XRCC6 RNA-Seq in K562

General Information


RBP	XRCC6
Cell_Line	K562
Method	CRISPR
Exp_Name	XRCC6-BGKcLV15-K562
ENCODE_series_ID	ENCSR342TEI
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR516EPT
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	XRCC6-BGKcLV15-61
Rep2	XRCC6-BGKcLV15-62
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	53.6
Rep2_qPCR	59.8
Rep1_WB	71.0
Rep2_WB	67.9
Antibody Cat#	MA5-13110
Antibody Lot#	LOT#TL2692924
Antibody DCC ID	ENCAB611VLV
Status	Released
Project	ENCODE4
ID	138

Experiment Information (Status: Released)

	BGKcLV15-61	BGKcLV15-62
idx	603	604
TRCN#_or_BGC#	BGC#0000373	BGC#0000373
shRNA_or_gRNA_sequence	GTTGCGGAAGGTTCGCGCCA	GTTGCGGAAGGTTCGCGCCA
PAM	AGG	AGG
Name	XRCC6-95	XRCC6-95
Sample_ID	BGKcLV15-61	BGKcLV15-62
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	XRCC6	XRCC6
qPCR_result	53.6	59.8
Ave_qPCR	56.7
RT-qPCR_primer-F	CAATGACAGTGCCAAAGCC
RT-qPCR_primer-R	AAGGATATGTCAAAGCCCCC
protein_conc	4410	4747
WB_result	71.0	67.9
Ave_WB	69.5
WB_DONE_date	4/11/19
MW	70KD
IP	Mouse / Ig
antibody_Cat#	MA5-13110	LOT#TL2692924
Antibody DCC ID	ENCAB611VLV
submitted_to_DCC_date	4/17/19
Rep1_TPM	260.9	0
Rep2_TPM	258.7	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4715	4716

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

	BGKcLV15-61	BGKcLV15-62
Sample_ID	BGKcLV15-61	BGKcLV15-62
Sample Name
Sample Name	XRCC6-BGKcLV15-61	XRCC6-BGKcLV15-62
RBP	XRCC6	XRCC6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5365	5366

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-61	BGKcLV15-62
Sample #	35	36
Sample Name	XRCC6-BGKcLV15-61	XRCC6-BGKcLV15-62
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	3-C1	3-D1
Tecan	41.60	34.72
Tecan_date	2019-12-10	2019-12-10
Size_bp	267	274
Peak_Molarity	26.50	20.50
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C5.png	DNA_Library_set43-44/set1/D5.png
RIN	9.4	9.8
libSample_RNA_Well	RNA_Library_set43-44/set1/C5.png	RNA_Library_set43-44/set1/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-61	BGKcLV15-62
RBP	XRCC6	XRCC6
Batch_ID	BGKcLV15	BGKcLV15
WB_result	71.000	67.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	611	612

Sequencing Information

	BGKcLV15-61	BGKcLV15-62
Sample_ID	BGKcLV15-61	BGKcLV15-62
Sample Name	XRCC6-BGKcLV15-61	XRCC6-BGKcLV15-62
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	109,284,818	93,322,644
total_aligned_reads	107,081,220	88,909,712
unique_aligned_reads	97,863,588	81,167,006
percent_uniqueAligned	0.89549	0.86975
correlation_replicates	0.995178	0.995178
spikein_reads	83,944	66,978
percent_spikeins	0.00077	0.00072
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	117	118

Data Submission Information

	BGKcLV15-61	BGKcLV15-61	BGKcLV15-61	BGKcLV15-61	BGKcLV15-61	BGKcLV15-61	BGKcLV15-62	BGKcLV15-62	BGKcLV15-62	BGKcLV15-62
ENCODE_alias	brenton-graveley:XRCC6-BGKcLV15	brenton-graveley:XRCC6-BGKcLV15-61	brenton-graveley:L-XRCC6-BGKcLV15-61	brenton-graveley:XRCC6-BGKcLV15-61_S35_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:XRCC6-BGKcLV15-61_S35_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:XRCC6-BGKcLV15-K562	brenton-graveley:XRCC6-BGKcLV15-62	brenton-graveley:L-XRCC6-BGKcLV15-62	brenton-graveley:XRCC6-BGKcLV15-62_S36_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:XRCC6-BGKcLV15-62_S36_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR516EPT	ENCBS954SAF	ENCLB845JQQ	ENCFF942QOY	ENCFF972IJW	ENCSR342TEI	ENCBS626UBX	ENCLB526OGT	ENCFF327VIY	ENCFF634DEZ
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	BGKcLV15-61	BGKcLV15-61	BGKcLV15-61	BGKcLV15-61	BGKcLV15-61	BGKcLV15-61	BGKcLV15-62	BGKcLV15-62	BGKcLV15-62	BGKcLV15-62
Sample Name	XRCC6-BGKcLV15-61	XRCC6-BGKcLV15-61	XRCC6-BGKcLV15-61	XRCC6-BGKcLV15-61	XRCC6-BGKcLV15-61	XRCC6-BGKcLV15-61	XRCC6-BGKcLV15-62	XRCC6-BGKcLV15-62	XRCC6-BGKcLV15-62	XRCC6-BGKcLV15-62
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		XRCC6-BGKcLV15-61.pdf	L-XRCC6-BGKcLV15-61.pdf				XRCC6-BGKcLV15-62.pdf	L-XRCC6-BGKcLV15-62.pdf
ID	34	150	314	512	564	7358	151	315	513	565

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-BGKcLV15-61_S35_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	117	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	113
XRCC6-BGKcLV15-61_S35_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	117	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	165
XRCC6-BGKcLV15-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	117					GRCh38	V40	XRCC6-BGKcLV15-61_S35_R1_001.filtered.trimmed.paired.fastq.gz,XRCC6-BGKcLV15-61_S35_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24404
XRCC6-BGKcLV15-61_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	117					GRCh38	V40	XRCC6-BGKcLV15-61/Aligned.sortedByCoord.out.bam		ENCORE2	24456
XRCC6-BGKcLV15-61_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	117					GRCh38	V40	XRCC6-BGKcLV15-61/Aligned.sortedByCoord.out.bam		ENCORE2	24508
XRCC6-BGKcLV15-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	117					GRCh38	V40	XRCC6-BGKcLV15-61/Aligned.sortedByCoord.out.bam		ENCORE2	24560
XRCC6-BGKcLV15-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	117					GRCh38	V40	XRCC6-BGKcLV15-61/Aligned.sortedByCoord.out.bam		ENCORE2	24612
XRCC6-BGKcLV15-61_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	117					GRCh38	V40	XRCC6-BGKcLV15-61_S35_R1_001.filtered.trimmed.paired.fastq.gz,XRCC6-BGKcLV15-61_S35_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24664
XRCC6-BGKcLV15-62_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	118	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	114
XRCC6-BGKcLV15-62_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	118	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	166
XRCC6-BGKcLV15-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	118					GRCh38	V40	XRCC6-BGKcLV15-62_S36_R1_001.filtered.trimmed.paired.fastq.gz,XRCC6-BGKcLV15-62_S36_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24405
XRCC6-BGKcLV15-62_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	118					GRCh38	V40	XRCC6-BGKcLV15-62/Aligned.sortedByCoord.out.bam		ENCORE2	24457
XRCC6-BGKcLV15-62_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	118					GRCh38	V40	XRCC6-BGKcLV15-62/Aligned.sortedByCoord.out.bam		ENCORE2	24509
XRCC6-BGKcLV15-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	118					GRCh38	V40	XRCC6-BGKcLV15-62/Aligned.sortedByCoord.out.bam		ENCORE2	24561
XRCC6-BGKcLV15-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	118					GRCh38	V40	XRCC6-BGKcLV15-62/Aligned.sortedByCoord.out.bam		ENCORE2	24613
XRCC6-BGKcLV15-62_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	118					GRCh38	V40	XRCC6-BGKcLV15-62_S36_R1_001.filtered.trimmed.paired.fastq.gz,XRCC6-BGKcLV15-62_S36_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24665