NSUN4 RNA-Seq in K562

General Information


RBP	NSUN4
Cell_Line	K562
Method	CRISPR
Exp_Name	NSUN4-BGKcLV15-K562
ENCODE_series_ID	ENCSR795RTD
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR550VEL
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	NSUN4-BGKcLV15-43
Rep2	NSUN4-BGKcLV15-44
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	77.2
Rep2_qPCR	74.9
Rep1_WB	86.1
Rep2_WB	81.6
Antibody Cat#	720212
Antibody Lot#	SA246721
Antibody DCC ID	ENCAB297AWK
Status	Released
Project	ENCODE4
ID	131

Experiment Information (Status: Released)

	BGKcLV15-43	BGKcLV15-44
idx	581	582
TRCN#_or_BGC#	BGC#0000358	BGC#0000358
shRNA_or_gRNA_sequence	TAGTCTGGCTATTCGGGACG	TAGTCTGGCTATTCGGGACG
PAM	GGG	GGG
Name	NSUN4-99	NSUN4-99
Sample_ID	BGKcLV15-43	BGKcLV15-44
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	NSUN4	NSUN4
qPCR_result	77.2	74.9
Ave_qPCR	76.1
RT-qPCR_primer-F	GGGATGGAAATCAAGTTCGAG
RT-qPCR_primer-R	GTGGTACAGGGCACATCCAC
protein_conc	5191	5017
WB_result	86.1	81.6
Ave_WB	83.8
WB_DONE_date	4/9/19
MW	43KD
IP	Rabbit / I
antibody_Cat#	720212
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	32.7	0
Rep2_TPM	30.7	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4693	4694

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NSUN4	Product_ID: 720212 Lot_ID: SA246721 Source: Thermo Fisher Target Name: NSUN4-human

Experiment Status

	BGKcLV15-43	BGKcLV15-44
Sample_ID	BGKcLV15-43	BGKcLV15-44
Sample Name
Sample Name	NSUN4-BGKcLV15-43	NSUN4-BGKcLV15-44
RBP	NSUN4	NSUN4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5351	5352

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-43	BGKcLV15-44
Sample #	21	22
Sample Name	NSUN4-BGKcLV15-43	NSUN4-BGKcLV15-44
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	2-E1	2-F1
Tecan	43.48	40.02
Tecan_date	2019-12-10	2019-12-10
Size_bp	273	277
Peak_Molarity	25.40	23.80
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E3.png	DNA_Library_set43-44/set1/F3.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set43-44/set1/E3.png	RNA_Library_set43-44/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-43	BGKcLV15-44
RBP	NSUN4	NSUN4
Batch_ID	BGKcLV15	BGKcLV15
WB_result	86.100	81.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	597	598

Sequencing Information

	BGKcLV15-43	BGKcLV15-44
Sample_ID	BGKcLV15-43	BGKcLV15-44
Sample Name	NSUN4-BGKcLV15-43	NSUN4-BGKcLV15-44
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	117,441,040	102,508,892
total_aligned_reads	110,050,418	97,560,212
unique_aligned_reads	100,522,544	89,052,016
percent_uniqueAligned	0.85594	0.86872
correlation_replicates	0.999201	0.999201
spikein_reads	72,488	70,116
percent_spikeins	0.00062	0.00068
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	103	104

Data Submission Information

	BGKcLV15-43	BGKcLV15-43	BGKcLV15-43	BGKcLV15-43	BGKcLV15-43	BGKcLV15-43	BGKcLV15-44	BGKcLV15-44	BGKcLV15-44	BGKcLV15-44
ENCODE_alias	brenton-graveley:NSUN4-BGKcLV15	brenton-graveley:NSUN4-BGKcLV15-43	brenton-graveley:L-NSUN4-BGKcLV15-43	brenton-graveley:NSUN4-BGKcLV15-43_S21_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NSUN4-BGKcLV15-43_S21_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NSUN4-BGKcLV15-K562	brenton-graveley:NSUN4-BGKcLV15-44	brenton-graveley:L-NSUN4-BGKcLV15-44	brenton-graveley:NSUN4-BGKcLV15-44_S22_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NSUN4-BGKcLV15-44_S22_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR550VEL	ENCBS871JRU	ENCLB414TDK	ENCFF550YSM	ENCFF046AMH	ENCSR795RTD	ENCBS864BAC	ENCLB691UVD	ENCFF612QCF	ENCFF781IVB
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	BGKcLV15-43	BGKcLV15-43	BGKcLV15-43	BGKcLV15-43	BGKcLV15-43	BGKcLV15-43	BGKcLV15-44	BGKcLV15-44	BGKcLV15-44	BGKcLV15-44
Sample Name	NSUN4-BGKcLV15-43	NSUN4-BGKcLV15-43	NSUN4-BGKcLV15-43	NSUN4-BGKcLV15-43	NSUN4-BGKcLV15-43	NSUN4-BGKcLV15-43	NSUN4-BGKcLV15-44	NSUN4-BGKcLV15-44	NSUN4-BGKcLV15-44	NSUN4-BGKcLV15-44
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		NSUN4-BGKcLV15-43.pdf	L-NPM1-BGKcLV15-41.pdf				NSUN4-BGKcLV15-44.pdf	L-NPM1-BGKcLV15-42.pdf
ID	27	136	300	498	550	7273	137	301	499	551

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
NSUN4-BGKcLV15-43_S21_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	103	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	97
NSUN4-BGKcLV15-43_S21_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	103	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	149
NSUN4-BGKcLV15-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	103					GRCh38	V40	NSUN4-BGKcLV15-43_S21_R1_001.filtered.trimmed.paired.fastq.gz,NSUN4-BGKcLV15-43_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24388
NSUN4-BGKcLV15-43_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	103					GRCh38	V40	NSUN4-BGKcLV15-43/Aligned.sortedByCoord.out.bam		ENCORE2	24440
NSUN4-BGKcLV15-43_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	103					GRCh38	V40	NSUN4-BGKcLV15-43/Aligned.sortedByCoord.out.bam		ENCORE2	24492
NSUN4-BGKcLV15-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	103					GRCh38	V40	NSUN4-BGKcLV15-43/Aligned.sortedByCoord.out.bam		ENCORE2	24544
NSUN4-BGKcLV15-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	103					GRCh38	V40	NSUN4-BGKcLV15-43/Aligned.sortedByCoord.out.bam		ENCORE2	24596
NSUN4-BGKcLV15-43_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	103					GRCh38	V40	NSUN4-BGKcLV15-43_S21_R1_001.filtered.trimmed.paired.fastq.gz,NSUN4-BGKcLV15-43_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24648
NSUN4-BGKcLV15-44_S22_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	104	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	98
NSUN4-BGKcLV15-44_S22_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	104	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	150
NSUN4-BGKcLV15-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	104					GRCh38	V40	NSUN4-BGKcLV15-44_S22_R1_001.filtered.trimmed.paired.fastq.gz,NSUN4-BGKcLV15-44_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24389
NSUN4-BGKcLV15-44_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	104					GRCh38	V40	NSUN4-BGKcLV15-44/Aligned.sortedByCoord.out.bam		ENCORE2	24441
NSUN4-BGKcLV15-44_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	104					GRCh38	V40	NSUN4-BGKcLV15-44/Aligned.sortedByCoord.out.bam		ENCORE2	24493
NSUN4-BGKcLV15-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	104					GRCh38	V40	NSUN4-BGKcLV15-44/Aligned.sortedByCoord.out.bam		ENCORE2	24545
NSUN4-BGKcLV15-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	104					GRCh38	V40	NSUN4-BGKcLV15-44/Aligned.sortedByCoord.out.bam		ENCORE2	24597
NSUN4-BGKcLV15-44_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	104					GRCh38	V40	NSUN4-BGKcLV15-44_S22_R1_001.filtered.trimmed.paired.fastq.gz,NSUN4-BGKcLV15-44_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24649