NPM1 RNA-Seq in HepG2

General Information


RBP	NPM1
Cell_Line	HepG2
Method	shRNA
Exp_Name	NPM1-BGHLV26-HepG2
ENCODE_series_ID	ENCSR066EXQ
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR016XPB
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	NPM1_BGHLV26_27
Rep2	NPM1_BGHLV26_28
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	62.4
Rep2_qPCR	72.1
Rep1_WB	66.4
Rep2_WB	61.2
Antibody Cat#	A302-402A
Antibody Lot#	A302-402A
Antibody DCC ID	ENCAB881HTO
Status	Released
Project	ENCODE3
ID	630

Experiment Information (Status: Released)

	BGHLV26-27	BGHLV26-27	BGHLV26-28	BGHLV26-28
idx	583	0	584	0
TRCN#_or_BGC#	TRCN0000062271	TRCN0000062271	TRCN0000062271	TRCN0000062271
shRNA_or_gRNA_sequence	GCAAAGGATGAGTTGCACATT	GCAAAGGATGAGTTGCACATT	GCAAAGGATGAGTTGCACATT	GCAAAGGATGAGTTGCACATT
PAM
Name	NPM1	NPM1	NPM1	NPM1
Sample_ID	BGHLV26-27	BGHLV26-27	BGHLV26-28	BGHLV26-28
transduction_Date	5/25/2015	5/25/2015	5/25/2015	5/25/2015
days
RBP_name	NPM1	NPM1	NPM1	NPM1
qPCR_result	62.4	62.4	72.1	72.1
Ave_qPCR	67.3	67.3
RT-qPCR_primer-F	ttgctgctgatgaagatgatg	ttgctgctgatgaagatgatg
RT-qPCR_primer-R	tttcttcactggcgcttttt	tttcttcactggcgcttttt
protein_conc	4293	4293	4944	4944
WB_result	66.4	52.2	61.2	60.6
Ave_WB	63.8	56.4
WB_DONE_date	6/26/2015	5/8/2019
MW	33kDa	33kDa
IP	1MB		1MB
antibody_Cat#	A302-402A	325200	A302-402A	LOT# TD268297
Antibody DCC ID	ENCAB881HTO	ENCAB147WFE	ENCAB881HTO
submitted_to_DCC_date	8/6/2015	4/17/2019
Rep1_TPM	419.7	0	0	0
Rep2_TPM	394.1	0	0	0
Action
Library_start_date	9/8/2015		9/8/2015
repeat_library
Note	x		x
ID	2664	2666	2665	2667

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
NPM1	Product_ID: 325200 Lot_ID: TD268297 Source: Thermo Fisher Target Name: NPM1-human

Experiment Status

	BGHLV26-27	BGHLV26-28
Sample_ID	BGHLV26-27	BGHLV26-28
Sample Name	NPM1_BGHLV26_27	NPM1_BGHLV26_28
Sample Name	NPM1_BGHLV26_27	NPM1_BGHLV26_28
RBP	NPM1	NPM1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	944	945

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-27	BGHLV26-28
Sample #
Sample Name	NPM1-BGHLV26-27	NPM1-BGHLV26-28
Sample_Name_Alias	NPM1_BGHLV26_27	NPM1_BGHLV26_28
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-08	2015-09-08
Lib_ID	Lib-150908	Lib-150908
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/E8.png	DNA_Library_LV24-25-26/set1/F8.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_LV25-26/set1/G1.png	RNA_Library_LV25-26/set1/H1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-27	BGHLV26-28
RBP	NPM1	NPM1
Batch_ID	BGHLV26	BGHLV26
WB_result	66.400	61.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2632	2633

Sequencing Information

	BGHLV26-27	BGHLV26-28
Sample_ID	BGHLV26-27	BGHLV26-28
Sample Name	NPM1_BGHLV26_27	NPM1_BGHLV26_28
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	117,037,156	85,255,204
total_aligned_reads	97,190,204	70,663,886
unique_aligned_reads	90,584,680	66,041,434
percent_uniqueAligned	0.77398	0.77463
correlation_replicates	0.997836	0.997836
spikein_reads	257,830	205,490
percent_spikeins	0.00220	0.00241
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1274	1275

Data Submission Information

	BGHLV26-27	BGHLV26-27
ENCODE_alias	brenton-graveley:NPM1_BGHLV26	brenton-graveley:NPM1-BGHLV26-HepG2
ENCODE_accession	ENCSR016XPB	ENCSR066EXQ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-27	BGHLV26-27
Sample Name	NPM1_BGHLV26_27	NPM1_BGHLV26_27
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3019	6830

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_BGHLV26_27_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1274	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19818
NPM1_BGHLV26_27_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1274	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19840
NPM1_BGHLV26_27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1274					GRCh38	V40	NPM1_BGHLV26_27_1.fastq.gz,NPM1_BGHLV26_27_2.fastq.gz		ENCORE2	19862
NPM1_BGHLV26_27_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1274					GRCh38	V40	NPM1_BGHLV26_27/Aligned.sortedByCoord.out.bam		ENCORE2	19884
NPM1_BGHLV26_27_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1274					GRCh38	V40	NPM1_BGHLV26_27/Aligned.sortedByCoord.out.bam		ENCORE2	19906
NPM1_BGHLV26_27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1274					GRCh38	V40	NPM1_BGHLV26_27/Aligned.sortedByCoord.out.bam		ENCORE2	19928
NPM1_BGHLV26_27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1274					GRCh38	V40	NPM1_BGHLV26_27/Aligned.sortedByCoord.out.bam		ENCORE2	19950
NPM1_BGHLV26_27_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1274					GRCh38	V40	NPM1_BGHLV26_27_1.fastq.gz,NPM1_BGHLV26_27_2.fastq.gz		ENCORE2	20658
NPM1_BGHLV26_28_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1275	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19819
NPM1_BGHLV26_28_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1275	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19841
NPM1_BGHLV26_28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1275					GRCh38	V40	NPM1_BGHLV26_28_1.fastq.gz,NPM1_BGHLV26_28_2.fastq.gz		ENCORE2	19863
NPM1_BGHLV26_28_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1275					GRCh38	V40	NPM1_BGHLV26_28/Aligned.sortedByCoord.out.bam		ENCORE2	19885
NPM1_BGHLV26_28_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1275					GRCh38	V40	NPM1_BGHLV26_28/Aligned.sortedByCoord.out.bam		ENCORE2	19907
NPM1_BGHLV26_28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1275					GRCh38	V40	NPM1_BGHLV26_28/Aligned.sortedByCoord.out.bam		ENCORE2	19929
NPM1_BGHLV26_28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1275					GRCh38	V40	NPM1_BGHLV26_28/Aligned.sortedByCoord.out.bam		ENCORE2	19951
NPM1_BGHLV26_28_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1275					GRCh38	V40	NPM1_BGHLV26_28_1.fastq.gz,NPM1_BGHLV26_28_2.fastq.gz		ENCORE2	20659