NSUN4 RNA-Seq in HepG2

General Information


RBP	NSUN4
Cell_Line	HepG2
Method	CRISPR
Exp_Name	NSUN4-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR372KFL
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR504CPZ
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	NSUN4-BGHcLV16-37
Rep2	NSUN4-BGHcLV16-38
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	74.9
Rep2_qPCR	59.2
Rep1_WB	72.9
Rep2_WB	83.3
Antibody Cat#	720212
Antibody Lot#	SA246721
Antibody DCC ID	ENCAB297AWK
Status	Released
Project	ENCODE4
ID	153

Experiment Information (Status: Released)

	BGHcLV16-37	BGHcLV16-38
idx	467	468
TRCN#_or_BGC#	BGC#0000358	BGC#0000358
shRNA_or_gRNA_sequence	TAGTCTGGCTATTCGGGACG	TAGTCTGGCTATTCGGGACG
PAM	GGG	GGG
Name	NSUN4-99	NSUN4-99
Sample_ID	BGHcLV16-37	BGHcLV16-38
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	NSUN4	NSUN4
qPCR_result	74.9	59.2
Ave_qPCR	67.1
RT-qPCR_primer-F	GGGATGGAAATCAAGTTCGAG
RT-qPCR_primer-R	GTGGTACAGGGCACATCCAC
protein_conc	4931	4358
WB_result	72.9	83.3
Ave_WB	78.1
WB_DONE_date	4/29/19
MW	43KD
IP	Rabbit / I
antibody_Cat#	720212
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	16	0
Rep2_TPM	15	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6616	6617

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

	BGHcLV16-37	BGHcLV16-38
Sample_ID	BGHcLV16-37	BGHcLV16-38
Sample Name
Sample Name	NSUN4-BGHcLV16-37	NSUN4-BGHcLV16-38
RBP	NSUN4	NSUN4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5425	5426

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-37	BGHcLV16-38
Sample #	59	60
Sample Name	NSUN4-BGHcLV16-37	NSUN4-BGHcLV16-38
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	2-A1	2-B1
Tecan	22.96	39.11
Tecan_date	2019-12-10	2019-12-10
Size_bp	279	279
Peak_Molarity	40.00	35.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/A3.png	DNA_Library_set43-44/set2/B3.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/A8.png	RNA_Library_set43-44/set1/B8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-37	BGHcLV16-38
RBP	NSUN4	NSUN4
Batch_ID	BGHcLV16	BGHcLV16
WB_result	72.900	83.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	635	636

Sequencing Information

	BGHcLV16-37	BGHcLV16-38
Sample_ID	BGHcLV16-37	BGHcLV16-38
Sample Name	NSUN4-BGHcLV16-37	NSUN4-BGHcLV16-38
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	111,551,664	130,908,226
total_aligned_reads	100,394,452	121,689,886
unique_aligned_reads	94,171,188	114,209,706
percent_uniqueAligned	0.84419	0.87244
correlation_replicates	0.998935	0.998935
spikein_reads	202,672	209,596
percent_spikeins	0.00182	0.00160
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	137	138

Data Submission Information

	BGHcLV16-37	BGHcLV16-37	BGHcLV16-37	BGHcLV16-37	BGHcLV16-37	BGHcLV16-37	BGHcLV16-38	BGHcLV16-38	BGHcLV16-38	BGHcLV16-38
ENCODE_alias	brenton-graveley:NSUN4-BGHcLV16	brenton-graveley:NSUN4-BGHcLV16-37	brenton-graveley:L-NSUN4-BGHcLV16-37	brenton-graveley:NSUN4-BGHcLV16-37_S55_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NSUN4-BGHcLV16-37_S55_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NSUN4-BGHcLV16-HepG2	brenton-graveley:NSUN4-BGHcLV16-38	brenton-graveley:L-NSUN4-BGHcLV16-38	brenton-graveley:NSUN4-BGHcLV16-38_S56_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NSUN4-BGHcLV16-38_S56_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR504CPZ	ENCBS530BMR	ENCLB484LAN	ENCFF356FYO	ENCFF719KCX	ENCSR372KFL	ENCBS065VXB	ENCLB514GAZ	ENCFF703EJH	ENCFF804RBE
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	BGHcLV16-37	BGHcLV16-37	BGHcLV16-37	BGHcLV16-37	BGHcLV16-37	BGHcLV16-37	BGHcLV16-38	BGHcLV16-38	BGHcLV16-38	BGHcLV16-38
Sample Name	NSUN4-BGHcLV16-37	NSUN4-BGHcLV16-37	NSUN4-BGHcLV16-37	NSUN4-BGHcLV16-37	NSUN4-BGHcLV16-37	NSUN4-BGHcLV16-37	NSUN4-BGHcLV16-38	NSUN4-BGHcLV16-38	NSUN4-BGHcLV16-38	NSUN4-BGHcLV16-38
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		NSUN4-BGHcLV16-37.pdf	L-NSUN4-BGHcLV16-37.pdf				NSUN4-BGHcLV16-38.pdf	L-NSUN4-BGHcLV16-38.pdf
ID	9	100	264	430	462	7272	101	265	431	463

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-BGHcLV16-37_S55_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	137	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	17
NSUN4-BGHcLV16-37_S55_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	137	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	49
NSUN4-BGHcLV16-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	137					GRCh38	V40	NSUN4-BGHcLV16-37_S55_R1_001.filtered.trimmed.paired.fastq.gz,NSUN4-BGHcLV16-37_S55_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24180
NSUN4-BGHcLV16-37_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	137					GRCh38	V40	NSUN4-BGHcLV16-37/Aligned.sortedByCoord.out.bam		ENCORE2	24212
NSUN4-BGHcLV16-37_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	137					GRCh38	V40	NSUN4-BGHcLV16-37/Aligned.sortedByCoord.out.bam		ENCORE2	24244
NSUN4-BGHcLV16-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	137					GRCh38	V40	NSUN4-BGHcLV16-37/Aligned.sortedByCoord.out.bam		ENCORE2	24276
NSUN4-BGHcLV16-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	137					GRCh38	V40	NSUN4-BGHcLV16-37/Aligned.sortedByCoord.out.bam		ENCORE2	24308
NSUN4-BGHcLV16-37_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	137					GRCh38	V40	NSUN4-BGHcLV16-37_S55_R1_001.filtered.trimmed.paired.fastq.gz,NSUN4-BGHcLV16-37_S55_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24340
NSUN4-BGHcLV16-38_S56_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	138	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	18
NSUN4-BGHcLV16-38_S56_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	138	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	50
NSUN4-BGHcLV16-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	138					GRCh38	V40	NSUN4-BGHcLV16-38_S56_R1_001.filtered.trimmed.paired.fastq.gz,NSUN4-BGHcLV16-38_S56_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24181
NSUN4-BGHcLV16-38_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	138					GRCh38	V40	NSUN4-BGHcLV16-38/Aligned.sortedByCoord.out.bam		ENCORE2	24213
NSUN4-BGHcLV16-38_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	138					GRCh38	V40	NSUN4-BGHcLV16-38/Aligned.sortedByCoord.out.bam		ENCORE2	24245
NSUN4-BGHcLV16-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	138					GRCh38	V40	NSUN4-BGHcLV16-38/Aligned.sortedByCoord.out.bam		ENCORE2	24277
NSUN4-BGHcLV16-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	138					GRCh38	V40	NSUN4-BGHcLV16-38/Aligned.sortedByCoord.out.bam		ENCORE2	24309
NSUN4-BGHcLV16-38_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	138					GRCh38	V40	NSUN4-BGHcLV16-38_S56_R1_001.filtered.trimmed.paired.fastq.gz,NSUN4-BGHcLV16-38_S56_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24341