ACO1 RNA-Seq in HepG2

General Information


RBP	ACO1
Cell_Line	HepG2
Method	shRNA
Exp_Name	ACO1-BGHLV31-HepG2
ENCODE_series_ID	ENCSR339RBD
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR511SYK
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	ACO1_BGHLV31-5
Rep2	ACO1_BGHLV31-6
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	59.2
Rep2_qPCR	51.6
Rep1_WB	58.8
Rep2_WB	50.3
Antibody Cat#	RN036PW
Antibody Lot#	RN036PW
Antibody DCC ID	ENCAB923LQZ
Status	Released
Project	ENCODE3
ID	691

Experiment Information (Status: Released)

	BGHLV31-5	BGHLV31-6
idx	753	754
TRCN#_or_BGC#	TRCN0000056555	TRCN0000056555
shRNA_or_gRNA_sequence	CGTATATCAAATCACCACCAT	CGTATATCAAATCACCACCAT
PAM
Name	ACO1	ACO1
Sample_ID	BGHLV31-5	BGHLV31-6
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	ACO1	ACO1
qPCR_result	59.2	51.6
Ave_qPCR	55.4
RT-qPCR_primer-F	gagccattgggagtaaatgc
RT-qPCR_primer-R	tgacatactgacgctccactg
protein_conc	4620	4581
WB_result	58.8	50.3
Ave_WB	54.6
WB_DONE_date	11/18/2015
MW	98kDa
IP	1MW	1MW
antibody_Cat#	RN036PW	RN036PW
Antibody DCC ID	ENCAB923LQZ	ENCAB923LQZ
submitted_to_DCC_date	12/7/2015
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2842	2843

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

	BGHLV31-5	BGHLV31-6
Sample_ID	BGHLV31-5	BGHLV31-6
Sample Name	ACO1_BGHLV31-5	ACO1_BGHLV31-6
Sample Name	ACO1_BGHLV31-5	ACO1_BGHLV31-6
RBP	ACO1	ACO1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1109	1110

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-5	BGHLV31-6
Sample #
Sample Name	ACO1-BGHLV31-5	ACO1-BGHLV31-6
Sample_Name_Alias	ACO1_BGHLV31-5	ACO1_BGHLV31-6
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set2/G9.png	DNA_Library_LV31-21B/set1/D5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C8.png	RNA_Library_LV29-30-31-32/set1/D8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-5	BGHLV31-6
RBP	ACO1	ACO1
Batch_ID	BGHLV31	BGHLV31
WB_result	58.800	50.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2806	2807

Sequencing Information

	BGHLV31-5	BGHLV31-6
Sample_ID	BGHLV31-5	BGHLV31-6
Sample Name	ACO1_BGHLV31-5	ACO1_BGHLV31-6
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	63,256,512	63,718,704
total_aligned_reads	54,565,254	56,191,528
unique_aligned_reads	51,273,880	52,874,016
percent_uniqueAligned	0.81057	0.82980
correlation_replicates	0.999328	0.999328
spikein_reads	271,464	240,672
percent_spikeins	0.00429	0.00378
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1455	1456

Data Submission Information

	BGHLV31-5	BGHLV31-5
ENCODE_alias	brenton-graveley:ACO1_BGHLV31	brenton-graveley:ACO1-BGHLV31-HepG2
ENCODE_accession	ENCSR511SYK	ENCSR339RBD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-5	BGHLV31-5
Sample Name	ACO1_BGHLV31-5	ACO1_BGHLV31-5
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3087	6578

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_BGHLV31-5_GGCTAC_L005_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1455	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20970
ACO1_BGHLV31-5_GGCTAC_L005_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1455	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20996
ACO1_BGHLV31-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1455					GRCh38	V40	ACO1_BGHLV31-5_GGCTAC_L005_001.R1.fastq.gz,ACO1_BGHLV31-5_GGCTAC_L005_001.R2.fastq.gz		ENCORE2	21030
ACO1_BGHLV31-5_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1455					GRCh38	V40	ACO1_BGHLV31-5/Aligned.sortedByCoord.out.bam		ENCORE2	21056
ACO1_BGHLV31-5_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1455					GRCh38	V40	ACO1_BGHLV31-5/Aligned.sortedByCoord.out.bam		ENCORE2	21082
ACO1_BGHLV31-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1455					GRCh38	V40	ACO1_BGHLV31-5/Aligned.sortedByCoord.out.bam		ENCORE2	21108
ACO1_BGHLV31-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1455					GRCh38	V40	ACO1_BGHLV31-5/Aligned.sortedByCoord.out.bam		ENCORE2	21134
ACO1_BGHLV31-5_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1455					GRCh38	V40	ACO1_BGHLV31-5_GGCTAC_L005_001.R1.fastq.gz,ACO1_BGHLV31-5_GGCTAC_L005_001.R2.fastq.gz		ENCORE2	21160
ACO1_BGHLV31-6_CTTGTA_L005_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1456	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20971
ACO1_BGHLV31-6_CTTGTA_L005_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1456	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20997
ACO1_BGHLV31-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1456					GRCh38	V40	ACO1_BGHLV31-6_CTTGTA_L005_001.R1.fastq.gz,ACO1_BGHLV31-6_CTTGTA_L005_001.R2.fastq.gz		ENCORE2	21031
ACO1_BGHLV31-6_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1456					GRCh38	V40	ACO1_BGHLV31-6/Aligned.sortedByCoord.out.bam		ENCORE2	21057
ACO1_BGHLV31-6_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1456					GRCh38	V40	ACO1_BGHLV31-6/Aligned.sortedByCoord.out.bam		ENCORE2	21083
ACO1_BGHLV31-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1456					GRCh38	V40	ACO1_BGHLV31-6/Aligned.sortedByCoord.out.bam		ENCORE2	21109
ACO1_BGHLV31-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1456					GRCh38	V40	ACO1_BGHLV31-6/Aligned.sortedByCoord.out.bam		ENCORE2	21135
ACO1_BGHLV31-6_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1456					GRCh38	V40	ACO1_BGHLV31-6_CTTGTA_L005_001.R1.fastq.gz,ACO1_BGHLV31-6_CTTGTA_L005_001.R2.fastq.gz		ENCORE2	21161