ACO2 RNA-Seq in HepG2

General Information


RBP	ACO2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ACO2-BGHcLV25-HepG2
ENCODE_series_ID	ENCSR955LXJ
Batch_ID	BGHcLV25
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR251SXS
ENCODE_CN_Exp_ID	ENCSR953VMB
Rep1	ACO2-BGHcLV25-3
Rep2	ACO2-BGHcLV25-4
CN1	NT-BGHcLV25-1
CN2	NT-BGHcLV25-2
Rep1_qPCR	49.4
Rep2_qPCR	65.6
Rep1_WB	59.3
Rep2_WB	59.8
Antibody Cat#	A305-302A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB412MAW
Status	Released
Project	ENCODE4
ID	12

Experiment Information (Status: Released)

	BGHcLV25-3	BGHcLV25-4
idx	710	711
TRCN#_or_BGC#	BGC#0000585	BGC#0000585
shRNA_or_gRNA_sequence	TCTCGGGGTTTGCGTCGTTG	TCTCGGGGTTTGCGTCGTTG
PAM	cgg	cgg
Name	ACO2_96	ACO2_96
Sample_ID	BGHcLV25-3	BGHcLV25-4
transduction_Date	2/18/21	2/18/21
days	D6	D6
RBP_name	ACO2	ACO2
qPCR_result	49.4	65.6
Ave_qPCR	57.5
RT-qPCR_primer-F	tgcgtaccctggtgttcttc
RT-qPCR_primer-R	ctgccaccttcaggatcaca
protein_conc	3152	3503
WB_result	59.3	59.8
Ave_WB	59.6
WB_DONE_date	4/22/21	JESS
MW	85.4KD
IP	Rabbit / I
antibody_Cat#	A305-302A	LOT# 1
Antibody DCC ID	ENCAB412MAW
submitted_to_DCC_date	10/26/21
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6865	6866

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

	BGHcLV25-3	BGHcLV25-4
Sample_ID	BGHcLV25-3	BGHcLV25-4
Sample Name
Sample Name	ACO2-BGHcLV25-3	ACO2-BGHcLV25-4
RBP	ACO2	ACO2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7829	7830

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV25-3	BGHcLV25-4
Sample #	27	28
Sample Name	ACO2-BGHcLV25-3	ACO2-BGHcLV25-4
Sample_Name_Alias
Index Well Position	C10	D10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	305	306
Peak_Molarity	72.50	89.30
libSampleQC_DNA_Well	DNA_Library_set47/set1/C7.png	DNA_Library_set47/set1/D7.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set47/set1/C4.png	RNA_Library_set47/set1/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV25-3	BGHcLV25-4
RBP	ACO2	ACO2
Batch_ID	BGHcLV25	BGHcLV25
WB_result	59.300	59.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1490	1491

Sequencing Information

	BGHcLV25-3	BGHcLV25-4
Sample_ID	BGHcLV25-3	BGHcLV25-4
Sample Name	ACO2-BGHcLV25-3	ACO2-BGHcLV25-4
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	123,407,214	94,541,490
total_aligned_reads	113,394,480	88,251,732
unique_aligned_reads	106,935,572	83,305,688
percent_uniqueAligned	0.86653	0.88115
correlation_replicates	0.998608	0.998608
spikein_reads	41,166	17,422
percent_spikeins	0.00033	0.00018
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	572	573

Data Submission Information

	BGHcLV25-3	BGHcLV25-3	BGHcLV25-3	BGHcLV25-3	BGHcLV25-3	BGHcLV25-3	BGHcLV25-4	BGHcLV25-4	BGHcLV25-4	BGHcLV25-4
ENCODE_alias	brenton-graveley:ACO2-BGHcLV25	brenton-graveley:ACO2-BGHcLV25-3	brenton-graveley:L-ACO2-BGHcLV25-3	brenton-graveley:ACO2-BGHcLV25-3_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACO2-BGHcLV25-3_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACO2-BGHcLV25-HepG2	brenton-graveley:ACO2-BGHcLV25-4	brenton-graveley:L-ACO2-BGHcLV25-4	brenton-graveley:ACO2-BGHcLV25-4_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACO2-BGHcLV25-4_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR251SXS	ENCBS720JSN	ENCLB886XUK	ENCFF935IMV	ENCFF810EUE	ENCSR955LXJ	ENCBS478QMB	ENCLB201PIV	ENCFF813ULK	ENCFF471QVZ
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	BGHcLV25-3	BGHcLV25-3	BGHcLV25-3	BGHcLV25-3	BGHcLV25-3	BGHcLV25-3	BGHcLV25-4	BGHcLV25-4	BGHcLV25-4	BGHcLV25-4
Sample Name	ACO2-BGHcLV25-3	ACO2-BGHcLV25-3	ACO2-BGHcLV25-3	ACO2-BGHcLV25-3	ACO2-BGHcLV25-3	ACO2-BGHcLV25-3	ACO2-BGHcLV25-4	ACO2-BGHcLV25-4	ACO2-BGHcLV25-4	ACO2-BGHcLV25-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		ACO2-BGHcLV25-3.pdf	L-ACO2-BGHcLV25-3.pdf				ACO2-BGHcLV25-4.pdf	L-ACO2-BGHcLV25-4.pdf
ID	3248	3283	3327	3371	3415	7061	3284	3328	3372	3416

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-BGHcLV25-3_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	572	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3735
ACO2-BGHcLV25-3_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	572	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3736
ACO2-BGHcLV25-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	572					GRCh38	V40	ACO2-BGHcLV25-3_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz,ACO2-BGHcLV25-3_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25379
ACO2-BGHcLV25-3_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	572					GRCh38	V40	ACO2-BGHcLV25-3_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz,ACO2-BGHcLV25-3_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25423
ACO2-BGHcLV25-3_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	572					GRCh38	V40	ACO2-BGHcLV25-3/Aligned.sortedByCoord.out.bam		ENCORE2	26255
ACO2-BGHcLV25-3_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	572					GRCh38	V40	ACO2-BGHcLV25-3/Aligned.sortedByCoord.out.bam		ENCORE2	26299
ACO2-BGHcLV25-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	572					GRCh38	V40	ACO2-BGHcLV25-3/Aligned.sortedByCoord.out.bam		ENCORE2	26343
ACO2-BGHcLV25-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	572					GRCh38	V40	ACO2-BGHcLV25-3/Aligned.sortedByCoord.out.bam		ENCORE2	26387
ACO2-BGHcLV25-4_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	573	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3691
ACO2-BGHcLV25-4_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	573	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3737
ACO2-BGHcLV25-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	573					GRCh38	V40	ACO2-BGHcLV25-4_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz,ACO2-BGHcLV25-4_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25380
ACO2-BGHcLV25-4_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	573					GRCh38	V40	ACO2-BGHcLV25-4_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz,ACO2-BGHcLV25-4_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25424
ACO2-BGHcLV25-4_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	573					GRCh38	V40	ACO2-BGHcLV25-4/Aligned.sortedByCoord.out.bam		ENCORE2	26256
ACO2-BGHcLV25-4_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	573					GRCh38	V40	ACO2-BGHcLV25-4/Aligned.sortedByCoord.out.bam		ENCORE2	26300
ACO2-BGHcLV25-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	573					GRCh38	V40	ACO2-BGHcLV25-4/Aligned.sortedByCoord.out.bam		ENCORE2	26344
ACO2-BGHcLV25-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	573					GRCh38	V40	ACO2-BGHcLV25-4/Aligned.sortedByCoord.out.bam		ENCORE2	26388