non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHcLV03-1 and BGHcLV03-2

NT-BGHcLV03-1,NT-BGHcLV03-2 (alias:NT_BGHcLV03-1,NT_BGHcLV03-2):

DDX21-BGHcLV03-HepG2

DEAF1-BGHcLV03-HepG2

DGCR8-BGHcLV03-HepG2

HNRNPF-BGHcLV03-HepG2

IGF2BP1-BGHcLV03-HepG2

NFX1-BGHcLV03-HepG2

RPLP0-BGHcLV03-HepG2

SRSF7-BGHcLV03-HepG2

Experiment Information (Status: Released)

	BGHcLV03-1	BGHcLV03-2
idx	1	2
TRCN#_or_BGC#	BGC#0000000	BGC#0000000
shRNA_or_gRNA_sequence	CAGTCGGGCGTCATCATGAT	CAGTCGGGCGTCATCATGAT
PAM
Name	non -target	non -target
Sample_ID	BGHcLV03-1	BGHcLV03-2
transduction_Date	12/16/2015	12/16/2015
days	D6	D6
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	2575
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	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	6142	6143

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV03-1	BGHcLV03-2
Sample_ID	BGHcLV03-1	BGHcLV03-2
Sample Name	NT_BGHcLV03-1	NT_BGHcLV03-2
Sample Name	NT_BGHcLV03-1	NT_BGHcLV03-2
RBP	non-target	non-target
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1103	1104

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV03-1	BGHcLV03-2
Sample #
Sample Name	NT-BGHcLV03-1	NT-BGHcLV03-2
Sample_Name_Alias	NT_BGHcLV03-1	NT_BGHcLV03-2
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/A1.png	DNA_Library_cLV02/set1/B1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_cLV02/set1/C2.png	RNA_Library_cLV02/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV03-1	BGHcLV03-2
RBP	NT	NT
Batch_ID	BGHcLV03	BGHcLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2800	2801

Sequencing Information

	BGHcLV03-1	BGHcLV03-2
Sample_ID	BGHcLV03-1	BGHcLV03-2
Sample Name	NT_BGHcLV03-1	NT_BGHcLV03-2
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGHcLV03	BGHcLV03
total_reads	43,857,540	94,762,382
total_aligned_reads	38,947,794	85,402,452
unique_aligned_reads	36,607,208	80,109,956
percent_uniqueAligned	0.83468	0.84538
correlation_replicates	0.992810	0.992810
spikein_reads	76,714	163,840
percent_spikeins	0.00175	0.00173
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1449	1450

Data Submission Information

	BGHcLV03-1
ENCODE_alias	brenton-graveley:NT_BGHcLV03
ENCODE_accession	ENCSR105NML
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHcLV03-1
Sample Name	NT_BGHcLV03-1
Selected	Yes
Status	Released
Status_Date	2016-03-08
Project	ENCODE3

protocol_URL
ID	3113

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_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1449	HiSeq2500	100	paired-ended	1				ENCODE3	22922
NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1449	HiSeq2500	100	paired-ended	2				ENCODE3	22940
NT_BGHcLV03-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1449					GRCh38	V40	NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz	ENCORE2	22958
NT_BGHcLV03-1_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1449					GRCh38	V40	NT_BGHcLV03-1/Aligned.sortedByCoord.out.bam	ENCORE2	22976
NT_BGHcLV03-1_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1449					GRCh38	V40	NT_BGHcLV03-1/Aligned.sortedByCoord.out.bam	ENCORE2	22994
NT_BGHcLV03-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1449					GRCh38	V40	NT_BGHcLV03-1/Aligned.sortedByCoord.out.bam	ENCORE2	23012
NT_BGHcLV03-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1449					GRCh38	V40	NT_BGHcLV03-1/Aligned.sortedByCoord.out.bam	ENCORE2	23030
NT_BGHcLV03-1_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1449					GRCh38	V40	NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz	ENCORE2	23048
NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1450	HiSeq2500	100	paired-ended	1				ENCODE3	22923
NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1450	HiSeq2500	100	paired-ended	2				ENCODE3	22941
NT_BGHcLV03-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1450					GRCh38	V40	NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCORE2	22959
NT_BGHcLV03-2_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1450					GRCh38	V40	NT_BGHcLV03-2/Aligned.sortedByCoord.out.bam	ENCORE2	22977
NT_BGHcLV03-2_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1450					GRCh38	V40	NT_BGHcLV03-2/Aligned.sortedByCoord.out.bam	ENCORE2	22995
NT_BGHcLV03-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1450					GRCh38	V40	NT_BGHcLV03-2/Aligned.sortedByCoord.out.bam	ENCORE2	23013
NT_BGHcLV03-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1450					GRCh38	V40	NT_BGHcLV03-2/Aligned.sortedByCoord.out.bam	ENCORE2	23031
NT_BGHcLV03-2_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1450					GRCh38	V40	NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCORE2	23049