AQR RNA-Seq in K562

General Information


RBP	AQR
Cell_Line	K562
Method	shRNA
Exp_Name	AQR-BGKLV38-K562
ENCODE_series_ID	ENCSR458PUT
Batch_ID	BGKLV38
Pool ID	Pool-161129
Local_Set_Name	set38
ENCODE_KD_Exp_ID	ENCSR624OUI
ENCODE_CN_Exp_ID	ENCSR718EWL
Rep1	AQR_BGKLV38-19
Rep2	AQR_BGKLV38-20
CN1	NT_BGKLV38-1
CN2	NT_BGKLV38-2
Rep1_qPCR	21.2
Rep2_qPCR	35.3
Rep1_WB	71.9
Rep2_WB	67.9
Antibody Cat#	A302-547A
Antibody Lot#	A302-547A
Antibody DCC ID	ENCAB609IGM
Status	Released
Project	ENCODE3
ID	755

Experiment Information (Status: Released)

	BGKLV38-19	BGKLV38-20
idx	790	791
TRCN#_or_BGC#	TRCN0000074871	TRCN0000074871
shRNA_or_gRNA_sequence	GCTAGGTTTCAAGTATGACAA	GCTAGGTTTCAAGTATGACAA
PAM
Name	AQR	AQR
Sample_ID	BGKLV38-19	BGKLV38-20
transduction_Date	9/15/16	9/15/16
days
RBP_name	AQR	AQR
qPCR_result	21.2	35.3
Ave_qPCR	28.2
RT-qPCR_primer-F	ccaacagaacctttcccaac
RT-qPCR_primer-R	gccatctggggcatattttt
protein_conc	2571	2481
WB_result	71.9	67.9
Ave_WB	69.9
WB_DONE_date	9/29/16	WES
MW	171kDa
IP	1	1
antibody_Cat#	A302-547A	A302-547A
Antibody DCC ID	ENCAB609IGM	ENCAB609IGM
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library
Note
ID	883	884

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AQR	Product_ID: A302-547A Lot_ID: 1 Source: Bethyl Labs Target Name: AQR-human

Experiment Status

	BGKLV38-19	BGKLV38-20
Sample_ID	BGKLV38-19	BGKLV38-20
Sample Name	AQR_BGKLV38-19	AQR_BGKLV38-20
Sample Name	AQR_BGKLV38-19	AQR_BGKLV38-20
RBP	AQR	AQR
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1305	1306

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-19	BGKLV38-20
Sample #
Sample Name	AQR-BGKLV38-19	AQR-BGKLV38-20
Sample_Name_Alias	AQR_BGKLV38-19	AQR_BGKLV38-20
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-03	2016-11-03
Lib_ID	Lib-161103	Lib-161103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/C5.png	DNA_Library_LV37-38/set1/D5.png
RIN	9.2	9.2
libSample_RNA_Well	RNA_Library_LV37_38/set2/F2.png	RNA_Library_LV37_38/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV38-19	BGKLV38-20
RBP	AQR	AQR
Batch_ID	BGKLV38	BGKLV38
WB_result	71.900	67.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2994	2995

Sequencing Information

	BGKLV38-19	BGKLV38-20
Sample_ID	BGKLV38-19	BGKLV38-20
Sample Name	AQR_BGKLV38-19	AQR_BGKLV38-20
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set38	set38
total_reads	105,000,000	58,602,988
total_aligned_reads	98,727,612	54,442,614
unique_aligned_reads	89,586,642	49,655,646
percent_uniqueAligned	0.85321	0.84732
correlation_replicates	0.997155	0.997155
spikein_reads	306,904	140,986
percent_spikeins	0.00292	0.00241
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1643	1644

Data Submission Information

	BGKLV38-19	BGKLV38-19
ENCODE_alias	brenton-graveley:AQR_BGKLV38	brenton-graveley:AQR-BGKLV38-K562
ENCODE_accession	ENCSR624OUI	ENCSR458PUT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV38-19	BGKLV38-19
Sample Name	AQR_BGKLV38-19	AQR_BGKLV38-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3192	6593

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
AQR_BGKLV38-19_GGCTAC_L007_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1643	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22174
AQR_BGKLV38-19_GGCTAC_L007_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1643	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22186
AQR_BGKLV38-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1643					GRCh38	V40	AQR_BGKLV38-19_GGCTAC_L007_001.R1.fastq.gz,AQR_BGKLV38-19_GGCTAC_L007_001.R2.fastq.gz		ENCORE2	22198
AQR_BGKLV38-19_Signal.Unique.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1643					GRCh38	V40	AQR_BGKLV38-19/Aligned.sortedByCoord.out.bam		ENCORE2	22210
AQR_BGKLV38-19_Signal.Unique.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1643					GRCh38	V40	AQR_BGKLV38-19/Aligned.sortedByCoord.out.bam		ENCORE2	22222
AQR_BGKLV38-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1643					GRCh38	V40	AQR_BGKLV38-19/Aligned.sortedByCoord.out.bam		ENCORE2	22234
AQR_BGKLV38-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1643					GRCh38	V40	AQR_BGKLV38-19/Aligned.sortedByCoord.out.bam		ENCORE2	22246
AQR_BGKLV38-19_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1643					GRCh38	V40	AQR_BGKLV38-19_GGCTAC_L007_001.R1.fastq.gz,AQR_BGKLV38-19_GGCTAC_L007_001.R2.fastq.gz		ENCORE2	22258
AQR_BGKLV38-20_CTTGTA_L007_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1644	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22175
AQR_BGKLV38-20_CTTGTA_L007_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1644	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22187
AQR_BGKLV38-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1644					GRCh38	V40	AQR_BGKLV38-20_CTTGTA_L007_001.R1.fastq.gz,AQR_BGKLV38-20_CTTGTA_L007_001.R2.fastq.gz		ENCORE2	22199
AQR_BGKLV38-20_Signal.Unique.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1644					GRCh38	V40	AQR_BGKLV38-20/Aligned.sortedByCoord.out.bam		ENCORE2	22211
AQR_BGKLV38-20_Signal.Unique.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1644					GRCh38	V40	AQR_BGKLV38-20/Aligned.sortedByCoord.out.bam		ENCORE2	22223
AQR_BGKLV38-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1644					GRCh38	V40	AQR_BGKLV38-20/Aligned.sortedByCoord.out.bam		ENCORE2	22235
AQR_BGKLV38-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1644					GRCh38	V40	AQR_BGKLV38-20/Aligned.sortedByCoord.out.bam		ENCORE2	22247
AQR_BGKLV38-20_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1644					GRCh38	V40	AQR_BGKLV38-20_CTTGTA_L007_001.R1.fastq.gz,AQR_BGKLV38-20_CTTGTA_L007_001.R2.fastq.gz		ENCORE2	22259