XPO1 RNA-Seq in HepG2

General Information


RBP	XPO1
Cell_Line	HepG2
Method	shRNA
Exp_Name	XPO1-BGHLV37-HepG2
ENCODE_series_ID	ENCSR807REK
Batch_ID	BGHLV37
Pool ID	Pool-180109
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR438UOT
ENCODE_CN_Exp_ID	ENCSR225PRV
Rep1	XPO1-BGHLV37-93C
Rep2	XPO1-BGHLV37-94C
CN1	non-target-BGHLV37-1C
CN2	non-target-BGHLV37-2C
Rep1_qPCR	20.2
Rep2_qPCR	0.0
Rep1_WB	72.3
Rep2_WB	69.2
Antibody Cat#	A300-469A
Antibody Lot#	A300-469A
Antibody DCC ID	ENCAB085DMF
Status	Released
Project	ENCODE4
ID	266

Experiment Information (Status: Released)

	BGHLV37-93	BGHLV37-94
idx	1005	1006
TRCN#_or_BGC#	TRCN0000153235	TRCN0000153235
shRNA_or_gRNA_sequence	GCTCAAGAAGTACTGACACAT	GCTCAAGAAGTACTGACACAT
PAM
Name	XPO1	XPO1
Sample_ID	BGHLV37-93	BGHLV37-94
transduction_Date	9/1/16	9/1/16
days
RBP_name	XPO1	XPO1
qPCR_result	20.2	0.0
Ave_qPCR	10.1
RT-qPCR_primer-F	gctctttgtgacagggcttt
RT-qPCR_primer-R	tgtcttcacctgcaaattcc
protein_conc	2263	1872
WB_result	72.3	69.2
Ave_WB	70.7
WB_DONE_date	9/19/16
MW	123kDa
IP	1	1
antibody_Cat#	A300-469A	A300-469A
Antibody DCC ID	ENCAB085DMF	ENCAB085DMF
submitted_to_DCC_date	10/26/16
Rep1_TPM	59.9	0
Rep2_TPM	46.2	0
Action
Library_start_date	12/18/17	12/18/17
repeat_library
Note
ID	3098	3099

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

Experiment Status

	BGHLV37-93	BGHLV37-94
Sample_ID	BGHLV37-93	BGHLV37-94
Sample Name
Sample Name	XPO1-BGHLV37-93C	XPO1-BGHLV37-94C
RBP	XPO1	XPO1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6443	6444

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-93	BGHLV37-94
Sample #	27	28
Sample Name	XPO1-BGHLV37-93C	XPO1-BGHLV37-94C
Sample_Name_Alias
Index Well Position	S13	S14
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	306	293
Peak_Molarity	25.30	6.56
libSampleQC_DNA_Well	DNA_Library_set40/set1/E6.png	DNA_Library_set40/set1/F6.png
RIN
libSample_RNA_Well	RNA_Library_set40/set1/C2.png	RNA_Library_set40/set1/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHLV37-93	BGHLV37-94
RBP	XPO1	XPO1
Batch_ID	BGHLV37	BGHLV37
WB_result	72.300	69.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	950	951

Sequencing Information

	BGHLV37-93	BGHLV37-94
Sample_ID	BGHLV37-93	BGHLV37-94
Sample Name	XPO1-BGHLV37-93C	XPO1-BGHLV37-94C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_H	set40_H
total_reads	29,136,210	96,394,800
total_aligned_reads	24,314,778	77,679,498
unique_aligned_reads	22,997,790	73,346,520
percent_uniqueAligned	0.78932	0.76090
correlation_replicates	0.981061	0.981061
spikein_reads	24,208	68,156
percent_spikeins	0.00083	0.00071
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	353	354

Data Submission Information

	BGHLV37-93	BGHLV37-93	BGHLV37-93	BGHLV37-93	BGHLV37-93	BGHLV37-93	BGHLV37-94	BGHLV37-94	BGHLV37-94	BGHLV37-94
ENCODE_alias	brenton-graveley:XPO1-BGHLV37-C	brenton-graveley:XPO1-BGHLV37-93C	brenton-graveley:L-XPO1-BGHLV37-93C	brenton-graveley:XPO1-BGHLV37-93C_AGTCAA_ACBYWVANXX_L002_001.R1.fastq.gz	brenton-graveley:XPO1-BGHLV37-93C_AGTCAA_ACBYWVANXX_L002_001.R2.fastq.gz	brenton-graveley:XPO1-BGHLV37-HepG2	brenton-graveley:XPO1-BGHLV37-94C	brenton-graveley:L-XPO1-BGHLV37-94C	brenton-graveley:XPO1-BGHLV37-94C_AGTTCC_ACBYWVANXX_L002_001.R1.fastq.gz	brenton-graveley:XPO1-BGHLV37-94C_AGTTCC_ACBYWVANXX_L002_001.R2.fastq.gz
ENCODE_accession	ENCSR438UOT	ENCBS426QLM	ENCLB537CRC	ENCFF553CUX	ENCFF373YSP	ENCSR807REK	ENCBS043LKR	ENCLB108JIX	ENCFF600DQH	ENCFF121ZRB
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	BGHLV37-93	BGHLV37-93	BGHLV37-93	BGHLV37-93	BGHLV37-93	BGHLV37-93	BGHLV37-94	BGHLV37-94	BGHLV37-94	BGHLV37-94
Sample Name	XPO1-BGHLV37-93C	XPO1-BGHLV37-93C	XPO1-BGHLV37-93C	XPO1-BGHLV37-93C	XPO1-BGHLV37-93C	XPO1-BGHLV37-93C	XPO1-BGHLV37-94C	XPO1-BGHLV37-94C	XPO1-BGHLV37-94C	XPO1-BGHLV37-94C
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-BGHLV37-93C.pdf	L-XPO1-BGHLV37-93C.pdf				XPO1-BGHLV37-94C.pdf	L-XPO1-BGHLV37-94C.pdf
ID	1452	1502	1558	1597	1634	7354	1503	1559	1598	1635

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-BGHLV37-93C_AGTCAA_ACBYWVANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	353	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	667
XPO1-BGHLV37-93C_AGTCAA_ACBYWVANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	353	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	709
XPO1-BGHLV37-93C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	353					GRCh38	V40	XPO1-BGHLV37-93C_AGTCAA_ACBYWVANXX_L002_001.R1.fastq.gz,XPO1-BGHLV37-93C_AGTCAA_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23270
XPO1-BGHLV37-93C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	353					GRCh38	V40	XPO1-BGHLV37-93C/Aligned.sortedByCoord.out.bam		ENCORE2	23304
XPO1-BGHLV37-93C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	353					GRCh38	V40	XPO1-BGHLV37-93C/Aligned.sortedByCoord.out.bam		ENCORE2	23338
XPO1-BGHLV37-93C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	353					GRCh38	V40	XPO1-BGHLV37-93C/Aligned.sortedByCoord.out.bam		ENCORE2	23372
XPO1-BGHLV37-93C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	353					GRCh38	V40	XPO1-BGHLV37-93C/Aligned.sortedByCoord.out.bam		ENCORE2	23406
XPO1-BGHLV37-93C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	353					GRCh38	V40	XPO1-BGHLV37-93C_AGTCAA_ACBYWVANXX_L002_001.R1.fastq.gz,XPO1-BGHLV37-93C_AGTCAA_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23440
XPO1-BGHLV37-94C_AGTTCC_ACBYWVANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	354	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	668
XPO1-BGHLV37-94C_AGTTCC_ACBYWVANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	354	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	710
XPO1-BGHLV37-94C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	354					GRCh38	V40	XPO1-BGHLV37-94C_AGTTCC_ACBYWVANXX_L002_001.R1.fastq.gz,XPO1-BGHLV37-94C_AGTTCC_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23271
XPO1-BGHLV37-94C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	354					GRCh38	V40	XPO1-BGHLV37-94C/Aligned.sortedByCoord.out.bam		ENCORE2	23305
XPO1-BGHLV37-94C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	354					GRCh38	V40	XPO1-BGHLV37-94C/Aligned.sortedByCoord.out.bam		ENCORE2	23339
XPO1-BGHLV37-94C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	354					GRCh38	V40	XPO1-BGHLV37-94C/Aligned.sortedByCoord.out.bam		ENCORE2	23373
XPO1-BGHLV37-94C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	354					GRCh38	V40	XPO1-BGHLV37-94C/Aligned.sortedByCoord.out.bam		ENCORE2	23407
XPO1-BGHLV37-94C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	354					GRCh38	V40	XPO1-BGHLV37-94C_AGTTCC_ACBYWVANXX_L002_001.R1.fastq.gz,XPO1-BGHLV37-94C_AGTTCC_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23441