NUP35 RNA-Seq in HepG2

General Information


RBP	NUP35
Cell_Line	HepG2
Method	shRNA
Exp_Name	NUP35-BGHLV27-HepG2
ENCODE_series_ID	ENCSR077SGY
Batch_ID	BGHLV27
Pool ID	Pool-160425
Local_Set_Name	set27
ENCODE_KD_Exp_ID	ENCSR457WBK
ENCODE_CN_Exp_ID	ENCSR960MSV
Rep1	NUP35_BGHLV27-39B
Rep2	NUP35_BGHLV27-40B
CN1	NT_BGHLV27-1B
CN2	NT_BGHLV27-2B
Rep1_qPCR	48.4
Rep2_qPCR	68.7
Rep1_WB	58.5
Rep2_WB	69.3
Antibody Cat#	A301-781A
Antibody Lot#	Lot 1
Antibody DCC ID	ENCAB697LIX
Status	Released
Project	ENCODE3
ID	647

Experiment Information (Status: Released)

	BGHLV27-39	BGHLV27-40
idx	659	660
TRCN#_or_BGC#	TRCN0000072378	TRCN0000072378
shRNA_or_gRNA_sequence	GCTGGTTCCTTCGGTTAGTTA	GCTGGTTCCTTCGGTTAGTTA
PAM
Name	NUP35	NUP35
Sample_ID	BGHLV27-39	BGHLV27-40
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	NUP35	NUP35
qPCR_result	48.4	68.7
Ave_qPCR	58.6
RT-qPCR_primer-F	caaagcctctactagtgattatcagg
RT-qPCR_primer-R	ccaaacatgtactccattgct
protein_conc	4851	4284
WB_result	58.5	69.3
Ave_WB	63.9
WB_DONE_date	10/20/2015
MW	35kDa
IP
antibody_Cat#	A301-781A	Lot 1
Antibody DCC ID	ENCAB697LIX	ENCAB697LIX
submitted_to_DCC_date	12/7/2015
Rep1_TPM	3.2	0
Rep2_TPM	3.6	0
Action
Library_start_date	3/10/2016	3/10/2016
repeat_library
Note
ID	2746	2747

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NUP35	Product_ID: A301-781A Lot_ID: 1 Source: Bethyl Labs Target Name: NUP35-human

Experiment Status

	BGHLV27-39	BGHLV27-40
Sample_ID	BGHLV27-39	BGHLV27-40
Sample Name	NUP35_BGHLV27-39B	NUP35_BGHLV27-40B
Sample Name	NUP35_BGHLV27-39B	NUP35_BGHLV27-40B
RBP	NUP35	NUP35
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1193	1194

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-39	BGHLV27-40
Sample #
Sample Name	NUP35-BGHLV27-39B	NUP35-BGHLV27-40B
Sample_Name_Alias	NUP35_BGHLV27-39B	NUP35_BGHLV27-40B
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-10	2016-03-10
Lib_ID	Lib-160310	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/G11.png	DNA_Library_LV33-34-25B-32/set1/H11.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/C5.png	RNA_Library_LV26-27-28-29/set1/D5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-39	BGHLV27-40
RBP	NUP35	NUP35
Batch_ID	BGHLV27	BGHLV27
WB_result	58.500	69.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2878	2879

Sequencing Information

	BGHLV27-39	BGHLV27-40
Sample_ID	BGHLV27-39	BGHLV27-40
Sample Name	NUP35_BGHLV27-39B	NUP35_BGHLV27-40B
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set27	set27
total_reads	130,295,012	98,264,152
total_aligned_reads	86,299,320	64,875,852
unique_aligned_reads	81,168,724	60,969,468
percent_uniqueAligned	0.62296	0.62047
correlation_replicates	0.995665	0.995665
spikein_reads	172,234	136,678
percent_spikeins	0.00132	0.00139
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1527	1528

Data Submission Information

	BGHLV27-39	BGHLV27-39
ENCODE_alias	brenton-graveley:NUP35_BGHLV27	brenton-graveley:NUP35-BGHLV27-HepG2
ENCODE_accession	ENCSR457WBK	ENCSR077SGY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-39	BGHLV27-39
Sample Name	NUP35_BGHLV27-39B	NUP35_BGHLV27-39B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3136	6836

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_BGHLV27-39B_AGTCAA_L006_001.R1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1527	HiSeq2500	100	paired-ended	1	GRCh38	V40		NT_BGHLV27-1B_GGCTAC_L006_001.R1.fastq.gz,NT_BGHLV27-2B_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	20016
NUP35_BGHLV27-39B_AGTCAA_L006_001.R2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1527	HiSeq2500	100	paired-ended	2				NT_BGHLV27-1B_GGCTAC_L006_001.R2.fastq.gz,NT_BGHLV27-2B_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	20038
NUP35_BGHLV27-39B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1527					GRCh38	V40	NUP35_BGHLV27-39B_AGTCAA_L006_001.R1.fastq.gz,NUP35_BGHLV27-39B_AGTCAA_L006_001.R2.fastq.gz		ENCORE2	20060
NUP35_BGHLV27-39B_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1527					GRCh38	V40	NUP35_BGHLV27-39B/Aligned.sortedByCoord.out.bam		ENCORE2	20082
NUP35_BGHLV27-39B_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1527					GRCh38	V40	NUP35_BGHLV27-39B/Aligned.sortedByCoord.out.bam		ENCORE2	20104
NUP35_BGHLV27-39B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1527					GRCh38	V40	NUP35_BGHLV27-39B/Aligned.sortedByCoord.out.bam		ENCORE2	20126
NUP35_BGHLV27-39B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1527					GRCh38	V40	NUP35_BGHLV27-39B/Aligned.sortedByCoord.out.bam		ENCORE2	20148
NUP35_BGHLV27-39B_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1527					GRCh38	V40	NUP35_BGHLV27-39B_AGTCAA_L006_001.R1.fastq.gz,NUP35_BGHLV27-39B_AGTCAA_L006_001.R2.fastq.gz		ENCORE2	20688
NUP35_BGHLV27-40B_AGTTCC_L006_001.R1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1528	HiSeq2500	100	paired-ended	1	GRCh38	V40		NT_BGHLV27-1B_GGCTAC_L006_001.R1.fastq.gz,NT_BGHLV27-2B_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	20017
NUP35_BGHLV27-40B_AGTTCC_L006_001.R2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1528	HiSeq2500	100	paired-ended	2				NT_BGHLV27-1B_GGCTAC_L006_001.R2.fastq.gz,NT_BGHLV27-2B_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	20039
NUP35_BGHLV27-40B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1528					GRCh38	V40	NUP35_BGHLV27-40B_AGTTCC_L006_001.R1.fastq.gz,NUP35_BGHLV27-40B_AGTTCC_L006_001.R2.fastq.gz		ENCORE2	20061
NUP35_BGHLV27-40B_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1528					GRCh38	V40	NUP35_BGHLV27-40B/Aligned.sortedByCoord.out.bam		ENCORE2	20083
NUP35_BGHLV27-40B_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1528					GRCh38	V40	NUP35_BGHLV27-40B/Aligned.sortedByCoord.out.bam		ENCORE2	20105
NUP35_BGHLV27-40B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1528					GRCh38	V40	NUP35_BGHLV27-40B/Aligned.sortedByCoord.out.bam		ENCORE2	20127
NUP35_BGHLV27-40B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1528					GRCh38	V40	NUP35_BGHLV27-40B/Aligned.sortedByCoord.out.bam		ENCORE2	20149
NUP35_BGHLV27-40B_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1528					GRCh38	V40	NUP35_BGHLV27-40B_AGTTCC_L006_001.R1.fastq.gz,NUP35_BGHLV27-40B_AGTTCC_L006_001.R2.fastq.gz		ENCORE2	20689