NONO RNA-Seq in HepG2

General Information


RBP	NONO
Cell_Line	HepG2
Method	shRNA
Exp_Name	NONO-BGHLV17-HepG2
ENCODE_series_ID	ENCSR905WEG
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR647NYX
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	NONO_BGHLV17_61
Rep2	NONO_BGHLV17_62
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	81.5
Rep2_qPCR	76.8
Rep1_WB	96.6
Rep2_WB	88.4
Antibody Cat#	A300-587A
Antibody Lot#	A300-587A
Antibody DCC ID	ENCAB467FVY
Status	Released
Project	ENCODE3
ID	434

Experiment Information (Status: Released)

	BGHLV17-61	BGHLV17-61	BGHLV17-62	BGHLV17-62
idx	297	299	298	300
TRCN#_or_BGC#	TRCN0000074559	TRCN0000074559	TRCN0000074559	TRCN0000074559
shRNA_or_gRNA_sequence	GCTGCTACAATGGAAGGAATT	GCTGCTACAATGGAAGGAATT	GCTGCTACAATGGAAGGAATT	GCTGCTACAATGGAAGGAATT
PAM
Name	NONO	NONO	NONO	NONO
Sample_ID	BGHLV17-61	BGHLV17-61	BGHLV17-62	BGHLV17-62
transduction_Date	8/19/2014	8/19/2014	8/19/2014	8/19/2014
days
RBP_name	NONO	NONO	NONO	NONO
qPCR_result	81.5	81.5	76.8	76.8
Ave_qPCR	79.1	79.1
RT-qPCR_primer-F	gagagcaggagattcggatg	gagagcaggagattcggatg
RT-qPCR_primer-R	gcatggcacctctgttgttt	gcatggcacctctgttgttt
protein_conc	2613	2613	3070	3070
WB_result	96.6	72.9	88.4	77.5
Ave_WB	92.5	75.2
WB_DONE_date	12/15/2014	2/26/2016
MW	54kDa	54kDa		wes
IP	1	fu's	1
antibody_Cat#	A300-587A	sc-166702	A300-587A	sc-166702
Antibody DCC ID	ENCAB467FVY	ENCAB097MPS	ENCAB467FVY	ENCAB097MPS
submitted_to_DCC_date	4/2/2015	3/8/2016
Rep1_TPM	98.7	0	0	0
Rep2_TPM	83.4	0	0	0
Action
Library_start_date	9/26/2014		9/26/2014
repeat_library
Note
ID	2362	2364	2363	2365

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NONO	Product_ID: A300-587A Lot_ID: 1 Source: Bethyl Labs Target Name: NONO-human
NONO	Product_ID: sc-166702 Lot_ID: C1810 Source: Santa Cruz Biotech Target Name: NONO-human

Experiment Status

	BGHLV17-61	BGHLV17-62
Sample_ID	BGHLV17-61	BGHLV17-62
Sample Name	NONO_BGHLV17_61	NONO_BGHLV17_62
Sample Name	NONO_BGHLV17_61	NONO_BGHLV17_62
RBP	NONO	NONO
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	594	595

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-61	BGHLV17-62
Sample #
Sample Name	NONO-BGHLV17-61	NONO-BGHLV17-62
Sample_Name_Alias	NONO_BGHLV17_61	NONO_BGHLV17_62
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/E5.png	DNA_Library_LV16-17/set1/F5.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/E7.png	RNA_Library_LV16-17-18/set1/F7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-61	BGHLV17-62
RBP	NONO	NONO
Batch_ID	BGHLV17	BGHLV17
WB_result	96.600	88.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2278	2279

Sequencing Information

	BGHLV17-61	BGHLV17-62
Sample_ID	BGHLV17-61	BGHLV17-62
Sample Name	NONO_BGHLV17_61	NONO_BGHLV17_62
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	65,360,000	50,660,000
total_aligned_reads	57,718,578	45,144,178
unique_aligned_reads	54,396,388	42,590,944
percent_uniqueAligned	0.83226	0.84072
correlation_replicates	0.990886	0.990886
spikein_reads	87,376	108,896
percent_spikeins	0.00134	0.00215
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	920	921

Data Submission Information

	BGHLV17-61	BGHLV17-61
ENCODE_alias	brenton-graveley:NONO_BGHLV17	brenton-graveley:NONO-BGHLV17-HepG2
ENCODE_accession	ENCSR647NYX	ENCSR905WEG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-61	BGHLV17-61
Sample Name	NONO_BGHLV17_61	NONO_BGHLV17_61
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2865	6828

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
NONO_BGHLV17_61_AGTCAA_L005_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	920	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14502
NONO_BGHLV17_61_AGTCAA_L005_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	920	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14540
NONO_BGHLV17_61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	920					GRCh38	V40	NONO_BGHLV17_61_AGTCAA_L005_R1_001.fastq.gz,NONO_BGHLV17_61_AGTCAA_L005_R2_001.fastq.gz		ENCORE2	14578
NONO_BGHLV17_61_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	920					GRCh38	V40	NONO_BGHLV17_61/Aligned.sortedByCoord.out.bam		ENCORE2	14616
NONO_BGHLV17_61_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	920					GRCh38	V40	NONO_BGHLV17_61/Aligned.sortedByCoord.out.bam		ENCORE2	14654
NONO_BGHLV17_61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	920					GRCh38	V40	NONO_BGHLV17_61/Aligned.sortedByCoord.out.bam		ENCORE2	14692
NONO_BGHLV17_61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	920					GRCh38	V40	NONO_BGHLV17_61/Aligned.sortedByCoord.out.bam		ENCORE2	14730
NONO_BGHLV17_61_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	920					GRCh38	V40	NONO_BGHLV17_61_AGTCAA_L005_R1_001.fastq.gz,NONO_BGHLV17_61_AGTCAA_L005_R2_001.fastq.gz		ENCORE2	14768
NONO_BGHLV17_62_AGTTCC_L005_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	921	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14503
NONO_BGHLV17_62_AGTTCC_L005_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	921	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14541
NONO_BGHLV17_62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	921					GRCh38	V40	NONO_BGHLV17_62_AGTTCC_L005_R1_001.fastq.gz,NONO_BGHLV17_62_AGTTCC_L005_R2_001.fastq.gz		ENCORE2	14579
NONO_BGHLV17_62_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	921					GRCh38	V40	NONO_BGHLV17_62/Aligned.sortedByCoord.out.bam		ENCORE2	14617
NONO_BGHLV17_62_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	921					GRCh38	V40	NONO_BGHLV17_62/Aligned.sortedByCoord.out.bam		ENCORE2	14655
NONO_BGHLV17_62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	921					GRCh38	V40	NONO_BGHLV17_62/Aligned.sortedByCoord.out.bam		ENCORE2	14693
NONO_BGHLV17_62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	921					GRCh38	V40	NONO_BGHLV17_62/Aligned.sortedByCoord.out.bam		ENCORE2	14731
NONO_BGHLV17_62_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	921					GRCh38	V40	NONO_BGHLV17_62_AGTTCC_L005_R1_001.fastq.gz,NONO_BGHLV17_62_AGTTCC_L005_R2_001.fastq.gz		ENCORE2	14769