XPO1 RNA-Seq in K562

General Information


RBP	XPO1
Cell_Line	K562
Method	shRNA
Exp_Name	XPO1-BGKLV38-K562
ENCODE_series_ID	ENCSR587VGW
Batch_ID	BGKLV38
Pool ID	Pool-180109
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR629XTS
ENCODE_CN_Exp_ID	ENCSR260BQC
Rep1	XPO1-BGKLV38-119C
Rep2	XPO1-BGKLV38-120C
CN1	NT-BGKLV38-1C
CN2	NT-BGKLV38-2C
Rep1_qPCR	55.2
Rep2_qPCR	51.9
Rep1_WB	54.5
Rep2_WB	58.7
Antibody Cat#	A300-469A
Antibody Lot#	A300-469A
Antibody DCC ID	ENCAB085DMF
Status	Released
Project	ENCODE4
ID	278

Experiment Information (Status: Released)

	BGKLV38-119	BGKLV38-119	BGKLV38-120	BGKLV38-120
idx	890	890	891	891
TRCN#_or_BGC#	TRCN0000153235	TRCN0000153235	TRCN0000153235	TRCN0000153235
shRNA_or_gRNA_sequence	GCTCAAGAAGTACTGACACAT	GCTCAAGAAGTACTGACACAT	GCTCAAGAAGTACTGACACAT	GCTCAAGAAGTACTGACACAT
PAM
Name	XPO1	XPO1	XPO1	XPO1
Sample_ID	BGKLV38-119	BGKLV38-119	BGKLV38-120	BGKLV38-120
transduction_Date	9/15/16	9/15/16	9/15/16	9/15/16
days
RBP_name	XPO1	XPO1	XPO1	XPO1
qPCR_result	55.2	55.2	51.9	51.9
Ave_qPCR	53.6	53.6
RT-qPCR_primer-F	tctccttaagtcggccttcc	tctccttaagtcggccttcc
RT-qPCR_primer-R	aagctgaaaagccctgtcac	aagctgaaaagccctgtcac
protein_conc	2849	2849	2852	2852
WB_result	54.5	74.3	58.7	68.2
Ave_WB	56.6	71.2
WB_DONE_date	10/6/16	4/18/24
MW	123kDa	123kDa
IP	1		1
antibody_Cat#	A300-469A	46249S	A300-469A	lot# 2
Antibody DCC ID	ENCAB085DMF		ENCAB085DMF
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action
Library_start_date	12/19/17		12/19/17
repeat_library
Note
ID	987	989	988	990

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
XPO1	Product_ID: A300-469A Lot_ID: 1 Source: Bethyl Labs Target Name: XPO1-human
XPO1	Product_ID: 46249S Lot_ID: 2 Source: Cell Signaling Technology Target Name: XPO1-human

Experiment Status

	BGKLV38-119	BGKLV38-120
Sample_ID	BGKLV38-119	BGKLV38-120
Sample Name
Sample Name	XPO1-BGKLV38-119C	XPO1-BGKLV38-120C
RBP	XPO1	XPO1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6481	6482

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-119	BGKLV38-120
Sample #	65	66
Sample Name	XPO1-BGKLV38-119C	XPO1-BGKLV38-120C
Sample_Name_Alias
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	282	289
Peak_Molarity	9.66	10.40
libSampleQC_DNA_Well	DNA_Library_set40/set1/C10.png	DNA_Library_set40/set1/D10.png
RIN	8.8	8.9
libSample_RNA_Well	RNA_Library_set40/set1/C5.png	RNA_Library_set40/set1/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGKLV38-119	BGKLV38-120
RBP	XPO1	XPO1
Batch_ID	BGKLV38	BGKLV38
WB_result	54.500	58.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	988	989

Sequencing Information

	BGKLV38-119	BGKLV38-120
Sample_ID	BGKLV38-119	BGKLV38-120
Sample Name	XPO1-BGKLV38-119C	XPO1-BGKLV38-120C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_K	set40_K
total_reads	57,003,900	52,635,748
total_aligned_reads	43,504,426	43,296,538
unique_aligned_reads	39,467,340	39,303,710
percent_uniqueAligned	0.69236	0.74671
correlation_replicates	0.999414	0.999414
spikein_reads	15,602	14,926
percent_spikeins	0.00027	0.00028
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	391	392

Data Submission Information

	BGKLV38-119	BGKLV38-119	BGKLV38-119	BGKLV38-119	BGKLV38-119	BGKLV38-119	BGKLV38-120	BGKLV38-120	BGKLV38-120	BGKLV38-120
ENCODE_alias	brenton-graveley:XPO1-BGKLV38-C	brenton-graveley:XPO1-BGKLV38-119C	brenton-graveley:L-XPO1-BGKLV38-119C	brenton-graveley:XPO1-BGKLV38-119C_GTGGCC_ACBYWVANXX_L006_001.R1.fastq.gz	brenton-graveley:XPO1-BGKLV38-119C_GTGGCC_ACBYWVANXX_L006_001.R2.fastq.gz	brenton-graveley:XPO1-BGKLV38-K562	brenton-graveley:XPO1-BGKLV38-120C	brenton-graveley:L-XPO1-BGKLV38-120C	brenton-graveley:XPO1-BGKLV38-120C_GTTTCG_ACBYWVANXX_L006_001.R1.fastq.gz	brenton-graveley:XPO1-BGKLV38-120C_GTTTCG_ACBYWVANXX_L006_001.R2.fastq.gz
ENCODE_accession	ENCSR629XTS	ENCBS186DPZ	ENCLB055IDC	ENCFF320IYT	ENCFF707BTF	ENCSR587VGW	ENCBS885KEV	ENCLB130WZH	ENCFF920NAJ	ENCFF881GGV
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	BGKLV38-119	BGKLV38-119	BGKLV38-119	BGKLV38-119	BGKLV38-119	BGKLV38-119	BGKLV38-120	BGKLV38-120	BGKLV38-120	BGKLV38-120
Sample Name	XPO1-BGKLV38-119C	XPO1-BGKLV38-119C	XPO1-BGKLV38-119C	XPO1-BGKLV38-119C	XPO1-BGKLV38-119C	XPO1-BGKLV38-119C	XPO1-BGKLV38-120C	XPO1-BGKLV38-120C	XPO1-BGKLV38-120C	XPO1-BGKLV38-120C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		XPO1-BGKLV38-119C.pdf	L-XPO1-BGKLV38-119C.pdf				XPO1-BGKLV38-120C.pdf	L-XPO1-BGKLV38-120C.pdf
ID	1453	1504	1560	1671	1704	7355	1505	1561	1672	1705

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
XPO1-BGKLV38-119C_GTGGCC_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	391	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	756
XPO1-BGKLV38-119C_GTGGCC_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	391	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	799
XPO1-BGKLV38-119C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	391					GRCh38	V40	XPO1-BGKLV38-119C_GTGGCC_ACBYWVANXX_L006_001.R1.fastq.gz,XPO1-BGKLV38-119C_GTGGCC_ACBYWVANXX_L006_001.R2.fastq.gz		ENCORE2	23496
XPO1-BGKLV38-119C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	391					GRCh38	V40	XPO1-BGKLV38-119C/Aligned.sortedByCoord.out.bam		ENCORE2	23530
XPO1-BGKLV38-119C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	391					GRCh38	V40	XPO1-BGKLV38-119C/Aligned.sortedByCoord.out.bam		ENCORE2	23564
XPO1-BGKLV38-119C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	391					GRCh38	V40	XPO1-BGKLV38-119C/Aligned.sortedByCoord.out.bam		ENCORE2	23598
XPO1-BGKLV38-119C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	391					GRCh38	V40	XPO1-BGKLV38-119C/Aligned.sortedByCoord.out.bam		ENCORE2	23632
XPO1-BGKLV38-119C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	391					GRCh38	V40	XPO1-BGKLV38-119C_GTGGCC_ACBYWVANXX_L006_001.R1.fastq.gz,XPO1-BGKLV38-119C_GTGGCC_ACBYWVANXX_L006_001.R2.fastq.gz		ENCORE2	23666
XPO1-BGKLV38-120C_GTTTCG_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	392	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	757
XPO1-BGKLV38-120C_GTTTCG_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	392	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	800
XPO1-BGKLV38-120C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	392					GRCh38	V40	XPO1-BGKLV38-120C_GTTTCG_ACBYWVANXX_L006_001.R1.fastq.gz,XPO1-BGKLV38-120C_GTTTCG_ACBYWVANXX_L006_001.R2.fastq.gz		ENCORE2	23497
XPO1-BGKLV38-120C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	392					GRCh38	V40	XPO1-BGKLV38-120C/Aligned.sortedByCoord.out.bam		ENCORE2	23531
XPO1-BGKLV38-120C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	392					GRCh38	V40	XPO1-BGKLV38-120C/Aligned.sortedByCoord.out.bam		ENCORE2	23565
XPO1-BGKLV38-120C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	392					GRCh38	V40	XPO1-BGKLV38-120C/Aligned.sortedByCoord.out.bam		ENCORE2	23599
XPO1-BGKLV38-120C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	392					GRCh38	V40	XPO1-BGKLV38-120C/Aligned.sortedByCoord.out.bam		ENCORE2	23633
XPO1-BGKLV38-120C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	392					GRCh38	V40	XPO1-BGKLV38-120C_GTTTCG_ACBYWVANXX_L006_001.R1.fastq.gz,XPO1-BGKLV38-120C_GTTTCG_ACBYWVANXX_L006_001.R2.fastq.gz		ENCORE2	23667