NOL12 RNA-Seq in HepG2

General Information


RBP	NOL12
Cell_Line	HepG2
Method	shRNA
Exp_Name	NOL12-BGHLV23-HepG2
ENCODE_series_ID	ENCSR994ZMV
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR643UFV
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	NOL12-BGHLV23-25
Rep2	NOL12-BGHLV23-26
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	62.3
Rep2_qPCR	59.8
Rep1_WB	75.5
Rep2_WB	76.9
Antibody Cat#	A302-733A
Antibody Lot#	A302-733A
Antibody DCC ID	ENCAB727RRN
Status	Released
Project	ENCODE3
ID	546

Experiment Information (Status: Released)

	BGHLV23-25	BGHLV23-26
idx	517	518
TRCN#_or_BGC#	TRCN0000181091	TRCN0000181091
shRNA_or_gRNA_sequence	CACAGCATCACTACATGCACA	CACAGCATCACTACATGCACA
PAM
Name	NOL12	NOL12
Sample_ID	BGHLV23-25	BGHLV23-26
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	NOL12	NOL12
qPCR_result	62.3	59.8
Ave_qPCR	61.1
RT-qPCR_primer-F	tgaccaccatcagtgacctg
RT-qPCR_primer-R	cctcctcagacctgtctcca
protein_conc	5713	5412
WB_result	75.5	76.9
Ave_WB	76.2
WB_DONE_date	5/14/2015
MW	30kDa
IP	1	1
antibody_Cat#	A302-733A	A302-733A
Antibody DCC ID	ENCAB727RRN	ENCAB727RRN
submitted_to_DCC_date	8/6/2015
Rep1_TPM	0.6	0
Rep2_TPM	1.2	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2598	2599

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NOL12	Product_ID: A302-733A Lot_ID: 1 Source: Bethyl Labs Target Name: NOL12-human

Experiment Status

	BGHLV23-25	BGHLV23-26
Sample_ID	BGHLV23-25	BGHLV23-26
Sample Name	NOL12-BGHLV23-25	NOL12-BGHLV23-26
Sample Name	NOL12-BGHLV23-25	NOL12-BGHLV23-26
RBP	NOL12	NOL12
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	828	829

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-25	BGHLV23-26
Sample #
Sample Name	NOL12-BGHLV23-25	NOL12-BGHLV23-26
Sample_Name_Alias	NOL12-BGHLV23-25	NOL12-BGHLV23-26
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set4/C1.png	DNA_Library_LV20-22-23/set4/D1.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/E6.png	RNA_Library_LV19-21-24/set2/F6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-25	BGHLV23-26
RBP	NOL12	NOL12
Batch_ID	BGHLV23	BGHLV23
WB_result	75.500	76.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2516	2517

Sequencing Information

	BGHLV23-25	BGHLV23-26
Sample_ID	BGHLV23-25	BGHLV23-26
Sample Name	NOL12-BGHLV23-25	NOL12-BGHLV23-26
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	59,220,000	58,240,000
total_aligned_reads	51,333,536	50,514,404
unique_aligned_reads	48,282,008	47,412,634
percent_uniqueAligned	0.81530	0.81409
correlation_replicates	0.997145	0.997145
spikein_reads	349,694	332,512
percent_spikeins	0.00590	0.00571
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1138	1139

Data Submission Information

	BGHLV23-25	BGHLV23-25
ENCODE_alias	brenton-graveley:NOL12-BGHLV23	brenton-graveley:NOL12-BGHLV23-HepG2
ENCODE_accession	ENCSR643UFV	ENCSR994ZMV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-25	BGHLV23-25
Sample Name	NOL12-BGHLV23-25	NOL12-BGHLV23-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2946	6825

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
NOL12-BGHLV23-25_GGCTAC_L006_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1138	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16666
NOL12-BGHLV23-25_GGCTAC_L006_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1138	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16704
NOL12-BGHLV23-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1138					GRCh38	V40	NOL12-BGHLV23-25_GGCTAC_L006_R1_001.fastq.gz,NOL12-BGHLV23-25_GGCTAC_L006_R2_001.fastq.gz		ENCORE2	16742
NOL12-BGHLV23-25_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1138					GRCh38	V40	NOL12-BGHLV23-25/Aligned.sortedByCoord.out.bam		ENCORE2	16780
NOL12-BGHLV23-25_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1138					GRCh38	V40	NOL12-BGHLV23-25/Aligned.sortedByCoord.out.bam		ENCORE2	16818
NOL12-BGHLV23-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1138					GRCh38	V40	NOL12-BGHLV23-25/Aligned.sortedByCoord.out.bam		ENCORE2	16856
NOL12-BGHLV23-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1138					GRCh38	V40	NOL12-BGHLV23-25/Aligned.sortedByCoord.out.bam		ENCORE2	16894
NOL12-BGHLV23-25_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1138					GRCh38	V40	NOL12-BGHLV23-25_GGCTAC_L006_R1_001.fastq.gz,NOL12-BGHLV23-25_GGCTAC_L006_R2_001.fastq.gz		ENCORE2	16932
NOL12-BGHLV23-26_CTTGTA_L006_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1139	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16667
NOL12-BGHLV23-26_CTTGTA_L006_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1139	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16705
NOL12-BGHLV23-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1139					GRCh38	V40	NOL12-BGHLV23-26_CTTGTA_L006_R1_001.fastq.gz,NOL12-BGHLV23-26_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	16743
NOL12-BGHLV23-26_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1139					GRCh38	V40	NOL12-BGHLV23-26/Aligned.sortedByCoord.out.bam		ENCORE2	16781
NOL12-BGHLV23-26_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1139					GRCh38	V40	NOL12-BGHLV23-26/Aligned.sortedByCoord.out.bam		ENCORE2	16819
NOL12-BGHLV23-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1139					GRCh38	V40	NOL12-BGHLV23-26/Aligned.sortedByCoord.out.bam		ENCORE2	16857
NOL12-BGHLV23-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1139					GRCh38	V40	NOL12-BGHLV23-26/Aligned.sortedByCoord.out.bam		ENCORE2	16895
NOL12-BGHLV23-26_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1139					GRCh38	V40	NOL12-BGHLV23-26_CTTGTA_L006_R1_001.fastq.gz,NOL12-BGHLV23-26_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	16933