CLTC RNA-Seq in HepG2

General Information


RBP	CLTC
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CLTC-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR957HNQ
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR576ASZ
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CLTC-BGHcLV29-23
Rep2	CLTC-BGHcLV29-24
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	81.6
Rep2_qPCR	80.1
Rep1_WB	85.1
Rep2_WB	88.2
Antibody Cat#	A304-743A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB019OFH
Status	Submitted
Project	ENCODE4
ID	852

Experiment Information (Status: Released)

	BGHcLV29-23	BGHcLV29-24
idx	854	855
TRCN#_or_BGC#	BGC#0000700	BGC#0000700
shRNA_or_gRNA_sequence	ATCGCCATTCTAGCCTTGCA	ATCGCCATTCTAGCCTTGCA
PAM	GGG	GGG
Name	CLTC_90	CLTC_90
Sample_ID	BGHcLV29-23	BGHcLV29-24
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	CLTC	CLTC
qPCR_result	81.6	80.1
Ave_qPCR	80.85
RT-qPCR_primer-F	acttagccggtgctgaagaa
RT-qPCR_primer-R	aaccgacggatagtgtctgg
protein_conc	0	3757
WB_result	85.1	88.2
Ave_WB	86.6
WB_DONE_date	9/14/21
MW	192k
IP	Rabbit / I
antibody_Cat#	A304-743A	LOT #1
Antibody DCC ID	ENCAB019OFH
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	7031	7032

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CLTC	Product_ID: A304-743A Lot_ID: 1 Source: Bethyl Labs Target Name: CLTC-human

Experiment Status

	BGHcLV29-23	BGHcLV29-24
Sample_ID	BGHcLV29-23	BGHcLV29-24
Sample Name
Sample Name	CLTC-BGHcLV29-23	CLTC-BGHcLV29-24
RBP	CLTC	CLTC
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9989	9990

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-23	BGHcLV29-24
Sample #	17	18
Sample Name	CLTC-BGHcLV29-23	CLTC-BGHcLV29-24
Sample_Name_Alias
Index Well Position	A03	B03
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	305	294
Peak_Molarity	34.40	29.50
libSampleQC_DNA_Well	DNA_Library_set50/set1/A3.png	DNA_Library_set50/set1/B3.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set50/set1/A9.png	RNA_Library_set50/set1/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-23	BGHcLV29-24
RBP	CLTC	CLTC
Batch_ID	BGHcLV29	BGHcLV29
WB_result	85.100	88.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3104	3105

Sequencing Information

	BGHcLV29-23	BGHcLV29-24
Sample_ID	BGHcLV29-23	BGHcLV29-24
Sample Name	CLTC-BGHcLV29-23	CLTC-BGHcLV29-24
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	86,892,020	68,530,284
total_aligned_reads	80,278,338	61,424,462
unique_aligned_reads	75,686,460	57,891,896
percent_uniqueAligned	0.87104	0.84476
correlation_replicates	0.991909	0.991909
spikein_reads	28,854	14,058
percent_spikeins	0.00033	0.00021
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1885	1886

Data Submission Information

	BGHcLV29-23	BGHcLV29-23	BGHcLV29-23	BGHcLV29-23	BGHcLV29-23	BGHcLV29-23	BGHcLV29-24	BGHcLV29-24	BGHcLV29-24	BGHcLV29-24
ENCODE_alias	brenton-graveley:CLTC-BGHcLV29	brenton-graveley:CLTC-BGHcLV29-23	brenton-graveley:L-CLTC-BGHcLV29-23	brenton-graveley:CLTC-BGHcLV29-23_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLTC-BGHcLV29-23_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLTC-BGHcLV29-HepG2	brenton-graveley:CLTC-BGHcLV29-24	brenton-graveley:L-CLTC-BGHcLV29-24	brenton-graveley:CLTC-BGHcLV29-24_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLTC-BGHcLV29-24_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR576ASZ	ENCBS620CUH	ENCLB411FZV	ENCFF713PHW	ENCFF381UTA	ENCSR957HNQ	ENCBS193FMX	ENCLB009WAO	ENCFF146LAL	ENCFF017WSV
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	BGHcLV29-23	BGHcLV29-23	BGHcLV29-23	BGHcLV29-23	BGHcLV29-23	BGHcLV29-23	BGHcLV29-24	BGHcLV29-24	BGHcLV29-24	BGHcLV29-24
Sample Name	CLTC-BGHcLV29-23	CLTC-BGHcLV29-23	CLTC-BGHcLV29-23	CLTC-BGHcLV29-23	CLTC-BGHcLV29-23	CLTC-BGHcLV29-23	CLTC-BGHcLV29-24	CLTC-BGHcLV29-24	CLTC-BGHcLV29-24	CLTC-BGHcLV29-24
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		CLTC-BGHcLV29-23.pdf	L-CLTC-BGHcLV29-23.pdf				CLTC-BGHcLV29-24.pdf	L-CLTC-BGHcLV29-24.pdf
ID	5850	5893	5965	6037	6109	6173	5894	5966	6038	6110

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
CLTC-BGHcLV29-23_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1885	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	5773
CLTC-BGHcLV29-23_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1885	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	5815
CLTC-BGHcLV29-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1885					GRCh38	V40	CLTC-BGHcLV29-23_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,CLTC-BGHcLV29-23_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18940
CLTC-BGHcLV29-23_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	1885					GRCh38	V40	CLTC-BGHcLV29-23/Aligned.sortedByCoord.out.bam		ENCORE2	18998
CLTC-BGHcLV29-23_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	1885					GRCh38	V40	CLTC-BGHcLV29-23/Aligned.sortedByCoord.out.bam		ENCORE2	19044
CLTC-BGHcLV29-23_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	1885					GRCh38	V40	CLTC-BGHcLV29-23/Aligned.sortedByCoord.out.bam		ENCORE2	19090
CLTC-BGHcLV29-23_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	1885					GRCh38	V40	CLTC-BGHcLV29-23/Aligned.sortedByCoord.out.bam		ENCORE2	19136
CLTC-BGHcLV29-23_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1885					GRCh38	V40	CLTC-BGHcLV29-23_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,CLTC-BGHcLV29-23_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19182
CLTC-BGHcLV29-24_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1886	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	5774
CLTC-BGHcLV29-24_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1886	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	5816
CLTC-BGHcLV29-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1886					GRCh38	V40	CLTC-BGHcLV29-24_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,CLTC-BGHcLV29-24_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18941
CLTC-BGHcLV29-24_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	1886					GRCh38	V40	CLTC-BGHcLV29-24/Aligned.sortedByCoord.out.bam		ENCORE2	18999
CLTC-BGHcLV29-24_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	1886					GRCh38	V40	CLTC-BGHcLV29-24/Aligned.sortedByCoord.out.bam		ENCORE2	19045
CLTC-BGHcLV29-24_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	1886					GRCh38	V40	CLTC-BGHcLV29-24/Aligned.sortedByCoord.out.bam		ENCORE2	19091
CLTC-BGHcLV29-24_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	1886					GRCh38	V40	CLTC-BGHcLV29-24/Aligned.sortedByCoord.out.bam		ENCORE2	19137
CLTC-BGHcLV29-24_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1886					GRCh38	V40	CLTC-BGHcLV29-24_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,CLTC-BGHcLV29-24_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19183