AARS RNA-Seq in HepG2

General Information


RBP	AARS
Cell_Line	HepG2
Method	shRNA
Exp_Name	AARS-BGHLV17-HepG2
ENCODE_series_ID	ENCSR642EFL
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR547NWD
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	AARS_BGHLV17_1
Rep2	AARS_BGHLV17_2
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	55.0
Rep2_qPCR	59.2
Rep1_WB	38.8
Rep2_WB	36.6
Antibody Cat#	A303-475A
Antibody Lot#	A303-475A
Antibody DCC ID	ENCAB346SAT
Status	Released
Project	ENCODE3
ID	426

Experiment Information (Status: Released)

	BGHLV17-1	BGHLV17-2
idx	237	238
TRCN#_or_BGC#	TRCN0000045691	TRCN0000045691
shRNA_or_gRNA_sequence	GACCTCATTATGCTGGACATT	GACCTCATTATGCTGGACATT
PAM
Name	AARS	AARS
Sample_ID	BGHLV17-1	BGHLV17-2
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	AARS	AARS
qPCR_result	55.0	59.2
Ave_qPCR	57.1
RT-qPCR_primer-F	tgctggagatctggaacctt
RT-qPCR_primer-R	ccatccctgtgtcaatgctt
protein_conc	2848	2204
WB_result	38.8	36.6
Ave_WB	37.7
WB_DONE_date	2/4/2015
MW	107kDa
IP	1	1
antibody_Cat#	A303-475A	A303-475A
Antibody DCC ID	ENCAB346SAT	ENCAB346SAT
submitted_to_DCC_date	4/2/2015
Rep1_TPM	81.8	0
Rep2_TPM	108.5	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2302	2303

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AARS	Product_ID: A303-475A Lot_ID: 1 Source: Bethyl Labs Target Name: AARS-human

Experiment Status

	BGHLV17-1	BGHLV17-2
Sample_ID	BGHLV17-1	BGHLV17-2
Sample Name	AARS_BGHLV17_1	AARS_BGHLV17_2
Sample Name	AARS_BGHLV17_1	AARS_BGHLV17_2
RBP	AARS	AARS
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	578	579

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-1	BGHLV17-2
Sample #
Sample Name	AARS-BGHLV17-1	AARS-BGHLV17-2
Sample_Name_Alias	AARS_BGHLV17_1	AARS_BGHLV17_2
Index Well Position	S03	S04
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/C1.png	DNA_Library_LV16-17/set1/D1.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/C3.png	RNA_Library_LV16-17-18/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-1	BGHLV17-2
RBP	AARS	AARS
Batch_ID	BGHLV17	BGHLV17
WB_result	38.800	36.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2262	2263

Sequencing Information

	BGHLV17-1	BGHLV17-2
Sample_ID	BGHLV17-1	BGHLV17-2
Sample Name	AARS_BGHLV17_1	AARS_BGHLV17_2
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	58,020,000	79,730,000
total_aligned_reads	51,534,958	70,451,084
unique_aligned_reads	48,525,166	66,356,740
percent_uniqueAligned	0.83635	0.83227
correlation_replicates	0.997170	0.997170
spikein_reads	149,994	246,788
percent_spikeins	0.00259	0.00310
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	904	905

Data Submission Information

	BGHLV17-1	BGHLV17-1
ENCODE_alias	brenton-graveley:AARS_BGHLV17	brenton-graveley:AARS-BGHLV17-HepG2
ENCODE_accession	ENCSR547NWD	ENCSR642EFL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-1	BGHLV17-1
Sample Name	AARS_BGHLV17_1	AARS_BGHLV17_1
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2857	6572

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
AARS_BGHLV17_1_TTAGGC_L001_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	904	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	14486
AARS_BGHLV17_1_TTAGGC_L001_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	904	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	14524
AARS_BGHLV17_1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	904					GRCh38	V40	AARS_BGHLV17_1_TTAGGC_L001_R1_001.fastq.gz,AARS_BGHLV17_1_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	14562
AARS_BGHLV17_1_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	904					GRCh38	V40	AARS_BGHLV17_1/Aligned.sortedByCoord.out.bam		ENCORE2	14600
AARS_BGHLV17_1_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	904					GRCh38	V40	AARS_BGHLV17_1/Aligned.sortedByCoord.out.bam		ENCORE2	14638
AARS_BGHLV17_1_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	904					GRCh38	V40	AARS_BGHLV17_1/Aligned.sortedByCoord.out.bam		ENCORE2	14676
AARS_BGHLV17_1_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	904					GRCh38	V40	AARS_BGHLV17_1/Aligned.sortedByCoord.out.bam		ENCORE2	14714
AARS_BGHLV17_1_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	904					GRCh38	V40	AARS_BGHLV17_1_TTAGGC_L001_R1_001.fastq.gz,AARS_BGHLV17_1_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	14752
AARS_BGHLV17_2_TGACCA_L001_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	905	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	14487
AARS_BGHLV17_2_TGACCA_L001_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	905	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	14525
AARS_BGHLV17_2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	905					GRCh38	V40	AARS_BGHLV17_2_TGACCA_L001_R1_001.fastq.gz,AARS_BGHLV17_2_TGACCA_L001_R2_001.fastq.gz		ENCORE2	14563
AARS_BGHLV17_2_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	905					GRCh38	V40	AARS_BGHLV17_2/Aligned.sortedByCoord.out.bam		ENCORE2	14601
AARS_BGHLV17_2_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	905					GRCh38	V40	AARS_BGHLV17_2/Aligned.sortedByCoord.out.bam		ENCORE2	14639
AARS_BGHLV17_2_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	905					GRCh38	V40	AARS_BGHLV17_2/Aligned.sortedByCoord.out.bam		ENCORE2	14677
AARS_BGHLV17_2_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	905					GRCh38	V40	AARS_BGHLV17_2/Aligned.sortedByCoord.out.bam		ENCORE2	14715
AARS_BGHLV17_2_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	905					GRCh38	V40	AARS_BGHLV17_2_TGACCA_L001_R1_001.fastq.gz,AARS_BGHLV17_2_TGACCA_L001_R2_001.fastq.gz		ENCORE2	14753