CNDP2 RNA-Seq in HepG2

General Information


RBP	CNDP2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CNDP2-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR097WOJ
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR085GSF
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CNDP2-BGHcLV29-27
Rep2	CNDP2-BGHcLV29-28
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	73
Rep2_qPCR	77.3
Rep1_WB	82.5
Rep2_WB	79.5
Antibody Cat#	A305-565A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB798DYU
Status	Submitted
Project	ENCODE4
ID	854

Experiment Information (Status: Released)

	BGHcLV29-27	BGHcLV29-28
idx	860	861
TRCN#_or_BGC#	BGC#0000704	BGC#0000704
shRNA_or_gRNA_sequence	GTGCTCCTCTTCCGTGACGG	GTGCTCCTCTTCCGTGACGG
PAM	CGG	CGG
Name	CNDP2_94	CNDP2_94
Sample_ID	BGHcLV29-27	BGHcLV29-28
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	CNDP2	CNDP2
qPCR_result	73	77.3
Ave_qPCR	75.15
RT-qPCR_primer-F	tggagtgcagcaacaaagac
RT-qPCR_primer-R	cctcttgtccaccaaagagc
protein_conc	4810	4767
WB_result	82.5	79.5
Ave_WB	81.0
WB_DONE_date	7/30/21	JESS
MW	53kd
IP	Rabbit / I
antibody_Cat#	A305-565A	LOT #1
Antibody DCC ID	ENCAB798DYU
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	7037	7038

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CNDP2	Product_ID: A305-565A Lot_ID: 1 Source: Bethyl Labs Target Name: CNDP2-human

Experiment Status

	BGHcLV29-27	BGHcLV29-28
Sample_ID	BGHcLV29-27	BGHcLV29-28
Sample Name
Sample Name	CNDP2-BGHcLV29-27	CNDP2-BGHcLV29-28
RBP	CNDP2	CNDP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9993	9994

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-27	BGHcLV29-28
Sample #	21	22
Sample Name	CNDP2-BGHcLV29-27	CNDP2-BGHcLV29-28
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	290	294
Peak_Molarity	36.40	39.60
libSampleQC_DNA_Well	DNA_Library_set50/set1/E3.png	DNA_Library_set50/set1/F3.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set50/set1/E9.png	RNA_Library_set50/set1/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-27	BGHcLV29-28
RBP	CNDP2	CNDP2
Batch_ID	BGHcLV29	BGHcLV29
WB_result	82.500	79.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3108	3109

Sequencing Information

	BGHcLV29-27	BGHcLV29-28
Sample_ID	BGHcLV29-27	BGHcLV29-28
Sample Name	CNDP2-BGHcLV29-27	CNDP2-BGHcLV29-28
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	116,060,344	68,741,430
total_aligned_reads	106,118,334	63,271,638
unique_aligned_reads	100,028,366	59,731,718
percent_uniqueAligned	0.86187	0.86893
correlation_replicates	0.999120	0.999120
spikein_reads	24,184	18,234
percent_spikeins	0.00021	0.00027
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1889	1890

Data Submission Information

	BGHcLV29-27	BGHcLV29-27	BGHcLV29-27	BGHcLV29-27	BGHcLV29-27	BGHcLV29-27	BGHcLV29-28	BGHcLV29-28	BGHcLV29-28	BGHcLV29-28
ENCODE_alias	brenton-graveley:CNDP2-BGHcLV29	brenton-graveley:CNDP2-BGHcLV29-27	brenton-graveley:L-CNDP2-BGHcLV29-27	brenton-graveley:CNDP2-BGHcLV29-27_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNDP2-BGHcLV29-27_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNDP2-BGHcLV29-HepG2	brenton-graveley:CNDP2-BGHcLV29-28	brenton-graveley:L-CNDP2-BGHcLV29-28	brenton-graveley:CNDP2-BGHcLV29-28_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CNDP2-BGHcLV29-28_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR085GSF	ENCBS355KGS	ENCLB947EFS	ENCFF612VED	ENCFF751EYT	ENCSR097WOJ	ENCBS458NJP	ENCLB063ZJC	ENCFF946QMR	ENCFF697RNI
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	BGHcLV29-27	BGHcLV29-27	BGHcLV29-27	BGHcLV29-27	BGHcLV29-27	BGHcLV29-27	BGHcLV29-28	BGHcLV29-28	BGHcLV29-28	BGHcLV29-28
Sample Name	CNDP2-BGHcLV29-27	CNDP2-BGHcLV29-27	CNDP2-BGHcLV29-27	CNDP2-BGHcLV29-27	CNDP2-BGHcLV29-27	CNDP2-BGHcLV29-27	CNDP2-BGHcLV29-28	CNDP2-BGHcLV29-28	CNDP2-BGHcLV29-28	CNDP2-BGHcLV29-28
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		CNDP2-BGHcLV29-27.pdf	L-CNDP2-BGHcLV29-27.pdf				CNDP2-BGHcLV29-28.pdf	L-CNDP2-BGHcLV29-28.pdf
ID	5852	5897	5969	6041	6113	6175	5898	5970	6042	6114

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
CNDP2-BGHcLV29-27_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1889	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5777
CNDP2-BGHcLV29-27_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1889	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5819
CNDP2-BGHcLV29-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1889					GRCh38	V40	CNDP2-BGHcLV29-27_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNDP2-BGHcLV29-27_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18944
CNDP2-BGHcLV29-27_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1889					GRCh38	V40	CNDP2-BGHcLV29-27/Aligned.sortedByCoord.out.bam		ENCORE2	19002
CNDP2-BGHcLV29-27_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1889					GRCh38	V40	CNDP2-BGHcLV29-27/Aligned.sortedByCoord.out.bam		ENCORE2	19048
CNDP2-BGHcLV29-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1889					GRCh38	V40	CNDP2-BGHcLV29-27/Aligned.sortedByCoord.out.bam		ENCORE2	19094
CNDP2-BGHcLV29-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1889					GRCh38	V40	CNDP2-BGHcLV29-27/Aligned.sortedByCoord.out.bam		ENCORE2	19140
CNDP2-BGHcLV29-27_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1889					GRCh38	V40	CNDP2-BGHcLV29-27_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNDP2-BGHcLV29-27_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19186
CNDP2-BGHcLV29-28_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1890	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5778
CNDP2-BGHcLV29-28_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1890	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5820
CNDP2-BGHcLV29-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1890					GRCh38	V40	CNDP2-BGHcLV29-28_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNDP2-BGHcLV29-28_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18945
CNDP2-BGHcLV29-28_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1890					GRCh38	V40	CNDP2-BGHcLV29-28/Aligned.sortedByCoord.out.bam		ENCORE2	19003
CNDP2-BGHcLV29-28_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1890					GRCh38	V40	CNDP2-BGHcLV29-28/Aligned.sortedByCoord.out.bam		ENCORE2	19049
CNDP2-BGHcLV29-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1890					GRCh38	V40	CNDP2-BGHcLV29-28/Aligned.sortedByCoord.out.bam		ENCORE2	19095
CNDP2-BGHcLV29-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1890					GRCh38	V40	CNDP2-BGHcLV29-28/Aligned.sortedByCoord.out.bam		ENCORE2	19141
CNDP2-BGHcLV29-28_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1890					GRCh38	V40	CNDP2-BGHcLV29-28_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,CNDP2-BGHcLV29-28_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19187