HNRNPD RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV47-39	BGHcLV47-40
idx	1643	1644
TRCN#_or_BGC#	BGC#0000192	BGC#0000192
shRNA_or_gRNA_sequence	GTCGGAGGAGCAGTTCGGCG	GTCGGAGGAGCAGTTCGGCG
PAM	GGG	GGG
Name	HNRNPD-93F	HNRNPD-93F
Sample_ID	BGHcLV47-39	BGHcLV47-40
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	HNRNPD	HNRNPD
qPCR_result	68.1	57.1
Ave_qPCR	62.6
RT-qPCR_primer-F	CTCCAGATACACCTGAAGAGAAA
RT-qPCR_primer-R	CGCCTCTTATTGGTCTTGTTG
protein_conc	4471	3965
WB_result	93.7	96.9
Ave_WB
WB_DONE_date	3/11/25
MW	38kd	TUBULIN
IP		fu's #18
antibody_Cat#	#12382	lot # 1
Antibody DCC ID	ENCAB870XOX
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9832	9833

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPD	Product_ID: 12382S Lot_ID: 1 Source: Cell Signaling Target Name: HNRNPD-human

Experiment Status

	BGHcLV47-39	BGHcLV47-40
Sample_ID	BGHcLV47-39	BGHcLV47-40
Sample Name
Sample Name	HNRNPD-BGHcLV47-39	HNRNPD-BGHcLV47-40
RBP	HNRNPD	HNRNPD
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14160	14161

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-39	BGHcLV47-40
Sample #	13	14
Sample Name	HNRNPD-BGHcLV47-39	HNRNPD-BGHcLV47-40
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	260	267
Peak_Molarity	55.90	36.00
libSampleQC_DNA_Well	DNA_Library_set78/set1/E7.png	DNA_Library_set78/set1/F7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set78/set1/E2.png	RNA_Library_set78/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-39	BGHcLV47-40
RBP	HNRNPD	HNRNPD
Batch_ID	BGHcLV47	BGHcLV47
WB_result	93.700	96.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4724	4725

Sequencing Information

	BGHcLV47-39	BGHcLV47-40	BGHcLV47-40
Sample_ID	BGHcLV47-39	BGHcLV47-40	BGHcLV47-40
Sample Name	HNRNPD-BGHcLV47-39	HNRNPD-BGHcLV47-40	HNRNPD-BGHcLV47-40
Pool ID	Pool-250422	Pool-250422	Pool-250822
LocalServer_folder	set78	set78	set78
total_reads	19,451,137	25,430,186	12,484,376
total_aligned_reads	17,027,103	19,478,100	9,600,998
unique_aligned_reads	16,021,096	18,324,479	9,035,136
percent_uniqueAligned	0.82366	0.72058	0.72372
correlation_replicates	0.995748	0.995748	0.996096
spikein_reads	17,122	21,532	10,432
percent_spikeins	0.00088	0.00085	0.00084
original_ReadLength	101	101	151
QC_Status	ReadyToSubmit	ReadyToSubmit	ReadyToSubmit
ID	3427	3428	3600

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
HNRNPD-BGHcLV47-39_S54_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3427	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32558
HNRNPD-BGHcLV47-39_S54_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3427	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32592
HNRNPD-BGHcLV47-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3427					GRCh38	V40	HNRNPD-BGHcLV47-39_S54_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPD-BGHcLV47-39_S54_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32626
HNRNPD-BGHcLV47-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3427					GRCh38	V40	HNRNPD-BGHcLV47-39_Aligned.sortedByCoord.out.bam		ENCORE2	32660
HNRNPD-BGHcLV47-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3427					GRCh38	V40	HNRNPD-BGHcLV47-39_Aligned.sortedByCoord.out.bam		ENCORE2	32694
HNRNPD-BGHcLV47-39_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3427					GRCh38	V40	HNRNPD-BGHcLV47-39_Aligned.sortedByCoord.out.bam		ENCORE2	32728
HNRNPD-BGHcLV47-39_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3427					GRCh38	V40	HNRNPD-BGHcLV47-39_Aligned.sortedByCoord.out.bam		ENCORE2	32762
HNRNPD-BGHcLV47-39_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3427					GRCh38	V40	HNRNPD-BGHcLV47-39_S54_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPD-BGHcLV47-39_S54_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32796
HNRNPD-BGHcLV47-40_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3428	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32559
HNRNPD-BGHcLV47-40_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3428	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32593
HNRNPD-BGHcLV47-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3428					GRCh38	V40	HNRNPD-BGHcLV47-40_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPD-BGHcLV47-40_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32627
HNRNPD-BGHcLV47-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3428					GRCh38	V40	HNRNPD-BGHcLV47-40_Aligned.sortedByCoord.out.bam		ENCORE2	32661
HNRNPD-BGHcLV47-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3428					GRCh38	V40	HNRNPD-BGHcLV47-40_Aligned.sortedByCoord.out.bam		ENCORE2	32695
HNRNPD-BGHcLV47-40_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3428					GRCh38	V40	HNRNPD-BGHcLV47-40_Aligned.sortedByCoord.out.bam		ENCORE2	32729
HNRNPD-BGHcLV47-40_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3428					GRCh38	V40	HNRNPD-BGHcLV47-40_Aligned.sortedByCoord.out.bam		ENCORE2	32763
HNRNPD-BGHcLV47-40_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3428					GRCh38	V40	HNRNPD-BGHcLV47-40_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,HNRNPD-BGHcLV47-40_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32797