non-target RNA-Seq in K562

General Information

List KD experiments controlled by BGKLV29-1 and BGKLV29-2

NT-BGKLV29-1,NT-BGKLV29-2 (alias:NT_BGKLV29-1,NT_BGKLV29-2):

ABCF1-BGKLV29-K562

NT-BGKLV29-1B,NT-BGKLV29-2B (alias:NTB_BGKLV29-1,NTB_BGKLV29-2):

EIF2S2-BGKLV29-K562

GRSF1-BGKLV29-K562

RBM17-BGKLV29-K562

Experiment Information (Status: Released)

	BGKLV29-1	BGKLV29-2
idx	534	535
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGKLV29-1	BGKLV29-2
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	3475
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	11/2/2015	11/2/2015
repeat_library
Note
ID	613	614

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV29-1	BGKLV29-1	BGKLV29-2	BGKLV29-2
Sample_ID	BGKLV29-1	BGKLV29-1	BGKLV29-2	BGKLV29-2
Sample Name	NTB_BGKLV29-1	NT_BGKLV29-1	NTB_BGKLV29-2	NT_BGKLV29-2
Sample Name	NTB_BGKLV29-1	NT_BGKLV29-1	NTB_BGKLV29-2	NT_BGKLV29-2
RBP	non-target	non-target	non-target	non-target
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	Released	Released	Released
Status_date	2016-03-03	2016-03-03	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note
ID	1028	1030	1029	1031

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-1	BGKLV29-1	BGKLV29-2	BGKLV29-2
Sample #
Sample Name	NT-BGKLV29-1	NT-BGKLV29-1B	NT-BGKLV29-2	NT-BGKLV29-2B
Sample_Name_Alias	NT_BGKLV29-1	NTB_BGKLV29-1	NT_BGKLV29-2	NTB_BGKLV29-2
Index Well Position	S09	S01	S10	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-03	2015-11-02	2015-11-03
Lib_ID	Lib-151102	Lib-151103	Lib-151102	Lib-151103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A5.png	DNA_Library_LV28-29-30/set1/A5.png	DNA_Library_LV28-29-30/set1/B5.png	DNA_Library_LV28-29-30/set2/G1.png
RIN	10.0	10.0	9.9	9.9
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/E10.png	RNA_Library_LV26-27-28-29/set1/E10.png	RNA_Library_LV26-27-28-29/set1/F10.png	RNA_Library_LV26-27-28-29/set1/F10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-1	BGKLV29-1	BGKLV29-2	BGKLV29-2
RBP	NT	NT	NT	NT
Batch_ID	BGKLV29	BGKLV29	BGKLV29	BGKLV29
WB_result	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2716	2730	2717	2731

Sequencing Information

	BGKLV29-1	BGKLV29-1	BGKLV29-2	BGKLV29-2
Sample_ID	BGKLV29-1	BGKLV29-1	BGKLV29-2	BGKLV29-2
Sample Name	NT_BGKLV29-1	NTB_BGKLV29-1	NT_BGKLV29-2	NTB_BGKLV29-2
Pool ID	Pool-151215C	Pool-151215B	Pool-151215C	Pool-151215B
LocalServer_folder	set29	set29	set29	set29
total_reads	94,643,022	52,813,884	74,199,310	60,452,200
total_aligned_reads	72,372,022	46,888,024	59,127,666	54,433,868
unique_aligned_reads	65,661,114	42,874,672	54,069,404	49,699,578
percent_uniqueAligned	0.69378	0.81181	0.72870	0.82213
correlation_replicates	0.986711	0.996461	0.986711	0.996461
spikein_reads	323,612	245,266	258,816	229,458
percent_spikeins	0.00342	0.00464	0.00349	0.00380
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1352	1393	1353	1394

Data Submission Information

	BGKLV29-1	BGKLV29-1
ENCODE_alias	brenton-graveley:NT_BGKLV29	brenton-graveley:NTB_BGKLV29
ENCODE_accession	ENCSR032YMP	ENCSR118EFE
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-1	BGKLV29-1
Sample Name	NT_BGKLV29-1	NTB_BGKLV29-1
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3

protocol_URL
ID	3063	3064

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
NTB_BGKLV29-1_ATCACG_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1393	HiSeq2500	100	paired-ended	1				ENCODE3	20430
NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1352	HiSeq2500	100	paired-ended	1				ENCODE3	20432
NTB_BGKLV29-1_ATCACG_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1393	HiSeq2500	100	paired-ended	2				ENCODE3	20460
NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1352	HiSeq2500	100	paired-ended	2				ENCODE3	20462
NTB_BGKLV29-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1393					GRCh38	V40	NTB_BGKLV29-1_ATCACG_L007_001.R1.fastq.gz,NTB_BGKLV29-1_ATCACG_L007_001.R2.fastq.gz	ENCORE2	20490
NT_BGKLV29-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1352					GRCh38	V40	NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz	ENCORE2	20492
NTB_BGKLV29-1_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1393					GRCh38	V40	NTB_BGKLV29-1/Aligned.sortedByCoord.out.bam	ENCORE2	20520
NT_BGKLV29-1_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1352					GRCh38	V40	NT_BGKLV29-1/Aligned.sortedByCoord.out.bam	ENCORE2	20522
NTB_BGKLV29-1_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1393					GRCh38	V40	NTB_BGKLV29-1/Aligned.sortedByCoord.out.bam	ENCORE2	20550
NT_BGKLV29-1_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1352					GRCh38	V40	NT_BGKLV29-1/Aligned.sortedByCoord.out.bam	ENCORE2	20552
NTB_BGKLV29-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1393					GRCh38	V40	NTB_BGKLV29-1/Aligned.sortedByCoord.out.bam	ENCORE2	20580
NT_BGKLV29-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1352					GRCh38	V40	NT_BGKLV29-1/Aligned.sortedByCoord.out.bam	ENCORE2	20582
NTB_BGKLV29-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1393					GRCh38	V40	NTB_BGKLV29-1/Aligned.sortedByCoord.out.bam	ENCORE2	20610
NT_BGKLV29-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1352					GRCh38	V40	NT_BGKLV29-1/Aligned.sortedByCoord.out.bam	ENCORE2	20612
NTB_BGKLV29-1_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1393					GRCh38	V40	NTB_BGKLV29-1_ATCACG_L007_001.R1.fastq.gz,NTB_BGKLV29-1_ATCACG_L007_001.R2.fastq.gz	ENCORE2	20640
NT_BGKLV29-1_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1352					GRCh38	V40	NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz	ENCORE2	20642
NTB_BGKLV29-2_CGATGT_L007_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1394	HiSeq2500	100	paired-ended	1				ENCODE3	20431
NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1353	HiSeq2500	100	paired-ended	1				ENCODE3	20433
NTB_BGKLV29-2_CGATGT_L007_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1394	HiSeq2500	100	paired-ended	2				ENCODE3	20461
NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1353	HiSeq2500	100	paired-ended	2				ENCODE3	20463
NTB_BGKLV29-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1394					GRCh38	V40	NTB_BGKLV29-2_CGATGT_L007_001.R1.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R2.fastq.gz	ENCORE2	20491
NT_BGKLV29-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1353					GRCh38	V40	NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCORE2	20493
NTB_BGKLV29-2_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1394					GRCh38	V40	NTB_BGKLV29-2/Aligned.sortedByCoord.out.bam	ENCORE2	20521
NT_BGKLV29-2_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1353					GRCh38	V40	NT_BGKLV29-2/Aligned.sortedByCoord.out.bam	ENCORE2	20523
NTB_BGKLV29-2_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1394					GRCh38	V40	NTB_BGKLV29-2/Aligned.sortedByCoord.out.bam	ENCORE2	20551
NT_BGKLV29-2_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1353					GRCh38	V40	NT_BGKLV29-2/Aligned.sortedByCoord.out.bam	ENCORE2	20553
NTB_BGKLV29-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1394					GRCh38	V40	NTB_BGKLV29-2/Aligned.sortedByCoord.out.bam	ENCORE2	20581
NT_BGKLV29-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1353					GRCh38	V40	NT_BGKLV29-2/Aligned.sortedByCoord.out.bam	ENCORE2	20583
NTB_BGKLV29-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1394					GRCh38	V40	NTB_BGKLV29-2/Aligned.sortedByCoord.out.bam	ENCORE2	20611
NT_BGKLV29-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1353					GRCh38	V40	NT_BGKLV29-2/Aligned.sortedByCoord.out.bam	ENCORE2	20613
NTB_BGKLV29-2_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1394					GRCh38	V40	NTB_BGKLV29-2_CGATGT_L007_001.R1.fastq.gz,NTB_BGKLV29-2_CGATGT_L007_001.R2.fastq.gz	ENCORE2	20641
NT_BGKLV29-2_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1353					GRCh38	V40	NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCORE2	20643