BARD1 RNA-Seq in K562

General Information


RBP	BARD1
Cell_Line	K562
Method	CRISPR
Exp_Name	BARD1-BGKcLV23-K562
ENCODE_series_ID	ENCSR451JFM
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR427KVG
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	BARD1-BGKcLV23-21
Rep2	BARD1-BGKcLV23-22
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	30.0
Rep2_qPCR	31.0
Rep1_WB	63.9
Rep2_WB	61.1
Antibody Cat#	PA5-85707
Antibody Lot#	LOT# UK2890668D
Antibody DCC ID	ENCAB064JSL
Status	Released
Project	ENCODE4
ID	24

Experiment Information (Status: Released)

	BGKcLV23-21	BGKcLV23-22
idx	807	808
TRCN#_or_BGC#	BGC#0000566	BGC#0000566
shRNA_or_gRNA_sequence	CTTCTCCAGGCGGTCGAGCG	CTTCTCCAGGCGGTCGAGCG
PAM	CGG	CGG
Name	BARD1_97	BARD1_97
Sample_ID	BGKcLV23-21	BGKcLV23-22
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	BARD1	BARD1
qPCR_result	30.0	31.0
Ave_qPCR	30.5
RT-qPCR_primer-F	attcctgaaggtccacgcag
RT-qPCR_primer-R	tggtgtttgaaggttcccca
protein_conc	2963	2753
WB_result	63.9	61.1
Ave_WB	62.5
WB_DONE_date	10/21/20
MW	86.6KD
IP	Rabbit / I
antibody_Cat#	PA5-85707	LOT# UK2890668D
Antibody DCC ID	ENCAB064JSL
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4927	4928

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BARD1	Product_ID: PA5-85707 Lot_ID: UK2890668D Source: Thermo Fisher Target Name: BARD1-human

Experiment Status

	BGKcLV23-21	BGKcLV23-22
Sample_ID	BGKcLV23-21	BGKcLV23-22
Sample Name
Sample Name	BARD1-BGKcLV23-21	BARD1-BGKcLV23-22
RBP	BARD1	BARD1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7437	7438

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-21	BGKcLV23-22
Sample #	39	40
Sample Name	BARD1-BGKcLV23-21	BARD1-BGKcLV23-22
Sample_Name_Alias
Index Well Position	G05	H05
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	295	292
Peak_Molarity	83.60	105.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/G5.png	DNA_Library_set46/set1/H5.png
RIN	9.5	9.3
libSample_RNA_Well	RNA_Library_set46/set2/G9.png	RNA_Library_set46/set2/H9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-21	BGKcLV23-22
RBP	BARD1	BARD1
Batch_ID	BGKcLV23	BGKcLV23
WB_result	63.900	61.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1414	1415

Sequencing Information

	BGKcLV23-21	BGKcLV23-22
Sample_ID	BGKcLV23-21	BGKcLV23-22
Sample Name	BARD1-BGKcLV23-21	BARD1-BGKcLV23-22
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	158,140,492	164,604,554
total_aligned_reads	147,341,430	151,581,148
unique_aligned_reads	133,992,296	138,242,626
percent_uniqueAligned	0.84730	0.83985
correlation_replicates	0.999499	0.999499
spikein_reads	62,188	67,968
percent_spikeins	0.00039	0.00041
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	520	521

Data Submission Information

	BGKcLV23-21	BGKcLV23-21	BGKcLV23-21	BGKcLV23-21	BGKcLV23-21	BGKcLV23-21	BGKcLV23-22	BGKcLV23-22	BGKcLV23-22	BGKcLV23-22
ENCODE_alias	brenton-graveley:BARD1-BGKcLV23	brenton-graveley:BARD1-BGKcLV23-21	brenton-graveley:L-BARD1-BGKcLV23-21	brenton-graveley:BARD1-BGKcLV23-21_TAAGTGGT+GGCTTAAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BARD1-BGKcLV23-21_TAAGTGGT+GGCTTAAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BARD1-BGKcLV23-K562	brenton-graveley:BARD1-BGKcLV23-22	brenton-graveley:L-BARD1-BGKcLV23-22	brenton-graveley:BARD1-BGKcLV23-22_CGGACAAC+AATCCGGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BARD1-BGKcLV23-22_CGGACAAC+AATCCGGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR427KVG	ENCBS024RMA	ENCLB049DBT	ENCFF742KSK	ENCFF865CKW	ENCSR451JFM	ENCBS476NAR	ENCLB170WJK	ENCFF404LQI	ENCFF468NMQ
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	BGKcLV23-21	BGKcLV23-21	BGKcLV23-21	BGKcLV23-21	BGKcLV23-21	BGKcLV23-21	BGKcLV23-22	BGKcLV23-22	BGKcLV23-22	BGKcLV23-22
Sample Name	BARD1-BGKcLV23-21	BARD1-BGKcLV23-21	BARD1-BGKcLV23-21	BARD1-BGKcLV23-21	BARD1-BGKcLV23-21	BARD1-BGKcLV23-21	BARD1-BGKcLV23-22	BARD1-BGKcLV23-22	BARD1-BGKcLV23-22	BARD1-BGKcLV23-22
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		BARD1-BGKcLV23-21.pdf	L-BARD1-BGKcLV23-21.pdf				BARD1-BGKcLV23-22.pdf	L-BARD1-BGKcLV23-22.pdf
ID	2414	2465	2529	2623	2657	7098	2466	2530	2624	2658

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
BARD1-BGKcLV23-21_TAAGTGGT+GGCTTAAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	520	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	1384
BARD1-BGKcLV23-21_TAAGTGGT+GGCTTAAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	520	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	1448
BARD1-BGKcLV23-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	520					GRCh38	V40	BARD1-BGKcLV23-21_TAAGTGGT+GGCTTAAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,BARD1-BGKcLV23-21_TAAGTGGT+GGCTTAAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25287
BARD1-BGKcLV23-21_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	520					GRCh38	V40	BARD1-BGKcLV23-21_TAAGTGGT+GGCTTAAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,BARD1-BGKcLV23-21_TAAGTGGT+GGCTTAAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25321
BARD1-BGKcLV23-21_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	520					GRCh38	V40	BARD1-BGKcLV23-21/Aligned.sortedByCoord.out.bam		ENCORE2	26125
BARD1-BGKcLV23-21_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	520					GRCh38	V40	BARD1-BGKcLV23-21/Aligned.sortedByCoord.out.bam		ENCORE2	26159
BARD1-BGKcLV23-21_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	520					GRCh38	V40	BARD1-BGKcLV23-21/Aligned.sortedByCoord.out.bam		ENCORE2	26193
BARD1-BGKcLV23-21_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	520					GRCh38	V40	BARD1-BGKcLV23-21/Aligned.sortedByCoord.out.bam		ENCORE2	26227
BARD1-BGKcLV23-22_CGGACAAC+AATCCGGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	521	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	1385
BARD1-BGKcLV23-22_CGGACAAC+AATCCGGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	521	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	1449
BARD1-BGKcLV23-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	521					GRCh38	V40	BARD1-BGKcLV23-22_CGGACAAC+AATCCGGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,BARD1-BGKcLV23-22_CGGACAAC+AATCCGGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25288
BARD1-BGKcLV23-22_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	521					GRCh38	V40	BARD1-BGKcLV23-22_CGGACAAC+AATCCGGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,BARD1-BGKcLV23-22_CGGACAAC+AATCCGGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25322
BARD1-BGKcLV23-22_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	521					GRCh38	V40	BARD1-BGKcLV23-22/Aligned.sortedByCoord.out.bam		ENCORE2	26126
BARD1-BGKcLV23-22_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	521					GRCh38	V40	BARD1-BGKcLV23-22/Aligned.sortedByCoord.out.bam		ENCORE2	26160
BARD1-BGKcLV23-22_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	521					GRCh38	V40	BARD1-BGKcLV23-22/Aligned.sortedByCoord.out.bam		ENCORE2	26194
BARD1-BGKcLV23-22_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	521					GRCh38	V40	BARD1-BGKcLV23-22/Aligned.sortedByCoord.out.bam		ENCORE2	26228