non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHLV33-1 and BGHLV33-2

NT-BGHLV33-1,NT-BGHLV33-2 (alias:NT_BGHLV33-1,NT_BGHLV33-2):

SF3A3-BGHLV33-HepG2

Experiment Information (Status: Released)

	BGHLV33-1	BGHLV33-2
idx	809	810
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non target	non target
Sample_ID	BGHLV33-1	BGHLV33-2
transduction_Date	11/17/2015	11/17/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	4179
WB_result
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	3/9/2016	3/9/2016
repeat_library
Note
ID	2898	2899

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV33-1	BGHLV33-2
Sample_ID	BGHLV33-1	BGHLV33-2
Sample Name	NT_BGHLV33-1	NT_BGHLV33-2
Sample Name	NT_BGHLV33-1	NT_BGHLV33-2
RBP	non-target	non-target
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1217	1218

Library-Prep
Sequencing

Library-Prep Information

	BGHLV33-1	BGHLV33-2
Sample #
Sample Name	NT-BGHLV33-1	NT-BGHLV33-2
Sample_Name_Alias	NT_BGHLV33-1	NT_BGHLV33-2
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/A1.png	DNA_Library_LV33-34-25B-32/set1/B1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/G2.png	RNA_Library_LV32-33-34/set1/H2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV33-1	BGHLV33-2
RBP	NT	NT
Batch_ID	BGHLV33	BGHLV33
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2902	2903

Sequencing Information

	BGHLV33-1	BGHLV33-2
Sample_ID	BGHLV33-1	BGHLV33-2
Sample Name	NT_BGHLV33-1	NT_BGHLV33-2
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set33	set33
total_reads	83,850,888	82,153,148
total_aligned_reads	68,053,214	67,134,886
unique_aligned_reads	64,004,058	63,215,356
percent_uniqueAligned	0.76331	0.76948
correlation_replicates	0.999014	0.999014
spikein_reads	246,770	272,688
percent_spikeins	0.00294	0.00332
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1551	1552

Data Submission Information

	BGHLV33-1
ENCODE_alias	brenton-graveley:NT_BGHLV33
ENCODE_accession	ENCSR691IVR
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV33-1
Sample Name	NT_BGHLV33-1
Selected	Yes
Status	Released
Status_Date	2016-09-23
Project	ENCODE3

protocol_URL
ID	3148

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	Project	FILE_ID
NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1551	HiSeq2500	100	paired-ended	1				ENCODE3	21426
NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1551	HiSeq2500	100	paired-ended	2				ENCODE3	21438
NT_BGHLV33-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1551					GRCh38	V40	NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz	ENCORE2	21450
NT_BGHLV33-1_Signal.Unique.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1551					GRCh38	V40	NT_BGHLV33-1/Aligned.sortedByCoord.out.bam	ENCORE2	21462
NT_BGHLV33-1_Signal.Unique.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1551					GRCh38	V40	NT_BGHLV33-1/Aligned.sortedByCoord.out.bam	ENCORE2	21474
NT_BGHLV33-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1551					GRCh38	V40	NT_BGHLV33-1/Aligned.sortedByCoord.out.bam	ENCORE2	21486
NT_BGHLV33-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1551					GRCh38	V40	NT_BGHLV33-1/Aligned.sortedByCoord.out.bam	ENCORE2	21498
NT_BGHLV33-1_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1551					GRCh38	V40	NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz	ENCORE2	21510
NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1552	HiSeq2500	100	paired-ended	1				ENCODE3	21427
NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1552	HiSeq2500	100	paired-ended	2				ENCODE3	21439
NT_BGHLV33-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1552					GRCh38	V40	NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCORE2	21451
NT_BGHLV33-2_Signal.Unique.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1552					GRCh38	V40	NT_BGHLV33-2/Aligned.sortedByCoord.out.bam	ENCORE2	21463
NT_BGHLV33-2_Signal.Unique.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1552					GRCh38	V40	NT_BGHLV33-2/Aligned.sortedByCoord.out.bam	ENCORE2	21475
NT_BGHLV33-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1552					GRCh38	V40	NT_BGHLV33-2/Aligned.sortedByCoord.out.bam	ENCORE2	21487
NT_BGHLV33-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1552					GRCh38	V40	NT_BGHLV33-2/Aligned.sortedByCoord.out.bam	ENCORE2	21499
NT_BGHLV33-2_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1552					GRCh38	V40	NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCORE2	21511