non-target RNA-Seq in K562

	BGKLV28-1	BGKLV28-2
idx	468	469
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGKLV28-1	BGKLV28-2
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	2248	0
WB_result		2935.5
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	10/28/2015	10/28/2015
repeat_library
Note
ID	543	544

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV28-1	BGKLV28-2
Sample_ID	BGKLV28-1	BGKLV28-2
Sample Name	non-target_BGKLV28-1	non-target_BGKLV28-2
Sample Name	non-target_BGKLV28-1	non-target_BGKLV28-2
RBP	non-target	non-target
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	986	987

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-1	BGKLV28-2
Sample #
Sample Name	NT-BGKLV28-1	NT-BGKLV28-2
Sample_Name_Alias	non-target_BGKLV28-1	non-target_BGKLV28-2
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A1.png	DNA_Library_LV28-29-30/set1/B1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/D7.png	RNA_Library_LV19-21-24/set2/E7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-1	BGKLV28-2
RBP	NT	NT
Batch_ID	BGKLV28	BGKLV28
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2678	2679

Sequencing Information

	BGKLV28-1	BGKLV28-2
Sample_ID	BGKLV28-1	BGKLV28-2
Sample Name	non-target_BGKLV28-1	non-target_BGKLV28-2
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	76,741,982	105,064,940
total_aligned_reads	56,848,842	84,751,712
unique_aligned_reads	51,146,664	76,799,226
percent_uniqueAligned	0.66648	0.73097
correlation_replicates	0.930000	0.934615
spikein_reads	207,638	248,416
percent_spikeins	0.00271	0.00236
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1320	1321

Data Submission Information

	BGKLV28-1
ENCODE_alias	brenton-graveley:non-target_BGKLV28
ENCODE_accession	ENCSR164MUK
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGKLV28-1
Sample Name	non-target_BGKLV28-1
Selected	Yes
Status	Released
Status_Date	2016-03-03
Project	ENCODE3

protocol_URL
ID	3042

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
non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1320	HiSeq2500	100	paired-ended	1				ENCODE3	20164
non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1320	HiSeq2500	100	paired-ended	2				ENCODE3	20196
non-target_BGKLV28-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1320					GRCh38	V40	non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz	ENCORE2	20228
non-target_BGKLV28-1_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1320					GRCh38	V40	non-target_BGKLV28-1/Aligned.sortedByCoord.out.bam	ENCORE2	20260
non-target_BGKLV28-1_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1320					GRCh38	V40	non-target_BGKLV28-1/Aligned.sortedByCoord.out.bam	ENCORE2	20292
non-target_BGKLV28-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1320					GRCh38	V40	non-target_BGKLV28-1/Aligned.sortedByCoord.out.bam	ENCORE2	20324
non-target_BGKLV28-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1320					GRCh38	V40	non-target_BGKLV28-1/Aligned.sortedByCoord.out.bam	ENCORE2	20356
non-target_BGKLV28-1_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1320					GRCh38	V40	non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz	ENCORE2	20388
non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1321	HiSeq2500	100	paired-ended	1				ENCODE3	20165
non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1321	HiSeq2500	100	paired-ended	2				ENCODE3	20197
non-target_BGKLV28-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1321					GRCh38	V40	non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCORE2	20229
non-target_BGKLV28-2_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1321					GRCh38	V40	non-target_BGKLV28-2/Aligned.sortedByCoord.out.bam	ENCORE2	20261
non-target_BGKLV28-2_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1321					GRCh38	V40	non-target_BGKLV28-2/Aligned.sortedByCoord.out.bam	ENCORE2	20293
non-target_BGKLV28-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1321					GRCh38	V40	non-target_BGKLV28-2/Aligned.sortedByCoord.out.bam	ENCORE2	20325
non-target_BGKLV28-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1321					GRCh38	V40	non-target_BGKLV28-2/Aligned.sortedByCoord.out.bam	ENCORE2	20357
non-target_BGKLV28-2_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1321					GRCh38	V40	non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCORE2	20389