non-target RNA-Seq in K562

General Information

List KD experiments controlled by BGKLV32-1 and BGKLV32-2

NT-BGKLV32-1,NT-BGKLV32-2 (alias:NT_BGKLV32-1,NT_BGKLV32-2):

AGGF1-BGKLV32-K562

Experiment Information (Status: Released)

	BGKLV32-1	BGKLV32-2
idx	600	601
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGKLV32-1	BGKLV32-2
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	2585
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	3/7/2016	3/7/2016
repeat_library
Note
ID	681	682

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV32-1	BGKLV32-2
Sample_ID	BGKLV32-1	BGKLV32-2
Sample Name	NT_BGKLV32-1	NT_BGKLV32-2
Sample Name	NT_BGKLV32-1	NT_BGKLV32-2
RBP	non-target	non-target
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1175	1176

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-1	BGKLV32-2
Sample #
Sample Name	NT-BGKLV32-1	NT-BGKLV32-2
Sample_Name_Alias	NT_BGKLV32-1	NT_BGKLV32-2
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/A6.png	DNA_Library_LV33-34-25B-32/set1/B6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A11.png	RNA_Library_LV29-30-31-32/set1/B11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-1	BGKLV32-2
RBP	NT	NT
Batch_ID	BGKLV32	BGKLV32
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2860	2861

Sequencing Information

	BGKLV32-1	BGKLV32-2
Sample_ID	BGKLV32-1	BGKLV32-2
Sample Name	NT_BGKLV32-1	NT_BGKLV32-2
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	137,000,000	83,474,516
total_aligned_reads	112,194,636	71,445,892
unique_aligned_reads	102,424,738	65,088,284
percent_uniqueAligned	0.74763	0.77974
correlation_replicates	0.998398	0.998398
spikein_reads	546,406	304,416
percent_spikeins	0.00399	0.00365
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1509	1510

Data Submission Information

	BGKLV32-1
ENCODE_alias	brenton-graveley:NT_BGKLV32B
ENCODE_accession	ENCSR143COQ
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGKLV32-1
Sample Name	NT_BGKLV32-1
Selected	Yes
Status	Released
Status_Date	2016-05-25
Project	ENCODE3

protocol_URL
ID	3127

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_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1509	HiSeq2500	100	paired-ended	1				ENCODE3	21208
NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1509	HiSeq2500	100	paired-ended	2				ENCODE3	21238
NT_BGKLV32-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1509					GRCh38	V40	NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz	ENCORE2	21268
NT_BGKLV32-1_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1509					GRCh38	V40	NT_BGKLV32-1/Aligned.sortedByCoord.out.bam	ENCORE2	21298
NT_BGKLV32-1_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1509					GRCh38	V40	NT_BGKLV32-1/Aligned.sortedByCoord.out.bam	ENCORE2	21328
NT_BGKLV32-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1509					GRCh38	V40	NT_BGKLV32-1/Aligned.sortedByCoord.out.bam	ENCORE2	21358
NT_BGKLV32-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1509					GRCh38	V40	NT_BGKLV32-1/Aligned.sortedByCoord.out.bam	ENCORE2	21388
NT_BGKLV32-1_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1509					GRCh38	V40	NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz	ENCORE2	21418
NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1510	HiSeq2500	100	paired-ended	1				ENCODE3	21209
NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1510	HiSeq2500	100	paired-ended	2				ENCODE3	21239
NT_BGKLV32-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1510					GRCh38	V40	NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCORE2	21269
NT_BGKLV32-2_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1510					GRCh38	V40	NT_BGKLV32-2/Aligned.sortedByCoord.out.bam	ENCORE2	21299
NT_BGKLV32-2_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1510					GRCh38	V40	NT_BGKLV32-2/Aligned.sortedByCoord.out.bam	ENCORE2	21329
NT_BGKLV32-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1510					GRCh38	V40	NT_BGKLV32-2/Aligned.sortedByCoord.out.bam	ENCORE2	21359
NT_BGKLV32-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1510					GRCh38	V40	NT_BGKLV32-2/Aligned.sortedByCoord.out.bam	ENCORE2	21389
NT_BGKLV32-2_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1510					GRCh38	V40	NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCORE2	21419