ALDOA RNA-Seq in HepG2

General Information


RBP	ALDOA
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ALDOA-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR112YSN
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR735FXX
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	ALDOA-BGHcLV27-7
Rep2	ALDOA-BGHcLV27-8
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	81.7
Rep2_qPCR	81.0
Rep1_WB	87.9
Rep2_WB	87.2
Antibody Cat#	A304-495A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB040UCI
Status	Released
Project	ENCODE4
ID	807

Experiment Information (Status: Released)

	BGHcLV27-7	BGHcLV27-8
idx	773	774
TRCN#_or_BGC#	BGC#0000629	BGC#0000629
shRNA_or_gRNA_sequence	ACGGAGCTGACTTCGCCAAG	ACGGAGCTGACTTCGCCAAG
PAM	TGG	TGG
Name	ALDOA_90	ALDOA_90
Sample_ID	BGHcLV27-7	BGHcLV27-8
transduction_Date	5/18/21	5/18/21
days	D6	D6
RBP_name	ALDOA	ALDOA
qPCR_result	81.7	81.0
Ave_qPCR	81.4
RT-qPCR_primer-F	agcctgagatcctccctgat
RT-qPCR_primer-R	ttgtagacagcagccagcac
protein_conc	3598	3487
WB_result	87.9	87.2
Ave_WB	87.5
WB_DONE_date	5/25/21	JESS
MW	39kDa
IP	Rabbit / I
antibody_Cat#	A304-495A	LOT# 1
Antibody DCC ID	ENCAB040UCI	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/03/21	09/03/21
repeat_library
Note
ID	6934	6935

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ALDOA	Product_ID: A304-495A Lot_ID: 1 Source: Bethyl Labs Target Name: ALDOA-human

Experiment Status

	BGHcLV27-7	BGHcLV27-8
Sample_ID	BGHcLV27-7	BGHcLV27-8
Sample Name
Sample Name	ALDOA-BGHcLV27-7	ALDOA-BGHcLV27-8
RBP	ALDOA	ALDOA
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9677	9678

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-7	BGHcLV27-8
Sample #	81	82
Sample Name	ALDOA-BGHcLV27-7	ALDOA-BGHcLV27-8
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	291	289
Peak_Molarity	176.00	161.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/E7.png	DNA_Library_set48-49/set2/F7.png
RIN	9.5	9.8
libSample_RNA_Well	RNA_Library_set48-49/set1/G7.png	RNA_Library_set48-49/set1/H7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-7	BGHcLV27-8
RBP	ALDOA	ALDOA
Batch_ID	BGHcLV27	BGHcLV27
WB_result	87.900	87.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1640	1641

Sequencing Information

	BGHcLV27-7	BGHcLV27-8
Sample_ID	BGHcLV27-7	BGHcLV27-8
Sample Name	ALDOA-BGHcLV27-7	ALDOA-BGHcLV27-8
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	66,392,234	76,984,838
total_aligned_reads	58,184,084	68,910,906
unique_aligned_reads	54,924,088	64,995,860
percent_uniqueAligned	0.82727	0.84427
correlation_replicates	0.997504	0.997504
spikein_reads	24,060	22,946
percent_spikeins	0.00036	0.00030
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1791	1792

Data Submission Information

	BGHcLV27-7	BGHcLV27-7	BGHcLV27-7	BGHcLV27-7	BGHcLV27-7	BGHcLV27-7	BGHcLV27-8	BGHcLV27-8	BGHcLV27-8	BGHcLV27-8
ENCODE_alias	brenton-graveley:ALDOA-BGHcLV27	brenton-graveley:ALDOA-BGHcLV27-7	brenton-graveley:L-ALDOA-BGHcLV27-7	brenton-graveley:ALDOA-BGHcLV27-7_S61_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALDOA-BGHcLV27-7_S61_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALDOA-BGHcLV27-HepG2	brenton-graveley:ALDOA-BGHcLV27-8	brenton-graveley:L-ALDOA-BGHcLV27-8	brenton-graveley:ALDOA-BGHcLV27-8_S62_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALDOA-BGHcLV27-8_S62_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR735FXX	ENCBS651VNU	ENCLB888EKF	ENCFF516YQA	ENCFF639FOJ	ENCSR112YSN	ENCBS084MWU	ENCLB265NKA	ENCFF362OKF	ENCFF919KMQ
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	BGHcLV27-7	BGHcLV27-7	BGHcLV27-7	BGHcLV27-7	BGHcLV27-7	BGHcLV27-7	BGHcLV27-8	BGHcLV27-8	BGHcLV27-8	BGHcLV27-8
Sample Name	ALDOA-BGHcLV27-7	ALDOA-BGHcLV27-7	ALDOA-BGHcLV27-7	ALDOA-BGHcLV27-7	ALDOA-BGHcLV27-7	ALDOA-BGHcLV27-7	ALDOA-BGHcLV27-8	ALDOA-BGHcLV27-8	ALDOA-BGHcLV27-8	ALDOA-BGHcLV27-8
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
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		ALDOA-BGHcLV27-7.pdf	L-ALDOA-BGHcLV27-7.pdf				ALDOA-BGHcLV27-8.pdf	L-ALDOA-BGHcLV27-8.pdf
ID	3435	3504	3638	3772	3906	7079	3505	3639	3773	3907

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
ALDOA-BGHcLV27-7_S61_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1791	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3782
ALDOA-BGHcLV27-7_S61_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1791	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3808
ALDOA-BGHcLV27-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1791					GRCh38	V40	ALDOA-BGHcLV27-7_S61_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDOA-BGHcLV27-7_S61_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25469
ALDOA-BGHcLV27-7_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1791					GRCh38	V40	ALDOA-BGHcLV27-7_S61_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDOA-BGHcLV27-7_S61_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25495
ALDOA-BGHcLV27-7_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1791					GRCh38	V40	ALDOA-BGHcLV27-7/Aligned.sortedByCoord.out.bam		ENCORE2	26433
ALDOA-BGHcLV27-7_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1791					GRCh38	V40	ALDOA-BGHcLV27-7/Aligned.sortedByCoord.out.bam		ENCORE2	26459
ALDOA-BGHcLV27-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1791					GRCh38	V40	ALDOA-BGHcLV27-7/Aligned.sortedByCoord.out.bam		ENCORE2	26485
ALDOA-BGHcLV27-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1791					GRCh38	V40	ALDOA-BGHcLV27-7/Aligned.sortedByCoord.out.bam		ENCORE2	26511
ALDOA-BGHcLV27-8_S62_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1792	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3783
ALDOA-BGHcLV27-8_S62_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1792	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3809
ALDOA-BGHcLV27-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1792					GRCh38	V40	ALDOA-BGHcLV27-8_S62_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDOA-BGHcLV27-8_S62_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25470
ALDOA-BGHcLV27-8_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1792					GRCh38	V40	ALDOA-BGHcLV27-8_S62_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDOA-BGHcLV27-8_S62_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25496
ALDOA-BGHcLV27-8_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1792					GRCh38	V40	ALDOA-BGHcLV27-8/Aligned.sortedByCoord.out.bam		ENCORE2	26434
ALDOA-BGHcLV27-8_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1792					GRCh38	V40	ALDOA-BGHcLV27-8/Aligned.sortedByCoord.out.bam		ENCORE2	26460
ALDOA-BGHcLV27-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1792					GRCh38	V40	ALDOA-BGHcLV27-8/Aligned.sortedByCoord.out.bam		ENCORE2	26486
ALDOA-BGHcLV27-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1792					GRCh38	V40	ALDOA-BGHcLV27-8/Aligned.sortedByCoord.out.bam		ENCORE2	26512