AQR RNA-Seq in HepG2

General Information


RBP	AQR
Cell_Line	HepG2
Method	shRNA
Exp_Name	AQR-BGHLV37-HepG2
ENCODE_series_ID	ENCSR354MEA
Batch_ID	BGHLV37
Pool ID	Pool-180109
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR431SXF
ENCODE_CN_Exp_ID	ENCSR225PRV
Rep1	AQR-BGHLV37-11C
Rep2	AQR-BGHLV37-12C
CN1	non-target-BGHLV37-1C
CN2	non-target-BGHLV37-2C
Rep1_qPCR	0.0
Rep2_qPCR	26.0
Rep1_WB	68.2
Rep2_WB	64.7
Antibody Cat#	A302-547A
Antibody Lot#	A302-547A
Antibody DCC ID	ENCAB609IGM
Status	Released
Project	ENCODE4
ID	262

Experiment Information (Status: Released)

	BGHLV37-11	BGHLV37-12
idx	923	924
TRCN#_or_BGC#	TRCN0000074870	TRCN0000074870
shRNA_or_gRNA_sequence	CCTGTCACTATGGACAAAGTT	CCTGTCACTATGGACAAAGTT
PAM
Name	AQR	AQR
Sample_ID	BGHLV37-11	BGHLV37-12
transduction_Date	9/1/16	9/1/16
days
RBP_name	AQR	AQR
qPCR_result	0.0	26.0
Ave_qPCR	13.0
RT-qPCR_primer-F	ccaacagaacctttcccaac
RT-qPCR_primer-R	gccatctggggcatattttt
protein_conc	3271	3173
WB_result	68.2	64.7
Ave_WB	66.4
WB_DONE_date	9/16/16	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	7.6	0
Rep2_TPM	5.8	0
Action
Library_start_date	12/18/17	12/18/17
repeat_library
Note
ID	3016	3017

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

	BGHLV37-11	BGHLV37-12
Sample_ID	BGHLV37-11	BGHLV37-12
Sample Name
Sample Name	AQR-BGHLV37-11C	AQR-BGHLV37-12C
RBP	AQR	AQR
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6435	6436

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-11	BGHLV37-12
Sample #	19	20
Sample Name	AQR-BGHLV37-11C	AQR-BGHLV37-12C
Sample_Name_Alias
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	286	292
Peak_Molarity	6.42	12.40
libSampleQC_DNA_Well	DNA_Library_set40/set1/E5.png	DNA_Library_set40/set1/F5.png
RIN	9.2	9.4
libSample_RNA_Well	RNA_Library_set40/set1/C1.png	RNA_Library_set40/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHLV37-11	BGHLV37-12
RBP	AQR	AQR
Batch_ID	BGHLV37	BGHLV37
WB_result	68.200	64.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	942	943

Sequencing Information

	BGHLV37-11	BGHLV37-12
Sample_ID	BGHLV37-11	BGHLV37-12
Sample Name	AQR-BGHLV37-11C	AQR-BGHLV37-12C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_H	set40_H
total_reads	77,652,938	44,353,692
total_aligned_reads	65,692,808	37,114,470
unique_aligned_reads	61,720,994	34,915,444
percent_uniqueAligned	0.79483	0.78720
correlation_replicates	0.998037	0.998037
spikein_reads	23,626	14,692
percent_spikeins	0.00030	0.00033
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	345	346

Data Submission Information

	BGHLV37-11	BGHLV37-11	BGHLV37-11	BGHLV37-11	BGHLV37-11	BGHLV37-11	BGHLV37-12	BGHLV37-12	BGHLV37-12	BGHLV37-12
ENCODE_alias	brenton-graveley:AQR-BGHLV37-C	brenton-graveley:AQR-BGHLV37-11C	brenton-graveley:L-AQR-BGHLV37-11C	brenton-graveley:AQR-BGHLV37-11C_ACAGTG_ACBYWVANXX_L001_001.R1.fastq.gz	brenton-graveley:AQR-BGHLV37-11C_ACAGTG_ACBYWVANXX_L001_001.R2.fastq.gz	brenton-graveley:AQR-BGHLV37-HepG2	brenton-graveley:AQR-BGHLV37-12C	brenton-graveley:L-AQR-BGHLV37-12C	brenton-graveley:AQR-BGHLV37-12C_GCCAAT_ACBYWVANXX_L001_001.R1.fastq.gz	brenton-graveley:AQR-BGHLV37-12C_GCCAAT_ACBYWVANXX_L001_001.R2.fastq.gz
ENCODE_accession	ENCSR431SXF	ENCBS246WPL	ENCLB867RJA	ENCFF727KCH	ENCFF926IHV	ENCSR354MEA	ENCBS775JOM	ENCLB281ZOM	ENCFF852TDH	ENCFF038WII
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV37-11	BGHLV37-11	BGHLV37-11	BGHLV37-11	BGHLV37-11	BGHLV37-11	BGHLV37-12	BGHLV37-12	BGHLV37-12	BGHLV37-12
Sample Name	AQR-BGHLV37-11C	AQR-BGHLV37-11C	AQR-BGHLV37-11C	AQR-BGHLV37-11C	AQR-BGHLV37-11C	AQR-BGHLV37-11C	AQR-BGHLV37-12C	AQR-BGHLV37-12C	AQR-BGHLV37-12C	AQR-BGHLV37-12C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		AQR-BGHLV37-11C.pdf	L-AQR-BGHLV37-11C.pdf				AQR-BGHLV37-12C.pdf	L-AQR-BGHLV37-12C.pdf
ID	1432	1462	1518	1574	1611	7092	1463	1519	1575	1612

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-BGHLV37-11C_ACAGTG_ACBYWVANXX_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	345	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	641
AQR-BGHLV37-11C_ACAGTG_ACBYWVANXX_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	345	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	683
AQR-BGHLV37-11C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	345					GRCh38	V40	AQR-BGHLV37-11C_ACAGTG_ACBYWVANXX_L001_001.R1.fastq.gz,AQR-BGHLV37-11C_ACAGTG_ACBYWVANXX_L001_001.R2.fastq.gz		ENCORE2	23248
AQR-BGHLV37-11C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	345					GRCh38	V40	AQR-BGHLV37-11C/Aligned.sortedByCoord.out.bam		ENCORE2	23282
AQR-BGHLV37-11C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	345					GRCh38	V40	AQR-BGHLV37-11C/Aligned.sortedByCoord.out.bam		ENCORE2	23316
AQR-BGHLV37-11C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	345					GRCh38	V40	AQR-BGHLV37-11C/Aligned.sortedByCoord.out.bam		ENCORE2	23350
AQR-BGHLV37-11C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	345					GRCh38	V40	AQR-BGHLV37-11C/Aligned.sortedByCoord.out.bam		ENCORE2	23384
AQR-BGHLV37-11C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	345					GRCh38	V40	AQR-BGHLV37-11C_ACAGTG_ACBYWVANXX_L001_001.R1.fastq.gz,AQR-BGHLV37-11C_ACAGTG_ACBYWVANXX_L001_001.R2.fastq.gz		ENCORE2	23418
AQR-BGHLV37-12C_GCCAAT_ACBYWVANXX_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	346	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	642
AQR-BGHLV37-12C_GCCAAT_ACBYWVANXX_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	346	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	684
AQR-BGHLV37-12C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	346					GRCh38	V40	AQR-BGHLV37-12C_GCCAAT_ACBYWVANXX_L001_001.R1.fastq.gz,AQR-BGHLV37-12C_GCCAAT_ACBYWVANXX_L001_001.R2.fastq.gz		ENCORE2	23249
AQR-BGHLV37-12C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	346					GRCh38	V40	AQR-BGHLV37-12C/Aligned.sortedByCoord.out.bam		ENCORE2	23283
AQR-BGHLV37-12C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	346					GRCh38	V40	AQR-BGHLV37-12C/Aligned.sortedByCoord.out.bam		ENCORE2	23317
AQR-BGHLV37-12C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	346					GRCh38	V40	AQR-BGHLV37-12C/Aligned.sortedByCoord.out.bam		ENCORE2	23351
AQR-BGHLV37-12C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	346					GRCh38	V40	AQR-BGHLV37-12C/Aligned.sortedByCoord.out.bam		ENCORE2	23385
AQR-BGHLV37-12C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	346					GRCh38	V40	AQR-BGHLV37-12C_GCCAAT_ACBYWVANXX_L001_001.R1.fastq.gz,AQR-BGHLV37-12C_GCCAAT_ACBYWVANXX_L001_001.R2.fastq.gz		ENCORE2	23419