non-target RNA-Seq in HepG2

	BGHLV20-1	BGHLV20-2
idx	365	366
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGHLV20-1	BGHLV20-2
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5002	0
WB_result		7558.5
Ave_WB		7299.6
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	5/29/2015	5/29/2015
repeat_library
Note
ID	2430	2431

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV20-1	BGHLV20-1	BGHLV20-2	BGHLV20-2
Sample_ID	BGHLV20-1	BGHLV20-1	BGHLV20-2	BGHLV20-2
Sample Name	non-target-BGHLV20-1_17706	NT_BGHLV20-1B	non-target-BGHLV20-2_17707	NT_BGHLV20-2B
Sample Name	non-target-BGHLV20-1_17706	NT_BGHLV20-1B	non-target-BGHLV20-2_17707	NT_BGHLV20-2B
RBP	non-target	non-target	non-target	non-target
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Released	Released	Released	Released
Status_date	2015-08-11	2016-09-24	2015-08-11	2016-09-24
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note
ID	730	1215	731	1216

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-1	BGHLV20-1	BGHLV20-2	BGHLV20-2
Sample #
Sample Name	NT-BGHLV20-1	NT-BGHLV20-1B	NT-BGHLV20-2	NT-BGHLV20-2B
Sample_Name_Alias	non-target-BGHLV20-1_17706	NT_BGHLV20-1B	non-target-BGHLV20-2_17707	NT_BGHLV20-2B
Index Well Position	S01	S18	S02	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2016-03-10	2015-05-29	2016-03-10
Lib_ID	Lib-150529	Lib-160310	Lib-150529	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set2/B1.png	DNA_Library_LV33-34-25B-32/set1/G9.png	DNA_Library_LV20-22-23/set1/B1.png	DNA_Library_LV33-34-25B-32/set1/H9.png
RIN	9.9	9.9	9.8	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/C7.png	RNA_Library_LV20-22-24/set1/C7.png	RNA_Library_LV20-22-24/set1/D7.png	RNA_Library_LV20-22-24/set1/D7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-1	BGHLV20-1	BGHLV20-2	BGHLV20-2
RBP	NT	NT	NT	NT
Batch_ID	BGHLV20	BGHLV20	BGHLV20	BGHLV20
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	2416	2892	2417	2893

Sequencing Information

	BGHLV20-1	BGHLV20-1	BGHLV20-2	BGHLV20-2
Sample_ID	BGHLV20-1	BGHLV20-1	BGHLV20-2	BGHLV20-2
Sample Name	non-target-BGHLV20-1_17706	NT_BGHLV20-1B	non-target-BGHLV20-2_17707	NT_BGHLV20-2B
Pool ID	Pool-150705	Pool-160425	Pool-150705	Pool-160425
LocalServer_folder	set20	set20	set20	set20
total_reads	48,560,000	86,071,038	45,810,000	86,590,952
total_aligned_reads	41,992,664	68,602,858	40,956,796	69,190,812
unique_aligned_reads	39,668,614	64,583,990	38,738,870	64,841,818
percent_uniqueAligned	0.81690	0.75036	0.84564	0.74883
correlation_replicates	0.995004	0.990639	0.995004	0.990639
spikein_reads	206,658	183,382	191,478	182,804
percent_spikeins	0.00426	0.00213	0.00418	0.00211
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1184	1541	1185	1542

Data Submission Information

	BGHLV20-1
ENCODE_alias	brenton-graveley:non-target-BGHLV20
ENCODE_accession	ENCSR305XWT
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV20-1
Sample Name	non-target-BGHLV20-1_17706
Selected	Yes
Status	Released
Status_Date	2015-08-11
Project	ENCODE3

protocol_URL
ID	2914

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-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1184	HiSeq2000	100	paired-ended	1				ENCODE3	15610
NT_BGHLV20-1B_GTCCGC_L004_001.R1.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1541	HiSeq2000	100	paired-ended	1				ENCODE3	15612
non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1184	HiSeq2000	100	paired-ended	2				ENCODE3	15652
NT_BGHLV20-1B_GTCCGC_L004_001.R2.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1541	HiSeq2000	100	paired-ended	2				ENCODE3	15654
non-target-BGHLV20-1_17706_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1184					GRCh38	V40	non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz	ENCORE2	15694
NT_BGHLV20-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1541					GRCh38	V40	NT_BGHLV20-1B_GTCCGC_L004_001.R1.fastq.gz,NT_BGHLV20-1B_GTCCGC_L004_001.R2.fastq.gz	ENCORE2	15696
non-target-BGHLV20-1_17706_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1184					GRCh38	V40	non-target-BGHLV20-1_17706/Aligned.sortedByCoord.out.bam	ENCORE2	15736
NT_BGHLV20-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1541					GRCh38	V40	NT_BGHLV20-1B/Aligned.sortedByCoord.out.bam	ENCORE2	15738
non-target-BGHLV20-1_17706_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1184					GRCh38	V40	non-target-BGHLV20-1_17706/Aligned.sortedByCoord.out.bam	ENCORE2	15778
NT_BGHLV20-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1541					GRCh38	V40	NT_BGHLV20-1B/Aligned.sortedByCoord.out.bam	ENCORE2	15780
non-target-BGHLV20-1_17706_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1184					GRCh38	V40	non-target-BGHLV20-1_17706/Aligned.sortedByCoord.out.bam	ENCORE2	15820
NT_BGHLV20-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1541					GRCh38	V40	NT_BGHLV20-1B/Aligned.sortedByCoord.out.bam	ENCORE2	15822
non-target-BGHLV20-1_17706_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1184					GRCh38	V40	non-target-BGHLV20-1_17706/Aligned.sortedByCoord.out.bam	ENCORE2	15862
NT_BGHLV20-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1541					GRCh38	V40	NT_BGHLV20-1B/Aligned.sortedByCoord.out.bam	ENCORE2	15864
non-target-BGHLV20-1_17706_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1184					GRCh38	V40	non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz	ENCORE2	15904
NT_BGHLV20-1B_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1541					GRCh38	V40	NT_BGHLV20-1B_GTCCGC_L004_001.R1.fastq.gz,NT_BGHLV20-1B_GTCCGC_L004_001.R2.fastq.gz	ENCORE2	15906
non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1185	HiSeq2000	100	paired-ended	1				ENCODE3	15611
NT_BGHLV20-2B_GTGAAA_L004_001.R1.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1542	HiSeq2000	100	paired-ended	1				ENCODE3	15613
non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1185	HiSeq2000	100	paired-ended	2				ENCODE3	15653
NT_BGHLV20-2B_GTGAAA_L004_001.R2.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1542	HiSeq2000	100	paired-ended	2				ENCODE3	15655
non-target-BGHLV20-2_17707_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1185					GRCh38	V40	non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCORE2	15695
NT_BGHLV20-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1542					GRCh38	V40	NT_BGHLV20-2B_GTGAAA_L004_001.R1.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R2.fastq.gz	ENCORE2	15697
non-target-BGHLV20-2_17707_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1185					GRCh38	V40	non-target-BGHLV20-2_17707/Aligned.sortedByCoord.out.bam	ENCORE2	15737
NT_BGHLV20-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1542					GRCh38	V40	NT_BGHLV20-2B/Aligned.sortedByCoord.out.bam	ENCORE2	15739
non-target-BGHLV20-2_17707_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1185					GRCh38	V40	non-target-BGHLV20-2_17707/Aligned.sortedByCoord.out.bam	ENCORE2	15779
NT_BGHLV20-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1542					GRCh38	V40	NT_BGHLV20-2B/Aligned.sortedByCoord.out.bam	ENCORE2	15781
non-target-BGHLV20-2_17707_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1185					GRCh38	V40	non-target-BGHLV20-2_17707/Aligned.sortedByCoord.out.bam	ENCORE2	15821
NT_BGHLV20-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1542					GRCh38	V40	NT_BGHLV20-2B/Aligned.sortedByCoord.out.bam	ENCORE2	15823
non-target-BGHLV20-2_17707_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1185					GRCh38	V40	non-target-BGHLV20-2_17707/Aligned.sortedByCoord.out.bam	ENCORE2	15863
NT_BGHLV20-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1542					GRCh38	V40	NT_BGHLV20-2B/Aligned.sortedByCoord.out.bam	ENCORE2	15865
non-target-BGHLV20-2_17707_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1185					GRCh38	V40	non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCORE2	15905
NT_BGHLV20-2B_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1542					GRCh38	V40	NT_BGHLV20-2B_GTGAAA_L004_001.R1.fastq.gz,NT_BGHLV20-2B_GTGAAA_L004_001.R2.fastq.gz	ENCORE2	15907