non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHLV16-1 and BGHLV16-2

NT-BGHLV16-1,NT-BGHLV16-2 (alias:NT_BGHLV16_1,NT_BGHLV16_2):

DDX52-BGHLV16-HepG2

EEF2-BGHLV16-HepG2

EFTUD2-BGHLV16-HepG2

EIF3D-BGHLV16-HepG2

FAM120A-BGHLV16-HepG2

Experiment Information (Status: Released)

	BGHLV16-1	BGHLV16-2
idx	169	170
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGHLV16-1	BGHLV16-2
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	5636
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	9/23/2014	9/23/2014
repeat_library
Note
ID	2234	2235

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV16-1	BGHLV16-2
Sample_ID	BGHLV16-1	BGHLV16-2
Sample Name	NT_BGHLV16_1	NT_BGHLV16_2
Sample Name	NT_BGHLV16_1	NT_BGHLV16_2
RBP	non-target	non-target
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	566	567

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-1	BGHLV16-2
Sample #
Sample Name	NT-BGHLV16-1	NT-BGHLV16-2
Sample_Name_Alias	NT_BGHLV16_1	NT_BGHLV16_2
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/A6.png	DNA_Library_LV16-17/set1/B6.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G11.png	RNA_Library_LV13-14-16/set1/H11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-1	BGHLV16-2
RBP	NT	NT
Batch_ID	BGHLV16	BGHLV16
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2250	2251

Sequencing Information

	BGHLV16-1	BGHLV16-2
Sample_ID	BGHLV16-1	BGHLV16-2
Sample Name	NT_BGHLV16_1	NT_BGHLV16_2
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	29,860,000	33,340,000
total_aligned_reads	27,173,664	30,158,250
unique_aligned_reads	25,718,096	28,523,716
percent_uniqueAligned	0.86129	0.85554
correlation_replicates	0.997733	0.997733
spikein_reads	64,554	54,050
percent_spikeins	0.00216	0.00162
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	892	893

Data Submission Information

	BGHLV16-1
ENCODE_alias	brenton-graveley:NT_BGHLV16
ENCODE_accession	ENCSR689PHN
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV16-1
Sample Name	NT_BGHLV16_1
Selected	Yes
Status	Released
Status_Date	2014-12-08
Project	ENCODE3

protocol_URL
ID	2851

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_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	892	HiSeq2000	100	paired-ended	1				ENCODE3	14292
NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	892	HiSeq2000	100	paired-ended	2				ENCODE3	14318
NT_BGHLV16_1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	892					GRCh38	V40	NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz	ENCORE2	14344
NT_BGHLV16_1_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	892					GRCh38	V40	NT_BGHLV16_1/Aligned.sortedByCoord.out.bam	ENCORE2	14370
NT_BGHLV16_1_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	892					GRCh38	V40	NT_BGHLV16_1/Aligned.sortedByCoord.out.bam	ENCORE2	14396
NT_BGHLV16_1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	892					GRCh38	V40	NT_BGHLV16_1/Aligned.sortedByCoord.out.bam	ENCORE2	14422
NT_BGHLV16_1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	892					GRCh38	V40	NT_BGHLV16_1/Aligned.sortedByCoord.out.bam	ENCORE2	14448
NT_BGHLV16_1_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	892					GRCh38	V40	NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz	ENCORE2	14474
NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	893	HiSeq2000	100	paired-ended	1				ENCODE3	14293
NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	893	HiSeq2000	100	paired-ended	2				ENCODE3	14319
NT_BGHLV16_2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	893					GRCh38	V40	NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCORE2	14345
NT_BGHLV16_2_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	893					GRCh38	V40	NT_BGHLV16_2/Aligned.sortedByCoord.out.bam	ENCORE2	14371
NT_BGHLV16_2_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	893					GRCh38	V40	NT_BGHLV16_2/Aligned.sortedByCoord.out.bam	ENCORE2	14397
NT_BGHLV16_2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	893					GRCh38	V40	NT_BGHLV16_2/Aligned.sortedByCoord.out.bam	ENCORE2	14423
NT_BGHLV16_2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	893					GRCh38	V40	NT_BGHLV16_2/Aligned.sortedByCoord.out.bam	ENCORE2	14449
NT_BGHLV16_2_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	893					GRCh38	V40	NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCORE2	14475