CTTN RNA-Seq in HepG2

General Information


RBP	CTTN
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CTTN-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR989JZM
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR755DOV
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CTTN-BGHcLV29-51
Rep2	CTTN-BGHcLV29-52
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	81.5
Rep2_WB	84.5
Antibody Cat#	A302-607A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB014AIG
Status	Submitted
Project	ENCODE4
ID	860

Experiment Information (Status: Released)

	BGHcLV29-51	BGHcLV29-52
idx	890	891
TRCN#_or_BGC#	BGC#0000727	BGC#0000727
shRNA_or_gRNA_sequence	CATCGCCCAGGATGACGCGG	CATCGCCCAGGATGACGCGG
PAM	GGG	GGG
Name	CTTN_93	CTTN_93
Sample_ID	BGHcLV29-51	BGHcLV29-52
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	CTTN	CTTN
qPCR_result	0	0
Ave_qPCR	0
RT-qPCR_primer-F	agcaagccagagccaaaac
RT-qPCR_primer-R	tcacagggcctctgtagctc
protein_conc	3549	3927
WB_result	81.5	84.5
Ave_WB	83.0
WB_DONE_date	9/27/21
MW	62KD
IP	Rabbit / I
antibody_Cat#	A302-607A	LOT #1
Antibody DCC ID	ENCAB014AIG
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	7069	7070

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CTTN	Product_ID: A302-607A Lot_ID: 1 Source: Bethyl Labs Target Name: CTTN-human

Experiment Status

	BGHcLV29-51	BGHcLV29-52
Sample_ID	BGHcLV29-51	BGHcLV29-52
Sample Name
Sample Name	CTTN-BGHcLV29-51	CTTN-BGHcLV29-52
RBP	CTTN	CTTN
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10005	10006

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-51	BGHcLV29-52
Sample #	33	34
Sample Name	CTTN-BGHcLV29-51	CTTN-BGHcLV29-52
Sample_Name_Alias
Index Well Position	A05	B05
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	306	302
Peak_Molarity	37.40	32.90
libSampleQC_DNA_Well	DNA_Library_set50/set1/A5.png	DNA_Library_set50/set1/B5.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set50/set1/A11.png	RNA_Library_set50/set1/B11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-51	BGHcLV29-52
RBP	CTTN	CTTN
Batch_ID	BGHcLV29	BGHcLV29
WB_result	81.500	84.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3120	3121

Sequencing Information

	BGHcLV29-51	BGHcLV29-52
Sample_ID	BGHcLV29-51	BGHcLV29-52
Sample Name	CTTN-BGHcLV29-51	CTTN-BGHcLV29-52
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	86,018,884	72,520,098
total_aligned_reads	78,739,996	66,572,662
unique_aligned_reads	74,272,402	62,795,430
percent_uniqueAligned	0.86344	0.86590
correlation_replicates	0.995508	0.995508
spikein_reads	17,354	15,286
percent_spikeins	0.00020	0.00021
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1901	1902

Data Submission Information

	BGHcLV29-51	BGHcLV29-51	BGHcLV29-51	BGHcLV29-51	BGHcLV29-51	BGHcLV29-51	BGHcLV29-52	BGHcLV29-52	BGHcLV29-52	BGHcLV29-52
ENCODE_alias	brenton-graveley:CTTN-BGHcLV29	brenton-graveley:CTTN-BGHcLV29-51	brenton-graveley:L-CTTN-BGHcLV29-51	brenton-graveley:CTTN-BGHcLV29-51_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTTN-BGHcLV29-51_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTTN-BGHcLV29-HepG2	brenton-graveley:CTTN-BGHcLV29-52	brenton-graveley:L-CTTN-BGHcLV29-52	brenton-graveley:CTTN-BGHcLV29-52_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTTN-BGHcLV29-52_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR755DOV	ENCBS094EUX	ENCLB725HCJ	ENCFF975ELD	ENCFF954BBU	ENCSR989JZM	ENCBS984YEV	ENCLB347ELK	ENCFF284VCQ	ENCFF557FXI
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	BGHcLV29-51	BGHcLV29-51	BGHcLV29-51	BGHcLV29-51	BGHcLV29-51	BGHcLV29-51	BGHcLV29-52	BGHcLV29-52	BGHcLV29-52	BGHcLV29-52
Sample Name	CTTN-BGHcLV29-51	CTTN-BGHcLV29-51	CTTN-BGHcLV29-51	CTTN-BGHcLV29-51	CTTN-BGHcLV29-51	CTTN-BGHcLV29-51	CTTN-BGHcLV29-52	CTTN-BGHcLV29-52	CTTN-BGHcLV29-52	CTTN-BGHcLV29-52
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		CTTN-BGHcLV29-51.pdf	L-CTTN-BGHcLV29-51.pdf				CTTN-BGHcLV29-52.pdf	L-CTTN-BGHcLV29-52.pdf
ID	5858	5909	5981	6053	6125	6181	5910	5982	6054	6126

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
CTTN-BGHcLV29-51_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1901	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	5789
CTTN-BGHcLV29-51_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1901	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	5831
CTTN-BGHcLV29-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1901					GRCh38	V40	CTTN-BGHcLV29-51_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTTN-BGHcLV29-51_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18956
CTTN-BGHcLV29-51_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	1901					GRCh38	V40	CTTN-BGHcLV29-51/Aligned.sortedByCoord.out.bam		ENCORE2	19014
CTTN-BGHcLV29-51_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	1901					GRCh38	V40	CTTN-BGHcLV29-51/Aligned.sortedByCoord.out.bam		ENCORE2	19060
CTTN-BGHcLV29-51_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	1901					GRCh38	V40	CTTN-BGHcLV29-51/Aligned.sortedByCoord.out.bam		ENCORE2	19106
CTTN-BGHcLV29-51_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	1901					GRCh38	V40	CTTN-BGHcLV29-51/Aligned.sortedByCoord.out.bam		ENCORE2	19152
CTTN-BGHcLV29-51_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1901					GRCh38	V40	CTTN-BGHcLV29-51_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTTN-BGHcLV29-51_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19198
CTTN-BGHcLV29-52_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1902	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	5790
CTTN-BGHcLV29-52_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1902	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	5832
CTTN-BGHcLV29-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1902					GRCh38	V40	CTTN-BGHcLV29-52_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTTN-BGHcLV29-52_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18957
CTTN-BGHcLV29-52_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	1902					GRCh38	V40	CTTN-BGHcLV29-52/Aligned.sortedByCoord.out.bam		ENCORE2	19015
CTTN-BGHcLV29-52_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	1902					GRCh38	V40	CTTN-BGHcLV29-52/Aligned.sortedByCoord.out.bam		ENCORE2	19061
CTTN-BGHcLV29-52_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	1902					GRCh38	V40	CTTN-BGHcLV29-52/Aligned.sortedByCoord.out.bam		ENCORE2	19107
CTTN-BGHcLV29-52_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	1902					GRCh38	V40	CTTN-BGHcLV29-52/Aligned.sortedByCoord.out.bam		ENCORE2	19153
CTTN-BGHcLV29-52_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1902					GRCh38	V40	CTTN-BGHcLV29-52_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,CTTN-BGHcLV29-52_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19199