015
MW
IP	1	1
antibody_Cat#	A303-779A	A303-779A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	28.661046	0
Rep2_TPM	21.7838373	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	147	148

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV11-63	BGKLV11-64
Sample_ID	BGKLV11-63	BGKLV11-64
Sample Name	TRA2A-LV11-63	TRA2A-LV11-64
Sample Name	TRA2A-LV11-63	TRA2A-LV11-64
RBP	TRA2A	TRA2A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	370	371

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-63	BGKLV11-64
Sample #
Sample Name	TRA2A-BGKLV11-63	TRA2A-BGKLV11-64
Sample_Name_Alias	TRA2A-LV11-63	TRA2A-LV11-64
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set4/C1.png	DNA_Library_LV11/set4/D1.png
RIN	8.9	9.2
libSample_RNA_Well	RNA_Library_LV11/set1/G6.png	RNA_Library_LV11/set1/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-63	BGKLV11-64
RBP	TRA2A	TRA2A
Batch_ID	BGKLV11	BGKLV11
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1992	1993

Sequencing Information

	BGKLV11-63	BGKLV11-64
Sample_ID	BGKLV11-63	BGKLV11-64
Sample Name	TRA2A-LV11-63	TRA2A-LV11-64
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	61,520,000	51,010,000
total_aligned_reads	50,292,380	42,640,318
unique_aligned_reads	46,049,342	39,078,280
percent_uniqueAligned	0.74853	0.76609
correlation_replicates	0.998877	0.998877
spikein_reads	247,292	275,918
percent_spikeins	0.00402	0.00541
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	692	693

Data Submission Information

	BGKLV11-63	BGKLV11-63
ENCODE_alias	brenton-graveley:TRA2A-LV11	brenton-graveley:TRA2A-BGKLV11-K562
ENCODE_accession	ENCSR916WOI	ENCSR352VCT
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-63	BGKLV11-63
Sample Name	TRA2A-LV11-63	TRA2A-LV11-63
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2734	7012

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
TRA2A-LV11-63_ACTGAT_L008_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	692	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12413
TRA2A-LV11-63_ACTGAT_L008_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	692	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12461
TRA2A-LV11-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	692					GRCh38	V40	TRA2A-LV11-63_ACTGAT_L008_R1_001.fastq.gz,TRA2A-LV11-63_ACTGAT_L008_R2_001.fastq.gz		ENCORE2	12509
TRA2A-LV11-63_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	692					GRCh38	V40	TRA2A-LV11-63/Aligned.sortedByCoord.out.bam		ENCORE2	12557
TRA2A-LV11-63_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	692					GRCh38	V40	TRA2A-LV11-63/Aligned.sortedByCoord.out.bam		ENCORE2	12605
TRA2A-LV11-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	692					GRCh38	V40	TRA2A-LV11-63/Aligned.sortedByCoord.out.bam		ENCORE2	12653
TRA2A-LV11-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	692					GRCh38	V40	TRA2A-LV11-63/Aligned.sortedByCoord.out.bam		ENCORE2	12701
TRA2A-LV11-63_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	692					GRCh38	V40	TRA2A-LV11-63_ACTGAT_L008_R1_001.fastq.gz,TRA2A-LV11-63_ACTGAT_L008_R2_001.fastq.gz		ENCORE2	12749
TRA2A-LV11-64_ATTCCT_L008_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	693	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12414
TRA2A-LV11-64_ATTCCT_L008_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	693	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12462
TRA2A-LV11-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	693					GRCh38	V40	TRA2A-LV11-64_ATTCCT_L008_R1_001.fastq.gz,TRA2A-LV11-64_ATTCCT_L008_R2_001.fastq.gz		ENCORE2	12510
TRA2A-LV11-64_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	693					GRCh38	V40	TRA2A-LV11-64/Aligned.sortedByCoord.out.bam		ENCORE2	12558
TRA2A-LV11-64_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	693					GRCh38	V40	TRA2A-LV11-64/Aligned.sortedByCoord.out.bam		ENCORE2	12606
TRA2A-LV11-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	693					GRCh38	V40	TRA2A-LV11-64/Aligned.sortedByCoord.out.bam		ENCORE2	12654
TRA2A-LV11-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	693					GRCh38	V40	TRA2A-LV11-64/Aligned.sortedByCoord.out.bam		ENCORE2	12702
TRA2A-LV11-64_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	693					GRCh38	V40	TRA2A-LV11-64_ATTCCT_L008_R1_001.fastq.gz,TRA2A-LV11-64_ATTCCT_L008_R2_001.fastq.gz		ENCORE2	12750