BRIX1 RNA-Seq in HepG2

General Information


RBP	BRIX1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	BRIX1-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR480STK
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR060SLE
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	BRIX1-BGHcLV24-19
Rep2	BRIX1-BGHcLV24-20
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	84.3
Rep2_WB	83.5
Antibody Cat#	PA5-89858
Antibody Lot#
Antibody DCC ID	ENCAB292SQJ
Status	Released
Project	ENCODE4
ID	4

Experiment Information (Status: Released)

	BGHcLV24-19	BGHcLV24-20
idx	677	678
TRCN#_or_BGC#	BGC#0000569	BGC#0000569
shRNA_or_gRNA_sequence	GTGGCGTGCCGCTTAGCTGG	GTGGCGTGCCGCTTAGCTGG
PAM	CGG	CGG
Name	BRIX1_91	BRIX1_91
Sample_ID	BGHcLV24-19	BGHcLV24-20
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	BRIX1	BRIX1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ACCTGGGCTCAAGTGGCTT
RT-qPCR_primer-R	CACCACAGAGCTGAAGGAGG
protein_conc	5475	5219
WB_result	84.3	83.5
Ave_WB	83.9
WB_DONE_date	12/14/20
MW	41.4KD
IP	Rabbit / I
antibody_Cat#	PA5-89858
Antibody DCC ID	ENCAB292SQJ
submitted_to_DCC_date	2/9/21
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6832	6833

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BRIX1	Product_ID: PA5-89858 Lot_ID: UK2881309A Source: Thermo Fisher Target Name: BRIX1-human

Experiment Status

	BGHcLV24-19	BGHcLV24-20
Sample_ID	BGHcLV24-19	BGHcLV24-20
Sample Name
Sample Name	BRIX1-BGHcLV24-19	BRIX1-BGHcLV24-20
RBP	BRIX1	BRIX1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7787	7788

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-19	BGHcLV24-20
Sample #	9	10
Sample Name	BRIX1-BGHcLV24-19	BRIX1-BGHcLV24-20
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	306	309
Peak_Molarity	83.50	68.80
libSampleQC_DNA_Well	DNA_Library_set47/set1/A5.png	DNA_Library_set47/set1/B5.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set47/set1/A2.png	RNA_Library_set47/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-19	BGHcLV24-20
RBP	BRIX1	BRIX1
Batch_ID	BGHcLV24	BGHcLV24
WB_result	84.300	83.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1472	1473

Sequencing Information

	BGHcLV24-19	BGHcLV24-20
Sample_ID	BGHcLV24-19	BGHcLV24-20
Sample Name	BRIX1-BGHcLV24-19	BRIX1-BGHcLV24-20
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	132,934,314	122,388,430
total_aligned_reads	118,481,060	109,372,622
unique_aligned_reads	111,612,844	103,084,510
percent_uniqueAligned	0.83961	0.84227
correlation_replicates	0.997952	0.997952
spikein_reads	65,490	57,112
percent_spikeins	0.00049	0.00047
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	554	555

Data Submission Information

	BGHcLV24-19	BGHcLV24-19	BGHcLV24-19	BGHcLV24-19	BGHcLV24-19	BGHcLV24-19	BGHcLV24-20	BGHcLV24-20	BGHcLV24-20	BGHcLV24-20
ENCODE_alias	brenton-graveley:BRIX1-BGHcLV24	brenton-graveley:BRIX1-BGHcLV24-19	brenton-graveley:L-BRIX1-BGHcLV24-19	brenton-graveley:BRIX1-BGHcLV24-19_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BRIX1-BGHcLV24-19_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BRIX1-BGHcLV24-HepG2	brenton-graveley:BRIX1-BGHcLV24-20	brenton-graveley:L-BRIX1-BGHcLV24-20	brenton-graveley:BRIX1-BGHcLV24-20_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BRIX1-BGHcLV24-20_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR060SLE	ENCBS185KSH	ENCLB419HQG	ENCFF203IOB	ENCFF144CPS	ENCSR480STK	ENCBS513DCS	ENCLB895QKE	ENCFF055BAY	ENCFF123XAQ
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	BGHcLV24-19	BGHcLV24-19	BGHcLV24-19	BGHcLV24-19	BGHcLV24-19	BGHcLV24-19	BGHcLV24-20	BGHcLV24-20	BGHcLV24-20	BGHcLV24-20
Sample Name	BRIX1-BGHcLV24-19	BRIX1-BGHcLV24-19	BRIX1-BGHcLV24-19	BRIX1-BGHcLV24-19	BRIX1-BGHcLV24-19	BRIX1-BGHcLV24-19	BRIX1-BGHcLV24-20	BRIX1-BGHcLV24-20	BRIX1-BGHcLV24-20	BRIX1-BGHcLV24-20
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		BRIX1-BGHcLV24-19.pdf	L-BRIX1-BGHcLV24-19.pdf				BRIX1-BGHcLV24-20.pdf	L-BRIX1-BGHcLV24-20.pdf
ID	3239	3265	3309	3353	3397	7102	3266	3310	3354	3398

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
BRIX1-BGHcLV24-19_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	554	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3712
BRIX1-BGHcLV24-19_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	554	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3758
BRIX1-BGHcLV24-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	554					GRCh38	V40	BRIX1-BGHcLV24-19_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,BRIX1-BGHcLV24-19_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25401
BRIX1-BGHcLV24-19_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	554					GRCh38	V40	BRIX1-BGHcLV24-19_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,BRIX1-BGHcLV24-19_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25445
BRIX1-BGHcLV24-19_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	554					GRCh38	V40	BRIX1-BGHcLV24-19/Aligned.sortedByCoord.out.bam		ENCORE2	26277
BRIX1-BGHcLV24-19_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	554					GRCh38	V40	BRIX1-BGHcLV24-19/Aligned.sortedByCoord.out.bam		ENCORE2	26321
BRIX1-BGHcLV24-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	554					GRCh38	V40	BRIX1-BGHcLV24-19/Aligned.sortedByCoord.out.bam		ENCORE2	26365
BRIX1-BGHcLV24-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	554					GRCh38	V40	BRIX1-BGHcLV24-19/Aligned.sortedByCoord.out.bam		ENCORE2	26409
BRIX1-BGHcLV24-20_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	555	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3713
BRIX1-BGHcLV24-20_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	555	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3759
BRIX1-BGHcLV24-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	555					GRCh38	V40	BRIX1-BGHcLV24-20_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,BRIX1-BGHcLV24-20_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25402
BRIX1-BGHcLV24-20_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	555					GRCh38	V40	BRIX1-BGHcLV24-20_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,BRIX1-BGHcLV24-20_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25446
BRIX1-BGHcLV24-20_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	555					GRCh38	V40	BRIX1-BGHcLV24-20/Aligned.sortedByCoord.out.bam		ENCORE2	26278
BRIX1-BGHcLV24-20_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	555					GRCh38	V40	BRIX1-BGHcLV24-20/Aligned.sortedByCoord.out.bam		ENCORE2	26322
BRIX1-BGHcLV24-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	555					GRCh38	V40	BRIX1-BGHcLV24-20/Aligned.sortedByCoord.out.bam		ENCORE2	26366
BRIX1-BGHcLV24-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	555					GRCh38	V40	BRIX1-BGHcLV24-20/Aligned.sortedByCoord.out.bam		ENCORE2	26410