NAA15 RNA-Seq in K562

General Information


RBP	NAA15
Cell_Line	K562
Method	shRNA
Exp_Name	NAA15-BGKLV32-K562
ENCODE_series_ID	ENCSR458HEM
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR945GUR
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	NAA15_BGKLV32-41
Rep2	NAA15_BGKLV32-42
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	78.9
Rep2_qPCR	89.8
Rep1_WB	87.0
Rep2_WB	85.5
Antibody Cat#	A302-147
Antibody Lot#	A302-147
Antibody DCC ID	ENCAB161WRM
Status	Released
Project	ENCODE3
ID	712

Experiment Information (Status: Released)

	BGKLV32-41	BGKLV32-42
idx	640	641
TRCN#_or_BGC#	TRCN0000061332	TRCN0000061332
shRNA_or_gRNA_sequence	CCAGTTTGACTTTCATACATA	CCAGTTTGACTTTCATACATA
PAM
Name	NAA15/NARG1	NAA15/NARG1
Sample_ID	BGKLV32-41	BGKLV32-42
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	NAA15	NAA15
qPCR_result	78.9	89.8
Ave_qPCR	84.4
RT-qPCR_primer-F	ggagcaacgaatccaaagaa
RT-qPCR_primer-R	tggcagctgataatctgtgtg
protein_conc	3194	3513
WB_result	87.0	85.5
Ave_WB	86.3
WB_DONE_date	2/8/2016
MW	101kDa	wes
IP
antibody_Cat#	A302-147	A302-147
Antibody DCC ID	ENCAB161WRM	ENCAB161WRM
submitted_to_DCC_date	3/8/2016
Rep1_TPM	26.45562768	0
Rep2_TPM	12.6415726	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	731	732

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NAA15	Product_ID: A302-147A Lot_ID: 1 Source: Bethyl Labs Target Name: NAA15-human

Experiment Status

	BGKLV32-41	BGKLV32-42
Sample_ID	BGKLV32-41	BGKLV32-42
Sample Name	NAA15_BGKLV32-41	NAA15_BGKLV32-42
Sample Name	NAA15_BGKLV32-41	NAA15_BGKLV32-42
RBP	NAA15	NAA15
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1173	1174

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-41	BGKLV32-42
Sample #
Sample Name	NAA15-BGKLV32-41	NAA15-BGKLV32-42
Sample_Name_Alias	NAA15_BGKLV32-41	NAA15_BGKLV32-42
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/G8.png	DNA_Library_LV33-34-25B-32/set1/H8.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/G1.png	RNA_Library_LV32-33-34/set1/H1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-41	BGKLV32-42
RBP	NAA15	NAA15
Batch_ID	BGKLV32	BGKLV32
WB_result	87.000	85.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2858	2859

Sequencing Information

	BGKLV32-41	BGKLV32-42
Sample_ID	BGKLV32-41	BGKLV32-42
Sample Name	NAA15_BGKLV32-41	NAA15_BGKLV32-42
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	57,119,604	64,616,122
total_aligned_reads	49,642,104	55,711,920
unique_aligned_reads	45,686,620	51,102,582
percent_uniqueAligned	0.79984	0.79086
correlation_replicates	0.995330	0.995330
spikein_reads	227,780	291,772
percent_spikeins	0.00399	0.00452
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1507	1508

Data Submission Information

	BGKLV32-41	BGKLV32-41
ENCODE_alias	brenton-graveley:NAA15_BGKLV32	brenton-graveley:NAA15-BGKLV32-K562
ENCODE_accession	ENCSR945GUR	ENCSR458HEM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-41	BGKLV32-41
Sample Name	NAA15_BGKLV32-41	NAA15_BGKLV32-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3126	6817

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
NAA15_BGKLV32-41_ACTGAT_L003_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1507	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21206
NAA15_BGKLV32-41_ACTGAT_L003_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1507	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21236
NAA15_BGKLV32-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1507					GRCh38	V40	NAA15_BGKLV32-41_ACTGAT_L003_001.R1.fastq.gz,NAA15_BGKLV32-41_ACTGAT_L003_001.R2.fastq.gz		ENCORE2	21266
NAA15_BGKLV32-41_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1507					GRCh38	V40	NAA15_BGKLV32-41/Aligned.sortedByCoord.out.bam		ENCORE2	21296
NAA15_BGKLV32-41_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1507					GRCh38	V40	NAA15_BGKLV32-41/Aligned.sortedByCoord.out.bam		ENCORE2	21326
NAA15_BGKLV32-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1507					GRCh38	V40	NAA15_BGKLV32-41/Aligned.sortedByCoord.out.bam		ENCORE2	21356
NAA15_BGKLV32-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1507					GRCh38	V40	NAA15_BGKLV32-41/Aligned.sortedByCoord.out.bam		ENCORE2	21386
NAA15_BGKLV32-41_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1507					GRCh38	V40	NAA15_BGKLV32-41_ACTGAT_L003_001.R1.fastq.gz,NAA15_BGKLV32-41_ACTGAT_L003_001.R2.fastq.gz		ENCORE2	21416
NAA15_BGKLV32-42_ATTCCT_L003_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1508	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21207
NAA15_BGKLV32-42_ATTCCT_L003_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1508	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21237
NAA15_BGKLV32-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1508					GRCh38	V40	NAA15_BGKLV32-42_ATTCCT_L003_001.R1.fastq.gz,NAA15_BGKLV32-42_ATTCCT_L003_001.R2.fastq.gz		ENCORE2	21267
NAA15_BGKLV32-42_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1508					GRCh38	V40	NAA15_BGKLV32-42/Aligned.sortedByCoord.out.bam		ENCORE2	21297
NAA15_BGKLV32-42_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1508					GRCh38	V40	NAA15_BGKLV32-42/Aligned.sortedByCoord.out.bam		ENCORE2	21327
NAA15_BGKLV32-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1508					GRCh38	V40	NAA15_BGKLV32-42/Aligned.sortedByCoord.out.bam		ENCORE2	21357
NAA15_BGKLV32-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1508					GRCh38	V40	NAA15_BGKLV32-42/Aligned.sortedByCoord.out.bam		ENCORE2	21387
NAA15_BGKLV32-42_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1508					GRCh38	V40	NAA15_BGKLV32-42_ATTCCT_L003_001.R1.fastq.gz,NAA15_BGKLV32-42_ATTCCT_L003_001.R2.fastq.gz		ENCORE2	21417