SBDS RNA-Seq in HepG2

General Information


RBP	SBDS
Cell_Line	HepG2
Method	shRNA
Exp_Name	SBDS-BGHLV22-HepG2
ENCODE_series_ID	ENCSR371FFJ
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR343DHN
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	SBDS-BGHLV22-47
Rep2	SBDS-BGHLV22-48
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	73.6
Rep2_qPCR	84.6
Rep1_WB	62.2
Rep2_WB	60.0
Antibody Cat#	GTX109168
Antibody Lot#	GTX109168
Antibody DCC ID	ENCAB894TLT
Status	Released
Project	ENCODE3
ID	529

Experiment Information (Status: Released)

	BGHLV22-47	BGHLV22-48
idx	475	476
TRCN#_or_BGC#	TRCN0000119047	TRCN0000119047
shRNA_or_gRNA_sequence	GCCAAATACTTGCTTAAACTA	GCCAAATACTTGCTTAAACTA
PAM
Name	SBDS	SBDS
Sample_ID	BGHLV22-47	BGHLV22-48
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	SBDS	SBDS
qPCR_result	73.6	84.6
Ave_qPCR	79.1
RT-qPCR_primer-F	aacagcaggctttggaagtg
RT-qPCR_primer-R	gatgaaccgaagcctcatgt
protein_conc	6410	6321
WB_result	62.2	60.0
Ave_WB	61.1
WB_DONE_date	5/4/2015
MW
IP	1	1
antibody_Cat#	GTX109168	GTX109168
Antibody DCC ID	ENCAB894TLT	ENCAB894TLT
submitted_to_DCC_date	5/6/2015
Rep1_TPM	67.3	0
Rep2_TPM	73.3	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2554	2555

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SBDS	Product_ID: GTX109168 Lot_ID: 40023 Source: GeneTex Target Name: SBDS-human

Experiment Status

	BGHLV22-47	BGHLV22-48
Sample_ID	BGHLV22-47	BGHLV22-48
Sample Name	SBDS-BGHLV22-47	SBDS-BGHLV22-48
Sample Name	SBDS-BGHLV22-47	SBDS-BGHLV22-48
RBP	SBDS	SBDS
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	808	809

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-47	BGHLV22-48
Sample #
Sample Name	SBDS-BGHLV22-47	SBDS-BGHLV22-48
Sample_Name_Alias	SBDS-BGHLV22-47	SBDS-BGHLV22-48
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/G9.png	DNA_Library_LV20-22-23/set1/H9.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G3.png	RNA_Library_LV22-23-25/set1/H3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-47	BGHLV22-48
RBP	SBDS	SBDS
Batch_ID	BGHLV22	BGHLV22
WB_result	62.200	60.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2494	2495

Sequencing Information

	BGHLV22-47	BGHLV22-48
Sample_ID	BGHLV22-47	BGHLV22-48
Sample Name	SBDS-BGHLV22-47	SBDS-BGHLV22-48
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	56,180,000	54,990,000
total_aligned_reads	51,468,126	49,699,256
unique_aligned_reads	48,384,570	46,609,466
percent_uniqueAligned	0.86124	0.84760
correlation_replicates	0.987733	0.987733
spikein_reads	286,508	337,494
percent_spikeins	0.00510	0.00614
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1116	1117

Data Submission Information

	BGHLV22-47	BGHLV22-47
ENCODE_alias	brenton-graveley:SBDS-BGHLV22	brenton-graveley:SBDS-BGHLV22-HepG2
ENCODE_accession	ENCSR343DHN	ENCSR371FFJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-47	BGHLV22-47
Sample Name	SBDS-BGHLV22-47	SBDS-BGHLV22-47
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2936	6932

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	controlled_by	Project	FILE_ID
SBDS-BGHLV22-47_CAGATC_L003_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1116	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16306
SBDS-BGHLV22-47_CAGATC_L003_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1116	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16346
SBDS-BGHLV22-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1116					GRCh38	V40	SBDS-BGHLV22-47_CAGATC_L003_R1_001.fastq.gz,SBDS-BGHLV22-47_CAGATC_L003_R2_001.fastq.gz		ENCORE2	16444
SBDS-BGHLV22-47_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	1116					GRCh38	V40	SBDS-BGHLV22-47/Aligned.sortedByCoord.out.bam		ENCORE2	16484
SBDS-BGHLV22-47_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	1116					GRCh38	V40	SBDS-BGHLV22-47/Aligned.sortedByCoord.out.bam		ENCORE2	16524
SBDS-BGHLV22-47_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	1116					GRCh38	V40	SBDS-BGHLV22-47/Aligned.sortedByCoord.out.bam		ENCORE2	16564
SBDS-BGHLV22-47_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	1116					GRCh38	V40	SBDS-BGHLV22-47/Aligned.sortedByCoord.out.bam		ENCORE2	16604
SBDS-BGHLV22-47_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1116					GRCh38	V40	SBDS-BGHLV22-47_CAGATC_L003_R1_001.fastq.gz,SBDS-BGHLV22-47_CAGATC_L003_R2_001.fastq.gz		ENCORE2	16644
SBDS-BGHLV22-48_ACTTGA_L003_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1117	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16307
SBDS-BGHLV22-48_ACTTGA_L003_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1117	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16347
SBDS-BGHLV22-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1117					GRCh38	V40	SBDS-BGHLV22-48_ACTTGA_L003_R1_001.fastq.gz,SBDS-BGHLV22-48_ACTTGA_L003_R2_001.fastq.gz		ENCORE2	16445
SBDS-BGHLV22-48_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	1117					GRCh38	V40	SBDS-BGHLV22-48/Aligned.sortedByCoord.out.bam		ENCORE2	16485
SBDS-BGHLV22-48_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	1117					GRCh38	V40	SBDS-BGHLV22-48/Aligned.sortedByCoord.out.bam		ENCORE2	16525
SBDS-BGHLV22-48_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	1117					GRCh38	V40	SBDS-BGHLV22-48/Aligned.sortedByCoord.out.bam		ENCORE2	16565
SBDS-BGHLV22-48_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	1117					GRCh38	V40	SBDS-BGHLV22-48/Aligned.sortedByCoord.out.bam		ENCORE2	16605
SBDS-BGHLV22-48_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1117					GRCh38	V40	SBDS-BGHLV22-48_ACTTGA_L003_R1_001.fastq.gz,SBDS-BGHLV22-48_ACTTGA_L003_R2_001.fastq.gz		ENCORE2	16645