non-target RNA-Seq in HepG2

	BGHLV30-1	BGHLV30-2
idx	685	686
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non target	non target
Sample_ID	BGHLV30-1	BGHLV30-2
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	4636
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	11/5/2015	11/5/2015
repeat_library
Note
ID	2772	2773

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV30-1	BGHLV30-1	BGHLV30-2	BGHLV30-2
Sample_ID	BGHLV30-1	BGHLV30-1	BGHLV30-2	BGHLV30-2
Sample Name	NT_BGHLV30-1	NT_BGHLV30-1B	NT_BGHLV30-2	NT_BGHLV30-2B
Sample Name	NT_BGHLV30-1	NT_BGHLV30-1B	NT_BGHLV30-2	NT_BGHLV30-2B
RBP	non-target	non-target	non-target	non-target
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Released	Released	Released	Released
Status_date	2016-03-04	2016-09-24	2016-03-04	2016-09-24
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note
ID	1064	1189	1065	1190

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-1	BGHLV30-1	BGHLV30-2	BGHLV30-2
Sample #
Sample Name	NT-BGHLV30-1	NT-BGHLV30-1B	NT-BGHLV30-2	NT-BGHLV30-2B
Sample_Name_Alias	NT_BGHLV30-1	NT_BGHLV30-1B	NT_BGHLV30-2	NT_BGHLV30-2B
Index Well Position	S18	S15	S19	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2016-03-10	2015-11-05	2016-03-10
Lib_ID	Lib-151105	Lib-160310	Lib-151105	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A9.png	DNA_Library_LV33-34-25B-32/set2/H2.png	DNA_Library_LV28-29-30/set1/B9.png	DNA_Library_LV33-34-25B-32/set1/B12.png
RIN	10.0	10.0	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A4.png	RNA_Library_LV29-30-31-32/set1/A4.png	RNA_Library_LV29-30-31-32/set1/B4.png	RNA_Library_LV29-30-31-32/set1/B4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-1	BGHLV30-1	BGHLV30-2	BGHLV30-2
RBP	NT	NT	NT	NT
Batch_ID	BGHLV30	BGHLV30	BGHLV30	BGHLV30
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	2756	2874	2757	2875

Sequencing Information

	BGHLV30-1	BGHLV30-1	BGHLV30-2	BGHLV30-2
Sample_ID	BGHLV30-1	BGHLV30-1	BGHLV30-2	BGHLV30-2
Sample Name	NT_BGHLV30-1	NT_BGHLV30-1B	NT_BGHLV30-2	NT_BGHLV30-2B
Pool ID	Pool-151215C	Pool-160425	Pool-151215C	Pool-160425
LocalServer_folder	set30	set30	set30	set30
total_reads	45,137,900	82,817,158	71,940,560	80,828,082
total_aligned_reads	35,535,796	57,798,288	59,675,280	58,282,754
unique_aligned_reads	33,480,268	54,356,434	56,141,062	54,901,516
percent_uniqueAligned	0.74173	0.65634	0.78038	0.67924
correlation_replicates	0.992748	0.996023	0.992748	0.996023
spikein_reads	110,934	121,472	192,594	152,452
percent_spikeins	0.00246	0.00147	0.00268	0.00189
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1364	1523	1365	1524

Data Submission Information

	BGHLV30-1	BGHLV30-1
ENCODE_alias	brenton-graveley:NT_BGHLV30	brenton-graveley:NT_BGHLV30B
ENCODE_accession	ENCSR067GHD	ENCSR776SXA
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-1	BGHLV30-1
Sample Name	NT_BGHLV30-1	NT_BGHLV30-1B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2016-05-25
Project	ENCODE3	ENCODE3

protocol_URL
ID	3081	3134

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_BGHLV30-1B_ATGTCA_L007_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1523	HiSeq2500	100	paired-ended	1				ENCODE3	20722
NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1364	HiSeq2500	100	paired-ended	1				ENCODE3	20723
NT_BGHLV30-1B_ATGTCA_L007_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1523	HiSeq2500	100	paired-ended	2				ENCODE3	20756
NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1364	HiSeq2500	100	paired-ended	2				ENCODE3	20757
NT_BGHLV30-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1523					GRCh38	V40	NT_BGHLV30-1B_ATGTCA_L007_001.R1.fastq.gz,NT_BGHLV30-1B_ATGTCA_L007_001.R2.fastq.gz	ENCORE2	20790
NT_BGHLV30-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1364					GRCh38	V40	NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz	ENCORE2	20791
NT_BGHLV30-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1523					GRCh38	V40	NT_BGHLV30-1B/Aligned.sortedByCoord.out.bam	ENCORE2	20824
NT_BGHLV30-1_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1364					GRCh38	V40	NT_BGHLV30-1/Aligned.sortedByCoord.out.bam	ENCORE2	20825
NT_BGHLV30-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1523					GRCh38	V40	NT_BGHLV30-1B/Aligned.sortedByCoord.out.bam	ENCORE2	20858
NT_BGHLV30-1_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1364					GRCh38	V40	NT_BGHLV30-1/Aligned.sortedByCoord.out.bam	ENCORE2	20859
NT_BGHLV30-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1523					GRCh38	V40	NT_BGHLV30-1B/Aligned.sortedByCoord.out.bam	ENCORE2	20892
NT_BGHLV30-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1364					GRCh38	V40	NT_BGHLV30-1/Aligned.sortedByCoord.out.bam	ENCORE2	20893
NT_BGHLV30-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1523					GRCh38	V40	NT_BGHLV30-1B/Aligned.sortedByCoord.out.bam	ENCORE2	20926
NT_BGHLV30-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1364					GRCh38	V40	NT_BGHLV30-1/Aligned.sortedByCoord.out.bam	ENCORE2	20927
NT_BGHLV30-1B_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1523					GRCh38	V40	NT_BGHLV30-1B_ATGTCA_L007_001.R1.fastq.gz,NT_BGHLV30-1B_ATGTCA_L007_001.R2.fastq.gz	ENCORE2	20960
NT_BGHLV30-1_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1364					GRCh38	V40	NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz	ENCORE2	20961
NT_BGHLV30-2B_CCGTCC_L007_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1524	HiSeq2500	100	paired-ended	1				ENCODE3	20724
NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1365	HiSeq2500	100	paired-ended	1				ENCODE3	20725
NT_BGHLV30-2B_CCGTCC_L007_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1524	HiSeq2500	100	paired-ended	2				ENCODE3	20758
NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1365	HiSeq2500	100	paired-ended	2				ENCODE3	20759
NT_BGHLV30-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1524					GRCh38	V40	NT_BGHLV30-2B_CCGTCC_L007_001.R1.fastq.gz,NT_BGHLV30-2B_CCGTCC_L007_001.R2.fastq.gz	ENCORE2	20792
NT_BGHLV30-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1365					GRCh38	V40	NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCORE2	20793
NT_BGHLV30-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1524					GRCh38	V40	NT_BGHLV30-2B/Aligned.sortedByCoord.out.bam	ENCORE2	20826
NT_BGHLV30-2_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1365					GRCh38	V40	NT_BGHLV30-2/Aligned.sortedByCoord.out.bam	ENCORE2	20827
NT_BGHLV30-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1524					GRCh38	V40	NT_BGHLV30-2B/Aligned.sortedByCoord.out.bam	ENCORE2	20860
NT_BGHLV30-2_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1365					GRCh38	V40	NT_BGHLV30-2/Aligned.sortedByCoord.out.bam	ENCORE2	20861
NT_BGHLV30-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1524					GRCh38	V40	NT_BGHLV30-2B/Aligned.sortedByCoord.out.bam	ENCORE2	20894
NT_BGHLV30-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1365					GRCh38	V40	NT_BGHLV30-2/Aligned.sortedByCoord.out.bam	ENCORE2	20895
NT_BGHLV30-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1524					GRCh38	V40	NT_BGHLV30-2B/Aligned.sortedByCoord.out.bam	ENCORE2	20928
NT_BGHLV30-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1365					GRCh38	V40	NT_BGHLV30-2/Aligned.sortedByCoord.out.bam	ENCORE2	20929
NT_BGHLV30-2B_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1524					GRCh38	V40	NT_BGHLV30-2B_CCGTCC_L007_001.R1.fastq.gz,NT_BGHLV30-2B_CCGTCC_L007_001.R2.fastq.gz	ENCORE2	20962
NT_BGHLV30-2_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1365					GRCh38	V40	NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCORE2	20963