XRCC6 RNA-Seq in K562

General Information


RBP	XRCC6
Cell_Line	K562
Method	shRNA
Exp_Name	XRCC6-BGKLV13-K562
ENCODE_series_ID	ENCSR927HSW
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR232CPD
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	XRCC6_BGKLV13_23
Rep2	XRCC6_BGKLV13_24
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	89.5
Rep2_qPCR	89.3
Rep1_WB	52.0
Rep2_WB	46.0
Antibody Cat#	A302-624A
Antibody Lot#	A302-624A
Antibody DCC ID	ENCAB462RZD
Status	Archived
Project	ENCODE3
ID	367

Experiment Information (Status: Released)

	BGKLV13-23	BGKLV13-24
idx	156	157
TRCN#_or_BGC#	TRCN0000039609	TRCN0000039609
shRNA_or_gRNA_sequence	GATGAGTCATAAGAGGATCAT	GATGAGTCATAAGAGGATCAT
PAM
Name	XRCC6	XRCC6
Sample_ID	BGKLV13-23	BGKLV13-24
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	XRCC6	XRCC6
qPCR_result	89.5	89.3
Ave_qPCR	89.4
RT-qPCR_primer-F	cgagcactcagcaggttaaa
RT-qPCR_primer-R	attggaggaggcttgagagc
protein_conc	1498	1634
WB_result	52.0	46.0
Ave_WB	49.0
WB_DONE_date	6/24/2015
MW	70kDa
IP	1	1
antibody_Cat#	A302-624A	A302-624A
Antibody DCC ID	ENCAB462RZD	ENCAB462RZD
submitted_to_DCC_date	8/6/2015
Rep1_TPM	115.133686	0
Rep2_TPM	85.2617666	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	171	172

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
XRCC6	Product_ID: A302-624A Lot_ID: 1 Source: Bethyl Labs Target Name: XRCC6-human

Experiment Status

	BGKLV13-23	BGKLV13-24
Sample_ID	BGKLV13-23	BGKLV13-24
Sample Name	XRCC6_BGKLV13_23	XRCC6_BGKLV13_24
Sample Name	XRCC6_BGKLV13_23	XRCC6_BGKLV13_24
RBP	XRCC6	XRCC6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	486	487

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-23	BGKLV13-24
Sample #
Sample Name	XRCC6-BGKLV13-23	XRCC6-BGKLV13-24
Sample_Name_Alias	XRCC6_BGKLV13_23	XRCC6_BGKLV13_24
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/B3.png	DNA_Library_LV13-14/set1/C3.png
RIN	9.1	9.3
libSample_RNA_Well	RNA_Library_LV12/set1/E11.png	RNA_Library_LV12/set1/F11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-23	BGKLV13-24
RBP	XRCC6	XRCC6
Batch_ID	BGKLV13	BGKLV13
WB_result	52.000	46.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2136	2137

Sequencing Information

	BGKLV13-23	BGKLV13-24
Sample_ID	BGKLV13-23	BGKLV13-24
Sample Name	XRCC6_BGKLV13_23	XRCC6_BGKLV13_24
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	48,940,000	43,640,000
total_aligned_reads	46,061,426	40,325,970
unique_aligned_reads	42,327,276	37,139,690
percent_uniqueAligned	0.86488	0.85105
correlation_replicates	0.997163	0.997163
spikein_reads	168,956	129,926
percent_spikeins	0.00345	0.00298
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	778	779

Data Submission Information

	BGKLV13-23	BGKLV13-23
ENCODE_alias	brenton-graveley:XRCC6_BGKLV13	brenton-graveley:XRCC6-BGKLV13-K562
ENCODE_accession	ENCSR232CPD	ENCSR927HSW
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-23	BGKLV13-23
Sample Name	XRCC6_BGKLV13_23	XRCC6_BGKLV13_23
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2792	7046

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
XRCC6_BGKLV13_23_GTCCGC_L003_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	778	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13414
XRCC6_BGKLV13_23_GTCCGC_L003_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	778	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13466
XRCC6_BGKLV13_23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	778					GRCh38	V40	XRCC6_BGKLV13_23_GTCCGC_L003_R1_001.fastq.gz,XRCC6_BGKLV13_23_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	13518
XRCC6_BGKLV13_23_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	778					GRCh38	V40	XRCC6_BGKLV13_23/Aligned.sortedByCoord.out.bam		ENCORE2	13570
XRCC6_BGKLV13_23_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	778					GRCh38	V40	XRCC6_BGKLV13_23/Aligned.sortedByCoord.out.bam		ENCORE2	13622
XRCC6_BGKLV13_23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	778					GRCh38	V40	XRCC6_BGKLV13_23/Aligned.sortedByCoord.out.bam		ENCORE2	13674
XRCC6_BGKLV13_23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	778					GRCh38	V40	XRCC6_BGKLV13_23/Aligned.sortedByCoord.out.bam		ENCORE2	13726
XRCC6_BGKLV13_23_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	778					GRCh38	V40	XRCC6_BGKLV13_23_GTCCGC_L003_R1_001.fastq.gz,XRCC6_BGKLV13_23_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	13778
XRCC6_BGKLV13_24_GTGAAA_L003_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	779	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13415
XRCC6_BGKLV13_24_GTGAAA_L003_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	779	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13467
XRCC6_BGKLV13_24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	779					GRCh38	V40	XRCC6_BGKLV13_24_GTGAAA_L003_R1_001.fastq.gz,XRCC6_BGKLV13_24_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	13519
XRCC6_BGKLV13_24_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	779					GRCh38	V40	XRCC6_BGKLV13_24/Aligned.sortedByCoord.out.bam		ENCORE2	13571
XRCC6_BGKLV13_24_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	779					GRCh38	V40	XRCC6_BGKLV13_24/Aligned.sortedByCoord.out.bam		ENCORE2	13623
XRCC6_BGKLV13_24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	779					GRCh38	V40	XRCC6_BGKLV13_24/Aligned.sortedByCoord.out.bam		ENCORE2	13675
XRCC6_BGKLV13_24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	779					GRCh38	V40	XRCC6_BGKLV13_24/Aligned.sortedByCoord.out.bam		ENCORE2	13727
XRCC6_BGKLV13_24_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	779					GRCh38	V40	XRCC6_BGKLV13_24_GTGAAA_L003_R1_001.fastq.gz,XRCC6_BGKLV13_24_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	13779