ACO2 RNA-Seq in K562

General Information


RBP	ACO2
Cell_Line	K562
Method	CRISPR
Exp_Name	ACO2-BGKcLV26-K562
ENCODE_series_ID	ENCSR531WIE
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR274ESZ
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	ACO2-BGKcLV26-3
Rep2	ACO2-BGKcLV26-4
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	70.1
Rep2_qPCR	78.1
Rep1_WB	76.7
Rep2_WB	73.7
Antibody Cat#	A305-302A
Antibody Lot#	LOT# 1
Antibody DCC ID	no ID
Status	Released
Project	ENCODE4
ID	782

Experiment Information (Status: Released)

	BGKcLV26-3	BGKcLV26-4
idx	856	857
TRCN#_or_BGC#	BGC#0000585	BGC#0000585
shRNA_or_gRNA_sequence	TCTCGGGGTTTGCGTCGTTG	TCTCGGGGTTTGCGTCGTTG
PAM	cgg	cgg
Name	ACO2_96	ACO2_96
Sample_ID	BGKcLV26-3	BGKcLV26-4
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	ACO2	ACO2
qPCR_result	70.1	78.1
Ave_qPCR	74.1
RT-qPCR_primer-F	tgcgtaccctggtgttcttc
RT-qPCR_primer-R	ctgccaccttcaggatcaca
protein_conc	4006	3997
WB_result	76.7	73.7
Ave_WB	75.2
WB_DONE_date	5/18/21	JESS
MW	85.4kd
IP	Rabbit / I
antibody_Cat#	A305-302A	LOT# 1
Antibody DCC ID	ENCAB412MAW	10/22/21
submitted_to_DCC_date
Rep1_TPM	79.2	0
Rep2_TPM	75.2	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	4988	4989

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ACO2	Product_ID: A305-302A Lot_ID: 1 Source: Bethyl Labs Target Name: ACO2-human

Experiment Status

	BGKcLV26-3	BGKcLV26-4
Sample_ID	BGKcLV26-3	BGKcLV26-4
Sample Name
Sample Name	ACO2-BGKcLV26-3	ACO2-BGKcLV26-4
RBP	ACO2	ACO2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9745	9746

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-3	BGKcLV26-4
Sample #	3	4
Sample Name	ACO2-BGKcLV26-3	ACO2-BGKcLV26-4
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	282	273
Peak_Molarity	73.70	41.90
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/C1.png	DNA_Library_set48-49/set1/D1.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set48-49/set1/C1.png	RNA_Library_set48-49/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-3	BGKcLV26-4
RBP	ACO2	ACO2
Batch_ID	BGKcLV26	BGKcLV26
WB_result	76.700	73.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1562	1563

Sequencing Information

	BGKcLV26-3	BGKcLV26-4
Sample_ID	BGKcLV26-3	BGKcLV26-4
Sample Name	ACO2-BGKcLV26-3	ACO2-BGKcLV26-4
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	78,451,630	108,541,134
total_aligned_reads	60,388,678	94,980,074
unique_aligned_reads	54,894,978	86,786,090
percent_uniqueAligned	0.69973	0.79957
correlation_replicates	0.991622	0.991622
spikein_reads	31,562	38,854
percent_spikeins	0.00040	0.00036
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1739	1740

Data Submission Information

	BGKcLV26-3	BGKcLV26-3	BGKcLV26-3	BGKcLV26-3	BGKcLV26-3	BGKcLV26-3	BGKcLV26-4	BGKcLV26-4	BGKcLV26-4	BGKcLV26-4
ENCODE_alias	brenton-graveley:ACO2-BGKcLV26	brenton-graveley:ACO2-BGKcLV26-3	brenton-graveley:L-ACO2-BGKcLV26-3	brenton-graveley:ACO2-BGKcLV26-3_S9_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACO2-BGKcLV26-3_S9_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACO2-BGKcLV26-K562	brenton-graveley:ACO2-BGKcLV26-4	brenton-graveley:L-ACO2-BGKcLV26-4	brenton-graveley:ACO2-BGKcLV26-4_S10_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACO2-BGKcLV26-4_S10_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR274ESZ	ENCBS367BPG	ENCLB007DXF	ENCFF206HGK	ENCFF463SPY	ENCSR531WIE	ENCBS136FWL	ENCLB617OLR	ENCFF351JIO	ENCFF714RRB
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	BGKcLV26-3	BGKcLV26-3	BGKcLV26-3	BGKcLV26-3	BGKcLV26-3	BGKcLV26-3	BGKcLV26-4	BGKcLV26-4	BGKcLV26-4	BGKcLV26-4
Sample Name	ACO2-BGKcLV26-3	ACO2-BGKcLV26-3	ACO2-BGKcLV26-3	ACO2-BGKcLV26-3	ACO2-BGKcLV26-3	ACO2-BGKcLV26-3	ACO2-BGKcLV26-4	ACO2-BGKcLV26-4	ACO2-BGKcLV26-4	ACO2-BGKcLV26-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		ACO2-BGKcLV26-3.pdf	L-ACO2-BGKcLV26-3.pdf				ACO2-BGKcLV26-4.pdf	L-ACO2-BGKcLV26-4.pdf
ID	3447	3528	3662	3796	3930	7062	3529	3663	3797	3931

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
ACO2-BGKcLV26-3_S9_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1739	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3832
ACO2-BGKcLV26-3_S9_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1739	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3882
ACO2-BGKcLV26-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1739					GRCh38	V40	ACO2-BGKcLV26-3_S9_L003_R1_001.filtered.trimmed.paired.fastq.gz,ACO2-BGKcLV26-3_S9_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25519
ACO2-BGKcLV26-3_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1739					GRCh38	V40	ACO2-BGKcLV26-3_S9_L003_R1_001.filtered.trimmed.paired.fastq.gz,ACO2-BGKcLV26-3_S9_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25569
ACO2-BGKcLV26-3_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1739					GRCh38	V40	ACO2-BGKcLV26-3/Aligned.sortedByCoord.out.bam		ENCORE2	26535
ACO2-BGKcLV26-3_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1739					GRCh38	V40	ACO2-BGKcLV26-3/Aligned.sortedByCoord.out.bam		ENCORE2	26585
ACO2-BGKcLV26-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1739					GRCh38	V40	ACO2-BGKcLV26-3/Aligned.sortedByCoord.out.bam		ENCORE2	26635
ACO2-BGKcLV26-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1739					GRCh38	V40	ACO2-BGKcLV26-3/Aligned.sortedByCoord.out.bam		ENCORE2	26685
ACO2-BGKcLV26-4_S10_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1740	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3833
ACO2-BGKcLV26-4_S10_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1740	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3883
ACO2-BGKcLV26-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1740					GRCh38	V40	ACO2-BGKcLV26-4_S10_L003_R1_001.filtered.trimmed.paired.fastq.gz,ACO2-BGKcLV26-4_S10_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25520
ACO2-BGKcLV26-4_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1740					GRCh38	V40	ACO2-BGKcLV26-4_S10_L003_R1_001.filtered.trimmed.paired.fastq.gz,ACO2-BGKcLV26-4_S10_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25570
ACO2-BGKcLV26-4_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1740					GRCh38	V40	ACO2-BGKcLV26-4/Aligned.sortedByCoord.out.bam		ENCORE2	26536
ACO2-BGKcLV26-4_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1740					GRCh38	V40	ACO2-BGKcLV26-4/Aligned.sortedByCoord.out.bam		ENCORE2	26586
ACO2-BGKcLV26-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1740					GRCh38	V40	ACO2-BGKcLV26-4/Aligned.sortedByCoord.out.bam		ENCORE2	26636
ACO2-BGKcLV26-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1740					GRCh38	V40	ACO2-BGKcLV26-4/Aligned.sortedByCoord.out.bam		ENCORE2	26686