NONO RNA-Seq in K562

General Information


RBP	NONO
Cell_Line	K562
Method	shRNA
Exp_Name	NONO-BGKLV19-K562
ENCODE_series_ID	ENCSR868GYG
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR398HXV
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	NONO_BGKLV19_35B
Rep2	NONO_BGKLV19_36B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	75.9
Rep2_qPCR	78.5
Rep1_WB	50.0
Rep2_WB	51.5
Antibody Cat#	A300-587A
Antibody Lot#	A300-587A
Antibody DCC ID	ENCAB467FVY
Status	Released
Project	ENCODE3
ID	475

Experiment Information (Status: Released)

	BGKLV19-35	BGKLV19-36
idx	242	243
TRCN#_or_BGC#	TRCN0000074559	TRCN0000074559
shRNA_or_gRNA_sequence	GCTGCTACAATGGAAGGAATT	GCTGCTACAATGGAAGGAATT
PAM
Name	NONO	NONO
Sample_ID	BGKLV19-35	BGKLV19-36
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	NONO	NONO
qPCR_result	75.9	78.5
Ave_qPCR	77.2
RT-qPCR_primer-F	gagagcaggagattcggatg
RT-qPCR_primer-R	gcatggcacctctgttgttt
protein_conc	2908	2895
WB_result	50.0	51.5
Ave_WB	50.8
WB_DONE_date	12/15/2014
MW	54kDa
IP	1	1
antibody_Cat#	A300-587A	A300-587A
Antibody DCC ID	ENCAB467FVY	ENCAB467FVY
submitted_to_DCC_date	4/2/2015
Rep1_TPM	105.842115	0
Rep2_TPM	136.766227	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	267	268

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

Experiment Status

	BGKLV19-35	BGKLV19-36
Sample_ID	BGKLV19-35	BGKLV19-36
Sample Name	NONO_BGKLV19_35B	NONO_BGKLV19_36B
Sample Name	NONO_BGKLV19_35B	NONO_BGKLV19_36B
RBP	NONO	NONO
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	680	681

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-35	BGKLV19-36
Sample #
Sample Name	NONO-BGKLV19-35B	NONO-BGKLV19-36B
Sample_Name_Alias	NONO_BGKLV19_35B	NONO_BGKLV19_36B
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/E9.png	DNA_Library_LV18-19/set1/F9.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/A4.png	RNA_Library_LV19-21-24/set1/B4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-35	BGKLV19-36
RBP	NONO	NONO
Batch_ID	BGKLV19	BGKLV19
WB_result	50.000	51.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2366	2367

Sequencing Information

	BGKLV19-35	BGKLV19-36
Sample_ID	BGKLV19-35	BGKLV19-36
Sample Name	NONO_BGKLV19_35B	NONO_BGKLV19_36B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	43,450,000	47,540,000
total_aligned_reads	40,244,690	43,839,808
unique_aligned_reads	36,713,582	40,099,890
percent_uniqueAligned	0.84496	0.84350
correlation_replicates	0.974924	0.974924
spikein_reads	172,254	195,810
percent_spikeins	0.00396	0.00412
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1008	1009

Data Submission Information

	BGKLV19-35	BGKLV19-35
ENCODE_alias	brenton-graveley:NONO_BGKLV19	brenton-graveley:NONO-BGKLV19-K562
ENCODE_accession	ENCSR398HXV	ENCSR868GYG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-35	BGKLV19-35
Sample Name	NONO_BGKLV19_35B	NONO_BGKLV19_35B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2889	6829

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_BGKLV19_35B_CGTACG_L004_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1008	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15120
NONO_BGKLV19_35B_CGTACG_L004_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1008	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15178
NONO_BGKLV19_35B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1008					GRCh38	V40	NONO_BGKLV19_35B_CGTACG_L004_R1_001.fastq.gz,NONO_BGKLV19_35B_CGTACG_L004_R2_001.fastq.gz		ENCORE2	15236
NONO_BGKLV19_35B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1008					GRCh38	V40	NONO_BGKLV19_35B/Aligned.sortedByCoord.out.bam		ENCORE2	15307
NONO_BGKLV19_35B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1008					GRCh38	V40	NONO_BGKLV19_35B/Aligned.sortedByCoord.out.bam		ENCORE2	15365
NONO_BGKLV19_35B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1008					GRCh38	V40	NONO_BGKLV19_35B/Aligned.sortedByCoord.out.bam		ENCORE2	15423
NONO_BGKLV19_35B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1008					GRCh38	V40	NONO_BGKLV19_35B/Aligned.sortedByCoord.out.bam		ENCORE2	15481
NONO_BGKLV19_35B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1008					GRCh38	V40	NONO_BGKLV19_35B_CGTACG_L004_R1_001.fastq.gz,NONO_BGKLV19_35B_CGTACG_L004_R2_001.fastq.gz		ENCORE2	16378
NONO_BGKLV19_36B_GAGTGG_L004_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1009	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15121
NONO_BGKLV19_36B_GAGTGG_L004_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1009	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15179
NONO_BGKLV19_36B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1009					GRCh38	V40	NONO_BGKLV19_36B_GAGTGG_L004_R1_001.fastq.gz,NONO_BGKLV19_36B_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	15237
NONO_BGKLV19_36B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1009					GRCh38	V40	NONO_BGKLV19_36B/Aligned.sortedByCoord.out.bam		ENCORE2	15308
NONO_BGKLV19_36B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1009					GRCh38	V40	NONO_BGKLV19_36B/Aligned.sortedByCoord.out.bam		ENCORE2	15366
NONO_BGKLV19_36B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1009					GRCh38	V40	NONO_BGKLV19_36B/Aligned.sortedByCoord.out.bam		ENCORE2	15424
NONO_BGKLV19_36B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1009					GRCh38	V40	NONO_BGKLV19_36B/Aligned.sortedByCoord.out.bam		ENCORE2	15482
NONO_BGKLV19_36B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1009					GRCh38	V40	NONO_BGKLV19_36B_GAGTGG_L004_R1_001.fastq.gz,NONO_BGKLV19_36B_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	16379