non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHLV27-1 and BGHLV27-2

NT-BGHLV27-1,NT-BGHLV27-2 (alias:non-target_BGHLV27-1,non-target_BGHLV27-2):

AKAP8-BGHLV27-HepG2

NT-BGHLV27-1B,NT-BGHLV27-2B (alias:NT_BGHLV27-1B,NT_BGHLV27-2B):

NUP35-BGHLV27-HepG2

Experiment Information (Status: Released)

	BGHLV27-1	BGHLV27-2
idx	621	622
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non target	non target
Sample_ID	BGHLV27-1	BGHLV27-2
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	5075
WB_result	4819.5
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	9/28/2015	9/28/2015
repeat_library
Note
ID	2708	2709

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV27-1	BGHLV27-1	BGHLV27-2	BGHLV27-2
Sample_ID	BGHLV27-1	BGHLV27-1	BGHLV27-2	BGHLV27-2
Sample Name	non-target_BGHLV27-1	NT_BGHLV27-1B	non-target_BGHLV27-2	NT_BGHLV27-2B
Sample Name	non-target_BGHLV27-1	NT_BGHLV27-1B	non-target_BGHLV27-2	NT_BGHLV27-2B
RBP	non-target	non-target	non-target	non-target
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Released	Released	Released	Released
Status_date	2016-01-16	2016-09-24	2016-01-16	2016-09-24
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note
ID	970	1191	971	1192

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-1	BGHLV27-1	BGHLV27-2	BGHLV27-2
Sample #
Sample Name	NT-BGHLV27-1	NT-BGHLV27-1B	NT-BGHLV27-2	NT-BGHLV27-2B
Sample_Name_Alias	non-target_BGHLV27-1	NT_BGHLV27-1B	non-target_BGHLV27-2	NT_BGHLV27-2B
Index Well Position	S01	S11	S02	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-28	2016-03-10	2015-09-28	2016-03-10
Lib_ID	Lib-150928	Lib-160310	Lib-150928	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV27/set1/A1.png	DNA_Library_LV33-34-25B-32/set1/E11.png	DNA_Library_LV27/set1/B1.png	DNA_Library_LV33-34-25B-32/set2/G2.png
RIN	9.8	9.8	9.8	9.8
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/A4.png	RNA_Library_LV26-27-28-29/set1/A4.png	RNA_Library_LV26-27-28-29/set1/B4.png	RNA_Library_LV26-27-28-29/set1/B4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-1	BGHLV27-1	BGHLV27-2	BGHLV27-2
RBP	NT	NT	NT	NT
Batch_ID	BGHLV27	BGHLV27	BGHLV27	BGHLV27
WB_result	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2662	2876	2663	2877

Sequencing Information

	BGHLV27-1	BGHLV27-1	BGHLV27-2	BGHLV27-2
Sample_ID	BGHLV27-1	BGHLV27-1	BGHLV27-2	BGHLV27-2
Sample Name	non-target_BGHLV27-1	NT_BGHLV27-1B	non-target_BGHLV27-2	NT_BGHLV27-2B
Pool ID	Pool-151201	Pool-160425	Pool-151201	Pool-160425
LocalServer_folder	set27	set27	set27	set27
total_reads	64,161,508	79,063,292	73,231,180	78,572,634
total_aligned_reads	56,677,506	51,305,932	63,576,426	53,153,640
unique_aligned_reads	53,439,534	48,224,190	59,722,386	49,944,640
percent_uniqueAligned	0.83289	0.60994	0.81553	0.63565
correlation_replicates	0.994332	0.999772	0.994332	0.999772
spikein_reads	233,148	116,862	247,504	119,352
percent_spikeins	0.00363	0.00148	0.00338	0.00152
original_ReadLength	101	100	101	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1304	1525	1305	1526

Data Submission Information

	BGHLV27-1	BGHLV27-1
ENCODE_alias	brenton-graveley:non-target_BGHLV27	brenton-graveley:NT_BGHLV27B
ENCODE_accession	ENCSR246RRQ	ENCSR960MSV
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-1	BGHLV27-1
Sample Name	non-target_BGHLV27-1	NT_BGHLV27-1B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2016-05-25
Project	ENCODE3	ENCODE3

protocol_URL
ID	3032	3135

File Information

Search:

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	Project	FILE_ID
non-target_BGHLV27-1_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1304	HiSeq2500	100	paired-ended	1	GRCh38	V40		ENCODE3	20012
non-target_BGHLV27-1_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1304	HiSeq2500	100	paired-ended	2				ENCODE3	20034
non-target_BGHLV27-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1304					GRCh38	V40	non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-1_2.fastq.gz	ENCORE2	20056
non-target_BGHLV27-1_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1304					GRCh38	V40	non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-1_2.fastq.gz	ENCORE2	20684
non-target_BGHLV27-1_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1304					GRCh38	V40	non-target_BGHLV27-1/Aligned.sortedByCoord.out.bam	ENCORE2	20078
non-target_BGHLV27-1_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1304					GRCh38	V40	non-target_BGHLV27-1/Aligned.sortedByCoord.out.bam	ENCORE2	20100
non-target_BGHLV27-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1304					GRCh38	V40	non-target_BGHLV27-1/Aligned.sortedByCoord.out.bam	ENCORE2	20122
non-target_BGHLV27-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1304					GRCh38	V40	non-target_BGHLV27-1/Aligned.sortedByCoord.out.bam	ENCORE2	20144
non-target_BGHLV27-2_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1305	HiSeq2500	100	paired-ended	1	GRCh38	V40		ENCODE3	20013
non-target_BGHLV27-2_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1305	HiSeq2500	100	paired-ended	2				ENCODE3	20035
non-target_BGHLV27-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1305					GRCh38	V40	non-target_BGHLV27-2_1.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCORE2	20057
non-target_BGHLV27-2_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1305					GRCh38	V40	non-target_BGHLV27-2_1.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCORE2	20685
non-target_BGHLV27-2_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1305					GRCh38	V40	non-target_BGHLV27-2/Aligned.sortedByCoord.out.bam	ENCORE2	20079
non-target_BGHLV27-2_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1305					GRCh38	V40	non-target_BGHLV27-2/Aligned.sortedByCoord.out.bam	ENCORE2	20101
non-target_BGHLV27-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1305					GRCh38	V40	non-target_BGHLV27-2/Aligned.sortedByCoord.out.bam	ENCORE2	20123
non-target_BGHLV27-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1305					GRCh38	V40	non-target_BGHLV27-2/Aligned.sortedByCoord.out.bam	ENCORE2	20145
NT_BGHLV27-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1525					GRCh38	V40	NT_BGHLV27-1B_GGCTAC_L006_001.R1.fastq.gz,NT_BGHLV27-1B_GGCTAC_L006_001.R2.fastq.gz	ENCORE2	20058
NT_BGHLV27-1B_GGCTAC_L006_001.R1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1525	HiSeq2500	100	paired-ended	1	GRCh38	V40		ENCODE3	20014
NT_BGHLV27-1B_GGCTAC_L006_001.R2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1525	HiSeq2500	100	paired-ended	2				ENCODE3	20036
NT_BGHLV27-1B_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1525					GRCh38	V40	NT_BGHLV27-1B_GGCTAC_L006_001.R1.fastq.gz,NT_BGHLV27-1B_GGCTAC_L006_001.R2.fastq.gz	ENCORE2	20686
NT_BGHLV27-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1525					GRCh38	V40	NT_BGHLV27-1B/Aligned.sortedByCoord.out.bam	ENCORE2	20080
NT_BGHLV27-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1525					GRCh38	V40	NT_BGHLV27-1B/Aligned.sortedByCoord.out.bam	ENCORE2	20102
NT_BGHLV27-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1525					GRCh38	V40	NT_BGHLV27-1B/Aligned.sortedByCoord.out.bam	ENCORE2	20124
NT_BGHLV27-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1525					GRCh38	V40	NT_BGHLV27-1B/Aligned.sortedByCoord.out.bam	ENCORE2	20146
NT_BGHLV27-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1526					GRCh38	V40	NT_BGHLV27-2B_CTTGTA_L006_001.R1.fastq.gz,NT_BGHLV27-2B_CTTGTA_L006_001.R2.fastq.gz	ENCORE2	20059
NT_BGHLV27-2B_CTTGTA_L006_001.R1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1526	HiSeq2500	100	paired-ended	1	GRCh38	V40		ENCODE3	20015
NT_BGHLV27-2B_CTTGTA_L006_001.R2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1526	HiSeq2500	100	paired-ended	2				ENCODE3	20037
NT_BGHLV27-2B_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1526					GRCh38	V40	NT_BGHLV27-2B_CTTGTA_L006_001.R1.fastq.gz,NT_BGHLV27-2B_CTTGTA_L006_001.R2.fastq.gz	ENCORE2	20687
NT_BGHLV27-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1526					GRCh38	V40	NT_BGHLV27-2B/Aligned.sortedByCoord.out.bam	ENCORE2	20081
NT_BGHLV27-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1526					GRCh38	V40	NT_BGHLV27-2B/Aligned.sortedByCoord.out.bam	ENCORE2	20103
NT_BGHLV27-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1526					GRCh38	V40	NT_BGHLV27-2B/Aligned.sortedByCoord.out.bam	ENCORE2	20125
NT_BGHLV27-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1526					GRCh38	V40	NT_BGHLV27-2B/Aligned.sortedByCoord.out.bam	ENCORE2	20147

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