XRCC5 RNA-Seq in K562

General Information


RBP	XRCC5
Cell_Line	K562
Method	CRISPR
Exp_Name	XRCC5-BGKcLV11-K562
ENCODE_series_ID	ENCSR678HMZ
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR276GMG
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	XRCC5-BGKcLV11-111
Rep2	XRCC5-BGKcLV11-112
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	12.4
Rep2_qPCR	0.0
Rep1_WB	69.5
Rep2_WB	70.8
Antibody Cat#	A302-627A
Antibody Lot#
Antibody DCC ID	ENCAB457QLP
Status	Released
Project	ENCODE4
ID	196

Experiment Information (Status: Released)

	BGKcLV11-111	BGKcLV11-112
idx	431	432
TRCN#_or_BGC#	BGC#0000299	BGC#0000299
shRNA_or_gRNA_sequence	CATGGCCACCTAAGCGAAAG	CATGGCCACCTAAGCGAAAG
PAM	ggg	ggg
Name	XRCC5_90	XRCC5_90
Sample_ID	BGKcLV11-111	BGKcLV11-112
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	XRCC5	XRCC5
qPCR_result	12.4	0.0
Ave_qPCR	6.2
RT-qPCR_primer-F	gcttggcaaagaaagatgaga
RT-qPCR_primer-R	gcttggcaaagaaagatgaga
protein_conc	2679	2786
WB_result	69.5	70.8
Ave_WB	70.1
WB_DONE_date	8/22/18	wes
MW	83 kDa
IP
antibody_Cat#	A302-627A
Antibody DCC ID	ENCAB457QLP
submitted_to_DCC_date	2/22/19
Rep1_TPM	183.4	0
Rep2_TPM	196	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4535	4536

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

Experiment Status

	BGKcLV11-111	BGKcLV11-112
Sample_ID	BGKcLV11-111	BGKcLV11-112
Sample Name	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-112
Sample Name	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-112
RBP	XRCC5	XRCC5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2699	2700

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-111	BGKcLV11-112
Sample #	27	28
Sample Name	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-112
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	2-C2	2-D2
Tecan	44.37	60.96
Tecan_date	2019-03-13	2019-03-13
Size_bp	296	297
Peak_Molarity	78.90	116.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/C4.png	DNA_Library_set42/set1/D4.png
RIN	9.6	9.0
libSample_RNA_Well	RNA_Library_set42/set1/C4.png	RNA_Library_set42/set1/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-111	BGKcLV11-112
RBP	XRCC5	XRCC5
Batch_ID	BGKcLV11	BGKcLV11
WB_result	69.500	70.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	27	28

Sequencing Information

	BGKcLV11-111	BGKcLV11-112
Sample_ID	BGKcLV11-111	BGKcLV11-112
Sample Name	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-112
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	100,354,220	52,734,478
total_aligned_reads	96,547,932	51,858,754
unique_aligned_reads	87,804,546	47,317,066
percent_uniqueAligned	0.87495	0.89727
correlation_replicates	0.992793	0.992793
spikein_reads	192,704	63,858
percent_spikeins	0.00192	0.00121
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	79	80

Data Submission Information

	BGKcLV11-111	BGKcLV11-111	BGKcLV11-111	BGKcLV11-111	BGKcLV11-111	BGKcLV11-111	BGKcLV11-112	BGKcLV11-112	BGKcLV11-112	BGKcLV11-112
ENCODE_alias	brenton-graveley:XRCC5-BGKcLV11	brenton-graveley:XRCC5-BGKcLV11-111	brenton-graveley:L-XRCC5-BGKcLV11-111	brenton-graveley:XRCC5-BGKcLV11-111_CTTGGTAT+CCAAGTCC_HK3H2DSXX_S27_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:XRCC5-BGKcLV11-111_CTTGGTAT+CCAAGTCC_HK3H2DSXX_S27_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:XRCC5-BGKcLV11-K562	brenton-graveley:XRCC5-BGKcLV11-112	brenton-graveley:L-XRCC5-BGKcLV11-112	brenton-graveley:XRCC5-BGKcLV11-112_TCCAACGC+TTGGACTT_HK3H2DSXX_S28_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:XRCC5-BGKcLV11-112_TCCAACGC+TTGGACTT_HK3H2DSXX_S28_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR276GMG	ENCBS567TJU	ENCLB669IKT	ENCFF281TTB	ENCFF232DIV	ENCSR678HMZ	ENCBS288OPM	ENCLB574JTF	ENCFF080NOC	ENCFF066ZVH
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	BGKcLV11-111	BGKcLV11-111	BGKcLV11-111	BGKcLV11-111	BGKcLV11-111	BGKcLV11-111	BGKcLV11-112	BGKcLV11-112	BGKcLV11-112	BGKcLV11-112
Sample Name	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-111	XRCC5-BGKcLV11-112	XRCC5-BGKcLV11-112	XRCC5-BGKcLV11-112	XRCC5-BGKcLV11-112
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		XRCC5-BGKcLV11-111.pdf	L-XRCC5-BGKcLV11-111.pdf				XRCC5-BGKcLV11-112.pdf	L-XRCC5-BGKcLV11-112.pdf
ID	774	843	925	1029	1111	7356	844	926	1030	1112

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-BGKcLV11-111_CTTGGTAT+CCAAGTCC_HK3H2DSXX_S27_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	79	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	411
XRCC5-BGKcLV11-111_CTTGGTAT+CCAAGTCC_HK3H2DSXX_S27_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	79	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	493
XRCC5-BGKcLV11-111_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	79					GRCh38	V40	XRCC5-BGKcLV11-111_CTTGGTAT+CCAAGTCC_HK3H2DSXX_S27_L004_R1_001.filtered.trimmed.paired.fastq.gz,XRCC5-BGKcLV11-111_CTTGGTAT+CCAAGTCC_HK3H2DSXX_S27_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23750
XRCC5-BGKcLV11-111_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	79					GRCh38	V40	XRCC5-BGKcLV11-111/Aligned.sortedByCoord.out.bam		ENCORE2	23832
XRCC5-BGKcLV11-111_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	79					GRCh38	V40	XRCC5-BGKcLV11-111/Aligned.sortedByCoord.out.bam		ENCORE2	23914
XRCC5-BGKcLV11-111_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	79					GRCh38	V40	XRCC5-BGKcLV11-111/Aligned.sortedByCoord.out.bam		ENCORE2	23996
XRCC5-BGKcLV11-111_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	79					GRCh38	V40	XRCC5-BGKcLV11-111/Aligned.sortedByCoord.out.bam		ENCORE2	24078
XRCC5-BGKcLV11-111_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	79					GRCh38	V40	XRCC5-BGKcLV11-111_CTTGGTAT+CCAAGTCC_HK3H2DSXX_S27_L004_R1_001.filtered.trimmed.paired.fastq.gz,XRCC5-BGKcLV11-111_CTTGGTAT+CCAAGTCC_HK3H2DSXX_S27_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24160
XRCC5-BGKcLV11-112_TCCAACGC+TTGGACTT_HK3H2DSXX_S28_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	80	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	412
XRCC5-BGKcLV11-112_TCCAACGC+TTGGACTT_HK3H2DSXX_S28_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	80	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	494
XRCC5-BGKcLV11-112_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	80					GRCh38	V40	XRCC5-BGKcLV11-112_TCCAACGC+TTGGACTT_HK3H2DSXX_S28_L004_R1_001.filtered.trimmed.paired.fastq.gz,XRCC5-BGKcLV11-112_TCCAACGC+TTGGACTT_HK3H2DSXX_S28_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23751
XRCC5-BGKcLV11-112_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	80					GRCh38	V40	XRCC5-BGKcLV11-112/Aligned.sortedByCoord.out.bam		ENCORE2	23833
XRCC5-BGKcLV11-112_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	80					GRCh38	V40	XRCC5-BGKcLV11-112/Aligned.sortedByCoord.out.bam		ENCORE2	23915
XRCC5-BGKcLV11-112_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	80					GRCh38	V40	XRCC5-BGKcLV11-112/Aligned.sortedByCoord.out.bam		ENCORE2	23997
XRCC5-BGKcLV11-112_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	80					GRCh38	V40	XRCC5-BGKcLV11-112/Aligned.sortedByCoord.out.bam		ENCORE2	24079
XRCC5-BGKcLV11-112_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	80					GRCh38	V40	XRCC5-BGKcLV11-112_TCCAACGC+TTGGACTT_HK3H2DSXX_S28_L004_R1_001.filtered.trimmed.paired.fastq.gz,XRCC5-BGKcLV11-112_TCCAACGC+TTGGACTT_HK3H2DSXX_S28_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24161