BRIX1 RNA-Seq in K562

General Information


RBP	BRIX1
Cell_Line	K562
Method	CRISPR
Exp_Name	BRIX1-BGKcLV23-K562
ENCODE_series_ID	ENCSR707SEA
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR162HOU
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	BRIX1-BGKcLV23-23
Rep2	BRIX1-BGKcLV23-24
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	70.1
Rep2_WB	70.4
Antibody Cat#	PA5-89858
Antibody Lot#	lot# UK2881309A
Antibody DCC ID	ENCAB292SQJ
Status	Released
Project	ENCODE4
ID	25

Experiment Information (Status: Released)

	BGKcLV23-23	BGKcLV23-24
idx	809	810
TRCN#_or_BGC#	BGC#0000569	BGC#0000569
shRNA_or_gRNA_sequence	GTGGCGTGCCGCTTAGCTGG	GTGGCGTGCCGCTTAGCTGG
PAM	CGG	CGG
Name	BRIX1_91	BRIX1_91
Sample_ID	BGKcLV23-23	BGKcLV23-24
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
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	2710	2909
WB_result	70.1	70.4
Ave_WB	70.2
WB_DONE_date	10/13/20
MW	41.4KD
IP	Rabbit / I
antibody_Cat#	PA5-89858	lot# UK2881309A
Antibody DCC ID	ENCAB292SQJ
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4929	4930

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

	BGKcLV23-23	BGKcLV23-24
Sample_ID	BGKcLV23-23	BGKcLV23-24
Sample Name
Sample Name	BRIX1-BGKcLV23-23	BRIX1-BGKcLV23-24
RBP	BRIX1	BRIX1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7439	7440

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-23	BGKcLV23-24
Sample #	41	42
Sample Name	BRIX1-BGKcLV23-23	BRIX1-BGKcLV23-24
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	299	305
Peak_Molarity	143.00	124.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/A6.png	DNA_Library_set46/set1/B6.png
RIN	9.2	9.2
libSample_RNA_Well	RNA_Library_set46/set2/A10.png	RNA_Library_set46/set2/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-23	BGKcLV23-24
RBP	BRIX1	BRIX1
Batch_ID	BGKcLV23	BGKcLV23
WB_result	70.100	70.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1416	1417

Sequencing Information

	BGKcLV23-23	BGKcLV23-24
Sample_ID	BGKcLV23-23	BGKcLV23-24
Sample Name	BRIX1-BGKcLV23-23	BRIX1-BGKcLV23-24
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	226,679,514	213,605,310
total_aligned_reads	209,573,980	196,544,094
unique_aligned_reads	190,429,132	178,472,552
percent_uniqueAligned	0.84008	0.83552
correlation_replicates	0.991704	0.991704
spikein_reads	182,220	114,972
percent_spikeins	0.00080	0.00054
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	522	523

Data Submission Information

	BGKcLV23-23	BGKcLV23-23	BGKcLV23-23	BGKcLV23-23	BGKcLV23-23	BGKcLV23-23	BGKcLV23-24	BGKcLV23-24	BGKcLV23-24	BGKcLV23-24
ENCODE_alias	brenton-graveley:BRIX1-BGKcLV23	brenton-graveley:BRIX1-BGKcLV23-23	brenton-graveley:L-BRIX1-BGKcLV23-23	brenton-graveley:BRIX1-BGKcLV23-23_ATATGGAT+TAATACAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BRIX1-BGKcLV23-23_ATATGGAT+TAATACAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BRIX1-BGKcLV23-K562	brenton-graveley:BRIX1-BGKcLV23-24	brenton-graveley:L-BRIX1-BGKcLV23-24	brenton-graveley:BRIX1-BGKcLV23-24_GCGCAAGC+CGGCGTGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BRIX1-BGKcLV23-24_GCGCAAGC+CGGCGTGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR162HOU	ENCBS883HOT	ENCLB151KAX	ENCFF923YDW	ENCFF450MLM	ENCSR707SEA	ENCBS846ABT	ENCLB561VMV	ENCFF495GOM	ENCFF951VVW
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	BGKcLV23-23	BGKcLV23-23	BGKcLV23-23	BGKcLV23-23	BGKcLV23-23	BGKcLV23-23	BGKcLV23-24	BGKcLV23-24	BGKcLV23-24	BGKcLV23-24
Sample Name	BRIX1-BGKcLV23-23	BRIX1-BGKcLV23-23	BRIX1-BGKcLV23-23	BRIX1-BGKcLV23-23	BRIX1-BGKcLV23-23	BRIX1-BGKcLV23-23	BRIX1-BGKcLV23-24	BRIX1-BGKcLV23-24	BRIX1-BGKcLV23-24	BRIX1-BGKcLV23-24
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		BRIX1-BGKcLV23-23.pdf	L-BRIX1-BGKcLV23-23.pdf				BRIX1-BGKcLV23-24.pdf	L-BRIX1-BGKcLV23-24.pdf
ID	2415	2467	2531	2625	2659	7103	2468	2532	2626	2660

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-BGKcLV23-23_ATATGGAT+TAATACAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	522	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1386
BRIX1-BGKcLV23-23_ATATGGAT+TAATACAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	522	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1450
BRIX1-BGKcLV23-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	522					GRCh38	V40	BRIX1-BGKcLV23-23_ATATGGAT+TAATACAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRIX1-BGKcLV23-23_ATATGGAT+TAATACAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25289
BRIX1-BGKcLV23-23_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	522					GRCh38	V40	BRIX1-BGKcLV23-23_ATATGGAT+TAATACAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRIX1-BGKcLV23-23_ATATGGAT+TAATACAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25323
BRIX1-BGKcLV23-23_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	522					GRCh38	V40	BRIX1-BGKcLV23-23/Aligned.sortedByCoord.out.bam		ENCORE2	26127
BRIX1-BGKcLV23-23_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	522					GRCh38	V40	BRIX1-BGKcLV23-23/Aligned.sortedByCoord.out.bam		ENCORE2	26161
BRIX1-BGKcLV23-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	522					GRCh38	V40	BRIX1-BGKcLV23-23/Aligned.sortedByCoord.out.bam		ENCORE2	26195
BRIX1-BGKcLV23-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	522					GRCh38	V40	BRIX1-BGKcLV23-23/Aligned.sortedByCoord.out.bam		ENCORE2	26229
BRIX1-BGKcLV23-24_GCGCAAGC+CGGCGTGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	523	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1387
BRIX1-BGKcLV23-24_GCGCAAGC+CGGCGTGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	523	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1451
BRIX1-BGKcLV23-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	523					GRCh38	V40	BRIX1-BGKcLV23-24_GCGCAAGC+CGGCGTGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRIX1-BGKcLV23-24_GCGCAAGC+CGGCGTGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25290
BRIX1-BGKcLV23-24_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	523					GRCh38	V40	BRIX1-BGKcLV23-24_GCGCAAGC+CGGCGTGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRIX1-BGKcLV23-24_GCGCAAGC+CGGCGTGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25324
BRIX1-BGKcLV23-24_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	523					GRCh38	V40	BRIX1-BGKcLV23-24/Aligned.sortedByCoord.out.bam		ENCORE2	26128
BRIX1-BGKcLV23-24_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	523					GRCh38	V40	BRIX1-BGKcLV23-24/Aligned.sortedByCoord.out.bam		ENCORE2	26162
BRIX1-BGKcLV23-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	523					GRCh38	V40	BRIX1-BGKcLV23-24/Aligned.sortedByCoord.out.bam		ENCORE2	26196
BRIX1-BGKcLV23-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	523					GRCh38	V40	BRIX1-BGKcLV23-24/Aligned.sortedByCoord.out.bam		ENCORE2	26230