NPM1 RNA-Seq in K562

General Information


RBP	NPM1
Cell_Line	K562
Method	shRNA
Exp_Name	NPM1-BGKLV28-K562
ENCODE_series_ID	ENCSR643PZS
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR346DZQ
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	NPM1_BGKLV28-31
Rep2	NPM1_BGKLV28-32
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	91.2
Rep2_qPCR	89.5
Rep1_WB	55.6
Rep2_WB	59.4
Antibody Cat#	A302-402A
Antibody Lot#	A302-402A
Antibody DCC ID	ENCAB881HTO
Status	Archived
Project	ENCODE3
ID	651

Experiment Information (Status: Released)

	BGKLV28-31	BGKLV28-32
idx	500	501
TRCN#_or_BGC#	TRCN0000062271	TRCN0000062271
shRNA_or_gRNA_sequence	GCAAAGGATGAGTTGCACATT	GCAAAGGATGAGTTGCACATT
PAM
Name	NPM1	NPM1
Sample_ID	BGKLV28-31	BGKLV28-32
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	NPM1	NPM1
qPCR_result	91.2	89.5
Ave_qPCR	90.4
RT-qPCR_primer-F	tggaggaagatgcagagtca
RT-qPCR_primer-R	tggaaccttgctaccacctc
protein_conc	2232	2515
WB_result	55.6	59.4
Ave_WB	57.5
WB_DONE_date	6/26/2015
MW	33kd
IP	1MB	1MB
antibody_Cat#	A302-402A	A302-402A
Antibody DCC ID	ENCAB881HTO	ENCAB881HTO
submitted_to_DCC_date	8/6/2015
Rep1_TPM	666.753217	0
Rep2_TPM	539.908879	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	575	576

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NPM1	Product_ID: A302-402A Lot_ID: 1 Source: Bethyl Labs Target Name: NPM1-human

Experiment Status

	BGKLV28-31	BGKLV28-32
Sample_ID	BGKLV28-31	BGKLV28-32
Sample Name	NPM1_BGKLV28-31	NPM1_BGKLV28-32
Sample Name	NPM1_BGKLV28-31	NPM1_BGKLV28-32
RBP	NPM1	NPM1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	988	989

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-31	BGKLV28-32
Sample #
Sample Name	NPM1-BGKLV28-31	NPM1-BGKLV28-32
Sample_Name_Alias	NPM1_BGKLV28-31	NPM1_BGKLV28-32
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A2.png	DNA_Library_LV28-29-30/set1/B2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/E7.png	RNA_Library_LV26-27-28-29/set1/F7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-31	BGKLV28-32
RBP	NPM1	NPM1
Batch_ID	BGKLV28	BGKLV28
WB_result	55.600	59.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2680	2681

Sequencing Information

	BGKLV28-31	BGKLV28-32
Sample_ID	BGKLV28-31	BGKLV28-32
Sample Name	NPM1_BGKLV28-31	NPM1_BGKLV28-32
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	86,231,004	80,544,910
total_aligned_reads	68,406,492	70,408,562
unique_aligned_reads	62,122,070	64,242,692
percent_uniqueAligned	0.72041	0.79760
correlation_replicates	0.972035	0.972035
spikein_reads	242,866	245,982
percent_spikeins	0.00282	0.00305
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1322	1323

Data Submission Information

	BGKLV28-31	BGKLV28-31
ENCODE_alias	brenton-graveley:NPM1_BGKLV28	brenton-graveley:NPM1-BGKLV28-K562
ENCODE_accession	ENCSR346DZQ	ENCSR643PZS
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-31	BGKLV28-31
Sample Name	NPM1_BGKLV28-31	NPM1_BGKLV28-31
Selected	Yes	No
Status	Released	Archived
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3043	6831

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_BGKLV28-31_GATCAG_L002_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1322	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20166
NPM1_BGKLV28-31_GATCAG_L002_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1322	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20198
NPM1_BGKLV28-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1322					GRCh38	V40	NPM1_BGKLV28-31_GATCAG_L002_001.R1.fastq.gz,NPM1_BGKLV28-31_GATCAG_L002_001.R2.fastq.gz		ENCORE2	20230
NPM1_BGKLV28-31_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1322					GRCh38	V40	NPM1_BGKLV28-31/Aligned.sortedByCoord.out.bam		ENCORE2	20262
NPM1_BGKLV28-31_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1322					GRCh38	V40	NPM1_BGKLV28-31/Aligned.sortedByCoord.out.bam		ENCORE2	20294
NPM1_BGKLV28-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1322					GRCh38	V40	NPM1_BGKLV28-31/Aligned.sortedByCoord.out.bam		ENCORE2	20326
NPM1_BGKLV28-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1322					GRCh38	V40	NPM1_BGKLV28-31/Aligned.sortedByCoord.out.bam		ENCORE2	20358
NPM1_BGKLV28-31_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1322					GRCh38	V40	NPM1_BGKLV28-31_GATCAG_L002_001.R1.fastq.gz,NPM1_BGKLV28-31_GATCAG_L002_001.R2.fastq.gz		ENCORE2	20390
NPM1_BGKLV28-32_TAGCTT_L002_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1323	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20167
NPM1_BGKLV28-32_TAGCTT_L002_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1323	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20199
NPM1_BGKLV28-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1323					GRCh38	V40	NPM1_BGKLV28-32_TAGCTT_L002_001.R1.fastq.gz,NPM1_BGKLV28-32_TAGCTT_L002_001.R2.fastq.gz		ENCORE2	20231
NPM1_BGKLV28-32_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1323					GRCh38	V40	NPM1_BGKLV28-32/Aligned.sortedByCoord.out.bam		ENCORE2	20263
NPM1_BGKLV28-32_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1323					GRCh38	V40	NPM1_BGKLV28-32/Aligned.sortedByCoord.out.bam		ENCORE2	20295
NPM1_BGKLV28-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1323					GRCh38	V40	NPM1_BGKLV28-32/Aligned.sortedByCoord.out.bam		ENCORE2	20327
NPM1_BGKLV28-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1323					GRCh38	V40	NPM1_BGKLV28-32/Aligned.sortedByCoord.out.bam		ENCORE2	20359
NPM1_BGKLV28-32_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1323					GRCh38	V40	NPM1_BGKLV28-32_TAGCTT_L002_001.R1.fastq.gz,NPM1_BGKLV28-32_TAGCTT_L002_001.R2.fastq.gz		ENCORE2	20391