XPO5 RNA-Seq in K562

General Information


RBP	XPO5
Cell_Line	K562
Method	shRNA
Exp_Name	XPO5-BGKLV28-K562
ENCODE_series_ID	ENCSR562QHN
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR453HKS
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	XPO5_BGKLV28-61
Rep2	XPO5_BGKLV28-62
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	66.8
Rep2_qPCR	71.6
Rep1_WB	67.1
Rep2_WB	67.1
Antibody Cat#	A303-991A
Antibody Lot#	A303-991A
Antibody DCC ID	ENCAB769WTH
Status	Released
Project	ENCODE3
ID	661

Experiment Information (Status: Released)

	BGKLV28-61	BGKLV28-62
idx	530	531
TRCN#_or_BGC#	TRCN0000158915	TRCN0000158915
shRNA_or_gRNA_sequence	CCAGATGTTTCGAACACTAAA	CCAGATGTTTCGAACACTAAA
PAM
Name	XPO5	XPO5
Sample_ID	BGKLV28-61	BGKLV28-62
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	XPO5	XPO5
qPCR_result	66.8	71.6
Ave_qPCR	69.2
RT-qPCR_primer-F	gctggggagtggctaaagta
RT-qPCR_primer-R	agacggaacagaggcttcct
protein_conc	2633	2795
WB_result	67.1	67.1
Ave_WB	67.1
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	44.2168938	0
Rep2_TPM	44.7303921	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	607	608

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

	BGKLV28-61	BGKLV28-62
Sample_ID	BGKLV28-61	BGKLV28-62
Sample Name	XPO5_BGKLV28-61	XPO5_BGKLV28-62
Sample Name	XPO5_BGKLV28-61	XPO5_BGKLV28-62
RBP	XPO5	XPO5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1008	1009

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-61	BGKLV28-62
Sample #
Sample Name	XPO5-BGKLV28-61	XPO5-BGKLV28-62
Sample_Name_Alias	XPO5_BGKLV28-61	XPO5_BGKLV28-62
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/E4.png	DNA_Library_LV28-29-30/set1/F4.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/A10.png	RNA_Library_LV26-27-28-29/set1/B10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-61	BGKLV28-62
RBP	XPO5	XPO5
Batch_ID	BGKLV28	BGKLV28
WB_result	67.100	67.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2700	2701

Sequencing Information

	BGKLV28-61	BGKLV28-62
Sample_ID	BGKLV28-61	BGKLV28-62
Sample Name	XPO5_BGKLV28-61	XPO5_BGKLV28-62
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	65,688,364	63,477,486
total_aligned_reads	53,945,276	52,066,154
unique_aligned_reads	49,294,466	47,745,726
percent_uniqueAligned	0.75043	0.75217
correlation_replicates	0.998278	0.998278
spikein_reads	223,930	182,108
percent_spikeins	0.00341	0.00287
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1342	1343

Data Submission Information

	BGKLV28-61	BGKLV28-61
ENCODE_alias	brenton-graveley:XPO5_BGKLV28	brenton-graveley:XPO5-BGKLV28-K562
ENCODE_accession	ENCSR453HKS	ENCSR562QHN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-61	BGKLV28-61
Sample Name	XPO5_BGKLV28-61	XPO5_BGKLV28-61
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3053	7042

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_BGKLV28-61_ACAGTG_L004_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1342	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20186
XPO5_BGKLV28-61_ACAGTG_L004_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1342	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20218
XPO5_BGKLV28-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1342					GRCh38	V40	XPO5_BGKLV28-61_ACAGTG_L004_001.R1.fastq.gz,XPO5_BGKLV28-61_ACAGTG_L004_001.R2.fastq.gz		ENCORE2	20250
XPO5_BGKLV28-61_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1342					GRCh38	V40	XPO5_BGKLV28-61/Aligned.sortedByCoord.out.bam		ENCORE2	20282
XPO5_BGKLV28-61_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1342					GRCh38	V40	XPO5_BGKLV28-61/Aligned.sortedByCoord.out.bam		ENCORE2	20314
XPO5_BGKLV28-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1342					GRCh38	V40	XPO5_BGKLV28-61/Aligned.sortedByCoord.out.bam		ENCORE2	20346
XPO5_BGKLV28-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1342					GRCh38	V40	XPO5_BGKLV28-61/Aligned.sortedByCoord.out.bam		ENCORE2	20378
XPO5_BGKLV28-61_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1342					GRCh38	V40	XPO5_BGKLV28-61_ACAGTG_L004_001.R1.fastq.gz,XPO5_BGKLV28-61_ACAGTG_L004_001.R2.fastq.gz		ENCORE2	20410
XPO5_BGKLV28-62_GCCAAT_L004_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1343	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20187
XPO5_BGKLV28-62_GCCAAT_L004_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1343	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20219
XPO5_BGKLV28-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1343					GRCh38	V40	XPO5_BGKLV28-62_GCCAAT_L004_001.R1.fastq.gz,XPO5_BGKLV28-62_GCCAAT_L004_001.R2.fastq.gz		ENCORE2	20251
XPO5_BGKLV28-62_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1343					GRCh38	V40	XPO5_BGKLV28-62/Aligned.sortedByCoord.out.bam		ENCORE2	20283
XPO5_BGKLV28-62_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1343					GRCh38	V40	XPO5_BGKLV28-62/Aligned.sortedByCoord.out.bam		ENCORE2	20315
XPO5_BGKLV28-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1343					GRCh38	V40	XPO5_BGKLV28-62/Aligned.sortedByCoord.out.bam		ENCORE2	20347
XPO5_BGKLV28-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1343					GRCh38	V40	XPO5_BGKLV28-62/Aligned.sortedByCoord.out.bam		ENCORE2	20379
XPO5_BGKLV28-62_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1343					GRCh38	V40	XPO5_BGKLV28-62_GCCAAT_L004_001.R1.fastq.gz,XPO5_BGKLV28-62_GCCAAT_L004_001.R2.fastq.gz		ENCORE2	20411