ACO1 RNA-Seq in K562

General Information


RBP	ACO1
Cell_Line	K562
Method	CRISPR
Exp_Name	ACO1-BGKcLV11-K562
ENCODE_series_ID	ENCSR370LQM
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR237QLO
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	ACO1-BGKcLV11-3
Rep2	ACO1-BGKcLV11-4
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	39.1
Rep2_qPCR	53.7
Rep1_WB	55.7
Rep2_WB	64.5
Antibody Cat#	RN036PW
Antibody Lot#
Antibody DCC ID	ENCAB923LQZ
Status	Released
Project	ENCODE4
ID	161

Experiment Information (Status: Released)

	BGKcLV11-3	BGKcLV11-4
idx	319	320
TRCN#_or_BGC#	BGC#0000240	BGC#0000240
shRNA_or_gRNA_sequence	TATTACCCAGACAGCCTCGT	TATTACCCAGACAGCCTCGT
PAM	ggg	ggg
Name	ACO1_90	ACO1_90
Sample_ID	BGKcLV11-3	BGKcLV11-4
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	ACO1	ACO1
qPCR_result	39.1	53.7
Ave_qPCR	46.4
RT-qPCR_primer-F	aggcagtggagcgtcagtat
RT-qPCR_primer-R	ttgctaaggcattccagctt
protein_conc	2694	2857
WB_result	55.7	64.5
Ave_WB	60.1
WB_DONE_date	8/13/18	wes
MW	98 kDa
IP
antibody_Cat#	RN036PW
Antibody DCC ID	ENCAB923LQZ	ENCAB923LQZ
submitted_to_DCC_date	2/22/19
Rep1_TPM	14	0
Rep2_TPM	15.4	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4419	4420

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ACO1	Product_ID: RN036PW Lot_ID: 1 Source: MBLI Target Name: ACO1-human

Experiment Status

	BGKcLV11-3	BGKcLV11-4
Sample_ID	BGKcLV11-3	BGKcLV11-4
Sample Name	ACO1-BGKcLV11-3	ACO1-BGKcLV11-4
Sample Name	ACO1-BGKcLV11-3	ACO1-BGKcLV11-4
RBP	ACO1	ACO1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2675	2676

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-3	BGKcLV11-4
Sample #	3	4
Sample Name	ACO1-BGKcLV11-3	ACO1-BGKcLV11-4
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	1-C1	1-D1
Tecan	34.31	45.79
Tecan_date	2019-03-13	2019-03-13
Size_bp	290	297
Peak_Molarity	74.10	65.30
libSampleQC_DNA_Well	DNA_Library_set42/set1/C1.png	DNA_Library_set42/set1/D1.png
RIN	9.0	9.7
libSample_RNA_Well	RNA_Library_set42/set1/C1.png	RNA_Library_set42/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-3	BGKcLV11-4
RBP	ACO1	ACO1
Batch_ID	BGKcLV11	BGKcLV11
WB_result	55.700	64.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3	4

Sequencing Information

	BGKcLV11-3	BGKcLV11-4
Sample_ID	BGKcLV11-3	BGKcLV11-4
Sample Name	ACO1-BGKcLV11-3	ACO1-BGKcLV11-4
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	33,542,332	41,667,584
total_aligned_reads	31,053,374	40,616,026
unique_aligned_reads	28,118,676	37,013,574
percent_uniqueAligned	0.83830	0.88831
correlation_replicates	0.997386	0.997386
spikein_reads	43,046	60,158
percent_spikeins	0.00128	0.00144
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1	2

Data Submission Information

	BGKcLV11-3	BGKcLV11-3	BGKcLV11-3	BGKcLV11-3	BGKcLV11-3	BGKcLV11-3	BGKcLV11-4	BGKcLV11-4	BGKcLV11-4	BGKcLV11-4
ENCODE_alias	brenton-graveley:ACO1-BGKcLV11	brenton-graveley:ACO1-BGKcLV11-3	brenton-graveley:L-ACO1-BGKcLV11-3	brenton-graveley:ACO1-BGKcLV11-3_GGACTTGG+CGCAGACG_HK3H2DSXX_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACO1-BGKcLV11-3_GGACTTGG+CGCAGACG_HK3H2DSXX_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACO1-BGKcLV11-K562	brenton-graveley:ACO1-BGKcLV11-4	brenton-graveley:L-ACO1-BGKcLV11-4	brenton-graveley:ACO1-BGKcLV11-4_AAGTCCAA+TATGAGTA_HK3H2DSXX_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACO1-BGKcLV11-4_AAGTCCAA+TATGAGTA_HK3H2DSXX_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR237QLO	ENCBS787BHM	ENCLB540JFY	ENCFF159WAI	ENCFF319OMM	ENCSR370LQM	ENCBS687AKW	ENCLB714ZWO	ENCFF137TWX	ENCFF205AZV
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	BGKcLV11-3	BGKcLV11-3	BGKcLV11-3	BGKcLV11-3	BGKcLV11-3	BGKcLV11-3	BGKcLV11-4	BGKcLV11-4	BGKcLV11-4	BGKcLV11-4
Sample Name	ACO1-BGKcLV11-3	ACO1-BGKcLV11-3	ACO1-BGKcLV11-3	ACO1-BGKcLV11-3	ACO1-BGKcLV11-3	ACO1-BGKcLV11-3	ACO1-BGKcLV11-4	ACO1-BGKcLV11-4	ACO1-BGKcLV11-4	ACO1-BGKcLV11-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		ACO1-BGKcLV11-3.pdf	L-ACO1-BGKcLV11-3.pdf				ACO1-BGKcLV11-4.pdf	L-ACO1-BGKcLV11-4.pdf
ID	761	817	899	951	1033	7060	818	900	952	1034

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
ACO1-BGKcLV11-3_GGACTTGG+CGCAGACG_HK3H2DSXX_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	333
ACO1-BGKcLV11-3_GGACTTGG+CGCAGACG_HK3H2DSXX_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	415
ACO1-BGKcLV11-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1					GRCh38	V40	ACO1-BGKcLV11-3_GGACTTGG+CGCAGACG_HK3H2DSXX_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,ACO1-BGKcLV11-3_GGACTTGG+CGCAGACG_HK3H2DSXX_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23672
ACO1-BGKcLV11-3_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1					GRCh38	V40	ACO1-BGKcLV11-3/Aligned.sortedByCoord.out.bam		ENCORE2	23754
ACO1-BGKcLV11-3_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1					GRCh38	V40	ACO1-BGKcLV11-3/Aligned.sortedByCoord.out.bam		ENCORE2	23836
ACO1-BGKcLV11-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1					GRCh38	V40	ACO1-BGKcLV11-3/Aligned.sortedByCoord.out.bam		ENCORE2	23918
ACO1-BGKcLV11-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1					GRCh38	V40	ACO1-BGKcLV11-3/Aligned.sortedByCoord.out.bam		ENCORE2	24000
ACO1-BGKcLV11-3_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1					GRCh38	V40	ACO1-BGKcLV11-3_GGACTTGG+CGCAGACG_HK3H2DSXX_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,ACO1-BGKcLV11-3_GGACTTGG+CGCAGACG_HK3H2DSXX_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24082
ACO1-BGKcLV11-4_AAGTCCAA+TATGAGTA_HK3H2DSXX_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	334
ACO1-BGKcLV11-4_AAGTCCAA+TATGAGTA_HK3H2DSXX_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	416
ACO1-BGKcLV11-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2					GRCh38	V40	ACO1-BGKcLV11-4_AAGTCCAA+TATGAGTA_HK3H2DSXX_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz,ACO1-BGKcLV11-4_AAGTCCAA+TATGAGTA_HK3H2DSXX_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23673
ACO1-BGKcLV11-4_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2					GRCh38	V40	ACO1-BGKcLV11-4/Aligned.sortedByCoord.out.bam		ENCORE2	23755
ACO1-BGKcLV11-4_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2					GRCh38	V40	ACO1-BGKcLV11-4/Aligned.sortedByCoord.out.bam		ENCORE2	23837
ACO1-BGKcLV11-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2					GRCh38	V40	ACO1-BGKcLV11-4/Aligned.sortedByCoord.out.bam		ENCORE2	23919
ACO1-BGKcLV11-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2					GRCh38	V40	ACO1-BGKcLV11-4/Aligned.sortedByCoord.out.bam		ENCORE2	24001
ACO1-BGKcLV11-4_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2					GRCh38	V40	ACO1-BGKcLV11-4_AAGTCCAA+TATGAGTA_HK3H2DSXX_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz,ACO1-BGKcLV11-4_AAGTCCAA+TATGAGTA_HK3H2DSXX_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24083