non-target RNA-Seq in HepG2

	BGHLV22-1	BGHLV22-2
idx	429	430
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non target	non target
Sample_ID	BGHLV22-1	BGHLV22-2
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	6488	0
WB_result	5989.5
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	6/5/2015	6/5/2015
repeat_library
Note
ID	2496	2497

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV22-1	BGHLV22-1	BGHLV22-2	BGHLV22-2
Sample_ID	BGHLV22-1	BGHLV22-1	BGHLV22-2	BGHLV22-2
Sample Name	non-target-BGHLV22-1_17746	NT_BGHLV22-1B	non-target-BGHLV22-2_17747	NT_BGHLV22-2B
Sample Name	non-target-BGHLV22-1_17746	NT_BGHLV22-1B	non-target-BGHLV22-2_17747	NT_BGHLV22-2B
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	2016-09-24	2015-08-13	2016-09-24
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note
ID	796	1209	797	1210

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-1	BGHLV22-1	BGHLV22-2	BGHLV22-2
Sample #
Sample Name	NT-BGHLV22-1	NT-BGHLV22-1B	NT-BGHLV22-2	NT-BGHLV22-2B
Sample_Name_Alias	non-target-BGHLV22-1_17746	NT_BGHLV22-1B	non-target-BGHLV22-2_17747	NT_BGHLV22-2B
Index Well Position	S01	S25	S02	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2016-03-10	2015-06-05	2016-03-10
Lib_ID	Lib-150605	Lib-160310	Lib-150605	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/A6.png	DNA_Library_LV33-34-25B-32/set2/C2.png	DNA_Library_LV20-22-23/set1/B6.png	DNA_Library_LV34_2-28/set2/D1.png
RIN	9.8	9.8	9.9	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G11.png	RNA_Library_LV20-22-24/set1/G11.png	RNA_Library_LV20-22-24/set1/H11.png	RNA_Library_LV20-22-24/set1/H11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-1	BGHLV22-1	BGHLV22-2	BGHLV22-2
RBP	NT	NT	NT	NT
Batch_ID	BGHLV22	BGHLV22	BGHLV22	BGHLV22
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	2482	2886	2483	2887

Sequencing Information

	BGHLV22-1	BGHLV22-1	BGHLV22-2	BGHLV22-2
Sample_ID	BGHLV22-1	BGHLV22-1	BGHLV22-2	BGHLV22-2
Sample Name	non-target-BGHLV22-1_17746	NT_BGHLV22-1B	non-target-BGHLV22-2_17747	NT_BGHLV22-2B
Pool ID	Pool-150705	Pool-160425	Pool-150705	Pool-160425
LocalServer_folder	set22	set22	set22	set22
total_reads	45,610,000	83,330,410	46,130,000	91,435,638
total_aligned_reads	42,256,200	67,091,016	42,335,090	71,663,182
unique_aligned_reads	39,824,716	62,916,310	39,852,406	67,069,098
percent_uniqueAligned	0.87316	0.75502	0.86392	0.73351
correlation_replicates	0.990847	0.997882	0.990847	0.997882
spikein_reads	263,640	159,700	245,678	181,914
percent_spikeins	0.00578	0.00192	0.00533	0.00199
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1212	1535	1213	1536

Data Submission Information

	BGHLV22-1	BGHLV22-1
ENCODE_alias	brenton-graveley:non-target-BGHLV22	brenton-graveley:NT_BGHLV22B
ENCODE_accession	ENCSR279HMU	ENCSR968BBQ
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-1	BGHLV22-1
Sample Name	non-target-BGHLV22-1_17746	NT_BGHLV22-1B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2016-05-25
Project	ENCODE3	ENCODE3

protocol_URL
ID	2930	3144

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-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1212	HiSeq2000	100	paired-ended	1				ENCODE3	16292
NT_BGHLV22-1B_ACTGAT_L005_001.R1.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1535	HiSeq2000	100	paired-ended	1				ENCODE3	16294
non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1212	HiSeq2000	100	paired-ended	2				ENCODE3	16332
NT_BGHLV22-1B_ACTGAT_L005_001.R2.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1535	HiSeq2000	100	paired-ended	2				ENCODE3	16334
non-target-BGHLV22-1_17746_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1212					GRCh38	V40	non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz	ENCORE2	16430
NT_BGHLV22-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1535					GRCh38	V40	NT_BGHLV22-1B_ACTGAT_L005_001.R1.fastq.gz,NT_BGHLV22-1B_ACTGAT_L005_001.R2.fastq.gz	ENCORE2	16432
non-target-BGHLV22-1_17746_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1212					GRCh38	V40	non-target-BGHLV22-1_17746/Aligned.sortedByCoord.out.bam	ENCORE2	16470
NT_BGHLV22-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1535					GRCh38	V40	NT_BGHLV22-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16472
non-target-BGHLV22-1_17746_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1212					GRCh38	V40	non-target-BGHLV22-1_17746/Aligned.sortedByCoord.out.bam	ENCORE2	16510
NT_BGHLV22-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1535					GRCh38	V40	NT_BGHLV22-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16512
non-target-BGHLV22-1_17746_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1212					GRCh38	V40	non-target-BGHLV22-1_17746/Aligned.sortedByCoord.out.bam	ENCORE2	16550
NT_BGHLV22-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1535					GRCh38	V40	NT_BGHLV22-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16552
non-target-BGHLV22-1_17746_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1212					GRCh38	V40	non-target-BGHLV22-1_17746/Aligned.sortedByCoord.out.bam	ENCORE2	16590
NT_BGHLV22-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1535					GRCh38	V40	NT_BGHLV22-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16592
non-target-BGHLV22-1_17746_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1212					GRCh38	V40	non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz	ENCORE2	16630
NT_BGHLV22-1B_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1535					GRCh38	V40	NT_BGHLV22-1B_ACTGAT_L005_001.R1.fastq.gz,NT_BGHLV22-1B_ACTGAT_L005_001.R2.fastq.gz	ENCORE2	16632
non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1213	HiSeq2000	100	paired-ended	1				ENCODE3	16293
NT_BGHLV22-2B_ATTCCT_L005_001.R1.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1536	HiSeq2000	100	paired-ended	1				ENCODE3	16295
non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1213	HiSeq2000	100	paired-ended	2				ENCODE3	16333
NT_BGHLV22-2B_ATTCCT_L005_001.R2.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1536	HiSeq2000	100	paired-ended	2				ENCODE3	16335
non-target-BGHLV22-2_17747_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1213					GRCh38	V40	non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCORE2	16431
NT_BGHLV22-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1536					GRCh38	V40	NT_BGHLV22-2B_ATTCCT_L005_001.R1.fastq.gz,NT_BGHLV22-2B_ATTCCT_L005_001.R2.fastq.gz	ENCORE2	16433
non-target-BGHLV22-2_17747_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1213					GRCh38	V40	non-target-BGHLV22-2_17747/Aligned.sortedByCoord.out.bam	ENCORE2	16471
NT_BGHLV22-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1536					GRCh38	V40	NT_BGHLV22-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16473
non-target-BGHLV22-2_17747_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1213					GRCh38	V40	non-target-BGHLV22-2_17747/Aligned.sortedByCoord.out.bam	ENCORE2	16511
NT_BGHLV22-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1536					GRCh38	V40	NT_BGHLV22-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16513
non-target-BGHLV22-2_17747_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1213					GRCh38	V40	non-target-BGHLV22-2_17747/Aligned.sortedByCoord.out.bam	ENCORE2	16551
NT_BGHLV22-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1536					GRCh38	V40	NT_BGHLV22-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16553
non-target-BGHLV22-2_17747_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1213					GRCh38	V40	non-target-BGHLV22-2_17747/Aligned.sortedByCoord.out.bam	ENCORE2	16591
NT_BGHLV22-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1536					GRCh38	V40	NT_BGHLV22-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16593
non-target-BGHLV22-2_17747_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1213					GRCh38	V40	non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCORE2	16631
NT_BGHLV22-2B_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1536					GRCh38	V40	NT_BGHLV22-2B_ATTCCT_L005_001.R1.fastq.gz,NT_BGHLV22-2B_ATTCCT_L005_001.R2.fastq.gz	ENCORE2	16633