SUCLG1 RNA-Seq in K562

General Information


RBP	SUCLG1
Cell_Line	K562
Method	shRNA
Exp_Name	SUCLG1-BGKLV25-K562
ENCODE_series_ID	ENCSR341IXU
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR101OPF
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	SUCLG1-BGKLV25-57
Rep2	SUCLG1-BGKLV25-58
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	98.6
Rep2_qPCR	87.3
Rep1_WB	59.1
Rep2_WB	61.5
Antibody Cat#	GTX109215
Antibody Lot#	GTX109215
Antibody DCC ID	ENCAB020DGN
Status	Released
Project	ENCODE3
ID	625

Experiment Information (Status: Released)

	BGKLV25-57	BGKLV25-57	BGKLV25-58	BGKLV25-58
idx	460	0	461	0
TRCN#_or_BGC#	TRCN0000048510	TRCN0000048510	TRCN0000048510	TRCN0000048510
shRNA_or_gRNA_sequence	CGGCAACATCTCTATGTTGAT	CGGCAACATCTCTATGTTGAT	CGGCAACATCTCTATGTTGAT	CGGCAACATCTCTATGTTGAT
PAM
Name	SUCLG1	SUCLG1	SUCLG1	SUCLG1
Sample_ID	BGKLV25-57	BGKLV25-57	BGKLV25-58	BGKLV25-58
transduction_Date	3/17/2015	3/17/2015	3/17/2015	3/17/2015
days
RBP_name	SUCLG1	SUCLG1	SUCLG1	SUCLG1
qPCR_result	98.6	98.6	87.3	87.3
Ave_qPCR	93.0	93.0
RT-qPCR_primer-F	ttcggcattgttcctacaca	ttcggcattgttcctacaca
RT-qPCR_primer-R	ctgtgaaaggtgccctgttt	ctgtgaaaggtgccctgttt
protein_conc	3445	3445	3179	3179
WB_result	59.1	88.6	61.5	92.2
Ave_WB	60.3	90.4
WB_DONE_date	5/13/2015	9/22/2022
MW	36kDa	36kd
IP	1		1
antibody_Cat#	GTX109215	8071	GTX109215	lot# 1
Antibody DCC ID	ENCAB020DGN		ENCAB020DGN
submitted_to_DCC_date	8/6/2015	1/9/2024
Rep1_TPM	53.4935237	0	0	0
Rep2_TPM	37.6692954	0	0	0
Action
Library_start_date	6/23/2015		6/23/2015
repeat_library
Note			11
ID	531	533	532	534

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUCLG1	Product_ID: GTX109215 Lot_ID: 40023 Source: GeneTex Target Name: SUCLG1-human
SUCLG1	Product_ID: 8071S Lot_ID: 1 Source: Cell Signaling Technology Target Name: SUCLG1-human

Experiment Status

	BGKLV25-57	BGKLV25-58
Sample_ID	BGKLV25-57	BGKLV25-58
Sample Name	SUCLG1-BGKLV25-57	SUCLG1-BGKLV25-58
Sample Name	SUCLG1-BGKLV25-57	SUCLG1-BGKLV25-58
RBP	SUCLG1	SUCLG1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	930	931

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-57	BGKLV25-58
Sample #
Sample Name	SUCLG1-BGKLV25-57	SUCLG1-BGKLV25-58
Sample_Name_Alias	SUCLG1-BGKLV25-57	SUCLG1-BGKLV25-58
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/C4.png	DNA_Library_LV24-25-26/set1/D4.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/E12.png	RNA_Library_LV22-23-25/set1/F12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-57	BGKLV25-58
RBP	SUCLG1	SUCLG1
Batch_ID	BGKLV25	BGKLV25
WB_result	59.100	61.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2622	2623

Sequencing Information

	BGKLV25-57	BGKLV25-58
Sample_ID	BGKLV25-57	BGKLV25-58
Sample Name	SUCLG1-BGKLV25-57	SUCLG1-BGKLV25-58
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	66,859,090	85,486,366
total_aligned_reads	68,251,052	87,701,578
unique_aligned_reads	62,153,794	79,964,538
percent_uniqueAligned	0.92962	0.93541
correlation_replicates	0.998967	0.998967
spikein_reads	342,408	418,346
percent_spikeins	0.00512	0.00489
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1264	1265

Data Submission Information

	BGKLV25-57	BGKLV25-57
ENCODE_alias	brenton-graveley:SUCLG1-BGKLV25	brenton-graveley:SUCLG1-BGKLV25-K562
ENCODE_accession	ENCSR101OPF	ENCSR341IXU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-57	BGKLV25-57
Sample Name	SUCLG1-BGKLV25-57	SUCLG1-BGKLV25-57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3014	6991

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
SUCLG1-BGKLV25-57_GGCTAC_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1264	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19592
SUCLG1-BGKLV25-57_GGCTAC_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1264	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19628
SUCLG1-BGKLV25-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1264					GRCh38	V40	SUCLG1-BGKLV25-57_GGCTAC_L008_001.R1.fastq.gz,SUCLG1-BGKLV25-57_GGCTAC_L008_001.R2.fastq.gz		ENCORE2	19664
SUCLG1-BGKLV25-57_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1264					GRCh38	V40	SUCLG1-BGKLV25-57/Aligned.sortedByCoord.out.bam		ENCORE2	19700
SUCLG1-BGKLV25-57_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1264					GRCh38	V40	SUCLG1-BGKLV25-57/Aligned.sortedByCoord.out.bam		ENCORE2	19736
SUCLG1-BGKLV25-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1264					GRCh38	V40	SUCLG1-BGKLV25-57/Aligned.sortedByCoord.out.bam		ENCORE2	19772
SUCLG1-BGKLV25-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1264					GRCh38	V40	SUCLG1-BGKLV25-57/Aligned.sortedByCoord.out.bam		ENCORE2	19808
SUCLG1-BGKLV25-57_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1264					GRCh38	V40	SUCLG1-BGKLV25-57_GGCTAC_L008_001.R1.fastq.gz,SUCLG1-BGKLV25-57_GGCTAC_L008_001.R2.fastq.gz		ENCORE2	19998
SUCLG1-BGKLV25-58_CTTGTA_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1265	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19593
SUCLG1-BGKLV25-58_CTTGTA_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1265	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19629
SUCLG1-BGKLV25-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1265					GRCh38	V40	SUCLG1-BGKLV25-58_CTTGTA_L008_001.R1.fastq.gz,SUCLG1-BGKLV25-58_CTTGTA_L008_001.R2.fastq.gz		ENCORE2	19665
SUCLG1-BGKLV25-58_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1265					GRCh38	V40	SUCLG1-BGKLV25-58/Aligned.sortedByCoord.out.bam		ENCORE2	19701
SUCLG1-BGKLV25-58_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1265					GRCh38	V40	SUCLG1-BGKLV25-58/Aligned.sortedByCoord.out.bam		ENCORE2	19737
SUCLG1-BGKLV25-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1265					GRCh38	V40	SUCLG1-BGKLV25-58/Aligned.sortedByCoord.out.bam		ENCORE2	19773
SUCLG1-BGKLV25-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1265					GRCh38	V40	SUCLG1-BGKLV25-58/Aligned.sortedByCoord.out.bam		ENCORE2	19809
SUCLG1-BGKLV25-58_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1265					GRCh38	V40	SUCLG1-BGKLV25-58_CTTGTA_L008_001.R1.fastq.gz,SUCLG1-BGKLV25-58_CTTGTA_L008_001.R2.fastq.gz		ENCORE2	19999