HNRNPCL1 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV04-33	BG293LV04-34
idx	0	0
TRCN#_or_BGC#	TRCN0000075086	TRCN0000075086
shRNA_or_gRNA_sequence	CCGGGCTTCAATTCTAAGAGTGGAACTCGAGTTCCACTCTTAGAATTGAAGCTTTTTG	CCGGGCTTCAATTCTAAGAGTGGAACTCGAGTTCCACTCTTAGAATTGAAGCTTTTTG
PAM
Name	HNRNPCL1	HNRNPCL1
Sample_ID	BG293LV04-33	BG293LV04-34
transduction_Date	9/7/23	9/7/23
days	D4	D4
RBP_name	HNRNPCL1	HNRNPCL1
qPCR_result	76.1	76.0
Ave_qPCR	76.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9920	9921

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV04-33	BG293LV04-34
Sample_ID	BG293LV04-33	BG293LV04-34
Sample Name
Sample Name	HNRNPCL1-BG293LV04-33	HNRNPCL1-BG293LV04-34
RBP	HNRNPCL1	HNRNPCL1
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	12522	12523

Library-Prep
Sequencing

Library-Prep Information

	BG293LV04-33	BG293LV04-34
Sample #	9	10
Sample Name	HNRNPCL1-BG293LV04-33	HNRNPCL1-BG293LV04-34
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-10	2023-10-10
Lib_ID	Lib-231010	Lib-231010
Tecan_Location
Tecan
Tecan_date
Size_bp	270	269
Peak_Molarity	77.10	55.10
libSampleQC_DNA_Well	DNA_Library_set64/set1/A10.png	DNA_Library_set64/set1/B10.png
RIN	10.0	9.7
libSample_RNA_Well	RNA_Library_set64/set1/A6.png	RNA_Library_set64/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-12	2023-10-12
Sample_ID	BG293LV04-33	BG293LV04-34
RBP	HNRNPCL1	HNRNPCL1
Batch_ID	BG293LV04	BG293LV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4014	4015

Sequencing Information

	BG293LV04-33	BG293LV04-34
Sample_ID	BG293LV04-33	BG293LV04-34
Sample Name	HNRNPCL1-BG293LV04-33	HNRNPCL1-BG293LV04-34
Pool ID	Pool-231012	Pool-231012
LocalServer_folder	set64	set64
total_reads	26,505,750	30,989,856
total_aligned_reads	23,978,209	27,724,172
unique_aligned_reads	22,474,251	25,970,684
percent_uniqueAligned	0.84790	0.83804
correlation_replicates	0.995393	0.995393
spikein_reads	12,658	8,124
percent_spikeins	0.00048	0.00026
original_ReadLength	100	100
QC_Status	Submitting	Submitting
ID	2623	2624

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
HNRNPCL1-BG293LV04-33_S9_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2623	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8686
HNRNPCL1-BG293LV04-33_S9_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2623	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8714
HNRNPCL1-BG293LV04-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2623					GRCh38	V40	HNRNPCL1-BG293LV04-33_S9_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPCL1-BG293LV04-33_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9763
HNRNPCL1-BG293LV04-33_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2623					GRCh38	V40	HNRNPCL1-BG293LV04-33/Aligned.sortedByCoord.out.bam		ENCORE2	9791
HNRNPCL1-BG293LV04-33_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2623					GRCh38	V40	HNRNPCL1-BG293LV04-33/Aligned.sortedByCoord.out.bam		ENCORE2	9819
HNRNPCL1-BG293LV04-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2623					GRCh38	V40	HNRNPCL1-BG293LV04-33/Aligned.sortedByCoord.out.bam		ENCORE2	9847
HNRNPCL1-BG293LV04-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2623					GRCh38	V40	HNRNPCL1-BG293LV04-33/Aligned.sortedByCoord.out.bam		ENCORE2	9875
HNRNPCL1-BG293LV04-33_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2623					GRCh38	V40	HNRNPCL1-BG293LV04-33_S9_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPCL1-BG293LV04-33_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9903
HNRNPCL1-BG293LV04-34_S10_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2624	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8687
HNRNPCL1-BG293LV04-34_S10_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2624	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8715
HNRNPCL1-BG293LV04-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2624					GRCh38	V40	HNRNPCL1-BG293LV04-34_S10_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPCL1-BG293LV04-34_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9764
HNRNPCL1-BG293LV04-34_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2624					GRCh38	V40	HNRNPCL1-BG293LV04-34/Aligned.sortedByCoord.out.bam		ENCORE2	9792
HNRNPCL1-BG293LV04-34_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2624					GRCh38	V40	HNRNPCL1-BG293LV04-34/Aligned.sortedByCoord.out.bam		ENCORE2	9820
HNRNPCL1-BG293LV04-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2624					GRCh38	V40	HNRNPCL1-BG293LV04-34/Aligned.sortedByCoord.out.bam		ENCORE2	9848
HNRNPCL1-BG293LV04-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2624					GRCh38	V40	HNRNPCL1-BG293LV04-34/Aligned.sortedByCoord.out.bam		ENCORE2	9876
HNRNPCL1-BG293LV04-34_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2624					GRCh38	V40	HNRNPCL1-BG293LV04-34_S10_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPCL1-BG293LV04-34_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9904