CAND1 RNA-Seq in K562

General Information


RBP	CAND1
Cell_Line	K562
Method	CRISPR
Exp_Name	CAND1-BGKcLV26-K562
ENCODE_series_ID	ENCSR124ARP
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR527XZI
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	CAND1-BGKcLV26-51
Rep2	CAND1-BGKcLV26-52
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	24.7
Rep2_qPCR	27.9
Rep1_WB	50.4
Rep2_WB	57.1660932
Antibody Cat#	A302-900A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB240SHA
Status	Released
Project	ENCODE4
ID	799

Experiment Information (Status: Released)

	BGKcLV26-51	BGKcLV26-52
idx	912	913
TRCN#_or_BGC#	BGC#0000660	BGC#0000660
shRNA_or_gRNA_sequence	TTTAGGGCATGCTCGAGTAA	TTTAGGGCATGCTCGAGTAA
PAM	GGG	GGG
Name	CAND1_95	CAND1_95
Sample_ID	BGKcLV26-51	BGKcLV26-52
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	CAND1	CAND1
qPCR_result	24.7	27.9
Ave_qPCR	26.3
RT-qPCR_primer-F	atcatatgcccgaagctcag
RT-qPCR_primer-R	cattcaaatctgggtcttcca
protein_conc	4282	5391
WB_result	50.4	57.2
Ave_WB	53.8
WB_DONE_date	5/28/21	jess
MW	136kDa
IP	Rabbit / I
antibody_Cat#	A302-900A	LOT# 1
Antibody DCC ID	ENCAB240SHA	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5044	5045

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CAND1	Product_ID: A302-900A Lot_ID: 1 Source: Bethyl Labs Target Name: CAND1-human

Experiment Status

	BGKcLV26-51	BGKcLV26-52
Sample_ID	BGKcLV26-51	BGKcLV26-52
Sample Name
Sample Name	CAND1-BGKcLV26-51	CAND1-BGKcLV26-52
RBP	CAND1	CAND1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9779	9780

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-51	BGKcLV26-52
Sample #	37	38
Sample Name	CAND1-BGKcLV26-51	CAND1-BGKcLV26-52
Sample_Name_Alias
Index Well Position	E05	F05
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	295
Peak_Molarity	136.00	117.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/E5.png	DNA_Library_set48-49/set1/F5.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set48-49/set1/E5.png	RNA_Library_set48-49/set1/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-51	BGKcLV26-52
RBP	CAND1	CAND1
Batch_ID	BGKcLV26	BGKcLV26
WB_result	50.400	57.166
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1596	1597

Sequencing Information

	BGKcLV26-51	BGKcLV26-52
Sample_ID	BGKcLV26-51	BGKcLV26-52
Sample Name	CAND1-BGKcLV26-51	CAND1-BGKcLV26-52
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	53,075,750	75,796,328
total_aligned_reads	46,223,762	67,474,536
unique_aligned_reads	42,374,886	61,809,582
percent_uniqueAligned	0.79839	0.81547
correlation_replicates	0.996239	0.996239
spikein_reads	19,094	23,602
percent_spikeins	0.00036	0.00031
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1773	1774

Data Submission Information

	BGKcLV26-51	BGKcLV26-51	BGKcLV26-51	BGKcLV26-51	BGKcLV26-51	BGKcLV26-51	BGKcLV26-52	BGKcLV26-52	BGKcLV26-52	BGKcLV26-52
ENCODE_alias	brenton-graveley:CAND1-BGKcLV26	brenton-graveley:CAND1-BGKcLV26-51	brenton-graveley:L-CAND1-BGKcLV26-51	brenton-graveley:CAND1-BGKcLV26-51_S43_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAND1-BGKcLV26-51_S43_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAND1-BGKcLV26-K562	brenton-graveley:CAND1-BGKcLV26-52	brenton-graveley:L-CAND1-BGKcLV26-52	brenton-graveley:CAND1-BGKcLV26-52_S44_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAND1-BGKcLV26-52_S44_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR527XZI	ENCBS010UIL	ENCLB373SXC	ENCFF688RAN	ENCFF521KBS	ENCSR124ARP	ENCBS338UWS	ENCLB799XBG	ENCFF267LTN	ENCFF146EFR
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	BGKcLV26-51	BGKcLV26-51	BGKcLV26-51	BGKcLV26-51	BGKcLV26-51	BGKcLV26-51	BGKcLV26-52	BGKcLV26-52	BGKcLV26-52	BGKcLV26-52
Sample Name	CAND1-BGKcLV26-51	CAND1-BGKcLV26-51	CAND1-BGKcLV26-51	CAND1-BGKcLV26-51	CAND1-BGKcLV26-51	CAND1-BGKcLV26-51	CAND1-BGKcLV26-52	CAND1-BGKcLV26-52	CAND1-BGKcLV26-52	CAND1-BGKcLV26-52
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		CAND1-BGKcLV26-51.pdf	L-CAND1-BGKcLV26-51.pdf				CAND1-BGKcLV26-52.pdf	L-CAND1-BGKcLV26-52.pdf
ID	3464	3562	3696	3830	3964	7111	3563	3697	3831	3965

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
CAND1-BGKcLV26-51_S43_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1773	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	3866
CAND1-BGKcLV26-51_S43_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1773	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	3916
CAND1-BGKcLV26-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1773					GRCh38	V40	CAND1-BGKcLV26-51_S43_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAND1-BGKcLV26-51_S43_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25553
CAND1-BGKcLV26-51_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1773					GRCh38	V40	CAND1-BGKcLV26-51_S43_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAND1-BGKcLV26-51_S43_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25603
CAND1-BGKcLV26-51_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	1773					GRCh38	V40	CAND1-BGKcLV26-51/Aligned.sortedByCoord.out.bam		ENCORE2	26569
CAND1-BGKcLV26-51_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	1773					GRCh38	V40	CAND1-BGKcLV26-51/Aligned.sortedByCoord.out.bam		ENCORE2	26619
CAND1-BGKcLV26-51_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	1773					GRCh38	V40	CAND1-BGKcLV26-51/Aligned.sortedByCoord.out.bam		ENCORE2	26669
CAND1-BGKcLV26-51_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	1773					GRCh38	V40	CAND1-BGKcLV26-51/Aligned.sortedByCoord.out.bam		ENCORE2	26719
CAND1-BGKcLV26-52_S44_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1774	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	3867
CAND1-BGKcLV26-52_S44_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1774	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	3917
CAND1-BGKcLV26-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1774					GRCh38	V40	CAND1-BGKcLV26-52_S44_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAND1-BGKcLV26-52_S44_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25554
CAND1-BGKcLV26-52_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1774					GRCh38	V40	CAND1-BGKcLV26-52_S44_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAND1-BGKcLV26-52_S44_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25604
CAND1-BGKcLV26-52_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	1774					GRCh38	V40	CAND1-BGKcLV26-52/Aligned.sortedByCoord.out.bam		ENCORE2	26570
CAND1-BGKcLV26-52_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	1774					GRCh38	V40	CAND1-BGKcLV26-52/Aligned.sortedByCoord.out.bam		ENCORE2	26620
CAND1-BGKcLV26-52_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	1774					GRCh38	V40	CAND1-BGKcLV26-52/Aligned.sortedByCoord.out.bam		ENCORE2	26670
CAND1-BGKcLV26-52_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	1774					GRCh38	V40	CAND1-BGKcLV26-52/Aligned.sortedByCoord.out.bam		ENCORE2	26720