CAT RNA-Seq in HepG2

General Information


RBP	CAT
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CAT-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR840UYV
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR051BQF
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	CAT-BGHcLV27-43
Rep2	CAT-BGHcLV27-44
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	56.0
Rep2_qPCR	60.5
Rep1_WB	53.3
Rep2_WB	56.0
Antibody Cat#	A304-767A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB661IMU
Status	Released
Project	ENCODE4
ID	816

Experiment Information (Status: Released)

	BGHcLV27-43	BGHcLV27-44
idx	809	810
TRCN#_or_BGC#	BGC#0000669	BGC#0000669
shRNA_or_gRNA_sequence	TTATTACAGTAGGGCCCCGT	TTATTACAGTAGGGCCCCGT
PAM	GGG	GGG
Name	CAT_96	CAT_96
Sample_ID	BGHcLV27-43	BGHcLV27-44
transduction_Date	5/18/21	5/18/21
days	D6	D6
RBP_name	CAT	CAT
qPCR_result	56.0	60.5
Ave_qPCR	58.3
RT-qPCR_primer-F	catcgccacatgaatggata
RT-qPCR_primer-R	tttttgatgccctggtcagt
protein_conc	3260	3359
WB_result	53.3	56.0
Ave_WB	54.7
WB_DONE_date	6/7/21	JESS
MW	60kDa
IP	Rabbit / I
antibody_Cat#	A304-767A	LOT# 1
Antibody DCC ID	ENCAB661IMU	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/03/21	09/03/21
repeat_library
Note
ID	6978	6979

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CAT	Product_ID: A304-767A Lot_ID: 1 Source: Bethyl Labs Target Name: CAT-human

Experiment Status

	BGHcLV27-43	BGHcLV27-44
Sample_ID	BGHcLV27-43	BGHcLV27-44
Sample Name
Sample Name	CAT-BGHcLV27-43	CAT-BGHcLV27-44
RBP	CAT	CAT
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9695	9696

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-43	BGHcLV27-44
Sample #	99	100
Sample Name	CAT-BGHcLV27-43	CAT-BGHcLV27-44
Sample_Name_Alias
Index Well Position	G10	H10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	292	289
Peak_Molarity	134.00	155.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/G9.png	DNA_Library_set48-49/set2/H9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set48-49/set1/A10.png	RNA_Library_set48-49/set1/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-43	BGHcLV27-44
RBP	CAT	CAT
Batch_ID	BGHcLV27	BGHcLV27
WB_result	53.300	56.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1658	1659

Sequencing Information

	BGHcLV27-43	BGHcLV27-44
Sample_ID	BGHcLV27-43	BGHcLV27-44
Sample Name	CAT-BGHcLV27-43	CAT-BGHcLV27-44
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	84,787,624	97,055,110
total_aligned_reads	74,370,790	84,312,530
unique_aligned_reads	70,105,070	79,411,548
percent_uniqueAligned	0.82683	0.81821
correlation_replicates	0.999306	0.999306
spikein_reads	17,122	16,784
percent_spikeins	0.00020	0.00017
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1809	1810

Data Submission Information

	BGHcLV27-43	BGHcLV27-43	BGHcLV27-43	BGHcLV27-43	BGHcLV27-43	BGHcLV27-43	BGHcLV27-44	BGHcLV27-44	BGHcLV27-44	BGHcLV27-44
ENCODE_alias	brenton-graveley:CAT-BGHcLV27	brenton-graveley:CAT-BGHcLV27-43	brenton-graveley:L-CAT-BGHcLV27-43	brenton-graveley:CAT-BGHcLV27-43_S79_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAT-BGHcLV27-43_S79_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAT-BGHcLV27-HepG2	brenton-graveley:CAT-BGHcLV27-44	brenton-graveley:L-CAT-BGHcLV27-44	brenton-graveley:CAT-BGHcLV27-44_S80_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAT-BGHcLV27-44_S80_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR051BQF	ENCBS659OBX	ENCLB709QSN	ENCFF358FBB	ENCFF254FXQ	ENCSR840UYV	ENCBS956SJA	ENCLB087HQC	ENCFF702ALB	ENCFF624WVS
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	BGHcLV27-43	BGHcLV27-43	BGHcLV27-43	BGHcLV27-43	BGHcLV27-43	BGHcLV27-43	BGHcLV27-44	BGHcLV27-44	BGHcLV27-44	BGHcLV27-44
Sample Name	CAT-BGHcLV27-43	CAT-BGHcLV27-43	CAT-BGHcLV27-43	CAT-BGHcLV27-43	CAT-BGHcLV27-43	CAT-BGHcLV27-43	CAT-BGHcLV27-44	CAT-BGHcLV27-44	CAT-BGHcLV27-44	CAT-BGHcLV27-44
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		CAT-BGHcLV27-43.pdf	L-CAT-BGHcLV27-43.pdf				CAT-BGHcLV27-44.pdf	L-CAT-BGHcLV27-44.pdf
ID	3444	3522	3656	3790	3924	7118	3523	3657	3791	3925

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
CAT-BGHcLV27-43_S79_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1809	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3800
CAT-BGHcLV27-43_S79_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1809	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3826
CAT-BGHcLV27-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1809					GRCh38	V40	CAT-BGHcLV27-43_S79_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAT-BGHcLV27-43_S79_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25487
CAT-BGHcLV27-43_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1809					GRCh38	V40	CAT-BGHcLV27-43_S79_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAT-BGHcLV27-43_S79_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25513
CAT-BGHcLV27-43_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1809					GRCh38	V40	CAT-BGHcLV27-43/Aligned.sortedByCoord.out.bam		ENCORE2	26451
CAT-BGHcLV27-43_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1809					GRCh38	V40	CAT-BGHcLV27-43/Aligned.sortedByCoord.out.bam		ENCORE2	26477
CAT-BGHcLV27-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1809					GRCh38	V40	CAT-BGHcLV27-43/Aligned.sortedByCoord.out.bam		ENCORE2	26503
CAT-BGHcLV27-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1809					GRCh38	V40	CAT-BGHcLV27-43/Aligned.sortedByCoord.out.bam		ENCORE2	26529
CAT-BGHcLV27-44_S80_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1810	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3801
CAT-BGHcLV27-44_S80_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1810	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3827
CAT-BGHcLV27-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1810					GRCh38	V40	CAT-BGHcLV27-44_S80_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAT-BGHcLV27-44_S80_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25488
CAT-BGHcLV27-44_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1810					GRCh38	V40	CAT-BGHcLV27-44_S80_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAT-BGHcLV27-44_S80_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25514
CAT-BGHcLV27-44_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1810					GRCh38	V40	CAT-BGHcLV27-44/Aligned.sortedByCoord.out.bam		ENCORE2	26452
CAT-BGHcLV27-44_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1810					GRCh38	V40	CAT-BGHcLV27-44/Aligned.sortedByCoord.out.bam		ENCORE2	26478
CAT-BGHcLV27-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1810					GRCh38	V40	CAT-BGHcLV27-44/Aligned.sortedByCoord.out.bam		ENCORE2	26504
CAT-BGHcLV27-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1810					GRCh38	V40	CAT-BGHcLV27-44/Aligned.sortedByCoord.out.bam		ENCORE2	26530