XRCC6 RNA-Seq in HepG2

General Information


RBP	XRCC6
Cell_Line	HepG2
Method	shRNA
Exp_Name	XRCC6-BGHLV14-HepG2
ENCODE_series_ID	ENCSR050PML
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR500WHE
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	XRCC6_BGHLV14-69
Rep2	XRCC6_BGHLV14-70
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	75.6
Rep2_qPCR	76.3
Rep1_WB	35.0
Rep2_WB	37.1
Antibody Cat#	A302-624A
Antibody Lot#	A302-624A
Antibody DCC ID	ENCAB462RZD
Status	Archived
Project	ENCODE3
ID	412

Experiment Information (Status: Released)

	BGHLV14-69	BGHLV14-70
idx	165	166
TRCN#_or_BGC#	TRCN0000039609	TRCN0000039609
shRNA_or_gRNA_sequence	GATGAGTCATAAGAGGATCAT	GATGAGTCATAAGAGGATCAT
PAM
Name	XRCC6	XRCC6
Sample_ID	BGHLV14-69	BGHLV14-70
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	XRCC6	XRCC6
qPCR_result	75.6	76.3
Ave_qPCR	76.0
RT-qPCR_primer-F	cgagcactcagcaggttaaa
RT-qPCR_primer-R	attggaggaggcttgagagc
protein_conc	2731	2881
WB_result	35.0	37.1
Ave_WB	36.1
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	122.6	0
Rep2_TPM	111.8	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2230	2231

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

	BGHLV14-69	BGHLV14-70
Sample_ID	BGHLV14-69	BGHLV14-70
Sample Name	XRCC6_BGHLV14-69	XRCC6_BGHLV14-70
Sample Name	XRCC6_BGHLV14-69	XRCC6_BGHLV14-70
RBP	XRCC6	XRCC6
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	548	549

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-69	BGHLV14-70
Sample #
Sample Name	XRCC6-BGHLV14-69	XRCC6-BGHLV14-70
Sample_Name_Alias	XRCC6_BGHLV14-69	XRCC6_BGHLV14-70
Index Well Position	S18	S19
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/D1.png	DNA_Library_LV13-14/set3/E1.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C11.png	RNA_Library_LV13-14-16/set1/D11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-69	BGHLV14-70
RBP	XRCC6	XRCC6
Batch_ID	BGHLV14	BGHLV14
WB_result	35.000	37.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2232	2233

Sequencing Information

	BGHLV14-69	BGHLV14-70
Sample_ID	BGHLV14-69	BGHLV14-70
Sample Name	XRCC6_BGHLV14-69	XRCC6_BGHLV14-70
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	52,970,000	50,180,000
total_aligned_reads	49,516,220	46,513,318
unique_aligned_reads	46,692,910	43,877,380
percent_uniqueAligned	0.88150	0.87440
correlation_replicates	0.999062	0.999062
spikein_reads	219,268	258,824
percent_spikeins	0.00414	0.00516
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	874	875

Data Submission Information

	BGHLV14-69	BGHLV14-69
ENCODE_alias	brenton-graveley:XRCC6_BGHLV14	brenton-graveley:XRCC6-BGHLV14-HepG2
ENCODE_accession	ENCSR500WHE	ENCSR050PML
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-69	BGHLV14-69
Sample Name	XRCC6_BGHLV14-69	XRCC6_BGHLV14-69
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2823	7045

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_BGHLV14-69_GTCCGC_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	874	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13840
XRCC6_BGHLV14-69_GTCCGC_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	874	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13902
XRCC6_BGHLV14-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	874					GRCh38	V40	XRCC6_BGHLV14-69_GTCCGC_L008_R1_001.fastq.gz,XRCC6_BGHLV14-69_GTCCGC_L008_R2_001.fastq.gz		ENCORE2	13964
XRCC6_BGHLV14-69_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	874					GRCh38	V40	XRCC6_BGHLV14-69/Aligned.sortedByCoord.out.bam		ENCORE2	14026
XRCC6_BGHLV14-69_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	874					GRCh38	V40	XRCC6_BGHLV14-69/Aligned.sortedByCoord.out.bam		ENCORE2	14088
XRCC6_BGHLV14-69_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	874					GRCh38	V40	XRCC6_BGHLV14-69/Aligned.sortedByCoord.out.bam		ENCORE2	14150
XRCC6_BGHLV14-69_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	874					GRCh38	V40	XRCC6_BGHLV14-69/Aligned.sortedByCoord.out.bam		ENCORE2	14212
XRCC6_BGHLV14-69_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	874					GRCh38	V40	XRCC6_BGHLV14-69_GTCCGC_L008_R1_001.fastq.gz,XRCC6_BGHLV14-69_GTCCGC_L008_R2_001.fastq.gz		ENCORE2	14274
XRCC6_BGHLV14-70_GTGAAA_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	875	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13841
XRCC6_BGHLV14-70_GTGAAA_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	875	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13903
XRCC6_BGHLV14-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	875					GRCh38	V40	XRCC6_BGHLV14-70_GTGAAA_L008_R1_001.fastq.gz,XRCC6_BGHLV14-70_GTGAAA_L008_R2_001.fastq.gz		ENCORE2	13965
XRCC6_BGHLV14-70_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	875					GRCh38	V40	XRCC6_BGHLV14-70/Aligned.sortedByCoord.out.bam		ENCORE2	14027
XRCC6_BGHLV14-70_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	875					GRCh38	V40	XRCC6_BGHLV14-70/Aligned.sortedByCoord.out.bam		ENCORE2	14089
XRCC6_BGHLV14-70_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	875					GRCh38	V40	XRCC6_BGHLV14-70/Aligned.sortedByCoord.out.bam		ENCORE2	14151
XRCC6_BGHLV14-70_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	875					GRCh38	V40	XRCC6_BGHLV14-70/Aligned.sortedByCoord.out.bam		ENCORE2	14213
XRCC6_BGHLV14-70_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	875					GRCh38	V40	XRCC6_BGHLV14-70_GTGAAA_L008_R1_001.fastq.gz,XRCC6_BGHLV14-70_GTGAAA_L008_R2_001.fastq.gz		ENCORE2	14275