GLRX3 RNA-Seq in K562

General Information


RBP	GLRX3
Cell_Line	K562
Method	shRNA
Exp_Name	GLRX3-BGKLV34-K562
ENCODE_series_ID	ENCSR367SEJ
Batch_ID	BGKLV34
Pool ID	Pool-160912
Local_Set_Name	set34
ENCODE_KD_Exp_ID	ENCSR874DVZ
ENCODE_CN_Exp_ID	ENCSR174OYC
Rep1	GLRX3_BGKLV34-17
Rep2	GLRX3_BGKLV34-18
CN1	NT_BGKLV34-1
CN2	NT_BGKLV34-2
Rep1_qPCR	73.7
Rep2_qPCR	75.4
Rep1_WB	69.7
Rep2_WB	66.1
Antibody Cat#	GTX118339
Antibody Lot#	GTX118339
Antibody DCC ID	ENCAB219JBV
Status	Released
Project	ENCODE3
ID	721

Experiment Information (Status: Released)

	BGKLV34-17	BGKLV34-18
idx	680	681
TRCN#_or_BGC#	TRCN0000064666	TRCN0000064666
shRNA_or_gRNA_sequence	CCTACCTATCCTCAGCTCTAT	CCTACCTATCCTCAGCTCTAT
PAM
Name	GLRX3/TXNL2	GLRX3/TXNL2
Sample_ID	BGKLV34-17	BGKLV34-18
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	GLRX3	GLRX3
qPCR_result	73.7	75.4
Ave_qPCR	74.5
RT-qPCR_primer-F	ggatgaagaagttcggcaag
RT-qPCR_primer-R	aatatccaatcctcccacca
protein_conc	2940	2586
WB_result	69.7	66.1
Ave_WB	67.9
WB_DONE_date	3/2/2016
MW	37kDa
IP	1	1
antibody_Cat#	GTX118339	GTX118339
Antibody DCC ID	ENCAB219JBV	ENCAB219JBV
submitted_to_DCC_date	3/8/2016
Rep1_TPM	26.1345306	0
Rep2_TPM	18.4274481	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	765	766

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GLRX3	Product_ID: GTX118339 Lot_ID: 40310 Source: GeneTex Target Name: GLRX3-human

Experiment Status

	BGKLV34-17	BGKLV34-18
Sample_ID	BGKLV34-17	BGKLV34-18
Sample Name	GLRX3_BGKLV34-17	GLRX3_BGKLV34-18
Sample Name	GLRX3_BGKLV34-17	GLRX3_BGKLV34-18
RBP	GLRX3	GLRX3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1229	1230

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-17	BGKLV34-18
Sample #
Sample Name	GLRX3-BGKLV34-17	GLRX3-BGKLV34-18
Sample_Name_Alias	GLRX3_BGKLV34-17	GLRX3_BGKLV34-18
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/G2.png	DNA_Library_LV33-34-25B-32/set1/H2.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/E4.png	RNA_Library_LV32-33-34/set1/F4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV34-17	BGKLV34-18
RBP	GLRX3	GLRX3
Batch_ID	BGKLV34	BGKLV34
WB_result	69.700	66.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2914	2915

Sequencing Information

	BGKLV34-17	BGKLV34-18
Sample_ID	BGKLV34-17	BGKLV34-18
Sample Name	GLRX3_BGKLV34-17	GLRX3_BGKLV34-18
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set34	set34
total_reads	60,905,234	62,232,200
total_aligned_reads	52,301,398	49,840,778
unique_aligned_reads	47,578,528	45,602,504
percent_uniqueAligned	0.78119	0.73278
correlation_replicates	0.995262	0.995262
spikein_reads	174,116	187,692
percent_spikeins	0.00286	0.00302
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1563	1564

Data Submission Information

	BGKLV34-17	BGKLV34-17
ENCODE_alias	brenton-graveley:GLRX3_BGKLV34	brenton-graveley:GLRX3-BGKLV34-K562
ENCODE_accession	ENCSR874DVZ	ENCSR367SEJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-17	BGKLV34-17
Sample Name	GLRX3_BGKLV34-17	GLRX3_BGKLV34-17
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3154	6733

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
GLRX3_BGKLV34-17_ACTGAT_L002_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1563	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21522
GLRX3_BGKLV34-17_ACTGAT_L002_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1563	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21542
GLRX3_BGKLV34-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1563					GRCh38	V40	GLRX3_BGKLV34-17_ACTGAT_L002_001.R1.fastq.gz,GLRX3_BGKLV34-17_ACTGAT_L002_001.R2.fastq.gz		ENCORE2	21562
GLRX3_BGKLV34-17_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1563					GRCh38	V40	GLRX3_BGKLV34-17/Aligned.sortedByCoord.out.bam		ENCORE2	21582
GLRX3_BGKLV34-17_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1563					GRCh38	V40	GLRX3_BGKLV34-17/Aligned.sortedByCoord.out.bam		ENCORE2	21602
GLRX3_BGKLV34-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1563					GRCh38	V40	GLRX3_BGKLV34-17/Aligned.sortedByCoord.out.bam		ENCORE2	21622
GLRX3_BGKLV34-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1563					GRCh38	V40	GLRX3_BGKLV34-17/Aligned.sortedByCoord.out.bam		ENCORE2	21642
GLRX3_BGKLV34-17_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1563					GRCh38	V40	GLRX3_BGKLV34-17_ACTGAT_L002_001.R1.fastq.gz,GLRX3_BGKLV34-17_ACTGAT_L002_001.R2.fastq.gz		ENCORE2	21662
GLRX3_BGKLV34-18_ATTCCT_L002_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1564	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21523
GLRX3_BGKLV34-18_ATTCCT_L002_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1564	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21543
GLRX3_BGKLV34-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1564					GRCh38	V40	GLRX3_BGKLV34-18_ATTCCT_L002_001.R1.fastq.gz,GLRX3_BGKLV34-18_ATTCCT_L002_001.R2.fastq.gz		ENCORE2	21563
GLRX3_BGKLV34-18_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1564					GRCh38	V40	GLRX3_BGKLV34-18/Aligned.sortedByCoord.out.bam		ENCORE2	21583
GLRX3_BGKLV34-18_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1564					GRCh38	V40	GLRX3_BGKLV34-18/Aligned.sortedByCoord.out.bam		ENCORE2	21603
GLRX3_BGKLV34-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1564					GRCh38	V40	GLRX3_BGKLV34-18/Aligned.sortedByCoord.out.bam		ENCORE2	21623
GLRX3_BGKLV34-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1564					GRCh38	V40	GLRX3_BGKLV34-18/Aligned.sortedByCoord.out.bam		ENCORE2	21643
GLRX3_BGKLV34-18_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1564					GRCh38	V40	GLRX3_BGKLV34-18_ATTCCT_L002_001.R1.fastq.gz,GLRX3_BGKLV34-18_ATTCCT_L002_001.R2.fastq.gz		ENCORE2	21663