NOL12 RNA-Seq in K562

General Information


RBP	NOL12
Cell_Line	K562
Method	shRNA
Exp_Name	NOL12-BGKLV25-K562
ENCODE_series_ID	ENCSR485ZZS
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR227AVS
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	NOL12-BGKLV25-35
Rep2	NOL12-BGKLV25-36
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	58.0
Rep2_qPCR	47.1
Rep1_WB	64.0
Rep2_WB	66.8
Antibody Cat#	A302-733A
Antibody Lot#	A302-733A
Antibody DCC ID	ENCAB727RRN
Status	Released
Project	ENCODE3
ID	620

Experiment Information (Status: Released)

	BGKLV25-35	BGKLV25-36
idx	438	439
TRCN#_or_BGC#	TRCN0000181091	TRCN0000181091
shRNA_or_gRNA_sequence	CACAGCATCACTACATGCACA	CACAGCATCACTACATGCACA
PAM
Name	NOL12	NOL12
Sample_ID	BGKLV25-35	BGKLV25-36
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	NOL12	NOL12
qPCR_result	58.0	47.1
Ave_qPCR	52.6
RT-qPCR_primer-F	tgaccaccatcagtgacctg
RT-qPCR_primer-R	cctcctcagacctgtctcca
protein_conc	3969	3943
WB_result	64.0	66.8
Ave_WB	65.4
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	1.83776162	0
Rep2_TPM	2.00211497	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	509	510

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

	BGKLV25-35	BGKLV25-36
Sample_ID	BGKLV25-35	BGKLV25-36
Sample Name	NOL12-BGKLV25-35	NOL12-BGKLV25-36
Sample Name	NOL12-BGKLV25-35	NOL12-BGKLV25-36
RBP	NOL12	NOL12
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	918	919

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-35	BGKLV25-36
Sample #
Sample Name	NOL12-BGKLV25-35	NOL12-BGKLV25-36
Sample_Name_Alias	NOL12-BGKLV25-35	NOL12-BGKLV25-36
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/A3.png	DNA_Library_LV24-25-26/set1/B3.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C11.png	RNA_Library_LV22-23-25/set1/D11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-35	BGKLV25-36
RBP	NOL12	NOL12
Batch_ID	BGKLV25	BGKLV25
WB_result	64.000	66.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2610	2611

Sequencing Information

	BGKLV25-35	BGKLV25-36
Sample_ID	BGKLV25-35	BGKLV25-36
Sample Name	NOL12-BGKLV25-35	NOL12-BGKLV25-36
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	89,485,556	113,075,578
total_aligned_reads	90,941,608	115,183,908
unique_aligned_reads	83,133,100	105,058,298
percent_uniqueAligned	0.92901	0.92910
correlation_replicates	0.998612	0.998612
spikein_reads	527,300	629,504
percent_spikeins	0.00589	0.00557
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1252	1253

Data Submission Information

	BGKLV25-35	BGKLV25-35
ENCODE_alias	brenton-graveley:NOL12-BGKLV25	brenton-graveley:NOL12-BGKLV25-K562
ENCODE_accession	ENCSR227AVS	ENCSR485ZZS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-35	BGKLV25-35
Sample Name	NOL12-BGKLV25-35	NOL12-BGKLV25-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3008	6826

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-BGKLV25-35_ATCACG_L007_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1252	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19578
NOL12-BGKLV25-35_ATCACG_L007_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1252	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19614
NOL12-BGKLV25-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1252					GRCh38	V40	NOL12-BGKLV25-35_ATCACG_L007_001.R1.fastq.gz,NOL12-BGKLV25-35_ATCACG_L007_001.R2.fastq.gz		ENCORE2	19650
NOL12-BGKLV25-35_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1252					GRCh38	V40	NOL12-BGKLV25-35/Aligned.sortedByCoord.out.bam		ENCORE2	19686
NOL12-BGKLV25-35_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1252					GRCh38	V40	NOL12-BGKLV25-35/Aligned.sortedByCoord.out.bam		ENCORE2	19722
NOL12-BGKLV25-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1252					GRCh38	V40	NOL12-BGKLV25-35/Aligned.sortedByCoord.out.bam		ENCORE2	19758
NOL12-BGKLV25-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1252					GRCh38	V40	NOL12-BGKLV25-35/Aligned.sortedByCoord.out.bam		ENCORE2	19794
NOL12-BGKLV25-35_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1252					GRCh38	V40	NOL12-BGKLV25-35_ATCACG_L007_001.R1.fastq.gz,NOL12-BGKLV25-35_ATCACG_L007_001.R2.fastq.gz		ENCORE2	19984
NOL12-BGKLV25-36_CGATGT_L007_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1253	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19579
NOL12-BGKLV25-36_CGATGT_L007_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1253	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19615
NOL12-BGKLV25-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1253					GRCh38	V40	NOL12-BGKLV25-36_CGATGT_L007_001.R1.fastq.gz,NOL12-BGKLV25-36_CGATGT_L007_001.R2.fastq.gz		ENCORE2	19651
NOL12-BGKLV25-36_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1253					GRCh38	V40	NOL12-BGKLV25-36/Aligned.sortedByCoord.out.bam		ENCORE2	19687
NOL12-BGKLV25-36_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1253					GRCh38	V40	NOL12-BGKLV25-36/Aligned.sortedByCoord.out.bam		ENCORE2	19723
NOL12-BGKLV25-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1253					GRCh38	V40	NOL12-BGKLV25-36/Aligned.sortedByCoord.out.bam		ENCORE2	19759
NOL12-BGKLV25-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1253					GRCh38	V40	NOL12-BGKLV25-36/Aligned.sortedByCoord.out.bam		ENCORE2	19795
NOL12-BGKLV25-36_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1253					GRCh38	V40	NOL12-BGKLV25-36_CGATGT_L007_001.R1.fastq.gz,NOL12-BGKLV25-36_CGATGT_L007_001.R2.fastq.gz		ENCORE2	19985