NUP35 RNA-Seq in K562

General Information


RBP	NUP35
Cell_Line	K562
Method	shRNA
Exp_Name	NUP35-BGKLV38-K562
ENCODE_series_ID	ENCSR040QNM
Batch_ID	BGKLV38
Pool ID	Pool-180109
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR953IQF
ENCODE_CN_Exp_ID	ENCSR260BQC
Rep1	NUP35-BGKLV38-41C
Rep2	NUP35-BGKLV38-42C
CN1	NT-BGKLV38-1C
CN2	NT-BGKLV38-2C
Rep1_qPCR	90.5
Rep2_qPCR	86.6
Rep1_WB	83.1
Rep2_WB	84.6
Antibody Cat#	A301-781A
Antibody Lot#	lot 1
Antibody DCC ID	ENCAB697LIX
Status	Released
Project	ENCODE4
ID	276

Experiment Information (Status: Released)

	BGKLV38-41	BGKLV38-41	BGKLV38-42	BGKLV38-42
idx	812	812	813	813
TRCN#_or_BGC#	TRCN0000072378	TRCN0000072378	TRCN0000072378	TRCN0000072378
shRNA_or_gRNA_sequence	GCTGGTTCCTTCGGTTAGTTA	GCTGGTTCCTTCGGTTAGTTA	GCTGGTTCCTTCGGTTAGTTA	GCTGGTTCCTTCGGTTAGTTA
PAM
Name	NUP35	NUP35	NUP35	NUP35
Sample_ID	BGKLV38-41	BGKLV38-41	BGKLV38-42	BGKLV38-42
transduction_Date	9/15/16	9/15/16	9/15/16	9/15/16
days
RBP_name	NUP35	NUP35	NUP35	NUP35
qPCR_result	90.5	90.5	86.6	86.6
Ave_qPCR	88.5	88.5
RT-qPCR_primer-F	TTGCTACAGCATACAAAGCCTC	TTGCTACAGCATACAAAGCCTC
RT-qPCR_primer-R	TCCATTGCTTTGGATACAAGACT	TCCATTGCTTTGGATACAAGACT
protein_conc	2702	2702	2748	2748
WB_result	83.1	65.0	84.6	75.0
Ave_WB	83.9	0.0
WB_DONE_date	10/14/16	6/12/19
MW	35kDa	35kDa
IP	1	2	1
antibody_Cat#	A301-781A	A301-781A	lot 1	lot 2
Antibody DCC ID	ENCAB697LIX	ENCAB117HMC
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	907	909	908	910

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NUP35	Product_ID: A301-781A Lot_ID: 2 Source: Bethyl Labs Target Name: NUP35-human

Experiment Status

	BGKLV38-41	BGKLV38-42
Sample_ID	BGKLV38-41	BGKLV38-42
Sample Name
Sample Name	NUP35-BGKLV38-41C	NUP35-BGKLV38-42C
RBP	NUP35	NUP35
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6477	6478

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-41	BGKLV38-42
Sample #	61	62
Sample Name	NUP35-BGKLV38-41C	NUP35-BGKLV38-42C
Sample_Name_Alias
Index Well Position	S15	S16
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	283	284
Peak_Molarity	11.60	8.64
libSampleQC_DNA_Well	DNA_Library_set40/set1/G9.png	DNA_Library_set40/set1/H9.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_set40/set1/G4.png	RNA_Library_set40/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGKLV38-41	BGKLV38-42
RBP	NUP35	NUP35
Batch_ID	BGKLV38	BGKLV38
WB_result	83.100	84.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	984	985

Sequencing Information

	BGKLV38-41	BGKLV38-42
Sample_ID	BGKLV38-41	BGKLV38-42
Sample Name	NUP35-BGKLV38-41C	NUP35-BGKLV38-42C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_K	set40_K
total_reads	42,685,938	51,434,946
total_aligned_reads	35,573,170	42,127,314
unique_aligned_reads	32,312,084	38,337,300
percent_uniqueAligned	0.75697	0.74536
correlation_replicates	0.999136	0.999136
spikein_reads	10,270	13,290
percent_spikeins	0.00024	0.00026
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	387	388

Data Submission Information

	BGKLV38-41	BGKLV38-41	BGKLV38-41	BGKLV38-41	BGKLV38-41	BGKLV38-41	BGKLV38-42	BGKLV38-42	BGKLV38-42	BGKLV38-42
ENCODE_alias	brenton-graveley:NUP35-BGKLV38-C	brenton-graveley:NUP35-BGKLV38-41C	brenton-graveley:L-NUP35-BGKLV38-41C	brenton-graveley:NUP35-BGKLV38-41C_ATGTCA_ACBYWVANXX_L005_001.R1.fastq.gz	brenton-graveley:NUP35-BGKLV38-41C_ATGTCA_ACBYWVANXX_L005_001.R2.fastq.gz	brenton-graveley:NUP35-BGKLV38-K562	brenton-graveley:NUP35-BGKLV38-42C	brenton-graveley:L-NUP35-BGKLV38-42C	brenton-graveley:NUP35-BGKLV38-42C_CCGTCC_ACBYWVANXX_L005_001.R1.fastq.gz	brenton-graveley:NUP35-BGKLV38-42C_CCGTCC_ACBYWVANXX_L005_001.R2.fastq.gz
ENCODE_accession	ENCSR953IQF	ENCBS893MGB	ENCLB669KKH	ENCFF340RAS	ENCFF119UJV	ENCSR040QNM	ENCBS863OOF	ENCLB459XYW	ENCFF574GXQ	ENCFF284IKH
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	BGKLV38-41	BGKLV38-41	BGKLV38-41	BGKLV38-41	BGKLV38-41	BGKLV38-41	BGKLV38-42	BGKLV38-42	BGKLV38-42	BGKLV38-42
Sample Name	NUP35-BGKLV38-41C	NUP35-BGKLV38-41C	NUP35-BGKLV38-41C	NUP35-BGKLV38-41C	NUP35-BGKLV38-41C	NUP35-BGKLV38-41C	NUP35-BGKLV38-42C	NUP35-BGKLV38-42C	NUP35-BGKLV38-42C	NUP35-BGKLV38-42C
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		NUP35-BGKLV38-41C.pdf	L-NUP35-BGKLV38-41C.pdf				NUP35-BGKLV38-42C.pdf	L-NUP35-BGKLV38-42C.pdf
ID	1447	1492	1548	1663	1696	7275	1493	1549	1664	1697

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
NUP35-BGKLV38-41C_ATGTCA_ACBYWVANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	387	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	746
NUP35-BGKLV38-41C_ATGTCA_ACBYWVANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	387	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	789
NUP35-BGKLV38-41C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	387					GRCh38	V40	NUP35-BGKLV38-41C_ATGTCA_ACBYWVANXX_L005_001.R1.fastq.gz,NUP35-BGKLV38-41C_ATGTCA_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23488
NUP35-BGKLV38-41C_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	387					GRCh38	V40	NUP35-BGKLV38-41C/Aligned.sortedByCoord.out.bam		ENCORE2	23522
NUP35-BGKLV38-41C_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	387					GRCh38	V40	NUP35-BGKLV38-41C/Aligned.sortedByCoord.out.bam		ENCORE2	23556
NUP35-BGKLV38-41C_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	387					GRCh38	V40	NUP35-BGKLV38-41C/Aligned.sortedByCoord.out.bam		ENCORE2	23590
NUP35-BGKLV38-41C_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	387					GRCh38	V40	NUP35-BGKLV38-41C/Aligned.sortedByCoord.out.bam		ENCORE2	23624
NUP35-BGKLV38-41C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	387					GRCh38	V40	NUP35-BGKLV38-41C_ATGTCA_ACBYWVANXX_L005_001.R1.fastq.gz,NUP35-BGKLV38-41C_ATGTCA_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23658
NUP35-BGKLV38-42C_CCGTCC_ACBYWVANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	388	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	747
NUP35-BGKLV38-42C_CCGTCC_ACBYWVANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	388	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	790
NUP35-BGKLV38-42C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	388					GRCh38	V40	NUP35-BGKLV38-42C_CCGTCC_ACBYWVANXX_L005_001.R1.fastq.gz,NUP35-BGKLV38-42C_CCGTCC_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23489
NUP35-BGKLV38-42C_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	388					GRCh38	V40	NUP35-BGKLV38-42C/Aligned.sortedByCoord.out.bam		ENCORE2	23523
NUP35-BGKLV38-42C_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	388					GRCh38	V40	NUP35-BGKLV38-42C/Aligned.sortedByCoord.out.bam		ENCORE2	23557
NUP35-BGKLV38-42C_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	388					GRCh38	V40	NUP35-BGKLV38-42C/Aligned.sortedByCoord.out.bam		ENCORE2	23591
NUP35-BGKLV38-42C_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	388					GRCh38	V40	NUP35-BGKLV38-42C/Aligned.sortedByCoord.out.bam		ENCORE2	23625
NUP35-BGKLV38-42C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	388					GRCh38	V40	NUP35-BGKLV38-42C_CCGTCC_ACBYWVANXX_L005_001.R1.fastq.gz,NUP35-BGKLV38-42C_CCGTCC_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23659