non-target RNA-Seq in HepG2

	BGHLV17-63	BGHLV17-64
idx	235	236
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGHLV17-63	BGHLV17-64
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	5208
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	9/26/2014	9/26/2014
repeat_library
Note
ID	2300	2301

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV17-63	BGHLV17-64
Sample_ID	BGHLV17-63	BGHLV17-64
Sample Name	NT_BGHLV17_63	NT_BGHLV17_64
Sample Name	NT_BGHLV17_63	NT_BGHLV17_64
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	596	597

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-63	BGHLV17-64
Sample #
Sample Name	NT-BGHLV17-63	NT-BGHLV17-64
Sample_Name_Alias	NT_BGHLV17_63	NT_BGHLV17_64
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/G5.png	DNA_Library_LV16-17/set1/B1.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/A3.png	RNA_Library_LV16-17-18/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-63	BGHLV17-64
RBP	NT	NT
Batch_ID	BGHLV17	BGHLV17
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2280	2281

Sequencing Information

	BGHLV17-63	BGHLV17-63	BGHLV17-64
Sample_ID	BGHLV17-63	BGHLV17-63	BGHLV17-64
Sample Name	NT_BGHLV17_63	NT_BGHLV17_63	NT_BGHLV17_64
Pool ID	Pool-141001	Pool-151215B	Pool-141001
LocalServer_folder	set17	set17	set17
total_reads	20,300,000	25,297,150	46,280,000
total_aligned_reads	17,990,054	23,306,814	40,506,990
unique_aligned_reads	16,990,680	22,011,582	38,203,806
percent_uniqueAligned	0.83698	0.87012	0.82549
correlation_replicates	0.990852		0.990852
spikein_reads	82,166	103,118	126,018
percent_spikeins	0.00405	0.00408	0.00272
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	922	1377	923

Data Submission Information

	BGHLV17-63
ENCODE_alias	brenton-graveley:NT_BGHLV17
ENCODE_accession	ENCSR856ZRV
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV17-63
Sample Name	NT_BGHLV17_63
Selected	Yes
Status	Released
Status_Date	2014-12-08
Project	ENCODE3

protocol_URL
ID	2875

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_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	922	HiSeq2000	100	paired-ended	1				ENCODE3	14504
NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	922	HiSeq2000	100	paired-ended	2				ENCODE3	14542
NT_BGHLV17_63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	922					GRCh38	V40	NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz	ENCORE2	14580
NT_BGHLV17_63_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	922					GRCh38	V40	NT_BGHLV17_63/Aligned.sortedByCoord.out.bam	ENCORE2	14618
NT_BGHLV17_63_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	922					GRCh38	V40	NT_BGHLV17_63/Aligned.sortedByCoord.out.bam	ENCORE2	14656
NT_BGHLV17_63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	922					GRCh38	V40	NT_BGHLV17_63/Aligned.sortedByCoord.out.bam	ENCORE2	14694
NT_BGHLV17_63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	922					GRCh38	V40	NT_BGHLV17_63/Aligned.sortedByCoord.out.bam	ENCORE2	14732
NT_BGHLV17_63_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	922					GRCh38	V40	NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz	ENCORE2	14770
NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	923	HiSeq2000	100	paired-ended	1				ENCODE3	14505
NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	923	HiSeq2000	100	paired-ended	2				ENCODE3	14543
NT_BGHLV17_64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	923					GRCh38	V40	NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCORE2	14581
NT_BGHLV17_64_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	923					GRCh38	V40	NT_BGHLV17_64/Aligned.sortedByCoord.out.bam	ENCORE2	14619
NT_BGHLV17_64_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	923					GRCh38	V40	NT_BGHLV17_64/Aligned.sortedByCoord.out.bam	ENCORE2	14657
NT_BGHLV17_64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	923					GRCh38	V40	NT_BGHLV17_64/Aligned.sortedByCoord.out.bam	ENCORE2	14695
NT_BGHLV17_64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	923					GRCh38	V40	NT_BGHLV17_64/Aligned.sortedByCoord.out.bam	ENCORE2	14733
NT_BGHLV17_64_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	923					GRCh38	V40	NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCORE2	14771