SART3 RNA-Seq in HepG2

General Information


RBP	SART3
Cell_Line	HepG2
Method	shRNA
Exp_Name	SART3-BGHLV22-HepG2
ENCODE_series_ID	ENCSR812YDZ
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR011BBS
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	SART3-BGHLV22-45
Rep2	SART3-BGHLV22-46
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	68.9
Rep2_qPCR	71.6
Rep1_WB	91.8
Rep2_WB	92.2
Antibody Cat#	GTX107684
Antibody Lot#	GTX107684
Antibody DCC ID	ENCAB956GLA
Status	Released
Project	ENCODE3
ID	528

Experiment Information (Status: Released)

	BGHLV22-45	BGHLV22-45	BGHLV22-45	BGHLV22-46	BGHLV22-46	BGHLV22-46
idx	473	473	473	474	474	474
TRCN#_or_BGC#	TRCN0000148806	TRCN0000148806	TRCN0000148806	TRCN0000148806	TRCN0000148806	TRCN0000148806
shRNA_or_gRNA_sequence	CGTTTCAATGAGAGTGGTGAT	CGTTTCAATGAGAGTGGTGAT	CGTTTCAATGAGAGTGGTGAT	CGTTTCAATGAGAGTGGTGAT	CGTTTCAATGAGAGTGGTGAT	CGTTTCAATGAGAGTGGTGAT
PAM
Name	SART3	SART3	SART3	SART3	SART3	SART3
Sample_ID	BGHLV22-45	BGHLV22-45	BGHLV22-45	BGHLV22-46	BGHLV22-46	BGHLV22-46
transduction_Date	10/16/2014	10/16/2014	10/16/2014	10/16/2014	10/16/2014	10/16/2014
days
RBP_name	SART3	SART3	SART3	SART3	SART3	SART3
qPCR_result	68.9	68.9	68.9	71.6	71.6	71.6
Ave_qPCR	70.2	70.2	70.2
RT-qPCR_primer-F	acccgattagctcgtgtcaa	acccgattagctcgtgtcaa	acccgattagctcgtgtcaa
RT-qPCR_primer-R	gctcttttccgttgttcagc	gctcttttccgttgttcagc	gctcttttccgttgttcagc
protein_conc	6426	6426	6426	6695	6695	6695
WB_result	91.8	74.4	91.3	92.2	81.2	89.2
Ave_WB	92.0	77.8	90.2
WB_DONE_date	5/11/2015	6/13/2022	6/16/2022
MW	110kDa	110kDa	110kDa
IP	1			1
antibody_Cat#	GTX107684	A301-521A	A301-522A	GTX107684		lot#1
Antibody DCC ID	ENCAB956GLA	ENCAB896HED	ENCAB589IXZ	ENCAB956GLA
submitted_to_DCC_date	8/6/2015
Rep1_TPM	27.6	0	0	0	0	0
Rep2_TPM	25.2	0	0	0	0	0
Action
Library_start_date	6/5/2015			6/5/2015
repeat_library
Note
ID	2544	2546	2548	2545	2547	2549

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SART3	Product_ID: GTX107684 Lot_ID: 39757 Source: GeneTex Target Name: SART3-human
SART3	Product_ID: A301-521A Lot_ID: 1 Source: Bethyl Labs Target Name: SART3-human
SART3	Product_ID: A301-522A Lot_ID: 1 Source: Bethyl Labs Target Name: SART3-human

Experiment Status

	BGHLV22-45	BGHLV22-46
Sample_ID	BGHLV22-45	BGHLV22-46
Sample Name	SART3-BGHLV22-45	SART3-BGHLV22-46
Sample Name	SART3-BGHLV22-45	SART3-BGHLV22-46
RBP	SART3	SART3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	806	807

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-45	BGHLV22-46
Sample #
Sample Name	SART3-BGHLV22-45	SART3-BGHLV22-46
Sample_Name_Alias	SART3-BGHLV22-45	SART3-BGHLV22-46
Index Well Position	S05	S06
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/E9.png	DNA_Library_LV20-22-23/set1/F9.png
RIN	9.5	9.8
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/E3.png	RNA_Library_LV22-23-25/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-45	BGHLV22-46
RBP	SART3	SART3
Batch_ID	BGHLV22	BGHLV22
WB_result	91.800	92.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2492	2493

Sequencing Information

	BGHLV22-45	BGHLV22-46
Sample_ID	BGHLV22-45	BGHLV22-46
Sample Name	SART3-BGHLV22-45	SART3-BGHLV22-46
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	53,330,000	64,510,000
total_aligned_reads	49,246,682	59,658,692
unique_aligned_reads	46,265,762	56,078,748
percent_uniqueAligned	0.86754	0.86930
correlation_replicates	0.999660	0.999660
spikein_reads	263,978	354,724
percent_spikeins	0.00495	0.00550
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1114	1115

Data Submission Information

	BGHLV22-45	BGHLV22-45
ENCODE_alias	brenton-graveley:SART3-BGHLV22	brenton-graveley:SART3-BGHLV22-HepG2
ENCODE_accession	ENCSR011BBS	ENCSR812YDZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-45	BGHLV22-45
Sample Name	SART3-BGHLV22-45	SART3-BGHLV22-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2935	6930

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
SART3-BGHLV22-45_ACAGTG_L002_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1114	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	16304
SART3-BGHLV22-45_ACAGTG_L002_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1114	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	16344
SART3-BGHLV22-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1114					GRCh38	V40	SART3-BGHLV22-45_ACAGTG_L002_R1_001.fastq.gz,SART3-BGHLV22-45_ACAGTG_L002_R2_001.fastq.gz		ENCORE2	16442
SART3-BGHLV22-45_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	1114					GRCh38	V40	SART3-BGHLV22-45/Aligned.sortedByCoord.out.bam		ENCORE2	16482
SART3-BGHLV22-45_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	1114					GRCh38	V40	SART3-BGHLV22-45/Aligned.sortedByCoord.out.bam		ENCORE2	16522
SART3-BGHLV22-45_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	1114					GRCh38	V40	SART3-BGHLV22-45/Aligned.sortedByCoord.out.bam		ENCORE2	16562
SART3-BGHLV22-45_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	1114					GRCh38	V40	SART3-BGHLV22-45/Aligned.sortedByCoord.out.bam		ENCORE2	16602
SART3-BGHLV22-45_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1114					GRCh38	V40	SART3-BGHLV22-45_ACAGTG_L002_R1_001.fastq.gz,SART3-BGHLV22-45_ACAGTG_L002_R2_001.fastq.gz		ENCORE2	16642
SART3-BGHLV22-46_GCCAAT_L002_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1115	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	16305
SART3-BGHLV22-46_GCCAAT_L002_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1115	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	16345
SART3-BGHLV22-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1115					GRCh38	V40	SART3-BGHLV22-46_GCCAAT_L002_R1_001.fastq.gz,SART3-BGHLV22-46_GCCAAT_L002_R2_001.fastq.gz		ENCORE2	16443
SART3-BGHLV22-46_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	1115					GRCh38	V40	SART3-BGHLV22-46/Aligned.sortedByCoord.out.bam		ENCORE2	16483
SART3-BGHLV22-46_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	1115					GRCh38	V40	SART3-BGHLV22-46/Aligned.sortedByCoord.out.bam		ENCORE2	16523
SART3-BGHLV22-46_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	1115					GRCh38	V40	SART3-BGHLV22-46/Aligned.sortedByCoord.out.bam		ENCORE2	16563
SART3-BGHLV22-46_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	1115					GRCh38	V40	SART3-BGHLV22-46/Aligned.sortedByCoord.out.bam		ENCORE2	16603
SART3-BGHLV22-46_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1115					GRCh38	V40	SART3-BGHLV22-46_GCCAAT_L002_R1_001.fastq.gz,SART3-BGHLV22-46_GCCAAT_L002_R2_001.fastq.gz		ENCORE2	16643