non-target RNA-Seq in K562

General Information

List KD experiments controlled by BGKcLV02-1 and BGKcLV02-2

NT-BGKcLV02-1,NT-BGKcLV02-2 (alias:NT_BGKcLV02-1,NT_BGKcLV02-2):

CEBPZ-BGKcLV02-K562

IGF2BP1-BGKcLV02-K562

NFX1-BGKcLV02-K562

PTBP1-BGKcLV02-K562

SRSF7-BGKcLV02-K562

Experiment Information (Status: Released)

	BGKcLV02-1	BGKcLV02-2
idx	1	2
TRCN#_or_BGC#	BGC#0000000	BGC#0000000
shRNA_or_gRNA_sequence	CAGTCGGGCGTCATCATGAT	CAGTCGGGCGTCATCATGAT
PAM
Name	non -target	non -target
Sample_ID	BGKcLV02-1	BGKcLV02-2
transduction_Date	12/15/2015	12/15/2015
days	day 6	day 6
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	3029
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	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	4095	4096

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV02-1	BGKcLV02-2
Sample_ID	BGKcLV02-1	BGKcLV02-2
Sample Name	NT_BGKcLV02-1	NT_BGKcLV02-2
Sample Name	NT_BGKcLV02-1	NT_BGKcLV02-2
RBP	non-target	non-target
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1091	1092

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-1	BGKcLV02-2
Sample #
Sample Name	NT-BGKcLV02-1	NT-BGKcLV02-2
Sample_Name_Alias	NT_BGKcLV02-1	NT_BGKcLV02-2
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/C3.png	DNA_Library_cLV02/set1/D3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_cLV02/set1/E4.png	RNA_Library_cLV02/set1/F4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-1	BGKcLV02-2
RBP	NT	NT
Batch_ID	BGKcLV02	BGKcLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2782	2783

Sequencing Information

	BGKcLV02-1	BGKcLV02-2
Sample_ID	BGKcLV02-1	BGKcLV02-2
Sample Name	NT_BGKcLV02-1	NT_BGKcLV02-2
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	71,710,812	44,284,954
total_aligned_reads	65,518,844	40,291,016
unique_aligned_reads	59,936,456	36,866,262
percent_uniqueAligned	0.83581	0.83248
correlation_replicates	0.980650	0.980650
spikein_reads	158,382	90,648
percent_spikeins	0.00221	0.00205
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1431	1432

Data Submission Information

	BGKcLV02-1
ENCODE_alias	brenton-graveley:NT_BGKcLV02
ENCODE_accession	ENCSR163JUC
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGKcLV02-1
Sample Name	NT_BGKcLV02-1
Selected	Yes
Status	Released
Status_Date	2016-03-08
Project	ENCODE3

protocol_URL
ID	3107

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_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1431	HiSeq2500	100	paired-ended	1				ENCODE3	22764
NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1431	HiSeq2500	100	paired-ended	2				ENCODE3	22784
NT_BGKcLV02-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1431					GRCh38	V40	NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz	ENCORE2	22804
NT_BGKcLV02-1_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1431					GRCh38	V40	NT_BGKcLV02-1/Aligned.sortedByCoord.out.bam	ENCORE2	22824
NT_BGKcLV02-1_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1431					GRCh38	V40	NT_BGKcLV02-1/Aligned.sortedByCoord.out.bam	ENCORE2	22844
NT_BGKcLV02-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1431					GRCh38	V40	NT_BGKcLV02-1/Aligned.sortedByCoord.out.bam	ENCORE2	22864
NT_BGKcLV02-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1431					GRCh38	V40	NT_BGKcLV02-1/Aligned.sortedByCoord.out.bam	ENCORE2	22884
NT_BGKcLV02-1_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1431					GRCh38	V40	NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz	ENCORE2	22904
NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1432	HiSeq2500	100	paired-ended	1				ENCODE3	22765
NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1432	HiSeq2500	100	paired-ended	2				ENCODE3	22785
NT_BGKcLV02-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1432					GRCh38	V40	NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCORE2	22805
NT_BGKcLV02-2_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1432					GRCh38	V40	NT_BGKcLV02-2/Aligned.sortedByCoord.out.bam	ENCORE2	22825
NT_BGKcLV02-2_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1432					GRCh38	V40	NT_BGKcLV02-2/Aligned.sortedByCoord.out.bam	ENCORE2	22845
NT_BGKcLV02-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1432					GRCh38	V40	NT_BGKcLV02-2/Aligned.sortedByCoord.out.bam	ENCORE2	22865
NT_BGKcLV02-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1432					GRCh38	V40	NT_BGKcLV02-2/Aligned.sortedByCoord.out.bam	ENCORE2	22885
NT_BGKcLV02-2_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1432					GRCh38	V40	NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCORE2	22905