CSTF3 RNA-Seq in K562

General Information


RBP	CSTF3
Cell_Line	K562
Method	CRISPR
Exp_Name	CSTF3-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CSTF3-BGKcLV35-17
Rep2	CSTF3-BGKcLV35-18
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	54.4
Rep2_WB	50.8
Antibody Cat#	A301-094A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB190TLL
Status	Submitted
Project	ENCORE2
ID	955

Experiment Information (Status: Submitting)

	BGKcLV35-17	BGKcLV35-18
idx	1294	1295
TRCN#_or_BGC#	BGC#0000724	BGC#0000724
shRNA_or_gRNA_sequence	GTCCGAAGAGTTTATCAACG	GTCCGAAGAGTTTATCAACG
PAM	AGG	AGG
Name	CSTF3_95	CSTF3_95
Sample_ID	BGKcLV35-17	BGKcLV35-18
transduction_Date	4/28/22	4/28/22
days	D6	D6
RBP_name	CSTF3	CSTF3
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ccctaaaccagacactcagca
RT-qPCR_primer-R	aggagggactgggaacactc
protein_conc	3280	2566
WB_result	54.4	50.8
Ave_WB	52.6
WB_DONE_date	6/2/22
MW	83KD
IP
antibody_Cat#	A301-094A	LOT #1
Antibody DCC ID	ENCAB190TLL
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	5438	5439

Western Blot

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

Experiment Status

	BGKcLV35-17	BGKcLV35-18
Sample_ID	BGKcLV35-17	BGKcLV35-18
Sample Name
Sample Name	CSTF3-BGKcLV35-17	CSTF3-BGKcLV35-18
RBP	CSTF3	CSTF3
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10867	10868

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-17	BGKcLV35-18
Sample #	33	34
Sample Name	CSTF3-BGKcLV35-17	CSTF3-BGKcLV35-18
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	288	287
Peak_Molarity	27.80	43.00
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/A9.png	DNA_Library_set54-56/set3/B9.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set54-56/set2/A5.png	RNA_Library_set54-56/set2/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-17	BGKcLV35-18
RBP	CSTF3	CSTF3
Batch_ID	BGKcLV35	BGKcLV35
WB_result	54.400	50.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3350	3351

Sequencing Information

	BGKcLV35-17	BGKcLV35-18
Sample_ID	BGKcLV35-17	BGKcLV35-18
Sample Name	CSTF3-BGKcLV35-17	CSTF3-BGKcLV35-18
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	48,801,436	35,525,616
total_aligned_reads	41,437,038	31,971,948
unique_aligned_reads	38,047,006	29,412,800
percent_uniqueAligned	0.77963	0.82793
correlation_replicates	0.997654	0.997654
spikein_reads	9,722	2,666
percent_spikeins	0.00020	0.00008
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2229	2230

Data Submission Information DCC submission information was not avaliable

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-BGKcLV35-17_S35_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2229	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8490
CSTF3-BGKcLV35-17_S35_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2229	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8540
CSTF3-BGKcLV35-17_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2229					GRCh38	V40	CSTF3-BGKcLV35-17/Aligned.sortedByCoord.out.bam		ENCORE2	17736
CSTF3-BGKcLV35-17_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2229					GRCh38	V40	CSTF3-BGKcLV35-17/Aligned.sortedByCoord.out.bam		ENCORE2	17786
CSTF3-BGKcLV35-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2229					GRCh38	V40	CSTF3-BGKcLV35-17/Aligned.sortedByCoord.out.bam		ENCORE2	17836
CSTF3-BGKcLV35-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2229					GRCh38	V40	CSTF3-BGKcLV35-17/Aligned.sortedByCoord.out.bam		ENCORE2	17886
CSTF3-BGKcLV35-17_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2229					GRCh38	V40	CSTF3-BGKcLV35-17_S35_R1_001.filtered.trimmed.paired.fastq.gz,CSTF3-BGKcLV35-17_S35_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17936
CSTF3-BGKcLV35-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2229					GRCh38	V40	CSTF3-BGKcLV35-17_S35_R1_001.filtered.trimmed.paired.fastq.gz,CSTF3-BGKcLV35-17_S35_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29277
CSTF3-BGKcLV35-18_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2230	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8491
CSTF3-BGKcLV35-18_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2230	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8541
CSTF3-BGKcLV35-18_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2230					GRCh38	V40	CSTF3-BGKcLV35-18/Aligned.sortedByCoord.out.bam		ENCORE2	17737
CSTF3-BGKcLV35-18_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2230					GRCh38	V40	CSTF3-BGKcLV35-18/Aligned.sortedByCoord.out.bam		ENCORE2	17787
CSTF3-BGKcLV35-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2230					GRCh38	V40	CSTF3-BGKcLV35-18/Aligned.sortedByCoord.out.bam		ENCORE2	17837
CSTF3-BGKcLV35-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2230					GRCh38	V40	CSTF3-BGKcLV35-18/Aligned.sortedByCoord.out.bam		ENCORE2	17887
CSTF3-BGKcLV35-18_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2230					GRCh38	V40	CSTF3-BGKcLV35-18_S36_R1_001.filtered.trimmed.paired.fastq.gz,CSTF3-BGKcLV35-18_S36_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17937
CSTF3-BGKcLV35-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2230					GRCh38	V40	CSTF3-BGKcLV35-18_S36_R1_001.filtered.trimmed.paired.fastq.gz,CSTF3-BGKcLV35-18_S36_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29278