non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHLV35-1 and BGHLV35-2

NT-BGHLV35-1,NT-BGHLV35-2 (alias:NT_BGHLV35-1,NT_BGHLV35-2):

BOP1-BGHLV35-HepG2

HNRNPLL-BGHLV35-HepG2

MTPAP-BGHLV35-HepG2

NSUN2-BGHLV35-HepG2

SF3B1-BGHLV35-HepG2

SNRNP70-BGHLV35-HepG2

SRSF3-BGHLV35-HepG2

TARDBP-BGHLV35-HepG2

Experiment Information (Status: Released)

	BGHLV35-1	BGHLV35-2
idx	857	858
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non target	non target
Sample_ID	BGHLV35-1	BGHLV35-2
transduction_Date	4/29/16	4/29/16
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	3793
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	07/18/16	07/18/16
repeat_library
Note
ID	2946	2947

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV35-1	BGHLV35-2
Sample_ID	BGHLV35-1	BGHLV35-2
Sample Name	NT_BGHLV35-1	NT_BGHLV35-2
Sample Name	NT_BGHLV35-1	NT_BGHLV35-2
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	1265	1266

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-1	BGHLV35-2
Sample #
Sample Name	NT-BGHLV35-1	NT-BGHLV35-2
Sample_Name_Alias	NT_BGHLV35-1	NT_BGHLV35-2
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set2/A1.png	DNA_Library_LV35/set2/B1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/A1.png	RNA_Library_LV35_LV36/set1/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-1	BGHLV35-2
RBP	NT	NT
Batch_ID	BGHLV35	BGHLV35
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2950	2951

Sequencing Information

	BGHLV35-1	BGHLV35-2
Sample_ID	BGHLV35-1	BGHLV35-2
Sample Name	NT_BGHLV35-1	NT_BGHLV35-2
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	76,979,034	82,763,436
total_aligned_reads	60,126,674	65,297,590
unique_aligned_reads	55,774,066	61,280,570
percent_uniqueAligned	0.72454	0.74043
correlation_replicates	0.996604	0.996604
spikein_reads	117,384	129,400
percent_spikeins	0.00152	0.00156
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1599	1600

Data Submission Information

	BGHLV35-1
ENCODE_alias	brenton-graveley:NT_BGHLV35
ENCODE_accession	ENCSR264TUE
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV35-1
Sample Name	NT_BGHLV35-1
Selected	Yes
Status	Released
Status_Date	2016-09-23
Project	ENCODE3

protocol_URL
ID	3172

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_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1599	HiSeq2500	100	paired-ended	1				ENCODE3	21698
NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1599	HiSeq2500	100	paired-ended	2				ENCODE3	21724
NT_BGHLV35-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1599					GRCh38	V40	NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz	ENCORE2	21750
NT_BGHLV35-1_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1599					GRCh38	V40	NT_BGHLV35-1/Aligned.sortedByCoord.out.bam	ENCORE2	21776
NT_BGHLV35-1_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1599					GRCh38	V40	NT_BGHLV35-1/Aligned.sortedByCoord.out.bam	ENCORE2	21802
NT_BGHLV35-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1599					GRCh38	V40	NT_BGHLV35-1/Aligned.sortedByCoord.out.bam	ENCORE2	21828
NT_BGHLV35-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1599					GRCh38	V40	NT_BGHLV35-1/Aligned.sortedByCoord.out.bam	ENCORE2	21854
NT_BGHLV35-1_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1599					GRCh38	V40	NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz	ENCORE2	21880
NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1600	HiSeq2500	100	paired-ended	1				ENCODE3	21699
NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1600	HiSeq2500	100	paired-ended	2				ENCODE3	21725
NT_BGHLV35-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1600					GRCh38	V40	NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCORE2	21751
NT_BGHLV35-2_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1600					GRCh38	V40	NT_BGHLV35-2/Aligned.sortedByCoord.out.bam	ENCORE2	21777
NT_BGHLV35-2_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1600					GRCh38	V40	NT_BGHLV35-2/Aligned.sortedByCoord.out.bam	ENCORE2	21803
NT_BGHLV35-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1600					GRCh38	V40	NT_BGHLV35-2/Aligned.sortedByCoord.out.bam	ENCORE2	21829
NT_BGHLV35-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1600					GRCh38	V40	NT_BGHLV35-2/Aligned.sortedByCoord.out.bam	ENCORE2	21855
NT_BGHLV35-2_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1600					GRCh38	V40	NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCORE2	21881