CAND1 RNA-Seq in HepG2

General Information


RBP	CAND1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CAND1-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR564DRD
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR297ONN
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	CAND1-BGHcLV27-33
Rep2	CAND1-BGHcLV27-34
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	65.2
Rep2_qPCR	64.8
Rep1_WB	95.5
Rep2_WB	95.7
Antibody Cat#	A302-900A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB240SHA
Status	Released
Project	ENCODE4
ID	813

Experiment Information (Status: Released)

	BGHcLV27-33	BGHcLV27-33	BGHcLV27-34	BGHcLV27-34
idx	799	799	800	800
TRCN#_or_BGC#	BGC#0000660	BGC#0000660	BGC#0000660	BGC#0000660
shRNA_or_gRNA_sequence	TTTAGGGCATGCTCGAGTAA	TTTAGGGCATGCTCGAGTAA	TTTAGGGCATGCTCGAGTAA	TTTAGGGCATGCTCGAGTAA
PAM	GGG	GGG	GGG	GGG
Name	CAND1_95	CAND1_95	CAND1_95	CAND1_95
Sample_ID	BGHcLV27-33	BGHcLV27-33	BGHcLV27-34	BGHcLV27-34
transduction_Date	5/18/21	5/18/21	5/18/21	5/18/21
days	D6	D6	D6	D6
RBP_name	CAND1	CAND1	CAND1	CAND1
qPCR_result	65.2	65.2	64.8	64.8
Ave_qPCR	65.0	65.0
RT-qPCR_primer-F	atcatatgcccgaagctcag	atcatatgcccgaagctcag
RT-qPCR_primer-R	cattcaaatctgggtcttcca	cattcaaatctgggtcttcca
protein_conc	3328	3328	4201	4201
WB_result	95.5	95.8	95.7	92.8
Ave_WB	95.6	94.3
WB_DONE_date	5/28/21	6/28/22	JESS
MW	136kDa	136kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A302-900A	A302-901A	LOT# 1	LOT # 1
Antibody DCC ID	ENCAB240SHA	ENCAB076TWD	10/22/21
submitted_to_DCC_date		8/16/22
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/03/21		09/03/21
repeat_library
Note
ID	6966	6968	6967	6969

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
CAND1	Product_ID: A302-901A Lot_ID: 1 Source: Bethyl Labs Target Name: CAND1-human

Experiment Status

	BGHcLV27-33	BGHcLV27-34
Sample_ID	BGHcLV27-33	BGHcLV27-34
Sample Name
Sample Name	CAND1-BGHcLV27-33	CAND1-BGHcLV27-34
RBP	CAND1	CAND1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9689	9690

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-33	BGHcLV27-34
Sample #	93	94
Sample Name	CAND1-BGHcLV27-33	CAND1-BGHcLV27-34
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	292	329
Peak_Molarity	126.00	90.50
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/A9.png	DNA_Library_set48-49/set2/B9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set48-49/set1/C9.png	RNA_Library_set48-49/set1/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-33	BGHcLV27-34
RBP	CAND1	CAND1
Batch_ID	BGHcLV27	BGHcLV27
WB_result	95.500	95.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1652	1653

Sequencing Information

	BGHcLV27-33	BGHcLV27-34
Sample_ID	BGHcLV27-33	BGHcLV27-34
Sample Name	CAND1-BGHcLV27-33	CAND1-BGHcLV27-34
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	73,867,792	90,435,444
total_aligned_reads	63,960,544	78,860,470
unique_aligned_reads	60,166,234	74,134,566
percent_uniqueAligned	0.81451	0.81975
correlation_replicates	0.996457	0.996457
spikein_reads	26,800	19,880
percent_spikeins	0.00036	0.00022
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1803	1804

Data Submission Information

	BGHcLV27-33	BGHcLV27-33	BGHcLV27-33	BGHcLV27-33	BGHcLV27-33	BGHcLV27-33	BGHcLV27-34	BGHcLV27-34	BGHcLV27-34	BGHcLV27-34
ENCODE_alias	brenton-graveley:CAND1-BGHcLV27	brenton-graveley:CAND1-BGHcLV27-33	brenton-graveley:L-CAND1-BGHcLV27-33	brenton-graveley:CAND1-BGHcLV27-33_S73_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAND1-BGHcLV27-33_S73_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAND1-BGHcLV27-HepG2	brenton-graveley:CAND1-BGHcLV27-34	brenton-graveley:L-CAND1-BGHcLV27-34	brenton-graveley:CAND1-BGHcLV27-34_S74_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAND1-BGHcLV27-34_S74_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR297ONN	ENCBS072RXM	ENCLB251PON	ENCFF453RGE	ENCFF644AUX	ENCSR564DRD	ENCBS144VMS	ENCLB993ALE	ENCFF021SBN	ENCFF965RWR
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	BGHcLV27-33	BGHcLV27-33	BGHcLV27-33	BGHcLV27-33	BGHcLV27-33	BGHcLV27-33	BGHcLV27-34	BGHcLV27-34	BGHcLV27-34	BGHcLV27-34
Sample Name	CAND1-BGHcLV27-33	CAND1-BGHcLV27-33	CAND1-BGHcLV27-33	CAND1-BGHcLV27-33	CAND1-BGHcLV27-33	CAND1-BGHcLV27-33	CAND1-BGHcLV27-34	CAND1-BGHcLV27-34	CAND1-BGHcLV27-34	CAND1-BGHcLV27-34
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
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		CAND1-BGHcLV27-33.pdf	L-CAND1-BGHcLV27-33.pdf				CAND1-BGHcLV27-34.pdf	L-CAND1-BGHcLV27-34.pdf
ID	3441	3516	3650	3784	3918	7110	3517	3651	3785	3919

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-BGHcLV27-33_S73_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1803	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3794
CAND1-BGHcLV27-33_S73_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1803	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3820
CAND1-BGHcLV27-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1803					GRCh38	V40	CAND1-BGHcLV27-33_S73_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAND1-BGHcLV27-33_S73_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25481
CAND1-BGHcLV27-33_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1803					GRCh38	V40	CAND1-BGHcLV27-33_S73_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAND1-BGHcLV27-33_S73_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25507
CAND1-BGHcLV27-33_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1803					GRCh38	V40	CAND1-BGHcLV27-33/Aligned.sortedByCoord.out.bam		ENCORE2	26445
CAND1-BGHcLV27-33_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1803					GRCh38	V40	CAND1-BGHcLV27-33/Aligned.sortedByCoord.out.bam		ENCORE2	26471
CAND1-BGHcLV27-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1803					GRCh38	V40	CAND1-BGHcLV27-33/Aligned.sortedByCoord.out.bam		ENCORE2	26497
CAND1-BGHcLV27-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1803					GRCh38	V40	CAND1-BGHcLV27-33/Aligned.sortedByCoord.out.bam		ENCORE2	26523
CAND1-BGHcLV27-34_S74_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1804	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3795
CAND1-BGHcLV27-34_S74_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1804	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3821
CAND1-BGHcLV27-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1804					GRCh38	V40	CAND1-BGHcLV27-34_S74_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAND1-BGHcLV27-34_S74_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25482
CAND1-BGHcLV27-34_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1804					GRCh38	V40	CAND1-BGHcLV27-34_S74_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAND1-BGHcLV27-34_S74_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25508
CAND1-BGHcLV27-34_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1804					GRCh38	V40	CAND1-BGHcLV27-34/Aligned.sortedByCoord.out.bam		ENCORE2	26446
CAND1-BGHcLV27-34_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1804					GRCh38	V40	CAND1-BGHcLV27-34/Aligned.sortedByCoord.out.bam		ENCORE2	26472
CAND1-BGHcLV27-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1804					GRCh38	V40	CAND1-BGHcLV27-34/Aligned.sortedByCoord.out.bam		ENCORE2	26498
CAND1-BGHcLV27-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1804					GRCh38	V40	CAND1-BGHcLV27-34/Aligned.sortedByCoord.out.bam		ENCORE2	26524