non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHLV26-1 and BGHLV26-2

NT-BGHLV26-1,NT-BGHLV26-2 (alias:non-target_BGHLV26-1,non-target_BGHLV26-2):

HNRNPUL1-BGHLV26-HepG2

SNRNP200-BGHLV26-HepG2

U2AF2-BGHLV26-HepG2

Experiment Information (Status: Released)

	BGHLV26-1	BGHLV26-2
idx	555	556
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non target	non target
Sample_ID	BGHLV26-1	BGHLV26-2
transduction_Date	5/25/2015	5/25/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	3777
WB_result	5494.3
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	9/8/2015	9/8/2015
repeat_library
Note
ID	2636	2637

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV26-1	BGHLV26-2
Sample_ID	BGHLV26-1	BGHLV26-2
Sample Name	non-target_BGHLV26-1	non-target_BGHLV26-2
Sample Name	non-target_BGHLV26-1	non-target_BGHLV26-2
RBP	non-target	non-target
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	942	943

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-1	BGHLV26-2
Sample #
Sample Name	NT-BGHLV26-1	NT-BGHLV26-2
Sample_Name_Alias	non-target_BGHLV26-1	non-target_BGHLV26-2
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-08	2015-09-08
Lib_ID	Lib-150908	Lib-150908
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/A8.png	DNA_Library_LV24-25-26/set1/B8.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV25-26/set1/C1.png	RNA_Library_LV25-26/set1/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-1	BGHLV26-2
RBP	NT	NT
Batch_ID	BGHLV26	BGHLV26
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2630	2631

Sequencing Information

	BGHLV26-1	BGHLV26-2
Sample_ID	BGHLV26-1	BGHLV26-2
Sample Name	non-target_BGHLV26-1	non-target_BGHLV26-2
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	54,289,294	62,190,962
total_aligned_reads	43,276,740	51,791,104
unique_aligned_reads	40,153,388	48,307,038
percent_uniqueAligned	0.73962	0.77675
correlation_replicates	0.977886	0.977886
spikein_reads	176,494	133,260
percent_spikeins	0.00325	0.00214
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1272	1273

Data Submission Information

	BGHLV26-1
ENCODE_alias	brenton-graveley:non-target_BGHLV26
ENCODE_accession	ENCSR104ABF
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV26-1
Sample Name	non-target_BGHLV26-1
Selected	Yes
Status	Released
Status_Date	2016-01-14
Project	ENCODE3

protocol_URL
ID	3018

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_BGHLV26-1_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1272	HiSeq2500	100	paired-ended	1				ENCODE3	19816
non-target_BGHLV26-1_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1272	HiSeq2500	100	paired-ended	2				ENCODE3	19838
non-target_BGHLV26-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1272					GRCh38	V40	non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-1_2.fastq.gz	ENCORE2	19860
non-target_BGHLV26-1_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1272					GRCh38	V40	non-target_BGHLV26-1/Aligned.sortedByCoord.out.bam	ENCORE2	19882
non-target_BGHLV26-1_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1272					GRCh38	V40	non-target_BGHLV26-1/Aligned.sortedByCoord.out.bam	ENCORE2	19904
non-target_BGHLV26-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1272					GRCh38	V40	non-target_BGHLV26-1/Aligned.sortedByCoord.out.bam	ENCORE2	19926
non-target_BGHLV26-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1272					GRCh38	V40	non-target_BGHLV26-1/Aligned.sortedByCoord.out.bam	ENCORE2	19948
non-target_BGHLV26-1_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1272					GRCh38	V40	non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-1_2.fastq.gz	ENCORE2	20656
non-target_BGHLV26-2_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1273	HiSeq2500	100	paired-ended	1				ENCODE3	19817
non-target_BGHLV26-2_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1273	HiSeq2500	100	paired-ended	2				ENCODE3	19839
non-target_BGHLV26-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1273					GRCh38	V40	non-target_BGHLV26-2_1.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCORE2	19861
non-target_BGHLV26-2_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1273					GRCh38	V40	non-target_BGHLV26-2/Aligned.sortedByCoord.out.bam	ENCORE2	19883
non-target_BGHLV26-2_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1273					GRCh38	V40	non-target_BGHLV26-2/Aligned.sortedByCoord.out.bam	ENCORE2	19905
non-target_BGHLV26-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1273					GRCh38	V40	non-target_BGHLV26-2/Aligned.sortedByCoord.out.bam	ENCORE2	19927
non-target_BGHLV26-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1273					GRCh38	V40	non-target_BGHLV26-2/Aligned.sortedByCoord.out.bam	ENCORE2	19949
non-target_BGHLV26-2_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1273					GRCh38	V40	non-target_BGHLV26-2_1.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCORE2	20657