CSTF1 RNA-Seq in HepG2

General Information


RBP	CSTF1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CSTF1-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR425FXE
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR751TUX
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	CSTF1-BGHcLV22-15
Rep2	CSTF1-BGHcLV22-16
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	61.1
Rep2_WB	59.9
Antibody Cat#	A301-250A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB678HIE
Status	Released
Project	ENCODE4
ID	40

Experiment Information (Status: Released)

	BGHcLV22-15	BGHcLV22-16
idx	608	609
TRCN#_or_BGC#	BGC#0000506	BGC#0000506
shRNA_or_gRNA_sequence	CTATAGGTAGCTACACGGCA	CTATAGGTAGCTACACGGCA
PAM	TGG	TGG
Name	CSTF1 _93	CSTF1 _93
Sample_ID	BGHcLV22-15	BGHcLV22-16
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	CSTF1	CSTF1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GGCTTCTGGTTCAAGGGATT
RT-qPCR_primer-R	GAAGGATGAAAAGAGATGGAACG
protein_conc	2355	2407
WB_result	61.1	59.9
Ave_WB	60.5
WB_DONE_date	9/2/20	JESS
MW	48.4kDa
IP	Rabbit / I
antibody_Cat#	A301-250A	Lot# 1
Antibody DCC ID	ENCAB678HIE
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	8811	8812

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSTF1	Product_ID: A301-250A Lot_ID: 1 Source: Bethyl Labs Target Name: CSTF1-human

Experiment Status

	BGHcLV22-15	BGHcLV22-16
Sample_ID	BGHcLV22-15	BGHcLV22-16
Sample Name
Sample Name	CSTF1-BGHcLV22-15	CSTF1-BGHcLV22-16
RBP	CSTF1	CSTF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7373	7374

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-15	BGHcLV22-16
Sample #	9	10
Sample Name	CSTF1-BGHcLV22-15	CSTF1-BGHcLV22-16
Sample_Name_Alias
Index Well Position	A02	B02
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	295	287
Peak_Molarity	55.50	139.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/A2.png	DNA_Library_set46/set1/B2.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_set46/set1/A10.png	RNA_Library_set46/set1/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-15	BGHcLV22-16
RBP	CSTF1	CSTF1
Batch_ID	BGHcLV22	BGHcLV22
WB_result	61.100	59.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1384	1385

Sequencing Information

	BGHcLV22-15	BGHcLV22-16
Sample_ID	BGHcLV22-15	BGHcLV22-16
Sample Name	CSTF1-BGHcLV22-15	CSTF1-BGHcLV22-16
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	194,498,834	139,274,444
total_aligned_reads	166,956,830	118,748,136
unique_aligned_reads	156,471,436	111,176,466
percent_uniqueAligned	0.80449	0.79825
correlation_replicates	0.979460	0.979460
spikein_reads	118,424	94,098
percent_spikeins	0.00061	0.00068
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	490	491

Data Submission Information

	BGHcLV22-15	BGHcLV22-15	BGHcLV22-15	BGHcLV22-15	BGHcLV22-15	BGHcLV22-15	BGHcLV22-16	BGHcLV22-16	BGHcLV22-16	BGHcLV22-16
ENCODE_alias	brenton-graveley:CSTF1-BGHcLV22	brenton-graveley:CSTF1-BGHcLV22-15	brenton-graveley:L-CSTF1-BGHcLV22-15	brenton-graveley:CSTF1-BGHcLV22-15_AGTTCAGG+TCTGTTGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSTF1-BGHcLV22-15_AGTTCAGG+TCTGTTGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSTF1-BGHcLV22-HepG2	brenton-graveley:CSTF1-BGHcLV22-16	brenton-graveley:L-CSTF1-BGHcLV22-16	brenton-graveley:CSTF1-BGHcLV22-16_GACCTGAA+CTCACCAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSTF1-BGHcLV22-16_GACCTGAA+CTCACCAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR751TUX	ENCBS138BKF	ENCLB222LZJ	ENCFF536NLJ	ENCFF727YFT	ENCSR425FXE	ENCBS830QUG	ENCLB064JKG	ENCFF142DJA	ENCFF115ETW
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	BGHcLV22-15	BGHcLV22-15	BGHcLV22-15	BGHcLV22-15	BGHcLV22-15	BGHcLV22-15	BGHcLV22-16	BGHcLV22-16	BGHcLV22-16	BGHcLV22-16
Sample Name	CSTF1-BGHcLV22-15	CSTF1-BGHcLV22-15	CSTF1-BGHcLV22-15	CSTF1-BGHcLV22-15	CSTF1-BGHcLV22-15	CSTF1-BGHcLV22-15	CSTF1-BGHcLV22-16	CSTF1-BGHcLV22-16	CSTF1-BGHcLV22-16	CSTF1-BGHcLV22-16
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		CSTF1-BGHcLV22-15.pdf	L-CSTF1-BGHcLV22-15.pdf				CSTF1-BGHcLV22-16.pdf	L-CSTF1-BGHcLV22-16.pdf
ID	2399	2435	2499	2563	2593	7159	2436	2500	2564	2594

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
CSTF1-BGHcLV22-15_AGTTCAGG+TCTGTTGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	490	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	1354
CSTF1-BGHcLV22-15_AGTTCAGG+TCTGTTGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	490	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	1418
CSTF1-BGHcLV22-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	490					GRCh38	V40	CSTF1-BGHcLV22-15_AGTTCAGG+TCTGTTGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF1-BGHcLV22-15_AGTTCAGG+TCTGTTGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25257
CSTF1-BGHcLV22-15_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	490					GRCh38	V40	CSTF1-BGHcLV22-15_AGTTCAGG+TCTGTTGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF1-BGHcLV22-15_AGTTCAGG+TCTGTTGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25355
CSTF1-BGHcLV22-15_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	490					GRCh38	V40	CSTF1-BGHcLV22-15/Aligned.sortedByCoord.out.bam		ENCORE2	26005
CSTF1-BGHcLV22-15_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	490					GRCh38	V40	CSTF1-BGHcLV22-15/Aligned.sortedByCoord.out.bam		ENCORE2	26035
CSTF1-BGHcLV22-15_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	490					GRCh38	V40	CSTF1-BGHcLV22-15/Aligned.sortedByCoord.out.bam		ENCORE2	26065
CSTF1-BGHcLV22-15_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	490					GRCh38	V40	CSTF1-BGHcLV22-15/Aligned.sortedByCoord.out.bam		ENCORE2	26095
CSTF1-BGHcLV22-16_GACCTGAA+CTCACCAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	491	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	1355
CSTF1-BGHcLV22-16_GACCTGAA+CTCACCAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	491	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	1419
CSTF1-BGHcLV22-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	491					GRCh38	V40	CSTF1-BGHcLV22-16_GACCTGAA+CTCACCAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF1-BGHcLV22-16_GACCTGAA+CTCACCAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25258
CSTF1-BGHcLV22-16_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	491					GRCh38	V40	CSTF1-BGHcLV22-16_GACCTGAA+CTCACCAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF1-BGHcLV22-16_GACCTGAA+CTCACCAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25356
CSTF1-BGHcLV22-16_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	491					GRCh38	V40	CSTF1-BGHcLV22-16/Aligned.sortedByCoord.out.bam		ENCORE2	26006
CSTF1-BGHcLV22-16_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	491					GRCh38	V40	CSTF1-BGHcLV22-16/Aligned.sortedByCoord.out.bam		ENCORE2	26036
CSTF1-BGHcLV22-16_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	491					GRCh38	V40	CSTF1-BGHcLV22-16/Aligned.sortedByCoord.out.bam		ENCORE2	26066
CSTF1-BGHcLV22-16_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	491					GRCh38	V40	CSTF1-BGHcLV22-16/Aligned.sortedByCoord.out.bam		ENCORE2	26096