XRN2 RNA-Seq in K562

General Information


RBP	XRN2
Cell_Line	K562
Method	shRNA
Exp_Name	XRN2-BGKLV19-K562
ENCODE_series_ID	ENCSR705HMQ
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR717SJA
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	XRN2_BGKLV19_63B
Rep2	XRN2_BGKLV19_64B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	49.0
Rep2_qPCR	46.1
Rep1_WB	59.1
Rep2_WB	64.2
Antibody Cat#	A301-103A
Antibody Lot#	A301-103A
Antibody DCC ID	ENCAB995BMT
Status	Released
Project	ENCODE3
ID	487

Experiment Information (Status: Released)

	BGKLV19-63	BGKLV19-64
idx	270	271
TRCN#_or_BGC#	TRCN0000049899	TRCN0000049899
shRNA_or_gRNA_sequence	CCCTGAACTATGTCATGGGAT	CCCTGAACTATGTCATGGGAT
PAM
Name	XRN2	XRN2
Sample_ID	BGKLV19-63	BGKLV19-64
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	XRN2	XRN2
qPCR_result	49.0	46.1
Ave_qPCR	47.6
RT-qPCR_primer-F	tgaaggactttgctgggttc
RT-qPCR_primer-R	tgcaatgccttcaaagtctg
protein_conc	2874	3235
WB_result	59.1	64.2
Ave_WB	61.7
WB_DONE_date	2/3/2015
MW	109kDa
IP	1	1
antibody_Cat#	A301-103A	A301-103A
Antibody DCC ID	ENCAB995BMT	ENCAB995BMT
submitted_to_DCC_date	4/2/2015
Rep1_TPM	26.1870312	0
Rep2_TPM	29.0078498	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	295	296

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
XRN2	Product_ID: A301-103A Lot_ID: 1 Source: Bethyl Labs Target Name: XRN2-human

Experiment Status

	BGKLV19-63	BGKLV19-64
Sample_ID	BGKLV19-63	BGKLV19-64
Sample Name	XRN2_BGKLV19_63B	XRN2_BGKLV19_64B
Sample Name	XRN2_BGKLV19_63B	XRN2_BGKLV19_64B
RBP	XRN2	XRN2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	706	707

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-63	BGKLV19-64
Sample #
Sample Name	XRN2-BGKLV19-63B	XRN2-BGKLV19-64B
Sample_Name_Alias	XRN2_BGKLV19_63B	XRN2_BGKLV19_64B
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/E12.png	DNA_Library_LV18-19/set1/F12.png
RIN	10.0	9.4
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/H1.png	RNA_Library_LV19-21-24/set1/B7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-63	BGKLV19-64
RBP	XRN2	XRN2
Batch_ID	BGKLV19	BGKLV19
WB_result	59.100	64.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2392	2393

Sequencing Information

	BGKLV19-63	BGKLV19-64
Sample_ID	BGKLV19-63	BGKLV19-64
Sample Name	XRN2_BGKLV19_63B	XRN2_BGKLV19_64B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	47,890,000	48,710,000
total_aligned_reads	44,375,366	44,920,030
unique_aligned_reads	40,727,904	41,219,334
percent_uniqueAligned	0.85045	0.84622
correlation_replicates	0.995324	0.995324
spikein_reads	188,960	175,972
percent_spikeins	0.00395	0.00361
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1034	1035

Data Submission Information

	BGKLV19-63	BGKLV19-63
ENCODE_alias	brenton-graveley:XRN2_BGKLV19	brenton-graveley:XRN2-BGKLV19-K562
ENCODE_accession	ENCSR717SJA	ENCSR705HMQ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-63	BGKLV19-63
Sample Name	XRN2_BGKLV19_63B	XRN2_BGKLV19_63B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2901	7048

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
XRN2_BGKLV19_63B_CGTACG_L007_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1034	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15150
XRN2_BGKLV19_63B_CGTACG_L007_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1034	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15208
XRN2_BGKLV19_63B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1034					GRCh38	V40	XRN2_BGKLV19_63B_CGTACG_L007_R1_001.fastq.gz,XRN2_BGKLV19_63B_CGTACG_L007_R2_001.fastq.gz		ENCORE2	15266
XRN2_BGKLV19_63B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1034					GRCh38	V40	XRN2_BGKLV19_63B/Aligned.sortedByCoord.out.bam		ENCORE2	15337
XRN2_BGKLV19_63B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1034					GRCh38	V40	XRN2_BGKLV19_63B/Aligned.sortedByCoord.out.bam		ENCORE2	15395
XRN2_BGKLV19_63B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1034					GRCh38	V40	XRN2_BGKLV19_63B/Aligned.sortedByCoord.out.bam		ENCORE2	15453
XRN2_BGKLV19_63B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1034					GRCh38	V40	XRN2_BGKLV19_63B/Aligned.sortedByCoord.out.bam		ENCORE2	15511
XRN2_BGKLV19_63B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1034					GRCh38	V40	XRN2_BGKLV19_63B_CGTACG_L007_R1_001.fastq.gz,XRN2_BGKLV19_63B_CGTACG_L007_R2_001.fastq.gz		ENCORE2	16408
XRN2_BGKLV19_64B_GAGTGG_L007_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1035	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15151
XRN2_BGKLV19_64B_GAGTGG_L007_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1035	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15209
XRN2_BGKLV19_64B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1035					GRCh38	V40	XRN2_BGKLV19_64B_GAGTGG_L007_R1_001.fastq.gz,XRN2_BGKLV19_64B_GAGTGG_L007_R2_001.fastq.gz		ENCORE2	15267
XRN2_BGKLV19_64B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1035					GRCh38	V40	XRN2_BGKLV19_64B/Aligned.sortedByCoord.out.bam		ENCORE2	15338
XRN2_BGKLV19_64B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1035					GRCh38	V40	XRN2_BGKLV19_64B/Aligned.sortedByCoord.out.bam		ENCORE2	15396
XRN2_BGKLV19_64B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1035					GRCh38	V40	XRN2_BGKLV19_64B/Aligned.sortedByCoord.out.bam		ENCORE2	15454
XRN2_BGKLV19_64B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1035					GRCh38	V40	XRN2_BGKLV19_64B/Aligned.sortedByCoord.out.bam		ENCORE2	15512
XRN2_BGKLV19_64B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1035					GRCh38	V40	XRN2_BGKLV19_64B_GAGTGG_L007_R1_001.fastq.gz,XRN2_BGKLV19_64B_GAGTGG_L007_R2_001.fastq.gz		ENCORE2	16409