GLRX3 RNA-Seq in HepG2

General Information


RBP	GLRX3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	GLRX3-BGHcLV12-HepG2
ENCODE_series_ID	ENCSR228IQO
Batch_ID	BGHcLV12
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR400SCX
ENCODE_CN_Exp_ID	ENCSR827PII
Rep1	GLRX3-BGHcLV12-77
Rep2	GLRX3-BGHcLV12-78
CN1	NT-BGHcLV12-1
CN2	NT-BGHcLV12-2
Rep1_qPCR	54.0
Rep2_qPCR	37.1
Rep1_WB	55.8
Rep2_WB	55.4
Antibody Cat#	GTX118339
Antibody Lot#
Antibody DCC ID	ENCAB219JBV
Status	Released
Project	ENCODE4
ID	173

Experiment Information (Status: Released)

	BGHcLV12-77	BGHcLV12-78
idx	337	338
TRCN#_or_BGC#	BGC#0000289	BGC#0000289
shRNA_or_gRNA_sequence	GGCAGCTGTAGCGGCCGTGG	GGCAGCTGTAGCGGCCGTGG
PAM	agg	agg
Name	TXNL2/GLRX3_63	TXNL2/GLRX3_63
Sample_ID	BGHcLV12-77	BGHcLV12-78
transduction_Date	8/17/18	8/17/18
days	D6	D6
RBP_name	GLRX3	GLRX3
qPCR_result	54.0	37.1
Ave_qPCR	45.6
RT-qPCR_primer-F	ggatgaagaagttcggcaag
RT-qPCR_primer-R	aatatccaatcctcccacca
protein_conc	5792	6302
WB_result	55.8	55.4
Ave_WB	55.6
WB_DONE_date	2/19/19
MW	37kDa
IP
antibody_Cat#	GTX118339
Antibody DCC ID	ENCAB219JBV
submitted_to_DCC_date	2/22/19
Rep1_TPM	62	0
Rep2_TPM	123	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	6482	6483

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

	BGHcLV12-77	BGHcLV12-78
Sample_ID	BGHcLV12-77	BGHcLV12-78
Sample Name	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-78
Sample Name	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-78
RBP	GLRX3	GLRX3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2815	2816

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV12-77	BGHcLV12-78
Sample #	45	46
Sample Name	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-78
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	3-E2	3-F2
Tecan	40.40	37.31
Tecan_date	2019-03-13	2019-03-13
Size_bp	301	292
Peak_Molarity	107.00	190.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/E6.png	DNA_Library_set42/set1/F6.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set42/set1/E6.png	RNA_Library_set42/set1/F6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGHcLV12-77	BGHcLV12-78
RBP	GLRX3	GLRX3
Batch_ID	BGHcLV12	BGHcLV12
WB_result	55.800	55.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	45	46

Sequencing Information

	BGHcLV12-77	BGHcLV12-78
Sample_ID	BGHcLV12-77	BGHcLV12-78
Sample Name	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-78
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	128,486,972	139,781,298
total_aligned_reads	123,070,948	132,137,276
unique_aligned_reads	115,601,070	124,121,854
percent_uniqueAligned	0.89971	0.88797
correlation_replicates	0.999088	0.999088
spikein_reads	130,826	132,596
percent_spikeins	0.00102	0.00095
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	25	26

Data Submission Information

	BGHcLV12-77	BGHcLV12-77	BGHcLV12-77	BGHcLV12-77	BGHcLV12-77	BGHcLV12-77	BGHcLV12-78	BGHcLV12-78	BGHcLV12-78	BGHcLV12-78
ENCODE_alias	brenton-graveley:GLRX3-BGHcLV12	brenton-graveley:GLRX3-BGHcLV12-77	brenton-graveley:L-GLRX3-BGHcLV12-77	brenton-graveley:GLRX3-BGHcLV12-77_ATGGCATG+AAGGTACC_HK3H2DSXX_S45_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GLRX3-BGHcLV12-77_ATGGCATG+AAGGTACC_HK3H2DSXX_S45_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GLRX3-BGHcLV12-HepG2	brenton-graveley:GLRX3-BGHcLV12-78	brenton-graveley:L-GLRX3-BGHcLV12-78	brenton-graveley:GLRX3-BGHcLV12-78_GCAATGCA+GGAACGTT_HK3H2DSXX_S46_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GLRX3-BGHcLV12-78_GCAATGCA+GGAACGTT_HK3H2DSXX_S46_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR400SCX	ENCBS041KFE	ENCLB862YPF	ENCFF029TOX	ENCFF545VHH	ENCSR228IQO	ENCBS869LGZ	ENCLB994EHQ	ENCFF101NQW	ENCFF169ZNY
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV12-77	BGHcLV12-77	BGHcLV12-77	BGHcLV12-77	BGHcLV12-77	BGHcLV12-77	BGHcLV12-78	BGHcLV12-78	BGHcLV12-78	BGHcLV12-78
Sample Name	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-77	GLRX3-BGHcLV12-78	GLRX3-BGHcLV12-78	GLRX3-BGHcLV12-78	GLRX3-BGHcLV12-78
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		GLRX3-BGHcLV12-77.pdf	L-GLRX3-BGHcLV12-77.pdf				GLRX3-BGHcLV12-78.pdf	L-GLRX3-BGHcLV12-78.pdf
ID	749	793	875	975	1057	7232	794	876	976	1058

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-BGHcLV12-77_ATGGCATG+AAGGTACC_HK3H2DSXX_S45_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	25	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	357
GLRX3-BGHcLV12-77_ATGGCATG+AAGGTACC_HK3H2DSXX_S45_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	25	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	439
GLRX3-BGHcLV12-77_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	25					GRCh38	V40	GLRX3-BGHcLV12-77_ATGGCATG+AAGGTACC_HK3H2DSXX_S45_L004_R1_001.filtered.trimmed.paired.fastq.gz,GLRX3-BGHcLV12-77_ATGGCATG+AAGGTACC_HK3H2DSXX_S45_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23696
GLRX3-BGHcLV12-77_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	25					GRCh38	V40	GLRX3-BGHcLV12-77/Aligned.sortedByCoord.out.bam		ENCORE2	23778
GLRX3-BGHcLV12-77_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	25					GRCh38	V40	GLRX3-BGHcLV12-77/Aligned.sortedByCoord.out.bam		ENCORE2	23860
GLRX3-BGHcLV12-77_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	25					GRCh38	V40	GLRX3-BGHcLV12-77/Aligned.sortedByCoord.out.bam		ENCORE2	23942
GLRX3-BGHcLV12-77_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	25					GRCh38	V40	GLRX3-BGHcLV12-77/Aligned.sortedByCoord.out.bam		ENCORE2	24024
GLRX3-BGHcLV12-77_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	25					GRCh38	V40	GLRX3-BGHcLV12-77_ATGGCATG+AAGGTACC_HK3H2DSXX_S45_L004_R1_001.filtered.trimmed.paired.fastq.gz,GLRX3-BGHcLV12-77_ATGGCATG+AAGGTACC_HK3H2DSXX_S45_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24106
GLRX3-BGHcLV12-78_GCAATGCA+GGAACGTT_HK3H2DSXX_S46_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	26	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	358
GLRX3-BGHcLV12-78_GCAATGCA+GGAACGTT_HK3H2DSXX_S46_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	26	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	440
GLRX3-BGHcLV12-78_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	26					GRCh38	V40	GLRX3-BGHcLV12-78_GCAATGCA+GGAACGTT_HK3H2DSXX_S46_L004_R1_001.filtered.trimmed.paired.fastq.gz,GLRX3-BGHcLV12-78_GCAATGCA+GGAACGTT_HK3H2DSXX_S46_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23697
GLRX3-BGHcLV12-78_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	26					GRCh38	V40	GLRX3-BGHcLV12-78/Aligned.sortedByCoord.out.bam		ENCORE2	23779
GLRX3-BGHcLV12-78_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	26					GRCh38	V40	GLRX3-BGHcLV12-78/Aligned.sortedByCoord.out.bam		ENCORE2	23861
GLRX3-BGHcLV12-78_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	26					GRCh38	V40	GLRX3-BGHcLV12-78/Aligned.sortedByCoord.out.bam		ENCORE2	23943
GLRX3-BGHcLV12-78_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	26					GRCh38	V40	GLRX3-BGHcLV12-78/Aligned.sortedByCoord.out.bam		ENCORE2	24025
GLRX3-BGHcLV12-78_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	26					GRCh38	V40	GLRX3-BGHcLV12-78_GCAATGCA+GGAACGTT_HK3H2DSXX_S46_L004_R1_001.filtered.trimmed.paired.fastq.gz,GLRX3-BGHcLV12-78_GCAATGCA+GGAACGTT_HK3H2DSXX_S46_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24107