CARS RNA-Seq in HepG2

General Information


RBP	CARS
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CARS-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR270IZY
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR077MFQ
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	CARS-BGHcLV27-39
Rep2	CARS-BGHcLV27-40
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	62.4
Rep2_WB	62.4
Antibody Cat#	A302-409A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB833ALL
Status	Released
Project	ENCODE4
ID	815

Experiment Information (Status: Released)

	BGHcLV27-39	BGHcLV27-40
idx	805	806
TRCN#_or_BGC#	BGC#0000666	BGC#0000666
shRNA_or_gRNA_sequence	TGAGATGCGTCATAGACGGT	TGAGATGCGTCATAGACGGT
PAM	TGG	TGG
Name	CARS1_96	CARS1_96
Sample_ID	BGHcLV27-39	BGHcLV27-40
transduction_Date	5/18/21	5/18/21
days	D6	D6
RBP_name	CARS	CARS
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	tggaaggacaccctggacta
RT-qPCR_primer-R	ccccacttctcaaactgacc
protein_conc	2467	2727
WB_result	62.4	62.4
Ave_WB	62.4
WB_DONE_date	5/27/21	JESS
MW	84kDa
IP	Rabbit / I
antibody_Cat#	A302-409A	LOT# 1
Antibody DCC ID	ENCAB833ALL	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	6974	6975

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CARS	Product_ID: A302-409A Lot_ID: 1 Source: Bethyl Labs Target Name: CARS-human

Experiment Status

	BGHcLV27-39	BGHcLV27-40
Sample_ID	BGHcLV27-39	BGHcLV27-40
Sample Name
Sample Name	CARS-BGHcLV27-39	CARS-BGHcLV27-40
RBP	CARS	CARS
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9693	9694

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-39	BGHcLV27-40
Sample #	97	98
Sample Name	CARS-BGHcLV27-39	CARS-BGHcLV27-40
Sample_Name_Alias
Index Well Position	E10	F10
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	297	298
Peak_Molarity	159.00	148.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/E9.png	DNA_Library_set48-49/set2/F9.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set48-49/set1/G9.png	RNA_Library_set48-49/set1/H9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-39	BGHcLV27-40
RBP	CARS	CARS
Batch_ID	BGHcLV27	BGHcLV27
WB_result	62.400	62.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1656	1657

Sequencing Information

	BGHcLV27-39	BGHcLV27-40
Sample_ID	BGHcLV27-39	BGHcLV27-40
Sample Name	CARS-BGHcLV27-39	CARS-BGHcLV27-40
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	73,967,290	66,110,800
total_aligned_reads	66,693,344	58,238,556
unique_aligned_reads	62,527,698	54,591,034
percent_uniqueAligned	0.84534	0.82575
correlation_replicates	0.997944	0.997944
spikein_reads	17,824	12,660
percent_spikeins	0.00024	0.00019
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1807	1808

Data Submission Information

	BGHcLV27-39	BGHcLV27-39	BGHcLV27-39	BGHcLV27-39	BGHcLV27-39	BGHcLV27-39	BGHcLV27-40	BGHcLV27-40	BGHcLV27-40	BGHcLV27-40
ENCODE_alias	brenton-graveley:CARS-BGHcLV27	brenton-graveley:CARS-BGHcLV27-39	brenton-graveley:L-CARS-BGHcLV27-39	brenton-graveley:CARS-BGHcLV27-39_S77_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARS-BGHcLV27-39_S77_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARS-BGHcLV27-HepG2	brenton-graveley:CARS-BGHcLV27-40	brenton-graveley:L-CARS-BGHcLV27-40	brenton-graveley:CARS-BGHcLV27-40_S78_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARS-BGHcLV27-40_S78_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR077MFQ	ENCBS916HYF	ENCLB391MVV	ENCFF268QCX	ENCFF096POD	ENCSR270IZY	ENCBS104KVQ	ENCLB576SAS	ENCFF104RHT	ENCFF156LGW
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	BGHcLV27-39	BGHcLV27-39	BGHcLV27-39	BGHcLV27-39	BGHcLV27-39	BGHcLV27-39	BGHcLV27-40	BGHcLV27-40	BGHcLV27-40	BGHcLV27-40
Sample Name	CARS-BGHcLV27-39	CARS-BGHcLV27-39	CARS-BGHcLV27-39	CARS-BGHcLV27-39	CARS-BGHcLV27-39	CARS-BGHcLV27-39	CARS-BGHcLV27-40	CARS-BGHcLV27-40	CARS-BGHcLV27-40	CARS-BGHcLV27-40
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		CARS-BGHcLV27-39.pdf	L-CARS-BGHcLV27-39.pdf				CARS-BGHcLV27-40.pdf	L-CARS-BGHcLV27-40.pdf
ID	3443	3520	3654	3788	3922	7115	3521	3655	3789	3923

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
CARS-BGHcLV27-39_S77_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1807	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	3798
CARS-BGHcLV27-39_S77_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1807	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	3824
CARS-BGHcLV27-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1807					GRCh38	V40	CARS-BGHcLV27-39_S77_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARS-BGHcLV27-39_S77_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25485
CARS-BGHcLV27-39_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1807					GRCh38	V40	CARS-BGHcLV27-39_S77_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARS-BGHcLV27-39_S77_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25511
CARS-BGHcLV27-39_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	1807					GRCh38	V40	CARS-BGHcLV27-39/Aligned.sortedByCoord.out.bam		ENCORE2	26449
CARS-BGHcLV27-39_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	1807					GRCh38	V40	CARS-BGHcLV27-39/Aligned.sortedByCoord.out.bam		ENCORE2	26475
CARS-BGHcLV27-39_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	1807					GRCh38	V40	CARS-BGHcLV27-39/Aligned.sortedByCoord.out.bam		ENCORE2	26501
CARS-BGHcLV27-39_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	1807					GRCh38	V40	CARS-BGHcLV27-39/Aligned.sortedByCoord.out.bam		ENCORE2	26527
CARS-BGHcLV27-40_S78_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1808	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	3799
CARS-BGHcLV27-40_S78_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1808	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	3825
CARS-BGHcLV27-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1808					GRCh38	V40	CARS-BGHcLV27-40_S78_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARS-BGHcLV27-40_S78_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25486
CARS-BGHcLV27-40_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1808					GRCh38	V40	CARS-BGHcLV27-40_S78_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARS-BGHcLV27-40_S78_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25512
CARS-BGHcLV27-40_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	1808					GRCh38	V40	CARS-BGHcLV27-40/Aligned.sortedByCoord.out.bam		ENCORE2	26450
CARS-BGHcLV27-40_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	1808					GRCh38	V40	CARS-BGHcLV27-40/Aligned.sortedByCoord.out.bam		ENCORE2	26476
CARS-BGHcLV27-40_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	1808					GRCh38	V40	CARS-BGHcLV27-40/Aligned.sortedByCoord.out.bam		ENCORE2	26502
CARS-BGHcLV27-40_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	1808					GRCh38	V40	CARS-BGHcLV27-40/Aligned.sortedByCoord.out.bam		ENCORE2	26528