AARS RNA-Seq in K562

General Information


RBP	AARS
Cell_Line	K562
Method	shRNA
Exp_Name	AARS-BGKLV21-K562
ENCODE_series_ID	ENCSR905BVF
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR599UDS
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	AARS_BGKLV21_3_17558
Rep2	AARS_BGKLV21_4_17559
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	43.8
Rep2_qPCR	47.5
Rep1_WB	66.9
Rep2_WB	73.9
Antibody Cat#	A303-475A
Antibody Lot#	A303-475A
Antibody DCC ID	ENCAB346SAT
Status	Released
Project	ENCODE3
ID	506

Experiment Information (Status: Released)

	BGKLV21-3	BGKLV21-4
idx	274	275
TRCN#_or_BGC#	TRCN0000045691	TRCN0000045691
shRNA_or_gRNA_sequence	GACCTCATTATGCTGGACATT	GACCTCATTATGCTGGACATT
PAM
Name	AARS	AARS
Sample_ID	BGKLV21-3	BGKLV21-4
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	AARS	AARS
qPCR_result	43.8	47.5
Ave_qPCR	45.6
RT-qPCR_primer-F	tgctggagatctggaacctt
RT-qPCR_primer-R	ccatccctgtgtcaatgctt
protein_conc	2759	2624
WB_result	66.9	73.9
Ave_WB	70.4
WB_DONE_date	2/4/2015
MW
IP	1	1
antibody_Cat#	A303-475A	A303-475A
Antibody DCC ID	ENCAB346SAT	ENCAB346SAT
submitted_to_DCC_date	4/2/2015
Rep1_TPM	105.869847	0
Rep2_TPM	275.495266	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	299	300

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

	BGKLV21-3	BGKLV21-4
Sample_ID	BGKLV21-3	BGKLV21-4
Sample Name	AARS_BGKLV21_3_17558	AARS_BGKLV21_4_17559
Sample Name	AARS_BGKLV21_3_17558	AARS_BGKLV21_4_17559
RBP	AARS	AARS
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	744	745

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-3	BGKLV21-4
Sample #
Sample Name	AARS-BGKLV21-3	AARS-BGKLV21-4
Sample_Name_Alias	AARS_BGKLV21_3_17558	AARS_BGKLV21_4_17559
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/C5.png	DNA_Library_LV21-24/set1/D5.png
RIN	9.9	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E7.png	RNA_Library_LV19-21-24/set1/F7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-3	BGKLV21-4
RBP	AARS	AARS
Batch_ID	BGKLV21	BGKLV21
WB_result	66.900	73.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2430	2431

Sequencing Information

	BGKLV21-3	BGKLV21-4
Sample_ID	BGKLV21-3	BGKLV21-4
Sample Name	AARS_BGKLV21_3_17558	AARS_BGKLV21_4_17559
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	38,090,000	45,760,000
total_aligned_reads	33,506,648	40,450,150
unique_aligned_reads	30,829,820	37,127,280
percent_uniqueAligned	0.80939	0.81135
correlation_replicates	0.998735	0.998735
spikein_reads	204,966	244,688
percent_spikeins	0.00538	0.00535
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1036	1037

Data Submission Information

	BGKLV21-3	BGKLV21-3
ENCODE_alias	brenton-graveley:AARS_BGKLV21	brenton-graveley:AARS-BGKLV21-K562
ENCODE_accession	ENCSR599UDS	ENCSR905BVF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-3	BGKLV21-3
Sample Name	AARS_BGKLV21_3_17558	AARS_BGKLV21_3_17558
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2958	6573

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_BGKLV21_3_17558_TTAGGC_L001_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1036	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15920
AARS_BGKLV21_3_17558_TTAGGC_L001_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1036	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15964
AARS_BGKLV21_3_17558_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1036					GRCh38	V40	AARS_BGKLV21_3_17558_TTAGGC_L001_R1_001.fastq.gz,AARS_BGKLV21_3_17558_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	16008
AARS_BGKLV21_3_17558_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1036					GRCh38	V40	AARS_BGKLV21_3_17558/Aligned.sortedByCoord.out.bam		ENCORE2	16052
AARS_BGKLV21_3_17558_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1036					GRCh38	V40	AARS_BGKLV21_3_17558/Aligned.sortedByCoord.out.bam		ENCORE2	16096
AARS_BGKLV21_3_17558_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1036					GRCh38	V40	AARS_BGKLV21_3_17558/Aligned.sortedByCoord.out.bam		ENCORE2	16140
AARS_BGKLV21_3_17558_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1036					GRCh38	V40	AARS_BGKLV21_3_17558/Aligned.sortedByCoord.out.bam		ENCORE2	16184
AARS_BGKLV21_3_17558_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1036					GRCh38	V40	AARS_BGKLV21_3_17558_TTAGGC_L001_R1_001.fastq.gz,AARS_BGKLV21_3_17558_TTAGGC_L001_R2_001.fastq.gz		ENCORE2	16228
AARS_BGKLV21_4_17559_TGACCA_L001_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1037	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15921
AARS_BGKLV21_4_17559_TGACCA_L001_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1037	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15965
AARS_BGKLV21_4_17559_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1037					GRCh38	V40	AARS_BGKLV21_4_17559_TGACCA_L001_R1_001.fastq.gz,AARS_BGKLV21_4_17559_TGACCA_L001_R2_001.fastq.gz		ENCORE2	16009
AARS_BGKLV21_4_17559_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1037					GRCh38	V40	AARS_BGKLV21_4_17559/Aligned.sortedByCoord.out.bam		ENCORE2	16053
AARS_BGKLV21_4_17559_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1037					GRCh38	V40	AARS_BGKLV21_4_17559/Aligned.sortedByCoord.out.bam		ENCORE2	16097
AARS_BGKLV21_4_17559_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1037					GRCh38	V40	AARS_BGKLV21_4_17559/Aligned.sortedByCoord.out.bam		ENCORE2	16141
AARS_BGKLV21_4_17559_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1037					GRCh38	V40	AARS_BGKLV21_4_17559/Aligned.sortedByCoord.out.bam		ENCORE2	16185
AARS_BGKLV21_4_17559_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1037					GRCh38	V40	AARS_BGKLV21_4_17559_TGACCA_L001_R1_001.fastq.gz,AARS_BGKLV21_4_17559_TGACCA_L001_R2_001.fastq.gz		ENCORE2	16229