non-target RNA-Seq in K562

General Information

List KD experiments controlled by BGKLV34-1 and BGKLV34-2

NT-BGKLV34-1B,NT-BGKLV34-2B:

RPS11-BGKLV34-K562

NT-BGKLV34-1,NT-BGKLV34-2 (alias:NT_BGKLV34-1,NT_BGKLV34-2):

Experiment Information (Status: Released)

	BGKLV34-1	BGKLV34-2
idx	664	665
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGKLV34-1	BGKLV34-2
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	4149
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	3/9/2016	3/9/2016
repeat_library
Note
ID	749	750

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV34-1	BGKLV34-1	BGKLV34-2	BGKLV34-2
Sample_ID	BGKLV34-1	BGKLV34-1	BGKLV34-2	BGKLV34-2
Sample Name	NT-BGKLV34-1B	NT_BGKLV34-1	NT-BGKLV34-2B	NT_BGKLV34-2
Sample Name	NT-BGKLV34-1B	NT_BGKLV34-1	NT-BGKLV34-2B	NT_BGKLV34-2
RBP	non-target	non-target	non-target	non-target
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	Released	Released	Released
Status_date	2021-03-18	2016-09-24	2021-03-18	2016-09-24
Project	ENCODE4	ENCODE3	ENCODE4	ENCODE3
Note
ID	106	1235	107	1236

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-1	BGKLV34-1	BGKLV34-2	BGKLV34-2
Sample #	39		40
Sample Name	NT-BGKLV34-1B	NT-BGKLV34-1	NT-BGKLV34-2B	NT-BGKLV34-2
Sample_Name_Alias		NT_BGKLV34-1		NT_BGKLV34-2
Index Well Position	S25	S22	S27	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2016-03-09	2018-01-02	2016-03-09
Lib_ID	Lib-180102	Lib-160309	Lib-180102	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp	287		284
Peak_Molarity	11.30		9.71
libSampleQC_DNA_Well	DNA_Library_set40/set1/G10.png	DNA_Library_LV33-34-25B-32/set1/E2.png	DNA_Library_set40/set1/H10.png	DNA_Library_LV34_2-28/set1/A1.png
RIN	10.0	10.0	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/C4.png	RNA_Library_LV32-33-34/set1/C4.png	RNA_Library_LV32-33-34/set1/D4.png	RNA_Library_LV32-33-34/set1/D4.png
SampleQC_method	TapeStation		TapeStation
SampleQC_date	2018-01-02		2018-01-02
Sample_ID	BGKLV34-1	BGKLV34-1	BGKLV34-2	BGKLV34-2
RBP	NT	NT	NT	NT
Batch_ID	BGKLV34	BGKLV34	BGKLV34	BGKLV34
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	ENCODE4	ENCODE3	ENCODE4	ENCODE3
ID	962	2920	963	2921

Sequencing Information

	BGKLV34-1	BGKLV34-1	BGKLV34-2	BGKLV34-2
Sample_ID	BGKLV34-1	BGKLV34-1	BGKLV34-2	BGKLV34-2
Sample Name	NT-BGKLV34-1B	NT_BGKLV34-1	NT-BGKLV34-2B	NT_BGKLV34-2
Pool ID	Pool-180109	Pool-160912	Pool-180109	Pool-160912
LocalServer_folder	set40_K	set34	set40_K	set34
total_reads	50,836,534	67,299,976	56,955,632	78,072,556
total_aligned_reads	42,877,480	57,140,988	47,603,678	67,436,380
unique_aligned_reads	39,171,108	52,373,790	43,298,558	61,716,572
percent_uniqueAligned	0.77053	0.77821	0.76022	0.79050
correlation_replicates	0.990971	0.998665	0.990971	0.998665
spikein_reads	10,016	172,746	19,136	261,216
percent_spikeins	0.00020	0.00257	0.00034	0.00335
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	365	1569	366	1570

Data Submission Information

	BGKLV34-1	BGKLV34-1	BGKLV34-1	BGKLV34-1	BGKLV34-1	BGKLV34-1	BGKLV34-2	BGKLV34-2	BGKLV34-2	BGKLV34-2
ENCODE_alias	brenton-graveley:NT-BGKLV34-B	brenton-graveley:NT_BGKLV34-1	brenton-graveley:L-NT-BGKLV34-1B	brenton-graveley:NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R1.fastq.gz	brenton-graveley:NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R2.fastq.gz	brenton-graveley:NT_BGKLV34	brenton-graveley:NT_BGKLV34-2	brenton-graveley:L-NT-BGKLV34-2B	brenton-graveley:NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R1.fastq.gz	brenton-graveley:NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R2.fastq.gz
ENCODE_accession	ENCSR774AEQ	ENCBS922JMC	ENCLB861VHS	ENCFF593EMC	ENCFF051YSC	ENCSR174OYC	ENCBS645VVV	ENCLB349BMJ	ENCFF108KTH	ENCFF060SHK
object_type	experiment	biosample	library	file_fastq1	file_fastq2	experiment	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-1	BGKLV34-1	BGKLV34-1	BGKLV34-1	BGKLV34-1	BGKLV34-1	BGKLV34-2	BGKLV34-2	BGKLV34-2	BGKLV34-2
Sample Name	NT-BGKLV34-1B	NT-BGKLV34-1B	NT-BGKLV34-1B	NT-BGKLV34-1B	NT-BGKLV34-1B	NT_BGKLV34-1	NT-BGKLV34-2B	NT-BGKLV34-2B	NT-BGKLV34-2B	NT-BGKLV34-2B
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2016-09-23	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE3	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV34_biosample_protocol_mix	LV40_library_protocol				LV34_biosample_protocol_mix	LV40_library_protocol
protocol_URL		NT_BGKLV34-1.pdf	L-NT-BGKLV34-1B.pdf				NT_BGKLV34-2.pdf	L-NT-BGKLV34-2B.pdf
ID	1444	1486	1542	1655	1688	3157	1487	1543	1656	1689

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-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	365	HiSeq2500	100	paired-ended	1				ENCODE4	738
NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	365	HiSeq2500	100	paired-ended	2				ENCODE4	781
NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1569	HiSeq2500	100	paired-ended	1				ENCODE3	21528
NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1569	HiSeq2500	100	paired-ended	2				ENCODE3	21548
NT_BGKLV34-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1569					GRCh38	V40	NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz	ENCORE2	21568
NT_BGKLV34-1_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1569					GRCh38	V40	NT_BGKLV34-1/Aligned.sortedByCoord.out.bam	ENCORE2	21588
NT_BGKLV34-1_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1569					GRCh38	V40	NT_BGKLV34-1/Aligned.sortedByCoord.out.bam	ENCORE2	21608
NT_BGKLV34-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1569					GRCh38	V40	NT_BGKLV34-1/Aligned.sortedByCoord.out.bam	ENCORE2	21628
NT_BGKLV34-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1569					GRCh38	V40	NT_BGKLV34-1/Aligned.sortedByCoord.out.bam	ENCORE2	21648
NT_BGKLV34-1_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1569					GRCh38	V40	NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz	ENCORE2	21668
NT-BGKLV34-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	365					GRCh38	V40	NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R1.fastq.gz,NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCORE2	23482
NT-BGKLV34-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	365					GRCh38	V40	NT-BGKLV34-1B/Aligned.sortedByCoord.out.bam	ENCORE2	23516
NT-BGKLV34-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	365					GRCh38	V40	NT-BGKLV34-1B/Aligned.sortedByCoord.out.bam	ENCORE2	23550
NT-BGKLV34-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	365					GRCh38	V40	NT-BGKLV34-1B/Aligned.sortedByCoord.out.bam	ENCORE2	23584
NT-BGKLV34-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	365					GRCh38	V40	NT-BGKLV34-1B/Aligned.sortedByCoord.out.bam	ENCORE2	23618
NT-BGKLV34-1B_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	365					GRCh38	V40	NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R1.fastq.gz,NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCORE2	23652
NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	366	HiSeq2500	100	paired-ended	1				ENCODE4	739
NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	366	HiSeq2500	100	paired-ended	2				ENCODE4	782
NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1570	HiSeq2500	100	paired-ended	1				ENCODE3	21529
NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1570	HiSeq2500	100	paired-ended	2				ENCODE3	21549
NT_BGKLV34-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1570					GRCh38	V40	NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCORE2	21569
NT_BGKLV34-2_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1570					GRCh38	V40	NT_BGKLV34-2/Aligned.sortedByCoord.out.bam	ENCORE2	21589
NT_BGKLV34-2_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1570					GRCh38	V40	NT_BGKLV34-2/Aligned.sortedByCoord.out.bam	ENCORE2	21609
NT_BGKLV34-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1570					GRCh38	V40	NT_BGKLV34-2/Aligned.sortedByCoord.out.bam	ENCORE2	21629
NT_BGKLV34-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1570					GRCh38	V40	NT_BGKLV34-2/Aligned.sortedByCoord.out.bam	ENCORE2	21649
NT_BGKLV34-2_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1570					GRCh38	V40	NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCORE2	21669
NT-BGKLV34-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	366					GRCh38	V40	NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R1.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCORE2	23483
NT-BGKLV34-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	366					GRCh38	V40	NT-BGKLV34-2B/Aligned.sortedByCoord.out.bam	ENCORE2	23517
NT-BGKLV34-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	366					GRCh38	V40	NT-BGKLV34-2B/Aligned.sortedByCoord.out.bam	ENCORE2	23551
NT-BGKLV34-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	366					GRCh38	V40	NT-BGKLV34-2B/Aligned.sortedByCoord.out.bam	ENCORE2	23585
NT-BGKLV34-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	366					GRCh38	V40	NT-BGKLV34-2B/Aligned.sortedByCoord.out.bam	ENCORE2	23619
NT-BGKLV34-2B_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	366					GRCh38	V40	NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R1.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCORE2	23653