NSUN2 RNA-Seq in K562

General Information


RBP	NSUN2
Cell_Line	K562
Method	shRNA
Exp_Name	NSUN2-BGKLV34-K562
ENCODE_series_ID	ENCSR951PTY
Batch_ID	BGKLV34
Pool ID	Pool-160912
Local_Set_Name	set34
ENCODE_KD_Exp_ID	ENCSR829EFL
ENCODE_CN_Exp_ID	ENCSR174OYC
Rep1	NSUN2_BGKLV34-25
Rep2	NSUN2_BGKLV34-26
CN1	NT_BGKLV34-1
CN2	NT_BGKLV34-2
Rep1_qPCR	58.8
Rep2_qPCR	56.9
Rep1_WB	65.3
Rep2_WB	56.9
Antibody Cat#	A303-912A
Antibody Lot#	A303-912A
Antibody DCC ID	ENCAB643VMO
Status	Released
Project	ENCODE3
ID	723

Experiment Information (Status: Released)

	BGKLV34-25	BGKLV34-25	BGKLV34-26	BGKLV34-26
idx	688	0	689	0
TRCN#_or_BGC#	TRCN0000166537	TRCN0000166537	TRCN0000166537	TRCN0000166537
shRNA_or_gRNA_sequence	CCCAAGAATGAACGGCTTCAT		CCCAAGAATGAACGGCTTCAT
PAM
Name	NSUN2	NSUN2	NSUN2	NSUN2
Sample_ID	BGKLV34-25	BGKLV34-25	BGKLV34-26	BGKLV34-26
transduction_Date	11/4/2015	11/4/2015	11/4/2015	11/4/2015
days
RBP_name	NSUN2	NSUN2	NSUN2	NSUN2
qPCR_result	58.8	58.8	56.9	56.9
Ave_qPCR	57.9	57.9
RT-qPCR_primer-F	ggaagcatcgtgctgaagta	ggaagcatcgtgctgaagta
RT-qPCR_primer-R	agttcgaatggaggccttt	agttcgaatggaggccttt
protein_conc	3558	3558	3019	3019
WB_result	65.3	68.6	56.9	62.8
Ave_WB	61.1	65.7
WB_DONE_date	2/2/2016	10/23/2018
MW	86kDa			wes
IP	1		1
antibody_Cat#	A303-912A	711068	A303-912A	Lot ID SA245649
Antibody DCC ID	ENCAB643VMO	ENCAB610PKS	ENCAB643VMO
submitted_to_DCC_date	3/8/2016	3/11/19
Rep1_TPM	110.799652	0	0	0
Rep2_TPM	57.5603108	0	0	0
Action
Library_start_date	3/9/2016		3/9/2016
repeat_library
Note
ID	779	781	780	782

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NSUN2	Product_ID: 711068 Lot_ID: SA245649 Source: Thermo Fisher Target Name: NSUN2-human
NSUN2	Product_ID: A303-912A Lot_ID: 1 Source: Bethyl Labs Target Name: NSUN2-human

Experiment Status

	BGKLV34-25	BGKLV34-26
Sample_ID	BGKLV34-25	BGKLV34-26
Sample Name	NSUN2_BGKLV34-25	NSUN2_BGKLV34-26
Sample Name	NSUN2_BGKLV34-25	NSUN2_BGKLV34-26
RBP	NSUN2	NSUN2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1233	1234

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-25	BGKLV34-26
Sample #
Sample Name	NSUN2-BGKLV34-25	NSUN2-BGKLV34-26
Sample_Name_Alias	NSUN2_BGKLV34-25	NSUN2_BGKLV34-26
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/C3.png	DNA_Library_LV33-34-25B-32/set1/D3.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/A5.png	RNA_Library_LV32-33-34/set1/B5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV34-25	BGKLV34-26
RBP	NSUN2	NSUN2
Batch_ID	BGKLV34	BGKLV34
WB_result	65.300	56.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2918	2919

Sequencing Information

	BGKLV34-25	BGKLV34-26
Sample_ID	BGKLV34-25	BGKLV34-26
Sample Name	NSUN2_BGKLV34-25	NSUN2_BGKLV34-26
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set34	set34
total_reads	90,082,108	79,710,518
total_aligned_reads	76,976,670	69,494,092
unique_aligned_reads	69,895,130	63,316,388
percent_uniqueAligned	0.77590	0.79433
correlation_replicates	0.999591	0.999591
spikein_reads	343,716	318,494
percent_spikeins	0.00382	0.00400
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1567	1568

Data Submission Information

	BGKLV34-25	BGKLV34-25
ENCODE_alias	brenton-graveley:NSUN2_BGKLV34	brenton-graveley:NSUN2-BGKLV34-K562
ENCODE_accession	ENCSR829EFL	ENCSR951PTY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-25	BGKLV34-25
Sample Name	NSUN2_BGKLV34-25	NSUN2_BGKLV34-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3156	6833

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
NSUN2_BGKLV34-25_TTAGGC_L003_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1567	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21526
NSUN2_BGKLV34-25_TTAGGC_L003_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1567	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21546
NSUN2_BGKLV34-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1567					GRCh38	V40	NSUN2_BGKLV34-25_TTAGGC_L003_001.R1.fastq.gz,NSUN2_BGKLV34-25_TTAGGC_L003_001.R2.fastq.gz		ENCORE2	21566
NSUN2_BGKLV34-25_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1567					GRCh38	V40	NSUN2_BGKLV34-25/Aligned.sortedByCoord.out.bam		ENCORE2	21586
NSUN2_BGKLV34-25_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1567					GRCh38	V40	NSUN2_BGKLV34-25/Aligned.sortedByCoord.out.bam		ENCORE2	21606
NSUN2_BGKLV34-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1567					GRCh38	V40	NSUN2_BGKLV34-25/Aligned.sortedByCoord.out.bam		ENCORE2	21626
NSUN2_BGKLV34-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1567					GRCh38	V40	NSUN2_BGKLV34-25/Aligned.sortedByCoord.out.bam		ENCORE2	21646
NSUN2_BGKLV34-25_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1567					GRCh38	V40	NSUN2_BGKLV34-25_TTAGGC_L003_001.R1.fastq.gz,NSUN2_BGKLV34-25_TTAGGC_L003_001.R2.fastq.gz		ENCORE2	21666
NSUN2_BGKLV34-26_TGACCA_L003_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1568	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21527
NSUN2_BGKLV34-26_TGACCA_L003_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1568	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21547
NSUN2_BGKLV34-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1568					GRCh38	V40	NSUN2_BGKLV34-26_TGACCA_L003_001.R1.fastq.gz,NSUN2_BGKLV34-26_TGACCA_L003_001.R2.fastq.gz		ENCORE2	21567
NSUN2_BGKLV34-26_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1568					GRCh38	V40	NSUN2_BGKLV34-26/Aligned.sortedByCoord.out.bam		ENCORE2	21587
NSUN2_BGKLV34-26_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1568					GRCh38	V40	NSUN2_BGKLV34-26/Aligned.sortedByCoord.out.bam		ENCORE2	21607
NSUN2_BGKLV34-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1568					GRCh38	V40	NSUN2_BGKLV34-26/Aligned.sortedByCoord.out.bam		ENCORE2	21627
NSUN2_BGKLV34-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1568					GRCh38	V40	NSUN2_BGKLV34-26/Aligned.sortedByCoord.out.bam		ENCORE2	21647
NSUN2_BGKLV34-26_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1568					GRCh38	V40	NSUN2_BGKLV34-26_TGACCA_L003_001.R1.fastq.gz,NSUN2_BGKLV34-26_TGACCA_L003_001.R2.fastq.gz		ENCORE2	21667