INTS11 RNA-Seq in HepG2

Experiment Information (Status: Submitting)

	BGHcLV34-13	BGHcLV34-14
idx	1083	1084
TRCN#_or_BGC#	BGC#0000714	BGC#0000714
shRNA_or_gRNA_sequence	GTCAGCAAAAGCCCGGTCGA	GTCAGCAAAAGCCCGGTCGA
PAM	AGG	AGG
Name	CPSF3L_93	CPSF3L_93
Sample_ID	BGHcLV34-13	BGHcLV34-14
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	INTS11	INTS11
qPCR_result	43.9	49.6
Ave_qPCR	46.8
RT-qPCR_primer-F	gtgcacctgcatgacacac
RT-qPCR_primer-R	aggacggactccacagtcac
protein_conc	3597	3675
WB_result	55.9	69.2
Ave_WB	62.6
WB_DONE_date	5/9/22	JESS
MW	68KD
IP	Rabbit / I
antibody_Cat#	A301-274A	LOT #4
Antibody DCC ID	ENCAB499MQV
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	7262	7263

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
INTS11	Product_ID: A301-274A Lot_ID: 4 Source: Bethyl Labs Target Name: INTS11-human

Experiment Status

	BGHcLV34-13	BGHcLV34-14
Sample_ID	BGHcLV34-13	BGHcLV34-14
Sample Name
Sample Name	CPSF3L-BGHcLV34-13	CPSF3L-BGHcLV34-14
RBP	CPSF3L	CPSF3L
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10799	10800

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-13	BGHcLV34-14
Sample #	3	4
Sample Name	CPSF3L-BGHcLV34-13	CPSF3L-BGHcLV34-14
Sample_Name_Alias
Index Well Position	C01	D01
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	279	277
Peak_Molarity	15.30	29.30
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/C5.png	DNA_Library_set54-56/set3/D5.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set54-56/set2/C1.png	RNA_Library_set54-56/set2/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGHcLV34-13	BGHcLV34-14
RBP	CPSF3L	CPSF3L
Batch_ID	BGHcLV34	BGHcLV34
WB_result	55.900	69.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3320	3321

Sequencing Information

	BGHcLV34-13	BGHcLV34-14
Sample_ID	BGHcLV34-13	BGHcLV34-14
Sample Name	CPSF3L-BGHcLV34-13	CPSF3L-BGHcLV34-14
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	68,988,846	56,781,088
total_aligned_reads	53,637,602	45,565,538
unique_aligned_reads	50,669,396	43,057,674
percent_uniqueAligned	0.73446	0.75831
correlation_replicates	0.995330	0.995330
spikein_reads	5,548	4,074
percent_spikeins	0.00008	0.00007
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2197	2198

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
CPSF3L-BGHcLV34-13_S3_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2197	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8484
CPSF3L-BGHcLV34-13_S3_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2197	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8534
CPSF3L-BGHcLV34-13_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	2197					GRCh38	V40	CPSF3L-BGHcLV34-13/Aligned.sortedByCoord.out.bam		ENCORE2	17730
CPSF3L-BGHcLV34-13_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	2197					GRCh38	V40	CPSF3L-BGHcLV34-13/Aligned.sortedByCoord.out.bam		ENCORE2	17780
CPSF3L-BGHcLV34-13_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	2197					GRCh38	V40	CPSF3L-BGHcLV34-13/Aligned.sortedByCoord.out.bam		ENCORE2	17830
CPSF3L-BGHcLV34-13_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	2197					GRCh38	V40	CPSF3L-BGHcLV34-13/Aligned.sortedByCoord.out.bam		ENCORE2	17880
CPSF3L-BGHcLV34-13_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2197					GRCh38	V40	CPSF3L-BGHcLV34-13_S3_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3L-BGHcLV34-13_S3_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17930
CPSF3L-BGHcLV34-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2197					GRCh38	V40	CPSF3L-BGHcLV34-13_S3_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3L-BGHcLV34-13_S3_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29271
CPSF3L-BGHcLV34-14_S4_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2198	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8485
CPSF3L-BGHcLV34-14_S4_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2198	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8535
CPSF3L-BGHcLV34-14_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	2198					GRCh38	V40	CPSF3L-BGHcLV34-14/Aligned.sortedByCoord.out.bam		ENCORE2	17731
CPSF3L-BGHcLV34-14_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	2198					GRCh38	V40	CPSF3L-BGHcLV34-14/Aligned.sortedByCoord.out.bam		ENCORE2	17781
CPSF3L-BGHcLV34-14_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	2198					GRCh38	V40	CPSF3L-BGHcLV34-14/Aligned.sortedByCoord.out.bam		ENCORE2	17831
CPSF3L-BGHcLV34-14_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	2198					GRCh38	V40	CPSF3L-BGHcLV34-14/Aligned.sortedByCoord.out.bam		ENCORE2	17881
CPSF3L-BGHcLV34-14_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2198					GRCh38	V40	CPSF3L-BGHcLV34-14_S4_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3L-BGHcLV34-14_S4_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17931
CPSF3L-BGHcLV34-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2198					GRCh38	V40	CPSF3L-BGHcLV34-14_S4_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3L-BGHcLV34-14_S4_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29272