non-target RNA-Seq in HepG2

	BGHLV23-1	BGHLV23-2
idx	493	494
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGHLV23-1	BGHLV23-2
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5393	0
WB_result	6442.8	6375.0
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	6/10/2015	6/10/2015
repeat_library
Note
ID	2568	2569

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV23-1	BGHLV23-1	BGHLV23-2	BGHLV23-2
Sample_ID	BGHLV23-1	BGHLV23-1	BGHLV23-2	BGHLV23-2
Sample Name	non-target-BGHLV23-1	NT_BGHLV23-1B	non-target-BGHLV23-2	NT_BGHLV23-2B
Sample Name	non-target-BGHLV23-1	NT_BGHLV23-1B	non-target-BGHLV23-2	NT_BGHLV23-2B
RBP	non-target	non-target	non-target	non-target
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Released	Released	Released	Released
Status_date	2015-08-13	2016-03-04	2015-08-13	2016-03-04
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note
ID	830	1079	831	1080

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-1	BGHLV23-1	BGHLV23-2	BGHLV23-2
Sample #
Sample Name	NT-BGHLV23-1	NT-BGHLV23-1B	NT-BGHLV23-2	NT-BGHLV23-2B
Sample_Name_Alias	non-target-BGHLV23-1	NT_BGHLV23-1B	non-target-BGHLV23-2	NT_BGHLV23-2B
Index Well Position	S18	S13	S19	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-11-03	2015-06-10	2015-11-03
Lib_ID	Lib-150610	Lib-151103	Lib-150610	Lib-151103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/A11.png	DNA_Library_LV28-29-30/set1/E8.png	DNA_Library_LV20-22-23/set1/B11.png	DNA_Library_LV28-29-30/set1/F8.png
RIN	9.7	9.7	9.6	9.6
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/E4.png	RNA_Library_LV22-23-25/set1/E4.png	RNA_Library_LV22-23-25/set1/F4.png	RNA_Library_LV22-23-25/set1/F4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-1	BGHLV23-1	BGHLV23-2	BGHLV23-2
RBP	NT	NT	NT	NT
Batch_ID	BGHLV23	BGHLV23	BGHLV23	BGHLV23
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	2518	2766	2519	2767

Sequencing Information

	BGHLV23-1	BGHLV23-1	BGHLV23-2	BGHLV23-2
Sample_ID	BGHLV23-1	BGHLV23-1	BGHLV23-2	BGHLV23-2
Sample Name	non-target-BGHLV23-1	NT_BGHLV23-1B	non-target-BGHLV23-2	NT_BGHLV23-2B
Pool ID	Pool-150701	Pool-151215B	Pool-150701	Pool-151215B
LocalServer_folder	set23	set23	set23	set23
total_reads	112,000,000	87,047,412	55,090,000	64,292,416
total_aligned_reads	99,686,424	74,350,148	50,656,016	56,823,480
unique_aligned_reads	93,841,724	69,925,596	47,678,806	53,627,064
percent_uniqueAligned	0.83787	0.80330	0.86547	0.83411
correlation_replicates	0.998985	0.990068	0.998985	0.990068
spikein_reads	725,986	172,452	409,054	112,444
percent_spikeins	0.00648	0.00198	0.00743	0.00175
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1140	1415	1141	1416

Data Submission Information

	BGHLV23-1	BGHLV23-1
ENCODE_alias	brenton-graveley:non-target-BGHLV23	brenton-graveley:NT_BGHLV23-B
ENCODE_accession	ENCSR042QTH	ENCSR364GRM
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-1	BGHLV23-1
Sample Name	non-target-BGHLV23-1	NT_BGHLV23-1B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2016-03-03
Project	ENCODE3	ENCODE3

protocol_URL
ID	2947	3086

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-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1140	HiSeq2000	100	paired-ended	1				ENCODE3	16668
NT_BGHLV23-1B_AGTCAA_L007_001.R1.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1415	HiSeq2000	100	paired-ended	1				ENCODE3	16670
non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1140	HiSeq2000	100	paired-ended	2				ENCODE3	16706
NT_BGHLV23-1B_AGTCAA_L007_001.R2.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1415	HiSeq2000	100	paired-ended	2				ENCODE3	16708
non-target-BGHLV23-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1140					GRCh38	V40	non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz	ENCORE2	16744
NT_BGHLV23-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1415					GRCh38	V40	NT_BGHLV23-1B_AGTCAA_L007_001.R1.fastq.gz,NT_BGHLV23-1B_AGTCAA_L007_001.R2.fastq.gz	ENCORE2	16746
non-target-BGHLV23-1_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1140					GRCh38	V40	non-target-BGHLV23-1/Aligned.sortedByCoord.out.bam	ENCORE2	16782
NT_BGHLV23-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1415					GRCh38	V40	NT_BGHLV23-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16784
non-target-BGHLV23-1_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1140					GRCh38	V40	non-target-BGHLV23-1/Aligned.sortedByCoord.out.bam	ENCORE2	16820
NT_BGHLV23-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1415					GRCh38	V40	NT_BGHLV23-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16822
non-target-BGHLV23-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1140					GRCh38	V40	non-target-BGHLV23-1/Aligned.sortedByCoord.out.bam	ENCORE2	16858
NT_BGHLV23-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1415					GRCh38	V40	NT_BGHLV23-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16860
non-target-BGHLV23-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1140					GRCh38	V40	non-target-BGHLV23-1/Aligned.sortedByCoord.out.bam	ENCORE2	16896
NT_BGHLV23-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1415					GRCh38	V40	NT_BGHLV23-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16898
non-target-BGHLV23-1_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1140					GRCh38	V40	non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz	ENCORE2	16934
NT_BGHLV23-1B_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1415					GRCh38	V40	NT_BGHLV23-1B_AGTCAA_L007_001.R1.fastq.gz,NT_BGHLV23-1B_AGTCAA_L007_001.R2.fastq.gz	ENCORE2	16936
non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1141	HiSeq2000	100	paired-ended	1				ENCODE3	16669
NT_BGHLV23-2B_AGTTCC_L007_001.R1.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1416	HiSeq2000	100	paired-ended	1				ENCODE3	16671
non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1141	HiSeq2000	100	paired-ended	2				ENCODE3	16707
NT_BGHLV23-2B_AGTTCC_L007_001.R2.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1416	HiSeq2000	100	paired-ended	2				ENCODE3	16709
non-target-BGHLV23-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1141					GRCh38	V40	non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCORE2	16745
NT_BGHLV23-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1416					GRCh38	V40	NT_BGHLV23-2B_AGTTCC_L007_001.R1.fastq.gz,NT_BGHLV23-2B_AGTTCC_L007_001.R2.fastq.gz	ENCORE2	16747
non-target-BGHLV23-2_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1141					GRCh38	V40	non-target-BGHLV23-2/Aligned.sortedByCoord.out.bam	ENCORE2	16783
NT_BGHLV23-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1416					GRCh38	V40	NT_BGHLV23-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16785
non-target-BGHLV23-2_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1141					GRCh38	V40	non-target-BGHLV23-2/Aligned.sortedByCoord.out.bam	ENCORE2	16821
NT_BGHLV23-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1416					GRCh38	V40	NT_BGHLV23-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16823
non-target-BGHLV23-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1141					GRCh38	V40	non-target-BGHLV23-2/Aligned.sortedByCoord.out.bam	ENCORE2	16859
NT_BGHLV23-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1416					GRCh38	V40	NT_BGHLV23-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16861
non-target-BGHLV23-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1141					GRCh38	V40	non-target-BGHLV23-2/Aligned.sortedByCoord.out.bam	ENCORE2	16897
NT_BGHLV23-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1416					GRCh38	V40	NT_BGHLV23-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16899
non-target-BGHLV23-2_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1141					GRCh38	V40	non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCORE2	16935
NT_BGHLV23-2B_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1416					GRCh38	V40	NT_BGHLV23-2B_AGTTCC_L007_001.R1.fastq.gz,NT_BGHLV23-2B_AGTTCC_L007_001.R2.fastq.gz	ENCORE2	16937