SART3 RNA-Seq in K562

General Information


RBP	SART3
Cell_Line	K562
Method	shRNA
Exp_Name	SART3-BGKLV24-K562
ENCODE_series_ID	ENCSR396HJG
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR954HAY
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	SART3_BGKLV24_53B
Rep2	SART3_BGKLV24_54B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	58.4
Rep2_qPCR	58.7
Rep1_WB	96.7
Rep2_WB	89.3
Antibody Cat#	GTX107684
Antibody Lot#	GTX107684
Antibody DCC ID	ENCAB956GLA
Status	Released
Project	ENCODE3
ID	609

Experiment Information (Status: Released)

	BGKLV24-53	BGKLV24-53	BGKLV24-54	BGKLV24-54
idx	390	390	391	391
TRCN#_or_BGC#	TRCN0000148806	TRCN0000148806	TRCN0000148806	TRCN0000148806
shRNA_or_gRNA_sequence	CGTTTCAATGAGAGTGGTGAT	CGTTTCAATGAGAGTGGTGAT	CGTTTCAATGAGAGTGGTGAT	CGTTTCAATGAGAGTGGTGAT
PAM
Name	SART3	SART3	SART3	SART3
Sample_ID	BGKLV24-53	BGKLV24-53	BGKLV24-54	BGKLV24-54
transduction_Date	2/27/2015	2/27/2015	2/27/2015	2/27/2015
days
RBP_name	SART3	SART3	SART3	SART3
qPCR_result	58.4	58.4	58.7	58.7
Ave_qPCR	58.6	58.6
RT-qPCR_primer-F	acccgattagctcgtgtcaa	acccgattagctcgtgtcaa
RT-qPCR_primer-R	gctcttttccgttgttcagc	gctcttttccgttgttcagc
protein_conc	3379	3379	3748	3748
WB_result	96.7	87.6	89.3	90.1
Ave_WB	93.0	88.8
WB_DONE_date	5/4/2015	6/13/2022
MW	110kDa	110kDa
IP	1		1
antibody_Cat#	GTX107684	A301-521A	GTX107684
Antibody DCC ID	ENCAB956GLA	ENCAB896HED	ENCAB956GLA
submitted_to_DCC_date	8/6/2015
Rep1_TPM	56.8370427	0	0	0
Rep2_TPM	48.6822599	0	0	0
Action
Library_start_date	9/2/2015		9/2/2015
repeat_library
Note	x		x
ID	447	449	448	450

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

Experiment Status

	BGKLV24-53	BGKLV24-54
Sample_ID	BGKLV24-53	BGKLV24-54
Sample Name	SART3_BGKLV24_53B	SART3_BGKLV24_54B
Sample Name	SART3_BGKLV24_53B	SART3_BGKLV24_54B
RBP	SART3	SART3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	900	901

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-53	BGKLV24-54
Sample #
Sample Name	SART3-BGKLV24-53B	SART3-BGKLV24-54B
Sample_Name_Alias	SART3_BGKLV24_53B	SART3_BGKLV24_54B
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/A7.png	DNA_Library_LV24-25-26/set1/B7.png
RIN	8.6	9.4
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A6.png	RNA_Library_LV20-22-24/set1/B6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-53	BGKLV24-54
RBP	SART3	SART3
Batch_ID	BGKLV24	BGKLV24
WB_result	96.700	89.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2588	2589

Sequencing Information

	BGKLV24-53	BGKLV24-54
Sample_ID	BGKLV24-53	BGKLV24-54
Sample Name	SART3_BGKLV24_53B	SART3_BGKLV24_54B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	88,539,956	98,717,876
total_aligned_reads	76,449,026	93,804,532
unique_aligned_reads	69,148,300	85,450,866
percent_uniqueAligned	0.78098	0.86561
correlation_replicates	0.991482	0.991482
spikein_reads	298,166	317,150
percent_spikeins	0.00337	0.00321
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1230	1231

Data Submission Information

	BGKLV24-53	BGKLV24-53
ENCODE_alias	brenton-graveley:SART3_BGKLV24_B	brenton-graveley:SART3-BGKLV24-K562
ENCODE_accession	ENCSR954HAY	ENCSR396HJG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-53	BGKLV24-53
Sample Name	SART3_BGKLV24_53B	SART3_BGKLV24_53B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2999	6931

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_BGKLV24_53B_GTCCGC_L003_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1230	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17486
SART3_BGKLV24_53B_GTCCGC_L003_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1230	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17510
SART3_BGKLV24_53B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1230					GRCh38	V40	SART3_BGKLV24_53B_GTCCGC_L003_001.R1.fastq.gz,SART3_BGKLV24_53B_GTCCGC_L003_001.R2.fastq.gz		ENCORE2	17534
SART3_BGKLV24_53B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1230					GRCh38	V40	SART3_BGKLV24_53B/Aligned.sortedByCoord.out.bam		ENCORE2	17558
SART3_BGKLV24_53B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1230					GRCh38	V40	SART3_BGKLV24_53B/Aligned.sortedByCoord.out.bam		ENCORE2	17582
SART3_BGKLV24_53B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1230					GRCh38	V40	SART3_BGKLV24_53B/Aligned.sortedByCoord.out.bam		ENCORE2	17606
SART3_BGKLV24_53B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1230					GRCh38	V40	SART3_BGKLV24_53B/Aligned.sortedByCoord.out.bam		ENCORE2	17630
SART3_BGKLV24_53B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1230					GRCh38	V40	SART3_BGKLV24_53B_GTCCGC_L003_001.R1.fastq.gz,SART3_BGKLV24_53B_GTCCGC_L003_001.R2.fastq.gz		ENCORE2	17654
SART3_BGKLV24_54B_GTGAAA_L003_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1231	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17487
SART3_BGKLV24_54B_GTGAAA_L003_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1231	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17511
SART3_BGKLV24_54B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1231					GRCh38	V40	SART3_BGKLV24_54B_GTGAAA_L003_001.R1.fastq.gz,SART3_BGKLV24_54B_GTGAAA_L003_001.R2.fastq.gz		ENCORE2	17535
SART3_BGKLV24_54B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1231					GRCh38	V40	SART3_BGKLV24_54B/Aligned.sortedByCoord.out.bam		ENCORE2	17559
SART3_BGKLV24_54B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1231					GRCh38	V40	SART3_BGKLV24_54B/Aligned.sortedByCoord.out.bam		ENCORE2	17583
SART3_BGKLV24_54B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1231					GRCh38	V40	SART3_BGKLV24_54B/Aligned.sortedByCoord.out.bam		ENCORE2	17607
SART3_BGKLV24_54B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1231					GRCh38	V40	SART3_BGKLV24_54B/Aligned.sortedByCoord.out.bam		ENCORE2	17631
SART3_BGKLV24_54B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1231					GRCh38	V40	SART3_BGKLV24_54B_GTGAAA_L003_001.R1.fastq.gz,SART3_BGKLV24_54B_GTGAAA_L003_001.R2.fastq.gz		ENCORE2	17655