NSUN2 RNA-Seq in HepG2

General Information


RBP	NSUN2
Cell_Line	HepG2
Method	shRNA
Exp_Name	NSUN2-BGHLV35-HepG2
ENCODE_series_ID	ENCSR825EXD
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR629RUG
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	NSUN2_BGHLV35-29
Rep2	NSUN2_BGHLV35-30
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	73.2
Rep2_qPCR	74.6
Rep1_WB	64.8
Rep2_WB	64.6
Antibody Cat#	A303-912A
Antibody Lot#	A303-912A
Antibody DCC ID	ENCAB643VMO
Status	Released
Project	ENCODE3
ID	737

Experiment Information (Status: Released)

	BGHLV35-29	BGHLV35-30
idx	885	886
TRCN#_or_BGC#	TRCN0000166537	TRCN0000166537
shRNA_or_gRNA_sequence	CCCAAGAATGAACGGCTTCAT	CCCAAGAATGAACGGCTTCAT
PAM
Name	NSUN2	NSUN2
Sample_ID	BGHLV35-29	BGHLV35-30
transduction_Date	4/29/16	4/29/16
days
RBP_name	NSUN2	NSUN2
qPCR_result	73.2	74.6
Ave_qPCR	73.9
RT-qPCR_primer-F	ggaagcatcgtgctgaagta
RT-qPCR_primer-R	agttcgaatggaggccttt
protein_conc	4133	4586
WB_result	64.8	64.6
Ave_WB	64.7
WB_DONE_date	5/10/2016	WES
MW	86kDa
IP	1	1
antibody_Cat#	A303-912A	A303-912A
Antibody DCC ID	ENCAB643VMO	ENCAB643VMO
submitted_to_DCC_date	10/26/16
Rep1_TPM	54.6	54.6
Rep2_TPM	48	48
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2974	2975

Western Blot

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

Experiment Status

	BGHLV35-29	BGHLV35-30
Sample_ID	BGHLV35-29	BGHLV35-30
Sample Name	NSUN2_BGHLV35-29	NSUN2_BGHLV35-30
Sample Name	NSUN2_BGHLV35-29	NSUN2_BGHLV35-30
RBP	NSUN2	NSUN2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1263	1264

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-29	BGHLV35-30
Sample #
Sample Name	NSUN2-BGHLV35-29	NSUN2-BGHLV35-30
Sample_Name_Alias	NSUN2_BGHLV35-29	NSUN2_BGHLV35-30
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set1/A3.png	DNA_Library_LV35/set1/B3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/A3.png	RNA_Library_LV35_LV36/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-29	BGHLV35-30
RBP	NSUN2	NSUN2
Batch_ID	BGHLV35	BGHLV35
WB_result	64.800	64.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2948	2949

Sequencing Information

	BGHLV35-29	BGHLV35-30
Sample_ID	BGHLV35-29	BGHLV35-30
Sample Name	NSUN2_BGHLV35-29	NSUN2_BGHLV35-30
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	67,508,796	74,325,872
total_aligned_reads	50,270,478	58,207,928
unique_aligned_reads	47,395,534	54,740,970
percent_uniqueAligned	0.70206	0.73650
correlation_replicates	0.996171	0.996171
spikein_reads	95,150	122,030
percent_spikeins	0.00141	0.00164
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1597	1598

Data Submission Information

	BGHLV35-29	BGHLV35-29
ENCODE_alias	brenton-graveley:NSUN2_BGHLV35	brenton-graveley:NSUN2-BGHLV35-HepG2
ENCODE_accession	ENCSR629RUG	ENCSR825EXD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-29	BGHLV35-29
Sample Name	NSUN2_BGHLV35-29	NSUN2_BGHLV35-29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3171	6832

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_BGHLV35-29_GTCCGC_L007_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1597	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21696
NSUN2_BGHLV35-29_GTCCGC_L007_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1597	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21722
NSUN2_BGHLV35-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1597					GRCh38	V40	NSUN2_BGHLV35-29_GTCCGC_L007_001.R1.fastq.gz,NSUN2_BGHLV35-29_GTCCGC_L007_001.R2.fastq.gz		ENCORE2	21748
NSUN2_BGHLV35-29_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1597					GRCh38	V40	NSUN2_BGHLV35-29/Aligned.sortedByCoord.out.bam		ENCORE2	21774
NSUN2_BGHLV35-29_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1597					GRCh38	V40	NSUN2_BGHLV35-29/Aligned.sortedByCoord.out.bam		ENCORE2	21800
NSUN2_BGHLV35-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1597					GRCh38	V40	NSUN2_BGHLV35-29/Aligned.sortedByCoord.out.bam		ENCORE2	21826
NSUN2_BGHLV35-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1597					GRCh38	V40	NSUN2_BGHLV35-29/Aligned.sortedByCoord.out.bam		ENCORE2	21852
NSUN2_BGHLV35-29_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1597					GRCh38	V40	NSUN2_BGHLV35-29_GTCCGC_L007_001.R1.fastq.gz,NSUN2_BGHLV35-29_GTCCGC_L007_001.R2.fastq.gz		ENCORE2	21878
NSUN2_BGHLV35-30_GTGAAA_L007_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1598	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21697
NSUN2_BGHLV35-30_GTGAAA_L007_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1598	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21723
NSUN2_BGHLV35-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1598					GRCh38	V40	NSUN2_BGHLV35-30_GTGAAA_L007_001.R1.fastq.gz,NSUN2_BGHLV35-30_GTGAAA_L007_001.R2.fastq.gz		ENCORE2	21749
NSUN2_BGHLV35-30_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1598					GRCh38	V40	NSUN2_BGHLV35-30/Aligned.sortedByCoord.out.bam		ENCORE2	21775
NSUN2_BGHLV35-30_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1598					GRCh38	V40	NSUN2_BGHLV35-30/Aligned.sortedByCoord.out.bam		ENCORE2	21801
NSUN2_BGHLV35-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1598					GRCh38	V40	NSUN2_BGHLV35-30/Aligned.sortedByCoord.out.bam		ENCORE2	21827
NSUN2_BGHLV35-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1598					GRCh38	V40	NSUN2_BGHLV35-30/Aligned.sortedByCoord.out.bam		ENCORE2	21853
NSUN2_BGHLV35-30_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1598					GRCh38	V40	NSUN2_BGHLV35-30_GTGAAA_L007_001.R1.fastq.gz,NSUN2_BGHLV35-30_GTGAAA_L007_001.R2.fastq.gz		ENCORE2	21879