NSD2 RNA-Seq in K562

General Information


RBP	NSD2
Cell_Line	K562
Method	CRISPR
Exp_Name	NSD2-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	NSD2-BGKcLV44-39
Rep2	NSD2-BGKcLV44-40
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	16.0
Rep2_qPCR	11.5
Rep1_WB	97.1
Rep2_WB	77.0
Antibody Cat#	65127S
Antibody Lot#	LOT# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1602

Experiment Information (Status: Submitting)

	BGKcLV44-39	BGKcLV44-40
idx	0	0
TRCN#_or_BGC#	BGC#0001035	BGC#0001035
shRNA_or_gRNA_sequence	GCAGCTCGGAGTCTTCCCGT	GCAGCTCGGAGTCTTCCCGT
PAM	TGG	TGG
Name	NSD2_90	NSD2_90
Sample_ID	BGKcLV44-39	BGKcLV44-40
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	NSD2	NSD2
qPCR_result	16.0	11.5
Ave_qPCR	13.7
RT-qPCR_primer-F	aaaacgccacctctcaacat
RT-qPCR_primer-R	gagggccataaggatcttcc
protein_conc	4695	4846
WB_result	97.1	77.0
Ave_WB
WB_DONE_date	8/12/24,8/22/24
MW	152kd
IP
antibody_Cat#	65127S	LOT# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5918	5919

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NSD2	Product_ID: 65127S Lot_ID: 1 Source: Cell Signaling Technology Target Name: NSD2-human

Experiment Status

	BGKcLV44-39	BGKcLV44-40
Sample_ID	BGKcLV44-39	BGKcLV44-40
Sample Name
Sample Name	NSD2-BGKcLV44-39	NSD2-BGKcLV44-40
RBP	NSD2	NSD2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13596	13597

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-39	BGKcLV44-40
Sample #	25	26
Sample Name	NSD2-BGKcLV44-39	NSD2-BGKcLV44-40
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	293	286
Peak_Molarity	101.00	86.90
libSampleQC_DNA_Well	DNA_Library_set75/set1/A9.png	DNA_Library_set75/set1/B9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/A3.png	RNA_Library_set75/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-39	BGKcLV44-40
RBP	NSD2	NSD2
Batch_ID	BGKcLV44	BGKcLV44
WB_result	97.100	77.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4584	4585

Sequencing Information

	BGKcLV44-39	BGKcLV44-40
Sample_ID	BGKcLV44-39	BGKcLV44-40
Sample Name	NSD2-BGKcLV44-39	NSD2-BGKcLV44-40
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	41,888,380	36,842,812
total_aligned_reads	39,707,535	34,701,404
unique_aligned_reads	36,766,871	32,139,334
percent_uniqueAligned	0.87773	0.87234
correlation_replicates	0.986626	0.986626
spikein_reads	103,534	82,744
percent_spikeins	0.00247	0.00225
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3295	3296

Data Submission Information DCC submission information was not avaliable

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
NSD2-BGKcLV44-39_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3295	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30950
NSD2-BGKcLV44-39_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3295	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30992
NSD2-BGKcLV44-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3295					GRCh38	V40	NSD2-BGKcLV44-39_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,NSD2-BGKcLV44-39_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31034
NSD2-BGKcLV44-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3295					GRCh38	V40	NSD2-BGKcLV44-39_Aligned.sortedByCoord.out.bam		ENCORE2	31076
NSD2-BGKcLV44-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3295					GRCh38	V40	NSD2-BGKcLV44-39_Aligned.sortedByCoord.out.bam		ENCORE2	31118
NSD2-BGKcLV44-39_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3295					GRCh38	V40	NSD2-BGKcLV44-39_Aligned.sortedByCoord.out.bam		ENCORE2	31160
NSD2-BGKcLV44-39_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3295					GRCh38	V40	NSD2-BGKcLV44-39_Aligned.sortedByCoord.out.bam		ENCORE2	31202
NSD2-BGKcLV44-39_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3295					GRCh38	V40	NSD2-BGKcLV44-39_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,NSD2-BGKcLV44-39_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31244
NSD2-BGKcLV44-40_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3296	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30951
NSD2-BGKcLV44-40_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3296	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30993
NSD2-BGKcLV44-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3296					GRCh38	V40	NSD2-BGKcLV44-40_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,NSD2-BGKcLV44-40_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31035
NSD2-BGKcLV44-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3296					GRCh38	V40	NSD2-BGKcLV44-40_Aligned.sortedByCoord.out.bam		ENCORE2	31077
NSD2-BGKcLV44-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3296					GRCh38	V40	NSD2-BGKcLV44-40_Aligned.sortedByCoord.out.bam		ENCORE2	31119
NSD2-BGKcLV44-40_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3296					GRCh38	V40	NSD2-BGKcLV44-40_Aligned.sortedByCoord.out.bam		ENCORE2	31161
NSD2-BGKcLV44-40_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3296					GRCh38	V40	NSD2-BGKcLV44-40_Aligned.sortedByCoord.out.bam		ENCORE2	31203
NSD2-BGKcLV44-40_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3296					GRCh38	V40	NSD2-BGKcLV44-40_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,NSD2-BGKcLV44-40_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31245