NOLC1 RNA-Seq in HepG2

General Information


RBP	NOLC1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	NOLC1-BGHcLV07-HepG2
ENCODE_series_ID	ENCSR115EVX
Batch_ID	BGHcLV07
Pool ID	Pool-170911
Local_Set_Name	set39_H
ENCODE_KD_Exp_ID	ENCSR959HPB
ENCODE_CN_Exp_ID	ENCSR521WAI
Rep1	NOLC1-BGHcLV07-19
Rep2	NOLC1-BGHcLV07-20
CN1	NT-BGHcLV07-1
CN2	NT-BGHcLV07-2
Rep1_qPCR	64.0
Rep2_qPCR	63.5
Rep1_WB	60.8
Rep2_WB	67.7
Antibody Cat#	A302-184A
Antibody Lot#
Antibody DCC ID	ENCAB287BXF
Status	Released
Project	ENCODE3
ID	765

Experiment Information (Status: Released)

	BGHcLV07-19	BGHcLV07-20
idx	131	132
TRCN#_or_BGC#	BGC#0000092	BGC#0000092
shRNA_or_gRNA_sequence	GGACGCCGGCATTCGCCGCG	GGACGCCGGCATTCGCCGCG
PAM
Name	NOLC1_92-1	NOLC1_92-1
Sample_ID	BGHcLV07-19	BGHcLV07-20
transduction_Date	6/13/17	6/13/17
days	D6	D6
RBP_name	NOLC1	NOLC1
qPCR_result	64.0	63.5
Ave_qPCR	63.8
RT-qPCR_primer-F	agcttctggctcaagtctgc
RT-qPCR_primer-R	gctgctgtcctcactgtcac
protein_conc	3573	4369
WB_result	60.8	67.7
Ave_WB	64.3
WB_DONE_date	7/25/17
MW	74kD
IP
antibody_Cat#	A302-184A
Antibody DCC ID	ENCAB287BXF	ENCAB287BXF
submitted_to_DCC_date	9/27/17
Rep1_TPM	98	0
Rep2_TPM	127	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	6274	6275

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NOLC1	Product_ID: A302-184A Lot_ID: 1 Source: Bethyl Labs Target Name: NOLC1-human

Experiment Status

	BGHcLV07-19	BGHcLV07-20
Sample_ID	BGHcLV07-19	BGHcLV07-20
Sample Name	NOLC1-BGHcLV07-19	NOLC1-BGHcLV07-20
Sample Name	NOLC1-BGHcLV07-19	NOLC1-BGHcLV07-20
RBP	NOLC1	NOLC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1383	1384

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV07-19	BGHcLV07-20
Sample #
Sample Name	NOLC1-BGHcLV07-19	NOLC1-BGHcLV07-20
Sample_Name_Alias	NOLC1-BGHcLV07-19	NOLC1-BGHcLV07-20
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/C4.png	DNA_Library_set39/set2/D4.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set39/set2/E1.png	RNA_Library_set39/set2/F1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV07-19	BGHcLV07-20
RBP	NOLC1	NOLC1
Batch_ID	BGHcLV07	BGHcLV07
WB_result	60.800	67.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3078	3079

Sequencing Information

	BGHcLV07-19	BGHcLV07-20
Sample_ID	BGHcLV07-19	BGHcLV07-20
Sample Name	NOLC1-BGHcLV07-19	NOLC1-BGHcLV07-20
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_H	set39_H
total_reads	45,686,188	85,595,518
total_aligned_reads	37,082,738	73,961,780
unique_aligned_reads	35,168,424	69,978,640
percent_uniqueAligned	0.76978	0.81755
correlation_replicates	0.957415	0.957415
spikein_reads	12,724	16,034
percent_spikeins	0.00028	0.00019
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1729	1730

Data Submission Information

	BGHcLV07-19	BGHcLV07-19
ENCODE_alias	brenton-graveley:NOLC1-BGHcLV07	brenton-graveley:NOLC1-BGHcLV07-HepG2
ENCODE_accession	ENCSR959HPB	ENCSR115EVX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV07-19	BGHcLV07-19
Sample Name	NOLC1-BGHcLV07-19	NOLC1-BGHcLV07-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3231	6827

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
NOLC1-BGHcLV07-19_GGCTAC_ACBE67ANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1729	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE3	22276
NOLC1-BGHcLV07-19_GGCTAC_ACBE67ANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1729	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE3	22300
NOLC1-BGHcLV07-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1729					GRCh38	V40	NOLC1-BGHcLV07-19_GGCTAC_ACBE67ANXX_L008_001.R1.fastq.gz,NOLC1-BGHcLV07-19_GGCTAC_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22324
NOLC1-BGHcLV07-19_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1729					GRCh38	V40	NOLC1-BGHcLV07-19/Aligned.sortedByCoord.out.bam		ENCORE2	22348
NOLC1-BGHcLV07-19_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1729					GRCh38	V40	NOLC1-BGHcLV07-19/Aligned.sortedByCoord.out.bam		ENCORE2	22372
NOLC1-BGHcLV07-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1729					GRCh38	V40	NOLC1-BGHcLV07-19/Aligned.sortedByCoord.out.bam		ENCORE2	22396
NOLC1-BGHcLV07-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1729					GRCh38	V40	NOLC1-BGHcLV07-19/Aligned.sortedByCoord.out.bam		ENCORE2	22420
NOLC1-BGHcLV07-19_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1729					GRCh38	V40	NOLC1-BGHcLV07-19_GGCTAC_ACBE67ANXX_L008_001.R1.fastq.gz,NOLC1-BGHcLV07-19_GGCTAC_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22444
NOLC1-BGHcLV07-20_CTTGTA_ACBE67ANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1730	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE3	22277
NOLC1-BGHcLV07-20_CTTGTA_ACBE67ANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1730	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE3	22301
NOLC1-BGHcLV07-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1730					GRCh38	V40	NOLC1-BGHcLV07-20_CTTGTA_ACBE67ANXX_L008_001.R1.fastq.gz,NOLC1-BGHcLV07-20_CTTGTA_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22325
NOLC1-BGHcLV07-20_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1730					GRCh38	V40	NOLC1-BGHcLV07-20/Aligned.sortedByCoord.out.bam		ENCORE2	22349
NOLC1-BGHcLV07-20_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1730					GRCh38	V40	NOLC1-BGHcLV07-20/Aligned.sortedByCoord.out.bam		ENCORE2	22373
NOLC1-BGHcLV07-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1730					GRCh38	V40	NOLC1-BGHcLV07-20/Aligned.sortedByCoord.out.bam		ENCORE2	22397
NOLC1-BGHcLV07-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1730					GRCh38	V40	NOLC1-BGHcLV07-20/Aligned.sortedByCoord.out.bam		ENCORE2	22421
NOLC1-BGHcLV07-20_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1730					GRCh38	V40	NOLC1-BGHcLV07-20_CTTGTA_ACBE67ANXX_L008_001.R1.fastq.gz,NOLC1-BGHcLV07-20_CTTGTA_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22445