CHTOP RNA-Seq in HepG2

General Information


RBP	CHTOP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CHTOP-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR005MID
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR298AQX
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	CHTOP-BGHcLV22-7
Rep2	CHTOP-BGHcLV22-8
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	79.4
Rep2_WB	82.2
Antibody Cat#	A303-411A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB775SVW
Status	Released
Project	ENCODE4
ID	38

Experiment Information (Status: Released)

	BGHcLV22-7	BGHcLV22-8
idx	600	601
TRCN#_or_BGC#	BGC#0000498	BGC#0000498
shRNA_or_gRNA_sequence	ACGGTTAGGCCGACCCATAG	ACGGTTAGGCCGACCCATAG
PAM	GGG	GGG
Name	CHTOP _98	CHTOP _98
Sample_ID	BGHcLV22-7	BGHcLV22-8
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	CHTOP	CHTOP
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	CGCCGAAAGTTGTGCTAAAA
RT-qPCR_primer-R	CGAAGCCCGAATATTCACTG
protein_conc	2219	2748
WB_result	79.4	82.2
Ave_WB	80.8
WB_DONE_date	1/7/21
MW	26.4kDa
IP	Rabbit / I
antibody_Cat#	A303-411A	Lot# 1
Antibody DCC ID	ENCAB775SVW
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	6755	6756

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CHTOP	Product_ID: A303-411A Lot_ID: 1 Source: Bethyl Labs Target Name: CHTOP-human

Experiment Status

	BGHcLV22-7	BGHcLV22-8
Sample_ID	BGHcLV22-7	BGHcLV22-8
Sample Name
Sample Name	CHTOP-BGHcLV22-7	CHTOP-BGHcLV22-8
RBP	CHTOP	CHTOP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7369	7370

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-7	BGHcLV22-8
Sample #	5	6
Sample Name	CHTOP-BGHcLV22-7	CHTOP-BGHcLV22-8
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	288	288
Peak_Molarity	72.20	67.60
libSampleQC_DNA_Well	DNA_Library_set46/set1/E1.png	DNA_Library_set46/set1/F1.png
RIN	9.8	9.5
libSample_RNA_Well	RNA_Library_set46/set1/E9.png	RNA_Library_set46/set1/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-7	BGHcLV22-8
RBP	CHTOP	CHTOP
Batch_ID	BGHcLV22	BGHcLV22
WB_result	69.000	70.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1380	1381

Sequencing Information

	BGHcLV22-7	BGHcLV22-8
Sample_ID	BGHcLV22-7	BGHcLV22-8
Sample Name	CHTOP-BGHcLV22-7	CHTOP-BGHcLV22-8
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	200,794,864	257,506,002
total_aligned_reads	151,047,344	214,354,954
unique_aligned_reads	141,606,446	200,884,528
percent_uniqueAligned	0.70523	0.78012
correlation_replicates	0.998028	0.998028
spikein_reads	91,894	129,308
percent_spikeins	0.00046	0.00050
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	486	487

Data Submission Information

	BGHcLV22-7	BGHcLV22-7	BGHcLV22-7	BGHcLV22-7	BGHcLV22-7	BGHcLV22-7	BGHcLV22-8	BGHcLV22-8	BGHcLV22-8	BGHcLV22-8
ENCODE_alias	brenton-graveley:CHTOP-BGHcLV22	brenton-graveley:CHTOP-BGHcLV22-7	brenton-graveley:L-CHTOP-BGHcLV22-7	brenton-graveley:CHTOP-BGHcLV22-7_ATCCACTG+ACGCACCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHTOP-BGHcLV22-7_ATCCACTG+ACGCACCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHTOP-BGHcLV22-HepG2	brenton-graveley:CHTOP-BGHcLV22-8	brenton-graveley:L-CHTOP-BGHcLV22-8	brenton-graveley:CHTOP-BGHcLV22-8_GCTTGTCA+GTATGTTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHTOP-BGHcLV22-8_GCTTGTCA+GTATGTTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR298AQX	ENCBS919KOR	ENCLB742HUO	ENCFF935YAO	ENCFF277KPO	ENCSR005MID	ENCBS641NAE	ENCLB381USO	ENCFF322UXW	ENCFF698FPU
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	BGHcLV22-7	BGHcLV22-7	BGHcLV22-7	BGHcLV22-7	BGHcLV22-7	BGHcLV22-7	BGHcLV22-8	BGHcLV22-8	BGHcLV22-8	BGHcLV22-8
Sample Name	CHTOP-BGHcLV22-7	CHTOP-BGHcLV22-7	CHTOP-BGHcLV22-7	CHTOP-BGHcLV22-7	CHTOP-BGHcLV22-7	CHTOP-BGHcLV22-7	CHTOP-BGHcLV22-8	CHTOP-BGHcLV22-8	CHTOP-BGHcLV22-8	CHTOP-BGHcLV22-8
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		CHTOP-BGHcLV22-7.pdf	L-CHTOP-BGHcLV22-7.pdf				CHTOP-BGHcLV22-8.pdf	L-CHTOP-BGHcLV22-8.pdf
ID	2397	2431	2495	2559	2589	7136	2432	2496	2560	2590

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
CHTOP-BGHcLV22-7_ATCCACTG+ACGCACCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	486	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1350
CHTOP-BGHcLV22-7_ATCCACTG+ACGCACCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	486	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1414
CHTOP-BGHcLV22-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	486					GRCh38	V40	CHTOP-BGHcLV22-7_ATCCACTG+ACGCACCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHTOP-BGHcLV22-7_ATCCACTG+ACGCACCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25253
CHTOP-BGHcLV22-7_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	486					GRCh38	V40	CHTOP-BGHcLV22-7_ATCCACTG+ACGCACCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHTOP-BGHcLV22-7_ATCCACTG+ACGCACCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25351
CHTOP-BGHcLV22-7_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	486					GRCh38	V40	CHTOP-BGHcLV22-7/Aligned.sortedByCoord.out.bam		ENCORE2	26001
CHTOP-BGHcLV22-7_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	486					GRCh38	V40	CHTOP-BGHcLV22-7/Aligned.sortedByCoord.out.bam		ENCORE2	26031
CHTOP-BGHcLV22-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	486					GRCh38	V40	CHTOP-BGHcLV22-7/Aligned.sortedByCoord.out.bam		ENCORE2	26061
CHTOP-BGHcLV22-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	486					GRCh38	V40	CHTOP-BGHcLV22-7/Aligned.sortedByCoord.out.bam		ENCORE2	26091
CHTOP-BGHcLV22-8_GCTTGTCA+GTATGTTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	487	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1351
CHTOP-BGHcLV22-8_GCTTGTCA+GTATGTTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	487	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1415
CHTOP-BGHcLV22-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	487					GRCh38	V40	CHTOP-BGHcLV22-8_GCTTGTCA+GTATGTTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHTOP-BGHcLV22-8_GCTTGTCA+GTATGTTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25254
CHTOP-BGHcLV22-8_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	487					GRCh38	V40	CHTOP-BGHcLV22-8_GCTTGTCA+GTATGTTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHTOP-BGHcLV22-8_GCTTGTCA+GTATGTTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25352
CHTOP-BGHcLV22-8_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	487					GRCh38	V40	CHTOP-BGHcLV22-8/Aligned.sortedByCoord.out.bam		ENCORE2	26002
CHTOP-BGHcLV22-8_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	487					GRCh38	V40	CHTOP-BGHcLV22-8/Aligned.sortedByCoord.out.bam		ENCORE2	26032
CHTOP-BGHcLV22-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	487					GRCh38	V40	CHTOP-BGHcLV22-8/Aligned.sortedByCoord.out.bam		ENCORE2	26062
CHTOP-BGHcLV22-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	487					GRCh38	V40	CHTOP-BGHcLV22-8/Aligned.sortedByCoord.out.bam		ENCORE2	26092