non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHLV31-1 and BGHLV31-2

NT-BGHLV31-1,NT-BGHLV31-2 (alias:NT-BGHLV31-1,NT-BGHLV31-2):

ACO1-BGHLV31-HepG2

NT-BGHLV31-1B,NT-BGHLV31-2B (alias:NT_BGHLV31-1B,NT_BGHLV31-2B):

RBM15-BGHLV31-HepG2

Experiment Information (Status: Released)

	BGHLV31-1	BGHLV31-2
idx	749	750
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non target	non target
Sample_ID	BGHLV31-1	BGHLV31-2
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	4180
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	2/4/2016	2/4/2016
repeat_library
Note
ID	2838	2839

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV31-1	BGHLV31-1	BGHLV31-2	BGHLV31-2
Sample_ID	BGHLV31-1	BGHLV31-1	BGHLV31-2	BGHLV31-2
Sample Name	NT-BGHLV31-1	NT_BGHLV31-1B	NT-BGHLV31-2	NT_BGHLV31-2B
Sample Name	NT-BGHLV31-1	NT_BGHLV31-1B	NT-BGHLV31-2	NT_BGHLV31-2B
RBP	non-target	non-target	non-target	non-target
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Released	Released	Released	Released
Status_date	2016-03-07	2016-09-24	2016-03-07	2016-09-24
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note
ID	1125	1183	1126	1184

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-1	BGHLV31-1	BGHLV31-2	BGHLV31-2
Sample #
Sample Name	NT-BGHLV31-1	NT-BGHLV31-1B	NT-BGHLV31-2	NT-BGHLV31-2B
Sample_Name_Alias	NT-BGHLV31-1	NT_BGHLV31-1B	NT-BGHLV31-2	NT_BGHLV31-2B
Index Well Position	S09	S20	S10	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-03-10	2016-02-04	2016-03-10
Lib_ID	Lib-160204	Lib-160310	Lib-160204	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set2/F9.png	DNA_Library_LV30-25B_31-1B/set1/B1.png	DNA_Library_LV31-21B/set1/B5.png	DNA_Library_LV33-34-25B-32/set1/F12.png
RIN	10.0	10.0	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A8.png	RNA_Library_LV29-30-31-32/set1/A8.png	RNA_Library_LV29-30-31-32/set1/B8.png	RNA_Library_LV29-30-31-32/set1/B8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-1	BGHLV31-1	BGHLV31-2	BGHLV31-2
RBP	NT	NT	NT	NT
Batch_ID	BGHLV31	BGHLV31	BGHLV31	BGHLV31
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	2822	2868	2823	2869

Sequencing Information

	BGHLV31-1	BGHLV31-1	BGHLV31-2	BGHLV31-2
Sample_ID	BGHLV31-1	BGHLV31-1	BGHLV31-2	BGHLV31-2
Sample Name	NT-BGHLV31-1	NT_BGHLV31-1B	NT-BGHLV31-2	NT_BGHLV31-2B
Pool ID	Pool-160229	Pool-160425	Pool-160229	Pool-160425
LocalServer_folder	set31	set31	set31	set31
total_reads	55,657,994	80,146,782	56,498,654	87,098,444
total_aligned_reads	49,325,058	58,250,658	49,869,452	62,062,672
unique_aligned_reads	46,505,000	54,747,484	46,997,462	58,385,586
percent_uniqueAligned	0.83555	0.68309	0.83183	0.67034
correlation_replicates	0.996713	0.997963	0.996713	0.997963
spikein_reads	257,050	141,682	250,554	130,250
percent_spikeins	0.00462	0.00177	0.00443	0.00150
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1471	1517	1472	1518

Data Submission Information

	BGHLV31-1	BGHLV31-1
ENCODE_alias	brenton-graveley:NT-BGHLV31	brenton-graveley:NT_BGHLV31B
ENCODE_accession	ENCSR538QOG	ENCSR585KOJ
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-1	BGHLV31-1
Sample Name	NT-BGHLV31-1	NT_BGHLV31-1B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2016-05-25
Project	ENCODE3	ENCODE3

protocol_URL
ID	3095	3131

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_BGHLV31-1B_GTGGCC_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1517	HiSeq2500	100	paired-ended	1				ENCODE3	21022
NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1471	HiSeq2500	100	paired-ended	1				ENCODE3	21023
NT_BGHLV31-1B_GTGGCC_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1517	HiSeq2500	100	paired-ended	2				ENCODE3	21026
NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1471	HiSeq2500	100	paired-ended	2				ENCODE3	21027
NT_BGHLV31-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1517					GRCh38	V40	NT_BGHLV31-1B_GTGGCC_L007_001.R1.fastq.gz,NT_BGHLV31-1B_GTGGCC_L007_001.R2.fastq.gz	ENCORE2	21046
NT-BGHLV31-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1471					GRCh38	V40	NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz	ENCORE2	21047
NT_BGHLV31-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1517					GRCh38	V40	NT_BGHLV31-1B/Aligned.sortedByCoord.out.bam	ENCORE2	21072
NT-BGHLV31-1_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1471					GRCh38	V40	NT-BGHLV31-1/Aligned.sortedByCoord.out.bam	ENCORE2	21073
NT_BGHLV31-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1517					GRCh38	V40	NT_BGHLV31-1B/Aligned.sortedByCoord.out.bam	ENCORE2	21098
NT-BGHLV31-1_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1471					GRCh38	V40	NT-BGHLV31-1/Aligned.sortedByCoord.out.bam	ENCORE2	21099
NT_BGHLV31-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1517					GRCh38	V40	NT_BGHLV31-1B/Aligned.sortedByCoord.out.bam	ENCORE2	21124
NT-BGHLV31-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1471					GRCh38	V40	NT-BGHLV31-1/Aligned.sortedByCoord.out.bam	ENCORE2	21125
NT_BGHLV31-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1517					GRCh38	V40	NT_BGHLV31-1B/Aligned.sortedByCoord.out.bam	ENCORE2	21150
NT-BGHLV31-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1471					GRCh38	V40	NT-BGHLV31-1/Aligned.sortedByCoord.out.bam	ENCORE2	21151
NT_BGHLV31-1B_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1517					GRCh38	V40	NT_BGHLV31-1B_GTGGCC_L007_001.R1.fastq.gz,NT_BGHLV31-1B_GTGGCC_L007_001.R2.fastq.gz	ENCORE2	21176
NT-BGHLV31-1_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1471					GRCh38	V40	NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz	ENCORE2	21177
NT_BGHLV31-2B_GTTTCG_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1518	HiSeq2500	100	paired-ended	1				ENCODE3	21024
NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1472	HiSeq2500	100	paired-ended	1				ENCODE3	21025
NT_BGHLV31-2B_GTTTCG_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1518	HiSeq2500	100	paired-ended	2				ENCODE3	21028
NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1472	HiSeq2500	100	paired-ended	2				ENCODE3	21029
NT_BGHLV31-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1518					GRCh38	V40	NT_BGHLV31-2B_GTTTCG_L007_001.R1.fastq.gz,NT_BGHLV31-2B_GTTTCG_L007_001.R2.fastq.gz	ENCORE2	21048
NT-BGHLV31-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1472					GRCh38	V40	NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCORE2	21049
NT_BGHLV31-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1518					GRCh38	V40	NT_BGHLV31-2B/Aligned.sortedByCoord.out.bam	ENCORE2	21074
NT-BGHLV31-2_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1472					GRCh38	V40	NT-BGHLV31-2/Aligned.sortedByCoord.out.bam	ENCORE2	21075
NT_BGHLV31-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1518					GRCh38	V40	NT_BGHLV31-2B/Aligned.sortedByCoord.out.bam	ENCORE2	21100
NT-BGHLV31-2_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1472					GRCh38	V40	NT-BGHLV31-2/Aligned.sortedByCoord.out.bam	ENCORE2	21101
NT_BGHLV31-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1518					GRCh38	V40	NT_BGHLV31-2B/Aligned.sortedByCoord.out.bam	ENCORE2	21126
NT-BGHLV31-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1472					GRCh38	V40	NT-BGHLV31-2/Aligned.sortedByCoord.out.bam	ENCORE2	21127
NT_BGHLV31-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1518					GRCh38	V40	NT_BGHLV31-2B/Aligned.sortedByCoord.out.bam	ENCORE2	21152
NT-BGHLV31-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1472					GRCh38	V40	NT-BGHLV31-2/Aligned.sortedByCoord.out.bam	ENCORE2	21153
NT_BGHLV31-2B_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1518					GRCh38	V40	NT_BGHLV31-2B_GTTTCG_L007_001.R1.fastq.gz,NT_BGHLV31-2B_GTTTCG_L007_001.R2.fastq.gz	ENCORE2	21178
NT-BGHLV31-2_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1472					GRCh38	V40	NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCORE2	21179