SLBP RNA-Seq in HepG2

General Information


RBP	SLBP
Cell_Line	HepG2
Method	shRNA
Exp_Name	SLBP-BGHLV23-HepG2
ENCODE_series_ID	ENCSR239VHY
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR519KXM
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	SLBP-BGHLV23-41
Rep2	SLBP-BGHLV23-42
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	87.9
Rep2_qPCR	86.9
Rep1_WB	89.2
Rep2_WB	93.8
Antibody Cat#	RN045P
Antibody Lot#	RN045P
Antibody DCC ID	ENCAB000BGB
Status	Released
Project	ENCODE3
ID	550

Experiment Information (Status: Released)

	BGHLV23-41	BGHLV23-42
idx	533	534
TRCN#_or_BGC#	TRCN0000106680	TRCN0000106680
shRNA_or_gRNA_sequence	CCAGCGAGCTTAATTGCGTAA	CCAGCGAGCTTAATTGCGTAA
PAM
Name	SLBP	SLBP
Sample_ID	BGHLV23-41	BGHLV23-42
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	SLBP	SLBP
qPCR_result	87.9	86.9
Ave_qPCR	87.4
RT-qPCR_primer-F	AGACCTTGAATCTGCAGAAAGC
RT-qPCR_primer-R	ACTGTCCATGTGTCTCACCTTG
protein_conc	6014	6700
WB_result	89.2	93.8
Ave_WB	91.5
WB_DONE_date	5/11/2015
MW	32kDa
IP	1	1
antibody_Cat#	RN045P	RN045P
Antibody DCC ID	ENCAB000BGB	ENCAB000BGB
submitted_to_DCC_date	8/6/2015
Rep1_TPM	24.6	0
Rep2_TPM	20.7	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2614	2615

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SLBP	Product_ID: RN045P Lot_ID: 1 Source: MBLI Target Name: SLBP-human

Experiment Status

	BGHLV23-41	BGHLV23-42
Sample_ID	BGHLV23-41	BGHLV23-42
Sample Name	SLBP-BGHLV23-41	SLBP-BGHLV23-42
Sample Name	SLBP-BGHLV23-41	SLBP-BGHLV23-42
RBP	SLBP	SLBP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	838	839

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-41	BGHLV23-42
Sample #
Sample Name	SLBP-BGHLV23-41	SLBP-BGHLV23-42
Sample_Name_Alias	SLBP-BGHLV23-41	SLBP-BGHLV23-42
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set4/C2.png	DNA_Library_LV20-22-23/set4/D2.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G7.png	RNA_Library_LV22-23-25/set1/H7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-41	BGHLV23-42
RBP	SLBP	SLBP
Batch_ID	BGHLV23	BGHLV23
WB_result	89.200	93.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2526	2527

Sequencing Information

	BGHLV23-41	BGHLV23-42
Sample_ID	BGHLV23-41	BGHLV23-42
Sample Name	SLBP-BGHLV23-41	SLBP-BGHLV23-42
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	57,390,000	59,850,000
total_aligned_reads	52,207,922	54,568,828
unique_aligned_reads	49,247,192	51,455,126
percent_uniqueAligned	0.85811	0.85973
correlation_replicates	0.999076	0.999076
spikein_reads	302,290	309,606
percent_spikeins	0.00527	0.00517
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1148	1149

Data Submission Information

	BGHLV23-41	BGHLV23-41
ENCODE_alias	brenton-graveley:SLBP-BGHLV23	brenton-graveley:SLBP-BGHLV23-HepG2
ENCODE_accession	ENCSR519KXM	ENCSR239VHY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-41	BGHLV23-41
Sample Name	SLBP-BGHLV23-41	SLBP-BGHLV23-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2951	6948

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
SLBP-BGHLV23-41_GTGGCC_L007_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1148	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16678
SLBP-BGHLV23-41_GTGGCC_L007_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1148	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16716
SLBP-BGHLV23-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1148					GRCh38	V40	SLBP-BGHLV23-41_GTGGCC_L007_R1_001.fastq.gz,SLBP-BGHLV23-41_GTGGCC_L007_R2_001.fastq.gz		ENCORE2	16754
SLBP-BGHLV23-41_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1148					GRCh38	V40	SLBP-BGHLV23-41/Aligned.sortedByCoord.out.bam		ENCORE2	16792
SLBP-BGHLV23-41_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1148					GRCh38	V40	SLBP-BGHLV23-41/Aligned.sortedByCoord.out.bam		ENCORE2	16830
SLBP-BGHLV23-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1148					GRCh38	V40	SLBP-BGHLV23-41/Aligned.sortedByCoord.out.bam		ENCORE2	16868
SLBP-BGHLV23-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1148					GRCh38	V40	SLBP-BGHLV23-41/Aligned.sortedByCoord.out.bam		ENCORE2	16906
SLBP-BGHLV23-41_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1148					GRCh38	V40	SLBP-BGHLV23-41_GTGGCC_L007_R1_001.fastq.gz,SLBP-BGHLV23-41_GTGGCC_L007_R2_001.fastq.gz		ENCORE2	16944
SLBP-BGHLV23-42_GTTTCG_L007_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1149	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16679
SLBP-BGHLV23-42_GTTTCG_L007_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1149	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16717
SLBP-BGHLV23-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1149					GRCh38	V40	SLBP-BGHLV23-42_GTTTCG_L007_R1_001.fastq.gz,SLBP-BGHLV23-42_GTTTCG_L007_R2_001.fastq.gz		ENCORE2	16755
SLBP-BGHLV23-42_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1149					GRCh38	V40	SLBP-BGHLV23-42/Aligned.sortedByCoord.out.bam		ENCORE2	16793
SLBP-BGHLV23-42_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1149					GRCh38	V40	SLBP-BGHLV23-42/Aligned.sortedByCoord.out.bam		ENCORE2	16831
SLBP-BGHLV23-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1149					GRCh38	V40	SLBP-BGHLV23-42/Aligned.sortedByCoord.out.bam		ENCORE2	16869
SLBP-BGHLV23-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1149					GRCh38	V40	SLBP-BGHLV23-42/Aligned.sortedByCoord.out.bam		ENCORE2	16907
SLBP-BGHLV23-42_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1149					GRCh38	V40	SLBP-BGHLV23-42_GTTTCG_L007_R1_001.fastq.gz,SLBP-BGHLV23-42_GTTTCG_L007_R2_001.fastq.gz		ENCORE2	16945