XRN2 RNA-Seq in HepG2

General Information


RBP	XRN2
Cell_Line	HepG2
Method	shRNA
Exp_Name	XRN2-BGHLV17-HepG2
ENCODE_series_ID	ENCSR542OTH
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR347ZHQ
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	XRN2_BGHLV17_41
Rep2	XRN2_BGHLV17_42
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	63.0
Rep2_qPCR	63.1
Rep1_WB	99.7
Rep2_WB	99.7
Antibody Cat#	A301-103A
Antibody Lot#	A301-103A
Antibody DCC ID	ENCAB995BMT
Status	Released
Project	ENCODE3
ID	443

Experiment Information (Status: Released)

	BGHLV17-41	BGHLV17-42
idx	277	278
TRCN#_or_BGC#	TRCN0000049899	TRCN0000049899
shRNA_or_gRNA_sequence	CCCTGAACTATGTCATGGGAT	CCCTGAACTATGTCATGGGAT
PAM
Name	XRN2	XRN2
Sample_ID	BGHLV17-41	BGHLV17-42
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	XRN2	XRN2
qPCR_result	63.0	63.1
Ave_qPCR	63.0
RT-qPCR_primer-F	tgaaggactttgctgggttc
RT-qPCR_primer-R	tgcaatgccttcaaagtctg
protein_conc	3259	3092
WB_result	99.7	99.7
Ave_WB	99.7
WB_DONE_date	3/19/2015
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	44.2	0
Rep2_TPM	41.4	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2342	2343

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

	BGHLV17-41	BGHLV17-42
Sample_ID	BGHLV17-41	BGHLV17-42
Sample Name	XRN2_BGHLV17_41	XRN2_BGHLV17_42
Sample Name	XRN2_BGHLV17_41	XRN2_BGHLV17_42
RBP	XRN2	XRN2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	614	615

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-41	BGHLV17-42
Sample #
Sample Name	XRN2-BGHLV17-41	XRN2-BGHLV17-42
Sample_Name_Alias	XRN2_BGHLV17_41	XRN2_BGHLV17_42
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/C4.png	DNA_Library_LV16-17/set1/D4.png
RIN	7.9	7.8
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/C6.png	RNA_Library_LV16-17-18/set1/D6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-41	BGHLV17-42
RBP	XRN2	XRN2
Batch_ID	BGHLV17	BGHLV17
WB_result	99.700	99.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2298	2299

Sequencing Information

	BGHLV17-41	BGHLV17-42
Sample_ID	BGHLV17-41	BGHLV17-42
Sample Name	XRN2_BGHLV17_41	XRN2_BGHLV17_42
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	61,580,000	62,740,000
total_aligned_reads	56,716,066	58,132,344
unique_aligned_reads	53,316,496	54,756,410
percent_uniqueAligned	0.86581	0.87275
correlation_replicates	0.999472	0.999472
spikein_reads	220,466	203,450
percent_spikeins	0.00358	0.00324
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	940	941

Data Submission Information

	BGHLV17-41	BGHLV17-41
ENCODE_alias	brenton-graveley:XRN2_BGHLV17	brenton-graveley:XRN2-BGHLV17-HepG2
ENCODE_accession	ENCSR347ZHQ	ENCSR542OTH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-41	BGHLV17-41
Sample Name	XRN2_BGHLV17_41	XRN2_BGHLV17_41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2874	7047

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_BGHLV17_41_TTAGGC_L004_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	940	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14522
XRN2_BGHLV17_41_TTAGGC_L004_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	940	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14560
XRN2_BGHLV17_41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	940					GRCh38	V40	XRN2_BGHLV17_41_TTAGGC_L004_R1_001.fastq.gz,XRN2_BGHLV17_41_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	14598
XRN2_BGHLV17_41_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	940					GRCh38	V40	XRN2_BGHLV17_41/Aligned.sortedByCoord.out.bam		ENCORE2	14636
XRN2_BGHLV17_41_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	940					GRCh38	V40	XRN2_BGHLV17_41/Aligned.sortedByCoord.out.bam		ENCORE2	14674
XRN2_BGHLV17_41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	940					GRCh38	V40	XRN2_BGHLV17_41/Aligned.sortedByCoord.out.bam		ENCORE2	14712
XRN2_BGHLV17_41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	940					GRCh38	V40	XRN2_BGHLV17_41/Aligned.sortedByCoord.out.bam		ENCORE2	14750
XRN2_BGHLV17_41_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	940					GRCh38	V40	XRN2_BGHLV17_41_TTAGGC_L004_R1_001.fastq.gz,XRN2_BGHLV17_41_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	14788
XRN2_BGHLV17_42_TGACCA_L004_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	941	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14523
XRN2_BGHLV17_42_TGACCA_L004_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	941	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14561
XRN2_BGHLV17_42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	941					GRCh38	V40	XRN2_BGHLV17_42_TGACCA_L004_R1_001.fastq.gz,XRN2_BGHLV17_42_TGACCA_L004_R2_001.fastq.gz		ENCORE2	14599
XRN2_BGHLV17_42_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	941					GRCh38	V40	XRN2_BGHLV17_42/Aligned.sortedByCoord.out.bam		ENCORE2	14637
XRN2_BGHLV17_42_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	941					GRCh38	V40	XRN2_BGHLV17_42/Aligned.sortedByCoord.out.bam		ENCORE2	14675
XRN2_BGHLV17_42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	941					GRCh38	V40	XRN2_BGHLV17_42/Aligned.sortedByCoord.out.bam		ENCORE2	14713
XRN2_BGHLV17_42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	941					GRCh38	V40	XRN2_BGHLV17_42/Aligned.sortedByCoord.out.bam		ENCORE2	14751
XRN2_BGHLV17_42_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	941					GRCh38	V40	XRN2_BGHLV17_42_TGACCA_L004_R1_001.fastq.gz,XRN2_BGHLV17_42_TGACCA_L004_R2_001.fastq.gz		ENCORE2	14789