title: NA14_120h, rep2

first: Xiaoqiang

last: Ma

address: 800 DONG CHUAN ROAD

institute: Shanghai Jiaotong University

description:
raw_count.txt
gene_FPKM.txt

data_processing:
The clean reads were obtained by removing adapter, ploy-N, and low quality raw reads and their quality were analyzed using the Fastp v.0.21.0.
The clean reads were mapped to the reference genome of Rhodotorula toruloides NP11 (NCBI Accession: GCA_000320785.2) using Hisat2 v2.0.5.
The numbers of reads mapped to each gene were counted using featureCounts v1.5.0-p3
The gene expression levels were estimated using FPKM, which was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: RHOziaDV1.0
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes FPKM values for each sample

organism: Rhodotorula toruloides

source_name: yeast cell

extract_protocol:
The WT, NA04, and NA14 were cultivated in the shake flasks containing 50 mL MMBOS medium and were sampled at 48h and 120h for transcriptome analysis. 1 mL diluted cell cultures with OD600 10 were centrifuged (6000 g at 4 ℃ for 5 min). The total RNA of the cell pellet was extracted using RNAprep pure kit (Tiangen, China) and assessed integrity using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina®。

value: yeast cell


title: NA04_120h, rep2

status: Public on Sep 14 2023

type: SRA

city: Shanghai

country: China

description:
raw_count.txt
gene_FPKM.txt

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: strain

tag: time


title: NA04_120h, rep3

description:
raw_count.txt
gene_FPKM.txt


title: NA14_48h, rep2

description:
raw_count.txt
gene_FPKM.txt


title: NA14_48h, rep1

description:
raw_count.txt
gene_FPKM.txt


title: NA14_120h, rep1

description:
raw_count.txt
gene_FPKM.txt


title: NA14_48h, rep3

description:
raw_count.txt
gene_FPKM.txt


title: NA14_120h, rep3

description:
raw_count.txt
gene_FPKM.txt


title: NA04_48h, rep3

description:
raw_count.txt
gene_FPKM.txt


title: Ctrl_2

status: Public on Sep 15 2023

city: Beijing

first: yuchen

last: lu

address: Yard 27, Taiping Road

institute: Beijing Institute of Basic Medical Sciences

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: Tab-delimited text files include FPKM and count values for each sample

organism: Mus musculus

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: age

tag: genotype

value: wild type


title: NA04_48h, rep2

description:
raw_count.txt
gene_FPKM.txt


title: P522R_5xFAD_M #31 (Neuropathology)

type: RNA

city: Stanford

first: Andy

middle: P

last: Tsai

state: California

address: 290 Jane Stanford Way E365

country: USA

institute: Stanford University

description:
X7M.M7.31.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels

hyb_protocol: standard NanoString protocol

scan_protocol: standard NanoString protocol

data_processing:
Data were processed, normalized, and combined using NanoString nSolver 4.0 analysis software.
Processed data matrix represents normalized log2 values.

label: NanoString

source_name: mouse cortex

label_protocol: standard NanoString protocol

extract_protocol: Total RNAs were prepared with Purelink RNA Mini Kit and subjected to NanoString analysis

tag: Sex

value: Male

tag: disease state

value: 5xFAD P522R mice

tag: tissue

value: brain cortex


title: P522R_5xFAD_M #30 (Neuropathology)

description:
X7M.M6.30.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: NA04_48h, rep1

description:
raw_count.txt
gene_FPKM.txt


title: P522R_5xFAD_M #29 (Neuropathology)

description:
X7M.M5.29.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: P522R_5xFAD_M #27 (Neuropathology)

description:
X7M.M4.27.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: WT_120h, rep2

description:
raw_count.txt
gene_FPKM.txt

value: WT


title: WT_120h, rep3

description:
raw_count.txt
gene_FPKM.txt


title: P522R_5xFAD_M #21 (Neuropathology)

description:
X7M.M2.21.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: P522R_5xFAD_F #8 (Neuropathology)

description:
X7M.F.8.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels

value: Female


title: WT_120h, rep1

description:
raw_count.txt
gene_FPKM.txt


title: P522R_5xFAD_F #49 (Neuropathology)

description:
X7M.F3.49.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: P522R_5xFAD_F #60 (Neuropathology)

description:
X7M.F6.60.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: P522R_5xFAD_M #23 (Neuropathology)

description:
X7M.M3.23.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: WT_48h, rep2

description:
raw_count.txt
gene_FPKM.txt


title: WT_48h, rep1

description:
raw_count.txt
gene_FPKM.txt


title: WT_48h, rep3

description:
raw_count.txt
gene_FPKM.txt


title: NA04_120h, rep1

description:
raw_count.txt
gene_FPKM.txt


title: P522R_5xFAD_F #54 (Neuropathology)

description:
X7M.F4.54.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: P522R_5xFAD_F #24 (Neuropathology)

description:
X7M.F2.24.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: P522R_5xFAD_F #106 (Neuropathology)

description:
X7M.F1.106.P522R.5xFAD.Ctx
nCounter® Neuropathology Panels


title: M28L_5xFAD_M #17 (Neuropathology)

description:
X7M.M9.17.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels

value: 5xFAD M28L mice


title: paired sgRNA-target library_input-lib_rep2_S26

city: CHICAGO

first: Yuan

last: Wu

state: Illinois

address: 929 E 57th St, GCIS E535

department: Chemistry

institute: University of Chicago

library_source: genomic

data_processing:
Adapter trimming and demultiplexing were performed using default algorithms provided by the NextSeq1000/2000 instrument.
Eeads were mapped to the designed sequences using Python v3.8. Reads were considered if 1) the R1 read contains “GTTTTAGAGCTAGA”, the first 14 nucleotides of the gRNA backbone; 2) the R1 read carries a spacer perfectly matched to the designed library; 3) the protospacer carries only C-to-T and A-to-G mutations compared to the spacer; 4) the R2 read contains a desired NGG PAM adjacent to the protospacer.
Assembly: Not applicable
Supplementary files format and content: Excel
Supplementary files format and content: All the mapped reads were output to excel with the corresponding information in Clinvar. Editing were showed as mismatched.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Transfected cells were incubated for an additional 3 days before harvesting. Genomic DNA was extracted using a Quick-DNA Miniprep Plus Kit (Zymo, D4069) following the manufacture’s protocol.
HEK293T cells were seeded into two 6 cm tissue culture dishes at a density of 1 x 106 cells per dish, and infected 18 h post-seeding with 2.5 mL lentiviral library at low multiplicity of infection (MOI) using 10 μg/mL polybrene. Cells were trypsinized 24 h post-infection, transferred into two 10 cm tissue culture dishes, and grown in DMEM medium supplemented with 10% FBS and 2 μg/mL puromycin. Cells were cultured and selected with 2 μg/mL puromycin for an additional 14 days. To maintain the diversity of the paired sgRNA-target library, cells were split and passaged at a minimum density of 1 x 107 cells per passage.

tag: cell line


title: M28L_5xFAD_M #21 (Neuropathology)

description:
X7M.M3.21.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: ABE8e_rep1_S29


title: M28L_5xFAD_M #15 (Neuropathology)

description:
X7M.M2.15.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: paired sgRNA-target library_input-lib_rep1_S21


title: ABE8r_rep1_S30


title: ABE8.20_rep2_S5


title: ABE8r_rep2_S7


title: M28L_5xFAD_M 9 (Neuropathology)

description:
X7M.M7.9.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: M28L_5xFAD_M #10 (Neuropathology)

description:
X7M.M8.10.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: ABE8e_rep2_S6


title: M28L_5xFAD_M #11 (Neuropathology)

description:
X7M.M1.11.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: ABE8.20_rep1_S28


title: ABE7.10_rep2_S4


title: M28L_5xFAD_F #28 (Neuropathology)

description:
X7M.F3.28.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: ABE7.10_rep1_S27


title: M28L_5xFAD_F #16 (Neuropathology)

description:
X7M.F9.16.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: M28L_5xFAD_F #20 (Neuropathology)

description:
X7M.F2.20.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: M28L_5xFAD_F8 #14 (Neuropathology)

description:
X7M.F8.14.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: M28L_5xFAD_F #12 (Neuropathology)

description:
X7M.F7.12.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: ABE-RA3.0_rep1_S8


title: ABE-RA3.0_rep2_S9


title: M28L_5xFAD_F1 #14 (Neuropathology)

description:
X7M.F1.14.M28L.5xFAD.Ctx
nCounter® Neuropathology Panels


title: ABE-RA2.0_rep2_S32


title: 5xFAD_M #1182 (Neuropathology)

description:
X7M.M3.1182.WT.5xFAD.Ctx
nCounter® Neuropathology Panels

value: 5xFAD mice


title: 5xFAD_M #1269 (Neuropathology)

description:
X7M.M5.1269.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: 5xFAD_M #1270 (Neuropathology)

description:
X7M.M6.1270.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: 5xFAD_M #1268 (Neuropathology)

description:
X7M.M4.1268.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: ABE-RA2.0_rep1_S31


title: 5xFAD_F #1253 (Neuropathology)

description:
X7M.F6.1253.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: 5xFAD_F #1248 (Neuropathology)

description:
X7M.F4.1248.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: 5xFAD_M #1181 (Neuropathology)

description:
X7M.M2.1181.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: 5xFAD_F #1190 (Neuropathology)

description:
X7M.F3.1190.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: 5xFAD_M #1177 (Neuropathology)

description:
X7M.M1.1177.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: 5xFAD_F #1249 (Neuropathology)

description:
X7M.F5.1249.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: 5xFAD_F #1180 (Neuropathology)

description:
X7M.F1.1180.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: 5xFAD_F #1189 (Neuropathology)

description:
X7M.F2.1189.WT.5xFAD.Ctx
nCounter® Neuropathology Panels


title: PER-403_taz+ABBV-07_IgG_rep2

city: Houston

first: Kyle

last: Eagen

state: TX

address: 1 Baylor Plaza

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Basecalling was performed using Illumina DRAGEN FASTQ Generation v3.7.4.
Reads were trimmed for adaptor sequences using trimmomatic v0.36.
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 (GRCh38) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using using bowtie2 v2.3 with options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Properly paired, mapped reads with a MAPQ ≥ 30 were retained using samtools v1.3.
PCR duplicates were removed with picard MarkDuplicates v2.9.
deepTools v3.4 was used to compute signal tracks by running bamCoverage with parameters --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2800000000 --extendReads --samFlagInclude 64 --scaleFactor $OR where the occupancy ratio ($OR) is used for spike-in normalization with D. melanogaster as the calibration genome, as previously described (Hu et al., 2015).
Epic2 v0.0 was used to identify broadly enriched domains with parameters -w 200 -g 5. IgG libraries were used as controls for domain annotation.
Called domains were filtered by signal strength and by domain size. Signal strength was determined by subtracting the rpm normalized input reads from rpm normalized sample reads for each called domain and subsequently ranked in increasing order of counts. The ROSE algorithm (Rank Ordering of Super-Enhancers) (Whyte et al., 2013) was applied to the ranked dataset to determine the cutoff threshold for signal strength by sliding a diagonal line and finding the point along the abscissa where the diagonal line was tangent to the rank-ordered curve. The cutoff for feature size was determined in a similar manner by ranking the domain length in base pairs and applying ROSE. Domains that exceeded both the signal cutoff and the size threshold were retained using bedtools intersect v2.30 with default parameters.
Often, we observed closely spaced domains and to span these domains and capture the entire domain, domains within 25 kb of one another were combined using bedtools v2.30 with command bedtools merge.
The above was performed for each biological replicate, and, then, to create the highest confidence domain list, domains identified in both replicates were merged using bedtools intersect v2.30 with default parameters. The resulting domains were considered “megadomains”. Epic2-identified domains that overlapped in each biological replicate but did not overlap with megadomains were considered "not Megadomains".
Assembly: GRCh38 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary files format and content: *.bw file of CUT&RUN track in bigWig format.
Supplementary files format and content: *.bed file of domain locations in bed format.
Library strategy: CUT&RUN

growth_protocol: 10-15 cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) + 1.25 µg/mL Plasmocin prophylactic (Invivogen #ant-mpp) at 37° C with 5% CO2.    PER-403 cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 20% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) + 1.25 µg/mL Plasmocin prophylactic (Invivogen #ant-mpp) at 37° C with 5% CO2.    Kc167 cells were grown in CCM3 Media (HyClone #SH30062.02) at 25° C.

extract_protocol:
Human cells were mixed with Drosophila cells at a 4:1 ratio and then cells were bound to magnetic beads and permeabilized with digitonin. Permeabilized cells were incubated with the indicated antibody plus an anti-Drosophila Histone H2Av antibody (Active Motif Spike-in Antibody, #61686) overnight. Antibody-bound chromatin was released by in situ protein A-MNase digestion and the soluble DNA then purified.
DNA was prepared for next-generation sequencing using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Tazemetostat and ABBV-075 were solubilized in DMSO. Cells were treated with 1 µM tazemetostat (0.1% final DMSO) or 1 µM tazemetostat + 0.702 nM ABBV-075 (0.1% final DMSO) for 96 hours. After the first 48 hours of treatment, cells were retreated with fresh growth media and compounds.

value: NUT carcinoma

tag: treatment

value: 1 µM Tazemetostat + 0.702 nM ABBV-075

tag: antibody

value: rabbit anti-mouse IgG H&L (Abcam #ab46540, RRID:AB_2614925)

tag: spike-in

value: Drosophila melanogaster Kc167 cells


title: K16_control

type: genomic

city: Liverpool

first: Christian

last: Hedrich

state: Please select...

address: Department of Women's & Children's Health,University of Liverpool, Alder Hey Children's NHS Foundation Trust,Eaton Road,

country: United Kingdom

description:
control
main analysis

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPICBeadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R environnment and packages Minfi and ChAMP
Average Beta

label: Cy5 and Cy3

source_name: PBMCs

label_protocol: Standard Illumina protocol

growth_protocol: cells obtained from patients PBMCs

extract_protocol: genomic DNA was extracted from sorted CD4+T cells using All prep Kit (Qiagen) according to manufacturer instructions

treatment_protocol: no treatment

tag: gender

tag: patient group

value: control

tag: pasi score


title: PER-403_taz_IgG_rep2

value: 1 µM Tazemetostat


title: PER-403_taz+ABBV-07_H3K27ac_rep2

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (Cell Signaling Technology #8173, RRID:AB_10949503)


title: K18_control

department: Department of Women's & Children's Health

description:
control
main analysis


title: K15_control

description:
control
main analysis


title: PER-403_taz_H3K27me3_rep2

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (Cell Signaling Technology #9733, RRID:AB_2616029)


title: PER-403_taz_H3K27ac_rep2


title: K14_control

description:
control
main analysis


title: K13_control

description:
control
main analysis


title: K12_control

description:
control
main analysis


title: PER-403_DMSO_IgG_rep2

value: 0.1% DMSO


title: PER-403_DMSO_H3K27me3_rep2


title: PER-403_DMSO_H3K27ac_rep2


title: K11_control

description:
control
main analysis


title: PER-403_taz+ABBV-07_IgG_rep1


title: K10_control

description:
control
main analysis


title: P12_secondAfter

description:
patient
main analysis


title: PER-403_taz+ABBV-07_H3K27me3_rep2


title: PER-403_taz+ABBV-07_H3K27ac_rep1


title: PER-403_taz+ABBV-07_H3K27me3_rep1


title: P18_After

description:
patient
main analysis

value: After


title: P18_before

description:
patient
main analysis

value: Male

value: Before


title: PER-403_taz_H3K27me3_rep1


title: P12_After

description:
patient
main analysis


title: PER-403_taz_H3K27ac_rep1


title: P17_secondAfter

description:
patient
main analysis


title: P17_before

description:
patient
main analysis


title: PER-403_DMSO_H3K27me3_rep1


title: 10-15_taz+ABBV-075_IgG_rep2


title: P17_After

description:
patient
main analysis


title: P2_after

description:
patient
main analysis


title: P5_after

description:
patient
main analysis


title: P1_after

description:
patient
main analysis


title: PER-403_DMSO_IgG_rep1


title: 10-15_taz+ABBV-075_H3K27me3_rep2


title: P22_After

description:
patient
main analysis


title: 10-15_taz+ABBV-075_H3K27ac_rep2


title: P12_before

description:
patient
main analysis


title: 10-15_taz_IgG_rep2


title: P2_before

description:
patient
main analysis


title: 10-15_taz_H3K27me3_rep2


title: 10-15_taz_H3K27ac_rep2


title: P1_before

description:
patient
main analysis


title: PER-403_taz_IgG_rep1


title: P31

description:
patient
main analysis
P31,PsA Patient,m,62,60_70_80N,6,2.05657E+11, R05C01

value: PsA Patient


title: 10-15_DMSO_IgG_rep2


title: P23

description:
patient
main analysis
P23,PsA Patient,w,81,60_70_80N,3.4,2.05657E+11, R04C01


title: 10-15_DMSO_H3K27ac_rep2


title: 10-15_DMSO_H3K27me3_rep2


title: PER-403_DMSO_H3K27ac_rep1


title: P18

description:
patient
main analysis
P18,psoriasis,m,68,60_70_80N,10.9,2.05657E+11, R02C01

value: psoriasis


title: P32

description:
patient
main analysis
P32,psoriasis,m,51,40_50N,21.3,2.05657E+11, R03C01


title: 10-15_taz+ABBV-075_IgG_rep1


title: P17

description:
patient
main analysis
P17,psoriasis,m,45,40_50N,21.8,2.05657E+11, R01C01


title: 10-15_taz+ABBV-075_H3K27ac_rep1


title: P16

description:
patient
main analysis
P16,psoriasis,w,27,20_30N,10.2,2.05657E+11, R06C01

value: Female


title: P14

description:
patient
main analysis
P14,psoriasis,m,49,40_50N,14.9,2.05657E+11, R04C01


title: P15

description:
patient
main analysis
P15,psoriasis,w,37,30_40N,10.5,2.05657E+11, R05C01


title: K18

description:
control
main analysis
K18,control,w,49,40_50N,-,2.05657E+11, R02C01


title: 10-15_taz_IgG_rep1


title: 10-15_DMSO_IgG_rep1


title: P11

description:
patient
main analysis
P11,PsA Patient,w,73,60_70_80N,10.2,2.05657E+11, R05C01


title: 10-15_DMSO_H3K27me3_rep1


title: 10-15_taz_H3K27me3_rep1


title: 10-15_DMSO_H3K27ac_rep1


title: P8

description:
patient
main analysis
P8,psoriasis,m,51,40_50N,12.4,2.05657E+11, R04C01


title: K16

description:
control
main analysis
K16,control,w,28,20_30N,-,2.05657E+11, R01C01


title: K15

description:
control
main analysis
K15,control,w,25,20_30N,-,2.05657E+11, R03C01


title: K14

description:
control
main analysis
K14,control,m,28,20_30N,-,2.05657E+11, R02C01


title: LNCaP_EHMT1_K450R451R_DOXUNC_B_rep2

city: Boston

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

description: LNCaP_EHMT1_K450RK451R_UNC_count_table.txt.gz

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (version 1.6.4) from GRCh37 Ensembl reference.
Assembly: hg19
Supplementary files format and content: txt file for raw counts of sequence reads

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
RNA-seq libraries  were performed by using TruSeq® Strnd Total RNA LT (Illumina).

value: Treated with 0.5ug/mL doxycyline and 2uM of UNC0642


title: LNCaP_EHMT1_K450R451R_DOXUNC_B_rep1


title: LNCaP_EHMT1_K450RK451R_UNC0642_B_rep2

value: Treated with 2uM of UNC0642


title: K13

description:
control
main analysis
K13,control,m,26,20_30N,-,2.05657E+11, R01C01


title: LNCaP_EHMT1_K450RK451R_UNC0642_B_rep1


title: P13

description:
patient
main analysis
P13,PsA Patient,m,70,60_70_80N,7.6,2.05657E+11, R06C01


title: P20

description:
patient
main analysis
P20,PsA Patient,m,49,40_50N,0.8,2.05657E+11, R07C01


title: LNCaP_EHMT1_K450RK451R_Veh_B_rep2

value: Treated with DMSO


title: 10-15_taz+ABBV-075_H3K27me3_rep1

value: NUT carcinoma

value: 1 µM Tazemetostat + 0.702 nM ABBV-075


title: P6

description:
patient
main analysis
P6,psoriasis,w,21,20_30N,16.5,2.05657E+11, R05C01


title: LNCaP_EHMT1_K450RK451R_Veh_B_rep1


title: LNCaP_siEHMT2_B_rep1

source_name: LNCaP

value: LNCaP

value: Treated with 20nM siEHMT2


title: P4

description:
patient
main analysis
P4,psoriasis,w,76,60_70_80N,33.1,2.05657E+11, R04C01


title: K12

description:
control
main analysis
K12,control,m,23,20_30N,-,2.05657E+11, R03C01

value: control


title: 10-15_taz_H3K27ac_rep1

value: 1 µM Tazemetostat

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (Cell Signaling Technology #8173, RRID:AB_10949503)

value: Drosophila melanogaster Kc167 cells


title: K11

description:
control
main analysis
K11,control,m,34,30_40N,-,2.05657E+11, R02C01


title: LNCaP_siNTC_B_rep2

value: Treated with 20nM siNTC


title: K10

description:
control
main analysis
K10,control,w,26,20_30N,-,2.05657E+11, R01C01


title: P12

description:
patient
main analysis
P12,PsA Patient,w,30,30_40N,25.1,2.05657E+11, R08C01


title: LNCaP_siNTC_B_rep1


title: P10

description:
patient
main analysis
P10,PsA Patient,m,40,30_40N,15,2.05657E+11, R07C01

value: Male


title: P2

description:
patient
main analysis
P2,psoriasis,m,25,20_30N,16.3,2.05657E+11, R06C01


title: H1-CA3-K27Ac

city: Trondheim

first: Stefan

last: Blankvoort

address: Olav Kyrresgt 9

department: Kavli Institute for systems Neuroscience

country: Norway

institute: NTNU

data_processing:
Aligning
Peak calling
Diffbind (details in methods)
Assembly:  mm10
Supplementary files format and content: Count table output from DiffBind in Rdata format.

growth_protocol: No culturing

extract_protocol:
Tissue was fixed with 1% formaldehyde for 10 minutes, quenched with 150mM Glycine, sonicated on a Qsonica Q800 for 30 minutes on a 10sec on-off schedule at 15-20W per tube
We used the Rubicon genomics Thruplex DNA-seq kit for library preparation
Three pools, 48 barcodeseach

value: WT

tag: chip antibody

value: K27Ac (Diagenode H3K27Ac Rabbit polyclonal, Cat# C15410196, lot# A1723-0041D)


title: J1-VentralHC-K27Ac

source_name: VentralHC

value: VentralHC


title: P4-VentralStriatum-K27Ac

source_name: VentralStriatum

value: VentralStriatum


title: B1-PreSubiculum-K27Ac

source_name: PreSubiculum

value: PreSubiculum


title: C1-Pre-Para-Subiculum-Input

source_name: Pre-Para-Subiculum

value: Pre-Para-Subiculum


title: B1-PreSubiculum-Input


title: T4-Claustrum-K27Ac

source_name: Claustrum

value: Claustrum


title: E2-DeepMEC-K27Ac

source_name: DeepMEC

value: DeepMEC


title: F1-Subiculum-Input

source_name: Subiculum

value: Subiculum


title: H1-CA3-Input


title: LNCaP_siEHMT2_B_rep2

value: LNCaP


title: F1-Subiculum-K27Ac


title: I2-CA1-Input


title: F2-Subiculum-Input


title: F2-Subiculum-K27Ac


title: P3-VentralStriatum-Input


title: T3-Claustrum-Input


title: J2-VentralHC-Input


title: H2-CA3-K27Ac


title: E1-DeepMEC-K27Ac


title: A2-VisCtx-Input

source_name: VisCtx

value: VisCtx


title: G2-DG-K27Ac

source_name: DG

value: DG


title: J2-VentralHC-K27Ac


title: P1

description:
patient
main analysis
P1,psoriasis,w,33,30_40N,19.5,2.05657E+11, R05C01

value: Female

value: psoriasis


title: T3-Claustrum-K27Ac


title: H2-CA3-Input


title: R4-AnteriorThalamus-Input

source_name: AnteriorThalamus

value: AnteriorThalamus


title: P3-VentralStriatum-K27Ac


title: K3-SomCtx-Input

source_name: SomCtx

value: SomCtx


title: A2-VisCtx-K27Ac


title: L3-PirCtx-K27Ac

source_name: PirCtx

value: PirCtx


title: T cells, tNGFR knockin, BATF antibody, donor 3

city: San Francisco

first: Franziska

last: Blaeschke

state: CA

address: 1650 Owens Street

institute: Gladstone Institutes

description:
tNGFR_BATF_3
dds.chip.batf2.rds

data_processing:
Sequencing adapters were trimmed using Trimmomatic.
The reads were aligned to the hg38 reference genome using Bowtie2 with the --very-sensitive option.
The resulting BAM files were sorted by genomic coordinates using Samtools to remove PCR duplicates. Duplicates after alignment and sorting were marked and removed by Picard.
Assembly: hg38 reference genome
Supplementary files format and content: Rds file generated after data processing including all samples

source_name: Blood

extract_protocol:
Sorted CAR T cells (5e6) were double crosslinked by 50 mM DSG (disuccinimidyl glutarate, ProteoChem) for 30 min followed by 10 min of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated using ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator using the following setup: Fill level – 10, Duty Cycle – 5, PIP – 140, Cycles/Burst – 200, Time – 4 min. Sheared chromatin was immunoprecipitated overnight with the following antibodies: BATF (brookwoodbiomedical – pab4003), TFAP4 (kind gift from Takeshi Egawa’s group). Antibody chromatin complexes were pulled down with Protein A magnetic beads and washed once in IP wash buffer I. (1% Triton, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer II. (1% Triton, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), once in IP wash buffer III. (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC) and once in TE buffer (10 mM EDTA and 200 mM Tris, pH 8.0). DNA was eluted from the beads by vigorous shaking for 20 minutes in elution buffer (100 mM NaHCO3, 1% SDS). DNA was decrosslinked overnight at 65C and purified with MinElute PCR purification kit (Qiagen).
DNA was quantified by Qubit and 10 ng DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 12 PCR cycles according to the manufacturer’s recommendations.

tag: individual

value: donor 3

value: Blood

value: Primary cells

value: T cells

value: tNGFR knockin

value: BATF


title: T cells, BATF knockin, BATF antibody, donor 3

description:
BATF_BATF_3
dds.chip.batf2.rds

tag: cell type

value: BATF knockin


title: T cells, TFAP4 knockin, BATF antibody, donor 3

description:
TFAP4_BATF_3
dds.chip.batf2.rds

value: TFAP4 knockin


title: T cells, BATF-TFAP4 knockin, BATF antibody, donor 3

description:
BATF-TFAP4_BATF_3
dds.chip.batf2.rds

value: BATF-TFAP4 knockin


title: Q4-MidlineThalamus-Input

source_name: MidlineThalamus

value: MidlineThalamus

value: WT


title: A1-VisCtx-Input

value: VisCtx


title: L3-PirCtx-Input


title: T cells, tNGFR knockin, BATF antibody, donor 2

description:
tNGFR_BATF_2
dds.chip.batf2.rds

value: donor 2


title: P4-VentralStriatum-Input

value: VentralStriatum


title: I2-CA1-K27Ac

value: K27Ac (Diagenode H3K27Ac Rabbit polyclonal, Cat# C15410196, lot# A1723-0041D)


title: T cells, TFAP4 knockin, BATF antibody, donor 2

description:
TFAP4_BATF_2
dds.chip.batf2.rds


title: O3-DorsalStriatum-K27Ac

source_name: DorsalStriatum

value: DorsalStriatum


title: Q4-MidlineThalamus-K27Ac


title: T cells, BATF knockin, BATF antibody, donor 2

description:
BATF_BATF_2
dds.chip.batf2.rds


title: S4-Thalamus-Input

source_name: Thalamus

value: Thalamus


title: T cells, TFAP4 knockin, BATF antibody, donor 1

description:
TFAP4_BATF_1
dds.chip.batf2.rds

value: donor 1


title: T cells, BATF-TFAP4 knockin, BATF antibody, donor 2

description:
BATF-TFAP4_BATF_2
dds.chip.batf2.rds

value: Blood


title: T cells, tNGFR knockin, BATF antibody, donor 1

description:
tNGFR_BATF_1
dds.chip.batf2.rds

value: Primary cells


title: S4-Thalamus-K27Ac


title: T cells, BATF knockin, BATF antibody, donor 1

description:
BATF_BATF_1
dds.chip.batf2.rds

value: T cells


title: T cells, BATF-TFAP4 knockin, BATF antibody, donor 1

description:
BATF-TFAP4_BATF_1
dds.chip.batf2.rds


title: E1-DeepMEC-Input

value: DeepMEC


title: T cells, tNGFR knockin, TFAP4 antibody, donor 3

description:
tNGFR_TFAP4_3
dds.chip.tfap4.2.rds

value: donor 3

value: tNGFR knockin


title: R4-AnteriroThalamus-K27Ac

source_name: AnteriroThalamus

value: AnteriorThalamus


title: T cells, TFAP4 knockin, TFAP4 antibody, donor 3

description:
TFAP4_TFAP4_3
dds.chip.tfap4.2.rds

value: TFAP4 knockin


title: K3-SomCtx-K27Ac

value: SomCtx


title: G1-DG-Input

value: DG

value: WT


title: T cells, BATF-TFAP4 knockin, TFAP4 antibody, donor 3

description:
BATF-TFAP4_TFAP4_3
dds.chip.tfap4.2.rds

value: BATF-TFAP4 knockin


title: T cells, tNGFR knockin, TFAP4 antibody, donor 2

description:
tNGFR_TFAP4_2
dds.chip.tfap4.2.rds

value: donor 2


title: G1-DG-K27Ac

value: K27Ac (Diagenode H3K27Ac Rabbit polyclonal, Cat# C15410196, lot# A1723-0041D)


title: C1-Pre-Para-Subiculum-K27Ac

value: Pre-Para-Subiculum


title: T cells, BATF knockin, TFAP4 antibody, donor 2

description:
BATF_TFAP4_2
dds.chip.tfap4.2.rds

value: BATF knockin


title: A1-VisCtx-K27Ac

value: VisCtx


title: T cells, BATF-TFAP4 knockin, TFAP4 antibody, donor 2

description:
BATF-TFAP4_TFAP4_2
dds.chip.tfap4.2.rds

value: Blood


title: E2-DeepMEC-Input


title: T cells, BATF knockin, TFAP4 antibody, donor 1

description:
BATF_TFAP4_1
dds.chip.tfap4.2.rds

value: donor 1

value: Primary cells


title: T cells, TFAP4 knockin, TFAP4 antibody, donor 1

description:
TFAP4_TFAP4_1
dds.chip.tfap4.2.rds

value: T cells


title: O3-DorsalStriatum-Input

value: DorsalStriatum


title: T cells, BATF-TFAP4 knockin, TFAP4 antibody, donor 1

description:
BATF-TFAP4_TFAP4_1
dds.chip.tfap4.2.rds


title: T cells, tNGFR knockin, TFAP4 antibody, donor 1

description:
tNGFR_TFAP4_1
dds.chip.tfap4.2.rds

value: tNGFR knockin


title: HEK293T_non-treat.rep2

data_processing:
Adapter-removed data were generated by Illumina Nextseq 550. Reads were mapped to hg37 genome using STAR v2.6.1b. Only uniquely mapped read were kept and deduplication were doen by rmdup function of samtools v1.16.1. Off targeting editing variants were called out by Reditools v2.0. Fisher exact test and filtration were performed with homemade python script.
Assembly: hg37

molecule: polyA RNA

extract_protocol: HEK293T cell were seeded into 24-welll plate (Corning) one day before transfection. After confluency of cell reach 80%, transfection of base editor and gRNA as plasmid DNA or RNA were done with Lipofectamine 2000 (Thermo Fisher Scientific), as described previously. After incubating 72h at 37 °C, cell were washed with 1x PBS and then lysed with TRIzol (THermo Fisher Scientific). Total RNA extraction, mRNA purification and RNA library preparation were done using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs), following the manufacturer's instruction. Final library were quantified using Library Quantification Kit (KAPA Biosystems) and sequenced on a NextSeq 500/550 High Output Kit v2.5 (75 Cyclies) as 85nt single-end reads.

value: no treatment

tag: library type

value: in vivo transcribed RNA


title: G2-DG-Input


title: HEK293T_non-treat.rep1


title: HEK293T_nCas9.rep2


title: T cells, BATF knockin, TFAP4 antibody, donor 3

description:
BATF_TFAP4_3
dds.chip.tfap4.2.rds

value: donor 3


title: HEK293T_nCas9.rep1


title: T4-Claustrum-Input

value: Claustrum


title: T cells, TFAP4 knockin, TFAP4 antibody, donor 2

description:
TFAP4_TFAP4_2
dds.chip.tfap4.2.rds

value: TFAP4 knockin


title: J1-VentralHC-Input

source_name: VentralHC

value: VentralHC

value: WT


title: HEK293T_nCas9-mRNA.rep2


title: 272LNnT2

first: Shuqi

last: Li

address: 60 Fenwood Rd.

department: Neurology

institute: Harvard Medical School and Brigham and Women's Hospital

description:
UMA272 HMO as N.txt
DESeq2-UMA272.299.302nagctrl.nagcys.summary.csv

data_processing:
The raw reads quality was checked by FastQC (v1.0.0).
For libraries prepared by NEBNext Ultra II Directional RNA library Prep Kit, the sequencing adapters were removed by Trimmomatic (v0.32). For libraries prepared by TruSeq Stranded mRNA Library Preparation Kit, the sequencing adapters were trimmed by using the Illumina FASTQ generation pipelines.
The quality-controlled and trimmed reads were then aligned to the Bifidobacterium longum subsp. infantis ATCC 15697T genome (NCBI accession number: NC_011593.1) using bowtie2 (v2.1.0)
The aligned reads were sorted by SAMtools (v1.0) and counted against specific genomic locus by using HTSeq (v0.6.1) for differential expression analysis.
Differentially expressed gene (DEG) analysis was performed using the R Package DESeq2 (v3.3.1) and log2 fold changes obtained for one condition relative to other
Assembly: Bifidobacterium longum subsp. infantis ATCC 15697
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Normalized abundance measurements from DeSeq2

organism: Bifidobacterium longum subsp. infantis

source_name: human infant feces

growth_protocol: Bifidobacterium infantis  was routinely propagated in De Man Rogosa Sharp medium supplemented with 0.05 % (m/v) L-cysteine hydrochloride at 37°C under anaerobic conditions.

extract_protocol:
Bacteria cells were harvested at exponential phase and pelleted immediately by centrifugation at 12,000 × g for 1 min and resuspended in 1 ml of RNAlater Ambion (Thermo Fisher Scientific, Waltham, MA, USA), and incubated at 4 °C overnight and then stored at – 80 °C until further analysis. RNA isolation was performed using a Ambion RNAqueousTM kit (Thermo Fisher Scientific) following manufacturer instructions. An additional step of bead-beating for cell disruption (FastPrep-24TM 5G, MP Biomedicals Inc, Santa Ana, CA, USA) was added to the RNA isolation procedure. Total RNA was immediately treated with the Turbo DNase free kit (Ambion, Thermo Fisher Scientific).
Total RNA was treated with Ribo-Zero rRNA Removal kit, Bacteria (Illumina, San Diego, CA, USA) to remove ribosomal RNA according to manufacturer instructions. The depleted RNA was purified with RNAeasy MinElute Cleanup kit (Qiagen, Valencia, CA, USA).  Whole transcriptome libraries were constructed using TruSeq Stranded mRNA Library Preparation Kit (Illumina) or NEBNext Ultra II Directional RNA library Prep Kit for Illumina (New England Biolabs Inc, MA, USA) following manufacturer instructions.

treatment_protocol: Bifidobacterium longum subsp. infantis were grown in mMRS media supplemented with pooled HMOs (2%, w/v), LNT (2%), LNnT (2%), NAG (2%), complex nitrogen (1% peptone, 0.5% yeast extract, 0.5% ammonium citrate) or L-cysteine (0.15%) as the nitrogen source, while 2% lactose as supplemented as the carbohydrate source.

tag: agent

value: LNnT

tag: strain

value: 2percent LNnT


title: 272LNnT1


title: CTRL_TMX [24d]

city: Ciudad de Mexico

first: Yalbi

middle: Itzel

last: Balderas-Martinez

state: Distrito Federal

address: Calzada de Tlalpan 4502, Sección XVI, Belisario Domínguez

country: Mexico

institute: INER

hyb_protocol: and hybridized on the array (Clariom S Assays Array Thermo Fisher), which detects both mRNA kit (Affymetrix, Santa Clara, CA, USA) and lncRNA

scan_protocol: Arrays were washed, stained, and scanned using a Genechip Scanner 3000 7G (Affymetrix).

data_processing: Quality analysis was performed using the affycoretools package version 1.64. The data were normalized with the Robust Multichip Analysis (RMA) function of the oligo package version 1.56, and for the differential analysis of gene expression, we used the limma package version 3.48.3, using a linear model based on the Bayes empirical method. Gene annotation was performed using the package pd.clariom.s.rat version 3.14.1

organism: Rattus norvegicus

source_name: No lesion and treatment LM- TMX+

label_protocol: labelled with the SensationPlusTM FFPE Amplification and WT Labelling

growth_protocol: Forty-four adult male, 269-365g Long-Evans rats were used in this study. After surgery, all animals were housed in individual cages in a 12 h light/dark cycle under controlled temperature and humidity. A standard diet based on rat chow and water was provided ad libitum.

extract_protocol: Frozen tissues were homogenized using a Kinematica™ Polytron™ PT2500E desktop homogenizer (Fisher Scientific). 200g of total RNA was extracted from homogenized tissues using the TRIzol (Invitrogen) method following the manufacturer's recommendations. RNA concentration and integrity were obtained using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only samples with RIN ≥ 7 were used for transcriptome analysis.

treatment_protocol: Animals were anesthetized with a mixture of ketamine (80 mg/kg) and xylazine (8 mg/kg) i.m. Afterwards, a laminectomy was performed under aseptic conditions to expose the dorsal surface of the dural sac at the  ninth thoracic (T9) level of the spine. The rats were positioned in the stereotactic frame by clamping T8 and T10 spinous processes to inflict the injury. The SCI consisted of a lesion by contusion using the New York University weight-drop device (MASCIS impactor) by dropping a 10 g rod from a height of 50 mm, resulting in an injury of severe intensity. After the lesion, the wound was sutured in layers. Non-injured (sham) animals only underwent soft tissue surgery without laminectomy or SCI. Intramuscular tramadol (5 mg/kg) was administered perioperatively to prevent pain. Neurogenic bladder handling was performed by manual expression twice a day.  A suspension of TMX (T5648, Sigma-Aldrich, Saint Louis, MO) was prepared by mixing each dose (5 mg/kg) in the vehicle (ethyl alcohol 100 μL + corn oil 1 mL). To achieve a homogenous mix, the suspension was prepared by heating the mixtures at 50 o C in a water bath for 5 min, followed by vortex agitation for 10 s three times. Rats received a single intraperitoneal dose of tamoxifen or vehicle 30 min after SCI or sham surgeries.

value: Long-Evans

value: male

tag: age

value: adult

value: No lesion and treatment LM- TMX+

tag: replicate


title: HEK293T_nCas9-mRNA.rep1


title: HEK293T_ABE8r.rep2


title: 272LNT2

value: LNT

value: 2percent LNT


title: CTRL_TMX [22d]

label: SensationPlusTM FFPE Amplification and WT Labelling

tag: Sex


title: 272LNT1


title: HEK293T_ABE8r-mRNA.rep2


title: HEK293T_ABE8r.rep1


title: HEK293T_ABE8r-R153dele.rep2


title: HEK293T_ABE8r-R153dele.rep1


title: CTRL_TMX [21d]


title: 272HMO2

value: pooled HMO

value: 2percent pooled HMO


title: HEK293T_ABE8r-A106W.rep2


title: 272HMO1


title: CTRL_TMX [19d]


title: HEK293T_ABE8r-A106W.rep1


title: HEK293T_ABE8r-mRNA.rep1


title: CTRL_TMX [23d]


title: LM_NoTMX [17c]

source_name: With lesion no treatment LM+ TMX-

value: With lesion no treatment LM+ TMX-


title: CTRL_TMX [20d]


title: LM_NoTMX [16c]


title: HEK293T_ABE7.10.rep2

value: in vivo transcribed RNA


title: 272ctrl1

value: control

value: 2percent complex nitrogen


title: HEK293T_ABE8.20.rep1


title: LM_TMX [11b]

source_name: With lesion and treatment LM+ TMX+

value: With lesion and treatment LM+ TMX+


title: LM_NoTMX [15c]


title: LM_TMX [12b]


title: LM_NoTMX [13c]


title: HEK293T_ABE7.10.rep1


title: LM_NoTMX [18c]


title: C, WTR, Day9, rpt5

city: Yamaguchi

first: Ryosuke

last: Mega

address: 1677-1, Yoshida

country: Japan

institute: Yamaguchi University

data_processing:
The raw sequence data were trimmed and qualified by trimmomatic (version 0.39) with default parameters.
The clean reads were aligned to the primary transcripts of the wheat reference genome by kallisto (version 0.46.2) with default parameters.
Assembly: IWGSC (ensembl49)
Supplementary files format and content: A fileset (an HDF5 and a tab-delimited table files for transcript abundance, and a JSON file for running log) for each kallisto run.

organism: Triticum aestivum

source_name: Spikelet

growth_protocol: The plants were cultivated at 25°C (14-h light)/15°C (10-h dark), with relative humidity levels of 40% (light)/60% (dark) until anthesis.

extract_protocol:
RNA was extracted using TRIzol from frozen spikelets. 6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEXTflex Rapid DIR mRNA Bundle following manufacturer's protocols.

treatment_protocol: The water supply was stopped for drought-treated samples (DR2, 5, 7, and 9) and continued for the well-watered ones (WTR2, 5, 7, and 9).

tag: tissue

value: Spikelet

tag: line

tag: genotype

value: Well-watered

tag: time


title: C, WTR, Day9, rpt4

tag: treatment


title: 302NAG2

description:
UMA272 UMA299 UMA302 NAG as N feature table.txt
DESeq2-UMA272.299.302nagctrl.nagcys.summary.csv

value: NAG

value: 2percent NAG


title: 299NAG2


title: C, WTR, Day9, rpt6


title: HEK293T_ABE8e.rep1


title: C, WTR, Day9, rpt3


title: HEK293T_ABE8.20.rep2


title: 299NAG1


title: C, WTR, Day9, rpt1


title: LM_TMX [9b]

value: Long-Evans


title: LM_TMX [10b]

value: male


title: LM_TMX [8b]

value: adult


title: 272NAG2


title: 302NAG1


title: C, WTR, Day7, rpt6

value: C


title: C, WTR, Day7, rpt4


title: C, WTR, Day7, rpt5


title: LM_TMX [7b]


title: C, WTR, Day7, rpt2


title: C, WTR, Day7, rpt3


title: C, WTR, Day7, rpt1


title: C, WTR, Day2, rpt6


title: C, WTR, Day9, rpt2


title: WT_Biological_Replicate_2

city: Brisbane

first: Carlos

middle: Horacio

last: Luna Flores

state: QLD

address: 2 george st, brisbane city

country: Australia

institute: Queensland University of Technology

data_processing:
FASTQC and Trimmomatic were used to remove poor quality reads.
Tophat was used to align RNA-seq reads against the reference genome of Phaffia rhodozyma CBS6938
Cufflinks was used to normilise and annotate the transcripts.
Cuffdiff was used to evaluate differential expression.
The cuttoff for significant differentially expressed genes was q < 0.05

organism: Phaffia rhodozyma

growth_protocol: Cells were grown in chemically defined media and sucrose as carbon source in instrumented fermenters. The pH, temperature, dissolved oxygen were measure and controlled at 5.5, 20 oC, and 70% across all the fermentation.

extract_protocol:
ZymoBiomics DNA/RNA Miniprep Kit was used for RNA extraction.
The library was prepared using the Illumina Stranded mRNA prep kit

tag: cell line

value: WT

value: Fermentation


title: WT_Biological_Replicate_3


title: C, WTR, Day2, rpt5


title: C, WTR, Day2, rpt4


title: mIgG2a 4

city: Indianapolis

first: Xavier

last: Taylor

state: Indiana

address: 307 E Merrill St

institute: Eli Lilly and Company

hyb_protocol: NanoString Technologies protocol

scan_protocol: NanoString Technologies protocol

data_processing: Counts for target genes were normalized to the best fitting house-keeping genes as determined by nSolver software to account for variability in RNA content. Background signal was calculated as a mean value of the negative hybridization control probes.

source_name: Primary BMDM

growth_protocol: The procedure used for bone marrow derived macrophage cultures was based on a previously described approach (Toda, G., et al STAR Protoc, 2021)

extract_protocol: Total RNA was isolated from primary cultures with Rneasy Plus Universal Mini Kit

treatment_protocol: Antibody coated plates were prepared using 24 well plates coated with 200 uL of 10ug/mL IgG2a, mIgG2a.LALAPG or left untreated (PBS vehicle) and sealed with parafilm and incubated overnight at 4C. After 5 days of culture (37C, 5% CO2) differentiated BMDMs were washed with PBS and detached with 5mL of 5mM EDTA for 5 minutes at 37C

value: BMDM

value: Brain


title: WT_Biological_Replicate_1


title: C, WTR, Day2, rpt3


title: CTRL_NoTMX [3a]

source_name: No lesion or treatment LM- TMX-

value: No lesion or treatment LM- TMX-


title: C, WTR, Day2, rpt2


title: CTRL_NoTMX [4a]


title: Mutant_Biological_Replicate_3

value: Mutagenised


title: mIgG2a 3


title: C, WTR, Day2, rpt1


title: CTRL_NoTMX [1a]


title: 272NAG1


title: CTRL_NoTMX [6a]


title: mIgG2a 2


title: Mutant_Biological_Replicate_2


title: C, DR, Day9, rpt4

value: Drought


title: C, DR, Day9, rpt5


title: CTRL_NoTMX [5a]


title: mIgG2a 1


title: C, DR, Day9, rpt3


title: C, DR, Day9, rpt2


title: LALAPG 4

value: +LALAPG


title: AB5075_3

city: Buenos Aires

first: Sieira

last: Rodrigo

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

data_processing:
Low-quality reads were removed using Trimmomatic v0.39
Reads were aligned witth Burrows Wheeler Alignment software (BWA) v0.7.17
Bigwig files were generated with custom bash scripts and BEDtools
Read counts per gene were determined using featureCounts v1.6.4
RNA-seq differential expression analysis was performed using DESeq2
Supplementary files format and content: .txt files containing the output of featureCounts for each sample

organism: Acinetobacter baumannii

source_name: Acinetobacter baumannii AB5075

growth_protocol: Overnight cultures of A. baumannii AB5075 and CRL 2244 with OD adjusted to 600 nm at 4.0 were centrifuged and resuspended in 3 mL of BHI broth and incubated for 90 min at 37°C.

extract_protocol:
Total RNA was extracted with Direct-zol RNA Kit (Zymo Research)
Illumina RNA-seq

value: Acinetobacter baumannii AB5075


title: AB5075_2


title: C, DR, Day7, rpt6

value: Spikelet


title: C, DR, Day9, rpt1


title: C, DR, Day7, rpt5


title: LALAPG 3


title: C, DR, Day7, rpt4


title: LALAPG 2


title: AB5075_1


title: C, DR, Day7, rpt2


title: C, DR, Day7, rpt3


title: COLO320-DM (rep)

city: WuHan

first: zou

last: yanyan

address: SHIZISHAN

institute: HZAU

data_processing:
library strategy: MGA-Seq
FastQC (version: 0.11.5) was used to assess the quality of raw reads, and FASTP (version: 0.23.2) was used to filter out the low-quality bases and adapter sequences. The clean read pairs which contained proximity ligation junction sequences “AAGCTAGCTT” were filtered out by Linux command line utility “grep”. The remaining reads were used for SNPs, indels, split reads, and CNV calling.
The remaining reads were aligned to the reference genome (hg19) and generated BAM file using BWA-MEM (version 0.7.17). The BAM file was sorted by SAMtools (version 1.15.1) and deduplicated by Sambamba (version 0.6.6). Next, we used BaseRecalibrator (GATK, version 4.2.2) to calibrate the base quality scores, and HaplotypeCaller (GATK, version 4.2.2) to detect SNPs and indels.
The deduplicated BAM file generated in SNP and indel calling step were used to identify split reads. The split alignment reads were extracted by SAMtools (version 1.15.1) with command line “samtools view test_deduplicated.bam | grep SA > test_split_reads.txt”
BIC-seq2 was used to derive CNV segments from reads coverage data. For details, refer to the software manual “http://www.compbio.med.harvard.edu/BIC-seq/”. For the segmentation step, parameters were designed as binsize = 50,000 bp and λ = 2 to determine the final CNV breakpoints. chrY and chrM were excluded from the analysis.
The types and breakpoints of translocations were identified according to the split reads and CNV information. For unbalanced translocations, the chromosomal copy number at the breakpoint were usually altered, while balanced translocations do not have any chromosomal copy number changes
Assembly: hg19
Supplementary files format and content: .hic  for  chromosome interaction information

extract_protocol: Cells were cross-linked with 0.5 % formaldehyde (Sigma) for 10 mins. The cross-linking reaction was terminated by glycine at a final concentration of 200 mM and lysed in lysis buffer (PBS contain 0.2% SDS) at room temperature for 5 min. After incubation, the nuclei were pelleted by centrifugation at 2,000 g/min for 5 min. The nuclei were transferred to 1.5 ml tubes and washed twice with PBS. For in situ restriction enzyme digestion, 140 μl of ddH2O, 20 μl of 10% Triton X-100, 20 μl of 10× NEBuffer 2.1, and 20 μl of HindIII (NEB, 20 units/μl) was added to the nuclei pellet and digested for 1.5 h at 37 °C in thermomixer (Eppendorf) with rotation at 1000 r.p.m. Add 5 μl of dNTP mix (10 mM each) and 5 μl of DNA polymerase I Klenow fragment (NEB, M0210) to the reaction system, place the sample in thermomixer with rotation at 37 °C at 1000 r.p.m for 30 mins. Add 27.5 μl of H2O, 3 μl of ATP (adenosine-triphosphate, 10mM), and 10 μl of T4 DNA ligase (Thermo, EL0011) to the reaction system, and placed the tube on the rotating mixers for 2 h at room temperature with rotation at 20 r.p.m. Add 20 μl of proteinase K (20 μg/ml) to the proximity ligation system, and then incubate at 60 °C for 2 hours. After digestion, the DNA was directly extracted using PCR Purification Kits (Zymo, D4013). DNA sequencing libraries were prepared using the VAHTS Universal Plus DNA Library Prep Kit (NDM627) according to manufacturer's protocol.


title: C, DR, Day9, rpt6


title: LALAPG 1


title: Mutant_Biological_Replicate_1


title: C, DR, Day2, rpt6


title: BMDM only 4


title: SW480 (rep)


title: K562 (rep)


title: C, DR, Day2, rpt5


title: 20% sample long-read

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

institute: The Walter and Eliza Hall Institute of Medical Research

description:
long_20
scM2_20_FLAMES_stats.txt

data_processing:
GEX + ATAC: base calling and quality scoring were performed using Illumina Real-Time Analysis on board software (version 2.11.3).
Raw base call files were demultiplexed into FASTQ files using the mkfastq pipeline in Cellranger ARC (version 2.0.0).
Reads were aligned to the human reference genome, filtering, barcode counting, peak calling were performed, and gene counts were generated using the count pipeline in CellRanger ARC (version 2.0.0).
Long reads: MinKNOW PromethION Release (version 20.06.9), base calling with Guppy (version 5.0.12).
Cell barcode matching and counting was performed with FLAMES (version 0.1.0, https://github.com/LuyiTian/FLAMES).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files with cell-associated barcodes, features, and matrix outputs from CellRanger.
Supplementary files format and content: scM2_20_FLAMES_stats.txt: comma-delimited file with cell IDs and counts

source_name: Lung adenocarcinoma

growth_protocol: The human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin.  The cells were grown independently at 37C  with 5% carbon dioxide until near 100% confluency.

extract_protocol:
The cell lines were mixed to achieve 16,000 nuclei captured, 9,700 nuclei in total, following the 10X Genomics nuclei preparation protocol.
GEX + ATAC:  10X Genomics Chromium nextgeM Single Cell Multiome ATAC +  Gene Expression kit,  Illumina NextSeq 500 sequencing chemistry v2.5. Long reads: Full length cDNA was obtained using 10X Multiome protocol to step 6. Elongation time was changed to 6 minutes. The ligation sequencing kit (SQK-LSK110) was used with the supplied ONT protocol. Libraries were loaded on 1 PromethION R9.4 flow cell and sequenced with ONT PromethION.

treatment_protocol: Cells were dissociated into single cell suspensions in FACS buffer, centrifuged and frozen at -80 °C.

value: Lung adenocarcinoma

value: mixture of cell lines:H2228, H1975, A549, H838, HCC827


title: C, DR, Day2, rpt4


title: BMDM only 3


title: Kidney cancer tissue

data_processing:
The nanopore sequencing reads with quality score more than 7 were mapped to the reference genome hg19 using minimap262 (version: 2.17 , -ax map-ont).
Structural variants were called using NanoSV63 (version: 1.2.4) with default parameters. Only SV supported by at least one definite split alignment read were retained for subsequent statistics.
Assembly: hg19
Supplementary files format and content: .vcf for variations

source_name: Kidney

extract_protocol:
DNA was extracted  according to manufacturer’s protocol.
Sequencing libraries were prepared according to manufacturer’s protocol.

value: Kidney


title: BMDM only 1


title: BMDM only 2


title: C, DR, Day2, rpt3


title: C, DR, Day2, rpt2


title: Healthy human peripheral blood cells [wgs]

data_processing:
FastQC (version: 0.11.5) was used to evaluate the quality of raw reads. FASTP (version: 0.23.2) was used to filter out the low-quality bases and adapter sequences.
Translocation identification were carried out using Delly259 (version: 0.8.6) and Gridss60 (version: 2.12.2) with default parameters. One WGS data from healthy person was served as control.
Assembly: hg19
Supplementary files format and content: .vcf for variations, .txt for copy number variation
Library strategy: WGS

source_name: Healthy human peripheral blood cells

value: Healthy human peripheral blood cells


title: SW480 [wgs]


title: C, DR, Day2, rpt1


title: C, Day0, rpt6

value: Before treatment


title: Infertile patient blood sample 2

data_processing:
FastQC49 (version: 0.11.5) was used to assess the quality of raw reads, and FASTP50 (version: 0.23.2) was used to filter out the low-quality bases and adapter sequences. The clean read pairs which contained proximity ligation junction sequences “AAGCTAGCTT” were filtered out by Linux command line utility “grep”. The remaining reads were used for SNPs, indels, split reads, and CNV calling.
The remaining reads were aligned to the reference genome (hg19) and generated BAM file using BWA-MEM51 (version 0.7.17). The BAM file was sorted by SAMtools52 (version 1.15.1) and deduplicated by Sambamba53 (version 0.6.6). Next, we used BaseRecalibrator (GATK54, version 4.2.2) to calibrate the base quality scores, and HaplotypeCaller (GATK, version 4.2.2) to detect SNPs and indels.
The deduplicated BAM file generated in SNP and indel calling step were used to identify split reads. The split alignment reads were extracted by SAMtools (version 1.15.1) with command line “samtools view test_deduplicated.bam | grep SA > test_split_reads.txt”
BIC-seq255 was used to derive CNV segments from reads coverage data. For details, refer to the software manual “http://www.compbio.med.harvard.edu/BIC-seq/”. For the segmentation step, parameters were designed as binsize = 50,000 bp and λ = 2 to determine the final CNV breakpoints. chrY and chrM were excluded from the analysis.
The types and breakpoints of translocations were identified according to the split reads and CNV information. For unbalanced translocations, the chromosomal copy number at the breakpoint were usually altered, while balanced translocations do not have any chromosomal copy number changes
Assembly: hg19
Supplementary files format and content: .vcf for variations, .txt for copy number variation
Library strategy: MSV-Seq

source_name: Infertile patient blood

treatment_protocol: For tumor tissue, 0.5 cm3 tissue blocks were selected and minced through a 40 μm strainer to obtain single cell suspension. For blood samples, we directly took 1 ml of anticoagulated whole blood, and centrifuged at 1500 g/min for 10 min to collect blood cells.

value: Infertile patient blood


title: C, DR, Day7, rpt1

value: C


title: Infertile patient blood sample 1


title: Healthy human peripheral blood cells


title: C, Day0, rpt4


title: C, Day0, rpt5


title: C, Day0, rpt3


title: Kidney cancer tissue replicate 1

source_name: Kidney cancer tissue

value: Kidney cancer tissue


title: C, Day0, rpt2


title: Kidney cancer tissue replicate 2


title: COLO320-DM


title: C, Day0, rpt1


title: PBMC from old research participant5

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Gene expression data of peripheral blood mononuclear cells isolated from an old voluntary human research participant.

hyb_protocol: For hybridization with the GeneChip (Affymetrix GeneChip Human genome U133 Plus 2.0 Array), 15 microg of fragmented cRNA in 200 microl of hybridization solution was used. Hybridization was performed in a Hybridization Oven 640 (Affymetrix) at 45 °C for 16h. Thereafter, washing and staining of gene chips was performed with the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 7G.

data_processing: Signals were processed with the Affymetrix GeneChip Operating Software (GCOS; v. 1.4. Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.

label: biotin

source_name: PBMC from old human research participant5

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix protocol (Affymetrix, GeneChip Expression Analysis Technical Manual; Rev. 5).

growth_protocol: Whole genome microarray gene expression profiling was performed with total RNA isolated from peripheral blood mononuclear cells from voluntary human research participants. The study compared two age groups. The old age group was aged 75-89 years (n=5), and the middle-aged group was aged 35-50 years (n=4).

extract_protocol: Total RNA was isolated from the PBMC with the RNeasy Mini kit following the instructions of the manufacturer (Qiagen).

treatment_protocol: For whole genome microarray gene expression profling, total RNA was isolated from peripheral blood mononuclear cells. Peripheral blood mononuclear cells were isolated from a fresh, heparinized blood sample (3 ml) by density gradient centrifugation with Ficoll® Paque Plus cell separation medium. Before addition of 3 ml of Ficoll® Paque plus, the anticoagulated blood sample was diluted with sterile PBS (1:1). The sample was centrifuged at 300 x g for 30 min, and the upper ring layer with the enriched mononuclear cells was collected. After dilution with PBS (1:3), peripheral blood mononuclear cells were isolated by a second centrifugation.

value: peripheral blood mononuclear cells

value: Old

tag: gender

value: Male


title: PBMC from old research participant4

source_name: PBMC from old human research participant4


title: PBMC from middle-aged research participant2

description: Gene expression data of peripheral blood mononuclear cells isolated from a middle-aged voluntary human research participant.

source_name: PBMC from middle-aged human research participant2

value: Middle-aged


title: PBMC from middle-aged research participant1

source_name: PBMC from middle-aged human research participant1


title: PBMC from middle-aged research participant3

source_name: PBMC from middle-aged human research participant3


title: PBMC from middle-aged research participant4

source_name: PBMC from middle-aged human research participant4


title: K562


title: PBMC from old research participant3

source_name: PBMC from old human research participant3


title: L8, WTR, Day9, rpt6

value: TaPYLox

value: Well-watered


title: Whole Blood, SAKI-4_miRNA

city: Yinchuan

first: Wen-jie

last: Zhou

address: No. 804, Shengli South Street, Xingqing District, Yinchuan City, Ningxia

institute: General Hospital of Ningxia Medical University

data_processing:
Genome Reference Consortium Human Build 38
Sequence reads were trimmed for adaptor sequence/low-quality sequence using hg38 genomic benchwork (parameter- Quality limit: 0.05)
The filtered reads were compared with the hg38 reference database using STAR software
Read count extraction and normalization were performed using hg38 genomic benchwork
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include expression quantity for each Sample

source_name: Whole Blood

extract_protocol:
In accordance with the manufacturer’s instructions, total RNA was isolated from clinical experimental specimens using TRizol reagent (Invitrogen RNA simple kit).
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

value: Whole Blood

value: SAKI


title: Whole Blood, SAKI-5_miRNA


title: TE-1 5um-D

city: Shantou

first: Yang

last: Chen

address: No.69, Dongxia North Road, Guangxia New Town, Shantou, Guangdong,

institute: Second Affiliated Hospital, Shantou University Medical College,

hyb_protocol: Add 500 µL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent supplied with the Agilent Gene Expression Hybridization Kit, or add 1250 µL of nuclease-free water to the vial containing lyophilized large volume 10X Blocking Agent (Agilent p/n 5188-5281).Mix by gently vortexing. If the pellet does not go into solution completely, heat the mix for 4 to 5 minutes at 37°C. Drive down any material adhering to the tube walls or cap by centrifuging  for 5 to 10 seconds.

scan_protocol: Put assembled slide holders with or without the ozone-barrier slide cover into the scanner carousel.In the Scan Control main window, choose the slot number of the first slide for Start Slot and the slot number for the last slide for End Slot.For 1x1M, 2x400K, 4x180K and 8x60K microarrays, select Profile AgilentG3_GX_1Color.Verify scan settings for one-color scans.Verify that the Scanner status in the main window says Scanner Ready.In the Scan Control main window, click Scan Slot m-n where m is the slot of the first slide, and n is the slot for the last slide.

data_processing:
Data analyses were performed with SPSS software ver. 20.0 (SPSS, Inc., Chicago, IL, USA) and GraphPad Prism 7.0 (GraphPad Software, La Jolla, CA, USA). All experimental data are expressed as the mean ± s.e.m. Probability (P) values <0.05 were considered statistically significant and were calculated using Student’s t-test as appropriate.
Probability (P) values <0.05 were considered statistically significant and were calculated using Student’s t-test as appropriate.

label_protocol: Add 100 µL of the Lysis Buffer to each reaction tube for a total volume of 116 µL.Mix on a vortex mixer, or pipette repeatedly until homogenized. Add an equal volume (116 µL) of 80% sulfolane (room temperature) to   the cell lysate. Mix thoroughly on a vortex mixer for 5 seconds.You must use equal volumes of 80% sulfolane and cell lysate. Mix on a vortex mixer until the lysate and sulfolane are thoroughly mixed.Put an RNA-binding nano-spin cup into a 2-mL collection tube.Transfer the 80% sulfolane and cell lysate mixture to the RNA-binding nano-spin cup and snap the cap onto the top of the spin cup. Spin the sample in a microcentrifuge at ≥12,000 x g for 60 seconds. Remove and keep the spin cup. Discard the filtrate. Put the spin cup back into the same 2-mL collection tube.Up to this point, the RNA has been protected from RNases by the presence of guanidine thiocyanate.Add 300 µL of 1x High-Salt Wash Buffer to the spin cup. Cap the spin cup, and spin the sample in a microcentrifuge at ≥12,000 x g for 60 seconds.Remove and keep the spin cup. Discard the filtrate. Put the spin cup   back into the same 2-mL collection tube.Add 300 µL of 1x Low-Salt Wash Buffer to the spin cup. Cap the spin cup, and spin the sample in a microcentrifuge at ≥12,000 x g for 60 seconds. Repeat step 9 and step 10 for a second low-salt wash.Remove and keep the spin cup. Discard the filtrate. Put the spin cup back into the same 2-mL collection tube.Add 300 µL of 1x Low-Salt Wash Buffer to the spin cup. Cap the spin cup, and spin the sample in a microcentrifuge at ≥12,000 x g for 3 minutes to dry the fiber matrix.Transfer the spin cup to a fresh 2-mL collection tube.Add 20 µL of Elution Buffer directly onto the fiber matrix inside the spin cup. Cap the spin cup and incubate the sample at room temperature for 2 minutes.Spin the sample in a microcentrifuge at ≥12,000 x g for 5 minutes.If needed, repeat the elution step (step 15 and step 16) to increase the yield of total RNA.Transfer the eluate in the collection tube to a capped microcentrifuge tube to store the RNA.The RNA can be stored at -20°C for up to one month, or at -80°C for long-term storage.

extract_protocol: Add 84 µL of nuclease-free water to your cRNA sample, for a total volume of 100 µL.Add 350 µL of Buffer RLT and mix well by pipetting.Add 250 µL of ethanol (96% to 100% purity) and mix thoroughly by pipetting. Do not centrifuge.Transfer the 700 µL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube.Transfer the RNeasy column to a new collection tube and add 500 µL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube.Add another 500 µL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube.If any buffer RPE remains on or near the frit of the column or on the   outside of the column, transfer the RNeasy column to a new 1.5-mL collection tube and centrifuge the sample at 4°C for 30 seconds at 13,000 rpm to remove any remaining traces of buffer RPE. Discard this collection tube and use a fresh tube to elute the cleaned cRNA sample.Elute the purified cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add 30 µL RNase-free water directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm.Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.

tag: group

value: drug-resistant


title: SW480


title: L8, WTR, Day9, rpt5

source_name: Spikelet

value: Spikelet


title: PBMC from old research participant1

source_name: PBMC from old human research participant1


title: Whole Blood, SAKI-3_miRNA


title: kidney cancer tissue rep3

data_processing:
FastQC (version: 0.11.5) was used to assess the quality of raw reads, and FASTP (version: 0.23.2) was used to filter out the low-quality bases and adapter sequences.
The clean reads were aligned to the hg19 using BWA-MEM (version: 0.7.17) with default parameters and sorted by Samtools (version: 1.15.1).
Gene expression levels were assessed using featureCounts51 (version: 2.0.0). Differential gene expression analysis was performed using the DEseq252 (version: 1.20.0) package.
The analysis outlined above was conducted with a complete pepline in https://github.com/GangCaoLab/NGS-pipelines/tree/master/RNA-Seq.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include differential gene expression analysis result

source_name: kidney cancer tissue

extract_protocol:
RNA was extracted using the RNAiso Plus (Takara, 9109) according to manufacturer’s protocol.
Sequencing libraries were prepared using the VAHTS Stranded mRNA-Seq Library Prep Kit (Vazyme, NR602-02) according to manufacturer's protocol.

value: kidney cancer tissue


title: PBMC from old research participant2

source_name: PBMC from old human research participant2


title: HEK293T_ABE8e.rep2

first: Yuan

last: Wu

address: 929 E 57th St, GCIS E535

value: in vivo transcribed RNA


title: 272ctrl2

source_name: human infant feces

value: control

value: 2percent complex nitrogen


title: TE-1 5um-C


title: L8, WTR, Day9, rpt4


title: L8, WTR, Day9, rpt3


title: chick retina, NMDA + clodronate vesicle treated

city: Columbus

first: Heithem

last: El-Hodiri

state: OH

address: 333 W 10th Ave

institute: Ohio State University College of Medicine

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger 7.0.1
Assembly: bGalGal1.mat.broiler.GRCg7b (Ensembl release 107)
Supplementary files format and content: filtered feature barcode matrix files from CellRanger output

organism: Gallus gallus

source_name: retina

extract_protocol:
Papain Dissociation Kit (Worthington Biochemicals), 15 minutes at 37 degrees C
10X Genomics Next GEM Single Cell 3' GEM, Bead, and Library Kits

value: retina

tag: developmental stage

value: chick

value: WT

value: clodronate liposome injection, NMDA injection


title: Whole Blood, SAKI-1_miRNA


title: Whole Blood, SAKI-2_miRNA


title: chick retina, clodronate vesicle treated

description: 10X Genomics

value: clodronate liposome injection, saline control


title: chick retina, NMDA treated

description: 10X Genomics

value: NMDA injection


title: TE-1-D

value: parental


title: kidney cancer tissue rep1


title: kidney cancer tissue rep2


title: L8, WTR, Day9, rpt2

value: TaPYLox


title: Whole Blood, HC-5_miRNA

value: healthy


title: chick retina, saline control

description: 10X Genomics

value: saline control


title: TE-1 5um-A


title: AB5075+CRL2244_3

organism:
Acinetobacter baumannii
Lacticaseibacillus rhamnosus

source_name: Acinetobacter baumannii AB5075 + Lacticaseibacillus rhamnosus CRL 2244


title: TE-1 5um-B


title: L8, WTR, Day9, rpt1

value: Well-watered


title: Whole Blood, HC-4_miRNA

value: Whole Blood


title: TE-1-B


title: TE-1-C


title: AB5075+CRL2244_2

value: Acinetobacter baumannii AB5075 + Lacticaseibacillus rhamnosus CRL 2244


title: L8, WTR, Day7, rpt6

value: Spikelet


title: HK2 cell ICCB2802

city: Shanghai

first: Ziru

last: Xia

address: 2nd Ruijin Road

institute: Shanghai Jiaotong University

data_processing:
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
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: excel file includes counts of each gene
Supplementary files format and content: excel file includes RPKM of each gene

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

value: renal tubular epithelial cell


title: HK2 cell ICCB2803


title: HK2 cell ICCB2801


title: Whole Blood, HC-3_miRNA


title: AB5075+CRL2244_1


title: HK2 cell control2

value: DMSO


title: Skin T cells at Day 100 (after transplantation) [ATAC-seq_Skin_100_742]

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
For ATAC-seq low quality peaks such as blacklisted peaks were eliminated.
Assembly: hg38
Supplementary files format and content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations
Supplementary files format and content: ATAC-seq peaks were identified by using the HOMER tool

source_name: T cells

growth_protocol: freshly isolated cells from human tissue

extract_protocol:
cells were isolated from heparinized blood using ficoll gradient and from skin biopsies using collagenase IV + mesh filtering
Illumina

value: Skin

value: T cells

value: Day 100 (after transplantation)


title: HK2 cell control3

value: WT


title: L8, WTR, Day7, rpt4


title: L8, WTR, Day7, rpt5


title: Whole Blood, HC-1_miRNA


title: Skin T cells at Day 100 (after transplantation) [ATAC-seq_Skin_100_741]


title: L8, WTR, Day7, rpt2


title: L8, WTR, Day7, rpt3


title: TE-1-A


title: LoVo shCLDN1 #2-2

city: New York

first: Spyros

last: Karaiskos

state: NY

department: Herbert Irving Cancer Center

institute: Columbia University

data_processing:
RNAseq data were processed with STAR and DEseq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: LoVo

extract_protocol:
Single metastatic CRC cells were isolated from metastatic liver tumors obtained after portal vein injection. After euthanization, the liver tissues were minced and digested in culture medium containing 200 U/mL collagenase IV at 37°C for 30 minutes. The undigested tissues were removed using a 70µm cell strainer and centrifuged. Red blood cells were lysed using ACK Lysing Buffer. The cell pellet was washed by PBS containing 0.04% BSA and resuspended in FACS buffer containing 0.5% BSA, 1 mM EDTA and 0.1% sodium azide in PBS. The metastatic CRC cells were sorted by flow cytometer based on the presence of mCherry fluorescence. Normal mouse liver tissues were used as a negative control for gating. Total RNAs were extracted using RNeasy Plus Micro Kit.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis. After end repair and addition of a single 'A' base, adaptors were ligated to the cDNA. The products were then purified and enriched by PCR to create the final cDNA library

value: LoVo

value: Colorectal cancer


title: Skin T cells at Day 100 (after transplantation) [ATAC-seq_Skin_100_738]


title: Skin T cells at Day 100 (after transplantation) [ATAC-seq_Skin_100_736]


title: HK2 cell control1


title: L8, WTR, Day7, rpt1

data_processing:
The raw sequence data were trimmed and qualified by trimmomatic (version 0.39) with default parameters.
The clean reads were aligned to the primary transcripts of the wheat reference genome by kallisto (version 0.46.2) with default parameters.
Assembly: IWGSC (ensembl49)
Supplementary files format and content: A fileset (an HDF5 and a tab-delimited table files for transcript abundance, and a JSON file for running log) for each kallisto run.


title: Skin T cells at Day 14 (after transplantation) [ATAC-seq_Skin_14_742]

value: Day 14 (after transplantation)


title: LoVo shCLDN1 #2-1


title: LoVo shCLDN1 #1-2


title: L8, WTR, Day2, rpt6


title: L8, WTR, Day2, rpt5


title: Whole Blood, HC-2_miRNA


title: Skin T cells at Day 14 (after transplantation) [ATAC-seq_Skin_14_741]


title: LoVo shNTC #2


title: RCMB56-ht, SHH, ATAC

city: La Jolla

first: Lukas

last: Chavez

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
ATAC-seq reads were trimmed on both ends using Trimmomatic v0.38, LEADING:15 TRAILING:15
ATAC-seq reads were aligned to the GRCh38 genome using bowtie v2.2.5 and deduplicated using Picard MarkDuplicates v2.18.27. Only primary alignments were retained.
Peaks were called using MACS2 v2.1.2 with significance cutoff q<0.05.
Coverage tracks were generated by extending reads to 200bp and shifting by 100bp, then converting to bigwig format using deeptools v3.5.1 bamCoverage.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak

source_name: medulloblastoma

extract_protocol:
Cells were cryopreserved in DMSO. Nuclei were thawed, lysed, stained (Trypan Blue), counted (Countess, Invitrogen), and tagmented (1X Tagment DNA Buffer, Illumina). DNA was purified using DNeasy Blood & Tissue Kit (Qiagen), and quantified using NanoDrop 2000 (Thermo Scientific), and purified using the Nextera DNA Library Preparation Kit (Illumina).
Between 50,000 and 100,000 nuclei were used in library construction. DNA was amplified by PCR (8 cycles), size-selected for nucleosome-free fragments (175-250bp) by gel electrophoresis (2% agarose gel, Invitrogen), and purified using the QIAquick Gel Extraction Kit (Qiagen). A second PCR amplification (4 cycles) and purification (Agencourt AMPure XP beads, Beckman Coulter) was performed on the size-selected fragments. The final library was validated using a Fragment Analyzer™ instrument (Advanced Analytical) and the KAPA Library Quantification Kit for Illumina Sequencing Platforms.

value: medulloblastoma


title: RCMB56-ht snRNA+ATAC-seq (RNA)

description:
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Sequencing data were uniformly processed using CellRanger ARC v2.0.0 with default parameters.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx are standard outputs from 10X single-cell pipelines. Mtx file is a table indexed by barcode on rows, and features on columns.

extract_protocol:
Disassociated cryopreserved cells stored in 10%DMSO/FBS were used. At least 50mg of tissue (1M cells) was used for both samples. Disassociated cells were prepared for Single Cell Multiome ATAC + Gene Expression sequencing (10X Genomics) according to the manufacturer’s instructions
Sequencing was performed on an Illumina NovaSeq S4 200 to a depth of at least 250M reads for snATAC-seq and 200M reads for snRNA-seq


title: L8, WTR, Day2, rpt4

extract_protocol:
RNA was extracted using TRIzol from frozen spikelets. 6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEXTflex Rapid DIR mRNA Bundle following manufacturer's protocols.

value: TaPYLox


title: RCMB56-ht snRNA+ATAC-seq (ATAC)

description:
MM_614 files are snATAC-seq sequenced over 2 lanes (technical replicate).
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz


title: D458, G3, ATAC


title: LoVo shNTC #1


title: Skin T cells at Day 0 (day of transplantation) [ATAC-seq_Skin_Tx_741]

value: Day 0 (day of transplantation)


title: DLD-1 shCLDN1 #2-2


title: L8, WTR, Day2, rpt2


title: Skin T cells at Day 0 (day of transplantation) [ATAC-seq_Skin_Tx_742]


title: D283 T21 rep B, pooled CRISPRi

description:
all.count.txt
D283_CRISPR-SURF_deconvolved_scores.bedgraph

data_processing:
Sequencing data QC, alignment and preprocessing was performed using MAGeCK-VISPR v0.4.1653.
CRISPRi score tracks were generated using CRISPR-SURF v1.0.
Assembly: GRCh38
Supplementary files format and content: all.count.txt: sgRNA abundance counts from MAGeCK.
Supplementary files format and content: *deconvolved_scores.bedgraph: essentiality score genomic tracks generated by CRISPR-SURF.
Library strategy: Pooled CRISPRi proliferation screen

extract_protocol:
Cells were harvested at T21, and genomic DNA extraction was performed using the NucleoSpin Blood XL kit.
The NGS samples were prepared by the SBP Functional Genomics Core Facility using two-step PCR amplification of the integrated sgRNA using the genomic DNA as a template. For the first PCR, “PCR1” sgRNAs were amplified using Herculase II Fusion DNA Polymerases (Agilent #600675) from total genomic DNA isolated from each replicate at T0 and T21. 4ug of genomic DNA was used for each 50ul reaction. PCR1 products were cleaned using QIAquick PCR Purification Kit (Qiagen). For the second PCR “PCR2”, 5µl of each cleaned PCR1 product was used for each 50ul reaction with primers designed to include Illumina Adaptors and unique barcodes to allow for multiplexed NGS. PCR2 products were bead-purified (AMPure XP, Beckman), and eluted in 30µl of low-EDTA TE buffer. Final concentrations of the desired products were determined by TapeStation (Agilent) and equimolar amounts from each sample were pooled for sequencing.


title: D283 T21 rep A, pooled CRISPRi


title: Skin T cells at Day 0 (day of transplantation) [ATAC-seq_Skin_Tx_736]


title: DLD-1 shCLDN1 #2-1


title: L8, WTR, Day2, rpt1


title: D283 T0 rep B,  pooled CRISPRi


title: Skin T cells at Baseline [ATAC-seq_Skin_B_742]

value: Baseline


title: DLD-1 shCLDN1 #1-2


title: L8, DR, Day9, rpt5

value: Drought


title: D283 T0 rep A, pooled CRISPRi


title: Skin T cells at Baseline [ATAC-seq_Skin_B_741]


title: LoVo shCLDN1 #1-1


title: L8, DR, Day9, rpt4


title: DLD-1 shNTC #2


title: Skin T cells at Baseline [ATAC-seq_Skin_B_738]


title: L8, DR, Day9, rpt3


title: D458 T21 rep A, pooled CRISPRi

description:
all.count.txt
D458_CRISPR-SURF_deconvolved_scores.bedgraph


title: DLD-1 shNTC #1


title: L8, WTR, Day2, rpt3

value: Well-watered


title: Skin T cells at Day 0 (day of transplantation) [ATAC-seq_Skin_Tx_738]


title: Whole Blood, SAKI-5

value: Whole Blood

tag: case

value: SAKI


title: D458 T0 rep B, pooled CRISPRi

tag: cell type


title: L8, DR, Day9, rpt2

value: Spikelet


title: Blood T cells at Day 100 (after transplantation) [ATAC-seq_Blood_100_742]

value: Blood


title: D458 T0 rep A, pooled CRISPRi


title: Whole Blood, SAKI-4


title: L8, DR, Day9, rpt1


title: L8, DR, Day7, rpt6


title: Blood T cells at Day 100 (after transplantation) [ATAC-seq_Blood_100_736]


title: Blood T cells at Day 100 (after transplantation) [ATAC-seq_Blood_100_741]


title: Whole Blood, SAKI-3


title: Whole Blood, SAKI-2


title: PWB EC 4221_3 derived from PWB iPSC 4221_3, replicate

city: Columbia

first: Wenbin

last: Tan

state: SC

address: 6311 Garners Ferry Road

department: Cell Biology and Anatomy

institute: University of South Carolina School of Medicine

description:
PWB_EC_4221_3R
EC_raw_counts.xls
EC_pseudo_counts.xls

data_processing:
The STAR (spliced transcripts alignment to a reference; https://github.com/alexdobin/STAR) RNA-seq aligner was used for raw reads’ alignment
The bam files generated by STAR were used as inputs to FeatureCounts (http://bioconductor.org/packages/Rsubread) for further validation and gene counts of RNA transcripts
Biostatistical analysis for differentially expressed genes (DEGs) among groups were carried out using edgeR (https://bioconductor.org/packages/edgeR/)
A set of scaling factors (effective library sizes) were used for downstream analyses after normalization of the original library sizes. Differential expressions were determined using either quasi-likelihood (QL) F-test or likelihood ratio test by glm functions in edgeR. A false discovery rate (FDR) < 0.05 was considered significant
Assembly: Human genome fasta and gtf annotation files from ensemble (Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz; Homo_sapiens.GRCh38.105.chr.gtf.gz) were retrieved for building the STAR genome index files
Supplementary files format and content: xls file includes raw counts for each sample
Supplementary files format and content: xls file includes pseudo counts for each sample

source_name: skin

growth_protocol: The iPSCs were grown in Essential 8 medium

extract_protocol:
Qiagen RNA isolation kit
Qiagen Standard RNA Library kit

treatment_protocol: The iPSCs were induced to MSCs, then differentiated into ECs

value: skin

value: PWB

value: EC


title: Blood T cells at Day 100 (after transplantation) [ATAC-seq_Blood_100_740]

value: T cells

value: Day 100 (after transplantation)


title: L8, DR, Day7, rpt5


title: Blood T cells at Day 100 (after transplantation) [ATAC-seq_Blood_100_738]


title: L8, DR, Day7, rpt4


title: PWB EC 4221_3 derived from PWB iPSC 4221_3

description:
PWB_EC_4221_3
EC_raw_counts.xls
EC_pseudo_counts.xls


title: Control EC 52521_9 derived from control iPSC 52521_9, replicate

description:
Control_EC_52521_9R
EC_raw_counts.xls
EC_pseudo_counts.xls

value: control


title: Blood T cells at Day 14 (after transplantation) [ATAC-seq_Blood_14_742]

value: Day 14 (after transplantation)


title: D458 T21 rep B, pooled CRISPRi

value: medulloblastoma


title: DLD-1 shCLDN1 #1-1

value: Colorectal cancer


title: L8, DR, Day7, rpt3

value: TaPYLox


title: Control EC 52521_9 derived from control iPSC 52521_9

description:
Control_EC_52521_9
EC_raw_counts.xls
EC_pseudo_counts.xls


title: Whole Blood, SAKI-1


title: Control EC 52521_4 derived from control iPSC 52521_4, replicate

description:
Control_EC_52521_4R
EC_raw_counts.xls
EC_pseudo_counts.xls


title: Blood T cells at Day 14 (after transplantation) [ATAC-seq_Blood_14_741]


title: L8, DR, Day7, rpt1


title: Whole Blood, HC-3

value: HC


title: Whole Blood, HC-5


title: L8, DR, Day2, rpt6

value: Drought


title: Whole Blood, HC-4


title: L8, DR, Day7, rpt2


title: Control EC 52521_4 derived from control iPSC 52521_4

description:
Control_EC_52521_4
EC_raw_counts.xls
EC_pseudo_counts.xls


title: Blood T cells at Day 14 (after transplantation) [ATAC-seq_Blood_14_740]


title: Whole Blood, HC-2


title: Blood T cells at Day 14 (after transplantation) [ATAC-seq_Blood_14_738]


title: PWB MSC 4221_3 derived from PWB iPSC 4221_3, replicate 3

description:
PWB_MSC_4221_3R3
MSC_raw_counts.xls
MSC_pseudo_counts.xls

value: MSC


title: Blood T cells at Day 14 (after transplantation) [ATAC-seq_Blood_14_736]


title: PWB MSC 4221_3 derived from PWB iPSC 4221_3

description:
PWB_MSC_4221_3
MSC_raw_counts.xls
MSC_pseudo_counts.xls


title: Blood T cells at Day 0 (day of transplantation) [ATAC-seq_Blood_Tx_741]

value: Day 0 (day of transplantation)


title: L8, DR, Day2, rpt2


title: PWB MSC 4221_3 derived from PWB iPSC 4221_3, replicate 1

description:
PWB_MSC_4221_3R1
MSC_raw_counts.xls
MSC_pseudo_counts.xls


title: Whole Blood, HC-1

value: Whole Blood


title: L8, DR, Day2, rpt3

value: Spikelet


title: Blood T cells at Day 0 (day of transplantation) [ATAC-seq_Blood_Tx_742]

value: Blood


title: Control MSC 52521_8 derived from control iPSC 52521_8

description:
Control_MSC_52521_8
MSC_raw_counts.xls
MSC_pseudo_counts.xls

value: skin


title: Blood T cells at Day 0 (day of transplantation) [ATAC-seq_Blood_Tx_740]


title: NB55

city: Edmonton

first: Najmeh

last: Bozorgmehr

state: Alberta

address: 11361 87th Ave NW, 7020L Katz Group Centre

department: Dentistry

country: Canada

institute: University of Alberta

description:
Non-responder1, Baseline
Female, Cervix

data_processing:
Raw data alligned to human genome cDNA database (GRCh38) using Kallisto software version 0.46.2. 100 permutations selected during allignment
Differential Expression analyses extracted from the count data using the DESeq2 R package version 4.2.0 (2022-04-22
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab delimited text file including transcript count values for each sample

source_name: Blood

extract_protocol:
TRIzol reagent, Direct-Zol RNA kit, Samples with RNA Integrity Numbers (RIN) more than 6.5 were selected
TruSeq RNA library Prep Kit v2 (Illumina), Poly A selection with oligo dTs conjugated to paramagnetic beads. Then first and second strands cDNA libraries were constructed from 100 ng of extracted RNA using the TruSeq RNA Library Prep kit v2 (Illumina) as per kit’s instruction. T-A ligation was added to the blunted and A-tailed cDNA, before doing 12 cycles of PCR to incorporate illumine adapters containing multiplexing barcodes.

value: Peripheral blood mononuclear cells


title: NB57

description:
Non-responder1, Cycle2
Female, Cervix

value: Valproic acid + Avelumab


title: Control MSC 52521_9 derived from control iPSC 52521_9

description:
Control_MSC_52521_9
MSC_raw_counts.xls
MSC_pseudo_counts.xls


title: NB58

description:
Non-responder1, Endpoint
Female, Cervix


title: Control MSC 52521_4 derived from control iPSC 52521_4R

description:
Control_MSC_52521_4R
MSC_raw_counts.xls
MSC_pseudo_counts.xls


title: L8, DR, Day2, rpt4

first: Ryosuke

last: Mega


title: NB54

description:
Non-responder6, Endpoint
Female, Anal


title: L8, DR, Day2, rpt1


title: L8, Day0, rpt6

value: Before treatment


title: Blood T cells at Baseline [ATAC-seq_Blood_B_742]

value: T cells

value: Baseline


title: Blood T cells at Baseline [ATAC-seq_Blood_B_740]


title: L8, DR, Day2, rpt5


title: Blood T cells at Day 0 (day of transplantation) [ATAC-seq_Blood_Tx_738]


title: L8, Day0, rpt5


title: NB52

description:
Non-responder6, Baseline
Female, Anal


title: Control MSC 52521_4 derived from control iPSC 52521_4

description:
Control_MSC_52521_4
MSC_raw_counts.xls
MSC_pseudo_counts.xls

value: control


title: Blood T cells at Baseline [ATAC-seq_Blood_B_741]


title: L8, Day0, rpt4


title: NB47

description:
Non-responder7, Endpoint
Male, Anal


title: PWB iPSC clone 4221_6 was generated from de-identified PWB skin tissues, replicate

description:
PWB_iPSC_4221_6R
Ipsc_raw_counts.xls
ipsc_pseudo_counts.xls

value: PWB

value: IPSC


title: PWB MSC 4221_3 derived from PWB iPSC 4221_3, replicate 2

description:
PWB_MSC_4221_3R2
MSC_raw_counts.xls
MSC_pseudo_counts.xls


title: PWB iPSC clone 4221_6 was generated from de-identified PWB skin tissues

description:
PWB_iPSC_4221_6
Ipsc_raw_counts.xls
ipsc_pseudo_counts.xls


title: L8, Day0, rpt3

value: TaPYLox


title: NB45

description:
Non-responder7, Cycle1
Male, Anal

value: Valproic acid


title: Blood T cells at Baseline [ATAC-seq_Blood_B_736]


title: NB44

description:
Non-responder7, Baseline
Male, Anal


title: Skin T cells at Day 100 (after transplantation) [RNA-seq_Skin_100_742]

value: Skin

value: Day 100 (after transplantation)


title: PWB iPSC clone 4221_3 was generated from de-identified PWB skin tissues

description:
PWB_iPSC_4221_3
Ipsc_raw_counts.xls
ipsc_pseudo_counts.xls


title: NB43

description:
Non-responder5, Endpoint
Female, Anal


title: L8, Day0, rpt1


title: NB42

description:
Non-responder5, Cycle2
Female, Anal


title: Skin T cells at Day 100 (after transplantation) [RNA-seq_Skin_100_738]


title: Skin T cells at Day 100 (after transplantation) [RNA-seq_Skin_100_736]


title: Skin T cells at Day 100 (after transplantation) [RNA-seq_Skin_100_741]


title: control iPSCs clone 52521_8 was generated from de-identified normal skin tissues, replicate

description:
Control_iPSC_52521_8R
Ipsc_raw_counts.xls
ipsc_pseudo_counts.xls


title: NB41

description:
Non-responder5, Cycle1
Female, Anal


title: control iPSCs clone 52521_9 was generated from de-identified normal skin tissues, replicate

description:
Control_iPSC_52521_9R
Ipsc_raw_counts.xls
ipsc_pseudo_counts.xls


title: NB40

description:
Non-responder5, Baseline
Female, Anal


title: Skin T cells at Day 14 (after transplantation) [RNA-seq_Skin_14_757]

value: Day 14 (after transplantation)


title: APP_Microglia, IL33, 24hours, rep1 [scRNAseq_IL33_24h_1]

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

description: Ilumina NextSeq 500/NovaSeq 6000

data_processing:
Demultiplexed FASTQ files (from Novogene) were aligned to mm10 mouse reference genome by Cell Ranger (v7.0.0) with the default settings. Then, we performed downstream quality control (QC) and analyses using Seurat. We further removed microglia with ≤500 genes, ≥15,000 unique molecular identifiers and ≥5% mitochondrial genes as second round of QC. After the QC, 72,519 microglia (from 86,288 CD11b+ cells) were retained for the downstream analysis.
Supplementary files format and content: mm10
Supplementary files format and content: filtered count matrix from Seurat

source_name: brain

extract_protocol:
In brief, we deeply anesthetized adult mice using isoflurane and then perfused them with ice-cold PBS. We minced the forebrain tissue into small pieces and mechanically dissociated them with a Dounce homogenizer on ice. We used a Percoll gradient (30%; Sigma-Aldrich) to remove myelin. We blocked the resultant mononuclear cell suspensions with an FcR blocker on ice for 10 min and then incubated them with antibody (all 1:100 dilution) in the dark on ice for 30 min. Next, we performed flow cytometry analysis and cell sorting with a BD Influx Cell Sorter. We used unstained controls to identify cell populations and visualized clear subpopulations of living microglia on scatter plots; the purity of microglial isolation was routinely >90% according to reanalysis of the sorted cells.
We generated scRNA-seq libraries using a Chromium Next GEM Single Cell 3′ Library Kit (v3.1 Chemistry; 10x Genomics) according to the manufacturer’s instructions. In brief, we counted sorted living CD11b+ cells on a hemocytometer. We mixed single-cell suspensions (400 cells µl−1) with reverse transcription reagent mix and loaded them into the chip for single-cell encapsulation. We immediately incubated the encapsulated cells in a thermocycler for reverse transcription. We obtained barcoded cDNA and used it for library construction according to the manufacturer’s instructions. We quantified the concentrations of the final libraries with Qubit (Thermo Fisher Scientific) and fragment lengths with Fragment Analyzer (Advanced Analytical). We performed paired-end sequencing of the libraries on a NovaSeq 6000 instrument (Novogene) according to the manufacturer’s instructions.

value: brain

value: Microglia


title: control iPSCs clone 52521_8 was generated from de-identified normal skin tissues

description:
Control_iPSC_52521_8
Ipsc_raw_counts.xls
ipsc_pseudo_counts.xls


title: APP_Microglia, IL33, 8hours, rep3 [scRNAseq_IL33_8h_3]

institute: Hong Kong University of Science and Technology

description: Ilumina NextSeq 500/NovaSeq 6000


title: NB46

description:
Non-responder7, Cycle2
Male, Anal

value: Blood


title: Skin T cells at Day 14 (after transplantation) [RNA-seq_Skin_14_754]


title: NB38

description:
Responder1, Endpoint
Female, Anal


title: L8, Day0, rpt2

city: Yamaguchi

address: 1677-1, Yoshida

institute: Yamaguchi University

value: Spikelet


title: PWB iPSC clone 4221_3 was generated from de-identified PWB skin tissues, replicate

description:
PWB_iPSC_4221_3R
Ipsc_raw_counts.xls
ipsc_pseudo_counts.xls

value: skin


title: Blood T cells at Baseline [ATAC-seq_Blood_B_738]


title: control iPSCs clone 52521_4 was generated from de-identified normal skin tissues

description:
Control_iPSC_52521_4
Ipsc_raw_counts.xls
ipsc_pseudo_counts.xls