non-target RNA-Seq in HepG2

	BGHLV18-1	BGHLV18-2
idx	301	302
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non -target	non -target
Sample_ID	BGHLV18-1	BGHLV18-2
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	5605
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	10/2/2014	10/2/2014
repeat_library
Note
ID	2366	2367

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV18-1	BGHLV18-2
Sample_ID	BGHLV18-1	BGHLV18-2
Sample Name	NT_BGHLV18_1	NT_BGHLV18_2
Sample Name	NT_BGHLV18_1	NT_BGHLV18_2
RBP	non-target	non-target
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	634	635

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-1	BGHLV18-2
Sample #
Sample Name	NT-BGHLV18-1	NT-BGHLV18-2
Sample_Name_Alias	NT_BGHLV18_1	NT_BGHLV18_2
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/G12.png	DNA_Library_LV18-19/set1/B1.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/G7.png	RNA_Library_LV16-17-18/set1/H7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-1	BGHLV18-2
RBP	NT	NT
Batch_ID	BGHLV18	BGHLV18
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2318	2319

Sequencing Information

	BGHLV18-1	BGHLV18-2
Sample_ID	BGHLV18-1	BGHLV18-2
Sample Name	NT_BGHLV18_1	NT_BGHLV18_2
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	31,770,000	55,920,000
total_aligned_reads	29,216,848	51,625,844
unique_aligned_reads	27,613,524	48,636,570
percent_uniqueAligned	0.86917	0.86975
correlation_replicates	0.995311	0.995311
spikein_reads	141,432	156,380
percent_spikeins	0.00445	0.00280
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	960	961

Data Submission Information

	BGHLV18-1
ENCODE_alias	brenton-graveley:NT_BGHLV18
ENCODE_accession	ENCSR674KEK
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV18-1
Sample Name	NT_BGHLV18_1
Selected	Yes
Status	Released
Status_Date	2014-12-08
Project	ENCODE3

protocol_URL
ID	2834

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	controlled_by	Project	FILE_ID
NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	960	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14808
NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	960	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14846
NT_BGHLV18_1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	960					GRCh38	V40	NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz		ENCORE2	14884
NT_BGHLV18_1_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	960					GRCh38	V40	NT_BGHLV18_1/Aligned.sortedByCoord.out.bam		ENCORE2	14922
NT_BGHLV18_1_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	960					GRCh38	V40	NT_BGHLV18_1/Aligned.sortedByCoord.out.bam		ENCORE2	14960
NT_BGHLV18_1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	960					GRCh38	V40	NT_BGHLV18_1/Aligned.sortedByCoord.out.bam		ENCORE2	14998
NT_BGHLV18_1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	960					GRCh38	V40	NT_BGHLV18_1/Aligned.sortedByCoord.out.bam		ENCORE2	15036
NT_BGHLV18_1_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	960					GRCh38	V40	NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz		ENCORE2	15074
NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	961	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14809
NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	961	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14847
NT_BGHLV18_2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	961					GRCh38	V40	NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz		ENCORE2	14885
NT_BGHLV18_2_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	961					GRCh38	V40	NT_BGHLV18_2/Aligned.sortedByCoord.out.bam		ENCORE2	14923
NT_BGHLV18_2_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	961					GRCh38	V40	NT_BGHLV18_2/Aligned.sortedByCoord.out.bam		ENCORE2	14961
NT_BGHLV18_2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	961					GRCh38	V40	NT_BGHLV18_2/Aligned.sortedByCoord.out.bam		ENCORE2	14999
NT_BGHLV18_2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	961					GRCh38	V40	NT_BGHLV18_2/Aligned.sortedByCoord.out.bam		ENCORE2	15037
NT_BGHLV18_2_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	961					GRCh38	V40	NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz		ENCORE2	15075