CSTF3 RNA-Seq in HepG2

General Information


RBP	CSTF3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CSTF3-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR089MTU
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR044GQU
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CSTF3-BGHcLV29-47
Rep2	CSTF3-BGHcLV29-48
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	15.5
Rep2_qPCR	3.1
Rep1_WB	71.5
Rep2_WB	87.4
Antibody Cat#	A301-094A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB194MWL
Status	Submitted
Project	ENCODE4
ID	859

Experiment Information (Status: Released)

	BGHcLV29-47	BGHcLV29-47	BGHcLV29-48	BGHcLV29-48
idx	882	884	883	885
TRCN#_or_BGC#	BGC#0000724	BGC#0000724	BGC#0000724	BGC#0000724
shRNA_or_gRNA_sequence	GTCCGAAGAGTTTATCAACG	GTCCGAAGAGTTTATCAACG	GTCCGAAGAGTTTATCAACG	GTCCGAAGAGTTTATCAACG
PAM	AGG	AGG	AGG	AGG
Name	CSTF3_95	CSTF3_95	CSTF3_95	CSTF3_95
Sample_ID	BGHcLV29-47	BGHcLV29-47	BGHcLV29-48	BGHcLV29-48
transduction_Date	7/20	7/20	7/20	7/20
days	D6	D6	D6	D6
RBP_name	CSTF3	CSTF3	CSTF3	CSTF3
qPCR_result	15.5	15.5	3.1	3.1
Ave_qPCR	9.3	9.3
RT-qPCR_primer-F	ccctaaaccagacactcagca	ccctaaaccagacactcagca
RT-qPCR_primer-R	aggagggactgggaacactc	aggagggactgggaacactc
protein_conc	5822	5822	4028	4028
WB_result	71.5	52.8	87.4	50.3287
Ave_WB	79.5	51.5
WB_DONE_date	10/8/21	6/16/22	JESS
MW	83KD	83KD
IP	Rabbit / I
antibody_Cat#	A301-094A	A301-096A	LOT #1	LOT #1
Antibody DCC ID	ENCAB194MWL	ENCAB190TLL
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	11/5/21		11/5/21
repeat_library
Note
ID	7061	7063	7062	7064

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSTF3	Product_ID: A301-094A Lot_ID: 1 Source: Bethyl Labs Target Name: CSTF3-human
CSTF3	Product_ID: A301-096A Lot_ID: 1 Source: Bethyl Labs Target Name: CSTF3-human

Experiment Status

	BGHcLV29-47	BGHcLV29-48
Sample_ID	BGHcLV29-47	BGHcLV29-48
Sample Name
Sample Name	CSTF3-BGHcLV29-47	CSTF3-BGHcLV29-48
RBP	CSTF3	CSTF3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10003	10004

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-47	BGHcLV29-48
Sample #	31	32
Sample Name	CSTF3-BGHcLV29-47	CSTF3-BGHcLV29-48
Sample_Name_Alias
Index Well Position	G04	H04
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	308	295
Peak_Molarity	45.60	42.70
libSampleQC_DNA_Well	DNA_Library_set50/set1/G4.png	DNA_Library_set50/set1/H4.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set50/set1/G10.png	RNA_Library_set50/set1/H10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-47	BGHcLV29-48
RBP	CSTF3	CSTF3
Batch_ID	BGHcLV29	BGHcLV29
WB_result	71.500	87.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3118	3119

Sequencing Information

	BGHcLV29-47	BGHcLV29-48
Sample_ID	BGHcLV29-47	BGHcLV29-48
Sample Name	CSTF3-BGHcLV29-47	CSTF3-BGHcLV29-48
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	76,200,994	69,527,522
total_aligned_reads	70,886,942	64,377,576
unique_aligned_reads	66,838,802	60,631,084
percent_uniqueAligned	0.87714	0.87204
correlation_replicates	0.980205	0.980205
spikein_reads	12,460	16,298
percent_spikeins	0.00016	0.00023
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1899	1900

Data Submission Information

	BGHcLV29-47	BGHcLV29-47	BGHcLV29-47	BGHcLV29-47	BGHcLV29-47	BGHcLV29-47	BGHcLV29-48	BGHcLV29-48	BGHcLV29-48	BGHcLV29-48
ENCODE_alias	brenton-graveley:CSTF3-BGHcLV29	brenton-graveley:CSTF3-BGHcLV29-47	brenton-graveley:L-CSTF3-BGHcLV29-47	brenton-graveley:CSTF3-BGHcLV29-47_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSTF3-BGHcLV29-47_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSTF3-BGHcLV29-HepG2	brenton-graveley:CSTF3-BGHcLV29-48	brenton-graveley:L-CSTF3-BGHcLV29-48	brenton-graveley:CSTF3-BGHcLV29-48_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSTF3-BGHcLV29-48_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR044GQU	ENCBS197FRN	ENCLB839ZVL	ENCFF322NJT	ENCFF519JJR	ENCSR089MTU	ENCBS986CSI	ENCLB991QAF	ENCFF018AVF	ENCFF197DUW
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	BGHcLV29-47	BGHcLV29-47	BGHcLV29-47	BGHcLV29-47	BGHcLV29-47	BGHcLV29-47	BGHcLV29-48	BGHcLV29-48	BGHcLV29-48	BGHcLV29-48
Sample Name	CSTF3-BGHcLV29-47	CSTF3-BGHcLV29-47	CSTF3-BGHcLV29-47	CSTF3-BGHcLV29-47	CSTF3-BGHcLV29-47	CSTF3-BGHcLV29-47	CSTF3-BGHcLV29-48	CSTF3-BGHcLV29-48	CSTF3-BGHcLV29-48	CSTF3-BGHcLV29-48
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		CSTF3-BGHcLV29-47.pdf	L-CSTF3-BGHcLV29-47.pdf				CSTF3-BGHcLV29-48.pdf	L-CSTF3-BGHcLV29-48.pdf
ID	5857	5907	5979	6051	6123	6180	5908	5980	6052	6124

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
CSTF3-BGHcLV29-47_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1899	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	5787
CSTF3-BGHcLV29-47_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1899	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	5829
CSTF3-BGHcLV29-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1899					GRCh38	V40	CSTF3-BGHcLV29-47_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF3-BGHcLV29-47_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18954
CSTF3-BGHcLV29-47_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	1899					GRCh38	V40	CSTF3-BGHcLV29-47/Aligned.sortedByCoord.out.bam		ENCORE2	19012
CSTF3-BGHcLV29-47_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	1899					GRCh38	V40	CSTF3-BGHcLV29-47/Aligned.sortedByCoord.out.bam		ENCORE2	19058
CSTF3-BGHcLV29-47_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	1899					GRCh38	V40	CSTF3-BGHcLV29-47/Aligned.sortedByCoord.out.bam		ENCORE2	19104
CSTF3-BGHcLV29-47_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	1899					GRCh38	V40	CSTF3-BGHcLV29-47/Aligned.sortedByCoord.out.bam		ENCORE2	19150
CSTF3-BGHcLV29-47_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1899					GRCh38	V40	CSTF3-BGHcLV29-47_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF3-BGHcLV29-47_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19196
CSTF3-BGHcLV29-48_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1900	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	5788
CSTF3-BGHcLV29-48_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1900	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	5830
CSTF3-BGHcLV29-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1900					GRCh38	V40	CSTF3-BGHcLV29-48_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF3-BGHcLV29-48_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18955
CSTF3-BGHcLV29-48_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	1900					GRCh38	V40	CSTF3-BGHcLV29-48/Aligned.sortedByCoord.out.bam		ENCORE2	19013
CSTF3-BGHcLV29-48_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	1900					GRCh38	V40	CSTF3-BGHcLV29-48/Aligned.sortedByCoord.out.bam		ENCORE2	19059
CSTF3-BGHcLV29-48_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	1900					GRCh38	V40	CSTF3-BGHcLV29-48/Aligned.sortedByCoord.out.bam		ENCORE2	19105
CSTF3-BGHcLV29-48_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	1900					GRCh38	V40	CSTF3-BGHcLV29-48/Aligned.sortedByCoord.out.bam		ENCORE2	19151
CSTF3-BGHcLV29-48_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1900					GRCh38	V40	CSTF3-BGHcLV29-48_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF3-BGHcLV29-48_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19197