CLNS1A RNA-Seq in HepG2

General Information


RBP	CLNS1A
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CLNS1A-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR298YMO
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR513CVF
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CLNS1A-BGHcLV29-21
Rep2	CLNS1A-BGHcLV29-22
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	60.5
Rep2_qPCR	62.6
Rep1_WB	73.3
Rep2_WB	73.6
Antibody Cat#	A304-521A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB677WEY
Status	Submitted
Project	ENCODE4
ID	851

Experiment Information (Status: Released)

	BGHcLV29-21	BGHcLV29-22
idx	852	853
TRCN#_or_BGC#	BGC#0000697	BGC#0000697
shRNA_or_gRNA_sequence	TGTAAAGGGTACCAGTGCCG	TGTAAAGGGTACCAGTGCCG
PAM	AGG	AGG
Name	CLNS1A_82	CLNS1A_82
Sample_ID	BGHcLV29-21	BGHcLV29-22
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	CLNS1A	CLNS1A
qPCR_result	60.5	62.6
Ave_qPCR	61.55
RT-qPCR_primer-F	tgttgctgatgaagaagaggaa
RT-qPCR_primer-R	ctcaggatctggatgcaagg
protein_conc	0	3622
WB_result	73.3	73.6
Ave_WB	73.5
WB_DONE_date	8/26/21
MW	26kd
IP	Rabbit / I
antibody_Cat#	A304-521A	LOT #1
Antibody DCC ID	ENCAB677WEY
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	7029	7030

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CLNS1A	Product_ID: A304-521A Lot_ID: 1 Source: Bethyl Labs Target Name: CLNS1A-human

Experiment Status

	BGHcLV29-21	BGHcLV29-22
Sample_ID	BGHcLV29-21	BGHcLV29-22
Sample Name
Sample Name	CLNS1A-BGHcLV29-21	CLNS1A-BGHcLV29-22
RBP	CLNS1A	CLNS1A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9987	9988

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-21	BGHcLV29-22
Sample #	15	16
Sample Name	CLNS1A-BGHcLV29-21	CLNS1A-BGHcLV29-22
Sample_Name_Alias
Index Well Position	G02	H02
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	293	288
Peak_Molarity	49.50	38.30
libSampleQC_DNA_Well	DNA_Library_set50/set1/G2.png	DNA_Library_set50/set1/H2.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set50/set1/G8.png	RNA_Library_set50/set1/H8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-21	BGHcLV29-22
RBP	CLNS1A	CLNS1A
Batch_ID	BGHcLV29	BGHcLV29
WB_result	73.300	73.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3102	3103

Sequencing Information

	BGHcLV29-21	BGHcLV29-22
Sample_ID	BGHcLV29-21	BGHcLV29-22
Sample Name	CLNS1A-BGHcLV29-21	CLNS1A-BGHcLV29-22
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	97,783,270	63,525,684
total_aligned_reads	92,537,202	58,349,442
unique_aligned_reads	87,399,638	55,027,794
percent_uniqueAligned	0.89381	0.86623
correlation_replicates	0.990230	0.990230
spikein_reads	18,510	13,724
percent_spikeins	0.00019	0.00022
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1883	1884

Data Submission Information

	BGHcLV29-21	BGHcLV29-21	BGHcLV29-21	BGHcLV29-21	BGHcLV29-21	BGHcLV29-21	BGHcLV29-22	BGHcLV29-22	BGHcLV29-22	BGHcLV29-22
ENCODE_alias	brenton-graveley:CLNS1A-BGHcLV29	brenton-graveley:CLNS1A-BGHcLV29-21	brenton-graveley:L-CLNS1A-BGHcLV29-21	brenton-graveley:CLNS1A-BGHcLV29-21_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLNS1A-BGHcLV29-21_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLNS1A-BGHcLV29-HepG2	brenton-graveley:CLNS1A-BGHcLV29-22	brenton-graveley:L-CLNS1A-BGHcLV29-22	brenton-graveley:CLNS1A-BGHcLV29-22_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLNS1A-BGHcLV29-22_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR513CVF	ENCBS418TNU	ENCLB108BSV	ENCFF140WEQ	ENCFF089RAQ	ENCSR298YMO	ENCBS286JRV	ENCLB667ZNE	ENCFF865LUZ	ENCFF197HIV
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	BGHcLV29-21	BGHcLV29-21	BGHcLV29-21	BGHcLV29-21	BGHcLV29-21	BGHcLV29-21	BGHcLV29-22	BGHcLV29-22	BGHcLV29-22	BGHcLV29-22
Sample Name	CLNS1A-BGHcLV29-21	CLNS1A-BGHcLV29-21	CLNS1A-BGHcLV29-21	CLNS1A-BGHcLV29-21	CLNS1A-BGHcLV29-21	CLNS1A-BGHcLV29-21	CLNS1A-BGHcLV29-22	CLNS1A-BGHcLV29-22	CLNS1A-BGHcLV29-22	CLNS1A-BGHcLV29-22
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		CLNS1A-BGHcLV29-21.pdf	L-CLNS1A-BGHcLV29-21.pdf				CLNS1A-BGHcLV29-22.pdf	L-CLNS1A-BGHcLV29-22.pdf
ID	5849	5891	5963	6035	6107	6172	5892	5964	6036	6108

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
CLNS1A-BGHcLV29-21_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1883	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	5771
CLNS1A-BGHcLV29-21_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1883	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	5813
CLNS1A-BGHcLV29-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1883					GRCh38	V40	CLNS1A-BGHcLV29-21_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,CLNS1A-BGHcLV29-21_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18938
CLNS1A-BGHcLV29-21_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	1883					GRCh38	V40	CLNS1A-BGHcLV29-21/Aligned.sortedByCoord.out.bam		ENCORE2	18996
CLNS1A-BGHcLV29-21_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	1883					GRCh38	V40	CLNS1A-BGHcLV29-21/Aligned.sortedByCoord.out.bam		ENCORE2	19042
CLNS1A-BGHcLV29-21_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	1883					GRCh38	V40	CLNS1A-BGHcLV29-21/Aligned.sortedByCoord.out.bam		ENCORE2	19088
CLNS1A-BGHcLV29-21_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	1883					GRCh38	V40	CLNS1A-BGHcLV29-21/Aligned.sortedByCoord.out.bam		ENCORE2	19134
CLNS1A-BGHcLV29-21_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1883					GRCh38	V40	CLNS1A-BGHcLV29-21_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,CLNS1A-BGHcLV29-21_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19180
CLNS1A-BGHcLV29-22_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1884	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	5772
CLNS1A-BGHcLV29-22_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1884	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	5814
CLNS1A-BGHcLV29-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1884					GRCh38	V40	CLNS1A-BGHcLV29-22_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,CLNS1A-BGHcLV29-22_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18939
CLNS1A-BGHcLV29-22_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	1884					GRCh38	V40	CLNS1A-BGHcLV29-22/Aligned.sortedByCoord.out.bam		ENCORE2	18997
CLNS1A-BGHcLV29-22_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	1884					GRCh38	V40	CLNS1A-BGHcLV29-22/Aligned.sortedByCoord.out.bam		ENCORE2	19043
CLNS1A-BGHcLV29-22_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	1884					GRCh38	V40	CLNS1A-BGHcLV29-22/Aligned.sortedByCoord.out.bam		ENCORE2	19089
CLNS1A-BGHcLV29-22_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	1884					GRCh38	V40	CLNS1A-BGHcLV29-22/Aligned.sortedByCoord.out.bam		ENCORE2	19135
CLNS1A-BGHcLV29-22_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1884					GRCh38	V40	CLNS1A-BGHcLV29-22_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,CLNS1A-BGHcLV29-22_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19181