NSUN5 RNA-Seq in K562

General Information


RBP	NSUN5
Cell_Line	K562
Method	CRISPR
Exp_Name	NSUN5-BGKcLV19-K562
ENCODE_series_ID	ENCSR613AQN
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR982XTO
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	NSUN5-BGKcLV19-29
Rep2	NSUN5-BGKcLV19-30
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	91.1
Rep2_WB	89.6687668
Antibody Cat#	PA5-54228
Antibody Lot#	LOT# TK2671522A
Antibody DCC ID	ENCAB884UJQ
Status	Released
Project	ENCODE4
ID	55

Experiment Information (Status: Released)

	BGKcLV19-29	BGKcLV19-30
idx	701	702
TRCN#_or_BGC#	BGC#0000475	BGC#0000475
shRNA_or_gRNA_sequence	CTGGTCTTTATTGCCTGGGG	CTGGTCTTTATTGCCTGGGG
PAM	TGG	TGG
Name	NSUN5_76	NSUN5_76
Sample_ID	BGKcLV19-29	BGKcLV19-30
transduction_Date	11/6/19	11/6/19
days	Day 6	Day 6
RBP_name	NSUN5	NSUN5
qPCR_result	0	0
Ave_qPCR	0.0
RT-qPCR_primer-F	TGAGCAGCTGGGATTATGAAG
RT-qPCR_primer-R	CAAGGGGTCCAGGAGAAAAT
protein_conc	3529	3926
WB_result	91.1	89.6687668
Ave_WB	90.4
WB_DONE_date	2/28/21	jess
MW	47kd
IP	Rabbit / I
antibody_Cat#	PA5-54228	LOT# TK2671522A
Antibody DCC ID	ENCAB884UJQ
submitted_to_DCC_date	11/16/20
Rep1_TPM	47.9	0
Rep2_TPM	29.2	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4821	4822

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NSUN5	Product_ID: PA5-54228 Lot_ID: TK2671522A Source: Thermo Fisher Target Name: NSUN5-human

Experiment Status

	BGKcLV19-29	BGKcLV19-30
Sample_ID	BGKcLV19-29	BGKcLV19-30
Sample Name
Sample Name	NSUN5-BGKcLV19-29	NSUN5-BGKcLV19-30
RBP	NSUN5	NSUN5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5703	5704

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-29	BGKcLV19-30
Sample #	17	18
Sample Name	NSUN5-BGKcLV19-29	NSUN5-BGKcLV19-30
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	303	309
Peak_Molarity	235.00	115.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/C2.png	DNA_Library_set45/set1/D2.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_set45/set1/C2.png	RNA_Library_set45/set2/A10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-29	BGKcLV19-30
RBP	NSUN5	NSUN5
Batch_ID	BGKcLV19	BGKcLV19
WB_result	83.200	81.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	791	792

Sequencing Information

	BGKcLV19-29	BGKcLV19-30
Sample_ID	BGKcLV19-29	BGKcLV19-30
Sample Name	NSUN5-BGKcLV19-29	NSUN5-BGKcLV19-30
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	142,462,766	72,815,944
total_aligned_reads	133,868,910	69,113,894
unique_aligned_reads	122,118,684	63,106,622
percent_uniqueAligned	0.85720	0.86666
correlation_replicates	0.989013	0.989013
spikein_reads	116,000	52,604
percent_spikeins	0.00081	0.00072
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	422	423

Data Submission Information

	BGKcLV19-29	BGKcLV19-29	BGKcLV19-29	BGKcLV19-29	BGKcLV19-29	BGKcLV19-29	BGKcLV19-30	BGKcLV19-30	BGKcLV19-30	BGKcLV19-30
ENCODE_alias	brenton-graveley:NSUN5-BGKcLV19	brenton-graveley:NSUN5-BGKcLV19-29	brenton-graveley:L-NSUN5-BGKcLV19-29	brenton-graveley:NSUN5-BGKcLV19-29_S11_R1_001.fastq.gz	brenton-graveley:NSUN5-BGKcLV19-29_S11_R2_001.fastq.gz	brenton-graveley:NSUN5-BGKcLV19-K562	brenton-graveley:NSUN5-BGKcLV19-30	brenton-graveley:L-NSUN5-BGKcLV19-30	brenton-graveley:NSUN5-BGKcLV19-30_S12_R1_001.fastq.gz	brenton-graveley:NSUN5-BGKcLV19-30_S12_R2_001.fastq.gz
ENCODE_accession	ENCSR982XTO	ENCBS660QBK	ENCLB792KWX	ENCFF398QBO	ENCFF367VTF	ENCSR613AQN	ENCBS332GWN	ENCLB243KUM	ENCFF861LVQ	ENCFF222PBD
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	BGKcLV19-29	BGKcLV19-29	BGKcLV19-29	BGKcLV19-29	BGKcLV19-29	BGKcLV19-29	BGKcLV19-30	BGKcLV19-30	BGKcLV19-30	BGKcLV19-30
Sample Name	NSUN5-BGKcLV19-29	NSUN5-BGKcLV19-29	NSUN5-BGKcLV19-29	NSUN5-BGKcLV19-29	NSUN5-BGKcLV19-29	NSUN5-BGKcLV19-29	NSUN5-BGKcLV19-30	NSUN5-BGKcLV19-30	NSUN5-BGKcLV19-30	NSUN5-BGKcLV19-30
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
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		NSUN5-BGKcLV19-29.pdf	L-NSUN5-BGKcLV19-29.pdf				NSUN5-BGKcLV19-30.pdf	L-NSUN5-BGKcLV19-30.pdf
ID	2095	2145	2215	2285	2355	7274	2146	2216	2286	2356

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
NSUN5-BGKcLV19-29_S11_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	422	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1234
NSUN5-BGKcLV19-29_S11_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	422	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1284
NSUN5-BGKcLV19-29_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	422					GRCh38	V40	NSUN5-BGKcLV19-29_S11_R1_001.filtered.trimmed.paired.fastq.gz,NSUN5-BGKcLV19-29_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25227
NSUN5-BGKcLV19-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	422					GRCh38	V40	NSUN5-BGKcLV19-29_S11_R1_001.filtered.trimmed.paired.fastq.gz,NSUN5-BGKcLV19-29_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27181
NSUN5-BGKcLV19-29_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	422					GRCh38	V40	NSUN5-BGKcLV19-29/Aligned.sortedByCoord.out.bam		ENCORE2	27231
NSUN5-BGKcLV19-29_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	422					GRCh38	V40	NSUN5-BGKcLV19-29/Aligned.sortedByCoord.out.bam		ENCORE2	27281
NSUN5-BGKcLV19-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	422					GRCh38	V40	NSUN5-BGKcLV19-29/Aligned.sortedByCoord.out.bam		ENCORE2	27331
NSUN5-BGKcLV19-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	422					GRCh38	V40	NSUN5-BGKcLV19-29/Aligned.sortedByCoord.out.bam		ENCORE2	27381
NSUN5-BGKcLV19-30_S12_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	423	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1235
NSUN5-BGKcLV19-30_S12_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	423	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1285
NSUN5-BGKcLV19-30_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	423					GRCh38	V40	NSUN5-BGKcLV19-30_S12_R1_001.filtered.trimmed.paired.fastq.gz,NSUN5-BGKcLV19-30_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25228
NSUN5-BGKcLV19-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	423					GRCh38	V40	NSUN5-BGKcLV19-30_S12_R1_001.filtered.trimmed.paired.fastq.gz,NSUN5-BGKcLV19-30_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27182
NSUN5-BGKcLV19-30_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	423					GRCh38	V40	NSUN5-BGKcLV19-30/Aligned.sortedByCoord.out.bam		ENCORE2	27232
NSUN5-BGKcLV19-30_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	423					GRCh38	V40	NSUN5-BGKcLV19-30/Aligned.sortedByCoord.out.bam		ENCORE2	27282
NSUN5-BGKcLV19-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	423					GRCh38	V40	NSUN5-BGKcLV19-30/Aligned.sortedByCoord.out.bam		ENCORE2	27332
NSUN5-BGKcLV19-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	423					GRCh38	V40	NSUN5-BGKcLV19-30/Aligned.sortedByCoord.out.bam		ENCORE2	27382