XPO5 RNA-Seq in HepG2

General Information


RBP	XPO5
Cell_Line	HepG2
Method	shRNA
Exp_Name	XPO5-BGHLV22-HepG2
ENCODE_series_ID	ENCSR879UEK
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR778RWJ
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	XPO5-BGHLV22-57
Rep2	XPO5-BGHLV22-58
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	73.4
Rep2_qPCR	77.1
Rep1_WB	62.1
Rep2_WB	59.5
Antibody Cat#	A303-991A
Antibody Lot#	A303-991A
Antibody DCC ID	ENCAB769WTH
Status	Released
Project	ENCODE3
ID	531

Experiment Information (Status: Released)

	BGHLV22-57	BGHLV22-58
idx	485	486
TRCN#_or_BGC#	TRCN0000158915	TRCN0000158915
shRNA_or_gRNA_sequence	CCAGATGTTTCGAACACTAAA	CCAGATGTTTCGAACACTAAA
PAM
Name	XPO5	XPO5
Sample_ID	BGHLV22-57	BGHLV22-58
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	XPO5	XPO5
qPCR_result	73.4	77.1
Ave_qPCR	75.2
RT-qPCR_primer-F	gctggggagtggctaaagta
RT-qPCR_primer-R	agacggaacagaggcttcct
protein_conc	5715	5953
WB_result	62.1	59.5
Ave_WB	60.8
WB_DONE_date	7/6/2015
MW	136kDa
IP	1	1
antibody_Cat#	A303-991A	A303-991A
Antibody DCC ID	ENCAB769WTH	ENCAB769WTH
submitted_to_DCC_date	8/6/2015
Rep1_TPM	16.7	0
Rep2_TPM	18.8	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2560	2561

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
XPO5	Product_ID: A303-991A Lot_ID: 1 Source: Bethyl Labs Target Name: XPO5-human

Experiment Status

	BGHLV22-57	BGHLV22-58
Sample_ID	BGHLV22-57	BGHLV22-58
Sample Name	XPO5-BGHLV22-57	XPO5-BGHLV22-58
Sample Name	XPO5-BGHLV22-57	XPO5-BGHLV22-58
RBP	XPO5	XPO5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	812	813

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-57	BGHLV22-58
Sample #
Sample Name	XPO5-BGHLV22-57	XPO5-BGHLV22-58
Sample_Name_Alias	XPO5-BGHLV22-57	XPO5-BGHLV22-58
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/C10.png	DNA_Library_LV20-22-23/set1/D10.png
RIN	9.2	9.2
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C4.png	RNA_Library_LV22-23-25/set1/D4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-57	BGHLV22-58
RBP	XPO5	XPO5
Batch_ID	BGHLV22	BGHLV22
WB_result	62.100	59.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2498	2499

Sequencing Information

	BGHLV22-57	BGHLV22-58
Sample_ID	BGHLV22-57	BGHLV22-58
Sample Name	XPO5-BGHLV22-57	XPO5-BGHLV22-58
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	54,190,000	44,900,000
total_aligned_reads	48,963,274	40,750,494
unique_aligned_reads	46,082,638	38,373,624
percent_uniqueAligned	0.85039	0.85465
correlation_replicates	0.994429	0.994429
spikein_reads	356,094	292,874
percent_spikeins	0.00657	0.00652
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1120	1121

Data Submission Information

	BGHLV22-57	BGHLV22-57
ENCODE_alias	brenton-graveley:XPO5-BGHLV22	brenton-graveley:XPO5-BGHLV22-HepG2
ENCODE_accession	ENCSR778RWJ	ENCSR879UEK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-57	BGHLV22-57
Sample Name	XPO5-BGHLV22-57	XPO5-BGHLV22-57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2938	7041

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
XPO5-BGHLV22-57_GGCTAC_L003_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1120	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16310
XPO5-BGHLV22-57_GGCTAC_L003_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1120	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16350
XPO5-BGHLV22-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1120					GRCh38	V40	XPO5-BGHLV22-57_GGCTAC_L003_R1_001.fastq.gz,XPO5-BGHLV22-57_GGCTAC_L003_R2_001.fastq.gz		ENCORE2	16448
XPO5-BGHLV22-57_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1120					GRCh38	V40	XPO5-BGHLV22-57/Aligned.sortedByCoord.out.bam		ENCORE2	16488
XPO5-BGHLV22-57_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1120					GRCh38	V40	XPO5-BGHLV22-57/Aligned.sortedByCoord.out.bam		ENCORE2	16528
XPO5-BGHLV22-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1120					GRCh38	V40	XPO5-BGHLV22-57/Aligned.sortedByCoord.out.bam		ENCORE2	16568
XPO5-BGHLV22-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1120					GRCh38	V40	XPO5-BGHLV22-57/Aligned.sortedByCoord.out.bam		ENCORE2	16608
XPO5-BGHLV22-57_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1120					GRCh38	V40	XPO5-BGHLV22-57_GGCTAC_L003_R1_001.fastq.gz,XPO5-BGHLV22-57_GGCTAC_L003_R2_001.fastq.gz		ENCORE2	16648
XPO5-BGHLV22-58_CTTGTA_L003_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1121	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16311
XPO5-BGHLV22-58_CTTGTA_L003_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1121	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16351
XPO5-BGHLV22-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1121					GRCh38	V40	XPO5-BGHLV22-58_CTTGTA_L003_R1_001.fastq.gz,XPO5-BGHLV22-58_CTTGTA_L003_R2_001.fastq.gz		ENCORE2	16449
XPO5-BGHLV22-58_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1121					GRCh38	V40	XPO5-BGHLV22-58/Aligned.sortedByCoord.out.bam		ENCORE2	16489
XPO5-BGHLV22-58_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1121					GRCh38	V40	XPO5-BGHLV22-58/Aligned.sortedByCoord.out.bam		ENCORE2	16529
XPO5-BGHLV22-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1121					GRCh38	V40	XPO5-BGHLV22-58/Aligned.sortedByCoord.out.bam		ENCORE2	16569
XPO5-BGHLV22-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1121					GRCh38	V40	XPO5-BGHLV22-58/Aligned.sortedByCoord.out.bam		ENCORE2	16609
XPO5-BGHLV22-58_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1121					GRCh38	V40	XPO5-BGHLV22-58_CTTGTA_L003_R1_001.fastq.gz,XPO5-BGHLV22-58_CTTGTA_L003_R2_001.fastq.gz		ENCORE2	16649