XRCC5 RNA-Seq in K562

General Information


RBP	XRCC5
Cell_Line	K562
Method	shRNA
Exp_Name	XRCC5-BGKLV13-K562
ENCODE_series_ID	ENCSR739QRH
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR715XZS
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	XRCC5_BGKLV13_35
Rep2	XRCC5_BGKLV13_36
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	54.6
Rep2_qPCR	51.0
Rep1_WB	27.6
Rep2_WB	35.1
Antibody Cat#	A302-627A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB457QLP
Status	Archived
Project	ENCODE3
ID	369

Experiment Information (Status: Released)

	BGKLV13-35	BGKLV13-35	BGKLV13-36	BGKLV13-36
idx	168	170	169	171
TRCN#_or_BGC#	TRCN0000010467	TRCN0000010467	TRCN0000010467	TRCN0000010467
shRNA_or_gRNA_sequence	TGAAGATGGACCTACAGCTAA	TGAAGATGGACCTACAGCTAA	TGAAGATGGACCTACAGCTAA	TGAAGATGGACCTACAGCTAA
PAM
Name	XRCC5	XRCC5	XRCC5	XRCC5
Sample_ID	BGKLV13-35	BGKLV13-35	BGKLV13-36	BGKLV13-36
transduction_Date	6/13/2014	6/13/2014	6/13/2014	6/13/2014
days
RBP_name	XRCC5	XRCC5	XRCC5	XRCC5
qPCR_result	54.6	54.6	51.0	51.0
Ave_qPCR	52.8	52.8
RT-qPCR_primer-F	gcttggcaaagaaagatgaga	gcttggcaaagaaagatgaga
RT-qPCR_primer-R	gcttggcaaagaaagatgaga	gcttggcaaagaaagatgaga
protein_conc	1979	1979	1978	1978
WB_result	27.6	0.0	35.1	0.0
Ave_WB	31.4	0.0
WB_DONE_date		2/22/2016
MW	83kDa	86kDa		wes
IP	1		1	fu's
antibody_Cat#	A302-627A	#201004	A302-627A	#201004
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	90.757142	0	0	0
Rep2_TPM	65.5916979	0	0	0
Action
Library_start_date	7/27/2014		7/27/2014
repeat_library
Note
ID	183	185	184	186

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV13-35	BGKLV13-36
Sample_ID	BGKLV13-35	BGKLV13-36
Sample Name	XRCC5_BGKLV13_35	XRCC5_BGKLV13_36
Sample Name	XRCC5_BGKLV13_35	XRCC5_BGKLV13_36
RBP	XRCC5	XRCC5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	484	485

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-35	BGKLV13-36
Sample #
Sample Name	XRCC5-BGKLV13-35	XRCC5-BGKLV13-36
Sample_Name_Alias	XRCC5_BGKLV13_35	XRCC5_BGKLV13_36
Index Well Position	S22	S23
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/F3.png	DNA_Library_LV13-14/set1/G3.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/A12.png	RNA_Library_LV12/set1/B12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-35	BGKLV13-36
RBP	XRCC5	XRCC5
Batch_ID	BGKLV13	BGKLV13
WB_result	27.600	35.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2140	2141

Sequencing Information

	BGKLV13-35	BGKLV13-36
Sample_ID	BGKLV13-35	BGKLV13-36
Sample Name	XRCC5_BGKLV13_35	XRCC5_BGKLV13_36
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	47,400,000	49,860,000
total_aligned_reads	44,552,610	46,352,958
unique_aligned_reads	41,066,366	42,708,228
percent_uniqueAligned	0.86638	0.85656
correlation_replicates	0.996430	0.996430
spikein_reads	285,418	196,860
percent_spikeins	0.00602	0.00395
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	782	783

Data Submission Information

	BGKLV13-35	BGKLV13-35
ENCODE_alias	brenton-graveley:XRCC5_BGKLV13	brenton-graveley:XRCC5-BGKLV13-K562
ENCODE_accession	ENCSR715XZS	ENCSR739QRH
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-35	BGKLV13-35
Sample Name	XRCC5_BGKLV13_35	XRCC5_BGKLV13_35
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2791	7044

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
XRCC5_BGKLV13_35_CGTACG_L003_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	782	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13412
XRCC5_BGKLV13_35_CGTACG_L003_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	782	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13464
XRCC5_BGKLV13_35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	782					GRCh38	V40	XRCC5_BGKLV13_35_CGTACG_L003_R1_001.fastq.gz,XRCC5_BGKLV13_35_CGTACG_L003_R2_001.fastq.gz		ENCORE2	13516
XRCC5_BGKLV13_35_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	782					GRCh38	V40	XRCC5_BGKLV13_35/Aligned.sortedByCoord.out.bam		ENCORE2	13568
XRCC5_BGKLV13_35_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	782					GRCh38	V40	XRCC5_BGKLV13_35/Aligned.sortedByCoord.out.bam		ENCORE2	13620
XRCC5_BGKLV13_35_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	782					GRCh38	V40	XRCC5_BGKLV13_35/Aligned.sortedByCoord.out.bam		ENCORE2	13672
XRCC5_BGKLV13_35_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	782					GRCh38	V40	XRCC5_BGKLV13_35/Aligned.sortedByCoord.out.bam		ENCORE2	13724
XRCC5_BGKLV13_35_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	782					GRCh38	V40	XRCC5_BGKLV13_35_CGTACG_L003_R1_001.fastq.gz,XRCC5_BGKLV13_35_CGTACG_L003_R2_001.fastq.gz		ENCORE2	13776
XRCC5_BGKLV13_36_GAGTGG_L004_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	783	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13413
XRCC5_BGKLV13_36_GAGTGG_L004_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	783	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13465
XRCC5_BGKLV13_36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	783					GRCh38	V40	XRCC5_BGKLV13_36_GAGTGG_L004_R1_001.fastq.gz,XRCC5_BGKLV13_36_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	13517
XRCC5_BGKLV13_36_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	783					GRCh38	V40	XRCC5_BGKLV13_36/Aligned.sortedByCoord.out.bam		ENCORE2	13569
XRCC5_BGKLV13_36_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	783					GRCh38	V40	XRCC5_BGKLV13_36/Aligned.sortedByCoord.out.bam		ENCORE2	13621
XRCC5_BGKLV13_36_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	783					GRCh38	V40	XRCC5_BGKLV13_36/Aligned.sortedByCoord.out.bam		ENCORE2	13673
XRCC5_BGKLV13_36_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	783					GRCh38	V40	XRCC5_BGKLV13_36/Aligned.sortedByCoord.out.bam		ENCORE2	13725
XRCC5_BGKLV13_36_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	783					GRCh38	V40	XRCC5_BGKLV13_36_GAGTGG_L004_R1_001.fastq.gz,XRCC5_BGKLV13_36_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	13777