XRCC6 RNA-Seq in HepG2

General Information


RBP	XRCC6
Cell_Line	HepG2
Method	CRISPR
Exp_Name	XRCC6-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR490GUT
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR312VLS
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	XRCC6-BGHcLV16-59
Rep2	XRCC6-BGHcLV16-60
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	56.4
Rep2_qPCR	60.7
Rep1_WB	80.2
Rep2_WB	71.6
Antibody Cat#	MA5-13110
Antibody Lot#	TL2692924
Antibody DCC ID	ENCAB611VLV
Status	Released
Project	ENCODE4
ID	159

Experiment Information (Status: Released)

	BGHcLV16-59	BGHcLV16-60
idx	489	490
TRCN#_or_BGC#	BGC#0000373	BGC#0000373
shRNA_or_gRNA_sequence	GTTGCGGAAGGTTCGCGCCA	GTTGCGGAAGGTTCGCGCCA
PAM	AGG	AGG
Name	XRCC6-95	XRCC6-95
Sample_ID	BGHcLV16-59	BGHcLV16-60
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	XRCC6	XRCC6
qPCR_result	56.4	60.7
Ave_qPCR	58.6
RT-qPCR_primer-F	CAATGACAGTGCCAAAGCC
RT-qPCR_primer-R	AAGGATATGTCAAAGCCCCC
protein_conc	3454	4537
WB_result	80.2	71.6
Ave_WB	75.9
WB_DONE_date	4/29/19
MW	70KD
IP	Mouse / Ig
antibody_Cat#	MA5-13110
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	326	0
Rep2_TPM	390	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6640	6641

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
XRCC6	Product_ID: MA5-13110 Lot_ID: TL2692924 Source: Thermo Fisher Target Name: XRCC6-human

Experiment Status

	BGHcLV16-59	BGHcLV16-60
Sample_ID	BGHcLV16-59	BGHcLV16-60
Sample Name
Sample Name	XRCC6-BGHcLV16-59	XRCC6-BGHcLV16-60
RBP	XRCC6	XRCC6
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5437	5438

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-59	BGHcLV16-60
Sample #	71	72
Sample Name	XRCC6-BGHcLV16-59	XRCC6-BGHcLV16-60
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	2-E2	2-F2
Tecan	35.30	31.97
Tecan_date	2019-12-10	2019-12-10
Size_bp	285	286
Peak_Molarity	71.80	71.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E4.png	DNA_Library_set43-44/set2/F4.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set43-44/set1/E9.png	RNA_Library_set43-44/set1/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-59	BGHcLV16-60
RBP	XRCC6	XRCC6
Batch_ID	BGHcLV16	BGHcLV16
WB_result	80.200	71.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	647	648

Sequencing Information

	BGHcLV16-59	BGHcLV16-60
Sample_ID	BGHcLV16-59	BGHcLV16-60
Sample Name	XRCC6-BGHcLV16-59	XRCC6-BGHcLV16-60
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	444,158,920	472,207,426
total_aligned_reads	420,757,330	444,409,120
unique_aligned_reads	393,458,570	415,229,036
percent_uniqueAligned	0.88585	0.87934
correlation_replicates	0.997170	0.997170
spikein_reads	513,572	547,160
percent_spikeins	0.00116	0.00116
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	149	150

Data Submission Information

	BGHcLV16-59	BGHcLV16-59	BGHcLV16-59	BGHcLV16-59	BGHcLV16-59	BGHcLV16-59	BGHcLV16-60	BGHcLV16-60	BGHcLV16-60	BGHcLV16-60
ENCODE_alias	brenton-graveley:XRCC6-BGHcLV16	brenton-graveley:XRCC6-BGHcLV16-59	brenton-graveley:L-XRCC6-BGHcLV16-59	brenton-graveley:XRCC6-BGHcLV16-59_S67_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:XRCC6-BGHcLV16-59_S67_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:XRCC6-BGHcLV16-HepG2	brenton-graveley:XRCC6-BGHcLV16-60	brenton-graveley:L-XRCC6-BGHcLV16-60	brenton-graveley:XRCC6-BGHcLV16-60_S68_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:XRCC6-BGHcLV16-60_S68_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR312VLS	ENCBS161WQQ	ENCLB226BJQ	ENCFF576DZS	ENCFF266RCZ	ENCSR490GUT	ENCBS393PMQ	ENCLB128OBL	ENCFF593ZLP	ENCFF334VPA
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV16-59	BGHcLV16-59	BGHcLV16-59	BGHcLV16-59	BGHcLV16-59	BGHcLV16-59	BGHcLV16-60	BGHcLV16-60	BGHcLV16-60	BGHcLV16-60
Sample Name	XRCC6-BGHcLV16-59	XRCC6-BGHcLV16-59	XRCC6-BGHcLV16-59	XRCC6-BGHcLV16-59	XRCC6-BGHcLV16-59	XRCC6-BGHcLV16-59	XRCC6-BGHcLV16-60	XRCC6-BGHcLV16-60	XRCC6-BGHcLV16-60	XRCC6-BGHcLV16-60
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		XRCC6-BGHcLV16-59.pdf	L-XRCC6-BGHcLV16-59.pdf				XRCC6-BGHcLV16-60.pdf	L-XRCC6-BGHcLV16-60.pdf
ID	15	112	276	442	474	7357	113	277	443	475

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-BGHcLV16-59_S67_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	149	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	29
XRCC6-BGHcLV16-59_S67_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	149	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	61
XRCC6-BGHcLV16-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	149					GRCh38	V40	XRCC6-BGHcLV16-59_S67_R1_001.filtered.trimmed.paired.fastq.gz,XRCC6-BGHcLV16-59_S67_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24192
XRCC6-BGHcLV16-59_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	149					GRCh38	V40	XRCC6-BGHcLV16-59/Aligned.sortedByCoord.out.bam		ENCORE2	24224
XRCC6-BGHcLV16-59_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	149					GRCh38	V40	XRCC6-BGHcLV16-59/Aligned.sortedByCoord.out.bam		ENCORE2	24256
XRCC6-BGHcLV16-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	149					GRCh38	V40	XRCC6-BGHcLV16-59/Aligned.sortedByCoord.out.bam		ENCORE2	24288
XRCC6-BGHcLV16-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	149					GRCh38	V40	XRCC6-BGHcLV16-59/Aligned.sortedByCoord.out.bam		ENCORE2	24320
XRCC6-BGHcLV16-59_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	149					GRCh38	V40	XRCC6-BGHcLV16-59_S67_R1_001.filtered.trimmed.paired.fastq.gz,XRCC6-BGHcLV16-59_S67_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24352
XRCC6-BGHcLV16-60_S68_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	150	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	30
XRCC6-BGHcLV16-60_S68_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	150	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	62
XRCC6-BGHcLV16-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	150					GRCh38	V40	XRCC6-BGHcLV16-60_S68_R1_001.filtered.trimmed.paired.fastq.gz,XRCC6-BGHcLV16-60_S68_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24193
XRCC6-BGHcLV16-60_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	150					GRCh38	V40	XRCC6-BGHcLV16-60/Aligned.sortedByCoord.out.bam		ENCORE2	24225
XRCC6-BGHcLV16-60_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	150					GRCh38	V40	XRCC6-BGHcLV16-60/Aligned.sortedByCoord.out.bam		ENCORE2	24257
XRCC6-BGHcLV16-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	150					GRCh38	V40	XRCC6-BGHcLV16-60/Aligned.sortedByCoord.out.bam		ENCORE2	24289
XRCC6-BGHcLV16-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	150					GRCh38	V40	XRCC6-BGHcLV16-60/Aligned.sortedByCoord.out.bam		ENCORE2	24321
XRCC6-BGHcLV16-60_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	150					GRCh38	V40	XRCC6-BGHcLV16-60_S68_R1_001.filtered.trimmed.paired.fastq.gz,XRCC6-BGHcLV16-60_S68_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24353