CAB39 RNA-Seq in HepG2

General Information


RBP	CAB39
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CAB39-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CAB39-BGHcLV45-7
Rep2	CAB39-BGHcLV45-8
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	59.0
Rep2_qPCR	65.1
Rep1_WB	80.9
Rep2_WB	83.8
Antibody Cat#	2716S
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1617

Experiment Information (Status: Submitting)

	BGHcLV45-7	BGHcLV45-8
idx	1440	1441
TRCN#_or_BGC#	BGC#0001117	BGC#0001117
shRNA_or_gRNA_sequence	GAGCTGTAAATCAGCTACCA	GAGCTGTAAATCAGCTACCA
PAM	GGG	GGG
Name	CAB39_76	CAB39_76
Sample_ID	BGHcLV45-7	BGHcLV45-8
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	CAB39	CAB39
qPCR_result	59.0	65.1
Ave_qPCR	62.1
RT-qPCR_primer-F	aggagagcatggctgttctg
RT-qPCR_primer-R	atggcaaccagatttttgga
protein_conc	4671	4861
WB_result	80.9	83.8
Ave_WB
WB_DONE_date	10/9/24
MW	39kd
IP
antibody_Cat#	2716S	lot # 2
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9695	9696

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CAB39	Product_ID: 2716S Lot_ID: 2 Source: Cell Signaling Technology Target Name: CAB39-human

Experiment Status

	BGHcLV45-7	BGHcLV45-8
Sample_ID	BGHcLV45-7	BGHcLV45-8
Sample Name
Sample Name	CAB39-BGHcLV45-7	CAB39-BGHcLV45-8
RBP	CAB39	CAB39
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13692	13693

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-7	BGHcLV45-8
Sample #	7	8
Sample Name	CAB39-BGHcLV45-7	CAB39-BGHcLV45-8
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	280	285
Peak_Molarity	62.90	58.70
libSampleQC_DNA_Well	DNA_Library_set76/set1/G7.png	DNA_Library_set76/set1/H7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set76/set1/G1.png	RNA_Library_set76/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-7	BGHcLV45-8
RBP	CAB39	CAB39
Batch_ID	BGHcLV45	BGHcLV45
WB_result	80.900	83.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4616	4617

Sequencing Information

	BGHcLV45-7	BGHcLV45-8
Sample_ID	BGHcLV45-7	BGHcLV45-8
Sample Name	CAB39-BGHcLV45-7	CAB39-BGHcLV45-8
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	32,516,495	37,941,270
total_aligned_reads	28,325,558	33,791,929
unique_aligned_reads	26,634,686	31,799,677
percent_uniqueAligned	0.81911	0.83813
correlation_replicates	0.999003	0.999003
spikein_reads	27,400	51,716
percent_spikeins	0.00084	0.00136
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3327	3328

Data Submission Information DCC submission information was not avaliable

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
CAB39-BGHcLV45-7_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3327	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31816
CAB39-BGHcLV45-7_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3327	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31858
CAB39-BGHcLV45-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3327					GRCh38	V40	CAB39-BGHcLV45-7_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAB39-BGHcLV45-7_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31900
CAB39-BGHcLV45-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3327					GRCh38	V40	CAB39-BGHcLV45-7_Aligned.sortedByCoord.out.bam		ENCORE2	31942
CAB39-BGHcLV45-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3327					GRCh38	V40	CAB39-BGHcLV45-7_Aligned.sortedByCoord.out.bam		ENCORE2	31984
CAB39-BGHcLV45-7_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3327					GRCh38	V40	CAB39-BGHcLV45-7_Aligned.sortedByCoord.out.bam		ENCORE2	32026
CAB39-BGHcLV45-7_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3327					GRCh38	V40	CAB39-BGHcLV45-7_Aligned.sortedByCoord.out.bam		ENCORE2	32068
CAB39-BGHcLV45-7_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3327					GRCh38	V40	CAB39-BGHcLV45-7_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAB39-BGHcLV45-7_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32110
CAB39-BGHcLV45-8_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3328	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31817
CAB39-BGHcLV45-8_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3328	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31859
CAB39-BGHcLV45-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3328					GRCh38	V40	CAB39-BGHcLV45-8_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAB39-BGHcLV45-8_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31901
CAB39-BGHcLV45-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3328					GRCh38	V40	CAB39-BGHcLV45-8_Aligned.sortedByCoord.out.bam		ENCORE2	31943
CAB39-BGHcLV45-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3328					GRCh38	V40	CAB39-BGHcLV45-8_Aligned.sortedByCoord.out.bam		ENCORE2	31985
CAB39-BGHcLV45-8_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3328					GRCh38	V40	CAB39-BGHcLV45-8_Aligned.sortedByCoord.out.bam		ENCORE2	32027
CAB39-BGHcLV45-8_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3328					GRCh38	V40	CAB39-BGHcLV45-8_Aligned.sortedByCoord.out.bam		ENCORE2	32069
CAB39-BGHcLV45-8_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3328					GRCh38	V40	CAB39-BGHcLV45-8_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAB39-BGHcLV45-8_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32111