XRCC5 RNA-Seq in HepG2

General Information


RBP	XRCC5
Cell_Line	HepG2
Method	shRNA
Exp_Name	XRCC5-BGHLV14-HepG2
ENCODE_series_ID	ENCSR379SEE
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR732IYM
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	XRCC5_BGHLV14-67
Rep2	XRCC5_BGHLV14-68
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	78.4
Rep2_qPCR	79.4
Rep1_WB	56.1
Rep2_WB	48.1
Antibody Cat#	A302-627A
Antibody Lot#	A302-627A
Antibody DCC ID	ENCAB457QLP
Status	Released
Project	ENCODE3
ID	411

Experiment Information (Status: Released)

	BGHLV14-67	BGHLV14-67	BGHLV14-68	BGHLV14-68
idx	163	0	164	0
TRCN#_or_BGC#	TRCN0000010467	TRCN0000010467	TRCN0000010467	TRCN0000010467
shRNA_or_gRNA_sequence	TGAAGATGGACCTACAGCTAA	TGAAGATGGACCTACAGCTAA	TGAAGATGGACCTACAGCTAA	TGAAGATGGACCTACAGCTAA
PAM
Name	XRCC5	XRCC5	XRCC5	XRCC5
Sample_ID	BGHLV14-67	BGHLV14-67	BGHLV14-68	BGHLV14-68
transduction_Date	7/4/2014	7/4/2014	7/4/2014	7/4/2014
days
RBP_name	XRCC5	XRCC5	XRCC5	XRCC5
qPCR_result	78.4	78.4	79.4	79.4
Ave_qPCR	78.9	78.9
RT-qPCR_primer-F	gcttggcaaagaaagatgaga	gcttggcaaagaaagatgaga
RT-qPCR_primer-R	gcttggcaaagaaagatgaga	gcttggcaaagaaagatgaga
protein_conc	2478	2478	2607	2607
WB_result	56.1	46.0	48.1	55.0
Ave_WB	52.1	50.5
WB_DONE_date	2/25/2016	8/17/2018	wes
MW	83kDa	86kDa
IP	1		1	fu's
antibody_Cat#	A302-627A	#201004	A302-627A	#201004
Antibody DCC ID	ENCAB457QLP	ENCAB308AOH		ENCAB308AOH
submitted_to_DCC_date	3/8/2016	8/20/2018
Rep1_TPM	87.5	0	0	0
Rep2_TPM	65.8	0	0	0
Action
Library_start_date	8/12/2014	8/12/2014	8/12/2014	8/12/2014
repeat_library
Note
ID	2226	2228	2227	2229

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
XRCC5	Product_ID: A302-627A Lot_ID: 1 Source: Bethyl Labs Target Name: XRCC5-human
XRCC5	Product_ID: 201004 Lot_ID: DD0729 Source: Zen Bioscience Target Name: XRCC5-human

Experiment Status

	BGHLV14-67	BGHLV14-68
Sample_ID	BGHLV14-67	BGHLV14-68
Sample Name	XRCC5_BGHLV14-67	XRCC5_BGHLV14-68
Sample Name	XRCC5_BGHLV14-67	XRCC5_BGHLV14-68
RBP	XRCC5	XRCC5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	546	547

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-67	BGHLV14-68
Sample #
Sample Name	XRCC5-BGHLV14-67	XRCC5-BGHLV14-68
Sample_Name_Alias	XRCC5_BGHLV14-67	XRCC5_BGHLV14-68
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set3/B1.png	DNA_Library_LV13-14/set3/C1.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A11.png	RNA_Library_LV13-14-16/set1/B11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-67	BGHLV14-68
RBP	XRCC5	XRCC5
Batch_ID	BGHLV14	BGHLV14
WB_result	56.100	48.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2230	2231

Sequencing Information

	BGHLV14-67	BGHLV14-68
Sample_ID	BGHLV14-67	BGHLV14-68
Sample Name	XRCC5_BGHLV14-67	XRCC5_BGHLV14-68
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	52,280,000	42,560,000
total_aligned_reads	48,198,624	38,077,352
unique_aligned_reads	45,566,446	36,016,378
percent_uniqueAligned	0.87158	0.84625
correlation_replicates	0.992130	0.992130
spikein_reads	203,420	145,654
percent_spikeins	0.00389	0.00342
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	872	873

Data Submission Information

	BGHLV14-67	BGHLV14-67
ENCODE_alias	brenton-graveley:XRCC5_BGHLV14	brenton-graveley:XRCC5-BGHLV14-HepG2
ENCODE_accession	ENCSR732IYM	ENCSR379SEE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-67	BGHLV14-67
Sample Name	XRCC5_BGHLV14-67	XRCC5_BGHLV14-67
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2822	7043

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_BGHLV14-67_ATGTCA_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	872	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13838
XRCC5_BGHLV14-67_ATGTCA_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	872	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13900
XRCC5_BGHLV14-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	872					GRCh38	V40	XRCC5_BGHLV14-67_ATGTCA_L008_R1_001.fastq.gz,XRCC5_BGHLV14-67_ATGTCA_L008_R2_001.fastq.gz		ENCORE2	13962
XRCC5_BGHLV14-67_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	872					GRCh38	V40	XRCC5_BGHLV14-67/Aligned.sortedByCoord.out.bam		ENCORE2	14024
XRCC5_BGHLV14-67_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	872					GRCh38	V40	XRCC5_BGHLV14-67/Aligned.sortedByCoord.out.bam		ENCORE2	14086
XRCC5_BGHLV14-67_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	872					GRCh38	V40	XRCC5_BGHLV14-67/Aligned.sortedByCoord.out.bam		ENCORE2	14148
XRCC5_BGHLV14-67_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	872					GRCh38	V40	XRCC5_BGHLV14-67/Aligned.sortedByCoord.out.bam		ENCORE2	14210
XRCC5_BGHLV14-67_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	872					GRCh38	V40	XRCC5_BGHLV14-67_ATGTCA_L008_R1_001.fastq.gz,XRCC5_BGHLV14-67_ATGTCA_L008_R2_001.fastq.gz		ENCORE2	14272
XRCC5_BGHLV14-68_CCGTCC_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	873	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13839
XRCC5_BGHLV14-68_CCGTCC_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	873	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13901
XRCC5_BGHLV14-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	873					GRCh38	V40	XRCC5_BGHLV14-68_CCGTCC_L008_R1_001.fastq.gz,XRCC5_BGHLV14-68_CCGTCC_L008_R2_001.fastq.gz		ENCORE2	13963
XRCC5_BGHLV14-68_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	873					GRCh38	V40	XRCC5_BGHLV14-68/Aligned.sortedByCoord.out.bam		ENCORE2	14025
XRCC5_BGHLV14-68_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	873					GRCh38	V40	XRCC5_BGHLV14-68/Aligned.sortedByCoord.out.bam		ENCORE2	14087
XRCC5_BGHLV14-68_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	873					GRCh38	V40	XRCC5_BGHLV14-68/Aligned.sortedByCoord.out.bam		ENCORE2	14149
XRCC5_BGHLV14-68_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	873					GRCh38	V40	XRCC5_BGHLV14-68/Aligned.sortedByCoord.out.bam		ENCORE2	14211
XRCC5_BGHLV14-68_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	873					GRCh38	V40	XRCC5_BGHLV14-68_CCGTCC_L008_R1_001.fastq.gz,XRCC5_BGHLV14-68_CCGTCC_L008_R2_001.fastq.gz		ENCORE2	14273