ALDH18A1 RNA-Seq in K562

General Information


RBP	ALDH18A1
Cell_Line	K562
Method	CRISPR
Exp_Name	ALDH18A1-BGKcLV26-K562
ENCODE_series_ID	ENCSR575TDU
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR642RCV
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	ALDH18A1-BGKcLV26-21
Rep2	ALDH18A1-BGKcLV26-22
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	54.5
Rep2_WB	66.4
Antibody Cat#	A304-802A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB436UBW
Status	Released
Project	ENCODE4
ID	789

Experiment Information (Status: Released)

	BGKcLV26-21	BGKcLV26-21	BGKcLV26-22	BGKcLV26-22
idx	876	878	877	879
TRCN#_or_BGC#	BGC#0000628	BGC#0000628	BGC#0000628	BGC#0000628
shRNA_or_gRNA_sequence	TGCGATCTGTCGCAGACCGA	TGCGATCTGTCGCAGACCGA	TGCGATCTGTCGCAGACCGA	TGCGATCTGTCGCAGACCGA
PAM	TGG	TGG	TGG	TGG
Name	ALDH18A1_99	ALDH18A1_99	ALDH18A1_99	ALDH18A1_99
Sample_ID	BGKcLV26-21	BGKcLV26-21	BGKcLV26-22	BGKcLV26-22
transduction_Date	3/30/21	3/30/21	3/30/21	3/30/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	ALDH18A1	ALDH18A1	ALDH18A1	ALDH18A1
qPCR_result	49.3	49.3	50.7	50.7
Ave_qPCR	50.0	50.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4404	4404	4451	4451
WB_result	54.5	78.8	66.4	80.3
Ave_WB	60.5	79.5
WB_DONE_date	4/22/21	4/20/22	jess
MW	87kDa	87kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A304-802A	A304-803A	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB436UBW	ENCAB658RVP	1/19/22
submitted_to_DCC_date
Rep1_TPM	39.2	0	0	0
Rep2_TPM	46	0	0	0
Action	Ready		Ready
Library_start_date	09/01/21		09/01/21
repeat_library
Note
ID	5008	5010	5009	5011

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ALDH18A1	Product_ID: A304-802A Lot_ID: 1 Source: Bethyl Labs Target Name: ALDH18A1-human
ALDH18A1	Product_ID: A304-803A Lot_ID: 1 Source: Bethyl Labs Target Name: ALDH18A1-human

Experiment Status

	BGKcLV26-21	BGKcLV26-22
Sample_ID	BGKcLV26-21	BGKcLV26-22
Sample Name
Sample Name	ALDH18A1-BGKcLV26-21	ALDH18A1-BGKcLV26-22
RBP	ALDH18A1	ALDH18A1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9759	9760

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-21	BGKcLV26-22
Sample #	17	18
Sample Name	ALDH18A1-BGKcLV26-21	ALDH18A1-BGKcLV26-22
Sample_Name_Alias
Index Well Position	A03	B03
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	321	294
Peak_Molarity	72.30	95.20
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/A3.png	DNA_Library_set48-49/set1/B3.png
RIN	9.4	9.7
libSample_RNA_Well	RNA_Library_set48-49/set1/A3.png	RNA_Library_set48-49/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-21	BGKcLV26-22
RBP	ALDH18A1	ALDH18A1
Batch_ID	BGKcLV26	BGKcLV26
WB_result	54.500	66.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1576	1577

Sequencing Information

	BGKcLV26-21	BGKcLV26-22
Sample_ID	BGKcLV26-21	BGKcLV26-22
Sample Name	ALDH18A1-BGKcLV26-21	ALDH18A1-BGKcLV26-22
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	103,938,894	69,307,836
total_aligned_reads	84,509,992	59,581,278
unique_aligned_reads	77,080,656	54,602,392
percent_uniqueAligned	0.74160	0.78782
correlation_replicates	0.999208	0.999208
spikein_reads	37,912	30,830
percent_spikeins	0.00036	0.00044
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1753	1754

Data Submission Information

	BGKcLV26-21	BGKcLV26-21	BGKcLV26-21	BGKcLV26-21	BGKcLV26-21	BGKcLV26-21	BGKcLV26-22	BGKcLV26-22	BGKcLV26-22	BGKcLV26-22
ENCODE_alias	brenton-graveley:ALDH18A1-BGKcLV26	brenton-graveley:ALDH18A1-BGKcLV26-21	brenton-graveley:L-ALDH18A1-BGKcLV26-21	brenton-graveley:ALDH18A1-BGKcLV26-21_S23_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALDH18A1-BGKcLV26-21_S23_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALDH18A1-BGKcLV26-K562	brenton-graveley:ALDH18A1-BGKcLV26-22	brenton-graveley:L-ALDH18A1-BGKcLV26-22	brenton-graveley:ALDH18A1-BGKcLV26-22_S24_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ALDH18A1-BGKcLV26-22_S24_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR642RCV	ENCBS747IVW	ENCLB544CHY	ENCFF735ULT	ENCFF209DVM	ENCSR575TDU	ENCBS138CBR	ENCLB822RLA	ENCFF171NZK	ENCFF504ZSJ
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	BGKcLV26-21	BGKcLV26-21	BGKcLV26-21	BGKcLV26-21	BGKcLV26-21	BGKcLV26-21	BGKcLV26-22	BGKcLV26-22	BGKcLV26-22	BGKcLV26-22
Sample Name	ALDH18A1-BGKcLV26-21	ALDH18A1-BGKcLV26-21	ALDH18A1-BGKcLV26-21	ALDH18A1-BGKcLV26-21	ALDH18A1-BGKcLV26-21	ALDH18A1-BGKcLV26-21	ALDH18A1-BGKcLV26-22	ALDH18A1-BGKcLV26-22	ALDH18A1-BGKcLV26-22	ALDH18A1-BGKcLV26-22
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-11-19	2022-02-04	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2022-02-04	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		ALDH18A1-BGKcLV26-21.pdf	L-ALDH18A1-BGKcLV26-21.pdf				ALDH18A1-BGKcLV26-22.pdf	L-ALDH18A1-BGKcLV26-22.pdf
ID	3454	3542	3676	3810	3944	7078	3543	3677	3811	3945

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
ALDH18A1-BGKcLV26-21_S23_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1753	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	3846
ALDH18A1-BGKcLV26-21_S23_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1753	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	3896
ALDH18A1-BGKcLV26-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1753					GRCh38	V40	ALDH18A1-BGKcLV26-21_S23_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDH18A1-BGKcLV26-21_S23_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25533
ALDH18A1-BGKcLV26-21_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1753					GRCh38	V40	ALDH18A1-BGKcLV26-21_S23_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDH18A1-BGKcLV26-21_S23_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25583
ALDH18A1-BGKcLV26-21_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	1753					GRCh38	V40	ALDH18A1-BGKcLV26-21/Aligned.sortedByCoord.out.bam		ENCORE2	26549
ALDH18A1-BGKcLV26-21_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	1753					GRCh38	V40	ALDH18A1-BGKcLV26-21/Aligned.sortedByCoord.out.bam		ENCORE2	26599
ALDH18A1-BGKcLV26-21_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	1753					GRCh38	V40	ALDH18A1-BGKcLV26-21/Aligned.sortedByCoord.out.bam		ENCORE2	26649
ALDH18A1-BGKcLV26-21_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	1753					GRCh38	V40	ALDH18A1-BGKcLV26-21/Aligned.sortedByCoord.out.bam		ENCORE2	26699
ALDH18A1-BGKcLV26-22_S24_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1754	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	3847
ALDH18A1-BGKcLV26-22_S24_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1754	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	3897
ALDH18A1-BGKcLV26-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1754					GRCh38	V40	ALDH18A1-BGKcLV26-22_S24_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDH18A1-BGKcLV26-22_S24_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25534
ALDH18A1-BGKcLV26-22_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1754					GRCh38	V40	ALDH18A1-BGKcLV26-22_S24_L003_R1_001.filtered.trimmed.paired.fastq.gz,ALDH18A1-BGKcLV26-22_S24_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25584
ALDH18A1-BGKcLV26-22_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	1754					GRCh38	V40	ALDH18A1-BGKcLV26-22/Aligned.sortedByCoord.out.bam		ENCORE2	26550
ALDH18A1-BGKcLV26-22_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	1754					GRCh38	V40	ALDH18A1-BGKcLV26-22/Aligned.sortedByCoord.out.bam		ENCORE2	26600
ALDH18A1-BGKcLV26-22_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	1754					GRCh38	V40	ALDH18A1-BGKcLV26-22/Aligned.sortedByCoord.out.bam		ENCORE2	26650
ALDH18A1-BGKcLV26-22_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	1754					GRCh38	V40	ALDH18A1-BGKcLV26-22/Aligned.sortedByCoord.out.bam		ENCORE2	26700