title: G450_CTCF

city: Göttingen

first: Argyris

last: Papantonis

state: Goettingen

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

data_processing:
Read pairs were aligned to the human reference genome GRCh38 using Bowtie2 (v2.3.4.1),PCR duplicates were removed using the MarkDuplicates function in Picard tools (v2.20.7),
Read coverage tracks (BigWig) were generated and normalized with the RPCG parameter using the bamCoverage function of deepTools2 (v3.5.1)
Peaks were called using SEACR (1.3) with an FDR cutoff of <0.01.
Assembly: GRCh38
Supplementary files format and content: *_RPGC.bw refers the bigwig track for each sample nornalizing with “RPGC” method in Deeptools
Supplementary files format and content: *_seacr_top0.01.peaks.stringent.bed refers peaks were called using SEACR (1.3) with an FDR cutoff of <0.01. Description of output fields: can be found here:https://github.com/FredHutch/SEACR.
Library strategy: CUT&Tag

source_name: glioblastoma stem-like cells

extract_protocol:
GSCs were lifted from plates using accutase (Sigma-Aldrich). Typically, 0.5 million cells were processed using the CUT&Tag-IT kit (Active Motif) as per manufacturer’s instructions.
CUT&Tag-IT kit (Active Motif) as per manufacturer’s instructions.

value: glioblastoma stem-like cells

tag: assay

value: CUT&TAG

tag: antibody

value: CTCF


title: Brain, water, db/db, rep1

status: Public on Mar 18 2024

type: SRA

city: seoul

first: sungguan

last: hong

address: 84, Heukseok-ro, Dongjak-gu, Seoul, 104-407

department: Chemistry

country: South Korea

institute: Chung-Ang

library_source: transcriptomic

data_processing:
Raw sequencing data were processed using Illumina bcl2fastq conversion tool to generate FASTQ files
Sequences were aligned to GRCm39 genome to gene expression count using New Tuxedo Protocol's default settings
Gene expression level of Refseq coding genes were quantified using Ballgown tool which inspect the distribution of abundance estimates.
Assembly: GRCm39
Supplementary files format and content: gene_expression_fpkm.txt

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Total RNA was isolated from tissue samples using the TRIzolTM Reagent. 1 mL of the reagent and a stainless-steel bead were added to the tissue samples, and tissues were fully homogenized by the TissueLyser LT homogenizer.
1000 ng of total RNA was processed to mRNA enrichment using NEBNext Poly(A) mRNA magnetic isolation module (New England BioLabs, MA, USA) and followed by fragmentation, cDNA synthesis, and library preparation with unique dual index using NEBNext Ultra II RNA library prep kit (New England BioLabs) according to the manufacturer’s manual.

tag: tissue

value: Brain

tag: Sex

value: Male

tag: strain

tag: genotype

value: db/+

tag: treatment

value: 16 weeks


title: Orc1_rep18

city: Somerville

first: Michal

last: Chappleboim

state: MA

address: 73A Bartlett

department: Systems Biology

country: USA

institute: Harvard Medical School

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1∆ ORC1_N'-3xFlag-MNase
ChEC-seq

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: be
Library strategy: ChEC-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Overnight cultures from fresh colonies were diluted (>1:10000) and grown to exponential growth in YPD medium
ChEC-Seq protocol as described in Zentner et al. MNase-seq modified from Yaakov et al. 2021
ChEC-seq: phenol chloroform
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

tag: background

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase


title: G351_CTCF

country: Germany

organism: Homo sapiens

tag: cell type


title: rDP4

type: RNA

city: New York

first: Ibrahim

last: Batal

state: NY

address: 630 W 168th street

department: Pathology & cell Biology

institute: Columbia University

description: Allograft GD control

hyb_protocol: 100 ng of isolated RNA was hybridized to the 770 genes PanCancer Immune Profiling Panel (NanoString Technologies) for 20 h at 65 °C according to the manufacturer’s instructions

scan_protocol: Digital counting was used to determine gene expression using the maximum 555 fields of

data_processing:
nSolver Analysis Software (version 4.0), including the nCounter Advanced Analysis (version 2.0), which uses the geNorm algorithm to normalize the data.
nSolver Analysis 4.0 Normalized count

label: Biotin

source_name: Allograft kidney biopsy

label_protocol: Genes of interest is detected by a pair of reporter probe (contains unique color code at the 5ʹend form molecular barcoding) and capture probe (contains 35 to 50 base pairs of target gene specific sequences). The capture probes are all biotin labeled at the 3ʹendfor the attachment of the genes of interest during digital detection.

extract_protocol: 10 μm x10 FFPE curls were sectioned from each biopsy. Total RNA was isolated from sectioned material using miRNeasy FFPE Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions and quantified by NanoDrop (Thermo Scientific, Wilmington, DE), Bioanalyzer 2100 (Agilent, Santa Clara, CA), and Qubit RNA BR (Thermo Fisher Scientific, Waltham, MA).

tag: age

value: Female


title: rDP5

description: Allograft GD control


title: G275_CTCF


title: Brain, sucrose, db/db, rep1


title: G394_CTCF


title: de novo IgAN1

description: Allograft GD control


title: Brain, brazzein, db/db, rep2


title: Orc1_rep16


title: Orc1_Orc1synCopy_rep1

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase


title: Orc1_rep17


title: G452P_CTCF


title: G450_H3K27ac


title: rIgAN3

description: Allograft GD control


title: Orc1_rep15


title: Brain, brazzein, db/db, rep1


title: G148_H3K27ac


title: Brain, water, db/+, rep2


title: G394_H3K27ac


title: Orc1_rep14


title: Orc1_rep19


title: Brain, sucrose, db/db, rep2


title: rIgAN4

description: Allograft GD control


title: G452C_H3K27ac


title: rC3GN1

description: Allograft rC3G


title: de novo MN4

description: Allograft GD control


title: de novo IgAN3

description: Allograft GD control


title: G412_H3K27ac


title: Orc1_rep12


title: rDP3

description: Allograft GD control


title: Brain, sucrose, db/+, rep1


title: G402_H3K27ac


title: Orc1_rep11


title: Brain, brazzein, db/+, rep2


title: de novo ICMGD NOS1

description: Allograft GD control


title: rC3GN11

description: Allograft rC3G


title: G402R_H3K27ac


title: rIgAN1

description: Allograft GD control


title: Brain, brazzein, db/+, rep1


title: Orc1_rep9


title: Orc1_rep10


title: Orc1_rep8


title: Brain, water, db/+, rep1


title: Orc1_rep13


title: de novo IgAN2

description: Allograft GD control


title: G275R_H3K27ac


title: rC3GN4

description: Allograft rC3G


title: G412R_H3K27ac


title: G275_H3K27ac


title: Orc1_rep7


title: Brain, sucrose, db/+, rep2


title: B16F10 tumor, rev day 10, replicate 2, bulkRNAseq

city: Philadelphia

first: Dennis

last: Discher

state: PA

address: 129 Towne Building

institute: University of Pennsylvania

description: CTTGTA

data_processing:
The reads were aligned to mouse reference, mm10 (GENCODE vM23/Ensembl 98) using star alignment.
Assembly: mm10
Supplementary files format and content: counts.txt files

extract_protocol:
Prior to tumor inoculation, B16F10 CD47 KO cells were treated with 2.5 μM MPS1i (reversine) or the equivalent volume of DMSO vehicle control. Cells were treated for 24 h, after which they were washed twice with PBS and allowed to recover for an additional 48 h. After the recovery period elapsed, all mice were subcutaneously injected with 5x105 B16F10 cells. Five or ten days after tumor inoculation, mice were euthanized, and tumors were excised and disaggregated for bulk RNA-sequencing.
RNA library was constructed using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina (E7770S, E7335) per the manufacturer’s instructions.

value: female

tag: cell line

value: CD47 KO

value: reversine


title: B16F10 tumor, rev day 5, replicate 2, bulkRNAseq

description: TAGCTT


title: Orc1_rep6


title: rHCV-GD1

description: Allograft GD control


title: B16F10 tumor, rev day 10, replicate 1, bulkRNAseq

description: GGCTAC


title: Orc1_rep5


title: B16F10 tumor, rev day 5, replicate 1, bulkRNAseq

description: GATCAG


title: rC3GN5

description: Allograft rC3G


title: B16F10 tumor, DMSO day 5, replicate 2, bulkRNAseq

description: CGATGT

value: DMSO


title: Reb1_rep1_seq2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 REB1-3xFlag-MNase::KanMX6
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 REB1-3xFlag-MNase::KanMX6


title: mLNs from KO mice, biological rep2

city: Shanghai

first: Zhaohua

last: Cai

state: Shanghai

address: 241 West Huaihai Road

country: China

institute: Shanghai Chest Hospital: Shanghai Jiao Tong University Affiliated Chest Hospital

description: Gene expression data from mLNs of KOmice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: mesenteric lymph node tissue from KO mice-2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: VE-cadherin-Cre mice were intercrossed with Fbw7flox/flox mice to generate Fbw7flox/flox;VE-cadherin-Cre mice.

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

treatment_protocol: Fbw7 KO mice spontaneously developed lymphoma.

value: lymphoma tissue


title: B16F10 tumor, DMSO day 5, replicate 1, bulkRNAseq

description: ATCACG


title: rDP1

description: Allograft GD control


title: rDDD6

description: Allograft rC3G


title: BMDM, B16 rev supernatant, scRNAseq

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (version 5.0.1) to generate FASTQ files, and the “count” command was used to generate raw count matrices aligned to mm10 (GENCODE vM23/Ensembl 98).
Assembly: mm10
Supplementary files format and content: tar of h5 files
Supplementary files format and content: provided as supplementary file

source_name: bone marrow

extract_protocol:
BMDMs that had successfully undergone 7 days of differentiation in 20 ng/mL M-CSF were used. Spent media was removed, BMDMs were gently washed once with phosphate-buffered saline (PBS), and fresh IMDM supplemented 10% FBS, 1% P/S, and 20 ng/mL M-CSF was added. Then, conditioned media from B16F10 cells treated with either MPS1i or DMSO was collected. Conditioned media was centrifuged for 5 min at 300 x g to remove any cellular debris. The supernatant was collected and then supplemented to 5% FBS, 1% P/S, and 20 ng/mL M-CSF. One whole volume of conditioned media was added to BMDMs with fresh media. 24 h after treatment, BMDMs were detached using 0.05% Trypsin and processed for single-cell RNA-sequencing.
RNA libraries were prepared using the 10X Genomics Chromium Single Cell Gene Expression kit (v3.1, single index, PN-1000128; PN-1000127; PN-1000213) per the manufacturer’s instructions.

value: bone marrow

value: M-CSF macrophage differentiation


title: Orc4_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 ORC4-N'-3xFlag-MNase
ChEC-seq

value: N-SWAT strain from Yofe et al.[1]

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 ORC4-N'-3xFlag-MNase


title: mLNs from KO mice, biological rep1

source_name: mesenteric lymph node tissue from KO mice-1


title: MN14

description: GD controls

source_name: native kidney biopsy


title: BMDM, control, scRNAseq

description: 10X Genomics


title: mLNs from WT mice, biological rep3

description: Gene expression data from mLNs of WT mice

source_name: mesenteric lymph node tissue from WT mice-3

value: normal lymph node


title: Orc2_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 ORC2-N'-3xFlag-MNase
ChEC-seq

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 ORC2-N'-3xFlag-MNase


title: HMPV, replicate 2, scRNAseq

city: Pittsburgh

first: John

last: Williams

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh School of Medicine

description: 10X Genomics

data_processing:
Sequencing outputs were processed with Cellranger.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
To ensure representation of both epithelial and hematopoietic lineage cells for each mouse sample, both right and left lungs  were inflated with a lower volume (0.25mL) dispase with agarose plug followed by digestion and processing into single cell  suspension as described above. Cells were next washed 5 times with 5-10mL of PBS+10%FBS and centrifuged at 500xg for  5’, followed by a final wash and centrifugation at 200xg for 10’ to remove debris. Dead cells were removed by magnetic  separation using Annexin V kit (STEMCELL Technologies).
Using the 10X Genomics 3’ CellPlex Kit, cells from each mouse sample were tagged using lipid-conjugated Barcode  oligonucleotides according to manufacturer’s instructions. Cells were passed through a 40-μM filter and cell viability was  determined using Cellometer 2000 (all showed >90% viability) prior to loading on 10X Chromium instrument. Following  established techniques using Chromium Single Cell 3’ Library V2 kit (10X), libraries were constructed and RNA-seq was  performed on each sample targeting 20,000 reads per cell.

value: Lung

value: 6-7 weeks old

value: C2-202 HMPV (5E5 PFU) intratracheally


title: Orc4_rep1


title: C3GN11

value: Female


title: mLNs from WT mice, biological rep1

source_name: mesenteric lymph node tissue from WT mice-1


title: IgAN15

description: GD controls

value: Male


title: Orc2_rep1


title: Orc1_rep4, seq2

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1::ORC1-synCopy ORC1-N'-3xFlag-MNase


title: mLNs from WT mice, biological rep2

source_name: mesenteric lymph node tissue from WT mice-2


title: Mock, replicate 2, scRNAseq

description: 10X Genomics

value: Mock lysate intratracheally


title: MN13

description: GD controls


title: HTGTS_Chr8_61Mb_DMSO_replicate_1_PW103

city: Heidelberg

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

institute: German Cancer Research Center

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_1; Bait Chr8_61Mb; Barcode T

data_processing:
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
GRO-seq: a sigularity pacakge https://github.com/brainbreaks/GROseq
DRIP-seq: Illumina adaptor sequences were trimed by trip-glaore, and the sequences were aligned with Bowtie2. same files were sorted, marjedup, and DRIP signal enrichment were determined by MACS2 callpeak (parameter: --nomodel --slocal 1000000 --llocal 10000000 --extsize 100000)
Assembly: mm10
Supplementary files format and content: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Bedgraph: display of continuous-valued data in track format
Library strategy: LAM-HTGTS

source_name: ESC-NPC

growth_protocol: The Xrcc4/p53-deficient mouse embryonic stem cells were cultured in DMEM medium supplemented with 15% ESC-grade fetal bovine serum, 20mM HEPES, non-essential amino acids, 100 U/ml Pen/Strep and glutamine mixture, 0.1mM beta-mercaptoethanol and 1000 U/mL ESGRO recombinant mouse leukemia inhibitory factor (LIF) on a monolayer of confluent irradiated mouse fibroblasts. The CAST x 129 hybrid mouse ES cells were cultured in 2i medium (50% DMEM/F12, 50% NeuralBasal, 0.5X N2 supplement, 0.5X B27 supplement, BSA, 10 mM PD03259010, 10 mM CHIR99021, 200 mM Glutamine, 11.9M Monothioglycerol, and 1x10^6 U/ml LIF). To induce mouse neural progenitor cells, Xrcc4/p53-deficient mouse ES cells were plated on laminine/poly-L-ornithine-coated plates and cultured in N2B27 medium (50% DMEM/F12, 50% NeuralBasal, 1% modified N2 supplement, 2% B27 supplement without RA, 1X Glutamax) for seven days. Cells were then passaged to laminin-coated plates and culture in NBBG medium (NeralBasalA, 2% B27 supplement without RA, 0.5 mM Glutamax, 10ng/ml human EGF, 10ng/ml mouse FGFb) for another five to six days. Neural progenitor cells were then collected for nucleofection, DRIP-seq, or Repli-seq experiments.

extract_protocol:
Genomic DNA for HTGTS: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. RNA were removed by treating samples with RNAseA prior phenol/chlroform extraction. Genomic DNA for DRIP-seq: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. Nascent RNA for GRO-seq: nuclei were lysed in TriZol reagents. RNA were extraced as manufacture instruction.
We follow the published protocol, as indicated below, to construct the libraries. DRIP-seq: https://www.nature.com/articles/s41596-019-0159-1 GRO-seq:https://www.sciencedirect.com/science/article/pii/S0092867415017031?via%3Dihub HTGTS: https://www.nature.com/articles/nprot.2016.043

treatment_protocol: Cells were treated with indicated concentration of aphidicolin or the veichle control DMSO for the indicated period.

value: ESC-NPC

value: Neural progenitor cells


title: rDP2

description: Allograft GD control


title: HTGTS_Chr8_61Mb_DMSO_replicate_2_PW115

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_2; Bait Chr8_61Mb; Barcode


title: HMPV, replicate 1, scRNAseq

description: 10X Genomics


title: Orc1_rep4


title: DP7

description: GD controls


title: Mock, replicate 1, scRNAseq

description: 10X Genomics


title: Reb1_rep1

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 REB1-3xFlag-MNase::KanMX6


title: IgAN14

description: GD controls


title: iWAT, estrogen treated group , Cold 7days, rep2

city: Chicago

first: Jooman

last: Park

state: IL

address: 909 S Wolcott Ave COMRB 1120

department: Dept. of Physiology and Biophysics

institute: University of Illinois at Chicago

data_processing:
Data Quality Control: filtering reads containing adapter or with low quality: Pastp
Mapping Reads to Reference Genome : HISAT2
Gene Expression Quantification : Feature Counts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: inguinal white adipose tissue

extract_protocol:
RNA was harvested using Trizol kit (Ambion). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene company (China).

value: inguinal white adipose tissue

value: Estrogen upon cold exposure


title: Orc1_rep3, seq2

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 bar1delta ORC1_N'-3xFlag-MNase


title: HTGTS_Chr8_61Mb_APH06_replicate_2_PW118

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_2; Bait Chr8_61Mb; Barcode GCG


title: IgAN13

description: GD controls


title: iWAT, estrogen treated group , Cold 7days, rep3


title: HTGTS_Chr8_61Mb_APH06_replicate_3_PW122

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_3; Bait Chr8_61Mb; Barcode TCA


title: Orc1_rep3


title: mLNs from KO mice, biological rep3

source_name: mesenteric lymph node tissue from KO mice-3

value: lymphoma tissue


title: Orc1_rep2

description:
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 ORC1-N'-3xFlag-MNase
ChEC-seq

value: N-SWAT strain from Yofe et al.[1]

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 ORC1-N'-3xFlag-MNase


title: HTGTS_Chr8_61Mb_APH06_replicate_1_PW106

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_1; Bait Chr8_61Mb; Barcode TAGT


title: iWAT, estrogen treated group , Cold 7days, rep1


title: IgAN12

description: GD controls


title: HTGTS_Chr8_61Mb_APH04_replicate_3_PW121

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_3; Bait Chr8_61Mb; Barcode AGT


title: iWAT, vehicle treated group , Cold 7days, rep3

value: Vehicle upon cold exposure


title: Orc1_rep1


title: C3GN9


title: iWAT, vehicle treated group , Cold 7days, rep2


title: HTGTS_Chr8_61Mb_APH04_replicate_2_PW117

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_2; Bait Chr8_61Mb; Barcode TA


title: IgAN11

description: GD controls


title: iWAT, vehicle treated group , Cold 7days, rep1


title: HTGTS_Chr8_61Mb_APH04_replicate_1_PW105

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_1; Bait Chr8_61Mb; Barcode GCG


title: HTGTS_Chr8_61Mb_DMSO_replicate_3_PW119

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_3; Bait Chr8_61Mb; Barcode TAGT


title: HTGTS_Chr8_61Mb_APH03_replicate_3_PW156_PW159

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_3; Bait Chr8_61Mb; Barcode T


title: DP6

description: GD controls


title: TBI animal S4, day 15

city: Leuven

first: Araks

last: Martirosyan

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

description: 10x Genomics v3

data_processing:
Data were demultiplexed, mapped and counted using a standard CellRanger 3.0.2 workflow making use of the UCSC mouse genome GRCm38/mm10 assembly and refdata-cellranger-mm10-3.0.0
Splice counts for velocyto analysis have been generated using standard velocyto --run10x pipeline using refdata-cellranger-mm10-3.0.0 reference genome
Assembly: mm10
Supplementary files format and content: tab-delimited text files include UMI counts for each Sample

source_name: Nestin-GFP

growth_protocol: All mice were bred in house and housed in groups of 3-4 animals per cage throughout the experiment under a 12-h light/dark cycle (lights on at 08.00AM) in a temperature and humidity-controlled room (21°C, 50%) with ad libitum access to food and water. All animal procedures were approved by the commission for Animal Welfare at the University of Amsterdam (CCD 4925) and/or VIB-KU Leuven (082/2018) and were performed according to the guidelines and regulations of the European Union for the use of animals for scientific purposes.

extract_protocol:
A single cell suspension was made from the micro-dissected dentate gyri using a neural tissue 562 dissociation kit (Miltenyi Biotech), according to the manufacturer’s protocol.
Library preparations for scRNA-seq were performed using a 10X Genomics Chromium Single Cell 3’ Kit, v3 (10X Genomics, Pleasanton, CA, USA).

treatment_protocol:
We studied sham craniotomized mice (Control) and mice subjected to unilateral controlled cortical impact (TBI) 15 days post-surgery.
To induce TBI, mice were placed in a stereotaxic frame and anesthetized using 2% isoflurane throughout the surgery. A craniotomy was performed, creating a window along the skull sutures from bregma to lambda over the left hemisphere. The impact piston was placed at an approximately 20-degree angle directly on the brain surface and an impact was performed using the following settings: 1 mm impact depth, 5.50 m/s velocity, dwell time 300 ms. After the impact, the skull bone was placed back and glued in place using Superglue. The skin was stitched to close the wound and animals were allowed to recover on a 37°C heat pad until fully awake.

value: 8 weeks

value: Nestin-GFP

value: TBI

tag: time

value: Day 15 post surgery


title: HTGTS_Chr8_61Mb_APH03_replicate_2_PW141

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_2; Bait Chr8_61Mb; Barcode T


title: TBI animal S3, day 15

description: 10x Genomics v3


title: C3GN8

value: Male


title: HTGTS_Chr8_61Mb_APH03_replicate_1_PW140

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_1; Bait Chr8_61Mb; Barcode


title: MN12

description: GD controls

value: Female


title: CTRL 3 (sample 1605)

city: Zürich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: D-HEST

country: Switzerland

institute: ETH Zürich

data_processing:
Reads were mapped to the GRCm39 genome with STAR 2.7.8a using the GENCODE M26 annotation as reference and quantified at the gene-level using featureCounts 1.6.4.
Genes were filtered using edgeR’s filterByExpr function before differential expression analysis with edgeR 3.32.1 using likelihood ratio tests with 3 surrogate variables estimated using sva 3.38.0.
Assembly: GRCm39
Supplementary files format and content: Matrix of reads counts per gene / sample.

source_name: hippocampus

growth_protocol: Mice were housed collectively in cages designed for 2 to 4 individuals, with unrestricted access to food and water. The animal facility maintained an inverted light-dark cycle of 12 hours.

extract_protocol:
Hippocampi were dissected and snap-frozen. RNA extraction was conducted with Trizol (Thermo Fisher) protocol and DNase treated.
TruSeq mRNA protocol

treatment_protocol: Mice underwent stereotactic injection in dorsal and ventral hippocampus.

value: hippocampus

tag: developmental stage

value: male

value: CTRL


title: CTRL 4 (sample 1620)


title: Hairpint 4 (sample 1607)

value: miR-708-5p overexpression


title: HTGTS_Chr8_61Mb_APH02_replicate_3_PW120

description: ESC-NPC; NXP010; Aphidicolin 0.2 uM 96h; LAM-HTGTS; replicate_3; Bait Chr8_61Mb; Barcode CATG

value: ESC-NPC

value: Neural progenitor cells


title: Hairpin 3 (sample 1604)


title: TBI animal S1, day 15

description: 10x Genomics v3


title: C3GN10


title: HTGTS_Chr8_61Mb_APH02_replicate_2_PW116

description: ESC-NPC; NXP010; Aphidicolin 0.2 uM 96h; LAM-HTGTS; replicate_2; Bait Chr8_61Mb; Barcode T


title: Hairpin 2 (sample 1603)


title: GROseq_NXP047_NXP047_Nrxn1_replicate_1_PW005

description:
Xrcc4-/-::p53-/-; ESC-NPC; NXP047; parental cell; a/b allels present (); replicate_1
nascent RNA

data_processing:
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
GRO-seq: a sigularity pacakge https://github.com/brainbreaks/GROseq
DRIP-seq: Illumina adaptor sequences were trimed by trip-glaore, and the sequences were aligned with Bowtie2. same files were sorted, marjedup, and DRIP signal enrichment were determined by MACS2 callpeak (parameter: --nomodel --slocal 1000000 --llocal 10000000 --extsize 100000)
Assembly: mm10
Supplementary files format and content: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Bedgraph: display of continuous-valued data in track format
Library strategy: GRO-seq


title: Sham animal S4, day 15

description: 10x Genomics v3

value: Sham


title: IgAN10

description: GD controls


title: MN11

description: GD controls


title: Hairpin 1 (sample 1602)


title: HTGTS_Chr8_61Mb_APH02_replicate_1_PW104

description: ESC-NPC; NXP010; Aphidicolin 0.2 uM 96h; LAM-HTGTS; replicate_1; Bait Chr8_61Mb; Barcode TA


title: CTRL 2 (sample 1601)


title: GROseq_NXP047_NXP047_Nrxn1_replicate_2_PW006

description:
Xrcc4-/-::p53-/-; ESC-NPC; NXP047; parental cell; a/b allels present (); replicate_2
nascent RNA


title: HTGTS_Chr6_70Mb_DMSO_replicate_9_PW111

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_9; Bait Chr6_70Mb; Barcode CGATT


title: Sham animal S3, day 15

description: 10x Genomics v3


title: DDD7


title: C3GN7


title: HTGTS_Chr6_70Mb_DMSO_replicate_8_PW107

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_8; Bait Chr6_70Mb; Barcode T


title: DP5

description: GD controls


title: TBI animal S2, day 15

description: 10x Genomics v3


title: Sham animal S2, day 15

description: 10x Genomics v3


title: PerC, B2, KO, 4

city: Charlottesville

first: Coleen

middle: A.

last: McNamara

state: VA

address: 345 Crispell Dr

department: Carter Immunology Center

institute: University of Virginia

data_processing:
The quality trimming was performed using fastp with default settings.
Mapping to the GRCm39 genome was performed with STAR
featureCounts was used to count reads mapped to genes.
Assembly: GRCm39, gencode.vM32
Supplementary files format and content: *_counts.txt contains raw counts data for the specified sample.
Supplementary files format and content: Aligned.sortedByCoord.out.bam containes reads aligned to reference in BAM format

source_name: Peritoneal cavity

extract_protocol:
Sort-purified peritoneal B-1a, B-1b, and B-2 cells obtained fromTET2KO andTET2WT C57BL/6 mice were RNA and DNA extracted by using the Qiagen AllPrep kit. The purified RNAs were stored at −80 °C and sent to Novogene to perform ultra-low input bulk RNA sequencing.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.  For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Peritoneal cavity

value: B cell

tag: cell subtype


title: DP4

description: GD controls


title: HTGTS_Chr6_70Mb_DMSO_replicate_7_VI059

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_7; Bait Chr6_70Mb; Barcode CATG

value: Xrcc4-/-::p53-/-,NXP010,Perental cell


title: CCL218_T3_Control_Rp2

city: Charleston

first: Joe

middle: R

last: Delaney

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description: three pulse-chases, replicate 2

data_processing:
Code and reference sgRNA data used to count sgRNAs in NGS data are available under https://github.com/jrdelaney/Published_Code/.
Supplementary files format and content: sgRNA count table by target genes and samples
Library strategy: AMPLICON

source_name: colorectal cancer

growth_protocol: A Brunello CRISPR-Cas9 library screen was performed with OVCAR3 and CCL218 cells in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After each pulse-chase, a pool of cells were collected for sgRNA quantitation. Three pulse chases were performed.

extract_protocol:
Invitrogen PureLink Genomic DNA Mini Kit
Cell pellets were processed for genomic DNA and sgRNA sequences amplified by PCR for NGS-based quantitation.

value: colorectal cancer

value: control


title: PerC, B2, KO, 3


title: IgAN9

description: GD controls


title: CCL218_T3_HCQ_Rp2

description: three pulse-chases, replicate 2

value: HCQ


title: HTGTS_Chr6_70Mb_DMSO_replicate_5_VI047

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_5; Bait Chr6_70Mb; Barcode CTGAC


title: PerC, B1a, KO, 4


title: CCL218_T3_HCQ_Rp1

description: three pulse-chases, replicate 1


title: IgAN8

description: GD controls


title: MN10

description: GD controls


title: PerC, B1a, KO, 3


title: HTGTS_Chr6_70Mb_DMSO_replicate_4_VI020

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_4; Bait Chr6_70Mb; Barcode


title: PerC, B1b, KO, 3


title: CTRL 1 (sample 1600)


title: CCL218_T2_Control_Rp1

description: two pulse-chases, replicate 1


title: HTGTS_Chr6_70Mb_DMSO_replicate_1_PW090

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_1; Bait Chr6_70Mb; Barcode T


title: HTGTS_Chr6_70Mb_DMSO_replicate_3_PW055

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_3; Bait Chr6_70Mb; Barcode T


title: Sham animal S1, day 15

description: 10x Genomics v3

value: 8 weeks

value: Nestin-GFP


title: CCL218_T3_Control_Rp1

description: three pulse-chases, replicate 1


title: DP3

description: GD controls

value: Male


title: CCL218_T2_Control_Rp2

description: two pulse-chases, replicate 2


title: MN8

description: GD controls


title: CCL218_T2_HCQ_Rp2

description: two pulse-chases, replicate 2


title: MN9

description: GD controls


title: HTGTS_Chr6_70Mb_APH06_replicate_3_PW114

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_3; Bait Chr6_70Mb; Barcode GTCAA


title: HTGTS_Chr6_70Mb_DMSO_replicate_2_LC0024

description: ESC-NPC; Nxp010; DMSO; LAM-HTGTS; replicate_2; Bait Chr6_70Mb; Barcode ATCGT


title: HTGTS_Chr6_70Mb_DMSO_replicate_6_VI053

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_6; Bait Chr6_70Mb; Barcode CTGAC


title: PerC, B2, KO, 1


title: PerC, B2, KO, 2


title: HTGTS_Chr6_70Mb_APH06_replicate_1_PW093

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_1; Bait Chr6_70Mb; Barcode TAGT


title: HTGTS_Chr6_70Mb_APH06_replicate_2_PW110

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_2; Bait Chr6_70Mb; Barcode TAGT


title: DP2

description: GD controls

value: Female


title: PerC, B1b, KO, 1


title: CCL218_T1_Control_Rp2

description: one pulse-chase, replicate 2


title: DP1

description: GD controls


title: PerC, B1b, KO, 2


title: HTGTS_Chr6_70Mb_APH05_replicate_8_VI060

description: ESC-NPC; NXP010; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_8; Bait Chr6_70Mb; Barcode CGATT


title: CCL218_T1_Control_Rp1

description: one pulse-chase, replicate 1


title: DDD6


title: HTGTS_Chr6_70Mb_APH05_replicate_7_VI054

description: ESC-NPC; NXP010; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_7; Bait Chr6_70Mb; Barcode CATGC


title: CCL218_T1_HCQ_Rp2

description: one pulse-chase, replicate 2


title: PerC, B1a, KO, 1


title: PerC, B2, WT, 4

value: WT


title: IgAN7

description: GD controls


title: IgAN6

description: GD controls


title: CCL218_T1_HCQ_Rp1

description: one pulse-chase, replicate 1


title: PerC, B1a, KO, 2


title: CCL218_T2_HCQ_Rp1

description: two pulse-chases, replicate 1


title: HTGTS_Chr6_70Mb_APH05_replicate_6_VI048

description: ESC-NPC; NXP010; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_6; Bait Chr6_70Mb; Barcode CATGC


title: IgAN5

description: GD controls


title: HTGTS_Chr6_70Mb_APH05_replicate_5_VI036

description: ESC-NPC; NXP010; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_5; Bait Chr6_70Mb; Barcode TG


title: CCL218_T0_Rp7

description: time zero, replicate 7


title: PerC, B1a, WT, 4


title: DDD5


title: HTGTS_Chr6_70Mb_APH05_replicate_4_VI028

description: ESC-NPC; NXP010; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_4; Bait Chr6_70Mb; Barcode AGT


title: PerC, B1b, WT, 3


title: CCL218_T0_Rp6

description: time zero, replicate 6


title: DDD4


title: HTGTS_Chr6_70Mb_APH05_replicate_3_VI021

description: ESC-NPC; NXP010; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_3; Bait Chr6_70Mb; Barcode A


title: CCL218_T0_Rp5

description: time zero, replicate 5


title: DDD3


title: PerC, B1b, WT, 2


title: CCL218_T0_Rp4

description: time zero, replicate 4


title: HTGTS_Chr6_70Mb_APH04_replicate_3_PW113

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_3; Bait Chr6_70Mb; Barcode CATGC


title: C3GN6


title: MN7

description: GD controls


title: PerC, B1a, WT, 2


title: CCL218_T0_Rp2

description: time zero, replicate 2


title: CCL218_T0_Rp3

description: time zero, replicate 3


title: PerC, B1a, WT, 3


title: DDD1


title: PerC, B1b, WT, 1


title: PerC, B2, WT, 1


title: HTGTS_Chr6_70Mb_APH05_replicate_1_PW056

description: ESC-NPC; NXP010; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_1; Bait Chr6_70Mb; Barcode TA


title: HTGTS_Chr6_70Mb_APH04_replicate_1_PW091

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_1; Bait Chr6_70Mb; Barcode TA


title: HTGTS_Chr6_70Mb_APH04_replicate_2_PW109

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_2; Bait Chr6_70Mb; Barcode GCG


title: PerC, B1b, WT, 4


title: CCL218_T0_Rp1

description: time zero, replicate 1


title: DDD2


title: CCL218_T0_Rp8

description: time zero, replicate 8


title: PerC, B1a, WT, 1


title: C3GN5


title: Repliseq-aph-G1

data_processing:
DRIPc-seq: Illumina adaptor sequences were trimed by trip-glaore, and the sequences were aligned with Bowtie2. same files were sorted, marjedup, and DRIP signal enrichment were determined by MACS2 callpeak (parameter: --nomodel --slocal 1000000 --llocal 10000000 --extsize 100000)
Hi-resolution repli-seq: a sigularity package https://github.com/brainbreaks/HighRes_RepliSeq
Assembly: mm10
Supplementary files format and content: bedgraph and bw: display of continuous-valued data in track format
Library strategy: Repli-seq

source_name: neural progenitor cells

extract_protocol:
Genomic DNA for Repliseq: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced by using a Zymo DNA extractin kit. RNA for DRIPc-seq: cells were lyzed in proteinase K digestion buffer, and genomic DNA/RNA complex were extraced with a standard phenol/chlorofomr protocol. DNA was degraded during the library prep procedure, and the RNA molecules were prerved.
We follow the published protocol, as indicated below, to construct the libraries. DRIPc-seq: https://www.nature.com/articles/s41596-019-0159-1 Repli-seq: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01983-8

value: neural progenitor cells

value: aphidicolin


title: HTGTS_Chr6_70Mb_APH03_replicate_4_PW158

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_4; Bait Chr6_70Mb; Barcode CATG


title: HTGTS_Chr6_70Mb_APH05_replicate_2_VI011

description: ESC-NPC; NXP010; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_2; Bait Chr6_70Mb; Barcode


title: MN6

description: GD controls


title: OVCAR3_T3_Control_Rp1

description: three pulse-chases, replicate 1

source_name: ovarian cancer

value: ovarian cancer


title: HTGTS_Chr6_70Mb_APH03_replicate_3_PW155

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_3; Bait Chr6_70Mb; Barcode ATCGT

value: ESC-NPC


title: C3GN4


title: Repliseq-untreated-G1

value: untreated


title: IgAN4

description: GD controls


title: OVCAR3_T2_Control_Rp2

description: two pulse-chases, replicate 2


title: Repliseq-aph-s16-rep2


title: C3GN3


title: OVCAR3_T3_HCQ_Rp2

description: three pulse-chases, replicate 2


title: Repliseq-aph-s12-rep2


title: MN5

description: GD controls


title: OVCAR3_T2_Control_Rp1

description: two pulse-chases, replicate 1


title: HTGTS_Chr6_70Mb_APH02_replicate_3_PW112

description: ESC-NPC; NXP010; Aphidicolin 0.2 uM 96h; LAM-HTGTS; replicate_3; Bait Chr6_70Mb; Barcode CTGAC

value: Neural progenitor cells


title: Repliseq-aph-s15-rep2


title: OVCAR3_T2_HCQ_Rp2

description: two pulse-chases, replicate 2


title: HTGTS_Chr6_70Mb_APH02_replicate_2_PW108

description: ESC-NPC; NXP010; Aphidicolin 0.2 uM 96h; LAM-HTGTS; replicate_2; Bait Chr6_70Mb; Barcode TA


title: OVCAR3_T3_Control_Rp2

description: three pulse-chases, replicate 2


title: HTGTS_Chr6_70Mb_APH02_replicate_1_PW092

description: ESC-NPC; NXP010; Aphidicolin 0.2 uM 96h; LAM-HTGTS; replicate_1; Bait Chr6_70Mb; Barcode GCG


title: Repliseq-aph-s11-rep2


title: Repliseq-aph-s10-rep2


title: MN3

description: GD controls


title: HTGTS_Chr5_101Mb_DMSO_replicate_3_PW131

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_3; Bait Chr5_101Mb; Barcode GATCAG


title: MN4

description: GD controls


title: OVCAR3_T1_Control_Rp2

description: one pulse-chase, replicate 2


title: Repliseq-aph-s9-rep2


title: C3GN2


title: HTGTS_Chr6_70Mb_APH03_replicate_2_PW139

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_2; Bait Chr6_70Mb; Barcode T


title: Repliseq-aph-s8-rep2


title: OVCAR3_T1_Control_Rp1

description: one pulse-chase, replicate 1


title: HTGTS_Chr6_70Mb_APH03_replicate_1_PW138

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_1; Bait Chr6_70Mb; Barcode TA


title: HTGTS_Chr5_101Mb_DMSO_replicate_1_PW123

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_1; Bait Chr5_101Mb; Barcode CGATGT


title: IgAN2

description: GD controls


title: OVCAR3_T1_HCQ_Rp2

description: one pulse-chase, replicate 2


title: Repliseq-aph-s7-rep2


title: Repliseq-aph-s6-rep2


title: C3GN1


title: HTGTS_Chr5_101Mb_APH06_replicate_2_PW130

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_2; Bait Chr5_101Mb; Barcode ACTTGA


title: IgAN1

description: GD controls


title: OVCAR3_T0_Rp8

description: time zero, replicate 8


title: Repliseq-aph-s5-rep2


title: HTGTS_Chr5_101Mb_APH06_replicate_1_PW126

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_1; Bait Chr5_101Mb; Barcode TGACCA


title: Repliseq-aph-s4-rep2


title: MN2

description: GD controls


title: OVCAR3_T1_HCQ_Rp1

description: one pulse-chase, replicate 1


title: HTGTS_Chr5_101Mb_APH04_replicate_3_PW133

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_3; Bait Chr5_101Mb; Barcode GGCTAC


title: OVCAR3_T0_Rp7

description: time zero, replicate 7


title: Repliseq-aph-s3-rep2


title: MN1

description: GD controls


title: OVCAR3_T0_Rp6

description: time zero, replicate 6


title: HTGTS_Chr5_101Mb_APH04_replicate_2_PW129

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_2; Bait Chr5_101Mb; Barcode CAGATC


title: OVCAR3_T0_Rp5

description: time zero, replicate 5


title: HTGTS_Chr5_101Mb_DMSO_replicate_2_PW127

description: ESC-NPC; NXP010; DMSO; LAM-HTGTS; replicate_2; Bait Chr5_101Mb; Barcode ACAGTG


title: Repliseq-aph-s1-rep2


title: IgAN3

description: GD controls


title: Repliseq-aph-s2-rep2


title: Rat_SEOV_4dpi_C

city: Rotterdam

first: Barry

last: Rockx

address: Wytemaweg 80

department: Viroscience

country: Netherlands

institute: Erasmus MC

data_processing:
Assembly: mRatBN7-2
Demultiplexing: Illumina bcl2fastq v2.20.0.422
adapter trimming (Illumina adapter sequences): Cutadapt
alignment: HiSat2 version 2.2.1
expression level counting: htseq-count version 0.12.4
gene filtering: keep only genes with count >=5 in at least 6 samples, separately for the 12 human and the 12 rat samples
Supplementary files format and content: .tsv file: tab-separated text file of raw counts, genes in rows and samples in columns.

organism: Rattus norvegicus

source_name: primary lung microvascular endothelial cells

growth_protocol: Commercially available primary cultures of Rattus norvegicus(Cell Biologics) or human (Cell Systems) were propagated in endothelial cell growth medium MV2 (PromoCell) supplemented with 1% penicillin/streptomycin (Lonza) at 37 degrees Celcius in a humidfied CO2 incubator

extract_protocol:
High pure RNA isolation kit (Roche)
Illumina TruSeq Stranded mRNA
ssRNA-seq (stranded RNA-seq)

treatment_protocol: Seoul 80-39 orthohantavirus (SEOV, European Virus Archive Global #008v-EVA1473, P+2) infection with MOI of 1.0 or mock infection with equal amounts of Dulbecco's modified Eagle's medium (Capricorn Scientific) supplemented with 5% fetal calf serum, HEPES, sodium bicarbonate, 1% pen/strep (Lonza) for two hours

tag: timepoint

value: SEOV


title: OVCAR3_T0_Rp3

description: time zero, replicate 3


title: Repliseq-aph-s16-rep1


title: Rat_SEOV_12dpi_B

value: primary lung microvascular endothelial cells


title: HTGTS_Chr5_101Mb_APH04_replicate_1_PW125

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_1; Bait Chr5_101Mb; Barcode TTAGGC


title: OVCAR3_T0_Rp4

description: time zero, replicate 4


title: OVCAR3_T0_Rp1

description: time zero, replicate 1


title: Repliseq-aph-s15-rep1


title: OVCAR3_T0_Rp2

description: time zero, replicate 2


title: HTGTS_Chr5_101Mb_APH06_replicate_3_PW134

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_3; Bait Chr5_101Mb; Barcode CTTGTA


title: HTGTS_Chr5_101Mb_APH03_replicate_2_PW136

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_2; Bait Chr5_101Mb; Barcode CGATGT


title: Rat_SEOV_4dpi_A


title: Rat_SEOV_12dpi_C


title: Repliseq-aph-s12-rep1


title: HTGTS_Chr5_101Mb_APH03_replicate_4_PW154_PW157

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_4; Bait Chr5_101Mb; Barcode ATCACG


title: HTGTS_Chr5_101Mb_APH03_replicate_3_PW137

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_3; Bait Chr5_101Mb; Barcode TTAGGC


title: Rat_Mock_12dpi_C

value: Mock


title: Repliseq-aph-s14-rep1


title: Rat_SEOV_12dpi_A


title: HTGTS_Chr5_101Mb_APH02_replicate_2_PW128

description: ESC-NPC; NXP010; Aphidicolin 0.2 uM 96h; LAM-HTGTS; replicate_2; Bait Chr5_101Mb; Barcode GCCAAT


title: Rat_SEOV_4dpi_B


title: HTGTS_Chr5_101Mb_APH03_replicate_1_PW135

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_1; Bait Chr5_101Mb; Barcode ATCACG


title: Repliseq-aph-s13-rep1


title: Rat_Mock_12dpi_B


title: control_CCL218_R_P19

description: "R" right sample

data_processing:
Transcriptome FASTQ data was aligned to hg38 reference genome using STAR on the UseGalaxy platform. RmDup removed duplicates. Transcripts were counted at the gene level using featureCounts
Assembly: hg38
Supplementary files format and content: featureCounts count table per gene per sample

molecule: polyA RNA

growth_protocol: OVCAR3 and CCL218 cells were passaged in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After 15 hydroxychloroquine pulse-chases, cells were allowed to proliferate for 7 days in drug-free media so that transient drug effects were no longer present. Cells were then pelleted and cell pellets were processed for concomitant bulk RNA-seq, whole-exome-sequencing, and single-cell RNA-seq. This project represents the bulk transcriptomic sequencing and analysis.

extract_protocol:
Cells were pooled, representing one-third of each 96-well plate, pelleted, and processed by Genewiz for RNA-seq and whole-exome sequencing (WES). Qiagen AllPrep DNA/RNA kits were used to isolate RNA and DNA from the same sample.
Agilent SureSelect Human All Exon V8 kits were used and polyA selection performed for transcriptomes.

treatment_protocol: see growth protocol

value: colorectal cancer


title: control_CCL218_M_P19

description: "M" middle sample

value: control


title: HTGTS_Chr5_101Mb_APH02_replicate_1_PW124

description: ESC-NPC; NXP010; Aphidicolin 0.2 uM 96h; LAM-HTGTS; replicate_1; Bait Chr5_101Mb; Barcode ATCACG


title: HCQevolved_CCL218_M_P15

description: "M" middle sample

value: HCQ-evolved


title: HTGTS_Chr5_101Mb_APH02_replicate_3_PW132

description: ESC-NPC; NXP010; Aphidicolin 0.2 uM 96h; LAM-HTGTS; replicate_3; Bait Chr5_101Mb; Barcode TAGCTT


title: HTGTS_Chr17_41Mb_DMSO_replicate_2_PW045

description: ESC-NPC; Nxp047; DMSO; LAM-HTGTS; replicate_2; Bait Chr17_41Mb; Barcode

value: Xrcc4-/-::p53-/-,NXP047,Parental cell


title: HCQevolved_CCL218_R_P15

description: "R" right sample


title: Repliseq-aph-s11-rep1


title: Repliseq-aph-s7-rep1


title: Rat_Mock_12dpi_A


title: HTGTS_Chr17_41Mb_DMSO_replicate_4_VI087

description: ESC-NPC; NXP047; DMSO; LAM-HTGTS; replicate_4; Bait Chr17_41Mb; Barcode T


title: HTGTS_Chr17_41Mb_DMSO_replicate_3_VI085

description: ESC-NPC; NXP047; DMSO; LAM-HTGTS; replicate_3; Bait Chr17_41Mb; Barcode


title: Repliseq-aph-s9-rep1


title: Repliseq-aph-s8-rep1


title: Rat_Mock_4dpi_A


title: control_CCL218_L_P19

description: "L" left sample


title: Rat_Mock_4dpi_C


title: HTGTS_Chr17_41Mb_DMSO_replicate_1_PW006

description: ESC-NPC; Nxp047; DMSO; LAM-HTGTS; replicate_1; Bait Chr17_41Mb; Barcode CATG


title: OVCAR3_T2_HCQ_Rp1

description: two pulse-chases, replicate 1

value: HCQ


title: Rat_Mock_4dpi_B


title: Repliseq-aph-s5-rep1


title: HCQevolved_OVCAR3_L_P15

description: "L" left sample


title: HCQevolved_OVCAR3_R_P15

description: "R" right sample


title: Repliseq-aph-s6-rep1


title: Repliseq-aph-s10-rep1


title: uCoTargetX.H1K562.RNA-3

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 20 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Assembly: hg19
Supplementary files format and content: The processed files were aggregate bigwig files.

growth_protocol: Following uCoTarget protocol.

extract_protocol:
Following uCoTarget protocol.
After PCR enrichment, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Cells were collocted by centrifugation at 300g for 3 minutes


title: uCoTargetX.H1K562.RNA-4


title: control_OVCAR3_R_P19

description: "R" right sample


title: HCQevolved_OVCAR3_M_P15

description: "M" middle sample


title: HTGTS_Chr17_41Mb_APH05_replicate_4_VI088

description: ESC-NPC; Nxp047; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_4; Bait Chr17_41Mb; Barcode GCG


title: Repliseq-aph-s4-rep1


title: control_OVCAR3_M_P19

description: "M" middle sample


title: Repliseq-aph-s3-rep1


title: HTGTS_Chr17_41Mb_APH05_replicate_3_VI086

description: ESC-NPC; Nxp047; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_3; Bait Chr17_41Mb; Barcode TA


title: HTGTS_Chr17_41Mb_APH05_replicate_1_PW005

description: ESC-NPC; Nxp047; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_1; Bait Chr17_41Mb; Barcode TAGT


title: HTGTS_Chr17_41Mb_APH05_replicate_2_PW046

description: ESC-NPC; Nxp047; Aphidicolin 0.5 uM 96h; LAM-HTGTS; replicate_2; Bait Chr17_41Mb; Barcode T


title: uCoTargetX.H1K562.RNA-1

description: RNA


title: HCQevolved_CCL218_L_P15

description: "L" left sample


title: Repliseq-aph-s2-rep1


title: uCoTargetX.H1K562.RNA-2

description: RNA


title: control_OVCAR3_L_P19

description: "L" left sample


title: HTGTS_Chr12_13Mb_APH06_replicate_3_PW153

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_3; Bait Chr12_13Mb; Barcode CAGATC


title: Repliseq-aph-s1-rep1


title: uCoTargetX.H1K562.DNA-4


title: uCoTargetX.H1K562.DNA-3


title: pSUPER_N4 miRNA

data_processing:
Analysis was performed with sports 1.0 with -M 1 , using the authors’ Rnor6 annotation.
Reads were aggregated between genome- and library-aligned.
Assembly: Rnor6
Supplementary files format and content: sports.SE.rds.gz contains a R SummarizedExperiment object with counts per sample / RNA and sample annotation.

source_name: Primary Cortical neuronal cultures (with glia)

growth_protocol: Cortical neuronal cultures after electroporation at DIV0 were maintained in Neurobasal-plus medium supplemented with 2% B27, 3mM GlutaMAX, 100ug/ml streptomycin and 100u/ml penicillin (Thermo) in a 37°C incubator with 5% CO2 until lysis at DIV5.

extract_protocol:
mirVana miRNA isolation kit with Total RNA Isolation Procedure
Eukaryotic Small RNA Sequencing (Novogene), with 18-40 bp insert, small RNA library was prepared with the NEB Next® Multiplex Small RNA Library Prep Set for Illumina®  according to the manufacturer’s instructions. Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing with SE50.

value: Empty vector


title: Repliseq-untreated-s16-rep2


title: pSUPER_N3 miRNA

value: Primary Cortical neuronal cultures (with glia)


title: uCoTargetX.H1K562.DNA-2


title: HTGTS_Chr12_13Mb_APH06_replicate_1_PW151

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_1; Bait Chr12_13Mb; Barcode ACAGTG


title: Repliseq-untreated-s15-rep2


title: pSUPER_N1 miRNA


title: uCoTargetX.H1K562.DNA-1


title: HTGTS_Chr12_13Mb_APH04_replicate_2_PW150

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_2; Bait Chr12_13Mb; Barcode TGACCA


title: Repliseq-untreated-s14-rep2


title: RERE2_N4 miRNA

value: shRNA against circRERE5


title: uCoTargetX.HSPC.RNA-4

source_name: HSPC

value: HSPC


title: RERE2_N3 miRNA

value: shRNA against circRERE4


title: Repliseq-untreated-s13-rep2

value: neural progenitor cells


title: HTGTS_Chr12_13Mb_APH04_replicate_1_PW149

description: ESC-NPC; NXP010; Aphidicolin 0.4 uM 96h; LAM-HTGTS; replicate_1; Bait Chr12_13Mb; Barcode TTAGGC

value: ESC-NPC


title: uCoTargetX.HSPC.RNA-3


title: HTGTS_Chr12_13Mb_APH03_replicate_3_PW148

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_3; Bait Chr12_13Mb; Barcode CGATGT


title: Repliseq-untreated-s12-rep2

value: untreated


title: RERE2_N2 miRNA

value: shRNA against circRERE3


title: HTGTS_Chr12_13Mb_APH06_replicate_2_PW152

description: ESC-NPC; NXP010; Aphidicolin 0.6 uM 96h; LAM-HTGTS; replicate_2; Bait Chr12_13Mb; Barcode GCCAAT

value: Neural progenitor cells


title: HTGTS_Chr12_13Mb_APH03_replicate_2_PW147

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_2; Bait Chr12_13Mb; Barcode ATCACG


title: RERE2_N1 miRNA

value: shRNA against circRERE2


title: uCoTargetX.HSPC.RNA-1

description: RNA


title: Repliseq-untreated-s10-rep2


title: HTGTS_Chr12_13Mb_APH03_replicate_1_PW146

description: ESC-NPC; NXP010; Aphidicolin 0.3 uM 96h; LAM-HTGTS; replicate_1; Bait Chr12_13Mb; Barcode


title: Pum2MM_N4 miRNA

value: Scrambled shRNA


title: Repliseq-untreated-s11-rep2


title: uCoTargetX.HSPC.DNA-4


title: Repliseq-untreated-s9-rep2


title: 543_CX_3_H3.3

city: Houston

first: Sharvari

last: Dharmaiah

state: TX

address: 2130 W. Holcombe Blvd.

institute: MD Anderson Cancer Center

data_processing:
*library strategy: CUT&Tag
The raw fastq files were subjected to FASTQC analysis for quality control analysis, followed by allignment to the human hg19 genome using Bowtie2 (version 2.4.5).
BAM files were filtered and coverage plots were generated after normalizing to IgG.
For peak calling, MACS2 callpeak (version 2.2.7.1) was used from BAM files with default parameters.
DiffBind (version 2.10.0) was used to compute differentially bound H3.3 sites in  samples.
Gene annotations were performed using BED files subjected to GREAT (version 4) analysis with Basal plus extension parameters ( Proximal: 5kb upstream, 1kb downstream, plus distal up to 1000kb), followed by pathway prediction analysis using Enrichr.
Peak annotation and visualization were performed using the PAVIS annotation tool.
Assembly: hg19
Supplementary files format and content: BED
Supplementary files format and content: bigwig

growth_protocol: Patient-derived glioma stem cells (GSCs) were grown and maintained in DMEM (Dulbecco's Modified Eagle Medium)/F-12 media (Gibco), B-27™ Supplement (Gibco), 20 ng/mL EGF, 10 ng/mL FGF, and 2 µg/mL heparin (Stemcell Technologies)

extract_protocol:
GSC DNA was extracted using the CUT&Tag-IT Assay Kit (Active Motif, #53160) following manufacturer's protocols.
Library pool was constructed using i7 and i5 indexing primers (following PCR conditions) following manufacturer's protocols (Active Motif, #53160)

treatment_protocol: Patient-derived glioma stem cells (GSCs) treated for 48 hours with either Vehicle (DMSO) or G4 stabilizer CX-5461 (1 µM).

value: Glioma stem cell

value: ATRX wildtype

value: 48 hours

tag: cut&tag antibody


title: Pum2MM_N3 miRNA


title: 543_CX_2_H3.3


title: uCoTargetX.HSPC.DNA-3


title: OVCAR3_T3_HCQ_Rp1

description: three pulse-chases, replicate 1

value: ovarian cancer


title: uCoTargetX.HSPC.DNA-2


title: Pum2MM_N2 miRNA


title: Repliseq-untreated-s7-rep2


title: 543_CX_1_H3.3


title: Pum2MM_N1 miRNA


title: uCoTargetX.HSPC.DNA-1


title: Repliseq-untreated-s6-rep2


title: uCoTargetX.HSPC.RNA-2

description: RNA


title: pSUPER_N4

data_processing:
Quantification performed using salmon 1.8.0 with --validateMappings on the mRatBN7.2 transcriptome.
Assembly: Rnor7
Supplementary files format and content: A R SummarizedExperiment object containing the read count matrix and sample annotation.

extract_protocol:
mirVana miRNA Isolation Kit
NEB Next® Ultra RNA Library Prep Kit for Illumina®. Indices were included to multiplex multiple samples. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, insert size of the library was validated on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).


title: 818_CX_3

data_processing:
The raw fastq files were subjected to FASTQC analysis for quality control analysis, followed by allignment to the human hg19 genome using RNASTAR (version 2.7.8a).
Raw transcript counts were determined using the HTseq-count Tool (version 0.9.1) and then subjected to Principal Component Analysis (PCA).
DESeq2 (version 2.11.40.7) was used to determine differentially expressed genes, which were subsequently analyzed using Gene Set Enrichment Analysis (GSEA) via a desktop version of the analysis tool.
Assembly: hg19
Supplementary files format and content: raw transcript counts

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy Plus Micro Kit (Qiagen, #74034) following  manufacturer's protocols.
RNA libraries for RNA-seq were prepared using Truseq library preparation kits (Illumina)  following  manufacturer's protocols.

value: ATRX deficient


title: 543_VEH_2_H3.3

value: DMSO


title: 543_VEH_3_H3.3


title: 818_CX_2


title: pSUPER_N3

value: Primary Cortical neuronal cultures (with glia)

value: Empty vector


title: 543_VEH_1_H3.3


title: Repliseq-untreated-s5-rep2


title: Repliseq-untreated-s4-rep2


title: pSUPER_N2


title: Repliseq-untreated-s3-rep2


title: SH590_CX_3_H3.3

value: ATRX knockdown


title: pSUPER_N1


title: 818_VEH_3


title: Repliseq-untreated-s8-rep2


title: 818_CX_1


title: RERE2_N4

value: shRNA against circRERE5


title: Repliseq-untreated-s2-rep2

value: neural progenitor cells


title: SH590_CX_1_H3.3


title: RERE2_N3

value: shRNA against circRERE4


title: SH590_VEH_3_H3.3


title: Repliseq-untreated-s1-rep2

value: untreated


title: RERE2_N2

value: shRNA against circRERE3


title: 522_CX_3


title: RERE2_N1


title: Repliseq-untreated-s16-rep1


title: 522_CX_2


title: 522_CX_1


title: SH590_VEH_2_H3.3


title: GR_965

description: Psychiatrically heatlhy subjects with genetic risk for mood disorders (at least one first-degree relative diagnosed with mood disorders)

data_processing:
Reads were processed using the ncPro 1.6.4 pipeline on the hg19 annotated (based on miRBase version 21). Only mature miRNA reads (accepting +2bp on either end) were considered for downstream analysis.
Differential expression analysis was then performed using limma/voom 3.46.0, with a model including a covariate to correct for the two technical batches.
Assembly: hg19
Supplementary files format and content: ncPRO read counts per sample and feature.

source_name: PBMC

growth_protocol: PBMCs were obtained from 10 ml of whole blood using the LeukoLOCK technology (Thermo Scientific) at the Biomaterialbank Marburg, Germany. Samples were frozen in DMSO.

extract_protocol:
Before RNA extractions, samples were thawed and washed with 1x PBS twice following centrifugation. After samples randomization, total RNA extraction from PBMCs was carried out using the the mirVana™ kit (Thermo Fisher)  following the manufacturer's protocol.
Illumina Truseq small RNA library protocol

value: PBMC

value: Female

tag: group

value: Genetic risk

tag: batch

value: B


title: Repliseq-untreated-s14-rep1


title: Pum2MM_N3

value: Scrambled shRNA


title: SH590_CX_2_H3.3

value: Glioma stem cell

value: 48 hours


title: 818_VEH_1

value: ATRX deficient


title: Repliseq-untreated-s13-rep1


title: GR_760


title: 818_VEH_2

value: DMSO


title: GR_599


title: Pum2MM_N1

value: Primary Cortical neuronal cultures (with glia)


title: 522_VEH_2


title: Repliseq-untreated-s11-rep1


title: Repliseq-untreated-s12-rep1


title: Repliseq-untreated-s15-rep1


title: GR_527


title: Repliseq-untreated-s10-rep1


title: 522_VEH_1


title: 603_CX_3

value: ATRX wildtype


title: SH590_VEH_1_H3.3

value: ATRX knockdown


title: Repliseq-untreated-s9-rep1


title: GR_476


title: PD.ASCC_7

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

data_processing:
QC analysis by fastqc and trimming by trimmomatic
mapping by star and counting by featurecount
generation of bw by sambamba, bedtools and wigtobigwig
Assembly: ensembl release-104
Supplementary files format and content: bw file per fastq file indicating coverage

source_name: primary tumor FFPE

extract_protocol:
Total RNA was isolated from FFPE samples using Qiagen RNeasy FFPE Kit (Qiagen) and depleted from ribosomal RNA (rRNA) to prepare sequencing libraries
Complete Stranded RNA Library

value: primary tumor FFPE

tag: disease state

value: PD


title: 603_CX_2


title: GR_454


title: PD.ASCC_5

tag: tissue


title: GR_2084

tag: Sex


title: PD.ASCC_6


title: 603_CX_1


title: Pum2MM_N2


title: 603_VEH_3


title: PD.ASCC_42


title: ER_872

description: Psychiatrically heatlhy subjects with environmental risk for mood disorders (suffered childhood maltreatment)


title: Repliseq-untreated-s6-rep1

value: neural progenitor cells


title: Repliseq-untreated-s7-rep1

value: untreated


title: PD.ASCC_41


title: Repliseq-untreated-s5-rep1


title: ER_850

value: Environmental Risk


title: 603_VEH_2


title: PD.ASCC_40


title: Repliseq-untreated-s4-rep1


title: 603_VEH_1


title: 543_CX_3


title: ER_778

value: PBMC


title: PD.ASCC_35


title: Repliseq-untreated-s3-rep1


title: Repliseq-untreated-s8-rep1


title: PD.ASCC_34


title: ER_651

value: Female


title: PD.ASCC_31


title: 543_CX_2


title: ER_628


title: PD.ASCC_30


title: 543_VEH_3


title: Ly6Clo-Mo_KO3

city: Saint Louis

first: Sunkyung

last: KIM

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in Saint Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: Mouse Ensembl GRCm38.76 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with merged differential expression results

source_name: Spleen

growth_protocol: Ly6Chi monocytes and Ly6Clo monocytes (approximately 40,000 – 50,000 cells/sample) were sort-purified from the spleens of WT or Cebpa +37–/– mice.

extract_protocol:
RNA was isolated from approximately 40,000-50,000 splenic monocytes using NucleoSpin RNA XS Kit (Macherey-Nagel).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: The monocytes were collected into 100 μL MACS buffer containing 40 U of Protector RNase inhibitor (Roche) to prevent RNA degradation

value: Spleen

tag: strain

value: Ly6Clo monocytes

value: Sort-purified (untreated)


title: 543_VEH_2

value: Glioma stem cell

tag: genotype


title: Ly6Clo-Mo_KO2

tag: treatment


title: 543_VEH_1

value: 48 hours


title: PD.ASCC_28


title: ER_636

value: B


title: Ly6Clo-Mo_KO1


title: ER_463


title: Repliseq-untreated-s2-rep1


title: SH590_CX_3


title: ER_43


title: 543_CX_1


title: Repliseq-untreated-s1-rep1


title: PD.ASCC_25


title: Ly6Clo-Mo_WT2

value: WT


title: SH590_CX_2


title: ER_305


title: PD.ASCC_24


title: ER_302


title: SH590_VEH_3

value: DMSO


title: SH590_CX_1


title: ER_565


title: PD.ASCC_22


title: Ly6Clo-Mo_WT1


title: Ly6Clo-Mo_WT3


title: ER_239


title: PD.ASCC_29


title: ER_59


title: PD.ASCC_27


title: SH590_VEH_2


title: PD.ASCC_18


title: Ly6Chi-Mo_WT2

value: Ly6Chi monocytes


title: SH590_VEH_1

value: ATRX knockdown


title: PD.ASCC_16

value: primary tumor FFPE


title: ER_2071


title: Ly6Chi-Mo_WT1


title: ER_2067


title: cCR.ASCC_99

value: cCR


title: cCR.ASCC_98


title: ER_2051


title: 4_0FSH_024CBern_A947-REP2_TCF7L2

city: San Fransisco

first: Xiaosai

last: Yao

state: CA

address: 1 DNA Way

department: Oncology Bioinformatics

institute: Roche/Genentech

data_processing:
ChIP-seq sequence data was processed using an ENCODE-DC/chip-seq-pipeline2 -based workflow (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Briefly .fastq files were aligned on the hg38 human genome reference using Bowtie2  (v2.2.6) followed by alignment sorting (samtools v1.7) of resulting bam files with filtering out of unmapped  reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s  MarkDuplicates  (v1.126) function followed by indexation of resulting bam files with samtools. For each bam  file, genome coverage was computed with bedtools (v2.26.0) followed by generation of bigwig  (wigToBigWig v377) files. Peaks were called with macs2 (v2.2.4) for each treatment sample using a pooled input alignment (.bam file) as control. Downstream analyses were performed with DiffBind v3.11.1 with default parameters, except for summits=250 in dba.count(). dba.contrast() and dba.analyzed() were used to  compute significant differential peaks with DESeq2.
Assembly: hg38
Supplementary files format and content: Macs2 peaks

source_name: Prostate

growth_protocol: Patient-derived CRPC organoids (WCM) were established and maintained as organoids in Matrigel drops according to the previously described protocol69. Cell cultures were regularly tested for Mycoplasma contamination and confirmed to be negative. Genentech Inc. synthesized A947 and its epimers (A858).

extract_protocol:
Whole cell lysates were prepared in 1x Cell lysis buffer (CST, 9803) supplemented with protease and phosphatase inhibitor cocktail (Thermo Fisher, 78440), and total protein was measured by Pierce BCA Protein Assay Kit (ThermoFisher Scientific, 23225).
Chromatin was prepared from 2 biological replicates of WCM1078 treated with A858 or A947 (1µM) for 24h, and ChIP-Seq assays were then performed by Active Motif Inc. using an antibody against TCF7L2 (Santa Cruz, cat# sc-8631, Lot# D0914).

value: Prostate

value: castrate-resistant prostate cancer (CRPC)

value: enriched in Wnt signaling

tag: chip-seq antibody

value: TCF4/TCF7L2 (Santa Cruz, cat# sc-8631, Lot# D0914)


title: 3_0FSG_024CBern_A947-REP1_TCF7L2

tag: cell type


title: ER_156

value: PBMC

value: Female

value: Environmental Risk


title: 0_0FWQ_024CBern_Pooled_Input


title: cCR.ASCC_96


title: 2_0FSF_024CBern_A858-REP2_TCF7L2


title: GR_99

value: Genetic risk

value: A


title: 1_0FBE_025CBern_A858-REP1_TCF7L2


title: cCR.ASCC_95


title: Ly6Chi-Mo_WT3

value: Spleen

value: Sort-purified (untreated)


title: KO

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description: 10x Genomics

data_processing:
Cell Ranger (10x Genomics, v7.1.0) was used to performalignment (GRCm38, Ensembl 93), filtering, barcode counting and UMI counting of sequencing reads from fastq files.
Assembly: GRCm38
Supplementary files format and content: Tab -separated values files and matrix files

source_name: aortic arch

growth_protocol: IRG-/- or control mice were placed on Western diet to induce development of atherosclerossis. 4O1 treatment was performed for 4 weeks, 3 times week. DMSO was used as vehicle control.

extract_protocol:
Chromium Next GEM Chip G Single Cell Kit: cd45+ cells were loaded into single-cell gel beads and barcoded with a unique molecular identifier, before being subjected to scRNA-seq
Chromium Next GEM Single Cell 3' Kit v3.1 10x platform for single cell RNAseq
Library Construction Kit: 10x platform for single cell RNAseq

treatment_protocol: Single-cell suspensions of the aortic arch were made and CD45+immune cells were isolated by staining (anti-CD45 PerCp-Cy5.5, BioLegend) and flow sorting viable (fixable viability dye e780, eBioscience) single cells on a Facs Aria II cytometer (BD) equipped with a 100 µm nozzle

value: aortic arch

value: immune

value: KO


title: GR_40


title: ER_207

value: B


title: cCR.ASCC_93

value: primary tumor FFPE


title: WT

description: 10x Genomics

value: WT


title: GR_342


title: knee chondrocytes rep8

city: Munich

first: Norbert

last: Bittner

address: Ingolstädter Landstraße 1

department: Computational Health

institute: Helmholtz Munich

data_processing:
Hi-C reads were quality filtered, trimmed, and adapters were removed using fastp v0.20.116 with the default settings. Reads were processed and mapped to the GRCh38 genome with HiC-pro v3.0.017, using default settings. To identify potential outliers, we conducted PCA analysis  of the single patient samples and removed sample 9 from the downstream analysis. For downstream analysis, single patient samples 1 - 8 were merged into a single file comprising of 3.520 billion reads. HiC juicebox files for visualization and further analysis were generated using the hicpro2juicebox.sh script using juicer tools v1.22.0122.
Assembly: GRCh38
Supplementary files format and content: Hi-C (.hic) format file containing the contact count matrix

source_name: primary chondrocytes form the knee

extract_protocol:
Cartilage samples were cut into tiny pieces and transferred into a Falcon tube, washed with PBS twice and then digested in DMEM with 3mg/mL Collagenase 1A (Sigma, #C9891) on a 37°C shaker overnight. Tissue suspensions were passed through a 70 µm cell strainer and single chondrocytes were collected. Cells were washed with PBS and split into aliquots. Approximately 2 million primary chondrocytes were crosslinked in 2% formaldehyde for 10 minutes at room temperature and the reaction was then quenched using a solution of 0.125M glycine (Sigma, #50046) + 3% BSA (Sigma, #A9647). Samples were then washed in PBS, snap frozen on dry ice and transferred to -80°C for long-term storage.
One million chondrocyte cells were used for library preparation using the two-restriction enzyme Arima Hi-C kit (Arima Genomics) and the KAPA HyperPrep kit (Roche #KK8504) following manufacturer’s protocols and using Illumina TruSeq dual indexes.

value: primary chondrocytes form the knee


title: PD.ASCC_11

value: PD


title: knee chondrocytes rep9


title: GR_269


title: cCR.ASCC_91

value: cCR


title: B2_PBS_4

city: Minneapolis

first: Anna

last: Carey

state: Minnesota

address: 312 Church Street SE

department: Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

data_processing:
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups was performed using the DESeq2Rpackage (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value<=0.05found by DESeq2 were assigned as differentially expressed.
Assembly: grcM39
Supplementary files format and content: txt counts file with each column as a different sample containing gene symbols and ensembl symbols

source_name: Visceral white adipose tissue (vWAT)

extract_protocol:
RNA was isolated using the Invitrogen purelink RNA micro kit (cat#12183-016) and processed as per manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: 20 month old female mice were treated with PBS or 0.1 mg/kg LPS (E. coli O111-B2) for 4 hours prior to euthanization by cervical dislocation under anaesthesia and harvest of visceral white adipose tissue (vWAT); vWAT was digested using collagenase II digestion buffer and a single cell suspension of the stromovascular fraction was isolated and stained prior to fluorescence associated cell sorting for the B1 (CD19+ CD11b+) and B2 (CD19+ CD11b-) B cell populations

value: female

value: Visceral white adipose tissue (vWAT)

value: In vivo 4 hour PBS


title: cCR.ASCC_90


title: B2_PBS_3


title: GR_215

value: PBMC

value: Female


title: cCR.ASCC_9


title: knee chondrocytes rep6


title: B2_PBS_2


title: knee chondrocytes rep5


title: B2_PBS_1


title: GR_142

value: Genetic risk

value: A


title: knee chondrocytes rep4


title: cCR.ASCC_88


title: control_80

description: Psychiatrically heatlhy subjects without genetic or environmental risk for mood disorders

value: healthy controls


title: B2_LPS_4

value: In vivo 4 hour 0.1 mg/kg LPS


title: cCR.ASCC_87


title: B2_LPS_3


title: knee chondrocytes rep3


title: control_749


title: cCR.ASCC_86


title: knee chondrocytes rep7


title: knee chondrocytes rep2


title: control_710


title: B2_LPS_2


title: cCR.ASCC_85


title: knee chondrocytes rep1


title: cCR.ASCC_84


title: control_706


title: Plasma+4OI

city: New York

description: 10x Genomics

data_processing:
Cell Ranger (10x Genomics, v7.0.0) was used to performalignment (GRCh38, Ensembl 93), filtering, barcode counting and UMI counting of sequencing reads from fastq files.
Assembly: GRCh38
Supplementary files format and content: Tab -separated values files and matrix files

growth_protocol: Human primary peripheral blood mononuclear cells (PBMCs) were isolated from whole blood obtained from the New York Blood Center. Whole blood was processed immediately upon receipt and diluted 1:1 (v:v) with PBS. Ficoll-Paque premium (Sigma Aldrich) was gently overlaid in Sepmate tubes (StemCell) with the diluted blood without breaking the surface plane, followed by centrifugation for 20 minutes (room temperature, without brake). The PBMC layer was collected, washed twice in PBS. The cell pellet was diluted in RPMI-1640 (ATCC) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Invitrogen) and cell concentration and viability were checked. Monocytes were magnetically labeled with magnetic anti-CD14 microbeads (Miltenyi Biotec), and collected within a MACS Column LS (Miltenyi Biotec) in the magnetic field of a MACS Separator, according to the manufacturer’s instructions. Monocytes were seeded in RPMI-1640 supplemented with 10% FBS, and differentiated with 50 ng/mL of recombinant human macrophage-colony stimulating factor (Peprotech) for 6 days in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
Chromium Next GEM Chip G Single Cell Kit: Cells were loaded into single-cell gel beads and barcoded with a unique molecular identifier, before being subjected to scRNA-seq
Chromium Next GEM Single Cell 3' Kit v3.1 10x platform for single cell RNAseq
Library Construction Kit: 10x platform for single cell RNAseq

treatment_protocol: Stimulation of PBMCs and staining protocols for CyTOF were based on methods described by (PMID: 21551058). Briefly, healthy PBMCs were co-incubated for 4 hours with patient plasma and 4OI (concentration, company), patient plasma or no plasma (control).

value: primary

value: plasma + 4O1


title: GR_171


title: B1_PBS_2


title: cCR.ASCC_89


title: control_676


title: cCR.ASCC_80


title: Plasma

description: 10x Genomics

value: plasma


title: B1_PBS_1


title: control_647


title: cCR.ASCC_8

value: primary tumor FFPE


title: CCL218_scRNApool

description: CCL218 pool containing control and HCQevolved cells from "L", "M", and "R"

data_processing:
Partek Flow was used to demultiplex samples, align reads to human genome hg38, flag and remove common contaminants including doublets, and generate RNA count tables per cell.
Assembly: hg38
Supplementary files format and content: Partek Flow counts table

extract_protocol:
Experimental procedures followed established techniques using the Chromium Single Cell 3’ Library v3.1 Kit (10x Genomics). Cultured cells in single-cell suspension were labeled with TotalSeq™-B anti-human Hashtag antibodies (Biolegend) and pooled in equal proportions prior to loading onto a 10X Genomics Next GEM Chip G and emulsified with 3’ Single Cell Next GEM beads using a Chromium™ Controller (10x Genomics).
From barcoded cDNAs, gene expression libraries were constructed using Chromium™ Next GEM Single Cell 3ʹ Library kit and hashtag oligo libraries were constructed using Chromium™ Single Cell 3ʹ Feature Barcode Library Kit (both from 10X Genomics)

value: colorectal cancer

value: control and HCQ evolved


title: B1_LPS_3

value: WT


title: cCR.ASCC_79

value: cCR


title: 522_VEH_3

value: Glioma stem cell

value: ATRX deficient

value: DMSO

value: 48 hours


title: control_664

value: PBMC

value: Female


title: control_582

value: A


title: cCR.ASCC_77


title: control_522

value: healthy controls


title: B1_LPS_2

value: female

value: Visceral white adipose tissue (vWAT)

value: In vivo 4 hour 0.1 mg/kg LPS


title: B2_LPS_1


title: OVCAR3_scRNApool

description: OVCAR3 pool containing control and HCQevolved cells from "L", "M", and "R"

value: ovarian cancer


title: Pum2MM_N4

value: Primary Cortical neuronal cultures (with glia)

value: Scrambled shRNA


title: cytarabine-persistent leukemia cells, M10

city: Boston

first: Qingyu

last: Luo

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
The raw FASTQ data were analyzed by the VIPER pipeline to generate gene expression data
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: PDX

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Plus XS (740990.250; Takara Bio) according to the manufacturer’s protocol.
Roche Kapa

value: PDX

value: AML

value: cytarabine


title: cKO EP cells  rep 3

city: Shanghai

first: Qirui

last: Wang

address: 639 Zhi Zao Ju Road

department: Department of Plastic and Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description:
RNA-seq sample for cKO
A-W6

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platformand 150 bppaired-endreadswere generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cKO Epidermis, FACS-sorted,P0

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructedusing VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: cKO Epidermis, FACS-sorted,P0

value: epidermal progenitor cell


title: cCR.ASCC_76

value: primary tumor FFPE

value: cCR


title: cytarabine-persistent leukemia cells, M9

value: WT


title: B1_LPS_1


title: cCR.ASCC_74


title: control_515

value: PBMC

value: Female


title: control_513

value: healthy controls

value: A


title: control_495


title: cCR.ASCC_70


title: No_plasma

description: 10x Genomics

value: primary


title: cytarabine-persistent leukemia cells, M8


title: cKO EP cells  rep 1

description:
RNA-seq sample for cKO
A-W2


title: cCR.ASCC_7


title: cKO EP cells  rep 2

description:
RNA-seq sample for cKO
A-W4


title: control_430


title: Ctrl EP cells  rep 3

description:
RNA-seq sample for ctrl
A-C5

source_name: Ctrl Epidermis, FACS-sorted,P0

value: Ctrl Epidermis, FACS-sorted,P0


title: cCR.ASCC_69


title: cytarabine-persistent leukemia cells, M6


title: Ctrl EP cells  rep 2

description:
RNA-seq sample for ctrl
A-C2


title: cCR.ASCC_68


title: control_434


title: Ctrl EP cells  rep 1

description:
RNA-seq sample for ctrl
A-C1


title: cCR.ASCC_67


title: cCR.ASCC_66


title: control, M4

value: Vehicle


title: control, M5


title: control_22


title: control, M3


title: MC3T3-E1 cells, NaHPO4, Rep 3, MC3T-2-3-C

first: Bram

middle: CJ

last: van der Eerden

department: Internal medicine

institute: Erasmus University MC

data_processing:
Sequencing was performed at 2x50 bp on a NovaSeq 6000 (Illumina).
To analyze RNA-seq data the Artificial Intelligence RNA-seq (AIR) was used (https:// sequentiabiotech.com/).
RNA-seq data validation, pairing and FastQC quality control were performed after which the reads were mapped against the mouse (GRCm39/Ensembl, release 104) genome.
For identification of differentially expressed genes (DEGs) the EdgeR method was used within AIR.
Assembly: GRCm39/Ensembl, release 104
Supplementary files format and content: Text filed including raw count for each sample
Supplementary files format and content: Text file including TMM normalized counts for each sample

source_name: Calvarial bone

growth_protocol: MC3T3-E1 were seeded in 12-wells plate, grown for 2 days in alpha-minimum essential medium (αMEM; A10490-01, Gibco, Paisley, UK), supplemented with 10% fetal bovine serum. Than cells were switched to osteogenic medium (αMEM, 10% FBS, 100 Units/mL penicillin and 100 µg/mL streptomycin, 10 mM β-glycerophosphate (BGP, Sigma-Aldrich, Missouri, United States), 50 µg/ml ascorbic acid (Sigma-Aldrich) and 0.1 µM dexamethasone (Sigma-Aldrich). Cells were differentiated for 27 days and refreshed 3 times a week.

extract_protocol:
Total RNA was isolated using TRIzol according to the manufacturer’s instructions. RNA concentration and size distribution profile were analyzed on an Agilent Bioanalyzer RNA 6000 Pico chip (Thermo Fisher Scientific, USA).
RNA sequencing library was prepared using the Truseq RNA stranded polyA library prep kit (Illumina, California, United States).

treatment_protocol: At day 27 cells were treated for 16 hours with 4 mM BGP or 4 mM Na2HPO4/NaH2PO4

value: Calvarial bone

value: Pre-osteoblast

value: 4 mM NaHPO4


title: control, M2

value: PDX

value: AML


title: cCR.ASCC_64


title: control_2004


title: control_134


title: MC3T3-E1 cells, NaHPO4, Rep 2, MC3T-2-3-B


title: cytarabine-persistent leukemia cells, M7

value: cytarabine


title: QL8

data_processing:
we used ChiLin pipeline 2.0.0 for QC and preprocessing, Burrows–Wheeler Aligner for read mapping, Model-based Analysis of ChIP-Seq (MACS) as a peak caller, and DESeq2 for differential peak analysis.
Assembly: hg19
Supplementary files format and content: bigWig, peaks

extract_protocol:
Genomic DNA was extracted using the Quick-DNA Microprep Kit (D3020; Zymo Research).
Briefly, 10^5cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2in water). Cells were centrifuged at 500×gfor 5 min in a prechilled fixed-angle centrifuge and the supernatant was carefully aspirated. Cell pellets were then resuspended in 50 µl RSB containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin y pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500×gin a prechilled fixed-angle centrifuge. Supernatant was removed, and nuclei were resuspended in 50 µl of transposition mix (2.5 µl transposase (100 nM final), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-10 and 5 µl water) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a shaking thermomixer. Reactions were cleaned up with QIAquick PCR spin columns. Library quantitation was used to determine the number of amplification cycles by plotting linear Rn vs. cycle and determining the cycle number corresponding to one-fourth of maximum fluorescent intensity

value: ALL

tag: pik3r5 expression

value: low


title: control, M1

tag: cell line


title: cCR.ASCC_63

value: primary tumor FFPE

value: cCR


title: cCR.ASCC_62


title: MC3T3-E1 cells, BGP, Rep 3, MC3T-2-2-C

value: WT

value: 4 mM BGP


title: PIK3R5i#2-Rep5

description:
18_QL
STAR_Gene_Counts

data_processing:
The raw FASTQ data were analyzed by the VIPER pipeline to generate gene expression data
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

value: BPDCN

value: PIK3R5 knockdown

value: DMSO


title: QL7


title: cCR.ASCC_61


title: PIK3R5i#2-Rep4

description:
17_QL
STAR_Gene_Counts


title: MC3T3-E1 cells, BGP, Rep 2, MC3T-2-2-B


title: MC3T3-E1 cells, BGP, Rep 1, MC3T-2-2-A


title: control_2013

value: PBMC

value: Female

value: healthy controls

value: A


title: cCR.ASCC_60


title: QL5


title: PIK3R5i#2-Rep3

description:
16_QL
STAR_Gene_Counts


title: MC3T3-E1 cells, NaHPO4, Rep 1, MC3T-2-3-A

value: Calvarial bone

value: Pre-osteoblast

value: 4 mM NaHPO4


title: MC3T3-E1 cells, Control, Rep 3, MC3T-2-1-C

value: Control


title: PIK3R5i#2-Rep1

description:
14_QL
STAR_Gene_Counts


title: MC3T3-E1 cells, Control, Rep 2, MC3T-2-1-B


title: cCR.ASCC_59


title: PIK3R5i#2-Rep2

description:
15_QL
STAR_Gene_Counts


title: PIK3R5i#1-Rep5

description:
13_QL
STAR_Gene_Counts


title: QL4

value: PDX

value: ALL

value: high


title: cCR.ASCC_56

value: primary tumor FFPE

value: cCR


title: QL2

value: WT


title: cCR.ASCC_55


title: PIK3R5i#1-Rep4

description:
12_QL
STAR_Gene_Counts

value: BPDCN


title: cCR.ASCC_54


title: QL1


title: cCR.ASCC_6


title: Brain, Aged Ethanol

city: Aurora

first: paige

last: Anton

state: COLORADO

address: 12850 E Monteview Blvd, School of Pharmacy V20-3470D

institute: University of Colorado Anschutz

description:
10x Genomics Visium Spatial Transcriptomics
D_Aged_Ethanol
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
filtered_feature_bc_matrix.h5
Aggr_cloupe.cloupe

data_processing:
FASTQ sequencing files were aligned to the mm10 mouse genome and gene expression counts generated using Space Ranger 2.0.0 (10X Genomics).
The `spaceranger count` command was used to generate tissue slice gene expression count matrices with default settings.
The `spaceranger aggr` command was used to aggregate all slice gene expression count matrices with default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz = list of barcodes
Supplementary files format and content: features.tsv.gz = list of gene IDs
Supplementary files format and content: matrix.mtx.gz = gene count data in Matrix Market Exchange Format
Supplementary files format and content: filtered_feature_bc_matrix.h5 = matrix of detected gene features
Supplementary files format and content: 01f00d4.TIF = high res image of tissue slice
Supplementary files format and content: Aggr_cloupe.cloupe = Gene expresssion data on loupe browser interface
Library strategy: Spatial Transcriptomics

source_name: Murine Brain (Hippocampal)

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Colorado Anschutz Medical Campus. Female C57BL/6 mice were obtained from the National Institutes of Aging (NIA) aged rodent colony and maintained for at least two weeks in an in-house animal facility prior to use.

extract_protocol:
Brain tissue was extracted, and meninges were removed. Left hemispheres were frozen in optimal cutting temperature (OCT) compound and sectioned for spatial transcriptomics. Brain tissue was sectioned coronally (10 um thickness; bregma -2.0 to -2.2) and slices were placed on a 10X Genomics Visium Spatial Gene Expression Slide.
Spatial trancriptomice sequenccing libraries were prepared with 10x Genomic Visium Gene Expression slides to manufacturer's instructions

treatment_protocol: Young (3–4-month-old) and aged (18–20-month-old) mice were randomized (2-3 mice/cage) into vehicle and ethanol treatment groups. All cage mates were matched by weight. Mice received intragastric gavages of vehicle (water) or ethanol (3 g/kg) every-other-day over the course of 18 days, totaling 10 exposures. All mice were allowed ad libitum access to chow and water during the treatment period and housed on a 12-hour/12-hour light/dark cycle. Eighteen hours after the final gavage, mice were anesthetized and sacrificed.

value: Murine Brain (Hippocampal)

tag: age

value: 18 months old

value: Ethanol


title: PF_MYST_overexpression_time point 6

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

description: This sample is of Plasmodium falciparum with PfMYST overexpression at six time point.

hyb_protocol: Hybridization was performed by Genomics Core Facility of Pennsylvania State University. Incubate at 95C for 5 minutes, followed by 42C for 5 minutes. Attach appropriate mixer to the array and add hybridizations solution according to the manufacturer’s instructions (Roche NimbleGen). Hybridize with mixing in a MAUI hybridization instrument overnight at 42C.

scan_protocol: Scanning was performed by Genomics Core Facility of Pennsylvania State University by using Axon GenePix 4000B.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in DNASTAR software-ArrayStar 4 (dnastar.com).
RMA-normalized, averaged gene-level signal intensity

organism: Plasmodium falciparum

source_name: Plasmodium falciparum PfMYST overexpression, time point 6

label_protocol: Labeling was done by Genomics Core Facility of Pennsylvania State Univerity. Amplify 1ug of each sample using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit. Dye couple 15 ug of aRNA with Cy3 or Cy5 (GE Health Care #RPN5661), as appropriate, and subsequently purify according to the Ambion Kit instructions.(AM1753).

growth_protocol:
P. falciparum were cultured as described previously (Trager and Jensen, 1976)
The parasite culture was synchronized by sorbital treatment (Lambros and Vanderberg, 1979).

extract_protocol: Total RNA was extracted using the Trizol reagent ((invirtogen.com)

tag: developmental stage

value: late schizont

tag: phenotype

value: a faster progression and shorter schizont development time


title: PIK3R5i#1-Rep3

description:
11_QL
STAR_Gene_Counts

value: PIK3R5 knockdown

value: DMSO


title: Brain, Aged Vehicle

description:
10x Genomics Visium Spatial Transcriptomics
C_Aged_Vehicle
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
filtered_feature_bc_matrix.h5
Aggr_cloupe.cloupe

value: Female

value: Vehicle


title: QL3

value: AML


title: MC3T3-E1 cells, Control, Rep 1, MC3T-2-1-A

value: Calvarial bone

value: Pre-osteoblast

value: Control


title: Brain, Young Vehicle

description:
10x Genomics Visium Spatial Transcriptomics
A_Young_Vehicle
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
filtered_feature_bc_matrix.h5
Aggr_cloupe.cloupe

value: 3 months old


title: PF_MYST_overexpression_time point 5

description: This sample is of Plasmodium falciparum with PfMYST overexpression at fifth time point.

source_name: Plasmodium falciparum PfMYST overexpression, time point 5

value: eraly schizont


title: cCR.ASCC_53

value: primary tumor FFPE

value: cCR


title: QL6

value: PDX

value: WT

value: low


title: PF_MYST_overexpression_time point 4

description: This sample is of Plasmodium falciparum with PfMYST overexpression at fouth time point.

source_name: Plasmodium falciparum PfMYST overexpression, time point 4

value: late trophozoite


title: PIK3R5i#1-Rep1

description:
9_QL
STAR_Gene_Counts

value: BPDCN


title: cCR.ASCC_50


title: cCR.ASCC_52


title: PF_MYST_overexpression_time point 3

description: This sample is of Plasmodium falciparum with PfMYST overexpression at third time point.

source_name: Plasmodium falciparum PfMYST overexpression, time point 3

value: middel trophozoite

value: a faster progression and shorter schizont development time


title: NTC#2+PI3Kγi-Rep2

description:
8_QL
STAR_Gene_Counts

value: eganelisib