title: Day 300, Q03, H48, Hepacam

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

description:
30 million PE reads
19094R-26Q1-40_S110_L003

data_processing:
Fastq files were first trimmed using Trimmomatic and mapped using STAR aligner with the paired end option selected (hg38)
We used FeatureCounts to assemble transcripts and generate raw count matrices. Following generation of raw count data, we used DESeq2 to normalize matrices and to determine differential gene expression statistics.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw expression values for each sample.

source_name: organoid

growth_protocol: hiPSCs were dissociated into single cells using Accutase (Innovate Cell Technologies, AT-104) and seeded into AggreWell plates (STEMCELL Technologies, 34815) at the density of 3 X 106 cells/well in Essential 8 medium (Life Technologies, A1517001) supplemented with 10 μ M Rock inhibitor Y-27632 (10 μ M, Selleckchem, S1049). Spheres formed the next day were collected and transferred to ultra-low-attachment 10 cm dishes (Corning, 3262). They were maintained in Essential 6 medium (Life Technologies, A1516401) supplemented with dual SMAD inhibitors SB-431542 (10 μ M, Tocris, 1614), dorsomorphin (2.5 μ M, Sigma-Aldrich, P5499) and Wnt pathway inhibitor XAV-939 (2.5 μ M, Tocris, 3748) for the first 6 days, with every day medium change. From Day 7, hCOs were cultured in Neurobasal A (Life Technologies, 10888) supplemented with B27 (Life Technologies, 12587), 20 ng ml–1 epidermal growth factor (R&D Systems, 236-EG) and 20 ng ml–1 basic fibroblast growth factor (R&D Systems, 233-FB), with every day medium change for another 8 days, and every other day medium change till Day 25. At this time point, hCOs were switched to neural basal medium supplemented with B27, 20 ng ml–1 brain-derived neurotrophic factor (BDNF; Peprotech, 450-02) and 20 ng ml–1 NT3 (Peprotech, 450-03) for another 20 days, with every other day medium change. From Day 45 onward, cells were maintained in Neurobasal A medium with B27, with medium change every 3-4 days.

extract_protocol:
RNA was harvested using RNAeasy Micro Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the NEB Next Ultra II kit using poly-A selection following manufacturer's protocols.

treatment_protocol: 48 hour hypoxia exposure

value: organoid

value: Hypoxia


title: Huh7 cells, 3D bioprinted with HUVEV cells, replicate 1

status: Public on Feb 12 2025

type: SRA

city: Hangzhou

first: Zhichao

last: Ye

address: Huajiachi Campus

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two samples was performed using the EBSeq R package. The resulting FDR (false discovery rate) were adjusted using the PPDE(posterior probability of being DE).The FDR < 0.05 & |log2（foldchange）| ≥1 was set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

molecule: total RNA

organism: Homo sapiens

source_name: Human Liver

extract_protocol:
RNA was isolated with TRIzol
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

tag: tissue

value: Human Liver

tag: cell line

tag: cell type

value: Hepatocytes

tag: genotype

value: WT

tag: treatment


title: SK36 EMV-inoculated TIGK cells, biological replicate 1

city: Portland

first: Emily

last: Helliwell

state: Oregon

address: 3181 SW Sam Jackson Park Rd, MRB433

country: USA

institute: Oregon Health and Science University

description: Library name: SK36_1

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample
Quality control of raw reads was carried out using FastQC v0.11.9. Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6
Trimmed reads were aligned to the reference genome Homo sapiens GRCh38 using STAR v2.6.1d
BAM file filtering and indexing was carried out using SAMtools v1.9
RNAseq library quality control was implemented using RSeQC v4.0.0 and QualiMap v2.2.2-dev; Duplicate reads were marked using Picard tools v2.23.9, Library complexity was estimated using Preseq v2.0.3, Duplication rate quality control was performed using dupRadar v1.18.0
Assembly: Reads overlapping with exons were assigned to genes using featureCounts v2.0.1
Supplementary files format and content: CSV file includes DEseq2-normalized counts across all samples "normalized_counts.csv"

source_name: TIGK CRL3397

growth_protocol: Gingival epithelial cell line TIGK CRL3397 was maintained in KBM Gold Keratinocyte Growth Basal Medium (Lonza) at 37°C, 5% CO2. 5x105 cells were seeded into each well of a 6-well plate and incubated for 24hr before inoculation.  KBM was replaced by RPMI prior to inoculation.

extract_protocol:
RNA was extracted from whole cells using a Trizol-based protocol, genomic DNA was digested using TURBO DNaseI according to manufacters protocol and samples were cleaned using Qiagen RNeasy kit. Total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat # R3000) according to the manufacturer’s instruction manual v1.3.0
RNA was reverse-transcribed into cDNA, which was followed by ribosomal RNA depletion. After that partial P7 adapter sequence was ligated at 3’ end of cDNAs, followed by second strand synthesis and partial P5 adapter ligation to 5’ end of the double stranded DNAs.  Lastly, libraries were amplified to incorporate full length adapters under the following conditions: initial denaturation at 95°C for 10 min; 10 - 16 cycles of denaturation at 95°C for 30 sec, annealing at 60°C for 30 sec, and extension at 72°C for 60 sec; and final extension at 72°C for 7 min

treatment_protocol: Streptococcus sanguinis SK36 was grown for 18hrs in chemically-defined media (CDM) for 18hrs, until late log-growth phase.  EMVs were isolated using differential centrifugation and quantified using nanoparticle tracking analysis.  Concentration was adjusted to 4x1011 particles per ml in 1X PBS, and 250μl of this suspension was used to inoculate 5x105 TIGK cells.  Control-treated cells were inoculated with 250μl of 1X PBS

value: TIGK CRL3397

value: Gingival epithelial cell

value: S. sanguinis SK36 EMVs (1011 particles)

tag: time


title: PBS-inoculated TIGK cells, biological replicate 1

description: Library name: PBS_1

value: PBS (control)


title: Huh7 cells, 3D bioprinted with HUVEV cells, replicate 2


title: Huh7 cells, 3D bioprinted, replicate 3

value: 3D bioprinted, replicate 3


title: Day 300, Q02, H48, Hepacam

description:
30 million PE reads
19094R-26Q1-39_S148_L003


title: Huh7 cells, 3D bioprinted, replicate 2

value: 3D bioprinted, replicate 2


title: Day 300, 2788, H48, Hepacam

description:
30 million PE reads
19094R-26Q1-38_S147_L003


title: Day 300, 2242, H48, Hepacam

description:
30 million PE reads
19094R-26Q1-37_S146_L003


title: p3_NB5

city: Guangzhou

first: lei

last: Miao

address: 9#, Jinsui Road,Tianhe District

institute: Guangzhou women and children's medical center

description: Library name: NB062

data_processing:
multiqc;hisat2;trimmomatic;trim-galore
Assembly: hg38_genome
Supplementary files format and content: raw counts for each Sample

source_name: Neuroblastoma

extract_protocol:
Total RNA in each sample was harvested and used for the construction of cDNA sequencing libraries.
cDNA libraries for RNA-seq were prepared  following manufacturer's protocols.

value: Neuroblastoma

value: Mediastinal tumor


title: wangG_FRAS192322945-1a

description: Library name: NB067


title: p1_xie1

description: Library name: NB060


title: p0_15

description: Library name: NB058


title: p3_lai2

description: Library name: NB061


title: Huh7 cells, 3D bioprinted, replicate 1

value: 3D bioprinted, replicate 1


title: Day 300, Q03, H48, Thy1

description:
30 million PE reads
19094R-26Q1-36_S130_L003


title: p4_11

description: Library name: NB063


title: p1_14

description: Library name: NB059


title: Huh7 cells, 2D cultured, replicate 2

value: 2D cultured, replicate 2


title: Day 300, 2788, H48, Thy1

description:
30 million PE reads
19094R-26Q1-34_S117_L003


title: NB79

description: Library name: NB056


title: p0_12

description: Library name: NB057


title: Huh7 cells, 2D cultured, replicate 1

value: 2D cultured, replicate 1


title: NB71

description: Library name: NB053


title: Day 300, 2242, H48, Thy1

description:
30 million PE reads
19094R-26Q1-33_S116_L003


title: NB70

description: Library name: NB052


title: NB69

description: Library name: NB051


title: Day 300, Q02, Control, Hepacam

description:
30 million PE reads
19094R-26Q1-31_S129_L003

value: Control


title: Day 300, Q03, Control, Hepacam

description:
30 million PE reads
19094R-26Q1-32_S115_L003

value: organoid


title: NB68

description: Library name: NB050


title: WGBS_H9_Naïve_ZFP57_OE

city: St. Louis

first: Thorold

middle: W.

last: Theunissen

state: MO

address: 4515 McKinley Ave, Room 3313

institute: Washington University in St. Louis

library_source: genomic

data_processing:
Paired-end Fastq files were trimmed with TrimGalore v0.6.6.
Reads were aligned with Bismark v0.23.0.
Methpipe package v4.1.1 was used to remove duplicate reads (duplicate-remover), calculate methylation levels (methcounts), extract and merge symmetric CpGs (symmetric-cpgs), and calculate methylation statistics for regions of interest.
Assembly: hg38
Supplementary files format and content: Imprint methylation xlsx file

molecule: genomic DNA

extract_protocol:
Genomic DNA was isolated using the Qiagen Dneasy Blood & Tissue kit.
Bisulfite conversion was performed on gDNA using the Zymo EZ DNA Methylation-Gold Kit. Libraries were constructed manually.

value: hESC


title: WGBS_H9_Naïve_rtTA


title: WGBS_H9-SRG_Naïve_ZFP57_OE


title: NB40

description: Library name: NB044


title: Day 300, 2242, Control, Hepacam

description:
30 million PE reads
19094R-26Q1-29_S145_L003


title: NB74

description: Library name: NB054


title: Day 300, Q03, Control, Thy1

description:
30 million PE reads
19094R-26Q1-28_S127_L003


title: NB43

description: Library name: NB045


title: WGBS_H9-SRG_1.0MEKi_0.1ERKi_d17_R+G-_Re-primed


title: NB64

description: Library name: NB048


title: Huh7 cells, 2D cultured, replicate 3

value: Human Liver

value: 2D cultured, replicate 3


title: Day 300, 2788, Control, Hepacam

description:
30 million PE reads
19094R-26Q1-30_S128_L003


title: WGBS_H9-SRG_0.5MEKi_0.5ERKi_d17_R+G-_Re-primed


title: NB4_13

description: Library name: NB4-13


title: Day 300, 2242, Control, Thy1

description:
30 million PE reads
19094R-26Q1-25_S143_L003


title: NB47

description: Library name: NB047


title: WGBS_H9-SRG_Naïve_rtTA


title: NB4_15

description: Library name: NB4-15


title: NB45

description: Library name: NB046


title: Day 300, 2788, Control, Thy1

description:
30 million PE reads
19094R-26Q1-26_S144_L003


title: NB4_12

description: Library name: NB4-12


title: NB4_10

description: Library name: NB4-10


title: NB4_14

description: Library name: NB4-14


title: NB65

description: Library name: NB049


title: WGBS_H9-SRG_1.0MEKi_2.5ERKi_d7_R+G-_Re-primed


title: Day 200, Q03, H48, Hepacam

description:
30 million PE reads
19094R-26Q1-16_S139_L003

value: Hypoxia


title: RNA-seq_H9-SRG_Naïve_ZFP57_OE_rep2

description:
RNA-seq_GeneCounts_CPM_2.xlsx
RNA-seq_GeneCounts_CPM_2.xlsx

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software.
Alignment was performed with STAR v2.5.1a or v2.7.9a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5 or 2.0.3.
Assembly: hg38
Supplementary files format and content: Gene counts xlsx files

extract_protocol:
Total RNA was isolated using the E.Z.N.A. total RNA kit I.
Library construction was performed using the Takara SMARTer Ultra Low RNA kit.


title: Day 200, Q02, H48, Hepacam

description:
30 million PE reads
19094R-26Q1-15_S138_L003


title: RNA-seq_H9-SRG_Naïve_ZFP57_OE_rep1


title: Day 200, 2788, H48, Hepacam

description:
30 million PE reads
19094R-26Q1-14_S137_L003


title: NB4_04

description: Library name: NB4-04


title: NB4_02

description: Library name: NB4-02


title: NB4_08

description: Library name: NB4-08


title: Day 200, 2242, H48, Hepacam

description:
30 million PE reads
19094R-26Q1-13_S136_L003


title: RNA-seq_H9-SRG_Naïve_rtTA_rep1


title: NB4_06

description: Library name: NB4-06


title: RNA-seq_H9-SRG_Naïve_rtTA_rep2


title: NB3_08

description: Library name: NB3-08


title: NB4_05

description: Library name: NB4-05


title: RNA-seq_H9_Naïve_ZFP57_OE_rep2


title: NB34

description: Library name: NB042


title: Day 200, Q03, H48, Thy1

description:
30 million PE reads
19094R-26Q1-12_S135_L003


title: NB3_07

description: Library name: NB3-07


title: NB4_11

description: Library name: NB4-11


title: Day 200, 2788, H48, Thy1

description:
30 million PE reads
19094R-26Q1-10_S134_L003


title: NB32

description: Library name: NB041


title: NB3_04

description: Library name: NB3-04


title: RNA-seq_H9_Naïve_rtTA_rep2


title: NB3_03

description: Library name: NB3-03


title: NB3_05

description: Library name: NB3-05


title: NB3_01

description: Library name: NB3-01


title: NB4_09

description: Library name: NB4-09


title: RNA-seq_H9_Naïve_ZFP57_OE_rep1


title: NB2_14

description: Library name: NB2-14


title: RNA-seq_H9_Naïve_rtTA_rep1


title: RNA-seq_H9_Primed_rep2


title: NB2_12

description: Library name: NB2-12


title: Day 200, 2788, Control, Hepacam

description:
30 million PE reads
19094R-26Q1-06_S131_L003


title: NB2_13

description: Library name: NB2-13


title: RNA-seq_H9_Primed_rep1


title: Day 200, Q03, Control, Thy1

description:
30 million PE reads
19094R-26Q1-04_S121_L003


title: NB36

description: Library name: NB043


title: NB2_08

description: Library name: NB2-08


title: NB2_09

description: Library name: NB2-09


title: NB2_10

description: Library name: NB2-10


title: Day 200, 2242, Control, Hepacam

description:
30 million PE reads
19094R-26Q1-05_S122_L003


title: RNA-seq_H9-SRG_1.0MEKi_0.1ERKi_rep2


title: NB2_06

description: Library name: NB2-06


title: NB2_04

description: Library name: NB2-04


title: Day 200, 2242, H48, Thy1

description:
30 million PE reads
19094R-26Q1-09_S133_L003


title: NB2_03

description: Library name: NB2-03


title: Day 200, 2788, Control, Thy1

description:
30 million PE reads
19094R-26Q1-02_S120_L003


title: RNA-seq_H9-SRG_1.0MEKi_0.1ERKi_rep1


title: Day 200, Q03, Control, Hepacam

description:
30 million PE reads
19094R-26Q1-08_S114_L003


title: Day 200, Q02, Control, Hepacam

description:
30 million PE reads
19094R-26Q1-07_S132_L003


title: Day 200, 2242, Control, Thy1

description:
30 million PE reads
19094R-26Q1-01_S113_L003


title: NB2_01

description: Library name: NB2-01


title: NB10110112

description: Library name: NB040


title: NB2_02

description: Library name: NB2-02


title: RNA-seq_H9-SRG_0.5MEKi_0.5ERKi_rep2


title: RNA-seq_H9-SRG_0.5MEKi_0.5ERKi_rep1


title: NB2_11

description: Library name: NB2-11


title: linG_FRAS192322946-1a

description: Library name: NB039


title: keG_FRAS192322944-1a

description: Library name: NB038


title: RNA-seq_H9-SRG_1.0MEKi_2.5ERKi_rep2


title: G_NB_liyf

description: Library name: NB037


title: CLL349

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
mRNA sequencing was generated using a HiSeq 4000 sequencer for 58 AA CLL and 292 EA CLL.  The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.4. Batch correction for all RNA samples was performed by removing protein coding genes with low counts, for each batch individually, resulting in 9,934 protein coding genes.  In addition, CombatSeq was run using the annotated reported race as a covariate, with CombatSeq corrected count values used for all downstream analyses.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes batch corrected gene counts each gene per sample

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using the Quagen miRNeasy Mini Kit
Illumina TruSeq Stranded mRNA library prep protocol

tag: ancestry

value: African Ancestry (AA)

value: Peripheral blood mononuclear cells

tag: disease state

value: Chronic Lymphocytic Leukemia (CLL)


title: CLL350

value: IGHV Unmutated


title: RNA-seq_H9-SRG_1.0MEKi_2.5ERKi_rep1


title: duB_FRAS192322948-1a

description: Library name: NB035


title: C4

description: Library name: NB028


title: RNA-seq_H9-SRG_0.5MEKi_1.0ERKi_rep1


title: caoB_FRAS192322949-1a

description: Library name: NB030


title: CHEN

description: Library name: NB031


title: C7

description: Library name: NB029


title: CLL347


title: CLL348


title: CLL346


title: C_NB_A6

description: Library name: NB032


title: B8

description: Library name: NB023


title: RNA-seq_H9-SRG_Primed_rep2


title: CLL345


title: RNA-seq_H9-SRG_Primed_rep1


title: B2

description: Library name: NB022


title: B_NB_B5

description: Library name: NB026


title: B_NB_B4

description: Library name: NB025


title: B_NB_A5

description: Library name: NB024


title: CLL343


title: C2

description: Library name: NB027


title: A9

description: Library name: NB021


title: CLL341


title: FLARE lineage recorder sequencing, 64 days of editing

city: Lebanon

first: Rachel

middle: Danielle

last: Saxe

state: New Hampshire

address: 1 Medical Center Dr

institute: Dartmouth Cancer Center

description: Library name: sample24_c1498_d64_editing

data_processing:
Basecalling with BCL2fastq or BCL Convert
Assembly: mm10
Supplementary files format and content: FLARE lineage tracing barcode pipeline output with aligned reads and edit patterns (.stats files)

organism: Mus musculus

extract_protocol:
Genomic DNA was extracted using the Qiagen Dneasy Blood and Tissue kit
Libraries were constructed with custom targeted PCR primers

value: AML

tag: genetic modification

value: FLARE lineage recording


title: RNA-seq_H9-SRG_0.5MEKi_1.0ERKi_rep2


title: F1 clone tag sequencing

description: Library name: sample25_F1_clonetags


title: CLL342


title: CLL344


title: A40

description: Library name: NB018

value: Neuroblastoma


title: A4

description: Library name: NB017

value: Mediastinal tumor


title: FLARE lineage recorder sequencing, 44 days of editing

description: Library name: sample23_c1498_d44_editing


title: CLL339

value: European Ancestry (EA)


title: CLL340

value: IGHV Mutated


title: A35

description: Library name: NB016


title: A31

description: Library name: NB014


title: FLARE lineage recorder sequencing, no Cas9 control

description: Library name: sample21_c1498_editing_control


title: A33

description: Library name: NB015


title: A28

description: Library name: NB012


title: F6 clone tag sequencing

description: Library name: sample26_F6_clonetags


title: CLL338


title: A30

description: Library name: NB013


title: A22

description: Library name: NB010


title: CLL337


title: A27

description: Library name: NB011


title: Mouse M4 clone tag sequencing, day 67 post C1498-FLARE injection, day of euthanasia

description: Library name: sample20_M4_d67_EP

value: AML, PBMC

value: 3x 100ul PBS


title: A21

description: Library name: NB009


title: A18

description: Library name: NB008


title: Mouse M4 clone tag sequencing, day 57 post C1498-FLARE injection

description: Library name: sample19_M4_d57


title: CLL336


title: A17

description: Library name: NB007


title: A44

description: Library name: NB019


title: A16

description: Library name: NB006


title: A12

description: Library name: NB004


title: CLL335


title: Mouse M3 clone tag sequencing, day 50 post C1498-FLARE injection, day of euthanasia

description: Library name: sample17_M3_d50_EP


title: Mouse M4 clone tag sequencing, day 28 post C1498-FLARE injection

description: Library name: sample18_M4_d28


title: CLL334


title: A15

description: Library name: NB005


title: A10110769

description: Library name: NB002


title: FLARE lineage recorder sequencing, 13 days of editing

description: Library name: sample22_c1498_d13_editing


title: A1

description: Library name: NB003


title: 1035620B_FRAS192322947-1a

description: Library name: NB001


title: Mouse M2 clone tag sequencing, day 67 post C1498-FLARE injection, day of euthanasia

description: Library name: sample14_M2_d67_EP

value: 3x 100mg/kg AraC


title: U251MG N2CR 2

city: La Jolla

first: Stacey

middle: Marie

last: Glasgow

state: California

address: 9500 Gilman Dr, 3216 Pacific Hall

institute: University of California San Diego

description:
Library name: Sample 5
Column name in raw_counts.csv:U251_N2KO_2

data_processing:
Demultiplexing was performed with the bcl2fastq Conversion Software (Illumina, San Diego, CA).
FASTQ files were processed in Galaxy using Trimmomatic with default parameters.
Read alignment was performed with HISAT2 using the hg38 reference genome and default parameters.
Raw expression data was obtained using featureCounts with default parameters.
Assembly: hg38
Supplementary files format and content: CSV file includes raw count data of all samples

source_name: Brain

extract_protocol:
Total RNA was isolated using TRIzol Reagent following the manufacturer's protocol.
The quality of total RNA was evaluated using an Agilent Tapestation 4200, and only samples with an RNA Integrity Number (RIN) above 9.0 were selected for RNA-seq library preparation with the Illumina® Stranded mRNA Prep kit (Illumina, San Diego, CA). Library preparation was conducted according to the manufacturer’s protocol by the UCSD Institute for Genomic Medicine (IGM) Core Facility.

value: Brain

value: Human glioblastoma astrocytoma


title: CLL332


title: U251MG N2CR 3

description:
Library name: Sample 6
Column name in raw_counts.csv:U251_N2KO_3


title: U251MG WT 3

description:
Library name: Sample 3
Column name in raw_counts.csv:U251_WT_3

value: WT


title: CLL331


title: Mouse M3 clone tag sequencing, day 28 post C1498-FLARE injection

description: Library name: sample15_M3_d28


title: Mouse M2 clone tag sequencing, day 28 post C1498-FLARE injection

description: Library name: sample13_M2_28


title: U251MG WT 2

description:
Library name: Sample 2
Column name in raw_counts.csv:U251_WT_2


title: CLL330


title: U251MG WT 1

description:
Library name: Sample 1
Column name in raw_counts.csv:U251_WT_1


title: DMSO_Cyt_3

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: DMSO_Cyt_3

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapters using trimmomatic v0.39
The SlamDunk pipeline v0.2.4 was used to align reads to a joint human genome (GRCh37.73) and Drosophila genome (Dm3), and the 3’ UTR of gene, and call T to C conversions and count the numbers of total and TC converted reads.
HiSAT2 was used to align reads to a joint human (GRCh37.73), Drosophila (Dm3) and ERCC genome and htseq was used to assign reads to genes, to calculate the size factors for spike-in normalisation.
The DESeq2 package in R was used to normalise the T to C converted read counts using the size factors calculated from the total ERCC read counts.
Assembly: hg19 and dm3
Supplementary files format and content: ERCC normalised TC counts

molecule: polyA RNA

source_name: Breast; Mammary gland

extract_protocol:
Cells were trypsinised, washed with cold PBS, counted, and Drosophila S2 cells spiked in prior to permeabilisation. Cells were permeabilised (1mg/ml Digitonin (SKU0215948050, MP Biomedicals), 100mM NaCl, 10mM Tris pH 8.0, 1:100 protease Inhibitor (Complete Mini EDTA-free, 4693159001 Sigma), 1:1000 RNase OUT (10-777-019, Invitrogen) for 10 min on ice. After centrifugation at 1000g for 3 min, the supernatant (cytoplasmic fraction) was set aside and the pelleted nuclei were resuspended in RLT buffer (Qiagen) and put through a QIAshredder column (Qiagen). Both cytoplasmic and nuclear fractions were then diluted 1:3 with RLT buffer (Qiagen), and ethanol added to a final concentration of 30%. RNA was recovered using a RNeasy mini spin column (Qiagen).carboxyamidomethylation of 4sU was performed using freshly prepared iodacetamide as described (Herzog et al Nature Methods 2017 PMID: 28945705). ERCC RNA (4456740, Ambion; 2l per 2g RNA) was spiked in according the manufacturer’s instructions. RNA was cleaned up using MinElute RNeasy kit (Qiagen).
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina with poly-A selection (NEB). Libraries were sequenced on a Novaseq with 150bp paired-end reads.

treatment_protocol: Drug added for 3 hours. 0.1 mM 4-thiouridine (4sU, Sigma-Aldrich) was added to the medium of drug-treated cells 60 min prior to harvesting.

value: Breast; Mammary gland

tag: cellular fraction

value: Cytoplasmic

value: Cyt

value: DMSO

tag: batch


title: CLL329

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Unmutated


title: Mouse M1 clone tag sequencing, day 57 post C1498-FLARE injection

description: Library name: sample11_M1_d57

value: FLARE lineage recording


title: CLL328


title: DMSO_Nuc_3

description: Library name: DMSO_Nuc_3

value: Nuclear

value: Nuc


title: Mouse M1 clone tag sequencing, day 67 post C1498-FLARE injection, day of euthanasia

description: Library name: sample12_M1_d67_EP


title: dBET_Nuc_3

description: Library name: dBET_Nuc_3


title: dBET_Cyt_3

description: Library name: dBET_Cyt_3


title: Mouse M1 clone tag sequencing, day 43 post C1498-FLARE injection

description: Library name: sample10_M1_d43


title: CLL333

value: European Ancestry (EA)

value: IGHV Mutated


title: Mouse M3 clone tag sequencing, day 43 post C1498-FLARE injection

description: Library name: sample16_M3_d43

value: AML, PBMC

value: 3x 100ul PBS


title: U251MG N2CR 1

description:
Library name: Sample 4
Column name in raw_counts.csv:U251_N2KO_1

value: Brain


title: DMSO_Nuc_2

description: Library name: DMSO_Nuc_2


title: dBET_Tot_3

description: Library name: dBET_Tot_3

value: Total

value: Tot


title: dBET_Tot_2

description: Library name: dBET_Tot_2

value: Breast; Mammary gland


title: Mouse M1 clone tag sequencing, day 28 post C1498-FLARE injection

description: Library name: sample9_M1_d28

value: 3x 100mg/kg AraC


title: CLL326


title: CLL325


title: DMSO_Tot_2

description: Library name: DMSO_Tot_2


title: dBET_Cyt_1

description: Library name: dBET_Cyt_1

value: Cytoplasmic

value: Cyt


title: DMSO_Tot_3

description: Library name: DMSO_Tot_3

value: DMSO


title: dBET_Nuc_2

description: Library name: dBET_Nuc_2


title: CLL323

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)


title: CLL324


title: DMSO_Cyt_2

description: Library name: DMSO_Cyt_2


title: CLL322


title: FLARE founder tag and clone tag sequencing associated with sample2 blood and bone marrow and sample 3

description: Library name: sample2_sample3_FLARE_barcodes

library_source: other

data_processing:
Basecalling with BCL2fastq or BCL Convert
scRNAseq samples processed with CellRanger count or multi
Assembly: mm10, GRch28
Supplementary files format and content: features, barcodes, and matrix output from CellRanger count or multi
Supplementary files format and content: FLARE lineage tracing barcode pipeline output with aligned reads and edit patterns (.stats files)

molecule: other

extract_protocol:
PBMCs from blood were isolated using a ficoll density gradient. All RNA was extracted following 10X 3' single cell RNA protocols
GEX and MULTIseq libraries were prepared following 10X 3' single cell library contruction protocols and MULTIseq multiplexing library construction protocols, respectively. FLARE barcode libraries were prepared with customn targeted PCR primers

tag: library type

value: FLARE

value: PBMC, AML, BMSC

value: FLARE lineage recording


title: DMSO_Nuc_1

description: Library name: DMSO_Nuc_1

value: Nuclear

value: Nuc


title: DMSO_Tot_1

description: Library name: DMSO_Tot_1


title: dBET_Tot_1

description: Library name: dBET_Tot_1


title: Bone marrow from mouse M1 collected at endpoint

description: Library name: sample2_scRNA_M1_endpoint_bone_marrow

library_source: transcriptomic single cell

value: GEX


title: CLL327

value: European Ancestry (EA)

value: IGHV Unmutated


title: CLL320


title: DIvA cell, IDH mutant, non treated, TETdCD, input, Rep2

city: Bethesda

first: Fengchao

last: Lang

state: MD

address: Convent Dr, Room 1142, Building 37

institute: NCI

description: Library name: IDHdCD_neg_input2

data_processing:
Basecalls were performed using RTA 3.10.30.
ChIP-seq and 4C-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Cutadapt 1.18, discarding reads left with < 20 bp.
ChIP-seq and 4C-seq reads were aligned to the UCSC hg38 genome using Bowtie2 2.3.4.1. Only uniquely mapping reads with at most two mismatches were retained.
For ChIP-seq, peaks were called using MACS v2-2.7.1 with the significance cut-off q-value <=0.01. bigWig files were generated using the Deeptools (bamCoverage). Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2. For 4C-seq, mapping was done using Pipe4C (R package) and peaks were called with PeakC (R package).
Assembly: hg38
Supplementary files format and content: For ChIP-seq, we have the bigWig, narrowPeak (except for Input sample), for 4C-seq, we have bigWig flies.

source_name: DIvA cell

growth_protocol: DMEM-Ham F-12 medium, 10% FBS, 1% antibiotics (100 U/mL penicillin and 10 mg/mL streptomycin), 2mM Glutamin. Cells are cultured in at 37 oC in humidified air with 5% CO2.

extract_protocol:
ChIP-seq was performed using ChIP-IT High Sensitivity (Active Motif, 53040) according to the manufacturer’s instructions. Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, sonication was performed with Covaris S220 at a power of 140 W for 20 min. For 4C-seq, The 4C–seq experiments were performed as described 24 with minor modifications. In brief, fifteen million DIvA cells were cross-linked with 2% formaldehyde for 10 min at room temperature, lysed and digested with DpnI (100 U, NEB). Digested DNA was then ligated with 50 U T4 DNA ligase (Promega), purified and digested with NlaIII overnight (NEB). After a second ligation step, DNA was purified before proceeding to library preparation.
ChIP library construction was performed with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Briefly, the steps include End Repair, dA-Tailing, Adaptor Ligation, ligation products purification and PCR process. 20 ng DNA was used for the starting material. For 4C–seq library preparation, eight hundred nanograms of 4C–seq template were amplified using two-step PCR reactions with inverse primers (PAGE-purified) and primers with Illumina adaptor sequences and a unique index for each condition. Libraries were purified with the QIAquick PCR Purification Kit (Qiagen), pooled and subjected to 150-bp single-end sequencing on the Illumina NextSeq2000 platform at the NCI/CCR Next Generation Sequencing Core Facility.

treatment_protocol: Three hundred nanomolar 4-OHT was added to the culture medium for 4 hr to induce AsisI expression and the cutting at AsisI recognition sites.

value: DIvA cell

value: osteosarcoma tumor cells


title: PBMCs from mouse M1 collected at endpoint

description: Library name: sample2_scRNA_M1_endpoint_blood


title: DIvA cell, IDH mutant, TETdCD4-OHT over expression, input, Rep1

description: Library name: IDHdCD_pos_input1


title: CLL319


title: DIvA cell, IDH mutant, TETdCD4-OHT over expression, input, Rep2

description: Library name: IDHdCD_pos_input2


title: dBET_Cyt_2

description: Library name: dBET_Cyt_2

value: Breast; Mammary gland


title: CLL318


title: DIvA cell, IDH mutant, non treated, TETCD, input, Rep2

description: Library name: IDHCD_neg_input2


title: DIvA cell, IDH mutant, TETCD4-OHT over expression, input, Rep2

description: Library name: IDHCD_pos_input2


title: MULTIseq barcodes for demultiplexing sample1_scRNA_c1498_pool

description:
Library name: sample1_MULTIseq_barcodes
"Antibody Capture" in processed data files

value: MULTIseq

value: AML

value: 0.05ug/mL AraC (persistent + resistant only)


title: DIvA cell, IDH mutant, non treated, TETCD, input, Rep1

description: Library name: IDHCD_neg_input1


title: DMSO_Cyt_1

description: Library name: DMSO_Cyt_1

value: Cytoplasmic

value: Cyt

value: DMSO


title: CLL317

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)


title: dBET_Nuc_1

description: Library name: dBET_Nuc_1


title: DIvA cell, IDH mutant, 4-OHT, input, Rep 2

description: Library name: IDHRH_pos_input2


title: DIvA cell, IDH mutant, non treated, TETdCD, input, Rep1

description: Library name: IDHdCD_neg_input1


title: CLL316


title: CLL321


title: DIvA cell, IDH wt, 4-OHT, input, Rep 2

description: Library name: IDHwt_pos_input2


title: FLARE founder tag and clone tag sequencing associated with sample1_scRNA_c1498_pool

description: Library name: sample1_FLARE_barcodes

value: FLARE

value: FLARE lineage recording


title: DIvA cell, IDH wt, 4-OHT, input, Rep 1

description: Library name: IDHwt_pos_input1


title: CLL312


title: DIvA cell, IDH wt, non treated, input, Rep 4

description: Library name: IDHwt_neg_input4


title: DIvA cell, IDH mutant, non treated, input, Rep 1

description: Library name: IDHRH_neg_input1


title: DIvA cell, IDH mutant, 4-OHT, input, Rep 1

description: Library name: IDHRH_pos_input1


title: CLL315


title: DIvA cell, IDH wt, non treated, input, Rep 2

description: Library name: IDHwt_neg_input2


title: CLL314

value: IGHV Mutated


title: DIvA cell, IDH wt, non treated, input, Rep 3

description: Library name: IDHwt_neg_input3


title: CLL313


title: DIvA cell, IDH mutant, TETCD4-OHT over expression, input, Rep1

description: Library name: IDHCD_pos_input1


title: DIvA cell, IDH wt, 4-OHT, input, Rep 3

description: Library name: IDHwt_pos_input3


title: CLL311


title: DIvA cell, IDH wt, non treated, input, Rep 1

description: Library name: IDHwt_neg_input1


title: CLL309


title: DIvA cell, IDH mutant, non treated, TETdCD, Rep2

description: Library name: IDHdCD_neg_2


title: DIvA cell, IDH mutant, non treated, TETdCD, Rep3

description: Library name: IDHdCD_neg_3


title: DIvA cell, IDH mutant, TETdCD4-OHT over expression, Rep1

description: Library name: IDHdCD_pos_1


title: DIvA cell, IDH mutant, TETCD4-OHT over expression, Rep2

description: Library name: IDHCD_pos_2


title: CLL308


title: DIvA cell, IDH mutant, non treated, TETdCD, Rep1

description: Library name: IDHdCD_neg_1


title: DIvA cell, IDH mutant, TETdCD4-OHT over expression, Rep2

description: Library name: IDHdCD_pos_2


title: LPS  2

city: Madrid

first: Ana Belen

last: Sanz

address: Avda. Reyes Catolicos 2

country: Spain

institute: IIS-Fundacion Jimenez Diaz

data_processing:
Prinseq processing to remove reads shorter than 60 nt
Prinseq processing to remove long polyA/T tails and bases assigned as N in the read ends
Mapping with TopHat using Bowtie (2.4.1.0)
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: bam files (mapped files)

source_name: Whole kidney

growth_protocol: Four or five mice were housed per cage at 25 ± 1°C on a 12-h light/dark cycle and given free access to food and water

extract_protocol:
Mice received a single intraperitoneal of 5 mg/kg bacterial lipopolysaccharide to induce a cytokine storm and resulting AKI. In indicated goups the Ro5-3335 (5 mg/kg) was injected i.p  3 h before LPS administration.
The library construction protocol includes these steps: mRNA isolation, cDNA generation, end prep, adaptor ligation, and PCR Enrichment of Adaptor Ligated DNA.

treatment_protocol: Cytokine storm-AKI was induced by L

value: Whole kidney

tag: strain

value: Wild type

value: 5 mg/kg bacterial lipopolysaccharide


title: DIvA cell, IDH mutant, non treated, input, Rep 2

description: Library name: IDHRH_neg_input2

value: DIvA cell


title: CLL306

value: European Ancestry (EA)

value: IGHV Unmutated


title: DIvA cell, IDH wt, 4-OHT, input, Rep 4

description: Library name: IDHwt_pos_input4

value: osteosarcoma tumor cells


title: DIvA cell, IDH mutant, 4-OHT,CTCF, Rep 3

description: Library name: IDHRH_pos_3


title: LPS  0


title: DIvA cell, IDH mutant, TETCD4-OHT over expression, Rep1

description: Library name: IDHCD_pos_1


title: CLL305


title: DIvA cell, IDH mutant, 4-OHT,CTCF, Rep 1

description: Library name: IDHRH_pos_1


title: DIvA cell, IDH mutant, 4-OHT,CTCF, Rep 2

description: Library name: IDHRH_pos_2


title: DIvA cell, IDH mutant, non treated, TETCD, Rep2

description: Library name: IDHCD_neg_2


title: CLL310


title: DIvA cell, IDH mutant, 4-OHT,CTCF, Rep 4

description: Library name: IDHRH_pos_4


title: LPS RUNX3 2

value: Ro5-3335 (5 mg/kg) was injected i.p  3 h before LPS administration


title: LPS  1


title: CLL304


title: DIvA cell, IDH mutant, non treated, CTCF, Rep 3

description: Library name: IDHRH_neg_3


title: DIvA cell, IDH mutant, non treated, CTCF, Rep 1

description: Library name: IDHRH_neg_1


title: LPS RUNX1 1


title: DIvA cell, IDH mutant, non treated, CTCF, Rep 2

description: Library name: IDHRH_neg_2


title: CLL303


title: DIvA cell, IDH wt, 4-OHT, CTCF, Rep 4

description: Library name: IDHwt_pos_4


title: LPS RUNX1 0


title: DIvA cell, IDH mutant, non treated, TETCD, Rep1

description: Library name: IDHCD_neg_1


title: DIvA cell, IDH wt, 4-OHT, CTCF, Rep 3

description: Library name: IDHwt_pos_3


title: CLL301


title: Runx1 1


title: Runx1 2


title: DIvA cell, IDH wt, 4-OHT, CTCF, Rep 2

description: Library name: IDHwt_pos_2


title: DIvA cell, IDH wt, 4-OHT, CTCF, Rep 1

description: Library name: IDHwt_pos_1


title: CLL300


title: DIvA cell, IDH wt, non treated, CTCF, ChIP, Rep 4

description: Library name: IDHwt_neg_4


title: DIvA cell, IDH wt, non treated, CTCF, ChIP, Rep 3

description: Library name: IDHwt_neg_3


title: Runx1 0


title: DIvA cell, IDH mutant, non treated, CTCF, Rep 4

description: Library name: IDHRH_neg_4


title: CLL299


title: Control 2

value: control


title: CLL298


title: Control 1


title: HepG2 cells, CREB5-2

city: Hefei

first: anqi

last: wang

address: 218 Jixi Road

institute: The First Affiliated Hospital of Anhui Medical University

data_processing:
Cutadapt was used to filter out unqualified sequences (sequencing adapters, low-quality sequences, etc.) from the raw data
Hisat2 was used for reference genome alignment
StringTie was ued to reconstruct transcripts and calculate the expressions of all genes in each sample
Assembly: homo sapiens Ensembl_v107
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

source_name: liver

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted and purified using TRIzol (Thermo Fisher, 15596018). A concentration>50ng/µL, RIN value>7.0, and total RNA>1µg are sufficient for downstream experiments. Use oligo (dT) magnetic beads (Dynabeads Oligo (dT), cat. 25-61005, Thermo Fisher, USA) to specifically capture mRNA containing PolyA (polyadenylation) through two rounds of purification. The captured mRNA was fragmented using the NEBNextR Magnesium RNA Fragmentation Module (cat. E6150S, USA) under high temperature conditions at 94 ℃ for 5-7 minutes.
cDNA was synthesized using Invitrogen SuperScriptTM II Reverse Transcriptase (cat. 1896649, CA, USA), and E Escherichia coli DNA polymerase I (NEB, cat. m0209, USA) and RNase H (NEB, cat. m0297, USA) were subjected to double stranded synthesis. The double stranded DNA was digested using UDG enzyme (NEB, cat. m0280, MA, US), and a library with fragment size of 300bp ± 50bp was formed by PCR (chain specific library)

treatment_protocol: HepG2 cells were transfected with lentivirus to overexpress CREB5 in the experimental group

value: liver

value: human hepatoma carcinoma cell

value: CREB5 overexpression


title: HepG2 cells, CREB5-3


title: CLL302

value: Peripheral blood mononuclear cells


title: DIvA cell, IDH wt, non treated, CTCF, ChIP, Rep 1

description: Library name: IDHwt_neg_1


title: DIvA cell, IDH wt, non treated, CTCF, ChIP, Rep 2

description: Library name: IDHwt_neg_2


title: C1498 founder pool, multiplexed control, resistant, and persistent flasks

description: Library name: sample1_scRNA_c1498_pool

value: GEX

value: AML

value: 0.05ug/mL AraC (persistent + resistant only)


title: CLL297

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Mutated


title: HepG2 cells, CREB5-1


title: HepG2 cells, Vector3

value: WT


title: CLL296


title: Control 0

value: Whole kidney

value: Wild type


title: HepG2 cells, Vector2


title: Tam-Bleo Day 14

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: 10x Genomics

data_processing:
Reads were aligned against the mouse genome (mm10) and counted by StarSolo.
Assembly: mm10
Supplementary files format and content: starsolo outputs
Supplementary files format and content: mtx

source_name: Lung

extract_protocol:
FACS sorted cells were stained with SytoxTM (Thermofisher Scientific) for dead cell exclusion. 9000 sorted viable tdTomato cells per time point were loaded into 10x Genomics Chromium.
Library preparation was conducted according to the manufacturer indications (Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 16 rxns PN-1000121).

value: Lung

value: Day 14

value: tdTomatopos cells

value: Bleomycin


title: HepG2 cells, Vector1


title: NKcells, Untreated, rep4

first: Neelam

last: Redekar

address: 9000 rockville pike

department: NIAID

institute: NIH

data_processing:
The mRNA sequencing data was processed using default parameter with RNA-seek workflow (https://github.com/OpenOmics/RNA-seek).
This included preprocessing of the raw sequencing reads to remove low quality bases, adapters, and shorter reads using Cutadapt v1.18, followed by alignment to human hg38 reference genome (GRCh38, Gencode Release 30) using STAR (v.2.7.6a) aligner in two-pass mapping mode.
The gene expression counts estimated from number of reads mapping to each annotated gene using RSEM (v.1.3.3).
Assembly: GRCh38, Gencode Release 30
Supplementary files format and content: tab-delimited text file inlcudes RSEM expected gene counts for NK92 sample libraries
Supplementary files format and content: tab-delimited text file inlcudes RSEM expected gene counts for NKcell sample libraries

source_name: Donor Blood

growth_protocol: For the obese/lean comparison NK cells were isolated from Heparin (green top) peripheral blood from African American women in the Washington, D.C. metropolitan area residing in under-resourced neighborhoods. For LDL/vehctr cmparisons NK cells were isolated from healthy donor buffy coats received from the NIH bloodbank. For both datasets PBMCs were isolated from the blood using the Ficoll technique. Afterwards NK cells were isolated using Miltenyi products in a two step process. First, CD3+ cells were removed in a positive selection step. The flowthrough of this selection step was than subjected to CD56 selection for CD3-/CD56+ NK cells. all cells were used immediately after isolation without expansion or cytokine treatment.

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (74104, Qiagen, USA) per manufacturers’ recommendation. An additional step of DNase I treatment was performed, and cells were washed twice thereafter. Concentration was determined using NanoDrop Spectrophotometer.
Libraries were prepared using SMART-Seq V4 (Takara Bio) and Nextera XT kit (Illumina) and were sequenced on Illumina Novaseq for paired-end 100bps using standard Illumina sequencing protocol.

treatment_protocol: RNA sequencing was performed from freshly isolated primary NK cells isolated from study participants’ peripheral blood (n=5 each lean or obese). Healthy donor buffy coats treated with vehicle (control) or LDL (n=4 sets). After isolation and/or treatment, NK cells were lysed in Trizol (15596026, Thermo Fisher Scientific, USA). DUSP1 or empty vector control were overexpressed in NK-92 cells using the Sleeping Beauty technique. NK-92 EV control or NK-92-DUSP1oe cells wee lysed in trizol for subsequent Sequencing analysis.

value: Donor Blood

value: NK

value: Control


title: CLL295

value: European Ancestry (EA)


title: NKcells, LDL, rep4

value: LDL


title: CLL294

value: Peripheral blood mononuclear cells

value: IGHV Unmutated


title: Bleo-Tam Day 60

description: 10x Genomics

value: Day 60


title: NKcells, LDL, rep3


title: NKcells, Untreated, rep3


title: CLL293

value: Chronic Lymphocytic Leukemia (CLL)


title: CLL307

value: IGHV Mutated


title: NKcells, LDL, rep2


title: Bleo-Tam Day 14

description: 10x Genomics


title: Saline Day 14

description: 10x Genomics

value: Saline


title: CLL292


title: NKcells, LDL, rep1


title: Proliferating CD4 T cells (120hr)

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: The sample used to obtain RNA for sequencing was 98.2% pure CD4 T cells activated for 120 hrs with anti-CD3/CD28 beads.

data_processing:
Sequencing was performed using one SMRTcell 8M per pool of two samples on the Sequel IIe system. Following data generation, multiple, iterative sequences covering a single molecule were collapsed to generate highly accurate circular consensus sequence (CCS) reads. These reads were demultiplexed and then used as input into the Iso-Seq v3 pipeline within SMRTLink v10.1, which filters out amplification artifacts, trims primers and polyA tails to produce de novo full-length non-chimeric (FLNC) transcripts.
The cDNA Cupcake protocol was used for post-processing of Iso-Seq clustered FLNC reads. The alignment files for the FLNC reads were converted to fastq and fasta format. Fasta files were aligned to the Homo sapiens reference genome assembly (hg38.p13) using minimap2 (v2.18-r1015) with the option -secondary=no. The resulting alignment files were collapsed into isoforms based on sequence similarity using the cDNA Cupcake Python script collapse_isoforms_by_sam.py. Isoform abundance was calculated using get_abundance_post_collapse.py, and isoforms were filtered to include those with at least two supporting reads with filter_by_count.py. Isoforms were also filtered to remove possible non-full length reads, indicated by a degraded 5’ prime region (filter_away_subset.py).
Assembly: hg38
Supplementary files format and content: ST143_4Hr_bs1_bc1018_flnc_ALIGNED_CUPCAKE.sorted.REDUCED.gff
Supplementary files format and content: ST143_16Hr_bs2_bc1019_flnc_ALIGNED_CUPCAKE.sorted.REDUCED.gff
Supplementary files format and content: ST143_48Hr_bs3_bc1020_flnc_ALIGNED_CUPCAKE.sorted.REDUCED.gff
Supplementary files format and content: ST143_120hr_bs4_bc1023_flnc_ALIGNED_CUPCAKE.sorted.REDUCED.gff
Library strategy: Iso-Seq

source_name: Peripheral Blood CD4 T Cell

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained from venous blood of the healthy female donor by density gradient separation using Lymphoprep Density Gradient Media and Sepmate PBMC Isolation Tubes Tubes (StemCell Technologies, 85450). CD4 T cells were then purified using negative magnetic selection via EasySep kit (Stemcell Technologies, Cat#17952). CD4 T cells were plated with Dynabeads Human T-Activator CD3/CD28 (Gibco Cat#11161D) and stimulated for 4, 16, 48, or 120hrs before RNA extraction for sequencing.

extract_protocol:
Activated cells were lysed in well with subsequent Dynabead removal. Total cellular RNA was extracted and purified using RNeasy Plus Mini Kit (Qiagen, 74134) following the manufacturer’s protocol with addition of on-column DNase digestion. High quality RNA (RIN>9) was used for library construction.
To generate IsoSeq libraries, 500ng of high-quality RNA (RIN>9) was used as input into oligodT primed cDNA synthesis (NEB). A Template Switch Oligo (PacBio) was utilized during the reverse transcriptase reaction for second strand synthesis. The resulting double stranded cDNA was amplified with unique barcoded primers and equimolar pooled into two separate pools containing 2 samples per pool. SMRTbell generation was performed according to manufacturer protocols (PacBio). Briefly, the amplified and pooled cDNA underwent enzymatic DNA damage and end repair prior to ligation of SMRTbell hairpin adapters. An enzyme cocktail was used to remove non-ligated template, then the final libraries were purified with magnetic beads. A sequencing primer (v4) was annealed and polymerase (v2.1) bound to the IsoSeq libraries, followed by a final purification on magnetic beads. Sequencing was performed using two SMRT cell 8M, one for each pool, on the Sequel IIe system in the UofL Sequencing Technology Center. Following data generation, multiple, iterative sequences covering a single molecule were collapsed to generate highly accurate circular consensus sequence (CCS) reads. These reads were demultiplexed and then used as input into the IsoSeq v3 pipeline within SMRTLink v10.1, which filters out amplification artifacts, trims primers and polyA tails to produce de novo full-length non-concatenated (FLNC) transcripts for downstream mapping and annotation.

treatment_protocol: CD4 T cells were stimulated with anti-CD3/CD28 Dynabeads at a bead:cell ratio of 1:1 (4, 16, and 48hr) or 3:1 (120hr) for the indicated times prior to RNA extraction. No additional cytokines or stimulants were added during this time. Cells stimulated for 120hrs were split  on day 2 of stimulation with 50% new media added.

value: Peripheral Blood CD4 T Cell

tag: Sex

value: female

tag: age

value: 24 years

tag: activation status

value: activated

tag: activation time_point


title: CLL291

tag: tissue


title: NKcells, Untreated, rep1

tag: cell line


title: Blasting CD4 T cells (48hr)

description: The sample used to obtain RNA for sequencing was 98.2% pure CD4 T cells activated for 48 hrs with anti-CD3/CD28 beads.

tag: cell type

value: 48 hr


title: NKcells, Lean AA, rep4

value: Lean


title: Mid-activated CD4 T cells (16hr)

description: The sample used to obtain RNA for sequencing was 98.2% pure CD4 T cells activated for 16 hrs with anti-CD3/CD28 beads.

value: 15 hr


title: NKcells, Lean AA, rep5

value: Donor Blood

value: NK


title: CLL290

value: European Ancestry (EA)

tag: genotype


title: NKcells, Lean AA, rep2

tag: treatment


title: CLL289


title: NKcells, Lean AA, rep1


title: NKcells, Obese AA, rep5

value: Obese


title: CLL288

value: Peripheral blood mononuclear cells


title: Early activated CD4 T Cells (4hr)

description: The sample used to obtain RNA for sequencing was 98.2% pure CD4 T cells activated for 4 hrs with anti-CD3/CD28 beads.

value: 4 hr


title: NKcells, Obese AA, rep4


title: NKcells, Obese AA, rep2


title: FLARE founder tag and clone tag sequencing associated with sample4_scRNA_humanAML_lines_postAraC

description: Library name: sample4_FLARE_barcodes

source_name: HL60, TF1

value: FLARE

value: HL60, TF1

value: AML

value: FLARE lineage recording

value: 0.01ug/mL AraC (treated HL60 flasks)


title: CLL286

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Mutated


title: NKcells, Obese AA, rep1

source_name: NK-92 cells

value: NK-92 cells


title: MULTIseq barcodes for demultiplexing sample4_scRNA_humanAML_lines_postAraC

description:
Library name: sample4_MULTIseq_barcodes
"Antibody Capture" in processed data files

value: MULTIseq


title: HL60 and TF1 post-AraC, control and treated flasks multiplexed

description: Library name: sample4_scRNA_humanAML_lines_postAraC

value: GEX


title: NK92cells, DUSP1 ORF, rep3

value: DUSP1 ORF


title: CLL287


title: CLL285

value: IGHV Unmutated


title: NK92cells, DUSP1 ORF, rep2

value: NK


title: MULTIseq barcodes for demultiplexing sample3_humanAML_lines

description:
Library name: sample3_MULTIseq_barcodes
"Antibody Capture" in processed data files

source_name: HL60, TF1, OCI-AML3

value: HL60, TF1, OCI-AML3


title: NKcells, Untreated, rep2

value: Donor Blood

value: Control


title: NK92cells, DUSP1 ORF, rep1


title: CLL284

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells


title: NK92cells, empty vector, rep2

value: empty vector


title: NK92cells, empty vector, rep3


title: NKcells, Lean AA, rep3

value: Lean


title: NK92cells, empty vector, rep1


title: HL60, TF1, and OCI-AML3 pre-AraC treatment multiplexed

description: Library name: sample3_scRNA_humanAML_lines_preAraC

value: AML

value: FLARE lineage recording


title: CLL283

value: Chronic Lymphocytic Leukemia (CLL)


title: HEK cells transfected with tRNA-Asp-GTC 3' tDR, replicate 4

city: Santa Cruz

first: Todd

last: Lowe

state: CA

address: 1156 High St

department: Biomolecular Engineering

institute: UC Santa Cruz

description: Library name: tDR_4

data_processing:
Raw fastq files were processed using the tRNA Analysis of eXpression (tRAX) pipeline.
Reads were split into mature tRNA fraction (>60nt) and fragment fraction (<60nt)
Fractions were re-processed through tRAX with --lazyremap option and differential expression of mature tRNAs was calculated from the "mature" fraction.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing read counts by feature (row) and sample (column)

growth_protocol: Human embryonic kidney 293 (HEK) cells were purchased from ATCC (ATCC, CRL-1573) and cultured in D10 medium, which consisted of DMEM with high glucose and pyruvate (Thermo Fisher, Cat# 11995073) supplemented with 10% fetal bovine serum (FBS) (ThermoFisher, Cat# 16000044) and 1% Penicillin/Streptomycin (Thermo Fisher, Cat# 15140122).

extract_protocol:
Total RNA was extracted following TRIzol protocol.
Libraries were prepared using Ordered Two-Template Relay sequencing (OTTR-seq)

treatment_protocol: HEK cells were transfected with 50nM tRNA-Asp-GTC-3'tDR or scramble control mimics with Lipofectamine RNAiMax. Cells were collected 48 hours after transfection.

value: transfected with tRNA-Asp-GTC 3' tDR


title: MMSC_DMSO_3.5d_rep1

city: San Antonio

first: Subash

last: Khadka

state: TX

address: 7703 Floyd Curl Dr

institute: UT Health San Antonio

data_processing:
RNAsik pipeline
Assembly: hg38
Supplementary files format and content: tab delimited text files includes raw counts for each sample

source_name: myometrium

extract_protocol:
Rneasy Plus mini kit (Qiagen)
Illumina

value: myometrium

value: primary cells

value: side population cells

value: WT

value: control

tag: time

value: 3.5 days


title: CLL282

tag: ancestry

value: IGHV Mutated


title: MMSC_DMSO_3.5d_rep3


title: NKcells, Obese AA, rep3

value: Donor Blood

value: NK

value: Obese


title: HEK cells transfected with tRNA-Asp-GTC 3' tDR, replicate 3

description: Library name: tDR_3


title: MMSC_CCT_3.5d_rep3

value: CDK8/19 inhibition


title: MMSC_CCT_3.5d_rep2


title: CLL280

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells

tag: disease state


title: HEK cells transfected with tRNA-Asp-GTC 3' tDR, replicate 1

description: Library name: tDR_1


title: MMSC_DMSO_4.5h_rep2

value: 4.5 hours


title: HEK cells transfected with tRNA-Asp-GTC 3' tDR, replicate 2

description: Library name: tDR_2


title: MMSC_DMSO_4.5h_rep3


title: CLL279

value: IGHV Unmutated


title: MMSC_CCT_3.5d_rep1


title: MMSC_CCT_4.5h_rep3


title: CLL278

value: Chronic Lymphocytic Leukemia (CLL)


title: MMSC_CCT_4.5h_rep2


title: MMSC_CCT_4.5h_rep1


title: HEK cells transfected with control scramble sequence, replicate 3

description: Library name: control_3


title: HEK cells transfected with control scramble sequence, replicate 4

description: Library name: control_4


title: MMSC_DMSO_4.5h_rep1


title: MMSC_CCT_3.5d_K27ac

data_processing:
Nextflow core CUT&RUN pipeline
Assembly: hg38
Supplementary files format and content: BED files
Library strategy: CUT&RUN

extract_protocol:
Specific DNA fragments pulled down with H3K27ac antibodies and non-specific background with IgG antibodies during CUT&RUN experiment extracted with Nucleospin Gel and PCR cleanup columns
KAPA Hyperprep Kit

tag: chip antibody


title: MMSC_DMSO_3.5d_rep2


title: HEK cells transfected with control scramble sequence, replicate 2

description: Library name: control_2


title: HEK cells transfected with control scramble sequence, replicate 1

description: Library name: control_1


title: CLL276


title: MMSC_DMSO_3.5d_K27ac

value: Control


title: CLL275


title: CLL277


title: MMSC_DMSO_3.5d_IgG

value: myometrium

value: anti-IgG


title: 95_EpithPLUSpl

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (Bolger, Lohse, and Usadel 2014) (version 0.39) using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20.
Trimmed sequences were mapped to the human reference genome provided by ENSEMBL, (version grch38_snp_tran) using Hisat2 (Kim, Langmead, and Salzberg 2015) with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK (McKenna et al. 2010) package (version 4.2.3.0) with default parameters except OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000.
Mapped reads were associated with transcripts from grch38 database (Zerbino et al. 2018) (Ensembl, version 112) using HTSeq-count (Anders, Pyl, and Huber 2015) (version 0.9.1) with default parameters except –stranded set to “reverse”.
Differentially expressed genes were selected using the DESeq2 package (Love, Huber, and Anders 2014) (version1.38.3).
Assembly: grch38 database, Ensembl version 112
Supplementary files format and content: Count normalized with "counts" function from Deseq2 package. Genes that haven't  reach 32 normalized counts in any group were removed.

source_name: epithelium

growth_protocol: Nasal epithelial cells were cultured at an air-liquid interface (ALI) for 21 days in PneumaCult medium (StemCell) within a two-chamber system (Greiner Bio-One).

extract_protocol:
Total RNA were then isolated by TRIzol method and further purified on collumns. A total of 1000 ng of intact total RNA was subjected to mRNA enrichment, heat fragmentation (94 ◦C, 5 min), cDNA synthesis and ligation of KAPA Unique Dual-Indexed Adapters (Roche). Ten cycles of library amplification were applied.
The size distribution of the final libraries was validated using an Agilent TapeStation 2200 and High Sensitivity D1000 Reagents (Agilent) and the concentration was determined by qPCR using a Kapa Library Quantifica-tion Kit (Roche).

treatment_protocol: Cells were stimulated with polyamide microplastic fibres (200 µg/cm2) for 48 hours.

value: epithelium

value: primary

value: nasal epithalial cells

value: microplastic

tag: disease

value: asthma

tag: growth condition

value: air-liquid interface


title: CLL274


title: 95_Epith


title: CLL281

value: IGHV Mutated


title: DIvA cell, IDH wt, non treated, Knock down (si2), 4C-seq, DSB2, Rep 2

description: Library name: DSB2_wtminus_KD2_2

data_processing:
Basecalls were performed using RTA 3.10.30.
ChIP-seq and 4C-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Cutadapt 1.18, discarding reads left with < 20 bp.
ChIP-seq and 4C-seq reads were aligned to the UCSC hg38 genome using Bowtie2 2.3.4.1. Only uniquely mapping reads with at most two mismatches were retained.
For ChIP-seq, peaks were called using MACS v2-2.7.1 with the significance cut-off q-value <=0.01. bigWig files were generated using the Deeptools (bamCoverage). Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2. For 4C-seq, mapping was done using Pipe4C (R package) and peaks were called with PeakC (R package).
Assembly: hg38
Supplementary files format and content: For ChIP-seq, we have the bigWig, narrowPeak (except for Input sample), for 4C-seq, we have bigWig flies.
Library strategy: 4C-seq

value: DIvA cell

value: osteosarcoma tumor cells


title: DIvA cell, IDH wt, non treated, Knock down (si2), 4C-seq, DSB2, Rep 1

description: Library name: DSB2_wtminus_KD2_1


title: 94_Epith


title: 94_EpithPLUSpl


title: DIvA cell, IDH wt, non treated, Knock down (si1), 4C-seq, DSB2, Rep 2

description: Library name: DSB2_wtminus_KD1_2


title: 92_EpithPLUSpl

value: control


title: CLL273

value: European Ancestry (EA)

value: Peripheral blood mononuclear cells


title: 92_Epith


title: 78_EpithPLUSpl


title: DIvA cell, IDH wt, 4-OHT, Knock down (si2), 4C-seq, DSB2, Rep 2

description: Library name: DSB2_wtplus_KD2_2


title: CLL270

value: IGHV Unmutated


title: 110_Epith

value: COPD


title: DIvA cell, IDH wt, non treated, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_wtminus_2


title: 113_Epith


title: CLL268

value: Chronic Lymphocytic Leukemia (CLL)


title: 113_EpithPLUSpl


title: 41_Epith


title: MMSC_CCT_3.5d_IgG

value: myometrium

value: primary cells

value: side population cells

value: WT

value: CDK8/19 inhibition


title: DIvA cell, IDH wt, non treated, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_wtminus_1


title: 44_Epith

value: epithelium

value: primary

value: nasal epithalial cells


title: CLL267


title: 110_EpithPLUSpl

value: microplastic

value: air-liquid interface


title: 41_EpithPLUSpl

value: asthma


title: CLL265


title: 104_EpithPLUSpl

value: control


title: 104_Epith


title: CLL269

value: European Ancestry (EA)


title: 44_EpithPLUSpl


title: DIvA cell, IDH wt, 4-OHT, Knock down (si1), 4C-seq, DSB2, Rep 1

description: Library name: DSB2_wtplus_KD1_1

value: DIvA cell

value: osteosarcoma tumor cells


title: 78_Epith


title: CLL272

value: Peripheral blood mononuclear cells

value: IGHV Mutated


title: 101_Epith


title: CLL271

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Unmutated


title: 109_EpithPLUSpl

value: COPD


title: CLL266


title: DIvA cell, IDH wt, 4-OHT, Knock down (si2), 4C-seq, DSB2, Rep 1

description: Library name: DSB2_wtplus_KD2_1


title: 109_Epith


title: DIvA cell, IDH wt, non treated, Knock down (si1), 4C-seq, DSB2, Rep 1

description: Library name: DSB2_wtminus_KD1_1


title: DIvA cell, IDH wt, 4-OHT, Knock down (si1), 4C-seq, DSB2, Rep 2

description: Library name: DSB2_wtplus_KD1_2


title: DIvA cell, IDH wt, TETCD4-OHT, over expression, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_wt_Qiaplus_2


title: CLL263


title: 100_EpithPLUSpl


title: 101_EpithPLUSpl


title: DIvA cell, IDH wt, TETCD4-OHT, over expression, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_wt_Qiaplus_1


title: DIvA cell, IDH mutant, non treated, Knock down (si2), 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHminus_KD2_2


title: 100_Epith


title: DJL1_rep3

city: Toronto

first: Lamisa

last: Ataei

state: ON

address: 25 Orde St

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

data_processing:
Library sequencing quality was evaluated using FastQC and presented in summary with MultiQC-seq.
Alignment to the human reference genome (GRCh38) was performed using Bowtie2 (v2.4.5)
Mitochondrial genome, unknown and random chromosome, and PCR duplicate reads were all removed using Samtools (v.1.18),
Peak calling was performed next using MACS3 command callpeaks with the following options: --nomodel --nolambda
BEDtools (v2.30.0) was used to remove blacklisted regions identified by ENCODE from peak files
Assembly: hg38
Supplementary files format and content: txt
Supplementary files format and content: bigwig

growth_protocol: H9 hES cells were cultured in RSeT media (STEM CELL) following manual instruction.

extract_protocol:
Cell pellets were resuspended by pipetting in 50μl of cold ATAC-Resuspension Buffer [RSB] (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin. Following tagmentation reactioin, DNA was cleaned up with the DNA Clean and Concentrator -5 Kit (Zymo) per manufacturer's instructions.
Library amplification was carried out according to the Omni-ATAC protocol (Corces et al. 2017), and pooled at equimolar concentration for paired-end 50bp read sequencing.

treatment_protocol: Transfections were performed in RSeT supplemented with 10 nM DZNep and 5nM TSA (RSeT+DT) and CEPT cocktail which includes 50nM Chroman 1, 5 µM Emricasan, Polyamine, and 0.7 µM Trans-ISRIB for the first 16 hours, and medium was then replaced thereafter with. RSeT+DT media. Cells were harvested for cell sorting and downstream assays 48 h after transfection.

value: Human embryonic stem cells


title: DJL1_rep4


title: CLL261

data_processing:
mRNA sequencing was generated using a HiSeq 4000 sequencer for 58 AA CLL and 292 EA CLL.  The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.4. Batch correction for all RNA samples was performed by removing protein coding genes with low counts, for each batch individually, resulting in 9,934 protein coding genes.  In addition, CombatSeq was run using the annotated reported race as a covariate, with CombatSeq corrected count values used for all downstream analyses.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes batch corrected gene counts each gene per sample


title: CLL262


title: DJL1_rep2


title: DIvA cell, IDH mutant, non treated, Knock down (si2), 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHminus_KD2_1


title: CLL260


title: CTRL_rep2


title: CTRL_rep4


title: DIvA cell, IDH mutant, non treated, Knock down (si1), 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHminus_KD1_1


title: CTRL_rep1


title: DJL1_rep1


title: CTRL_rep3


title: DJL1_rep2

data_processing:
RNA-seq reads were quality-checked and trimmed using Trim Galore! v0.4.0
The the trimmed reads were aligned to GRCh38 with hisat2 v2.2.1, which generated .bam files
FeatureCounts function from the subread package (v1.5.0) was applied to count reads of each gene to generate the raw counts table.
Assembly: hg38
Supplementary files format and content: txt

extract_protocol:
RNA extraction was performed using the RNeasy mini kit (QIAGEN), according to the manufacturer’s instructions.
200ng of RNA from each sample was used to prepare sequencing libraries. Libraries were prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB # E7490S) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB # E7760L), per manufacturer’s instructions. Library cDNA were equally pooled at 10 nM for sequencing.


title: DIvA cell, IDH mutant, non treated, Knock down (si1), 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHminus_KD1_2


title: DJL1_rep3


title: CLL258

extract_protocol:
RNA was extracted using the Quagen miRNeasy Mini Kit
Illumina TruSeq Stranded mRNA library prep protocol


title: CLL259


title: DJL1_rep1


title: DIvA cell, IDH mutant, non treated, empty vector, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHminus_EVminus_1


title: DIvA cell, IDH mutant, non treated, empty vector, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHminus_EVminus_2


title: CLL264


title: CTRL_rep4


title: CLL257


title: CTRL_rep2


title: DIvA cell, IDH mutant, non treated, TETdCD, over expression, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHminus_dCD_2


title: DIvA cell, IDH mutatnt, non treated, TETdCD, over expression, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHminus_dCD_1


title: CTRL_rep1


title: CTRL_rep3


title: Primed-ESC_3_pre-rDNA

description:
Primed_pre-rDNA_chr13.bedGraph
Primed_pre-rDNA_chr15.bedGraph

data_processing:
T2T genome indices for bowtie2 were generated containing only 1 of the 5 acrocentric chromosomes and all non acrocentric chromosomes using the T2T-CHMv2.0 assembly using bowtie2-build
A DpnII digested T2T genome was built using digestGenome() from  the UMI4Cats R package (Ramos-Rodriguez et al. 2021)
Samples were demultiplexed, separated, aligned, and count files were generated using the nested function contactsUMI4C() with default settings. prepUMI4C() was run separately to prepare the demultiplexed fastq files for submission
UMI4C objects were built for plotting using the function makeUMI4C() with default settings but a bait_exclusion=10000, and bait_expansion=1500000 or bait_expansion=5000000
Regions to test for statistical analysis were generated with makeWindowFragments() with default settings, and then tested with callInteractions() using default settings but a padj_threshold=0.05
Assembly: T2T-CHMv2.0
Supplementary files format and content: bedGraph
Library strategy: UMI-4C-seq

growth_protocol: H9 hES cells were cultured in RSeT media or mTeSR Plus media (STEM CELL) following manual instruction.

extract_protocol:
To isolate 3C DNA, cells were thawed and gently lysed on ice for 30 minutes to release nuclei. Nuclei were washed and permeabilized by incubating in 1% SDS and 1.15X NEB3.1 buffer for 1 h, and then in the presence of 2.85% Triton-X100 for 1 h. Following digestion and re-ligation protcols, DNA was purified using standard phenol-chloroform and ethanol extraction.
Library amplification was carried out according to the UMI-4C protocol (Schwartzman et al. 2016).

treatment_protocol: Cells were crosslinked in 1% formaldehyde prior to harvesting and sample collection.


title: CLL255


title: DIvA cell, IDH mutatnt, non treated, TETCD, over expression, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHminus_CD1_2


title: CLL254


title: Primed-ESC_3_5primeL1DJ

description:
Primed_5primeL1DJ_1_chr13.bedGraph
Primed_5primeL1DJ_1_chr15.bedGraph
Primed_5primeL1DJ_2_chr13.bedGraph
Primed_5primeL1DJ_2_chr15.bedGraph


title: DIvA cell, IDH mutatnt, non treated, TETCD, over expression, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHminus_CD1_1


title: CLL253


title: Primed-ESC_2_pre-IR

description:
Primed_pre-IR_chr13.bedGraph
Primed_pre-IR_chr15.bedGraph


title: DIvA cell, IDH mutant, non treated, 4-OHT, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHminus_2


title: Primed-ESC_2_pre-rDNA


title: Primed-ESC_3_DJ_IR


title: CLL252


title: Primed-ESC_2_DJ_IR


title: DIvA cell, IDH mutant, non treated, 4-OHT, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHminus_1


title: Primed-ESC_2_5primeL1DJ


title: Primed-ESC_3_3primeL1DJ

description:
Primed_3primeL1DJ_1_chr13.bedGraph
Primed_3primeL1DJ_1_chr15.bedGraph
Primed_3primeL1DJ_2_chr13.bedGraph
Primed_3primeL1DJ_2_chr15.bedGraph


title: Primed-ESC_2_3primeL1DJ


title: CLL251


title: CLL250


title: DIvA cell, IDH mutant, 4-OHT, Knock down (si2), 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHplus_KD2_2


title: Primed-ESC_1_pre-rDNA


title: CLL256


title: Primed-ESC_1_pre-IR


title: DIvA cell, IDH mutant, 4-OHT, Knock down (si2), 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHplus_KD2_1


title: CLL249


title: Primed-ESC_3_pre-IR


title: Primed-ESC_1_3primeL1DJ


title: Primed-ESC_1_5primeL1DJ


title: DIvA cell, IDH mutant, 4-OHT, Knock down (si1), 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHplus_KD1_2


title: CLL248


title: Naïve-ESC_3_pre-IR

description:
Rset_DT_pre-IR_chr13.bedGraph
Rset_DT_pre-IR_chr15.bedGraph


title: Naïve-ESC_3_pre-rDNA

description:
Rset_DT_pre-rDNA_chr13.bedGraph
Rset_DT_pre-rDNA_chr15.bedGraph


title: Naïve-ESC_3_DJ_IR


title: DIvA cell, IDH mutant, 4-OHT, Knock down (si1), 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHplus_KD1_1


title: CLL247


title: CLL246


title: Naïve-ESC_3_5primeL1DJ

description:
Rset_DT_5primeL1DJ_1_chr13.bedGraph
Rset_DT_5primeL1DJ_1_chr15.bedGraph
Rset_DT_5primeL1DJ_2_chr13.bedGraph
Rset_DT_5primeL1DJ_2_chr15.bedGraph


title: DIvA cell, IDH mutant, 4-OHT, empty vector, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHplus_EVminus_2


title: Naïve-ESC_3_3primeL1DJ

description:
Rset_DT_3primeL1DJ_1_chr13.bedGraph
Rset_DT_3primeL1DJ_1_chr15.bedGraph
Rset_DT_3primeL1DJ_2_chr13.bedGraph
Rset_DT_3primeL1DJ_2_chr15.bedGraph


title: DIvA cell, IDH mutant, 4-OHT, empty vector, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHplus_EVminus_1


title: Naïve-ESC_2_DJ_IR


title: Naïve-ESC_2_pre-rDNA


title: DIvA cell, IDH mutant, TETdCD4-OHT, over expression, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHplus_dCD_2


title: CLL244


title: Naïve-ESC_2_5primeL1DJ


title: DIvA cell, IDH mutant, TETdCD4-OHT, over expression, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHplus_dCD_1


title: Naïve-ESC_2_3primeL1DJ


title: CLL243


title: Naïve-ESC_1_pre-rDNA


title: Primed-ESC_1_DJ_IR


title: DIvA cell, IDH mutant, 4-OHT, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RHplus_2


title: Naïve-ESC_1_DJ_IR


title: DIvA cell, IDH mutant, 4-OHT, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RHplus_1


title: Naïve-ESC_1_5primeL1DJ


title: DIvA cell, IDH mutant, TETCD4-OHT, over expression, 4C-seq, DSB2, Rep 2

description: Library name: DSB2_RH_CD_Qiaplus_2


title: CLL245


title: WGBS_H9-SRG_Re-primed_R+G+

data_processing:
Paired-end Fastq files were trimmed with TrimGalore v0.6.6.
Reads were aligned with Bismark v0.23.0.
Methpipe package v4.1.1 was used to remove duplicate reads (duplicate-remover), calculate methylation levels (methcounts), extract and merge symmetric CpGs (symmetric-cpgs), and calculate methylation statistics for regions of interest.
Assembly: hg38
Supplementary files format and content: Imprint methylation xlsx file

extract_protocol:
Genomic DNA was isolated using the Qiagen Dneasy Blood & Tissue kit.
Bisulfite conversion was performed on gDNA using the Zymo EZ DNA Methylation-Gold Kit. Libraries were constructed manually.

value: hESC


title: WGBS_H9-SRG_Re-primed_R+G-


title: WGBS_H9-SRG_Naïve_P5_R+G+


title: Naïve-ESC_1_3primeL1DJ


title: WGBS_H9-SRG_Naïve_P1_R+G+


title: Naïve-ESC_2_pre-IR


title: CLL241


title: CLL239


title: CLL240


title: WGBS_H9-SRG_Naïve_P5_R+G-


title: CLL237

value: African Ancestry (AA)


title: RNA-seq_H9-SRG_Clone2_PXGGYA_P5_R+G+

description:
RNA-seq_GeneCounts_CPM_1.xlsx
RNA-seq_GeneCounts_CPM_1.xlsx

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software.
Alignment was performed with STAR v2.5.1a or v2.7.9a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5 or 2.0.3.
Assembly: hg38
Supplementary files format and content: Gene counts xlsx files

extract_protocol:
Total RNA was isolated using the E.Z.N.A. total RNA kit I.
Library construction was performed using the Takara SMARTer Ultra Low RNA kit.


title: CLL242


title: Naïve-ESC_1_pre-IR


title: WGBS_H9-SRG_Primed


title: DIvA cell, IDH wt, non treated, Knock down (si2), 4C-seq, DSB1, Rep 2

description: Library name: DSB1_wtminus_KD2_2


title: WGBS_H9-SRG_Naïve_P1_R+G-


title: DIvA cell, IDH wt, non treated, Knock down (si2), 4C-seq, DSB1, Rep 1

description: Library name: DSB1_wtminus_KD2_1


title: RNA-seq_H9-SRG_Clone2_NoERKi_P1


title: CLL236


title: DIvA cell, IDH wt, 4-OHT, Knock down (si2), 4C-seq, DSB1, Rep 2

description: Library name: DSB1_wtplus_KD2_2


title: RNA-seq_H9-SRG_Clone1_PXGGYA_P1_R+G-


title: DIvA cell, IDH wt, non treated, Knock down (si1), 4C-seq, DSB1, Rep 2

description: Library name: DSB1_wtminus_KD1_2


title: RNA-seq_H9-SRG_Clone1_Primed


title: RNA-seq_H9-SRG_Clone2_PXGGYA_P1_R+G+


title: DIvA cell, IDH wt, non treated, Knock down (si1), 4C-seq, DSB1, Rep 1

description: Library name: DSB1_wtminus_KD1_1


title: RNA-seq_H9-SRG_Clone2_PXGGYA_P1_R+G-


title: RNA-seq_H9-SRG_Clone2_Primed


title: RNA-seq_H9-SRG_Clone1_NoERKi_P1


title: DIvA cell, IDH wt, non treated, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_wtminus_2


title: CLL234


title: DIvA cell, IDH wt, non treated, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_wtminus_1


title: DIvA cell, IDH wt, 4-OHT, Knock down (si1), 4C-seq, DSB1, Rep 2

description: Library name: DSB1_wtplus_KD1_2


title: CLL238


title: RNA-seq_H9-SRG_Clone1_PXGGYA_P5_R+G-


title: CLL233


title: RNA-seq_H9-SRG_Clone1_PXGGYA_P1_R+G+


title: RIVA-BCL10-R58Q-2

city: miami

first: Jonathan

middle: H

last: Schatz

state: Florida

address: 1580 NW 10th Ave 1st floor

department: Department of Medicine

institute: university of miami

data_processing:
Picard was used to analyze the reads.
STAR was used to align the reads to Hg38.
Cutadapt was used to process the data.
Assembly: Hg38
Supplementary files format and content: tab delimited text file containing raw counts for each sample

source_name: RIVA

growth_protocol: RIVA cells infected with indicated plvx-Tetone vectors

extract_protocol:
RNA was extracted with the Qiagen RNAeasy Mini Kit with optional on-column DNAse
Total RNA was prepped with the Nugen Universal Plus mRNA-Seq with NuQuant (M01485 v6) using 500ng via Qubit and 14 cycles PCR. Libraries were sequenced on Illumina Novaseq 6000 across 2 runs.  Fastq files were combined for analysis.

treatment_protocol: RIVA cells were induced with 200ng/ml of doxycycline x24 hours

value: RIVA

value: DLBCL

value: BCL10 R58Q

value: 200ng/uL doxycycline


title: DIvA cell, IDH mutant, TETCD4-OHT, over expression, 4C-seq, DSB2, Rep 1

description: Library name: DSB2_RH_CD_Qiaplus_1

extract_protocol:
ChIP-seq was performed using ChIP-IT High Sensitivity (Active Motif, 53040) according to the manufacturer’s instructions. Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, sonication was performed with Covaris S220 at a power of 140 W for 20 min. For 4C-seq, The 4C–seq experiments were performed as described 24 with minor modifications. In brief, fifteen million DIvA cells were cross-linked with 2% formaldehyde for 10 min at room temperature, lysed and digested with DpnI (100 U, NEB). Digested DNA was then ligated with 50 U T4 DNA ligase (Promega), purified and digested with NlaIII overnight (NEB). After a second ligation step, DNA was purified before proceeding to library preparation.
ChIP library construction was performed with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Briefly, the steps include End Repair, dA-Tailing, Adaptor Ligation, ligation products purification and PCR process. 20 ng DNA was used for the starting material. For 4C–seq library preparation, eight hundred nanograms of 4C–seq template were amplified using two-step PCR reactions with inverse primers (PAGE-purified) and primers with Illumina adaptor sequences and a unique index for each condition. Libraries were purified with the QIAquick PCR Purification Kit (Qiagen), pooled and subjected to 150-bp single-end sequencing on the Illumina NextSeq2000 platform at the NCI/CCR Next Generation Sequencing Core Facility.


title: RIVA-BCL10-S136X-3

value: BCL10 S136X


title: CLL229


title: DIvA cell, IDH wt, 4-OHT, Knock down (si2), 4C-seq, DSB1, Rep 1

description: Library name: DSB1_wtplus_KD2_1


title: RNA-seq_H9-SRG_Clone2_PXGGYA_P5_R+G-


title: DIvA cell, IDH wt, TETCD4-OHT, over expression, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_wt_Qiaplus_2


title: RIVA-vector-3

value: BCL10 wild type


title: CLL231

value: European Ancestry (EA)


title: RIVA-BCL10-R58Q-3


title: CLL235


title: RIVA-vector-1


title: RNA-seq_H9-SRG_Clone1_PXGGYA_P5_R+G+


title: RIVA-BCL10-R58Q-1


title: DIvA cell, IDH wt, 4-OHT, Knock down (si1), 4C-seq, DSB1, Rep 1

description: Library name: DSB1_wtplus_KD1_1

value: DIvA cell


title: DIvA cell, IDH mutant, non treated, Knock down (si2), 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHminus_KD2_1

value: osteosarcoma tumor cells


title: P043, Pre-treatment, scRNA-seq

city: Beijing

first: Yuanyuan

last: Zhang

state: Beijing

address: Panjiayuan nanli #17, Chaoyang District

department: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description:
10x Genomics
P043.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

data_processing:
Demultiplexing, barcode processing, alignment, gene counting, and the generation of raw count matrix were performed by the Cell Ranger toolkit (version 3.1.0)
Assembly: GRCh38, mm10
Supplementary files format and content: Excel file, and matrix files enclosed in RDS

source_name: Chest wall

extract_protocol:
Tumor biopsy samples were first stored in RNAlater RNA stabilization reagent (QIAGEN) after collection and kept on ice to avoid RNA degradation. Samples were then collected in the RPMI-1640 medium (Gibco), and enzymatically digested with gentle MACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37 °C according to the manufacturer’s protocol. The dissociated cells were next passed through a 40-μm cell-strainer (BD) in the RPMI-1640 medium (Invitrogen) with 10% FBS until uniform cell suspensions were obtained. Subsequently, the suspended cells were passed through cell strainers and centrifuged at 400 g for 10 min. Red blood cells were removed via the same procedure described above. After washing twice with 1x PBS (Invitrogen), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 5’ Kit from 10x Genomics, following the manufacturer’s instructions; Bulk RNA-seq libraries were constructed in Sequanta Technologies Co., Ltd at Shanghai.

tag: patient

value: Chest wall

value: Immune cells

tag: group

value: Pre-treatment

value: Nab-paclitaxel plus Atezolizumab

tag: response

value: NR


title: CLL232

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)

value: IGHV Unmutated


title: P046, Pre-treatment, scRNA-seq

description:
10x Genomics
P046.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

source_name: Breast

value: Breast


title: RIVA-BCL10-S136X-1

value: RIVA

value: DLBCL


title: CLL228

source_name: Peripheral blood mononuclear cells


title: CLL227

value: IGHV Mutated


title: RIVA-BCL10-S136X-2

value: BCL10 S136X

value: 200ng/uL doxycycline


title: RIVA-vector-2

value: BCL10 wild type


title: DIvA cell, IDH wt, TETCD4-OHT, over expression, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_wt_Qiaplus_1

value: DIvA cell


title: P055, Pre-treatment, scRNA-seq

description:
10x Genomics
P055.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P055, Post-treatment, scRNA-seq

description:
10x Genomics
P055.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Post-treatment


title: P042, Post-treatment, scRNA-seq

description:
10x Genomics
P042.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P035, Pre-treatment, scRNA-seq

description:
10x Genomics
P035.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

source_name: Liver

value: Liver


title: CLL226

value: European Ancestry (EA)


title: DIvA cell, IDH mutant, non treated, empty vector, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHminus_EVminus_2

value: osteosarcoma tumor cells


title: DIvA cell, IDH mutant, non treated, Knock down (si2), 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHminus_KD2_2


title: P046, Post-treatment, scRNA-seq

description:
10x Genomics
P046.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Immune cells

value: Nab-paclitaxel plus Atezolizumab


title: P057, Post-treatment, scRNA-seq

description:
10x Genomics
P057.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: NR


title: CLL225

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)


title: CLL224


title: DIvA cell, IDH mutant, non treated, Knock down (si1), 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHminus_KD1_2


title: DIvA cell, IDH mutant, non treated, Knock down (si1), 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHminus_KD1_1


title: CLL223


title: CLL230


title: P042, Pre-treatment, scRNA-seq

description:
10x Genomics
P042.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Breast

value: Pre-treatment


title: P053, Post-treatment, scRNA-seq

description:
10x Genomics
P053.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P057, Pre-treatment, scRNA-seq

description:
10x Genomics
P057.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: CLL220


title: P053, Pre-treatment, scRNA-seq

description:
10x Genomics
P053.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: CLL221


title: DIvA cell, IDH mutant, non treated, TETdCD, over expression, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHminus_dCD_2


title: P047, Pre-treatment, scRNA-seq

description:
10x Genomics
P047.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

source_name: Lymph node

value: Lymph node


title: P047, Post-treatment, scRNA-seq

description:
10x Genomics
P047.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: CLL218

value: IGHV Unmutated


title: DIvA cell, IDH mutant, non treated, TETdCD, over expression, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHminus_dCD_1

source_name: DIvA cell


title: DIvA cell, IDH mutant, non treated, TETCD, over expression, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHminus_CD1_2


title: P056, Pre-treatment, scRNA-seq

description:
10x Genomics
P056.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: R


title: P052, Post-treatment, scRNA-seq

description:
10x Genomics
P052.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P052, Pre-treatment, scRNA-seq

description:
10x Genomics
P052.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P058, Pre-treatment, scRNA-seq

description:
10x Genomics
P058.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P058, Post-treatment, scRNA-seq

description:
10x Genomics
P058.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P062, Pre-treatment, scRNA-seq

description:
10x Genomics
P062.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: DIvA cell, IDH mutant, non treated, TETCD, over expression, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHminus_CD1_1


title: CLL222


title: DIvA cell, IDH mutant, non treated, empty vector, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHminus_EVminus_1


title: DIvA cell, IDH mutant, non treated, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHminus_2


title: CLL216


title: CLL217


title: DIvA cell, IDH mutant, non treated, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHminus_1


title: P049, Pre-treatment, scRNA-seq

description:
10x Genomics
P049.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: CLL215


title: P051, Post-treatment, scRNA-seq

description:
10x Genomics
P051.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: CLL219


title: P051, Pre-treatment, scRNA-seq

description:
10x Genomics
P051.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P045, Post-treatment, scRNA-seq

description:
10x Genomics
P045.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P045, Pre-treatment, scRNA-seq

description:
10x Genomics
P045.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: CLL214


title: DIvA cell, IDH mutant, TETdCD4-OHT, Knock down (si2), 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHplus_KD2_1


title: DIvA cell, IDH mutant, TETdCD4-OHT, Knock down (si2), 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHplus_KD2_2


title: CLL213


title: P056, Post-treatment, scRNA-seq

description:
10x Genomics
P056.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: DIvA cell, IDH mutant, TETdCD4-OHT, Knock down (si1), 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHplus_KD1_2


title: P054, Post-treatment, scRNA-seq

description:
10x Genomics
P054.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P060, Post-treatment, scRNA-seq

description:
10x Genomics
P060.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Chest wall

value: Nab-paclitaxel


title: P054, Pre-treatment, scRNA-seq

description:
10x Genomics
P054.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: DIvA cell, IDH mutant, TETdCD4-OHT, Knock down (si1), 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHplus_KD1_1

value: DIvA cell


title: P049, Post-treatment, scRNA-seq

description:
10x Genomics
P049.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Post-treatment


title: P060, Pre-treatment, scRNA-seq

description:
10x Genomics
P060.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

source_name: Chest walll

value: Chest walll


title: CLL211

value: European Ancestry (EA)

value: IGHV Mutated


title: P059, Post-treatment, scRNA-seq

description:
10x Genomics
P059.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Immune cells


title: P040-L, Post-treatment, scRNA-seq

description:
10x Genomics
P040-L.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: CLL209


title: P059, Pre-treatment, scRNA-seq

description:
10x Genomics
P059.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P061, Pre-treatment, scRNA-seq

description:
10x Genomics
P061.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: CLL210


title: CLL208


title: DIvA cell, IDH mutant, TETdCD4-OHT, empty vector, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHplus_EVminus_2

value: osteosarcoma tumor cells


title: DIvA cell, IDH mutant, TETdCD4-OHT, empty vector, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHplus_EVminus_1


title: P040, Pre-treatment, scRNA-seq

description:
10x Genomics
P040.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: NR


title: P040-L, Pre-treatment, scRNA-seq

description:
10x Genomics
P040-L.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: DIvA cell, IDH mutant, TETdCD4-OHT, over expression, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHplus_dCD_2


title: DIvA cell, IDH mutant, TETdCD4-OHT, over expression, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHplus_dCD_1


title: P040, Post-treatment, scRNA-seq

description:
10x Genomics
P040.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P044, Pre-treatment, scRNA-seq

description:
10x Genomics
P044.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: CLL212

value: Peripheral blood mononuclear cells


title: CLL206

value: Chronic Lymphocytic Leukemia (CLL)


title: P031, Pre-treatment, scRNA-seq

description:
10x Genomics
P031.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Breast


title: P034, Post-treatment, scRNA-seq

description:
10x Genomics
P034.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: DIvA cell, IDH mutant, TETCD4-OHT, over expression, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RH_CD_Qiaplus_2


title: P034, Pre-treatment, scRNA-seq

description:
10x Genomics
P034.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Pre-treatment


title: P039, Post-treatment, scRNA-seq

description:
10x Genomics
P039.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: DIvA cell, IDH mutant, 4-OHT, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RHplus_1


title: P032, Pre-treatment, scRNA-seq

description:
10x Genomics
P032.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Liver


title: CLL204

value: IGHV Unmutated


title: CLL205


title: CLL207


title: P039, Pre-treatment, scRNA-seq

description:
10x Genomics
P039.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: R


title: P041, Post-treatment, scRNA-seq

description:
10x Genomics
P041.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P041, Pre-treatment, scRNA-seq

description:
10x Genomics
P041.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: P037, Pre-treatment, scRNA-seq

description:
10x Genomics
P037.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds


title: shNAT10, IP, RIP 3

city: Wu Han

first: Gongcai

last: Tao

state: Hu Bei Province

address: No. 9, Zhangzhidong Road, Wuchang District

department: Department of Gastrointestinal Surgery

institute: Renmin Hospital of Wuhan University

data_processing:
Sample preparation and RNA library construction
Quality control and mapping
Transcript-level quantification, analysis of differential acetylation, cluster analysis, GO and KEGG enrichment of differential acetylation.(P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.)
Assembly: human genome (GRCh38)
Supplementary files format and content: Exctab-delimited bed files include MACS_peak for each Sample
Supplementary files format and content: Excel files include comprehensive information for all Samples
Library strategy: ac4CRIP-Seq

source_name: colorectal cancer

growth_protocol: SW620 cells were maintained in L15 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated using the TRIZOL reagent and subjected to multiple purification steps to obtain an RNA solution of suitable concentration and purity.
RNA libraries for ac4CRIP-seq were prepared using GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) following manufacturer's protocols.

value: colorectal cancer

value: colorectal cancer cells

value: NAT10 knockdown


title: CLL203

first: Jessica

last: Hohenstein

address: 200 1st St SW

institute: Mayo Clinic


title: shNAT10, IP, RIP 2


title: DIvA cell, IDH mutant, 4-OHT, 4C-seq, DSB1, Rep 2

description: Library name: DSB1_RHplus_2

value: DIvA cell


title: P038, Pre-treatment, scRNA-seq

description:
10x Genomics
P038.Pre
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Nab-paclitaxel


title: P037, Post-treatment, scRNA-seq

description:
10x Genomics
P037.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Post-treatment


title: ctrl3_NAWM9

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

data_processing:
All raw fastq files were processed with the Nanostring GeoMxNGSPipeline v2.3.3.10, and counts per gene were exported as Nanostring DCC files per sample.
Assembly: hg38
Supplementary files format and content: Nanostring GeoMx DCC files with read counts per gene
Library strategy: Spatial Transcriptomics

source_name: Brain, MS Autopsie

extract_protocol:
5µm thick sections were cut under RNase free codtions and processed according to the GeoMx RNA FFPE workflow (MAN-10150-02) with 10min antigen retrival at 100°C and 15min Proteinase K (0.1µg/ml in PBS) at 37°C for RNA Target exposure.
Spatial Transcriptomics libararys were prepared according to GeoMx DSP workflow (MAN-10153-02)

value: Brain, MS Autopsie

value: CD68 positive

tag: location

value: NAWM


title: CLL201

city: Rochester

value: European Ancestry (EA)


title: ctrl3_NAWM8


title: ctrl3_NAWM7


title: P038, Post-treatment, scRNA-seq

description:
10x Genomics
P038.Post
CD8T.counts.rds
CD4T.counts.rds
Bcell.counts.rds
NK.counts.rds
Myeloid.counts.rds

value: Immune cells


title: CLL202

value: Peripheral blood mononuclear cells

value: Chronic Lymphocytic Leukemia (CLL)


title: shControl, IP, RIP 3

value: WT


title: ctrl3_NAWM6


title: CLL200


title: shNAT10, IP, RIP 1


title: CLL199


title: DIvA cell, IDH mutant, TETCD4-OHT, over expression, 4C-seq, DSB1, Rep 1

description: Library name: DSB1_RH_CD_Qiaplus_1

value: osteosarcoma tumor cells


title: shControl, IP, RIP 2


title: ctrl3_NAWM5


title: CLL198

value: IGHV Unmutated


title: ctrl3_NAWM4


title: shNAT10, Input, RIP 2


title: CLL197

value: IGHV Mutated


title: shNAT10, Input, RIP 3

value: colorectal cancer


title: shNAT10, Input, RIP 1

value: colorectal cancer cells


title: ctrl3_NAWM3


title: shControl, Input, RIP 2


title: shControl, Input, RIP 1