ALDOA RNA-Seq in K562

General Information


RBP	ALDOA
Cell_Line	K562
Method	CRISPR
Exp_Name	ALDOA-BGKcLV26-K562
ENCODE_series_ID	ENCSR379PIL
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR071DBC
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	ALDOA-BGKcLV26-23
Rep2	ALDOA-BGKcLV26-24
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	81.7
Rep2_qPCR	78.7
Rep1_WB	70.0
Rep2_WB	72.0
Antibody Cat#	A304-495A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB040UCI
Status	Released
Project	ENCODE4
ID	790

Experiment Information (Status: Released)

	BGKcLV26-23	BGKcLV26-24
idx	880	881
TRCN#_or_BGC#	BGC#0000629	BGC#0000629
shRNA_or_gRNA_sequence	ACGGAGCTGACTTCGCCAAG	ACGGAGCTGACTTCGCCAAG
PAM	TGG	TGG
Name	ALDOA_90	ALDOA_90
Sample_ID	BGKcLV26-23	BGKcLV26-24
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	ALDOA	ALDOA
qPCR_result	81.7	78.7
Ave_qPCR	80.2
RT-qPCR_primer-F	agcctgagatcctccctgat
RT-qPCR_primer-R	ttgtagacagcagccagcac
protein_conc	4973	4865
WB_result	70.0	72.0
Ave_WB	71.0
WB_DONE_date	6/23/21	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	09/01/21	09/01/21
repeat_library
Note
ID	5012	5013

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

	BGKcLV26-23	BGKcLV26-24
Sample_ID	BGKcLV26-23	BGKcLV26-24
Sample Name
Sample Name	ALDOA-BGKcLV26-23	ALDOA-BGKcLV26-24
RBP	ALDOA	ALDOA
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9761	9762

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-23	BGKcLV26-24
Sample #	19	20
Sample Name	ALDOA-BGKcLV26-23	ALDOA-BGKcLV26-24
Sample_Name_Alias
Index Well Position	C03	D03
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	300	288
Peak_Molarity	98.40	87.20
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/C3.png	DNA_Library_set48-49/set1/D3.png
RIN	9.6	9.1
libSample_RNA_Well	RNA_Library_set48-49/set1/C3.png	RNA_Library_set48-49/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-23	BGKcLV26-24
RBP	ALDOA	ALDOA
Batch_ID	BGKcLV26	BGKcLV26
WB_result	70.000	72.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1578	1579

Sequencing Information

	BGKcLV26-23	BGKcLV26-24
Sample_ID	BGKcLV26-23	BGKcLV26-24
Sample Name	ALDOA-BGKcLV26-23	ALDOA-BGKcLV26-24
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	94,426,640	87,202,522
total_aligned_reads	82,709,628	77,240,514
unique_aligned_reads	75,552,150	70,656,832
percent_uniqueAligned	0.80011	0.81026
correlation_replicates	0.999436	0.999436
spikein_reads	40,650	20,604
percent_spikeins	0.00043	0.00024
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1755	1756

Data Submission Information

	BGKcLV26-23	BGKcLV26-23	BGKcLV26-23	BGKcLV26-23	BGKcLV26-23	BGKcLV26-23	BGKcLV26-24	BGKcLV26-24	BGKcLV26-24	BGKcLV26-24
ENCODE_alias	brenton-graveley:ALDOA-BGKcLV26	brenton-graveley:ALDOA-BGKcLV26-23	brenton-graveley:L-ALDOA-BGKcLV26-23	brenton-graveley:ALDOA-BGKcLV26-23_S25_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALDOA-BGKcLV26-23_S25_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALDOA-BGKcLV26-K562	brenton-graveley:ALDOA-BGKcLV26-24	brenton-graveley:L-ALDOA-BGKcLV26-24	brenton-graveley:ALDOA-BGKcLV26-24_S26_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALDOA-BGKcLV26-24_S26_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR071DBC	ENCBS166ZET	ENCLB822KJN	ENCFF741XWF	ENCFF952SFH	ENCSR379PIL	ENCBS326SBM	ENCLB075JLP	ENCFF249YHE	ENCFF999NBF
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	BGKcLV26-23	BGKcLV26-23	BGKcLV26-23	BGKcLV26-23	BGKcLV26-23	BGKcLV26-23	BGKcLV26-24	BGKcLV26-24	BGKcLV26-24	BGKcLV26-24
Sample Name	ALDOA-BGKcLV26-23	ALDOA-BGKcLV26-23	ALDOA-BGKcLV26-23	ALDOA-BGKcLV26-23	ALDOA-BGKcLV26-23	ALDOA-BGKcLV26-23	ALDOA-BGKcLV26-24	ALDOA-BGKcLV26-24	ALDOA-BGKcLV26-24	ALDOA-BGKcLV26-24
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		ALDOA-BGKcLV26-23.pdf	L-ALDOA-BGKcLV26-23.pdf				ALDOA-BGKcLV26-24.pdf	L-ALDOA-BGKcLV26-24.pdf
ID	3455	3544	3678	3812	3946	7080	3545	3679	3813	3947

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-BGKcLV26-23_S25_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1755	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	3848
ALDOA-BGKcLV26-23_S25_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1755	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	3898
ALDOA-BGKcLV26-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1755					GRCh38	V40	ALDOA-BGKcLV26-23_S25_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDOA-BGKcLV26-23_S25_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25535
ALDOA-BGKcLV26-23_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1755					GRCh38	V40	ALDOA-BGKcLV26-23_S25_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDOA-BGKcLV26-23_S25_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25585
ALDOA-BGKcLV26-23_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	1755					GRCh38	V40	ALDOA-BGKcLV26-23/Aligned.sortedByCoord.out.bam		ENCORE2	26551
ALDOA-BGKcLV26-23_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	1755					GRCh38	V40	ALDOA-BGKcLV26-23/Aligned.sortedByCoord.out.bam		ENCORE2	26601
ALDOA-BGKcLV26-23_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	1755					GRCh38	V40	ALDOA-BGKcLV26-23/Aligned.sortedByCoord.out.bam		ENCORE2	26651
ALDOA-BGKcLV26-23_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	1755					GRCh38	V40	ALDOA-BGKcLV26-23/Aligned.sortedByCoord.out.bam		ENCORE2	26701
ALDOA-BGKcLV26-24_S26_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1756	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	3849
ALDOA-BGKcLV26-24_S26_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1756	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	3899
ALDOA-BGKcLV26-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1756					GRCh38	V40	ALDOA-BGKcLV26-24_S26_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDOA-BGKcLV26-24_S26_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25536
ALDOA-BGKcLV26-24_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1756					GRCh38	V40	ALDOA-BGKcLV26-24_S26_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDOA-BGKcLV26-24_S26_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25586
ALDOA-BGKcLV26-24_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	1756					GRCh38	V40	ALDOA-BGKcLV26-24/Aligned.sortedByCoord.out.bam		ENCORE2	26552
ALDOA-BGKcLV26-24_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	1756					GRCh38	V40	ALDOA-BGKcLV26-24/Aligned.sortedByCoord.out.bam		ENCORE2	26602
ALDOA-BGKcLV26-24_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	1756					GRCh38	V40	ALDOA-BGKcLV26-24/Aligned.sortedByCoord.out.bam		ENCORE2	26652
ALDOA-BGKcLV26-24_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	1756					GRCh38	V40	ALDOA-BGKcLV26-24/Aligned.sortedByCoord.out.bam		ENCORE2	26702