NAA15 RNA-Seq in HepG2

General Information


RBP	NAA15
Cell_Line	HepG2
Method	shRNA
Exp_Name	NAA15-BGHLV30-HepG2
ENCODE_series_ID	ENCSR396BIJ
Batch_ID	BGHLV30
Pool ID	Pool-151215B
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR355OQC
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	NAA15_BGHLV30-45
Rep2	NAA15_BGHLV30-46
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	76.7
Rep2_qPCR	65.4
Rep1_WB	88.3
Rep2_WB	89.1
Antibody Cat#	A302-147A
Antibody Lot#	A302-147A
Antibody DCC ID	ENCAB161WRM
Status	Released
Project	ENCODE3
ID	686

Experiment Information (Status: Released)

	BGHLV30-45	BGHLV30-46
idx	733	734
TRCN#_or_BGC#	TRCN0000061332	TRCN0000061332
shRNA_or_gRNA_sequence	CCAGTTTGACTTTCATACATA	CCAGTTTGACTTTCATACATA
PAM
Name	NAA15/NARG1	NAA15/NARG1
Sample_ID	BGHLV30-45	BGHLV30-46
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	NAA15	NAA15
qPCR_result	76.7	65.4
Ave_qPCR	71.1
RT-qPCR_primer-F	ggagcaacgaatccaaagaa
RT-qPCR_primer-R	tggcagctgataatctgtgtg
protein_conc	4813	5056
WB_result	88.3	89.1
Ave_WB	88.7
WB_DONE_date	9/22/2015
MW	101kDa
IP	1	1
antibody_Cat#	A302-147A	A302-147A
Antibody DCC ID	ENCAB161WRM	ENCAB161WRM
submitted_to_DCC_date	12/7/2015
Rep1_TPM	9.6	0
Rep2_TPM	8.7	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2824	2825

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

	BGHLV30-45	BGHLV30-46
Sample_ID	BGHLV30-45	BGHLV30-46
Sample Name	NAA15_BGHLV30-45	NAA15_BGHLV30-46
Sample Name	NAA15_BGHLV30-45	NAA15_BGHLV30-46
RBP	NAA15	NAA15
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1062	1063

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-45	BGHLV30-46
Sample #
Sample Name	NAA15-BGHLV30-45	NAA15-BGHLV30-46
Sample_Name_Alias	NAA15_BGHLV30-45	NAA15_BGHLV30-46
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/G11.png	DNA_Library_LV28-29-30/set1/H11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A7.png	RNA_Library_LV29-30-31-32/set1/B7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-45	BGHLV30-46
RBP	NAA15	NAA15
Batch_ID	BGHLV30	BGHLV30
WB_result	88.300	89.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2754	2755

Sequencing Information

	BGHLV30-45	BGHLV30-46
Sample_ID	BGHLV30-45	BGHLV30-46
Sample Name	NAA15_BGHLV30-45	NAA15_BGHLV30-46
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set30	set30
total_reads	69,128,276	58,761,332
total_aligned_reads	60,624,448	51,113,806
unique_aligned_reads	57,243,576	48,258,676
percent_uniqueAligned	0.82808	0.82127
correlation_replicates	0.999414	0.999414
spikein_reads	178,990	148,614
percent_spikeins	0.00259	0.00253
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1405	1406

Data Submission Information

	BGHLV30-45	BGHLV30-45
ENCODE_alias	brenton-graveley:NAA15_BGHLV30	brenton-graveley:NAA15-BGHLV30-HepG2
ENCODE_accession	ENCSR355OQC	ENCSR396BIJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-45	BGHLV30-45
Sample Name	NAA15_BGHLV30-45	NAA15_BGHLV30-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3080	6816

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_BGHLV30-45_ATGTCA_L004_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1405	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20720
NAA15_BGHLV30-45_ATGTCA_L004_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1405	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20754
NAA15_BGHLV30-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1405					GRCh38	V40	NAA15_BGHLV30-45_ATGTCA_L004_001.R1.fastq.gz,NAA15_BGHLV30-45_ATGTCA_L004_001.R2.fastq.gz		ENCORE2	20788
NAA15_BGHLV30-45_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1405					GRCh38	V40	NAA15_BGHLV30-45/Aligned.sortedByCoord.out.bam		ENCORE2	20822
NAA15_BGHLV30-45_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1405					GRCh38	V40	NAA15_BGHLV30-45/Aligned.sortedByCoord.out.bam		ENCORE2	20856
NAA15_BGHLV30-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1405					GRCh38	V40	NAA15_BGHLV30-45/Aligned.sortedByCoord.out.bam		ENCORE2	20890
NAA15_BGHLV30-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1405					GRCh38	V40	NAA15_BGHLV30-45/Aligned.sortedByCoord.out.bam		ENCORE2	20924
NAA15_BGHLV30-45_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1405					GRCh38	V40	NAA15_BGHLV30-45_ATGTCA_L004_001.R1.fastq.gz,NAA15_BGHLV30-45_ATGTCA_L004_001.R2.fastq.gz		ENCORE2	20958
NAA15_BGHLV30-46_CCGTCC_L004_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1406	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20721
NAA15_BGHLV30-46_CCGTCC_L004_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1406	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20755
NAA15_BGHLV30-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1406					GRCh38	V40	NAA15_BGHLV30-46_CCGTCC_L004_001.R1.fastq.gz,NAA15_BGHLV30-46_CCGTCC_L004_001.R2.fastq.gz		ENCORE2	20789
NAA15_BGHLV30-46_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1406					GRCh38	V40	NAA15_BGHLV30-46/Aligned.sortedByCoord.out.bam		ENCORE2	20823
NAA15_BGHLV30-46_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1406					GRCh38	V40	NAA15_BGHLV30-46/Aligned.sortedByCoord.out.bam		ENCORE2	20857
NAA15_BGHLV30-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1406					GRCh38	V40	NAA15_BGHLV30-46/Aligned.sortedByCoord.out.bam		ENCORE2	20891
NAA15_BGHLV30-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1406					GRCh38	V40	NAA15_BGHLV30-46/Aligned.sortedByCoord.out.bam		ENCORE2	20925
NAA15_BGHLV30-46_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1406					GRCh38	V40	NAA15_BGHLV30-46_CCGTCC_L004_001.R1.fastq.gz,NAA15_BGHLV30-46_CCGTCC_L004_001.R2.fastq.gz		ENCORE2	20959