BYSL RNA-Seq in K562

General Information


RBP	BYSL
Cell_Line	K562
Method	CRISPR
Exp_Name	BYSL-BGKcLV26-K562
ENCODE_series_ID	ENCSR075BGQ
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR012OCK
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	BYSL-BGKcLV26-43
Rep2	BYSL-BGKcLV26-44
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	66.3
Rep2_qPCR	74.5
Rep1_WB	69.6
Rep2_WB	61.6008935
Antibody Cat#	A304-568A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB273OKQ
Status	Released
Project	ENCODE4
ID	797

Experiment Information (Status: Released)

	BGKcLV26-43	BGKcLV26-44
idx	904	905
TRCN#_or_BGC#	BGC#0000651	BGC#0000651
shRNA_or_gRNA_sequence	CAAATTCAAGGCGGCCCGTG	CAAATTCAAGGCGGCCCGTG
PAM	GGG	GGG
Name	BYSL_91	BYSL_91
Sample_ID	BGKcLV26-43	BGKcLV26-44
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	BYSL	BYSL
qPCR_result	66.3	74.5
Ave_qPCR	70.4
RT-qPCR_primer-F	ccccgggtcctagaagtgta
RT-qPCR_primer-R	agttggagagtgcagggatg
protein_conc	4255	5436
WB_result	69.6	61.6
Ave_WB	65.6
WB_DONE_date	6/25/21	jess
MW	50kDa
IP	Rabbit / I
antibody_Cat#	A304-568A	LOT# 1
Antibody DCC ID	ENCAB273OKQ	10/22/21
submitted_to_DCC_date
Rep1_TPM	49.2	0
Rep2_TPM	49.4	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5036	5037

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BYSL	Product_ID: A304-568A Lot_ID: 1 Source: Bethyl Labs Target Name: BYSL-human

Experiment Status

	BGKcLV26-43	BGKcLV26-44
Sample_ID	BGKcLV26-43	BGKcLV26-44
Sample Name
Sample Name	BYSL-BGKcLV26-43	BYSL-BGKcLV26-44
RBP	BYSL	BYSL
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9775	9776

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-43	BGKcLV26-44
Sample #	33	34
Sample Name	BYSL-BGKcLV26-43	BYSL-BGKcLV26-44
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	297	297
Peak_Molarity	102.00	109.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/A5.png	DNA_Library_set48-49/set1/B5.png
RIN	9.1	9.5
libSample_RNA_Well	RNA_Library_set48-49/set1/A5.png	RNA_Library_set48-49/set1/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-43	BGKcLV26-44
RBP	BYSL	BYSL
Batch_ID	BGKcLV26	BGKcLV26
WB_result	69.600	61.601
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1592	1593

Sequencing Information

	BGKcLV26-43	BGKcLV26-44
Sample_ID	BGKcLV26-43	BGKcLV26-44
Sample Name	BYSL-BGKcLV26-43	BYSL-BGKcLV26-44
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	93,719,258	69,254,148
total_aligned_reads	82,568,776	62,010,556
unique_aligned_reads	75,644,298	56,572,962
percent_uniqueAligned	0.80714	0.81689
correlation_replicates	0.999438	0.999438
spikein_reads	44,258	22,478
percent_spikeins	0.00047	0.00032
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1769	1770

Data Submission Information

	BGKcLV26-43	BGKcLV26-43	BGKcLV26-43	BGKcLV26-43	BGKcLV26-43	BGKcLV26-43	BGKcLV26-44	BGKcLV26-44	BGKcLV26-44	BGKcLV26-44
ENCODE_alias	brenton-graveley:BYSL-BGKcLV26	brenton-graveley:BYSL-BGKcLV26-43	brenton-graveley:L-BYSL-BGKcLV26-43	brenton-graveley:BYSL-BGKcLV26-43_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BYSL-BGKcLV26-43_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BYSL-BGKcLV26-K562	brenton-graveley:BYSL-BGKcLV26-44	brenton-graveley:L-BYSL-BGKcLV26-44	brenton-graveley:BYSL-BGKcLV26-44_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BYSL-BGKcLV26-44_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR012OCK	ENCBS842HKQ	ENCLB435ULD	ENCFF063RTP	ENCFF995QXS	ENCSR075BGQ	ENCBS033RQQ	ENCLB775UIS	ENCFF781HTW	ENCFF696BUC
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	BGKcLV26-43	BGKcLV26-43	BGKcLV26-43	BGKcLV26-43	BGKcLV26-43	BGKcLV26-43	BGKcLV26-44	BGKcLV26-44	BGKcLV26-44	BGKcLV26-44
Sample Name	BYSL-BGKcLV26-43	BYSL-BGKcLV26-43	BYSL-BGKcLV26-43	BYSL-BGKcLV26-43	BYSL-BGKcLV26-43	BYSL-BGKcLV26-43	BYSL-BGKcLV26-44	BYSL-BGKcLV26-44	BYSL-BGKcLV26-44	BYSL-BGKcLV26-44
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		BYSL-BGKcLV26-43.pdf	L-BYSL-BGKcLV26-43.pdf				BYSL-BGKcLV26-44.pdf	L-BYSL-BGKcLV26-44.pdf
ID	3462	3558	3692	3826	3960	7104	3559	3693	3827	3961

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
BYSL-BGKcLV26-43_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1769	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3862
BYSL-BGKcLV26-43_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1769	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3912
BYSL-BGKcLV26-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1769					GRCh38	V40	BYSL-BGKcLV26-43_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,BYSL-BGKcLV26-43_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25549
BYSL-BGKcLV26-43_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1769					GRCh38	V40	BYSL-BGKcLV26-43_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,BYSL-BGKcLV26-43_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25599
BYSL-BGKcLV26-43_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1769					GRCh38	V40	BYSL-BGKcLV26-43/Aligned.sortedByCoord.out.bam		ENCORE2	26565
BYSL-BGKcLV26-43_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1769					GRCh38	V40	BYSL-BGKcLV26-43/Aligned.sortedByCoord.out.bam		ENCORE2	26615
BYSL-BGKcLV26-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1769					GRCh38	V40	BYSL-BGKcLV26-43/Aligned.sortedByCoord.out.bam		ENCORE2	26665
BYSL-BGKcLV26-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1769					GRCh38	V40	BYSL-BGKcLV26-43/Aligned.sortedByCoord.out.bam		ENCORE2	26715
BYSL-BGKcLV26-44_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1770	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3863
BYSL-BGKcLV26-44_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1770	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3913
BYSL-BGKcLV26-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1770					GRCh38	V40	BYSL-BGKcLV26-44_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz,BYSL-BGKcLV26-44_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25550
BYSL-BGKcLV26-44_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1770					GRCh38	V40	BYSL-BGKcLV26-44_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz,BYSL-BGKcLV26-44_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25600
BYSL-BGKcLV26-44_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1770					GRCh38	V40	BYSL-BGKcLV26-44/Aligned.sortedByCoord.out.bam		ENCORE2	26566
BYSL-BGKcLV26-44_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1770					GRCh38	V40	BYSL-BGKcLV26-44/Aligned.sortedByCoord.out.bam		ENCORE2	26616
BYSL-BGKcLV26-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1770					GRCh38	V40	BYSL-BGKcLV26-44/Aligned.sortedByCoord.out.bam		ENCORE2	26666
BYSL-BGKcLV26-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1770					GRCh38	V40	BYSL-BGKcLV26-44/Aligned.sortedByCoord.out.bam		ENCORE2	26716