HMGB1 RNA-Seq in K562

Experiment Information (Status: Sequenced)

	BGKcLV53-67	BGKcLV53-68
idx	0	0
TRCN#_or_BGC#	BGC#0001515	BGC#0001515
shRNA_or_gRNA_sequence	TGTGTGTCCTGTGTACCCGA	TGTGTGTCCTGTGTACCCGA
PAM	GGG	GGG
Name	HMGB1_88U	HMGB1_88U
Sample_ID	BGKcLV53-67	BGKcLV53-68
transduction_Date	2/24/26	2/24/26
days	D6	D6
RBP_name	HMGB1	HMGB1
qPCR_result	0.0	22.0
Ave_qPCR	11.0
RT-qPCR_primer-F	tatggcaaaagcggacaagg
RT-qPCR_primer-R	tttgggcgatactcagagca
protein_conc	1881	1777
WB_result	58.8	59.7
Ave_WB
WB_DONE_date	3/24/26,3/20/26
MW	25kd	#69
IP
antibody_Cat#	GTX101277	lot# 39742
Antibody DCC ID	ENCAB976FQA
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	6429	6430

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HMGB1	Product_ID: GTX101277 Lot_ID: 39742 Source: GeneTex Target Name: HMGB1-human

Experiment Status

	BGKcLV53-67	BGKcLV53-68
Sample_ID	BGKcLV53-67	BGKcLV53-68
Sample Name
Sample Name	HMGB1-BGKcLV53-67	HMGB1-BGKcLV53-68
RBP	HMGB1	HMGB1
Cell_Line	K562	K562
Exp UID
Status	Sequenced	Sequenced
Status_date	2026-09-16	2026-09-16
Project	ENCORE2	ENCORE2
Note
ID	14796	14797

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV53-67	BGKcLV53-68
Sample #	47	48
Sample Name	HMGB1-BGKcLV53-67	HMGB1-BGKcLV53-68
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-26	2026-05-26
Lib_ID	Lib-260526	Lib-260526
Tecan_Location
Tecan
Tecan_date
Size_bp	296	307
Peak_Molarity	85.30	66.50
libSampleQC_DNA_Well	DNA_Library_set82/set2/E10.png	DNA_Library_set82/set2/F10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set82/set2/E7.png	RNA_Library_set82/set2/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-27	2026-05-27
Sample_ID	BGKcLV53-67	BGKcLV53-68
RBP	HMGB1	HMGB1
Batch_ID	BGKcLV53	BGKcLV53
WB_result	58.800	59.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4886	4887

Sequencing Information

	BGKcLV53-67	BGKcLV53-68
Sample_ID	BGKcLV53-67	BGKcLV53-68
Sample Name	HMGB1-BGKcLV53-67	HMGB1-BGKcLV53-68
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	34,743,377	34,683,503
total_aligned_reads	30,724,332	31,945,499
unique_aligned_reads	28,534,332	29,688,725
percent_uniqueAligned	0.82129	0.85599
correlation_replicates	0.998315	0.998315
spikein_reads	43,434	57,860
percent_spikeins	0.00125	0.00167
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3587	3588

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
HMGB1-BGKcLV53-67_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3587	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33670
HMGB1-BGKcLV53-67_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3587	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33728
HMGB1-BGKcLV53-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3587					GRCh38	V40	HMGB1-BGKcLV53-67_R1.filtered.trimmed.paired.fastq.gz,HMGB1-BGKcLV53-67_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33786
HMGB1-BGKcLV53-67_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3587					GRCh38	V40	HMGB1-BGKcLV53-67_Aligned.sortedByCoord.out.bam		ENCORE2	33844
HMGB1-BGKcLV53-67_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3587					GRCh38	V40	HMGB1-BGKcLV53-67_Aligned.sortedByCoord.out.bam		ENCORE2	33902
HMGB1-BGKcLV53-67_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3587					GRCh38	V40	HMGB1-BGKcLV53-67_Aligned.sortedByCoord.out.bam		ENCORE2	33960
HMGB1-BGKcLV53-67_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3587					GRCh38	V40	HMGB1-BGKcLV53-67_Aligned.sortedByCoord.out.bam		ENCORE2	34018
HMGB1-BGKcLV53-67_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3587					GRCh38	V40	HMGB1-BGKcLV53-67_R1.filtered.trimmed.paired.fastq.gz,HMGB1-BGKcLV53-67_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34076
HMGB1-BGKcLV53-68_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3588	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33671
HMGB1-BGKcLV53-68_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3588	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33729
HMGB1-BGKcLV53-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3588					GRCh38	V40	HMGB1-BGKcLV53-68_R1.filtered.trimmed.paired.fastq.gz,HMGB1-BGKcLV53-68_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33787
HMGB1-BGKcLV53-68_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3588					GRCh38	V40	HMGB1-BGKcLV53-68_Aligned.sortedByCoord.out.bam		ENCORE2	33845
HMGB1-BGKcLV53-68_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3588					GRCh38	V40	HMGB1-BGKcLV53-68_Aligned.sortedByCoord.out.bam		ENCORE2	33903
HMGB1-BGKcLV53-68_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3588					GRCh38	V40	HMGB1-BGKcLV53-68_Aligned.sortedByCoord.out.bam		ENCORE2	33961
HMGB1-BGKcLV53-68_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3588					GRCh38	V40	HMGB1-BGKcLV53-68_Aligned.sortedByCoord.out.bam		ENCORE2	34019
HMGB1-BGKcLV53-68_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3588					GRCh38	V40	HMGB1-BGKcLV53-68_R1.filtered.trimmed.paired.fastq.gz,HMGB1-BGKcLV53-68_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34077