title: 3128869_G401_PHIPmarc_siCtrl_3_ChIP

description: Library name: 3128869_G401_PHIPmarc_siCtrl_3_ChIP_HAM


title: CHLA266_RNAseq_siPHIP_NA_1

status: Public on Feb 09 2026

type: SRA

city: Memphis

first: John

last: Navarro

state: Tennessee

address: 262 Danny Thomas Place

country: USA

institute: St. Jude Children's Research Hospital

description:
Library name: 3399701_CHLA266_RNAseq_siPHIP_NA_1_HAM
20251104 RNAseq after PHIP KD CHLA266
ROBERTS-864304-STRANDED_RSEM_gene_count.txt

library_source: transcriptomic

data_processing:
trim_galore v0.6.3 remove adapter sequences
alignment with STAR2.7.9a --twopassMode Basic
read counts quantified by RSEMv1.3.3
Assembly: hg19/GRCh37.p13
Supplementary files format and content: tab delimited table of read counts for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: McCoy's Medium + 10% FBS + 10% GlutaMAX

extract_protocol:
ZymoResearch Direct-zol™ RNA MiniPrep Plus Cat # R2070 according to manufacturer's instructions
TruSeq Stranded mRNA Library Prep Kit, Illumina, PN 20020595

treatment_protocol: 48 hour transfection with individual siRNAs

tag: cell line

tag: cell type

value: ATRT

tag: genotype

value: siPHIP


title: BIN67_RNAseq_siPHIP_NA_1

description:
Library name: 3396600_BIN67_RNAseq_siPHIP_NA_1_HAM
20251020 RNAseq after PHIP KD BIN67
ROBERTS-863692-STRANDED_RSEM_gene_count.txt

value: SCCOHT


title: CHLA266_RNAseq_siCtrl_NA_2

description:
Library name: 3399699_CHLA266_RNAseq_siCtrl_NA_2_HAM
20251104 RNAseq after PHIP KD CHLA266
ROBERTS-864304-STRANDED_RSEM_gene_count.txt

value: siCtrl


title: 3334382_G401_CHD4ab240640_GFP_2_ChIP

description: Library name: 3334382_G401_CHD4ab240640_GFP_2_ChIP_HAM

library_source: genomic

data_processing:
Raw reads were processed using Trim-Galore (v0.6.3, Krueger F. (2012)
Reads were mapped to human-drosophila reference hybrid genome (merged hg19/GRCh37.p13 and dm6 genomes) with bwa aln, followed by bwa samse or sampe (v0.7.17-r1039, PMID: 19451168)
Reads mapping to human reference genome were extracted for further analysis using samtools, duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) and Cross-Correlation analysis was conducted with SPP (v1.11, PMID: 19029915)
Uniquely mapped reads were then extracted with samtools, extended with bedtools (v2.24.0, PMID: 20110278) using the fragment size value previously estimated with Cross-Correlation analysis, and then converted to bigwig track files by UCSC tools (v4, PMID: 22908213).
Peaks were called using MACS2 (PMID: 18798982) program with –nomodel -q 0.05 flags (high confidence peaks).
Assembly: merged hg19/GRCh37.p13 and dm6
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

molecule: genomic DNA

source_name: cell line

growth_protocol: McCoy's Media + 10% FBS

extract_protocol:
Covaris truCHIP Chromatin Shearing Kit
KAPA Library Prep Kit

tag: tissue

value: cell line

value: rhabdoid tumor

value: GFP


title: 3128874_G401_PHIPmarc_siPHIP_2_ChIP

description: Library name: 3128874_G401_PHIPmarc_siPHIP_2_ChIP_HAM


title: CHLA266_RNAseq_siCtrl_NA_3

description:
Library name: 3399700_CHLA266_RNAseq_siCtrl_NA_3_HAM
20251104 RNAseq after PHIP KD CHLA266
ROBERTS-864304-STRANDED_RSEM_gene_count.txt


title: HA-PHIPG401cB7_RNAseq_siPHIP_plusDOX_1

description:
Library name: 3392857_HA-PHIPG401cB7_RNAseq_siPHIP_plusDOX_1_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt

tag: treatment

value: plusDOX


title: HA-PHIPG401cB7_RNAseq_siPHIP_plusDOX_2

description:
Library name: 3392858_HA-PHIPG401cB7_RNAseq_siPHIP_plusDOX_2_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: HA-PHIPG401cB7_RNAseq_siPHIP_plusDOX_3

description:
Library name: 3392859_HA-PHIPG401cB7_RNAseq_siPHIP_plusDOX_3_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: BIN67_RNAseq_siCtrl_NA_1

description:
Library name: 3396597_BIN67_RNAseq_siCtrl_NA_1_HAM
20251020 RNAseq after PHIP KD BIN67
ROBERTS-863692-STRANDED_RSEM_gene_count.txt


title: HA-PHIPG401cB7_RNAseq_siPHIP_noDOX_2

description:
Library name: 3392855_HA-PHIPG401cB7_RNAseq_siPHIP_noDOX_2_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt

value: noDOX


title: HA-PHIPG401cB7_RNAseq_siPHIP_noDOX_1

description:
Library name: 3392854_HA-PHIPG401cB7_RNAseq_siPHIP_noDOX_1_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: HA-PHIPG401cB7_RNAseq_siCtrl_plusDOX_1

description:
Library name: 3392851_HA-PHIPG401cB7_RNAseq_siCtrl_plusDOX_1_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: HA-PHIPG401cB7_RNAseq_siCtrl_plusDOX_3

description:
Library name: 3392853_HA-PHIPG401cB7_RNAseq_siCtrl_plusDOX_3_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: HA-PHIPG401cB7_RNAseq_siCtrl_plusDOX_2

description:
Library name: 3392852_HA-PHIPG401cB7_RNAseq_siCtrl_plusDOX_2_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: HA-PHIPG401cB7_RNAseq_siCtrl_noDOX_2

description:
Library name: 3392849_HA-PHIPG401cB7_RNAseq_siCtrl_noDOX_2_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: HA-PHIPG401cB7_RNAseq_siCtrl_noDOX_3

description:
Library name: 3392850_HA-PHIPG401cB7_RNAseq_siCtrl_noDOX_3_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: 3404924_G401_input_PHIP-rescue_1_ChIP

description:
Library name: 3404924_G401_input_PHIP-rescue_1_ChIP_HAM
input for PHIP-rescue samples

value: PHIP-rescue


title: HA-PHIPG401cB7_RNAseq_siCtrl_noDOX_1

description:
Library name: 3392848_HA-PHIPG401cB7_RNAseq_siCtrl_noDOX_1_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: 3404923_G401_input_PHIP-KD_3_ChIP

description:
Library name: 3404923_G401_input_PHIP-KD_3_ChIP_HAM
input for PHIP-KD samples

value: PHIP-KD


title: 3404918_G401_input_PHIP-OE_1_ChIP

description:
Library name: 3404918_G401_input_PHIP-OE_1_ChIP_HAM
input for PHIP-OE samples

value: PHIP-OE


title: 3404926_G401_input_PHIP-rescue_3_ChIP

description:
Library name: 3404926_G401_input_PHIP-rescue_3_ChIP_HAM
input for PHIP-rescue samples


title: 3404919_G401_input_PHIP-OE_2_ChIP

description:
Library name: 3404919_G401_input_PHIP-OE_2_ChIP_HAM
input for PHIP-OE samples


title: 3404917_G401_input_control_3_ChIP

description:
Library name: 3404917_G401_input_control_3_ChIP_HAM
input for control samples

value: control


title: 3404921_G401_input_PHIP-KD_1_ChIP

description:
Library name: 3404921_G401_input_PHIP-KD_1_ChIP_HAM
input for PHIP-KD samples


title: 3404916_G401_input_control_2_ChIP

description:
Library name: 3404916_G401_input_control_2_ChIP_HAM
input for control samples


title: HA-PHIPG401cB7_RNAseq_siPHIP_noDOX_3

description:
Library name: 3392856_HA-PHIPG401cB7_RNAseq_siPHIP_noDOX_3_HAM
20251013 HA-PHIP rescue G401 RNAseq
ROBERTS-862930-STRANDED_RSEM_gene_count.txt


title: SAMPLE 12_Cd72+/-;Pax5+/- preleukemic precursor B-cells

type: RNA

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from Cd72+/-;Pax5+/- preleukemic proB cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Affymetrix Transcriptome Analysis Console (TAC) Software Version 4.0.3.14 was used for the normalization, summarization and quality control of the microarray data.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: The animals were bred and maintained in the SPF (specific pathogen-free) area of the animal facility.  At 1 months of age, they were sacrificed to obtain purified bone marrow proB cells.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Bone marrow proB cells


title: 3404920_G401_input_PHIP-OE_3_ChIP

description:
Library name: 3404920_G401_input_PHIP-OE_3_ChIP_HAM
input for PHIP-OE samples


title: 3404922_G401_input_PHIP-KD_2_ChIP

description:
Library name: 3404922_G401_input_PHIP-KD_2_ChIP_HAM
input for PHIP-KD samples


title: BIN67_RNAseq_siCtrl_NA_2

description:
Library name: 3396598_BIN67_RNAseq_siCtrl_NA_2_HAM
20251020 RNAseq after PHIP KD BIN67
ROBERTS-863692-STRANDED_RSEM_gene_count.txt


title: SAMPLE 11_Cd72+/-;Pax5+/- preleukemic precursor B-cells


title: SAMPLE 8_WT pro-B cells

description: Gene expression data from WTproB cells

source_name: WT

value: WT pro-B cells


title: 3404915_G401_input_control_1_ChIP

description:
Library name: 3404915_G401_input_control_1_ChIP_HAM
input for control samples


description:
Library name: 3404898_G401_H3K27ac-ab4729_PHIP-rescue_3_ChIP_HAM
H3K27ac ChIP-seq in PHIP-rescue cells


title: 3404925_G401_input_PHIP-rescue_2_ChIP

description:
Library name: 3404925_G401_input_PHIP-rescue_2_ChIP_HAM
input for PHIP-rescue samples


description:
Library name: 3404896_G401_H3K27ac-ab4729_PHIP-rescue_1_ChIP_HAM
H3K27ac ChIP-seq in PHIP-rescue cells


description:
Library name: 3404897_G401_H3K27ac-ab4729_PHIP-rescue_2_ChIP_HAM
H3K27ac ChIP-seq in PHIP-rescue cells


title: SAMPLE 9_Cd72+/-;Pax5+/- preleukemic precursor B-cells


description:
Library name: 3404895_G401_H3K27ac-ab4729_PHIP-KD_3_ChIP_HAM
H3K27ac ChIP-seq in PHIP-KD cells


title: SAMPLE 5_WT pro-B cells

description: Gene expression data from WTproB cells


title: SAMPLE 6_WT pro-B cells

description: Gene expression data from WTproB cells


description:
Library name: 3404893_G401_H3K27ac-ab4729_PHIP-KD_1_ChIP_HAM
H3K27ac ChIP-seq in PHIP-KD cells


description:
Library name: 3404892_G401_H3K27ac-ab4729_PHIP-OE_3_ChIP_HAM
H3K27ac ChIP-seq in PHIP-OE cells


title: SAMPLE 10_Cd72+/-;Pax5+/- preleukemic precursor B-cells


title: SAMPLE 7_WT pro-B cells

description: Gene expression data from WTproB cells


description:
Library name: 3404891_G401_H3K27ac-ab4729_PHIP-OE_2_ChIP_HAM
H3K27ac ChIP-seq in PHIP-OE cells


title: SAMPLE 2_Pax5+/- preleukemic precursor B-cells

description: Gene expression data from Pax5+/- preleukemic proB cells

value: Pax5+/- preleukemic precursor B-cells


title: SAMPLE 3_Pax5+/- preleukemic precursor B-cells


title: Ribo_hSLFN14_K219N_-Dox

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

description:
Library name: Sample_3
shift_Asite_hSLFN14_K219N_+Dox_hSLFN14_K219N_-Dox.csv

library_source: other

data_processing:
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Assembly: GRCh39.p13
Supplementary files format and content: comma-delimited text files including codon subsequence abundance shift for each codon.
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
WT or K219N SLFN14-inducible 293T cells were seeded in 6-well plates and left untreated or induced with doxycycline (2 μg/mL) for 24 h. The 6-well plates were pre-coated with poly-D-lysine (Gibco) for 5 min at room temperature to enhance the cell attachment. Following treatment, cells were washed once with ice-cold PBS and lysed in polysome lysis buffer (10 mM HEPES, pH 7.4, 5 mM MgCl₂, 100 mM KCl, 1% Triton X-100, 100 μg/mL cycloheximide). Lysates were clarified by centrifugation at maximum speed (≥ 13,000 × g) for 15 min at 4 °C, and the supernatant was collected for downstream ribo-seq analysis.
Ribo-seq libraries were constructed by modifying the Ezra-seq method, as previously described. In brief, the whole cell lysates were digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by agitation at 4°C for 1 h. RNAs were extracted using Trizol LS reagent (Invitrogen) followed by isopropanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 μl RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μl SUPERase·In (Invitrogen)) for 10 min at 70 °C. The gel debris was removed using a Spin-X column (Corning), followed by isopropanol precipitation. 4 μl RNAs (10~200 ng) were mixed with 1 nmol ATP, 1 μl T4 PNK (NEB), 20 U SUPERase·In, 1 μl Poly(A) Polymerase (NEB), and 1 μl homemade Ezra enzyme in 1 × T4 PNK buffer and incubated at 37 °C for 30 min followed by 70 °C for 10 min. Then ligation was performed for 90 min at 25 °C by mixing with a 10 μl reaction mixture (1 pmol biotinylated 5’ end adaptor, 1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 12.5% PEG8000 and 200 U T4 RNA ligase 2 truncated KQ (NEB)). The ligated RNA samples were pulled down after incubation with 20 uL pre-washed streptavidin magnetic beads (NEB) at room temperature for 10 min. After washing once with 100 uL 2 × SSC (Invitrogen), beads were resuspended in 12 μl nuclease-free water and mixed with 8 μl cDNA synthesis mixture (1 poml RT primer, 1 × first strand buffer, 100 nmol DTT, 1 nmol dNTP, 20 U SUPERase·In and 100 ng m-MLV) followed by incubation at 50 °C for 20 min. After washing once with 2 × SSC, beads were resuspended in 20 μl nuclease-free water and incubated at 95 °C for 2 min, then immediately placed on the ice for 1 min. After placing on magnet stand for 1 min, the supernatant cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 °C, 30 s; (98 °C, 5 s; 67 °C, 15 s; 72 °C, 20 s) for 13 cycles; 72 °C, 2 min. PCR products were separated on an 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size 170 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA). After quantification by Qubit 4 Fluorometer (Invitrogen), equal amounts of barcoded samples were pooled and sequenced using MiniSeq (Illumina).

value: WT

value: Dox


title: Ribo_hSLFN14_WT_+Dox

description:
Library name: Sample_2
shift_Asite_hSLFN14_WT_+Dox_hSLFN14_WT_-Dox.csv


title: SAMPLE 1_Pax5+/- preleukemic precursor B-cells


description:
Library name: 3404889_G401_H3K27ac-ab4729_control_3_ChIP_HAM
H3K27ac ChIP-seq in control cells


title: p1558_T-PLL_longitudinal_p1486

city: Leipzig

first: Dennis

last: Jungherz

address: Johannisallee 32a

department: Hematology

country: Germany

institute: University of Leipzig Medical Center

description:
Library name: 110000
N019

data_processing:
Indexing and sorting of mapped reads as well as removal of secondary alignments was performed using samtools (v1.5)
FeatureCounts (v1.5.3)3 was used for summarizing gene-mapped reads. Ensembl annotations (GRCh 38.89) were used for assigning mapped reads to known genes.
Assembly: Reads were aligned to the human genome (UCSC hg38) using Hisat2 (v2.1.0)
Supplementary files format and content: Sample annotation table with associated gene expression values (FPKM) for protein-coding genes

source_name: peripheral blood

growth_protocol: For in-vitro culture, cells were seeded at 1-2x10^6/mL in RPMI supplemented with 10% heat-inactivated FBS and 1% Penicillin-Streptomycin (Gibco, life technologies, Carlsbad, California, USA).

extract_protocol:
Total RNA was isolated from PBMCs of 46 T-PLL patients and CD3+ pan-T-cells of 6 age_x0002_matched healthy controls using the mirVana kit (Thermofisher, Waltham, Massachusetts, USA) according to manufacturer’s guidelines (total RNA isolation, no enrichment for small RNAs). In order to remove remaining DNA, DNAse treatment of samples was performed by using the DNA-free kit (Invitrogen, Carlsbad, California, USA). RNA quality was assessed using the 4150 TapeStation (Agilent, Santa Clara, California, USA) and samples with RNA  integrity number (RIN) < 6 were excluded (median RIN=8.76).
For polyA-RNA sequencing, samples were subjected to library preparation using the TruSeq® Stranded mRNA Library Prep kit (Illumina, San Diego, California, USA) and then sequenced on the NovaSeq 6000 platform (Illumina, San Diego, California, USA) according to standard protocols.

treatment_protocol: Primary isolates of 50 well-annotated T-PLL patients and of T cells from six age-matched healthy donors were studied (banked 2009-2019). CD3+ pan-T-cells of 6 age-matched healthy donors were used as controls (age older than 55 years). For that peripheral-blood mononuclear cells (PBMCs) were isolated from buffy coats by density gradient centrifugation (Histopaque, Sigma-Aldrich, St. Louis, Missouri, USA). Enrichment of CD3+ T-cells was performed by negative selection from PBMCs using magnetic-bead based cell enrichment (Biolegend, San Diego, California, USA) according to manufacturer’s guidelines.

value: peripheral blood

value: PBMCs derived from T-PLL patient


description:
Library name: 3404888_G401_H3K27ac-ab4729_control_2_ChIP_HAM
H3K27ac ChIP-seq in control cells


description:
Library name: 3404887_G401_H3K27ac-ab4729_control_1_ChIP_HAM
H3K27ac ChIP-seq in control cells


title: WT_iPSC_3

city: Hangzhou

first: Jiayang

last: Wan

address: No. 79, Qingchun Road, Shangcheng District

country: China

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

description: Library name: Sample 6

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: FPKM_all_samples.txt
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample.

source_name: stem cell

extract_protocol:
Total RNA was extracted from the samples using the  RNA-Quick Purification Kit (Yishan Bio, RN001), followed by library preparation and sequencing on the Illumina platform.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: stem cell

value: induced pluripotent stem cell


title: Ribo_hSLFN14_K219N_+Dox

description:
Library name: Sample_4
shift_Asite_hSLFN14_K219N_+Dox_hSLFN14_K219N_-Dox.csv


title: WT_iPSC_2

description: Library name: Sample 5


title: p1486_T-PLL

description:
Library name: 109996
N019


description:
Library name: 3404894_G401_H3K27ac-ab4729_PHIP-KD_2_ChIP_HAM
H3K27ac ChIP-seq in PHIP-KD cells

value: rhabdoid tumor


title: Ribo_hSLFN14_WT_-Dox

description:
Library name: Sample_1
shift_Asite_hSLFN14_WT_+Dox_hSLFN14_WT_-Dox.csv


title: WT_iPSC_1

description: Library name: Sample 4


title: p1553_T-PLL_longitudinal_p1486

description:
Library name: 109998
N019


description:
Library name: 3404890_G401_H3K27ac-ab4729_PHIP-OE_1_ChIP_HAM
H3K27ac ChIP-seq in PHIP-OE cells


title: p1500_T-PLL

description:
Library name: 109994
N021


title: R693Q_iPSC_3

description: Library name: Sample 3


title: p2545_T-PLL

description:
Library name: 109992
Helsinki_p2545


title: p1364_T-PLL

description:
Library name: 109990
Helsinki_p1364


title: p1408_T-PLL

description:
Library name: 109988
N002


title: p1417_T-PLL

description:
Library name: 109984
TP111


title: R693Q_iPSC_1

description: Library name: Sample 1


title: p1419_T-PLL

description:
Library name: 109982
TP112


title: R693Q_iPSC_2

description: Library name: Sample 2


title: p1404_T-PLL

description:
Library name: 109986
TP109


title: G401_input_siPHIP_3_MTA2_RBBP4

description:
Library name: 3274178_G401_input_siPHIP_3_ChIP_HAM
input for siPHIP RBBP4 and MTA2

value: siPHIP


title: G401_input_siPHIP_1_MTA2_RBBP4

description:
Library name: 3274176_G401_input_siPHIP_1_ChIP_HAM
input for siPHIP RBBP4 and MTA2


title: G401_input_siCtrl_2_MTA2_RBBP4

description:
Library name: 3274174_G401_input_siCtrl_2_ChIP_HAM
input for siCtrl RBBP4 and MTA2

value: siCtrl


title: G401_input_siCtrl_3_MTA2_RBBP4

description:
Library name: 3274175_G401_input_siCtrl_3_ChIP_HAM
input for siCtrl RBBP4 and MTA2


title: G401_input_siPHIP_2_MTA2_RBBP4

description:
Library name: 3274177_G401_input_siPHIP_2_ChIP_HAM
input for siPHIP RBBP4 and MTA2


title: p1549_T-PLL

description:
Library name: 109980
N047


title: p1567_T-PLL

description:
Library name: 109976
N058


title: SAMPLE 4_Pax5+/- preleukemic precursor B-cells


title: G401_input_siCtrl_1_MTA2_RBBP4

description:
Library name: 3274173_G401_input_siCtrl_1_ChIP_HAM
input for siCtrl RBBP4 and MTA2


title: G401_MTA2ab8106_siPHIP_3

description:
Library name: 3274172_G401_MTA2ab8106_siPHIP_3_ChIP_HAM
ChIP for MTA2 in siPHIP


title: p1532_T-PLL

description:
Library name: 109978
N034


title: p1376_T-PLL

description:
Library name: 109972
TP060


title: p1080_T-PLL

description:
Library name: 109968
TP023


title: G401_MTA2ab8106_siPHIP_2

description:
Library name: 3274171_G401_MTA2ab8106_siPHIP_2_ChIP_HAM
ChIP for MTA2 in siPHIP


title: G401_MTA2ab8106_siPHIP_1

description:
Library name: 3274170_G401_MTA2ab8106_siPHIP_1_ChIP_HAM
ChIP for MTA2 in siPHIP


title: G401_MTA2ab8106_siCtrl_3

description:
Library name: 3274169_G401_MTA2ab8106_siCtrl_3_ChIP_HAM
ChIP for MTA2 in siCtrl


title: p1332_T-PLL

description:
Library name: 109966
TP049


title: p1495_T-PLL

description:
Library name: 109964
TP100


title: p1557_T-PLL

description:
Library name: 109962
N055


title: G401_MTA2ab8106_siCtrl_2

description:
Library name: 3274168_G401_MTA2ab8106_siCtrl_2_ChIP_HAM
ChIP for MTA2 in siCtrl


title: p1434_T-PLL

description:
Library name: 109960
TP102


title: p1599_T-PLL

description:
Library name: 109956
N069


title: G401_RBBP4ab79416_siPHIP_3

description:
Library name: 3274166_G401_RBBP4ab79416_siPHIP_3_ChIP_HAM
ChIP for RBBP4 in siPHIP


title: p1528_T-PLL

description:
Library name: 109970
N030


title: p1432_T-PLL

description:
Library name: 109958
N007


title: G401_RBBP4ab79416_siPHIP_2

description:
Library name: 3274165_G401_RBBP4ab79416_siPHIP_2_ChIP_HAM
ChIP for RBBP4 in siPHIP


title: G401_RBBP4ab79416_siCtrl_2

description:
Library name: 3274162_G401_RBBP4ab79416_siCtrl_2_ChIP_HAM
ChIP for RBBP4 in siCtrl


title: G401_RBBP4ab79416_siPHIP_1

description:
Library name: 3274164_G401_RBBP4ab79416_siPHIP_1_ChIP_HAM
ChIP for RBBP4 in siPHIP


title: G401_HDAC1-40967_siPHIP_3

description:
Library name: 3198097_G401_HDAC1-40967_siPHIP_3_ChIP_HAM
ChIP for HDAC1 in siPHIP


title: G401_MTA2ab8106_siCtrl_1

description:
Library name: 3274167_G401_MTA2ab8106_siCtrl_1_ChIP_HAM
ChIP for MTA2 in siCtrl


title: p1581_T-PLL

description:
Library name: 109954
N061


title: G401_RBBP4ab79416_siCtrl_3

description:
Library name: 3274163_G401_RBBP4ab79416_siCtrl_3_ChIP_HAM
ChIP for RBBP4 in siCtrl


title: p1570_T-PLL

description:
Library name: 109952
N060


title: G401_RBBP4ab79416_siCtrl_1

description:
Library name: 3274161_G401_RBBP4ab79416_siCtrl_1_ChIP_HAM
ChIP for RBBP4 in siCtrl


title: p1383_T-PLL

description:
Library name: 109948
TP065


title: p1561_T-PLL

description:
Library name: 109950
N059


title: G401_HDAC1-40967_siPHIP_2

description:
Library name: 3198096_G401_HDAC1-40967_siPHIP_2_ChIP_HAM
ChIP for HDAC1 in siPHIP


title: p1485_T-PLL

description:
Library name: 109946
TP106


title: p1481_T-PLL

description:
Library name: 109944
N017


title: G401_HDAC1-40967_siCtrl_3

description:
Library name: 3198094_G401_HDAC1-40967_siCtrl_3_ChIP_HAM
ChIP for HDAC1 in siCtrl


title: p1375_T-PLL

description:
Library name: 109942
TP059


title: BC005_control

description:
Library name: 109928
Healthy_BC005

value: pan CD3+ T-cells derived from healthy donor


title: G401_HDAC1-40967_siCtrl_1

description:
Library name: 3198092_G401_HDAC1-40967_siCtrl_1_ChIP_HAM
ChIP for HDAC1 in siCtrl


title: p1339_T-PLL

description:
Library name: 109940
TP026


title: G401_inputHDAC1_siCtrl_3

description:
Library name: 3198088_G401_inputHDAC1_siCtrl_3_ChIP_HAM
input for siCtrl HDAC1


title: G401_HDAC1-40967_siPHIP_1

description:
Library name: 3198095_G401_HDAC1-40967_siPHIP_1_ChIP_HAM
ChIP for HDAC1 in siPHIP


title: BC003_control

description:
Library name: 109926
Healthy_BC003


title: p1499_T-PLL

description:
Library name: 109908
N020


title: G401_inputHDAC1_siPHIP_2

description:
Library name: 3198090_G401_inputHDAC1_siPHIP_2_ChIP_HAM
input for siPHIP HDAC1


title: BC002_control

description:
Library name: 109924
Healthy_BC002


title: G401_inputHDAC1_siPHIP_3

description:
Library name: 3198091_G401_inputHDAC1_siPHIP_3_ChIP_HAM
input for siPHIP HDAC1


title: G401_HDAC1-40967_siCtrl_2

description:
Library name: 3198093_G401_HDAC1-40967_siCtrl_2_ChIP_HAM
ChIP for HDAC1 in siCtrl


title: G401_inputHDAC1_siCtrl_1

description:
Library name: 3198086_G401_inputHDAC1_siCtrl_1_ChIP_HAM
input for siCtrl HDAC1


title: G401_inputHDAC1_siCtrl_2

description:
Library name: 3198087_G401_inputHDAC1_siCtrl_2_ChIP_HAM
input for siCtrl HDAC1


title: p1326_T-PLL

description:
Library name: 109902
TP006


title: p1371_T-PLL

description:
Library name: 109904
TP013


title: BC001_control

description:
Library name: 109922
Healthy_BC001


title: p598_T-PLL

description:
Library name: 109896
TP015


title: G401_inputCHD4_siPHIP_1

description:
Library name: 3220446_G401_inputCHD4_siPHIP_1_ChIP_HAM
input for siPHIP CHD4 samples


title: G401_inputH3K27_siCtrl_1

description:
Library name: 3220443_G401_inputH3K27_siCtrl_1_ChIP_HAM
input for siCtrl PE H3K27ac samples


title: G401_inputCHD4_siCtrl_1

description:
Library name: 3220445_G401_inputCHD4_siCtrl_1_ChIP_HAM
input for siCtrl CHD4 samples


title: p1308_T-PLL

description:
Library name: 109900
TP004


title: G401_CHD4-ab240640_siPHIP_3

description:
Library name: 3220442_G401_CHD4-ab240640_siPHIP_3_ChIP_HAM
ChIP for CHD4 in siPHIP


title: G401_inputH3K27_siPHIP_1

description:
Library name: 3220444_G401_inputH3K27_siPHIP_1_ChIP_HAM
input for siPHIP PE H3K27ac


title: G401_inputHDAC1_siPHIP_1

description:
Library name: 3198089_G401_inputHDAC1_siPHIP_1_ChIP_HAM
input for siPHIP HDAC1


title: BC4_control

description:
Library name: 109882
Healthy_BC004


title: G401_CHD4-ab240640_siPHIP_1

description:
Library name: 3220440_G401_CHD4-ab240640_siPHIP_1_ChIP_HAM
ChIP for CHD4 in siPHIP


title: G401_H3K27acab4729_siPHIP_3_inputscale

description:
Library name: 3220436_G401_H3K27acab4729_siPHIP_3_ChIP_HAM
ChIP for H3K27ac in siPHIP


title: G401_CHD4-ab240640_siCtrl_3

description:
Library name: 3220439_G401_CHD4-ab240640_siCtrl_3_ChIP_HAM
ChIP for CHD4 in siCtrl


title: G401_CHD4-ab240640_siPHIP_2

description:
Library name: 3220441_G401_CHD4-ab240640_siPHIP_2_ChIP_HAM
ChIP for CHD4 in siPHIP


title: p1077_T-PLL

description:
Library name: 109898
TP022


title: p210_T-PLL

description:
Library name: 109894
TP043


title: G401_CHD4-ab240640_siCtrl_2

description:
Library name: 3220438_G401_CHD4-ab240640_siCtrl_2_ChIP_HAM
ChIP for CHD4 in siCtrl


title: p1483_T-PLL

description:
Library name: 109872
TP105


title: p1478_T-PLL

description:
Library name: 109870
N014


title: p1391_T-PLL

description:
Library name: 109878
TP099


title: G401_CHD4-ab240640_siCtrl_1

description:
Library name: 3220437_G401_CHD4-ab240640_siCtrl_1_ChIP_HAM
ChIP for CHD4 in siCtrl


title: G401_H3K27acab4729_siPHIP_2_inputscale

description:
Library name: 3220435_G401_H3K27acab4729_siPHIP_2_ChIP_HAM
ChIP for H3K27ac in siPHIP


title: p1488_T-PLL

description:
Library name: 109892
N053


title: p1368_T-PLL

description:
Library name: 109874
TP054


title: p1359_T-PLL

description:
Library name: 109880
TP056


title: p1548_T-PLL

description:
Library name: 109876
N046


title: G401_H3K27acab4729_siPHIP_1_inputscale

description:
Library name: 3220434_G401_H3K27acab4729_siPHIP_1_ChIP_HAM
ChIP for H3K27ac in siPHIP


title: G401_H3K27acab4729_siCtrl_3_inputscale

description:
Library name: 3220433_G401_H3K27acab4729_siCtrl_3_ChIP_HAM
ChIP for H3K27ac in siCtrl


title: BC7_control

description:
Library name: 109884
Healthy_BC007


title: p1402_T-PLL

description:
Library name: 109868
TP092


title: G401_inputH4ac_siPHIP_1

description:
Library name: 3198085_G401_inputH4ac_siPHIP_1_ChIP_HAM
input for siPHIP H4ac samples


title: p1400_T-PLL

description:
Library name: 109866
TP108


title: p1381_T-PLL

description:
Library name: 109862
TP063


title: G401_H3K27acab4729_siCtrl_2_inputscale

description:
Library name: 3220432_G401_H3K27acab4729_siCtrl_2_ChIP_HAM
ChIP for H3K27ac in siCtrl


title: p1395_T-PLL

description:
Library name: 109864
N001


title: p1367_T-PLL

description:
Library name: 109860
TP057


title: G401_H3K27acab4729_siCtrl_1_inputscale

description:
Library name: 3220431_G401_H3K27acab4729_siCtrl_1_ChIP_HAM
ChIP for H3K27ac in siCtrl


title: H4, adeno-STAG2, RNA-Seq, rep3

city: CLEVELAND

first: Fulai

last: Jin

state: Ohio

address: 10900 Euclid Avenue

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: Library name: H4_10_3

data_processing:
Data were aligned to hg19 assembly with HISAT2 the maximum and minimum panelties for soft-flipping per base are both set to 1000. Genes were annotated and counted using featureCounts.
RNA-seq data was normalized and statical tested with DESeq2.
Assembly: hg19
Supplementary files format and content: DESeq2 results for each cell line are provided

source_name: Brain

growth_protocol: All cell lines were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% Pen/Strep at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using the RNEasy mini kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the NEB Next® Ultra™ II RNA Library Prep Kit (NEB).

treatment_protocol: 70 ul of virus was added to cells at 70% confluence in a 10 cm dish in 10 mL of media.

value: Brain

value: Human Glioma

value: adeno-STAG2 infection

tag: time


title: G401_inputH4ac_siCtrl_1

description:
Library name: 3198084_G401_inputH4ac_siCtrl_1_ChIP_HAM
input for siCtrl H4ac samples


title: G401_H4ac06866_siPHIP_3

description:
Library name: 3198083_G401_H4ac06866_siPHIP_3_ChIP_HAM
ChIP for H4ac in siPHIP


title: H4, adeno-STAG2, RNA-Seq, rep2

description: Library name: H4_10_2


title: H4, adenoviral vector, RNA-Seq, rep3

description: Library name: H4_7_3

value: adenoviral vector infection


title: G401_H4ac06866_siPHIP_1

description:
Library name: 3198081_G401_H4ac06866_siPHIP_1_ChIP_HAM
ChIP for H4ac in siPHIP


title: G401_H4ac06866_siCtrl_2

description:
Library name: 3198079_G401_H4ac06866_siCtrl_2_ChIP_HAM
ChIP for H4ac in siCtrl


title: H4, adeno-STAG2, RNA-Seq, rep1

description: Library name: H4_10_1


title: G401_H4ac06866_siCtrl_3

description:
Library name: 3198080_G401_H4ac06866_siCtrl_3_ChIP_HAM
ChIP for H4ac in siCtrl


title: G401_input_siPHIP_1_H3K14ac

description:
Library name: 3125128_G401_input_siPHIP_1_ChIP_HAM
input for siPHIP H3K14ac samples


title: MOG, adeno-STAG2, RNA-Seq, rep3

description: Library name: MOG_8

value: MOG-G-UVW


title: H4, adenoviral vector, RNA-Seq, rep2

description: Library name: H4_7_2


title: MOG, adeno-STAG2, RNA-Seq, rep2

description: Library name: MOG_7


title: MOG, adeno-STAG2, RNA-Seq, rep1

description: Library name: MOG_6


title: G401_H4ac06866_siPHIP_2

description:
Library name: 3198082_G401_H4ac06866_siPHIP_2_ChIP_HAM
ChIP for H4ac in siPHIP


title: MOG, adenoviral vector, RNA-Seq, rep3

description: Library name: MOG_3


title: G401_H3K14ac-ab52946_siPHIP_3

description:
Library name: 3125123_G401_H3K14ac-ab52946_siPHIP_3_ChIP_HAM
ChIP for H3K14ac in siPHIP


title: G401_H3K14ac-ab52946_siPHIP_2

description:
Library name: 3125122_G401_H3K14ac-ab52946_siPHIP_2_ChIP_HAM
ChIP for H3K14ac in siPHIP


title: G401_H4ac06866_siCtrl_1

description:
Library name: 3198078_G401_H4ac06866_siCtrl_1_ChIP_HAM
ChIP for H4ac in siCtrl


title: H4, adenoviral vector, RNA-Seq, rep1

description: Library name: H4_7_1


title: G401_input_siCtrl_1_H3K14ac

description:
Library name: 3125127_G401_input_siCtrl_1_ChIP_HAM
input for siCtrl H3K14ac samples


title: G401_H3K14ac-ab52946_siPHIP_1

description:
Library name: 3125121_G401_H3K14ac-ab52946_siPHIP_1_ChIP_HAM
ChIP for H3K14ac in siPHIP


title: G401_H3K14ac-ab52946_siCtrl_2

description:
Library name: 3125119_G401_H3K14ac-ab52946_siCtrl_2_ChIP_HAM
ChIP for H3K14ac in siCtrl


title: G401_H3K14ac-ab52946_siCtrl_3

description:
Library name: 3125120_G401_H3K14ac-ab52946_siCtrl_3_ChIP_HAM
ChIP for H3K14ac in siCtrl


title: MOG, adenoviral vector, RNA-Seq, rep1

description: Library name: MOG_1


title: H4, adeno-STAG2, rep2

description: Library name: H4_STAG2_B

data_processing:
Data were aligned to hg19 assembly with BWA. The replicates were merged and then downsampled the cis reads within 2 million bp to 100M. Mapped data was processed with HiCorr for bias correction and then enhanced with DeepLoop.
Assembly: hg19
Supplementary files format and content: For each HiC, the top300k loop of each celline is provided.

extract_protocol:
Genomic DNA was crosslinked and harvested using the Arima Hi-C+ kit (Arima Genomics) as described in the kit instructions.
Hi-C libraries were generated using the Arima Hi-C+ kit (Arima Genomics) as described in the kit instructions.


title: H4, adeno-STAG2, rep1

description: Library name: H4_STAG2_A


title: MOG, adenoviral vector, RNA-Seq, rep2

description: Library name: MOG_2


title: G401_H3K14ac-ab52946_siCtrl_1

description:
Library name: 3125118_G401_H3K14ac-ab52946_siCtrl_1_ChIP_HAM
ChIP for H3K14ac in siCtrl


title: MOG, adeno-STAG2, rep1

description: Library name: MOG_STAG2_A


title: MOG, adeno-STAG2, rep2

description: Library name: MOG_STAG2_B


title: G401_DDB1ab109027_siPHIP_3

description:
Library name: 2697826_G401_DDB1ab109027_siPHIP_3_ChIP_HAM
ChIP for DDB1 in siPHIP


title: MOG, adenoviral vector, rep2

description: Library name: MOG_vector_B


title: G401_DDB1ab109027_siPHIP_2

description:
Library name: 2697825_G401_DDB1ab109027_siPHIP_2_ChIP_HAM
ChIP for DDB1 in siPHIP


title: G401_DDB1ab109027_siCtrl_3

description:
Library name: 2697823_G401_DDB1ab109027_siCtrl_3_ChIP_HAM
ChIP for DDB1 in siCtrl


title: H4, adenoviral vector, rep1

description: Library name: H4_vector_A


title: G401_DDB1ab109027_siPHIP_1

description:
Library name: 2697824_G401_DDB1ab109027_siPHIP_1_ChIP_HAM
ChIP for DDB1 in siPHIP


title: RNA-seq, Primary Human Macrophages, IFNγ 20 ng/mL, Replicate 3

city: Cambridge

first: Jooho

last: Chung

state: MA

address: 300 Binney Street

institute: Broad Institute//Massachusetts General Hospital

description: Library name: MacrophageIFN20-3

data_processing:
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
Transcript counts were quantified by pseudoalignment of trimmed reads to hg38 using Kallisto (v0.46.0)
Gene counts were aggregated from transcript counts using the tximport (v1.24.0) R package
Assembly: hg38
Supplementary files format and content: comma-separated text file includes raw gene counts in each sample

source_name: Peripheral blood

growth_protocol: Macrophages were differentiated with M-CSF from peripheral blood-derived monocytes

extract_protocol:
RNA was isolated with the Qiagen RNAeasy kit per the manufacturer's instructions
cDNA library was prepared by Azenta/GeneWiz

treatment_protocol: Adherent macrophages were stimulated overnight with PBS, IFNg 4 ng/mL, or IFNg 20 ng/mL before cell processing

value: Peripheral blood

value: Macrophage

value: IFNg 20 ng/mL


title: RNA-seq, Primary Human Macrophages, IFNγ 20 ng/mL, Replicate 1

description: Library name: MacrophageIFN20-1


title: H4, adenoviral vector, rep2

description: Library name: H4_vector_B


title: G401_input_siPHIP_1_DDB1

description:
Library name: 2697828_G401_input_siPHIP_1_ChIP_HAM
input control for siPHIP DDB1 samples


title: G401_DDB1ab109027_siCtrl_1

description:
Library name: 2697821_G401_DDB1ab109027_siCtrl_1_ChIP_HAM
ChIP for DDB1 in siCtrl


title: G401_DDB1ab109027_siCtrl_2

description:
Library name: 2697822_G401_DDB1ab109027_siCtrl_2_ChIP_HAM
ChIP for DDB1 in siCtrl


title: MOG, adenoviral vector, rep1

description: Library name: MOG_vector_A


title: G401_input_siCtrl_1_DDB1

description:
Library name: 2697827_G401_input_siCtrl_1_ChIP_HAM
input control for siCtrl DDB1 samples


title: RNA-seq, Primary Human Macrophages, IFNγ 20 ng/mL, Replicate 2

description: Library name: MacrophageIFN20-2


title: G401_HAcst3724S_GFP_2

description:
Library name: 2695629_G401_HAcst3724S_GFP_2_ChIP_HAM
HA tag GFP

value: GFP


title: RNA-seq, Primary Human Macrophages, IFNγ 4 ng/mL, Replicate 2

description: Library name: MacrophageIFN4-2

value: IFNg 4 ng/mL


title: G401_HAcst3724S_HA-PHIP_1

description:
Library name: 2695630_G401_HAcst3724S_HA-PHIP_1_ChIP_HAM
HA tag HA-PHIP

value: HA-PHIP


title: RNA-seq, Primary Human Macrophages, IFNγ 4 ng/mL, Replicate 1

description: Library name: MacrophageIFN4-1


title: G401_HAcst3724S_HA-PHIP_2

description:
Library name: 2695631_G401_HAcst3724S_HA-PHIP_2_ChIP_HAM
HA tag HA-PHIP


title: G401_HAcst3724S_GFP_1

description:
Library name: 2695628_G401_HAcst3724S_GFP_1_ChIP_HAM
HA tag GFP


title: RNA-seq, Primary Human Macrophages, IFNγ 4 ng/mL, Replicate 3

description: Library name: MacrophageIFN4-3


title: RNA-seq, Primary Human Macrophages, Untreated, Replicate 1

description: Library name: MacrophageUntreated-1

value: PBS


title: RNA-seq, Primary Human Macrophages, Untreated, Replicate 2

description: Library name: MacrophageUntreated-2


title: G401_H3K27me3cst9733S_siCtrl_3

description:
Library name: 2667514_G401_H3K27me3cst9733S_siCtrl_3_ChIP_HAM
ChIP for H3K27me3 in siCtrl


title: Hepatocellular carcinoma, patient A-30, tumor tissue, live-sorted

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE

institute: University of California San Francisco

description: Library name: A-30-Tumor

library_source: transcriptomic single cell

data_processing:
CellRanger version 7.0.0 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data.
Doubletdetection to identify doublet cells from the single cell data. The scanpy data analysis pipeline was used for pre-processing and analysis of scRNAseq data, with the following software versions: scanpy 1.6.0, anndata 0.7.4, umap 0.4.1, numpy 1.19.1, scipy 1.5.2, pandas 1.1.2, scikit-learn 0.23.2, statsmodels 0.12.0, python-igraph 0.8.2, and louvain 0.8.2. Cells with less than 100 genes, greater than 2500 genes, or with >10% of genes being mitochondrial were removed. Additionally, platelets and red blood cells were also removed. We filtered out ribosomal and mitochondrial genes and genes detected in less than 3 cells. Gene counts were then normalized, log transformed, scaled, and corrected for batch effects. Principal component analysis was used to reduce the dimensionality of the dataset, and the top 50 principal components were used as input for clustering via the Leiden algorithm.
Assembly: GRCh38 3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hepatocellular carcinoma

extract_protocol:
Tumor resection samples and adjacent liver tissue were digested in RPMI containing Collagenase I & II (0.1 mg/ml, Thermo Fisher Scientific) and DNAse I, minced, and digested for one hour using the GentleMACS system (Miltenyi Biotec). Isolation of live and CD45+ cells was performed using MACS LS columns (Miltenyi Biotec).
Library was performed according to the manufacter’s instructions (single cell 10x 5’ version 1 protocol, 10x Genomics). Briefly, cell suspensions were combined with master mix and loaded into the chip with gel beads to generate the gel bead-in-emulsion (GEM), which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. Reverse transcription was performed on the poly-A RNA within each GEM. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads and amplified by PCR. To prepare libraries from cDNA, SPRIselect beads were used to isolate the correct size fragments. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added during library construction.

value: hepatocellular carcinoma


title: G401_H3K27me3cst9733S_siPHIP_2

description:
Library name: 2667516_G401_H3K27me3cst9733S_siPHIP_2_ChIP_HAM
ChIP for H3K27me3 in siPHIP

value: rhabdoid tumor


title: G401_H3K27me3cst9733S_siPHIP_1

description:
Library name: 2667515_G401_H3K27me3cst9733S_siPHIP_1_ChIP_HAM
ChIP for H3K27me3 in siPHIP

value: siPHIP


title: Hepatocellular carcinoma, patient A-24, tumor tissue, live-sorted

description: Library name: A-24-Tumor


title: Hepatocellular carcinoma, patient A-24, tumor tissue, live and CD45-sorted

description: Library name: A-24-Tumor-CD45+


title: G401_H3K27me3cst9733S_siPHIP_3

description:
Library name: 2667517_G401_H3K27me3cst9733S_siPHIP_3_ChIP_HAM
ChIP for H3K27me3 in siPHIP


title: Hepatocellular carcinoma, patient A-30, tissue adjacent to tumor, live-sorted

description: Library name: A-30-Adjacent


title: G401_H3K27me3cst9733S_siCtrl_2

description:
Library name: 2667513_G401_H3K27me3cst9733S_siCtrl_2_ChIP_HAM
ChIP for H3K27me3 in siCtrl

value: siCtrl


title: G401_H3K27me3cst9733S_siCtrl_1

description:
Library name: 2667512_G401_H3K27me3cst9733S_siCtrl_1_ChIP_HAM
ChIP for H3K27me3 in siCtrl


title: G401_H3K4me3ab8580_siPHIP_3

description:
Library name: 2667511_G401_H3K4me3ab8580_siPHIP_3_ChIP_HAM
ChIP for H3K4me3 in siPHIP


title: p1336_T-PLL

description:
Library name: 109974
TP009

value: peripheral blood

value: PBMCs derived from T-PLL patient


title: Hepatocellular carcinoma, patient A-23, tumor tissue, live-sorted

description: Library name: A-23-Tumor


title: G401_H3K4me3ab8580_siCtrl_1

description:
Library name: 2667506_G401_H3K4me3ab8580_siCtrl_1_ChIP_HAM
ChIP for H3K4me3 in siCtrl


title: G401_H3K4me3ab8580_siPHIP_1

description:
Library name: 2667509_G401_H3K4me3ab8580_siPHIP_1_ChIP_HAM
ChIP for H3K4me3 in siPHIP


title: G401_input_siPHIP_1_histone

description:
Library name: 2644054_G401_input_siPHIP_1_ChIP_HAM
input control for siPHIP samples (used with the single-end histone mark ChIP-seq samples)


title: Hepatocellular carcinoma, patient A-20, tissue adjacent to tumor, live-sorted

description: Library name: A-20-Adjacent


title: G401_H3K4me3ab8580_siCtrl_2

description:
Library name: 2667507_G401_H3K4me3ab8580_siCtrl_2_ChIP_HAM
ChIP for H3K4me3 in siCtrl


title: G401_input_siCtrl_1_histone

description:
Library name: 2644053_G401_input_siCtrl_1_ChIP_HAM
input control for siCtrl samples (used with the single-end histone mark ChIP-seq samples)


title: G401_siPHIP-D_rep3

description:
Library name: 3083556_G401_NA_siPHIP-D_NA_3_HAM
RNA-seq in siPHIP in G401


title: G401_H3K4me3ab8580_siCtrl_3

description:
Library name: 2667508_G401_H3K4me3ab8580_siCtrl_3_ChIP_HAM
ChIP for H3K4me3 in siCtrl


title: Hepatocellular carcinoma, patient A-24, tissue adjacent to tumor, live-sorted

description: Library name: A-24-Adjacent


title: G401_siPHIP-D_rep2

description:
Library name: 3083555_G401_NA_siPHIP-D_NA_2_HAM
RNA-seq in siPHIP in G401


title: Hepatocellular carcinoma, patient A-19, tumor tissue, live-sorted

description: Library name: A-19-Tumor


title: Hepatocellular carcinoma, patient A-24, tissue adjacent to tumor, live and CD45-sorted

description: Library name: A-24-Adjacent-CD45+


title: Hepatocellular carcinoma, patient A-20, tumor tissue, live-sorted

description: Library name: A-20-Tumor


title: Hepatocellular carcinoma, patient A-20, tumor tissue, live and CD45-sorted

description: Library name: A-20-Tumor-CD45+


title: Hepatocellular carcinoma, patient A-19, tissue adjacent to tumor, live and CD45-sorted

description: Library name: A-19-Adjacent-CD45+


title: Hepatocellular carcinoma, patient A-20, tissue adjacent to tumor, live and CD45-sorted

description: Library name: A-20-Adjacent-CD45+


title: G401_siPHIP-B_rep3

description:
Library name: 3083553_G401_NA_siPHIP-B_NA_3_HAM
RNA-seq in siPHIP in G401


title: Hepatocellular carcinoma, patient A-18, tissue adjacent to tumor, live-sorted

description: Library name: A-18-Adjacent


title: Hepatocellular carcinoma, patient A-23, tumor tissue, live and CD45-sorted

description: Library name: A-23-Tumor-CD45+


title: G401_siPHIP-D_rep1

description:
Library name: 3083554_G401_NA_siPHIP-D_NA_1_HAM
RNA-seq in siPHIP in G401


title: G401_H3K4me3ab8580_siPHIP_2

description:
Library name: 2667510_G401_H3K4me3ab8580_siPHIP_2_ChIP_HAM
ChIP for H3K4me3 in siPHIP


title: G401_siPHIP-B_rep2

description:
Library name: 3083552_G401_NA_siPHIP-B_NA_2_HAM
RNA-seq in siPHIP in G401


title: G401_siPHIP-B_rep1

description:
Library name: 3083551_G401_NA_siPHIP-B_NA_1_HAM
RNA-seq in siPHIP in G401


title: G401_siCtrl-2_rep2

description:
Library name: 3083549_G401_NA_siCtrl-2_NA_2_HAM
RNA-seq in siCtrl in G401


title: Multiome, BM, ATAC

city: Tucson

first: Deepta

last: Bhattacharya

state: AZ

address: 1656 East Mabel St

department: Immunobiology

institute: University of Arizona

description:
Library name: BM ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

library_source: genomic single cell

data_processing:
Files were demultiplexed using Cellranger mkfastq
Demultiplexed data were processed using the Cellranger count pipeline.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: ATAC_fragments.tsv.gz, mRNA_martix.h5

source_name: Bone Marrow

extract_protocol:
B cells were FACS purified and processed according to 10X Genomics Multiome manufacturer protcols.
Libraries were constructed according to 10X Genomics Multiome manufacturer protocols.

value: Bone Marrow


title: Multiome, A366_D13, ATAC

description:
Library name: A366 D13 ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

source_name: Tonsil

value: Tonsil


title: Multiome, BM, GEX

description:
Library name: BM RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: G401_siCtrl-2_rep3

description:
Library name: 3083550_G401_NA_siCtrl-2_NA_3_HAM
RNA-seq in siCtrl in G401


title: Multiome, A366_D13, GEX

description:
Library name: A366 D13 RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: G401_siCtrl-2_rep1

description:
Library name: 3083548_G401_NA_siCtrl-2_NA_1_HAM
RNA-seq in siCtrl in G401


title: G401_siCtrl-1_rep2

description:
Library name: 3083546_G401_NA_siCtrl-1_NA_2_HAM
RNA-seq in siCtrl in G401


title: G401_siCtrl-1_rep1

description:
Library name: 3083545_G401_NA_siCtrl-1_NA_1_HAM
RNA-seq in siCtrl in G401


title: Multiome, A366_D7, GEX

description:
Library name: A366 D7 RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: Multiome, A366_D10, ATAC

description:
Library name: A366 D10 ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Hepatocellular carcinoma, patient A-12, tumor tissue, live-sorted

description: Library name: A-12-Tumor


title: Multiome, A366_D7, ATAC

description:
Library name: A366 D7 ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, A366_D10, GEX

description:
Library name: A366 D10 RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: A204_siPHIP_rep2

description:
Library name: 2702446_A204_NA_siPHIP_NA_2_HAM
RNA-seq in siPHIP in A204


title: Multiome, A366_D4, GEX

description:
Library name: A366 D4 RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: A204_siPHIP_rep3

description:
Library name: 2702447_A204_NA_siPHIP_NA_3_HAM
RNA-seq in siPHIP in A204


title: A204_siPHIP_rep1

description:
Library name: 2702445_A204_NA_siPHIP_NA_1_HAM
RNA-seq in siPHIP in A204


title: Multiome, DMSO_D13, ATAC

description:
Library name: DMSO D13 ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, A366_D4, ATAC

description:
Library name: A366 D4 ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: A204_siCtrl_rep2

description:
Library name: 2702443_A204_NA_siCtrl_NA_2_HAM
RNA-seq in siCtrl in A204


title: Multiome, DMSO_D13, GEX

description:
Library name: DMSO D13 RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: Multiome, DMSO_D10, ATAC

description:
Library name: DMSO D10 ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, DMSO_D10, GEX

description:
Library name: DMSO D10 RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: A204_siCtrl_rep1

description:
Library name: 2702442_A204_NA_siCtrl_NA_1_HAM
RNA-seq in siCtrl in A204


title: SPTAN1+/- clone2_2

city: Charlestown

first: Ryuji

last: Morizane

address: 149 13th Street

institute: Massachusetts General Hospital

description: Library name: HSC10_2

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Remove reads with adapter contamination.
Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).
Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Assembly: Reference genome (GRCh38) and gene model annotation files were downloaded  from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: txt file includes raw counts of all samples.

source_name: H9 ESCs

growth_protocol: H9-derived PKHD1 mutants were maintained on hESC-qualified Geltrex coated plates using StemFit ® Basic04 Complete Type. The hPSC lines were passaged weekly, using Accutase for dissociation and Y27632 to facilitate adhesion on passaging. Kidney organoids were then differentiated and maintained following protocol reported in Morizane R et al Nat. Protoc. 2017; 12(1): 195-207.

extract_protocol:
Total RNA samples were isolated from kidney organoids with TRIzol (Thermo Fisher Scientific) according to the manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Kidney organoids on day 14 of differentiation were placed on miclofluidics chips with 10% geltrex. Fluid shear stress was applied to whole organoids at a pulsatile flow rate of 0.4 ml/min 0.5 sec; 0.04 ml/min 0.5sec  from day 15 to day 35. Half of the medium in reservoir was replaced every 2 to 3 day.

value: H9 ESCs

value: kidney organoids derived from human embryonic stem cells


title: A204_siCtrl_rep3

description:
Library name: 2702444_A204_NA_siCtrl_NA_3_HAM
RNA-seq in siCtrl in A204


title: G401_siCtrl-1_rep3

description:
Library name: 3083547_G401_NA_siCtrl-1_NA_3_HAM
RNA-seq in siCtrl in G401


title: Multiome, DMSO_D7, ATAC

description:
Library name: DMSO D7 ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, DMSO_D7, GEX

description:
Library name: DMSO D7 RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: SPTAN1+/- clone1_2

description: Library name: HSC2_2


title: SPTAN1+/- clone2_1

description: Library name: HSC10_1


title: Multiome, DMSO_D4, ATAC

description:
Library name: DMSO D4 ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: Multiome, DMSO_D4, GEX

description:
Library name: DMSO D4 RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: Multiome, Tonsil, GEX

description:
Library name: Tonsil_RNA
3’ mRNA (v3.1 10x Genomics): read 1 contains cell barcode and UMI; read2 contains transcript sequence


title: Multiome, Tonsil, ATAC

description:
Library name: Tonsil_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: SPTAN1+/+ clone2_2

description: Library name: HSC3_2


title: SPTAN1+/+ clone1_2

description: Library name: HSC1_2


title: WT_5

city: Ann Arbor

first: David

middle: Kelly

last: Jones

state: Mi

address: 1150 W Medical Center Drive

institute: University of Michigan

description:
Library name: Sample_4090-AJ-20
4090-AJ-20

data_processing:
Data were pre-filtered to remove genes with 0 counts in all samples. Differential gene expression analysis was performed using DESeq2, using a negative binomial generalized linear model (thresholds: linear fold change >1.5 or <-1.5, Benjamini-Hochberg FDR (Padj) <0.05). Plots were generated using variations of DESeq2 plotting functions and other packages with R version 3.6.3. Genes were annotated with NCBI Entrez GeneIDs and text descriptions. Functional analysis, including candidate pathways activated or inhibited in comparison(s) and GO-term enrichments, was performed using iPathway Guide (Advaita).
Assembly: hg38
Supplementary files format and content: counts

growth_protocol: WT and KCNH2-/- hESCs were maintained on Matrigel-coated plates in TeSR-E8 and mTeSR plus medium, respectively, and kept in a humidified atmosphere with 5% CO2 at 37 °C. Cells were cultured for at least 4 days until they reached ~80 % confluency.

extract_protocol:
RNA was extracted with the RNAeasy Mini Kit (Qiagen). RNA samples were quantified, and only samples with concentrations of at least 250 ng/µL were used.
Sequencing was performed by the UM AdvancedGenomics Core, with libraries constructed and subsequently subjected to 150 paired end cycles on the NovaSeq-6000 platform (Illumina).

value: human Eembryonic Stem Cells

value: WT


title: SPTAN1+/+ clone2_1

description: Library name: HSC3_1


title: WT_4

description:
Library name: Sample_4090-AJ-19
4090-AJ-19


title: SPTAN1+/+ clone1_1

description: Library name: HSC1_1


title: WT_3

description:
Library name: Sample_4090-AJ-18
4090-AJ-18


title: Ber_minus_2-2_S14, Control

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Department of Biomedical Sciences

institute: Florida State University

description:
Library name: Ber_minus_2-2_S14
CUT&Tag

data_processing:
The CUT&Tag sequencing reads were pre-processed to remove Illumina adaptor sequences using BBduk (ktrim=r k=23 mink=11 hdist=1 tpe tbo (https://sourceforge.net/projects/bbmap/).
The adaptor trimmed reads were aligned to the D. melanogaster genome (BDGP6) genome assembly, using Bowtie2 (--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 8 -x /; v. 2.2.5)
The mapped reads then underwent a series of file format conversion steps to prepare for SEACR peak calling. The mapped read files, in the .sam format, were converted to .bam files using Samtools view command (view -bS -F 0x04). These .bam files were sorted using the Samtools sort command (sort -n -O bam -@ 12). The sorted .bam files were converted to .bed files using bedtools bamtobed command (bamtobed -bedpe -i). These files were filtered to keep read pairs on the same chromosome with a fragment length <1000bp (awk '$1==$4 && $6-$2 < 1000 {print $0}) and the fragment related columns were extracted using ‘cut -f 1,2,6’.
The .bed files were converted to .bedgraph files for peak calling using bedtools (genomecov -bg -i).
Assembly: D. melamogaster BDGP6
Supplementary files format and content: .bedgraph files for SEACR peak calling.
Library strategy: CUT&Tag

organism: Drosophila melanogaster

growth_protocol: Males used in CUT&Tag were 15-24 hours old. To collect these males, bottles with D. melanogaster and D. simulans were cleared at 10:00 AM, flies were collected at 5:00 PM, and aged overnight to allow for recovery from CO2 anesthesia. The male flies were stored individually in small vials with food, in a 25°C incubator. The next day, brain dissections started at 8:00 AM and ended at 10:00 AM.

extract_protocol:
Ten brains were used for each CUT&Tag sequencing library. The CUT&Tag procedure and sequencing library preparation protocol was previously described, with some modifications (Ahmad 2020). After dissection, brains were fixed in 1% paraformaldehyde/1X PBS for 1 minute, then transferred to 1X PBS. Brains were washed two additional times for 5 minutes per wash. The rat polyclonal anti-FruM antibody was used at a 1:50 dilution (Sanders and Arbeitman 2008). The secondary rabbit anti-rat IgG (abcam ab6703) was used at 1:100 dilution. For control libraries, the brains were only incubated in secondary antibody. DNA recovery was performed as previously described (Kaya-Okur et al. 2019). Samples underwent 21 cycles of PCR and were purified by agencourt bead purification before sequencing (Ahmad 2020).
CUT&Tag

value: Brain

value: Male


title: SPTAN1+/- clone1_1

description: Library name: HSC2_1


title: Ber_plus_2-2_S13, FruM

description:
Library name: Ber_plus_2-2_S13
CUT&Tag


title: WT_2

description:
Library name: Sample_4090-AJ-17
4090-AJ-17


title: 57-KO_5

description:
Library name: Sample_4090-AJ-15
4090-AJ-15

value: KCNH2 knockdown


title: WT_1

description:
Library name: Sample_4090-AJ-16
4090-AJ-16


title: SCC25 cells, JK184 0.02 μM, 24h, replicate 3

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

description: Library name: RNA36

data_processing:
Quality check of raw paired-end fastq reads was carried out by FastQC.
The Illumina adapters clipping and quality trimming of raw fastq reads were performed using cutadapt v4.3 with settings --quality-base=33 -q 0,20 -m 35 -M 250. Trimmed RNA-Seq reads were mapped to the reference genome using STAR v2.7.3a as a splice-aware short read aligner and default parameters except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic.
Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, mapped regions, read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools – namely, RSeQC v4.0.0, Picard toolkit v2.25.6, and Qualimap v.2.2.2. All statistics were processed by MultiQC v1.10.1.
Mapped read counts were obtain using featureCounts from the Subread package v2.0.
Assembly: Homo sapiens genome (GRCh38) with Ensembl annotation (release 111)
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: JK184_vs_CTRL-featureCount_exon_table.tsv

growth_protocol: HNSCC cells (CAL27 and SCC25) were grown in a humidified atmosphere at 37°C, 5% CO2 in DMEM+++ (DMEM supplemented with 10% fetal bovine serum (FCS), 1% GlutMAX and 1% Penicilin/Streptomycin (P/S)). Cells were grown until 80% confluency and then passaged using Trypsin/EDTA.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit from HNSCC cell lines (CAL27 or SCC25), and 500 ng of total RNA were used for the construction of the sequencing libraries.
Sequencing libraries were prepared using (i) NEBNext Poly(A) mRNA Magnetic Isolation Module and sequencing library was prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using NEBNext Multiplex Oligos for Illumina and Agencourt Ampure XP Beads for cell line samples and (ii) QuantSeq 3′ mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt in combination with UMI Second Strand Synthesis Module for QuantSeq FWD.

treatment_protocol: Cells were either treated with DMEM+++ and vehicle (DMSO) or JK184 at the indicated concentrations for 6, 12 or 24 hours. For the patient samples no specific treatment was performed.


title: 57-KO_4

description:
Library name: Sample_4090-AJ-14
4090-AJ-14


title: Ber_minus_2-1_S11, Control

description:
Library name: Ber_minus_2-1_S11
CUT&Tag


title: SCC25 cells, JK184 0.02 μM, 24h, replicate 1

description: Library name: RNA34


title: SCC25 cells, Control, 24h, replicate 3

description: Library name: RNA33


title: 57-KO_3

description:
Library name: Sample_4090-AJ-13
4090-AJ-13


title: 57-KO_1

description:
Library name: Sample_4090-AJ-11
4090-AJ-11


title: SCC25 cells, JK184 0.02 μM, 24h, replicate 2

description: Library name: RNA35


title: 57-KO_2

description:
Library name: Sample_4090-AJ-12
4090-AJ-12


title: HCT116 cells, FLAG-RING1B

city: Seoul

first: Hyebin

last: Park

address: 84 Heukseok-ro, Dongjak-gu

department: Life science

country: South Korea

institute: Chung-Ang University

description: Library name: FLAG-RING1B

data_processing:
Raw FASTQ files were assessed for quality using FastQC (v0.11.7). Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.38) with default parameters.
Reads were aligned to the human reference genome (GRCh38/hg38) using Bowtie (v1.1.2) with default settings. Duplicated reads were marked and removed using Picard (v0.118).
Peak calling was performed using MACS2 (v2.1.1)
The chromosomal distribution of ChIP-seq peaks was visualized using the ChIPseeker R package (v1.26.2).
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: colon

growth_protocol: HCT116 cells were maintained in RPMI 1640 with 10% fetal bivine serum (FBS) and 1% penicillin-streptomycin

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min, followed by addition of 125mM glycine for 5min. Cells were lysed using SDS lysis buffer and then sonicated.
ChIP-seq libraries were prepared using the TruSeq DNA sample preparation kit (Illumina).

value: colon

value: Colorectal carcinoma

value: RING1B overexpression

value: ANTI-FLAG (Sigma, F3165)


title: Ber_plus_2-1_S10, FruM

description:
Library name: Ber_plus_2-1_S10
CUT&Tag


title: HCT116 cells, FLAG-MIB1

description: Library name: FLAG-MIB1

value: MIB1 overexpression


title: SCC25 cells, Control, 24h, replicate 2

description: Library name: RNA32


title: CAL27 cells, JK184 0.2 μM, 24h, replicate 3

description: Library name: RNA30


title: HCT116 cells, H2AK119ub

description: Library name: H2AK119ub

value: ANTI-H2AK119ub (CST, 8240S)


title: CAL27 cells, JK184 0.2 μM, 24h, replicate 1

description: Library name: RNA28


title: CAL27 cells, JK184 0.2 μM, 24h, replicate 2

description: Library name: RNA29


title: BJ fibroblasts, replicate 4, siFH, Day 5

city: Paris

first: Mikel

last: Rezola Artero

state: Ile de France

address: 15 Rue de l'École de Médecine

department: Centre de Recherche des Cordeliers

country: France

institute: Inserm

description:
Library name: BJ_siFH_4
Column name in All_RSEMexpectedcounts.csv: siFH_4

data_processing:
FASTQ files were aligned using STAR algorithm (version 2.7.6a), on the Ensembl release 101 reference.
RSEM (v1.3.1) was used for quantification.
Statistical analyses on the read counts were performed with R (version 3.6.3) and the DESeq2 package (DESeq2_1.26.0)
Assembly: hg38
Supplementary files format and content: RSEM ".genes.results" files contain gene-level expression estimates including expected counts, TPM, and gene length.
Supplementary files format and content: The CSV file contains a combined gene-level expected count matrix for all samples.

source_name: BJ (ATCC CRL-2522)

growth_protocol: BJ fibroblasts were cultured in Eagle Minimum Essential Medium (ATCC 30-2003) + 10% heat-inactivated FCS + 1× penicillin/streptomycin + 1× HEPES (Gibco 15630-080) in a humidified atmosphere of 5% CO2 at 37°C and routinely tested for Mycoplasma (Lonza LT07-318). BJ fibroblasts were used up to four passages.

extract_protocol:
RNA extraction was performed using the Maxwell® 16 LEV kit (Promega AS1270). RNA quality was evaluated with the Agilent 2100 Bioanalyzer system and 2100 Expert software. RNA integrity numbers for all samples were above 8.
Libraries were prepared following the Stranded mRNA Prep protocol from Illumina, starting from 250 ng of high quality total RNA. Paired end (2 × 51 bp) sequencing was performed on an Illumina NovaSeq platform.

treatment_protocol: Cells were transfected with a pre-incubated siRNA mixture (30 min, room temperature) containing: 2 CFH siRNAs (Qiagen SI00003983 and SI00003990) at 50 nM with lipofectamine RNAimax (ThermoFisher 13778150) in OptiMEM. Silencing was performed at 50% confluence in 6-well plates, 10cm² petri dishes or T75 flasks, and stopped after 24 hours.

value: BJ (ATCC CRL-2522)

value: human dermal fibroblast

value: silencing with siFH

tag: batch


title: HCT116 cells, input

description: Library name: Input


title: BJ fibroblasts, replicate 3, siFH, Day 5

description:
Library name: BJ_siFH_3
Column name in All_RSEMexpectedcounts.csv: siFH_3


title: SCC25 cells, Control, 24h, replicate 1

description: Library name: RNA31


title: CAL27 cells, Control, 24h, replicate 2

description: Library name: RNA26


title: CAL27 cells, Control, 24h, replicate 3

description: Library name: RNA27


title: CAL27 cells, Control, 24h, replicate 1

description: Library name: RNA25


title: BJ fibroblasts, replicate 1, siFH, Day 5

description:
Library name: BJ_siFH_1
Column name in All_RSEMexpectedcounts.csv: siFH_1


title: BJ fibroblasts, replicate 4, siCtrl, Day 5

description:
Library name: BJ_Ctrl_4
Column name in All_RSEMexpectedcounts.csv: siCtrl_4

value: silencing with siCtrl


title: SCC25 cells, JK184 0.02 μM, 12h, replicate 3

description: Library name: RNA24


title: SCC25 cells, JK184 0.02 μM, 12h, replicate 2

description: Library name: RNA23


title: SCC25 cells, JK184 0.02 μM, 12h, replicate 1

description: Library name: RNA22


title: BJ fibroblasts, replicate 3, siCtrl, Day 5

description:
Library name: BJ_Ctrl_3
Column name in All_RSEMexpectedcounts.csv: siCtrl_3


title: BJ fibroblasts, replicate 2, siCtrl, Day 5

description:
Library name: BJ_Ctrl_2
Column name in All_RSEMexpectedcounts.csv: siCtrl_2


title: BJ fibroblasts, replicate 1, siCtrl, Day 5

description:
Library name: BJ_Ctrl_1
Column name in All_RSEMexpectedcounts.csv: siCtrl_1


title: SCC25 cells, Control, 12h, replicate 3

description: Library name: RNA21


title: P7_input_ChIP

city: Guangzhou

first: Ming

last: Yuan

state: Guangdong

address: 26 Yuancun Erheng Rd

institute: The sixth affiliated hostpital, sun yat-sen university

description:
Library name: P7_input_ChIP
P7_input_ChIP

data_processing:
Raw data were cleaned by fastp software to filter reads with low quality.
Clean data were aligned to UCSC hg38 genome using Bowtie2 software. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using MACS2 with the significance cut-off q-value <=0.01.
bigWig files were generated using bedtools software.
The heatmap of peak distribution were generated by deeptools software.
Assembly: hg38
Supplementary files format and content: bigWig files for each sample (except the input samples)

growth_protocol: ADSCs were maintained in DMEM with 1 g/L glucose containing 1% streptomycin–penicillin and 10% FBS in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Genomic DNA were extrated using ChIP Kit (MERCK) and processed for antibodies crosslink following the instruction.
DNA fragments with indicated antibody crosslinking were isolated and purified for library construction by amplification and adapter addition.

value: cell line

value: ADSCs

value: Adipose-derived Stem Cells

value: Passage 7


title: P7_H3K9cr_ChIP

description:
Library name: P7_H3K9cr_ChIP
P7_H3K9cr_ChIP

value: WT

value: Passage 3


title: BJ fibroblasts, replicate 2, siFH, Day 5

description:
Library name: BJ_siFH_2
Column name in All_RSEMexpectedcounts.csv: siFH_2


title: CAL27 cells, JK184 0.2 μM, 12h, replicate 2

description: Library name: RNA17


title: CAL27 cells, JK184 0.2 μM, 12h, replicate 1

description: Library name: RNA16


title: P3_H3K9cr_ChIP

description:
Library name: P3_H3K9cr_ChIP
P3_H3K9cr_ChIP


title: SCC25 cells, Control, 12h, replicate 2

description: Library name: RNA20


title: CAL27 cells, JK184 0.2 μM, 12h, replicate 3

description: Library name: RNA18


title: SCC25 cells, Control, 12h, replicate 1

description: Library name: RNA19


title: CAL27 cells, Control, 12h, replicate 3

description: Library name: RNA15


title: Micro-C of Homo sapiens: IsoCtrl hiPSC neuron sample 5

city: Chapel Hill

first: Hyejung

last: Won

state: North Carolina

address: 116 Manning Dr

department: Genetics

institute: University of North Carolina at Chapel Hill

description: Library name: Ctrl_hiPSC_Neu_5

data_processing:
Hi-C and Micro-C processing: Read quality of fastq files was first assessed using FastQC (v0.12.1). Sequencing reads were then aligned to the GRCh38 reference genome using bwa mem (v0.7.17). Duplicate reads were removed with Pairtools (v1.1.3). Resulting BAM files were converted to multi-resolution contact matrices using cooler (v0.10.4) for downstream analysis.
CHART procossing: CHART reads were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). Duplicate reads were removed with Picard (v3.1.1), and replicates were merged using Samtools (v1.6). Peaks were called using MACS2 (v2.2.9.1) with the following parameters: -t STR_nodups_sorted.bam -f BAMPE -q 0.05 -g hs --keep-dup all -B –SPMR. Read counts per peak were quantified using bedtools multicov (v2.31.0) on the merged BAM files for each control and STR replicate. C9-STR gained CHART peaks were defined if the mean CPM-normalized read count in C9-STR samples was at least two-fold higher than that in control samples.
CUT&RUN processing: CHART reads were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). Duplicate reads were removed with Picard (v3.1.1), and replicates were merged using Samtools (v1.6). Replicates were merged separately for C9-STR and isogenic control conditions. Peaks were called using MACS2 (v2.2.9.1) with the following parameters: -t CTCF_STR_isoCtrl.bam -c input_nodups_sorted.bam -f BAM -q 0.01 -g hs --nomodel --shift 0 --extsize 200 --keep-dup all -B –SPMR. Differential peaks were identified using DESeq2 (v1.44.0) with an LRT comparing a full model that adjusts for replication and condition against a reduced model that includes replication only. Log fold change shrinkage was performed using the apeglm method. C9-STR gained CTCF peaks were defined as those with padj < 0.05 and LFC > log₂(1.5), while C9-STR lost CTCF peaks were defined as padj < 0.05 and LFC < −log₂(1.5).
RNA-seq processing: RNA-seq reads were aligned to the reference genome using STAR (v2.7.11b), and gene-level quantification was performed using HTSeq (v2.0.5). Differential expression analysis was conducted using DESeq2 (v1.44.0), with a model that included replication and condition as design factors. A likelihood ratio test (LRT) was used to assess the effect of condition by comparing the full model (replication + condition) against a reduced model containing only replication. We defined upregulated DEGs as an adjusted p-value (padj) < 0.05 and log2 fold change (LFC) > 0, whereas downregulated DEGs were identified using padj < 0.05 and LFC < 0.
Assembly: GRCh38
Supplementary files format and content: 10kb cooler files of Hi-C and Micro-C data, along with bigwig files of CUT&RUN, CHART, and RNA-seq data.

source_name: iPSC derived neurons

extract_protocol:
Hi-C libraries: Nuclei were isolated from the visual cortex of three individuals with C9-ALS and three neurotypical controls. Neuronal (NeuN-positive) and glial (NeuN-negative) nuclei were separated using fluorescence-activated nuclei sorting (FANS).
Micro-C libraries: Micro-C was performed using the Dovetail Genomics Cantata Bio Micro-C kit (Dovetail Proximity Ligation Core Box 1, PN DG-REF-001; Dovetail Micro-C Module Box 2, PN DG-NUC-001), following the manufacturer’s user guide (version 1.0).
CHART libraries: Cells were first fixed with 1% PFA for 10 minutes at room temperature to preserve chromatin architecture, followed by nuclei isolation. A second crosslinking step was performed on isolated nuclei using 3% formaldehyde for 10 minutes at room temperature. After washing, nuclei were resuspended in sonication buffer (50 mM HEPES-OH pH 7.5, 75 mM NaCl, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate, 0.1 mM EGTA) and sonicated using a Covaris M220 Focused-ultrasonicator (75 Peak Incident Power, 10% Duty Factor, 200 Cycles per Burst, 3 minutes) to obtain 2-10 kb chromatin fragments. Crosslinks were then reversed, and the DNA was purified and assessed for fragmentation.
CUT&RUN libraries: CUT&RUN was performed using the CUTANA CUT&RUN Kit (Epicypher, 14-1048) using 4 replicates per condition (C9-STR neurons and isogenic control neurons, totaling 8 samples).
RNA-seq libraries: RNA was extracted from 1 million hiPSC-derived neurons per sample for each of 6 biological replicates per condition (C9-STR neurons and isogenic control neurons, n=12 samples total) using the Zymo Quick-RNA Miniprep Kit (R10564).
Hi-C libraries: Sorted nuclei were fixed in 1% formaldehyde to preserve chromatin interactions. Crosslinked chromatin was then digested with MboI (NEB, R0147S), followed by end repair, biotin labeling, and proximity-based ligation. The resulting DNA was sheared to 300-600 base-pair (bp) fragments, and biotinylated fragments were selectively captured via streptavidin pulldown. Illumina sequencing adapters were ligated to the recovered fragments, which were then amplified by PCR.
Micro-C libraries: Micro-C was performed using the Dovetail Library Module, PN DG-LIB-001, following the manufacturer’s user guide (version 1.0).
CHART libraries: DNA libraries were prepared using the CUTANA CUT&RUN Library Prep Kit (EpiCypher, 14-1001).
CUT&RUN libraries: DNA (calculated with the Qubit dsDNA HS Assay Kit) using the CUTANA CUT&RUN Library Prep Kit (EpiCypher 14-1001) according to the manufacturer’s recommendations.
RNA-seq libraries: Library preparation was performed by the UNC Integrated Genomics Core High-Throughput Sequencing Facility (RRID: SCR_022620) using the KAPA Stranded mRNA-Seq Kit (Roche Diagnostics, 07962193001), following the manufacturer’s protocol.

value: iPSC derived neurons

tag: condition

value: Neuron


title: CAL27 cells, Control, 12h, replicate 1

description: Library name: RNA13


title: SCC25 cells, JK184 0.02 μM, 6h, replicate 3

description: Library name: RNA12


title: Micro-C of Homo sapiens: C9STR hiPSC neuron sample 5

description: Library name: STR_hiPSC_Neu_5


title: Micro-C of Homo sapiens: C9STR hiPSC neuron sample 6

description: Library name: STR_hiPSC_Neu_6


title: P3_input_ChIP

description:
Library name: P3_input_ChIP
P3_input_ChIP


title: Micro-C of Homo sapiens: IsoCtrl hiPSC neuron sample 6

description: Library name: Ctrl_hiPSC_Neu_6


title: SCC25 cells, JK184 0.02 μM, 6h, replicate 1

description: Library name: RNA10


title: SCC25 cells, JK184 0.02 μM, 6h, replicate 2

description: Library name: RNA11


title: SCC25 cells, Control, 6h, replicate 3

description: Library name: RNA9


title: CAL27 cells, Control, 12h, replicate 2

description: Library name: RNA14


title: SCC25 cells, Control, 6h, replicate 2

description: Library name: RNA8


title: Micro-C of Homo sapiens: IsoCtrl hiPSC neuron sample 2

description: Library name: Ctrl_hiPSC_Neu_2


title: Micro-C of Homo sapiens: C9STR hiPSC neuron sample 4

description: Library name: STR_hiPSC_Neu_4


title: Micro-C of Homo sapiens: IsoCtrl hiPSC neuron sample 4

description: Library name: Ctrl_hiPSC_Neu_4


title: Micro-C of Homo sapiens: C9STR hiPSC neuron sample 3

description: Library name: STR_hiPSC_Neu_3


title: Micro-C of Homo sapiens: IsoCtrl hiPSC neuron sample 1

description: Library name: Ctrl_hiPSC_Neu_1


title: SCC25 cells, Control, 6h, replicate 1

description: Library name: RNA7


title: CAL27 cells, JK184 0.2 μM, 6h, replicate 2

description: Library name: RNA5


title: Micro-C of Homo sapiens: C9STR hiPSC neuron sample 1

description: Library name: STR_hiPSC_Neu_1


title: Micro-C of Homo sapiens: IsoCtrl hiPSC neuron sample 3

description: Library name: Ctrl_hiPSC_Neu_3


title: CAL27 cells, JK184 0.2 μM, 6h, replicate 3

description: Library name: RNA6


title: CAL27 cells, JK184 0.2 μM, 6h, replicate 1

description: Library name: RNA4


title: Hi-C of Homo sapiens: Ctrl postmortem glia sample 2

description: Library name: Ctrl_Post_Glia_2

source_name: postmortem brain

value: postmortem brain

value: Control

value: Glia


title: CAL27 cells, Control, 6h, replicate 3

description: Library name: RNA3


title: Hi-C of Homo sapiens: Ctrl postmortem glia sample 1

description: Library name: Ctrl_Post_Glia_1


title: Micro-C of Homo sapiens: C9STR hiPSC neuron sample 2

description: Library name: STR_hiPSC_Neu_2


title: CUTRUN of Homo sapiens: Negative Control

description: Library name: Ctrl_hiPSC_Neu_CUTRUN_NegCtrl

data_processing:
Hi-C and Micro-C processing: Read quality of fastq files was first assessed using FastQC (v0.12.1). Sequencing reads were then aligned to the GRCh38 reference genome using bwa mem (v0.7.17). Duplicate reads were removed with Pairtools (v1.1.3). Resulting BAM files were converted to multi-resolution contact matrices using cooler (v0.10.4) for downstream analysis.
CHART procossing: CHART reads were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). Duplicate reads were removed with Picard (v3.1.1), and replicates were merged using Samtools (v1.6). Peaks were called using MACS2 (v2.2.9.1) with the following parameters: -t STR_nodups_sorted.bam -f BAMPE -q 0.05 -g hs --keep-dup all -B –SPMR. Read counts per peak were quantified using bedtools multicov (v2.31.0) on the merged BAM files for each control and STR replicate. C9-STR gained CHART peaks were defined if the mean CPM-normalized read count in C9-STR samples was at least two-fold higher than that in control samples.
CUT&RUN processing: CHART reads were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). Duplicate reads were removed with Picard (v3.1.1), and replicates were merged using Samtools (v1.6). Replicates were merged separately for C9-STR and isogenic control conditions. Peaks were called using MACS2 (v2.2.9.1) with the following parameters: -t CTCF_STR_isoCtrl.bam -c input_nodups_sorted.bam -f BAM -q 0.01 -g hs --nomodel --shift 0 --extsize 200 --keep-dup all -B –SPMR. Differential peaks were identified using DESeq2 (v1.44.0) with an LRT comparing a full model that adjusts for replication and condition against a reduced model that includes replication only. Log fold change shrinkage was performed using the apeglm method. C9-STR gained CTCF peaks were defined as those with padj < 0.05 and LFC > log₂(1.5), while C9-STR lost CTCF peaks were defined as padj < 0.05 and LFC < −log₂(1.5).
RNA-seq processing: RNA-seq reads were aligned to the reference genome using STAR (v2.7.11b), and gene-level quantification was performed using HTSeq (v2.0.5). Differential expression analysis was conducted using DESeq2 (v1.44.0), with a model that included replication and condition as design factors. A likelihood ratio test (LRT) was used to assess the effect of condition by comparing the full model (replication + condition) against a reduced model containing only replication. We defined upregulated DEGs as an adjusted p-value (padj) < 0.05 and log2 fold change (LFC) > 0, whereas downregulated DEGs were identified using padj < 0.05 and LFC < 0.
Assembly: GRCh38
Supplementary files format and content: 10kb cooler files of Hi-C and Micro-C data, along with bigwig files of CUT&RUN, CHART, and RNA-seq data.
Library strategy: CUT&Run


title: CAL27 cells, Control, 6h, replicate 1

description: Library name: RNA1


title: Hi-C of Homo sapiens: Ctrl postmortem neuron sample 3

description: Library name: Ctrl_Post_Neu_3


title: Hi-C of Homo sapiens: C9ALS postmortem glia sample 1

description: Library name: ALS_Post_Glia_1

value: ALS


title: CUTRUN of Homo sapiens: C9STR hiPSC neuron sample 1, 2, 3, and 4

description: Library name: STR_hiPSC_Neu_CUTRUN


title: CUTRUN of Homo sapiens: IsoCtrl hiPSC neuron sample 1, 2, 3, and 4

description: Library name: Ctrl_hiPSC_Neu_CUTRUN


title: CHART of Homo sapiens: IsoCtrl hiPSC neuron sample 1, 2, and input

description: Library name: Ctrl_hiPSC_Neu_CHART


title: Hi-C of Homo sapiens: Ctrl postmortem neuron sample 1

description: Library name: Ctrl_Post_Neu_1


title: CAL27 cells, Control, 6h, replicate 2

description: Library name: RNA2


title: Hi-C of Homo sapiens: C9ALS postmortem neuron sample 2

description: Library name: ALS_Post_Neu_2


title: Hi-C of Homo sapiens: C9ALS postmortem neuron sample 3

description: Library name: ALS_Post_Neu_3


title: Hi-C of Homo sapiens: C9ALS postmortem neuron sample 1

description: Library name: ALS_Post_Neu_1


title: 8084, plasma sample, IFNβ-1a, 6days

city: Silver Spring

first: Lakshmi Manasa

middle: Sakuntala

last: Chekka

state: Maryland

address: 10903 New Hampshire Avenue

department: DARS, CDER

institute: U.S. FDA

description: Library name: F14865791

data_processing:
CLC Genomics Workbench v21.0.1
Samples were processed using Toolbox "Ready to use workflow" for "Small RNA sequencing" and "Qiaseq miRNAquantification"
Sequence reads were trimmed for adapters and size, UMI reads are generated from grouping greads with the same or similar UMI and similar sequence.
Mature miRNA reads are considered as expression counts.
Raw data was normalized using Deseq2 R package
Assembly: mirBase v22
Supplementary files format and content: csv file includes raw counts for each sample

source_name: plasma

growth_protocol: EDTA Plasma from healthy subjects was collected and stored at -80 degrees centigrade.

extract_protocol:
EDTA plasma from whole blood. RNA was extracted using miRNeasy® Serum/Plasma Kit (Cat. 217184, Qiagen LLC).
Library preparations were carried out using the QIAseq miRNA Library Kit [96] (# 331505) together with QIAseq miRNA [96] Index IL (#331565), and an automated liquid handling method developed for preparation of 96 cDNA using the Biomek i7 Automated Liquid Handler (Beckman).

treatment_protocol: Subjects were randomized between IFNβ-1a, pegIFNβ-1a and placebo groups

value: plasma

tag: disease state

value: Healthy


title: hESC, L1TD1, rep3 (second run)

city: Beijing

first: Yuan

last: Zhou

address: 38 college road

institute: Peking University

description:
Library name: L1TD1-3 (second run)
L1TD1-3 (second run)

data_processing:
Firstly, use cutadapt (v3.7) to remove the adaptor and low-quality reads to obtain high-quality clean FASTQ reads.
Clean reads were then aligned to the reference genome (hg38) by using STAR software (v2.7.8a).
The aligned SAM-format reads were sorted, transformed to BAM format, and indexed via samtools (v1.12).
Next, run Picard to remove duplicates and sort the output BAM files. To identify editing sites, we used Bullseye (https://github.com/mflamand/Bullseye) .
Assembly: hg38
Supplementary files format and content: Files show the renew target sites of DDX6, FUBP3, FXR2 and L1TD1 identified by HyperTRIBE in hESCs.

source_name: early embryo

growth_protocol: Human embryonic stem cells (hESCs) were cultivated in serum-free, defined mTeSR1 medium (STEMCELL, catalog#85850) and grown on plates coated with growth-factor-reduced Matrigel.

extract_protocol:
Sanger sequencing was used to conﬁrm proper insertion and then control and RBP-ADAR plasmids were infected into hESCs by transfection reagent jetOPTIMUS (Polyplus, catalog#101000051). After transient transfection into target cells for 24 h, the cells containing RBP-ADAR fusion proteins or mCherry-ADAR proteins were sorted by GFP and mCherry ﬂuorescence and using TRIzol reagent to extract the mRNA from the sorted cells. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
After library quality control, quantified libraries were pooled and sequenced on Illumina NovaSeq 6000 with paired-end 150-bp reads, providing sequencing data at 40 Gb per library.

treatment_protocol: hESCs were passaged with non-enzymatic dissociation by 0.5 mM EDTA (Beyotime, catalog#C0196-100ml).

value: early embryo

value: hESC

value: human embryonic stem cell

value: Experimental group


title: 8084, plasma sample, IFNβ-1a, 5days

description: Library name: F14865616


title: hESC, L1TD1, rep2 (second run)

description:
Library name: L1TD1-2 (second run)
L1TD1-2 (second run)


title: 8084, plasma sample, IFNβ-1a, 4days

description: Library name: F14865501


title: 8084, plasma sample, IFNβ-1a, 2days

description: Library name: F14865255


title: Hi-C of Homo sapiens: C9ALS postmortem glia sample 2

description: Library name: ALS_Post_Glia_2


title: 8084, plasma sample, IFNβ-1a, 0.67days

description: Library name: F14865043


title: 8084, plasma sample, IFNβ-1a, 0.33days

description: Library name: F14864962


title: hESC, FXR2, rep2 (second run)

description:
Library name: FXR2-2 (second run)
FXR2-2 (second run)


title: hESC, FXR2, rep3 (second run)

description:
Library name: FXR2-3 (second run)
FXR2-3 (second run)


title: hESC, L1TD1, rep1 (second run)

description:
Library name: L1TD1-1 (second run)
L1TD1-1 (second run)


title: 8084, plasma sample, IFNβ-1a, 0.125days

description: Library name: F14864868


title: Hi-C of Homo sapiens: Ctrl postmortem neuron sample 2

description: Library name: Ctrl_Post_Neu_2


title: 8084, plasma sample, IFNβ-1a, 0.25days

description: Library name: F14864946


title: CHART of Homo sapiens: C9STR hiPSC neuron sample 1, 2, and input

description: Library name: STR_hiPSC_Neu_CHART


title: 8084, plasma sample, IFNβ-1a, Baseline

description: Library name: F14864744


title: 8080, plasma sample, pegIFNβ-1a, 13days

description: Library name: F14858268


title: hESC, FUBP3, rep3 (second run)

description:
Library name: FUBP3-3 (second run)
FUBP3-3 (second run)


title: hESC, FXR2, rep1 (second run)

description:
Library name: FXR2-1 (second run)
FXR2-1 (second run)


title: hESC, FUBP3, rep2 (second run)

description:
Library name: FUBP3-2 (second run)
FUBP3-2 (second run)


title: 8080, plasma sample, pegIFNβ-1a, 9days

description: Library name: F14857996


title: 8080, plasma sample, pegIFNβ-1a, 6days

description: Library name: F14857549


title: hESC, DDX6, rep3 (second run)

description:
Library name: DDX6-3 (second run)
DDX6-3 (second run)


title: 8080, plasma sample, pegIFNβ-1a, 5days

description: Library name: F14857372


title: JURKAT, METTL3 KD, rep1

description:
Library name: JURKAT-1
JURKAT-METTL3-KD-1

data_processing:
After sequencing, image analysis, base identification and QC, raw reads (Raw Data) are generated. QC was first performed using Q30.
Then cutadapt software (v1.9.3) was used to de-join and remove low quality reads to obtain clean reads.
Clean reads were aligned to the reference genome (hg38) and BAM files were obtained using STAR (v.2.7) and bowtie2 (v.2.2.4) software.
GLORI-tools took cleaned reads as input and finally reported the conversion rate (A-to-G) of GLORI and single-base loci of m6A sites with corresponding “A” rate as modification level.
Assembly: hg38
Supplementary files format and content: The data represent authentic m6A modification sites in WT A549 cells, human embryonic stem cells, and JURKAT cells, identified by filtering out sites that persist in METTL3-knockdown (KD) cells.

source_name: lymphocyte

growth_protocol: A549 cell lines were cultured in DMEM medium supplemented with 10% fetal bovine serum and antibiotics. Jurkat cell line was maintained in RPMI 1640 medium with 10% FBS and antibiotics. Human embryonic stem cells (hESCs) were cultivated in serum-free, defined mTeSR1 medium and grown on plates coated with growth-factor-reduced Matrigel. The clean vein of the umbilical cord was first lavaged with 0.25% trypsin at 37°C for 15 min. Cells were grown at 37°C with 5% CO2.

extract_protocol:
Total RNA from the samples was extracted using TRIzol, and RNA was purified according to the MEGA clear transcription purification kit. RNA was incubated with fragmentation buffer for 4 min at 94°C and glyoxal solution and DMSO were added, and the mixture was incubated for 30 min at 50°C in a preheated thermal cycler. Minutes, and at the end of the incubation, the tubes were brought to room temperature, and then saturated H3BO3 solution was added. The incubation was continued at 50 °C for 30 min. Then add to the pre-configured deamination buffer (750 mM NaNO2, 40 mM MES (pH 6.0), and 10 μl of glyoxal solution) for a total of 8 h of incubation.
Finally, RNA was purified by ethanol precipitation, and sequencing libraries were constructed by GenSeq® Low Input RNA Library Prep Kit following the process of the instructions provided by the manufacturer. The constructed sequencing libraries were subjected to quality control and quantification by BioAnalyzer 2100 system, followed by 150 bp double-end sequencing.

treatment_protocol: hESCs were passaged with non-enzymatic dissociation by 0.5 mM EDTA. Other cells were digested with 0.25% trypsin at 37°C for 2-5 min.

value: lymphocyte

value: JURKAT

value: acute T-cell lymphoblastic leukemia

value: METTL3 KD


title: hESC, DDX6, rep1 (second run)

description:
Library name: DDX6-1 (second run)
DDX6-1 (second run)


title: JURKAT, METTL3 KD, rep2

description:
Library name: JURKAT-2
JURKAT-METTL3-KD-2


title: 8080, plasma sample, pegIFNβ-1a, 2days

description: Library name: F14857011


title: hESC, METTL3 KD, rep2

description:
Library name: hESC-2
hESC-METTL3-KD-2


title: hESC, FUBP3, rep1 (second run)

description:
Library name: FUBP3-1 (second run)
FUBP3-1 (second run)


title: 8080, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F14856500


title: A549, METTL3 KD, rep2

description:
Library name: A549-2
A549-METTL3-KD-2

source_name: lung

value: lung

value: human lung adenocarcinoma cell


title: 8080, plasma sample, pegIFNβ-1a, 4days

description: Library name: F14857257


title: 8080, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F14856702


title: 8078, plasma sample, pegIFNβ-1a _placebo, 6days

description: Library name: F14853444

value: pegIFNβ-1a _placebo


title: 8080, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F14856799


title: A549, METTL3 KD, rep1

description:
Library name: A549-1
A549-METTL3-KD-1


title: S34F_SMG1_2

city: St Louis

first: Sridhar

last: Nonavinkere Srivatsan

address: 660 S Eucild Ave

institute: WashU School Of Medicine

description: Library name: Sample_23

data_processing:
Illumina Novaseq 6000 using paired reads extending 150 bases
Mouse: The reads were then mapped using STAR (v2.7.0) against the GRCm38.95 version of the mouse genome from the Ensembl consortium. Human: The reads were then mapped using STAR (v2.7.0) against the GRCh38.95 version of the human genome from the Ensembl consortium
Gene counts were determined by  processing the resulting reads using using kallisto v0.43.1
Assembly: mm10/hg38
Supplementary files format and content: tab seperated text file that includes raw counts for each sample

source_name: K562 cell line

extract_protocol:
RNA was isolated from sorted GFP+ mouse MLL::AF9 BM cells after SMG1i-63 or vehicle treatment using the Quick-RNA MicroPrep Kit (Fisher-Zymo, No. R1050). Quality of isolated RNA was determined using Agilent RNA 6000 Nano chip using the Agilent 4200 TapeStation platform. Quantification was performed using Qubit Fluorometer (Thermo-Fisher Scientific). Total RNA samples with RNA integrity number (RIN) >9 were selected for Illumina sequencing library preparation. For K562 same protocol was used for library preparation.
The RNA-sequencing libraries were constructed using KAPA RNA HyperPrep Kit with RiboErase (Roche, Catalog # KK8560/61), per the manufacturer’s protocol. After amplification, final libraries (~360 bp mean size) were sequenced on Illumina NovaSeq 6000, generating 2 x 150bp paired-end reads.

value: K562 cell line

value: 36 hrs


title: 8078, plasma sample, pegIFNβ-1a _placebo, 2days

description: Library name: F14852901


title: hESC, DDX6, rep2 (second run)

description:
Library name: DDX6-2 (second run)
DDX6-2 (second run)


title: S34F_SMG1_3

description: Library name: Sample_24


title: hESC, METTL3 KD, rep1

description:
Library name: hESC-1
hESC-METTL3-KD-1


title: 8078, plasma sample, pegIFNβ-1a _placebo, 5days

description: Library name: F14853267


title: CD1

first: Fang

last: Xie

address: Southern Medical University, No. 1838, North Guangzhou Avenue

department: Nanfang Hospital

institute: Southern Medical University

description: Library name: SAMPLE1

data_processing:
Raw sequencing data were processed using Space Ranger (v3.0), which aligned FASTQ files to the human reference genome (GRCh38), detected the tissue area on the slide, and generated spatially resolved gene-barcode matrices. Downstream analyses were performed using Seurat (v4.3.2) in R. Data were normalized, clustered, and annotated using default parameters.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: The strictured and fibrotic ileum sample from Crohn's disease patient.

extract_protocol:
Fresh full-thickness ileal tissues were paraffin-embedded, and five-micrometer sections were cut from FFPE tissue blocks using a microtome.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics VisiumSpatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

value: ileum


title: 8078, plasma sample, pegIFNβ-1a _placebo, 4days

description: Library name: F14853147


title: S34F_SMG1_1

description: Library name: Sample_22


title: CD2

description: Library name: SAMPLE2

source_name: The non-strictured and non-fibrotic ileum sample from Crohn's disease patient.


title: 8077, plasma sample, pegIFNβ-1a, 13days

description: Library name: F14852108


title: 8078, plasma sample, pegIFNβ-1a _placebo, Baseline

description: Library name: F14852390


title: 8080, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F14856624


title: WT_SMG1_1

description: Library name: Sample_16


title: 8078, plasma sample, pegIFNβ-1a _placebo, 1.33days

description: Library name: F14852839


title: S34F_DMSO_3

description: Library name: Sample_21

value: DMSO


title: 8078, plasma sample, pegIFNβ-1a _placebo, 9days

description: Library name: F14853891

value: plasma


title: S34F_DMSO_2

description: Library name: Sample_20


title: 8078, plasma sample, pegIFNβ-1a _placebo, 13days

description: Library name: F14854163

value: Healthy


title: WT_DMSO_3

description: Library name: Sample_15


title: WT_DMSO_2

description: Library name: Sample_14


title: 8077, plasma sample, pegIFNβ-1a, 5days

description: Library name: F14851178


title: WT_SMG1_3

description: Library name: Sample_18


title: 8077, plasma sample, pegIFNβ-1a, 9days

description: Library name: F14851836


title: 8078, plasma sample, pegIFNβ-1a _placebo, 0.67days

description: Library name: F14852689


title: 8078, plasma sample, pegIFNβ-1a _placebo, 0.25days

description: Library name: F14852592


title: WT_SMG1_2

description: Library name: Sample_17


title: 8077, plasma sample, pegIFNβ-1a, 6days

description: Library name: F14851355


title: S34F_DMSO_1

description: Library name: Sample_19


title: WT_DMSO_1

description: Library name: Sample_13