NPM1 RNA-Seq in K562

General Information


RBP	NPM1
Cell_Line	K562
Method	CRISPR
Exp_Name	NPM1-BGKcLV15-K562
ENCODE_series_ID	ENCSR463EFP
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR034NAT
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	NPM1-BGKcLV15-41
Rep2	NPM1-BGKcLV15-42
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	85.0
Rep2_qPCR	83.3
Rep1_WB	92.1
Rep2_WB	86.4
Antibody Cat#	325200
Antibody Lot#	LOT# TD268297
Antibody DCC ID	ENCAB147WFE
Status	Released
Project	ENCODE4
ID	130

Experiment Information (Status: Released)

	BGKcLV15-41	BGKcLV15-42
idx	579	580
TRCN#_or_BGC#	BGC#0000377	BGC#0000377
shRNA_or_gRNA_sequence	TATGTAAGTGCCCTTACCGT	TATGTAAGTGCCCTTACCGT
PAM	tgg	tgg
Name	NPM1-96	NPM1-96
Sample_ID	BGKcLV15-41	BGKcLV15-42
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	NPM1	NPM1
qPCR_result	85.0	83.3
Ave_qPCR	84.2
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5616	5785
WB_result	92.1	86.4
Ave_WB	89.2
WB_DONE_date	4/9/19,4/18/19,5/8/1
MW	33KD
IP	Mouse / Ig
antibody_Cat#	325200	LOT# TD268297
Antibody DCC ID	ENCAB147WFE
submitted_to_DCC_date	4/17/19
Rep1_TPM	3076.8	0
Rep2_TPM	3879	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4691	4692

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NPM1	Product_ID: 325200 Lot_ID: TD268297 Source: Thermo Fisher Target Name: NPM1-human

Experiment Status

	BGKcLV15-41	BGKcLV15-42
Sample_ID	BGKcLV15-41	BGKcLV15-42
Sample Name
Sample Name	NPM1-BGKcLV15-41	NPM1-BGKcLV15-42
RBP	NPM1	NPM1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5349	5350

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-41	BGKcLV15-42
Sample #	19	20
Sample Name	NPM1-BGKcLV15-41	NPM1-BGKcLV15-42
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	2-C1	2-D1
Tecan	40.84	41.40
Tecan_date	2019-12-10	2019-12-10
Size_bp	262	272
Peak_Molarity	17.80	19.50
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C3.png	DNA_Library_set43-44/set1/D3.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/C3.png	RNA_Library_set43-44/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-41	BGKcLV15-42
RBP	NPM1	NPM1
Batch_ID	BGKcLV15	BGKcLV15
WB_result	92.100	86.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	595	596

Sequencing Information

	BGKcLV15-41	BGKcLV15-42
Sample_ID	BGKcLV15-41	BGKcLV15-42
Sample Name	NPM1-BGKcLV15-41	NPM1-BGKcLV15-42
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	122,254,406	108,085,552
total_aligned_reads	117,701,930	103,635,890
unique_aligned_reads	107,343,504	94,604,488
percent_uniqueAligned	0.87803	0.87527
correlation_replicates	0.999167	0.999167
spikein_reads	92,104	89,326
percent_spikeins	0.00075	0.00083
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	101	102

Data Submission Information

	BGKcLV15-41	BGKcLV15-41	BGKcLV15-41	BGKcLV15-41	BGKcLV15-41	BGKcLV15-41	BGKcLV15-42	BGKcLV15-42	BGKcLV15-42	BGKcLV15-42
ENCODE_alias	brenton-graveley:NPM1-BGKcLV15	brenton-graveley:NPM1-BGKcLV15-41	brenton-graveley:L-NPM1-BGKcLV15-41	brenton-graveley:NPM1-BGKcLV15-41_S19_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NPM1-BGKcLV15-41_S19_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NPM1-BGKcLV15-K562	brenton-graveley:NPM1-BGKcLV15-42	brenton-graveley:L-NPM1-BGKcLV15-42	brenton-graveley:NPM1-BGKcLV15-42_S20_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NPM1-BGKcLV15-42_S20_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR034NAT	ENCBS665YAY	ENCLB322SVK	ENCFF794WJO	ENCFF521CAR	ENCSR463EFP	ENCBS868KHZ	ENCLB655CII	ENCFF371ANT	ENCFF637YYZ
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	BGKcLV15-41	BGKcLV15-41	BGKcLV15-41	BGKcLV15-41	BGKcLV15-41	BGKcLV15-41	BGKcLV15-42	BGKcLV15-42	BGKcLV15-42	BGKcLV15-42
Sample Name	NPM1-BGKcLV15-41	NPM1-BGKcLV15-41	NPM1-BGKcLV15-41	NPM1-BGKcLV15-41	NPM1-BGKcLV15-41	NPM1-BGKcLV15-41	NPM1-BGKcLV15-42	NPM1-BGKcLV15-42	NPM1-BGKcLV15-42	NPM1-BGKcLV15-42
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
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		NPM1-BGKcLV15-41.pdf	L-MECP2-BGKcLV15-39.pdf				NPM1-BGKcLV15-42.pdf	L-MECP2-BGKcLV15-40.pdf
ID	26	134	298	496	548	7271	135	299	497	549

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
NPM1-BGKcLV15-41_S19_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	101	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	95
NPM1-BGKcLV15-41_S19_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	101	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	147
NPM1-BGKcLV15-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	101					GRCh38	V40	NPM1-BGKcLV15-41_S19_R1_001.filtered.trimmed.paired.fastq.gz,NPM1-BGKcLV15-41_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24386
NPM1-BGKcLV15-41_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	101					GRCh38	V40	NPM1-BGKcLV15-41/Aligned.sortedByCoord.out.bam		ENCORE2	24438
NPM1-BGKcLV15-41_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	101					GRCh38	V40	NPM1-BGKcLV15-41/Aligned.sortedByCoord.out.bam		ENCORE2	24490
NPM1-BGKcLV15-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	101					GRCh38	V40	NPM1-BGKcLV15-41/Aligned.sortedByCoord.out.bam		ENCORE2	24542
NPM1-BGKcLV15-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	101					GRCh38	V40	NPM1-BGKcLV15-41/Aligned.sortedByCoord.out.bam		ENCORE2	24594
NPM1-BGKcLV15-41_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	101					GRCh38	V40	NPM1-BGKcLV15-41_S19_R1_001.filtered.trimmed.paired.fastq.gz,NPM1-BGKcLV15-41_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24646
NPM1-BGKcLV15-42_S20_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	102	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	96
NPM1-BGKcLV15-42_S20_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	102	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	148
NPM1-BGKcLV15-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	102					GRCh38	V40	NPM1-BGKcLV15-42_S20_R1_001.filtered.trimmed.paired.fastq.gz,NPM1-BGKcLV15-42_S20_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24387
NPM1-BGKcLV15-42_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	102					GRCh38	V40	NPM1-BGKcLV15-42/Aligned.sortedByCoord.out.bam		ENCORE2	24439
NPM1-BGKcLV15-42_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	102					GRCh38	V40	NPM1-BGKcLV15-42/Aligned.sortedByCoord.out.bam		ENCORE2	24491
NPM1-BGKcLV15-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	102					GRCh38	V40	NPM1-BGKcLV15-42/Aligned.sortedByCoord.out.bam		ENCORE2	24543
NPM1-BGKcLV15-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	102					GRCh38	V40	NPM1-BGKcLV15-42/Aligned.sortedByCoord.out.bam		ENCORE2	24595
NPM1-BGKcLV15-42_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	102					GRCh38	V40	NPM1-BGKcLV15-42_S20_R1_001.filtered.trimmed.paired.fastq.gz,NPM1-BGKcLV15-42_S20_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24647